diff --git a/.circleci/common.sh b/.circleci/common.sh deleted file mode 100644 index be66a12ad023a..0000000000000 --- a/.circleci/common.sh +++ /dev/null @@ -1,2 +0,0 @@ -MINICONDA_VER=4.5.4 -BIOCONDA_UTILS_TAG=master diff --git a/.gitignore b/.gitignore index f9640a3ae617a..b93a35e8da1f2 100644 --- a/.gitignore +++ b/.gitignore @@ -17,3 +17,6 @@ cached_bioconductor_tarballs #Ignore hidden files from Dolphin window manager .directory + +#People sometimes mistakenly upload their local copy of this file +.circleci/common.sh diff --git a/build-fail-blacklist b/build-fail-blacklist index 68fc2b661b2da..3277cb73f49c2 100644 --- a/build-fail-blacklist +++ b/build-fail-blacklist @@ -21,19 +21,6 @@ recipes/gqt recipes/diamond_add_taxonomy recipes/shapemapper recipes/biom-format -recipes/bioconductor-sictools -recipes/bioconductor-bsgenome.amellifera.beebase.assembly4 -recipes/bioconductor-bsgenome.btaurus.ucsc.bostau6 -recipes/bioconductor-bsgenome.dmelanogaster.ucsc.dm2 -recipes/bioconductor-bsgenome.drerio.ucsc.danrer7 -recipes/bioconductor-bsgenome.gaculeatus.ucsc.gasacu1.masked -recipes/bioconductor-bsgenome.ggallus.ucsc.galgal3.masked -recipes/bioconductor-bsgenome.ggallus.ucsc.galgal4.masked -recipes/bioconductor-bsgenome.ggallus.ucsc.galgal5 -recipes/bioconductor-bsgenome.mmulatta.ucsc.rhemac2.masked -recipes/bioconductor-bsgenome.ptroglodytes.ucsc.pantro5 -recipes/bioconductor-bsgenome.sscrofa.ucsc.susscr3 -recipes/bioconductor-xtrasnplocs.hsapiens.dbsnp144.grch38 recipes/circulator recipes/igdiscover recipes/rnftools @@ -48,6 +35,13 @@ recipes/andi recipes/lcfit recipes/musicc recipes/treekin/0.4.2 +recipes/blast/2.5.0 +recipes/quast +recipes/w4mclassfilter +recipes/tobias +recipes/tadarida-c +recipes/w4mclstrpeakpics +recipes/rsem # Broken due to changes in nalgebra on crates.io https://github.com/varlociraptor/prosic2/issues/1 recipes/prosic @@ -686,7 +680,7 @@ recipes/r-dbchip recipes/r-asics recipes/r-biom -# Deprecated/build fail in Bioconductor +# Deprecated/build fail in Bioconductor 3.8 recipes/bioconductor-atlasrdf recipes/bioconductor-jmosaics recipes/bioconductor-meshsim @@ -696,7 +690,6 @@ recipes/bioconductor-rcytoscape recipes/bioconductor-browservizdemo recipes/bioconductor-pannbuilder recipes/bioconductor-splicer -recipes/bioconductor-flowq recipes/bioconductor-pbcmc recipes/bioconductor-mqtl.nmr recipes/bioconductor-nudge @@ -728,55 +721,2635 @@ recipes/bioconductor-diffbind/2.2.12 recipes/bioconductor-xcms/1.52.0 recipes/bioconductor-s4vectors/0.8.11 -# r-dagitity missing -> missing of V8 in conda-forge -recipes/r-pcalg -recipes/bioconductor-epinem -recipes/bioconductor-debrowser -recipes/bioconductor-mirlab - # r-bibitr missing -> missing V8 in conda-forge recipes/bioconductor-mirsm -# system call failed: Cannot allocate memory -recipes/bioconductor-conumee -recipes/bioconductor-remp +# Build never completes +recipes/bioconductor-cancer -# Missing r-magick -recipes/bioconductor-omicspca +# Marked as build fails in bioconductor release 3.9 +recipes/bioconductor-birte +recipes/bioconductor-dsimer +recipes/bioconductor-flipflop +recipes/bioconductor-gpumagic +recipes/bioconductor-flowq +recipes/bioconductor-procona +recipes/bioconductor-pgpc -# Needs running X server for testing -recipes/bioconductor-mcagui -recipes/bioconductor-easyqpcr +# stringify can't find libmysqlclient.18 +recipes/ucsc-overlapselect +recipes/ucsc-pslmap +recipes/ucsc-pslcdnafilter -# package ‘rjags’ could not be loaded (linking issue) -recipes/bioconductor-madseq +# Only compatible with R >=3.6, which isn't supported by conda-forge yet +recipes/bioconductor-ssrch +recipes/bioconductor-depecher +recipes/bioconductor-msstats +recipes/bioconductor-msstatstmt +recipes/bioconductor-simlr +recipes/bioconductor-smad +recipes/bioconductor-graper +recipes/bioconductor-sitepath +recipes/bioconductor-alevinqc +recipes/bioconductor-topconfects +recipes/bioconductor-specl +recipes/bioconductor-pathwaypca +recipes/bioconductor-biocversion +recipes/bioconductor-rmelting +recipes/bioconductor-tpp2d +recipes/bioconductor-isocorrectorgui +recipes/bioconductor-dcanr +recipes/bioconductor-bigpint +recipes/bioconductor-subcellbarcode +recipes/bioconductor-gladiatox +recipes/bioconductor-biocgenerics + +# Build and rendering failures that are breaking bulk and the nightly uploads +recipes/sqt +recipes/tepid +recipes/aragorn/1.2.38 +recipes/art/3.11.14 +recipes/autodock-vina +recipes/bcbiogff/0.6.2 +recipes/bcbiogff +recipes/biopet/0.8.0 +recipes/biopet +recipes/blockbuster +recipes/metfrag +recipes/metfrag/2.3.1 +recipes/metfrag/2.4.2 +recipes/varscan/2.4.2 +recipes/discovar +recipes/ccat/3.0 +recipes/transabyss +recipes/soapdenovo2-prepare +recipes/damidseq_pipeline +recipes/repeatmodeler +recipes/detonate +recipes/pal_finder +recipes/dfam + +# ld: unknown option: -T +recipes/bioconductor-lpsymphony + +# Requires GTK+ +recipes/bioconductor-hilbertvisgui -# Missing root5 dependency -recipes/bioconductor-xps +# fatal error: zlib.h: No such file or directory +recipes/bioconductor-rbowtie2 -# Build never completes -recipes/bioconductor-cancer +# cannot find -llapack +recipes/bioconductor-tofsims -# Compilation errors (and dependencies) -recipes/bioconductor-bgmix -recipes/bioconductor-chemmineob -recipes/bioconductor-flipflop -recipes/bioconductor-hilbertvisgui -recipes/bioconductor-rsbml -recipes/bioconductor-bgx +# missing r-reldist +recipes/bioconductor-m3drop + +# missing r-saver>=1.1.1 and r-rmagic>=1.3.0 +recipes/bioconductor-screcover + +# Unsupported fortran compiler recipes/bioconductor-iclusterplus -recipes/bioconductor-explorase -recipes/bioconductor-dsimer -recipes/bioconductor-interactivedisplay + +# configure: error: cannot find sources (GLAD) in . or .. recipes/bioconductor-glad recipes/bioconductor-manor recipes/bioconductor-seqcna + +# r-base 3.5.1 and root5 5.34.36 are incompatible +recipes/bioconductor-xps + +# Build fails in bulk +recipes/rmblast +recipes/perl-bio-db-hts + +# missing r-numbers +recipes/bioconductor-dnabarcodecompatibility + +# missing r-sybil +recipes/bioconductor-coregflux + +# missing r-msigdbr +recipes/bioconductor-hyper + +# export LD_LIBRARY_PATH=${BUILD_PREFIX}/x86_64-conda_cos6-linux-gnu/sysroot/usr/lib64 +recipes/bioconductor-bgmix + +# requires a functional X server +recipes/bioconductor-easyqpcr + +# missing dependency r-dagitty +recipes/r-pcalg + +# Unclear why these fail +recipes/bioconductor-encodexplorerdata +recipes/bioconductor-nanotubes +recipes/bioconductor-msqc1 +recipes/bioconductor-clumsiddata + +# Rendering errors that are breaking bulk and the nightly upload +recipes/adam +recipes/albatradis +recipes/anise_basil +recipes/bamclipper +recipes/bbmap/37.10 +recipes/bbmap/37.17 +recipes/bbmap/37.52 +recipes/bbmap/37.62 +recipes/bbmap/37.99 +recipes/bcftools-snvphyl-plugin +recipes/biotradis +recipes/bsmap +recipes/cannoli +recipes/cgview +recipes/crisper_recognition_tool +recipes/Drop-seq_tools +recipes/dsh-bio +recipes/dwgsim +recipes/dxua +recipes/fastindep +recipes/fgbio +recipes/gatk4/4.0.3.0 +recipes/gatk-framework +recipes/gb_taxonomy_tools +recipes/genblastg +recipes/gromacs/2018 +recipes/hr2 +recipes/indelfixer +recipes/je-suite +recipes/mdust +recipes/metacherchant +recipes/mgltools +recipes/mira +recipes/mira/3.4.1.1 +recipes/mira/4.9.5 +recipes/mira/4.9.6 +recipes/mobster +recipes/mummer4 +recipes/mvicuna +recipes/netreg +recipes/ngmlr/0.2.3 +recipes/ngmlr/0.2.4 +recipes/npinv +recipes/opsin/1.4.0 +recipes/opsin/2.1.0 +recipes/opsin/2.4.0 +recipes/pathwaymatcher +recipes/pauda +recipes/pepnovo +recipes/pyteomics +recipes/qorts +recipes/rabix-bunny +recipes/ragout +recipes/rawtools +recipes/rdp_classifier/2.2 +recipes/recon +recipes/regtools +recipes/repeatscout +recipes/rnacode/0.3 +recipes/rna-seqc +recipes/rnastructure +recipes/rnastructure/5.7 +recipes/rnastructure/6.0 +recipes/seqbuster +recipes/seqcluster +recipes/shorah/1.1.3 +recipes/snpeff/4.1l +recipes/snpeff/4.2 +recipes/snver +recipes/soapdenovo2-errorcorrection +recipes/soapec +recipes/socru +recipes/ssake +recipes/subread +recipes/tantan +recipes/tophat-recondition +recipes/tracer +recipes/vcfsamplecompare +recipes/watchdog-wms +recipes/wdltool +recipes/womtool +recipes/xtandem +recipes/yaha + +# Depends on bioconductor-biocgenerics, which can't be built until after R 3.6.1 is released and conda-forge moves its pinnings +recipes/bioconductor-a4 +recipes/bioconductor-a4base +recipes/bioconductor-a4classif +recipes/bioconductor-a4core +recipes/bioconductor-a4preproc +recipes/bioconductor-a4reporting +recipes/bioconductor-abaenrichment +recipes/bioconductor-abarray +recipes/bioconductor-ace +recipes/bioconductor-acgh +recipes/bioconductor-acme recipes/bioconductor-adacgh2 -recipes/bioconductor-snapcgh -recipes/bioconductor-italics +recipes/bioconductor-adam +recipes/bioconductor-adamgui +recipes/bioconductor-adaptest +recipes/bioconductor-adductdata +recipes/bioconductor-adductomicsr +recipes/bioconductor-adme16cod.db +recipes/bioconductor-adsplit +recipes/bioconductor-affixcan +recipes/bioconductor-affy +recipes/bioconductor-affycomp +recipes/bioconductor-affycompatible +recipes/bioconductor-affycompdata +recipes/bioconductor-affycontam +recipes/bioconductor-affycoretools +recipes/bioconductor-affydata +recipes/bioconductor-affyexpress +recipes/bioconductor-affyilm +recipes/bioconductor-affylmgui +recipes/bioconductor-affypara +recipes/bioconductor-affypdnn +recipes/bioconductor-affyplm +recipes/bioconductor-affyqcreport +recipes/bioconductor-affyrnadegradation +recipes/bioconductor-agcdf +recipes/bioconductor-ag.db +recipes/bioconductor-agdex +recipes/bioconductor-agimicrorna +recipes/bioconductor-agprobe +recipes/bioconductor-ahensdbs +recipes/bioconductor-aims +recipes/bioconductor-airway +recipes/bioconductor-aldex2 +recipes/bioconductor-all +recipes/bioconductor-allelicimbalance +recipes/bioconductor-allenpvc +recipes/bioconductor-allmll +recipes/bioconductor-alpine +recipes/bioconductor-alpinedata +recipes/bioconductor-altcdfenvs +recipes/bioconductor-alternativesplicingevents.hg19 +recipes/bioconductor-alternativesplicingevents.hg38 +recipes/bioconductor-amaretto +recipes/bioconductor-ampaffyexample +recipes/bioconductor-amplican +recipes/bioconductor-ampliqueso +recipes/bioconductor-analysispageserver +recipes/bioconductor-anamir +recipes/bioconductor-anaquin +recipes/bioconductor-aneufinder +recipes/bioconductor-anf +recipes/bioconductor-animalcules +recipes/bioconductor-annaffy +recipes/bioconductor-annmap +recipes/bioconductor-annotate +recipes/bioconductor-annotationdbi +recipes/bioconductor-annotationfilter +recipes/bioconductor-annotationforge +recipes/bioconductor-annotationfuncs +recipes/bioconductor-annotationhub +recipes/bioconductor-annotationhubdata +recipes/bioconductor-annotationtools +recipes/bioconductor-annotatr +recipes/bioconductor-anopheles.db0 +recipes/bioconductor-anota +recipes/bioconductor-anota2seq +recipes/bioconductor-antiprofilesdata +recipes/bioconductor-apcomplex +recipes/bioconductor-apeglm +recipes/bioconductor-appreci8r +recipes/bioconductor-arabidopsis.db0 +recipes/bioconductor-aracne.networks +recipes/bioconductor-arrayexpress +recipes/bioconductor-arrayexpresshts +recipes/bioconductor-arraymvout +recipes/bioconductor-arrayqualitymetrics +recipes/bioconductor-arraytools +recipes/bioconductor-arraytv +recipes/bioconductor-artms +recipes/bioconductor-asics +recipes/bioconductor-aspli +recipes/bioconductor-assessorf +recipes/bioconductor-assessorfdata +recipes/bioconductor-assign +recipes/bioconductor-atacseqqc +recipes/bioconductor-ath1121501cdf +recipes/bioconductor-ath1121501.db +recipes/bioconductor-ath1121501probe +recipes/bioconductor-atsnp +recipes/bioconductor-attract +recipes/bioconductor-aucell +recipes/bioconductor-baalchip +recipes/bioconductor-badregionfinder +recipes/bioconductor-bags +recipes/bioconductor-ballgown +recipes/bioconductor-bamsignals +recipes/bioconductor-bandits +recipes/bioconductor-barley1cdf +recipes/bioconductor-barley1probe +recipes/bioconductor-basecallqc +recipes/bioconductor-basic4cseq +recipes/bioconductor-basics +recipes/bioconductor-basicstarrseq +recipes/bioconductor-batchelor +recipes/bioconductor-batchqc +recipes/bioconductor-bayesknockdown +recipes/bioconductor-bayespeak +recipes/bioconductor-baynorm +recipes/bioconductor-bayseq +recipes/bioconductor-bbcanalyzer +recipes/bioconductor-bcellviper +recipes/bioconductor-bcrank +recipes/bioconductor-bcseq +recipes/bioconductor-bdmmacorrect +recipes/bioconductor-beachmat +recipes/bioconductor-beadarray +recipes/bioconductor-beadarrayexampledata +recipes/bioconductor-beadarraysnp +recipes/bioconductor-beadarrayusecases +recipes/bioconductor-bearscc +recipes/bioconductor-beat +recipes/bioconductor-bgeedb +recipes/bioconductor-bgx +recipes/bioconductor-bicare +recipes/bioconductor-bifet recipes/bioconductor-biggr - -# stringify can't find libmysqlclient.18 -recipes/ucsc-overlapselect -recipes/ucsc-pslmap -recipes/ucsc-pslcdnafilter +recipes/bioconductor-bigmelon +recipes/bioconductor-bioassayr +recipes/bioconductor-biobase +recipes/bioconductor-biobroom +recipes/bioconductor-biocancer +recipes/bioconductor-bioccasestudies +recipes/bioconductor-bioccheck +recipes/bioconductor-biocgraph +recipes/bioconductor-biocneighbors +recipes/bioconductor-bioconcotk +recipes/bioconductor-biocor +recipes/bioconductor-biocpkgtools +recipes/bioconductor-biocsingular +recipes/bioconductor-biocsklearn +recipes/bioconductor-biocviews +recipes/bioconductor-biodist +recipes/bioconductor-biomart +recipes/bioconductor-biomm +recipes/bioconductor-biomvcclass +recipes/bioconductor-biomvrcns +recipes/bioconductor-bionet +recipes/bioconductor-bionetstat +recipes/bioconductor-bioqc +recipes/bioconductor-bioseqclass +recipes/bioconductor-biosigner +recipes/bioconductor-biostrings +recipes/bioconductor-biosvd +recipes/bioconductor-biotmle +recipes/bioconductor-biovizbase +recipes/bioconductor-birta +recipes/bioconductor-biseq +recipes/bioconductor-bitseq +recipes/bioconductor-bladderbatch +recipes/bioconductor-blima +recipes/bioconductor-blma +recipes/bioconductor-bloodcancermultiomics2017 +recipes/bioconductor-bnbc +recipes/bioconductor-bodymaprat +recipes/bioconductor-bovinecdf +recipes/bioconductor-bovine.db +recipes/bioconductor-bovine.db0 +recipes/bioconductor-bovineprobe +recipes/bioconductor-bprmeth +recipes/bioconductor-brain +recipes/bioconductor-brainimager +recipes/bioconductor-brainimagerdata +recipes/bioconductor-brainstars +recipes/bioconductor-branchpointer +recipes/bioconductor-breakpointr +recipes/bioconductor-brgedata +recipes/bioconductor-bronchialil13 +recipes/bioconductor-browserviz +recipes/bioconductor-bsgenome +recipes/bioconductor-bsgenome.alyrata.jgi.v1 +recipes/bioconductor-bsgenome.amellifera.beebase.assembly4 +recipes/bioconductor-bsgenome.amellifera.ucsc.apimel2 +recipes/bioconductor-bsgenome.amellifera.ucsc.apimel2.masked +recipes/bioconductor-bsgenome.aofficinalis.ncbi.v1 +recipes/bioconductor-bsgenome.athaliana.tair.04232008 +recipes/bioconductor-bsgenome.athaliana.tair.tair9 +recipes/bioconductor-bsgenome.btaurus.ucsc.bostau3 +recipes/bioconductor-bsgenome.btaurus.ucsc.bostau3.masked +recipes/bioconductor-bsgenome.btaurus.ucsc.bostau4 +recipes/bioconductor-bsgenome.btaurus.ucsc.bostau4.masked +recipes/bioconductor-bsgenome.btaurus.ucsc.bostau6 +recipes/bioconductor-bsgenome.btaurus.ucsc.bostau6.masked +recipes/bioconductor-bsgenome.btaurus.ucsc.bostau8 +recipes/bioconductor-bsgenome.carietinum.ncbi.v1 +recipes/bioconductor-bsgenome.celegans.ucsc.ce10 +recipes/bioconductor-bsgenome.celegans.ucsc.ce11 +recipes/bioconductor-bsgenome.celegans.ucsc.ce2 +recipes/bioconductor-bsgenome.celegans.ucsc.ce6 +recipes/bioconductor-bsgenome.cfamiliaris.ucsc.canfam2 +recipes/bioconductor-bsgenome.cfamiliaris.ucsc.canfam2.masked +recipes/bioconductor-bsgenome.cfamiliaris.ucsc.canfam3 +recipes/bioconductor-bsgenome.cfamiliaris.ucsc.canfam3.masked +recipes/bioconductor-bsgenome.cjacchus.ucsc.caljac3 +recipes/bioconductor-bsgenome.dmelanogaster.ucsc.dm2 +recipes/bioconductor-bsgenome.dmelanogaster.ucsc.dm2.masked +recipes/bioconductor-bsgenome.dmelanogaster.ucsc.dm3 +recipes/bioconductor-bsgenome.dmelanogaster.ucsc.dm3.masked +recipes/bioconductor-bsgenome.dmelanogaster.ucsc.dm6 +recipes/bioconductor-bsgenome.drerio.ucsc.danrer10 +recipes/bioconductor-bsgenome.drerio.ucsc.danrer5 +recipes/bioconductor-bsgenome.drerio.ucsc.danrer5.masked +recipes/bioconductor-bsgenome.drerio.ucsc.danrer6 +recipes/bioconductor-bsgenome.drerio.ucsc.danrer6.masked +recipes/bioconductor-bsgenome.drerio.ucsc.danrer7 +recipes/bioconductor-bsgenome.drerio.ucsc.danrer7.masked +recipes/bioconductor-bsgenome.ecoli.ncbi.20080805 +recipes/bioconductor-bsgenome.gaculeatus.ucsc.gasacu1 +recipes/bioconductor-bsgenome.gaculeatus.ucsc.gasacu1.masked +recipes/bioconductor-bsgenome.ggallus.ucsc.galgal3 +recipes/bioconductor-bsgenome.ggallus.ucsc.galgal3.masked +recipes/bioconductor-bsgenome.ggallus.ucsc.galgal4 +recipes/bioconductor-bsgenome.ggallus.ucsc.galgal4.masked +recipes/bioconductor-bsgenome.ggallus.ucsc.galgal5 +recipes/bioconductor-bsgenome.hsapiens.1000genomes.hs37d5 +recipes/bioconductor-bsgenome.hsapiens.ncbi.grch38 +recipes/bioconductor-bsgenome.hsapiens.ucsc.hg17 +recipes/bioconductor-bsgenome.hsapiens.ucsc.hg17.masked +recipes/bioconductor-bsgenome.hsapiens.ucsc.hg18 +recipes/bioconductor-bsgenome.hsapiens.ucsc.hg18.masked +recipes/bioconductor-bsgenome.hsapiens.ucsc.hg19 +recipes/bioconductor-bsgenome.hsapiens.ucsc.hg19.masked +recipes/bioconductor-bsgenome.hsapiens.ucsc.hg38 +recipes/bioconductor-bsgenome.hsapiens.ucsc.hg38.masked +recipes/bioconductor-bsgenome.mdomestica.ucsc.mondom5 +recipes/bioconductor-bsgenome.mfascicularis.ncbi.5.0 +recipes/bioconductor-bsgenome.mfuro.ucsc.musfur1 +recipes/bioconductor-bsgenome.mmulatta.ucsc.rhemac2 +recipes/bioconductor-bsgenome.mmulatta.ucsc.rhemac2.masked +recipes/bioconductor-bsgenome.mmulatta.ucsc.rhemac3 +recipes/bioconductor-bsgenome.mmulatta.ucsc.rhemac3.masked +recipes/bioconductor-bsgenome.mmulatta.ucsc.rhemac8 +recipes/bioconductor-bsgenome.mmusculus.ucsc.mm10 +recipes/bioconductor-bsgenome.mmusculus.ucsc.mm10.masked +recipes/bioconductor-bsgenome.mmusculus.ucsc.mm8 +recipes/bioconductor-bsgenome.mmusculus.ucsc.mm8.masked +recipes/bioconductor-bsgenome.mmusculus.ucsc.mm9 +recipes/bioconductor-bsgenome.mmusculus.ucsc.mm9.masked +recipes/bioconductor-bsgenome.osativa.msu.msu7 +recipes/bioconductor-bsgenome.ptroglodytes.ucsc.pantro2 +recipes/bioconductor-bsgenome.ptroglodytes.ucsc.pantro2.masked +recipes/bioconductor-bsgenome.ptroglodytes.ucsc.pantro3 +recipes/bioconductor-bsgenome.ptroglodytes.ucsc.pantro3.masked +recipes/bioconductor-bsgenome.ptroglodytes.ucsc.pantro5 +recipes/bioconductor-bsgenome.ptroglodytes.ucsc.pantro6 +recipes/bioconductor-bsgenome.rnorvegicus.ucsc.rn4 +recipes/bioconductor-bsgenome.rnorvegicus.ucsc.rn4.masked +recipes/bioconductor-bsgenome.rnorvegicus.ucsc.rn5 +recipes/bioconductor-bsgenome.rnorvegicus.ucsc.rn5.masked +recipes/bioconductor-bsgenome.rnorvegicus.ucsc.rn6 +recipes/bioconductor-bsgenome.scerevisiae.ucsc.saccer1 +recipes/bioconductor-bsgenome.scerevisiae.ucsc.saccer2 +recipes/bioconductor-bsgenome.scerevisiae.ucsc.saccer3 +recipes/bioconductor-bsgenome.sscrofa.ucsc.susscr11 +recipes/bioconductor-bsgenome.sscrofa.ucsc.susscr3 +recipes/bioconductor-bsgenome.sscrofa.ucsc.susscr3.masked +recipes/bioconductor-bsgenome.tgondii.toxodb.7.0 +recipes/bioconductor-bsgenome.tguttata.ucsc.taegut1 +recipes/bioconductor-bsgenome.tguttata.ucsc.taegut1.masked +recipes/bioconductor-bsgenome.tguttata.ucsc.taegut2 +recipes/bioconductor-bsgenome.vvinifera.urgi.iggp12xv0 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+recipes/bioconductor-yri1kgv +recipes/bioconductor-yrimulti +recipes/bioconductor-zebrafishcdf +recipes/bioconductor-zebrafish.db +recipes/bioconductor-zebrafish.db0 +recipes/bioconductor-zebrafishprobe +recipes/bioconductor-zfpkm +recipes/bioconductor-zinbwave diff --git a/recipes/bioconductor-a4/meta.yaml b/recipes/bioconductor-a4/meta.yaml index 42d6a2cac7379..d9d1dbf30fb6d 100644 --- a/recipes/bioconductor-a4/meta.yaml +++ b/recipes/bioconductor-a4/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.30.0" %} +{% set version = "1.32.0" %} {% set name = "a4" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 4e44a4273b805b3fda0cbbd476566c25 + md5: 00e7562c4412f2a31b54919b66137388 build: number: 0 rpaths: @@ -20,18 +20,18 @@ build: # Suggests: MLP, nlcv, ALL, Cairo requirements: host: - - 'bioconductor-a4base >=1.30.0,<1.31.0' - - 'bioconductor-a4classif >=1.30.0,<1.31.0' - - 'bioconductor-a4core >=1.30.0,<1.31.0' - - 'bioconductor-a4preproc >=1.30.0,<1.31.0' - - 'bioconductor-a4reporting >=1.30.0,<1.31.0' + - 'bioconductor-a4base >=1.32.0,<1.33.0' + - 'bioconductor-a4classif >=1.32.0,<1.33.0' + - 'bioconductor-a4core >=1.32.0,<1.33.0' + - 'bioconductor-a4preproc >=1.32.0,<1.33.0' + - 'bioconductor-a4reporting >=1.32.0,<1.33.0' - r-base run: - - 'bioconductor-a4base >=1.30.0,<1.31.0' - - 'bioconductor-a4classif >=1.30.0,<1.31.0' - - 'bioconductor-a4core >=1.30.0,<1.31.0' - - 'bioconductor-a4preproc >=1.30.0,<1.31.0' - - 'bioconductor-a4reporting >=1.30.0,<1.31.0' + - 'bioconductor-a4base >=1.32.0,<1.33.0' + - 'bioconductor-a4classif >=1.32.0,<1.33.0' + - 'bioconductor-a4core >=1.32.0,<1.33.0' + - 'bioconductor-a4preproc >=1.32.0,<1.33.0' + - 'bioconductor-a4reporting >=1.32.0,<1.33.0' - r-base test: commands: diff --git a/recipes/bioconductor-a4base/meta.yaml b/recipes/bioconductor-a4base/meta.yaml index 6056bbc7ad27c..39916fb8498db 100644 --- a/recipes/bioconductor-a4base/meta.yaml +++ b/recipes/bioconductor-a4base/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.30.0" %} +{% set version = "1.32.0" %} {% set name = "a4Base" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: a8238f64848e4f0974867b0a5f3dc920 + md5: 077a2873fd1bea468bc86307a1eee4e7 build: number: 0 rpaths: @@ -20,27 +20,27 @@ build: # Suggests: Cairo, ALL requirements: host: - - 'bioconductor-a4core >=1.30.0,<1.31.0' - - 'bioconductor-a4preproc >=1.30.0,<1.31.0' - - 'bioconductor-annaffy >=1.54.0,<1.55.0' - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' - - 'bioconductor-biobase >=2.42.0,<2.43.0' - - 'bioconductor-genefilter >=1.64.0,<1.65.0' - - 'bioconductor-limma >=3.38.0,<3.39.0' - - 'bioconductor-multtest >=2.38.0,<2.39.0' + - 'bioconductor-a4core >=1.32.0,<1.33.0' + - 'bioconductor-a4preproc >=1.32.0,<1.33.0' + - 'bioconductor-annaffy >=1.56.0,<1.57.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' + - 'bioconductor-genefilter >=1.66.0,<1.67.0' + - 'bioconductor-limma >=3.40.0,<3.41.0' + - 'bioconductor-multtest >=2.40.0,<2.41.0' - r-base - r-glmnet - r-gplots - r-mpm run: - - 'bioconductor-a4core >=1.30.0,<1.31.0' - - 'bioconductor-a4preproc >=1.30.0,<1.31.0' - - 'bioconductor-annaffy >=1.54.0,<1.55.0' - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' - - 'bioconductor-biobase >=2.42.0,<2.43.0' - - 'bioconductor-genefilter >=1.64.0,<1.65.0' - - 'bioconductor-limma >=3.38.0,<3.39.0' - - 'bioconductor-multtest >=2.38.0,<2.39.0' + - 'bioconductor-a4core >=1.32.0,<1.33.0' + - 'bioconductor-a4preproc >=1.32.0,<1.33.0' + - 'bioconductor-annaffy >=1.56.0,<1.57.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' + - 'bioconductor-genefilter >=1.66.0,<1.67.0' + - 'bioconductor-limma >=3.40.0,<3.41.0' + - 'bioconductor-multtest >=2.40.0,<2.41.0' - r-base - r-glmnet - r-gplots diff --git a/recipes/bioconductor-a4classif/meta.yaml b/recipes/bioconductor-a4classif/meta.yaml index 310ad67c2e993..dfb7bdaf5045a 100644 --- a/recipes/bioconductor-a4classif/meta.yaml +++ b/recipes/bioconductor-a4classif/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.30.0" %} +{% set version = "1.32.0" %} {% set name = "a4Classif" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: f3c574a15569caf4bc36badf16e2403a + md5: c194b90cc4d80c9d589d6c1269ac4da2 build: number: 0 rpaths: @@ -20,18 +20,18 @@ build: # Suggests: ALL requirements: host: - - 'bioconductor-a4core >=1.30.0,<1.31.0' - - 'bioconductor-a4preproc >=1.30.0,<1.31.0' - - 'bioconductor-mlinterfaces >=1.62.0,<1.63.0' + - 'bioconductor-a4core >=1.32.0,<1.33.0' + - 'bioconductor-a4preproc >=1.32.0,<1.33.0' + - 'bioconductor-mlinterfaces >=1.64.0,<1.65.0' - r-base - r-glmnet - r-pamr - r-rocr - r-varselrf run: - - 'bioconductor-a4core >=1.30.0,<1.31.0' - - 'bioconductor-a4preproc >=1.30.0,<1.31.0' - - 'bioconductor-mlinterfaces >=1.62.0,<1.63.0' + - 'bioconductor-a4core >=1.32.0,<1.33.0' + - 'bioconductor-a4preproc >=1.32.0,<1.33.0' + - 'bioconductor-mlinterfaces >=1.64.0,<1.65.0' - r-base - r-glmnet - r-pamr diff --git a/recipes/bioconductor-a4core/meta.yaml b/recipes/bioconductor-a4core/meta.yaml index 1a8c96f6c1344..56c6e345d6b57 100644 --- a/recipes/bioconductor-a4core/meta.yaml +++ b/recipes/bioconductor-a4core/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.30.0" %} +{% set version = "1.32.0" %} {% set name = "a4Core" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 1c18ebb284225195642263519f84089b + md5: 0764afbd62979e811eaf99fda4807e15 build: number: 0 rpaths: @@ -19,11 +19,11 @@ build: noarch: generic requirements: host: - - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' - r-base - r-glmnet run: - - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' - r-base - r-glmnet test: diff --git a/recipes/bioconductor-a4preproc/meta.yaml b/recipes/bioconductor-a4preproc/meta.yaml index e2c637e3f572b..85836c4d307e3 100644 --- a/recipes/bioconductor-a4preproc/meta.yaml +++ b/recipes/bioconductor-a4preproc/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.30.0" %} +{% set version = "1.32.0" %} {% set name = "a4Preproc" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 79f088fcd94c8cf56ca40b40a59b8e97 + md5: f28197ecba4a5696660442d33aa6638d build: number: 0 rpaths: @@ -20,10 +20,10 @@ build: # Suggests: ALL, hgu95av2.db requirements: host: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' - r-base run: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' - r-base test: commands: diff --git a/recipes/bioconductor-a4reporting/meta.yaml b/recipes/bioconductor-a4reporting/meta.yaml index cc3f99a348bab..5d80fc980a701 100644 --- a/recipes/bioconductor-a4reporting/meta.yaml +++ b/recipes/bioconductor-a4reporting/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.30.0" %} +{% set version = "1.32.0" %} {% set name = "a4Reporting" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 4a7eb752a3ac2e746930c0166c248d3d + md5: c37278b81f6909876a48043145cbdacc build: number: 0 rpaths: @@ -19,11 +19,11 @@ build: noarch: generic requirements: host: - - 'bioconductor-annaffy >=1.54.0,<1.55.0' + - 'bioconductor-annaffy >=1.56.0,<1.57.0' - r-base - r-xtable run: - - 'bioconductor-annaffy >=1.54.0,<1.55.0' + - 'bioconductor-annaffy >=1.56.0,<1.57.0' - r-base - r-xtable test: diff --git a/recipes/bioconductor-abadata/meta.yaml b/recipes/bioconductor-abadata/meta.yaml index bb3879f1e95e1..f188da61b39aa 100644 --- a/recipes/bioconductor-abadata/meta.yaml +++ b/recipes/bioconductor-abadata/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.12.0" %} +{% set version = "1.14.0" %} {% set name = "ABAData" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,9 +10,9 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 617a2967ed10a6b1f90406420a28545e + md5: 14527790b75fc139b5bbed7981c1a1ea build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ @@ -23,7 +23,7 @@ requirements: - r-base run: - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-abadata/post-link.sh b/recipes/bioconductor-abadata/post-link.sh index 50b809e3ecd35..a9a53fcc1c885 100644 --- a/recipes/bioconductor-abadata/post-link.sh +++ b/recipes/bioconductor-abadata/post-link.sh @@ -1,11 +1,11 @@ #!/bin/bash -FN="ABAData_1.12.0.tar.gz" +FN="ABAData_1.14.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/experiment/src/contrib/ABAData_1.12.0.tar.gz" - "https://bioarchive.galaxyproject.org/ABAData_1.12.0.tar.gz" - "https://depot.galaxyproject.org/software/bioconductor-abadata/bioconductor-abadata_1.12.0_src_all.tar.gz" + "https://bioconductor.org/packages/3.9/data/experiment/src/contrib/ABAData_1.14.0.tar.gz" + "https://bioarchive.galaxyproject.org/ABAData_1.14.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-abadata/bioconductor-abadata_1.14.0_src_all.tar.gz" ) -MD5="617a2967ed10a6b1f90406420a28545e" +MD5="14527790b75fc139b5bbed7981c1a1ea" # Use a staging area in the conda dir rather than temp dirs, both to avoid # permission issues as well as to have things downloaded in a predictable @@ -16,7 +16,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-abaenrichment/meta.yaml b/recipes/bioconductor-abaenrichment/meta.yaml index 68af8a5a138eb..cb809e652c75e 100644 --- a/recipes/bioconductor-abaenrichment/meta.yaml +++ b/recipes/bioconductor-abaenrichment/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.12.0" %} +{% set version = "1.14.0" %} {% set name = "ABAEnrichment" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: f5934cab26c8b62087ed9242aa0cbf8a + md5: 1a51e6bb3d1686f966c8a12ce6e08c9f build: number: 0 rpaths: @@ -19,16 +19,16 @@ build: # Suggests: BiocStyle, knitr, testthat requirements: host: - - 'bioconductor-abadata >=1.12.0,<1.13.0' - - 'bioconductor-gofuncr >=1.2.0,<1.3.0' + - 'bioconductor-abadata >=1.14.0,<1.15.0' + - 'bioconductor-gofuncr >=1.4.0,<1.5.0' - r-base - 'r-data.table >=1.10.4' - 'r-gplots >=2.14.2' - 'r-gtools >=3.5.0' - 'r-rcpp >=0.11.5' run: - - 'bioconductor-abadata >=1.12.0,<1.13.0' - - 'bioconductor-gofuncr >=1.2.0,<1.3.0' + - 'bioconductor-abadata >=1.14.0,<1.15.0' + - 'bioconductor-gofuncr >=1.4.0,<1.5.0' - r-base - 'r-data.table >=1.10.4' - 'r-gplots >=2.14.2' diff --git a/recipes/bioconductor-abarray/meta.yaml b/recipes/bioconductor-abarray/meta.yaml index 19e12280a1143..b161992225c13 100644 --- a/recipes/bioconductor-abarray/meta.yaml +++ b/recipes/bioconductor-abarray/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.50.0" %} +{% set version = "1.52.0" %} {% set name = "ABarray" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 84761cfa2828e57c5ef0daa712f741d8 + md5: 549b89684d9e319caac557f517acc7e3 build: number: 0 rpaths: @@ -20,12 +20,12 @@ build: # Suggests: limma, LPE requirements: host: - - 'bioconductor-biobase >=2.42.0,<2.43.0' - - 'bioconductor-multtest >=2.38.0,<2.39.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' + - 'bioconductor-multtest >=2.40.0,<2.41.0' - r-base run: - - 'bioconductor-biobase >=2.42.0,<2.43.0' - - 'bioconductor-multtest >=2.38.0,<2.39.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' + - 'bioconductor-multtest >=2.40.0,<2.41.0' - r-base test: commands: diff --git a/recipes/bioconductor-abseqr/meta.yaml b/recipes/bioconductor-abseqr/meta.yaml index 77f7ba37ab596..15cb1cf9e4fae 100644 --- a/recipes/bioconductor-abseqr/meta.yaml +++ b/recipes/bioconductor-abseqr/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.0.0" %} +{% set version = "1.2.0" %} {% set name = "abseqR" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,9 +10,9 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: de9e8be03e84433a1fc776c563ec4426 + md5: a1cf442849ec89bc9937730094727705 build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ @@ -21,8 +21,8 @@ build: # SystemRequirements: pandoc (>= 1.19.2.1) requirements: host: - - 'bioconductor-biocparallel >=1.16.0,<1.17.0' - - 'bioconductor-biocstyle >=2.10.0,<2.11.0' + - 'bioconductor-biocparallel >=1.18.0,<1.19.0' + - 'bioconductor-biocstyle >=2.12.0,<2.13.0' - r-base - r-circlize - r-flexdashboard @@ -40,9 +40,10 @@ requirements: - r-stringr - r-vegan - r-venndiagram + - pandoc >=1.19.2.1 run: - - 'bioconductor-biocparallel >=1.16.0,<1.17.0' - - 'bioconductor-biocstyle >=2.10.0,<2.11.0' + - 'bioconductor-biocparallel >=1.18.0,<1.19.0' + - 'bioconductor-biocstyle >=2.12.0,<2.13.0' - r-base - r-circlize - r-flexdashboard @@ -60,6 +61,7 @@ requirements: - r-stringr - r-vegan - r-venndiagram + - pandoc >=1.19.2.1 test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-absseq/meta.yaml b/recipes/bioconductor-absseq/meta.yaml index 9fabb26ead2d6..8d8cc01a6df64 100644 --- a/recipes/bioconductor-absseq/meta.yaml +++ b/recipes/bioconductor-absseq/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.36.0" %} +{% set version = "1.38.0" %} {% set name = "ABSSeq" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 030589f236271c0cfa666af69b74e223 + md5: 3b22e021c165c711734201fe2d8c9503 build: number: 0 rpaths: @@ -20,11 +20,11 @@ build: # Suggests: edgeR requirements: host: - - 'bioconductor-limma >=3.38.0,<3.39.0' + - 'bioconductor-limma >=3.40.0,<3.41.0' - r-base - r-locfit run: - - 'bioconductor-limma >=3.38.0,<3.39.0' + - 'bioconductor-limma >=3.40.0,<3.41.0' - r-base - r-locfit test: diff --git a/recipes/bioconductor-acde/meta.yaml b/recipes/bioconductor-acde/meta.yaml index 2ba01cd6a1028..10d2875d99772 100644 --- a/recipes/bioconductor-acde/meta.yaml +++ b/recipes/bioconductor-acde/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.12.0" %} +{% set version = "1.14.0" %} {% set name = "acde" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: f5bf1b85bb7436813020a5aec3765d12 + md5: 5bca02d14050dab364619ac2f3fc1dd0 build: number: 0 rpaths: diff --git a/recipes/bioconductor-ace/meta.yaml b/recipes/bioconductor-ace/meta.yaml index 4c4fb59a45bf5..5c5b3499ef47b 100644 --- a/recipes/bioconductor-ace/meta.yaml +++ b/recipes/bioconductor-ace/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.0.0" %} +{% set version = "1.2.0" %} {% set name = "ACE" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 20953839cc1ce4ab6b8a3689954c3c74 + md5: 6190b52169f64b8372c05c2c920a2e55 build: number: 0 rpaths: @@ -20,13 +20,15 @@ build: # Suggests: knitr, rmarkdown, BiocStyle requirements: host: - - 'bioconductor-biobase >=2.42.0,<2.43.0' - - 'bioconductor-qdnaseq >=1.18.0,<1.19.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' + - 'bioconductor-genomicranges >=1.36.0,<1.37.0' + - 'bioconductor-qdnaseq >=1.20.0,<1.21.0' - r-base - r-ggplot2 run: - - 'bioconductor-biobase >=2.42.0,<2.43.0' - - 'bioconductor-qdnaseq >=1.18.0,<1.19.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' + - 'bioconductor-genomicranges >=1.36.0,<1.37.0' + - 'bioconductor-qdnaseq >=1.20.0,<1.21.0' - r-base - r-ggplot2 test: diff --git a/recipes/bioconductor-acgh/meta.yaml b/recipes/bioconductor-acgh/meta.yaml index 095c8593716a9..d43ac499b80fa 100644 --- a/recipes/bioconductor-acgh/meta.yaml +++ b/recipes/bioconductor-acgh/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.60.0" %} +{% set version = "1.62.0" %} {% set name = "aCGH" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 4bdcf0503d13c9393ea12593e769d165 + md5: be0bef86c5af1ecdb9c23f26dcea7595 build: number: 0 rpaths: @@ -18,14 +18,14 @@ build: - lib/ requirements: host: - - 'bioconductor-biobase >=2.42.0,<2.43.0' - - 'bioconductor-multtest >=2.38.0,<2.39.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' + - 'bioconductor-multtest >=2.40.0,<2.41.0' - r-base - r-cluster - r-survival run: - - 'bioconductor-biobase >=2.42.0,<2.43.0' - - 'bioconductor-multtest >=2.38.0,<2.39.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' + - 'bioconductor-multtest >=2.40.0,<2.41.0' - r-base - r-cluster - r-survival diff --git a/recipes/bioconductor-acme/meta.yaml b/recipes/bioconductor-acme/meta.yaml index 747a7761320d0..aa3b465eea6a7 100644 --- a/recipes/bioconductor-acme/meta.yaml +++ b/recipes/bioconductor-acme/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "2.38.0" %} +{% set version = "2.40.0" %} {% set name = "ACME" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 02fba578c93d2cf28d7f548400bae520 + md5: dda3b6d9d427487387d71d30ec8ac676 build: number: 0 rpaths: @@ -18,12 +18,12 @@ build: - lib/ requirements: host: - - 'bioconductor-biobase >=2.42.0,<2.43.0' - - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' + - 'bioconductor-biocgenerics >=0.30.0,<0.31.0' - r-base run: - - 'bioconductor-biobase >=2.42.0,<2.43.0' - - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' + - 'bioconductor-biocgenerics >=0.30.0,<0.31.0' - r-base build: - {{ compiler('c') }} diff --git a/recipes/bioconductor-adacgh2/meta.yaml b/recipes/bioconductor-adacgh2/meta.yaml index 73cf53ff509c6..7bd9fe1dbfee6 100644 --- a/recipes/bioconductor-adacgh2/meta.yaml +++ b/recipes/bioconductor-adacgh2/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "2.22.0" %} +{% set version = "2.24.0" %} {% set name = "ADaCGH2" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: cd000cb277c242ba358cade134fc5a4d + md5: 61c8ba54a1304c9c18fc0d47b8d75dae build: number: 0 rpaths: @@ -19,11 +19,11 @@ build: # Suggests: CGHregions, Cairo, limma requirements: host: - - 'bioconductor-acgh >=1.60.0,<1.61.0' - - 'bioconductor-dnacopy >=1.56.0,<1.57.0' - - 'bioconductor-glad >=2.46.0,<2.47.0' - - 'bioconductor-snapcgh >=1.52.0,<1.53.0' - - 'bioconductor-tilingarray >=1.60.0,<1.61.0' + - 'bioconductor-acgh >=1.62.0,<1.63.0' + - 'bioconductor-dnacopy >=1.58.0,<1.59.0' + - 'bioconductor-glad >=2.48.0,<2.49.0' + - 'bioconductor-snapcgh >=1.54.0,<1.55.0' + - 'bioconductor-tilingarray >=1.62.0,<1.63.0' - r-base - r-bit - r-cluster @@ -31,11 +31,11 @@ requirements: - r-ffbase - r-waveslim run: - - 'bioconductor-acgh >=1.60.0,<1.61.0' - - 'bioconductor-dnacopy >=1.56.0,<1.57.0' - - 'bioconductor-glad >=2.46.0,<2.47.0' - - 'bioconductor-snapcgh >=1.52.0,<1.53.0' - - 'bioconductor-tilingarray >=1.60.0,<1.61.0' + - 'bioconductor-acgh >=1.62.0,<1.63.0' + - 'bioconductor-dnacopy >=1.58.0,<1.59.0' + - 'bioconductor-glad >=2.48.0,<2.49.0' + - 'bioconductor-snapcgh >=1.54.0,<1.55.0' + - 'bioconductor-tilingarray >=1.62.0,<1.63.0' - r-base - r-bit - r-cluster diff --git a/recipes/bioconductor-adam/build.sh b/recipes/bioconductor-adam/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-adam/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-adam/meta.yaml b/recipes/bioconductor-adam/meta.yaml new file mode 100644 index 0000000000000..7761f3009962a --- /dev/null +++ b/recipes/bioconductor-adam/meta.yaml @@ -0,0 +1,55 @@ +{% set version = "1.0.0" %} +{% set name = "ADAM" %} +{% set bioc = "3.9" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: 7d35a54f2e960ec7a7ec8f6f8f9a2e54 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ +# Suggests: testthat +# SystemRequirements: C++11 +requirements: + host: + - 'bioconductor-go.db >=3.8.0,<3.9.0' + - 'bioconductor-keggrest >=1.24.0,<1.25.0' + - 'bioconductor-summarizedexperiment >=1.14.0,<1.15.0' + - r-base + - 'r-dplyr >=0.7.6' + - 'r-dt >=0.4' + - r-knitr + - 'r-pbapply >=1.3-4' + - 'r-rcpp >=0.12.18' + - 'r-stringr >=1.3.1' + run: + - 'bioconductor-go.db >=3.8.0,<3.9.0' + - 'bioconductor-keggrest >=1.24.0,<1.25.0' + - 'bioconductor-summarizedexperiment >=1.14.0,<1.15.0' + - r-base + - 'r-dplyr >=0.7.6' + - 'r-dt >=0.4' + - r-knitr + - 'r-pbapply >=1.3-4' + - 'r-rcpp >=0.12.18' + - 'r-stringr >=1.3.1' + build: + - {{ compiler('c') }} + - {{ compiler('cxx') }} + - make +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: 'GPL (>= 2)' + summary: 'ADAM is a GSEA R package created to group a set of genes from comparative samples (control versus experiment) belonging to different species according to their respective functions (Gene Ontology and KEGG pathways as default) and show their significance by calculating p-values referring togene diversity and activity. Each group of genes is called GFAG (Group of Functionally Associated Genes).' + diff --git a/recipes/bioconductor-adamgui/build.sh b/recipes/bioconductor-adamgui/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-adamgui/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-adamgui/meta.yaml b/recipes/bioconductor-adamgui/meta.yaml new file mode 100644 index 0000000000000..ce6c5bb56efb1 --- /dev/null +++ b/recipes/bioconductor-adamgui/meta.yaml @@ -0,0 +1,73 @@ +{% set version = "1.0.0" %} +{% set name = "ADAMgui" %} +{% set bioc = "3.9" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: 1c158e0c42e546c9f3eba19fb76a486a +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: BiocStyle +requirements: + host: + - 'bioconductor-adam >=1.0.0,<1.1.0' + - 'bioconductor-go.db >=3.8.0,<3.9.0' + - r-base + - 'r-colorramps >=2.3' + - 'r-data.table >=1.11.4' + - 'r-dplyr >=0.7.6' + - 'r-dt >=0.4' + - 'r-ggplot2 >=3.0.0' + - 'r-ggpubr >=0.1.8' + - 'r-ggrepel >=0.8.0' + - 'r-ggsignif >=0.4.0' + - 'r-gridextra >=2.3' + - r-knitr + - 'r-rcolorbrewer >=1.1-2' + - 'r-reshape2 >=1.4.3' + - 'r-shiny >=1.1.0' + - 'r-shinyjs >=1.0' + - 'r-stringi >=1.2.4' + - 'r-stringr >=1.3.1' + - r-testthat + - 'r-varhandle >=2.0.3' + run: + - 'bioconductor-adam >=1.0.0,<1.1.0' + - 'bioconductor-go.db >=3.8.0,<3.9.0' + - r-base + - 'r-colorramps >=2.3' + - 'r-data.table >=1.11.4' + - 'r-dplyr >=0.7.6' + - 'r-dt >=0.4' + - 'r-ggplot2 >=3.0.0' + - 'r-ggpubr >=0.1.8' + - 'r-ggrepel >=0.8.0' + - 'r-ggsignif >=0.4.0' + - 'r-gridextra >=2.3' + - r-knitr + - 'r-rcolorbrewer >=1.1-2' + - 'r-reshape2 >=1.4.3' + - 'r-shiny >=1.1.0' + - 'r-shinyjs >=1.0' + - 'r-stringi >=1.2.4' + - 'r-stringr >=1.3.1' + - r-testthat + - 'r-varhandle >=2.0.3' +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: 'GPL (>= 2)' + summary: 'ADAMgui is a Graphical User Interface for the ADAM package. The ADAMgui package provides 2 shiny-based applications that allows the user to study the output of the ADAM package files through different plots. It''s possible, for example, to choose a specific GFAG and observe the gene expression behavior with the plots created with the GFAGtargetUi function. Features such as differential expression and foldchange can be easily seen with aid of the plots made with GFAGpathUi function.' + diff --git a/recipes/bioconductor-adaptest/meta.yaml b/recipes/bioconductor-adaptest/meta.yaml index 8ee6327b13445..57bec680b2f28 100644 --- a/recipes/bioconductor-adaptest/meta.yaml +++ b/recipes/bioconductor-adaptest/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.2.0" %} +{% set version = "1.4.0" %} {% set name = "adaptest" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 1535857a21f2819c2930aded9d404325 + md5: 01ac7bda196917f184b581d772f2b112 build: number: 0 rpaths: @@ -20,13 +20,13 @@ build: # Suggests: testthat, Matrix, SuperLearner, earth, gam, nnls, airway, rmarkdown, knitr, BiocStyle requirements: host: - - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' + - 'bioconductor-summarizedexperiment >=1.14.0,<1.15.0' - r-base - r-calibrate - 'r-origami >=1.0.0' - r-tmle run: - - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' + - 'bioconductor-summarizedexperiment >=1.14.0,<1.15.0' - r-base - r-calibrate - 'r-origami >=1.0.0' diff --git a/recipes/bioconductor-adductdata/meta.yaml b/recipes/bioconductor-adductdata/meta.yaml new file mode 100644 index 0000000000000..56f295f881662 --- /dev/null +++ b/recipes/bioconductor-adductdata/meta.yaml @@ -0,0 +1,38 @@ +{% set version = "1.0.0" %} +{% set name = "adductData" %} +{% set bioc = "3.9" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: ee38a871976b2c0f4eba667771f3b3a0 +build: + number: 1 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: knitr (>= 1.15.1), rmarkdown (>= 1.5) +requirements: + host: + - 'bioconductor-annotationhub >=2.16.0,<2.17.0' + - 'bioconductor-experimenthub >=1.10.0,<1.11.0' + - r-base + run: + - 'bioconductor-annotationhub >=2.16.0,<2.17.0' + - 'bioconductor-experimenthub >=1.10.0,<1.11.0' + - r-base + - curl +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'mzXML files from Grigoryan et al 2016 (Anal Chem).' + diff --git a/recipes/bioconductor-adductdata/post-link.sh b/recipes/bioconductor-adductdata/post-link.sh new file mode 100644 index 0000000000000..fccfc82a0537c --- /dev/null +++ b/recipes/bioconductor-adductdata/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="adductData_1.0.0.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.9/data/experiment/src/contrib/adductData_1.0.0.tar.gz" + "https://bioarchive.galaxyproject.org/adductData_1.0.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-adductdata/bioconductor-adductdata_1.0.0_src_all.tar.gz" +) +MD5="ee38a871976b2c0f4eba667771f3b3a0" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + curl $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-adductdata/pre-unlink.sh b/recipes/bioconductor-adductdata/pre-unlink.sh new file mode 100644 index 0000000000000..ae9c01d8a812e --- /dev/null +++ b/recipes/bioconductor-adductdata/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ adductData diff --git a/recipes/bioconductor-adductomicsr/build.sh b/recipes/bioconductor-adductomicsr/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-adductomicsr/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-adductomicsr/meta.yaml b/recipes/bioconductor-adductomicsr/meta.yaml new file mode 100644 index 0000000000000..a848d13ebf4d5 --- /dev/null +++ b/recipes/bioconductor-adductomicsr/meta.yaml @@ -0,0 +1,75 @@ +{% set version = "1.0.0" %} +{% set name = "adductomicsR" %} +{% set bioc = "3.9" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: f46d8533250c8bb1e9c5c85409c1b96d +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: knitr (>= 1.15.1), rmarkdown (>= 1.5), Rdisop (>= 1.34.0), testthat +requirements: + host: + - 'bioconductor-adductdata >=1.0.0,<1.1.0' + - 'bioconductor-annotationhub >=2.16.0,<2.17.0' + - 'bioconductor-experimenthub >=1.10.0,<1.11.0' + - 'bioconductor-mzr >=2.18.0,<2.19.0' + - 'r-ade4 >=1.7.6' + - r-base + - 'r-bootstrap >=2017.2' + - 'r-data.table >=1.10.4' + - 'r-dosnow >=1.0.14' + - 'r-dplyr >=0.7.5' + - 'r-dt >=0.2' + - 'r-fastcluster >=1.1.22' + - 'r-foreach >=1.4.3' + - 'r-fpc >=2.1.10' + - 'r-orgmassspecr >=0.4.6' + - 'r-pastecs >=1.3.18' + - 'r-pracma >=2.0.4' + - 'r-rcppeigen >=0.3.3.3.0' + - 'r-reshape2 >=1.4.2' + - 'r-rvest >=0.3.2' + - 'r-smoother >=1.1' + - 'r-zoo >=1.8' + run: + - 'bioconductor-adductdata >=1.0.0,<1.1.0' + - 'bioconductor-annotationhub >=2.16.0,<2.17.0' + - 'bioconductor-experimenthub >=1.10.0,<1.11.0' + - 'bioconductor-mzr >=2.18.0,<2.19.0' + - 'r-ade4 >=1.7.6' + - r-base + - 'r-bootstrap >=2017.2' + - 'r-data.table >=1.10.4' + - 'r-dosnow >=1.0.14' + - 'r-dplyr >=0.7.5' + - 'r-dt >=0.2' + - 'r-fastcluster >=1.1.22' + - 'r-foreach >=1.4.3' + - 'r-fpc >=2.1.10' + - 'r-orgmassspecr >=0.4.6' + - 'r-pastecs >=1.3.18' + - 'r-pracma >=2.0.4' + - 'r-rcppeigen >=0.3.3.3.0' + - 'r-reshape2 >=1.4.2' + - 'r-rvest >=0.3.2' + - 'r-smoother >=1.1' + - 'r-zoo >=1.8' +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'Processes MS2 data to identify potentially adducted peptides from spectra that has been corrected for mass drift and retention time drift and quantifies MS1 level mass spectral peaks.' + diff --git a/recipes/bioconductor-adme16cod.db/meta.yaml b/recipes/bioconductor-adme16cod.db/meta.yaml index a8c10c48572b6..24327cf4dbfd1 100644 --- a/recipes/bioconductor-adme16cod.db/meta.yaml +++ b/recipes/bioconductor-adme16cod.db/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.4.0" %} {% set name = "adme16cod.db" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -12,7 +12,7 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 3902516a40a503302ef732143b2394b9 build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ @@ -20,14 +20,14 @@ build: # Suggests: annotate, RUnit requirements: host: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' - - 'bioconductor-org.rn.eg.db >=3.7.0,<3.8.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' + - 'bioconductor-org.rn.eg.db >=3.8.0,<3.9.0' - r-base run: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' - - 'bioconductor-org.rn.eg.db >=3.7.0,<3.8.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' + - 'bioconductor-org.rn.eg.db >=3.8.0,<3.9.0' - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-adme16cod.db/post-link.sh b/recipes/bioconductor-adme16cod.db/post-link.sh index bc38bb05eb812..31480d35ab688 100644 --- a/recipes/bioconductor-adme16cod.db/post-link.sh +++ b/recipes/bioconductor-adme16cod.db/post-link.sh @@ -1,9 +1,10 @@ #!/bin/bash FN="adme16cod.db_3.4.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/adme16cod.db_3.4.0.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/adme16cod.db_3.4.0.tar.gz" "https://bioarchive.galaxyproject.org/adme16cod.db_3.4.0.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-adme16cod.db/bioconductor-adme16cod.db_3.4.0_src_all.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-adme16cod.db/bioconductor-adme16cod.db_3.4.0_src_all.tar.gz" ) MD5="3902516a40a503302ef732143b2394b9" @@ -16,7 +17,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-adsplit/meta.yaml b/recipes/bioconductor-adsplit/meta.yaml index 69252cc0de95d..03cfd2373398e 100644 --- a/recipes/bioconductor-adsplit/meta.yaml +++ b/recipes/bioconductor-adsplit/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.52.0" %} +{% set version = "1.54.0" %} {% set name = "adSplit" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: a5cd67644a93b10c454e0584b002e08d + md5: a392edf9d83df7654bce88050c3d9a61 build: number: 0 rpaths: @@ -19,19 +19,19 @@ build: # Suggests: golubEsets (>= 1.0), vsn (>= 1.5.0), hu6800.db (>= 1.8.1) requirements: host: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' - - 'bioconductor-biobase >=2.42.0,<2.43.0' - - 'bioconductor-go.db >=3.7.0,<3.8.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' + - 'bioconductor-go.db >=3.8.0,<3.9.0' - 'bioconductor-kegg.db >=3.2.0,<3.3.0' - - 'bioconductor-multtest >=2.38.0,<2.39.0' + - 'bioconductor-multtest >=2.40.0,<2.41.0' - r-base - 'r-cluster >=1.9.1' run: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' - - 'bioconductor-biobase >=2.42.0,<2.43.0' - - 'bioconductor-go.db >=3.7.0,<3.8.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' + - 'bioconductor-go.db >=3.8.0,<3.9.0' - 'bioconductor-kegg.db >=3.2.0,<3.3.0' - - 'bioconductor-multtest >=2.38.0,<2.39.0' + - 'bioconductor-multtest >=2.40.0,<2.41.0' - r-base - 'r-cluster >=1.9.1' build: diff --git a/recipes/bioconductor-affixcan/meta.yaml b/recipes/bioconductor-affixcan/meta.yaml index dfd673e9a880b..d10bf3a42fb78 100644 --- a/recipes/bioconductor-affixcan/meta.yaml +++ b/recipes/bioconductor-affixcan/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.0.0" %} +{% set version = "1.2.0" %} {% set name = "AffiXcan" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 20b361ce24b3fbf71f7d3a032655a98d + md5: 1ecf671ff853da1943fa93927c9a84d9 build: number: 0 rpaths: @@ -20,14 +20,14 @@ build: # Suggests: BiocStyle, knitr, rmarkdown requirements: host: - - 'bioconductor-biocparallel >=1.16.0,<1.17.0' - - 'bioconductor-multiassayexperiment >=1.8.0,<1.9.0' - - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' + - 'bioconductor-biocparallel >=1.18.0,<1.19.0' + - 'bioconductor-multiassayexperiment >=1.10.0,<1.11.0' + - 'bioconductor-summarizedexperiment >=1.14.0,<1.15.0' - r-base run: - - 'bioconductor-biocparallel >=1.16.0,<1.17.0' - - 'bioconductor-multiassayexperiment >=1.8.0,<1.9.0' - - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' + - 'bioconductor-biocparallel >=1.18.0,<1.19.0' + - 'bioconductor-multiassayexperiment >=1.10.0,<1.11.0' + - 'bioconductor-summarizedexperiment >=1.14.0,<1.15.0' - r-base test: commands: diff --git a/recipes/bioconductor-affxparser/meta.yaml b/recipes/bioconductor-affxparser/meta.yaml index 99184ff5fc6c7..e6adf7a797d8a 100644 --- a/recipes/bioconductor-affxparser/meta.yaml +++ b/recipes/bioconductor-affxparser/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.54.0" %} +{% set version = "1.56.0" %} {% set name = "affxparser" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 1c7cbf0945cc1504d16ba19d68b0f192 + md5: 27535bccec824509ea79df83a641e32d build: number: 0 rpaths: diff --git a/recipes/bioconductor-affy/meta.yaml b/recipes/bioconductor-affy/meta.yaml index 11864893d1214..b0c0fbd50c8eb 100644 --- a/recipes/bioconductor-affy/meta.yaml +++ b/recipes/bioconductor-affy/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.60.0" %} +{% set version = "1.62.0" %} {% set name = "affy" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 0f37ad355a3b6a6b501c65a3deec2d41 + md5: 0eb552db00c271587a6736744dfa0218 build: number: 0 rpaths: @@ -19,19 +19,19 @@ build: # Suggests: tkWidgets (>= 1.19.0), affydata, widgetTools requirements: host: - - 'bioconductor-affyio >=1.52.0,<1.53.0' - - 'bioconductor-biobase >=2.42.0,<2.43.0' - - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' - - 'bioconductor-preprocesscore >=1.44.0,<1.45.0' - - 'bioconductor-zlibbioc >=1.28.0,<1.29.0' + - 'bioconductor-affyio >=1.54.0,<1.55.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' + - 'bioconductor-biocgenerics >=0.30.0,<0.31.0' + - 'bioconductor-preprocesscore >=1.46.0,<1.47.0' + - 'bioconductor-zlibbioc >=1.30.0,<1.31.0' - r-base - r-biocmanager run: - - 'bioconductor-affyio >=1.52.0,<1.53.0' - - 'bioconductor-biobase >=2.42.0,<2.43.0' - - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' - - 'bioconductor-preprocesscore >=1.44.0,<1.45.0' - - 'bioconductor-zlibbioc >=1.28.0,<1.29.0' + - 'bioconductor-affyio >=1.54.0,<1.55.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' + - 'bioconductor-biocgenerics >=0.30.0,<0.31.0' + - 'bioconductor-preprocesscore >=1.46.0,<1.47.0' + - 'bioconductor-zlibbioc >=1.30.0,<1.31.0' - r-base - r-biocmanager build: diff --git a/recipes/bioconductor-affycomp/meta.yaml b/recipes/bioconductor-affycomp/meta.yaml index 2755a2e54757a..3af261350c3d4 100644 --- a/recipes/bioconductor-affycomp/meta.yaml +++ b/recipes/bioconductor-affycomp/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.58.0" %} +{% set version = "1.60.0" %} {% set name = "affycomp" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 76bd3762a9a1589fd157be1a543de1d7 + md5: 2e6ae6a236b15e9d2fd7f376611e4841 build: number: 0 rpaths: @@ -20,10 +20,10 @@ build: # Suggests: splines, affycompData requirements: host: - - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' - r-base run: - - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' - r-base test: commands: diff --git a/recipes/bioconductor-affycompatible/meta.yaml b/recipes/bioconductor-affycompatible/meta.yaml index 85f2057e51217..002f5217656a3 100644 --- a/recipes/bioconductor-affycompatible/meta.yaml +++ b/recipes/bioconductor-affycompatible/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.42.0" %} +{% set version = "1.44.0" %} {% set name = "AffyCompatible" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 7d2ab32e48872dcba0cdf268543d15c9 + md5: 997af0dcfd3582138684f9d81580588b build: number: 0 rpaths: @@ -19,12 +19,12 @@ build: noarch: generic requirements: host: - - 'bioconductor-biostrings >=2.50.0,<2.51.0' + - 'bioconductor-biostrings >=2.52.0,<2.53.0' - r-base - 'r-rcurl >=0.8-1' - 'r-xml >=2.8-1' run: - - 'bioconductor-biostrings >=2.50.0,<2.51.0' + - 'bioconductor-biostrings >=2.52.0,<2.53.0' - r-base - 'r-rcurl >=0.8-1' - 'r-xml >=2.8-1' diff --git a/recipes/bioconductor-affycompdata/meta.yaml b/recipes/bioconductor-affycompdata/meta.yaml index 28c67a3e46440..8819e27313f20 100644 --- a/recipes/bioconductor-affycompdata/meta.yaml +++ b/recipes/bioconductor-affycompdata/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.20.0" %} +{% set version = "1.22.0" %} {% set name = "affycompData" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,23 +10,23 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 7dd3ccd7ee103e5fabc1beb000d08af2 + md5: a334dbc9b6dc766a2f496d967de5e918 build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ noarch: generic requirements: host: - - 'bioconductor-affycomp >=1.58.0,<1.59.0' - - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-affycomp >=1.60.0,<1.61.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' - r-base run: - - 'bioconductor-affycomp >=1.58.0,<1.59.0' - - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-affycomp >=1.60.0,<1.61.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-affycompdata/post-link.sh b/recipes/bioconductor-affycompdata/post-link.sh index f9d3ac54f36da..328b20d800413 100644 --- a/recipes/bioconductor-affycompdata/post-link.sh +++ b/recipes/bioconductor-affycompdata/post-link.sh @@ -1,11 +1,11 @@ #!/bin/bash -FN="affycompData_1.20.0.tar.gz" +FN="affycompData_1.22.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/experiment/src/contrib/affycompData_1.20.0.tar.gz" - "https://bioarchive.galaxyproject.org/affycompData_1.20.0.tar.gz" - "https://depot.galaxyproject.org/software/bioconductor-affycompdata/bioconductor-affycompdata_1.20.0_src_all.tar.gz" + "https://bioconductor.org/packages/3.9/data/experiment/src/contrib/affycompData_1.22.0.tar.gz" + "https://bioarchive.galaxyproject.org/affycompData_1.22.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-affycompdata/bioconductor-affycompdata_1.22.0_src_all.tar.gz" ) -MD5="7dd3ccd7ee103e5fabc1beb000d08af2" +MD5="a334dbc9b6dc766a2f496d967de5e918" # Use a staging area in the conda dir rather than temp dirs, both to avoid # permission issues as well as to have things downloaded in a predictable @@ -16,7 +16,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-affycontam/meta.yaml b/recipes/bioconductor-affycontam/meta.yaml index 5fa9abbf6345b..2986202d84ab4 100644 --- a/recipes/bioconductor-affycontam/meta.yaml +++ b/recipes/bioconductor-affycontam/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.40.0" %} +{% set version = "1.42.0" %} {% set name = "affyContam" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: a2f70361f7e473c963c0e46202b8004f + md5: 39f0ab0f6b0ae300d20a01ff7bb67a55 build: number: 0 rpaths: @@ -20,14 +20,14 @@ build: # Suggests: hgu95av2cdf requirements: host: - - 'bioconductor-affy >=1.60.0,<1.61.0' - - 'bioconductor-affydata >=1.30.0,<1.31.0' - - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-affy >=1.62.0,<1.63.0' + - 'bioconductor-affydata >=1.32.0,<1.33.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' - r-base run: - - 'bioconductor-affy >=1.60.0,<1.61.0' - - 'bioconductor-affydata >=1.30.0,<1.31.0' - - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-affy >=1.62.0,<1.63.0' + - 'bioconductor-affydata >=1.32.0,<1.33.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' - r-base test: commands: diff --git a/recipes/bioconductor-affycoretools/meta.yaml b/recipes/bioconductor-affycoretools/meta.yaml index e201766063164..c988583b91346 100644 --- a/recipes/bioconductor-affycoretools/meta.yaml +++ b/recipes/bioconductor-affycoretools/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.54.0" %} +{% set version = "1.56.0" %} {% set name = "affycoretools" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: f9ed1862b102e59df1f5177ce547cecc + md5: ce4c6af2de95858a0223ca0fc00c0fca build: number: 0 rpaths: @@ -20,17 +20,17 @@ build: # Suggests: affydata, hgfocuscdf, BiocStyle, knitr, hgu95av2.db, rgl, rmarkdown requirements: host: - - 'bioconductor-affy >=1.60.0,<1.61.0' - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' - - 'bioconductor-biobase >=2.42.0,<2.43.0' - - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' - - 'bioconductor-edger >=3.24.0,<3.25.0' - - 'bioconductor-gcrma >=2.54.0,<2.55.0' - - 'bioconductor-gostats >=2.48.0,<2.49.0' - - 'bioconductor-limma >=3.38.0,<3.39.0' - - 'bioconductor-oligoclasses >=1.44.0,<1.45.0' - - 'bioconductor-reportingtools >=2.22.0,<2.23.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-affy >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' + - 'bioconductor-biocgenerics >=0.30.0,<0.31.0' + - 'bioconductor-edger >=3.26.0,<3.27.0' + - 'bioconductor-gcrma >=2.56.0,<2.57.0' + - 'bioconductor-gostats >=2.50.0,<2.51.0' + - 'bioconductor-limma >=3.40.0,<3.41.0' + - 'bioconductor-oligoclasses >=1.46.0,<1.47.0' + - 'bioconductor-reportingtools >=2.24.0,<2.25.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' - r-base - r-dbi - r-ggplot2 @@ -40,17 +40,17 @@ requirements: - r-rsqlite - r-xtable run: - - 'bioconductor-affy >=1.60.0,<1.61.0' - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' - - 'bioconductor-biobase >=2.42.0,<2.43.0' - - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' - - 'bioconductor-edger >=3.24.0,<3.25.0' - - 'bioconductor-gcrma >=2.54.0,<2.55.0' - - 'bioconductor-gostats >=2.48.0,<2.49.0' - - 'bioconductor-limma >=3.38.0,<3.39.0' - - 'bioconductor-oligoclasses >=1.44.0,<1.45.0' - - 'bioconductor-reportingtools >=2.22.0,<2.23.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-affy >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' + - 'bioconductor-biocgenerics >=0.30.0,<0.31.0' + - 'bioconductor-edger >=3.26.0,<3.27.0' + - 'bioconductor-gcrma >=2.56.0,<2.57.0' + - 'bioconductor-gostats >=2.50.0,<2.51.0' + - 'bioconductor-limma >=3.40.0,<3.41.0' + - 'bioconductor-oligoclasses >=1.46.0,<1.47.0' + - 'bioconductor-reportingtools >=2.24.0,<2.25.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' - r-base - r-dbi - r-ggplot2 diff --git a/recipes/bioconductor-affydata/meta.yaml b/recipes/bioconductor-affydata/meta.yaml index 99e25bfea91cf..cdf0b6158d53f 100644 --- a/recipes/bioconductor-affydata/meta.yaml +++ b/recipes/bioconductor-affydata/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.30.0" %} +{% set version = "1.32.0" %} {% set name = "affydata" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: c4edc5ad12670675bc7fc5b993f29a36 + md5: a37af61d647439e98b7b03e7fe349ca1 build: number: 1 rpaths: @@ -20,12 +20,12 @@ build: # Suggests: hgu95av2cdf, hgu133acdf requirements: host: - - 'bioconductor-affy >=1.60.0,<1.61.0' + - 'bioconductor-affy >=1.62.0,<1.63.0' - r-base run: - - 'bioconductor-affy >=1.60.0,<1.61.0' + - 'bioconductor-affy >=1.62.0,<1.63.0' - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-affydata/post-link.sh b/recipes/bioconductor-affydata/post-link.sh index 8f860f057ea33..08ce8a4f95a34 100644 --- a/recipes/bioconductor-affydata/post-link.sh +++ b/recipes/bioconductor-affydata/post-link.sh @@ -1,11 +1,11 @@ #!/bin/bash -FN="affydata_1.30.0.tar.gz" +FN="affydata_1.32.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/experiment/src/contrib/affydata_1.30.0.tar.gz" - "https://bioarchive.galaxyproject.org/affydata_1.30.0.tar.gz" - "https://depot.galaxyproject.org/software/bioconductor-affydata/bioconductor-affydata_1.30.0_src_all.tar.gz" + "https://bioconductor.org/packages/3.9/data/experiment/src/contrib/affydata_1.32.0.tar.gz" + "https://bioarchive.galaxyproject.org/affydata_1.32.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-affydata/bioconductor-affydata_1.32.0_src_all.tar.gz" ) -MD5="c4edc5ad12670675bc7fc5b993f29a36" +MD5="a37af61d647439e98b7b03e7fe349ca1" # Use a staging area in the conda dir rather than temp dirs, both to avoid # permission issues as well as to have things downloaded in a predictable @@ -16,7 +16,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-affyexpress/meta.yaml b/recipes/bioconductor-affyexpress/meta.yaml index 5884954d13242..1cd5d7f086543 100644 --- a/recipes/bioconductor-affyexpress/meta.yaml +++ b/recipes/bioconductor-affyexpress/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.48.0" %} +{% set version = "1.50.0" %} {% set name = "AffyExpress" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 4afe8bb6ec8b571cacfd6faa5cb7284c + md5: 428dc21416445e4ca92bbe44502f26a7 build: number: 0 rpaths: @@ -20,12 +20,12 @@ build: # Suggests: simpleaffy, R2HTML, affyPLM, hgu95av2cdf, hgu95av2, test3cdf, genefilter, estrogen, annaffy, gcrma requirements: host: - - 'bioconductor-affy >=1.60.0,<1.61.0' - - 'bioconductor-limma >=3.38.0,<3.39.0' + - 'bioconductor-affy >=1.62.0,<1.63.0' + - 'bioconductor-limma >=3.40.0,<3.41.0' - r-base run: - - 'bioconductor-affy >=1.60.0,<1.61.0' - - 'bioconductor-limma >=3.38.0,<3.39.0' + - 'bioconductor-affy >=1.62.0,<1.63.0' + - 'bioconductor-limma >=3.40.0,<3.41.0' - r-base test: commands: diff --git a/recipes/bioconductor-affyhgu133a2expr/meta.yaml b/recipes/bioconductor-affyhgu133a2expr/meta.yaml index 3895b1ab1fbf9..6bd6a2fb9c05a 100644 --- a/recipes/bioconductor-affyhgu133a2expr/meta.yaml +++ b/recipes/bioconductor-affyhgu133a2expr/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.18.0" %} +{% set version = "1.20.0" %} {% set name = "Affyhgu133A2Expr" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,9 +10,9 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 5944ee99dfc56eaedd6ca8a95dfd59dc + md5: 1eab8a17b6f940ee9d980b39ac66874b build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ @@ -22,7 +22,7 @@ requirements: - r-base run: - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-affyhgu133a2expr/post-link.sh b/recipes/bioconductor-affyhgu133a2expr/post-link.sh index ce7e4b9518b66..047d9cd8eefef 100644 --- a/recipes/bioconductor-affyhgu133a2expr/post-link.sh +++ b/recipes/bioconductor-affyhgu133a2expr/post-link.sh @@ -1,11 +1,11 @@ #!/bin/bash -FN="Affyhgu133A2Expr_1.18.0.tar.gz" +FN="Affyhgu133A2Expr_1.20.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/experiment/src/contrib/Affyhgu133A2Expr_1.18.0.tar.gz" - "https://bioarchive.galaxyproject.org/Affyhgu133A2Expr_1.18.0.tar.gz" - "https://depot.galaxyproject.org/software/bioconductor-affyhgu133a2expr/bioconductor-affyhgu133a2expr_1.18.0_src_all.tar.gz" + "https://bioconductor.org/packages/3.9/data/experiment/src/contrib/Affyhgu133A2Expr_1.20.0.tar.gz" + "https://bioarchive.galaxyproject.org/Affyhgu133A2Expr_1.20.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-affyhgu133a2expr/bioconductor-affyhgu133a2expr_1.20.0_src_all.tar.gz" ) -MD5="5944ee99dfc56eaedd6ca8a95dfd59dc" +MD5="1eab8a17b6f940ee9d980b39ac66874b" # Use a staging area in the conda dir rather than temp dirs, both to avoid # permission issues as well as to have things downloaded in a predictable @@ -16,7 +16,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-affyhgu133aexpr/meta.yaml b/recipes/bioconductor-affyhgu133aexpr/meta.yaml index 129f700b224b2..a76ebef89af84 100644 --- a/recipes/bioconductor-affyhgu133aexpr/meta.yaml +++ b/recipes/bioconductor-affyhgu133aexpr/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.20.0" %} +{% set version = "1.22.0" %} {% set name = "Affyhgu133aExpr" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,9 +10,9 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 9254b9cb76829110172cb80b01921ddc + md5: 39428013cde8719e8b487042fdea7f47 build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ @@ -22,7 +22,7 @@ requirements: - r-base run: - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-affyhgu133aexpr/post-link.sh b/recipes/bioconductor-affyhgu133aexpr/post-link.sh index 930322bc4de5c..122e2ac7cd5f8 100644 --- a/recipes/bioconductor-affyhgu133aexpr/post-link.sh +++ b/recipes/bioconductor-affyhgu133aexpr/post-link.sh @@ -1,11 +1,11 @@ #!/bin/bash -FN="Affyhgu133aExpr_1.20.0.tar.gz" +FN="Affyhgu133aExpr_1.22.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/experiment/src/contrib/Affyhgu133aExpr_1.20.0.tar.gz" - "https://bioarchive.galaxyproject.org/Affyhgu133aExpr_1.20.0.tar.gz" - "https://depot.galaxyproject.org/software/bioconductor-affyhgu133aexpr/bioconductor-affyhgu133aexpr_1.20.0_src_all.tar.gz" + "https://bioconductor.org/packages/3.9/data/experiment/src/contrib/Affyhgu133aExpr_1.22.0.tar.gz" + "https://bioarchive.galaxyproject.org/Affyhgu133aExpr_1.22.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-affyhgu133aexpr/bioconductor-affyhgu133aexpr_1.22.0_src_all.tar.gz" ) -MD5="9254b9cb76829110172cb80b01921ddc" +MD5="39428013cde8719e8b487042fdea7f47" # Use a staging area in the conda dir rather than temp dirs, both to avoid # permission issues as well as to have things downloaded in a predictable @@ -16,7 +16,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-affyhgu133plus2expr/meta.yaml b/recipes/bioconductor-affyhgu133plus2expr/meta.yaml index d302bae8fc2c5..a27999db95371 100644 --- a/recipes/bioconductor-affyhgu133plus2expr/meta.yaml +++ b/recipes/bioconductor-affyhgu133plus2expr/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.16.0" %} +{% set version = "1.18.0" %} {% set name = "Affyhgu133Plus2Expr" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,9 +10,9 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 86ff16e83ac8445c7242525e1cbc146a + md5: f1d335aef3a0fb1371144a6f81e70fa4 build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ @@ -22,7 +22,7 @@ requirements: - r-base run: - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-affyhgu133plus2expr/post-link.sh b/recipes/bioconductor-affyhgu133plus2expr/post-link.sh index 2d7cab54a13ce..1f065607577c6 100644 --- a/recipes/bioconductor-affyhgu133plus2expr/post-link.sh +++ b/recipes/bioconductor-affyhgu133plus2expr/post-link.sh @@ -1,11 +1,11 @@ #!/bin/bash -FN="Affyhgu133Plus2Expr_1.16.0.tar.gz" +FN="Affyhgu133Plus2Expr_1.18.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/experiment/src/contrib/Affyhgu133Plus2Expr_1.16.0.tar.gz" - "https://bioarchive.galaxyproject.org/Affyhgu133Plus2Expr_1.16.0.tar.gz" - "https://depot.galaxyproject.org/software/bioconductor-affyhgu133plus2expr/bioconductor-affyhgu133plus2expr_1.16.0_src_all.tar.gz" + "https://bioconductor.org/packages/3.9/data/experiment/src/contrib/Affyhgu133Plus2Expr_1.18.0.tar.gz" + "https://bioarchive.galaxyproject.org/Affyhgu133Plus2Expr_1.18.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-affyhgu133plus2expr/bioconductor-affyhgu133plus2expr_1.18.0_src_all.tar.gz" ) -MD5="86ff16e83ac8445c7242525e1cbc146a" +MD5="f1d335aef3a0fb1371144a6f81e70fa4" # Use a staging area in the conda dir rather than temp dirs, both to avoid # permission issues as well as to have things downloaded in a predictable @@ -16,7 +16,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-affyilm/meta.yaml b/recipes/bioconductor-affyilm/meta.yaml index ee2b7437346d0..d36ca74659dee 100644 --- a/recipes/bioconductor-affyilm/meta.yaml +++ b/recipes/bioconductor-affyilm/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.34.0" %} +{% set version = "1.36.0" %} {% set name = "affyILM" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 87811dbf7c0589e74a9c5858811ffb61 + md5: 1d882d602cf45f48b6ccec53d761dc31 build: number: 0 rpaths: @@ -20,16 +20,16 @@ build: # Suggests: AffymetrixDataTestFiles, hgfocusprobe requirements: host: - - 'bioconductor-affxparser >=1.54.0,<1.55.0' - - 'bioconductor-affy >=1.60.0,<1.61.0' - - 'bioconductor-biobase >=2.42.0,<2.43.0' - - 'bioconductor-gcrma >=2.54.0,<2.55.0' + - 'bioconductor-affxparser >=1.56.0,<1.57.0' + - 'bioconductor-affy >=1.62.0,<1.63.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' + - 'bioconductor-gcrma >=2.56.0,<2.57.0' - r-base run: - - 'bioconductor-affxparser >=1.54.0,<1.55.0' - - 'bioconductor-affy >=1.60.0,<1.61.0' - - 'bioconductor-biobase >=2.42.0,<2.43.0' - - 'bioconductor-gcrma >=2.54.0,<2.55.0' + - 'bioconductor-affxparser >=1.56.0,<1.57.0' + - 'bioconductor-affy >=1.62.0,<1.63.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' + - 'bioconductor-gcrma >=2.56.0,<2.57.0' - r-base test: commands: diff --git a/recipes/bioconductor-affyio/meta.yaml b/recipes/bioconductor-affyio/meta.yaml index 190f270160157..b3cb6aa620ee7 100644 --- a/recipes/bioconductor-affyio/meta.yaml +++ b/recipes/bioconductor-affyio/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.52.0" %} +{% set version = "1.54.0" %} {% set name = "affyio" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 4f0bb750a68406e25541e19a5dd1f5a2 + md5: 4a115565876093c68f17dc28c9274592 build: number: 0 rpaths: @@ -18,10 +18,10 @@ build: - lib/ requirements: host: - - 'bioconductor-zlibbioc >=1.28.0,<1.29.0' + - 'bioconductor-zlibbioc >=1.30.0,<1.31.0' - r-base run: - - 'bioconductor-zlibbioc >=1.28.0,<1.29.0' + - 'bioconductor-zlibbioc >=1.30.0,<1.31.0' - r-base build: - {{ compiler('c') }} diff --git a/recipes/bioconductor-affylmgui/meta.yaml b/recipes/bioconductor-affylmgui/meta.yaml index ae3b5d435abb4..20bfc84627384 100644 --- a/recipes/bioconductor-affylmgui/meta.yaml +++ b/recipes/bioconductor-affylmgui/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.56.0" %} +{% set version = "1.58.0" %} {% set name = "affylmGUI" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 1c03dfb6477d26f31f544c7f60d3a0d3 + md5: 6cf0ca5e075473d5e96e59febe8f630c build: number: 0 rpaths: @@ -19,24 +19,24 @@ build: noarch: generic requirements: host: - - 'bioconductor-affy >=1.60.0,<1.61.0' - - 'bioconductor-affyio >=1.52.0,<1.53.0' - - 'bioconductor-affyplm >=1.58.0,<1.59.0' - - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' - - 'bioconductor-gcrma >=2.54.0,<2.55.0' - - 'bioconductor-limma >=3.38.0,<3.39.0' + - 'bioconductor-affy >=1.62.0,<1.63.0' + - 'bioconductor-affyio >=1.54.0,<1.55.0' + - 'bioconductor-affyplm >=1.60.0,<1.61.0' + - 'bioconductor-biocgenerics >=0.30.0,<0.31.0' + - 'bioconductor-gcrma >=2.56.0,<2.57.0' + - 'bioconductor-limma >=3.40.0,<3.41.0' - r-base - r-biocmanager - r-r2html - r-tkrplot - r-xtable run: - - 'bioconductor-affy >=1.60.0,<1.61.0' - - 'bioconductor-affyio >=1.52.0,<1.53.0' - - 'bioconductor-affyplm >=1.58.0,<1.59.0' - - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' - - 'bioconductor-gcrma >=2.54.0,<2.55.0' - - 'bioconductor-limma >=3.38.0,<3.39.0' + - 'bioconductor-affy >=1.62.0,<1.63.0' + - 'bioconductor-affyio >=1.54.0,<1.55.0' + - 'bioconductor-affyplm >=1.60.0,<1.61.0' + - 'bioconductor-biocgenerics >=0.30.0,<0.31.0' + - 'bioconductor-gcrma >=2.56.0,<2.57.0' + - 'bioconductor-limma >=3.40.0,<3.41.0' - r-base - r-biocmanager - r-r2html diff --git a/recipes/bioconductor-affymetrixdatatestfiles/meta.yaml b/recipes/bioconductor-affymetrixdatatestfiles/meta.yaml index 607f37d6567dc..9b92d8b9ffe3c 100644 --- a/recipes/bioconductor-affymetrixdatatestfiles/meta.yaml +++ b/recipes/bioconductor-affymetrixdatatestfiles/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "0.20.0" %} +{% set version = "0.22.0" %} {% set name = "AffymetrixDataTestFiles" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 9ba84883ca62f5f7b73d9cd3fa1f36a5 + md5: c2cdbf27e487b9877c00fb8c60e22959 build: number: 0 rpaths: @@ -22,7 +22,7 @@ requirements: - r-base run: - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-affymetrixdatatestfiles/post-link.sh b/recipes/bioconductor-affymetrixdatatestfiles/post-link.sh index 14b0334c71899..b7988ce02dcdd 100644 --- a/recipes/bioconductor-affymetrixdatatestfiles/post-link.sh +++ b/recipes/bioconductor-affymetrixdatatestfiles/post-link.sh @@ -1,11 +1,11 @@ #!/bin/bash -FN="AffymetrixDataTestFiles_0.20.0.tar.gz" +FN="AffymetrixDataTestFiles_0.22.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/experiment/src/contrib/AffymetrixDataTestFiles_0.20.0.tar.gz" - "https://bioarchive.galaxyproject.org/AffymetrixDataTestFiles_0.20.0.tar.gz" - "https://depot.galaxyproject.org/software/bioconductor-affymetrixdatatestfiles/bioconductor-affymetrixdatatestfiles_0.20.0_src_all.tar.gz" + "https://bioconductor.org/packages/3.9/data/experiment/src/contrib/AffymetrixDataTestFiles_0.22.0.tar.gz" + "https://bioarchive.galaxyproject.org/AffymetrixDataTestFiles_0.22.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-affymetrixdatatestfiles/bioconductor-affymetrixdatatestfiles_0.22.0_src_all.tar.gz" ) -MD5="9ba84883ca62f5f7b73d9cd3fa1f36a5" +MD5="c2cdbf27e487b9877c00fb8c60e22959" # Use a staging area in the conda dir rather than temp dirs, both to avoid # permission issues as well as to have things downloaded in a predictable @@ -16,7 +16,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-affymoe4302expr/meta.yaml b/recipes/bioconductor-affymoe4302expr/meta.yaml index 02977b3d0e0ea..4998a35961d7d 100644 --- a/recipes/bioconductor-affymoe4302expr/meta.yaml +++ b/recipes/bioconductor-affymoe4302expr/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.20.0" %} +{% set version = "1.22.0" %} {% set name = "Affymoe4302Expr" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: e21ed8d45f198ac957d5343b48dd8d2c + md5: f9c8f9273ae064ffc30074388b43f8ed build: number: 0 rpaths: @@ -22,7 +22,7 @@ requirements: - r-base run: - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-affymoe4302expr/post-link.sh b/recipes/bioconductor-affymoe4302expr/post-link.sh index 6eedcfc633997..1a9cc217d0609 100644 --- a/recipes/bioconductor-affymoe4302expr/post-link.sh +++ b/recipes/bioconductor-affymoe4302expr/post-link.sh @@ -1,11 +1,11 @@ #!/bin/bash -FN="Affymoe4302Expr_1.20.0.tar.gz" +FN="Affymoe4302Expr_1.22.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/experiment/src/contrib/Affymoe4302Expr_1.20.0.tar.gz" - "https://bioarchive.galaxyproject.org/Affymoe4302Expr_1.20.0.tar.gz" - "https://depot.galaxyproject.org/software/bioconductor-affymoe4302expr/bioconductor-affymoe4302expr_1.20.0_src_all.tar.gz" + "https://bioconductor.org/packages/3.9/data/experiment/src/contrib/Affymoe4302Expr_1.22.0.tar.gz" + "https://bioarchive.galaxyproject.org/Affymoe4302Expr_1.22.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-affymoe4302expr/bioconductor-affymoe4302expr_1.22.0_src_all.tar.gz" ) -MD5="e21ed8d45f198ac957d5343b48dd8d2c" +MD5="f9c8f9273ae064ffc30074388b43f8ed" # Use a staging area in the conda dir rather than temp dirs, both to avoid # permission issues as well as to have things downloaded in a predictable @@ -16,7 +16,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-affypara/meta.yaml b/recipes/bioconductor-affypara/meta.yaml index 32f3362f5b2b8..755fd394aa4d6 100644 --- a/recipes/bioconductor-affypara/meta.yaml +++ b/recipes/bioconductor-affypara/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.42.0" %} +{% set version = "1.44.0" %} {% set name = "affyPara" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 7a05c33daf0b6393e7ff928bf134b47f + md5: 0b8f11ce29ec0e877c3b010974975502 build: number: 0 rpaths: @@ -20,16 +20,16 @@ build: # Suggests: affydata requirements: host: - - 'bioconductor-affy >=1.60.0,<1.61.0' - - 'bioconductor-affyio >=1.52.0,<1.53.0' - - 'bioconductor-vsn >=3.50.0,<3.51.0' + - 'bioconductor-affy >=1.62.0,<1.63.0' + - 'bioconductor-affyio >=1.54.0,<1.55.0' + - 'bioconductor-vsn >=3.52.0,<3.53.0' - 'r-aplpack >=1.1.1' - r-base - 'r-snow >=0.2-3' run: - - 'bioconductor-affy >=1.60.0,<1.61.0' - - 'bioconductor-affyio >=1.52.0,<1.53.0' - - 'bioconductor-vsn >=3.50.0,<3.51.0' + - 'bioconductor-affy >=1.62.0,<1.63.0' + - 'bioconductor-affyio >=1.54.0,<1.55.0' + - 'bioconductor-vsn >=3.52.0,<3.53.0' - 'r-aplpack >=1.1.1' - r-base - 'r-snow >=0.2-3' diff --git a/recipes/bioconductor-affypdnn/meta.yaml b/recipes/bioconductor-affypdnn/meta.yaml index 1a4224db0ee10..009b48b571335 100644 --- a/recipes/bioconductor-affypdnn/meta.yaml +++ b/recipes/bioconductor-affypdnn/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.56.0" %} +{% set version = "1.58.0" %} {% set name = "affypdnn" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: cc5feb90eb660fee35c0cab8846cb443 + md5: 3bdf72549b4a89495ee30df5b025338f build: number: 0 rpaths: @@ -20,10 +20,10 @@ build: # Suggests: affydata, hgu95av2probe requirements: host: - - 'bioconductor-affy >=1.60.0,<1.61.0' + - 'bioconductor-affy >=1.62.0,<1.63.0' - r-base run: - - 'bioconductor-affy >=1.60.0,<1.61.0' + - 'bioconductor-affy >=1.62.0,<1.63.0' - r-base test: commands: diff --git a/recipes/bioconductor-affyplm/meta.yaml b/recipes/bioconductor-affyplm/meta.yaml index 01cd75976bef9..61fdde53a8d4f 100644 --- a/recipes/bioconductor-affyplm/meta.yaml +++ b/recipes/bioconductor-affyplm/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.58.0" %} +{% set version = "1.60.0" %} {% set name = "affyPLM" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 4d9e87db1f232700fec8543fc83fd8be + md5: 8070d4cba459fb7998c26c3d7c0ed571 build: number: 0 rpaths: @@ -19,20 +19,20 @@ build: # Suggests: affydata, MASS requirements: host: - - 'bioconductor-affy >=1.60.0,<1.61.0' - - 'bioconductor-biobase >=2.42.0,<2.43.0' - - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' - - 'bioconductor-gcrma >=2.54.0,<2.55.0' - - 'bioconductor-preprocesscore >=1.44.0,<1.45.0' - - 'bioconductor-zlibbioc >=1.28.0,<1.29.0' + - 'bioconductor-affy >=1.62.0,<1.63.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' + - 'bioconductor-biocgenerics >=0.30.0,<0.31.0' + - 'bioconductor-gcrma >=2.56.0,<2.57.0' + - 'bioconductor-preprocesscore >=1.46.0,<1.47.0' + - 'bioconductor-zlibbioc >=1.30.0,<1.31.0' - r-base run: - - 'bioconductor-affy >=1.60.0,<1.61.0' - - 'bioconductor-biobase >=2.42.0,<2.43.0' - - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' - - 'bioconductor-gcrma >=2.54.0,<2.55.0' - - 'bioconductor-preprocesscore >=1.44.0,<1.45.0' - - 'bioconductor-zlibbioc >=1.28.0,<1.29.0' + - 'bioconductor-affy >=1.62.0,<1.63.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' + - 'bioconductor-biocgenerics >=0.30.0,<0.31.0' + - 'bioconductor-gcrma >=2.56.0,<2.57.0' + - 'bioconductor-preprocesscore >=1.46.0,<1.47.0' + - 'bioconductor-zlibbioc >=1.30.0,<1.31.0' - r-base build: - {{ compiler('c') }} diff --git a/recipes/bioconductor-affyqcreport/meta.yaml b/recipes/bioconductor-affyqcreport/meta.yaml index 4137ab14dc2ca..5df91e0d1d2d4 100644 --- a/recipes/bioconductor-affyqcreport/meta.yaml +++ b/recipes/bioconductor-affyqcreport/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.60.0" %} +{% set version = "1.62.0" %} {% set name = "affyQCReport" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 639c5ee5befbf01b8f090eacc2a81f67 + md5: de5e5962fb74cd0b4deed0ebc0898b88 build: number: 0 rpaths: @@ -20,21 +20,21 @@ build: # Suggests: tkWidgets (>= 1.5.23), affydata (>= 1.4.1) requirements: host: - - 'bioconductor-affy >=1.60.0,<1.61.0' - - 'bioconductor-affyplm >=1.58.0,<1.59.0' - - 'bioconductor-biobase >=2.42.0,<2.43.0' - - 'bioconductor-genefilter >=1.64.0,<1.65.0' - - 'bioconductor-simpleaffy >=2.58.0,<2.59.0' + - 'bioconductor-affy >=1.62.0,<1.63.0' + - 'bioconductor-affyplm >=1.60.0,<1.61.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' + - 'bioconductor-genefilter >=1.66.0,<1.67.0' + - 'bioconductor-simpleaffy >=2.60.0,<2.61.0' - r-base - r-lattice - r-rcolorbrewer - r-xtable run: - - 'bioconductor-affy >=1.60.0,<1.61.0' - - 'bioconductor-affyplm >=1.58.0,<1.59.0' - - 'bioconductor-biobase >=2.42.0,<2.43.0' - - 'bioconductor-genefilter >=1.64.0,<1.65.0' - - 'bioconductor-simpleaffy >=2.58.0,<2.59.0' + - 'bioconductor-affy >=1.62.0,<1.63.0' + - 'bioconductor-affyplm >=1.60.0,<1.61.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' + - 'bioconductor-genefilter >=1.66.0,<1.67.0' + - 'bioconductor-simpleaffy >=2.60.0,<2.61.0' - r-base - r-lattice - r-rcolorbrewer diff --git a/recipes/bioconductor-affyrnadegradation/meta.yaml b/recipes/bioconductor-affyrnadegradation/meta.yaml index 0d3ba3a05941d..51c76dc6f3a88 100644 --- a/recipes/bioconductor-affyrnadegradation/meta.yaml +++ b/recipes/bioconductor-affyrnadegradation/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.28.0" %} +{% set version = "1.30.0" %} {% set name = "AffyRNADegradation" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: cad1f5fe8dd49d21d9409975dfb9bb32 + md5: bd6cf71aecceb26a25b7b6b8a4e651a1 build: number: 0 rpaths: @@ -20,10 +20,10 @@ build: # Suggests: AmpAffyExample requirements: host: - - 'bioconductor-affy >=1.60.0,<1.61.0' + - 'bioconductor-affy >=1.62.0,<1.63.0' - r-base run: - - 'bioconductor-affy >=1.60.0,<1.61.0' + - 'bioconductor-affy >=1.62.0,<1.63.0' - r-base test: commands: diff --git a/recipes/bioconductor-ag.db/meta.yaml b/recipes/bioconductor-ag.db/meta.yaml index d6a46ad9de471..50a6814d6a4d6 100644 --- a/recipes/bioconductor-ag.db/meta.yaml +++ b/recipes/bioconductor-ag.db/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.2.3" %} {% set name = "ag.db" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -12,7 +12,7 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: e5913da38fe4487202306cacd885840d build: - number: 1 + number: 2 rpaths: - lib/R/lib/ - lib/ @@ -20,14 +20,14 @@ build: # Suggests: DBI, annotate, RUnit requirements: host: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' - - 'bioconductor-org.at.tair.db >=3.7.0,<3.8.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' + - 'bioconductor-org.at.tair.db >=3.8.0,<3.9.0' - r-base run: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' - - 'bioconductor-org.at.tair.db >=3.7.0,<3.8.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' + - 'bioconductor-org.at.tair.db >=3.8.0,<3.9.0' - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-ag.db/post-link.sh b/recipes/bioconductor-ag.db/post-link.sh index 4918e248e708b..d23dae5127828 100644 --- a/recipes/bioconductor-ag.db/post-link.sh +++ b/recipes/bioconductor-ag.db/post-link.sh @@ -1,9 +1,10 @@ #!/bin/bash FN="ag.db_3.2.3.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/ag.db_3.2.3.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/ag.db_3.2.3.tar.gz" "https://bioarchive.galaxyproject.org/ag.db_3.2.3.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-ag.db/bioconductor-ag.db_3.2.3_src_all.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-ag.db/bioconductor-ag.db_3.2.3_src_all.tar.gz" ) MD5="e5913da38fe4487202306cacd885840d" @@ -16,7 +17,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-agcdf/meta.yaml b/recipes/bioconductor-agcdf/meta.yaml index 31a6de20756c8..ba7af64aad11b 100644 --- a/recipes/bioconductor-agcdf/meta.yaml +++ b/recipes/bioconductor-agcdf/meta.yaml @@ -1,6 +1,6 @@ {% set version = "2.18.0" %} {% set name = "agcdf" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -12,19 +12,19 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 5dd14bc6a6d2729f5e7b170105c78e48 build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' - r-base run: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-agcdf/post-link.sh b/recipes/bioconductor-agcdf/post-link.sh index bf5d8be1dec95..005bed7600299 100644 --- a/recipes/bioconductor-agcdf/post-link.sh +++ b/recipes/bioconductor-agcdf/post-link.sh @@ -1,9 +1,10 @@ #!/bin/bash FN="agcdf_2.18.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/agcdf_2.18.0.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/agcdf_2.18.0.tar.gz" "https://bioarchive.galaxyproject.org/agcdf_2.18.0.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-agcdf/bioconductor-agcdf_2.18.0_src_all.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-agcdf/bioconductor-agcdf_2.18.0_src_all.tar.gz" ) MD5="5dd14bc6a6d2729f5e7b170105c78e48" @@ -16,7 +17,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-agdex/meta.yaml b/recipes/bioconductor-agdex/meta.yaml index c19c605bfeba7..c60d78dfed188 100644 --- a/recipes/bioconductor-agdex/meta.yaml +++ b/recipes/bioconductor-agdex/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.30.0" %} +{% set version = "1.32.0" %} {% set name = "AGDEX" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 0a82c526b05e7fbac77480ea0a93b42c + md5: eef4f67c480d45fa194afd886da71abc build: number: 0 rpaths: @@ -19,12 +19,12 @@ build: noarch: generic requirements: host: - - 'bioconductor-biobase >=2.42.0,<2.43.0' - - 'bioconductor-gseabase >=1.44.0,<1.45.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' + - 'bioconductor-gseabase >=1.46.0,<1.47.0' - r-base run: - - 'bioconductor-biobase >=2.42.0,<2.43.0' - - 'bioconductor-gseabase >=1.44.0,<1.45.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' + - 'bioconductor-gseabase >=1.46.0,<1.47.0' - r-base test: commands: diff --git a/recipes/bioconductor-agilp/meta.yaml b/recipes/bioconductor-agilp/meta.yaml index aae07b7866fb1..373f7f92fc3ef 100644 --- a/recipes/bioconductor-agilp/meta.yaml +++ b/recipes/bioconductor-agilp/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "3.14.0" %} +{% set version = "3.16.0" %} {% set name = "agilp" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: c9c79b9c0a8bf313d6426266e1cac965 + md5: 1445a40d1bf7d80b5c2b32b093dac65b build: number: 0 rpaths: diff --git a/recipes/bioconductor-agimicrorna/meta.yaml b/recipes/bioconductor-agimicrorna/meta.yaml index 0f85b982da20b..dc5f495702ea8 100644 --- a/recipes/bioconductor-agimicrorna/meta.yaml +++ b/recipes/bioconductor-agimicrorna/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "2.32.0" %} +{% set version = "2.34.0" %} {% set name = "AgiMicroRna" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,9 +10,9 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: c28be6c85e4bf0e0fdfd1bf17df43814 + md5: 4a07273782f1b205dddbb221aeae7c7c build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ @@ -20,18 +20,18 @@ build: # Suggests: geneplotter,marray,gplots,gtools,gdata,codelink requirements: host: - - 'bioconductor-affy >=1.60.0,<1.61.0' - - 'bioconductor-affycoretools >=1.54.0,<1.55.0' - - 'bioconductor-biobase >=2.42.0,<2.43.0' - - 'bioconductor-limma >=3.38.0,<3.39.0' - - 'bioconductor-preprocesscore >=1.44.0,<1.45.0' + - 'bioconductor-affy >=1.62.0,<1.63.0' + - 'bioconductor-affycoretools >=1.56.0,<1.57.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' + - 'bioconductor-limma >=3.40.0,<3.41.0' + - 'bioconductor-preprocesscore >=1.46.0,<1.47.0' - r-base run: - - 'bioconductor-affy >=1.60.0,<1.61.0' - - 'bioconductor-affycoretools >=1.54.0,<1.55.0' - - 'bioconductor-biobase >=2.42.0,<2.43.0' - - 'bioconductor-limma >=3.38.0,<3.39.0' - - 'bioconductor-preprocesscore >=1.44.0,<1.45.0' + - 'bioconductor-affy >=1.62.0,<1.63.0' + - 'bioconductor-affycoretools >=1.56.0,<1.57.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' + - 'bioconductor-limma >=3.40.0,<3.41.0' + - 'bioconductor-preprocesscore >=1.46.0,<1.47.0' - r-base test: commands: diff --git a/recipes/bioconductor-agprobe/meta.yaml b/recipes/bioconductor-agprobe/meta.yaml index 5bb5c0e0a8b1e..6446be6f5cc22 100644 --- a/recipes/bioconductor-agprobe/meta.yaml +++ b/recipes/bioconductor-agprobe/meta.yaml @@ -1,6 +1,6 @@ {% set version = "2.18.0" %} {% set name = "agprobe" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -12,19 +12,19 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 08f7527d4c8a30d8b2f86016a53f075a build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' - r-base run: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-agprobe/post-link.sh b/recipes/bioconductor-agprobe/post-link.sh index 95d7df3c4a9a0..dba9e788fa05c 100644 --- a/recipes/bioconductor-agprobe/post-link.sh +++ b/recipes/bioconductor-agprobe/post-link.sh @@ -1,9 +1,10 @@ #!/bin/bash FN="agprobe_2.18.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/agprobe_2.18.0.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/agprobe_2.18.0.tar.gz" "https://bioarchive.galaxyproject.org/agprobe_2.18.0.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-agprobe/bioconductor-agprobe_2.18.0_src_all.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-agprobe/bioconductor-agprobe_2.18.0_src_all.tar.gz" ) MD5="08f7527d4c8a30d8b2f86016a53f075a" @@ -16,7 +17,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-ahcytobands/meta.yaml b/recipes/bioconductor-ahcytobands/meta.yaml index afc5050a6952f..51a23e6c33e8d 100644 --- a/recipes/bioconductor-ahcytobands/meta.yaml +++ b/recipes/bioconductor-ahcytobands/meta.yaml @@ -1,6 +1,6 @@ {% set version = "0.99.0" %} {% set name = "AHCytoBands" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -12,7 +12,7 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' md5: 87b801fe5699cae422a661711272c0a2 build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ @@ -22,7 +22,7 @@ requirements: - r-base run: - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-ahcytobands/post-link.sh b/recipes/bioconductor-ahcytobands/post-link.sh index 06fe7624f755e..6f316564fd98e 100644 --- a/recipes/bioconductor-ahcytobands/post-link.sh +++ b/recipes/bioconductor-ahcytobands/post-link.sh @@ -1,9 +1,10 @@ #!/bin/bash FN="AHCytoBands_0.99.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/AHCytoBands_0.99.0.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/AHCytoBands_0.99.0.tar.gz" "https://bioarchive.galaxyproject.org/AHCytoBands_0.99.0.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-ahcytobands/bioconductor-ahcytobands_0.99.0_src_all.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-ahcytobands/bioconductor-ahcytobands_0.99.0_src_all.tar.gz" ) MD5="87b801fe5699cae422a661711272c0a2" @@ -16,7 +17,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-ahensdbs/meta.yaml b/recipes/bioconductor-ahensdbs/meta.yaml index a8c37920286d0..b78c315eaf2a7 100644 --- a/recipes/bioconductor-ahensdbs/meta.yaml +++ b/recipes/bioconductor-ahensdbs/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.0.8" %} +{% set version = "1.0.9" %} {% set name = "AHEnsDbs" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: a325efcf47764e6a2fd3945661016c17 + md5: f00a5fbd590a9337f295a58270f2a8d0 build: number: 0 rpaths: @@ -20,14 +20,14 @@ build: # Suggests: BiocStyle, knitr, AnnotationHub (>= 2.7.13) requirements: host: - - 'bioconductor-annotationhubdata >=1.12.0,<1.13.0' - - 'bioconductor-ensembldb >=2.6.0,<2.7.0' + - 'bioconductor-annotationhubdata >=1.14.0,<1.15.0' + - 'bioconductor-ensembldb >=2.8.0,<2.9.0' - r-base run: - - 'bioconductor-annotationhubdata >=1.12.0,<1.13.0' - - 'bioconductor-ensembldb >=2.6.0,<2.7.0' + - 'bioconductor-annotationhubdata >=1.14.0,<1.15.0' + - 'bioconductor-ensembldb >=2.8.0,<2.9.0' - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-ahensdbs/post-link.sh b/recipes/bioconductor-ahensdbs/post-link.sh index 3eb5320c7550f..dca491de4733f 100644 --- a/recipes/bioconductor-ahensdbs/post-link.sh +++ b/recipes/bioconductor-ahensdbs/post-link.sh @@ -1,11 +1,11 @@ #!/bin/bash -FN="AHEnsDbs_1.0.8.tar.gz" +FN="AHEnsDbs_1.0.9.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/AHEnsDbs_1.0.8.tar.gz" - "https://bioarchive.galaxyproject.org/AHEnsDbs_1.0.8.tar.gz" - "https://depot.galaxyproject.org/software/bioconductor-ahensdbs/bioconductor-ahensdbs_1.0.8_src_all.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/AHEnsDbs_1.0.9.tar.gz" + "https://bioarchive.galaxyproject.org/AHEnsDbs_1.0.9.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-ahensdbs/bioconductor-ahensdbs_1.0.9_src_all.tar.gz" ) -MD5="a325efcf47764e6a2fd3945661016c17" +MD5="f00a5fbd590a9337f295a58270f2a8d0" # Use a staging area in the conda dir rather than temp dirs, both to avoid # permission issues as well as to have things downloaded in a predictable @@ -16,7 +16,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-aims/meta.yaml b/recipes/bioconductor-aims/meta.yaml index 64f9d19351638..3e25cb530d37b 100644 --- a/recipes/bioconductor-aims/meta.yaml +++ b/recipes/bioconductor-aims/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.14.1" %} +{% set version = "1.16.0" %} {% set name = "AIMS" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: 2bd7a201281f56b30a2b77e994f53ac41931d87955d6a9f82d744481d2c8e7da + md5: bd6fd76b022c0aeaeadc06cfe332a09a build: number: 0 rpaths: @@ -20,11 +20,11 @@ build: # Suggests: breastCancerVDX, hgu133a.db, RUnit, BiocGenerics requirements: host: - - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' - r-base - r-e1071 run: - - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' - r-base - r-e1071 test: diff --git a/recipes/bioconductor-airway/meta.yaml b/recipes/bioconductor-airway/meta.yaml index 45f30594abc1f..ec317bbc2824b 100644 --- a/recipes/bioconductor-airway/meta.yaml +++ b/recipes/bioconductor-airway/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.2.0" %} +{% set version = "1.4.0" %} {% set name = "airway" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 1b539cecd5b5a3b3550b659ec1f21b89 + md5: ef609098c2893c759ddabbcb47cd4b6b build: number: 0 rpaths: @@ -20,12 +20,12 @@ build: # Suggests: knitr, GEOquery requirements: host: - - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' + - 'bioconductor-summarizedexperiment >=1.14.0,<1.15.0' - r-base run: - - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' + - 'bioconductor-summarizedexperiment >=1.14.0,<1.15.0' - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-airway/post-link.sh b/recipes/bioconductor-airway/post-link.sh index c81a400d94cd4..1d7b965f0c15d 100644 --- a/recipes/bioconductor-airway/post-link.sh +++ b/recipes/bioconductor-airway/post-link.sh @@ -1,11 +1,11 @@ #!/bin/bash -FN="airway_1.2.0.tar.gz" +FN="airway_1.4.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/experiment/src/contrib/airway_1.2.0.tar.gz" - "https://bioarchive.galaxyproject.org/airway_1.2.0.tar.gz" - "https://depot.galaxyproject.org/software/bioconductor-airway/bioconductor-airway_1.2.0_src_all.tar.gz" + "https://bioconductor.org/packages/3.9/data/experiment/src/contrib/airway_1.4.0.tar.gz" + "https://bioarchive.galaxyproject.org/airway_1.4.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-airway/bioconductor-airway_1.4.0_src_all.tar.gz" ) -MD5="1b539cecd5b5a3b3550b659ec1f21b89" +MD5="ef609098c2893c759ddabbcb47cd4b6b" # Use a staging area in the conda dir rather than temp dirs, both to avoid # permission issues as well as to have things downloaded in a predictable @@ -16,7 +16,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-aldex2/meta.yaml b/recipes/bioconductor-aldex2/meta.yaml index a0653e1b53a33..1c79b05fa9d7f 100644 --- a/recipes/bioconductor-aldex2/meta.yaml +++ b/recipes/bioconductor-aldex2/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.14.1" %} +{% set version = "1.16.0" %} {% set name = "ALDEx2" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,30 +10,30 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: de6ce7be75ca2f1b8082a9c91108a046 + md5: 87792c8bd9d78c5b5ffdf069ce52fa8d build: number: 0 rpaths: - lib/R/lib/ - lib/ noarch: generic -# Suggests: testthat +# Suggests: testthat, BiocStyle, knitr, rmarkdown requirements: host: - - 'bioconductor-biocparallel >=1.16.0,<1.17.0' - - 'bioconductor-genomicranges >=1.34.0,<1.35.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-multtest >=2.38.0,<2.39.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' - - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' + - 'bioconductor-biocparallel >=1.18.0,<1.19.0' + - 'bioconductor-genomicranges >=1.36.0,<1.37.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-multtest >=2.40.0,<2.41.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' + - 'bioconductor-summarizedexperiment >=1.14.0,<1.15.0' - r-base run: - - 'bioconductor-biocparallel >=1.16.0,<1.17.0' - - 'bioconductor-genomicranges >=1.34.0,<1.35.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-multtest >=2.38.0,<2.39.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' - - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' + - 'bioconductor-biocparallel >=1.18.0,<1.19.0' + - 'bioconductor-genomicranges >=1.36.0,<1.37.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-multtest >=2.40.0,<2.41.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' + - 'bioconductor-summarizedexperiment >=1.14.0,<1.15.0' - r-base test: commands: @@ -41,7 +41,7 @@ test: about: home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: 'file LICENSE' - summary: 'A differential abundance analysis for the comparison of two or more conditions. Useful for analyzing data from standard RNA-seq or meta-RNA-seq assays as well as selected and unselected values from in-vitro sequence selections. Uses a Dirichlet-multinomial model to infer abundance from counts, optimized for three or more experimental replicates. The method infers biological and sampling variation to calculate the expected false discovery rate, given the variation, based on a Wilcox rank test or Welch t-test (via aldex.ttest), or a glm and Kruskal-Wallis test (via aldex.glm). Reports p-values and Benjamini-Hochberg corrected p-values.' + summary: 'A differential abundance analysis for the comparison of two or more conditions. Useful for analyzing data from standard RNA-seq or meta-RNA-seq assays as well as selected and unselected values from in-vitro sequence selections. Uses a Dirichlet-multinomial model to infer abundance from counts, optimized for three or more experimental replicates. The method infers biological and sampling variation to calculate the expected false discovery rate, given the variation, based on a Wilcoxon Rank Sum test and Welch''s t-test (via aldex.ttest), a Kruskal-Wallis test (via aldex.kw), a generalized linear model (via aldex.glm), or a correlation test (via aldex.corr). All tests report p-values and Benjamini-Hochberg corrected p-values.' extra: identifiers: - biotools:aldex2 diff --git a/recipes/bioconductor-alevinqc/build.sh b/recipes/bioconductor-alevinqc/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-alevinqc/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-alevinqc/meta.yaml b/recipes/bioconductor-alevinqc/meta.yaml new file mode 100644 index 0000000000000..0f9645618c6cd --- /dev/null +++ b/recipes/bioconductor-alevinqc/meta.yaml @@ -0,0 +1,53 @@ +{% set version = "1.0.0" %} +{% set name = "alevinQC" %} +{% set bioc = "3.9" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: 89abd6266744805e6da89f345a75b12c +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: knitr, BiocStyle, testthat, +requirements: + host: + - 'bioconductor-tximport >=1.12.0,<1.13.0' + - r-base + - r-cowplot + - r-dplyr + - r-dt + - r-ggally + - r-ggplot2 + - r-rjson + - r-rmarkdown + - r-shiny + - r-shinydashboard + run: + - 'bioconductor-tximport >=1.12.0,<1.13.0' + - r-base + - r-cowplot + - r-dplyr + - r-dt + - r-ggally + - r-ggplot2 + - r-rjson + - r-rmarkdown + - r-shiny + - r-shinydashboard +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: 'MIT + file LICENSE' + summary: 'Generate QC reports summarizing the output from an alevin run. Reports can be generated as html or pdf files, or as shiny applications.' + diff --git a/recipes/bioconductor-all/meta.yaml b/recipes/bioconductor-all/meta.yaml index 71b3660102990..8f236287649a0 100644 --- a/recipes/bioconductor-all/meta.yaml +++ b/recipes/bioconductor-all/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.24.0" %} +{% set version = "1.26.0" %} {% set name = "ALL" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_{{ name|lower }}.tar.gz' - md5: 815e7ffa1cb6eb8d71d29a5f450ff804 + md5: 10195f32f47c4af7bcb37ed7bdba04cb build: number: 0 rpaths: @@ -20,12 +20,12 @@ build: # Suggests: rpart requirements: host: - - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' - r-base run: - - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-all/post-link.sh b/recipes/bioconductor-all/post-link.sh index 52efd5a566822..ca7b56fa25b7e 100644 --- a/recipes/bioconductor-all/post-link.sh +++ b/recipes/bioconductor-all/post-link.sh @@ -1,11 +1,11 @@ #!/bin/bash -FN="ALL_1.24.0.tar.gz" +FN="ALL_1.26.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/experiment/src/contrib/ALL_1.24.0.tar.gz" - "https://bioarchive.galaxyproject.org/ALL_1.24.0.tar.gz" - "https://depot.galaxyproject.org/software/bioconductor-all/bioconductor-all_1.24.0_src_all.tar.gz" + "https://bioconductor.org/packages/3.9/data/experiment/src/contrib/ALL_1.26.0.tar.gz" + "https://bioarchive.galaxyproject.org/ALL_1.26.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-all/bioconductor-all_1.26.0_src_all.tar.gz" ) -MD5="815e7ffa1cb6eb8d71d29a5f450ff804" +MD5="10195f32f47c4af7bcb37ed7bdba04cb" # Use a staging area in the conda dir rather than temp dirs, both to avoid # permission issues as well as to have things downloaded in a predictable @@ -16,7 +16,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-allelicimbalance/meta.yaml b/recipes/bioconductor-allelicimbalance/meta.yaml index b01f33794b2b6..47989f8eb8b04 100644 --- a/recipes/bioconductor-allelicimbalance/meta.yaml +++ b/recipes/bioconductor-allelicimbalance/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.20.0" %} +{% set version = "1.22.0" %} {% set name = "AllelicImbalance" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,9 +10,9 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 6a2b9b7e9957cf227690060862bd280c + md5: 807f1eb3d123bed77822e239fc05029b build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ @@ -20,20 +20,20 @@ build: # Suggests: testthat, org.Hs.eg.db, TxDb.Hsapiens.UCSC.hg19.knownGene, SNPlocs.Hsapiens.dbSNP144.GRCh37, BiocStyle, knitr, rmarkdown requirements: host: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' - - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' - - 'bioconductor-biostrings >=2.50.0,<2.51.0' - - 'bioconductor-bsgenome >=1.50.0,<1.51.0' - - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' - - 'bioconductor-genomicalignments >=1.18.0,<1.19.0' - - 'bioconductor-genomicfeatures >=1.34.0,<1.35.0' - - 'bioconductor-genomicranges >=1.34.0,<1.35.0' - - 'bioconductor-gviz >=1.26.0,<1.27.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-rsamtools >=1.34.0,<1.35.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' - - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' - - 'bioconductor-variantannotation >=1.28.0,<1.29.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' + - 'bioconductor-biocgenerics >=0.30.0,<0.31.0' + - 'bioconductor-biostrings >=2.52.0,<2.53.0' + - 'bioconductor-bsgenome >=1.52.0,<1.53.0' + - 'bioconductor-genomeinfodb >=1.20.0,<1.21.0' + - 'bioconductor-genomicalignments >=1.20.0,<1.21.0' + - 'bioconductor-genomicfeatures >=1.36.0,<1.37.0' + - 'bioconductor-genomicranges >=1.36.0,<1.37.0' + - 'bioconductor-gviz >=1.28.0,<1.29.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-rsamtools >=2.0.0,<2.1.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' + - 'bioconductor-summarizedexperiment >=1.14.0,<1.15.0' + - 'bioconductor-variantannotation >=1.30.0,<1.31.0' - r-base - r-gridextra - r-lattice @@ -41,20 +41,20 @@ requirements: - r-nlme - r-seqinr run: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' - - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' - - 'bioconductor-biostrings >=2.50.0,<2.51.0' - - 'bioconductor-bsgenome >=1.50.0,<1.51.0' - - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' - - 'bioconductor-genomicalignments >=1.18.0,<1.19.0' - - 'bioconductor-genomicfeatures >=1.34.0,<1.35.0' - - 'bioconductor-genomicranges >=1.34.0,<1.35.0' - - 'bioconductor-gviz >=1.26.0,<1.27.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-rsamtools >=1.34.0,<1.35.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' - - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' - - 'bioconductor-variantannotation >=1.28.0,<1.29.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' + - 'bioconductor-biocgenerics >=0.30.0,<0.31.0' + - 'bioconductor-biostrings >=2.52.0,<2.53.0' + - 'bioconductor-bsgenome >=1.52.0,<1.53.0' + - 'bioconductor-genomeinfodb >=1.20.0,<1.21.0' + - 'bioconductor-genomicalignments >=1.20.0,<1.21.0' + - 'bioconductor-genomicfeatures >=1.36.0,<1.37.0' + - 'bioconductor-genomicranges >=1.36.0,<1.37.0' + - 'bioconductor-gviz >=1.28.0,<1.29.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-rsamtools >=2.0.0,<2.1.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' + - 'bioconductor-summarizedexperiment >=1.14.0,<1.15.0' + - 'bioconductor-variantannotation >=1.30.0,<1.31.0' - r-base - r-gridextra - r-lattice diff --git a/recipes/bioconductor-allenpvc/meta.yaml b/recipes/bioconductor-allenpvc/meta.yaml index d2f86a5626605..3ad2ee4023a66 100644 --- a/recipes/bioconductor-allenpvc/meta.yaml +++ b/recipes/bioconductor-allenpvc/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.0.0" %} +{% set version = "1.2.0" %} {% set name = "allenpvc" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: e77a28b830842ee034930432e95fdfaf + md5: 37da5faac1aeef26425a1f0ac4b3981c build: number: 0 rpaths: @@ -20,16 +20,16 @@ build: # Suggests: BiocStyle, knitr, rmarkdown requirements: host: - - 'bioconductor-annotationhub >=2.14.0,<2.15.0' - - 'bioconductor-experimenthub >=1.8.0,<1.9.0' - - 'bioconductor-singlecellexperiment >=1.4.0,<1.5.0' + - 'bioconductor-annotationhub >=2.16.0,<2.17.0' + - 'bioconductor-experimenthub >=1.10.0,<1.11.0' + - 'bioconductor-singlecellexperiment >=1.6.0,<1.7.0' - r-base run: - - 'bioconductor-annotationhub >=2.14.0,<2.15.0' - - 'bioconductor-experimenthub >=1.8.0,<1.9.0' - - 'bioconductor-singlecellexperiment >=1.4.0,<1.5.0' + - 'bioconductor-annotationhub >=2.16.0,<2.17.0' + - 'bioconductor-experimenthub >=1.10.0,<1.11.0' + - 'bioconductor-singlecellexperiment >=1.6.0,<1.7.0' - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-allenpvc/post-link.sh b/recipes/bioconductor-allenpvc/post-link.sh index 98f33105d04c2..485b268c80b2c 100644 --- a/recipes/bioconductor-allenpvc/post-link.sh +++ b/recipes/bioconductor-allenpvc/post-link.sh @@ -1,11 +1,11 @@ #!/bin/bash -FN="allenpvc_1.0.0.tar.gz" +FN="allenpvc_1.2.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/experiment/src/contrib/allenpvc_1.0.0.tar.gz" - "https://bioarchive.galaxyproject.org/allenpvc_1.0.0.tar.gz" - "https://depot.galaxyproject.org/software/bioconductor-allenpvc/bioconductor-allenpvc_1.0.0_src_all.tar.gz" + "https://bioconductor.org/packages/3.9/data/experiment/src/contrib/allenpvc_1.2.0.tar.gz" + "https://bioarchive.galaxyproject.org/allenpvc_1.2.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-allenpvc/bioconductor-allenpvc_1.2.0_src_all.tar.gz" ) -MD5="e77a28b830842ee034930432e95fdfaf" +MD5="37da5faac1aeef26425a1f0ac4b3981c" # Use a staging area in the conda dir rather than temp dirs, both to avoid # permission issues as well as to have things downloaded in a predictable @@ -16,7 +16,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-allmll/meta.yaml b/recipes/bioconductor-allmll/meta.yaml index a50031f6ba3bc..7b8ef0cdde52b 100644 --- a/recipes/bioconductor-allmll/meta.yaml +++ b/recipes/bioconductor-allmll/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.22.0" %} +{% set version = "1.24.0" %} {% set name = "ALLMLL" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: fc9e850c94ac9ec9c377f5e8843e7673 + md5: 90b0a2dc8092018739e3c8b195888311 build: number: 0 rpaths: @@ -19,12 +19,12 @@ build: noarch: generic requirements: host: - - 'bioconductor-affy >=1.60.0,<1.61.0' + - 'bioconductor-affy >=1.62.0,<1.63.0' - r-base run: - - 'bioconductor-affy >=1.60.0,<1.61.0' + - 'bioconductor-affy >=1.62.0,<1.63.0' - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-allmll/post-link.sh b/recipes/bioconductor-allmll/post-link.sh index f725e86035a27..89d1f2e2d7191 100644 --- a/recipes/bioconductor-allmll/post-link.sh +++ b/recipes/bioconductor-allmll/post-link.sh @@ -1,11 +1,11 @@ #!/bin/bash -FN="ALLMLL_1.22.0.tar.gz" +FN="ALLMLL_1.24.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/experiment/src/contrib/ALLMLL_1.22.0.tar.gz" - "https://bioarchive.galaxyproject.org/ALLMLL_1.22.0.tar.gz" - "https://depot.galaxyproject.org/software/bioconductor-allmll/bioconductor-allmll_1.22.0_src_all.tar.gz" + "https://bioconductor.org/packages/3.9/data/experiment/src/contrib/ALLMLL_1.24.0.tar.gz" + "https://bioarchive.galaxyproject.org/ALLMLL_1.24.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-allmll/bioconductor-allmll_1.24.0_src_all.tar.gz" ) -MD5="fc9e850c94ac9ec9c377f5e8843e7673" +MD5="90b0a2dc8092018739e3c8b195888311" # Use a staging area in the conda dir rather than temp dirs, both to avoid # permission issues as well as to have things downloaded in a predictable @@ -16,7 +16,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-alpine/meta.yaml b/recipes/bioconductor-alpine/meta.yaml index bfe30b46fcdff..b6953b0201e52 100644 --- a/recipes/bioconductor-alpine/meta.yaml +++ b/recipes/bioconductor-alpine/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.8.0" %} +{% set version = "1.10.0" %} {% set name = "alpine" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 2f5f6264027f585b0c8a25a7d90095a2 + md5: 406b4cea9ae12ceead4a586e194c567d build: number: 0 rpaths: @@ -20,32 +20,32 @@ build: # Suggests: knitr, testthat, alpineData, rtracklayer, ensembldb, BSgenome.Hsapiens.NCBI.GRCh38, RColorBrewer requirements: host: - - 'bioconductor-biostrings >=2.50.0,<2.51.0' - - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' - - 'bioconductor-genomicalignments >=1.18.0,<1.19.0' - - 'bioconductor-genomicfeatures >=1.34.0,<1.35.0' - - 'bioconductor-genomicranges >=1.34.0,<1.35.0' - - 'bioconductor-graph >=1.60.0,<1.61.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-rbgl >=1.58.0,<1.59.0' - - 'bioconductor-rsamtools >=1.34.0,<1.35.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' - - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' + - 'bioconductor-biostrings >=2.52.0,<2.53.0' + - 'bioconductor-genomeinfodb >=1.20.0,<1.21.0' + - 'bioconductor-genomicalignments >=1.20.0,<1.21.0' + - 'bioconductor-genomicfeatures >=1.36.0,<1.37.0' + - 'bioconductor-genomicranges >=1.36.0,<1.37.0' + - 'bioconductor-graph >=1.62.0,<1.63.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-rbgl >=1.60.0,<1.61.0' + - 'bioconductor-rsamtools >=2.0.0,<2.1.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' + - 'bioconductor-summarizedexperiment >=1.14.0,<1.15.0' - r-base - r-speedglm - r-stringr run: - - 'bioconductor-biostrings >=2.50.0,<2.51.0' - - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' - - 'bioconductor-genomicalignments >=1.18.0,<1.19.0' - - 'bioconductor-genomicfeatures >=1.34.0,<1.35.0' - - 'bioconductor-genomicranges >=1.34.0,<1.35.0' - - 'bioconductor-graph >=1.60.0,<1.61.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-rbgl >=1.58.0,<1.59.0' - - 'bioconductor-rsamtools >=1.34.0,<1.35.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' - - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' + - 'bioconductor-biostrings >=2.52.0,<2.53.0' + - 'bioconductor-genomeinfodb >=1.20.0,<1.21.0' + - 'bioconductor-genomicalignments >=1.20.0,<1.21.0' + - 'bioconductor-genomicfeatures >=1.36.0,<1.37.0' + - 'bioconductor-genomicranges >=1.36.0,<1.37.0' + - 'bioconductor-graph >=1.62.0,<1.63.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-rbgl >=1.60.0,<1.61.0' + - 'bioconductor-rsamtools >=2.0.0,<2.1.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' + - 'bioconductor-summarizedexperiment >=1.14.0,<1.15.0' - r-base - r-speedglm - r-stringr diff --git a/recipes/bioconductor-alpinedata/meta.yaml b/recipes/bioconductor-alpinedata/meta.yaml index af5d3c973159b..6d8351253264e 100644 --- a/recipes/bioconductor-alpinedata/meta.yaml +++ b/recipes/bioconductor-alpinedata/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.8.0" %} +{% set version = "1.10.0" %} {% set name = "alpineData" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 56b8097bf76942789ec2694ad0fa51e7 + md5: b97dd0b4c0e4b0b3b55308ffe850740f build: number: 0 rpaths: @@ -20,16 +20,16 @@ build: # Suggests: GenomicAlignments, knitr requirements: host: - - 'bioconductor-annotationhub >=2.14.0,<2.15.0' - - 'bioconductor-experimenthub >=1.8.0,<1.9.0' - - 'bioconductor-genomicalignments >=1.18.0,<1.19.0' + - 'bioconductor-annotationhub >=2.16.0,<2.17.0' + - 'bioconductor-experimenthub >=1.10.0,<1.11.0' + - 'bioconductor-genomicalignments >=1.20.0,<1.21.0' - r-base run: - - 'bioconductor-annotationhub >=2.14.0,<2.15.0' - - 'bioconductor-experimenthub >=1.8.0,<1.9.0' - - 'bioconductor-genomicalignments >=1.18.0,<1.19.0' + - 'bioconductor-annotationhub >=2.16.0,<2.17.0' + - 'bioconductor-experimenthub >=1.10.0,<1.11.0' + - 'bioconductor-genomicalignments >=1.20.0,<1.21.0' - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-alpinedata/post-link.sh b/recipes/bioconductor-alpinedata/post-link.sh index c06a2fe90d186..cbdee4fe1921d 100644 --- a/recipes/bioconductor-alpinedata/post-link.sh +++ b/recipes/bioconductor-alpinedata/post-link.sh @@ -1,11 +1,11 @@ #!/bin/bash -FN="alpineData_1.8.0.tar.gz" +FN="alpineData_1.10.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/experiment/src/contrib/alpineData_1.8.0.tar.gz" - "https://bioarchive.galaxyproject.org/alpineData_1.8.0.tar.gz" - "https://depot.galaxyproject.org/software/bioconductor-alpinedata/bioconductor-alpinedata_1.8.0_src_all.tar.gz" + "https://bioconductor.org/packages/3.9/data/experiment/src/contrib/alpineData_1.10.0.tar.gz" + "https://bioarchive.galaxyproject.org/alpineData_1.10.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-alpinedata/bioconductor-alpinedata_1.10.0_src_all.tar.gz" ) -MD5="56b8097bf76942789ec2694ad0fa51e7" +MD5="b97dd0b4c0e4b0b3b55308ffe850740f" # Use a staging area in the conda dir rather than temp dirs, both to avoid # permission issues as well as to have things downloaded in a predictable @@ -16,7 +16,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-alsace/meta.yaml b/recipes/bioconductor-alsace/meta.yaml index ba72c0d0ef0c7..5b558c36b0d7d 100644 --- a/recipes/bioconductor-alsace/meta.yaml +++ b/recipes/bioconductor-alsace/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.18.0" %} +{% set version = "1.20.0" %} {% set name = "alsace" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: a26103b4ba914dab96374e4e7be3b78b + md5: d93cfabbc11b8b2d27bfabde5067437c build: number: 0 rpaths: diff --git a/recipes/bioconductor-altcdfenvs/meta.yaml b/recipes/bioconductor-altcdfenvs/meta.yaml index dd1cf79935093..3fd298d18e0a5 100644 --- a/recipes/bioconductor-altcdfenvs/meta.yaml +++ b/recipes/bioconductor-altcdfenvs/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "2.44.0" %} +{% set version = "2.46.0" %} {% set name = "altcdfenvs" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 3d5ddd23cc69e649a27a607a98d5d4dc + md5: 47a0200f44c54dd06492e69bd03cd051 build: number: 0 rpaths: @@ -20,22 +20,22 @@ build: # Suggests: plasmodiumanophelescdf, hgu95acdf, hgu133aprobe, hgu133a.db, hgu133acdf, Rgraphviz, RColorBrewer requirements: host: - - 'bioconductor-affy >=1.60.0,<1.61.0' - - 'bioconductor-biobase >=2.42.0,<2.43.0' - - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' - - 'bioconductor-biostrings >=2.50.0,<2.51.0' - - 'bioconductor-hypergraph >=1.54.0,<1.55.0' - - 'bioconductor-makecdfenv >=1.58.0,<1.59.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-affy >=1.62.0,<1.63.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' + - 'bioconductor-biocgenerics >=0.30.0,<0.31.0' + - 'bioconductor-biostrings >=2.52.0,<2.53.0' + - 'bioconductor-hypergraph >=1.56.0,<1.57.0' + - 'bioconductor-makecdfenv >=1.60.0,<1.61.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' - r-base run: - - 'bioconductor-affy >=1.60.0,<1.61.0' - - 'bioconductor-biobase >=2.42.0,<2.43.0' - - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' - - 'bioconductor-biostrings >=2.50.0,<2.51.0' - - 'bioconductor-hypergraph >=1.54.0,<1.55.0' - - 'bioconductor-makecdfenv >=1.58.0,<1.59.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-affy >=1.62.0,<1.63.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' + - 'bioconductor-biocgenerics >=0.30.0,<0.31.0' + - 'bioconductor-biostrings >=2.52.0,<2.53.0' + - 'bioconductor-hypergraph >=1.56.0,<1.57.0' + - 'bioconductor-makecdfenv >=1.60.0,<1.61.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' - r-base test: commands: diff --git a/recipes/bioconductor-alternativesplicingevents.hg19/meta.yaml b/recipes/bioconductor-alternativesplicingevents.hg19/meta.yaml index 574be0bd566f8..f70852f7c8b88 100644 --- a/recipes/bioconductor-alternativesplicingevents.hg19/meta.yaml +++ b/recipes/bioconductor-alternativesplicingevents.hg19/meta.yaml @@ -1,6 +1,6 @@ {% set version = "1.0.1" %} {% set name = "alternativeSplicingEvents.hg19" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -12,7 +12,7 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' md5: 3e694353233e7d5d3abd22bfb5887513 build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ @@ -20,12 +20,12 @@ build: # Suggests: data.frame, dplyr, GenomicRanges, S4Vectors requirements: host: - - 'bioconductor-annotationhub >=2.14.0,<2.15.0' + - 'bioconductor-annotationhub >=2.16.0,<2.17.0' - r-base run: - - 'bioconductor-annotationhub >=2.14.0,<2.15.0' + - 'bioconductor-annotationhub >=2.16.0,<2.17.0' - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-alternativesplicingevents.hg19/post-link.sh b/recipes/bioconductor-alternativesplicingevents.hg19/post-link.sh index c926ecd7596ea..fb3ba54e629a9 100644 --- a/recipes/bioconductor-alternativesplicingevents.hg19/post-link.sh +++ b/recipes/bioconductor-alternativesplicingevents.hg19/post-link.sh @@ -1,9 +1,10 @@ #!/bin/bash FN="alternativeSplicingEvents.hg19_1.0.1.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/alternativeSplicingEvents.hg19_1.0.1.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/alternativeSplicingEvents.hg19_1.0.1.tar.gz" "https://bioarchive.galaxyproject.org/alternativeSplicingEvents.hg19_1.0.1.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-alternativesplicingevents.hg19/bioconductor-alternativesplicingevents.hg19_1.0.1_src_all.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-alternativesplicingevents.hg19/bioconductor-alternativesplicingevents.hg19_1.0.1_src_all.tar.gz" ) MD5="3e694353233e7d5d3abd22bfb5887513" @@ -16,7 +17,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-alternativesplicingevents.hg38/meta.yaml b/recipes/bioconductor-alternativesplicingevents.hg38/meta.yaml index 327aa4258a2a6..e1d26e50ec949 100644 --- a/recipes/bioconductor-alternativesplicingevents.hg38/meta.yaml +++ b/recipes/bioconductor-alternativesplicingevents.hg38/meta.yaml @@ -1,6 +1,6 @@ {% set version = "1.0.1" %} {% set name = "alternativeSplicingEvents.hg38" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -12,7 +12,7 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' md5: 9ce2e10cfe00ec4451670e1fd18d2e37 build: - number: 1 + number: 2 rpaths: - lib/R/lib/ - lib/ @@ -20,12 +20,12 @@ build: # Suggests: dplyr, GenomicRanges, S4Vectors requirements: host: - - 'bioconductor-annotationhub >=2.14.0,<2.15.0' + - 'bioconductor-annotationhub >=2.16.0,<2.17.0' - r-base run: - - 'bioconductor-annotationhub >=2.14.0,<2.15.0' + - 'bioconductor-annotationhub >=2.16.0,<2.17.0' - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-alternativesplicingevents.hg38/post-link.sh b/recipes/bioconductor-alternativesplicingevents.hg38/post-link.sh index 6e4e45d2d7b67..bc0529f63927a 100644 --- a/recipes/bioconductor-alternativesplicingevents.hg38/post-link.sh +++ b/recipes/bioconductor-alternativesplicingevents.hg38/post-link.sh @@ -1,9 +1,10 @@ #!/bin/bash FN="alternativeSplicingEvents.hg38_1.0.1.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/alternativeSplicingEvents.hg38_1.0.1.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/alternativeSplicingEvents.hg38_1.0.1.tar.gz" "https://bioarchive.galaxyproject.org/alternativeSplicingEvents.hg38_1.0.1.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-alternativesplicingevents.hg38/bioconductor-alternativesplicingevents.hg38_1.0.1_src_all.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-alternativesplicingevents.hg38/bioconductor-alternativesplicingevents.hg38_1.0.1_src_all.tar.gz" ) MD5="9ce2e10cfe00ec4451670e1fd18d2e37" @@ -16,7 +17,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-amaretto/build.sh b/recipes/bioconductor-amaretto/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-amaretto/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-amaretto/meta.yaml b/recipes/bioconductor-amaretto/meta.yaml new file mode 100644 index 0000000000000..3c271b64ca427 --- /dev/null +++ b/recipes/bioconductor-amaretto/meta.yaml @@ -0,0 +1,77 @@ +{% set version = "1.0.0" %} +{% set name = "AMARETTO" %} +{% set bioc = "3.9" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: 58c63ba233527e4f2b24d85aad2d857c +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ +# Suggests: testthat, MASS, knitr +requirements: + host: + - 'bioconductor-biocfilecache >=1.8.0,<1.9.0' + - 'bioconductor-complexheatmap >=2.0.0,<2.1.0' + - 'bioconductor-curatedtcgadata >=1.6.0,<1.7.0' + - 'bioconductor-impute >=1.58.0,<1.59.0' + - 'bioconductor-limma >=3.40.0,<3.41.0' + - 'bioconductor-multiassayexperiment >=1.10.0,<1.11.0' + - r-base + - 'r-callr >=3.0.0.9001' + - r-circlize + - r-doparallel + - r-dplyr + - r-dt + - r-foreach + - r-glmnet + - r-httr + - r-matrix + - r-matrixstats + - r-rcpp + - r-readr + - r-reshape2 + - r-rmarkdown + - r-tibble + run: + - 'bioconductor-biocfilecache >=1.8.0,<1.9.0' + - 'bioconductor-complexheatmap >=2.0.0,<2.1.0' + - 'bioconductor-curatedtcgadata >=1.6.0,<1.7.0' + - 'bioconductor-impute >=1.58.0,<1.59.0' + - 'bioconductor-limma >=3.40.0,<3.41.0' + - 'bioconductor-multiassayexperiment >=1.10.0,<1.11.0' + - r-base + - 'r-callr >=3.0.0.9001' + - r-circlize + - r-doparallel + - r-dplyr + - r-dt + - r-foreach + - r-glmnet + - r-httr + - r-matrix + - r-matrixstats + - r-rcpp + - r-readr + - r-reshape2 + - r-rmarkdown + - r-tibble + build: + - {{ compiler('c') }} + - {{ compiler('cxx') }} +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: 'Apache License (== 2.0) + file LICENSE' + summary: 'Integrating an increasing number of available multi-omics cancer data remains one of the main challenges to improve our understanding of cancer. One of the main challenges is using multi-omics data for identifying novel cancer driver genes. We have developed an algorithm, called AMARETTO, that integrates copy number, DNA methylation and gene expression data to identify a set of driver genes by analyzing cancer samples and connects them to clusters of co-expressed genes, which we define as modules. We applied AMARETTO in a pancancer setting to identify cancer driver genes and their modules on multiple cancer sites. AMARETTO captures modules enriched in angiogenesis, cell cycle and EMT, and modules that accurately predict survival and molecular subtypes. This allows AMARETTO to identify novel cancer driver genes directing canonical cancer pathways.' + diff --git a/recipes/bioconductor-amountain/meta.yaml b/recipes/bioconductor-amountain/meta.yaml index fbf6ceaf824b2..15d32d3f5a94f 100644 --- a/recipes/bioconductor-amountain/meta.yaml +++ b/recipes/bioconductor-amountain/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.8.0" %} +{% set version = "1.10.0" %} {% set name = "AMOUNTAIN" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 394ae847017425e30abdaf18107b02b7 + md5: 4511063e0919b9b89aacee901f2273b3 build: number: 0 rpaths: @@ -22,11 +22,9 @@ requirements: host: - r-base - gsl - - openblas run: - r-base - gsl - - openblas build: - {{ compiler('c') }} - make diff --git a/recipes/bioconductor-ampaffyexample/meta.yaml b/recipes/bioconductor-ampaffyexample/meta.yaml index 30d81a0845bf1..5632c920cab6f 100644 --- a/recipes/bioconductor-ampaffyexample/meta.yaml +++ b/recipes/bioconductor-ampaffyexample/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.22.0" %} +{% set version = "1.24.0" %} {% set name = "AmpAffyExample" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 89fc3d6d5cff3852ec8b8748898bf8af + md5: 90cc999d9d645e4478c8ca9bee8900b3 build: number: 0 rpaths: @@ -20,12 +20,12 @@ build: # Suggests: hgu133acdf requirements: host: - - 'bioconductor-affy >=1.60.0,<1.61.0' + - 'bioconductor-affy >=1.62.0,<1.63.0' - r-base run: - - 'bioconductor-affy >=1.60.0,<1.61.0' + - 'bioconductor-affy >=1.62.0,<1.63.0' - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-ampaffyexample/post-link.sh b/recipes/bioconductor-ampaffyexample/post-link.sh index dfeecc7c3b58c..89faa8ac2e09a 100644 --- a/recipes/bioconductor-ampaffyexample/post-link.sh +++ b/recipes/bioconductor-ampaffyexample/post-link.sh @@ -1,11 +1,11 @@ #!/bin/bash -FN="AmpAffyExample_1.22.0.tar.gz" +FN="AmpAffyExample_1.24.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/experiment/src/contrib/AmpAffyExample_1.22.0.tar.gz" - "https://bioarchive.galaxyproject.org/AmpAffyExample_1.22.0.tar.gz" - "https://depot.galaxyproject.org/software/bioconductor-ampaffyexample/bioconductor-ampaffyexample_1.22.0_src_all.tar.gz" + "https://bioconductor.org/packages/3.9/data/experiment/src/contrib/AmpAffyExample_1.24.0.tar.gz" + "https://bioarchive.galaxyproject.org/AmpAffyExample_1.24.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-ampaffyexample/bioconductor-ampaffyexample_1.24.0_src_all.tar.gz" ) -MD5="89fc3d6d5cff3852ec8b8748898bf8af" +MD5="90cc999d9d645e4478c8ca9bee8900b3" # Use a staging area in the conda dir rather than temp dirs, both to avoid # permission issues as well as to have things downloaded in a predictable @@ -16,7 +16,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-amplican/meta.yaml b/recipes/bioconductor-amplican/meta.yaml index 90545d0347209..ae6355a3d1145 100644 --- a/recipes/bioconductor-amplican/meta.yaml +++ b/recipes/bioconductor-amplican/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.4.0" %} +{% set version = "1.6.0" %} {% set name = "amplican" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,29 +10,27 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 10c9662fb6df49f5d796ae7a40287749 + md5: f4acd20d0f4f701b1e7dcc93a3c95f9f build: number: 0 rpaths: - lib/R/lib/ - lib/ - noarch: generic # Suggests: testthat, BiocStyle, GenomicAlignments requirements: host: - - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' - - 'bioconductor-biocparallel >=1.16.0,<1.17.0' - - 'bioconductor-biostrings >=2.50.0,<2.51.0' - - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' - - 'bioconductor-genomicranges >=1.34.0,<1.35.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' - - 'bioconductor-shortread >=1.40.0,<1.41.0' + - 'bioconductor-biocgenerics >=0.30.0,<0.31.0' + - 'bioconductor-biocparallel >=1.18.0,<1.19.0' + - 'bioconductor-biostrings >=2.52.0,<2.53.0' + - 'bioconductor-genomeinfodb >=1.20.0,<1.21.0' + - 'bioconductor-genomicranges >=1.36.0,<1.37.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' + - 'bioconductor-shortread >=1.42.0,<1.43.0' - r-base - 'r-clustercrit >=1.2.7' - 'r-data.table >=1.10.4-3' - 'r-dplyr >=0.7.2' - - 'r-ggforce >=0.1.2' - 'r-ggplot2 >=2.2.0' - 'r-ggthemes >=3.4.0' - 'r-gridextra >=2.2.1' @@ -40,23 +38,23 @@ requirements: - 'r-knitr >=1.16' - 'r-matrix >=1.2-10' - 'r-matrixstats >=0.52.2' + - r-rcpp - 'r-rmarkdown >=1.6' - 'r-stringr >=1.2.0' - 'r-waffle >=0.7.0' run: - - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' - - 'bioconductor-biocparallel >=1.16.0,<1.17.0' - - 'bioconductor-biostrings >=2.50.0,<2.51.0' - - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' - - 'bioconductor-genomicranges >=1.34.0,<1.35.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' - - 'bioconductor-shortread >=1.40.0,<1.41.0' + - 'bioconductor-biocgenerics >=0.30.0,<0.31.0' + - 'bioconductor-biocparallel >=1.18.0,<1.19.0' + - 'bioconductor-biostrings >=2.52.0,<2.53.0' + - 'bioconductor-genomeinfodb >=1.20.0,<1.21.0' + - 'bioconductor-genomicranges >=1.36.0,<1.37.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' + - 'bioconductor-shortread >=1.42.0,<1.43.0' - r-base - 'r-clustercrit >=1.2.7' - 'r-data.table >=1.10.4-3' - 'r-dplyr >=0.7.2' - - 'r-ggforce >=0.1.2' - 'r-ggplot2 >=2.2.0' - 'r-ggthemes >=3.4.0' - 'r-gridextra >=2.2.1' @@ -64,9 +62,14 @@ requirements: - 'r-knitr >=1.16' - 'r-matrix >=1.2-10' - 'r-matrixstats >=0.52.2' + - r-rcpp - 'r-rmarkdown >=1.6' - 'r-stringr >=1.2.0' - 'r-waffle >=0.7.0' + build: + - {{ compiler('c') }} + - {{ compiler('cxx') }} + - make test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-analysispageserver/meta.yaml b/recipes/bioconductor-analysispageserver/meta.yaml index 3e67c394a509f..d8d17169e84ee 100644 --- a/recipes/bioconductor-analysispageserver/meta.yaml +++ b/recipes/bioconductor-analysispageserver/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.16.0" %} +{% set version = "1.18.0" %} {% set name = "AnalysisPageServer" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 85095095c94e346b6c74c85b3a8ee6dc + md5: 0ffa66c286ebe271f01c493b88607b75 build: number: 0 rpaths: @@ -19,14 +19,14 @@ build: # Suggests: RUnit, XML, knitr requirements: host: - - 'bioconductor-biobase >=2.42.0,<2.43.0' - - 'bioconductor-graph >=1.60.0,<1.61.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' + - 'bioconductor-graph >=1.62.0,<1.63.0' - r-base - r-log4r - r-rjson run: - - 'bioconductor-biobase >=2.42.0,<2.43.0' - - 'bioconductor-graph >=1.60.0,<1.61.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' + - 'bioconductor-graph >=1.62.0,<1.63.0' - r-base - r-log4r - r-rjson diff --git a/recipes/bioconductor-anamir/meta.yaml b/recipes/bioconductor-anamir/meta.yaml index e187018ff2244..7e3ee55ba3e9e 100644 --- a/recipes/bioconductor-anamir/meta.yaml +++ b/recipes/bioconductor-anamir/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.10.0" %} +{% set version = "1.11.0" %} {% set name = "anamiR" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 0743887caa63267607e4165602f90951 + md5: 88695f2755b1a925eba6c3742bcdd64c build: number: 0 rpaths: @@ -20,24 +20,24 @@ build: # Suggests: knitr, rmarkdown, data.table requirements: host: - - 'bioconductor-deseq2 >=1.22.0,<1.23.0' - - 'bioconductor-gage >=2.32.0,<2.33.0' - - 'bioconductor-limma >=3.38.0,<3.39.0' - - 'bioconductor-lumi >=2.34.0,<2.35.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' - - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' + - 'bioconductor-deseq2 >=1.24.0,<1.25.0' + - 'bioconductor-gage >=2.34.0,<2.35.0' + - 'bioconductor-limma >=3.40.0,<3.41.0' + - 'bioconductor-lumi >=2.36.0,<2.37.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' + - 'bioconductor-summarizedexperiment >=1.14.0,<1.15.0' - r-agricolae - r-base - r-dbi - r-gplots - r-rmysql run: - - 'bioconductor-deseq2 >=1.22.0,<1.23.0' - - 'bioconductor-gage >=2.32.0,<2.33.0' - - 'bioconductor-limma >=3.38.0,<3.39.0' - - 'bioconductor-lumi >=2.34.0,<2.35.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' - - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' + - 'bioconductor-deseq2 >=1.24.0,<1.25.0' + - 'bioconductor-gage >=2.34.0,<2.35.0' + - 'bioconductor-limma >=3.40.0,<3.41.0' + - 'bioconductor-lumi >=2.36.0,<2.37.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' + - 'bioconductor-summarizedexperiment >=1.14.0,<1.15.0' - r-agricolae - r-base - r-dbi diff --git a/recipes/bioconductor-anaquin/meta.yaml b/recipes/bioconductor-anaquin/meta.yaml index 33d9502ce3ccf..ef6e377603100 100644 --- a/recipes/bioconductor-anaquin/meta.yaml +++ b/recipes/bioconductor-anaquin/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "2.6.0" %} +{% set version = "2.8.0" %} {% set name = "Anaquin" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 8f1bc0e8a7c1e4762e4c561b8461f068 + md5: a151bd5028a663f00df34bd73274a841 build: number: 0 rpaths: @@ -20,8 +20,8 @@ build: # Suggests: RUnit, rmarkdown requirements: host: - - 'bioconductor-deseq2 >=1.22.0,<1.23.0' - - 'bioconductor-qvalue >=2.14.0,<2.15.0' + - 'bioconductor-deseq2 >=1.24.0,<1.25.0' + - 'bioconductor-qvalue >=2.16.0,<2.17.0' - r-base - 'r-ggplot2 >=2.2.0' - r-knitr @@ -29,8 +29,8 @@ requirements: - r-plyr - r-rocr run: - - 'bioconductor-deseq2 >=1.22.0,<1.23.0' - - 'bioconductor-qvalue >=2.14.0,<2.15.0' + - 'bioconductor-deseq2 >=1.24.0,<1.25.0' + - 'bioconductor-qvalue >=2.16.0,<2.17.0' - r-base - 'r-ggplot2 >=2.2.0' - r-knitr diff --git a/recipes/bioconductor-aneufinder/meta.yaml b/recipes/bioconductor-aneufinder/meta.yaml index 2df5118ba3de4..f950d1cd57599 100644 --- a/recipes/bioconductor-aneufinder/meta.yaml +++ b/recipes/bioconductor-aneufinder/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.10.1" %} +{% set version = "1.12.0" %} {% set name = "AneuFinder" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: aef30798edd6bd379f288ef13dce3cc8 + md5: f4039076c73890e1ea9803a294f6dfe4 build: number: 0 rpaths: @@ -19,16 +19,16 @@ build: # Suggests: knitr, BiocStyle, testthat, BSgenome.Hsapiens.UCSC.hg19, BSgenome.Mmusculus.UCSC.mm10 requirements: host: - - 'bioconductor-aneufinderdata >=1.10.0,<1.11.0' - - 'bioconductor-bamsignals >=1.14.0,<1.15.0' - - 'bioconductor-biostrings >=2.50.0,<2.51.0' - - 'bioconductor-dnacopy >=1.56.0,<1.57.0' - - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' - - 'bioconductor-genomicalignments >=1.18.0,<1.19.0' - - 'bioconductor-genomicranges >=1.34.0,<1.35.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-rsamtools >=1.34.0,<1.35.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-aneufinderdata >=1.12.0,<1.13.0' + - 'bioconductor-bamsignals >=1.16.0,<1.17.0' + - 'bioconductor-biostrings >=2.52.0,<2.53.0' + - 'bioconductor-dnacopy >=1.58.0,<1.59.0' + - 'bioconductor-genomeinfodb >=1.20.0,<1.21.0' + - 'bioconductor-genomicalignments >=1.20.0,<1.21.0' + - 'bioconductor-genomicranges >=1.36.0,<1.37.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-rsamtools >=2.0.0,<2.1.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' - r-base - r-cowplot - r-doparallel @@ -41,16 +41,16 @@ requirements: - r-reordercluster - r-reshape2 run: - - 'bioconductor-aneufinderdata >=1.10.0,<1.11.0' - - 'bioconductor-bamsignals >=1.14.0,<1.15.0' - - 'bioconductor-biostrings >=2.50.0,<2.51.0' - - 'bioconductor-dnacopy >=1.56.0,<1.57.0' - - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' - - 'bioconductor-genomicalignments >=1.18.0,<1.19.0' - - 'bioconductor-genomicranges >=1.34.0,<1.35.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-rsamtools >=1.34.0,<1.35.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-aneufinderdata >=1.12.0,<1.13.0' + - 'bioconductor-bamsignals >=1.16.0,<1.17.0' + - 'bioconductor-biostrings >=2.52.0,<2.53.0' + - 'bioconductor-dnacopy >=1.58.0,<1.59.0' + - 'bioconductor-genomeinfodb >=1.20.0,<1.21.0' + - 'bioconductor-genomicalignments >=1.20.0,<1.21.0' + - 'bioconductor-genomicranges >=1.36.0,<1.37.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-rsamtools >=2.0.0,<2.1.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' - r-base - r-cowplot - r-doparallel diff --git a/recipes/bioconductor-aneufinderdata/meta.yaml b/recipes/bioconductor-aneufinderdata/meta.yaml index 6240769b088de..7fd7d4e6e1e29 100644 --- a/recipes/bioconductor-aneufinderdata/meta.yaml +++ b/recipes/bioconductor-aneufinderdata/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.10.0" %} +{% set version = "1.12.0" %} {% set name = "AneuFinderData" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: aeee3783942cb420cfb1a39dbbe1b9cc + md5: 1c7d8037814fe4ba56e13c74d85175c1 build: number: 0 rpaths: @@ -22,7 +22,7 @@ requirements: - r-base run: - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-aneufinderdata/post-link.sh b/recipes/bioconductor-aneufinderdata/post-link.sh index aaaaf625be0f2..7472b6753f6d4 100644 --- a/recipes/bioconductor-aneufinderdata/post-link.sh +++ b/recipes/bioconductor-aneufinderdata/post-link.sh @@ -1,11 +1,11 @@ #!/bin/bash -FN="AneuFinderData_1.10.0.tar.gz" +FN="AneuFinderData_1.12.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/experiment/src/contrib/AneuFinderData_1.10.0.tar.gz" - "https://bioarchive.galaxyproject.org/AneuFinderData_1.10.0.tar.gz" - "https://depot.galaxyproject.org/software/bioconductor-aneufinderdata/bioconductor-aneufinderdata_1.10.0_src_all.tar.gz" + "https://bioconductor.org/packages/3.9/data/experiment/src/contrib/AneuFinderData_1.12.0.tar.gz" + "https://bioarchive.galaxyproject.org/AneuFinderData_1.12.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-aneufinderdata/bioconductor-aneufinderdata_1.12.0_src_all.tar.gz" ) -MD5="aeee3783942cb420cfb1a39dbbe1b9cc" +MD5="1c7d8037814fe4ba56e13c74d85175c1" # Use a staging area in the conda dir rather than temp dirs, both to avoid # permission issues as well as to have things downloaded in a predictable @@ -16,7 +16,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-anf/meta.yaml b/recipes/bioconductor-anf/meta.yaml index 15c18397f9b07..377c0a2f206ae 100644 --- a/recipes/bioconductor-anf/meta.yaml +++ b/recipes/bioconductor-anf/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.4.0" %} +{% set version = "1.6.0" %} {% set name = "ANF" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 78709ee747b31ed759c515fd36ae9960 + md5: 8faf0a5e89310c253b504a30aa8e0287 build: number: 0 rpaths: @@ -20,14 +20,14 @@ build: # Suggests: ExperimentHub, SNFtool, knitr, rmarkdown, testthat requirements: host: - - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' - r-base - r-igraph - r-mass - r-rcolorbrewer - r-survival run: - - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' - r-base - r-igraph - r-mass diff --git a/recipes/bioconductor-animalcules/build.sh b/recipes/bioconductor-animalcules/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-animalcules/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-animalcules/meta.yaml b/recipes/bioconductor-animalcules/meta.yaml new file mode 100644 index 0000000000000..6e3f17846d54f --- /dev/null +++ b/recipes/bioconductor-animalcules/meta.yaml @@ -0,0 +1,91 @@ +{% set version = "1.0.0" %} +{% set name = "animalcules" %} +{% set bioc = "3.9" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + md5: f975ef9dbb18ecdfb265f0c6fc4c611d +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: BiocStyle, knitr, rmarkdown, testthat, usethis +requirements: + host: + - 'bioconductor-deseq2 >=1.24.0,<1.25.0' + - 'bioconductor-limma >=3.40.0,<3.41.0' + - 'bioconductor-multiassayexperiment >=1.10.0,<1.11.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' + - 'bioconductor-summarizedexperiment >=1.14.0,<1.15.0' + - r-ape + - r-assertthat + - r-base + - r-caret + - r-covr + - r-dmwr + - r-dplyr + - r-dt + - r-forcats + - r-ggplot2 + - r-glmnet + - r-httr + - r-lattice + - r-magrittr + - r-plotly + - r-plotroc + - r-rentrez + - r-reshape2 + - r-scales + - r-shiny + - r-shinyjs + - r-tibble + - r-tsne + - r-vegan + - r-xml + run: + - 'bioconductor-deseq2 >=1.24.0,<1.25.0' + - 'bioconductor-limma >=3.40.0,<3.41.0' + - 'bioconductor-multiassayexperiment >=1.10.0,<1.11.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' + - 'bioconductor-summarizedexperiment >=1.14.0,<1.15.0' + - r-ape + - r-assertthat + - r-base + - r-caret + - r-covr + - r-dmwr + - r-dplyr + - r-dt + - r-forcats + - r-ggplot2 + - r-glmnet + - r-httr + - r-lattice + - r-magrittr + - r-plotly + - r-plotroc + - r-rentrez + - r-reshape2 + - r-scales + - r-shiny + - r-shinyjs + - r-tibble + - r-tsne + - r-vegan + - r-xml +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'animalcules is an R package for utilizing up-to-date data analytics, visualization methods, and machine learning models to provide users an easy-to-use interactive microbiome analysis framework. It can be used as a standalone software package or users can explore their data with the accompanying interactive R Shiny application. Traditional microbiome analysis such as alpha/beta diversity and differential abundance analysis are enhanced, while new methods like biomarker identification are introduced by animalcules. Powerful interactive and dynamic figures generated by animalcules enable users to understand their data better and discover new insights.' + diff --git a/recipes/bioconductor-annaffy/meta.yaml b/recipes/bioconductor-annaffy/meta.yaml index ee605741c842a..266a9299d0d20 100644 --- a/recipes/bioconductor-annaffy/meta.yaml +++ b/recipes/bioconductor-annaffy/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.54.0" %} +{% set version = "1.56.0" %} {% set name = "annaffy" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 1417af7e94aa576c88bb823ac42e6f9e + md5: a8a02ef5f29978804a1d2c8e013829a5 build: number: 0 rpaths: @@ -20,16 +20,16 @@ build: # Suggests: hgu95av2.db, multtest, tcltk requirements: host: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' - - 'bioconductor-biobase >=2.42.0,<2.43.0' - - 'bioconductor-go.db >=3.7.0,<3.8.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' + - 'bioconductor-go.db >=3.8.0,<3.9.0' - 'bioconductor-kegg.db >=3.2.0,<3.3.0' - r-base - r-dbi run: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' - - 'bioconductor-biobase >=2.42.0,<2.43.0' - - 'bioconductor-go.db >=3.7.0,<3.8.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' + - 'bioconductor-go.db >=3.8.0,<3.9.0' - 'bioconductor-kegg.db >=3.2.0,<3.3.0' - r-base - r-dbi diff --git a/recipes/bioconductor-annmap/meta.yaml b/recipes/bioconductor-annmap/meta.yaml index bc8906fc165a3..0efaccf66ab99 100644 --- a/recipes/bioconductor-annmap/meta.yaml +++ b/recipes/bioconductor-annmap/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.24.0" %} +{% set version = "1.26.0" %} {% set name = "annmap" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 004c0c2fc7fe6be4898c97449f568b62 + md5: 721ffaaaab01aabd5bbbf20d7c25d1ce build: number: 0 rpaths: @@ -20,24 +20,24 @@ build: # Suggests: RUnit, rjson, Gviz requirements: host: - - 'bioconductor-biobase >=2.42.0,<2.43.0' - - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' - - 'bioconductor-genefilter >=1.64.0,<1.65.0' - - 'bioconductor-genomicranges >=1.34.0,<1.35.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-rsamtools >=1.34.0,<1.35.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' + - 'bioconductor-biocgenerics >=0.30.0,<0.31.0' + - 'bioconductor-genefilter >=1.66.0,<1.67.0' + - 'bioconductor-genomicranges >=1.36.0,<1.37.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-rsamtools >=2.0.0,<2.1.0' - r-base - r-dbi - r-digest - r-lattice - 'r-rmysql >=0.6-0' run: - - 'bioconductor-biobase >=2.42.0,<2.43.0' - - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' - - 'bioconductor-genefilter >=1.64.0,<1.65.0' - - 'bioconductor-genomicranges >=1.34.0,<1.35.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-rsamtools >=1.34.0,<1.35.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' + - 'bioconductor-biocgenerics >=0.30.0,<0.31.0' + - 'bioconductor-genefilter >=1.66.0,<1.67.0' + - 'bioconductor-genomicranges >=1.36.0,<1.37.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-rsamtools >=2.0.0,<2.1.0' - r-base - r-dbi - r-digest diff --git a/recipes/bioconductor-annotate/meta.yaml b/recipes/bioconductor-annotate/meta.yaml index 87efb600c2205..10de48c28239b 100644 --- a/recipes/bioconductor-annotate/meta.yaml +++ b/recipes/bioconductor-annotate/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.60.1" %} +{% set version = "1.62.0" %} {% set name = "annotate" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - sha256: 974bf61f765e989b31d8b42f86ddb3028d4868f46b4a0a0a9a1dfb3db257665e + md5: 8f03aad5fa522e027f0446f15eeaa1ea build: number: 0 rpaths: @@ -20,18 +20,18 @@ build: # Suggests: hgu95av2.db, genefilter, Biostrings (>= 2.25.10), IRanges, rae230a.db, rae230aprobe, tkWidgets, GO.db, org.Hs.eg.db, org.Mm.eg.db, hom.Hs.inp.db, humanCHRLOC, Rgraphviz, RUnit, requirements: host: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' - - 'bioconductor-biobase >=2.42.0,<2.43.0' - - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' + - 'bioconductor-biocgenerics >=0.30.0,<0.31.0' - r-base - r-dbi - r-rcurl - r-xml - r-xtable run: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' - - 'bioconductor-biobase >=2.42.0,<2.43.0' - - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' + - 'bioconductor-biocgenerics >=0.30.0,<0.31.0' - r-base - r-dbi - r-rcurl diff --git a/recipes/bioconductor-annotationdbi/meta.yaml b/recipes/bioconductor-annotationdbi/meta.yaml index f562b0826bd17..c65476d8af625 100644 --- a/recipes/bioconductor-annotationdbi/meta.yaml +++ b/recipes/bioconductor-annotationdbi/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.44.0" %} +{% set version = "1.46.0" %} {% set name = "AnnotationDbi" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 65b98cea76650046e4287a093092269a + md5: 1a415419b12be8f26f698d38a97d1cfe build: number: 0 rpaths: @@ -20,18 +20,18 @@ build: # Suggests: hgu95av2.db, GO.db, org.Sc.sgd.db, org.At.tair.db, KEGG.db, RUnit, TxDb.Hsapiens.UCSC.hg19.knownGene, hom.Hs.inp.db, org.Hs.eg.db, reactome.db, AnnotationForge, graph, EnsDb.Hsapiens.v75, BiocStyle, knitr requirements: host: - - 'bioconductor-biobase >=2.42.0,<2.43.0' - - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' + - 'bioconductor-biocgenerics >=0.30.0,<0.31.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' - r-base - r-dbi - r-rsqlite run: - - 'bioconductor-biobase >=2.42.0,<2.43.0' - - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' + - 'bioconductor-biocgenerics >=0.30.0,<0.31.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' - r-base - r-dbi - r-rsqlite @@ -41,7 +41,7 @@ test: about: home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: Artistic-2.0 - summary: 'Provides user interface and database connection code for annotation data packages using SQLite data storage.' + summary: 'Implements a user-friendly interface for querying SQLite-based annotation data packages.' extra: identifiers: - biotools:annotationdbi diff --git a/recipes/bioconductor-annotationfilter/meta.yaml b/recipes/bioconductor-annotationfilter/meta.yaml index bad6ae7e2302b..d18a431789ed1 100644 --- a/recipes/bioconductor-annotationfilter/meta.yaml +++ b/recipes/bioconductor-annotationfilter/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.6.0" %} +{% set version = "1.8.0" %} {% set name = "AnnotationFilter" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 607d1a6cc3e97499cb79ff01e24f03c6 + md5: 603cfc35bf42d7549f2643e31b79a7a3 build: number: 0 rpaths: @@ -20,11 +20,11 @@ build: # Suggests: BiocStyle, knitr, testthat, RSQLite, org.Hs.eg.db requirements: host: - - 'bioconductor-genomicranges >=1.34.0,<1.35.0' + - 'bioconductor-genomicranges >=1.36.0,<1.37.0' - r-base - r-lazyeval run: - - 'bioconductor-genomicranges >=1.34.0,<1.35.0' + - 'bioconductor-genomicranges >=1.36.0,<1.37.0' - r-base - r-lazyeval test: diff --git a/recipes/bioconductor-annotationforge/meta.yaml b/recipes/bioconductor-annotationforge/meta.yaml index f1130276e6f62..f67801a1a780c 100644 --- a/recipes/bioconductor-annotationforge/meta.yaml +++ b/recipes/bioconductor-annotationforge/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.24.0" %} +{% set version = "1.26.0" %} {% set name = "AnnotationForge" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 2f5509af2751bdbc94f0f08b2ec6950e + md5: f2394220b4915aa9338cf5173a83dcd5 build: number: 0 rpaths: @@ -20,20 +20,20 @@ build: # Suggests: biomaRt, httr, GenomeInfoDb (>= 1.17.1), Biostrings, affy, hgu95av2.db, human.db0, org.Hs.eg.db, Homo.sapiens, hom.Hs.inp.db, GO.db, BiocStyle, knitr, BiocManager requirements: host: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' - - 'bioconductor-biobase >=2.42.0,<2.43.0' - - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' + - 'bioconductor-biocgenerics >=0.30.0,<0.31.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' - r-base - r-dbi - r-rcurl - r-rsqlite - r-xml run: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' - - 'bioconductor-biobase >=2.42.0,<2.43.0' - - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' + - 'bioconductor-biocgenerics >=0.30.0,<0.31.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' - r-base - r-dbi - r-rcurl diff --git a/recipes/bioconductor-annotationfuncs/meta.yaml b/recipes/bioconductor-annotationfuncs/meta.yaml index e88a768e1eb90..1f3ef3c584942 100644 --- a/recipes/bioconductor-annotationfuncs/meta.yaml +++ b/recipes/bioconductor-annotationfuncs/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.32.0" %} +{% set version = "1.34.0" %} {% set name = "AnnotationFuncs" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 80fb2ac0e0b19ff0abdce58fc2c53933 + md5: be945cfe20ec22abb94c68865e053fac build: number: 0 rpaths: @@ -20,11 +20,11 @@ build: # Suggests: org.Bt.eg.db, GO.db, org.Hs.eg.db, hom.Hs.inp.db requirements: host: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' - r-base - r-dbi run: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' - r-base - r-dbi test: diff --git a/recipes/bioconductor-annotationhub/meta.yaml b/recipes/bioconductor-annotationhub/meta.yaml index 77f640fc1989f..8fcab1c20bb63 100644 --- a/recipes/bioconductor-annotationhub/meta.yaml +++ b/recipes/bioconductor-annotationhub/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "2.14.5" %} +{% set version = "2.16.0" %} {% set name = "AnnotationHub" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: 715a302680cb33fa3883a7af714d394ff87e84184506567e24c1102aa3ead947 + md5: a361fea7f2fbddb542ab9a50ef3ba27e build: number: 0 rpaths: @@ -20,25 +20,31 @@ build: # Suggests: IRanges, GenomicRanges, GenomeInfoDb, VariantAnnotation, Rsamtools, rtracklayer, BiocStyle, knitr, AnnotationForge, rBiopaxParser, RUnit, GenomicFeatures, MSnbase, mzR, Biostrings, SummarizedExperiment, ExperimentHub, gdsfmt requirements: host: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' - - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' - - 'bioconductor-interactivedisplaybase >=1.20.0,<1.21.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' + - 'bioconductor-biocfilecache >=1.8.0,<1.9.0' + - 'bioconductor-biocgenerics >=0.30.0,<0.31.0' + - 'bioconductor-interactivedisplaybase >=1.22.0,<1.23.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' - r-base - r-biocmanager - r-curl + - r-dplyr - r-httr + - r-rappdirs - r-rsqlite - r-yaml run: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' - - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' - - 'bioconductor-interactivedisplaybase >=1.20.0,<1.21.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' + - 'bioconductor-biocfilecache >=1.8.0,<1.9.0' + - 'bioconductor-biocgenerics >=0.30.0,<0.31.0' + - 'bioconductor-interactivedisplaybase >=1.22.0,<1.23.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' - r-base - r-biocmanager - r-curl + - r-dplyr - r-httr + - r-rappdirs - r-rsqlite - r-yaml test: diff --git a/recipes/bioconductor-annotationhubdata/meta.yaml b/recipes/bioconductor-annotationhubdata/meta.yaml index 16a36b2d552bd..aa3644973ec6e 100644 --- a/recipes/bioconductor-annotationhubdata/meta.yaml +++ b/recipes/bioconductor-annotationhubdata/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.12.0" %} +{% set version = "1.14.0" %} {% set name = "AnnotationHubData" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 523c97f501f82a3ea206a80e4d99c3e4 + md5: 8b2804206858012619e1ea021ac13d3f build: number: 0 rpaths: @@ -20,22 +20,22 @@ build: # Suggests: RUnit, knitr, BiocStyle, grasp2db, GenomeInfoDbData requirements: host: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' - - 'bioconductor-annotationforge >=1.24.0,<1.25.0' - - 'bioconductor-annotationhub >=2.14.0,<2.15.0' - - 'bioconductor-biobase >=2.42.0,<2.43.0' - - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' - - 'bioconductor-biocviews >=1.50.0,<1.51.0' - - 'bioconductor-biostrings >=2.50.0,<2.51.0' - - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' - - 'bioconductor-genomicfeatures >=1.34.0,<1.35.0' - - 'bioconductor-genomicranges >=1.34.0,<1.35.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-organismdbi >=1.24.0,<1.25.0' - - 'bioconductor-rbiopaxparser >=2.22.0,<2.23.0' - - 'bioconductor-rsamtools >=1.34.0,<1.35.0' - - 'bioconductor-rtracklayer >=1.42.0,<1.43.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' + - 'bioconductor-annotationforge >=1.26.0,<1.27.0' + - 'bioconductor-annotationhub >=2.16.0,<2.17.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' + - 'bioconductor-biocgenerics >=0.30.0,<0.31.0' + - 'bioconductor-biocviews >=1.52.0,<1.53.0' + - 'bioconductor-biostrings >=2.52.0,<2.53.0' + - 'bioconductor-genomeinfodb >=1.20.0,<1.21.0' + - 'bioconductor-genomicfeatures >=1.36.0,<1.37.0' + - 'bioconductor-genomicranges >=1.36.0,<1.37.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-organismdbi >=1.26.0,<1.27.0' + - 'bioconductor-rbiopaxparser >=2.24.0,<2.25.0' + - 'bioconductor-rsamtools >=2.0.0,<2.1.0' + - 'bioconductor-rtracklayer >=1.44.0,<1.45.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' - r-base - r-biocmanager - r-dbi @@ -45,22 +45,22 @@ requirements: - r-rsqlite - r-xml run: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' - - 'bioconductor-annotationforge >=1.24.0,<1.25.0' - - 'bioconductor-annotationhub >=2.14.0,<2.15.0' - - 'bioconductor-biobase >=2.42.0,<2.43.0' - - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' - - 'bioconductor-biocviews >=1.50.0,<1.51.0' - - 'bioconductor-biostrings >=2.50.0,<2.51.0' - - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' - - 'bioconductor-genomicfeatures >=1.34.0,<1.35.0' - - 'bioconductor-genomicranges >=1.34.0,<1.35.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-organismdbi >=1.24.0,<1.25.0' - - 'bioconductor-rbiopaxparser >=2.22.0,<2.23.0' - - 'bioconductor-rsamtools >=1.34.0,<1.35.0' - - 'bioconductor-rtracklayer >=1.42.0,<1.43.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' + - 'bioconductor-annotationforge >=1.26.0,<1.27.0' + - 'bioconductor-annotationhub >=2.16.0,<2.17.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' + - 'bioconductor-biocgenerics >=0.30.0,<0.31.0' + - 'bioconductor-biocviews >=1.52.0,<1.53.0' + - 'bioconductor-biostrings >=2.52.0,<2.53.0' + - 'bioconductor-genomeinfodb >=1.20.0,<1.21.0' + - 'bioconductor-genomicfeatures >=1.36.0,<1.37.0' + - 'bioconductor-genomicranges >=1.36.0,<1.37.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-organismdbi >=1.26.0,<1.27.0' + - 'bioconductor-rbiopaxparser >=2.24.0,<2.25.0' + - 'bioconductor-rsamtools >=2.0.0,<2.1.0' + - 'bioconductor-rtracklayer >=1.44.0,<1.45.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' - r-base - r-biocmanager - r-dbi diff --git a/recipes/bioconductor-annotationtools/meta.yaml b/recipes/bioconductor-annotationtools/meta.yaml index fe0cc657d1862..c7e5f31547f75 100644 --- a/recipes/bioconductor-annotationtools/meta.yaml +++ b/recipes/bioconductor-annotationtools/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.56.0" %} +{% set version = "1.58.0" %} {% set name = "annotationTools" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 9371efaf0751aa8d26710245cba18825 + md5: a3d93246437cc2a1e60e4c83e1dc14c2 build: number: 0 rpaths: @@ -19,10 +19,10 @@ build: noarch: generic requirements: host: - - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' - r-base run: - - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' - r-base test: commands: diff --git a/recipes/bioconductor-annotatr/meta.yaml b/recipes/bioconductor-annotatr/meta.yaml index 3c10b576a5f7a..63101863f6220 100644 --- a/recipes/bioconductor-annotatr/meta.yaml +++ b/recipes/bioconductor-annotatr/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.8.0" %} +{% set version = "1.10.0" %} {% set name = "annotatr" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: e91b2cc81be539c201d2c518d37b764f + md5: bebb93f6f3a99c3cdb56158c49e26029 build: number: 0 rpaths: @@ -20,30 +20,30 @@ build: # Suggests: BiocStyle, devtools, knitr, org.Dm.eg.db, org.Gg.eg.db, org.Hs.eg.db, org.Mm.eg.db, org.Rn.eg.db, rmarkdown, roxygen2, testthat, TxDb.Dmelanogaster.UCSC.dm3.ensGene, TxDb.Dmelanogaster.UCSC.dm6.ensGene, TxDb.Ggallus.UCSC.galGal5.refGene, TxDb.Hsapiens.UCSC.hg19.knownGene, TxDb.Hsapiens.UCSC.hg38.knownGene, TxDb.Mmusculus.UCSC.mm9.knownGene, TxDb.Mmusculus.UCSC.mm10.knownGene, TxDb.Rnorvegicus.UCSC.rn4.ensGene, TxDb.Rnorvegicus.UCSC.rn5.refGene, TxDb.Rnorvegicus.UCSC.rn6.refGene requirements: host: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' - - 'bioconductor-annotationhub >=2.14.0,<2.15.0' - - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' - - 'bioconductor-genomicfeatures >=1.34.0,<1.35.0' - - 'bioconductor-genomicranges >=1.34.0,<1.35.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-regioner >=1.14.0,<1.15.0' - - 'bioconductor-rtracklayer >=1.42.0,<1.43.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' + - 'bioconductor-annotationhub >=2.16.0,<2.17.0' + - 'bioconductor-genomeinfodb >=1.20.0,<1.21.0' + - 'bioconductor-genomicfeatures >=1.36.0,<1.37.0' + - 'bioconductor-genomicranges >=1.36.0,<1.37.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-regioner >=1.16.0,<1.17.0' + - 'bioconductor-rtracklayer >=1.44.0,<1.45.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' - r-base - r-dplyr - r-ggplot2 - r-readr - r-reshape2 run: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' - - 'bioconductor-annotationhub >=2.14.0,<2.15.0' - - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' - - 'bioconductor-genomicfeatures >=1.34.0,<1.35.0' - - 'bioconductor-genomicranges >=1.34.0,<1.35.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-regioner >=1.14.0,<1.15.0' - - 'bioconductor-rtracklayer >=1.42.0,<1.43.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' + - 'bioconductor-annotationhub >=2.16.0,<2.17.0' + - 'bioconductor-genomeinfodb >=1.20.0,<1.21.0' + - 'bioconductor-genomicfeatures >=1.36.0,<1.37.0' + - 'bioconductor-genomicranges >=1.36.0,<1.37.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-regioner >=1.16.0,<1.17.0' + - 'bioconductor-rtracklayer >=1.44.0,<1.45.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' - r-base - r-dplyr - r-ggplot2 diff --git a/recipes/bioconductor-anopheles.db0/meta.yaml b/recipes/bioconductor-anopheles.db0/meta.yaml index 1388bda1a7789..7e0344b864e57 100644 --- a/recipes/bioconductor-anopheles.db0/meta.yaml +++ b/recipes/bioconductor-anopheles.db0/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "3.7.1" %} +{% set version = "3.8.2" %} {% set name = "anopheles.db0" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,21 +10,21 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: c19b72aa3fa5aaefa84b3abf3cd5c303 + md5: 8ee605dc6b30694688ffe67e71259ca8 build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' - r-base run: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-anopheles.db0/post-link.sh b/recipes/bioconductor-anopheles.db0/post-link.sh index efe7988fa0ff1..92fc74403942e 100644 --- a/recipes/bioconductor-anopheles.db0/post-link.sh +++ b/recipes/bioconductor-anopheles.db0/post-link.sh @@ -1,11 +1,11 @@ #!/bin/bash -FN="anopheles.db0_3.7.1.tar.gz" +FN="anopheles.db0_3.8.2.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/anopheles.db0_3.7.1.tar.gz" - "https://bioarchive.galaxyproject.org/anopheles.db0_3.7.1.tar.gz" - "https://depot.galaxyproject.org/software/bioconductor-anopheles.db0/bioconductor-anopheles.db0_3.7.1_src_all.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/anopheles.db0_3.8.2.tar.gz" + "https://bioarchive.galaxyproject.org/anopheles.db0_3.8.2.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-anopheles.db0/bioconductor-anopheles.db0_3.8.2_src_all.tar.gz" ) -MD5="c19b72aa3fa5aaefa84b3abf3cd5c303" +MD5="8ee605dc6b30694688ffe67e71259ca8" # Use a staging area in the conda dir rather than temp dirs, both to avoid # permission issues as well as to have things downloaded in a predictable @@ -16,7 +16,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-anota/meta.yaml b/recipes/bioconductor-anota/meta.yaml index 0c3f57ac7a038..7da21688617aa 100644 --- a/recipes/bioconductor-anota/meta.yaml +++ b/recipes/bioconductor-anota/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.30.0" %} +{% set version = "1.32.0" %} {% set name = "anota" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: c3cc7015b78f0b9283107019ce4fd4ad + md5: 6b3a90ec4a197d10eb21ba9197e542c2 build: number: 0 rpaths: @@ -19,12 +19,12 @@ build: noarch: generic requirements: host: - - 'bioconductor-multtest >=2.38.0,<2.39.0' - - 'bioconductor-qvalue >=2.14.0,<2.15.0' + - 'bioconductor-multtest >=2.40.0,<2.41.0' + - 'bioconductor-qvalue >=2.16.0,<2.17.0' - r-base run: - - 'bioconductor-multtest >=2.38.0,<2.39.0' - - 'bioconductor-qvalue >=2.14.0,<2.15.0' + - 'bioconductor-multtest >=2.40.0,<2.41.0' + - 'bioconductor-qvalue >=2.16.0,<2.17.0' - r-base test: commands: diff --git a/recipes/bioconductor-anota2seq/meta.yaml b/recipes/bioconductor-anota2seq/meta.yaml index f0171ad91ed6e..9f6374f717ef4 100644 --- a/recipes/bioconductor-anota2seq/meta.yaml +++ b/recipes/bioconductor-anota2seq/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.4.0" %} +{% set version = "1.6.0" %} {% set name = "anota2seq" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 5841a54f1413e576c45b5aec77d03c98 + md5: 10fc0941a5f771a929f463e9a386b763 build: number: 0 rpaths: @@ -20,21 +20,21 @@ build: # Suggests: BiocStyle,knitr requirements: host: - - 'bioconductor-deseq2 >=1.22.0,<1.23.0' - - 'bioconductor-edger >=3.24.0,<3.25.0' - - 'bioconductor-limma >=3.38.0,<3.39.0' - - 'bioconductor-multtest >=2.38.0,<2.39.0' - - 'bioconductor-qvalue >=2.14.0,<2.15.0' - - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' + - 'bioconductor-deseq2 >=1.24.0,<1.25.0' + - 'bioconductor-edger >=3.26.0,<3.27.0' + - 'bioconductor-limma >=3.40.0,<3.41.0' + - 'bioconductor-multtest >=2.40.0,<2.41.0' + - 'bioconductor-qvalue >=2.16.0,<2.17.0' + - 'bioconductor-summarizedexperiment >=1.14.0,<1.15.0' - r-base - r-rcolorbrewer run: - - 'bioconductor-deseq2 >=1.22.0,<1.23.0' - - 'bioconductor-edger >=3.24.0,<3.25.0' - - 'bioconductor-limma >=3.38.0,<3.39.0' - - 'bioconductor-multtest >=2.38.0,<2.39.0' - - 'bioconductor-qvalue >=2.14.0,<2.15.0' - - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' + - 'bioconductor-deseq2 >=1.24.0,<1.25.0' + - 'bioconductor-edger >=3.26.0,<3.27.0' + - 'bioconductor-limma >=3.40.0,<3.41.0' + - 'bioconductor-multtest >=2.40.0,<2.41.0' + - 'bioconductor-qvalue >=2.16.0,<2.17.0' + - 'bioconductor-summarizedexperiment >=1.14.0,<1.15.0' - r-base - r-rcolorbrewer test: diff --git a/recipes/bioconductor-antiprofiles/meta.yaml b/recipes/bioconductor-antiprofiles/meta.yaml index cf16d177f6200..8d2a05b131e80 100644 --- a/recipes/bioconductor-antiprofiles/meta.yaml +++ b/recipes/bioconductor-antiprofiles/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.22.0" %} +{% set version = "1.24.0" %} {% set name = "antiProfiles" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 5f45e664940f6ea8925cb91e62f3e6e7 + md5: bdd8104b20e733ee81f7ebfd42810921 build: number: 0 rpaths: diff --git a/recipes/bioconductor-antiprofilesdata/meta.yaml b/recipes/bioconductor-antiprofilesdata/meta.yaml index 8a06586e49aff..2788f7a5c6a5b 100644 --- a/recipes/bioconductor-antiprofilesdata/meta.yaml +++ b/recipes/bioconductor-antiprofilesdata/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.18.0" %} +{% set version = "1.20.0" %} {% set name = "antiProfilesData" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 6db261abb425b57ede7976f9b0a0ca90 + md5: 939e6ebc361769f5198676a9502baba7 build: number: 0 rpaths: @@ -20,12 +20,12 @@ build: # Suggests: frma, GEOquery, GEOmetadb requirements: host: - - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' - r-base run: - - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-antiprofilesdata/post-link.sh b/recipes/bioconductor-antiprofilesdata/post-link.sh index 93eda78912940..2a8cd31eefa5f 100644 --- a/recipes/bioconductor-antiprofilesdata/post-link.sh +++ b/recipes/bioconductor-antiprofilesdata/post-link.sh @@ -1,11 +1,11 @@ #!/bin/bash -FN="antiProfilesData_1.18.0.tar.gz" +FN="antiProfilesData_1.20.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/experiment/src/contrib/antiProfilesData_1.18.0.tar.gz" - "https://bioarchive.galaxyproject.org/antiProfilesData_1.18.0.tar.gz" - "https://depot.galaxyproject.org/software/bioconductor-antiprofilesdata/bioconductor-antiprofilesdata_1.18.0_src_all.tar.gz" + "https://bioconductor.org/packages/3.9/data/experiment/src/contrib/antiProfilesData_1.20.0.tar.gz" + "https://bioarchive.galaxyproject.org/antiProfilesData_1.20.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-antiprofilesdata/bioconductor-antiprofilesdata_1.20.0_src_all.tar.gz" ) -MD5="6db261abb425b57ede7976f9b0a0ca90" +MD5="939e6ebc361769f5198676a9502baba7" # Use a staging area in the conda dir rather than temp dirs, both to avoid # permission issues as well as to have things downloaded in a predictable @@ -16,7 +16,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-apcomplex/meta.yaml b/recipes/bioconductor-apcomplex/meta.yaml index 7ea71bf3ed35b..253c5a6a01b71 100644 --- a/recipes/bioconductor-apcomplex/meta.yaml +++ b/recipes/bioconductor-apcomplex/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "2.48.0" %} +{% set version = "2.50.0" %} {% set name = "apComplex" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 82bb7fd1f58e41e1479feac11932084b + md5: 97c9a7b9d83a2e280c6731ba19fd40a6 build: number: 0 rpaths: @@ -19,16 +19,16 @@ build: noarch: generic requirements: host: - - 'bioconductor-graph >=1.60.0,<1.61.0' - - 'bioconductor-org.sc.sgd.db >=3.7.0,<3.8.0' - - 'bioconductor-rbgl >=1.58.0,<1.59.0' - - 'bioconductor-rgraphviz >=2.26.0,<2.27.0' + - 'bioconductor-graph >=1.62.0,<1.63.0' + - 'bioconductor-org.sc.sgd.db >=3.8.0,<3.9.0' + - 'bioconductor-rbgl >=1.60.0,<1.61.0' + - 'bioconductor-rgraphviz >=2.28.0,<2.29.0' - r-base run: - - 'bioconductor-graph >=1.60.0,<1.61.0' - - 'bioconductor-org.sc.sgd.db >=3.7.0,<3.8.0' - - 'bioconductor-rbgl >=1.58.0,<1.59.0' - - 'bioconductor-rgraphviz >=2.26.0,<2.27.0' + - 'bioconductor-graph >=1.62.0,<1.63.0' + - 'bioconductor-org.sc.sgd.db >=3.8.0,<3.9.0' + - 'bioconductor-rbgl >=1.60.0,<1.61.0' + - 'bioconductor-rgraphviz >=2.28.0,<2.29.0' - r-base test: commands: diff --git a/recipes/bioconductor-apeglm/meta.yaml b/recipes/bioconductor-apeglm/meta.yaml index af0e48b9f6e7e..a3c1b706196c3 100644 --- a/recipes/bioconductor-apeglm/meta.yaml +++ b/recipes/bioconductor-apeglm/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.4.1" %} +{% set version = "1.6.0" %} {% set name = "apeglm" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 9ea5ccdba700813f59686a9fef116c26 + md5: be62827e5f20cdd38a44f3c163417486 build: number: 0 rpaths: @@ -19,16 +19,16 @@ build: # Suggests: DESeq2, airway, knitr, rmarkdown, testthat requirements: host: - - 'bioconductor-genomicranges >=1.34.0,<1.35.0' - - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' + - 'bioconductor-genomicranges >=1.36.0,<1.37.0' + - 'bioconductor-summarizedexperiment >=1.14.0,<1.15.0' - r-base - r-emdbook - r-rcpp - r-rcppeigen - r-rcppnumerical run: - - 'bioconductor-genomicranges >=1.34.0,<1.35.0' - - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' + - 'bioconductor-genomicranges >=1.36.0,<1.37.0' + - 'bioconductor-summarizedexperiment >=1.14.0,<1.15.0' - r-base - r-emdbook - r-rcpp diff --git a/recipes/bioconductor-appreci8r/meta.yaml b/recipes/bioconductor-appreci8r/meta.yaml index 55c526695043c..15bbe7d8d2585 100644 --- a/recipes/bioconductor-appreci8r/meta.yaml +++ b/recipes/bioconductor-appreci8r/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.0.0" %} +{% set version = "1.2.0" %} {% set name = "appreci8R" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 425813a17e39960bc786393fbf3ac7ee + md5: d0ae21a6be2fd7919476f6bb03172e48 build: number: 0 rpaths: @@ -20,30 +20,30 @@ build: # Suggests: GO.db, org.Hs.eg.db requirements: host: - - 'bioconductor-biostrings >=2.50.0,<2.51.0' - - 'bioconductor-bsgenome >=1.50.0,<1.51.0' + - 'bioconductor-biostrings >=2.52.0,<2.53.0' + - 'bioconductor-bsgenome >=1.52.0,<1.53.0' - 'bioconductor-bsgenome.hsapiens.ucsc.hg19 >=1.4.0,<1.5.0' - - 'bioconductor-cosmic.67 >=1.18.0,<1.19.0' - - 'bioconductor-genomicfeatures >=1.34.0,<1.35.0' - - 'bioconductor-genomicranges >=1.34.0,<1.35.0' - - 'bioconductor-genomicscores >=1.6.0,<1.7.0' - - 'bioconductor-homo.sapiens >=1.3.0,<1.4.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-mafdb.1kgenomes.phase3.hs37d5 >=3.7.0,<3.8.0' - - 'bioconductor-mafdb.esp6500si.v2.ssa137.hs37d5 >=3.7.0,<3.8.0' - - 'bioconductor-mafdb.exac.r1.0.hs37d5 >=3.7.0,<3.8.0' - - 'bioconductor-mafdb.gnomadex.r2.0.1.hs37d5 >=3.8.0,<3.9.0' + - 'bioconductor-cosmic.67 >=1.20.0,<1.21.0' + - 'bioconductor-genomicfeatures >=1.36.0,<1.37.0' + - 'bioconductor-genomicranges >=1.36.0,<1.37.0' + - 'bioconductor-genomicscores >=1.8.0,<1.9.0' + - 'bioconductor-homo.sapiens >=1.4.0,<1.5.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-mafdb.1kgenomes.phase3.hs37d5 >=3.8.0,<3.9.0' + - 'bioconductor-mafdb.esp6500si.v2.ssa137.hs37d5 >=3.8.0,<3.9.0' + - 'bioconductor-mafdb.exac.r1.0.hs37d5 >=3.8.0,<3.9.0' - 'bioconductor-polyphen.hsapiens.dbsnp131 >=1.0.0,<1.1.0' - - 'bioconductor-rsamtools >=1.34.0,<1.35.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-rsamtools >=2.0.0,<2.1.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' - 'bioconductor-sift.hsapiens.dbsnp137 >=1.0.0,<1.1.0' - - 'bioconductor-snplocs.hsapiens.dbsnp144.grch37 >=0.99.0,<0.100.0' - - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' + - 'bioconductor-snplocs.hsapiens.dbsnp144.grch37 >=1.0.0,<1.1.0' + - 'bioconductor-summarizedexperiment >=1.14.0,<1.15.0' - 'bioconductor-txdb.hsapiens.ucsc.hg19.knowngene >=3.2.0,<3.3.0' - - 'bioconductor-variantannotation >=1.28.0,<1.29.0' - - 'bioconductor-xtrasnplocs.hsapiens.dbsnp144.grch37 >=0.99.0,<0.100.0' + - 'bioconductor-variantannotation >=1.30.0,<1.31.0' + - 'bioconductor-xtrasnplocs.hsapiens.dbsnp144.grch37 >=1.0.0,<1.1.0' - r-base - r-dt + - r-mafdb.gnomadex.r2.0.1.hs37d5 - r-openxlsx - r-rentrez - r-rsnps @@ -52,30 +52,30 @@ requirements: - r-shinyjs - r-stringr run: - - 'bioconductor-biostrings >=2.50.0,<2.51.0' - - 'bioconductor-bsgenome >=1.50.0,<1.51.0' + - 'bioconductor-biostrings >=2.52.0,<2.53.0' + - 'bioconductor-bsgenome >=1.52.0,<1.53.0' - 'bioconductor-bsgenome.hsapiens.ucsc.hg19 >=1.4.0,<1.5.0' - - 'bioconductor-cosmic.67 >=1.18.0,<1.19.0' - - 'bioconductor-genomicfeatures >=1.34.0,<1.35.0' - - 'bioconductor-genomicranges >=1.34.0,<1.35.0' - - 'bioconductor-genomicscores >=1.6.0,<1.7.0' - - 'bioconductor-homo.sapiens >=1.3.0,<1.4.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-mafdb.1kgenomes.phase3.hs37d5 >=3.7.0,<3.8.0' - - 'bioconductor-mafdb.esp6500si.v2.ssa137.hs37d5 >=3.7.0,<3.8.0' - - 'bioconductor-mafdb.exac.r1.0.hs37d5 >=3.7.0,<3.8.0' - - 'bioconductor-mafdb.gnomadex.r2.0.1.hs37d5 >=3.8.0,<3.9.0' + - 'bioconductor-cosmic.67 >=1.20.0,<1.21.0' + - 'bioconductor-genomicfeatures >=1.36.0,<1.37.0' + - 'bioconductor-genomicranges >=1.36.0,<1.37.0' + - 'bioconductor-genomicscores >=1.8.0,<1.9.0' + - 'bioconductor-homo.sapiens >=1.4.0,<1.5.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-mafdb.1kgenomes.phase3.hs37d5 >=3.8.0,<3.9.0' + - 'bioconductor-mafdb.esp6500si.v2.ssa137.hs37d5 >=3.8.0,<3.9.0' + - 'bioconductor-mafdb.exac.r1.0.hs37d5 >=3.8.0,<3.9.0' - 'bioconductor-polyphen.hsapiens.dbsnp131 >=1.0.0,<1.1.0' - - 'bioconductor-rsamtools >=1.34.0,<1.35.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-rsamtools >=2.0.0,<2.1.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' - 'bioconductor-sift.hsapiens.dbsnp137 >=1.0.0,<1.1.0' - - 'bioconductor-snplocs.hsapiens.dbsnp144.grch37 >=0.99.0,<0.100.0' - - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' + - 'bioconductor-snplocs.hsapiens.dbsnp144.grch37 >=1.0.0,<1.1.0' + - 'bioconductor-summarizedexperiment >=1.14.0,<1.15.0' - 'bioconductor-txdb.hsapiens.ucsc.hg19.knowngene >=3.2.0,<3.3.0' - - 'bioconductor-variantannotation >=1.28.0,<1.29.0' - - 'bioconductor-xtrasnplocs.hsapiens.dbsnp144.grch37 >=0.99.0,<0.100.0' + - 'bioconductor-variantannotation >=1.30.0,<1.31.0' + - 'bioconductor-xtrasnplocs.hsapiens.dbsnp144.grch37 >=1.0.0,<1.1.0' - r-base - r-dt + - r-mafdb.gnomadex.r2.0.1.hs37d5 - r-openxlsx - r-rentrez - r-rsnps diff --git a/recipes/bioconductor-arabidopsis.db0/meta.yaml b/recipes/bioconductor-arabidopsis.db0/meta.yaml index 25ddf02d67245..71beb5550455f 100644 --- a/recipes/bioconductor-arabidopsis.db0/meta.yaml +++ b/recipes/bioconductor-arabidopsis.db0/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "3.7.1" %} +{% set version = "3.8.2" %} {% set name = "arabidopsis.db0" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,21 +10,21 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 1366b9a8107e13d674be15d742537f2a + md5: 8a9e7a715dee82af3056db3a41416049 build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' - r-base run: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-arabidopsis.db0/post-link.sh b/recipes/bioconductor-arabidopsis.db0/post-link.sh index ac39216e6583f..b540c2af6699b 100644 --- a/recipes/bioconductor-arabidopsis.db0/post-link.sh +++ b/recipes/bioconductor-arabidopsis.db0/post-link.sh @@ -1,11 +1,11 @@ #!/bin/bash -FN="arabidopsis.db0_3.7.1.tar.gz" +FN="arabidopsis.db0_3.8.2.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/arabidopsis.db0_3.7.1.tar.gz" - "https://bioarchive.galaxyproject.org/arabidopsis.db0_3.7.1.tar.gz" - "https://depot.galaxyproject.org/software/bioconductor-arabidopsis.db0/bioconductor-arabidopsis.db0_3.7.1_src_all.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/arabidopsis.db0_3.8.2.tar.gz" + "https://bioarchive.galaxyproject.org/arabidopsis.db0_3.8.2.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-arabidopsis.db0/bioconductor-arabidopsis.db0_3.8.2_src_all.tar.gz" ) -MD5="1366b9a8107e13d674be15d742537f2a" +MD5="8a9e7a715dee82af3056db3a41416049" # Use a staging area in the conda dir rather than temp dirs, both to avoid # permission issues as well as to have things downloaded in a predictable @@ -16,7 +16,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-aracne.networks/meta.yaml b/recipes/bioconductor-aracne.networks/meta.yaml index 11203b2eba781..3125efd8a430e 100644 --- a/recipes/bioconductor-aracne.networks/meta.yaml +++ b/recipes/bioconductor-aracne.networks/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.8.0" %} +{% set version = "1.10.0" %} {% set name = "aracne.networks" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 1dd61303e99861938db45495480b8dea + md5: 3dafc172cee133222db156054e3bf6f9 build: number: 0 rpaths: @@ -19,12 +19,12 @@ build: noarch: generic requirements: host: - - 'bioconductor-viper >=1.16.0,<1.17.0' + - 'bioconductor-viper >=1.18.0,<1.19.0' - r-base run: - - 'bioconductor-viper >=1.16.0,<1.17.0' + - 'bioconductor-viper >=1.18.0,<1.19.0' - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-aracne.networks/post-link.sh b/recipes/bioconductor-aracne.networks/post-link.sh index 87e22c1ba0a6d..85a289aacaef4 100644 --- a/recipes/bioconductor-aracne.networks/post-link.sh +++ b/recipes/bioconductor-aracne.networks/post-link.sh @@ -1,11 +1,11 @@ #!/bin/bash -FN="aracne.networks_1.8.0.tar.gz" +FN="aracne.networks_1.10.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/experiment/src/contrib/aracne.networks_1.8.0.tar.gz" - "https://bioarchive.galaxyproject.org/aracne.networks_1.8.0.tar.gz" - "https://depot.galaxyproject.org/software/bioconductor-aracne.networks/bioconductor-aracne.networks_1.8.0_src_all.tar.gz" + "https://bioconductor.org/packages/3.9/data/experiment/src/contrib/aracne.networks_1.10.0.tar.gz" + "https://bioarchive.galaxyproject.org/aracne.networks_1.10.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-aracne.networks/bioconductor-aracne.networks_1.10.0_src_all.tar.gz" ) -MD5="1dd61303e99861938db45495480b8dea" +MD5="3dafc172cee133222db156054e3bf6f9" # Use a staging area in the conda dir rather than temp dirs, both to avoid # permission issues as well as to have things downloaded in a predictable @@ -16,7 +16,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-aroma.light/meta.yaml b/recipes/bioconductor-aroma.light/meta.yaml index 0b6ae4b61fe3d..d5da50ae71b47 100644 --- a/recipes/bioconductor-aroma.light/meta.yaml +++ b/recipes/bioconductor-aroma.light/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "3.12.0" %} +{% set version = "3.14.0" %} {% set name = "aroma.light" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,9 +10,9 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: f98a7b55b903ecd0334b7d3afed5ce95 + md5: b088ab52f1b5adc3ec73956627927728 build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ diff --git a/recipes/bioconductor-arrayexpress/meta.yaml b/recipes/bioconductor-arrayexpress/meta.yaml index fb77dbc20ed6e..f9f0885dff32e 100644 --- a/recipes/bioconductor-arrayexpress/meta.yaml +++ b/recipes/bioconductor-arrayexpress/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.42.0" %} +{% set version = "1.44.0" %} {% set name = "ArrayExpress" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 718b770b408424f6141d1ce8c818b00a + md5: 76ff83867cd18b53bffdab25bd564245 build: number: 0 rpaths: @@ -20,15 +20,15 @@ build: # Suggests: affy requirements: host: - - 'bioconductor-biobase >=2.42.0,<2.43.0' - - 'bioconductor-limma >=3.38.0,<3.39.0' - - 'bioconductor-oligo >=1.46.0,<1.47.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' + - 'bioconductor-limma >=3.40.0,<3.41.0' + - 'bioconductor-oligo >=1.48.0,<1.49.0' - r-base - r-xml run: - - 'bioconductor-biobase >=2.42.0,<2.43.0' - - 'bioconductor-limma >=3.38.0,<3.39.0' - - 'bioconductor-oligo >=1.46.0,<1.47.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' + - 'bioconductor-limma >=3.40.0,<3.41.0' + - 'bioconductor-oligo >=1.48.0,<1.49.0' - r-base - r-xml test: diff --git a/recipes/bioconductor-arrayexpresshts/meta.yaml b/recipes/bioconductor-arrayexpresshts/meta.yaml index 186f870dcf3c2..57db506929d40 100644 --- a/recipes/bioconductor-arrayexpresshts/meta.yaml +++ b/recipes/bioconductor-arrayexpresshts/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.32.1" %} +{% set version = "1.33.1" %} {% set name = "ArrayExpressHTS" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 999bbee605ec5abb2c4328916301e33a + md5: 0fd123cf9a46084572632cd06b919a7d build: number: 0 rpaths: @@ -18,16 +18,16 @@ build: - lib/ requirements: host: - - 'bioconductor-biobase >=2.42.0,<2.43.0' - - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' - - 'bioconductor-biomart >=2.38.0,<2.39.0' - - 'bioconductor-biostrings >=2.50.0,<2.51.0' - - 'bioconductor-deseq >=1.34.0,<1.35.0' - - 'bioconductor-edger >=3.24.0,<3.25.0' - - 'bioconductor-genomicranges >=1.34.0,<1.35.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-rsamtools >=1.34.0,<1.35.0' - - 'bioconductor-shortread >=1.40.0,<1.41.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' + - 'bioconductor-biocgenerics >=0.30.0,<0.31.0' + - 'bioconductor-biomart >=2.40.0,<2.41.0' + - 'bioconductor-biostrings >=2.52.0,<2.53.0' + - 'bioconductor-deseq >=1.36.0,<1.37.0' + - 'bioconductor-edger >=3.26.0,<3.27.0' + - 'bioconductor-genomicranges >=1.36.0,<1.37.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-rsamtools >=2.0.0,<2.1.0' + - 'bioconductor-shortread >=1.42.0,<1.43.0' - r-base - r-bitops - r-hmisc @@ -40,16 +40,16 @@ requirements: - r-svmisc - r-xml run: - - 'bioconductor-biobase >=2.42.0,<2.43.0' - - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' - - 'bioconductor-biomart >=2.38.0,<2.39.0' - - 'bioconductor-biostrings >=2.50.0,<2.51.0' - - 'bioconductor-deseq >=1.34.0,<1.35.0' - - 'bioconductor-edger >=3.24.0,<3.25.0' - - 'bioconductor-genomicranges >=1.34.0,<1.35.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-rsamtools >=1.34.0,<1.35.0' - - 'bioconductor-shortread >=1.40.0,<1.41.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' + - 'bioconductor-biocgenerics >=0.30.0,<0.31.0' + - 'bioconductor-biomart >=2.40.0,<2.41.0' + - 'bioconductor-biostrings >=2.52.0,<2.53.0' + - 'bioconductor-deseq >=1.36.0,<1.37.0' + - 'bioconductor-edger >=3.26.0,<3.27.0' + - 'bioconductor-genomicranges >=1.36.0,<1.37.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-rsamtools >=2.0.0,<2.1.0' + - 'bioconductor-shortread >=1.42.0,<1.43.0' - r-base - r-bitops - r-hmisc diff --git a/recipes/bioconductor-arraymvout/meta.yaml b/recipes/bioconductor-arraymvout/meta.yaml index c4351cae7e2b7..d8a72e29713cc 100644 --- a/recipes/bioconductor-arraymvout/meta.yaml +++ b/recipes/bioconductor-arraymvout/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.40.0" %} +{% set version = "1.42.0" %} {% set name = "arrayMvout" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: c9c9ec7b5f1774bab6514b85fb9db8a8 + md5: 27e2ed35f77af3c61d937e7694dfd814 build: number: 0 rpaths: @@ -20,22 +20,22 @@ build: # Suggests: MAQCsubset, mvoutData, lumiBarnes, affyPLM, affydata, hgu133atagcdf requirements: host: - - 'bioconductor-affy >=1.60.0,<1.61.0' - - 'bioconductor-affycontam >=1.40.0,<1.41.0' - - 'bioconductor-biobase >=2.42.0,<2.43.0' - - 'bioconductor-lumi >=2.34.0,<2.35.0' - - 'bioconductor-mdqc >=1.44.0,<1.45.0' - - 'bioconductor-parody >=1.40.0,<1.41.0' - - 'bioconductor-simpleaffy >=2.58.0,<2.59.0' + - 'bioconductor-affy >=1.62.0,<1.63.0' + - 'bioconductor-affycontam >=1.42.0,<1.43.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' + - 'bioconductor-lumi >=2.36.0,<2.37.0' + - 'bioconductor-mdqc >=1.46.0,<1.47.0' + - 'bioconductor-parody >=1.42.0,<1.43.0' + - 'bioconductor-simpleaffy >=2.60.0,<2.61.0' - r-base run: - - 'bioconductor-affy >=1.60.0,<1.61.0' - - 'bioconductor-affycontam >=1.40.0,<1.41.0' - - 'bioconductor-biobase >=2.42.0,<2.43.0' - - 'bioconductor-lumi >=2.34.0,<2.35.0' - - 'bioconductor-mdqc >=1.44.0,<1.45.0' - - 'bioconductor-parody >=1.40.0,<1.41.0' - - 'bioconductor-simpleaffy >=2.58.0,<2.59.0' + - 'bioconductor-affy >=1.62.0,<1.63.0' + - 'bioconductor-affycontam >=1.42.0,<1.43.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' + - 'bioconductor-lumi >=2.36.0,<2.37.0' + - 'bioconductor-mdqc >=1.46.0,<1.47.0' + - 'bioconductor-parody >=1.42.0,<1.43.0' + - 'bioconductor-simpleaffy >=2.60.0,<2.61.0' - r-base test: commands: diff --git a/recipes/bioconductor-arrayquality/meta.yaml b/recipes/bioconductor-arrayquality/meta.yaml index 1bfe93385a325..9fb985d4a4437 100644 --- a/recipes/bioconductor-arrayquality/meta.yaml +++ b/recipes/bioconductor-arrayquality/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.60.0" %} +{% set version = "1.62.0" %} {% set name = "arrayQuality" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: e217db056836d45c77da1fa228ea7d87 + md5: 23f5d66736b23ca32f6db3b55b2f0b59 build: number: 0 rpaths: @@ -20,15 +20,15 @@ build: # Suggests: mclust, MEEBOdata, HEEBOdata requirements: host: - - 'bioconductor-limma >=3.38.0,<3.39.0' - - 'bioconductor-marray >=1.60.0,<1.61.0' + - 'bioconductor-limma >=3.40.0,<3.41.0' + - 'bioconductor-marray >=1.62.0,<1.63.0' - r-base - r-gridbase - r-hexbin - r-rcolorbrewer run: - - 'bioconductor-limma >=3.38.0,<3.39.0' - - 'bioconductor-marray >=1.60.0,<1.61.0' + - 'bioconductor-limma >=3.40.0,<3.41.0' + - 'bioconductor-marray >=1.62.0,<1.63.0' - r-base - r-gridbase - r-hexbin diff --git a/recipes/bioconductor-arrayqualitymetrics/meta.yaml b/recipes/bioconductor-arrayqualitymetrics/meta.yaml index 837e3d81435b0..a8fb732b191d1 100644 --- a/recipes/bioconductor-arrayqualitymetrics/meta.yaml +++ b/recipes/bioconductor-arrayqualitymetrics/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "3.38.0" %} +{% set version = "3.40.0" %} {% set name = "arrayQualityMetrics" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: c85ba7444832fd3da35ebeb206ac5dbc + md5: feb4513176dad1e95c490dcf866092cc build: number: 0 rpaths: @@ -20,15 +20,14 @@ build: # Suggests: ALLMLL, CCl4, BiocStyle, knitr requirements: host: - - 'bioconductor-affy >=1.60.0,<1.61.0' - - 'bioconductor-affyplm >=1.58.0,<1.59.0' - - 'bioconductor-beadarray >=2.32.0,<2.33.0' - - 'bioconductor-biobase >=2.42.0,<2.43.0' - - 'bioconductor-genefilter >=1.64.0,<1.65.0' - - 'bioconductor-limma >=3.38.0,<3.39.0' - - 'bioconductor-vsn >=3.50.0,<3.51.0' + - 'bioconductor-affy >=1.62.0,<1.63.0' + - 'bioconductor-affyplm >=1.60.0,<1.61.0' + - 'bioconductor-beadarray >=2.34.0,<2.35.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' + - 'bioconductor-genefilter >=1.66.0,<1.67.0' + - 'bioconductor-limma >=3.40.0,<3.41.0' + - 'bioconductor-vsn >=3.52.0,<3.53.0' - r-base - - 'r-cairo >=1.4-6' - 'r-gridsvg >=1.4-3' - r-hmisc - r-hwriter @@ -36,17 +35,17 @@ requirements: - r-latticeextra - r-rcolorbrewer - r-setrng + - r-svglite - r-xml run: - - 'bioconductor-affy >=1.60.0,<1.61.0' - - 'bioconductor-affyplm >=1.58.0,<1.59.0' - - 'bioconductor-beadarray >=2.32.0,<2.33.0' - - 'bioconductor-biobase >=2.42.0,<2.43.0' - - 'bioconductor-genefilter >=1.64.0,<1.65.0' - - 'bioconductor-limma >=3.38.0,<3.39.0' - - 'bioconductor-vsn >=3.50.0,<3.51.0' + - 'bioconductor-affy >=1.62.0,<1.63.0' + - 'bioconductor-affyplm >=1.60.0,<1.61.0' + - 'bioconductor-beadarray >=2.34.0,<2.35.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' + - 'bioconductor-genefilter >=1.66.0,<1.67.0' + - 'bioconductor-limma >=3.40.0,<3.41.0' + - 'bioconductor-vsn >=3.52.0,<3.53.0' - r-base - - 'r-cairo >=1.4-6' - 'r-gridsvg >=1.4-3' - r-hmisc - r-hwriter @@ -54,6 +53,7 @@ requirements: - r-latticeextra - r-rcolorbrewer - r-setrng + - r-svglite - r-xml test: commands: diff --git a/recipes/bioconductor-arraytools/meta.yaml b/recipes/bioconductor-arraytools/meta.yaml index 7e326f1e73f9c..6eafd6eae0a88 100644 --- a/recipes/bioconductor-arraytools/meta.yaml +++ b/recipes/bioconductor-arraytools/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.42.0" %} +{% set version = "1.44.0" %} {% set name = "ArrayTools" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 2111784fb075319520ca6b6f1add616b + md5: 3e41b9280d67c39c0002721d521906d5 build: number: 0 rpaths: @@ -20,15 +20,15 @@ build: # Suggests: simpleaffy, R2HTML, affydata, affyPLM, genefilter, annaffy, gcrma, hugene10sttranscriptcluster.db requirements: host: - - 'bioconductor-affy >=1.60.0,<1.61.0' - - 'bioconductor-biobase >=2.42.0,<2.43.0' - - 'bioconductor-limma >=3.38.0,<3.39.0' + - 'bioconductor-affy >=1.62.0,<1.63.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' + - 'bioconductor-limma >=3.40.0,<3.41.0' - r-base - r-xtable run: - - 'bioconductor-affy >=1.60.0,<1.61.0' - - 'bioconductor-biobase >=2.42.0,<2.43.0' - - 'bioconductor-limma >=3.38.0,<3.39.0' + - 'bioconductor-affy >=1.62.0,<1.63.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' + - 'bioconductor-limma >=3.40.0,<3.41.0' - r-base - r-xtable test: diff --git a/recipes/bioconductor-arraytv/meta.yaml b/recipes/bioconductor-arraytv/meta.yaml index f3df951222fc6..84ba03a056493 100644 --- a/recipes/bioconductor-arraytv/meta.yaml +++ b/recipes/bioconductor-arraytv/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.20.0" %} +{% set version = "1.22.0" %} {% set name = "ArrayTV" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 5cf6ce896c57f219ee738b6d9dfa8a7f + md5: e73af58a14b0d432bb15491156f492bc build: number: 0 rpaths: @@ -20,17 +20,17 @@ build: # Suggests: RColorBrewer, crlmm, ff, BSgenome.Hsapiens.UCSC.hg18,BSgenome.Hsapiens.UCSC.hg19, lattice, latticeExtra, RUnit, BiocGenerics requirements: host: - - 'bioconductor-dnacopy >=1.56.0,<1.57.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-oligoclasses >=1.44.0,<1.45.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-dnacopy >=1.58.0,<1.59.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-oligoclasses >=1.46.0,<1.47.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' - r-base - r-foreach run: - - 'bioconductor-dnacopy >=1.56.0,<1.57.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-oligoclasses >=1.44.0,<1.45.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-dnacopy >=1.58.0,<1.59.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-oligoclasses >=1.46.0,<1.47.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' - r-base - r-foreach test: diff --git a/recipes/bioconductor-arrmdata/meta.yaml b/recipes/bioconductor-arrmdata/meta.yaml index 1cb3170c45b91..8d5a3cd6bc4a3 100644 --- a/recipes/bioconductor-arrmdata/meta.yaml +++ b/recipes/bioconductor-arrmdata/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.18.0" %} +{% set version = "1.20.0" %} {% set name = "ARRmData" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 16ccdc6a5bc334b90c45e81103075a58 + md5: a31c9743207a9e6e802284323c235412 build: number: 0 rpaths: @@ -22,7 +22,7 @@ requirements: - r-base run: - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-arrmdata/post-link.sh b/recipes/bioconductor-arrmdata/post-link.sh index 95d96b40cfdaa..9174ad851b0ae 100644 --- a/recipes/bioconductor-arrmdata/post-link.sh +++ b/recipes/bioconductor-arrmdata/post-link.sh @@ -1,11 +1,11 @@ #!/bin/bash -FN="ARRmData_1.18.0.tar.gz" +FN="ARRmData_1.20.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/experiment/src/contrib/ARRmData_1.18.0.tar.gz" - "https://bioarchive.galaxyproject.org/ARRmData_1.18.0.tar.gz" - "https://depot.galaxyproject.org/software/bioconductor-arrmdata/bioconductor-arrmdata_1.18.0_src_all.tar.gz" + "https://bioconductor.org/packages/3.9/data/experiment/src/contrib/ARRmData_1.20.0.tar.gz" + "https://bioarchive.galaxyproject.org/ARRmData_1.20.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-arrmdata/bioconductor-arrmdata_1.20.0_src_all.tar.gz" ) -MD5="16ccdc6a5bc334b90c45e81103075a58" +MD5="a31c9743207a9e6e802284323c235412" # Use a staging area in the conda dir rather than temp dirs, both to avoid # permission issues as well as to have things downloaded in a predictable @@ -16,7 +16,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-arrmnormalization/meta.yaml b/recipes/bioconductor-arrmnormalization/meta.yaml index 3e8cf3285e30c..6ffa2e4a5fbfa 100644 --- a/recipes/bioconductor-arrmnormalization/meta.yaml +++ b/recipes/bioconductor-arrmnormalization/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.22.0" %} +{% set version = "1.24.0" %} {% set name = "ARRmNormalization" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 0007af10085c49def9f420ab8a14bfa0 + md5: fa44aea8216cb0a17a0719b10e276e89 build: number: 0 rpaths: @@ -19,10 +19,10 @@ build: noarch: generic requirements: host: - - 'bioconductor-arrmdata >=1.18.0,<1.19.0' + - 'bioconductor-arrmdata >=1.20.0,<1.21.0' - r-base run: - - 'bioconductor-arrmdata >=1.18.0,<1.19.0' + - 'bioconductor-arrmdata >=1.20.0,<1.21.0' - r-base test: commands: diff --git a/recipes/bioconductor-artms/meta.yaml b/recipes/bioconductor-artms/meta.yaml index 64ea897b7bd7d..2f751182e18c7 100644 --- a/recipes/bioconductor-artms/meta.yaml +++ b/recipes/bioconductor-artms/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.0.10" %} +{% set version = "1.2.0" %} {% set name = "artMS" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: ad314ff7f1e8ef4203a483ee6aac53c8 + md5: 1b1ad8a15d8db237f9a932446f95d474 build: number: 0 rpaths: @@ -20,13 +20,13 @@ build: # Suggests: BiocStyle, knitr, rmarkdown, testthat requirements: host: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' - - 'bioconductor-biomart >=2.38.0,<2.39.0' - - 'bioconductor-complexheatmap >=1.20.0,<1.21.0' - - 'bioconductor-limma >=3.38.0,<3.39.0' - - 'bioconductor-msstats >=3.14.0,<3.15.0' - - 'bioconductor-org.hs.eg.db >=3.7.0,<3.8.0' - - 'bioconductor-org.mm.eg.db >=3.7.0,<3.8.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' + - 'bioconductor-biomart >=2.40.0,<2.41.0' + - 'bioconductor-complexheatmap >=2.0.0,<2.1.0' + - 'bioconductor-limma >=3.40.0,<3.41.0' + - 'bioconductor-msstats >=3.16.0,<3.17.0' + - 'bioconductor-org.hs.eg.db >=3.8.0,<3.9.0' + - 'bioconductor-org.mm.eg.db >=3.8.0,<3.9.0' - r-base - r-bit64 - r-circlize @@ -56,13 +56,13 @@ requirements: - r-venndiagram - r-yaml run: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' - - 'bioconductor-biomart >=2.38.0,<2.39.0' - - 'bioconductor-complexheatmap >=1.20.0,<1.21.0' - - 'bioconductor-limma >=3.38.0,<3.39.0' - - 'bioconductor-msstats >=3.14.0,<3.15.0' - - 'bioconductor-org.hs.eg.db >=3.7.0,<3.8.0' - - 'bioconductor-org.mm.eg.db >=3.7.0,<3.8.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' + - 'bioconductor-biomart >=2.40.0,<2.41.0' + - 'bioconductor-complexheatmap >=2.0.0,<2.1.0' + - 'bioconductor-limma >=3.40.0,<3.41.0' + - 'bioconductor-msstats >=3.16.0,<3.17.0' + - 'bioconductor-org.hs.eg.db >=3.8.0,<3.9.0' + - 'bioconductor-org.mm.eg.db >=3.8.0,<3.9.0' - r-base - r-bit64 - r-circlize @@ -97,5 +97,5 @@ test: about: home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: 'GPL (>= 3) + file LICENSE' - summary: 'artMS provides a set of tools for the analysis of proteomics label-free datasets. It takes as input the MaxQuant search result output (evidence.txt file) and performs quality control, relative quantification using MSstats, downstream analysis and integration. artMS also provides a set of functions to re-format and make it compatible with other analytical tools, including, SAINTq, SAINTexpress, Phosfate, and PHOTON.' + summary: 'artMS provides a set of tools for the analysis of proteomics label-free datasets. It takes as input the MaxQuant search result output (evidence.txt file) and performs quality control, relative quantification using MSstats, downstream analysis and integration. artMS also provides a set of functions to re-format and make it compatible with other analytical tools, including, SAINTq, SAINTexpress, Phosfate, and PHOTON. Check [http://artms.org](http://artms.org) for details.' diff --git a/recipes/bioconductor-asafe/meta.yaml b/recipes/bioconductor-asafe/meta.yaml index 79a14cf565bfa..94002b0408e89 100644 --- a/recipes/bioconductor-asafe/meta.yaml +++ b/recipes/bioconductor-asafe/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.8.0" %} +{% set version = "1.10.0" %} {% set name = "ASAFE" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 514dbf478d594a68fd86ba799f35b51d + md5: 607a5a93f3de7de64f09dea96c0526d6 build: number: 0 rpaths: diff --git a/recipes/bioconductor-aseb/meta.yaml b/recipes/bioconductor-aseb/meta.yaml index a2764b6cf6d7d..20b4f4c3b2981 100644 --- a/recipes/bioconductor-aseb/meta.yaml +++ b/recipes/bioconductor-aseb/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.26.0" %} +{% set version = "1.28.0" %} {% set name = "ASEB" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 3051785401668b2ad729c669a876699e + md5: 72879a9c7bf18ea45b4cd0fd9855fe3c build: number: 0 rpaths: diff --git a/recipes/bioconductor-asgsca/meta.yaml b/recipes/bioconductor-asgsca/meta.yaml index 9eb87d13cc87a..d0d8e894e8517 100644 --- a/recipes/bioconductor-asgsca/meta.yaml +++ b/recipes/bioconductor-asgsca/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.16.0" %} +{% set version = "1.18.0" %} {% set name = "ASGSCA" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 1a540dfd5b527f46d89a54056ea29339 + md5: 8684a6a76f7d751d64bd09bf5f090a7e build: number: 0 rpaths: diff --git a/recipes/bioconductor-ashkenazimsonchr21/meta.yaml b/recipes/bioconductor-ashkenazimsonchr21/meta.yaml index a066f58e8bfdf..3bfca252800b8 100644 --- a/recipes/bioconductor-ashkenazimsonchr21/meta.yaml +++ b/recipes/bioconductor-ashkenazimsonchr21/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.12.0" %} +{% set version = "1.14.0" %} {% set name = "AshkenazimSonChr21" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: b565b952357149f37240f4fa62dfc425 + md5: afcd79416fd2b6fb83f2ad1793dcbc2b build: number: 0 rpaths: @@ -23,7 +23,7 @@ requirements: - r-base run: - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-ashkenazimsonchr21/post-link.sh b/recipes/bioconductor-ashkenazimsonchr21/post-link.sh index 05947210831fb..f26121d5ed7d4 100644 --- a/recipes/bioconductor-ashkenazimsonchr21/post-link.sh +++ b/recipes/bioconductor-ashkenazimsonchr21/post-link.sh @@ -1,11 +1,11 @@ #!/bin/bash -FN="AshkenazimSonChr21_1.12.0.tar.gz" +FN="AshkenazimSonChr21_1.14.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/experiment/src/contrib/AshkenazimSonChr21_1.12.0.tar.gz" - "https://bioarchive.galaxyproject.org/AshkenazimSonChr21_1.12.0.tar.gz" - "https://depot.galaxyproject.org/software/bioconductor-ashkenazimsonchr21/bioconductor-ashkenazimsonchr21_1.12.0_src_all.tar.gz" + "https://bioconductor.org/packages/3.9/data/experiment/src/contrib/AshkenazimSonChr21_1.14.0.tar.gz" + "https://bioarchive.galaxyproject.org/AshkenazimSonChr21_1.14.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-ashkenazimsonchr21/bioconductor-ashkenazimsonchr21_1.14.0_src_all.tar.gz" ) -MD5="b565b952357149f37240f4fa62dfc425" +MD5="afcd79416fd2b6fb83f2ad1793dcbc2b" # Use a staging area in the conda dir rather than temp dirs, both to avoid # permission issues as well as to have things downloaded in a predictable @@ -16,7 +16,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-asics/meta.yaml b/recipes/bioconductor-asics/meta.yaml index aa64cd7c8ba0f..15827c45b233f 100644 --- a/recipes/bioconductor-asics/meta.yaml +++ b/recipes/bioconductor-asics/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.2.0" %} +{% set version = "2.0.0" %} {% set name = "ASICS" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 96b660a838b9d9edcf46b98c866ce4c1 + md5: 53c51cd55179c23fff2f9e2a767168cc build: number: 0 rpaths: @@ -20,26 +20,30 @@ build: # Suggests: knitr, rmarkdown, BiocStyle, testthat, ASICSdata requirements: host: - - 'bioconductor-biocparallel >=1.16.0,<1.17.0' - - 'bioconductor-ropls >=1.14.0,<1.15.0' - - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' + - 'bioconductor-biocparallel >=1.18.0,<1.19.0' + - 'bioconductor-pepsnmr >=1.2.0,<1.3.0' + - 'bioconductor-ropls >=1.16.0,<1.17.0' + - 'bioconductor-summarizedexperiment >=1.14.0,<1.15.0' - r-base - r-ggplot2 - r-gridextra + - r-matrix - r-plyr - r-quadprog - - r-speaq + - r-tsdist - r-zoo run: - - 'bioconductor-biocparallel >=1.16.0,<1.17.0' - - 'bioconductor-ropls >=1.14.0,<1.15.0' - - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' + - 'bioconductor-biocparallel >=1.18.0,<1.19.0' + - 'bioconductor-pepsnmr >=1.2.0,<1.3.0' + - 'bioconductor-ropls >=1.16.0,<1.17.0' + - 'bioconductor-summarizedexperiment >=1.14.0,<1.15.0' - r-base - r-ggplot2 - r-gridextra + - r-matrix - r-plyr - r-quadprog - - r-speaq + - r-tsdist - r-zoo test: commands: diff --git a/recipes/bioconductor-asicsdata/meta.yaml b/recipes/bioconductor-asicsdata/meta.yaml index eec44629ea8fa..7ab561a4acb1d 100644 --- a/recipes/bioconductor-asicsdata/meta.yaml +++ b/recipes/bioconductor-asicsdata/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.2.0" %} +{% set version = "1.4.0" %} {% set name = "ASICSdata" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: bb4f0522ab312de30adfa029a55e023b + md5: c8a51bb2154a98248afedc0b926acd7d build: number: 0 rpaths: @@ -23,7 +23,7 @@ requirements: - r-base run: - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-asicsdata/post-link.sh b/recipes/bioconductor-asicsdata/post-link.sh index d162b6f821b79..170805375db61 100644 --- a/recipes/bioconductor-asicsdata/post-link.sh +++ b/recipes/bioconductor-asicsdata/post-link.sh @@ -1,11 +1,11 @@ #!/bin/bash -FN="ASICSdata_1.2.0.tar.gz" +FN="ASICSdata_1.4.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/experiment/src/contrib/ASICSdata_1.2.0.tar.gz" - "https://bioarchive.galaxyproject.org/ASICSdata_1.2.0.tar.gz" - "https://depot.galaxyproject.org/software/bioconductor-asicsdata/bioconductor-asicsdata_1.2.0_src_all.tar.gz" + "https://bioconductor.org/packages/3.9/data/experiment/src/contrib/ASICSdata_1.4.0.tar.gz" + "https://bioarchive.galaxyproject.org/ASICSdata_1.4.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-asicsdata/bioconductor-asicsdata_1.4.0_src_all.tar.gz" ) -MD5="bb4f0522ab312de30adfa029a55e023b" +MD5="c8a51bb2154a98248afedc0b926acd7d" # Use a staging area in the conda dir rather than temp dirs, both to avoid # permission issues as well as to have things downloaded in a predictable @@ -16,7 +16,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-aspli/meta.yaml b/recipes/bioconductor-aspli/meta.yaml index 7308bea8912cf..99022a71454cb 100644 --- a/recipes/bioconductor-aspli/meta.yaml +++ b/recipes/bioconductor-aspli/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.8.0" %} +{% set version = "1.10.0" %} {% set name = "ASpli" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: f0c1e25d140f97ae3a5df84f8a8c190a + md5: 552cdc96a5dfd1b28a87c9f9928e3036 build: number: 0 rpaths: @@ -19,30 +19,30 @@ build: noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' - - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' - - 'bioconductor-biocstyle >=2.10.0,<2.11.0' - - 'bioconductor-edger >=3.24.0,<3.25.0' - - 'bioconductor-genomicalignments >=1.18.0,<1.19.0' - - 'bioconductor-genomicfeatures >=1.34.0,<1.35.0' - - 'bioconductor-genomicranges >=1.34.0,<1.35.0' - - 'bioconductor-gviz >=1.26.0,<1.27.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-rsamtools >=1.34.0,<1.35.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' + - 'bioconductor-biocgenerics >=0.30.0,<0.31.0' + - 'bioconductor-biocstyle >=2.12.0,<2.13.0' + - 'bioconductor-edger >=3.26.0,<3.27.0' + - 'bioconductor-genomicalignments >=1.20.0,<1.21.0' + - 'bioconductor-genomicfeatures >=1.36.0,<1.37.0' + - 'bioconductor-genomicranges >=1.36.0,<1.37.0' + - 'bioconductor-gviz >=1.28.0,<1.29.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-rsamtools >=2.0.0,<2.1.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' - r-base run: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' - - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' - - 'bioconductor-biocstyle >=2.10.0,<2.11.0' - - 'bioconductor-edger >=3.24.0,<3.25.0' - - 'bioconductor-genomicalignments >=1.18.0,<1.19.0' - - 'bioconductor-genomicfeatures >=1.34.0,<1.35.0' - - 'bioconductor-genomicranges >=1.34.0,<1.35.0' - - 'bioconductor-gviz >=1.26.0,<1.27.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-rsamtools >=1.34.0,<1.35.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' + - 'bioconductor-biocgenerics >=0.30.0,<0.31.0' + - 'bioconductor-biocstyle >=2.12.0,<2.13.0' + - 'bioconductor-edger >=3.26.0,<3.27.0' + - 'bioconductor-genomicalignments >=1.20.0,<1.21.0' + - 'bioconductor-genomicfeatures >=1.36.0,<1.37.0' + - 'bioconductor-genomicranges >=1.36.0,<1.37.0' + - 'bioconductor-gviz >=1.28.0,<1.29.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-rsamtools >=2.0.0,<2.1.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' - r-base test: commands: diff --git a/recipes/bioconductor-assessorf/meta.yaml b/recipes/bioconductor-assessorf/meta.yaml index 463e3a845fea2..81ed2d8e88e9c 100644 --- a/recipes/bioconductor-assessorf/meta.yaml +++ b/recipes/bioconductor-assessorf/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.0.2" %} +{% set version = "1.2.0" %} {% set name = "AssessORF" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 2e28b613ca3a146a5e719e2ce6366ccf + md5: 7fe2617641b7963168599745ebbc2598 build: number: 0 rpaths: @@ -20,16 +20,16 @@ build: # Suggests: AssessORFData, BiocStyle, knitr, rmarkdown requirements: host: - - 'bioconductor-biostrings >=2.50.0,<2.51.0' - - 'bioconductor-decipher >=2.10.0,<2.11.0' - - 'bioconductor-genomicranges >=1.34.0,<1.35.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-biostrings >=2.52.0,<2.53.0' + - 'bioconductor-decipher >=2.12.0,<2.13.0' + - 'bioconductor-genomicranges >=1.36.0,<1.37.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' - r-base run: - - 'bioconductor-biostrings >=2.50.0,<2.51.0' - - 'bioconductor-decipher >=2.10.0,<2.11.0' - - 'bioconductor-genomicranges >=1.34.0,<1.35.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-biostrings >=2.52.0,<2.53.0' + - 'bioconductor-decipher >=2.12.0,<2.13.0' + - 'bioconductor-genomicranges >=1.36.0,<1.37.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' - r-base test: commands: diff --git a/recipes/bioconductor-assessorfdata/meta.yaml b/recipes/bioconductor-assessorfdata/meta.yaml index 21abe1017a981..101662ca43483 100644 --- a/recipes/bioconductor-assessorfdata/meta.yaml +++ b/recipes/bioconductor-assessorfdata/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.0.0" %} +{% set version = "1.2.0" %} {% set name = "AssessORFData" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,9 +10,9 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 53b9314533795f7344f755bccd72a1ec + md5: d8fb320aa512adb3b5c4656d7f2809b2 build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ @@ -20,12 +20,12 @@ build: # Suggests: AssessORF, BiocStyle, knitr, rmarkdown requirements: host: - - 'bioconductor-decipher >=2.10.0,<2.11.0' + - 'bioconductor-decipher >=2.12.0,<2.13.0' - r-base run: - - 'bioconductor-decipher >=2.10.0,<2.11.0' + - 'bioconductor-decipher >=2.12.0,<2.13.0' - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-assessorfdata/post-link.sh b/recipes/bioconductor-assessorfdata/post-link.sh index 4b1a394b96e2d..d4302b3e232f9 100644 --- a/recipes/bioconductor-assessorfdata/post-link.sh +++ b/recipes/bioconductor-assessorfdata/post-link.sh @@ -1,11 +1,11 @@ #!/bin/bash -FN="AssessORFData_1.0.0.tar.gz" +FN="AssessORFData_1.2.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/experiment/src/contrib/AssessORFData_1.0.0.tar.gz" - "https://bioarchive.galaxyproject.org/AssessORFData_1.0.0.tar.gz" - "https://depot.galaxyproject.org/software/bioconductor-assessorfdata/bioconductor-assessorfdata_1.0.0_src_all.tar.gz" + "https://bioconductor.org/packages/3.9/data/experiment/src/contrib/AssessORFData_1.2.0.tar.gz" + "https://bioarchive.galaxyproject.org/AssessORFData_1.2.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-assessorfdata/bioconductor-assessorfdata_1.2.0_src_all.tar.gz" ) -MD5="53b9314533795f7344f755bccd72a1ec" +MD5="d8fb320aa512adb3b5c4656d7f2809b2" # Use a staging area in the conda dir rather than temp dirs, both to avoid # permission issues as well as to have things downloaded in a predictable @@ -16,7 +16,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-asset/meta.yaml b/recipes/bioconductor-asset/meta.yaml index 8654243801b46..d18d4b13154fb 100644 --- a/recipes/bioconductor-asset/meta.yaml +++ b/recipes/bioconductor-asset/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "2.0.0" %} +{% set version = "2.2.0" %} {% set name = "ASSET" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 70928d9e0f7dac81d168732658f53b69 + md5: 962772db656337d51d15eac8b0a3fc86 build: number: 0 rpaths: diff --git a/recipes/bioconductor-assign/meta.yaml b/recipes/bioconductor-assign/meta.yaml index 017c2c36b72ec..da9437800fada 100644 --- a/recipes/bioconductor-assign/meta.yaml +++ b/recipes/bioconductor-assign/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.18.0" %} +{% set version = "1.20.1" %} {% set name = "ASSIGN" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,17 +10,17 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: cd78a27ed8e521787729a557227ceba6 + md5: 92fc35d4e6b9944a41e5cf84e702f25a build: number: 0 rpaths: - lib/R/lib/ - lib/ noarch: generic -# Suggests: testthat, BiocStyle, knitr, rmarkdown +# Suggests: testthat, BiocStyle, lintr, knitr, rmarkdown requirements: host: - - 'bioconductor-sva >=3.30.0,<3.31.0' + - 'bioconductor-sva >=3.32.0,<3.33.0' - r-base - r-ggplot2 - r-gplots @@ -28,7 +28,7 @@ requirements: - r-rlab - r-yaml run: - - 'bioconductor-sva >=3.30.0,<3.31.0' + - 'bioconductor-sva >=3.32.0,<3.33.0' - r-base - r-ggplot2 - r-gplots diff --git a/recipes/bioconductor-atacseqqc/meta.yaml b/recipes/bioconductor-atacseqqc/meta.yaml index 851e0d5b0e1a5..826d6eed6e468 100644 --- a/recipes/bioconductor-atacseqqc/meta.yaml +++ b/recipes/bioconductor-atacseqqc/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.6.4" %} +{% set version = "1.8.0" %} {% set name = "ATACseqQC" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: beb49cf02e2d39c45810d19cbea2dd59 + md5: 24706d6fc7038f2f94d1b9caf85acdad build: number: 0 rpaths: @@ -20,39 +20,41 @@ build: # Suggests: BiocStyle, knitr, BSgenome.Hsapiens.UCSC.hg19, TxDb.Hsapiens.UCSC.hg19.knownGene, phastCons100way.UCSC.hg19, MotifDb, trackViewer, testthat requirements: host: - - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' - - 'bioconductor-biostrings >=2.50.0,<2.51.0' - - 'bioconductor-bsgenome >=1.50.0,<1.51.0' - - 'bioconductor-chippeakanno >=3.16.0,<3.17.0' - - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' - - 'bioconductor-genomicalignments >=1.18.0,<1.19.0' - - 'bioconductor-genomicranges >=1.34.0,<1.35.0' - - 'bioconductor-genomicscores >=1.6.0,<1.7.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-limma >=3.38.0,<3.39.0' - - 'bioconductor-motifstack >=1.26.0,<1.27.0' - - 'bioconductor-rsamtools >=1.34.0,<1.35.0' - - 'bioconductor-rtracklayer >=1.42.0,<1.43.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-biocgenerics >=0.30.0,<0.31.0' + - 'bioconductor-biostrings >=2.52.0,<2.53.0' + - 'bioconductor-bsgenome >=1.52.0,<1.53.0' + - 'bioconductor-chippeakanno >=3.18.0,<3.19.0' + - 'bioconductor-edger >=3.26.0,<3.27.0' + - 'bioconductor-genomeinfodb >=1.20.0,<1.21.0' + - 'bioconductor-genomicalignments >=1.20.0,<1.21.0' + - 'bioconductor-genomicranges >=1.36.0,<1.37.0' + - 'bioconductor-genomicscores >=1.8.0,<1.9.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-limma >=3.40.0,<3.41.0' + - 'bioconductor-motifstack >=1.28.0,<1.29.0' + - 'bioconductor-rsamtools >=2.0.0,<2.1.0' + - 'bioconductor-rtracklayer >=1.44.0,<1.45.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' - r-base - r-kernsmooth - r-preseqr - r-randomforest run: - - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' - - 'bioconductor-biostrings >=2.50.0,<2.51.0' - - 'bioconductor-bsgenome >=1.50.0,<1.51.0' - - 'bioconductor-chippeakanno >=3.16.0,<3.17.0' - - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' - - 'bioconductor-genomicalignments >=1.18.0,<1.19.0' - - 'bioconductor-genomicranges >=1.34.0,<1.35.0' - - 'bioconductor-genomicscores >=1.6.0,<1.7.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-limma >=3.38.0,<3.39.0' - - 'bioconductor-motifstack >=1.26.0,<1.27.0' - - 'bioconductor-rsamtools >=1.34.0,<1.35.0' - - 'bioconductor-rtracklayer >=1.42.0,<1.43.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-biocgenerics >=0.30.0,<0.31.0' + - 'bioconductor-biostrings >=2.52.0,<2.53.0' + - 'bioconductor-bsgenome >=1.52.0,<1.53.0' + - 'bioconductor-chippeakanno >=3.18.0,<3.19.0' + - 'bioconductor-edger >=3.26.0,<3.27.0' + - 'bioconductor-genomeinfodb >=1.20.0,<1.21.0' + - 'bioconductor-genomicalignments >=1.20.0,<1.21.0' + - 'bioconductor-genomicranges >=1.36.0,<1.37.0' + - 'bioconductor-genomicscores >=1.8.0,<1.9.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-limma >=3.40.0,<3.41.0' + - 'bioconductor-motifstack >=1.28.0,<1.29.0' + - 'bioconductor-rsamtools >=2.0.0,<2.1.0' + - 'bioconductor-rtracklayer >=1.44.0,<1.45.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' - r-base - r-kernsmooth - r-preseqr diff --git a/recipes/bioconductor-ath1121501.db/meta.yaml b/recipes/bioconductor-ath1121501.db/meta.yaml index eabfcb01990cd..cf071a8de49e7 100644 --- a/recipes/bioconductor-ath1121501.db/meta.yaml +++ b/recipes/bioconductor-ath1121501.db/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.2.3" %} {% set name = "ath1121501.db" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -12,7 +12,7 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: ff9977848321463b27a379ed31fffbc3 build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ @@ -20,14 +20,14 @@ build: # Suggests: DBI, annotate, RUnit requirements: host: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' - - 'bioconductor-org.at.tair.db >=3.7.0,<3.8.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' + - 'bioconductor-org.at.tair.db >=3.8.0,<3.9.0' - r-base run: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' - - 'bioconductor-org.at.tair.db >=3.7.0,<3.8.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' + - 'bioconductor-org.at.tair.db >=3.8.0,<3.9.0' - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-ath1121501.db/post-link.sh b/recipes/bioconductor-ath1121501.db/post-link.sh index bc78c065e4d59..0299cb81e9ffd 100644 --- a/recipes/bioconductor-ath1121501.db/post-link.sh +++ b/recipes/bioconductor-ath1121501.db/post-link.sh @@ -1,9 +1,10 @@ #!/bin/bash FN="ath1121501.db_3.2.3.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/ath1121501.db_3.2.3.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/ath1121501.db_3.2.3.tar.gz" "https://bioarchive.galaxyproject.org/ath1121501.db_3.2.3.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-ath1121501.db/bioconductor-ath1121501.db_3.2.3_src_all.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-ath1121501.db/bioconductor-ath1121501.db_3.2.3_src_all.tar.gz" ) MD5="ff9977848321463b27a379ed31fffbc3" @@ -16,7 +17,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-ath1121501cdf/meta.yaml b/recipes/bioconductor-ath1121501cdf/meta.yaml index ccbfe821e5384..a098dd0f6cb0d 100644 --- a/recipes/bioconductor-ath1121501cdf/meta.yaml +++ b/recipes/bioconductor-ath1121501cdf/meta.yaml @@ -1,6 +1,6 @@ {% set version = "2.18.0" %} {% set name = "ath1121501cdf" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -12,19 +12,19 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 8b63798143219b7c1c2666a91a1a2440 build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' - r-base run: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-ath1121501cdf/post-link.sh b/recipes/bioconductor-ath1121501cdf/post-link.sh index 1be820ba446b5..5fafa83ffebce 100644 --- a/recipes/bioconductor-ath1121501cdf/post-link.sh +++ b/recipes/bioconductor-ath1121501cdf/post-link.sh @@ -1,9 +1,10 @@ #!/bin/bash FN="ath1121501cdf_2.18.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/ath1121501cdf_2.18.0.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/ath1121501cdf_2.18.0.tar.gz" "https://bioarchive.galaxyproject.org/ath1121501cdf_2.18.0.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-ath1121501cdf/bioconductor-ath1121501cdf_2.18.0_src_all.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-ath1121501cdf/bioconductor-ath1121501cdf_2.18.0_src_all.tar.gz" ) MD5="8b63798143219b7c1c2666a91a1a2440" @@ -16,7 +17,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-ath1121501probe/meta.yaml b/recipes/bioconductor-ath1121501probe/meta.yaml index 23d2663830778..618aa52401810 100644 --- a/recipes/bioconductor-ath1121501probe/meta.yaml +++ b/recipes/bioconductor-ath1121501probe/meta.yaml @@ -1,6 +1,6 @@ {% set version = "2.18.0" %} {% set name = "ath1121501probe" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -12,19 +12,19 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: eeeae5e6550bb472ba3419d71bbd7dfb build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' - r-base run: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-ath1121501probe/post-link.sh b/recipes/bioconductor-ath1121501probe/post-link.sh index 6eb81b3a5f721..e2b9e26d38f59 100644 --- a/recipes/bioconductor-ath1121501probe/post-link.sh +++ b/recipes/bioconductor-ath1121501probe/post-link.sh @@ -1,9 +1,10 @@ #!/bin/bash FN="ath1121501probe_2.18.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/ath1121501probe_2.18.0.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/ath1121501probe_2.18.0.tar.gz" "https://bioarchive.galaxyproject.org/ath1121501probe_2.18.0.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-ath1121501probe/bioconductor-ath1121501probe_2.18.0_src_all.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-ath1121501probe/bioconductor-ath1121501probe_2.18.0_src_all.tar.gz" ) MD5="eeeae5e6550bb472ba3419d71bbd7dfb" @@ -16,7 +17,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-atsnp/build.sh b/recipes/bioconductor-atsnp/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-atsnp/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-atsnp/meta.yaml b/recipes/bioconductor-atsnp/meta.yaml new file mode 100644 index 0000000000000..92dd51b0500ae --- /dev/null +++ b/recipes/bioconductor-atsnp/meta.yaml @@ -0,0 +1,50 @@ +{% set version = "1.0.0" %} +{% set name = "atSNP" %} +{% set bioc = "3.9" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: 3af26fbd4c4878de74d0e4abedef8462 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ +# Suggests: testthat, BiocStyle, knitr, rmarkdown +requirements: + host: + - 'bioconductor-biocfilecache >=1.8.0,<1.9.0' + - 'bioconductor-biocparallel >=1.18.0,<1.19.0' + - 'bioconductor-bsgenome >=1.52.0,<1.53.0' + - 'bioconductor-motifstack >=1.28.0,<1.29.0' + - r-base + - r-data.table + - r-rappdirs + - r-rcpp + run: + - 'bioconductor-biocfilecache >=1.8.0,<1.9.0' + - 'bioconductor-biocparallel >=1.18.0,<1.19.0' + - 'bioconductor-bsgenome >=1.52.0,<1.53.0' + - 'bioconductor-motifstack >=1.28.0,<1.29.0' + - r-base + - r-data.table + - r-rappdirs + - r-rcpp + build: + - {{ compiler('c') }} + - {{ compiler('cxx') }} + - make +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: GPL-2 + summary: 'atSNP performs affinity tests of motif matches with the SNP or the reference genomes and SNP-led changes in motif matches.' + diff --git a/recipes/bioconductor-attract/meta.yaml b/recipes/bioconductor-attract/meta.yaml index 7cdf9a7b4d4d3..f7568044e94ee 100644 --- a/recipes/bioconductor-attract/meta.yaml +++ b/recipes/bioconductor-attract/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.34.0" %} +{% set version = "1.36.0" %} {% set name = "attract" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: e01ada5c2cde36bc4f0ec78e81344a13 + md5: 84ae2e3cffca1dc87cc4adc53a2da5ee build: number: 0 rpaths: @@ -20,23 +20,23 @@ build: # Suggests: illuminaHumanv1.db requirements: host: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' - - 'bioconductor-biobase >=2.42.0,<2.43.0' - - 'bioconductor-gostats >=2.48.0,<2.49.0' - - 'bioconductor-keggrest >=1.22.0,<1.23.0' - - 'bioconductor-limma >=3.38.0,<3.39.0' - - 'bioconductor-org.hs.eg.db >=3.7.0,<3.8.0' - - 'bioconductor-reactome.db >=1.66.0,<1.67.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' + - 'bioconductor-gostats >=2.50.0,<2.51.0' + - 'bioconductor-keggrest >=1.24.0,<1.25.0' + - 'bioconductor-limma >=3.40.0,<3.41.0' + - 'bioconductor-org.hs.eg.db >=3.8.0,<3.9.0' + - 'bioconductor-reactome.db >=1.68.0,<1.69.0' - r-base - r-cluster run: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' - - 'bioconductor-biobase >=2.42.0,<2.43.0' - - 'bioconductor-gostats >=2.48.0,<2.49.0' - - 'bioconductor-keggrest >=1.22.0,<1.23.0' - - 'bioconductor-limma >=3.38.0,<3.39.0' - - 'bioconductor-org.hs.eg.db >=3.7.0,<3.8.0' - - 'bioconductor-reactome.db >=1.66.0,<1.67.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' + - 'bioconductor-gostats >=2.50.0,<2.51.0' + - 'bioconductor-keggrest >=1.24.0,<1.25.0' + - 'bioconductor-limma >=3.40.0,<3.41.0' + - 'bioconductor-org.hs.eg.db >=3.8.0,<3.9.0' + - 'bioconductor-reactome.db >=1.68.0,<1.69.0' - r-base - r-cluster test: diff --git a/recipes/bioconductor-aucell/meta.yaml b/recipes/bioconductor-aucell/meta.yaml index 6141f55a0f0f0..417facc8358de 100644 --- a/recipes/bioconductor-aucell/meta.yaml +++ b/recipes/bioconductor-aucell/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.4.1" %} +{% set version = "1.6.0" %} {% set name = "AUCell" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,26 +10,26 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 170badbf1b074c59b28b7fb467f06897 + md5: 60e912117110a72c8c328d69c52c59d3 build: number: 0 rpaths: - lib/R/lib/ - lib/ noarch: generic -# Suggests: Biobase, BiocStyle, devtools, DT, GEOquery, knitr, NMF, plotly, R2HTML, rbokeh, rmarkdown, Rtsne, testthat, zoo +# Suggests: Biobase, BiocStyle, devtools, dynamicTreeCut, DT, GEOquery, knitr, NMF, plotly, R2HTML, rbokeh, rmarkdown, Rtsne, testthat, zoo requirements: host: - - 'bioconductor-gseabase >=1.44.0,<1.45.0' - - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' + - 'bioconductor-gseabase >=1.46.0,<1.47.0' + - 'bioconductor-summarizedexperiment >=1.14.0,<1.15.0' - r-base - r-data.table - r-mixtools - r-r.utils - r-shiny run: - - 'bioconductor-gseabase >=1.44.0,<1.45.0' - - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' + - 'bioconductor-gseabase >=1.46.0,<1.47.0' + - 'bioconductor-summarizedexperiment >=1.14.0,<1.15.0' - r-base - r-data.table - r-mixtools diff --git a/recipes/bioconductor-baalchip/meta.yaml b/recipes/bioconductor-baalchip/meta.yaml index 3aa815d18e8f9..32ae0a5222fe8 100644 --- a/recipes/bioconductor-baalchip/meta.yaml +++ b/recipes/bioconductor-baalchip/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.8.0" %} +{% set version = "1.10.0" %} {% set name = "BaalChIP" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: d2f63d691155d6831cae2aa3a10277a7 + md5: d9cae5f88c75467961335bd0e1bd88de build: number: 0 rpaths: @@ -20,11 +20,11 @@ build: # Suggests: RUnit, BiocGenerics, knitr, rmarkdown, BiocStyle requirements: host: - - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' - - 'bioconductor-genomicalignments >=1.18.0,<1.19.0' - - 'bioconductor-genomicranges >=1.34.0,<1.35.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-rsamtools >=1.34.0,<1.35.0' + - 'bioconductor-genomeinfodb >=1.20.0,<1.21.0' + - 'bioconductor-genomicalignments >=1.20.0,<1.21.0' + - 'bioconductor-genomicranges >=1.36.0,<1.37.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-rsamtools >=2.0.0,<2.1.0' - r-base - r-coda - r-doby @@ -34,11 +34,11 @@ requirements: - r-reshape2 - r-scales run: - - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' - - 'bioconductor-genomicalignments >=1.18.0,<1.19.0' - - 'bioconductor-genomicranges >=1.34.0,<1.35.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-rsamtools >=1.34.0,<1.35.0' + - 'bioconductor-genomeinfodb >=1.20.0,<1.21.0' + - 'bioconductor-genomicalignments >=1.20.0,<1.21.0' + - 'bioconductor-genomicranges >=1.36.0,<1.37.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-rsamtools >=2.0.0,<2.1.0' - r-base - r-coda - r-doby diff --git a/recipes/bioconductor-bac/meta.yaml b/recipes/bioconductor-bac/meta.yaml index c5cc2ead24108..f50b2f370a970 100644 --- a/recipes/bioconductor-bac/meta.yaml +++ b/recipes/bioconductor-bac/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.42.0" %} +{% set version = "1.44.0" %} {% set name = "BAC" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 1d862459cdf5b19fa4d1f45825a2ef46 + md5: 7503cab362d622450435212c7aca4436 build: number: 0 rpaths: diff --git a/recipes/bioconductor-bacon/meta.yaml b/recipes/bioconductor-bacon/meta.yaml index 295853672aff9..cece414f608ab 100644 --- a/recipes/bioconductor-bacon/meta.yaml +++ b/recipes/bioconductor-bacon/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.10.1" %} +{% set version = "1.12.0" %} {% set name = "bacon" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - sha256: aea1214f7253a88cf4746467ce3096a5fea087d7f46e5408023ebee758b8a3dd + md5: 86a2cea86bb1adf7f064f2558665b7c0 build: number: 0 rpaths: @@ -19,12 +19,12 @@ build: # Suggests: BiocStyle, knitr, rmarkdown, testthat, roxygen2 requirements: host: - - 'bioconductor-biocparallel >=1.16.0,<1.17.0' + - 'bioconductor-biocparallel >=1.18.0,<1.19.0' - r-base - r-ellipse - r-ggplot2 run: - - 'bioconductor-biocparallel >=1.16.0,<1.17.0' + - 'bioconductor-biocparallel >=1.18.0,<1.19.0' - r-base - r-ellipse - r-ggplot2 diff --git a/recipes/bioconductor-bader/meta.yaml b/recipes/bioconductor-bader/meta.yaml index 44e76e385e110..95dcc96e99a41 100644 --- a/recipes/bioconductor-bader/meta.yaml +++ b/recipes/bioconductor-bader/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.20.1" %} +{% set version = "1.22.0" %} {% set name = "BADER" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 7cea340eb46d86d415094f8ee014a934 + md5: c12c151e27efae47af5137305a7d6f75 build: number: 0 rpaths: diff --git a/recipes/bioconductor-badregionfinder/meta.yaml b/recipes/bioconductor-badregionfinder/meta.yaml index ff5a909d02e51..3b3e497767789 100644 --- a/recipes/bioconductor-badregionfinder/meta.yaml +++ b/recipes/bioconductor-badregionfinder/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.10.0" %} +{% set version = "1.12.0" %} {% set name = "BadRegionFinder" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 1e8c8450b18124340da912960d9a7d13 + md5: 6e3813a39cffe2ded4ee72248cf704e2 build: number: 0 rpaths: @@ -20,18 +20,18 @@ build: # Suggests: BSgenome.Hsapiens.UCSC.hg19 requirements: host: - - 'bioconductor-biomart >=2.38.0,<2.39.0' - - 'bioconductor-genomicranges >=1.34.0,<1.35.0' - - 'bioconductor-rsamtools >=1.34.0,<1.35.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' - - 'bioconductor-variantannotation >=1.28.0,<1.29.0' + - 'bioconductor-biomart >=2.40.0,<2.41.0' + - 'bioconductor-genomicranges >=1.36.0,<1.37.0' + - 'bioconductor-rsamtools >=2.0.0,<2.1.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' + - 'bioconductor-variantannotation >=1.30.0,<1.31.0' - r-base run: - - 'bioconductor-biomart >=2.38.0,<2.39.0' - - 'bioconductor-genomicranges >=1.34.0,<1.35.0' - - 'bioconductor-rsamtools >=1.34.0,<1.35.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' - - 'bioconductor-variantannotation >=1.28.0,<1.29.0' + - 'bioconductor-biomart >=2.40.0,<2.41.0' + - 'bioconductor-genomicranges >=1.36.0,<1.37.0' + - 'bioconductor-rsamtools >=2.0.0,<2.1.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' + - 'bioconductor-variantannotation >=1.30.0,<1.31.0' - r-base test: commands: diff --git a/recipes/bioconductor-bags/meta.yaml b/recipes/bioconductor-bags/meta.yaml index 794a3f4c33e38..fb0a96652b83d 100644 --- a/recipes/bioconductor-bags/meta.yaml +++ b/recipes/bioconductor-bags/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "2.22.0" %} +{% set version = "2.24.0" %} {% set name = "BAGS" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 2d000e29d269eb8f93a2eabcd1436182 + md5: bf7b643c639d196d99411a851f5215cb build: number: 0 rpaths: @@ -18,12 +18,12 @@ build: - lib/ requirements: host: - - 'bioconductor-biobase >=2.42.0,<2.43.0' - - 'bioconductor-breastcancervdx >=1.20.0,<1.21.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' + - 'bioconductor-breastcancervdx >=1.22.0,<1.23.0' - r-base run: - - 'bioconductor-biobase >=2.42.0,<2.43.0' - - 'bioconductor-breastcancervdx >=1.20.0,<1.21.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' + - 'bioconductor-breastcancervdx >=1.22.0,<1.23.0' - r-base build: - {{ compiler('c') }} diff --git a/recipes/bioconductor-ballgown/meta.yaml b/recipes/bioconductor-ballgown/meta.yaml index 35653c9318649..27b5fd8311a2b 100644 --- a/recipes/bioconductor-ballgown/meta.yaml +++ b/recipes/bioconductor-ballgown/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "2.14.0" %} +{% set version = "2.16.0" %} {% set name = "ballgown" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: d71a9350866c532da0a81b77fe36628e + md5: 80c05edb3007ae4bd8774ee870d4c9de build: number: 0 rpaths: @@ -20,25 +20,25 @@ build: # Suggests: testthat, knitr requirements: host: - - 'bioconductor-biobase >=2.42.0,<2.43.0' - - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' - - 'bioconductor-genomicranges >=1.34.0,<1.35.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-limma >=3.38.0,<3.39.0' - - 'bioconductor-rtracklayer >=1.42.0,<1.43.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' - - 'bioconductor-sva >=3.30.0,<3.31.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' + - 'bioconductor-genomeinfodb >=1.20.0,<1.21.0' + - 'bioconductor-genomicranges >=1.36.0,<1.37.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-limma >=3.40.0,<3.41.0' + - 'bioconductor-rtracklayer >=1.44.0,<1.45.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' + - 'bioconductor-sva >=3.32.0,<3.33.0' - r-base - r-rcolorbrewer run: - - 'bioconductor-biobase >=2.42.0,<2.43.0' - - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' - - 'bioconductor-genomicranges >=1.34.0,<1.35.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-limma >=3.38.0,<3.39.0' - - 'bioconductor-rtracklayer >=1.42.0,<1.43.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' - - 'bioconductor-sva >=3.30.0,<3.31.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' + - 'bioconductor-genomeinfodb >=1.20.0,<1.21.0' + - 'bioconductor-genomicranges >=1.36.0,<1.37.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-limma >=3.40.0,<3.41.0' + - 'bioconductor-rtracklayer >=1.44.0,<1.45.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' + - 'bioconductor-sva >=3.32.0,<3.33.0' - r-base - r-rcolorbrewer test: diff --git a/recipes/bioconductor-bamsignals/meta.yaml b/recipes/bioconductor-bamsignals/meta.yaml index 925a1ea35b9dd..d081bd14a07f5 100644 --- a/recipes/bioconductor-bamsignals/meta.yaml +++ b/recipes/bioconductor-bamsignals/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.14.0" %} +{% set version = "1.16.0" %} {% set name = "bamsignals" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 5d36b092f1a9e17de3b7f39ea838f7dc + md5: d193458eb5ac2b8af0c95ed0a6ef48dd build: number: 0 rpaths: @@ -19,19 +19,19 @@ build: # Suggests: testthat (>= 0.9), Rsamtools, BiocStyle, knitr, rmarkdown requirements: host: - - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' - - 'bioconductor-genomicranges >=1.34.0,<1.35.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-rhtslib >=1.14.0,<1.15.0' - - 'bioconductor-zlibbioc >=1.28.0,<1.29.0' + - 'bioconductor-biocgenerics >=0.30.0,<0.31.0' + - 'bioconductor-genomicranges >=1.36.0,<1.37.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-rhtslib >=1.16.0,<1.17.0' + - 'bioconductor-zlibbioc >=1.30.0,<1.31.0' - r-base - 'r-rcpp >=0.10.6' run: - - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' - - 'bioconductor-genomicranges >=1.34.0,<1.35.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-rhtslib >=1.14.0,<1.15.0' - - 'bioconductor-zlibbioc >=1.28.0,<1.29.0' + - 'bioconductor-biocgenerics >=0.30.0,<0.31.0' + - 'bioconductor-genomicranges >=1.36.0,<1.37.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-rhtslib >=1.16.0,<1.17.0' + - 'bioconductor-zlibbioc >=1.30.0,<1.31.0' - r-base - 'r-rcpp >=0.10.6' build: diff --git a/recipes/bioconductor-bandits/build.sh b/recipes/bioconductor-bandits/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-bandits/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-bandits/meta.yaml b/recipes/bioconductor-bandits/meta.yaml new file mode 100644 index 0000000000000..1a9496a5a34b5 --- /dev/null +++ b/recipes/bioconductor-bandits/meta.yaml @@ -0,0 +1,57 @@ +{% set version = "1.0.0" %} +{% set name = "BANDITS" %} +{% set bioc = "3.9" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: d2a9930abcadaa225c59afe1fd0e6097 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ +# Suggests: knitr, rmarkdown, testthat, tximport, BiocStyle, GenomicFeatures, Biostrings +# SystemRequirements: C++11 +requirements: + host: + - 'bioconductor-biocparallel >=1.18.0,<1.19.0' + - 'bioconductor-drimseq >=1.12.0,<1.13.0' + - r-base + - r-data.table + - r-doparallel + - r-dorng + - r-foreach + - r-ggplot2 + - r-mass + - r-rcpp + - r-rcpparmadillo + run: + - 'bioconductor-biocparallel >=1.18.0,<1.19.0' + - 'bioconductor-drimseq >=1.12.0,<1.13.0' + - r-base + - r-data.table + - r-doparallel + - r-dorng + - r-foreach + - r-ggplot2 + - r-mass + - r-rcpp + - r-rcpparmadillo + build: + - {{ compiler('c') }} + - {{ compiler('cxx') }} + - make +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: 'GPL (>= 3)' + summary: 'BANDITS is a Bayesian hierarchical model for detecting differential splicing of genes and transcripts, via differential transcript usage (DTU), between two or more conditions. The method uses a Bayesian hierarchical framework, which allows for sample specific proportions in a Dirichlet-Multinomial model, and samples the allocation of fragments to the transcripts. Parameters are inferred via Markov chain Monte Carlo (MCMC) techniques and a DTU test is performed via a multivariate Wald test on the posterior densities for the average relative abundance of transcripts.' + diff --git a/recipes/bioconductor-banocc/meta.yaml b/recipes/bioconductor-banocc/meta.yaml index f6f7fe0217076..ded8b27d9ebb2 100644 --- a/recipes/bioconductor-banocc/meta.yaml +++ b/recipes/bioconductor-banocc/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.6.1" %} +{% set version = "1.8.0" %} {% set name = "banocc" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 1803b7e6681726b610bd4e7ea3f5bce3 + md5: 2efc9ad31f51961ccb514914002cf5f9 build: number: 0 rpaths: diff --git a/recipes/bioconductor-barley1cdf/meta.yaml b/recipes/bioconductor-barley1cdf/meta.yaml index 4c9d633ece424..b7914f3555193 100644 --- a/recipes/bioconductor-barley1cdf/meta.yaml +++ b/recipes/bioconductor-barley1cdf/meta.yaml @@ -1,6 +1,6 @@ {% set version = "2.18.0" %} {% set name = "barley1cdf" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -12,19 +12,19 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 16a2ca83f550518756d9fa3273672157 build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' - r-base run: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-barley1cdf/post-link.sh b/recipes/bioconductor-barley1cdf/post-link.sh index e8b400df14186..5e205ab092816 100644 --- a/recipes/bioconductor-barley1cdf/post-link.sh +++ b/recipes/bioconductor-barley1cdf/post-link.sh @@ -1,9 +1,10 @@ #!/bin/bash FN="barley1cdf_2.18.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/barley1cdf_2.18.0.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/barley1cdf_2.18.0.tar.gz" "https://bioarchive.galaxyproject.org/barley1cdf_2.18.0.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-barley1cdf/bioconductor-barley1cdf_2.18.0_src_all.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-barley1cdf/bioconductor-barley1cdf_2.18.0_src_all.tar.gz" ) MD5="16a2ca83f550518756d9fa3273672157" @@ -16,7 +17,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-barley1probe/meta.yaml b/recipes/bioconductor-barley1probe/meta.yaml index 926d7db678b32..4f5c00969b4dc 100644 --- a/recipes/bioconductor-barley1probe/meta.yaml +++ b/recipes/bioconductor-barley1probe/meta.yaml @@ -1,6 +1,6 @@ {% set version = "2.18.0" %} {% set name = "barley1probe" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -12,19 +12,19 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 80595d8ecf83ba83ea84a722a24ab474 build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' - r-base run: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-barley1probe/post-link.sh b/recipes/bioconductor-barley1probe/post-link.sh index 8738af1967302..32742fd53fe7d 100644 --- a/recipes/bioconductor-barley1probe/post-link.sh +++ b/recipes/bioconductor-barley1probe/post-link.sh @@ -1,9 +1,10 @@ #!/bin/bash FN="barley1probe_2.18.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/barley1probe_2.18.0.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/barley1probe_2.18.0.tar.gz" "https://bioarchive.galaxyproject.org/barley1probe_2.18.0.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-barley1probe/bioconductor-barley1probe_2.18.0_src_all.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-barley1probe/bioconductor-barley1probe_2.18.0_src_all.tar.gz" ) MD5="80595d8ecf83ba83ea84a722a24ab474" @@ -16,7 +17,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-basecallqc/meta.yaml b/recipes/bioconductor-basecallqc/meta.yaml index db2ff1fa77fa9..38da8e94c1d3a 100644 --- a/recipes/bioconductor-basecallqc/meta.yaml +++ b/recipes/bioconductor-basecallqc/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.6.0" %} +{% set version = "1.8.0" %} {% set name = "basecallQC" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 88e03b7e9ba40099f69694c3b228bbe5 + md5: 1833033cf86b2c75d24b284a3bb3700f build: number: 0 rpaths: @@ -21,7 +21,7 @@ build: # SystemRequirements: bcl2Fastq (versions >= 2.1.7) requirements: host: - - 'bioconductor-shortread >=1.40.0,<1.41.0' + - 'bioconductor-shortread >=1.42.0,<1.43.0' - r-base - r-data.table - r-dplyr @@ -38,7 +38,7 @@ requirements: - r-xml - r-yaml run: - - 'bioconductor-shortread >=1.40.0,<1.41.0' + - 'bioconductor-shortread >=1.42.0,<1.43.0' - r-base - r-data.table - r-dplyr diff --git a/recipes/bioconductor-basespacer/meta.yaml b/recipes/bioconductor-basespacer/meta.yaml index dbaaa393c796a..45c2b91b41f5d 100644 --- a/recipes/bioconductor-basespacer/meta.yaml +++ b/recipes/bioconductor-basespacer/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.26.0" %} +{% set version = "1.28.0" %} {% set name = "BaseSpaceR" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 25da31488eb0751ca13b4c24ef1d27f0 + md5: bf914f2845df6896b289430c7dda8fb7 build: number: 0 rpaths: diff --git a/recipes/bioconductor-basic4cseq/meta.yaml b/recipes/bioconductor-basic4cseq/meta.yaml index 370460b60cf8d..20272cfaf0eae 100644 --- a/recipes/bioconductor-basic4cseq/meta.yaml +++ b/recipes/bioconductor-basic4cseq/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.18.0" %} +{% set version = "1.20.0" %} {% set name = "Basic4Cseq" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 2be7b773728e3e0f11702a26a7891b3f + md5: 60ecce3e0bfa529c4a4a99c72a55b046 build: number: 0 rpaths: @@ -20,18 +20,18 @@ build: # Suggests: BSgenome.Hsapiens.UCSC.hg19 requirements: host: - - 'bioconductor-biostrings >=2.50.0,<2.51.0' - - 'bioconductor-bsgenome.ecoli.ncbi.20080805 >=1.3.0,<1.4.0' - - 'bioconductor-genomicalignments >=1.18.0,<1.19.0' - - 'bioconductor-genomicranges >=1.34.0,<1.35.0' + - 'bioconductor-biostrings >=2.52.0,<2.53.0' + - 'bioconductor-bsgenome.ecoli.ncbi.20080805 >=1.4.0,<1.5.0' + - 'bioconductor-genomicalignments >=1.20.0,<1.21.0' + - 'bioconductor-genomicranges >=1.36.0,<1.37.0' - r-base - r-catools - r-rcircos run: - - 'bioconductor-biostrings >=2.50.0,<2.51.0' - - 'bioconductor-bsgenome.ecoli.ncbi.20080805 >=1.3.0,<1.4.0' - - 'bioconductor-genomicalignments >=1.18.0,<1.19.0' - - 'bioconductor-genomicranges >=1.34.0,<1.35.0' + - 'bioconductor-biostrings >=2.52.0,<2.53.0' + - 'bioconductor-bsgenome.ecoli.ncbi.20080805 >=1.4.0,<1.5.0' + - 'bioconductor-genomicalignments >=1.20.0,<1.21.0' + - 'bioconductor-genomicranges >=1.36.0,<1.37.0' - r-base - r-catools - r-rcircos diff --git a/recipes/bioconductor-basics/meta.yaml b/recipes/bioconductor-basics/meta.yaml index 7771c6f918ee1..13e98cda1d296 100644 --- a/recipes/bioconductor-basics/meta.yaml +++ b/recipes/bioconductor-basics/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.4.0" %} +{% set version = "1.6.0" %} {% set name = "BASiCS" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,47 +10,53 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: e695dfb2ea1fd76c8674873beb4eb3a4 + md5: 2313c99d85e93025a11ad67d50a931ad build: number: 0 rpaths: - lib/R/lib/ - lib/ -# Suggests: BiocStyle, knitr, rmarkdown +# Suggests: BiocStyle, knitr, rmarkdown, testthat # SystemRequirements: C++11 requirements: host: - - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' - - 'bioconductor-scran >=1.10.0,<1.11.0' - - 'bioconductor-singlecellexperiment >=1.4.0,<1.5.0' - - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' + - 'bioconductor-biocgenerics >=0.30.0,<0.31.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' + - 'bioconductor-scran >=1.12.0,<1.13.0' + - 'bioconductor-singlecellexperiment >=1.6.0,<1.7.0' + - 'bioconductor-summarizedexperiment >=1.14.0,<1.15.0' - r-base - r-coda + - r-cowplot - r-data.table + - r-ggextra - r-ggplot2 - r-kernsmooth - r-mass - r-matrixstats - 'r-rcpp >=0.11.3' - r-rcpparmadillo - - r-testthat + - r-viridis run: - - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' - - 'bioconductor-scran >=1.10.0,<1.11.0' - - 'bioconductor-singlecellexperiment >=1.4.0,<1.5.0' - - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' + - 'bioconductor-biocgenerics >=0.30.0,<0.31.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' + - 'bioconductor-scran >=1.12.0,<1.13.0' + - 'bioconductor-singlecellexperiment >=1.6.0,<1.7.0' + - 'bioconductor-summarizedexperiment >=1.14.0,<1.15.0' - r-base - r-coda + - r-cowplot - r-data.table + - r-ggextra - r-ggplot2 - r-kernsmooth - r-mass - r-matrixstats - 'r-rcpp >=0.11.3' - r-rcpparmadillo - - r-testthat + - r-viridis build: - {{ compiler('c') }} - {{ compiler('cxx') }} diff --git a/recipes/bioconductor-basicstarrseq/meta.yaml b/recipes/bioconductor-basicstarrseq/meta.yaml index 6f3e55845b9be..064864be92650 100644 --- a/recipes/bioconductor-basicstarrseq/meta.yaml +++ b/recipes/bioconductor-basicstarrseq/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.10.0" %} +{% set version = "1.12.0" %} {% set name = "BasicSTARRseq" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,9 +10,9 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 6ef49c32242bce2db8d44a695ed756a8 + md5: d2511adf3fc8177f9135ba710a978b98 build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ @@ -20,18 +20,18 @@ build: # Suggests: knitr requirements: host: - - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' - - 'bioconductor-genomicalignments >=1.18.0,<1.19.0' - - 'bioconductor-genomicranges >=1.34.0,<1.35.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-genomeinfodb >=1.20.0,<1.21.0' + - 'bioconductor-genomicalignments >=1.20.0,<1.21.0' + - 'bioconductor-genomicranges >=1.36.0,<1.37.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' - r-base run: - - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' - - 'bioconductor-genomicalignments >=1.18.0,<1.19.0' - - 'bioconductor-genomicranges >=1.34.0,<1.35.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-genomeinfodb >=1.20.0,<1.21.0' + - 'bioconductor-genomicalignments >=1.20.0,<1.21.0' + - 'bioconductor-genomicranges >=1.36.0,<1.37.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' - r-base test: commands: diff --git a/recipes/bioconductor-batchelor/build.sh b/recipes/bioconductor-batchelor/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-batchelor/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-batchelor/meta.yaml b/recipes/bioconductor-batchelor/meta.yaml new file mode 100644 index 0000000000000..bf96dd7e6823d --- /dev/null +++ b/recipes/bioconductor-batchelor/meta.yaml @@ -0,0 +1,63 @@ +{% set version = "1.0.0" %} +{% set name = "batchelor" %} +{% set bioc = "3.9" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + md5: dae9ed9c63eb9de4e21f8d826ac09eef +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ +# Suggests: testthat, BiocStyle, knitr, beachmat, scRNAseq +# SystemRequirements: C++11 +requirements: + host: + - 'bioconductor-beachmat >=2.0.0,<2.1.0' + - 'bioconductor-biocgenerics >=0.30.0,<0.31.0' + - 'bioconductor-biocneighbors >=1.2.0,<1.3.0' + - 'bioconductor-biocparallel >=1.18.0,<1.19.0' + - 'bioconductor-biocsingular >=1.0.0,<1.1.0' + - 'bioconductor-delayedarray >=0.10.0,<0.11.0' + - 'bioconductor-delayedmatrixstats >=1.6.0,<1.7.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' + - 'bioconductor-scater >=1.12.0,<1.13.0' + - 'bioconductor-singlecellexperiment >=1.6.0,<1.7.0' + - 'bioconductor-summarizedexperiment >=1.14.0,<1.15.0' + - r-base + - r-matrix + - r-rcpp + run: + - 'bioconductor-beachmat >=2.0.0,<2.1.0' + - 'bioconductor-biocgenerics >=0.30.0,<0.31.0' + - 'bioconductor-biocneighbors >=1.2.0,<1.3.0' + - 'bioconductor-biocparallel >=1.18.0,<1.19.0' + - 'bioconductor-biocsingular >=1.0.0,<1.1.0' + - 'bioconductor-delayedarray >=0.10.0,<0.11.0' + - 'bioconductor-delayedmatrixstats >=1.6.0,<1.7.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' + - 'bioconductor-scater >=1.12.0,<1.13.0' + - 'bioconductor-singlecellexperiment >=1.6.0,<1.7.0' + - 'bioconductor-summarizedexperiment >=1.14.0,<1.15.0' + - r-base + - r-matrix + - r-rcpp + build: + - {{ compiler('c') }} + - {{ compiler('cxx') }} + - make +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: GPL-3 + summary: 'Implements a variety of methods for batch correction of single-cell (RNA sequencing) data. This includes methods based on detecting mutually nearest neighbors as well as a simple sparsity-preserving translation of the population means. Functions are also provided for global rescaling to remove differences in depth between batches, and to perform a principal components analysis that is robust to differences in the numbers of cells across different batches.' + diff --git a/recipes/bioconductor-batchqc/meta.yaml b/recipes/bioconductor-batchqc/meta.yaml index 2eb38476eead9..5e17ec4ba2ca6 100644 --- a/recipes/bioconductor-batchqc/meta.yaml +++ b/recipes/bioconductor-batchqc/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.10.1" %} +{% set version = "1.12.0" %} {% set name = "BatchQC" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 5011c3bec69aa680c0d3e6130b483dcd + md5: e34082012f9e8d1689143057dd6ec626 build: number: 0 rpaths: @@ -21,8 +21,8 @@ build: # SystemRequirements: pandoc (http://pandoc.org/installing.html) for generating reports from markdown files. requirements: host: - - 'bioconductor-limma >=3.38.0,<3.39.0' - - 'bioconductor-sva >=3.30.0,<3.31.0' + - 'bioconductor-limma >=3.40.0,<3.41.0' + - 'bioconductor-sva >=3.32.0,<3.33.0' - r-base - r-corpcor - r-d3heatmap @@ -37,9 +37,10 @@ requirements: - r-reshape2 - r-rmarkdown - r-shiny + - pandoc run: - - 'bioconductor-limma >=3.38.0,<3.39.0' - - 'bioconductor-sva >=3.30.0,<3.31.0' + - 'bioconductor-limma >=3.40.0,<3.41.0' + - 'bioconductor-sva >=3.32.0,<3.33.0' - r-base - r-corpcor - r-d3heatmap @@ -54,6 +55,7 @@ requirements: - r-reshape2 - r-rmarkdown - r-shiny + - pandoc test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-bayesknockdown/meta.yaml b/recipes/bioconductor-bayesknockdown/meta.yaml index ee3f63c5655d2..9ece09d289a1d 100644 --- a/recipes/bioconductor-bayesknockdown/meta.yaml +++ b/recipes/bioconductor-bayesknockdown/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.8.0" %} +{% set version = "1.10.0" %} {% set name = "BayesKnockdown" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 75b7426ec5da2b1e3513f9f78c739412 + md5: c3790c39334419427105d2404a4e8155 build: number: 0 rpaths: @@ -19,10 +19,10 @@ build: noarch: generic requirements: host: - - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' - r-base run: - - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' - r-base test: commands: diff --git a/recipes/bioconductor-bayespeak/meta.yaml b/recipes/bioconductor-bayespeak/meta.yaml index d2de8b09d8675..107548af45f3f 100644 --- a/recipes/bioconductor-bayespeak/meta.yaml +++ b/recipes/bioconductor-bayespeak/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.34.0" %} +{% set version = "1.36.0" %} {% set name = "BayesPeak" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,19 +10,19 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: e92c2c9940b0329142b613fe625eba15 + md5: 5cbdcb27c5f5fd239bb1a3b0521d5e3c build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ # Suggests: BiocStyle, parallel requirements: host: - - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' - r-base run: - - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' - r-base build: - {{ compiler('c') }} diff --git a/recipes/bioconductor-baynorm/meta.yaml b/recipes/bioconductor-baynorm/meta.yaml index ebf34e5b26271..c0538303c2806 100644 --- a/recipes/bioconductor-baynorm/meta.yaml +++ b/recipes/bioconductor-baynorm/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.0.6" %} +{% set version = "1.2.0" %} {% set name = "bayNorm" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: b4f6f28c11a1448671eb4b01b8b09a07 + md5: 32d5215e13ae5eccf197f760b8c2f368 build: number: 0 rpaths: @@ -19,9 +19,9 @@ build: # Suggests: knitr, rmarkdown, BiocStyle, devtools, testthat requirements: host: - - 'bioconductor-biocparallel >=1.16.0,<1.17.0' - - 'bioconductor-singlecellexperiment >=1.4.0,<1.5.0' - - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' + - 'bioconductor-biocparallel >=1.18.0,<1.19.0' + - 'bioconductor-singlecellexperiment >=1.6.0,<1.7.0' + - 'bioconductor-summarizedexperiment >=1.14.0,<1.15.0' - r-base - r-bb - r-dosnow @@ -34,9 +34,9 @@ requirements: - r-rcpparmadillo - r-rcppprogress run: - - 'bioconductor-biocparallel >=1.16.0,<1.17.0' - - 'bioconductor-singlecellexperiment >=1.4.0,<1.5.0' - - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' + - 'bioconductor-biocparallel >=1.18.0,<1.19.0' + - 'bioconductor-singlecellexperiment >=1.6.0,<1.7.0' + - 'bioconductor-summarizedexperiment >=1.14.0,<1.15.0' - r-base - r-bb - r-dosnow diff --git a/recipes/bioconductor-bayseq/meta.yaml b/recipes/bioconductor-bayseq/meta.yaml index 4e8cea35b8f55..2ee3df5cb469a 100644 --- a/recipes/bioconductor-bayseq/meta.yaml +++ b/recipes/bioconductor-bayseq/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "2.16.0" %} +{% set version = "2.18.0" %} {% set name = "baySeq" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 640b6b622f46258525fecc4304ffbac5 + md5: db957567c040f3240610ab767f1bb0c4 build: number: 0 rpaths: @@ -20,13 +20,13 @@ build: # Suggests: BiocStyle, BiocGenerics requirements: host: - - 'bioconductor-edger >=3.24.0,<3.25.0' - - 'bioconductor-genomicranges >=1.34.0,<1.35.0' + - 'bioconductor-edger >=3.26.0,<3.27.0' + - 'bioconductor-genomicranges >=1.36.0,<1.37.0' - r-abind - r-base run: - - 'bioconductor-edger >=3.24.0,<3.25.0' - - 'bioconductor-genomicranges >=1.34.0,<1.35.0' + - 'bioconductor-edger >=3.26.0,<3.27.0' + - 'bioconductor-genomicranges >=1.36.0,<1.37.0' - r-abind - r-base test: diff --git a/recipes/bioconductor-bbcanalyzer/meta.yaml b/recipes/bioconductor-bbcanalyzer/meta.yaml index 48e176fca2799..4d1b0f2cb1ecf 100644 --- a/recipes/bioconductor-bbcanalyzer/meta.yaml +++ b/recipes/bioconductor-bbcanalyzer/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.12.0" %} +{% set version = "1.14.0" %} {% set name = "BBCAnalyzer" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: a43ebce794b431b5600923809bbd81f8 + md5: 350d7307122713cb15aab5eee510c524 build: number: 0 rpaths: @@ -20,20 +20,20 @@ build: # Suggests: BSgenome.Hsapiens.UCSC.hg19 requirements: host: - - 'bioconductor-biostrings >=2.50.0,<2.51.0' - - 'bioconductor-genomicranges >=1.34.0,<1.35.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-rsamtools >=1.34.0,<1.35.0' - - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' - - 'bioconductor-variantannotation >=1.28.0,<1.29.0' + - 'bioconductor-biostrings >=2.52.0,<2.53.0' + - 'bioconductor-genomicranges >=1.36.0,<1.37.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-rsamtools >=2.0.0,<2.1.0' + - 'bioconductor-summarizedexperiment >=1.14.0,<1.15.0' + - 'bioconductor-variantannotation >=1.30.0,<1.31.0' - r-base run: - - 'bioconductor-biostrings >=2.50.0,<2.51.0' - - 'bioconductor-genomicranges >=1.34.0,<1.35.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-rsamtools >=1.34.0,<1.35.0' - - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' - - 'bioconductor-variantannotation >=1.28.0,<1.29.0' + - 'bioconductor-biostrings >=2.52.0,<2.53.0' + - 'bioconductor-genomicranges >=1.36.0,<1.37.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-rsamtools >=2.0.0,<2.1.0' + - 'bioconductor-summarizedexperiment >=1.14.0,<1.15.0' + - 'bioconductor-variantannotation >=1.30.0,<1.31.0' - r-base test: commands: diff --git a/recipes/bioconductor-bcellviper/meta.yaml b/recipes/bioconductor-bcellviper/meta.yaml index ed110e74888a6..38cea8f2bbf04 100644 --- a/recipes/bioconductor-bcellviper/meta.yaml +++ b/recipes/bioconductor-bcellviper/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.18.0" %} +{% set version = "1.20.0" %} {% set name = "bcellViper" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 9fb04cd65ec9c1bd6673bf0e53878c28 + md5: e0533eed79305a8a39db5051ba7fb9a5 build: number: 0 rpaths: @@ -19,12 +19,12 @@ build: noarch: generic requirements: host: - - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' - r-base run: - - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-bcellviper/post-link.sh b/recipes/bioconductor-bcellviper/post-link.sh index 0041861654664..992f568e3e754 100644 --- a/recipes/bioconductor-bcellviper/post-link.sh +++ b/recipes/bioconductor-bcellviper/post-link.sh @@ -1,11 +1,11 @@ #!/bin/bash -FN="bcellViper_1.18.0.tar.gz" +FN="bcellViper_1.20.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/experiment/src/contrib/bcellViper_1.18.0.tar.gz" - "https://bioarchive.galaxyproject.org/bcellViper_1.18.0.tar.gz" - "https://depot.galaxyproject.org/software/bioconductor-bcellviper/bioconductor-bcellviper_1.18.0_src_all.tar.gz" + "https://bioconductor.org/packages/3.9/data/experiment/src/contrib/bcellViper_1.20.0.tar.gz" + "https://bioarchive.galaxyproject.org/bcellViper_1.20.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-bcellviper/bioconductor-bcellviper_1.20.0_src_all.tar.gz" ) -MD5="9fb04cd65ec9c1bd6673bf0e53878c28" +MD5="e0533eed79305a8a39db5051ba7fb9a5" # Use a staging area in the conda dir rather than temp dirs, both to avoid # permission issues as well as to have things downloaded in a predictable @@ -16,7 +16,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-bcrank/meta.yaml b/recipes/bioconductor-bcrank/meta.yaml index 66fd7f0898de2..a0fabc013470e 100644 --- a/recipes/bioconductor-bcrank/meta.yaml +++ b/recipes/bioconductor-bcrank/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.44.0" %} +{% set version = "1.46.0" %} {% set name = "BCRANK" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 69400b8a8212a30ece13daec99343f3d + md5: 1e9103225b4ac26e8252a559d9622498 build: number: 0 rpaths: @@ -19,10 +19,10 @@ build: # Suggests: seqLogo requirements: host: - - 'bioconductor-biostrings >=2.50.0,<2.51.0' + - 'bioconductor-biostrings >=2.52.0,<2.53.0' - r-base run: - - 'bioconductor-biostrings >=2.50.0,<2.51.0' + - 'bioconductor-biostrings >=2.52.0,<2.53.0' - r-base build: - {{ compiler('c') }} diff --git a/recipes/bioconductor-bcseq/meta.yaml b/recipes/bioconductor-bcseq/meta.yaml index bbee61677cacb..8e02d1fda18c6 100644 --- a/recipes/bioconductor-bcseq/meta.yaml +++ b/recipes/bioconductor-bcseq/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.4.0" %} +{% set version = "1.6.0" %} {% set name = "bcSeq" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 045854c6264a3f8f1f80931333d0b477 + md5: 522909473d50d079a1b737a997d24414 build: number: 0 rpaths: @@ -19,12 +19,12 @@ build: # Suggests: knitr requirements: host: - - 'bioconductor-biostrings >=2.50.0,<2.51.0' + - 'bioconductor-biostrings >=2.52.0,<2.53.0' - r-base - r-matrix - 'r-rcpp >=0.12.12' run: - - 'bioconductor-biostrings >=2.50.0,<2.51.0' + - 'bioconductor-biostrings >=2.52.0,<2.53.0' - r-base - r-matrix - 'r-rcpp >=0.12.12' diff --git a/recipes/bioconductor-bdmmacorrect/meta.yaml b/recipes/bioconductor-bdmmacorrect/meta.yaml index 5f685a1b8bd7b..63edece99c271 100644 --- a/recipes/bioconductor-bdmmacorrect/meta.yaml +++ b/recipes/bioconductor-bdmmacorrect/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.0.0" %} +{% set version = "1.2.0" %} {% set name = "BDMMAcorrect" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 4a778faf834a0328b8493cbd3f3dd198 + md5: 08b2cfecf96d63befb59e857ad9b7bf4 build: number: 0 rpaths: @@ -19,7 +19,7 @@ build: # Suggests: knitr, rmarkdown, BiocGenerics requirements: host: - - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' + - 'bioconductor-summarizedexperiment >=1.14.0,<1.15.0' - r-ape - r-base - r-ellipse @@ -29,7 +29,7 @@ requirements: - r-rcppeigen - r-vegan run: - - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' + - 'bioconductor-summarizedexperiment >=1.14.0,<1.15.0' - r-ape - r-base - r-ellipse diff --git a/recipes/bioconductor-beachmat/meta.yaml b/recipes/bioconductor-beachmat/meta.yaml index fc8a61ea2c3e6..34d1dcf191fee 100644 --- a/recipes/bioconductor-beachmat/meta.yaml +++ b/recipes/bioconductor-beachmat/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.4.0" %} +{% set version = "2.0.0" %} {% set name = "beachmat" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,9 +10,9 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 41e56c5e6b9366f13fca35053c15fced + md5: c0c0ea857cbfc243f4350ef48527b6f5 build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ @@ -20,21 +20,13 @@ build: # SystemRequirements: C++11 requirements: host: - - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' - - 'bioconductor-delayedarray >=0.8.0,<0.9.0' - - 'bioconductor-hdf5array >=1.10.0,<1.11.0' - - 'bioconductor-rhdf5 >=2.26.0,<2.27.0' - - 'bioconductor-rhdf5lib >=1.4.0,<1.5.0' + - 'bioconductor-biocgenerics >=0.30.0,<0.31.0' + - 'bioconductor-delayedarray >=0.10.0,<0.11.0' - r-base - - 'r-rcpp >=0.12.14' run: - - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' - - 'bioconductor-delayedarray >=0.8.0,<0.9.0' - - 'bioconductor-hdf5array >=1.10.0,<1.11.0' - - 'bioconductor-rhdf5 >=2.26.0,<2.27.0' - - 'bioconductor-rhdf5lib >=1.4.0,<1.5.0' + - 'bioconductor-biocgenerics >=0.30.0,<0.31.0' + - 'bioconductor-delayedarray >=0.10.0,<0.11.0' - r-base - - 'r-rcpp >=0.12.14' build: - {{ compiler('c') }} - {{ compiler('cxx') }} @@ -45,7 +37,7 @@ test: about: home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: GPL-3 - summary: 'Provides a consistent C++ class interface for a variety of commonly used matrix types, including sparse and HDF5-backed matrices.' + summary: 'Provides a consistent C++ class interface for reading from and writing data to a variety of commonly used matrix types. Ordinary matrices and several sparse/dense Matrix classes are directly supported, third-party S4 classes may be supported by external linkage, while all other matrices are handled by DelayedArray block processing.' extra: parent_recipe: name: bioconductor-beachmat diff --git a/recipes/bioconductor-beadarray/meta.yaml b/recipes/bioconductor-beadarray/meta.yaml index 11b11e169407a..0f8f7cf8e364b 100644 --- a/recipes/bioconductor-beadarray/meta.yaml +++ b/recipes/bioconductor-beadarray/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "2.32.0" %} +{% set version = "2.34.0" %} {% set name = "beadarray" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 3a4e97e6601c7dd23ecc9581624fe74e + md5: 4f03d3bd7e45479f800e943ef7e4384d build: number: 0 rpaths: @@ -19,28 +19,30 @@ build: # Suggests: lumi, vsn, affy, hwriter, beadarrayExampleData, illuminaHumanv3.db, gridExtra, BiocStyle, TxDb.Hsapiens.UCSC.hg19.knownGene, ggbio, Nozzle.R1, knitr requirements: host: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' - - 'bioconductor-beaddatapackr >=1.34.0,<1.35.0' - - 'bioconductor-biobase >=2.42.0,<2.43.0' - - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' - - 'bioconductor-genomicranges >=1.34.0,<1.35.0' - - 'bioconductor-illuminaio >=0.24.0,<0.25.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-limma >=3.38.0,<3.39.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' + - 'bioconductor-beaddatapackr >=1.36.0,<1.37.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' + - 'bioconductor-biocgenerics >=0.30.0,<0.31.0' + - 'bioconductor-genomicranges >=1.36.0,<1.37.0' + - 'bioconductor-illuminaio >=0.26.0,<0.27.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-limma >=3.40.0,<3.41.0' - r-base - r-ggplot2 + - r-hexbin - r-reshape2 run: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' - - 'bioconductor-beaddatapackr >=1.34.0,<1.35.0' - - 'bioconductor-biobase >=2.42.0,<2.43.0' - - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' - - 'bioconductor-genomicranges >=1.34.0,<1.35.0' - - 'bioconductor-illuminaio >=0.24.0,<0.25.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-limma >=3.38.0,<3.39.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' + - 'bioconductor-beaddatapackr >=1.36.0,<1.37.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' + - 'bioconductor-biocgenerics >=0.30.0,<0.31.0' + - 'bioconductor-genomicranges >=1.36.0,<1.37.0' + - 'bioconductor-illuminaio >=0.26.0,<0.27.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-limma >=3.40.0,<3.41.0' - r-base - r-ggplot2 + - r-hexbin - r-reshape2 build: - {{ compiler('c') }} @@ -50,8 +52,8 @@ test: - '$R -e "library(''{{ name }}'')"' about: home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: GPL-2 - summary: 'The package is able to read bead-level data (raw TIFFs and text files) output by BeadScan as well as bead-summary data from BeadStudio. Methods for quality assessment and low-level analysis are provided.' + license: 'MIT + file LICENSE' + summary: 'The package is able to read bead-level data (raw TIFFs and text files) output by BeadScan as well as bead-summary data from BeadStudio. Methods for quality assessment and low-level analysis are provided.' extra: identifiers: - biotools:beadarray diff --git a/recipes/bioconductor-beadarrayexampledata/meta.yaml b/recipes/bioconductor-beadarrayexampledata/meta.yaml index 182c2f952bc11..34480b138460b 100644 --- a/recipes/bioconductor-beadarrayexampledata/meta.yaml +++ b/recipes/bioconductor-beadarrayexampledata/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.20.0" %} +{% set version = "1.22.0" %} {% set name = "beadarrayExampleData" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 256c9a9bb54f750aba53708c59e3c132 + md5: ade87a63114d99fd5a48b24d7b08bfbb build: number: 0 rpaths: @@ -19,14 +19,14 @@ build: noarch: generic requirements: host: - - 'bioconductor-beadarray >=2.32.0,<2.33.0' - - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-beadarray >=2.34.0,<2.35.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' - r-base run: - - 'bioconductor-beadarray >=2.32.0,<2.33.0' - - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-beadarray >=2.34.0,<2.35.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-beadarrayexampledata/post-link.sh b/recipes/bioconductor-beadarrayexampledata/post-link.sh index eff5b62b36d65..6aaeecbebdee3 100644 --- a/recipes/bioconductor-beadarrayexampledata/post-link.sh +++ b/recipes/bioconductor-beadarrayexampledata/post-link.sh @@ -1,11 +1,11 @@ #!/bin/bash -FN="beadarrayExampleData_1.20.0.tar.gz" +FN="beadarrayExampleData_1.22.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/experiment/src/contrib/beadarrayExampleData_1.20.0.tar.gz" - "https://bioarchive.galaxyproject.org/beadarrayExampleData_1.20.0.tar.gz" - "https://depot.galaxyproject.org/software/bioconductor-beadarrayexampledata/bioconductor-beadarrayexampledata_1.20.0_src_all.tar.gz" + "https://bioconductor.org/packages/3.9/data/experiment/src/contrib/beadarrayExampleData_1.22.0.tar.gz" + "https://bioarchive.galaxyproject.org/beadarrayExampleData_1.22.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-beadarrayexampledata/bioconductor-beadarrayexampledata_1.22.0_src_all.tar.gz" ) -MD5="256c9a9bb54f750aba53708c59e3c132" +MD5="ade87a63114d99fd5a48b24d7b08bfbb" # Use a staging area in the conda dir rather than temp dirs, both to avoid # permission issues as well as to have things downloaded in a predictable @@ -16,7 +16,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-beadarraysnp/meta.yaml b/recipes/bioconductor-beadarraysnp/meta.yaml index 5b058e50cb783..48b24585e4ff5 100644 --- a/recipes/bioconductor-beadarraysnp/meta.yaml +++ b/recipes/bioconductor-beadarraysnp/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.48.0" %} +{% set version = "1.50.0" %} {% set name = "beadarraySNP" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 6022599758a0d8487f62868a6b0895ad + md5: be8d5f6c4373eb5b19bef26fe6f9fb48 build: number: 0 rpaths: @@ -20,12 +20,12 @@ build: # Suggests: aCGH, affy, limma, snapCGH, beadarray, DNAcopy requirements: host: - - 'bioconductor-biobase >=2.42.0,<2.43.0' - - 'bioconductor-quantsmooth >=1.48.0,<1.49.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' + - 'bioconductor-quantsmooth >=1.50.0,<1.51.0' - r-base run: - - 'bioconductor-biobase >=2.42.0,<2.43.0' - - 'bioconductor-quantsmooth >=1.48.0,<1.49.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' + - 'bioconductor-quantsmooth >=1.50.0,<1.51.0' - r-base test: commands: diff --git a/recipes/bioconductor-beadarrayusecases/meta.yaml b/recipes/bioconductor-beadarrayusecases/meta.yaml index a9d42c154e973..f752203c0e502 100644 --- a/recipes/bioconductor-beadarrayusecases/meta.yaml +++ b/recipes/bioconductor-beadarrayusecases/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.20.0" %} +{% set version = "1.22.0" %} {% set name = "BeadArrayUseCases" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: aa5309f7583a03c59235ce459a749cd6 + md5: f137cb510837fa607e144c2c1290d846 build: number: 0 rpaths: @@ -20,16 +20,16 @@ build: # Suggests: Biostrings, GenomicRanges, illuminaHumanv1.db, illuminaHumanv2.db, illuminaHumanv3.db requirements: host: - - 'bioconductor-beadarray >=2.32.0,<2.33.0' - - 'bioconductor-geoquery >=2.50.0,<2.51.0' - - 'bioconductor-limma >=3.38.0,<3.39.0' + - 'bioconductor-beadarray >=2.34.0,<2.35.0' + - 'bioconductor-geoquery >=2.52.0,<2.53.0' + - 'bioconductor-limma >=3.40.0,<3.41.0' - r-base run: - - 'bioconductor-beadarray >=2.32.0,<2.33.0' - - 'bioconductor-geoquery >=2.50.0,<2.51.0' - - 'bioconductor-limma >=3.38.0,<3.39.0' + - 'bioconductor-beadarray >=2.34.0,<2.35.0' + - 'bioconductor-geoquery >=2.52.0,<2.53.0' + - 'bioconductor-limma >=3.40.0,<3.41.0' - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-beadarrayusecases/post-link.sh b/recipes/bioconductor-beadarrayusecases/post-link.sh index c20ea3b397810..aa43710cb94e7 100644 --- a/recipes/bioconductor-beadarrayusecases/post-link.sh +++ b/recipes/bioconductor-beadarrayusecases/post-link.sh @@ -1,11 +1,11 @@ #!/bin/bash -FN="BeadArrayUseCases_1.20.0.tar.gz" +FN="BeadArrayUseCases_1.22.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/experiment/src/contrib/BeadArrayUseCases_1.20.0.tar.gz" - "https://bioarchive.galaxyproject.org/BeadArrayUseCases_1.20.0.tar.gz" - "https://depot.galaxyproject.org/software/bioconductor-beadarrayusecases/bioconductor-beadarrayusecases_1.20.0_src_all.tar.gz" + "https://bioconductor.org/packages/3.9/data/experiment/src/contrib/BeadArrayUseCases_1.22.0.tar.gz" + "https://bioarchive.galaxyproject.org/BeadArrayUseCases_1.22.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-beadarrayusecases/bioconductor-beadarrayusecases_1.22.0_src_all.tar.gz" ) -MD5="aa5309f7583a03c59235ce459a749cd6" +MD5="f137cb510837fa607e144c2c1290d846" # Use a staging area in the conda dir rather than temp dirs, both to avoid # permission issues as well as to have things downloaded in a predictable @@ -16,7 +16,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-beaddatapackr/meta.yaml b/recipes/bioconductor-beaddatapackr/meta.yaml index 9c19af64948bc..6f516ce9d6c03 100644 --- a/recipes/bioconductor-beaddatapackr/meta.yaml +++ b/recipes/bioconductor-beaddatapackr/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.34.0" %} +{% set version = "1.36.0" %} {% set name = "BeadDataPackR" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 0e53726240d897ac98a7fc3044bc198e + md5: caf869b373fa5fbd3820f7760d2cf84f build: number: 0 rpaths: diff --git a/recipes/bioconductor-bearscc/meta.yaml b/recipes/bioconductor-bearscc/meta.yaml index 1b25ad37e2bea..92d070aded0cc 100644 --- a/recipes/bioconductor-bearscc/meta.yaml +++ b/recipes/bioconductor-bearscc/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.2.0" %} +{% set version = "1.4.0" %} {% set name = "BEARscc" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: fbc3fa284b714e75f62395ac202b9ac3 + md5: 74b837640990a0c334f1ec70bc269165 build: number: 0 rpaths: @@ -20,12 +20,12 @@ build: # Suggests: testthat, cowplot, knitr, rmarkdown, BiocStyle, NMF requirements: host: - - 'bioconductor-singlecellexperiment >=1.4.0,<1.5.0' + - 'bioconductor-singlecellexperiment >=1.6.0,<1.7.0' - r-base - r-data.table - r-ggplot2 run: - - 'bioconductor-singlecellexperiment >=1.4.0,<1.5.0' + - 'bioconductor-singlecellexperiment >=1.6.0,<1.7.0' - r-base - r-data.table - r-ggplot2 diff --git a/recipes/bioconductor-beat/meta.yaml b/recipes/bioconductor-beat/meta.yaml index 6ee392b701a70..aead314d4f9c6 100644 --- a/recipes/bioconductor-beat/meta.yaml +++ b/recipes/bioconductor-beat/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.20.1" %} +{% set version = "1.22.0" %} {% set name = "BEAT" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 896ce4cb9595b2d7455ded6750f5fa90 + md5: 5ca0f1e34e04fd2c3293960760fd7b80 build: number: 0 rpaths: @@ -19,16 +19,16 @@ build: noarch: generic requirements: host: - - 'bioconductor-biostrings >=2.50.0,<2.51.0' - - 'bioconductor-bsgenome >=1.50.0,<1.51.0' - - 'bioconductor-genomicranges >=1.34.0,<1.35.0' - - 'bioconductor-shortread >=1.40.0,<1.41.0' + - 'bioconductor-biostrings >=2.52.0,<2.53.0' + - 'bioconductor-bsgenome >=1.52.0,<1.53.0' + - 'bioconductor-genomicranges >=1.36.0,<1.37.0' + - 'bioconductor-shortread >=1.42.0,<1.43.0' - r-base run: - - 'bioconductor-biostrings >=2.50.0,<2.51.0' - - 'bioconductor-bsgenome >=1.50.0,<1.51.0' - - 'bioconductor-genomicranges >=1.34.0,<1.35.0' - - 'bioconductor-shortread >=1.40.0,<1.41.0' + - 'bioconductor-biostrings >=2.52.0,<2.53.0' + - 'bioconductor-bsgenome >=1.52.0,<1.53.0' + - 'bioconductor-genomicranges >=1.36.0,<1.37.0' + - 'bioconductor-shortread >=1.42.0,<1.43.0' - r-base test: commands: diff --git a/recipes/bioconductor-beclear/meta.yaml b/recipes/bioconductor-beclear/meta.yaml index f6074d3950770..ae725fe0536ad 100644 --- a/recipes/bioconductor-beclear/meta.yaml +++ b/recipes/bioconductor-beclear/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.14.0" %} +{% set version = "2.0.0" %} {% set name = "BEclear" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,36 +10,42 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: f7d173d8b8e409c822746bced7049a1e + md5: 92515d8f34e66403c62df8b192d0dbdf build: number: 0 rpaths: - lib/R/lib/ - lib/ - noarch: generic -# Suggests: testthat +# Suggests: testthat, BiocStyle, knitr, rmarkdown, pander +# SystemRequirements: C++11 requirements: host: - - 'bioconductor-biocparallel >=1.16.0,<1.17.0' + - 'bioconductor-biocparallel >=1.18.0,<1.19.0' - r-base - 'r-data.table >=1.11.8' - r-futile.logger - r-matrix + - r-rcpp - r-rdpack run: - - 'bioconductor-biocparallel >=1.16.0,<1.17.0' + - 'bioconductor-biocparallel >=1.18.0,<1.19.0' - r-base - 'r-data.table >=1.11.8' - r-futile.logger - r-matrix + - r-rcpp - r-rdpack + build: + - {{ compiler('c') }} + - {{ compiler('cxx') }} + - make test: commands: - '$R -e "library(''{{ name }}'')"' about: home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: GPL-2 - summary: 'Provides some functions to detect and correct for batch effects in DNA methylation data. The core function is based on latent factor models and can also be used to predict missing values in any other matrix containing real numbers.' + license: GPL-3 + summary: 'Provides functions to detect and correct for batch effects in DNA methylation data. The core function is based on latent factor models and can also be used to predict missing values in any other matrix containing real numbers.' extra: identifiers: - biotools:beclear diff --git a/recipes/bioconductor-beta7/meta.yaml b/recipes/bioconductor-beta7/meta.yaml index c7f3bbe7ba680..370ef1fc81ed6 100644 --- a/recipes/bioconductor-beta7/meta.yaml +++ b/recipes/bioconductor-beta7/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.20.0" %} +{% set version = "1.22.0" %} {% set name = "beta7" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,21 +10,21 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 135330c43b9aa93aedc4559f15e83c76 + md5: 60b008e68244a7e355d290ac76aa0b04 build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ noarch: generic requirements: host: - - 'bioconductor-marray >=1.60.0,<1.61.0' + - 'bioconductor-marray >=1.62.0,<1.63.0' - r-base run: - - 'bioconductor-marray >=1.60.0,<1.61.0' + - 'bioconductor-marray >=1.62.0,<1.63.0' - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-beta7/post-link.sh b/recipes/bioconductor-beta7/post-link.sh index 92587f096045c..f979e87954980 100644 --- a/recipes/bioconductor-beta7/post-link.sh +++ b/recipes/bioconductor-beta7/post-link.sh @@ -1,11 +1,11 @@ #!/bin/bash -FN="beta7_1.20.0.tar.gz" +FN="beta7_1.22.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/experiment/src/contrib/beta7_1.20.0.tar.gz" - "https://bioarchive.galaxyproject.org/beta7_1.20.0.tar.gz" - "https://depot.galaxyproject.org/software/bioconductor-beta7/bioconductor-beta7_1.20.0_src_all.tar.gz" + "https://bioconductor.org/packages/3.9/data/experiment/src/contrib/beta7_1.22.0.tar.gz" + "https://bioarchive.galaxyproject.org/beta7_1.22.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-beta7/bioconductor-beta7_1.22.0_src_all.tar.gz" ) -MD5="135330c43b9aa93aedc4559f15e83c76" +MD5="60b008e68244a7e355d290ac76aa0b04" # Use a staging area in the conda dir rather than temp dirs, both to avoid # permission issues as well as to have things downloaded in a predictable @@ -16,7 +16,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-bgafun/meta.yaml b/recipes/bioconductor-bgafun/meta.yaml index 098b8dd39cb5b..013addceb64ef 100644 --- a/recipes/bioconductor-bgafun/meta.yaml +++ b/recipes/bioconductor-bgafun/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.44.0" %} +{% set version = "1.46.0" %} {% set name = "bgafun" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 592bfaec5b579e3e9b2cd37afb26e9d3 + md5: 62e6be628d01e80d2193cd34d29602ac build: number: 0 rpaths: @@ -19,12 +19,12 @@ build: noarch: generic requirements: host: - - 'bioconductor-made4 >=1.56.0,<1.57.0' + - 'bioconductor-made4 >=1.58.0,<1.59.0' - r-ade4 - r-base - r-seqinr run: - - 'bioconductor-made4 >=1.56.0,<1.57.0' + - 'bioconductor-made4 >=1.58.0,<1.59.0' - r-ade4 - r-base - r-seqinr diff --git a/recipes/bioconductor-bgeedb/meta.yaml b/recipes/bioconductor-bgeedb/meta.yaml index 515facb9d1023..a2463d484255d 100644 --- a/recipes/bioconductor-bgeedb/meta.yaml +++ b/recipes/bioconductor-bgeedb/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "2.8.0" %} +{% set version = "2.10.0" %} {% set name = "BgeeDB" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 124a63f929213a6fc1b30f964cf3e1b5 + md5: 4da20080e790bd0121458d873a9d525b build: number: 0 rpaths: @@ -20,9 +20,9 @@ build: # Suggests: knitr, BiocStyle, testthat, rmarkdown requirements: host: - - 'bioconductor-biobase >=2.42.0,<2.43.0' - - 'bioconductor-graph >=1.60.0,<1.61.0' - - 'bioconductor-topgo >=2.34.0,<2.35.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' + - 'bioconductor-graph >=1.62.0,<1.63.0' + - 'bioconductor-topgo >=2.36.0,<2.37.0' - r-base - r-data.table - r-digest @@ -30,9 +30,9 @@ requirements: - r-rcurl - r-tidyr run: - - 'bioconductor-biobase >=2.42.0,<2.43.0' - - 'bioconductor-graph >=1.60.0,<1.61.0' - - 'bioconductor-topgo >=2.34.0,<2.35.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' + - 'bioconductor-graph >=1.62.0,<1.63.0' + - 'bioconductor-topgo >=2.36.0,<2.37.0' - r-base - r-data.table - r-digest diff --git a/recipes/bioconductor-bgmix/meta.yaml b/recipes/bioconductor-bgmix/meta.yaml index f85866820e5b6..9fa64a6ed20f8 100644 --- a/recipes/bioconductor-bgmix/meta.yaml +++ b/recipes/bioconductor-bgmix/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.42.0" %} +{% set version = "1.44.0" %} {% set name = "BGmix" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 0fe9456585e4fa7c1ef2e87e2c93fd26 + md5: ed5d6b4d0fdcbc4b26fa57154d9e8cba build: number: 0 rpaths: diff --git a/recipes/bioconductor-bgx/meta.yaml b/recipes/bioconductor-bgx/meta.yaml index d8fbcef88d5f8..e110c46fcb9c1 100644 --- a/recipes/bioconductor-bgx/meta.yaml +++ b/recipes/bioconductor-bgx/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.48.1" %} +{% set version = "1.50.0" %} {% set name = "bgx" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 16b83dd458322f39c457d82c63b37602 + md5: 0249dde7f7644bf8aee843004a9deb93 build: number: 0 rpaths: @@ -19,15 +19,15 @@ build: # Suggests: affydata, hgu95av2cdf requirements: host: - - 'bioconductor-affy >=1.60.0,<1.61.0' - - 'bioconductor-biobase >=2.42.0,<2.43.0' - - 'bioconductor-gcrma >=2.54.0,<2.55.0' + - 'bioconductor-affy >=1.62.0,<1.63.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' + - 'bioconductor-gcrma >=2.56.0,<2.57.0' - r-base - 'r-rcpp >=0.11.0' run: - - 'bioconductor-affy >=1.60.0,<1.61.0' - - 'bioconductor-biobase >=2.42.0,<2.43.0' - - 'bioconductor-gcrma >=2.54.0,<2.55.0' + - 'bioconductor-affy >=1.62.0,<1.63.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' + - 'bioconductor-gcrma >=2.56.0,<2.57.0' - r-base - 'r-rcpp >=0.11.0' build: diff --git a/recipes/bioconductor-bhc/meta.yaml b/recipes/bioconductor-bhc/meta.yaml index c5e47b1b9c089..5e992b480beb2 100644 --- a/recipes/bioconductor-bhc/meta.yaml +++ b/recipes/bioconductor-bhc/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.34.0" %} +{% set version = "1.36.0" %} {% set name = "BHC" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 7779188efbd83088fc32df257617e208 + md5: 068199f15d449715b3a74a4065f548ec build: number: 0 rpaths: diff --git a/recipes/bioconductor-bicare/meta.yaml b/recipes/bioconductor-bicare/meta.yaml index f485716d8c4da..2070e4b3b0966 100644 --- a/recipes/bioconductor-bicare/meta.yaml +++ b/recipes/bioconductor-bicare/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.40.0" %} +{% set version = "1.42.0" %} {% set name = "BicARE" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 90878d870f7ec218fc9eea9fe9b5d839 + md5: db034e853c41bbe8c9bbd029b4810082 build: number: 0 rpaths: @@ -18,14 +18,14 @@ build: - lib/ requirements: host: - - 'bioconductor-biobase >=2.42.0,<2.43.0' - - 'bioconductor-gseabase >=1.44.0,<1.45.0' - - 'bioconductor-multtest >=2.38.0,<2.39.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' + - 'bioconductor-gseabase >=1.46.0,<1.47.0' + - 'bioconductor-multtest >=2.40.0,<2.41.0' - r-base run: - - 'bioconductor-biobase >=2.42.0,<2.43.0' - - 'bioconductor-gseabase >=1.44.0,<1.45.0' - - 'bioconductor-multtest >=2.38.0,<2.39.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' + - 'bioconductor-gseabase >=1.46.0,<1.47.0' + - 'bioconductor-multtest >=2.40.0,<2.41.0' - r-base build: - {{ compiler('c') }} diff --git a/recipes/bioconductor-bifet/meta.yaml b/recipes/bioconductor-bifet/meta.yaml index eb7ec3eea3dd1..49d0011c5be37 100644 --- a/recipes/bioconductor-bifet/meta.yaml +++ b/recipes/bioconductor-bifet/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.2.0" %} +{% set version = "1.4.0" %} {% set name = "BiFET" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: a4fb307fab64ae9ffcf38919bb865d72 + md5: 9d5de94f76d910215de96b965bc1eaab build: number: 0 rpaths: @@ -20,11 +20,11 @@ build: # Suggests: testthat, knitr requirements: host: - - 'bioconductor-genomicranges >=1.34.0,<1.35.0' + - 'bioconductor-genomicranges >=1.36.0,<1.37.0' - r-base - r-poibin run: - - 'bioconductor-genomicranges >=1.34.0,<1.35.0' + - 'bioconductor-genomicranges >=1.36.0,<1.37.0' - r-base - r-poibin test: diff --git a/recipes/bioconductor-biggr/meta.yaml b/recipes/bioconductor-biggr/meta.yaml index 365e9d7b0972c..13a50c83b636d 100644 --- a/recipes/bioconductor-biggr/meta.yaml +++ b/recipes/bioconductor-biggr/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.18.0" %} +{% set version = "1.20.0" %} {% set name = "BiGGR" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: c0bbb2a19b06bc77e802c9f131b5bd0e + md5: b10464c305eafcdb9f52d932a36f0382 build: number: 0 rpaths: @@ -19,17 +19,17 @@ build: noarch: generic requirements: host: - - 'bioconductor-hyperdraw >=1.34.0,<1.35.0' - - 'bioconductor-hypergraph >=1.54.0,<1.55.0' - - 'bioconductor-rsbml >=2.40.0,<2.41.0' + - 'bioconductor-hyperdraw >=1.36.0,<1.37.0' + - 'bioconductor-hypergraph >=1.56.0,<1.57.0' + - 'bioconductor-rsbml >=2.42.0,<2.43.0' - r-base - r-lim - r-limsolve - r-stringr run: - - 'bioconductor-hyperdraw >=1.34.0,<1.35.0' - - 'bioconductor-hypergraph >=1.54.0,<1.55.0' - - 'bioconductor-rsbml >=2.40.0,<2.41.0' + - 'bioconductor-hyperdraw >=1.36.0,<1.37.0' + - 'bioconductor-hypergraph >=1.56.0,<1.57.0' + - 'bioconductor-rsbml >=2.42.0,<2.43.0' - r-base - r-lim - r-limsolve diff --git a/recipes/bioconductor-bigmelon/meta.yaml b/recipes/bioconductor-bigmelon/meta.yaml index 6ad31c415ea85..4547ac6bb9c87 100644 --- a/recipes/bioconductor-bigmelon/meta.yaml +++ b/recipes/bioconductor-bigmelon/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.8.0" %} +{% set version = "1.10.0" %} {% set name = "bigmelon" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 3b7456161c012f3441cffda28e3ce9ca + md5: fb80cb687a5702ad151f2217b577da3e build: number: 0 rpaths: @@ -20,22 +20,22 @@ build: # Suggests: BiocGenerics, BiocStyle, minfiData, parallel, IlluminaHumanMethylation450kanno.ilmn12.hg19, IlluminaHumanMethylationEPICanno.ilm10b2.hg19, bumphunter requirements: host: - - 'bioconductor-biobase >=2.42.0,<2.43.0' - - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' - - 'bioconductor-gdsfmt >=1.18.0,<1.19.0' - - 'bioconductor-geoquery >=2.50.0,<2.51.0' - - 'bioconductor-methylumi >=2.28.0,<2.29.0' - - 'bioconductor-minfi >=1.28.0,<1.29.0' - - 'bioconductor-watermelon >=1.26.0,<1.27.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' + - 'bioconductor-biocgenerics >=0.30.0,<0.31.0' + - 'bioconductor-gdsfmt >=1.20.0,<1.21.0' + - 'bioconductor-geoquery >=2.52.0,<2.53.0' + - 'bioconductor-methylumi >=2.30.0,<2.31.0' + - 'bioconductor-minfi >=1.30.0,<1.31.0' + - 'bioconductor-watermelon >=1.28.0,<1.29.0' - r-base run: - - 'bioconductor-biobase >=2.42.0,<2.43.0' - - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' - - 'bioconductor-gdsfmt >=1.18.0,<1.19.0' - - 'bioconductor-geoquery >=2.50.0,<2.51.0' - - 'bioconductor-methylumi >=2.28.0,<2.29.0' - - 'bioconductor-minfi >=1.28.0,<1.29.0' - - 'bioconductor-watermelon >=1.26.0,<1.27.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' + - 'bioconductor-biocgenerics >=0.30.0,<0.31.0' + - 'bioconductor-gdsfmt >=1.20.0,<1.21.0' + - 'bioconductor-geoquery >=2.52.0,<2.53.0' + - 'bioconductor-methylumi >=2.30.0,<2.31.0' + - 'bioconductor-minfi >=1.30.0,<1.31.0' + - 'bioconductor-watermelon >=1.28.0,<1.29.0' - r-base test: commands: diff --git a/recipes/bioconductor-bigmemoryextras/meta.yaml b/recipes/bioconductor-bigmemoryextras/meta.yaml index c30746165c20e..57b9f1bff4666 100644 --- a/recipes/bioconductor-bigmemoryextras/meta.yaml +++ b/recipes/bioconductor-bigmemoryextras/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.30.0" %} +{% set version = "1.32.0" %} {% set name = "bigmemoryExtras" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: fea9a5d5915ed5832554e56d06b8389a + md5: f8f4f43d3318d5118883e89803205d49 build: number: 0 rpaths: diff --git a/recipes/bioconductor-bigpint/build.sh b/recipes/bioconductor-bigpint/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-bigpint/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-bigpint/meta.yaml b/recipes/bioconductor-bigpint/meta.yaml new file mode 100644 index 0000000000000..200e6389d5b9c --- /dev/null +++ b/recipes/bioconductor-bigpint/meta.yaml @@ -0,0 +1,65 @@ +{% set version = "1.0.0" %} +{% set name = "bigPint" %} +{% set bioc = "3.9" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: e088f5debc65a3f6b74f6f47b9949bc3 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: BiocGenerics (>= 0.29.1), data.table (>= 1.11.8), EDASeq (>= 2.14.0), edgeR (>= 3.22.2), gtools (>= 3.5.0), knitr (>= 1.13), matrixStats (>= 0.53.1), rmarkdown (>= 1.10), roxygen2 (>= 3.0.0), RUnit (>= 0.4.32), tibble (>= 1.4.2), +requirements: + host: + - r-base + - 'r-dplyr >=0.7.2' + - 'r-ggally >=1.3.2' + - 'r-ggplot2 >=2.2.1' + - 'r-gridextra >=2.3' + - 'r-hexbin >=1.27.1' + - 'r-hmisc >=4.0.3' + - 'r-htmlwidgets >=0.9' + - 'r-plotly >=4.7.1' + - 'r-plyr >=1.8.4' + - 'r-rcolorbrewer >=1.1.2' + - 'r-reshape >=0.8.7' + - 'r-shiny >=1.0.5' + - 'r-shinycssloaders >=0.2.0' + - 'r-shinydashboard >=0.6.1' + - 'r-stringr >=1.3.1' + - 'r-tidyr >=0.7.0' + run: + - r-base + - 'r-dplyr >=0.7.2' + - 'r-ggally >=1.3.2' + - 'r-ggplot2 >=2.2.1' + - 'r-gridextra >=2.3' + - 'r-hexbin >=1.27.1' + - 'r-hmisc >=4.0.3' + - 'r-htmlwidgets >=0.9' + - 'r-plotly >=4.7.1' + - 'r-plyr >=1.8.4' + - 'r-rcolorbrewer >=1.1.2' + - 'r-reshape >=0.8.7' + - 'r-shiny >=1.0.5' + - 'r-shinycssloaders >=0.2.0' + - 'r-shinydashboard >=0.6.1' + - 'r-stringr >=1.3.1' + - 'r-tidyr >=0.7.0' +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: GPL-3 + summary: 'Methods for visualizing large multivariate datasets using static and interactive scatterplot matrices, parallel coordinate plots, volcano plots, and litre plots. Includes examples for visualizing RNA-sequencing datasets and differentially expressed genes.' + diff --git a/recipes/bioconductor-bioassayr/meta.yaml b/recipes/bioconductor-bioassayr/meta.yaml index d7e9ce545310d..e31b560d1248a 100644 --- a/recipes/bioconductor-bioassayr/meta.yaml +++ b/recipes/bioconductor-bioassayr/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.20.1" %} +{% set version = "1.22.0" %} {% set name = "bioassayR" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: ff00435c3bf6e16fa6e865f4e33d8154f2a22c06608769569706f361ebf4c1fd + md5: 78c3d0f8997a2ad15ca8cce89222bc9c build: number: 0 rpaths: @@ -20,8 +20,8 @@ build: # Suggests: BiocStyle, RCurl, biomaRt, cellHTS2, knitr, knitcitations, knitrBootstrap, testthat, ggplot2, rmarkdown requirements: host: - - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' - - 'bioconductor-chemminer >=3.34.0,<3.35.0' + - 'bioconductor-biocgenerics >=0.30.0,<0.31.0' + - 'bioconductor-chemminer >=3.36.0,<3.37.0' - r-base - 'r-dbi >=0.3.1' - r-matrix @@ -29,8 +29,8 @@ requirements: - 'r-rsqlite >=1.0.0' - r-xml run: - - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' - - 'bioconductor-chemminer >=3.34.0,<3.35.0' + - 'bioconductor-biocgenerics >=0.30.0,<0.31.0' + - 'bioconductor-chemminer >=3.36.0,<3.37.0' - r-base - 'r-dbi >=0.3.1' - r-matrix diff --git a/recipes/bioconductor-biobase/meta.yaml b/recipes/bioconductor-biobase/meta.yaml index 8f278175c02dc..cb74b3d2294fe 100644 --- a/recipes/bioconductor-biobase/meta.yaml +++ b/recipes/bioconductor-biobase/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "2.42.0" %} +{% set version = "2.44.0" %} {% set name = "Biobase" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,19 +10,19 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: a7137201a04682443ec0a418309e006b + md5: 2f8f240f9146ececcd4e297c86705ae0 build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ # Suggests: tools, tkWidgets, ALL, RUnit, golubEsets requirements: host: - - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' + - 'bioconductor-biocgenerics >=0.30.0,<0.31.0' - r-base run: - - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' + - 'bioconductor-biocgenerics >=0.30.0,<0.31.0' - r-base build: - {{ compiler('c') }} diff --git a/recipes/bioconductor-biobroom/meta.yaml b/recipes/bioconductor-biobroom/meta.yaml index dde88b982a020..252e79d2b8196 100644 --- a/recipes/bioconductor-biobroom/meta.yaml +++ b/recipes/bioconductor-biobroom/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.14.0" %} +{% set version = "1.16.0" %} {% set name = "biobroom" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 8e8a35fc42f28c672f6f5b8b144cc2b1 + md5: 4541701fe3cbd912a008c0254029b54a build: number: 0 rpaths: @@ -20,13 +20,13 @@ build: # Suggests: limma, DESeq2, airway, ggplot2, plyr, GenomicRanges, testthat, magrittr, edgeR, qvalue, knitr, data.table, MSnbase, SummarizedExperiment requirements: host: - - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' - r-base - r-broom - r-dplyr - r-tidyr run: - - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' - r-base - r-broom - r-dplyr diff --git a/recipes/bioconductor-biocancer/meta.yaml b/recipes/bioconductor-biocancer/meta.yaml index 6cb7c1cb4add0..2eca818fc1f9a 100644 --- a/recipes/bioconductor-biocancer/meta.yaml +++ b/recipes/bioconductor-biocancer/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.10.0" %} +{% set version = "1.12.0" %} {% set name = "bioCancer" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 9365942b5cc542b374bb471501a93e49 + md5: ff8c79305222e25cf02716f9ceb953e6 build: number: 0 rpaths: @@ -20,14 +20,14 @@ build: # Suggests: BiocStyle, rmarkdown, knitr, testthat (>= 0.10.0) requirements: host: - - 'bioconductor-annotationfuncs >=1.32.0,<1.33.0' - - 'bioconductor-biobase >=2.42.0,<2.43.0' - - 'bioconductor-clusterprofiler >=3.10.0,<3.11.0' - - 'bioconductor-dose >=3.8.0,<3.9.0' - - 'bioconductor-genetclassifier >=1.22.0,<1.23.0' - - 'bioconductor-org.hs.eg.db >=3.7.0,<3.8.0' - - 'bioconductor-reactome.db >=1.66.0,<1.67.0' - - 'bioconductor-reactomepa >=1.26.0,<1.27.0' + - 'bioconductor-annotationfuncs >=1.34.0,<1.35.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' + - 'bioconductor-clusterprofiler >=3.12.0,<3.13.0' + - 'bioconductor-dose >=3.10.0,<3.11.0' + - 'bioconductor-genetclassifier >=1.24.0,<1.25.0' + - 'bioconductor-org.hs.eg.db >=3.8.0,<3.9.0' + - 'bioconductor-reactome.db >=1.68.0,<1.69.0' + - 'bioconductor-reactomepa >=1.28.0,<1.29.0' - 'r-algdesign >=1.1.7.3' - r-base - 'r-cgdsr >=1.2.6' @@ -44,14 +44,14 @@ requirements: - r-visnetwork - 'r-xml >=3.98' run: - - 'bioconductor-annotationfuncs >=1.32.0,<1.33.0' - - 'bioconductor-biobase >=2.42.0,<2.43.0' - - 'bioconductor-clusterprofiler >=3.10.0,<3.11.0' - - 'bioconductor-dose >=3.8.0,<3.9.0' - - 'bioconductor-genetclassifier >=1.22.0,<1.23.0' - - 'bioconductor-org.hs.eg.db >=3.7.0,<3.8.0' - - 'bioconductor-reactome.db >=1.66.0,<1.67.0' - - 'bioconductor-reactomepa >=1.26.0,<1.27.0' + - 'bioconductor-annotationfuncs >=1.34.0,<1.35.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' + - 'bioconductor-clusterprofiler >=3.12.0,<3.13.0' + - 'bioconductor-dose >=3.10.0,<3.11.0' + - 'bioconductor-genetclassifier >=1.24.0,<1.25.0' + - 'bioconductor-org.hs.eg.db >=3.8.0,<3.9.0' + - 'bioconductor-reactome.db >=1.68.0,<1.69.0' + - 'bioconductor-reactomepa >=1.28.0,<1.29.0' - 'r-algdesign >=1.1.7.3' - r-base - 'r-cgdsr >=1.2.6' diff --git a/recipes/bioconductor-bioccasestudies/meta.yaml b/recipes/bioconductor-bioccasestudies/meta.yaml index 655ee84b42a4b..75542a421a587 100644 --- a/recipes/bioconductor-bioccasestudies/meta.yaml +++ b/recipes/bioconductor-bioccasestudies/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.44.0" %} +{% set version = "1.46.0" %} {% set name = "BiocCaseStudies" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,9 +10,9 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: b42e2a90273bbc029e3163dddc35656c + md5: 04e12153b18240289d6891b6000e5e1a build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ @@ -20,10 +20,10 @@ build: # Suggests: affy (>= 1.17.3), affyPLM (>= 1.15.1), affyQCReport (>= 1.17.0), ALL (>= 1.4.3), annaffy (>= 1.11.1), annotate (>= 1.17.3), AnnotationDbi (>= 1.1.6), apComplex (>= 2.5.0), Biobase (>= 1.17.5), bioDist (>= 1.11.3), biocGraph (>= 1.1.1), biomaRt (>= 1.13.5), CCl4 (>= 1.0.6), CLL (>= 1.2.4), Category (>= 2.5.0), class (>= 7.2-38), cluster (>= 1.11.9), convert (>= 1.15.0), gcrma (>= 2.11.1), genefilter (>= 1.17.6), geneplotter (>= 1.17.2), GO.db (>= 2.0.2), GOstats (>= 2.5.0), graph (>= 1.17.4), GSEABase (>= 1.1.13), hgu133a.db (>= 2.0.2), hgu95av2.db, hgu95av2cdf (>= 2.0.0), hgu95av2probe (>= 2.0.0), hopach (>= 1.13.0), KEGG.db (>= 2.0.2), kohonen (>= 2.0.2), lattice (>= 0.17.2), latticeExtra (>= 0.3-1), limma (>= 2.13.1), MASS (>= 7.2-38), MLInterfaces (>= 1.13.17), multtest (>= 1.19.0), org.Hs.eg.db (>= 2.0.2), ppiStats (>= 1.5.4), randomForest (>= 4.5-20), RBGL (>= 1.15.6), RColorBrewer (>= 1.0-2), Rgraphviz (>= 1.17.11), vsn (>= 3.4.0), weaver (>= 1.5.0), xtable (>= 1.5-2), yeastExpData (>= 0.9.11) requirements: host: - - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' - r-base run: - - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' - r-base test: commands: diff --git a/recipes/bioconductor-bioccheck/meta.yaml b/recipes/bioconductor-bioccheck/meta.yaml index 7990c51e330f5..cc0ed80c1f4d8 100644 --- a/recipes/bioconductor-bioccheck/meta.yaml +++ b/recipes/bioconductor-bioccheck/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.18.0" %} +{% set version = "1.20.0" %} {% set name = "BiocCheck" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,18 +10,18 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 89d98a97234600db83aa55aa628bbeef + md5: f7f9dcecc38c06d20364dc756d21f324 build: number: 0 rpaths: - lib/R/lib/ - lib/ noarch: generic -# Suggests: RUnit, BiocGenerics, Biobase, RJSONIO, rmarkdown, devtools (>= 1.4.1) +# Suggests: RUnit, BiocGenerics, Biobase, RJSONIO, rmarkdown, devtools (>= 1.4.1), usethis, BiocStyle requirements: host: - - 'bioconductor-biocviews >=1.50.0,<1.51.0' - - 'bioconductor-graph >=1.60.0,<1.61.0' + - 'bioconductor-biocviews >=1.52.0,<1.53.0' + - 'bioconductor-graph >=1.62.0,<1.63.0' - r-base - r-biocmanager - r-codetools @@ -30,8 +30,8 @@ requirements: - r-optparse - r-stringdist run: - - 'bioconductor-biocviews >=1.50.0,<1.51.0' - - 'bioconductor-graph >=1.60.0,<1.61.0' + - 'bioconductor-biocviews >=1.52.0,<1.53.0' + - 'bioconductor-graph >=1.62.0,<1.63.0' - r-base - r-biocmanager - r-codetools diff --git a/recipes/bioconductor-biocfilecache/meta.yaml b/recipes/bioconductor-biocfilecache/meta.yaml index fb47a6f0e0689..d28a1ba6fbb63 100644 --- a/recipes/bioconductor-biocfilecache/meta.yaml +++ b/recipes/bioconductor-biocfilecache/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.6.0" %} +{% set version = "1.8.0" %} {% set name = "BiocFileCache" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: c5b4282a6191a520567d03508bf46652 + md5: e362534e2cd232efbe27190cbd15fbb9 build: number: 0 rpaths: diff --git a/recipes/bioconductor-biocgenerics/meta.yaml b/recipes/bioconductor-biocgenerics/meta.yaml index 09b90292a59f3..cb1748e69a63c 100644 --- a/recipes/bioconductor-biocgenerics/meta.yaml +++ b/recipes/bioconductor-biocgenerics/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "0.28.0" %} +{% set version = "0.30.0" %} {% set name = "BiocGenerics" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,9 +10,9 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 39b4dfb1f9526c64ddcb9b994130a7c0 + md5: 77e2d121cec79b2656c24621b77923da build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ @@ -29,7 +29,7 @@ test: about: home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: Artistic-2.0 - summary: 'S4 generic functions needed by many Bioconductor packages.' + summary: 'The package defines S4 generic functions used in Bioconductor.' extra: identifiers: - biotools:biocgenerics diff --git a/recipes/bioconductor-biocgraph/meta.yaml b/recipes/bioconductor-biocgraph/meta.yaml index 90fe3917e0c36..0f8706fdd1429 100644 --- a/recipes/bioconductor-biocgraph/meta.yaml +++ b/recipes/bioconductor-biocgraph/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.44.0" %} +{% set version = "1.46.0" %} {% set name = "biocGraph" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: eca6aee70c90d6a42c92bcada35490eb + md5: 8c4c19f08f543393ec056e3c14fcafca build: number: 0 rpaths: @@ -20,16 +20,16 @@ build: # Suggests: fibroEset, geneplotter, hgu95av2.db requirements: host: - - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' - - 'bioconductor-geneplotter >=1.60.0,<1.61.0' - - 'bioconductor-graph >=1.60.0,<1.61.0' - - 'bioconductor-rgraphviz >=2.26.0,<2.27.0' + - 'bioconductor-biocgenerics >=0.30.0,<0.31.0' + - 'bioconductor-geneplotter >=1.62.0,<1.63.0' + - 'bioconductor-graph >=1.62.0,<1.63.0' + - 'bioconductor-rgraphviz >=2.28.0,<2.29.0' - r-base run: - - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' - - 'bioconductor-geneplotter >=1.60.0,<1.61.0' - - 'bioconductor-graph >=1.60.0,<1.61.0' - - 'bioconductor-rgraphviz >=2.26.0,<2.27.0' + - 'bioconductor-biocgenerics >=0.30.0,<0.31.0' + - 'bioconductor-geneplotter >=1.62.0,<1.63.0' + - 'bioconductor-graph >=1.62.0,<1.63.0' + - 'bioconductor-rgraphviz >=2.28.0,<2.29.0' - r-base test: commands: diff --git a/recipes/bioconductor-biocneighbors/meta.yaml b/recipes/bioconductor-biocneighbors/meta.yaml index e7d97d0d48065..999efe65dae6d 100644 --- a/recipes/bioconductor-biocneighbors/meta.yaml +++ b/recipes/bioconductor-biocneighbors/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.0.0" %} +{% set version = "1.2.0" %} {% set name = "BiocNeighbors" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,27 +10,31 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 654e4deee2cadb9901f8137142719b16 + md5: ea04a1707a7374e2de38e2f0310eaf80 build: number: 0 rpaths: - lib/R/lib/ - lib/ -# Suggests: testthat, BiocStyle, knitr, rmarkdown, FNN, RcppAnnoy +# Suggests: testthat, BiocStyle, knitr, rmarkdown, FNN, RcppAnnoy, RcppHNSW # SystemRequirements: C++11 requirements: host: - - 'bioconductor-biocparallel >=1.16.0,<1.17.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-biocgenerics >=0.30.0,<0.31.0' + - 'bioconductor-biocparallel >=1.18.0,<1.19.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' - r-base - r-rcpp - r-rcppannoy + - r-rcpphnsw run: - - 'bioconductor-biocparallel >=1.16.0,<1.17.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-biocgenerics >=0.30.0,<0.31.0' + - 'bioconductor-biocparallel >=1.18.0,<1.19.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' - r-base - r-rcpp - r-rcppannoy + - r-rcpphnsw build: - {{ compiler('c') }} - {{ compiler('cxx') }} @@ -41,5 +45,5 @@ test: about: home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: GPL-3 - summary: 'Implements exact and approximate methods for nearest neighbor detection, in a framework that allows them to be easily switched within Bioconductor packages or workflows. The exact algorithm is implemented using pre-clustering with the k-means algorithm, as described by Wang (2012). This is faster than conventional kd-trees for neighbor searching in higher (> 20) dimensional data. The approximate method uses the Annoy algorithm. Functions are also provided to search for all neighbors within a given distance. Parallelization is achieved for all methods using the BiocParallel framework.' + summary: 'Implements exact and approximate methods for nearest neighbor detection, in a framework that allows them to be easily switched within Bioconductor packages or workflows. Exact searches can be performed using the k-means for k-nearest neighbors algorithm or with vantage point trees. Approximate searches can be performed using the Annoy or HNSW libraries. Searching on either Euclidean or Manhattan distances is supported. Parallelization is achieved for all methods by using BiocParallel. Functions are also provided to search for all neighbors within a given distance.' diff --git a/recipes/bioconductor-bioconcotk/meta.yaml b/recipes/bioconductor-bioconcotk/meta.yaml index d6897fbc276ab..a037922e73af6 100644 --- a/recipes/bioconductor-bioconcotk/meta.yaml +++ b/recipes/bioconductor-bioconcotk/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.2.0" %} +{% set version = "1.4.0" %} {% set name = "BiocOncoTK" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 26a8f3e8a0262f795f4e1ebba65f7022 + md5: 16fba5eb15058c62c7f28924a3c28223 build: number: 0 rpaths: @@ -20,12 +20,12 @@ build: # Suggests: knitr, dbplyr, DBI, org.Hs.eg.db, MultiAssayExperiment, BiocStyle, ontoProc, ontologyPlot, pogos, GenomeInfoDb, restfulSE (>= 1.3.7), BiocFileCache, TxDb.Hsapiens.UCSC.hg19.knownGene, Biobase, TxDb.Hsapiens.UCSC.hg18.knownGene, reshape2, testthat, AnnotationDbi, FDb.InfiniumMethylation.hg19, EnsDb.Hsapiens.v75 requirements: host: - - 'bioconductor-complexheatmap >=1.20.0,<1.21.0' - - 'bioconductor-genomicfeatures >=1.34.0,<1.35.0' - - 'bioconductor-genomicranges >=1.34.0,<1.35.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' - - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' + - 'bioconductor-complexheatmap >=2.0.0,<2.1.0' + - 'bioconductor-genomicfeatures >=1.36.0,<1.37.0' + - 'bioconductor-genomicranges >=1.36.0,<1.37.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' + - 'bioconductor-summarizedexperiment >=1.14.0,<1.15.0' - r-base - r-bigrquery - r-dbi @@ -37,12 +37,12 @@ requirements: - r-rjson - r-shiny run: - - 'bioconductor-complexheatmap >=1.20.0,<1.21.0' - - 'bioconductor-genomicfeatures >=1.34.0,<1.35.0' - - 'bioconductor-genomicranges >=1.34.0,<1.35.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' - - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' + - 'bioconductor-complexheatmap >=2.0.0,<2.1.0' + - 'bioconductor-genomicfeatures >=1.36.0,<1.37.0' + - 'bioconductor-genomicranges >=1.36.0,<1.37.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' + - 'bioconductor-summarizedexperiment >=1.14.0,<1.15.0' - r-base - r-bigrquery - r-dbi diff --git a/recipes/bioconductor-biocor/meta.yaml b/recipes/bioconductor-biocor/meta.yaml index 0cafbf55eaec4..3fefe9b9a579e 100644 --- a/recipes/bioconductor-biocor/meta.yaml +++ b/recipes/bioconductor-biocor/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.6.0" %} +{% set version = "1.8.0" %} {% set name = "BioCor" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: b242a547b800e76229cb0e0e2af8acee + md5: 96d1d1f5f124ad493f0ff15c88c8daaa build: number: 0 rpaths: @@ -20,13 +20,13 @@ build: # Suggests: reactome.db, org.Hs.eg.db, WGCNA, methods, GOSemSim, testthat, knitr, rmarkdown, BiocStyle, airway, DESeq2, boot, targetscan.Hs.eg.db, Hmisc, spelling requirements: host: - - 'bioconductor-biocparallel >=1.16.0,<1.17.0' - - 'bioconductor-gseabase >=1.44.0,<1.45.0' + - 'bioconductor-biocparallel >=1.18.0,<1.19.0' + - 'bioconductor-gseabase >=1.46.0,<1.47.0' - r-base - r-matrix run: - - 'bioconductor-biocparallel >=1.16.0,<1.17.0' - - 'bioconductor-gseabase >=1.44.0,<1.45.0' + - 'bioconductor-biocparallel >=1.18.0,<1.19.0' + - 'bioconductor-gseabase >=1.46.0,<1.47.0' - r-base - r-matrix test: diff --git a/recipes/bioconductor-biocparallel/meta.yaml b/recipes/bioconductor-biocparallel/meta.yaml index 554d65e1fcbbf..a0acd89a8f449 100644 --- a/recipes/bioconductor-biocparallel/meta.yaml +++ b/recipes/bioconductor-biocparallel/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.16.6" %} +{% set version = "1.18.0" %} {% set name = "BiocParallel" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: 424fc59e6c69cad310c3c1592e21e04e165621a29d414ac10f677c6aeaef62c7 + md5: 7b6606106480c45a0876c42db947ebe7 build: number: 0 rpaths: @@ -32,7 +32,7 @@ requirements: build: - {{ compiler('c') }} - {{ compiler('cxx') }} - - {{ compiler('fortran') }} + - automake - make test: commands: diff --git a/recipes/bioconductor-biocpkgtools/meta.yaml b/recipes/bioconductor-biocpkgtools/meta.yaml index a556ca05a6145..d7fc0f1a7c467 100644 --- a/recipes/bioconductor-biocpkgtools/meta.yaml +++ b/recipes/bioconductor-biocpkgtools/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.0.2" %} +{% set version = "1.2.0" %} {% set name = "BiocPkgTools" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,25 +10,30 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 175524fc5f0f2d9566e13705c7cf0d46 + md5: 579be6f301bf4c99ebdfd01c757b751c build: number: 0 rpaths: - lib/R/lib/ - lib/ noarch: generic -# Suggests: BiocStyle, knitr, rmarkdown, testthat, tm, SnowballC, pdftools, visNetwork, biocViews +# Suggests: BiocStyle, knitr, rmarkdown, testthat, tm, SnowballC, pdftools, visNetwork, clipr requirements: host: + - 'bioconductor-biocviews >=1.52.0,<1.53.0' + - 'bioconductor-graph >=1.62.0,<1.63.0' + - 'bioconductor-rbgl >=1.60.0,<1.61.0' - r-base - r-biocmanager - r-dplyr - r-dt + - r-gh - r-htmltools - r-htmlwidgets - r-httr - r-igraph - r-jsonlite + - r-magrittr - r-readr - r-rex - r-rvest @@ -37,15 +42,20 @@ requirements: - r-tidyr - r-xml2 run: + - 'bioconductor-biocviews >=1.52.0,<1.53.0' + - 'bioconductor-graph >=1.62.0,<1.63.0' + - 'bioconductor-rbgl >=1.60.0,<1.61.0' - r-base - r-biocmanager - r-dplyr - r-dt + - r-gh - r-htmltools - r-htmlwidgets - r-httr - r-igraph - r-jsonlite + - r-magrittr - r-readr - r-rex - r-rvest diff --git a/recipes/bioconductor-biocsingular/build.sh b/recipes/bioconductor-biocsingular/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-biocsingular/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-biocsingular/meta.yaml b/recipes/bioconductor-biocsingular/meta.yaml new file mode 100644 index 0000000000000..d423d5359df82 --- /dev/null +++ b/recipes/bioconductor-biocsingular/meta.yaml @@ -0,0 +1,55 @@ +{% set version = "1.0.0" %} +{% set name = "BiocSingular" %} +{% set bioc = "3.9" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: 529a83b1188e9db77f65c5b51fa67ded +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ +# Suggests: testthat, BiocStyle, knitr, rmarkdown, beachmat +# SystemRequirements: C++11 +requirements: + host: + - 'bioconductor-beachmat >=2.0.0,<2.1.0' + - 'bioconductor-biocgenerics >=0.30.0,<0.31.0' + - 'bioconductor-biocparallel >=1.18.0,<1.19.0' + - 'bioconductor-delayedarray >=0.10.0,<0.11.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' + - r-base + - r-irlba + - r-matrix + - r-rcpp + - r-rsvd + run: + - 'bioconductor-beachmat >=2.0.0,<2.1.0' + - 'bioconductor-biocgenerics >=0.30.0,<0.31.0' + - 'bioconductor-biocparallel >=1.18.0,<1.19.0' + - 'bioconductor-delayedarray >=0.10.0,<0.11.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' + - r-base + - r-irlba + - r-matrix + - r-rcpp + - r-rsvd + build: + - {{ compiler('c') }} + - {{ compiler('cxx') }} + - make +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: GPL-3 + summary: 'Implements exact and approximate methods for singular value decomposition and principal components analysis, in a framework that allows them to be easily switched within Bioconductor packages or workflows. Where possible, parallelization is achieved using the BiocParallel framework.' + diff --git a/recipes/bioconductor-biocsklearn/meta.yaml b/recipes/bioconductor-biocsklearn/meta.yaml index df4f0b622af0c..cffc4cf67b547 100644 --- a/recipes/bioconductor-biocsklearn/meta.yaml +++ b/recipes/bioconductor-biocsklearn/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.4.0" %} +{% set version = "1.6.0" %} {% set name = "BiocSklearn" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,36 +10,38 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 789848b2d360055fa151d1d1724d9e37 + md5: 08d1933cf9d02f67c3eb8bbda351afd5 build: number: 0 rpaths: - lib/R/lib/ - lib/ noarch: generic -# Suggests: testthat, restfulSE, HDF5Array +# Suggests: testthat, restfulSE, HDF5Array, BiocStyle # SystemRequirements: python (>= 2.7), sklearn, numpy, pandas, h5py requirements: host: - - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' + - 'bioconductor-summarizedexperiment >=1.14.0,<1.15.0' - r-base - r-bbmisc - r-knitr - r-reticulate - python + - sklearn + - numpy - pandas - h5py - - scikit-learn run: - - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' + - 'bioconductor-summarizedexperiment >=1.14.0,<1.15.0' - r-base - r-bbmisc - r-knitr - r-reticulate - python + - sklearn + - numpy - pandas - h5py - - scikit-learn test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-biocstyle/meta.yaml b/recipes/bioconductor-biocstyle/meta.yaml index 7c9ab087a8816..013fed5a5ff99 100644 --- a/recipes/bioconductor-biocstyle/meta.yaml +++ b/recipes/bioconductor-biocstyle/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "2.10.0" %} +{% set version = "2.12.0" %} {% set name = "BiocStyle" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 7f0128f86d5c39d959ad11312d343e1d + md5: ef988ecd950940e6d7f9dcaa76bbdeb4 build: number: 0 rpaths: diff --git a/recipes/bioconductor-biocversion/meta.yaml b/recipes/bioconductor-biocversion/meta.yaml index 3c0f8e8ee20fd..f115a56603f60 100644 --- a/recipes/bioconductor-biocversion/meta.yaml +++ b/recipes/bioconductor-biocversion/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "3.8.0" %} +{% set version = "3.9.0" %} {% set name = "BiocVersion" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 7ebb61bfd78dcc1567b649a35dee075a + md5: 82c8be204ec54af118c304eee89b1ca7 build: number: 0 rpaths: diff --git a/recipes/bioconductor-biocviews/meta.yaml b/recipes/bioconductor-biocviews/meta.yaml index dc2e035c72ce2..6dbfc5af63a9d 100644 --- a/recipes/bioconductor-biocviews/meta.yaml +++ b/recipes/bioconductor-biocviews/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.50.9" %} +{% set version = "1.52.0" %} {% set name = "biocViews" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,27 +10,27 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 4e7e0b4cb13c29161ecc38e0a7f8d0b8 + md5: 13ae0c16ad260e4c54f1857437111055 build: number: 0 rpaths: - lib/R/lib/ - lib/ noarch: generic -# Suggests: BiocGenerics, knitr +# Suggests: BiocGenerics, knitr, commonmark requirements: host: - - 'bioconductor-biobase >=2.42.0,<2.43.0' - - 'bioconductor-graph >=1.60.0,<1.61.0' - - 'bioconductor-rbgl >=1.58.0,<1.59.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' + - 'bioconductor-graph >=1.62.0,<1.63.0' + - 'bioconductor-rbgl >=1.60.0,<1.61.0' - r-base - r-rcurl - r-runit - r-xml run: - - 'bioconductor-biobase >=2.42.0,<2.43.0' - - 'bioconductor-graph >=1.60.0,<1.61.0' - - 'bioconductor-rbgl >=1.58.0,<1.59.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' + - 'bioconductor-graph >=1.62.0,<1.63.0' + - 'bioconductor-rbgl >=1.60.0,<1.61.0' - r-base - r-rcurl - r-runit @@ -41,7 +41,7 @@ test: about: home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: Artistic-2.0 - summary: 'Infrastructure to support Bioconductor ''views'' used to classify software packages. ''biocViews'' are directed acyclic graphs of terms from a controlled vocabulary. There are three major classifications, corresponding to ''software'', ''annotation'', and ''experiment data'' packages.' + summary: 'Infrastructure to support ''views'' used to classify Bioconductor packages. ''biocViews'' are directed acyclic graphs of terms from a controlled vocabulary. There are three major classifications, corresponding to ''software'', ''annotation'', and ''experiment data'' packages.' extra: identifiers: - biotools:biocviews diff --git a/recipes/bioconductor-biocworkflowtools/meta.yaml b/recipes/bioconductor-biocworkflowtools/meta.yaml index cd39744d2304a..644c7ad5a1936 100644 --- a/recipes/bioconductor-biocworkflowtools/meta.yaml +++ b/recipes/bioconductor-biocworkflowtools/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.8.0" %} +{% set version = "1.10.0" %} {% set name = "BiocWorkflowTools" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 6c344c8e215be2318eca98bc8f579a67 + md5: b35b8354e016215f29f0fa4c7108e4ef build: number: 0 rpaths: @@ -19,7 +19,7 @@ build: noarch: generic requirements: host: - - 'bioconductor-biocstyle >=2.10.0,<2.11.0' + - 'bioconductor-biocstyle >=2.12.0,<2.13.0' - r-base - r-bookdown - r-devtools @@ -29,8 +29,9 @@ requirements: - r-rmarkdown - r-rstudioapi - r-stringr + - r-usethis run: - - 'bioconductor-biocstyle >=2.10.0,<2.11.0' + - 'bioconductor-biocstyle >=2.12.0,<2.13.0' - r-base - r-bookdown - r-devtools @@ -40,6 +41,7 @@ requirements: - r-rmarkdown - r-rstudioapi - r-stringr + - r-usethis test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-biodist/meta.yaml b/recipes/bioconductor-biodist/meta.yaml index 402f7738896de..87ae25391acc3 100644 --- a/recipes/bioconductor-biodist/meta.yaml +++ b/recipes/bioconductor-biodist/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.54.0" %} +{% set version = "1.56.0" %} {% set name = "bioDist" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: fed70af697577a8e3f3f7065be6b790b + md5: 2d840412a1cb4aa5a70a225fa5be7a4b build: number: 0 rpaths: @@ -20,11 +20,11 @@ build: # Suggests: locfit requirements: host: - - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' - r-base - r-kernsmooth run: - - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' - r-base - r-kernsmooth test: diff --git a/recipes/bioconductor-biomart/meta.yaml b/recipes/bioconductor-biomart/meta.yaml index b4df06623c7a8..d7f9135bc38cb 100644 --- a/recipes/bioconductor-biomart/meta.yaml +++ b/recipes/bioconductor-biomart/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "2.38.0" %} +{% set version = "2.40.0" %} {% set name = "biomaRt" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 4a9185e87108865494abcd7340cab002 + md5: 4056c9f0f519c2024075419323a3191b build: number: 0 rpaths: @@ -20,7 +20,7 @@ build: # Suggests: annotate, BiocStyle, knitr, rmarkdown, testthat requirements: host: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' - r-base - r-httr - r-progress @@ -28,7 +28,7 @@ requirements: - r-stringr - r-xml run: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' - r-base - r-httr - r-progress @@ -41,7 +41,7 @@ test: about: home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: Artistic-2.0 - summary: 'In recent years a wealth of biological data has become available in public data repositories. Easy access to these valuable data resources and firm integration with data analysis is needed for comprehensive bioinformatics data analysis. biomaRt provides an interface to a growing collection of databases implementing the BioMart software suite (http://www.biomart.org). The package enables retrieval of large amounts of data in a uniform way without the need to know the underlying database schemas or write complex SQL queries. The most prominent examples of BioMart databases are Ensembl, which provides biomaRt users direct access to a diverse set of data and enables a wide range of powerful online queries from gene annotation to database mining.' + summary: 'In recent years a wealth of biological data has become available in public data repositories. Easy access to these valuable data resources and firm integration with data analysis is needed for comprehensive bioinformatics data analysis. biomaRt provides an interface to a growing collection of databases implementing the BioMart software suite (). The package enables retrieval of large amounts of data in a uniform way without the need to know the underlying database schemas or write complex SQL queries. The most prominent examples of BioMart databases are maintain by Ensembl, which provides biomaRt users direct access to a diverse set of data and enables a wide range of powerful online queries from gene annotation to database mining.' extra: identifiers: - biotools:biomaRt diff --git a/recipes/bioconductor-biomformat/meta.yaml b/recipes/bioconductor-biomformat/meta.yaml index 91d2f3fe79668..7decee5febe08 100644 --- a/recipes/bioconductor-biomformat/meta.yaml +++ b/recipes/bioconductor-biomformat/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.10.1" %} +{% set version = "1.12.0" %} {% set name = "biomformat" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - sha256: f8ddc44ed0a1897fdc172eb4cd98ca1899666f2b914ab87ca3b72db52b868ea8 + md5: d2a93f141e43ac49d4e7ded308ecb29f build: number: 0 rpaths: @@ -20,13 +20,13 @@ build: # Suggests: testthat (>= 0.10), knitr (>= 1.10), BiocStyle (>= 1.6), rmarkdown (>= 0.7) requirements: host: - - 'bioconductor-rhdf5 >=2.26.0,<2.27.0' + - 'bioconductor-rhdf5 >=2.28.0,<2.29.0' - r-base - 'r-jsonlite >=0.9.16' - 'r-matrix >=1.2' - 'r-plyr >=1.8' run: - - 'bioconductor-rhdf5 >=2.26.0,<2.27.0' + - 'bioconductor-rhdf5 >=2.28.0,<2.29.0' - r-base - 'r-jsonlite >=0.9.16' - 'r-matrix >=1.2' diff --git a/recipes/bioconductor-biomm/build.sh b/recipes/bioconductor-biomm/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-biomm/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-biomm/meta.yaml b/recipes/bioconductor-biomm/meta.yaml new file mode 100644 index 0000000000000..1e815ca31cea3 --- /dev/null +++ b/recipes/bioconductor-biomm/meta.yaml @@ -0,0 +1,51 @@ +{% set version = "1.0.0" %} +{% set name = "BioMM" %} +{% set bioc = "3.9" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: c82d385b2460620296de121163c9b500 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: BiocStyle, knitr, RUnit, BiocGenerics +requirements: + host: + - 'bioconductor-biocparallel >=1.18.0,<1.19.0' + - 'bioconductor-variancepartition >=1.14.0,<1.15.0' + - r-base + - r-e1071 + - r-ggplot2 + - r-glmnet + - r-lattice + - r-nsprcomp + - r-ranger + - r-rms + run: + - 'bioconductor-biocparallel >=1.18.0,<1.19.0' + - 'bioconductor-variancepartition >=1.14.0,<1.15.0' + - r-base + - r-e1071 + - r-ggplot2 + - r-glmnet + - r-lattice + - r-nsprcomp + - r-ranger + - r-rms +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: GPL-3 + summary: 'The identification of reproducible biological patterns from high-dimensional omics data is a key factor in understanding the biology of complex disease or traits. Incorporating prior biological knowledge into machine learning is an important step in advancing such research. We have proposed a biologically informed multi-stage machine learing framework termed BioMM specifically for phenotype prediction based on omics-scale data where we can evaluate different machine learning models with various prior biological meta information.' + diff --git a/recipes/bioconductor-biomvcclass/meta.yaml b/recipes/bioconductor-biomvcclass/meta.yaml index f620842beb20f..ff0b4dfa26211 100644 --- a/recipes/bioconductor-biomvcclass/meta.yaml +++ b/recipes/bioconductor-biomvcclass/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.50.0" %} +{% set version = "1.52.0" %} {% set name = "BioMVCClass" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: a37c816ced8ff46c22e7493f9e10997f + md5: dc40cf1df6b1793993401d3f8438625f build: number: 0 rpaths: @@ -19,16 +19,16 @@ build: noarch: generic requirements: host: - - 'bioconductor-biobase >=2.42.0,<2.43.0' - - 'bioconductor-graph >=1.60.0,<1.61.0' - - 'bioconductor-mvcclass >=1.56.0,<1.57.0' - - 'bioconductor-rgraphviz >=2.26.0,<2.27.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' + - 'bioconductor-graph >=1.62.0,<1.63.0' + - 'bioconductor-mvcclass >=1.58.0,<1.59.0' + - 'bioconductor-rgraphviz >=2.28.0,<2.29.0' - r-base run: - - 'bioconductor-biobase >=2.42.0,<2.43.0' - - 'bioconductor-graph >=1.60.0,<1.61.0' - - 'bioconductor-mvcclass >=1.56.0,<1.57.0' - - 'bioconductor-rgraphviz >=2.26.0,<2.27.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' + - 'bioconductor-graph >=1.62.0,<1.63.0' + - 'bioconductor-mvcclass >=1.58.0,<1.59.0' + - 'bioconductor-rgraphviz >=2.28.0,<2.29.0' - r-base test: commands: diff --git a/recipes/bioconductor-biomvrcns/meta.yaml b/recipes/bioconductor-biomvrcns/meta.yaml index e257e5f12e0c1..dd94425d94f98 100644 --- a/recipes/bioconductor-biomvrcns/meta.yaml +++ b/recipes/bioconductor-biomvrcns/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.22.0" %} +{% set version = "1.24.0" %} {% set name = "biomvRCNS" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 43649cec95f927eace8290ffe12e756d + md5: abf2ba8352f9473e8e489f55569a307e build: number: 0 rpaths: @@ -19,15 +19,15 @@ build: # Suggests: cluster, parallel, GenomicFeatures, dynamicTreeCut, Rsamtools, TxDb.Hsapiens.UCSC.hg19.knownGene requirements: host: - - 'bioconductor-genomicranges >=1.34.0,<1.35.0' - - 'bioconductor-gviz >=1.26.0,<1.27.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-genomicranges >=1.36.0,<1.37.0' + - 'bioconductor-gviz >=1.28.0,<1.29.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' - r-base - r-mvtnorm run: - - 'bioconductor-genomicranges >=1.34.0,<1.35.0' - - 'bioconductor-gviz >=1.26.0,<1.27.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-genomicranges >=1.36.0,<1.37.0' + - 'bioconductor-gviz >=1.28.0,<1.29.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' - r-base - r-mvtnorm build: diff --git a/recipes/bioconductor-bionet/meta.yaml b/recipes/bioconductor-bionet/meta.yaml index d0c3a172034e5..8e84ae6279f50 100644 --- a/recipes/bioconductor-bionet/meta.yaml +++ b/recipes/bioconductor-bionet/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.42.0" %} +{% set version = "1.44.0" %} {% set name = "BioNet" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: c87b42a860906cd6ec25b02150e4b763 + md5: 33b3f5065ff53b5414ca11432a489261 build: number: 0 rpaths: @@ -20,17 +20,17 @@ build: # Suggests: rgl, impute, DLBCL, genefilter, xtable, ALL, limma, hgu95av2.db, XML requirements: host: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' - - 'bioconductor-biobase >=2.42.0,<2.43.0' - - 'bioconductor-graph >=1.60.0,<1.61.0' - - 'bioconductor-rbgl >=1.58.0,<1.59.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' + - 'bioconductor-graph >=1.62.0,<1.63.0' + - 'bioconductor-rbgl >=1.60.0,<1.61.0' - r-base - 'r-igraph >=1.0.1' run: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' - - 'bioconductor-biobase >=2.42.0,<2.43.0' - - 'bioconductor-graph >=1.60.0,<1.61.0' - - 'bioconductor-rbgl >=1.58.0,<1.59.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' + - 'bioconductor-graph >=1.62.0,<1.63.0' + - 'bioconductor-rbgl >=1.60.0,<1.61.0' - r-base - 'r-igraph >=1.0.1' test: diff --git a/recipes/bioconductor-bionetstat/meta.yaml b/recipes/bioconductor-bionetstat/meta.yaml index 3e3f408e99cc9..f38ceeb590dd7 100644 --- a/recipes/bioconductor-bionetstat/meta.yaml +++ b/recipes/bioconductor-bionetstat/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.2.2" %} +{% set version = "1.4.0" %} {% set name = "BioNetStat" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: d815407c6d2c3bb0387ae0e22fc2ee81 + md5: d846bf02baf8bedceb371250c12810dc build: number: 0 rpaths: @@ -19,8 +19,8 @@ build: noarch: generic requirements: host: - - 'bioconductor-biocparallel >=1.16.0,<1.17.0' - - 'bioconductor-pathview >=1.22.0,<1.23.0' + - 'bioconductor-biocparallel >=1.18.0,<1.19.0' + - 'bioconductor-pathview >=1.24.0,<1.25.0' - r-base - r-ggplot2 - r-hmisc @@ -36,8 +36,8 @@ requirements: - r-whisker - r-yaml run: - - 'bioconductor-biocparallel >=1.16.0,<1.17.0' - - 'bioconductor-pathview >=1.22.0,<1.23.0' + - 'bioconductor-biocparallel >=1.18.0,<1.19.0' + - 'bioconductor-pathview >=1.24.0,<1.25.0' - r-base - r-ggplot2 - r-hmisc diff --git a/recipes/bioconductor-bioqc/meta.yaml b/recipes/bioconductor-bioqc/meta.yaml index 4d120ef1c597a..c128d407ae47d 100644 --- a/recipes/bioconductor-bioqc/meta.yaml +++ b/recipes/bioconductor-bioqc/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.10.0" %} +{% set version = "1.12.0" %} {% set name = "BioQC" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 47b14e1b9485410002bb96d5346fb525 + md5: acd4981f54d129a02e19563063f8be27 build: number: 0 rpaths: @@ -19,11 +19,11 @@ build: # Suggests: testthat, knitr, rmarkdown, lattice, latticeExtra, rbenchmark, gplots, gridExtra, hgu133plus2.db, ineq requirements: host: - - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' - r-base - r-rcpp run: - - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' - r-base - r-rcpp build: diff --git a/recipes/bioconductor-bioseqclass/meta.yaml b/recipes/bioconductor-bioseqclass/meta.yaml index 738ec4695c788..f4793b528be14 100644 --- a/recipes/bioconductor-bioseqclass/meta.yaml +++ b/recipes/bioconductor-bioseqclass/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.40.0" %} +{% set version = "1.42.0" %} {% set name = "BioSeqClass" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 9bb1fbea1848a6ffe2e020deaa1f3777 + md5: f84297e07369bf7aeeef25aad3e45261 build: number: 0 rpaths: @@ -20,8 +20,8 @@ build: # Suggests: scatterplot3d requirements: host: - - 'bioconductor-biobase >=2.42.0,<2.43.0' - - 'bioconductor-biostrings >=2.50.0,<2.51.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' + - 'bioconductor-biostrings >=2.52.0,<2.53.0' - r-base - r-class - r-e1071 @@ -35,8 +35,8 @@ requirements: - r-scatterplot3d - r-tree run: - - 'bioconductor-biobase >=2.42.0,<2.43.0' - - 'bioconductor-biostrings >=2.50.0,<2.51.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' + - 'bioconductor-biostrings >=2.52.0,<2.53.0' - r-base - r-class - r-e1071 diff --git a/recipes/bioconductor-biosigner/meta.yaml b/recipes/bioconductor-biosigner/meta.yaml index 173a47f5d06fb..7f6fe20ae909e 100644 --- a/recipes/bioconductor-biosigner/meta.yaml +++ b/recipes/bioconductor-biosigner/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.10.0" %} +{% set version = "1.12.0" %} {% set name = "biosigner" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,24 +10,24 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 5a7f57cd3552ed1c2cf21cf18f33da77 + md5: 370b5493603495a810a607df9587e081 build: number: 0 rpaths: - lib/R/lib/ - lib/ noarch: generic -# Suggests: BioMark, RUnit, BiocGenerics, BiocStyle, golubEsets, hu6800.db, knitr, rmarkdown +# Suggests: BioMark, BiocGenerics, BiocStyle, golubEsets, hu6800.db, knitr, rmarkdown, testthat requirements: host: - - 'bioconductor-biobase >=2.42.0,<2.43.0' - - 'bioconductor-ropls >=1.14.0,<1.15.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' + - 'bioconductor-ropls >=1.16.0,<1.17.0' - r-base - r-e1071 - r-randomforest run: - - 'bioconductor-biobase >=2.42.0,<2.43.0' - - 'bioconductor-ropls >=1.14.0,<1.15.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' + - 'bioconductor-ropls >=1.16.0,<1.17.0' - r-base - r-e1071 - r-randomforest diff --git a/recipes/bioconductor-biostrings/meta.yaml b/recipes/bioconductor-biostrings/meta.yaml index d4fd966ca6c19..edfc979c76cdb 100644 --- a/recipes/bioconductor-biostrings/meta.yaml +++ b/recipes/bioconductor-biostrings/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "2.50.2" %} +{% set version = "2.52.0" %} {% set name = "Biostrings" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 40233fb2ae38e2e1d5900cdd2e578ad7 + md5: 288b4398c81188be1a32bfd27241492d build: number: 0 rpaths: @@ -19,16 +19,16 @@ build: # Suggests: BSgenome (>= 1.13.14), BSgenome.Celegans.UCSC.ce2 (>= 1.3.11), BSgenome.Dmelanogaster.UCSC.dm3 (>= 1.3.11), BSgenome.Hsapiens.UCSC.hg18, drosophila2probe, hgu95av2probe, hgu133aprobe, GenomicFeatures (>= 1.3.14), hgu95av2cdf, affy (>= 1.41.3), affydata (>= 1.11.5), RUnit requirements: host: - - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' - - 'bioconductor-xvector >=0.22.0,<0.23.0' + - 'bioconductor-biocgenerics >=0.30.0,<0.31.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' + - 'bioconductor-xvector >=0.24.0,<0.25.0' - r-base run: - - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' - - 'bioconductor-xvector >=0.22.0,<0.23.0' + - 'bioconductor-biocgenerics >=0.30.0,<0.31.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' + - 'bioconductor-xvector >=0.24.0,<0.25.0' - r-base build: - {{ compiler('c') }} diff --git a/recipes/bioconductor-biosvd/meta.yaml b/recipes/bioconductor-biosvd/meta.yaml index 740ea5d82809d..5291589f7ae01 100644 --- a/recipes/bioconductor-biosvd/meta.yaml +++ b/recipes/bioconductor-biosvd/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "2.18.0" %} +{% set version = "2.20.0" %} {% set name = "biosvd" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,22 +10,22 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: aeb5728b6822575a2e87140073a2de84 + md5: c445ae7cb8f2f00107f38edc234a92c8 build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ noarch: generic requirements: host: - - 'bioconductor-biobase >=2.42.0,<2.43.0' - - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' + - 'bioconductor-biocgenerics >=0.30.0,<0.31.0' - r-base - r-nmf run: - - 'bioconductor-biobase >=2.42.0,<2.43.0' - - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' + - 'bioconductor-biocgenerics >=0.30.0,<0.31.0' - r-base - r-nmf test: diff --git a/recipes/bioconductor-biotmle/meta.yaml b/recipes/bioconductor-biotmle/meta.yaml index 78b9b5de9386e..2a5cb095b4dab 100644 --- a/recipes/bioconductor-biotmle/meta.yaml +++ b/recipes/bioconductor-biotmle/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.6.0" %} +{% set version = "1.8.0" %} {% set name = "biotmle" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 19b83e8aa5038a0a939357fa63638a44 + md5: c19bed4db37f90de3029d5374f65d94a build: number: 0 rpaths: @@ -20,11 +20,12 @@ build: # Suggests: testthat, knitr, rmarkdown, BiocStyle, SuperLearner, Matrix, DBI, biotmleData (>= 1.1.1) requirements: host: - - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' - - 'bioconductor-biocparallel >=1.16.0,<1.17.0' - - 'bioconductor-limma >=3.38.0,<3.39.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' - - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' + - 'bioconductor-biocgenerics >=0.30.0,<0.31.0' + - 'bioconductor-biocparallel >=1.18.0,<1.19.0' + - 'bioconductor-limma >=3.40.0,<3.41.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' + - 'bioconductor-summarizedexperiment >=1.14.0,<1.15.0' + - r-assertthat - r-base - r-dofuture - r-dplyr @@ -32,13 +33,15 @@ requirements: - r-ggplot2 - r-ggsci - r-superheat + - r-tibble - r-tmle run: - - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' - - 'bioconductor-biocparallel >=1.16.0,<1.17.0' - - 'bioconductor-limma >=3.38.0,<3.39.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' - - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' + - 'bioconductor-biocgenerics >=0.30.0,<0.31.0' + - 'bioconductor-biocparallel >=1.18.0,<1.19.0' + - 'bioconductor-limma >=3.40.0,<3.41.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' + - 'bioconductor-summarizedexperiment >=1.14.0,<1.15.0' + - r-assertthat - r-base - r-dofuture - r-dplyr @@ -46,6 +49,7 @@ requirements: - r-ggplot2 - r-ggsci - r-superheat + - r-tibble - r-tmle test: commands: @@ -53,5 +57,5 @@ test: about: home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: 'file LICENSE' - summary: 'This package facilitates the discovery of biomarkers from biological sequencing data (e.g., microarrays, RNA-seq) based on the associations of potential biomarkers with exposure and outcome variables by implementing an estimation procedure that combines a generalization of moderated statistics with targeted minimum loss-based estimates (TMLE) of parameters defined via causal inference (e.g., Average Treatment Effect) whose estimators admit asymptotically linear representations.' + summary: 'This package facilitates the discovery of biomarkers from biological sequencing data (e.g., microarrays, RNA-seq) based on the associations of potential biomarkers with exposure and outcome variables by implementing an estimation procedure that combines a generalization of moderated statistics with targeted minimum loss-based estimates (TMLE) of causal parameters (e.g., Average Treatment Effect) whose estimators admit asymptotically linear representations (in terms of influence functions).' diff --git a/recipes/bioconductor-biotmledata/meta.yaml b/recipes/bioconductor-biotmledata/meta.yaml index 32c9a28a71506..e9c4f551a1a56 100644 --- a/recipes/bioconductor-biotmledata/meta.yaml +++ b/recipes/bioconductor-biotmledata/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.6.0" %} +{% set version = "1.8.0" %} {% set name = "biotmleData" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 14d22102df0583c9d12c3bc003a4c544 + md5: 81e38ef555e606146c1a7c8358a2f3a6 build: number: 0 rpaths: @@ -23,7 +23,7 @@ requirements: - r-base run: - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-biotmledata/post-link.sh b/recipes/bioconductor-biotmledata/post-link.sh index 66ace8661c31e..e50d0e89006c9 100644 --- a/recipes/bioconductor-biotmledata/post-link.sh +++ b/recipes/bioconductor-biotmledata/post-link.sh @@ -1,11 +1,11 @@ #!/bin/bash -FN="biotmleData_1.6.0.tar.gz" +FN="biotmleData_1.8.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/experiment/src/contrib/biotmleData_1.6.0.tar.gz" - "https://bioarchive.galaxyproject.org/biotmleData_1.6.0.tar.gz" - "https://depot.galaxyproject.org/software/bioconductor-biotmledata/bioconductor-biotmledata_1.6.0_src_all.tar.gz" + "https://bioconductor.org/packages/3.9/data/experiment/src/contrib/biotmleData_1.8.0.tar.gz" + "https://bioarchive.galaxyproject.org/biotmleData_1.8.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-biotmledata/bioconductor-biotmledata_1.8.0_src_all.tar.gz" ) -MD5="14d22102df0583c9d12c3bc003a4c544" +MD5="81e38ef555e606146c1a7c8358a2f3a6" # Use a staging area in the conda dir rather than temp dirs, both to avoid # permission issues as well as to have things downloaded in a predictable @@ -16,7 +16,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-biovizbase/meta.yaml b/recipes/bioconductor-biovizbase/meta.yaml index 867282010f1bb..67dbc9747b77e 100644 --- a/recipes/bioconductor-biovizbase/meta.yaml +++ b/recipes/bioconductor-biovizbase/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.30.1" %} +{% set version = "1.32.0" %} {% set name = "biovizBase" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 43a32d6cc270b0edf67938d30f9d1ce5 + md5: cae76703fef55cb32ba79461f815b86e build: number: 0 rpaths: @@ -19,20 +19,20 @@ build: # Suggests: BSgenome.Hsapiens.UCSC.hg19, TxDb.Hsapiens.UCSC.hg19.knownGene, BSgenome, rtracklayer, EnsDb.Hsapiens.v75, RUnit requirements: host: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' - - 'bioconductor-annotationfilter >=1.6.0,<1.7.0' - - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' - - 'bioconductor-biostrings >=2.50.0,<2.51.0' - - 'bioconductor-ensembldb >=2.6.0,<2.7.0' - - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' - - 'bioconductor-genomicalignments >=1.18.0,<1.19.0' - - 'bioconductor-genomicfeatures >=1.34.0,<1.35.0' - - 'bioconductor-genomicranges >=1.34.0,<1.35.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-rsamtools >=1.34.0,<1.35.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' - - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' - - 'bioconductor-variantannotation >=1.28.0,<1.29.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' + - 'bioconductor-annotationfilter >=1.8.0,<1.9.0' + - 'bioconductor-biocgenerics >=0.30.0,<0.31.0' + - 'bioconductor-biostrings >=2.52.0,<2.53.0' + - 'bioconductor-ensembldb >=2.8.0,<2.9.0' + - 'bioconductor-genomeinfodb >=1.20.0,<1.21.0' + - 'bioconductor-genomicalignments >=1.20.0,<1.21.0' + - 'bioconductor-genomicfeatures >=1.36.0,<1.37.0' + - 'bioconductor-genomicranges >=1.36.0,<1.37.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-rsamtools >=2.0.0,<2.1.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' + - 'bioconductor-summarizedexperiment >=1.14.0,<1.15.0' + - 'bioconductor-variantannotation >=1.30.0,<1.31.0' - r-base - r-dichromat - r-hmisc @@ -40,20 +40,20 @@ requirements: - r-rlang - r-scales run: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' - - 'bioconductor-annotationfilter >=1.6.0,<1.7.0' - - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' - - 'bioconductor-biostrings >=2.50.0,<2.51.0' - - 'bioconductor-ensembldb >=2.6.0,<2.7.0' - - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' - - 'bioconductor-genomicalignments >=1.18.0,<1.19.0' - - 'bioconductor-genomicfeatures >=1.34.0,<1.35.0' - - 'bioconductor-genomicranges >=1.34.0,<1.35.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-rsamtools >=1.34.0,<1.35.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' - - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' - - 'bioconductor-variantannotation >=1.28.0,<1.29.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' + - 'bioconductor-annotationfilter >=1.8.0,<1.9.0' + - 'bioconductor-biocgenerics >=0.30.0,<0.31.0' + - 'bioconductor-biostrings >=2.52.0,<2.53.0' + - 'bioconductor-ensembldb >=2.8.0,<2.9.0' + - 'bioconductor-genomeinfodb >=1.20.0,<1.21.0' + - 'bioconductor-genomicalignments >=1.20.0,<1.21.0' + - 'bioconductor-genomicfeatures >=1.36.0,<1.37.0' + - 'bioconductor-genomicranges >=1.36.0,<1.37.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-rsamtools >=2.0.0,<2.1.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' + - 'bioconductor-summarizedexperiment >=1.14.0,<1.15.0' + - 'bioconductor-variantannotation >=1.30.0,<1.31.0' - r-base - r-dichromat - r-hmisc diff --git a/recipes/bioconductor-birewire/meta.yaml b/recipes/bioconductor-birewire/meta.yaml index 7f61935190187..045e8ae1ff5bf 100644 --- a/recipes/bioconductor-birewire/meta.yaml +++ b/recipes/bioconductor-birewire/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "3.14.0" %} +{% set version = "3.16.0" %} {% set name = "BiRewire" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: dfa755b6535050e3c39865feedb53c55 + md5: f0ffa84bfc1b5a61653bfdc3fa10d25e build: number: 0 rpaths: diff --git a/recipes/bioconductor-birta/meta.yaml b/recipes/bioconductor-birta/meta.yaml index 783f517362b43..6b5c61c92155c 100644 --- a/recipes/bioconductor-birta/meta.yaml +++ b/recipes/bioconductor-birta/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.26.0" %} +{% set version = "1.28.0" %} {% set name = "birta" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 16a30ffecfc786f5ba64e8796f4a8266 + md5: d4c84a404a92d5698e1af22fd17da36b build: number: 0 rpaths: @@ -18,13 +18,13 @@ build: - lib/ requirements: host: - - 'bioconductor-biobase >=2.42.0,<2.43.0' - - 'bioconductor-limma >=3.38.0,<3.39.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' + - 'bioconductor-limma >=3.40.0,<3.41.0' - r-base - r-mass run: - - 'bioconductor-biobase >=2.42.0,<2.43.0' - - 'bioconductor-limma >=3.38.0,<3.39.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' + - 'bioconductor-limma >=3.40.0,<3.41.0' - r-base - r-mass build: diff --git a/recipes/bioconductor-biseq/meta.yaml b/recipes/bioconductor-biseq/meta.yaml index 97093604097ef..2217c1f4627bd 100644 --- a/recipes/bioconductor-biseq/meta.yaml +++ b/recipes/bioconductor-biseq/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.22.0" %} +{% set version = "1.24.0" %} {% set name = "BiSeq" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,38 +10,38 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 2a92d9e431dba31d85eb4b55a7239214 + md5: c460a1ce9835304b0c0caaed08b7e828 build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ noarch: generic requirements: host: - - 'bioconductor-biobase >=2.42.0,<2.43.0' - - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' - - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' - - 'bioconductor-genomicranges >=1.34.0,<1.35.0' - - 'bioconductor-globaltest >=5.36.0,<5.37.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-rtracklayer >=1.42.0,<1.43.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' - - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' + - 'bioconductor-biocgenerics >=0.30.0,<0.31.0' + - 'bioconductor-genomeinfodb >=1.20.0,<1.21.0' + - 'bioconductor-genomicranges >=1.36.0,<1.37.0' + - 'bioconductor-globaltest >=5.38.0,<5.39.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-rtracklayer >=1.44.0,<1.45.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' + - 'bioconductor-summarizedexperiment >=1.14.0,<1.15.0' - r-base - r-betareg - r-formula - r-lokern run: - - 'bioconductor-biobase >=2.42.0,<2.43.0' - - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' - - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' - - 'bioconductor-genomicranges >=1.34.0,<1.35.0' - - 'bioconductor-globaltest >=5.36.0,<5.37.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-rtracklayer >=1.42.0,<1.43.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' - - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' + - 'bioconductor-biocgenerics >=0.30.0,<0.31.0' + - 'bioconductor-genomeinfodb >=1.20.0,<1.21.0' + - 'bioconductor-genomicranges >=1.36.0,<1.37.0' + - 'bioconductor-globaltest >=5.38.0,<5.39.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-rtracklayer >=1.44.0,<1.45.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' + - 'bioconductor-summarizedexperiment >=1.14.0,<1.15.0' - r-base - r-betareg - r-formula diff --git a/recipes/bioconductor-bitseq/meta.yaml b/recipes/bioconductor-bitseq/meta.yaml index 83286885dbed2..6658215aead35 100644 --- a/recipes/bioconductor-bitseq/meta.yaml +++ b/recipes/bioconductor-bitseq/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.26.0" %} +{% set version = "1.28.0" %} {% set name = "BitSeq" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 563db99a022384f3bb02354a18ca1397 + md5: 813708121ae472700424da3cde5fdf22 build: number: 0 rpaths: @@ -19,16 +19,16 @@ build: # Suggests: edgeR, DESeq, BiocStyle requirements: host: - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-rsamtools >=1.34.0,<1.35.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' - - 'bioconductor-zlibbioc >=1.28.0,<1.29.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-rhtslib >=1.16.0,<1.17.0' + - 'bioconductor-rsamtools >=2.0.0,<2.1.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' - r-base run: - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-rsamtools >=1.34.0,<1.35.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' - - 'bioconductor-zlibbioc >=1.28.0,<1.29.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-rhtslib >=1.16.0,<1.17.0' + - 'bioconductor-rsamtools >=2.0.0,<2.1.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' - r-base build: - {{ compiler('c') }} diff --git a/recipes/bioconductor-bladderbatch/meta.yaml b/recipes/bioconductor-bladderbatch/meta.yaml index 35443e01d4fb6..13374c785f4ed 100644 --- a/recipes/bioconductor-bladderbatch/meta.yaml +++ b/recipes/bioconductor-bladderbatch/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.20.0" %} +{% set version = "1.22.0" %} {% set name = "bladderbatch" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 27cf90b928cffce1c1ae3e0b3a99e687 + md5: 218fc2ffe79cb78448361adc8c9a3c2b build: number: 0 rpaths: @@ -19,12 +19,12 @@ build: noarch: generic requirements: host: - - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' - r-base run: - - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-bladderbatch/post-link.sh b/recipes/bioconductor-bladderbatch/post-link.sh index e5a7808b57944..9db120950b6a3 100644 --- a/recipes/bioconductor-bladderbatch/post-link.sh +++ b/recipes/bioconductor-bladderbatch/post-link.sh @@ -1,11 +1,11 @@ #!/bin/bash -FN="bladderbatch_1.20.0.tar.gz" +FN="bladderbatch_1.22.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/experiment/src/contrib/bladderbatch_1.20.0.tar.gz" - "https://bioarchive.galaxyproject.org/bladderbatch_1.20.0.tar.gz" - "https://depot.galaxyproject.org/software/bioconductor-bladderbatch/bioconductor-bladderbatch_1.20.0_src_all.tar.gz" + "https://bioconductor.org/packages/3.9/data/experiment/src/contrib/bladderbatch_1.22.0.tar.gz" + "https://bioarchive.galaxyproject.org/bladderbatch_1.22.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-bladderbatch/bioconductor-bladderbatch_1.22.0_src_all.tar.gz" ) -MD5="27cf90b928cffce1c1ae3e0b3a99e687" +MD5="218fc2ffe79cb78448361adc8c9a3c2b" # Use a staging area in the conda dir rather than temp dirs, both to avoid # permission issues as well as to have things downloaded in a predictable @@ -16,7 +16,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-blima/meta.yaml b/recipes/bioconductor-blima/meta.yaml index 853a126673e1b..f4baf6f66e1ca 100644 --- a/recipes/bioconductor-blima/meta.yaml +++ b/recipes/bioconductor-blima/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.16.0" %} +{% set version = "1.18.0" %} {% set name = "blima" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: a12b89fa5b76052797843be0affdd48c + md5: 2e95ea07342f80f96e6893c08a11ef12 build: number: 0 rpaths: @@ -19,15 +19,15 @@ build: # Suggests: xtable, blimaTestingData, BiocStyle, illuminaHumanv4.db, lumi, knitr requirements: host: - - 'bioconductor-beadarray >=2.32.0,<2.33.0' - - 'bioconductor-biobase >=2.42.0,<2.43.0' - - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' + - 'bioconductor-beadarray >=2.34.0,<2.35.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' + - 'bioconductor-biocgenerics >=0.30.0,<0.31.0' - r-base - 'r-rcpp >=0.12.8' run: - - 'bioconductor-beadarray >=2.32.0,<2.33.0' - - 'bioconductor-biobase >=2.42.0,<2.43.0' - - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' + - 'bioconductor-beadarray >=2.34.0,<2.35.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' + - 'bioconductor-biocgenerics >=0.30.0,<0.31.0' - r-base - 'r-rcpp >=0.12.8' build: diff --git a/recipes/bioconductor-blimatestingdata/meta.yaml b/recipes/bioconductor-blimatestingdata/meta.yaml index 216db70d0daee..61018d8fd702d 100644 --- a/recipes/bioconductor-blimatestingdata/meta.yaml +++ b/recipes/bioconductor-blimatestingdata/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.2.0" %} +{% set version = "1.4.0" %} {% set name = "blimaTestingData" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 7e41a94448ab84c270161d5e9cb5a623 + md5: 0b979387eeedb8a9e0c32e120f2c6593 build: number: 0 rpaths: @@ -23,7 +23,7 @@ requirements: - r-base run: - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-blimatestingdata/post-link.sh b/recipes/bioconductor-blimatestingdata/post-link.sh index e2b36c5324549..eb5f45104c7a1 100644 --- a/recipes/bioconductor-blimatestingdata/post-link.sh +++ b/recipes/bioconductor-blimatestingdata/post-link.sh @@ -1,11 +1,11 @@ #!/bin/bash -FN="blimaTestingData_1.2.0.tar.gz" +FN="blimaTestingData_1.4.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/experiment/src/contrib/blimaTestingData_1.2.0.tar.gz" - "https://bioarchive.galaxyproject.org/blimaTestingData_1.2.0.tar.gz" - "https://depot.galaxyproject.org/software/bioconductor-blimatestingdata/bioconductor-blimatestingdata_1.2.0_src_all.tar.gz" + "https://bioconductor.org/packages/3.9/data/experiment/src/contrib/blimaTestingData_1.4.0.tar.gz" + "https://bioarchive.galaxyproject.org/blimaTestingData_1.4.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-blimatestingdata/bioconductor-blimatestingdata_1.4.0_src_all.tar.gz" ) -MD5="7e41a94448ab84c270161d5e9cb5a623" +MD5="0b979387eeedb8a9e0c32e120f2c6593" # Use a staging area in the conda dir rather than temp dirs, both to avoid # permission issues as well as to have things downloaded in a predictable @@ -16,7 +16,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-blma/meta.yaml b/recipes/bioconductor-blma/meta.yaml index 3d424c5bde083..f74fb2566fb53 100644 --- a/recipes/bioconductor-blma/meta.yaml +++ b/recipes/bioconductor-blma/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.6.0" %} +{% set version = "1.8.0" %} {% set name = "BLMA" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 42b39994812056f775ef77969f32ccdc + md5: 03448e027232a4ce824f5981f73f3858 build: number: 0 rpaths: @@ -20,19 +20,19 @@ build: # Suggests: RUnit, BiocGenerics requirements: host: - - 'bioconductor-biobase >=2.42.0,<2.43.0' - - 'bioconductor-graph >=1.60.0,<1.61.0' - - 'bioconductor-limma >=3.38.0,<3.39.0' - - 'bioconductor-padog >=1.24.0,<1.25.0' - - 'bioconductor-rontotools >=2.10.0,<2.11.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' + - 'bioconductor-graph >=1.62.0,<1.63.0' + - 'bioconductor-limma >=3.40.0,<3.41.0' + - 'bioconductor-padog >=1.26.0,<1.27.0' + - 'bioconductor-rontotools >=2.12.0,<2.13.0' - r-base - r-gsa run: - - 'bioconductor-biobase >=2.42.0,<2.43.0' - - 'bioconductor-graph >=1.60.0,<1.61.0' - - 'bioconductor-limma >=3.38.0,<3.39.0' - - 'bioconductor-padog >=1.24.0,<1.25.0' - - 'bioconductor-rontotools >=2.10.0,<2.11.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' + - 'bioconductor-graph >=1.62.0,<1.63.0' + - 'bioconductor-limma >=3.40.0,<3.41.0' + - 'bioconductor-padog >=1.26.0,<1.27.0' + - 'bioconductor-rontotools >=2.12.0,<2.13.0' - r-base - r-gsa test: diff --git a/recipes/bioconductor-bloodcancermultiomics2017/meta.yaml b/recipes/bioconductor-bloodcancermultiomics2017/meta.yaml index 213fd155cb387..f2bd2a148cede 100644 --- a/recipes/bioconductor-bloodcancermultiomics2017/meta.yaml +++ b/recipes/bioconductor-bloodcancermultiomics2017/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.2.0" %} +{% set version = "1.4.0" %} {% set name = "BloodCancerMultiOmics2017" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 15b928a89d53d59a59901c520a2368f6 + md5: 5836db39c714421d8cd32c63030483b9 build: number: 0 rpaths: @@ -20,9 +20,9 @@ build: # Suggests: BiocStyle, knitr, rmarkdown, abind, AnnotationDbi, biomaRt, broom, colorspace, cowplot, dendsort, doParallel, foreach, forestplot, genefilter, ggbeeswarm, ggtern, gridExtra, hexbin, IHW, limma, magrittr, Matrix, maxstat, nat, org.Hs.eg.db, pheatmap, piano, readxl, Rtsne, tidyr, tidyverse, xtable requirements: host: - - 'bioconductor-biobase >=2.42.0,<2.43.0' - - 'bioconductor-deseq2 >=1.22.0,<1.23.0' - - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' + - 'bioconductor-deseq2 >=1.24.0,<1.25.0' + - 'bioconductor-summarizedexperiment >=1.14.0,<1.15.0' - r-base - r-beeswarm - r-devtools @@ -38,9 +38,9 @@ requirements: - r-survival - r-tibble run: - - 'bioconductor-biobase >=2.42.0,<2.43.0' - - 'bioconductor-deseq2 >=1.22.0,<1.23.0' - - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' + - 'bioconductor-deseq2 >=1.24.0,<1.25.0' + - 'bioconductor-summarizedexperiment >=1.14.0,<1.15.0' - r-base - r-beeswarm - r-devtools @@ -55,7 +55,7 @@ requirements: - r-scales - r-survival - r-tibble - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-bloodcancermultiomics2017/post-link.sh b/recipes/bioconductor-bloodcancermultiomics2017/post-link.sh index 09dd5f367bc23..9a53f6298095e 100644 --- a/recipes/bioconductor-bloodcancermultiomics2017/post-link.sh +++ b/recipes/bioconductor-bloodcancermultiomics2017/post-link.sh @@ -1,11 +1,11 @@ #!/bin/bash -FN="BloodCancerMultiOmics2017_1.2.0.tar.gz" +FN="BloodCancerMultiOmics2017_1.4.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/experiment/src/contrib/BloodCancerMultiOmics2017_1.2.0.tar.gz" - "https://bioarchive.galaxyproject.org/BloodCancerMultiOmics2017_1.2.0.tar.gz" - "https://depot.galaxyproject.org/software/bioconductor-bloodcancermultiomics2017/bioconductor-bloodcancermultiomics2017_1.2.0_src_all.tar.gz" + "https://bioconductor.org/packages/3.9/data/experiment/src/contrib/BloodCancerMultiOmics2017_1.4.0.tar.gz" + "https://bioarchive.galaxyproject.org/BloodCancerMultiOmics2017_1.4.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-bloodcancermultiomics2017/bioconductor-bloodcancermultiomics2017_1.4.0_src_all.tar.gz" ) -MD5="15b928a89d53d59a59901c520a2368f6" +MD5="5836db39c714421d8cd32c63030483b9" # Use a staging area in the conda dir rather than temp dirs, both to avoid # permission issues as well as to have things downloaded in a predictable @@ -16,7 +16,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-bnbc/meta.yaml b/recipes/bioconductor-bnbc/meta.yaml index 36cfe9b3ea8bc..3c4daf1a01986 100644 --- a/recipes/bioconductor-bnbc/meta.yaml +++ b/recipes/bioconductor-bnbc/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.4.0" %} +{% set version = "1.6.0" %} {% set name = "bnbc" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 5aa07b96e10124cc3d9ce6f1b30aa935 + md5: 2ac97c91b275868cae06795309f84f1c build: number: 0 rpaths: @@ -19,28 +19,28 @@ build: # Suggests: BiocStyle, knitr, rmarkdown, RUnit requirements: host: - - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' - - 'bioconductor-ebimage >=4.24.0,<4.25.0' - - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' - - 'bioconductor-genomicranges >=1.34.0,<1.35.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-preprocesscore >=1.44.0,<1.45.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' - - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' - - 'bioconductor-sva >=3.30.0,<3.31.0' + - 'bioconductor-biocgenerics >=0.30.0,<0.31.0' + - 'bioconductor-ebimage >=4.26.0,<4.27.0' + - 'bioconductor-genomeinfodb >=1.20.0,<1.21.0' + - 'bioconductor-genomicranges >=1.36.0,<1.37.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-preprocesscore >=1.46.0,<1.47.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' + - 'bioconductor-summarizedexperiment >=1.14.0,<1.15.0' + - 'bioconductor-sva >=3.32.0,<3.33.0' - r-base - r-matrixstats - 'r-rcpp >=0.12.12' run: - - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' - - 'bioconductor-ebimage >=4.24.0,<4.25.0' - - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' - - 'bioconductor-genomicranges >=1.34.0,<1.35.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-preprocesscore >=1.44.0,<1.45.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' - - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' - - 'bioconductor-sva >=3.30.0,<3.31.0' + - 'bioconductor-biocgenerics >=0.30.0,<0.31.0' + - 'bioconductor-ebimage >=4.26.0,<4.27.0' + - 'bioconductor-genomeinfodb >=1.20.0,<1.21.0' + - 'bioconductor-genomicranges >=1.36.0,<1.37.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-preprocesscore >=1.46.0,<1.47.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' + - 'bioconductor-summarizedexperiment >=1.14.0,<1.15.0' + - 'bioconductor-sva >=3.32.0,<3.33.0' - r-base - r-matrixstats - 'r-rcpp >=0.12.12' diff --git a/recipes/bioconductor-bodymaprat/meta.yaml b/recipes/bioconductor-bodymaprat/meta.yaml new file mode 100644 index 0000000000000..5db9973f0169b --- /dev/null +++ b/recipes/bioconductor-bodymaprat/meta.yaml @@ -0,0 +1,38 @@ +{% set version = "1.0.0" %} +{% set name = "bodymapRat" %} +{% set bioc = "3.9" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: 828a327a3b634d6861595baea00c4ac3 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: knitr, BiocStyle, testthat +requirements: + host: + - 'bioconductor-experimenthub >=1.10.0,<1.11.0' + - 'bioconductor-summarizedexperiment >=1.14.0,<1.15.0' + - r-base + run: + - 'bioconductor-experimenthub >=1.10.0,<1.11.0' + - 'bioconductor-summarizedexperiment >=1.14.0,<1.15.0' + - r-base + - curl +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html' + license: 'CC BY 4.0' + summary: 'This package contains a SummarizedExperiment from the Yu et al. (2013) paper that performed the rat BodyMap across 11 organs and 4 developmental stages. Raw FASTQ files were downloaded and mapped using STAR. Data is available on ExperimentHub as a data package.' + diff --git a/recipes/bioconductor-bodymaprat/post-link.sh b/recipes/bioconductor-bodymaprat/post-link.sh new file mode 100644 index 0000000000000..4e0849692c39a --- /dev/null +++ b/recipes/bioconductor-bodymaprat/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="bodymapRat_1.0.0.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.9/data/experiment/src/contrib/bodymapRat_1.0.0.tar.gz" + "https://bioarchive.galaxyproject.org/bodymapRat_1.0.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-bodymaprat/bioconductor-bodymaprat_1.0.0_src_all.tar.gz" +) +MD5="828a327a3b634d6861595baea00c4ac3" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + curl $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-bodymaprat/pre-unlink.sh b/recipes/bioconductor-bodymaprat/pre-unlink.sh new file mode 100644 index 0000000000000..15db36347b103 --- /dev/null +++ b/recipes/bioconductor-bodymaprat/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ bodymapRat diff --git a/recipes/bioconductor-bovine.db/meta.yaml b/recipes/bioconductor-bovine.db/meta.yaml index 2d74db4665b52..acd1368c373f7 100644 --- a/recipes/bioconductor-bovine.db/meta.yaml +++ b/recipes/bioconductor-bovine.db/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.2.3" %} {% set name = "bovine.db" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -12,7 +12,7 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 0006dd79279fa1bf69a275e0586f2197 build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ @@ -20,14 +20,14 @@ build: # Suggests: DBI, annotate, RUnit requirements: host: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' - - 'bioconductor-org.bt.eg.db >=3.7.0,<3.8.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' + - 'bioconductor-org.bt.eg.db >=3.8.0,<3.9.0' - r-base run: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' - - 'bioconductor-org.bt.eg.db >=3.7.0,<3.8.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' + - 'bioconductor-org.bt.eg.db >=3.8.0,<3.9.0' - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-bovine.db/post-link.sh b/recipes/bioconductor-bovine.db/post-link.sh index fa327eb20d587..639b670c6b682 100644 --- a/recipes/bioconductor-bovine.db/post-link.sh +++ b/recipes/bioconductor-bovine.db/post-link.sh @@ -1,9 +1,10 @@ #!/bin/bash FN="bovine.db_3.2.3.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/bovine.db_3.2.3.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/bovine.db_3.2.3.tar.gz" "https://bioarchive.galaxyproject.org/bovine.db_3.2.3.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-bovine.db/bioconductor-bovine.db_3.2.3_src_all.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-bovine.db/bioconductor-bovine.db_3.2.3_src_all.tar.gz" ) MD5="0006dd79279fa1bf69a275e0586f2197" @@ -16,7 +17,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-bovine.db0/meta.yaml b/recipes/bioconductor-bovine.db0/meta.yaml index a70955401d4fd..d7bb01459043c 100644 --- a/recipes/bioconductor-bovine.db0/meta.yaml +++ b/recipes/bioconductor-bovine.db0/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "3.7.1" %} +{% set version = "3.8.2" %} {% set name = "bovine.db0" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 26ad273e690096d02697afa70888c38c + md5: b7c423c42b6aa3519636b4b7f204840a build: number: 0 rpaths: @@ -19,12 +19,12 @@ build: noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' - r-base run: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-bovine.db0/post-link.sh b/recipes/bioconductor-bovine.db0/post-link.sh index 3249cd9c9462c..f47a0bfb214ec 100644 --- a/recipes/bioconductor-bovine.db0/post-link.sh +++ b/recipes/bioconductor-bovine.db0/post-link.sh @@ -1,11 +1,11 @@ #!/bin/bash -FN="bovine.db0_3.7.1.tar.gz" +FN="bovine.db0_3.8.2.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/bovine.db0_3.7.1.tar.gz" - "https://bioarchive.galaxyproject.org/bovine.db0_3.7.1.tar.gz" - "https://depot.galaxyproject.org/software/bioconductor-bovine.db0/bioconductor-bovine.db0_3.7.1_src_all.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/bovine.db0_3.8.2.tar.gz" + "https://bioarchive.galaxyproject.org/bovine.db0_3.8.2.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-bovine.db0/bioconductor-bovine.db0_3.8.2_src_all.tar.gz" ) -MD5="26ad273e690096d02697afa70888c38c" +MD5="b7c423c42b6aa3519636b4b7f204840a" # Use a staging area in the conda dir rather than temp dirs, both to avoid # permission issues as well as to have things downloaded in a predictable @@ -16,7 +16,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-bovinecdf/meta.yaml b/recipes/bioconductor-bovinecdf/meta.yaml index 5967e371f11df..ea2919cd2f6bd 100644 --- a/recipes/bioconductor-bovinecdf/meta.yaml +++ b/recipes/bioconductor-bovinecdf/meta.yaml @@ -1,6 +1,6 @@ {% set version = "2.18.0" %} {% set name = "bovinecdf" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -12,19 +12,19 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: e155fc7d5f84ee420d9b250a639af305 build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' - r-base run: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-bovinecdf/post-link.sh b/recipes/bioconductor-bovinecdf/post-link.sh index 959cc29725a63..7f1eff55ce22e 100644 --- a/recipes/bioconductor-bovinecdf/post-link.sh +++ b/recipes/bioconductor-bovinecdf/post-link.sh @@ -1,9 +1,10 @@ #!/bin/bash FN="bovinecdf_2.18.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/bovinecdf_2.18.0.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/bovinecdf_2.18.0.tar.gz" "https://bioarchive.galaxyproject.org/bovinecdf_2.18.0.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-bovinecdf/bioconductor-bovinecdf_2.18.0_src_all.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-bovinecdf/bioconductor-bovinecdf_2.18.0_src_all.tar.gz" ) MD5="e155fc7d5f84ee420d9b250a639af305" @@ -16,7 +17,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-bovineprobe/meta.yaml b/recipes/bioconductor-bovineprobe/meta.yaml index 66f0294de4222..0ff972a797a6b 100644 --- a/recipes/bioconductor-bovineprobe/meta.yaml +++ b/recipes/bioconductor-bovineprobe/meta.yaml @@ -1,6 +1,6 @@ {% set version = "2.18.0" %} {% set name = "bovineprobe" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -12,19 +12,19 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 9f9e25fc8c7a76acf541745b7c09748b build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' - r-base run: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-bovineprobe/post-link.sh b/recipes/bioconductor-bovineprobe/post-link.sh index 4a7e958e3ae3f..bbf830bca6084 100644 --- a/recipes/bioconductor-bovineprobe/post-link.sh +++ b/recipes/bioconductor-bovineprobe/post-link.sh @@ -1,9 +1,10 @@ #!/bin/bash FN="bovineprobe_2.18.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/bovineprobe_2.18.0.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/bovineprobe_2.18.0.tar.gz" "https://bioarchive.galaxyproject.org/bovineprobe_2.18.0.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-bovineprobe/bioconductor-bovineprobe_2.18.0_src_all.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-bovineprobe/bioconductor-bovineprobe_2.18.0_src_all.tar.gz" ) MD5="9f9e25fc8c7a76acf541745b7c09748b" @@ -16,7 +17,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-bprmeth/meta.yaml b/recipes/bioconductor-bprmeth/meta.yaml index 0e1d9e914b923..ec69158060ac5 100644 --- a/recipes/bioconductor-bprmeth/meta.yaml +++ b/recipes/bioconductor-bprmeth/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.8.1" %} +{% set version = "1.10.0" %} {% set name = "BPRMeth" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 06448d58568d7bd992940a07b65acc79 + md5: bbcac2501e39ec8cc0610666f24dafa7 build: number: 0 rpaths: @@ -19,10 +19,10 @@ build: # Suggests: testthat, knitr, rmarkdown requirements: host: - - 'bioconductor-biocstyle >=2.10.0,<2.11.0' - - 'bioconductor-genomicranges >=1.34.0,<1.35.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-biocstyle >=2.12.0,<2.13.0' + - 'bioconductor-genomicranges >=1.36.0,<1.37.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' - r-assertthat - r-base - r-cowplot @@ -42,10 +42,10 @@ requirements: - r-rcpparmadillo - r-truncnorm run: - - 'bioconductor-biocstyle >=2.10.0,<2.11.0' - - 'bioconductor-genomicranges >=1.34.0,<1.35.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-biocstyle >=2.12.0,<2.13.0' + - 'bioconductor-genomicranges >=1.36.0,<1.37.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' - r-assertthat - r-base - r-cowplot diff --git a/recipes/bioconductor-brain/meta.yaml b/recipes/bioconductor-brain/meta.yaml index 0d56d5ff75c15..7fa3e1a4a611f 100644 --- a/recipes/bioconductor-brain/meta.yaml +++ b/recipes/bioconductor-brain/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.28.1" %} +{% set version = "1.30.0" %} {% set name = "BRAIN" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 363be3229f287c660f2150891538bf4d + md5: 66a32ce11265c7b523f7e4736aa777c4 build: number: 0 rpaths: @@ -19,12 +19,12 @@ build: noarch: generic requirements: host: - - 'bioconductor-biostrings >=2.50.0,<2.51.0' + - 'bioconductor-biostrings >=2.52.0,<2.53.0' - r-base - r-lattice - r-polynomf run: - - 'bioconductor-biostrings >=2.50.0,<2.51.0' + - 'bioconductor-biostrings >=2.52.0,<2.53.0' - r-base - r-lattice - r-polynomf diff --git a/recipes/bioconductor-brainimager/meta.yaml b/recipes/bioconductor-brainimager/meta.yaml index 01dc3279c8bcd..76e7fb00034b4 100644 --- a/recipes/bioconductor-brainimager/meta.yaml +++ b/recipes/bioconductor-brainimager/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.0.0" %} +{% set version = "1.1.0" %} {% set name = "brainImageR" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: c77706bbf26dc837b806693cba2728d3 + md5: 4e4558bdb154e1bad002543fca8f1c10 build: number: 0 rpaths: @@ -20,8 +20,8 @@ build: # Suggests: knitr, rmarkdown requirements: host: - - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' - - 'bioconductor-experimenthub >=1.8.0,<1.9.0' + - 'bioconductor-biocgenerics >=0.30.0,<0.31.0' + - 'bioconductor-experimenthub >=1.10.0,<1.11.0' - r-base - r-ggplot2 - r-gridextra @@ -29,8 +29,8 @@ requirements: - r-rcolorbrewer - r-testthat run: - - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' - - 'bioconductor-experimenthub >=1.8.0,<1.9.0' + - 'bioconductor-biocgenerics >=0.30.0,<0.31.0' + - 'bioconductor-experimenthub >=1.10.0,<1.11.0' - r-base - r-ggplot2 - r-gridextra diff --git a/recipes/bioconductor-brainimagerdata/meta.yaml b/recipes/bioconductor-brainimagerdata/meta.yaml index a7615c52d92f0..f13464a1d7480 100644 --- a/recipes/bioconductor-brainimagerdata/meta.yaml +++ b/recipes/bioconductor-brainimagerdata/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.0.0" %} +{% set version = "1.2.0" %} {% set name = "brainImageRdata" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 87e676b7cde0a2abb781670ade0e68d9 + md5: 54c39516d8efa96d6404737c09bddb94 build: number: 0 rpaths: @@ -20,12 +20,12 @@ build: # Suggests: knitr requirements: host: - - 'bioconductor-experimenthub >=1.8.0,<1.9.0' + - 'bioconductor-experimenthub >=1.10.0,<1.11.0' - r-base run: - - 'bioconductor-experimenthub >=1.8.0,<1.9.0' + - 'bioconductor-experimenthub >=1.10.0,<1.11.0' - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-brainimagerdata/post-link.sh b/recipes/bioconductor-brainimagerdata/post-link.sh index ceb99527cac88..dcc75f61e1cf7 100644 --- a/recipes/bioconductor-brainimagerdata/post-link.sh +++ b/recipes/bioconductor-brainimagerdata/post-link.sh @@ -1,11 +1,11 @@ #!/bin/bash -FN="brainImageRdata_1.0.0.tar.gz" +FN="brainImageRdata_1.2.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/experiment/src/contrib/brainImageRdata_1.0.0.tar.gz" - "https://bioarchive.galaxyproject.org/brainImageRdata_1.0.0.tar.gz" - "https://depot.galaxyproject.org/software/bioconductor-brainimagerdata/bioconductor-brainimagerdata_1.0.0_src_all.tar.gz" + "https://bioconductor.org/packages/3.9/data/experiment/src/contrib/brainImageRdata_1.2.0.tar.gz" + "https://bioarchive.galaxyproject.org/brainImageRdata_1.2.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-brainimagerdata/bioconductor-brainimagerdata_1.2.0_src_all.tar.gz" ) -MD5="87e676b7cde0a2abb781670ade0e68d9" +MD5="54c39516d8efa96d6404737c09bddb94" # Use a staging area in the conda dir rather than temp dirs, both to avoid # permission issues as well as to have things downloaded in a predictable @@ -16,7 +16,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-brainstars/meta.yaml b/recipes/bioconductor-brainstars/meta.yaml index 9484ef8d76f14..f28efe3e33151 100644 --- a/recipes/bioconductor-brainstars/meta.yaml +++ b/recipes/bioconductor-brainstars/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.26.0" %} +{% set version = "1.28.0" %} {% set name = "BrainStars" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 163e6ff00d0a1c573ddbcc5631fb1c1e + md5: 56f8fb333636c6039354361fb6ea6c7e build: number: 0 rpaths: @@ -19,12 +19,12 @@ build: noarch: generic requirements: host: - - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' - r-base - r-rcurl - r-rjsonio run: - - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' - r-base - r-rcurl - r-rjsonio diff --git a/recipes/bioconductor-branchpointer/meta.yaml b/recipes/bioconductor-branchpointer/meta.yaml index 7bdfff05dfcd0..8720191366608 100644 --- a/recipes/bioconductor-branchpointer/meta.yaml +++ b/recipes/bioconductor-branchpointer/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.8.0" %} +{% set version = "1.10.0" %} {% set name = "branchpointer" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 6632b483e3c0cbcf604ec23b145ce82a + md5: 3b81c925b5c40c1767e6b923782bf57e build: number: 0 rpaths: @@ -20,14 +20,14 @@ build: # Suggests: knitr, BiocStyle requirements: host: - - 'bioconductor-biomart >=2.38.0,<2.39.0' - - 'bioconductor-biostrings >=2.50.0,<2.51.0' + - 'bioconductor-biomart >=2.40.0,<2.41.0' + - 'bioconductor-biostrings >=2.52.0,<2.53.0' - 'bioconductor-bsgenome.hsapiens.ucsc.hg38 >=1.4.0,<1.5.0' - - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' - - 'bioconductor-genomicranges >=1.34.0,<1.35.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-rtracklayer >=1.42.0,<1.43.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-genomeinfodb >=1.20.0,<1.21.0' + - 'bioconductor-genomicranges >=1.36.0,<1.37.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-rtracklayer >=1.44.0,<1.45.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' - r-base - r-caret - r-cowplot @@ -38,14 +38,14 @@ requirements: - r-plyr - r-stringr run: - - 'bioconductor-biomart >=2.38.0,<2.39.0' - - 'bioconductor-biostrings >=2.50.0,<2.51.0' + - 'bioconductor-biomart >=2.40.0,<2.41.0' + - 'bioconductor-biostrings >=2.52.0,<2.53.0' - 'bioconductor-bsgenome.hsapiens.ucsc.hg38 >=1.4.0,<1.5.0' - - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' - - 'bioconductor-genomicranges >=1.34.0,<1.35.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-rtracklayer >=1.42.0,<1.43.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-genomeinfodb >=1.20.0,<1.21.0' + - 'bioconductor-genomicranges >=1.36.0,<1.37.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-rtracklayer >=1.44.0,<1.45.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' - r-base - r-caret - r-cowplot diff --git a/recipes/bioconductor-breakpointr/meta.yaml b/recipes/bioconductor-breakpointr/meta.yaml index 341124a37b723..9b02f4a8804b7 100644 --- a/recipes/bioconductor-breakpointr/meta.yaml +++ b/recipes/bioconductor-breakpointr/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.0.0" %} +{% set version = "1.2.0" %} {% set name = "breakpointR" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,9 +10,9 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: a9e609669b8ffbc8116345d14dc59e42 + md5: acb110bb2c43c9bfac81309de7281960 build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ @@ -20,14 +20,14 @@ build: # Suggests: knitr, BiocStyle, testthat requirements: host: - - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' - - 'bioconductor-breakpointrdata >=1.0.0,<1.1.0' - - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' - - 'bioconductor-genomicalignments >=1.18.0,<1.19.0' - - 'bioconductor-genomicranges >=1.34.0,<1.35.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-rsamtools >=1.34.0,<1.35.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-biocgenerics >=0.30.0,<0.31.0' + - 'bioconductor-breakpointrdata >=1.2.0,<1.3.0' + - 'bioconductor-genomeinfodb >=1.20.0,<1.21.0' + - 'bioconductor-genomicalignments >=1.20.0,<1.21.0' + - 'bioconductor-genomicranges >=1.36.0,<1.37.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-rsamtools >=2.0.0,<2.1.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' - r-base - r-cowplot - r-doparallel @@ -35,14 +35,14 @@ requirements: - r-ggplot2 - r-gtools run: - - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' - - 'bioconductor-breakpointrdata >=1.0.0,<1.1.0' - - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' - - 'bioconductor-genomicalignments >=1.18.0,<1.19.0' - - 'bioconductor-genomicranges >=1.34.0,<1.35.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-rsamtools >=1.34.0,<1.35.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-biocgenerics >=0.30.0,<0.31.0' + - 'bioconductor-breakpointrdata >=1.2.0,<1.3.0' + - 'bioconductor-genomeinfodb >=1.20.0,<1.21.0' + - 'bioconductor-genomicalignments >=1.20.0,<1.21.0' + - 'bioconductor-genomicranges >=1.36.0,<1.37.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-rsamtools >=2.0.0,<2.1.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' - r-base - r-cowplot - r-doparallel diff --git a/recipes/bioconductor-breakpointrdata/meta.yaml b/recipes/bioconductor-breakpointrdata/meta.yaml index 6f39f0351b27e..6cffb384b004d 100644 --- a/recipes/bioconductor-breakpointrdata/meta.yaml +++ b/recipes/bioconductor-breakpointrdata/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.0.0" %} +{% set version = "1.2.0" %} {% set name = "breakpointRdata" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 6484ead0a5a57fe29f9bd0edba517f10 + md5: 5bb31f8819f87705c211d99636af87eb build: number: 0 rpaths: @@ -23,7 +23,7 @@ requirements: - r-base run: - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-breakpointrdata/post-link.sh b/recipes/bioconductor-breakpointrdata/post-link.sh index 8e36317a9d93a..cd81585f6eb00 100644 --- a/recipes/bioconductor-breakpointrdata/post-link.sh +++ b/recipes/bioconductor-breakpointrdata/post-link.sh @@ -1,11 +1,11 @@ #!/bin/bash -FN="breakpointRdata_1.0.0.tar.gz" +FN="breakpointRdata_1.2.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/experiment/src/contrib/breakpointRdata_1.0.0.tar.gz" - "https://bioarchive.galaxyproject.org/breakpointRdata_1.0.0.tar.gz" - "https://depot.galaxyproject.org/software/bioconductor-breakpointrdata/bioconductor-breakpointrdata_1.0.0_src_all.tar.gz" + "https://bioconductor.org/packages/3.9/data/experiment/src/contrib/breakpointRdata_1.2.0.tar.gz" + "https://bioarchive.galaxyproject.org/breakpointRdata_1.2.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-breakpointrdata/bioconductor-breakpointrdata_1.2.0_src_all.tar.gz" ) -MD5="6484ead0a5a57fe29f9bd0edba517f10" +MD5="5bb31f8819f87705c211d99636af87eb" # Use a staging area in the conda dir rather than temp dirs, both to avoid # permission issues as well as to have things downloaded in a predictable @@ -16,7 +16,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-breastcancermainz/meta.yaml b/recipes/bioconductor-breastcancermainz/meta.yaml index 006ee5e7ecd49..f3fc563ea0cb0 100644 --- a/recipes/bioconductor-breastcancermainz/meta.yaml +++ b/recipes/bioconductor-breastcancermainz/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.20.0" %} +{% set version = "1.22.0" %} {% set name = "breastCancerMAINZ" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: d3c2b64b8798cb80b9f214fcb4958dfd + md5: f04819049e4092504c4f5a7c84f0ce4b build: number: 0 rpaths: @@ -23,7 +23,7 @@ requirements: - r-base run: - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-breastcancermainz/post-link.sh b/recipes/bioconductor-breastcancermainz/post-link.sh index 358ea9380b52c..53e7f99ecc0ca 100644 --- a/recipes/bioconductor-breastcancermainz/post-link.sh +++ b/recipes/bioconductor-breastcancermainz/post-link.sh @@ -1,11 +1,11 @@ #!/bin/bash -FN="breastCancerMAINZ_1.20.0.tar.gz" +FN="breastCancerMAINZ_1.22.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/experiment/src/contrib/breastCancerMAINZ_1.20.0.tar.gz" - "https://bioarchive.galaxyproject.org/breastCancerMAINZ_1.20.0.tar.gz" - "https://depot.galaxyproject.org/software/bioconductor-breastcancermainz/bioconductor-breastcancermainz_1.20.0_src_all.tar.gz" + "https://bioconductor.org/packages/3.9/data/experiment/src/contrib/breastCancerMAINZ_1.22.0.tar.gz" + "https://bioarchive.galaxyproject.org/breastCancerMAINZ_1.22.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-breastcancermainz/bioconductor-breastcancermainz_1.22.0_src_all.tar.gz" ) -MD5="d3c2b64b8798cb80b9f214fcb4958dfd" +MD5="f04819049e4092504c4f5a7c84f0ce4b" # Use a staging area in the conda dir rather than temp dirs, both to avoid # permission issues as well as to have things downloaded in a predictable @@ -16,7 +16,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-breastcancernki/meta.yaml b/recipes/bioconductor-breastcancernki/meta.yaml index 33eb5847d7ead..7cb83c4db41b4 100644 --- a/recipes/bioconductor-breastcancernki/meta.yaml +++ b/recipes/bioconductor-breastcancernki/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.20.0" %} +{% set version = "1.22.0" %} {% set name = "breastCancerNKI" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 2f70179c1ded047824519512d9eed41b + md5: 60ba238770e734f7995c540e52ced5d7 build: number: 0 rpaths: @@ -23,7 +23,7 @@ requirements: - r-base run: - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-breastcancernki/post-link.sh b/recipes/bioconductor-breastcancernki/post-link.sh index 6c7748940f8e8..48f4a93072aca 100644 --- a/recipes/bioconductor-breastcancernki/post-link.sh +++ b/recipes/bioconductor-breastcancernki/post-link.sh @@ -1,11 +1,11 @@ #!/bin/bash -FN="breastCancerNKI_1.20.0.tar.gz" +FN="breastCancerNKI_1.22.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/experiment/src/contrib/breastCancerNKI_1.20.0.tar.gz" - "https://bioarchive.galaxyproject.org/breastCancerNKI_1.20.0.tar.gz" - "https://depot.galaxyproject.org/software/bioconductor-breastcancernki/bioconductor-breastcancernki_1.20.0_src_all.tar.gz" + "https://bioconductor.org/packages/3.9/data/experiment/src/contrib/breastCancerNKI_1.22.0.tar.gz" + "https://bioarchive.galaxyproject.org/breastCancerNKI_1.22.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-breastcancernki/bioconductor-breastcancernki_1.22.0_src_all.tar.gz" ) -MD5="2f70179c1ded047824519512d9eed41b" +MD5="60ba238770e734f7995c540e52ced5d7" # Use a staging area in the conda dir rather than temp dirs, both to avoid # permission issues as well as to have things downloaded in a predictable @@ -16,7 +16,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-breastcancertransbig/meta.yaml b/recipes/bioconductor-breastcancertransbig/meta.yaml index 5a9727b80c727..edef622c831af 100644 --- a/recipes/bioconductor-breastcancertransbig/meta.yaml +++ b/recipes/bioconductor-breastcancertransbig/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.20.0" %} +{% set version = "1.22.0" %} {% set name = "breastCancerTRANSBIG" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: c3fe59c8cf826647a2f11320f6b7a3bd + md5: 1752abd0640ff2958d4b91752b68b28c build: number: 0 rpaths: @@ -23,7 +23,7 @@ requirements: - r-base run: - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-breastcancertransbig/post-link.sh b/recipes/bioconductor-breastcancertransbig/post-link.sh index 3545bfadb41ac..656991656a6aa 100644 --- a/recipes/bioconductor-breastcancertransbig/post-link.sh +++ b/recipes/bioconductor-breastcancertransbig/post-link.sh @@ -1,11 +1,11 @@ #!/bin/bash -FN="breastCancerTRANSBIG_1.20.0.tar.gz" +FN="breastCancerTRANSBIG_1.22.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/experiment/src/contrib/breastCancerTRANSBIG_1.20.0.tar.gz" - "https://bioarchive.galaxyproject.org/breastCancerTRANSBIG_1.20.0.tar.gz" - "https://depot.galaxyproject.org/software/bioconductor-breastcancertransbig/bioconductor-breastcancertransbig_1.20.0_src_all.tar.gz" + "https://bioconductor.org/packages/3.9/data/experiment/src/contrib/breastCancerTRANSBIG_1.22.0.tar.gz" + "https://bioarchive.galaxyproject.org/breastCancerTRANSBIG_1.22.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-breastcancertransbig/bioconductor-breastcancertransbig_1.22.0_src_all.tar.gz" ) -MD5="c3fe59c8cf826647a2f11320f6b7a3bd" +MD5="1752abd0640ff2958d4b91752b68b28c" # Use a staging area in the conda dir rather than temp dirs, both to avoid # permission issues as well as to have things downloaded in a predictable @@ -16,7 +16,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-breastcancerunt/meta.yaml b/recipes/bioconductor-breastcancerunt/meta.yaml index 496ce28ada225..a6d79704c060f 100644 --- a/recipes/bioconductor-breastcancerunt/meta.yaml +++ b/recipes/bioconductor-breastcancerunt/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.20.0" %} +{% set version = "1.22.0" %} {% set name = "breastCancerUNT" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: f70937326bfeab71ab497ce4ea46ff76 + md5: 4abb8ad6dee3b46bfe38e5712993418d build: number: 0 rpaths: @@ -23,7 +23,7 @@ requirements: - r-base run: - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-breastcancerunt/post-link.sh b/recipes/bioconductor-breastcancerunt/post-link.sh index ba326183a48fc..b06b8293ccbdb 100644 --- a/recipes/bioconductor-breastcancerunt/post-link.sh +++ b/recipes/bioconductor-breastcancerunt/post-link.sh @@ -1,11 +1,11 @@ #!/bin/bash -FN="breastCancerUNT_1.20.0.tar.gz" +FN="breastCancerUNT_1.22.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/experiment/src/contrib/breastCancerUNT_1.20.0.tar.gz" - "https://bioarchive.galaxyproject.org/breastCancerUNT_1.20.0.tar.gz" - "https://depot.galaxyproject.org/software/bioconductor-breastcancerunt/bioconductor-breastcancerunt_1.20.0_src_all.tar.gz" + "https://bioconductor.org/packages/3.9/data/experiment/src/contrib/breastCancerUNT_1.22.0.tar.gz" + "https://bioarchive.galaxyproject.org/breastCancerUNT_1.22.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-breastcancerunt/bioconductor-breastcancerunt_1.22.0_src_all.tar.gz" ) -MD5="f70937326bfeab71ab497ce4ea46ff76" +MD5="4abb8ad6dee3b46bfe38e5712993418d" # Use a staging area in the conda dir rather than temp dirs, both to avoid # permission issues as well as to have things downloaded in a predictable @@ -16,7 +16,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-breastcancerupp/meta.yaml b/recipes/bioconductor-breastcancerupp/meta.yaml index db2cbf669c63c..4779dc3959746 100644 --- a/recipes/bioconductor-breastcancerupp/meta.yaml +++ b/recipes/bioconductor-breastcancerupp/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.20.0" %} +{% set version = "1.22.0" %} {% set name = "breastCancerUPP" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 8a54948ea0e0328b3035e3f4d4551960 + md5: 2c41fe7534c5a603b6aeef57e7b4600e build: number: 0 rpaths: @@ -23,7 +23,7 @@ requirements: - r-base run: - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-breastcancerupp/post-link.sh b/recipes/bioconductor-breastcancerupp/post-link.sh index 827a9c2b33a30..16a66b82aedf7 100644 --- a/recipes/bioconductor-breastcancerupp/post-link.sh +++ b/recipes/bioconductor-breastcancerupp/post-link.sh @@ -1,11 +1,11 @@ #!/bin/bash -FN="breastCancerUPP_1.20.0.tar.gz" +FN="breastCancerUPP_1.22.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/experiment/src/contrib/breastCancerUPP_1.20.0.tar.gz" - "https://bioarchive.galaxyproject.org/breastCancerUPP_1.20.0.tar.gz" - "https://depot.galaxyproject.org/software/bioconductor-breastcancerupp/bioconductor-breastcancerupp_1.20.0_src_all.tar.gz" + "https://bioconductor.org/packages/3.9/data/experiment/src/contrib/breastCancerUPP_1.22.0.tar.gz" + "https://bioarchive.galaxyproject.org/breastCancerUPP_1.22.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-breastcancerupp/bioconductor-breastcancerupp_1.22.0_src_all.tar.gz" ) -MD5="8a54948ea0e0328b3035e3f4d4551960" +MD5="2c41fe7534c5a603b6aeef57e7b4600e" # Use a staging area in the conda dir rather than temp dirs, both to avoid # permission issues as well as to have things downloaded in a predictable @@ -16,7 +16,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-breastcancervdx/meta.yaml b/recipes/bioconductor-breastcancervdx/meta.yaml index 571d409e31527..e4276dc93d4e3 100644 --- a/recipes/bioconductor-breastcancervdx/meta.yaml +++ b/recipes/bioconductor-breastcancervdx/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.20.0" %} +{% set version = "1.22.0" %} {% set name = "breastCancerVDX" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 4b05a31ca8f4a0a069137dfc614039e8 + md5: b437da5fd7abf3b1f10276dd6543217d build: number: 0 rpaths: @@ -23,7 +23,7 @@ requirements: - r-base run: - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-breastcancervdx/post-link.sh b/recipes/bioconductor-breastcancervdx/post-link.sh index be586e50bc278..146654fd3f79e 100644 --- a/recipes/bioconductor-breastcancervdx/post-link.sh +++ b/recipes/bioconductor-breastcancervdx/post-link.sh @@ -1,11 +1,11 @@ #!/bin/bash -FN="breastCancerVDX_1.20.0.tar.gz" +FN="breastCancerVDX_1.22.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/experiment/src/contrib/breastCancerVDX_1.20.0.tar.gz" - "https://bioarchive.galaxyproject.org/breastCancerVDX_1.20.0.tar.gz" - "https://depot.galaxyproject.org/software/bioconductor-breastcancervdx/bioconductor-breastcancervdx_1.20.0_src_all.tar.gz" + "https://bioconductor.org/packages/3.9/data/experiment/src/contrib/breastCancerVDX_1.22.0.tar.gz" + "https://bioarchive.galaxyproject.org/breastCancerVDX_1.22.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-breastcancervdx/bioconductor-breastcancervdx_1.22.0_src_all.tar.gz" ) -MD5="4b05a31ca8f4a0a069137dfc614039e8" +MD5="b437da5fd7abf3b1f10276dd6543217d" # Use a staging area in the conda dir rather than temp dirs, both to avoid # permission issues as well as to have things downloaded in a predictable @@ -16,7 +16,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-brgedata/meta.yaml b/recipes/bioconductor-brgedata/meta.yaml index 3efe817c4f260..706dd334187e0 100644 --- a/recipes/bioconductor-brgedata/meta.yaml +++ b/recipes/bioconductor-brgedata/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.4.0" %} +{% set version = "1.6.0" %} {% set name = "brgedata" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: d2ad8ac2f818311243fa6afe0907e93c + md5: cb1cdff76c21aabfa29e0004360532d8 build: number: 0 rpaths: @@ -20,14 +20,14 @@ build: # Suggests: minfi, MultiAssayExperiment, knitr, rexposome requirements: host: - - 'bioconductor-biobase >=2.42.0,<2.43.0' - - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' + - 'bioconductor-summarizedexperiment >=1.14.0,<1.15.0' - r-base run: - - 'bioconductor-biobase >=2.42.0,<2.43.0' - - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' + - 'bioconductor-summarizedexperiment >=1.14.0,<1.15.0' - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-brgedata/post-link.sh b/recipes/bioconductor-brgedata/post-link.sh index e80ec005b06bc..badabad739d48 100644 --- a/recipes/bioconductor-brgedata/post-link.sh +++ b/recipes/bioconductor-brgedata/post-link.sh @@ -1,11 +1,11 @@ #!/bin/bash -FN="brgedata_1.4.0.tar.gz" +FN="brgedata_1.6.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/experiment/src/contrib/brgedata_1.4.0.tar.gz" - "https://bioarchive.galaxyproject.org/brgedata_1.4.0.tar.gz" - "https://depot.galaxyproject.org/software/bioconductor-brgedata/bioconductor-brgedata_1.4.0_src_all.tar.gz" + "https://bioconductor.org/packages/3.9/data/experiment/src/contrib/brgedata_1.6.0.tar.gz" + "https://bioarchive.galaxyproject.org/brgedata_1.6.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-brgedata/bioconductor-brgedata_1.6.0_src_all.tar.gz" ) -MD5="d2ad8ac2f818311243fa6afe0907e93c" +MD5="cb1cdff76c21aabfa29e0004360532d8" # Use a staging area in the conda dir rather than temp dirs, both to avoid # permission issues as well as to have things downloaded in a predictable @@ -16,7 +16,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-bridge/meta.yaml b/recipes/bioconductor-bridge/meta.yaml index 14205ddcf7298..b11592ba80c28 100644 --- a/recipes/bioconductor-bridge/meta.yaml +++ b/recipes/bioconductor-bridge/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.46.0" %} +{% set version = "1.48.0" %} {% set name = "bridge" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 6c1d00b6b26a2ba3ae999dac684e71eb + md5: 480a9c00864b54d93b8c319a3db68795 build: number: 0 rpaths: @@ -18,10 +18,10 @@ build: - lib/ requirements: host: - - 'bioconductor-rama >=1.56.0,<1.57.0' + - 'bioconductor-rama >=1.58.0,<1.59.0' - r-base run: - - 'bioconductor-rama >=1.56.0,<1.57.0' + - 'bioconductor-rama >=1.58.0,<1.59.0' - r-base build: - {{ compiler('c') }} diff --git a/recipes/bioconductor-bridgedbr/meta.yaml b/recipes/bioconductor-bridgedbr/meta.yaml index d1c88ffa16010..ed6f116c78947 100644 --- a/recipes/bioconductor-bridgedbr/meta.yaml +++ b/recipes/bioconductor-bridgedbr/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.16.1" %} +{% set version = "1.18.0" %} {% set name = "BridgeDbR" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: b83ee15b26b1686871641054744343b8 + md5: 791900b33b1997d6e5308c888d4ca2ea build: number: 0 rpaths: diff --git a/recipes/bioconductor-bronchialil13/meta.yaml b/recipes/bioconductor-bronchialil13/meta.yaml index 76daf40174509..a8422543f9de1 100644 --- a/recipes/bioconductor-bronchialil13/meta.yaml +++ b/recipes/bioconductor-bronchialil13/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.20.0" %} +{% set version = "1.22.0" %} {% set name = "bronchialIL13" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,21 +10,21 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 985ae91a81f525c68653969a59631523 + md5: a7b5cbe220c3ad028b87560217dca192 build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ noarch: generic requirements: host: - - 'bioconductor-affy >=1.60.0,<1.61.0' + - 'bioconductor-affy >=1.62.0,<1.63.0' - r-base run: - - 'bioconductor-affy >=1.60.0,<1.61.0' + - 'bioconductor-affy >=1.62.0,<1.63.0' - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-bronchialil13/post-link.sh b/recipes/bioconductor-bronchialil13/post-link.sh index 9b5b7148554c9..e5575a5fe7528 100644 --- a/recipes/bioconductor-bronchialil13/post-link.sh +++ b/recipes/bioconductor-bronchialil13/post-link.sh @@ -1,11 +1,11 @@ #!/bin/bash -FN="bronchialIL13_1.20.0.tar.gz" +FN="bronchialIL13_1.22.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/experiment/src/contrib/bronchialIL13_1.20.0.tar.gz" - "https://bioarchive.galaxyproject.org/bronchialIL13_1.20.0.tar.gz" - "https://depot.galaxyproject.org/software/bioconductor-bronchialil13/bioconductor-bronchialil13_1.20.0_src_all.tar.gz" + "https://bioconductor.org/packages/3.9/data/experiment/src/contrib/bronchialIL13_1.22.0.tar.gz" + "https://bioarchive.galaxyproject.org/bronchialIL13_1.22.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-bronchialil13/bioconductor-bronchialil13_1.22.0_src_all.tar.gz" ) -MD5="985ae91a81f525c68653969a59631523" +MD5="a7b5cbe220c3ad028b87560217dca192" # Use a staging area in the conda dir rather than temp dirs, both to avoid # permission issues as well as to have things downloaded in a predictable @@ -16,7 +16,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-browserviz/meta.yaml b/recipes/bioconductor-browserviz/meta.yaml index 96f8e6f217d2e..b86bbbb1c3be2 100644 --- a/recipes/bioconductor-browserviz/meta.yaml +++ b/recipes/bioconductor-browserviz/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "2.4.0" %} +{% set version = "2.6.0" %} {% set name = "BrowserViz" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: bb0a3c4799dfc95dc9b9467437ccb23c + md5: 263756ed6328875b0b8f1890a17f3ef5 build: number: 0 rpaths: @@ -20,14 +20,14 @@ build: # Suggests: RUnit, BiocStyle requirements: host: - - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' + - 'bioconductor-biocgenerics >=0.30.0,<0.31.0' - r-base - - 'r-httpuv >=1.4.0' + - 'r-httpuv >=1.5.0' - 'r-jsonlite >=1.5' run: - - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' + - 'bioconductor-biocgenerics >=0.30.0,<0.31.0' - r-base - - 'r-httpuv >=1.4.0' + - 'r-httpuv >=1.5.0' - 'r-jsonlite >=1.5' test: commands: diff --git a/recipes/bioconductor-bsgenome.alyrata.jgi.v1/meta.yaml b/recipes/bioconductor-bsgenome.alyrata.jgi.v1/meta.yaml index 69798a5b573da..5e8ccfc26e1c6 100644 --- a/recipes/bioconductor-bsgenome.alyrata.jgi.v1/meta.yaml +++ b/recipes/bioconductor-bsgenome.alyrata.jgi.v1/meta.yaml @@ -1,6 +1,6 @@ {% set version = "1.0.0" %} {% set name = "BSgenome.Alyrata.JGI.v1" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -12,19 +12,19 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' md5: 2119e78ebb1957fd55ab186b167e0995 build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ noarch: generic requirements: host: - - 'bioconductor-bsgenome >=1.50.0,<1.51.0' + - 'bioconductor-bsgenome >=1.52.0,<1.53.0' - r-base run: - - 'bioconductor-bsgenome >=1.50.0,<1.51.0' + - 'bioconductor-bsgenome >=1.52.0,<1.53.0' - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-bsgenome.alyrata.jgi.v1/post-link.sh b/recipes/bioconductor-bsgenome.alyrata.jgi.v1/post-link.sh index 5420f308f28d7..12cbb73fa0c3a 100644 --- a/recipes/bioconductor-bsgenome.alyrata.jgi.v1/post-link.sh +++ b/recipes/bioconductor-bsgenome.alyrata.jgi.v1/post-link.sh @@ -1,9 +1,10 @@ #!/bin/bash FN="BSgenome.Alyrata.JGI.v1_1.0.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/BSgenome.Alyrata.JGI.v1_1.0.0.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/BSgenome.Alyrata.JGI.v1_1.0.0.tar.gz" "https://bioarchive.galaxyproject.org/BSgenome.Alyrata.JGI.v1_1.0.0.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-bsgenome.alyrata.jgi.v1/bioconductor-bsgenome.alyrata.jgi.v1_1.0.0_src_all.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-bsgenome.alyrata.jgi.v1/bioconductor-bsgenome.alyrata.jgi.v1_1.0.0_src_all.tar.gz" ) MD5="2119e78ebb1957fd55ab186b167e0995" @@ -16,7 +17,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-bsgenome.amellifera.beebase.assembly4/meta.yaml b/recipes/bioconductor-bsgenome.amellifera.beebase.assembly4/meta.yaml index 8a087272b2e24..d63826e2d220d 100644 --- a/recipes/bioconductor-bsgenome.amellifera.beebase.assembly4/meta.yaml +++ b/recipes/bioconductor-bsgenome.amellifera.beebase.assembly4/meta.yaml @@ -1,6 +1,6 @@ {% set version = "1.4.0" %} {% set name = "BSgenome.Amellifera.BeeBase.assembly4" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -12,19 +12,19 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' md5: 77495ee5eba48fe52902c9cc4f9ba7cc build: - number: 1 + number: 2 rpaths: - lib/R/lib/ - lib/ noarch: generic requirements: host: - - 'bioconductor-bsgenome >=1.50.0,<1.51.0' + - 'bioconductor-bsgenome >=1.52.0,<1.53.0' - r-base run: - - 'bioconductor-bsgenome >=1.50.0,<1.51.0' + - 'bioconductor-bsgenome >=1.52.0,<1.53.0' - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-bsgenome.amellifera.beebase.assembly4/post-link.sh b/recipes/bioconductor-bsgenome.amellifera.beebase.assembly4/post-link.sh index 2543f1b66c387..973413cd33c09 100644 --- a/recipes/bioconductor-bsgenome.amellifera.beebase.assembly4/post-link.sh +++ b/recipes/bioconductor-bsgenome.amellifera.beebase.assembly4/post-link.sh @@ -1,9 +1,10 @@ #!/bin/bash FN="BSgenome.Amellifera.BeeBase.assembly4_1.4.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/BSgenome.Amellifera.BeeBase.assembly4_1.4.0.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/BSgenome.Amellifera.BeeBase.assembly4_1.4.0.tar.gz" "https://bioarchive.galaxyproject.org/BSgenome.Amellifera.BeeBase.assembly4_1.4.0.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-bsgenome.amellifera.beebase.assembly4/bioconductor-bsgenome.amellifera.beebase.assembly4_1.4.0_src_all.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-bsgenome.amellifera.beebase.assembly4/bioconductor-bsgenome.amellifera.beebase.assembly4_1.4.0_src_all.tar.gz" ) MD5="77495ee5eba48fe52902c9cc4f9ba7cc" @@ -16,7 +17,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-bsgenome.amellifera.ucsc.apimel2.masked/meta.yaml b/recipes/bioconductor-bsgenome.amellifera.ucsc.apimel2.masked/meta.yaml index 3f258398320f9..bfdfe0d22b68b 100644 --- a/recipes/bioconductor-bsgenome.amellifera.ucsc.apimel2.masked/meta.yaml +++ b/recipes/bioconductor-bsgenome.amellifera.ucsc.apimel2.masked/meta.yaml @@ -1,6 +1,6 @@ {% set version = "1.3.99" %} {% set name = "BSgenome.Amellifera.UCSC.apiMel2.masked" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -12,21 +12,21 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' md5: e7a7ff8cfce8e239b22116855456f23d build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ noarch: generic requirements: host: - - 'bioconductor-bsgenome >=1.50.0,<1.51.0' + - 'bioconductor-bsgenome >=1.52.0,<1.53.0' - 'bioconductor-bsgenome.amellifera.ucsc.apimel2 >=1.4.0,<1.5.0' - r-base run: - - 'bioconductor-bsgenome >=1.50.0,<1.51.0' + - 'bioconductor-bsgenome >=1.52.0,<1.53.0' - 'bioconductor-bsgenome.amellifera.ucsc.apimel2 >=1.4.0,<1.5.0' - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-bsgenome.amellifera.ucsc.apimel2.masked/post-link.sh b/recipes/bioconductor-bsgenome.amellifera.ucsc.apimel2.masked/post-link.sh index da1e7b022c374..855b9d02f2efb 100644 --- a/recipes/bioconductor-bsgenome.amellifera.ucsc.apimel2.masked/post-link.sh +++ b/recipes/bioconductor-bsgenome.amellifera.ucsc.apimel2.masked/post-link.sh @@ -1,9 +1,10 @@ #!/bin/bash FN="BSgenome.Amellifera.UCSC.apiMel2.masked_1.3.99.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/BSgenome.Amellifera.UCSC.apiMel2.masked_1.3.99.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/BSgenome.Amellifera.UCSC.apiMel2.masked_1.3.99.tar.gz" "https://bioarchive.galaxyproject.org/BSgenome.Amellifera.UCSC.apiMel2.masked_1.3.99.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-bsgenome.amellifera.ucsc.apimel2.masked/bioconductor-bsgenome.amellifera.ucsc.apimel2.masked_1.3.99_src_all.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-bsgenome.amellifera.ucsc.apimel2.masked/bioconductor-bsgenome.amellifera.ucsc.apimel2.masked_1.3.99_src_all.tar.gz" ) MD5="e7a7ff8cfce8e239b22116855456f23d" @@ -16,7 +17,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-bsgenome.amellifera.ucsc.apimel2/meta.yaml b/recipes/bioconductor-bsgenome.amellifera.ucsc.apimel2/meta.yaml index e4dd223a046ac..7e2b0c3d5f25b 100644 --- a/recipes/bioconductor-bsgenome.amellifera.ucsc.apimel2/meta.yaml +++ b/recipes/bioconductor-bsgenome.amellifera.ucsc.apimel2/meta.yaml @@ -1,6 +1,6 @@ {% set version = "1.4.0" %} {% set name = "BSgenome.Amellifera.UCSC.apiMel2" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -12,19 +12,19 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' md5: 436ddf54868906e7d1135369d41a2ffe build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ noarch: generic requirements: host: - - 'bioconductor-bsgenome >=1.50.0,<1.51.0' + - 'bioconductor-bsgenome >=1.52.0,<1.53.0' - r-base run: - - 'bioconductor-bsgenome >=1.50.0,<1.51.0' + - 'bioconductor-bsgenome >=1.52.0,<1.53.0' - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-bsgenome.amellifera.ucsc.apimel2/post-link.sh b/recipes/bioconductor-bsgenome.amellifera.ucsc.apimel2/post-link.sh index bc09999c3772a..cf6a10ab79f44 100644 --- a/recipes/bioconductor-bsgenome.amellifera.ucsc.apimel2/post-link.sh +++ b/recipes/bioconductor-bsgenome.amellifera.ucsc.apimel2/post-link.sh @@ -1,9 +1,10 @@ #!/bin/bash FN="BSgenome.Amellifera.UCSC.apiMel2_1.4.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/BSgenome.Amellifera.UCSC.apiMel2_1.4.0.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/BSgenome.Amellifera.UCSC.apiMel2_1.4.0.tar.gz" "https://bioarchive.galaxyproject.org/BSgenome.Amellifera.UCSC.apiMel2_1.4.0.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-bsgenome.amellifera.ucsc.apimel2/bioconductor-bsgenome.amellifera.ucsc.apimel2_1.4.0_src_all.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-bsgenome.amellifera.ucsc.apimel2/bioconductor-bsgenome.amellifera.ucsc.apimel2_1.4.0_src_all.tar.gz" ) MD5="436ddf54868906e7d1135369d41a2ffe" @@ -16,7 +17,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-bsgenome.aofficinalis.ncbi.v1/meta.yaml b/recipes/bioconductor-bsgenome.aofficinalis.ncbi.v1/meta.yaml index ea2665a8a77da..8067ee6e160c7 100644 --- a/recipes/bioconductor-bsgenome.aofficinalis.ncbi.v1/meta.yaml +++ b/recipes/bioconductor-bsgenome.aofficinalis.ncbi.v1/meta.yaml @@ -1,6 +1,6 @@ {% set version = "1.0.0" %} {% set name = "BSgenome.Aofficinalis.NCBI.V1" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -12,19 +12,19 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' md5: 3f8fd13e74eee63895a5ef528004b60b build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ noarch: generic requirements: host: - - 'bioconductor-bsgenome >=1.50.0,<1.51.0' + - 'bioconductor-bsgenome >=1.52.0,<1.53.0' - r-base run: - - 'bioconductor-bsgenome >=1.50.0,<1.51.0' + - 'bioconductor-bsgenome >=1.52.0,<1.53.0' - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-bsgenome.aofficinalis.ncbi.v1/post-link.sh b/recipes/bioconductor-bsgenome.aofficinalis.ncbi.v1/post-link.sh index 7212469ff8c77..58ba88a5fa964 100644 --- a/recipes/bioconductor-bsgenome.aofficinalis.ncbi.v1/post-link.sh +++ b/recipes/bioconductor-bsgenome.aofficinalis.ncbi.v1/post-link.sh @@ -1,9 +1,10 @@ #!/bin/bash FN="BSgenome.Aofficinalis.NCBI.V1_1.0.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/BSgenome.Aofficinalis.NCBI.V1_1.0.0.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/BSgenome.Aofficinalis.NCBI.V1_1.0.0.tar.gz" "https://bioarchive.galaxyproject.org/BSgenome.Aofficinalis.NCBI.V1_1.0.0.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-bsgenome.aofficinalis.ncbi.v1/bioconductor-bsgenome.aofficinalis.ncbi.v1_1.0.0_src_all.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-bsgenome.aofficinalis.ncbi.v1/bioconductor-bsgenome.aofficinalis.ncbi.v1_1.0.0_src_all.tar.gz" ) MD5="3f8fd13e74eee63895a5ef528004b60b" @@ -16,7 +17,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-bsgenome.athaliana.tair.04232008/meta.yaml b/recipes/bioconductor-bsgenome.athaliana.tair.04232008/meta.yaml index 491027f18c476..faabfdaa4da1a 100644 --- a/recipes/bioconductor-bsgenome.athaliana.tair.04232008/meta.yaml +++ b/recipes/bioconductor-bsgenome.athaliana.tair.04232008/meta.yaml @@ -1,6 +1,6 @@ {% set version = "1.3.1000" %} {% set name = "BSgenome.Athaliana.TAIR.04232008" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -12,19 +12,19 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' md5: 6b8a31a228dbcf4468974f5ec1d98467 build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ noarch: generic requirements: host: - - 'bioconductor-bsgenome >=1.50.0,<1.51.0' + - 'bioconductor-bsgenome >=1.52.0,<1.53.0' - r-base run: - - 'bioconductor-bsgenome >=1.50.0,<1.51.0' + - 'bioconductor-bsgenome >=1.52.0,<1.53.0' - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-bsgenome.athaliana.tair.04232008/post-link.sh b/recipes/bioconductor-bsgenome.athaliana.tair.04232008/post-link.sh index c7c73a235c134..a972c613afc48 100644 --- a/recipes/bioconductor-bsgenome.athaliana.tair.04232008/post-link.sh +++ b/recipes/bioconductor-bsgenome.athaliana.tair.04232008/post-link.sh @@ -1,9 +1,10 @@ #!/bin/bash FN="BSgenome.Athaliana.TAIR.04232008_1.3.1000.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/BSgenome.Athaliana.TAIR.04232008_1.3.1000.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/BSgenome.Athaliana.TAIR.04232008_1.3.1000.tar.gz" "https://bioarchive.galaxyproject.org/BSgenome.Athaliana.TAIR.04232008_1.3.1000.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-bsgenome.athaliana.tair.04232008/bioconductor-bsgenome.athaliana.tair.04232008_1.3.1000_src_all.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-bsgenome.athaliana.tair.04232008/bioconductor-bsgenome.athaliana.tair.04232008_1.3.1000_src_all.tar.gz" ) MD5="6b8a31a228dbcf4468974f5ec1d98467" @@ -16,7 +17,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-bsgenome.athaliana.tair.tair9/meta.yaml b/recipes/bioconductor-bsgenome.athaliana.tair.tair9/meta.yaml index 1333fdbe54030..7354c387a9572 100644 --- a/recipes/bioconductor-bsgenome.athaliana.tair.tair9/meta.yaml +++ b/recipes/bioconductor-bsgenome.athaliana.tair.tair9/meta.yaml @@ -1,6 +1,6 @@ {% set version = "1.3.1000" %} {% set name = "BSgenome.Athaliana.TAIR.TAIR9" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -12,19 +12,19 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' md5: 8c6709a5f544616d59f4d39aac5787a7 build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ noarch: generic requirements: host: - - 'bioconductor-bsgenome >=1.50.0,<1.51.0' + - 'bioconductor-bsgenome >=1.52.0,<1.53.0' - r-base run: - - 'bioconductor-bsgenome >=1.50.0,<1.51.0' + - 'bioconductor-bsgenome >=1.52.0,<1.53.0' - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-bsgenome.athaliana.tair.tair9/post-link.sh b/recipes/bioconductor-bsgenome.athaliana.tair.tair9/post-link.sh index 1569f3e1d69e0..3b0f40243f898 100644 --- a/recipes/bioconductor-bsgenome.athaliana.tair.tair9/post-link.sh +++ b/recipes/bioconductor-bsgenome.athaliana.tair.tair9/post-link.sh @@ -1,9 +1,10 @@ #!/bin/bash FN="BSgenome.Athaliana.TAIR.TAIR9_1.3.1000.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/BSgenome.Athaliana.TAIR.TAIR9_1.3.1000.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/BSgenome.Athaliana.TAIR.TAIR9_1.3.1000.tar.gz" "https://bioarchive.galaxyproject.org/BSgenome.Athaliana.TAIR.TAIR9_1.3.1000.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-bsgenome.athaliana.tair.tair9/bioconductor-bsgenome.athaliana.tair.tair9_1.3.1000_src_all.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-bsgenome.athaliana.tair.tair9/bioconductor-bsgenome.athaliana.tair.tair9_1.3.1000_src_all.tar.gz" ) MD5="8c6709a5f544616d59f4d39aac5787a7" @@ -16,7 +17,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-bsgenome.btaurus.ucsc.bostau3.masked/meta.yaml b/recipes/bioconductor-bsgenome.btaurus.ucsc.bostau3.masked/meta.yaml index 5567929dd890a..e8d1c581ab081 100644 --- a/recipes/bioconductor-bsgenome.btaurus.ucsc.bostau3.masked/meta.yaml +++ b/recipes/bioconductor-bsgenome.btaurus.ucsc.bostau3.masked/meta.yaml @@ -1,6 +1,6 @@ {% set version = "1.3.99" %} {% set name = "BSgenome.Btaurus.UCSC.bosTau3.masked" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -12,21 +12,21 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' md5: 50f7da5907cbe0d08183dc7161a8ca56 build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ noarch: generic requirements: host: - - 'bioconductor-bsgenome >=1.50.0,<1.51.0' + - 'bioconductor-bsgenome >=1.52.0,<1.53.0' - 'bioconductor-bsgenome.btaurus.ucsc.bostau3 >=1.4.0,<1.5.0' - r-base run: - - 'bioconductor-bsgenome >=1.50.0,<1.51.0' + - 'bioconductor-bsgenome >=1.52.0,<1.53.0' - 'bioconductor-bsgenome.btaurus.ucsc.bostau3 >=1.4.0,<1.5.0' - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-bsgenome.btaurus.ucsc.bostau3.masked/post-link.sh b/recipes/bioconductor-bsgenome.btaurus.ucsc.bostau3.masked/post-link.sh index 496a53e8d3fa7..c9e3b284a3c5a 100644 --- a/recipes/bioconductor-bsgenome.btaurus.ucsc.bostau3.masked/post-link.sh +++ b/recipes/bioconductor-bsgenome.btaurus.ucsc.bostau3.masked/post-link.sh @@ -1,9 +1,10 @@ #!/bin/bash FN="BSgenome.Btaurus.UCSC.bosTau3.masked_1.3.99.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/BSgenome.Btaurus.UCSC.bosTau3.masked_1.3.99.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/BSgenome.Btaurus.UCSC.bosTau3.masked_1.3.99.tar.gz" "https://bioarchive.galaxyproject.org/BSgenome.Btaurus.UCSC.bosTau3.masked_1.3.99.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-bsgenome.btaurus.ucsc.bostau3.masked/bioconductor-bsgenome.btaurus.ucsc.bostau3.masked_1.3.99_src_all.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-bsgenome.btaurus.ucsc.bostau3.masked/bioconductor-bsgenome.btaurus.ucsc.bostau3.masked_1.3.99_src_all.tar.gz" ) MD5="50f7da5907cbe0d08183dc7161a8ca56" @@ -16,7 +17,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-bsgenome.btaurus.ucsc.bostau3/meta.yaml b/recipes/bioconductor-bsgenome.btaurus.ucsc.bostau3/meta.yaml index 06c2ce1632fe6..c4d0c1b9270b9 100644 --- a/recipes/bioconductor-bsgenome.btaurus.ucsc.bostau3/meta.yaml +++ b/recipes/bioconductor-bsgenome.btaurus.ucsc.bostau3/meta.yaml @@ -1,6 +1,6 @@ {% set version = "1.4.0" %} {% set name = "BSgenome.Btaurus.UCSC.bosTau3" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -12,7 +12,7 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' md5: fe6c4d5853f91c3db3e716ddbc773580 build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ @@ -20,12 +20,12 @@ build: # Suggests: GenomicFeatures requirements: host: - - 'bioconductor-bsgenome >=1.50.0,<1.51.0' + - 'bioconductor-bsgenome >=1.52.0,<1.53.0' - r-base run: - - 'bioconductor-bsgenome >=1.50.0,<1.51.0' + - 'bioconductor-bsgenome >=1.52.0,<1.53.0' - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-bsgenome.btaurus.ucsc.bostau3/post-link.sh b/recipes/bioconductor-bsgenome.btaurus.ucsc.bostau3/post-link.sh index 4bd7c65209a53..0db15d6012077 100644 --- a/recipes/bioconductor-bsgenome.btaurus.ucsc.bostau3/post-link.sh +++ b/recipes/bioconductor-bsgenome.btaurus.ucsc.bostau3/post-link.sh @@ -1,9 +1,10 @@ #!/bin/bash FN="BSgenome.Btaurus.UCSC.bosTau3_1.4.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/BSgenome.Btaurus.UCSC.bosTau3_1.4.0.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/BSgenome.Btaurus.UCSC.bosTau3_1.4.0.tar.gz" "https://bioarchive.galaxyproject.org/BSgenome.Btaurus.UCSC.bosTau3_1.4.0.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-bsgenome.btaurus.ucsc.bostau3/bioconductor-bsgenome.btaurus.ucsc.bostau3_1.4.0_src_all.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-bsgenome.btaurus.ucsc.bostau3/bioconductor-bsgenome.btaurus.ucsc.bostau3_1.4.0_src_all.tar.gz" ) MD5="fe6c4d5853f91c3db3e716ddbc773580" @@ -16,7 +17,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-bsgenome.btaurus.ucsc.bostau4.masked/meta.yaml b/recipes/bioconductor-bsgenome.btaurus.ucsc.bostau4.masked/meta.yaml index 95f877065a86e..a5cf4208cef20 100644 --- a/recipes/bioconductor-bsgenome.btaurus.ucsc.bostau4.masked/meta.yaml +++ b/recipes/bioconductor-bsgenome.btaurus.ucsc.bostau4.masked/meta.yaml @@ -1,6 +1,6 @@ {% set version = "1.3.99" %} {% set name = "BSgenome.Btaurus.UCSC.bosTau4.masked" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -12,21 +12,21 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' md5: 7c5294349c7061adfb3948bc5659afeb build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ noarch: generic requirements: host: - - 'bioconductor-bsgenome >=1.50.0,<1.51.0' + - 'bioconductor-bsgenome >=1.52.0,<1.53.0' - 'bioconductor-bsgenome.btaurus.ucsc.bostau4 >=1.4.0,<1.5.0' - r-base run: - - 'bioconductor-bsgenome >=1.50.0,<1.51.0' + - 'bioconductor-bsgenome >=1.52.0,<1.53.0' - 'bioconductor-bsgenome.btaurus.ucsc.bostau4 >=1.4.0,<1.5.0' - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-bsgenome.btaurus.ucsc.bostau4.masked/post-link.sh b/recipes/bioconductor-bsgenome.btaurus.ucsc.bostau4.masked/post-link.sh index c6099db4648a3..eb128ad99aac9 100644 --- a/recipes/bioconductor-bsgenome.btaurus.ucsc.bostau4.masked/post-link.sh +++ b/recipes/bioconductor-bsgenome.btaurus.ucsc.bostau4.masked/post-link.sh @@ -1,9 +1,10 @@ #!/bin/bash FN="BSgenome.Btaurus.UCSC.bosTau4.masked_1.3.99.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/BSgenome.Btaurus.UCSC.bosTau4.masked_1.3.99.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/BSgenome.Btaurus.UCSC.bosTau4.masked_1.3.99.tar.gz" "https://bioarchive.galaxyproject.org/BSgenome.Btaurus.UCSC.bosTau4.masked_1.3.99.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-bsgenome.btaurus.ucsc.bostau4.masked/bioconductor-bsgenome.btaurus.ucsc.bostau4.masked_1.3.99_src_all.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-bsgenome.btaurus.ucsc.bostau4.masked/bioconductor-bsgenome.btaurus.ucsc.bostau4.masked_1.3.99_src_all.tar.gz" ) MD5="7c5294349c7061adfb3948bc5659afeb" @@ -16,7 +17,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-bsgenome.btaurus.ucsc.bostau4/meta.yaml b/recipes/bioconductor-bsgenome.btaurus.ucsc.bostau4/meta.yaml index 0620b7907b08a..9f7ae70436587 100644 --- a/recipes/bioconductor-bsgenome.btaurus.ucsc.bostau4/meta.yaml +++ b/recipes/bioconductor-bsgenome.btaurus.ucsc.bostau4/meta.yaml @@ -1,6 +1,6 @@ {% set version = "1.4.0" %} {% set name = "BSgenome.Btaurus.UCSC.bosTau4" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -12,7 +12,7 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' md5: 162cd253c719e347df5748ebb407a191 build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ @@ -20,12 +20,12 @@ build: # Suggests: GenomicFeatures requirements: host: - - 'bioconductor-bsgenome >=1.50.0,<1.51.0' + - 'bioconductor-bsgenome >=1.52.0,<1.53.0' - r-base run: - - 'bioconductor-bsgenome >=1.50.0,<1.51.0' + - 'bioconductor-bsgenome >=1.52.0,<1.53.0' - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-bsgenome.btaurus.ucsc.bostau4/post-link.sh b/recipes/bioconductor-bsgenome.btaurus.ucsc.bostau4/post-link.sh index e6002c52b8c98..43eacf7440563 100644 --- a/recipes/bioconductor-bsgenome.btaurus.ucsc.bostau4/post-link.sh +++ b/recipes/bioconductor-bsgenome.btaurus.ucsc.bostau4/post-link.sh @@ -1,9 +1,10 @@ #!/bin/bash FN="BSgenome.Btaurus.UCSC.bosTau4_1.4.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/BSgenome.Btaurus.UCSC.bosTau4_1.4.0.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/BSgenome.Btaurus.UCSC.bosTau4_1.4.0.tar.gz" "https://bioarchive.galaxyproject.org/BSgenome.Btaurus.UCSC.bosTau4_1.4.0.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-bsgenome.btaurus.ucsc.bostau4/bioconductor-bsgenome.btaurus.ucsc.bostau4_1.4.0_src_all.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-bsgenome.btaurus.ucsc.bostau4/bioconductor-bsgenome.btaurus.ucsc.bostau4_1.4.0_src_all.tar.gz" ) MD5="162cd253c719e347df5748ebb407a191" @@ -16,7 +17,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-bsgenome.btaurus.ucsc.bostau6.masked/meta.yaml b/recipes/bioconductor-bsgenome.btaurus.ucsc.bostau6.masked/meta.yaml index ff5d633929b16..27e7d2cb6688e 100644 --- a/recipes/bioconductor-bsgenome.btaurus.ucsc.bostau6.masked/meta.yaml +++ b/recipes/bioconductor-bsgenome.btaurus.ucsc.bostau6.masked/meta.yaml @@ -1,6 +1,6 @@ {% set version = "1.3.99" %} {% set name = "BSgenome.Btaurus.UCSC.bosTau6.masked" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -12,21 +12,21 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' md5: a176de6b1b91854d47e783b8249dbf58 build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ noarch: generic requirements: host: - - 'bioconductor-bsgenome >=1.50.0,<1.51.0' + - 'bioconductor-bsgenome >=1.52.0,<1.53.0' - 'bioconductor-bsgenome.btaurus.ucsc.bostau6 >=1.4.0,<1.5.0' - r-base run: - - 'bioconductor-bsgenome >=1.50.0,<1.51.0' + - 'bioconductor-bsgenome >=1.52.0,<1.53.0' - 'bioconductor-bsgenome.btaurus.ucsc.bostau6 >=1.4.0,<1.5.0' - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-bsgenome.btaurus.ucsc.bostau6.masked/post-link.sh b/recipes/bioconductor-bsgenome.btaurus.ucsc.bostau6.masked/post-link.sh index dc0f359db335b..84459bca1ad83 100644 --- a/recipes/bioconductor-bsgenome.btaurus.ucsc.bostau6.masked/post-link.sh +++ b/recipes/bioconductor-bsgenome.btaurus.ucsc.bostau6.masked/post-link.sh @@ -1,9 +1,10 @@ #!/bin/bash FN="BSgenome.Btaurus.UCSC.bosTau6.masked_1.3.99.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/BSgenome.Btaurus.UCSC.bosTau6.masked_1.3.99.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/BSgenome.Btaurus.UCSC.bosTau6.masked_1.3.99.tar.gz" "https://bioarchive.galaxyproject.org/BSgenome.Btaurus.UCSC.bosTau6.masked_1.3.99.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-bsgenome.btaurus.ucsc.bostau6.masked/bioconductor-bsgenome.btaurus.ucsc.bostau6.masked_1.3.99_src_all.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-bsgenome.btaurus.ucsc.bostau6.masked/bioconductor-bsgenome.btaurus.ucsc.bostau6.masked_1.3.99_src_all.tar.gz" ) MD5="a176de6b1b91854d47e783b8249dbf58" @@ -16,7 +17,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-bsgenome.btaurus.ucsc.bostau6/meta.yaml b/recipes/bioconductor-bsgenome.btaurus.ucsc.bostau6/meta.yaml index aa57afdc68061..d50d29a798007 100644 --- a/recipes/bioconductor-bsgenome.btaurus.ucsc.bostau6/meta.yaml +++ b/recipes/bioconductor-bsgenome.btaurus.ucsc.bostau6/meta.yaml @@ -1,6 +1,6 @@ {% set version = "1.4.0" %} {% set name = "BSgenome.Btaurus.UCSC.bosTau6" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -12,7 +12,7 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' md5: b22391e0678fc3743daa4b77ecc55f66 build: - number: 1 + number: 2 rpaths: - lib/R/lib/ - lib/ @@ -20,12 +20,12 @@ build: # Suggests: GenomicFeatures requirements: host: - - 'bioconductor-bsgenome >=1.50.0,<1.51.0' + - 'bioconductor-bsgenome >=1.52.0,<1.53.0' - r-base run: - - 'bioconductor-bsgenome >=1.50.0,<1.51.0' + - 'bioconductor-bsgenome >=1.52.0,<1.53.0' - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-bsgenome.btaurus.ucsc.bostau6/post-link.sh b/recipes/bioconductor-bsgenome.btaurus.ucsc.bostau6/post-link.sh index 6460206f50708..88fbc9018c5d1 100644 --- a/recipes/bioconductor-bsgenome.btaurus.ucsc.bostau6/post-link.sh +++ b/recipes/bioconductor-bsgenome.btaurus.ucsc.bostau6/post-link.sh @@ -1,9 +1,10 @@ #!/bin/bash FN="BSgenome.Btaurus.UCSC.bosTau6_1.4.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/BSgenome.Btaurus.UCSC.bosTau6_1.4.0.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/BSgenome.Btaurus.UCSC.bosTau6_1.4.0.tar.gz" "https://bioarchive.galaxyproject.org/BSgenome.Btaurus.UCSC.bosTau6_1.4.0.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-bsgenome.btaurus.ucsc.bostau6/bioconductor-bsgenome.btaurus.ucsc.bostau6_1.4.0_src_all.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-bsgenome.btaurus.ucsc.bostau6/bioconductor-bsgenome.btaurus.ucsc.bostau6_1.4.0_src_all.tar.gz" ) MD5="b22391e0678fc3743daa4b77ecc55f66" @@ -16,7 +17,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-bsgenome.btaurus.ucsc.bostau8/meta.yaml b/recipes/bioconductor-bsgenome.btaurus.ucsc.bostau8/meta.yaml index dc6ddd13aad19..0fc59bbe06900 100644 --- a/recipes/bioconductor-bsgenome.btaurus.ucsc.bostau8/meta.yaml +++ b/recipes/bioconductor-bsgenome.btaurus.ucsc.bostau8/meta.yaml @@ -1,6 +1,6 @@ {% set version = "1.4.2" %} {% set name = "BSgenome.Btaurus.UCSC.bosTau8" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -12,7 +12,7 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' md5: 61ababa7b2b5360fceeb06f0bf49b208 build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ @@ -20,12 +20,12 @@ build: # Suggests: GenomicFeatures requirements: host: - - 'bioconductor-bsgenome >=1.50.0,<1.51.0' + - 'bioconductor-bsgenome >=1.52.0,<1.53.0' - r-base run: - - 'bioconductor-bsgenome >=1.50.0,<1.51.0' + - 'bioconductor-bsgenome >=1.52.0,<1.53.0' - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-bsgenome.btaurus.ucsc.bostau8/post-link.sh b/recipes/bioconductor-bsgenome.btaurus.ucsc.bostau8/post-link.sh index 5a0965df29b08..5a86172b520b8 100644 --- a/recipes/bioconductor-bsgenome.btaurus.ucsc.bostau8/post-link.sh +++ b/recipes/bioconductor-bsgenome.btaurus.ucsc.bostau8/post-link.sh @@ -1,9 +1,10 @@ #!/bin/bash FN="BSgenome.Btaurus.UCSC.bosTau8_1.4.2.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/BSgenome.Btaurus.UCSC.bosTau8_1.4.2.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/BSgenome.Btaurus.UCSC.bosTau8_1.4.2.tar.gz" "https://bioarchive.galaxyproject.org/BSgenome.Btaurus.UCSC.bosTau8_1.4.2.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-bsgenome.btaurus.ucsc.bostau8/bioconductor-bsgenome.btaurus.ucsc.bostau8_1.4.2_src_all.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-bsgenome.btaurus.ucsc.bostau8/bioconductor-bsgenome.btaurus.ucsc.bostau8_1.4.2_src_all.tar.gz" ) MD5="61ababa7b2b5360fceeb06f0bf49b208" @@ -16,7 +17,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-bsgenome.carietinum.ncbi.v1/meta.yaml b/recipes/bioconductor-bsgenome.carietinum.ncbi.v1/meta.yaml index e3af808a3a687..e105dcd598cb3 100644 --- a/recipes/bioconductor-bsgenome.carietinum.ncbi.v1/meta.yaml +++ b/recipes/bioconductor-bsgenome.carietinum.ncbi.v1/meta.yaml @@ -1,6 +1,6 @@ {% set version = "1.0.0" %} {% set name = "BSgenome.Carietinum.NCBI.v1" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -12,19 +12,19 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' md5: eef018ecce6d32852aa18ac39cf377c6 build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ noarch: generic requirements: host: - - 'bioconductor-bsgenome >=1.50.0,<1.51.0' + - 'bioconductor-bsgenome >=1.52.0,<1.53.0' - r-base run: - - 'bioconductor-bsgenome >=1.50.0,<1.51.0' + - 'bioconductor-bsgenome >=1.52.0,<1.53.0' - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-bsgenome.carietinum.ncbi.v1/post-link.sh b/recipes/bioconductor-bsgenome.carietinum.ncbi.v1/post-link.sh index b2f0d4b788064..bdf7b045d3391 100644 --- a/recipes/bioconductor-bsgenome.carietinum.ncbi.v1/post-link.sh +++ b/recipes/bioconductor-bsgenome.carietinum.ncbi.v1/post-link.sh @@ -1,9 +1,10 @@ #!/bin/bash FN="BSgenome.Carietinum.NCBI.v1_1.0.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/BSgenome.Carietinum.NCBI.v1_1.0.0.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/BSgenome.Carietinum.NCBI.v1_1.0.0.tar.gz" "https://bioarchive.galaxyproject.org/BSgenome.Carietinum.NCBI.v1_1.0.0.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-bsgenome.carietinum.ncbi.v1/bioconductor-bsgenome.carietinum.ncbi.v1_1.0.0_src_all.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-bsgenome.carietinum.ncbi.v1/bioconductor-bsgenome.carietinum.ncbi.v1_1.0.0_src_all.tar.gz" ) MD5="eef018ecce6d32852aa18ac39cf377c6" @@ -16,7 +17,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-bsgenome.celegans.ucsc.ce10/meta.yaml b/recipes/bioconductor-bsgenome.celegans.ucsc.ce10/meta.yaml index d04271e0d65c2..899852e81dc0b 100644 --- a/recipes/bioconductor-bsgenome.celegans.ucsc.ce10/meta.yaml +++ b/recipes/bioconductor-bsgenome.celegans.ucsc.ce10/meta.yaml @@ -1,6 +1,6 @@ {% set version = "1.4.0" %} {% set name = "BSgenome.Celegans.UCSC.ce10" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -12,7 +12,7 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' md5: 98a8ca836d6db23e46674552669d7942 build: - number: 5 + number: 6 rpaths: - lib/R/lib/ - lib/ @@ -20,12 +20,12 @@ build: # Suggests: GenomicFeatures requirements: host: - - 'bioconductor-bsgenome >=1.50.0,<1.51.0' + - 'bioconductor-bsgenome >=1.52.0,<1.53.0' - r-base run: - - 'bioconductor-bsgenome >=1.50.0,<1.51.0' + - 'bioconductor-bsgenome >=1.52.0,<1.53.0' - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-bsgenome.celegans.ucsc.ce10/post-link.sh b/recipes/bioconductor-bsgenome.celegans.ucsc.ce10/post-link.sh index abbb8bfed82e0..586179abfc31d 100644 --- a/recipes/bioconductor-bsgenome.celegans.ucsc.ce10/post-link.sh +++ b/recipes/bioconductor-bsgenome.celegans.ucsc.ce10/post-link.sh @@ -1,7 +1,7 @@ #!/bin/bash FN="BSgenome.Celegans.UCSC.ce10_1.4.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/BSgenome.Celegans.UCSC.ce10_1.4.0.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/BSgenome.Celegans.UCSC.ce10_1.4.0.tar.gz" "https://bioarchive.galaxyproject.org/BSgenome.Celegans.UCSC.ce10_1.4.0.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-bsgenome.celegans.ucsc.ce10/bioconductor-bsgenome.celegans.ucsc.ce10_1.4.0_src_all.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-bsgenome.celegans.ucsc.ce10/bioconductor-bsgenome.celegans.ucsc.ce10_1.4.0_src_all.tar.gz" @@ -17,7 +17,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-bsgenome.celegans.ucsc.ce11/meta.yaml b/recipes/bioconductor-bsgenome.celegans.ucsc.ce11/meta.yaml index 50fd52d697181..7b4b11ebfc9db 100644 --- a/recipes/bioconductor-bsgenome.celegans.ucsc.ce11/meta.yaml +++ b/recipes/bioconductor-bsgenome.celegans.ucsc.ce11/meta.yaml @@ -1,6 +1,6 @@ {% set version = "1.4.2" %} {% set name = "BSgenome.Celegans.UCSC.ce11" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -12,7 +12,7 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' md5: b80e24149a0c6ed323d0c9a6d112ef52 build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ @@ -20,12 +20,12 @@ build: # Suggests: GenomicFeatures requirements: host: - - 'bioconductor-bsgenome >=1.50.0,<1.51.0' + - 'bioconductor-bsgenome >=1.52.0,<1.53.0' - r-base run: - - 'bioconductor-bsgenome >=1.50.0,<1.51.0' + - 'bioconductor-bsgenome >=1.52.0,<1.53.0' - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-bsgenome.celegans.ucsc.ce11/post-link.sh b/recipes/bioconductor-bsgenome.celegans.ucsc.ce11/post-link.sh index 71849f1a23522..3c2cbf00b7b38 100644 --- a/recipes/bioconductor-bsgenome.celegans.ucsc.ce11/post-link.sh +++ b/recipes/bioconductor-bsgenome.celegans.ucsc.ce11/post-link.sh @@ -1,9 +1,10 @@ #!/bin/bash FN="BSgenome.Celegans.UCSC.ce11_1.4.2.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/BSgenome.Celegans.UCSC.ce11_1.4.2.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/BSgenome.Celegans.UCSC.ce11_1.4.2.tar.gz" "https://bioarchive.galaxyproject.org/BSgenome.Celegans.UCSC.ce11_1.4.2.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-bsgenome.celegans.ucsc.ce11/bioconductor-bsgenome.celegans.ucsc.ce11_1.4.2_src_all.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-bsgenome.celegans.ucsc.ce11/bioconductor-bsgenome.celegans.ucsc.ce11_1.4.2_src_all.tar.gz" ) MD5="b80e24149a0c6ed323d0c9a6d112ef52" @@ -16,7 +17,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-bsgenome.celegans.ucsc.ce2/meta.yaml b/recipes/bioconductor-bsgenome.celegans.ucsc.ce2/meta.yaml index 32d3c283ca42c..1b06de4b41e7d 100644 --- a/recipes/bioconductor-bsgenome.celegans.ucsc.ce2/meta.yaml +++ b/recipes/bioconductor-bsgenome.celegans.ucsc.ce2/meta.yaml @@ -1,6 +1,6 @@ {% set version = "1.4.0" %} {% set name = "BSgenome.Celegans.UCSC.ce2" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -12,7 +12,7 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' md5: b2bf7eec2b07685cf9dcdf42840db208 build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ @@ -20,12 +20,12 @@ build: # Suggests: GenomicFeatures requirements: host: - - 'bioconductor-bsgenome >=1.50.0,<1.51.0' + - 'bioconductor-bsgenome >=1.52.0,<1.53.0' - r-base run: - - 'bioconductor-bsgenome >=1.50.0,<1.51.0' + - 'bioconductor-bsgenome >=1.52.0,<1.53.0' - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-bsgenome.celegans.ucsc.ce2/post-link.sh b/recipes/bioconductor-bsgenome.celegans.ucsc.ce2/post-link.sh index b6088b50a7f2a..fe4fef4819eee 100644 --- a/recipes/bioconductor-bsgenome.celegans.ucsc.ce2/post-link.sh +++ b/recipes/bioconductor-bsgenome.celegans.ucsc.ce2/post-link.sh @@ -1,9 +1,10 @@ #!/bin/bash FN="BSgenome.Celegans.UCSC.ce2_1.4.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/BSgenome.Celegans.UCSC.ce2_1.4.0.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/BSgenome.Celegans.UCSC.ce2_1.4.0.tar.gz" "https://bioarchive.galaxyproject.org/BSgenome.Celegans.UCSC.ce2_1.4.0.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-bsgenome.celegans.ucsc.ce2/bioconductor-bsgenome.celegans.ucsc.ce2_1.4.0_src_all.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-bsgenome.celegans.ucsc.ce2/bioconductor-bsgenome.celegans.ucsc.ce2_1.4.0_src_all.tar.gz" ) MD5="b2bf7eec2b07685cf9dcdf42840db208" @@ -16,7 +17,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-bsgenome.celegans.ucsc.ce6/meta.yaml b/recipes/bioconductor-bsgenome.celegans.ucsc.ce6/meta.yaml index 11a043d84d096..d41c29d53075d 100644 --- a/recipes/bioconductor-bsgenome.celegans.ucsc.ce6/meta.yaml +++ b/recipes/bioconductor-bsgenome.celegans.ucsc.ce6/meta.yaml @@ -1,6 +1,6 @@ {% set version = "1.4.0" %} {% set name = "BSgenome.Celegans.UCSC.ce6" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -12,7 +12,7 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' md5: cb86ff861d8f660c2abd8fc1907d84a6 build: - number: 5 + number: 6 rpaths: - lib/R/lib/ - lib/ @@ -20,12 +20,12 @@ build: # Suggests: TxDb.Celegans.UCSC.ce6.ensGene requirements: host: - - 'bioconductor-bsgenome >=1.50.0,<1.51.0' + - 'bioconductor-bsgenome >=1.52.0,<1.53.0' - r-base run: - - 'bioconductor-bsgenome >=1.50.0,<1.51.0' + - 'bioconductor-bsgenome >=1.52.0,<1.53.0' - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-bsgenome.celegans.ucsc.ce6/post-link.sh b/recipes/bioconductor-bsgenome.celegans.ucsc.ce6/post-link.sh index 496a98adabf50..e8e088c35058d 100644 --- a/recipes/bioconductor-bsgenome.celegans.ucsc.ce6/post-link.sh +++ b/recipes/bioconductor-bsgenome.celegans.ucsc.ce6/post-link.sh @@ -1,7 +1,7 @@ #!/bin/bash FN="BSgenome.Celegans.UCSC.ce6_1.4.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/BSgenome.Celegans.UCSC.ce6_1.4.0.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/BSgenome.Celegans.UCSC.ce6_1.4.0.tar.gz" "https://bioarchive.galaxyproject.org/BSgenome.Celegans.UCSC.ce6_1.4.0.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-bsgenome.celegans.ucsc.ce6/bioconductor-bsgenome.celegans.ucsc.ce6_1.4.0_src_all.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-bsgenome.celegans.ucsc.ce6/bioconductor-bsgenome.celegans.ucsc.ce6_1.4.0_src_all.tar.gz" @@ -17,7 +17,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-bsgenome.cfamiliaris.ucsc.canfam2.masked/meta.yaml b/recipes/bioconductor-bsgenome.cfamiliaris.ucsc.canfam2.masked/meta.yaml index 390d645c0fd1e..fcad8bbf2497b 100644 --- a/recipes/bioconductor-bsgenome.cfamiliaris.ucsc.canfam2.masked/meta.yaml +++ b/recipes/bioconductor-bsgenome.cfamiliaris.ucsc.canfam2.masked/meta.yaml @@ -1,6 +1,6 @@ {% set version = "1.3.99" %} {% set name = "BSgenome.Cfamiliaris.UCSC.canFam2.masked" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -12,21 +12,21 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' md5: 6f921533bb83f83f43b8d227b00a48cb build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ noarch: generic requirements: host: - - 'bioconductor-bsgenome >=1.50.0,<1.51.0' + - 'bioconductor-bsgenome >=1.52.0,<1.53.0' - 'bioconductor-bsgenome.cfamiliaris.ucsc.canfam2 >=1.4.0,<1.5.0' - r-base run: - - 'bioconductor-bsgenome >=1.50.0,<1.51.0' + - 'bioconductor-bsgenome >=1.52.0,<1.53.0' - 'bioconductor-bsgenome.cfamiliaris.ucsc.canfam2 >=1.4.0,<1.5.0' - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-bsgenome.cfamiliaris.ucsc.canfam2.masked/post-link.sh b/recipes/bioconductor-bsgenome.cfamiliaris.ucsc.canfam2.masked/post-link.sh index 66ec46c290d4b..2a48aaf509bec 100644 --- a/recipes/bioconductor-bsgenome.cfamiliaris.ucsc.canfam2.masked/post-link.sh +++ b/recipes/bioconductor-bsgenome.cfamiliaris.ucsc.canfam2.masked/post-link.sh @@ -1,9 +1,10 @@ #!/bin/bash FN="BSgenome.Cfamiliaris.UCSC.canFam2.masked_1.3.99.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/BSgenome.Cfamiliaris.UCSC.canFam2.masked_1.3.99.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/BSgenome.Cfamiliaris.UCSC.canFam2.masked_1.3.99.tar.gz" "https://bioarchive.galaxyproject.org/BSgenome.Cfamiliaris.UCSC.canFam2.masked_1.3.99.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-bsgenome.cfamiliaris.ucsc.canfam2.masked/bioconductor-bsgenome.cfamiliaris.ucsc.canfam2.masked_1.3.99_src_all.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-bsgenome.cfamiliaris.ucsc.canfam2.masked/bioconductor-bsgenome.cfamiliaris.ucsc.canfam2.masked_1.3.99_src_all.tar.gz" ) MD5="6f921533bb83f83f43b8d227b00a48cb" @@ -16,7 +17,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-bsgenome.cfamiliaris.ucsc.canfam2/meta.yaml b/recipes/bioconductor-bsgenome.cfamiliaris.ucsc.canfam2/meta.yaml index c2b95b893c742..ff38d59cd1473 100644 --- a/recipes/bioconductor-bsgenome.cfamiliaris.ucsc.canfam2/meta.yaml +++ b/recipes/bioconductor-bsgenome.cfamiliaris.ucsc.canfam2/meta.yaml @@ -1,6 +1,6 @@ {% set version = "1.4.0" %} {% set name = "BSgenome.Cfamiliaris.UCSC.canFam2" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -12,7 +12,7 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' md5: b98f5289ed5d362cd815db9352598634 build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ @@ -20,12 +20,12 @@ build: # Suggests: GenomicFeatures requirements: host: - - 'bioconductor-bsgenome >=1.50.0,<1.51.0' + - 'bioconductor-bsgenome >=1.52.0,<1.53.0' - r-base run: - - 'bioconductor-bsgenome >=1.50.0,<1.51.0' + - 'bioconductor-bsgenome >=1.52.0,<1.53.0' - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-bsgenome.cfamiliaris.ucsc.canfam2/post-link.sh b/recipes/bioconductor-bsgenome.cfamiliaris.ucsc.canfam2/post-link.sh index 57f6fe216e81b..c2d3e4515e2cc 100644 --- a/recipes/bioconductor-bsgenome.cfamiliaris.ucsc.canfam2/post-link.sh +++ b/recipes/bioconductor-bsgenome.cfamiliaris.ucsc.canfam2/post-link.sh @@ -1,9 +1,10 @@ #!/bin/bash FN="BSgenome.Cfamiliaris.UCSC.canFam2_1.4.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/BSgenome.Cfamiliaris.UCSC.canFam2_1.4.0.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/BSgenome.Cfamiliaris.UCSC.canFam2_1.4.0.tar.gz" "https://bioarchive.galaxyproject.org/BSgenome.Cfamiliaris.UCSC.canFam2_1.4.0.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-bsgenome.cfamiliaris.ucsc.canfam2/bioconductor-bsgenome.cfamiliaris.ucsc.canfam2_1.4.0_src_all.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-bsgenome.cfamiliaris.ucsc.canfam2/bioconductor-bsgenome.cfamiliaris.ucsc.canfam2_1.4.0_src_all.tar.gz" ) MD5="b98f5289ed5d362cd815db9352598634" @@ -16,7 +17,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-bsgenome.cfamiliaris.ucsc.canfam3.masked/meta.yaml b/recipes/bioconductor-bsgenome.cfamiliaris.ucsc.canfam3.masked/meta.yaml index f3f4c3f8b21c8..0490881a33f7a 100644 --- a/recipes/bioconductor-bsgenome.cfamiliaris.ucsc.canfam3.masked/meta.yaml +++ b/recipes/bioconductor-bsgenome.cfamiliaris.ucsc.canfam3.masked/meta.yaml @@ -1,6 +1,6 @@ {% set version = "1.3.99" %} {% set name = "BSgenome.Cfamiliaris.UCSC.canFam3.masked" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -12,21 +12,21 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' md5: 8e2246f51fc967dc2ed748cf967a7649 build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ noarch: generic requirements: host: - - 'bioconductor-bsgenome >=1.50.0,<1.51.0' + - 'bioconductor-bsgenome >=1.52.0,<1.53.0' - 'bioconductor-bsgenome.cfamiliaris.ucsc.canfam3 >=1.4.0,<1.5.0' - r-base run: - - 'bioconductor-bsgenome >=1.50.0,<1.51.0' + - 'bioconductor-bsgenome >=1.52.0,<1.53.0' - 'bioconductor-bsgenome.cfamiliaris.ucsc.canfam3 >=1.4.0,<1.5.0' - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-bsgenome.cfamiliaris.ucsc.canfam3.masked/post-link.sh b/recipes/bioconductor-bsgenome.cfamiliaris.ucsc.canfam3.masked/post-link.sh index fffe5785b22a2..ecede54919e6e 100644 --- a/recipes/bioconductor-bsgenome.cfamiliaris.ucsc.canfam3.masked/post-link.sh +++ b/recipes/bioconductor-bsgenome.cfamiliaris.ucsc.canfam3.masked/post-link.sh @@ -1,9 +1,10 @@ #!/bin/bash FN="BSgenome.Cfamiliaris.UCSC.canFam3.masked_1.3.99.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/BSgenome.Cfamiliaris.UCSC.canFam3.masked_1.3.99.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/BSgenome.Cfamiliaris.UCSC.canFam3.masked_1.3.99.tar.gz" "https://bioarchive.galaxyproject.org/BSgenome.Cfamiliaris.UCSC.canFam3.masked_1.3.99.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-bsgenome.cfamiliaris.ucsc.canfam3.masked/bioconductor-bsgenome.cfamiliaris.ucsc.canfam3.masked_1.3.99_src_all.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-bsgenome.cfamiliaris.ucsc.canfam3.masked/bioconductor-bsgenome.cfamiliaris.ucsc.canfam3.masked_1.3.99_src_all.tar.gz" ) MD5="8e2246f51fc967dc2ed748cf967a7649" @@ -16,7 +17,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-bsgenome.cfamiliaris.ucsc.canfam3/meta.yaml b/recipes/bioconductor-bsgenome.cfamiliaris.ucsc.canfam3/meta.yaml index 77a7df8a7533a..4726c61104209 100644 --- a/recipes/bioconductor-bsgenome.cfamiliaris.ucsc.canfam3/meta.yaml +++ b/recipes/bioconductor-bsgenome.cfamiliaris.ucsc.canfam3/meta.yaml @@ -1,6 +1,6 @@ {% set version = "1.4.0" %} {% set name = "BSgenome.Cfamiliaris.UCSC.canFam3" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -12,7 +12,7 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' md5: efcdc531042be86f99a734cd69c0688c build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ @@ -20,12 +20,12 @@ build: # Suggests: GenomicFeatures requirements: host: - - 'bioconductor-bsgenome >=1.50.0,<1.51.0' + - 'bioconductor-bsgenome >=1.52.0,<1.53.0' - r-base run: - - 'bioconductor-bsgenome >=1.50.0,<1.51.0' + - 'bioconductor-bsgenome >=1.52.0,<1.53.0' - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-bsgenome.cfamiliaris.ucsc.canfam3/post-link.sh b/recipes/bioconductor-bsgenome.cfamiliaris.ucsc.canfam3/post-link.sh index 244d8b4e03a73..3474a32e868dc 100644 --- a/recipes/bioconductor-bsgenome.cfamiliaris.ucsc.canfam3/post-link.sh +++ b/recipes/bioconductor-bsgenome.cfamiliaris.ucsc.canfam3/post-link.sh @@ -1,9 +1,10 @@ #!/bin/bash FN="BSgenome.Cfamiliaris.UCSC.canFam3_1.4.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/BSgenome.Cfamiliaris.UCSC.canFam3_1.4.0.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/BSgenome.Cfamiliaris.UCSC.canFam3_1.4.0.tar.gz" "https://bioarchive.galaxyproject.org/BSgenome.Cfamiliaris.UCSC.canFam3_1.4.0.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-bsgenome.cfamiliaris.ucsc.canfam3/bioconductor-bsgenome.cfamiliaris.ucsc.canfam3_1.4.0_src_all.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-bsgenome.cfamiliaris.ucsc.canfam3/bioconductor-bsgenome.cfamiliaris.ucsc.canfam3_1.4.0_src_all.tar.gz" ) MD5="efcdc531042be86f99a734cd69c0688c" @@ -16,7 +17,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-bsgenome.cjacchus.ucsc.caljac3/meta.yaml b/recipes/bioconductor-bsgenome.cjacchus.ucsc.caljac3/meta.yaml new file mode 100644 index 0000000000000..d581e85277321 --- /dev/null +++ b/recipes/bioconductor-bsgenome.cjacchus.ucsc.caljac3/meta.yaml @@ -0,0 +1,35 @@ +{% set version = "1.4.2" %} +{% set name = "BSgenome.Cjacchus.UCSC.calJac3" %} +{% set bioc = "3.9" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: 41f927aa0d6ffbdaa6ad93c9135409e6 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +requirements: + host: + - 'bioconductor-bsgenome >=1.52.0,<1.53.0' + - r-base + run: + - 'bioconductor-bsgenome >=1.52.0,<1.53.0' + - r-base + - curl +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'Full genome sequences for Callithrix jacchus (Marmoset) as provided by UCSC (calJac3, Mar. 2009) and stored in Biostrings objects.' + diff --git a/recipes/bioconductor-bsgenome.cjacchus.ucsc.caljac3/post-link.sh b/recipes/bioconductor-bsgenome.cjacchus.ucsc.caljac3/post-link.sh new file mode 100644 index 0000000000000..298d52c3de1ff --- /dev/null +++ b/recipes/bioconductor-bsgenome.cjacchus.ucsc.caljac3/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="BSgenome.Cjacchus.UCSC.calJac3_1.4.2.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/BSgenome.Cjacchus.UCSC.calJac3_1.4.2.tar.gz" + "https://bioarchive.galaxyproject.org/BSgenome.Cjacchus.UCSC.calJac3_1.4.2.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-bsgenome.cjacchus.ucsc.caljac3/bioconductor-bsgenome.cjacchus.ucsc.caljac3_1.4.2_src_all.tar.gz" +) +MD5="41f927aa0d6ffbdaa6ad93c9135409e6" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + curl $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-bsgenome.cjacchus.ucsc.caljac3/pre-unlink.sh b/recipes/bioconductor-bsgenome.cjacchus.ucsc.caljac3/pre-unlink.sh new file mode 100644 index 0000000000000..afc8135320934 --- /dev/null +++ b/recipes/bioconductor-bsgenome.cjacchus.ucsc.caljac3/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ BSgenome.Cjacchus.UCSC.calJac3 diff --git a/recipes/bioconductor-bsgenome.dmelanogaster.ucsc.dm2.masked/meta.yaml b/recipes/bioconductor-bsgenome.dmelanogaster.ucsc.dm2.masked/meta.yaml index d5b5384b88a43..56e7bc36642af 100644 --- a/recipes/bioconductor-bsgenome.dmelanogaster.ucsc.dm2.masked/meta.yaml +++ b/recipes/bioconductor-bsgenome.dmelanogaster.ucsc.dm2.masked/meta.yaml @@ -1,6 +1,6 @@ {% set version = "1.3.99" %} {% set name = "BSgenome.Dmelanogaster.UCSC.dm2.masked" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -12,21 +12,21 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' md5: ae7ca3053e97a0d6bd20bc2b9635ecce build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ noarch: generic requirements: host: - - 'bioconductor-bsgenome >=1.50.0,<1.51.0' + - 'bioconductor-bsgenome >=1.52.0,<1.53.0' - 'bioconductor-bsgenome.dmelanogaster.ucsc.dm2 >=1.4.0,<1.5.0' - r-base run: - - 'bioconductor-bsgenome >=1.50.0,<1.51.0' + - 'bioconductor-bsgenome >=1.52.0,<1.53.0' - 'bioconductor-bsgenome.dmelanogaster.ucsc.dm2 >=1.4.0,<1.5.0' - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-bsgenome.dmelanogaster.ucsc.dm2.masked/post-link.sh b/recipes/bioconductor-bsgenome.dmelanogaster.ucsc.dm2.masked/post-link.sh index f09e0ee4499ca..8808cab55e077 100644 --- a/recipes/bioconductor-bsgenome.dmelanogaster.ucsc.dm2.masked/post-link.sh +++ b/recipes/bioconductor-bsgenome.dmelanogaster.ucsc.dm2.masked/post-link.sh @@ -1,9 +1,10 @@ #!/bin/bash FN="BSgenome.Dmelanogaster.UCSC.dm2.masked_1.3.99.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/BSgenome.Dmelanogaster.UCSC.dm2.masked_1.3.99.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/BSgenome.Dmelanogaster.UCSC.dm2.masked_1.3.99.tar.gz" "https://bioarchive.galaxyproject.org/BSgenome.Dmelanogaster.UCSC.dm2.masked_1.3.99.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-bsgenome.dmelanogaster.ucsc.dm2.masked/bioconductor-bsgenome.dmelanogaster.ucsc.dm2.masked_1.3.99_src_all.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-bsgenome.dmelanogaster.ucsc.dm2.masked/bioconductor-bsgenome.dmelanogaster.ucsc.dm2.masked_1.3.99_src_all.tar.gz" ) MD5="ae7ca3053e97a0d6bd20bc2b9635ecce" @@ -16,7 +17,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-bsgenome.dmelanogaster.ucsc.dm2/meta.yaml b/recipes/bioconductor-bsgenome.dmelanogaster.ucsc.dm2/meta.yaml index 5c9b8a05a5f5b..a66036d83d0e5 100644 --- a/recipes/bioconductor-bsgenome.dmelanogaster.ucsc.dm2/meta.yaml +++ b/recipes/bioconductor-bsgenome.dmelanogaster.ucsc.dm2/meta.yaml @@ -1,6 +1,6 @@ {% set version = "1.4.0" %} {% set name = "BSgenome.Dmelanogaster.UCSC.dm2" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -12,7 +12,7 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' md5: ebc88df5595fc7aad588b8f3f7de4784 build: - number: 1 + number: 2 rpaths: - lib/R/lib/ - lib/ @@ -20,12 +20,12 @@ build: # Suggests: GenomicFeatures requirements: host: - - 'bioconductor-bsgenome >=1.50.0,<1.51.0' + - 'bioconductor-bsgenome >=1.52.0,<1.53.0' - r-base run: - - 'bioconductor-bsgenome >=1.50.0,<1.51.0' + - 'bioconductor-bsgenome >=1.52.0,<1.53.0' - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-bsgenome.dmelanogaster.ucsc.dm2/post-link.sh b/recipes/bioconductor-bsgenome.dmelanogaster.ucsc.dm2/post-link.sh index 966be3f58fe32..9531bad7b3cf4 100644 --- a/recipes/bioconductor-bsgenome.dmelanogaster.ucsc.dm2/post-link.sh +++ b/recipes/bioconductor-bsgenome.dmelanogaster.ucsc.dm2/post-link.sh @@ -1,9 +1,10 @@ #!/bin/bash FN="BSgenome.Dmelanogaster.UCSC.dm2_1.4.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/BSgenome.Dmelanogaster.UCSC.dm2_1.4.0.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/BSgenome.Dmelanogaster.UCSC.dm2_1.4.0.tar.gz" "https://bioarchive.galaxyproject.org/BSgenome.Dmelanogaster.UCSC.dm2_1.4.0.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-bsgenome.dmelanogaster.ucsc.dm2/bioconductor-bsgenome.dmelanogaster.ucsc.dm2_1.4.0_src_all.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-bsgenome.dmelanogaster.ucsc.dm2/bioconductor-bsgenome.dmelanogaster.ucsc.dm2_1.4.0_src_all.tar.gz" ) MD5="ebc88df5595fc7aad588b8f3f7de4784" @@ -16,7 +17,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-bsgenome.dmelanogaster.ucsc.dm3.masked/meta.yaml b/recipes/bioconductor-bsgenome.dmelanogaster.ucsc.dm3.masked/meta.yaml index 72cfc08f7343e..3c6000ddc8151 100644 --- a/recipes/bioconductor-bsgenome.dmelanogaster.ucsc.dm3.masked/meta.yaml +++ b/recipes/bioconductor-bsgenome.dmelanogaster.ucsc.dm3.masked/meta.yaml @@ -1,6 +1,6 @@ {% set version = "1.3.99" %} {% set name = "BSgenome.Dmelanogaster.UCSC.dm3.masked" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -12,21 +12,21 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' md5: 592e7ec451d126b2d314ab6c75d86830 build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ noarch: generic requirements: host: - - 'bioconductor-bsgenome >=1.50.0,<1.51.0' + - 'bioconductor-bsgenome >=1.52.0,<1.53.0' - 'bioconductor-bsgenome.dmelanogaster.ucsc.dm3 >=1.4.0,<1.5.0' - r-base run: - - 'bioconductor-bsgenome >=1.50.0,<1.51.0' + - 'bioconductor-bsgenome >=1.52.0,<1.53.0' - 'bioconductor-bsgenome.dmelanogaster.ucsc.dm3 >=1.4.0,<1.5.0' - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-bsgenome.dmelanogaster.ucsc.dm3.masked/post-link.sh b/recipes/bioconductor-bsgenome.dmelanogaster.ucsc.dm3.masked/post-link.sh index 03ddf17262cf7..9b29eb330e3bd 100644 --- a/recipes/bioconductor-bsgenome.dmelanogaster.ucsc.dm3.masked/post-link.sh +++ b/recipes/bioconductor-bsgenome.dmelanogaster.ucsc.dm3.masked/post-link.sh @@ -1,9 +1,10 @@ #!/bin/bash FN="BSgenome.Dmelanogaster.UCSC.dm3.masked_1.3.99.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/BSgenome.Dmelanogaster.UCSC.dm3.masked_1.3.99.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/BSgenome.Dmelanogaster.UCSC.dm3.masked_1.3.99.tar.gz" "https://bioarchive.galaxyproject.org/BSgenome.Dmelanogaster.UCSC.dm3.masked_1.3.99.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-bsgenome.dmelanogaster.ucsc.dm3.masked/bioconductor-bsgenome.dmelanogaster.ucsc.dm3.masked_1.3.99_src_all.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-bsgenome.dmelanogaster.ucsc.dm3.masked/bioconductor-bsgenome.dmelanogaster.ucsc.dm3.masked_1.3.99_src_all.tar.gz" ) MD5="592e7ec451d126b2d314ab6c75d86830" @@ -16,7 +17,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-bsgenome.dmelanogaster.ucsc.dm3/meta.yaml b/recipes/bioconductor-bsgenome.dmelanogaster.ucsc.dm3/meta.yaml index 201b0742317be..86d07e66c2a57 100644 --- a/recipes/bioconductor-bsgenome.dmelanogaster.ucsc.dm3/meta.yaml +++ b/recipes/bioconductor-bsgenome.dmelanogaster.ucsc.dm3/meta.yaml @@ -1,6 +1,6 @@ {% set version = "1.4.0" %} {% set name = "BSgenome.Dmelanogaster.UCSC.dm3" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -12,7 +12,7 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' md5: b7ceebf7bfee766596f602f9e808d069 build: - number: 5 + number: 6 rpaths: - lib/R/lib/ - lib/ @@ -20,12 +20,12 @@ build: # Suggests: TxDb.Dmelanogaster.UCSC.dm3.ensGene requirements: host: - - 'bioconductor-bsgenome >=1.50.0,<1.51.0' + - 'bioconductor-bsgenome >=1.52.0,<1.53.0' - r-base run: - - 'bioconductor-bsgenome >=1.50.0,<1.51.0' + - 'bioconductor-bsgenome >=1.52.0,<1.53.0' - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-bsgenome.dmelanogaster.ucsc.dm3/post-link.sh b/recipes/bioconductor-bsgenome.dmelanogaster.ucsc.dm3/post-link.sh index 8850fce984937..ac1f377f6dda3 100644 --- a/recipes/bioconductor-bsgenome.dmelanogaster.ucsc.dm3/post-link.sh +++ b/recipes/bioconductor-bsgenome.dmelanogaster.ucsc.dm3/post-link.sh @@ -1,7 +1,7 @@ #!/bin/bash FN="BSgenome.Dmelanogaster.UCSC.dm3_1.4.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/BSgenome.Dmelanogaster.UCSC.dm3_1.4.0.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/BSgenome.Dmelanogaster.UCSC.dm3_1.4.0.tar.gz" "https://bioarchive.galaxyproject.org/BSgenome.Dmelanogaster.UCSC.dm3_1.4.0.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-bsgenome.dmelanogaster.ucsc.dm3/bioconductor-bsgenome.dmelanogaster.ucsc.dm3_1.4.0_src_all.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-bsgenome.dmelanogaster.ucsc.dm3/bioconductor-bsgenome.dmelanogaster.ucsc.dm3_1.4.0_src_all.tar.gz" @@ -17,7 +17,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-bsgenome.dmelanogaster.ucsc.dm6/meta.yaml b/recipes/bioconductor-bsgenome.dmelanogaster.ucsc.dm6/meta.yaml index 380242721ad2d..dd9c287c523a8 100644 --- a/recipes/bioconductor-bsgenome.dmelanogaster.ucsc.dm6/meta.yaml +++ b/recipes/bioconductor-bsgenome.dmelanogaster.ucsc.dm6/meta.yaml @@ -1,6 +1,6 @@ {% set version = "1.4.1" %} {% set name = "BSgenome.Dmelanogaster.UCSC.dm6" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -12,7 +12,7 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' md5: f9d6e406b7893a17c08edd4521c2802f build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ @@ -20,12 +20,12 @@ build: # Suggests: GenomicFeatures requirements: host: - - 'bioconductor-bsgenome >=1.50.0,<1.51.0' + - 'bioconductor-bsgenome >=1.52.0,<1.53.0' - r-base run: - - 'bioconductor-bsgenome >=1.50.0,<1.51.0' + - 'bioconductor-bsgenome >=1.52.0,<1.53.0' - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-bsgenome.dmelanogaster.ucsc.dm6/post-link.sh b/recipes/bioconductor-bsgenome.dmelanogaster.ucsc.dm6/post-link.sh index 7898ecb68f5dd..8e68b728250a0 100644 --- a/recipes/bioconductor-bsgenome.dmelanogaster.ucsc.dm6/post-link.sh +++ b/recipes/bioconductor-bsgenome.dmelanogaster.ucsc.dm6/post-link.sh @@ -1,9 +1,10 @@ #!/bin/bash FN="BSgenome.Dmelanogaster.UCSC.dm6_1.4.1.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/BSgenome.Dmelanogaster.UCSC.dm6_1.4.1.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/BSgenome.Dmelanogaster.UCSC.dm6_1.4.1.tar.gz" "https://bioarchive.galaxyproject.org/BSgenome.Dmelanogaster.UCSC.dm6_1.4.1.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-bsgenome.dmelanogaster.ucsc.dm6/bioconductor-bsgenome.dmelanogaster.ucsc.dm6_1.4.1_src_all.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-bsgenome.dmelanogaster.ucsc.dm6/bioconductor-bsgenome.dmelanogaster.ucsc.dm6_1.4.1_src_all.tar.gz" ) MD5="f9d6e406b7893a17c08edd4521c2802f" @@ -16,7 +17,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-bsgenome.drerio.ucsc.danrer10/meta.yaml b/recipes/bioconductor-bsgenome.drerio.ucsc.danrer10/meta.yaml index d4de3ba1bab5b..ddbd222c0cef2 100644 --- a/recipes/bioconductor-bsgenome.drerio.ucsc.danrer10/meta.yaml +++ b/recipes/bioconductor-bsgenome.drerio.ucsc.danrer10/meta.yaml @@ -1,6 +1,6 @@ {% set version = "1.4.2" %} {% set name = "BSgenome.Drerio.UCSC.danRer10" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -12,7 +12,7 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' md5: b8dbcc8a338a021ed35656b27b3dd4c0 build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ @@ -20,12 +20,12 @@ build: # Suggests: GenomicFeatures requirements: host: - - 'bioconductor-bsgenome >=1.50.0,<1.51.0' + - 'bioconductor-bsgenome >=1.52.0,<1.53.0' - r-base run: - - 'bioconductor-bsgenome >=1.50.0,<1.51.0' + - 'bioconductor-bsgenome >=1.52.0,<1.53.0' - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-bsgenome.drerio.ucsc.danrer10/post-link.sh b/recipes/bioconductor-bsgenome.drerio.ucsc.danrer10/post-link.sh index ae87b8fc245aa..1270073812872 100644 --- a/recipes/bioconductor-bsgenome.drerio.ucsc.danrer10/post-link.sh +++ b/recipes/bioconductor-bsgenome.drerio.ucsc.danrer10/post-link.sh @@ -1,9 +1,10 @@ #!/bin/bash FN="BSgenome.Drerio.UCSC.danRer10_1.4.2.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/BSgenome.Drerio.UCSC.danRer10_1.4.2.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/BSgenome.Drerio.UCSC.danRer10_1.4.2.tar.gz" "https://bioarchive.galaxyproject.org/BSgenome.Drerio.UCSC.danRer10_1.4.2.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-bsgenome.drerio.ucsc.danrer10/bioconductor-bsgenome.drerio.ucsc.danrer10_1.4.2_src_all.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-bsgenome.drerio.ucsc.danrer10/bioconductor-bsgenome.drerio.ucsc.danrer10_1.4.2_src_all.tar.gz" ) MD5="b8dbcc8a338a021ed35656b27b3dd4c0" @@ -16,7 +17,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-bsgenome.drerio.ucsc.danrer5.masked/meta.yaml b/recipes/bioconductor-bsgenome.drerio.ucsc.danrer5.masked/meta.yaml index c98de599cb509..a2bdb33cb8917 100644 --- a/recipes/bioconductor-bsgenome.drerio.ucsc.danrer5.masked/meta.yaml +++ b/recipes/bioconductor-bsgenome.drerio.ucsc.danrer5.masked/meta.yaml @@ -1,6 +1,6 @@ {% set version = "1.3.99" %} {% set name = "BSgenome.Drerio.UCSC.danRer5.masked" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -12,21 +12,21 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' md5: 8f0623bcbe1743754a56c55599b535f3 build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ noarch: generic requirements: host: - - 'bioconductor-bsgenome >=1.50.0,<1.51.0' + - 'bioconductor-bsgenome >=1.52.0,<1.53.0' - 'bioconductor-bsgenome.drerio.ucsc.danrer5 >=1.4.0,<1.5.0' - r-base run: - - 'bioconductor-bsgenome >=1.50.0,<1.51.0' + - 'bioconductor-bsgenome >=1.52.0,<1.53.0' - 'bioconductor-bsgenome.drerio.ucsc.danrer5 >=1.4.0,<1.5.0' - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-bsgenome.drerio.ucsc.danrer5.masked/post-link.sh b/recipes/bioconductor-bsgenome.drerio.ucsc.danrer5.masked/post-link.sh index 56a947c85df3d..2e2892c69db87 100644 --- a/recipes/bioconductor-bsgenome.drerio.ucsc.danrer5.masked/post-link.sh +++ b/recipes/bioconductor-bsgenome.drerio.ucsc.danrer5.masked/post-link.sh @@ -1,9 +1,10 @@ #!/bin/bash FN="BSgenome.Drerio.UCSC.danRer5.masked_1.3.99.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/BSgenome.Drerio.UCSC.danRer5.masked_1.3.99.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/BSgenome.Drerio.UCSC.danRer5.masked_1.3.99.tar.gz" "https://bioarchive.galaxyproject.org/BSgenome.Drerio.UCSC.danRer5.masked_1.3.99.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-bsgenome.drerio.ucsc.danrer5.masked/bioconductor-bsgenome.drerio.ucsc.danrer5.masked_1.3.99_src_all.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-bsgenome.drerio.ucsc.danrer5.masked/bioconductor-bsgenome.drerio.ucsc.danrer5.masked_1.3.99_src_all.tar.gz" ) MD5="8f0623bcbe1743754a56c55599b535f3" @@ -16,7 +17,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-bsgenome.drerio.ucsc.danrer5/meta.yaml b/recipes/bioconductor-bsgenome.drerio.ucsc.danrer5/meta.yaml index ad2802f3bff83..a6c5dd27c37ea 100644 --- a/recipes/bioconductor-bsgenome.drerio.ucsc.danrer5/meta.yaml +++ b/recipes/bioconductor-bsgenome.drerio.ucsc.danrer5/meta.yaml @@ -1,6 +1,6 @@ {% set version = "1.4.0" %} {% set name = "BSgenome.Drerio.UCSC.danRer5" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -12,7 +12,7 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' md5: b1fee4bcc0d9cebb2bbdec5cb851f00d build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ @@ -20,12 +20,12 @@ build: # Suggests: GenomicFeatures requirements: host: - - 'bioconductor-bsgenome >=1.50.0,<1.51.0' + - 'bioconductor-bsgenome >=1.52.0,<1.53.0' - r-base run: - - 'bioconductor-bsgenome >=1.50.0,<1.51.0' + - 'bioconductor-bsgenome >=1.52.0,<1.53.0' - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-bsgenome.drerio.ucsc.danrer5/post-link.sh b/recipes/bioconductor-bsgenome.drerio.ucsc.danrer5/post-link.sh index 5fb6e5e771e4c..5ca0a5dfec8b4 100644 --- a/recipes/bioconductor-bsgenome.drerio.ucsc.danrer5/post-link.sh +++ b/recipes/bioconductor-bsgenome.drerio.ucsc.danrer5/post-link.sh @@ -1,9 +1,10 @@ #!/bin/bash FN="BSgenome.Drerio.UCSC.danRer5_1.4.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/BSgenome.Drerio.UCSC.danRer5_1.4.0.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/BSgenome.Drerio.UCSC.danRer5_1.4.0.tar.gz" "https://bioarchive.galaxyproject.org/BSgenome.Drerio.UCSC.danRer5_1.4.0.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-bsgenome.drerio.ucsc.danrer5/bioconductor-bsgenome.drerio.ucsc.danrer5_1.4.0_src_all.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-bsgenome.drerio.ucsc.danrer5/bioconductor-bsgenome.drerio.ucsc.danrer5_1.4.0_src_all.tar.gz" ) MD5="b1fee4bcc0d9cebb2bbdec5cb851f00d" @@ -16,7 +17,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-bsgenome.drerio.ucsc.danrer6.masked/meta.yaml b/recipes/bioconductor-bsgenome.drerio.ucsc.danrer6.masked/meta.yaml index f34b6c82ff70c..e0f7aaf6fdd78 100644 --- a/recipes/bioconductor-bsgenome.drerio.ucsc.danrer6.masked/meta.yaml +++ b/recipes/bioconductor-bsgenome.drerio.ucsc.danrer6.masked/meta.yaml @@ -1,6 +1,6 @@ {% set version = "1.3.99" %} {% set name = "BSgenome.Drerio.UCSC.danRer6.masked" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -12,21 +12,21 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' md5: 71c9b05c27b8d2e05735e6494a8f17ba build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ noarch: generic requirements: host: - - 'bioconductor-bsgenome >=1.50.0,<1.51.0' + - 'bioconductor-bsgenome >=1.52.0,<1.53.0' - 'bioconductor-bsgenome.drerio.ucsc.danrer6 >=1.4.0,<1.5.0' - r-base run: - - 'bioconductor-bsgenome >=1.50.0,<1.51.0' + - 'bioconductor-bsgenome >=1.52.0,<1.53.0' - 'bioconductor-bsgenome.drerio.ucsc.danrer6 >=1.4.0,<1.5.0' - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-bsgenome.drerio.ucsc.danrer6.masked/post-link.sh b/recipes/bioconductor-bsgenome.drerio.ucsc.danrer6.masked/post-link.sh index 7a41c8a32b18f..88892932c0187 100644 --- a/recipes/bioconductor-bsgenome.drerio.ucsc.danrer6.masked/post-link.sh +++ b/recipes/bioconductor-bsgenome.drerio.ucsc.danrer6.masked/post-link.sh @@ -1,9 +1,10 @@ #!/bin/bash FN="BSgenome.Drerio.UCSC.danRer6.masked_1.3.99.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/BSgenome.Drerio.UCSC.danRer6.masked_1.3.99.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/BSgenome.Drerio.UCSC.danRer6.masked_1.3.99.tar.gz" "https://bioarchive.galaxyproject.org/BSgenome.Drerio.UCSC.danRer6.masked_1.3.99.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-bsgenome.drerio.ucsc.danrer6.masked/bioconductor-bsgenome.drerio.ucsc.danrer6.masked_1.3.99_src_all.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-bsgenome.drerio.ucsc.danrer6.masked/bioconductor-bsgenome.drerio.ucsc.danrer6.masked_1.3.99_src_all.tar.gz" ) MD5="71c9b05c27b8d2e05735e6494a8f17ba" @@ -16,7 +17,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-bsgenome.drerio.ucsc.danrer6/meta.yaml b/recipes/bioconductor-bsgenome.drerio.ucsc.danrer6/meta.yaml index 747128e3dd1a9..fb22be194ea59 100644 --- a/recipes/bioconductor-bsgenome.drerio.ucsc.danrer6/meta.yaml +++ b/recipes/bioconductor-bsgenome.drerio.ucsc.danrer6/meta.yaml @@ -1,6 +1,6 @@ {% set version = "1.4.0" %} {% set name = "BSgenome.Drerio.UCSC.danRer6" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -12,7 +12,7 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' md5: 537d37d29d97ae0c31d77decc67b25b0 build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ @@ -20,12 +20,12 @@ build: # Suggests: GenomicFeatures requirements: host: - - 'bioconductor-bsgenome >=1.50.0,<1.51.0' + - 'bioconductor-bsgenome >=1.52.0,<1.53.0' - r-base run: - - 'bioconductor-bsgenome >=1.50.0,<1.51.0' + - 'bioconductor-bsgenome >=1.52.0,<1.53.0' - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-bsgenome.drerio.ucsc.danrer6/post-link.sh b/recipes/bioconductor-bsgenome.drerio.ucsc.danrer6/post-link.sh index 37d83f0728b41..75c2089eec3a3 100644 --- a/recipes/bioconductor-bsgenome.drerio.ucsc.danrer6/post-link.sh +++ b/recipes/bioconductor-bsgenome.drerio.ucsc.danrer6/post-link.sh @@ -1,9 +1,10 @@ #!/bin/bash FN="BSgenome.Drerio.UCSC.danRer6_1.4.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/BSgenome.Drerio.UCSC.danRer6_1.4.0.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/BSgenome.Drerio.UCSC.danRer6_1.4.0.tar.gz" "https://bioarchive.galaxyproject.org/BSgenome.Drerio.UCSC.danRer6_1.4.0.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-bsgenome.drerio.ucsc.danrer6/bioconductor-bsgenome.drerio.ucsc.danrer6_1.4.0_src_all.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-bsgenome.drerio.ucsc.danrer6/bioconductor-bsgenome.drerio.ucsc.danrer6_1.4.0_src_all.tar.gz" ) MD5="537d37d29d97ae0c31d77decc67b25b0" @@ -16,7 +17,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-bsgenome.drerio.ucsc.danrer7.masked/meta.yaml b/recipes/bioconductor-bsgenome.drerio.ucsc.danrer7.masked/meta.yaml index 74d9528b4b17e..1fd326cb59f28 100644 --- a/recipes/bioconductor-bsgenome.drerio.ucsc.danrer7.masked/meta.yaml +++ b/recipes/bioconductor-bsgenome.drerio.ucsc.danrer7.masked/meta.yaml @@ -1,6 +1,6 @@ {% set version = "1.3.99" %} {% set name = "BSgenome.Drerio.UCSC.danRer7.masked" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -12,21 +12,21 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' md5: 5d68af24477d006ed22e7342ff97ac16 build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ noarch: generic requirements: host: - - 'bioconductor-bsgenome >=1.50.0,<1.51.0' + - 'bioconductor-bsgenome >=1.52.0,<1.53.0' - 'bioconductor-bsgenome.drerio.ucsc.danrer7 >=1.4.0,<1.5.0' - r-base run: - - 'bioconductor-bsgenome >=1.50.0,<1.51.0' + - 'bioconductor-bsgenome >=1.52.0,<1.53.0' - 'bioconductor-bsgenome.drerio.ucsc.danrer7 >=1.4.0,<1.5.0' - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-bsgenome.drerio.ucsc.danrer7.masked/post-link.sh b/recipes/bioconductor-bsgenome.drerio.ucsc.danrer7.masked/post-link.sh index 705dd689e88be..3f99d38aecced 100644 --- a/recipes/bioconductor-bsgenome.drerio.ucsc.danrer7.masked/post-link.sh +++ b/recipes/bioconductor-bsgenome.drerio.ucsc.danrer7.masked/post-link.sh @@ -1,9 +1,10 @@ #!/bin/bash FN="BSgenome.Drerio.UCSC.danRer7.masked_1.3.99.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/BSgenome.Drerio.UCSC.danRer7.masked_1.3.99.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/BSgenome.Drerio.UCSC.danRer7.masked_1.3.99.tar.gz" "https://bioarchive.galaxyproject.org/BSgenome.Drerio.UCSC.danRer7.masked_1.3.99.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-bsgenome.drerio.ucsc.danrer7.masked/bioconductor-bsgenome.drerio.ucsc.danrer7.masked_1.3.99_src_all.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-bsgenome.drerio.ucsc.danrer7.masked/bioconductor-bsgenome.drerio.ucsc.danrer7.masked_1.3.99_src_all.tar.gz" ) MD5="5d68af24477d006ed22e7342ff97ac16" @@ -16,7 +17,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-bsgenome.drerio.ucsc.danrer7/meta.yaml b/recipes/bioconductor-bsgenome.drerio.ucsc.danrer7/meta.yaml index e1b4b697d78c7..97398a832918e 100644 --- a/recipes/bioconductor-bsgenome.drerio.ucsc.danrer7/meta.yaml +++ b/recipes/bioconductor-bsgenome.drerio.ucsc.danrer7/meta.yaml @@ -1,6 +1,6 @@ {% set version = "1.4.0" %} {% set name = "BSgenome.Drerio.UCSC.danRer7" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -12,7 +12,7 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' md5: 766b407a46f20d69a143eab0809eb10a build: - number: 4 + number: 5 rpaths: - lib/R/lib/ - lib/ @@ -20,12 +20,12 @@ build: # Suggests: GenomicFeatures requirements: host: - - 'bioconductor-bsgenome >=1.50.0,<1.51.0' + - 'bioconductor-bsgenome >=1.52.0,<1.53.0' - r-base run: - - 'bioconductor-bsgenome >=1.50.0,<1.51.0' + - 'bioconductor-bsgenome >=1.52.0,<1.53.0' - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-bsgenome.drerio.ucsc.danrer7/post-link.sh b/recipes/bioconductor-bsgenome.drerio.ucsc.danrer7/post-link.sh index be9038e829adc..b12eb6fcefa6c 100644 --- a/recipes/bioconductor-bsgenome.drerio.ucsc.danrer7/post-link.sh +++ b/recipes/bioconductor-bsgenome.drerio.ucsc.danrer7/post-link.sh @@ -1,7 +1,7 @@ #!/bin/bash FN="BSgenome.Drerio.UCSC.danRer7_1.4.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/BSgenome.Drerio.UCSC.danRer7_1.4.0.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/BSgenome.Drerio.UCSC.danRer7_1.4.0.tar.gz" "https://bioarchive.galaxyproject.org/BSgenome.Drerio.UCSC.danRer7_1.4.0.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-bsgenome.drerio.ucsc.danrer7/bioconductor-bsgenome.drerio.ucsc.danrer7_1.4.0_src_all.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-bsgenome.drerio.ucsc.danrer7/bioconductor-bsgenome.drerio.ucsc.danrer7_1.4.0_src_all.tar.gz" @@ -17,7 +17,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-bsgenome.ecoli.ncbi.20080805/meta.yaml b/recipes/bioconductor-bsgenome.ecoli.ncbi.20080805/meta.yaml index 84346d1fdfd65..8955aa1eb4b27 100644 --- a/recipes/bioconductor-bsgenome.ecoli.ncbi.20080805/meta.yaml +++ b/recipes/bioconductor-bsgenome.ecoli.ncbi.20080805/meta.yaml @@ -1,6 +1,6 @@ {% set version = "1.3.1000" %} {% set name = "BSgenome.Ecoli.NCBI.20080805" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -12,19 +12,19 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' md5: c653e9cbee3faeb6fd5759b7575f234d build: - number: 5 + number: 6 rpaths: - lib/R/lib/ - lib/ noarch: generic requirements: host: - - 'bioconductor-bsgenome >=1.50.0,<1.51.0' + - 'bioconductor-bsgenome >=1.52.0,<1.53.0' - r-base run: - - 'bioconductor-bsgenome >=1.50.0,<1.51.0' + - 'bioconductor-bsgenome >=1.52.0,<1.53.0' - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-bsgenome.ecoli.ncbi.20080805/post-link.sh b/recipes/bioconductor-bsgenome.ecoli.ncbi.20080805/post-link.sh index 23826e14a44cb..2151a960ef1cf 100644 --- a/recipes/bioconductor-bsgenome.ecoli.ncbi.20080805/post-link.sh +++ b/recipes/bioconductor-bsgenome.ecoli.ncbi.20080805/post-link.sh @@ -1,7 +1,7 @@ #!/bin/bash FN="BSgenome.Ecoli.NCBI.20080805_1.3.1000.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/BSgenome.Ecoli.NCBI.20080805_1.3.1000.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/BSgenome.Ecoli.NCBI.20080805_1.3.1000.tar.gz" "https://bioarchive.galaxyproject.org/BSgenome.Ecoli.NCBI.20080805_1.3.1000.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-bsgenome.ecoli.ncbi.20080805/bioconductor-bsgenome.ecoli.ncbi.20080805_1.3.1000_src_all.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-bsgenome.ecoli.ncbi.20080805/bioconductor-bsgenome.ecoli.ncbi.20080805_1.3.1000_src_all.tar.gz" @@ -17,7 +17,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-bsgenome.gaculeatus.ucsc.gasacu1.masked/meta.yaml b/recipes/bioconductor-bsgenome.gaculeatus.ucsc.gasacu1.masked/meta.yaml index a7081f96f4ae0..f1c24f71f9b9d 100644 --- a/recipes/bioconductor-bsgenome.gaculeatus.ucsc.gasacu1.masked/meta.yaml +++ b/recipes/bioconductor-bsgenome.gaculeatus.ucsc.gasacu1.masked/meta.yaml @@ -1,6 +1,6 @@ {% set version = "1.3.99" %} {% set name = "BSgenome.Gaculeatus.UCSC.gasAcu1.masked" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -12,21 +12,21 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' md5: 9d9b9e70f4f4624ee4a2b09a59d44510 build: - number: 1 + number: 2 rpaths: - lib/R/lib/ - lib/ noarch: generic requirements: host: - - 'bioconductor-bsgenome >=1.50.0,<1.51.0' + - 'bioconductor-bsgenome >=1.52.0,<1.53.0' - 'bioconductor-bsgenome.gaculeatus.ucsc.gasacu1 >=1.4.0,<1.5.0' - r-base run: - - 'bioconductor-bsgenome >=1.50.0,<1.51.0' + - 'bioconductor-bsgenome >=1.52.0,<1.53.0' - 'bioconductor-bsgenome.gaculeatus.ucsc.gasacu1 >=1.4.0,<1.5.0' - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-bsgenome.gaculeatus.ucsc.gasacu1.masked/post-link.sh b/recipes/bioconductor-bsgenome.gaculeatus.ucsc.gasacu1.masked/post-link.sh index 79d771acd2b00..257bf86afd8d7 100644 --- a/recipes/bioconductor-bsgenome.gaculeatus.ucsc.gasacu1.masked/post-link.sh +++ b/recipes/bioconductor-bsgenome.gaculeatus.ucsc.gasacu1.masked/post-link.sh @@ -1,9 +1,10 @@ #!/bin/bash FN="BSgenome.Gaculeatus.UCSC.gasAcu1.masked_1.3.99.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/BSgenome.Gaculeatus.UCSC.gasAcu1.masked_1.3.99.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/BSgenome.Gaculeatus.UCSC.gasAcu1.masked_1.3.99.tar.gz" "https://bioarchive.galaxyproject.org/BSgenome.Gaculeatus.UCSC.gasAcu1.masked_1.3.99.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-bsgenome.gaculeatus.ucsc.gasacu1.masked/bioconductor-bsgenome.gaculeatus.ucsc.gasacu1.masked_1.3.99_src_all.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-bsgenome.gaculeatus.ucsc.gasacu1.masked/bioconductor-bsgenome.gaculeatus.ucsc.gasacu1.masked_1.3.99_src_all.tar.gz" ) MD5="9d9b9e70f4f4624ee4a2b09a59d44510" @@ -16,7 +17,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-bsgenome.gaculeatus.ucsc.gasacu1/meta.yaml b/recipes/bioconductor-bsgenome.gaculeatus.ucsc.gasacu1/meta.yaml index c20b01d9c4f37..eee42169fd9e2 100644 --- a/recipes/bioconductor-bsgenome.gaculeatus.ucsc.gasacu1/meta.yaml +++ b/recipes/bioconductor-bsgenome.gaculeatus.ucsc.gasacu1/meta.yaml @@ -1,6 +1,6 @@ {% set version = "1.4.0" %} {% set name = "BSgenome.Gaculeatus.UCSC.gasAcu1" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -12,7 +12,7 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' md5: 412aa0570d9c556861b7bb9a5bbc2007 build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ @@ -20,12 +20,12 @@ build: # Suggests: GenomicFeatures requirements: host: - - 'bioconductor-bsgenome >=1.50.0,<1.51.0' + - 'bioconductor-bsgenome >=1.52.0,<1.53.0' - r-base run: - - 'bioconductor-bsgenome >=1.50.0,<1.51.0' + - 'bioconductor-bsgenome >=1.52.0,<1.53.0' - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-bsgenome.gaculeatus.ucsc.gasacu1/post-link.sh b/recipes/bioconductor-bsgenome.gaculeatus.ucsc.gasacu1/post-link.sh index 3da9a1e5d4e48..3aa3e14e4009d 100644 --- a/recipes/bioconductor-bsgenome.gaculeatus.ucsc.gasacu1/post-link.sh +++ b/recipes/bioconductor-bsgenome.gaculeatus.ucsc.gasacu1/post-link.sh @@ -1,9 +1,10 @@ #!/bin/bash FN="BSgenome.Gaculeatus.UCSC.gasAcu1_1.4.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/BSgenome.Gaculeatus.UCSC.gasAcu1_1.4.0.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/BSgenome.Gaculeatus.UCSC.gasAcu1_1.4.0.tar.gz" "https://bioarchive.galaxyproject.org/BSgenome.Gaculeatus.UCSC.gasAcu1_1.4.0.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-bsgenome.gaculeatus.ucsc.gasacu1/bioconductor-bsgenome.gaculeatus.ucsc.gasacu1_1.4.0_src_all.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-bsgenome.gaculeatus.ucsc.gasacu1/bioconductor-bsgenome.gaculeatus.ucsc.gasacu1_1.4.0_src_all.tar.gz" ) MD5="412aa0570d9c556861b7bb9a5bbc2007" @@ -16,7 +17,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-bsgenome.ggallus.ucsc.galgal3.masked/meta.yaml b/recipes/bioconductor-bsgenome.ggallus.ucsc.galgal3.masked/meta.yaml index 08df5d09e16f8..ae3f29438d68d 100644 --- a/recipes/bioconductor-bsgenome.ggallus.ucsc.galgal3.masked/meta.yaml +++ b/recipes/bioconductor-bsgenome.ggallus.ucsc.galgal3.masked/meta.yaml @@ -1,6 +1,6 @@ {% set version = "1.3.99" %} {% set name = "BSgenome.Ggallus.UCSC.galGal3.masked" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -12,21 +12,21 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' md5: b3224e3a2b15de379c068e61cedfefa6 build: - number: 1 + number: 2 rpaths: - lib/R/lib/ - lib/ noarch: generic requirements: host: - - 'bioconductor-bsgenome >=1.50.0,<1.51.0' + - 'bioconductor-bsgenome >=1.52.0,<1.53.0' - 'bioconductor-bsgenome.ggallus.ucsc.galgal3 >=1.4.0,<1.5.0' - r-base run: - - 'bioconductor-bsgenome >=1.50.0,<1.51.0' + - 'bioconductor-bsgenome >=1.52.0,<1.53.0' - 'bioconductor-bsgenome.ggallus.ucsc.galgal3 >=1.4.0,<1.5.0' - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-bsgenome.ggallus.ucsc.galgal3.masked/post-link.sh b/recipes/bioconductor-bsgenome.ggallus.ucsc.galgal3.masked/post-link.sh index 4d37b1aead325..b87a8311a3778 100644 --- a/recipes/bioconductor-bsgenome.ggallus.ucsc.galgal3.masked/post-link.sh +++ b/recipes/bioconductor-bsgenome.ggallus.ucsc.galgal3.masked/post-link.sh @@ -1,9 +1,10 @@ #!/bin/bash FN="BSgenome.Ggallus.UCSC.galGal3.masked_1.3.99.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/BSgenome.Ggallus.UCSC.galGal3.masked_1.3.99.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/BSgenome.Ggallus.UCSC.galGal3.masked_1.3.99.tar.gz" "https://bioarchive.galaxyproject.org/BSgenome.Ggallus.UCSC.galGal3.masked_1.3.99.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-bsgenome.ggallus.ucsc.galgal3.masked/bioconductor-bsgenome.ggallus.ucsc.galgal3.masked_1.3.99_src_all.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-bsgenome.ggallus.ucsc.galgal3.masked/bioconductor-bsgenome.ggallus.ucsc.galgal3.masked_1.3.99_src_all.tar.gz" ) MD5="b3224e3a2b15de379c068e61cedfefa6" @@ -16,7 +17,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-bsgenome.ggallus.ucsc.galgal3/meta.yaml b/recipes/bioconductor-bsgenome.ggallus.ucsc.galgal3/meta.yaml index 48b392f7c0e8f..199568c70f831 100644 --- a/recipes/bioconductor-bsgenome.ggallus.ucsc.galgal3/meta.yaml +++ b/recipes/bioconductor-bsgenome.ggallus.ucsc.galgal3/meta.yaml @@ -1,6 +1,6 @@ {% set version = "1.4.0" %} {% set name = "BSgenome.Ggallus.UCSC.galGal3" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -12,7 +12,7 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' md5: a463e5ccfc8c6d2c62a6ade0da65dbc4 build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ @@ -20,12 +20,12 @@ build: # Suggests: GenomicFeatures requirements: host: - - 'bioconductor-bsgenome >=1.50.0,<1.51.0' + - 'bioconductor-bsgenome >=1.52.0,<1.53.0' - r-base run: - - 'bioconductor-bsgenome >=1.50.0,<1.51.0' + - 'bioconductor-bsgenome >=1.52.0,<1.53.0' - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-bsgenome.ggallus.ucsc.galgal3/post-link.sh b/recipes/bioconductor-bsgenome.ggallus.ucsc.galgal3/post-link.sh index ce402b4c5bc15..7d03a25347974 100644 --- a/recipes/bioconductor-bsgenome.ggallus.ucsc.galgal3/post-link.sh +++ b/recipes/bioconductor-bsgenome.ggallus.ucsc.galgal3/post-link.sh @@ -1,9 +1,10 @@ #!/bin/bash FN="BSgenome.Ggallus.UCSC.galGal3_1.4.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/BSgenome.Ggallus.UCSC.galGal3_1.4.0.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/BSgenome.Ggallus.UCSC.galGal3_1.4.0.tar.gz" "https://bioarchive.galaxyproject.org/BSgenome.Ggallus.UCSC.galGal3_1.4.0.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-bsgenome.ggallus.ucsc.galgal3/bioconductor-bsgenome.ggallus.ucsc.galgal3_1.4.0_src_all.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-bsgenome.ggallus.ucsc.galgal3/bioconductor-bsgenome.ggallus.ucsc.galgal3_1.4.0_src_all.tar.gz" ) MD5="a463e5ccfc8c6d2c62a6ade0da65dbc4" @@ -16,7 +17,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-bsgenome.ggallus.ucsc.galgal4.masked/meta.yaml b/recipes/bioconductor-bsgenome.ggallus.ucsc.galgal4.masked/meta.yaml index 14d66e8676c79..83bcfd24776d2 100644 --- a/recipes/bioconductor-bsgenome.ggallus.ucsc.galgal4.masked/meta.yaml +++ b/recipes/bioconductor-bsgenome.ggallus.ucsc.galgal4.masked/meta.yaml @@ -1,6 +1,6 @@ {% set version = "1.3.99" %} {% set name = "BSgenome.Ggallus.UCSC.galGal4.masked" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -12,21 +12,21 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' md5: 0166121ebd8d0b6a4d24d67e175cfe81 build: - number: 1 + number: 2 rpaths: - lib/R/lib/ - lib/ noarch: generic requirements: host: - - 'bioconductor-bsgenome >=1.50.0,<1.51.0' + - 'bioconductor-bsgenome >=1.52.0,<1.53.0' - 'bioconductor-bsgenome.ggallus.ucsc.galgal4 >=1.4.0,<1.5.0' - r-base run: - - 'bioconductor-bsgenome >=1.50.0,<1.51.0' + - 'bioconductor-bsgenome >=1.52.0,<1.53.0' - 'bioconductor-bsgenome.ggallus.ucsc.galgal4 >=1.4.0,<1.5.0' - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-bsgenome.ggallus.ucsc.galgal4.masked/post-link.sh b/recipes/bioconductor-bsgenome.ggallus.ucsc.galgal4.masked/post-link.sh index 2a8b04474e125..81e1df0618055 100644 --- a/recipes/bioconductor-bsgenome.ggallus.ucsc.galgal4.masked/post-link.sh +++ b/recipes/bioconductor-bsgenome.ggallus.ucsc.galgal4.masked/post-link.sh @@ -1,9 +1,10 @@ #!/bin/bash FN="BSgenome.Ggallus.UCSC.galGal4.masked_1.3.99.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/BSgenome.Ggallus.UCSC.galGal4.masked_1.3.99.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/BSgenome.Ggallus.UCSC.galGal4.masked_1.3.99.tar.gz" "https://bioarchive.galaxyproject.org/BSgenome.Ggallus.UCSC.galGal4.masked_1.3.99.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-bsgenome.ggallus.ucsc.galgal4.masked/bioconductor-bsgenome.ggallus.ucsc.galgal4.masked_1.3.99_src_all.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-bsgenome.ggallus.ucsc.galgal4.masked/bioconductor-bsgenome.ggallus.ucsc.galgal4.masked_1.3.99_src_all.tar.gz" ) MD5="0166121ebd8d0b6a4d24d67e175cfe81" @@ -16,7 +17,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-bsgenome.ggallus.ucsc.galgal4/meta.yaml b/recipes/bioconductor-bsgenome.ggallus.ucsc.galgal4/meta.yaml index 3f792dcdc54cc..a59834437d247 100644 --- a/recipes/bioconductor-bsgenome.ggallus.ucsc.galgal4/meta.yaml +++ b/recipes/bioconductor-bsgenome.ggallus.ucsc.galgal4/meta.yaml @@ -1,6 +1,6 @@ {% set version = "1.4.0" %} {% set name = "BSgenome.Ggallus.UCSC.galGal4" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -12,7 +12,7 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' md5: c2cb4bfc39db93c060e78d8d12542c11 build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ @@ -20,12 +20,12 @@ build: # Suggests: GenomicFeatures requirements: host: - - 'bioconductor-bsgenome >=1.50.0,<1.51.0' + - 'bioconductor-bsgenome >=1.52.0,<1.53.0' - r-base run: - - 'bioconductor-bsgenome >=1.50.0,<1.51.0' + - 'bioconductor-bsgenome >=1.52.0,<1.53.0' - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-bsgenome.ggallus.ucsc.galgal4/post-link.sh b/recipes/bioconductor-bsgenome.ggallus.ucsc.galgal4/post-link.sh index b27f923b428b5..dc63ddc21c159 100644 --- a/recipes/bioconductor-bsgenome.ggallus.ucsc.galgal4/post-link.sh +++ b/recipes/bioconductor-bsgenome.ggallus.ucsc.galgal4/post-link.sh @@ -1,9 +1,10 @@ #!/bin/bash FN="BSgenome.Ggallus.UCSC.galGal4_1.4.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/BSgenome.Ggallus.UCSC.galGal4_1.4.0.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/BSgenome.Ggallus.UCSC.galGal4_1.4.0.tar.gz" "https://bioarchive.galaxyproject.org/BSgenome.Ggallus.UCSC.galGal4_1.4.0.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-bsgenome.ggallus.ucsc.galgal4/bioconductor-bsgenome.ggallus.ucsc.galgal4_1.4.0_src_all.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-bsgenome.ggallus.ucsc.galgal4/bioconductor-bsgenome.ggallus.ucsc.galgal4_1.4.0_src_all.tar.gz" ) MD5="c2cb4bfc39db93c060e78d8d12542c11" @@ -16,7 +17,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-bsgenome.ggallus.ucsc.galgal5/meta.yaml b/recipes/bioconductor-bsgenome.ggallus.ucsc.galgal5/meta.yaml index 0aff5ddc0dfba..d12009b150201 100644 --- a/recipes/bioconductor-bsgenome.ggallus.ucsc.galgal5/meta.yaml +++ b/recipes/bioconductor-bsgenome.ggallus.ucsc.galgal5/meta.yaml @@ -1,6 +1,6 @@ {% set version = "1.4.2" %} {% set name = "BSgenome.Ggallus.UCSC.galGal5" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -12,19 +12,19 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' md5: 93b42354404edd848b21ea6781ca135c build: - number: 1 + number: 2 rpaths: - lib/R/lib/ - lib/ noarch: generic requirements: host: - - 'bioconductor-bsgenome >=1.50.0,<1.51.0' + - 'bioconductor-bsgenome >=1.52.0,<1.53.0' - r-base run: - - 'bioconductor-bsgenome >=1.50.0,<1.51.0' + - 'bioconductor-bsgenome >=1.52.0,<1.53.0' - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-bsgenome.ggallus.ucsc.galgal5/post-link.sh b/recipes/bioconductor-bsgenome.ggallus.ucsc.galgal5/post-link.sh index 9d7aa568c94f4..e58c1d206e9a8 100644 --- a/recipes/bioconductor-bsgenome.ggallus.ucsc.galgal5/post-link.sh +++ b/recipes/bioconductor-bsgenome.ggallus.ucsc.galgal5/post-link.sh @@ -1,9 +1,10 @@ #!/bin/bash FN="BSgenome.Ggallus.UCSC.galGal5_1.4.2.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/BSgenome.Ggallus.UCSC.galGal5_1.4.2.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/BSgenome.Ggallus.UCSC.galGal5_1.4.2.tar.gz" "https://bioarchive.galaxyproject.org/BSgenome.Ggallus.UCSC.galGal5_1.4.2.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-bsgenome.ggallus.ucsc.galgal5/bioconductor-bsgenome.ggallus.ucsc.galgal5_1.4.2_src_all.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-bsgenome.ggallus.ucsc.galgal5/bioconductor-bsgenome.ggallus.ucsc.galgal5_1.4.2_src_all.tar.gz" ) MD5="93b42354404edd848b21ea6781ca135c" @@ -16,7 +17,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-bsgenome.hsapiens.1000genomes.hs37d5/meta.yaml b/recipes/bioconductor-bsgenome.hsapiens.1000genomes.hs37d5/meta.yaml index 550b21f3e379d..0dc67b3cc3693 100644 --- a/recipes/bioconductor-bsgenome.hsapiens.1000genomes.hs37d5/meta.yaml +++ b/recipes/bioconductor-bsgenome.hsapiens.1000genomes.hs37d5/meta.yaml @@ -1,6 +1,6 @@ {% set version = "0.99.1" %} {% set name = "BSgenome.Hsapiens.1000genomes.hs37d5" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -12,19 +12,19 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' md5: 164e1692d38fefa499c2c8ac5fc22793 build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ noarch: generic requirements: host: - - 'bioconductor-bsgenome >=1.50.0,<1.51.0' + - 'bioconductor-bsgenome >=1.52.0,<1.53.0' - r-base run: - - 'bioconductor-bsgenome >=1.50.0,<1.51.0' + - 'bioconductor-bsgenome >=1.52.0,<1.53.0' - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-bsgenome.hsapiens.1000genomes.hs37d5/post-link.sh b/recipes/bioconductor-bsgenome.hsapiens.1000genomes.hs37d5/post-link.sh index bfc3daabdeaba..4ff20cc9fd0dd 100644 --- a/recipes/bioconductor-bsgenome.hsapiens.1000genomes.hs37d5/post-link.sh +++ b/recipes/bioconductor-bsgenome.hsapiens.1000genomes.hs37d5/post-link.sh @@ -1,9 +1,10 @@ #!/bin/bash FN="BSgenome.Hsapiens.1000genomes.hs37d5_0.99.1.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/BSgenome.Hsapiens.1000genomes.hs37d5_0.99.1.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/BSgenome.Hsapiens.1000genomes.hs37d5_0.99.1.tar.gz" "https://bioarchive.galaxyproject.org/BSgenome.Hsapiens.1000genomes.hs37d5_0.99.1.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-bsgenome.hsapiens.1000genomes.hs37d5/bioconductor-bsgenome.hsapiens.1000genomes.hs37d5_0.99.1_src_all.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-bsgenome.hsapiens.1000genomes.hs37d5/bioconductor-bsgenome.hsapiens.1000genomes.hs37d5_0.99.1_src_all.tar.gz" ) MD5="164e1692d38fefa499c2c8ac5fc22793" @@ -16,7 +17,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-bsgenome.hsapiens.ncbi.grch38/meta.yaml b/recipes/bioconductor-bsgenome.hsapiens.ncbi.grch38/meta.yaml index ff2edbc51d6de..6f595233442bc 100644 --- a/recipes/bioconductor-bsgenome.hsapiens.ncbi.grch38/meta.yaml +++ b/recipes/bioconductor-bsgenome.hsapiens.ncbi.grch38/meta.yaml @@ -1,6 +1,6 @@ {% set version = "1.3.1000" %} {% set name = "BSgenome.Hsapiens.NCBI.GRCh38" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -12,19 +12,19 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' md5: 733d324b34d34d7da8c4bf38459f4fae build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ noarch: generic requirements: host: - - 'bioconductor-bsgenome >=1.50.0,<1.51.0' + - 'bioconductor-bsgenome >=1.52.0,<1.53.0' - r-base run: - - 'bioconductor-bsgenome >=1.50.0,<1.51.0' + - 'bioconductor-bsgenome >=1.52.0,<1.53.0' - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-bsgenome.hsapiens.ncbi.grch38/post-link.sh b/recipes/bioconductor-bsgenome.hsapiens.ncbi.grch38/post-link.sh index ff702951a6d4b..5a47fe308c625 100644 --- a/recipes/bioconductor-bsgenome.hsapiens.ncbi.grch38/post-link.sh +++ b/recipes/bioconductor-bsgenome.hsapiens.ncbi.grch38/post-link.sh @@ -1,9 +1,10 @@ #!/bin/bash FN="BSgenome.Hsapiens.NCBI.GRCh38_1.3.1000.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/BSgenome.Hsapiens.NCBI.GRCh38_1.3.1000.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/BSgenome.Hsapiens.NCBI.GRCh38_1.3.1000.tar.gz" "https://bioarchive.galaxyproject.org/BSgenome.Hsapiens.NCBI.GRCh38_1.3.1000.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-bsgenome.hsapiens.ncbi.grch38/bioconductor-bsgenome.hsapiens.ncbi.grch38_1.3.1000_src_all.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-bsgenome.hsapiens.ncbi.grch38/bioconductor-bsgenome.hsapiens.ncbi.grch38_1.3.1000_src_all.tar.gz" ) MD5="733d324b34d34d7da8c4bf38459f4fae" @@ -16,7 +17,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-bsgenome.hsapiens.ucsc.hg17.masked/meta.yaml b/recipes/bioconductor-bsgenome.hsapiens.ucsc.hg17.masked/meta.yaml index 0a480d04bbe19..7f5aecd019f3b 100644 --- a/recipes/bioconductor-bsgenome.hsapiens.ucsc.hg17.masked/meta.yaml +++ b/recipes/bioconductor-bsgenome.hsapiens.ucsc.hg17.masked/meta.yaml @@ -1,6 +1,6 @@ {% set version = "1.3.99" %} {% set name = "BSgenome.Hsapiens.UCSC.hg17.masked" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -12,21 +12,21 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' md5: ff6ee5196f234c5a2a3bcdd052c3c08e build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ noarch: generic requirements: host: - - 'bioconductor-bsgenome >=1.50.0,<1.51.0' - - 'bioconductor-bsgenome.hsapiens.ucsc.hg17 >=1.3.0,<1.4.0' + - 'bioconductor-bsgenome >=1.52.0,<1.53.0' + - 'bioconductor-bsgenome.hsapiens.ucsc.hg17 >=1.4.0,<1.5.0' - r-base run: - - 'bioconductor-bsgenome >=1.50.0,<1.51.0' - - 'bioconductor-bsgenome.hsapiens.ucsc.hg17 >=1.3.0,<1.4.0' + - 'bioconductor-bsgenome >=1.52.0,<1.53.0' + - 'bioconductor-bsgenome.hsapiens.ucsc.hg17 >=1.4.0,<1.5.0' - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-bsgenome.hsapiens.ucsc.hg17.masked/post-link.sh b/recipes/bioconductor-bsgenome.hsapiens.ucsc.hg17.masked/post-link.sh index b02348d8a0cc2..525dd3eb30734 100644 --- a/recipes/bioconductor-bsgenome.hsapiens.ucsc.hg17.masked/post-link.sh +++ b/recipes/bioconductor-bsgenome.hsapiens.ucsc.hg17.masked/post-link.sh @@ -1,9 +1,10 @@ #!/bin/bash FN="BSgenome.Hsapiens.UCSC.hg17.masked_1.3.99.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/BSgenome.Hsapiens.UCSC.hg17.masked_1.3.99.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/BSgenome.Hsapiens.UCSC.hg17.masked_1.3.99.tar.gz" "https://bioarchive.galaxyproject.org/BSgenome.Hsapiens.UCSC.hg17.masked_1.3.99.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-bsgenome.hsapiens.ucsc.hg17.masked/bioconductor-bsgenome.hsapiens.ucsc.hg17.masked_1.3.99_src_all.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-bsgenome.hsapiens.ucsc.hg17.masked/bioconductor-bsgenome.hsapiens.ucsc.hg17.masked_1.3.99_src_all.tar.gz" ) MD5="ff6ee5196f234c5a2a3bcdd052c3c08e" @@ -16,7 +17,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-bsgenome.hsapiens.ucsc.hg17/meta.yaml b/recipes/bioconductor-bsgenome.hsapiens.ucsc.hg17/meta.yaml index 2f445de455c1b..fb9f20df25141 100644 --- a/recipes/bioconductor-bsgenome.hsapiens.ucsc.hg17/meta.yaml +++ b/recipes/bioconductor-bsgenome.hsapiens.ucsc.hg17/meta.yaml @@ -1,6 +1,6 @@ {% set version = "1.3.1000" %} {% set name = "BSgenome.Hsapiens.UCSC.hg17" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -12,7 +12,7 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' md5: cbea3029c3d3125a88e6c061c3d3abde build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ @@ -20,12 +20,12 @@ build: # Suggests: GenomicFeatures requirements: host: - - 'bioconductor-bsgenome >=1.50.0,<1.51.0' + - 'bioconductor-bsgenome >=1.52.0,<1.53.0' - r-base run: - - 'bioconductor-bsgenome >=1.50.0,<1.51.0' + - 'bioconductor-bsgenome >=1.52.0,<1.53.0' - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-bsgenome.hsapiens.ucsc.hg17/post-link.sh b/recipes/bioconductor-bsgenome.hsapiens.ucsc.hg17/post-link.sh index 881150aec75fe..db9e1ac053230 100644 --- a/recipes/bioconductor-bsgenome.hsapiens.ucsc.hg17/post-link.sh +++ b/recipes/bioconductor-bsgenome.hsapiens.ucsc.hg17/post-link.sh @@ -1,9 +1,10 @@ #!/bin/bash FN="BSgenome.Hsapiens.UCSC.hg17_1.3.1000.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/BSgenome.Hsapiens.UCSC.hg17_1.3.1000.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/BSgenome.Hsapiens.UCSC.hg17_1.3.1000.tar.gz" "https://bioarchive.galaxyproject.org/BSgenome.Hsapiens.UCSC.hg17_1.3.1000.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-bsgenome.hsapiens.ucsc.hg17/bioconductor-bsgenome.hsapiens.ucsc.hg17_1.3.1000_src_all.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-bsgenome.hsapiens.ucsc.hg17/bioconductor-bsgenome.hsapiens.ucsc.hg17_1.3.1000_src_all.tar.gz" ) MD5="cbea3029c3d3125a88e6c061c3d3abde" @@ -16,7 +17,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-bsgenome.hsapiens.ucsc.hg18.masked/meta.yaml b/recipes/bioconductor-bsgenome.hsapiens.ucsc.hg18.masked/meta.yaml index a93051e22acac..9eac2fb3cdd81 100644 --- a/recipes/bioconductor-bsgenome.hsapiens.ucsc.hg18.masked/meta.yaml +++ b/recipes/bioconductor-bsgenome.hsapiens.ucsc.hg18.masked/meta.yaml @@ -1,6 +1,6 @@ {% set version = "1.3.99" %} {% set name = "BSgenome.Hsapiens.UCSC.hg18.masked" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -12,21 +12,21 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' md5: e6a31e3cba34ce5e0eb6f76d2c19870c build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ noarch: generic requirements: host: - - 'bioconductor-bsgenome >=1.50.0,<1.51.0' - - 'bioconductor-bsgenome.hsapiens.ucsc.hg18 >=1.3.0,<1.4.0' + - 'bioconductor-bsgenome >=1.52.0,<1.53.0' + - 'bioconductor-bsgenome.hsapiens.ucsc.hg18 >=1.4.0,<1.5.0' - r-base run: - - 'bioconductor-bsgenome >=1.50.0,<1.51.0' - - 'bioconductor-bsgenome.hsapiens.ucsc.hg18 >=1.3.0,<1.4.0' + - 'bioconductor-bsgenome >=1.52.0,<1.53.0' + - 'bioconductor-bsgenome.hsapiens.ucsc.hg18 >=1.4.0,<1.5.0' - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-bsgenome.hsapiens.ucsc.hg18.masked/post-link.sh b/recipes/bioconductor-bsgenome.hsapiens.ucsc.hg18.masked/post-link.sh index 9611a772b601e..127cc3fa145e8 100644 --- a/recipes/bioconductor-bsgenome.hsapiens.ucsc.hg18.masked/post-link.sh +++ b/recipes/bioconductor-bsgenome.hsapiens.ucsc.hg18.masked/post-link.sh @@ -1,9 +1,10 @@ #!/bin/bash FN="BSgenome.Hsapiens.UCSC.hg18.masked_1.3.99.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/BSgenome.Hsapiens.UCSC.hg18.masked_1.3.99.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/BSgenome.Hsapiens.UCSC.hg18.masked_1.3.99.tar.gz" "https://bioarchive.galaxyproject.org/BSgenome.Hsapiens.UCSC.hg18.masked_1.3.99.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-bsgenome.hsapiens.ucsc.hg18.masked/bioconductor-bsgenome.hsapiens.ucsc.hg18.masked_1.3.99_src_all.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-bsgenome.hsapiens.ucsc.hg18.masked/bioconductor-bsgenome.hsapiens.ucsc.hg18.masked_1.3.99_src_all.tar.gz" ) MD5="e6a31e3cba34ce5e0eb6f76d2c19870c" @@ -16,7 +17,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-bsgenome.hsapiens.ucsc.hg18/meta.yaml b/recipes/bioconductor-bsgenome.hsapiens.ucsc.hg18/meta.yaml index 1ffe6b5aa9014..cd8fb036d30d8 100644 --- a/recipes/bioconductor-bsgenome.hsapiens.ucsc.hg18/meta.yaml +++ b/recipes/bioconductor-bsgenome.hsapiens.ucsc.hg18/meta.yaml @@ -1,6 +1,6 @@ {% set version = "1.3.1000" %} {% set name = "BSgenome.Hsapiens.UCSC.hg18" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -12,7 +12,7 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' md5: 51bb2e1ed4009860bb21aaac32fffd9c build: - number: 3 + number: 4 rpaths: - lib/R/lib/ - lib/ @@ -20,12 +20,12 @@ build: # Suggests: TxDb.Hsapiens.UCSC.hg18.knownGene requirements: host: - - 'bioconductor-bsgenome >=1.50.0,<1.51.0' + - 'bioconductor-bsgenome >=1.52.0,<1.53.0' - r-base run: - - 'bioconductor-bsgenome >=1.50.0,<1.51.0' + - 'bioconductor-bsgenome >=1.52.0,<1.53.0' - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-bsgenome.hsapiens.ucsc.hg18/post-link.sh b/recipes/bioconductor-bsgenome.hsapiens.ucsc.hg18/post-link.sh index d2aebf5da7d09..8c97b7072c839 100644 --- a/recipes/bioconductor-bsgenome.hsapiens.ucsc.hg18/post-link.sh +++ b/recipes/bioconductor-bsgenome.hsapiens.ucsc.hg18/post-link.sh @@ -1,7 +1,7 @@ #!/bin/bash FN="BSgenome.Hsapiens.UCSC.hg18_1.3.1000.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/BSgenome.Hsapiens.UCSC.hg18_1.3.1000.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/BSgenome.Hsapiens.UCSC.hg18_1.3.1000.tar.gz" "https://bioarchive.galaxyproject.org/BSgenome.Hsapiens.UCSC.hg18_1.3.1000.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-bsgenome.hsapiens.ucsc.hg18/bioconductor-bsgenome.hsapiens.ucsc.hg18_1.3.1000_src_all.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-bsgenome.hsapiens.ucsc.hg18/bioconductor-bsgenome.hsapiens.ucsc.hg18_1.3.1000_src_all.tar.gz" @@ -17,7 +17,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-bsgenome.hsapiens.ucsc.hg19.masked/meta.yaml b/recipes/bioconductor-bsgenome.hsapiens.ucsc.hg19.masked/meta.yaml index c1bdbf89c852b..efe28a6a3c245 100644 --- a/recipes/bioconductor-bsgenome.hsapiens.ucsc.hg19.masked/meta.yaml +++ b/recipes/bioconductor-bsgenome.hsapiens.ucsc.hg19.masked/meta.yaml @@ -1,6 +1,6 @@ {% set version = "1.3.99" %} {% set name = "BSgenome.Hsapiens.UCSC.hg19.masked" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -12,21 +12,21 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' md5: 8abeb2afb811e1a38cf822d1bc0cb50a build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ noarch: generic requirements: host: - - 'bioconductor-bsgenome >=1.50.0,<1.51.0' + - 'bioconductor-bsgenome >=1.52.0,<1.53.0' - 'bioconductor-bsgenome.hsapiens.ucsc.hg19 >=1.4.0,<1.5.0' - r-base run: - - 'bioconductor-bsgenome >=1.50.0,<1.51.0' + - 'bioconductor-bsgenome >=1.52.0,<1.53.0' - 'bioconductor-bsgenome.hsapiens.ucsc.hg19 >=1.4.0,<1.5.0' - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-bsgenome.hsapiens.ucsc.hg19.masked/post-link.sh b/recipes/bioconductor-bsgenome.hsapiens.ucsc.hg19.masked/post-link.sh index 27847b9725eb3..4c57a2815631a 100644 --- a/recipes/bioconductor-bsgenome.hsapiens.ucsc.hg19.masked/post-link.sh +++ b/recipes/bioconductor-bsgenome.hsapiens.ucsc.hg19.masked/post-link.sh @@ -1,9 +1,10 @@ #!/bin/bash FN="BSgenome.Hsapiens.UCSC.hg19.masked_1.3.99.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/BSgenome.Hsapiens.UCSC.hg19.masked_1.3.99.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/BSgenome.Hsapiens.UCSC.hg19.masked_1.3.99.tar.gz" "https://bioarchive.galaxyproject.org/BSgenome.Hsapiens.UCSC.hg19.masked_1.3.99.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-bsgenome.hsapiens.ucsc.hg19.masked/bioconductor-bsgenome.hsapiens.ucsc.hg19.masked_1.3.99_src_all.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-bsgenome.hsapiens.ucsc.hg19.masked/bioconductor-bsgenome.hsapiens.ucsc.hg19.masked_1.3.99_src_all.tar.gz" ) MD5="8abeb2afb811e1a38cf822d1bc0cb50a" @@ -16,7 +17,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-bsgenome.hsapiens.ucsc.hg19/meta.yaml b/recipes/bioconductor-bsgenome.hsapiens.ucsc.hg19/meta.yaml index c0018e5414c7c..5f9658921556d 100644 --- a/recipes/bioconductor-bsgenome.hsapiens.ucsc.hg19/meta.yaml +++ b/recipes/bioconductor-bsgenome.hsapiens.ucsc.hg19/meta.yaml @@ -1,6 +1,6 @@ {% set version = "1.4.0" %} {% set name = "BSgenome.Hsapiens.UCSC.hg19" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -12,7 +12,7 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' md5: 672a988b28d8602afb2bd5595db7303b build: - number: 5 + number: 6 rpaths: - lib/R/lib/ - lib/ @@ -20,12 +20,12 @@ build: # Suggests: TxDb.Hsapiens.UCSC.hg19.knownGene requirements: host: - - 'bioconductor-bsgenome >=1.50.0,<1.51.0' + - 'bioconductor-bsgenome >=1.52.0,<1.53.0' - r-base run: - - 'bioconductor-bsgenome >=1.50.0,<1.51.0' + - 'bioconductor-bsgenome >=1.52.0,<1.53.0' - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-bsgenome.hsapiens.ucsc.hg19/post-link.sh b/recipes/bioconductor-bsgenome.hsapiens.ucsc.hg19/post-link.sh index a4e6d31a11474..51242ecb7fd13 100644 --- a/recipes/bioconductor-bsgenome.hsapiens.ucsc.hg19/post-link.sh +++ b/recipes/bioconductor-bsgenome.hsapiens.ucsc.hg19/post-link.sh @@ -1,7 +1,7 @@ #!/bin/bash FN="BSgenome.Hsapiens.UCSC.hg19_1.4.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/BSgenome.Hsapiens.UCSC.hg19_1.4.0.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/BSgenome.Hsapiens.UCSC.hg19_1.4.0.tar.gz" "https://bioarchive.galaxyproject.org/BSgenome.Hsapiens.UCSC.hg19_1.4.0.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-bsgenome.hsapiens.ucsc.hg19/bioconductor-bsgenome.hsapiens.ucsc.hg19_1.4.0_src_all.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-bsgenome.hsapiens.ucsc.hg19/bioconductor-bsgenome.hsapiens.ucsc.hg19_1.4.0_src_all.tar.gz" @@ -17,7 +17,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-bsgenome.hsapiens.ucsc.hg38.masked/meta.yaml b/recipes/bioconductor-bsgenome.hsapiens.ucsc.hg38.masked/meta.yaml index 8e8cf83f93edd..d0c4b6cf3c276 100644 --- a/recipes/bioconductor-bsgenome.hsapiens.ucsc.hg38.masked/meta.yaml +++ b/recipes/bioconductor-bsgenome.hsapiens.ucsc.hg38.masked/meta.yaml @@ -1,6 +1,6 @@ {% set version = "1.3.99" %} {% set name = "BSgenome.Hsapiens.UCSC.hg38.masked" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -12,21 +12,21 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' md5: 50c9fc14be05113dc56651ea7a49beb1 build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ noarch: generic requirements: host: - - 'bioconductor-bsgenome >=1.50.0,<1.51.0' + - 'bioconductor-bsgenome >=1.52.0,<1.53.0' - 'bioconductor-bsgenome.hsapiens.ucsc.hg38 >=1.4.0,<1.5.0' - r-base run: - - 'bioconductor-bsgenome >=1.50.0,<1.51.0' + - 'bioconductor-bsgenome >=1.52.0,<1.53.0' - 'bioconductor-bsgenome.hsapiens.ucsc.hg38 >=1.4.0,<1.5.0' - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-bsgenome.hsapiens.ucsc.hg38.masked/post-link.sh b/recipes/bioconductor-bsgenome.hsapiens.ucsc.hg38.masked/post-link.sh index 17f04c351ad20..f48595b43bf03 100644 --- a/recipes/bioconductor-bsgenome.hsapiens.ucsc.hg38.masked/post-link.sh +++ b/recipes/bioconductor-bsgenome.hsapiens.ucsc.hg38.masked/post-link.sh @@ -1,9 +1,10 @@ #!/bin/bash FN="BSgenome.Hsapiens.UCSC.hg38.masked_1.3.99.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/BSgenome.Hsapiens.UCSC.hg38.masked_1.3.99.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/BSgenome.Hsapiens.UCSC.hg38.masked_1.3.99.tar.gz" "https://bioarchive.galaxyproject.org/BSgenome.Hsapiens.UCSC.hg38.masked_1.3.99.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-bsgenome.hsapiens.ucsc.hg38.masked/bioconductor-bsgenome.hsapiens.ucsc.hg38.masked_1.3.99_src_all.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-bsgenome.hsapiens.ucsc.hg38.masked/bioconductor-bsgenome.hsapiens.ucsc.hg38.masked_1.3.99_src_all.tar.gz" ) MD5="50c9fc14be05113dc56651ea7a49beb1" @@ -16,7 +17,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-bsgenome.hsapiens.ucsc.hg38/meta.yaml b/recipes/bioconductor-bsgenome.hsapiens.ucsc.hg38/meta.yaml index 4ffda28b395ca..d0e19e1bfd971 100644 --- a/recipes/bioconductor-bsgenome.hsapiens.ucsc.hg38/meta.yaml +++ b/recipes/bioconductor-bsgenome.hsapiens.ucsc.hg38/meta.yaml @@ -1,6 +1,6 @@ {% set version = "1.4.1" %} {% set name = "BSgenome.Hsapiens.UCSC.hg38" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -12,7 +12,7 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' md5: 1b95bfdc9763351b04611666cd624b30 build: - number: 5 + number: 6 rpaths: - lib/R/lib/ - lib/ @@ -20,12 +20,12 @@ build: # Suggests: TxDb.Hsapiens.UCSC.hg38.knownGene requirements: host: - - 'bioconductor-bsgenome >=1.50.0,<1.51.0' + - 'bioconductor-bsgenome >=1.52.0,<1.53.0' - r-base run: - - 'bioconductor-bsgenome >=1.50.0,<1.51.0' + - 'bioconductor-bsgenome >=1.52.0,<1.53.0' - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-bsgenome.hsapiens.ucsc.hg38/post-link.sh b/recipes/bioconductor-bsgenome.hsapiens.ucsc.hg38/post-link.sh index 5620f9356e402..16c0dc7ac9ff7 100644 --- a/recipes/bioconductor-bsgenome.hsapiens.ucsc.hg38/post-link.sh +++ b/recipes/bioconductor-bsgenome.hsapiens.ucsc.hg38/post-link.sh @@ -1,7 +1,7 @@ #!/bin/bash FN="BSgenome.Hsapiens.UCSC.hg38_1.4.1.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/BSgenome.Hsapiens.UCSC.hg38_1.4.1.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/BSgenome.Hsapiens.UCSC.hg38_1.4.1.tar.gz" "https://bioarchive.galaxyproject.org/BSgenome.Hsapiens.UCSC.hg38_1.4.1.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-bsgenome.hsapiens.ucsc.hg38/bioconductor-bsgenome.hsapiens.ucsc.hg38_1.4.1_src_all.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-bsgenome.hsapiens.ucsc.hg38/bioconductor-bsgenome.hsapiens.ucsc.hg38_1.4.1_src_all.tar.gz" @@ -17,7 +17,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-bsgenome.mdomestica.ucsc.mondom5/meta.yaml b/recipes/bioconductor-bsgenome.mdomestica.ucsc.mondom5/meta.yaml new file mode 100644 index 0000000000000..1cb5cde4e07e2 --- /dev/null +++ b/recipes/bioconductor-bsgenome.mdomestica.ucsc.mondom5/meta.yaml @@ -0,0 +1,35 @@ +{% set version = "1.4.2" %} +{% set name = "BSgenome.Mdomestica.UCSC.monDom5" %} +{% set bioc = "3.9" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: ff940f7446a275962f69a6f4cb84724c +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +requirements: + host: + - 'bioconductor-bsgenome >=1.52.0,<1.53.0' + - r-base + run: + - 'bioconductor-bsgenome >=1.52.0,<1.53.0' + - r-base + - curl +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'Full genome sequences for Monodelphis domestica (Opossum) as provided by UCSC (monDom5, Oct. 2006) and stored in Biostrings objects.' + diff --git a/recipes/bioconductor-bsgenome.mdomestica.ucsc.mondom5/post-link.sh b/recipes/bioconductor-bsgenome.mdomestica.ucsc.mondom5/post-link.sh new file mode 100644 index 0000000000000..4abe6464058ad --- /dev/null +++ b/recipes/bioconductor-bsgenome.mdomestica.ucsc.mondom5/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="BSgenome.Mdomestica.UCSC.monDom5_1.4.2.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/BSgenome.Mdomestica.UCSC.monDom5_1.4.2.tar.gz" + "https://bioarchive.galaxyproject.org/BSgenome.Mdomestica.UCSC.monDom5_1.4.2.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-bsgenome.mdomestica.ucsc.mondom5/bioconductor-bsgenome.mdomestica.ucsc.mondom5_1.4.2_src_all.tar.gz" +) +MD5="ff940f7446a275962f69a6f4cb84724c" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + curl $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-bsgenome.mdomestica.ucsc.mondom5/pre-unlink.sh b/recipes/bioconductor-bsgenome.mdomestica.ucsc.mondom5/pre-unlink.sh new file mode 100644 index 0000000000000..e06754481fb90 --- /dev/null +++ b/recipes/bioconductor-bsgenome.mdomestica.ucsc.mondom5/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ BSgenome.Mdomestica.UCSC.monDom5 diff --git a/recipes/bioconductor-bsgenome.mfascicularis.ncbi.5.0/meta.yaml b/recipes/bioconductor-bsgenome.mfascicularis.ncbi.5.0/meta.yaml index b6ed65d2c063a..ad35f20f296bb 100644 --- a/recipes/bioconductor-bsgenome.mfascicularis.ncbi.5.0/meta.yaml +++ b/recipes/bioconductor-bsgenome.mfascicularis.ncbi.5.0/meta.yaml @@ -1,6 +1,6 @@ {% set version = "1.4.2" %} {% set name = "BSgenome.Mfascicularis.NCBI.5.0" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -12,19 +12,19 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' md5: dba6ade39dc6b4f6d06f488141b5550b build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ noarch: generic requirements: host: - - 'bioconductor-bsgenome >=1.50.0,<1.51.0' + - 'bioconductor-bsgenome >=1.52.0,<1.53.0' - r-base run: - - 'bioconductor-bsgenome >=1.50.0,<1.51.0' + - 'bioconductor-bsgenome >=1.52.0,<1.53.0' - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-bsgenome.mfascicularis.ncbi.5.0/post-link.sh b/recipes/bioconductor-bsgenome.mfascicularis.ncbi.5.0/post-link.sh index af953c892d414..77786133fd95a 100644 --- a/recipes/bioconductor-bsgenome.mfascicularis.ncbi.5.0/post-link.sh +++ b/recipes/bioconductor-bsgenome.mfascicularis.ncbi.5.0/post-link.sh @@ -1,9 +1,10 @@ #!/bin/bash FN="BSgenome.Mfascicularis.NCBI.5.0_1.4.2.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/BSgenome.Mfascicularis.NCBI.5.0_1.4.2.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/BSgenome.Mfascicularis.NCBI.5.0_1.4.2.tar.gz" "https://bioarchive.galaxyproject.org/BSgenome.Mfascicularis.NCBI.5.0_1.4.2.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-bsgenome.mfascicularis.ncbi.5.0/bioconductor-bsgenome.mfascicularis.ncbi.5.0_1.4.2_src_all.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-bsgenome.mfascicularis.ncbi.5.0/bioconductor-bsgenome.mfascicularis.ncbi.5.0_1.4.2_src_all.tar.gz" ) MD5="dba6ade39dc6b4f6d06f488141b5550b" @@ -16,7 +17,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-bsgenome.mfuro.ucsc.musfur1/meta.yaml b/recipes/bioconductor-bsgenome.mfuro.ucsc.musfur1/meta.yaml index 2bb2b9cda6784..659c495a0524a 100644 --- a/recipes/bioconductor-bsgenome.mfuro.ucsc.musfur1/meta.yaml +++ b/recipes/bioconductor-bsgenome.mfuro.ucsc.musfur1/meta.yaml @@ -1,6 +1,6 @@ {% set version = "1.4.1" %} {% set name = "BSgenome.Mfuro.UCSC.musFur1" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -12,19 +12,19 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' md5: c33e71746ce551bcbcd22be1979aee63 build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ noarch: generic requirements: host: - - 'bioconductor-bsgenome >=1.50.0,<1.51.0' + - 'bioconductor-bsgenome >=1.52.0,<1.53.0' - r-base run: - - 'bioconductor-bsgenome >=1.50.0,<1.51.0' + - 'bioconductor-bsgenome >=1.52.0,<1.53.0' - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-bsgenome.mfuro.ucsc.musfur1/post-link.sh b/recipes/bioconductor-bsgenome.mfuro.ucsc.musfur1/post-link.sh index d64c1caf066fa..a3d114d5e4b22 100644 --- a/recipes/bioconductor-bsgenome.mfuro.ucsc.musfur1/post-link.sh +++ b/recipes/bioconductor-bsgenome.mfuro.ucsc.musfur1/post-link.sh @@ -1,9 +1,10 @@ #!/bin/bash FN="BSgenome.Mfuro.UCSC.musFur1_1.4.1.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/BSgenome.Mfuro.UCSC.musFur1_1.4.1.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/BSgenome.Mfuro.UCSC.musFur1_1.4.1.tar.gz" "https://bioarchive.galaxyproject.org/BSgenome.Mfuro.UCSC.musFur1_1.4.1.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-bsgenome.mfuro.ucsc.musfur1/bioconductor-bsgenome.mfuro.ucsc.musfur1_1.4.1_src_all.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-bsgenome.mfuro.ucsc.musfur1/bioconductor-bsgenome.mfuro.ucsc.musfur1_1.4.1_src_all.tar.gz" ) MD5="c33e71746ce551bcbcd22be1979aee63" @@ -16,7 +17,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-bsgenome.mmulatta.ucsc.rhemac2.masked/meta.yaml b/recipes/bioconductor-bsgenome.mmulatta.ucsc.rhemac2.masked/meta.yaml index 2bb2d8474b633..02d4af8cef228 100644 --- a/recipes/bioconductor-bsgenome.mmulatta.ucsc.rhemac2.masked/meta.yaml +++ b/recipes/bioconductor-bsgenome.mmulatta.ucsc.rhemac2.masked/meta.yaml @@ -1,6 +1,6 @@ {% set version = "1.3.99" %} {% set name = "BSgenome.Mmulatta.UCSC.rheMac2.masked" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -12,21 +12,21 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' md5: 7602d86b68df7e4c8d336fede4090a62 build: - number: 1 + number: 2 rpaths: - lib/R/lib/ - lib/ noarch: generic requirements: host: - - 'bioconductor-bsgenome >=1.50.0,<1.51.0' + - 'bioconductor-bsgenome >=1.52.0,<1.53.0' - 'bioconductor-bsgenome.mmulatta.ucsc.rhemac2 >=1.4.0,<1.5.0' - r-base run: - - 'bioconductor-bsgenome >=1.50.0,<1.51.0' + - 'bioconductor-bsgenome >=1.52.0,<1.53.0' - 'bioconductor-bsgenome.mmulatta.ucsc.rhemac2 >=1.4.0,<1.5.0' - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-bsgenome.mmulatta.ucsc.rhemac2.masked/post-link.sh b/recipes/bioconductor-bsgenome.mmulatta.ucsc.rhemac2.masked/post-link.sh index b67c79ab70cfb..84989613d4167 100644 --- a/recipes/bioconductor-bsgenome.mmulatta.ucsc.rhemac2.masked/post-link.sh +++ b/recipes/bioconductor-bsgenome.mmulatta.ucsc.rhemac2.masked/post-link.sh @@ -1,9 +1,10 @@ #!/bin/bash FN="BSgenome.Mmulatta.UCSC.rheMac2.masked_1.3.99.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/BSgenome.Mmulatta.UCSC.rheMac2.masked_1.3.99.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/BSgenome.Mmulatta.UCSC.rheMac2.masked_1.3.99.tar.gz" "https://bioarchive.galaxyproject.org/BSgenome.Mmulatta.UCSC.rheMac2.masked_1.3.99.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-bsgenome.mmulatta.ucsc.rhemac2.masked/bioconductor-bsgenome.mmulatta.ucsc.rhemac2.masked_1.3.99_src_all.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-bsgenome.mmulatta.ucsc.rhemac2.masked/bioconductor-bsgenome.mmulatta.ucsc.rhemac2.masked_1.3.99_src_all.tar.gz" ) MD5="7602d86b68df7e4c8d336fede4090a62" @@ -16,7 +17,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-bsgenome.mmulatta.ucsc.rhemac2/meta.yaml b/recipes/bioconductor-bsgenome.mmulatta.ucsc.rhemac2/meta.yaml index 56cae92713421..44ababa2c036e 100644 --- a/recipes/bioconductor-bsgenome.mmulatta.ucsc.rhemac2/meta.yaml +++ b/recipes/bioconductor-bsgenome.mmulatta.ucsc.rhemac2/meta.yaml @@ -1,6 +1,6 @@ {% set version = "1.4.0" %} {% set name = "BSgenome.Mmulatta.UCSC.rheMac2" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -12,7 +12,7 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' md5: 90c43e127e76dfd7cea90de9e1af9a50 build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ @@ -20,12 +20,12 @@ build: # Suggests: GenomicFeatures requirements: host: - - 'bioconductor-bsgenome >=1.50.0,<1.51.0' + - 'bioconductor-bsgenome >=1.52.0,<1.53.0' - r-base run: - - 'bioconductor-bsgenome >=1.50.0,<1.51.0' + - 'bioconductor-bsgenome >=1.52.0,<1.53.0' - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-bsgenome.mmulatta.ucsc.rhemac2/post-link.sh b/recipes/bioconductor-bsgenome.mmulatta.ucsc.rhemac2/post-link.sh index b30c078b8fbfd..25a15ac9c1217 100644 --- a/recipes/bioconductor-bsgenome.mmulatta.ucsc.rhemac2/post-link.sh +++ b/recipes/bioconductor-bsgenome.mmulatta.ucsc.rhemac2/post-link.sh @@ -1,9 +1,10 @@ #!/bin/bash FN="BSgenome.Mmulatta.UCSC.rheMac2_1.4.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/BSgenome.Mmulatta.UCSC.rheMac2_1.4.0.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/BSgenome.Mmulatta.UCSC.rheMac2_1.4.0.tar.gz" "https://bioarchive.galaxyproject.org/BSgenome.Mmulatta.UCSC.rheMac2_1.4.0.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-bsgenome.mmulatta.ucsc.rhemac2/bioconductor-bsgenome.mmulatta.ucsc.rhemac2_1.4.0_src_all.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-bsgenome.mmulatta.ucsc.rhemac2/bioconductor-bsgenome.mmulatta.ucsc.rhemac2_1.4.0_src_all.tar.gz" ) MD5="90c43e127e76dfd7cea90de9e1af9a50" @@ -16,7 +17,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-bsgenome.mmulatta.ucsc.rhemac3.masked/meta.yaml b/recipes/bioconductor-bsgenome.mmulatta.ucsc.rhemac3.masked/meta.yaml index f58f935695c36..9299cdfd62e4e 100644 --- a/recipes/bioconductor-bsgenome.mmulatta.ucsc.rhemac3.masked/meta.yaml +++ b/recipes/bioconductor-bsgenome.mmulatta.ucsc.rhemac3.masked/meta.yaml @@ -1,6 +1,6 @@ {% set version = "1.3.99" %} {% set name = "BSgenome.Mmulatta.UCSC.rheMac3.masked" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -12,21 +12,21 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' md5: 94f8714865655d3144e14f6fc5c24e76 build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ noarch: generic requirements: host: - - 'bioconductor-bsgenome >=1.50.0,<1.51.0' + - 'bioconductor-bsgenome >=1.52.0,<1.53.0' - 'bioconductor-bsgenome.mmulatta.ucsc.rhemac3 >=1.4.0,<1.5.0' - r-base run: - - 'bioconductor-bsgenome >=1.50.0,<1.51.0' + - 'bioconductor-bsgenome >=1.52.0,<1.53.0' - 'bioconductor-bsgenome.mmulatta.ucsc.rhemac3 >=1.4.0,<1.5.0' - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-bsgenome.mmulatta.ucsc.rhemac3.masked/post-link.sh b/recipes/bioconductor-bsgenome.mmulatta.ucsc.rhemac3.masked/post-link.sh index 2032568ccead0..c2737bec54ca8 100644 --- a/recipes/bioconductor-bsgenome.mmulatta.ucsc.rhemac3.masked/post-link.sh +++ b/recipes/bioconductor-bsgenome.mmulatta.ucsc.rhemac3.masked/post-link.sh @@ -1,9 +1,10 @@ #!/bin/bash FN="BSgenome.Mmulatta.UCSC.rheMac3.masked_1.3.99.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/BSgenome.Mmulatta.UCSC.rheMac3.masked_1.3.99.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/BSgenome.Mmulatta.UCSC.rheMac3.masked_1.3.99.tar.gz" "https://bioarchive.galaxyproject.org/BSgenome.Mmulatta.UCSC.rheMac3.masked_1.3.99.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-bsgenome.mmulatta.ucsc.rhemac3.masked/bioconductor-bsgenome.mmulatta.ucsc.rhemac3.masked_1.3.99_src_all.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-bsgenome.mmulatta.ucsc.rhemac3.masked/bioconductor-bsgenome.mmulatta.ucsc.rhemac3.masked_1.3.99_src_all.tar.gz" ) MD5="94f8714865655d3144e14f6fc5c24e76" @@ -16,7 +17,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-bsgenome.mmulatta.ucsc.rhemac3/meta.yaml b/recipes/bioconductor-bsgenome.mmulatta.ucsc.rhemac3/meta.yaml index 17af3a9649e30..6e5a0c658ce94 100644 --- a/recipes/bioconductor-bsgenome.mmulatta.ucsc.rhemac3/meta.yaml +++ b/recipes/bioconductor-bsgenome.mmulatta.ucsc.rhemac3/meta.yaml @@ -1,6 +1,6 @@ {% set version = "1.4.0" %} {% set name = "BSgenome.Mmulatta.UCSC.rheMac3" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -12,7 +12,7 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' md5: dfa1ecb9d0bb7a5d9fa628092fb1c354 build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ @@ -20,12 +20,12 @@ build: # Suggests: GenomicFeatures requirements: host: - - 'bioconductor-bsgenome >=1.50.0,<1.51.0' + - 'bioconductor-bsgenome >=1.52.0,<1.53.0' - r-base run: - - 'bioconductor-bsgenome >=1.50.0,<1.51.0' + - 'bioconductor-bsgenome >=1.52.0,<1.53.0' - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-bsgenome.mmulatta.ucsc.rhemac3/post-link.sh b/recipes/bioconductor-bsgenome.mmulatta.ucsc.rhemac3/post-link.sh index 83a666bc84d52..3bb7e0efc0da9 100644 --- a/recipes/bioconductor-bsgenome.mmulatta.ucsc.rhemac3/post-link.sh +++ b/recipes/bioconductor-bsgenome.mmulatta.ucsc.rhemac3/post-link.sh @@ -1,9 +1,10 @@ #!/bin/bash FN="BSgenome.Mmulatta.UCSC.rheMac3_1.4.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/BSgenome.Mmulatta.UCSC.rheMac3_1.4.0.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/BSgenome.Mmulatta.UCSC.rheMac3_1.4.0.tar.gz" "https://bioarchive.galaxyproject.org/BSgenome.Mmulatta.UCSC.rheMac3_1.4.0.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-bsgenome.mmulatta.ucsc.rhemac3/bioconductor-bsgenome.mmulatta.ucsc.rhemac3_1.4.0_src_all.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-bsgenome.mmulatta.ucsc.rhemac3/bioconductor-bsgenome.mmulatta.ucsc.rhemac3_1.4.0_src_all.tar.gz" ) MD5="dfa1ecb9d0bb7a5d9fa628092fb1c354" @@ -16,7 +17,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-bsgenome.mmulatta.ucsc.rhemac8/meta.yaml b/recipes/bioconductor-bsgenome.mmulatta.ucsc.rhemac8/meta.yaml index 298a61b62ec93..aba6b1c9142ca 100644 --- a/recipes/bioconductor-bsgenome.mmulatta.ucsc.rhemac8/meta.yaml +++ b/recipes/bioconductor-bsgenome.mmulatta.ucsc.rhemac8/meta.yaml @@ -1,6 +1,6 @@ {% set version = "1.4.2" %} {% set name = "BSgenome.Mmulatta.UCSC.rheMac8" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -12,19 +12,19 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' md5: e9ad1f70f652c62554e2c5af7638c015 build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ noarch: generic requirements: host: - - 'bioconductor-bsgenome >=1.50.0,<1.51.0' + - 'bioconductor-bsgenome >=1.52.0,<1.53.0' - r-base run: - - 'bioconductor-bsgenome >=1.50.0,<1.51.0' + - 'bioconductor-bsgenome >=1.52.0,<1.53.0' - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-bsgenome.mmulatta.ucsc.rhemac8/post-link.sh b/recipes/bioconductor-bsgenome.mmulatta.ucsc.rhemac8/post-link.sh index 8881ddde3e188..308a367fe62c8 100644 --- a/recipes/bioconductor-bsgenome.mmulatta.ucsc.rhemac8/post-link.sh +++ b/recipes/bioconductor-bsgenome.mmulatta.ucsc.rhemac8/post-link.sh @@ -1,9 +1,10 @@ #!/bin/bash FN="BSgenome.Mmulatta.UCSC.rheMac8_1.4.2.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/BSgenome.Mmulatta.UCSC.rheMac8_1.4.2.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/BSgenome.Mmulatta.UCSC.rheMac8_1.4.2.tar.gz" "https://bioarchive.galaxyproject.org/BSgenome.Mmulatta.UCSC.rheMac8_1.4.2.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-bsgenome.mmulatta.ucsc.rhemac8/bioconductor-bsgenome.mmulatta.ucsc.rhemac8_1.4.2_src_all.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-bsgenome.mmulatta.ucsc.rhemac8/bioconductor-bsgenome.mmulatta.ucsc.rhemac8_1.4.2_src_all.tar.gz" ) MD5="e9ad1f70f652c62554e2c5af7638c015" @@ -16,7 +17,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-bsgenome.mmusculus.ucsc.mm10.masked/meta.yaml b/recipes/bioconductor-bsgenome.mmusculus.ucsc.mm10.masked/meta.yaml index 627ac243ada86..388415d826fa7 100644 --- a/recipes/bioconductor-bsgenome.mmusculus.ucsc.mm10.masked/meta.yaml +++ b/recipes/bioconductor-bsgenome.mmusculus.ucsc.mm10.masked/meta.yaml @@ -1,6 +1,6 @@ {% set version = "1.3.99" %} {% set name = "BSgenome.Mmusculus.UCSC.mm10.masked" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -12,21 +12,21 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' md5: c6a5365fa1a0d2a5ecb63752960eb3d7 build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ noarch: generic requirements: host: - - 'bioconductor-bsgenome >=1.50.0,<1.51.0' + - 'bioconductor-bsgenome >=1.52.0,<1.53.0' - 'bioconductor-bsgenome.mmusculus.ucsc.mm10 >=1.4.0,<1.5.0' - r-base run: - - 'bioconductor-bsgenome >=1.50.0,<1.51.0' + - 'bioconductor-bsgenome >=1.52.0,<1.53.0' - 'bioconductor-bsgenome.mmusculus.ucsc.mm10 >=1.4.0,<1.5.0' - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-bsgenome.mmusculus.ucsc.mm10.masked/post-link.sh b/recipes/bioconductor-bsgenome.mmusculus.ucsc.mm10.masked/post-link.sh index c3896a6559802..67a883382fa26 100644 --- a/recipes/bioconductor-bsgenome.mmusculus.ucsc.mm10.masked/post-link.sh +++ b/recipes/bioconductor-bsgenome.mmusculus.ucsc.mm10.masked/post-link.sh @@ -1,9 +1,10 @@ #!/bin/bash FN="BSgenome.Mmusculus.UCSC.mm10.masked_1.3.99.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/BSgenome.Mmusculus.UCSC.mm10.masked_1.3.99.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/BSgenome.Mmusculus.UCSC.mm10.masked_1.3.99.tar.gz" "https://bioarchive.galaxyproject.org/BSgenome.Mmusculus.UCSC.mm10.masked_1.3.99.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-bsgenome.mmusculus.ucsc.mm10.masked/bioconductor-bsgenome.mmusculus.ucsc.mm10.masked_1.3.99_src_all.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-bsgenome.mmusculus.ucsc.mm10.masked/bioconductor-bsgenome.mmusculus.ucsc.mm10.masked_1.3.99_src_all.tar.gz" ) MD5="c6a5365fa1a0d2a5ecb63752960eb3d7" @@ -16,7 +17,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-bsgenome.mmusculus.ucsc.mm10/meta.yaml b/recipes/bioconductor-bsgenome.mmusculus.ucsc.mm10/meta.yaml index eafc6a150e051..3e83c965f24b3 100644 --- a/recipes/bioconductor-bsgenome.mmusculus.ucsc.mm10/meta.yaml +++ b/recipes/bioconductor-bsgenome.mmusculus.ucsc.mm10/meta.yaml @@ -1,6 +1,6 @@ {% set version = "1.4.0" %} {% set name = "BSgenome.Mmusculus.UCSC.mm10" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -12,7 +12,7 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' md5: 929f8bd0ea9ad416ecc0c2c002500414 build: - number: 5 + number: 6 rpaths: - lib/R/lib/ - lib/ @@ -20,12 +20,12 @@ build: # Suggests: TxDb.Mmusculus.UCSC.mm10.knownGene requirements: host: - - 'bioconductor-bsgenome >=1.50.0,<1.51.0' + - 'bioconductor-bsgenome >=1.52.0,<1.53.0' - r-base run: - - 'bioconductor-bsgenome >=1.50.0,<1.51.0' + - 'bioconductor-bsgenome >=1.52.0,<1.53.0' - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-bsgenome.mmusculus.ucsc.mm10/post-link.sh b/recipes/bioconductor-bsgenome.mmusculus.ucsc.mm10/post-link.sh index 56bd4d6eddee8..df60f4301c9b2 100644 --- a/recipes/bioconductor-bsgenome.mmusculus.ucsc.mm10/post-link.sh +++ b/recipes/bioconductor-bsgenome.mmusculus.ucsc.mm10/post-link.sh @@ -1,7 +1,7 @@ #!/bin/bash FN="BSgenome.Mmusculus.UCSC.mm10_1.4.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/BSgenome.Mmusculus.UCSC.mm10_1.4.0.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/BSgenome.Mmusculus.UCSC.mm10_1.4.0.tar.gz" "https://bioarchive.galaxyproject.org/BSgenome.Mmusculus.UCSC.mm10_1.4.0.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-bsgenome.mmusculus.ucsc.mm10/bioconductor-bsgenome.mmusculus.ucsc.mm10_1.4.0_src_all.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-bsgenome.mmusculus.ucsc.mm10/bioconductor-bsgenome.mmusculus.ucsc.mm10_1.4.0_src_all.tar.gz" @@ -17,7 +17,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-bsgenome.mmusculus.ucsc.mm8.masked/meta.yaml b/recipes/bioconductor-bsgenome.mmusculus.ucsc.mm8.masked/meta.yaml index 12f4b224e9838..9f23d31da202c 100644 --- a/recipes/bioconductor-bsgenome.mmusculus.ucsc.mm8.masked/meta.yaml +++ b/recipes/bioconductor-bsgenome.mmusculus.ucsc.mm8.masked/meta.yaml @@ -1,6 +1,6 @@ {% set version = "1.3.99" %} {% set name = "BSgenome.Mmusculus.UCSC.mm8.masked" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -12,21 +12,21 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' md5: 5809f925e0fe7c4b73b78a90c9a36fdd build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ noarch: generic requirements: host: - - 'bioconductor-bsgenome >=1.50.0,<1.51.0' + - 'bioconductor-bsgenome >=1.52.0,<1.53.0' - 'bioconductor-bsgenome.mmusculus.ucsc.mm8 >=1.4.0,<1.5.0' - r-base run: - - 'bioconductor-bsgenome >=1.50.0,<1.51.0' + - 'bioconductor-bsgenome >=1.52.0,<1.53.0' - 'bioconductor-bsgenome.mmusculus.ucsc.mm8 >=1.4.0,<1.5.0' - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-bsgenome.mmusculus.ucsc.mm8.masked/post-link.sh b/recipes/bioconductor-bsgenome.mmusculus.ucsc.mm8.masked/post-link.sh index 6ae61ca9fc4cb..c9d84403f8e0d 100644 --- a/recipes/bioconductor-bsgenome.mmusculus.ucsc.mm8.masked/post-link.sh +++ b/recipes/bioconductor-bsgenome.mmusculus.ucsc.mm8.masked/post-link.sh @@ -1,9 +1,10 @@ #!/bin/bash FN="BSgenome.Mmusculus.UCSC.mm8.masked_1.3.99.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/BSgenome.Mmusculus.UCSC.mm8.masked_1.3.99.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/BSgenome.Mmusculus.UCSC.mm8.masked_1.3.99.tar.gz" "https://bioarchive.galaxyproject.org/BSgenome.Mmusculus.UCSC.mm8.masked_1.3.99.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-bsgenome.mmusculus.ucsc.mm8.masked/bioconductor-bsgenome.mmusculus.ucsc.mm8.masked_1.3.99_src_all.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-bsgenome.mmusculus.ucsc.mm8.masked/bioconductor-bsgenome.mmusculus.ucsc.mm8.masked_1.3.99_src_all.tar.gz" ) MD5="5809f925e0fe7c4b73b78a90c9a36fdd" @@ -16,7 +17,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-bsgenome.mmusculus.ucsc.mm8/meta.yaml b/recipes/bioconductor-bsgenome.mmusculus.ucsc.mm8/meta.yaml index ffcb9e70ba209..7c7cd90cde27b 100644 --- a/recipes/bioconductor-bsgenome.mmusculus.ucsc.mm8/meta.yaml +++ b/recipes/bioconductor-bsgenome.mmusculus.ucsc.mm8/meta.yaml @@ -1,6 +1,6 @@ {% set version = "1.4.0" %} {% set name = "BSgenome.Mmusculus.UCSC.mm8" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -12,7 +12,7 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' md5: f6aa91cdce2607f30a34f6dd0d678aff build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ @@ -20,12 +20,12 @@ build: # Suggests: GenomicFeatures requirements: host: - - 'bioconductor-bsgenome >=1.50.0,<1.51.0' + - 'bioconductor-bsgenome >=1.52.0,<1.53.0' - r-base run: - - 'bioconductor-bsgenome >=1.50.0,<1.51.0' + - 'bioconductor-bsgenome >=1.52.0,<1.53.0' - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-bsgenome.mmusculus.ucsc.mm8/post-link.sh b/recipes/bioconductor-bsgenome.mmusculus.ucsc.mm8/post-link.sh index 7ff91773a76e3..ccc7f9acd4c4f 100644 --- a/recipes/bioconductor-bsgenome.mmusculus.ucsc.mm8/post-link.sh +++ b/recipes/bioconductor-bsgenome.mmusculus.ucsc.mm8/post-link.sh @@ -1,9 +1,10 @@ #!/bin/bash FN="BSgenome.Mmusculus.UCSC.mm8_1.4.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/BSgenome.Mmusculus.UCSC.mm8_1.4.0.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/BSgenome.Mmusculus.UCSC.mm8_1.4.0.tar.gz" "https://bioarchive.galaxyproject.org/BSgenome.Mmusculus.UCSC.mm8_1.4.0.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-bsgenome.mmusculus.ucsc.mm8/bioconductor-bsgenome.mmusculus.ucsc.mm8_1.4.0_src_all.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-bsgenome.mmusculus.ucsc.mm8/bioconductor-bsgenome.mmusculus.ucsc.mm8_1.4.0_src_all.tar.gz" ) MD5="f6aa91cdce2607f30a34f6dd0d678aff" @@ -16,7 +17,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-bsgenome.mmusculus.ucsc.mm9.masked/meta.yaml b/recipes/bioconductor-bsgenome.mmusculus.ucsc.mm9.masked/meta.yaml index 11a9983fe8ac0..0d120a1012f2b 100644 --- a/recipes/bioconductor-bsgenome.mmusculus.ucsc.mm9.masked/meta.yaml +++ b/recipes/bioconductor-bsgenome.mmusculus.ucsc.mm9.masked/meta.yaml @@ -1,6 +1,6 @@ {% set version = "1.3.99" %} {% set name = "BSgenome.Mmusculus.UCSC.mm9.masked" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -12,21 +12,21 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' md5: a5dadab14e55cdfc39649ede7a8483d5 build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ noarch: generic requirements: host: - - 'bioconductor-bsgenome >=1.50.0,<1.51.0' + - 'bioconductor-bsgenome >=1.52.0,<1.53.0' - 'bioconductor-bsgenome.mmusculus.ucsc.mm9 >=1.4.0,<1.5.0' - r-base run: - - 'bioconductor-bsgenome >=1.50.0,<1.51.0' + - 'bioconductor-bsgenome >=1.52.0,<1.53.0' - 'bioconductor-bsgenome.mmusculus.ucsc.mm9 >=1.4.0,<1.5.0' - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-bsgenome.mmusculus.ucsc.mm9.masked/post-link.sh b/recipes/bioconductor-bsgenome.mmusculus.ucsc.mm9.masked/post-link.sh index b8dbc797780d4..7f2774c9f0db1 100644 --- a/recipes/bioconductor-bsgenome.mmusculus.ucsc.mm9.masked/post-link.sh +++ b/recipes/bioconductor-bsgenome.mmusculus.ucsc.mm9.masked/post-link.sh @@ -1,9 +1,10 @@ #!/bin/bash FN="BSgenome.Mmusculus.UCSC.mm9.masked_1.3.99.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/BSgenome.Mmusculus.UCSC.mm9.masked_1.3.99.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/BSgenome.Mmusculus.UCSC.mm9.masked_1.3.99.tar.gz" "https://bioarchive.galaxyproject.org/BSgenome.Mmusculus.UCSC.mm9.masked_1.3.99.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-bsgenome.mmusculus.ucsc.mm9.masked/bioconductor-bsgenome.mmusculus.ucsc.mm9.masked_1.3.99_src_all.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-bsgenome.mmusculus.ucsc.mm9.masked/bioconductor-bsgenome.mmusculus.ucsc.mm9.masked_1.3.99_src_all.tar.gz" ) MD5="a5dadab14e55cdfc39649ede7a8483d5" @@ -16,7 +17,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-bsgenome.mmusculus.ucsc.mm9/meta.yaml b/recipes/bioconductor-bsgenome.mmusculus.ucsc.mm9/meta.yaml index 7840558f80878..75fbb5ed12021 100644 --- a/recipes/bioconductor-bsgenome.mmusculus.ucsc.mm9/meta.yaml +++ b/recipes/bioconductor-bsgenome.mmusculus.ucsc.mm9/meta.yaml @@ -1,6 +1,6 @@ {% set version = "1.4.0" %} {% set name = "BSgenome.Mmusculus.UCSC.mm9" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -12,7 +12,7 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' md5: 5a30ba2b4481a17e8e6979eb69eabf78 build: - number: 5 + number: 6 rpaths: - lib/R/lib/ - lib/ @@ -20,12 +20,12 @@ build: # Suggests: TxDb.Mmusculus.UCSC.mm9.knownGene requirements: host: - - 'bioconductor-bsgenome >=1.50.0,<1.51.0' + - 'bioconductor-bsgenome >=1.52.0,<1.53.0' - r-base run: - - 'bioconductor-bsgenome >=1.50.0,<1.51.0' + - 'bioconductor-bsgenome >=1.52.0,<1.53.0' - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-bsgenome.mmusculus.ucsc.mm9/post-link.sh b/recipes/bioconductor-bsgenome.mmusculus.ucsc.mm9/post-link.sh index 356ff7b3d7a3a..b91ba504ff692 100644 --- a/recipes/bioconductor-bsgenome.mmusculus.ucsc.mm9/post-link.sh +++ b/recipes/bioconductor-bsgenome.mmusculus.ucsc.mm9/post-link.sh @@ -1,7 +1,7 @@ #!/bin/bash FN="BSgenome.Mmusculus.UCSC.mm9_1.4.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/BSgenome.Mmusculus.UCSC.mm9_1.4.0.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/BSgenome.Mmusculus.UCSC.mm9_1.4.0.tar.gz" "https://bioarchive.galaxyproject.org/BSgenome.Mmusculus.UCSC.mm9_1.4.0.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-bsgenome.mmusculus.ucsc.mm9/bioconductor-bsgenome.mmusculus.ucsc.mm9_1.4.0_src_all.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-bsgenome.mmusculus.ucsc.mm9/bioconductor-bsgenome.mmusculus.ucsc.mm9_1.4.0_src_all.tar.gz" @@ -17,7 +17,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-bsgenome.osativa.msu.msu7/meta.yaml b/recipes/bioconductor-bsgenome.osativa.msu.msu7/meta.yaml index ca58d27608d7e..2a5d9439d6b43 100644 --- a/recipes/bioconductor-bsgenome.osativa.msu.msu7/meta.yaml +++ b/recipes/bioconductor-bsgenome.osativa.msu.msu7/meta.yaml @@ -1,6 +1,6 @@ {% set version = "0.99.1" %} {% set name = "BSgenome.Osativa.MSU.MSU7" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -12,19 +12,19 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' md5: 459fe50be785d06ab680565aacca1c57 build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ noarch: generic requirements: host: - - 'bioconductor-bsgenome >=1.50.0,<1.51.0' + - 'bioconductor-bsgenome >=1.52.0,<1.53.0' - r-base run: - - 'bioconductor-bsgenome >=1.50.0,<1.51.0' + - 'bioconductor-bsgenome >=1.52.0,<1.53.0' - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-bsgenome.osativa.msu.msu7/post-link.sh b/recipes/bioconductor-bsgenome.osativa.msu.msu7/post-link.sh index 0d94fc46a583c..7ef4f0d0e20aa 100644 --- a/recipes/bioconductor-bsgenome.osativa.msu.msu7/post-link.sh +++ b/recipes/bioconductor-bsgenome.osativa.msu.msu7/post-link.sh @@ -1,9 +1,10 @@ #!/bin/bash FN="BSgenome.Osativa.MSU.MSU7_0.99.1.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/BSgenome.Osativa.MSU.MSU7_0.99.1.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/BSgenome.Osativa.MSU.MSU7_0.99.1.tar.gz" "https://bioarchive.galaxyproject.org/BSgenome.Osativa.MSU.MSU7_0.99.1.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-bsgenome.osativa.msu.msu7/bioconductor-bsgenome.osativa.msu.msu7_0.99.1_src_all.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-bsgenome.osativa.msu.msu7/bioconductor-bsgenome.osativa.msu.msu7_0.99.1_src_all.tar.gz" ) MD5="459fe50be785d06ab680565aacca1c57" @@ -16,7 +17,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-bsgenome.ptroglodytes.ucsc.pantro2.masked/meta.yaml b/recipes/bioconductor-bsgenome.ptroglodytes.ucsc.pantro2.masked/meta.yaml index e40627060e3e5..aae753763bcbd 100644 --- a/recipes/bioconductor-bsgenome.ptroglodytes.ucsc.pantro2.masked/meta.yaml +++ b/recipes/bioconductor-bsgenome.ptroglodytes.ucsc.pantro2.masked/meta.yaml @@ -1,6 +1,6 @@ {% set version = "1.3.99" %} {% set name = "BSgenome.Ptroglodytes.UCSC.panTro2.masked" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -12,21 +12,21 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' md5: e6d069be23712b483b4e4c71554594cf build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ noarch: generic requirements: host: - - 'bioconductor-bsgenome >=1.50.0,<1.51.0' + - 'bioconductor-bsgenome >=1.52.0,<1.53.0' - 'bioconductor-bsgenome.ptroglodytes.ucsc.pantro2 >=1.4.0,<1.5.0' - r-base run: - - 'bioconductor-bsgenome >=1.50.0,<1.51.0' + - 'bioconductor-bsgenome >=1.52.0,<1.53.0' - 'bioconductor-bsgenome.ptroglodytes.ucsc.pantro2 >=1.4.0,<1.5.0' - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-bsgenome.ptroglodytes.ucsc.pantro2.masked/post-link.sh b/recipes/bioconductor-bsgenome.ptroglodytes.ucsc.pantro2.masked/post-link.sh index dd89722671c24..518a63fffc3b9 100644 --- a/recipes/bioconductor-bsgenome.ptroglodytes.ucsc.pantro2.masked/post-link.sh +++ b/recipes/bioconductor-bsgenome.ptroglodytes.ucsc.pantro2.masked/post-link.sh @@ -1,9 +1,10 @@ #!/bin/bash FN="BSgenome.Ptroglodytes.UCSC.panTro2.masked_1.3.99.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/BSgenome.Ptroglodytes.UCSC.panTro2.masked_1.3.99.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/BSgenome.Ptroglodytes.UCSC.panTro2.masked_1.3.99.tar.gz" "https://bioarchive.galaxyproject.org/BSgenome.Ptroglodytes.UCSC.panTro2.masked_1.3.99.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-bsgenome.ptroglodytes.ucsc.pantro2.masked/bioconductor-bsgenome.ptroglodytes.ucsc.pantro2.masked_1.3.99_src_all.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-bsgenome.ptroglodytes.ucsc.pantro2.masked/bioconductor-bsgenome.ptroglodytes.ucsc.pantro2.masked_1.3.99_src_all.tar.gz" ) MD5="e6d069be23712b483b4e4c71554594cf" @@ -16,7 +17,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-bsgenome.ptroglodytes.ucsc.pantro2/meta.yaml b/recipes/bioconductor-bsgenome.ptroglodytes.ucsc.pantro2/meta.yaml index 66645a5a45d53..282d862c88123 100644 --- a/recipes/bioconductor-bsgenome.ptroglodytes.ucsc.pantro2/meta.yaml +++ b/recipes/bioconductor-bsgenome.ptroglodytes.ucsc.pantro2/meta.yaml @@ -1,6 +1,6 @@ {% set version = "1.4.0" %} {% set name = "BSgenome.Ptroglodytes.UCSC.panTro2" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -12,7 +12,7 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' md5: 780200c315779ac75fcf0bdeb9a2eb8c build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ @@ -20,12 +20,12 @@ build: # Suggests: GenomicFeatures requirements: host: - - 'bioconductor-bsgenome >=1.50.0,<1.51.0' + - 'bioconductor-bsgenome >=1.52.0,<1.53.0' - r-base run: - - 'bioconductor-bsgenome >=1.50.0,<1.51.0' + - 'bioconductor-bsgenome >=1.52.0,<1.53.0' - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-bsgenome.ptroglodytes.ucsc.pantro2/post-link.sh b/recipes/bioconductor-bsgenome.ptroglodytes.ucsc.pantro2/post-link.sh index beac98c21853b..8322409fe9f99 100644 --- a/recipes/bioconductor-bsgenome.ptroglodytes.ucsc.pantro2/post-link.sh +++ b/recipes/bioconductor-bsgenome.ptroglodytes.ucsc.pantro2/post-link.sh @@ -1,9 +1,10 @@ #!/bin/bash FN="BSgenome.Ptroglodytes.UCSC.panTro2_1.4.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/BSgenome.Ptroglodytes.UCSC.panTro2_1.4.0.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/BSgenome.Ptroglodytes.UCSC.panTro2_1.4.0.tar.gz" "https://bioarchive.galaxyproject.org/BSgenome.Ptroglodytes.UCSC.panTro2_1.4.0.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-bsgenome.ptroglodytes.ucsc.pantro2/bioconductor-bsgenome.ptroglodytes.ucsc.pantro2_1.4.0_src_all.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-bsgenome.ptroglodytes.ucsc.pantro2/bioconductor-bsgenome.ptroglodytes.ucsc.pantro2_1.4.0_src_all.tar.gz" ) MD5="780200c315779ac75fcf0bdeb9a2eb8c" @@ -16,7 +17,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-bsgenome.ptroglodytes.ucsc.pantro3.masked/meta.yaml b/recipes/bioconductor-bsgenome.ptroglodytes.ucsc.pantro3.masked/meta.yaml index c65123d76fb65..9bd7f10e1afff 100644 --- a/recipes/bioconductor-bsgenome.ptroglodytes.ucsc.pantro3.masked/meta.yaml +++ b/recipes/bioconductor-bsgenome.ptroglodytes.ucsc.pantro3.masked/meta.yaml @@ -1,6 +1,6 @@ {% set version = "1.3.99" %} {% set name = "BSgenome.Ptroglodytes.UCSC.panTro3.masked" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -12,21 +12,21 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' md5: 89e96b3796d3b8e8793146597506e3f5 build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ noarch: generic requirements: host: - - 'bioconductor-bsgenome >=1.50.0,<1.51.0' + - 'bioconductor-bsgenome >=1.52.0,<1.53.0' - 'bioconductor-bsgenome.ptroglodytes.ucsc.pantro3 >=1.4.0,<1.5.0' - r-base run: - - 'bioconductor-bsgenome >=1.50.0,<1.51.0' + - 'bioconductor-bsgenome >=1.52.0,<1.53.0' - 'bioconductor-bsgenome.ptroglodytes.ucsc.pantro3 >=1.4.0,<1.5.0' - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-bsgenome.ptroglodytes.ucsc.pantro3.masked/post-link.sh b/recipes/bioconductor-bsgenome.ptroglodytes.ucsc.pantro3.masked/post-link.sh index 68d2e4bd1010e..509f96a5cb8ef 100644 --- a/recipes/bioconductor-bsgenome.ptroglodytes.ucsc.pantro3.masked/post-link.sh +++ b/recipes/bioconductor-bsgenome.ptroglodytes.ucsc.pantro3.masked/post-link.sh @@ -1,9 +1,10 @@ #!/bin/bash FN="BSgenome.Ptroglodytes.UCSC.panTro3.masked_1.3.99.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/BSgenome.Ptroglodytes.UCSC.panTro3.masked_1.3.99.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/BSgenome.Ptroglodytes.UCSC.panTro3.masked_1.3.99.tar.gz" "https://bioarchive.galaxyproject.org/BSgenome.Ptroglodytes.UCSC.panTro3.masked_1.3.99.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-bsgenome.ptroglodytes.ucsc.pantro3.masked/bioconductor-bsgenome.ptroglodytes.ucsc.pantro3.masked_1.3.99_src_all.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-bsgenome.ptroglodytes.ucsc.pantro3.masked/bioconductor-bsgenome.ptroglodytes.ucsc.pantro3.masked_1.3.99_src_all.tar.gz" ) MD5="89e96b3796d3b8e8793146597506e3f5" @@ -16,7 +17,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-bsgenome.ptroglodytes.ucsc.pantro3/meta.yaml b/recipes/bioconductor-bsgenome.ptroglodytes.ucsc.pantro3/meta.yaml index 8cf6705dd4895..deea19e56463e 100644 --- a/recipes/bioconductor-bsgenome.ptroglodytes.ucsc.pantro3/meta.yaml +++ b/recipes/bioconductor-bsgenome.ptroglodytes.ucsc.pantro3/meta.yaml @@ -1,6 +1,6 @@ {% set version = "1.4.0" %} {% set name = "BSgenome.Ptroglodytes.UCSC.panTro3" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -12,7 +12,7 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' md5: 4677c75befd60742f3fc2a54c7f60666 build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ @@ -20,12 +20,12 @@ build: # Suggests: GenomicFeatures requirements: host: - - 'bioconductor-bsgenome >=1.50.0,<1.51.0' + - 'bioconductor-bsgenome >=1.52.0,<1.53.0' - r-base run: - - 'bioconductor-bsgenome >=1.50.0,<1.51.0' + - 'bioconductor-bsgenome >=1.52.0,<1.53.0' - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-bsgenome.ptroglodytes.ucsc.pantro3/post-link.sh b/recipes/bioconductor-bsgenome.ptroglodytes.ucsc.pantro3/post-link.sh index 8449ec40795e1..b250aeb18542e 100644 --- a/recipes/bioconductor-bsgenome.ptroglodytes.ucsc.pantro3/post-link.sh +++ b/recipes/bioconductor-bsgenome.ptroglodytes.ucsc.pantro3/post-link.sh @@ -1,9 +1,10 @@ #!/bin/bash FN="BSgenome.Ptroglodytes.UCSC.panTro3_1.4.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/BSgenome.Ptroglodytes.UCSC.panTro3_1.4.0.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/BSgenome.Ptroglodytes.UCSC.panTro3_1.4.0.tar.gz" "https://bioarchive.galaxyproject.org/BSgenome.Ptroglodytes.UCSC.panTro3_1.4.0.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-bsgenome.ptroglodytes.ucsc.pantro3/bioconductor-bsgenome.ptroglodytes.ucsc.pantro3_1.4.0_src_all.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-bsgenome.ptroglodytes.ucsc.pantro3/bioconductor-bsgenome.ptroglodytes.ucsc.pantro3_1.4.0_src_all.tar.gz" ) MD5="4677c75befd60742f3fc2a54c7f60666" @@ -16,7 +17,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-bsgenome.ptroglodytes.ucsc.pantro5/meta.yaml b/recipes/bioconductor-bsgenome.ptroglodytes.ucsc.pantro5/meta.yaml index 43e227f1e80f8..04a4e667f0e83 100644 --- a/recipes/bioconductor-bsgenome.ptroglodytes.ucsc.pantro5/meta.yaml +++ b/recipes/bioconductor-bsgenome.ptroglodytes.ucsc.pantro5/meta.yaml @@ -1,6 +1,6 @@ {% set version = "1.4.2" %} {% set name = "BSgenome.Ptroglodytes.UCSC.panTro5" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -12,19 +12,19 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' md5: 5b88573dd9c3ef838699b65934f8abe3 build: - number: 1 + number: 2 rpaths: - lib/R/lib/ - lib/ noarch: generic requirements: host: - - 'bioconductor-bsgenome >=1.50.0,<1.51.0' + - 'bioconductor-bsgenome >=1.52.0,<1.53.0' - r-base run: - - 'bioconductor-bsgenome >=1.50.0,<1.51.0' + - 'bioconductor-bsgenome >=1.52.0,<1.53.0' - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-bsgenome.ptroglodytes.ucsc.pantro5/post-link.sh b/recipes/bioconductor-bsgenome.ptroglodytes.ucsc.pantro5/post-link.sh index 147f9f9420711..6e77c602934bf 100644 --- a/recipes/bioconductor-bsgenome.ptroglodytes.ucsc.pantro5/post-link.sh +++ b/recipes/bioconductor-bsgenome.ptroglodytes.ucsc.pantro5/post-link.sh @@ -1,9 +1,10 @@ #!/bin/bash FN="BSgenome.Ptroglodytes.UCSC.panTro5_1.4.2.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/BSgenome.Ptroglodytes.UCSC.panTro5_1.4.2.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/BSgenome.Ptroglodytes.UCSC.panTro5_1.4.2.tar.gz" "https://bioarchive.galaxyproject.org/BSgenome.Ptroglodytes.UCSC.panTro5_1.4.2.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-bsgenome.ptroglodytes.ucsc.pantro5/bioconductor-bsgenome.ptroglodytes.ucsc.pantro5_1.4.2_src_all.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-bsgenome.ptroglodytes.ucsc.pantro5/bioconductor-bsgenome.ptroglodytes.ucsc.pantro5_1.4.2_src_all.tar.gz" ) MD5="5b88573dd9c3ef838699b65934f8abe3" @@ -16,7 +17,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-bsgenome.ptroglodytes.ucsc.pantro6/meta.yaml b/recipes/bioconductor-bsgenome.ptroglodytes.ucsc.pantro6/meta.yaml index 877b0b92e061a..682ab01c29989 100644 --- a/recipes/bioconductor-bsgenome.ptroglodytes.ucsc.pantro6/meta.yaml +++ b/recipes/bioconductor-bsgenome.ptroglodytes.ucsc.pantro6/meta.yaml @@ -1,6 +1,6 @@ {% set version = "1.4.2" %} {% set name = "BSgenome.Ptroglodytes.UCSC.panTro6" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -12,19 +12,19 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' md5: 1df05d985374e9edc1dd7c3df5118338 build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ noarch: generic requirements: host: - - 'bioconductor-bsgenome >=1.50.0,<1.51.0' + - 'bioconductor-bsgenome >=1.52.0,<1.53.0' - r-base run: - - 'bioconductor-bsgenome >=1.50.0,<1.51.0' + - 'bioconductor-bsgenome >=1.52.0,<1.53.0' - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-bsgenome.ptroglodytes.ucsc.pantro6/post-link.sh b/recipes/bioconductor-bsgenome.ptroglodytes.ucsc.pantro6/post-link.sh index 2e297f45726d5..237dbbb36f68d 100644 --- a/recipes/bioconductor-bsgenome.ptroglodytes.ucsc.pantro6/post-link.sh +++ b/recipes/bioconductor-bsgenome.ptroglodytes.ucsc.pantro6/post-link.sh @@ -1,9 +1,10 @@ #!/bin/bash FN="BSgenome.Ptroglodytes.UCSC.panTro6_1.4.2.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/BSgenome.Ptroglodytes.UCSC.panTro6_1.4.2.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/BSgenome.Ptroglodytes.UCSC.panTro6_1.4.2.tar.gz" "https://bioarchive.galaxyproject.org/BSgenome.Ptroglodytes.UCSC.panTro6_1.4.2.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-bsgenome.ptroglodytes.ucsc.pantro6/bioconductor-bsgenome.ptroglodytes.ucsc.pantro6_1.4.2_src_all.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-bsgenome.ptroglodytes.ucsc.pantro6/bioconductor-bsgenome.ptroglodytes.ucsc.pantro6_1.4.2_src_all.tar.gz" ) MD5="1df05d985374e9edc1dd7c3df5118338" @@ -16,7 +17,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-bsgenome.rnorvegicus.ucsc.rn4.masked/meta.yaml b/recipes/bioconductor-bsgenome.rnorvegicus.ucsc.rn4.masked/meta.yaml index 625109cf69ef2..afa07a9a37e2e 100644 --- a/recipes/bioconductor-bsgenome.rnorvegicus.ucsc.rn4.masked/meta.yaml +++ b/recipes/bioconductor-bsgenome.rnorvegicus.ucsc.rn4.masked/meta.yaml @@ -1,6 +1,6 @@ {% set version = "1.3.99" %} {% set name = "BSgenome.Rnorvegicus.UCSC.rn4.masked" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -12,21 +12,21 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' md5: 7e2ea7df588b6b10515e07ea3868c568 build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ noarch: generic requirements: host: - - 'bioconductor-bsgenome >=1.50.0,<1.51.0' + - 'bioconductor-bsgenome >=1.52.0,<1.53.0' - 'bioconductor-bsgenome.rnorvegicus.ucsc.rn4 >=1.4.0,<1.5.0' - r-base run: - - 'bioconductor-bsgenome >=1.50.0,<1.51.0' + - 'bioconductor-bsgenome >=1.52.0,<1.53.0' - 'bioconductor-bsgenome.rnorvegicus.ucsc.rn4 >=1.4.0,<1.5.0' - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-bsgenome.rnorvegicus.ucsc.rn4.masked/post-link.sh b/recipes/bioconductor-bsgenome.rnorvegicus.ucsc.rn4.masked/post-link.sh index aae11f1722ac9..6a223e1856fe6 100644 --- a/recipes/bioconductor-bsgenome.rnorvegicus.ucsc.rn4.masked/post-link.sh +++ b/recipes/bioconductor-bsgenome.rnorvegicus.ucsc.rn4.masked/post-link.sh @@ -1,9 +1,10 @@ #!/bin/bash FN="BSgenome.Rnorvegicus.UCSC.rn4.masked_1.3.99.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/BSgenome.Rnorvegicus.UCSC.rn4.masked_1.3.99.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/BSgenome.Rnorvegicus.UCSC.rn4.masked_1.3.99.tar.gz" "https://bioarchive.galaxyproject.org/BSgenome.Rnorvegicus.UCSC.rn4.masked_1.3.99.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-bsgenome.rnorvegicus.ucsc.rn4.masked/bioconductor-bsgenome.rnorvegicus.ucsc.rn4.masked_1.3.99_src_all.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-bsgenome.rnorvegicus.ucsc.rn4.masked/bioconductor-bsgenome.rnorvegicus.ucsc.rn4.masked_1.3.99_src_all.tar.gz" ) MD5="7e2ea7df588b6b10515e07ea3868c568" @@ -16,7 +17,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-bsgenome.rnorvegicus.ucsc.rn4/meta.yaml b/recipes/bioconductor-bsgenome.rnorvegicus.ucsc.rn4/meta.yaml index b28a76eb79373..f7fe0c6568dd9 100644 --- a/recipes/bioconductor-bsgenome.rnorvegicus.ucsc.rn4/meta.yaml +++ b/recipes/bioconductor-bsgenome.rnorvegicus.ucsc.rn4/meta.yaml @@ -1,6 +1,6 @@ {% set version = "1.4.0" %} {% set name = "BSgenome.Rnorvegicus.UCSC.rn4" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -12,7 +12,7 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' md5: 3afe6729237781445d99ec38228ee1a8 build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ @@ -20,12 +20,12 @@ build: # Suggests: TxDb.Rnorvegicus.UCSC.rn4.ensGene requirements: host: - - 'bioconductor-bsgenome >=1.50.0,<1.51.0' + - 'bioconductor-bsgenome >=1.52.0,<1.53.0' - r-base run: - - 'bioconductor-bsgenome >=1.50.0,<1.51.0' + - 'bioconductor-bsgenome >=1.52.0,<1.53.0' - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-bsgenome.rnorvegicus.ucsc.rn4/post-link.sh b/recipes/bioconductor-bsgenome.rnorvegicus.ucsc.rn4/post-link.sh index 7813879e0e7b8..929a093599eed 100644 --- a/recipes/bioconductor-bsgenome.rnorvegicus.ucsc.rn4/post-link.sh +++ b/recipes/bioconductor-bsgenome.rnorvegicus.ucsc.rn4/post-link.sh @@ -1,9 +1,10 @@ #!/bin/bash FN="BSgenome.Rnorvegicus.UCSC.rn4_1.4.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/BSgenome.Rnorvegicus.UCSC.rn4_1.4.0.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/BSgenome.Rnorvegicus.UCSC.rn4_1.4.0.tar.gz" "https://bioarchive.galaxyproject.org/BSgenome.Rnorvegicus.UCSC.rn4_1.4.0.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-bsgenome.rnorvegicus.ucsc.rn4/bioconductor-bsgenome.rnorvegicus.ucsc.rn4_1.4.0_src_all.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-bsgenome.rnorvegicus.ucsc.rn4/bioconductor-bsgenome.rnorvegicus.ucsc.rn4_1.4.0_src_all.tar.gz" ) MD5="3afe6729237781445d99ec38228ee1a8" @@ -16,7 +17,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-bsgenome.rnorvegicus.ucsc.rn5.masked/meta.yaml b/recipes/bioconductor-bsgenome.rnorvegicus.ucsc.rn5.masked/meta.yaml index b19990b56d57a..f90c7c2767121 100644 --- a/recipes/bioconductor-bsgenome.rnorvegicus.ucsc.rn5.masked/meta.yaml +++ b/recipes/bioconductor-bsgenome.rnorvegicus.ucsc.rn5.masked/meta.yaml @@ -1,6 +1,6 @@ {% set version = "1.3.99" %} {% set name = "BSgenome.Rnorvegicus.UCSC.rn5.masked" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -12,21 +12,21 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' md5: 663233774b79012cb2cc08224ac275ed build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ noarch: generic requirements: host: - - 'bioconductor-bsgenome >=1.50.0,<1.51.0' + - 'bioconductor-bsgenome >=1.52.0,<1.53.0' - 'bioconductor-bsgenome.rnorvegicus.ucsc.rn5 >=1.4.0,<1.5.0' - r-base run: - - 'bioconductor-bsgenome >=1.50.0,<1.51.0' + - 'bioconductor-bsgenome >=1.52.0,<1.53.0' - 'bioconductor-bsgenome.rnorvegicus.ucsc.rn5 >=1.4.0,<1.5.0' - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-bsgenome.rnorvegicus.ucsc.rn5.masked/post-link.sh b/recipes/bioconductor-bsgenome.rnorvegicus.ucsc.rn5.masked/post-link.sh index 38418a2e57a23..d9bea86b17360 100644 --- a/recipes/bioconductor-bsgenome.rnorvegicus.ucsc.rn5.masked/post-link.sh +++ b/recipes/bioconductor-bsgenome.rnorvegicus.ucsc.rn5.masked/post-link.sh @@ -1,9 +1,10 @@ #!/bin/bash FN="BSgenome.Rnorvegicus.UCSC.rn5.masked_1.3.99.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/BSgenome.Rnorvegicus.UCSC.rn5.masked_1.3.99.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/BSgenome.Rnorvegicus.UCSC.rn5.masked_1.3.99.tar.gz" "https://bioarchive.galaxyproject.org/BSgenome.Rnorvegicus.UCSC.rn5.masked_1.3.99.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-bsgenome.rnorvegicus.ucsc.rn5.masked/bioconductor-bsgenome.rnorvegicus.ucsc.rn5.masked_1.3.99_src_all.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-bsgenome.rnorvegicus.ucsc.rn5.masked/bioconductor-bsgenome.rnorvegicus.ucsc.rn5.masked_1.3.99_src_all.tar.gz" ) MD5="663233774b79012cb2cc08224ac275ed" @@ -16,7 +17,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-bsgenome.rnorvegicus.ucsc.rn5/meta.yaml b/recipes/bioconductor-bsgenome.rnorvegicus.ucsc.rn5/meta.yaml index c36691b8dc09b..66e5fdd5ab546 100644 --- a/recipes/bioconductor-bsgenome.rnorvegicus.ucsc.rn5/meta.yaml +++ b/recipes/bioconductor-bsgenome.rnorvegicus.ucsc.rn5/meta.yaml @@ -1,6 +1,6 @@ {% set version = "1.4.0" %} {% set name = "BSgenome.Rnorvegicus.UCSC.rn5" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -12,7 +12,7 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' md5: 723b1f3ced395ef638b2d68053b05c86 build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ @@ -20,12 +20,12 @@ build: # Suggests: TxDb.Rnorvegicus.UCSC.rn5.refGene requirements: host: - - 'bioconductor-bsgenome >=1.50.0,<1.51.0' + - 'bioconductor-bsgenome >=1.52.0,<1.53.0' - r-base run: - - 'bioconductor-bsgenome >=1.50.0,<1.51.0' + - 'bioconductor-bsgenome >=1.52.0,<1.53.0' - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-bsgenome.rnorvegicus.ucsc.rn5/post-link.sh b/recipes/bioconductor-bsgenome.rnorvegicus.ucsc.rn5/post-link.sh index bd3444c37264d..845c969124dc8 100644 --- a/recipes/bioconductor-bsgenome.rnorvegicus.ucsc.rn5/post-link.sh +++ b/recipes/bioconductor-bsgenome.rnorvegicus.ucsc.rn5/post-link.sh @@ -1,9 +1,10 @@ #!/bin/bash FN="BSgenome.Rnorvegicus.UCSC.rn5_1.4.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/BSgenome.Rnorvegicus.UCSC.rn5_1.4.0.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/BSgenome.Rnorvegicus.UCSC.rn5_1.4.0.tar.gz" "https://bioarchive.galaxyproject.org/BSgenome.Rnorvegicus.UCSC.rn5_1.4.0.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-bsgenome.rnorvegicus.ucsc.rn5/bioconductor-bsgenome.rnorvegicus.ucsc.rn5_1.4.0_src_all.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-bsgenome.rnorvegicus.ucsc.rn5/bioconductor-bsgenome.rnorvegicus.ucsc.rn5_1.4.0_src_all.tar.gz" ) MD5="723b1f3ced395ef638b2d68053b05c86" @@ -16,7 +17,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-bsgenome.rnorvegicus.ucsc.rn6/meta.yaml b/recipes/bioconductor-bsgenome.rnorvegicus.ucsc.rn6/meta.yaml index 3d6047efb4d5d..4f8b699400427 100644 --- a/recipes/bioconductor-bsgenome.rnorvegicus.ucsc.rn6/meta.yaml +++ b/recipes/bioconductor-bsgenome.rnorvegicus.ucsc.rn6/meta.yaml @@ -1,6 +1,6 @@ {% set version = "1.4.1" %} {% set name = "BSgenome.Rnorvegicus.UCSC.rn6" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -12,7 +12,7 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' md5: 60d3fb201e0b1475912aaf681927096d build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ @@ -20,12 +20,12 @@ build: # Suggests: GenomicFeatures requirements: host: - - 'bioconductor-bsgenome >=1.50.0,<1.51.0' + - 'bioconductor-bsgenome >=1.52.0,<1.53.0' - r-base run: - - 'bioconductor-bsgenome >=1.50.0,<1.51.0' + - 'bioconductor-bsgenome >=1.52.0,<1.53.0' - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-bsgenome.rnorvegicus.ucsc.rn6/post-link.sh b/recipes/bioconductor-bsgenome.rnorvegicus.ucsc.rn6/post-link.sh index ff2dae830af46..e1649b846e61d 100644 --- a/recipes/bioconductor-bsgenome.rnorvegicus.ucsc.rn6/post-link.sh +++ b/recipes/bioconductor-bsgenome.rnorvegicus.ucsc.rn6/post-link.sh @@ -1,9 +1,10 @@ #!/bin/bash FN="BSgenome.Rnorvegicus.UCSC.rn6_1.4.1.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/BSgenome.Rnorvegicus.UCSC.rn6_1.4.1.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/BSgenome.Rnorvegicus.UCSC.rn6_1.4.1.tar.gz" "https://bioarchive.galaxyproject.org/BSgenome.Rnorvegicus.UCSC.rn6_1.4.1.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-bsgenome.rnorvegicus.ucsc.rn6/bioconductor-bsgenome.rnorvegicus.ucsc.rn6_1.4.1_src_all.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-bsgenome.rnorvegicus.ucsc.rn6/bioconductor-bsgenome.rnorvegicus.ucsc.rn6_1.4.1_src_all.tar.gz" ) MD5="60d3fb201e0b1475912aaf681927096d" @@ -16,7 +17,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-bsgenome.scerevisiae.ucsc.saccer1/meta.yaml b/recipes/bioconductor-bsgenome.scerevisiae.ucsc.saccer1/meta.yaml index fb6e644b30bf2..ba834fe85f262 100644 --- a/recipes/bioconductor-bsgenome.scerevisiae.ucsc.saccer1/meta.yaml +++ b/recipes/bioconductor-bsgenome.scerevisiae.ucsc.saccer1/meta.yaml @@ -1,6 +1,6 @@ {% set version = "1.4.0" %} {% set name = "BSgenome.Scerevisiae.UCSC.sacCer1" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -12,19 +12,19 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' md5: ad4c29c16a9635088bf13872b4a02ed4 build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ noarch: generic requirements: host: - - 'bioconductor-bsgenome >=1.50.0,<1.51.0' + - 'bioconductor-bsgenome >=1.52.0,<1.53.0' - r-base run: - - 'bioconductor-bsgenome >=1.50.0,<1.51.0' + - 'bioconductor-bsgenome >=1.52.0,<1.53.0' - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-bsgenome.scerevisiae.ucsc.saccer1/post-link.sh b/recipes/bioconductor-bsgenome.scerevisiae.ucsc.saccer1/post-link.sh index 1367fdeeb5b10..d189b784c046d 100644 --- a/recipes/bioconductor-bsgenome.scerevisiae.ucsc.saccer1/post-link.sh +++ b/recipes/bioconductor-bsgenome.scerevisiae.ucsc.saccer1/post-link.sh @@ -1,9 +1,10 @@ #!/bin/bash FN="BSgenome.Scerevisiae.UCSC.sacCer1_1.4.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/BSgenome.Scerevisiae.UCSC.sacCer1_1.4.0.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/BSgenome.Scerevisiae.UCSC.sacCer1_1.4.0.tar.gz" "https://bioarchive.galaxyproject.org/BSgenome.Scerevisiae.UCSC.sacCer1_1.4.0.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-bsgenome.scerevisiae.ucsc.saccer1/bioconductor-bsgenome.scerevisiae.ucsc.saccer1_1.4.0_src_all.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-bsgenome.scerevisiae.ucsc.saccer1/bioconductor-bsgenome.scerevisiae.ucsc.saccer1_1.4.0_src_all.tar.gz" ) MD5="ad4c29c16a9635088bf13872b4a02ed4" @@ -16,7 +17,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-bsgenome.scerevisiae.ucsc.saccer2/meta.yaml b/recipes/bioconductor-bsgenome.scerevisiae.ucsc.saccer2/meta.yaml index b61f4f2e57edd..e6a734b6ee95f 100644 --- a/recipes/bioconductor-bsgenome.scerevisiae.ucsc.saccer2/meta.yaml +++ b/recipes/bioconductor-bsgenome.scerevisiae.ucsc.saccer2/meta.yaml @@ -1,6 +1,6 @@ {% set version = "1.4.0" %} {% set name = "BSgenome.Scerevisiae.UCSC.sacCer2" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -12,19 +12,19 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' md5: f1025b4d0fa7891dc46301550163753e build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ noarch: generic requirements: host: - - 'bioconductor-bsgenome >=1.50.0,<1.51.0' + - 'bioconductor-bsgenome >=1.52.0,<1.53.0' - r-base run: - - 'bioconductor-bsgenome >=1.50.0,<1.51.0' + - 'bioconductor-bsgenome >=1.52.0,<1.53.0' - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-bsgenome.scerevisiae.ucsc.saccer2/post-link.sh b/recipes/bioconductor-bsgenome.scerevisiae.ucsc.saccer2/post-link.sh index 3a1cc98f61ebe..734624214f66e 100644 --- a/recipes/bioconductor-bsgenome.scerevisiae.ucsc.saccer2/post-link.sh +++ b/recipes/bioconductor-bsgenome.scerevisiae.ucsc.saccer2/post-link.sh @@ -1,9 +1,10 @@ #!/bin/bash FN="BSgenome.Scerevisiae.UCSC.sacCer2_1.4.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/BSgenome.Scerevisiae.UCSC.sacCer2_1.4.0.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/BSgenome.Scerevisiae.UCSC.sacCer2_1.4.0.tar.gz" "https://bioarchive.galaxyproject.org/BSgenome.Scerevisiae.UCSC.sacCer2_1.4.0.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-bsgenome.scerevisiae.ucsc.saccer2/bioconductor-bsgenome.scerevisiae.ucsc.saccer2_1.4.0_src_all.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-bsgenome.scerevisiae.ucsc.saccer2/bioconductor-bsgenome.scerevisiae.ucsc.saccer2_1.4.0_src_all.tar.gz" ) MD5="f1025b4d0fa7891dc46301550163753e" @@ -16,7 +17,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-bsgenome.scerevisiae.ucsc.saccer3/meta.yaml b/recipes/bioconductor-bsgenome.scerevisiae.ucsc.saccer3/meta.yaml index 7ab884006c8f4..b385dab2ebf54 100644 --- a/recipes/bioconductor-bsgenome.scerevisiae.ucsc.saccer3/meta.yaml +++ b/recipes/bioconductor-bsgenome.scerevisiae.ucsc.saccer3/meta.yaml @@ -1,6 +1,6 @@ {% set version = "1.4.0" %} {% set name = "BSgenome.Scerevisiae.UCSC.sacCer3" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -12,19 +12,19 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' md5: 7f2d8bba69c3dcebf426d9b19a6bed30 build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ noarch: generic requirements: host: - - 'bioconductor-bsgenome >=1.50.0,<1.51.0' + - 'bioconductor-bsgenome >=1.52.0,<1.53.0' - r-base run: - - 'bioconductor-bsgenome >=1.50.0,<1.51.0' + - 'bioconductor-bsgenome >=1.52.0,<1.53.0' - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-bsgenome.scerevisiae.ucsc.saccer3/post-link.sh b/recipes/bioconductor-bsgenome.scerevisiae.ucsc.saccer3/post-link.sh index 513cb0038e836..e28f8ccf90541 100644 --- a/recipes/bioconductor-bsgenome.scerevisiae.ucsc.saccer3/post-link.sh +++ b/recipes/bioconductor-bsgenome.scerevisiae.ucsc.saccer3/post-link.sh @@ -1,9 +1,10 @@ #!/bin/bash FN="BSgenome.Scerevisiae.UCSC.sacCer3_1.4.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/BSgenome.Scerevisiae.UCSC.sacCer3_1.4.0.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/BSgenome.Scerevisiae.UCSC.sacCer3_1.4.0.tar.gz" "https://bioarchive.galaxyproject.org/BSgenome.Scerevisiae.UCSC.sacCer3_1.4.0.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-bsgenome.scerevisiae.ucsc.saccer3/bioconductor-bsgenome.scerevisiae.ucsc.saccer3_1.4.0_src_all.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-bsgenome.scerevisiae.ucsc.saccer3/bioconductor-bsgenome.scerevisiae.ucsc.saccer3_1.4.0_src_all.tar.gz" ) MD5="7f2d8bba69c3dcebf426d9b19a6bed30" @@ -16,7 +17,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-bsgenome.sscrofa.ucsc.susscr11/meta.yaml b/recipes/bioconductor-bsgenome.sscrofa.ucsc.susscr11/meta.yaml index d74510e5c8916..d1440f317f831 100644 --- a/recipes/bioconductor-bsgenome.sscrofa.ucsc.susscr11/meta.yaml +++ b/recipes/bioconductor-bsgenome.sscrofa.ucsc.susscr11/meta.yaml @@ -1,6 +1,6 @@ {% set version = "1.4.2" %} {% set name = "BSgenome.Sscrofa.UCSC.susScr11" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -12,19 +12,19 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' md5: db22832229e31e1a629d107df522dff9 build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ noarch: generic requirements: host: - - 'bioconductor-bsgenome >=1.50.0,<1.51.0' + - 'bioconductor-bsgenome >=1.52.0,<1.53.0' - r-base run: - - 'bioconductor-bsgenome >=1.50.0,<1.51.0' + - 'bioconductor-bsgenome >=1.52.0,<1.53.0' - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-bsgenome.sscrofa.ucsc.susscr11/post-link.sh b/recipes/bioconductor-bsgenome.sscrofa.ucsc.susscr11/post-link.sh index 647b6e12067c6..9d20f61af9055 100644 --- a/recipes/bioconductor-bsgenome.sscrofa.ucsc.susscr11/post-link.sh +++ b/recipes/bioconductor-bsgenome.sscrofa.ucsc.susscr11/post-link.sh @@ -1,9 +1,10 @@ #!/bin/bash FN="BSgenome.Sscrofa.UCSC.susScr11_1.4.2.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/BSgenome.Sscrofa.UCSC.susScr11_1.4.2.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/BSgenome.Sscrofa.UCSC.susScr11_1.4.2.tar.gz" "https://bioarchive.galaxyproject.org/BSgenome.Sscrofa.UCSC.susScr11_1.4.2.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-bsgenome.sscrofa.ucsc.susscr11/bioconductor-bsgenome.sscrofa.ucsc.susscr11_1.4.2_src_all.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-bsgenome.sscrofa.ucsc.susscr11/bioconductor-bsgenome.sscrofa.ucsc.susscr11_1.4.2_src_all.tar.gz" ) MD5="db22832229e31e1a629d107df522dff9" @@ -16,7 +17,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-bsgenome.sscrofa.ucsc.susscr3.masked/meta.yaml b/recipes/bioconductor-bsgenome.sscrofa.ucsc.susscr3.masked/meta.yaml index 72a23487da301..bed5cd19c49c2 100644 --- a/recipes/bioconductor-bsgenome.sscrofa.ucsc.susscr3.masked/meta.yaml +++ b/recipes/bioconductor-bsgenome.sscrofa.ucsc.susscr3.masked/meta.yaml @@ -1,6 +1,6 @@ {% set version = "1.3.99" %} {% set name = "BSgenome.Sscrofa.UCSC.susScr3.masked" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -12,21 +12,21 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' md5: fd240651d22d169fd1e27a2b66e40dd7 build: - number: 1 + number: 2 rpaths: - lib/R/lib/ - lib/ noarch: generic requirements: host: - - 'bioconductor-bsgenome >=1.50.0,<1.51.0' + - 'bioconductor-bsgenome >=1.52.0,<1.53.0' - 'bioconductor-bsgenome.sscrofa.ucsc.susscr3 >=1.4.0,<1.5.0' - r-base run: - - 'bioconductor-bsgenome >=1.50.0,<1.51.0' + - 'bioconductor-bsgenome >=1.52.0,<1.53.0' - 'bioconductor-bsgenome.sscrofa.ucsc.susscr3 >=1.4.0,<1.5.0' - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-bsgenome.sscrofa.ucsc.susscr3.masked/post-link.sh b/recipes/bioconductor-bsgenome.sscrofa.ucsc.susscr3.masked/post-link.sh index 53232dfc7b96e..59781f20eed99 100644 --- a/recipes/bioconductor-bsgenome.sscrofa.ucsc.susscr3.masked/post-link.sh +++ b/recipes/bioconductor-bsgenome.sscrofa.ucsc.susscr3.masked/post-link.sh @@ -1,9 +1,10 @@ #!/bin/bash FN="BSgenome.Sscrofa.UCSC.susScr3.masked_1.3.99.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/BSgenome.Sscrofa.UCSC.susScr3.masked_1.3.99.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/BSgenome.Sscrofa.UCSC.susScr3.masked_1.3.99.tar.gz" "https://bioarchive.galaxyproject.org/BSgenome.Sscrofa.UCSC.susScr3.masked_1.3.99.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-bsgenome.sscrofa.ucsc.susscr3.masked/bioconductor-bsgenome.sscrofa.ucsc.susscr3.masked_1.3.99_src_all.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-bsgenome.sscrofa.ucsc.susscr3.masked/bioconductor-bsgenome.sscrofa.ucsc.susscr3.masked_1.3.99_src_all.tar.gz" ) MD5="fd240651d22d169fd1e27a2b66e40dd7" @@ -16,7 +17,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-bsgenome.sscrofa.ucsc.susscr3/meta.yaml b/recipes/bioconductor-bsgenome.sscrofa.ucsc.susscr3/meta.yaml index cfe48b5eef4c7..0203ef20b838f 100644 --- a/recipes/bioconductor-bsgenome.sscrofa.ucsc.susscr3/meta.yaml +++ b/recipes/bioconductor-bsgenome.sscrofa.ucsc.susscr3/meta.yaml @@ -1,6 +1,6 @@ {% set version = "1.4.0" %} {% set name = "BSgenome.Sscrofa.UCSC.susScr3" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -12,19 +12,19 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' md5: 0457ca52a81c9d7ceadad5830169e6cf build: - number: 1 + number: 2 rpaths: - lib/R/lib/ - lib/ noarch: generic requirements: host: - - 'bioconductor-bsgenome >=1.50.0,<1.51.0' + - 'bioconductor-bsgenome >=1.52.0,<1.53.0' - r-base run: - - 'bioconductor-bsgenome >=1.50.0,<1.51.0' + - 'bioconductor-bsgenome >=1.52.0,<1.53.0' - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-bsgenome.sscrofa.ucsc.susscr3/post-link.sh b/recipes/bioconductor-bsgenome.sscrofa.ucsc.susscr3/post-link.sh index c882a46e5c133..00e7cf42343e5 100644 --- a/recipes/bioconductor-bsgenome.sscrofa.ucsc.susscr3/post-link.sh +++ b/recipes/bioconductor-bsgenome.sscrofa.ucsc.susscr3/post-link.sh @@ -1,9 +1,10 @@ #!/bin/bash FN="BSgenome.Sscrofa.UCSC.susScr3_1.4.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/BSgenome.Sscrofa.UCSC.susScr3_1.4.0.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/BSgenome.Sscrofa.UCSC.susScr3_1.4.0.tar.gz" "https://bioarchive.galaxyproject.org/BSgenome.Sscrofa.UCSC.susScr3_1.4.0.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-bsgenome.sscrofa.ucsc.susscr3/bioconductor-bsgenome.sscrofa.ucsc.susscr3_1.4.0_src_all.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-bsgenome.sscrofa.ucsc.susscr3/bioconductor-bsgenome.sscrofa.ucsc.susscr3_1.4.0_src_all.tar.gz" ) MD5="0457ca52a81c9d7ceadad5830169e6cf" @@ -16,7 +17,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-bsgenome.tgondii.toxodb.7.0/meta.yaml b/recipes/bioconductor-bsgenome.tgondii.toxodb.7.0/meta.yaml index ad1cccf276ab8..f947b64499560 100644 --- a/recipes/bioconductor-bsgenome.tgondii.toxodb.7.0/meta.yaml +++ b/recipes/bioconductor-bsgenome.tgondii.toxodb.7.0/meta.yaml @@ -1,6 +1,6 @@ {% set version = "0.99.0" %} {% set name = "BSgenome.Tgondii.ToxoDB.7.0" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -12,19 +12,19 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' md5: 8f204871f73f8d1c5194f3748e28878e build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ noarch: generic requirements: host: - - 'bioconductor-bsgenome >=1.50.0,<1.51.0' + - 'bioconductor-bsgenome >=1.52.0,<1.53.0' - r-base run: - - 'bioconductor-bsgenome >=1.50.0,<1.51.0' + - 'bioconductor-bsgenome >=1.52.0,<1.53.0' - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-bsgenome.tgondii.toxodb.7.0/post-link.sh b/recipes/bioconductor-bsgenome.tgondii.toxodb.7.0/post-link.sh index cf4201c036138..a550bbb25bd55 100644 --- a/recipes/bioconductor-bsgenome.tgondii.toxodb.7.0/post-link.sh +++ b/recipes/bioconductor-bsgenome.tgondii.toxodb.7.0/post-link.sh @@ -1,9 +1,10 @@ #!/bin/bash FN="BSgenome.Tgondii.ToxoDB.7.0_0.99.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/BSgenome.Tgondii.ToxoDB.7.0_0.99.0.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/BSgenome.Tgondii.ToxoDB.7.0_0.99.0.tar.gz" "https://bioarchive.galaxyproject.org/BSgenome.Tgondii.ToxoDB.7.0_0.99.0.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-bsgenome.tgondii.toxodb.7.0/bioconductor-bsgenome.tgondii.toxodb.7.0_0.99.0_src_all.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-bsgenome.tgondii.toxodb.7.0/bioconductor-bsgenome.tgondii.toxodb.7.0_0.99.0_src_all.tar.gz" ) MD5="8f204871f73f8d1c5194f3748e28878e" @@ -16,7 +17,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-bsgenome.tguttata.ucsc.taegut1.masked/meta.yaml b/recipes/bioconductor-bsgenome.tguttata.ucsc.taegut1.masked/meta.yaml index a0dac90b902b0..e938ed4913c03 100644 --- a/recipes/bioconductor-bsgenome.tguttata.ucsc.taegut1.masked/meta.yaml +++ b/recipes/bioconductor-bsgenome.tguttata.ucsc.taegut1.masked/meta.yaml @@ -1,6 +1,6 @@ {% set version = "1.3.99" %} {% set name = "BSgenome.Tguttata.UCSC.taeGut1.masked" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -12,21 +12,21 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' md5: 63684abb5b330bb54ff89fe78f2e6444 build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ noarch: generic requirements: host: - - 'bioconductor-bsgenome >=1.50.0,<1.51.0' + - 'bioconductor-bsgenome >=1.52.0,<1.53.0' - 'bioconductor-bsgenome.tguttata.ucsc.taegut1 >=1.4.0,<1.5.0' - r-base run: - - 'bioconductor-bsgenome >=1.50.0,<1.51.0' + - 'bioconductor-bsgenome >=1.52.0,<1.53.0' - 'bioconductor-bsgenome.tguttata.ucsc.taegut1 >=1.4.0,<1.5.0' - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-bsgenome.tguttata.ucsc.taegut1.masked/post-link.sh b/recipes/bioconductor-bsgenome.tguttata.ucsc.taegut1.masked/post-link.sh index c2125b874c6c1..0fc8a8a8032fb 100644 --- a/recipes/bioconductor-bsgenome.tguttata.ucsc.taegut1.masked/post-link.sh +++ b/recipes/bioconductor-bsgenome.tguttata.ucsc.taegut1.masked/post-link.sh @@ -1,9 +1,10 @@ #!/bin/bash FN="BSgenome.Tguttata.UCSC.taeGut1.masked_1.3.99.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/BSgenome.Tguttata.UCSC.taeGut1.masked_1.3.99.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/BSgenome.Tguttata.UCSC.taeGut1.masked_1.3.99.tar.gz" "https://bioarchive.galaxyproject.org/BSgenome.Tguttata.UCSC.taeGut1.masked_1.3.99.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-bsgenome.tguttata.ucsc.taegut1.masked/bioconductor-bsgenome.tguttata.ucsc.taegut1.masked_1.3.99_src_all.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-bsgenome.tguttata.ucsc.taegut1.masked/bioconductor-bsgenome.tguttata.ucsc.taegut1.masked_1.3.99_src_all.tar.gz" ) MD5="63684abb5b330bb54ff89fe78f2e6444" @@ -16,7 +17,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-bsgenome.tguttata.ucsc.taegut1/meta.yaml b/recipes/bioconductor-bsgenome.tguttata.ucsc.taegut1/meta.yaml index 9cf3df48e63b4..775ac462eff7e 100644 --- a/recipes/bioconductor-bsgenome.tguttata.ucsc.taegut1/meta.yaml +++ b/recipes/bioconductor-bsgenome.tguttata.ucsc.taegut1/meta.yaml @@ -1,6 +1,6 @@ {% set version = "1.4.0" %} {% set name = "BSgenome.Tguttata.UCSC.taeGut1" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -12,19 +12,19 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' md5: 9753d9568d2a866a627673a518a1dd8a build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ noarch: generic requirements: host: - - 'bioconductor-bsgenome >=1.50.0,<1.51.0' + - 'bioconductor-bsgenome >=1.52.0,<1.53.0' - r-base run: - - 'bioconductor-bsgenome >=1.50.0,<1.51.0' + - 'bioconductor-bsgenome >=1.52.0,<1.53.0' - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-bsgenome.tguttata.ucsc.taegut1/post-link.sh b/recipes/bioconductor-bsgenome.tguttata.ucsc.taegut1/post-link.sh index c8e93e38b82d3..ab3bd80eba7dd 100644 --- a/recipes/bioconductor-bsgenome.tguttata.ucsc.taegut1/post-link.sh +++ b/recipes/bioconductor-bsgenome.tguttata.ucsc.taegut1/post-link.sh @@ -1,9 +1,10 @@ #!/bin/bash FN="BSgenome.Tguttata.UCSC.taeGut1_1.4.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/BSgenome.Tguttata.UCSC.taeGut1_1.4.0.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/BSgenome.Tguttata.UCSC.taeGut1_1.4.0.tar.gz" "https://bioarchive.galaxyproject.org/BSgenome.Tguttata.UCSC.taeGut1_1.4.0.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-bsgenome.tguttata.ucsc.taegut1/bioconductor-bsgenome.tguttata.ucsc.taegut1_1.4.0_src_all.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-bsgenome.tguttata.ucsc.taegut1/bioconductor-bsgenome.tguttata.ucsc.taegut1_1.4.0_src_all.tar.gz" ) MD5="9753d9568d2a866a627673a518a1dd8a" @@ -16,7 +17,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-bsgenome.tguttata.ucsc.taegut2/meta.yaml b/recipes/bioconductor-bsgenome.tguttata.ucsc.taegut2/meta.yaml index 4b22b69d131f6..1ca2004680554 100644 --- a/recipes/bioconductor-bsgenome.tguttata.ucsc.taegut2/meta.yaml +++ b/recipes/bioconductor-bsgenome.tguttata.ucsc.taegut2/meta.yaml @@ -1,6 +1,6 @@ {% set version = "1.4.2" %} {% set name = "BSgenome.Tguttata.UCSC.taeGut2" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -12,19 +12,19 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' md5: 1d39678fb060e643f7e9c4ec25e828c0 build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ noarch: generic requirements: host: - - 'bioconductor-bsgenome >=1.50.0,<1.51.0' + - 'bioconductor-bsgenome >=1.52.0,<1.53.0' - r-base run: - - 'bioconductor-bsgenome >=1.50.0,<1.51.0' + - 'bioconductor-bsgenome >=1.52.0,<1.53.0' - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-bsgenome.tguttata.ucsc.taegut2/post-link.sh b/recipes/bioconductor-bsgenome.tguttata.ucsc.taegut2/post-link.sh index 78dfd39087ec1..83f85a25ebfd3 100644 --- a/recipes/bioconductor-bsgenome.tguttata.ucsc.taegut2/post-link.sh +++ b/recipes/bioconductor-bsgenome.tguttata.ucsc.taegut2/post-link.sh @@ -1,9 +1,10 @@ #!/bin/bash FN="BSgenome.Tguttata.UCSC.taeGut2_1.4.2.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/BSgenome.Tguttata.UCSC.taeGut2_1.4.2.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/BSgenome.Tguttata.UCSC.taeGut2_1.4.2.tar.gz" "https://bioarchive.galaxyproject.org/BSgenome.Tguttata.UCSC.taeGut2_1.4.2.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-bsgenome.tguttata.ucsc.taegut2/bioconductor-bsgenome.tguttata.ucsc.taegut2_1.4.2_src_all.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-bsgenome.tguttata.ucsc.taegut2/bioconductor-bsgenome.tguttata.ucsc.taegut2_1.4.2_src_all.tar.gz" ) MD5="1d39678fb060e643f7e9c4ec25e828c0" @@ -16,7 +17,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-bsgenome.vvinifera.urgi.iggp12xv0/meta.yaml b/recipes/bioconductor-bsgenome.vvinifera.urgi.iggp12xv0/meta.yaml index 58d7463116fc4..b8e46dc0ee62e 100644 --- a/recipes/bioconductor-bsgenome.vvinifera.urgi.iggp12xv0/meta.yaml +++ b/recipes/bioconductor-bsgenome.vvinifera.urgi.iggp12xv0/meta.yaml @@ -1,6 +1,6 @@ {% set version = "0.1" %} {% set name = "BSgenome.Vvinifera.URGI.IGGP12Xv0" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -12,19 +12,19 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' md5: 3f791de6d699325a97080cd98be86d89 build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ noarch: generic requirements: host: - - 'bioconductor-bsgenome >=1.50.0,<1.51.0' + - 'bioconductor-bsgenome >=1.52.0,<1.53.0' - r-base run: - - 'bioconductor-bsgenome >=1.50.0,<1.51.0' + - 'bioconductor-bsgenome >=1.52.0,<1.53.0' - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-bsgenome.vvinifera.urgi.iggp12xv0/post-link.sh b/recipes/bioconductor-bsgenome.vvinifera.urgi.iggp12xv0/post-link.sh index 384b6fd25186f..74ee20cbae0a5 100644 --- a/recipes/bioconductor-bsgenome.vvinifera.urgi.iggp12xv0/post-link.sh +++ b/recipes/bioconductor-bsgenome.vvinifera.urgi.iggp12xv0/post-link.sh @@ -1,9 +1,10 @@ #!/bin/bash FN="BSgenome.Vvinifera.URGI.IGGP12Xv0_0.1.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/BSgenome.Vvinifera.URGI.IGGP12Xv0_0.1.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/BSgenome.Vvinifera.URGI.IGGP12Xv0_0.1.tar.gz" "https://bioarchive.galaxyproject.org/BSgenome.Vvinifera.URGI.IGGP12Xv0_0.1.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-bsgenome.vvinifera.urgi.iggp12xv0/bioconductor-bsgenome.vvinifera.urgi.iggp12xv0_0.1_src_all.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-bsgenome.vvinifera.urgi.iggp12xv0/bioconductor-bsgenome.vvinifera.urgi.iggp12xv0_0.1_src_all.tar.gz" ) MD5="3f791de6d699325a97080cd98be86d89" @@ -16,7 +17,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-bsgenome.vvinifera.urgi.iggp12xv2/meta.yaml b/recipes/bioconductor-bsgenome.vvinifera.urgi.iggp12xv2/meta.yaml index 2ae3de04058a9..0fbb9460960d6 100644 --- a/recipes/bioconductor-bsgenome.vvinifera.urgi.iggp12xv2/meta.yaml +++ b/recipes/bioconductor-bsgenome.vvinifera.urgi.iggp12xv2/meta.yaml @@ -1,6 +1,6 @@ {% set version = "0.1" %} {% set name = "BSgenome.Vvinifera.URGI.IGGP12Xv2" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -12,19 +12,19 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' md5: 95472e574ab46327c19e241c381b26a2 build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ noarch: generic requirements: host: - - 'bioconductor-bsgenome >=1.50.0,<1.51.0' + - 'bioconductor-bsgenome >=1.52.0,<1.53.0' - r-base run: - - 'bioconductor-bsgenome >=1.50.0,<1.51.0' + - 'bioconductor-bsgenome >=1.52.0,<1.53.0' - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-bsgenome.vvinifera.urgi.iggp12xv2/post-link.sh b/recipes/bioconductor-bsgenome.vvinifera.urgi.iggp12xv2/post-link.sh index 39fd328f8f52c..80265a0ee4f82 100644 --- a/recipes/bioconductor-bsgenome.vvinifera.urgi.iggp12xv2/post-link.sh +++ b/recipes/bioconductor-bsgenome.vvinifera.urgi.iggp12xv2/post-link.sh @@ -1,9 +1,10 @@ #!/bin/bash FN="BSgenome.Vvinifera.URGI.IGGP12Xv2_0.1.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/BSgenome.Vvinifera.URGI.IGGP12Xv2_0.1.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/BSgenome.Vvinifera.URGI.IGGP12Xv2_0.1.tar.gz" "https://bioarchive.galaxyproject.org/BSgenome.Vvinifera.URGI.IGGP12Xv2_0.1.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-bsgenome.vvinifera.urgi.iggp12xv2/bioconductor-bsgenome.vvinifera.urgi.iggp12xv2_0.1_src_all.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-bsgenome.vvinifera.urgi.iggp12xv2/bioconductor-bsgenome.vvinifera.urgi.iggp12xv2_0.1_src_all.tar.gz" ) MD5="95472e574ab46327c19e241c381b26a2" @@ -16,7 +17,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-bsgenome.vvinifera.urgi.iggp8x/meta.yaml b/recipes/bioconductor-bsgenome.vvinifera.urgi.iggp8x/meta.yaml index 12b2376f59d8b..b0135383851db 100644 --- a/recipes/bioconductor-bsgenome.vvinifera.urgi.iggp8x/meta.yaml +++ b/recipes/bioconductor-bsgenome.vvinifera.urgi.iggp8x/meta.yaml @@ -1,6 +1,6 @@ {% set version = "0.1" %} {% set name = "BSgenome.Vvinifera.URGI.IGGP8X" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -12,19 +12,19 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' md5: fccaf60e5c9352b9c454f7a8ecac2a20 build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ noarch: generic requirements: host: - - 'bioconductor-bsgenome >=1.50.0,<1.51.0' + - 'bioconductor-bsgenome >=1.52.0,<1.53.0' - r-base run: - - 'bioconductor-bsgenome >=1.50.0,<1.51.0' + - 'bioconductor-bsgenome >=1.52.0,<1.53.0' - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-bsgenome.vvinifera.urgi.iggp8x/post-link.sh b/recipes/bioconductor-bsgenome.vvinifera.urgi.iggp8x/post-link.sh index a1381a0ecae46..d69b306e54c0f 100644 --- a/recipes/bioconductor-bsgenome.vvinifera.urgi.iggp8x/post-link.sh +++ b/recipes/bioconductor-bsgenome.vvinifera.urgi.iggp8x/post-link.sh @@ -1,9 +1,10 @@ #!/bin/bash FN="BSgenome.Vvinifera.URGI.IGGP8X_0.1.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/BSgenome.Vvinifera.URGI.IGGP8X_0.1.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/BSgenome.Vvinifera.URGI.IGGP8X_0.1.tar.gz" "https://bioarchive.galaxyproject.org/BSgenome.Vvinifera.URGI.IGGP8X_0.1.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-bsgenome.vvinifera.urgi.iggp8x/bioconductor-bsgenome.vvinifera.urgi.iggp8x_0.1_src_all.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-bsgenome.vvinifera.urgi.iggp8x/bioconductor-bsgenome.vvinifera.urgi.iggp8x_0.1_src_all.tar.gz" ) MD5="fccaf60e5c9352b9c454f7a8ecac2a20" @@ -16,7 +17,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-bsgenome/meta.yaml b/recipes/bioconductor-bsgenome/meta.yaml index ae0befa1ed030..58613741157ce 100644 --- a/recipes/bioconductor-bsgenome/meta.yaml +++ b/recipes/bioconductor-bsgenome/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.50.0" %} +{% set version = "1.52.0" %} {% set name = "BSgenome" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: f395bece508475220d86ec87f694436b + md5: 6af1de03fa89f6a029a86d70ea8e9fe8 build: number: 0 rpaths: @@ -20,26 +20,26 @@ build: # Suggests: BiocManager, Biobase, BSgenome.Celegans.UCSC.ce2, BSgenome.Hsapiens.UCSC.hg38, BSgenome.Hsapiens.UCSC.hg38.masked, BSgenome.Mmusculus.UCSC.mm10, BSgenome.Rnorvegicus.UCSC.rn5, BSgenome.Scerevisiae.UCSC.sacCer1, TxDb.Hsapiens.UCSC.hg38.knownGene, TxDb.Mmusculus.UCSC.mm10.knownGene, SNPlocs.Hsapiens.dbSNP144.GRCh38, XtraSNPlocs.Hsapiens.dbSNP144.GRCh38, hgu95av2probe, RUnit requirements: host: - - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' - - 'bioconductor-biostrings >=2.50.0,<2.51.0' - - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' - - 'bioconductor-genomicranges >=1.34.0,<1.35.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-rsamtools >=1.34.0,<1.35.0' - - 'bioconductor-rtracklayer >=1.42.0,<1.43.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' - - 'bioconductor-xvector >=0.22.0,<0.23.0' + - 'bioconductor-biocgenerics >=0.30.0,<0.31.0' + - 'bioconductor-biostrings >=2.52.0,<2.53.0' + - 'bioconductor-genomeinfodb >=1.20.0,<1.21.0' + - 'bioconductor-genomicranges >=1.36.0,<1.37.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-rsamtools >=2.0.0,<2.1.0' + - 'bioconductor-rtracklayer >=1.44.0,<1.45.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' + - 'bioconductor-xvector >=0.24.0,<0.25.0' - r-base run: - - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' - - 'bioconductor-biostrings >=2.50.0,<2.51.0' - - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' - - 'bioconductor-genomicranges >=1.34.0,<1.35.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-rsamtools >=1.34.0,<1.35.0' - - 'bioconductor-rtracklayer >=1.42.0,<1.43.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' - - 'bioconductor-xvector >=0.22.0,<0.23.0' + - 'bioconductor-biocgenerics >=0.30.0,<0.31.0' + - 'bioconductor-biostrings >=2.52.0,<2.53.0' + - 'bioconductor-genomeinfodb >=1.20.0,<1.21.0' + - 'bioconductor-genomicranges >=1.36.0,<1.37.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-rsamtools >=2.0.0,<2.1.0' + - 'bioconductor-rtracklayer >=1.44.0,<1.45.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' + - 'bioconductor-xvector >=0.24.0,<0.25.0' - r-base test: commands: diff --git a/recipes/bioconductor-bsseq/meta.yaml b/recipes/bioconductor-bsseq/meta.yaml index 55fc373a6d536..8e399b266a5e7 100644 --- a/recipes/bioconductor-bsseq/meta.yaml +++ b/recipes/bioconductor-bsseq/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.18.0" %} +{% set version = "1.20.0" %} {% set name = "bsseq" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,33 +10,32 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 27d165f57d1a2fdfd2fb2af640039d90 + md5: fafc60de775b2523fd161a7711106a9a build: number: 0 rpaths: - lib/R/lib/ - lib/ -# Suggests: testthat, bsseqData, BiocStyle, rmarkdown, knitr, Matrix, doParallel, rtracklayer, BSgenome.Hsapiens.UCSC.hg38, beachmat +# Suggests: testthat, bsseqData, BiocStyle, rmarkdown, knitr, Matrix, doParallel, rtracklayer, BSgenome.Hsapiens.UCSC.hg38, beachmat (>= 1.5.2), BatchJobs # SystemRequirements: C++11 requirements: host: - - 'bioconductor-beachmat >=1.4.0,<1.5.0' - - 'bioconductor-biobase >=2.42.0,<2.43.0' - - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' - - 'bioconductor-biocparallel >=1.16.0,<1.17.0' - - 'bioconductor-biostrings >=2.50.0,<2.51.0' - - 'bioconductor-bsgenome >=1.50.0,<1.51.0' - - 'bioconductor-delayedarray >=0.8.0,<0.9.0' - - 'bioconductor-delayedmatrixstats >=1.4.0,<1.5.0' - - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' - - 'bioconductor-genomicranges >=1.34.0,<1.35.0' - - 'bioconductor-hdf5array >=1.10.0,<1.11.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-limma >=3.38.0,<3.39.0' - - 'bioconductor-rhdf5 >=2.26.0,<2.27.0' - - 'bioconductor-rhdf5lib >=1.4.0,<1.5.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' - - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' + - 'bioconductor-beachmat >=2.0.0,<2.1.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' + - 'bioconductor-biocgenerics >=0.30.0,<0.31.0' + - 'bioconductor-biocparallel >=1.18.0,<1.19.0' + - 'bioconductor-biostrings >=2.52.0,<2.53.0' + - 'bioconductor-bsgenome >=1.52.0,<1.53.0' + - 'bioconductor-delayedarray >=0.10.0,<0.11.0' + - 'bioconductor-delayedmatrixstats >=1.6.0,<1.7.0' + - 'bioconductor-genomeinfodb >=1.20.0,<1.21.0' + - 'bioconductor-genomicranges >=1.36.0,<1.37.0' + - 'bioconductor-hdf5array >=1.12.0,<1.13.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-limma >=3.40.0,<3.41.0' + - 'bioconductor-rhdf5 >=2.28.0,<2.29.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' + - 'bioconductor-summarizedexperiment >=1.14.0,<1.15.0' - r-base - 'r-data.table >=1.11.8' - r-gtools @@ -46,23 +45,22 @@ requirements: - r-rcpp - r-scales run: - - 'bioconductor-beachmat >=1.4.0,<1.5.0' - - 'bioconductor-biobase >=2.42.0,<2.43.0' - - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' - - 'bioconductor-biocparallel >=1.16.0,<1.17.0' - - 'bioconductor-biostrings >=2.50.0,<2.51.0' - - 'bioconductor-bsgenome >=1.50.0,<1.51.0' - - 'bioconductor-delayedarray >=0.8.0,<0.9.0' - - 'bioconductor-delayedmatrixstats >=1.4.0,<1.5.0' - - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' - - 'bioconductor-genomicranges >=1.34.0,<1.35.0' - - 'bioconductor-hdf5array >=1.10.0,<1.11.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-limma >=3.38.0,<3.39.0' - - 'bioconductor-rhdf5 >=2.26.0,<2.27.0' - - 'bioconductor-rhdf5lib >=1.4.0,<1.5.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' - - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' + - 'bioconductor-beachmat >=2.0.0,<2.1.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' + - 'bioconductor-biocgenerics >=0.30.0,<0.31.0' + - 'bioconductor-biocparallel >=1.18.0,<1.19.0' + - 'bioconductor-biostrings >=2.52.0,<2.53.0' + - 'bioconductor-bsgenome >=1.52.0,<1.53.0' + - 'bioconductor-delayedarray >=0.10.0,<0.11.0' + - 'bioconductor-delayedmatrixstats >=1.6.0,<1.7.0' + - 'bioconductor-genomeinfodb >=1.20.0,<1.21.0' + - 'bioconductor-genomicranges >=1.36.0,<1.37.0' + - 'bioconductor-hdf5array >=1.12.0,<1.13.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-limma >=3.40.0,<3.41.0' + - 'bioconductor-rhdf5 >=2.28.0,<2.29.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' + - 'bioconductor-summarizedexperiment >=1.14.0,<1.15.0' - r-base - 'r-data.table >=1.11.8' - r-gtools diff --git a/recipes/bioconductor-bsseqdata/meta.yaml b/recipes/bioconductor-bsseqdata/meta.yaml index dd74f194bc515..5859717e85a6c 100644 --- a/recipes/bioconductor-bsseqdata/meta.yaml +++ b/recipes/bioconductor-bsseqdata/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "0.20.0" %} +{% set version = "0.22.0" %} {% set name = "bsseqData" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: fb6e98b0545c71b6447d69747244036c + md5: e7675043ef714d778044e826b0dd2b1d build: number: 0 rpaths: @@ -19,12 +19,12 @@ build: noarch: generic requirements: host: - - 'bioconductor-bsseq >=1.18.0,<1.19.0' + - 'bioconductor-bsseq >=1.20.0,<1.21.0' - r-base run: - - 'bioconductor-bsseq >=1.18.0,<1.19.0' + - 'bioconductor-bsseq >=1.20.0,<1.21.0' - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-bsseqdata/post-link.sh b/recipes/bioconductor-bsseqdata/post-link.sh index 2f8679f403870..bbaf0cfae382c 100644 --- a/recipes/bioconductor-bsseqdata/post-link.sh +++ b/recipes/bioconductor-bsseqdata/post-link.sh @@ -1,11 +1,11 @@ #!/bin/bash -FN="bsseqData_0.20.0.tar.gz" +FN="bsseqData_0.22.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/experiment/src/contrib/bsseqData_0.20.0.tar.gz" - "https://bioarchive.galaxyproject.org/bsseqData_0.20.0.tar.gz" - "https://depot.galaxyproject.org/software/bioconductor-bsseqdata/bioconductor-bsseqdata_0.20.0_src_all.tar.gz" + "https://bioconductor.org/packages/3.9/data/experiment/src/contrib/bsseqData_0.22.0.tar.gz" + "https://bioarchive.galaxyproject.org/bsseqData_0.22.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-bsseqdata/bioconductor-bsseqdata_0.22.0_src_all.tar.gz" ) -MD5="fb6e98b0545c71b6447d69747244036c" +MD5="e7675043ef714d778044e826b0dd2b1d" # Use a staging area in the conda dir rather than temp dirs, both to avoid # permission issues as well as to have things downloaded in a predictable @@ -16,7 +16,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-bsubtiliscdf/meta.yaml b/recipes/bioconductor-bsubtiliscdf/meta.yaml index eff2885d2ee36..2fac17b09d610 100644 --- a/recipes/bioconductor-bsubtiliscdf/meta.yaml +++ b/recipes/bioconductor-bsubtiliscdf/meta.yaml @@ -1,6 +1,6 @@ {% set version = "2.18.0" %} {% set name = "bsubtiliscdf" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -12,19 +12,19 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 7d7893d28c601206805819ae0e49b31b build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' - r-base run: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-bsubtiliscdf/post-link.sh b/recipes/bioconductor-bsubtiliscdf/post-link.sh index 54baf47f6e017..6e4ddbdea9e17 100644 --- a/recipes/bioconductor-bsubtiliscdf/post-link.sh +++ b/recipes/bioconductor-bsubtiliscdf/post-link.sh @@ -1,9 +1,10 @@ #!/bin/bash FN="bsubtiliscdf_2.18.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/bsubtiliscdf_2.18.0.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/bsubtiliscdf_2.18.0.tar.gz" "https://bioarchive.galaxyproject.org/bsubtiliscdf_2.18.0.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-bsubtiliscdf/bioconductor-bsubtiliscdf_2.18.0_src_all.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-bsubtiliscdf/bioconductor-bsubtiliscdf_2.18.0_src_all.tar.gz" ) MD5="7d7893d28c601206805819ae0e49b31b" @@ -16,7 +17,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-bsubtilisprobe/meta.yaml b/recipes/bioconductor-bsubtilisprobe/meta.yaml index b6e1111a9053e..67ae6faa414c2 100644 --- a/recipes/bioconductor-bsubtilisprobe/meta.yaml +++ b/recipes/bioconductor-bsubtilisprobe/meta.yaml @@ -1,6 +1,6 @@ {% set version = "2.18.0" %} {% set name = "bsubtilisprobe" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -12,19 +12,19 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 83568fcea2122350b7ce982e79b7ec53 build: - number: 1 + number: 2 rpaths: - lib/R/lib/ - lib/ noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' - r-base run: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-bsubtilisprobe/post-link.sh b/recipes/bioconductor-bsubtilisprobe/post-link.sh index 1d9c54028d7c0..2116f649a8a32 100644 --- a/recipes/bioconductor-bsubtilisprobe/post-link.sh +++ b/recipes/bioconductor-bsubtilisprobe/post-link.sh @@ -1,9 +1,10 @@ #!/bin/bash FN="bsubtilisprobe_2.18.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/bsubtilisprobe_2.18.0.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/bsubtilisprobe_2.18.0.tar.gz" "https://bioarchive.galaxyproject.org/bsubtilisprobe_2.18.0.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-bsubtilisprobe/bioconductor-bsubtilisprobe_2.18.0_src_all.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-bsubtilisprobe/bioconductor-bsubtilisprobe_2.18.0_src_all.tar.gz" ) MD5="83568fcea2122350b7ce982e79b7ec53" @@ -16,7 +17,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-bubbletree/meta.yaml b/recipes/bioconductor-bubbletree/meta.yaml index f437494d0bbb2..1b1fedf3f5f0c 100644 --- a/recipes/bioconductor-bubbletree/meta.yaml +++ b/recipes/bioconductor-bubbletree/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "2.12.0" %} +{% set version = "2.14.0" %} {% set name = "BubbleTree" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 7a76991a141f4d831fbea768e01d76bd + md5: 742ca18c07acb22717ae1dea849bed4a build: number: 0 rpaths: @@ -20,13 +20,13 @@ build: # Suggests: knitr, rmarkdown requirements: host: - - 'bioconductor-biobase >=2.42.0,<2.43.0' - - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' - - 'bioconductor-biocstyle >=2.10.0,<2.11.0' - - 'bioconductor-biovizbase >=1.30.0,<1.31.0' - - 'bioconductor-genomicranges >=1.34.0,<1.35.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-limma >=3.38.0,<3.39.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' + - 'bioconductor-biocgenerics >=0.30.0,<0.31.0' + - 'bioconductor-biocstyle >=2.12.0,<2.13.0' + - 'bioconductor-biovizbase >=1.32.0,<1.33.0' + - 'bioconductor-genomicranges >=1.36.0,<1.37.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-limma >=3.40.0,<3.41.0' - r-base - r-dplyr - r-e1071 @@ -39,13 +39,13 @@ requirements: - r-rcolorbrewer - r-writexls run: - - 'bioconductor-biobase >=2.42.0,<2.43.0' - - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' - - 'bioconductor-biocstyle >=2.10.0,<2.11.0' - - 'bioconductor-biovizbase >=1.30.0,<1.31.0' - - 'bioconductor-genomicranges >=1.34.0,<1.35.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-limma >=3.38.0,<3.39.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' + - 'bioconductor-biocgenerics >=0.30.0,<0.31.0' + - 'bioconductor-biocstyle >=2.12.0,<2.13.0' + - 'bioconductor-biovizbase >=1.32.0,<1.33.0' + - 'bioconductor-genomicranges >=1.36.0,<1.37.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-limma >=3.40.0,<3.41.0' - r-base - r-dplyr - r-e1071 diff --git a/recipes/bioconductor-bufferedmatrix/meta.yaml b/recipes/bioconductor-bufferedmatrix/meta.yaml index 9b99b7625774a..cff7fb9ad4d08 100644 --- a/recipes/bioconductor-bufferedmatrix/meta.yaml +++ b/recipes/bioconductor-bufferedmatrix/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.46.0" %} +{% set version = "1.48.0" %} {% set name = "BufferedMatrix" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: ac35d5e400ae81406bd70ca1f631b593 + md5: c4fbf25d9fb604528e65ad5c8fb14309 build: number: 0 rpaths: diff --git a/recipes/bioconductor-bufferedmatrixmethods/meta.yaml b/recipes/bioconductor-bufferedmatrixmethods/meta.yaml index 4937771b0c390..6a0003bc2c095 100644 --- a/recipes/bioconductor-bufferedmatrixmethods/meta.yaml +++ b/recipes/bioconductor-bufferedmatrixmethods/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.46.0" %} +{% set version = "1.48.0" %} {% set name = "BufferedMatrixMethods" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: fd0c01ee09b195d76b9b4e76ccda07ca + md5: 8a3abe17de06403a2ea5ead96663ef3f build: number: 0 rpaths: @@ -19,10 +19,10 @@ build: # Suggests: affyio, affy requirements: host: - - 'bioconductor-bufferedmatrix >=1.46.0,<1.47.0' + - 'bioconductor-bufferedmatrix >=1.48.0,<1.49.0' - r-base run: - - 'bioconductor-bufferedmatrix >=1.46.0,<1.47.0' + - 'bioconductor-bufferedmatrix >=1.48.0,<1.49.0' - r-base build: - {{ compiler('c') }} diff --git a/recipes/bioconductor-bumhmm/meta.yaml b/recipes/bioconductor-bumhmm/meta.yaml index 5842d6e9975f5..ea40a5e934536 100644 --- a/recipes/bioconductor-bumhmm/meta.yaml +++ b/recipes/bioconductor-bumhmm/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.6.0" %} +{% set version = "1.8.0" %} {% set name = "BUMHMM" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 1a6387144538ea8c29eb322172c268d6 + md5: abc7caecb419e680be1f0a5523c2a71a build: number: 0 rpaths: @@ -20,17 +20,17 @@ build: # Suggests: testthat, knitr, BiocStyle requirements: host: - - 'bioconductor-biostrings >=2.50.0,<2.51.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' + - 'bioconductor-biostrings >=2.52.0,<2.53.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-summarizedexperiment >=1.14.0,<1.15.0' - r-base - r-devtools - r-gtools - r-stringi run: - - 'bioconductor-biostrings >=2.50.0,<2.51.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' + - 'bioconductor-biostrings >=2.52.0,<2.53.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-summarizedexperiment >=1.14.0,<1.15.0' - r-base - r-devtools - r-gtools diff --git a/recipes/bioconductor-bumphunter/meta.yaml b/recipes/bioconductor-bumphunter/meta.yaml index 08c599fb44514..2d7eeb772a0f1 100644 --- a/recipes/bioconductor-bumphunter/meta.yaml +++ b/recipes/bioconductor-bumphunter/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.24.5" %} +{% set version = "1.26.0" %} {% set name = "bumphunter" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,9 +10,9 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 7c38a75e34594b999dbe13f58de13d2d + md5: e25e9e6a64a16dcef24c87e798527c93 build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ @@ -20,14 +20,14 @@ build: # Suggests: testthat, RUnit, doParallel, org.Hs.eg.db, TxDb.Hsapiens.UCSC.hg19.knownGene requirements: host: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' - - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' - - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' - - 'bioconductor-genomicfeatures >=1.34.0,<1.35.0' - - 'bioconductor-genomicranges >=1.34.0,<1.35.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-limma >=3.38.0,<3.39.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' + - 'bioconductor-biocgenerics >=0.30.0,<0.31.0' + - 'bioconductor-genomeinfodb >=1.20.0,<1.21.0' + - 'bioconductor-genomicfeatures >=1.36.0,<1.37.0' + - 'bioconductor-genomicranges >=1.36.0,<1.37.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-limma >=3.40.0,<3.41.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' - r-base - r-dorng - r-foreach @@ -35,14 +35,14 @@ requirements: - r-locfit - r-matrixstats run: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' - - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' - - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' - - 'bioconductor-genomicfeatures >=1.34.0,<1.35.0' - - 'bioconductor-genomicranges >=1.34.0,<1.35.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-limma >=3.38.0,<3.39.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' + - 'bioconductor-biocgenerics >=0.30.0,<0.31.0' + - 'bioconductor-genomeinfodb >=1.20.0,<1.21.0' + - 'bioconductor-genomicfeatures >=1.36.0,<1.37.0' + - 'bioconductor-genomicranges >=1.36.0,<1.37.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-limma >=3.40.0,<3.41.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' - r-base - r-dorng - r-foreach diff --git a/recipes/bioconductor-bus/meta.yaml b/recipes/bioconductor-bus/meta.yaml index bfa1f473abafd..6607ab6b27b7d 100644 --- a/recipes/bioconductor-bus/meta.yaml +++ b/recipes/bioconductor-bus/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.38.0" %} +{% set version = "1.40.0" %} {% set name = "BUS" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: ebdfc2420596f5fdc284694c57183488 + md5: ff29430aa926268c7089a76acc9f2844 build: number: 0 rpaths: @@ -18,11 +18,11 @@ build: - lib/ requirements: host: - - 'bioconductor-minet >=3.40.0,<3.41.0' + - 'bioconductor-minet >=3.42.0,<3.43.0' - r-base - r-infotheo run: - - 'bioconductor-minet >=3.40.0,<3.41.0' + - 'bioconductor-minet >=3.42.0,<3.43.0' - r-base - r-infotheo build: diff --git a/recipes/bioconductor-buscorrect/meta.yaml b/recipes/bioconductor-buscorrect/meta.yaml index 19e95d5dd71cb..9350c15a56eca 100644 --- a/recipes/bioconductor-buscorrect/meta.yaml +++ b/recipes/bioconductor-buscorrect/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.0.0" %} +{% set version = "1.2.0" %} {% set name = "BUScorrect" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: aadd22d922c6821cf37445835612c4b7 + md5: 9feb05c8c1adf79f5c5aa54125456483 build: number: 0 rpaths: @@ -19,11 +19,11 @@ build: # Suggests: BiocStyle, knitr, RUnit, BiocGenerics requirements: host: - - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' + - 'bioconductor-summarizedexperiment >=1.14.0,<1.15.0' - r-base - r-gplots run: - - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' + - 'bioconductor-summarizedexperiment >=1.14.0,<1.15.0' - r-base - r-gplots build: diff --git a/recipes/bioconductor-cafe/meta.yaml b/recipes/bioconductor-cafe/meta.yaml index b5c66dafcffcf..ceb00c5e8f505 100644 --- a/recipes/bioconductor-cafe/meta.yaml +++ b/recipes/bioconductor-cafe/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.18.0" %} +{% set version = "1.20.0" %} {% set name = "CAFE" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: db87b028e56b69c3372cf9e8b0f04836 + md5: 4aa05a6bf30967eec73b6a616e1c0a00 build: number: 0 rpaths: @@ -20,24 +20,24 @@ build: # Suggests: RUnit, BiocGenerics, BiocStyle requirements: host: - - 'bioconductor-affy >=1.60.0,<1.61.0' - - 'bioconductor-annotate >=1.60.0,<1.61.0' - - 'bioconductor-biobase >=2.42.0,<2.43.0' - - 'bioconductor-biovizbase >=1.30.0,<1.31.0' - - 'bioconductor-genomicranges >=1.34.0,<1.35.0' - - 'bioconductor-ggbio >=1.30.0,<1.31.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-affy >=1.62.0,<1.63.0' + - 'bioconductor-annotate >=1.62.0,<1.63.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' + - 'bioconductor-biovizbase >=1.32.0,<1.33.0' + - 'bioconductor-genomicranges >=1.36.0,<1.37.0' + - 'bioconductor-ggbio >=1.32.0,<1.33.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' - r-base - r-ggplot2 - r-gridextra run: - - 'bioconductor-affy >=1.60.0,<1.61.0' - - 'bioconductor-annotate >=1.60.0,<1.61.0' - - 'bioconductor-biobase >=2.42.0,<2.43.0' - - 'bioconductor-biovizbase >=1.30.0,<1.31.0' - - 'bioconductor-genomicranges >=1.34.0,<1.35.0' - - 'bioconductor-ggbio >=1.30.0,<1.31.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-affy >=1.62.0,<1.63.0' + - 'bioconductor-annotate >=1.62.0,<1.63.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' + - 'bioconductor-biovizbase >=1.32.0,<1.33.0' + - 'bioconductor-genomicranges >=1.36.0,<1.37.0' + - 'bioconductor-ggbio >=1.32.0,<1.33.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' - r-base - r-ggplot2 - r-gridextra diff --git a/recipes/bioconductor-cagefightr/meta.yaml b/recipes/bioconductor-cagefightr/meta.yaml index f151d99631cd6..02aefd829ab29 100644 --- a/recipes/bioconductor-cagefightr/meta.yaml +++ b/recipes/bioconductor-cagefightr/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.2.0" %} +{% set version = "1.4.0" %} {% set name = "CAGEfightR" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,9 +10,9 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: bed28d787f521b9fb0ee568b6188041f + md5: b4d4fe760ca5f2d924c4ad980502a530 build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ @@ -20,19 +20,19 @@ build: # Suggests: knitr, rmarkdown, BiocStyle, org.Mm.eg.db, TxDb.Mmusculus.UCSC.mm9.knownGene requirements: host: - - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' - - 'bioconductor-biocparallel >=1.16.0,<1.17.0' - - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' - - 'bioconductor-genomicfeatures >=1.34.0,<1.35.0' - - 'bioconductor-genomicfiles >=1.18.0,<1.19.0' - - 'bioconductor-genomicinteractions >=1.16.0,<1.17.0' - - 'bioconductor-genomicranges >=1.34.0,<1.35.0' - - 'bioconductor-gviz >=1.26.0,<1.27.0' - - 'bioconductor-interactionset >=1.10.0,<1.11.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-rtracklayer >=1.42.0,<1.43.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' - - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' + - 'bioconductor-biocgenerics >=0.30.0,<0.31.0' + - 'bioconductor-biocparallel >=1.18.0,<1.19.0' + - 'bioconductor-genomeinfodb >=1.20.0,<1.21.0' + - 'bioconductor-genomicfeatures >=1.36.0,<1.37.0' + - 'bioconductor-genomicfiles >=1.20.0,<1.21.0' + - 'bioconductor-genomicinteractions >=1.18.0,<1.19.0' + - 'bioconductor-genomicranges >=1.36.0,<1.37.0' + - 'bioconductor-gviz >=1.28.0,<1.29.0' + - 'bioconductor-interactionset >=1.12.0,<1.13.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-rtracklayer >=1.44.0,<1.45.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' + - 'bioconductor-summarizedexperiment >=1.14.0,<1.15.0' - 'r-assertthat >=0.2.0' - r-base - 'r-grr >=0.9.5' @@ -40,19 +40,19 @@ requirements: - 'r-matrix.utils >=0.9.6' - 'r-pryr >=0.1.3' run: - - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' - - 'bioconductor-biocparallel >=1.16.0,<1.17.0' - - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' - - 'bioconductor-genomicfeatures >=1.34.0,<1.35.0' - - 'bioconductor-genomicfiles >=1.18.0,<1.19.0' - - 'bioconductor-genomicinteractions >=1.16.0,<1.17.0' - - 'bioconductor-genomicranges >=1.34.0,<1.35.0' - - 'bioconductor-gviz >=1.26.0,<1.27.0' - - 'bioconductor-interactionset >=1.10.0,<1.11.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-rtracklayer >=1.42.0,<1.43.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' - - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' + - 'bioconductor-biocgenerics >=0.30.0,<0.31.0' + - 'bioconductor-biocparallel >=1.18.0,<1.19.0' + - 'bioconductor-genomeinfodb >=1.20.0,<1.21.0' + - 'bioconductor-genomicfeatures >=1.36.0,<1.37.0' + - 'bioconductor-genomicfiles >=1.20.0,<1.21.0' + - 'bioconductor-genomicinteractions >=1.18.0,<1.19.0' + - 'bioconductor-genomicranges >=1.36.0,<1.37.0' + - 'bioconductor-gviz >=1.28.0,<1.29.0' + - 'bioconductor-interactionset >=1.12.0,<1.13.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-rtracklayer >=1.44.0,<1.45.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' + - 'bioconductor-summarizedexperiment >=1.14.0,<1.15.0' - 'r-assertthat >=0.2.0' - r-base - 'r-grr >=0.9.5' diff --git a/recipes/bioconductor-cager/meta.yaml b/recipes/bioconductor-cager/meta.yaml index a13c3c74c52e4..aacd4ab26ad51 100644 --- a/recipes/bioconductor-cager/meta.yaml +++ b/recipes/bioconductor-cager/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.24.0" %} +{% set version = "1.26.0" %} {% set name = "CAGEr" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 9ecbf3e0bb2fb6d00e1de0a3652d845e + md5: a772349f5b6bdf941e81f52030ee226a build: number: 0 rpaths: @@ -20,19 +20,19 @@ build: # Suggests: BSgenome.Drerio.UCSC.danRer7, DESeq2, FANTOM3and4CAGE, BiocStyle, knitr, rmarkdown requirements: host: - - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' - - 'bioconductor-biocparallel >=1.16.0,<1.17.0' - - 'bioconductor-bsgenome >=1.50.0,<1.51.0' - - 'bioconductor-delayedarray >=0.8.0,<0.9.0' - - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' - - 'bioconductor-genomicalignments >=1.18.0,<1.19.0' - - 'bioconductor-genomicranges >=1.34.0,<1.35.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-multiassayexperiment >=1.8.0,<1.9.0' - - 'bioconductor-rsamtools >=1.34.0,<1.35.0' - - 'bioconductor-rtracklayer >=1.42.0,<1.43.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' - - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' + - 'bioconductor-biocgenerics >=0.30.0,<0.31.0' + - 'bioconductor-biocparallel >=1.18.0,<1.19.0' + - 'bioconductor-bsgenome >=1.52.0,<1.53.0' + - 'bioconductor-delayedarray >=0.10.0,<0.11.0' + - 'bioconductor-genomeinfodb >=1.20.0,<1.21.0' + - 'bioconductor-genomicalignments >=1.20.0,<1.21.0' + - 'bioconductor-genomicranges >=1.36.0,<1.37.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-multiassayexperiment >=1.10.0,<1.11.0' + - 'bioconductor-rsamtools >=2.0.0,<2.1.0' + - 'bioconductor-rtracklayer >=1.44.0,<1.45.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' + - 'bioconductor-summarizedexperiment >=1.14.0,<1.15.0' - r-base - r-beanplot - r-data.table @@ -49,19 +49,19 @@ requirements: - r-vegan - r-vgam run: - - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' - - 'bioconductor-biocparallel >=1.16.0,<1.17.0' - - 'bioconductor-bsgenome >=1.50.0,<1.51.0' - - 'bioconductor-delayedarray >=0.8.0,<0.9.0' - - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' - - 'bioconductor-genomicalignments >=1.18.0,<1.19.0' - - 'bioconductor-genomicranges >=1.34.0,<1.35.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-multiassayexperiment >=1.8.0,<1.9.0' - - 'bioconductor-rsamtools >=1.34.0,<1.35.0' - - 'bioconductor-rtracklayer >=1.42.0,<1.43.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' - - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' + - 'bioconductor-biocgenerics >=0.30.0,<0.31.0' + - 'bioconductor-biocparallel >=1.18.0,<1.19.0' + - 'bioconductor-bsgenome >=1.52.0,<1.53.0' + - 'bioconductor-delayedarray >=0.10.0,<0.11.0' + - 'bioconductor-genomeinfodb >=1.20.0,<1.21.0' + - 'bioconductor-genomicalignments >=1.20.0,<1.21.0' + - 'bioconductor-genomicranges >=1.36.0,<1.37.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-multiassayexperiment >=1.10.0,<1.11.0' + - 'bioconductor-rsamtools >=2.0.0,<2.1.0' + - 'bioconductor-rtracklayer >=1.44.0,<1.45.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' + - 'bioconductor-summarizedexperiment >=1.14.0,<1.15.0' - r-base - r-beanplot - r-data.table diff --git a/recipes/bioconductor-calib/meta.yaml b/recipes/bioconductor-calib/meta.yaml index 6b6179dd13fbe..bc667078e065c 100644 --- a/recipes/bioconductor-calib/meta.yaml +++ b/recipes/bioconductor-calib/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.48.0" %} +{% set version = "1.50.0" %} {% set name = "CALIB" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 1b50dd84b955b6ca81e18509167b4896 + md5: 9c5e453a09daa9f258cc2c396d127781 build: number: 0 rpaths: @@ -18,10 +18,10 @@ build: - lib/ requirements: host: - - 'bioconductor-limma >=3.38.0,<3.39.0' + - 'bioconductor-limma >=3.40.0,<3.41.0' - r-base run: - - 'bioconductor-limma >=3.38.0,<3.39.0' + - 'bioconductor-limma >=3.40.0,<3.41.0' - r-base build: - {{ compiler('c') }} diff --git a/recipes/bioconductor-camera/build.sh b/recipes/bioconductor-camera/build.sh index 5ea71a1203cac..c1d13421f5f1e 100644 --- a/recipes/bioconductor-camera/build.sh +++ b/recipes/bioconductor-camera/build.sh @@ -8,4 +8,4 @@ CXX=$CXX CXX98=$CXX CXX11=$CXX CXX14=$CXX" > ~/.R/Makevars -$R CMD INSTALL --build . +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-camera/meta.yaml b/recipes/bioconductor-camera/meta.yaml index 47a95468877d4..2d7ffac95175a 100644 --- a/recipes/bioconductor-camera/meta.yaml +++ b/recipes/bioconductor-camera/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.38.1" %} +{% set version = "1.40.0" %} {% set name = "CAMERA" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: f4ebd02dfe4bf266473696c109d86544 + md5: b69c86dafe1b112ee23bfce67a9725a3 build: number: 0 rpaths: @@ -19,18 +19,18 @@ build: # Suggests: faahKO, RUnit, BiocGenerics requirements: host: - - 'bioconductor-biobase >=2.42.0,<2.43.0' - - 'bioconductor-graph >=1.60.0,<1.61.0' - - 'bioconductor-rbgl >=1.58.0,<1.59.0' - - 'bioconductor-xcms >=3.4.0,<3.5.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' + - 'bioconductor-graph >=1.62.0,<1.63.0' + - 'bioconductor-rbgl >=1.60.0,<1.61.0' + - 'bioconductor-xcms >=3.6.0,<3.7.0' - r-base - r-hmisc - r-igraph run: - - 'bioconductor-biobase >=2.42.0,<2.43.0' - - 'bioconductor-graph >=1.60.0,<1.61.0' - - 'bioconductor-rbgl >=1.58.0,<1.59.0' - - 'bioconductor-xcms >=3.4.0,<3.5.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' + - 'bioconductor-graph >=1.62.0,<1.63.0' + - 'bioconductor-rbgl >=1.60.0,<1.61.0' + - 'bioconductor-xcms >=3.6.0,<3.7.0' - r-base - r-hmisc - r-igraph diff --git a/recipes/bioconductor-camthc/meta.yaml b/recipes/bioconductor-camthc/meta.yaml index 92309001dd6b7..951b5cdbbade7 100644 --- a/recipes/bioconductor-camthc/meta.yaml +++ b/recipes/bioconductor-camthc/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.0.0" %} +{% set version = "1.2.0" %} {% set name = "CAMTHC" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: cb62c6d7934584f5d24869db7d927437 + md5: 29259f9a6a2be58c0e648edf17b0adc9 build: number: 0 rpaths: @@ -21,27 +21,29 @@ build: # SystemRequirements: Java (>= 1.8) requirements: host: - - 'bioconductor-biobase >=2.42.0,<2.43.0' - - 'bioconductor-biocparallel >=1.16.0,<1.17.0' - - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' + - 'bioconductor-biocparallel >=1.18.0,<1.19.0' + - 'bioconductor-summarizedexperiment >=1.14.0,<1.15.0' - r-apcluster - r-base - r-corpcor - r-dmwr - r-geometry - r-nmf + - r-nnls - r-pcapp - r-rjava run: - - 'bioconductor-biobase >=2.42.0,<2.43.0' - - 'bioconductor-biocparallel >=1.16.0,<1.17.0' - - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' + - 'bioconductor-biocparallel >=1.18.0,<1.19.0' + - 'bioconductor-summarizedexperiment >=1.14.0,<1.15.0' - r-apcluster - r-base - r-corpcor - r-dmwr - r-geometry - r-nmf + - r-nnls - r-pcapp - r-rjava test: diff --git a/recipes/bioconductor-cancer/meta.yaml b/recipes/bioconductor-cancer/meta.yaml index 0c4f570b505ad..5035504046d86 100644 --- a/recipes/bioconductor-cancer/meta.yaml +++ b/recipes/bioconductor-cancer/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.16.0" %} +{% set version = "1.18.0" %} {% set name = "canceR" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 6194127d4d1248ea09dfcaa420cedb1e + md5: bf364aa1ed5ae2d3502f26e5a4e01bba build: number: 0 rpaths: @@ -20,11 +20,11 @@ build: # Suggests: testthat (>= 0.10.0), R.rsp requirements: host: - - 'bioconductor-biobase >=2.42.0,<2.43.0' - - 'bioconductor-genetclassifier >=1.22.0,<1.23.0' - - 'bioconductor-gseabase >=1.44.0,<1.45.0' - - 'bioconductor-gsealm >=1.42.0,<1.43.0' - - 'bioconductor-phenotest >=1.30.0,<1.31.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' + - 'bioconductor-genetclassifier >=1.24.0,<1.25.0' + - 'bioconductor-gseabase >=1.46.0,<1.47.0' + - 'bioconductor-gsealm >=1.44.0,<1.45.0' + - 'bioconductor-phenotest >=1.32.0,<1.33.0' - r-base - r-cgdsr - r-circlize @@ -36,11 +36,11 @@ requirements: - r-tcltk2 - r-tkrplot run: - - 'bioconductor-biobase >=2.42.0,<2.43.0' - - 'bioconductor-genetclassifier >=1.22.0,<1.23.0' - - 'bioconductor-gseabase >=1.44.0,<1.45.0' - - 'bioconductor-gsealm >=1.42.0,<1.43.0' - - 'bioconductor-phenotest >=1.30.0,<1.31.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' + - 'bioconductor-genetclassifier >=1.24.0,<1.25.0' + - 'bioconductor-gseabase >=1.46.0,<1.47.0' + - 'bioconductor-gsealm >=1.44.0,<1.45.0' + - 'bioconductor-phenotest >=1.32.0,<1.33.0' - r-base - r-cgdsr - r-circlize diff --git a/recipes/bioconductor-cancerclass/meta.yaml b/recipes/bioconductor-cancerclass/meta.yaml index 87a58892d74fe..b59ab8762a1bc 100644 --- a/recipes/bioconductor-cancerclass/meta.yaml +++ b/recipes/bioconductor-cancerclass/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.26.0" %} +{% set version = "1.28.0" %} {% set name = "cancerclass" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 046f83f4ae882a6cc05716c51e2cfee2 + md5: 96e541e72420dee85bc2abcb91ff3f36 build: number: 0 rpaths: @@ -19,11 +19,11 @@ build: # Suggests: cancerdata requirements: host: - - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' - r-base - r-binom run: - - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' - r-base - r-binom build: diff --git a/recipes/bioconductor-cancerdata/meta.yaml b/recipes/bioconductor-cancerdata/meta.yaml index 1830ca2a52c93..00a6a584b7e1e 100644 --- a/recipes/bioconductor-cancerdata/meta.yaml +++ b/recipes/bioconductor-cancerdata/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.20.0" %} +{% set version = "1.22.0" %} {% set name = "cancerdata" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 2fb3c2815ba70f6edcf0254c19afed66 + md5: e7527824c67a7dc60e2345b78ee01da7 build: number: 0 rpaths: @@ -19,12 +19,12 @@ build: noarch: generic requirements: host: - - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' - r-base run: - - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-cancerdata/post-link.sh b/recipes/bioconductor-cancerdata/post-link.sh index 86e4cc27ae742..62a48680917c4 100644 --- a/recipes/bioconductor-cancerdata/post-link.sh +++ b/recipes/bioconductor-cancerdata/post-link.sh @@ -1,11 +1,11 @@ #!/bin/bash -FN="cancerdata_1.20.0.tar.gz" +FN="cancerdata_1.22.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/experiment/src/contrib/cancerdata_1.20.0.tar.gz" - "https://bioarchive.galaxyproject.org/cancerdata_1.20.0.tar.gz" - "https://depot.galaxyproject.org/software/bioconductor-cancerdata/bioconductor-cancerdata_1.20.0_src_all.tar.gz" + "https://bioconductor.org/packages/3.9/data/experiment/src/contrib/cancerdata_1.22.0.tar.gz" + "https://bioarchive.galaxyproject.org/cancerdata_1.22.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-cancerdata/bioconductor-cancerdata_1.22.0_src_all.tar.gz" ) -MD5="2fb3c2815ba70f6edcf0254c19afed66" +MD5="e7527824c67a7dc60e2345b78ee01da7" # Use a staging area in the conda dir rather than temp dirs, both to avoid # permission issues as well as to have things downloaded in a predictable @@ -16,7 +16,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-cancerinsilico/meta.yaml b/recipes/bioconductor-cancerinsilico/meta.yaml index 47dfc45bbb3a0..c901bf3f83402 100644 --- a/recipes/bioconductor-cancerinsilico/meta.yaml +++ b/recipes/bioconductor-cancerinsilico/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "2.2.1" %} +{% set version = "2.4.0" %} {% set name = "CancerInSilico" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: a87a2d1778e80e9df154575bc9bc05d0 + md5: 19bdc49294e17f67b6cffbc0fd53e67b build: number: 0 rpaths: diff --git a/recipes/bioconductor-cancermutationanalysis/meta.yaml b/recipes/bioconductor-cancermutationanalysis/meta.yaml index 54d3fa32dbeca..31f8ae2fe958d 100644 --- a/recipes/bioconductor-cancermutationanalysis/meta.yaml +++ b/recipes/bioconductor-cancermutationanalysis/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.24.0" %} +{% set version = "1.26.0" %} {% set name = "CancerMutationAnalysis" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 6b4c874482fba54cb147332073586193 + md5: b68cb94aaffc396c1fb4db092acbae91 build: number: 0 rpaths: @@ -19,14 +19,14 @@ build: # Suggests: KEGG.db requirements: host: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' - - 'bioconductor-limma >=3.38.0,<3.39.0' - - 'bioconductor-qvalue >=2.14.0,<2.15.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' + - 'bioconductor-limma >=3.40.0,<3.41.0' + - 'bioconductor-qvalue >=2.16.0,<2.17.0' - r-base run: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' - - 'bioconductor-limma >=3.38.0,<3.39.0' - - 'bioconductor-qvalue >=2.14.0,<2.15.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' + - 'bioconductor-limma >=3.40.0,<3.41.0' + - 'bioconductor-qvalue >=2.16.0,<2.17.0' - r-base build: - {{ compiler('c') }} diff --git a/recipes/bioconductor-cancersubtypes/meta.yaml b/recipes/bioconductor-cancersubtypes/meta.yaml index 00a10ae771fa6..dfece30ba2130 100644 --- a/recipes/bioconductor-cancersubtypes/meta.yaml +++ b/recipes/bioconductor-cancersubtypes/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.8.0" %} +{% set version = "1.10.0" %} {% set name = "CancerSubtypes" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: f5f9711de5b16e3b4f2ddb908bc44aa7 + md5: cfa0a35941d1046859161ffd2fbacb9f build: number: 0 rpaths: @@ -20,9 +20,9 @@ build: # Suggests: BiocGenerics, RUnit, knitr, RTCGA.mRNA, RTCGA.clinical requirements: host: - - 'bioconductor-consensusclusterplus >=1.46.0,<1.47.0' - - 'bioconductor-impute >=1.56.0,<1.57.0' - - 'bioconductor-limma >=3.38.0,<3.39.0' + - 'bioconductor-consensusclusterplus >=1.48.0,<1.49.0' + - 'bioconductor-impute >=1.58.0,<1.59.0' + - 'bioconductor-limma >=3.40.0,<3.41.0' - r-base - r-cluster - r-icluster @@ -31,9 +31,9 @@ requirements: - r-snftool - r-survival run: - - 'bioconductor-consensusclusterplus >=1.46.0,<1.47.0' - - 'bioconductor-impute >=1.56.0,<1.57.0' - - 'bioconductor-limma >=3.38.0,<3.39.0' + - 'bioconductor-consensusclusterplus >=1.48.0,<1.49.0' + - 'bioconductor-impute >=1.58.0,<1.59.0' + - 'bioconductor-limma >=3.40.0,<3.41.0' - r-base - r-cluster - r-icluster diff --git a/recipes/bioconductor-cand/meta.yaml b/recipes/bioconductor-cand/meta.yaml index c6ba36df57a50..0586c99e87b7f 100644 --- a/recipes/bioconductor-cand/meta.yaml +++ b/recipes/bioconductor-cand/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.14.0" %} +{% set version = "1.16.0" %} {% set name = "CAnD" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: fd13a36a530e102aa5f1b9c2ba8eb65f + md5: b37b73d94fb166e98936f40b91f3f3f3 build: number: 0 rpaths: diff --git a/recipes/bioconductor-canine.db/meta.yaml b/recipes/bioconductor-canine.db/meta.yaml index 6e96260c1fc3f..f93bba976d643 100644 --- a/recipes/bioconductor-canine.db/meta.yaml +++ b/recipes/bioconductor-canine.db/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.2.3" %} {% set name = "canine.db" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -12,7 +12,7 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 313097118354c68b3b6fb348eb55720e build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ @@ -20,14 +20,14 @@ build: # Suggests: DBI, annotate, RUnit requirements: host: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' - - 'bioconductor-org.cf.eg.db >=3.7.0,<3.8.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' + - 'bioconductor-org.cf.eg.db >=3.8.0,<3.9.0' - r-base run: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' - - 'bioconductor-org.cf.eg.db >=3.7.0,<3.8.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' + - 'bioconductor-org.cf.eg.db >=3.8.0,<3.9.0' - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-canine.db/post-link.sh b/recipes/bioconductor-canine.db/post-link.sh index 8a443b6905c29..088020ede0f65 100644 --- a/recipes/bioconductor-canine.db/post-link.sh +++ b/recipes/bioconductor-canine.db/post-link.sh @@ -1,9 +1,10 @@ #!/bin/bash FN="canine.db_3.2.3.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/canine.db_3.2.3.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/canine.db_3.2.3.tar.gz" "https://bioarchive.galaxyproject.org/canine.db_3.2.3.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-canine.db/bioconductor-canine.db_3.2.3_src_all.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-canine.db/bioconductor-canine.db_3.2.3_src_all.tar.gz" ) MD5="313097118354c68b3b6fb348eb55720e" @@ -16,7 +17,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-canine.db0/meta.yaml b/recipes/bioconductor-canine.db0/meta.yaml index b057a8de02b7a..211ebc1206dda 100644 --- a/recipes/bioconductor-canine.db0/meta.yaml +++ b/recipes/bioconductor-canine.db0/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "3.7.1" %} +{% set version = "3.8.2" %} {% set name = "canine.db0" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: f2c7805b097ff757f07a47efcdd17f4f + md5: 56742a475a81dacaedd6c100df27eff0 build: number: 0 rpaths: @@ -19,12 +19,12 @@ build: noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' - r-base run: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-canine.db0/post-link.sh b/recipes/bioconductor-canine.db0/post-link.sh index 679bbf721d23b..0ea5cb0165c78 100644 --- a/recipes/bioconductor-canine.db0/post-link.sh +++ b/recipes/bioconductor-canine.db0/post-link.sh @@ -1,11 +1,11 @@ #!/bin/bash -FN="canine.db0_3.7.1.tar.gz" +FN="canine.db0_3.8.2.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/canine.db0_3.7.1.tar.gz" - "https://bioarchive.galaxyproject.org/canine.db0_3.7.1.tar.gz" - "https://depot.galaxyproject.org/software/bioconductor-canine.db0/bioconductor-canine.db0_3.7.1_src_all.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/canine.db0_3.8.2.tar.gz" + "https://bioarchive.galaxyproject.org/canine.db0_3.8.2.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-canine.db0/bioconductor-canine.db0_3.8.2_src_all.tar.gz" ) -MD5="f2c7805b097ff757f07a47efcdd17f4f" +MD5="56742a475a81dacaedd6c100df27eff0" # Use a staging area in the conda dir rather than temp dirs, both to avoid # permission issues as well as to have things downloaded in a predictable @@ -16,7 +16,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-canine2.db/meta.yaml b/recipes/bioconductor-canine2.db/meta.yaml index b18bddc919b40..76a819eef7fae 100644 --- a/recipes/bioconductor-canine2.db/meta.yaml +++ b/recipes/bioconductor-canine2.db/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.2.3" %} {% set name = "canine2.db" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -12,7 +12,7 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 5c393ea8e91c4d3eb08137bc2f301ca7 build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ @@ -20,14 +20,14 @@ build: # Suggests: DBI, annotate, RUnit requirements: host: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' - - 'bioconductor-org.cf.eg.db >=3.7.0,<3.8.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' + - 'bioconductor-org.cf.eg.db >=3.8.0,<3.9.0' - r-base run: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' - - 'bioconductor-org.cf.eg.db >=3.7.0,<3.8.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' + - 'bioconductor-org.cf.eg.db >=3.8.0,<3.9.0' - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-canine2.db/post-link.sh b/recipes/bioconductor-canine2.db/post-link.sh index f1dd2bc14bbdc..2503198f44cdb 100644 --- a/recipes/bioconductor-canine2.db/post-link.sh +++ b/recipes/bioconductor-canine2.db/post-link.sh @@ -1,9 +1,10 @@ #!/bin/bash FN="canine2.db_3.2.3.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/canine2.db_3.2.3.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/canine2.db_3.2.3.tar.gz" "https://bioarchive.galaxyproject.org/canine2.db_3.2.3.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-canine2.db/bioconductor-canine2.db_3.2.3_src_all.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-canine2.db/bioconductor-canine2.db_3.2.3_src_all.tar.gz" ) MD5="5c393ea8e91c4d3eb08137bc2f301ca7" @@ -16,7 +17,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-canine2cdf/meta.yaml b/recipes/bioconductor-canine2cdf/meta.yaml index 0afc2fd42139b..1bcc0449fa091 100644 --- a/recipes/bioconductor-canine2cdf/meta.yaml +++ b/recipes/bioconductor-canine2cdf/meta.yaml @@ -1,6 +1,6 @@ {% set version = "2.18.0" %} {% set name = "canine2cdf" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -12,19 +12,19 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 78740cde98c75e6680470564a4df74c3 build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' - r-base run: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-canine2cdf/post-link.sh b/recipes/bioconductor-canine2cdf/post-link.sh index 38f8978039d24..d59ab4ad7fd0f 100644 --- a/recipes/bioconductor-canine2cdf/post-link.sh +++ b/recipes/bioconductor-canine2cdf/post-link.sh @@ -1,9 +1,10 @@ #!/bin/bash FN="canine2cdf_2.18.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/canine2cdf_2.18.0.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/canine2cdf_2.18.0.tar.gz" "https://bioarchive.galaxyproject.org/canine2cdf_2.18.0.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-canine2cdf/bioconductor-canine2cdf_2.18.0_src_all.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-canine2cdf/bioconductor-canine2cdf_2.18.0_src_all.tar.gz" ) MD5="78740cde98c75e6680470564a4df74c3" @@ -16,7 +17,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-canine2probe/meta.yaml b/recipes/bioconductor-canine2probe/meta.yaml index 902ba243c21a1..98e0d86022110 100644 --- a/recipes/bioconductor-canine2probe/meta.yaml +++ b/recipes/bioconductor-canine2probe/meta.yaml @@ -1,6 +1,6 @@ {% set version = "2.18.0" %} {% set name = "canine2probe" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -12,19 +12,19 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 7de0f4ea616e8662dc2eaa9ab78d1f13 build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' - r-base run: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-canine2probe/post-link.sh b/recipes/bioconductor-canine2probe/post-link.sh index 8bf3e02d73a2b..48cea5e3dc09d 100644 --- a/recipes/bioconductor-canine2probe/post-link.sh +++ b/recipes/bioconductor-canine2probe/post-link.sh @@ -1,9 +1,10 @@ #!/bin/bash FN="canine2probe_2.18.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/canine2probe_2.18.0.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/canine2probe_2.18.0.tar.gz" "https://bioarchive.galaxyproject.org/canine2probe_2.18.0.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-canine2probe/bioconductor-canine2probe_2.18.0_src_all.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-canine2probe/bioconductor-canine2probe_2.18.0_src_all.tar.gz" ) MD5="7de0f4ea616e8662dc2eaa9ab78d1f13" @@ -16,7 +17,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-caninecdf/meta.yaml b/recipes/bioconductor-caninecdf/meta.yaml index aeb97a6b98f25..beebb3e4a3441 100644 --- a/recipes/bioconductor-caninecdf/meta.yaml +++ b/recipes/bioconductor-caninecdf/meta.yaml @@ -1,6 +1,6 @@ {% set version = "2.18.0" %} {% set name = "caninecdf" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -12,19 +12,19 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 656f845cc66890015a4e13c5304ec262 build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' - r-base run: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-caninecdf/post-link.sh b/recipes/bioconductor-caninecdf/post-link.sh index 93bed19dd6070..37620d1b080ba 100644 --- a/recipes/bioconductor-caninecdf/post-link.sh +++ b/recipes/bioconductor-caninecdf/post-link.sh @@ -1,9 +1,10 @@ #!/bin/bash FN="caninecdf_2.18.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/caninecdf_2.18.0.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/caninecdf_2.18.0.tar.gz" "https://bioarchive.galaxyproject.org/caninecdf_2.18.0.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-caninecdf/bioconductor-caninecdf_2.18.0_src_all.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-caninecdf/bioconductor-caninecdf_2.18.0_src_all.tar.gz" ) MD5="656f845cc66890015a4e13c5304ec262" @@ -16,7 +17,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-canineprobe/meta.yaml b/recipes/bioconductor-canineprobe/meta.yaml index bf637da974db7..43604203c215c 100644 --- a/recipes/bioconductor-canineprobe/meta.yaml +++ b/recipes/bioconductor-canineprobe/meta.yaml @@ -1,6 +1,6 @@ {% set version = "2.18.0" %} {% set name = "canineprobe" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -12,19 +12,19 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: e5467bc9b7e54c5adce6b409ba7df767 build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' - r-base run: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-canineprobe/post-link.sh b/recipes/bioconductor-canineprobe/post-link.sh index e0e06346be571..3c1a569e6a2b2 100644 --- a/recipes/bioconductor-canineprobe/post-link.sh +++ b/recipes/bioconductor-canineprobe/post-link.sh @@ -1,9 +1,10 @@ #!/bin/bash FN="canineprobe_2.18.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/canineprobe_2.18.0.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/canineprobe_2.18.0.tar.gz" "https://bioarchive.galaxyproject.org/canineprobe_2.18.0.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-canineprobe/bioconductor-canineprobe_2.18.0_src_all.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-canineprobe/bioconductor-canineprobe_2.18.0_src_all.tar.gz" ) MD5="e5467bc9b7e54c5adce6b409ba7df767" @@ -16,7 +17,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-caomicsv/meta.yaml b/recipes/bioconductor-caomicsv/meta.yaml index a7b71b58a6e48..1277f67c74a2e 100644 --- a/recipes/bioconductor-caomicsv/meta.yaml +++ b/recipes/bioconductor-caomicsv/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.12.1" %} +{% set version = "1.14.0" %} {% set name = "caOmicsV" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 1557453c140c78a3dde7d88e542031c7 + md5: 94c63ecbfe0401c88974fa774831ed1e build: number: 0 rpaths: diff --git a/recipes/bioconductor-cardinal/meta.yaml b/recipes/bioconductor-cardinal/meta.yaml index bcdfa85aca9fe..5fb65b79aae2b 100644 --- a/recipes/bioconductor-cardinal/meta.yaml +++ b/recipes/bioconductor-cardinal/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "2.0.4" %} +{% set version = "2.2.0" %} {% set name = "Cardinal" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,44 +10,52 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: f99423a9fdcb27ca44a9b6c5ebdd1a7b2daaebd8f8dc4963a356d79112ca2984 + md5: f48e36871776ac1321b1c6de73d23345 build: number: 0 rpaths: - lib/R/lib/ - lib/ -# Suggests: BiocStyle, testthat +# Suggests: BiocStyle, testthat, knitr, rmarkdown requirements: host: - - 'bioconductor-biobase >=2.42.0,<2.43.0' - - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' - - 'bioconductor-biocparallel >=1.16.0,<1.17.0' - - 'bioconductor-ebimage >=4.24.0,<4.25.0' - - 'bioconductor-matter >=1.8.0,<1.9.0' - - 'bioconductor-protgenerics >=1.14.0,<1.15.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' + - 'bioconductor-biocgenerics >=0.30.0,<0.31.0' + - 'bioconductor-biocparallel >=1.18.0,<1.19.0' + - 'bioconductor-ebimage >=4.26.0,<4.27.0' + - 'bioconductor-matter >=1.10.0,<1.11.0' + - 'bioconductor-protgenerics >=1.16.0,<1.17.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' - r-base - r-dplyr - r-irlba - r-lattice - r-magrittr + - r-matrix + - r-mclust + - r-nlme - r-signal - r-sp + - r-viridislite run: - - 'bioconductor-biobase >=2.42.0,<2.43.0' - - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' - - 'bioconductor-biocparallel >=1.16.0,<1.17.0' - - 'bioconductor-ebimage >=4.24.0,<4.25.0' - - 'bioconductor-matter >=1.8.0,<1.9.0' - - 'bioconductor-protgenerics >=1.14.0,<1.15.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' + - 'bioconductor-biocgenerics >=0.30.0,<0.31.0' + - 'bioconductor-biocparallel >=1.18.0,<1.19.0' + - 'bioconductor-ebimage >=4.26.0,<4.27.0' + - 'bioconductor-matter >=1.10.0,<1.11.0' + - 'bioconductor-protgenerics >=1.16.0,<1.17.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' - r-base - r-dplyr - r-irlba - r-lattice - r-magrittr + - r-matrix + - r-mclust + - r-nlme - r-signal - r-sp + - r-viridislite build: - {{ compiler('c') }} - {{ compiler('cxx') }} diff --git a/recipes/bioconductor-cardinalworkflows/meta.yaml b/recipes/bioconductor-cardinalworkflows/meta.yaml index 2ead086df4572..8e7ee81e28260 100644 --- a/recipes/bioconductor-cardinalworkflows/meta.yaml +++ b/recipes/bioconductor-cardinalworkflows/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.14.0" %} +{% set version = "1.16.0" %} {% set name = "CardinalWorkflows" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 5c7621b5e018a39a1dc3f2ea76532695 + md5: 1d61193cff92e95a54c8a79cf2148ba7 build: number: 0 rpaths: @@ -20,12 +20,12 @@ build: # Suggests: BiocStyle requirements: host: - - 'bioconductor-cardinal >=2.0.0,<2.1.0' + - 'bioconductor-cardinal >=2.2.0,<2.3.0' - r-base run: - - 'bioconductor-cardinal >=2.0.0,<2.1.0' + - 'bioconductor-cardinal >=2.2.0,<2.3.0' - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-cardinalworkflows/post-link.sh b/recipes/bioconductor-cardinalworkflows/post-link.sh index a36bd132eb299..4176d5c96401f 100644 --- a/recipes/bioconductor-cardinalworkflows/post-link.sh +++ b/recipes/bioconductor-cardinalworkflows/post-link.sh @@ -1,11 +1,11 @@ #!/bin/bash -FN="CardinalWorkflows_1.14.0.tar.gz" +FN="CardinalWorkflows_1.16.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/experiment/src/contrib/CardinalWorkflows_1.14.0.tar.gz" - "https://bioarchive.galaxyproject.org/CardinalWorkflows_1.14.0.tar.gz" - "https://depot.galaxyproject.org/software/bioconductor-cardinalworkflows/bioconductor-cardinalworkflows_1.14.0_src_all.tar.gz" + "https://bioconductor.org/packages/3.9/data/experiment/src/contrib/CardinalWorkflows_1.16.0.tar.gz" + "https://bioarchive.galaxyproject.org/CardinalWorkflows_1.16.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-cardinalworkflows/bioconductor-cardinalworkflows_1.16.0_src_all.tar.gz" ) -MD5="5c7621b5e018a39a1dc3f2ea76532695" +MD5="1d61193cff92e95a54c8a79cf2148ba7" # Use a staging area in the conda dir rather than temp dirs, both to avoid # permission issues as well as to have things downloaded in a predictable @@ -16,7 +16,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-casper/meta.yaml b/recipes/bioconductor-casper/meta.yaml index d4d50160598bb..3d1f8b68702ac 100644 --- a/recipes/bioconductor-casper/meta.yaml +++ b/recipes/bioconductor-casper/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "2.16.0" %} +{% set version = "2.18.0" %} {% set name = "casper" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: f6de73dd1b5f4e0ee0118b65837c547b + md5: 6217e8fdb4348566354428667313e3f4 build: number: 0 rpaths: @@ -18,18 +18,18 @@ build: - lib/ requirements: host: - - 'bioconductor-biobase >=2.42.0,<2.43.0' - - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' - - 'bioconductor-ebarrays >=2.46.0,<2.47.0' - - 'bioconductor-gaga >=2.28.0,<2.29.0' - - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' - - 'bioconductor-genomicfeatures >=1.34.0,<1.35.0' - - 'bioconductor-genomicranges >=1.34.0,<1.35.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-limma >=3.38.0,<3.39.0' - - 'bioconductor-rsamtools >=1.34.0,<1.35.0' - - 'bioconductor-rtracklayer >=1.42.0,<1.43.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' + - 'bioconductor-biocgenerics >=0.30.0,<0.31.0' + - 'bioconductor-ebarrays >=2.48.0,<2.49.0' + - 'bioconductor-gaga >=2.30.0,<2.31.0' + - 'bioconductor-genomeinfodb >=1.20.0,<1.21.0' + - 'bioconductor-genomicfeatures >=1.36.0,<1.37.0' + - 'bioconductor-genomicranges >=1.36.0,<1.37.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-limma >=3.40.0,<3.41.0' + - 'bioconductor-rsamtools >=2.0.0,<2.1.0' + - 'bioconductor-rtracklayer >=1.44.0,<1.45.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' - r-base - r-coda - r-gtools @@ -38,18 +38,18 @@ requirements: - r-survival - r-vgam run: - - 'bioconductor-biobase >=2.42.0,<2.43.0' - - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' - - 'bioconductor-ebarrays >=2.46.0,<2.47.0' - - 'bioconductor-gaga >=2.28.0,<2.29.0' - - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' - - 'bioconductor-genomicfeatures >=1.34.0,<1.35.0' - - 'bioconductor-genomicranges >=1.34.0,<1.35.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-limma >=3.38.0,<3.39.0' - - 'bioconductor-rsamtools >=1.34.0,<1.35.0' - - 'bioconductor-rtracklayer >=1.42.0,<1.43.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' + - 'bioconductor-biocgenerics >=0.30.0,<0.31.0' + - 'bioconductor-ebarrays >=2.48.0,<2.49.0' + - 'bioconductor-gaga >=2.30.0,<2.31.0' + - 'bioconductor-genomeinfodb >=1.20.0,<1.21.0' + - 'bioconductor-genomicfeatures >=1.36.0,<1.37.0' + - 'bioconductor-genomicranges >=1.36.0,<1.37.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-limma >=3.40.0,<3.41.0' + - 'bioconductor-rsamtools >=2.0.0,<2.1.0' + - 'bioconductor-rtracklayer >=1.44.0,<1.45.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' - r-base - r-coda - r-gtools diff --git a/recipes/bioconductor-catalyst/meta.yaml b/recipes/bioconductor-catalyst/meta.yaml index 41b5780bf7462..a8bfaccae9d60 100644 --- a/recipes/bioconductor-catalyst/meta.yaml +++ b/recipes/bioconductor-catalyst/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.6.0" %} +{% set version = "1.8.0" %} {% set name = "CATALYST" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,26 +10,29 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 023f69e0aaf615cfb1acc1efa8093b2f + md5: f0438af8c6a337b96c52bb5d190a5b1b build: number: 0 rpaths: - lib/R/lib/ - lib/ noarch: generic -# Suggests: BiocStyle, knitr, rmarkdown, testthat, diffcyt +# Suggests: BiocStyle, knitr, rmarkdown, testthat, diffcyt, umap requirements: host: - - 'bioconductor-biobase >=2.42.0,<2.43.0' - - 'bioconductor-complexheatmap >=1.20.0,<1.21.0' - - 'bioconductor-consensusclusterplus >=1.46.0,<1.47.0' - - 'bioconductor-flowcore >=1.48.0,<1.49.0' - - 'bioconductor-flowsom >=1.14.0,<1.15.0' - - 'bioconductor-limma >=3.38.0,<3.39.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' - - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' + - 'bioconductor-complexheatmap >=2.0.0,<2.1.0' + - 'bioconductor-consensusclusterplus >=1.48.0,<1.49.0' + - 'bioconductor-flowcore >=1.50.0,<1.51.0' + - 'bioconductor-flowsom >=1.16.0,<1.17.0' + - 'bioconductor-limma >=3.40.0,<3.41.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' + - 'bioconductor-scater >=1.12.0,<1.13.0' + - 'bioconductor-singlecellexperiment >=1.6.0,<1.7.0' + - 'bioconductor-summarizedexperiment >=1.14.0,<1.15.0' - r-base - r-circlize + - r-data.table - r-dplyr - r-drc - r-dt @@ -39,10 +42,10 @@ requirements: - r-gridextra - r-htmltools - r-magrittr - - r-matrix - r-matrixstats - r-nnls - r-plotly + - r-purrr - r-rcolorbrewer - r-reshape2 - r-rtsne @@ -51,18 +54,20 @@ requirements: - r-shinybs - r-shinydashboard - r-shinyjs - - r-tidyr run: - - 'bioconductor-biobase >=2.42.0,<2.43.0' - - 'bioconductor-complexheatmap >=1.20.0,<1.21.0' - - 'bioconductor-consensusclusterplus >=1.46.0,<1.47.0' - - 'bioconductor-flowcore >=1.48.0,<1.49.0' - - 'bioconductor-flowsom >=1.14.0,<1.15.0' - - 'bioconductor-limma >=3.38.0,<3.39.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' - - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' + - 'bioconductor-complexheatmap >=2.0.0,<2.1.0' + - 'bioconductor-consensusclusterplus >=1.48.0,<1.49.0' + - 'bioconductor-flowcore >=1.50.0,<1.51.0' + - 'bioconductor-flowsom >=1.16.0,<1.17.0' + - 'bioconductor-limma >=3.40.0,<3.41.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' + - 'bioconductor-scater >=1.12.0,<1.13.0' + - 'bioconductor-singlecellexperiment >=1.6.0,<1.7.0' + - 'bioconductor-summarizedexperiment >=1.14.0,<1.15.0' - r-base - r-circlize + - r-data.table - r-dplyr - r-drc - r-dt @@ -72,10 +77,10 @@ requirements: - r-gridextra - r-htmltools - r-magrittr - - r-matrix - r-matrixstats - r-nnls - r-plotly + - r-purrr - r-rcolorbrewer - r-reshape2 - r-rtsne @@ -84,7 +89,6 @@ requirements: - r-shinybs - r-shinydashboard - r-shinyjs - - r-tidyr test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-category/meta.yaml b/recipes/bioconductor-category/meta.yaml index fe1909125660d..6d229e59d44ad 100644 --- a/recipes/bioconductor-category/meta.yaml +++ b/recipes/bioconductor-category/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "2.48.0" %} +{% set version = "2.50.0" %} {% set name = "Category" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 062f06f66067dcbb4d21fe9dd714eff9 + md5: 610c7927a696661781795a3d1ca41539 build: number: 0 rpaths: @@ -20,26 +20,26 @@ build: # Suggests: EBarrays, ALL, Rgraphviz, RColorBrewer, xtable (>= 1.4-6), hgu95av2.db, KEGG.db, SNPchip, geneplotter, limma, lattice, RUnit, org.Sc.sgd.db, GOstats, GO.db requirements: host: - - 'bioconductor-annotate >=1.60.0,<1.61.0' - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' - - 'bioconductor-biobase >=2.42.0,<2.43.0' - - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' - - 'bioconductor-genefilter >=1.64.0,<1.65.0' - - 'bioconductor-graph >=1.60.0,<1.61.0' - - 'bioconductor-gseabase >=1.44.0,<1.45.0' - - 'bioconductor-rbgl >=1.58.0,<1.59.0' + - 'bioconductor-annotate >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' + - 'bioconductor-biocgenerics >=0.30.0,<0.31.0' + - 'bioconductor-genefilter >=1.66.0,<1.67.0' + - 'bioconductor-graph >=1.62.0,<1.63.0' + - 'bioconductor-gseabase >=1.46.0,<1.47.0' + - 'bioconductor-rbgl >=1.60.0,<1.61.0' - r-base - r-dbi - r-matrix run: - - 'bioconductor-annotate >=1.60.0,<1.61.0' - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' - - 'bioconductor-biobase >=2.42.0,<2.43.0' - - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' - - 'bioconductor-genefilter >=1.64.0,<1.65.0' - - 'bioconductor-graph >=1.60.0,<1.61.0' - - 'bioconductor-gseabase >=1.44.0,<1.45.0' - - 'bioconductor-rbgl >=1.58.0,<1.59.0' + - 'bioconductor-annotate >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' + - 'bioconductor-biocgenerics >=0.30.0,<0.31.0' + - 'bioconductor-genefilter >=1.66.0,<1.67.0' + - 'bioconductor-graph >=1.62.0,<1.63.0' + - 'bioconductor-gseabase >=1.46.0,<1.47.0' + - 'bioconductor-rbgl >=1.60.0,<1.61.0' - r-base - r-dbi - r-matrix diff --git a/recipes/bioconductor-categorycompare/meta.yaml b/recipes/bioconductor-categorycompare/meta.yaml index 802f4d8d2377b..b1a23137dd007 100644 --- a/recipes/bioconductor-categorycompare/meta.yaml +++ b/recipes/bioconductor-categorycompare/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.26.0" %} +{% set version = "1.28.0" %} {% set name = "categoryCompare" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 0651838e9b5b0d85c2100aee6deca3c7 + md5: d3bd6209e65811fef8df62ffb93bd150 build: number: 0 rpaths: @@ -21,31 +21,33 @@ build: # SystemRequirements: Cytoscape (>= 3.6.1) (if used for visualization of results, heavily suggested) requirements: host: - - 'bioconductor-annotate >=1.60.0,<1.61.0' - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' - - 'bioconductor-biobase >=2.42.0,<2.43.0' - - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' - - 'bioconductor-category >=2.48.0,<2.49.0' - - 'bioconductor-gostats >=2.48.0,<2.49.0' - - 'bioconductor-graph >=1.60.0,<1.61.0' - - 'bioconductor-gseabase >=1.44.0,<1.45.0' - - 'bioconductor-rcy3 >=2.2.0,<2.3.0' + - 'bioconductor-annotate >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' + - 'bioconductor-biocgenerics >=0.30.0,<0.31.0' + - 'bioconductor-category >=2.50.0,<2.51.0' + - 'bioconductor-gostats >=2.50.0,<2.51.0' + - 'bioconductor-graph >=1.62.0,<1.63.0' + - 'bioconductor-gseabase >=1.46.0,<1.47.0' + - 'bioconductor-rcy3 >=2.4.0,<2.5.0' - r-base - r-colorspace - r-hwriter + - cytoscape >=3.6.1 run: - - 'bioconductor-annotate >=1.60.0,<1.61.0' - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' - - 'bioconductor-biobase >=2.42.0,<2.43.0' - - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' - - 'bioconductor-category >=2.48.0,<2.49.0' - - 'bioconductor-gostats >=2.48.0,<2.49.0' - - 'bioconductor-graph >=1.60.0,<1.61.0' - - 'bioconductor-gseabase >=1.44.0,<1.45.0' - - 'bioconductor-rcy3 >=2.2.0,<2.3.0' + - 'bioconductor-annotate >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' + - 'bioconductor-biocgenerics >=0.30.0,<0.31.0' + - 'bioconductor-category >=2.50.0,<2.51.0' + - 'bioconductor-gostats >=2.50.0,<2.51.0' + - 'bioconductor-graph >=1.62.0,<1.63.0' + - 'bioconductor-gseabase >=1.46.0,<1.47.0' + - 'bioconductor-rcy3 >=2.4.0,<2.5.0' - r-base - r-colorspace - r-hwriter + - cytoscape >=3.6.1 test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-causalr/meta.yaml b/recipes/bioconductor-causalr/meta.yaml index ef1dc26fe4fac..1651ecc0e46f6 100644 --- a/recipes/bioconductor-causalr/meta.yaml +++ b/recipes/bioconductor-causalr/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.14.1" %} +{% set version = "1.16.0" %} {% set name = "CausalR" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,9 +10,9 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: b28781d608123d026005d9388166057d + md5: e1eee612fc9cb8f492e5d61d5cb07823 build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ diff --git a/recipes/bioconductor-cbaf/meta.yaml b/recipes/bioconductor-cbaf/meta.yaml index f21eb571010a6..7b5327ccc70c5 100644 --- a/recipes/bioconductor-cbaf/meta.yaml +++ b/recipes/bioconductor-cbaf/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.4.0" %} +{% set version = "1.6.0" %} {% set name = "cbaf" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: c9f3c048d7b4e87473f694c927c9dc71 + md5: 41ce506cab60b7ac4d85c024f43eca84 build: number: 0 rpaths: @@ -20,16 +20,16 @@ build: # Suggests: knitr, rmarkdown, BiocStyle requirements: host: - - 'bioconductor-biocfilecache >=1.6.0,<1.7.0' - - 'bioconductor-genefilter >=1.64.0,<1.65.0' + - 'bioconductor-biocfilecache >=1.8.0,<1.9.0' + - 'bioconductor-genefilter >=1.66.0,<1.67.0' - r-base - r-cgdsr - r-gplots - r-rcolorbrewer - r-xlsx run: - - 'bioconductor-biocfilecache >=1.6.0,<1.7.0' - - 'bioconductor-genefilter >=1.64.0,<1.65.0' + - 'bioconductor-biocfilecache >=1.8.0,<1.9.0' + - 'bioconductor-genefilter >=1.66.0,<1.67.0' - r-base - r-cgdsr - r-gplots diff --git a/recipes/bioconductor-ccdata/meta.yaml b/recipes/bioconductor-ccdata/meta.yaml index 0e0c56adc4b5e..27f374e640ecf 100644 --- a/recipes/bioconductor-ccdata/meta.yaml +++ b/recipes/bioconductor-ccdata/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.8.0" %} +{% set version = "1.10.0" %} {% set name = "ccdata" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 43a2ecfa4bf126deb0a2ef4abf1c349e + md5: 5b120a35642d1ef94a586f18fc5fc7d5 build: number: 0 rpaths: @@ -22,7 +22,7 @@ requirements: - r-base run: - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-ccdata/post-link.sh b/recipes/bioconductor-ccdata/post-link.sh index d993090a7a313..ba8347684d51d 100644 --- a/recipes/bioconductor-ccdata/post-link.sh +++ b/recipes/bioconductor-ccdata/post-link.sh @@ -1,11 +1,11 @@ #!/bin/bash -FN="ccdata_1.8.0.tar.gz" +FN="ccdata_1.10.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/experiment/src/contrib/ccdata_1.8.0.tar.gz" - "https://bioarchive.galaxyproject.org/ccdata_1.8.0.tar.gz" - "https://depot.galaxyproject.org/software/bioconductor-ccdata/bioconductor-ccdata_1.8.0_src_all.tar.gz" + "https://bioconductor.org/packages/3.9/data/experiment/src/contrib/ccdata_1.10.0.tar.gz" + "https://bioarchive.galaxyproject.org/ccdata_1.10.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-ccdata/bioconductor-ccdata_1.10.0_src_all.tar.gz" ) -MD5="43a2ecfa4bf126deb0a2ef4abf1c349e" +MD5="5b120a35642d1ef94a586f18fc5fc7d5" # Use a staging area in the conda dir rather than temp dirs, both to avoid # permission issues as well as to have things downloaded in a predictable @@ -16,7 +16,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-ccfindr/meta.yaml b/recipes/bioconductor-ccfindr/meta.yaml index 221a16bd17d0a..cc48952df7339 100644 --- a/recipes/bioconductor-ccfindr/meta.yaml +++ b/recipes/bioconductor-ccfindr/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.2.0" %} +{% set version = "1.4.0" %} {% set name = "ccfindR" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: d2dae166f7d062b6fe3aded90a1ba724 + md5: 13cbf66d6dfc90661a5b2b1604aa2f6b build: number: 0 rpaths: @@ -19,9 +19,9 @@ build: # Suggests: BiocStyle, knitr, rmarkdown requirements: host: - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' - - 'bioconductor-singlecellexperiment >=1.4.0,<1.5.0' - - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' + - 'bioconductor-singlecellexperiment >=1.6.0,<1.7.0' + - 'bioconductor-summarizedexperiment >=1.14.0,<1.15.0' - r-ape - r-base - r-gtools @@ -32,12 +32,10 @@ requirements: - r-rcppeigen - r-rmpi - r-rtsne - - gsl - - openblas run: - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' - - 'bioconductor-singlecellexperiment >=1.4.0,<1.5.0' - - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' + - 'bioconductor-singlecellexperiment >=1.6.0,<1.7.0' + - 'bioconductor-summarizedexperiment >=1.14.0,<1.15.0' - r-ape - r-base - r-gtools @@ -48,8 +46,6 @@ requirements: - r-rcppeigen - r-rmpi - r-rtsne - - gsl - - openblas build: - {{ compiler('c') }} - {{ compiler('cxx') }} diff --git a/recipes/bioconductor-ccl4/meta.yaml b/recipes/bioconductor-ccl4/meta.yaml index 7b796019164c2..4e764729a0313 100644 --- a/recipes/bioconductor-ccl4/meta.yaml +++ b/recipes/bioconductor-ccl4/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.20.0" %} +{% set version = "1.22.0" %} {% set name = "CCl4" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: f8e6ef164ec15f7b8af5bfcd78fcc34b + md5: 465604e9af49594dd9bfdfe6c059edc1 build: number: 0 rpaths: @@ -19,14 +19,14 @@ build: noarch: generic requirements: host: - - 'bioconductor-biobase >=2.42.0,<2.43.0' - - 'bioconductor-limma >=3.38.0,<3.39.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' + - 'bioconductor-limma >=3.40.0,<3.41.0' - r-base run: - - 'bioconductor-biobase >=2.42.0,<2.43.0' - - 'bioconductor-limma >=3.38.0,<3.39.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' + - 'bioconductor-limma >=3.40.0,<3.41.0' - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-ccl4/post-link.sh b/recipes/bioconductor-ccl4/post-link.sh index 3c72b4825ea52..96adbcab70c19 100644 --- a/recipes/bioconductor-ccl4/post-link.sh +++ b/recipes/bioconductor-ccl4/post-link.sh @@ -1,11 +1,11 @@ #!/bin/bash -FN="CCl4_1.20.0.tar.gz" +FN="CCl4_1.22.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/experiment/src/contrib/CCl4_1.20.0.tar.gz" - "https://bioarchive.galaxyproject.org/CCl4_1.20.0.tar.gz" - "https://depot.galaxyproject.org/software/bioconductor-ccl4/bioconductor-ccl4_1.20.0_src_all.tar.gz" + "https://bioconductor.org/packages/3.9/data/experiment/src/contrib/CCl4_1.22.0.tar.gz" + "https://bioarchive.galaxyproject.org/CCl4_1.22.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-ccl4/bioconductor-ccl4_1.22.0_src_all.tar.gz" ) -MD5="f8e6ef164ec15f7b8af5bfcd78fcc34b" +MD5="465604e9af49594dd9bfdfe6c059edc1" # Use a staging area in the conda dir rather than temp dirs, both to avoid # permission issues as well as to have things downloaded in a predictable @@ -16,7 +16,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-ccmap/meta.yaml b/recipes/bioconductor-ccmap/meta.yaml index 45b4bf36ee117..6824f07b913e4 100644 --- a/recipes/bioconductor-ccmap/meta.yaml +++ b/recipes/bioconductor-ccmap/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.8.0" %} +{% set version = "1.10.0" %} {% set name = "ccmap" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: d603b7771a6fac35514db7eb9818bf57 + md5: 4d904def7978b58e57ea2bd1a941179f build: number: 0 rpaths: @@ -20,8 +20,8 @@ build: # Suggests: crossmeta, knitr, rmarkdown, testthat, lydata requirements: host: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' - - 'bioconductor-ccdata >=1.8.0,<1.9.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' + - 'bioconductor-ccdata >=1.10.0,<1.11.0' - r-base - 'r-biocmanager >=1.24.0' - 'r-data.table >=1.10.4' @@ -30,8 +30,8 @@ requirements: - 'r-lsa >=0.73.1' - 'r-xgboost >=0.6.4' run: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' - - 'bioconductor-ccdata >=1.8.0,<1.9.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' + - 'bioconductor-ccdata >=1.10.0,<1.11.0' - r-base - 'r-biocmanager >=1.24.0' - 'r-data.table >=1.10.4' diff --git a/recipes/bioconductor-ccpromise/meta.yaml b/recipes/bioconductor-ccpromise/meta.yaml index 3255d36bc831d..89b0557d1ff77 100644 --- a/recipes/bioconductor-ccpromise/meta.yaml +++ b/recipes/bioconductor-ccpromise/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.8.0" %} +{% set version = "1.10.0" %} {% set name = "CCPROMISE" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 73f58481f1fabc4fbd97d0b1e9647071 + md5: c914d856d7feb2613b26d682f881a9ee build: number: 0 rpaths: @@ -19,15 +19,15 @@ build: noarch: generic requirements: host: - - 'bioconductor-biobase >=2.42.0,<2.43.0' - - 'bioconductor-gseabase >=1.44.0,<1.45.0' - - 'bioconductor-promise >=1.34.0,<1.35.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' + - 'bioconductor-gseabase >=1.46.0,<1.47.0' + - 'bioconductor-promise >=1.36.0,<1.37.0' - r-base - r-ccp run: - - 'bioconductor-biobase >=2.42.0,<2.43.0' - - 'bioconductor-gseabase >=1.44.0,<1.45.0' - - 'bioconductor-promise >=1.34.0,<1.35.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' + - 'bioconductor-gseabase >=1.46.0,<1.47.0' + - 'bioconductor-promise >=1.36.0,<1.37.0' - r-base - r-ccp test: diff --git a/recipes/bioconductor-ccrepe/meta.yaml b/recipes/bioconductor-ccrepe/meta.yaml index 15654e29d9973..1fd201bceccbe 100644 --- a/recipes/bioconductor-ccrepe/meta.yaml +++ b/recipes/bioconductor-ccrepe/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.18.1" %} +{% set version = "1.20.0" %} {% set name = "ccrepe" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 4a8ab1db992aa0909e6bc3917d7900b7 + md5: a6aec5acadb248eb94a14fa114bbc658 build: number: 0 rpaths: diff --git a/recipes/bioconductor-cctutorial/meta.yaml b/recipes/bioconductor-cctutorial/meta.yaml index 3ba732d14aa62..69a03dc773586 100644 --- a/recipes/bioconductor-cctutorial/meta.yaml +++ b/recipes/bioconductor-cctutorial/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.20.0" %} +{% set version = "1.22.0" %} {% set name = "ccTutorial" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: bf29fe20285bcedbd73d52a641ebb751 + md5: 9a7ab28f231b5b046e61a1fa80385ef3 build: number: 0 rpaths: @@ -20,18 +20,18 @@ build: # Suggests: biomaRt, Biobase(>= 2.5.5), xtable requirements: host: - - 'bioconductor-affy >=1.60.0,<1.61.0' - - 'bioconductor-biobase >=2.42.0,<2.43.0' - - 'bioconductor-ringo >=1.46.0,<1.47.0' - - 'bioconductor-topgo >=2.34.0,<2.35.0' + - 'bioconductor-affy >=1.62.0,<1.63.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' + - 'bioconductor-ringo >=1.48.0,<1.49.0' + - 'bioconductor-topgo >=2.36.0,<2.37.0' - r-base run: - - 'bioconductor-affy >=1.60.0,<1.61.0' - - 'bioconductor-biobase >=2.42.0,<2.43.0' - - 'bioconductor-ringo >=1.46.0,<1.47.0' - - 'bioconductor-topgo >=2.34.0,<2.35.0' + - 'bioconductor-affy >=1.62.0,<1.63.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' + - 'bioconductor-ringo >=1.48.0,<1.49.0' + - 'bioconductor-topgo >=2.36.0,<2.37.0' - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-cctutorial/post-link.sh b/recipes/bioconductor-cctutorial/post-link.sh index a6db3d439b25f..d98d83b43994b 100644 --- a/recipes/bioconductor-cctutorial/post-link.sh +++ b/recipes/bioconductor-cctutorial/post-link.sh @@ -1,11 +1,11 @@ #!/bin/bash -FN="ccTutorial_1.20.0.tar.gz" +FN="ccTutorial_1.22.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/experiment/src/contrib/ccTutorial_1.20.0.tar.gz" - "https://bioarchive.galaxyproject.org/ccTutorial_1.20.0.tar.gz" - "https://depot.galaxyproject.org/software/bioconductor-cctutorial/bioconductor-cctutorial_1.20.0_src_all.tar.gz" + "https://bioconductor.org/packages/3.9/data/experiment/src/contrib/ccTutorial_1.22.0.tar.gz" + "https://bioarchive.galaxyproject.org/ccTutorial_1.22.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-cctutorial/bioconductor-cctutorial_1.22.0_src_all.tar.gz" ) -MD5="bf29fe20285bcedbd73d52a641ebb751" +MD5="9a7ab28f231b5b046e61a1fa80385ef3" # Use a staging area in the conda dir rather than temp dirs, both to avoid # permission issues as well as to have things downloaded in a predictable @@ -16,7 +16,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-celaref/meta.yaml b/recipes/bioconductor-celaref/meta.yaml index 0ec433e941990..a893707152ccd 100644 --- a/recipes/bioconductor-celaref/meta.yaml +++ b/recipes/bioconductor-celaref/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.0.0" %} +{% set version = "1.2.0" %} {% set name = "celaref" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,20 +10,21 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: d19bfcefa4ddc3730276a4b44b81ba18 + md5: 050a0789e0fa54d29ff8ddb134e05710 build: number: 0 rpaths: - lib/R/lib/ - lib/ noarch: generic -# Suggests: limma, parallel, knitr, rmarkdown, ExperimentHub +# Suggests: limma, parallel, knitr, rmarkdown, ExperimentHub, testthat requirements: host: - - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' - - 'bioconductor-mast >=1.8.0,<1.9.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' - - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' + - 'bioconductor-biocgenerics >=0.30.0,<0.31.0' + - 'bioconductor-delayedarray >=0.10.0,<0.11.0' + - 'bioconductor-mast >=1.10.0,<1.11.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' + - 'bioconductor-summarizedexperiment >=1.14.0,<1.15.0' - r-base - r-dplyr - r-ggplot2 @@ -33,10 +34,11 @@ requirements: - r-rlang - r-tibble run: - - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' - - 'bioconductor-mast >=1.8.0,<1.9.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' - - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' + - 'bioconductor-biocgenerics >=0.30.0,<0.31.0' + - 'bioconductor-delayedarray >=0.10.0,<0.11.0' + - 'bioconductor-mast >=1.10.0,<1.11.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' + - 'bioconductor-summarizedexperiment >=1.14.0,<1.15.0' - r-base - r-dplyr - r-ggplot2 diff --git a/recipes/bioconductor-celarefdata/meta.yaml b/recipes/bioconductor-celarefdata/meta.yaml index 99df8611a3a57..25e25e50c92e4 100644 --- a/recipes/bioconductor-celarefdata/meta.yaml +++ b/recipes/bioconductor-celarefdata/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.0.0" %} +{% set version = "1.2.0" %} {% set name = "celarefData" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: fcf4c1723f025947fa6012f02e2aa33c + md5: 45c742f3a1047a409cc2ab112c2712e7 build: number: 0 rpaths: @@ -23,7 +23,7 @@ requirements: - r-base run: - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-celarefdata/post-link.sh b/recipes/bioconductor-celarefdata/post-link.sh index 1859b9b54adc2..f4d8fc87f3a80 100644 --- a/recipes/bioconductor-celarefdata/post-link.sh +++ b/recipes/bioconductor-celarefdata/post-link.sh @@ -1,11 +1,11 @@ #!/bin/bash -FN="celarefData_1.0.0.tar.gz" +FN="celarefData_1.2.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/experiment/src/contrib/celarefData_1.0.0.tar.gz" - "https://bioarchive.galaxyproject.org/celarefData_1.0.0.tar.gz" - "https://depot.galaxyproject.org/software/bioconductor-celarefdata/bioconductor-celarefdata_1.0.0_src_all.tar.gz" + "https://bioconductor.org/packages/3.9/data/experiment/src/contrib/celarefData_1.2.0.tar.gz" + "https://bioarchive.galaxyproject.org/celarefData_1.2.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-celarefdata/bioconductor-celarefdata_1.2.0_src_all.tar.gz" ) -MD5="fcf4c1723f025947fa6012f02e2aa33c" +MD5="45c742f3a1047a409cc2ab112c2712e7" # Use a staging area in the conda dir rather than temp dirs, both to avoid # permission issues as well as to have things downloaded in a predictable @@ -16,7 +16,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-celda/build.sh b/recipes/bioconductor-celda/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-celda/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-celda/meta.yaml b/recipes/bioconductor-celda/meta.yaml new file mode 100644 index 0000000000000..5f5186fbff6a4 --- /dev/null +++ b/recipes/bioconductor-celda/meta.yaml @@ -0,0 +1,82 @@ +{% set version = "1.0.0" %} +{% set name = "celda" %} +{% set bioc = "3.9" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + md5: 3ebbc9c388bfabc68ede6165fd4a675f +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ +# Suggests: testthat, knitr, roxygen2, rmarkdown, corrplot, Matrix, biomaRt, covr, M3DExampleData, BiocManager, BiocStyle +requirements: + host: + - 'bioconductor-mast >=1.10.0,<1.11.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' + - 'bioconductor-summarizedexperiment >=1.14.0,<1.15.0' + - r-base + - r-data.table + - r-digest + - r-doparallel + - r-enrichr + - r-foreach + - r-ggplot2 + - r-ggrepel + - r-gridextra + - r-gtable + - r-matrixstats + - r-mcmcprecision + - r-plyr + - r-rcolorbrewer + - r-rcpp + - r-rcppeigen + - r-reshape2 + - r-rtsne + - r-scales + - r-stringi + - r-umap + run: + - 'bioconductor-mast >=1.10.0,<1.11.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' + - 'bioconductor-summarizedexperiment >=1.14.0,<1.15.0' + - r-base + - r-data.table + - r-digest + - r-doparallel + - r-enrichr + - r-foreach + - r-ggplot2 + - r-ggrepel + - r-gridextra + - r-gtable + - r-matrixstats + - r-mcmcprecision + - r-plyr + - r-rcolorbrewer + - r-rcpp + - r-rcppeigen + - r-reshape2 + - r-rtsne + - r-scales + - r-stringi + - r-umap + build: + - {{ compiler('c') }} + - {{ compiler('cxx') }} + - make +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: 'MIT + file LICENSE' + summary: 'celda leverages Bayesian hierarchical modeling to cluster genes, cells, or both simultaneously from single cell sequencing data.' + diff --git a/recipes/bioconductor-celegans.db/meta.yaml b/recipes/bioconductor-celegans.db/meta.yaml index 31ee2555f7880..ee139285499ff 100644 --- a/recipes/bioconductor-celegans.db/meta.yaml +++ b/recipes/bioconductor-celegans.db/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.2.3" %} {% set name = "celegans.db" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -12,7 +12,7 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: fb4631ee29a20c20d5766aed4c04cac1 build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ @@ -20,14 +20,14 @@ build: # Suggests: DBI, annotate, RUnit requirements: host: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' - - 'bioconductor-org.ce.eg.db >=3.7.0,<3.8.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' + - 'bioconductor-org.ce.eg.db >=3.8.0,<3.9.0' - r-base run: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' - - 'bioconductor-org.ce.eg.db >=3.7.0,<3.8.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' + - 'bioconductor-org.ce.eg.db >=3.8.0,<3.9.0' - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-celegans.db/post-link.sh b/recipes/bioconductor-celegans.db/post-link.sh index 32c78c87b4d04..8e59fb6c11acb 100644 --- a/recipes/bioconductor-celegans.db/post-link.sh +++ b/recipes/bioconductor-celegans.db/post-link.sh @@ -1,9 +1,10 @@ #!/bin/bash FN="celegans.db_3.2.3.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/celegans.db_3.2.3.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/celegans.db_3.2.3.tar.gz" "https://bioarchive.galaxyproject.org/celegans.db_3.2.3.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-celegans.db/bioconductor-celegans.db_3.2.3_src_all.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-celegans.db/bioconductor-celegans.db_3.2.3_src_all.tar.gz" ) MD5="fb4631ee29a20c20d5766aed4c04cac1" @@ -16,7 +17,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-celeganscdf/meta.yaml b/recipes/bioconductor-celeganscdf/meta.yaml index 586ccb512e9f3..c69c8e448bf89 100644 --- a/recipes/bioconductor-celeganscdf/meta.yaml +++ b/recipes/bioconductor-celeganscdf/meta.yaml @@ -1,6 +1,6 @@ {% set version = "2.18.0" %} {% set name = "celeganscdf" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -12,19 +12,19 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 1098cd99bfc5000bf9858e4a3acaf452 build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' - r-base run: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-celeganscdf/post-link.sh b/recipes/bioconductor-celeganscdf/post-link.sh index 5b6c47b20da91..751e28c19b1f8 100644 --- a/recipes/bioconductor-celeganscdf/post-link.sh +++ b/recipes/bioconductor-celeganscdf/post-link.sh @@ -1,9 +1,10 @@ #!/bin/bash FN="celeganscdf_2.18.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/celeganscdf_2.18.0.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/celeganscdf_2.18.0.tar.gz" "https://bioarchive.galaxyproject.org/celeganscdf_2.18.0.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-celeganscdf/bioconductor-celeganscdf_2.18.0_src_all.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-celeganscdf/bioconductor-celeganscdf_2.18.0_src_all.tar.gz" ) MD5="1098cd99bfc5000bf9858e4a3acaf452" @@ -16,7 +17,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-celegansprobe/meta.yaml b/recipes/bioconductor-celegansprobe/meta.yaml index 9dd5d3cbdd8b0..bd8a7d77eeafb 100644 --- a/recipes/bioconductor-celegansprobe/meta.yaml +++ b/recipes/bioconductor-celegansprobe/meta.yaml @@ -1,6 +1,6 @@ {% set version = "2.18.0" %} {% set name = "celegansprobe" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -12,19 +12,19 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 7454bba10ff2dd7c03bfe0f9d450f148 build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' - r-base run: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-celegansprobe/post-link.sh b/recipes/bioconductor-celegansprobe/post-link.sh index 32c59e2cd641b..a6ddb57cec9ec 100644 --- a/recipes/bioconductor-celegansprobe/post-link.sh +++ b/recipes/bioconductor-celegansprobe/post-link.sh @@ -1,9 +1,10 @@ #!/bin/bash FN="celegansprobe_2.18.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/celegansprobe_2.18.0.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/celegansprobe_2.18.0.tar.gz" "https://bioarchive.galaxyproject.org/celegansprobe_2.18.0.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-celegansprobe/bioconductor-celegansprobe_2.18.0_src_all.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-celegansprobe/bioconductor-celegansprobe_2.18.0_src_all.tar.gz" ) MD5="7454bba10ff2dd7c03bfe0f9d450f148" @@ -16,7 +17,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-cellbaser/meta.yaml b/recipes/bioconductor-cellbaser/meta.yaml index 763bfd6026732..26dd2e734d69e 100644 --- a/recipes/bioconductor-cellbaser/meta.yaml +++ b/recipes/bioconductor-cellbaser/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.6.0" %} +{% set version = "1.8.0" %} {% set name = "cellbaseR" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 9078d93a013e860fe491397e945ddd0a + md5: 50b708255d2fa47c96c4db9d5918ec85 build: number: 0 rpaths: @@ -20,8 +20,8 @@ build: # Suggests: BiocStyle, knitr, rmarkdown, Gviz, VariantAnnotation requirements: host: - - 'bioconductor-biocparallel >=1.16.0,<1.17.0' - - 'bioconductor-rsamtools >=1.34.0,<1.35.0' + - 'bioconductor-biocparallel >=1.18.0,<1.19.0' + - 'bioconductor-rsamtools >=2.0.0,<2.1.0' - r-base - r-data.table - r-doparallel @@ -32,8 +32,8 @@ requirements: - r-r.utils - r-tidyr run: - - 'bioconductor-biocparallel >=1.16.0,<1.17.0' - - 'bioconductor-rsamtools >=1.34.0,<1.35.0' + - 'bioconductor-biocparallel >=1.18.0,<1.19.0' + - 'bioconductor-rsamtools >=2.0.0,<2.1.0' - r-base - r-data.table - r-doparallel diff --git a/recipes/bioconductor-cellbench/build.sh b/recipes/bioconductor-cellbench/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-cellbench/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-cellbench/meta.yaml b/recipes/bioconductor-cellbench/meta.yaml new file mode 100644 index 0000000000000..56c2a80825e63 --- /dev/null +++ b/recipes/bioconductor-cellbench/meta.yaml @@ -0,0 +1,59 @@ +{% set version = "1.0.0" %} +{% set name = "CellBench" %} +{% set bioc = "3.9" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: a77973ea7c9f31801559a17a7251af96 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: BiocStyle, covr, knitr, rmarkdown, testthat, limma, ggplot2 +requirements: + host: + - 'bioconductor-biocfilecache >=1.8.0,<1.9.0' + - 'bioconductor-biocparallel >=1.18.0,<1.19.0' + - 'bioconductor-singlecellexperiment >=1.6.0,<1.7.0' + - r-base + - r-dplyr + - r-glue + - r-lubridate + - r-magrittr + - r-memoise + - 'r-purrr >=0.3.0' + - r-rappdirs + - r-rlang + - r-tibble + - r-tidyr + run: + - 'bioconductor-biocfilecache >=1.8.0,<1.9.0' + - 'bioconductor-biocparallel >=1.18.0,<1.19.0' + - 'bioconductor-singlecellexperiment >=1.6.0,<1.7.0' + - r-base + - r-dplyr + - r-glue + - r-lubridate + - r-magrittr + - r-memoise + - 'r-purrr >=0.3.0' + - r-rappdirs + - r-rlang + - r-tibble + - r-tidyr +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: GPL-3 + summary: 'This package contains infrastructure for benchmarking analysis methods and access to single cell mixture benchmarking data. It provides a framework for organising analysis methods and testing combinations of methods in a pipeline without explicitly laying out each combination. It also provides utilities for sampling and filtering SingleCellExperiment objects, constructing lists of functions with varying parameters, and multithreaded evaluation of analysis methods.' + diff --git a/recipes/bioconductor-cellgrowth/meta.yaml b/recipes/bioconductor-cellgrowth/meta.yaml index 5c0e9f1393e7d..4706304871547 100644 --- a/recipes/bioconductor-cellgrowth/meta.yaml +++ b/recipes/bioconductor-cellgrowth/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.26.1" %} +{% set version = "1.28.0" %} {% set name = "cellGrowth" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 1d0750c5cdb6784f3a972f2e195377c6 + md5: 25a0f256421f38c8a6fd36b95900aacc build: number: 0 rpaths: diff --git a/recipes/bioconductor-cellhts2/meta.yaml b/recipes/bioconductor-cellhts2/meta.yaml index d449342d967aa..69c4406d12299 100644 --- a/recipes/bioconductor-cellhts2/meta.yaml +++ b/recipes/bioconductor-cellhts2/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "2.46.0" %} +{% set version = "2.48.0" %} {% set name = "cellHTS2" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: b0b4a06e25549a92e8239883e2fb533b + md5: 47d1c36b22194c71761ee17bf05f35b0 build: number: 0 rpaths: @@ -20,27 +20,27 @@ build: # Suggests: ggplot2 requirements: host: - - 'bioconductor-biobase >=2.42.0,<2.43.0' - - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' - - 'bioconductor-category >=2.48.0,<2.49.0' - - 'bioconductor-genefilter >=1.64.0,<1.65.0' - - 'bioconductor-gseabase >=1.44.0,<1.45.0' - - 'bioconductor-prada >=1.58.0,<1.59.0' - - 'bioconductor-splots >=1.48.0,<1.49.0' - - 'bioconductor-vsn >=3.50.0,<3.51.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' + - 'bioconductor-biocgenerics >=0.30.0,<0.31.0' + - 'bioconductor-category >=2.50.0,<2.51.0' + - 'bioconductor-genefilter >=1.66.0,<1.67.0' + - 'bioconductor-gseabase >=1.46.0,<1.47.0' + - 'bioconductor-prada >=1.60.0,<1.61.0' + - 'bioconductor-splots >=1.50.0,<1.51.0' + - 'bioconductor-vsn >=3.52.0,<3.53.0' - r-base - r-hwriter - r-locfit - r-rcolorbrewer run: - - 'bioconductor-biobase >=2.42.0,<2.43.0' - - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' - - 'bioconductor-category >=2.48.0,<2.49.0' - - 'bioconductor-genefilter >=1.64.0,<1.65.0' - - 'bioconductor-gseabase >=1.44.0,<1.45.0' - - 'bioconductor-prada >=1.58.0,<1.59.0' - - 'bioconductor-splots >=1.48.0,<1.49.0' - - 'bioconductor-vsn >=3.50.0,<3.51.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' + - 'bioconductor-biocgenerics >=0.30.0,<0.31.0' + - 'bioconductor-category >=2.50.0,<2.51.0' + - 'bioconductor-genefilter >=1.66.0,<1.67.0' + - 'bioconductor-gseabase >=1.46.0,<1.47.0' + - 'bioconductor-prada >=1.60.0,<1.61.0' + - 'bioconductor-splots >=1.50.0,<1.51.0' + - 'bioconductor-vsn >=3.52.0,<3.53.0' - r-base - r-hwriter - r-locfit diff --git a/recipes/bioconductor-cellity/meta.yaml b/recipes/bioconductor-cellity/meta.yaml index 57561730b97a8..ac9e5e84ba86a 100644 --- a/recipes/bioconductor-cellity/meta.yaml +++ b/recipes/bioconductor-cellity/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.10.0" %} +{% set version = "1.12.0" %} {% set name = "cellity" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: f3b201ec288008e1ecba4a4937573082 + md5: 292c57c85e717761e9acefbfab0e4894 build: number: 0 rpaths: @@ -20,20 +20,20 @@ build: # Suggests: BiocStyle, caret, knitr, testthat, rmarkdown requirements: host: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' - - 'bioconductor-org.hs.eg.db >=3.7.0,<3.8.0' - - 'bioconductor-org.mm.eg.db >=3.7.0,<3.8.0' - - 'bioconductor-topgo >=2.34.0,<2.35.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' + - 'bioconductor-org.hs.eg.db >=3.8.0,<3.9.0' + - 'bioconductor-org.mm.eg.db >=3.8.0,<3.9.0' + - 'bioconductor-topgo >=2.36.0,<2.37.0' - r-base - r-e1071 - r-ggplot2 - r-mvoutlier - r-robustbase run: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' - - 'bioconductor-org.hs.eg.db >=3.7.0,<3.8.0' - - 'bioconductor-org.mm.eg.db >=3.7.0,<3.8.0' - - 'bioconductor-topgo >=2.34.0,<2.35.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' + - 'bioconductor-org.hs.eg.db >=3.8.0,<3.9.0' + - 'bioconductor-org.mm.eg.db >=3.8.0,<3.9.0' + - 'bioconductor-topgo >=2.36.0,<2.37.0' - r-base - r-e1071 - r-ggplot2 diff --git a/recipes/bioconductor-cellmapper/meta.yaml b/recipes/bioconductor-cellmapper/meta.yaml index 90906331e98cb..81793ec006681 100644 --- a/recipes/bioconductor-cellmapper/meta.yaml +++ b/recipes/bioconductor-cellmapper/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.8.0" %} +{% set version = "1.10.0" %} {% set name = "CellMapper" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: a7a9cd05f7a9f5fad346faf0cdbd8224 + md5: 46b337915bc344f73f8942e2f20f7f09 build: number: 0 rpaths: @@ -20,10 +20,10 @@ build: # Suggests: CellMapperData, Biobase, HumanAffyData, ALL, BiocStyle, ExperimentHub requirements: host: - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' - r-base run: - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' - r-base test: commands: diff --git a/recipes/bioconductor-cellmapperdata/meta.yaml b/recipes/bioconductor-cellmapperdata/meta.yaml index b9abbf5412dbd..47cc9d7f94302 100644 --- a/recipes/bioconductor-cellmapperdata/meta.yaml +++ b/recipes/bioconductor-cellmapperdata/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.8.0" %} +{% set version = "1.10.0" %} {% set name = "CellMapperData" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: ac7ff311f02953168d5cb3f829fd1e1c + md5: ad6ececf308dc29a5ebc1e56a6bf7632 build: number: 0 rpaths: @@ -20,14 +20,14 @@ build: # Suggests: BiocStyle requirements: host: - - 'bioconductor-cellmapper >=1.8.0,<1.9.0' - - 'bioconductor-experimenthub >=1.8.0,<1.9.0' + - 'bioconductor-cellmapper >=1.10.0,<1.11.0' + - 'bioconductor-experimenthub >=1.10.0,<1.11.0' - r-base run: - - 'bioconductor-cellmapper >=1.8.0,<1.9.0' - - 'bioconductor-experimenthub >=1.8.0,<1.9.0' + - 'bioconductor-cellmapper >=1.10.0,<1.11.0' + - 'bioconductor-experimenthub >=1.10.0,<1.11.0' - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-cellmapperdata/post-link.sh b/recipes/bioconductor-cellmapperdata/post-link.sh index 1b1de2c5f9880..8171103a1dce2 100644 --- a/recipes/bioconductor-cellmapperdata/post-link.sh +++ b/recipes/bioconductor-cellmapperdata/post-link.sh @@ -1,11 +1,11 @@ #!/bin/bash -FN="CellMapperData_1.8.0.tar.gz" +FN="CellMapperData_1.10.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/experiment/src/contrib/CellMapperData_1.8.0.tar.gz" - "https://bioarchive.galaxyproject.org/CellMapperData_1.8.0.tar.gz" - "https://depot.galaxyproject.org/software/bioconductor-cellmapperdata/bioconductor-cellmapperdata_1.8.0_src_all.tar.gz" + "https://bioconductor.org/packages/3.9/data/experiment/src/contrib/CellMapperData_1.10.0.tar.gz" + "https://bioarchive.galaxyproject.org/CellMapperData_1.10.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-cellmapperdata/bioconductor-cellmapperdata_1.10.0_src_all.tar.gz" ) -MD5="ac7ff311f02953168d5cb3f829fd1e1c" +MD5="ad6ececf308dc29a5ebc1e56a6bf7632" # Use a staging area in the conda dir rather than temp dirs, both to avoid # permission issues as well as to have things downloaded in a predictable @@ -16,7 +16,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-cellmixs/build.sh b/recipes/bioconductor-cellmixs/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-cellmixs/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-cellmixs/meta.yaml b/recipes/bioconductor-cellmixs/meta.yaml new file mode 100644 index 0000000000000..80e177b249589 --- /dev/null +++ b/recipes/bioconductor-cellmixs/meta.yaml @@ -0,0 +1,63 @@ +{% set version = "1.0.0" %} +{% set name = "CellMixS" %} +{% set bioc = "3.9" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: 2cbd063d78358d8bbaa59042397917ec +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: BiocStyle, knitr, rmarkdown, testthat, limma +requirements: + host: + - 'bioconductor-biocneighbors >=1.2.0,<1.3.0' + - 'bioconductor-biocparallel >=1.18.0,<1.19.0' + - 'bioconductor-scater >=1.12.0,<1.13.0' + - 'bioconductor-singlecellexperiment >=1.6.0,<1.7.0' + - 'bioconductor-summarizedexperiment >=1.14.0,<1.15.0' + - r-base + - r-cowplot + - r-dplyr + - r-ggplot2 + - r-ggridges + - r-ksamples + - r-listarrays + - r-magrittr + - r-purrr + - r-tidyr + - r-viridis + run: + - 'bioconductor-biocneighbors >=1.2.0,<1.3.0' + - 'bioconductor-biocparallel >=1.18.0,<1.19.0' + - 'bioconductor-scater >=1.12.0,<1.13.0' + - 'bioconductor-singlecellexperiment >=1.6.0,<1.7.0' + - 'bioconductor-summarizedexperiment >=1.14.0,<1.15.0' + - r-base + - r-cowplot + - r-dplyr + - r-ggplot2 + - r-ggridges + - r-ksamples + - r-listarrays + - r-magrittr + - r-purrr + - r-tidyr + - r-viridis +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: 'GPL (>=2)' + summary: 'Evaluate Cellspecific Mixing Scores (CMS) for different batches/groups in scRNA-seq data.' + diff --git a/recipes/bioconductor-cellnoptr/meta.yaml b/recipes/bioconductor-cellnoptr/meta.yaml index 29f3596e35d71..10946dea52724 100644 --- a/recipes/bioconductor-cellnoptr/meta.yaml +++ b/recipes/bioconductor-cellnoptr/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.28.0" %} +{% set version = "1.30.0" %} {% set name = "CellNOptR" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,33 +10,41 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 896919b3c3f1d53863345c5afb1d3a69 + md5: 9b0dba0616690fed7ae50cc60e5def8a build: number: 0 rpaths: - lib/R/lib/ - lib/ -# Suggests: RUnit, BiocGenerics, igraph, stringi, stringr +# Suggests: data.table, plyr, dplyr, tidyr, readr, RUnit, BiocGenerics, # SystemRequirements: Graphviz version >= 2.2 requirements: host: - - 'bioconductor-graph >=1.60.0,<1.61.0' - - 'bioconductor-rbgl >=1.58.0,<1.59.0' - - 'bioconductor-rgraphviz >=2.26.0,<2.27.0' + - 'bioconductor-graph >=1.62.0,<1.63.0' + - 'bioconductor-rbgl >=1.60.0,<1.61.0' + - 'bioconductor-rgraphviz >=2.28.0,<2.29.0' - r-base - r-ggplot2 - r-hash + - r-igraph - r-rcurl + - r-stringi + - r-stringr - r-xml + - graphviz >=2.2 run: - - 'bioconductor-graph >=1.60.0,<1.61.0' - - 'bioconductor-rbgl >=1.58.0,<1.59.0' - - 'bioconductor-rgraphviz >=2.26.0,<2.27.0' + - 'bioconductor-graph >=1.62.0,<1.63.0' + - 'bioconductor-rbgl >=1.60.0,<1.61.0' + - 'bioconductor-rgraphviz >=2.28.0,<2.29.0' - r-base - r-ggplot2 - r-hash + - r-igraph - r-rcurl + - r-stringi + - r-stringr - r-xml + - graphviz >=2.2 build: - {{ compiler('c') }} - make diff --git a/recipes/bioconductor-cellscape/meta.yaml b/recipes/bioconductor-cellscape/meta.yaml index 1f67b4dc0f7ad..f53d087c2b92c 100644 --- a/recipes/bioconductor-cellscape/meta.yaml +++ b/recipes/bioconductor-cellscape/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.6.0" %} +{% set version = "1.8.0" %} {% set name = "cellscape" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: fca7882d296832aed78b674d1bb92f18 + md5: a3879c530dadeea94b728acea78ef4cc build: number: 0 rpaths: diff --git a/recipes/bioconductor-cellscore/meta.yaml b/recipes/bioconductor-cellscore/meta.yaml index 1851641bac91e..fbc67f5f7464d 100644 --- a/recipes/bioconductor-cellscore/meta.yaml +++ b/recipes/bioconductor-cellscore/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.2.0" %} +{% set version = "1.4.0" %} {% set name = "CellScore" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: e9b84c8c0cbd7bbe43cbe7c71af89342 + md5: a574b7a8e836c7ab3c26c00a14810ac0 build: number: 0 rpaths: @@ -20,14 +20,14 @@ build: # Suggests: hgu133plus2CellScore, knitr requirements: host: - - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' - r-base - 'r-gplots >=3.0.1' - 'r-lsa >=0.73.1' - 'r-rcolorbrewer >=1.1-2' - 'r-squash >=1.0.8' run: - - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' - r-base - 'r-gplots >=3.0.1' - 'r-lsa >=0.73.1' diff --git a/recipes/bioconductor-celltrails/meta.yaml b/recipes/bioconductor-celltrails/meta.yaml index 789e7edc792de..bc9df5bb5e8b0 100644 --- a/recipes/bioconductor-celltrails/meta.yaml +++ b/recipes/bioconductor-celltrails/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.0.0" %} +{% set version = "1.2.0" %} {% set name = "CellTrails" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: ae463a8b64790828bda20cc7d0521655 + md5: e64c7c273fb506b9cc1931e4ec63558d build: number: 0 rpaths: @@ -20,10 +20,10 @@ build: # Suggests: AnnotationDbi, destiny, RUnit, scater, scran, knitr, org.Mm.eg.db, rmarkdown requirements: host: - - 'bioconductor-biobase >=2.42.0,<2.43.0' - - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' - - 'bioconductor-singlecellexperiment >=1.4.0,<1.5.0' - - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' + - 'bioconductor-biocgenerics >=0.30.0,<0.31.0' + - 'bioconductor-singlecellexperiment >=1.6.0,<1.7.0' + - 'bioconductor-summarizedexperiment >=1.14.0,<1.15.0' - r-base - r-cba - r-dendextend @@ -37,10 +37,10 @@ requirements: - r-reshape2 - r-rtsne run: - - 'bioconductor-biobase >=2.42.0,<2.43.0' - - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' - - 'bioconductor-singlecellexperiment >=1.4.0,<1.5.0' - - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' + - 'bioconductor-biocgenerics >=0.30.0,<0.31.0' + - 'bioconductor-singlecellexperiment >=1.6.0,<1.7.0' + - 'bioconductor-summarizedexperiment >=1.14.0,<1.15.0' - r-base - r-cba - r-dendextend diff --git a/recipes/bioconductor-celltree/meta.yaml b/recipes/bioconductor-celltree/meta.yaml index b70794a49087f..052a363877d0a 100644 --- a/recipes/bioconductor-celltree/meta.yaml +++ b/recipes/bioconductor-celltree/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.12.0" %} +{% set version = "1.14.0" %} {% set name = "cellTree" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: d9840be22b8ca149f718dc8f5d7a07c7 + md5: 0d509562248089909780d86511d479f6 build: number: 0 rpaths: @@ -20,7 +20,7 @@ build: # Suggests: BiocStyle, knitr, HSMMSingleCell, biomaRt, org.Hs.eg.db, Biobase, tools requirements: host: - - 'bioconductor-topgo >=2.34.0,<2.35.0' + - 'bioconductor-topgo >=2.36.0,<2.37.0' - r-base - r-gplots - r-igraph @@ -29,7 +29,7 @@ requirements: - r-topicmodels - r-xtable run: - - 'bioconductor-topgo >=2.34.0,<2.35.0' + - 'bioconductor-topgo >=2.36.0,<2.37.0' - r-base - r-gplots - r-igraph diff --git a/recipes/bioconductor-cemitool/meta.yaml b/recipes/bioconductor-cemitool/meta.yaml index 9e9429ff5664e..d8240fd3738f3 100644 --- a/recipes/bioconductor-cemitool/meta.yaml +++ b/recipes/bioconductor-cemitool/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.6.10" %} +{% set version = "1.8.0" %} {% set name = "CEMiTool" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 5eacaa2f654c93c4e0c816397df1607e + md5: 865a41a9b9aa8bce4c9c2db3ec55bd64 build: number: 0 rpaths: @@ -20,10 +20,10 @@ build: # Suggests: testthat, BiocManager requirements: host: - - 'bioconductor-clusterprofiler >=3.10.0,<3.11.0' - - 'bioconductor-fgsea >=1.8.0,<1.9.0' - - 'bioconductor-geneoverlap >=1.18.0,<1.19.0' - - 'bioconductor-limma >=3.38.0,<3.39.0' + - 'bioconductor-clusterprofiler >=3.12.0,<3.13.0' + - 'bioconductor-fgsea >=1.10.0,<1.11.0' + - 'bioconductor-geneoverlap >=1.20.0,<1.21.0' + - 'bioconductor-limma >=3.40.0,<3.41.0' - r-base - 'r-data.table >=1.9.4' - r-dplyr @@ -54,10 +54,10 @@ requirements: - r-tidyr - r-wgcna run: - - 'bioconductor-clusterprofiler >=3.10.0,<3.11.0' - - 'bioconductor-fgsea >=1.8.0,<1.9.0' - - 'bioconductor-geneoverlap >=1.18.0,<1.19.0' - - 'bioconductor-limma >=3.38.0,<3.39.0' + - 'bioconductor-clusterprofiler >=3.12.0,<3.13.0' + - 'bioconductor-fgsea >=1.10.0,<1.11.0' + - 'bioconductor-geneoverlap >=1.20.0,<1.21.0' + - 'bioconductor-limma >=3.40.0,<3.41.0' - r-base - 'r-data.table >=1.9.4' - r-dplyr diff --git a/recipes/bioconductor-ceu1kg/meta.yaml b/recipes/bioconductor-ceu1kg/meta.yaml index 16e7c5b072082..946c47efe384b 100644 --- a/recipes/bioconductor-ceu1kg/meta.yaml +++ b/recipes/bioconductor-ceu1kg/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "0.20.0" %} +{% set version = "0.22.0" %} {% set name = "ceu1kg" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 039d5e0ba8ee673cbd97d636f30d379e + md5: c755c9ed3fded070eb1c8acb518e3d15 build: number: 0 rpaths: @@ -20,16 +20,16 @@ build: # Suggests: SNPlocs.Hsapiens.dbSNP.20101109 requirements: host: - - 'bioconductor-biobase >=2.42.0,<2.43.0' - - 'bioconductor-ggbase >=3.44.0,<3.45.0' - - 'bioconductor-ggtools >=5.18.0,<5.19.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' + - 'bioconductor-ggbase >=3.46.0,<3.47.0' + - 'bioconductor-ggtools >=5.20.0,<5.21.0' - r-base run: - - 'bioconductor-biobase >=2.42.0,<2.43.0' - - 'bioconductor-ggbase >=3.44.0,<3.45.0' - - 'bioconductor-ggtools >=5.18.0,<5.19.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' + - 'bioconductor-ggbase >=3.46.0,<3.47.0' + - 'bioconductor-ggtools >=5.20.0,<5.21.0' - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-ceu1kg/post-link.sh b/recipes/bioconductor-ceu1kg/post-link.sh index 9dee80c1528fc..e5ca29fd6f298 100644 --- a/recipes/bioconductor-ceu1kg/post-link.sh +++ b/recipes/bioconductor-ceu1kg/post-link.sh @@ -1,11 +1,11 @@ #!/bin/bash -FN="ceu1kg_0.20.0.tar.gz" +FN="ceu1kg_0.22.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/experiment/src/contrib/ceu1kg_0.20.0.tar.gz" - "https://bioarchive.galaxyproject.org/ceu1kg_0.20.0.tar.gz" - "https://depot.galaxyproject.org/software/bioconductor-ceu1kg/bioconductor-ceu1kg_0.20.0_src_all.tar.gz" + "https://bioconductor.org/packages/3.9/data/experiment/src/contrib/ceu1kg_0.22.0.tar.gz" + "https://bioarchive.galaxyproject.org/ceu1kg_0.22.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-ceu1kg/bioconductor-ceu1kg_0.22.0_src_all.tar.gz" ) -MD5="039d5e0ba8ee673cbd97d636f30d379e" +MD5="c755c9ed3fded070eb1c8acb518e3d15" # Use a staging area in the conda dir rather than temp dirs, both to avoid # permission issues as well as to have things downloaded in a predictable @@ -16,7 +16,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-ceu1kgv/meta.yaml b/recipes/bioconductor-ceu1kgv/meta.yaml index e0100536c73ce..0fbeae1fd422c 100644 --- a/recipes/bioconductor-ceu1kgv/meta.yaml +++ b/recipes/bioconductor-ceu1kgv/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "0.24.0" %} +{% set version = "0.26.0" %} {% set name = "ceu1kgv" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: c972c7288208ef044f986bbfd8fab71c + md5: 287b778e75815512fa403979131b628d build: number: 0 rpaths: @@ -19,14 +19,14 @@ build: noarch: generic requirements: host: - - 'bioconductor-biobase >=2.42.0,<2.43.0' - - 'bioconductor-ggbase >=3.44.0,<3.45.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' + - 'bioconductor-ggbase >=3.46.0,<3.47.0' - r-base run: - - 'bioconductor-biobase >=2.42.0,<2.43.0' - - 'bioconductor-ggbase >=3.44.0,<3.45.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' + - 'bioconductor-ggbase >=3.46.0,<3.47.0' - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-ceu1kgv/post-link.sh b/recipes/bioconductor-ceu1kgv/post-link.sh index 5ac623df8befe..8b10ceecf731f 100644 --- a/recipes/bioconductor-ceu1kgv/post-link.sh +++ b/recipes/bioconductor-ceu1kgv/post-link.sh @@ -1,11 +1,11 @@ #!/bin/bash -FN="ceu1kgv_0.24.0.tar.gz" +FN="ceu1kgv_0.26.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/experiment/src/contrib/ceu1kgv_0.24.0.tar.gz" - "https://bioarchive.galaxyproject.org/ceu1kgv_0.24.0.tar.gz" - "https://depot.galaxyproject.org/software/bioconductor-ceu1kgv/bioconductor-ceu1kgv_0.24.0_src_all.tar.gz" + "https://bioconductor.org/packages/3.9/data/experiment/src/contrib/ceu1kgv_0.26.0.tar.gz" + "https://bioarchive.galaxyproject.org/ceu1kgv_0.26.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-ceu1kgv/bioconductor-ceu1kgv_0.26.0_src_all.tar.gz" ) -MD5="c972c7288208ef044f986bbfd8fab71c" +MD5="287b778e75815512fa403979131b628d" # Use a staging area in the conda dir rather than temp dirs, both to avoid # permission issues as well as to have things downloaded in a predictable @@ -16,7 +16,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-ceuhm3/meta.yaml b/recipes/bioconductor-ceuhm3/meta.yaml index 1937bb99e7b1b..e10af411e80a0 100644 --- a/recipes/bioconductor-ceuhm3/meta.yaml +++ b/recipes/bioconductor-ceuhm3/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "0.20.0" %} +{% set version = "0.22.0" %} {% set name = "ceuhm3" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 0255a0481a74261e5d40cbc1c00bd46f + md5: c3036effe82163927a9658279be42c81 build: number: 0 rpaths: @@ -19,16 +19,16 @@ build: noarch: generic requirements: host: - - 'bioconductor-biobase >=2.42.0,<2.43.0' - - 'bioconductor-ggbase >=3.44.0,<3.45.0' - - 'bioconductor-ggtools >=5.18.0,<5.19.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' + - 'bioconductor-ggbase >=3.46.0,<3.47.0' + - 'bioconductor-ggtools >=5.20.0,<5.21.0' - r-base run: - - 'bioconductor-biobase >=2.42.0,<2.43.0' - - 'bioconductor-ggbase >=3.44.0,<3.45.0' - - 'bioconductor-ggtools >=5.18.0,<5.19.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' + - 'bioconductor-ggbase >=3.46.0,<3.47.0' + - 'bioconductor-ggtools >=5.20.0,<5.21.0' - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-ceuhm3/post-link.sh b/recipes/bioconductor-ceuhm3/post-link.sh index 5570db21a6baa..d1c57583e50ca 100644 --- a/recipes/bioconductor-ceuhm3/post-link.sh +++ b/recipes/bioconductor-ceuhm3/post-link.sh @@ -1,11 +1,11 @@ #!/bin/bash -FN="ceuhm3_0.20.0.tar.gz" +FN="ceuhm3_0.22.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/experiment/src/contrib/ceuhm3_0.20.0.tar.gz" - "https://bioarchive.galaxyproject.org/ceuhm3_0.20.0.tar.gz" - "https://depot.galaxyproject.org/software/bioconductor-ceuhm3/bioconductor-ceuhm3_0.20.0_src_all.tar.gz" + "https://bioconductor.org/packages/3.9/data/experiment/src/contrib/ceuhm3_0.22.0.tar.gz" + "https://bioarchive.galaxyproject.org/ceuhm3_0.22.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-ceuhm3/bioconductor-ceuhm3_0.22.0_src_all.tar.gz" ) -MD5="0255a0481a74261e5d40cbc1c00bd46f" +MD5="c3036effe82163927a9658279be42c81" # Use a staging area in the conda dir rather than temp dirs, both to avoid # permission issues as well as to have things downloaded in a predictable @@ -16,7 +16,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-cexor/meta.yaml b/recipes/bioconductor-cexor/meta.yaml index 5ab15527834ee..240fd526337b0 100644 --- a/recipes/bioconductor-cexor/meta.yaml +++ b/recipes/bioconductor-cexor/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.20.0" %} +{% set version = "1.22.0" %} {% set name = "CexoR" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: adc301c13a685ebcb765a611268f6612 + md5: d511dfadd09f06ab9ab73f2de560b815 build: number: 0 rpaths: @@ -20,24 +20,24 @@ build: # Suggests: RUnit, BiocGenerics, BiocStyle requirements: host: - - 'bioconductor-genomation >=1.14.0,<1.15.0' - - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' - - 'bioconductor-genomicranges >=1.34.0,<1.35.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-rsamtools >=1.34.0,<1.35.0' - - 'bioconductor-rtracklayer >=1.42.0,<1.43.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-genomation >=1.16.0,<1.17.0' + - 'bioconductor-genomeinfodb >=1.20.0,<1.21.0' + - 'bioconductor-genomicranges >=1.36.0,<1.37.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-rsamtools >=2.0.0,<2.1.0' + - 'bioconductor-rtracklayer >=1.44.0,<1.45.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' - r-base - r-idr - r-rcolorbrewer run: - - 'bioconductor-genomation >=1.14.0,<1.15.0' - - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' - - 'bioconductor-genomicranges >=1.34.0,<1.35.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-rsamtools >=1.34.0,<1.35.0' - - 'bioconductor-rtracklayer >=1.42.0,<1.43.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-genomation >=1.16.0,<1.17.0' + - 'bioconductor-genomeinfodb >=1.20.0,<1.21.0' + - 'bioconductor-genomicranges >=1.36.0,<1.37.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-rsamtools >=2.0.0,<2.1.0' + - 'bioconductor-rtracklayer >=1.44.0,<1.45.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' - r-base - r-idr - r-rcolorbrewer diff --git a/recipes/bioconductor-cfassay/meta.yaml b/recipes/bioconductor-cfassay/meta.yaml index c7443080a6bd7..69ad0c05e7f4e 100644 --- a/recipes/bioconductor-cfassay/meta.yaml +++ b/recipes/bioconductor-cfassay/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.16.1" %} +{% set version = "1.18.0" %} {% set name = "CFAssay" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 8ed2b2e9908e3cf38d77a8747dd6a409 + md5: c0704e737f2e2b56f14e679d98a7b092 build: number: 0 rpaths: diff --git a/recipes/bioconductor-cgdv17/meta.yaml b/recipes/bioconductor-cgdv17/meta.yaml index 7dde6bf14ac01..6c17db2571d8b 100644 --- a/recipes/bioconductor-cgdv17/meta.yaml +++ b/recipes/bioconductor-cgdv17/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "0.20.0" %} +{% set version = "0.22.0" %} {% set name = "cgdv17" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: f099ccc73aef5fb29585a9f7a026f29f + md5: f7d6c5564f18afe12623a4b6f184e787 build: number: 0 rpaths: @@ -20,22 +20,22 @@ build: # Suggests: parallel, GGtools, TxDb.Hsapiens.UCSC.hg19.knownGene, org.Hs.eg.db, illuminaHumanv1.db requirements: host: - - 'bioconductor-biobase >=2.42.0,<2.43.0' - - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' - - 'bioconductor-genomicranges >=1.34.0,<1.35.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' - - 'bioconductor-variantannotation >=1.28.0,<1.29.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' + - 'bioconductor-biocgenerics >=0.30.0,<0.31.0' + - 'bioconductor-genomicranges >=1.36.0,<1.37.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' + - 'bioconductor-variantannotation >=1.30.0,<1.31.0' - r-base run: - - 'bioconductor-biobase >=2.42.0,<2.43.0' - - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' - - 'bioconductor-genomicranges >=1.34.0,<1.35.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' - - 'bioconductor-variantannotation >=1.28.0,<1.29.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' + - 'bioconductor-biocgenerics >=0.30.0,<0.31.0' + - 'bioconductor-genomicranges >=1.36.0,<1.37.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' + - 'bioconductor-variantannotation >=1.30.0,<1.31.0' - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-cgdv17/post-link.sh b/recipes/bioconductor-cgdv17/post-link.sh index a3b38f46eb94b..d0d13be6e5359 100644 --- a/recipes/bioconductor-cgdv17/post-link.sh +++ b/recipes/bioconductor-cgdv17/post-link.sh @@ -1,11 +1,11 @@ #!/bin/bash -FN="cgdv17_0.20.0.tar.gz" +FN="cgdv17_0.22.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/experiment/src/contrib/cgdv17_0.20.0.tar.gz" - "https://bioarchive.galaxyproject.org/cgdv17_0.20.0.tar.gz" - "https://depot.galaxyproject.org/software/bioconductor-cgdv17/bioconductor-cgdv17_0.20.0_src_all.tar.gz" + "https://bioconductor.org/packages/3.9/data/experiment/src/contrib/cgdv17_0.22.0.tar.gz" + "https://bioarchive.galaxyproject.org/cgdv17_0.22.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-cgdv17/bioconductor-cgdv17_0.22.0_src_all.tar.gz" ) -MD5="f099ccc73aef5fb29585a9f7a026f29f" +MD5="f7d6c5564f18afe12623a4b6f184e787" # Use a staging area in the conda dir rather than temp dirs, both to avoid # permission issues as well as to have things downloaded in a predictable @@ -16,7 +16,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-cgen/meta.yaml b/recipes/bioconductor-cgen/meta.yaml index 8354391ad1caf..2a79648eb3eb4 100644 --- a/recipes/bioconductor-cgen/meta.yaml +++ b/recipes/bioconductor-cgen/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "3.18.0" %} +{% set version = "3.20.0" %} {% set name = "CGEN" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 8de652a5e02f957223ebbe1923ed9886 + md5: 767b43ecdbf0996bfd4cca6de398c669 build: number: 0 rpaths: diff --git a/recipes/bioconductor-cghbase/meta.yaml b/recipes/bioconductor-cghbase/meta.yaml index 1f2ed670a0338..536903adfe7ed 100644 --- a/recipes/bioconductor-cghbase/meta.yaml +++ b/recipes/bioconductor-cghbase/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.42.0" %} +{% set version = "1.44.0" %} {% set name = "CGHbase" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 8e5a1db8a434a7a03a7f0298a6e466a1 + md5: 6407dc3137d1d4cdbea47d20cb2a2a81 build: number: 0 rpaths: @@ -19,12 +19,12 @@ build: noarch: generic requirements: host: - - 'bioconductor-biobase >=2.42.0,<2.43.0' - - 'bioconductor-marray >=1.60.0,<1.61.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' + - 'bioconductor-marray >=1.62.0,<1.63.0' - r-base run: - - 'bioconductor-biobase >=2.42.0,<2.43.0' - - 'bioconductor-marray >=1.60.0,<1.61.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' + - 'bioconductor-marray >=1.62.0,<1.63.0' - r-base test: commands: diff --git a/recipes/bioconductor-cghcall/meta.yaml b/recipes/bioconductor-cghcall/meta.yaml index 120bc58d2b5c2..5246d656d93ea 100644 --- a/recipes/bioconductor-cghcall/meta.yaml +++ b/recipes/bioconductor-cghcall/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "2.44.0" %} +{% set version = "2.46.0" %} {% set name = "CGHcall" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,26 +10,26 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 6adfe221a755373d03ab61d68c575c06 + md5: 892aae691ef9ebd057fa867b487e309e build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ noarch: generic requirements: host: - - 'bioconductor-biobase >=2.42.0,<2.43.0' - - 'bioconductor-cghbase >=1.42.0,<1.43.0' - - 'bioconductor-dnacopy >=1.56.0,<1.57.0' - - 'bioconductor-impute >=1.56.0,<1.57.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' + - 'bioconductor-cghbase >=1.44.0,<1.45.0' + - 'bioconductor-dnacopy >=1.58.0,<1.59.0' + - 'bioconductor-impute >=1.58.0,<1.59.0' - r-base - r-snowfall run: - - 'bioconductor-biobase >=2.42.0,<2.43.0' - - 'bioconductor-cghbase >=1.42.0,<1.43.0' - - 'bioconductor-dnacopy >=1.56.0,<1.57.0' - - 'bioconductor-impute >=1.56.0,<1.57.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' + - 'bioconductor-cghbase >=1.44.0,<1.45.0' + - 'bioconductor-dnacopy >=1.58.0,<1.59.0' + - 'bioconductor-impute >=1.58.0,<1.59.0' - r-base - r-snowfall test: diff --git a/recipes/bioconductor-cghmcr/meta.yaml b/recipes/bioconductor-cghmcr/meta.yaml index 7b9a8e3bd36a5..df6299994da22 100644 --- a/recipes/bioconductor-cghmcr/meta.yaml +++ b/recipes/bioconductor-cghmcr/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.40.0" %} +{% set version = "1.42.0" %} {% set name = "cghMCR" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: ee9010fd0cda4e0454890e547be251fa + md5: eaf9fbdce3b0f3a370e021769e05db83 build: number: 0 rpaths: @@ -19,16 +19,16 @@ build: noarch: generic requirements: host: - - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' - - 'bioconductor-cntools >=1.38.0,<1.39.0' - - 'bioconductor-dnacopy >=1.56.0,<1.57.0' - - 'bioconductor-limma >=3.38.0,<3.39.0' + - 'bioconductor-biocgenerics >=0.30.0,<0.31.0' + - 'bioconductor-cntools >=1.40.0,<1.41.0' + - 'bioconductor-dnacopy >=1.58.0,<1.59.0' + - 'bioconductor-limma >=3.40.0,<3.41.0' - r-base run: - - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' - - 'bioconductor-cntools >=1.38.0,<1.39.0' - - 'bioconductor-dnacopy >=1.56.0,<1.57.0' - - 'bioconductor-limma >=3.38.0,<3.39.0' + - 'bioconductor-biocgenerics >=0.30.0,<0.31.0' + - 'bioconductor-cntools >=1.40.0,<1.41.0' + - 'bioconductor-dnacopy >=1.58.0,<1.59.0' + - 'bioconductor-limma >=3.40.0,<3.41.0' - r-base test: commands: diff --git a/recipes/bioconductor-cghnormaliter/meta.yaml b/recipes/bioconductor-cghnormaliter/meta.yaml index b9e3f21cc4ece..a3e761b8fc4ca 100644 --- a/recipes/bioconductor-cghnormaliter/meta.yaml +++ b/recipes/bioconductor-cghnormaliter/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.36.0" %} +{% set version = "1.38.0" %} {% set name = "CGHnormaliter" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 864c1f86399bde28c8deea6390e8f03f + md5: ced0a49c575405ab70d0728b3b32a9f9 build: number: 0 rpaths: @@ -19,14 +19,14 @@ build: noarch: generic requirements: host: - - 'bioconductor-biobase >=2.42.0,<2.43.0' - - 'bioconductor-cghbase >=1.42.0,<1.43.0' - - 'bioconductor-cghcall >=2.44.0,<2.45.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' + - 'bioconductor-cghbase >=1.44.0,<1.45.0' + - 'bioconductor-cghcall >=2.46.0,<2.47.0' - r-base run: - - 'bioconductor-biobase >=2.42.0,<2.43.0' - - 'bioconductor-cghbase >=1.42.0,<1.43.0' - - 'bioconductor-cghcall >=2.44.0,<2.45.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' + - 'bioconductor-cghbase >=1.44.0,<1.45.0' + - 'bioconductor-cghcall >=2.46.0,<2.47.0' - r-base test: commands: diff --git a/recipes/bioconductor-cghregions/meta.yaml b/recipes/bioconductor-cghregions/meta.yaml index 337ee48b81f81..4986f6df4d728 100644 --- a/recipes/bioconductor-cghregions/meta.yaml +++ b/recipes/bioconductor-cghregions/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.40.0" %} +{% set version = "1.42.0" %} {% set name = "CGHregions" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 83a3b0748e057ec4ca72aa1866f9b030 + md5: 78e9736273b569e7f6eba6f2024f2a40 build: number: 0 rpaths: @@ -19,12 +19,12 @@ build: noarch: generic requirements: host: - - 'bioconductor-biobase >=2.42.0,<2.43.0' - - 'bioconductor-cghbase >=1.42.0,<1.43.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' + - 'bioconductor-cghbase >=1.44.0,<1.45.0' - r-base run: - - 'bioconductor-biobase >=2.42.0,<2.43.0' - - 'bioconductor-cghbase >=1.42.0,<1.43.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' + - 'bioconductor-cghbase >=1.44.0,<1.45.0' - r-base test: commands: diff --git a/recipes/bioconductor-champ/meta.yaml b/recipes/bioconductor-champ/meta.yaml index 18818562707ac..2380007ba96ae 100644 --- a/recipes/bioconductor-champ/meta.yaml +++ b/recipes/bioconductor-champ/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "2.12.2" %} +{% set version = "2.14.0" %} {% set name = "ChAMP" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: ceb70607b5f5384692320a6264b0a635 + md5: c9aee84f402874745f1c5289f6de38b3 build: number: 0 rpaths: @@ -20,28 +20,28 @@ build: # Suggests: knitr,rmarkdown requirements: host: - - 'bioconductor-bumphunter >=1.24.0,<1.25.0' - - 'bioconductor-champdata >=2.14.0,<2.15.0' - - 'bioconductor-dmrcate >=1.18.0,<1.19.0' - - 'bioconductor-dnacopy >=1.56.0,<1.57.0' - - 'bioconductor-fem >=3.10.0,<3.11.0' - - 'bioconductor-genomicranges >=1.34.0,<1.35.0' - - 'bioconductor-globaltest >=5.36.0,<5.37.0' - - 'bioconductor-goseq >=1.34.0,<1.35.0' - - 'bioconductor-illumina450probevariants.db >=1.18.0,<1.19.0' + - 'bioconductor-bumphunter >=1.26.0,<1.27.0' + - 'bioconductor-champdata >=2.16.0,<2.17.0' + - 'bioconductor-dmrcate >=1.20.0,<1.21.0' + - 'bioconductor-dnacopy >=1.58.0,<1.59.0' + - 'bioconductor-fem >=3.12.0,<3.13.0' + - 'bioconductor-genomicranges >=1.36.0,<1.37.0' + - 'bioconductor-globaltest >=5.38.0,<5.39.0' + - 'bioconductor-goseq >=1.36.0,<1.37.0' + - 'bioconductor-illumina450probevariants.db >=1.20.0,<1.21.0' - 'bioconductor-illuminahumanmethylation450kmanifest >=0.4.0,<0.5.0' - 'bioconductor-illuminahumanmethylationepicanno.ilm10b2.hg19 >=0.6.0,<0.7.0' - - 'bioconductor-illuminahumanmethylationepicmanifest >=0.3.0,<0.4.0' - - 'bioconductor-illuminaio >=0.24.0,<0.25.0' - - 'bioconductor-impute >=1.56.0,<1.57.0' - - 'bioconductor-limma >=3.38.0,<3.39.0' - - 'bioconductor-marray >=1.60.0,<1.61.0' - - 'bioconductor-minfi >=1.28.0,<1.29.0' - - 'bioconductor-missmethyl >=1.16.0,<1.17.0' - - 'bioconductor-preprocesscore >=1.44.0,<1.45.0' - - 'bioconductor-qvalue >=2.14.0,<2.15.0' - - 'bioconductor-sva >=3.30.0,<3.31.0' - - 'bioconductor-watermelon >=1.26.0,<1.27.0' + - 'bioconductor-illuminahumanmethylationepicmanifest >=0.4.0,<0.5.0' + - 'bioconductor-illuminaio >=0.26.0,<0.27.0' + - 'bioconductor-impute >=1.58.0,<1.59.0' + - 'bioconductor-limma >=3.40.0,<3.41.0' + - 'bioconductor-marray >=1.62.0,<1.63.0' + - 'bioconductor-minfi >=1.30.0,<1.31.0' + - 'bioconductor-missmethyl >=1.18.0,<1.19.0' + - 'bioconductor-preprocesscore >=1.46.0,<1.47.0' + - 'bioconductor-qvalue >=2.16.0,<2.17.0' + - 'bioconductor-sva >=3.32.0,<3.33.0' + - 'bioconductor-watermelon >=1.28.0,<1.29.0' - r-base - r-combinat - r-dendextend @@ -60,28 +60,28 @@ requirements: - r-shiny - r-shinythemes run: - - 'bioconductor-bumphunter >=1.24.0,<1.25.0' - - 'bioconductor-champdata >=2.14.0,<2.15.0' - - 'bioconductor-dmrcate >=1.18.0,<1.19.0' - - 'bioconductor-dnacopy >=1.56.0,<1.57.0' - - 'bioconductor-fem >=3.10.0,<3.11.0' - - 'bioconductor-genomicranges >=1.34.0,<1.35.0' - - 'bioconductor-globaltest >=5.36.0,<5.37.0' - - 'bioconductor-goseq >=1.34.0,<1.35.0' - - 'bioconductor-illumina450probevariants.db >=1.18.0,<1.19.0' + - 'bioconductor-bumphunter >=1.26.0,<1.27.0' + - 'bioconductor-champdata >=2.16.0,<2.17.0' + - 'bioconductor-dmrcate >=1.20.0,<1.21.0' + - 'bioconductor-dnacopy >=1.58.0,<1.59.0' + - 'bioconductor-fem >=3.12.0,<3.13.0' + - 'bioconductor-genomicranges >=1.36.0,<1.37.0' + - 'bioconductor-globaltest >=5.38.0,<5.39.0' + - 'bioconductor-goseq >=1.36.0,<1.37.0' + - 'bioconductor-illumina450probevariants.db >=1.20.0,<1.21.0' - 'bioconductor-illuminahumanmethylation450kmanifest >=0.4.0,<0.5.0' - 'bioconductor-illuminahumanmethylationepicanno.ilm10b2.hg19 >=0.6.0,<0.7.0' - - 'bioconductor-illuminahumanmethylationepicmanifest >=0.3.0,<0.4.0' - - 'bioconductor-illuminaio >=0.24.0,<0.25.0' - - 'bioconductor-impute >=1.56.0,<1.57.0' - - 'bioconductor-limma >=3.38.0,<3.39.0' - - 'bioconductor-marray >=1.60.0,<1.61.0' - - 'bioconductor-minfi >=1.28.0,<1.29.0' - - 'bioconductor-missmethyl >=1.16.0,<1.17.0' - - 'bioconductor-preprocesscore >=1.44.0,<1.45.0' - - 'bioconductor-qvalue >=2.14.0,<2.15.0' - - 'bioconductor-sva >=3.30.0,<3.31.0' - - 'bioconductor-watermelon >=1.26.0,<1.27.0' + - 'bioconductor-illuminahumanmethylationepicmanifest >=0.4.0,<0.5.0' + - 'bioconductor-illuminaio >=0.26.0,<0.27.0' + - 'bioconductor-impute >=1.58.0,<1.59.0' + - 'bioconductor-limma >=3.40.0,<3.41.0' + - 'bioconductor-marray >=1.62.0,<1.63.0' + - 'bioconductor-minfi >=1.30.0,<1.31.0' + - 'bioconductor-missmethyl >=1.18.0,<1.19.0' + - 'bioconductor-preprocesscore >=1.46.0,<1.47.0' + - 'bioconductor-qvalue >=2.16.0,<2.17.0' + - 'bioconductor-sva >=3.32.0,<3.33.0' + - 'bioconductor-watermelon >=1.28.0,<1.29.0' - r-base - r-combinat - r-dendextend diff --git a/recipes/bioconductor-champdata/meta.yaml b/recipes/bioconductor-champdata/meta.yaml index b3cb39985fee2..ac9074e2fbd5f 100644 --- a/recipes/bioconductor-champdata/meta.yaml +++ b/recipes/bioconductor-champdata/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "2.14.0" %} +{% set version = "2.16.0" %} {% set name = "ChAMPdata" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 45ef9f402b16c268d28853e51b26ffd0 + md5: 41023a6402403275016b865f07eba6a5 build: number: 0 rpaths: @@ -19,14 +19,14 @@ build: noarch: generic requirements: host: - - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' - - 'bioconductor-genomicranges >=1.34.0,<1.35.0' + - 'bioconductor-biocgenerics >=0.30.0,<0.31.0' + - 'bioconductor-genomicranges >=1.36.0,<1.37.0' - r-base run: - - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' - - 'bioconductor-genomicranges >=1.34.0,<1.35.0' + - 'bioconductor-biocgenerics >=0.30.0,<0.31.0' + - 'bioconductor-genomicranges >=1.36.0,<1.37.0' - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-champdata/post-link.sh b/recipes/bioconductor-champdata/post-link.sh index a9ab679e049df..da5b9befe8ece 100644 --- a/recipes/bioconductor-champdata/post-link.sh +++ b/recipes/bioconductor-champdata/post-link.sh @@ -1,11 +1,11 @@ #!/bin/bash -FN="ChAMPdata_2.14.0.tar.gz" +FN="ChAMPdata_2.16.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/experiment/src/contrib/ChAMPdata_2.14.0.tar.gz" - "https://bioarchive.galaxyproject.org/ChAMPdata_2.14.0.tar.gz" - "https://depot.galaxyproject.org/software/bioconductor-champdata/bioconductor-champdata_2.14.0_src_all.tar.gz" + "https://bioconductor.org/packages/3.9/data/experiment/src/contrib/ChAMPdata_2.16.0.tar.gz" + "https://bioarchive.galaxyproject.org/ChAMPdata_2.16.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-champdata/bioconductor-champdata_2.16.0_src_all.tar.gz" ) -MD5="45ef9f402b16c268d28853e51b26ffd0" +MD5="41023a6402403275016b865f07eba6a5" # Use a staging area in the conda dir rather than temp dirs, both to avoid # permission issues as well as to have things downloaded in a predictable @@ -16,7 +16,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-charge/meta.yaml b/recipes/bioconductor-charge/meta.yaml index b8fc6c400748d..70e20ffd4ff1f 100644 --- a/recipes/bioconductor-charge/meta.yaml +++ b/recipes/bioconductor-charge/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.2.0" %} +{% set version = "1.4.0" %} {% set name = "CHARGE" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 5c4c8debe46ce9db6a724b4bc94e6f06 + md5: 68a0b860a2dc6ecc2e64eb5496954d0b build: number: 0 rpaths: @@ -20,9 +20,9 @@ build: # Suggests: roxygen2, EnsDb.Hsapiens.v86 requirements: host: - - 'bioconductor-genomicranges >=1.34.0,<1.35.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' + - 'bioconductor-genomicranges >=1.36.0,<1.37.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-summarizedexperiment >=1.14.0,<1.15.0' - r-base - r-cluster - r-diptest @@ -32,9 +32,9 @@ requirements: - r-modes - r-plyr run: - - 'bioconductor-genomicranges >=1.34.0,<1.35.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' + - 'bioconductor-genomicranges >=1.36.0,<1.37.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-summarizedexperiment >=1.14.0,<1.15.0' - r-base - r-cluster - r-diptest diff --git a/recipes/bioconductor-charm/meta.yaml b/recipes/bioconductor-charm/meta.yaml index d866f710106d6..d84724608767c 100644 --- a/recipes/bioconductor-charm/meta.yaml +++ b/recipes/bioconductor-charm/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "2.28.0" %} +{% set version = "2.29.0" %} {% set name = "charm" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 63fa78f4ef43f5c8ea4f2fe33885e184 + md5: f8013190e4d25c45eb4999a6a2c4a883 build: number: 0 rpaths: @@ -20,17 +20,17 @@ build: # Suggests: charmData, BSgenome.Hsapiens.UCSC.hg18, corpcor requirements: host: - - 'bioconductor-biobase >=2.42.0,<2.43.0' - - 'bioconductor-biostrings >=2.50.0,<2.51.0' - - 'bioconductor-bsgenome >=1.50.0,<1.51.0' - - 'bioconductor-genefilter >=1.64.0,<1.65.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-limma >=3.38.0,<3.39.0' - - 'bioconductor-oligo >=1.46.0,<1.47.0' - - 'bioconductor-oligoclasses >=1.44.0,<1.45.0' - - 'bioconductor-preprocesscore >=1.44.0,<1.45.0' - - 'bioconductor-siggenes >=1.56.0,<1.57.0' - - 'bioconductor-sva >=3.30.0,<3.31.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' + - 'bioconductor-biostrings >=2.52.0,<2.53.0' + - 'bioconductor-bsgenome >=1.52.0,<1.53.0' + - 'bioconductor-genefilter >=1.66.0,<1.67.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-limma >=3.40.0,<3.41.0' + - 'bioconductor-oligo >=1.48.0,<1.49.0' + - 'bioconductor-oligoclasses >=1.46.0,<1.47.0' + - 'bioconductor-preprocesscore >=1.46.0,<1.47.0' + - 'bioconductor-siggenes >=1.58.0,<1.59.0' + - 'bioconductor-sva >=3.32.0,<3.33.0' - r-base - r-ff - r-fields @@ -39,17 +39,17 @@ requirements: - r-rcolorbrewer - r-sqn run: - - 'bioconductor-biobase >=2.42.0,<2.43.0' - - 'bioconductor-biostrings >=2.50.0,<2.51.0' - - 'bioconductor-bsgenome >=1.50.0,<1.51.0' - - 'bioconductor-genefilter >=1.64.0,<1.65.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-limma >=3.38.0,<3.39.0' - - 'bioconductor-oligo >=1.46.0,<1.47.0' - - 'bioconductor-oligoclasses >=1.44.0,<1.45.0' - - 'bioconductor-preprocesscore >=1.44.0,<1.45.0' - - 'bioconductor-siggenes >=1.56.0,<1.57.0' - - 'bioconductor-sva >=3.30.0,<3.31.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' + - 'bioconductor-biostrings >=2.52.0,<2.53.0' + - 'bioconductor-bsgenome >=1.52.0,<1.53.0' + - 'bioconductor-genefilter >=1.66.0,<1.67.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-limma >=3.40.0,<3.41.0' + - 'bioconductor-oligo >=1.48.0,<1.49.0' + - 'bioconductor-oligoclasses >=1.46.0,<1.47.0' + - 'bioconductor-preprocesscore >=1.46.0,<1.47.0' + - 'bioconductor-siggenes >=1.58.0,<1.59.0' + - 'bioconductor-sva >=3.32.0,<3.33.0' - r-base - r-ff - r-fields diff --git a/recipes/bioconductor-charmdata/meta.yaml b/recipes/bioconductor-charmdata/meta.yaml index bd7aaef89b145..de911355f9972 100644 --- a/recipes/bioconductor-charmdata/meta.yaml +++ b/recipes/bioconductor-charmdata/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.18.0" %} +{% set version = "1.19.0" %} {% set name = "charmData" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,23 +10,23 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: b8a33b09e3b618b0aae3f3ca0ec5acc9 + md5: b01273cf14a402015dc5a26f6b3780ef build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ noarch: generic requirements: host: - - 'bioconductor-charm >=2.28.0,<2.29.0' - - 'bioconductor-pd.charm.hg18.example >=0.99.0,<0.100.0' + - 'bioconductor-charm >=2.30.0,<2.31.0' + - 'bioconductor-pd.charm.hg18.example >=1.0.0,<1.1.0' - r-base run: - - 'bioconductor-charm >=2.28.0,<2.29.0' - - 'bioconductor-pd.charm.hg18.example >=0.99.0,<0.100.0' + - 'bioconductor-charm >=2.30.0,<2.31.0' + - 'bioconductor-pd.charm.hg18.example >=1.0.0,<1.1.0' - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-charmdata/post-link.sh b/recipes/bioconductor-charmdata/post-link.sh index 043d3e4c0b774..354bbe2382c12 100644 --- a/recipes/bioconductor-charmdata/post-link.sh +++ b/recipes/bioconductor-charmdata/post-link.sh @@ -1,11 +1,11 @@ #!/bin/bash -FN="charmData_1.18.0.tar.gz" +FN="charmData_1.19.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/experiment/src/contrib/charmData_1.18.0.tar.gz" - "https://bioarchive.galaxyproject.org/charmData_1.18.0.tar.gz" - "https://depot.galaxyproject.org/software/bioconductor-charmdata/bioconductor-charmdata_1.18.0_src_all.tar.gz" + "https://bioconductor.org/packages/3.9/data/experiment/src/contrib/charmData_1.19.0.tar.gz" + "https://bioarchive.galaxyproject.org/charmData_1.19.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-charmdata/bioconductor-charmdata_1.19.0_src_all.tar.gz" ) -MD5="b8a33b09e3b618b0aae3f3ca0ec5acc9" +MD5="b01273cf14a402015dc5a26f6b3780ef" # Use a staging area in the conda dir rather than temp dirs, both to avoid # permission issues as well as to have things downloaded in a predictable @@ -16,7 +16,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-chemminedrugs/meta.yaml b/recipes/bioconductor-chemminedrugs/meta.yaml index f2b83a5228653..97b4701923690 100644 --- a/recipes/bioconductor-chemminedrugs/meta.yaml +++ b/recipes/bioconductor-chemminedrugs/meta.yaml @@ -1,6 +1,6 @@ {% set version = "1.0.2" %} {% set name = "ChemmineDrugs" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -12,7 +12,7 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' md5: 2a3646e5173e93080fb5b49564f5d545 build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ @@ -20,16 +20,16 @@ build: # Suggests: BiocStyle,knitcitations,knitr requirements: host: - - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' - - 'bioconductor-chemminer >=3.34.0,<3.35.0' + - 'bioconductor-biocgenerics >=0.30.0,<0.31.0' + - 'bioconductor-chemminer >=3.36.0,<3.37.0' - r-base - r-rsqlite run: - - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' - - 'bioconductor-chemminer >=3.34.0,<3.35.0' + - 'bioconductor-biocgenerics >=0.30.0,<0.31.0' + - 'bioconductor-chemminer >=3.36.0,<3.37.0' - r-base - r-rsqlite - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-chemminedrugs/post-link.sh b/recipes/bioconductor-chemminedrugs/post-link.sh index e582a5c13f482..ecf5d3ce45cb4 100644 --- a/recipes/bioconductor-chemminedrugs/post-link.sh +++ b/recipes/bioconductor-chemminedrugs/post-link.sh @@ -1,9 +1,10 @@ #!/bin/bash FN="ChemmineDrugs_1.0.2.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/ChemmineDrugs_1.0.2.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/ChemmineDrugs_1.0.2.tar.gz" "https://bioarchive.galaxyproject.org/ChemmineDrugs_1.0.2.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-chemminedrugs/bioconductor-chemminedrugs_1.0.2_src_all.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-chemminedrugs/bioconductor-chemminedrugs_1.0.2_src_all.tar.gz" ) MD5="2a3646e5173e93080fb5b49564f5d545" @@ -16,7 +17,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-chemmineob/meta.yaml b/recipes/bioconductor-chemmineob/meta.yaml index fd71fb2af1a2b..3ae0968e94202 100644 --- a/recipes/bioconductor-chemmineob/meta.yaml +++ b/recipes/bioconductor-chemmineob/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.20.0" %} +{% set version = "1.22.0" %} {% set name = "ChemmineOB" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: e22ab70101dfc90ee6432269eb9d2adb + md5: 7fe4e4182986ff317665bf0db03aab31 build: number: 0 rpaths: @@ -20,15 +20,15 @@ build: # SystemRequirements: OpenBabel (>= 2.3.1) with headers (http://openbabel.org). requirements: host: - - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' - - 'bioconductor-zlibbioc >=1.28.0,<1.29.0' + - 'bioconductor-biocgenerics >=0.30.0,<0.31.0' + - 'bioconductor-zlibbioc >=1.30.0,<1.31.0' - r-base - r-bh - 'r-rcpp >=0.11.0' - openbabel >=2.3.1 run: - - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' - - 'bioconductor-zlibbioc >=1.28.0,<1.29.0' + - 'bioconductor-biocgenerics >=0.30.0,<0.31.0' + - 'bioconductor-zlibbioc >=1.30.0,<1.31.0' - r-base - r-bh - 'r-rcpp >=0.11.0' diff --git a/recipes/bioconductor-chemminer/meta.yaml b/recipes/bioconductor-chemminer/meta.yaml index ceb4604e63dbe..99cba2b9fa594 100644 --- a/recipes/bioconductor-chemminer/meta.yaml +++ b/recipes/bioconductor-chemminer/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "3.34.1" %} +{% set version = "3.36.0" %} {% set name = "ChemmineR" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: e271de186e07cdbb5195645bbab04f13 + md5: 8d49bddc3a3375ead2711b55cd405930 build: number: 0 rpaths: @@ -20,7 +20,7 @@ build: # SystemRequirements: GNU make requirements: host: - - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' + - 'bioconductor-biocgenerics >=0.30.0,<0.31.0' - r-base - r-base64enc - r-bh @@ -35,7 +35,7 @@ requirements: - r-rjson - r-rsvg run: - - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' + - 'bioconductor-biocgenerics >=0.30.0,<0.31.0' - r-base - r-base64enc - r-bh diff --git a/recipes/bioconductor-chetah/build.sh b/recipes/bioconductor-chetah/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-chetah/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-chetah/meta.yaml b/recipes/bioconductor-chetah/meta.yaml new file mode 100644 index 0000000000000..13fb7d73ebf95 --- /dev/null +++ b/recipes/bioconductor-chetah/meta.yaml @@ -0,0 +1,59 @@ +{% set version = "1.0.0" %} +{% set name = "CHETAH" %} +{% set bioc = "3.9" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: f249890b29eed4f6cf36b36700f1a39d +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: knitr, rmarkdown, Matrix, testthat, vdiffr +requirements: + host: + - 'bioconductor-biodist >=1.56.0,<1.57.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' + - 'bioconductor-singlecellexperiment >=1.6.0,<1.7.0' + - 'bioconductor-summarizedexperiment >=1.14.0,<1.15.0' + - r-base + - r-corrplot + - r-cowplot + - r-dendextend + - r-ggplot2 + - r-gplots + - r-pheatmap + - r-plotly + - r-reshape2 + - r-shiny + run: + - 'bioconductor-biodist >=1.56.0,<1.57.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' + - 'bioconductor-singlecellexperiment >=1.6.0,<1.7.0' + - 'bioconductor-summarizedexperiment >=1.14.0,<1.15.0' + - r-base + - r-corrplot + - r-cowplot + - r-dendextend + - r-ggplot2 + - r-gplots + - r-pheatmap + - r-plotly + - r-reshape2 + - r-shiny +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: 'file LICENSE' + summary: 'CHETAH is a accurate, selective and fast scRNA-seq classifier. Classification is guided by a reference dataset, preferentially also a scRNA-seq dataset. By hierarchical clustering of the reference data, CHETAH creates a classification tree that enables a step-wise, top-to-bottom classification. Using a novel stopping rule, CHETAH classifies the input cells to the cell types of the references and to "intermediate types": more general classifications that ended in an intermediate node of the tree.' + diff --git a/recipes/bioconductor-chic.data/meta.yaml b/recipes/bioconductor-chic.data/meta.yaml index 8b81764b11aa5..ef6af94f93abc 100644 --- a/recipes/bioconductor-chic.data/meta.yaml +++ b/recipes/bioconductor-chic.data/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.2.0" %} +{% set version = "1.4.0" %} {% set name = "ChIC.data" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 4bee195762ecb4bfce23bc3f841cc5cb + md5: 363188008f53ea5cab5ae873be14365a build: number: 0 rpaths: @@ -24,7 +24,7 @@ requirements: run: - r-base - 'r-caret >=6.0-78' - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-chic.data/post-link.sh b/recipes/bioconductor-chic.data/post-link.sh index d01b740e31baf..6836990103440 100644 --- a/recipes/bioconductor-chic.data/post-link.sh +++ b/recipes/bioconductor-chic.data/post-link.sh @@ -1,11 +1,11 @@ #!/bin/bash -FN="ChIC.data_1.2.0.tar.gz" +FN="ChIC.data_1.4.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/experiment/src/contrib/ChIC.data_1.2.0.tar.gz" - "https://bioarchive.galaxyproject.org/ChIC.data_1.2.0.tar.gz" - "https://depot.galaxyproject.org/software/bioconductor-chic.data/bioconductor-chic.data_1.2.0_src_all.tar.gz" + "https://bioconductor.org/packages/3.9/data/experiment/src/contrib/ChIC.data_1.4.0.tar.gz" + "https://bioarchive.galaxyproject.org/ChIC.data_1.4.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-chic.data/bioconductor-chic.data_1.4.0_src_all.tar.gz" ) -MD5="4bee195762ecb4bfce23bc3f841cc5cb" +MD5="363188008f53ea5cab5ae873be14365a" # Use a staging area in the conda dir rather than temp dirs, both to avoid # permission issues as well as to have things downloaded in a predictable @@ -16,7 +16,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-chic/meta.yaml b/recipes/bioconductor-chic/meta.yaml index ccb5272995b21..e8d303ef1b788 100644 --- a/recipes/bioconductor-chic/meta.yaml +++ b/recipes/bioconductor-chic/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.2.0" %} +{% set version = "1.4.0" %} {% set name = "ChIC" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,31 +10,31 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: dcf74f7e88f59bb8965f1d0202651109 + md5: 36c70a76294c44a3740a1aca9aa5a9b5 build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ noarch: generic requirements: host: - - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' - - 'bioconductor-chic.data >=1.2.0,<1.3.0' - - 'bioconductor-genomicranges >=1.34.0,<1.35.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-biocgenerics >=0.30.0,<0.31.0' + - 'bioconductor-chic.data >=1.4.0,<1.5.0' + - 'bioconductor-genomicranges >=1.36.0,<1.37.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' - r-base - r-caret - r-catools - r-progress - r-spp run: - - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' - - 'bioconductor-chic.data >=1.2.0,<1.3.0' - - 'bioconductor-genomicranges >=1.34.0,<1.35.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-biocgenerics >=0.30.0,<0.31.0' + - 'bioconductor-chic.data >=1.4.0,<1.5.0' + - 'bioconductor-genomicranges >=1.36.0,<1.37.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' - r-base - r-caret - r-catools diff --git a/recipes/bioconductor-chicago/meta.yaml b/recipes/bioconductor-chicago/meta.yaml index 0c8e7f73f7dba..b1de726806884 100644 --- a/recipes/bioconductor-chicago/meta.yaml +++ b/recipes/bioconductor-chicago/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.10.1" %} +{% set version = "1.12.0" %} {% set name = "Chicago" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 4dd883d54c606ec9c47a78bc942ca5bb + md5: d5ed2c8bd98b169b431f2aef87a65aa6 build: number: 0 rpaths: diff --git a/recipes/bioconductor-chicken.db/meta.yaml b/recipes/bioconductor-chicken.db/meta.yaml index bd190acbf18eb..4b0d86814e428 100644 --- a/recipes/bioconductor-chicken.db/meta.yaml +++ b/recipes/bioconductor-chicken.db/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.2.3" %} {% set name = "chicken.db" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -12,7 +12,7 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: e093b861c4688cf10e53a3124ee8bfc0 build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ @@ -20,14 +20,14 @@ build: # Suggests: DBI, annotate, RUnit requirements: host: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' - - 'bioconductor-org.gg.eg.db >=3.7.0,<3.8.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' + - 'bioconductor-org.gg.eg.db >=3.8.0,<3.9.0' - r-base run: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' - - 'bioconductor-org.gg.eg.db >=3.7.0,<3.8.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' + - 'bioconductor-org.gg.eg.db >=3.8.0,<3.9.0' - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-chicken.db/post-link.sh b/recipes/bioconductor-chicken.db/post-link.sh index efcf3f7a17cc1..6d4329feedd8f 100644 --- a/recipes/bioconductor-chicken.db/post-link.sh +++ b/recipes/bioconductor-chicken.db/post-link.sh @@ -1,9 +1,10 @@ #!/bin/bash FN="chicken.db_3.2.3.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/chicken.db_3.2.3.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/chicken.db_3.2.3.tar.gz" "https://bioarchive.galaxyproject.org/chicken.db_3.2.3.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-chicken.db/bioconductor-chicken.db_3.2.3_src_all.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-chicken.db/bioconductor-chicken.db_3.2.3_src_all.tar.gz" ) MD5="e093b861c4688cf10e53a3124ee8bfc0" @@ -16,7 +17,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-chicken.db0/meta.yaml b/recipes/bioconductor-chicken.db0/meta.yaml index b3fa5f26582a1..1f9badf85640d 100644 --- a/recipes/bioconductor-chicken.db0/meta.yaml +++ b/recipes/bioconductor-chicken.db0/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "3.7.1" %} +{% set version = "3.8.2" %} {% set name = "chicken.db0" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 948b616eea6f7bda986dfc115842279e + md5: a205de7be26047ac1d45287320d4efc6 build: number: 0 rpaths: @@ -19,12 +19,12 @@ build: noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' - r-base run: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-chicken.db0/post-link.sh b/recipes/bioconductor-chicken.db0/post-link.sh index 8cb76018eb88c..bf16884125ce1 100644 --- a/recipes/bioconductor-chicken.db0/post-link.sh +++ b/recipes/bioconductor-chicken.db0/post-link.sh @@ -1,11 +1,11 @@ #!/bin/bash -FN="chicken.db0_3.7.1.tar.gz" +FN="chicken.db0_3.8.2.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/chicken.db0_3.7.1.tar.gz" - "https://bioarchive.galaxyproject.org/chicken.db0_3.7.1.tar.gz" - "https://depot.galaxyproject.org/software/bioconductor-chicken.db0/bioconductor-chicken.db0_3.7.1_src_all.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/chicken.db0_3.8.2.tar.gz" + "https://bioarchive.galaxyproject.org/chicken.db0_3.8.2.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-chicken.db0/bioconductor-chicken.db0_3.8.2_src_all.tar.gz" ) -MD5="948b616eea6f7bda986dfc115842279e" +MD5="a205de7be26047ac1d45287320d4efc6" # Use a staging area in the conda dir rather than temp dirs, both to avoid # permission issues as well as to have things downloaded in a predictable @@ -16,7 +16,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-chickencdf/meta.yaml b/recipes/bioconductor-chickencdf/meta.yaml index 333741b4a4fdb..c3b7828d60e04 100644 --- a/recipes/bioconductor-chickencdf/meta.yaml +++ b/recipes/bioconductor-chickencdf/meta.yaml @@ -1,6 +1,6 @@ {% set version = "2.18.0" %} {% set name = "chickencdf" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -12,19 +12,19 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: ab0097b4b7b6c4d94360feb84ab69972 build: - number: 1 + number: 2 rpaths: - lib/R/lib/ - lib/ noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' - r-base run: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-chickencdf/post-link.sh b/recipes/bioconductor-chickencdf/post-link.sh index 53fe7ec7d2034..c1ae022c54422 100644 --- a/recipes/bioconductor-chickencdf/post-link.sh +++ b/recipes/bioconductor-chickencdf/post-link.sh @@ -1,9 +1,10 @@ #!/bin/bash FN="chickencdf_2.18.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/chickencdf_2.18.0.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/chickencdf_2.18.0.tar.gz" "https://bioarchive.galaxyproject.org/chickencdf_2.18.0.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-chickencdf/bioconductor-chickencdf_2.18.0_src_all.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-chickencdf/bioconductor-chickencdf_2.18.0_src_all.tar.gz" ) MD5="ab0097b4b7b6c4d94360feb84ab69972" @@ -16,7 +17,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-chickenprobe/meta.yaml b/recipes/bioconductor-chickenprobe/meta.yaml index 59d38673354c4..3bc5ccea6fe1d 100644 --- a/recipes/bioconductor-chickenprobe/meta.yaml +++ b/recipes/bioconductor-chickenprobe/meta.yaml @@ -1,6 +1,6 @@ {% set version = "2.18.0" %} {% set name = "chickenprobe" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -12,19 +12,19 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: b33599081ce1ba768ff7992e143c01d0 build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' - r-base run: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-chickenprobe/post-link.sh b/recipes/bioconductor-chickenprobe/post-link.sh index 705ddb10b71e1..3d32d7506d694 100644 --- a/recipes/bioconductor-chickenprobe/post-link.sh +++ b/recipes/bioconductor-chickenprobe/post-link.sh @@ -1,9 +1,10 @@ #!/bin/bash FN="chickenprobe_2.18.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/chickenprobe_2.18.0.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/chickenprobe_2.18.0.tar.gz" "https://bioarchive.galaxyproject.org/chickenprobe_2.18.0.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-chickenprobe/bioconductor-chickenprobe_2.18.0_src_all.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-chickenprobe/bioconductor-chickenprobe_2.18.0_src_all.tar.gz" ) MD5="b33599081ce1ba768ff7992e143c01d0" @@ -16,7 +17,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-chimera/meta.yaml b/recipes/bioconductor-chimera/meta.yaml index 00c58ba18ab14..d6934b41a379c 100644 --- a/recipes/bioconductor-chimera/meta.yaml +++ b/recipes/bioconductor-chimera/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.24.0" %} +{% set version = "1.26.0" %} {% set name = "chimera" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 3245d0c076c17bc1b850d377cf15070a + md5: 1260ef67ee085f1a61374ae3a7deafed build: number: 0 rpaths: @@ -20,25 +20,33 @@ build: # SystemRequirements: STAR, TopHat, bowtie and samtools are required for some functionalities requirements: host: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' - - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' - 'bioconductor-bsgenome.hsapiens.ucsc.hg19 >=1.4.0,<1.5.0' - - 'bioconductor-genomicalignments >=1.18.0,<1.19.0' - - 'bioconductor-genomicranges >=1.34.0,<1.35.0' - - 'bioconductor-homo.sapiens >=1.3.0,<1.4.0' - - 'bioconductor-rsamtools >=1.34.0,<1.35.0' + - 'bioconductor-genomicalignments >=1.20.0,<1.21.0' + - 'bioconductor-genomicranges >=1.36.0,<1.37.0' + - 'bioconductor-homo.sapiens >=1.4.0,<1.5.0' + - 'bioconductor-rsamtools >=2.0.0,<2.1.0' - 'bioconductor-txdb.hsapiens.ucsc.hg19.knowngene >=3.2.0,<3.3.0' - r-base + - star + - tophat + - bowtie2 + - samtools run: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' - - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' - 'bioconductor-bsgenome.hsapiens.ucsc.hg19 >=1.4.0,<1.5.0' - - 'bioconductor-genomicalignments >=1.18.0,<1.19.0' - - 'bioconductor-genomicranges >=1.34.0,<1.35.0' - - 'bioconductor-homo.sapiens >=1.3.0,<1.4.0' - - 'bioconductor-rsamtools >=1.34.0,<1.35.0' + - 'bioconductor-genomicalignments >=1.20.0,<1.21.0' + - 'bioconductor-genomicranges >=1.36.0,<1.37.0' + - 'bioconductor-homo.sapiens >=1.4.0,<1.5.0' + - 'bioconductor-rsamtools >=2.0.0,<2.1.0' - 'bioconductor-txdb.hsapiens.ucsc.hg19.knowngene >=3.2.0,<3.3.0' - r-base + - star + - tophat + - bowtie2 + - samtools build: - {{ compiler('c') }} - {{ compiler('cxx') }} diff --git a/recipes/bioconductor-chimeraviz/meta.yaml b/recipes/bioconductor-chimeraviz/meta.yaml index 1687deeefd57e..028b1d0c964a1 100644 --- a/recipes/bioconductor-chimeraviz/meta.yaml +++ b/recipes/bioconductor-chimeraviz/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.8.0" %} +{% set version = "1.10.0" %} {% set name = "chimeraviz" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 88df77f2bd025b9416ec3b0538c97b19 + md5: 1232b731506b98afc592ea7cc9bb3732 build: number: 0 rpaths: @@ -21,57 +21,65 @@ build: # SystemRequirements: bowtie, samtools, and egrep are required for some functionalities requirements: host: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' - - 'bioconductor-annotationfilter >=1.6.0,<1.7.0' - - 'bioconductor-biocstyle >=2.10.0,<2.11.0' - - 'bioconductor-biostrings >=2.50.0,<2.51.0' - - 'bioconductor-ensembldb >=2.6.0,<2.7.0' - - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' - - 'bioconductor-genomicalignments >=1.18.0,<1.19.0' - - 'bioconductor-genomicranges >=1.34.0,<1.35.0' - - 'bioconductor-graph >=1.60.0,<1.61.0' - - 'bioconductor-gviz >=1.26.0,<1.27.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-org.hs.eg.db >=3.7.0,<3.8.0' - - 'bioconductor-org.mm.eg.db >=3.7.0,<3.8.0' - - 'bioconductor-rgraphviz >=2.26.0,<2.27.0' - - 'bioconductor-rsamtools >=1.34.0,<1.35.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' + - 'bioconductor-annotationfilter >=1.8.0,<1.9.0' + - 'bioconductor-biocstyle >=2.12.0,<2.13.0' + - 'bioconductor-biostrings >=2.52.0,<2.53.0' + - 'bioconductor-ensembldb >=2.8.0,<2.9.0' + - 'bioconductor-genomeinfodb >=1.20.0,<1.21.0' + - 'bioconductor-genomicalignments >=1.20.0,<1.21.0' + - 'bioconductor-genomicranges >=1.36.0,<1.37.0' + - 'bioconductor-graph >=1.62.0,<1.63.0' + - 'bioconductor-gviz >=1.28.0,<1.29.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-org.hs.eg.db >=3.8.0,<3.9.0' + - 'bioconductor-org.mm.eg.db >=3.8.0,<3.9.0' + - 'bioconductor-rgraphviz >=2.28.0,<2.29.0' + - 'bioconductor-rsamtools >=2.0.0,<2.1.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' - r-argumentcheck - r-base - r-data.table - r-dplyr - r-dt + - r-gtools - r-plyr - r-rcircos - r-rcolorbrewer - r-rmarkdown + - bowtie2 + - samtools + - grep run: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' - - 'bioconductor-annotationfilter >=1.6.0,<1.7.0' - - 'bioconductor-biocstyle >=2.10.0,<2.11.0' - - 'bioconductor-biostrings >=2.50.0,<2.51.0' - - 'bioconductor-ensembldb >=2.6.0,<2.7.0' - - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' - - 'bioconductor-genomicalignments >=1.18.0,<1.19.0' - - 'bioconductor-genomicranges >=1.34.0,<1.35.0' - - 'bioconductor-graph >=1.60.0,<1.61.0' - - 'bioconductor-gviz >=1.26.0,<1.27.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-org.hs.eg.db >=3.7.0,<3.8.0' - - 'bioconductor-org.mm.eg.db >=3.7.0,<3.8.0' - - 'bioconductor-rgraphviz >=2.26.0,<2.27.0' - - 'bioconductor-rsamtools >=1.34.0,<1.35.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' + - 'bioconductor-annotationfilter >=1.8.0,<1.9.0' + - 'bioconductor-biocstyle >=2.12.0,<2.13.0' + - 'bioconductor-biostrings >=2.52.0,<2.53.0' + - 'bioconductor-ensembldb >=2.8.0,<2.9.0' + - 'bioconductor-genomeinfodb >=1.20.0,<1.21.0' + - 'bioconductor-genomicalignments >=1.20.0,<1.21.0' + - 'bioconductor-genomicranges >=1.36.0,<1.37.0' + - 'bioconductor-graph >=1.62.0,<1.63.0' + - 'bioconductor-gviz >=1.28.0,<1.29.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-org.hs.eg.db >=3.8.0,<3.9.0' + - 'bioconductor-org.mm.eg.db >=3.8.0,<3.9.0' + - 'bioconductor-rgraphviz >=2.28.0,<2.29.0' + - 'bioconductor-rsamtools >=2.0.0,<2.1.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' - r-argumentcheck - r-base - r-data.table - r-dplyr - r-dt + - r-gtools - r-plyr - r-rcircos - r-rcolorbrewer - r-rmarkdown + - bowtie2 + - samtools + - grep test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-chimp.db0/meta.yaml b/recipes/bioconductor-chimp.db0/meta.yaml index d81afbe73f9e7..6e81733b9e375 100644 --- a/recipes/bioconductor-chimp.db0/meta.yaml +++ b/recipes/bioconductor-chimp.db0/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "3.7.1" %} +{% set version = "3.8.2" %} {% set name = "chimp.db0" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: e9b8c6525777c4474e79ed1edc5c5f05 + md5: 7a3202440652fd2c5a4c95c5439e92a8 build: number: 0 rpaths: @@ -19,12 +19,12 @@ build: noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' - r-base run: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-chimp.db0/post-link.sh b/recipes/bioconductor-chimp.db0/post-link.sh index 145c60524fdde..6af6c8efff57e 100644 --- a/recipes/bioconductor-chimp.db0/post-link.sh +++ b/recipes/bioconductor-chimp.db0/post-link.sh @@ -1,11 +1,11 @@ #!/bin/bash -FN="chimp.db0_3.7.1.tar.gz" +FN="chimp.db0_3.8.2.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/chimp.db0_3.7.1.tar.gz" - "https://bioarchive.galaxyproject.org/chimp.db0_3.7.1.tar.gz" - "https://depot.galaxyproject.org/software/bioconductor-chimp.db0/bioconductor-chimp.db0_3.7.1_src_all.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/chimp.db0_3.8.2.tar.gz" + "https://bioarchive.galaxyproject.org/chimp.db0_3.8.2.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-chimp.db0/bioconductor-chimp.db0_3.8.2_src_all.tar.gz" ) -MD5="e9b8c6525777c4474e79ed1edc5c5f05" +MD5="7a3202440652fd2c5a4c95c5439e92a8" # Use a staging area in the conda dir rather than temp dirs, both to avoid # permission issues as well as to have things downloaded in a predictable @@ -16,7 +16,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-chimphumanbraindata/meta.yaml b/recipes/bioconductor-chimphumanbraindata/meta.yaml index 313b306c3a162..fc2f26e0d9387 100644 --- a/recipes/bioconductor-chimphumanbraindata/meta.yaml +++ b/recipes/bioconductor-chimphumanbraindata/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.20.0" %} +{% set version = "1.22.0" %} {% set name = "ChimpHumanBrainData" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: ea5241df1f05ea48aa510de5a2a3efb9 + md5: d7a381464a431897c78431f93a64998d build: number: 0 rpaths: @@ -19,20 +19,20 @@ build: noarch: generic requirements: host: - - 'bioconductor-affy >=1.60.0,<1.61.0' - - 'bioconductor-limma >=3.38.0,<3.39.0' - - 'bioconductor-qvalue >=2.14.0,<2.15.0' + - 'bioconductor-affy >=1.62.0,<1.63.0' + - 'bioconductor-limma >=3.40.0,<3.41.0' + - 'bioconductor-qvalue >=2.16.0,<2.17.0' - r-base - r-hexbin - r-statmod run: - - 'bioconductor-affy >=1.60.0,<1.61.0' - - 'bioconductor-limma >=3.38.0,<3.39.0' - - 'bioconductor-qvalue >=2.14.0,<2.15.0' + - 'bioconductor-affy >=1.62.0,<1.63.0' + - 'bioconductor-limma >=3.40.0,<3.41.0' + - 'bioconductor-qvalue >=2.16.0,<2.17.0' - r-base - r-hexbin - r-statmod - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-chimphumanbraindata/post-link.sh b/recipes/bioconductor-chimphumanbraindata/post-link.sh index 0e79dca87316b..b60711fbb1a63 100644 --- a/recipes/bioconductor-chimphumanbraindata/post-link.sh +++ b/recipes/bioconductor-chimphumanbraindata/post-link.sh @@ -1,11 +1,11 @@ #!/bin/bash -FN="ChimpHumanBrainData_1.20.0.tar.gz" +FN="ChimpHumanBrainData_1.22.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/experiment/src/contrib/ChimpHumanBrainData_1.20.0.tar.gz" - "https://bioarchive.galaxyproject.org/ChimpHumanBrainData_1.20.0.tar.gz" - "https://depot.galaxyproject.org/software/bioconductor-chimphumanbraindata/bioconductor-chimphumanbraindata_1.20.0_src_all.tar.gz" + "https://bioconductor.org/packages/3.9/data/experiment/src/contrib/ChimpHumanBrainData_1.22.0.tar.gz" + "https://bioarchive.galaxyproject.org/ChimpHumanBrainData_1.22.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-chimphumanbraindata/bioconductor-chimphumanbraindata_1.22.0_src_all.tar.gz" ) -MD5="ea5241df1f05ea48aa510de5a2a3efb9" +MD5="d7a381464a431897c78431f93a64998d" # Use a staging area in the conda dir rather than temp dirs, both to avoid # permission issues as well as to have things downloaded in a predictable @@ -16,7 +16,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-chipanalyser/meta.yaml b/recipes/bioconductor-chipanalyser/meta.yaml index d5218b1126936..1afcc39444780 100644 --- a/recipes/bioconductor-chipanalyser/meta.yaml +++ b/recipes/bioconductor-chipanalyser/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.4.0" %} +{% set version = "1.6.0" %} {% set name = "ChIPanalyser" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 4f3fdeed3fb1ba02a78e56d70f1a9098 + md5: 9bd347492da8d4964d74601513538ea7 build: number: 0 rpaths: @@ -20,25 +20,25 @@ build: # Suggests: BSgenome.Dmelanogaster.UCSC.dm3,knitr, RUnit, BiocGenerics requirements: host: - - 'bioconductor-biostrings >=2.50.0,<2.51.0' - - 'bioconductor-bsgenome >=1.50.0,<1.51.0' - - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' - - 'bioconductor-genomicranges >=1.34.0,<1.35.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-rtracklayer >=1.42.0,<1.43.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-biostrings >=2.52.0,<2.53.0' + - 'bioconductor-bsgenome >=1.52.0,<1.53.0' + - 'bioconductor-genomeinfodb >=1.20.0,<1.21.0' + - 'bioconductor-genomicranges >=1.36.0,<1.37.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-rtracklayer >=1.44.0,<1.45.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' - r-base - r-biocmanager - r-rcpproll - r-rocr run: - - 'bioconductor-biostrings >=2.50.0,<2.51.0' - - 'bioconductor-bsgenome >=1.50.0,<1.51.0' - - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' - - 'bioconductor-genomicranges >=1.34.0,<1.35.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-rtracklayer >=1.42.0,<1.43.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-biostrings >=2.52.0,<2.53.0' + - 'bioconductor-bsgenome >=1.52.0,<1.53.0' + - 'bioconductor-genomeinfodb >=1.20.0,<1.21.0' + - 'bioconductor-genomicranges >=1.36.0,<1.37.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-rtracklayer >=1.44.0,<1.45.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' - r-base - r-biocmanager - r-rcpproll diff --git a/recipes/bioconductor-chipcomp/meta.yaml b/recipes/bioconductor-chipcomp/meta.yaml index 71e3eb7516049..86de48b677e5c 100644 --- a/recipes/bioconductor-chipcomp/meta.yaml +++ b/recipes/bioconductor-chipcomp/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.12.0" %} +{% set version = "1.14.0" %} {% set name = "ChIPComp" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: de5f56eb79ef4dab25dd22ac8aa20b0e + md5: 7cefdbab363e65223863f0845cb2c840 build: number: 0 rpaths: @@ -19,28 +19,28 @@ build: # Suggests: BiocStyle,RUnit requirements: host: - - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' + - 'bioconductor-biocgenerics >=0.30.0,<0.31.0' - 'bioconductor-bsgenome.hsapiens.ucsc.hg19 >=1.4.0,<1.5.0' - 'bioconductor-bsgenome.mmusculus.ucsc.mm9 >=1.4.0,<1.5.0' - - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' - - 'bioconductor-genomicranges >=1.34.0,<1.35.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-limma >=3.38.0,<3.39.0' - - 'bioconductor-rsamtools >=1.34.0,<1.35.0' - - 'bioconductor-rtracklayer >=1.42.0,<1.43.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-genomeinfodb >=1.20.0,<1.21.0' + - 'bioconductor-genomicranges >=1.36.0,<1.37.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-limma >=3.40.0,<3.41.0' + - 'bioconductor-rsamtools >=2.0.0,<2.1.0' + - 'bioconductor-rtracklayer >=1.44.0,<1.45.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' - r-base run: - - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' + - 'bioconductor-biocgenerics >=0.30.0,<0.31.0' - 'bioconductor-bsgenome.hsapiens.ucsc.hg19 >=1.4.0,<1.5.0' - 'bioconductor-bsgenome.mmusculus.ucsc.mm9 >=1.4.0,<1.5.0' - - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' - - 'bioconductor-genomicranges >=1.34.0,<1.35.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-limma >=3.38.0,<3.39.0' - - 'bioconductor-rsamtools >=1.34.0,<1.35.0' - - 'bioconductor-rtracklayer >=1.42.0,<1.43.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-genomeinfodb >=1.20.0,<1.21.0' + - 'bioconductor-genomicranges >=1.36.0,<1.37.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-limma >=3.40.0,<3.41.0' + - 'bioconductor-rsamtools >=2.0.0,<2.1.0' + - 'bioconductor-rtracklayer >=1.44.0,<1.45.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' - r-base build: - {{ compiler('c') }} diff --git a/recipes/bioconductor-chipenrich.data/meta.yaml b/recipes/bioconductor-chipenrich.data/meta.yaml index 3ae9fa7344a7e..f5dbcc0585182 100644 --- a/recipes/bioconductor-chipenrich.data/meta.yaml +++ b/recipes/bioconductor-chipenrich.data/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "2.6.0" %} +{% set version = "2.8.0" %} {% set name = "chipenrich.data" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: cd762813ed7fcc7e0ef6d0be7de5047b + md5: 26d744a980e0698a991565fb0beea5a1 build: number: 0 rpaths: @@ -20,26 +20,26 @@ build: # Suggests: BiocStyle, devtools, knitr, rmarkdown, roxygen2, testthat, GO.db, org.Dm.eg.db, org.Dr.eg.db, org.Hs.eg.db, org.Mm.eg.db, org.Rn.eg.db, TxDb.Dmelanogaster.UCSC.dm3.ensGene, TxDb.Dmelanogaster.UCSC.dm6.ensGene, TxDb.Drerio.UCSC.danRer10.refGene, TxDb.Hsapiens.UCSC.hg19.knownGene, TxDb.Hsapiens.UCSC.hg38.knownGene, TxDb.Mmusculus.UCSC.mm9.knownGene, TxDb.Mmusculus.UCSC.mm10.knownGene, TxDb.Rnorvegicus.UCSC.rn4.ensGene, TxDb.Rnorvegicus.UCSC.rn5.refGene, TxDb.Rnorvegicus.UCSC.rn6.refGene requirements: host: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' - - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' - - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' - - 'bioconductor-genomicranges >=1.34.0,<1.35.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-rtracklayer >=1.42.0,<1.43.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' + - 'bioconductor-biocgenerics >=0.30.0,<0.31.0' + - 'bioconductor-genomeinfodb >=1.20.0,<1.21.0' + - 'bioconductor-genomicranges >=1.36.0,<1.37.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-rtracklayer >=1.44.0,<1.45.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' - r-base - r-readr run: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' - - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' - - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' - - 'bioconductor-genomicranges >=1.34.0,<1.35.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-rtracklayer >=1.42.0,<1.43.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' + - 'bioconductor-biocgenerics >=0.30.0,<0.31.0' + - 'bioconductor-genomeinfodb >=1.20.0,<1.21.0' + - 'bioconductor-genomicranges >=1.36.0,<1.37.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-rtracklayer >=1.44.0,<1.45.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' - r-base - r-readr - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-chipenrich.data/post-link.sh b/recipes/bioconductor-chipenrich.data/post-link.sh index e567dee9fa807..51e035fda0d39 100644 --- a/recipes/bioconductor-chipenrich.data/post-link.sh +++ b/recipes/bioconductor-chipenrich.data/post-link.sh @@ -1,11 +1,11 @@ #!/bin/bash -FN="chipenrich.data_2.6.0.tar.gz" +FN="chipenrich.data_2.8.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/experiment/src/contrib/chipenrich.data_2.6.0.tar.gz" - "https://bioarchive.galaxyproject.org/chipenrich.data_2.6.0.tar.gz" - "https://depot.galaxyproject.org/software/bioconductor-chipenrich.data/bioconductor-chipenrich.data_2.6.0_src_all.tar.gz" + "https://bioconductor.org/packages/3.9/data/experiment/src/contrib/chipenrich.data_2.8.0.tar.gz" + "https://bioarchive.galaxyproject.org/chipenrich.data_2.8.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-chipenrich.data/bioconductor-chipenrich.data_2.8.0_src_all.tar.gz" ) -MD5="cd762813ed7fcc7e0ef6d0be7de5047b" +MD5="26d744a980e0698a991565fb0beea5a1" # Use a staging area in the conda dir rather than temp dirs, both to avoid # permission issues as well as to have things downloaded in a predictable @@ -16,7 +16,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-chipenrich/meta.yaml b/recipes/bioconductor-chipenrich/meta.yaml index 18d496d26c5d8..df6124b8a6288 100644 --- a/recipes/bioconductor-chipenrich/meta.yaml +++ b/recipes/bioconductor-chipenrich/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "2.6.0" %} +{% set version = "2.8.0" %} {% set name = "chipenrich" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: de5edd323cf961e677b6b7fc52f1c0d3 + md5: 70a5e2c7704314c3f01ab8571cc47769 build: number: 0 rpaths: @@ -20,19 +20,19 @@ build: # Suggests: BiocStyle, devtools, knitr, rmarkdown, roxygen2, testthat requirements: host: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' - - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' - - 'bioconductor-chipenrich.data >=2.6.0,<2.7.0' - - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' - - 'bioconductor-genomicranges >=1.34.0,<1.35.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-org.dm.eg.db >=3.7.0,<3.8.0' - - 'bioconductor-org.dr.eg.db >=3.7.0,<3.8.0' - - 'bioconductor-org.hs.eg.db >=3.7.0,<3.8.0' - - 'bioconductor-org.mm.eg.db >=3.7.0,<3.8.0' - - 'bioconductor-org.rn.eg.db >=3.7.0,<3.8.0' - - 'bioconductor-rtracklayer >=1.42.0,<1.43.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' + - 'bioconductor-biocgenerics >=0.30.0,<0.31.0' + - 'bioconductor-chipenrich.data >=2.8.0,<2.9.0' + - 'bioconductor-genomeinfodb >=1.20.0,<1.21.0' + - 'bioconductor-genomicranges >=1.36.0,<1.37.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-org.dm.eg.db >=3.8.0,<3.9.0' + - 'bioconductor-org.dr.eg.db >=3.8.0,<3.9.0' + - 'bioconductor-org.hs.eg.db >=3.8.0,<3.9.0' + - 'bioconductor-org.mm.eg.db >=3.8.0,<3.9.0' + - 'bioconductor-org.rn.eg.db >=3.8.0,<3.9.0' + - 'bioconductor-rtracklayer >=1.44.0,<1.45.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' - r-base - r-lattice - r-latticeextra @@ -41,19 +41,19 @@ requirements: - r-rms - r-stringr run: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' - - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' - - 'bioconductor-chipenrich.data >=2.6.0,<2.7.0' - - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' - - 'bioconductor-genomicranges >=1.34.0,<1.35.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-org.dm.eg.db >=3.7.0,<3.8.0' - - 'bioconductor-org.dr.eg.db >=3.7.0,<3.8.0' - - 'bioconductor-org.hs.eg.db >=3.7.0,<3.8.0' - - 'bioconductor-org.mm.eg.db >=3.7.0,<3.8.0' - - 'bioconductor-org.rn.eg.db >=3.7.0,<3.8.0' - - 'bioconductor-rtracklayer >=1.42.0,<1.43.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' + - 'bioconductor-biocgenerics >=0.30.0,<0.31.0' + - 'bioconductor-chipenrich.data >=2.8.0,<2.9.0' + - 'bioconductor-genomeinfodb >=1.20.0,<1.21.0' + - 'bioconductor-genomicranges >=1.36.0,<1.37.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-org.dm.eg.db >=3.8.0,<3.9.0' + - 'bioconductor-org.dr.eg.db >=3.8.0,<3.9.0' + - 'bioconductor-org.hs.eg.db >=3.8.0,<3.9.0' + - 'bioconductor-org.mm.eg.db >=3.8.0,<3.9.0' + - 'bioconductor-org.rn.eg.db >=3.8.0,<3.9.0' + - 'bioconductor-rtracklayer >=1.44.0,<1.45.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' - r-base - r-lattice - r-latticeextra diff --git a/recipes/bioconductor-chipexoqual/meta.yaml b/recipes/bioconductor-chipexoqual/meta.yaml index c4ff40299cc1a..4dbb7ee84e0ec 100644 --- a/recipes/bioconductor-chipexoqual/meta.yaml +++ b/recipes/bioconductor-chipexoqual/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.6.0" %} +{% set version = "1.8.0" %} {% set name = "ChIPexoQual" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 611bcc06f4a538ad75e2233cbf3c88ec + md5: 9f41cb7adca04bb0dea5fd142061d18d build: number: 0 rpaths: @@ -20,14 +20,14 @@ build: # Suggests: ChIPexoQualExample (>= 0.99.1), knitr (>= 1.10), BiocStyle, gridExtra (>= 2.2), testthat requirements: host: - - 'bioconductor-biocparallel >=1.16.0,<1.17.0' - - 'bioconductor-biovizbase >=1.30.0,<1.31.0' - - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' - - 'bioconductor-genomicalignments >=1.18.0,<1.19.0' - - 'bioconductor-genomicranges >=1.34.0,<1.35.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-rsamtools >=1.34.0,<1.35.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-biocparallel >=1.18.0,<1.19.0' + - 'bioconductor-biovizbase >=1.32.0,<1.33.0' + - 'bioconductor-genomeinfodb >=1.20.0,<1.21.0' + - 'bioconductor-genomicalignments >=1.20.0,<1.21.0' + - 'bioconductor-genomicranges >=1.36.0,<1.37.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-rsamtools >=2.0.0,<2.1.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' - r-base - 'r-broom >=0.4' - 'r-data.table >=1.9.6' @@ -39,14 +39,14 @@ requirements: - 'r-scales >=0.4.0' - 'r-viridis >=0.3' run: - - 'bioconductor-biocparallel >=1.16.0,<1.17.0' - - 'bioconductor-biovizbase >=1.30.0,<1.31.0' - - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' - - 'bioconductor-genomicalignments >=1.18.0,<1.19.0' - - 'bioconductor-genomicranges >=1.34.0,<1.35.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-rsamtools >=1.34.0,<1.35.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-biocparallel >=1.18.0,<1.19.0' + - 'bioconductor-biovizbase >=1.32.0,<1.33.0' + - 'bioconductor-genomeinfodb >=1.20.0,<1.21.0' + - 'bioconductor-genomicalignments >=1.20.0,<1.21.0' + - 'bioconductor-genomicranges >=1.36.0,<1.37.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-rsamtools >=2.0.0,<2.1.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' - r-base - 'r-broom >=0.4' - 'r-data.table >=1.9.6' diff --git a/recipes/bioconductor-chipexoqualexample/meta.yaml b/recipes/bioconductor-chipexoqualexample/meta.yaml index ebadeacbb80e1..a4401dcfcad76 100644 --- a/recipes/bioconductor-chipexoqualexample/meta.yaml +++ b/recipes/bioconductor-chipexoqualexample/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.6.0" %} +{% set version = "1.8.0" %} {% set name = "ChIPexoQualExample" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 18e7a340ba4586efebd01c0eaa2de1b4 + md5: 991058493c34afddf1ea08c093d52206 build: number: 0 rpaths: @@ -22,7 +22,7 @@ requirements: - r-base run: - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-chipexoqualexample/post-link.sh b/recipes/bioconductor-chipexoqualexample/post-link.sh index 646b804921e47..bd9babbd87acb 100644 --- a/recipes/bioconductor-chipexoqualexample/post-link.sh +++ b/recipes/bioconductor-chipexoqualexample/post-link.sh @@ -1,11 +1,11 @@ #!/bin/bash -FN="ChIPexoQualExample_1.6.0.tar.gz" +FN="ChIPexoQualExample_1.8.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/experiment/src/contrib/ChIPexoQualExample_1.6.0.tar.gz" - "https://bioarchive.galaxyproject.org/ChIPexoQualExample_1.6.0.tar.gz" - "https://depot.galaxyproject.org/software/bioconductor-chipexoqualexample/bioconductor-chipexoqualexample_1.6.0_src_all.tar.gz" + "https://bioconductor.org/packages/3.9/data/experiment/src/contrib/ChIPexoQualExample_1.8.0.tar.gz" + "https://bioarchive.galaxyproject.org/ChIPexoQualExample_1.8.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-chipexoqualexample/bioconductor-chipexoqualexample_1.8.0_src_all.tar.gz" ) -MD5="18e7a340ba4586efebd01c0eaa2de1b4" +MD5="991058493c34afddf1ea08c093d52206" # Use a staging area in the conda dir rather than temp dirs, both to avoid # permission issues as well as to have things downloaded in a predictable @@ -16,7 +16,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-chippeakanno/meta.yaml b/recipes/bioconductor-chippeakanno/meta.yaml index 85b2ab2c8ae07..d06afa968eb65 100644 --- a/recipes/bioconductor-chippeakanno/meta.yaml +++ b/recipes/bioconductor-chippeakanno/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "3.16.0" %} +{% set version = "3.18.0" %} {% set name = "ChIPpeakAnno" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,38 +10,39 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 5e52ae5329247caf5e5b29de1051c5b3 + md5: ce563c6fe91bb8422e9cfecdc831238b build: number: 0 rpaths: - lib/R/lib/ - lib/ noarch: generic -# Suggests: reactome.db, BSgenome.Ecoli.NCBI.20080805, BSgenome.Hsapiens.UCSC.hg19, org.Ce.eg.db, org.Hs.eg.db, BSgenome.Celegans.UCSC.ce10, BSgenome.Drerio.UCSC.danRer7, EnsDb.Hsapiens.v75, EnsDb.Hsapiens.v79, TxDb.Hsapiens.UCSC.hg19.knownGene, TxDb.Hsapiens.UCSC.hg38.knownGene, gplots, BiocStyle, rtracklayer, knitr, rmarkdown, testthat, trackViewer, motifStack, OrganismDbi +# Suggests: reactome.db, BSgenome.Ecoli.NCBI.20080805, BSgenome.Hsapiens.UCSC.hg19, org.Ce.eg.db, org.Hs.eg.db, BSgenome.Celegans.UCSC.ce10, BSgenome.Drerio.UCSC.danRer7, EnsDb.Hsapiens.v75, EnsDb.Hsapiens.v79, TxDb.Hsapiens.UCSC.hg19.knownGene, TxDb.Hsapiens.UCSC.hg38.knownGene, gplots, BiocStyle, knitr, rmarkdown, testthat, trackViewer, motifStack, OrganismDbi requirements: host: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' - - 'bioconductor-biobase >=2.42.0,<2.43.0' - - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' - - 'bioconductor-biomart >=2.38.0,<2.39.0' - - 'bioconductor-biostrings >=2.50.0,<2.51.0' - - 'bioconductor-bsgenome >=1.50.0,<1.51.0' - - 'bioconductor-delayedarray >=0.8.0,<0.9.0' - - 'bioconductor-ensembldb >=2.6.0,<2.7.0' - - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' - - 'bioconductor-genomicalignments >=1.18.0,<1.19.0' - - 'bioconductor-genomicfeatures >=1.34.0,<1.35.0' - - 'bioconductor-genomicranges >=1.34.0,<1.35.0' - - 'bioconductor-go.db >=3.7.0,<3.8.0' - - 'bioconductor-graph >=1.60.0,<1.61.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-limma >=3.38.0,<3.39.0' - - 'bioconductor-multtest >=2.38.0,<2.39.0' - - 'bioconductor-rbgl >=1.58.0,<1.59.0' - - 'bioconductor-regioner >=1.14.0,<1.15.0' - - 'bioconductor-rsamtools >=1.34.0,<1.35.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' - - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' + - 'bioconductor-biocgenerics >=0.30.0,<0.31.0' + - 'bioconductor-biomart >=2.40.0,<2.41.0' + - 'bioconductor-biostrings >=2.52.0,<2.53.0' + - 'bioconductor-bsgenome >=1.52.0,<1.53.0' + - 'bioconductor-delayedarray >=0.10.0,<0.11.0' + - 'bioconductor-ensembldb >=2.8.0,<2.9.0' + - 'bioconductor-genomeinfodb >=1.20.0,<1.21.0' + - 'bioconductor-genomicalignments >=1.20.0,<1.21.0' + - 'bioconductor-genomicfeatures >=1.36.0,<1.37.0' + - 'bioconductor-genomicranges >=1.36.0,<1.37.0' + - 'bioconductor-go.db >=3.8.0,<3.9.0' + - 'bioconductor-graph >=1.62.0,<1.63.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-limma >=3.40.0,<3.41.0' + - 'bioconductor-multtest >=2.40.0,<2.41.0' + - 'bioconductor-rbgl >=1.60.0,<1.61.0' + - 'bioconductor-regioner >=1.16.0,<1.17.0' + - 'bioconductor-rsamtools >=2.0.0,<2.1.0' + - 'bioconductor-rtracklayer >=1.44.0,<1.45.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' + - 'bioconductor-summarizedexperiment >=1.14.0,<1.15.0' - r-base - r-biocmanager - r-dbi @@ -50,28 +51,29 @@ requirements: - r-seqinr - r-venndiagram run: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' - - 'bioconductor-biobase >=2.42.0,<2.43.0' - - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' - - 'bioconductor-biomart >=2.38.0,<2.39.0' - - 'bioconductor-biostrings >=2.50.0,<2.51.0' - - 'bioconductor-bsgenome >=1.50.0,<1.51.0' - - 'bioconductor-delayedarray >=0.8.0,<0.9.0' - - 'bioconductor-ensembldb >=2.6.0,<2.7.0' - - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' - - 'bioconductor-genomicalignments >=1.18.0,<1.19.0' - - 'bioconductor-genomicfeatures >=1.34.0,<1.35.0' - - 'bioconductor-genomicranges >=1.34.0,<1.35.0' - - 'bioconductor-go.db >=3.7.0,<3.8.0' - - 'bioconductor-graph >=1.60.0,<1.61.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-limma >=3.38.0,<3.39.0' - - 'bioconductor-multtest >=2.38.0,<2.39.0' - - 'bioconductor-rbgl >=1.58.0,<1.59.0' - - 'bioconductor-regioner >=1.14.0,<1.15.0' - - 'bioconductor-rsamtools >=1.34.0,<1.35.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' - - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' + - 'bioconductor-biocgenerics >=0.30.0,<0.31.0' + - 'bioconductor-biomart >=2.40.0,<2.41.0' + - 'bioconductor-biostrings >=2.52.0,<2.53.0' + - 'bioconductor-bsgenome >=1.52.0,<1.53.0' + - 'bioconductor-delayedarray >=0.10.0,<0.11.0' + - 'bioconductor-ensembldb >=2.8.0,<2.9.0' + - 'bioconductor-genomeinfodb >=1.20.0,<1.21.0' + - 'bioconductor-genomicalignments >=1.20.0,<1.21.0' + - 'bioconductor-genomicfeatures >=1.36.0,<1.37.0' + - 'bioconductor-genomicranges >=1.36.0,<1.37.0' + - 'bioconductor-go.db >=3.8.0,<3.9.0' + - 'bioconductor-graph >=1.62.0,<1.63.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-limma >=3.40.0,<3.41.0' + - 'bioconductor-multtest >=2.40.0,<2.41.0' + - 'bioconductor-rbgl >=1.60.0,<1.61.0' + - 'bioconductor-regioner >=1.16.0,<1.17.0' + - 'bioconductor-rsamtools >=2.0.0,<2.1.0' + - 'bioconductor-rtracklayer >=1.44.0,<1.45.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' + - 'bioconductor-summarizedexperiment >=1.14.0,<1.15.0' - r-base - r-biocmanager - r-dbi diff --git a/recipes/bioconductor-chipqc/meta.yaml b/recipes/bioconductor-chipqc/meta.yaml index 039660483e354..aa54ad4126c26 100644 --- a/recipes/bioconductor-chipqc/meta.yaml +++ b/recipes/bioconductor-chipqc/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.18.2" %} +{% set version = "1.20.0" %} {% set name = "ChIPQC" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 16de65710a6d40872b208d6bdad77a9f + md5: 1eeef062ff28b32273a925872e9b4de0 build: number: 0 rpaths: @@ -20,17 +20,17 @@ build: # Suggests: BiocStyle requirements: host: - - 'bioconductor-biobase >=2.42.0,<2.43.0' - - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' - - 'bioconductor-biocparallel >=1.16.0,<1.17.0' - - 'bioconductor-chipseq >=1.32.0,<1.33.0' - - 'bioconductor-diffbind >=2.10.0,<2.11.0' - - 'bioconductor-genomicalignments >=1.18.0,<1.19.0' - - 'bioconductor-genomicfeatures >=1.34.0,<1.35.0' - - 'bioconductor-genomicranges >=1.34.0,<1.35.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-rsamtools >=1.34.0,<1.35.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' + - 'bioconductor-biocgenerics >=0.30.0,<0.31.0' + - 'bioconductor-biocparallel >=1.18.0,<1.19.0' + - 'bioconductor-chipseq >=1.34.0,<1.35.0' + - 'bioconductor-diffbind >=2.12.0,<2.13.0' + - 'bioconductor-genomicalignments >=1.20.0,<1.21.0' + - 'bioconductor-genomicfeatures >=1.36.0,<1.37.0' + - 'bioconductor-genomicranges >=1.36.0,<1.37.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-rsamtools >=2.0.0,<2.1.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' - 'bioconductor-txdb.celegans.ucsc.ce6.ensgene >=3.2.0,<3.3.0' - 'bioconductor-txdb.dmelanogaster.ucsc.dm3.ensgene >=3.2.0,<3.3.0' - 'bioconductor-txdb.hsapiens.ucsc.hg18.knowngene >=3.2.0,<3.3.0' @@ -44,17 +44,17 @@ requirements: - r-nozzle.r1 - r-reshape2 run: - - 'bioconductor-biobase >=2.42.0,<2.43.0' - - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' - - 'bioconductor-biocparallel >=1.16.0,<1.17.0' - - 'bioconductor-chipseq >=1.32.0,<1.33.0' - - 'bioconductor-diffbind >=2.10.0,<2.11.0' - - 'bioconductor-genomicalignments >=1.18.0,<1.19.0' - - 'bioconductor-genomicfeatures >=1.34.0,<1.35.0' - - 'bioconductor-genomicranges >=1.34.0,<1.35.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-rsamtools >=1.34.0,<1.35.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' + - 'bioconductor-biocgenerics >=0.30.0,<0.31.0' + - 'bioconductor-biocparallel >=1.18.0,<1.19.0' + - 'bioconductor-chipseq >=1.34.0,<1.35.0' + - 'bioconductor-diffbind >=2.12.0,<2.13.0' + - 'bioconductor-genomicalignments >=1.20.0,<1.21.0' + - 'bioconductor-genomicfeatures >=1.36.0,<1.37.0' + - 'bioconductor-genomicranges >=1.36.0,<1.37.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-rsamtools >=2.0.0,<2.1.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' - 'bioconductor-txdb.celegans.ucsc.ce6.ensgene >=3.2.0,<3.3.0' - 'bioconductor-txdb.dmelanogaster.ucsc.dm3.ensgene >=3.2.0,<3.3.0' - 'bioconductor-txdb.hsapiens.ucsc.hg18.knowngene >=3.2.0,<3.3.0' diff --git a/recipes/bioconductor-chipseeker/meta.yaml b/recipes/bioconductor-chipseeker/meta.yaml index 73c680fdbf297..1240a5742c2df 100644 --- a/recipes/bioconductor-chipseeker/meta.yaml +++ b/recipes/bioconductor-chipseeker/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.18.0" %} +{% set version = "1.20.0" %} {% set name = "ChIPseeker" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: ef4405a995f3e80a672528ddb20d0279 + md5: bb0609bdaf4de9d9423bfd758bad1e12 build: number: 0 rpaths: @@ -20,15 +20,15 @@ build: # Suggests: clusterProfiler, ReactomePA, org.Hs.eg.db, knitr, BiocStyle, rmarkdown, testthat requirements: host: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' - - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' - - 'bioconductor-enrichplot >=1.2.0,<1.3.0' - - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' - - 'bioconductor-genomicfeatures >=1.34.0,<1.35.0' - - 'bioconductor-genomicranges >=1.34.0,<1.35.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-rtracklayer >=1.42.0,<1.43.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' + - 'bioconductor-biocgenerics >=0.30.0,<0.31.0' + - 'bioconductor-enrichplot >=1.4.0,<1.5.0' + - 'bioconductor-genomeinfodb >=1.20.0,<1.21.0' + - 'bioconductor-genomicfeatures >=1.36.0,<1.37.0' + - 'bioconductor-genomicranges >=1.36.0,<1.37.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-rtracklayer >=1.44.0,<1.45.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' - 'bioconductor-txdb.hsapiens.ucsc.hg19.knowngene >=3.2.0,<3.3.0' - r-base - r-boot @@ -42,15 +42,15 @@ requirements: - r-rcolorbrewer - r-upsetr run: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' - - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' - - 'bioconductor-enrichplot >=1.2.0,<1.3.0' - - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' - - 'bioconductor-genomicfeatures >=1.34.0,<1.35.0' - - 'bioconductor-genomicranges >=1.34.0,<1.35.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-rtracklayer >=1.42.0,<1.43.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' + - 'bioconductor-biocgenerics >=0.30.0,<0.31.0' + - 'bioconductor-enrichplot >=1.4.0,<1.5.0' + - 'bioconductor-genomeinfodb >=1.20.0,<1.21.0' + - 'bioconductor-genomicfeatures >=1.36.0,<1.37.0' + - 'bioconductor-genomicranges >=1.36.0,<1.37.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-rtracklayer >=1.44.0,<1.45.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' - 'bioconductor-txdb.hsapiens.ucsc.hg19.knowngene >=3.2.0,<3.3.0' - r-base - r-boot diff --git a/recipes/bioconductor-chipseq/meta.yaml b/recipes/bioconductor-chipseq/meta.yaml index 4e289832adcb5..667a63b76e8bd 100644 --- a/recipes/bioconductor-chipseq/meta.yaml +++ b/recipes/bioconductor-chipseq/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.32.0" %} +{% set version = "1.34.0" %} {% set name = "chipseq" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,28 +10,28 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 290f7ce079aa0d77772ce81d8499f3af + md5: 0789cf5bd49a71364a763517cb219aea build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ # Suggests: BSgenome, GenomicFeatures, TxDb.Mmusculus.UCSC.mm9.knownGene requirements: host: - - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' - - 'bioconductor-genomicranges >=1.34.0,<1.35.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' - - 'bioconductor-shortread >=1.40.0,<1.41.0' + - 'bioconductor-biocgenerics >=0.30.0,<0.31.0' + - 'bioconductor-genomicranges >=1.36.0,<1.37.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' + - 'bioconductor-shortread >=1.42.0,<1.43.0' - r-base - r-lattice run: - - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' - - 'bioconductor-genomicranges >=1.34.0,<1.35.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' - - 'bioconductor-shortread >=1.40.0,<1.41.0' + - 'bioconductor-biocgenerics >=0.30.0,<0.31.0' + - 'bioconductor-genomicranges >=1.36.0,<1.37.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' + - 'bioconductor-shortread >=1.42.0,<1.43.0' - r-base - r-lattice build: diff --git a/recipes/bioconductor-chipseqdbdata/meta.yaml b/recipes/bioconductor-chipseqdbdata/meta.yaml new file mode 100644 index 0000000000000..2db079015db39 --- /dev/null +++ b/recipes/bioconductor-chipseqdbdata/meta.yaml @@ -0,0 +1,40 @@ +{% set version = "1.0.0" %} +{% set name = "chipseqDBData" %} +{% set bioc = "3.9" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: 89f8ca03e19a3107510d93bb3a082625 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: knitr, BiocStyle, Rsamtools +requirements: + host: + - 'bioconductor-annotationhub >=2.16.0,<2.17.0' + - 'bioconductor-experimenthub >=1.10.0,<1.11.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' + - r-base + run: + - 'bioconductor-annotationhub >=2.16.0,<2.17.0' + - 'bioconductor-experimenthub >=1.10.0,<1.11.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' + - r-base + - curl +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html' + license: 'CC BY 4.0' + summary: 'Sorted and indexed BAM files for ChIP-seq libraries, for use in the chipseqDB workflow. BAM indices are also included.' + diff --git a/recipes/bioconductor-chipseqdbdata/post-link.sh b/recipes/bioconductor-chipseqdbdata/post-link.sh new file mode 100644 index 0000000000000..4d6acb42e303f --- /dev/null +++ b/recipes/bioconductor-chipseqdbdata/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="chipseqDBData_1.0.0.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.9/data/experiment/src/contrib/chipseqDBData_1.0.0.tar.gz" + "https://bioarchive.galaxyproject.org/chipseqDBData_1.0.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-chipseqdbdata/bioconductor-chipseqdbdata_1.0.0_src_all.tar.gz" +) +MD5="89f8ca03e19a3107510d93bb3a082625" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + curl $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-chipseqdbdata/pre-unlink.sh b/recipes/bioconductor-chipseqdbdata/pre-unlink.sh new file mode 100644 index 0000000000000..b71f387271e23 --- /dev/null +++ b/recipes/bioconductor-chipseqdbdata/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ chipseqDBData diff --git a/recipes/bioconductor-chipseqr/meta.yaml b/recipes/bioconductor-chipseqr/meta.yaml index 2da8c55a1528e..00476971d6d2c 100644 --- a/recipes/bioconductor-chipseqr/meta.yaml +++ b/recipes/bioconductor-chipseqr/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.36.0" %} +{% set version = "1.38.0" %} {% set name = "ChIPseqR" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,32 +10,32 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 546c295c55884109a0a1e834b58c41b2 + md5: b1ce207d55454fdc59df12255e6d3f0f build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ requirements: host: - - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' - - 'bioconductor-biostrings >=2.50.0,<2.51.0' - - 'bioconductor-genomicranges >=1.34.0,<1.35.0' - - 'bioconductor-hilbertvis >=1.40.0,<1.41.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' - - 'bioconductor-shortread >=1.40.0,<1.41.0' + - 'bioconductor-biocgenerics >=0.30.0,<0.31.0' + - 'bioconductor-biostrings >=2.52.0,<2.53.0' + - 'bioconductor-genomicranges >=1.36.0,<1.37.0' + - 'bioconductor-hilbertvis >=1.42.0,<1.43.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' + - 'bioconductor-shortread >=1.42.0,<1.43.0' - r-base - r-fbasics - r-timsac run: - - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' - - 'bioconductor-biostrings >=2.50.0,<2.51.0' - - 'bioconductor-genomicranges >=1.34.0,<1.35.0' - - 'bioconductor-hilbertvis >=1.40.0,<1.41.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' - - 'bioconductor-shortread >=1.40.0,<1.41.0' + - 'bioconductor-biocgenerics >=0.30.0,<0.31.0' + - 'bioconductor-biostrings >=2.52.0,<2.53.0' + - 'bioconductor-genomicranges >=1.36.0,<1.37.0' + - 'bioconductor-hilbertvis >=1.42.0,<1.43.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' + - 'bioconductor-shortread >=1.42.0,<1.43.0' - r-base - r-fbasics - r-timsac diff --git a/recipes/bioconductor-chipseqspike/meta.yaml b/recipes/bioconductor-chipseqspike/meta.yaml index aabcf4db3dcd5..40651c3137ca6 100644 --- a/recipes/bioconductor-chipseqspike/meta.yaml +++ b/recipes/bioconductor-chipseqspike/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.2.0" %} +{% set version = "1.4.0" %} {% set name = "ChIPSeqSpike" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 4d22e39a23ca76f29f3d1ad621c608f8 + md5: f36d97df712bd1d40d5ccddda86dcc05 build: number: 0 rpaths: @@ -20,26 +20,26 @@ build: # Suggests: BiocStyle, knitr, rmarkdown, testthat requirements: host: - - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' - - 'bioconductor-genomicranges >=1.34.0,<1.35.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-rsamtools >=1.34.0,<1.35.0' - - 'bioconductor-rtracklayer >=1.42.0,<1.43.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' - - 'bioconductor-seqplots >=1.20.0,<1.21.0' + - 'bioconductor-biocgenerics >=0.30.0,<0.31.0' + - 'bioconductor-genomicranges >=1.36.0,<1.37.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-rsamtools >=2.0.0,<2.1.0' + - 'bioconductor-rtracklayer >=1.44.0,<1.45.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' + - 'bioconductor-seqplots >=1.22.0,<1.23.0' - r-base - r-corrplot - r-ggplot2 - r-lsd - r-stringr run: - - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' - - 'bioconductor-genomicranges >=1.34.0,<1.35.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-rsamtools >=1.34.0,<1.35.0' - - 'bioconductor-rtracklayer >=1.42.0,<1.43.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' - - 'bioconductor-seqplots >=1.20.0,<1.21.0' + - 'bioconductor-biocgenerics >=0.30.0,<0.31.0' + - 'bioconductor-genomicranges >=1.36.0,<1.37.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-rsamtools >=2.0.0,<2.1.0' + - 'bioconductor-rtracklayer >=1.44.0,<1.45.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' + - 'bioconductor-seqplots >=1.22.0,<1.23.0' - r-base - r-corrplot - r-ggplot2 diff --git a/recipes/bioconductor-chipsim/meta.yaml b/recipes/bioconductor-chipsim/meta.yaml index 9fd4a68c795af..d77fb1a41fcd3 100644 --- a/recipes/bioconductor-chipsim/meta.yaml +++ b/recipes/bioconductor-chipsim/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.36.0" %} +{% set version = "1.38.0" %} {% set name = "ChIPsim" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 807aa8e54aeac47c04e3b4173118482a + md5: 21a19dd3b1a20aa6feabae9db8193bd3 build: number: 0 rpaths: @@ -20,16 +20,16 @@ build: # Suggests: actuar, zoo requirements: host: - - 'bioconductor-biostrings >=2.50.0,<2.51.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-shortread >=1.40.0,<1.41.0' - - 'bioconductor-xvector >=0.22.0,<0.23.0' + - 'bioconductor-biostrings >=2.52.0,<2.53.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-shortread >=1.42.0,<1.43.0' + - 'bioconductor-xvector >=0.24.0,<0.25.0' - r-base run: - - 'bioconductor-biostrings >=2.50.0,<2.51.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-shortread >=1.40.0,<1.41.0' - - 'bioconductor-xvector >=0.22.0,<0.23.0' + - 'bioconductor-biostrings >=2.52.0,<2.53.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-shortread >=1.42.0,<1.43.0' + - 'bioconductor-xvector >=0.24.0,<0.25.0' - r-base test: commands: diff --git a/recipes/bioconductor-chipxpress/meta.yaml b/recipes/bioconductor-chipxpress/meta.yaml index 79397fe7400eb..516f06807dfca 100644 --- a/recipes/bioconductor-chipxpress/meta.yaml +++ b/recipes/bioconductor-chipxpress/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.26.0" %} +{% set version = "1.28.0" %} {% set name = "ChIPXpress" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 42bb787851b0c8b7875266dff5128c4e + md5: 9680fbb73971f9b76b2099d0b0ca8161 build: number: 0 rpaths: @@ -20,20 +20,20 @@ build: # Suggests: mouse4302frmavecs, mouse4302.db, mouse4302cdf, RUnit, BiocGenerics requirements: host: - - 'bioconductor-affy >=1.60.0,<1.61.0' - - 'bioconductor-biobase >=2.42.0,<2.43.0' - - 'bioconductor-chipxpressdata >=1.20.0,<1.21.0' - - 'bioconductor-frma >=1.34.0,<1.35.0' - - 'bioconductor-geoquery >=2.50.0,<2.51.0' + - 'bioconductor-affy >=1.62.0,<1.63.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' + - 'bioconductor-chipxpressdata >=1.22.0,<1.23.0' + - 'bioconductor-frma >=1.36.0,<1.37.0' + - 'bioconductor-geoquery >=2.52.0,<2.53.0' - r-base - r-biganalytics - r-bigmemory run: - - 'bioconductor-affy >=1.60.0,<1.61.0' - - 'bioconductor-biobase >=2.42.0,<2.43.0' - - 'bioconductor-chipxpressdata >=1.20.0,<1.21.0' - - 'bioconductor-frma >=1.34.0,<1.35.0' - - 'bioconductor-geoquery >=2.50.0,<2.51.0' + - 'bioconductor-affy >=1.62.0,<1.63.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' + - 'bioconductor-chipxpressdata >=1.22.0,<1.23.0' + - 'bioconductor-frma >=1.36.0,<1.37.0' + - 'bioconductor-geoquery >=2.52.0,<2.53.0' - r-base - r-biganalytics - r-bigmemory diff --git a/recipes/bioconductor-chipxpressdata/meta.yaml b/recipes/bioconductor-chipxpressdata/meta.yaml index 392d73f7396e7..6e01150aa6bbe 100644 --- a/recipes/bioconductor-chipxpressdata/meta.yaml +++ b/recipes/bioconductor-chipxpressdata/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.20.0" %} +{% set version = "1.22.0" %} {% set name = "ChIPXpressData" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: a22a580a546729aa51a3e5899c047f1e + md5: 4dc8f6accadaa504672e7f40d144460a build: number: 0 rpaths: @@ -24,7 +24,7 @@ requirements: run: - r-base - r-bigmemory - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-chipxpressdata/post-link.sh b/recipes/bioconductor-chipxpressdata/post-link.sh index e98475ddc773f..570324777bc1d 100644 --- a/recipes/bioconductor-chipxpressdata/post-link.sh +++ b/recipes/bioconductor-chipxpressdata/post-link.sh @@ -1,11 +1,11 @@ #!/bin/bash -FN="ChIPXpressData_1.20.0.tar.gz" +FN="ChIPXpressData_1.22.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/experiment/src/contrib/ChIPXpressData_1.20.0.tar.gz" - "https://bioarchive.galaxyproject.org/ChIPXpressData_1.20.0.tar.gz" - "https://depot.galaxyproject.org/software/bioconductor-chipxpressdata/bioconductor-chipxpressdata_1.20.0_src_all.tar.gz" + "https://bioconductor.org/packages/3.9/data/experiment/src/contrib/ChIPXpressData_1.22.0.tar.gz" + "https://bioarchive.galaxyproject.org/ChIPXpressData_1.22.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-chipxpressdata/bioconductor-chipxpressdata_1.22.0_src_all.tar.gz" ) -MD5="a22a580a546729aa51a3e5899c047f1e" +MD5="4dc8f6accadaa504672e7f40d144460a" # Use a staging area in the conda dir rather than temp dirs, both to avoid # permission issues as well as to have things downloaded in a predictable @@ -16,7 +16,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-chopsticks/meta.yaml b/recipes/bioconductor-chopsticks/meta.yaml index 86dc8bcbc2245..34b97afcd54c3 100644 --- a/recipes/bioconductor-chopsticks/meta.yaml +++ b/recipes/bioconductor-chopsticks/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.48.0" %} +{% set version = "1.50.0" %} {% set name = "chopsticks" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: b808bcd49f1f23d35a2189e46df3a6de + md5: 6971614767463f422261c871144d0de4 build: number: 0 rpaths: diff --git a/recipes/bioconductor-chrogps/meta.yaml b/recipes/bioconductor-chrogps/meta.yaml index 553b80ce32629..d02882ecfd6f4 100644 --- a/recipes/bioconductor-chrogps/meta.yaml +++ b/recipes/bioconductor-chrogps/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "2.0.1" %} +{% set version = "2.2.0" %} {% set name = "chroGPS" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: e2d2fbcc1addfcf53cac565380b86399 + md5: 1c20015597fc1f3d3e4f99320344c4bf build: number: 0 rpaths: @@ -19,9 +19,9 @@ build: noarch: generic requirements: host: - - 'bioconductor-biobase >=2.42.0,<2.43.0' - - 'bioconductor-genomicranges >=1.34.0,<1.35.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' + - 'bioconductor-genomicranges >=1.36.0,<1.37.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' - r-base - r-changepoint - r-cluster @@ -31,9 +31,9 @@ requirements: - r-mass - r-vegan run: - - 'bioconductor-biobase >=2.42.0,<2.43.0' - - 'bioconductor-genomicranges >=1.34.0,<1.35.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' + - 'bioconductor-genomicranges >=1.36.0,<1.37.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' - r-base - r-changepoint - r-cluster diff --git a/recipes/bioconductor-chromdraw/meta.yaml b/recipes/bioconductor-chromdraw/meta.yaml index 0b1f91a0bbb06..c1b01692f9fd1 100644 --- a/recipes/bioconductor-chromdraw/meta.yaml +++ b/recipes/bioconductor-chromdraw/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "2.12.0" %} +{% set version = "2.14.0" %} {% set name = "chromDraw" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: c54bc321ee938793b8fcbb474ef540f1 + md5: e577a789a88f7d82e8e6fc7a9388cbb5 build: number: 0 rpaths: @@ -19,11 +19,11 @@ build: # SystemRequirements: Rtools (>= 3.1) requirements: host: - - 'bioconductor-genomicranges >=1.34.0,<1.35.0' + - 'bioconductor-genomicranges >=1.36.0,<1.37.0' - r-base - 'r-rcpp >=0.11.1' run: - - 'bioconductor-genomicranges >=1.34.0,<1.35.0' + - 'bioconductor-genomicranges >=1.36.0,<1.37.0' - r-base - 'r-rcpp >=0.11.1' build: diff --git a/recipes/bioconductor-chromheatmap/meta.yaml b/recipes/bioconductor-chromheatmap/meta.yaml index 19398e5f69d82..b4a52d6b57dc0 100644 --- a/recipes/bioconductor-chromheatmap/meta.yaml +++ b/recipes/bioconductor-chromheatmap/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.36.0" %} +{% set version = "1.38.0" %} {% set name = "ChromHeatMap" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 8c849b949219b4a16234dc8850dd594e + md5: 86424fcf2665a84797efb9977b73449f build: number: 0 rpaths: @@ -20,22 +20,22 @@ build: # Suggests: ALL, hgu95av2.db requirements: host: - - 'bioconductor-annotate >=1.60.0,<1.61.0' - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' - - 'bioconductor-biobase >=2.42.0,<2.43.0' - - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' - - 'bioconductor-genomicranges >=1.34.0,<1.35.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-rtracklayer >=1.42.0,<1.43.0' + - 'bioconductor-annotate >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' + - 'bioconductor-biocgenerics >=0.30.0,<0.31.0' + - 'bioconductor-genomicranges >=1.36.0,<1.37.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-rtracklayer >=1.44.0,<1.45.0' - r-base run: - - 'bioconductor-annotate >=1.60.0,<1.61.0' - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' - - 'bioconductor-biobase >=2.42.0,<2.43.0' - - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' - - 'bioconductor-genomicranges >=1.34.0,<1.35.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-rtracklayer >=1.42.0,<1.43.0' + - 'bioconductor-annotate >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' + - 'bioconductor-biocgenerics >=0.30.0,<0.31.0' + - 'bioconductor-genomicranges >=1.36.0,<1.37.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-rtracklayer >=1.44.0,<1.45.0' - r-base test: commands: diff --git a/recipes/bioconductor-chromplot/meta.yaml b/recipes/bioconductor-chromplot/meta.yaml index 409b39de15bb2..5d09846614c89 100644 --- a/recipes/bioconductor-chromplot/meta.yaml +++ b/recipes/bioconductor-chromplot/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.10.0" %} +{% set version = "1.12.0" %} {% set name = "chromPlot" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: fd2da81e6c20c564f5b23a49c65e6847 + md5: a83b3a023294deec5184eb5f7af01ec1 build: number: 0 rpaths: @@ -20,12 +20,12 @@ build: # Suggests: qtl, GenomicFeatures, TxDb.Hsapiens.UCSC.hg19.knownGene requirements: host: - - 'bioconductor-biomart >=2.38.0,<2.39.0' - - 'bioconductor-genomicranges >=1.34.0,<1.35.0' + - 'bioconductor-biomart >=2.40.0,<2.41.0' + - 'bioconductor-genomicranges >=1.36.0,<1.37.0' - r-base run: - - 'bioconductor-biomart >=2.38.0,<2.39.0' - - 'bioconductor-genomicranges >=1.34.0,<1.35.0' + - 'bioconductor-biomart >=2.40.0,<2.41.0' + - 'bioconductor-genomicranges >=1.36.0,<1.37.0' - r-base test: commands: diff --git a/recipes/bioconductor-chromstar/meta.yaml b/recipes/bioconductor-chromstar/meta.yaml index 79e2dbe121073..e88454b8db5ff 100644 --- a/recipes/bioconductor-chromstar/meta.yaml +++ b/recipes/bioconductor-chromstar/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.8.1" %} +{% set version = "1.10.0" %} {% set name = "chromstaR" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 55388dee59d7db8dd9042778d0ff9f79 + md5: 021eb8e6f24bb476a42ceefcaf19b883 build: number: 0 rpaths: @@ -19,14 +19,14 @@ build: # Suggests: knitr, BiocStyle, testthat, biomaRt requirements: host: - - 'bioconductor-bamsignals >=1.14.0,<1.15.0' - - 'bioconductor-chromstardata >=1.8.0,<1.9.0' - - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' - - 'bioconductor-genomicalignments >=1.18.0,<1.19.0' - - 'bioconductor-genomicranges >=1.34.0,<1.35.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-rsamtools >=1.34.0,<1.35.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-bamsignals >=1.16.0,<1.17.0' + - 'bioconductor-chromstardata >=1.10.0,<1.11.0' + - 'bioconductor-genomeinfodb >=1.20.0,<1.21.0' + - 'bioconductor-genomicalignments >=1.20.0,<1.21.0' + - 'bioconductor-genomicranges >=1.36.0,<1.37.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-rsamtools >=2.0.0,<2.1.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' - r-base - r-doparallel - r-foreach @@ -34,14 +34,14 @@ requirements: - r-mvtnorm - r-reshape2 run: - - 'bioconductor-bamsignals >=1.14.0,<1.15.0' - - 'bioconductor-chromstardata >=1.8.0,<1.9.0' - - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' - - 'bioconductor-genomicalignments >=1.18.0,<1.19.0' - - 'bioconductor-genomicranges >=1.34.0,<1.35.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-rsamtools >=1.34.0,<1.35.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-bamsignals >=1.16.0,<1.17.0' + - 'bioconductor-chromstardata >=1.10.0,<1.11.0' + - 'bioconductor-genomeinfodb >=1.20.0,<1.21.0' + - 'bioconductor-genomicalignments >=1.20.0,<1.21.0' + - 'bioconductor-genomicranges >=1.36.0,<1.37.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-rsamtools >=2.0.0,<2.1.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' - r-base - r-doparallel - r-foreach @@ -52,7 +52,6 @@ requirements: - {{ compiler('c') }} - {{ compiler('cxx') }} - make - - llvm-openmp # [osx] test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-chromstardata/meta.yaml b/recipes/bioconductor-chromstardata/meta.yaml index c445e57853988..df043114650bc 100644 --- a/recipes/bioconductor-chromstardata/meta.yaml +++ b/recipes/bioconductor-chromstardata/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.8.0" %} +{% set version = "1.10.0" %} {% set name = "chromstaRData" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 6de05adbae8cdeacaad09e20b18bbf95 + md5: 10d6c6236f90681d268ddb75e36f8549 build: number: 0 rpaths: @@ -22,7 +22,7 @@ requirements: - r-base run: - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-chromstardata/post-link.sh b/recipes/bioconductor-chromstardata/post-link.sh index 237bb7d6576a5..1b598c295859d 100644 --- a/recipes/bioconductor-chromstardata/post-link.sh +++ b/recipes/bioconductor-chromstardata/post-link.sh @@ -1,11 +1,11 @@ #!/bin/bash -FN="chromstaRData_1.8.0.tar.gz" +FN="chromstaRData_1.10.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/experiment/src/contrib/chromstaRData_1.8.0.tar.gz" - "https://bioarchive.galaxyproject.org/chromstaRData_1.8.0.tar.gz" - "https://depot.galaxyproject.org/software/bioconductor-chromstardata/bioconductor-chromstardata_1.8.0_src_all.tar.gz" + "https://bioconductor.org/packages/3.9/data/experiment/src/contrib/chromstaRData_1.10.0.tar.gz" + "https://bioarchive.galaxyproject.org/chromstaRData_1.10.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-chromstardata/bioconductor-chromstardata_1.10.0_src_all.tar.gz" ) -MD5="6de05adbae8cdeacaad09e20b18bbf95" +MD5="10d6c6236f90681d268ddb75e36f8549" # Use a staging area in the conda dir rather than temp dirs, both to avoid # permission issues as well as to have things downloaded in a predictable @@ -16,7 +16,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-chromswitch/meta.yaml b/recipes/bioconductor-chromswitch/meta.yaml index 8279d3af3f330..a2ef5604fb087 100644 --- a/recipes/bioconductor-chromswitch/meta.yaml +++ b/recipes/bioconductor-chromswitch/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.4.1" %} +{% set version = "1.6.0" %} {% set name = "chromswitch" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 36c5d3dc74c17ed9d82bc8f1bc7b46df + md5: a4818e3957bc869fe4f87d9c38066fc3 build: number: 0 rpaths: @@ -20,12 +20,12 @@ build: # Suggests: BiocStyle, DescTools (>= 0.99.19), devtools (>= 1.13.3), GenomeInfoDb (>= 1.16.0), knitr, rmarkdown, mclust (>= 5.3), testthat requirements: host: - - 'bioconductor-biobase >=2.42.0,<2.43.0' - - 'bioconductor-biocparallel >=1.16.0,<1.17.0' - - 'bioconductor-genomicranges >=1.34.0,<1.35.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-rtracklayer >=1.42.0,<1.43.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' + - 'bioconductor-biocparallel >=1.18.0,<1.19.0' + - 'bioconductor-genomicranges >=1.36.0,<1.37.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-rtracklayer >=1.44.0,<1.45.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' - r-base - 'r-cluster >=2.0.6' - 'r-dplyr >=0.5.0' @@ -36,12 +36,12 @@ requirements: - 'r-nmf >=0.20.6' - 'r-tidyr >=0.6.3' run: - - 'bioconductor-biobase >=2.42.0,<2.43.0' - - 'bioconductor-biocparallel >=1.16.0,<1.17.0' - - 'bioconductor-genomicranges >=1.34.0,<1.35.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-rtracklayer >=1.42.0,<1.43.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' + - 'bioconductor-biocparallel >=1.18.0,<1.19.0' + - 'bioconductor-genomicranges >=1.36.0,<1.37.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-rtracklayer >=1.44.0,<1.45.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' - r-base - 'r-cluster >=2.0.6' - 'r-dplyr >=0.5.0' diff --git a/recipes/bioconductor-chromvar/meta.yaml b/recipes/bioconductor-chromvar/meta.yaml index bf2a7110be7fa..eddcef5e5ef90 100644 --- a/recipes/bioconductor-chromvar/meta.yaml +++ b/recipes/bioconductor-chromvar/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.4.1" %} +{% set version = "1.6.0" %} {% set name = "chromVAR" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 7dcbe9c69e7956109f77d47d3a69edea + md5: 00a21c0ce9d872f74f6a5206daaaaaa4 build: number: 0 rpaths: @@ -20,17 +20,17 @@ build: # SystemRequirements: C++11 requirements: host: - - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' - - 'bioconductor-biocparallel >=1.16.0,<1.17.0' - - 'bioconductor-biostrings >=2.50.0,<2.51.0' - - 'bioconductor-bsgenome >=1.50.0,<1.51.0' - - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' - - 'bioconductor-genomicranges >=1.34.0,<1.35.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-rsamtools >=1.34.0,<1.35.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' - - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' - - 'bioconductor-tfbstools >=1.20.0,<1.21.0' + - 'bioconductor-biocgenerics >=0.30.0,<0.31.0' + - 'bioconductor-biocparallel >=1.18.0,<1.19.0' + - 'bioconductor-biostrings >=2.52.0,<2.53.0' + - 'bioconductor-bsgenome >=1.52.0,<1.53.0' + - 'bioconductor-genomeinfodb >=1.20.0,<1.21.0' + - 'bioconductor-genomicranges >=1.36.0,<1.37.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-rsamtools >=2.0.0,<2.1.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' + - 'bioconductor-summarizedexperiment >=1.14.0,<1.15.0' + - 'bioconductor-tfbstools >=1.22.0,<1.23.0' - r-base - r-dt - r-ggplot2 @@ -44,17 +44,17 @@ requirements: - r-rtsne - r-shiny run: - - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' - - 'bioconductor-biocparallel >=1.16.0,<1.17.0' - - 'bioconductor-biostrings >=2.50.0,<2.51.0' - - 'bioconductor-bsgenome >=1.50.0,<1.51.0' - - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' - - 'bioconductor-genomicranges >=1.34.0,<1.35.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-rsamtools >=1.34.0,<1.35.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' - - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' - - 'bioconductor-tfbstools >=1.20.0,<1.21.0' + - 'bioconductor-biocgenerics >=0.30.0,<0.31.0' + - 'bioconductor-biocparallel >=1.18.0,<1.19.0' + - 'bioconductor-biostrings >=2.52.0,<2.53.0' + - 'bioconductor-bsgenome >=1.52.0,<1.53.0' + - 'bioconductor-genomeinfodb >=1.20.0,<1.21.0' + - 'bioconductor-genomicranges >=1.36.0,<1.37.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-rsamtools >=2.0.0,<2.1.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' + - 'bioconductor-summarizedexperiment >=1.14.0,<1.15.0' + - 'bioconductor-tfbstools >=1.22.0,<1.23.0' - r-base - r-dt - r-ggplot2 diff --git a/recipes/bioconductor-chronos/meta.yaml b/recipes/bioconductor-chronos/meta.yaml index 5b36eb53ba4dc..110cb71d9ce67 100644 --- a/recipes/bioconductor-chronos/meta.yaml +++ b/recipes/bioconductor-chronos/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.10.0" %} +{% set version = "1.12.0" %} {% set name = "CHRONOS" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 0fdab9e25f3a8db821e653397297b081 + md5: 23549499ee1be61c2fe468de10d353b0 build: number: 0 rpaths: @@ -21,27 +21,34 @@ build: # SystemRequirements: Java version >= 1.7, Pandoc requirements: host: - - 'bioconductor-biomart >=2.38.0,<2.39.0' - - 'bioconductor-graph >=1.60.0,<1.61.0' - - 'bioconductor-rbgl >=1.58.0,<1.59.0' + - 'bioconductor-biomart >=2.40.0,<2.41.0' + - 'bioconductor-graph >=1.62.0,<1.63.0' + - 'bioconductor-rbgl >=1.60.0,<1.61.0' - r-base - r-circlize - r-doparallel - r-foreach + - r-igraph - r-openxlsx - r-rcurl - r-xml + - openjdk 8.* + - pandoc run: - - 'bioconductor-biomart >=2.38.0,<2.39.0' - - 'bioconductor-graph >=1.60.0,<1.61.0' - - 'bioconductor-rbgl >=1.58.0,<1.59.0' + - 'bioconductor-biomart >=2.40.0,<2.41.0' + - 'bioconductor-graph >=1.62.0,<1.63.0' + - 'bioconductor-rbgl >=1.60.0,<1.61.0' - r-base - r-circlize - r-doparallel - r-foreach + - r-igraph - r-openxlsx - r-rcurl - r-xml + - openjdk 8.* + - pandoc + test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-cicero/meta.yaml b/recipes/bioconductor-cicero/meta.yaml index 89d596a586da1..baf63a352d182 100644 --- a/recipes/bioconductor-cicero/meta.yaml +++ b/recipes/bioconductor-cicero/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.0.14" %} +{% set version = "1.2.0" %} {% set name = "cicero" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: b1fc55ada12056f198b3e707f0de715d + md5: 20ceee0cf038811ec4b611da2d8248c7 build: number: 0 rpaths: @@ -20,13 +20,13 @@ build: # Suggests: AnnotationDbi (>= 1.38.2), knitr, rmarkdown, rtracklayer (>= 1.36.6), testthat, vdiffr (>= 0.2.3), covr requirements: host: - - 'bioconductor-biobase >=2.42.0,<2.43.0' - - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' - - 'bioconductor-genomicranges >=1.34.0,<1.35.0' - - 'bioconductor-gviz >=1.26.0,<1.27.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-monocle >=2.10.0,<2.11.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' + - 'bioconductor-biocgenerics >=0.30.0,<0.31.0' + - 'bioconductor-genomicranges >=1.36.0,<1.37.0' + - 'bioconductor-gviz >=1.28.0,<1.29.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-monocle >=2.12.0,<2.13.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' - 'r-assertthat >=0.2.0' - r-base - 'r-data.table >=1.10.4' @@ -42,13 +42,13 @@ requirements: - 'r-tibble >=1.4.2' - 'r-vgam >=1.0-5' run: - - 'bioconductor-biobase >=2.42.0,<2.43.0' - - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' - - 'bioconductor-genomicranges >=1.34.0,<1.35.0' - - 'bioconductor-gviz >=1.26.0,<1.27.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-monocle >=2.10.0,<2.11.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' + - 'bioconductor-biocgenerics >=0.30.0,<0.31.0' + - 'bioconductor-genomicranges >=1.36.0,<1.37.0' + - 'bioconductor-gviz >=1.28.0,<1.29.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-monocle >=2.12.0,<2.13.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' - 'r-assertthat >=0.2.0' - r-base - 'r-data.table >=1.10.4' diff --git a/recipes/bioconductor-cindex/meta.yaml b/recipes/bioconductor-cindex/meta.yaml index a4d5fb5aeccdd..012b591395bfc 100644 --- a/recipes/bioconductor-cindex/meta.yaml +++ b/recipes/bioconductor-cindex/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.10.0" %} +{% set version = "1.12.0" %} {% set name = "CINdex" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,9 +10,9 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 429ec61774d457ec691f01d418bb6ff1 + md5: 5194827a892d59246818e56c5c65cf59 build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ @@ -20,10 +20,10 @@ build: # Suggests: knitr, testthat, ReactomePA, RUnit, BiocGenerics, AnnotationHub, rtracklayer, pd.genomewidesnp.6, org.Hs.eg.db, biovizBase, TxDb.Hsapiens.UCSC.hg18.knownGene, methods, Biostrings,Homo.sapiens requirements: host: - - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' - - 'bioconductor-genomicranges >=1.34.0,<1.35.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-genomeinfodb >=1.20.0,<1.21.0' + - 'bioconductor-genomicranges >=1.36.0,<1.37.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' - r-base - r-bitops - r-dplyr @@ -33,10 +33,10 @@ requirements: - r-som - r-stringr run: - - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' - - 'bioconductor-genomicranges >=1.34.0,<1.35.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-genomeinfodb >=1.20.0,<1.21.0' + - 'bioconductor-genomicranges >=1.36.0,<1.37.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' - r-base - r-bitops - r-dplyr diff --git a/recipes/bioconductor-cispath/meta.yaml b/recipes/bioconductor-cispath/meta.yaml index 0542d6b1237e4..38195bffe4ac0 100644 --- a/recipes/bioconductor-cispath/meta.yaml +++ b/recipes/bioconductor-cispath/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.22.0" %} +{% set version = "1.24.0" %} {% set name = "cisPath" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: f599dcd8049193817764ff0114785078 + md5: bf2dfa76883e6262aabd0a67e7e3e6be build: number: 0 rpaths: diff --git a/recipes/bioconductor-citruscdf/meta.yaml b/recipes/bioconductor-citruscdf/meta.yaml index 493097039a05f..311282c261089 100644 --- a/recipes/bioconductor-citruscdf/meta.yaml +++ b/recipes/bioconductor-citruscdf/meta.yaml @@ -1,6 +1,6 @@ {% set version = "2.18.0" %} {% set name = "citruscdf" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -12,19 +12,19 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 4af821a0c1ae1adf42b7dc5ce7458593 build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' - r-base run: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-citruscdf/post-link.sh b/recipes/bioconductor-citruscdf/post-link.sh index 266f10bd165ed..3193cd6b4199a 100644 --- a/recipes/bioconductor-citruscdf/post-link.sh +++ b/recipes/bioconductor-citruscdf/post-link.sh @@ -1,9 +1,10 @@ #!/bin/bash FN="citruscdf_2.18.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/citruscdf_2.18.0.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/citruscdf_2.18.0.tar.gz" "https://bioarchive.galaxyproject.org/citruscdf_2.18.0.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-citruscdf/bioconductor-citruscdf_2.18.0_src_all.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-citruscdf/bioconductor-citruscdf_2.18.0_src_all.tar.gz" ) MD5="4af821a0c1ae1adf42b7dc5ce7458593" @@ -16,7 +17,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-citrusprobe/meta.yaml b/recipes/bioconductor-citrusprobe/meta.yaml index 1edc7075239a7..77190f4700e93 100644 --- a/recipes/bioconductor-citrusprobe/meta.yaml +++ b/recipes/bioconductor-citrusprobe/meta.yaml @@ -1,6 +1,6 @@ {% set version = "2.18.0" %} {% set name = "citrusprobe" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -12,19 +12,19 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 259b114f96d5307c447d000bd27a7d15 build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' - r-base run: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-citrusprobe/post-link.sh b/recipes/bioconductor-citrusprobe/post-link.sh index c1b5e46c67e4f..59244acdb2a60 100644 --- a/recipes/bioconductor-citrusprobe/post-link.sh +++ b/recipes/bioconductor-citrusprobe/post-link.sh @@ -1,9 +1,10 @@ #!/bin/bash FN="citrusprobe_2.18.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/citrusprobe_2.18.0.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/citrusprobe_2.18.0.tar.gz" "https://bioarchive.galaxyproject.org/citrusprobe_2.18.0.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-citrusprobe/bioconductor-citrusprobe_2.18.0_src_all.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-citrusprobe/bioconductor-citrusprobe_2.18.0_src_all.tar.gz" ) MD5="259b114f96d5307c447d000bd27a7d15" @@ -16,7 +17,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-clariomdhumanprobeset.db/meta.yaml b/recipes/bioconductor-clariomdhumanprobeset.db/meta.yaml index 6a6490e1c7677..29f989548cc94 100644 --- a/recipes/bioconductor-clariomdhumanprobeset.db/meta.yaml +++ b/recipes/bioconductor-clariomdhumanprobeset.db/meta.yaml @@ -1,6 +1,6 @@ {% set version = "8.7.0" %} {% set name = "clariomdhumanprobeset.db" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -12,7 +12,7 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 3f390b06a44187e10e4e8a60af16375b build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ @@ -20,14 +20,14 @@ build: # Suggests: DBI, annotate, RUnit requirements: host: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' - - 'bioconductor-org.hs.eg.db >=3.7.0,<3.8.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' + - 'bioconductor-org.hs.eg.db >=3.8.0,<3.9.0' - r-base run: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' - - 'bioconductor-org.hs.eg.db >=3.7.0,<3.8.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' + - 'bioconductor-org.hs.eg.db >=3.8.0,<3.9.0' - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-clariomdhumanprobeset.db/post-link.sh b/recipes/bioconductor-clariomdhumanprobeset.db/post-link.sh index 4e840b8594fd6..bf2c0d4c940e9 100644 --- a/recipes/bioconductor-clariomdhumanprobeset.db/post-link.sh +++ b/recipes/bioconductor-clariomdhumanprobeset.db/post-link.sh @@ -1,9 +1,10 @@ #!/bin/bash FN="clariomdhumanprobeset.db_8.7.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/clariomdhumanprobeset.db_8.7.0.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/clariomdhumanprobeset.db_8.7.0.tar.gz" "https://bioarchive.galaxyproject.org/clariomdhumanprobeset.db_8.7.0.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-clariomdhumanprobeset.db/bioconductor-clariomdhumanprobeset.db_8.7.0_src_all.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-clariomdhumanprobeset.db/bioconductor-clariomdhumanprobeset.db_8.7.0_src_all.tar.gz" ) MD5="3f390b06a44187e10e4e8a60af16375b" @@ -16,7 +17,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-clariomdhumantranscriptcluster.db/meta.yaml b/recipes/bioconductor-clariomdhumantranscriptcluster.db/meta.yaml index 8173e6ce75810..eae3e5441e151 100644 --- a/recipes/bioconductor-clariomdhumantranscriptcluster.db/meta.yaml +++ b/recipes/bioconductor-clariomdhumantranscriptcluster.db/meta.yaml @@ -1,6 +1,6 @@ {% set version = "8.7.0" %} {% set name = "clariomdhumantranscriptcluster.db" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -12,7 +12,7 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: a460203ad96a4ada92b495ac0811cbe3 build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ @@ -20,14 +20,14 @@ build: # Suggests: DBI, annotate, RUnit requirements: host: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' - - 'bioconductor-org.hs.eg.db >=3.7.0,<3.8.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' + - 'bioconductor-org.hs.eg.db >=3.8.0,<3.9.0' - r-base run: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' - - 'bioconductor-org.hs.eg.db >=3.7.0,<3.8.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' + - 'bioconductor-org.hs.eg.db >=3.8.0,<3.9.0' - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-clariomdhumantranscriptcluster.db/post-link.sh b/recipes/bioconductor-clariomdhumantranscriptcluster.db/post-link.sh index 0f69e7cf22dab..13b1d8e0788ce 100644 --- a/recipes/bioconductor-clariomdhumantranscriptcluster.db/post-link.sh +++ b/recipes/bioconductor-clariomdhumantranscriptcluster.db/post-link.sh @@ -1,9 +1,10 @@ #!/bin/bash FN="clariomdhumantranscriptcluster.db_8.7.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/clariomdhumantranscriptcluster.db_8.7.0.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/clariomdhumantranscriptcluster.db_8.7.0.tar.gz" "https://bioarchive.galaxyproject.org/clariomdhumantranscriptcluster.db_8.7.0.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-clariomdhumantranscriptcluster.db/bioconductor-clariomdhumantranscriptcluster.db_8.7.0_src_all.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-clariomdhumantranscriptcluster.db/bioconductor-clariomdhumantranscriptcluster.db_8.7.0_src_all.tar.gz" ) MD5="a460203ad96a4ada92b495ac0811cbe3" @@ -16,7 +17,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-clariomshumanhttranscriptcluster.db/meta.yaml b/recipes/bioconductor-clariomshumanhttranscriptcluster.db/meta.yaml index 7dc188a8b7553..fd95a20b93f88 100644 --- a/recipes/bioconductor-clariomshumanhttranscriptcluster.db/meta.yaml +++ b/recipes/bioconductor-clariomshumanhttranscriptcluster.db/meta.yaml @@ -1,6 +1,6 @@ {% set version = "8.7.0" %} {% set name = "clariomshumanhttranscriptcluster.db" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -12,7 +12,7 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: fce4e730f50b068d8f91319754f8024f build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ @@ -20,14 +20,14 @@ build: # Suggests: DBI, annotate, RUnit requirements: host: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' - - 'bioconductor-org.hs.eg.db >=3.7.0,<3.8.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' + - 'bioconductor-org.hs.eg.db >=3.8.0,<3.9.0' - r-base run: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' - - 'bioconductor-org.hs.eg.db >=3.7.0,<3.8.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' + - 'bioconductor-org.hs.eg.db >=3.8.0,<3.9.0' - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-clariomshumanhttranscriptcluster.db/post-link.sh b/recipes/bioconductor-clariomshumanhttranscriptcluster.db/post-link.sh index 971a1d44f30a5..f9dc9352c6328 100644 --- a/recipes/bioconductor-clariomshumanhttranscriptcluster.db/post-link.sh +++ b/recipes/bioconductor-clariomshumanhttranscriptcluster.db/post-link.sh @@ -1,9 +1,10 @@ #!/bin/bash FN="clariomshumanhttranscriptcluster.db_8.7.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/clariomshumanhttranscriptcluster.db_8.7.0.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/clariomshumanhttranscriptcluster.db_8.7.0.tar.gz" "https://bioarchive.galaxyproject.org/clariomshumanhttranscriptcluster.db_8.7.0.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-clariomshumanhttranscriptcluster.db/bioconductor-clariomshumanhttranscriptcluster.db_8.7.0_src_all.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-clariomshumanhttranscriptcluster.db/bioconductor-clariomshumanhttranscriptcluster.db_8.7.0_src_all.tar.gz" ) MD5="fce4e730f50b068d8f91319754f8024f" @@ -16,7 +17,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-clariomshumantranscriptcluster.db/meta.yaml b/recipes/bioconductor-clariomshumantranscriptcluster.db/meta.yaml index 7060dbd8345bc..c0fb2975fd066 100644 --- a/recipes/bioconductor-clariomshumantranscriptcluster.db/meta.yaml +++ b/recipes/bioconductor-clariomshumantranscriptcluster.db/meta.yaml @@ -1,6 +1,6 @@ {% set version = "8.7.0" %} {% set name = "clariomshumantranscriptcluster.db" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -12,7 +12,7 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 0b92969a4bb4a2d8e972602f68c7ad1b build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ @@ -20,14 +20,14 @@ build: # Suggests: DBI, annotate, RUnit requirements: host: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' - - 'bioconductor-org.hs.eg.db >=3.7.0,<3.8.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' + - 'bioconductor-org.hs.eg.db >=3.8.0,<3.9.0' - r-base run: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' - - 'bioconductor-org.hs.eg.db >=3.7.0,<3.8.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' + - 'bioconductor-org.hs.eg.db >=3.8.0,<3.9.0' - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-clariomshumantranscriptcluster.db/post-link.sh b/recipes/bioconductor-clariomshumantranscriptcluster.db/post-link.sh index 0e8f413578139..8552100d28f23 100644 --- a/recipes/bioconductor-clariomshumantranscriptcluster.db/post-link.sh +++ b/recipes/bioconductor-clariomshumantranscriptcluster.db/post-link.sh @@ -1,9 +1,10 @@ #!/bin/bash FN="clariomshumantranscriptcluster.db_8.7.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/clariomshumantranscriptcluster.db_8.7.0.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/clariomshumantranscriptcluster.db_8.7.0.tar.gz" "https://bioarchive.galaxyproject.org/clariomshumantranscriptcluster.db_8.7.0.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-clariomshumantranscriptcluster.db/bioconductor-clariomshumantranscriptcluster.db_8.7.0_src_all.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-clariomshumantranscriptcluster.db/bioconductor-clariomshumantranscriptcluster.db_8.7.0_src_all.tar.gz" ) MD5="0b92969a4bb4a2d8e972602f68c7ad1b" @@ -16,7 +17,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-clariomsmousehttranscriptcluster.db/meta.yaml b/recipes/bioconductor-clariomsmousehttranscriptcluster.db/meta.yaml index fa983f6e50b0d..464c1cd5fdf35 100644 --- a/recipes/bioconductor-clariomsmousehttranscriptcluster.db/meta.yaml +++ b/recipes/bioconductor-clariomsmousehttranscriptcluster.db/meta.yaml @@ -1,6 +1,6 @@ {% set version = "8.7.0" %} {% set name = "clariomsmousehttranscriptcluster.db" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -12,7 +12,7 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: ba6fdb1816669b4ffb2707a0fe89ef59 build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ @@ -20,14 +20,14 @@ build: # Suggests: DBI, annotate, RUnit requirements: host: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' - - 'bioconductor-org.mm.eg.db >=3.7.0,<3.8.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' + - 'bioconductor-org.mm.eg.db >=3.8.0,<3.9.0' - r-base run: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' - - 'bioconductor-org.mm.eg.db >=3.7.0,<3.8.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' + - 'bioconductor-org.mm.eg.db >=3.8.0,<3.9.0' - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-clariomsmousehttranscriptcluster.db/post-link.sh b/recipes/bioconductor-clariomsmousehttranscriptcluster.db/post-link.sh index de2bb4041027c..9088928daeba2 100644 --- a/recipes/bioconductor-clariomsmousehttranscriptcluster.db/post-link.sh +++ b/recipes/bioconductor-clariomsmousehttranscriptcluster.db/post-link.sh @@ -1,9 +1,10 @@ #!/bin/bash FN="clariomsmousehttranscriptcluster.db_8.7.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/clariomsmousehttranscriptcluster.db_8.7.0.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/clariomsmousehttranscriptcluster.db_8.7.0.tar.gz" "https://bioarchive.galaxyproject.org/clariomsmousehttranscriptcluster.db_8.7.0.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-clariomsmousehttranscriptcluster.db/bioconductor-clariomsmousehttranscriptcluster.db_8.7.0_src_all.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-clariomsmousehttranscriptcluster.db/bioconductor-clariomsmousehttranscriptcluster.db_8.7.0_src_all.tar.gz" ) MD5="ba6fdb1816669b4ffb2707a0fe89ef59" @@ -16,7 +17,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-clariomsmousetranscriptcluster.db/meta.yaml b/recipes/bioconductor-clariomsmousetranscriptcluster.db/meta.yaml index 01e5a799e42b9..c5633a9c6a794 100644 --- a/recipes/bioconductor-clariomsmousetranscriptcluster.db/meta.yaml +++ b/recipes/bioconductor-clariomsmousetranscriptcluster.db/meta.yaml @@ -1,6 +1,6 @@ {% set version = "8.7.0" %} {% set name = "clariomsmousetranscriptcluster.db" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -12,7 +12,7 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: a70687be504281a4ec08c0535da4121f build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ @@ -20,14 +20,14 @@ build: # Suggests: DBI, annotate, RUnit requirements: host: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' - - 'bioconductor-org.mm.eg.db >=3.7.0,<3.8.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' + - 'bioconductor-org.mm.eg.db >=3.8.0,<3.9.0' - r-base run: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' - - 'bioconductor-org.mm.eg.db >=3.7.0,<3.8.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' + - 'bioconductor-org.mm.eg.db >=3.8.0,<3.9.0' - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-clariomsmousetranscriptcluster.db/post-link.sh b/recipes/bioconductor-clariomsmousetranscriptcluster.db/post-link.sh index 72ff07bef19d2..1258e5cd908e9 100644 --- a/recipes/bioconductor-clariomsmousetranscriptcluster.db/post-link.sh +++ b/recipes/bioconductor-clariomsmousetranscriptcluster.db/post-link.sh @@ -1,9 +1,10 @@ #!/bin/bash FN="clariomsmousetranscriptcluster.db_8.7.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/clariomsmousetranscriptcluster.db_8.7.0.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/clariomsmousetranscriptcluster.db_8.7.0.tar.gz" "https://bioarchive.galaxyproject.org/clariomsmousetranscriptcluster.db_8.7.0.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-clariomsmousetranscriptcluster.db/bioconductor-clariomsmousetranscriptcluster.db_8.7.0_src_all.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-clariomsmousetranscriptcluster.db/bioconductor-clariomsmousetranscriptcluster.db_8.7.0_src_all.tar.gz" ) MD5="a70687be504281a4ec08c0535da4121f" @@ -16,7 +17,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-clariomsrathttranscriptcluster.db/meta.yaml b/recipes/bioconductor-clariomsrathttranscriptcluster.db/meta.yaml index 8c0a08bb3ed68..7ce438ddb45cf 100644 --- a/recipes/bioconductor-clariomsrathttranscriptcluster.db/meta.yaml +++ b/recipes/bioconductor-clariomsrathttranscriptcluster.db/meta.yaml @@ -1,6 +1,6 @@ {% set version = "8.7.0" %} {% set name = "clariomsrathttranscriptcluster.db" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -12,7 +12,7 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 50399fde7380b015da941f36362a3f78 build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ @@ -20,14 +20,14 @@ build: # Suggests: DBI, annotate, RUnit requirements: host: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' - - 'bioconductor-org.rn.eg.db >=3.7.0,<3.8.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' + - 'bioconductor-org.rn.eg.db >=3.8.0,<3.9.0' - r-base run: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' - - 'bioconductor-org.rn.eg.db >=3.7.0,<3.8.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' + - 'bioconductor-org.rn.eg.db >=3.8.0,<3.9.0' - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-clariomsrathttranscriptcluster.db/post-link.sh b/recipes/bioconductor-clariomsrathttranscriptcluster.db/post-link.sh index dff9d73bb5269..9354a1ce21604 100644 --- a/recipes/bioconductor-clariomsrathttranscriptcluster.db/post-link.sh +++ b/recipes/bioconductor-clariomsrathttranscriptcluster.db/post-link.sh @@ -1,9 +1,10 @@ #!/bin/bash FN="clariomsrathttranscriptcluster.db_8.7.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/clariomsrathttranscriptcluster.db_8.7.0.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/clariomsrathttranscriptcluster.db_8.7.0.tar.gz" "https://bioarchive.galaxyproject.org/clariomsrathttranscriptcluster.db_8.7.0.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-clariomsrathttranscriptcluster.db/bioconductor-clariomsrathttranscriptcluster.db_8.7.0_src_all.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-clariomsrathttranscriptcluster.db/bioconductor-clariomsrathttranscriptcluster.db_8.7.0_src_all.tar.gz" ) MD5="50399fde7380b015da941f36362a3f78" @@ -16,7 +17,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-clariomsrattranscriptcluster.db/meta.yaml b/recipes/bioconductor-clariomsrattranscriptcluster.db/meta.yaml index 10346dbed76d3..2e1ed5d5a6fb1 100644 --- a/recipes/bioconductor-clariomsrattranscriptcluster.db/meta.yaml +++ b/recipes/bioconductor-clariomsrattranscriptcluster.db/meta.yaml @@ -1,6 +1,6 @@ {% set version = "8.7.0" %} {% set name = "clariomsrattranscriptcluster.db" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -12,7 +12,7 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 34d0c761a038f5f28f6b5db4b7e575a7 build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ @@ -20,14 +20,14 @@ build: # Suggests: DBI, annotate, RUnit requirements: host: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' - - 'bioconductor-org.rn.eg.db >=3.7.0,<3.8.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' + - 'bioconductor-org.rn.eg.db >=3.8.0,<3.9.0' - r-base run: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' - - 'bioconductor-org.rn.eg.db >=3.7.0,<3.8.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' + - 'bioconductor-org.rn.eg.db >=3.8.0,<3.9.0' - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-clariomsrattranscriptcluster.db/post-link.sh b/recipes/bioconductor-clariomsrattranscriptcluster.db/post-link.sh index 353d6ec67de40..d7a8514ad98e2 100644 --- a/recipes/bioconductor-clariomsrattranscriptcluster.db/post-link.sh +++ b/recipes/bioconductor-clariomsrattranscriptcluster.db/post-link.sh @@ -1,9 +1,10 @@ #!/bin/bash FN="clariomsrattranscriptcluster.db_8.7.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/clariomsrattranscriptcluster.db_8.7.0.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/clariomsrattranscriptcluster.db_8.7.0.tar.gz" "https://bioarchive.galaxyproject.org/clariomsrattranscriptcluster.db_8.7.0.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-clariomsrattranscriptcluster.db/bioconductor-clariomsrattranscriptcluster.db_8.7.0_src_all.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-clariomsrattranscriptcluster.db/bioconductor-clariomsrattranscriptcluster.db_8.7.0_src_all.tar.gz" ) MD5="34d0c761a038f5f28f6b5db4b7e575a7" @@ -16,7 +17,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-classifyr/meta.yaml b/recipes/bioconductor-classifyr/meta.yaml index 35343e33cf4d1..62a27ab79ba03 100644 --- a/recipes/bioconductor-classifyr/meta.yaml +++ b/recipes/bioconductor-classifyr/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "2.2.6" %} +{% set version = "2.4.0" %} {% set name = "ClassifyR" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 5e17ba0d5c16354d00145a3dc9adbb79 + md5: 156be11086908fd5f050915742c96f7b build: number: 0 rpaths: @@ -20,16 +20,16 @@ build: # Suggests: limma, genefilter, edgeR, car, Rmixmod, ggplot2 (>= 3.0.0), gridExtra (>= 2.0.0), cowplot, BiocStyle, pamr, PoiClaClu, parathyroidSE, knitr, htmltools, gtable, scales, e1071, rmarkdown, IRanges, randomForest, robustbase, glmnet, class requirements: host: - - 'bioconductor-biocparallel >=1.16.0,<1.17.0' - - 'bioconductor-multiassayexperiment >=1.8.0,<1.9.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-biocparallel >=1.18.0,<1.19.0' + - 'bioconductor-multiassayexperiment >=1.10.0,<1.11.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' - r-base - r-locfit - r-plyr run: - - 'bioconductor-biocparallel >=1.16.0,<1.17.0' - - 'bioconductor-multiassayexperiment >=1.8.0,<1.9.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-biocparallel >=1.18.0,<1.19.0' + - 'bioconductor-multiassayexperiment >=1.10.0,<1.11.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' - r-base - r-locfit - r-plyr diff --git a/recipes/bioconductor-cleanupdtseq/meta.yaml b/recipes/bioconductor-cleanupdtseq/meta.yaml index 7ca85ac775ee7..6b20f0c5e3d3c 100644 --- a/recipes/bioconductor-cleanupdtseq/meta.yaml +++ b/recipes/bioconductor-cleanupdtseq/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.20.0" %} +{% set version = "1.22.0" %} {% set name = "cleanUpdTSeq" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 4bcb20170e1ccbcfc1c93d2adb6e0e0d + md5: de3acfeb36d648850cfbac428cfc1418 build: number: 0 rpaths: @@ -20,18 +20,22 @@ build: # Suggests: BiocStyle, knitr, RUnit requirements: host: - - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' - - 'bioconductor-bsgenome >=1.50.0,<1.51.0' + - 'bioconductor-biocgenerics >=0.30.0,<0.31.0' + - 'bioconductor-bsgenome >=1.52.0,<1.53.0' - 'bioconductor-bsgenome.drerio.ucsc.danrer7 >=1.4.0,<1.5.0' - - 'bioconductor-genomicranges >=1.34.0,<1.35.0' + - 'bioconductor-genomeinfodb >=1.20.0,<1.21.0' + - 'bioconductor-genomicranges >=1.36.0,<1.37.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' - r-base - r-e1071 - r-seqinr run: - - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' - - 'bioconductor-bsgenome >=1.50.0,<1.51.0' + - 'bioconductor-biocgenerics >=0.30.0,<0.31.0' + - 'bioconductor-bsgenome >=1.52.0,<1.53.0' - 'bioconductor-bsgenome.drerio.ucsc.danrer7 >=1.4.0,<1.5.0' - - 'bioconductor-genomicranges >=1.34.0,<1.35.0' + - 'bioconductor-genomeinfodb >=1.20.0,<1.21.0' + - 'bioconductor-genomicranges >=1.36.0,<1.37.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' - r-base - r-e1071 - r-seqinr diff --git a/recipes/bioconductor-cleaver/meta.yaml b/recipes/bioconductor-cleaver/meta.yaml index 80824c48a3ea5..3b4ad3d333a57 100644 --- a/recipes/bioconductor-cleaver/meta.yaml +++ b/recipes/bioconductor-cleaver/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.20.0" %} +{% set version = "1.22.0" %} {% set name = "cleaver" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,24 +10,24 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 3ac18493a9e15c2f5e9679b96d9d3da7 + md5: 9759e3cc9a1c9f2be7e029ceb462b4a3 build: number: 0 rpaths: - lib/R/lib/ - lib/ noarch: generic -# Suggests: testthat (>= 0.8), knitr, BiocStyle (>= 0.0.14), BRAIN, UniProt.ws (>= 2.1.4) +# Suggests: testthat (>= 0.8), knitr, BiocStyle (>= 0.0.14), rmarkdown, BRAIN, UniProt.ws (>= 2.1.4) requirements: host: - - 'bioconductor-biostrings >=2.50.0,<2.51.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-biostrings >=2.52.0,<2.53.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' - r-base run: - - 'bioconductor-biostrings >=2.50.0,<2.51.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-biostrings >=2.52.0,<2.53.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' - r-base test: commands: diff --git a/recipes/bioconductor-clippda/meta.yaml b/recipes/bioconductor-clippda/meta.yaml index 51739b3be0d29..5c45cf07bdfa5 100644 --- a/recipes/bioconductor-clippda/meta.yaml +++ b/recipes/bioconductor-clippda/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.32.0" %} +{% set version = "1.34.0" %} {% set name = "clippda" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 0d4835a20f6d5153606e6338f6933a85 + md5: 9555259a3e4435bdbdd750f255b16918 build: number: 0 rpaths: @@ -19,22 +19,21 @@ build: noarch: generic requirements: host: - - 'bioconductor-biobase >=2.42.0,<2.43.0' - - 'bioconductor-limma >=3.38.0,<3.39.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' + - 'bioconductor-limma >=3.40.0,<3.41.0' - r-base - r-lattice - r-rgl - r-scatterplot3d - r-statmod run: - - 'bioconductor-biobase >=2.42.0,<2.43.0' - - 'bioconductor-limma >=3.38.0,<3.39.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' + - 'bioconductor-limma >=3.40.0,<3.41.0' - r-base - r-lattice - r-rgl - r-scatterplot3d - r-statmod - test: commands: - '$R -e "library(''{{ name }}'')"' @@ -42,8 +41,7 @@ about: home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: 'GPL (>=2)' summary: 'Methods for the nalysis of data from clinical proteomic profiling studies. The focus is on the studies of human subjects, which are often observational case-control by design and have technical replicates. A method for sample size determination for planning these studies is proposed. It incorporates routines for adjusting for the expected heterogeneities and imbalances in the data and the within-sample replicate correlations.' - extra: container: - # libgl.so extended-base: true + diff --git a/recipes/bioconductor-clipper/meta.yaml b/recipes/bioconductor-clipper/meta.yaml index b7cc3a9f109cf..22cbfad7f979c 100644 --- a/recipes/bioconductor-clipper/meta.yaml +++ b/recipes/bioconductor-clipper/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.22.0" %} +{% set version = "1.24.0" %} {% set name = "clipper" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: eb3ea7c60842da6cb778e932d303688f + md5: 5ffbf94bc0991428351e2c32de0cec5c build: number: 0 rpaths: @@ -19,11 +19,11 @@ build: # Suggests: RUnit, BiocGenerics, graphite, ALL, hgu95av2.db, MASS, BiocStyle requirements: host: - - 'bioconductor-biobase >=2.42.0,<2.43.0' - - 'bioconductor-graph >=1.60.0,<1.61.0' - - 'bioconductor-kegggraph >=1.42.0,<1.43.0' - - 'bioconductor-qpgraph >=2.16.0,<2.17.0' - - 'bioconductor-rbgl >=1.58.0,<1.59.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' + - 'bioconductor-graph >=1.62.0,<1.63.0' + - 'bioconductor-kegggraph >=1.44.0,<1.45.0' + - 'bioconductor-qpgraph >=2.18.0,<2.19.0' + - 'bioconductor-rbgl >=1.60.0,<1.61.0' - r-base - r-corpcor - 'r-grbase >=1.6.6' @@ -31,11 +31,11 @@ requirements: - r-matrix - r-rcpp run: - - 'bioconductor-biobase >=2.42.0,<2.43.0' - - 'bioconductor-graph >=1.60.0,<1.61.0' - - 'bioconductor-kegggraph >=1.42.0,<1.43.0' - - 'bioconductor-qpgraph >=2.16.0,<2.17.0' - - 'bioconductor-rbgl >=1.58.0,<1.59.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' + - 'bioconductor-graph >=1.62.0,<1.63.0' + - 'bioconductor-kegggraph >=1.44.0,<1.45.0' + - 'bioconductor-qpgraph >=2.18.0,<2.19.0' + - 'bioconductor-rbgl >=1.60.0,<1.61.0' - r-base - r-corpcor - 'r-grbase >=1.6.6' diff --git a/recipes/bioconductor-cll/meta.yaml b/recipes/bioconductor-cll/meta.yaml index 3d0f56e98689e..9ce579a774870 100644 --- a/recipes/bioconductor-cll/meta.yaml +++ b/recipes/bioconductor-cll/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.22.0" %} +{% set version = "1.24.0" %} {% set name = "CLL" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 3851a86f9abc1159d405cbbc03ecf405 + md5: c7e9da38377b6a30c1a4969b4175a543 build: number: 0 rpaths: @@ -19,14 +19,14 @@ build: noarch: generic requirements: host: - - 'bioconductor-affy >=1.60.0,<1.61.0' - - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-affy >=1.62.0,<1.63.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' - r-base run: - - 'bioconductor-affy >=1.60.0,<1.61.0' - - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-affy >=1.62.0,<1.63.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-cll/post-link.sh b/recipes/bioconductor-cll/post-link.sh index ea682058d28c1..cc593fc4e71c3 100644 --- a/recipes/bioconductor-cll/post-link.sh +++ b/recipes/bioconductor-cll/post-link.sh @@ -1,11 +1,11 @@ #!/bin/bash -FN="CLL_1.22.0.tar.gz" +FN="CLL_1.24.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/experiment/src/contrib/CLL_1.22.0.tar.gz" - "https://bioarchive.galaxyproject.org/CLL_1.22.0.tar.gz" - "https://depot.galaxyproject.org/software/bioconductor-cll/bioconductor-cll_1.22.0_src_all.tar.gz" + "https://bioconductor.org/packages/3.9/data/experiment/src/contrib/CLL_1.24.0.tar.gz" + "https://bioarchive.galaxyproject.org/CLL_1.24.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-cll/bioconductor-cll_1.24.0_src_all.tar.gz" ) -MD5="3851a86f9abc1159d405cbbc03ecf405" +MD5="c7e9da38377b6a30c1a4969b4175a543" # Use a staging area in the conda dir rather than temp dirs, both to avoid # permission issues as well as to have things downloaded in a predictable @@ -16,7 +16,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-cllmethylation/meta.yaml b/recipes/bioconductor-cllmethylation/meta.yaml index 69e88fba44b0b..47462f3d25e52 100644 --- a/recipes/bioconductor-cllmethylation/meta.yaml +++ b/recipes/bioconductor-cllmethylation/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.2.0" %} +{% set version = "1.4.0" %} {% set name = "CLLmethylation" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: cd8a30818dd72030144bd4216d915569 + md5: 2b2496c6f9a26e10a55c87b5a1087859 build: number: 0 rpaths: @@ -20,14 +20,14 @@ build: # Suggests: BiocStyle, ggplot2, knitr, rmarkdown requirements: host: - - 'bioconductor-experimenthub >=1.8.0,<1.9.0' - - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' + - 'bioconductor-experimenthub >=1.10.0,<1.11.0' + - 'bioconductor-summarizedexperiment >=1.14.0,<1.15.0' - r-base run: - - 'bioconductor-experimenthub >=1.8.0,<1.9.0' - - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' + - 'bioconductor-experimenthub >=1.10.0,<1.11.0' + - 'bioconductor-summarizedexperiment >=1.14.0,<1.15.0' - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-cllmethylation/post-link.sh b/recipes/bioconductor-cllmethylation/post-link.sh index 0b5a50efe06f0..b59432230a53c 100644 --- a/recipes/bioconductor-cllmethylation/post-link.sh +++ b/recipes/bioconductor-cllmethylation/post-link.sh @@ -1,11 +1,11 @@ #!/bin/bash -FN="CLLmethylation_1.2.0.tar.gz" +FN="CLLmethylation_1.4.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/experiment/src/contrib/CLLmethylation_1.2.0.tar.gz" - "https://bioarchive.galaxyproject.org/CLLmethylation_1.2.0.tar.gz" - "https://depot.galaxyproject.org/software/bioconductor-cllmethylation/bioconductor-cllmethylation_1.2.0_src_all.tar.gz" + "https://bioconductor.org/packages/3.9/data/experiment/src/contrib/CLLmethylation_1.4.0.tar.gz" + "https://bioarchive.galaxyproject.org/CLLmethylation_1.4.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-cllmethylation/bioconductor-cllmethylation_1.4.0_src_all.tar.gz" ) -MD5="cd8a30818dd72030144bd4216d915569" +MD5="2b2496c6f9a26e10a55c87b5a1087859" # Use a staging area in the conda dir rather than temp dirs, both to avoid # permission issues as well as to have things downloaded in a predictable @@ -16,7 +16,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-clomial/meta.yaml b/recipes/bioconductor-clomial/meta.yaml index 4627242b78748..228cf8efe8383 100644 --- a/recipes/bioconductor-clomial/meta.yaml +++ b/recipes/bioconductor-clomial/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.18.1" %} +{% set version = "1.20.0" %} {% set name = "Clomial" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 6b28f8d222ff2b4d8101cf3f2bd0c670 + md5: 483932cc2911c5055e2972fbeb3005b2 build: number: 0 rpaths: diff --git a/recipes/bioconductor-clonality/meta.yaml b/recipes/bioconductor-clonality/meta.yaml index 416716e5c38d0..ca476cdc2ee7e 100644 --- a/recipes/bioconductor-clonality/meta.yaml +++ b/recipes/bioconductor-clonality/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.30.0" %} +{% set version = "1.32.0" %} {% set name = "Clonality" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: aa1dccf7e9baf578b9be782ec99278e2 + md5: 16951e83e9b7565b99dca3cb450eebf9 build: number: 0 rpaths: @@ -20,10 +20,10 @@ build: # Suggests: gdata requirements: host: - - 'bioconductor-dnacopy >=1.56.0,<1.57.0' + - 'bioconductor-dnacopy >=1.58.0,<1.59.0' - r-base run: - - 'bioconductor-dnacopy >=1.56.0,<1.57.0' + - 'bioconductor-dnacopy >=1.58.0,<1.59.0' - r-base test: commands: diff --git a/recipes/bioconductor-clonotyper/meta.yaml b/recipes/bioconductor-clonotyper/meta.yaml index 6b1750589a24e..da47ad639020b 100644 --- a/recipes/bioconductor-clonotyper/meta.yaml +++ b/recipes/bioconductor-clonotyper/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.20.0" %} +{% set version = "1.22.0" %} {% set name = "clonotypeR" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: ce60c01fcc6b07e75ad0047f74e308ec + md5: d123ef6f87bc8411f75011922537ad38 build: number: 0 rpaths: diff --git a/recipes/bioconductor-clst/meta.yaml b/recipes/bioconductor-clst/meta.yaml index 9dc37212eb2b9..549b64c06f39e 100644 --- a/recipes/bioconductor-clst/meta.yaml +++ b/recipes/bioconductor-clst/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.30.0" %} +{% set version = "1.32.0" %} {% set name = "clst" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 03379c8704e8e7843e96d8feb82ac307 + md5: a9b3a5b2342ff43e0946b8c17c81816c build: number: 0 rpaths: @@ -20,11 +20,11 @@ build: # Suggests: RUnit requirements: host: - - 'bioconductor-roc >=1.58.0,<1.59.0' + - 'bioconductor-roc >=1.60.0,<1.61.0' - r-base - r-lattice run: - - 'bioconductor-roc >=1.58.0,<1.59.0' + - 'bioconductor-roc >=1.60.0,<1.61.0' - r-base - r-lattice test: diff --git a/recipes/bioconductor-clstutils/meta.yaml b/recipes/bioconductor-clstutils/meta.yaml index c8052498b4dfa..0bd2bce49d622 100644 --- a/recipes/bioconductor-clstutils/meta.yaml +++ b/recipes/bioconductor-clstutils/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.30.0" %} +{% set version = "1.32.0" %} {% set name = "clstutils" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: e63fa92d5f3812877f3c9904b7530fe7 + md5: f31a1566acdc40319644a1c7ec1969ab build: number: 0 rpaths: @@ -20,14 +20,14 @@ build: # Suggests: RUnit, RSVGTipsDevice requirements: host: - - 'bioconductor-clst >=1.30.0,<1.31.0' + - 'bioconductor-clst >=1.32.0,<1.33.0' - r-ape - r-base - r-lattice - r-rjson - r-rsqlite run: - - 'bioconductor-clst >=1.30.0,<1.31.0' + - 'bioconductor-clst >=1.32.0,<1.33.0' - r-ape - r-base - r-lattice diff --git a/recipes/bioconductor-clumsid/build.sh b/recipes/bioconductor-clumsid/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-clumsid/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-clumsid/meta.yaml b/recipes/bioconductor-clumsid/meta.yaml new file mode 100644 index 0000000000000..28c55b7b40e1c --- /dev/null +++ b/recipes/bioconductor-clumsid/meta.yaml @@ -0,0 +1,59 @@ +{% set version = "1.0.0" %} +{% set name = "CluMSID" %} +{% set bioc = "3.9" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: 48db07b1d9a97a89ad03a97253e8e24a +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: knitr, rmarkdown, testthat, dplyr, readr, stringr, magrittr, CluMSIDdata, metaMS, metaMSdata, xcms +requirements: + host: + - 'bioconductor-biobase >=2.44.0,<2.45.0' + - 'bioconductor-msnbase >=2.10.0,<2.11.0' + - 'bioconductor-mzr >=2.18.0,<2.19.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' + - r-ape + - r-base + - r-dbscan + - r-ggally + - r-ggplot2 + - r-gplots + - r-network + - r-plotly + - r-rcolorbrewer + - r-sna + run: + - 'bioconductor-biobase >=2.44.0,<2.45.0' + - 'bioconductor-msnbase >=2.10.0,<2.11.0' + - 'bioconductor-mzr >=2.18.0,<2.19.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' + - r-ape + - r-base + - r-dbscan + - r-ggally + - r-ggplot2 + - r-gplots + - r-network + - r-plotly + - r-rcolorbrewer + - r-sna +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: 'MIT + file LICENSE' + summary: 'CluMSID is a tool that aids the identification of features in untargeted LC-MS/MS analysis by the use of MS2 spectra similarity and unsupervised statistical methods. It offers functions for a complete and customisable workflow from raw data to visualisations and is interfaceable with the xmcs family of preprocessing packages.' + diff --git a/recipes/bioconductor-clumsiddata/meta.yaml b/recipes/bioconductor-clumsiddata/meta.yaml new file mode 100644 index 0000000000000..22a399acf1905 --- /dev/null +++ b/recipes/bioconductor-clumsiddata/meta.yaml @@ -0,0 +1,33 @@ +{% set version = "1.0.0" %} +{% set name = "CluMSIDdata" %} +{% set bioc = "3.9" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: a9ba9176bf862de81836a3b74f60af5e +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +requirements: + host: + - r-base + run: + - r-base + - curl +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html' + license: 'MIT + file LICENSE' + summary: 'This package contains various LC-MS/MS and GC-MS data that is used in vignettes and examples in the CluMSID package.' + diff --git a/recipes/bioconductor-clumsiddata/post-link.sh b/recipes/bioconductor-clumsiddata/post-link.sh new file mode 100644 index 0000000000000..97af019b93ecf --- /dev/null +++ b/recipes/bioconductor-clumsiddata/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="CluMSIDdata_1.0.0.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.9/data/experiment/src/contrib/CluMSIDdata_1.0.0.tar.gz" + "https://bioarchive.galaxyproject.org/CluMSIDdata_1.0.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-clumsiddata/bioconductor-clumsiddata_1.0.0_src_all.tar.gz" +) +MD5="a9ba9176bf862de81836a3b74f60af5e" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + curl $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-clumsiddata/pre-unlink.sh b/recipes/bioconductor-clumsiddata/pre-unlink.sh new file mode 100644 index 0000000000000..4944d73795f6e --- /dev/null +++ b/recipes/bioconductor-clumsiddata/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ CluMSIDdata diff --git a/recipes/bioconductor-clustcomp/meta.yaml b/recipes/bioconductor-clustcomp/meta.yaml index 79e4f867941fb..ecff4088d40c8 100644 --- a/recipes/bioconductor-clustcomp/meta.yaml +++ b/recipes/bioconductor-clustcomp/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.10.0" %} +{% set version = "1.12.0" %} {% set name = "clustComp" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: e6750fcee97be0e5706cb50e8d87f610 + md5: 5d6c72bdfdab1828b794fe80e5b2bf4e build: number: 0 rpaths: diff --git a/recipes/bioconductor-clusterexperiment/meta.yaml b/recipes/bioconductor-clusterexperiment/meta.yaml index 49b215ba80a32..3c17cefb3ada1 100644 --- a/recipes/bioconductor-clusterexperiment/meta.yaml +++ b/recipes/bioconductor-clusterexperiment/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "2.2.0" %} +{% set version = "2.4.0" %} {% set name = "clusterExperiment" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: d8125f0b838d2d47f45701e1ee5fc54a + md5: bf9ef5b681063b83d8452cdb0f9a95f9 build: number: 0 rpaths: @@ -19,22 +19,22 @@ build: # Suggests: BiocStyle, knitr, testthat, scRNAseq, MAST, Rtsne, scran, igraph requirements: host: - - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' - - 'bioconductor-delayedarray >=0.8.0,<0.9.0' - - 'bioconductor-edger >=3.24.0,<3.25.0' - - 'bioconductor-hdf5array >=1.10.0,<1.11.0' - - 'bioconductor-limma >=3.38.0,<3.39.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' - - 'bioconductor-singlecellexperiment >=1.4.0,<1.5.0' - - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' - - 'bioconductor-zinbwave >=1.4.0,<1.5.0' + - 'bioconductor-biocgenerics >=0.30.0,<0.31.0' + - 'bioconductor-delayedarray >=0.10.0,<0.11.0' + - 'bioconductor-edger >=3.26.0,<3.27.0' + - 'bioconductor-hdf5array >=1.12.0,<1.13.0' + - 'bioconductor-limma >=3.40.0,<3.41.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' + - 'bioconductor-singlecellexperiment >=1.6.0,<1.7.0' + - 'bioconductor-summarizedexperiment >=1.14.0,<1.15.0' + - 'bioconductor-zinbwave >=1.6.0,<1.7.0' - 'r-ape >=5.0' - r-base - r-cluster - - r-dendextend - r-howmany - r-kernlab - r-locfdr + - r-matrix - r-matrixstats - r-nmf - r-phylobase @@ -44,22 +44,22 @@ requirements: - r-scales - r-stringr run: - - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' - - 'bioconductor-delayedarray >=0.8.0,<0.9.0' - - 'bioconductor-edger >=3.24.0,<3.25.0' - - 'bioconductor-hdf5array >=1.10.0,<1.11.0' - - 'bioconductor-limma >=3.38.0,<3.39.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' - - 'bioconductor-singlecellexperiment >=1.4.0,<1.5.0' - - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' - - 'bioconductor-zinbwave >=1.4.0,<1.5.0' + - 'bioconductor-biocgenerics >=0.30.0,<0.31.0' + - 'bioconductor-delayedarray >=0.10.0,<0.11.0' + - 'bioconductor-edger >=3.26.0,<3.27.0' + - 'bioconductor-hdf5array >=1.12.0,<1.13.0' + - 'bioconductor-limma >=3.40.0,<3.41.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' + - 'bioconductor-singlecellexperiment >=1.6.0,<1.7.0' + - 'bioconductor-summarizedexperiment >=1.14.0,<1.15.0' + - 'bioconductor-zinbwave >=1.6.0,<1.7.0' - 'r-ape >=5.0' - r-base - r-cluster - - r-dendextend - r-howmany - r-kernlab - r-locfdr + - r-matrix - r-matrixstats - r-nmf - r-phylobase diff --git a/recipes/bioconductor-clusterjudge/meta.yaml b/recipes/bioconductor-clusterjudge/meta.yaml index 1b9e2e200e651..12cc77b6cae63 100644 --- a/recipes/bioconductor-clusterjudge/meta.yaml +++ b/recipes/bioconductor-clusterjudge/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.4.0" %} +{% set version = "1.6.0" %} {% set name = "ClusterJudge" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 87cb47cba4bc6d197a97d2e50b814e0c + md5: 8355965d9a38957058a66a8a28535160 build: number: 0 rpaths: diff --git a/recipes/bioconductor-clusterprofiler/meta.yaml b/recipes/bioconductor-clusterprofiler/meta.yaml index f7380424d6368..595c2cee17e7e 100644 --- a/recipes/bioconductor-clusterprofiler/meta.yaml +++ b/recipes/bioconductor-clusterprofiler/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "3.10.1" %} +{% set version = "3.12.0" %} {% set name = "clusterProfiler" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,22 +10,22 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 4b67eff75b931da94b8862db7f9e8776 + md5: a8c02c3af86ebc0916bae80c64419b18 build: number: 0 rpaths: - lib/R/lib/ - lib/ noarch: generic -# Suggests: AnnotationHub, GSEABase, KEGG.db, knitr, org.Hs.eg.db, prettydoc, pathview, ReactomePA, testthat +# Suggests: AnnotationHub, dplyr, KEGG.db, knitr, org.Hs.eg.db, prettydoc, ReactomePA, testthat requirements: host: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' - - 'bioconductor-dose >=3.8.0,<3.9.0' - - 'bioconductor-enrichplot >=1.2.0,<1.3.0' - - 'bioconductor-go.db >=3.7.0,<3.8.0' - - 'bioconductor-gosemsim >=2.8.0,<2.9.0' - - 'bioconductor-qvalue >=2.14.0,<2.15.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' + - 'bioconductor-dose >=3.10.0,<3.11.0' + - 'bioconductor-enrichplot >=1.4.0,<1.5.0' + - 'bioconductor-go.db >=3.8.0,<3.9.0' + - 'bioconductor-gosemsim >=2.10.0,<2.11.0' + - 'bioconductor-qvalue >=2.16.0,<2.17.0' - r-base - r-ggplot2 - r-magrittr @@ -33,12 +33,12 @@ requirements: - r-rvcheck - r-tidyr run: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' - - 'bioconductor-dose >=3.8.0,<3.9.0' - - 'bioconductor-enrichplot >=1.2.0,<1.3.0' - - 'bioconductor-go.db >=3.7.0,<3.8.0' - - 'bioconductor-gosemsim >=2.8.0,<2.9.0' - - 'bioconductor-qvalue >=2.14.0,<2.15.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' + - 'bioconductor-dose >=3.10.0,<3.11.0' + - 'bioconductor-enrichplot >=1.4.0,<1.5.0' + - 'bioconductor-go.db >=3.8.0,<3.9.0' + - 'bioconductor-gosemsim >=2.10.0,<2.11.0' + - 'bioconductor-qvalue >=2.16.0,<2.17.0' - r-base - r-ggplot2 - r-magrittr diff --git a/recipes/bioconductor-clusterseq/meta.yaml b/recipes/bioconductor-clusterseq/meta.yaml index 7116b8433c9a1..899fa83064981 100644 --- a/recipes/bioconductor-clusterseq/meta.yaml +++ b/recipes/bioconductor-clusterseq/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.6.0" %} +{% set version = "1.8.0" %} {% set name = "clusterSeq" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: de87aa6662095dfe988eff1c8c2c6bce + md5: f82bb977baa0ce56344f8732a4fbdca0 build: number: 0 rpaths: @@ -20,14 +20,14 @@ build: # Suggests: BiocStyle requirements: host: - - 'bioconductor-bayseq >=2.16.0,<2.17.0' - - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' - - 'bioconductor-biocparallel >=1.16.0,<1.17.0' + - 'bioconductor-bayseq >=2.18.0,<2.19.0' + - 'bioconductor-biocgenerics >=0.30.0,<0.31.0' + - 'bioconductor-biocparallel >=1.18.0,<1.19.0' - r-base run: - - 'bioconductor-bayseq >=2.16.0,<2.17.0' - - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' - - 'bioconductor-biocparallel >=1.16.0,<1.17.0' + - 'bioconductor-bayseq >=2.18.0,<2.19.0' + - 'bioconductor-biocgenerics >=0.30.0,<0.31.0' + - 'bioconductor-biocparallel >=1.18.0,<1.19.0' - r-base test: commands: diff --git a/recipes/bioconductor-clustersignificance/meta.yaml b/recipes/bioconductor-clustersignificance/meta.yaml index 4c69142fe6d6d..7bbf9cc388dcd 100644 --- a/recipes/bioconductor-clustersignificance/meta.yaml +++ b/recipes/bioconductor-clustersignificance/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.10.0" %} +{% set version = "1.12.0" %} {% set name = "ClusterSignificance" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: e9d0e4317b1a056b26796c4158d5b63f + md5: b97eb45eafae8a055983244ffd40d33a build: number: 0 rpaths: diff --git a/recipes/bioconductor-clusterstab/meta.yaml b/recipes/bioconductor-clusterstab/meta.yaml index 2cd1469300114..c0c0f9e60d8d1 100644 --- a/recipes/bioconductor-clusterstab/meta.yaml +++ b/recipes/bioconductor-clusterstab/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.54.0" %} +{% set version = "1.56.0" %} {% set name = "clusterStab" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 13e2412428edb769e74ebf828778f9e0 + md5: d55549ed704e0e7d13c80c9d6a13b1b2 build: number: 0 rpaths: @@ -20,10 +20,10 @@ build: # Suggests: fibroEset, genefilter requirements: host: - - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' - r-base run: - - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' - r-base test: commands: diff --git a/recipes/bioconductor-cma/meta.yaml b/recipes/bioconductor-cma/meta.yaml index 985b9ed400636..d66933073e589 100644 --- a/recipes/bioconductor-cma/meta.yaml +++ b/recipes/bioconductor-cma/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.40.0" %} +{% set version = "1.42.0" %} {% set name = "CMA" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: ae7cd551d9e6cf48713f81726e421044 + md5: a1fd257a7b975dd6c6c31b60dd072e36 build: number: 0 rpaths: @@ -20,10 +20,10 @@ build: # Suggests: MASS, class, nnet, glmnet, e1071, randomForest, plsgenomics, gbm, mgcv, corpcor, limma, st, mvtnorm requirements: host: - - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' - r-base run: - - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' - r-base test: commands: diff --git a/recipes/bioconductor-cmap/meta.yaml b/recipes/bioconductor-cmap/meta.yaml index bf2c78f959e64..75bef602469c7 100644 --- a/recipes/bioconductor-cmap/meta.yaml +++ b/recipes/bioconductor-cmap/meta.yaml @@ -1,6 +1,6 @@ {% set version = "1.15.1" %} {% set name = "cMAP" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -12,7 +12,7 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' md5: dbf8df4d4540151936884e1c5d747bcf build: - number: 3 + number: 4 rpaths: - lib/R/lib/ - lib/ @@ -22,7 +22,7 @@ requirements: - r-base run: - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-cmap/post-link.sh b/recipes/bioconductor-cmap/post-link.sh index 171ddc53d512b..1ac1ea8bc5cdc 100644 --- a/recipes/bioconductor-cmap/post-link.sh +++ b/recipes/bioconductor-cmap/post-link.sh @@ -1,7 +1,7 @@ #!/bin/bash FN="cMAP_1.15.1.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/cMAP_1.15.1.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/cMAP_1.15.1.tar.gz" "https://bioarchive.galaxyproject.org/cMAP_1.15.1.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-cmap/bioconductor-cmap_1.15.1_src_all.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-cmap/bioconductor-cmap_1.15.1_src_all.tar.gz" @@ -17,7 +17,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-cmap2data/meta.yaml b/recipes/bioconductor-cmap2data/meta.yaml index 5631f39bc3e24..953cb77d62e38 100644 --- a/recipes/bioconductor-cmap2data/meta.yaml +++ b/recipes/bioconductor-cmap2data/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.18.0" %} +{% set version = "1.20.0" %} {% set name = "cMap2data" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 174f2e6265ede0b5e9163d7557f9e608 + md5: 5a816640a2b0fbe93e9398b460320ed7 build: number: 0 rpaths: @@ -22,7 +22,7 @@ requirements: - r-base run: - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-cmap2data/post-link.sh b/recipes/bioconductor-cmap2data/post-link.sh index 87f4f0cb57f30..ae10a79392a58 100644 --- a/recipes/bioconductor-cmap2data/post-link.sh +++ b/recipes/bioconductor-cmap2data/post-link.sh @@ -1,11 +1,11 @@ #!/bin/bash -FN="cMap2data_1.18.0.tar.gz" +FN="cMap2data_1.20.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/experiment/src/contrib/cMap2data_1.18.0.tar.gz" - "https://bioarchive.galaxyproject.org/cMap2data_1.18.0.tar.gz" - "https://depot.galaxyproject.org/software/bioconductor-cmap2data/bioconductor-cmap2data_1.18.0_src_all.tar.gz" + "https://bioconductor.org/packages/3.9/data/experiment/src/contrib/cMap2data_1.20.0.tar.gz" + "https://bioarchive.galaxyproject.org/cMap2data_1.20.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-cmap2data/bioconductor-cmap2data_1.20.0_src_all.tar.gz" ) -MD5="174f2e6265ede0b5e9163d7557f9e608" +MD5="5a816640a2b0fbe93e9398b460320ed7" # Use a staging area in the conda dir rather than temp dirs, both to avoid # permission issues as well as to have things downloaded in a predictable @@ -16,7 +16,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-cn.farms/meta.yaml b/recipes/bioconductor-cn.farms/meta.yaml index 12c853ac590e0..5be8689d1a56a 100644 --- a/recipes/bioconductor-cn.farms/meta.yaml +++ b/recipes/bioconductor-cn.farms/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.30.0" %} +{% set version = "1.32.0" %} {% set name = "cn.farms" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 0182f9e0aa8c1ab548b761a264cf0926 + md5: fb0b30634c95a67c17e7b8f652c0b1a3 build: number: 0 rpaths: @@ -19,24 +19,24 @@ build: # Suggests: pd.mapping250k.sty, pd.mapping250k.nsp, pd.genomewidesnp.5, pd.genomewidesnp.6 requirements: host: - - 'bioconductor-affxparser >=1.54.0,<1.55.0' - - 'bioconductor-biobase >=2.42.0,<2.43.0' - - 'bioconductor-dnacopy >=1.56.0,<1.57.0' - - 'bioconductor-oligo >=1.46.0,<1.47.0' - - 'bioconductor-oligoclasses >=1.44.0,<1.45.0' - - 'bioconductor-preprocesscore >=1.44.0,<1.45.0' + - 'bioconductor-affxparser >=1.56.0,<1.57.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' + - 'bioconductor-dnacopy >=1.58.0,<1.59.0' + - 'bioconductor-oligo >=1.48.0,<1.49.0' + - 'bioconductor-oligoclasses >=1.46.0,<1.47.0' + - 'bioconductor-preprocesscore >=1.46.0,<1.47.0' - r-base - r-dbi - r-ff - r-lattice - r-snow run: - - 'bioconductor-affxparser >=1.54.0,<1.55.0' - - 'bioconductor-biobase >=2.42.0,<2.43.0' - - 'bioconductor-dnacopy >=1.56.0,<1.57.0' - - 'bioconductor-oligo >=1.46.0,<1.47.0' - - 'bioconductor-oligoclasses >=1.44.0,<1.45.0' - - 'bioconductor-preprocesscore >=1.44.0,<1.45.0' + - 'bioconductor-affxparser >=1.56.0,<1.57.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' + - 'bioconductor-dnacopy >=1.58.0,<1.59.0' + - 'bioconductor-oligo >=1.48.0,<1.49.0' + - 'bioconductor-oligoclasses >=1.46.0,<1.47.0' + - 'bioconductor-preprocesscore >=1.46.0,<1.47.0' - r-base - r-dbi - r-ff diff --git a/recipes/bioconductor-cn.mops/meta.yaml b/recipes/bioconductor-cn.mops/meta.yaml index 8dad2803eb29d..35a6fc18590c3 100644 --- a/recipes/bioconductor-cn.mops/meta.yaml +++ b/recipes/bioconductor-cn.mops/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.28.0" %} +{% set version = "1.30.0" %} {% set name = "cn.mops" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: c6736a533b5a4a5832b974bf0f33389b + md5: 503588f63a7ee549f7bb6f001b147cb5 build: number: 0 rpaths: @@ -19,24 +19,24 @@ build: # Suggests: DNAcopy requirements: host: - - 'bioconductor-biobase >=2.42.0,<2.43.0' - - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' - - 'bioconductor-exomecopy >=1.28.0,<1.29.0' - - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' - - 'bioconductor-genomicranges >=1.34.0,<1.35.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-rsamtools >=1.34.0,<1.35.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' + - 'bioconductor-biocgenerics >=0.30.0,<0.31.0' + - 'bioconductor-exomecopy >=1.30.0,<1.31.0' + - 'bioconductor-genomeinfodb >=1.20.0,<1.21.0' + - 'bioconductor-genomicranges >=1.36.0,<1.37.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-rsamtools >=2.0.0,<2.1.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' - r-base run: - - 'bioconductor-biobase >=2.42.0,<2.43.0' - - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' - - 'bioconductor-exomecopy >=1.28.0,<1.29.0' - - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' - - 'bioconductor-genomicranges >=1.34.0,<1.35.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-rsamtools >=1.34.0,<1.35.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' + - 'bioconductor-biocgenerics >=0.30.0,<0.31.0' + - 'bioconductor-exomecopy >=1.30.0,<1.31.0' + - 'bioconductor-genomeinfodb >=1.20.0,<1.21.0' + - 'bioconductor-genomicranges >=1.36.0,<1.37.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-rsamtools >=2.0.0,<2.1.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' - r-base build: - {{ compiler('c') }} diff --git a/recipes/bioconductor-cnanorm/meta.yaml b/recipes/bioconductor-cnanorm/meta.yaml index a837b4902f344..7e12450eb7da4 100644 --- a/recipes/bioconductor-cnanorm/meta.yaml +++ b/recipes/bioconductor-cnanorm/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.28.0" %} +{% set version = "1.30.0" %} {% set name = "CNAnorm" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: edd5ffe29a6af7360a99b61e85ae5292 + md5: 30e28ca6bb87d15fa7c5a6f464f4f55e build: number: 0 rpaths: @@ -18,10 +18,10 @@ build: - lib/ requirements: host: - - 'bioconductor-dnacopy >=1.56.0,<1.57.0' + - 'bioconductor-dnacopy >=1.58.0,<1.59.0' - r-base run: - - 'bioconductor-dnacopy >=1.56.0,<1.57.0' + - 'bioconductor-dnacopy >=1.58.0,<1.59.0' - r-base build: - {{ compiler('c') }} diff --git a/recipes/bioconductor-cner/meta.yaml b/recipes/bioconductor-cner/meta.yaml index 0aa2e0f79d51c..3ac370de135bd 100644 --- a/recipes/bioconductor-cner/meta.yaml +++ b/recipes/bioconductor-cner/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.18.1" %} +{% set version = "1.20.0" %} {% set name = "CNEr" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: d14b070544db2a224af7ddacd34e24ad + md5: cf1a825dd6ed04ab61022de008fd5535 build: number: 0 rpaths: @@ -19,18 +19,18 @@ build: # Suggests: Gviz (>= 1.7.4), BiocStyle, knitr, rmarkdown, testthat, BSgenome.Drerio.UCSC.danRer10, BSgenome.Hsapiens.UCSC.hg38, TxDb.Drerio.UCSC.danRer10.refGene, BSgenome.Hsapiens.UCSC.hg19, BSgenome.Ggallus.UCSC.galGal3 requirements: host: - - 'bioconductor-annotate >=1.60.0,<1.61.0' - - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' - - 'bioconductor-biostrings >=2.50.0,<2.51.0' - - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' - - 'bioconductor-genomicalignments >=1.18.0,<1.19.0' - - 'bioconductor-genomicranges >=1.34.0,<1.35.0' - - 'bioconductor-go.db >=3.7.0,<3.8.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-keggrest >=1.22.0,<1.23.0' - - 'bioconductor-rtracklayer >=1.42.0,<1.43.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' - - 'bioconductor-xvector >=0.22.0,<0.23.0' + - 'bioconductor-annotate >=1.62.0,<1.63.0' + - 'bioconductor-biocgenerics >=0.30.0,<0.31.0' + - 'bioconductor-biostrings >=2.52.0,<2.53.0' + - 'bioconductor-genomeinfodb >=1.20.0,<1.21.0' + - 'bioconductor-genomicalignments >=1.20.0,<1.21.0' + - 'bioconductor-genomicranges >=1.36.0,<1.37.0' + - 'bioconductor-go.db >=3.8.0,<3.9.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-keggrest >=1.24.0,<1.25.0' + - 'bioconductor-rtracklayer >=1.44.0,<1.45.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' + - 'bioconductor-xvector >=0.24.0,<0.25.0' - r-base - 'r-dbi >=0.7' - 'r-ggplot2 >=2.1.0' @@ -40,18 +40,18 @@ requirements: - 'r-reshape2 >=1.4.1' - 'r-rsqlite >=0.11.4' run: - - 'bioconductor-annotate >=1.60.0,<1.61.0' - - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' - - 'bioconductor-biostrings >=2.50.0,<2.51.0' - - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' - - 'bioconductor-genomicalignments >=1.18.0,<1.19.0' - - 'bioconductor-genomicranges >=1.34.0,<1.35.0' - - 'bioconductor-go.db >=3.7.0,<3.8.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-keggrest >=1.22.0,<1.23.0' - - 'bioconductor-rtracklayer >=1.42.0,<1.43.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' - - 'bioconductor-xvector >=0.22.0,<0.23.0' + - 'bioconductor-annotate >=1.62.0,<1.63.0' + - 'bioconductor-biocgenerics >=0.30.0,<0.31.0' + - 'bioconductor-biostrings >=2.52.0,<2.53.0' + - 'bioconductor-genomeinfodb >=1.20.0,<1.21.0' + - 'bioconductor-genomicalignments >=1.20.0,<1.21.0' + - 'bioconductor-genomicranges >=1.36.0,<1.37.0' + - 'bioconductor-go.db >=3.8.0,<3.9.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-keggrest >=1.24.0,<1.25.0' + - 'bioconductor-rtracklayer >=1.44.0,<1.45.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' + - 'bioconductor-xvector >=0.24.0,<0.25.0' - r-base - 'r-dbi >=0.7' - 'r-ggplot2 >=2.1.0' diff --git a/recipes/bioconductor-cnordt/meta.yaml b/recipes/bioconductor-cnordt/meta.yaml index 9c932bd3d2130..74ba69606ad7c 100644 --- a/recipes/bioconductor-cnordt/meta.yaml +++ b/recipes/bioconductor-cnordt/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.24.1" %} +{% set version = "1.26.0" %} {% set name = "CNORdt" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: cf70dff7dc7563f6896b09d7af84d9fd + md5: 4de4604fc7299bfdab6568b3bc769da1 build: number: 0 rpaths: @@ -18,11 +18,11 @@ build: - lib/ requirements: host: - - 'bioconductor-cellnoptr >=1.28.0,<1.29.0' + - 'bioconductor-cellnoptr >=1.30.0,<1.31.0' - r-abind - r-base run: - - 'bioconductor-cellnoptr >=1.28.0,<1.29.0' + - 'bioconductor-cellnoptr >=1.30.0,<1.31.0' - r-abind - r-base build: diff --git a/recipes/bioconductor-cnorfeeder/meta.yaml b/recipes/bioconductor-cnorfeeder/meta.yaml index d0b066d9fa379..5a2932a5a4249 100644 --- a/recipes/bioconductor-cnorfeeder/meta.yaml +++ b/recipes/bioconductor-cnorfeeder/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.22.0" %} +{% set version = "1.24.0" %} {% set name = "CNORfeeder" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: d939f756f949292243ea621b99d9cf69 + md5: 2d7828bfb2c79b93ed53013e0d0f1fff build: number: 0 rpaths: @@ -20,12 +20,12 @@ build: # Suggests: minet, catnet, Rgraphviz, RUnit, BiocGenerics, igraph requirements: host: - - 'bioconductor-cellnoptr >=1.28.0,<1.29.0' - - 'bioconductor-graph >=1.60.0,<1.61.0' + - 'bioconductor-cellnoptr >=1.30.0,<1.31.0' + - 'bioconductor-graph >=1.62.0,<1.63.0' - r-base run: - - 'bioconductor-cellnoptr >=1.28.0,<1.29.0' - - 'bioconductor-graph >=1.60.0,<1.61.0' + - 'bioconductor-cellnoptr >=1.30.0,<1.31.0' + - 'bioconductor-graph >=1.62.0,<1.63.0' - r-base test: commands: diff --git a/recipes/bioconductor-cnorfuzzy/meta.yaml b/recipes/bioconductor-cnorfuzzy/meta.yaml index f51a9c51f732b..2c43ef0bbc3d3 100644 --- a/recipes/bioconductor-cnorfuzzy/meta.yaml +++ b/recipes/bioconductor-cnorfuzzy/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.24.0" %} +{% set version = "1.26.0" %} {% set name = "CNORfuzzy" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: a81e01df30c7acdb9a966953fa009109 + md5: e309f6b2e672b473f696368fd2a62595 build: number: 0 rpaths: @@ -19,11 +19,11 @@ build: # Suggests: xtable, Rgraphviz, RUnit, BiocGenerics requirements: host: - - 'bioconductor-cellnoptr >=1.28.0,<1.29.0' + - 'bioconductor-cellnoptr >=1.30.0,<1.31.0' - r-base - 'r-nloptr >=0.8.5' run: - - 'bioconductor-cellnoptr >=1.28.0,<1.29.0' + - 'bioconductor-cellnoptr >=1.30.0,<1.31.0' - r-base - 'r-nloptr >=0.8.5' build: diff --git a/recipes/bioconductor-cnorode/meta.yaml b/recipes/bioconductor-cnorode/meta.yaml index df3828e5ec538..5d2c06d4e502a 100644 --- a/recipes/bioconductor-cnorode/meta.yaml +++ b/recipes/bioconductor-cnorode/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.24.0" %} +{% set version = "1.26.0" %} {% set name = "CNORode" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: f3ea74252b1ad73d7342f763e5ad55be + md5: 800cc2ee0114d43e824ce48573f517d0 build: number: 0 rpaths: @@ -18,11 +18,11 @@ build: - lib/ requirements: host: - - 'bioconductor-cellnoptr >=1.28.0,<1.29.0' + - 'bioconductor-cellnoptr >=1.30.0,<1.31.0' - r-base - r-genalg run: - - 'bioconductor-cellnoptr >=1.28.0,<1.29.0' + - 'bioconductor-cellnoptr >=1.30.0,<1.31.0' - r-base - r-genalg build: diff --git a/recipes/bioconductor-cnpbayes/meta.yaml b/recipes/bioconductor-cnpbayes/meta.yaml index 727d7223e3a7c..71d66af58ffe8 100644 --- a/recipes/bioconductor-cnpbayes/meta.yaml +++ b/recipes/bioconductor-cnpbayes/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.12.0" %} +{% set version = "1.13.5" %} {% set name = "CNPBayes" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: b9231a3d34f0e502f273043d299f125d + md5: 8e50d11d4d4152779c2f999901665d93 build: number: 0 rpaths: @@ -19,15 +19,16 @@ build: # Suggests: testthat, knitr, BiocStyle, rmarkdown, BiocCheck, MASS, VanillaICE, tidyverse requirements: host: - - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' - - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' - - 'bioconductor-genomicranges >=1.34.0,<1.35.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' - - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' + - 'bioconductor-biocgenerics >=0.30.0,<0.31.0' + - 'bioconductor-genomeinfodb >=1.20.0,<1.21.0' + - 'bioconductor-genomicranges >=1.36.0,<1.37.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' + - 'bioconductor-summarizedexperiment >=1.14.0,<1.15.0' - r-base - r-coda - r-combinat + - r-data.table - r-dplyr - r-ggplot2 - r-gtools @@ -37,20 +38,22 @@ requirements: - r-purrr - r-rcolorbrewer - 'r-rcpp >=0.12.1' + - r-rcpparmadillo - r-reshape2 - r-scales - r-tibble - r-tidyr run: - - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' - - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' - - 'bioconductor-genomicranges >=1.34.0,<1.35.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' - - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' + - 'bioconductor-biocgenerics >=0.30.0,<0.31.0' + - 'bioconductor-genomeinfodb >=1.20.0,<1.21.0' + - 'bioconductor-genomicranges >=1.36.0,<1.37.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' + - 'bioconductor-summarizedexperiment >=1.14.0,<1.15.0' - r-base - r-coda - r-combinat + - r-data.table - r-dplyr - r-ggplot2 - r-gtools @@ -60,6 +63,7 @@ requirements: - r-purrr - r-rcolorbrewer - 'r-rcpp >=0.12.1' + - r-rcpparmadillo - r-reshape2 - r-scales - r-tibble diff --git a/recipes/bioconductor-cntools/meta.yaml b/recipes/bioconductor-cntools/meta.yaml index 927653b7bbcef..b1bbba03582ec 100644 --- a/recipes/bioconductor-cntools/meta.yaml +++ b/recipes/bioconductor-cntools/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.38.0" %} +{% set version = "1.40.0" %} {% set name = "CNTools" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 0a41c86ddaddf77e73f344fe7fa3c915 + md5: d3fab8b1e26b17398d947fb7785b06f5 build: number: 0 rpaths: @@ -18,10 +18,10 @@ build: - lib/ requirements: host: - - 'bioconductor-genefilter >=1.64.0,<1.65.0' + - 'bioconductor-genefilter >=1.66.0,<1.67.0' - r-base run: - - 'bioconductor-genefilter >=1.64.0,<1.65.0' + - 'bioconductor-genefilter >=1.66.0,<1.67.0' - r-base build: - {{ compiler('c') }} diff --git a/recipes/bioconductor-cnvgsa/meta.yaml b/recipes/bioconductor-cnvgsa/meta.yaml index 04b3b88565924..84bf45e091ce4 100644 --- a/recipes/bioconductor-cnvgsa/meta.yaml +++ b/recipes/bioconductor-cnvgsa/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.26.0" %} +{% set version = "1.28.0" %} {% set name = "cnvGSA" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: f178bf3793415071fcb3504af847f843 + md5: c0795147bf7c9c04734e76a4a9d5ad28 build: number: 0 rpaths: @@ -20,14 +20,14 @@ build: # Suggests: cnvGSAdata, org.Hs.eg.db requirements: host: - - 'bioconductor-genomicranges >=1.34.0,<1.35.0' + - 'bioconductor-genomicranges >=1.36.0,<1.37.0' - r-base - r-brglm - r-doparallel - r-foreach - r-splitstackshape run: - - 'bioconductor-genomicranges >=1.34.0,<1.35.0' + - 'bioconductor-genomicranges >=1.36.0,<1.37.0' - r-base - r-brglm - r-doparallel diff --git a/recipes/bioconductor-cnvgsadata/meta.yaml b/recipes/bioconductor-cnvgsadata/meta.yaml index 32edd34854046..be0de5cf78f06 100644 --- a/recipes/bioconductor-cnvgsadata/meta.yaml +++ b/recipes/bioconductor-cnvgsadata/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.18.0" %} +{% set version = "1.20.0" %} {% set name = "cnvGSAdata" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 9068308f3e9af11c862659158fc77687 + md5: 084bb4dde34828a90051aec087948cf1 build: number: 0 rpaths: @@ -19,12 +19,12 @@ build: noarch: generic requirements: host: - - 'bioconductor-cnvgsa >=1.26.0,<1.27.0' + - 'bioconductor-cnvgsa >=1.28.0,<1.29.0' - r-base run: - - 'bioconductor-cnvgsa >=1.26.0,<1.27.0' + - 'bioconductor-cnvgsa >=1.28.0,<1.29.0' - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-cnvgsadata/post-link.sh b/recipes/bioconductor-cnvgsadata/post-link.sh index 6acc2ba8baecb..231ea4395dcb6 100644 --- a/recipes/bioconductor-cnvgsadata/post-link.sh +++ b/recipes/bioconductor-cnvgsadata/post-link.sh @@ -1,11 +1,11 @@ #!/bin/bash -FN="cnvGSAdata_1.18.0.tar.gz" +FN="cnvGSAdata_1.20.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/experiment/src/contrib/cnvGSAdata_1.18.0.tar.gz" - "https://bioarchive.galaxyproject.org/cnvGSAdata_1.18.0.tar.gz" - "https://depot.galaxyproject.org/software/bioconductor-cnvgsadata/bioconductor-cnvgsadata_1.18.0_src_all.tar.gz" + "https://bioconductor.org/packages/3.9/data/experiment/src/contrib/cnvGSAdata_1.20.0.tar.gz" + "https://bioarchive.galaxyproject.org/cnvGSAdata_1.20.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-cnvgsadata/bioconductor-cnvgsadata_1.20.0_src_all.tar.gz" ) -MD5="9068308f3e9af11c862659158fc77687" +MD5="084bb4dde34828a90051aec087948cf1" # Use a staging area in the conda dir rather than temp dirs, both to avoid # permission issues as well as to have things downloaded in a predictable @@ -16,7 +16,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-cnvpanelizer/meta.yaml b/recipes/bioconductor-cnvpanelizer/meta.yaml index 24139a6ce3790..80d69b39a8059 100644 --- a/recipes/bioconductor-cnvpanelizer/meta.yaml +++ b/recipes/bioconductor-cnvpanelizer/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.14.0" %} +{% set version = "1.16.0" %} {% set name = "CNVPanelizer" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 98e25515072bab932fb127f75cbfe980 + md5: cb6a6ddd87aff3639c36971aa6260251 build: number: 0 rpaths: @@ -20,13 +20,13 @@ build: # Suggests: knitr, RUnit, BiocGenerics requirements: host: - - 'bioconductor-exomecopy >=1.28.0,<1.29.0' - - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' - - 'bioconductor-genomicranges >=1.34.0,<1.35.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-noiseq >=2.26.0,<2.27.0' - - 'bioconductor-rsamtools >=1.34.0,<1.35.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-exomecopy >=1.30.0,<1.31.0' + - 'bioconductor-genomeinfodb >=1.20.0,<1.21.0' + - 'bioconductor-genomicranges >=1.36.0,<1.37.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-noiseq >=2.28.0,<2.29.0' + - 'bioconductor-rsamtools >=2.0.0,<2.1.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' - r-base - r-foreach - r-ggplot2 @@ -40,13 +40,13 @@ requirements: - r-stringr - r-testthat run: - - 'bioconductor-exomecopy >=1.28.0,<1.29.0' - - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' - - 'bioconductor-genomicranges >=1.34.0,<1.35.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-noiseq >=2.26.0,<2.27.0' - - 'bioconductor-rsamtools >=1.34.0,<1.35.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-exomecopy >=1.30.0,<1.31.0' + - 'bioconductor-genomeinfodb >=1.20.0,<1.21.0' + - 'bioconductor-genomicranges >=1.36.0,<1.37.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-noiseq >=2.28.0,<2.29.0' + - 'bioconductor-rsamtools >=2.0.0,<2.1.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' - r-base - r-foreach - r-ggplot2 diff --git a/recipes/bioconductor-cnvranger/build.sh b/recipes/bioconductor-cnvranger/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-cnvranger/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-cnvranger/meta.yaml b/recipes/bioconductor-cnvranger/meta.yaml new file mode 100644 index 0000000000000..ac00b7bb839dd --- /dev/null +++ b/recipes/bioconductor-cnvranger/meta.yaml @@ -0,0 +1,69 @@ +{% set version = "1.0.0" %} +{% set name = "CNVRanger" %} +{% set bioc = "3.9" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: 31c5cdcaaebf77a8fc1407058886db5d +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: AnnotationHub, BSgenome.Btaurus.UCSC.bosTau6.masked, BiocStyle, MultiAssayExperiment, TCGAutils, curatedTCGAData, ensembldb, knitr, regioneR, rmarkdown +requirements: + host: + - 'bioconductor-biocparallel >=1.18.0,<1.19.0' + - 'bioconductor-edger >=3.26.0,<3.27.0' + - 'bioconductor-gdsarray >=1.4.0,<1.5.0' + - 'bioconductor-gdsfmt >=1.20.0,<1.21.0' + - 'bioconductor-genomeinfodb >=1.20.0,<1.21.0' + - 'bioconductor-genomicranges >=1.36.0,<1.37.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-limma >=3.40.0,<3.41.0' + - 'bioconductor-raggedexperiment >=1.8.0,<1.9.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' + - 'bioconductor-snprelate >=1.18.0,<1.19.0' + - 'bioconductor-summarizedexperiment >=1.14.0,<1.15.0' + - r-base + - r-data.table + - r-lattice + - r-plyr + - r-qqman + - r-rappdirs + - r-reshape2 + run: + - 'bioconductor-biocparallel >=1.18.0,<1.19.0' + - 'bioconductor-edger >=3.26.0,<3.27.0' + - 'bioconductor-gdsarray >=1.4.0,<1.5.0' + - 'bioconductor-gdsfmt >=1.20.0,<1.21.0' + - 'bioconductor-genomeinfodb >=1.20.0,<1.21.0' + - 'bioconductor-genomicranges >=1.36.0,<1.37.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-limma >=3.40.0,<3.41.0' + - 'bioconductor-raggedexperiment >=1.8.0,<1.9.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' + - 'bioconductor-snprelate >=1.18.0,<1.19.0' + - 'bioconductor-summarizedexperiment >=1.14.0,<1.15.0' + - r-base + - r-data.table + - r-lattice + - r-plyr + - r-qqman + - r-rappdirs + - r-reshape2 +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'The CNVRanger package implements a comprehensive tool suite for CNV analysis. This includes functionality for summarizing individual CNV calls across a population, assessing overlap with functional genomic regions, and association analysis with gene expression and quantitative phenotypes.' + diff --git a/recipes/bioconductor-cnvrd2/meta.yaml b/recipes/bioconductor-cnvrd2/meta.yaml index f0f63c89923c7..f15d69a35acbb 100644 --- a/recipes/bioconductor-cnvrd2/meta.yaml +++ b/recipes/bioconductor-cnvrd2/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.20.0" %} +{% set version = "1.22.0" %} {% set name = "CNVrd2" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 43748a826e927c6f6c8a24789b709688 + md5: 4794f092465ee552756f69506e6a0b93 build: number: 0 rpaths: @@ -20,25 +20,23 @@ build: # Suggests: knitr requirements: host: - - 'bioconductor-dnacopy >=1.56.0,<1.57.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-rsamtools >=1.34.0,<1.35.0' - - 'bioconductor-variantannotation >=1.28.0,<1.29.0' + - 'bioconductor-dnacopy >=1.58.0,<1.59.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-rsamtools >=2.0.0,<2.1.0' + - 'bioconductor-variantannotation >=1.30.0,<1.31.0' - r-base - r-ggplot2 - r-gridextra - r-rjags - - jags run: - - 'bioconductor-dnacopy >=1.56.0,<1.57.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-rsamtools >=1.34.0,<1.35.0' - - 'bioconductor-variantannotation >=1.28.0,<1.29.0' + - 'bioconductor-dnacopy >=1.58.0,<1.59.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-rsamtools >=2.0.0,<2.1.0' + - 'bioconductor-variantannotation >=1.30.0,<1.31.0' - r-base - r-ggplot2 - r-gridextra - r-rjags - - jags test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-cnvtools/meta.yaml b/recipes/bioconductor-cnvtools/meta.yaml index 5b048d3137f22..308a97bba6d09 100644 --- a/recipes/bioconductor-cnvtools/meta.yaml +++ b/recipes/bioconductor-cnvtools/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.76.0" %} +{% set version = "1.78.0" %} {% set name = "CNVtools" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 8c7a391861a596b79dec372a8ed5fd92 + md5: f9844ca1cd5bb736dc47736f3848b3e4 build: number: 0 rpaths: diff --git a/recipes/bioconductor-cobindr/meta.yaml b/recipes/bioconductor-cobindr/meta.yaml index b39a3eb00770b..b411be8af30a0 100644 --- a/recipes/bioconductor-cobindr/meta.yaml +++ b/recipes/bioconductor-cobindr/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.20.0" %} +{% set version = "1.22.0" %} {% set name = "cobindR" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,9 +10,9 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: a311dfeeec28c8f77c993ace8a77b5c7 + md5: 435e9185e8656279a82919a21d95a5fd build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ @@ -20,11 +20,11 @@ build: # Suggests: RUnit requirements: host: - - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' - - 'bioconductor-biomart >=2.38.0,<2.39.0' - - 'bioconductor-biostrings >=2.50.0,<2.51.0' - - 'bioconductor-bsgenome >=1.50.0,<1.51.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-biocgenerics >=0.30.0,<0.31.0' + - 'bioconductor-biomart >=2.40.0,<2.41.0' + - 'bioconductor-biostrings >=2.52.0,<2.53.0' + - 'bioconductor-bsgenome >=1.52.0,<1.53.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' - r-base - r-gmp - r-gplots @@ -33,11 +33,11 @@ requirements: - r-seqinr - r-yaml run: - - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' - - 'bioconductor-biomart >=2.38.0,<2.39.0' - - 'bioconductor-biostrings >=2.50.0,<2.51.0' - - 'bioconductor-bsgenome >=1.50.0,<1.51.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-biocgenerics >=0.30.0,<0.31.0' + - 'bioconductor-biomart >=2.40.0,<2.41.0' + - 'bioconductor-biostrings >=2.52.0,<2.53.0' + - 'bioconductor-bsgenome >=1.52.0,<1.53.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' - r-base - r-gmp - r-gplots diff --git a/recipes/bioconductor-cocitestats/meta.yaml b/recipes/bioconductor-cocitestats/meta.yaml index 859af5949fbe8..bfb6ac11fc978 100644 --- a/recipes/bioconductor-cocitestats/meta.yaml +++ b/recipes/bioconductor-cocitestats/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.54.0" %} +{% set version = "1.56.0" %} {% set name = "CoCiteStats" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 631d2c987e3945ab37065b400165fd2f + md5: 4b07800c4a99cf17a31094fd78d7ce6e build: number: 0 rpaths: @@ -19,12 +19,12 @@ build: noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' - - 'bioconductor-org.hs.eg.db >=3.7.0,<3.8.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' + - 'bioconductor-org.hs.eg.db >=3.8.0,<3.9.0' - r-base run: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' - - 'bioconductor-org.hs.eg.db >=3.7.0,<3.8.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' + - 'bioconductor-org.hs.eg.db >=3.8.0,<3.9.0' - r-base test: commands: diff --git a/recipes/bioconductor-cocoa/meta.yaml b/recipes/bioconductor-cocoa/meta.yaml index 519c81e7f8199..5c8a1840368d1 100644 --- a/recipes/bioconductor-cocoa/meta.yaml +++ b/recipes/bioconductor-cocoa/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.0.1" %} +{% set version = "1.2.0" %} {% set name = "COCOA" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 4daa8635624853e5bd208d15853d55d0 + md5: 2a3284970a78abe427089c9bc74f4076 build: number: 0 rpaths: @@ -20,25 +20,25 @@ build: # Suggests: knitr, parallel, testthat, BiocStyle, rmarkdown, AnnotationHub, LOLA requirements: host: - - 'bioconductor-biobase >=2.42.0,<2.43.0' - - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' - - 'bioconductor-complexheatmap >=1.20.0,<1.21.0' - - 'bioconductor-genomicranges >=1.34.0,<1.35.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-mira >=1.4.0,<1.5.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' + - 'bioconductor-biocgenerics >=0.30.0,<0.31.0' + - 'bioconductor-complexheatmap >=2.0.0,<2.1.0' + - 'bioconductor-genomicranges >=1.36.0,<1.37.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-mira >=1.6.0,<1.7.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' - r-base - r-data.table - r-ggplot2 - r-tidyr run: - - 'bioconductor-biobase >=2.42.0,<2.43.0' - - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' - - 'bioconductor-complexheatmap >=1.20.0,<1.21.0' - - 'bioconductor-genomicranges >=1.34.0,<1.35.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-mira >=1.4.0,<1.5.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' + - 'bioconductor-biocgenerics >=0.30.0,<0.31.0' + - 'bioconductor-complexheatmap >=2.0.0,<2.1.0' + - 'bioconductor-genomicranges >=1.36.0,<1.37.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-mira >=1.6.0,<1.7.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' - r-base - r-data.table - r-ggplot2 diff --git a/recipes/bioconductor-codelink/meta.yaml b/recipes/bioconductor-codelink/meta.yaml index fcc8e141e3b47..838f251919067 100644 --- a/recipes/bioconductor-codelink/meta.yaml +++ b/recipes/bioconductor-codelink/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.50.0" %} +{% set version = "1.52.0" %} {% set name = "codelink" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 581f0dafd469d47a78e5c59c019d20fc + md5: b7c747213e454bfb4f6f8191815d36ec build: number: 0 rpaths: @@ -20,16 +20,16 @@ build: # Suggests: genefilter, parallel, knitr requirements: host: - - 'bioconductor-annotate >=1.60.0,<1.61.0' - - 'bioconductor-biobase >=2.42.0,<2.43.0' - - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' - - 'bioconductor-limma >=3.38.0,<3.39.0' + - 'bioconductor-annotate >=1.62.0,<1.63.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' + - 'bioconductor-biocgenerics >=0.30.0,<0.31.0' + - 'bioconductor-limma >=3.40.0,<3.41.0' - r-base run: - - 'bioconductor-annotate >=1.60.0,<1.61.0' - - 'bioconductor-biobase >=2.42.0,<2.43.0' - - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' - - 'bioconductor-limma >=3.38.0,<3.39.0' + - 'bioconductor-annotate >=1.62.0,<1.63.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' + - 'bioconductor-biocgenerics >=0.30.0,<0.31.0' + - 'bioconductor-limma >=3.40.0,<3.41.0' - r-base test: commands: diff --git a/recipes/bioconductor-codex/meta.yaml b/recipes/bioconductor-codex/meta.yaml index c66e3258865d9..822136f4ddd84 100644 --- a/recipes/bioconductor-codex/meta.yaml +++ b/recipes/bioconductor-codex/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.14.0" %} +{% set version = "1.16.0" %} {% set name = "CODEX" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: d25cc0d3a2df50fff53a274b3d634724 + md5: a17ebe2c29dccb53f92d0417d22f2363 build: number: 0 rpaths: @@ -20,20 +20,20 @@ build: # Suggests: WES.1KG.WUGSC requirements: host: - - 'bioconductor-biostrings >=2.50.0,<2.51.0' + - 'bioconductor-biostrings >=2.52.0,<2.53.0' - 'bioconductor-bsgenome.hsapiens.ucsc.hg19 >=1.4.0,<1.5.0' - - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-rsamtools >=1.34.0,<1.35.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-genomeinfodb >=1.20.0,<1.21.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-rsamtools >=2.0.0,<2.1.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' - r-base run: - - 'bioconductor-biostrings >=2.50.0,<2.51.0' + - 'bioconductor-biostrings >=2.52.0,<2.53.0' - 'bioconductor-bsgenome.hsapiens.ucsc.hg19 >=1.4.0,<1.5.0' - - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-rsamtools >=1.34.0,<1.35.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-genomeinfodb >=1.20.0,<1.21.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-rsamtools >=2.0.0,<2.1.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' - r-base test: commands: diff --git a/recipes/bioconductor-coexnet/meta.yaml b/recipes/bioconductor-coexnet/meta.yaml index a1d2870e66a35..97f8102a1acea 100644 --- a/recipes/bioconductor-coexnet/meta.yaml +++ b/recipes/bioconductor-coexnet/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.4.0" %} +{% set version = "1.6.0" %} {% set name = "coexnet" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 9d8e6b5ab48da4a1ca2db90f2160c94f + md5: 2dc427a31e354e132cf875cf6378ed8f build: number: 0 rpaths: @@ -20,30 +20,30 @@ build: # Suggests: RUnit, BiocGenerics, knitr requirements: host: - - 'bioconductor-acde >=1.12.0,<1.13.0' - - 'bioconductor-affy >=1.60.0,<1.61.0' - - 'bioconductor-biobase >=2.42.0,<2.43.0' - - 'bioconductor-geoquery >=2.50.0,<2.51.0' - - 'bioconductor-limma >=3.38.0,<3.39.0' - - 'bioconductor-minet >=3.40.0,<3.41.0' - - 'bioconductor-siggenes >=1.56.0,<1.57.0' - - 'bioconductor-stringdb >=1.22.0,<1.23.0' - - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' - - 'bioconductor-vsn >=3.50.0,<3.51.0' + - 'bioconductor-acde >=1.14.0,<1.15.0' + - 'bioconductor-affy >=1.62.0,<1.63.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' + - 'bioconductor-geoquery >=2.52.0,<2.53.0' + - 'bioconductor-limma >=3.40.0,<3.41.0' + - 'bioconductor-minet >=3.42.0,<3.43.0' + - 'bioconductor-siggenes >=1.58.0,<1.59.0' + - 'bioconductor-stringdb >=1.24.0,<1.25.0' + - 'bioconductor-summarizedexperiment >=1.14.0,<1.15.0' + - 'bioconductor-vsn >=3.52.0,<3.53.0' - r-base - r-igraph - r-rmarkdown run: - - 'bioconductor-acde >=1.12.0,<1.13.0' - - 'bioconductor-affy >=1.60.0,<1.61.0' - - 'bioconductor-biobase >=2.42.0,<2.43.0' - - 'bioconductor-geoquery >=2.50.0,<2.51.0' - - 'bioconductor-limma >=3.38.0,<3.39.0' - - 'bioconductor-minet >=3.40.0,<3.41.0' - - 'bioconductor-siggenes >=1.56.0,<1.57.0' - - 'bioconductor-stringdb >=1.22.0,<1.23.0' - - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' - - 'bioconductor-vsn >=3.50.0,<3.51.0' + - 'bioconductor-acde >=1.14.0,<1.15.0' + - 'bioconductor-affy >=1.62.0,<1.63.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' + - 'bioconductor-geoquery >=2.52.0,<2.53.0' + - 'bioconductor-limma >=3.40.0,<3.41.0' + - 'bioconductor-minet >=3.42.0,<3.43.0' + - 'bioconductor-siggenes >=1.58.0,<1.59.0' + - 'bioconductor-stringdb >=1.24.0,<1.25.0' + - 'bioconductor-summarizedexperiment >=1.14.0,<1.15.0' + - 'bioconductor-vsn >=3.52.0,<3.53.0' - r-base - r-igraph - r-rmarkdown diff --git a/recipes/bioconductor-cogaps/meta.yaml b/recipes/bioconductor-cogaps/meta.yaml index 06a7ee5cafc7a..604d41f7bc488 100644 --- a/recipes/bioconductor-cogaps/meta.yaml +++ b/recipes/bioconductor-cogaps/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "3.2.1" %} +{% set version = "3.4.0" %} {% set name = "CoGAPS" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: fe3ec2e7eb8cb5fb23894fd27bf856df + md5: cc5ad88f7e8fcfc7db45e24c979149ea build: number: 0 rpaths: @@ -19,24 +19,24 @@ build: # Suggests: testthat, knitr, rmarkdown, BiocStyle requirements: host: - - 'bioconductor-biocparallel >=1.16.0,<1.17.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' - - 'bioconductor-singlecellexperiment >=1.4.0,<1.5.0' - - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' + - 'bioconductor-biocparallel >=1.18.0,<1.19.0' + - 'bioconductor-rhdf5 >=2.28.0,<2.29.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' + - 'bioconductor-singlecellexperiment >=1.6.0,<1.7.0' + - 'bioconductor-summarizedexperiment >=1.14.0,<1.15.0' - r-base - - r-bh - r-cluster - r-data.table - r-gplots - r-rcolorbrewer - r-rcpp run: - - 'bioconductor-biocparallel >=1.16.0,<1.17.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' - - 'bioconductor-singlecellexperiment >=1.4.0,<1.5.0' - - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' + - 'bioconductor-biocparallel >=1.18.0,<1.19.0' + - 'bioconductor-rhdf5 >=2.28.0,<2.29.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' + - 'bioconductor-singlecellexperiment >=1.6.0,<1.7.0' + - 'bioconductor-summarizedexperiment >=1.14.0,<1.15.0' - r-base - - r-bh - r-cluster - r-data.table - r-gplots diff --git a/recipes/bioconductor-cogena/meta.yaml b/recipes/bioconductor-cogena/meta.yaml index 9cb7d778b7abf..d2c0b2bdfe006 100644 --- a/recipes/bioconductor-cogena/meta.yaml +++ b/recipes/bioconductor-cogena/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.16.0" %} +{% set version = "1.18.0" %} {% set name = "cogena" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: e2c7d73b261ab79838296c26f8b38878 + md5: b785e1765e816c29bfaeb53b57fdf454 build: number: 0 rpaths: @@ -20,7 +20,7 @@ build: # Suggests: knitr, rmarkdown requirements: host: - - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' - r-amap - r-apcluster - r-base @@ -39,7 +39,7 @@ requirements: - r-mclust - r-reshape2 run: - - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' - r-amap - r-apcluster - r-base diff --git a/recipes/bioconductor-cogps/meta.yaml b/recipes/bioconductor-cogps/meta.yaml index f3e1d372d58b7..b07ee571651ef 100644 --- a/recipes/bioconductor-cogps/meta.yaml +++ b/recipes/bioconductor-cogps/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.26.0" %} +{% set version = "1.28.0" %} {% set name = "coGPS" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: e471e9f7a0a57988cbe0729d35712e77 + md5: 49800c742e5b6176809de49f5a58a938 build: number: 0 rpaths: diff --git a/recipes/bioconductor-cohcap/meta.yaml b/recipes/bioconductor-cohcap/meta.yaml index ebc68854ce81b..a177bb5ce2cdb 100644 --- a/recipes/bioconductor-cohcap/meta.yaml +++ b/recipes/bioconductor-cohcap/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.28.1" %} +{% set version = "1.30.0" %} {% set name = "COHCAP" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: a00f1b04b6e4a464ab245bf79ebbb764 + md5: 8009dc2a7a0bf2f7bdaee07a0802496b build: number: 0 rpaths: @@ -19,7 +19,7 @@ build: # SystemRequirements: Perl requirements: host: - - 'bioconductor-cohcapanno >=1.18.0,<1.19.0' + - 'bioconductor-cohcapanno >=1.20.0,<1.21.0' - r-base - r-bh - r-gplots @@ -27,8 +27,9 @@ requirements: - r-rcpp - r-rcpparmadillo - r-writexls + - perl run: - - 'bioconductor-cohcapanno >=1.18.0,<1.19.0' + - 'bioconductor-cohcapanno >=1.20.0,<1.21.0' - r-base - r-bh - r-gplots @@ -36,6 +37,7 @@ requirements: - r-rcpp - r-rcpparmadillo - r-writexls + - perl build: - {{ compiler('c') }} - {{ compiler('cxx') }} @@ -46,7 +48,7 @@ test: about: home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: GPL-3 - summary: 'This package provides a pipeline to analyze single-nucleotide resolution methylation data (Illumina 450k/EPIC methylation array, targeted BS-Seq, etc.). It provides differential methylation for CpG Sites, differential methylation for CpG Islands, integration with gene expression data, with visualizaton options. Discussion Group: https://sourceforge.net/p/cohcap/discussion/bioconductor/' + summary: 'COHCAP (pronounced "co-cap") provides a pipeline to analyze single-nucleotide resolution methylation data (Illumina 450k/EPIC methylation array, targeted BS-Seq, etc.). It provides differential methylation for CpG Sites, differential methylation for CpG Islands, integration with gene expression data, with visualizaton options. Discussion Group: https://sourceforge.net/p/cohcap/discussion/bioconductor/' extra: identifiers: - biotools:cohcap diff --git a/recipes/bioconductor-cohcapanno/meta.yaml b/recipes/bioconductor-cohcapanno/meta.yaml index f637d1c09f67a..48727a57dee25 100644 --- a/recipes/bioconductor-cohcapanno/meta.yaml +++ b/recipes/bioconductor-cohcapanno/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.18.0" %} +{% set version = "1.20.0" %} {% set name = "COHCAPanno" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,9 +10,9 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: b68214a25ae7726c488dd5893cf6417a + md5: 7372e4f9927b5c9b1060be2105a3e3f4 build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ @@ -22,7 +22,7 @@ requirements: - r-base run: - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-cohcapanno/post-link.sh b/recipes/bioconductor-cohcapanno/post-link.sh index d69ac98cef541..2c439a47a460c 100644 --- a/recipes/bioconductor-cohcapanno/post-link.sh +++ b/recipes/bioconductor-cohcapanno/post-link.sh @@ -1,11 +1,11 @@ #!/bin/bash -FN="COHCAPanno_1.18.0.tar.gz" +FN="COHCAPanno_1.20.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/experiment/src/contrib/COHCAPanno_1.18.0.tar.gz" - "https://bioarchive.galaxyproject.org/COHCAPanno_1.18.0.tar.gz" - "https://depot.galaxyproject.org/software/bioconductor-cohcapanno/bioconductor-cohcapanno_1.18.0_src_all.tar.gz" + "https://bioconductor.org/packages/3.9/data/experiment/src/contrib/COHCAPanno_1.20.0.tar.gz" + "https://bioarchive.galaxyproject.org/COHCAPanno_1.20.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-cohcapanno/bioconductor-cohcapanno_1.20.0_src_all.tar.gz" ) -MD5="b68214a25ae7726c488dd5893cf6417a" +MD5="7372e4f9927b5c9b1060be2105a3e3f4" # Use a staging area in the conda dir rather than temp dirs, both to avoid # permission issues as well as to have things downloaded in a predictable @@ -16,7 +16,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-cola/build.sh b/recipes/bioconductor-cola/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-cola/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-cola/meta.yaml b/recipes/bioconductor-cola/meta.yaml new file mode 100644 index 0000000000000..fe728c7214b4e --- /dev/null +++ b/recipes/bioconductor-cola/meta.yaml @@ -0,0 +1,80 @@ +{% set version = "1.0.0" %} +{% set name = "cola" %} +{% set bioc = "3.9" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + md5: 70e16effbf24c03503860821b8a95175 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ +# Suggests: genefilter, mvtnorm, testthat (>= 0.3), data.tree, dendextend, samr, pamr, venneuler, kohonen, NMF, WGCNA, Rtsne, umap +requirements: + host: + - 'bioconductor-complexheatmap >=2.0.0,<2.1.0' + - 'bioconductor-impute >=1.58.0,<1.59.0' + - r-base + - r-brew + - 'r-circlize >=0.4.5' + - r-clue + - r-cluster + - r-crayon + - r-digest + - r-getoptlong + - 'r-globaloptions >=0.1.0' + - r-gplots + - r-httr + - r-knitr + - r-markdown + - r-matrixstats + - r-mclust + - r-microbenchmark + - r-png + - r-rcolorbrewer + - 'r-rcpp >=0.11.0' + - r-skmeans + - r-xml2 + run: + - 'bioconductor-complexheatmap >=2.0.0,<2.1.0' + - 'bioconductor-impute >=1.58.0,<1.59.0' + - r-base + - r-brew + - 'r-circlize >=0.4.5' + - r-clue + - r-cluster + - r-crayon + - r-digest + - r-getoptlong + - 'r-globaloptions >=0.1.0' + - r-gplots + - r-httr + - r-knitr + - r-markdown + - r-matrixstats + - r-mclust + - r-microbenchmark + - r-png + - r-rcolorbrewer + - 'r-rcpp >=0.11.0' + - r-skmeans + - r-xml2 + build: + - {{ compiler('c') }} + - {{ compiler('cxx') }} + - make +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: 'MIT + file LICENSE' + summary: 'Subgroup classification is a basic task in genomic data analysis, especially for gene expression data and methylation data. It can predict novel subgroups when there is nothing known about the data or it can test consistency between predicted subgroups with known annotations. The cola package provides a general framework for subgroup classification by consensus clustering. It has following features: 1. It modularizes the consensus clustering processes that various methods can be easily integrated. 2. It provides rich visualizations for interpreting the results. 3. It allows running multiple methods at the same time and provides functionalities to compare results in a straightforward way. 4. It provides a new method to extract features which are more efficient to separate subgroups. 5. It allows doing partitioning in a hierarchical way to detect subgroups with relatively smaller difference. 6. It generates detailed reports for the complete analysis.' + diff --git a/recipes/bioconductor-colonca/meta.yaml b/recipes/bioconductor-colonca/meta.yaml index 3baabfc07215f..58e9e83c96678 100644 --- a/recipes/bioconductor-colonca/meta.yaml +++ b/recipes/bioconductor-colonca/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.24.0" %} +{% set version = "1.26.0" %} {% set name = "colonCA" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 60d8c68d5e87c89a3fb08e63169e3ab0 + md5: 26823f01a5ba01edf9e744c98dcb74b3 build: number: 0 rpaths: @@ -19,12 +19,12 @@ build: noarch: generic requirements: host: - - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' - r-base run: - - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-colonca/post-link.sh b/recipes/bioconductor-colonca/post-link.sh index 3d43078230712..c6fcc5287ff0f 100644 --- a/recipes/bioconductor-colonca/post-link.sh +++ b/recipes/bioconductor-colonca/post-link.sh @@ -1,11 +1,11 @@ #!/bin/bash -FN="colonCA_1.24.0.tar.gz" +FN="colonCA_1.26.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/experiment/src/contrib/colonCA_1.24.0.tar.gz" - "https://bioarchive.galaxyproject.org/colonCA_1.24.0.tar.gz" - "https://depot.galaxyproject.org/software/bioconductor-colonca/bioconductor-colonca_1.24.0_src_all.tar.gz" + "https://bioconductor.org/packages/3.9/data/experiment/src/contrib/colonCA_1.26.0.tar.gz" + "https://bioarchive.galaxyproject.org/colonCA_1.26.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-colonca/bioconductor-colonca_1.26.0_src_all.tar.gz" ) -MD5="60d8c68d5e87c89a3fb08e63169e3ab0" +MD5="26823f01a5ba01edf9e744c98dcb74b3" # Use a staging area in the conda dir rather than temp dirs, both to avoid # permission issues as well as to have things downloaded in a predictable @@ -16,7 +16,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-comet/meta.yaml b/recipes/bioconductor-comet/meta.yaml index 95c65d35f9597..5c9c29446a6be 100644 --- a/recipes/bioconductor-comet/meta.yaml +++ b/recipes/bioconductor-comet/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.14.0" %} +{% set version = "1.16.0" %} {% set name = "coMET" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 47824d638de57c2c0bc0c22a624fb0f2 + md5: bd89b930a424c677834857e55b7237f3 build: number: 0 rpaths: @@ -20,12 +20,12 @@ build: # Suggests: BiocStyle, knitr, RUnit, BiocGenerics requirements: host: - - 'bioconductor-biomart >=2.38.0,<2.39.0' - - 'bioconductor-genomicranges >=1.34.0,<1.35.0' - - 'bioconductor-gviz >=1.26.0,<1.27.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-rtracklayer >=1.42.0,<1.43.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-biomart >=2.40.0,<2.41.0' + - 'bioconductor-genomicranges >=1.36.0,<1.37.0' + - 'bioconductor-gviz >=1.28.0,<1.29.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-rtracklayer >=1.44.0,<1.45.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' - r-base - r-colortools - r-corrplot @@ -33,12 +33,12 @@ requirements: - r-hash - r-psych run: - - 'bioconductor-biomart >=2.38.0,<2.39.0' - - 'bioconductor-genomicranges >=1.34.0,<1.35.0' - - 'bioconductor-gviz >=1.26.0,<1.27.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-rtracklayer >=1.42.0,<1.43.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-biomart >=2.40.0,<2.41.0' + - 'bioconductor-genomicranges >=1.36.0,<1.37.0' + - 'bioconductor-gviz >=1.28.0,<1.29.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-rtracklayer >=1.44.0,<1.45.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' - r-base - r-colortools - r-corrplot diff --git a/recipes/bioconductor-compartmap/meta.yaml b/recipes/bioconductor-compartmap/meta.yaml index 6ffcafe1d519a..117639b5f695c 100644 --- a/recipes/bioconductor-compartmap/meta.yaml +++ b/recipes/bioconductor-compartmap/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.0.2" %} +{% set version = "1.2.0" %} {% set name = "compartmap" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 232abc83b25db9468001591dabba0f76 + md5: 3a5b9a72c01eaef3aafd6f7e8124e83c build: number: 0 rpaths: @@ -20,19 +20,19 @@ build: # Suggests: covr, testthat, knitr requirements: host: - - 'bioconductor-genomicranges >=1.34.0,<1.35.0' - - 'bioconductor-homo.sapiens >=1.3.0,<1.4.0' - - 'bioconductor-minfi >=1.28.0,<1.29.0' - - 'bioconductor-mixomics >=6.6.0,<6.7.0' - - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' + - 'bioconductor-genomicranges >=1.36.0,<1.37.0' + - 'bioconductor-homo.sapiens >=1.4.0,<1.5.0' + - 'bioconductor-minfi >=1.30.0,<1.31.0' + - 'bioconductor-mixomics >=6.8.0,<6.9.0' + - 'bioconductor-summarizedexperiment >=1.14.0,<1.15.0' - r-base - r-gtools run: - - 'bioconductor-genomicranges >=1.34.0,<1.35.0' - - 'bioconductor-homo.sapiens >=1.3.0,<1.4.0' - - 'bioconductor-minfi >=1.28.0,<1.29.0' - - 'bioconductor-mixomics >=6.6.0,<6.7.0' - - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' + - 'bioconductor-genomicranges >=1.36.0,<1.37.0' + - 'bioconductor-homo.sapiens >=1.4.0,<1.5.0' + - 'bioconductor-minfi >=1.30.0,<1.31.0' + - 'bioconductor-mixomics >=6.8.0,<6.9.0' + - 'bioconductor-summarizedexperiment >=1.14.0,<1.15.0' - r-base - r-gtools test: diff --git a/recipes/bioconductor-compass/meta.yaml b/recipes/bioconductor-compass/meta.yaml index cf18190a44e3f..3434a828b42ec 100644 --- a/recipes/bioconductor-compass/meta.yaml +++ b/recipes/bioconductor-compass/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.20.1" %} +{% set version = "1.22.0" %} {% set name = "COMPASS" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,16 +10,16 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: 1f71a2ee813f4a1161caee370673b2334ea8d94e58c8e5ab4bcc36e7614b114a + md5: f3efd33af8043c6ec9b8e668e645e2a5 build: number: 0 rpaths: - lib/R/lib/ - lib/ -# Suggests: flowWorkspace (>= 3.9.66), flowCore, ncdfFlow, shiny, testthat, devtools, flowWorkspaceData +# Suggests: flowWorkspace (>= 3.9.66), flowCore, ncdfFlow, shiny, testthat, devtools, flowWorkspaceData, ggplot2 requirements: host: - - 'bioconductor-biocstyle >=2.10.0,<2.11.0' + - 'bioconductor-biocstyle >=2.12.0,<2.13.0' - r-abind - r-base - r-clue @@ -37,7 +37,7 @@ requirements: - r-scales - r-tidyr run: - - 'bioconductor-biocstyle >=2.10.0,<2.11.0' + - 'bioconductor-biocstyle >=2.12.0,<2.13.0' - r-abind - r-base - r-clue diff --git a/recipes/bioconductor-compcoder/meta.yaml b/recipes/bioconductor-compcoder/meta.yaml index 775dce296fe59..8f934374075fb 100644 --- a/recipes/bioconductor-compcoder/meta.yaml +++ b/recipes/bioconductor-compcoder/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.18.1" %} +{% set version = "1.20.0" %} {% set name = "compcodeR" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: 3a570348305566bda5fa339d239830f7fad09e72da9a4cf3d0f6dd5fb2fa6320 + md5: a5213f6c6339bb117e50a815146de05a build: number: 0 rpaths: @@ -20,8 +20,8 @@ build: # Suggests: BiocStyle, EBSeq, DESeq, DESeq2 (>= 1.1.31), baySeq (>= 2.2.0), genefilter, NOISeq, TCC, NBPSeq (>= 0.3.0) requirements: host: - - 'bioconductor-edger >=3.24.0,<3.25.0' - - 'bioconductor-limma >=3.38.0,<3.39.0' + - 'bioconductor-edger >=3.26.0,<3.27.0' + - 'bioconductor-limma >=3.40.0,<3.41.0' - r-base - r-catools - r-gdata @@ -39,8 +39,8 @@ requirements: - r-stringr - r-vioplot run: - - 'bioconductor-edger >=3.24.0,<3.25.0' - - 'bioconductor-limma >=3.38.0,<3.39.0' + - 'bioconductor-edger >=3.26.0,<3.27.0' + - 'bioconductor-limma >=3.40.0,<3.41.0' - r-base - r-catools - r-gdata diff --git a/recipes/bioconductor-compepitools/meta.yaml b/recipes/bioconductor-compepitools/meta.yaml index 2af08a34c7bcd..0bffbfe6360d7 100644 --- a/recipes/bioconductor-compepitools/meta.yaml +++ b/recipes/bioconductor-compepitools/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.16.0" %} +{% set version = "1.18.0" %} {% set name = "compEpiTools" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: fb61333b079671d747268fb10a6b1188 + md5: 5634de2c34a8a8006e7025d34234797e build: number: 0 rpaths: @@ -20,35 +20,35 @@ build: # Suggests: BSgenome.Mmusculus.UCSC.mm9, TxDb.Mmusculus.UCSC.mm9.knownGene, org.Mm.eg.db, knitr, rtracklayer requirements: host: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' - - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' - - 'bioconductor-biostrings >=2.50.0,<2.51.0' - - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' - - 'bioconductor-genomicfeatures >=1.34.0,<1.35.0' - - 'bioconductor-genomicranges >=1.34.0,<1.35.0' - - 'bioconductor-go.db >=3.7.0,<3.8.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-methylpipe >=1.16.0,<1.17.0' - - 'bioconductor-rsamtools >=1.34.0,<1.35.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' - - 'bioconductor-topgo >=2.34.0,<2.35.0' - - 'bioconductor-xvector >=0.22.0,<0.23.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' + - 'bioconductor-biocgenerics >=0.30.0,<0.31.0' + - 'bioconductor-biostrings >=2.52.0,<2.53.0' + - 'bioconductor-genomeinfodb >=1.20.0,<1.21.0' + - 'bioconductor-genomicfeatures >=1.36.0,<1.37.0' + - 'bioconductor-genomicranges >=1.36.0,<1.37.0' + - 'bioconductor-go.db >=3.8.0,<3.9.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-methylpipe >=1.18.0,<1.19.0' + - 'bioconductor-rsamtools >=2.0.0,<2.1.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' + - 'bioconductor-topgo >=2.36.0,<2.37.0' + - 'bioconductor-xvector >=0.24.0,<0.25.0' - r-base - r-gplots run: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' - - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' - - 'bioconductor-biostrings >=2.50.0,<2.51.0' - - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' - - 'bioconductor-genomicfeatures >=1.34.0,<1.35.0' - - 'bioconductor-genomicranges >=1.34.0,<1.35.0' - - 'bioconductor-go.db >=3.7.0,<3.8.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-methylpipe >=1.16.0,<1.17.0' - - 'bioconductor-rsamtools >=1.34.0,<1.35.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' - - 'bioconductor-topgo >=2.34.0,<2.35.0' - - 'bioconductor-xvector >=0.22.0,<0.23.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' + - 'bioconductor-biocgenerics >=0.30.0,<0.31.0' + - 'bioconductor-biostrings >=2.52.0,<2.53.0' + - 'bioconductor-genomeinfodb >=1.20.0,<1.21.0' + - 'bioconductor-genomicfeatures >=1.36.0,<1.37.0' + - 'bioconductor-genomicranges >=1.36.0,<1.37.0' + - 'bioconductor-go.db >=3.8.0,<3.9.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-methylpipe >=1.18.0,<1.19.0' + - 'bioconductor-rsamtools >=2.0.0,<2.1.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' + - 'bioconductor-topgo >=2.36.0,<2.37.0' + - 'bioconductor-xvector >=0.24.0,<0.25.0' - r-base - r-gplots test: diff --git a/recipes/bioconductor-compgo/meta.yaml b/recipes/bioconductor-compgo/meta.yaml index 57cda3fdea4a4..80271de18554a 100644 --- a/recipes/bioconductor-compgo/meta.yaml +++ b/recipes/bioconductor-compgo/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.18.0" %} +{% set version = "1.20.0" %} {% set name = "CompGO" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 8d55397e57562db724c8714f2ca5b0c1 + md5: f5dd5a91ff4f0dec75db80fddf3731f5 build: number: 0 rpaths: @@ -19,23 +19,23 @@ build: noarch: generic requirements: host: - - 'bioconductor-genomicfeatures >=1.34.0,<1.35.0' - - 'bioconductor-pathview >=1.22.0,<1.23.0' - - 'bioconductor-pcamethods >=1.74.0,<1.75.0' - - 'bioconductor-rdavidwebservice >=1.20.0,<1.21.0' - - 'bioconductor-rgraphviz >=2.26.0,<2.27.0' - - 'bioconductor-rtracklayer >=1.42.0,<1.43.0' + - 'bioconductor-genomicfeatures >=1.36.0,<1.37.0' + - 'bioconductor-pathview >=1.24.0,<1.25.0' + - 'bioconductor-pcamethods >=1.76.0,<1.77.0' + - 'bioconductor-rdavidwebservice >=1.22.0,<1.23.0' + - 'bioconductor-rgraphviz >=2.28.0,<2.29.0' + - 'bioconductor-rtracklayer >=1.44.0,<1.45.0' - 'bioconductor-txdb.mmusculus.ucsc.mm9.knowngene >=3.2.0,<3.3.0' - r-base - r-ggplot2 - r-reshape2 run: - - 'bioconductor-genomicfeatures >=1.34.0,<1.35.0' - - 'bioconductor-pathview >=1.22.0,<1.23.0' - - 'bioconductor-pcamethods >=1.74.0,<1.75.0' - - 'bioconductor-rdavidwebservice >=1.20.0,<1.21.0' - - 'bioconductor-rgraphviz >=2.26.0,<2.27.0' - - 'bioconductor-rtracklayer >=1.42.0,<1.43.0' + - 'bioconductor-genomicfeatures >=1.36.0,<1.37.0' + - 'bioconductor-pathview >=1.24.0,<1.25.0' + - 'bioconductor-pcamethods >=1.76.0,<1.77.0' + - 'bioconductor-rdavidwebservice >=1.22.0,<1.23.0' + - 'bioconductor-rgraphviz >=2.28.0,<2.29.0' + - 'bioconductor-rtracklayer >=1.44.0,<1.45.0' - 'bioconductor-txdb.mmusculus.ucsc.mm9.knowngene >=3.2.0,<3.3.0' - r-base - r-ggplot2 diff --git a/recipes/bioconductor-complexheatmap/meta.yaml b/recipes/bioconductor-complexheatmap/meta.yaml index e05dee47ded00..8178a91d0faa7 100644 --- a/recipes/bioconductor-complexheatmap/meta.yaml +++ b/recipes/bioconductor-complexheatmap/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.20.0" %} +{% set version = "2.0.0" %} {% set name = "ComplexHeatmap" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,28 +10,32 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 456f36170972af9de5e366781054c561 + md5: 9c18a94275f005a74bf2d7e5a30ff3ea build: number: 0 rpaths: - lib/R/lib/ - lib/ noarch: generic -# Suggests: testthat (>= 0.3), knitr, markdown, cluster, MASS, pvclust, dendsort, HilbertCurve, Cairo, png, jpeg, tiff, fastcluster, dendextend (>= 1.0.1) +# Suggests: testthat (>= 1.0.0), knitr, markdown, dendsort, Cairo, jpeg, tiff, fastcluster, dendextend (>= 1.0.1), grImport, grImport2, glue, GenomicRanges requirements: host: - r-base - - 'r-circlize >=0.4.1' + - 'r-circlize >=0.4.5' + - r-clue - r-colorspace - r-getoptlong - 'r-globaloptions >=0.1.0' + - r-png - r-rcolorbrewer run: - r-base - - 'r-circlize >=0.4.1' + - 'r-circlize >=0.4.5' + - r-clue - r-colorspace - r-getoptlong - 'r-globaloptions >=0.1.0' + - r-png - r-rcolorbrewer test: commands: @@ -39,7 +43,7 @@ test: about: home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: 'MIT + file LICENSE' - summary: 'Complex heatmaps are efficient to visualize associations between different sources of data sets and reveal potential structures. Here the ComplexHeatmap package provides a highly flexible way to arrange multiple heatmaps and supports self-defined annotation graphics.' + summary: 'Complex heatmaps are efficient to visualize associations between different sources of data sets and reveal potential patterns. Here the ComplexHeatmap package provides a highly flexible way to arrange multiple heatmaps and supports various annotation graphics.' extra: identifiers: - biotools:complexheatmap diff --git a/recipes/bioconductor-condcomp/meta.yaml b/recipes/bioconductor-condcomp/meta.yaml index 12e56d07b43db..068770f382f50 100644 --- a/recipes/bioconductor-condcomp/meta.yaml +++ b/recipes/bioconductor-condcomp/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.0.1" %} +{% set version = "1.1.1" %} {% set name = "condcomp" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 19e58e283d0ffc5e9a5fccf562513f20 + md5: 0f1919283cb85a0552f82365b33d193e build: number: 0 rpaths: diff --git a/recipes/bioconductor-confess/meta.yaml b/recipes/bioconductor-confess/meta.yaml index 7e1200ec558b5..49e3e49faadf1 100644 --- a/recipes/bioconductor-confess/meta.yaml +++ b/recipes/bioconductor-confess/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.10.1" %} +{% set version = "1.12.0" %} {% set name = "CONFESS" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 5fa9f3d2b4d02fdf8964f10fa9bf83b0 + md5: 9d796e40ddb6520234e5a68e3bbb7d2b build: number: 0 rpaths: @@ -20,14 +20,14 @@ build: # Suggests: BiocStyle, knitr, rmarkdown, CONFESSdata requirements: host: - - 'bioconductor-ebimage >=4.24.0,<4.25.0' - - 'bioconductor-flowclust >=3.20.0,<3.21.0' - - 'bioconductor-flowcore >=1.48.0,<1.49.0' - - 'bioconductor-flowmeans >=1.42.0,<1.43.0' - - 'bioconductor-flowmerge >=2.30.0,<2.31.0' - - 'bioconductor-flowpeaks >=1.28.0,<1.29.0' - - 'bioconductor-limma >=3.38.0,<3.39.0' - - 'bioconductor-samspectral >=1.36.0,<1.37.0' + - 'bioconductor-ebimage >=4.26.0,<4.27.0' + - 'bioconductor-flowclust >=3.22.0,<3.23.0' + - 'bioconductor-flowcore >=1.50.0,<1.51.0' + - 'bioconductor-flowmeans >=1.44.0,<1.45.0' + - 'bioconductor-flowmerge >=2.32.0,<2.33.0' + - 'bioconductor-flowpeaks >=1.30.0,<1.31.0' + - 'bioconductor-limma >=3.40.0,<3.41.0' + - 'bioconductor-samspectral >=1.38.0,<1.39.0' - r-base - r-changepoint - r-cluster @@ -48,14 +48,14 @@ requirements: - r-wavethresh - r-zoo run: - - 'bioconductor-ebimage >=4.24.0,<4.25.0' - - 'bioconductor-flowclust >=3.20.0,<3.21.0' - - 'bioconductor-flowcore >=1.48.0,<1.49.0' - - 'bioconductor-flowmeans >=1.42.0,<1.43.0' - - 'bioconductor-flowmerge >=2.30.0,<2.31.0' - - 'bioconductor-flowpeaks >=1.28.0,<1.29.0' - - 'bioconductor-limma >=3.38.0,<3.39.0' - - 'bioconductor-samspectral >=1.36.0,<1.37.0' + - 'bioconductor-ebimage >=4.26.0,<4.27.0' + - 'bioconductor-flowclust >=3.22.0,<3.23.0' + - 'bioconductor-flowcore >=1.50.0,<1.51.0' + - 'bioconductor-flowmeans >=1.44.0,<1.45.0' + - 'bioconductor-flowmerge >=2.32.0,<2.33.0' + - 'bioconductor-flowpeaks >=1.30.0,<1.31.0' + - 'bioconductor-limma >=3.40.0,<3.41.0' + - 'bioconductor-samspectral >=1.38.0,<1.39.0' - r-base - r-changepoint - r-cluster @@ -82,7 +82,7 @@ about: home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: GPL-2 summary: 'Single Cell Fluidigm Spot Detector.' - extra: container: - extended-base: True + extended-base: true + diff --git a/recipes/bioconductor-confessdata/meta.yaml b/recipes/bioconductor-confessdata/meta.yaml index 7de5b14bcb8ed..9955ddb4cfddb 100644 --- a/recipes/bioconductor-confessdata/meta.yaml +++ b/recipes/bioconductor-confessdata/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.10.0" %} +{% set version = "1.12.0" %} {% set name = "CONFESSdata" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 3e44ef1d35b8701069ba3908770dbb1e + md5: 5a94a77fec0407c04bc72f89934775a1 build: number: 0 rpaths: @@ -22,7 +22,7 @@ requirements: - r-base run: - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-confessdata/post-link.sh b/recipes/bioconductor-confessdata/post-link.sh index c5e9aa7d1b533..6f7b6e6b9cb4c 100644 --- a/recipes/bioconductor-confessdata/post-link.sh +++ b/recipes/bioconductor-confessdata/post-link.sh @@ -1,11 +1,11 @@ #!/bin/bash -FN="CONFESSdata_1.10.0.tar.gz" +FN="CONFESSdata_1.12.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/experiment/src/contrib/CONFESSdata_1.10.0.tar.gz" - "https://bioarchive.galaxyproject.org/CONFESSdata_1.10.0.tar.gz" - "https://depot.galaxyproject.org/software/bioconductor-confessdata/bioconductor-confessdata_1.10.0_src_all.tar.gz" + "https://bioconductor.org/packages/3.9/data/experiment/src/contrib/CONFESSdata_1.12.0.tar.gz" + "https://bioarchive.galaxyproject.org/CONFESSdata_1.12.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-confessdata/bioconductor-confessdata_1.12.0_src_all.tar.gz" ) -MD5="3e44ef1d35b8701069ba3908770dbb1e" +MD5="5a94a77fec0407c04bc72f89934775a1" # Use a staging area in the conda dir rather than temp dirs, both to avoid # permission issues as well as to have things downloaded in a predictable @@ -16,7 +16,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-connectivitymap/meta.yaml b/recipes/bioconductor-connectivitymap/meta.yaml index 9d26bc50ebb58..d9bdc8f0fc30c 100644 --- a/recipes/bioconductor-connectivitymap/meta.yaml +++ b/recipes/bioconductor-connectivitymap/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.18.0" %} +{% set version = "1.20.0" %} {% set name = "ConnectivityMap" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: ff3bb449f67cd01953a13682b3496fff + md5: 0556684e97c094a8206e314400bb5165 build: number: 0 rpaths: @@ -23,7 +23,7 @@ requirements: - r-base run: - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-connectivitymap/post-link.sh b/recipes/bioconductor-connectivitymap/post-link.sh index 26df838ebd549..7556bb6080c1d 100644 --- a/recipes/bioconductor-connectivitymap/post-link.sh +++ b/recipes/bioconductor-connectivitymap/post-link.sh @@ -1,11 +1,11 @@ #!/bin/bash -FN="ConnectivityMap_1.18.0.tar.gz" +FN="ConnectivityMap_1.20.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/experiment/src/contrib/ConnectivityMap_1.18.0.tar.gz" - "https://bioarchive.galaxyproject.org/ConnectivityMap_1.18.0.tar.gz" - "https://depot.galaxyproject.org/software/bioconductor-connectivitymap/bioconductor-connectivitymap_1.18.0_src_all.tar.gz" + "https://bioconductor.org/packages/3.9/data/experiment/src/contrib/ConnectivityMap_1.20.0.tar.gz" + "https://bioarchive.galaxyproject.org/ConnectivityMap_1.20.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-connectivitymap/bioconductor-connectivitymap_1.20.0_src_all.tar.gz" ) -MD5="ff3bb449f67cd01953a13682b3496fff" +MD5="0556684e97c094a8206e314400bb5165" # Use a staging area in the conda dir rather than temp dirs, both to avoid # permission issues as well as to have things downloaded in a predictable @@ -16,7 +16,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-consensus/meta.yaml b/recipes/bioconductor-consensus/meta.yaml index dfd644a398e84..7f8989332fc65 100644 --- a/recipes/bioconductor-consensus/meta.yaml +++ b/recipes/bioconductor-consensus/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.0.2" %} +{% set version = "1.2.0" %} {% set name = "consensus" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: d1eb7d315a9299d8c4f2b69819f93b02 + md5: f3a7d31b7219d56cd48a3b5bc41e9f4d build: number: 0 rpaths: diff --git a/recipes/bioconductor-consensusclusterplus/meta.yaml b/recipes/bioconductor-consensusclusterplus/meta.yaml index b4226ed40597f..96ef56f4b52ac 100644 --- a/recipes/bioconductor-consensusclusterplus/meta.yaml +++ b/recipes/bioconductor-consensusclusterplus/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.46.0" %} +{% set version = "1.48.0" %} {% set name = "ConsensusClusterPlus" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: e53f78c29f4dc2a0a9feaf93acb4c71f + md5: 866829344d197d481e17c6101abd0856 build: number: 0 rpaths: @@ -19,13 +19,13 @@ build: noarch: generic requirements: host: - - 'bioconductor-all >=1.24.0,<1.25.0' - - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-all >=1.26.0,<1.27.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' - r-base - r-cluster run: - - 'bioconductor-all >=1.24.0,<1.25.0' - - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-all >=1.26.0,<1.27.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' - r-base - r-cluster test: diff --git a/recipes/bioconductor-consensusde/meta.yaml b/recipes/bioconductor-consensusde/meta.yaml index fde497af711db..2c35afd0b0cb0 100644 --- a/recipes/bioconductor-consensusde/meta.yaml +++ b/recipes/bioconductor-consensusde/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.0.0" %} +{% set version = "1.2.0" %} {% set name = "consensusDE" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 11e5c9a0b5eb21efed6daa2b0dde82ac + md5: 63d574c54e5e9f7305359f14d6c63352 build: number: 0 rpaths: @@ -20,43 +20,51 @@ build: # Suggests: knitr, rmarkdown requirements: host: - - 'bioconductor-airway >=1.2.0,<1.3.0' - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' - - 'bioconductor-biobase >=2.42.0,<2.43.0' - - 'bioconductor-biocparallel >=1.16.0,<1.17.0' - - 'bioconductor-biostrings >=2.50.0,<2.51.0' - - 'bioconductor-deseq2 >=1.22.0,<1.23.0' - - 'bioconductor-edaseq >=2.16.0,<2.17.0' - - 'bioconductor-edger >=3.24.0,<3.25.0' - - 'bioconductor-genomicalignments >=1.18.0,<1.19.0' - - 'bioconductor-genomicfeatures >=1.34.0,<1.35.0' - - 'bioconductor-limma >=3.38.0,<3.39.0' - - 'bioconductor-pcamethods >=1.74.0,<1.75.0' - - 'bioconductor-rsamtools >=1.34.0,<1.35.0' - - 'bioconductor-ruvseq >=1.16.0,<1.17.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' - - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' + - 'bioconductor-airway >=1.4.0,<1.5.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' + - 'bioconductor-biocgenerics >=0.30.0,<0.31.0' + - 'bioconductor-biocparallel >=1.18.0,<1.19.0' + - 'bioconductor-biostrings >=2.52.0,<2.53.0' + - 'bioconductor-deseq2 >=1.24.0,<1.25.0' + - 'bioconductor-edaseq >=2.18.0,<2.19.0' + - 'bioconductor-edger >=3.26.0,<3.27.0' + - 'bioconductor-ensdb.hsapiens.v86 >=3.0.0,<3.1.0' + - 'bioconductor-ensembldb >=2.8.0,<2.9.0' + - 'bioconductor-genomicalignments >=1.20.0,<1.21.0' + - 'bioconductor-genomicfeatures >=1.36.0,<1.37.0' + - 'bioconductor-limma >=3.40.0,<3.41.0' + - 'bioconductor-org.hs.eg.db >=3.8.0,<3.9.0' + - 'bioconductor-pcamethods >=1.76.0,<1.77.0' + - 'bioconductor-rsamtools >=2.0.0,<2.1.0' + - 'bioconductor-ruvseq >=1.18.0,<1.19.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' + - 'bioconductor-summarizedexperiment >=1.14.0,<1.15.0' - 'bioconductor-txdb.dmelanogaster.ucsc.dm3.ensgene >=3.2.0,<3.3.0' - r-base - r-dendextend - r-rcolorbrewer run: - - 'bioconductor-airway >=1.2.0,<1.3.0' - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' - - 'bioconductor-biobase >=2.42.0,<2.43.0' - - 'bioconductor-biocparallel >=1.16.0,<1.17.0' - - 'bioconductor-biostrings >=2.50.0,<2.51.0' - - 'bioconductor-deseq2 >=1.22.0,<1.23.0' - - 'bioconductor-edaseq >=2.16.0,<2.17.0' - - 'bioconductor-edger >=3.24.0,<3.25.0' - - 'bioconductor-genomicalignments >=1.18.0,<1.19.0' - - 'bioconductor-genomicfeatures >=1.34.0,<1.35.0' - - 'bioconductor-limma >=3.38.0,<3.39.0' - - 'bioconductor-pcamethods >=1.74.0,<1.75.0' - - 'bioconductor-rsamtools >=1.34.0,<1.35.0' - - 'bioconductor-ruvseq >=1.16.0,<1.17.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' - - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' + - 'bioconductor-airway >=1.4.0,<1.5.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' + - 'bioconductor-biocgenerics >=0.30.0,<0.31.0' + - 'bioconductor-biocparallel >=1.18.0,<1.19.0' + - 'bioconductor-biostrings >=2.52.0,<2.53.0' + - 'bioconductor-deseq2 >=1.24.0,<1.25.0' + - 'bioconductor-edaseq >=2.18.0,<2.19.0' + - 'bioconductor-edger >=3.26.0,<3.27.0' + - 'bioconductor-ensdb.hsapiens.v86 >=3.0.0,<3.1.0' + - 'bioconductor-ensembldb >=2.8.0,<2.9.0' + - 'bioconductor-genomicalignments >=1.20.0,<1.21.0' + - 'bioconductor-genomicfeatures >=1.36.0,<1.37.0' + - 'bioconductor-limma >=3.40.0,<3.41.0' + - 'bioconductor-org.hs.eg.db >=3.8.0,<3.9.0' + - 'bioconductor-pcamethods >=1.76.0,<1.77.0' + - 'bioconductor-rsamtools >=2.0.0,<2.1.0' + - 'bioconductor-ruvseq >=1.18.0,<1.19.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' + - 'bioconductor-summarizedexperiment >=1.14.0,<1.15.0' - 'bioconductor-txdb.dmelanogaster.ucsc.dm3.ensgene >=3.2.0,<3.3.0' - r-base - r-dendextend @@ -67,5 +75,5 @@ test: about: home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: GPL-3 - summary: 'This package allows users to perform DE analysis using multiple algorithms. It seeks consensus from multiple methods. Currently it supports "Voom", "EdgeR" and "DESeq", but can be easily extended. It uses RUV-seq (optional) to remove batch effects.' + summary: 'This package allows users to perform DE analysis using multiple algorithms. It seeks consensus from multiple methods. Currently it supports "Voom", "EdgeR" and "DESeq". It uses RUV-seq (optional) to remove batch effects.' diff --git a/recipes/bioconductor-consensusov/meta.yaml b/recipes/bioconductor-consensusov/meta.yaml index d20a9e4442095..5a0231baff16b 100644 --- a/recipes/bioconductor-consensusov/meta.yaml +++ b/recipes/bioconductor-consensusov/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.4.1" %} +{% set version = "1.6.0" %} {% set name = "consensusOV" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: bae7c5cf0c2d5174dcde8cba046e1222 + md5: edacb8fa98a32c5388bfed32307b3496 build: number: 0 rpaths: @@ -20,19 +20,19 @@ build: # Suggests: knitr, ggplot2 requirements: host: - - 'bioconductor-biobase >=2.42.0,<2.43.0' - - 'bioconductor-genefu >=2.14.0,<2.15.0' - - 'bioconductor-gsva >=1.30.0,<1.31.0' - - 'bioconductor-limma >=3.38.0,<3.39.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' + - 'bioconductor-genefu >=2.16.0,<2.17.0' + - 'bioconductor-gsva >=1.32.0,<1.33.0' + - 'bioconductor-limma >=3.40.0,<3.41.0' - r-base - r-gdata - r-matrixstats - r-randomforest run: - - 'bioconductor-biobase >=2.42.0,<2.43.0' - - 'bioconductor-genefu >=2.14.0,<2.15.0' - - 'bioconductor-gsva >=1.30.0,<1.31.0' - - 'bioconductor-limma >=3.38.0,<3.39.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' + - 'bioconductor-genefu >=2.16.0,<2.17.0' + - 'bioconductor-gsva >=1.32.0,<1.33.0' + - 'bioconductor-limma >=3.40.0,<3.41.0' - r-base - r-gdata - r-matrixstats diff --git a/recipes/bioconductor-consensusseeker/meta.yaml b/recipes/bioconductor-consensusseeker/meta.yaml index bd96947d86300..0cafa21deefbb 100644 --- a/recipes/bioconductor-consensusseeker/meta.yaml +++ b/recipes/bioconductor-consensusseeker/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.10.0" %} +{% set version = "1.12.0" %} {% set name = "consensusSeekeR" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 32baf724416cf72420acc402a030cc1a + md5: ddf046f4b7cc24ef7da7f0172594de24 build: number: 0 rpaths: @@ -20,23 +20,23 @@ build: # Suggests: BiocStyle, ggplot2, knitr, rmarkdown, RUnit requirements: host: - - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' - - 'bioconductor-biocparallel >=1.16.0,<1.17.0' - - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' - - 'bioconductor-genomicranges >=1.34.0,<1.35.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-rtracklayer >=1.42.0,<1.43.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-biocgenerics >=0.30.0,<0.31.0' + - 'bioconductor-biocparallel >=1.18.0,<1.19.0' + - 'bioconductor-genomeinfodb >=1.20.0,<1.21.0' + - 'bioconductor-genomicranges >=1.36.0,<1.37.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-rtracklayer >=1.44.0,<1.45.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' - r-base - r-stringr run: - - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' - - 'bioconductor-biocparallel >=1.16.0,<1.17.0' - - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' - - 'bioconductor-genomicranges >=1.34.0,<1.35.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-rtracklayer >=1.42.0,<1.43.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-biocgenerics >=0.30.0,<0.31.0' + - 'bioconductor-biocparallel >=1.18.0,<1.19.0' + - 'bioconductor-genomeinfodb >=1.20.0,<1.21.0' + - 'bioconductor-genomicranges >=1.36.0,<1.37.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-rtracklayer >=1.44.0,<1.45.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' - r-base - r-stringr test: diff --git a/recipes/bioconductor-contibait/meta.yaml b/recipes/bioconductor-contibait/meta.yaml index 2e6367748d3e6..a1045033f6cd0 100644 --- a/recipes/bioconductor-contibait/meta.yaml +++ b/recipes/bioconductor-contibait/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.10.0" %} +{% set version = "1.12.0" %} {% set name = "contiBAIT" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 8854ac11a9aaab81bf63b0f3ffee1168 + md5: d6a506be45a84ec08ecd8a6434d47fc8 build: number: 0 rpaths: @@ -19,16 +19,16 @@ build: # Suggests: BiocStyle requirements: host: - - 'bioconductor-biocparallel >=1.16.0,<1.17.0' - - 'bioconductor-dnacopy >=1.56.0,<1.57.0' - - 'bioconductor-exomecopy >=1.28.0,<1.29.0' - - 'bioconductor-genomicalignments >=1.18.0,<1.19.0' - - 'bioconductor-genomicfiles >=1.18.0,<1.19.0' - - 'bioconductor-genomicranges >=1.34.0,<1.35.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-rsamtools >=1.34.0,<1.35.0' - - 'bioconductor-rtracklayer >=1.42.0,<1.43.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-biocparallel >=1.18.0,<1.19.0' + - 'bioconductor-dnacopy >=1.58.0,<1.59.0' + - 'bioconductor-exomecopy >=1.30.0,<1.31.0' + - 'bioconductor-genomicalignments >=1.20.0,<1.21.0' + - 'bioconductor-genomicfiles >=1.20.0,<1.21.0' + - 'bioconductor-genomicranges >=1.36.0,<1.37.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-rsamtools >=2.0.0,<2.1.0' + - 'bioconductor-rtracklayer >=1.44.0,<1.45.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' - r-base - 'r-bh >=1.51.0-3' - r-clue @@ -43,16 +43,16 @@ requirements: - r-reshape2 - r-tsp run: - - 'bioconductor-biocparallel >=1.16.0,<1.17.0' - - 'bioconductor-dnacopy >=1.56.0,<1.57.0' - - 'bioconductor-exomecopy >=1.28.0,<1.29.0' - - 'bioconductor-genomicalignments >=1.18.0,<1.19.0' - - 'bioconductor-genomicfiles >=1.18.0,<1.19.0' - - 'bioconductor-genomicranges >=1.34.0,<1.35.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-rsamtools >=1.34.0,<1.35.0' - - 'bioconductor-rtracklayer >=1.42.0,<1.43.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-biocparallel >=1.18.0,<1.19.0' + - 'bioconductor-dnacopy >=1.58.0,<1.59.0' + - 'bioconductor-exomecopy >=1.30.0,<1.31.0' + - 'bioconductor-genomicalignments >=1.20.0,<1.21.0' + - 'bioconductor-genomicfiles >=1.20.0,<1.21.0' + - 'bioconductor-genomicranges >=1.36.0,<1.37.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-rsamtools >=2.0.0,<2.1.0' + - 'bioconductor-rtracklayer >=1.44.0,<1.45.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' - r-base - 'r-bh >=1.51.0-3' - r-clue diff --git a/recipes/bioconductor-conumee/meta.yaml b/recipes/bioconductor-conumee/meta.yaml index 9ac8038f845f8..c726638cc6bda 100644 --- a/recipes/bioconductor-conumee/meta.yaml +++ b/recipes/bioconductor-conumee/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.16.0" %} +{% set version = "1.18.0" %} {% set name = "conumee" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: cbf7b1712e25b8433f543f3d9d6459a1 + md5: 19965541916026a8a1ddd80627772222 build: number: 0 rpaths: @@ -20,28 +20,28 @@ build: # Suggests: BiocStyle, knitr, rmarkdown, minfiData, RCurl requirements: host: - - 'bioconductor-dnacopy >=1.56.0,<1.57.0' - - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' - - 'bioconductor-genomicranges >=1.34.0,<1.35.0' + - 'bioconductor-dnacopy >=1.58.0,<1.59.0' + - 'bioconductor-genomeinfodb >=1.20.0,<1.21.0' + - 'bioconductor-genomicranges >=1.36.0,<1.37.0' - 'bioconductor-illuminahumanmethylation450kanno.ilmn12.hg19 >=0.6.0,<0.7.0' - 'bioconductor-illuminahumanmethylation450kmanifest >=0.4.0,<0.5.0' - 'bioconductor-illuminahumanmethylationepicanno.ilm10b2.hg19 >=0.6.0,<0.7.0' - - 'bioconductor-illuminahumanmethylationepicmanifest >=0.3.0,<0.4.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-minfi >=1.28.0,<1.29.0' - - 'bioconductor-rtracklayer >=1.42.0,<1.43.0' + - 'bioconductor-illuminahumanmethylationepicmanifest >=0.4.0,<0.5.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-minfi >=1.30.0,<1.31.0' + - 'bioconductor-rtracklayer >=1.44.0,<1.45.0' - r-base run: - - 'bioconductor-dnacopy >=1.56.0,<1.57.0' - - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' - - 'bioconductor-genomicranges >=1.34.0,<1.35.0' + - 'bioconductor-dnacopy >=1.58.0,<1.59.0' + - 'bioconductor-genomeinfodb >=1.20.0,<1.21.0' + - 'bioconductor-genomicranges >=1.36.0,<1.37.0' - 'bioconductor-illuminahumanmethylation450kanno.ilmn12.hg19 >=0.6.0,<0.7.0' - 'bioconductor-illuminahumanmethylation450kmanifest >=0.4.0,<0.5.0' - 'bioconductor-illuminahumanmethylationepicanno.ilm10b2.hg19 >=0.6.0,<0.7.0' - - 'bioconductor-illuminahumanmethylationepicmanifest >=0.3.0,<0.4.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-minfi >=1.28.0,<1.29.0' - - 'bioconductor-rtracklayer >=1.42.0,<1.43.0' + - 'bioconductor-illuminahumanmethylationepicmanifest >=0.4.0,<0.5.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-minfi >=1.30.0,<1.31.0' + - 'bioconductor-rtracklayer >=1.44.0,<1.45.0' - r-base test: commands: diff --git a/recipes/bioconductor-convert/meta.yaml b/recipes/bioconductor-convert/meta.yaml index 917c03eab128e..f7c35ac57ec1a 100644 --- a/recipes/bioconductor-convert/meta.yaml +++ b/recipes/bioconductor-convert/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.58.0" %} +{% set version = "1.60.0" %} {% set name = "convert" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 315f0cead1c62a2d4e898a1d7136c625 + md5: f4e2775a7a35742a6ce8265d2156a2d9 build: number: 0 rpaths: @@ -19,14 +19,14 @@ build: noarch: generic requirements: host: - - 'bioconductor-biobase >=2.42.0,<2.43.0' - - 'bioconductor-limma >=3.38.0,<3.39.0' - - 'bioconductor-marray >=1.60.0,<1.61.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' + - 'bioconductor-limma >=3.40.0,<3.41.0' + - 'bioconductor-marray >=1.62.0,<1.63.0' - r-base run: - - 'bioconductor-biobase >=2.42.0,<2.43.0' - - 'bioconductor-limma >=3.38.0,<3.39.0' - - 'bioconductor-marray >=1.60.0,<1.61.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' + - 'bioconductor-limma >=3.40.0,<3.41.0' + - 'bioconductor-marray >=1.62.0,<1.63.0' - r-base test: commands: diff --git a/recipes/bioconductor-copa/meta.yaml b/recipes/bioconductor-copa/meta.yaml index 0cdcb2ce9d2fc..81cd3d936af90 100644 --- a/recipes/bioconductor-copa/meta.yaml +++ b/recipes/bioconductor-copa/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.50.0" %} +{% set version = "1.52.0" %} {% set name = "copa" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 0b6d430c7136ee40abaae1d099d2dfd1 + md5: ebc47c86e5c884013d3b4f0fd4366c42 build: number: 0 rpaths: @@ -19,10 +19,10 @@ build: # Suggests: colonCA requirements: host: - - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' - r-base run: - - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' - r-base build: - {{ compiler('c') }} diff --git a/recipes/bioconductor-copdsexualdimorphism.data/meta.yaml b/recipes/bioconductor-copdsexualdimorphism.data/meta.yaml index 58e238c3b4da5..8505e1c032665 100644 --- a/recipes/bioconductor-copdsexualdimorphism.data/meta.yaml +++ b/recipes/bioconductor-copdsexualdimorphism.data/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.18.0" %} +{% set version = "1.20.0" %} {% set name = "COPDSexualDimorphism.data" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 4089a6b6e4d5537d8b1c4352800ab0a4 + md5: 47555d52e02a3b6d87bbe39a18174531 build: number: 0 rpaths: @@ -22,7 +22,7 @@ requirements: - r-base run: - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-copdsexualdimorphism.data/post-link.sh b/recipes/bioconductor-copdsexualdimorphism.data/post-link.sh index 8546ee245a480..fd8a19f2cef01 100644 --- a/recipes/bioconductor-copdsexualdimorphism.data/post-link.sh +++ b/recipes/bioconductor-copdsexualdimorphism.data/post-link.sh @@ -1,11 +1,11 @@ #!/bin/bash -FN="COPDSexualDimorphism.data_1.18.0.tar.gz" +FN="COPDSexualDimorphism.data_1.20.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/experiment/src/contrib/COPDSexualDimorphism.data_1.18.0.tar.gz" - "https://bioarchive.galaxyproject.org/COPDSexualDimorphism.data_1.18.0.tar.gz" - "https://depot.galaxyproject.org/software/bioconductor-copdsexualdimorphism.data/bioconductor-copdsexualdimorphism.data_1.18.0_src_all.tar.gz" + "https://bioconductor.org/packages/3.9/data/experiment/src/contrib/COPDSexualDimorphism.data_1.20.0.tar.gz" + "https://bioarchive.galaxyproject.org/COPDSexualDimorphism.data_1.20.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-copdsexualdimorphism.data/bioconductor-copdsexualdimorphism.data_1.20.0_src_all.tar.gz" ) -MD5="4089a6b6e4d5537d8b1c4352800ab0a4" +MD5="47555d52e02a3b6d87bbe39a18174531" # Use a staging area in the conda dir rather than temp dirs, both to avoid # permission issues as well as to have things downloaded in a predictable @@ -16,7 +16,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-copyhelper/meta.yaml b/recipes/bioconductor-copyhelper/meta.yaml index f0eecafa07659..09c190580586b 100644 --- a/recipes/bioconductor-copyhelper/meta.yaml +++ b/recipes/bioconductor-copyhelper/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.14.0" %} +{% set version = "1.16.0" %} {% set name = "CopyhelpeR" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: d1141ae0fe9aa075e083042ededcafce + md5: d2c50c7ac853e6f631111da79fe7bc03 build: number: 0 rpaths: @@ -23,7 +23,7 @@ requirements: - r-base run: - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-copyhelper/post-link.sh b/recipes/bioconductor-copyhelper/post-link.sh index c75091947f326..c7693001c26c4 100644 --- a/recipes/bioconductor-copyhelper/post-link.sh +++ b/recipes/bioconductor-copyhelper/post-link.sh @@ -1,11 +1,11 @@ #!/bin/bash -FN="CopyhelpeR_1.14.0.tar.gz" +FN="CopyhelpeR_1.16.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/experiment/src/contrib/CopyhelpeR_1.14.0.tar.gz" - "https://bioarchive.galaxyproject.org/CopyhelpeR_1.14.0.tar.gz" - "https://depot.galaxyproject.org/software/bioconductor-copyhelper/bioconductor-copyhelper_1.14.0_src_all.tar.gz" + "https://bioconductor.org/packages/3.9/data/experiment/src/contrib/CopyhelpeR_1.16.0.tar.gz" + "https://bioarchive.galaxyproject.org/CopyhelpeR_1.16.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-copyhelper/bioconductor-copyhelper_1.16.0_src_all.tar.gz" ) -MD5="d1141ae0fe9aa075e083042ededcafce" +MD5="d2c50c7ac853e6f631111da79fe7bc03" # Use a staging area in the conda dir rather than temp dirs, both to avoid # permission issues as well as to have things downloaded in a predictable @@ -16,7 +16,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-copyneutralima/meta.yaml b/recipes/bioconductor-copyneutralima/meta.yaml index fce9fd0f21316..c6e0a8f2399d7 100644 --- a/recipes/bioconductor-copyneutralima/meta.yaml +++ b/recipes/bioconductor-copyneutralima/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.0.0" %} +{% set version = "1.2.0" %} {% set name = "CopyNeutralIMA" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 88e8d2b42e4512161e2c2a7fa95b6a5b + md5: 99b9b248b03ad09a1b274a986d0a6b54 build: number: 0 rpaths: @@ -20,14 +20,14 @@ build: # Suggests: BiocStyle,knitr,rmarkdown,minfi,conumee,minfiData requirements: host: - - 'bioconductor-experimenthub >=1.8.0,<1.9.0' + - 'bioconductor-experimenthub >=1.10.0,<1.11.0' - r-base - 'r-rdpack >=0.8' run: - - 'bioconductor-experimenthub >=1.8.0,<1.9.0' + - 'bioconductor-experimenthub >=1.10.0,<1.11.0' - r-base - 'r-rdpack >=0.8' - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-copyneutralima/post-link.sh b/recipes/bioconductor-copyneutralima/post-link.sh index ee9106d0fa38a..2a0a463bc6595 100644 --- a/recipes/bioconductor-copyneutralima/post-link.sh +++ b/recipes/bioconductor-copyneutralima/post-link.sh @@ -1,11 +1,11 @@ #!/bin/bash -FN="CopyNeutralIMA_1.0.0.tar.gz" +FN="CopyNeutralIMA_1.2.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/experiment/src/contrib/CopyNeutralIMA_1.0.0.tar.gz" - "https://bioarchive.galaxyproject.org/CopyNeutralIMA_1.0.0.tar.gz" - "https://depot.galaxyproject.org/software/bioconductor-copyneutralima/bioconductor-copyneutralima_1.0.0_src_all.tar.gz" + "https://bioconductor.org/packages/3.9/data/experiment/src/contrib/CopyNeutralIMA_1.2.0.tar.gz" + "https://bioarchive.galaxyproject.org/CopyNeutralIMA_1.2.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-copyneutralima/bioconductor-copyneutralima_1.2.0_src_all.tar.gz" ) -MD5="88e8d2b42e4512161e2c2a7fa95b6a5b" +MD5="99b9b248b03ad09a1b274a986d0a6b54" # Use a staging area in the conda dir rather than temp dirs, both to avoid # permission issues as well as to have things downloaded in a predictable @@ -16,7 +16,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-copynumber/meta.yaml b/recipes/bioconductor-copynumber/meta.yaml index a722ea4dde3be..5ccd4cc16629a 100644 --- a/recipes/bioconductor-copynumber/meta.yaml +++ b/recipes/bioconductor-copynumber/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.22.0" %} +{% set version = "1.24.0" %} {% set name = "copynumber" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: d2ce25bf392279699524af3cf45cf4c2 + md5: 465a840dd46f78b16e9eb8f9b2d31865 build: number: 0 rpaths: @@ -19,16 +19,16 @@ build: noarch: generic requirements: host: - - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' - - 'bioconductor-genomicranges >=1.34.0,<1.35.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-biocgenerics >=0.30.0,<0.31.0' + - 'bioconductor-genomicranges >=1.36.0,<1.37.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' - r-base run: - - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' - - 'bioconductor-genomicranges >=1.34.0,<1.35.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-biocgenerics >=0.30.0,<0.31.0' + - 'bioconductor-genomicranges >=1.36.0,<1.37.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' - r-base test: commands: diff --git a/recipes/bioconductor-copynumberplots/build.sh b/recipes/bioconductor-copynumberplots/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-copynumberplots/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-copynumberplots/meta.yaml b/recipes/bioconductor-copynumberplots/meta.yaml new file mode 100644 index 0000000000000..1d1646287e5df --- /dev/null +++ b/recipes/bioconductor-copynumberplots/meta.yaml @@ -0,0 +1,51 @@ +{% set version = "1.0.0" %} +{% set name = "CopyNumberPlots" %} +{% set bioc = "3.9" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: b71e6933cfcd629d6f4ce65f5f5eabed +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: BiocStyle, knitr, panelcn.mops, BSgenome.Hsapiens.UCSC.hg19.masked, DNAcopy +requirements: + host: + - 'bioconductor-cn.mops >=1.30.0,<1.31.0' + - 'bioconductor-genomeinfodb >=1.20.0,<1.21.0' + - 'bioconductor-genomicranges >=1.36.0,<1.37.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-karyoploter >=1.10.0,<1.11.0' + - 'bioconductor-regioner >=1.16.0,<1.17.0' + - 'bioconductor-rsamtools >=2.0.0,<2.1.0' + - 'bioconductor-summarizedexperiment >=1.14.0,<1.15.0' + - 'bioconductor-variantannotation >=1.30.0,<1.31.0' + - r-base + run: + - 'bioconductor-cn.mops >=1.30.0,<1.31.0' + - 'bioconductor-genomeinfodb >=1.20.0,<1.21.0' + - 'bioconductor-genomicranges >=1.36.0,<1.37.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-karyoploter >=1.10.0,<1.11.0' + - 'bioconductor-regioner >=1.16.0,<1.17.0' + - 'bioconductor-rsamtools >=2.0.0,<2.1.0' + - 'bioconductor-summarizedexperiment >=1.14.0,<1.15.0' + - 'bioconductor-variantannotation >=1.30.0,<1.31.0' + - r-base +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'CopyNumberPlots have a set of functions extending karyoploteRs functionality to create beautiful, customizable and flexible plots of copy-number related data.' + diff --git a/recipes/bioconductor-copywriter/meta.yaml b/recipes/bioconductor-copywriter/meta.yaml index 0150aa881f1e2..c632f2264c834 100644 --- a/recipes/bioconductor-copywriter/meta.yaml +++ b/recipes/bioconductor-copywriter/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "2.14.0" %} +{% set version = "2.16.0" %} {% set name = "CopywriteR" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: a34d836b32a16c62c84c49b14030018b + md5: b3ff89f23a907740463bf7282689f384 build: number: 0 rpaths: @@ -20,32 +20,32 @@ build: # Suggests: BiocStyle, SCLCBam, snow requirements: host: - - 'bioconductor-biocparallel >=1.16.0,<1.17.0' - - 'bioconductor-chipseq >=1.32.0,<1.33.0' - - 'bioconductor-copyhelper >=1.14.0,<1.15.0' - - 'bioconductor-dnacopy >=1.56.0,<1.57.0' - - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' - - 'bioconductor-genomicalignments >=1.18.0,<1.19.0' - - 'bioconductor-genomicranges >=1.34.0,<1.35.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-rsamtools >=1.34.0,<1.35.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-biocparallel >=1.18.0,<1.19.0' + - 'bioconductor-chipseq >=1.34.0,<1.35.0' + - 'bioconductor-copyhelper >=1.16.0,<1.17.0' + - 'bioconductor-dnacopy >=1.58.0,<1.59.0' + - 'bioconductor-genomeinfodb >=1.20.0,<1.21.0' + - 'bioconductor-genomicalignments >=1.20.0,<1.21.0' + - 'bioconductor-genomicranges >=1.36.0,<1.37.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-rsamtools >=2.0.0,<2.1.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' - r-base - r-data.table - r-futile.logger - r-gtools - r-matrixstats run: - - 'bioconductor-biocparallel >=1.16.0,<1.17.0' - - 'bioconductor-chipseq >=1.32.0,<1.33.0' - - 'bioconductor-copyhelper >=1.14.0,<1.15.0' - - 'bioconductor-dnacopy >=1.56.0,<1.57.0' - - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' - - 'bioconductor-genomicalignments >=1.18.0,<1.19.0' - - 'bioconductor-genomicranges >=1.34.0,<1.35.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-rsamtools >=1.34.0,<1.35.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-biocparallel >=1.18.0,<1.19.0' + - 'bioconductor-chipseq >=1.34.0,<1.35.0' + - 'bioconductor-copyhelper >=1.16.0,<1.17.0' + - 'bioconductor-dnacopy >=1.58.0,<1.59.0' + - 'bioconductor-genomeinfodb >=1.20.0,<1.21.0' + - 'bioconductor-genomicalignments >=1.20.0,<1.21.0' + - 'bioconductor-genomicranges >=1.36.0,<1.37.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-rsamtools >=2.0.0,<2.1.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' - r-base - r-data.table - r-futile.logger diff --git a/recipes/bioconductor-cordon/meta.yaml b/recipes/bioconductor-cordon/meta.yaml index 65ef8eb4acc7a..a4a5b53e9cac7 100644 --- a/recipes/bioconductor-cordon/meta.yaml +++ b/recipes/bioconductor-cordon/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.0.1" %} +{% set version = "1.2.0" %} {% set name = "coRdon" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: cce2223c43430259ba3291816ecd36ad + md5: 9fbd4bba3bbbd8fb23a683170a77cf0f build: number: 0 rpaths: @@ -20,21 +20,23 @@ build: # Suggests: BiocStyle, testthat, knitr, rmarkdown requirements: host: - - 'bioconductor-biobase >=2.42.0,<2.43.0' - - 'bioconductor-biostrings >=2.50.0,<2.51.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' + - 'bioconductor-biostrings >=2.52.0,<2.53.0' - r-base - r-data.table - r-dplyr - r-ggplot2 - r-purrr + - r-stringr run: - - 'bioconductor-biobase >=2.42.0,<2.43.0' - - 'bioconductor-biostrings >=2.50.0,<2.51.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' + - 'bioconductor-biostrings >=2.52.0,<2.53.0' - r-base - r-data.table - r-dplyr - r-ggplot2 - r-purrr + - r-stringr test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-coregflux/build.sh b/recipes/bioconductor-coregflux/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-coregflux/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-coregflux/meta.yaml b/recipes/bioconductor-coregflux/meta.yaml new file mode 100644 index 0000000000000..246425a2120f0 --- /dev/null +++ b/recipes/bioconductor-coregflux/meta.yaml @@ -0,0 +1,40 @@ +{% set version = "1.0.0" %} +{% set name = "CoRegFlux" %} +{% set bioc = "3.9" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: 1166cd531721136b6d1825bc83c82cbd +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: glpkAPI, testthat, knitr, rmarkdown, digest, R.cache, ggplot2, plyr, igraph, methods, latex2exp, rBayesianOptimization +# SystemRequirements: GLPK (>= 4.42) +requirements: + host: + - 'bioconductor-coregnet >=1.22.0,<1.23.0' + - glpk + - r-base + - r-sybil + run: + - 'bioconductor-coregnet >=1.22.0,<1.23.0' + - glpk + - r-base + - r-sybil +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: GPL-3 + summary: 'CoRegFlux aims at providing tools to integrate reverse engineered gene regulatory networks and gene-expression into metabolic models to improve prediction of phenotypes, both for metabolic engineering, through transcription factor or gene (TF) knock-out or overexpression in various conditions as well as to improve our understanding of the interactions and cell inner-working.' + diff --git a/recipes/bioconductor-coregnet/meta.yaml b/recipes/bioconductor-coregnet/meta.yaml index f1a80d043534a..5d109ab6d913e 100644 --- a/recipes/bioconductor-coregnet/meta.yaml +++ b/recipes/bioconductor-coregnet/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.20.0" %} +{% set version = "1.22.0" %} {% set name = "CoRegNet" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 9271a02c25c486a3becae3002e02590a + md5: 15562e61d7856a361e519160696701e1 build: number: 0 rpaths: diff --git a/recipes/bioconductor-cormotif/meta.yaml b/recipes/bioconductor-cormotif/meta.yaml index 252eed210b4f1..9741acaea8cee 100644 --- a/recipes/bioconductor-cormotif/meta.yaml +++ b/recipes/bioconductor-cormotif/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.28.0" %} +{% set version = "1.30.0" %} {% set name = "Cormotif" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 23da3810b5bd4632e8cec7e5a23d132f + md5: f2fb657c778e48018575f928a729f606 build: number: 0 rpaths: @@ -19,12 +19,12 @@ build: noarch: generic requirements: host: - - 'bioconductor-affy >=1.60.0,<1.61.0' - - 'bioconductor-limma >=3.38.0,<3.39.0' + - 'bioconductor-affy >=1.62.0,<1.63.0' + - 'bioconductor-limma >=3.40.0,<3.41.0' - r-base run: - - 'bioconductor-affy >=1.60.0,<1.61.0' - - 'bioconductor-limma >=3.38.0,<3.39.0' + - 'bioconductor-affy >=1.62.0,<1.63.0' + - 'bioconductor-limma >=3.40.0,<3.41.0' - r-base test: commands: diff --git a/recipes/bioconductor-cormut/meta.yaml b/recipes/bioconductor-cormut/meta.yaml index 5682eb39dab7f..d2a59cac9326a 100644 --- a/recipes/bioconductor-cormut/meta.yaml +++ b/recipes/bioconductor-cormut/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.24.0" %} +{% set version = "1.26.0" %} {% set name = "CorMut" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 87d0c12fe94d44ee994cf211b377db63 + md5: 7b38f2d9cd75e9410e2cce41b0b45f40 build: number: 0 rpaths: diff --git a/recipes/bioconductor-correp/meta.yaml b/recipes/bioconductor-correp/meta.yaml index 2b536fd208fa5..853a3ef31ac7f 100644 --- a/recipes/bioconductor-correp/meta.yaml +++ b/recipes/bioconductor-correp/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.48.0" %} +{% set version = "1.50.0" %} {% set name = "CORREP" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: bb75ae6c927d9b6ab112864dad047cf5 + md5: 337c57abb391e1b24492671e8e479594 build: number: 0 rpaths: diff --git a/recipes/bioconductor-coseq/meta.yaml b/recipes/bioconductor-coseq/meta.yaml index d1da376060d75..93c15546b7b6b 100644 --- a/recipes/bioconductor-coseq/meta.yaml +++ b/recipes/bioconductor-coseq/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.6.0" %} +{% set version = "1.8.0" %} {% set name = "coseq" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 82a886ded142822f3f84ef320ee3d51b + md5: ca85966ba23706ba1f3ce752d4c43a17 build: number: 0 rpaths: @@ -20,12 +20,12 @@ build: # Suggests: Biobase, knitr, rmarkdown, testthat requirements: host: - - 'bioconductor-biocparallel >=1.16.0,<1.17.0' - - 'bioconductor-deseq2 >=1.22.0,<1.23.0' - - 'bioconductor-edger >=3.24.0,<3.25.0' - - 'bioconductor-htsfilter >=1.22.0,<1.23.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' - - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' + - 'bioconductor-biocparallel >=1.18.0,<1.19.0' + - 'bioconductor-deseq2 >=1.24.0,<1.25.0' + - 'bioconductor-edger >=3.26.0,<3.27.0' + - 'bioconductor-htsfilter >=1.24.0,<1.25.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' + - 'bioconductor-summarizedexperiment >=1.14.0,<1.15.0' - r-base - r-capushe - r-compositions @@ -37,12 +37,12 @@ requirements: - r-rmixmod - r-scales run: - - 'bioconductor-biocparallel >=1.16.0,<1.17.0' - - 'bioconductor-deseq2 >=1.22.0,<1.23.0' - - 'bioconductor-edger >=3.24.0,<3.25.0' - - 'bioconductor-htsfilter >=1.22.0,<1.23.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' - - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' + - 'bioconductor-biocparallel >=1.18.0,<1.19.0' + - 'bioconductor-deseq2 >=1.24.0,<1.25.0' + - 'bioconductor-edger >=3.26.0,<3.27.0' + - 'bioconductor-htsfilter >=1.24.0,<1.25.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' + - 'bioconductor-summarizedexperiment >=1.14.0,<1.15.0' - r-base - r-capushe - r-compositions diff --git a/recipes/bioconductor-cosmic.67/meta.yaml b/recipes/bioconductor-cosmic.67/meta.yaml index bad388b85efda..eb42029cedfa5 100644 --- a/recipes/bioconductor-cosmic.67/meta.yaml +++ b/recipes/bioconductor-cosmic.67/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.18.0" %} +{% set version = "1.20.0" %} {% set name = "COSMIC.67" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: db1bb894b11d6e1f9d2675e68bdf3291 + md5: 4ddee996e33164a4f0d0034c438b7783 build: number: 0 rpaths: @@ -20,16 +20,16 @@ build: # Suggests: testthat, BiocStyle, knitr requirements: host: - - 'bioconductor-genomicranges >=1.34.0,<1.35.0' - - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' - - 'bioconductor-variantannotation >=1.28.0,<1.29.0' + - 'bioconductor-genomicranges >=1.36.0,<1.37.0' + - 'bioconductor-summarizedexperiment >=1.14.0,<1.15.0' + - 'bioconductor-variantannotation >=1.30.0,<1.31.0' - r-base run: - - 'bioconductor-genomicranges >=1.34.0,<1.35.0' - - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' - - 'bioconductor-variantannotation >=1.28.0,<1.29.0' + - 'bioconductor-genomicranges >=1.36.0,<1.37.0' + - 'bioconductor-summarizedexperiment >=1.14.0,<1.15.0' + - 'bioconductor-variantannotation >=1.30.0,<1.31.0' - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-cosmic.67/post-link.sh b/recipes/bioconductor-cosmic.67/post-link.sh index 2505a2a1f7393..cf6e46d32a492 100644 --- a/recipes/bioconductor-cosmic.67/post-link.sh +++ b/recipes/bioconductor-cosmic.67/post-link.sh @@ -1,11 +1,11 @@ #!/bin/bash -FN="COSMIC.67_1.18.0.tar.gz" +FN="COSMIC.67_1.20.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/experiment/src/contrib/COSMIC.67_1.18.0.tar.gz" - "https://bioarchive.galaxyproject.org/COSMIC.67_1.18.0.tar.gz" - "https://depot.galaxyproject.org/software/bioconductor-cosmic.67/bioconductor-cosmic.67_1.18.0_src_all.tar.gz" + "https://bioconductor.org/packages/3.9/data/experiment/src/contrib/COSMIC.67_1.20.0.tar.gz" + "https://bioarchive.galaxyproject.org/COSMIC.67_1.20.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-cosmic.67/bioconductor-cosmic.67_1.20.0_src_all.tar.gz" ) -MD5="db1bb894b11d6e1f9d2675e68bdf3291" +MD5="4ddee996e33164a4f0d0034c438b7783" # Use a staging area in the conda dir rather than temp dirs, both to avoid # permission issues as well as to have things downloaded in a predictable @@ -16,7 +16,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-cosmiq/build.sh b/recipes/bioconductor-cosmiq/build.sh index 5ea71a1203cac..c1d13421f5f1e 100644 --- a/recipes/bioconductor-cosmiq/build.sh +++ b/recipes/bioconductor-cosmiq/build.sh @@ -8,4 +8,4 @@ CXX=$CXX CXX98=$CXX CXX11=$CXX CXX14=$CXX" > ~/.R/Makevars -$R CMD INSTALL --build . +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-cosmiq/meta.yaml b/recipes/bioconductor-cosmiq/meta.yaml index 2985031f69e36..a4bcf544ebb79 100644 --- a/recipes/bioconductor-cosmiq/meta.yaml +++ b/recipes/bioconductor-cosmiq/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.16.1" %} +{% set version = "1.18.0" %} {% set name = "cosmiq" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: b26dc394e45a3ce9eac78550972aae03 + md5: 7280905e37ca78bd4d6557311fe07d18 build: number: 0 rpaths: @@ -19,16 +19,16 @@ build: # Suggests: RUnit, BiocGenerics, BiocStyle requirements: host: - - 'bioconductor-faahko >=1.22.0,<1.23.0' - - 'bioconductor-massspecwavelet >=1.48.0,<1.49.0' - - 'bioconductor-xcms >=3.4.0,<3.5.0' + - 'bioconductor-faahko >=1.24.0,<1.25.0' + - 'bioconductor-massspecwavelet >=1.50.0,<1.51.0' + - 'bioconductor-xcms >=3.6.0,<3.7.0' - r-base - r-pracma - r-rcpp run: - - 'bioconductor-faahko >=1.22.0,<1.23.0' - - 'bioconductor-massspecwavelet >=1.48.0,<1.49.0' - - 'bioconductor-xcms >=3.4.0,<3.5.0' + - 'bioconductor-faahko >=1.24.0,<1.25.0' + - 'bioconductor-massspecwavelet >=1.50.0,<1.51.0' + - 'bioconductor-xcms >=3.6.0,<3.7.0' - r-base - r-pracma - r-rcpp diff --git a/recipes/bioconductor-cosnet/meta.yaml b/recipes/bioconductor-cosnet/meta.yaml index 42fdf99cee87c..1f5eb987b7db7 100644 --- a/recipes/bioconductor-cosnet/meta.yaml +++ b/recipes/bioconductor-cosnet/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.16.0" %} +{% set version = "1.18.0" %} {% set name = "COSNet" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: ca0dbf84990b9770b2179ff397e5c407 + md5: 5db1fd2a292bb507438470c11477910c build: number: 0 rpaths: diff --git a/recipes/bioconductor-cottoncdf/meta.yaml b/recipes/bioconductor-cottoncdf/meta.yaml index 1d231e4e94f00..8b6bc4600348f 100644 --- a/recipes/bioconductor-cottoncdf/meta.yaml +++ b/recipes/bioconductor-cottoncdf/meta.yaml @@ -1,6 +1,6 @@ {% set version = "2.18.0" %} {% set name = "cottoncdf" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -12,19 +12,19 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: b9d2a4b43235c6e531b78cca006e84b2 build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' - r-base run: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-cottoncdf/post-link.sh b/recipes/bioconductor-cottoncdf/post-link.sh index ba38c815ebcf4..e9e558149d98b 100644 --- a/recipes/bioconductor-cottoncdf/post-link.sh +++ b/recipes/bioconductor-cottoncdf/post-link.sh @@ -1,9 +1,10 @@ #!/bin/bash FN="cottoncdf_2.18.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/cottoncdf_2.18.0.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/cottoncdf_2.18.0.tar.gz" "https://bioarchive.galaxyproject.org/cottoncdf_2.18.0.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-cottoncdf/bioconductor-cottoncdf_2.18.0_src_all.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-cottoncdf/bioconductor-cottoncdf_2.18.0_src_all.tar.gz" ) MD5="b9d2a4b43235c6e531b78cca006e84b2" @@ -16,7 +17,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-cottonprobe/meta.yaml b/recipes/bioconductor-cottonprobe/meta.yaml index fea33b15b3432..adc0c03a7648f 100644 --- a/recipes/bioconductor-cottonprobe/meta.yaml +++ b/recipes/bioconductor-cottonprobe/meta.yaml @@ -1,6 +1,6 @@ {% set version = "2.18.0" %} {% set name = "cottonprobe" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -12,19 +12,19 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 032fa94876685820d94526fd56dd0b65 build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' - r-base run: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-cottonprobe/post-link.sh b/recipes/bioconductor-cottonprobe/post-link.sh index 2e1b6131d4b85..01e1e3a01bfc6 100644 --- a/recipes/bioconductor-cottonprobe/post-link.sh +++ b/recipes/bioconductor-cottonprobe/post-link.sh @@ -1,9 +1,10 @@ #!/bin/bash FN="cottonprobe_2.18.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/cottonprobe_2.18.0.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/cottonprobe_2.18.0.tar.gz" "https://bioarchive.galaxyproject.org/cottonprobe_2.18.0.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-cottonprobe/bioconductor-cottonprobe_2.18.0_src_all.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-cottonprobe/bioconductor-cottonprobe_2.18.0_src_all.tar.gz" ) MD5="032fa94876685820d94526fd56dd0b65" @@ -16,7 +17,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-countclust/meta.yaml b/recipes/bioconductor-countclust/meta.yaml index c496ae8032bc2..8b4e2469996d4 100644 --- a/recipes/bioconductor-countclust/meta.yaml +++ b/recipes/bioconductor-countclust/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.10.1" %} +{% set version = "1.12.0" %} {% set name = "CountClust" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,18 +10,17 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: 06f7e8468d61658aaf82f7860fbd3487885b57798c8d798ba86f6c7e524e22ac + md5: b9aa36dedfc2a7fb087e027e2e40d7bf build: number: 0 rpaths: - lib/R/lib/ - lib/ + noarch: generic # Suggests: knitr, kableExtra, BiocStyle, Biobase, roxygen2, RColorBrewer, devtools, xtable requirements: - build: - - {{ compiler('fortran') }} host: - - 'bioconductor-limma >=3.38.0,<3.39.0' + - 'bioconductor-limma >=3.40.0,<3.41.0' - r-base - r-cowplot - r-flexmix @@ -34,7 +33,7 @@ requirements: - r-slam - r-squarem run: - - 'bioconductor-limma >=3.38.0,<3.39.0' + - 'bioconductor-limma >=3.40.0,<3.41.0' - r-base - r-cowplot - r-flexmix diff --git a/recipes/bioconductor-countsimqc/meta.yaml b/recipes/bioconductor-countsimqc/meta.yaml index 7deacb599286a..d645dc639a4b7 100644 --- a/recipes/bioconductor-countsimqc/meta.yaml +++ b/recipes/bioconductor-countsimqc/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.0.0" %} +{% set version = "1.2.0" %} {% set name = "countsimQC" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 57a8e42b86fec1cd161aa644697d7d37 + md5: 0cff7db1e83c85c84ad72f5e24fac4ef build: number: 0 rpaths: @@ -20,11 +20,11 @@ build: # Suggests: knitr, testthat requirements: host: - - 'bioconductor-deseq2 >=1.22.0,<1.23.0' - - 'bioconductor-edger >=3.24.0,<3.25.0' - - 'bioconductor-genefilter >=1.64.0,<1.65.0' + - 'bioconductor-deseq2 >=1.24.0,<1.25.0' + - 'bioconductor-edger >=3.26.0,<3.27.0' + - 'bioconductor-genefilter >=1.66.0,<1.67.0' - 'bioconductor-genomeinfodbdata >=1.2.0,<1.3.0' - - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' + - 'bioconductor-summarizedexperiment >=1.14.0,<1.15.0' - r-base - r-catools - r-dplyr @@ -34,11 +34,11 @@ requirements: - 'r-rmarkdown >=0.9.5' - r-tidyr run: - - 'bioconductor-deseq2 >=1.22.0,<1.23.0' - - 'bioconductor-edger >=3.24.0,<3.25.0' - - 'bioconductor-genefilter >=1.64.0,<1.65.0' + - 'bioconductor-deseq2 >=1.24.0,<1.25.0' + - 'bioconductor-edger >=3.26.0,<3.27.0' + - 'bioconductor-genefilter >=1.66.0,<1.67.0' - 'bioconductor-genomeinfodbdata >=1.2.0,<1.3.0' - - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' + - 'bioconductor-summarizedexperiment >=1.14.0,<1.15.0' - r-base - r-catools - r-dplyr diff --git a/recipes/bioconductor-coveb/meta.yaml b/recipes/bioconductor-coveb/meta.yaml index 6125ccacea843..ddfef7c1118c2 100644 --- a/recipes/bioconductor-coveb/meta.yaml +++ b/recipes/bioconductor-coveb/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.8.1" %} +{% set version = "1.10.0" %} {% set name = "covEB" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: aab7041e42cc915452b0d7c1b9b03557954f172820b8de9323b2275c2b4df1a4 + md5: d936d0ebb4fe7540db44a8d77c60f770 build: number: 0 rpaths: @@ -20,7 +20,7 @@ build: # Suggests: curatedBladderData requirements: host: - - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' - r-base - r-gsl - r-igraph @@ -28,7 +28,7 @@ requirements: - r-matrix - r-mvtnorm run: - - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' - r-base - r-gsl - r-igraph diff --git a/recipes/bioconductor-coverageview/meta.yaml b/recipes/bioconductor-coverageview/meta.yaml index f614db3768ce7..c09d3c623149d 100644 --- a/recipes/bioconductor-coverageview/meta.yaml +++ b/recipes/bioconductor-coverageview/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.20.0" %} +{% set version = "1.22.0" %} {% set name = "CoverageView" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 7022b9de2a05fe8e1f1da1ca1d7482b3 + md5: 3713144fc6a492d347e4d0088705dd06 build: number: 0 rpaths: @@ -19,20 +19,20 @@ build: noarch: generic requirements: host: - - 'bioconductor-genomicalignments >=1.18.0,<1.19.0' - - 'bioconductor-genomicranges >=1.34.0,<1.35.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-rsamtools >=1.34.0,<1.35.0' - - 'bioconductor-rtracklayer >=1.42.0,<1.43.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-genomicalignments >=1.20.0,<1.21.0' + - 'bioconductor-genomicranges >=1.36.0,<1.37.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-rsamtools >=2.0.0,<2.1.0' + - 'bioconductor-rtracklayer >=1.44.0,<1.45.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' - r-base run: - - 'bioconductor-genomicalignments >=1.18.0,<1.19.0' - - 'bioconductor-genomicranges >=1.34.0,<1.35.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-rsamtools >=1.34.0,<1.35.0' - - 'bioconductor-rtracklayer >=1.42.0,<1.43.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-genomicalignments >=1.20.0,<1.21.0' + - 'bioconductor-genomicranges >=1.36.0,<1.37.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-rsamtools >=2.0.0,<2.1.0' + - 'bioconductor-rtracklayer >=1.44.0,<1.45.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' - r-base test: commands: diff --git a/recipes/bioconductor-covrna/meta.yaml b/recipes/bioconductor-covrna/meta.yaml index 11e68574e3cae..61350bf35df46 100644 --- a/recipes/bioconductor-covrna/meta.yaml +++ b/recipes/bioconductor-covrna/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.8.0" %} +{% set version = "1.10.0" %} {% set name = "covRNA" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 808e8c797079d7a87f802b5d45935d73 + md5: 45420d33aa33dc000e6d93bd9631c602 build: number: 0 rpaths: @@ -20,13 +20,13 @@ build: # Suggests: BiocStyle, knitr, rmarkdown requirements: host: - - 'bioconductor-biobase >=2.42.0,<2.43.0' - - 'bioconductor-genefilter >=1.64.0,<1.65.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' + - 'bioconductor-genefilter >=1.66.0,<1.67.0' - r-ade4 - r-base run: - - 'bioconductor-biobase >=2.42.0,<2.43.0' - - 'bioconductor-genefilter >=1.64.0,<1.65.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' + - 'bioconductor-genefilter >=1.66.0,<1.67.0' - r-ade4 - r-base test: diff --git a/recipes/bioconductor-cpvsnp/meta.yaml b/recipes/bioconductor-cpvsnp/meta.yaml index b60fb45e398be..d3512e252126d 100644 --- a/recipes/bioconductor-cpvsnp/meta.yaml +++ b/recipes/bioconductor-cpvsnp/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.14.0" %} +{% set version = "1.16.0" %} {% set name = "cpvSNP" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 398ce7f3fde5ae72b9a0c171902351b0 + md5: fe5f5b8dd0f39d5fec228b88b0a702a4 build: number: 0 rpaths: @@ -20,17 +20,17 @@ build: # Suggests: TxDb.Hsapiens.UCSC.hg19.knownGene, RUnit, BiocGenerics, ReportingTools, BiocStyle requirements: host: - - 'bioconductor-biocparallel >=1.16.0,<1.17.0' - - 'bioconductor-genomicfeatures >=1.34.0,<1.35.0' - - 'bioconductor-gseabase >=1.44.0,<1.45.0' + - 'bioconductor-biocparallel >=1.18.0,<1.19.0' + - 'bioconductor-genomicfeatures >=1.36.0,<1.37.0' + - 'bioconductor-gseabase >=1.46.0,<1.47.0' - r-base - r-corpcor - r-ggplot2 - r-plyr run: - - 'bioconductor-biocparallel >=1.16.0,<1.17.0' - - 'bioconductor-genomicfeatures >=1.34.0,<1.35.0' - - 'bioconductor-gseabase >=1.44.0,<1.45.0' + - 'bioconductor-biocparallel >=1.18.0,<1.19.0' + - 'bioconductor-genomicfeatures >=1.36.0,<1.37.0' + - 'bioconductor-gseabase >=1.46.0,<1.47.0' - r-base - r-corpcor - r-ggplot2 diff --git a/recipes/bioconductor-cqn/meta.yaml b/recipes/bioconductor-cqn/meta.yaml index 751dfb2e8e15b..08ac8fefe6518 100644 --- a/recipes/bioconductor-cqn/meta.yaml +++ b/recipes/bioconductor-cqn/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.28.1" %} +{% set version = "1.30.0" %} {% set name = "cqn" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - sha256: 3824c9f340df64134801c0ecbca011bbc8005f0a0a11b33ffa54cd72fd414818 + md5: 3cdf1037d31884fe295ff7ab0bdc68da build: number: 0 rpaths: @@ -20,13 +20,13 @@ build: # Suggests: scales, edgeR requirements: host: - - 'bioconductor-preprocesscore >=1.44.0,<1.45.0' + - 'bioconductor-preprocesscore >=1.46.0,<1.47.0' - r-base - r-mclust - r-nor1mix - r-quantreg run: - - 'bioconductor-preprocesscore >=1.44.0,<1.45.0' + - 'bioconductor-preprocesscore >=1.46.0,<1.47.0' - r-base - r-mclust - r-nor1mix diff --git a/recipes/bioconductor-crcl18/meta.yaml b/recipes/bioconductor-crcl18/meta.yaml index 4fc8602f99e8d..5bbccb442f584 100644 --- a/recipes/bioconductor-crcl18/meta.yaml +++ b/recipes/bioconductor-crcl18/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.2.0" %} +{% set version = "1.4.0" %} {% set name = "CRCL18" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,21 +10,21 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 552108f3a1772e108e845fea9ac04fa8 + md5: acaf9fea6a3b3fc312d3fe77a0157e93 build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ noarch: generic requirements: host: - - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' - r-base run: - - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-crcl18/post-link.sh b/recipes/bioconductor-crcl18/post-link.sh index 329a00cc047ea..5b6927e204fc9 100644 --- a/recipes/bioconductor-crcl18/post-link.sh +++ b/recipes/bioconductor-crcl18/post-link.sh @@ -1,11 +1,11 @@ #!/bin/bash -FN="CRCL18_1.2.0.tar.gz" +FN="CRCL18_1.4.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/experiment/src/contrib/CRCL18_1.2.0.tar.gz" - "https://bioarchive.galaxyproject.org/CRCL18_1.2.0.tar.gz" - "https://depot.galaxyproject.org/software/bioconductor-crcl18/bioconductor-crcl18_1.2.0_src_all.tar.gz" + "https://bioconductor.org/packages/3.9/data/experiment/src/contrib/CRCL18_1.4.0.tar.gz" + "https://bioarchive.galaxyproject.org/CRCL18_1.4.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-crcl18/bioconductor-crcl18_1.4.0_src_all.tar.gz" ) -MD5="552108f3a1772e108e845fea9ac04fa8" +MD5="acaf9fea6a3b3fc312d3fe77a0157e93" # Use a staging area in the conda dir rather than temp dirs, both to avoid # permission issues as well as to have things downloaded in a predictable @@ -16,7 +16,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-crimage/meta.yaml b/recipes/bioconductor-crimage/meta.yaml index 4c17c413de0f5..58eb38d22d211 100644 --- a/recipes/bioconductor-crimage/meta.yaml +++ b/recipes/bioconductor-crimage/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.30.0" %} +{% set version = "1.32.0" %} {% set name = "CRImage" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: fcab4dae1b32b2a00aedf7c509307ac9 + md5: 7ace556d1951e5c55d93d081953153a2 build: number: 0 rpaths: @@ -19,18 +19,18 @@ build: noarch: generic requirements: host: - - 'bioconductor-acgh >=1.60.0,<1.61.0' - - 'bioconductor-dnacopy >=1.56.0,<1.57.0' - - 'bioconductor-ebimage >=4.24.0,<4.25.0' + - 'bioconductor-acgh >=1.62.0,<1.63.0' + - 'bioconductor-dnacopy >=1.58.0,<1.59.0' + - 'bioconductor-ebimage >=4.26.0,<4.27.0' - r-base - r-e1071 - r-foreach - r-mass - r-sgeostat run: - - 'bioconductor-acgh >=1.60.0,<1.61.0' - - 'bioconductor-dnacopy >=1.56.0,<1.57.0' - - 'bioconductor-ebimage >=4.24.0,<4.25.0' + - 'bioconductor-acgh >=1.62.0,<1.63.0' + - 'bioconductor-dnacopy >=1.58.0,<1.59.0' + - 'bioconductor-ebimage >=4.26.0,<4.27.0' - r-base - r-e1071 - r-foreach diff --git a/recipes/bioconductor-crisprseek/meta.yaml b/recipes/bioconductor-crisprseek/meta.yaml index 83345e89aef74..f1c759b1d751e 100644 --- a/recipes/bioconductor-crisprseek/meta.yaml +++ b/recipes/bioconductor-crisprseek/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.22.0" %} +{% set version = "1.24.0" %} {% set name = "CRISPRseek" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 73f09ccf2c434036da758ab88e0f280c + md5: 9dbb4cffe40d991680210919a4db879d build: number: 0 rpaths: @@ -20,23 +20,23 @@ build: # Suggests: RUnit, BiocStyle, BSgenome.Hsapiens.UCSC.hg19, TxDb.Hsapiens.UCSC.hg19.knownGene, org.Hs.eg.db requirements: host: - - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' - - 'bioconductor-biocparallel >=1.16.0,<1.17.0' - - 'bioconductor-biostrings >=2.50.0,<2.51.0' - - 'bioconductor-bsgenome >=1.50.0,<1.51.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-biocgenerics >=0.30.0,<0.31.0' + - 'bioconductor-biocparallel >=1.18.0,<1.19.0' + - 'bioconductor-biostrings >=2.52.0,<2.53.0' + - 'bioconductor-bsgenome >=1.52.0,<1.53.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' - r-base - r-data.table - r-hash - r-seqinr run: - - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' - - 'bioconductor-biocparallel >=1.16.0,<1.17.0' - - 'bioconductor-biostrings >=2.50.0,<2.51.0' - - 'bioconductor-bsgenome >=1.50.0,<1.51.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-biocgenerics >=0.30.0,<0.31.0' + - 'bioconductor-biocparallel >=1.18.0,<1.19.0' + - 'bioconductor-biostrings >=2.52.0,<2.53.0' + - 'bioconductor-bsgenome >=1.52.0,<1.53.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' - r-base - r-data.table - r-hash diff --git a/recipes/bioconductor-crisprseekplus/meta.yaml b/recipes/bioconductor-crisprseekplus/meta.yaml index a7a6b265b2a9f..7b7b78d471674 100644 --- a/recipes/bioconductor-crisprseekplus/meta.yaml +++ b/recipes/bioconductor-crisprseekplus/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.8.0" %} +{% set version = "1.10.0" %} {% set name = "crisprseekplus" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 555d70d98d046f584dc4ec325ba9c6cd + md5: 14baca0d404914db60ec75a333550e12 build: number: 0 rpaths: @@ -20,12 +20,12 @@ build: # Suggests: testthat, rmarkdown, knitr, R.rsp requirements: host: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' - - 'bioconductor-bsgenome >=1.50.0,<1.51.0' - - 'bioconductor-crisprseek >=1.22.0,<1.23.0' - - 'bioconductor-genomicfeatures >=1.34.0,<1.35.0' - - 'bioconductor-genomicranges >=1.34.0,<1.35.0' - - 'bioconductor-guideseq >=1.12.0,<1.13.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' + - 'bioconductor-bsgenome >=1.52.0,<1.53.0' + - 'bioconductor-crisprseek >=1.24.0,<1.25.0' + - 'bioconductor-genomicfeatures >=1.36.0,<1.37.0' + - 'bioconductor-genomicranges >=1.36.0,<1.37.0' + - 'bioconductor-guideseq >=1.14.0,<1.15.0' - r-base - r-biocmanager - r-dt @@ -33,12 +33,12 @@ requirements: - r-shiny - r-shinyjs run: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' - - 'bioconductor-bsgenome >=1.50.0,<1.51.0' - - 'bioconductor-crisprseek >=1.22.0,<1.23.0' - - 'bioconductor-genomicfeatures >=1.34.0,<1.35.0' - - 'bioconductor-genomicranges >=1.34.0,<1.35.0' - - 'bioconductor-guideseq >=1.12.0,<1.13.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' + - 'bioconductor-bsgenome >=1.52.0,<1.53.0' + - 'bioconductor-crisprseek >=1.24.0,<1.25.0' + - 'bioconductor-genomicfeatures >=1.36.0,<1.37.0' + - 'bioconductor-genomicranges >=1.36.0,<1.37.0' + - 'bioconductor-guideseq >=1.14.0,<1.15.0' - r-base - r-biocmanager - r-dt diff --git a/recipes/bioconductor-crisprvariants/meta.yaml b/recipes/bioconductor-crisprvariants/meta.yaml index 3916b59316ce8..949ea8cdc8168 100644 --- a/recipes/bioconductor-crisprvariants/meta.yaml +++ b/recipes/bioconductor-crisprvariants/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.10.0" %} +{% set version = "1.12.0" %} {% set name = "CrispRVariants" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 23ba6adc80afcdf68fb73bd81f648097 + md5: ef9f95207557f57a1c1818c45a21eb7b build: number: 0 rpaths: @@ -20,29 +20,29 @@ build: # Suggests: BiocStyle, gdata, GenomicFeatures, knitr, rmarkdown, rtracklayer, sangerseqR, testthat, VariantAnnotation requirements: host: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' - - 'bioconductor-biocparallel >=1.16.0,<1.17.0' - - 'bioconductor-biostrings >=2.50.0,<2.51.0' - - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' - - 'bioconductor-genomicalignments >=1.18.0,<1.19.0' - - 'bioconductor-genomicranges >=1.34.0,<1.35.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-rsamtools >=1.34.0,<1.35.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' + - 'bioconductor-biocparallel >=1.18.0,<1.19.0' + - 'bioconductor-biostrings >=2.52.0,<2.53.0' + - 'bioconductor-genomeinfodb >=1.20.0,<1.21.0' + - 'bioconductor-genomicalignments >=1.20.0,<1.21.0' + - 'bioconductor-genomicranges >=1.36.0,<1.37.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-rsamtools >=2.0.0,<2.1.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' - r-base - 'r-ggplot2 >=2.2.0' - r-gridextra - r-reshape2 run: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' - - 'bioconductor-biocparallel >=1.16.0,<1.17.0' - - 'bioconductor-biostrings >=2.50.0,<2.51.0' - - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' - - 'bioconductor-genomicalignments >=1.18.0,<1.19.0' - - 'bioconductor-genomicranges >=1.34.0,<1.35.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-rsamtools >=1.34.0,<1.35.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' + - 'bioconductor-biocparallel >=1.18.0,<1.19.0' + - 'bioconductor-biostrings >=2.52.0,<2.53.0' + - 'bioconductor-genomeinfodb >=1.20.0,<1.21.0' + - 'bioconductor-genomicalignments >=1.20.0,<1.21.0' + - 'bioconductor-genomicranges >=1.36.0,<1.37.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-rsamtools >=2.0.0,<2.1.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' - r-base - 'r-ggplot2 >=2.2.0' - r-gridextra diff --git a/recipes/bioconductor-crlmm/meta.yaml b/recipes/bioconductor-crlmm/meta.yaml index 0a8b185874e25..16cc0af663de5 100644 --- a/recipes/bioconductor-crlmm/meta.yaml +++ b/recipes/bioconductor-crlmm/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.40.0" %} +{% set version = "1.42.0" %} {% set name = "crlmm" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 0297a5176d679d97b5465292552b151b + md5: 73c3522b65b499db015b7027fd1d349f build: number: 0 rpaths: @@ -19,14 +19,14 @@ build: # Suggests: hapmapsnp6, genomewidesnp6Crlmm (>= 1.0.7), GGdata, snpStats, RUnit requirements: host: - - 'bioconductor-affyio >=1.52.0,<1.53.0' - - 'bioconductor-biobase >=2.42.0,<2.43.0' - - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' - - 'bioconductor-illuminaio >=0.24.0,<0.25.0' - - 'bioconductor-limma >=3.38.0,<3.39.0' - - 'bioconductor-oligoclasses >=1.44.0,<1.45.0' - - 'bioconductor-preprocesscore >=1.44.0,<1.45.0' - - 'bioconductor-snpchip >=2.28.0,<2.29.0' + - 'bioconductor-affyio >=1.54.0,<1.55.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' + - 'bioconductor-biocgenerics >=0.30.0,<0.31.0' + - 'bioconductor-illuminaio >=0.26.0,<0.27.0' + - 'bioconductor-limma >=3.40.0,<3.41.0' + - 'bioconductor-oligoclasses >=1.46.0,<1.47.0' + - 'bioconductor-preprocesscore >=1.46.0,<1.47.0' + - 'bioconductor-snpchip >=2.30.0,<2.31.0' - r-base - r-beanplot - r-ellipse @@ -38,14 +38,14 @@ requirements: - 'r-rcppeigen >=0.3.1.2.1' - r-vgam run: - - 'bioconductor-affyio >=1.52.0,<1.53.0' - - 'bioconductor-biobase >=2.42.0,<2.43.0' - - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' - - 'bioconductor-illuminaio >=0.24.0,<0.25.0' - - 'bioconductor-limma >=3.38.0,<3.39.0' - - 'bioconductor-oligoclasses >=1.44.0,<1.45.0' - - 'bioconductor-preprocesscore >=1.44.0,<1.45.0' - - 'bioconductor-snpchip >=2.28.0,<2.29.0' + - 'bioconductor-affyio >=1.54.0,<1.55.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' + - 'bioconductor-biocgenerics >=0.30.0,<0.31.0' + - 'bioconductor-illuminaio >=0.26.0,<0.27.0' + - 'bioconductor-limma >=3.40.0,<3.41.0' + - 'bioconductor-oligoclasses >=1.46.0,<1.47.0' + - 'bioconductor-preprocesscore >=1.46.0,<1.47.0' + - 'bioconductor-snpchip >=2.30.0,<2.31.0' - r-base - r-beanplot - r-ellipse diff --git a/recipes/bioconductor-crossmeta/meta.yaml b/recipes/bioconductor-crossmeta/meta.yaml index 73c2ecebb7645..3a6c8721b83e4 100644 --- a/recipes/bioconductor-crossmeta/meta.yaml +++ b/recipes/bioconductor-crossmeta/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.8.0" %} +{% set version = "1.10.0" %} {% set name = "crossmeta" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 8ca286bce5ef78116e67a41eea184ed2 + md5: a7e2ea603db3fedc20fb7783003eeedb build: number: 0 rpaths: @@ -20,19 +20,20 @@ build: # Suggests: knitr, rmarkdown, lydata, org.Hs.eg.db, testthat, ccdata requirements: host: - - 'bioconductor-affxparser >=1.54.0,<1.55.0' - - 'bioconductor-affy >=1.60.0,<1.61.0' - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' - - 'bioconductor-biobase >=2.42.0,<2.43.0' - - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' - - 'bioconductor-ccmap >=1.8.0,<1.9.0' - - 'bioconductor-geoquery >=2.50.0,<2.51.0' - - 'bioconductor-limma >=3.38.0,<3.39.0' - - 'bioconductor-oligo >=1.46.0,<1.47.0' - - 'bioconductor-sva >=3.30.0,<3.31.0' + - 'bioconductor-affxparser >=1.56.0,<1.57.0' + - 'bioconductor-affy >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' + - 'bioconductor-biocgenerics >=0.30.0,<0.31.0' + - 'bioconductor-ccmap >=1.10.0,<1.11.0' + - 'bioconductor-geoquery >=2.52.0,<2.53.0' + - 'bioconductor-limma >=3.40.0,<3.41.0' + - 'bioconductor-oligo >=1.48.0,<1.49.0' + - 'bioconductor-sva >=3.32.0,<3.33.0' - r-base - - 'r-biocmanager >=1.24.0' + - 'r-biocmanager >=1.30.4' - 'r-data.table >=1.10.4' + - 'r-dbi >=1.0.0' - 'r-doparallel >=1.0.10' - 'r-dorng >=1.6' - 'r-dt >=0.2' @@ -43,27 +44,31 @@ requirements: - 'r-metama >=3.1.2' - 'r-metap >=0.8' - 'r-miniui >=0.1.1' - - 'r-pander >=0.6.0' - 'r-plotly >=4.5.6' - 'r-rcolorbrewer >=1.1.2' + - 'r-rcurl >=1.95.4.11' - 'r-rdrop2 >=0.7.0' + - 'r-reader >=1.0.6' - 'r-reshape >=0.8.6' + - 'r-rsqlite >=2.1.1' - 'r-shiny >=1.0.0' - 'r-stringr >=1.2.0' + - 'r-xml >=3.98.1.17' run: - - 'bioconductor-affxparser >=1.54.0,<1.55.0' - - 'bioconductor-affy >=1.60.0,<1.61.0' - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' - - 'bioconductor-biobase >=2.42.0,<2.43.0' - - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' - - 'bioconductor-ccmap >=1.8.0,<1.9.0' - - 'bioconductor-geoquery >=2.50.0,<2.51.0' - - 'bioconductor-limma >=3.38.0,<3.39.0' - - 'bioconductor-oligo >=1.46.0,<1.47.0' - - 'bioconductor-sva >=3.30.0,<3.31.0' + - 'bioconductor-affxparser >=1.56.0,<1.57.0' + - 'bioconductor-affy >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' + - 'bioconductor-biocgenerics >=0.30.0,<0.31.0' + - 'bioconductor-ccmap >=1.10.0,<1.11.0' + - 'bioconductor-geoquery >=2.52.0,<2.53.0' + - 'bioconductor-limma >=3.40.0,<3.41.0' + - 'bioconductor-oligo >=1.48.0,<1.49.0' + - 'bioconductor-sva >=3.32.0,<3.33.0' - r-base - - 'r-biocmanager >=1.24.0' + - 'r-biocmanager >=1.30.4' - 'r-data.table >=1.10.4' + - 'r-dbi >=1.0.0' - 'r-doparallel >=1.0.10' - 'r-dorng >=1.6' - 'r-dt >=0.2' @@ -74,13 +79,16 @@ requirements: - 'r-metama >=3.1.2' - 'r-metap >=0.8' - 'r-miniui >=0.1.1' - - 'r-pander >=0.6.0' - 'r-plotly >=4.5.6' - 'r-rcolorbrewer >=1.1.2' + - 'r-rcurl >=1.95.4.11' - 'r-rdrop2 >=0.7.0' + - 'r-reader >=1.0.6' - 'r-reshape >=0.8.6' + - 'r-rsqlite >=2.1.1' - 'r-shiny >=1.0.0' - 'r-stringr >=1.2.0' + - 'r-xml >=3.98.1.17' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-csar/meta.yaml b/recipes/bioconductor-csar/meta.yaml index 94d729c986c6c..41442376039a3 100644 --- a/recipes/bioconductor-csar/meta.yaml +++ b/recipes/bioconductor-csar/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.34.0" %} +{% set version = "1.36.0" %} {% set name = "CSAR" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,25 +10,25 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: cb843cd969ee7b70323486c565279993 + md5: a7187a296ff5f634727e0d4d8c277b6f build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ # Suggests: ShortRead, Biostrings requirements: host: - - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' - - 'bioconductor-genomicranges >=1.34.0,<1.35.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-genomeinfodb >=1.20.0,<1.21.0' + - 'bioconductor-genomicranges >=1.36.0,<1.37.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' - r-base run: - - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' - - 'bioconductor-genomicranges >=1.34.0,<1.35.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-genomeinfodb >=1.20.0,<1.21.0' + - 'bioconductor-genomicranges >=1.36.0,<1.37.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' - r-base build: - {{ compiler('c') }} diff --git a/recipes/bioconductor-csaw/meta.yaml b/recipes/bioconductor-csaw/meta.yaml index e00530b4e1e14..055ae2c6fe5e8 100644 --- a/recipes/bioconductor-csaw/meta.yaml +++ b/recipes/bioconductor-csaw/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.16.1" %} +{% set version = "1.18.0" %} {% set name = "csaw" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,47 +10,47 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 82d3daa64a0e7d2fc765c0194bae718a + md5: 9bd64f602a67ea5a18eabc7ecef5d031 build: number: 0 rpaths: - lib/R/lib/ - lib/ -# Suggests: org.Mm.eg.db, TxDb.Mmusculus.UCSC.mm10.knownGene, testthat +# Suggests: org.Mm.eg.db, TxDb.Mmusculus.UCSC.mm10.knownGene, testthat, GenomicAlignments, knitr, BiocStyle, rmarkdown, BiocManager # SystemRequirements: C++11 requirements: host: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' - - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' - - 'bioconductor-biocparallel >=1.16.0,<1.17.0' - - 'bioconductor-edger >=3.24.0,<3.25.0' - - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' - - 'bioconductor-genomicfeatures >=1.34.0,<1.35.0' - - 'bioconductor-genomicranges >=1.34.0,<1.35.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-limma >=3.38.0,<3.39.0' - - 'bioconductor-rhtslib >=1.14.0,<1.15.0' - - 'bioconductor-rsamtools >=1.34.0,<1.35.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' - - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' - - 'bioconductor-zlibbioc >=1.28.0,<1.29.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' + - 'bioconductor-biocgenerics >=0.30.0,<0.31.0' + - 'bioconductor-biocparallel >=1.18.0,<1.19.0' + - 'bioconductor-edger >=3.26.0,<3.27.0' + - 'bioconductor-genomeinfodb >=1.20.0,<1.21.0' + - 'bioconductor-genomicfeatures >=1.36.0,<1.37.0' + - 'bioconductor-genomicranges >=1.36.0,<1.37.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-limma >=3.40.0,<3.41.0' + - 'bioconductor-rhtslib >=1.16.0,<1.17.0' + - 'bioconductor-rsamtools >=2.0.0,<2.1.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' + - 'bioconductor-summarizedexperiment >=1.14.0,<1.15.0' + - 'bioconductor-zlibbioc >=1.30.0,<1.31.0' - r-base - r-rcpp run: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' - - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' - - 'bioconductor-biocparallel >=1.16.0,<1.17.0' - - 'bioconductor-edger >=3.24.0,<3.25.0' - - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' - - 'bioconductor-genomicfeatures >=1.34.0,<1.35.0' - - 'bioconductor-genomicranges >=1.34.0,<1.35.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-limma >=3.38.0,<3.39.0' - - 'bioconductor-rhtslib >=1.14.0,<1.15.0' - - 'bioconductor-rsamtools >=1.34.0,<1.35.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' - - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' - - 'bioconductor-zlibbioc >=1.28.0,<1.29.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' + - 'bioconductor-biocgenerics >=0.30.0,<0.31.0' + - 'bioconductor-biocparallel >=1.18.0,<1.19.0' + - 'bioconductor-edger >=3.26.0,<3.27.0' + - 'bioconductor-genomeinfodb >=1.20.0,<1.21.0' + - 'bioconductor-genomicfeatures >=1.36.0,<1.37.0' + - 'bioconductor-genomicranges >=1.36.0,<1.37.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-limma >=3.40.0,<3.41.0' + - 'bioconductor-rhtslib >=1.16.0,<1.17.0' + - 'bioconductor-rsamtools >=2.0.0,<2.1.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' + - 'bioconductor-summarizedexperiment >=1.14.0,<1.15.0' + - 'bioconductor-zlibbioc >=1.30.0,<1.31.0' - r-base - r-rcpp build: diff --git a/recipes/bioconductor-cssp/meta.yaml b/recipes/bioconductor-cssp/meta.yaml index 5d3eea5b8ba02..c628376cd4a9d 100644 --- a/recipes/bioconductor-cssp/meta.yaml +++ b/recipes/bioconductor-cssp/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.20.0" %} +{% set version = "1.22.0" %} {% set name = "CSSP" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 80255d123a4ba68f4b7bc8eafa0f30f8 + md5: 0df8f08ebb21ddcea13f1b3a096f28dc build: number: 0 rpaths: diff --git a/recipes/bioconductor-ctc/meta.yaml b/recipes/bioconductor-ctc/meta.yaml index 946fc3ab61669..0b6dca1c9fff8 100644 --- a/recipes/bioconductor-ctc/meta.yaml +++ b/recipes/bioconductor-ctc/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.56.0" %} +{% set version = "1.58.0" %} {% set name = "ctc" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: fe42ef0d23d5e1861c71b74a423f17e6 + md5: 8c4c2f9b987498ff1fe4f73d0354ae23 build: number: 0 rpaths: diff --git a/recipes/bioconductor-ctdquerier/meta.yaml b/recipes/bioconductor-ctdquerier/meta.yaml index ecccae8ca9ed9..72ab4ffb40500 100644 --- a/recipes/bioconductor-ctdquerier/meta.yaml +++ b/recipes/bioconductor-ctdquerier/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.2.0" %} +{% set version = "1.4.0" %} {% set name = "CTDquerier" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 30fbafbd91f9c7191e26145edd756856 + md5: b17b3506564035fe23a6e0e92d163fac build: number: 0 rpaths: @@ -20,8 +20,8 @@ build: # Suggests: BiocStyle, knitr requirements: host: - - 'bioconductor-biocfilecache >=1.6.0,<1.7.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-biocfilecache >=1.8.0,<1.9.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' - r-base - r-ggplot2 - r-gridextra @@ -31,8 +31,8 @@ requirements: - r-stringdist - r-stringr run: - - 'bioconductor-biocfilecache >=1.6.0,<1.7.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-biocfilecache >=1.8.0,<1.9.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' - r-base - r-ggplot2 - r-gridextra diff --git a/recipes/bioconductor-ctrap/meta.yaml b/recipes/bioconductor-ctrap/meta.yaml index f32b6236c3fd9..bb713504a42ef 100644 --- a/recipes/bioconductor-ctrap/meta.yaml +++ b/recipes/bioconductor-ctrap/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.0.3" %} +{% set version = "1.2.0" %} {% set name = "cTRAP" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: df4aabaf7896ba049296d92bd7885506 + md5: a3b7c8688824fa8c631f6675c0438dd2 build: number: 0 rpaths: @@ -20,10 +20,10 @@ build: # Suggests: testthat, knitr, covr, biomaRt requirements: host: - - 'bioconductor-fgsea >=1.8.0,<1.9.0' - - 'bioconductor-limma >=3.38.0,<3.39.0' - - 'bioconductor-piano >=1.22.0,<1.23.0' - - 'bioconductor-rhdf5 >=2.26.0,<2.27.0' + - 'bioconductor-fgsea >=1.10.0,<1.11.0' + - 'bioconductor-limma >=3.40.0,<3.41.0' + - 'bioconductor-piano >=2.0.0,<2.1.0' + - 'bioconductor-rhdf5 >=2.28.0,<2.29.0' - r-base - r-cowplot - r-data.table @@ -34,10 +34,10 @@ requirements: - r-r.utils - r-readr run: - - 'bioconductor-fgsea >=1.8.0,<1.9.0' - - 'bioconductor-limma >=3.38.0,<3.39.0' - - 'bioconductor-piano >=1.22.0,<1.23.0' - - 'bioconductor-rhdf5 >=2.26.0,<2.27.0' + - 'bioconductor-fgsea >=1.10.0,<1.11.0' + - 'bioconductor-limma >=3.40.0,<3.41.0' + - 'bioconductor-piano >=2.0.0,<2.1.0' + - 'bioconductor-rhdf5 >=2.28.0,<2.29.0' - r-base - r-cowplot - r-data.table diff --git a/recipes/bioconductor-ctsge/meta.yaml b/recipes/bioconductor-ctsge/meta.yaml index 089c7ed518a5c..6489ecff6e131 100644 --- a/recipes/bioconductor-ctsge/meta.yaml +++ b/recipes/bioconductor-ctsge/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.8.1" %} +{% set version = "1.10.0" %} {% set name = "ctsGE" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: 2bcbefebb2d4a221406894232538b72af0115cc9c470f1b148e6c0af829f8a7f + md5: 82dbb0de98157d7ddc1ecde7ed463bdc build: number: 0 rpaths: @@ -20,7 +20,7 @@ build: # Suggests: BiocStyle, dplyr, DT, GEOquery, knitr, pander, rmarkdown, testthat requirements: host: - - 'bioconductor-limma >=3.38.0,<3.39.0' + - 'bioconductor-limma >=3.40.0,<3.41.0' - r-base - r-ccapp - r-ggplot2 @@ -28,7 +28,7 @@ requirements: - r-shiny - r-stringr run: - - 'bioconductor-limma >=3.38.0,<3.39.0' + - 'bioconductor-limma >=3.40.0,<3.41.0' - r-base - r-ccapp - r-ggplot2 diff --git a/recipes/bioconductor-cummerbund/meta.yaml b/recipes/bioconductor-cummerbund/meta.yaml index 8db061dc53887..937a7ada787d5 100644 --- a/recipes/bioconductor-cummerbund/meta.yaml +++ b/recipes/bioconductor-cummerbund/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "2.24.0" %} +{% set version = "2.26.0" %} {% set name = "cummeRbund" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: a713a35d1c8f2a837d9c5a8ab86b8f72 + md5: 9d6f7bf9e12be69be7391f2f369f9f0d build: number: 0 rpaths: @@ -20,11 +20,11 @@ build: # Suggests: cluster, plyr, NMFN, stringr, GenomicFeatures, GenomicRanges, rjson requirements: host: - - 'bioconductor-biobase >=2.42.0,<2.43.0' - - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' - - 'bioconductor-gviz >=1.26.0,<1.27.0' - - 'bioconductor-rtracklayer >=1.42.0,<1.43.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' + - 'bioconductor-biocgenerics >=0.30.0,<0.31.0' + - 'bioconductor-gviz >=1.28.0,<1.29.0' + - 'bioconductor-rtracklayer >=1.44.0,<1.45.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' - r-base - r-fastcluster - r-ggplot2 @@ -32,11 +32,11 @@ requirements: - r-reshape2 - r-rsqlite run: - - 'bioconductor-biobase >=2.42.0,<2.43.0' - - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' - - 'bioconductor-gviz >=1.26.0,<1.27.0' - - 'bioconductor-rtracklayer >=1.42.0,<1.43.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' + - 'bioconductor-biocgenerics >=0.30.0,<0.31.0' + - 'bioconductor-gviz >=1.28.0,<1.29.0' + - 'bioconductor-rtracklayer >=1.44.0,<1.45.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' - r-base - r-fastcluster - r-ggplot2 diff --git a/recipes/bioconductor-curatedadipochip/meta.yaml b/recipes/bioconductor-curatedadipochip/meta.yaml new file mode 100644 index 0000000000000..9a5cd5bb3ffb4 --- /dev/null +++ b/recipes/bioconductor-curatedadipochip/meta.yaml @@ -0,0 +1,38 @@ +{% set version = "1.0.0" %} +{% set name = "curatedAdipoChIP" %} +{% set bioc = "3.9" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: bd1152653faf9424562c638ea8fc1ded +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: knitr, rmarkdown, GenomicFeatures, ChIPseeker, AnnotationDbi, S4Vectors, DESeq2, fastqcr, devtools, testthat, readr, dplyr, tidyr, ggplot2 +requirements: + host: + - 'bioconductor-experimenthub >=1.10.0,<1.11.0' + - 'bioconductor-summarizedexperiment >=1.14.0,<1.15.0' + - r-base + run: + - 'bioconductor-experimenthub >=1.10.0,<1.11.0' + - 'bioconductor-summarizedexperiment >=1.14.0,<1.15.0' + - r-base + - curl +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html' + license: GPL-3 + summary: 'A curated dataset of publicly available ChIP-sequencing of transcription factors, chromatin remodelers and histone modifications in the 3T3-L1 pre-adipocyte cell line. The package document the data collection, pre-processing and processing of the data. In addition to the documentation, the package contains the scripts that was used to generated the data.' + diff --git a/recipes/bioconductor-curatedadipochip/post-link.sh b/recipes/bioconductor-curatedadipochip/post-link.sh new file mode 100644 index 0000000000000..954f9c81a2581 --- /dev/null +++ b/recipes/bioconductor-curatedadipochip/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="curatedAdipoChIP_1.0.0.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.9/data/experiment/src/contrib/curatedAdipoChIP_1.0.0.tar.gz" + "https://bioarchive.galaxyproject.org/curatedAdipoChIP_1.0.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-curatedadipochip/bioconductor-curatedadipochip_1.0.0_src_all.tar.gz" +) +MD5="bd1152653faf9424562c638ea8fc1ded" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + curl $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-curatedadipochip/pre-unlink.sh b/recipes/bioconductor-curatedadipochip/pre-unlink.sh new file mode 100644 index 0000000000000..89d66ce01417e --- /dev/null +++ b/recipes/bioconductor-curatedadipochip/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ curatedAdipoChIP diff --git a/recipes/bioconductor-curatedadiporna/meta.yaml b/recipes/bioconductor-curatedadiporna/meta.yaml new file mode 100644 index 0000000000000..093b65889e844 --- /dev/null +++ b/recipes/bioconductor-curatedadiporna/meta.yaml @@ -0,0 +1,36 @@ +{% set version = "1.0.0" %} +{% set name = "curatedAdipoRNA" %} +{% set bioc = "3.9" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: 4424c4af38fa09e6d09b81c4d485c830 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: knitr, rmarkdown, DESeq2, fastqcr, devtools, testthat, readr, dplyr, tidyr, ggplot2, S4Vectors +requirements: + host: + - 'bioconductor-summarizedexperiment >=1.14.0,<1.15.0' + - r-base + run: + - 'bioconductor-summarizedexperiment >=1.14.0,<1.15.0' + - r-base + - curl +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html' + license: GPL-3 + summary: 'A curated dataset of RNA-Seq samples. The samples are MDI-induced pre-phagocytes (3T3-L1) at different time points/stage of differentiation. The package document the data collection, pre-processing and processing. In addition to the documentation, the package contains the scripts that was used to generated the data.' + diff --git a/recipes/bioconductor-curatedadiporna/post-link.sh b/recipes/bioconductor-curatedadiporna/post-link.sh new file mode 100644 index 0000000000000..51d44ccebb596 --- /dev/null +++ b/recipes/bioconductor-curatedadiporna/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="curatedAdipoRNA_1.0.0.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.9/data/experiment/src/contrib/curatedAdipoRNA_1.0.0.tar.gz" + "https://bioarchive.galaxyproject.org/curatedAdipoRNA_1.0.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-curatedadiporna/bioconductor-curatedadiporna_1.0.0_src_all.tar.gz" +) +MD5="4424c4af38fa09e6d09b81c4d485c830" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + curl $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-curatedadiporna/pre-unlink.sh b/recipes/bioconductor-curatedadiporna/pre-unlink.sh new file mode 100644 index 0000000000000..1c1803b04e644 --- /dev/null +++ b/recipes/bioconductor-curatedadiporna/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ curatedAdipoRNA diff --git a/recipes/bioconductor-curatedbladderdata/meta.yaml b/recipes/bioconductor-curatedbladderdata/meta.yaml index 4f2eec7eaadca..405bc958b75cb 100644 --- a/recipes/bioconductor-curatedbladderdata/meta.yaml +++ b/recipes/bioconductor-curatedbladderdata/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.18.0" %} +{% set version = "1.20.0" %} {% set name = "curatedBladderData" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 9626900fba87d603d8a0d7b068f3ce02 + md5: e81603412d05d4aeef774fb278648872 build: number: 0 rpaths: @@ -20,12 +20,12 @@ build: # Suggests: BiocStyle, survival, xtable, sva, genefilter, logging requirements: host: - - 'bioconductor-affy >=1.60.0,<1.61.0' + - 'bioconductor-affy >=1.62.0,<1.63.0' - r-base run: - - 'bioconductor-affy >=1.60.0,<1.61.0' + - 'bioconductor-affy >=1.62.0,<1.63.0' - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-curatedbladderdata/post-link.sh b/recipes/bioconductor-curatedbladderdata/post-link.sh index 34b380fbcd462..8ea7e7f375a88 100644 --- a/recipes/bioconductor-curatedbladderdata/post-link.sh +++ b/recipes/bioconductor-curatedbladderdata/post-link.sh @@ -1,11 +1,11 @@ #!/bin/bash -FN="curatedBladderData_1.18.0.tar.gz" +FN="curatedBladderData_1.20.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/experiment/src/contrib/curatedBladderData_1.18.0.tar.gz" - "https://bioarchive.galaxyproject.org/curatedBladderData_1.18.0.tar.gz" - "https://depot.galaxyproject.org/software/bioconductor-curatedbladderdata/bioconductor-curatedbladderdata_1.18.0_src_all.tar.gz" + "https://bioconductor.org/packages/3.9/data/experiment/src/contrib/curatedBladderData_1.20.0.tar.gz" + "https://bioarchive.galaxyproject.org/curatedBladderData_1.20.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-curatedbladderdata/bioconductor-curatedbladderdata_1.20.0_src_all.tar.gz" ) -MD5="9626900fba87d603d8a0d7b068f3ce02" +MD5="e81603412d05d4aeef774fb278648872" # Use a staging area in the conda dir rather than temp dirs, both to avoid # permission issues as well as to have things downloaded in a predictable @@ -16,7 +16,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-curatedbreastdata/meta.yaml b/recipes/bioconductor-curatedbreastdata/meta.yaml index 22e3d229baad8..51552c6d2b316 100644 --- a/recipes/bioconductor-curatedbreastdata/meta.yaml +++ b/recipes/bioconductor-curatedbreastdata/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "2.10.0" %} +{% set version = "2.12.0" %} {% set name = "curatedBreastData" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: f331996cfe36abc88dbc84a8fde187c5 + md5: 945c48e2f40b55c017fcb7acf33c86d8 build: number: 0 rpaths: @@ -19,20 +19,20 @@ build: noarch: generic requirements: host: - - 'bioconductor-biobase >=2.42.0,<2.43.0' - - 'bioconductor-biocstyle >=2.10.0,<2.11.0' - - 'bioconductor-impute >=1.56.0,<1.57.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' + - 'bioconductor-biocstyle >=2.12.0,<2.13.0' + - 'bioconductor-impute >=1.58.0,<1.59.0' - r-base - r-ggplot2 - r-xml run: - - 'bioconductor-biobase >=2.42.0,<2.43.0' - - 'bioconductor-biocstyle >=2.10.0,<2.11.0' - - 'bioconductor-impute >=1.56.0,<1.57.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' + - 'bioconductor-biocstyle >=2.12.0,<2.13.0' + - 'bioconductor-impute >=1.58.0,<1.59.0' - r-base - r-ggplot2 - r-xml - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-curatedbreastdata/post-link.sh b/recipes/bioconductor-curatedbreastdata/post-link.sh index 2ff59a64889aa..e8e0ca4f0802f 100644 --- a/recipes/bioconductor-curatedbreastdata/post-link.sh +++ b/recipes/bioconductor-curatedbreastdata/post-link.sh @@ -1,11 +1,11 @@ #!/bin/bash -FN="curatedBreastData_2.10.0.tar.gz" +FN="curatedBreastData_2.12.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/experiment/src/contrib/curatedBreastData_2.10.0.tar.gz" - "https://bioarchive.galaxyproject.org/curatedBreastData_2.10.0.tar.gz" - "https://depot.galaxyproject.org/software/bioconductor-curatedbreastdata/bioconductor-curatedbreastdata_2.10.0_src_all.tar.gz" + "https://bioconductor.org/packages/3.9/data/experiment/src/contrib/curatedBreastData_2.12.0.tar.gz" + "https://bioarchive.galaxyproject.org/curatedBreastData_2.12.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-curatedbreastdata/bioconductor-curatedbreastdata_2.12.0_src_all.tar.gz" ) -MD5="f331996cfe36abc88dbc84a8fde187c5" +MD5="945c48e2f40b55c017fcb7acf33c86d8" # Use a staging area in the conda dir rather than temp dirs, both to avoid # permission issues as well as to have things downloaded in a predictable @@ -16,7 +16,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-curatedcrcdata/meta.yaml b/recipes/bioconductor-curatedcrcdata/meta.yaml index 3542d0d1fea45..f511c1c8d6337 100644 --- a/recipes/bioconductor-curatedcrcdata/meta.yaml +++ b/recipes/bioconductor-curatedcrcdata/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "2.14.0" %} +{% set version = "2.16.0" %} {% set name = "curatedCRCData" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 930dbdba821daa1232beb01eee233d80 + md5: e9df2a3ae6a0b51c081cc3a653045805 build: number: 0 rpaths: @@ -20,14 +20,14 @@ build: # Suggests: survival, RUnit, metafor, genefilter, logging, sva, xtable, futile.logger, BiocStyle requirements: host: - - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' + - 'bioconductor-biocgenerics >=0.30.0,<0.31.0' - r-base - r-nlme run: - - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' + - 'bioconductor-biocgenerics >=0.30.0,<0.31.0' - r-base - r-nlme - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-curatedcrcdata/post-link.sh b/recipes/bioconductor-curatedcrcdata/post-link.sh index 71f39b75f3357..4180107330394 100644 --- a/recipes/bioconductor-curatedcrcdata/post-link.sh +++ b/recipes/bioconductor-curatedcrcdata/post-link.sh @@ -1,11 +1,11 @@ #!/bin/bash -FN="curatedCRCData_2.14.0.tar.gz" +FN="curatedCRCData_2.16.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/experiment/src/contrib/curatedCRCData_2.14.0.tar.gz" - "https://bioarchive.galaxyproject.org/curatedCRCData_2.14.0.tar.gz" - "https://depot.galaxyproject.org/software/bioconductor-curatedcrcdata/bioconductor-curatedcrcdata_2.14.0_src_all.tar.gz" + "https://bioconductor.org/packages/3.9/data/experiment/src/contrib/curatedCRCData_2.16.0.tar.gz" + "https://bioarchive.galaxyproject.org/curatedCRCData_2.16.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-curatedcrcdata/bioconductor-curatedcrcdata_2.16.0_src_all.tar.gz" ) -MD5="930dbdba821daa1232beb01eee233d80" +MD5="e9df2a3ae6a0b51c081cc3a653045805" # Use a staging area in the conda dir rather than temp dirs, both to avoid # permission issues as well as to have things downloaded in a predictable @@ -16,7 +16,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-curatedmetagenomicdata/meta.yaml b/recipes/bioconductor-curatedmetagenomicdata/meta.yaml index 5b3537252deb0..2e99dd69efcb2 100644 --- a/recipes/bioconductor-curatedmetagenomicdata/meta.yaml +++ b/recipes/bioconductor-curatedmetagenomicdata/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.12.3" %} +{% set version = "1.13.3" %} {% set name = "curatedMetagenomicData" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,9 +10,9 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 647d57c43704bee51d7d54327e419cd4 + md5: 524c855267709a5288cbe910d9f81dec build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ @@ -20,24 +20,24 @@ build: # Suggests: BiocManager, devtools, roxygen2, testthat, covr, knitr, rmarkdown, BiocCheck, BiocStyle, BiocParallel, readr, RISmed, ggplot2, metagenomeSeq, phyloseq, ape requirements: host: - - 'bioconductor-annotationhub >=2.14.0,<2.15.0' - - 'bioconductor-biobase >=2.42.0,<2.43.0' - - 'bioconductor-experimenthub >=1.8.0,<1.9.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-annotationhub >=2.16.0,<2.17.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' + - 'bioconductor-experimenthub >=1.10.0,<1.11.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' - r-base - 'r-dplyr >=0.5.0' - r-magrittr - r-tidyr run: - - 'bioconductor-annotationhub >=2.14.0,<2.15.0' - - 'bioconductor-biobase >=2.42.0,<2.43.0' - - 'bioconductor-experimenthub >=1.8.0,<1.9.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-annotationhub >=2.16.0,<2.17.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' + - 'bioconductor-experimenthub >=1.10.0,<1.11.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' - r-base - 'r-dplyr >=0.5.0' - r-magrittr - r-tidyr - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-curatedmetagenomicdata/post-link.sh b/recipes/bioconductor-curatedmetagenomicdata/post-link.sh index 31be771a6b2cb..232480056f811 100644 --- a/recipes/bioconductor-curatedmetagenomicdata/post-link.sh +++ b/recipes/bioconductor-curatedmetagenomicdata/post-link.sh @@ -1,11 +1,11 @@ #!/bin/bash -FN="curatedMetagenomicData_1.12.3.tar.gz" +FN="curatedMetagenomicData_1.13.3.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/experiment/src/contrib/curatedMetagenomicData_1.12.3.tar.gz" - "https://bioarchive.galaxyproject.org/curatedMetagenomicData_1.12.3.tar.gz" - "https://depot.galaxyproject.org/software/bioconductor-curatedmetagenomicdata/bioconductor-curatedmetagenomicdata_1.12.3_src_all.tar.gz" + "https://bioconductor.org/packages/3.9/data/experiment/src/contrib/curatedMetagenomicData_1.13.3.tar.gz" + "https://bioarchive.galaxyproject.org/curatedMetagenomicData_1.13.3.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-curatedmetagenomicdata/bioconductor-curatedmetagenomicdata_1.13.3_src_all.tar.gz" ) -MD5="647d57c43704bee51d7d54327e419cd4" +MD5="524c855267709a5288cbe910d9f81dec" # Use a staging area in the conda dir rather than temp dirs, both to avoid # permission issues as well as to have things downloaded in a predictable @@ -16,7 +16,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-curatedovariandata/meta.yaml b/recipes/bioconductor-curatedovariandata/meta.yaml index b80df52bbb3ad..f8e8b5c2b56dc 100644 --- a/recipes/bioconductor-curatedovariandata/meta.yaml +++ b/recipes/bioconductor-curatedovariandata/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.20.0" %} +{% set version = "1.22.0" %} {% set name = "curatedOvarianData" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 7c3a22afa72323d96332d78df1478c8a + md5: 1af5517292618a6a05871dbf02953866 build: number: 0 rpaths: @@ -20,14 +20,14 @@ build: # Suggests: survival, RUnit, metafor, genefilter, logging, sva, xtable, futile.logger, BiocStyle requirements: host: - - 'bioconductor-affy >=1.60.0,<1.61.0' - - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' + - 'bioconductor-affy >=1.62.0,<1.63.0' + - 'bioconductor-biocgenerics >=0.30.0,<0.31.0' - r-base run: - - 'bioconductor-affy >=1.60.0,<1.61.0' - - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' + - 'bioconductor-affy >=1.62.0,<1.63.0' + - 'bioconductor-biocgenerics >=0.30.0,<0.31.0' - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-curatedovariandata/post-link.sh b/recipes/bioconductor-curatedovariandata/post-link.sh index 65e509d207d67..df05f7c5d78b5 100644 --- a/recipes/bioconductor-curatedovariandata/post-link.sh +++ b/recipes/bioconductor-curatedovariandata/post-link.sh @@ -1,11 +1,11 @@ #!/bin/bash -FN="curatedOvarianData_1.20.0.tar.gz" +FN="curatedOvarianData_1.22.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/experiment/src/contrib/curatedOvarianData_1.20.0.tar.gz" - "https://bioarchive.galaxyproject.org/curatedOvarianData_1.20.0.tar.gz" - "https://depot.galaxyproject.org/software/bioconductor-curatedovariandata/bioconductor-curatedovariandata_1.20.0_src_all.tar.gz" + "https://bioconductor.org/packages/3.9/data/experiment/src/contrib/curatedOvarianData_1.22.0.tar.gz" + "https://bioarchive.galaxyproject.org/curatedOvarianData_1.22.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-curatedovariandata/bioconductor-curatedovariandata_1.22.0_src_all.tar.gz" ) -MD5="7c3a22afa72323d96332d78df1478c8a" +MD5="1af5517292618a6a05871dbf02953866" # Use a staging area in the conda dir rather than temp dirs, both to avoid # permission issues as well as to have things downloaded in a predictable @@ -16,7 +16,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-curatedtcgadata/meta.yaml b/recipes/bioconductor-curatedtcgadata/meta.yaml index a62774f47ddc9..ee0902a328202 100644 --- a/recipes/bioconductor-curatedtcgadata/meta.yaml +++ b/recipes/bioconductor-curatedtcgadata/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.4.0" %} +{% set version = "1.6.0" %} {% set name = "curatedTCGAData" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,33 +10,37 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 2bb34b9c62fc697c3fff464396c08b91 + md5: 3389cf6624a52501366bbccdcf9d2534 build: number: 0 rpaths: - lib/R/lib/ - lib/ noarch: generic -# Suggests: BiocStyle, knitr, readr, rmarkdown, testthat +# Suggests: BiocStyle, knitr, readr, rmarkdown, TCGAutils, testthat requirements: host: - - 'bioconductor-annotationhub >=2.14.0,<2.15.0' - - 'bioconductor-experimenthub >=1.8.0,<1.9.0' - - 'bioconductor-multiassayexperiment >=1.8.0,<1.9.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-annotationhub >=2.16.0,<2.17.0' + - 'bioconductor-experimenthub >=1.10.0,<1.11.0' + - 'bioconductor-hdf5array >=1.12.0,<1.13.0' + - 'bioconductor-multiassayexperiment >=1.10.0,<1.11.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' + - 'bioconductor-summarizedexperiment >=1.14.0,<1.15.0' - r-base run: - - 'bioconductor-annotationhub >=2.14.0,<2.15.0' - - 'bioconductor-experimenthub >=1.8.0,<1.9.0' - - 'bioconductor-multiassayexperiment >=1.8.0,<1.9.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-annotationhub >=2.16.0,<2.17.0' + - 'bioconductor-experimenthub >=1.10.0,<1.11.0' + - 'bioconductor-hdf5array >=1.12.0,<1.13.0' + - 'bioconductor-multiassayexperiment >=1.10.0,<1.11.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' + - 'bioconductor-summarizedexperiment >=1.14.0,<1.15.0' - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' about: home: 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html' license: Artistic-2.0 - summary: 'This package provides publicly available data from The Cancer Genome Atlas (TCGA) Bioconductor MultiAssayExperiment class objects. These objects integrate multiple assays (e.g. RNA-seq, copy number, mutation, microRNA, protein, and others) with clinical / pathological data. The MultiAssayExperiment class links assay barcodes with patient IDs, enabling harmonized subsetting of rows (features) and columns (patients / samples) across the entire experiment.' + summary: 'This package provides publicly available data from The Cancer Genome Atlas (TCGA) as MultiAssayExperiment objects. MultiAssayExperiment integrates multiple assays (e.g., RNA-seq, copy number, mutation, microRNA, protein, and others) with clinical / pathological data. It also links assay barcodes with patient identifiers, enabling harmonized subsetting of rows (features) and columns (patients / samples) across the entire multi-''omics experiment.' diff --git a/recipes/bioconductor-curatedtcgadata/post-link.sh b/recipes/bioconductor-curatedtcgadata/post-link.sh index 65821a4340406..7cfb2734a6de7 100644 --- a/recipes/bioconductor-curatedtcgadata/post-link.sh +++ b/recipes/bioconductor-curatedtcgadata/post-link.sh @@ -1,11 +1,11 @@ #!/bin/bash -FN="curatedTCGAData_1.4.0.tar.gz" +FN="curatedTCGAData_1.6.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/experiment/src/contrib/curatedTCGAData_1.4.0.tar.gz" - "https://bioarchive.galaxyproject.org/curatedTCGAData_1.4.0.tar.gz" - "https://depot.galaxyproject.org/software/bioconductor-curatedtcgadata/bioconductor-curatedtcgadata_1.4.0_src_all.tar.gz" + "https://bioconductor.org/packages/3.9/data/experiment/src/contrib/curatedTCGAData_1.6.0.tar.gz" + "https://bioarchive.galaxyproject.org/curatedTCGAData_1.6.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-curatedtcgadata/bioconductor-curatedtcgadata_1.6.0_src_all.tar.gz" ) -MD5="2bb34b9c62fc697c3fff464396c08b91" +MD5="3389cf6624a52501366bbccdcf9d2534" # Use a staging area in the conda dir rather than temp dirs, both to avoid # permission issues as well as to have things downloaded in a predictable @@ -16,7 +16,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-customprodb/meta.yaml b/recipes/bioconductor-customprodb/meta.yaml index a975bd7f339b7..b24ebff86fe77 100644 --- a/recipes/bioconductor-customprodb/meta.yaml +++ b/recipes/bioconductor-customprodb/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.22.0" %} +{% set version = "1.24.0" %} {% set name = "customProDB" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 971e7cda62bc25dfa59f452ce73b1d09 + md5: f0480be5b51b492ef68898710c8c56aa build: number: 0 rpaths: @@ -20,18 +20,18 @@ build: # Suggests: RMariaDB, BSgenome.Hsapiens.UCSC.hg19 requirements: host: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' - - 'bioconductor-biomart >=2.38.0,<2.39.0' - - 'bioconductor-biostrings >=2.50.0,<2.51.0' - - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' - - 'bioconductor-genomicalignments >=1.18.0,<1.19.0' - - 'bioconductor-genomicfeatures >=1.34.0,<1.35.0' - - 'bioconductor-genomicranges >=1.34.0,<1.35.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-rsamtools >=1.34.0,<1.35.0' - - 'bioconductor-rtracklayer >=1.42.0,<1.43.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' - - 'bioconductor-variantannotation >=1.28.0,<1.29.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' + - 'bioconductor-biomart >=2.40.0,<2.41.0' + - 'bioconductor-biostrings >=2.52.0,<2.53.0' + - 'bioconductor-genomeinfodb >=1.20.0,<1.21.0' + - 'bioconductor-genomicalignments >=1.20.0,<1.21.0' + - 'bioconductor-genomicfeatures >=1.36.0,<1.37.0' + - 'bioconductor-genomicranges >=1.36.0,<1.37.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-rsamtools >=2.0.0,<2.1.0' + - 'bioconductor-rtracklayer >=1.44.0,<1.45.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' + - 'bioconductor-variantannotation >=1.30.0,<1.31.0' - r-ahocorasicktrie - r-base - r-dbi @@ -40,18 +40,18 @@ requirements: - r-rsqlite - r-stringr run: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' - - 'bioconductor-biomart >=2.38.0,<2.39.0' - - 'bioconductor-biostrings >=2.50.0,<2.51.0' - - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' - - 'bioconductor-genomicalignments >=1.18.0,<1.19.0' - - 'bioconductor-genomicfeatures >=1.34.0,<1.35.0' - - 'bioconductor-genomicranges >=1.34.0,<1.35.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-rsamtools >=1.34.0,<1.35.0' - - 'bioconductor-rtracklayer >=1.42.0,<1.43.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' - - 'bioconductor-variantannotation >=1.28.0,<1.29.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' + - 'bioconductor-biomart >=2.40.0,<2.41.0' + - 'bioconductor-biostrings >=2.52.0,<2.53.0' + - 'bioconductor-genomeinfodb >=1.20.0,<1.21.0' + - 'bioconductor-genomicalignments >=1.20.0,<1.21.0' + - 'bioconductor-genomicfeatures >=1.36.0,<1.37.0' + - 'bioconductor-genomicranges >=1.36.0,<1.37.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-rsamtools >=2.0.0,<2.1.0' + - 'bioconductor-rtracklayer >=1.44.0,<1.45.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' + - 'bioconductor-variantannotation >=1.30.0,<1.31.0' - r-ahocorasicktrie - r-base - r-dbi diff --git a/recipes/bioconductor-cve/meta.yaml b/recipes/bioconductor-cve/meta.yaml index 36c87775f82f6..441e818f83a2b 100644 --- a/recipes/bioconductor-cve/meta.yaml +++ b/recipes/bioconductor-cve/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.8.0" %} +{% set version = "1.10.0" %} {% set name = "CVE" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: b21a70bfa5c7401ffd91e3eb8be07d39 + md5: 2396cfaf7ce6b60195a6af560d5c1d66 build: number: 0 rpaths: @@ -20,7 +20,7 @@ build: # Suggests: knitr, rmarkdown, RTCGAToolbox, testthat, BiocStyle requirements: host: - - 'bioconductor-consensusclusterplus >=1.46.0,<1.47.0' + - 'bioconductor-consensusclusterplus >=1.48.0,<1.49.0' - r-ape - r-base - r-ggplot2 @@ -32,7 +32,7 @@ requirements: - r-tidyverse - r-wgcna run: - - 'bioconductor-consensusclusterplus >=1.46.0,<1.47.0' + - 'bioconductor-consensusclusterplus >=1.48.0,<1.49.0' - r-ape - r-base - r-ggplot2 diff --git a/recipes/bioconductor-cycle/meta.yaml b/recipes/bioconductor-cycle/meta.yaml index eff1f19f26bbe..9a1ab04f5e5f0 100644 --- a/recipes/bioconductor-cycle/meta.yaml +++ b/recipes/bioconductor-cycle/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.36.0" %} +{% set version = "1.38.0" %} {% set name = "cycle" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 20c0540915e76d5897c280c086256c36 + md5: 2cd209230387fc9f0631f2d0e1fcd46a build: number: 0 rpaths: @@ -19,12 +19,12 @@ build: noarch: generic requirements: host: - - 'bioconductor-biobase >=2.42.0,<2.43.0' - - 'bioconductor-mfuzz >=2.42.0,<2.43.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' + - 'bioconductor-mfuzz >=2.44.0,<2.45.0' - r-base run: - - 'bioconductor-biobase >=2.42.0,<2.43.0' - - 'bioconductor-mfuzz >=2.42.0,<2.43.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' + - 'bioconductor-mfuzz >=2.44.0,<2.45.0' - r-base test: commands: diff --git a/recipes/bioconductor-cydar/meta.yaml b/recipes/bioconductor-cydar/meta.yaml index 2f26bba532060..16ee52632c032 100644 --- a/recipes/bioconductor-cydar/meta.yaml +++ b/recipes/bioconductor-cydar/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.6.0" %} +{% set version = "1.8.0" %} {% set name = "cydar" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: dd6fc3308e6af0aa4eb5a496c287f63d + md5: ce5632a0901f34dd03c93f5d6389a375 build: number: 0 rpaths: @@ -20,27 +20,27 @@ build: # SystemRequirements: C++11 requirements: host: - - 'bioconductor-biobase >=2.42.0,<2.43.0' - - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' - - 'bioconductor-biocneighbors >=1.0.0,<1.1.0' - - 'bioconductor-biocparallel >=1.16.0,<1.17.0' - - 'bioconductor-flowcore >=1.48.0,<1.49.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' - - 'bioconductor-singlecellexperiment >=1.4.0,<1.5.0' - - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' + - 'bioconductor-biocgenerics >=0.30.0,<0.31.0' + - 'bioconductor-biocneighbors >=1.2.0,<1.3.0' + - 'bioconductor-biocparallel >=1.18.0,<1.19.0' + - 'bioconductor-flowcore >=1.50.0,<1.51.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' + - 'bioconductor-singlecellexperiment >=1.6.0,<1.7.0' + - 'bioconductor-summarizedexperiment >=1.14.0,<1.15.0' - r-base - r-rcpp - r-shiny - r-viridis run: - - 'bioconductor-biobase >=2.42.0,<2.43.0' - - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' - - 'bioconductor-biocneighbors >=1.0.0,<1.1.0' - - 'bioconductor-biocparallel >=1.16.0,<1.17.0' - - 'bioconductor-flowcore >=1.48.0,<1.49.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' - - 'bioconductor-singlecellexperiment >=1.4.0,<1.5.0' - - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' + - 'bioconductor-biocgenerics >=0.30.0,<0.31.0' + - 'bioconductor-biocneighbors >=1.2.0,<1.3.0' + - 'bioconductor-biocparallel >=1.18.0,<1.19.0' + - 'bioconductor-flowcore >=1.50.0,<1.51.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' + - 'bioconductor-singlecellexperiment >=1.6.0,<1.7.0' + - 'bioconductor-summarizedexperiment >=1.14.0,<1.15.0' - r-base - r-rcpp - r-shiny diff --git a/recipes/bioconductor-cyp450cdf/meta.yaml b/recipes/bioconductor-cyp450cdf/meta.yaml index 956b267bd0954..89e2a8ace07e2 100644 --- a/recipes/bioconductor-cyp450cdf/meta.yaml +++ b/recipes/bioconductor-cyp450cdf/meta.yaml @@ -1,6 +1,6 @@ {% set version = "2.18.0" %} {% set name = "cyp450cdf" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -12,19 +12,19 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 7923c4d24b7b654d0f59d52ed2258eb9 build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' - r-base run: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-cyp450cdf/post-link.sh b/recipes/bioconductor-cyp450cdf/post-link.sh index aaa49374be2eb..978c61cf5b625 100644 --- a/recipes/bioconductor-cyp450cdf/post-link.sh +++ b/recipes/bioconductor-cyp450cdf/post-link.sh @@ -1,9 +1,10 @@ #!/bin/bash FN="cyp450cdf_2.18.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/cyp450cdf_2.18.0.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/cyp450cdf_2.18.0.tar.gz" "https://bioarchive.galaxyproject.org/cyp450cdf_2.18.0.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-cyp450cdf/bioconductor-cyp450cdf_2.18.0_src_all.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-cyp450cdf/bioconductor-cyp450cdf_2.18.0_src_all.tar.gz" ) MD5="7923c4d24b7b654d0f59d52ed2258eb9" @@ -16,7 +17,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-cytodx/meta.yaml b/recipes/bioconductor-cytodx/meta.yaml index bbe4976eb2724..ec44264388f57 100644 --- a/recipes/bioconductor-cytodx/meta.yaml +++ b/recipes/bioconductor-cytodx/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.2.1" %} +{% set version = "1.4.0" %} {% set name = "CytoDx" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,9 +10,9 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 9e2a90f9e0816c38eb2c0d4c17a146e7 + md5: 28c899b94fb5cac16103e4cd83d76037 build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ @@ -20,7 +20,7 @@ build: # Suggests: knitr requirements: host: - - 'bioconductor-flowcore >=1.48.0,<1.49.0' + - 'bioconductor-flowcore >=1.50.0,<1.51.0' - r-base - r-doparallel - r-dplyr @@ -28,7 +28,7 @@ requirements: - r-rpart - r-rpart.plot run: - - 'bioconductor-flowcore >=1.48.0,<1.49.0' + - 'bioconductor-flowcore >=1.50.0,<1.51.0' - r-base - r-doparallel - r-dplyr diff --git a/recipes/bioconductor-cytofast/build.sh b/recipes/bioconductor-cytofast/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-cytofast/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-cytofast/meta.yaml b/recipes/bioconductor-cytofast/meta.yaml new file mode 100644 index 0000000000000..a584ce275df04 --- /dev/null +++ b/recipes/bioconductor-cytofast/meta.yaml @@ -0,0 +1,47 @@ +{% set version = "1.0.0" %} +{% set name = "cytofast" %} +{% set bioc = "3.9" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + md5: 4400b4f61df017e6f5a9f902d39da411 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: BiocStyle, knitr, rmarkdown +requirements: + host: + - 'bioconductor-flowcore >=1.50.0,<1.51.0' + - 'bioconductor-flowsom >=1.16.0,<1.17.0' + - r-base + - r-ggplot2 + - r-ggridges + - r-rcolorbrewer + - r-rdpack + - r-reshape2 + run: + - 'bioconductor-flowcore >=1.50.0,<1.51.0' + - 'bioconductor-flowsom >=1.16.0,<1.17.0' + - r-base + - r-ggplot2 + - r-ggridges + - r-rcolorbrewer + - r-rdpack + - r-reshape2 +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: GPL-3 + summary: 'Multi-parametric flow and mass cytometry allows exceptional high-resolution exploration of the cellular composition of the immune system. Together with tools like FlowSOM and Cytosplore it is possible to identify novel cell types. By introducing cytofast we hope to offer a workflow for visualization and quantification of cell clusters for an efficient discovery of cell populations associated with diseases or other clinical outcomes.' + diff --git a/recipes/bioconductor-cytolib/meta.yaml b/recipes/bioconductor-cytolib/meta.yaml index 9ad77bd42ae4e..1e2f9cdef6f6f 100644 --- a/recipes/bioconductor-cytolib/meta.yaml +++ b/recipes/bioconductor-cytolib/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.4.1" %} +{% set version = "1.6.0" %} {% set name = "cytolib" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 3b9d823ae09d6d83d05e088afc955e4b + md5: b485d248ce7346c0beafaff56d68dcd7 build: number: 0 rpaths: @@ -21,11 +21,11 @@ build: # SystemRequirements: GNU make, C++11 requirements: host: - - 'bioconductor-rprotobuflib >=1.4.0,<1.5.0' + - 'bioconductor-rprotobuflib >=1.6.0,<1.7.0' - r-base - 'r-bh >=1.62.0-1' run: - - 'bioconductor-rprotobuflib >=1.4.0,<1.5.0' + - 'bioconductor-rprotobuflib >=1.6.0,<1.7.0' - r-base - 'r-bh >=1.62.0-1' test: diff --git a/recipes/bioconductor-cytoml/meta.yaml b/recipes/bioconductor-cytoml/meta.yaml index 96fb34e8cd8ac..4ae535dea934e 100644 --- a/recipes/bioconductor-cytoml/meta.yaml +++ b/recipes/bioconductor-cytoml/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.8.1" %} +{% set version = "1.10.0" %} {% set name = "CytoML" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,49 +10,70 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 9be209a388efba16dd699e4c85542c51 + md5: 9b02fad08a21f76fc73cc24fff7211b1 build: number: 0 rpaths: - lib/R/lib/ - lib/ - noarch: generic # Suggests: testthat, flowWorkspaceData (>= 2.11.1), knitr, parallel +# SystemRequirements: xml2, GNU make, C++11 requirements: host: - - 'bioconductor-biobase >=2.42.0,<2.43.0' - - 'bioconductor-flowcore >=1.48.0,<1.49.0' - - 'bioconductor-flowutils >=1.46.0,<1.47.0' - - 'bioconductor-flowworkspace >=3.30.0,<3.31.0' - - 'bioconductor-ggcyto >=1.10.0,<1.11.0' - - 'bioconductor-graph >=1.60.0,<1.61.0' - - 'bioconductor-ncdfflow >=2.28.0,<2.29.0' - - 'bioconductor-opencyto >=1.20.0,<1.21.0' - - 'bioconductor-rbgl >=1.58.0,<1.59.0' - - 'bioconductor-rgraphviz >=2.26.0,<2.27.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' + - 'bioconductor-cytolib >=1.6.0,<1.7.0' + - 'bioconductor-flowcore >=1.50.0,<1.51.0' + - 'bioconductor-flowutils >=1.48.0,<1.49.0' + - 'bioconductor-flowworkspace >=3.32.0,<3.33.0' + - 'bioconductor-ggcyto >=1.12.0,<1.13.0' + - 'bioconductor-graph >=1.62.0,<1.63.0' + - 'bioconductor-ncdfflow >=2.30.0,<2.31.0' + - 'bioconductor-opencyto >=1.22.0,<1.23.0' + - 'bioconductor-rbgl >=1.60.0,<1.61.0' + - 'bioconductor-rgraphviz >=2.28.0,<2.29.0' + - 'bioconductor-rprotobuflib >=1.6.0,<1.7.0' - r-base - r-base64enc + - 'r-bh >=1.62.0-1' - r-data.table + - r-dplyr - r-jsonlite + - r-lattice - r-plyr + - r-rcpp + - r-rcppparallel - r-xml + - r-yaml run: - - 'bioconductor-biobase >=2.42.0,<2.43.0' - - 'bioconductor-flowcore >=1.48.0,<1.49.0' - - 'bioconductor-flowutils >=1.46.0,<1.47.0' - - 'bioconductor-flowworkspace >=3.30.0,<3.31.0' - - 'bioconductor-ggcyto >=1.10.0,<1.11.0' - - 'bioconductor-graph >=1.60.0,<1.61.0' - - 'bioconductor-ncdfflow >=2.28.0,<2.29.0' - - 'bioconductor-opencyto >=1.20.0,<1.21.0' - - 'bioconductor-rbgl >=1.58.0,<1.59.0' - - 'bioconductor-rgraphviz >=2.26.0,<2.27.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' + - 'bioconductor-cytolib >=1.6.0,<1.7.0' + - 'bioconductor-flowcore >=1.50.0,<1.51.0' + - 'bioconductor-flowutils >=1.48.0,<1.49.0' + - 'bioconductor-flowworkspace >=3.32.0,<3.33.0' + - 'bioconductor-ggcyto >=1.12.0,<1.13.0' + - 'bioconductor-graph >=1.62.0,<1.63.0' + - 'bioconductor-ncdfflow >=2.30.0,<2.31.0' + - 'bioconductor-opencyto >=1.22.0,<1.23.0' + - 'bioconductor-rbgl >=1.60.0,<1.61.0' + - 'bioconductor-rgraphviz >=2.28.0,<2.29.0' + - 'bioconductor-rprotobuflib >=1.6.0,<1.7.0' - r-base - r-base64enc + - 'r-bh >=1.62.0-1' - r-data.table + - r-dplyr - r-jsonlite + - r-lattice - r-plyr + - r-rcpp + - r-rcppparallel - r-xml + - r-yaml + build: + - {{ compiler('c') }} + - {{ compiler('cxx') }} + - automake + - make test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-dada2/meta.yaml b/recipes/bioconductor-dada2/meta.yaml index beb4c3cb6586f..5cc2358d035e2 100644 --- a/recipes/bioconductor-dada2/meta.yaml +++ b/recipes/bioconductor-dada2/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.10.0" %} +{% set version = "1.12.0" %} {% set name = "dada2" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 4ee982f882667aefb39624b5b71df387 + md5: 2aef8b16a4b716f9ad8f42cb0c778483 build: number: 0 rpaths: @@ -20,27 +20,25 @@ build: # SystemRequirements: GNU make requirements: host: - - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' - - 'bioconductor-biostrings >=2.50.0,<2.51.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-shortread >=1.40.0,<1.41.0' - - 'bioconductor-xvector >=0.22.0,<0.23.0' + - 'bioconductor-biocgenerics >=0.30.0,<0.31.0' + - 'bioconductor-biostrings >=2.52.0,<2.53.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-shortread >=1.42.0,<1.43.0' + - 'bioconductor-xvector >=0.24.0,<0.25.0' - r-base - - 'r-data.table >=1.9.4' - 'r-ggplot2 >=2.1.0' - - 'r-rcpp >=0.11.2' + - 'r-rcpp >=0.12.0' - 'r-rcppparallel >=4.3.0' - 'r-reshape2 >=1.4.1' run: - - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' - - 'bioconductor-biostrings >=2.50.0,<2.51.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-shortread >=1.40.0,<1.41.0' - - 'bioconductor-xvector >=0.22.0,<0.23.0' + - 'bioconductor-biocgenerics >=0.30.0,<0.31.0' + - 'bioconductor-biostrings >=2.52.0,<2.53.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-shortread >=1.42.0,<1.43.0' + - 'bioconductor-xvector >=0.24.0,<0.25.0' - r-base - - 'r-data.table >=1.9.4' - 'r-ggplot2 >=2.1.0' - - 'r-rcpp >=0.11.2' + - 'r-rcpp >=0.12.0' - 'r-rcppparallel >=4.3.0' - 'r-reshape2 >=1.4.1' build: diff --git a/recipes/bioconductor-daglogo/meta.yaml b/recipes/bioconductor-daglogo/meta.yaml index a5775ecd8ae6c..a5c6ee001e08b 100644 --- a/recipes/bioconductor-daglogo/meta.yaml +++ b/recipes/bioconductor-daglogo/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.20.0" %} +{% set version = "1.22.0" %} {% set name = "dagLogo" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,28 +10,32 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: eb5d6fe6ff233fd79d7c1ed8fff34965 + md5: d8af40ea859ed3684e1749780be525b7 build: number: 0 rpaths: - lib/R/lib/ - lib/ noarch: generic -# Suggests: XML, BiocStyle, knitr, rmarkdown, testthat, UniProt.ws +# Suggests: XML, BiocStyle, knitr, rmarkdown, testthat requirements: host: - - 'bioconductor-biomart >=2.38.0,<2.39.0' - - 'bioconductor-biostrings >=2.50.0,<2.51.0' - - 'bioconductor-motifstack >=1.26.0,<1.27.0' + - 'bioconductor-biocgenerics >=0.30.0,<0.31.0' + - 'bioconductor-biomart >=2.40.0,<2.41.0' + - 'bioconductor-biostrings >=2.52.0,<2.53.0' + - 'bioconductor-motifstack >=1.28.0,<1.29.0' + - 'bioconductor-uniprot.ws >=2.24.0,<2.25.0' - r-base - - r-grimport + - r-grimport2 - r-pheatmap run: - - 'bioconductor-biomart >=2.38.0,<2.39.0' - - 'bioconductor-biostrings >=2.50.0,<2.51.0' - - 'bioconductor-motifstack >=1.26.0,<1.27.0' + - 'bioconductor-biocgenerics >=0.30.0,<0.31.0' + - 'bioconductor-biomart >=2.40.0,<2.41.0' + - 'bioconductor-biostrings >=2.52.0,<2.53.0' + - 'bioconductor-motifstack >=1.28.0,<1.29.0' + - 'bioconductor-uniprot.ws >=2.24.0,<2.25.0' - r-base - - r-grimport + - r-grimport2 - r-pheatmap test: commands: diff --git a/recipes/bioconductor-dama/meta.yaml b/recipes/bioconductor-dama/meta.yaml index 445853cf45c4b..adf30197a5f76 100644 --- a/recipes/bioconductor-dama/meta.yaml +++ b/recipes/bioconductor-dama/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.54.0" %} +{% set version = "1.56.0" %} {% set name = "daMA" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 51df11f7dc90a9ac4ab8f24e61584a0a + md5: 062d03b002e2ef63716ffbc7d709c9dd build: number: 0 rpaths: diff --git a/recipes/bioconductor-damirseq/meta.yaml b/recipes/bioconductor-damirseq/meta.yaml index 3b34e178f6030..8530b3c7d39c2 100644 --- a/recipes/bioconductor-damirseq/meta.yaml +++ b/recipes/bioconductor-damirseq/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.6.2" %} +{% set version = "1.8.0" %} {% set name = "DaMiRseq" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 4cd2d065024ce3981840b0bfa27d2e2e + md5: 39e1c34e6e3b181a85b1a4ed9f7324f4 build: number: 0 rpaths: @@ -20,12 +20,12 @@ build: # Suggests: BiocStyle, knitr, testthat requirements: host: - - 'bioconductor-deseq2 >=1.22.0,<1.23.0' - - 'bioconductor-edaseq >=2.16.0,<2.17.0' - - 'bioconductor-edger >=3.24.0,<3.25.0' - - 'bioconductor-limma >=3.38.0,<3.39.0' - - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' - - 'bioconductor-sva >=3.30.0,<3.31.0' + - 'bioconductor-deseq2 >=1.24.0,<1.25.0' + - 'bioconductor-edaseq >=2.18.0,<2.19.0' + - 'bioconductor-edger >=3.26.0,<3.27.0' + - 'bioconductor-limma >=3.40.0,<3.41.0' + - 'bioconductor-summarizedexperiment >=1.14.0,<1.15.0' + - 'bioconductor-sva >=3.32.0,<3.33.0' - r-arm - r-base - r-caret @@ -47,12 +47,12 @@ requirements: - r-reshape2 - r-rsnns run: - - 'bioconductor-deseq2 >=1.22.0,<1.23.0' - - 'bioconductor-edaseq >=2.16.0,<2.17.0' - - 'bioconductor-edger >=3.24.0,<3.25.0' - - 'bioconductor-limma >=3.38.0,<3.39.0' - - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' - - 'bioconductor-sva >=3.30.0,<3.31.0' + - 'bioconductor-deseq2 >=1.24.0,<1.25.0' + - 'bioconductor-edaseq >=2.18.0,<2.19.0' + - 'bioconductor-edger >=3.26.0,<3.27.0' + - 'bioconductor-limma >=3.40.0,<3.41.0' + - 'bioconductor-summarizedexperiment >=1.14.0,<1.15.0' + - 'bioconductor-sva >=3.32.0,<3.33.0' - r-arm - r-base - r-caret diff --git a/recipes/bioconductor-dapar/meta.yaml b/recipes/bioconductor-dapar/meta.yaml index c835e356923bb..1597bc7aba919 100644 --- a/recipes/bioconductor-dapar/meta.yaml +++ b/recipes/bioconductor-dapar/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.14.4" %} +{% set version = "1.16.0" %} {% set name = "DAPAR" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: cea5c0670db7ebc03f3bbcb71d918678 + md5: 50aa903d308f8f41039217f5e4a22a24 build: number: 0 rpaths: @@ -20,17 +20,17 @@ build: # Suggests: BiocGenerics, Biobase, testthat, BiocStyle requirements: host: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' - - 'bioconductor-clusterprofiler >=3.10.0,<3.11.0' - - 'bioconductor-dapardata >=1.12.0,<1.13.0' - - 'bioconductor-graph >=1.60.0,<1.61.0' - - 'bioconductor-impute >=1.56.0,<1.57.0' - - 'bioconductor-limma >=3.38.0,<3.39.0' - - 'bioconductor-msnbase >=2.8.0,<2.9.0' - - 'bioconductor-pcamethods >=1.74.0,<1.75.0' - - 'bioconductor-preprocesscore >=1.44.0,<1.45.0' - - 'bioconductor-siggenes >=1.56.0,<1.57.0' - - 'bioconductor-vsn >=3.50.0,<3.51.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' + - 'bioconductor-clusterprofiler >=3.12.0,<3.13.0' + - 'bioconductor-dapardata >=1.14.0,<1.15.0' + - 'bioconductor-graph >=1.62.0,<1.63.0' + - 'bioconductor-impute >=1.58.0,<1.59.0' + - 'bioconductor-limma >=3.40.0,<3.41.0' + - 'bioconductor-msnbase >=2.10.0,<2.11.0' + - 'bioconductor-pcamethods >=1.76.0,<1.77.0' + - 'bioconductor-preprocesscore >=1.46.0,<1.47.0' + - 'bioconductor-siggenes >=1.58.0,<1.59.0' + - 'bioconductor-vsn >=3.52.0,<3.53.0' - r-base - r-cairo - 'r-cp4p >=0.3.5' @@ -60,17 +60,17 @@ requirements: - r-tmvtnorm - r-vioplot run: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' - - 'bioconductor-clusterprofiler >=3.10.0,<3.11.0' - - 'bioconductor-dapardata >=1.12.0,<1.13.0' - - 'bioconductor-graph >=1.60.0,<1.61.0' - - 'bioconductor-impute >=1.56.0,<1.57.0' - - 'bioconductor-limma >=3.38.0,<3.39.0' - - 'bioconductor-msnbase >=2.8.0,<2.9.0' - - 'bioconductor-pcamethods >=1.74.0,<1.75.0' - - 'bioconductor-preprocesscore >=1.44.0,<1.45.0' - - 'bioconductor-siggenes >=1.56.0,<1.57.0' - - 'bioconductor-vsn >=3.50.0,<3.51.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' + - 'bioconductor-clusterprofiler >=3.12.0,<3.13.0' + - 'bioconductor-dapardata >=1.14.0,<1.15.0' + - 'bioconductor-graph >=1.62.0,<1.63.0' + - 'bioconductor-impute >=1.58.0,<1.59.0' + - 'bioconductor-limma >=3.40.0,<3.41.0' + - 'bioconductor-msnbase >=2.10.0,<2.11.0' + - 'bioconductor-pcamethods >=1.76.0,<1.77.0' + - 'bioconductor-preprocesscore >=1.46.0,<1.47.0' + - 'bioconductor-siggenes >=1.58.0,<1.59.0' + - 'bioconductor-vsn >=3.52.0,<3.53.0' - r-base - r-cairo - 'r-cp4p >=0.3.5' diff --git a/recipes/bioconductor-dapardata/meta.yaml b/recipes/bioconductor-dapardata/meta.yaml index 961cc24649b34..3bd968f4dab19 100644 --- a/recipes/bioconductor-dapardata/meta.yaml +++ b/recipes/bioconductor-dapardata/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.12.1" %} +{% set version = "1.14.0" %} {% set name = "DAPARdata" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 5db15dae7303ec5f823c84377aa5c12c + md5: 4807b95a2b0aea5cc46adb360a165383 build: number: 0 rpaths: @@ -20,14 +20,14 @@ build: # Suggests: DAPAR, Prostar requirements: host: - - 'bioconductor-msnbase >=2.8.0,<2.9.0' + - 'bioconductor-msnbase >=2.10.0,<2.11.0' - r-base - r-knitr run: - - 'bioconductor-msnbase >=2.8.0,<2.9.0' + - 'bioconductor-msnbase >=2.10.0,<2.11.0' - r-base - r-knitr - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-dapardata/post-link.sh b/recipes/bioconductor-dapardata/post-link.sh index 0e24a67331a56..6083615b41b12 100644 --- a/recipes/bioconductor-dapardata/post-link.sh +++ b/recipes/bioconductor-dapardata/post-link.sh @@ -1,11 +1,11 @@ #!/bin/bash -FN="DAPARdata_1.12.1.tar.gz" +FN="DAPARdata_1.14.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/experiment/src/contrib/DAPARdata_1.12.1.tar.gz" - "https://bioarchive.galaxyproject.org/DAPARdata_1.12.1.tar.gz" - "https://depot.galaxyproject.org/software/bioconductor-dapardata/bioconductor-dapardata_1.12.1_src_all.tar.gz" + "https://bioconductor.org/packages/3.9/data/experiment/src/contrib/DAPARdata_1.14.0.tar.gz" + "https://bioarchive.galaxyproject.org/DAPARdata_1.14.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-dapardata/bioconductor-dapardata_1.14.0_src_all.tar.gz" ) -MD5="5db15dae7303ec5f823c84377aa5c12c" +MD5="4807b95a2b0aea5cc46adb360a165383" # Use a staging area in the conda dir rather than temp dirs, both to avoid # permission issues as well as to have things downloaded in a predictable @@ -16,7 +16,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-dart/meta.yaml b/recipes/bioconductor-dart/meta.yaml index f714076b59c2e..465d3cef25617 100644 --- a/recipes/bioconductor-dart/meta.yaml +++ b/recipes/bioconductor-dart/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.30.0" %} +{% set version = "1.32.0" %} {% set name = "DART" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: a2c0ddeb30154385e9b4672c8d137fac + md5: 3e0b9ba160194b3200963009133620ba build: number: 0 rpaths: diff --git a/recipes/bioconductor-davidtiling/meta.yaml b/recipes/bioconductor-davidtiling/meta.yaml index 5b85384265c14..2150f47894fa3 100644 --- a/recipes/bioconductor-davidtiling/meta.yaml +++ b/recipes/bioconductor-davidtiling/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.22.0" %} +{% set version = "1.24.0" %} {% set name = "davidTiling" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: ace6b4becfd62c19a8b353de336d6ca6 + md5: fc322c673362b180aacb0e2f381db62c build: number: 0 rpaths: @@ -19,16 +19,16 @@ build: noarch: generic requirements: host: - - 'bioconductor-biobase >=2.42.0,<2.43.0' - - 'bioconductor-go.db >=3.7.0,<3.8.0' - - 'bioconductor-tilingarray >=1.60.0,<1.61.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' + - 'bioconductor-go.db >=3.8.0,<3.9.0' + - 'bioconductor-tilingarray >=1.62.0,<1.63.0' - r-base run: - - 'bioconductor-biobase >=2.42.0,<2.43.0' - - 'bioconductor-go.db >=3.7.0,<3.8.0' - - 'bioconductor-tilingarray >=1.60.0,<1.61.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' + - 'bioconductor-go.db >=3.8.0,<3.9.0' + - 'bioconductor-tilingarray >=1.62.0,<1.63.0' - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-davidtiling/post-link.sh b/recipes/bioconductor-davidtiling/post-link.sh index 47cec70bdc6ff..d3975a1b290f2 100644 --- a/recipes/bioconductor-davidtiling/post-link.sh +++ b/recipes/bioconductor-davidtiling/post-link.sh @@ -1,11 +1,11 @@ #!/bin/bash -FN="davidTiling_1.22.0.tar.gz" +FN="davidTiling_1.24.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/experiment/src/contrib/davidTiling_1.22.0.tar.gz" - "https://bioarchive.galaxyproject.org/davidTiling_1.22.0.tar.gz" - "https://depot.galaxyproject.org/software/bioconductor-davidtiling/bioconductor-davidtiling_1.22.0_src_all.tar.gz" + "https://bioconductor.org/packages/3.9/data/experiment/src/contrib/davidTiling_1.24.0.tar.gz" + "https://bioarchive.galaxyproject.org/davidTiling_1.24.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-davidtiling/bioconductor-davidtiling_1.24.0_src_all.tar.gz" ) -MD5="ace6b4becfd62c19a8b353de336d6ca6" +MD5="fc322c673362b180aacb0e2f381db62c" # Use a staging area in the conda dir rather than temp dirs, both to avoid # permission issues as well as to have things downloaded in a predictable @@ -16,7 +16,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-dbchip/meta.yaml b/recipes/bioconductor-dbchip/meta.yaml index 5dc0e15bdbbf6..e9ba801a9fab5 100644 --- a/recipes/bioconductor-dbchip/meta.yaml +++ b/recipes/bioconductor-dbchip/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.26.0" %} +{% set version = "1.28.0" %} {% set name = "DBChIP" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: d2ca8f6a4e640074c6de45eba4db9a50 + md5: 8a7945a976f67ca5f9a0e0416c25f485 build: number: 0 rpaths: @@ -20,12 +20,12 @@ build: # Suggests: ShortRead, BiocGenerics requirements: host: - - 'bioconductor-deseq >=1.34.0,<1.35.0' - - 'bioconductor-edger >=3.24.0,<3.25.0' + - 'bioconductor-deseq >=1.36.0,<1.37.0' + - 'bioconductor-edger >=3.26.0,<3.27.0' - r-base run: - - 'bioconductor-deseq >=1.34.0,<1.35.0' - - 'bioconductor-edger >=3.24.0,<3.25.0' + - 'bioconductor-deseq >=1.36.0,<1.37.0' + - 'bioconductor-edger >=3.26.0,<3.27.0' - r-base test: commands: diff --git a/recipes/bioconductor-dcanr/build.sh b/recipes/bioconductor-dcanr/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-dcanr/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-dcanr/meta.yaml b/recipes/bioconductor-dcanr/meta.yaml new file mode 100644 index 0000000000000..99e98ee9441d2 --- /dev/null +++ b/recipes/bioconductor-dcanr/meta.yaml @@ -0,0 +1,51 @@ +{% set version = "1.0.0" %} +{% set name = "dcanr" %} +{% set bioc = "3.9" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + md5: 3d8ea0c3dd1aec60c5f1cb87bd55cbd3 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: EBcoexpress, testthat, EBarrays, GeneNet, COSINE, mclust, minqa, SummarizedExperiment, Biobase, knitr, rmarkdown, BiocStyle, edgeR +requirements: + host: + - r-base + - r-circlize + - r-dorng + - r-foreach + - r-igraph + - r-matrix + - r-plyr + - r-rcolorbrewer + - r-reshape2 + - r-stringr + run: + - r-base + - r-circlize + - r-dorng + - r-foreach + - r-igraph + - r-matrix + - r-plyr + - r-rcolorbrewer + - r-reshape2 + - r-stringr +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: GPL-3 + summary: 'Methods and an evaluation framework for the inference of differential co-expression/association networks.' + diff --git a/recipes/bioconductor-dcgsa/meta.yaml b/recipes/bioconductor-dcgsa/meta.yaml index 849abf8bd6382..2014c89198346 100644 --- a/recipes/bioconductor-dcgsa/meta.yaml +++ b/recipes/bioconductor-dcgsa/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.10.1" %} +{% set version = "1.12.0" %} {% set name = "dcGSA" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: d2b2a3fc8f779844fb894f2613b3b74c5236807802b0fe8fac28aa44f93baaee + md5: e0657f2cdbcd15aed33108d311ffc6f6 build: number: 0 rpaths: @@ -20,11 +20,11 @@ build: # Suggests: knitr requirements: host: - - 'bioconductor-biocparallel >=1.16.0,<1.17.0' + - 'bioconductor-biocparallel >=1.18.0,<1.19.0' - r-base - r-matrix run: - - 'bioconductor-biocparallel >=1.16.0,<1.17.0' + - 'bioconductor-biocparallel >=1.18.0,<1.19.0' - r-base - r-matrix test: diff --git a/recipes/bioconductor-dchiprep/meta.yaml b/recipes/bioconductor-dchiprep/meta.yaml index 15bccd72e5ae1..0d089d8bac8db 100644 --- a/recipes/bioconductor-dchiprep/meta.yaml +++ b/recipes/bioconductor-dchiprep/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.12.0" %} +{% set version = "1.14.0" %} {% set name = "DChIPRep" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 16c51ba26b30d3f5466e7aa8676a4441 + md5: f2de5544bb683f3c476ac945450a0ac7 build: number: 0 rpaths: @@ -20,12 +20,12 @@ build: # Suggests: mgcv, testthat, BiocStyle, knitr, rmarkdown requirements: host: - - 'bioconductor-chippeakanno >=3.16.0,<3.17.0' - - 'bioconductor-deseq2 >=1.22.0,<1.23.0' - - 'bioconductor-genomicranges >=1.34.0,<1.35.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' - - 'bioconductor-soggi >=1.14.0,<1.15.0' - - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' + - 'bioconductor-chippeakanno >=3.18.0,<3.19.0' + - 'bioconductor-deseq2 >=1.24.0,<1.25.0' + - 'bioconductor-genomicranges >=1.36.0,<1.37.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' + - 'bioconductor-soggi >=1.16.0,<1.17.0' + - 'bioconductor-summarizedexperiment >=1.14.0,<1.15.0' - r-assertthat - r-base - r-fdrtool @@ -36,12 +36,12 @@ requirements: - r-smoothmest - r-tidyr run: - - 'bioconductor-chippeakanno >=3.16.0,<3.17.0' - - 'bioconductor-deseq2 >=1.22.0,<1.23.0' - - 'bioconductor-genomicranges >=1.34.0,<1.35.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' - - 'bioconductor-soggi >=1.14.0,<1.15.0' - - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' + - 'bioconductor-chippeakanno >=3.18.0,<3.19.0' + - 'bioconductor-deseq2 >=1.24.0,<1.25.0' + - 'bioconductor-genomicranges >=1.36.0,<1.37.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' + - 'bioconductor-soggi >=1.16.0,<1.17.0' + - 'bioconductor-summarizedexperiment >=1.14.0,<1.15.0' - r-assertthat - r-base - r-fdrtool diff --git a/recipes/bioconductor-ddct/meta.yaml b/recipes/bioconductor-ddct/meta.yaml index ef3042a6e5d47..dfd658c45e4be 100644 --- a/recipes/bioconductor-ddct/meta.yaml +++ b/recipes/bioconductor-ddct/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.38.0" %} +{% set version = "1.40.0" %} {% set name = "ddCt" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: a0d6affcd7f9fac5b22389a3657bba99 + md5: b211d12a2de05a10f8fa66d8449b8522 build: number: 0 rpaths: @@ -20,15 +20,15 @@ build: # Suggests: RUnit requirements: host: - - 'bioconductor-biobase >=2.42.0,<2.43.0' - - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' + - 'bioconductor-biocgenerics >=0.30.0,<0.31.0' - r-base - r-lattice - 'r-rcolorbrewer >=0.1-3' - r-xtable run: - - 'bioconductor-biobase >=2.42.0,<2.43.0' - - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' + - 'bioconductor-biocgenerics >=0.30.0,<0.31.0' - r-base - r-lattice - 'r-rcolorbrewer >=0.1-3' diff --git a/recipes/bioconductor-ddpcrclust/meta.yaml b/recipes/bioconductor-ddpcrclust/meta.yaml index d117ad01f0c49..21a2fb3dd5bdc 100644 --- a/recipes/bioconductor-ddpcrclust/meta.yaml +++ b/recipes/bioconductor-ddpcrclust/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.2.0" %} +{% set version = "1.4.0" %} {% set name = "ddPCRclust" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: cf65901cbc08efe813fa358b52244059 + md5: aab48e900fbc6ea52c57c297b0850f62 build: number: 0 rpaths: @@ -20,10 +20,10 @@ build: # Suggests: BiocStyle requirements: host: - - 'bioconductor-flowcore >=1.48.0,<1.49.0' - - 'bioconductor-flowdensity >=1.16.0,<1.17.0' - - 'bioconductor-flowpeaks >=1.28.0,<1.29.0' - - 'bioconductor-samspectral >=1.36.0,<1.37.0' + - 'bioconductor-flowcore >=1.50.0,<1.51.0' + - 'bioconductor-flowdensity >=1.18.0,<1.19.0' + - 'bioconductor-flowpeaks >=1.30.0,<1.31.0' + - 'bioconductor-samspectral >=1.38.0,<1.39.0' - r-base - r-clue - r-ggplot2 @@ -31,10 +31,10 @@ requirements: - r-plotrix - r-r.utils run: - - 'bioconductor-flowcore >=1.48.0,<1.49.0' - - 'bioconductor-flowdensity >=1.16.0,<1.17.0' - - 'bioconductor-flowpeaks >=1.28.0,<1.29.0' - - 'bioconductor-samspectral >=1.36.0,<1.37.0' + - 'bioconductor-flowcore >=1.50.0,<1.51.0' + - 'bioconductor-flowdensity >=1.18.0,<1.19.0' + - 'bioconductor-flowpeaks >=1.30.0,<1.31.0' + - 'bioconductor-samspectral >=1.38.0,<1.39.0' - r-base - r-clue - r-ggplot2 diff --git a/recipes/bioconductor-debrowser/meta.yaml b/recipes/bioconductor-debrowser/meta.yaml index c284caf6679b8..8910efdb23864 100644 --- a/recipes/bioconductor-debrowser/meta.yaml +++ b/recipes/bioconductor-debrowser/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.10.4" %} +{% set version = "1.12.0" %} {% set name = "debrowser" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: c5f863a0ba5f1df02036146e3e83fc04 + md5: 94479c5a1dcccb68dea8c894008bb2e9 build: number: 0 rpaths: @@ -20,30 +20,28 @@ build: # Suggests: testthat, rmarkdown, knitr, R.rsp requirements: host: - - 'bioconductor-annotate >=1.60.0,<1.61.0' - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' - - 'bioconductor-bayseq >=2.16.0,<2.17.0' - - 'bioconductor-clusterprofiler >=3.10.0,<3.11.0' - - 'bioconductor-deseq2 >=1.22.0,<1.23.0' - - 'bioconductor-dose >=3.8.0,<3.9.0' - - 'bioconductor-edger >=3.24.0,<3.25.0' - - 'bioconductor-enrichplot >=1.2.0,<1.3.0' - - 'bioconductor-genomicranges >=1.34.0,<1.35.0' - - 'bioconductor-harman >=1.10.0,<1.11.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-limma >=3.38.0,<3.39.0' - - 'bioconductor-org.hs.eg.db >=3.7.0,<3.8.0' - - 'bioconductor-org.mm.eg.db >=3.7.0,<3.8.0' - - 'bioconductor-pathview >=1.22.0,<1.23.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' - - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' - - 'bioconductor-sva >=3.30.0,<3.31.0' + - 'bioconductor-annotate >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' + - 'bioconductor-clusterprofiler >=3.12.0,<3.13.0' + - 'bioconductor-deseq2 >=1.24.0,<1.25.0' + - 'bioconductor-dose >=3.10.0,<3.11.0' + - 'bioconductor-edger >=3.26.0,<3.27.0' + - 'bioconductor-enrichplot >=1.4.0,<1.5.0' + - 'bioconductor-genomicranges >=1.36.0,<1.37.0' + - 'bioconductor-harman >=1.12.0,<1.13.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-limma >=3.40.0,<3.41.0' + - 'bioconductor-org.hs.eg.db >=3.8.0,<3.9.0' + - 'bioconductor-org.mm.eg.db >=3.8.0,<3.9.0' + - 'bioconductor-pathview >=1.24.0,<1.25.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' + - 'bioconductor-summarizedexperiment >=1.14.0,<1.15.0' + - 'bioconductor-sva >=3.32.0,<3.33.0' - r-base - r-colourpicker - r-d3heatmap - r-dt - r-ggplot2 - - r-googleauthr - r-gplots - r-heatmaply - r-igraph @@ -57,32 +55,29 @@ requirements: - r-shinydashboard - r-shinyjs - r-stringi - - r-v8 run: - - 'bioconductor-annotate >=1.60.0,<1.61.0' - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' - - 'bioconductor-bayseq >=2.16.0,<2.17.0' - - 'bioconductor-clusterprofiler >=3.10.0,<3.11.0' - - 'bioconductor-deseq2 >=1.22.0,<1.23.0' - - 'bioconductor-dose >=3.8.0,<3.9.0' - - 'bioconductor-edger >=3.24.0,<3.25.0' - - 'bioconductor-enrichplot >=1.2.0,<1.3.0' - - 'bioconductor-genomicranges >=1.34.0,<1.35.0' - - 'bioconductor-harman >=1.10.0,<1.11.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-limma >=3.38.0,<3.39.0' - - 'bioconductor-org.hs.eg.db >=3.7.0,<3.8.0' - - 'bioconductor-org.mm.eg.db >=3.7.0,<3.8.0' - - 'bioconductor-pathview >=1.22.0,<1.23.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' - - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' - - 'bioconductor-sva >=3.30.0,<3.31.0' + - 'bioconductor-annotate >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' + - 'bioconductor-clusterprofiler >=3.12.0,<3.13.0' + - 'bioconductor-deseq2 >=1.24.0,<1.25.0' + - 'bioconductor-dose >=3.10.0,<3.11.0' + - 'bioconductor-edger >=3.26.0,<3.27.0' + - 'bioconductor-enrichplot >=1.4.0,<1.5.0' + - 'bioconductor-genomicranges >=1.36.0,<1.37.0' + - 'bioconductor-harman >=1.12.0,<1.13.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-limma >=3.40.0,<3.41.0' + - 'bioconductor-org.hs.eg.db >=3.8.0,<3.9.0' + - 'bioconductor-org.mm.eg.db >=3.8.0,<3.9.0' + - 'bioconductor-pathview >=1.24.0,<1.25.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' + - 'bioconductor-summarizedexperiment >=1.14.0,<1.15.0' + - 'bioconductor-sva >=3.32.0,<3.33.0' - r-base - r-colourpicker - r-d3heatmap - r-dt - r-ggplot2 - - r-googleauthr - r-gplots - r-heatmaply - r-igraph @@ -96,7 +91,6 @@ requirements: - r-shinydashboard - r-shinyjs - r-stringi - - r-v8 test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-decipher/meta.yaml b/recipes/bioconductor-decipher/meta.yaml index 0f79433aa2080..4bd3f029dabd5 100644 --- a/recipes/bioconductor-decipher/meta.yaml +++ b/recipes/bioconductor-decipher/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "2.10.0" %} +{% set version = "2.12.0" %} {% set name = "DECIPHER" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: c3d5e6617b7bcfae06453241cf97d1a2 + md5: 0bcfc1d4493c22bc9287d6b4525a6f73 build: number: 0 rpaths: @@ -18,18 +18,18 @@ build: - lib/ requirements: host: - - 'bioconductor-biostrings >=2.50.0,<2.51.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' - - 'bioconductor-xvector >=0.22.0,<0.23.0' + - 'bioconductor-biostrings >=2.52.0,<2.53.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' + - 'bioconductor-xvector >=0.24.0,<0.25.0' - r-base - r-dbi - 'r-rsqlite >=1.1' run: - - 'bioconductor-biostrings >=2.50.0,<2.51.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' - - 'bioconductor-xvector >=0.22.0,<0.23.0' + - 'bioconductor-biostrings >=2.52.0,<2.53.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' + - 'bioconductor-xvector >=0.24.0,<0.25.0' - r-base - r-dbi - 'r-rsqlite >=1.1' diff --git a/recipes/bioconductor-deco/build.sh b/recipes/bioconductor-deco/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-deco/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-deco/meta.yaml b/recipes/bioconductor-deco/meta.yaml new file mode 100644 index 0000000000000..372e321257e0a --- /dev/null +++ b/recipes/bioconductor-deco/meta.yaml @@ -0,0 +1,71 @@ +{% set version = "1.0.0" %} +{% set name = "deco" %} +{% set bioc = "3.9" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + md5: c0f8d851c4d54bbb75d233024b60c2e5 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: knitr, curatedTCGAData, MultiAssayExperiment, Homo.sapiens +requirements: + host: + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' + - 'bioconductor-biocparallel >=1.18.0,<1.19.0' + - 'bioconductor-biocstyle >=2.12.0,<2.13.0' + - 'bioconductor-limma >=3.40.0,<3.41.0' + - 'bioconductor-made4 >=1.58.0,<1.59.0' + - 'bioconductor-summarizedexperiment >=1.14.0,<1.15.0' + - r-ade4 + - r-base + - r-cluster + - r-foreign + - r-gdata + - r-ggplot2 + - r-gplots + - r-gridextra + - r-locfit + - r-rcolorbrewer + - r-reshape2 + - r-scatterplot3d + - r-sfsmisc + run: + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' + - 'bioconductor-biocparallel >=1.18.0,<1.19.0' + - 'bioconductor-biocstyle >=2.12.0,<2.13.0' + - 'bioconductor-limma >=3.40.0,<3.41.0' + - 'bioconductor-made4 >=1.58.0,<1.59.0' + - 'bioconductor-summarizedexperiment >=1.14.0,<1.15.0' + - r-ade4 + - r-base + - r-cluster + - r-foreign + - r-gdata + - r-ggplot2 + - r-gplots + - r-gridextra + - r-locfit + - r-rcolorbrewer + - r-reshape2 + - r-scatterplot3d + - r-sfsmisc +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: 'GPL (>=3)' + summary: 'This package discovers differential features in hetero- and homogeneous omic data by a two-step method including subsampling LIMMA and NSCA. DECO reveals feature associations to hidden subclasses not exclusively related to higher deregulation levels.' + diff --git a/recipes/bioconductor-decomplexdisease/meta.yaml b/recipes/bioconductor-decomplexdisease/meta.yaml index 97b0f5826df0c..36773ac6904a8 100644 --- a/recipes/bioconductor-decomplexdisease/meta.yaml +++ b/recipes/bioconductor-decomplexdisease/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.2.0" %} +{% set version = "1.4.0" %} {% set name = "DEComplexDisease" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 8939bc37f0e9520bb74d734800f681d7 + md5: 513c04ff3be9a08ec70f54c148c44879 build: number: 0 rpaths: @@ -19,19 +19,19 @@ build: # Suggests: knitr requirements: host: - - 'bioconductor-biocparallel >=1.16.0,<1.17.0' - - 'bioconductor-complexheatmap >=1.20.0,<1.21.0' - - 'bioconductor-deseq2 >=1.22.0,<1.23.0' - - 'bioconductor-edger >=3.24.0,<3.25.0' - - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' + - 'bioconductor-biocparallel >=1.18.0,<1.19.0' + - 'bioconductor-complexheatmap >=2.0.0,<2.1.0' + - 'bioconductor-deseq2 >=1.24.0,<1.25.0' + - 'bioconductor-edger >=3.26.0,<3.27.0' + - 'bioconductor-summarizedexperiment >=1.14.0,<1.15.0' - r-base - 'r-rcpp >=0.12.7' run: - - 'bioconductor-biocparallel >=1.16.0,<1.17.0' - - 'bioconductor-complexheatmap >=1.20.0,<1.21.0' - - 'bioconductor-deseq2 >=1.22.0,<1.23.0' - - 'bioconductor-edger >=3.24.0,<3.25.0' - - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' + - 'bioconductor-biocparallel >=1.18.0,<1.19.0' + - 'bioconductor-complexheatmap >=2.0.0,<2.1.0' + - 'bioconductor-deseq2 >=1.24.0,<1.25.0' + - 'bioconductor-edger >=3.26.0,<3.27.0' + - 'bioconductor-summarizedexperiment >=1.14.0,<1.15.0' - r-base - 'r-rcpp >=0.12.7' build: diff --git a/recipes/bioconductor-decomptumor2sig/build.sh b/recipes/bioconductor-decomptumor2sig/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-decomptumor2sig/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-decomptumor2sig/meta.yaml b/recipes/bioconductor-decomptumor2sig/meta.yaml new file mode 100644 index 0000000000000..b42a2b825ed2a --- /dev/null +++ b/recipes/bioconductor-decomptumor2sig/meta.yaml @@ -0,0 +1,67 @@ +{% set version = "2.0.0" %} +{% set name = "decompTumor2Sig" %} +{% set bioc = "3.9" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: a1ad320d7db408fc59c16dfc97b0578d +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: knitr, rmarkdown, BiocStyle +requirements: + host: + - 'bioconductor-biocgenerics >=0.30.0,<0.31.0' + - 'bioconductor-biostrings >=2.52.0,<2.53.0' + - 'bioconductor-bsgenome.hsapiens.ucsc.hg19 >=1.4.0,<1.5.0' + - 'bioconductor-genomicfeatures >=1.36.0,<1.37.0' + - 'bioconductor-genomicranges >=1.36.0,<1.37.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' + - 'bioconductor-summarizedexperiment >=1.14.0,<1.15.0' + - 'bioconductor-txdb.hsapiens.ucsc.hg19.knowngene >=3.2.0,<3.3.0' + - 'bioconductor-variantannotation >=1.30.0,<1.31.0' + - r-base + - r-data.table + - r-ggplot2 + - r-ggseqlogo + - r-gridextra + - r-matrix + - r-plyr + - 'r-quadprog >=1.5-5' + - r-vcfr + run: + - 'bioconductor-biocgenerics >=0.30.0,<0.31.0' + - 'bioconductor-biostrings >=2.52.0,<2.53.0' + - 'bioconductor-bsgenome.hsapiens.ucsc.hg19 >=1.4.0,<1.5.0' + - 'bioconductor-genomicfeatures >=1.36.0,<1.37.0' + - 'bioconductor-genomicranges >=1.36.0,<1.37.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' + - 'bioconductor-summarizedexperiment >=1.14.0,<1.15.0' + - 'bioconductor-txdb.hsapiens.ucsc.hg19.knowngene >=3.2.0,<3.3.0' + - 'bioconductor-variantannotation >=1.30.0,<1.31.0' + - r-base + - r-data.table + - r-ggplot2 + - r-ggseqlogo + - r-gridextra + - r-matrix + - r-plyr + - 'r-quadprog >=1.5-5' + - r-vcfr +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: GPL-2 + summary: 'Uses quadratic programming for signature refitting, i.e., to decompose the mutation catalog from an individual tumor sample into a set of given mutational signatures (either Alexandrov-model signatures or Shiraishi-model signatures), computing weights that reflect the contributions of the signatures to the mutation load of the tumor.' + diff --git a/recipes/bioconductor-deconrnaseq/meta.yaml b/recipes/bioconductor-deconrnaseq/meta.yaml index 9837c2c33b127..abf86ebd6d110 100644 --- a/recipes/bioconductor-deconrnaseq/meta.yaml +++ b/recipes/bioconductor-deconrnaseq/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.24.0" %} +{% set version = "1.26.0" %} {% set name = "DeconRNASeq" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,21 +10,21 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 22cb44d707c7ce74ce46d782949aaad7 + md5: e5ef95e4fa67c3af0692a3fc2fbd4f64 build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ noarch: generic requirements: host: - - 'bioconductor-pcamethods >=1.74.0,<1.75.0' + - 'bioconductor-pcamethods >=1.76.0,<1.77.0' - r-base - r-ggplot2 - r-limsolve run: - - 'bioconductor-pcamethods >=1.74.0,<1.75.0' + - 'bioconductor-pcamethods >=1.76.0,<1.77.0' - r-base - r-ggplot2 - r-limsolve diff --git a/recipes/bioconductor-decontam/meta.yaml b/recipes/bioconductor-decontam/meta.yaml index e677be3b50cf4..f30a5ca4d924f 100644 --- a/recipes/bioconductor-decontam/meta.yaml +++ b/recipes/bioconductor-decontam/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.2.1" %} +{% set version = "1.4.0" %} {% set name = "decontam" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 9ff6703e6bc65320f3eeffb89ef3a097 + md5: ac1669c915a51167c800d83b008ad20c build: number: 0 rpaths: diff --git a/recipes/bioconductor-deds/meta.yaml b/recipes/bioconductor-deds/meta.yaml index 4db0b653381f3..9225e3e3ab3a9 100644 --- a/recipes/bioconductor-deds/meta.yaml +++ b/recipes/bioconductor-deds/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.56.0" %} +{% set version = "1.58.0" %} {% set name = "DEDS" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 520ca60c57d58412dd6eaede77dcd215 + md5: 7ac7e8cf17dab9cd14df45cd2beb9fe8 build: number: 0 rpaths: diff --git a/recipes/bioconductor-deepbluer/meta.yaml b/recipes/bioconductor-deepbluer/meta.yaml index 38caee386f537..e79fcbc24dcb0 100644 --- a/recipes/bioconductor-deepbluer/meta.yaml +++ b/recipes/bioconductor-deepbluer/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.8.0" %} +{% set version = "1.10.0" %} {% set name = "DeepBlueR" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 34d71a046cc37a278f8f36fc41358513 + md5: 40b7e1b2d6736d0ce796bfad122568c4 build: number: 0 rpaths: @@ -20,9 +20,9 @@ build: # Suggests: knitr, rmarkdown, LOLA, Gviz, gplots, ggplot2, tidyr, RColorBrewer, matrixStats requirements: host: - - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' - - 'bioconductor-genomicranges >=1.34.0,<1.35.0' - - 'bioconductor-rtracklayer >=1.42.0,<1.43.0' + - 'bioconductor-genomeinfodb >=1.20.0,<1.21.0' + - 'bioconductor-genomicranges >=1.36.0,<1.37.0' + - 'bioconductor-rtracklayer >=1.44.0,<1.45.0' - r-base - r-data.table - r-diffr @@ -37,9 +37,9 @@ requirements: - r-withr - r-xml run: - - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' - - 'bioconductor-genomicranges >=1.34.0,<1.35.0' - - 'bioconductor-rtracklayer >=1.42.0,<1.43.0' + - 'bioconductor-genomeinfodb >=1.20.0,<1.21.0' + - 'bioconductor-genomicranges >=1.36.0,<1.37.0' + - 'bioconductor-rtracklayer >=1.44.0,<1.45.0' - r-base - r-data.table - r-diffr diff --git a/recipes/bioconductor-deepsnv/meta.yaml b/recipes/bioconductor-deepsnv/meta.yaml index 265c7ecba8b96..530ec7980cfe3 100644 --- a/recipes/bioconductor-deepsnv/meta.yaml +++ b/recipes/bioconductor-deepsnv/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.28.0" %} +{% set version = "1.30.0" %} {% set name = "deepSNV" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: e75cbb2a6a32b486dd4f525de48d8f40 + md5: 2547a2cad930d74948b182b285df1c07 build: number: 0 rpaths: @@ -19,21 +19,21 @@ build: # Suggests: RColorBrewer, knitr, rmarkdown requirements: host: - - 'bioconductor-biostrings >=2.50.0,<2.51.0' - - 'bioconductor-genomicranges >=1.34.0,<1.35.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-rhtslib >=1.14.0,<1.15.0' - - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' - - 'bioconductor-variantannotation >=1.28.0,<1.29.0' + - 'bioconductor-biostrings >=2.52.0,<2.53.0' + - 'bioconductor-genomicranges >=1.36.0,<1.37.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-rhtslib >=1.16.0,<1.17.0' + - 'bioconductor-summarizedexperiment >=1.14.0,<1.15.0' + - 'bioconductor-variantannotation >=1.30.0,<1.31.0' - r-base - r-vgam run: - - 'bioconductor-biostrings >=2.50.0,<2.51.0' - - 'bioconductor-genomicranges >=1.34.0,<1.35.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-rhtslib >=1.14.0,<1.15.0' - - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' - - 'bioconductor-variantannotation >=1.28.0,<1.29.0' + - 'bioconductor-biostrings >=2.52.0,<2.53.0' + - 'bioconductor-genomicranges >=1.36.0,<1.37.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-rhtslib >=1.16.0,<1.17.0' + - 'bioconductor-summarizedexperiment >=1.14.0,<1.15.0' + - 'bioconductor-variantannotation >=1.30.0,<1.31.0' - r-base - r-vgam build: diff --git a/recipes/bioconductor-deformats/meta.yaml b/recipes/bioconductor-deformats/meta.yaml index 0f83c2135e75d..46b2862b76fe0 100644 --- a/recipes/bioconductor-deformats/meta.yaml +++ b/recipes/bioconductor-deformats/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.10.0" %} +{% set version = "1.12.0" %} {% set name = "DEFormats" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 69f526fa202b52de33804e15791a1243 + md5: 5d280ee04668d89bdf8065b18451f7aa build: number: 0 rpaths: @@ -20,20 +20,20 @@ build: # Suggests: BiocStyle (>= 1.8.0), knitr, rmarkdown, testthat requirements: host: - - 'bioconductor-deseq2 >=1.22.0,<1.23.0' - - 'bioconductor-edger >=3.24.0,<3.25.0' - - 'bioconductor-genomicranges >=1.34.0,<1.35.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' - - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' + - 'bioconductor-deseq2 >=1.24.0,<1.25.0' + - 'bioconductor-edger >=3.26.0,<3.27.0' + - 'bioconductor-genomicranges >=1.36.0,<1.37.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' + - 'bioconductor-summarizedexperiment >=1.14.0,<1.15.0' - r-base - r-checkmate - r-data.table run: - - 'bioconductor-deseq2 >=1.22.0,<1.23.0' - - 'bioconductor-edger >=3.24.0,<3.25.0' - - 'bioconductor-genomicranges >=1.34.0,<1.35.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' - - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' + - 'bioconductor-deseq2 >=1.24.0,<1.25.0' + - 'bioconductor-edger >=3.26.0,<3.27.0' + - 'bioconductor-genomicranges >=1.36.0,<1.37.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' + - 'bioconductor-summarizedexperiment >=1.14.0,<1.15.0' - r-base - r-checkmate - r-data.table diff --git a/recipes/bioconductor-degraph/meta.yaml b/recipes/bioconductor-degraph/meta.yaml index a1e3bb072aff1..e19fefe66c90d 100644 --- a/recipes/bioconductor-degraph/meta.yaml +++ b/recipes/bioconductor-degraph/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.34.0" %} +{% set version = "1.36.0" %} {% set name = "DEGraph" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 51a9e855c83c270117e9cd3ed052d86e + md5: 29e1cfa7fe5e9ea44f6ac99e847e9fde build: number: 0 rpaths: @@ -20,11 +20,11 @@ build: # Suggests: corpcor, fields, graph, KEGGgraph, lattice, marray, RBGL, rrcov, Rgraphviz, NCIgraph requirements: host: - - 'bioconductor-graph >=1.60.0,<1.61.0' - - 'bioconductor-kegggraph >=1.42.0,<1.43.0' - - 'bioconductor-ncigraph >=1.30.0,<1.31.0' - - 'bioconductor-rbgl >=1.58.0,<1.59.0' - - 'bioconductor-rgraphviz >=2.26.0,<2.27.0' + - 'bioconductor-graph >=1.62.0,<1.63.0' + - 'bioconductor-kegggraph >=1.44.0,<1.45.0' + - 'bioconductor-ncigraph >=1.32.0,<1.33.0' + - 'bioconductor-rbgl >=1.60.0,<1.61.0' + - 'bioconductor-rgraphviz >=2.28.0,<2.29.0' - r-base - r-lattice - r-mvtnorm @@ -32,11 +32,11 @@ requirements: - r-r.utils - r-rrcov run: - - 'bioconductor-graph >=1.60.0,<1.61.0' - - 'bioconductor-kegggraph >=1.42.0,<1.43.0' - - 'bioconductor-ncigraph >=1.30.0,<1.31.0' - - 'bioconductor-rbgl >=1.58.0,<1.59.0' - - 'bioconductor-rgraphviz >=2.26.0,<2.27.0' + - 'bioconductor-graph >=1.62.0,<1.63.0' + - 'bioconductor-kegggraph >=1.44.0,<1.45.0' + - 'bioconductor-ncigraph >=1.32.0,<1.33.0' + - 'bioconductor-rbgl >=1.60.0,<1.61.0' + - 'bioconductor-rgraphviz >=2.28.0,<2.29.0' - r-base - r-lattice - r-mvtnorm diff --git a/recipes/bioconductor-degreport/meta.yaml b/recipes/bioconductor-degreport/meta.yaml index f6bc2ac51274b..07ca4aa9622f3 100644 --- a/recipes/bioconductor-degreport/meta.yaml +++ b/recipes/bioconductor-degreport/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.19.1" %} +{% set version = "1.20.0" %} {% set name = "DEGreport" %} -{% set bioc = "devel" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,24 +10,24 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: c30386fc78d062e49c22fa0845c93871affa9289281169c5e42a0f958c875de7 + md5: d46192672effa5839311e532c523465f build: number: 0 rpaths: - lib/R/lib/ - lib/ noarch: generic -# Suggests: BiocStyle, AnnotationDbi, limma, pheatmap, knitr, rmarkdown, statmod, testthat +# Suggests: BiocStyle, AnnotationDbi, limma, pheatmap, rmarkdown, statmod, testthat requirements: host: - - bioconductor-biobase - - bioconductor-biocgenerics - - bioconductor-complexheatmap - - bioconductor-consensusclusterplus - - bioconductor-deseq2 - - bioconductor-edger - - bioconductor-s4vectors - - bioconductor-summarizedexperiment + - 'bioconductor-biobase >=2.44.0,<2.45.0' + - 'bioconductor-biocgenerics >=0.30.0,<0.31.0' + - 'bioconductor-complexheatmap >=2.0.0,<2.1.0' + - 'bioconductor-consensusclusterplus >=1.48.0,<1.49.0' + - 'bioconductor-deseq2 >=1.24.0,<1.25.0' + - 'bioconductor-edger >=3.26.0,<3.27.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' + - 'bioconductor-summarizedexperiment >=1.14.0,<1.15.0' - r-base - r-broom - r-circlize @@ -51,14 +51,14 @@ requirements: - r-tibble - r-tidyr run: - - bioconductor-biobase - - bioconductor-biocgenerics - - bioconductor-complexheatmap - - bioconductor-consensusclusterplus - - bioconductor-deseq2 - - bioconductor-edger - - bioconductor-s4vectors - - bioconductor-summarizedexperiment + - 'bioconductor-biobase >=2.44.0,<2.45.0' + - 'bioconductor-biocgenerics >=0.30.0,<0.31.0' + - 'bioconductor-complexheatmap >=2.0.0,<2.1.0' + - 'bioconductor-consensusclusterplus >=1.48.0,<1.49.0' + - 'bioconductor-deseq2 >=1.24.0,<1.25.0' + - 'bioconductor-edger >=3.26.0,<3.27.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' + - 'bioconductor-summarizedexperiment >=1.14.0,<1.15.0' - r-base - r-broom - r-circlize diff --git a/recipes/bioconductor-degseq/meta.yaml b/recipes/bioconductor-degseq/meta.yaml index e4a46d257fa10..c1689dd952da9 100644 --- a/recipes/bioconductor-degseq/meta.yaml +++ b/recipes/bioconductor-degseq/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.36.1" %} +{% set version = "1.38.0" %} {% set name = "DEGseq" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: b8923f545fdf7ddeece5e9abd038cc00 + md5: 6c69744cb13c43d7a0d91bb0b045c5b0 build: number: 0 rpaths: @@ -18,10 +18,10 @@ build: - lib/ requirements: host: - - 'bioconductor-qvalue >=2.14.0,<2.15.0' + - 'bioconductor-qvalue >=2.16.0,<2.17.0' - r-base run: - - 'bioconductor-qvalue >=2.14.0,<2.15.0' + - 'bioconductor-qvalue >=2.16.0,<2.17.0' - r-base build: - {{ compiler('c') }} diff --git a/recipes/bioconductor-delayedarray/meta.yaml b/recipes/bioconductor-delayedarray/meta.yaml index a5627fc94e3e9..c0c909bcb8637 100644 --- a/recipes/bioconductor-delayedarray/meta.yaml +++ b/recipes/bioconductor-delayedarray/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "0.8.0" %} +{% set version = "0.10.0" %} {% set name = "DelayedArray" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: f8365083bd320d946db08c9aa34c335c + md5: 7ae9f998c8c10a0807dd4fc56c6c90c9 build: number: 0 rpaths: @@ -19,18 +19,20 @@ build: # Suggests: Matrix, HDF5Array, genefilter, SummarizedExperiment, airway, pryr, DelayedMatrixStats, knitr, BiocStyle, RUnit requirements: host: - - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' - - 'bioconductor-biocparallel >=1.16.0,<1.17.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-biocgenerics >=0.30.0,<0.31.0' + - 'bioconductor-biocparallel >=1.18.0,<1.19.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' - r-base + - r-matrix - r-matrixstats run: - - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' - - 'bioconductor-biocparallel >=1.16.0,<1.17.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-biocgenerics >=0.30.0,<0.31.0' + - 'bioconductor-biocparallel >=1.18.0,<1.19.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' - r-base + - r-matrix - r-matrixstats build: - {{ compiler('c') }} diff --git a/recipes/bioconductor-delayeddataframe/build.sh b/recipes/bioconductor-delayeddataframe/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-delayeddataframe/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-delayeddataframe/meta.yaml b/recipes/bioconductor-delayeddataframe/meta.yaml new file mode 100644 index 0000000000000..6fd9db6831f09 --- /dev/null +++ b/recipes/bioconductor-delayeddataframe/meta.yaml @@ -0,0 +1,39 @@ +{% set version = "1.0.0" %} +{% set name = "DelayedDataFrame" %} +{% set bioc = "3.9" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: 60d192f4f76c29989e1feb0e47d23660 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: testthat, knitr, rmarkdown, SeqArray, GDSArray +requirements: + host: + - 'bioconductor-biocgenerics >=0.30.0,<0.31.0' + - 'bioconductor-delayedarray >=0.10.0,<0.11.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' + - r-base + run: + - 'bioconductor-biocgenerics >=0.30.0,<0.31.0' + - 'bioconductor-delayedarray >=0.10.0,<0.11.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' + - r-base +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: GPL-3 + summary: 'Based on the standard DataFrame metaphor, we are trying to implement the feature of delayed operation on the DelayedDataFrame, with a slot of lazyIndex, which saves the mapping indexes for each column of DelayedDataFrame. Methods like show, validity check, [/[[ subsetting, rbind/cbind are implemented for DelayedDataFrame to be operated around lazyIndex. The listData slot stays untouched until a realization call e.g., DataFrame constructor OR as.list() is invoked.' + diff --git a/recipes/bioconductor-delayedmatrixstats/meta.yaml b/recipes/bioconductor-delayedmatrixstats/meta.yaml index b8f82b9e3679e..07227e0f29344 100644 --- a/recipes/bioconductor-delayedmatrixstats/meta.yaml +++ b/recipes/bioconductor-delayedmatrixstats/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.4.0" %} +{% set version = "1.6.0" %} {% set name = "DelayedMatrixStats" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,9 +10,9 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 7393b93bd0df9dfc1964e1d05f3e474b + md5: 9e0435b260c7b5e1d7608a7214ae93f8 build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ @@ -20,20 +20,20 @@ build: # Suggests: testthat, knitr, rmarkdown, covr, BiocStyle, microbenchmark, profmem requirements: host: - - 'bioconductor-biocparallel >=1.16.0,<1.17.0' - - 'bioconductor-delayedarray >=0.8.0,<0.9.0' - - 'bioconductor-hdf5array >=1.10.0,<1.11.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-biocparallel >=1.18.0,<1.19.0' + - 'bioconductor-delayedarray >=0.10.0,<0.11.0' + - 'bioconductor-hdf5array >=1.12.0,<1.13.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' - r-base - r-matrix - 'r-matrixstats >=0.53.1' run: - - 'bioconductor-biocparallel >=1.16.0,<1.17.0' - - 'bioconductor-delayedarray >=0.8.0,<0.9.0' - - 'bioconductor-hdf5array >=1.10.0,<1.11.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-biocparallel >=1.18.0,<1.19.0' + - 'bioconductor-delayedarray >=0.10.0,<0.11.0' + - 'bioconductor-hdf5array >=1.12.0,<1.13.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' - r-base - r-matrix - 'r-matrixstats >=0.53.1' diff --git a/recipes/bioconductor-deltagseg/meta.yaml b/recipes/bioconductor-deltagseg/meta.yaml index ccc5e6859ded3..07e17322be6e3 100644 --- a/recipes/bioconductor-deltagseg/meta.yaml +++ b/recipes/bioconductor-deltagseg/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.22.0" %} +{% set version = "1.24.0" %} {% set name = "deltaGseg" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: fa281178cf227dc36cbc08c12954a7cb + md5: 05b04ca791d4530c8edd16df31f2a2c4 build: number: 0 rpaths: diff --git a/recipes/bioconductor-demand/meta.yaml b/recipes/bioconductor-demand/meta.yaml index 4ed10bb08cc15..90000a6f4ff4e 100644 --- a/recipes/bioconductor-demand/meta.yaml +++ b/recipes/bioconductor-demand/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.12.0" %} +{% set version = "1.14.0" %} {% set name = "DeMAND" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 7407289aa62fd7f774451b158ee89d6d + md5: 2dbb15daf66fb5efe935fee33d49fd7b build: number: 0 rpaths: diff --git a/recipes/bioconductor-demixt/build.sh b/recipes/bioconductor-demixt/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-demixt/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-demixt/meta.yaml b/recipes/bioconductor-demixt/meta.yaml new file mode 100644 index 0000000000000..781f08a78564a --- /dev/null +++ b/recipes/bioconductor-demixt/meta.yaml @@ -0,0 +1,42 @@ +{% set version = "1.0.0" %} +{% set name = "DeMixT" %} +{% set bioc = "3.9" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: 4799674f409a64b478d86eda7f08ec26 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ +requirements: + host: + - 'bioconductor-summarizedexperiment >=1.14.0,<1.15.0' + - r-base + - r-kernsmooth + - r-knitr + - r-matrixstats + run: + - 'bioconductor-summarizedexperiment >=1.14.0,<1.15.0' + - r-base + - r-kernsmooth + - r-knitr + - r-matrixstats + build: + - {{ compiler('c') }} + - make +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: GPL-3 + summary: 'DeMixT is a software package that performs deconvolution on transcriptome data from a mixture of two or three components.' + diff --git a/recipes/bioconductor-dep/meta.yaml b/recipes/bioconductor-dep/meta.yaml index 43132170452c7..65ea28f13ca34 100644 --- a/recipes/bioconductor-dep/meta.yaml +++ b/recipes/bioconductor-dep/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.4.0" %} +{% set version = "1.6.0" %} {% set name = "DEP" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://{{ name|lower }}ot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: ea171465a54d5eadb6474de86bacf5cd + md5: e28b75342a72f73f471ecd755df87539 build: number: 0 rpaths: @@ -20,11 +20,11 @@ build: # Suggests: testthat, enrichR, knitr, BiocStyle requirements: host: - - 'bioconductor-complexheatmap >=1.20.0,<1.21.0' - - 'bioconductor-limma >=3.38.0,<3.39.0' - - 'bioconductor-msnbase >=2.8.0,<2.9.0' - - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' - - 'bioconductor-vsn >=3.50.0,<3.51.0' + - 'bioconductor-complexheatmap >=2.0.0,<2.1.0' + - 'bioconductor-limma >=3.40.0,<3.41.0' + - 'bioconductor-msnbase >=2.10.0,<2.11.0' + - 'bioconductor-summarizedexperiment >=1.14.0,<1.15.0' + - 'bioconductor-vsn >=3.52.0,<3.53.0' - r-assertthat - r-base - r-circlize @@ -45,11 +45,11 @@ requirements: - r-tibble - r-tidyr run: - - 'bioconductor-complexheatmap >=1.20.0,<1.21.0' - - 'bioconductor-limma >=3.38.0,<3.39.0' - - 'bioconductor-msnbase >=2.8.0,<2.9.0' - - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' - - 'bioconductor-vsn >=3.50.0,<3.51.0' + - 'bioconductor-complexheatmap >=2.0.0,<2.1.0' + - 'bioconductor-limma >=3.40.0,<3.41.0' + - 'bioconductor-msnbase >=2.10.0,<2.11.0' + - 'bioconductor-summarizedexperiment >=1.14.0,<1.15.0' + - 'bioconductor-vsn >=3.52.0,<3.53.0' - r-assertthat - r-base - r-circlize diff --git a/recipes/bioconductor-depecher/build.sh b/recipes/bioconductor-depecher/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-depecher/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-depecher/meta.yaml b/recipes/bioconductor-depecher/meta.yaml new file mode 100644 index 0000000000000..10a234aa6cd49 --- /dev/null +++ b/recipes/bioconductor-depecher/meta.yaml @@ -0,0 +1,66 @@ +{% set version = "1.0.0" %} +{% set name = "DepecheR" %} +{% set bioc = "3.9" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: 40ab211d17a4e171dc6605b97f060268 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ +# Suggests: Rtsne, testthat, knitr, rmarkdown, BiocStyle +requirements: + host: + - 'bioconductor-biocparallel >=1.18.0,<1.19.0' + - 'bioconductor-mixomics >=6.8.0,<6.9.0' + - r-base + - 'r-beanplot >=1.2' + - 'r-dosnow >=1.0.16' + - 'r-dplyr >=0.7.8' + - 'r-foreach >=1.4.4' + - 'r-ggplot2 >=3.1.0' + - 'r-gplots >=3.0.1' + - 'r-mass >=7.3.51' + - 'r-matrixstats >=0.54.0' + - 'r-moments >=0.14' + - 'r-rcpp >=1.0.0' + - r-rcppeigen + - 'r-reshape2 >=1.4.3' + - 'r-viridis >=0.5.1' + run: + - 'bioconductor-biocparallel >=1.18.0,<1.19.0' + - 'bioconductor-mixomics >=6.8.0,<6.9.0' + - r-base + - 'r-beanplot >=1.2' + - 'r-dosnow >=1.0.16' + - 'r-dplyr >=0.7.8' + - 'r-foreach >=1.4.4' + - 'r-ggplot2 >=3.1.0' + - 'r-gplots >=3.0.1' + - 'r-mass >=7.3.51' + - 'r-matrixstats >=0.54.0' + - 'r-moments >=0.14' + - 'r-rcpp >=1.0.0' + - r-rcppeigen + - 'r-reshape2 >=1.4.3' + - 'r-viridis >=0.5.1' + build: + - {{ compiler('c') }} + - {{ compiler('cxx') }} + - make +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: 'MIT + file LICENSE' + summary: 'The purpose of this package is to identify traits in a dataset that can separate groups. This is done on two levels. First, clustering is performed, using an implementation of sparse K-means. Secondly, the generated clusters are used to predict outcomes of groups of individuals based on their distribution of observations in the different clusters. As certain clusters with separating information will be identified, and these clusters are defined by a sparse number of variables, this method can reduce the complexity of data, to only emphasize the data that actually matters.' + diff --git a/recipes/bioconductor-deqms/meta.yaml b/recipes/bioconductor-deqms/meta.yaml index 0f34891d64897..8718f60c084cc 100644 --- a/recipes/bioconductor-deqms/meta.yaml +++ b/recipes/bioconductor-deqms/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.0.1" %} +{% set version = "1.2.0" %} {% set name = "DEqMS" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,21 +10,21 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: e1cc1f30d361427422477667d5f6e8c4d55fefcc5357903df009f603bcaec9a0 + md5: 06cffbc05f01e49b60ca5cadfe31bc04 build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ noarch: generic -# Suggests: BiocStyle,knitr,rmarkdown,plyr,matrixStats,reshape2,farms,RColorBrewer,utils,ggrepel,pheatmap,ExperimentHub +# Suggests: BiocStyle,knitr,rmarkdown,plyr,matrixStats,reshape2,farms,utils,ggrepel,ExperimentHub,LSD requirements: host: - - 'bioconductor-limma >=3.38.0,<3.39.0' + - 'bioconductor-limma >=3.40.0,<3.41.0' - r-base - r-ggplot2 run: - - 'bioconductor-limma >=3.38.0,<3.39.0' + - 'bioconductor-limma >=3.40.0,<3.41.0' - r-base - r-ggplot2 test: diff --git a/recipes/bioconductor-derfinder/meta.yaml b/recipes/bioconductor-derfinder/meta.yaml index a8b0870de6d22..a260039572416 100644 --- a/recipes/bioconductor-derfinder/meta.yaml +++ b/recipes/bioconductor-derfinder/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.16.1" %} +{% set version = "1.18.0" %} {% set name = "derfinder" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 7899d9344b5d359f2fb65d88a8bd3bfc + md5: 80d3695d822c0007da6786c5bbdbd937 build: number: 0 rpaths: @@ -20,39 +20,39 @@ build: # Suggests: BiocStyle (>= 2.5.19), biovizBase, sessioninfo, derfinderData (>= 0.99.0), derfinderPlot, DESeq2, ggplot2, knitcitations (>= 1.0.1), knitr (>= 1.6), limma, RefManageR, rmarkdown (>= 0.3.3), testthat, TxDb.Hsapiens.UCSC.hg19.knownGene requirements: host: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' - - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' - - 'bioconductor-biocparallel >=1.16.0,<1.17.0' - - 'bioconductor-bumphunter >=1.24.0,<1.25.0' - - 'bioconductor-derfinderhelper >=1.16.0,<1.17.0' - - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' - - 'bioconductor-genomicalignments >=1.18.0,<1.19.0' - - 'bioconductor-genomicfeatures >=1.34.0,<1.35.0' - - 'bioconductor-genomicfiles >=1.18.0,<1.19.0' - - 'bioconductor-genomicranges >=1.34.0,<1.35.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-qvalue >=2.14.0,<2.15.0' - - 'bioconductor-rsamtools >=1.34.0,<1.35.0' - - 'bioconductor-rtracklayer >=1.42.0,<1.43.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' + - 'bioconductor-biocgenerics >=0.30.0,<0.31.0' + - 'bioconductor-biocparallel >=1.18.0,<1.19.0' + - 'bioconductor-bumphunter >=1.26.0,<1.27.0' + - 'bioconductor-derfinderhelper >=1.18.0,<1.19.0' + - 'bioconductor-genomeinfodb >=1.20.0,<1.21.0' + - 'bioconductor-genomicalignments >=1.20.0,<1.21.0' + - 'bioconductor-genomicfeatures >=1.36.0,<1.37.0' + - 'bioconductor-genomicfiles >=1.20.0,<1.21.0' + - 'bioconductor-genomicranges >=1.36.0,<1.37.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-qvalue >=2.16.0,<2.17.0' + - 'bioconductor-rsamtools >=2.0.0,<2.1.0' + - 'bioconductor-rtracklayer >=1.44.0,<1.45.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' - r-base - r-hmisc run: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' - - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' - - 'bioconductor-biocparallel >=1.16.0,<1.17.0' - - 'bioconductor-bumphunter >=1.24.0,<1.25.0' - - 'bioconductor-derfinderhelper >=1.16.0,<1.17.0' - - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' - - 'bioconductor-genomicalignments >=1.18.0,<1.19.0' - - 'bioconductor-genomicfeatures >=1.34.0,<1.35.0' - - 'bioconductor-genomicfiles >=1.18.0,<1.19.0' - - 'bioconductor-genomicranges >=1.34.0,<1.35.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-qvalue >=2.14.0,<2.15.0' - - 'bioconductor-rsamtools >=1.34.0,<1.35.0' - - 'bioconductor-rtracklayer >=1.42.0,<1.43.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' + - 'bioconductor-biocgenerics >=0.30.0,<0.31.0' + - 'bioconductor-biocparallel >=1.18.0,<1.19.0' + - 'bioconductor-bumphunter >=1.26.0,<1.27.0' + - 'bioconductor-derfinderhelper >=1.18.0,<1.19.0' + - 'bioconductor-genomeinfodb >=1.20.0,<1.21.0' + - 'bioconductor-genomicalignments >=1.20.0,<1.21.0' + - 'bioconductor-genomicfeatures >=1.36.0,<1.37.0' + - 'bioconductor-genomicfiles >=1.20.0,<1.21.0' + - 'bioconductor-genomicranges >=1.36.0,<1.37.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-qvalue >=2.16.0,<2.17.0' + - 'bioconductor-rsamtools >=2.0.0,<2.1.0' + - 'bioconductor-rtracklayer >=1.44.0,<1.45.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' - r-base - r-hmisc test: @@ -61,10 +61,7 @@ test: about: home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: Artistic-2.0 - summary: | - This package provides functions for annotation-agnostic differential expression analysis of RNA-seq data. - Two implementations of the DER Finder approach are included in this package: (1) single base-level F-statistics and (2) DER identification at the expressed regions-level. - The DER Finder approach can also be used to identify differentially bounded ChIP-seq peaks. + summary: 'This package provides functions for annotation-agnostic differential expression analysis of RNA-seq data. Two implementations of the DER Finder approach are included in this package: (1) single base-level F-statistics and (2) DER identification at the expressed regions-level. The DER Finder approach can also be used to identify differentially bounded ChIP-seq peaks.' extra: identifiers: - biotools:derfinder diff --git a/recipes/bioconductor-derfinderdata/meta.yaml b/recipes/bioconductor-derfinderdata/meta.yaml index b230e5f4c069f..3da62139789f2 100644 --- a/recipes/bioconductor-derfinderdata/meta.yaml +++ b/recipes/bioconductor-derfinderdata/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "2.0.0" %} +{% set version = "2.2.0" %} {% set name = "derfinderData" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: a33f63fe0dc553cdb09434a7b243535b + md5: f2762c86e4e2d3ec958485e9fc1dae37 build: number: 0 rpaths: @@ -23,7 +23,7 @@ requirements: - r-base run: - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-derfinderdata/post-link.sh b/recipes/bioconductor-derfinderdata/post-link.sh index 307c7cbc43023..ea3970e2995ab 100644 --- a/recipes/bioconductor-derfinderdata/post-link.sh +++ b/recipes/bioconductor-derfinderdata/post-link.sh @@ -1,11 +1,11 @@ #!/bin/bash -FN="derfinderData_2.0.0.tar.gz" +FN="derfinderData_2.2.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/experiment/src/contrib/derfinderData_2.0.0.tar.gz" - "https://bioarchive.galaxyproject.org/derfinderData_2.0.0.tar.gz" - "https://depot.galaxyproject.org/software/bioconductor-derfinderdata/bioconductor-derfinderdata_2.0.0_src_all.tar.gz" + "https://bioconductor.org/packages/3.9/data/experiment/src/contrib/derfinderData_2.2.0.tar.gz" + "https://bioarchive.galaxyproject.org/derfinderData_2.2.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-derfinderdata/bioconductor-derfinderdata_2.2.0_src_all.tar.gz" ) -MD5="a33f63fe0dc553cdb09434a7b243535b" +MD5="f2762c86e4e2d3ec958485e9fc1dae37" # Use a staging area in the conda dir rather than temp dirs, both to avoid # permission issues as well as to have things downloaded in a predictable @@ -16,7 +16,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-derfinderhelper/meta.yaml b/recipes/bioconductor-derfinderhelper/meta.yaml index 967400cf19f37..fb14b4a55fa93 100644 --- a/recipes/bioconductor-derfinderhelper/meta.yaml +++ b/recipes/bioconductor-derfinderhelper/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.16.1" %} +{% set version = "1.18.0" %} {% set name = "derfinderHelper" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 0aa279c6fed199400564d6cdc3f1ffd3 + md5: 5ecad5c048563c1ab581036c2af62db8 build: number: 0 rpaths: @@ -20,13 +20,13 @@ build: # Suggests: sessioninfo, knitcitations (>= 1.0.1), knitr (>= 1.6), BiocStyle (>= 2.5.19), rmarkdown (>= 0.3.3), testthat requirements: host: - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' - r-base - r-matrix run: - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' - r-base - r-matrix test: diff --git a/recipes/bioconductor-derfinderplot/meta.yaml b/recipes/bioconductor-derfinderplot/meta.yaml index 41ff4b9e98809..f860d2f21ff98 100644 --- a/recipes/bioconductor-derfinderplot/meta.yaml +++ b/recipes/bioconductor-derfinderplot/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.16.1" %} +{% set version = "1.18.0" %} {% set name = "derfinderPlot" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: fb39127239320c43ca5180870017ecb2 + md5: 445aea23faddd720a00df2e5d9aee4cc build: number: 0 rpaths: @@ -20,14 +20,14 @@ build: # Suggests: biovizBase (>= 1.27.2), bumphunter (>= 1.7.6), derfinderData (>= 0.99.0), sessioninfo, knitcitations (>= 1.0.1), knitr (>= 1.6), BiocStyle (>= 2.5.19), org.Hs.eg.db, rmarkdown (>= 0.3.3), testthat, TxDb.Hsapiens.UCSC.hg19.knownGene requirements: host: - - 'bioconductor-derfinder >=1.16.0,<1.17.0' - - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' - - 'bioconductor-genomicfeatures >=1.34.0,<1.35.0' - - 'bioconductor-genomicranges >=1.34.0,<1.35.0' - - 'bioconductor-ggbio >=1.30.0,<1.31.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-limma >=3.38.0,<3.39.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-derfinder >=1.18.0,<1.19.0' + - 'bioconductor-genomeinfodb >=1.20.0,<1.21.0' + - 'bioconductor-genomicfeatures >=1.36.0,<1.37.0' + - 'bioconductor-genomicranges >=1.36.0,<1.37.0' + - 'bioconductor-ggbio >=1.32.0,<1.33.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-limma >=3.40.0,<3.41.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' - r-base - r-ggplot2 - r-plyr @@ -36,14 +36,14 @@ requirements: - r-reshape2 - r-scales run: - - 'bioconductor-derfinder >=1.16.0,<1.17.0' - - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' - - 'bioconductor-genomicfeatures >=1.34.0,<1.35.0' - - 'bioconductor-genomicranges >=1.34.0,<1.35.0' - - 'bioconductor-ggbio >=1.30.0,<1.31.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-limma >=3.38.0,<3.39.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-derfinder >=1.18.0,<1.19.0' + - 'bioconductor-genomeinfodb >=1.20.0,<1.21.0' + - 'bioconductor-genomicfeatures >=1.36.0,<1.37.0' + - 'bioconductor-genomicranges >=1.36.0,<1.37.0' + - 'bioconductor-ggbio >=1.32.0,<1.33.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-limma >=3.40.0,<3.41.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' - r-base - r-ggplot2 - r-plyr diff --git a/recipes/bioconductor-descan2/meta.yaml b/recipes/bioconductor-descan2/meta.yaml index 9f2d9bc293004..20cc20125bae5 100644 --- a/recipes/bioconductor-descan2/meta.yaml +++ b/recipes/bioconductor-descan2/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.2.0" %} +{% set version = "1.4.0" %} {% set name = "DEScan2" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 6d6d1d534831bb5fefe9a82eedec0af4 + md5: 601fc7fa0c23f543e35db969282faea5 build: number: 0 rpaths: @@ -19,17 +19,17 @@ build: # Suggests: BiocStyle, knitr, rmarkdown, testthat, edgeR, limma, EDASeq, RUVSeq, RColorBrewer, statmod requirements: host: - - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' - - 'bioconductor-biocparallel >=1.16.0,<1.17.0' - - 'bioconductor-chippeakanno >=3.16.0,<3.17.0' - - 'bioconductor-delayedarray >=0.8.0,<0.9.0' - - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' - - 'bioconductor-genomicalignments >=1.18.0,<1.19.0' - - 'bioconductor-genomicranges >=1.34.0,<1.35.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-rtracklayer >=1.42.0,<1.43.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' - - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' + - 'bioconductor-biocgenerics >=0.30.0,<0.31.0' + - 'bioconductor-biocparallel >=1.18.0,<1.19.0' + - 'bioconductor-chippeakanno >=3.18.0,<3.19.0' + - 'bioconductor-delayedarray >=0.10.0,<0.11.0' + - 'bioconductor-genomeinfodb >=1.20.0,<1.21.0' + - 'bioconductor-genomicalignments >=1.20.0,<1.21.0' + - 'bioconductor-genomicranges >=1.36.0,<1.37.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-rtracklayer >=1.44.0,<1.45.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' + - 'bioconductor-summarizedexperiment >=1.14.0,<1.15.0' - r-base - r-data.table - r-glue @@ -37,17 +37,17 @@ requirements: - 'r-rcpp >=0.12.13' - r-rcpparmadillo run: - - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' - - 'bioconductor-biocparallel >=1.16.0,<1.17.0' - - 'bioconductor-chippeakanno >=3.16.0,<3.17.0' - - 'bioconductor-delayedarray >=0.8.0,<0.9.0' - - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' - - 'bioconductor-genomicalignments >=1.18.0,<1.19.0' - - 'bioconductor-genomicranges >=1.34.0,<1.35.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-rtracklayer >=1.42.0,<1.43.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' - - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' + - 'bioconductor-biocgenerics >=0.30.0,<0.31.0' + - 'bioconductor-biocparallel >=1.18.0,<1.19.0' + - 'bioconductor-chippeakanno >=3.18.0,<3.19.0' + - 'bioconductor-delayedarray >=0.10.0,<0.11.0' + - 'bioconductor-genomeinfodb >=1.20.0,<1.21.0' + - 'bioconductor-genomicalignments >=1.20.0,<1.21.0' + - 'bioconductor-genomicranges >=1.36.0,<1.37.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-rtracklayer >=1.44.0,<1.45.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' + - 'bioconductor-summarizedexperiment >=1.14.0,<1.15.0' - r-base - r-data.table - r-glue diff --git a/recipes/bioconductor-deseq/meta.yaml b/recipes/bioconductor-deseq/meta.yaml index 23b5f2906d07d..15653fc254516 100644 --- a/recipes/bioconductor-deseq/meta.yaml +++ b/recipes/bioconductor-deseq/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.34.1" %} +{% set version = "1.36.0" %} {% set name = "DESeq" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: e292a4df25b50cfa0ce0b62f73f012539c5d6fee86ae6b63549ec2f5598ff12e + md5: 2f4ef93911b4e75bc0b470bb0b9d70d0 build: number: 0 rpaths: @@ -19,20 +19,20 @@ build: # Suggests: pasilla (>= 0.2.10), vsn, gplots requirements: host: - - 'bioconductor-biobase >=2.42.0,<2.43.0' - - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' - - 'bioconductor-genefilter >=1.64.0,<1.65.0' - - 'bioconductor-geneplotter >=1.60.0,<1.61.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' + - 'bioconductor-biocgenerics >=0.30.0,<0.31.0' + - 'bioconductor-genefilter >=1.66.0,<1.67.0' + - 'bioconductor-geneplotter >=1.62.0,<1.63.0' - r-base - r-lattice - r-locfit - r-mass - r-rcolorbrewer run: - - 'bioconductor-biobase >=2.42.0,<2.43.0' - - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' - - 'bioconductor-genefilter >=1.64.0,<1.65.0' - - 'bioconductor-geneplotter >=1.60.0,<1.61.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' + - 'bioconductor-biocgenerics >=0.30.0,<0.31.0' + - 'bioconductor-genefilter >=1.66.0,<1.67.0' + - 'bioconductor-geneplotter >=1.62.0,<1.63.0' - r-base - r-lattice - r-locfit diff --git a/recipes/bioconductor-deseq2/meta.yaml b/recipes/bioconductor-deseq2/meta.yaml index 0593f604374b3..e2839aa0f36a3 100644 --- a/recipes/bioconductor-deseq2/meta.yaml +++ b/recipes/bioconductor-deseq2/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.22.1" %} +{% set version = "1.24.0" %} {% set name = "DESeq2" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: b7cf6da541d28dcd9abe09425dc43447 + md5: 51a2fd660c9f615e5819e795b62c125e build: number: 0 rpaths: @@ -19,15 +19,15 @@ build: # Suggests: testthat, knitr, rmarkdown, vsn, pheatmap, RColorBrewer, IHW, apeglm, ashr, tximport, tximportData, readr, pbapply, airway, pasilla (>= 0.2.10) requirements: host: - - 'bioconductor-biobase >=2.42.0,<2.43.0' - - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' - - 'bioconductor-biocparallel >=1.16.0,<1.17.0' - - 'bioconductor-genefilter >=1.64.0,<1.65.0' - - 'bioconductor-geneplotter >=1.60.0,<1.61.0' - - 'bioconductor-genomicranges >=1.34.0,<1.35.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' - - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' + - 'bioconductor-biocgenerics >=0.30.0,<0.31.0' + - 'bioconductor-biocparallel >=1.18.0,<1.19.0' + - 'bioconductor-genefilter >=1.66.0,<1.67.0' + - 'bioconductor-geneplotter >=1.62.0,<1.63.0' + - 'bioconductor-genomicranges >=1.36.0,<1.37.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' + - 'bioconductor-summarizedexperiment >=1.14.0,<1.15.0' - r-base - r-ggplot2 - r-hmisc @@ -35,15 +35,15 @@ requirements: - 'r-rcpp >=0.11.0' - r-rcpparmadillo run: - - 'bioconductor-biobase >=2.42.0,<2.43.0' - - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' - - 'bioconductor-biocparallel >=1.16.0,<1.17.0' - - 'bioconductor-genefilter >=1.64.0,<1.65.0' - - 'bioconductor-geneplotter >=1.60.0,<1.61.0' - - 'bioconductor-genomicranges >=1.34.0,<1.35.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' - - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' + - 'bioconductor-biocgenerics >=0.30.0,<0.31.0' + - 'bioconductor-biocparallel >=1.18.0,<1.19.0' + - 'bioconductor-genefilter >=1.66.0,<1.67.0' + - 'bioconductor-geneplotter >=1.62.0,<1.63.0' + - 'bioconductor-genomicranges >=1.36.0,<1.37.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' + - 'bioconductor-summarizedexperiment >=1.14.0,<1.15.0' - r-base - r-ggplot2 - r-hmisc diff --git a/recipes/bioconductor-desingle/meta.yaml b/recipes/bioconductor-desingle/meta.yaml index a19f0d67ba751..1efb64b57883a 100644 --- a/recipes/bioconductor-desingle/meta.yaml +++ b/recipes/bioconductor-desingle/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.2.1" %} +{% set version = "1.4.0" %} {% set name = "DEsingle" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 8d446c9bd3e760ae2c67426a1911e42c + md5: f9d286f5314f05cf0ac1f38da3a691ad build: number: 0 rpaths: @@ -20,7 +20,7 @@ build: # Suggests: knitr, rmarkdown, SingleCellExperiment requirements: host: - - 'bioconductor-biocparallel >=1.16.0,<1.17.0' + - 'bioconductor-biocparallel >=1.18.0,<1.19.0' - r-base - 'r-bbmle >=1.0.18' - 'r-gamlss >=4.4-0' @@ -30,7 +30,7 @@ requirements: - 'r-pscl >=1.4.9' - 'r-vgam >=1.0-2' run: - - 'bioconductor-biocparallel >=1.16.0,<1.17.0' + - 'bioconductor-biocparallel >=1.18.0,<1.19.0' - r-base - 'r-bbmle >=1.0.18' - 'r-gamlss >=4.4-0' diff --git a/recipes/bioconductor-desousa2013/meta.yaml b/recipes/bioconductor-desousa2013/meta.yaml index ff91541e59185..d3ceeeac019a2 100644 --- a/recipes/bioconductor-desousa2013/meta.yaml +++ b/recipes/bioconductor-desousa2013/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.18.0" %} +{% set version = "1.20.0" %} {% set name = "DeSousa2013" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 6059d057fb2eb7d4b64896680da57226 + md5: 6772bbad387e983a0f1ba536055635ca build: number: 0 rpaths: @@ -19,16 +19,16 @@ build: noarch: generic requirements: host: - - 'bioconductor-affy >=1.60.0,<1.61.0' - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' - - 'bioconductor-biobase >=2.42.0,<2.43.0' - - 'bioconductor-consensusclusterplus >=1.46.0,<1.47.0' - - 'bioconductor-frma >=1.34.0,<1.35.0' - - 'bioconductor-frmatools >=1.34.0,<1.35.0' + - 'bioconductor-affy >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' + - 'bioconductor-consensusclusterplus >=1.48.0,<1.49.0' + - 'bioconductor-frma >=1.36.0,<1.37.0' + - 'bioconductor-frmatools >=1.36.0,<1.37.0' - 'bioconductor-hgu133plus2.db >=3.2.0,<3.3.0' - - 'bioconductor-hgu133plus2frmavecs >=1.5.0,<1.6.0' - - 'bioconductor-siggenes >=1.56.0,<1.57.0' - - 'bioconductor-sva >=3.30.0,<3.31.0' + - 'bioconductor-hgu133plus2frmavecs >=1.6.0,<1.7.0' + - 'bioconductor-siggenes >=1.58.0,<1.59.0' + - 'bioconductor-sva >=3.32.0,<3.33.0' - r-base - r-cluster - r-gplots @@ -37,16 +37,16 @@ requirements: - r-rocr - r-survival run: - - 'bioconductor-affy >=1.60.0,<1.61.0' - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' - - 'bioconductor-biobase >=2.42.0,<2.43.0' - - 'bioconductor-consensusclusterplus >=1.46.0,<1.47.0' - - 'bioconductor-frma >=1.34.0,<1.35.0' - - 'bioconductor-frmatools >=1.34.0,<1.35.0' + - 'bioconductor-affy >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' + - 'bioconductor-consensusclusterplus >=1.48.0,<1.49.0' + - 'bioconductor-frma >=1.36.0,<1.37.0' + - 'bioconductor-frmatools >=1.36.0,<1.37.0' - 'bioconductor-hgu133plus2.db >=3.2.0,<3.3.0' - - 'bioconductor-hgu133plus2frmavecs >=1.5.0,<1.6.0' - - 'bioconductor-siggenes >=1.56.0,<1.57.0' - - 'bioconductor-sva >=3.30.0,<3.31.0' + - 'bioconductor-hgu133plus2frmavecs >=1.6.0,<1.7.0' + - 'bioconductor-siggenes >=1.58.0,<1.59.0' + - 'bioconductor-sva >=3.32.0,<3.33.0' - r-base - r-cluster - r-gplots @@ -54,7 +54,7 @@ requirements: - r-rgl - r-rocr - r-survival - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-desousa2013/post-link.sh b/recipes/bioconductor-desousa2013/post-link.sh index b810f8a5a3215..13ae1399a28a1 100644 --- a/recipes/bioconductor-desousa2013/post-link.sh +++ b/recipes/bioconductor-desousa2013/post-link.sh @@ -1,11 +1,11 @@ #!/bin/bash -FN="DeSousa2013_1.18.0.tar.gz" +FN="DeSousa2013_1.20.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/experiment/src/contrib/DeSousa2013_1.18.0.tar.gz" - "https://bioarchive.galaxyproject.org/DeSousa2013_1.18.0.tar.gz" - "https://depot.galaxyproject.org/software/bioconductor-desousa2013/bioconductor-desousa2013_1.18.0_src_all.tar.gz" + "https://bioconductor.org/packages/3.9/data/experiment/src/contrib/DeSousa2013_1.20.0.tar.gz" + "https://bioarchive.galaxyproject.org/DeSousa2013_1.20.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-desousa2013/bioconductor-desousa2013_1.20.0_src_all.tar.gz" ) -MD5="6059d057fb2eb7d4b64896680da57226" +MD5="6772bbad387e983a0f1ba536055635ca" # Use a staging area in the conda dir rather than temp dirs, both to avoid # permission issues as well as to have things downloaded in a predictable @@ -16,7 +16,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-destiny/meta.yaml b/recipes/bioconductor-destiny/meta.yaml index f99c18f5df3c6..78c1b6ff9d718 100644 --- a/recipes/bioconductor-destiny/meta.yaml +++ b/recipes/bioconductor-destiny/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "2.12.0" %} +{% set version = "2.14.0" %} {% set name = "destiny" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: ac5c9847de79461d53d1ad996f155d19 + md5: 4b2e28a4eb7022cfad8589c8c6d45ded build: number: 0 rpaths: @@ -20,9 +20,9 @@ build: # SystemRequirements: C++11 requirements: host: - - 'bioconductor-biobase >=2.42.0,<2.43.0' - - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' - - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' + - 'bioconductor-biocgenerics >=0.30.0,<0.31.0' + - 'bioconductor-summarizedexperiment >=1.14.0,<1.15.0' - r-base - r-ggplot2 - r-ggthemes @@ -36,9 +36,9 @@ requirements: - r-smoother - r-vim run: - - 'bioconductor-biobase >=2.42.0,<2.43.0' - - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' - - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' + - 'bioconductor-biocgenerics >=0.30.0,<0.31.0' + - 'bioconductor-summarizedexperiment >=1.14.0,<1.15.0' - r-base - r-ggplot2 - r-ggthemes diff --git a/recipes/bioconductor-desubs/meta.yaml b/recipes/bioconductor-desubs/meta.yaml index 9ba4bd5c2b186..97c227dd97aa0 100644 --- a/recipes/bioconductor-desubs/meta.yaml +++ b/recipes/bioconductor-desubs/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.8.1" %} +{% set version = "1.10.0" %} {% set name = "DEsubs" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,9 +10,9 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 90cc0ee693e5b17182604558c98ab38a + md5: 3401c12e1b7b956a302c894862bbff72 build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ @@ -20,13 +20,13 @@ build: # Suggests: RUnit, BiocGenerics, knitr requirements: host: - - 'bioconductor-deseq >=1.34.0,<1.35.0' - - 'bioconductor-deseq2 >=1.22.0,<1.23.0' - - 'bioconductor-ebseq >=1.22.0,<1.23.0' - - 'bioconductor-edger >=3.24.0,<3.25.0' - - 'bioconductor-graph >=1.60.0,<1.61.0' - - 'bioconductor-limma >=3.38.0,<3.39.0' - - 'bioconductor-rbgl >=1.58.0,<1.59.0' + - 'bioconductor-deseq >=1.36.0,<1.37.0' + - 'bioconductor-deseq2 >=1.24.0,<1.25.0' + - 'bioconductor-ebseq >=1.24.0,<1.25.0' + - 'bioconductor-edger >=3.26.0,<3.27.0' + - 'bioconductor-graph >=1.62.0,<1.63.0' + - 'bioconductor-limma >=3.40.0,<3.41.0' + - 'bioconductor-rbgl >=1.60.0,<1.61.0' - r-base - r-circlize - r-ggplot2 @@ -37,13 +37,13 @@ requirements: - r-nbpseq - r-pheatmap run: - - 'bioconductor-deseq >=1.34.0,<1.35.0' - - 'bioconductor-deseq2 >=1.22.0,<1.23.0' - - 'bioconductor-ebseq >=1.22.0,<1.23.0' - - 'bioconductor-edger >=3.24.0,<3.25.0' - - 'bioconductor-graph >=1.60.0,<1.61.0' - - 'bioconductor-limma >=3.38.0,<3.39.0' - - 'bioconductor-rbgl >=1.58.0,<1.59.0' + - 'bioconductor-deseq >=1.36.0,<1.37.0' + - 'bioconductor-deseq2 >=1.24.0,<1.25.0' + - 'bioconductor-ebseq >=1.24.0,<1.25.0' + - 'bioconductor-edger >=3.26.0,<3.27.0' + - 'bioconductor-graph >=1.62.0,<1.63.0' + - 'bioconductor-limma >=3.40.0,<3.41.0' + - 'bioconductor-rbgl >=1.60.0,<1.61.0' - r-base - r-circlize - r-ggplot2 diff --git a/recipes/bioconductor-dexseq/build.sh b/recipes/bioconductor-dexseq/build.sh index a413a860554c3..c1d13421f5f1e 100644 --- a/recipes/bioconductor-dexseq/build.sh +++ b/recipes/bioconductor-dexseq/build.sh @@ -8,11 +8,4 @@ CXX=$CXX CXX98=$CXX CXX11=$CXX CXX14=$CXX" > ~/.R/Makevars -$R CMD INSTALL --build . -mkdir -p "$PREFIX/bin" -PYTHON_SCRIPTS_DIR=$PREFIX/lib/R/library/DEXSeq/python_scripts -for f in dexseq_count.py dexseq_prepare_annotation.py; do - sed -i.bak '1s|^|#!/usr/bin/env python\'$'\n|g' "$PYTHON_SCRIPTS_DIR/$f" - chmod +x "$PYTHON_SCRIPTS_DIR/$f" - ln -s "$PYTHON_SCRIPTS_DIR/$f" $PREFIX/bin/ -done +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-dexseq/meta.yaml b/recipes/bioconductor-dexseq/meta.yaml index 6c3ed4919e414..4460f26e8bd5d 100644 --- a/recipes/bioconductor-dexseq/meta.yaml +++ b/recipes/bioconductor-dexseq/meta.yaml @@ -1,77 +1,69 @@ -{% set version = "1.28.1" %} +{% set version = "1.30.0" %} {% set name = "DEXSeq" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' - source: url: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: df4aee7ee509042297b0d58d258dcc27 - + md5: 756246353a1779eebec78015ca33d881 build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ noarch: generic -# Suggests: GenomicFeatures (>= 1.13.29), pasilla (>= 0.2.22), parathyroidSE, BiocStyle, knitr +# Suggests: GenomicFeatures (>= 1.13.29), pasilla (>= 0.2.22), parathyroidSE, BiocStyle, knitr, rmarkdown requirements: host: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' - - 'bioconductor-biobase >=2.42.0,<2.43.0' - - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' - - 'bioconductor-biocparallel >=1.16.0,<1.17.0' - - 'bioconductor-biomart >=2.38.0,<2.39.0' - - 'bioconductor-deseq2 >=1.22.0,<1.23.0' - - 'bioconductor-genefilter >=1.64.0,<1.65.0' - - 'bioconductor-geneplotter >=1.60.0,<1.61.0' - - 'bioconductor-genomicranges >=1.34.0,<1.35.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-rsamtools >=1.34.0,<1.35.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' - - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' + - 'bioconductor-biocgenerics >=0.30.0,<0.31.0' + - 'bioconductor-biocparallel >=1.18.0,<1.19.0' + - 'bioconductor-biomart >=2.40.0,<2.41.0' + - 'bioconductor-deseq2 >=1.24.0,<1.25.0' + - 'bioconductor-genefilter >=1.66.0,<1.67.0' + - 'bioconductor-geneplotter >=1.62.0,<1.63.0' + - 'bioconductor-genomicranges >=1.36.0,<1.37.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-rsamtools >=2.0.0,<2.1.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' + - 'bioconductor-summarizedexperiment >=1.14.0,<1.15.0' - r-base - r-hwriter - r-rcolorbrewer - r-statmod - r-stringr run: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' - - 'bioconductor-biobase >=2.42.0,<2.43.0' - - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' - - 'bioconductor-biocparallel >=1.16.0,<1.17.0' - - 'bioconductor-biomart >=2.38.0,<2.39.0' - - 'bioconductor-deseq2 >=1.22.0,<1.23.0' - - 'bioconductor-genefilter >=1.64.0,<1.65.0' - - 'bioconductor-geneplotter >=1.60.0,<1.61.0' - - 'bioconductor-genomicranges >=1.34.0,<1.35.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-rsamtools >=1.34.0,<1.35.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' - - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' + - 'bioconductor-biocgenerics >=0.30.0,<0.31.0' + - 'bioconductor-biocparallel >=1.18.0,<1.19.0' + - 'bioconductor-biomart >=2.40.0,<2.41.0' + - 'bioconductor-deseq2 >=1.24.0,<1.25.0' + - 'bioconductor-genefilter >=1.66.0,<1.67.0' + - 'bioconductor-geneplotter >=1.62.0,<1.63.0' + - 'bioconductor-genomicranges >=1.36.0,<1.37.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-rsamtools >=2.0.0,<2.1.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' + - 'bioconductor-summarizedexperiment >=1.14.0,<1.15.0' - r-base - r-hwriter - r-rcolorbrewer - r-statmod - r-stringr - - python <3 - - 'htseq >=0.6.1,<0.10.0' # dexseq_count.py performes an overly simplistic version check test: commands: - '$R -e "library(''{{ name }}'')"' - - dexseq_count.py --help - - dexseq_prepare_annotation.py --help - about: home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: 'GPL (>= 3)' summary: 'The package is focused on finding differential exon usage using RNA-seq exon counts between samples with different experimental designs. It provides functions that allows the user to make the necessary statistical tests based on a model that uses the negative binomial distribution to estimate the variance between biological replicates and generalized linear models for testing. The package also provides functions for the visualization and exploration of the results.' - extra: identifiers: - biotools:dexseq diff --git a/recipes/bioconductor-dexus/meta.yaml b/recipes/bioconductor-dexus/meta.yaml index 767b18abc0195..8338f77e67463 100644 --- a/recipes/bioconductor-dexus/meta.yaml +++ b/recipes/bioconductor-dexus/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.22.1" %} +{% set version = "1.24.0" %} {% set name = "dexus" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: df149bdc24e61ffbe4bdb9f9ed34095c + md5: cb34d5e04455977ed9a0bd3d0f275c1c build: number: 0 rpaths: @@ -19,10 +19,10 @@ build: # Suggests: parallel, statmod, DESeq, RColorBrewer requirements: host: - - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' + - 'bioconductor-biocgenerics >=0.30.0,<0.31.0' - r-base run: - - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' + - 'bioconductor-biocgenerics >=0.30.0,<0.31.0' - r-base build: - {{ compiler('c') }} diff --git a/recipes/bioconductor-dfp/meta.yaml b/recipes/bioconductor-dfp/meta.yaml index 3cce5dad5f13a..23191220eeb46 100644 --- a/recipes/bioconductor-dfp/meta.yaml +++ b/recipes/bioconductor-dfp/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.40.0" %} +{% set version = "1.42.0" %} {% set name = "DFP" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 12981b09b4c4c8d2738eb7d9ae20e399 + md5: 2101788ecc7a5ee2507bfb52ade1a716 build: number: 0 rpaths: @@ -19,10 +19,10 @@ build: noarch: generic requirements: host: - - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' - r-base run: - - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' - r-base test: commands: diff --git a/recipes/bioconductor-diffbind/meta.yaml b/recipes/bioconductor-diffbind/meta.yaml index 4415c263183bd..86eed58fbf8c0 100644 --- a/recipes/bioconductor-diffbind/meta.yaml +++ b/recipes/bioconductor-diffbind/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "2.10.0" %} +{% set version = "2.12.0" %} {% set name = "DiffBind" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,27 +10,27 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: cebf717d82d269302bb10819892d6b6e + md5: ae0905af5e87e5525769294d162ef611 build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ # Suggests: DESeq, BiocStyle, testthat requirements: host: - - 'bioconductor-biocparallel >=1.16.0,<1.17.0' - - 'bioconductor-deseq2 >=1.22.0,<1.23.0' - - 'bioconductor-edger >=3.24.0,<3.25.0' - - 'bioconductor-genomicalignments >=1.18.0,<1.19.0' - - 'bioconductor-genomicranges >=1.34.0,<1.35.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-limma >=3.38.0,<3.39.0' - - 'bioconductor-rsamtools >=1.34.0,<1.35.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' - - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' - - 'bioconductor-systempiper >=1.16.0,<1.17.0' - - 'bioconductor-zlibbioc >=1.28.0,<1.29.0' + - 'bioconductor-biocparallel >=1.18.0,<1.19.0' + - 'bioconductor-deseq2 >=1.24.0,<1.25.0' + - 'bioconductor-edger >=3.26.0,<3.27.0' + - 'bioconductor-genomicalignments >=1.20.0,<1.21.0' + - 'bioconductor-genomicranges >=1.36.0,<1.37.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-limma >=3.40.0,<3.41.0' + - 'bioconductor-rhtslib >=1.16.0,<1.17.0' + - 'bioconductor-rsamtools >=2.0.0,<2.1.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' + - 'bioconductor-summarizedexperiment >=1.14.0,<1.15.0' + - 'bioconductor-systempiper >=1.18.0,<1.19.0' - r-amap - r-base - r-dplyr @@ -42,18 +42,18 @@ requirements: - r-rcolorbrewer - r-rcpp run: - - 'bioconductor-biocparallel >=1.16.0,<1.17.0' - - 'bioconductor-deseq2 >=1.22.0,<1.23.0' - - 'bioconductor-edger >=3.24.0,<3.25.0' - - 'bioconductor-genomicalignments >=1.18.0,<1.19.0' - - 'bioconductor-genomicranges >=1.34.0,<1.35.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-limma >=3.38.0,<3.39.0' - - 'bioconductor-rsamtools >=1.34.0,<1.35.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' - - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' - - 'bioconductor-systempiper >=1.16.0,<1.17.0' - - 'bioconductor-zlibbioc >=1.28.0,<1.29.0' + - 'bioconductor-biocparallel >=1.18.0,<1.19.0' + - 'bioconductor-deseq2 >=1.24.0,<1.25.0' + - 'bioconductor-edger >=3.26.0,<3.27.0' + - 'bioconductor-genomicalignments >=1.20.0,<1.21.0' + - 'bioconductor-genomicranges >=1.36.0,<1.37.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-limma >=3.40.0,<3.41.0' + - 'bioconductor-rhtslib >=1.16.0,<1.17.0' + - 'bioconductor-rsamtools >=2.0.0,<2.1.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' + - 'bioconductor-summarizedexperiment >=1.14.0,<1.15.0' + - 'bioconductor-systempiper >=1.18.0,<1.19.0' - r-amap - r-base - r-dplyr diff --git a/recipes/bioconductor-diffcoexp/meta.yaml b/recipes/bioconductor-diffcoexp/meta.yaml index 9049dd7c39c24..66d6577218423 100644 --- a/recipes/bioconductor-diffcoexp/meta.yaml +++ b/recipes/bioconductor-diffcoexp/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.2.0" %} +{% set version = "1.4.0" %} {% set name = "diffcoexp" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 84d4b05956389705839485018b5aa33c + md5: 49a4bd12fa99f28a09013c7e2dbd9fd5 build: number: 0 rpaths: @@ -20,16 +20,16 @@ build: # Suggests: GEOquery requirements: host: - - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' - - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' + - 'bioconductor-biocgenerics >=0.30.0,<0.31.0' + - 'bioconductor-summarizedexperiment >=1.14.0,<1.15.0' - r-base - r-diffcorr - r-igraph - r-psych - r-wgcna run: - - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' - - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' + - 'bioconductor-biocgenerics >=0.30.0,<0.31.0' + - 'bioconductor-summarizedexperiment >=1.14.0,<1.15.0' - r-base - r-diffcorr - r-igraph diff --git a/recipes/bioconductor-diffcyt/meta.yaml b/recipes/bioconductor-diffcyt/meta.yaml index cc852df365102..1b59a844f006b 100644 --- a/recipes/bioconductor-diffcyt/meta.yaml +++ b/recipes/bioconductor-diffcyt/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.2.23" %} +{% set version = "1.4.0" %} {% set name = "diffcyt" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,23 +10,23 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 1aaf7d62abe990792f52e699dc1777f1 + md5: a442d99ed8adbb5ff80214110a777e67 build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ noarch: generic -# Suggests: BiocStyle, knitr, rmarkdown, HDCytoData, CATALYST +# Suggests: BiocStyle, knitr, rmarkdown, testthat, HDCytoData, CATALYST requirements: host: - - 'bioconductor-complexheatmap >=1.20.0,<1.21.0' - - 'bioconductor-edger >=3.24.0,<3.25.0' - - 'bioconductor-flowcore >=1.48.0,<1.49.0' - - 'bioconductor-flowsom >=1.14.0,<1.15.0' - - 'bioconductor-limma >=3.38.0,<3.39.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' - - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' + - 'bioconductor-complexheatmap >=2.0.0,<2.1.0' + - 'bioconductor-edger >=3.26.0,<3.27.0' + - 'bioconductor-flowcore >=1.50.0,<1.51.0' + - 'bioconductor-flowsom >=1.16.0,<1.17.0' + - 'bioconductor-limma >=3.40.0,<3.41.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' + - 'bioconductor-summarizedexperiment >=1.14.0,<1.15.0' - r-base - r-circlize - r-dplyr @@ -36,13 +36,13 @@ requirements: - r-reshape2 - r-tidyr run: - - 'bioconductor-complexheatmap >=1.20.0,<1.21.0' - - 'bioconductor-edger >=3.24.0,<3.25.0' - - 'bioconductor-flowcore >=1.48.0,<1.49.0' - - 'bioconductor-flowsom >=1.14.0,<1.15.0' - - 'bioconductor-limma >=3.38.0,<3.39.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' - - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' + - 'bioconductor-complexheatmap >=2.0.0,<2.1.0' + - 'bioconductor-edger >=3.26.0,<3.27.0' + - 'bioconductor-flowcore >=1.50.0,<1.51.0' + - 'bioconductor-flowsom >=1.16.0,<1.17.0' + - 'bioconductor-limma >=3.40.0,<3.41.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' + - 'bioconductor-summarizedexperiment >=1.14.0,<1.15.0' - r-base - r-circlize - r-dplyr @@ -57,5 +57,5 @@ test: about: home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: 'MIT + file LICENSE' - summary: 'Statistical methods for differential discovery analyses in high-dimensional cytometry data (including flow cytometry, mass cytometry or CyTOF, and oligonucleotide-tagged cytometry), based on (i) high-resolution clustering and (ii) empirical Bayes moderated tests adapted from transcriptomics.' + summary: 'Statistical methods for differential discovery analyses in high-dimensional cytometry data (including flow cytometry, mass cytometry or CyTOF, and oligonucleotide-tagged cytometry), based on a combination of high-resolution clustering and empirical Bayes moderated tests adapted from transcriptomics.' diff --git a/recipes/bioconductor-diffgeneanalysis/meta.yaml b/recipes/bioconductor-diffgeneanalysis/meta.yaml index d7db5cb7f4ea1..fb2acf7854fe2 100644 --- a/recipes/bioconductor-diffgeneanalysis/meta.yaml +++ b/recipes/bioconductor-diffgeneanalysis/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.64.0" %} +{% set version = "1.66.0" %} {% set name = "diffGeneAnalysis" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 506fc6d4eb0b4d2d23cee89b0f19c704 + md5: fba381a248d6938a6eb4eae857a11d76 build: number: 0 rpaths: diff --git a/recipes/bioconductor-diffhic/meta.yaml b/recipes/bioconductor-diffhic/meta.yaml index 532ad782ad190..f67366b49ea53 100644 --- a/recipes/bioconductor-diffhic/meta.yaml +++ b/recipes/bioconductor-diffhic/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.14.0" %} +{% set version = "1.16.0" %} {% set name = "diffHic" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: b3a4a022ba4b42c3c84d13a12a2e3e79 + md5: 1b82b5c50751576e1e81fdc2493d7b64 build: number: 0 rpaths: @@ -20,44 +20,44 @@ build: # SystemRequirements: C++11 requirements: host: - - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' - - 'bioconductor-biostrings >=2.50.0,<2.51.0' - - 'bioconductor-bsgenome >=1.50.0,<1.51.0' - - 'bioconductor-csaw >=1.16.0,<1.17.0' - - 'bioconductor-edger >=3.24.0,<3.25.0' - - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' - - 'bioconductor-genomicranges >=1.34.0,<1.35.0' - - 'bioconductor-interactionset >=1.10.0,<1.11.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-limma >=3.38.0,<3.39.0' - - 'bioconductor-rhdf5 >=2.26.0,<2.27.0' - - 'bioconductor-rhtslib >=1.14.0,<1.15.0' - - 'bioconductor-rsamtools >=1.34.0,<1.35.0' - - 'bioconductor-rtracklayer >=1.42.0,<1.43.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' - - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' - - 'bioconductor-zlibbioc >=1.28.0,<1.29.0' + - 'bioconductor-biocgenerics >=0.30.0,<0.31.0' + - 'bioconductor-biostrings >=2.52.0,<2.53.0' + - 'bioconductor-bsgenome >=1.52.0,<1.53.0' + - 'bioconductor-csaw >=1.18.0,<1.19.0' + - 'bioconductor-edger >=3.26.0,<3.27.0' + - 'bioconductor-genomeinfodb >=1.20.0,<1.21.0' + - 'bioconductor-genomicranges >=1.36.0,<1.37.0' + - 'bioconductor-interactionset >=1.12.0,<1.13.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-limma >=3.40.0,<3.41.0' + - 'bioconductor-rhdf5 >=2.28.0,<2.29.0' + - 'bioconductor-rhtslib >=1.16.0,<1.17.0' + - 'bioconductor-rsamtools >=2.0.0,<2.1.0' + - 'bioconductor-rtracklayer >=1.44.0,<1.45.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' + - 'bioconductor-summarizedexperiment >=1.14.0,<1.15.0' + - 'bioconductor-zlibbioc >=1.30.0,<1.31.0' - r-base - r-locfit - r-rcpp run: - - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' - - 'bioconductor-biostrings >=2.50.0,<2.51.0' - - 'bioconductor-bsgenome >=1.50.0,<1.51.0' - - 'bioconductor-csaw >=1.16.0,<1.17.0' - - 'bioconductor-edger >=3.24.0,<3.25.0' - - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' - - 'bioconductor-genomicranges >=1.34.0,<1.35.0' - - 'bioconductor-interactionset >=1.10.0,<1.11.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-limma >=3.38.0,<3.39.0' - - 'bioconductor-rhdf5 >=2.26.0,<2.27.0' - - 'bioconductor-rhtslib >=1.14.0,<1.15.0' - - 'bioconductor-rsamtools >=1.34.0,<1.35.0' - - 'bioconductor-rtracklayer >=1.42.0,<1.43.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' - - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' - - 'bioconductor-zlibbioc >=1.28.0,<1.29.0' + - 'bioconductor-biocgenerics >=0.30.0,<0.31.0' + - 'bioconductor-biostrings >=2.52.0,<2.53.0' + - 'bioconductor-bsgenome >=1.52.0,<1.53.0' + - 'bioconductor-csaw >=1.18.0,<1.19.0' + - 'bioconductor-edger >=3.26.0,<3.27.0' + - 'bioconductor-genomeinfodb >=1.20.0,<1.21.0' + - 'bioconductor-genomicranges >=1.36.0,<1.37.0' + - 'bioconductor-interactionset >=1.12.0,<1.13.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-limma >=3.40.0,<3.41.0' + - 'bioconductor-rhdf5 >=2.28.0,<2.29.0' + - 'bioconductor-rhtslib >=1.16.0,<1.17.0' + - 'bioconductor-rsamtools >=2.0.0,<2.1.0' + - 'bioconductor-rtracklayer >=1.44.0,<1.45.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' + - 'bioconductor-summarizedexperiment >=1.14.0,<1.15.0' + - 'bioconductor-zlibbioc >=1.30.0,<1.31.0' - r-base - r-locfit - r-rcpp diff --git a/recipes/bioconductor-difflogo/meta.yaml b/recipes/bioconductor-difflogo/meta.yaml index 7011e42c6038d..be8a689240f07 100644 --- a/recipes/bioconductor-difflogo/meta.yaml +++ b/recipes/bioconductor-difflogo/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "2.6.0" %} +{% set version = "2.8.0" %} {% set name = "DiffLogo" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 7135a21ee77702fa93080a7076f9d314 + md5: dcc3efcb7888d29382b8aee7dc141c8e build: number: 0 rpaths: diff --git a/recipes/bioconductor-diffloop/meta.yaml b/recipes/bioconductor-diffloop/meta.yaml index 0fdf4551e19a0..d4b0e42f48792 100644 --- a/recipes/bioconductor-diffloop/meta.yaml +++ b/recipes/bioconductor-diffloop/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.10.0" %} +{% set version = "1.12.0" %} {% set name = "diffloop" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: a5f0e706ebe5ef31bbea8c497fe7ad90 + md5: 9d151ba0bf75463de9f3b0d13d96b5dc build: number: 0 rpaths: @@ -20,16 +20,16 @@ build: # Suggests: DESeq2, diffloopdata, ggrepel, knitr, rmarkdown, testthat requirements: host: - - 'bioconductor-biobase >=2.42.0,<2.43.0' - - 'bioconductor-biomart >=2.38.0,<2.39.0' - - 'bioconductor-edger >=3.24.0,<3.25.0' - - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' - - 'bioconductor-genomicranges >=1.34.0,<1.35.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-limma >=3.38.0,<3.39.0' - - 'bioconductor-rtracklayer >=1.42.0,<1.43.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' - - 'bioconductor-sushi >=1.20.0,<1.21.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' + - 'bioconductor-biomart >=2.40.0,<2.41.0' + - 'bioconductor-edger >=3.26.0,<3.27.0' + - 'bioconductor-genomeinfodb >=1.20.0,<1.21.0' + - 'bioconductor-genomicranges >=1.36.0,<1.37.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-limma >=3.40.0,<3.41.0' + - 'bioconductor-rtracklayer >=1.44.0,<1.45.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' + - 'bioconductor-sushi >=1.22.0,<1.23.0' - r-base - r-data.table - r-dplyr @@ -43,16 +43,16 @@ requirements: - r-reshape2 - r-statmod run: - - 'bioconductor-biobase >=2.42.0,<2.43.0' - - 'bioconductor-biomart >=2.38.0,<2.39.0' - - 'bioconductor-edger >=3.24.0,<3.25.0' - - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' - - 'bioconductor-genomicranges >=1.34.0,<1.35.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-limma >=3.38.0,<3.39.0' - - 'bioconductor-rtracklayer >=1.42.0,<1.43.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' - - 'bioconductor-sushi >=1.20.0,<1.21.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' + - 'bioconductor-biomart >=2.40.0,<2.41.0' + - 'bioconductor-edger >=3.26.0,<3.27.0' + - 'bioconductor-genomeinfodb >=1.20.0,<1.21.0' + - 'bioconductor-genomicranges >=1.36.0,<1.37.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-limma >=3.40.0,<3.41.0' + - 'bioconductor-rtracklayer >=1.44.0,<1.45.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' + - 'bioconductor-sushi >=1.22.0,<1.23.0' - r-base - r-data.table - r-dplyr diff --git a/recipes/bioconductor-diffloopdata/meta.yaml b/recipes/bioconductor-diffloopdata/meta.yaml index ef719cfa797e0..ae74cebd526f5 100644 --- a/recipes/bioconductor-diffloopdata/meta.yaml +++ b/recipes/bioconductor-diffloopdata/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.10.0" %} +{% set version = "1.12.0" %} {% set name = "diffloopdata" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 157263c6bb6d391cab4e51e575e014c3 + md5: eb6194f78579441878992b842aa3cbea build: number: 0 rpaths: @@ -23,7 +23,7 @@ requirements: - r-base run: - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-diffloopdata/post-link.sh b/recipes/bioconductor-diffloopdata/post-link.sh index f6d2241193456..c0d52a78466da 100644 --- a/recipes/bioconductor-diffloopdata/post-link.sh +++ b/recipes/bioconductor-diffloopdata/post-link.sh @@ -1,11 +1,11 @@ #!/bin/bash -FN="diffloopdata_1.10.0.tar.gz" +FN="diffloopdata_1.12.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/experiment/src/contrib/diffloopdata_1.10.0.tar.gz" - "https://bioarchive.galaxyproject.org/diffloopdata_1.10.0.tar.gz" - "https://depot.galaxyproject.org/software/bioconductor-diffloopdata/bioconductor-diffloopdata_1.10.0_src_all.tar.gz" + "https://bioconductor.org/packages/3.9/data/experiment/src/contrib/diffloopdata_1.12.0.tar.gz" + "https://bioarchive.galaxyproject.org/diffloopdata_1.12.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-diffloopdata/bioconductor-diffloopdata_1.12.0_src_all.tar.gz" ) -MD5="157263c6bb6d391cab4e51e575e014c3" +MD5="eb6194f78579441878992b842aa3cbea" # Use a staging area in the conda dir rather than temp dirs, both to avoid # permission issues as well as to have things downloaded in a predictable @@ -16,7 +16,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-diffustats/meta.yaml b/recipes/bioconductor-diffustats/meta.yaml index a1835e37667e8..bab99461cf5b0 100644 --- a/recipes/bioconductor-diffustats/meta.yaml +++ b/recipes/bioconductor-diffustats/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.2.0" %} +{% set version = "1.4.0" %} {% set name = "diffuStats" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 98921980a28a6e7ce21bf8b1d83eb6f3 + md5: 2d28196f508d79d81d396b315e840fa8 build: number: 0 rpaths: diff --git a/recipes/bioconductor-diggit/meta.yaml b/recipes/bioconductor-diggit/meta.yaml index c9ab3c9e21575..2a9837dcf03c4 100644 --- a/recipes/bioconductor-diggit/meta.yaml +++ b/recipes/bioconductor-diggit/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.14.0" %} +{% set version = "1.15.0" %} {% set name = "diggit" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,9 +10,9 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: a21bdc5d8e8cbb24df4dd989df2d1450 + md5: 222d6a6fca5fd8865aa8d43f99813558 build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ @@ -20,13 +20,13 @@ build: # Suggests: diggitdata requirements: host: - - 'bioconductor-biobase >=2.42.0,<2.43.0' - - 'bioconductor-viper >=1.16.0,<1.17.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' + - 'bioconductor-viper >=1.18.0,<1.19.0' - r-base - r-ks run: - - 'bioconductor-biobase >=2.42.0,<2.43.0' - - 'bioconductor-viper >=1.16.0,<1.17.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' + - 'bioconductor-viper >=1.18.0,<1.19.0' - r-base - r-ks test: diff --git a/recipes/bioconductor-diggitdata/meta.yaml b/recipes/bioconductor-diggitdata/meta.yaml index 30a740dfbbcd6..dbf5a7719420d 100644 --- a/recipes/bioconductor-diggitdata/meta.yaml +++ b/recipes/bioconductor-diggitdata/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.14.0" %} +{% set version = "1.16.0" %} {% set name = "diggitdata" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 5129f39e50ca1fa38fe4e56ef691e868 + md5: a16c7ace0ba38076d549222dc0afb374 build: number: 0 rpaths: @@ -19,14 +19,14 @@ build: noarch: generic requirements: host: - - 'bioconductor-biobase >=2.42.0,<2.43.0' - - 'bioconductor-viper >=1.16.0,<1.17.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' + - 'bioconductor-viper >=1.18.0,<1.19.0' - r-base run: - - 'bioconductor-biobase >=2.42.0,<2.43.0' - - 'bioconductor-viper >=1.16.0,<1.17.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' + - 'bioconductor-viper >=1.18.0,<1.19.0' - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-diggitdata/post-link.sh b/recipes/bioconductor-diggitdata/post-link.sh index 60356cb2acbb5..2d259a77534bb 100644 --- a/recipes/bioconductor-diggitdata/post-link.sh +++ b/recipes/bioconductor-diggitdata/post-link.sh @@ -1,11 +1,11 @@ #!/bin/bash -FN="diggitdata_1.14.0.tar.gz" +FN="diggitdata_1.16.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/experiment/src/contrib/diggitdata_1.14.0.tar.gz" - "https://bioarchive.galaxyproject.org/diggitdata_1.14.0.tar.gz" - "https://depot.galaxyproject.org/software/bioconductor-diggitdata/bioconductor-diggitdata_1.14.0_src_all.tar.gz" + "https://bioconductor.org/packages/3.9/data/experiment/src/contrib/diggitdata_1.16.0.tar.gz" + "https://bioarchive.galaxyproject.org/diggitdata_1.16.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-diggitdata/bioconductor-diggitdata_1.16.0_src_all.tar.gz" ) -MD5="5129f39e50ca1fa38fe4e56ef691e868" +MD5="a16c7ace0ba38076d549222dc0afb374" # Use a staging area in the conda dir rather than temp dirs, both to avoid # permission issues as well as to have things downloaded in a predictable @@ -16,7 +16,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-director/meta.yaml b/recipes/bioconductor-director/meta.yaml index 6426cf6c1e66e..d12906c19743a 100644 --- a/recipes/bioconductor-director/meta.yaml +++ b/recipes/bioconductor-director/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.8.0" %} +{% set version = "1.10.0" %} {% set name = "Director" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 2f4bce6a06d8920880b28603880e9284 + md5: 531b8d69150abadd2afb8c87c6f7929a build: number: 0 rpaths: diff --git a/recipes/bioconductor-dirichletmultinomial/meta.yaml b/recipes/bioconductor-dirichletmultinomial/meta.yaml index ccdc3a4d2d523..2a5f15401c44f 100644 --- a/recipes/bioconductor-dirichletmultinomial/meta.yaml +++ b/recipes/bioconductor-dirichletmultinomial/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.24.1" %} +{% set version = "1.26.0" %} {% set name = "DirichletMultinomial" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: aaa3d35ca05178de9e815c34a73ec17011b9f0a2606cdbce2b171d8fbf745f6d + md5: ff77746ada0149b0fb99d375f17c4b4d build: number: 0 rpaths: @@ -20,19 +20,17 @@ build: # SystemRequirements: gsl requirements: host: - - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-biocgenerics >=0.30.0,<0.31.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' - r-base - gsl - - openblas run: - - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-biocgenerics >=0.30.0,<0.31.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' - r-base - - openblas - + - gsl build: - {{ compiler('c') }} - make diff --git a/recipes/bioconductor-discordant/meta.yaml b/recipes/bioconductor-discordant/meta.yaml index 77f90fbbc9652..50bfd13b6d79c 100644 --- a/recipes/bioconductor-discordant/meta.yaml +++ b/recipes/bioconductor-discordant/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.6.1" %} +{% set version = "1.8.0" %} {% set name = "discordant" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - sha256: 98a705429f40594f69047905a4e2a87dcaa0628dae58e24118f81f7a2a0ef08b + md5: 59e96c19225caa973d164391632985a2 build: number: 0 rpaths: @@ -19,13 +19,13 @@ build: # Suggests: BiocStyle, knitr requirements: host: - - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' - r-base - r-biwt - r-gtools - r-mass run: - - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' - r-base - r-biwt - r-gtools diff --git a/recipes/bioconductor-discorhythm/build.sh b/recipes/bioconductor-discorhythm/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-discorhythm/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-discorhythm/meta.yaml b/recipes/bioconductor-discorhythm/meta.yaml new file mode 100644 index 0000000000000..f54d1d2be550e --- /dev/null +++ b/recipes/bioconductor-discorhythm/meta.yaml @@ -0,0 +1,92 @@ +{% set version = "1.0.0" %} +{% set name = "DiscoRhythm" %} +{% set bioc = "3.9" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: 850593d2b075f4bae3be34fad5eb7727 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: testthat +# SystemRequirements: To generate html reports pandoc (http://pandoc.org/installing.html) is required. +requirements: + host: + - 'bioconductor-biocgenerics >=0.30.0,<0.31.0' + - 'bioconductor-biocstyle >=2.12.0,<2.13.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' + - 'bioconductor-summarizedexperiment >=1.14.0,<1.15.0' + - r-base + - r-broom + - r-data.table + - r-dplyr + - r-dt + - r-ggextra + - r-ggplot2 + - r-gridextra + - r-heatmaply + - r-kableextra + - r-knitr + - r-magick + - r-matrixstats + - r-matrixtests + - 'r-metacycle >=1.2.0' + - r-plotly + - r-rmarkdown + - r-shiny + - r-shinybs + - r-shinycssloaders + - r-shinydashboard + - r-shinyjs + - r-upsetr + - r-venndiagram + - r-viridis + - pandoc + run: + - 'bioconductor-biocgenerics >=0.30.0,<0.31.0' + - 'bioconductor-biocstyle >=2.12.0,<2.13.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' + - 'bioconductor-summarizedexperiment >=1.14.0,<1.15.0' + - r-base + - r-broom + - r-data.table + - r-dplyr + - r-dt + - r-ggextra + - r-ggplot2 + - r-gridextra + - r-heatmaply + - r-kableextra + - r-knitr + - r-magick + - r-matrixstats + - r-matrixtests + - 'r-metacycle >=1.2.0' + - r-plotly + - r-rmarkdown + - r-shiny + - r-shinybs + - r-shinycssloaders + - r-shinydashboard + - r-shinyjs + - r-upsetr + - r-venndiagram + - r-viridis + - pandoc +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: GPL-3 + summary: 'Set of functions for estimation of cyclical characteristics, such as period, phase, amplitude, and statistical significance in large temporal datasets. Supporting functions are available for quality control, dimensionality reduction, spectral analysis, and analysis of experimental replicates. Contains a R Shiny web interface to execute all workflow steps.' + diff --git a/recipes/bioconductor-divergence/build.sh b/recipes/bioconductor-divergence/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-divergence/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-divergence/meta.yaml b/recipes/bioconductor-divergence/meta.yaml new file mode 100644 index 0000000000000..1d7696e3d9c7c --- /dev/null +++ b/recipes/bioconductor-divergence/meta.yaml @@ -0,0 +1,35 @@ +{% set version = "1.0.0" %} +{% set name = "divergence" %} +{% set bioc = "3.9" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + md5: 4aa6ee4b37d749a4349d8da511e87cee +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: knitr, rmarkdown +requirements: + host: + - 'bioconductor-summarizedexperiment >=1.14.0,<1.15.0' + - r-base + run: + - 'bioconductor-summarizedexperiment >=1.14.0,<1.15.0' + - r-base +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: GPL-2 + summary: 'This package provides functionality for performing divergence analysis as presented in Dinalankara et al, "Digitizing omics profiles by divergence from a baseline", PANS 2018. This allows the user to simplify high dimensional omics data into a binary or ternary format which encapsulates how the data is divergent from a specified baseline group with the same univariate or multivariate features.' + diff --git a/recipes/bioconductor-dks/meta.yaml b/recipes/bioconductor-dks/meta.yaml index f1e889d6fc430..e00269c164dd2 100644 --- a/recipes/bioconductor-dks/meta.yaml +++ b/recipes/bioconductor-dks/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.28.0" %} +{% set version = "1.30.0" %} {% set name = "dks" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 5ef3fc109a885dd0a57afc15b4e1892e + md5: 01287b09c7acdd4a20edba7351bdb187 build: number: 0 rpaths: diff --git a/recipes/bioconductor-dlbcl/meta.yaml b/recipes/bioconductor-dlbcl/meta.yaml index 609f552281a8c..317177887b6b3 100644 --- a/recipes/bioconductor-dlbcl/meta.yaml +++ b/recipes/bioconductor-dlbcl/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.22.0" %} +{% set version = "1.24.0" %} {% set name = "DLBCL" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: a031da595f9e721bc23ff580d3fa5bd4 + md5: 730b96fa17675ada97131b40a2466c94 build: number: 0 rpaths: @@ -19,12 +19,12 @@ build: noarch: generic requirements: host: - - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' - r-base run: - - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-dlbcl/post-link.sh b/recipes/bioconductor-dlbcl/post-link.sh index 609338118d811..f49e9f9332f91 100644 --- a/recipes/bioconductor-dlbcl/post-link.sh +++ b/recipes/bioconductor-dlbcl/post-link.sh @@ -1,11 +1,11 @@ #!/bin/bash -FN="DLBCL_1.22.0.tar.gz" +FN="DLBCL_1.24.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/experiment/src/contrib/DLBCL_1.22.0.tar.gz" - "https://bioarchive.galaxyproject.org/DLBCL_1.22.0.tar.gz" - "https://depot.galaxyproject.org/software/bioconductor-dlbcl/bioconductor-dlbcl_1.22.0_src_all.tar.gz" + "https://bioconductor.org/packages/3.9/data/experiment/src/contrib/DLBCL_1.24.0.tar.gz" + "https://bioarchive.galaxyproject.org/DLBCL_1.24.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-dlbcl/bioconductor-dlbcl_1.24.0_src_all.tar.gz" ) -MD5="a031da595f9e721bc23ff580d3fa5bd4" +MD5="730b96fa17675ada97131b40a2466c94" # Use a staging area in the conda dir rather than temp dirs, both to avoid # permission issues as well as to have things downloaded in a predictable @@ -16,7 +16,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-dmchmm/meta.yaml b/recipes/bioconductor-dmchmm/meta.yaml index a7a21f2aad802..ffedb5c04a024 100644 --- a/recipes/bioconductor-dmchmm/meta.yaml +++ b/recipes/bioconductor-dmchmm/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.4.0" %} +{% set version = "1.6.0" %} {% set name = "DMCHMM" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 18d395ae88598cefb95eefe00606bef5 + md5: 4b451c76bb34a68bc240b018e31eec15 build: number: 0 rpaths: @@ -20,23 +20,23 @@ build: # Suggests: testthat, knitr requirements: host: - - 'bioconductor-biocparallel >=1.16.0,<1.17.0' - - 'bioconductor-genomicranges >=1.34.0,<1.35.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-rtracklayer >=1.42.0,<1.43.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' - - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' + - 'bioconductor-biocparallel >=1.18.0,<1.19.0' + - 'bioconductor-genomicranges >=1.36.0,<1.37.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-rtracklayer >=1.44.0,<1.45.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' + - 'bioconductor-summarizedexperiment >=1.14.0,<1.15.0' - r-base - r-calibrate - r-fdrtool - r-multcomp run: - - 'bioconductor-biocparallel >=1.16.0,<1.17.0' - - 'bioconductor-genomicranges >=1.34.0,<1.35.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-rtracklayer >=1.42.0,<1.43.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' - - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' + - 'bioconductor-biocparallel >=1.18.0,<1.19.0' + - 'bioconductor-genomicranges >=1.36.0,<1.37.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-rtracklayer >=1.44.0,<1.45.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' + - 'bioconductor-summarizedexperiment >=1.14.0,<1.15.0' - r-base - r-calibrate - r-fdrtool diff --git a/recipes/bioconductor-dmelsgi/meta.yaml b/recipes/bioconductor-dmelsgi/meta.yaml index a6675415f275d..b4b8edf1b513c 100644 --- a/recipes/bioconductor-dmelsgi/meta.yaml +++ b/recipes/bioconductor-dmelsgi/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.14.0" %} +{% set version = "1.16.0" %} {% set name = "DmelSGI" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 9eda48b2f405f9995dcd517916961e93 + md5: 42c76634466b104f1c93c49d14757b49 build: number: 0 rpaths: @@ -20,8 +20,8 @@ build: # Suggests: BiocStyle, EBImage, RColorBrewer, RNAinteractMAPK, RSVGTipsDevice, cgdsr, hwriter, xtable, beeswarm requirements: host: - - 'bioconductor-limma >=3.38.0,<3.39.0' - - 'bioconductor-rhdf5 >=2.26.0,<2.27.0' + - 'bioconductor-limma >=3.40.0,<3.41.0' + - 'bioconductor-rhdf5 >=2.28.0,<2.29.0' - r-abind - r-base - r-gplots @@ -29,15 +29,15 @@ requirements: - r-knitr - r-tsp run: - - 'bioconductor-limma >=3.38.0,<3.39.0' - - 'bioconductor-rhdf5 >=2.26.0,<2.27.0' + - 'bioconductor-limma >=3.40.0,<3.41.0' + - 'bioconductor-rhdf5 >=2.28.0,<2.29.0' - r-abind - r-base - r-gplots - r-igraph - r-knitr - r-tsp - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-dmelsgi/post-link.sh b/recipes/bioconductor-dmelsgi/post-link.sh index dc1582005a955..4dba9e99f1d82 100644 --- a/recipes/bioconductor-dmelsgi/post-link.sh +++ b/recipes/bioconductor-dmelsgi/post-link.sh @@ -1,11 +1,11 @@ #!/bin/bash -FN="DmelSGI_1.14.0.tar.gz" +FN="DmelSGI_1.16.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/experiment/src/contrib/DmelSGI_1.14.0.tar.gz" - "https://bioarchive.galaxyproject.org/DmelSGI_1.14.0.tar.gz" - "https://depot.galaxyproject.org/software/bioconductor-dmelsgi/bioconductor-dmelsgi_1.14.0_src_all.tar.gz" + "https://bioconductor.org/packages/3.9/data/experiment/src/contrib/DmelSGI_1.16.0.tar.gz" + "https://bioarchive.galaxyproject.org/DmelSGI_1.16.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-dmelsgi/bioconductor-dmelsgi_1.16.0_src_all.tar.gz" ) -MD5="9eda48b2f405f9995dcd517916961e93" +MD5="42c76634466b104f1c93c49d14757b49" # Use a staging area in the conda dir rather than temp dirs, both to avoid # permission issues as well as to have things downloaded in a predictable @@ -16,7 +16,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-dmrcaller/meta.yaml b/recipes/bioconductor-dmrcaller/meta.yaml index eb05d65f55b04..020295165eedc 100644 --- a/recipes/bioconductor-dmrcaller/meta.yaml +++ b/recipes/bioconductor-dmrcaller/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.14.0" %} +{% set version = "1.16.0" %} {% set name = "DMRcaller" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: ce092dcceace356aa8cc520295eb8fea + md5: 23001b628eb991beec5ef7ad3921f1b1 build: number: 0 rpaths: @@ -19,17 +19,17 @@ build: # Suggests: knitr, RUnit, BiocGenerics requirements: host: - - 'bioconductor-genomicranges >=1.34.0,<1.35.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-genomicranges >=1.36.0,<1.37.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' - r-base - r-betareg - r-rcpp - r-rcpproll run: - - 'bioconductor-genomicranges >=1.34.0,<1.35.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-genomicranges >=1.36.0,<1.37.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' - r-base - r-betareg - r-rcpp diff --git a/recipes/bioconductor-dmrcate/meta.yaml b/recipes/bioconductor-dmrcate/meta.yaml index bf304769dab11..b260dfb9e3a79 100644 --- a/recipes/bioconductor-dmrcate/meta.yaml +++ b/recipes/bioconductor-dmrcate/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.18.0" %} +{% set version = "1.20.0" %} {% set name = "DMRcate" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 4bfe58dbc6445926f73996a187c6aa1f + md5: 835c193be0468ad25fb4eb90bda45c77 build: number: 0 rpaths: @@ -20,27 +20,27 @@ build: # Suggests: knitr, RUnit, BiocGenerics, IlluminaHumanMethylation450kanno.ilmn12.hg19, IlluminaHumanMethylationEPICanno.ilm10b4.hg19 requirements: host: - - 'bioconductor-dmrcatedata >=1.18.0,<1.19.0' - - 'bioconductor-dss >=2.30.0,<2.31.0' - - 'bioconductor-genomicranges >=1.34.0,<1.35.0' - - 'bioconductor-gviz >=1.26.0,<1.27.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-limma >=3.38.0,<3.39.0' - - 'bioconductor-minfi >=1.28.0,<1.29.0' - - 'bioconductor-missmethyl >=1.16.0,<1.17.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-dmrcatedata >=1.20.0,<1.21.0' + - 'bioconductor-dss >=2.32.0,<2.33.0' + - 'bioconductor-genomicranges >=1.36.0,<1.37.0' + - 'bioconductor-gviz >=1.28.0,<1.29.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-limma >=3.40.0,<3.41.0' + - 'bioconductor-minfi >=1.30.0,<1.31.0' + - 'bioconductor-missmethyl >=1.18.0,<1.19.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' - r-base - r-plyr run: - - 'bioconductor-dmrcatedata >=1.18.0,<1.19.0' - - 'bioconductor-dss >=2.30.0,<2.31.0' - - 'bioconductor-genomicranges >=1.34.0,<1.35.0' - - 'bioconductor-gviz >=1.26.0,<1.27.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-limma >=3.38.0,<3.39.0' - - 'bioconductor-minfi >=1.28.0,<1.29.0' - - 'bioconductor-missmethyl >=1.16.0,<1.17.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-dmrcatedata >=1.20.0,<1.21.0' + - 'bioconductor-dss >=2.32.0,<2.33.0' + - 'bioconductor-genomicranges >=1.36.0,<1.37.0' + - 'bioconductor-gviz >=1.28.0,<1.29.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-limma >=3.40.0,<3.41.0' + - 'bioconductor-minfi >=1.30.0,<1.31.0' + - 'bioconductor-missmethyl >=1.18.0,<1.19.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' - r-base - r-plyr test: diff --git a/recipes/bioconductor-dmrcatedata/meta.yaml b/recipes/bioconductor-dmrcatedata/meta.yaml index 9a779a868a7cc..74ce0b2484283 100644 --- a/recipes/bioconductor-dmrcatedata/meta.yaml +++ b/recipes/bioconductor-dmrcatedata/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.18.0" %} +{% set version = "1.20.0" %} {% set name = "DMRcatedata" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: b929cb1b0888f6cbd0e41219b3807b84 + md5: 4401fe1a28b3d313d4ec38d5ca48b7fe build: number: 0 rpaths: @@ -20,12 +20,12 @@ build: # Suggests: knitr requirements: host: - - 'bioconductor-genomicranges >=1.34.0,<1.35.0' + - 'bioconductor-genomicranges >=1.36.0,<1.37.0' - r-base run: - - 'bioconductor-genomicranges >=1.34.0,<1.35.0' + - 'bioconductor-genomicranges >=1.36.0,<1.37.0' - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-dmrcatedata/post-link.sh b/recipes/bioconductor-dmrcatedata/post-link.sh index 87b74409ac6b8..ecc509268c5dc 100644 --- a/recipes/bioconductor-dmrcatedata/post-link.sh +++ b/recipes/bioconductor-dmrcatedata/post-link.sh @@ -1,11 +1,11 @@ #!/bin/bash -FN="DMRcatedata_1.18.0.tar.gz" +FN="DMRcatedata_1.20.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/experiment/src/contrib/DMRcatedata_1.18.0.tar.gz" - "https://bioarchive.galaxyproject.org/DMRcatedata_1.18.0.tar.gz" - "https://depot.galaxyproject.org/software/bioconductor-dmrcatedata/bioconductor-dmrcatedata_1.18.0_src_all.tar.gz" + "https://bioconductor.org/packages/3.9/data/experiment/src/contrib/DMRcatedata_1.20.0.tar.gz" + "https://bioarchive.galaxyproject.org/DMRcatedata_1.20.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-dmrcatedata/bioconductor-dmrcatedata_1.20.0_src_all.tar.gz" ) -MD5="b929cb1b0888f6cbd0e41219b3807b84" +MD5="4401fe1a28b3d313d4ec38d5ca48b7fe" # Use a staging area in the conda dir rather than temp dirs, both to avoid # permission issues as well as to have things downloaded in a predictable @@ -16,7 +16,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-dmrforpairs/meta.yaml b/recipes/bioconductor-dmrforpairs/meta.yaml index e2edc4b3970e0..8f79f51779ffd 100644 --- a/recipes/bioconductor-dmrforpairs/meta.yaml +++ b/recipes/bioconductor-dmrforpairs/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.18.0" %} +{% set version = "1.20.0" %} {% set name = "DMRforPairs" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 0f972e67a117c8be0dc1cc2fcf831ab7 + md5: 4f92ad08fcb9bdbd584cac54e4ed788c build: number: 0 rpaths: @@ -19,13 +19,13 @@ build: noarch: generic requirements: host: - - 'bioconductor-genomicranges >=1.34.0,<1.35.0' - - 'bioconductor-gviz >=1.26.0,<1.27.0' + - 'bioconductor-genomicranges >=1.36.0,<1.37.0' + - 'bioconductor-gviz >=1.28.0,<1.29.0' - r-base - 'r-r2html >=2.2.1' run: - - 'bioconductor-genomicranges >=1.34.0,<1.35.0' - - 'bioconductor-gviz >=1.26.0,<1.27.0' + - 'bioconductor-genomicranges >=1.36.0,<1.37.0' + - 'bioconductor-gviz >=1.28.0,<1.29.0' - r-base - 'r-r2html >=2.2.1' test: diff --git a/recipes/bioconductor-dmrscan/meta.yaml b/recipes/bioconductor-dmrscan/meta.yaml index 60552464d5e8a..7266e9bf3d959 100644 --- a/recipes/bioconductor-dmrscan/meta.yaml +++ b/recipes/bioconductor-dmrscan/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.8.0" %} +{% set version = "1.10.0" %} {% set name = "DMRScan" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 0e746f249607060c44d9f4591fc72a1d + md5: b5ecc41efedcac307eea126809b029a4 build: number: 0 rpaths: @@ -20,18 +20,18 @@ build: # Suggests: testthat, knitr, rmarkdown requirements: host: - - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' - - 'bioconductor-genomicranges >=1.34.0,<1.35.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-genomeinfodb >=1.20.0,<1.21.0' + - 'bioconductor-genomicranges >=1.36.0,<1.37.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' - r-base - r-mass - r-matrix - r-mvtnorm - r-rcpproll run: - - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' - - 'bioconductor-genomicranges >=1.34.0,<1.35.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-genomeinfodb >=1.20.0,<1.21.0' + - 'bioconductor-genomicranges >=1.36.0,<1.37.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' - r-base - r-mass - r-matrix diff --git a/recipes/bioconductor-dmrseq/meta.yaml b/recipes/bioconductor-dmrseq/meta.yaml index e01b30c46942c..7532b5bd4baca 100644 --- a/recipes/bioconductor-dmrseq/meta.yaml +++ b/recipes/bioconductor-dmrseq/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.2.1" %} +{% set version = "1.4.0" %} {% set name = "dmrseq" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: e388d10623aea75e8909ccc6ef875fa5 + md5: cef5b646ee11d99f8fbba86e93a2f9d0 build: number: 0 rpaths: @@ -20,17 +20,17 @@ build: # Suggests: knitr, rmarkdown, BiocStyle requirements: host: - - 'bioconductor-annotationhub >=2.14.0,<2.15.0' - - 'bioconductor-annotatr >=1.8.0,<1.9.0' - - 'bioconductor-biocparallel >=1.16.0,<1.17.0' - - 'bioconductor-bsseq >=1.18.0,<1.19.0' - - 'bioconductor-bumphunter >=1.24.0,<1.25.0' - - 'bioconductor-delayedmatrixstats >=1.4.0,<1.5.0' - - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' - - 'bioconductor-genomicranges >=1.34.0,<1.35.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-rtracklayer >=1.42.0,<1.43.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-annotationhub >=2.16.0,<2.17.0' + - 'bioconductor-annotatr >=1.10.0,<1.11.0' + - 'bioconductor-biocparallel >=1.18.0,<1.19.0' + - 'bioconductor-bsseq >=1.20.0,<1.21.0' + - 'bioconductor-bumphunter >=1.26.0,<1.27.0' + - 'bioconductor-delayedmatrixstats >=1.6.0,<1.7.0' + - 'bioconductor-genomeinfodb >=1.20.0,<1.21.0' + - 'bioconductor-genomicranges >=1.36.0,<1.37.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-rtracklayer >=1.44.0,<1.45.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' - r-base - r-ggplot2 - r-locfit @@ -39,17 +39,17 @@ requirements: - r-outliers - r-rcolorbrewer run: - - 'bioconductor-annotationhub >=2.14.0,<2.15.0' - - 'bioconductor-annotatr >=1.8.0,<1.9.0' - - 'bioconductor-biocparallel >=1.16.0,<1.17.0' - - 'bioconductor-bsseq >=1.18.0,<1.19.0' - - 'bioconductor-bumphunter >=1.24.0,<1.25.0' - - 'bioconductor-delayedmatrixstats >=1.4.0,<1.5.0' - - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' - - 'bioconductor-genomicranges >=1.34.0,<1.35.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-rtracklayer >=1.42.0,<1.43.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-annotationhub >=2.16.0,<2.17.0' + - 'bioconductor-annotatr >=1.10.0,<1.11.0' + - 'bioconductor-biocparallel >=1.18.0,<1.19.0' + - 'bioconductor-bsseq >=1.20.0,<1.21.0' + - 'bioconductor-bumphunter >=1.26.0,<1.27.0' + - 'bioconductor-delayedmatrixstats >=1.6.0,<1.7.0' + - 'bioconductor-genomeinfodb >=1.20.0,<1.21.0' + - 'bioconductor-genomicranges >=1.36.0,<1.37.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-rtracklayer >=1.44.0,<1.45.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' - r-base - r-ggplot2 - r-locfit diff --git a/recipes/bioconductor-dnabarcodecompatibility/build.sh b/recipes/bioconductor-dnabarcodecompatibility/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-dnabarcodecompatibility/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-dnabarcodecompatibility/meta.yaml b/recipes/bioconductor-dnabarcodecompatibility/meta.yaml new file mode 100644 index 0000000000000..bd0f7f7bb71fa --- /dev/null +++ b/recipes/bioconductor-dnabarcodecompatibility/meta.yaml @@ -0,0 +1,45 @@ +{% set version = "1.0.0" %} +{% set name = "DNABarcodeCompatibility" %} +{% set bioc = "3.9" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: 29d41c899bb70efb83f22cf7405c9122 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: knitr, rmarkdown, BiocStyle, testthat +requirements: + host: + - 'bioconductor-dnabarcodes >=1.14.0,<1.15.0' + - r-base + - r-dplyr + - r-numbers + - r-purrr + - r-stringr + - r-tidyr + run: + - 'bioconductor-dnabarcodes >=1.14.0,<1.15.0' + - r-base + - r-dplyr + - r-numbers + - r-purrr + - r-stringr + - r-tidyr +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: GPL-2 + summary: 'The package allows one to obtain optimized combinations of DNA barcodes to be used for multiplex sequencing. In each barcode combination, barcodes are pooled with respect to Illumina chemistry constraints. Combinations can be filtered to keep those that are robust against substitution and insertion/deletion errors thereby facilitating the demultiplexing step. In addition, the package provides an optimizer function to further favor the selection of barcode combinations with least redundancy of DNA barcodes.' + diff --git a/recipes/bioconductor-dnabarcodes/meta.yaml b/recipes/bioconductor-dnabarcodes/meta.yaml index 10c314bd88f35..586784af4292a 100644 --- a/recipes/bioconductor-dnabarcodes/meta.yaml +++ b/recipes/bioconductor-dnabarcodes/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.12.0" %} +{% set version = "1.14.0" %} {% set name = "DNABarcodes" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 7c3ceda6d5afa1322c928dab20a28f74 + md5: d5e24b79f158ae0aa4641b8215e81f7c build: number: 0 rpaths: @@ -28,12 +28,10 @@ requirements: - r-bh - r-matrix - 'r-rcpp >=0.11.2' - - llvm-openmp # [osx] build: - {{ compiler('c') }} - {{ compiler('cxx') }} - make - - llvm-openmp # [osx] test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-dnacopy/meta.yaml b/recipes/bioconductor-dnacopy/meta.yaml index f7e24d9bcfe42..cf5fd383a73ec 100644 --- a/recipes/bioconductor-dnacopy/meta.yaml +++ b/recipes/bioconductor-dnacopy/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.56.0" %} +{% set version = "1.58.0" %} {% set name = "DNAcopy" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 184fc2c7f242fcfe49504ad1e135f34f + md5: 459165b252a246b8cfe1b1dc792079c8 build: number: 0 rpaths: diff --git a/recipes/bioconductor-dnashaper/meta.yaml b/recipes/bioconductor-dnashaper/meta.yaml index 1317fd25f9211..22d64e7b5e885 100644 --- a/recipes/bioconductor-dnashaper/meta.yaml +++ b/recipes/bioconductor-dnashaper/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.10.0" %} +{% set version = "1.12.0" %} {% set name = "DNAshapeR" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: d0da206934c751b45cc8606a22dbeb6d + md5: 7f27913e977cf523165f72f81957c94e build: number: 0 rpaths: @@ -19,14 +19,14 @@ build: # Suggests: AnnotationHub, knitr, rmarkdown, testthat, BSgenome.Scerevisiae.UCSC.sacCer3, BSgenome.Hsapiens.UCSC.hg19, caret requirements: host: - - 'bioconductor-biostrings >=2.50.0,<2.51.0' - - 'bioconductor-genomicranges >=1.34.0,<1.35.0' + - 'bioconductor-biostrings >=2.52.0,<2.53.0' + - 'bioconductor-genomicranges >=1.36.0,<1.37.0' - r-base - r-fields - 'r-rcpp >=0.12.1' run: - - 'bioconductor-biostrings >=2.50.0,<2.51.0' - - 'bioconductor-genomicranges >=1.34.0,<1.35.0' + - 'bioconductor-biostrings >=2.52.0,<2.53.0' + - 'bioconductor-genomicranges >=1.36.0,<1.37.0' - r-base - r-fields - 'r-rcpp >=0.12.1' diff --git a/recipes/bioconductor-do.db/meta.yaml b/recipes/bioconductor-do.db/meta.yaml index 4b4b452f717c3..5c4027251e89f 100644 --- a/recipes/bioconductor-do.db/meta.yaml +++ b/recipes/bioconductor-do.db/meta.yaml @@ -1,6 +1,6 @@ {% set version = "2.9" %} {% set name = "DO.db" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -12,19 +12,19 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' md5: 63dda6d46d2fe40c52a2e79260a7fb9d build: - number: 4 + number: 5 rpaths: - lib/R/lib/ - lib/ noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' - r-base run: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-do.db/post-link.sh b/recipes/bioconductor-do.db/post-link.sh index 3b3a029afa379..86ce9ed3bf995 100644 --- a/recipes/bioconductor-do.db/post-link.sh +++ b/recipes/bioconductor-do.db/post-link.sh @@ -1,7 +1,7 @@ #!/bin/bash FN="DO.db_2.9.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/DO.db_2.9.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/DO.db_2.9.tar.gz" "https://bioarchive.galaxyproject.org/DO.db_2.9.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-do.db/bioconductor-do.db_2.9_src_all.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-do.db/bioconductor-do.db_2.9_src_all.tar.gz" @@ -17,7 +17,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-dominoeffect/meta.yaml b/recipes/bioconductor-dominoeffect/meta.yaml index c08e4a420596c..068947e2101e1 100644 --- a/recipes/bioconductor-dominoeffect/meta.yaml +++ b/recipes/bioconductor-dominoeffect/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.2.1" %} +{% set version = "1.4.0" %} {% set name = "DominoEffect" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: b4ff1d47e6409ad76352e13709577d25 + md5: 72e2fad413e30de2ff92289505bebbb7 build: number: 0 rpaths: @@ -20,25 +20,25 @@ build: # Suggests: knitr, testthat requirements: host: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' - - 'bioconductor-biomart >=2.38.0,<2.39.0' - - 'bioconductor-biostrings >=2.50.0,<2.51.0' - - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' - - 'bioconductor-genomicranges >=1.34.0,<1.35.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' - - 'bioconductor-variantannotation >=1.28.0,<1.29.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' + - 'bioconductor-biomart >=2.40.0,<2.41.0' + - 'bioconductor-biostrings >=2.52.0,<2.53.0' + - 'bioconductor-genomeinfodb >=1.20.0,<1.21.0' + - 'bioconductor-genomicranges >=1.36.0,<1.37.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-summarizedexperiment >=1.14.0,<1.15.0' + - 'bioconductor-variantannotation >=1.30.0,<1.31.0' - r-base - r-data.table run: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' - - 'bioconductor-biomart >=2.38.0,<2.39.0' - - 'bioconductor-biostrings >=2.50.0,<2.51.0' - - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' - - 'bioconductor-genomicranges >=1.34.0,<1.35.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' - - 'bioconductor-variantannotation >=1.28.0,<1.29.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' + - 'bioconductor-biomart >=2.40.0,<2.41.0' + - 'bioconductor-biostrings >=2.52.0,<2.53.0' + - 'bioconductor-genomeinfodb >=1.20.0,<1.21.0' + - 'bioconductor-genomicranges >=1.36.0,<1.37.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-summarizedexperiment >=1.14.0,<1.15.0' + - 'bioconductor-variantannotation >=1.30.0,<1.31.0' - r-base - r-data.table test: diff --git a/recipes/bioconductor-donapllp2013/meta.yaml b/recipes/bioconductor-donapllp2013/meta.yaml index eaf0805c0896e..173b0bb68a587 100644 --- a/recipes/bioconductor-donapllp2013/meta.yaml +++ b/recipes/bioconductor-donapllp2013/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.20.0" %} +{% set version = "1.22.0" %} {% set name = "DonaPLLP2013" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 5a228295986fdfe1ad44a66ca2f1d947 + md5: dc254e899f0e9368fea3d2543408970c build: number: 0 rpaths: @@ -19,12 +19,12 @@ build: noarch: generic requirements: host: - - 'bioconductor-ebimage >=4.24.0,<4.25.0' + - 'bioconductor-ebimage >=4.26.0,<4.27.0' - r-base run: - - 'bioconductor-ebimage >=4.24.0,<4.25.0' + - 'bioconductor-ebimage >=4.26.0,<4.27.0' - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-donapllp2013/post-link.sh b/recipes/bioconductor-donapllp2013/post-link.sh index 67cbeb1413547..f52fd2e345ba8 100644 --- a/recipes/bioconductor-donapllp2013/post-link.sh +++ b/recipes/bioconductor-donapllp2013/post-link.sh @@ -1,11 +1,11 @@ #!/bin/bash -FN="DonaPLLP2013_1.20.0.tar.gz" +FN="DonaPLLP2013_1.22.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/experiment/src/contrib/DonaPLLP2013_1.20.0.tar.gz" - "https://bioarchive.galaxyproject.org/DonaPLLP2013_1.20.0.tar.gz" - "https://depot.galaxyproject.org/software/bioconductor-donapllp2013/bioconductor-donapllp2013_1.20.0_src_all.tar.gz" + "https://bioconductor.org/packages/3.9/data/experiment/src/contrib/DonaPLLP2013_1.22.0.tar.gz" + "https://bioarchive.galaxyproject.org/DonaPLLP2013_1.22.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-donapllp2013/bioconductor-donapllp2013_1.22.0_src_all.tar.gz" ) -MD5="5a228295986fdfe1ad44a66ca2f1d947" +MD5="dc254e899f0e9368fea3d2543408970c" # Use a staging area in the conda dir rather than temp dirs, both to avoid # permission issues as well as to have things downloaded in a predictable @@ -16,7 +16,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-doppelgangr/meta.yaml b/recipes/bioconductor-doppelgangr/meta.yaml index 066821bd5a403..62f6ad4d96bdb 100644 --- a/recipes/bioconductor-doppelgangr/meta.yaml +++ b/recipes/bioconductor-doppelgangr/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.10.1" %} +{% set version = "1.12.0" %} {% set name = "doppelgangR" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 81743278a4db71d5b8881189df2c08af + md5: e592f39c775f1c9ab21a45f3b9261c6d build: number: 0 rpaths: @@ -20,20 +20,20 @@ build: # Suggests: BiocStyle, knitr, rmarkdown, curatedOvarianData, ROCR, pROC, RUnit, simulatorZ, proxy requirements: host: - - 'bioconductor-biobase >=2.42.0,<2.43.0' - - 'bioconductor-biocparallel >=1.16.0,<1.17.0' - - 'bioconductor-impute >=1.56.0,<1.57.0' - - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' - - 'bioconductor-sva >=3.30.0,<3.31.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' + - 'bioconductor-biocparallel >=1.18.0,<1.19.0' + - 'bioconductor-impute >=1.58.0,<1.59.0' + - 'bioconductor-summarizedexperiment >=1.14.0,<1.15.0' + - 'bioconductor-sva >=3.32.0,<3.33.0' - r-base - r-digest - r-mnormt run: - - 'bioconductor-biobase >=2.42.0,<2.43.0' - - 'bioconductor-biocparallel >=1.16.0,<1.17.0' - - 'bioconductor-impute >=1.56.0,<1.57.0' - - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' - - 'bioconductor-sva >=3.30.0,<3.31.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' + - 'bioconductor-biocparallel >=1.18.0,<1.19.0' + - 'bioconductor-impute >=1.58.0,<1.59.0' + - 'bioconductor-summarizedexperiment >=1.14.0,<1.15.0' + - 'bioconductor-sva >=3.32.0,<3.33.0' - r-base - r-digest - r-mnormt diff --git a/recipes/bioconductor-doqtl/meta.yaml b/recipes/bioconductor-doqtl/meta.yaml index df479a1f46808..d3ae4e69b82a0 100644 --- a/recipes/bioconductor-doqtl/meta.yaml +++ b/recipes/bioconductor-doqtl/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.18.0" %} +{% set version = "1.19.0" %} {% set name = "DOQTL" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 8b15a6d126d98936877e94434c13b3b5 + md5: 680f81e25019ae46bc2eb0ea51bdd72e build: number: 0 rpaths: @@ -19,17 +19,17 @@ build: # Suggests: MUGAExampleData requirements: host: - - 'bioconductor-annotate >=1.60.0,<1.61.0' - - 'bioconductor-annotationtools >=1.56.0,<1.57.0' - - 'bioconductor-biobase >=2.42.0,<2.43.0' - - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' - - 'bioconductor-biomart >=2.38.0,<2.39.0' + - 'bioconductor-annotate >=1.62.0,<1.63.0' + - 'bioconductor-annotationtools >=1.58.0,<1.59.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' + - 'bioconductor-biocgenerics >=0.30.0,<0.31.0' + - 'bioconductor-biomart >=2.40.0,<2.41.0' - 'bioconductor-bsgenome.mmusculus.ucsc.mm10 >=1.4.0,<1.5.0' - - 'bioconductor-genomicranges >=1.34.0,<1.35.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-rhdf5 >=2.26.0,<2.27.0' - - 'bioconductor-rsamtools >=1.34.0,<1.35.0' - - 'bioconductor-variantannotation >=1.28.0,<1.29.0' + - 'bioconductor-genomicranges >=1.36.0,<1.37.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-rhdf5 >=2.28.0,<2.29.0' + - 'bioconductor-rsamtools >=2.0.0,<2.1.0' + - 'bioconductor-variantannotation >=1.30.0,<1.31.0' - r-base - r-corpcor - r-doparallel @@ -43,17 +43,17 @@ requirements: - r-runit - r-xml run: - - 'bioconductor-annotate >=1.60.0,<1.61.0' - - 'bioconductor-annotationtools >=1.56.0,<1.57.0' - - 'bioconductor-biobase >=2.42.0,<2.43.0' - - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' - - 'bioconductor-biomart >=2.38.0,<2.39.0' + - 'bioconductor-annotate >=1.62.0,<1.63.0' + - 'bioconductor-annotationtools >=1.58.0,<1.59.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' + - 'bioconductor-biocgenerics >=0.30.0,<0.31.0' + - 'bioconductor-biomart >=2.40.0,<2.41.0' - 'bioconductor-bsgenome.mmusculus.ucsc.mm10 >=1.4.0,<1.5.0' - - 'bioconductor-genomicranges >=1.34.0,<1.35.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-rhdf5 >=2.26.0,<2.27.0' - - 'bioconductor-rsamtools >=1.34.0,<1.35.0' - - 'bioconductor-variantannotation >=1.28.0,<1.29.0' + - 'bioconductor-genomicranges >=1.36.0,<1.37.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-rhdf5 >=2.28.0,<2.29.0' + - 'bioconductor-rsamtools >=2.0.0,<2.1.0' + - 'bioconductor-variantannotation >=1.30.0,<1.31.0' - r-base - r-corpcor - r-doparallel diff --git a/recipes/bioconductor-doscheda/meta.yaml b/recipes/bioconductor-doscheda/meta.yaml index b27ddce5d445b..7fcae1551d602 100644 --- a/recipes/bioconductor-doscheda/meta.yaml +++ b/recipes/bioconductor-doscheda/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.4.0" %} +{% set version = "1.6.0" %} {% set name = "Doscheda" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: f10e02e1255d3fc585c0710e482d75e5 + md5: 6f97a7a6534ee3d3c09d0c35e23e71d8 build: number: 0 rpaths: @@ -20,9 +20,9 @@ build: # Suggests: BiocStyle, knitr, rmarkdown, testthat requirements: host: - - 'bioconductor-affy >=1.60.0,<1.61.0' - - 'bioconductor-limma >=3.38.0,<3.39.0' - - 'bioconductor-vsn >=3.50.0,<3.51.0' + - 'bioconductor-affy >=1.62.0,<1.63.0' + - 'bioconductor-limma >=3.40.0,<3.41.0' + - 'bioconductor-vsn >=3.52.0,<3.53.0' - r-base - r-calibrate - r-corrgram @@ -41,9 +41,9 @@ requirements: - r-shinydashboard - r-stringr run: - - 'bioconductor-affy >=1.60.0,<1.61.0' - - 'bioconductor-limma >=3.38.0,<3.39.0' - - 'bioconductor-vsn >=3.50.0,<3.51.0' + - 'bioconductor-affy >=1.62.0,<1.63.0' + - 'bioconductor-limma >=3.40.0,<3.41.0' + - 'bioconductor-vsn >=3.52.0,<3.53.0' - r-base - r-calibrate - r-corrgram diff --git a/recipes/bioconductor-dose/meta.yaml b/recipes/bioconductor-dose/meta.yaml index 86aa6afc2e424..eea8dbd74da96 100644 --- a/recipes/bioconductor-dose/meta.yaml +++ b/recipes/bioconductor-dose/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "3.8.0" %} +{% set version = "3.10.0" %} {% set name = "DOSE" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,34 +10,34 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: a179a5c31428292643cadb40577409f7 + md5: d3c54fe039819f2fec31d8da313ee06e build: number: 0 rpaths: - lib/R/lib/ - lib/ noarch: generic -# Suggests: BiocStyle, clusterProfiler, knitr, org.Hs.eg.db, testthat +# Suggests: prettydoc, clusterProfiler, knitr, org.Hs.eg.db, testthat requirements: host: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' - - 'bioconductor-biocparallel >=1.16.0,<1.17.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' + - 'bioconductor-biocparallel >=1.18.0,<1.19.0' - 'bioconductor-do.db 2.9' - - 'bioconductor-fgsea >=1.8.0,<1.9.0' - - 'bioconductor-gosemsim >=2.8.0,<2.9.0' - - 'bioconductor-qvalue >=2.14.0,<2.15.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-fgsea >=1.10.0,<1.11.0' + - 'bioconductor-gosemsim >=2.10.0,<2.11.0' + - 'bioconductor-qvalue >=2.16.0,<2.17.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' - r-base - r-ggplot2 - r-reshape2 run: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' - - 'bioconductor-biocparallel >=1.16.0,<1.17.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' + - 'bioconductor-biocparallel >=1.18.0,<1.19.0' - 'bioconductor-do.db 2.9' - - 'bioconductor-fgsea >=1.8.0,<1.9.0' - - 'bioconductor-gosemsim >=2.8.0,<2.9.0' - - 'bioconductor-qvalue >=2.14.0,<2.15.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-fgsea >=1.10.0,<1.11.0' + - 'bioconductor-gosemsim >=2.10.0,<2.11.0' + - 'bioconductor-qvalue >=2.16.0,<2.17.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' - r-base - r-ggplot2 - r-reshape2 diff --git a/recipes/bioconductor-doser/build.sh b/recipes/bioconductor-doser/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-doser/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-doser/meta.yaml b/recipes/bioconductor-doser/meta.yaml new file mode 100644 index 0000000000000..42e597b8c689a --- /dev/null +++ b/recipes/bioconductor-doser/meta.yaml @@ -0,0 +1,49 @@ +{% set version = "1.0.0" %} +{% set name = "doseR" %} +{% set bioc = "3.9" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: 66d789556a8eadf0bc626496ca65b490 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: BiocStyle, knitr, rmarkdown +requirements: + host: + - 'bioconductor-edger >=3.26.0,<3.27.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' + - 'bioconductor-summarizedexperiment >=1.14.0,<1.15.0' + - r-base + - r-digest + - r-lme4 + - r-matrixstats + - r-mclust + - r-runit + run: + - 'bioconductor-edger >=3.26.0,<3.27.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' + - 'bioconductor-summarizedexperiment >=1.14.0,<1.15.0' + - r-base + - r-digest + - r-lme4 + - r-matrixstats + - r-mclust + - r-runit +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: GPL + summary: 'doseR package is a next generation sequencing package for sex chromosome dosage compensation which can be applied broadly to detect shifts in gene expression among an arbitrary number of pre-defined groups of loci. doseR is a differential gene expression package for count data, that detects directional shifts in expression for multiple, specific subsets of genes, broad utility in systems biology research. doseR has been prepared to manage the nature of the data and the desired set of inferences. doseR uses S4 classes to store count data from sequencing experiment. It contains functions to normalize and filter count data, as well as to plot and calculate statistics of count data. It contains a framework for linear modeling of count data. The package has been tested using real and simulated data.' + diff --git a/recipes/bioconductor-drawproteins/meta.yaml b/recipes/bioconductor-drawproteins/meta.yaml index 5b9d438daa076..584dcf181fe90 100644 --- a/recipes/bioconductor-drawproteins/meta.yaml +++ b/recipes/bioconductor-drawproteins/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.2.0" %} +{% set version = "1.4.0" %} {% set name = "drawProteins" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 206c89be262e17a9c1f9611aa69272c5 + md5: cea2f328f8d1343ea7c79eb07a7c0774 build: number: 0 rpaths: @@ -26,6 +26,7 @@ requirements: - r-httr - r-readr - r-stringr + - r-tidyr run: - r-base - r-dplyr @@ -33,6 +34,7 @@ requirements: - r-httr - r-readr - r-stringr + - r-tidyr test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-dream4/meta.yaml b/recipes/bioconductor-dream4/meta.yaml index 4e6bf3a212cdf..fbb105bee0064 100644 --- a/recipes/bioconductor-dream4/meta.yaml +++ b/recipes/bioconductor-dream4/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.18.0" %} +{% set version = "1.20.0" %} {% set name = "DREAM4" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 47e37f3d98279f6f1f1e5dfa1198f1b3 + md5: 00d929e1410ebea22bae8e2f9b15ea6e build: number: 0 rpaths: @@ -20,12 +20,12 @@ build: # Suggests: RUnit, networkBMA requirements: host: - - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' + - 'bioconductor-summarizedexperiment >=1.14.0,<1.15.0' - r-base run: - - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' + - 'bioconductor-summarizedexperiment >=1.14.0,<1.15.0' - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-dream4/post-link.sh b/recipes/bioconductor-dream4/post-link.sh index 8b276626a350f..6fddfaffbf332 100644 --- a/recipes/bioconductor-dream4/post-link.sh +++ b/recipes/bioconductor-dream4/post-link.sh @@ -1,11 +1,11 @@ #!/bin/bash -FN="DREAM4_1.18.0.tar.gz" +FN="DREAM4_1.20.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/experiment/src/contrib/DREAM4_1.18.0.tar.gz" - "https://bioarchive.galaxyproject.org/DREAM4_1.18.0.tar.gz" - "https://depot.galaxyproject.org/software/bioconductor-dream4/bioconductor-dream4_1.18.0_src_all.tar.gz" + "https://bioconductor.org/packages/3.9/data/experiment/src/contrib/DREAM4_1.20.0.tar.gz" + "https://bioarchive.galaxyproject.org/DREAM4_1.20.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-dream4/bioconductor-dream4_1.20.0_src_all.tar.gz" ) -MD5="47e37f3d98279f6f1f1e5dfa1198f1b3" +MD5="00d929e1410ebea22bae8e2f9b15ea6e" # Use a staging area in the conda dir rather than temp dirs, both to avoid # permission issues as well as to have things downloaded in a predictable @@ -16,7 +16,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-dresscheck/meta.yaml b/recipes/bioconductor-dresscheck/meta.yaml index e7ad67cf00c18..8376dc3981749 100644 --- a/recipes/bioconductor-dresscheck/meta.yaml +++ b/recipes/bioconductor-dresscheck/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "0.20.0" %} +{% set version = "0.22.0" %} {% set name = "dressCheck" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: dad61d2a1cfae86bc1f1b9f132291ae6 + md5: 7584cc6c48fa1c394fe41c524f7b3854 build: number: 0 rpaths: @@ -20,12 +20,12 @@ build: # Suggests: survival, chron requirements: host: - - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' - r-base run: - - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-dresscheck/post-link.sh b/recipes/bioconductor-dresscheck/post-link.sh index e30625c962d74..73786ed6afbca 100644 --- a/recipes/bioconductor-dresscheck/post-link.sh +++ b/recipes/bioconductor-dresscheck/post-link.sh @@ -1,11 +1,11 @@ #!/bin/bash -FN="dressCheck_0.20.0.tar.gz" +FN="dressCheck_0.22.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/experiment/src/contrib/dressCheck_0.20.0.tar.gz" - "https://bioarchive.galaxyproject.org/dressCheck_0.20.0.tar.gz" - "https://depot.galaxyproject.org/software/bioconductor-dresscheck/bioconductor-dresscheck_0.20.0_src_all.tar.gz" + "https://bioconductor.org/packages/3.9/data/experiment/src/contrib/dressCheck_0.22.0.tar.gz" + "https://bioarchive.galaxyproject.org/dressCheck_0.22.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-dresscheck/bioconductor-dresscheck_0.22.0_src_all.tar.gz" ) -MD5="dad61d2a1cfae86bc1f1b9f132291ae6" +MD5="7584cc6c48fa1c394fe41c524f7b3854" # Use a staging area in the conda dir rather than temp dirs, both to avoid # permission issues as well as to have things downloaded in a predictable @@ -16,7 +16,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-drimseq/meta.yaml b/recipes/bioconductor-drimseq/meta.yaml index 887a639e2a881..f47c6e3aaa2a7 100644 --- a/recipes/bioconductor-drimseq/meta.yaml +++ b/recipes/bioconductor-drimseq/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.10.0" %} +{% set version = "1.12.0" %} {% set name = "DRIMSeq" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 1f674b2ade74a9c629045f01def425ff + md5: 399bc7fe47de2da27d0f357470c7037e build: number: 0 rpaths: @@ -20,25 +20,25 @@ build: # Suggests: PasillaTranscriptExpr, GeuvadisTranscriptExpr, grid, BiocStyle, knitr, testthat requirements: host: - - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' - - 'bioconductor-biocparallel >=1.16.0,<1.17.0' - - 'bioconductor-edger >=3.24.0,<3.25.0' - - 'bioconductor-genomicranges >=1.34.0,<1.35.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-limma >=3.38.0,<3.39.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-biocgenerics >=0.30.0,<0.31.0' + - 'bioconductor-biocparallel >=1.18.0,<1.19.0' + - 'bioconductor-edger >=3.26.0,<3.27.0' + - 'bioconductor-genomicranges >=1.36.0,<1.37.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-limma >=3.40.0,<3.41.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' - r-base - r-ggplot2 - r-mass - r-reshape2 run: - - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' - - 'bioconductor-biocparallel >=1.16.0,<1.17.0' - - 'bioconductor-edger >=3.24.0,<3.25.0' - - 'bioconductor-genomicranges >=1.34.0,<1.35.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-limma >=3.38.0,<3.39.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-biocgenerics >=0.30.0,<0.31.0' + - 'bioconductor-biocparallel >=1.18.0,<1.19.0' + - 'bioconductor-edger >=3.26.0,<3.27.0' + - 'bioconductor-genomicranges >=1.36.0,<1.37.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-limma >=3.40.0,<3.41.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' - r-base - r-ggplot2 - r-mass diff --git a/recipes/bioconductor-drivernet/meta.yaml b/recipes/bioconductor-drivernet/meta.yaml index 2324d3eef717e..0a7d79988f6ff 100644 --- a/recipes/bioconductor-drivernet/meta.yaml +++ b/recipes/bioconductor-drivernet/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.22.0" %} +{% set version = "1.24.0" %} {% set name = "DriverNet" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 0a220e7958f082c4c716ee19f77f735a + md5: 5fa9c7883dd6b274a3e22bc1e4b25678 build: number: 0 rpaths: diff --git a/recipes/bioconductor-dropletutils/meta.yaml b/recipes/bioconductor-dropletutils/meta.yaml index 51a89bce5c178..e536835350af3 100644 --- a/recipes/bioconductor-dropletutils/meta.yaml +++ b/recipes/bioconductor-dropletutils/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.2.1" %} +{% set version = "1.4.0" %} {% set name = "DropletUtils" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 756b633ad77b92d78bd632eaa02c14ba + md5: 0678545b0c0f7bb478c1205d9edbc106 build: number: 0 rpaths: @@ -20,28 +20,34 @@ build: # SystemRequirements: C++11 requirements: host: - - 'bioconductor-beachmat >=1.4.0,<1.5.0' - - 'bioconductor-biocparallel >=1.16.0,<1.17.0' - - 'bioconductor-edger >=3.24.0,<3.25.0' - - 'bioconductor-hdf5array >=1.10.0,<1.11.0' - - 'bioconductor-rhdf5 >=2.26.0,<2.27.0' - - 'bioconductor-rhdf5lib >=1.4.0,<1.5.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' - - 'bioconductor-singlecellexperiment >=1.4.0,<1.5.0' + - 'bioconductor-beachmat >=2.0.0,<2.1.0' + - 'bioconductor-biocparallel >=1.18.0,<1.19.0' + - 'bioconductor-edger >=3.26.0,<3.27.0' + - 'bioconductor-hdf5array >=1.12.0,<1.13.0' + - 'bioconductor-rhdf5 >=2.28.0,<2.29.0' + - 'bioconductor-rhdf5lib >=1.6.0,<1.7.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' + - 'bioconductor-singlecellexperiment >=1.6.0,<1.7.0' - r-base + - r-bh + - r-dqrng - r-matrix + - r-r.utils - r-rcpp run: - - 'bioconductor-beachmat >=1.4.0,<1.5.0' - - 'bioconductor-biocparallel >=1.16.0,<1.17.0' - - 'bioconductor-edger >=3.24.0,<3.25.0' - - 'bioconductor-hdf5array >=1.10.0,<1.11.0' - - 'bioconductor-rhdf5 >=2.26.0,<2.27.0' - - 'bioconductor-rhdf5lib >=1.4.0,<1.5.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' - - 'bioconductor-singlecellexperiment >=1.4.0,<1.5.0' + - 'bioconductor-beachmat >=2.0.0,<2.1.0' + - 'bioconductor-biocparallel >=1.18.0,<1.19.0' + - 'bioconductor-edger >=3.26.0,<3.27.0' + - 'bioconductor-hdf5array >=1.12.0,<1.13.0' + - 'bioconductor-rhdf5 >=2.28.0,<2.29.0' + - 'bioconductor-rhdf5lib >=1.6.0,<1.7.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' + - 'bioconductor-singlecellexperiment >=1.6.0,<1.7.0' - r-base + - r-bh + - r-dqrng - r-matrix + - r-r.utils - r-rcpp build: - {{ compiler('c') }} @@ -53,7 +59,7 @@ test: about: home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: GPL-3 - summary: 'Provides a number of utility functions for handling single-cell (RNA-seq) data from droplet technologies such as 10X Genomics. This includes data loading, identification of cells from empty droplets, removal of barcode-swapped pseudo-cells, and downsampling of the count matrix.' + summary: 'Provides a number of utility functions for handling single-cell (RNA-seq) data from droplet technologies such as 10X Genomics. This includes data loading from count matrices or molecule information files, identification of cells from empty droplets, removal of barcode-swapped pseudo-cells, and downsampling of the count matrix.' extra: identifiers: - biotools:DropletUtils diff --git a/recipes/bioconductor-drosgenome1.db/meta.yaml b/recipes/bioconductor-drosgenome1.db/meta.yaml index 5a4c4edca09ec..2b1be173a2ed4 100644 --- a/recipes/bioconductor-drosgenome1.db/meta.yaml +++ b/recipes/bioconductor-drosgenome1.db/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.2.3" %} {% set name = "drosgenome1.db" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -12,7 +12,7 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 44bc6356bc04226cba8cb2f3544c4688 build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ @@ -20,14 +20,14 @@ build: # Suggests: DBI, annotate, RUnit requirements: host: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' - - 'bioconductor-org.dm.eg.db >=3.7.0,<3.8.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' + - 'bioconductor-org.dm.eg.db >=3.8.0,<3.9.0' - r-base run: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' - - 'bioconductor-org.dm.eg.db >=3.7.0,<3.8.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' + - 'bioconductor-org.dm.eg.db >=3.8.0,<3.9.0' - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-drosgenome1.db/post-link.sh b/recipes/bioconductor-drosgenome1.db/post-link.sh index 6e304888a1b8d..dce0a33b828ba 100644 --- a/recipes/bioconductor-drosgenome1.db/post-link.sh +++ b/recipes/bioconductor-drosgenome1.db/post-link.sh @@ -1,9 +1,10 @@ #!/bin/bash FN="drosgenome1.db_3.2.3.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/drosgenome1.db_3.2.3.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/drosgenome1.db_3.2.3.tar.gz" "https://bioarchive.galaxyproject.org/drosgenome1.db_3.2.3.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-drosgenome1.db/bioconductor-drosgenome1.db_3.2.3_src_all.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-drosgenome1.db/bioconductor-drosgenome1.db_3.2.3_src_all.tar.gz" ) MD5="44bc6356bc04226cba8cb2f3544c4688" @@ -16,7 +17,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-drosgenome1cdf/meta.yaml b/recipes/bioconductor-drosgenome1cdf/meta.yaml index 18a9b42b4d25b..fd360a507fe36 100644 --- a/recipes/bioconductor-drosgenome1cdf/meta.yaml +++ b/recipes/bioconductor-drosgenome1cdf/meta.yaml @@ -1,6 +1,6 @@ {% set version = "2.18.0" %} {% set name = "drosgenome1cdf" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -12,19 +12,19 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: e12983f2148c10ef1faa50f810b6eee3 build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' - r-base run: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-drosgenome1cdf/post-link.sh b/recipes/bioconductor-drosgenome1cdf/post-link.sh index 7e717a0fa859a..73af38e4e35b0 100644 --- a/recipes/bioconductor-drosgenome1cdf/post-link.sh +++ b/recipes/bioconductor-drosgenome1cdf/post-link.sh @@ -1,9 +1,10 @@ #!/bin/bash FN="drosgenome1cdf_2.18.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/drosgenome1cdf_2.18.0.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/drosgenome1cdf_2.18.0.tar.gz" "https://bioarchive.galaxyproject.org/drosgenome1cdf_2.18.0.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-drosgenome1cdf/bioconductor-drosgenome1cdf_2.18.0_src_all.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-drosgenome1cdf/bioconductor-drosgenome1cdf_2.18.0_src_all.tar.gz" ) MD5="e12983f2148c10ef1faa50f810b6eee3" @@ -16,7 +17,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-drosgenome1probe/meta.yaml b/recipes/bioconductor-drosgenome1probe/meta.yaml index 769246245c50a..0d5408499ba7a 100644 --- a/recipes/bioconductor-drosgenome1probe/meta.yaml +++ b/recipes/bioconductor-drosgenome1probe/meta.yaml @@ -1,6 +1,6 @@ {% set version = "2.18.0" %} {% set name = "drosgenome1probe" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -12,19 +12,19 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 1f12abdfeee65e8a6554f57507d86fb3 build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' - r-base run: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-drosgenome1probe/post-link.sh b/recipes/bioconductor-drosgenome1probe/post-link.sh index c28b5005a2559..f386bdd4e3f77 100644 --- a/recipes/bioconductor-drosgenome1probe/post-link.sh +++ b/recipes/bioconductor-drosgenome1probe/post-link.sh @@ -1,9 +1,10 @@ #!/bin/bash FN="drosgenome1probe_2.18.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/drosgenome1probe_2.18.0.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/drosgenome1probe_2.18.0.tar.gz" "https://bioarchive.galaxyproject.org/drosgenome1probe_2.18.0.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-drosgenome1probe/bioconductor-drosgenome1probe_2.18.0_src_all.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-drosgenome1probe/bioconductor-drosgenome1probe_2.18.0_src_all.tar.gz" ) MD5="1f12abdfeee65e8a6554f57507d86fb3" @@ -16,7 +17,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-drosophila2.db/meta.yaml b/recipes/bioconductor-drosophila2.db/meta.yaml index 4d0c88424ce60..58c594958eee6 100644 --- a/recipes/bioconductor-drosophila2.db/meta.yaml +++ b/recipes/bioconductor-drosophila2.db/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.2.3" %} {% set name = "drosophila2.db" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -12,7 +12,7 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 04a372eff398f79691216ed9fcc34bc8 build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ @@ -20,14 +20,14 @@ build: # Suggests: DBI, annotate, RUnit requirements: host: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' - - 'bioconductor-org.dm.eg.db >=3.7.0,<3.8.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' + - 'bioconductor-org.dm.eg.db >=3.8.0,<3.9.0' - r-base run: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' - - 'bioconductor-org.dm.eg.db >=3.7.0,<3.8.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' + - 'bioconductor-org.dm.eg.db >=3.8.0,<3.9.0' - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-drosophila2.db/post-link.sh b/recipes/bioconductor-drosophila2.db/post-link.sh index da47bcf20ed7b..3e3ac211fe660 100644 --- a/recipes/bioconductor-drosophila2.db/post-link.sh +++ b/recipes/bioconductor-drosophila2.db/post-link.sh @@ -1,9 +1,10 @@ #!/bin/bash FN="drosophila2.db_3.2.3.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/drosophila2.db_3.2.3.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/drosophila2.db_3.2.3.tar.gz" "https://bioarchive.galaxyproject.org/drosophila2.db_3.2.3.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-drosophila2.db/bioconductor-drosophila2.db_3.2.3_src_all.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-drosophila2.db/bioconductor-drosophila2.db_3.2.3_src_all.tar.gz" ) MD5="04a372eff398f79691216ed9fcc34bc8" @@ -16,7 +17,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-drosophila2cdf/meta.yaml b/recipes/bioconductor-drosophila2cdf/meta.yaml index cd31fe0d27b4e..90891f9d7dd85 100644 --- a/recipes/bioconductor-drosophila2cdf/meta.yaml +++ b/recipes/bioconductor-drosophila2cdf/meta.yaml @@ -1,6 +1,6 @@ {% set version = "2.18.0" %} {% set name = "drosophila2cdf" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -12,19 +12,19 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 3323e723c133ff2b6188e22bebf3e20a build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' - r-base run: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-drosophila2cdf/post-link.sh b/recipes/bioconductor-drosophila2cdf/post-link.sh index e8e6163f5f5fb..1d816298c744e 100644 --- a/recipes/bioconductor-drosophila2cdf/post-link.sh +++ b/recipes/bioconductor-drosophila2cdf/post-link.sh @@ -1,9 +1,10 @@ #!/bin/bash FN="drosophila2cdf_2.18.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/drosophila2cdf_2.18.0.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/drosophila2cdf_2.18.0.tar.gz" "https://bioarchive.galaxyproject.org/drosophila2cdf_2.18.0.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-drosophila2cdf/bioconductor-drosophila2cdf_2.18.0_src_all.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-drosophila2cdf/bioconductor-drosophila2cdf_2.18.0_src_all.tar.gz" ) MD5="3323e723c133ff2b6188e22bebf3e20a" @@ -16,7 +17,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-drosophila2probe/meta.yaml b/recipes/bioconductor-drosophila2probe/meta.yaml index 892260d8a7543..c7ab7aee54fe2 100644 --- a/recipes/bioconductor-drosophila2probe/meta.yaml +++ b/recipes/bioconductor-drosophila2probe/meta.yaml @@ -1,6 +1,6 @@ {% set version = "2.18.0" %} {% set name = "drosophila2probe" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -12,19 +12,19 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: ba0251902ea0a5f0db61105bdcdc3530 build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' - r-base run: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-drosophila2probe/post-link.sh b/recipes/bioconductor-drosophila2probe/post-link.sh index 36dc692f4d401..74be4b46ddb70 100644 --- a/recipes/bioconductor-drosophila2probe/post-link.sh +++ b/recipes/bioconductor-drosophila2probe/post-link.sh @@ -1,9 +1,10 @@ #!/bin/bash FN="drosophila2probe_2.18.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/drosophila2probe_2.18.0.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/drosophila2probe_2.18.0.tar.gz" "https://bioarchive.galaxyproject.org/drosophila2probe_2.18.0.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-drosophila2probe/bioconductor-drosophila2probe_2.18.0_src_all.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-drosophila2probe/bioconductor-drosophila2probe_2.18.0_src_all.tar.gz" ) MD5="ba0251902ea0a5f0db61105bdcdc3530" @@ -16,7 +17,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-drugvsdisease/build.sh b/recipes/bioconductor-drugvsdisease/build.sh index 5ea71a1203cac..c1d13421f5f1e 100644 --- a/recipes/bioconductor-drugvsdisease/build.sh +++ b/recipes/bioconductor-drugvsdisease/build.sh @@ -8,4 +8,4 @@ CXX=$CXX CXX98=$CXX CXX11=$CXX CXX14=$CXX" > ~/.R/Makevars -$R CMD INSTALL --build . +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-drugvsdisease/meta.yaml b/recipes/bioconductor-drugvsdisease/meta.yaml index 122063e9525ff..0afaf2d5e98f4 100644 --- a/recipes/bioconductor-drugvsdisease/meta.yaml +++ b/recipes/bioconductor-drugvsdisease/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "2.24.2" %} +{% set version = "2.26.0" %} {% set name = "DrugVsDisease" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 70b3c0ce3a8af1afa7f2d08b718092f8 + md5: 548b0dc940cdc16bec2d6b9d610d463c build: number: 0 rpaths: @@ -19,36 +19,36 @@ build: noarch: generic requirements: host: - - 'bioconductor-affy >=1.60.0,<1.61.0' - - 'bioconductor-annotate >=1.60.0,<1.61.0' - - 'bioconductor-arrayexpress >=1.42.0,<1.43.0' - - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' - - 'bioconductor-biomart >=2.38.0,<2.39.0' - - 'bioconductor-cmap2data >=1.18.0,<1.19.0' - - 'bioconductor-drugvsdiseasedata >=1.18.0,<1.19.0' - - 'bioconductor-geoquery >=2.50.0,<2.51.0' + - 'bioconductor-affy >=1.62.0,<1.63.0' + - 'bioconductor-annotate >=1.62.0,<1.63.0' + - 'bioconductor-arrayexpress >=1.44.0,<1.45.0' + - 'bioconductor-biocgenerics >=0.30.0,<0.31.0' + - 'bioconductor-biomart >=2.40.0,<2.41.0' + - 'bioconductor-cmap2data >=1.20.0,<1.21.0' + - 'bioconductor-drugvsdiseasedata >=1.20.0,<1.21.0' + - 'bioconductor-geoquery >=2.52.0,<2.53.0' - 'bioconductor-hgu133a.db >=3.2.0,<3.3.0' - 'bioconductor-hgu133a2.db >=3.2.0,<3.3.0' - 'bioconductor-hgu133plus2.db >=3.2.0,<3.3.0' - - 'bioconductor-limma >=3.38.0,<3.39.0' - - 'bioconductor-qvalue >=2.14.0,<2.15.0' + - 'bioconductor-limma >=3.40.0,<3.41.0' + - 'bioconductor-qvalue >=2.16.0,<2.17.0' - r-base - r-runit - r-xtable run: - - 'bioconductor-affy >=1.60.0,<1.61.0' - - 'bioconductor-annotate >=1.60.0,<1.61.0' - - 'bioconductor-arrayexpress >=1.42.0,<1.43.0' - - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' - - 'bioconductor-biomart >=2.38.0,<2.39.0' - - 'bioconductor-cmap2data >=1.18.0,<1.19.0' - - 'bioconductor-drugvsdiseasedata >=1.18.0,<1.19.0' - - 'bioconductor-geoquery >=2.50.0,<2.51.0' + - 'bioconductor-affy >=1.62.0,<1.63.0' + - 'bioconductor-annotate >=1.62.0,<1.63.0' + - 'bioconductor-arrayexpress >=1.44.0,<1.45.0' + - 'bioconductor-biocgenerics >=0.30.0,<0.31.0' + - 'bioconductor-biomart >=2.40.0,<2.41.0' + - 'bioconductor-cmap2data >=1.20.0,<1.21.0' + - 'bioconductor-drugvsdiseasedata >=1.20.0,<1.21.0' + - 'bioconductor-geoquery >=2.52.0,<2.53.0' - 'bioconductor-hgu133a.db >=3.2.0,<3.3.0' - 'bioconductor-hgu133a2.db >=3.2.0,<3.3.0' - 'bioconductor-hgu133plus2.db >=3.2.0,<3.3.0' - - 'bioconductor-limma >=3.38.0,<3.39.0' - - 'bioconductor-qvalue >=2.14.0,<2.15.0' + - 'bioconductor-limma >=3.40.0,<3.41.0' + - 'bioconductor-qvalue >=2.16.0,<2.17.0' - r-base - r-runit - r-xtable diff --git a/recipes/bioconductor-drugvsdiseasedata/meta.yaml b/recipes/bioconductor-drugvsdiseasedata/meta.yaml index d9ac51ec2ddb9..13de9ba7c89dc 100644 --- a/recipes/bioconductor-drugvsdiseasedata/meta.yaml +++ b/recipes/bioconductor-drugvsdiseasedata/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.18.0" %} +{% set version = "1.20.0" %} {% set name = "DrugVsDiseasedata" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: e6cddb699ec1351eda47cbb3fb40e705 + md5: 70457ffd167a803e7b9572c3ee8de757 build: number: 0 rpaths: @@ -22,7 +22,7 @@ requirements: - r-base run: - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-drugvsdiseasedata/post-link.sh b/recipes/bioconductor-drugvsdiseasedata/post-link.sh index b41469b0541d2..efda0beba3f01 100644 --- a/recipes/bioconductor-drugvsdiseasedata/post-link.sh +++ b/recipes/bioconductor-drugvsdiseasedata/post-link.sh @@ -1,11 +1,11 @@ #!/bin/bash -FN="DrugVsDiseasedata_1.18.0.tar.gz" +FN="DrugVsDiseasedata_1.20.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/experiment/src/contrib/DrugVsDiseasedata_1.18.0.tar.gz" - "https://bioarchive.galaxyproject.org/DrugVsDiseasedata_1.18.0.tar.gz" - "https://depot.galaxyproject.org/software/bioconductor-drugvsdiseasedata/bioconductor-drugvsdiseasedata_1.18.0_src_all.tar.gz" + "https://bioconductor.org/packages/3.9/data/experiment/src/contrib/DrugVsDiseasedata_1.20.0.tar.gz" + "https://bioarchive.galaxyproject.org/DrugVsDiseasedata_1.20.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-drugvsdiseasedata/bioconductor-drugvsdiseasedata_1.20.0_src_all.tar.gz" ) -MD5="e6cddb699ec1351eda47cbb3fb40e705" +MD5="70457ffd167a803e7b9572c3ee8de757" # Use a staging area in the conda dir rather than temp dirs, both to avoid # permission issues as well as to have things downloaded in a predictable @@ -16,7 +16,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-dsimer/meta.yaml b/recipes/bioconductor-dsimer/meta.yaml index 53bddefd9c9cd..62f25709eef74 100644 --- a/recipes/bioconductor-dsimer/meta.yaml +++ b/recipes/bioconductor-dsimer/meta.yaml @@ -20,8 +20,8 @@ build: requirements: host: - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' - - 'bioconductor-go.db >=3.7.0,<3.8.0' - - 'bioconductor-org.hs.eg.db >=3.7.0,<3.8.0' + - 'bioconductor-go.db >=3.8.0,<3.9.0' + - 'bioconductor-org.hs.eg.db >=3.8.0,<3.9.0' - r-base - r-ggplot2 - 'r-igraph >=1.0.1' @@ -29,8 +29,8 @@ requirements: - r-reshape2 run: - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' - - 'bioconductor-go.db >=3.7.0,<3.8.0' - - 'bioconductor-org.hs.eg.db >=3.7.0,<3.8.0' + - 'bioconductor-go.db >=3.8.0,<3.9.0' + - 'bioconductor-org.hs.eg.db >=3.8.0,<3.9.0' - r-base - r-ggplot2 - 'r-igraph >=1.0.1' diff --git a/recipes/bioconductor-dsqtl/meta.yaml b/recipes/bioconductor-dsqtl/meta.yaml index 1131c45ab0f25..b799655d4b710 100644 --- a/recipes/bioconductor-dsqtl/meta.yaml +++ b/recipes/bioconductor-dsqtl/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "0.20.0" %} +{% set version = "0.22.0" %} {% set name = "dsQTL" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 077dd1342d0cc842c44937a61e90ea10 + md5: 832fc2afb33890374a5efa553fe276ab build: number: 0 rpaths: @@ -20,16 +20,16 @@ build: # Suggests: GGtools, rtracklayer requirements: host: - - 'bioconductor-biobase >=2.42.0,<2.43.0' - - 'bioconductor-ggbase >=3.44.0,<3.45.0' - - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' + - 'bioconductor-ggbase >=3.46.0,<3.47.0' + - 'bioconductor-summarizedexperiment >=1.14.0,<1.15.0' - r-base run: - - 'bioconductor-biobase >=2.42.0,<2.43.0' - - 'bioconductor-ggbase >=3.44.0,<3.45.0' - - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' + - 'bioconductor-ggbase >=3.46.0,<3.47.0' + - 'bioconductor-summarizedexperiment >=1.14.0,<1.15.0' - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-dsqtl/post-link.sh b/recipes/bioconductor-dsqtl/post-link.sh index 478a0c3dfaa70..ad7b12af4e35b 100644 --- a/recipes/bioconductor-dsqtl/post-link.sh +++ b/recipes/bioconductor-dsqtl/post-link.sh @@ -1,11 +1,11 @@ #!/bin/bash -FN="dsQTL_0.20.0.tar.gz" +FN="dsQTL_0.22.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/experiment/src/contrib/dsQTL_0.20.0.tar.gz" - "https://bioarchive.galaxyproject.org/dsQTL_0.20.0.tar.gz" - "https://depot.galaxyproject.org/software/bioconductor-dsqtl/bioconductor-dsqtl_0.20.0_src_all.tar.gz" + "https://bioconductor.org/packages/3.9/data/experiment/src/contrib/dsQTL_0.22.0.tar.gz" + "https://bioarchive.galaxyproject.org/dsQTL_0.22.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-dsqtl/bioconductor-dsqtl_0.22.0_src_all.tar.gz" ) -MD5="077dd1342d0cc842c44937a61e90ea10" +MD5="832fc2afb33890374a5efa553fe276ab" # Use a staging area in the conda dir rather than temp dirs, both to avoid # permission issues as well as to have things downloaded in a predictable @@ -16,7 +16,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-dss/meta.yaml b/recipes/bioconductor-dss/meta.yaml index e2d24b560941a..4adfc9c3d7f5c 100644 --- a/recipes/bioconductor-dss/meta.yaml +++ b/recipes/bioconductor-dss/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "2.30.0" %} +{% set version = "2.32.0" %} {% set name = "DSS" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,23 +10,23 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 6ea15f25bbe6c4c2afb12976d575cefc + md5: 24e4aa2a0263452f0a28e93a660789f1 build: number: 0 rpaths: - lib/R/lib/ - lib/ -# Suggests: BiocStyle +# Suggests: BiocStyle, knitr, rmarkdown requirements: host: - - 'bioconductor-biobase >=2.42.0,<2.43.0' - - 'bioconductor-bsseq >=1.18.0,<1.19.0' - - 'bioconductor-delayedarray >=0.8.0,<0.9.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' + - 'bioconductor-bsseq >=1.20.0,<1.21.0' + - 'bioconductor-delayedarray >=0.10.0,<0.11.0' - r-base run: - - 'bioconductor-biobase >=2.42.0,<2.43.0' - - 'bioconductor-bsseq >=1.18.0,<1.19.0' - - 'bioconductor-delayedarray >=0.8.0,<0.9.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' + - 'bioconductor-bsseq >=1.20.0,<1.21.0' + - 'bioconductor-delayedarray >=0.10.0,<0.11.0' - r-base build: - {{ compiler('c') }} diff --git a/recipes/bioconductor-dta/meta.yaml b/recipes/bioconductor-dta/meta.yaml index d005d1a0c4739..01c5d59f22c9c 100644 --- a/recipes/bioconductor-dta/meta.yaml +++ b/recipes/bioconductor-dta/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "2.28.0" %} +{% set version = "2.30.0" %} {% set name = "DTA" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 7af46c4b3ca3d98a4c9398b0d68a1c71 + md5: e4fe6eb840110181a531da530d2ddee4 build: number: 0 rpaths: diff --git a/recipes/bioconductor-dualks/meta.yaml b/recipes/bioconductor-dualks/meta.yaml index fc347a269569f..d665b53c474a0 100644 --- a/recipes/bioconductor-dualks/meta.yaml +++ b/recipes/bioconductor-dualks/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.42.0" %} +{% set version = "1.44.0" %} {% set name = "dualKS" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: aef440fc9d6a7971b3ca41a51f7368c1 + md5: 8179aa4020d4188a630cccc07313bc4e build: number: 0 rpaths: @@ -19,12 +19,12 @@ build: noarch: generic requirements: host: - - 'bioconductor-affy >=1.60.0,<1.61.0' - - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-affy >=1.62.0,<1.63.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' - r-base run: - - 'bioconductor-affy >=1.60.0,<1.61.0' - - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-affy >=1.62.0,<1.63.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' - r-base test: commands: diff --git a/recipes/bioconductor-duoclustering2018/meta.yaml b/recipes/bioconductor-duoclustering2018/meta.yaml index f34f0280f267e..99537d9b2d3ca 100644 --- a/recipes/bioconductor-duoclustering2018/meta.yaml +++ b/recipes/bioconductor-duoclustering2018/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.0.0" %} +{% set version = "1.2.0" %} {% set name = "DuoClustering2018" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 533a6230137770c646ced387a5ecd4fd + md5: 49e45aac011f59a54755d13f314949c3 build: number: 0 rpaths: @@ -20,7 +20,7 @@ build: # Suggests: knitr, rmarkdown, BiocStyle, iSEE, scater, SingleCellExperiment, SummarizedExperiment, plyr requirements: host: - - 'bioconductor-experimenthub >=1.8.0,<1.9.0' + - 'bioconductor-experimenthub >=1.10.0,<1.11.0' - r-base - r-dplyr - r-ggplot2 @@ -32,7 +32,7 @@ requirements: - r-tidyr - r-viridis run: - - 'bioconductor-experimenthub >=1.8.0,<1.9.0' + - 'bioconductor-experimenthub >=1.10.0,<1.11.0' - r-base - r-dplyr - r-ggplot2 @@ -43,7 +43,7 @@ requirements: - r-reshape2 - r-tidyr - r-viridis - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-duoclustering2018/post-link.sh b/recipes/bioconductor-duoclustering2018/post-link.sh index 38d8d1d122004..4e77422fa8084 100644 --- a/recipes/bioconductor-duoclustering2018/post-link.sh +++ b/recipes/bioconductor-duoclustering2018/post-link.sh @@ -1,11 +1,11 @@ #!/bin/bash -FN="DuoClustering2018_1.0.0.tar.gz" +FN="DuoClustering2018_1.2.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/experiment/src/contrib/DuoClustering2018_1.0.0.tar.gz" - "https://bioarchive.galaxyproject.org/DuoClustering2018_1.0.0.tar.gz" - "https://depot.galaxyproject.org/software/bioconductor-duoclustering2018/bioconductor-duoclustering2018_1.0.0_src_all.tar.gz" + "https://bioconductor.org/packages/3.9/data/experiment/src/contrib/DuoClustering2018_1.2.0.tar.gz" + "https://bioarchive.galaxyproject.org/DuoClustering2018_1.2.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-duoclustering2018/bioconductor-duoclustering2018_1.2.0_src_all.tar.gz" ) -MD5="533a6230137770c646ced387a5ecd4fd" +MD5="49e45aac011f59a54755d13f314949c3" # Use a staging area in the conda dir rather than temp dirs, both to avoid # permission issues as well as to have things downloaded in a predictable @@ -16,7 +16,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-dupchecker/meta.yaml b/recipes/bioconductor-dupchecker/meta.yaml index 7d7480fc03dcc..c3b20dddf3183 100644 --- a/recipes/bioconductor-dupchecker/meta.yaml +++ b/recipes/bioconductor-dupchecker/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.20.0" %} +{% set version = "1.22.0" %} {% set name = "DupChecker" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: c5867bb93e37d69cb72527f796de4e0f + md5: f9c7509c929ec424905a344d2a4bf81e build: number: 0 rpaths: diff --git a/recipes/bioconductor-dupradar/meta.yaml b/recipes/bioconductor-dupradar/meta.yaml index 0be13e6efdc8e..72bea7b46f439 100644 --- a/recipes/bioconductor-dupradar/meta.yaml +++ b/recipes/bioconductor-dupradar/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.12.1" %} +{% set version = "1.14.0" %} {% set name = "dupRadar" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,9 +10,9 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 58ff3f96c44230db7e9483621a213421 + md5: f97053380896eef28891a1ea2f6fca70 build: - number: 2 + number: 0 rpaths: - lib/R/lib/ - lib/ @@ -20,13 +20,11 @@ build: # Suggests: BiocStyle, knitr, rmarkdown, AnnotationHub requirements: host: - - 'bioconductor-rsubread >=1.32.0,<1.33.0' + - 'bioconductor-rsubread >=1.34.0,<1.35.0' - r-base - - r-kernsmooth run: - - 'bioconductor-rsubread >=1.32.0,<1.33.0' + - 'bioconductor-rsubread >=1.34.0,<1.35.0' - r-base - - r-kernsmooth test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-dvddata/meta.yaml b/recipes/bioconductor-dvddata/meta.yaml index 24c6da4746cd9..e18a3ab13d1ad 100644 --- a/recipes/bioconductor-dvddata/meta.yaml +++ b/recipes/bioconductor-dvddata/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.18.0" %} +{% set version = "1.20.0" %} {% set name = "DvDdata" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: c2b58da21a872a2757fb6928e7fd155e + md5: 532227658b29e36af2d13ba3d27c4ae5 build: number: 0 rpaths: @@ -22,7 +22,7 @@ requirements: - r-base run: - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-dvddata/post-link.sh b/recipes/bioconductor-dvddata/post-link.sh index 37956bd966240..499098991b39b 100644 --- a/recipes/bioconductor-dvddata/post-link.sh +++ b/recipes/bioconductor-dvddata/post-link.sh @@ -1,11 +1,11 @@ #!/bin/bash -FN="DvDdata_1.18.0.tar.gz" +FN="DvDdata_1.20.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/experiment/src/contrib/DvDdata_1.18.0.tar.gz" - "https://bioarchive.galaxyproject.org/DvDdata_1.18.0.tar.gz" - "https://depot.galaxyproject.org/software/bioconductor-dvddata/bioconductor-dvddata_1.18.0_src_all.tar.gz" + "https://bioconductor.org/packages/3.9/data/experiment/src/contrib/DvDdata_1.20.0.tar.gz" + "https://bioarchive.galaxyproject.org/DvDdata_1.20.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-dvddata/bioconductor-dvddata_1.20.0_src_all.tar.gz" ) -MD5="c2b58da21a872a2757fb6928e7fd155e" +MD5="532227658b29e36af2d13ba3d27c4ae5" # Use a staging area in the conda dir rather than temp dirs, both to avoid # permission issues as well as to have things downloaded in a predictable @@ -16,7 +16,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-dyebias/meta.yaml b/recipes/bioconductor-dyebias/meta.yaml index 869ecc22af231..92ef298516865 100644 --- a/recipes/bioconductor-dyebias/meta.yaml +++ b/recipes/bioconductor-dyebias/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.42.0" %} +{% set version = "1.44.0" %} {% set name = "dyebias" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: a5c7c84939a73cac498807188f7c8ee8 + md5: 2f434cc8b244800f94d4301d29ae1b25 build: number: 0 rpaths: @@ -20,12 +20,12 @@ build: # Suggests: limma, convert, GEOquery, dyebiasexamples, methods requirements: host: - - 'bioconductor-biobase >=2.42.0,<2.43.0' - - 'bioconductor-marray >=1.60.0,<1.61.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' + - 'bioconductor-marray >=1.62.0,<1.63.0' - r-base run: - - 'bioconductor-biobase >=2.42.0,<2.43.0' - - 'bioconductor-marray >=1.60.0,<1.61.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' + - 'bioconductor-marray >=1.62.0,<1.63.0' - r-base test: commands: diff --git a/recipes/bioconductor-dyebiasexamples/meta.yaml b/recipes/bioconductor-dyebiasexamples/meta.yaml index b7124dec80ee2..e64f6a6c0315c 100644 --- a/recipes/bioconductor-dyebiasexamples/meta.yaml +++ b/recipes/bioconductor-dyebiasexamples/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.22.0" %} +{% set version = "1.24.0" %} {% set name = "dyebiasexamples" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 21da0022921c7f6e6eeb997e1bc56fa4 + md5: 5b5ecedcc8fc4ec91f6180788357b69a build: number: 0 rpaths: @@ -20,14 +20,14 @@ build: # Suggests: dyebias, convert, Biobase requirements: host: - - 'bioconductor-geoquery >=2.50.0,<2.51.0' - - 'bioconductor-marray >=1.60.0,<1.61.0' + - 'bioconductor-geoquery >=2.52.0,<2.53.0' + - 'bioconductor-marray >=1.62.0,<1.63.0' - r-base run: - - 'bioconductor-geoquery >=2.50.0,<2.51.0' - - 'bioconductor-marray >=1.60.0,<1.61.0' + - 'bioconductor-geoquery >=2.52.0,<2.53.0' + - 'bioconductor-marray >=1.62.0,<1.63.0' - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-dyebiasexamples/post-link.sh b/recipes/bioconductor-dyebiasexamples/post-link.sh index 18a14ea13d57f..6dae841167b44 100644 --- a/recipes/bioconductor-dyebiasexamples/post-link.sh +++ b/recipes/bioconductor-dyebiasexamples/post-link.sh @@ -1,11 +1,11 @@ #!/bin/bash -FN="dyebiasexamples_1.22.0.tar.gz" +FN="dyebiasexamples_1.24.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/experiment/src/contrib/dyebiasexamples_1.22.0.tar.gz" - "https://bioarchive.galaxyproject.org/dyebiasexamples_1.22.0.tar.gz" - "https://depot.galaxyproject.org/software/bioconductor-dyebiasexamples/bioconductor-dyebiasexamples_1.22.0_src_all.tar.gz" + "https://bioconductor.org/packages/3.9/data/experiment/src/contrib/dyebiasexamples_1.24.0.tar.gz" + "https://bioarchive.galaxyproject.org/dyebiasexamples_1.24.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-dyebiasexamples/bioconductor-dyebiasexamples_1.24.0_src_all.tar.gz" ) -MD5="21da0022921c7f6e6eeb997e1bc56fa4" +MD5="5b5ecedcc8fc4ec91f6180788357b69a" # Use a staging area in the conda dir rather than temp dirs, both to avoid # permission issues as well as to have things downloaded in a predictable @@ -16,7 +16,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-dyndoc/meta.yaml b/recipes/bioconductor-dyndoc/meta.yaml index 2d41257170297..aefa92b1fff21 100644 --- a/recipes/bioconductor-dyndoc/meta.yaml +++ b/recipes/bioconductor-dyndoc/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.60.0" %} +{% set version = "1.62.0" %} {% set name = "DynDoc" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 9ab4d310071f59bab69bad2f75c152e7 + md5: 3e9372cbe7a1d407f48e62f87e984c1b build: number: 0 rpaths: diff --git a/recipes/bioconductor-easyqpcr/meta.yaml b/recipes/bioconductor-easyqpcr/meta.yaml index 1092840651022..020e609fc67b9 100644 --- a/recipes/bioconductor-easyqpcr/meta.yaml +++ b/recipes/bioconductor-easyqpcr/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.24.0" %} +{% set version = "1.26.0" %} {% set name = "EasyqpcR" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 858ce6239d7775d581f9dd188ea167df + md5: f1bfda9188d2d66721b5035c0bd4bd46 build: number: 0 rpaths: diff --git a/recipes/bioconductor-easyrnaseq/meta.yaml b/recipes/bioconductor-easyrnaseq/meta.yaml index 72add9461662a..a3db0f4992f8d 100644 --- a/recipes/bioconductor-easyrnaseq/meta.yaml +++ b/recipes/bioconductor-easyrnaseq/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "2.18.2" %} +{% set version = "2.20.0" %} {% set name = "easyRNASeq" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,55 +10,59 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: e2daba492e062c9fae75030c5b3e280c + md5: 7db78c0f10e0bac811550c80ae29c372 build: number: 0 rpaths: - lib/R/lib/ - lib/ noarch: generic -# Suggests: BiocStyle (>= 2.7.8), BSgenome (>= 1.39.0), BSgenome.Dmelanogaster.UCSC.dm3 (>= 1.4.0), curl, knitr, rmarkdown, RUnit (>= 0.4.31) +# Suggests: BiocStyle (>= 2.9.6), BSgenome (>= 1.49.5), BSgenome.Dmelanogaster.UCSC.dm3 (>= 1.4.0), curl, knitr, rmarkdown, RUnit (>= 0.4.32) requirements: host: - - 'bioconductor-biobase >=2.42.0,<2.43.0' - - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' - - 'bioconductor-biocparallel >=1.16.0,<1.17.0' - - 'bioconductor-biomart >=2.38.0,<2.39.0' - - 'bioconductor-biostrings >=2.50.0,<2.51.0' - - 'bioconductor-deseq >=1.34.0,<1.35.0' - - 'bioconductor-edger >=3.24.0,<3.25.0' - - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' - - 'bioconductor-genomeintervals >=1.38.0,<1.39.0' - - 'bioconductor-genomicalignments >=1.18.0,<1.19.0' - - 'bioconductor-genomicranges >=1.34.0,<1.35.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-rsamtools >=1.34.0,<1.35.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' - - 'bioconductor-shortread >=1.40.0,<1.41.0' - - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' + - 'bioconductor-biocfilecache >=1.8.0,<1.9.0' + - 'bioconductor-biocgenerics >=0.30.0,<0.31.0' + - 'bioconductor-biocparallel >=1.18.0,<1.19.0' + - 'bioconductor-biomart >=2.40.0,<2.41.0' + - 'bioconductor-biostrings >=2.52.0,<2.53.0' + - 'bioconductor-deseq >=1.36.0,<1.37.0' + - 'bioconductor-edger >=3.26.0,<3.27.0' + - 'bioconductor-genomeinfodb >=1.20.0,<1.21.0' + - 'bioconductor-genomeintervals >=1.40.0,<1.41.0' + - 'bioconductor-genomicalignments >=1.20.0,<1.21.0' + - 'bioconductor-genomicranges >=1.36.0,<1.37.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-rsamtools >=2.0.0,<2.1.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' + - 'bioconductor-shortread >=1.42.0,<1.43.0' + - 'bioconductor-summarizedexperiment >=1.14.0,<1.15.0' - r-base - r-locfit - - 'r-lsd >=3.0' + - 'r-lsd >=4.0' + - 'r-rappdirs >=0.3.1' run: - - 'bioconductor-biobase >=2.42.0,<2.43.0' - - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' - - 'bioconductor-biocparallel >=1.16.0,<1.17.0' - - 'bioconductor-biomart >=2.38.0,<2.39.0' - - 'bioconductor-biostrings >=2.50.0,<2.51.0' - - 'bioconductor-deseq >=1.34.0,<1.35.0' - - 'bioconductor-edger >=3.24.0,<3.25.0' - - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' - - 'bioconductor-genomeintervals >=1.38.0,<1.39.0' - - 'bioconductor-genomicalignments >=1.18.0,<1.19.0' - - 'bioconductor-genomicranges >=1.34.0,<1.35.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-rsamtools >=1.34.0,<1.35.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' - - 'bioconductor-shortread >=1.40.0,<1.41.0' - - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' + - 'bioconductor-biocfilecache >=1.8.0,<1.9.0' + - 'bioconductor-biocgenerics >=0.30.0,<0.31.0' + - 'bioconductor-biocparallel >=1.18.0,<1.19.0' + - 'bioconductor-biomart >=2.40.0,<2.41.0' + - 'bioconductor-biostrings >=2.52.0,<2.53.0' + - 'bioconductor-deseq >=1.36.0,<1.37.0' + - 'bioconductor-edger >=3.26.0,<3.27.0' + - 'bioconductor-genomeinfodb >=1.20.0,<1.21.0' + - 'bioconductor-genomeintervals >=1.40.0,<1.41.0' + - 'bioconductor-genomicalignments >=1.20.0,<1.21.0' + - 'bioconductor-genomicranges >=1.36.0,<1.37.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-rsamtools >=2.0.0,<2.1.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' + - 'bioconductor-shortread >=1.42.0,<1.43.0' + - 'bioconductor-summarizedexperiment >=1.14.0,<1.15.0' - r-base - r-locfit - - 'r-lsd >=3.0' + - 'r-lsd >=4.0' + - 'r-rappdirs >=0.3.1' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-eatonetalchipseq/meta.yaml b/recipes/bioconductor-eatonetalchipseq/meta.yaml index 5611c93590f7b..316be9d5549d2 100644 --- a/recipes/bioconductor-eatonetalchipseq/meta.yaml +++ b/recipes/bioconductor-eatonetalchipseq/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "0.20.0" %} +{% set version = "0.22.0" %} {% set name = "EatonEtAlChIPseq" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 4733fad7f34d353e3dbe267587fe2198 + md5: e6375a109bfe89cab8a89d343dd1105c build: number: 0 rpaths: @@ -19,16 +19,16 @@ build: noarch: generic requirements: host: - - 'bioconductor-genomicranges >=1.34.0,<1.35.0' - - 'bioconductor-rtracklayer >=1.42.0,<1.43.0' - - 'bioconductor-shortread >=1.40.0,<1.41.0' + - 'bioconductor-genomicranges >=1.36.0,<1.37.0' + - 'bioconductor-rtracklayer >=1.44.0,<1.45.0' + - 'bioconductor-shortread >=1.42.0,<1.43.0' - r-base run: - - 'bioconductor-genomicranges >=1.34.0,<1.35.0' - - 'bioconductor-rtracklayer >=1.42.0,<1.43.0' - - 'bioconductor-shortread >=1.40.0,<1.41.0' + - 'bioconductor-genomicranges >=1.36.0,<1.37.0' + - 'bioconductor-rtracklayer >=1.44.0,<1.45.0' + - 'bioconductor-shortread >=1.42.0,<1.43.0' - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-eatonetalchipseq/post-link.sh b/recipes/bioconductor-eatonetalchipseq/post-link.sh index 65f5f40833c67..8a472f1a0cd8b 100644 --- a/recipes/bioconductor-eatonetalchipseq/post-link.sh +++ b/recipes/bioconductor-eatonetalchipseq/post-link.sh @@ -1,11 +1,11 @@ #!/bin/bash -FN="EatonEtAlChIPseq_0.20.0.tar.gz" +FN="EatonEtAlChIPseq_0.22.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/experiment/src/contrib/EatonEtAlChIPseq_0.20.0.tar.gz" - "https://bioarchive.galaxyproject.org/EatonEtAlChIPseq_0.20.0.tar.gz" - "https://depot.galaxyproject.org/software/bioconductor-eatonetalchipseq/bioconductor-eatonetalchipseq_0.20.0_src_all.tar.gz" + "https://bioconductor.org/packages/3.9/data/experiment/src/contrib/EatonEtAlChIPseq_0.22.0.tar.gz" + "https://bioarchive.galaxyproject.org/EatonEtAlChIPseq_0.22.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-eatonetalchipseq/bioconductor-eatonetalchipseq_0.22.0_src_all.tar.gz" ) -MD5="4733fad7f34d353e3dbe267587fe2198" +MD5="e6375a109bfe89cab8a89d343dd1105c" # Use a staging area in the conda dir rather than temp dirs, both to avoid # permission issues as well as to have things downloaded in a predictable @@ -16,7 +16,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-ebarrays/meta.yaml b/recipes/bioconductor-ebarrays/meta.yaml index c2e84bb53a995..66d05ad0b9a36 100644 --- a/recipes/bioconductor-ebarrays/meta.yaml +++ b/recipes/bioconductor-ebarrays/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "2.46.0" %} +{% set version = "2.48.0" %} {% set name = "EBarrays" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 4a42f6740313e671fbd0433896b6f227 + md5: 608cdd3e7a7efa9de797cc7cd8076e2a build: number: 0 rpaths: @@ -18,12 +18,12 @@ build: - lib/ requirements: host: - - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' - r-base - r-cluster - r-lattice run: - - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' - r-base - r-cluster - r-lattice diff --git a/recipes/bioconductor-ebcoexpress/meta.yaml b/recipes/bioconductor-ebcoexpress/meta.yaml index bea9508059c84..609feb65cc644 100644 --- a/recipes/bioconductor-ebcoexpress/meta.yaml +++ b/recipes/bioconductor-ebcoexpress/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.26.0" %} +{% set version = "1.28.0" %} {% set name = "EBcoexpress" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 391a4f44e4fc3c4578121104a30877c6 + md5: 9a21fccfdac28510fb2cf51bae19638d build: number: 0 rpaths: @@ -19,12 +19,12 @@ build: # Suggests: graph, igraph, colorspace requirements: host: - - 'bioconductor-ebarrays >=2.46.0,<2.47.0' + - 'bioconductor-ebarrays >=2.48.0,<2.49.0' - r-base - r-mclust - r-minqa run: - - 'bioconductor-ebarrays >=2.46.0,<2.47.0' + - 'bioconductor-ebarrays >=2.48.0,<2.49.0' - r-base - r-mclust - r-minqa diff --git a/recipes/bioconductor-ebimage/meta.yaml b/recipes/bioconductor-ebimage/meta.yaml index 175b332c7c580..4749cdc43f160 100644 --- a/recipes/bioconductor-ebimage/meta.yaml +++ b/recipes/bioconductor-ebimage/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "4.24.0" %} +{% set version = "4.26.0" %} {% set name = "EBImage" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 3ddadf0e47dfe26013b10378dee62c55 + md5: 098cfb9ab5b7d4f10ad9cbba2bf6a3cb build: number: 0 rpaths: @@ -19,7 +19,7 @@ build: # Suggests: BiocStyle, digest, knitr, rmarkdown, shiny requirements: host: - - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' + - 'bioconductor-biocgenerics >=0.30.0,<0.31.0' - r-abind - r-base - 'r-fftwtools >=0.9-7' @@ -31,7 +31,7 @@ requirements: - r-rcurl - r-tiff run: - - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' + - 'bioconductor-biocgenerics >=0.30.0,<0.31.0' - r-abind - r-base - 'r-fftwtools >=0.9-7' diff --git a/recipes/bioconductor-ebsea/meta.yaml b/recipes/bioconductor-ebsea/meta.yaml index 6ac1071f188b7..4293e5bf2c707 100644 --- a/recipes/bioconductor-ebsea/meta.yaml +++ b/recipes/bioconductor-ebsea/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.10.0" %} +{% set version = "1.12.0" %} {% set name = "EBSEA" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 6e9147314c2308892969992ca042ddec + md5: fd19e2b5af8e9eb07c0991802c63068c build: number: 0 rpaths: @@ -19,13 +19,13 @@ build: noarch: generic requirements: host: - - 'bioconductor-edger >=3.24.0,<3.25.0' - - 'bioconductor-limma >=3.38.0,<3.39.0' + - 'bioconductor-edger >=3.26.0,<3.27.0' + - 'bioconductor-limma >=3.40.0,<3.41.0' - r-base - r-plyr run: - - 'bioconductor-edger >=3.24.0,<3.25.0' - - 'bioconductor-limma >=3.38.0,<3.39.0' + - 'bioconductor-edger >=3.26.0,<3.27.0' + - 'bioconductor-limma >=3.40.0,<3.41.0' - r-base - r-plyr test: diff --git a/recipes/bioconductor-ebseq/meta.yaml b/recipes/bioconductor-ebseq/meta.yaml index b64eeb835511c..fb9fec7e5bbe1 100644 --- a/recipes/bioconductor-ebseq/meta.yaml +++ b/recipes/bioconductor-ebseq/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.22.1" %} +{% set version = "1.24.0" %} {% set name = "EBSeq" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: a0a9b5dffd4c6192174e60598939c0516fe7b34708aa3082045635be6098ebbf + md5: becd6c60c5358cfc63ca19c6ce33f87c build: number: 0 rpaths: diff --git a/recipes/bioconductor-ebseqhmm/meta.yaml b/recipes/bioconductor-ebseqhmm/meta.yaml index 7d2639e506b01..fe6b25a5892fa 100644 --- a/recipes/bioconductor-ebseqhmm/meta.yaml +++ b/recipes/bioconductor-ebseqhmm/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.16.1" %} +{% set version = "1.18.0" %} {% set name = "EBSeqHMM" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: bc9f5011aac248573761e9eee788749e8c35163578548ad08ab61ea7293eb48a + md5: 8f2f866cd05535d159b93b39e59c7ce5 build: number: 0 rpaths: @@ -19,10 +19,10 @@ build: noarch: generic requirements: host: - - 'bioconductor-ebseq >=1.22.0,<1.23.0' + - 'bioconductor-ebseq >=1.24.0,<1.25.0' - r-base run: - - 'bioconductor-ebseq >=1.22.0,<1.23.0' + - 'bioconductor-ebseq >=1.24.0,<1.25.0' - r-base test: commands: diff --git a/recipes/bioconductor-ecoli2.db/meta.yaml b/recipes/bioconductor-ecoli2.db/meta.yaml index bc547a1055123..29cecdbe06170 100644 --- a/recipes/bioconductor-ecoli2.db/meta.yaml +++ b/recipes/bioconductor-ecoli2.db/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.2.3" %} {% set name = "ecoli2.db" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -12,7 +12,7 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 1fe0877a59b63453df6667944818e66b build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ @@ -20,14 +20,14 @@ build: # Suggests: DBI, annotate, RUnit requirements: host: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' - - 'bioconductor-org.eck12.eg.db >=3.7.0,<3.8.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' + - 'bioconductor-org.eck12.eg.db >=3.8.0,<3.9.0' - r-base run: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' - - 'bioconductor-org.eck12.eg.db >=3.7.0,<3.8.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' + - 'bioconductor-org.eck12.eg.db >=3.8.0,<3.9.0' - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-ecoli2.db/post-link.sh b/recipes/bioconductor-ecoli2.db/post-link.sh index 4967e375ba169..325f65f0d6cec 100644 --- a/recipes/bioconductor-ecoli2.db/post-link.sh +++ b/recipes/bioconductor-ecoli2.db/post-link.sh @@ -1,9 +1,10 @@ #!/bin/bash FN="ecoli2.db_3.2.3.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/ecoli2.db_3.2.3.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/ecoli2.db_3.2.3.tar.gz" "https://bioarchive.galaxyproject.org/ecoli2.db_3.2.3.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-ecoli2.db/bioconductor-ecoli2.db_3.2.3_src_all.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-ecoli2.db/bioconductor-ecoli2.db_3.2.3_src_all.tar.gz" ) MD5="1fe0877a59b63453df6667944818e66b" @@ -16,7 +17,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-ecoli2cdf/meta.yaml b/recipes/bioconductor-ecoli2cdf/meta.yaml index 8d571c1663050..8b4fcf096d302 100644 --- a/recipes/bioconductor-ecoli2cdf/meta.yaml +++ b/recipes/bioconductor-ecoli2cdf/meta.yaml @@ -1,6 +1,6 @@ {% set version = "2.18.0" %} {% set name = "ecoli2cdf" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -12,19 +12,19 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: b5cd1f05322ce494132ff649de9806c6 build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' - r-base run: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-ecoli2cdf/post-link.sh b/recipes/bioconductor-ecoli2cdf/post-link.sh index 9856100a0a7ee..e307b34aa183f 100644 --- a/recipes/bioconductor-ecoli2cdf/post-link.sh +++ b/recipes/bioconductor-ecoli2cdf/post-link.sh @@ -1,9 +1,10 @@ #!/bin/bash FN="ecoli2cdf_2.18.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/ecoli2cdf_2.18.0.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/ecoli2cdf_2.18.0.tar.gz" "https://bioarchive.galaxyproject.org/ecoli2cdf_2.18.0.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-ecoli2cdf/bioconductor-ecoli2cdf_2.18.0_src_all.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-ecoli2cdf/bioconductor-ecoli2cdf_2.18.0_src_all.tar.gz" ) MD5="b5cd1f05322ce494132ff649de9806c6" @@ -16,7 +17,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-ecoli2probe/meta.yaml b/recipes/bioconductor-ecoli2probe/meta.yaml index 43c6be8e89252..95790da04ae14 100644 --- a/recipes/bioconductor-ecoli2probe/meta.yaml +++ b/recipes/bioconductor-ecoli2probe/meta.yaml @@ -1,6 +1,6 @@ {% set version = "2.18.0" %} {% set name = "ecoli2probe" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -12,19 +12,19 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 061fcb782ee9da3aa5108881677a4531 build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' - r-base run: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-ecoli2probe/post-link.sh b/recipes/bioconductor-ecoli2probe/post-link.sh index 8cb5aee73b4d9..86346bce46bc3 100644 --- a/recipes/bioconductor-ecoli2probe/post-link.sh +++ b/recipes/bioconductor-ecoli2probe/post-link.sh @@ -1,9 +1,10 @@ #!/bin/bash FN="ecoli2probe_2.18.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/ecoli2probe_2.18.0.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/ecoli2probe_2.18.0.tar.gz" "https://bioarchive.galaxyproject.org/ecoli2probe_2.18.0.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-ecoli2probe/bioconductor-ecoli2probe_2.18.0_src_all.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-ecoli2probe/bioconductor-ecoli2probe_2.18.0_src_all.tar.gz" ) MD5="061fcb782ee9da3aa5108881677a4531" @@ -16,7 +17,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-ecoliasv2cdf/meta.yaml b/recipes/bioconductor-ecoliasv2cdf/meta.yaml index 9109458b8c483..526e9cb242742 100644 --- a/recipes/bioconductor-ecoliasv2cdf/meta.yaml +++ b/recipes/bioconductor-ecoliasv2cdf/meta.yaml @@ -1,6 +1,6 @@ {% set version = "2.18.0" %} {% set name = "ecoliasv2cdf" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -12,19 +12,19 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: d7771ca1648b26a6af5bfb7582c6c778 build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' - r-base run: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-ecoliasv2cdf/post-link.sh b/recipes/bioconductor-ecoliasv2cdf/post-link.sh index 6cf2684b2b8f3..27ca84d4e8044 100644 --- a/recipes/bioconductor-ecoliasv2cdf/post-link.sh +++ b/recipes/bioconductor-ecoliasv2cdf/post-link.sh @@ -1,9 +1,10 @@ #!/bin/bash FN="ecoliasv2cdf_2.18.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/ecoliasv2cdf_2.18.0.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/ecoliasv2cdf_2.18.0.tar.gz" "https://bioarchive.galaxyproject.org/ecoliasv2cdf_2.18.0.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-ecoliasv2cdf/bioconductor-ecoliasv2cdf_2.18.0_src_all.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-ecoliasv2cdf/bioconductor-ecoliasv2cdf_2.18.0_src_all.tar.gz" ) MD5="d7771ca1648b26a6af5bfb7582c6c778" @@ -16,7 +17,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-ecoliasv2probe/meta.yaml b/recipes/bioconductor-ecoliasv2probe/meta.yaml index c4b1411afdc3f..7dfeaf7c6979b 100644 --- a/recipes/bioconductor-ecoliasv2probe/meta.yaml +++ b/recipes/bioconductor-ecoliasv2probe/meta.yaml @@ -1,6 +1,6 @@ {% set version = "2.18.0" %} {% set name = "ecoliasv2probe" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -12,19 +12,19 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: b3e4332266184576279c3a478f286dc9 build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' - r-base run: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-ecoliasv2probe/post-link.sh b/recipes/bioconductor-ecoliasv2probe/post-link.sh index 384c866f1d197..e766612ff54fd 100644 --- a/recipes/bioconductor-ecoliasv2probe/post-link.sh +++ b/recipes/bioconductor-ecoliasv2probe/post-link.sh @@ -1,9 +1,10 @@ #!/bin/bash FN="ecoliasv2probe_2.18.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/ecoliasv2probe_2.18.0.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/ecoliasv2probe_2.18.0.tar.gz" "https://bioarchive.galaxyproject.org/ecoliasv2probe_2.18.0.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-ecoliasv2probe/bioconductor-ecoliasv2probe_2.18.0_src_all.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-ecoliasv2probe/bioconductor-ecoliasv2probe_2.18.0_src_all.tar.gz" ) MD5="b3e4332266184576279c3a478f286dc9" @@ -16,7 +17,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-ecolicdf/meta.yaml b/recipes/bioconductor-ecolicdf/meta.yaml index dcaf486e91e36..52306807dd872 100644 --- a/recipes/bioconductor-ecolicdf/meta.yaml +++ b/recipes/bioconductor-ecolicdf/meta.yaml @@ -1,6 +1,6 @@ {% set version = "2.18.0" %} {% set name = "ecolicdf" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -12,19 +12,19 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 4e664c1ac41a8ab68ef22f8a889b916c build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' - r-base run: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-ecolicdf/post-link.sh b/recipes/bioconductor-ecolicdf/post-link.sh index 73410dba35bcb..c1b601e8f8404 100644 --- a/recipes/bioconductor-ecolicdf/post-link.sh +++ b/recipes/bioconductor-ecolicdf/post-link.sh @@ -1,9 +1,10 @@ #!/bin/bash FN="ecolicdf_2.18.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/ecolicdf_2.18.0.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/ecolicdf_2.18.0.tar.gz" "https://bioarchive.galaxyproject.org/ecolicdf_2.18.0.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-ecolicdf/bioconductor-ecolicdf_2.18.0_src_all.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-ecolicdf/bioconductor-ecolicdf_2.18.0_src_all.tar.gz" ) MD5="4e664c1ac41a8ab68ef22f8a889b916c" @@ -16,7 +17,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-ecolik12.db0/meta.yaml b/recipes/bioconductor-ecolik12.db0/meta.yaml index 0125036171024..b0b7958638438 100644 --- a/recipes/bioconductor-ecolik12.db0/meta.yaml +++ b/recipes/bioconductor-ecolik12.db0/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "3.7.1" %} +{% set version = "3.8.2" %} {% set name = "ecoliK12.db0" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: d2ee48a340d6222a8e78582748849d42 + md5: 98364b33380367953ef27050c72d8d5c build: number: 0 rpaths: @@ -19,12 +19,12 @@ build: noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' - r-base run: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-ecolik12.db0/post-link.sh b/recipes/bioconductor-ecolik12.db0/post-link.sh index c3c1e97d0798d..c141677f9fccd 100644 --- a/recipes/bioconductor-ecolik12.db0/post-link.sh +++ b/recipes/bioconductor-ecolik12.db0/post-link.sh @@ -1,11 +1,11 @@ #!/bin/bash -FN="ecoliK12.db0_3.7.1.tar.gz" +FN="ecoliK12.db0_3.8.2.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/ecoliK12.db0_3.7.1.tar.gz" - "https://bioarchive.galaxyproject.org/ecoliK12.db0_3.7.1.tar.gz" - "https://depot.galaxyproject.org/software/bioconductor-ecolik12.db0/bioconductor-ecolik12.db0_3.7.1_src_all.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/ecoliK12.db0_3.8.2.tar.gz" + "https://bioarchive.galaxyproject.org/ecoliK12.db0_3.8.2.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-ecolik12.db0/bioconductor-ecolik12.db0_3.8.2_src_all.tar.gz" ) -MD5="d2ee48a340d6222a8e78582748849d42" +MD5="98364b33380367953ef27050c72d8d5c" # Use a staging area in the conda dir rather than temp dirs, both to avoid # permission issues as well as to have things downloaded in a predictable @@ -16,7 +16,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-ecolileucine/meta.yaml b/recipes/bioconductor-ecolileucine/meta.yaml index 13703c2fe18cc..edfedc58d56ab 100644 --- a/recipes/bioconductor-ecolileucine/meta.yaml +++ b/recipes/bioconductor-ecolileucine/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.22.0" %} +{% set version = "1.24.0" %} {% set name = "ecoliLeucine" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 8b615a131951847086512158b0d6c876 + md5: 6b94fceec7ba510c24754b9fcd8c6ac5 build: number: 0 rpaths: @@ -19,14 +19,14 @@ build: noarch: generic requirements: host: - - 'bioconductor-affy >=1.60.0,<1.61.0' + - 'bioconductor-affy >=1.62.0,<1.63.0' - 'bioconductor-ecolicdf >=2.18.0,<2.19.0' - r-base run: - - 'bioconductor-affy >=1.60.0,<1.61.0' + - 'bioconductor-affy >=1.62.0,<1.63.0' - 'bioconductor-ecolicdf >=2.18.0,<2.19.0' - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-ecolileucine/post-link.sh b/recipes/bioconductor-ecolileucine/post-link.sh index 977f8324f8e3c..89bbec308929d 100644 --- a/recipes/bioconductor-ecolileucine/post-link.sh +++ b/recipes/bioconductor-ecolileucine/post-link.sh @@ -1,11 +1,11 @@ #!/bin/bash -FN="ecoliLeucine_1.22.0.tar.gz" +FN="ecoliLeucine_1.24.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/experiment/src/contrib/ecoliLeucine_1.22.0.tar.gz" - "https://bioarchive.galaxyproject.org/ecoliLeucine_1.22.0.tar.gz" - "https://depot.galaxyproject.org/software/bioconductor-ecolileucine/bioconductor-ecolileucine_1.22.0_src_all.tar.gz" + "https://bioconductor.org/packages/3.9/data/experiment/src/contrib/ecoliLeucine_1.24.0.tar.gz" + "https://bioarchive.galaxyproject.org/ecoliLeucine_1.24.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-ecolileucine/bioconductor-ecolileucine_1.24.0_src_all.tar.gz" ) -MD5="8b615a131951847086512158b0d6c876" +MD5="6b94fceec7ba510c24754b9fcd8c6ac5" # Use a staging area in the conda dir rather than temp dirs, both to avoid # permission issues as well as to have things downloaded in a predictable @@ -16,7 +16,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-ecoliprobe/meta.yaml b/recipes/bioconductor-ecoliprobe/meta.yaml index 1343b9072c32c..27027c02cfaf6 100644 --- a/recipes/bioconductor-ecoliprobe/meta.yaml +++ b/recipes/bioconductor-ecoliprobe/meta.yaml @@ -1,6 +1,6 @@ {% set version = "2.18.0" %} {% set name = "ecoliprobe" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -12,19 +12,19 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 09586f9907bdbc43ba5ea4ce07c1f756 build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' - r-base run: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-ecoliprobe/post-link.sh b/recipes/bioconductor-ecoliprobe/post-link.sh index b4929ffe15fb4..912069cffe7fc 100644 --- a/recipes/bioconductor-ecoliprobe/post-link.sh +++ b/recipes/bioconductor-ecoliprobe/post-link.sh @@ -1,9 +1,10 @@ #!/bin/bash FN="ecoliprobe_2.18.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/ecoliprobe_2.18.0.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/ecoliprobe_2.18.0.tar.gz" "https://bioarchive.galaxyproject.org/ecoliprobe_2.18.0.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-ecoliprobe/bioconductor-ecoliprobe_2.18.0_src_all.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-ecoliprobe/bioconductor-ecoliprobe_2.18.0_src_all.tar.gz" ) MD5="09586f9907bdbc43ba5ea4ce07c1f756" @@ -16,7 +17,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-ecolisakai.db0/meta.yaml b/recipes/bioconductor-ecolisakai.db0/meta.yaml index 058b9f4669b02..71607d80578b7 100644 --- a/recipes/bioconductor-ecolisakai.db0/meta.yaml +++ b/recipes/bioconductor-ecolisakai.db0/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "3.7.1" %} +{% set version = "3.8.2" %} {% set name = "ecoliSakai.db0" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: b0d399ca92ed5899e7c5770d86f38de2 + md5: 5307f40dff484dfd8427111bfc8312ce build: number: 0 rpaths: @@ -19,12 +19,12 @@ build: noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' - r-base run: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-ecolisakai.db0/post-link.sh b/recipes/bioconductor-ecolisakai.db0/post-link.sh index 31258e8b6818b..c0ddd373b7700 100644 --- a/recipes/bioconductor-ecolisakai.db0/post-link.sh +++ b/recipes/bioconductor-ecolisakai.db0/post-link.sh @@ -1,11 +1,11 @@ #!/bin/bash -FN="ecoliSakai.db0_3.7.1.tar.gz" +FN="ecoliSakai.db0_3.8.2.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/ecoliSakai.db0_3.7.1.tar.gz" - "https://bioarchive.galaxyproject.org/ecoliSakai.db0_3.7.1.tar.gz" - "https://depot.galaxyproject.org/software/bioconductor-ecolisakai.db0/bioconductor-ecolisakai.db0_3.7.1_src_all.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/ecoliSakai.db0_3.8.2.tar.gz" + "https://bioarchive.galaxyproject.org/ecoliSakai.db0_3.8.2.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-ecolisakai.db0/bioconductor-ecolisakai.db0_3.8.2_src_all.tar.gz" ) -MD5="b0d399ca92ed5899e7c5770d86f38de2" +MD5="5307f40dff484dfd8427111bfc8312ce" # Use a staging area in the conda dir rather than temp dirs, both to avoid # permission issues as well as to have things downloaded in a predictable @@ -16,7 +16,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-ecolitk/meta.yaml b/recipes/bioconductor-ecolitk/meta.yaml index 0d9ff2c8d5ae0..30e3247b9605d 100644 --- a/recipes/bioconductor-ecolitk/meta.yaml +++ b/recipes/bioconductor-ecolitk/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.54.0" %} +{% set version = "1.56.0" %} {% set name = "ecolitk" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: a0d9620024909dcbb12b20e3b5ebf92f + md5: d7eeb11fad631ce3934581f5f7606aeb build: number: 0 rpaths: @@ -20,10 +20,10 @@ build: # Suggests: ecoliLeucine, ecolicdf, graph, multtest, affy requirements: host: - - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' - r-base run: - - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' - r-base test: commands: diff --git a/recipes/bioconductor-edaseq/meta.yaml b/recipes/bioconductor-edaseq/meta.yaml index 520b63889c718..1850a8e9b59af 100644 --- a/recipes/bioconductor-edaseq/meta.yaml +++ b/recipes/bioconductor-edaseq/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "2.16.0" %} +{% set version = "2.18.0" %} {% set name = "EDASeq" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: ed8283ab13f07c4d7a182c240471dd89 + md5: 478a1ed2c78ff2d606de4fae097f6776 build: number: 0 rpaths: @@ -20,33 +20,35 @@ build: # Suggests: BiocStyle, knitr, yeastRNASeq, leeBamViews, edgeR, KernSmooth, testthat requirements: host: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' - - 'bioconductor-aroma.light >=3.12.0,<3.13.0' - - 'bioconductor-biobase >=2.42.0,<2.43.0' - - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' - - 'bioconductor-biomart >=2.38.0,<2.39.0' - - 'bioconductor-biostrings >=2.50.0,<2.51.0' - - 'bioconductor-deseq >=1.34.0,<1.35.0' - - 'bioconductor-genomicfeatures >=1.34.0,<1.35.0' - - 'bioconductor-genomicranges >=1.34.0,<1.35.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-rsamtools >=1.34.0,<1.35.0' - - 'bioconductor-shortread >=1.40.0,<1.41.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' + - 'bioconductor-aroma.light >=3.14.0,<3.15.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' + - 'bioconductor-biocgenerics >=0.30.0,<0.31.0' + - 'bioconductor-biomart >=2.40.0,<2.41.0' + - 'bioconductor-biostrings >=2.52.0,<2.53.0' + - 'bioconductor-deseq >=1.36.0,<1.37.0' + - 'bioconductor-genomicfeatures >=1.36.0,<1.37.0' + - 'bioconductor-genomicranges >=1.36.0,<1.37.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-rsamtools >=2.0.0,<2.1.0' + - 'bioconductor-shortread >=1.42.0,<1.43.0' - r-base + - r-biocmanager run: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' - - 'bioconductor-aroma.light >=3.12.0,<3.13.0' - - 'bioconductor-biobase >=2.42.0,<2.43.0' - - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' - - 'bioconductor-biomart >=2.38.0,<2.39.0' - - 'bioconductor-biostrings >=2.50.0,<2.51.0' - - 'bioconductor-deseq >=1.34.0,<1.35.0' - - 'bioconductor-genomicfeatures >=1.34.0,<1.35.0' - - 'bioconductor-genomicranges >=1.34.0,<1.35.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-rsamtools >=1.34.0,<1.35.0' - - 'bioconductor-shortread >=1.40.0,<1.41.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' + - 'bioconductor-aroma.light >=3.14.0,<3.15.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' + - 'bioconductor-biocgenerics >=0.30.0,<0.31.0' + - 'bioconductor-biomart >=2.40.0,<2.41.0' + - 'bioconductor-biostrings >=2.52.0,<2.53.0' + - 'bioconductor-deseq >=1.36.0,<1.37.0' + - 'bioconductor-genomicfeatures >=1.36.0,<1.37.0' + - 'bioconductor-genomicranges >=1.36.0,<1.37.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-rsamtools >=2.0.0,<2.1.0' + - 'bioconductor-shortread >=1.42.0,<1.43.0' - r-base + - r-biocmanager test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-edda/meta.yaml b/recipes/bioconductor-edda/meta.yaml index 512e287b8cd97..90d27432d1fec 100644 --- a/recipes/bioconductor-edda/meta.yaml +++ b/recipes/bioconductor-edda/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.20.1" %} +{% set version = "1.22.0" %} {% set name = "EDDA" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 28bedf0b293d64808ba970c681b891f7 + md5: 644dc53ad78a4e34f618d4f76ef7a04f build: number: 0 rpaths: @@ -18,17 +18,17 @@ build: - lib/ requirements: host: - - 'bioconductor-bayseq >=2.16.0,<2.17.0' - - 'bioconductor-deseq >=1.34.0,<1.35.0' - - 'bioconductor-edger >=3.24.0,<3.25.0' + - 'bioconductor-bayseq >=2.18.0,<2.19.0' + - 'bioconductor-deseq >=1.36.0,<1.37.0' + - 'bioconductor-edger >=3.26.0,<3.27.0' - r-base - 'r-rcpp >=0.10.4' - r-rocr - r-snow run: - - 'bioconductor-bayseq >=2.16.0,<2.17.0' - - 'bioconductor-deseq >=1.34.0,<1.35.0' - - 'bioconductor-edger >=3.24.0,<3.25.0' + - 'bioconductor-bayseq >=2.18.0,<2.19.0' + - 'bioconductor-deseq >=1.36.0,<1.37.0' + - 'bioconductor-edger >=3.26.0,<3.27.0' - r-base - 'r-rcpp >=0.10.4' - r-rocr diff --git a/recipes/bioconductor-edge/meta.yaml b/recipes/bioconductor-edge/meta.yaml index 45838191d091d..2adae5a4dd713 100644 --- a/recipes/bioconductor-edge/meta.yaml +++ b/recipes/bioconductor-edge/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "2.14.0" %} +{% set version = "2.16.0" %} {% set name = "edge" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 6797ccce69d0cfc8d172ead461d3cec7 + md5: 48cb021c6bd3677e96f44d419ef4382f build: number: 0 rpaths: @@ -19,18 +19,18 @@ build: # Suggests: testthat, knitr, ggplot2, reshape2 requirements: host: - - 'bioconductor-biobase >=2.42.0,<2.43.0' - - 'bioconductor-qvalue >=2.14.0,<2.15.0' - - 'bioconductor-snm >=1.30.0,<1.31.0' - - 'bioconductor-sva >=3.30.0,<3.31.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' + - 'bioconductor-qvalue >=2.16.0,<2.17.0' + - 'bioconductor-snm >=1.32.0,<1.33.0' + - 'bioconductor-sva >=3.32.0,<3.33.0' - r-base - r-jackstraw - r-mass run: - - 'bioconductor-biobase >=2.42.0,<2.43.0' - - 'bioconductor-qvalue >=2.14.0,<2.15.0' - - 'bioconductor-snm >=1.30.0,<1.31.0' - - 'bioconductor-sva >=3.30.0,<3.31.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' + - 'bioconductor-qvalue >=2.16.0,<2.17.0' + - 'bioconductor-snm >=1.32.0,<1.33.0' + - 'bioconductor-sva >=3.32.0,<3.33.0' - r-base - r-jackstraw - r-mass diff --git a/recipes/bioconductor-edger/meta.yaml b/recipes/bioconductor-edger/meta.yaml index 88f0957e3c6bf..fddd47238e48d 100644 --- a/recipes/bioconductor-edger/meta.yaml +++ b/recipes/bioconductor-edger/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "3.24.3" %} +{% set version = "3.26.0" %} {% set name = "edgeR" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: af0be10708ac096b58c83177dcc9ff08588c9a3bb2f0579da6b0d7ae97aed197 + md5: 52bd63ccc21c97aee7334aabc64e0fec build: number: 0 rpaths: @@ -20,12 +20,12 @@ build: # SystemRequirements: C++11 requirements: host: - - 'bioconductor-limma >=3.38.0,<3.39.0' + - 'bioconductor-limma >=3.40.0,<3.41.0' - r-base - r-locfit - r-rcpp run: - - 'bioconductor-limma >=3.38.0,<3.39.0' + - 'bioconductor-limma >=3.40.0,<3.41.0' - r-base - r-locfit - r-rcpp diff --git a/recipes/bioconductor-eegc/meta.yaml b/recipes/bioconductor-eegc/meta.yaml index 4e9949f3c26aa..9565642947682 100644 --- a/recipes/bioconductor-eegc/meta.yaml +++ b/recipes/bioconductor-eegc/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.8.1" %} +{% set version = "1.10.0" %} {% set name = "eegc" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: acac7f97fcfcc9641aab15beda10c60c + md5: b05f2f7a3f6e39f65f1deea5ee9e874d build: number: 0 rpaths: @@ -20,15 +20,15 @@ build: # Suggests: knitr requirements: host: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' - - 'bioconductor-clusterprofiler >=3.10.0,<3.11.0' - - 'bioconductor-deseq2 >=1.22.0,<1.23.0' - - 'bioconductor-dose >=3.8.0,<3.9.0' - - 'bioconductor-edger >=3.24.0,<3.25.0' - - 'bioconductor-limma >=3.38.0,<3.39.0' - - 'bioconductor-org.hs.eg.db >=3.7.0,<3.8.0' - - 'bioconductor-org.mm.eg.db >=3.7.0,<3.8.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' + - 'bioconductor-clusterprofiler >=3.12.0,<3.13.0' + - 'bioconductor-deseq2 >=1.24.0,<1.25.0' + - 'bioconductor-dose >=3.10.0,<3.11.0' + - 'bioconductor-edger >=3.26.0,<3.27.0' + - 'bioconductor-limma >=3.40.0,<3.41.0' + - 'bioconductor-org.hs.eg.db >=3.8.0,<3.9.0' + - 'bioconductor-org.mm.eg.db >=3.8.0,<3.9.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' - r-base - r-ggplot2 - r-gplots @@ -38,15 +38,15 @@ requirements: - r-sna - r-wordcloud run: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' - - 'bioconductor-clusterprofiler >=3.10.0,<3.11.0' - - 'bioconductor-deseq2 >=1.22.0,<1.23.0' - - 'bioconductor-dose >=3.8.0,<3.9.0' - - 'bioconductor-edger >=3.24.0,<3.25.0' - - 'bioconductor-limma >=3.38.0,<3.39.0' - - 'bioconductor-org.hs.eg.db >=3.7.0,<3.8.0' - - 'bioconductor-org.mm.eg.db >=3.7.0,<3.8.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' + - 'bioconductor-clusterprofiler >=3.12.0,<3.13.0' + - 'bioconductor-deseq2 >=1.24.0,<1.25.0' + - 'bioconductor-dose >=3.10.0,<3.11.0' + - 'bioconductor-edger >=3.26.0,<3.27.0' + - 'bioconductor-limma >=3.40.0,<3.41.0' + - 'bioconductor-org.hs.eg.db >=3.8.0,<3.9.0' + - 'bioconductor-org.mm.eg.db >=3.8.0,<3.9.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' - r-base - r-ggplot2 - r-gplots diff --git a/recipes/bioconductor-egad/meta.yaml b/recipes/bioconductor-egad/meta.yaml index 2da78f43b6bda..593b103955d0e 100644 --- a/recipes/bioconductor-egad/meta.yaml +++ b/recipes/bioconductor-egad/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.10.0" %} +{% set version = "1.12.0" %} {% set name = "EGAD" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 798b2f43513b64bec9a70c5a6b387efe + md5: 51baa1af3e40ef6ac8b84484d61c8091 build: number: 0 rpaths: @@ -20,12 +20,12 @@ build: # Suggests: knitr, rmarkdown, testthat requirements: host: - - 'bioconductor-affy >=1.60.0,<1.61.0' - - 'bioconductor-arrayqualitymetrics >=3.38.0,<3.39.0' - - 'bioconductor-biobase >=2.42.0,<2.43.0' - - 'bioconductor-geoquery >=2.50.0,<2.51.0' - - 'bioconductor-impute >=1.56.0,<1.57.0' - - 'bioconductor-limma >=3.38.0,<3.39.0' + - 'bioconductor-affy >=1.62.0,<1.63.0' + - 'bioconductor-arrayqualitymetrics >=3.40.0,<3.41.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' + - 'bioconductor-geoquery >=2.52.0,<2.53.0' + - 'bioconductor-impute >=1.58.0,<1.59.0' + - 'bioconductor-limma >=3.40.0,<3.41.0' - r-base - r-gplots - r-igraph @@ -36,12 +36,12 @@ requirements: - r-rcurl - r-zoo run: - - 'bioconductor-affy >=1.60.0,<1.61.0' - - 'bioconductor-arrayqualitymetrics >=3.38.0,<3.39.0' - - 'bioconductor-biobase >=2.42.0,<2.43.0' - - 'bioconductor-geoquery >=2.50.0,<2.51.0' - - 'bioconductor-impute >=1.56.0,<1.57.0' - - 'bioconductor-limma >=3.38.0,<3.39.0' + - 'bioconductor-affy >=1.62.0,<1.63.0' + - 'bioconductor-arrayqualitymetrics >=3.40.0,<3.41.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' + - 'bioconductor-geoquery >=2.52.0,<2.53.0' + - 'bioconductor-impute >=1.58.0,<1.59.0' + - 'bioconductor-limma >=3.40.0,<3.41.0' - r-base - r-gplots - r-igraph diff --git a/recipes/bioconductor-egsea/meta.yaml b/recipes/bioconductor-egsea/meta.yaml index 9136863f191f3..ff4e1473c6f39 100644 --- a/recipes/bioconductor-egsea/meta.yaml +++ b/recipes/bioconductor-egsea/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.10.0" %} +{% set version = "1.12.0" %} {% set name = "EGSEA" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 8f51d5d82b08d86f6c433712921d2596 + md5: 74eecf4e7b394954f7616a2fe86d926e build: number: 0 rpaths: @@ -20,22 +20,22 @@ build: # Suggests: BiocStyle, knitr, testthat requirements: host: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' - - 'bioconductor-biobase >=2.42.0,<2.43.0' - - 'bioconductor-edger >=3.24.0,<3.25.0' - - 'bioconductor-egseadata >=1.10.0,<1.11.0' - - 'bioconductor-gage >=2.32.0,<2.33.0' - - 'bioconductor-glimma >=1.10.0,<1.11.0' - - 'bioconductor-globaltest >=5.36.0,<5.37.0' - - 'bioconductor-gsva >=1.30.0,<1.31.0' - - 'bioconductor-limma >=3.38.0,<3.39.0' - - 'bioconductor-org.hs.eg.db >=3.7.0,<3.8.0' - - 'bioconductor-org.mm.eg.db >=3.7.0,<3.8.0' - - 'bioconductor-org.rn.eg.db >=3.7.0,<3.8.0' - - 'bioconductor-padog >=1.24.0,<1.25.0' - - 'bioconductor-pathview >=1.22.0,<1.23.0' - - 'bioconductor-safe >=3.22.0,<3.23.0' - - 'bioconductor-topgo >=2.34.0,<2.35.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' + - 'bioconductor-edger >=3.26.0,<3.27.0' + - 'bioconductor-egseadata >=1.12.0,<1.13.0' + - 'bioconductor-gage >=2.34.0,<2.35.0' + - 'bioconductor-glimma >=1.12.0,<1.13.0' + - 'bioconductor-globaltest >=5.38.0,<5.39.0' + - 'bioconductor-gsva >=1.32.0,<1.33.0' + - 'bioconductor-limma >=3.40.0,<3.41.0' + - 'bioconductor-org.hs.eg.db >=3.8.0,<3.9.0' + - 'bioconductor-org.mm.eg.db >=3.8.0,<3.9.0' + - 'bioconductor-org.rn.eg.db >=3.8.0,<3.9.0' + - 'bioconductor-padog >=1.26.0,<1.27.0' + - 'bioconductor-pathview >=1.24.0,<1.25.0' + - 'bioconductor-safe >=3.24.0,<3.25.0' + - 'bioconductor-topgo >=2.36.0,<2.37.0' - r-base - r-dt - 'r-ggplot2 >=1.0.0' @@ -48,22 +48,22 @@ requirements: - r-rcolorbrewer - 'r-stringi >=0.5.0' run: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' - - 'bioconductor-biobase >=2.42.0,<2.43.0' - - 'bioconductor-edger >=3.24.0,<3.25.0' - - 'bioconductor-egseadata >=1.10.0,<1.11.0' - - 'bioconductor-gage >=2.32.0,<2.33.0' - - 'bioconductor-glimma >=1.10.0,<1.11.0' - - 'bioconductor-globaltest >=5.36.0,<5.37.0' - - 'bioconductor-gsva >=1.30.0,<1.31.0' - - 'bioconductor-limma >=3.38.0,<3.39.0' - - 'bioconductor-org.hs.eg.db >=3.7.0,<3.8.0' - - 'bioconductor-org.mm.eg.db >=3.7.0,<3.8.0' - - 'bioconductor-org.rn.eg.db >=3.7.0,<3.8.0' - - 'bioconductor-padog >=1.24.0,<1.25.0' - - 'bioconductor-pathview >=1.22.0,<1.23.0' - - 'bioconductor-safe >=3.22.0,<3.23.0' - - 'bioconductor-topgo >=2.34.0,<2.35.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' + - 'bioconductor-edger >=3.26.0,<3.27.0' + - 'bioconductor-egseadata >=1.12.0,<1.13.0' + - 'bioconductor-gage >=2.34.0,<2.35.0' + - 'bioconductor-glimma >=1.12.0,<1.13.0' + - 'bioconductor-globaltest >=5.38.0,<5.39.0' + - 'bioconductor-gsva >=1.32.0,<1.33.0' + - 'bioconductor-limma >=3.40.0,<3.41.0' + - 'bioconductor-org.hs.eg.db >=3.8.0,<3.9.0' + - 'bioconductor-org.mm.eg.db >=3.8.0,<3.9.0' + - 'bioconductor-org.rn.eg.db >=3.8.0,<3.9.0' + - 'bioconductor-padog >=1.26.0,<1.27.0' + - 'bioconductor-pathview >=1.24.0,<1.25.0' + - 'bioconductor-safe >=3.24.0,<3.25.0' + - 'bioconductor-topgo >=2.36.0,<2.37.0' - r-base - r-dt - 'r-ggplot2 >=1.0.0' diff --git a/recipes/bioconductor-egseadata/meta.yaml b/recipes/bioconductor-egseadata/meta.yaml index a8b5c136ec935..a7bdf3b4374ff 100644 --- a/recipes/bioconductor-egseadata/meta.yaml +++ b/recipes/bioconductor-egseadata/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.10.0" %} +{% set version = "1.12.0" %} {% set name = "EGSEAdata" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 666b85ee723e0125632a40a30b3f602e + md5: 66cb1885c1cc1a378884e34c41ef2e25 build: number: 0 rpaths: @@ -23,7 +23,7 @@ requirements: - r-base run: - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-egseadata/post-link.sh b/recipes/bioconductor-egseadata/post-link.sh index cefd8f7c81cb9..2eb77657e1991 100644 --- a/recipes/bioconductor-egseadata/post-link.sh +++ b/recipes/bioconductor-egseadata/post-link.sh @@ -1,11 +1,11 @@ #!/bin/bash -FN="EGSEAdata_1.10.0.tar.gz" +FN="EGSEAdata_1.12.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/experiment/src/contrib/EGSEAdata_1.10.0.tar.gz" - "https://bioarchive.galaxyproject.org/EGSEAdata_1.10.0.tar.gz" - "https://depot.galaxyproject.org/software/bioconductor-egseadata/bioconductor-egseadata_1.10.0_src_all.tar.gz" + "https://bioconductor.org/packages/3.9/data/experiment/src/contrib/EGSEAdata_1.12.0.tar.gz" + "https://bioarchive.galaxyproject.org/EGSEAdata_1.12.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-egseadata/bioconductor-egseadata_1.12.0_src_all.tar.gz" ) -MD5="666b85ee723e0125632a40a30b3f602e" +MD5="66cb1885c1cc1a378884e34c41ef2e25" # Use a staging area in the conda dir rather than temp dirs, both to avoid # permission issues as well as to have things downloaded in a predictable @@ -16,7 +16,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-eir/meta.yaml b/recipes/bioconductor-eir/meta.yaml index 1a32a5624d29a..32ed96b75ec03 100644 --- a/recipes/bioconductor-eir/meta.yaml +++ b/recipes/bioconductor-eir/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.22.0" %} +{% set version = "1.24.0" %} {% set name = "eiR" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 02df663489eb5a3924b07e84a86f38e4 + md5: aa753e91c09aeb6f53c66957e36d7d99 build: number: 0 rpaths: @@ -19,9 +19,9 @@ build: # Suggests: BiocStyle, knitcitations, knitr, knitrBootstrap requirements: host: - - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' - - 'bioconductor-chemminer >=3.34.0,<3.35.0' - - 'bioconductor-gesper >=1.14.0,<1.15.0' + - 'bioconductor-biocgenerics >=0.30.0,<0.31.0' + - 'bioconductor-chemminer >=3.36.0,<3.37.0' + - 'bioconductor-gesper >=1.16.0,<1.17.0' - r-base - r-dbi - r-digest @@ -31,9 +31,9 @@ requirements: - r-snow - r-snowfall run: - - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' - - 'bioconductor-chemminer >=3.34.0,<3.35.0' - - 'bioconductor-gesper >=1.14.0,<1.15.0' + - 'bioconductor-biocgenerics >=0.30.0,<0.31.0' + - 'bioconductor-chemminer >=3.36.0,<3.37.0' + - 'bioconductor-gesper >=1.16.0,<1.17.0' - r-base - r-dbi - r-digest diff --git a/recipes/bioconductor-eisa/meta.yaml b/recipes/bioconductor-eisa/meta.yaml index fa6486423c200..4491d05b19c60 100644 --- a/recipes/bioconductor-eisa/meta.yaml +++ b/recipes/bioconductor-eisa/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.34.0" %} +{% set version = "1.36.0" %} {% set name = "eisa" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 114415b5b584378e8c2f93e081833045 + md5: cf034edc59e97a5ba8fd5322bc36c876 build: number: 0 rpaths: @@ -20,20 +20,20 @@ build: # Suggests: igraph (>= 0.6), Matrix, GOstats, GO.db, KEGG.db, biclust, MASS, xtable, ALL, hgu95av2.db, targetscan.Hs.eg.db, org.Hs.eg.db requirements: host: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' - - 'bioconductor-biobase >=2.42.0,<2.43.0' - - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' - - 'bioconductor-category >=2.48.0,<2.49.0' - - 'bioconductor-genefilter >=1.64.0,<1.65.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' + - 'bioconductor-biocgenerics >=0.30.0,<0.31.0' + - 'bioconductor-category >=2.50.0,<2.51.0' + - 'bioconductor-genefilter >=1.66.0,<1.67.0' - r-base - r-dbi - r-isa2 run: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' - - 'bioconductor-biobase >=2.42.0,<2.43.0' - - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' - - 'bioconductor-category >=2.48.0,<2.49.0' - - 'bioconductor-genefilter >=1.64.0,<1.65.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' + - 'bioconductor-biocgenerics >=0.30.0,<0.31.0' + - 'bioconductor-category >=2.50.0,<2.51.0' + - 'bioconductor-genefilter >=1.66.0,<1.67.0' - r-base - r-dbi - r-isa2 diff --git a/recipes/bioconductor-elbow/meta.yaml b/recipes/bioconductor-elbow/meta.yaml index b288e376ecc0f..4fef861d88289 100644 --- a/recipes/bioconductor-elbow/meta.yaml +++ b/recipes/bioconductor-elbow/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.18.1" %} +{% set version = "1.20.0" %} {% set name = "ELBOW" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 66a2e8881b2fb3ea5cd7d76785a8c123 + md5: a7f6650044af31c238c8d98c0d56e437 build: number: 0 rpaths: diff --git a/recipes/bioconductor-elmer.data/meta.yaml b/recipes/bioconductor-elmer.data/meta.yaml index af2d6e57b3e76..8aa4ad82049b1 100644 --- a/recipes/bioconductor-elmer.data/meta.yaml +++ b/recipes/bioconductor-elmer.data/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "2.6.0" %} +{% set version = "2.8.0" %} {% set name = "ELMER.data" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 6c2fe2971cd966175cb61c146921107f + md5: 11271a22a29147bc8f11c3039399d191 build: number: 0 rpaths: @@ -20,12 +20,12 @@ build: # Suggests: BiocStyle, knitr, dplyr, devtools, DT requirements: host: - - 'bioconductor-genomicranges >=1.34.0,<1.35.0' + - 'bioconductor-genomicranges >=1.36.0,<1.37.0' - r-base run: - - 'bioconductor-genomicranges >=1.34.0,<1.35.0' + - 'bioconductor-genomicranges >=1.36.0,<1.37.0' - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-elmer.data/post-link.sh b/recipes/bioconductor-elmer.data/post-link.sh index 2c387eb156f28..0381f1727d66f 100644 --- a/recipes/bioconductor-elmer.data/post-link.sh +++ b/recipes/bioconductor-elmer.data/post-link.sh @@ -1,11 +1,11 @@ #!/bin/bash -FN="ELMER.data_2.6.0.tar.gz" +FN="ELMER.data_2.8.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/experiment/src/contrib/ELMER.data_2.6.0.tar.gz" - "https://bioarchive.galaxyproject.org/ELMER.data_2.6.0.tar.gz" - "https://depot.galaxyproject.org/software/bioconductor-elmer.data/bioconductor-elmer.data_2.6.0_src_all.tar.gz" + "https://bioconductor.org/packages/3.9/data/experiment/src/contrib/ELMER.data_2.8.0.tar.gz" + "https://bioarchive.galaxyproject.org/ELMER.data_2.8.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-elmer.data/bioconductor-elmer.data_2.8.0_src_all.tar.gz" ) -MD5="6c2fe2971cd966175cb61c146921107f" +MD5="11271a22a29147bc8f11c3039399d191" # Use a staging area in the conda dir rather than temp dirs, both to avoid # permission issues as well as to have things downloaded in a predictable @@ -16,7 +16,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-elmer/meta.yaml b/recipes/bioconductor-elmer/meta.yaml index 73219a6b653b8..8623e90635f44 100644 --- a/recipes/bioconductor-elmer/meta.yaml +++ b/recipes/bioconductor-elmer/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "2.6.1" %} +{% set version = "2.8.0" %} {% set name = "ELMER" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,28 +10,30 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: ee51a1a511d97cfa74ffd82100c16f10 + md5: 98495928178bb60dd260ca5317b0ddb3 build: number: 0 rpaths: - lib/R/lib/ - lib/ noarch: generic -# Suggests: BiocStyle, knitr, testthat, data.table, DT, GenomicInteractions, webshot, rtracklayer, R.utils, covr +# Suggests: BiocStyle, knitr, testthat, data.table, DT, GenomicInteractions, webshot, R.utils, covr requirements: host: - - 'bioconductor-biomart >=2.38.0,<2.39.0' - - 'bioconductor-complexheatmap >=1.20.0,<1.21.0' - - 'bioconductor-elmer.data >=2.6.0,<2.7.0' - - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' - - 'bioconductor-genomicfeatures >=1.34.0,<1.35.0' - - 'bioconductor-genomicranges >=1.34.0,<1.35.0' - - 'bioconductor-gviz >=1.26.0,<1.27.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-multiassayexperiment >=1.8.0,<1.9.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' - - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' - - 'bioconductor-tcgabiolinks >=2.10.0,<2.11.0' + - 'bioconductor-biomart >=2.40.0,<2.41.0' + - 'bioconductor-complexheatmap >=2.0.0,<2.1.0' + - 'bioconductor-delayedarray >=0.10.0,<0.11.0' + - 'bioconductor-elmer.data >=2.8.0,<2.9.0' + - 'bioconductor-genomeinfodb >=1.20.0,<1.21.0' + - 'bioconductor-genomicfeatures >=1.36.0,<1.37.0' + - 'bioconductor-genomicranges >=1.36.0,<1.37.0' + - 'bioconductor-gviz >=1.28.0,<1.29.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-multiassayexperiment >=1.10.0,<1.11.0' + - 'bioconductor-rtracklayer >=1.44.0,<1.45.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' + - 'bioconductor-summarizedexperiment >=1.14.0,<1.15.0' + - 'bioconductor-tcgabiolinks >=2.12.0,<2.13.0' - r-base - r-circlize - r-doparallel @@ -45,6 +47,8 @@ requirements: - r-matrix - r-plotly - r-plyr + - r-progress + - r-purrr - r-readr - r-reshape - r-rmarkdown @@ -54,18 +58,20 @@ requirements: - r-tidyr - r-xml2 run: - - 'bioconductor-biomart >=2.38.0,<2.39.0' - - 'bioconductor-complexheatmap >=1.20.0,<1.21.0' - - 'bioconductor-elmer.data >=2.6.0,<2.7.0' - - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' - - 'bioconductor-genomicfeatures >=1.34.0,<1.35.0' - - 'bioconductor-genomicranges >=1.34.0,<1.35.0' - - 'bioconductor-gviz >=1.26.0,<1.27.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-multiassayexperiment >=1.8.0,<1.9.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' - - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' - - 'bioconductor-tcgabiolinks >=2.10.0,<2.11.0' + - 'bioconductor-biomart >=2.40.0,<2.41.0' + - 'bioconductor-complexheatmap >=2.0.0,<2.1.0' + - 'bioconductor-delayedarray >=0.10.0,<0.11.0' + - 'bioconductor-elmer.data >=2.8.0,<2.9.0' + - 'bioconductor-genomeinfodb >=1.20.0,<1.21.0' + - 'bioconductor-genomicfeatures >=1.36.0,<1.37.0' + - 'bioconductor-genomicranges >=1.36.0,<1.37.0' + - 'bioconductor-gviz >=1.28.0,<1.29.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-multiassayexperiment >=1.10.0,<1.11.0' + - 'bioconductor-rtracklayer >=1.44.0,<1.45.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' + - 'bioconductor-summarizedexperiment >=1.14.0,<1.15.0' + - 'bioconductor-tcgabiolinks >=2.12.0,<2.13.0' - r-base - r-circlize - r-doparallel @@ -79,6 +85,8 @@ requirements: - r-matrix - r-plotly - r-plyr + - r-progress + - r-purrr - r-readr - r-reshape - r-rmarkdown diff --git a/recipes/bioconductor-emdomics/meta.yaml b/recipes/bioconductor-emdomics/meta.yaml index 962bc46bb2afb..80c75a1b980fe 100644 --- a/recipes/bioconductor-emdomics/meta.yaml +++ b/recipes/bioconductor-emdomics/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "2.12.0" %} +{% set version = "2.14.0" %} {% set name = "EMDomics" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,9 +10,9 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 0f9d117d39c59207bccc6f6ecad2f5e9 + md5: baabbdfdbaf4306ac2d89804857133a0 build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ @@ -20,16 +20,16 @@ build: # Suggests: knitr requirements: host: - - 'bioconductor-biocparallel >=1.16.0,<1.17.0' - - 'bioconductor-preprocesscore >=1.44.0,<1.45.0' + - 'bioconductor-biocparallel >=1.18.0,<1.19.0' + - 'bioconductor-preprocesscore >=1.46.0,<1.47.0' - r-base - r-cdft - r-emdist - r-ggplot2 - r-matrixstats run: - - 'bioconductor-biocparallel >=1.16.0,<1.17.0' - - 'bioconductor-preprocesscore >=1.44.0,<1.45.0' + - 'bioconductor-biocparallel >=1.18.0,<1.19.0' + - 'bioconductor-preprocesscore >=1.46.0,<1.47.0' - r-base - r-cdft - r-emdist diff --git a/recipes/bioconductor-empiricalbrownsmethod/meta.yaml b/recipes/bioconductor-empiricalbrownsmethod/meta.yaml index 27bac5005b59b..2e888f708a37e 100644 --- a/recipes/bioconductor-empiricalbrownsmethod/meta.yaml +++ b/recipes/bioconductor-empiricalbrownsmethod/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.10.0" %} +{% set version = "1.12.0" %} {% set name = "EmpiricalBrownsMethod" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 2d91e211bf843eefad77a8526c65a370 + md5: e4b0403a9ba17adcf61cba37e292cf0f build: number: 0 rpaths: diff --git a/recipes/bioconductor-encodexplorer/meta.yaml b/recipes/bioconductor-encodexplorer/meta.yaml index 530d38104976d..839817d66cc96 100644 --- a/recipes/bioconductor-encodexplorer/meta.yaml +++ b/recipes/bioconductor-encodexplorer/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "2.8.0" %} +{% set version = "2.10.0" %} {% set name = "ENCODExplorer" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 6bd1aa3aa9897fbd1d85c19d47c9aaaf + md5: cfc6d5a72878ec794ac0be88938cedfa build: number: 0 rpaths: @@ -20,6 +20,7 @@ build: # Suggests: RUnit,BiocGenerics,knitr, curl, httr requirements: host: + - 'bioconductor-annotationhub >=2.16.0,<2.17.0' - r-base - r-data.table - r-dplyr @@ -32,6 +33,7 @@ requirements: - r-stringr - r-tidyr run: + - 'bioconductor-annotationhub >=2.16.0,<2.17.0' - r-base - r-data.table - r-dplyr diff --git a/recipes/bioconductor-encodexplorerdata/meta.yaml b/recipes/bioconductor-encodexplorerdata/meta.yaml new file mode 100644 index 0000000000000..4ac9f186921fc --- /dev/null +++ b/recipes/bioconductor-encodexplorerdata/meta.yaml @@ -0,0 +1,42 @@ +{% set version = "0.99.1" %} +{% set name = "ENCODExplorerData" %} +{% set bioc = "3.9" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: 61788c5c9d248ce4b4488b0be98ea879 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: AnnotationHub, RUnit, BiocGenerics, knitr, curl, httr +requirements: + host: + - r-base + - r-data.table + - r-jsonlite + - r-rcurl + - r-tidyr + run: + - r-base + - r-data.table + - r-jsonlite + - r-rcurl + - r-tidyr + - curl +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'This package allows user to quickly access ENCODE project files metadata and give access to helper functions to query the ENCODE rest api, download ENCODE datasets and save the database in SQLite format.' + diff --git a/recipes/bioconductor-encodexplorerdata/post-link.sh b/recipes/bioconductor-encodexplorerdata/post-link.sh new file mode 100644 index 0000000000000..0bf77c5224f3e --- /dev/null +++ b/recipes/bioconductor-encodexplorerdata/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="ENCODExplorerData_0.99.1.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/ENCODExplorerData_0.99.1.tar.gz" + "https://bioarchive.galaxyproject.org/ENCODExplorerData_0.99.1.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-encodexplorerdata/bioconductor-encodexplorerdata_0.99.1_src_all.tar.gz" +) +MD5="61788c5c9d248ce4b4488b0be98ea879" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + curl $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-encodexplorerdata/pre-unlink.sh b/recipes/bioconductor-encodexplorerdata/pre-unlink.sh new file mode 100644 index 0000000000000..f4dcc207027a8 --- /dev/null +++ b/recipes/bioconductor-encodexplorerdata/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ ENCODExplorerData diff --git a/recipes/bioconductor-enhancedvolcano/meta.yaml b/recipes/bioconductor-enhancedvolcano/meta.yaml index 1861447eb7add..f21ecdd513878 100644 --- a/recipes/bioconductor-enhancedvolcano/meta.yaml +++ b/recipes/bioconductor-enhancedvolcano/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.0.1" %} +{% set version = "1.2.0" %} {% set name = "EnhancedVolcano" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 2981aa06d982fff46fbbf4728e8d957e + md5: e07947292645c861e847cab9fcf60f84 build: number: 0 rpaths: @@ -33,7 +33,7 @@ test: about: home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: GPL-3 - summary: 'Volcano plots represent a useful way to visualise the results of differential expression analyses. Here, we present a highly-configurable function that produces publication-ready volcano plots. EnhancedVolcano will attempt to fit as many transcript names in the plot window as possible, thus avoiding ''clogging'' up the plot with labels that could not otherwise have been read.' + summary: 'Volcano plots represent a useful way to visualise the results of differential expression analyses. Here, we present a highly-configurable function that produces publication-ready volcano plots. EnhancedVolcano will attempt to fit as many transcript names in the plot window as possible, thus avoiding clogging up the plot with labels that could not otherwise have been read. Other functionality allows the user to identify up to 3 different types of attributes in the same plot space via colour, shape, and shade parameter configurations.' extra: parent_recipe: name: bioconductor-enhancedvolcano diff --git a/recipes/bioconductor-enmix/meta.yaml b/recipes/bioconductor-enmix/meta.yaml index 053bcc1a58786..5045b00bb8352 100644 --- a/recipes/bioconductor-enmix/meta.yaml +++ b/recipes/bioconductor-enmix/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.18.0" %} +{% set version = "1.20.0" %} {% set name = "ENmix" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 0553f4e4210daa532f8686ec4ea8cc46 + md5: 0cbb33604739295704994fda97f10698 build: number: 0 rpaths: @@ -20,25 +20,25 @@ build: # Suggests: minfiData (>= 0.4.1), RPMM, RUnit, BiocGenerics requirements: host: - - 'bioconductor-geneplotter >=1.60.0,<1.61.0' - - 'bioconductor-impute >=1.56.0,<1.57.0' - - 'bioconductor-minfi >=1.28.0,<1.29.0' - - 'bioconductor-preprocesscore >=1.44.0,<1.45.0' - - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' - - 'bioconductor-sva >=3.30.0,<3.31.0' - - 'bioconductor-watermelon >=1.26.0,<1.27.0' + - 'bioconductor-geneplotter >=1.62.0,<1.63.0' + - 'bioconductor-impute >=1.58.0,<1.59.0' + - 'bioconductor-minfi >=1.30.0,<1.31.0' + - 'bioconductor-preprocesscore >=1.46.0,<1.47.0' + - 'bioconductor-summarizedexperiment >=1.14.0,<1.15.0' + - 'bioconductor-sva >=3.32.0,<3.33.0' + - 'bioconductor-watermelon >=1.28.0,<1.29.0' - r-base - r-doparallel - r-foreach - r-mass run: - - 'bioconductor-geneplotter >=1.60.0,<1.61.0' - - 'bioconductor-impute >=1.56.0,<1.57.0' - - 'bioconductor-minfi >=1.28.0,<1.29.0' - - 'bioconductor-preprocesscore >=1.44.0,<1.45.0' - - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' - - 'bioconductor-sva >=3.30.0,<3.31.0' - - 'bioconductor-watermelon >=1.26.0,<1.27.0' + - 'bioconductor-geneplotter >=1.62.0,<1.63.0' + - 'bioconductor-impute >=1.58.0,<1.59.0' + - 'bioconductor-minfi >=1.30.0,<1.31.0' + - 'bioconductor-preprocesscore >=1.46.0,<1.47.0' + - 'bioconductor-summarizedexperiment >=1.14.0,<1.15.0' + - 'bioconductor-sva >=3.32.0,<3.33.0' + - 'bioconductor-watermelon >=1.28.0,<1.29.0' - r-base - r-doparallel - r-foreach diff --git a/recipes/bioconductor-enrichedheatmap/meta.yaml b/recipes/bioconductor-enrichedheatmap/meta.yaml index 192c24854b533..31e945be93ff1 100644 --- a/recipes/bioconductor-enrichedheatmap/meta.yaml +++ b/recipes/bioconductor-enrichedheatmap/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.12.0" %} +{% set version = "1.14.0" %} {% set name = "EnrichedHeatmap" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 7e80d59a04785ab940be2ecb1c3b942e + md5: 354f237782eaf57e6c3ace742398e126 build: number: 0 rpaths: @@ -19,21 +19,21 @@ build: # Suggests: testthat (>= 0.3), knitr, markdown, genefilter, RColorBrewer requirements: host: - - 'bioconductor-complexheatmap >=1.20.0,<1.21.0' - - 'bioconductor-genomicranges >=1.34.0,<1.35.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-complexheatmap >=2.0.0,<2.1.0' + - 'bioconductor-genomicranges >=1.36.0,<1.37.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' - r-base - - 'r-circlize >=0.4.1' + - 'r-circlize >=0.4.5' - r-getoptlong - r-locfit - r-matrixstats - r-rcpp run: - - 'bioconductor-complexheatmap >=1.20.0,<1.21.0' - - 'bioconductor-genomicranges >=1.34.0,<1.35.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-complexheatmap >=2.0.0,<2.1.0' + - 'bioconductor-genomicranges >=1.36.0,<1.37.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' - r-base - - 'r-circlize >=0.4.1' + - 'r-circlize >=0.4.5' - r-getoptlong - r-locfit - r-matrixstats diff --git a/recipes/bioconductor-enrichmentbrowser/meta.yaml b/recipes/bioconductor-enrichmentbrowser/meta.yaml index b91297eedc041..9d2b0e809549f 100644 --- a/recipes/bioconductor-enrichmentbrowser/meta.yaml +++ b/recipes/bioconductor-enrichmentbrowser/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "2.12.0" %} +{% set version = "2.14.0" %} {% set name = "EnrichmentBrowser" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: d1ef550adea70fa1584228da5dc23de7 + md5: 39f8abc6a8734944c73965b43fb91195 build: number: 0 rpaths: @@ -20,58 +20,58 @@ build: # Suggests: ALL, BiocStyle, airway, hgu95av2.db, knitr requirements: host: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' - - 'bioconductor-biocfilecache >=1.6.0,<1.7.0' - - 'bioconductor-biocgraph >=1.44.0,<1.45.0' - - 'bioconductor-complexheatmap >=1.20.0,<1.21.0' - - 'bioconductor-deseq2 >=1.22.0,<1.23.0' - - 'bioconductor-edaseq >=2.16.0,<2.17.0' - - 'bioconductor-edger >=3.24.0,<3.25.0' - - 'bioconductor-geneplotter >=1.60.0,<1.61.0' - - 'bioconductor-go.db >=3.7.0,<3.8.0' - - 'bioconductor-graph >=1.60.0,<1.61.0' - - 'bioconductor-graphite >=1.28.0,<1.29.0' - - 'bioconductor-gseabase >=1.44.0,<1.45.0' - - 'bioconductor-kegggraph >=1.42.0,<1.43.0' - - 'bioconductor-keggrest >=1.22.0,<1.23.0' - - 'bioconductor-limma >=3.38.0,<3.39.0' - - 'bioconductor-pathview >=1.22.0,<1.23.0' - - 'bioconductor-reportingtools >=2.22.0,<2.23.0' - - 'bioconductor-rgraphviz >=2.26.0,<2.27.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' - - 'bioconductor-safe >=3.22.0,<3.23.0' - - 'bioconductor-spia >=2.34.0,<2.35.0' - - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' - - 'bioconductor-topgo >=2.34.0,<2.35.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' + - 'bioconductor-biocfilecache >=1.8.0,<1.9.0' + - 'bioconductor-biocgraph >=1.46.0,<1.47.0' + - 'bioconductor-complexheatmap >=2.0.0,<2.1.0' + - 'bioconductor-deseq2 >=1.24.0,<1.25.0' + - 'bioconductor-edaseq >=2.18.0,<2.19.0' + - 'bioconductor-edger >=3.26.0,<3.27.0' + - 'bioconductor-geneplotter >=1.62.0,<1.63.0' + - 'bioconductor-go.db >=3.8.0,<3.9.0' + - 'bioconductor-graph >=1.62.0,<1.63.0' + - 'bioconductor-graphite >=1.30.0,<1.31.0' + - 'bioconductor-gseabase >=1.46.0,<1.47.0' + - 'bioconductor-kegggraph >=1.44.0,<1.45.0' + - 'bioconductor-keggrest >=1.24.0,<1.25.0' + - 'bioconductor-limma >=3.40.0,<3.41.0' + - 'bioconductor-pathview >=1.24.0,<1.25.0' + - 'bioconductor-reportingtools >=2.24.0,<2.25.0' + - 'bioconductor-rgraphviz >=2.28.0,<2.29.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' + - 'bioconductor-safe >=3.24.0,<3.25.0' + - 'bioconductor-spia >=2.36.0,<2.37.0' + - 'bioconductor-summarizedexperiment >=1.14.0,<1.15.0' + - 'bioconductor-topgo >=2.36.0,<2.37.0' - r-base - r-biocmanager - r-hwriter - r-mass - r-rappdirs run: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' - - 'bioconductor-biocfilecache >=1.6.0,<1.7.0' - - 'bioconductor-biocgraph >=1.44.0,<1.45.0' - - 'bioconductor-complexheatmap >=1.20.0,<1.21.0' - - 'bioconductor-deseq2 >=1.22.0,<1.23.0' - - 'bioconductor-edaseq >=2.16.0,<2.17.0' - - 'bioconductor-edger >=3.24.0,<3.25.0' - - 'bioconductor-geneplotter >=1.60.0,<1.61.0' - - 'bioconductor-go.db >=3.7.0,<3.8.0' - - 'bioconductor-graph >=1.60.0,<1.61.0' - - 'bioconductor-graphite >=1.28.0,<1.29.0' - - 'bioconductor-gseabase >=1.44.0,<1.45.0' - - 'bioconductor-kegggraph >=1.42.0,<1.43.0' - - 'bioconductor-keggrest >=1.22.0,<1.23.0' - - 'bioconductor-limma >=3.38.0,<3.39.0' - - 'bioconductor-pathview >=1.22.0,<1.23.0' - - 'bioconductor-reportingtools >=2.22.0,<2.23.0' - - 'bioconductor-rgraphviz >=2.26.0,<2.27.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' - - 'bioconductor-safe >=3.22.0,<3.23.0' - - 'bioconductor-spia >=2.34.0,<2.35.0' - - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' - - 'bioconductor-topgo >=2.34.0,<2.35.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' + - 'bioconductor-biocfilecache >=1.8.0,<1.9.0' + - 'bioconductor-biocgraph >=1.46.0,<1.47.0' + - 'bioconductor-complexheatmap >=2.0.0,<2.1.0' + - 'bioconductor-deseq2 >=1.24.0,<1.25.0' + - 'bioconductor-edaseq >=2.18.0,<2.19.0' + - 'bioconductor-edger >=3.26.0,<3.27.0' + - 'bioconductor-geneplotter >=1.62.0,<1.63.0' + - 'bioconductor-go.db >=3.8.0,<3.9.0' + - 'bioconductor-graph >=1.62.0,<1.63.0' + - 'bioconductor-graphite >=1.30.0,<1.31.0' + - 'bioconductor-gseabase >=1.46.0,<1.47.0' + - 'bioconductor-kegggraph >=1.44.0,<1.45.0' + - 'bioconductor-keggrest >=1.24.0,<1.25.0' + - 'bioconductor-limma >=3.40.0,<3.41.0' + - 'bioconductor-pathview >=1.24.0,<1.25.0' + - 'bioconductor-reportingtools >=2.24.0,<2.25.0' + - 'bioconductor-rgraphviz >=2.28.0,<2.29.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' + - 'bioconductor-safe >=3.24.0,<3.25.0' + - 'bioconductor-spia >=2.36.0,<2.37.0' + - 'bioconductor-summarizedexperiment >=1.14.0,<1.15.0' + - 'bioconductor-topgo >=2.36.0,<2.37.0' - r-base - r-biocmanager - r-hwriter diff --git a/recipes/bioconductor-enrichplot/meta.yaml b/recipes/bioconductor-enrichplot/meta.yaml index 53b223637a20c..b5cda3b7b324e 100644 --- a/recipes/bioconductor-enrichplot/meta.yaml +++ b/recipes/bioconductor-enrichplot/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.2.0" %} +{% set version = "1.4.0" %} {% set name = "enrichplot" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,19 +10,19 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 27648033d0cf6a3a71f8ecbef075b0b8 + md5: 3842cd6f24eede4adb94dad3374f50a1 build: number: 0 rpaths: - lib/R/lib/ - lib/ noarch: generic -# Suggests: clusterProfiler, knitr, org.Hs.eg.db, prettydoc +# Suggests: clusterProfiler, dplyr, knitr, org.Hs.eg.db, prettydoc requirements: host: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' - - 'bioconductor-dose >=3.8.0,<3.9.0' - - 'bioconductor-gosemsim >=2.8.0,<2.9.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' + - 'bioconductor-dose >=3.10.0,<3.11.0' + - 'bioconductor-gosemsim >=2.10.0,<2.11.0' - r-base - r-cowplot - r-europepmc @@ -37,9 +37,9 @@ requirements: - r-reshape2 - r-upsetr run: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' - - 'bioconductor-dose >=3.8.0,<3.9.0' - - 'bioconductor-gosemsim >=2.8.0,<2.9.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' + - 'bioconductor-dose >=3.10.0,<3.11.0' + - 'bioconductor-gosemsim >=2.10.0,<2.11.0' - r-base - r-cowplot - r-europepmc diff --git a/recipes/bioconductor-enrichtf/build.sh b/recipes/bioconductor-enrichtf/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-enrichtf/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-enrichtf/meta.yaml b/recipes/bioconductor-enrichtf/meta.yaml new file mode 100644 index 0000000000000..aa3e95202db20 --- /dev/null +++ b/recipes/bioconductor-enrichtf/meta.yaml @@ -0,0 +1,57 @@ +{% set version = "1.0.0" %} +{% set name = "enrichTF" %} +{% set bioc = "3.9" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: 6d32698632dc4bd6b099d48325581b09 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: knitr, magrittr, testthat +requirements: + host: + - 'bioconductor-biocgenerics >=0.30.0,<0.31.0' + - 'bioconductor-bsgenome >=1.52.0,<1.53.0' + - 'bioconductor-genomeinfodb >=1.20.0,<1.21.0' + - 'bioconductor-genomicranges >=1.36.0,<1.37.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-jaspar2018 >=1.2.0,<1.3.0' + - 'bioconductor-motifmatchr >=1.6.0,<1.7.0' + - 'bioconductor-pipeframe >=1.0.0,<1.1.0' + - 'bioconductor-rtracklayer >=1.44.0,<1.45.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' + - 'bioconductor-tfbstools >=1.22.0,<1.23.0' + - r-base + - r-r.utils + run: + - 'bioconductor-biocgenerics >=0.30.0,<0.31.0' + - 'bioconductor-bsgenome >=1.52.0,<1.53.0' + - 'bioconductor-genomeinfodb >=1.20.0,<1.21.0' + - 'bioconductor-genomicranges >=1.36.0,<1.37.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-jaspar2018 >=1.2.0,<1.3.0' + - 'bioconductor-motifmatchr >=1.6.0,<1.7.0' + - 'bioconductor-pipeframe >=1.0.0,<1.1.0' + - 'bioconductor-rtracklayer >=1.44.0,<1.45.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' + - 'bioconductor-tfbstools >=1.22.0,<1.23.0' + - r-base + - r-r.utils +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: GPL-3 + summary: 'As transcription factors (TFs) play a crucial role in regulating the transcription process through binding on the genome alone or in a combinatorial manner, TF enrichment analysis is an efficient and important procedure to locate the candidate functional TFs from a set of experimentally defined regulatory regions. While it is commonly accepted that structurally related TFs may have similar binding preference to sequences (i.e. motifs) and one TF may have multiple motifs, TF enrichment analysis is much more challenging than motif enrichment analysis. Here we present a R package for TF enrichment analysis which combine motif enrichment with the PECA model.' + diff --git a/recipes/bioconductor-ensdb.hsapiens.v75/meta.yaml b/recipes/bioconductor-ensdb.hsapiens.v75/meta.yaml index 74a79c4133df4..67f2130633f31 100644 --- a/recipes/bioconductor-ensdb.hsapiens.v75/meta.yaml +++ b/recipes/bioconductor-ensdb.hsapiens.v75/meta.yaml @@ -1,6 +1,6 @@ {% set version = "2.99.0" %} {% set name = "EnsDb.Hsapiens.v75" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -12,19 +12,19 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' md5: 6c896475252903972bfc6c0eb0d8f334 build: - number: 3 + number: 4 rpaths: - lib/R/lib/ - lib/ noarch: generic requirements: host: - - 'bioconductor-ensembldb >=2.6.0,<2.7.0' + - 'bioconductor-ensembldb >=2.8.0,<2.9.0' - r-base run: - - 'bioconductor-ensembldb >=2.6.0,<2.7.0' + - 'bioconductor-ensembldb >=2.8.0,<2.9.0' - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-ensdb.hsapiens.v75/post-link.sh b/recipes/bioconductor-ensdb.hsapiens.v75/post-link.sh index 7f5f8d69d7739..110a97c08ab56 100644 --- a/recipes/bioconductor-ensdb.hsapiens.v75/post-link.sh +++ b/recipes/bioconductor-ensdb.hsapiens.v75/post-link.sh @@ -1,7 +1,7 @@ #!/bin/bash FN="EnsDb.Hsapiens.v75_2.99.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/EnsDb.Hsapiens.v75_2.99.0.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/EnsDb.Hsapiens.v75_2.99.0.tar.gz" "https://bioarchive.galaxyproject.org/EnsDb.Hsapiens.v75_2.99.0.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-ensdb.hsapiens.v75/bioconductor-ensdb.hsapiens.v75_2.99.0_src_all.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-ensdb.hsapiens.v75/bioconductor-ensdb.hsapiens.v75_2.99.0_src_all.tar.gz" @@ -17,7 +17,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-ensdb.hsapiens.v79/meta.yaml b/recipes/bioconductor-ensdb.hsapiens.v79/meta.yaml index 9e713cc2bced6..8c6d0b7afb1ff 100644 --- a/recipes/bioconductor-ensdb.hsapiens.v79/meta.yaml +++ b/recipes/bioconductor-ensdb.hsapiens.v79/meta.yaml @@ -1,6 +1,6 @@ {% set version = "2.99.0" %} {% set name = "EnsDb.Hsapiens.v79" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -12,19 +12,19 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' md5: 16b5629805c07649b2aa501d34fcc588 build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ noarch: generic requirements: host: - - 'bioconductor-ensembldb >=2.6.0,<2.7.0' + - 'bioconductor-ensembldb >=2.8.0,<2.9.0' - r-base run: - - 'bioconductor-ensembldb >=2.6.0,<2.7.0' + - 'bioconductor-ensembldb >=2.8.0,<2.9.0' - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-ensdb.hsapiens.v79/post-link.sh b/recipes/bioconductor-ensdb.hsapiens.v79/post-link.sh index f8ef604b80fdd..870b63ca59c28 100644 --- a/recipes/bioconductor-ensdb.hsapiens.v79/post-link.sh +++ b/recipes/bioconductor-ensdb.hsapiens.v79/post-link.sh @@ -1,9 +1,10 @@ #!/bin/bash FN="EnsDb.Hsapiens.v79_2.99.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/EnsDb.Hsapiens.v79_2.99.0.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/EnsDb.Hsapiens.v79_2.99.0.tar.gz" "https://bioarchive.galaxyproject.org/EnsDb.Hsapiens.v79_2.99.0.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-ensdb.hsapiens.v79/bioconductor-ensdb.hsapiens.v79_2.99.0_src_all.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-ensdb.hsapiens.v79/bioconductor-ensdb.hsapiens.v79_2.99.0_src_all.tar.gz" ) MD5="16b5629805c07649b2aa501d34fcc588" @@ -16,7 +17,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-ensdb.hsapiens.v86/meta.yaml b/recipes/bioconductor-ensdb.hsapiens.v86/meta.yaml index db596488669b6..fa797e63afed7 100644 --- a/recipes/bioconductor-ensdb.hsapiens.v86/meta.yaml +++ b/recipes/bioconductor-ensdb.hsapiens.v86/meta.yaml @@ -1,6 +1,6 @@ {% set version = "2.99.0" %} {% set name = "EnsDb.Hsapiens.v86" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -12,19 +12,19 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' md5: 0c9e52512ff6dbbbdb754c4d41149939 build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ noarch: generic requirements: host: - - 'bioconductor-ensembldb >=2.6.0,<2.7.0' + - 'bioconductor-ensembldb >=2.8.0,<2.9.0' - r-base run: - - 'bioconductor-ensembldb >=2.6.0,<2.7.0' + - 'bioconductor-ensembldb >=2.8.0,<2.9.0' - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-ensdb.hsapiens.v86/post-link.sh b/recipes/bioconductor-ensdb.hsapiens.v86/post-link.sh index 4c8b47133682e..2e1f9aa5fa13f 100644 --- a/recipes/bioconductor-ensdb.hsapiens.v86/post-link.sh +++ b/recipes/bioconductor-ensdb.hsapiens.v86/post-link.sh @@ -1,9 +1,10 @@ #!/bin/bash FN="EnsDb.Hsapiens.v86_2.99.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/EnsDb.Hsapiens.v86_2.99.0.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/EnsDb.Hsapiens.v86_2.99.0.tar.gz" "https://bioarchive.galaxyproject.org/EnsDb.Hsapiens.v86_2.99.0.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-ensdb.hsapiens.v86/bioconductor-ensdb.hsapiens.v86_2.99.0_src_all.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-ensdb.hsapiens.v86/bioconductor-ensdb.hsapiens.v86_2.99.0_src_all.tar.gz" ) MD5="0c9e52512ff6dbbbdb754c4d41149939" @@ -16,7 +17,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-ensdb.mmusculus.v75/meta.yaml b/recipes/bioconductor-ensdb.mmusculus.v75/meta.yaml index dd3ef93ec2011..624533cef53ec 100644 --- a/recipes/bioconductor-ensdb.mmusculus.v75/meta.yaml +++ b/recipes/bioconductor-ensdb.mmusculus.v75/meta.yaml @@ -1,6 +1,6 @@ {% set version = "2.99.0" %} {% set name = "EnsDb.Mmusculus.v75" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -12,19 +12,19 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' md5: 081bf6f90ff77031b634b4fe32e00be8 build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ noarch: generic requirements: host: - - 'bioconductor-ensembldb >=2.6.0,<2.7.0' + - 'bioconductor-ensembldb >=2.8.0,<2.9.0' - r-base run: - - 'bioconductor-ensembldb >=2.6.0,<2.7.0' + - 'bioconductor-ensembldb >=2.8.0,<2.9.0' - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-ensdb.mmusculus.v75/post-link.sh b/recipes/bioconductor-ensdb.mmusculus.v75/post-link.sh index 544e068e619a9..5466d2d6151ca 100644 --- a/recipes/bioconductor-ensdb.mmusculus.v75/post-link.sh +++ b/recipes/bioconductor-ensdb.mmusculus.v75/post-link.sh @@ -1,9 +1,10 @@ #!/bin/bash FN="EnsDb.Mmusculus.v75_2.99.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/EnsDb.Mmusculus.v75_2.99.0.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/EnsDb.Mmusculus.v75_2.99.0.tar.gz" "https://bioarchive.galaxyproject.org/EnsDb.Mmusculus.v75_2.99.0.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-ensdb.mmusculus.v75/bioconductor-ensdb.mmusculus.v75_2.99.0_src_all.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-ensdb.mmusculus.v75/bioconductor-ensdb.mmusculus.v75_2.99.0_src_all.tar.gz" ) MD5="081bf6f90ff77031b634b4fe32e00be8" @@ -16,7 +17,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-ensdb.mmusculus.v79/meta.yaml b/recipes/bioconductor-ensdb.mmusculus.v79/meta.yaml index e1880b0484d4e..3cc254504adf7 100644 --- a/recipes/bioconductor-ensdb.mmusculus.v79/meta.yaml +++ b/recipes/bioconductor-ensdb.mmusculus.v79/meta.yaml @@ -1,6 +1,6 @@ {% set version = "2.99.0" %} {% set name = "EnsDb.Mmusculus.v79" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -12,19 +12,19 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' md5: 28bbab743b0d2d550dbfa0bcd3274fad build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ noarch: generic requirements: host: - - 'bioconductor-ensembldb >=2.6.0,<2.7.0' + - 'bioconductor-ensembldb >=2.8.0,<2.9.0' - r-base run: - - 'bioconductor-ensembldb >=2.6.0,<2.7.0' + - 'bioconductor-ensembldb >=2.8.0,<2.9.0' - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-ensdb.mmusculus.v79/post-link.sh b/recipes/bioconductor-ensdb.mmusculus.v79/post-link.sh index db6d6bc699b6f..18f86d6beb595 100644 --- a/recipes/bioconductor-ensdb.mmusculus.v79/post-link.sh +++ b/recipes/bioconductor-ensdb.mmusculus.v79/post-link.sh @@ -1,9 +1,10 @@ #!/bin/bash FN="EnsDb.Mmusculus.v79_2.99.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/EnsDb.Mmusculus.v79_2.99.0.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/EnsDb.Mmusculus.v79_2.99.0.tar.gz" "https://bioarchive.galaxyproject.org/EnsDb.Mmusculus.v79_2.99.0.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-ensdb.mmusculus.v79/bioconductor-ensdb.mmusculus.v79_2.99.0_src_all.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-ensdb.mmusculus.v79/bioconductor-ensdb.mmusculus.v79_2.99.0_src_all.tar.gz" ) MD5="28bbab743b0d2d550dbfa0bcd3274fad" @@ -16,7 +17,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-ensdb.rnorvegicus.v75/meta.yaml b/recipes/bioconductor-ensdb.rnorvegicus.v75/meta.yaml index 0a3f7c503ca90..f85dac116c7ee 100644 --- a/recipes/bioconductor-ensdb.rnorvegicus.v75/meta.yaml +++ b/recipes/bioconductor-ensdb.rnorvegicus.v75/meta.yaml @@ -1,6 +1,6 @@ {% set version = "2.99.0" %} {% set name = "EnsDb.Rnorvegicus.v75" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -12,19 +12,19 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' md5: 40ff53b41aa6fad0d5bd15f9c6f3bad8 build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ noarch: generic requirements: host: - - 'bioconductor-ensembldb >=2.6.0,<2.7.0' + - 'bioconductor-ensembldb >=2.8.0,<2.9.0' - r-base run: - - 'bioconductor-ensembldb >=2.6.0,<2.7.0' + - 'bioconductor-ensembldb >=2.8.0,<2.9.0' - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-ensdb.rnorvegicus.v75/post-link.sh b/recipes/bioconductor-ensdb.rnorvegicus.v75/post-link.sh index 72bcd438b5f69..5dfeeb1eaa869 100644 --- a/recipes/bioconductor-ensdb.rnorvegicus.v75/post-link.sh +++ b/recipes/bioconductor-ensdb.rnorvegicus.v75/post-link.sh @@ -1,9 +1,10 @@ #!/bin/bash FN="EnsDb.Rnorvegicus.v75_2.99.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/EnsDb.Rnorvegicus.v75_2.99.0.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/EnsDb.Rnorvegicus.v75_2.99.0.tar.gz" "https://bioarchive.galaxyproject.org/EnsDb.Rnorvegicus.v75_2.99.0.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-ensdb.rnorvegicus.v75/bioconductor-ensdb.rnorvegicus.v75_2.99.0_src_all.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-ensdb.rnorvegicus.v75/bioconductor-ensdb.rnorvegicus.v75_2.99.0_src_all.tar.gz" ) MD5="40ff53b41aa6fad0d5bd15f9c6f3bad8" @@ -16,7 +17,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-ensdb.rnorvegicus.v79/meta.yaml b/recipes/bioconductor-ensdb.rnorvegicus.v79/meta.yaml index 6360aafc9a7d6..7b025aee97698 100644 --- a/recipes/bioconductor-ensdb.rnorvegicus.v79/meta.yaml +++ b/recipes/bioconductor-ensdb.rnorvegicus.v79/meta.yaml @@ -1,6 +1,6 @@ {% set version = "2.99.0" %} {% set name = "EnsDb.Rnorvegicus.v79" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -12,19 +12,19 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' md5: 7d305bd0d1a073bd8c60063ae210a7a9 build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ noarch: generic requirements: host: - - 'bioconductor-ensembldb >=2.6.0,<2.7.0' + - 'bioconductor-ensembldb >=2.8.0,<2.9.0' - r-base run: - - 'bioconductor-ensembldb >=2.6.0,<2.7.0' + - 'bioconductor-ensembldb >=2.8.0,<2.9.0' - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-ensdb.rnorvegicus.v79/post-link.sh b/recipes/bioconductor-ensdb.rnorvegicus.v79/post-link.sh index bee10abd82f46..375afd65f128b 100644 --- a/recipes/bioconductor-ensdb.rnorvegicus.v79/post-link.sh +++ b/recipes/bioconductor-ensdb.rnorvegicus.v79/post-link.sh @@ -1,9 +1,10 @@ #!/bin/bash FN="EnsDb.Rnorvegicus.v79_2.99.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/EnsDb.Rnorvegicus.v79_2.99.0.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/EnsDb.Rnorvegicus.v79_2.99.0.tar.gz" "https://bioarchive.galaxyproject.org/EnsDb.Rnorvegicus.v79_2.99.0.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-ensdb.rnorvegicus.v79/bioconductor-ensdb.rnorvegicus.v79_2.99.0_src_all.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-ensdb.rnorvegicus.v79/bioconductor-ensdb.rnorvegicus.v79_2.99.0_src_all.tar.gz" ) MD5="7d305bd0d1a073bd8c60063ae210a7a9" @@ -16,7 +17,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-ensembldb/meta.yaml b/recipes/bioconductor-ensembldb/meta.yaml index 61f73310a4f76..a63321bd06b09 100644 --- a/recipes/bioconductor-ensembldb/meta.yaml +++ b/recipes/bioconductor-ensembldb/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "2.6.3" %} +{% set version = "2.8.0" %} {% set name = "ensembldb" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 1541d39916d19f6a8c573d5b97955453 + md5: 147470cfa8481113890772fffaad3153 build: number: 0 rpaths: @@ -20,37 +20,37 @@ build: # Suggests: BiocStyle, knitr, EnsDb.Hsapiens.v86 (>= 0.99.8), testthat, BSgenome.Hsapiens.NCBI.GRCh38, ggbio (>= 1.24.0), Gviz (>= 1.20.0), magrittr, AnnotationHub requirements: host: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' - - 'bioconductor-annotationfilter >=1.6.0,<1.7.0' - - 'bioconductor-biobase >=2.42.0,<2.43.0' - - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' - - 'bioconductor-biostrings >=2.50.0,<2.51.0' - - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' - - 'bioconductor-genomicfeatures >=1.34.0,<1.35.0' - - 'bioconductor-genomicranges >=1.34.0,<1.35.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-protgenerics >=1.14.0,<1.15.0' - - 'bioconductor-rsamtools >=1.34.0,<1.35.0' - - 'bioconductor-rtracklayer >=1.42.0,<1.43.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' + - 'bioconductor-annotationfilter >=1.8.0,<1.9.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' + - 'bioconductor-biocgenerics >=0.30.0,<0.31.0' + - 'bioconductor-biostrings >=2.52.0,<2.53.0' + - 'bioconductor-genomeinfodb >=1.20.0,<1.21.0' + - 'bioconductor-genomicfeatures >=1.36.0,<1.37.0' + - 'bioconductor-genomicranges >=1.36.0,<1.37.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-protgenerics >=1.16.0,<1.17.0' + - 'bioconductor-rsamtools >=2.0.0,<2.1.0' + - 'bioconductor-rtracklayer >=1.44.0,<1.45.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' - r-base - r-curl - r-dbi - 'r-rsqlite >=1.1' run: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' - - 'bioconductor-annotationfilter >=1.6.0,<1.7.0' - - 'bioconductor-biobase >=2.42.0,<2.43.0' - - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' - - 'bioconductor-biostrings >=2.50.0,<2.51.0' - - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' - - 'bioconductor-genomicfeatures >=1.34.0,<1.35.0' - - 'bioconductor-genomicranges >=1.34.0,<1.35.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-protgenerics >=1.14.0,<1.15.0' - - 'bioconductor-rsamtools >=1.34.0,<1.35.0' - - 'bioconductor-rtracklayer >=1.42.0,<1.43.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' + - 'bioconductor-annotationfilter >=1.8.0,<1.9.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' + - 'bioconductor-biocgenerics >=0.30.0,<0.31.0' + - 'bioconductor-biostrings >=2.52.0,<2.53.0' + - 'bioconductor-genomeinfodb >=1.20.0,<1.21.0' + - 'bioconductor-genomicfeatures >=1.36.0,<1.37.0' + - 'bioconductor-genomicranges >=1.36.0,<1.37.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-protgenerics >=1.16.0,<1.17.0' + - 'bioconductor-rsamtools >=2.0.0,<2.1.0' + - 'bioconductor-rtracklayer >=1.44.0,<1.45.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' - r-base - r-curl - r-dbi diff --git a/recipes/bioconductor-ensemblvep/meta.yaml b/recipes/bioconductor-ensemblvep/meta.yaml index b582b4003e4ca..910c301655444 100644 --- a/recipes/bioconductor-ensemblvep/meta.yaml +++ b/recipes/bioconductor-ensemblvep/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.24.0" %} +{% set version = "1.26.0" %} {% set name = "ensemblVEP" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: fdbeb189d18514fa1631a98270057bcf + md5: eaead079b2b775cc2cb532b895186c34 build: number: 0 rpaths: @@ -18,26 +18,32 @@ build: - lib/ noarch: generic # Suggests: RUnit -# SystemRequirements: Ensembl VEP (API version 94) and the Perl modules DBI and DBD::mysql must be installed. See the package README and Ensembl installation instructions: http://www.ensembl.org/info/docs/tools/vep/script/vep_download.html#installer +# SystemRequirements: Ensembl VEP (API version 96) and the Perl modules DBI and DBD::mysql must be installed. See the package README and Ensembl installation instructions: http://www.ensembl.org/info/docs/tools/vep/script/vep_download.html#installer requirements: host: - - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' - - 'bioconductor-biostrings >=2.50.0,<2.51.0' - - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' - - 'bioconductor-genomicranges >=1.34.0,<1.35.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' - - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' - - 'bioconductor-variantannotation >=1.28.0,<1.29.0' + - 'bioconductor-biocgenerics >=0.30.0,<0.31.0' + - 'bioconductor-biostrings >=2.52.0,<2.53.0' + - 'bioconductor-genomeinfodb >=1.20.0,<1.21.0' + - 'bioconductor-genomicranges >=1.36.0,<1.37.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' + - 'bioconductor-summarizedexperiment >=1.14.0,<1.15.0' + - 'bioconductor-variantannotation >=1.30.0,<1.31.0' - r-base + - ensembl-vep + - perl-dbi + - perl-dbd-mysql run: - - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' - - 'bioconductor-biostrings >=2.50.0,<2.51.0' - - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' - - 'bioconductor-genomicranges >=1.34.0,<1.35.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' - - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' - - 'bioconductor-variantannotation >=1.28.0,<1.29.0' + - 'bioconductor-biocgenerics >=0.30.0,<0.31.0' + - 'bioconductor-biostrings >=2.52.0,<2.53.0' + - 'bioconductor-genomeinfodb >=1.20.0,<1.21.0' + - 'bioconductor-genomicranges >=1.36.0,<1.37.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' + - 'bioconductor-summarizedexperiment >=1.14.0,<1.15.0' + - 'bioconductor-variantannotation >=1.30.0,<1.31.0' - r-base + - ensembl-vep + - perl-dbi + - perl-dbd-mysql test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-envisionquery/meta.yaml b/recipes/bioconductor-envisionquery/meta.yaml index cfbc6fe09badc..48e40c79822e9 100644 --- a/recipes/bioconductor-envisionquery/meta.yaml +++ b/recipes/bioconductor-envisionquery/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.30.0" %} +{% set version = "1.32.0" %} {% set name = "ENVISIONQuery" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: c5c1fc6faa77de4dce984b8311aad152 + md5: 8e08095cda9c1a95d101e7568cf49d34 build: number: 0 rpaths: diff --git a/recipes/bioconductor-epidish/meta.yaml b/recipes/bioconductor-epidish/meta.yaml index 70fe404b7e334..4685372a0d471 100644 --- a/recipes/bioconductor-epidish/meta.yaml +++ b/recipes/bioconductor-epidish/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.4.1" %} +{% set version = "2.0.2" %} {% set name = "EpiDISH" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 4acbfaf1f6e45ca12fef51b9b3e8f1eb + md5: 0924ada71c8694d640b3181de1bfc7e5 build: number: 0 rpaths: @@ -23,17 +23,21 @@ requirements: - r-base - r-e1071 - r-mass + - r-matrixstats - r-quadprog + - r-stringr run: - r-base - r-e1071 - r-mass + - r-matrixstats - r-quadprog + - r-stringr test: commands: - '$R -e "library(''{{ name }}'')"' about: home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: GPL-2 - summary: 'EpiDISH is a R package to infer the proportions of a priori known cell subtypes present in a sample representing a mixture of such cell-types. Inference proceeds via one of 3 methods (Robust Partial Correlations-RPC, Cibersort (CBS), Constrained Projection (CP)), as determined by user.' + summary: 'EpiDISH is a R package to infer the proportions of a priori known cell-types present in a sample representing a mixture of such cell-types. Right now, the package can be used on DNAm data of whole blood, generic epithelial tissue and breast tissue. Besides, the package provides a function that allows the identification of differentially methylated cell-types and their directionality of change in Epigenome-Wide Association Studies.' diff --git a/recipes/bioconductor-epigenomix/meta.yaml b/recipes/bioconductor-epigenomix/meta.yaml index 02e8941369116..6e6e44ed26d1a 100644 --- a/recipes/bioconductor-epigenomix/meta.yaml +++ b/recipes/bioconductor-epigenomix/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.22.0" %} +{% set version = "1.24.0" %} {% set name = "epigenomix" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 290798e17819a26cfa3171ecefab0307 + md5: 25ef016294642eea92f5861defac13f5 build: number: 0 rpaths: @@ -19,27 +19,27 @@ build: noarch: generic requirements: host: - - 'bioconductor-beadarray >=2.32.0,<2.33.0' - - 'bioconductor-biobase >=2.42.0,<2.43.0' - - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' - - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' - - 'bioconductor-genomicranges >=1.34.0,<1.35.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-rsamtools >=1.34.0,<1.35.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' - - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' + - 'bioconductor-beadarray >=2.34.0,<2.35.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' + - 'bioconductor-biocgenerics >=0.30.0,<0.31.0' + - 'bioconductor-genomeinfodb >=1.20.0,<1.21.0' + - 'bioconductor-genomicranges >=1.36.0,<1.37.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-rsamtools >=2.0.0,<2.1.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' + - 'bioconductor-summarizedexperiment >=1.14.0,<1.15.0' - r-base - r-mcmcpack run: - - 'bioconductor-beadarray >=2.32.0,<2.33.0' - - 'bioconductor-biobase >=2.42.0,<2.43.0' - - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' - - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' - - 'bioconductor-genomicranges >=1.34.0,<1.35.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-rsamtools >=1.34.0,<1.35.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' - - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' + - 'bioconductor-beadarray >=2.34.0,<2.35.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' + - 'bioconductor-biocgenerics >=0.30.0,<0.31.0' + - 'bioconductor-genomeinfodb >=1.20.0,<1.21.0' + - 'bioconductor-genomicranges >=1.36.0,<1.37.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-rsamtools >=2.0.0,<2.1.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' + - 'bioconductor-summarizedexperiment >=1.14.0,<1.15.0' - r-base - r-mcmcpack test: diff --git a/recipes/bioconductor-epihet/build.sh b/recipes/bioconductor-epihet/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-epihet/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-epihet/meta.yaml b/recipes/bioconductor-epihet/meta.yaml new file mode 100644 index 0000000000000..eb2da2c3236c0 --- /dev/null +++ b/recipes/bioconductor-epihet/meta.yaml @@ -0,0 +1,61 @@ +{% set version = "1.0.0" %} +{% set name = "epihet" %} +{% set bioc = "3.9" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + md5: c06c440713eb659c25de200098c28c1c +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: knitr, clusterProfiler, ggfortify, org.Hs.eg.db, rmarkdown +requirements: + host: + - 'bioconductor-genomicranges >=1.36.0,<1.37.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-qvalue >=2.16.0,<2.17.0' + - 'bioconductor-reactomepa >=1.28.0,<1.29.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' + - r-base + - r-data.table + - r-doparallel + - r-entropyexplorer + - r-foreach + - r-ggplot2 + - r-igraph + - r-pheatmap + - r-rtsne + - r-wgcna + run: + - 'bioconductor-genomicranges >=1.36.0,<1.37.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-qvalue >=2.16.0,<2.17.0' + - 'bioconductor-reactomepa >=1.28.0,<1.29.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' + - r-base + - r-data.table + - r-doparallel + - r-entropyexplorer + - r-foreach + - r-ggplot2 + - r-igraph + - r-pheatmap + - r-rtsne + - r-wgcna +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'epihet is an R-package that calculates the epigenetic heterogeneity between cancer cells and/or normal cells. The functions establish a pipeline that take in bisulfite sequencing data from multiple samples and use the data to track similarities and differences in epipolymorphism,proportion of discordantly methylated sequencing reads (PDR),and Shannon entropy values at epialleles that are shared between the samples.epihet can be used to perform analysis on the data by creating pheatmaps, box plots, PCA plots, and t-SNE plots. MA plots can also be created by calculating the differential heterogeneity of the samples. And we construct co-epihet network and perform network analysis.' + diff --git a/recipes/bioconductor-epinem/meta.yaml b/recipes/bioconductor-epinem/meta.yaml index 2d19f1d97edfd..a3a7f3cf33c92 100644 --- a/recipes/bioconductor-epinem/meta.yaml +++ b/recipes/bioconductor-epinem/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.6.0" %} +{% set version = "1.8.0" %} {% set name = "epiNEM" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 6e8ad9c7f2ce1f6fa87bc01d4b0ab653 + md5: 76377c06686a8e5e8300c0c983923261 build: number: 0 rpaths: @@ -20,9 +20,9 @@ build: # Suggests: knitr, RUnit, BiocGenerics, STRINGdb, devtools, rmarkdown, GOSemSim, AnnotationHub, org.Sc.sgd.db requirements: host: - - 'bioconductor-graph >=1.60.0,<1.61.0' - - 'bioconductor-minet >=3.40.0,<3.41.0' - - 'bioconductor-nem >=2.56.0,<2.57.0' + - 'bioconductor-graph >=1.62.0,<1.63.0' + - 'bioconductor-minet >=3.42.0,<3.43.0' + - 'bioconductor-nem >=2.58.0,<2.59.0' - r-base - r-boolnet - r-e1071 @@ -33,9 +33,9 @@ requirements: - r-pcalg - r-rcolorbrewer run: - - 'bioconductor-graph >=1.60.0,<1.61.0' - - 'bioconductor-minet >=3.40.0,<3.41.0' - - 'bioconductor-nem >=2.56.0,<2.57.0' + - 'bioconductor-graph >=1.62.0,<1.63.0' + - 'bioconductor-minet >=3.42.0,<3.43.0' + - 'bioconductor-nem >=2.58.0,<2.59.0' - r-base - r-boolnet - r-e1071 diff --git a/recipes/bioconductor-epivizr/meta.yaml b/recipes/bioconductor-epivizr/meta.yaml index 90ffb710d8b5a..50674c61243b5 100644 --- a/recipes/bioconductor-epivizr/meta.yaml +++ b/recipes/bioconductor-epivizr/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "2.12.0" %} +{% set version = "2.14.0" %} {% set name = "epivizr" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 598be3e3e7c653398de1a63851e204e1 + md5: e8327fa8707402547bf84be7693df002 build: number: 0 rpaths: @@ -20,18 +20,18 @@ build: # Suggests: testthat, roxygen2, knitr, Biobase, SummarizedExperiment, antiProfilesData, hgu133plus2.db, Mus.musculus, BiocStyle requirements: host: - - 'bioconductor-epivizrdata >=1.10.0,<1.11.0' - - 'bioconductor-epivizrserver >=1.10.0,<1.11.0' - - 'bioconductor-genomicranges >=1.34.0,<1.35.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-epivizrdata >=1.12.0,<1.13.0' + - 'bioconductor-epivizrserver >=1.12.0,<1.13.0' + - 'bioconductor-genomicranges >=1.36.0,<1.37.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' - r-base run: - - 'bioconductor-epivizrdata >=1.10.0,<1.11.0' - - 'bioconductor-epivizrserver >=1.10.0,<1.11.0' - - 'bioconductor-genomicranges >=1.34.0,<1.35.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-epivizrdata >=1.12.0,<1.13.0' + - 'bioconductor-epivizrserver >=1.12.0,<1.13.0' + - 'bioconductor-genomicranges >=1.36.0,<1.37.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' - r-base test: commands: diff --git a/recipes/bioconductor-epivizrchart/meta.yaml b/recipes/bioconductor-epivizrchart/meta.yaml index dd4a90919d80b..159650d7af414 100644 --- a/recipes/bioconductor-epivizrchart/meta.yaml +++ b/recipes/bioconductor-epivizrchart/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.4.0" %} +{% set version = "1.6.0" %} {% set name = "epivizrChart" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: a0c65f110f53a24eb774b181b4cd21b7 + md5: 67b9da7932bddf6246b6b86f84e153b1 build: number: 0 rpaths: @@ -20,16 +20,16 @@ build: # Suggests: testthat, roxygen2, knitr, Biobase, GenomicRanges, S4Vectors, IRanges, SummarizedExperiment, antiProfilesData, hgu133plus2.db, Mus.musculus, BiocStyle, Homo.sapiens, shiny, minfi, Rsamtools, rtracklayer, RColorBrewer, magrittr, AnnotationHub requirements: host: - - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' - - 'bioconductor-epivizrdata >=1.10.0,<1.11.0' - - 'bioconductor-epivizrserver >=1.10.0,<1.11.0' + - 'bioconductor-biocgenerics >=0.30.0,<0.31.0' + - 'bioconductor-epivizrdata >=1.12.0,<1.13.0' + - 'bioconductor-epivizrserver >=1.12.0,<1.13.0' - r-base - r-htmltools - r-rjson run: - - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' - - 'bioconductor-epivizrdata >=1.10.0,<1.11.0' - - 'bioconductor-epivizrserver >=1.10.0,<1.11.0' + - 'bioconductor-biocgenerics >=0.30.0,<0.31.0' + - 'bioconductor-epivizrdata >=1.12.0,<1.13.0' + - 'bioconductor-epivizrserver >=1.12.0,<1.13.0' - r-base - r-htmltools - r-rjson diff --git a/recipes/bioconductor-epivizrdata/meta.yaml b/recipes/bioconductor-epivizrdata/meta.yaml index 411f5f72dded0..56d2c83aa8db5 100644 --- a/recipes/bioconductor-epivizrdata/meta.yaml +++ b/recipes/bioconductor-epivizrdata/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.10.0" %} +{% set version = "1.12.0" %} {% set name = "epivizrData" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: a9fd3870de8f49edaf48ebfbc400d35b + md5: 2f11801b5495e63deab2497ed1b92286 build: number: 0 rpaths: @@ -20,28 +20,28 @@ build: # Suggests: testthat, roxygen2, bumphunter, hgu133plus2.db, Mus.musculus, TxDb.Mmusculus.UCSC.mm10.knownGene, rjson, knitr, rmarkdown, BiocStyle, EnsDb.Mmusculus.v79, AnnotationHub, rtracklayer, utils, RMySQL, DBI requirements: host: - - 'bioconductor-biobase >=2.42.0,<2.43.0' - - 'bioconductor-ensembldb >=2.6.0,<2.7.0' - - 'bioconductor-epivizrserver >=1.10.0,<1.11.0' - - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' - - 'bioconductor-genomicfeatures >=1.34.0,<1.35.0' - - 'bioconductor-genomicranges >=1.34.0,<1.35.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-organismdbi >=1.24.0,<1.25.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' - - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' + - 'bioconductor-ensembldb >=2.8.0,<2.9.0' + - 'bioconductor-epivizrserver >=1.12.0,<1.13.0' + - 'bioconductor-genomeinfodb >=1.20.0,<1.21.0' + - 'bioconductor-genomicfeatures >=1.36.0,<1.37.0' + - 'bioconductor-genomicranges >=1.36.0,<1.37.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-organismdbi >=1.26.0,<1.27.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' + - 'bioconductor-summarizedexperiment >=1.14.0,<1.15.0' - r-base run: - - 'bioconductor-biobase >=2.42.0,<2.43.0' - - 'bioconductor-ensembldb >=2.6.0,<2.7.0' - - 'bioconductor-epivizrserver >=1.10.0,<1.11.0' - - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' - - 'bioconductor-genomicfeatures >=1.34.0,<1.35.0' - - 'bioconductor-genomicranges >=1.34.0,<1.35.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-organismdbi >=1.24.0,<1.25.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' - - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' + - 'bioconductor-ensembldb >=2.8.0,<2.9.0' + - 'bioconductor-epivizrserver >=1.12.0,<1.13.0' + - 'bioconductor-genomeinfodb >=1.20.0,<1.21.0' + - 'bioconductor-genomicfeatures >=1.36.0,<1.37.0' + - 'bioconductor-genomicranges >=1.36.0,<1.37.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-organismdbi >=1.26.0,<1.27.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' + - 'bioconductor-summarizedexperiment >=1.14.0,<1.15.0' - r-base test: commands: diff --git a/recipes/bioconductor-epivizrserver/meta.yaml b/recipes/bioconductor-epivizrserver/meta.yaml index e5d98608d2a7e..4b82718c018c7 100644 --- a/recipes/bioconductor-epivizrserver/meta.yaml +++ b/recipes/bioconductor-epivizrserver/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.10.0" %} +{% set version = "1.12.0" %} {% set name = "epivizrServer" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 537fc02d780e78830cd3d470cdee219a + md5: 1ebe50b859db578f50ff6068288efd38 build: number: 0 rpaths: diff --git a/recipes/bioconductor-epivizrstandalone/meta.yaml b/recipes/bioconductor-epivizrstandalone/meta.yaml index ccd6881f88e2d..b24c7637053f2 100644 --- a/recipes/bioconductor-epivizrstandalone/meta.yaml +++ b/recipes/bioconductor-epivizrstandalone/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.10.0" %} +{% set version = "1.12.0" %} {% set name = "epivizrStandalone" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,9 +10,9 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 1c5b85237ceb90203bab2c0e7e9f5f7c + md5: cab65c8a4b24d30beb55a608d6fbdc62 build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ @@ -20,21 +20,21 @@ build: # Suggests: testthat, knitr, rmarkdown, OrganismDbi (>= 1.13.9), Mus.musculus, Biobase, BiocStyle requirements: host: - - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' - - 'bioconductor-epivizr >=2.12.0,<2.13.0' - - 'bioconductor-epivizrserver >=1.10.0,<1.11.0' - - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' - - 'bioconductor-genomicfeatures >=1.34.0,<1.35.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-biocgenerics >=0.30.0,<0.31.0' + - 'bioconductor-epivizr >=2.14.0,<2.15.0' + - 'bioconductor-epivizrserver >=1.12.0,<1.13.0' + - 'bioconductor-genomeinfodb >=1.20.0,<1.21.0' + - 'bioconductor-genomicfeatures >=1.36.0,<1.37.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' - r-base - r-git2r run: - - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' - - 'bioconductor-epivizr >=2.12.0,<2.13.0' - - 'bioconductor-epivizrserver >=1.10.0,<1.11.0' - - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' - - 'bioconductor-genomicfeatures >=1.34.0,<1.35.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-biocgenerics >=0.30.0,<0.31.0' + - 'bioconductor-epivizr >=2.14.0,<2.15.0' + - 'bioconductor-epivizrserver >=1.12.0,<1.13.0' + - 'bioconductor-genomeinfodb >=1.20.0,<1.21.0' + - 'bioconductor-genomicfeatures >=1.36.0,<1.37.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' - r-base - r-git2r test: diff --git a/recipes/bioconductor-erccdashboard/meta.yaml b/recipes/bioconductor-erccdashboard/meta.yaml index d07b8afe073ff..a93dbc1238a15 100644 --- a/recipes/bioconductor-erccdashboard/meta.yaml +++ b/recipes/bioconductor-erccdashboard/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.16.1" %} +{% set version = "1.18.0" %} {% set name = "erccdashboard" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - sha256: e9377dc42ea308cc68e679bffec600ad329e91ec0ba8c8b6874b822bbfb3c575 + md5: 1032ec195ee26ce0239d120c955a83f9 build: number: 0 rpaths: @@ -19,9 +19,9 @@ build: noarch: generic requirements: host: - - 'bioconductor-edger >=3.24.0,<3.25.0' - - 'bioconductor-limma >=3.38.0,<3.39.0' - - 'bioconductor-qvalue >=2.14.0,<2.15.0' + - 'bioconductor-edger >=3.26.0,<3.27.0' + - 'bioconductor-limma >=3.40.0,<3.41.0' + - 'bioconductor-qvalue >=2.16.0,<2.17.0' - r-base - 'r-ggplot2 >=2.1.0' - r-gplots @@ -35,9 +35,9 @@ requirements: - r-scales - r-stringr run: - - 'bioconductor-edger >=3.24.0,<3.25.0' - - 'bioconductor-limma >=3.38.0,<3.39.0' - - 'bioconductor-qvalue >=2.14.0,<2.15.0' + - 'bioconductor-edger >=3.26.0,<3.27.0' + - 'bioconductor-limma >=3.40.0,<3.41.0' + - 'bioconductor-qvalue >=2.16.0,<2.17.0' - r-base - 'r-ggplot2 >=2.1.0' - r-gplots diff --git a/recipes/bioconductor-erma/meta.yaml b/recipes/bioconductor-erma/meta.yaml index 82b0a03912a3d..39820c8dfc627 100644 --- a/recipes/bioconductor-erma/meta.yaml +++ b/recipes/bioconductor-erma/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "0.14.0" %} +{% set version = "1.0.0" %} {% set name = "erma" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 4cba185c4cd0cc49bf6d10bc4864f2f9 + md5: b42e8f00156c28d2698ba16c5585b758 build: number: 0 rpaths: @@ -20,34 +20,34 @@ build: # Suggests: rmarkdown, BiocStyle, knitr, GO.db, png, DT, doParallel requirements: host: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' - - 'bioconductor-biobase >=2.42.0,<2.43.0' - - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' - - 'bioconductor-biocparallel >=1.16.0,<1.17.0' - - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' - - 'bioconductor-genomicfiles >=1.18.0,<1.19.0' - - 'bioconductor-genomicranges >=1.34.0,<1.35.0' - - 'bioconductor-homo.sapiens >=1.3.0,<1.4.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-rtracklayer >=1.42.0,<1.43.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' - - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' + - 'bioconductor-biocgenerics >=0.30.0,<0.31.0' + - 'bioconductor-biocparallel >=1.18.0,<1.19.0' + - 'bioconductor-genomeinfodb >=1.20.0,<1.21.0' + - 'bioconductor-genomicfiles >=1.20.0,<1.21.0' + - 'bioconductor-genomicranges >=1.36.0,<1.37.0' + - 'bioconductor-homo.sapiens >=1.4.0,<1.5.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-rtracklayer >=1.44.0,<1.45.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' + - 'bioconductor-summarizedexperiment >=1.14.0,<1.15.0' - r-base - r-ggplot2 - r-shiny run: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' - - 'bioconductor-biobase >=2.42.0,<2.43.0' - - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' - - 'bioconductor-biocparallel >=1.16.0,<1.17.0' - - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' - - 'bioconductor-genomicfiles >=1.18.0,<1.19.0' - - 'bioconductor-genomicranges >=1.34.0,<1.35.0' - - 'bioconductor-homo.sapiens >=1.3.0,<1.4.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-rtracklayer >=1.42.0,<1.43.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' - - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' + - 'bioconductor-biocgenerics >=0.30.0,<0.31.0' + - 'bioconductor-biocparallel >=1.18.0,<1.19.0' + - 'bioconductor-genomeinfodb >=1.20.0,<1.21.0' + - 'bioconductor-genomicfiles >=1.20.0,<1.21.0' + - 'bioconductor-genomicranges >=1.36.0,<1.37.0' + - 'bioconductor-homo.sapiens >=1.4.0,<1.5.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-rtracklayer >=1.44.0,<1.45.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' + - 'bioconductor-summarizedexperiment >=1.14.0,<1.15.0' - r-base - r-ggplot2 - r-shiny diff --git a/recipes/bioconductor-erssa/meta.yaml b/recipes/bioconductor-erssa/meta.yaml index 075ef21347ceb..b5da311975fdb 100644 --- a/recipes/bioconductor-erssa/meta.yaml +++ b/recipes/bioconductor-erssa/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.0.0" %} +{% set version = "1.2.0" %} {% set name = "ERSSA" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 9e7e15475b35dd6b76178e7d122d339b + md5: 96c579e7c9d1351f8c6dc94e2c3bb38c build: number: 0 rpaths: @@ -20,17 +20,17 @@ build: # Suggests: BiocStyle, knitr, rmarkdown requirements: host: - - 'bioconductor-biocparallel >=1.16.0,<1.17.0' - - 'bioconductor-deseq2 >=1.22.0,<1.23.0' - - 'bioconductor-edger >=3.24.0,<3.25.0' + - 'bioconductor-biocparallel >=1.18.0,<1.19.0' + - 'bioconductor-deseq2 >=1.24.0,<1.25.0' + - 'bioconductor-edger >=3.26.0,<3.27.0' - r-base - 'r-ggplot2 >=3.0.0' - 'r-plyr >=1.8.4' - 'r-rcolorbrewer >=1.1-2' run: - - 'bioconductor-biocparallel >=1.16.0,<1.17.0' - - 'bioconductor-deseq2 >=1.22.0,<1.23.0' - - 'bioconductor-edger >=3.24.0,<3.25.0' + - 'bioconductor-biocparallel >=1.18.0,<1.19.0' + - 'bioconductor-deseq2 >=1.24.0,<1.25.0' + - 'bioconductor-edger >=3.26.0,<3.27.0' - r-base - 'r-ggplot2 >=3.0.0' - 'r-plyr >=1.8.4' diff --git a/recipes/bioconductor-esatac/meta.yaml b/recipes/bioconductor-esatac/meta.yaml index 78e3a20741eba..c72176ea0d2dd 100644 --- a/recipes/bioconductor-esatac/meta.yaml +++ b/recipes/bioconductor-esatac/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.4.3" %} +{% set version = "1.6.0" %} {% set name = "esATAC" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: e196b9f855c19bbdf03ccf43109417e2 + md5: 2099b8e6a287346bd8bff922615fe429 build: number: 0 rpaths: @@ -20,24 +20,24 @@ build: # SystemRequirements: C++11 requirements: host: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' - - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' - - 'bioconductor-biostrings >=2.50.0,<2.51.0' - - 'bioconductor-bsgenome >=1.50.0,<1.51.0' - - 'bioconductor-chipseeker >=1.18.0,<1.19.0' - - 'bioconductor-clusterprofiler >=3.10.0,<3.11.0' - - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' - - 'bioconductor-genomicfeatures >=1.34.0,<1.35.0' - - 'bioconductor-genomicranges >=1.34.0,<1.35.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-jaspar2016 >=1.10.0,<1.11.0' - - 'bioconductor-motifmatchr >=1.4.0,<1.5.0' - - 'bioconductor-rbowtie2 >=1.4.0,<1.5.0' - - 'bioconductor-rsamtools >=1.34.0,<1.35.0' - - 'bioconductor-rtracklayer >=1.42.0,<1.43.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' - - 'bioconductor-shortread >=1.40.0,<1.41.0' - - 'bioconductor-tfbstools >=1.20.0,<1.21.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' + - 'bioconductor-biocgenerics >=0.30.0,<0.31.0' + - 'bioconductor-biostrings >=2.52.0,<2.53.0' + - 'bioconductor-bsgenome >=1.52.0,<1.53.0' + - 'bioconductor-chipseeker >=1.20.0,<1.21.0' + - 'bioconductor-clusterprofiler >=3.12.0,<3.13.0' + - 'bioconductor-genomeinfodb >=1.20.0,<1.21.0' + - 'bioconductor-genomicfeatures >=1.36.0,<1.37.0' + - 'bioconductor-genomicranges >=1.36.0,<1.37.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-jaspar2016 >=1.12.0,<1.13.0' + - 'bioconductor-motifmatchr >=1.6.0,<1.7.0' + - 'bioconductor-rbowtie2 >=1.6.0,<1.7.0' + - 'bioconductor-rsamtools >=2.0.0,<2.1.0' + - 'bioconductor-rtracklayer >=1.44.0,<1.45.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' + - 'bioconductor-shortread >=1.42.0,<1.43.0' + - 'bioconductor-tfbstools >=1.22.0,<1.23.0' - r-base - r-biocmanager - r-corrplot @@ -53,24 +53,24 @@ requirements: - r-rmarkdown - r-venndiagram run: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' - - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' - - 'bioconductor-biostrings >=2.50.0,<2.51.0' - - 'bioconductor-bsgenome >=1.50.0,<1.51.0' - - 'bioconductor-chipseeker >=1.18.0,<1.19.0' - - 'bioconductor-clusterprofiler >=3.10.0,<3.11.0' - - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' - - 'bioconductor-genomicfeatures >=1.34.0,<1.35.0' - - 'bioconductor-genomicranges >=1.34.0,<1.35.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-jaspar2016 >=1.10.0,<1.11.0' - - 'bioconductor-motifmatchr >=1.4.0,<1.5.0' - - 'bioconductor-rbowtie2 >=1.4.0,<1.5.0' - - 'bioconductor-rsamtools >=1.34.0,<1.35.0' - - 'bioconductor-rtracklayer >=1.42.0,<1.43.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' - - 'bioconductor-shortread >=1.40.0,<1.41.0' - - 'bioconductor-tfbstools >=1.20.0,<1.21.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' + - 'bioconductor-biocgenerics >=0.30.0,<0.31.0' + - 'bioconductor-biostrings >=2.52.0,<2.53.0' + - 'bioconductor-bsgenome >=1.52.0,<1.53.0' + - 'bioconductor-chipseeker >=1.20.0,<1.21.0' + - 'bioconductor-clusterprofiler >=3.12.0,<3.13.0' + - 'bioconductor-genomeinfodb >=1.20.0,<1.21.0' + - 'bioconductor-genomicfeatures >=1.36.0,<1.37.0' + - 'bioconductor-genomicranges >=1.36.0,<1.37.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-jaspar2016 >=1.12.0,<1.13.0' + - 'bioconductor-motifmatchr >=1.6.0,<1.7.0' + - 'bioconductor-rbowtie2 >=1.6.0,<1.7.0' + - 'bioconductor-rsamtools >=2.0.0,<2.1.0' + - 'bioconductor-rtracklayer >=1.44.0,<1.45.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' + - 'bioconductor-shortread >=1.42.0,<1.43.0' + - 'bioconductor-tfbstools >=1.22.0,<1.23.0' - r-base - r-biocmanager - r-corrplot diff --git a/recipes/bioconductor-esetvis/meta.yaml b/recipes/bioconductor-esetvis/meta.yaml index 08c072b4626ff..3898789d95776 100644 --- a/recipes/bioconductor-esetvis/meta.yaml +++ b/recipes/bioconductor-esetvis/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.8.0" %} +{% set version = "1.10.0" %} {% set name = "esetVis" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 00dabd51d6f8ed126f3c6a53ef514e96 + md5: 0d9a30c4788017d0dd9aa162ce949901 build: number: 0 rpaths: @@ -20,16 +20,16 @@ build: # Suggests: ggplot2, ggvis, rbokeh, ggrepel, knitr, rmarkdown, ALL, hgu95av2.db, AnnotationDbi, pander, SummarizedExperiment requirements: host: - - 'bioconductor-biobase >=2.42.0,<2.43.0' - - 'bioconductor-mlp >=1.30.0,<1.31.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' + - 'bioconductor-mlp >=1.32.0,<1.33.0' - r-base - r-hexbin - r-mass - r-mpm - r-rtsne run: - - 'bioconductor-biobase >=2.42.0,<2.43.0' - - 'bioconductor-mlp >=1.30.0,<1.31.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' + - 'bioconductor-mlp >=1.32.0,<1.33.0' - r-base - r-hexbin - r-mass diff --git a/recipes/bioconductor-estrogen/meta.yaml b/recipes/bioconductor-estrogen/meta.yaml index 83128e6d8dd9a..933690dbbdb52 100644 --- a/recipes/bioconductor-estrogen/meta.yaml +++ b/recipes/bioconductor-estrogen/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.28.0" %} +{% set version = "1.30.0" %} {% set name = "estrogen" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 5a2bbc25340ef7cc6c9cf4a579e4c190 + md5: fe5ddaafa6641e710a5cf76fb47a9989 build: number: 0 rpaths: @@ -23,7 +23,7 @@ requirements: - r-base run: - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-estrogen/post-link.sh b/recipes/bioconductor-estrogen/post-link.sh index 37691a91d6210..b46a677b4d812 100644 --- a/recipes/bioconductor-estrogen/post-link.sh +++ b/recipes/bioconductor-estrogen/post-link.sh @@ -1,11 +1,11 @@ #!/bin/bash -FN="estrogen_1.28.0.tar.gz" +FN="estrogen_1.30.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/experiment/src/contrib/estrogen_1.28.0.tar.gz" - "https://bioarchive.galaxyproject.org/estrogen_1.28.0.tar.gz" - "https://depot.galaxyproject.org/software/bioconductor-estrogen/bioconductor-estrogen_1.28.0_src_all.tar.gz" + "https://bioconductor.org/packages/3.9/data/experiment/src/contrib/estrogen_1.30.0.tar.gz" + "https://bioarchive.galaxyproject.org/estrogen_1.30.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-estrogen/bioconductor-estrogen_1.30.0_src_all.tar.gz" ) -MD5="5a2bbc25340ef7cc6c9cf4a579e4c190" +MD5="fe5ddaafa6641e710a5cf76fb47a9989" # Use a staging area in the conda dir rather than temp dirs, both to avoid # permission issues as well as to have things downloaded in a predictable @@ -16,7 +16,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-etec16s/meta.yaml b/recipes/bioconductor-etec16s/meta.yaml index 1e2711484c4d9..8ef898e0ee024 100644 --- a/recipes/bioconductor-etec16s/meta.yaml +++ b/recipes/bioconductor-etec16s/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.10.0" %} +{% set version = "1.12.0" %} {% set name = "etec16s" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: ab6de328373655b42c1915fa52fcb47e + md5: d59c6663c4df8f745e0b326cb712137b build: number: 0 rpaths: @@ -19,14 +19,14 @@ build: noarch: generic requirements: host: - - 'bioconductor-biobase >=2.42.0,<2.43.0' - - 'bioconductor-metagenomeseq >=1.24.0,<1.25.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' + - 'bioconductor-metagenomeseq >=1.26.0,<1.27.0' - r-base run: - - 'bioconductor-biobase >=2.42.0,<2.43.0' - - 'bioconductor-metagenomeseq >=1.24.0,<1.25.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' + - 'bioconductor-metagenomeseq >=1.26.0,<1.27.0' - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-etec16s/post-link.sh b/recipes/bioconductor-etec16s/post-link.sh index 0db9292d24c60..c1d2569af1e83 100644 --- a/recipes/bioconductor-etec16s/post-link.sh +++ b/recipes/bioconductor-etec16s/post-link.sh @@ -1,11 +1,11 @@ #!/bin/bash -FN="etec16s_1.10.0.tar.gz" +FN="etec16s_1.12.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/experiment/src/contrib/etec16s_1.10.0.tar.gz" - "https://bioarchive.galaxyproject.org/etec16s_1.10.0.tar.gz" - "https://depot.galaxyproject.org/software/bioconductor-etec16s/bioconductor-etec16s_1.10.0_src_all.tar.gz" + "https://bioconductor.org/packages/3.9/data/experiment/src/contrib/etec16s_1.12.0.tar.gz" + "https://bioarchive.galaxyproject.org/etec16s_1.12.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-etec16s/bioconductor-etec16s_1.12.0_src_all.tar.gz" ) -MD5="ab6de328373655b42c1915fa52fcb47e" +MD5="d59c6663c4df8f745e0b326cb712137b" # Use a staging area in the conda dir rather than temp dirs, both to avoid # permission issues as well as to have things downloaded in a predictable @@ -16,7 +16,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-eudysbiome/meta.yaml b/recipes/bioconductor-eudysbiome/meta.yaml index 52e4a587e3258..03f1839a8ca84 100644 --- a/recipes/bioconductor-eudysbiome/meta.yaml +++ b/recipes/bioconductor-eudysbiome/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.12.0" %} +{% set version = "1.14.0" %} {% set name = "eudysbiome" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,23 +10,23 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: b8a7504e2d5c6793c7d82819f060cd3c + md5: 047a92ad163d17b14f550850e37eb0e7 build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ noarch: generic requirements: host: - - 'bioconductor-biostrings >=2.50.0,<2.51.0' - - 'bioconductor-rsamtools >=1.34.0,<1.35.0' + - 'bioconductor-biostrings >=2.52.0,<2.53.0' + - 'bioconductor-rsamtools >=2.0.0,<2.1.0' - r-base - r-plyr - r-r.utils run: - - 'bioconductor-biostrings >=2.50.0,<2.51.0' - - 'bioconductor-rsamtools >=1.34.0,<1.35.0' + - 'bioconductor-biostrings >=2.52.0,<2.53.0' + - 'bioconductor-rsamtools >=2.0.0,<2.1.0' - r-base - r-plyr - r-r.utils diff --git a/recipes/bioconductor-eupathdb/meta.yaml b/recipes/bioconductor-eupathdb/meta.yaml index e3d11bee53dc6..a673524688354 100644 --- a/recipes/bioconductor-eupathdb/meta.yaml +++ b/recipes/bioconductor-eupathdb/meta.yaml @@ -1,6 +1,6 @@ {% set version = "1.0.1" %} {% set name = "EuPathDB" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -12,7 +12,7 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' md5: 1451c3ab6c224d9a4cfbdf27dc5c2680 build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ @@ -20,24 +20,24 @@ build: # Suggests: dplyr, knitr, BiocStyle, rmarkdown, jsonlite requirements: host: - - 'bioconductor-annotationhub >=2.14.0,<2.15.0' - - 'bioconductor-annotationhubdata >=1.12.0,<1.13.0' - - 'bioconductor-biobase >=2.42.0,<2.43.0' - - 'bioconductor-biostrings >=2.50.0,<2.51.0' + - 'bioconductor-annotationhub >=2.16.0,<2.17.0' + - 'bioconductor-annotationhubdata >=1.14.0,<1.15.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' + - 'bioconductor-biostrings >=2.52.0,<2.53.0' - 'bioconductor-genomeinfodbdata >=1.2.0,<1.3.0' - - 'bioconductor-genomicranges >=1.34.0,<1.35.0' + - 'bioconductor-genomicranges >=1.36.0,<1.37.0' - r-base - r-biocmanager run: - - 'bioconductor-annotationhub >=2.14.0,<2.15.0' - - 'bioconductor-annotationhubdata >=1.12.0,<1.13.0' - - 'bioconductor-biobase >=2.42.0,<2.43.0' - - 'bioconductor-biostrings >=2.50.0,<2.51.0' + - 'bioconductor-annotationhub >=2.16.0,<2.17.0' + - 'bioconductor-annotationhubdata >=1.14.0,<1.15.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' + - 'bioconductor-biostrings >=2.52.0,<2.53.0' - 'bioconductor-genomeinfodbdata >=1.2.0,<1.3.0' - - 'bioconductor-genomicranges >=1.34.0,<1.35.0' + - 'bioconductor-genomicranges >=1.36.0,<1.37.0' - r-base - r-biocmanager - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-eupathdb/post-link.sh b/recipes/bioconductor-eupathdb/post-link.sh index a6829e4930814..608f29515bb9d 100644 --- a/recipes/bioconductor-eupathdb/post-link.sh +++ b/recipes/bioconductor-eupathdb/post-link.sh @@ -1,9 +1,10 @@ #!/bin/bash FN="EuPathDB_1.0.1.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/EuPathDB_1.0.1.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/EuPathDB_1.0.1.tar.gz" "https://bioarchive.galaxyproject.org/EuPathDB_1.0.1.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-eupathdb/bioconductor-eupathdb_1.0.1_src_all.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-eupathdb/bioconductor-eupathdb_1.0.1_src_all.tar.gz" ) MD5="1451c3ab6c224d9a4cfbdf27dc5c2680" @@ -16,7 +17,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-evaluomer/build.sh b/recipes/bioconductor-evaluomer/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-evaluomer/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-evaluomer/meta.yaml b/recipes/bioconductor-evaluomer/meta.yaml new file mode 100644 index 0000000000000..86c3ec5cc17ed --- /dev/null +++ b/recipes/bioconductor-evaluomer/meta.yaml @@ -0,0 +1,43 @@ +{% set version = "1.0.0" %} +{% set name = "evaluomeR" %} +{% set bioc = "3.9" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: 06a1b1383ff3000956f41296b02850cb +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: BiocStyle, knitr, rmarkdown, kableExtra, magrittr +requirements: + host: + - 'bioconductor-multiassayexperiment >=1.10.0,<1.11.0' + - 'bioconductor-summarizedexperiment >=1.14.0,<1.15.0' + - r-base + - 'r-cluster >=2.0.7-1' + - 'r-corrplot >=0.84' + - r-rdpack + run: + - 'bioconductor-multiassayexperiment >=1.10.0,<1.11.0' + - 'bioconductor-summarizedexperiment >=1.14.0,<1.15.0' + - r-base + - 'r-cluster >=2.0.7-1' + - 'r-corrplot >=0.84' + - r-rdpack +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: GPL-3 + summary: 'Evaluating the reliability of your own metrics and the measurements done on your own datasets by analysing the stability and goodness of the classifications of such metrics.' + diff --git a/recipes/bioconductor-eventpointer/meta.yaml b/recipes/bioconductor-eventpointer/meta.yaml index b1053f1727ee0..cceb8e1d1c44b 100644 --- a/recipes/bioconductor-eventpointer/meta.yaml +++ b/recipes/bioconductor-eventpointer/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "2.0.1" %} +{% set version = "2.2.0" %} {% set name = "EventPointer" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,29 +10,32 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: ecd974e8c801868993f80115b6dc07fe + md5: 390e6ac5a06cc6d500f4c6796fb65ae5 build: number: 0 rpaths: - lib/R/lib/ - lib/ noarch: generic -# Suggests: knitr, rmarkdown, BiocStyle, RUnit, BiocGenerics +# Suggests: knitr, rmarkdown, BiocStyle, RUnit, BiocGenerics, dplyr, kableExtra requirements: host: - - 'bioconductor-affxparser >=1.54.0,<1.55.0' - - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' - - 'bioconductor-genomicfeatures >=1.34.0,<1.35.0' - - 'bioconductor-genomicranges >=1.34.0,<1.35.0' - - 'bioconductor-graph >=1.60.0,<1.61.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-limma >=3.38.0,<3.39.0' - - 'bioconductor-qvalue >=2.14.0,<2.15.0' - - 'bioconductor-rbgl >=1.58.0,<1.59.0' - - 'bioconductor-rhdf5 >=2.26.0,<2.27.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' - - 'bioconductor-sgseq >=1.16.0,<1.17.0' - - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' + - 'bioconductor-affxparser >=1.56.0,<1.57.0' + - 'bioconductor-biostrings >=2.52.0,<2.53.0' + - 'bioconductor-bsgenome >=1.52.0,<1.53.0' + - 'bioconductor-bsgenome.hsapiens.ucsc.hg38 >=1.4.0,<1.5.0' + - 'bioconductor-genomeinfodb >=1.20.0,<1.21.0' + - 'bioconductor-genomicfeatures >=1.36.0,<1.37.0' + - 'bioconductor-genomicranges >=1.36.0,<1.37.0' + - 'bioconductor-graph >=1.62.0,<1.63.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-limma >=3.40.0,<3.41.0' + - 'bioconductor-qvalue >=2.16.0,<2.17.0' + - 'bioconductor-rbgl >=1.60.0,<1.61.0' + - 'bioconductor-rhdf5 >=2.28.0,<2.29.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' + - 'bioconductor-sgseq >=1.18.0,<1.19.0' + - 'bioconductor-summarizedexperiment >=1.14.0,<1.15.0' - r-base - r-cobs - r-doparallel @@ -45,19 +48,22 @@ requirements: - r-prodlim - r-stringr run: - - 'bioconductor-affxparser >=1.54.0,<1.55.0' - - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' - - 'bioconductor-genomicfeatures >=1.34.0,<1.35.0' - - 'bioconductor-genomicranges >=1.34.0,<1.35.0' - - 'bioconductor-graph >=1.60.0,<1.61.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-limma >=3.38.0,<3.39.0' - - 'bioconductor-qvalue >=2.14.0,<2.15.0' - - 'bioconductor-rbgl >=1.58.0,<1.59.0' - - 'bioconductor-rhdf5 >=2.26.0,<2.27.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' - - 'bioconductor-sgseq >=1.16.0,<1.17.0' - - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' + - 'bioconductor-affxparser >=1.56.0,<1.57.0' + - 'bioconductor-biostrings >=2.52.0,<2.53.0' + - 'bioconductor-bsgenome >=1.52.0,<1.53.0' + - 'bioconductor-bsgenome.hsapiens.ucsc.hg38 >=1.4.0,<1.5.0' + - 'bioconductor-genomeinfodb >=1.20.0,<1.21.0' + - 'bioconductor-genomicfeatures >=1.36.0,<1.37.0' + - 'bioconductor-genomicranges >=1.36.0,<1.37.0' + - 'bioconductor-graph >=1.62.0,<1.63.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-limma >=3.40.0,<3.41.0' + - 'bioconductor-qvalue >=2.16.0,<2.17.0' + - 'bioconductor-rbgl >=1.60.0,<1.61.0' + - 'bioconductor-rhdf5 >=2.28.0,<2.29.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' + - 'bioconductor-sgseq >=1.18.0,<1.19.0' + - 'bioconductor-summarizedexperiment >=1.14.0,<1.15.0' - r-base - r-cobs - r-doparallel diff --git a/recipes/bioconductor-excluster/meta.yaml b/recipes/bioconductor-excluster/meta.yaml index 5aa414f3f4e9c..7ff16da1ec6f6 100644 --- a/recipes/bioconductor-excluster/meta.yaml +++ b/recipes/bioconductor-excluster/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.0.0" %} +{% set version = "1.2.0" %} {% set name = "ExCluster" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: f46f2947dbef303b274520f5ae7e3531 + md5: 5028118a73918c8857db5fd7e96db56f build: number: 0 rpaths: @@ -19,17 +19,17 @@ build: noarch: generic requirements: host: - - 'bioconductor-genomicranges >=1.34.0,<1.35.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-rsubread >=1.32.0,<1.33.0' - - 'bioconductor-rtracklayer >=1.42.0,<1.43.0' + - 'bioconductor-genomicranges >=1.36.0,<1.37.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-rsubread >=1.34.0,<1.35.0' + - 'bioconductor-rtracklayer >=1.44.0,<1.45.0' - r-base - r-matrixstats run: - - 'bioconductor-genomicranges >=1.34.0,<1.35.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-rsubread >=1.32.0,<1.33.0' - - 'bioconductor-rtracklayer >=1.42.0,<1.43.0' + - 'bioconductor-genomicranges >=1.36.0,<1.37.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-rsubread >=1.34.0,<1.35.0' + - 'bioconductor-rtracklayer >=1.44.0,<1.45.0' - r-base - r-matrixstats test: diff --git a/recipes/bioconductor-eximir/meta.yaml b/recipes/bioconductor-eximir/meta.yaml index 4bed43979eb61..929fb0d9670a1 100644 --- a/recipes/bioconductor-eximir/meta.yaml +++ b/recipes/bioconductor-eximir/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "2.24.0" %} +{% set version = "2.26.0" %} {% set name = "ExiMiR" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 541711a5a0c2f740bc70a23b50d3b432 + md5: 4dd952a0c5f77f86265721357dc47d1f build: number: 0 rpaths: @@ -20,18 +20,18 @@ build: # Suggests: mirna10cdf requirements: host: - - 'bioconductor-affy >=1.60.0,<1.61.0' - - 'bioconductor-affyio >=1.52.0,<1.53.0' - - 'bioconductor-biobase >=2.42.0,<2.43.0' - - 'bioconductor-limma >=3.38.0,<3.39.0' - - 'bioconductor-preprocesscore >=1.44.0,<1.45.0' + - 'bioconductor-affy >=1.62.0,<1.63.0' + - 'bioconductor-affyio >=1.54.0,<1.55.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' + - 'bioconductor-limma >=3.40.0,<3.41.0' + - 'bioconductor-preprocesscore >=1.46.0,<1.47.0' - r-base run: - - 'bioconductor-affy >=1.60.0,<1.61.0' - - 'bioconductor-affyio >=1.52.0,<1.53.0' - - 'bioconductor-biobase >=2.42.0,<2.43.0' - - 'bioconductor-limma >=3.38.0,<3.39.0' - - 'bioconductor-preprocesscore >=1.44.0,<1.45.0' + - 'bioconductor-affy >=1.62.0,<1.63.0' + - 'bioconductor-affyio >=1.54.0,<1.55.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' + - 'bioconductor-limma >=3.40.0,<3.41.0' + - 'bioconductor-preprocesscore >=1.46.0,<1.47.0' - r-base test: commands: diff --git a/recipes/bioconductor-exomecopy/meta.yaml b/recipes/bioconductor-exomecopy/meta.yaml index 9c9f550553528..3527b70d63fdc 100644 --- a/recipes/bioconductor-exomecopy/meta.yaml +++ b/recipes/bioconductor-exomecopy/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.28.0" %} +{% set version = "1.30.0" %} {% set name = "exomeCopy" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 4512e1db1fe55da16916eccd3a45fd14 + md5: e68955655de5d7df8b919f6b029b3be0 build: number: 0 rpaths: @@ -19,16 +19,16 @@ build: # Suggests: Biostrings requirements: host: - - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' - - 'bioconductor-genomicranges >=1.34.0,<1.35.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-rsamtools >=1.34.0,<1.35.0' + - 'bioconductor-genomeinfodb >=1.20.0,<1.21.0' + - 'bioconductor-genomicranges >=1.36.0,<1.37.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-rsamtools >=2.0.0,<2.1.0' - r-base run: - - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' - - 'bioconductor-genomicranges >=1.34.0,<1.35.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-rsamtools >=1.34.0,<1.35.0' + - 'bioconductor-genomeinfodb >=1.20.0,<1.21.0' + - 'bioconductor-genomicranges >=1.36.0,<1.37.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-rsamtools >=2.0.0,<2.1.0' - r-base build: - {{ compiler('c') }} diff --git a/recipes/bioconductor-exomepeak/meta.yaml b/recipes/bioconductor-exomepeak/meta.yaml index 38c66e1982b53..5dcb566f6fac0 100644 --- a/recipes/bioconductor-exomepeak/meta.yaml +++ b/recipes/bioconductor-exomepeak/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "2.16.0" %} +{% set version = "2.17.0" %} {% set name = "exomePeak" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 966b325c0553337d4f866c6ad8978bd4 + md5: 3456fc99d03482a26b4cd24a3333f7eb build: number: 0 rpaths: @@ -19,16 +19,16 @@ build: noarch: generic requirements: host: - - 'bioconductor-genomicalignments >=1.18.0,<1.19.0' - - 'bioconductor-genomicfeatures >=1.34.0,<1.35.0' - - 'bioconductor-rsamtools >=1.34.0,<1.35.0' - - 'bioconductor-rtracklayer >=1.42.0,<1.43.0' + - 'bioconductor-genomicalignments >=1.20.0,<1.21.0' + - 'bioconductor-genomicfeatures >=1.36.0,<1.37.0' + - 'bioconductor-rsamtools >=2.0.0,<2.1.0' + - 'bioconductor-rtracklayer >=1.44.0,<1.45.0' - r-base run: - - 'bioconductor-genomicalignments >=1.18.0,<1.19.0' - - 'bioconductor-genomicfeatures >=1.34.0,<1.35.0' - - 'bioconductor-rsamtools >=1.34.0,<1.35.0' - - 'bioconductor-rtracklayer >=1.42.0,<1.43.0' + - 'bioconductor-genomicalignments >=1.20.0,<1.21.0' + - 'bioconductor-genomicfeatures >=1.36.0,<1.37.0' + - 'bioconductor-rsamtools >=2.0.0,<2.1.0' + - 'bioconductor-rtracklayer >=1.44.0,<1.45.0' - r-base test: commands: diff --git a/recipes/bioconductor-experimenthub/meta.yaml b/recipes/bioconductor-experimenthub/meta.yaml index b111bc873058c..de3266420a65a 100644 --- a/recipes/bioconductor-experimenthub/meta.yaml +++ b/recipes/bioconductor-experimenthub/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.8.0" %} +{% set version = "1.10.0" %} {% set name = "ExperimentHub" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: c4a23733d1283fbc667b67cb0a630110 + md5: de16efc050b3675e822fbd241b1068c3 build: number: 0 rpaths: @@ -20,19 +20,23 @@ build: # Suggests: knitr, BiocStyle requirements: host: - - 'bioconductor-annotationhub >=2.14.0,<2.15.0' - - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-annotationhub >=2.16.0,<2.17.0' + - 'bioconductor-biocfilecache >=1.8.0,<1.9.0' + - 'bioconductor-biocgenerics >=0.30.0,<0.31.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' - r-base - r-biocmanager - r-curl + - r-rappdirs run: - - 'bioconductor-annotationhub >=2.14.0,<2.15.0' - - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-annotationhub >=2.16.0,<2.17.0' + - 'bioconductor-biocfilecache >=1.8.0,<1.9.0' + - 'bioconductor-biocgenerics >=0.30.0,<0.31.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' - r-base - r-biocmanager - r-curl + - r-rappdirs test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-experimenthubdata/meta.yaml b/recipes/bioconductor-experimenthubdata/meta.yaml index 0ec8068db0d4c..0d4be4c84a269 100644 --- a/recipes/bioconductor-experimenthubdata/meta.yaml +++ b/recipes/bioconductor-experimenthubdata/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.8.0" %} +{% set version = "1.10.0" %} {% set name = "ExperimentHubData" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: d12ea3b540ea4e10072c39cf6637d576 + md5: a7707d43fbbd0db88936ba6a99a53400 build: number: 0 rpaths: @@ -20,26 +20,26 @@ build: # Suggests: GenomeInfoDb, RUnit, knitr, BiocStyle requirements: host: - - 'bioconductor-annotationhubdata >=1.12.0,<1.13.0' - - 'bioconductor-bioccheck >=1.18.0,<1.19.0' - - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' - - 'bioconductor-biocviews >=1.50.0,<1.51.0' - - 'bioconductor-experimenthub >=1.8.0,<1.9.0' - - 'bioconductor-graph >=1.60.0,<1.61.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-annotationhubdata >=1.14.0,<1.15.0' + - 'bioconductor-bioccheck >=1.20.0,<1.21.0' + - 'bioconductor-biocgenerics >=0.30.0,<0.31.0' + - 'bioconductor-biocviews >=1.52.0,<1.53.0' + - 'bioconductor-experimenthub >=1.10.0,<1.11.0' + - 'bioconductor-graph >=1.62.0,<1.63.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' - r-base - r-biocmanager - r-curl - r-dbi - r-httr run: - - 'bioconductor-annotationhubdata >=1.12.0,<1.13.0' - - 'bioconductor-bioccheck >=1.18.0,<1.19.0' - - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' - - 'bioconductor-biocviews >=1.50.0,<1.51.0' - - 'bioconductor-experimenthub >=1.8.0,<1.9.0' - - 'bioconductor-graph >=1.60.0,<1.61.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-annotationhubdata >=1.14.0,<1.15.0' + - 'bioconductor-bioccheck >=1.20.0,<1.21.0' + - 'bioconductor-biocgenerics >=0.30.0,<0.31.0' + - 'bioconductor-biocviews >=1.52.0,<1.53.0' + - 'bioconductor-experimenthub >=1.10.0,<1.11.0' + - 'bioconductor-graph >=1.62.0,<1.63.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' - r-base - r-biocmanager - r-curl diff --git a/recipes/bioconductor-explorase/meta.yaml b/recipes/bioconductor-explorase/meta.yaml index 6c07e54f25c72..3aa89e251e4b2 100644 --- a/recipes/bioconductor-explorase/meta.yaml +++ b/recipes/bioconductor-explorase/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.46.0" %} +{% set version = "1.48.0" %} {% set name = "explorase" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 2064b8b45518a6a033abc5e46c312bf7 + md5: 21248c0c7488ee0bf6077ccb03290d0c build: number: 0 rpaths: @@ -20,12 +20,12 @@ build: # Suggests: cairoDevice requirements: host: - - 'bioconductor-limma >=3.38.0,<3.39.0' + - 'bioconductor-limma >=3.40.0,<3.41.0' - r-base - r-rggobi - r-rgtk2 run: - - 'bioconductor-limma >=3.38.0,<3.39.0' + - 'bioconductor-limma >=3.40.0,<3.41.0' - r-base - r-rggobi - r-rgtk2 diff --git a/recipes/bioconductor-expressionatlas/meta.yaml b/recipes/bioconductor-expressionatlas/meta.yaml index cf2e1e6aaf9cb..79beb2a130935 100644 --- a/recipes/bioconductor-expressionatlas/meta.yaml +++ b/recipes/bioconductor-expressionatlas/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.10.0" %} +{% set version = "1.12.0" %} {% set name = "ExpressionAtlas" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: fa4131206692f3b828491081f9468738 + md5: a14c5b3cbe7c1c11e6f7b12290762eae build: number: 0 rpaths: @@ -20,19 +20,19 @@ build: # Suggests: knitr, testthat, rmarkdown requirements: host: - - 'bioconductor-biobase >=2.42.0,<2.43.0' - - 'bioconductor-limma >=3.38.0,<3.39.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' - - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' + - 'bioconductor-limma >=3.40.0,<3.41.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' + - 'bioconductor-summarizedexperiment >=1.14.0,<1.15.0' - r-base - r-httr - r-xml - r-xml2 run: - - 'bioconductor-biobase >=2.42.0,<2.43.0' - - 'bioconductor-limma >=3.38.0,<3.39.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' - - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' + - 'bioconductor-limma >=3.40.0,<3.41.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' + - 'bioconductor-summarizedexperiment >=1.14.0,<1.15.0' - r-base - r-httr - r-xml diff --git a/recipes/bioconductor-expressionview/meta.yaml b/recipes/bioconductor-expressionview/meta.yaml index 493e9f063cba2..df50bade65aaa 100644 --- a/recipes/bioconductor-expressionview/meta.yaml +++ b/recipes/bioconductor-expressionview/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.34.0" %} +{% set version = "1.36.0" %} {% set name = "ExpressionView" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 24263ace50dde80c1d85d8382ca5a612 + md5: 42823dd1a231c96c1c8484403e95b652 build: number: 0 rpaths: @@ -19,18 +19,18 @@ build: # Suggests: ALL, hgu95av2.db, biclust, affy requirements: host: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' - - 'bioconductor-eisa >=1.34.0,<1.35.0' - - 'bioconductor-go.db >=3.7.0,<3.8.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' + - 'bioconductor-eisa >=1.36.0,<1.37.0' + - 'bioconductor-go.db >=3.8.0,<3.9.0' - 'bioconductor-kegg.db >=3.2.0,<3.3.0' - r-base - r-bitops - r-catools - r-isa2 run: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' - - 'bioconductor-eisa >=1.34.0,<1.35.0' - - 'bioconductor-go.db >=3.7.0,<3.8.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' + - 'bioconductor-eisa >=1.36.0,<1.37.0' + - 'bioconductor-go.db >=3.8.0,<3.9.0' - 'bioconductor-kegg.db >=3.2.0,<3.3.0' - r-base - r-bitops diff --git a/recipes/bioconductor-faahko/meta.yaml b/recipes/bioconductor-faahko/meta.yaml index a493273971de9..72b5e315b0998 100644 --- a/recipes/bioconductor-faahko/meta.yaml +++ b/recipes/bioconductor-faahko/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.22.0" %} +{% set version = "1.24.0" %} {% set name = "faahKO" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: c59e4588f572f3b56555cfd8d905107e + md5: c2d5a234c32448986696671867e5fbca build: number: 0 rpaths: @@ -19,12 +19,12 @@ build: noarch: generic requirements: host: - - 'bioconductor-xcms >=3.4.0,<3.5.0' + - 'bioconductor-xcms >=3.6.0,<3.7.0' - r-base run: - - 'bioconductor-xcms >=3.4.0,<3.5.0' + - 'bioconductor-xcms >=3.6.0,<3.7.0' - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-faahko/post-link.sh b/recipes/bioconductor-faahko/post-link.sh index afe71cbc3dd03..5275e4a2f275a 100644 --- a/recipes/bioconductor-faahko/post-link.sh +++ b/recipes/bioconductor-faahko/post-link.sh @@ -1,11 +1,11 @@ #!/bin/bash -FN="faahKO_1.22.0.tar.gz" +FN="faahKO_1.24.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/experiment/src/contrib/faahKO_1.22.0.tar.gz" - "https://bioarchive.galaxyproject.org/faahKO_1.22.0.tar.gz" - "https://depot.galaxyproject.org/software/bioconductor-faahko/bioconductor-faahko_1.22.0_src_all.tar.gz" + "https://bioconductor.org/packages/3.9/data/experiment/src/contrib/faahKO_1.24.0.tar.gz" + "https://bioarchive.galaxyproject.org/faahKO_1.24.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-faahko/bioconductor-faahko_1.24.0_src_all.tar.gz" ) -MD5="c59e4588f572f3b56555cfd8d905107e" +MD5="c2d5a234c32448986696671867e5fbca" # Use a staging area in the conda dir rather than temp dirs, both to avoid # permission issues as well as to have things downloaded in a predictable @@ -16,7 +16,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-fabia/meta.yaml b/recipes/bioconductor-fabia/meta.yaml index 6a69d6c799d7f..b0139a23226f7 100644 --- a/recipes/bioconductor-fabia/meta.yaml +++ b/recipes/bioconductor-fabia/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "2.28.0" %} +{% set version = "2.30.0" %} {% set name = "fabia" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: f98407e943a5d51e71b5d14cda70fa18 + md5: 6c36dc1231f55f6469d11f4b76a49acc build: number: 0 rpaths: @@ -18,10 +18,10 @@ build: - lib/ requirements: host: - - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' - r-base run: - - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' - r-base build: - {{ compiler('c') }} diff --git a/recipes/bioconductor-fabiadata/meta.yaml b/recipes/bioconductor-fabiadata/meta.yaml index 7df8948349865..de3dcc6bff1c2 100644 --- a/recipes/bioconductor-fabiadata/meta.yaml +++ b/recipes/bioconductor-fabiadata/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.20.0" %} +{% set version = "1.22.0" %} {% set name = "fabiaData" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 1e781ec38c4767dd2ab23517fae76c59 + md5: ebba780603b8886835107e4653c27d6d build: number: 0 rpaths: @@ -20,12 +20,12 @@ build: # Suggests: fabia requirements: host: - - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' - r-base run: - - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-fabiadata/post-link.sh b/recipes/bioconductor-fabiadata/post-link.sh index aa26e26965a32..3fb4c6acd84e1 100644 --- a/recipes/bioconductor-fabiadata/post-link.sh +++ b/recipes/bioconductor-fabiadata/post-link.sh @@ -1,11 +1,11 @@ #!/bin/bash -FN="fabiaData_1.20.0.tar.gz" +FN="fabiaData_1.22.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/experiment/src/contrib/fabiaData_1.20.0.tar.gz" - "https://bioarchive.galaxyproject.org/fabiaData_1.20.0.tar.gz" - "https://depot.galaxyproject.org/software/bioconductor-fabiadata/bioconductor-fabiadata_1.20.0_src_all.tar.gz" + "https://bioconductor.org/packages/3.9/data/experiment/src/contrib/fabiaData_1.22.0.tar.gz" + "https://bioarchive.galaxyproject.org/fabiaData_1.22.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-fabiadata/bioconductor-fabiadata_1.22.0_src_all.tar.gz" ) -MD5="1e781ec38c4767dd2ab23517fae76c59" +MD5="ebba780603b8886835107e4653c27d6d" # Use a staging area in the conda dir rather than temp dirs, both to avoid # permission issues as well as to have things downloaded in a predictable @@ -16,7 +16,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-facopy.annot/meta.yaml b/recipes/bioconductor-facopy.annot/meta.yaml index 868edcb4b84e8..0691d37df5f3f 100644 --- a/recipes/bioconductor-facopy.annot/meta.yaml +++ b/recipes/bioconductor-facopy.annot/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.2.0" %} +{% set version = "1.4.0" %} {% set name = "facopy.annot" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: db7545bcf43738e8ba6894a2ec423c19 + md5: 5a332eb0a856a4bd83e8d6e2236fabc4 build: number: 0 rpaths: @@ -22,7 +22,7 @@ requirements: - r-base run: - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-facopy.annot/post-link.sh b/recipes/bioconductor-facopy.annot/post-link.sh index be1f3e5d13e2a..b3859560a5c7a 100644 --- a/recipes/bioconductor-facopy.annot/post-link.sh +++ b/recipes/bioconductor-facopy.annot/post-link.sh @@ -1,11 +1,11 @@ #!/bin/bash -FN="facopy.annot_1.2.0.tar.gz" +FN="facopy.annot_1.4.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/experiment/src/contrib/facopy.annot_1.2.0.tar.gz" - "https://bioarchive.galaxyproject.org/facopy.annot_1.2.0.tar.gz" - "https://depot.galaxyproject.org/software/bioconductor-facopy.annot/bioconductor-facopy.annot_1.2.0_src_all.tar.gz" + "https://bioconductor.org/packages/3.9/data/experiment/src/contrib/facopy.annot_1.4.0.tar.gz" + "https://bioarchive.galaxyproject.org/facopy.annot_1.4.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-facopy.annot/bioconductor-facopy.annot_1.4.0_src_all.tar.gz" ) -MD5="db7545bcf43738e8ba6894a2ec423c19" +MD5="5a332eb0a856a4bd83e8d6e2236fabc4" # Use a staging area in the conda dir rather than temp dirs, both to avoid # permission issues as well as to have things downloaded in a predictable @@ -16,7 +16,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-facsdorit/meta.yaml b/recipes/bioconductor-facsdorit/meta.yaml index af2e9e2f2cb25..44c49d5007ab6 100644 --- a/recipes/bioconductor-facsdorit/meta.yaml +++ b/recipes/bioconductor-facsdorit/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.24.0" %} +{% set version = "1.26.0" %} {% set name = "facsDorit" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 9072988b0ba231cb46fb323fd326c7fe + md5: dcf6e4b99ee9e013e30ebd0f8ec678d0 build: number: 0 rpaths: @@ -19,12 +19,12 @@ build: noarch: generic requirements: host: - - 'bioconductor-prada >=1.58.0,<1.59.0' + - 'bioconductor-prada >=1.60.0,<1.61.0' - r-base run: - - 'bioconductor-prada >=1.58.0,<1.59.0' + - 'bioconductor-prada >=1.60.0,<1.61.0' - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-facsdorit/post-link.sh b/recipes/bioconductor-facsdorit/post-link.sh index 0c6ff92abf036..6a670721d56bb 100644 --- a/recipes/bioconductor-facsdorit/post-link.sh +++ b/recipes/bioconductor-facsdorit/post-link.sh @@ -1,11 +1,11 @@ #!/bin/bash -FN="facsDorit_1.24.0.tar.gz" +FN="facsDorit_1.26.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/experiment/src/contrib/facsDorit_1.24.0.tar.gz" - "https://bioarchive.galaxyproject.org/facsDorit_1.24.0.tar.gz" - "https://depot.galaxyproject.org/software/bioconductor-facsdorit/bioconductor-facsdorit_1.24.0_src_all.tar.gz" + "https://bioconductor.org/packages/3.9/data/experiment/src/contrib/facsDorit_1.26.0.tar.gz" + "https://bioarchive.galaxyproject.org/facsDorit_1.26.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-facsdorit/bioconductor-facsdorit_1.26.0_src_all.tar.gz" ) -MD5="9072988b0ba231cb46fb323fd326c7fe" +MD5="dcf6e4b99ee9e013e30ebd0f8ec678d0" # Use a staging area in the conda dir rather than temp dirs, both to avoid # permission issues as well as to have things downloaded in a predictable @@ -16,7 +16,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-factdesign/meta.yaml b/recipes/bioconductor-factdesign/meta.yaml index 7346671625fa6..ac78e0215eb27 100644 --- a/recipes/bioconductor-factdesign/meta.yaml +++ b/recipes/bioconductor-factdesign/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.58.0" %} +{% set version = "1.60.0" %} {% set name = "factDesign" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 19e692c687b778b8a0a5cb377ba8b4ac + md5: 9db80d51dde4fe4debf4bcd1317e331d build: number: 0 rpaths: @@ -20,10 +20,10 @@ build: # Suggests: affy, genefilter, multtest requirements: host: - - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' - r-base run: - - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' - r-base test: commands: diff --git a/recipes/bioconductor-famagg/meta.yaml b/recipes/bioconductor-famagg/meta.yaml index e41661c257554..be73682865ecb 100644 --- a/recipes/bioconductor-famagg/meta.yaml +++ b/recipes/bioconductor-famagg/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.10.4" %} +{% set version = "1.12.0" %} {% set name = "FamAgg" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: d0b065157cbadbae389a5ba19ab3353f59f70f35b415099ea6166ca5aa62773a + md5: 7d73b990b471a5bbc9a5f4a52010fdc1 build: number: 0 rpaths: @@ -20,7 +20,7 @@ build: # Suggests: BiocStyle, knitr, RUnit, rmarkdown requirements: host: - - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' + - 'bioconductor-biocgenerics >=0.30.0,<0.31.0' - r-base - 'r-gap >=1.1-17' - r-igraph @@ -28,7 +28,7 @@ requirements: - r-matrix - r-survey run: - - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' + - 'bioconductor-biocgenerics >=0.30.0,<0.31.0' - r-base - 'r-gap >=1.1-17' - r-igraph diff --git a/recipes/bioconductor-fantom3and4cage/meta.yaml b/recipes/bioconductor-fantom3and4cage/meta.yaml index e413b71c143bc..b3294356529a1 100644 --- a/recipes/bioconductor-fantom3and4cage/meta.yaml +++ b/recipes/bioconductor-fantom3and4cage/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.18.0" %} +{% set version = "1.20.0" %} {% set name = "FANTOM3and4CAGE" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: c55a0fa84038a6e16773118479ae213c + md5: bfadfb9fe266c14e13c78de6887e8270 build: number: 0 rpaths: @@ -22,7 +22,7 @@ requirements: - r-base run: - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-fantom3and4cage/post-link.sh b/recipes/bioconductor-fantom3and4cage/post-link.sh index 28f77a65fd969..86ba8f3688179 100644 --- a/recipes/bioconductor-fantom3and4cage/post-link.sh +++ b/recipes/bioconductor-fantom3and4cage/post-link.sh @@ -1,11 +1,11 @@ #!/bin/bash -FN="FANTOM3and4CAGE_1.18.0.tar.gz" +FN="FANTOM3and4CAGE_1.20.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/experiment/src/contrib/FANTOM3and4CAGE_1.18.0.tar.gz" - "https://bioarchive.galaxyproject.org/FANTOM3and4CAGE_1.18.0.tar.gz" - "https://depot.galaxyproject.org/software/bioconductor-fantom3and4cage/bioconductor-fantom3and4cage_1.18.0_src_all.tar.gz" + "https://bioconductor.org/packages/3.9/data/experiment/src/contrib/FANTOM3and4CAGE_1.20.0.tar.gz" + "https://bioarchive.galaxyproject.org/FANTOM3and4CAGE_1.20.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-fantom3and4cage/bioconductor-fantom3and4cage_1.20.0_src_all.tar.gz" ) -MD5="c55a0fa84038a6e16773118479ae213c" +MD5="bfadfb9fe266c14e13c78de6887e8270" # Use a staging area in the conda dir rather than temp dirs, both to avoid # permission issues as well as to have things downloaded in a predictable @@ -16,7 +16,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-farms/meta.yaml b/recipes/bioconductor-farms/meta.yaml index 5370afc153fa5..5ca38a23ff7f4 100644 --- a/recipes/bioconductor-farms/meta.yaml +++ b/recipes/bioconductor-farms/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.34.0" %} +{% set version = "1.36.0" %} {% set name = "farms" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: a16c7d5833eabebebe06a37ab2c92ead + md5: e03fed5237d059cc504f8311600938e1 build: number: 0 rpaths: @@ -20,13 +20,13 @@ build: # Suggests: affydata, Biobase, utils requirements: host: - - 'bioconductor-affy >=1.60.0,<1.61.0' - - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-affy >=1.62.0,<1.63.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' - r-base - r-mass run: - - 'bioconductor-affy >=1.60.0,<1.61.0' - - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-affy >=1.62.0,<1.63.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' - r-base - r-mass test: diff --git a/recipes/bioconductor-fastliquidassociation/meta.yaml b/recipes/bioconductor-fastliquidassociation/meta.yaml index b8bde60637eda..650ca668fc32b 100644 --- a/recipes/bioconductor-fastliquidassociation/meta.yaml +++ b/recipes/bioconductor-fastliquidassociation/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.18.0" %} +{% set version = "1.20.0" %} {% set name = "fastLiquidAssociation" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: f264e290f452047d63defed48f91ada0 + md5: 86c29b5cd8edd17a1844abbc2c40281d build: number: 0 rpaths: @@ -20,17 +20,17 @@ build: # Suggests: GOstats, yeastCC, org.Sc.sgd.db requirements: host: - - 'bioconductor-impute >=1.56.0,<1.57.0' - - 'bioconductor-liquidassociation >=1.36.0,<1.37.0' - - 'bioconductor-preprocesscore >=1.44.0,<1.45.0' + - 'bioconductor-impute >=1.58.0,<1.59.0' + - 'bioconductor-liquidassociation >=1.38.0,<1.39.0' + - 'bioconductor-preprocesscore >=1.46.0,<1.47.0' - r-base - r-doparallel - r-hmisc - r-wgcna run: - - 'bioconductor-impute >=1.56.0,<1.57.0' - - 'bioconductor-liquidassociation >=1.36.0,<1.37.0' - - 'bioconductor-preprocesscore >=1.44.0,<1.45.0' + - 'bioconductor-impute >=1.58.0,<1.59.0' + - 'bioconductor-liquidassociation >=1.38.0,<1.39.0' + - 'bioconductor-preprocesscore >=1.46.0,<1.47.0' - r-base - r-doparallel - r-hmisc diff --git a/recipes/bioconductor-fastqcleaner/meta.yaml b/recipes/bioconductor-fastqcleaner/meta.yaml index 7efd8d5061c9e..19edb052b0eaf 100644 --- a/recipes/bioconductor-fastqcleaner/meta.yaml +++ b/recipes/bioconductor-fastqcleaner/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.0.0" %} +{% set version = "1.2.0" %} {% set name = "FastqCleaner" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 24a7168bea8c5d1abfd726fd43e53484 + md5: 9fd90848cb095f8768c8aa22cf426ab4 build: number: 0 rpaths: @@ -19,10 +19,10 @@ build: # Suggests: BiocStyle, testthat, knitr, rmarkdown requirements: host: - - 'bioconductor-biostrings >=2.50.0,<2.51.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' - - 'bioconductor-shortread >=1.40.0,<1.41.0' + - 'bioconductor-biostrings >=2.52.0,<2.53.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' + - 'bioconductor-shortread >=1.42.0,<1.43.0' - r-base - r-dt - r-htmltools @@ -30,10 +30,10 @@ requirements: - r-shiny - r-shinybs run: - - 'bioconductor-biostrings >=2.50.0,<2.51.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' - - 'bioconductor-shortread >=1.40.0,<1.41.0' + - 'bioconductor-biostrings >=2.52.0,<2.53.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' + - 'bioconductor-shortread >=1.42.0,<1.43.0' - r-base - r-dt - r-htmltools diff --git a/recipes/bioconductor-fastseg/meta.yaml b/recipes/bioconductor-fastseg/meta.yaml index 4af5939d18398..47fcc28c8eeb9 100644 --- a/recipes/bioconductor-fastseg/meta.yaml +++ b/recipes/bioconductor-fastseg/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.28.0" %} +{% set version = "1.30.0" %} {% set name = "fastseg" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,27 +10,27 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: f47179909801546c1b8cbadd9d487295 + md5: 3f4f576809b0b9de45d4e8ef2947eea6 build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ # Suggests: DNAcopy, oligo requirements: host: - - 'bioconductor-biobase >=2.42.0,<2.43.0' - - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' - - 'bioconductor-genomicranges >=1.34.0,<1.35.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' + - 'bioconductor-biocgenerics >=0.30.0,<0.31.0' + - 'bioconductor-genomicranges >=1.36.0,<1.37.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' - r-base run: - - 'bioconductor-biobase >=2.42.0,<2.43.0' - - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' - - 'bioconductor-genomicranges >=1.34.0,<1.35.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' + - 'bioconductor-biocgenerics >=0.30.0,<0.31.0' + - 'bioconductor-genomicranges >=1.36.0,<1.37.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' - r-base build: - {{ compiler('c') }} diff --git a/recipes/bioconductor-fcbf/meta.yaml b/recipes/bioconductor-fcbf/meta.yaml index e4f43d2eb4c47..e198faaf2fba0 100644 --- a/recipes/bioconductor-fcbf/meta.yaml +++ b/recipes/bioconductor-fcbf/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.0.1" %} +{% set version = "1.1.1" %} {% set name = "FCBF" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 28449b73200091dccba49241087286f0 + md5: 4e239aa44d73220cddf8a7c7bf6855a2 build: number: 0 rpaths: @@ -20,12 +20,12 @@ build: # Suggests: caret, mlbench, SingleCellExperiment, knitr, rmarkdown, testthat, BiocManager requirements: host: - - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' + - 'bioconductor-summarizedexperiment >=1.14.0,<1.15.0' - r-base - r-ggplot2 - r-gridextra run: - - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' + - 'bioconductor-summarizedexperiment >=1.14.0,<1.15.0' - r-base - r-ggplot2 - r-gridextra diff --git a/recipes/bioconductor-fccac/meta.yaml b/recipes/bioconductor-fccac/meta.yaml index be97adbfc2835..cda912e4c57ee 100644 --- a/recipes/bioconductor-fccac/meta.yaml +++ b/recipes/bioconductor-fccac/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.8.0" %} +{% set version = "1.10.0" %} {% set name = "fCCAC" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 20e26204e5c9d0726a0a060b5c2e41cd + md5: 6614471a57447b3ba938fb723cd9e661 build: number: 0 rpaths: @@ -20,21 +20,21 @@ build: # Suggests: RUnit, BiocGenerics, BiocStyle requirements: host: - - 'bioconductor-complexheatmap >=1.20.0,<1.21.0' - - 'bioconductor-genomation >=1.14.0,<1.15.0' - - 'bioconductor-genomicranges >=1.34.0,<1.35.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-complexheatmap >=2.0.0,<2.1.0' + - 'bioconductor-genomation >=1.16.0,<1.17.0' + - 'bioconductor-genomicranges >=1.36.0,<1.37.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' - r-base - r-fda - r-ggplot2 - r-rcolorbrewer run: - - 'bioconductor-complexheatmap >=1.20.0,<1.21.0' - - 'bioconductor-genomation >=1.14.0,<1.15.0' - - 'bioconductor-genomicranges >=1.34.0,<1.35.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-complexheatmap >=2.0.0,<2.1.0' + - 'bioconductor-genomation >=1.16.0,<1.17.0' + - 'bioconductor-genomicranges >=1.36.0,<1.37.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' - r-base - r-fda - r-ggplot2 diff --git a/recipes/bioconductor-fci/build.sh b/recipes/bioconductor-fci/build.sh index c1d13421f5f1e..068014183bd4e 100644 --- a/recipes/bioconductor-fci/build.sh +++ b/recipes/bioconductor-fci/build.sh @@ -1,4 +1,5 @@ #!/bin/bash +export LD_LIBRARY_PATH=${BUILD_PREFIX}/x86_64-conda_cos6-linux-gnu/sysroot/usr/lib64 mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION mkdir -p ~/.R @@ -8,4 +9,4 @@ CXX=$CXX CXX98=$CXX CXX11=$CXX CXX14=$CXX" > ~/.R/Makevars -$R CMD INSTALL --build . \ No newline at end of file +$R CMD INSTALL --build . diff --git a/recipes/bioconductor-fci/meta.yaml b/recipes/bioconductor-fci/meta.yaml index 87b04fd384227..279e2c30eebd9 100644 --- a/recipes/bioconductor-fci/meta.yaml +++ b/recipes/bioconductor-fci/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.12.0" %} +{% set version = "1.14.0" %} {% set name = "fCI" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: a3c20a38535de3aeba64aa906ac0d37a + md5: d886adcdcb84a88b0c24d8f4ae4d910a build: number: 0 rpaths: @@ -19,6 +19,13 @@ build: noarch: generic # Suggests: knitr, rmarkdown, BiocStyle requirements: + build: + - {{ cdt('mesa-libgl-devel') }} + - {{ cdt('mesa-dri-drivers') }} + - {{ cdt('libselinux') }} + - {{ cdt('libxdamage') }} + - {{ cdt('libxxf86vm') }} + - {{ cdt('libxfixes') }} host: - r-base - r-fnn @@ -37,13 +44,12 @@ requirements: - r-zoo test: commands: - - '$R -e "library(''{{ name }}'')"' + - LD_LIBRARY_PATH="${BUILD_PREFIX}/x86_64-conda_cos6-linux-gnu/sysroot/usr/lib64:/usr/lib/x86_64-linux-gnu/" $R -e "library('{{ name }}')" about: home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: 'GPL (>= 2)' summary: '(f-divergence Cutoff Index), is to find DEGs in the transcriptomic & proteomic data, and identify DEGs by computing the difference between the distribution of fold-changes for the control-control and remaining (non-differential) case-control gene expression ratio data. fCI provides several advantages compared to existing methods.' - extra: container: - # needed for libGL.so.1 extended-base: true + diff --git a/recipes/bioconductor-fdb.fantom4.promoters.hg19/meta.yaml b/recipes/bioconductor-fdb.fantom4.promoters.hg19/meta.yaml index 9a98a8912e91c..ac31c114bb17e 100644 --- a/recipes/bioconductor-fdb.fantom4.promoters.hg19/meta.yaml +++ b/recipes/bioconductor-fdb.fantom4.promoters.hg19/meta.yaml @@ -1,6 +1,6 @@ {% set version = "1.0.0" %} {% set name = "FDb.FANTOM4.promoters.hg19" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -12,7 +12,7 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' md5: 99a610eb895470e3d945acc5cfb3ebe6 build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ @@ -20,16 +20,16 @@ build: # Suggests: BSgenome.Hsapiens.UCSC.hg19, rtracklayer, matrixStats requirements: host: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' - - 'bioconductor-biostrings >=2.50.0,<2.51.0' - - 'bioconductor-genomicfeatures >=1.34.0,<1.35.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' + - 'bioconductor-biostrings >=2.52.0,<2.53.0' + - 'bioconductor-genomicfeatures >=1.36.0,<1.37.0' - r-base run: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' - - 'bioconductor-biostrings >=2.50.0,<2.51.0' - - 'bioconductor-genomicfeatures >=1.34.0,<1.35.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' + - 'bioconductor-biostrings >=2.52.0,<2.53.0' + - 'bioconductor-genomicfeatures >=1.36.0,<1.37.0' - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-fdb.fantom4.promoters.hg19/post-link.sh b/recipes/bioconductor-fdb.fantom4.promoters.hg19/post-link.sh index a12b17294b7e9..70e29aec3baf7 100644 --- a/recipes/bioconductor-fdb.fantom4.promoters.hg19/post-link.sh +++ b/recipes/bioconductor-fdb.fantom4.promoters.hg19/post-link.sh @@ -1,9 +1,10 @@ #!/bin/bash FN="FDb.FANTOM4.promoters.hg19_1.0.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/FDb.FANTOM4.promoters.hg19_1.0.0.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/FDb.FANTOM4.promoters.hg19_1.0.0.tar.gz" "https://bioarchive.galaxyproject.org/FDb.FANTOM4.promoters.hg19_1.0.0.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-fdb.fantom4.promoters.hg19/bioconductor-fdb.fantom4.promoters.hg19_1.0.0_src_all.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-fdb.fantom4.promoters.hg19/bioconductor-fdb.fantom4.promoters.hg19_1.0.0_src_all.tar.gz" ) MD5="99a610eb895470e3d945acc5cfb3ebe6" @@ -16,7 +17,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-fdb.infiniummethylation.hg18/meta.yaml b/recipes/bioconductor-fdb.infiniummethylation.hg18/meta.yaml index 900fcb98dfc38..81c7861a00c03 100644 --- a/recipes/bioconductor-fdb.infiniummethylation.hg18/meta.yaml +++ b/recipes/bioconductor-fdb.infiniummethylation.hg18/meta.yaml @@ -1,6 +1,6 @@ {% set version = "2.2.0" %} {% set name = "FDb.InfiniumMethylation.hg18" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -12,27 +12,27 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' md5: 95ceab50d0a7c3d417cee12fbe3defb3 build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' - - 'bioconductor-biostrings >=2.50.0,<2.51.0' - - 'bioconductor-genomicfeatures >=1.34.0,<1.35.0' - - 'bioconductor-org.hs.eg.db >=3.7.0,<3.8.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' + - 'bioconductor-biostrings >=2.52.0,<2.53.0' + - 'bioconductor-genomicfeatures >=1.36.0,<1.37.0' + - 'bioconductor-org.hs.eg.db >=3.8.0,<3.9.0' - 'bioconductor-txdb.hsapiens.ucsc.hg18.knowngene >=3.2.0,<3.3.0' - r-base run: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' - - 'bioconductor-biostrings >=2.50.0,<2.51.0' - - 'bioconductor-genomicfeatures >=1.34.0,<1.35.0' - - 'bioconductor-org.hs.eg.db >=3.7.0,<3.8.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' + - 'bioconductor-biostrings >=2.52.0,<2.53.0' + - 'bioconductor-genomicfeatures >=1.36.0,<1.37.0' + - 'bioconductor-org.hs.eg.db >=3.8.0,<3.9.0' - 'bioconductor-txdb.hsapiens.ucsc.hg18.knowngene >=3.2.0,<3.3.0' - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-fdb.infiniummethylation.hg18/post-link.sh b/recipes/bioconductor-fdb.infiniummethylation.hg18/post-link.sh index 2ff12a22bddb3..b6f8c14ce1e28 100644 --- a/recipes/bioconductor-fdb.infiniummethylation.hg18/post-link.sh +++ b/recipes/bioconductor-fdb.infiniummethylation.hg18/post-link.sh @@ -1,9 +1,10 @@ #!/bin/bash FN="FDb.InfiniumMethylation.hg18_2.2.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/FDb.InfiniumMethylation.hg18_2.2.0.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/FDb.InfiniumMethylation.hg18_2.2.0.tar.gz" "https://bioarchive.galaxyproject.org/FDb.InfiniumMethylation.hg18_2.2.0.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-fdb.infiniummethylation.hg18/bioconductor-fdb.infiniummethylation.hg18_2.2.0_src_all.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-fdb.infiniummethylation.hg18/bioconductor-fdb.infiniummethylation.hg18_2.2.0_src_all.tar.gz" ) MD5="95ceab50d0a7c3d417cee12fbe3defb3" @@ -16,7 +17,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-fdb.infiniummethylation.hg19/meta.yaml b/recipes/bioconductor-fdb.infiniummethylation.hg19/meta.yaml index 7b669b972c24a..18fc3c478e0b7 100644 --- a/recipes/bioconductor-fdb.infiniummethylation.hg19/meta.yaml +++ b/recipes/bioconductor-fdb.infiniummethylation.hg19/meta.yaml @@ -1,6 +1,6 @@ {% set version = "2.2.0" %} {% set name = "FDb.InfiniumMethylation.hg19" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -12,7 +12,7 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' md5: b8b1abc599b9556b9fe9c6e824cb2697 build: - number: 4 + number: 5 rpaths: - lib/R/lib/ - lib/ @@ -20,20 +20,20 @@ build: # Suggests: FDb.UCSC.snp135common.hg19 requirements: host: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' - - 'bioconductor-biostrings >=2.50.0,<2.51.0' - - 'bioconductor-genomicfeatures >=1.34.0,<1.35.0' - - 'bioconductor-org.hs.eg.db >=3.7.0,<3.8.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' + - 'bioconductor-biostrings >=2.52.0,<2.53.0' + - 'bioconductor-genomicfeatures >=1.36.0,<1.37.0' + - 'bioconductor-org.hs.eg.db >=3.8.0,<3.9.0' - 'bioconductor-txdb.hsapiens.ucsc.hg19.knowngene >=3.2.0,<3.3.0' - r-base run: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' - - 'bioconductor-biostrings >=2.50.0,<2.51.0' - - 'bioconductor-genomicfeatures >=1.34.0,<1.35.0' - - 'bioconductor-org.hs.eg.db >=3.7.0,<3.8.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' + - 'bioconductor-biostrings >=2.52.0,<2.53.0' + - 'bioconductor-genomicfeatures >=1.36.0,<1.37.0' + - 'bioconductor-org.hs.eg.db >=3.8.0,<3.9.0' - 'bioconductor-txdb.hsapiens.ucsc.hg19.knowngene >=3.2.0,<3.3.0' - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-fdb.infiniummethylation.hg19/post-link.sh b/recipes/bioconductor-fdb.infiniummethylation.hg19/post-link.sh index ba59def2f0797..fa4d4f5933402 100644 --- a/recipes/bioconductor-fdb.infiniummethylation.hg19/post-link.sh +++ b/recipes/bioconductor-fdb.infiniummethylation.hg19/post-link.sh @@ -1,7 +1,7 @@ #!/bin/bash FN="FDb.InfiniumMethylation.hg19_2.2.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/FDb.InfiniumMethylation.hg19_2.2.0.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/FDb.InfiniumMethylation.hg19_2.2.0.tar.gz" "https://bioarchive.galaxyproject.org/FDb.InfiniumMethylation.hg19_2.2.0.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-fdb.infiniummethylation.hg19/bioconductor-fdb.infiniummethylation.hg19_2.2.0_src_all.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-fdb.infiniummethylation.hg19/bioconductor-fdb.infiniummethylation.hg19_2.2.0_src_all.tar.gz" @@ -17,7 +17,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-fdb.ucsc.snp135common.hg19/meta.yaml b/recipes/bioconductor-fdb.ucsc.snp135common.hg19/meta.yaml index 7344bf3a0b899..ea7b8a1891179 100644 --- a/recipes/bioconductor-fdb.ucsc.snp135common.hg19/meta.yaml +++ b/recipes/bioconductor-fdb.ucsc.snp135common.hg19/meta.yaml @@ -1,6 +1,6 @@ {% set version = "1.0.0" %} {% set name = "FDb.UCSC.snp135common.hg19" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -12,7 +12,7 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' md5: 0cdca5fa595bb69464016ceb97635f78 build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ @@ -20,14 +20,14 @@ build: # Suggests: BSgenome.Hsapiens.UCSC.hg19, SNPlocs.Hsapiens.dbSNP.20111119 requirements: host: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' - - 'bioconductor-genomicfeatures >=1.34.0,<1.35.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' + - 'bioconductor-genomicfeatures >=1.36.0,<1.37.0' - r-base run: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' - - 'bioconductor-genomicfeatures >=1.34.0,<1.35.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' + - 'bioconductor-genomicfeatures >=1.36.0,<1.37.0' - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-fdb.ucsc.snp135common.hg19/post-link.sh b/recipes/bioconductor-fdb.ucsc.snp135common.hg19/post-link.sh index 56d6c7400a000..408e965c7d8f0 100644 --- a/recipes/bioconductor-fdb.ucsc.snp135common.hg19/post-link.sh +++ b/recipes/bioconductor-fdb.ucsc.snp135common.hg19/post-link.sh @@ -1,9 +1,10 @@ #!/bin/bash FN="FDb.UCSC.snp135common.hg19_1.0.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/FDb.UCSC.snp135common.hg19_1.0.0.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/FDb.UCSC.snp135common.hg19_1.0.0.tar.gz" "https://bioarchive.galaxyproject.org/FDb.UCSC.snp135common.hg19_1.0.0.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-fdb.ucsc.snp135common.hg19/bioconductor-fdb.ucsc.snp135common.hg19_1.0.0_src_all.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-fdb.ucsc.snp135common.hg19/bioconductor-fdb.ucsc.snp135common.hg19_1.0.0_src_all.tar.gz" ) MD5="0cdca5fa595bb69464016ceb97635f78" @@ -16,7 +17,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-fdb.ucsc.snp137common.hg19/meta.yaml b/recipes/bioconductor-fdb.ucsc.snp137common.hg19/meta.yaml index 87c7999eafba5..55b24c86938ad 100644 --- a/recipes/bioconductor-fdb.ucsc.snp137common.hg19/meta.yaml +++ b/recipes/bioconductor-fdb.ucsc.snp137common.hg19/meta.yaml @@ -1,6 +1,6 @@ {% set version = "1.0.0" %} {% set name = "FDb.UCSC.snp137common.hg19" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -12,7 +12,7 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' md5: dac83f2d2f9ea9f033e50beac5c44838 build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ @@ -20,14 +20,14 @@ build: # Suggests: BSgenome.Hsapiens.UCSC.hg19 requirements: host: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' - - 'bioconductor-genomicfeatures >=1.34.0,<1.35.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' + - 'bioconductor-genomicfeatures >=1.36.0,<1.37.0' - r-base run: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' - - 'bioconductor-genomicfeatures >=1.34.0,<1.35.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' + - 'bioconductor-genomicfeatures >=1.36.0,<1.37.0' - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-fdb.ucsc.snp137common.hg19/post-link.sh b/recipes/bioconductor-fdb.ucsc.snp137common.hg19/post-link.sh index b94795333fba5..0706c44cca39c 100644 --- a/recipes/bioconductor-fdb.ucsc.snp137common.hg19/post-link.sh +++ b/recipes/bioconductor-fdb.ucsc.snp137common.hg19/post-link.sh @@ -1,9 +1,10 @@ #!/bin/bash FN="FDb.UCSC.snp137common.hg19_1.0.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/FDb.UCSC.snp137common.hg19_1.0.0.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/FDb.UCSC.snp137common.hg19_1.0.0.tar.gz" "https://bioarchive.galaxyproject.org/FDb.UCSC.snp137common.hg19_1.0.0.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-fdb.ucsc.snp137common.hg19/bioconductor-fdb.ucsc.snp137common.hg19_1.0.0_src_all.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-fdb.ucsc.snp137common.hg19/bioconductor-fdb.ucsc.snp137common.hg19_1.0.0_src_all.tar.gz" ) MD5="dac83f2d2f9ea9f033e50beac5c44838" @@ -16,7 +17,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-fdb.ucsc.trnas/meta.yaml b/recipes/bioconductor-fdb.ucsc.trnas/meta.yaml index 4ce40cd9a1f8b..ebc7aa91e90f7 100644 --- a/recipes/bioconductor-fdb.ucsc.trnas/meta.yaml +++ b/recipes/bioconductor-fdb.ucsc.trnas/meta.yaml @@ -1,6 +1,6 @@ {% set version = "1.0.1" %} {% set name = "FDb.UCSC.tRNAs" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -12,21 +12,21 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' md5: 77bfdadd4d9f995a72b001e4e41792fa build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' - - 'bioconductor-genomicfeatures >=1.34.0,<1.35.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' + - 'bioconductor-genomicfeatures >=1.36.0,<1.37.0' - r-base run: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' - - 'bioconductor-genomicfeatures >=1.34.0,<1.35.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' + - 'bioconductor-genomicfeatures >=1.36.0,<1.37.0' - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-fdb.ucsc.trnas/post-link.sh b/recipes/bioconductor-fdb.ucsc.trnas/post-link.sh index 5303c7972f626..444f6d9dc3980 100644 --- a/recipes/bioconductor-fdb.ucsc.trnas/post-link.sh +++ b/recipes/bioconductor-fdb.ucsc.trnas/post-link.sh @@ -1,9 +1,10 @@ #!/bin/bash FN="FDb.UCSC.tRNAs_1.0.1.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/FDb.UCSC.tRNAs_1.0.1.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/FDb.UCSC.tRNAs_1.0.1.tar.gz" "https://bioarchive.galaxyproject.org/FDb.UCSC.tRNAs_1.0.1.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-fdb.ucsc.trnas/bioconductor-fdb.ucsc.trnas_1.0.1_src_all.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-fdb.ucsc.trnas/bioconductor-fdb.ucsc.trnas_1.0.1_src_all.tar.gz" ) MD5="77bfdadd4d9f995a72b001e4e41792fa" @@ -16,7 +17,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-fdrame/meta.yaml b/recipes/bioconductor-fdrame/meta.yaml index 68dc8c642ffa8..ce67dbbf0e0a4 100644 --- a/recipes/bioconductor-fdrame/meta.yaml +++ b/recipes/bioconductor-fdrame/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.54.0" %} +{% set version = "1.56.0" %} {% set name = "fdrame" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 1cb9ad63d92d24dae60d42ba7ed28916 + md5: 8bb3059973a217274a7d8dec8a1250a3 build: number: 0 rpaths: diff --git a/recipes/bioconductor-fella/meta.yaml b/recipes/bioconductor-fella/meta.yaml index 66d7733beb2fd..1fdaca533f436 100644 --- a/recipes/bioconductor-fella/meta.yaml +++ b/recipes/bioconductor-fella/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.2.0" %} +{% set version = "1.4.0" %} {% set name = "FELLA" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,9 +10,9 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 57cc316a2cfa0eed827576e28c8e7fd6 + md5: 25073ad00d5fbb978994cd4da5b403d5 build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ @@ -20,13 +20,13 @@ build: # Suggests: shiny, DT, magrittr, visNetwork, knitr, BiocStyle, rmarkdown, testthat, biomaRt, org.Hs.eg.db, org.Mm.eg.db, AnnotationDbi, GOSemSim requirements: host: - - 'bioconductor-keggrest >=1.22.0,<1.23.0' + - 'bioconductor-keggrest >=1.24.0,<1.25.0' - r-base - r-igraph - r-matrix - r-plyr run: - - 'bioconductor-keggrest >=1.22.0,<1.23.0' + - 'bioconductor-keggrest >=1.24.0,<1.25.0' - r-base - r-igraph - r-matrix diff --git a/recipes/bioconductor-fem/meta.yaml b/recipes/bioconductor-fem/meta.yaml index 56167b72f82ab..cd12a6d988ba1 100644 --- a/recipes/bioconductor-fem/meta.yaml +++ b/recipes/bioconductor-fem/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "3.10.0" %} +{% set version = "3.12.0" %} {% set name = "FEM" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: bdcb6f1671541b2849ed9ca57a974b9b + md5: 0dfe9b41772263030ef193759c90acc3 build: number: 0 rpaths: @@ -19,25 +19,25 @@ build: noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' - - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' - - 'bioconductor-graph >=1.60.0,<1.61.0' - - 'bioconductor-impute >=1.56.0,<1.57.0' - - 'bioconductor-limma >=3.38.0,<3.39.0' - - 'bioconductor-marray >=1.60.0,<1.61.0' - - 'bioconductor-org.hs.eg.db >=3.7.0,<3.8.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' + - 'bioconductor-biocgenerics >=0.30.0,<0.31.0' + - 'bioconductor-graph >=1.62.0,<1.63.0' + - 'bioconductor-impute >=1.58.0,<1.59.0' + - 'bioconductor-limma >=3.40.0,<3.41.0' + - 'bioconductor-marray >=1.62.0,<1.63.0' + - 'bioconductor-org.hs.eg.db >=3.8.0,<3.9.0' - r-base - r-corrplot - r-igraph - r-matrix run: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' - - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' - - 'bioconductor-graph >=1.60.0,<1.61.0' - - 'bioconductor-impute >=1.56.0,<1.57.0' - - 'bioconductor-limma >=3.38.0,<3.39.0' - - 'bioconductor-marray >=1.60.0,<1.61.0' - - 'bioconductor-org.hs.eg.db >=3.7.0,<3.8.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' + - 'bioconductor-biocgenerics >=0.30.0,<0.31.0' + - 'bioconductor-graph >=1.62.0,<1.63.0' + - 'bioconductor-impute >=1.58.0,<1.59.0' + - 'bioconductor-limma >=3.40.0,<3.41.0' + - 'bioconductor-marray >=1.62.0,<1.63.0' + - 'bioconductor-org.hs.eg.db >=3.8.0,<3.9.0' - r-base - r-corrplot - r-igraph diff --git a/recipes/bioconductor-ffpe/meta.yaml b/recipes/bioconductor-ffpe/meta.yaml index b408593af6e07..0c3e44583628e 100644 --- a/recipes/bioconductor-ffpe/meta.yaml +++ b/recipes/bioconductor-ffpe/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.26.0" %} +{% set version = "1.28.0" %} {% set name = "ffpe" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 0854fb74a6463f5e5c6fd54a18ad20e8 + md5: 05ad7dc16b2f849f392123a3a6a8b7d2 build: number: 0 rpaths: @@ -20,20 +20,20 @@ build: # Suggests: genefilter, ffpeExampleData requirements: host: - - 'bioconductor-affy >=1.60.0,<1.61.0' - - 'bioconductor-biobase >=2.42.0,<2.43.0' - - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' - - 'bioconductor-lumi >=2.34.0,<2.35.0' - - 'bioconductor-methylumi >=2.28.0,<2.29.0' + - 'bioconductor-affy >=1.62.0,<1.63.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' + - 'bioconductor-biocgenerics >=0.30.0,<0.31.0' + - 'bioconductor-lumi >=2.36.0,<2.37.0' + - 'bioconductor-methylumi >=2.30.0,<2.31.0' - r-base - r-sfsmisc - r-ttr run: - - 'bioconductor-affy >=1.60.0,<1.61.0' - - 'bioconductor-biobase >=2.42.0,<2.43.0' - - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' - - 'bioconductor-lumi >=2.34.0,<2.35.0' - - 'bioconductor-methylumi >=2.28.0,<2.29.0' + - 'bioconductor-affy >=1.62.0,<1.63.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' + - 'bioconductor-biocgenerics >=0.30.0,<0.31.0' + - 'bioconductor-lumi >=2.36.0,<2.37.0' + - 'bioconductor-methylumi >=2.30.0,<2.31.0' - r-base - r-sfsmisc - r-ttr diff --git a/recipes/bioconductor-ffpeexampledata/meta.yaml b/recipes/bioconductor-ffpeexampledata/meta.yaml index 4d29741b0bc74..9edbd9420a46d 100644 --- a/recipes/bioconductor-ffpeexampledata/meta.yaml +++ b/recipes/bioconductor-ffpeexampledata/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.20.0" %} +{% set version = "1.22.0" %} {% set name = "ffpeExampleData" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 3e1855c53c4cef163383ef8921a86ab1 + md5: cc909cc2b13a7cc9a8238bdab9f68d08 build: number: 0 rpaths: @@ -20,12 +20,12 @@ build: # Suggests: genefilter, affy requirements: host: - - 'bioconductor-lumi >=2.34.0,<2.35.0' + - 'bioconductor-lumi >=2.36.0,<2.37.0' - r-base run: - - 'bioconductor-lumi >=2.34.0,<2.35.0' + - 'bioconductor-lumi >=2.36.0,<2.37.0' - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-ffpeexampledata/post-link.sh b/recipes/bioconductor-ffpeexampledata/post-link.sh index d8216c828de7f..1990920b2e0a0 100644 --- a/recipes/bioconductor-ffpeexampledata/post-link.sh +++ b/recipes/bioconductor-ffpeexampledata/post-link.sh @@ -1,11 +1,11 @@ #!/bin/bash -FN="ffpeExampleData_1.20.0.tar.gz" +FN="ffpeExampleData_1.22.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/experiment/src/contrib/ffpeExampleData_1.20.0.tar.gz" - "https://bioarchive.galaxyproject.org/ffpeExampleData_1.20.0.tar.gz" - "https://depot.galaxyproject.org/software/bioconductor-ffpeexampledata/bioconductor-ffpeexampledata_1.20.0_src_all.tar.gz" + "https://bioconductor.org/packages/3.9/data/experiment/src/contrib/ffpeExampleData_1.22.0.tar.gz" + "https://bioarchive.galaxyproject.org/ffpeExampleData_1.22.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-ffpeexampledata/bioconductor-ffpeexampledata_1.22.0_src_all.tar.gz" ) -MD5="3e1855c53c4cef163383ef8921a86ab1" +MD5="cc909cc2b13a7cc9a8238bdab9f68d08" # Use a staging area in the conda dir rather than temp dirs, both to avoid # permission issues as well as to have things downloaded in a predictable @@ -16,7 +16,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-fgnet/meta.yaml b/recipes/bioconductor-fgnet/meta.yaml index e424c3ed6ed55..bc4945b2605c2 100644 --- a/recipes/bioconductor-fgnet/meta.yaml +++ b/recipes/bioconductor-fgnet/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "3.16.0" %} +{% set version = "3.18.0" %} {% set name = "FGNet" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 8e0ffafc6f001f952cf23b176de7d099 + md5: 86c490d5ddaab231d0dfdd862f6aed95 build: number: 0 rpaths: diff --git a/recipes/bioconductor-fgsea/meta.yaml b/recipes/bioconductor-fgsea/meta.yaml index 660bf73b180d9..07f23100632c7 100644 --- a/recipes/bioconductor-fgsea/meta.yaml +++ b/recipes/bioconductor-fgsea/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.8.0" %} +{% set version = "1.10.0" %} {% set name = "fgsea" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 1ede6d5cb80ae8f3832581da55ee5cc0 + md5: 4e28e16ce0ef3b3cd01eecd80e51a4fe build: number: 0 rpaths: @@ -20,8 +20,9 @@ build: # SystemRequirements: C++11 requirements: host: - - 'bioconductor-biocparallel >=1.16.0,<1.17.0' + - 'bioconductor-biocparallel >=1.18.0,<1.19.0' - r-base + - r-bh - r-data.table - r-fastmatch - 'r-ggplot2 >=2.2.0' @@ -29,8 +30,9 @@ requirements: - r-matrix - r-rcpp run: - - 'bioconductor-biocparallel >=1.16.0,<1.17.0' + - 'bioconductor-biocparallel >=1.18.0,<1.19.0' - r-base + - r-bh - r-data.table - r-fastmatch - 'r-ggplot2 >=2.2.0' diff --git a/recipes/bioconductor-fibroeset/meta.yaml b/recipes/bioconductor-fibroeset/meta.yaml index a7c4dd03915cd..99d6161d2db77 100644 --- a/recipes/bioconductor-fibroeset/meta.yaml +++ b/recipes/bioconductor-fibroeset/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.24.0" %} +{% set version = "1.26.0" %} {% set name = "fibroEset" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 62d8b288008e726bd897b0a7296aade1 + md5: cb7df36fe536a6bdbefeddf2086ec477 build: number: 0 rpaths: @@ -19,12 +19,12 @@ build: noarch: generic requirements: host: - - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' - r-base run: - - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-fibroeset/post-link.sh b/recipes/bioconductor-fibroeset/post-link.sh index 429da1db2d7c9..b2dd0d815d9b8 100644 --- a/recipes/bioconductor-fibroeset/post-link.sh +++ b/recipes/bioconductor-fibroeset/post-link.sh @@ -1,11 +1,11 @@ #!/bin/bash -FN="fibroEset_1.24.0.tar.gz" +FN="fibroEset_1.26.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/experiment/src/contrib/fibroEset_1.24.0.tar.gz" - "https://bioarchive.galaxyproject.org/fibroEset_1.24.0.tar.gz" - "https://depot.galaxyproject.org/software/bioconductor-fibroeset/bioconductor-fibroeset_1.24.0_src_all.tar.gz" + "https://bioconductor.org/packages/3.9/data/experiment/src/contrib/fibroEset_1.26.0.tar.gz" + "https://bioarchive.galaxyproject.org/fibroEset_1.26.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-fibroeset/bioconductor-fibroeset_1.26.0_src_all.tar.gz" ) -MD5="62d8b288008e726bd897b0a7296aade1" +MD5="cb7df36fe536a6bdbefeddf2086ec477" # Use a staging area in the conda dir rather than temp dirs, both to avoid # permission issues as well as to have things downloaded in a predictable @@ -16,7 +16,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-findmyfriends/meta.yaml b/recipes/bioconductor-findmyfriends/meta.yaml index f77c7344290e7..eaaa4f4d6d7eb 100644 --- a/recipes/bioconductor-findmyfriends/meta.yaml +++ b/recipes/bioconductor-findmyfriends/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.12.0" %} +{% set version = "1.14.0" %} {% set name = "FindMyFriends" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 1b49ddefa018ab07f89bc316d119f099 + md5: 8f41164987f56ae09297da848cc88b31 build: number: 0 rpaths: @@ -19,13 +19,13 @@ build: # Suggests: BiocStyle, testthat, knitr, rmarkdown, reutils requirements: host: - - 'bioconductor-biobase >=2.42.0,<2.43.0' - - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' - - 'bioconductor-biocparallel >=1.16.0,<1.17.0' - - 'bioconductor-biostrings >=2.50.0,<2.51.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-kebabs >=1.16.0,<1.17.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' + - 'bioconductor-biocgenerics >=0.30.0,<0.31.0' + - 'bioconductor-biocparallel >=1.18.0,<1.19.0' + - 'bioconductor-biostrings >=2.52.0,<2.53.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-kebabs >=1.18.0,<1.19.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' - r-base - r-digest - r-dplyr @@ -38,13 +38,13 @@ requirements: - r-rcpp - r-reshape2 run: - - 'bioconductor-biobase >=2.42.0,<2.43.0' - - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' - - 'bioconductor-biocparallel >=1.16.0,<1.17.0' - - 'bioconductor-biostrings >=2.50.0,<2.51.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-kebabs >=1.16.0,<1.17.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' + - 'bioconductor-biocgenerics >=0.30.0,<0.31.0' + - 'bioconductor-biocparallel >=1.18.0,<1.19.0' + - 'bioconductor-biostrings >=2.52.0,<2.53.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-kebabs >=1.18.0,<1.19.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' - r-base - r-digest - r-dplyr diff --git a/recipes/bioconductor-fis/meta.yaml b/recipes/bioconductor-fis/meta.yaml index e24ac53ea669e..eba0486a83911 100644 --- a/recipes/bioconductor-fis/meta.yaml +++ b/recipes/bioconductor-fis/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.10.0" %} +{% set version = "1.12.0" %} {% set name = "FIs" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: b7e898f0a018f003f8268ed5b255049f + md5: 26a808973c479d338754411a994a3df9 build: number: 0 rpaths: @@ -22,7 +22,7 @@ requirements: - r-base run: - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-fis/post-link.sh b/recipes/bioconductor-fis/post-link.sh index 6bc14e4a701c7..88f123c3c6291 100644 --- a/recipes/bioconductor-fis/post-link.sh +++ b/recipes/bioconductor-fis/post-link.sh @@ -1,11 +1,11 @@ #!/bin/bash -FN="FIs_1.10.0.tar.gz" +FN="FIs_1.12.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/experiment/src/contrib/FIs_1.10.0.tar.gz" - "https://bioarchive.galaxyproject.org/FIs_1.10.0.tar.gz" - "https://depot.galaxyproject.org/software/bioconductor-fis/bioconductor-fis_1.10.0_src_all.tar.gz" + "https://bioconductor.org/packages/3.9/data/experiment/src/contrib/FIs_1.12.0.tar.gz" + "https://bioarchive.galaxyproject.org/FIs_1.12.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-fis/bioconductor-fis_1.12.0_src_all.tar.gz" ) -MD5="b7e898f0a018f003f8268ed5b255049f" +MD5="26a808973c479d338754411a994a3df9" # Use a staging area in the conda dir rather than temp dirs, both to avoid # permission issues as well as to have things downloaded in a predictable @@ -16,7 +16,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-fishalyser/meta.yaml b/recipes/bioconductor-fishalyser/meta.yaml index c10ac0d43ffc4..daefe252124a2 100644 --- a/recipes/bioconductor-fishalyser/meta.yaml +++ b/recipes/bioconductor-fishalyser/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.16.0" %} +{% set version = "1.18.0" %} {% set name = "FISHalyseR" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,9 +10,9 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 18f4ac8d3e1695713f0953102e3105f5 + md5: be6da4b0fcd9884da0ee3d01c3dcdf37 build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ @@ -20,11 +20,11 @@ build: # Suggests: knitr requirements: host: - - 'bioconductor-ebimage >=4.24.0,<4.25.0' + - 'bioconductor-ebimage >=4.26.0,<4.27.0' - r-abind - r-base run: - - 'bioconductor-ebimage >=4.24.0,<4.25.0' + - 'bioconductor-ebimage >=4.26.0,<4.27.0' - r-abind - r-base test: diff --git a/recipes/bioconductor-fishpond/build.sh b/recipes/bioconductor-fishpond/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-fishpond/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-fishpond/meta.yaml b/recipes/bioconductor-fishpond/meta.yaml new file mode 100644 index 0000000000000..a379f025b0251 --- /dev/null +++ b/recipes/bioconductor-fishpond/meta.yaml @@ -0,0 +1,47 @@ +{% set version = "1.0.0" %} +{% set name = "fishpond" %} +{% set bioc = "3.9" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + md5: 388955bba65408b9a29e29a2e9bff2ee +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: testthat, knitr, rmarkdown, macrophage, tximeta, org.Hs.eg.db, DESeq2, apeglm +requirements: + host: + - 'bioconductor-qvalue >=2.16.0,<2.17.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' + - 'bioconductor-summarizedexperiment >=1.14.0,<1.15.0' + - r-abind + - r-base + - r-matrixstats + - r-samr + - r-svmisc + run: + - 'bioconductor-qvalue >=2.16.0,<2.17.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' + - 'bioconductor-summarizedexperiment >=1.14.0,<1.15.0' + - r-abind + - r-base + - r-matrixstats + - r-samr + - r-svmisc +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: GPL-2 + summary: 'Fishpond contains methods for differential transcript and gene expression analysis of RNA-seq data using inferential replicates for uncertainty of abundance quantification, as generated by Gibbs sampling or bootstrap sampling.' + diff --git a/recipes/bioconductor-fission/meta.yaml b/recipes/bioconductor-fission/meta.yaml index e38e1a7bb4331..0be7436eba0a3 100644 --- a/recipes/bioconductor-fission/meta.yaml +++ b/recipes/bioconductor-fission/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.2.0" %} +{% set version = "1.4.0" %} {% set name = "fission" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 9576468d0dd81fb3edc7e7b550e0dc86 + md5: 9e37bceecdb13c6f82799730387e02d0 build: number: 0 rpaths: @@ -20,12 +20,12 @@ build: # Suggests: knitr requirements: host: - - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' + - 'bioconductor-summarizedexperiment >=1.14.0,<1.15.0' - r-base run: - - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' + - 'bioconductor-summarizedexperiment >=1.14.0,<1.15.0' - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-fission/post-link.sh b/recipes/bioconductor-fission/post-link.sh index f59abe1a67c66..d05557795a17a 100644 --- a/recipes/bioconductor-fission/post-link.sh +++ b/recipes/bioconductor-fission/post-link.sh @@ -1,11 +1,11 @@ #!/bin/bash -FN="fission_1.2.0.tar.gz" +FN="fission_1.4.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/experiment/src/contrib/fission_1.2.0.tar.gz" - "https://bioarchive.galaxyproject.org/fission_1.2.0.tar.gz" - "https://depot.galaxyproject.org/software/bioconductor-fission/bioconductor-fission_1.2.0_src_all.tar.gz" + "https://bioconductor.org/packages/3.9/data/experiment/src/contrib/fission_1.4.0.tar.gz" + "https://bioarchive.galaxyproject.org/fission_1.4.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-fission/bioconductor-fission_1.4.0_src_all.tar.gz" ) -MD5="9576468d0dd81fb3edc7e7b550e0dc86" +MD5="9e37bceecdb13c6f82799730387e02d0" # Use a staging area in the conda dir rather than temp dirs, both to avoid # permission issues as well as to have things downloaded in a predictable @@ -16,7 +16,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-fitcons.ucsc.hg19/meta.yaml b/recipes/bioconductor-fitcons.ucsc.hg19/meta.yaml index 2c7d1a2ebf8d1..53062f7468dc7 100644 --- a/recipes/bioconductor-fitcons.ucsc.hg19/meta.yaml +++ b/recipes/bioconductor-fitcons.ucsc.hg19/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.7.1" %} {% set name = "fitCons.UCSC.hg19" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -12,29 +12,29 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' md5: 53d954890ec9b91084664a10161ce391 build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ noarch: generic requirements: host: - - 'bioconductor-bsgenome >=1.50.0,<1.51.0' - - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' - - 'bioconductor-genomicranges >=1.34.0,<1.35.0' - - 'bioconductor-genomicscores >=1.6.0,<1.7.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-bsgenome >=1.52.0,<1.53.0' + - 'bioconductor-genomeinfodb >=1.20.0,<1.21.0' + - 'bioconductor-genomicranges >=1.36.0,<1.37.0' + - 'bioconductor-genomicscores >=1.8.0,<1.9.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' - r-base run: - - 'bioconductor-bsgenome >=1.50.0,<1.51.0' - - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' - - 'bioconductor-genomicranges >=1.34.0,<1.35.0' - - 'bioconductor-genomicscores >=1.6.0,<1.7.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-bsgenome >=1.52.0,<1.53.0' + - 'bioconductor-genomeinfodb >=1.20.0,<1.21.0' + - 'bioconductor-genomicranges >=1.36.0,<1.37.0' + - 'bioconductor-genomicscores >=1.8.0,<1.9.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-fitcons.ucsc.hg19/post-link.sh b/recipes/bioconductor-fitcons.ucsc.hg19/post-link.sh index 78f796e6774e6..b9043a5772a87 100644 --- a/recipes/bioconductor-fitcons.ucsc.hg19/post-link.sh +++ b/recipes/bioconductor-fitcons.ucsc.hg19/post-link.sh @@ -1,9 +1,10 @@ #!/bin/bash FN="fitCons.UCSC.hg19_3.7.1.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/fitCons.UCSC.hg19_3.7.1.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/fitCons.UCSC.hg19_3.7.1.tar.gz" "https://bioarchive.galaxyproject.org/fitCons.UCSC.hg19_3.7.1.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-fitcons.ucsc.hg19/bioconductor-fitcons.ucsc.hg19_3.7.1_src_all.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-fitcons.ucsc.hg19/bioconductor-fitcons.ucsc.hg19_3.7.1_src_all.tar.gz" ) MD5="53d954890ec9b91084664a10161ce391" @@ -16,7 +17,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-fithic/meta.yaml b/recipes/bioconductor-fithic/meta.yaml index 74adc06980102..033d608ddf2d9 100644 --- a/recipes/bioconductor-fithic/meta.yaml +++ b/recipes/bioconductor-fithic/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.8.0" %} +{% set version = "1.10.0" %} {% set name = "FitHiC" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: e61cb471638915e53858418b543fe1af + md5: 9ad2ef5671bfce808db7f9f61c64b93d build: number: 0 rpaths: diff --git a/recipes/bioconductor-flagme/meta.yaml b/recipes/bioconductor-flagme/meta.yaml index c09297bcb3150..0aa3eb906a143 100644 --- a/recipes/bioconductor-flagme/meta.yaml +++ b/recipes/bioconductor-flagme/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.38.1" %} +{% set version = "1.40.0" %} {% set name = "flagme" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 6a2fbf22b7ee2036539b05d38295b111 + md5: 836cd0c2d6ef6d6f58af43228416412d build: number: 0 rpaths: @@ -18,17 +18,17 @@ build: - lib/ requirements: host: - - 'bioconductor-camera >=1.38.0,<1.39.0' - - 'bioconductor-gcspikelite >=1.20.0,<1.21.0' - - 'bioconductor-xcms >=3.4.0,<3.5.0' + - 'bioconductor-camera >=1.40.0,<1.41.0' + - 'bioconductor-gcspikelite >=1.22.0,<1.23.0' + - 'bioconductor-xcms >=3.6.0,<3.7.0' - r-base - r-gplots - r-mass - r-sparsem run: - - 'bioconductor-camera >=1.38.0,<1.39.0' - - 'bioconductor-gcspikelite >=1.20.0,<1.21.0' - - 'bioconductor-xcms >=3.4.0,<3.5.0' + - 'bioconductor-camera >=1.40.0,<1.41.0' + - 'bioconductor-gcspikelite >=1.22.0,<1.23.0' + - 'bioconductor-xcms >=3.6.0,<3.7.0' - r-base - r-gplots - r-mass diff --git a/recipes/bioconductor-fletcher2013a/meta.yaml b/recipes/bioconductor-fletcher2013a/meta.yaml index 04e80d1d01955..91f886c28312a 100644 --- a/recipes/bioconductor-fletcher2013a/meta.yaml +++ b/recipes/bioconductor-fletcher2013a/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.18.0" %} +{% set version = "1.20.0" %} {% set name = "Fletcher2013a" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 8fc3c9e06927fa7a6508ea42fee23dd7 + md5: 3e34329457960bd66816855ecaba1584 build: number: 0 rpaths: @@ -19,18 +19,18 @@ build: noarch: generic requirements: host: - - 'bioconductor-biobase >=2.42.0,<2.43.0' - - 'bioconductor-limma >=3.38.0,<3.39.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' + - 'bioconductor-limma >=3.40.0,<3.41.0' - r-base - r-gplots - r-venndiagram run: - - 'bioconductor-biobase >=2.42.0,<2.43.0' - - 'bioconductor-limma >=3.38.0,<3.39.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' + - 'bioconductor-limma >=3.40.0,<3.41.0' - r-base - r-gplots - r-venndiagram - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-fletcher2013a/post-link.sh b/recipes/bioconductor-fletcher2013a/post-link.sh index cd38b663aaa9e..d37c55311fbff 100644 --- a/recipes/bioconductor-fletcher2013a/post-link.sh +++ b/recipes/bioconductor-fletcher2013a/post-link.sh @@ -1,11 +1,11 @@ #!/bin/bash -FN="Fletcher2013a_1.18.0.tar.gz" +FN="Fletcher2013a_1.20.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/experiment/src/contrib/Fletcher2013a_1.18.0.tar.gz" - "https://bioarchive.galaxyproject.org/Fletcher2013a_1.18.0.tar.gz" - "https://depot.galaxyproject.org/software/bioconductor-fletcher2013a/bioconductor-fletcher2013a_1.18.0_src_all.tar.gz" + "https://bioconductor.org/packages/3.9/data/experiment/src/contrib/Fletcher2013a_1.20.0.tar.gz" + "https://bioarchive.galaxyproject.org/Fletcher2013a_1.20.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-fletcher2013a/bioconductor-fletcher2013a_1.20.0_src_all.tar.gz" ) -MD5="8fc3c9e06927fa7a6508ea42fee23dd7" +MD5="3e34329457960bd66816855ecaba1584" # Use a staging area in the conda dir rather than temp dirs, both to avoid # permission issues as well as to have things downloaded in a predictable @@ -16,7 +16,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-fletcher2013b/meta.yaml b/recipes/bioconductor-fletcher2013b/meta.yaml index 2a1fc73fef911..d132dd9af2154 100644 --- a/recipes/bioconductor-fletcher2013b/meta.yaml +++ b/recipes/bioconductor-fletcher2013b/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.18.0" %} +{% set version = "1.20.0" %} {% set name = "Fletcher2013b" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 02757b2d756e7d7fb48641ad9a81aaf4 + md5: 5da665ab15174d34747bfea5b972d48b build: number: 0 rpaths: @@ -19,20 +19,20 @@ build: noarch: generic requirements: host: - - 'bioconductor-fletcher2013a >=1.18.0,<1.19.0' - - 'bioconductor-reder >=1.30.0,<1.31.0' - - 'bioconductor-rtn >=2.6.0,<2.7.0' + - 'bioconductor-fletcher2013a >=1.20.0,<1.21.0' + - 'bioconductor-reder >=1.32.0,<1.33.0' + - 'bioconductor-rtn >=2.8.0,<2.9.0' - r-base - r-igraph - r-rcolorbrewer run: - - 'bioconductor-fletcher2013a >=1.18.0,<1.19.0' - - 'bioconductor-reder >=1.30.0,<1.31.0' - - 'bioconductor-rtn >=2.6.0,<2.7.0' + - 'bioconductor-fletcher2013a >=1.20.0,<1.21.0' + - 'bioconductor-reder >=1.32.0,<1.33.0' + - 'bioconductor-rtn >=2.8.0,<2.9.0' - r-base - r-igraph - r-rcolorbrewer - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-fletcher2013b/post-link.sh b/recipes/bioconductor-fletcher2013b/post-link.sh index 12fbdb6d8669e..29df460366431 100644 --- a/recipes/bioconductor-fletcher2013b/post-link.sh +++ b/recipes/bioconductor-fletcher2013b/post-link.sh @@ -1,11 +1,11 @@ #!/bin/bash -FN="Fletcher2013b_1.18.0.tar.gz" +FN="Fletcher2013b_1.20.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/experiment/src/contrib/Fletcher2013b_1.18.0.tar.gz" - "https://bioarchive.galaxyproject.org/Fletcher2013b_1.18.0.tar.gz" - "https://depot.galaxyproject.org/software/bioconductor-fletcher2013b/bioconductor-fletcher2013b_1.18.0_src_all.tar.gz" + "https://bioconductor.org/packages/3.9/data/experiment/src/contrib/Fletcher2013b_1.20.0.tar.gz" + "https://bioarchive.galaxyproject.org/Fletcher2013b_1.20.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-fletcher2013b/bioconductor-fletcher2013b_1.20.0_src_all.tar.gz" ) -MD5="02757b2d756e7d7fb48641ad9a81aaf4" +MD5="5da665ab15174d34747bfea5b972d48b" # Use a staging area in the conda dir rather than temp dirs, both to avoid # permission issues as well as to have things downloaded in a predictable @@ -16,7 +16,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-flowai/meta.yaml b/recipes/bioconductor-flowai/meta.yaml index d2dce84254956..3c12e06edf5a6 100644 --- a/recipes/bioconductor-flowai/meta.yaml +++ b/recipes/bioconductor-flowai/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.12.7" %} +{% set version = "1.14.0" %} {% set name = "flowAI" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: 8429431151e15433b370279c9d05963183a399a2215d041c6d04d9f613a595e8 + md5: c887df5730d374cb7db2a7ef93524fe8 build: number: 0 rpaths: @@ -20,7 +20,7 @@ build: # Suggests: testthat, shiny requirements: host: - - 'bioconductor-flowcore >=1.48.0,<1.49.0' + - 'bioconductor-flowcore >=1.50.0,<1.51.0' - r-base - r-changepoint - r-ggplot2 @@ -31,7 +31,7 @@ requirements: - r-rmarkdown - r-scales run: - - 'bioconductor-flowcore >=1.48.0,<1.49.0' + - 'bioconductor-flowcore >=1.50.0,<1.51.0' - r-base - r-changepoint - r-ggplot2 diff --git a/recipes/bioconductor-flowbeads/meta.yaml b/recipes/bioconductor-flowbeads/meta.yaml index 6a3d749c131b0..c350a5adc3658 100644 --- a/recipes/bioconductor-flowbeads/meta.yaml +++ b/recipes/bioconductor-flowbeads/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.20.0" %} +{% set version = "1.22.0" %} {% set name = "flowBeads" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: fc8ae810a91f127ff4ad0bbe8ae888ae + md5: aa74d00c38b7ea468cf450e3ab01001e build: number: 0 rpaths: @@ -20,15 +20,15 @@ build: # Suggests: flowViz requirements: host: - - 'bioconductor-biobase >=2.42.0,<2.43.0' - - 'bioconductor-flowcore >=1.48.0,<1.49.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' + - 'bioconductor-flowcore >=1.50.0,<1.51.0' - r-base - r-knitr - r-rrcov - r-xtable run: - - 'bioconductor-biobase >=2.42.0,<2.43.0' - - 'bioconductor-flowcore >=1.48.0,<1.49.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' + - 'bioconductor-flowcore >=1.50.0,<1.51.0' - r-base - r-knitr - r-rrcov diff --git a/recipes/bioconductor-flowbin/meta.yaml b/recipes/bioconductor-flowbin/meta.yaml index 900021f43fbc5..4228f1307e21b 100644 --- a/recipes/bioconductor-flowbin/meta.yaml +++ b/recipes/bioconductor-flowbin/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.18.0" %} +{% set version = "1.20.0" %} {% set name = "flowBin" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 4adf63836576460151cff9e5022bcbec + md5: bb3ae805b33e7df21ecf640f8cd5874f build: number: 0 rpaths: @@ -20,18 +20,18 @@ build: # Suggests: parallel requirements: host: - - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' - - 'bioconductor-flowcore >=1.48.0,<1.49.0' - - 'bioconductor-flowfp >=1.40.0,<1.41.0' - - 'bioconductor-limma >=3.38.0,<3.39.0' + - 'bioconductor-biocgenerics >=0.30.0,<0.31.0' + - 'bioconductor-flowcore >=1.50.0,<1.51.0' + - 'bioconductor-flowfp >=1.42.0,<1.43.0' + - 'bioconductor-limma >=3.40.0,<3.41.0' - r-base - r-class - r-snow run: - - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' - - 'bioconductor-flowcore >=1.48.0,<1.49.0' - - 'bioconductor-flowfp >=1.40.0,<1.41.0' - - 'bioconductor-limma >=3.38.0,<3.39.0' + - 'bioconductor-biocgenerics >=0.30.0,<0.31.0' + - 'bioconductor-flowcore >=1.50.0,<1.51.0' + - 'bioconductor-flowfp >=1.42.0,<1.43.0' + - 'bioconductor-limma >=3.40.0,<3.41.0' - r-base - r-class - r-snow diff --git a/recipes/bioconductor-flowcatchr/meta.yaml b/recipes/bioconductor-flowcatchr/meta.yaml index 4bb6f7d180877..e889e36f0ef02 100644 --- a/recipes/bioconductor-flowcatchr/meta.yaml +++ b/recipes/bioconductor-flowcatchr/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.16.0" %} +{% set version = "1.18.0" %} {% set name = "flowcatchR" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: e6cce882873b92da15dcc28e0bff415d + md5: 9c3d6e42f7c1073343ca5c0854422759 build: number: 0 rpaths: @@ -21,21 +21,23 @@ build: # SystemRequirements: ImageMagick requirements: host: - - 'bioconductor-biocparallel >=1.16.0,<1.17.0' - - 'bioconductor-ebimage >=4.24.0,<4.25.0' + - 'bioconductor-biocparallel >=1.18.0,<1.19.0' + - 'bioconductor-ebimage >=4.26.0,<4.27.0' - r-abind - r-base - r-colorramps - r-plotly - r-shiny + - imagemagick run: - - 'bioconductor-biocparallel >=1.16.0,<1.17.0' - - 'bioconductor-ebimage >=4.24.0,<4.25.0' + - 'bioconductor-biocparallel >=1.18.0,<1.19.0' + - 'bioconductor-ebimage >=4.26.0,<4.27.0' - r-abind - r-base - r-colorramps - r-plotly - r-shiny + - imagemagick test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-flowchic/meta.yaml b/recipes/bioconductor-flowchic/meta.yaml index 03de49d9c1fbb..3a5fc4c317ec2 100644 --- a/recipes/bioconductor-flowchic/meta.yaml +++ b/recipes/bioconductor-flowchic/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.16.0" %} +{% set version = "1.18.0" %} {% set name = "flowCHIC" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 2ed608da9c12a446d191101b5bc30ee7 + md5: 63c39e1f2a05a49e65601574812b1a21 build: number: 0 rpaths: @@ -19,15 +19,15 @@ build: noarch: generic requirements: host: - - 'bioconductor-ebimage >=4.24.0,<4.25.0' - - 'bioconductor-flowcore >=1.48.0,<1.49.0' + - 'bioconductor-ebimage >=4.26.0,<4.27.0' + - 'bioconductor-flowcore >=1.50.0,<1.51.0' - r-base - r-ggplot2 - r-hexbin - r-vegan run: - - 'bioconductor-ebimage >=4.24.0,<4.25.0' - - 'bioconductor-flowcore >=1.48.0,<1.49.0' + - 'bioconductor-ebimage >=4.26.0,<4.27.0' + - 'bioconductor-flowcore >=1.50.0,<1.51.0' - r-base - r-ggplot2 - r-hexbin diff --git a/recipes/bioconductor-flowcl/meta.yaml b/recipes/bioconductor-flowcl/meta.yaml index a6c5aab51b3e5..032da59e63ebd 100644 --- a/recipes/bioconductor-flowcl/meta.yaml +++ b/recipes/bioconductor-flowcl/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.20.1" %} +{% set version = "1.22.0" %} {% set name = "flowCL" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: cb31d847de5e1c0582c3b12d778a1931 + md5: 0144cde0951e98a4f7a8471693807a52 build: number: 0 rpaths: @@ -20,13 +20,13 @@ build: # Suggests: RUnit, BiocGenerics requirements: host: - - 'bioconductor-graph >=1.60.0,<1.61.0' - - 'bioconductor-rgraphviz >=2.26.0,<2.27.0' + - 'bioconductor-graph >=1.62.0,<1.63.0' + - 'bioconductor-rgraphviz >=2.28.0,<2.29.0' - r-base - r-sparql run: - - 'bioconductor-graph >=1.60.0,<1.61.0' - - 'bioconductor-rgraphviz >=2.26.0,<2.27.0' + - 'bioconductor-graph >=1.62.0,<1.63.0' + - 'bioconductor-rgraphviz >=2.28.0,<2.29.0' - r-base - r-sparql test: diff --git a/recipes/bioconductor-flowclean/meta.yaml b/recipes/bioconductor-flowclean/meta.yaml index 03f74063f2e60..4a40740dd39c8 100644 --- a/recipes/bioconductor-flowclean/meta.yaml +++ b/recipes/bioconductor-flowclean/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.20.0" %} +{% set version = "1.22.0" %} {% set name = "flowClean" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 5aee35d8d33660b091d930a61da84b11 + md5: 2b64b477a320b1858313596eb698a805 build: number: 0 rpaths: @@ -20,13 +20,13 @@ build: # Suggests: flowViz, grid, gridExtra requirements: host: - - 'bioconductor-flowcore >=1.48.0,<1.49.0' + - 'bioconductor-flowcore >=1.50.0,<1.51.0' - r-base - r-bit - r-changepoint - r-sfsmisc run: - - 'bioconductor-flowcore >=1.48.0,<1.49.0' + - 'bioconductor-flowcore >=1.50.0,<1.51.0' - r-base - r-bit - r-changepoint diff --git a/recipes/bioconductor-flowclust/meta.yaml b/recipes/bioconductor-flowclust/meta.yaml index 904ddb74a6eff..1657f467a6347 100644 --- a/recipes/bioconductor-flowclust/meta.yaml +++ b/recipes/bioconductor-flowclust/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "3.20.0" %} +{% set version = "3.22.0" %} {% set name = "flowClust" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,32 +10,32 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: a53bc9c6beaa0a76bb4023ade9b38116 + md5: 53d5656c14e1ba05708c2492ec629315 build: number: 0 rpaths: - lib/R/lib/ - lib/ -# Suggests: testthat, flowWorkspace, flowWorkspaceData +# Suggests: testthat, flowWorkspace, flowWorkspaceData, knitr, rmarkdown, openCyto # SystemRequirements: GNU make requirements: host: - - 'bioconductor-biobase >=2.42.0,<2.43.0' - - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' - - 'bioconductor-flowcore >=1.48.0,<1.49.0' - - 'bioconductor-flowviz >=1.46.0,<1.47.0' - - 'bioconductor-graph >=1.60.0,<1.61.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' + - 'bioconductor-biocgenerics >=0.30.0,<0.31.0' + - 'bioconductor-flowcore >=1.50.0,<1.51.0' + - 'bioconductor-flowviz >=1.48.0,<1.49.0' + - 'bioconductor-graph >=1.62.0,<1.63.0' - r-base - r-clue - r-corpcor - r-ellipse - r-mnormt run: - - 'bioconductor-biobase >=2.42.0,<2.43.0' - - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' - - 'bioconductor-flowcore >=1.48.0,<1.49.0' - - 'bioconductor-flowviz >=1.46.0,<1.47.0' - - 'bioconductor-graph >=1.60.0,<1.61.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' + - 'bioconductor-biocgenerics >=0.30.0,<0.31.0' + - 'bioconductor-flowcore >=1.50.0,<1.51.0' + - 'bioconductor-flowviz >=1.48.0,<1.49.0' + - 'bioconductor-graph >=1.62.0,<1.63.0' - r-base - r-clue - r-corpcor diff --git a/recipes/bioconductor-flowcore/meta.yaml b/recipes/bioconductor-flowcore/meta.yaml index 1434c9fd6a80e..118e69aa559ca 100644 --- a/recipes/bioconductor-flowcore/meta.yaml +++ b/recipes/bioconductor-flowcore/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.48.1" %} +{% set version = "1.50.0" %} {% set name = "flowCore" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: f7bc97563b5e3329cabdef957a445d0a8688f6a94ab29144cb3f44107cf39511 + md5: fd5fe2da3e045833d245472bfb1d92df build: number: 0 rpaths: @@ -20,9 +20,9 @@ build: # SystemRequirements: GNU make, C++11 requirements: host: - - 'bioconductor-biobase >=2.42.0,<2.43.0' - - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' - - 'bioconductor-graph >=1.60.0,<1.61.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' + - 'bioconductor-biocgenerics >=0.30.0,<0.31.0' + - 'bioconductor-graph >=1.62.0,<1.63.0' - r-base - 'r-bh >=1.65.0.1' - r-corpcor @@ -31,9 +31,9 @@ requirements: - r-rcpp - r-rrcov run: - - 'bioconductor-biobase >=2.42.0,<2.43.0' - - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' - - 'bioconductor-graph >=1.60.0,<1.61.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' + - 'bioconductor-biocgenerics >=0.30.0,<0.31.0' + - 'bioconductor-graph >=1.62.0,<1.63.0' - r-base - 'r-bh >=1.65.0.1' - r-corpcor diff --git a/recipes/bioconductor-flowcybar/meta.yaml b/recipes/bioconductor-flowcybar/meta.yaml index 8380c3b3eed00..6d561e1b06197 100644 --- a/recipes/bioconductor-flowcybar/meta.yaml +++ b/recipes/bioconductor-flowcybar/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.18.1" %} +{% set version = "1.20.0" %} {% set name = "flowCyBar" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 6a4ece4b4aa8ca2d846ec89e431a9abc + md5: 3a40a7203f7e9b7ea9fd8b14a61e30cc build: number: 0 rpaths: diff --git a/recipes/bioconductor-flowdensity/meta.yaml b/recipes/bioconductor-flowdensity/meta.yaml index cb259823ad9b9..09446f44044e7 100644 --- a/recipes/bioconductor-flowdensity/meta.yaml +++ b/recipes/bioconductor-flowdensity/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.16.1" %} +{% set version = "1.18.0" %} {% set name = "flowDensity" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: 04f786145fff289cfb5921e2a06e74bda1ecf92d9ededae60e1b3e45ca1cbe4e + md5: 8f3b83a8621c85305349c9e6e4a07e73 build: number: 0 rpaths: @@ -20,23 +20,25 @@ build: # SystemRequirements: GEOS (>= 3.2.0);for building from source: GEOS from http://trac.osgeo.org/geos/; GEOS OSX frameworks built by William Kyngesburye at http://www.kyngchaos.com/ may be used for source installs on OSX. requirements: host: - - 'bioconductor-flowcore >=1.48.0,<1.49.0' - - 'bioconductor-flowworkspace >=3.30.0,<3.31.0' + - 'bioconductor-flowcore >=1.50.0,<1.51.0' + - 'bioconductor-flowworkspace >=3.32.0,<3.33.0' - r-base - r-car - r-gplots - r-rfoc - r-rgeos - r-sp + - geos >=3.2.0 run: - - 'bioconductor-flowcore >=1.48.0,<1.49.0' - - 'bioconductor-flowworkspace >=3.30.0,<3.31.0' + - 'bioconductor-flowcore >=1.50.0,<1.51.0' + - 'bioconductor-flowworkspace >=3.32.0,<3.33.0' - r-base - r-car - r-gplots - r-rfoc - r-rgeos - r-sp + - geos >=3.2.0 test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-flowfit/meta.yaml b/recipes/bioconductor-flowfit/meta.yaml index 9e3082c64eb72..18bc12ddb7d33 100644 --- a/recipes/bioconductor-flowfit/meta.yaml +++ b/recipes/bioconductor-flowfit/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.20.1" %} +{% set version = "1.22.0" %} {% set name = "flowFit" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 175d3d9b13e2263b591cbf40ccbbae37 + md5: bebb60e166df9b96234595340d3ce45e build: number: 0 rpaths: @@ -20,15 +20,15 @@ build: # Suggests: flowFitExampleData requirements: host: - - 'bioconductor-flowcore >=1.48.0,<1.49.0' - - 'bioconductor-flowviz >=1.46.0,<1.47.0' + - 'bioconductor-flowcore >=1.50.0,<1.51.0' + - 'bioconductor-flowviz >=1.48.0,<1.49.0' - r-base - r-gplots - r-kza - r-minpack.lm run: - - 'bioconductor-flowcore >=1.48.0,<1.49.0' - - 'bioconductor-flowviz >=1.46.0,<1.47.0' + - 'bioconductor-flowcore >=1.50.0,<1.51.0' + - 'bioconductor-flowviz >=1.48.0,<1.49.0' - r-base - r-gplots - r-kza diff --git a/recipes/bioconductor-flowfitexampledata/meta.yaml b/recipes/bioconductor-flowfitexampledata/meta.yaml index 8f31f2e28536e..af992b41ef0bc 100644 --- a/recipes/bioconductor-flowfitexampledata/meta.yaml +++ b/recipes/bioconductor-flowfitexampledata/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.18.0" %} +{% set version = "1.20.0" %} {% set name = "flowFitExampleData" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 1ffa4e31d23b8df9f4df96504a893639 + md5: d5627c525cb0ab48377638d0af2e8c3c build: number: 0 rpaths: @@ -19,12 +19,12 @@ build: noarch: generic requirements: host: - - 'bioconductor-flowcore >=1.48.0,<1.49.0' + - 'bioconductor-flowcore >=1.50.0,<1.51.0' - r-base run: - - 'bioconductor-flowcore >=1.48.0,<1.49.0' + - 'bioconductor-flowcore >=1.50.0,<1.51.0' - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-flowfitexampledata/post-link.sh b/recipes/bioconductor-flowfitexampledata/post-link.sh index 2b88b27a8aaa2..a43ffc8891c3d 100644 --- a/recipes/bioconductor-flowfitexampledata/post-link.sh +++ b/recipes/bioconductor-flowfitexampledata/post-link.sh @@ -1,11 +1,11 @@ #!/bin/bash -FN="flowFitExampleData_1.18.0.tar.gz" +FN="flowFitExampleData_1.20.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/experiment/src/contrib/flowFitExampleData_1.18.0.tar.gz" - "https://bioarchive.galaxyproject.org/flowFitExampleData_1.18.0.tar.gz" - "https://depot.galaxyproject.org/software/bioconductor-flowfitexampledata/bioconductor-flowfitexampledata_1.18.0_src_all.tar.gz" + "https://bioconductor.org/packages/3.9/data/experiment/src/contrib/flowFitExampleData_1.20.0.tar.gz" + "https://bioarchive.galaxyproject.org/flowFitExampleData_1.20.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-flowfitexampledata/bioconductor-flowfitexampledata_1.20.0_src_all.tar.gz" ) -MD5="1ffa4e31d23b8df9f4df96504a893639" +MD5="d5627c525cb0ab48377638d0af2e8c3c" # Use a staging area in the conda dir rather than temp dirs, both to avoid # permission issues as well as to have things downloaded in a predictable @@ -16,7 +16,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-flowfp/meta.yaml b/recipes/bioconductor-flowfp/meta.yaml index 348de7bb20be9..f2080bae7fd3e 100644 --- a/recipes/bioconductor-flowfp/meta.yaml +++ b/recipes/bioconductor-flowfp/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.40.0" %} +{% set version = "1.42.0" %} {% set name = "flowFP" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: d3a2bfd5a4e4b74002838cabd1b26066 + md5: 42394f73038de936b2d9ad3b82bceee4 build: number: 0 rpaths: @@ -19,16 +19,16 @@ build: # Suggests: RUnit requirements: host: - - 'bioconductor-biobase >=2.42.0,<2.43.0' - - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' - - 'bioconductor-flowcore >=1.48.0,<1.49.0' - - 'bioconductor-flowviz >=1.46.0,<1.47.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' + - 'bioconductor-biocgenerics >=0.30.0,<0.31.0' + - 'bioconductor-flowcore >=1.50.0,<1.51.0' + - 'bioconductor-flowviz >=1.48.0,<1.49.0' - r-base run: - - 'bioconductor-biobase >=2.42.0,<2.43.0' - - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' - - 'bioconductor-flowcore >=1.48.0,<1.49.0' - - 'bioconductor-flowviz >=1.46.0,<1.47.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' + - 'bioconductor-biocgenerics >=0.30.0,<0.31.0' + - 'bioconductor-flowcore >=1.50.0,<1.51.0' + - 'bioconductor-flowviz >=1.48.0,<1.49.0' - r-base build: - {{ compiler('c') }} diff --git a/recipes/bioconductor-flowmap/meta.yaml b/recipes/bioconductor-flowmap/meta.yaml index e438e335d64f8..a6efb5832047a 100644 --- a/recipes/bioconductor-flowmap/meta.yaml +++ b/recipes/bioconductor-flowmap/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.20.1" %} +{% set version = "1.22.0" %} {% set name = "flowMap" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: b92e0c86d27f34410419826317e8277f + md5: 1956f3a204de01fecfbeb7ad53d2f824 build: number: 0 rpaths: diff --git a/recipes/bioconductor-flowmatch/meta.yaml b/recipes/bioconductor-flowmatch/meta.yaml index b607b5d18ebb0..8ad5c98196721 100644 --- a/recipes/bioconductor-flowmatch/meta.yaml +++ b/recipes/bioconductor-flowmatch/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.18.0" %} +{% set version = "1.20.0" %} {% set name = "flowMatch" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 7d6d3eea6d0f74416629b825d8bcd6a2 + md5: a9f89f20a689dcf0acfb8f6f72fe47e8 build: number: 0 rpaths: @@ -19,13 +19,13 @@ build: # Suggests: healthyFlowData requirements: host: - - 'bioconductor-biobase >=2.42.0,<2.43.0' - - 'bioconductor-flowcore >=1.48.0,<1.49.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' + - 'bioconductor-flowcore >=1.50.0,<1.51.0' - r-base - 'r-rcpp >=0.11.0' run: - - 'bioconductor-biobase >=2.42.0,<2.43.0' - - 'bioconductor-flowcore >=1.48.0,<1.49.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' + - 'bioconductor-flowcore >=1.50.0,<1.51.0' - r-base - 'r-rcpp >=0.11.0' build: diff --git a/recipes/bioconductor-flowmeans/meta.yaml b/recipes/bioconductor-flowmeans/meta.yaml index c7c8ae401ae63..60820f0c34b88 100644 --- a/recipes/bioconductor-flowmeans/meta.yaml +++ b/recipes/bioconductor-flowmeans/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.42.1" %} +{% set version = "1.44.0" %} {% set name = "flowMeans" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 0b5ac87aa94096b505c62a49f57a0252 + md5: 26cf203fb97eed85439fc524aa63c39a build: number: 0 rpaths: @@ -19,14 +19,14 @@ build: noarch: generic requirements: host: - - 'bioconductor-biobase >=2.42.0,<2.43.0' - - 'bioconductor-flowcore >=1.48.0,<1.49.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' + - 'bioconductor-flowcore >=1.50.0,<1.51.0' - r-base - r-feature - r-rrcov run: - - 'bioconductor-biobase >=2.42.0,<2.43.0' - - 'bioconductor-flowcore >=1.48.0,<1.49.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' + - 'bioconductor-flowcore >=1.50.0,<1.51.0' - r-base - r-feature - r-rrcov @@ -37,7 +37,7 @@ about: home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: Artistic-2.0 summary: 'Identifies cell populations in Flow Cytometry data using non-parametric clustering and segmented-regression-based change point detection. Note: R 2.11.0 or newer is required.' - extra: container: - extended-base: True + extended-base: true + diff --git a/recipes/bioconductor-flowmerge/meta.yaml b/recipes/bioconductor-flowmerge/meta.yaml index b81395b72ecb1..92dc2c511586e 100644 --- a/recipes/bioconductor-flowmerge/meta.yaml +++ b/recipes/bioconductor-flowmerge/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "2.30.1" %} +{% set version = "2.32.0" %} {% set name = "flowMerge" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,29 +10,30 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 6594ae374303f35932dca812d021147b + md5: aa5796d15c5bbe1e10f1d1204cafe657 build: number: 0 rpaths: - lib/R/lib/ - lib/ noarch: generic +# Suggests: knitr, rmarkdown requirements: host: - - 'bioconductor-flowclust >=3.20.0,<3.21.0' - - 'bioconductor-flowcore >=1.48.0,<1.49.0' - - 'bioconductor-graph >=1.60.0,<1.61.0' - - 'bioconductor-rgraphviz >=2.26.0,<2.27.0' + - 'bioconductor-flowclust >=3.22.0,<3.23.0' + - 'bioconductor-flowcore >=1.50.0,<1.51.0' + - 'bioconductor-graph >=1.62.0,<1.63.0' + - 'bioconductor-rgraphviz >=2.28.0,<2.29.0' - r-base - r-feature - r-foreach - r-rrcov - r-snow run: - - 'bioconductor-flowclust >=3.20.0,<3.21.0' - - 'bioconductor-flowcore >=1.48.0,<1.49.0' - - 'bioconductor-graph >=1.60.0,<1.61.0' - - 'bioconductor-rgraphviz >=2.26.0,<2.27.0' + - 'bioconductor-flowclust >=3.22.0,<3.23.0' + - 'bioconductor-flowcore >=1.50.0,<1.51.0' + - 'bioconductor-graph >=1.62.0,<1.63.0' + - 'bioconductor-rgraphviz >=2.28.0,<2.29.0' - r-base - r-feature - r-foreach @@ -45,7 +46,7 @@ about: home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: Artistic-2.0 summary: 'Merging of mixture components for model-based automated gating of flow cytometry data using the flowClust framework. Note: users should have a working copy of flowClust 2.0 installed.' - extra: container: - extended-base: True + extended-base: true + diff --git a/recipes/bioconductor-flowpeaks/meta.yaml b/recipes/bioconductor-flowpeaks/meta.yaml index 6e0902054c1fc..7e495ad5914a0 100644 --- a/recipes/bioconductor-flowpeaks/meta.yaml +++ b/recipes/bioconductor-flowpeaks/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.28.1" %} +{% set version = "1.30.0" %} {% set name = "flowPeaks" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: 26527ccb6b7130aebf7adff190b969dd659e72692f84d23119ec2568965de821 + md5: 8af65bebd3bc3545a27d8f0d9da6c741 build: number: 0 rpaths: @@ -20,11 +20,9 @@ build: requirements: host: - r-base - - openblas - gsl run: - r-base - - openblas - gsl build: - {{ compiler('c') }} diff --git a/recipes/bioconductor-flowploidy/meta.yaml b/recipes/bioconductor-flowploidy/meta.yaml index cc638d088ec0c..b0293ff578585 100644 --- a/recipes/bioconductor-flowploidy/meta.yaml +++ b/recipes/bioconductor-flowploidy/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.8.0" %} +{% set version = "1.10.0" %} {% set name = "flowPloidy" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 4866ee71a93962a34151e674a0a26895 + md5: 8e4270702378029e598d7b82be4177a4 build: number: 0 rpaths: @@ -20,7 +20,7 @@ build: # Suggests: flowPloidyData, testthat requirements: host: - - 'bioconductor-flowcore >=1.48.0,<1.49.0' + - 'bioconductor-flowcore >=1.50.0,<1.51.0' - r-base - r-car - r-catools @@ -29,7 +29,7 @@ requirements: - r-rmarkdown - r-shiny run: - - 'bioconductor-flowcore >=1.48.0,<1.49.0' + - 'bioconductor-flowcore >=1.50.0,<1.51.0' - r-base - r-car - r-catools diff --git a/recipes/bioconductor-flowploidydata/meta.yaml b/recipes/bioconductor-flowploidydata/meta.yaml index 3ab1f2f651adf..35b30d51475ea 100644 --- a/recipes/bioconductor-flowploidydata/meta.yaml +++ b/recipes/bioconductor-flowploidydata/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.8.0" %} +{% set version = "1.10.0" %} {% set name = "flowPloidyData" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 86881aa99d32cc1ce20304591cb599ab + md5: e207b89cdef6679d0ee10063a582c930 build: number: 0 rpaths: @@ -23,7 +23,7 @@ requirements: - r-base run: - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-flowploidydata/post-link.sh b/recipes/bioconductor-flowploidydata/post-link.sh index 5a405567262a9..c60bfa5265ddb 100644 --- a/recipes/bioconductor-flowploidydata/post-link.sh +++ b/recipes/bioconductor-flowploidydata/post-link.sh @@ -1,11 +1,11 @@ #!/bin/bash -FN="flowPloidyData_1.8.0.tar.gz" +FN="flowPloidyData_1.10.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/experiment/src/contrib/flowPloidyData_1.8.0.tar.gz" - "https://bioarchive.galaxyproject.org/flowPloidyData_1.8.0.tar.gz" - "https://depot.galaxyproject.org/software/bioconductor-flowploidydata/bioconductor-flowploidydata_1.8.0_src_all.tar.gz" + "https://bioconductor.org/packages/3.9/data/experiment/src/contrib/flowPloidyData_1.10.0.tar.gz" + "https://bioarchive.galaxyproject.org/flowPloidyData_1.10.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-flowploidydata/bioconductor-flowploidydata_1.10.0_src_all.tar.gz" ) -MD5="86881aa99d32cc1ce20304591cb599ab" +MD5="e207b89cdef6679d0ee10063a582c930" # Use a staging area in the conda dir rather than temp dirs, both to avoid # permission issues as well as to have things downloaded in a predictable @@ -16,7 +16,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-flowplots/meta.yaml b/recipes/bioconductor-flowplots/meta.yaml index ac6f1654ccf60..e5d64b6b49503 100644 --- a/recipes/bioconductor-flowplots/meta.yaml +++ b/recipes/bioconductor-flowplots/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.30.1" %} +{% set version = "1.32.0" %} {% set name = "flowPlots" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 99408a38d1bddc7dca85ef37e60d4b27 + md5: 7006726f05d103ef51ab895d105c2b5e build: number: 0 rpaths: diff --git a/recipes/bioconductor-flowqb/meta.yaml b/recipes/bioconductor-flowqb/meta.yaml index 1e0970ec187fa..74929b0101b88 100644 --- a/recipes/bioconductor-flowqb/meta.yaml +++ b/recipes/bioconductor-flowqb/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "2.10.1" %} +{% set version = "2.11.1" %} {% set name = "flowQB" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: a324990ad4dec51636d4d825b3161215 + md5: 3326238deb71a39ac4cfa69c29dc76c1 build: number: 0 rpaths: @@ -20,11 +20,11 @@ build: # Suggests: flowQBData, FlowRepositoryR, xlsx, RUnit, BiocGenerics requirements: host: - - 'bioconductor-flowcore >=1.48.0,<1.49.0' + - 'bioconductor-flowcore >=1.50.0,<1.51.0' - r-base - r-extremevalues run: - - 'bioconductor-flowcore >=1.48.0,<1.49.0' + - 'bioconductor-flowcore >=1.50.0,<1.51.0' - r-base - r-extremevalues test: diff --git a/recipes/bioconductor-flowqbdata/meta.yaml b/recipes/bioconductor-flowqbdata/meta.yaml index 2e4b39b9e1ecb..d77b2f93528b9 100644 --- a/recipes/bioconductor-flowqbdata/meta.yaml +++ b/recipes/bioconductor-flowqbdata/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.8.0" %} +{% set version = "1.10.0" %} {% set name = "flowQBData" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 4692d5e5b2c714b9b1d55636c65b90d4 + md5: e5d94c8fb66f811c34a7a92ef607f20d build: number: 0 rpaths: @@ -23,7 +23,7 @@ requirements: - r-base run: - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-flowqbdata/post-link.sh b/recipes/bioconductor-flowqbdata/post-link.sh index 13b3ba3f63116..4d7d117294267 100644 --- a/recipes/bioconductor-flowqbdata/post-link.sh +++ b/recipes/bioconductor-flowqbdata/post-link.sh @@ -1,11 +1,11 @@ #!/bin/bash -FN="flowQBData_1.8.0.tar.gz" +FN="flowQBData_1.10.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/experiment/src/contrib/flowQBData_1.8.0.tar.gz" - "https://bioarchive.galaxyproject.org/flowQBData_1.8.0.tar.gz" - "https://depot.galaxyproject.org/software/bioconductor-flowqbdata/bioconductor-flowqbdata_1.8.0_src_all.tar.gz" + "https://bioconductor.org/packages/3.9/data/experiment/src/contrib/flowQBData_1.10.0.tar.gz" + "https://bioarchive.galaxyproject.org/flowQBData_1.10.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-flowqbdata/bioconductor-flowqbdata_1.10.0_src_all.tar.gz" ) -MD5="4692d5e5b2c714b9b1d55636c65b90d4" +MD5="e5d94c8fb66f811c34a7a92ef607f20d" # Use a staging area in the conda dir rather than temp dirs, both to avoid # permission issues as well as to have things downloaded in a predictable @@ -16,7 +16,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-flowrepositoryr/meta.yaml b/recipes/bioconductor-flowrepositoryr/meta.yaml index be416c824dc00..399c4294982ce 100644 --- a/recipes/bioconductor-flowrepositoryr/meta.yaml +++ b/recipes/bioconductor-flowrepositoryr/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.14.1" %} +{% set version = "1.16.0" %} {% set name = "FlowRepositoryR" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: e634ffe0fd712764deadd08271b7bc2e + md5: 412477b926637675d6c9b2dbd0d07c1f build: number: 0 rpaths: diff --git a/recipes/bioconductor-flowsom/meta.yaml b/recipes/bioconductor-flowsom/meta.yaml index 15c43ff967d41..e8990fe77c7f9 100644 --- a/recipes/bioconductor-flowsom/meta.yaml +++ b/recipes/bioconductor-flowsom/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.14.1" %} +{% set version = "1.16.0" %} {% set name = "FlowSOM" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: 18f0d8e895305e0d3db91133aefad7bdfe7e5487ecf3a7808167932fc7931ee8 + md5: b28182a7c8e7d0a062c93d7e709ab789 build: number: 0 rpaths: @@ -19,19 +19,19 @@ build: # Suggests: BiocStyle requirements: host: - - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' - - 'bioconductor-consensusclusterplus >=1.46.0,<1.47.0' - - 'bioconductor-flowcore >=1.48.0,<1.49.0' - - 'bioconductor-flowutils >=1.46.0,<1.47.0' + - 'bioconductor-biocgenerics >=0.30.0,<0.31.0' + - 'bioconductor-consensusclusterplus >=1.48.0,<1.49.0' + - 'bioconductor-flowcore >=1.50.0,<1.51.0' + - 'bioconductor-flowutils >=1.48.0,<1.49.0' - r-base - r-igraph - r-tsne - r-xml run: - - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' - - 'bioconductor-consensusclusterplus >=1.46.0,<1.47.0' - - 'bioconductor-flowcore >=1.48.0,<1.49.0' - - 'bioconductor-flowutils >=1.46.0,<1.47.0' + - 'bioconductor-biocgenerics >=0.30.0,<0.31.0' + - 'bioconductor-consensusclusterplus >=1.48.0,<1.49.0' + - 'bioconductor-flowcore >=1.50.0,<1.51.0' + - 'bioconductor-flowutils >=1.48.0,<1.49.0' - r-base - r-igraph - r-tsne diff --git a/recipes/bioconductor-flowsorted.blood.450k/meta.yaml b/recipes/bioconductor-flowsorted.blood.450k/meta.yaml index 49a0bcb7ee331..b2d1c9e768aac 100644 --- a/recipes/bioconductor-flowsorted.blood.450k/meta.yaml +++ b/recipes/bioconductor-flowsorted.blood.450k/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.20.0" %} +{% set version = "1.22.0" %} {% set name = "FlowSorted.Blood.450k" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: de53e97b7b4dd6b5930d22cef0cf7a64 + md5: d2a79cbca36828a67db9655e7e23e059 build: number: 0 rpaths: @@ -19,12 +19,12 @@ build: noarch: generic requirements: host: - - 'bioconductor-minfi >=1.28.0,<1.29.0' + - 'bioconductor-minfi >=1.30.0,<1.31.0' - r-base run: - - 'bioconductor-minfi >=1.28.0,<1.29.0' + - 'bioconductor-minfi >=1.30.0,<1.31.0' - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-flowsorted.blood.450k/post-link.sh b/recipes/bioconductor-flowsorted.blood.450k/post-link.sh index 00b542a759cb3..9e1faa7cefcca 100644 --- a/recipes/bioconductor-flowsorted.blood.450k/post-link.sh +++ b/recipes/bioconductor-flowsorted.blood.450k/post-link.sh @@ -1,11 +1,11 @@ #!/bin/bash -FN="FlowSorted.Blood.450k_1.20.0.tar.gz" +FN="FlowSorted.Blood.450k_1.22.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/experiment/src/contrib/FlowSorted.Blood.450k_1.20.0.tar.gz" - "https://bioarchive.galaxyproject.org/FlowSorted.Blood.450k_1.20.0.tar.gz" - "https://depot.galaxyproject.org/software/bioconductor-flowsorted.blood.450k/bioconductor-flowsorted.blood.450k_1.20.0_src_all.tar.gz" + "https://bioconductor.org/packages/3.9/data/experiment/src/contrib/FlowSorted.Blood.450k_1.22.0.tar.gz" + "https://bioarchive.galaxyproject.org/FlowSorted.Blood.450k_1.22.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-flowsorted.blood.450k/bioconductor-flowsorted.blood.450k_1.22.0_src_all.tar.gz" ) -MD5="de53e97b7b4dd6b5930d22cef0cf7a64" +MD5="d2a79cbca36828a67db9655e7e23e059" # Use a staging area in the conda dir rather than temp dirs, both to avoid # permission issues as well as to have things downloaded in a predictable @@ -16,7 +16,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-flowsorted.blood.epic/meta.yaml b/recipes/bioconductor-flowsorted.blood.epic/meta.yaml index ac8dbc36d373b..5ce566669829b 100644 --- a/recipes/bioconductor-flowsorted.blood.epic/meta.yaml +++ b/recipes/bioconductor-flowsorted.blood.epic/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.0.0" %} +{% set version = "1.2.0" %} {% set name = "FlowSorted.Blood.EPIC" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 8d567155aab1d5b96ad468d0f0632acd + md5: 4e6f8a48f8d8504c3027429fb164eb98 build: number: 0 rpaths: @@ -20,26 +20,26 @@ build: # Suggests: knitr, rmarkdown, EpiDISH, FlowSorted.Blood.450k(>= 1.0.1), FlowSorted.CordBlood.450k, FlowSorted.CordBloodNorway.450k, testthat, IlluminaHumanMethylation450kmanifest(>= 0.2.0), IlluminaHumanMethylation450kanno.ilmn12.hg19(>= 0.2.1), IlluminaHumanMethylationEPICanno.ilm10b2.hg19 requirements: host: - - 'bioconductor-experimenthub >=1.8.0,<1.9.0' - - 'bioconductor-genefilter >=1.64.0,<1.65.0' + - 'bioconductor-experimenthub >=1.10.0,<1.11.0' + - 'bioconductor-genefilter >=1.66.0,<1.67.0' - 'bioconductor-illuminahumanmethylationepicanno.ilm10b4.hg19 >=0.6.0,<0.7.0' - - 'bioconductor-minfi >=1.28.0,<1.29.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' - - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' + - 'bioconductor-minfi >=1.30.0,<1.31.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' + - 'bioconductor-summarizedexperiment >=1.14.0,<1.15.0' - r-base - r-nlme - r-quadprog run: - - 'bioconductor-experimenthub >=1.8.0,<1.9.0' - - 'bioconductor-genefilter >=1.64.0,<1.65.0' + - 'bioconductor-experimenthub >=1.10.0,<1.11.0' + - 'bioconductor-genefilter >=1.66.0,<1.67.0' - 'bioconductor-illuminahumanmethylationepicanno.ilm10b4.hg19 >=0.6.0,<0.7.0' - - 'bioconductor-minfi >=1.28.0,<1.29.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' - - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' + - 'bioconductor-minfi >=1.30.0,<1.31.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' + - 'bioconductor-summarizedexperiment >=1.14.0,<1.15.0' - r-base - r-nlme - r-quadprog - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-flowsorted.blood.epic/post-link.sh b/recipes/bioconductor-flowsorted.blood.epic/post-link.sh index 73fbbc3d3ebae..551376e03a159 100644 --- a/recipes/bioconductor-flowsorted.blood.epic/post-link.sh +++ b/recipes/bioconductor-flowsorted.blood.epic/post-link.sh @@ -1,11 +1,11 @@ #!/bin/bash -FN="FlowSorted.Blood.EPIC_1.0.0.tar.gz" +FN="FlowSorted.Blood.EPIC_1.2.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/experiment/src/contrib/FlowSorted.Blood.EPIC_1.0.0.tar.gz" - "https://bioarchive.galaxyproject.org/FlowSorted.Blood.EPIC_1.0.0.tar.gz" - "https://depot.galaxyproject.org/software/bioconductor-flowsorted.blood.epic/bioconductor-flowsorted.blood.epic_1.0.0_src_all.tar.gz" + "https://bioconductor.org/packages/3.9/data/experiment/src/contrib/FlowSorted.Blood.EPIC_1.2.0.tar.gz" + "https://bioarchive.galaxyproject.org/FlowSorted.Blood.EPIC_1.2.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-flowsorted.blood.epic/bioconductor-flowsorted.blood.epic_1.2.0_src_all.tar.gz" ) -MD5="8d567155aab1d5b96ad468d0f0632acd" +MD5="4e6f8a48f8d8504c3027429fb164eb98" # Use a staging area in the conda dir rather than temp dirs, both to avoid # permission issues as well as to have things downloaded in a predictable @@ -16,7 +16,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-flowsorted.cordblood.450k/meta.yaml b/recipes/bioconductor-flowsorted.cordblood.450k/meta.yaml index 13db95bdadde7..2553aca8a0148 100644 --- a/recipes/bioconductor-flowsorted.cordblood.450k/meta.yaml +++ b/recipes/bioconductor-flowsorted.cordblood.450k/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.10.0" %} +{% set version = "1.12.0" %} {% set name = "FlowSorted.CordBlood.450k" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,21 +10,21 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 5a049ecac95e4b77ea0d497838edb2e0 + md5: 35c1420b23f1016c0953af3f67a48e07 build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ noarch: generic requirements: host: - - 'bioconductor-minfi >=1.28.0,<1.29.0' + - 'bioconductor-minfi >=1.30.0,<1.31.0' - r-base run: - - 'bioconductor-minfi >=1.28.0,<1.29.0' + - 'bioconductor-minfi >=1.30.0,<1.31.0' - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-flowsorted.cordblood.450k/post-link.sh b/recipes/bioconductor-flowsorted.cordblood.450k/post-link.sh index 1c3e500ac45ed..b8560d8858d90 100644 --- a/recipes/bioconductor-flowsorted.cordblood.450k/post-link.sh +++ b/recipes/bioconductor-flowsorted.cordblood.450k/post-link.sh @@ -1,11 +1,11 @@ #!/bin/bash -FN="FlowSorted.CordBlood.450k_1.10.0.tar.gz" +FN="FlowSorted.CordBlood.450k_1.12.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/experiment/src/contrib/FlowSorted.CordBlood.450k_1.10.0.tar.gz" - "https://bioarchive.galaxyproject.org/FlowSorted.CordBlood.450k_1.10.0.tar.gz" - "https://depot.galaxyproject.org/software/bioconductor-flowsorted.cordblood.450k/bioconductor-flowsorted.cordblood.450k_1.10.0_src_all.tar.gz" + "https://bioconductor.org/packages/3.9/data/experiment/src/contrib/FlowSorted.CordBlood.450k_1.12.0.tar.gz" + "https://bioarchive.galaxyproject.org/FlowSorted.CordBlood.450k_1.12.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-flowsorted.cordblood.450k/bioconductor-flowsorted.cordblood.450k_1.12.0_src_all.tar.gz" ) -MD5="5a049ecac95e4b77ea0d497838edb2e0" +MD5="35c1420b23f1016c0953af3f67a48e07" # Use a staging area in the conda dir rather than temp dirs, both to avoid # permission issues as well as to have things downloaded in a predictable @@ -16,7 +16,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-flowsorted.cordbloodcombined.450k/meta.yaml b/recipes/bioconductor-flowsorted.cordbloodcombined.450k/meta.yaml new file mode 100644 index 0000000000000..3d53291d71cb8 --- /dev/null +++ b/recipes/bioconductor-flowsorted.cordbloodcombined.450k/meta.yaml @@ -0,0 +1,46 @@ +{% set version = "1.0.0" %} +{% set name = "FlowSorted.CordBloodCombined.450k" %} +{% set bioc = "3.9" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: 526f5a9879e6ae163dcbea71951cd91c +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: knitr, rmarkdown, testthat, IlluminaHumanMethylation450kmanifest(>= 0.2.0), IlluminaHumanMethylationEPICanno.ilm10b2.hg19 +requirements: + host: + - 'bioconductor-experimenthub >=1.10.0,<1.11.0' + - 'bioconductor-flowsorted.blood.epic >=1.2.0,<1.3.0' + - 'bioconductor-illuminahumanmethylation450kanno.ilmn12.hg19 >=0.6.0,<0.7.0' + - 'bioconductor-illuminahumanmethylationepicanno.ilm10b4.hg19 >=0.6.0,<0.7.0' + - 'bioconductor-minfi >=1.30.0,<1.31.0' + - 'bioconductor-summarizedexperiment >=1.14.0,<1.15.0' + - r-base + run: + - 'bioconductor-experimenthub >=1.10.0,<1.11.0' + - 'bioconductor-flowsorted.blood.epic >=1.2.0,<1.3.0' + - 'bioconductor-illuminahumanmethylation450kanno.ilmn12.hg19 >=0.6.0,<0.7.0' + - 'bioconductor-illuminahumanmethylationepicanno.ilm10b4.hg19 >=0.6.0,<0.7.0' + - 'bioconductor-minfi >=1.30.0,<1.31.0' + - 'bioconductor-summarizedexperiment >=1.14.0,<1.15.0' + - r-base + - curl +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html' + license: GPL-3 + summary: 'Raw data objects to be used for umbilical cord blood cell proportion estimation in minfi and similar packages. The FlowSorted.CordBloodCombined.450k object is based in samples assayed by Bakulski et al, Gervin et al., de Goede et al., and Lin et al.' + diff --git a/recipes/bioconductor-flowsorted.cordbloodcombined.450k/post-link.sh b/recipes/bioconductor-flowsorted.cordbloodcombined.450k/post-link.sh new file mode 100644 index 0000000000000..af235037c9d3c --- /dev/null +++ b/recipes/bioconductor-flowsorted.cordbloodcombined.450k/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="FlowSorted.CordBloodCombined.450k_1.0.0.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.9/data/experiment/src/contrib/FlowSorted.CordBloodCombined.450k_1.0.0.tar.gz" + "https://bioarchive.galaxyproject.org/FlowSorted.CordBloodCombined.450k_1.0.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-flowsorted.cordbloodcombined.450k/bioconductor-flowsorted.cordbloodcombined.450k_1.0.0_src_all.tar.gz" +) +MD5="526f5a9879e6ae163dcbea71951cd91c" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + curl $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-flowsorted.cordbloodcombined.450k/pre-unlink.sh b/recipes/bioconductor-flowsorted.cordbloodcombined.450k/pre-unlink.sh new file mode 100644 index 0000000000000..5ee46736b73d2 --- /dev/null +++ b/recipes/bioconductor-flowsorted.cordbloodcombined.450k/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ FlowSorted.CordBloodCombined.450k diff --git a/recipes/bioconductor-flowsorted.cordbloodnorway.450k/meta.yaml b/recipes/bioconductor-flowsorted.cordbloodnorway.450k/meta.yaml index 6153184cdba8c..3f64e57a79159 100644 --- a/recipes/bioconductor-flowsorted.cordbloodnorway.450k/meta.yaml +++ b/recipes/bioconductor-flowsorted.cordbloodnorway.450k/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.8.0" %} +{% set version = "1.10.0" %} {% set name = "FlowSorted.CordBloodNorway.450k" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: f8a375e9ed900e593e944cbd95f13750 + md5: 83e0a618318a466dbb7df19db7340909 build: number: 0 rpaths: @@ -19,12 +19,12 @@ build: noarch: generic requirements: host: - - 'bioconductor-minfi >=1.28.0,<1.29.0' + - 'bioconductor-minfi >=1.30.0,<1.31.0' - r-base run: - - 'bioconductor-minfi >=1.28.0,<1.29.0' + - 'bioconductor-minfi >=1.30.0,<1.31.0' - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-flowsorted.cordbloodnorway.450k/post-link.sh b/recipes/bioconductor-flowsorted.cordbloodnorway.450k/post-link.sh index a223416d99d8e..48207917a5635 100644 --- a/recipes/bioconductor-flowsorted.cordbloodnorway.450k/post-link.sh +++ b/recipes/bioconductor-flowsorted.cordbloodnorway.450k/post-link.sh @@ -1,11 +1,11 @@ #!/bin/bash -FN="FlowSorted.CordBloodNorway.450k_1.8.0.tar.gz" +FN="FlowSorted.CordBloodNorway.450k_1.10.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/experiment/src/contrib/FlowSorted.CordBloodNorway.450k_1.8.0.tar.gz" - "https://bioarchive.galaxyproject.org/FlowSorted.CordBloodNorway.450k_1.8.0.tar.gz" - "https://depot.galaxyproject.org/software/bioconductor-flowsorted.cordbloodnorway.450k/bioconductor-flowsorted.cordbloodnorway.450k_1.8.0_src_all.tar.gz" + "https://bioconductor.org/packages/3.9/data/experiment/src/contrib/FlowSorted.CordBloodNorway.450k_1.10.0.tar.gz" + "https://bioarchive.galaxyproject.org/FlowSorted.CordBloodNorway.450k_1.10.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-flowsorted.cordbloodnorway.450k/bioconductor-flowsorted.cordbloodnorway.450k_1.10.0_src_all.tar.gz" ) -MD5="f8a375e9ed900e593e944cbd95f13750" +MD5="83e0a618318a466dbb7df19db7340909" # Use a staging area in the conda dir rather than temp dirs, both to avoid # permission issues as well as to have things downloaded in a predictable @@ -16,7 +16,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-flowsorted.dlpfc.450k/meta.yaml b/recipes/bioconductor-flowsorted.dlpfc.450k/meta.yaml index 8ae27298dad6b..f1f015780513c 100644 --- a/recipes/bioconductor-flowsorted.dlpfc.450k/meta.yaml +++ b/recipes/bioconductor-flowsorted.dlpfc.450k/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.18.0" %} +{% set version = "1.20.0" %} {% set name = "FlowSorted.DLPFC.450k" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: de071e70f511a405aad3ee9b3196fd43 + md5: 2079268ebe8b094cc960b96c9ab94876 build: number: 0 rpaths: @@ -19,12 +19,12 @@ build: noarch: generic requirements: host: - - 'bioconductor-minfi >=1.28.0,<1.29.0' + - 'bioconductor-minfi >=1.30.0,<1.31.0' - r-base run: - - 'bioconductor-minfi >=1.28.0,<1.29.0' + - 'bioconductor-minfi >=1.30.0,<1.31.0' - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-flowsorted.dlpfc.450k/post-link.sh b/recipes/bioconductor-flowsorted.dlpfc.450k/post-link.sh index 9c455116de7f5..00e3b87b053e8 100644 --- a/recipes/bioconductor-flowsorted.dlpfc.450k/post-link.sh +++ b/recipes/bioconductor-flowsorted.dlpfc.450k/post-link.sh @@ -1,11 +1,11 @@ #!/bin/bash -FN="FlowSorted.DLPFC.450k_1.18.0.tar.gz" +FN="FlowSorted.DLPFC.450k_1.20.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/experiment/src/contrib/FlowSorted.DLPFC.450k_1.18.0.tar.gz" - "https://bioarchive.galaxyproject.org/FlowSorted.DLPFC.450k_1.18.0.tar.gz" - "https://depot.galaxyproject.org/software/bioconductor-flowsorted.dlpfc.450k/bioconductor-flowsorted.dlpfc.450k_1.18.0_src_all.tar.gz" + "https://bioconductor.org/packages/3.9/data/experiment/src/contrib/FlowSorted.DLPFC.450k_1.20.0.tar.gz" + "https://bioarchive.galaxyproject.org/FlowSorted.DLPFC.450k_1.20.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-flowsorted.dlpfc.450k/bioconductor-flowsorted.dlpfc.450k_1.20.0_src_all.tar.gz" ) -MD5="de071e70f511a405aad3ee9b3196fd43" +MD5="2079268ebe8b094cc960b96c9ab94876" # Use a staging area in the conda dir rather than temp dirs, both to avoid # permission issues as well as to have things downloaded in a predictable @@ -16,7 +16,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-flowstats/meta.yaml b/recipes/bioconductor-flowstats/meta.yaml index f1ce634ee404a..bf9ef04525ff9 100644 --- a/recipes/bioconductor-flowstats/meta.yaml +++ b/recipes/bioconductor-flowstats/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "3.40.1" %} +{% set version = "3.42.0" %} {% set name = "flowStats" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,22 +10,22 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 43c7c4367a8c80d147feb7030425e5fc + md5: e79d22f2752f9f575bd057c3bed7fd5b build: number: 0 rpaths: - lib/R/lib/ - lib/ noarch: generic -# Suggests: xtable +# Suggests: xtable, testthat requirements: host: - - 'bioconductor-biobase >=2.42.0,<2.43.0' - - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' - - 'bioconductor-flowcore >=1.48.0,<1.49.0' - - 'bioconductor-flowviz >=1.46.0,<1.47.0' - - 'bioconductor-flowworkspace >=3.30.0,<3.31.0' - - 'bioconductor-ncdfflow >=2.28.0,<2.29.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' + - 'bioconductor-biocgenerics >=0.30.0,<0.31.0' + - 'bioconductor-flowcore >=1.50.0,<1.51.0' + - 'bioconductor-flowviz >=1.48.0,<1.49.0' + - 'bioconductor-flowworkspace >=3.32.0,<3.33.0' + - 'bioconductor-ncdfflow >=2.30.0,<2.31.0' - r-base - r-cluster - 'r-fda >=2.2.6' @@ -35,12 +35,12 @@ requirements: - r-mass - r-rcolorbrewer run: - - 'bioconductor-biobase >=2.42.0,<2.43.0' - - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' - - 'bioconductor-flowcore >=1.48.0,<1.49.0' - - 'bioconductor-flowviz >=1.46.0,<1.47.0' - - 'bioconductor-flowworkspace >=3.30.0,<3.31.0' - - 'bioconductor-ncdfflow >=2.28.0,<2.29.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' + - 'bioconductor-biocgenerics >=0.30.0,<0.31.0' + - 'bioconductor-flowcore >=1.50.0,<1.51.0' + - 'bioconductor-flowviz >=1.48.0,<1.49.0' + - 'bioconductor-flowworkspace >=3.32.0,<3.33.0' + - 'bioconductor-ncdfflow >=2.30.0,<2.31.0' - r-base - r-cluster - 'r-fda >=2.2.6' diff --git a/recipes/bioconductor-flowtime/meta.yaml b/recipes/bioconductor-flowtime/meta.yaml index fd10d7533da6c..d3f10bafe4d19 100644 --- a/recipes/bioconductor-flowtime/meta.yaml +++ b/recipes/bioconductor-flowtime/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.6.0" %} +{% set version = "1.8.0" %} {% set name = "flowTime" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 6dc8563724ec85842899e6784f515be0 + md5: d14bb00e157e0c1204f1304d9106b693 build: number: 0 rpaths: @@ -20,11 +20,11 @@ build: # Suggests: knitr, rmarkdown, flowViz, ggplot2, BiocGenerics, moments, stats requirements: host: - - 'bioconductor-flowcore >=1.48.0,<1.49.0' + - 'bioconductor-flowcore >=1.50.0,<1.51.0' - r-base - r-plyr run: - - 'bioconductor-flowcore >=1.48.0,<1.49.0' + - 'bioconductor-flowcore >=1.50.0,<1.51.0' - r-base - r-plyr test: diff --git a/recipes/bioconductor-flowtrans/meta.yaml b/recipes/bioconductor-flowtrans/meta.yaml index 33db22b62d5e4..7a6acb09cda4a 100644 --- a/recipes/bioconductor-flowtrans/meta.yaml +++ b/recipes/bioconductor-flowtrans/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.34.0" %} +{% set version = "1.36.0" %} {% set name = "flowTrans" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: b5ebb0150ba77abab998b93e3a5cb255 + md5: 5be3fa82b2892bc99ad35307f9395b35 build: number: 0 rpaths: @@ -19,14 +19,14 @@ build: noarch: generic requirements: host: - - 'bioconductor-flowclust >=3.20.0,<3.21.0' - - 'bioconductor-flowcore >=1.48.0,<1.49.0' - - 'bioconductor-flowviz >=1.46.0,<1.47.0' + - 'bioconductor-flowclust >=3.22.0,<3.23.0' + - 'bioconductor-flowcore >=1.50.0,<1.51.0' + - 'bioconductor-flowviz >=1.48.0,<1.49.0' - r-base run: - - 'bioconductor-flowclust >=3.20.0,<3.21.0' - - 'bioconductor-flowcore >=1.48.0,<1.49.0' - - 'bioconductor-flowviz >=1.46.0,<1.47.0' + - 'bioconductor-flowclust >=3.22.0,<3.23.0' + - 'bioconductor-flowcore >=1.50.0,<1.51.0' + - 'bioconductor-flowviz >=1.48.0,<1.49.0' - r-base test: commands: diff --git a/recipes/bioconductor-flowtype/meta.yaml b/recipes/bioconductor-flowtype/meta.yaml index 9bf8cfeec7c31..e991013d11b86 100644 --- a/recipes/bioconductor-flowtype/meta.yaml +++ b/recipes/bioconductor-flowtype/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "2.20.1" %} +{% set version = "2.22.0" %} {% set name = "flowType" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,32 +10,31 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 49e8b8b49790cb4941b43a831022fc89 + md5: ee8256e879c82ce3ea542245b829c72a build: number: 0 - skip: True # [osx] rpaths: - lib/R/lib/ - lib/ # Suggests: xtable requirements: host: - - 'bioconductor-biobase >=2.42.0,<2.43.0' - - 'bioconductor-flowclust >=3.20.0,<3.21.0' - - 'bioconductor-flowcore >=1.48.0,<1.49.0' - - 'bioconductor-flowmeans >=1.42.0,<1.43.0' - - 'bioconductor-flowmerge >=2.30.0,<2.31.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' + - 'bioconductor-flowclust >=3.22.0,<3.23.0' + - 'bioconductor-flowcore >=1.50.0,<1.51.0' + - 'bioconductor-flowmeans >=1.44.0,<1.45.0' + - 'bioconductor-flowmerge >=2.32.0,<2.33.0' - r-base - 'r-bh >=1.51.0-3' - 'r-rcpp >=0.10.4' - r-rrcov - r-sfsmisc run: - - 'bioconductor-biobase >=2.42.0,<2.43.0' - - 'bioconductor-flowclust >=3.20.0,<3.21.0' - - 'bioconductor-flowcore >=1.48.0,<1.49.0' - - 'bioconductor-flowmeans >=1.42.0,<1.43.0' - - 'bioconductor-flowmerge >=2.30.0,<2.31.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' + - 'bioconductor-flowclust >=3.22.0,<3.23.0' + - 'bioconductor-flowcore >=1.50.0,<1.51.0' + - 'bioconductor-flowmeans >=1.44.0,<1.45.0' + - 'bioconductor-flowmerge >=2.32.0,<2.33.0' - r-base - 'r-bh >=1.51.0-3' - 'r-rcpp >=0.10.4' @@ -52,7 +51,7 @@ about: home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: Artistic-2.0 summary: 'Phenotyping Flow Cytometry Assays using multidimentional expansion of single dimentional partitions.' - extra: container: - extended-base: True + extended-base: true + diff --git a/recipes/bioconductor-flowutils/meta.yaml b/recipes/bioconductor-flowutils/meta.yaml index 4a03a6313c393..de8a21c2090eb 100644 --- a/recipes/bioconductor-flowutils/meta.yaml +++ b/recipes/bioconductor-flowutils/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.46.1" %} +{% set version = "1.48.0" %} {% set name = "flowUtils" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: ffdf1baeb708cd98dad8863594b8488bd4eeb7509f5227d275d7dc210cee686e + md5: 6e5a358c3a1fef2abfe65b50f0dbc32f build: number: 0 rpaths: @@ -20,17 +20,17 @@ build: # Suggests: gatingMLData requirements: host: - - 'bioconductor-biobase >=2.42.0,<2.43.0' - - 'bioconductor-flowcore >=1.48.0,<1.49.0' - - 'bioconductor-graph >=1.60.0,<1.61.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' + - 'bioconductor-flowcore >=1.50.0,<1.51.0' + - 'bioconductor-graph >=1.62.0,<1.63.0' - r-base - r-corpcor - r-runit - r-xml run: - - 'bioconductor-biobase >=2.42.0,<2.43.0' - - 'bioconductor-flowcore >=1.48.0,<1.49.0' - - 'bioconductor-graph >=1.60.0,<1.61.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' + - 'bioconductor-flowcore >=1.50.0,<1.51.0' + - 'bioconductor-graph >=1.62.0,<1.63.0' - r-base - r-corpcor - r-runit diff --git a/recipes/bioconductor-flowviz/meta.yaml b/recipes/bioconductor-flowviz/meta.yaml index 355723cf6e72f..d410cc69c277d 100644 --- a/recipes/bioconductor-flowviz/meta.yaml +++ b/recipes/bioconductor-flowviz/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.46.1" %} +{% set version = "1.48.0" %} {% set name = "flowViz" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: 2102c0f41b3c053a89c717574cf3c41693942a77b3ee8cd2944735f26c16175e + md5: 6919f8a0332621f4805e2b395c9c58b7 build: number: 0 rpaths: @@ -20,8 +20,8 @@ build: # Suggests: colorspace, flowStats,knitr requirements: host: - - 'bioconductor-biobase >=2.42.0,<2.43.0' - - 'bioconductor-flowcore >=1.48.0,<1.49.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' + - 'bioconductor-flowcore >=1.50.0,<1.51.0' - r-base - r-hexbin - r-idpmisc @@ -31,8 +31,8 @@ requirements: - r-mass - r-rcolorbrewer run: - - 'bioconductor-biobase >=2.42.0,<2.43.0' - - 'bioconductor-flowcore >=1.48.0,<1.49.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' + - 'bioconductor-flowcore >=1.50.0,<1.51.0' - r-base - r-hexbin - r-idpmisc diff --git a/recipes/bioconductor-flowvs/meta.yaml b/recipes/bioconductor-flowvs/meta.yaml index 7c94e0ac7e41f..095886d516c2d 100644 --- a/recipes/bioconductor-flowvs/meta.yaml +++ b/recipes/bioconductor-flowvs/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.14.1" %} +{% set version = "1.16.0" %} {% set name = "flowVS" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: a1f53e1a4431e5172e5ca33be1584e08 + md5: b664e794b1e3998631475b893d92bc39 build: number: 0 rpaths: @@ -20,14 +20,14 @@ build: # Suggests: knitr, vsn, requirements: host: - - 'bioconductor-flowcore >=1.48.0,<1.49.0' - - 'bioconductor-flowstats >=3.40.0,<3.41.0' - - 'bioconductor-flowviz >=1.46.0,<1.47.0' + - 'bioconductor-flowcore >=1.50.0,<1.51.0' + - 'bioconductor-flowstats >=3.42.0,<3.43.0' + - 'bioconductor-flowviz >=1.48.0,<1.49.0' - r-base run: - - 'bioconductor-flowcore >=1.48.0,<1.49.0' - - 'bioconductor-flowstats >=3.40.0,<3.41.0' - - 'bioconductor-flowviz >=1.46.0,<1.47.0' + - 'bioconductor-flowcore >=1.50.0,<1.51.0' + - 'bioconductor-flowstats >=3.42.0,<3.43.0' + - 'bioconductor-flowviz >=1.48.0,<1.49.0' - r-base test: commands: diff --git a/recipes/bioconductor-flowworkspace/meta.yaml b/recipes/bioconductor-flowworkspace/meta.yaml index 83a8f885e907d..70ed901e91f3d 100644 --- a/recipes/bioconductor-flowworkspace/meta.yaml +++ b/recipes/bioconductor-flowworkspace/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "3.30.2" %} +{% set version = "3.32.0" %} {% set name = "flowWorkspace" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,29 +10,30 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: 81d43db4a9edbdd509a0e534055644ca4250660aa4fe434c75b5e6342fbf2ea6 + md5: 797fa4879c1d4bab3f8daf1a845eac98 build: number: 0 rpaths: - lib/R/lib/ - lib/ -# Suggests: testthat, flowWorkspaceData, knitr, ggcyto, parallel -# SystemRequirements: xml2, GNU make, C++11 +# Suggests: testthat, flowWorkspaceData, knitr, ggcyto, parallel, CytoML +# SystemRequirements: GNU make, C++11 requirements: host: - - 'bioconductor-biobase >=2.42.0,<2.43.0' - - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' - - 'bioconductor-cytolib >=1.4.0,<1.5.0' - - 'bioconductor-flowcore >=1.48.0,<1.49.0' - - 'bioconductor-flowviz >=1.46.0,<1.47.0' - - 'bioconductor-graph >=1.60.0,<1.61.0' - - 'bioconductor-ncdfflow >=2.28.0,<2.29.0' - - 'bioconductor-rbgl >=1.58.0,<1.59.0' - - 'bioconductor-rgraphviz >=2.26.0,<2.27.0' - - 'bioconductor-rprotobuflib >=1.4.0,<1.5.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' + - 'bioconductor-biocgenerics >=0.30.0,<0.31.0' + - 'bioconductor-cytolib >=1.6.0,<1.7.0' + - 'bioconductor-flowcore >=1.50.0,<1.51.0' + - 'bioconductor-flowviz >=1.48.0,<1.49.0' + - 'bioconductor-graph >=1.62.0,<1.63.0' + - 'bioconductor-ncdfflow >=2.30.0,<2.31.0' + - 'bioconductor-rbgl >=1.60.0,<1.61.0' + - 'bioconductor-rgraphviz >=2.28.0,<2.29.0' + - 'bioconductor-rprotobuflib >=1.6.0,<1.7.0' - r-base - 'r-bh >=1.62.0-1' - r-data.table + - r-digest - r-dplyr - r-gridextra - r-lattice @@ -40,23 +41,24 @@ requirements: - r-matrixstats - r-rcolorbrewer - r-rcpp + - r-rcppparallel - r-scales - r-stringr - - r-xml run: - - 'bioconductor-biobase >=2.42.0,<2.43.0' - - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' - - 'bioconductor-cytolib >=1.4.0,<1.5.0' - - 'bioconductor-flowcore >=1.48.0,<1.49.0' - - 'bioconductor-flowviz >=1.46.0,<1.47.0' - - 'bioconductor-graph >=1.60.0,<1.61.0' - - 'bioconductor-ncdfflow >=2.28.0,<2.29.0' - - 'bioconductor-rbgl >=1.58.0,<1.59.0' - - 'bioconductor-rgraphviz >=2.26.0,<2.27.0' - - 'bioconductor-rprotobuflib >=1.4.0,<1.5.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' + - 'bioconductor-biocgenerics >=0.30.0,<0.31.0' + - 'bioconductor-cytolib >=1.6.0,<1.7.0' + - 'bioconductor-flowcore >=1.50.0,<1.51.0' + - 'bioconductor-flowviz >=1.48.0,<1.49.0' + - 'bioconductor-graph >=1.62.0,<1.63.0' + - 'bioconductor-ncdfflow >=2.30.0,<2.31.0' + - 'bioconductor-rbgl >=1.60.0,<1.61.0' + - 'bioconductor-rgraphviz >=2.28.0,<2.29.0' + - 'bioconductor-rprotobuflib >=1.6.0,<1.7.0' - r-base - 'r-bh >=1.62.0-1' - r-data.table + - r-digest - r-dplyr - r-gridextra - r-lattice @@ -64,13 +66,12 @@ requirements: - r-matrixstats - r-rcolorbrewer - r-rcpp + - r-rcppparallel - r-scales - r-stringr - - r-xml build: - {{ compiler('c') }} - {{ compiler('cxx') }} - - automake - make test: commands: diff --git a/recipes/bioconductor-flowworkspacedata/meta.yaml b/recipes/bioconductor-flowworkspacedata/meta.yaml index 5022171efb946..5f7900cf7336d 100644 --- a/recipes/bioconductor-flowworkspacedata/meta.yaml +++ b/recipes/bioconductor-flowworkspacedata/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "2.18.0" %} +{% set version = "2.20.0" %} {% set name = "flowWorkspaceData" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 67cd786b29a27ccdbb1b1c423bfce42d + md5: c729e940217ce7298e58ddb4b654b85a build: number: 0 rpaths: @@ -22,7 +22,7 @@ requirements: - r-base run: - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-flowworkspacedata/post-link.sh b/recipes/bioconductor-flowworkspacedata/post-link.sh index fbc81bdd768dd..2be33751d0472 100644 --- a/recipes/bioconductor-flowworkspacedata/post-link.sh +++ b/recipes/bioconductor-flowworkspacedata/post-link.sh @@ -1,11 +1,11 @@ #!/bin/bash -FN="flowWorkspaceData_2.18.0.tar.gz" +FN="flowWorkspaceData_2.20.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/experiment/src/contrib/flowWorkspaceData_2.18.0.tar.gz" - "https://bioarchive.galaxyproject.org/flowWorkspaceData_2.18.0.tar.gz" - "https://depot.galaxyproject.org/software/bioconductor-flowworkspacedata/bioconductor-flowworkspacedata_2.18.0_src_all.tar.gz" + "https://bioconductor.org/packages/3.9/data/experiment/src/contrib/flowWorkspaceData_2.20.0.tar.gz" + "https://bioarchive.galaxyproject.org/flowWorkspaceData_2.20.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-flowworkspacedata/bioconductor-flowworkspacedata_2.20.0_src_all.tar.gz" ) -MD5="67cd786b29a27ccdbb1b1c423bfce42d" +MD5="c729e940217ce7298e58ddb4b654b85a" # Use a staging area in the conda dir rather than temp dirs, both to avoid # permission issues as well as to have things downloaded in a predictable @@ -16,7 +16,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-fly.db0/meta.yaml b/recipes/bioconductor-fly.db0/meta.yaml index 4d3a76998d629..af3766cad685a 100644 --- a/recipes/bioconductor-fly.db0/meta.yaml +++ b/recipes/bioconductor-fly.db0/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "3.7.1" %} +{% set version = "3.8.2" %} {% set name = "fly.db0" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 5158fc82a6d73d7ca2f20010e7f18149 + md5: 96b1c49edc7c11bc6a76f74c15308053 build: number: 0 rpaths: @@ -19,12 +19,12 @@ build: noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' - r-base run: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-fly.db0/post-link.sh b/recipes/bioconductor-fly.db0/post-link.sh index 2bc220aa32ed5..7f8de655203a4 100644 --- a/recipes/bioconductor-fly.db0/post-link.sh +++ b/recipes/bioconductor-fly.db0/post-link.sh @@ -1,11 +1,11 @@ #!/bin/bash -FN="fly.db0_3.7.1.tar.gz" +FN="fly.db0_3.8.2.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/fly.db0_3.7.1.tar.gz" - "https://bioarchive.galaxyproject.org/fly.db0_3.7.1.tar.gz" - "https://depot.galaxyproject.org/software/bioconductor-fly.db0/bioconductor-fly.db0_3.7.1_src_all.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/fly.db0_3.8.2.tar.gz" + "https://bioarchive.galaxyproject.org/fly.db0_3.8.2.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-fly.db0/bioconductor-fly.db0_3.8.2_src_all.tar.gz" ) -MD5="5158fc82a6d73d7ca2f20010e7f18149" +MD5="96b1c49edc7c11bc6a76f74c15308053" # Use a staging area in the conda dir rather than temp dirs, both to avoid # permission issues as well as to have things downloaded in a predictable @@ -16,7 +16,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-fmcsr/meta.yaml b/recipes/bioconductor-fmcsr/meta.yaml index 53378a4e42a4f..21a0babb5ec03 100644 --- a/recipes/bioconductor-fmcsr/meta.yaml +++ b/recipes/bioconductor-fmcsr/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.24.0" %} +{% set version = "1.26.0" %} {% set name = "fmcsR" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 62865bc0fa2c4ac4a6f437220ff05e8e + md5: a4e4eb7851b2c51f6f21a85ac7af7247 build: number: 0 rpaths: @@ -19,13 +19,13 @@ build: # Suggests: BiocStyle, knitr, knitcitations, knitrBootstrap requirements: host: - - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' - - 'bioconductor-chemminer >=3.34.0,<3.35.0' + - 'bioconductor-biocgenerics >=0.30.0,<0.31.0' + - 'bioconductor-chemminer >=3.36.0,<3.37.0' - r-base - r-runit run: - - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' - - 'bioconductor-chemminer >=3.34.0,<3.35.0' + - 'bioconductor-biocgenerics >=0.30.0,<0.31.0' + - 'bioconductor-chemminer >=3.36.0,<3.37.0' - r-base - r-runit build: diff --git a/recipes/bioconductor-focalcall/meta.yaml b/recipes/bioconductor-focalcall/meta.yaml index 5c443072164be..db906285ce0d5 100644 --- a/recipes/bioconductor-focalcall/meta.yaml +++ b/recipes/bioconductor-focalcall/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.16.0" %} +{% set version = "1.18.0" %} {% set name = "focalCall" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: b19052a468311959ee34805929344404 + md5: c555b50351bca8977b62353027cc35f1 build: number: 0 rpaths: @@ -20,10 +20,10 @@ build: # Suggests: RUnit, BiocGenerics requirements: host: - - 'bioconductor-cghcall >=2.44.0,<2.45.0' + - 'bioconductor-cghcall >=2.46.0,<2.47.0' - r-base run: - - 'bioconductor-cghcall >=2.44.0,<2.45.0' + - 'bioconductor-cghcall >=2.46.0,<2.47.0' - r-base test: commands: diff --git a/recipes/bioconductor-foldgo/meta.yaml b/recipes/bioconductor-foldgo/meta.yaml index dbcbdc696caa6..afe1083242c72 100644 --- a/recipes/bioconductor-foldgo/meta.yaml +++ b/recipes/bioconductor-foldgo/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.0.1" %} +{% set version = "1.2.0" %} {% set name = "FoldGO" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 48dac3b597db9819387033f7f5030e60 + md5: 38aba737bd38b3346c7ef5457cffe0ae build: number: 0 rpaths: @@ -20,12 +20,12 @@ build: # Suggests: knitr, rmarkdown, devtools, kableExtra requirements: host: - - 'bioconductor-topgo >=2.34.0,<2.35.0' + - 'bioconductor-topgo >=2.36.0,<2.37.0' - r-base - 'r-ggplot2 >=2.2.1' - 'r-tidyr >=0.8.0' run: - - 'bioconductor-topgo >=2.34.0,<2.35.0' + - 'bioconductor-topgo >=2.36.0,<2.37.0' - r-base - 'r-ggplot2 >=2.2.1' - 'r-tidyr >=0.8.0' diff --git a/recipes/bioconductor-fourcseq/meta.yaml b/recipes/bioconductor-fourcseq/meta.yaml index 57ac89bfd550f..cfd2220fad20b 100644 --- a/recipes/bioconductor-fourcseq/meta.yaml +++ b/recipes/bioconductor-fourcseq/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.16.0" %} +{% set version = "1.18.0" %} {% set name = "FourCSeq" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,9 +10,9 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 53c2a29adaf6ec73c43ccb06f633a330 + md5: 8433a631778a0686ed1107a965e96e8b build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ @@ -20,15 +20,15 @@ build: # Suggests: BiocStyle, knitr, TxDb.Dmelanogaster.UCSC.dm3.ensGene requirements: host: - - 'bioconductor-biobase >=2.42.0,<2.43.0' - - 'bioconductor-biostrings >=2.50.0,<2.51.0' - - 'bioconductor-deseq2 >=1.22.0,<1.23.0' - - 'bioconductor-genomicalignments >=1.18.0,<1.19.0' - - 'bioconductor-genomicranges >=1.34.0,<1.35.0' - - 'bioconductor-ggbio >=1.30.0,<1.31.0' - - 'bioconductor-rsamtools >=1.34.0,<1.35.0' - - 'bioconductor-rtracklayer >=1.42.0,<1.43.0' - - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' + - 'bioconductor-biostrings >=2.52.0,<2.53.0' + - 'bioconductor-deseq2 >=1.24.0,<1.25.0' + - 'bioconductor-genomicalignments >=1.20.0,<1.21.0' + - 'bioconductor-genomicranges >=1.36.0,<1.37.0' + - 'bioconductor-ggbio >=1.32.0,<1.33.0' + - 'bioconductor-rsamtools >=2.0.0,<2.1.0' + - 'bioconductor-rtracklayer >=1.44.0,<1.45.0' + - 'bioconductor-summarizedexperiment >=1.14.0,<1.15.0' - r-base - r-fda - r-ggplot2 @@ -37,15 +37,15 @@ requirements: - r-matrix - r-reshape2 run: - - 'bioconductor-biobase >=2.42.0,<2.43.0' - - 'bioconductor-biostrings >=2.50.0,<2.51.0' - - 'bioconductor-deseq2 >=1.22.0,<1.23.0' - - 'bioconductor-genomicalignments >=1.18.0,<1.19.0' - - 'bioconductor-genomicranges >=1.34.0,<1.35.0' - - 'bioconductor-ggbio >=1.30.0,<1.31.0' - - 'bioconductor-rsamtools >=1.34.0,<1.35.0' - - 'bioconductor-rtracklayer >=1.42.0,<1.43.0' - - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' + - 'bioconductor-biostrings >=2.52.0,<2.53.0' + - 'bioconductor-deseq2 >=1.24.0,<1.25.0' + - 'bioconductor-genomicalignments >=1.20.0,<1.21.0' + - 'bioconductor-genomicranges >=1.36.0,<1.37.0' + - 'bioconductor-ggbio >=1.32.0,<1.33.0' + - 'bioconductor-rsamtools >=2.0.0,<2.1.0' + - 'bioconductor-rtracklayer >=1.44.0,<1.45.0' + - 'bioconductor-summarizedexperiment >=1.14.0,<1.15.0' - r-base - r-fda - r-ggplot2 diff --git a/recipes/bioconductor-frgepistasis/meta.yaml b/recipes/bioconductor-frgepistasis/meta.yaml index d8d7128bfa4c9..77cdf7c0342e3 100644 --- a/recipes/bioconductor-frgepistasis/meta.yaml +++ b/recipes/bioconductor-frgepistasis/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.18.0" %} +{% set version = "1.20.0" %} {% set name = "FRGEpistasis" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 69714b75285540f4339872f28b55ca84 + md5: 37952e856c57599225394728b3730b97 build: number: 0 rpaths: diff --git a/recipes/bioconductor-frma/meta.yaml b/recipes/bioconductor-frma/meta.yaml index 3daf0fbbc7060..90bebae641438 100644 --- a/recipes/bioconductor-frma/meta.yaml +++ b/recipes/bioconductor-frma/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.34.0" %} +{% set version = "1.36.0" %} {% set name = "frma" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: b37d6b5a88ba58da47c33d6d7f09b93a + md5: 94bf551993ea56f77e48330bfe13b0db build: number: 0 rpaths: @@ -20,22 +20,22 @@ build: # Suggests: hgu133afrmavecs, frmaExampleData requirements: host: - - 'bioconductor-affy >=1.60.0,<1.61.0' - - 'bioconductor-biobase >=2.42.0,<2.43.0' - - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' - - 'bioconductor-oligo >=1.46.0,<1.47.0' - - 'bioconductor-oligoclasses >=1.44.0,<1.45.0' - - 'bioconductor-preprocesscore >=1.44.0,<1.45.0' + - 'bioconductor-affy >=1.62.0,<1.63.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' + - 'bioconductor-biocgenerics >=0.30.0,<0.31.0' + - 'bioconductor-oligo >=1.48.0,<1.49.0' + - 'bioconductor-oligoclasses >=1.46.0,<1.47.0' + - 'bioconductor-preprocesscore >=1.46.0,<1.47.0' - r-base - r-dbi - r-mass run: - - 'bioconductor-affy >=1.60.0,<1.61.0' - - 'bioconductor-biobase >=2.42.0,<2.43.0' - - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' - - 'bioconductor-oligo >=1.46.0,<1.47.0' - - 'bioconductor-oligoclasses >=1.44.0,<1.45.0' - - 'bioconductor-preprocesscore >=1.44.0,<1.45.0' + - 'bioconductor-affy >=1.62.0,<1.63.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' + - 'bioconductor-biocgenerics >=0.30.0,<0.31.0' + - 'bioconductor-oligo >=1.48.0,<1.49.0' + - 'bioconductor-oligoclasses >=1.46.0,<1.47.0' + - 'bioconductor-preprocesscore >=1.46.0,<1.47.0' - r-base - r-dbi - r-mass diff --git a/recipes/bioconductor-frmaexampledata/meta.yaml b/recipes/bioconductor-frmaexampledata/meta.yaml index e87a5eab3f57b..fc255e347fdb4 100644 --- a/recipes/bioconductor-frmaexampledata/meta.yaml +++ b/recipes/bioconductor-frmaexampledata/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.18.0" %} +{% set version = "1.20.0" %} {% set name = "frmaExampleData" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: d4faf0fddd05a0522bb832c1569b052d + md5: 3eb2349bbcc2b56bc60f2f7911e6d7cc build: number: 0 rpaths: @@ -22,7 +22,7 @@ requirements: - r-base run: - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-frmaexampledata/post-link.sh b/recipes/bioconductor-frmaexampledata/post-link.sh index d1796dbd5fd69..331be912b1c37 100644 --- a/recipes/bioconductor-frmaexampledata/post-link.sh +++ b/recipes/bioconductor-frmaexampledata/post-link.sh @@ -1,11 +1,11 @@ #!/bin/bash -FN="frmaExampleData_1.18.0.tar.gz" +FN="frmaExampleData_1.20.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/experiment/src/contrib/frmaExampleData_1.18.0.tar.gz" - "https://bioarchive.galaxyproject.org/frmaExampleData_1.18.0.tar.gz" - "https://depot.galaxyproject.org/software/bioconductor-frmaexampledata/bioconductor-frmaexampledata_1.18.0_src_all.tar.gz" + "https://bioconductor.org/packages/3.9/data/experiment/src/contrib/frmaExampleData_1.20.0.tar.gz" + "https://bioarchive.galaxyproject.org/frmaExampleData_1.20.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-frmaexampledata/bioconductor-frmaexampledata_1.20.0_src_all.tar.gz" ) -MD5="d4faf0fddd05a0522bb832c1569b052d" +MD5="3eb2349bbcc2b56bc60f2f7911e6d7cc" # Use a staging area in the conda dir rather than temp dirs, both to avoid # permission issues as well as to have things downloaded in a predictable @@ -16,7 +16,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-frmatools/meta.yaml b/recipes/bioconductor-frmatools/meta.yaml index 0f695c23ba05b..662f0ac01e822 100644 --- a/recipes/bioconductor-frmatools/meta.yaml +++ b/recipes/bioconductor-frmatools/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.34.0" %} +{% set version = "1.36.0" %} {% set name = "frmaTools" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: a62d9d619c2495c994c3ef00f8d44708 + md5: db1ec01c20b52ddc34d3c8161bf13da4 build: number: 0 rpaths: @@ -20,15 +20,15 @@ build: # Suggests: oligo, pd.huex.1.0.st.v2, pd.hugene.1.0.st.v1, frma, affyPLM, hgu133aprobe, hgu133atagprobe, hgu133plus2probe, hgu133acdf, hgu133atagcdf, hgu133plus2cdf, hgu133afrmavecs, frmaExampleData requirements: host: - - 'bioconductor-affy >=1.60.0,<1.61.0' - - 'bioconductor-biobase >=2.42.0,<2.43.0' - - 'bioconductor-preprocesscore >=1.44.0,<1.45.0' + - 'bioconductor-affy >=1.62.0,<1.63.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' + - 'bioconductor-preprocesscore >=1.46.0,<1.47.0' - r-base - r-dbi run: - - 'bioconductor-affy >=1.60.0,<1.61.0' - - 'bioconductor-biobase >=2.42.0,<2.43.0' - - 'bioconductor-preprocesscore >=1.44.0,<1.45.0' + - 'bioconductor-affy >=1.62.0,<1.63.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' + - 'bioconductor-preprocesscore >=1.46.0,<1.47.0' - r-base - r-dbi test: diff --git a/recipes/bioconductor-funchip/meta.yaml b/recipes/bioconductor-funchip/meta.yaml index 6037f7f60a750..db0b9f29a388b 100644 --- a/recipes/bioconductor-funchip/meta.yaml +++ b/recipes/bioconductor-funchip/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.8.0" %} +{% set version = "1.10.0" %} {% set name = "FunChIP" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: c8c104f2587cb6dad1645d758e3ef9f2 + md5: 24e2ce91810cb2a528e349b51e968597 build: number: 0 rpaths: @@ -18,10 +18,10 @@ build: - lib/ requirements: host: - - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' - - 'bioconductor-genomicalignments >=1.18.0,<1.19.0' - - 'bioconductor-genomicranges >=1.34.0,<1.35.0' - - 'bioconductor-rsamtools >=1.34.0,<1.35.0' + - 'bioconductor-genomeinfodb >=1.20.0,<1.21.0' + - 'bioconductor-genomicalignments >=1.20.0,<1.21.0' + - 'bioconductor-genomicranges >=1.36.0,<1.37.0' + - 'bioconductor-rsamtools >=2.0.0,<2.1.0' - r-base - r-doparallel - r-fda @@ -30,10 +30,10 @@ requirements: - r-rcpp - r-shiny run: - - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' - - 'bioconductor-genomicalignments >=1.18.0,<1.19.0' - - 'bioconductor-genomicranges >=1.34.0,<1.35.0' - - 'bioconductor-rsamtools >=1.34.0,<1.35.0' + - 'bioconductor-genomeinfodb >=1.20.0,<1.21.0' + - 'bioconductor-genomicalignments >=1.20.0,<1.21.0' + - 'bioconductor-genomicranges >=1.36.0,<1.37.0' + - 'bioconductor-rsamtools >=2.0.0,<2.1.0' - r-base - r-doparallel - r-fda diff --git a/recipes/bioconductor-funcisnp.data/meta.yaml b/recipes/bioconductor-funcisnp.data/meta.yaml index f5f1263acf769..9e480cd0a42db 100644 --- a/recipes/bioconductor-funcisnp.data/meta.yaml +++ b/recipes/bioconductor-funcisnp.data/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.18.0" %} +{% set version = "1.20.0" %} {% set name = "FunciSNP.data" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: d92989e8bb3e92138d3a597266fd0770 + md5: 693316a2d7cea94fbf95e20e011ae1be build: number: 0 rpaths: @@ -19,14 +19,14 @@ build: noarch: generic requirements: host: - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-rtracklayer >=1.42.0,<1.43.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-rtracklayer >=1.44.0,<1.45.0' - r-base run: - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-rtracklayer >=1.42.0,<1.43.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-rtracklayer >=1.44.0,<1.45.0' - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-funcisnp.data/post-link.sh b/recipes/bioconductor-funcisnp.data/post-link.sh index 5d620a1bde67d..bd2816173965a 100644 --- a/recipes/bioconductor-funcisnp.data/post-link.sh +++ b/recipes/bioconductor-funcisnp.data/post-link.sh @@ -1,11 +1,11 @@ #!/bin/bash -FN="FunciSNP.data_1.18.0.tar.gz" +FN="FunciSNP.data_1.20.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/experiment/src/contrib/FunciSNP.data_1.18.0.tar.gz" - "https://bioarchive.galaxyproject.org/FunciSNP.data_1.18.0.tar.gz" - "https://depot.galaxyproject.org/software/bioconductor-funcisnp.data/bioconductor-funcisnp.data_1.18.0_src_all.tar.gz" + "https://bioconductor.org/packages/3.9/data/experiment/src/contrib/FunciSNP.data_1.20.0.tar.gz" + "https://bioarchive.galaxyproject.org/FunciSNP.data_1.20.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-funcisnp.data/bioconductor-funcisnp.data_1.20.0_src_all.tar.gz" ) -MD5="d92989e8bb3e92138d3a597266fd0770" +MD5="693316a2d7cea94fbf95e20e011ae1be" # Use a staging area in the conda dir rather than temp dirs, both to avoid # permission issues as well as to have things downloaded in a predictable @@ -16,7 +16,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-funcisnp/meta.yaml b/recipes/bioconductor-funcisnp/meta.yaml index 4d3225458f8d2..b0c6e3a43ef83 100644 --- a/recipes/bioconductor-funcisnp/meta.yaml +++ b/recipes/bioconductor-funcisnp/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.26.0" %} +{% set version = "1.28.0" %} {% set name = "FunciSNP" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: e55399c304732cc26e706341e659018c + md5: 62d1b1948e8ebd9737593809f8644870 build: number: 0 rpaths: @@ -20,36 +20,36 @@ build: # Suggests: org.Hs.eg.db requirements: host: - - 'bioconductor-biobase >=2.42.0,<2.43.0' - - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' - - 'bioconductor-chippeakanno >=3.16.0,<3.17.0' - - 'bioconductor-funcisnp.data >=1.18.0,<1.19.0' - - 'bioconductor-genomicranges >=1.34.0,<1.35.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-rsamtools >=1.34.0,<1.35.0' - - 'bioconductor-rtracklayer >=1.42.0,<1.43.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' - - 'bioconductor-snpstats >=1.32.0,<1.33.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' + - 'bioconductor-biocgenerics >=0.30.0,<0.31.0' + - 'bioconductor-chippeakanno >=3.18.0,<3.19.0' + - 'bioconductor-funcisnp.data >=1.20.0,<1.21.0' + - 'bioconductor-genomicranges >=1.36.0,<1.37.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-rsamtools >=2.0.0,<2.1.0' + - 'bioconductor-rtracklayer >=1.44.0,<1.45.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' + - 'bioconductor-snpstats >=1.34.0,<1.35.0' - 'bioconductor-txdb.hsapiens.ucsc.hg19.knowngene >=3.2.0,<3.3.0' - - 'bioconductor-variantannotation >=1.28.0,<1.29.0' + - 'bioconductor-variantannotation >=1.30.0,<1.31.0' - r-base - 'r-ggplot2 >=0.9.0' - r-plyr - 'r-reshape >=0.8.4' - r-scales run: - - 'bioconductor-biobase >=2.42.0,<2.43.0' - - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' - - 'bioconductor-chippeakanno >=3.16.0,<3.17.0' - - 'bioconductor-funcisnp.data >=1.18.0,<1.19.0' - - 'bioconductor-genomicranges >=1.34.0,<1.35.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-rsamtools >=1.34.0,<1.35.0' - - 'bioconductor-rtracklayer >=1.42.0,<1.43.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' - - 'bioconductor-snpstats >=1.32.0,<1.33.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' + - 'bioconductor-biocgenerics >=0.30.0,<0.31.0' + - 'bioconductor-chippeakanno >=3.18.0,<3.19.0' + - 'bioconductor-funcisnp.data >=1.20.0,<1.21.0' + - 'bioconductor-genomicranges >=1.36.0,<1.37.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-rsamtools >=2.0.0,<2.1.0' + - 'bioconductor-rtracklayer >=1.44.0,<1.45.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' + - 'bioconductor-snpstats >=1.34.0,<1.35.0' - 'bioconductor-txdb.hsapiens.ucsc.hg19.knowngene >=3.2.0,<3.3.0' - - 'bioconductor-variantannotation >=1.28.0,<1.29.0' + - 'bioconductor-variantannotation >=1.30.0,<1.31.0' - r-base - 'r-ggplot2 >=0.9.0' - r-plyr diff --git a/recipes/bioconductor-funtoonorm/meta.yaml b/recipes/bioconductor-funtoonorm/meta.yaml index 7d01724a1960a..efe51cf97599a 100644 --- a/recipes/bioconductor-funtoonorm/meta.yaml +++ b/recipes/bioconductor-funtoonorm/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.6.0" %} +{% set version = "1.8.0" %} {% set name = "funtooNorm" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: c580cc3077ad762b790f4ccbc1ca9de8 + md5: b6d50989a81ea88fe52f9bf110a7bd17 build: number: 0 rpaths: @@ -20,18 +20,18 @@ build: # Suggests: prettydoc, minfiData, knitr, rmarkdown requirements: host: - - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' + - 'bioconductor-genomeinfodb >=1.20.0,<1.21.0' - 'bioconductor-illuminahumanmethylation450kanno.ilmn12.hg19 >=0.6.0,<0.7.0' - 'bioconductor-illuminahumanmethylation450kmanifest >=0.4.0,<0.5.0' - - 'bioconductor-minfi >=1.28.0,<1.29.0' + - 'bioconductor-minfi >=1.30.0,<1.31.0' - r-base - r-matrixstats - r-pls run: - - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' + - 'bioconductor-genomeinfodb >=1.20.0,<1.21.0' - 'bioconductor-illuminahumanmethylation450kanno.ilmn12.hg19 >=0.6.0,<0.7.0' - 'bioconductor-illuminahumanmethylation450kmanifest >=0.4.0,<0.5.0' - - 'bioconductor-minfi >=1.28.0,<1.29.0' + - 'bioconductor-minfi >=1.30.0,<1.31.0' - r-base - r-matrixstats - r-pls diff --git a/recipes/bioconductor-furrowseg/meta.yaml b/recipes/bioconductor-furrowseg/meta.yaml index fcab9d0a4dfb8..3114c05e37be3 100644 --- a/recipes/bioconductor-furrowseg/meta.yaml +++ b/recipes/bioconductor-furrowseg/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.10.0" %} +{% set version = "1.12.0" %} {% set name = "furrowSeg" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: dc60909e3fe7d7b517d4aaa5693fbe83 + md5: ce4d21cb772147f45976e3e47612cfb0 build: number: 0 rpaths: @@ -20,20 +20,20 @@ build: # Suggests: BiocStyle, ggplot2, knitr requirements: host: - - 'bioconductor-ebimage >=4.24.0,<4.25.0' + - 'bioconductor-ebimage >=4.26.0,<4.27.0' - r-abind - r-base - r-dplyr - r-locfit - r-tiff run: - - 'bioconductor-ebimage >=4.24.0,<4.25.0' + - 'bioconductor-ebimage >=4.26.0,<4.27.0' - r-abind - r-base - r-dplyr - r-locfit - r-tiff - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-furrowseg/post-link.sh b/recipes/bioconductor-furrowseg/post-link.sh index 1d398f03d3df9..12dee654afd50 100644 --- a/recipes/bioconductor-furrowseg/post-link.sh +++ b/recipes/bioconductor-furrowseg/post-link.sh @@ -1,11 +1,11 @@ #!/bin/bash -FN="furrowSeg_1.10.0.tar.gz" +FN="furrowSeg_1.12.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/experiment/src/contrib/furrowSeg_1.10.0.tar.gz" - "https://bioarchive.galaxyproject.org/furrowSeg_1.10.0.tar.gz" - "https://depot.galaxyproject.org/software/bioconductor-furrowseg/bioconductor-furrowseg_1.10.0_src_all.tar.gz" + "https://bioconductor.org/packages/3.9/data/experiment/src/contrib/furrowSeg_1.12.0.tar.gz" + "https://bioarchive.galaxyproject.org/furrowSeg_1.12.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-furrowseg/bioconductor-furrowseg_1.12.0_src_all.tar.gz" ) -MD5="dc60909e3fe7d7b517d4aaa5693fbe83" +MD5="ce4d21cb772147f45976e3e47612cfb0" # Use a staging area in the conda dir rather than temp dirs, both to avoid # permission issues as well as to have things downloaded in a predictable @@ -16,7 +16,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-ga4ghclient/meta.yaml b/recipes/bioconductor-ga4ghclient/meta.yaml index 41435097f8847..e64030c3c5995 100644 --- a/recipes/bioconductor-ga4ghclient/meta.yaml +++ b/recipes/bioconductor-ga4ghclient/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.6.0" %} +{% set version = "1.8.0" %} {% set name = "GA4GHclient" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: f69a308636d5abd8d6c3e071e0182437 + md5: 8ef72497f8aed503e012fa063162a496 build: number: 0 rpaths: @@ -20,25 +20,25 @@ build: # Suggests: AnnotationDbi, BiocStyle, DT, knitr, org.Hs.eg.db, rmarkdown, testthat, TxDb.Hsapiens.UCSC.hg19.knownGene requirements: host: - - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' - - 'bioconductor-biostrings >=2.50.0,<2.51.0' - - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' - - 'bioconductor-genomicranges >=1.34.0,<1.35.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' - - 'bioconductor-variantannotation >=1.28.0,<1.29.0' + - 'bioconductor-biocgenerics >=0.30.0,<0.31.0' + - 'bioconductor-biostrings >=2.52.0,<2.53.0' + - 'bioconductor-genomeinfodb >=1.20.0,<1.21.0' + - 'bioconductor-genomicranges >=1.36.0,<1.37.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' + - 'bioconductor-variantannotation >=1.30.0,<1.31.0' - r-base - r-dplyr - r-httr - r-jsonlite run: - - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' - - 'bioconductor-biostrings >=2.50.0,<2.51.0' - - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' - - 'bioconductor-genomicranges >=1.34.0,<1.35.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' - - 'bioconductor-variantannotation >=1.28.0,<1.29.0' + - 'bioconductor-biocgenerics >=0.30.0,<0.31.0' + - 'bioconductor-biostrings >=2.52.0,<2.53.0' + - 'bioconductor-genomeinfodb >=1.20.0,<1.21.0' + - 'bioconductor-genomicranges >=1.36.0,<1.37.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' + - 'bioconductor-variantannotation >=1.30.0,<1.31.0' - r-base - r-dplyr - r-httr diff --git a/recipes/bioconductor-ga4ghshiny/meta.yaml b/recipes/bioconductor-ga4ghshiny/meta.yaml index 39a62032f93f3..8b3bf27dbf9cc 100644 --- a/recipes/bioconductor-ga4ghshiny/meta.yaml +++ b/recipes/bioconductor-ga4ghshiny/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.4.0" %} +{% set version = "1.6.0" %} {% set name = "GA4GHshiny" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 5798bf389bc3818bb6508788039afce7 + md5: a619b2ae29713b73728f89295c804fe0 build: number: 0 rpaths: @@ -20,12 +20,12 @@ build: # Suggests: BiocStyle, org.Hs.eg.db, knitr, rmarkdown, testthat, TxDb.Hsapiens.UCSC.hg19.knownGene requirements: host: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' - - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' - - 'bioconductor-ga4ghclient >=1.6.0,<1.7.0' - - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' - - 'bioconductor-genomicfeatures >=1.34.0,<1.35.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' + - 'bioconductor-biocgenerics >=0.30.0,<0.31.0' + - 'bioconductor-ga4ghclient >=1.8.0,<1.9.0' + - 'bioconductor-genomeinfodb >=1.20.0,<1.21.0' + - 'bioconductor-genomicfeatures >=1.36.0,<1.37.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' - r-base - r-dplyr - r-dt @@ -36,12 +36,12 @@ requirements: - r-shinythemes - r-tidyr run: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' - - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' - - 'bioconductor-ga4ghclient >=1.6.0,<1.7.0' - - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' - - 'bioconductor-genomicfeatures >=1.34.0,<1.35.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' + - 'bioconductor-biocgenerics >=0.30.0,<0.31.0' + - 'bioconductor-ga4ghclient >=1.8.0,<1.9.0' + - 'bioconductor-genomeinfodb >=1.20.0,<1.21.0' + - 'bioconductor-genomicfeatures >=1.36.0,<1.37.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' - r-base - r-dplyr - r-dt diff --git a/recipes/bioconductor-gaga/meta.yaml b/recipes/bioconductor-gaga/meta.yaml index 51d07a4e90711..9265b259ad70e 100644 --- a/recipes/bioconductor-gaga/meta.yaml +++ b/recipes/bioconductor-gaga/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "2.28.1" %} +{% set version = "2.30.0" %} {% set name = "gaga" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - sha256: a599e317c2c9b6670657075cf71ecadb0036a3a6f18df0b6dbfde382ea51ef04 + md5: fe0fd738660de0e168906463bee2143c build: number: 0 rpaths: @@ -18,14 +18,14 @@ build: - lib/ requirements: host: - - 'bioconductor-biobase >=2.42.0,<2.43.0' - - 'bioconductor-ebarrays >=2.46.0,<2.47.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' + - 'bioconductor-ebarrays >=2.48.0,<2.49.0' - r-base - r-coda - r-mgcv run: - - 'bioconductor-biobase >=2.42.0,<2.43.0' - - 'bioconductor-ebarrays >=2.46.0,<2.47.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' + - 'bioconductor-ebarrays >=2.48.0,<2.49.0' - r-base - r-coda - r-mgcv diff --git a/recipes/bioconductor-gage/meta.yaml b/recipes/bioconductor-gage/meta.yaml index 03ae136a61bc4..0ca92cdc85ff4 100644 --- a/recipes/bioconductor-gage/meta.yaml +++ b/recipes/bioconductor-gage/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "2.32.0" %} +{% set version = "2.34.0" %} {% set name = "gage" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 2f57d55ae9a703d93f8205f19e900c5e + md5: 986f20d5fa1a55d8f9a6f90e42ffbf73 build: number: 0 rpaths: @@ -20,14 +20,14 @@ build: # Suggests: pathview, gageData, GO.db, org.Hs.eg.db, hgu133a.db, GSEABase, Rsamtools, GenomicAlignments, TxDb.Hsapiens.UCSC.hg19.knownGene, DESeq, DESeq2, edgeR, limma requirements: host: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' - - 'bioconductor-graph >=1.60.0,<1.61.0' - - 'bioconductor-keggrest >=1.22.0,<1.23.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' + - 'bioconductor-graph >=1.62.0,<1.63.0' + - 'bioconductor-keggrest >=1.24.0,<1.25.0' - r-base run: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' - - 'bioconductor-graph >=1.60.0,<1.61.0' - - 'bioconductor-keggrest >=1.22.0,<1.23.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' + - 'bioconductor-graph >=1.62.0,<1.63.0' + - 'bioconductor-keggrest >=1.24.0,<1.25.0' - r-base test: commands: diff --git a/recipes/bioconductor-gagedata/meta.yaml b/recipes/bioconductor-gagedata/meta.yaml index 72a3500f1b2b4..0dd14d07c4c6e 100644 --- a/recipes/bioconductor-gagedata/meta.yaml +++ b/recipes/bioconductor-gagedata/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "2.20.0" %} +{% set version = "2.22.0" %} {% set name = "gageData" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: d483527aa3d7520e62154c90057f7d23 + md5: b20e038013ae19b70c5dc543fea69efe build: number: 0 rpaths: @@ -23,7 +23,7 @@ requirements: - r-base run: - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-gagedata/post-link.sh b/recipes/bioconductor-gagedata/post-link.sh index c25427fe26941..37a294261e5c2 100644 --- a/recipes/bioconductor-gagedata/post-link.sh +++ b/recipes/bioconductor-gagedata/post-link.sh @@ -1,11 +1,11 @@ #!/bin/bash -FN="gageData_2.20.0.tar.gz" +FN="gageData_2.22.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/experiment/src/contrib/gageData_2.20.0.tar.gz" - "https://bioarchive.galaxyproject.org/gageData_2.20.0.tar.gz" - "https://depot.galaxyproject.org/software/bioconductor-gagedata/bioconductor-gagedata_2.20.0_src_all.tar.gz" + "https://bioconductor.org/packages/3.9/data/experiment/src/contrib/gageData_2.22.0.tar.gz" + "https://bioarchive.galaxyproject.org/gageData_2.22.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-gagedata/bioconductor-gagedata_2.22.0_src_all.tar.gz" ) -MD5="d483527aa3d7520e62154c90057f7d23" +MD5="b20e038013ae19b70c5dc543fea69efe" # Use a staging area in the conda dir rather than temp dirs, both to avoid # permission issues as well as to have things downloaded in a predictable @@ -16,7 +16,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-gaggle/meta.yaml b/recipes/bioconductor-gaggle/meta.yaml index b5c9d0c8a259e..1ccf4dac6729b 100644 --- a/recipes/bioconductor-gaggle/meta.yaml +++ b/recipes/bioconductor-gaggle/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.50.0" %} +{% set version = "1.52.0" %} {% set name = "gaggle" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 0941a1c5621659082664ba61b3e33a61 + md5: 4c1228a547ec5dd7bc84989fe799167c build: number: 0 rpaths: @@ -19,12 +19,12 @@ build: noarch: generic requirements: host: - - 'bioconductor-graph >=1.60.0,<1.61.0' + - 'bioconductor-graph >=1.62.0,<1.63.0' - r-base - 'r-rjava >=0.4' - 'r-runit >=0.4.17' run: - - 'bioconductor-graph >=1.60.0,<1.61.0' + - 'bioconductor-graph >=1.62.0,<1.63.0' - r-base - 'r-rjava >=0.4' - 'r-runit >=0.4.17' diff --git a/recipes/bioconductor-gaia/meta.yaml b/recipes/bioconductor-gaia/meta.yaml index 66b7c5949c6d0..2a0c4860d0ed1 100644 --- a/recipes/bioconductor-gaia/meta.yaml +++ b/recipes/bioconductor-gaia/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "2.26.0" %} +{% set version = "2.28.0" %} {% set name = "gaia" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: e4d353ce4c66796d457f0a54189ed840 + md5: 1f9c21a6827807196e692492a66421a4 build: number: 0 rpaths: diff --git a/recipes/bioconductor-gapgom/build.sh b/recipes/bioconductor-gapgom/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-gapgom/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-gapgom/meta.yaml b/recipes/bioconductor-gapgom/meta.yaml new file mode 100644 index 0000000000000..4f31438ede8ba --- /dev/null +++ b/recipes/bioconductor-gapgom/meta.yaml @@ -0,0 +1,69 @@ +{% set version = "1.0.0" %} +{% set name = "GAPGOM" %} +{% set bioc = "3.9" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: f759c198b3ba235a97ca2aa9774957c6 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: org.Dm.eg.db, org.Rn.eg.db, org.Sc.sgd.db, org.Dr.eg.db, org.Ce.eg.db, org.At.tair.db, org.EcK12.eg.db, org.Bt.eg.db, org.Cf.eg.db, org.Ag.eg.db, org.EcSakai.eg.db, org.Gg.eg.db, org.Pt.eg.db, org.Pf.plasmo.db, org.Mmu.eg.db, org.Ss.eg.db, org.Xl.eg.db, testthat, pryr, knitr, rmarkdown, prettydoc, ggplot2, kableExtra, profvis, reshape2 +requirements: + host: + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' + - 'bioconductor-biocfilecache >=1.8.0,<1.9.0' + - 'bioconductor-geoquery >=2.52.0,<2.53.0' + - 'bioconductor-go.db >=3.8.0,<3.9.0' + - 'bioconductor-gosemsim >=2.10.0,<2.11.0' + - 'bioconductor-graph >=1.62.0,<1.63.0' + - 'bioconductor-org.hs.eg.db >=3.8.0,<3.9.0' + - 'bioconductor-org.mm.eg.db >=3.8.0,<3.9.0' + - 'bioconductor-rbgl >=1.60.0,<1.61.0' + - r-base + - r-data.table + - r-dplyr + - r-fastmatch + - r-igraph + - r-magrittr + - r-matrix + - r-matrixstats + - r-plyr + run: + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' + - 'bioconductor-biocfilecache >=1.8.0,<1.9.0' + - 'bioconductor-geoquery >=2.52.0,<2.53.0' + - 'bioconductor-go.db >=3.8.0,<3.9.0' + - 'bioconductor-gosemsim >=2.10.0,<2.11.0' + - 'bioconductor-graph >=1.62.0,<1.63.0' + - 'bioconductor-org.hs.eg.db >=3.8.0,<3.9.0' + - 'bioconductor-org.mm.eg.db >=3.8.0,<3.9.0' + - 'bioconductor-rbgl >=1.60.0,<1.61.0' + - r-base + - r-data.table + - r-dplyr + - r-fastmatch + - r-igraph + - r-magrittr + - r-matrix + - r-matrixstats + - r-plyr +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: 'MIT + file LICENSE' + summary: 'Collection of various measures and tools for lncRNA annotation prediction put inside a redistributable R package. The package contains two main algorithms; lncRNA2GOA and TopoICSim. lncRNA2GOA tries to annotate novel genes (in this specific case lncRNAs) by using various correlation/geometric scoring methods on correlated expression data. After correlating/scoring, the results are annotated and enriched. TopoICSim is a topologically based method, that compares gene similarity based on the topology of the GO DAG by information content (IC) between GO terms.' + diff --git a/recipes/bioconductor-gaprediction/meta.yaml b/recipes/bioconductor-gaprediction/meta.yaml index 19d9b028335cb..15ba8aa66c192 100644 --- a/recipes/bioconductor-gaprediction/meta.yaml +++ b/recipes/bioconductor-gaprediction/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.8.1" %} +{% set version = "1.10.0" %} {% set name = "GAprediction" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 181fe65adf80c170982cfe2c8b21e273 + md5: 90976d9f97e8ca28b0f6f54e07a142a5 build: number: 0 rpaths: diff --git a/recipes/bioconductor-garfield/meta.yaml b/recipes/bioconductor-garfield/meta.yaml index 5cf399aa58e94..b614e8b65eb84 100644 --- a/recipes/bioconductor-garfield/meta.yaml +++ b/recipes/bioconductor-garfield/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.10.0" %} +{% set version = "1.12.0" %} {% set name = "garfield" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: a32182358d9332b323393b06db079a20 + md5: 6716cb811197c02cd261b63f47272001 build: number: 0 rpaths: diff --git a/recipes/bioconductor-gars/meta.yaml b/recipes/bioconductor-gars/meta.yaml index 1c94778bd5eab..1abe5e20240be 100644 --- a/recipes/bioconductor-gars/meta.yaml +++ b/recipes/bioconductor-gars/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.2.0" %} +{% set version = "1.4.0" %} {% set name = "GARS" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 682be28045f9dab362947bae60f43b76 + md5: b665e44406eda49f0709b6fd442b69ec build: number: 0 rpaths: @@ -20,16 +20,16 @@ build: # Suggests: BiocStyle, knitr, testthat requirements: host: - - 'bioconductor-damirseq >=1.6.0,<1.7.0' - - 'bioconductor-mlseq >=2.0.0,<2.1.0' - - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' + - 'bioconductor-damirseq >=1.8.0,<1.9.0' + - 'bioconductor-mlseq >=2.2.0,<2.3.0' + - 'bioconductor-summarizedexperiment >=1.14.0,<1.15.0' - r-base - r-cluster - r-ggplot2 run: - - 'bioconductor-damirseq >=1.6.0,<1.7.0' - - 'bioconductor-mlseq >=2.0.0,<2.1.0' - - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' + - 'bioconductor-damirseq >=1.8.0,<1.9.0' + - 'bioconductor-mlseq >=2.2.0,<2.3.0' + - 'bioconductor-summarizedexperiment >=1.14.0,<1.15.0' - r-base - r-cluster - r-ggplot2 diff --git a/recipes/bioconductor-gaschyhs/meta.yaml b/recipes/bioconductor-gaschyhs/meta.yaml index 6f8cdddf039c9..03bc7146350a8 100644 --- a/recipes/bioconductor-gaschyhs/meta.yaml +++ b/recipes/bioconductor-gaschyhs/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.20.0" %} +{% set version = "1.22.0" %} {% set name = "gaschYHS" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: c6348bdc5404d69a6c6e4726478d2e62 + md5: 640ea3dc1bccf57861211b0f6395ec1b build: number: 0 rpaths: @@ -19,12 +19,12 @@ build: noarch: generic requirements: host: - - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' - r-base run: - - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-gaschyhs/post-link.sh b/recipes/bioconductor-gaschyhs/post-link.sh index 04fc385ee47a9..58ee910de7082 100644 --- a/recipes/bioconductor-gaschyhs/post-link.sh +++ b/recipes/bioconductor-gaschyhs/post-link.sh @@ -1,11 +1,11 @@ #!/bin/bash -FN="gaschYHS_1.20.0.tar.gz" +FN="gaschYHS_1.22.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/experiment/src/contrib/gaschYHS_1.20.0.tar.gz" - "https://bioarchive.galaxyproject.org/gaschYHS_1.20.0.tar.gz" - "https://depot.galaxyproject.org/software/bioconductor-gaschyhs/bioconductor-gaschyhs_1.20.0_src_all.tar.gz" + "https://bioconductor.org/packages/3.9/data/experiment/src/contrib/gaschYHS_1.22.0.tar.gz" + "https://bioarchive.galaxyproject.org/gaschYHS_1.22.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-gaschyhs/bioconductor-gaschyhs_1.22.0_src_all.tar.gz" ) -MD5="c6348bdc5404d69a6c6e4726478d2e62" +MD5="640ea3dc1bccf57861211b0f6395ec1b" # Use a staging area in the conda dir rather than temp dirs, both to avoid # permission issues as well as to have things downloaded in a predictable @@ -16,7 +16,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-gatefinder/meta.yaml b/recipes/bioconductor-gatefinder/meta.yaml index 2bc06363740e3..9a9dd1f210626 100644 --- a/recipes/bioconductor-gatefinder/meta.yaml +++ b/recipes/bioconductor-gatefinder/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.2.0" %} +{% set version = "1.4.0" %} {% set name = "GateFinder" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,25 +10,25 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 72c29a720bc9634230ca614f8cd47619 + md5: 761325ed0ae4c8fd95f7e6209b21a4ce build: number: 0 rpaths: - lib/R/lib/ - lib/ noarch: generic -# Suggests: RUnit, flowUtils, BiocGenerics +# Suggests: RUnit, BiocGenerics requirements: host: - - 'bioconductor-flowcore >=1.48.0,<1.49.0' - - 'bioconductor-flowfp >=1.40.0,<1.41.0' + - 'bioconductor-flowcore >=1.50.0,<1.51.0' + - 'bioconductor-flowfp >=1.42.0,<1.43.0' - r-base - r-diptest - r-mvoutlier - r-splancs run: - - 'bioconductor-flowcore >=1.48.0,<1.49.0' - - 'bioconductor-flowfp >=1.40.0,<1.41.0' + - 'bioconductor-flowcore >=1.50.0,<1.51.0' + - 'bioconductor-flowfp >=1.42.0,<1.43.0' - r-base - r-diptest - r-mvoutlier diff --git a/recipes/bioconductor-gatingmldata/meta.yaml b/recipes/bioconductor-gatingmldata/meta.yaml index 51b66eb20160f..21fa073f61adc 100644 --- a/recipes/bioconductor-gatingmldata/meta.yaml +++ b/recipes/bioconductor-gatingmldata/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "2.22.0" %} +{% set version = "2.24.0" %} {% set name = "gatingMLData" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: ea5dc27900b34bcf1588ec22100f1d95 + md5: 8738620aac52004fefa9a3af7194df75 build: number: 0 rpaths: @@ -23,7 +23,7 @@ requirements: - r-base run: - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-gatingmldata/post-link.sh b/recipes/bioconductor-gatingmldata/post-link.sh index 663c264881652..1a7bf1df165b3 100644 --- a/recipes/bioconductor-gatingmldata/post-link.sh +++ b/recipes/bioconductor-gatingmldata/post-link.sh @@ -1,11 +1,11 @@ #!/bin/bash -FN="gatingMLData_2.22.0.tar.gz" +FN="gatingMLData_2.24.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/experiment/src/contrib/gatingMLData_2.22.0.tar.gz" - "https://bioarchive.galaxyproject.org/gatingMLData_2.22.0.tar.gz" - "https://depot.galaxyproject.org/software/bioconductor-gatingmldata/bioconductor-gatingmldata_2.22.0_src_all.tar.gz" + "https://bioconductor.org/packages/3.9/data/experiment/src/contrib/gatingMLData_2.24.0.tar.gz" + "https://bioarchive.galaxyproject.org/gatingMLData_2.24.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-gatingmldata/bioconductor-gatingmldata_2.24.0_src_all.tar.gz" ) -MD5="ea5dc27900b34bcf1588ec22100f1d95" +MD5="8738620aac52004fefa9a3af7194df75" # Use a staging area in the conda dir rather than temp dirs, both to avoid # permission issues as well as to have things downloaded in a predictable @@ -16,7 +16,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-gcapc/meta.yaml b/recipes/bioconductor-gcapc/meta.yaml index 38ea00db785eb..0f4ac33ab79ec 100644 --- a/recipes/bioconductor-gcapc/meta.yaml +++ b/recipes/bioconductor-gcapc/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.6.0" %} +{% set version = "1.8.0" %} {% set name = "gcapc" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: ac19d863951e0b659a1d4605aafeb1c6 + md5: f607d7621f7ace1805fcd7a3afd84641 build: number: 0 rpaths: @@ -20,28 +20,28 @@ build: # Suggests: BiocStyle, knitr, rmarkdown, BSgenome.Hsapiens.UCSC.hg19, BSgenome.Mmusculus.UCSC.mm10 requirements: host: - - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' - - 'bioconductor-biostrings >=2.50.0,<2.51.0' - - 'bioconductor-bsgenome >=1.50.0,<1.51.0' - - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' - - 'bioconductor-genomicalignments >=1.18.0,<1.19.0' - - 'bioconductor-genomicranges >=1.34.0,<1.35.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-rsamtools >=1.34.0,<1.35.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-biocgenerics >=0.30.0,<0.31.0' + - 'bioconductor-biostrings >=2.52.0,<2.53.0' + - 'bioconductor-bsgenome >=1.52.0,<1.53.0' + - 'bioconductor-genomeinfodb >=1.20.0,<1.21.0' + - 'bioconductor-genomicalignments >=1.20.0,<1.21.0' + - 'bioconductor-genomicranges >=1.36.0,<1.37.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-rsamtools >=2.0.0,<2.1.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' - r-base - r-mass - r-matrixstats run: - - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' - - 'bioconductor-biostrings >=2.50.0,<2.51.0' - - 'bioconductor-bsgenome >=1.50.0,<1.51.0' - - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' - - 'bioconductor-genomicalignments >=1.18.0,<1.19.0' - - 'bioconductor-genomicranges >=1.34.0,<1.35.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-rsamtools >=1.34.0,<1.35.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-biocgenerics >=0.30.0,<0.31.0' + - 'bioconductor-biostrings >=2.52.0,<2.53.0' + - 'bioconductor-bsgenome >=1.52.0,<1.53.0' + - 'bioconductor-genomeinfodb >=1.20.0,<1.21.0' + - 'bioconductor-genomicalignments >=1.20.0,<1.21.0' + - 'bioconductor-genomicranges >=1.36.0,<1.37.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-rsamtools >=2.0.0,<2.1.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' - r-base - r-mass - r-matrixstats diff --git a/recipes/bioconductor-gcatest/meta.yaml b/recipes/bioconductor-gcatest/meta.yaml index 00613102cb8fd..2f8fb8efe4c4f 100644 --- a/recipes/bioconductor-gcatest/meta.yaml +++ b/recipes/bioconductor-gcatest/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.12.0" %} +{% set version = "1.14.0" %} {% set name = "gcatest" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 4fdd3965d7db773c137fbd281f34d6e8 + md5: 443b739eb0572f57d9a0a6d7e4a2a620 build: number: 0 rpaths: @@ -19,10 +19,10 @@ build: # Suggests: knitr, ggplot2 requirements: host: - - 'bioconductor-lfa >=1.12.0,<1.13.0' + - 'bioconductor-lfa >=1.14.0,<1.15.0' - r-base run: - - 'bioconductor-lfa >=1.12.0,<1.13.0' + - 'bioconductor-lfa >=1.14.0,<1.15.0' - r-base build: - {{ compiler('c') }} diff --git a/recipes/bioconductor-gcmap/meta.yaml b/recipes/bioconductor-gcmap/meta.yaml index ab1d955ccef89..f923b2c8977d3 100644 --- a/recipes/bioconductor-gcmap/meta.yaml +++ b/recipes/bioconductor-gcmap/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.26.0" %} +{% set version = "1.28.0" %} {% set name = "gCMAP" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 3753b67183a2d0c21be53cf900eda12a + md5: 059af72e07332cff9038a6abe84cf21a build: number: 0 rpaths: @@ -20,30 +20,30 @@ build: # Suggests: BiocGenerics, KEGG.db, reactome.db, RUnit, GO.db, mgsa requirements: host: - - 'bioconductor-annotate >=1.60.0,<1.61.0' - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' - - 'bioconductor-bigmemoryextras >=1.30.0,<1.31.0' - - 'bioconductor-biobase >=2.42.0,<2.43.0' - - 'bioconductor-category >=2.48.0,<2.49.0' - - 'bioconductor-deseq >=1.34.0,<1.35.0' - - 'bioconductor-genefilter >=1.64.0,<1.65.0' - - 'bioconductor-gseabase >=1.44.0,<1.45.0' - - 'bioconductor-gsealm >=1.42.0,<1.43.0' - - 'bioconductor-limma >=3.38.0,<3.39.0' + - 'bioconductor-annotate >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' + - 'bioconductor-bigmemoryextras >=1.32.0,<1.33.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' + - 'bioconductor-category >=2.50.0,<2.51.0' + - 'bioconductor-deseq >=1.36.0,<1.37.0' + - 'bioconductor-genefilter >=1.66.0,<1.67.0' + - 'bioconductor-gseabase >=1.46.0,<1.47.0' + - 'bioconductor-gsealm >=1.44.0,<1.45.0' + - 'bioconductor-limma >=3.40.0,<3.41.0' - r-base - r-bigmemory - 'r-matrix >=1.0.9' run: - - 'bioconductor-annotate >=1.60.0,<1.61.0' - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' - - 'bioconductor-bigmemoryextras >=1.30.0,<1.31.0' - - 'bioconductor-biobase >=2.42.0,<2.43.0' - - 'bioconductor-category >=2.48.0,<2.49.0' - - 'bioconductor-deseq >=1.34.0,<1.35.0' - - 'bioconductor-genefilter >=1.64.0,<1.65.0' - - 'bioconductor-gseabase >=1.44.0,<1.45.0' - - 'bioconductor-gsealm >=1.42.0,<1.43.0' - - 'bioconductor-limma >=3.38.0,<3.39.0' + - 'bioconductor-annotate >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' + - 'bioconductor-bigmemoryextras >=1.32.0,<1.33.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' + - 'bioconductor-category >=2.50.0,<2.51.0' + - 'bioconductor-deseq >=1.36.0,<1.37.0' + - 'bioconductor-genefilter >=1.66.0,<1.67.0' + - 'bioconductor-gseabase >=1.46.0,<1.47.0' + - 'bioconductor-gsealm >=1.44.0,<1.45.0' + - 'bioconductor-limma >=3.40.0,<3.41.0' - r-base - r-bigmemory - 'r-matrix >=1.0.9' diff --git a/recipes/bioconductor-gcmapweb/meta.yaml b/recipes/bioconductor-gcmapweb/meta.yaml index f7ea7d1567e53..37db43f251bc9 100644 --- a/recipes/bioconductor-gcmapweb/meta.yaml +++ b/recipes/bioconductor-gcmapweb/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.22.0" %} +{% set version = "1.24.0" %} {% set name = "gCMAPWeb" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 2d2b869ba468ba3932dc14580d96f88f + md5: 271ff957589aeabcef3b64198399ad4d build: number: 0 rpaths: @@ -20,24 +20,24 @@ build: # Suggests: affy, ArrayExpress, hgfocus.db, hgu133a.db, mgug4104a.db, org.Hs.eg.db, org.Mm.eg.db, RUnit requirements: host: - - 'bioconductor-annotate >=1.60.0,<1.61.0' - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' - - 'bioconductor-biobase >=2.42.0,<2.43.0' - - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' - - 'bioconductor-gcmap >=1.26.0,<1.27.0' - - 'bioconductor-gseabase >=1.44.0,<1.45.0' + - 'bioconductor-annotate >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' + - 'bioconductor-biocgenerics >=0.30.0,<0.31.0' + - 'bioconductor-gcmap >=1.28.0,<1.29.0' + - 'bioconductor-gseabase >=1.46.0,<1.47.0' - r-base - r-brew - r-hwriter - r-rook - r-yaml run: - - 'bioconductor-annotate >=1.60.0,<1.61.0' - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' - - 'bioconductor-biobase >=2.42.0,<2.43.0' - - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' - - 'bioconductor-gcmap >=1.26.0,<1.27.0' - - 'bioconductor-gseabase >=1.44.0,<1.45.0' + - 'bioconductor-annotate >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' + - 'bioconductor-biocgenerics >=0.30.0,<0.31.0' + - 'bioconductor-gcmap >=1.28.0,<1.29.0' + - 'bioconductor-gseabase >=1.46.0,<1.47.0' - r-base - r-brew - r-hwriter diff --git a/recipes/bioconductor-gcrisprtools/meta.yaml b/recipes/bioconductor-gcrisprtools/meta.yaml index 3f7824867863e..40f3cc1084f09 100644 --- a/recipes/bioconductor-gcrisprtools/meta.yaml +++ b/recipes/bioconductor-gcrisprtools/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.10.0" %} +{% set version = "1.12.0" %} {% set name = "gCrisprTools" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 1c5860fdfdf165520493eecf72540ce8 + md5: e5485064448e1a89aedae9dbb1725be1 build: number: 0 rpaths: @@ -20,16 +20,16 @@ build: # Suggests: edgeR, knitr, grid, AnnotationDbi, org.Mm.eg.db, org.Hs.eg.db, RUnit, BiocGenerics requirements: host: - - 'bioconductor-biobase >=2.42.0,<2.43.0' - - 'bioconductor-limma >=3.38.0,<3.39.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' + - 'bioconductor-limma >=3.40.0,<3.41.0' - 'bioconductor-panther.db >=1.0.0,<1.1.0' - r-base - r-ggplot2 - r-rmarkdown - r-robustrankaggreg run: - - 'bioconductor-biobase >=2.42.0,<2.43.0' - - 'bioconductor-limma >=3.38.0,<3.39.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' + - 'bioconductor-limma >=3.40.0,<3.41.0' - 'bioconductor-panther.db >=1.0.0,<1.1.0' - r-base - r-ggplot2 diff --git a/recipes/bioconductor-gcrma/meta.yaml b/recipes/bioconductor-gcrma/meta.yaml index 945290c8a17de..860aa082f72d2 100644 --- a/recipes/bioconductor-gcrma/meta.yaml +++ b/recipes/bioconductor-gcrma/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "2.54.0" %} +{% set version = "2.56.0" %} {% set name = "gcrma" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 413897a1c3888e7ee57ee6c5f238934c + md5: 62510ade73f9c0b8823e51b6bff2c322 build: number: 0 rpaths: @@ -19,19 +19,19 @@ build: # Suggests: affydata, tools, splines, hgu95av2cdf, hgu95av2probe requirements: host: - - 'bioconductor-affy >=1.60.0,<1.61.0' - - 'bioconductor-affyio >=1.52.0,<1.53.0' - - 'bioconductor-biobase >=2.42.0,<2.43.0' - - 'bioconductor-biostrings >=2.50.0,<2.51.0' - - 'bioconductor-xvector >=0.22.0,<0.23.0' + - 'bioconductor-affy >=1.62.0,<1.63.0' + - 'bioconductor-affyio >=1.54.0,<1.55.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' + - 'bioconductor-biostrings >=2.52.0,<2.53.0' + - 'bioconductor-xvector >=0.24.0,<0.25.0' - r-base - r-biocmanager run: - - 'bioconductor-affy >=1.60.0,<1.61.0' - - 'bioconductor-affyio >=1.52.0,<1.53.0' - - 'bioconductor-biobase >=2.42.0,<2.43.0' - - 'bioconductor-biostrings >=2.50.0,<2.51.0' - - 'bioconductor-xvector >=0.22.0,<0.23.0' + - 'bioconductor-affy >=1.62.0,<1.63.0' + - 'bioconductor-affyio >=1.54.0,<1.55.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' + - 'bioconductor-biostrings >=2.52.0,<2.53.0' + - 'bioconductor-xvector >=0.24.0,<0.25.0' - r-base - r-biocmanager build: diff --git a/recipes/bioconductor-gcspikelite/meta.yaml b/recipes/bioconductor-gcspikelite/meta.yaml index f32e532bf3882..6aca6897360ea 100644 --- a/recipes/bioconductor-gcspikelite/meta.yaml +++ b/recipes/bioconductor-gcspikelite/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.20.0" %} +{% set version = "1.22.0" %} {% set name = "gcspikelite" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: d365d11462a9a1ed68634ff8e9e0cfa4 + md5: 008f920fa946568d0e31d4333e2fe28c build: number: 0 rpaths: @@ -22,7 +22,7 @@ requirements: - r-base run: - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-gcspikelite/post-link.sh b/recipes/bioconductor-gcspikelite/post-link.sh index 43f3c952bc38e..25ba2a28abbb5 100644 --- a/recipes/bioconductor-gcspikelite/post-link.sh +++ b/recipes/bioconductor-gcspikelite/post-link.sh @@ -1,11 +1,11 @@ #!/bin/bash -FN="gcspikelite_1.20.0.tar.gz" +FN="gcspikelite_1.22.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/experiment/src/contrib/gcspikelite_1.20.0.tar.gz" - "https://bioarchive.galaxyproject.org/gcspikelite_1.20.0.tar.gz" - "https://depot.galaxyproject.org/software/bioconductor-gcspikelite/bioconductor-gcspikelite_1.20.0_src_all.tar.gz" + "https://bioconductor.org/packages/3.9/data/experiment/src/contrib/gcspikelite_1.22.0.tar.gz" + "https://bioarchive.galaxyproject.org/gcspikelite_1.22.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-gcspikelite/bioconductor-gcspikelite_1.22.0_src_all.tar.gz" ) -MD5="d365d11462a9a1ed68634ff8e9e0cfa4" +MD5="008f920fa946568d0e31d4333e2fe28c" # Use a staging area in the conda dir rather than temp dirs, both to avoid # permission issues as well as to have things downloaded in a predictable @@ -16,7 +16,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-gdcrnatools/meta.yaml b/recipes/bioconductor-gdcrnatools/meta.yaml index efc9c13989db8..3690eec145f25 100644 --- a/recipes/bioconductor-gdcrnatools/meta.yaml +++ b/recipes/bioconductor-gdcrnatools/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.2.0" %} +{% set version = "1.4.0" %} {% set name = "GDCRNATools" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: e702d575672f68f5b46c0ec7f872442d + md5: 4dcda733dd967b458c3c2299a5ac3f0e build: number: 0 rpaths: @@ -20,16 +20,16 @@ build: # Suggests: knitr, testthat requirements: host: - - 'bioconductor-biocparallel >=1.16.0,<1.17.0' - - 'bioconductor-biomart >=2.38.0,<2.39.0' - - 'bioconductor-clusterprofiler >=3.10.0,<3.11.0' - - 'bioconductor-deseq2 >=1.22.0,<1.23.0' - - 'bioconductor-dose >=3.8.0,<3.9.0' - - 'bioconductor-edger >=3.24.0,<3.25.0' - - 'bioconductor-genomicdatacommons >=1.6.0,<1.7.0' - - 'bioconductor-limma >=3.38.0,<3.39.0' - - 'bioconductor-org.hs.eg.db >=3.7.0,<3.8.0' - - 'bioconductor-pathview >=1.22.0,<1.23.0' + - 'bioconductor-biocparallel >=1.18.0,<1.19.0' + - 'bioconductor-biomart >=2.40.0,<2.41.0' + - 'bioconductor-clusterprofiler >=3.12.0,<3.13.0' + - 'bioconductor-deseq2 >=1.24.0,<1.25.0' + - 'bioconductor-dose >=3.10.0,<3.11.0' + - 'bioconductor-edger >=3.26.0,<3.27.0' + - 'bioconductor-genomicdatacommons >=1.8.0,<1.9.0' + - 'bioconductor-limma >=3.40.0,<3.41.0' + - 'bioconductor-org.hs.eg.db >=3.8.0,<3.9.0' + - 'bioconductor-pathview >=1.24.0,<1.25.0' - r-base - r-dt - r-ggplot2 @@ -41,16 +41,16 @@ requirements: - r-survminer - r-xml run: - - 'bioconductor-biocparallel >=1.16.0,<1.17.0' - - 'bioconductor-biomart >=2.38.0,<2.39.0' - - 'bioconductor-clusterprofiler >=3.10.0,<3.11.0' - - 'bioconductor-deseq2 >=1.22.0,<1.23.0' - - 'bioconductor-dose >=3.8.0,<3.9.0' - - 'bioconductor-edger >=3.24.0,<3.25.0' - - 'bioconductor-genomicdatacommons >=1.6.0,<1.7.0' - - 'bioconductor-limma >=3.38.0,<3.39.0' - - 'bioconductor-org.hs.eg.db >=3.7.0,<3.8.0' - - 'bioconductor-pathview >=1.22.0,<1.23.0' + - 'bioconductor-biocparallel >=1.18.0,<1.19.0' + - 'bioconductor-biomart >=2.40.0,<2.41.0' + - 'bioconductor-clusterprofiler >=3.12.0,<3.13.0' + - 'bioconductor-deseq2 >=1.24.0,<1.25.0' + - 'bioconductor-dose >=3.10.0,<3.11.0' + - 'bioconductor-edger >=3.26.0,<3.27.0' + - 'bioconductor-genomicdatacommons >=1.8.0,<1.9.0' + - 'bioconductor-limma >=3.40.0,<3.41.0' + - 'bioconductor-org.hs.eg.db >=3.8.0,<3.9.0' + - 'bioconductor-pathview >=1.24.0,<1.25.0' - r-base - r-dt - r-ggplot2 diff --git a/recipes/bioconductor-gdsarray/meta.yaml b/recipes/bioconductor-gdsarray/meta.yaml index d0340c460ea2b..b2eeb4a003a0d 100644 --- a/recipes/bioconductor-gdsarray/meta.yaml +++ b/recipes/bioconductor-gdsarray/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.2.0" %} +{% set version = "1.4.0" %} {% set name = "GDSArray" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,9 +10,9 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 6c3b4ae29009e0e1bf5c6cee249a25a5 + md5: 182eb14be19507ec332ea86f92eec9c1 build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ @@ -20,20 +20,20 @@ build: # Suggests: testthat, knitr, BiocStyle, BiocManager requirements: host: - - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' - - 'bioconductor-delayedarray >=0.8.0,<0.9.0' - - 'bioconductor-gdsfmt >=1.18.0,<1.19.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' - - 'bioconductor-seqarray >=1.22.0,<1.23.0' - - 'bioconductor-snprelate >=1.16.0,<1.17.0' + - 'bioconductor-biocgenerics >=0.30.0,<0.31.0' + - 'bioconductor-delayedarray >=0.10.0,<0.11.0' + - 'bioconductor-gdsfmt >=1.20.0,<1.21.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' + - 'bioconductor-seqarray >=1.24.0,<1.25.0' + - 'bioconductor-snprelate >=1.18.0,<1.19.0' - r-base run: - - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' - - 'bioconductor-delayedarray >=0.8.0,<0.9.0' - - 'bioconductor-gdsfmt >=1.18.0,<1.19.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' - - 'bioconductor-seqarray >=1.22.0,<1.23.0' - - 'bioconductor-snprelate >=1.16.0,<1.17.0' + - 'bioconductor-biocgenerics >=0.30.0,<0.31.0' + - 'bioconductor-delayedarray >=0.10.0,<0.11.0' + - 'bioconductor-gdsfmt >=1.20.0,<1.21.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' + - 'bioconductor-seqarray >=1.24.0,<1.25.0' + - 'bioconductor-snprelate >=1.18.0,<1.19.0' - r-base test: commands: diff --git a/recipes/bioconductor-gdsfmt/meta.yaml b/recipes/bioconductor-gdsfmt/meta.yaml index 3edc7ffe286f1..5fedf30373cda 100644 --- a/recipes/bioconductor-gdsfmt/meta.yaml +++ b/recipes/bioconductor-gdsfmt/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.18.1" %} +{% set version = "1.20.0" %} {% set name = "gdsfmt" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 7538626e88124c3fc733b67512f7179d + md5: 5778f3ca0a10bc914759350f8d42e091 build: number: 0 rpaths: diff --git a/recipes/bioconductor-geecc/meta.yaml b/recipes/bioconductor-geecc/meta.yaml index 9ac2f15ee6caf..d6176c4be0acf 100644 --- a/recipes/bioconductor-geecc/meta.yaml +++ b/recipes/bioconductor-geecc/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.16.1" %} +{% set version = "1.18.0" %} {% set name = "geecc" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 48ad185a3e1ba4bdf4b1bb868221b507 + md5: 4f779900b8bc8e0953aa230712cc1f61 build: number: 0 rpaths: diff --git a/recipes/bioconductor-gem/meta.yaml b/recipes/bioconductor-gem/meta.yaml index 6f5336e43be8b..f07928c80e411 100644 --- a/recipes/bioconductor-gem/meta.yaml +++ b/recipes/bioconductor-gem/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.8.0" %} +{% set version = "1.10.0" %} {% set name = "GEM" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 06d08b08b90d67d3bfd976aef192dc52 + md5: 2e92486e419e74aa7da4884e857cb7ad build: number: 0 rpaths: diff --git a/recipes/bioconductor-genarise/meta.yaml b/recipes/bioconductor-genarise/meta.yaml index 6c0b2f104e4a0..30203a403c61b 100644 --- a/recipes/bioconductor-genarise/meta.yaml +++ b/recipes/bioconductor-genarise/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.58.0" %} +{% set version = "1.60.0" %} {% set name = "genArise" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 4b848ac87c655ce850a42af452508f99 + md5: 402bb601fc9494da58dacac7c66457f6 build: number: 0 rpaths: diff --git a/recipes/bioconductor-genbankr/meta.yaml b/recipes/bioconductor-genbankr/meta.yaml index 7af1401c5e586..79fe08524ec24 100644 --- a/recipes/bioconductor-genbankr/meta.yaml +++ b/recipes/bioconductor-genbankr/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.10.0" %} +{% set version = "1.12.0" %} {% set name = "genbankr" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 3eb9b0da2de16e06cbf5adcf518b27ac + md5: 282798884cfbad30dc4ff75b1498c910 build: number: 0 rpaths: @@ -20,28 +20,28 @@ build: # Suggests: RUnit, rentrez, knitr, rmarkdown, BiocStyle requirements: host: - - 'bioconductor-biobase >=2.42.0,<2.43.0' - - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' - - 'bioconductor-biostrings >=2.50.0,<2.51.0' - - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' - - 'bioconductor-genomicfeatures >=1.34.0,<1.35.0' - - 'bioconductor-genomicranges >=1.34.0,<1.35.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-rtracklayer >=1.42.0,<1.43.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' - - 'bioconductor-variantannotation >=1.28.0,<1.29.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' + - 'bioconductor-biocgenerics >=0.30.0,<0.31.0' + - 'bioconductor-biostrings >=2.52.0,<2.53.0' + - 'bioconductor-genomeinfodb >=1.20.0,<1.21.0' + - 'bioconductor-genomicfeatures >=1.36.0,<1.37.0' + - 'bioconductor-genomicranges >=1.36.0,<1.37.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-rtracklayer >=1.44.0,<1.45.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' + - 'bioconductor-variantannotation >=1.30.0,<1.31.0' - r-base run: - - 'bioconductor-biobase >=2.42.0,<2.43.0' - - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' - - 'bioconductor-biostrings >=2.50.0,<2.51.0' - - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' - - 'bioconductor-genomicfeatures >=1.34.0,<1.35.0' - - 'bioconductor-genomicranges >=1.34.0,<1.35.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-rtracklayer >=1.42.0,<1.43.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' - - 'bioconductor-variantannotation >=1.28.0,<1.29.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' + - 'bioconductor-biocgenerics >=0.30.0,<0.31.0' + - 'bioconductor-biostrings >=2.52.0,<2.53.0' + - 'bioconductor-genomeinfodb >=1.20.0,<1.21.0' + - 'bioconductor-genomicfeatures >=1.36.0,<1.37.0' + - 'bioconductor-genomicranges >=1.36.0,<1.37.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-rtracklayer >=1.44.0,<1.45.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' + - 'bioconductor-variantannotation >=1.30.0,<1.31.0' - r-base test: commands: diff --git a/recipes/bioconductor-geneaccord/meta.yaml b/recipes/bioconductor-geneaccord/meta.yaml index 4a14e1a1da938..671a769eeffec 100644 --- a/recipes/bioconductor-geneaccord/meta.yaml +++ b/recipes/bioconductor-geneaccord/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.0.0" %} +{% set version = "1.2.0" %} {% set name = "GeneAccord" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 20327d63683336b7ae0f47d9757727b3 + md5: 2af2f56aea9f6d6e079a19365ece474a build: number: 0 rpaths: @@ -20,7 +20,7 @@ build: # Suggests: assertthat, BiocStyle, devtools, knitr, rmarkdown, testthat requirements: host: - - 'bioconductor-biomart >=2.38.0,<2.39.0' + - 'bioconductor-biomart >=2.40.0,<2.41.0' - r-base - r-catools - r-dplyr @@ -33,7 +33,7 @@ requirements: - r-reshape2 - r-tibble run: - - 'bioconductor-biomart >=2.38.0,<2.39.0' + - 'bioconductor-biomart >=2.40.0,<2.41.0' - r-base - r-catools - r-dplyr diff --git a/recipes/bioconductor-geneanswers/meta.yaml b/recipes/bioconductor-geneanswers/meta.yaml index 227fe81b544be..a8177c41a2376 100644 --- a/recipes/bioconductor-geneanswers/meta.yaml +++ b/recipes/bioconductor-geneanswers/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "2.24.0" %} +{% set version = "2.26.0" %} {% set name = "GeneAnswers" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 0d3cf555819cf8b8d71029082abc33e1 + md5: fd8e5e90f98efbb2045e11d42e1b1f36 build: number: 0 rpaths: @@ -20,10 +20,10 @@ build: # Suggests: GO.db, KEGG.db, reactome.db, biomaRt, AnnotationDbi, org.Hs.eg.db, org.Rn.eg.db, org.Mm.eg.db, org.Dm.eg.db, graph requirements: host: - - 'bioconductor-annotate >=1.60.0,<1.61.0' - - 'bioconductor-biobase >=2.42.0,<2.43.0' - - 'bioconductor-heatplus >=2.28.0,<2.29.0' - - 'bioconductor-rbgl >=1.58.0,<1.59.0' + - 'bioconductor-annotate >=1.62.0,<1.63.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' + - 'bioconductor-heatplus >=2.30.0,<2.31.0' + - 'bioconductor-rbgl >=1.60.0,<1.61.0' - r-base - r-downloader - r-igraph @@ -33,10 +33,10 @@ requirements: - r-rsqlite - r-xml run: - - 'bioconductor-annotate >=1.60.0,<1.61.0' - - 'bioconductor-biobase >=2.42.0,<2.43.0' - - 'bioconductor-heatplus >=2.28.0,<2.29.0' - - 'bioconductor-rbgl >=1.58.0,<1.59.0' + - 'bioconductor-annotate >=1.62.0,<1.63.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' + - 'bioconductor-heatplus >=2.30.0,<2.31.0' + - 'bioconductor-rbgl >=1.60.0,<1.61.0' - r-base - r-downloader - r-igraph diff --git a/recipes/bioconductor-geneattribution/meta.yaml b/recipes/bioconductor-geneattribution/meta.yaml index 956b3de14db15..4db4000922b5d 100644 --- a/recipes/bioconductor-geneattribution/meta.yaml +++ b/recipes/bioconductor-geneattribution/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.8.0" %} +{% set version = "1.10.0" %} {% set name = "geneAttribution" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: f789b0c41a0d5bcce055f113b718d583 + md5: 37a9d2c93f2b96fd64ca5e27574680a0 build: number: 0 rpaths: @@ -20,22 +20,22 @@ build: # Suggests: TxDb.Hsapiens.UCSC.hg38.knownGene, TxDb.Hsapiens.UCSC.hg19.knownGene, knitr, rmarkdown, testthat requirements: host: - - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' - - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' - - 'bioconductor-genomicfeatures >=1.34.0,<1.35.0' - - 'bioconductor-genomicranges >=1.34.0,<1.35.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-org.hs.eg.db >=3.7.0,<3.8.0' - - 'bioconductor-rtracklayer >=1.42.0,<1.43.0' + - 'bioconductor-biocgenerics >=0.30.0,<0.31.0' + - 'bioconductor-genomeinfodb >=1.20.0,<1.21.0' + - 'bioconductor-genomicfeatures >=1.36.0,<1.37.0' + - 'bioconductor-genomicranges >=1.36.0,<1.37.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-org.hs.eg.db >=3.8.0,<3.9.0' + - 'bioconductor-rtracklayer >=1.44.0,<1.45.0' - r-base run: - - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' - - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' - - 'bioconductor-genomicfeatures >=1.34.0,<1.35.0' - - 'bioconductor-genomicranges >=1.34.0,<1.35.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-org.hs.eg.db >=3.7.0,<3.8.0' - - 'bioconductor-rtracklayer >=1.42.0,<1.43.0' + - 'bioconductor-biocgenerics >=0.30.0,<0.31.0' + - 'bioconductor-genomeinfodb >=1.20.0,<1.21.0' + - 'bioconductor-genomicfeatures >=1.36.0,<1.37.0' + - 'bioconductor-genomicranges >=1.36.0,<1.37.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-org.hs.eg.db >=3.8.0,<3.9.0' + - 'bioconductor-rtracklayer >=1.44.0,<1.45.0' - r-base test: commands: diff --git a/recipes/bioconductor-genebreak/meta.yaml b/recipes/bioconductor-genebreak/meta.yaml index bc98de079d832..3f6dc5acbf301 100644 --- a/recipes/bioconductor-genebreak/meta.yaml +++ b/recipes/bioconductor-genebreak/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.12.0" %} +{% set version = "1.14.0" %} {% set name = "GeneBreak" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 6210aae2a4a0e02205f7fcb10831f943 + md5: dc709035c22b79fe16ce899a4e300857 build: number: 0 rpaths: @@ -19,16 +19,16 @@ build: noarch: generic requirements: host: - - 'bioconductor-cghbase >=1.42.0,<1.43.0' - - 'bioconductor-cghcall >=2.44.0,<2.45.0' - - 'bioconductor-genomicranges >=1.34.0,<1.35.0' - - 'bioconductor-qdnaseq >=1.18.0,<1.19.0' + - 'bioconductor-cghbase >=1.44.0,<1.45.0' + - 'bioconductor-cghcall >=2.46.0,<2.47.0' + - 'bioconductor-genomicranges >=1.36.0,<1.37.0' + - 'bioconductor-qdnaseq >=1.20.0,<1.21.0' - r-base run: - - 'bioconductor-cghbase >=1.42.0,<1.43.0' - - 'bioconductor-cghcall >=2.44.0,<2.45.0' - - 'bioconductor-genomicranges >=1.34.0,<1.35.0' - - 'bioconductor-qdnaseq >=1.18.0,<1.19.0' + - 'bioconductor-cghbase >=1.44.0,<1.45.0' + - 'bioconductor-cghcall >=2.46.0,<2.47.0' + - 'bioconductor-genomicranges >=1.36.0,<1.37.0' + - 'bioconductor-qdnaseq >=1.20.0,<1.21.0' - r-base test: commands: diff --git a/recipes/bioconductor-geneclassifiers/meta.yaml b/recipes/bioconductor-geneclassifiers/meta.yaml index 22fa21219908a..2274568a3ec8d 100644 --- a/recipes/bioconductor-geneclassifiers/meta.yaml +++ b/recipes/bioconductor-geneclassifiers/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.6.0" %} +{% set version = "1.8.0" %} {% set name = "geneClassifiers" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 2af1e841e8a184c21b9d0d1c6907d376 + md5: 70331d8e3d86ebc811c144dd58759ca4 build: number: 0 rpaths: @@ -20,12 +20,12 @@ build: # Suggests: testthat requirements: host: - - 'bioconductor-biobase >=2.42.0,<2.43.0' - - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' + - 'bioconductor-biocgenerics >=0.30.0,<0.31.0' - r-base run: - - 'bioconductor-biobase >=2.42.0,<2.43.0' - - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' + - 'bioconductor-biocgenerics >=0.30.0,<0.31.0' - r-base test: commands: diff --git a/recipes/bioconductor-geneexpressionsignature/meta.yaml b/recipes/bioconductor-geneexpressionsignature/meta.yaml index cc1406088fc6e..cea78c036ed00 100644 --- a/recipes/bioconductor-geneexpressionsignature/meta.yaml +++ b/recipes/bioconductor-geneexpressionsignature/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.28.0" %} +{% set version = "1.30.0" %} {% set name = "GeneExpressionSignature" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 00e1e0a915a2a1455f65c1dd159427cc + md5: 295460a18d140851e6f3852e80973cd4 build: number: 0 rpaths: @@ -20,12 +20,12 @@ build: # Suggests: apcluster,GEOquery requirements: host: - - 'bioconductor-biobase >=2.42.0,<2.43.0' - - 'bioconductor-pgsea >=1.56.0,<1.57.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' + - 'bioconductor-pgsea >=1.58.0,<1.59.0' - r-base run: - - 'bioconductor-biobase >=2.42.0,<2.43.0' - - 'bioconductor-pgsea >=1.56.0,<1.57.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' + - 'bioconductor-pgsea >=1.58.0,<1.59.0' - r-base test: commands: diff --git a/recipes/bioconductor-genefilter/meta.yaml b/recipes/bioconductor-genefilter/meta.yaml index 86227c15b5dc6..0fb34033dd65b 100644 --- a/recipes/bioconductor-genefilter/meta.yaml +++ b/recipes/bioconductor-genefilter/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.64.0" %} +{% set version = "1.66.0" %} {% set name = "genefilter" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,26 +10,26 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 88bde15c167b64adeaeb6396a4adafed + md5: 89a16c8a1c9ec26f6429981b785a15b0 build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ # Suggests: class, hgu95av2.db, tkWidgets, ALL, ROC, DESeq, pasilla, RColorBrewer, BiocStyle, knitr requirements: host: - - 'bioconductor-annotate >=1.60.0,<1.61.0' - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' - - 'bioconductor-biobase >=2.42.0,<2.43.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-annotate >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' - r-base - r-survival run: - - 'bioconductor-annotate >=1.60.0,<1.61.0' - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' - - 'bioconductor-biobase >=2.42.0,<2.43.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-annotate >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' - r-base - r-survival build: diff --git a/recipes/bioconductor-genefu/meta.yaml b/recipes/bioconductor-genefu/meta.yaml index 6f871b132794d..ecba655532a0e 100644 --- a/recipes/bioconductor-genefu/meta.yaml +++ b/recipes/bioconductor-genefu/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "2.14.0" %} +{% set version = "2.16.0" %} {% set name = "genefu" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 26fd028d750b137edebcdbf8966c0324 + md5: 55607b25477679e847b5febd2b8345e0 build: number: 0 rpaths: @@ -20,19 +20,21 @@ build: # Suggests: GeneMeta, breastCancerVDX, breastCancerMAINZ, breastCancerTRANSBIG, breastCancerUPP, breastCancerUNT, breastCancerNKI, rmeta, Biobase, xtable, knitr, caret, survival requirements: host: - - 'bioconductor-aims >=1.14.0,<1.15.0' - - 'bioconductor-biomart >=2.38.0,<2.39.0' - - 'bioconductor-limma >=3.38.0,<3.39.0' - - 'bioconductor-survcomp >=1.32.0,<1.33.0' + - 'bioconductor-aims >=1.16.0,<1.17.0' + - 'bioconductor-biomart >=2.40.0,<2.41.0' + - 'bioconductor-impute >=1.58.0,<1.59.0' + - 'bioconductor-limma >=3.40.0,<3.41.0' + - 'bioconductor-survcomp >=1.34.0,<1.35.0' - r-amap - r-base - r-ic10 - r-mclust run: - - 'bioconductor-aims >=1.14.0,<1.15.0' - - 'bioconductor-biomart >=2.38.0,<2.39.0' - - 'bioconductor-limma >=3.38.0,<3.39.0' - - 'bioconductor-survcomp >=1.32.0,<1.33.0' + - 'bioconductor-aims >=1.16.0,<1.17.0' + - 'bioconductor-biomart >=2.40.0,<2.41.0' + - 'bioconductor-impute >=1.58.0,<1.59.0' + - 'bioconductor-limma >=3.40.0,<3.41.0' + - 'bioconductor-survcomp >=1.34.0,<1.35.0' - r-amap - r-base - r-ic10 diff --git a/recipes/bioconductor-genega/meta.yaml b/recipes/bioconductor-genega/meta.yaml index 2b0b99c0f0068..1e812c0f99c18 100644 --- a/recipes/bioconductor-genega/meta.yaml +++ b/recipes/bioconductor-genega/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.32.0" %} +{% set version = "1.34.0" %} {% set name = "GeneGA" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 4d664e7a6933501a3286da527d3f306c + md5: e4fe3036db49cde6d708962fd1ed1739 build: number: 0 rpaths: diff --git a/recipes/bioconductor-genegeneinter/meta.yaml b/recipes/bioconductor-genegeneinter/meta.yaml index ab227e81ed466..fbe335bb23020 100644 --- a/recipes/bioconductor-genegeneinter/meta.yaml +++ b/recipes/bioconductor-genegeneinter/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.8.0" %} +{% set version = "1.10.0" %} {% set name = "GeneGeneInteR" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,20 +10,19 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: aa36bdccea1e40711a5ed4b583c8e602 + md5: 31d000883a38923e0e8b964c92f73d40 build: number: 0 rpaths: - lib/R/lib/ - lib/ - noarch: generic requirements: host: - - 'bioconductor-genomicranges >=1.34.0,<1.35.0' - - 'bioconductor-ggtools >=5.18.0,<5.19.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-rsamtools >=1.34.0,<1.35.0' - - 'bioconductor-snpstats >=1.32.0,<1.33.0' + - 'bioconductor-genomicranges >=1.36.0,<1.37.0' + - 'bioconductor-ggtools >=5.20.0,<5.21.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-rsamtools >=2.0.0,<2.1.0' + - 'bioconductor-snpstats >=1.34.0,<1.35.0' - r-base - r-data.table - r-factominer @@ -31,13 +30,12 @@ requirements: - r-kernlab - r-mvtnorm - r-plspm - - r-rioja run: - - 'bioconductor-genomicranges >=1.34.0,<1.35.0' - - 'bioconductor-ggtools >=5.18.0,<5.19.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-rsamtools >=1.34.0,<1.35.0' - - 'bioconductor-snpstats >=1.32.0,<1.33.0' + - 'bioconductor-genomicranges >=1.36.0,<1.37.0' + - 'bioconductor-ggtools >=5.20.0,<5.21.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-rsamtools >=2.0.0,<2.1.0' + - 'bioconductor-snpstats >=1.34.0,<1.35.0' - r-base - r-data.table - r-factominer @@ -45,7 +43,10 @@ requirements: - r-kernlab - r-mvtnorm - r-plspm - - r-rioja + build: + - {{ compiler('c') }} + - {{ compiler('cxx') }} + - make test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-genelendatabase/meta.yaml b/recipes/bioconductor-genelendatabase/meta.yaml index b74abd93168d3..8e76dbf29cb25 100644 --- a/recipes/bioconductor-genelendatabase/meta.yaml +++ b/recipes/bioconductor-genelendatabase/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.18.0" %} +{% set version = "1.20.0" %} {% set name = "geneLenDataBase" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 6bb5df37b2b3472202006a767123ac34 + md5: 53df16996486e637bf7a98b5498525ff build: number: 0 rpaths: @@ -19,14 +19,14 @@ build: noarch: generic requirements: host: - - 'bioconductor-genomicfeatures >=1.34.0,<1.35.0' - - 'bioconductor-rtracklayer >=1.42.0,<1.43.0' + - 'bioconductor-genomicfeatures >=1.36.0,<1.37.0' + - 'bioconductor-rtracklayer >=1.44.0,<1.45.0' - r-base run: - - 'bioconductor-genomicfeatures >=1.34.0,<1.35.0' - - 'bioconductor-rtracklayer >=1.42.0,<1.43.0' + - 'bioconductor-genomicfeatures >=1.36.0,<1.37.0' + - 'bioconductor-rtracklayer >=1.44.0,<1.45.0' - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-genelendatabase/post-link.sh b/recipes/bioconductor-genelendatabase/post-link.sh index 90871542d0e8b..98b1ccd642d7f 100644 --- a/recipes/bioconductor-genelendatabase/post-link.sh +++ b/recipes/bioconductor-genelendatabase/post-link.sh @@ -1,11 +1,11 @@ #!/bin/bash -FN="geneLenDataBase_1.18.0.tar.gz" +FN="geneLenDataBase_1.20.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/experiment/src/contrib/geneLenDataBase_1.18.0.tar.gz" - "https://bioarchive.galaxyproject.org/geneLenDataBase_1.18.0.tar.gz" - "https://depot.galaxyproject.org/software/bioconductor-genelendatabase/bioconductor-genelendatabase_1.18.0_src_all.tar.gz" + "https://bioconductor.org/packages/3.9/data/experiment/src/contrib/geneLenDataBase_1.20.0.tar.gz" + "https://bioarchive.galaxyproject.org/geneLenDataBase_1.20.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-genelendatabase/bioconductor-genelendatabase_1.20.0_src_all.tar.gz" ) -MD5="6bb5df37b2b3472202006a767123ac34" +MD5="53df16996486e637bf7a98b5498525ff" # Use a staging area in the conda dir rather than temp dirs, both to avoid # permission issues as well as to have things downloaded in a predictable @@ -16,7 +16,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-genemeta/meta.yaml b/recipes/bioconductor-genemeta/meta.yaml index bbda7f1c356b7..d07dd603952b0 100644 --- a/recipes/bioconductor-genemeta/meta.yaml +++ b/recipes/bioconductor-genemeta/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.54.0" %} +{% set version = "1.56.0" %} {% set name = "GeneMeta" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: f6cc399bae052e2cbeb38d2bcbe3cd10 + md5: edea7656bc37bd90cf806f5bffead15f build: number: 0 rpaths: @@ -20,12 +20,12 @@ build: # Suggests: RColorBrewer requirements: host: - - 'bioconductor-biobase >=2.42.0,<2.43.0' - - 'bioconductor-genefilter >=1.64.0,<1.65.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' + - 'bioconductor-genefilter >=1.66.0,<1.67.0' - r-base run: - - 'bioconductor-biobase >=2.42.0,<2.43.0' - - 'bioconductor-genefilter >=1.64.0,<1.65.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' + - 'bioconductor-genefilter >=1.66.0,<1.67.0' - r-base test: commands: diff --git a/recipes/bioconductor-genenetworkbuilder/meta.yaml b/recipes/bioconductor-genenetworkbuilder/meta.yaml index afae91fe57f2c..6c5765a3110ee 100644 --- a/recipes/bioconductor-genenetworkbuilder/meta.yaml +++ b/recipes/bioconductor-genenetworkbuilder/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.24.1" %} +{% set version = "1.26.0" %} {% set name = "GeneNetworkBuilder" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: 5a3d0a76f6a427cc189b6b24d7dbeafa324917017156346e9e5ffbff05c74ac2 + md5: a7c3a4d30cfa4fb7df90b203456c5497 build: number: 0 rpaths: @@ -19,8 +19,8 @@ build: # Suggests: RUnit, BiocGenerics, RBGL, knitr, simpIntLists, shiny, STRINGdb requirements: host: - - 'bioconductor-graph >=1.60.0,<1.61.0' - - 'bioconductor-rgraphviz >=2.26.0,<2.27.0' + - 'bioconductor-graph >=1.62.0,<1.63.0' + - 'bioconductor-rgraphviz >=2.28.0,<2.29.0' - r-base - r-htmlwidgets - r-plyr @@ -28,8 +28,8 @@ requirements: - r-rjson - r-xml run: - - 'bioconductor-graph >=1.60.0,<1.61.0' - - 'bioconductor-rgraphviz >=2.26.0,<2.27.0' + - 'bioconductor-graph >=1.62.0,<1.63.0' + - 'bioconductor-rgraphviz >=2.28.0,<2.29.0' - r-base - r-htmlwidgets - r-plyr diff --git a/recipes/bioconductor-geneoverlap/meta.yaml b/recipes/bioconductor-geneoverlap/meta.yaml index c2aeee3ef6102..f86415b5bba11 100644 --- a/recipes/bioconductor-geneoverlap/meta.yaml +++ b/recipes/bioconductor-geneoverlap/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.18.0" %} +{% set version = "1.20.0" %} {% set name = "GeneOverlap" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: dd4b8465cdd86f717727612caef4f1af + md5: c16764bedae345b804a1178d788f2ce0 build: number: 0 rpaths: diff --git a/recipes/bioconductor-geneplast.data.string.v91/meta.yaml b/recipes/bioconductor-geneplast.data.string.v91/meta.yaml index c709c0c4eac15..aea2e46c075e4 100644 --- a/recipes/bioconductor-geneplast.data.string.v91/meta.yaml +++ b/recipes/bioconductor-geneplast.data.string.v91/meta.yaml @@ -1,6 +1,6 @@ {% set version = "0.99.6" %} {% set name = "geneplast.data.string.v91" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -12,7 +12,7 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 86433f8489d9228c5ed73e2b75a55398 build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ @@ -22,7 +22,7 @@ requirements: - r-base run: - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-geneplast.data.string.v91/post-link.sh b/recipes/bioconductor-geneplast.data.string.v91/post-link.sh index 914e1e5611b42..0026fe7f4c150 100644 --- a/recipes/bioconductor-geneplast.data.string.v91/post-link.sh +++ b/recipes/bioconductor-geneplast.data.string.v91/post-link.sh @@ -1,9 +1,10 @@ #!/bin/bash FN="geneplast.data.string.v91_0.99.6.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/geneplast.data.string.v91_0.99.6.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/geneplast.data.string.v91_0.99.6.tar.gz" "https://bioarchive.galaxyproject.org/geneplast.data.string.v91_0.99.6.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-geneplast.data.string.v91/bioconductor-geneplast.data.string.v91_0.99.6_src_all.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-geneplast.data.string.v91/bioconductor-geneplast.data.string.v91_0.99.6_src_all.tar.gz" ) MD5="86433f8489d9228c5ed73e2b75a55398" @@ -16,7 +17,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-geneplast/meta.yaml b/recipes/bioconductor-geneplast/meta.yaml index d17c73447a434..1800639081e76 100644 --- a/recipes/bioconductor-geneplast/meta.yaml +++ b/recipes/bioconductor-geneplast/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.8.0" %} +{% set version = "1.10.0" %} {% set name = "geneplast" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: bcdbc3f90a41dc19ce54893cbc0cf1b5 + md5: 3430edc008f854a9b733136da225883b build: number: 0 rpaths: diff --git a/recipes/bioconductor-geneplotter/meta.yaml b/recipes/bioconductor-geneplotter/meta.yaml index 21c93d4992ee7..233827497f8ff 100644 --- a/recipes/bioconductor-geneplotter/meta.yaml +++ b/recipes/bioconductor-geneplotter/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.60.0" %} +{% set version = "1.62.0" %} {% set name = "geneplotter" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 077d06670401f046e762f770a0815a25 + md5: f682017835f9a7eeffa925eaac8f71f9 build: number: 0 rpaths: @@ -20,18 +20,18 @@ build: # Suggests: Rgraphviz, fibroEset, hgu95av2.db, hu6800.db, hgu133a.db requirements: host: - - 'bioconductor-annotate >=1.60.0,<1.61.0' - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' - - 'bioconductor-biobase >=2.42.0,<2.43.0' - - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' + - 'bioconductor-annotate >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' + - 'bioconductor-biocgenerics >=0.30.0,<0.31.0' - r-base - r-lattice - r-rcolorbrewer run: - - 'bioconductor-annotate >=1.60.0,<1.61.0' - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' - - 'bioconductor-biobase >=2.42.0,<2.43.0' - - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' + - 'bioconductor-annotate >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' + - 'bioconductor-biocgenerics >=0.30.0,<0.31.0' - r-base - r-lattice - r-rcolorbrewer diff --git a/recipes/bioconductor-generecommender/meta.yaml b/recipes/bioconductor-generecommender/meta.yaml index 16838cfa199cd..ada1d66c7ba12 100644 --- a/recipes/bioconductor-generecommender/meta.yaml +++ b/recipes/bioconductor-generecommender/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.54.0" %} +{% set version = "1.56.0" %} {% set name = "geneRecommender" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,19 +10,19 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: fa33e09ffa3ace8332c399d2d48728a8 + md5: 3d86561defb5cdd99161a27b05877bab build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ noarch: generic requirements: host: - - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' - r-base run: - - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' - r-base test: commands: diff --git a/recipes/bioconductor-generegionscan/meta.yaml b/recipes/bioconductor-generegionscan/meta.yaml index ef4649df09ddc..345b0cc2c25dd 100644 --- a/recipes/bioconductor-generegionscan/meta.yaml +++ b/recipes/bioconductor-generegionscan/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.38.0" %} +{% set version = "1.40.0" %} {% set name = "GeneRegionScan" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 2260cef9b94226c671ee7b49585b48c2 + md5: 68b83d6f500c10572e4d015ba84ccb66 build: number: 0 rpaths: @@ -20,17 +20,17 @@ build: # Suggests: BSgenome, affy, AnnotationDbi requirements: host: - - 'bioconductor-affxparser >=1.54.0,<1.55.0' - - 'bioconductor-biobase >=2.42.0,<2.43.0' - - 'bioconductor-biostrings >=2.50.0,<2.51.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-affxparser >=1.56.0,<1.57.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' + - 'bioconductor-biostrings >=2.52.0,<2.53.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' - r-base - r-rcolorbrewer run: - - 'bioconductor-affxparser >=1.54.0,<1.55.0' - - 'bioconductor-biobase >=2.42.0,<2.43.0' - - 'bioconductor-biostrings >=2.50.0,<2.51.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-affxparser >=1.56.0,<1.57.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' + - 'bioconductor-biostrings >=2.52.0,<2.53.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' - r-base - r-rcolorbrewer test: diff --git a/recipes/bioconductor-generxcluster/meta.yaml b/recipes/bioconductor-generxcluster/meta.yaml index 2ccfcd9709d1f..c437788e5cb37 100644 --- a/recipes/bioconductor-generxcluster/meta.yaml +++ b/recipes/bioconductor-generxcluster/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.18.0" %} +{% set version = "1.20.0" %} {% set name = "geneRxCluster" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,21 +10,21 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 8d1ada8668cffaf687eb24c1313cf667 + md5: 8c38b2da8fef36460b58499de0326f98 build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ # Suggests: RUnit, BiocGenerics requirements: host: - - 'bioconductor-genomicranges >=1.34.0,<1.35.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-genomicranges >=1.36.0,<1.37.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' - r-base run: - - 'bioconductor-genomicranges >=1.34.0,<1.35.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-genomicranges >=1.36.0,<1.37.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' - r-base build: - {{ compiler('c') }} diff --git a/recipes/bioconductor-geneselectmmd/meta.yaml b/recipes/bioconductor-geneselectmmd/meta.yaml index 817aacb37ddba..c15b2af846975 100644 --- a/recipes/bioconductor-geneselectmmd/meta.yaml +++ b/recipes/bioconductor-geneselectmmd/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "2.26.0" %} +{% set version = "2.28.0" %} {% set name = "GeneSelectMMD" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,23 +10,23 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: d3e9c106d9ae273e16d315dc1e37f123 + md5: d872e68b8285183d0d7ab04aa7233f22 build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ # Suggests: ALL requirements: host: - - 'bioconductor-biobase >=2.42.0,<2.43.0' - - 'bioconductor-limma >=3.38.0,<3.39.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' + - 'bioconductor-limma >=3.40.0,<3.41.0' - r-base - r-mass - r-survival run: - - 'bioconductor-biobase >=2.42.0,<2.43.0' - - 'bioconductor-limma >=3.38.0,<3.39.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' + - 'bioconductor-limma >=3.40.0,<3.41.0' - r-base - r-mass - r-survival diff --git a/recipes/bioconductor-genesis/meta.yaml b/recipes/bioconductor-genesis/meta.yaml index 20df0a83b5a20..38b8bba984a56 100644 --- a/recipes/bioconductor-genesis/meta.yaml +++ b/recipes/bioconductor-genesis/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "2.12.0" %} +{% set version = "2.14.0" %} {% set name = "GENESIS" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,26 +10,26 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: a0cf436a8357cd15fdaec5c6c8b7574b + md5: d2d7616788ab5d2621a7aa0fe65780d7 build: number: 0 rpaths: - lib/R/lib/ - lib/ noarch: generic -# Suggests: CompQuadForm, poibin, survey, testthat, knitr, rmarkdown, GWASdata, ggplot2, GGally, RColorBrewer, TxDb.Hsapiens.UCSC.hg19.knownGene +# Suggests: CompQuadForm, poibin, survey, testthat, BiocStyle, knitr, rmarkdown, GWASdata, ggplot2, GGally, RColorBrewer, TxDb.Hsapiens.UCSC.hg19.knownGene requirements: host: - - 'bioconductor-biobase >=2.42.0,<2.43.0' - - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' - - 'bioconductor-gdsfmt >=1.18.0,<1.19.0' - - 'bioconductor-genomicranges >=1.34.0,<1.35.0' - - 'bioconductor-gwastools >=1.28.0,<1.29.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' - - 'bioconductor-seqarray >=1.22.0,<1.23.0' - - 'bioconductor-seqvartools >=1.20.0,<1.21.0' - - 'bioconductor-snprelate >=1.16.0,<1.17.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' + - 'bioconductor-biocgenerics >=0.30.0,<0.31.0' + - 'bioconductor-gdsfmt >=1.20.0,<1.21.0' + - 'bioconductor-genomicranges >=1.36.0,<1.37.0' + - 'bioconductor-gwastools >=1.30.0,<1.31.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' + - 'bioconductor-seqarray >=1.24.0,<1.25.0' + - 'bioconductor-seqvartools >=1.22.0,<1.23.0' + - 'bioconductor-snprelate >=1.18.0,<1.19.0' - r-base - r-data.table - r-dplyr @@ -38,16 +38,16 @@ requirements: - r-matrix - r-reshape2 run: - - 'bioconductor-biobase >=2.42.0,<2.43.0' - - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' - - 'bioconductor-gdsfmt >=1.18.0,<1.19.0' - - 'bioconductor-genomicranges >=1.34.0,<1.35.0' - - 'bioconductor-gwastools >=1.28.0,<1.29.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' - - 'bioconductor-seqarray >=1.22.0,<1.23.0' - - 'bioconductor-seqvartools >=1.20.0,<1.21.0' - - 'bioconductor-snprelate >=1.16.0,<1.17.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' + - 'bioconductor-biocgenerics >=0.30.0,<0.31.0' + - 'bioconductor-gdsfmt >=1.20.0,<1.21.0' + - 'bioconductor-genomicranges >=1.36.0,<1.37.0' + - 'bioconductor-gwastools >=1.30.0,<1.31.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' + - 'bioconductor-seqarray >=1.24.0,<1.25.0' + - 'bioconductor-seqvartools >=1.22.0,<1.23.0' + - 'bioconductor-snprelate >=1.18.0,<1.19.0' - r-base - r-data.table - r-dplyr diff --git a/recipes/bioconductor-genestructuretools/meta.yaml b/recipes/bioconductor-genestructuretools/meta.yaml index 6147b3f3bddc7..5406a72cbbe5f 100644 --- a/recipes/bioconductor-genestructuretools/meta.yaml +++ b/recipes/bioconductor-genestructuretools/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.2.0" %} +{% set version = "1.4.0" %} {% set name = "GeneStructureTools" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: df6de751d9ef353cd61d4e51488f0c5e + md5: 05cb8f5f2ca9b74c09c5633ff75050d9 build: number: 0 rpaths: @@ -20,26 +20,26 @@ build: # Suggests: BiocStyle, knitr, rmarkdown requirements: host: - - 'bioconductor-biostrings >=2.50.0,<2.51.0' + - 'bioconductor-biostrings >=2.52.0,<2.53.0' - 'bioconductor-bsgenome.mmusculus.ucsc.mm10 >=1.4.0,<1.5.0' - - 'bioconductor-genomicranges >=1.34.0,<1.35.0' - - 'bioconductor-gviz >=1.26.0,<1.27.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-rtracklayer >=1.42.0,<1.43.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-genomicranges >=1.36.0,<1.37.0' + - 'bioconductor-gviz >=1.28.0,<1.29.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-rtracklayer >=1.44.0,<1.45.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' - r-base - r-data.table - r-plyr - r-stringdist - r-stringr run: - - 'bioconductor-biostrings >=2.50.0,<2.51.0' + - 'bioconductor-biostrings >=2.52.0,<2.53.0' - 'bioconductor-bsgenome.mmusculus.ucsc.mm10 >=1.4.0,<1.5.0' - - 'bioconductor-genomicranges >=1.34.0,<1.35.0' - - 'bioconductor-gviz >=1.26.0,<1.27.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-rtracklayer >=1.42.0,<1.43.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-genomicranges >=1.36.0,<1.37.0' + - 'bioconductor-gviz >=1.28.0,<1.29.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-rtracklayer >=1.44.0,<1.45.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' - r-base - r-data.table - r-plyr diff --git a/recipes/bioconductor-genetclassifier/meta.yaml b/recipes/bioconductor-genetclassifier/meta.yaml index 2635eaf786674..b792228fa69dc 100644 --- a/recipes/bioconductor-genetclassifier/meta.yaml +++ b/recipes/bioconductor-genetclassifier/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.22.0" %} +{% set version = "1.24.0" %} {% set name = "geNetClassifier" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 7ed135e01c9a31922be170711651ed12 + md5: 47c050a36340a35356171d886ccd9cf7 build: number: 0 rpaths: @@ -20,15 +20,15 @@ build: # Suggests: leukemiasEset, RUnit, BiocGenerics requirements: host: - - 'bioconductor-biobase >=2.42.0,<2.43.0' - - 'bioconductor-ebarrays >=2.46.0,<2.47.0' - - 'bioconductor-minet >=3.40.0,<3.41.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' + - 'bioconductor-ebarrays >=2.48.0,<2.49.0' + - 'bioconductor-minet >=3.42.0,<3.43.0' - r-base - r-e1071 run: - - 'bioconductor-biobase >=2.42.0,<2.43.0' - - 'bioconductor-ebarrays >=2.46.0,<2.47.0' - - 'bioconductor-minet >=3.40.0,<3.41.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' + - 'bioconductor-ebarrays >=2.48.0,<2.49.0' + - 'bioconductor-minet >=3.42.0,<3.43.0' - r-base - r-e1071 test: diff --git a/recipes/bioconductor-geneticsdesign/meta.yaml b/recipes/bioconductor-geneticsdesign/meta.yaml index a002676773d6c..aa5030191f87f 100644 --- a/recipes/bioconductor-geneticsdesign/meta.yaml +++ b/recipes/bioconductor-geneticsdesign/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.50.0" %} +{% set version = "1.52.0" %} {% set name = "GeneticsDesign" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: c1cc329cd3f43602ab706b0988a01ae7 + md5: 5219e9f8a29fe16b38de31f69c170236 build: number: 0 rpaths: diff --git a/recipes/bioconductor-geneticsped/meta.yaml b/recipes/bioconductor-geneticsped/meta.yaml index 45e82afb50a3f..fe5b0d115e287 100644 --- a/recipes/bioconductor-geneticsped/meta.yaml +++ b/recipes/bioconductor-geneticsped/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.44.0" %} +{% set version = "1.46.0" %} {% set name = "GeneticsPed" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 596538e0ee1818d212af9d5e61296166 + md5: bbe9e968038a3b327d34e53292cdbbd5 build: number: 0 rpaths: diff --git a/recipes/bioconductor-genextender/meta.yaml b/recipes/bioconductor-genextender/meta.yaml index 59cddcaab9d51..eaba77d6c7a8c 100644 --- a/recipes/bioconductor-genextender/meta.yaml +++ b/recipes/bioconductor-genextender/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.8.0" %} +{% set version = "1.10.0" %} {% set name = "geneXtendeR" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 967c99eb692b4bff278ddd7d808b1806 + md5: 450c027fe6c2ae4934dd24a8686e2236 build: number: 0 rpaths: @@ -19,11 +19,11 @@ build: # Suggests: knitr, rmarkdown, testthat, org.Ag.eg.db, org.Bt.eg.db, org.Ce.eg.db, org.Cf.eg.db, org.Dm.eg.db, org.Dr.eg.db, org.Gg.eg.db, org.Hs.eg.db, org.Mm.eg.db, org.Pt.eg.db, org.Sc.sgd.db, org.Ss.eg.db, org.Xl.eg.db, rtracklayer requirements: host: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' - - 'bioconductor-biocstyle >=2.10.0,<2.11.0' - - 'bioconductor-go.db >=3.7.0,<3.8.0' - - 'bioconductor-org.rn.eg.db >=3.7.0,<3.8.0' - - 'bioconductor-rtracklayer >=1.42.0,<1.43.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' + - 'bioconductor-biocstyle >=2.12.0,<2.13.0' + - 'bioconductor-go.db >=3.8.0,<3.9.0' + - 'bioconductor-org.rn.eg.db >=3.8.0,<3.9.0' + - 'bioconductor-rtracklayer >=1.44.0,<1.45.0' - r-base - r-data.table - r-dplyr @@ -33,11 +33,11 @@ requirements: - r-tm - r-wordcloud run: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' - - 'bioconductor-biocstyle >=2.10.0,<2.11.0' - - 'bioconductor-go.db >=3.7.0,<3.8.0' - - 'bioconductor-org.rn.eg.db >=3.7.0,<3.8.0' - - 'bioconductor-rtracklayer >=1.42.0,<1.43.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' + - 'bioconductor-biocstyle >=2.12.0,<2.13.0' + - 'bioconductor-go.db >=3.8.0,<3.9.0' + - 'bioconductor-org.rn.eg.db >=3.8.0,<3.9.0' + - 'bioconductor-rtracklayer >=1.44.0,<1.45.0' - r-base - r-data.table - r-dplyr diff --git a/recipes/bioconductor-genie3/meta.yaml b/recipes/bioconductor-genie3/meta.yaml index 68d54d74be815..43f2b999e8f7a 100644 --- a/recipes/bioconductor-genie3/meta.yaml +++ b/recipes/bioconductor-genie3/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.4.3" %} +{% set version = "1.6.0" %} {% set name = "GENIE3" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: e748062a232c1b7dc7af6b02c7ac4b3c6695907ed0b2706896cd182176756ff1 + md5: 535e4bf9a25c52f26feb09ac5e790016 build: number: 0 rpaths: diff --git a/recipes/bioconductor-genocn/meta.yaml b/recipes/bioconductor-genocn/meta.yaml index c4c3cd4b4f4de..d748ac68eed11 100644 --- a/recipes/bioconductor-genocn/meta.yaml +++ b/recipes/bioconductor-genocn/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.34.0" %} +{% set version = "1.36.0" %} {% set name = "genoCN" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 7b95b4cd827c5f41d1b35f5537be32f9 + md5: 90b9be077f52a563e6d3a046c3c8a6af build: number: 0 rpaths: diff --git a/recipes/bioconductor-genogam/meta.yaml b/recipes/bioconductor-genogam/meta.yaml index 54d3f02e4a72c..e03a6e97fc53e 100644 --- a/recipes/bioconductor-genogam/meta.yaml +++ b/recipes/bioconductor-genogam/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "2.0.2" %} +{% set version = "2.2.0" %} {% set name = "GenoGAM" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: eef4cf97be75a9660e31856b0cb711cf + md5: 10eeda50dcae803a3fc0cffcce6eefad build: number: 0 rpaths: @@ -19,19 +19,19 @@ build: # Suggests: BiocStyle, chipseq (>= 1.21.2), LSD (>= 3.0.0), genefilter (>= 1.54.2), ggplot2 (>= 2.1.0), testthat, knitr, rmarkdown requirements: host: - - 'bioconductor-biocparallel >=1.16.0,<1.17.0' - - 'bioconductor-biostrings >=2.50.0,<2.51.0' - - 'bioconductor-delayedarray >=0.8.0,<0.9.0' - - 'bioconductor-deseq2 >=1.22.0,<1.23.0' - - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' - - 'bioconductor-genomicalignments >=1.18.0,<1.19.0' - - 'bioconductor-genomicranges >=1.34.0,<1.35.0' - - 'bioconductor-hdf5array >=1.10.0,<1.11.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-rhdf5 >=2.26.0,<2.27.0' - - 'bioconductor-rsamtools >=1.34.0,<1.35.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' - - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' + - 'bioconductor-biocparallel >=1.18.0,<1.19.0' + - 'bioconductor-biostrings >=2.52.0,<2.53.0' + - 'bioconductor-delayedarray >=0.10.0,<0.11.0' + - 'bioconductor-deseq2 >=1.24.0,<1.25.0' + - 'bioconductor-genomeinfodb >=1.20.0,<1.21.0' + - 'bioconductor-genomicalignments >=1.20.0,<1.21.0' + - 'bioconductor-genomicranges >=1.36.0,<1.37.0' + - 'bioconductor-hdf5array >=1.12.0,<1.13.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-rhdf5 >=2.28.0,<2.29.0' + - 'bioconductor-rsamtools >=2.0.0,<2.1.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' + - 'bioconductor-summarizedexperiment >=1.14.0,<1.15.0' - r-base - 'r-data.table >=1.9.4' - 'r-futile.logger >=1.4.1' @@ -40,19 +40,19 @@ requirements: - r-rcpparmadillo - 'r-sparseinv >=0.1.1' run: - - 'bioconductor-biocparallel >=1.16.0,<1.17.0' - - 'bioconductor-biostrings >=2.50.0,<2.51.0' - - 'bioconductor-delayedarray >=0.8.0,<0.9.0' - - 'bioconductor-deseq2 >=1.22.0,<1.23.0' - - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' - - 'bioconductor-genomicalignments >=1.18.0,<1.19.0' - - 'bioconductor-genomicranges >=1.34.0,<1.35.0' - - 'bioconductor-hdf5array >=1.10.0,<1.11.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-rhdf5 >=2.26.0,<2.27.0' - - 'bioconductor-rsamtools >=1.34.0,<1.35.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' - - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' + - 'bioconductor-biocparallel >=1.18.0,<1.19.0' + - 'bioconductor-biostrings >=2.52.0,<2.53.0' + - 'bioconductor-delayedarray >=0.10.0,<0.11.0' + - 'bioconductor-deseq2 >=1.24.0,<1.25.0' + - 'bioconductor-genomeinfodb >=1.20.0,<1.21.0' + - 'bioconductor-genomicalignments >=1.20.0,<1.21.0' + - 'bioconductor-genomicranges >=1.36.0,<1.37.0' + - 'bioconductor-hdf5array >=1.12.0,<1.13.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-rhdf5 >=2.28.0,<2.29.0' + - 'bioconductor-rsamtools >=2.0.0,<2.1.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' + - 'bioconductor-summarizedexperiment >=1.14.0,<1.15.0' - r-base - 'r-data.table >=1.9.4' - 'r-futile.logger >=1.4.1' diff --git a/recipes/bioconductor-genomation/meta.yaml b/recipes/bioconductor-genomation/meta.yaml index ae8b4283e7ffb..4c40eedcef42b 100644 --- a/recipes/bioconductor-genomation/meta.yaml +++ b/recipes/bioconductor-genomation/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.14.0" %} +{% set version = "1.16.0" %} {% set name = "genomation" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: b5adfde48396a2fd9ffd760e880690f8 + md5: a7ad497efb9e2fda03c6c37ce19eed8c build: number: 0 rpaths: @@ -19,17 +19,17 @@ build: # Suggests: BiocGenerics, genomationData, knitr, RColorBrewer, rmarkdown requirements: host: - - 'bioconductor-biostrings >=2.50.0,<2.51.0' - - 'bioconductor-bsgenome >=1.50.0,<1.51.0' - - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' - - 'bioconductor-genomicalignments >=1.18.0,<1.19.0' - - 'bioconductor-genomicranges >=1.34.0,<1.35.0' - - 'bioconductor-impute >=1.56.0,<1.57.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-rsamtools >=1.34.0,<1.35.0' - - 'bioconductor-rtracklayer >=1.42.0,<1.43.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' - - 'bioconductor-seqpattern >=1.14.0,<1.15.0' + - 'bioconductor-biostrings >=2.52.0,<2.53.0' + - 'bioconductor-bsgenome >=1.52.0,<1.53.0' + - 'bioconductor-genomeinfodb >=1.20.0,<1.21.0' + - 'bioconductor-genomicalignments >=1.20.0,<1.21.0' + - 'bioconductor-genomicranges >=1.36.0,<1.37.0' + - 'bioconductor-impute >=1.58.0,<1.59.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-rsamtools >=2.0.0,<2.1.0' + - 'bioconductor-rtracklayer >=1.44.0,<1.45.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' + - 'bioconductor-seqpattern >=1.16.0,<1.17.0' - r-base - r-data.table - r-ggplot2 @@ -42,17 +42,17 @@ requirements: - r-reshape2 - r-runit run: - - 'bioconductor-biostrings >=2.50.0,<2.51.0' - - 'bioconductor-bsgenome >=1.50.0,<1.51.0' - - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' - - 'bioconductor-genomicalignments >=1.18.0,<1.19.0' - - 'bioconductor-genomicranges >=1.34.0,<1.35.0' - - 'bioconductor-impute >=1.56.0,<1.57.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-rsamtools >=1.34.0,<1.35.0' - - 'bioconductor-rtracklayer >=1.42.0,<1.43.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' - - 'bioconductor-seqpattern >=1.14.0,<1.15.0' + - 'bioconductor-biostrings >=2.52.0,<2.53.0' + - 'bioconductor-bsgenome >=1.52.0,<1.53.0' + - 'bioconductor-genomeinfodb >=1.20.0,<1.21.0' + - 'bioconductor-genomicalignments >=1.20.0,<1.21.0' + - 'bioconductor-genomicranges >=1.36.0,<1.37.0' + - 'bioconductor-impute >=1.58.0,<1.59.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-rsamtools >=2.0.0,<2.1.0' + - 'bioconductor-rtracklayer >=1.44.0,<1.45.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' + - 'bioconductor-seqpattern >=1.16.0,<1.17.0' - r-base - r-data.table - r-ggplot2 diff --git a/recipes/bioconductor-genomationdata/meta.yaml b/recipes/bioconductor-genomationdata/meta.yaml index 296fc359bfcf2..8f7592de7fa31 100644 --- a/recipes/bioconductor-genomationdata/meta.yaml +++ b/recipes/bioconductor-genomationdata/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.14.0" %} +{% set version = "1.16.0" %} {% set name = "genomationData" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: c0a8b50d7fbe4e4179d172ce02204bf6 + md5: e9b054305d2ce85aeb1bca338eb07b66 build: number: 0 rpaths: @@ -23,7 +23,7 @@ requirements: - r-base run: - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-genomationdata/post-link.sh b/recipes/bioconductor-genomationdata/post-link.sh index b562ebef54849..6ad7d7899939b 100644 --- a/recipes/bioconductor-genomationdata/post-link.sh +++ b/recipes/bioconductor-genomationdata/post-link.sh @@ -1,11 +1,11 @@ #!/bin/bash -FN="genomationData_1.14.0.tar.gz" +FN="genomationData_1.16.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/experiment/src/contrib/genomationData_1.14.0.tar.gz" - "https://bioarchive.galaxyproject.org/genomationData_1.14.0.tar.gz" - "https://depot.galaxyproject.org/software/bioconductor-genomationdata/bioconductor-genomationdata_1.14.0_src_all.tar.gz" + "https://bioconductor.org/packages/3.9/data/experiment/src/contrib/genomationData_1.16.0.tar.gz" + "https://bioarchive.galaxyproject.org/genomationData_1.16.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-genomationdata/bioconductor-genomationdata_1.16.0_src_all.tar.gz" ) -MD5="c0a8b50d7fbe4e4179d172ce02204bf6" +MD5="e9b054305d2ce85aeb1bca338eb07b66" # Use a staging area in the conda dir rather than temp dirs, both to avoid # permission issues as well as to have things downloaded in a predictable @@ -16,7 +16,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-genomegraphs/meta.yaml b/recipes/bioconductor-genomegraphs/meta.yaml index 1a22328692682..027ee231edd19 100644 --- a/recipes/bioconductor-genomegraphs/meta.yaml +++ b/recipes/bioconductor-genomegraphs/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.42.0" %} +{% set version = "1.44.0" %} {% set name = "GenomeGraphs" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 7be8b00de248fe8b5b73d43d17c9ea7a + md5: 67809498b9dfae83aabac0bf220eb35f build: number: 0 rpaths: @@ -19,10 +19,10 @@ build: noarch: generic requirements: host: - - 'bioconductor-biomart >=2.38.0,<2.39.0' + - 'bioconductor-biomart >=2.40.0,<2.41.0' - r-base run: - - 'bioconductor-biomart >=2.38.0,<2.39.0' + - 'bioconductor-biomart >=2.40.0,<2.41.0' - r-base test: commands: diff --git a/recipes/bioconductor-genomeinfodb/meta.yaml b/recipes/bioconductor-genomeinfodb/meta.yaml index 06df2a6b077cd..ff934a4ba7475 100644 --- a/recipes/bioconductor-genomeinfodb/meta.yaml +++ b/recipes/bioconductor-genomeinfodb/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.18.1" %} +{% set version = "1.20.0" %} {% set name = "GenomeInfoDb" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: b680b6c792d677f90541bdfdd0eb0bfb + md5: cecf189c70fce6130d357c0a8c46eb01 build: number: 0 rpaths: @@ -20,17 +20,17 @@ build: # Suggests: GenomicRanges, Rsamtools, GenomicAlignments, BSgenome, GenomicFeatures, BSgenome.Scerevisiae.UCSC.sacCer2, BSgenome.Celegans.UCSC.ce2, BSgenome.Hsapiens.NCBI.GRCh38, TxDb.Dmelanogaster.UCSC.dm3.ensGene, RUnit, BiocStyle, knitr requirements: host: - - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' + - 'bioconductor-biocgenerics >=0.30.0,<0.31.0' - 'bioconductor-genomeinfodbdata >=1.2.0,<1.3.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' - r-base - r-rcurl run: - - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' + - 'bioconductor-biocgenerics >=0.30.0,<0.31.0' - 'bioconductor-genomeinfodbdata >=1.2.0,<1.3.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' - r-base - r-rcurl test: diff --git a/recipes/bioconductor-genomeinfodbdata/meta.yaml b/recipes/bioconductor-genomeinfodbdata/meta.yaml index 788e20b1ab7aa..39ae7e375d46e 100644 --- a/recipes/bioconductor-genomeinfodbdata/meta.yaml +++ b/recipes/bioconductor-genomeinfodbdata/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.2.0" %} +{% set version = "1.2.1" %} {% set name = "GenomeInfoDbData" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 8fdbaf72a91aa676a3d521f0f307f10b + md5: 2fd536521151e2ff37217b5cfee8cec4 build: number: 0 rpaths: @@ -22,7 +22,7 @@ requirements: - r-base run: - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-genomeinfodbdata/post-link.sh b/recipes/bioconductor-genomeinfodbdata/post-link.sh index a974e47e62ffa..3275453cefde4 100644 --- a/recipes/bioconductor-genomeinfodbdata/post-link.sh +++ b/recipes/bioconductor-genomeinfodbdata/post-link.sh @@ -1,11 +1,11 @@ #!/bin/bash -FN="GenomeInfoDbData_1.2.0.tar.gz" +FN="GenomeInfoDbData_1.2.1.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/GenomeInfoDbData_1.2.0.tar.gz" - "https://bioarchive.galaxyproject.org/GenomeInfoDbData_1.2.0.tar.gz" - "https://depot.galaxyproject.org/software/bioconductor-genomeinfodbdata/bioconductor-genomeinfodbdata_1.2.0_src_all.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/GenomeInfoDbData_1.2.1.tar.gz" + "https://bioarchive.galaxyproject.org/GenomeInfoDbData_1.2.1.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-genomeinfodbdata/bioconductor-genomeinfodbdata_1.2.1_src_all.tar.gz" ) -MD5="8fdbaf72a91aa676a3d521f0f307f10b" +MD5="2fd536521151e2ff37217b5cfee8cec4" # Use a staging area in the conda dir rather than temp dirs, both to avoid # permission issues as well as to have things downloaded in a predictable @@ -16,7 +16,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-genomeintervals/meta.yaml b/recipes/bioconductor-genomeintervals/meta.yaml index 57d605664d9ff..c207458c1f8fb 100644 --- a/recipes/bioconductor-genomeintervals/meta.yaml +++ b/recipes/bioconductor-genomeintervals/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.38.0" %} +{% set version = "1.40.0" %} {% set name = "genomeIntervals" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 4944f98e184cd5b015136453854d8bad + md5: 43bb686102c90ce961b0b6351e0e3589 build: number: 0 rpaths: @@ -19,19 +19,19 @@ build: noarch: generic requirements: host: - - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' - - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' - - 'bioconductor-genomicranges >=1.34.0,<1.35.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-biocgenerics >=0.30.0,<0.31.0' + - 'bioconductor-genomeinfodb >=1.20.0,<1.21.0' + - 'bioconductor-genomicranges >=1.36.0,<1.37.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' - r-base - 'r-intervals >=0.14.0' run: - - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' - - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' - - 'bioconductor-genomicranges >=1.34.0,<1.35.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-biocgenerics >=0.30.0,<0.31.0' + - 'bioconductor-genomeinfodb >=1.20.0,<1.21.0' + - 'bioconductor-genomicranges >=1.36.0,<1.37.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' - r-base - 'r-intervals >=0.14.0' test: diff --git a/recipes/bioconductor-genomes/meta.yaml b/recipes/bioconductor-genomes/meta.yaml index 27e2a195c36bb..a55f4d23dc9bc 100644 --- a/recipes/bioconductor-genomes/meta.yaml +++ b/recipes/bioconductor-genomes/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "3.12.0" %} +{% set version = "3.14.0" %} {% set name = "genomes" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 725ed613b762b70263f03f55a1792cd4 + md5: a077a69631cbe6acd0cd2e691c7cae06 build: number: 0 rpaths: diff --git a/recipes/bioconductor-genomewidesnp5crlmm/meta.yaml b/recipes/bioconductor-genomewidesnp5crlmm/meta.yaml index a3479e9f06524..c1dba211cf865 100644 --- a/recipes/bioconductor-genomewidesnp5crlmm/meta.yaml +++ b/recipes/bioconductor-genomewidesnp5crlmm/meta.yaml @@ -1,6 +1,6 @@ {% set version = "1.0.6" %} {% set name = "genomewidesnp5Crlmm" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -12,7 +12,7 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' md5: cc24140cd17758b8e09f4fe6c931526a build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ @@ -22,7 +22,7 @@ requirements: - r-base run: - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-genomewidesnp5crlmm/post-link.sh b/recipes/bioconductor-genomewidesnp5crlmm/post-link.sh index 0185d129605b1..38d8aab565f85 100644 --- a/recipes/bioconductor-genomewidesnp5crlmm/post-link.sh +++ b/recipes/bioconductor-genomewidesnp5crlmm/post-link.sh @@ -1,9 +1,10 @@ #!/bin/bash FN="genomewidesnp5Crlmm_1.0.6.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/genomewidesnp5Crlmm_1.0.6.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/genomewidesnp5Crlmm_1.0.6.tar.gz" "https://bioarchive.galaxyproject.org/genomewidesnp5Crlmm_1.0.6.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-genomewidesnp5crlmm/bioconductor-genomewidesnp5crlmm_1.0.6_src_all.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-genomewidesnp5crlmm/bioconductor-genomewidesnp5crlmm_1.0.6_src_all.tar.gz" ) MD5="cc24140cd17758b8e09f4fe6c931526a" @@ -16,7 +17,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-genomewidesnp6crlmm/meta.yaml b/recipes/bioconductor-genomewidesnp6crlmm/meta.yaml index 816a4d2060ac3..5f556fe7315df 100644 --- a/recipes/bioconductor-genomewidesnp6crlmm/meta.yaml +++ b/recipes/bioconductor-genomewidesnp6crlmm/meta.yaml @@ -1,6 +1,6 @@ {% set version = "1.0.7" %} {% set name = "genomewidesnp6Crlmm" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -12,7 +12,7 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' md5: 13dd5aef3d814524896f2f3013beb78b build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ @@ -22,7 +22,7 @@ requirements: - r-base run: - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-genomewidesnp6crlmm/post-link.sh b/recipes/bioconductor-genomewidesnp6crlmm/post-link.sh index b86df4588d0c7..3980871e36132 100644 --- a/recipes/bioconductor-genomewidesnp6crlmm/post-link.sh +++ b/recipes/bioconductor-genomewidesnp6crlmm/post-link.sh @@ -1,9 +1,10 @@ #!/bin/bash FN="genomewidesnp6Crlmm_1.0.7.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/genomewidesnp6Crlmm_1.0.7.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/genomewidesnp6Crlmm_1.0.7.tar.gz" "https://bioarchive.galaxyproject.org/genomewidesnp6Crlmm_1.0.7.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-genomewidesnp6crlmm/bioconductor-genomewidesnp6crlmm_1.0.7_src_all.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-genomewidesnp6crlmm/bioconductor-genomewidesnp6crlmm_1.0.7_src_all.tar.gz" ) MD5="13dd5aef3d814524896f2f3013beb78b" @@ -16,7 +17,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-genomicalignments/meta.yaml b/recipes/bioconductor-genomicalignments/meta.yaml index cda44b056e5e7..d14a204d4e904 100644 --- a/recipes/bioconductor-genomicalignments/meta.yaml +++ b/recipes/bioconductor-genomicalignments/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.18.1" %} +{% set version = "1.20.0" %} {% set name = "GenomicAlignments" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 0220afca94e1abcdb173b1df36f1cc60 + md5: 2db1b0e1295c63bca03ea88183210c80 build: number: 0 rpaths: @@ -19,26 +19,26 @@ build: # Suggests: ShortRead, rtracklayer, BSgenome, GenomicFeatures, RNAseqData.HNRNPC.bam.chr14, pasillaBamSubset, TxDb.Hsapiens.UCSC.hg19.knownGene, TxDb.Dmelanogaster.UCSC.dm3.ensGene, BSgenome.Dmelanogaster.UCSC.dm3, BSgenome.Hsapiens.UCSC.hg19, DESeq2, edgeR, RUnit, BiocStyle requirements: host: - - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' - - 'bioconductor-biocparallel >=1.16.0,<1.17.0' - - 'bioconductor-biostrings >=2.50.0,<2.51.0' - - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' - - 'bioconductor-genomicranges >=1.34.0,<1.35.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-rsamtools >=1.34.0,<1.35.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' - - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' + - 'bioconductor-biocgenerics >=0.30.0,<0.31.0' + - 'bioconductor-biocparallel >=1.18.0,<1.19.0' + - 'bioconductor-biostrings >=2.52.0,<2.53.0' + - 'bioconductor-genomeinfodb >=1.20.0,<1.21.0' + - 'bioconductor-genomicranges >=1.36.0,<1.37.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-rsamtools >=2.0.0,<2.1.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' + - 'bioconductor-summarizedexperiment >=1.14.0,<1.15.0' - r-base run: - - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' - - 'bioconductor-biocparallel >=1.16.0,<1.17.0' - - 'bioconductor-biostrings >=2.50.0,<2.51.0' - - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' - - 'bioconductor-genomicranges >=1.34.0,<1.35.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-rsamtools >=1.34.0,<1.35.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' - - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' + - 'bioconductor-biocgenerics >=0.30.0,<0.31.0' + - 'bioconductor-biocparallel >=1.18.0,<1.19.0' + - 'bioconductor-biostrings >=2.52.0,<2.53.0' + - 'bioconductor-genomeinfodb >=1.20.0,<1.21.0' + - 'bioconductor-genomicranges >=1.36.0,<1.37.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-rsamtools >=2.0.0,<2.1.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' + - 'bioconductor-summarizedexperiment >=1.14.0,<1.15.0' - r-base build: - {{ compiler('c') }} diff --git a/recipes/bioconductor-genomicdatacommons/meta.yaml b/recipes/bioconductor-genomicdatacommons/meta.yaml index 4c24d9d3e9681..573e9a8dfb08f 100644 --- a/recipes/bioconductor-genomicdatacommons/meta.yaml +++ b/recipes/bioconductor-genomicdatacommons/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.6.0" %} +{% set version = "1.8.0" %} {% set name = "GenomicDataCommons" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 390615fd4999a0564cea10c4242c878e + md5: 7a1b67231b1ccc299aa857334cc6b8fb build: number: 0 rpaths: @@ -20,32 +20,34 @@ build: # Suggests: BiocStyle, knitr, rmarkdown, DT, testthat, listviewer, ggplot2, GenomicAlignments, Rsamtools requirements: host: - - 'bioconductor-genomicranges >=1.34.0,<1.35.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' - - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' + - 'bioconductor-genomicranges >=1.36.0,<1.37.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' + - 'bioconductor-summarizedexperiment >=1.14.0,<1.15.0' - r-base - r-dplyr - r-httr - r-jsonlite - - r-lazyeval - r-magrittr - r-rappdirs - r-readr + - r-rlang + - r-tibble - r-xml2 run: - - 'bioconductor-genomicranges >=1.34.0,<1.35.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' - - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' + - 'bioconductor-genomicranges >=1.36.0,<1.37.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' + - 'bioconductor-summarizedexperiment >=1.14.0,<1.15.0' - r-base - r-dplyr - r-httr - r-jsonlite - - r-lazyeval - r-magrittr - r-rappdirs - r-readr + - r-rlang + - r-tibble - r-xml2 test: commands: diff --git a/recipes/bioconductor-genomicfeatures/meta.yaml b/recipes/bioconductor-genomicfeatures/meta.yaml index dc9c71d563d33..047aa963305a6 100644 --- a/recipes/bioconductor-genomicfeatures/meta.yaml +++ b/recipes/bioconductor-genomicfeatures/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.34.1" %} +{% set version = "1.36.0" %} {% set name = "GenomicFeatures" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,43 +10,43 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: b227cf5cd1a3cbabc3df6381060234ab + md5: 2ad51098b8d4532a76224a93cf862657 build: number: 0 rpaths: - lib/R/lib/ - lib/ noarch: generic -# Suggests: RMariaDB, org.Mm.eg.db, org.Hs.eg.db, BSgenome, BSgenome.Hsapiens.UCSC.hg19 (>= 1.3.17), BSgenome.Celegans.UCSC.ce2, BSgenome.Dmelanogaster.UCSC.dm3 (>= 1.3.17), mirbase.db, FDb.UCSC.tRNAs, TxDb.Hsapiens.UCSC.hg19.knownGene, TxDb.Dmelanogaster.UCSC.dm3.ensGene (>= 2.7.1), TxDb.Mmusculus.UCSC.mm10.knownGene, TxDb.Hsapiens.UCSC.hg19.lincRNAsTranscripts, TxDb.Hsapiens.UCSC.hg38.knownGene, SNPlocs.Hsapiens.dbSNP144.GRCh38, Rsamtools, pasillaBamSubset (>= 0.0.5), GenomicAlignments (>= 1.15.7), ensembldb, RUnit, BiocStyle, knitr +# Suggests: RMariaDB, org.Mm.eg.db, org.Hs.eg.db, BSgenome, BSgenome.Hsapiens.UCSC.hg19 (>= 1.3.17), BSgenome.Celegans.UCSC.ce2, BSgenome.Dmelanogaster.UCSC.dm3 (>= 1.3.17), mirbase.db, FDb.UCSC.tRNAs, TxDb.Hsapiens.UCSC.hg19.knownGene, TxDb.Dmelanogaster.UCSC.dm3.ensGene (>= 2.7.1), TxDb.Mmusculus.UCSC.mm10.knownGene (>= 3.4.7), TxDb.Hsapiens.UCSC.hg19.lincRNAsTranscripts, TxDb.Hsapiens.UCSC.hg38.knownGene (>= 3.4.6), SNPlocs.Hsapiens.dbSNP144.GRCh38, Rsamtools, pasillaBamSubset (>= 0.0.5), GenomicAlignments (>= 1.15.7), ensembldb, RUnit, BiocStyle, knitr requirements: host: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' - - 'bioconductor-biobase >=2.42.0,<2.43.0' - - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' - - 'bioconductor-biomart >=2.38.0,<2.39.0' - - 'bioconductor-biostrings >=2.50.0,<2.51.0' - - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' - - 'bioconductor-genomicranges >=1.34.0,<1.35.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-rtracklayer >=1.42.0,<1.43.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' - - 'bioconductor-xvector >=0.22.0,<0.23.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' + - 'bioconductor-biocgenerics >=0.30.0,<0.31.0' + - 'bioconductor-biomart >=2.40.0,<2.41.0' + - 'bioconductor-biostrings >=2.52.0,<2.53.0' + - 'bioconductor-genomeinfodb >=1.20.0,<1.21.0' + - 'bioconductor-genomicranges >=1.36.0,<1.37.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-rtracklayer >=1.44.0,<1.45.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' + - 'bioconductor-xvector >=0.24.0,<0.25.0' - r-base - r-dbi - r-rcurl - 'r-rsqlite >=2.0' run: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' - - 'bioconductor-biobase >=2.42.0,<2.43.0' - - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' - - 'bioconductor-biomart >=2.38.0,<2.39.0' - - 'bioconductor-biostrings >=2.50.0,<2.51.0' - - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' - - 'bioconductor-genomicranges >=1.34.0,<1.35.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-rtracklayer >=1.42.0,<1.43.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' - - 'bioconductor-xvector >=0.22.0,<0.23.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' + - 'bioconductor-biocgenerics >=0.30.0,<0.31.0' + - 'bioconductor-biomart >=2.40.0,<2.41.0' + - 'bioconductor-biostrings >=2.52.0,<2.53.0' + - 'bioconductor-genomeinfodb >=1.20.0,<1.21.0' + - 'bioconductor-genomicranges >=1.36.0,<1.37.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-rtracklayer >=1.44.0,<1.45.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' + - 'bioconductor-xvector >=0.24.0,<0.25.0' - r-base - r-dbi - r-rcurl diff --git a/recipes/bioconductor-genomicfiles/meta.yaml b/recipes/bioconductor-genomicfiles/meta.yaml index f3c91c1f08af7..3028155aa588d 100644 --- a/recipes/bioconductor-genomicfiles/meta.yaml +++ b/recipes/bioconductor-genomicfiles/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.18.0" %} +{% set version = "1.20.0" %} {% set name = "GenomicFiles" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,9 +10,9 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 2776040839b95869d3c9686fedb8144a + md5: 315822cd8b9c8a8be88deb9aebf37e56 build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ @@ -20,30 +20,30 @@ build: # Suggests: BiocStyle, RUnit, genefilter, deepSNV, RNAseqData.HNRNPC.bam.chr14, Biostrings, Homo.sapiens requirements: host: - - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' - - 'bioconductor-biocparallel >=1.16.0,<1.17.0' - - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' - - 'bioconductor-genomicalignments >=1.18.0,<1.19.0' - - 'bioconductor-genomicranges >=1.34.0,<1.35.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-rsamtools >=1.34.0,<1.35.0' - - 'bioconductor-rtracklayer >=1.42.0,<1.43.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' - - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' - - 'bioconductor-variantannotation >=1.28.0,<1.29.0' + - 'bioconductor-biocgenerics >=0.30.0,<0.31.0' + - 'bioconductor-biocparallel >=1.18.0,<1.19.0' + - 'bioconductor-genomeinfodb >=1.20.0,<1.21.0' + - 'bioconductor-genomicalignments >=1.20.0,<1.21.0' + - 'bioconductor-genomicranges >=1.36.0,<1.37.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-rsamtools >=2.0.0,<2.1.0' + - 'bioconductor-rtracklayer >=1.44.0,<1.45.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' + - 'bioconductor-summarizedexperiment >=1.14.0,<1.15.0' + - 'bioconductor-variantannotation >=1.30.0,<1.31.0' - r-base run: - - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' - - 'bioconductor-biocparallel >=1.16.0,<1.17.0' - - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' - - 'bioconductor-genomicalignments >=1.18.0,<1.19.0' - - 'bioconductor-genomicranges >=1.34.0,<1.35.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-rsamtools >=1.34.0,<1.35.0' - - 'bioconductor-rtracklayer >=1.42.0,<1.43.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' - - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' - - 'bioconductor-variantannotation >=1.28.0,<1.29.0' + - 'bioconductor-biocgenerics >=0.30.0,<0.31.0' + - 'bioconductor-biocparallel >=1.18.0,<1.19.0' + - 'bioconductor-genomeinfodb >=1.20.0,<1.21.0' + - 'bioconductor-genomicalignments >=1.20.0,<1.21.0' + - 'bioconductor-genomicranges >=1.36.0,<1.37.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-rsamtools >=2.0.0,<2.1.0' + - 'bioconductor-rtracklayer >=1.44.0,<1.45.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' + - 'bioconductor-summarizedexperiment >=1.14.0,<1.15.0' + - 'bioconductor-variantannotation >=1.30.0,<1.31.0' - r-base test: commands: diff --git a/recipes/bioconductor-genomicinteractions/meta.yaml b/recipes/bioconductor-genomicinteractions/meta.yaml index d058c5cab0269..1c4d2609fd060 100644 --- a/recipes/bioconductor-genomicinteractions/meta.yaml +++ b/recipes/bioconductor-genomicinteractions/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.16.0" %} +{% set version = "1.18.0" %} {% set name = "GenomicInteractions" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,9 +10,9 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: c1beef4055b4d2e6cd2ccba99b7f331b + md5: e3c3434c6842987b4e120331c50d2f38 build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ @@ -20,16 +20,16 @@ build: # Suggests: knitr, BiocStyle, testthat requirements: host: - - 'bioconductor-biobase >=2.42.0,<2.43.0' - - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' - - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' - - 'bioconductor-genomicranges >=1.34.0,<1.35.0' - - 'bioconductor-gviz >=1.26.0,<1.27.0' - - 'bioconductor-interactionset >=1.10.0,<1.11.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-rsamtools >=1.34.0,<1.35.0' - - 'bioconductor-rtracklayer >=1.42.0,<1.43.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' + - 'bioconductor-biocgenerics >=0.30.0,<0.31.0' + - 'bioconductor-genomeinfodb >=1.20.0,<1.21.0' + - 'bioconductor-genomicranges >=1.36.0,<1.37.0' + - 'bioconductor-gviz >=1.28.0,<1.29.0' + - 'bioconductor-interactionset >=1.12.0,<1.13.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-rsamtools >=2.0.0,<2.1.0' + - 'bioconductor-rtracklayer >=1.44.0,<1.45.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' - r-base - r-data.table - r-dplyr @@ -38,16 +38,16 @@ requirements: - r-igraph - r-stringr run: - - 'bioconductor-biobase >=2.42.0,<2.43.0' - - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' - - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' - - 'bioconductor-genomicranges >=1.34.0,<1.35.0' - - 'bioconductor-gviz >=1.26.0,<1.27.0' - - 'bioconductor-interactionset >=1.10.0,<1.11.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-rsamtools >=1.34.0,<1.35.0' - - 'bioconductor-rtracklayer >=1.42.0,<1.43.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' + - 'bioconductor-biocgenerics >=0.30.0,<0.31.0' + - 'bioconductor-genomeinfodb >=1.20.0,<1.21.0' + - 'bioconductor-genomicranges >=1.36.0,<1.37.0' + - 'bioconductor-gviz >=1.28.0,<1.29.0' + - 'bioconductor-interactionset >=1.12.0,<1.13.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-rsamtools >=2.0.0,<2.1.0' + - 'bioconductor-rtracklayer >=1.44.0,<1.45.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' - r-base - r-data.table - r-dplyr diff --git a/recipes/bioconductor-genomicranges/meta.yaml b/recipes/bioconductor-genomicranges/meta.yaml index b861fecd91ae8..526c928942de2 100644 --- a/recipes/bioconductor-genomicranges/meta.yaml +++ b/recipes/bioconductor-genomicranges/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.34.0" %} +{% set version = "1.36.0" %} {% set name = "GenomicRanges" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: efe660c341dcd0c0b07d2e9086b63434 + md5: 3b37cea5d6fcdef3ed57e80cdd7dc5b0 build: number: 0 rpaths: @@ -19,18 +19,18 @@ build: # Suggests: Matrix, Biobase, AnnotationDbi, annotate, Biostrings (>= 2.25.3), SummarizedExperiment (>= 0.1.5), Rsamtools (>= 1.13.53), GenomicAlignments, rtracklayer, BSgenome, GenomicFeatures, Gviz, VariantAnnotation, AnnotationHub, DESeq2, DEXSeq, edgeR, KEGGgraph, RNAseqData.HNRNPC.bam.chr14, pasillaBamSubset, KEGG.db, hgu95av2.db, hgu95av2probe, BSgenome.Scerevisiae.UCSC.sacCer2, BSgenome.Hsapiens.UCSC.hg19, BSgenome.Mmusculus.UCSC.mm10, TxDb.Athaliana.BioMart.plantsmart22, TxDb.Dmelanogaster.UCSC.dm3.ensGene, TxDb.Hsapiens.UCSC.hg19.knownGene, TxDb.Mmusculus.UCSC.mm10.knownGene, RUnit, digest, knitr, BiocStyle requirements: host: - - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' - - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' - - 'bioconductor-xvector >=0.22.0,<0.23.0' + - 'bioconductor-biocgenerics >=0.30.0,<0.31.0' + - 'bioconductor-genomeinfodb >=1.20.0,<1.21.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' + - 'bioconductor-xvector >=0.24.0,<0.25.0' - r-base run: - - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' - - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' - - 'bioconductor-xvector >=0.22.0,<0.23.0' + - 'bioconductor-biocgenerics >=0.30.0,<0.31.0' + - 'bioconductor-genomeinfodb >=1.20.0,<1.21.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' + - 'bioconductor-xvector >=0.24.0,<0.25.0' - r-base build: - {{ compiler('c') }} diff --git a/recipes/bioconductor-genomicscores/meta.yaml b/recipes/bioconductor-genomicscores/meta.yaml index 7541d7cefb792..30ab2a0b9aa4c 100644 --- a/recipes/bioconductor-genomicscores/meta.yaml +++ b/recipes/bioconductor-genomicscores/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.6.0" %} +{% set version = "1.8.0" %} {% set name = "GenomicScores" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 002dca8198727b7629cf69f5b17b6240 + md5: c030f1bdb93d85cecc0b039cc07462df build: number: 0 rpaths: @@ -20,27 +20,27 @@ build: # Suggests: BiocStyle, knitr, rmarkdown, BSgenome.Hsapiens.UCSC.hg19, phastCons100way.UCSC.hg19, MafDb.1Kgenomes.phase1.hs37d5, SNPlocs.Hsapiens.dbSNP144.GRCh37, VariantAnnotation, TxDb.Hsapiens.UCSC.hg19.knownGene, gwascat, RColorBrewer requirements: host: - - 'bioconductor-annotationhub >=2.14.0,<2.15.0' - - 'bioconductor-biobase >=2.42.0,<2.43.0' - - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' - - 'bioconductor-biostrings >=2.50.0,<2.51.0' - - 'bioconductor-bsgenome >=1.50.0,<1.51.0' - - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' - - 'bioconductor-genomicranges >=1.34.0,<1.35.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-annotationhub >=2.16.0,<2.17.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' + - 'bioconductor-biocgenerics >=0.30.0,<0.31.0' + - 'bioconductor-biostrings >=2.52.0,<2.53.0' + - 'bioconductor-bsgenome >=1.52.0,<1.53.0' + - 'bioconductor-genomeinfodb >=1.20.0,<1.21.0' + - 'bioconductor-genomicranges >=1.36.0,<1.37.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' - r-base - r-xml run: - - 'bioconductor-annotationhub >=2.14.0,<2.15.0' - - 'bioconductor-biobase >=2.42.0,<2.43.0' - - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' - - 'bioconductor-biostrings >=2.50.0,<2.51.0' - - 'bioconductor-bsgenome >=1.50.0,<1.51.0' - - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' - - 'bioconductor-genomicranges >=1.34.0,<1.35.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-annotationhub >=2.16.0,<2.17.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' + - 'bioconductor-biocgenerics >=0.30.0,<0.31.0' + - 'bioconductor-biostrings >=2.52.0,<2.53.0' + - 'bioconductor-bsgenome >=1.52.0,<1.53.0' + - 'bioconductor-genomeinfodb >=1.20.0,<1.21.0' + - 'bioconductor-genomicranges >=1.36.0,<1.37.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' - r-base - r-xml test: diff --git a/recipes/bioconductor-genomictuples/meta.yaml b/recipes/bioconductor-genomictuples/meta.yaml index abfb320b0c272..b8b5b06dec510 100644 --- a/recipes/bioconductor-genomictuples/meta.yaml +++ b/recipes/bioconductor-genomictuples/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.16.0" %} +{% set version = "1.18.0" %} {% set name = "GenomicTuples" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 9b7b5ed8d0fbd6a214f5556b2c38a4b0 + md5: 31d317d5a9fcdcea3e3f3944e8cd9a6e build: number: 0 rpaths: @@ -19,20 +19,20 @@ build: # Suggests: testthat, knitr, BiocStyle, rmarkdown requirements: host: - - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' - - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' - - 'bioconductor-genomicranges >=1.34.0,<1.35.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-biocgenerics >=0.30.0,<0.31.0' + - 'bioconductor-genomeinfodb >=1.20.0,<1.21.0' + - 'bioconductor-genomicranges >=1.36.0,<1.37.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' - r-base - r-data.table - 'r-rcpp >=0.11.2' run: - - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' - - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' - - 'bioconductor-genomicranges >=1.34.0,<1.35.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-biocgenerics >=0.30.0,<0.31.0' + - 'bioconductor-genomeinfodb >=1.20.0,<1.21.0' + - 'bioconductor-genomicranges >=1.36.0,<1.37.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' - r-base - r-data.table - 'r-rcpp >=0.11.2' diff --git a/recipes/bioconductor-genominator/meta.yaml b/recipes/bioconductor-genominator/meta.yaml index 4b3b0d750bf3d..cd13d599de298 100644 --- a/recipes/bioconductor-genominator/meta.yaml +++ b/recipes/bioconductor-genominator/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.36.0" %} +{% set version = "1.38.0" %} {% set name = "Genominator" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,9 +10,9 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: a787b87c5fee3feaea76a0151ccdee50 + md5: 3d84c0c525066a75bba4249dc5676d07 build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ @@ -20,16 +20,16 @@ build: # Suggests: biomaRt, ShortRead, yeastRNASeq requirements: host: - - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' - - 'bioconductor-genomegraphs >=1.42.0,<1.43.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-biocgenerics >=0.30.0,<0.31.0' + - 'bioconductor-genomegraphs >=1.44.0,<1.45.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' - r-base - 'r-dbi >=0.2-5' - r-rsqlite run: - - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' - - 'bioconductor-genomegraphs >=1.42.0,<1.43.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-biocgenerics >=0.30.0,<0.31.0' + - 'bioconductor-genomegraphs >=1.44.0,<1.45.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' - r-base - 'r-dbi >=0.2-5' - r-rsqlite diff --git a/recipes/bioconductor-genoset/meta.yaml b/recipes/bioconductor-genoset/meta.yaml index eb78b02ca9264..f7f6b4d8602bc 100644 --- a/recipes/bioconductor-genoset/meta.yaml +++ b/recipes/bioconductor-genoset/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.38.0" %} +{% set version = "1.40.0" %} {% set name = "genoset" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 68336a575e2390f041edb49ed5b68477 + md5: 9c639a14b97c90b50581c7c44fa2575e build: number: 0 rpaths: @@ -19,20 +19,20 @@ build: # Suggests: testthat, knitr, BiocStyle, rmarkdown, DNAcopy, stats, BSgenome, Biostrings requirements: host: - - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' - - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' - - 'bioconductor-genomicranges >=1.34.0,<1.35.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' - - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' + - 'bioconductor-biocgenerics >=0.30.0,<0.31.0' + - 'bioconductor-genomeinfodb >=1.20.0,<1.21.0' + - 'bioconductor-genomicranges >=1.36.0,<1.37.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' + - 'bioconductor-summarizedexperiment >=1.14.0,<1.15.0' - r-base run: - - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' - - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' - - 'bioconductor-genomicranges >=1.34.0,<1.35.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' - - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' + - 'bioconductor-biocgenerics >=0.30.0,<0.31.0' + - 'bioconductor-genomeinfodb >=1.20.0,<1.21.0' + - 'bioconductor-genomicranges >=1.36.0,<1.37.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' + - 'bioconductor-summarizedexperiment >=1.14.0,<1.15.0' - r-base build: - {{ compiler('c') }} diff --git a/recipes/bioconductor-genotypeeval/meta.yaml b/recipes/bioconductor-genotypeeval/meta.yaml index 02d10822274a6..45a2fe67a2abc 100644 --- a/recipes/bioconductor-genotypeeval/meta.yaml +++ b/recipes/bioconductor-genotypeeval/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.14.0" %} +{% set version = "1.16.0" %} {% set name = "genotypeeval" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: d8c0444b34549730384bdad50312d814 + md5: 5f5c8d95fb9dd6fa0487c43c400d5515 build: number: 0 rpaths: @@ -20,23 +20,23 @@ build: # Suggests: rmarkdown, testthat, SNPlocs.Hsapiens.dbSNP141.GRCh38, TxDb.Hsapiens.UCSC.hg38.knownGene requirements: host: - - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' - - 'bioconductor-biocparallel >=1.16.0,<1.17.0' - - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' - - 'bioconductor-genomicranges >=1.34.0,<1.35.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-rtracklayer >=1.42.0,<1.43.0' - - 'bioconductor-variantannotation >=1.28.0,<1.29.0' + - 'bioconductor-biocgenerics >=0.30.0,<0.31.0' + - 'bioconductor-biocparallel >=1.18.0,<1.19.0' + - 'bioconductor-genomeinfodb >=1.20.0,<1.21.0' + - 'bioconductor-genomicranges >=1.36.0,<1.37.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-rtracklayer >=1.44.0,<1.45.0' + - 'bioconductor-variantannotation >=1.30.0,<1.31.0' - r-base - r-ggplot2 run: - - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' - - 'bioconductor-biocparallel >=1.16.0,<1.17.0' - - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' - - 'bioconductor-genomicranges >=1.34.0,<1.35.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-rtracklayer >=1.42.0,<1.43.0' - - 'bioconductor-variantannotation >=1.28.0,<1.29.0' + - 'bioconductor-biocgenerics >=0.30.0,<0.31.0' + - 'bioconductor-biocparallel >=1.18.0,<1.19.0' + - 'bioconductor-genomeinfodb >=1.20.0,<1.21.0' + - 'bioconductor-genomicranges >=1.36.0,<1.37.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-rtracklayer >=1.44.0,<1.45.0' + - 'bioconductor-variantannotation >=1.30.0,<1.31.0' - r-base - r-ggplot2 test: diff --git a/recipes/bioconductor-genphen/meta.yaml b/recipes/bioconductor-genphen/meta.yaml index ed8ed4e1b0268..26a01aa5bacea 100644 --- a/recipes/bioconductor-genphen/meta.yaml +++ b/recipes/bioconductor-genphen/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.10.0" %} +{% set version = "1.12.0" %} {% set name = "genphen" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,29 +10,43 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: c7be09e60a56d52fcdffa12b85b6e028 + md5: 639411d203a20fcf40382048173545e7 build: number: 0 rpaths: - lib/R/lib/ - lib/ +# Suggests: testthat +# SystemRequirements: GNU make requirements: host: - - 'bioconductor-biostrings >=2.50.0,<2.51.0' + - 'bioconductor-biostrings >=2.52.0,<2.53.0' - r-base + - 'r-bh >=1.66.0-1' - r-doparallel - r-e1071 - r-foreach - r-ranger - - r-rstan + - 'r-rcpp >=0.12.17' + - 'r-rcppeigen >=0.3.3.4.0' + - r-rpref + - 'r-rstan >=2.17.3' + - 'r-rstantools >=1.5.0' + - 'r-stanheaders >=2.17.2' run: - - 'bioconductor-biostrings >=2.50.0,<2.51.0' + - 'bioconductor-biostrings >=2.52.0,<2.53.0' - r-base + - 'r-bh >=1.66.0-1' - r-doparallel - r-e1071 - r-foreach - r-ranger - - r-rstan + - 'r-rcpp >=0.12.17' + - 'r-rcppeigen >=0.3.3.4.0' + - r-rpref + - 'r-rstan >=2.17.3' + - 'r-rstantools >=1.5.0' + - 'r-stanheaders >=2.17.2' build: - {{ compiler('c') }} - {{ compiler('cxx') }} @@ -43,5 +57,5 @@ test: about: home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: 'GPL (>= 2)' - summary: 'Genetic association studies are an essential tool for studying the relationship between genotypes and phenotypes. With genphen we can quantify the association between genotypes and phenotypes using a hybrid method which uses statistical learning techniques such as random forest and support vector machines, and Bayesian inference using hierarchical models.' + summary: 'Genetic association studies are an essential tool for studying the relationship between genotypes and phenotypes. With genphen we can jointly study multiple phenotypes of different types, by quantifying the association between different genotypes and each phenotype using a hybrid method which uses statistical learning techniques such as random forest and support vector machines, and Bayesian inference using hierarchical models.' diff --git a/recipes/bioconductor-genrank/meta.yaml b/recipes/bioconductor-genrank/meta.yaml index 222d422e5471f..5c796cd7cd82b 100644 --- a/recipes/bioconductor-genrank/meta.yaml +++ b/recipes/bioconductor-genrank/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.10.0" %} +{% set version = "1.12.0" %} {% set name = "GenRank" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 68b7b5b4ad252221ec675ee9f40e0037 + md5: dad9e212df456a6ccd2c25ca658ec132 build: number: 0 rpaths: @@ -20,12 +20,12 @@ build: # Suggests: knitr, rmarkdown, testthat requirements: host: - - 'bioconductor-survcomp >=1.32.0,<1.33.0' + - 'bioconductor-survcomp >=1.34.0,<1.35.0' - r-base - r-matrixstats - r-reshape2 run: - - 'bioconductor-survcomp >=1.32.0,<1.33.0' + - 'bioconductor-survcomp >=1.34.0,<1.35.0' - r-base - r-matrixstats - r-reshape2 diff --git a/recipes/bioconductor-genvisr/meta.yaml b/recipes/bioconductor-genvisr/meta.yaml index 3951b2ac72d0d..7d29994d3bbe2 100644 --- a/recipes/bioconductor-genvisr/meta.yaml +++ b/recipes/bioconductor-genvisr/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.14.2" %} +{% set version = "1.16.0" %} {% set name = "GenVisR" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 970d7bdf968cc909da48746af4f61700 + md5: 742fdff945254b0cc3f72e99d46065e1 build: number: 0 rpaths: @@ -20,17 +20,17 @@ build: # Suggests: BiocStyle, BSgenome.Hsapiens.UCSC.hg19, knitr, RMySQL, roxygen2, testthat, TxDb.Hsapiens.UCSC.hg19.knownGene, rmarkdown, vdiffr, formatR, TxDb.Hsapiens.UCSC.hg38.knownGene, BSgenome.Hsapiens.UCSC.hg38 requirements: host: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' - - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' - - 'bioconductor-biomart >=2.38.0,<2.39.0' - - 'bioconductor-biostrings >=2.50.0,<2.51.0' - - 'bioconductor-bsgenome >=1.50.0,<1.51.0' - - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' - - 'bioconductor-genomicfeatures >=1.34.0,<1.35.0' - - 'bioconductor-genomicranges >=1.34.0,<1.35.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-rsamtools >=1.34.0,<1.35.0' - - 'bioconductor-variantannotation >=1.28.0,<1.29.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' + - 'bioconductor-biocgenerics >=0.30.0,<0.31.0' + - 'bioconductor-biomart >=2.40.0,<2.41.0' + - 'bioconductor-biostrings >=2.52.0,<2.53.0' + - 'bioconductor-bsgenome >=1.52.0,<1.53.0' + - 'bioconductor-genomeinfodb >=1.20.0,<1.21.0' + - 'bioconductor-genomicfeatures >=1.36.0,<1.37.0' + - 'bioconductor-genomicranges >=1.36.0,<1.37.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-rsamtools >=2.0.0,<2.1.0' + - 'bioconductor-variantannotation >=1.30.0,<1.31.0' - r-base - r-data.table - r-dbi @@ -44,17 +44,17 @@ requirements: - r-scales - r-viridis run: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' - - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' - - 'bioconductor-biomart >=2.38.0,<2.39.0' - - 'bioconductor-biostrings >=2.50.0,<2.51.0' - - 'bioconductor-bsgenome >=1.50.0,<1.51.0' - - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' - - 'bioconductor-genomicfeatures >=1.34.0,<1.35.0' - - 'bioconductor-genomicranges >=1.34.0,<1.35.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-rsamtools >=1.34.0,<1.35.0' - - 'bioconductor-variantannotation >=1.28.0,<1.29.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' + - 'bioconductor-biocgenerics >=0.30.0,<0.31.0' + - 'bioconductor-biomart >=2.40.0,<2.41.0' + - 'bioconductor-biostrings >=2.52.0,<2.53.0' + - 'bioconductor-bsgenome >=1.52.0,<1.53.0' + - 'bioconductor-genomeinfodb >=1.20.0,<1.21.0' + - 'bioconductor-genomicfeatures >=1.36.0,<1.37.0' + - 'bioconductor-genomicranges >=1.36.0,<1.37.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-rsamtools >=2.0.0,<2.1.0' + - 'bioconductor-variantannotation >=1.30.0,<1.31.0' - r-base - r-data.table - r-dbi diff --git a/recipes/bioconductor-geometadb/meta.yaml b/recipes/bioconductor-geometadb/meta.yaml index 277b1c68be2ca..09defaa5e0b87 100644 --- a/recipes/bioconductor-geometadb/meta.yaml +++ b/recipes/bioconductor-geometadb/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.44.0" %} +{% set version = "1.46.0" %} {% set name = "GEOmetadb" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 9c85e98fb9e4f41fa76e8bac68ff4d35 + md5: f6d5d27fe6addf6f4daf72b82372b8ad build: number: 0 rpaths: @@ -20,11 +20,11 @@ build: # Suggests: knitr, rmarkdown, dplyr, tm, wordcloud requirements: host: - - 'bioconductor-geoquery >=2.50.0,<2.51.0' + - 'bioconductor-geoquery >=2.52.0,<2.53.0' - r-base - r-rsqlite run: - - 'bioconductor-geoquery >=2.50.0,<2.51.0' + - 'bioconductor-geoquery >=2.52.0,<2.53.0' - r-base - r-rsqlite test: diff --git a/recipes/bioconductor-geoquery/meta.yaml b/recipes/bioconductor-geoquery/meta.yaml index 438a019aa2264..ec97ca99fbe97 100644 --- a/recipes/bioconductor-geoquery/meta.yaml +++ b/recipes/bioconductor-geoquery/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "2.50.5" %} +{% set version = "2.52.0" %} {% set name = "GEOquery" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: e6c104433f3c731029045682156fdcef41e177a2fbf0292f8c217ac400a08d1c + md5: ab0f2d2a69f1cbd845ab7cbe225c3ba9 build: number: 0 rpaths: @@ -20,23 +20,23 @@ build: # Suggests: knitr, rmarkdown, BiocGenerics, testthat, covr requirements: host: - - 'bioconductor-biobase >=2.42.0,<2.43.0' - - 'bioconductor-limma >=3.38.0,<3.39.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' + - 'bioconductor-limma >=3.40.0,<3.41.0' - r-base - r-dplyr - r-httr - r-magrittr - - r-readr + - 'r-readr >=1.3.1' - r-tidyr - r-xml2 run: - - 'bioconductor-biobase >=2.42.0,<2.43.0' - - 'bioconductor-limma >=3.38.0,<3.39.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' + - 'bioconductor-limma >=3.40.0,<3.41.0' - r-base - r-dplyr - r-httr - r-magrittr - - r-readr + - 'r-readr >=1.3.1' - r-tidyr - r-xml2 test: diff --git a/recipes/bioconductor-geosubmission/meta.yaml b/recipes/bioconductor-geosubmission/meta.yaml index 1e64433e553d3..b1735db6aadc0 100644 --- a/recipes/bioconductor-geosubmission/meta.yaml +++ b/recipes/bioconductor-geosubmission/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.34.0" %} +{% set version = "1.36.0" %} {% set name = "GEOsubmission" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 54b2359778553d53725c9974f1cda515 + md5: 4bc67c34e3a62253a1b0e79e6cc915e7 build: number: 0 rpaths: @@ -19,12 +19,12 @@ build: noarch: generic requirements: host: - - 'bioconductor-affy >=1.60.0,<1.61.0' - - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-affy >=1.62.0,<1.63.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' - r-base run: - - 'bioconductor-affy >=1.60.0,<1.61.0' - - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-affy >=1.62.0,<1.63.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' - r-base test: commands: diff --git a/recipes/bioconductor-gep2pep/meta.yaml b/recipes/bioconductor-gep2pep/meta.yaml index 399ba00737555..84d233ea9ac44 100644 --- a/recipes/bioconductor-gep2pep/meta.yaml +++ b/recipes/bioconductor-gep2pep/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.2.0" %} +{% set version = "1.4.0" %} {% set name = "gep2pep" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: fd48276c9acea753df8d96b68a5b5ab0 + md5: d4bdd65369f474f7b3d17ac060fc0347 build: number: 0 rpaths: @@ -20,9 +20,9 @@ build: # Suggests: WriteXLS, testthat, knitr, rmarkdown requirements: host: - - 'bioconductor-biobase >=2.42.0,<2.43.0' - - 'bioconductor-gseabase >=1.44.0,<1.45.0' - - 'bioconductor-rhdf5 >=2.26.0,<2.27.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' + - 'bioconductor-gseabase >=1.46.0,<1.47.0' + - 'bioconductor-rhdf5 >=2.28.0,<2.29.0' - r-base - r-digest - r-foreach @@ -30,9 +30,9 @@ requirements: - 'r-repo >=2.1.1' - r-xml run: - - 'bioconductor-biobase >=2.42.0,<2.43.0' - - 'bioconductor-gseabase >=1.44.0,<1.45.0' - - 'bioconductor-rhdf5 >=2.26.0,<2.27.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' + - 'bioconductor-gseabase >=1.46.0,<1.47.0' + - 'bioconductor-rhdf5 >=2.28.0,<2.29.0' - r-base - r-digest - r-foreach diff --git a/recipes/bioconductor-gesper/meta.yaml b/recipes/bioconductor-gesper/meta.yaml index 8895942bf37d3..67179b305f12c 100644 --- a/recipes/bioconductor-gesper/meta.yaml +++ b/recipes/bioconductor-gesper/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.14.0" %} +{% set version = "1.16.0" %} {% set name = "gespeR" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: d646d9eae2ab8798944be04aed1fa303 + md5: d2b3ea34d9d1c043f889a02fb111451b build: number: 0 rpaths: @@ -20,9 +20,9 @@ build: # Suggests: knitr requirements: host: - - 'bioconductor-biobase >=2.42.0,<2.43.0' - - 'bioconductor-biomart >=2.38.0,<2.39.0' - - 'bioconductor-cellhts2 >=2.46.0,<2.47.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' + - 'bioconductor-biomart >=2.40.0,<2.41.0' + - 'bioconductor-cellhts2 >=2.48.0,<2.49.0' - r-base - r-doparallel - r-dplyr @@ -32,9 +32,9 @@ requirements: - r-matrix - r-reshape2 run: - - 'bioconductor-biobase >=2.42.0,<2.43.0' - - 'bioconductor-biomart >=2.38.0,<2.39.0' - - 'bioconductor-cellhts2 >=2.46.0,<2.47.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' + - 'bioconductor-biomart >=2.40.0,<2.41.0' + - 'bioconductor-cellhts2 >=2.48.0,<2.49.0' - r-base - r-doparallel - r-dplyr diff --git a/recipes/bioconductor-geuvadistranscriptexpr/meta.yaml b/recipes/bioconductor-geuvadistranscriptexpr/meta.yaml index 53c8bc70796f2..076fe501abf68 100644 --- a/recipes/bioconductor-geuvadistranscriptexpr/meta.yaml +++ b/recipes/bioconductor-geuvadistranscriptexpr/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.10.0" %} +{% set version = "1.12.0" %} {% set name = "GeuvadisTranscriptExpr" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: e7df5c58da3c1e58245c8b0d12263735 + md5: ece1f0f2d431b75bca527b79f319c9a0 build: number: 0 rpaths: @@ -23,7 +23,7 @@ requirements: - r-base run: - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-geuvadistranscriptexpr/post-link.sh b/recipes/bioconductor-geuvadistranscriptexpr/post-link.sh index ddcc63ee69362..2c3f0f3cd141f 100644 --- a/recipes/bioconductor-geuvadistranscriptexpr/post-link.sh +++ b/recipes/bioconductor-geuvadistranscriptexpr/post-link.sh @@ -1,11 +1,11 @@ #!/bin/bash -FN="GeuvadisTranscriptExpr_1.10.0.tar.gz" +FN="GeuvadisTranscriptExpr_1.12.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/experiment/src/contrib/GeuvadisTranscriptExpr_1.10.0.tar.gz" - "https://bioarchive.galaxyproject.org/GeuvadisTranscriptExpr_1.10.0.tar.gz" - "https://depot.galaxyproject.org/software/bioconductor-geuvadistranscriptexpr/bioconductor-geuvadistranscriptexpr_1.10.0_src_all.tar.gz" + "https://bioconductor.org/packages/3.9/data/experiment/src/contrib/GeuvadisTranscriptExpr_1.12.0.tar.gz" + "https://bioarchive.galaxyproject.org/GeuvadisTranscriptExpr_1.12.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-geuvadistranscriptexpr/bioconductor-geuvadistranscriptexpr_1.12.0_src_all.tar.gz" ) -MD5="e7df5c58da3c1e58245c8b0d12263735" +MD5="ece1f0f2d431b75bca527b79f319c9a0" # Use a staging area in the conda dir rather than temp dirs, both to avoid # permission issues as well as to have things downloaded in a predictable @@ -16,7 +16,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-geuvpack/meta.yaml b/recipes/bioconductor-geuvpack/meta.yaml index 054fc78590ba5..6c72bbb8629b7 100644 --- a/recipes/bioconductor-geuvpack/meta.yaml +++ b/recipes/bioconductor-geuvpack/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.14.0" %} +{% set version = "1.16.0" %} {% set name = "geuvPack" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 0fddefe9a5285b6545e39af655ef2502 + md5: ab9980646eee0afbfb64f8009fc0862e build: number: 0 rpaths: @@ -19,12 +19,12 @@ build: noarch: generic requirements: host: - - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' + - 'bioconductor-summarizedexperiment >=1.14.0,<1.15.0' - r-base run: - - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' + - 'bioconductor-summarizedexperiment >=1.14.0,<1.15.0' - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-geuvpack/post-link.sh b/recipes/bioconductor-geuvpack/post-link.sh index 27215be2a17f6..869b1ff9d8557 100644 --- a/recipes/bioconductor-geuvpack/post-link.sh +++ b/recipes/bioconductor-geuvpack/post-link.sh @@ -1,11 +1,11 @@ #!/bin/bash -FN="geuvPack_1.14.0.tar.gz" +FN="geuvPack_1.16.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/experiment/src/contrib/geuvPack_1.14.0.tar.gz" - "https://bioarchive.galaxyproject.org/geuvPack_1.14.0.tar.gz" - "https://depot.galaxyproject.org/software/bioconductor-geuvpack/bioconductor-geuvpack_1.14.0_src_all.tar.gz" + "https://bioconductor.org/packages/3.9/data/experiment/src/contrib/geuvPack_1.16.0.tar.gz" + "https://bioarchive.galaxyproject.org/geuvPack_1.16.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-geuvpack/bioconductor-geuvpack_1.16.0_src_all.tar.gz" ) -MD5="0fddefe9a5285b6545e39af655ef2502" +MD5="ab9980646eee0afbfb64f8009fc0862e" # Use a staging area in the conda dir rather than temp dirs, both to avoid # permission issues as well as to have things downloaded in a predictable @@ -16,7 +16,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-geuvstore2/meta.yaml b/recipes/bioconductor-geuvstore2/meta.yaml index 4b678c202fc4d..bb99454f2c3d0 100644 --- a/recipes/bioconductor-geuvstore2/meta.yaml +++ b/recipes/bioconductor-geuvstore2/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.12.0" %} +{% set version = "1.14.0" %} {% set name = "geuvStore2" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 4a979fce43756a969ef30510fc7edd7f + md5: ca0b70a5e2a1b47dd19f9e9566dc8411 build: number: 0 rpaths: @@ -20,16 +20,16 @@ build: # Suggests: Homo.sapiens, knitr (>= 1.7), rmarkdown requirements: host: - - 'bioconductor-genomicranges >=1.34.0,<1.35.0' - - 'bioconductor-gqtlbase >=1.14.0,<1.15.0' + - 'bioconductor-genomicranges >=1.36.0,<1.37.0' + - 'bioconductor-gqtlbase >=1.16.0,<1.17.0' - r-base - r-batchjobs run: - - 'bioconductor-genomicranges >=1.34.0,<1.35.0' - - 'bioconductor-gqtlbase >=1.14.0,<1.15.0' + - 'bioconductor-genomicranges >=1.36.0,<1.37.0' + - 'bioconductor-gqtlbase >=1.16.0,<1.17.0' - r-base - r-batchjobs - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-geuvstore2/post-link.sh b/recipes/bioconductor-geuvstore2/post-link.sh index 2fc765b3a909f..4e7d956324fa5 100644 --- a/recipes/bioconductor-geuvstore2/post-link.sh +++ b/recipes/bioconductor-geuvstore2/post-link.sh @@ -1,11 +1,11 @@ #!/bin/bash -FN="geuvStore2_1.12.0.tar.gz" +FN="geuvStore2_1.14.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/experiment/src/contrib/geuvStore2_1.12.0.tar.gz" - "https://bioarchive.galaxyproject.org/geuvStore2_1.12.0.tar.gz" - "https://depot.galaxyproject.org/software/bioconductor-geuvstore2/bioconductor-geuvstore2_1.12.0_src_all.tar.gz" + "https://bioconductor.org/packages/3.9/data/experiment/src/contrib/geuvStore2_1.14.0.tar.gz" + "https://bioarchive.galaxyproject.org/geuvStore2_1.14.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-geuvstore2/bioconductor-geuvstore2_1.14.0_src_all.tar.gz" ) -MD5="4a979fce43756a969ef30510fc7edd7f" +MD5="ca0b70a5e2a1b47dd19f9e9566dc8411" # Use a staging area in the conda dir rather than temp dirs, both to avoid # permission issues as well as to have things downloaded in a predictable @@ -16,7 +16,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-gewist/meta.yaml b/recipes/bioconductor-gewist/meta.yaml index 3da9a77fa5885..4ad5fbaeac5e2 100644 --- a/recipes/bioconductor-gewist/meta.yaml +++ b/recipes/bioconductor-gewist/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.26.0" %} +{% set version = "1.28.0" %} {% set name = "GEWIST" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: d056905b8d6521e06a936955e8fdab08 + md5: eed2a055a18ee166af153d06ca0410ee build: number: 0 rpaths: diff --git a/recipes/bioconductor-ggbase/meta.yaml b/recipes/bioconductor-ggbase/meta.yaml index 97155cac51a9f..d536687fc9ec4 100644 --- a/recipes/bioconductor-ggbase/meta.yaml +++ b/recipes/bioconductor-ggbase/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "3.44.0" %} +{% set version = "3.46.0" %} {% set name = "GGBase" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 126306447c411a4c114df4a7f83fdce7 + md5: 40c2bc7b7cb9bfdb3fca63e092e29888 build: number: 0 rpaths: @@ -20,30 +20,30 @@ build: # Suggests: GGtools, illuminaHumanv1.db, knitr requirements: host: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' - - 'bioconductor-biobase >=2.42.0,<2.43.0' - - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' - - 'bioconductor-genefilter >=1.64.0,<1.65.0' - - 'bioconductor-genomicranges >=1.34.0,<1.35.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-limma >=3.38.0,<3.39.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' - - 'bioconductor-snpstats >=1.32.0,<1.33.0' - - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' + - 'bioconductor-biocgenerics >=0.30.0,<0.31.0' + - 'bioconductor-genefilter >=1.66.0,<1.67.0' + - 'bioconductor-genomicranges >=1.36.0,<1.37.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-limma >=3.40.0,<3.41.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' + - 'bioconductor-snpstats >=1.34.0,<1.35.0' + - 'bioconductor-summarizedexperiment >=1.14.0,<1.15.0' - r-base - r-digest - r-matrix run: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' - - 'bioconductor-biobase >=2.42.0,<2.43.0' - - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' - - 'bioconductor-genefilter >=1.64.0,<1.65.0' - - 'bioconductor-genomicranges >=1.34.0,<1.35.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-limma >=3.38.0,<3.39.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' - - 'bioconductor-snpstats >=1.32.0,<1.33.0' - - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' + - 'bioconductor-biocgenerics >=0.30.0,<0.31.0' + - 'bioconductor-genefilter >=1.66.0,<1.67.0' + - 'bioconductor-genomicranges >=1.36.0,<1.37.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-limma >=3.40.0,<3.41.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' + - 'bioconductor-snpstats >=1.34.0,<1.35.0' + - 'bioconductor-summarizedexperiment >=1.14.0,<1.15.0' - r-base - r-digest - r-matrix diff --git a/recipes/bioconductor-ggbio/meta.yaml b/recipes/bioconductor-ggbio/meta.yaml index 4e27ee449d09e..32050b340b5fd 100644 --- a/recipes/bioconductor-ggbio/meta.yaml +++ b/recipes/bioconductor-ggbio/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.30.0" %} +{% set version = "1.32.0" %} {% set name = "ggbio" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: fff6ae2022a12bfc785903fa9f64e7a8 + md5: 5ee3dd6b46d554ca569c2b9dc71e429d build: number: 0 rpaths: @@ -20,25 +20,25 @@ build: # Suggests: vsn, BSgenome.Hsapiens.UCSC.hg19, Homo.sapiens, TxDb.Hsapiens.UCSC.hg19.knownGene, chipseq, TxDb.Mmusculus.UCSC.mm9.knownGene, knitr, BiocStyle, testthat, EnsDb.Hsapiens.v75, tinytex requirements: host: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' - - 'bioconductor-annotationfilter >=1.6.0,<1.7.0' - - 'bioconductor-biobase >=2.42.0,<2.43.0' - - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' - - 'bioconductor-biostrings >=2.50.0,<2.51.0' - - 'bioconductor-biovizbase >=1.30.0,<1.31.0' - - 'bioconductor-bsgenome >=1.50.0,<1.51.0' - - 'bioconductor-ensembldb >=2.6.0,<2.7.0' - - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' - - 'bioconductor-genomicalignments >=1.18.0,<1.19.0' - - 'bioconductor-genomicfeatures >=1.34.0,<1.35.0' - - 'bioconductor-genomicranges >=1.34.0,<1.35.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-organismdbi >=1.24.0,<1.25.0' - - 'bioconductor-rsamtools >=1.34.0,<1.35.0' - - 'bioconductor-rtracklayer >=1.42.0,<1.43.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' - - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' - - 'bioconductor-variantannotation >=1.28.0,<1.29.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' + - 'bioconductor-annotationfilter >=1.8.0,<1.9.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' + - 'bioconductor-biocgenerics >=0.30.0,<0.31.0' + - 'bioconductor-biostrings >=2.52.0,<2.53.0' + - 'bioconductor-biovizbase >=1.32.0,<1.33.0' + - 'bioconductor-bsgenome >=1.52.0,<1.53.0' + - 'bioconductor-ensembldb >=2.8.0,<2.9.0' + - 'bioconductor-genomeinfodb >=1.20.0,<1.21.0' + - 'bioconductor-genomicalignments >=1.20.0,<1.21.0' + - 'bioconductor-genomicfeatures >=1.36.0,<1.37.0' + - 'bioconductor-genomicranges >=1.36.0,<1.37.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-organismdbi >=1.26.0,<1.27.0' + - 'bioconductor-rsamtools >=2.0.0,<2.1.0' + - 'bioconductor-rtracklayer >=1.44.0,<1.45.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' + - 'bioconductor-summarizedexperiment >=1.14.0,<1.15.0' + - 'bioconductor-variantannotation >=1.30.0,<1.31.0' - r-base - r-ggally - 'r-ggplot2 >=1.0.0' @@ -49,25 +49,25 @@ requirements: - r-rlang - r-scales run: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' - - 'bioconductor-annotationfilter >=1.6.0,<1.7.0' - - 'bioconductor-biobase >=2.42.0,<2.43.0' - - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' - - 'bioconductor-biostrings >=2.50.0,<2.51.0' - - 'bioconductor-biovizbase >=1.30.0,<1.31.0' - - 'bioconductor-bsgenome >=1.50.0,<1.51.0' - - 'bioconductor-ensembldb >=2.6.0,<2.7.0' - - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' - - 'bioconductor-genomicalignments >=1.18.0,<1.19.0' - - 'bioconductor-genomicfeatures >=1.34.0,<1.35.0' - - 'bioconductor-genomicranges >=1.34.0,<1.35.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-organismdbi >=1.24.0,<1.25.0' - - 'bioconductor-rsamtools >=1.34.0,<1.35.0' - - 'bioconductor-rtracklayer >=1.42.0,<1.43.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' - - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' - - 'bioconductor-variantannotation >=1.28.0,<1.29.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' + - 'bioconductor-annotationfilter >=1.8.0,<1.9.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' + - 'bioconductor-biocgenerics >=0.30.0,<0.31.0' + - 'bioconductor-biostrings >=2.52.0,<2.53.0' + - 'bioconductor-biovizbase >=1.32.0,<1.33.0' + - 'bioconductor-bsgenome >=1.52.0,<1.53.0' + - 'bioconductor-ensembldb >=2.8.0,<2.9.0' + - 'bioconductor-genomeinfodb >=1.20.0,<1.21.0' + - 'bioconductor-genomicalignments >=1.20.0,<1.21.0' + - 'bioconductor-genomicfeatures >=1.36.0,<1.37.0' + - 'bioconductor-genomicranges >=1.36.0,<1.37.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-organismdbi >=1.26.0,<1.27.0' + - 'bioconductor-rsamtools >=2.0.0,<2.1.0' + - 'bioconductor-rtracklayer >=1.44.0,<1.45.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' + - 'bioconductor-summarizedexperiment >=1.14.0,<1.15.0' + - 'bioconductor-variantannotation >=1.30.0,<1.31.0' - r-base - r-ggally - 'r-ggplot2 >=1.0.0' diff --git a/recipes/bioconductor-ggcyto/meta.yaml b/recipes/bioconductor-ggcyto/meta.yaml index fe69409a61c2a..b56cca3099f67 100644 --- a/recipes/bioconductor-ggcyto/meta.yaml +++ b/recipes/bioconductor-ggcyto/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.10.2" %} +{% set version = "1.12.0" %} {% set name = "ggcyto" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - sha256: 4170b273932d37d3873da4ff099448f173067081630f6ebebf5ce74698ce1c5a + md5: 4c9443a3bbee4ff09ef9b8e413b40328 build: number: 0 rpaths: @@ -20,9 +20,9 @@ build: # Suggests: testthat, flowWorkspaceData, knitr, rmarkdown, flowStats, openCyto, flowViz, ggridges, vdiffr requirements: host: - - 'bioconductor-flowcore >=1.48.0,<1.49.0' - - 'bioconductor-flowworkspace >=3.30.0,<3.31.0' - - 'bioconductor-ncdfflow >=2.28.0,<2.29.0' + - 'bioconductor-flowcore >=1.50.0,<1.51.0' + - 'bioconductor-flowworkspace >=3.32.0,<3.33.0' + - 'bioconductor-ncdfflow >=2.30.0,<2.31.0' - r-base - r-data.table - 'r-ggplot2 >=2.2.1.9000' @@ -32,9 +32,9 @@ requirements: - r-rlang - r-scales run: - - 'bioconductor-flowcore >=1.48.0,<1.49.0' - - 'bioconductor-flowworkspace >=3.30.0,<3.31.0' - - 'bioconductor-ncdfflow >=2.28.0,<2.29.0' + - 'bioconductor-flowcore >=1.50.0,<1.51.0' + - 'bioconductor-flowworkspace >=3.32.0,<3.33.0' + - 'bioconductor-ncdfflow >=2.30.0,<2.31.0' - r-base - r-data.table - 'r-ggplot2 >=2.2.1.9000' diff --git a/recipes/bioconductor-ggdata/meta.yaml b/recipes/bioconductor-ggdata/meta.yaml index 34a135232c979..843405a2882f9 100644 --- a/recipes/bioconductor-ggdata/meta.yaml +++ b/recipes/bioconductor-ggdata/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.20.0" %} +{% set version = "1.22.0" %} {% set name = "GGdata" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: dffb9127f0d21be6e27478b178bf9d13 + md5: afba50713e07d019b729a86fda04580e build: number: 0 rpaths: @@ -19,20 +19,20 @@ build: noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' - - 'bioconductor-biobase >=2.42.0,<2.43.0' - - 'bioconductor-ggbase >=3.44.0,<3.45.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' + - 'bioconductor-ggbase >=3.46.0,<3.47.0' - 'bioconductor-illuminahumanv1.db >=1.26.0,<1.27.0' - - 'bioconductor-snpstats >=1.32.0,<1.33.0' + - 'bioconductor-snpstats >=1.34.0,<1.35.0' - r-base run: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' - - 'bioconductor-biobase >=2.42.0,<2.43.0' - - 'bioconductor-ggbase >=3.44.0,<3.45.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' + - 'bioconductor-ggbase >=3.46.0,<3.47.0' - 'bioconductor-illuminahumanv1.db >=1.26.0,<1.27.0' - - 'bioconductor-snpstats >=1.32.0,<1.33.0' + - 'bioconductor-snpstats >=1.34.0,<1.35.0' - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-ggdata/post-link.sh b/recipes/bioconductor-ggdata/post-link.sh index c57b7dfc0e72d..91831c7a0580b 100644 --- a/recipes/bioconductor-ggdata/post-link.sh +++ b/recipes/bioconductor-ggdata/post-link.sh @@ -1,11 +1,11 @@ #!/bin/bash -FN="GGdata_1.20.0.tar.gz" +FN="GGdata_1.22.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/experiment/src/contrib/GGdata_1.20.0.tar.gz" - "https://bioarchive.galaxyproject.org/GGdata_1.20.0.tar.gz" - "https://depot.galaxyproject.org/software/bioconductor-ggdata/bioconductor-ggdata_1.20.0_src_all.tar.gz" + "https://bioconductor.org/packages/3.9/data/experiment/src/contrib/GGdata_1.22.0.tar.gz" + "https://bioarchive.galaxyproject.org/GGdata_1.22.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-ggdata/bioconductor-ggdata_1.22.0_src_all.tar.gz" ) -MD5="dffb9127f0d21be6e27478b178bf9d13" +MD5="afba50713e07d019b729a86fda04580e" # Use a staging area in the conda dir rather than temp dirs, both to avoid # permission issues as well as to have things downloaded in a predictable @@ -16,7 +16,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-gghumanmethcancerpanelv1.db/meta.yaml b/recipes/bioconductor-gghumanmethcancerpanelv1.db/meta.yaml index 56c52d0b42921..b8ca1c123352d 100644 --- a/recipes/bioconductor-gghumanmethcancerpanelv1.db/meta.yaml +++ b/recipes/bioconductor-gghumanmethcancerpanelv1.db/meta.yaml @@ -1,6 +1,6 @@ {% set version = "1.4.1" %} {% set name = "GGHumanMethCancerPanelv1.db" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -12,7 +12,7 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' md5: e8f4a37182b175fb33dd54f8093e6f52 build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ @@ -20,16 +20,16 @@ build: # Suggests: annotate requirements: host: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' - - 'bioconductor-annotationforge >=1.24.0,<1.25.0' - - 'bioconductor-org.hs.eg.db >=3.7.0,<3.8.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' + - 'bioconductor-annotationforge >=1.26.0,<1.27.0' + - 'bioconductor-org.hs.eg.db >=3.8.0,<3.9.0' - r-base run: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' - - 'bioconductor-annotationforge >=1.24.0,<1.25.0' - - 'bioconductor-org.hs.eg.db >=3.7.0,<3.8.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' + - 'bioconductor-annotationforge >=1.26.0,<1.27.0' + - 'bioconductor-org.hs.eg.db >=3.8.0,<3.9.0' - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-gghumanmethcancerpanelv1.db/post-link.sh b/recipes/bioconductor-gghumanmethcancerpanelv1.db/post-link.sh index c57236256cec9..1f02187501497 100644 --- a/recipes/bioconductor-gghumanmethcancerpanelv1.db/post-link.sh +++ b/recipes/bioconductor-gghumanmethcancerpanelv1.db/post-link.sh @@ -1,9 +1,10 @@ #!/bin/bash FN="GGHumanMethCancerPanelv1.db_1.4.1.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/GGHumanMethCancerPanelv1.db_1.4.1.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/GGHumanMethCancerPanelv1.db_1.4.1.tar.gz" "https://bioarchive.galaxyproject.org/GGHumanMethCancerPanelv1.db_1.4.1.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-gghumanmethcancerpanelv1.db/bioconductor-gghumanmethcancerpanelv1.db_1.4.1_src_all.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-gghumanmethcancerpanelv1.db/bioconductor-gghumanmethcancerpanelv1.db_1.4.1_src_all.tar.gz" ) MD5="e8f4a37182b175fb33dd54f8093e6f52" @@ -16,7 +17,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-ggtools/meta.yaml b/recipes/bioconductor-ggtools/meta.yaml index c85288cb634e8..3af6d97a86bb2 100644 --- a/recipes/bioconductor-ggtools/meta.yaml +++ b/recipes/bioconductor-ggtools/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "5.18.0" %} +{% set version = "5.20.0" %} {% set name = "GGtools" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 7c5237419693c7989d912bd329dd982b + md5: b54d30694006d2f291c7b717a39c56d3 build: number: 0 rpaths: @@ -20,21 +20,21 @@ build: # Suggests: GGdata, illuminaHumanv1.db, SNPlocs.Hsapiens.dbSNP144.GRCh37, multtest, aod, rmeta requirements: host: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' - - 'bioconductor-biobase >=2.42.0,<2.43.0' - - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' - - 'bioconductor-biostrings >=2.50.0,<2.51.0' - - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' - - 'bioconductor-genomicranges >=1.34.0,<1.35.0' - - 'bioconductor-ggbase >=3.44.0,<3.45.0' - - 'bioconductor-gviz >=1.26.0,<1.27.0' - - 'bioconductor-homo.sapiens >=1.3.0,<1.4.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-rsamtools >=1.34.0,<1.35.0' - - 'bioconductor-rtracklayer >=1.42.0,<1.43.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' - - 'bioconductor-snpstats >=1.32.0,<1.33.0' - - 'bioconductor-variantannotation >=1.28.0,<1.29.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' + - 'bioconductor-biocgenerics >=0.30.0,<0.31.0' + - 'bioconductor-biostrings >=2.52.0,<2.53.0' + - 'bioconductor-genomeinfodb >=1.20.0,<1.21.0' + - 'bioconductor-genomicranges >=1.36.0,<1.37.0' + - 'bioconductor-ggbase >=3.46.0,<3.47.0' + - 'bioconductor-gviz >=1.28.0,<1.29.0' + - 'bioconductor-homo.sapiens >=1.4.0,<1.5.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-rsamtools >=2.0.0,<2.1.0' + - 'bioconductor-rtracklayer >=1.44.0,<1.45.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' + - 'bioconductor-snpstats >=1.34.0,<1.35.0' + - 'bioconductor-variantannotation >=1.30.0,<1.31.0' - r-base - r-biglm - r-bit @@ -46,21 +46,21 @@ requirements: - r-reshape2 - r-rocr run: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' - - 'bioconductor-biobase >=2.42.0,<2.43.0' - - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' - - 'bioconductor-biostrings >=2.50.0,<2.51.0' - - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' - - 'bioconductor-genomicranges >=1.34.0,<1.35.0' - - 'bioconductor-ggbase >=3.44.0,<3.45.0' - - 'bioconductor-gviz >=1.26.0,<1.27.0' - - 'bioconductor-homo.sapiens >=1.3.0,<1.4.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-rsamtools >=1.34.0,<1.35.0' - - 'bioconductor-rtracklayer >=1.42.0,<1.43.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' - - 'bioconductor-snpstats >=1.32.0,<1.33.0' - - 'bioconductor-variantannotation >=1.28.0,<1.29.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' + - 'bioconductor-biocgenerics >=0.30.0,<0.31.0' + - 'bioconductor-biostrings >=2.52.0,<2.53.0' + - 'bioconductor-genomeinfodb >=1.20.0,<1.21.0' + - 'bioconductor-genomicranges >=1.36.0,<1.37.0' + - 'bioconductor-ggbase >=3.46.0,<3.47.0' + - 'bioconductor-gviz >=1.28.0,<1.29.0' + - 'bioconductor-homo.sapiens >=1.4.0,<1.5.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-rsamtools >=2.0.0,<2.1.0' + - 'bioconductor-rtracklayer >=1.44.0,<1.45.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' + - 'bioconductor-snpstats >=1.34.0,<1.35.0' + - 'bioconductor-variantannotation >=1.30.0,<1.31.0' - r-base - r-biglm - r-bit diff --git a/recipes/bioconductor-ggtree/meta.yaml b/recipes/bioconductor-ggtree/meta.yaml index 0d9876b277af7..56562b7adc642 100644 --- a/recipes/bioconductor-ggtree/meta.yaml +++ b/recipes/bioconductor-ggtree/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.14.6" %} +{% set version = "1.16.0" %} {% set name = "ggtree" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,17 +10,17 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - sha256: 249120b4acd7d3b6d213943acc5581facb7c44c19c1016d16d71c32da76ce44a + md5: 82f310db99b36c69f5118195d6a37596 build: number: 0 rpaths: - lib/R/lib/ - lib/ noarch: generic -# Suggests: colorspace, cowplot, emojifont, ggimage, knitr, prettydoc, rmarkdown, testthat +# Suggests: emojifont, ggimage, ggplotify, grDevices, knitr, prettydoc, rmarkdown, scales, testthat, tibble requirements: host: - - 'bioconductor-treeio >=1.6.0,<1.7.0' + - 'bioconductor-treeio >=1.8.0,<1.9.0' - r-ape - r-base - r-dplyr @@ -29,12 +29,10 @@ requirements: - r-purrr - r-rlang - 'r-rvcheck >=0.1.0' - - r-scales - - r-tibble - r-tidyr - - 'r-tidytree >=0.1.9' + - 'r-tidytree >=0.2.4' run: - - 'bioconductor-treeio >=1.6.0,<1.7.0' + - 'bioconductor-treeio >=1.8.0,<1.9.0' - r-ape - r-base - r-dplyr @@ -43,10 +41,8 @@ requirements: - r-purrr - r-rlang - 'r-rvcheck >=0.1.0' - - r-scales - - r-tibble - r-tidyr - - 'r-tidytree >=0.1.9' + - 'r-tidytree >=0.2.4' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-gigsea/meta.yaml b/recipes/bioconductor-gigsea/meta.yaml index 288341a1bd4f8..8b4ebc2a46bb3 100644 --- a/recipes/bioconductor-gigsea/meta.yaml +++ b/recipes/bioconductor-gigsea/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.0.0" %} +{% set version = "1.2.0" %} {% set name = "GIGSEA" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: b2a1158dd46f573307badd416a2c2206 + md5: 722ecfa98d287f8380af786f160492f9 build: number: 0 rpaths: diff --git a/recipes/bioconductor-gigseadata/meta.yaml b/recipes/bioconductor-gigseadata/meta.yaml index 388658b12b881..4ac57b022fbc3 100644 --- a/recipes/bioconductor-gigseadata/meta.yaml +++ b/recipes/bioconductor-gigseadata/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.0.0" %} +{% set version = "1.2.0" %} {% set name = "GIGSEAdata" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 9036142a6d2c9eecdfec8023c032aa7f + md5: 9179864b9233f0010eb2f0fb58317ae5 build: number: 0 rpaths: @@ -23,7 +23,7 @@ requirements: - r-base run: - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-gigseadata/post-link.sh b/recipes/bioconductor-gigseadata/post-link.sh index b389d98e38e3e..6cb9258f48ea5 100644 --- a/recipes/bioconductor-gigseadata/post-link.sh +++ b/recipes/bioconductor-gigseadata/post-link.sh @@ -1,11 +1,11 @@ #!/bin/bash -FN="GIGSEAdata_1.0.0.tar.gz" +FN="GIGSEAdata_1.2.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/experiment/src/contrib/GIGSEAdata_1.0.0.tar.gz" - "https://bioarchive.galaxyproject.org/GIGSEAdata_1.0.0.tar.gz" - "https://depot.galaxyproject.org/software/bioconductor-gigseadata/bioconductor-gigseadata_1.0.0_src_all.tar.gz" + "https://bioconductor.org/packages/3.9/data/experiment/src/contrib/GIGSEAdata_1.2.0.tar.gz" + "https://bioarchive.galaxyproject.org/GIGSEAdata_1.2.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-gigseadata/bioconductor-gigseadata_1.2.0_src_all.tar.gz" ) -MD5="9036142a6d2c9eecdfec8023c032aa7f" +MD5="9179864b9233f0010eb2f0fb58317ae5" # Use a staging area in the conda dir rather than temp dirs, both to avoid # permission issues as well as to have things downloaded in a predictable @@ -16,7 +16,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-girafe/meta.yaml b/recipes/bioconductor-girafe/meta.yaml index e74813b3dc35d..a704d35f7ff5c 100644 --- a/recipes/bioconductor-girafe/meta.yaml +++ b/recipes/bioconductor-girafe/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.34.0" %} +{% set version = "1.36.0" %} {% set name = "girafe" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 18a9eabd7dba531cefb42bbd99372c25 + md5: da9585bea6624a78478137c4ccb901c1 build: number: 0 rpaths: @@ -19,25 +19,25 @@ build: # Suggests: MASS, org.Mm.eg.db, RColorBrewer requirements: host: - - 'bioconductor-biobase >=2.42.0,<2.43.0' - - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' - - 'bioconductor-biostrings >=2.50.0,<2.51.0' - - 'bioconductor-genomeintervals >=1.38.0,<1.39.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-rsamtools >=1.34.0,<1.35.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' - - 'bioconductor-shortread >=1.40.0,<1.41.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' + - 'bioconductor-biocgenerics >=0.30.0,<0.31.0' + - 'bioconductor-biostrings >=2.52.0,<2.53.0' + - 'bioconductor-genomeintervals >=1.40.0,<1.41.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-rsamtools >=2.0.0,<2.1.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' + - 'bioconductor-shortread >=1.42.0,<1.43.0' - r-base - 'r-intervals >=0.13.1' run: - - 'bioconductor-biobase >=2.42.0,<2.43.0' - - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' - - 'bioconductor-biostrings >=2.50.0,<2.51.0' - - 'bioconductor-genomeintervals >=1.38.0,<1.39.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-rsamtools >=1.34.0,<1.35.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' - - 'bioconductor-shortread >=1.40.0,<1.41.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' + - 'bioconductor-biocgenerics >=0.30.0,<0.31.0' + - 'bioconductor-biostrings >=2.52.0,<2.53.0' + - 'bioconductor-genomeintervals >=1.40.0,<1.41.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-rsamtools >=2.0.0,<2.1.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' + - 'bioconductor-shortread >=1.42.0,<1.43.0' - r-base - 'r-intervals >=0.13.1' build: diff --git a/recipes/bioconductor-gispa/meta.yaml b/recipes/bioconductor-gispa/meta.yaml index 6429f6fbb831d..7ea719713018a 100644 --- a/recipes/bioconductor-gispa/meta.yaml +++ b/recipes/bioconductor-gispa/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.6.0" %} +{% set version = "1.8.0" %} {% set name = "GISPA" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,9 +10,9 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 6f8b3bfbd6ddbb19055508854568fa4b + md5: 375f9485d8ba68a0267fa3d38fcaba0f build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ @@ -20,9 +20,9 @@ build: # Suggests: knitr requirements: host: - - 'bioconductor-biobase >=2.42.0,<2.43.0' - - 'bioconductor-genefilter >=1.64.0,<1.65.0' - - 'bioconductor-gseabase >=1.44.0,<1.45.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' + - 'bioconductor-genefilter >=1.66.0,<1.67.0' + - 'bioconductor-gseabase >=1.46.0,<1.47.0' - r-base - r-changepoint - r-data.table @@ -32,9 +32,9 @@ requirements: - r-plyr - r-scatterplot3d run: - - 'bioconductor-biobase >=2.42.0,<2.43.0' - - 'bioconductor-genefilter >=1.64.0,<1.65.0' - - 'bioconductor-gseabase >=1.44.0,<1.45.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' + - 'bioconductor-genefilter >=1.66.0,<1.67.0' + - 'bioconductor-gseabase >=1.46.0,<1.47.0' - r-base - r-changepoint - r-data.table diff --git a/recipes/bioconductor-glad/build.sh b/recipes/bioconductor-glad/build.sh index 9729b1f9bb736..c1d13421f5f1e 100644 --- a/recipes/bioconductor-glad/build.sh +++ b/recipes/bioconductor-glad/build.sh @@ -8,4 +8,4 @@ CXX=$CXX CXX98=$CXX CXX11=$CXX CXX14=$CXX" > ~/.R/Makevars -$R CMD INSTALL --build --configure-args="--srcdir src" . +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-glad/meta.yaml b/recipes/bioconductor-glad/meta.yaml index 9324eb90ef9c6..463ac6d9937c3 100644 --- a/recipes/bioconductor-glad/meta.yaml +++ b/recipes/bioconductor-glad/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "2.46.0" %} +{% set version = "2.48.0" %} {% set name = "GLAD" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: a27d757cf431fe1ca45706b90060d032 + md5: 3f5b35a21a75186227d262647b59f35b build: number: 0 rpaths: diff --git a/recipes/bioconductor-gladiatox/build.sh b/recipes/bioconductor-gladiatox/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-gladiatox/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-gladiatox/meta.yaml b/recipes/bioconductor-gladiatox/meta.yaml new file mode 100644 index 0000000000000..514cd73afba09 --- /dev/null +++ b/recipes/bioconductor-gladiatox/meta.yaml @@ -0,0 +1,63 @@ +{% set version = "1.0.0" %} +{% set name = "GladiaTOX" %} +{% set bioc = "3.9" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: bd7ad2050bd0e42d250712d6d72be21f +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: roxygen2, knitr, rmarkdown, testthat, BiocStyle +requirements: + host: + - r-base + - r-brew + - 'r-data.table >=1.9.4' + - r-dbi + - r-ggplot2 + - r-ggrepel + - r-numderiv + - r-rcolorbrewer + - r-rcurl + - r-rjsonio + - r-rmysql + - r-rsqlite + - r-stringr + - r-tidyr + - r-xml + - r-xtable + run: + - r-base + - r-brew + - 'r-data.table >=1.9.4' + - r-dbi + - r-ggplot2 + - r-ggrepel + - r-numderiv + - r-rcolorbrewer + - r-rcurl + - r-rjsonio + - r-rmysql + - r-rsqlite + - r-stringr + - r-tidyr + - r-xml + - r-xtable +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: GPL-2 + summary: 'GladiaTOX R package is an open-source, flexible solution to high-content screening data processing and reporting in biomedical research. GladiaTOX takes advantage of the tcpl core functionalities and provides a number of extensions: it provides a web-service solution to fetch raw data; it computes severity scores and exports ToxPi formatted files; furthermore it contains a suite of functionalities to generate pdf reports for quality control and data processing.' + diff --git a/recipes/bioconductor-glimma/meta.yaml b/recipes/bioconductor-glimma/meta.yaml index f41fd48a5094a..1ff7d6ac27247 100644 --- a/recipes/bioconductor-glimma/meta.yaml +++ b/recipes/bioconductor-glimma/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.10.1" %} +{% set version = "1.12.0" %} {% set name = "Glimma" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: 9badc670ef21cbec3e18bf965a1b6f78e98080ad19dc9b43bcf1285d0ae719c6 + md5: 8fe9db52a5ebc432f8cab7071d33a14d build: number: 0 rpaths: @@ -20,13 +20,13 @@ build: # Suggests: BiocStyle, IRanges, GenomicRanges, SummarizedExperiment, DESeq2, limma, testthat, knitr, rmarkdown, pryr requirements: host: - - 'bioconductor-edger >=3.24.0,<3.25.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-edger >=3.26.0,<3.27.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' - r-base - r-jsonlite run: - - 'bioconductor-edger >=3.24.0,<3.25.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-edger >=3.26.0,<3.27.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' - r-base - r-jsonlite test: diff --git a/recipes/bioconductor-glmsparsenet/meta.yaml b/recipes/bioconductor-glmsparsenet/meta.yaml index 1b3f933cbe790..103bb9d8dc882 100644 --- a/recipes/bioconductor-glmsparsenet/meta.yaml +++ b/recipes/bioconductor-glmsparsenet/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.0.0" %} +{% set version = "1.1.2" %} {% set name = "glmSparseNet" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 9ed879fd69f8bd537dcefa694c561bce + md5: 1c15c6b25738dd2382996f65c9385a39 build: number: 0 rpaths: @@ -20,10 +20,10 @@ build: # Suggests: testthat, knitr, rmarkdown, survival, survcomp, pROC, VennDiagram, BiocStyle, curatedTCGAData, TCGAutils requirements: host: - - 'bioconductor-biomart >=2.38.0,<2.39.0' - - 'bioconductor-multiassayexperiment >=1.8.0,<1.9.0' - - 'bioconductor-stringdb >=1.22.0,<1.23.0' - - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' + - 'bioconductor-biomart >=2.40.0,<2.41.0' + - 'bioconductor-multiassayexperiment >=1.10.0,<1.11.0' + - 'bioconductor-stringdb >=1.24.0,<1.25.0' + - 'bioconductor-summarizedexperiment >=1.14.0,<1.15.0' - r-base - r-dplyr - r-forcats @@ -40,10 +40,10 @@ requirements: - r-stringr - r-survminer run: - - 'bioconductor-biomart >=2.38.0,<2.39.0' - - 'bioconductor-multiassayexperiment >=1.8.0,<1.9.0' - - 'bioconductor-stringdb >=1.22.0,<1.23.0' - - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' + - 'bioconductor-biomart >=2.40.0,<2.41.0' + - 'bioconductor-multiassayexperiment >=1.10.0,<1.11.0' + - 'bioconductor-stringdb >=1.24.0,<1.25.0' + - 'bioconductor-summarizedexperiment >=1.14.0,<1.15.0' - r-base - r-dplyr - r-forcats diff --git a/recipes/bioconductor-globalancova/meta.yaml b/recipes/bioconductor-globalancova/meta.yaml index ec91b7a2509a0..c2b973257efc2 100644 --- a/recipes/bioconductor-globalancova/meta.yaml +++ b/recipes/bioconductor-globalancova/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "4.0.0" %} +{% set version = "4.2.0" %} {% set name = "GlobalAncova" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 9f9fd66217449c73f94bf8bd70ba82bb + md5: 24e42662d9e3fd5eea193bad02300c8f build: number: 0 rpaths: @@ -19,21 +19,21 @@ build: # Suggests: GO.db, KEGG.db, golubEsets, hu6800.db, vsn, Rgraphviz requirements: host: - - 'bioconductor-annotate >=1.60.0,<1.61.0' - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' - - 'bioconductor-biobase >=2.42.0,<2.43.0' - - 'bioconductor-globaltest >=5.36.0,<5.37.0' - - 'bioconductor-gseabase >=1.44.0,<1.45.0' + - 'bioconductor-annotate >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' + - 'bioconductor-globaltest >=5.38.0,<5.39.0' + - 'bioconductor-gseabase >=1.46.0,<1.47.0' - r-base - r-corpcor - r-dendextend - r-vgam run: - - 'bioconductor-annotate >=1.60.0,<1.61.0' - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' - - 'bioconductor-biobase >=2.42.0,<2.43.0' - - 'bioconductor-globaltest >=5.36.0,<5.37.0' - - 'bioconductor-gseabase >=1.44.0,<1.45.0' + - 'bioconductor-annotate >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' + - 'bioconductor-globaltest >=5.38.0,<5.39.0' + - 'bioconductor-gseabase >=1.46.0,<1.47.0' - r-base - r-corpcor - r-dendextend diff --git a/recipes/bioconductor-globalseq/meta.yaml b/recipes/bioconductor-globalseq/meta.yaml index 25e809863a47c..cc1536873bbba 100644 --- a/recipes/bioconductor-globalseq/meta.yaml +++ b/recipes/bioconductor-globalseq/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.10.1" %} +{% set version = "1.12.0" %} {% set name = "globalSeq" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: b8378c9ceb14159be27fb3fcd47ee8fc + md5: 0052e28fb11a8c9575baa1a55b4a3b74 build: number: 0 rpaths: diff --git a/recipes/bioconductor-globaltest/meta.yaml b/recipes/bioconductor-globaltest/meta.yaml index cb142a203a5d1..2889153bad05a 100644 --- a/recipes/bioconductor-globaltest/meta.yaml +++ b/recipes/bioconductor-globaltest/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "5.36.0" %} +{% set version = "5.38.0" %} {% set name = "globaltest" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,25 +10,25 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 0c2d22bf1ee33788c7ab870b595e78b0 + md5: a93ffe229a13c2b8ae1e0bfab3ae7088 build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ noarch: generic -# Suggests: vsn, golubEsets, KEGG.db, hu6800.db, Rgraphviz, GO.db, lungExpression, org.Hs.eg.db, GSEABase, penalized, gss, MASS, boot, rpart +# Suggests: vsn, golubEsets, KEGG.db, hu6800.db, Rgraphviz, GO.db, lungExpression, org.Hs.eg.db, GSEABase, penalized, gss, MASS, boot, rpart, mstate requirements: host: - - 'bioconductor-annotate >=1.60.0,<1.61.0' - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' - - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-annotate >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' - r-base - r-survival run: - - 'bioconductor-annotate >=1.60.0,<1.61.0' - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' - - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-annotate >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' - r-base - r-survival test: diff --git a/recipes/bioconductor-gmapr/meta.yaml b/recipes/bioconductor-gmapr/meta.yaml index 505cd0849610c..bfd53924ce3c1 100644 --- a/recipes/bioconductor-gmapr/meta.yaml +++ b/recipes/bioconductor-gmapr/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.24.1" %} +{% set version = "1.26.0" %} {% set name = "gmapR" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: de783ca018e6fd1ef451a819819bb1de + md5: f7730c3b5581e3ce7b4ef1b3093ba1ee build: number: 0 rpaths: @@ -19,36 +19,36 @@ build: # Suggests: RUnit, BSgenome.Dmelanogaster.UCSC.dm3, BSgenome.Scerevisiae.UCSC.sacCer3, org.Hs.eg.db, TxDb.Hsapiens.UCSC.hg19.knownGene, BSgenome.Hsapiens.UCSC.hg19, LungCancerLines requirements: host: - - 'bioconductor-biobase >=2.42.0,<2.43.0' - - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' - - 'bioconductor-biocparallel >=1.16.0,<1.17.0' - - 'bioconductor-biostrings >=2.50.0,<2.51.0' - - 'bioconductor-bsgenome >=1.50.0,<1.51.0' - - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' - - 'bioconductor-genomicalignments >=1.18.0,<1.19.0' - - 'bioconductor-genomicfeatures >=1.34.0,<1.35.0' - - 'bioconductor-genomicranges >=1.34.0,<1.35.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-rsamtools >=1.34.0,<1.35.0' - - 'bioconductor-rtracklayer >=1.42.0,<1.43.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' - - 'bioconductor-variantannotation >=1.28.0,<1.29.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' + - 'bioconductor-biocgenerics >=0.30.0,<0.31.0' + - 'bioconductor-biocparallel >=1.18.0,<1.19.0' + - 'bioconductor-biostrings >=2.52.0,<2.53.0' + - 'bioconductor-bsgenome >=1.52.0,<1.53.0' + - 'bioconductor-genomeinfodb >=1.20.0,<1.21.0' + - 'bioconductor-genomicalignments >=1.20.0,<1.21.0' + - 'bioconductor-genomicfeatures >=1.36.0,<1.37.0' + - 'bioconductor-genomicranges >=1.36.0,<1.37.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-rsamtools >=2.0.0,<2.1.0' + - 'bioconductor-rtracklayer >=1.44.0,<1.45.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' + - 'bioconductor-variantannotation >=1.30.0,<1.31.0' - r-base run: - - 'bioconductor-biobase >=2.42.0,<2.43.0' - - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' - - 'bioconductor-biocparallel >=1.16.0,<1.17.0' - - 'bioconductor-biostrings >=2.50.0,<2.51.0' - - 'bioconductor-bsgenome >=1.50.0,<1.51.0' - - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' - - 'bioconductor-genomicalignments >=1.18.0,<1.19.0' - - 'bioconductor-genomicfeatures >=1.34.0,<1.35.0' - - 'bioconductor-genomicranges >=1.34.0,<1.35.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-rsamtools >=1.34.0,<1.35.0' - - 'bioconductor-rtracklayer >=1.42.0,<1.43.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' - - 'bioconductor-variantannotation >=1.28.0,<1.29.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' + - 'bioconductor-biocgenerics >=0.30.0,<0.31.0' + - 'bioconductor-biocparallel >=1.18.0,<1.19.0' + - 'bioconductor-biostrings >=2.52.0,<2.53.0' + - 'bioconductor-bsgenome >=1.52.0,<1.53.0' + - 'bioconductor-genomeinfodb >=1.20.0,<1.21.0' + - 'bioconductor-genomicalignments >=1.20.0,<1.21.0' + - 'bioconductor-genomicfeatures >=1.36.0,<1.37.0' + - 'bioconductor-genomicranges >=1.36.0,<1.37.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-rsamtools >=2.0.0,<2.1.0' + - 'bioconductor-rtracklayer >=1.44.0,<1.45.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' + - 'bioconductor-variantannotation >=1.30.0,<1.31.0' - r-base build: - {{ compiler('c') }} diff --git a/recipes/bioconductor-gmrp/meta.yaml b/recipes/bioconductor-gmrp/meta.yaml index 9a21469d09bc2..9eb169f6b53d5 100644 --- a/recipes/bioconductor-gmrp/meta.yaml +++ b/recipes/bioconductor-gmrp/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.10.1" %} +{% set version = "1.12.0" %} {% set name = "GMRP" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 4103cc393e2719f8324e96f4fcc67c9c + md5: e11678c64a96380d6c9e45e55d4625a8 build: number: 0 rpaths: @@ -20,12 +20,12 @@ build: # Suggests: BiocStyle, BiocGenerics requirements: host: - - 'bioconductor-genomicranges >=1.34.0,<1.35.0' + - 'bioconductor-genomicranges >=1.36.0,<1.37.0' - r-base - r-diagram - r-plotrix run: - - 'bioconductor-genomicranges >=1.34.0,<1.35.0' + - 'bioconductor-genomicranges >=1.36.0,<1.37.0' - r-base - r-diagram - r-plotrix diff --git a/recipes/bioconductor-gnet2/build.sh b/recipes/bioconductor-gnet2/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-gnet2/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-gnet2/meta.yaml b/recipes/bioconductor-gnet2/meta.yaml new file mode 100644 index 0000000000000..6e48719b4f613 --- /dev/null +++ b/recipes/bioconductor-gnet2/meta.yaml @@ -0,0 +1,50 @@ +{% set version = "1.0.0" %} +{% set name = "GNET2" %} +{% set bioc = "3.9" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: 2bf1f758fca46085479a0bde5375fc15 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ +# Suggests: knitr, rmarkdown +requirements: + host: + - 'bioconductor-summarizedexperiment >=1.14.0,<1.15.0' + - r-base + - r-diagrammer + - r-ggplot2 + - r-matrixstats + - r-rcpp + - r-reshape2 + - r-xgboost + run: + - 'bioconductor-summarizedexperiment >=1.14.0,<1.15.0' + - r-base + - r-diagrammer + - r-ggplot2 + - r-matrixstats + - r-rcpp + - r-reshape2 + - r-xgboost + build: + - {{ compiler('c') }} + - {{ compiler('cxx') }} + - make +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: 'Apache License 2.0' + summary: 'Cluster genes to functional groups with E-M process. Iteratively perform TF assigning and Gene assigning, until the assignment of genes did not change, or max number of iterations is reached.' + diff --git a/recipes/bioconductor-go.db/meta.yaml b/recipes/bioconductor-go.db/meta.yaml index 0f0ba213374b8..ca2a4ac0b0c70 100644 --- a/recipes/bioconductor-go.db/meta.yaml +++ b/recipes/bioconductor-go.db/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "3.7.0" %} +{% set version = "3.8.2" %} {% set name = "GO.db" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: bc452e3dd445711b27de93c15abd414c + md5: 63669b6fceef7ba0d6a2c36b7d8cf796 build: number: 0 rpaths: @@ -20,12 +20,12 @@ build: # Suggests: DBI requirements: host: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' - r-base run: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-go.db/post-link.sh b/recipes/bioconductor-go.db/post-link.sh index 2f94f23fedf5f..75539cf062ba9 100644 --- a/recipes/bioconductor-go.db/post-link.sh +++ b/recipes/bioconductor-go.db/post-link.sh @@ -1,11 +1,11 @@ #!/bin/bash -FN="GO.db_3.7.0.tar.gz" +FN="GO.db_3.8.2.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/GO.db_3.7.0.tar.gz" - "https://bioarchive.galaxyproject.org/GO.db_3.7.0.tar.gz" - "https://depot.galaxyproject.org/software/bioconductor-go.db/bioconductor-go.db_3.7.0_src_all.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/GO.db_3.8.2.tar.gz" + "https://bioarchive.galaxyproject.org/GO.db_3.8.2.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-go.db/bioconductor-go.db_3.8.2_src_all.tar.gz" ) -MD5="bc452e3dd445711b27de93c15abd414c" +MD5="63669b6fceef7ba0d6a2c36b7d8cf796" # Use a staging area in the conda dir rather than temp dirs, both to avoid # permission issues as well as to have things downloaded in a predictable @@ -16,7 +16,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-goexpress/meta.yaml b/recipes/bioconductor-goexpress/meta.yaml index df617bae71834..cb1c18e5c6329 100644 --- a/recipes/bioconductor-goexpress/meta.yaml +++ b/recipes/bioconductor-goexpress/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.16.0" %} +{% set version = "1.18.0" %} {% set name = "GOexpress" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 7444623130b12f9cb3659718b52d190b + md5: 629c508e879921a4a5e8e8a77f8d0bd6 build: number: 0 rpaths: @@ -20,8 +20,8 @@ build: # Suggests: BiocStyle requirements: host: - - 'bioconductor-biobase >=2.42.0,<2.43.0' - - 'bioconductor-biomart >=2.38.0,<2.39.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' + - 'bioconductor-biomart >=2.40.0,<2.41.0' - r-base - 'r-ggplot2 >=0.9.0' - 'r-gplots >=2.13.0' @@ -30,8 +30,8 @@ requirements: - 'r-rcurl >=1.95' - 'r-stringr >=0.6.2' run: - - 'bioconductor-biobase >=2.42.0,<2.43.0' - - 'bioconductor-biomart >=2.38.0,<2.39.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' + - 'bioconductor-biomart >=2.40.0,<2.41.0' - r-base - 'r-ggplot2 >=0.9.0' - 'r-gplots >=2.13.0' diff --git a/recipes/bioconductor-gofuncr/meta.yaml b/recipes/bioconductor-gofuncr/meta.yaml index bdc8bea6fa54e..3bd2166d1bb93 100644 --- a/recipes/bioconductor-gofuncr/meta.yaml +++ b/recipes/bioconductor-gofuncr/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.2.0" %} +{% set version = "1.4.0" %} {% set name = "GOfuncR" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 751400dc73371df5c86c87511fecdede + md5: 74726fe990476fa6b666cf2b5bb9eba4 build: number: 0 rpaths: @@ -19,18 +19,18 @@ build: # Suggests: Homo.sapiens, BiocStyle, knitr, testthat requirements: host: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' - - 'bioconductor-genomicranges >=1.34.0,<1.35.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' + - 'bioconductor-genomicranges >=1.36.0,<1.37.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' - r-base - 'r-gtools >=3.5.0' - 'r-mapplots >=1.5' - 'r-rcpp >=0.11.5' - 'r-vioplot >=0.2' run: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' - - 'bioconductor-genomicranges >=1.34.0,<1.35.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' + - 'bioconductor-genomicranges >=1.36.0,<1.37.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' - r-base - 'r-gtools >=3.5.0' - 'r-mapplots >=1.5' @@ -46,5 +46,5 @@ test: about: home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: 'GPL (>= 2)' - summary: 'GOfuncR performs a gene ontology enrichment analysis based on the ontology enrichment software FUNC. GO-annotations are obtained from OrganismDb or OrgDb packages (''Homo.sapiens'' by default); the GO-graph is included in the package and updated regularly (11-Oct-2018). GOfuncR provides the standard candidate vs. background enrichment analysis using the hypergeometric test, as well as three additional tests: (i) the Wilcoxon rank-sum test that is used when genes are ranked, (ii) a binomial test that is used when genes are associated with two counts and (iii) a Chi-square or Fisher''s exact test that is used in cases when genes are associated with four counts. To correct for multiple testing and interdependency of the tests, family-wise error rates are computed based on random permutations of the gene-associated variables. GOfuncR also provides tools for exploring the ontology graph and the annotations, and options to take gene-length or spatial clustering of genes into account. It is also possible to provide custom gene coordinates, annotations and ontologies.' + summary: 'GOfuncR performs a gene ontology enrichment analysis based on the ontology enrichment software FUNC. GO-annotations are obtained from OrganismDb or OrgDb packages (''Homo.sapiens'' by default); the GO-graph is included in the package and updated regularly (27-Mar-2019). GOfuncR provides the standard candidate vs. background enrichment analysis using the hypergeometric test, as well as three additional tests: (i) the Wilcoxon rank-sum test that is used when genes are ranked, (ii) a binomial test that is used when genes are associated with two counts and (iii) a Chi-square or Fisher''s exact test that is used in cases when genes are associated with four counts. To correct for multiple testing and interdependency of the tests, family-wise error rates are computed based on random permutations of the gene-associated variables. GOfuncR also provides tools for exploring the ontology graph and the annotations, and options to take gene-length or spatial clustering of genes into account. It is also possible to provide custom gene coordinates, annotations and ontologies.' diff --git a/recipes/bioconductor-gofunction/meta.yaml b/recipes/bioconductor-gofunction/meta.yaml index 6337f7fae6e01..ddf3896d74880 100644 --- a/recipes/bioconductor-gofunction/meta.yaml +++ b/recipes/bioconductor-gofunction/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.30.0" %} +{% set version = "1.32.0" %} {% set name = "GOFunction" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 72307dd4950cad125f42856c1153729b + md5: 2c06746ecbd128cf9b3015f1b02562e7 build: number: 0 rpaths: @@ -19,20 +19,20 @@ build: noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' - - 'bioconductor-biobase >=2.42.0,<2.43.0' - - 'bioconductor-go.db >=3.7.0,<3.8.0' - - 'bioconductor-graph >=1.60.0,<1.61.0' - - 'bioconductor-rgraphviz >=2.26.0,<2.27.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' + - 'bioconductor-go.db >=3.8.0,<3.9.0' + - 'bioconductor-graph >=1.62.0,<1.63.0' + - 'bioconductor-rgraphviz >=2.28.0,<2.29.0' - r-base - r-dbi - 'r-sparsem >=0.85' run: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' - - 'bioconductor-biobase >=2.42.0,<2.43.0' - - 'bioconductor-go.db >=3.7.0,<3.8.0' - - 'bioconductor-graph >=1.60.0,<1.61.0' - - 'bioconductor-rgraphviz >=2.26.0,<2.27.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' + - 'bioconductor-go.db >=3.8.0,<3.9.0' + - 'bioconductor-graph >=1.62.0,<1.63.0' + - 'bioconductor-rgraphviz >=2.28.0,<2.29.0' - r-base - r-dbi - 'r-sparsem >=0.85' diff --git a/recipes/bioconductor-golubesets/meta.yaml b/recipes/bioconductor-golubesets/meta.yaml index 9dddd76337257..4bcfb87ea46fd 100644 --- a/recipes/bioconductor-golubesets/meta.yaml +++ b/recipes/bioconductor-golubesets/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.24.0" %} +{% set version = "1.26.0" %} {% set name = "golubEsets" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 0fe60bd861eca25969193aeadcd0bc59 + md5: 3e7e78f951be8c6542fd6de61eabd92e build: number: 0 rpaths: @@ -19,12 +19,12 @@ build: noarch: generic requirements: host: - - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' - r-base run: - - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-golubesets/post-link.sh b/recipes/bioconductor-golubesets/post-link.sh index 15372b4c016ed..36839d8027073 100644 --- a/recipes/bioconductor-golubesets/post-link.sh +++ b/recipes/bioconductor-golubesets/post-link.sh @@ -1,11 +1,11 @@ #!/bin/bash -FN="golubEsets_1.24.0.tar.gz" +FN="golubEsets_1.26.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/experiment/src/contrib/golubEsets_1.24.0.tar.gz" - "https://bioarchive.galaxyproject.org/golubEsets_1.24.0.tar.gz" - "https://depot.galaxyproject.org/software/bioconductor-golubesets/bioconductor-golubesets_1.24.0_src_all.tar.gz" + "https://bioconductor.org/packages/3.9/data/experiment/src/contrib/golubEsets_1.26.0.tar.gz" + "https://bioarchive.galaxyproject.org/golubEsets_1.26.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-golubesets/bioconductor-golubesets_1.26.0_src_all.tar.gz" ) -MD5="0fe60bd861eca25969193aeadcd0bc59" +MD5="3e7e78f951be8c6542fd6de61eabd92e" # Use a staging area in the conda dir rather than temp dirs, both to avoid # permission issues as well as to have things downloaded in a predictable @@ -16,7 +16,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-gopro/meta.yaml b/recipes/bioconductor-gopro/meta.yaml index e11bd548c3aee..58da93836e16b 100644 --- a/recipes/bioconductor-gopro/meta.yaml +++ b/recipes/bioconductor-gopro/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.8.0" %} +{% set version = "1.10.0" %} {% set name = "GOpro" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 5d1245837ea8262a04366bef11ae4cf7 + md5: 32d15cff75940d97854d32a844fa5fdb build: number: 0 rpaths: @@ -19,12 +19,12 @@ build: # Suggests: knitr, rmarkdown, RTCGA.PANCAN12, BiocStyle, testthat requirements: host: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' - - 'bioconductor-go.db >=3.7.0,<3.8.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-multiassayexperiment >=1.8.0,<1.9.0' - - 'bioconductor-org.hs.eg.db >=3.7.0,<3.8.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' + - 'bioconductor-go.db >=3.8.0,<3.9.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-multiassayexperiment >=1.10.0,<1.11.0' + - 'bioconductor-org.hs.eg.db >=3.8.0,<3.9.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' - r-base - r-bh - r-dendextend @@ -32,12 +32,12 @@ requirements: - r-foreach - r-rcpp run: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' - - 'bioconductor-go.db >=3.7.0,<3.8.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-multiassayexperiment >=1.8.0,<1.9.0' - - 'bioconductor-org.hs.eg.db >=3.7.0,<3.8.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' + - 'bioconductor-go.db >=3.8.0,<3.9.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-multiassayexperiment >=1.10.0,<1.11.0' + - 'bioconductor-org.hs.eg.db >=3.8.0,<3.9.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' - r-base - r-bh - r-dendextend diff --git a/recipes/bioconductor-goprofiles/meta.yaml b/recipes/bioconductor-goprofiles/meta.yaml index 8f1135b726918..7f0a95fd303e8 100644 --- a/recipes/bioconductor-goprofiles/meta.yaml +++ b/recipes/bioconductor-goprofiles/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.44.0" %} +{% set version = "1.46.0" %} {% set name = "goProfiles" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,9 +10,9 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: cee2739892a0f493ca62346297a00d42 + md5: fd64c57600d8c94f0e32f8dd51e0f2f3 build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ @@ -20,16 +20,16 @@ build: # Suggests: org.Hs.eg.db requirements: host: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' - - 'bioconductor-biobase >=2.42.0,<2.43.0' - - 'bioconductor-go.db >=3.7.0,<3.8.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' + - 'bioconductor-go.db >=3.8.0,<3.9.0' - r-base - r-compquadform - r-stringr run: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' - - 'bioconductor-biobase >=2.42.0,<2.43.0' - - 'bioconductor-go.db >=3.7.0,<3.8.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' + - 'bioconductor-go.db >=3.8.0,<3.9.0' - r-base - r-compquadform - r-stringr diff --git a/recipes/bioconductor-gosemsim/meta.yaml b/recipes/bioconductor-gosemsim/meta.yaml index 13d1293059fef..3e414a59927de 100644 --- a/recipes/bioconductor-gosemsim/meta.yaml +++ b/recipes/bioconductor-gosemsim/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "2.8.0" %} +{% set version = "2.10.0" %} {% set name = "GOSemSim" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 8f4ba171e35070a482be6ea54d0cc814 + md5: 7c3863de574a9827b66b3fec462ae4d8 build: number: 0 rpaths: @@ -19,13 +19,13 @@ build: # Suggests: AnnotationHub, BiocManager, clusterProfiler, DOSE, knitr, org.Hs.eg.db, prettydoc, testthat requirements: host: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' - - 'bioconductor-go.db >=3.7.0,<3.8.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' + - 'bioconductor-go.db >=3.8.0,<3.9.0' - r-base - r-rcpp run: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' - - 'bioconductor-go.db >=3.7.0,<3.8.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' + - 'bioconductor-go.db >=3.8.0,<3.9.0' - r-base - r-rcpp build: diff --git a/recipes/bioconductor-goseq/meta.yaml b/recipes/bioconductor-goseq/meta.yaml index f7c8d33e81ad2..f0869e33d48db 100644 --- a/recipes/bioconductor-goseq/meta.yaml +++ b/recipes/bioconductor-goseq/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.34.1" %} +{% set version = "1.36.0" %} {% set name = "goseq" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: f521a65052ddd286a3b0aa5a5f106f85 + md5: 4d129450dfb15d6d4c0dfaad38049082 build: number: 0 rpaths: @@ -20,18 +20,18 @@ build: # Suggests: edgeR, org.Hs.eg.db, rtracklayer requirements: host: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' - - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' - - 'bioconductor-genelendatabase >=1.18.0,<1.19.0' - - 'bioconductor-go.db >=3.7.0,<3.8.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' + - 'bioconductor-biocgenerics >=0.30.0,<0.31.0' + - 'bioconductor-genelendatabase >=1.20.0,<1.21.0' + - 'bioconductor-go.db >=3.8.0,<3.9.0' - r-base - r-biasedurn - r-mgcv run: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' - - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' - - 'bioconductor-genelendatabase >=1.18.0,<1.19.0' - - 'bioconductor-go.db >=3.7.0,<3.8.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' + - 'bioconductor-biocgenerics >=0.30.0,<0.31.0' + - 'bioconductor-genelendatabase >=1.20.0,<1.21.0' + - 'bioconductor-go.db >=3.8.0,<3.9.0' - r-base - r-biasedurn - r-mgcv diff --git a/recipes/bioconductor-gosim/meta.yaml b/recipes/bioconductor-gosim/meta.yaml index 5399625b89872..eaa75c24ce5a0 100644 --- a/recipes/bioconductor-gosim/meta.yaml +++ b/recipes/bioconductor-gosim/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.20.0" %} +{% set version = "1.22.0" %} {% set name = "GOSim" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 87d1eb1841be4fa7d9c2e145051806c5 + md5: a40a2a17bb04a80fa603731be6cc7874 build: number: 0 rpaths: @@ -18,13 +18,13 @@ build: - lib/ requirements: host: - - 'bioconductor-annotate >=1.60.0,<1.61.0' - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' - - 'bioconductor-go.db >=3.7.0,<3.8.0' - - 'bioconductor-graph >=1.60.0,<1.61.0' - - 'bioconductor-org.hs.eg.db >=3.7.0,<3.8.0' - - 'bioconductor-rbgl >=1.58.0,<1.59.0' - - 'bioconductor-topgo >=2.34.0,<2.35.0' + - 'bioconductor-annotate >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' + - 'bioconductor-go.db >=3.8.0,<3.9.0' + - 'bioconductor-graph >=1.62.0,<1.63.0' + - 'bioconductor-org.hs.eg.db >=3.8.0,<3.9.0' + - 'bioconductor-rbgl >=1.60.0,<1.61.0' + - 'bioconductor-topgo >=2.36.0,<2.37.0' - r-base - r-cluster - r-corpcor @@ -32,13 +32,13 @@ requirements: - r-matrix - r-rcpp run: - - 'bioconductor-annotate >=1.60.0,<1.61.0' - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' - - 'bioconductor-go.db >=3.7.0,<3.8.0' - - 'bioconductor-graph >=1.60.0,<1.61.0' - - 'bioconductor-org.hs.eg.db >=3.7.0,<3.8.0' - - 'bioconductor-rbgl >=1.58.0,<1.59.0' - - 'bioconductor-topgo >=2.34.0,<2.35.0' + - 'bioconductor-annotate >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' + - 'bioconductor-go.db >=3.8.0,<3.9.0' + - 'bioconductor-graph >=1.62.0,<1.63.0' + - 'bioconductor-org.hs.eg.db >=3.8.0,<3.9.0' + - 'bioconductor-rbgl >=1.60.0,<1.61.0' + - 'bioconductor-topgo >=2.36.0,<2.37.0' - r-base - r-cluster - r-corpcor diff --git a/recipes/bioconductor-gostag/meta.yaml b/recipes/bioconductor-gostag/meta.yaml index d73d0b0bf15db..116c314be3a17 100644 --- a/recipes/bioconductor-gostag/meta.yaml +++ b/recipes/bioconductor-gostag/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.6.1" %} +{% set version = "1.8.0" %} {% set name = "goSTAG" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 7e6c56c3730f5b5601d6ca456d4a8922 + md5: 9cc1c101e786c4d899963065072348c0 build: number: 0 rpaths: @@ -20,15 +20,15 @@ build: # Suggests: BiocStyle, knitr, rmarkdown, testthat requirements: host: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' - - 'bioconductor-biomart >=2.38.0,<2.39.0' - - 'bioconductor-go.db >=3.7.0,<3.8.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' + - 'bioconductor-biomart >=2.40.0,<2.41.0' + - 'bioconductor-go.db >=3.8.0,<3.9.0' - r-base - r-memoise run: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' - - 'bioconductor-biomart >=2.38.0,<2.39.0' - - 'bioconductor-go.db >=3.7.0,<3.8.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' + - 'bioconductor-biomart >=2.40.0,<2.41.0' + - 'bioconductor-go.db >=3.8.0,<3.9.0' - r-base - r-memoise test: diff --git a/recipes/bioconductor-gostats/meta.yaml b/recipes/bioconductor-gostats/meta.yaml index 6f3c31537494c..e793569efc3ad 100644 --- a/recipes/bioconductor-gostats/meta.yaml +++ b/recipes/bioconductor-gostats/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "2.48.0" %} +{% set version = "2.50.0" %} {% set name = "GOstats" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 5f5df1dbb7717f909a32a5ed83159006 + md5: 18ba9b92fb8f33ed241d15ea0a6c8b06 build: number: 0 rpaths: @@ -20,26 +20,26 @@ build: # Suggests: hgu95av2.db (>= 1.13.0), ALL, multtest, genefilter, RColorBrewer, xtable, SparseM, GSEABase, geneplotter, org.Hs.eg.db, RUnit, BiocGenerics requirements: host: - - 'bioconductor-annotate >=1.60.0,<1.61.0' - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' - - 'bioconductor-annotationforge >=1.24.0,<1.25.0' - - 'bioconductor-biobase >=2.42.0,<2.43.0' - - 'bioconductor-category >=2.48.0,<2.49.0' - - 'bioconductor-go.db >=3.7.0,<3.8.0' - - 'bioconductor-graph >=1.60.0,<1.61.0' - - 'bioconductor-rbgl >=1.58.0,<1.59.0' - - 'bioconductor-rgraphviz >=2.26.0,<2.27.0' + - 'bioconductor-annotate >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' + - 'bioconductor-annotationforge >=1.26.0,<1.27.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' + - 'bioconductor-category >=2.50.0,<2.51.0' + - 'bioconductor-go.db >=3.8.0,<3.9.0' + - 'bioconductor-graph >=1.62.0,<1.63.0' + - 'bioconductor-rbgl >=1.60.0,<1.61.0' + - 'bioconductor-rgraphviz >=2.28.0,<2.29.0' - r-base run: - - 'bioconductor-annotate >=1.60.0,<1.61.0' - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' - - 'bioconductor-annotationforge >=1.24.0,<1.25.0' - - 'bioconductor-biobase >=2.42.0,<2.43.0' - - 'bioconductor-category >=2.48.0,<2.49.0' - - 'bioconductor-go.db >=3.7.0,<3.8.0' - - 'bioconductor-graph >=1.60.0,<1.61.0' - - 'bioconductor-rbgl >=1.58.0,<1.59.0' - - 'bioconductor-rgraphviz >=2.26.0,<2.27.0' + - 'bioconductor-annotate >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' + - 'bioconductor-annotationforge >=1.26.0,<1.27.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' + - 'bioconductor-category >=2.50.0,<2.51.0' + - 'bioconductor-go.db >=3.8.0,<3.9.0' + - 'bioconductor-graph >=1.62.0,<1.63.0' + - 'bioconductor-rbgl >=1.60.0,<1.61.0' + - 'bioconductor-rgraphviz >=2.28.0,<2.29.0' - r-base test: commands: diff --git a/recipes/bioconductor-gosummaries/meta.yaml b/recipes/bioconductor-gosummaries/meta.yaml index e18bdbff12f2c..252288e719c07 100644 --- a/recipes/bioconductor-gosummaries/meta.yaml +++ b/recipes/bioconductor-gosummaries/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "2.18.0" %} +{% set version = "2.20.0" %} {% set name = "GOsummaries" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: ea44c2e32bb5f0d12f0aad1b5ffdcdce + md5: 58fda5df6b523c4d578e9fdc3ae05ee1 build: number: 0 rpaths: @@ -19,7 +19,7 @@ build: # Suggests: vegan requirements: host: - - 'bioconductor-limma >=3.38.0,<3.39.0' + - 'bioconductor-limma >=3.40.0,<3.41.0' - r-base - r-ggplot2 - r-gprofiler @@ -28,7 +28,7 @@ requirements: - r-rcpp - r-reshape2 run: - - 'bioconductor-limma >=3.38.0,<3.39.0' + - 'bioconductor-limma >=3.40.0,<3.41.0' - r-base - r-ggplot2 - r-gprofiler diff --git a/recipes/bioconductor-gothic/meta.yaml b/recipes/bioconductor-gothic/meta.yaml index 54aa3f85c5a7a..9123e56294987 100644 --- a/recipes/bioconductor-gothic/meta.yaml +++ b/recipes/bioconductor-gothic/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.18.0" %} +{% set version = "1.19.0" %} {% set name = "GOTHiC" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: b9d8f7ee06dab41f8d1bf9dc03cc13dd + md5: 83bc5e03acace1872290c6c134ca2014 build: number: 0 rpaths: @@ -20,28 +20,28 @@ build: # Suggests: HiCDataLymphoblast requirements: host: - - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' - - 'bioconductor-biostrings >=2.50.0,<2.51.0' - - 'bioconductor-bsgenome >=1.50.0,<1.51.0' - - 'bioconductor-genomicranges >=1.34.0,<1.35.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-rsamtools >=1.34.0,<1.35.0' - - 'bioconductor-rtracklayer >=1.42.0,<1.43.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' - - 'bioconductor-shortread >=1.40.0,<1.41.0' + - 'bioconductor-biocgenerics >=0.30.0,<0.31.0' + - 'bioconductor-biostrings >=2.52.0,<2.53.0' + - 'bioconductor-bsgenome >=1.52.0,<1.53.0' + - 'bioconductor-genomicranges >=1.36.0,<1.37.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-rsamtools >=2.0.0,<2.1.0' + - 'bioconductor-rtracklayer >=1.44.0,<1.45.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' + - 'bioconductor-shortread >=1.42.0,<1.43.0' - r-base - r-data.table - r-ggplot2 run: - - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' - - 'bioconductor-biostrings >=2.50.0,<2.51.0' - - 'bioconductor-bsgenome >=1.50.0,<1.51.0' - - 'bioconductor-genomicranges >=1.34.0,<1.35.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-rsamtools >=1.34.0,<1.35.0' - - 'bioconductor-rtracklayer >=1.42.0,<1.43.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' - - 'bioconductor-shortread >=1.40.0,<1.41.0' + - 'bioconductor-biocgenerics >=0.30.0,<0.31.0' + - 'bioconductor-biostrings >=2.52.0,<2.53.0' + - 'bioconductor-bsgenome >=1.52.0,<1.53.0' + - 'bioconductor-genomicranges >=1.36.0,<1.37.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-rsamtools >=2.0.0,<2.1.0' + - 'bioconductor-rtracklayer >=1.44.0,<1.45.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' + - 'bioconductor-shortread >=1.42.0,<1.43.0' - r-base - r-data.table - r-ggplot2 diff --git a/recipes/bioconductor-gotools/meta.yaml b/recipes/bioconductor-gotools/meta.yaml index 9cc43c3be4986..6379d7387978e 100644 --- a/recipes/bioconductor-gotools/meta.yaml +++ b/recipes/bioconductor-gotools/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.56.0" %} +{% set version = "1.58.0" %} {% set name = "goTools" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 61fbb92f3f3abdcb58dfdf024fe10d84 + md5: e2d72bfb02d9979dfeef7e6bc5d17c65 build: number: 0 rpaths: @@ -20,12 +20,12 @@ build: # Suggests: hgu133a.db requirements: host: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' - - 'bioconductor-go.db >=3.7.0,<3.8.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' + - 'bioconductor-go.db >=3.8.0,<3.9.0' - r-base run: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' - - 'bioconductor-go.db >=3.7.0,<3.8.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' + - 'bioconductor-go.db >=3.8.0,<3.9.0' - r-base test: commands: diff --git a/recipes/bioconductor-gp53cdf/meta.yaml b/recipes/bioconductor-gp53cdf/meta.yaml index a2839c0ae5d8b..f8ebc247e57c6 100644 --- a/recipes/bioconductor-gp53cdf/meta.yaml +++ b/recipes/bioconductor-gp53cdf/meta.yaml @@ -1,6 +1,6 @@ {% set version = "2.18.0" %} {% set name = "gp53cdf" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -12,19 +12,19 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 2887dd15d3fa29b5c13b068c8d641f61 build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' - r-base run: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-gp53cdf/post-link.sh b/recipes/bioconductor-gp53cdf/post-link.sh index 9333e907245eb..6c92be5bda5e1 100644 --- a/recipes/bioconductor-gp53cdf/post-link.sh +++ b/recipes/bioconductor-gp53cdf/post-link.sh @@ -1,9 +1,10 @@ #!/bin/bash FN="gp53cdf_2.18.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/gp53cdf_2.18.0.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/gp53cdf_2.18.0.tar.gz" "https://bioarchive.galaxyproject.org/gp53cdf_2.18.0.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-gp53cdf/bioconductor-gp53cdf_2.18.0_src_all.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-gp53cdf/bioconductor-gp53cdf_2.18.0_src_all.tar.gz" ) MD5="2887dd15d3fa29b5c13b068c8d641f61" @@ -16,7 +17,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-gpart/meta.yaml b/recipes/bioconductor-gpart/meta.yaml index c0b8cef97ec6f..0489ddd85f269 100644 --- a/recipes/bioconductor-gpart/meta.yaml +++ b/recipes/bioconductor-gpart/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.0.0" %} +{% set version = "1.2.0" %} {% set name = "gpart" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 823ed883bf941ecae5644533d1ba464a + md5: 1331072984139386a31e1218ad5d5203 build: number: 0 rpaths: @@ -19,24 +19,24 @@ build: # Suggests: knitr, rmarkdown, BiocStyle, testthat requirements: host: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' - - 'bioconductor-biomart >=2.38.0,<2.39.0' - - 'bioconductor-genomicranges >=1.34.0,<1.35.0' - - 'bioconductor-homo.sapiens >=1.3.0,<1.4.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-organismdbi >=1.24.0,<1.25.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' + - 'bioconductor-biomart >=2.40.0,<2.41.0' + - 'bioconductor-genomicranges >=1.36.0,<1.37.0' + - 'bioconductor-homo.sapiens >=1.4.0,<1.5.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-organismdbi >=1.26.0,<1.27.0' - 'bioconductor-txdb.hsapiens.ucsc.hg38.knowngene >=3.4.0,<3.5.0' - r-base - r-data.table - r-igraph - r-rcpp run: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' - - 'bioconductor-biomart >=2.38.0,<2.39.0' - - 'bioconductor-genomicranges >=1.34.0,<1.35.0' - - 'bioconductor-homo.sapiens >=1.3.0,<1.4.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-organismdbi >=1.24.0,<1.25.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' + - 'bioconductor-biomart >=2.40.0,<2.41.0' + - 'bioconductor-genomicranges >=1.36.0,<1.37.0' + - 'bioconductor-homo.sapiens >=1.4.0,<1.5.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-organismdbi >=1.26.0,<1.27.0' - 'bioconductor-txdb.hsapiens.ucsc.hg38.knowngene >=3.4.0,<3.5.0' - r-base - r-data.table diff --git a/recipes/bioconductor-gpls/meta.yaml b/recipes/bioconductor-gpls/meta.yaml index a4c2d247f8a36..90e009b752a4f 100644 --- a/recipes/bioconductor-gpls/meta.yaml +++ b/recipes/bioconductor-gpls/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.54.0" %} +{% set version = "1.56.0" %} {% set name = "gpls" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 0ff76e002a0dcaa8da6bfb4435129896 + md5: 13093d7b8ea0811da3ff37cb5f332ac3 build: number: 0 rpaths: diff --git a/recipes/bioconductor-gprege/meta.yaml b/recipes/bioconductor-gprege/meta.yaml index b5d526a2bbcf9..9cddf5fe60088 100644 --- a/recipes/bioconductor-gprege/meta.yaml +++ b/recipes/bioconductor-gprege/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.26.0" %} +{% set version = "1.28.0" %} {% set name = "gprege" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 8c3464efa7978c37ba0203de3ae063ae + md5: 9c0b44c318ff09818ff49a50e0fee651 build: number: 0 rpaths: diff --git a/recipes/bioconductor-gqtlbase/meta.yaml b/recipes/bioconductor-gqtlbase/meta.yaml index b126b4bcd55b9..3cba63d905ebe 100644 --- a/recipes/bioconductor-gqtlbase/meta.yaml +++ b/recipes/bioconductor-gqtlbase/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.14.0" %} +{% set version = "1.16.0" %} {% set name = "gQTLBase" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 0b4b30b4c1152b7f98e2c7a8f2f130d9 + md5: 73e850aa5a1ff008660ac575a99e8006 build: number: 0 rpaths: @@ -20,12 +20,12 @@ build: # Suggests: geuvStore2, knitr, rmarkdown, BiocStyle, RUnit, GGtools, Homo.sapiens, IRanges, erma, GenomeInfoDb, gwascat, geuvPack requirements: host: - - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' - - 'bioconductor-genomicfiles >=1.18.0,<1.19.0' - - 'bioconductor-genomicranges >=1.34.0,<1.35.0' - - 'bioconductor-rtracklayer >=1.42.0,<1.43.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' - - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' + - 'bioconductor-biocgenerics >=0.30.0,<0.31.0' + - 'bioconductor-genomicfiles >=1.20.0,<1.21.0' + - 'bioconductor-genomicranges >=1.36.0,<1.37.0' + - 'bioconductor-rtracklayer >=1.44.0,<1.45.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' + - 'bioconductor-summarizedexperiment >=1.14.0,<1.15.0' - r-base - r-batchjobs - r-bbmisc @@ -35,12 +35,12 @@ requirements: - r-ffbase - r-foreach run: - - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' - - 'bioconductor-genomicfiles >=1.18.0,<1.19.0' - - 'bioconductor-genomicranges >=1.34.0,<1.35.0' - - 'bioconductor-rtracklayer >=1.42.0,<1.43.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' - - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' + - 'bioconductor-biocgenerics >=0.30.0,<0.31.0' + - 'bioconductor-genomicfiles >=1.20.0,<1.21.0' + - 'bioconductor-genomicranges >=1.36.0,<1.37.0' + - 'bioconductor-rtracklayer >=1.44.0,<1.45.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' + - 'bioconductor-summarizedexperiment >=1.14.0,<1.15.0' - r-base - r-batchjobs - r-bbmisc diff --git a/recipes/bioconductor-gqtlstats/meta.yaml b/recipes/bioconductor-gqtlstats/meta.yaml index 755ddbbe5212a..ce164e51b9cdf 100644 --- a/recipes/bioconductor-gqtlstats/meta.yaml +++ b/recipes/bioconductor-gqtlstats/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.14.0" %} +{% set version = "1.16.0" %} {% set name = "gQTLstats" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: df3a3589b6080c6b24d7364536fe302f + md5: ebda0ef678142318e1aa07668efea57f build: number: 0 rpaths: @@ -20,22 +20,22 @@ build: # Suggests: geuvPack, geuvStore2, Rsamtools, knitr, rmarkdown, ggbio, BiocStyle, RUnit, multtest, gwascat, org.Hs.eg.db, TxDb.Hsapiens.UCSC.hg19.knownGene, ldblock requirements: host: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' - - 'bioconductor-biobase >=2.42.0,<2.43.0' - - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' - - 'bioconductor-erma >=0.14.0,<0.15.0' - - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' - - 'bioconductor-genomicfeatures >=1.34.0,<1.35.0' - - 'bioconductor-genomicfiles >=1.18.0,<1.19.0' - - 'bioconductor-genomicranges >=1.34.0,<1.35.0' - - 'bioconductor-gqtlbase >=1.14.0,<1.15.0' - - 'bioconductor-homo.sapiens >=1.3.0,<1.4.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-limma >=3.38.0,<3.39.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' - - 'bioconductor-snpstats >=1.32.0,<1.33.0' - - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' - - 'bioconductor-variantannotation >=1.28.0,<1.29.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' + - 'bioconductor-biocgenerics >=0.30.0,<0.31.0' + - 'bioconductor-erma >=1.0.0,<1.1.0' + - 'bioconductor-genomeinfodb >=1.20.0,<1.21.0' + - 'bioconductor-genomicfeatures >=1.36.0,<1.37.0' + - 'bioconductor-genomicfiles >=1.20.0,<1.21.0' + - 'bioconductor-genomicranges >=1.36.0,<1.37.0' + - 'bioconductor-gqtlbase >=1.16.0,<1.17.0' + - 'bioconductor-homo.sapiens >=1.4.0,<1.5.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-limma >=3.40.0,<3.41.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' + - 'bioconductor-snpstats >=1.34.0,<1.35.0' + - 'bioconductor-summarizedexperiment >=1.14.0,<1.15.0' + - 'bioconductor-variantannotation >=1.30.0,<1.31.0' - r-base - r-batchjobs - r-bbmisc @@ -52,22 +52,22 @@ requirements: - r-reshape2 - r-shiny run: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' - - 'bioconductor-biobase >=2.42.0,<2.43.0' - - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' - - 'bioconductor-erma >=0.14.0,<0.15.0' - - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' - - 'bioconductor-genomicfeatures >=1.34.0,<1.35.0' - - 'bioconductor-genomicfiles >=1.18.0,<1.19.0' - - 'bioconductor-genomicranges >=1.34.0,<1.35.0' - - 'bioconductor-gqtlbase >=1.14.0,<1.15.0' - - 'bioconductor-homo.sapiens >=1.3.0,<1.4.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-limma >=3.38.0,<3.39.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' - - 'bioconductor-snpstats >=1.32.0,<1.33.0' - - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' - - 'bioconductor-variantannotation >=1.28.0,<1.29.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' + - 'bioconductor-biocgenerics >=0.30.0,<0.31.0' + - 'bioconductor-erma >=1.0.0,<1.1.0' + - 'bioconductor-genomeinfodb >=1.20.0,<1.21.0' + - 'bioconductor-genomicfeatures >=1.36.0,<1.37.0' + - 'bioconductor-genomicfiles >=1.20.0,<1.21.0' + - 'bioconductor-genomicranges >=1.36.0,<1.37.0' + - 'bioconductor-gqtlbase >=1.16.0,<1.17.0' + - 'bioconductor-homo.sapiens >=1.4.0,<1.5.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-limma >=3.40.0,<3.41.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' + - 'bioconductor-snpstats >=1.34.0,<1.35.0' + - 'bioconductor-summarizedexperiment >=1.14.0,<1.15.0' + - 'bioconductor-variantannotation >=1.30.0,<1.31.0' - r-base - r-batchjobs - r-bbmisc diff --git a/recipes/bioconductor-graper/build.sh b/recipes/bioconductor-graper/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-graper/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-graper/meta.yaml b/recipes/bioconductor-graper/meta.yaml new file mode 100644 index 0000000000000..9c1d8020c254f --- /dev/null +++ b/recipes/bioconductor-graper/meta.yaml @@ -0,0 +1,50 @@ +{% set version = "1.0.0" %} +{% set name = "graper" %} +{% set bioc = "3.9" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + md5: 3cf8669879141e500e5f69ec7004637b +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ +# Suggests: knitr, rmarkdown, BiocStyle, testthat +requirements: + host: + - r-base + - r-bh + - r-cowplot + - r-ggplot2 + - r-matrix + - r-matrixstats + - r-rcpp + - r-rcpparmadillo + run: + - r-base + - r-bh + - r-cowplot + - r-ggplot2 + - r-matrix + - r-matrixstats + - r-rcpp + - r-rcpparmadillo + build: + - {{ compiler('c') }} + - {{ compiler('cxx') }} + - make +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: 'GPL (>= 2)' + summary: 'This package enables regression and classification on high-dimensional data with different relative strengths of penalization for different feature groups, such as different assays or omic types. The optimal relative strengths are chosen adaptively. Optimisation is performed using a variational Bayes approach.' + diff --git a/recipes/bioconductor-graph/build.sh b/recipes/bioconductor-graph/build.sh index 603165b2d72f6..c1d13421f5f1e 100644 --- a/recipes/bioconductor-graph/build.sh +++ b/recipes/bioconductor-graph/build.sh @@ -8,6 +8,4 @@ CXX=$CXX CXX98=$CXX CXX11=$CXX CXX14=$CXX" > ~/.R/Makevars -$R CMD INSTALL --build . - -ln -s ${PREFIX}/lib/R/library/graph/libs/BioC_graph.so ${PREFIX}/lib/R/library/graph/libs/graph.so +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-graph/meta.yaml b/recipes/bioconductor-graph/meta.yaml index cc2ef113d04b1..72f9b03f8a193 100644 --- a/recipes/bioconductor-graph/meta.yaml +++ b/recipes/bioconductor-graph/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.60.0" %} +{% set version = "1.62.0" %} {% set name = "graph" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,22 +10,19 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: ee2a677386e14496f7efcdb18b033bff + md5: 5b665791d49e3e87757e6f0cf1c27acf build: number: 0 rpaths: - lib/R/lib/ - lib/ - patches: - - Makevars.patch - # Suggests: SparseM (>= 0.36), XML, RBGL, RUnit, cluster requirements: host: - - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' + - 'bioconductor-biocgenerics >=0.30.0,<0.31.0' - r-base run: - - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' + - 'bioconductor-biocgenerics >=0.30.0,<0.31.0' - r-base build: - {{ compiler('c') }} diff --git a/recipes/bioconductor-graphalignment/meta.yaml b/recipes/bioconductor-graphalignment/meta.yaml index fb5b2cf76ffb2..b670cf85964b3 100644 --- a/recipes/bioconductor-graphalignment/meta.yaml +++ b/recipes/bioconductor-graphalignment/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.46.0" %} +{% set version = "1.48.0" %} {% set name = "GraphAlignment" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: bdea26bff023e6e73179fc7d34097a1a + md5: 7001972152fb1cd966f873d62f6100ff build: number: 0 rpaths: diff --git a/recipes/bioconductor-graphat/meta.yaml b/recipes/bioconductor-graphat/meta.yaml index 1e14500876201..7f166dc2b2b0a 100644 --- a/recipes/bioconductor-graphat/meta.yaml +++ b/recipes/bioconductor-graphat/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.54.0" %} +{% set version = "1.56.0" %} {% set name = "GraphAT" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 01fbc5e58324e882d6885a62e4c037c5 + md5: 1cb0ccafa1dc19eda5c0dd9c628df925 build: number: 0 rpaths: @@ -19,11 +19,11 @@ build: noarch: generic requirements: host: - - 'bioconductor-graph >=1.60.0,<1.61.0' + - 'bioconductor-graph >=1.62.0,<1.63.0' - r-base - r-mcmcpack run: - - 'bioconductor-graph >=1.60.0,<1.61.0' + - 'bioconductor-graph >=1.62.0,<1.63.0' - r-base - r-mcmcpack test: diff --git a/recipes/bioconductor-graphite/meta.yaml b/recipes/bioconductor-graphite/meta.yaml index aae535c2bcfda..3df5a8f0ca1a2 100644 --- a/recipes/bioconductor-graphite/meta.yaml +++ b/recipes/bioconductor-graphite/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.28.2" %} +{% set version = "1.30.0" %} {% set name = "graphite" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - sha256: c53349b3993fb786a8bffe4624c6e66535b2369236cc953bb7fa50e78e2eb149 + md5: 559dbd9b8368b238afaa3784083fb4dc build: number: 0 rpaths: @@ -20,15 +20,15 @@ build: # Suggests: a4Preproc, ALL, BiocStyle, clipper, codetools, hgu133plus2.db, hgu95av2.db, impute, knitr, org.Hs.eg.db, parallel, R.rsp, RCy3, rmarkdown, SPIA (>= 2.2), testthat, topologyGSA (>= 1.4.0) requirements: host: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' - - 'bioconductor-graph >=1.60.0,<1.61.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' + - 'bioconductor-graph >=1.62.0,<1.63.0' - r-base - r-checkmate - r-httr - r-rappdirs run: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' - - 'bioconductor-graph >=1.60.0,<1.61.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' + - 'bioconductor-graph >=1.62.0,<1.63.0' - r-base - r-checkmate - r-httr diff --git a/recipes/bioconductor-graphpac/meta.yaml b/recipes/bioconductor-graphpac/meta.yaml index 2b901d093c167..7eae07d7123e7 100644 --- a/recipes/bioconductor-graphpac/meta.yaml +++ b/recipes/bioconductor-graphpac/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.24.0" %} +{% set version = "1.26.0" %} {% set name = "GraphPAC" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: a4ca5bc3f6a808a8fbdadf2da251e745 + md5: 9b4dbec7c57284685df2391f3d95e8c0 build: number: 0 rpaths: @@ -20,13 +20,13 @@ build: # Suggests: RUnit, BiocGenerics requirements: host: - - 'bioconductor-ipac >=1.26.0,<1.27.0' + - 'bioconductor-ipac >=1.28.0,<1.29.0' - r-base - r-igraph - r-rmallow - r-tsp run: - - 'bioconductor-ipac >=1.26.0,<1.27.0' + - 'bioconductor-ipac >=1.28.0,<1.29.0' - r-base - r-igraph - r-rmallow diff --git a/recipes/bioconductor-grasp2db/meta.yaml b/recipes/bioconductor-grasp2db/meta.yaml index 5bfa047ea3fb1..3f2b663d691d7 100644 --- a/recipes/bioconductor-grasp2db/meta.yaml +++ b/recipes/bioconductor-grasp2db/meta.yaml @@ -1,6 +1,6 @@ {% set version = "1.1.0" %} {% set name = "grasp2db" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -12,7 +12,7 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 3fc90fc7c99e7da51dcbb687fd2d5515 build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ @@ -20,22 +20,22 @@ build: # Suggests: gwascat, knitr requirements: host: - - 'bioconductor-annotationhub >=2.14.0,<2.15.0' - - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' + - 'bioconductor-annotationhub >=2.16.0,<2.17.0' + - 'bioconductor-genomeinfodb >=1.20.0,<1.21.0' - r-base - r-dbplyr - r-digest - r-dplyr - r-rsqlite run: - - 'bioconductor-annotationhub >=2.14.0,<2.15.0' - - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' + - 'bioconductor-annotationhub >=2.16.0,<2.17.0' + - 'bioconductor-genomeinfodb >=1.20.0,<1.21.0' - r-base - r-dbplyr - r-digest - r-dplyr - r-rsqlite - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-grasp2db/post-link.sh b/recipes/bioconductor-grasp2db/post-link.sh index 514eaf8383bc0..c8ec0b950e3c4 100644 --- a/recipes/bioconductor-grasp2db/post-link.sh +++ b/recipes/bioconductor-grasp2db/post-link.sh @@ -1,9 +1,10 @@ #!/bin/bash FN="grasp2db_1.1.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/grasp2db_1.1.0.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/grasp2db_1.1.0.tar.gz" "https://bioarchive.galaxyproject.org/grasp2db_1.1.0.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-grasp2db/bioconductor-grasp2db_1.1.0_src_all.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-grasp2db/bioconductor-grasp2db_1.1.0_src_all.tar.gz" ) MD5="3fc90fc7c99e7da51dcbb687fd2d5515" @@ -16,7 +17,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-greengenes13.5mgdb/meta.yaml b/recipes/bioconductor-greengenes13.5mgdb/meta.yaml index b5dac48de249a..25041777efad6 100644 --- a/recipes/bioconductor-greengenes13.5mgdb/meta.yaml +++ b/recipes/bioconductor-greengenes13.5mgdb/meta.yaml @@ -1,6 +1,6 @@ {% set version = "2.0.0" %} {% set name = "greengenes13.5MgDb" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -12,19 +12,19 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' md5: c06d8d5b702636bb5fb3e6229869578c build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ noarch: generic requirements: host: - - 'bioconductor-metagenomefeatures >=2.2.0,<2.3.0' + - 'bioconductor-metagenomefeatures >=2.4.0,<2.5.0' - r-base run: - - 'bioconductor-metagenomefeatures >=2.2.0,<2.3.0' + - 'bioconductor-metagenomefeatures >=2.4.0,<2.5.0' - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-greengenes13.5mgdb/post-link.sh b/recipes/bioconductor-greengenes13.5mgdb/post-link.sh index 05b2b5934d983..99a23e26423e2 100644 --- a/recipes/bioconductor-greengenes13.5mgdb/post-link.sh +++ b/recipes/bioconductor-greengenes13.5mgdb/post-link.sh @@ -1,9 +1,10 @@ #!/bin/bash FN="greengenes13.5MgDb_2.0.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/greengenes13.5MgDb_2.0.0.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/greengenes13.5MgDb_2.0.0.tar.gz" "https://bioarchive.galaxyproject.org/greengenes13.5MgDb_2.0.0.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-greengenes13.5mgdb/bioconductor-greengenes13.5mgdb_2.0.0_src_all.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-greengenes13.5mgdb/bioconductor-greengenes13.5mgdb_2.0.0_src_all.tar.gz" ) MD5="c06d8d5b702636bb5fb3e6229869578c" @@ -16,7 +17,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-grenits/meta.yaml b/recipes/bioconductor-grenits/meta.yaml index 7ebe519a31e36..58f28f83aa011 100644 --- a/recipes/bioconductor-grenits/meta.yaml +++ b/recipes/bioconductor-grenits/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.34.0" %} +{% set version = "1.36.0" %} {% set name = "GRENITS" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 70f49c97897e351c99d0b6c2394f520b + md5: 92261713a716c49379d2ee4b6e2c6308 build: number: 0 rpaths: diff --git a/recipes/bioconductor-greylistchip/meta.yaml b/recipes/bioconductor-greylistchip/meta.yaml index c02085d032bce..875b3b188a057 100644 --- a/recipes/bioconductor-greylistchip/meta.yaml +++ b/recipes/bioconductor-greylistchip/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.14.0" %} +{% set version = "1.16.0" %} {% set name = "GreyListChIP" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: ff01f53cc4c0b6c6a42e908cc436bdb4 + md5: c0294f8e0ec2b37ace8520022cc71000 build: number: 0 rpaths: @@ -20,23 +20,23 @@ build: # Suggests: BiocStyle, BiocGenerics, RUnit requirements: host: - - 'bioconductor-bsgenome >=1.50.0,<1.51.0' - - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' - - 'bioconductor-genomicalignments >=1.18.0,<1.19.0' - - 'bioconductor-genomicranges >=1.34.0,<1.35.0' - - 'bioconductor-rsamtools >=1.34.0,<1.35.0' - - 'bioconductor-rtracklayer >=1.42.0,<1.43.0' - - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' + - 'bioconductor-bsgenome >=1.52.0,<1.53.0' + - 'bioconductor-genomeinfodb >=1.20.0,<1.21.0' + - 'bioconductor-genomicalignments >=1.20.0,<1.21.0' + - 'bioconductor-genomicranges >=1.36.0,<1.37.0' + - 'bioconductor-rsamtools >=2.0.0,<2.1.0' + - 'bioconductor-rtracklayer >=1.44.0,<1.45.0' + - 'bioconductor-summarizedexperiment >=1.14.0,<1.15.0' - r-base - r-mass run: - - 'bioconductor-bsgenome >=1.50.0,<1.51.0' - - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' - - 'bioconductor-genomicalignments >=1.18.0,<1.19.0' - - 'bioconductor-genomicranges >=1.34.0,<1.35.0' - - 'bioconductor-rsamtools >=1.34.0,<1.35.0' - - 'bioconductor-rtracklayer >=1.42.0,<1.43.0' - - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' + - 'bioconductor-bsgenome >=1.52.0,<1.53.0' + - 'bioconductor-genomeinfodb >=1.20.0,<1.21.0' + - 'bioconductor-genomicalignments >=1.20.0,<1.21.0' + - 'bioconductor-genomicranges >=1.36.0,<1.37.0' + - 'bioconductor-rsamtools >=2.0.0,<2.1.0' + - 'bioconductor-rtracklayer >=1.44.0,<1.45.0' + - 'bioconductor-summarizedexperiment >=1.14.0,<1.15.0' - r-base - r-mass test: diff --git a/recipes/bioconductor-grmetrics/meta.yaml b/recipes/bioconductor-grmetrics/meta.yaml index 66d7d1d35badc..612ad8765fc1a 100644 --- a/recipes/bioconductor-grmetrics/meta.yaml +++ b/recipes/bioconductor-grmetrics/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.8.1" %} +{% set version = "1.10.0" %} {% set name = "GRmetrics" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: b8489f60afaf6fdd7a7d8607051bf841 + md5: 30fe04b3ef445896e2551fcc7ba75eaa build: number: 0 rpaths: @@ -20,15 +20,15 @@ build: # Suggests: knitr, rmarkdown, BiocStyle requirements: host: - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' - - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' + - 'bioconductor-summarizedexperiment >=1.14.0,<1.15.0' - r-base - r-drc - r-ggplot2 - r-plotly run: - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' - - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' + - 'bioconductor-summarizedexperiment >=1.14.0,<1.15.0' - r-base - r-drc - r-ggplot2 diff --git a/recipes/bioconductor-grndata/meta.yaml b/recipes/bioconductor-grndata/meta.yaml index 89cac523febe2..be9ae9ac49245 100644 --- a/recipes/bioconductor-grndata/meta.yaml +++ b/recipes/bioconductor-grndata/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.14.0" %} +{% set version = "1.16.0" %} {% set name = "grndata" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,9 +10,9 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: aacdf027236c99022b11fdabb983bbe4 + md5: f68d2293bf9ad882ff9f061266f63fd1 build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ @@ -23,7 +23,7 @@ requirements: - r-base run: - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-grndata/post-link.sh b/recipes/bioconductor-grndata/post-link.sh index 91d12a31080d4..6e024cbebfb5f 100644 --- a/recipes/bioconductor-grndata/post-link.sh +++ b/recipes/bioconductor-grndata/post-link.sh @@ -1,11 +1,11 @@ #!/bin/bash -FN="grndata_1.14.0.tar.gz" +FN="grndata_1.16.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/experiment/src/contrib/grndata_1.14.0.tar.gz" - "https://bioarchive.galaxyproject.org/grndata_1.14.0.tar.gz" - "https://depot.galaxyproject.org/software/bioconductor-grndata/bioconductor-grndata_1.14.0_src_all.tar.gz" + "https://bioconductor.org/packages/3.9/data/experiment/src/contrib/grndata_1.16.0.tar.gz" + "https://bioarchive.galaxyproject.org/grndata_1.16.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-grndata/bioconductor-grndata_1.16.0_src_all.tar.gz" ) -MD5="aacdf027236c99022b11fdabb983bbe4" +MD5="f68d2293bf9ad882ff9f061266f63fd1" # Use a staging area in the conda dir rather than temp dirs, both to avoid # permission issues as well as to have things downloaded in a predictable @@ -16,7 +16,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-grohmm/meta.yaml b/recipes/bioconductor-grohmm/meta.yaml index 73d6684271a83..057ccb38c8835 100644 --- a/recipes/bioconductor-grohmm/meta.yaml +++ b/recipes/bioconductor-grohmm/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.16.0" %} +{% set version = "1.18.0" %} {% set name = "groHMM" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 3d1cc353a06a4bc8d282f3712167ade0 + md5: 8983dcbac6cd3cf84433640e07ea4207 build: number: 0 rpaths: @@ -19,21 +19,21 @@ build: # Suggests: BiocStyle, GenomicFeatures, edgeR, org.Hs.eg.db, TxDb.Hsapiens.UCSC.hg19.knownGene requirements: host: - - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' - - 'bioconductor-genomicalignments >=1.18.0,<1.19.0' - - 'bioconductor-genomicranges >=1.34.0,<1.35.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-rtracklayer >=1.42.0,<1.43.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-genomeinfodb >=1.20.0,<1.21.0' + - 'bioconductor-genomicalignments >=1.20.0,<1.21.0' + - 'bioconductor-genomicranges >=1.36.0,<1.37.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-rtracklayer >=1.44.0,<1.45.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' - r-base - r-mass run: - - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' - - 'bioconductor-genomicalignments >=1.18.0,<1.19.0' - - 'bioconductor-genomicranges >=1.34.0,<1.35.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-rtracklayer >=1.42.0,<1.43.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-genomeinfodb >=1.20.0,<1.21.0' + - 'bioconductor-genomicalignments >=1.20.0,<1.21.0' + - 'bioconductor-genomicranges >=1.36.0,<1.37.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-rtracklayer >=1.44.0,<1.45.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' - r-base - r-mass build: diff --git a/recipes/bioconductor-grridge/meta.yaml b/recipes/bioconductor-grridge/meta.yaml index 5df7a9c2f7ffc..398aaaf4885e5 100644 --- a/recipes/bioconductor-grridge/meta.yaml +++ b/recipes/bioconductor-grridge/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.6.0" %} +{% set version = "1.8.0" %} {% set name = "GRridge" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: d5da4e835e460089ca8be2f16538e44c + md5: 15d439eaf17d228970bce90e32c35825 build: number: 0 rpaths: @@ -20,7 +20,7 @@ build: # Suggests: testthat requirements: host: - - 'bioconductor-graph >=1.60.0,<1.61.0' + - 'bioconductor-graph >=1.62.0,<1.63.0' - r-base - r-glmnet - r-iso @@ -28,7 +28,7 @@ requirements: - r-penalized - r-survival run: - - 'bioconductor-graph >=1.60.0,<1.61.0' + - 'bioconductor-graph >=1.62.0,<1.63.0' - r-base - r-glmnet - r-iso diff --git a/recipes/bioconductor-gsalightning/meta.yaml b/recipes/bioconductor-gsalightning/meta.yaml index f944353572a0a..0021e22322b12 100644 --- a/recipes/bioconductor-gsalightning/meta.yaml +++ b/recipes/bioconductor-gsalightning/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.10.0" %} +{% set version = "1.12.0" %} {% set name = "GSALightning" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 28383657aa63e5f8fe8140563135c3d0 + md5: 88df9d921afbca1265815c27f4f4532b build: number: 0 rpaths: diff --git a/recipes/bioconductor-gsar/meta.yaml b/recipes/bioconductor-gsar/meta.yaml index aa60c48887d09..2da9bf431b8ce 100644 --- a/recipes/bioconductor-gsar/meta.yaml +++ b/recipes/bioconductor-gsar/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.16.0" %} +{% set version = "1.18.0" %} {% set name = "GSAR" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: dfc4fe251c7b1129b68af45dfb7a3d4d + md5: f53c56d21969b346b9ddd9da63bb45c0 build: number: 0 rpaths: diff --git a/recipes/bioconductor-gsbenchmark/meta.yaml b/recipes/bioconductor-gsbenchmark/meta.yaml index 70e064bcf540a..5f2629567c676 100644 --- a/recipes/bioconductor-gsbenchmark/meta.yaml +++ b/recipes/bioconductor-gsbenchmark/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.2.0" %} +{% set version = "1.4.0" %} {% set name = "GSBenchMark" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,9 +10,9 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 5fa1f183443b3841de7e075441d47c5d + md5: a59a7b4328531cb827db30a0cabe0c5f build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ @@ -22,7 +22,7 @@ requirements: - r-base run: - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-gsbenchmark/post-link.sh b/recipes/bioconductor-gsbenchmark/post-link.sh index c196735a78565..ac84063b34e4f 100644 --- a/recipes/bioconductor-gsbenchmark/post-link.sh +++ b/recipes/bioconductor-gsbenchmark/post-link.sh @@ -1,11 +1,11 @@ #!/bin/bash -FN="GSBenchMark_1.2.0.tar.gz" +FN="GSBenchMark_1.4.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/experiment/src/contrib/GSBenchMark_1.2.0.tar.gz" - "https://bioarchive.galaxyproject.org/GSBenchMark_1.2.0.tar.gz" - "https://depot.galaxyproject.org/software/bioconductor-gsbenchmark/bioconductor-gsbenchmark_1.2.0_src_all.tar.gz" + "https://bioconductor.org/packages/3.9/data/experiment/src/contrib/GSBenchMark_1.4.0.tar.gz" + "https://bioarchive.galaxyproject.org/GSBenchMark_1.4.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-gsbenchmark/bioconductor-gsbenchmark_1.4.0_src_all.tar.gz" ) -MD5="5fa1f183443b3841de7e075441d47c5d" +MD5="a59a7b4328531cb827db30a0cabe0c5f" # Use a staging area in the conda dir rather than temp dirs, both to avoid # permission issues as well as to have things downloaded in a predictable @@ -16,7 +16,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-gsca/meta.yaml b/recipes/bioconductor-gsca/meta.yaml index 9ceeb878f6823..6a17d5aef044f 100644 --- a/recipes/bioconductor-gsca/meta.yaml +++ b/recipes/bioconductor-gsca/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "2.12.0" %} +{% set version = "2.14.0" %} {% set name = "GSCA" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,9 +10,9 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 5c525cb073c7ab3b0d0d2db4e4dc2f9c + md5: 8ff07dab7380213bff28935f8f9d362b build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ @@ -20,7 +20,7 @@ build: # Suggests: Affyhgu133aExpr, Affymoe4302Expr, Affyhgu133A2Expr, Affyhgu133Plus2Expr requirements: host: - - 'bioconductor-rhdf5 >=2.26.0,<2.27.0' + - 'bioconductor-rhdf5 >=2.28.0,<2.29.0' - r-base - r-ggplot2 - r-gplots @@ -29,7 +29,7 @@ requirements: - r-shiny - r-sp run: - - 'bioconductor-rhdf5 >=2.26.0,<2.27.0' + - 'bioconductor-rhdf5 >=2.28.0,<2.29.0' - r-base - r-ggplot2 - r-gplots diff --git a/recipes/bioconductor-gse62944/meta.yaml b/recipes/bioconductor-gse62944/meta.yaml index e9802af3acf3e..f5f05108b688b 100644 --- a/recipes/bioconductor-gse62944/meta.yaml +++ b/recipes/bioconductor-gse62944/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.10.0" %} +{% set version = "1.12.0" %} {% set name = "GSE62944" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: fecc45362eda757435ba7a0735c96b11 + md5: 817f3700ad4889d79e78336b42bd802b build: number: 0 rpaths: @@ -20,14 +20,14 @@ build: # Suggests: ExperimentHub (>= 0.99.6), knitr, BiocStyle requirements: host: - - 'bioconductor-biobase >=2.42.0,<2.43.0' - - 'bioconductor-geoquery >=2.50.0,<2.51.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' + - 'bioconductor-geoquery >=2.52.0,<2.53.0' - r-base run: - - 'bioconductor-biobase >=2.42.0,<2.43.0' - - 'bioconductor-geoquery >=2.50.0,<2.51.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' + - 'bioconductor-geoquery >=2.52.0,<2.53.0' - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-gse62944/post-link.sh b/recipes/bioconductor-gse62944/post-link.sh index dbb15005e76c1..10eb305aeacf2 100644 --- a/recipes/bioconductor-gse62944/post-link.sh +++ b/recipes/bioconductor-gse62944/post-link.sh @@ -1,11 +1,11 @@ #!/bin/bash -FN="GSE62944_1.10.0.tar.gz" +FN="GSE62944_1.12.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/experiment/src/contrib/GSE62944_1.10.0.tar.gz" - "https://bioarchive.galaxyproject.org/GSE62944_1.10.0.tar.gz" - "https://depot.galaxyproject.org/software/bioconductor-gse62944/bioconductor-gse62944_1.10.0_src_all.tar.gz" + "https://bioconductor.org/packages/3.9/data/experiment/src/contrib/GSE62944_1.12.0.tar.gz" + "https://bioarchive.galaxyproject.org/GSE62944_1.12.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-gse62944/bioconductor-gse62944_1.12.0_src_all.tar.gz" ) -MD5="fecc45362eda757435ba7a0735c96b11" +MD5="817f3700ad4889d79e78336b42bd802b" # Use a staging area in the conda dir rather than temp dirs, both to avoid # permission issues as well as to have things downloaded in a predictable @@ -16,7 +16,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-gseabase/meta.yaml b/recipes/bioconductor-gseabase/meta.yaml index ba73d42e5672e..359b1e1799bc0 100644 --- a/recipes/bioconductor-gseabase/meta.yaml +++ b/recipes/bioconductor-gseabase/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.44.0" %} +{% set version = "1.46.0" %} {% set name = "GSEABase" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 5b59c4714c169230996c60cf235300bc + md5: 6e562d9bbdc3e1305b0af55f106e418f build: number: 0 rpaths: @@ -20,19 +20,19 @@ build: # Suggests: hgu95av2.db, GO.db, org.Hs.eg.db, Rgraphviz, ReportingTools, testthat, BiocStyle, knitr requirements: host: - - 'bioconductor-annotate >=1.60.0,<1.61.0' - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' - - 'bioconductor-biobase >=2.42.0,<2.43.0' - - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' - - 'bioconductor-graph >=1.60.0,<1.61.0' + - 'bioconductor-annotate >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' + - 'bioconductor-biocgenerics >=0.30.0,<0.31.0' + - 'bioconductor-graph >=1.62.0,<1.63.0' - r-base - r-xml run: - - 'bioconductor-annotate >=1.60.0,<1.61.0' - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' - - 'bioconductor-biobase >=2.42.0,<2.43.0' - - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' - - 'bioconductor-graph >=1.60.0,<1.61.0' + - 'bioconductor-annotate >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' + - 'bioconductor-biocgenerics >=0.30.0,<0.31.0' + - 'bioconductor-graph >=1.62.0,<1.63.0' - r-base - r-xml test: diff --git a/recipes/bioconductor-gseabenchmarker/meta.yaml b/recipes/bioconductor-gseabenchmarker/meta.yaml index 4ec64a318faf9..de20edfa5c70f 100644 --- a/recipes/bioconductor-gseabenchmarker/meta.yaml +++ b/recipes/bioconductor-gseabenchmarker/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.2.0" %} +{% set version = "1.4.0" %} {% set name = "GSEABenchmarkeR" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 9955f0c7c9c12de28436f4d794eec517 + md5: 6666b019e68213e8fb990d28955ade35 build: number: 0 rpaths: @@ -20,35 +20,35 @@ build: # Suggests: BiocStyle, knitr, rmarkdown requirements: host: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' - - 'bioconductor-annotationhub >=2.14.0,<2.15.0' - - 'bioconductor-biobase >=2.42.0,<2.43.0' - - 'bioconductor-biocfilecache >=1.6.0,<1.7.0' - - 'bioconductor-biocparallel >=1.16.0,<1.17.0' - - 'bioconductor-edger >=3.24.0,<3.25.0' - - 'bioconductor-enrichmentbrowser >=2.12.0,<2.13.0' - - 'bioconductor-experimenthub >=1.8.0,<1.9.0' - - 'bioconductor-geoquery >=2.50.0,<2.51.0' - - 'bioconductor-keggandmetacoredzpathwaysgeo >=1.2.0,<1.3.0' - - 'bioconductor-keggdzpathwaysgeo >=1.20.0,<1.21.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' - - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' + - 'bioconductor-annotationhub >=2.16.0,<2.17.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' + - 'bioconductor-biocfilecache >=1.8.0,<1.9.0' + - 'bioconductor-biocparallel >=1.18.0,<1.19.0' + - 'bioconductor-edger >=3.26.0,<3.27.0' + - 'bioconductor-enrichmentbrowser >=2.14.0,<2.15.0' + - 'bioconductor-experimenthub >=1.10.0,<1.11.0' + - 'bioconductor-geoquery >=2.52.0,<2.53.0' + - 'bioconductor-keggandmetacoredzpathwaysgeo >=1.4.0,<1.5.0' + - 'bioconductor-keggdzpathwaysgeo >=1.22.0,<1.23.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' + - 'bioconductor-summarizedexperiment >=1.14.0,<1.15.0' - r-base - r-rappdirs run: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' - - 'bioconductor-annotationhub >=2.14.0,<2.15.0' - - 'bioconductor-biobase >=2.42.0,<2.43.0' - - 'bioconductor-biocfilecache >=1.6.0,<1.7.0' - - 'bioconductor-biocparallel >=1.16.0,<1.17.0' - - 'bioconductor-edger >=3.24.0,<3.25.0' - - 'bioconductor-enrichmentbrowser >=2.12.0,<2.13.0' - - 'bioconductor-experimenthub >=1.8.0,<1.9.0' - - 'bioconductor-geoquery >=2.50.0,<2.51.0' - - 'bioconductor-keggandmetacoredzpathwaysgeo >=1.2.0,<1.3.0' - - 'bioconductor-keggdzpathwaysgeo >=1.20.0,<1.21.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' - - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' + - 'bioconductor-annotationhub >=2.16.0,<2.17.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' + - 'bioconductor-biocfilecache >=1.8.0,<1.9.0' + - 'bioconductor-biocparallel >=1.18.0,<1.19.0' + - 'bioconductor-edger >=3.26.0,<3.27.0' + - 'bioconductor-enrichmentbrowser >=2.14.0,<2.15.0' + - 'bioconductor-experimenthub >=1.10.0,<1.11.0' + - 'bioconductor-geoquery >=2.52.0,<2.53.0' + - 'bioconductor-keggandmetacoredzpathwaysgeo >=1.4.0,<1.5.0' + - 'bioconductor-keggdzpathwaysgeo >=1.22.0,<1.23.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' + - 'bioconductor-summarizedexperiment >=1.14.0,<1.15.0' - r-base - r-rappdirs test: diff --git a/recipes/bioconductor-gsealm/meta.yaml b/recipes/bioconductor-gsealm/meta.yaml index a60e0c6e9ec4e..fef76d4c261d4 100644 --- a/recipes/bioconductor-gsealm/meta.yaml +++ b/recipes/bioconductor-gsealm/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.42.0" %} +{% set version = "1.44.0" %} {% set name = "GSEAlm" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 042abec16df906184e23c4677d4ab42d + md5: 44954c57f7ebdd5e32d0a86d2961a28c build: number: 0 rpaths: @@ -20,10 +20,10 @@ build: # Suggests: GSEABase,Category, multtest, ALL, annotate, hgu95av2.db, genefilter, GOstats, RColorBrewer requirements: host: - - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' - r-base run: - - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' - r-base test: commands: diff --git a/recipes/bioconductor-gsean/meta.yaml b/recipes/bioconductor-gsean/meta.yaml index 63bb63ffb9d36..58d6e55e40bbf 100644 --- a/recipes/bioconductor-gsean/meta.yaml +++ b/recipes/bioconductor-gsean/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.2.0" %} +{% set version = "1.4.0" %} {% set name = "gsean" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,22 +10,22 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 03265cedf007c831dba2d78d84309d67 + md5: f6381b7ee7c8d515568c970921768f54 build: number: 0 rpaths: - lib/R/lib/ - lib/ noarch: generic -# Suggests: DESeq2, knitr, plotly, RANKS, WGCNA +# Suggests: SummarizedExperiment, knitr, plotly, RANKS, WGCNA requirements: host: - - 'bioconductor-fgsea >=1.8.0,<1.9.0' - - 'bioconductor-ppinfer >=1.8.0,<1.9.0' + - 'bioconductor-fgsea >=1.10.0,<1.11.0' + - 'bioconductor-ppinfer >=1.10.0,<1.11.0' - r-base run: - - 'bioconductor-fgsea >=1.8.0,<1.9.0' - - 'bioconductor-ppinfer >=1.8.0,<1.9.0' + - 'bioconductor-fgsea >=1.10.0,<1.11.0' + - 'bioconductor-ppinfer >=1.10.0,<1.11.0' - r-base test: commands: diff --git a/recipes/bioconductor-gskb/meta.yaml b/recipes/bioconductor-gskb/meta.yaml index 05f1d15bdee08..4b143b0f3c490 100644 --- a/recipes/bioconductor-gskb/meta.yaml +++ b/recipes/bioconductor-gskb/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.14.0" %} +{% set version = "1.16.0" %} {% set name = "gskb" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: d2053bb9fd322f0c71360f6721761443 + md5: b6a505908c6339c2cc3e5f9b937737aa build: number: 0 rpaths: @@ -23,7 +23,7 @@ requirements: - r-base run: - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-gskb/post-link.sh b/recipes/bioconductor-gskb/post-link.sh index a4a08a2beeb43..5d0002ec95edb 100644 --- a/recipes/bioconductor-gskb/post-link.sh +++ b/recipes/bioconductor-gskb/post-link.sh @@ -1,11 +1,11 @@ #!/bin/bash -FN="gskb_1.14.0.tar.gz" +FN="gskb_1.16.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/experiment/src/contrib/gskb_1.14.0.tar.gz" - "https://bioarchive.galaxyproject.org/gskb_1.14.0.tar.gz" - "https://depot.galaxyproject.org/software/bioconductor-gskb/bioconductor-gskb_1.14.0_src_all.tar.gz" + "https://bioconductor.org/packages/3.9/data/experiment/src/contrib/gskb_1.16.0.tar.gz" + "https://bioarchive.galaxyproject.org/gskb_1.16.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-gskb/bioconductor-gskb_1.16.0_src_all.tar.gz" ) -MD5="d2053bb9fd322f0c71360f6721761443" +MD5="b6a505908c6339c2cc3e5f9b937737aa" # Use a staging area in the conda dir rather than temp dirs, both to avoid # permission issues as well as to have things downloaded in a predictable @@ -16,7 +16,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-gsreg/meta.yaml b/recipes/bioconductor-gsreg/meta.yaml index 1b1c8bb3c61f4..36090b31dbe1e 100644 --- a/recipes/bioconductor-gsreg/meta.yaml +++ b/recipes/bioconductor-gsreg/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.16.0" %} +{% set version = "1.18.0" %} {% set name = "GSReg" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 723ed94d28d5f414bde41f093c8409b9 + md5: 75a7727c6c3ec5dddbd7fe272c65b2d1 build: number: 0 rpaths: @@ -19,16 +19,16 @@ build: # Suggests: GenomicRanges, GSBenchMark requirements: host: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' - - 'bioconductor-genomicfeatures >=1.34.0,<1.35.0' - - 'bioconductor-homo.sapiens >=1.3.0,<1.4.0' - - 'bioconductor-org.hs.eg.db >=3.7.0,<3.8.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' + - 'bioconductor-genomicfeatures >=1.36.0,<1.37.0' + - 'bioconductor-homo.sapiens >=1.4.0,<1.5.0' + - 'bioconductor-org.hs.eg.db >=3.8.0,<3.9.0' - r-base run: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' - - 'bioconductor-genomicfeatures >=1.34.0,<1.35.0' - - 'bioconductor-homo.sapiens >=1.3.0,<1.4.0' - - 'bioconductor-org.hs.eg.db >=3.7.0,<3.8.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' + - 'bioconductor-genomicfeatures >=1.36.0,<1.37.0' + - 'bioconductor-homo.sapiens >=1.4.0,<1.5.0' + - 'bioconductor-org.hs.eg.db >=3.8.0,<3.9.0' - r-base build: - {{ compiler('c') }} diff --git a/recipes/bioconductor-gsri/meta.yaml b/recipes/bioconductor-gsri/meta.yaml index f32bd472881bf..3090efbb14589 100644 --- a/recipes/bioconductor-gsri/meta.yaml +++ b/recipes/bioconductor-gsri/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "2.30.0" %} +{% set version = "2.32.0" %} {% set name = "GSRI" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: f57c37cdbe4fd009e96b330b0c6d4272 + md5: fb44aa45a4375a0e2b7b6ed0c4604285 build: number: 0 rpaths: @@ -20,17 +20,17 @@ build: # Suggests: limma, hgu95av2.db requirements: host: - - 'bioconductor-biobase >=2.42.0,<2.43.0' - - 'bioconductor-genefilter >=1.64.0,<1.65.0' - - 'bioconductor-gseabase >=1.44.0,<1.45.0' - - 'bioconductor-les >=1.32.0,<1.33.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' + - 'bioconductor-genefilter >=1.66.0,<1.67.0' + - 'bioconductor-gseabase >=1.46.0,<1.47.0' + - 'bioconductor-les >=1.34.0,<1.35.0' - r-base - r-fdrtool run: - - 'bioconductor-biobase >=2.42.0,<2.43.0' - - 'bioconductor-genefilter >=1.64.0,<1.65.0' - - 'bioconductor-gseabase >=1.44.0,<1.45.0' - - 'bioconductor-les >=1.32.0,<1.33.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' + - 'bioconductor-genefilter >=1.66.0,<1.67.0' + - 'bioconductor-gseabase >=1.46.0,<1.47.0' + - 'bioconductor-les >=1.34.0,<1.35.0' - r-base - r-fdrtool test: diff --git a/recipes/bioconductor-gsva/meta.yaml b/recipes/bioconductor-gsva/meta.yaml index 538e838918dc4..cfd70fd35ec50 100644 --- a/recipes/bioconductor-gsva/meta.yaml +++ b/recipes/bioconductor-gsva/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.30.0" %} +{% set version = "1.32.0" %} {% set name = "GSVA" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,27 +10,27 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: eab560c63cf486e47723ab7d6292bc76 + md5: fbf37c12f2e4ddbefffe06d68a49c54c build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ # Suggests: limma, RColorBrewer, genefilter, mclust, edgeR, snow, parallel, GSVAdata requirements: host: - - 'bioconductor-biobase >=2.42.0,<2.43.0' - - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' - - 'bioconductor-geneplotter >=1.60.0,<1.61.0' - - 'bioconductor-gseabase >=1.44.0,<1.45.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' + - 'bioconductor-biocgenerics >=0.30.0,<0.31.0' + - 'bioconductor-geneplotter >=1.62.0,<1.63.0' + - 'bioconductor-gseabase >=1.46.0,<1.47.0' - r-base - r-shiny - r-shinythemes run: - - 'bioconductor-biobase >=2.42.0,<2.43.0' - - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' - - 'bioconductor-geneplotter >=1.60.0,<1.61.0' - - 'bioconductor-gseabase >=1.44.0,<1.45.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' + - 'bioconductor-biocgenerics >=0.30.0,<0.31.0' + - 'bioconductor-geneplotter >=1.62.0,<1.63.0' + - 'bioconductor-gseabase >=1.46.0,<1.47.0' - r-base - r-shiny - r-shinythemes diff --git a/recipes/bioconductor-gsvadata/meta.yaml b/recipes/bioconductor-gsvadata/meta.yaml index 8ad4798171329..d529cf46ebdaa 100644 --- a/recipes/bioconductor-gsvadata/meta.yaml +++ b/recipes/bioconductor-gsvadata/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.18.0" %} +{% set version = "1.20.0" %} {% set name = "GSVAdata" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 10c95ec0b4214f43609e0bfdfc860bc8 + md5: 484d17c3ba9983370f7d91f8db3899e7 build: number: 0 rpaths: @@ -19,16 +19,16 @@ build: noarch: generic requirements: host: - - 'bioconductor-biobase >=2.42.0,<2.43.0' - - 'bioconductor-gseabase >=1.44.0,<1.45.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' + - 'bioconductor-gseabase >=1.46.0,<1.47.0' - 'bioconductor-hgu95a.db >=3.2.0,<3.3.0' - r-base run: - - 'bioconductor-biobase >=2.42.0,<2.43.0' - - 'bioconductor-gseabase >=1.44.0,<1.45.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' + - 'bioconductor-gseabase >=1.46.0,<1.47.0' - 'bioconductor-hgu95a.db >=3.2.0,<3.3.0' - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-gsvadata/post-link.sh b/recipes/bioconductor-gsvadata/post-link.sh index c228480ee0d3c..bc937217fa2f7 100644 --- a/recipes/bioconductor-gsvadata/post-link.sh +++ b/recipes/bioconductor-gsvadata/post-link.sh @@ -1,11 +1,11 @@ #!/bin/bash -FN="GSVAdata_1.18.0.tar.gz" +FN="GSVAdata_1.20.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/experiment/src/contrib/GSVAdata_1.18.0.tar.gz" - "https://bioarchive.galaxyproject.org/GSVAdata_1.18.0.tar.gz" - "https://depot.galaxyproject.org/software/bioconductor-gsvadata/bioconductor-gsvadata_1.18.0_src_all.tar.gz" + "https://bioconductor.org/packages/3.9/data/experiment/src/contrib/GSVAdata_1.20.0.tar.gz" + "https://bioarchive.galaxyproject.org/GSVAdata_1.20.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-gsvadata/bioconductor-gsvadata_1.20.0_src_all.tar.gz" ) -MD5="10c95ec0b4214f43609e0bfdfc860bc8" +MD5="484d17c3ba9983370f7d91f8db3899e7" # Use a staging area in the conda dir rather than temp dirs, both to avoid # permission issues as well as to have things downloaded in a predictable @@ -16,7 +16,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-gtrellis/meta.yaml b/recipes/bioconductor-gtrellis/meta.yaml index 3c06ddff1b61f..af68174f67f90 100644 --- a/recipes/bioconductor-gtrellis/meta.yaml +++ b/recipes/bioconductor-gtrellis/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.14.0" %} +{% set version = "1.16.0" %} {% set name = "gtrellis" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,24 +10,24 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 8fc5688a3249a05d5088b29ea8885535 + md5: b3c146b4dab9ee1afcdceefd70895da3 build: number: 0 rpaths: - lib/R/lib/ - lib/ noarch: generic -# Suggests: testthat (>= 1.0.0), knitr, RColorBrewer, markdown, ComplexHeatmap (>= 1.9.7), Cairo, png, jpeg, tiff +# Suggests: testthat (>= 1.0.0), knitr, RColorBrewer, markdown, ComplexHeatmap (>= 1.99.0), Cairo, png, jpeg, tiff requirements: host: - - 'bioconductor-genomicranges >=1.34.0,<1.35.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-genomicranges >=1.36.0,<1.37.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' - r-base - 'r-circlize >=0.3.3' - r-getoptlong run: - - 'bioconductor-genomicranges >=1.34.0,<1.35.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-genomicranges >=1.36.0,<1.37.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' - r-base - 'r-circlize >=0.3.3' - r-getoptlong diff --git a/recipes/bioconductor-guideseq/meta.yaml b/recipes/bioconductor-guideseq/meta.yaml index ee86b59cfb1f5..7d2d7bf4887ac 100644 --- a/recipes/bioconductor-guideseq/meta.yaml +++ b/recipes/bioconductor-guideseq/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.12.0" %} +{% set version = "1.14.0" %} {% set name = "GUIDEseq" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: eeef16c619ade79a8efac593cde02193 + md5: 1f6c785e409fd430fd39babe82a8b53d build: number: 0 rpaths: @@ -20,37 +20,37 @@ build: # Suggests: knitr, RUnit, BiocStyle, BSgenome.Hsapiens.UCSC.hg19, TxDb.Hsapiens.UCSC.hg19.knownGene, org.Hs.eg.db requirements: host: - - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' - - 'bioconductor-biocparallel >=1.16.0,<1.17.0' - - 'bioconductor-biostrings >=2.50.0,<2.51.0' - - 'bioconductor-bsgenome >=1.50.0,<1.51.0' - - 'bioconductor-chippeakanno >=3.16.0,<3.17.0' - - 'bioconductor-crisprseek >=1.22.0,<1.23.0' - - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' - - 'bioconductor-genomicalignments >=1.18.0,<1.19.0' - - 'bioconductor-genomicranges >=1.34.0,<1.35.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-limma >=3.38.0,<3.39.0' - - 'bioconductor-rsamtools >=1.34.0,<1.35.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-biocgenerics >=0.30.0,<0.31.0' + - 'bioconductor-biocparallel >=1.18.0,<1.19.0' + - 'bioconductor-biostrings >=2.52.0,<2.53.0' + - 'bioconductor-bsgenome >=1.52.0,<1.53.0' + - 'bioconductor-chippeakanno >=3.18.0,<3.19.0' + - 'bioconductor-crisprseek >=1.24.0,<1.25.0' + - 'bioconductor-genomeinfodb >=1.20.0,<1.21.0' + - 'bioconductor-genomicalignments >=1.20.0,<1.21.0' + - 'bioconductor-genomicranges >=1.36.0,<1.37.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-limma >=3.40.0,<3.41.0' + - 'bioconductor-rsamtools >=2.0.0,<2.1.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' - r-base - r-data.table - r-hash - r-matrixstats run: - - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' - - 'bioconductor-biocparallel >=1.16.0,<1.17.0' - - 'bioconductor-biostrings >=2.50.0,<2.51.0' - - 'bioconductor-bsgenome >=1.50.0,<1.51.0' - - 'bioconductor-chippeakanno >=3.16.0,<3.17.0' - - 'bioconductor-crisprseek >=1.22.0,<1.23.0' - - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' - - 'bioconductor-genomicalignments >=1.18.0,<1.19.0' - - 'bioconductor-genomicranges >=1.34.0,<1.35.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-limma >=3.38.0,<3.39.0' - - 'bioconductor-rsamtools >=1.34.0,<1.35.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-biocgenerics >=0.30.0,<0.31.0' + - 'bioconductor-biocparallel >=1.18.0,<1.19.0' + - 'bioconductor-biostrings >=2.52.0,<2.53.0' + - 'bioconductor-bsgenome >=1.52.0,<1.53.0' + - 'bioconductor-chippeakanno >=3.18.0,<3.19.0' + - 'bioconductor-crisprseek >=1.24.0,<1.25.0' + - 'bioconductor-genomeinfodb >=1.20.0,<1.21.0' + - 'bioconductor-genomicalignments >=1.20.0,<1.21.0' + - 'bioconductor-genomicranges >=1.36.0,<1.37.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-limma >=3.40.0,<3.41.0' + - 'bioconductor-rsamtools >=2.0.0,<2.1.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' - r-base - r-data.table - r-hash diff --git a/recipes/bioconductor-guitar/meta.yaml b/recipes/bioconductor-guitar/meta.yaml index aa1979bcdb922..70d3501e5cb17 100644 --- a/recipes/bioconductor-guitar/meta.yaml +++ b/recipes/bioconductor-guitar/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.20.1" %} +{% set version = "2.0.0" %} {% set name = "Guitar" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 2a40227682263aa6cd477bbcfc80c729 + md5: 6d39650e6b2647c97fdb54ff80fa1357 build: number: 0 rpaths: @@ -19,23 +19,25 @@ build: noarch: generic requirements: host: - - 'bioconductor-genomicalignments >=1.18.0,<1.19.0' - - 'bioconductor-genomicfeatures >=1.34.0,<1.35.0' - - 'bioconductor-genomicranges >=1.34.0,<1.35.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-rsamtools >=1.34.0,<1.35.0' - - 'bioconductor-rtracklayer >=1.42.0,<1.43.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' + - 'bioconductor-genomicfeatures >=1.36.0,<1.37.0' + - 'bioconductor-genomicranges >=1.36.0,<1.37.0' + - 'bioconductor-rtracklayer >=1.44.0,<1.45.0' - r-base + - r-dplyr - r-ggplot2 + - r-knitr + - r-magrittr run: - - 'bioconductor-genomicalignments >=1.18.0,<1.19.0' - - 'bioconductor-genomicfeatures >=1.34.0,<1.35.0' - - 'bioconductor-genomicranges >=1.34.0,<1.35.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-rsamtools >=1.34.0,<1.35.0' - - 'bioconductor-rtracklayer >=1.42.0,<1.43.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' + - 'bioconductor-genomicfeatures >=1.36.0,<1.37.0' + - 'bioconductor-genomicranges >=1.36.0,<1.37.0' + - 'bioconductor-rtracklayer >=1.44.0,<1.45.0' - r-base + - r-dplyr - r-ggplot2 + - r-knitr + - r-magrittr test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-gviz/meta.yaml b/recipes/bioconductor-gviz/meta.yaml index b257bdfffd23b..9759173a80c23 100644 --- a/recipes/bioconductor-gviz/meta.yaml +++ b/recipes/bioconductor-gviz/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.26.4" %} +{% set version = "1.28.0" %} {% set name = "Gviz" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,32 +10,32 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: ef0cbfbcf333f436de1a3e34acf04dd1 + md5: e8371fbbacb745b624330b721c905be2 build: number: 0 rpaths: - lib/R/lib/ - lib/ noarch: generic -# Suggests: xtable, BSgenome.Hsapiens.UCSC.hg19, BiocStyle +# Suggests: BSgenome.Hsapiens.UCSC.hg19, BiocStyle, knitr, kableExtra, rmarkdown, testthat requirements: host: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' - - 'bioconductor-biobase >=2.42.0,<2.43.0' - - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' - - 'bioconductor-biomart >=2.38.0,<2.39.0' - - 'bioconductor-biostrings >=2.50.0,<2.51.0' - - 'bioconductor-biovizbase >=1.30.0,<1.31.0' - - 'bioconductor-bsgenome >=1.50.0,<1.51.0' - - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' - - 'bioconductor-genomicalignments >=1.18.0,<1.19.0' - - 'bioconductor-genomicfeatures >=1.34.0,<1.35.0' - - 'bioconductor-genomicranges >=1.34.0,<1.35.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-rsamtools >=1.34.0,<1.35.0' - - 'bioconductor-rtracklayer >=1.42.0,<1.43.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' - - 'bioconductor-xvector >=0.22.0,<0.23.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' + - 'bioconductor-biocgenerics >=0.30.0,<0.31.0' + - 'bioconductor-biomart >=2.40.0,<2.41.0' + - 'bioconductor-biostrings >=2.52.0,<2.53.0' + - 'bioconductor-biovizbase >=1.32.0,<1.33.0' + - 'bioconductor-bsgenome >=1.52.0,<1.53.0' + - 'bioconductor-genomeinfodb >=1.20.0,<1.21.0' + - 'bioconductor-genomicalignments >=1.20.0,<1.21.0' + - 'bioconductor-genomicfeatures >=1.36.0,<1.37.0' + - 'bioconductor-genomicranges >=1.36.0,<1.37.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-rsamtools >=2.0.0,<2.1.0' + - 'bioconductor-rtracklayer >=1.44.0,<1.45.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' + - 'bioconductor-xvector >=0.24.0,<0.25.0' - r-base - 'r-digest >=0.6.8' - r-lattice @@ -43,22 +43,22 @@ requirements: - 'r-matrixstats >=0.8.14' - r-rcolorbrewer run: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' - - 'bioconductor-biobase >=2.42.0,<2.43.0' - - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' - - 'bioconductor-biomart >=2.38.0,<2.39.0' - - 'bioconductor-biostrings >=2.50.0,<2.51.0' - - 'bioconductor-biovizbase >=1.30.0,<1.31.0' - - 'bioconductor-bsgenome >=1.50.0,<1.51.0' - - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' - - 'bioconductor-genomicalignments >=1.18.0,<1.19.0' - - 'bioconductor-genomicfeatures >=1.34.0,<1.35.0' - - 'bioconductor-genomicranges >=1.34.0,<1.35.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-rsamtools >=1.34.0,<1.35.0' - - 'bioconductor-rtracklayer >=1.42.0,<1.43.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' - - 'bioconductor-xvector >=0.22.0,<0.23.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' + - 'bioconductor-biocgenerics >=0.30.0,<0.31.0' + - 'bioconductor-biomart >=2.40.0,<2.41.0' + - 'bioconductor-biostrings >=2.52.0,<2.53.0' + - 'bioconductor-biovizbase >=1.32.0,<1.33.0' + - 'bioconductor-bsgenome >=1.52.0,<1.53.0' + - 'bioconductor-genomeinfodb >=1.20.0,<1.21.0' + - 'bioconductor-genomicalignments >=1.20.0,<1.21.0' + - 'bioconductor-genomicfeatures >=1.36.0,<1.37.0' + - 'bioconductor-genomicranges >=1.36.0,<1.37.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-rsamtools >=2.0.0,<2.1.0' + - 'bioconductor-rtracklayer >=1.44.0,<1.45.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' + - 'bioconductor-xvector >=0.24.0,<0.25.0' - r-base - 'r-digest >=0.6.8' - r-lattice diff --git a/recipes/bioconductor-gwascat/meta.yaml b/recipes/bioconductor-gwascat/meta.yaml index c5d5492b6fdff..0536c2284bf66 100644 --- a/recipes/bioconductor-gwascat/meta.yaml +++ b/recipes/bioconductor-gwascat/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "2.14.0" %} +{% set version = "2.16.0" %} {% set name = "gwascat" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,59 +10,41 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 4a30aafb9ce69767d6b21553fbba9607 + md5: 2d207fdbf68b17a46b2c3b78ea275455 build: number: 0 rpaths: - lib/R/lib/ - lib/ noarch: generic -# Suggests: DO.db, DT, utils, knitr, RBGL, RUnit +# Suggests: DO.db, DT, utils, knitr, RBGL, RUnit, snpStats, Gviz, VariantAnnotation, AnnotationHub, gQTLstats, graph, ggbio, ggplot2, DelayedArray requirements: host: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' - - 'bioconductor-annotationhub >=2.14.0,<2.15.0' - - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' - - 'bioconductor-biostrings >=2.50.0,<2.51.0' - - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' - - 'bioconductor-genomicfeatures >=1.34.0,<1.35.0' - - 'bioconductor-genomicranges >=1.34.0,<1.35.0' - - 'bioconductor-ggbio >=1.30.0,<1.31.0' - - 'bioconductor-gqtlstats >=1.14.0,<1.15.0' - - 'bioconductor-graph >=1.60.0,<1.61.0' - - 'bioconductor-gviz >=1.26.0,<1.27.0' - - 'bioconductor-homo.sapiens >=1.3.0,<1.4.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-rsamtools >=1.34.0,<1.35.0' - - 'bioconductor-rtracklayer >=1.42.0,<1.43.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' - - 'bioconductor-snpstats >=1.32.0,<1.33.0' - - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' - - 'bioconductor-variantannotation >=1.28.0,<1.29.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' + - 'bioconductor-biocgenerics >=0.30.0,<0.31.0' + - 'bioconductor-biostrings >=2.52.0,<2.53.0' + - 'bioconductor-genomeinfodb >=1.20.0,<1.21.0' + - 'bioconductor-genomicfeatures >=1.36.0,<1.37.0' + - 'bioconductor-genomicranges >=1.36.0,<1.37.0' + - 'bioconductor-homo.sapiens >=1.4.0,<1.5.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-rsamtools >=2.0.0,<2.1.0' + - 'bioconductor-rtracklayer >=1.44.0,<1.45.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' - r-base - - r-ggplot2 run: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' - - 'bioconductor-annotationhub >=2.14.0,<2.15.0' - - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' - - 'bioconductor-biostrings >=2.50.0,<2.51.0' - - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' - - 'bioconductor-genomicfeatures >=1.34.0,<1.35.0' - - 'bioconductor-genomicranges >=1.34.0,<1.35.0' - - 'bioconductor-ggbio >=1.30.0,<1.31.0' - - 'bioconductor-gqtlstats >=1.14.0,<1.15.0' - - 'bioconductor-graph >=1.60.0,<1.61.0' - - 'bioconductor-gviz >=1.26.0,<1.27.0' - - 'bioconductor-homo.sapiens >=1.3.0,<1.4.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-rsamtools >=1.34.0,<1.35.0' - - 'bioconductor-rtracklayer >=1.42.0,<1.43.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' - - 'bioconductor-snpstats >=1.32.0,<1.33.0' - - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' - - 'bioconductor-variantannotation >=1.28.0,<1.29.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' + - 'bioconductor-biocgenerics >=0.30.0,<0.31.0' + - 'bioconductor-biostrings >=2.52.0,<2.53.0' + - 'bioconductor-genomeinfodb >=1.20.0,<1.21.0' + - 'bioconductor-genomicfeatures >=1.36.0,<1.37.0' + - 'bioconductor-genomicranges >=1.36.0,<1.37.0' + - 'bioconductor-homo.sapiens >=1.4.0,<1.5.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-rsamtools >=2.0.0,<2.1.0' + - 'bioconductor-rtracklayer >=1.44.0,<1.45.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' - r-base - - r-ggplot2 test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-gwasdata/meta.yaml b/recipes/bioconductor-gwasdata/meta.yaml index 09b34f7ec74b1..9c4c70bbd844c 100644 --- a/recipes/bioconductor-gwasdata/meta.yaml +++ b/recipes/bioconductor-gwasdata/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.20.0" %} +{% set version = "1.22.0" %} {% set name = "GWASdata" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 6b7ab74910c712639fa896f6b19e2934 + md5: 4e1c2ce5dfcb6411e5b6d6690aeeb369 build: number: 0 rpaths: @@ -19,12 +19,12 @@ build: noarch: generic requirements: host: - - 'bioconductor-gwastools >=1.28.0,<1.29.0' + - 'bioconductor-gwastools >=1.30.0,<1.31.0' - r-base run: - - 'bioconductor-gwastools >=1.28.0,<1.29.0' + - 'bioconductor-gwastools >=1.30.0,<1.31.0' - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-gwasdata/post-link.sh b/recipes/bioconductor-gwasdata/post-link.sh index d395df474b575..58082a4e227bb 100644 --- a/recipes/bioconductor-gwasdata/post-link.sh +++ b/recipes/bioconductor-gwasdata/post-link.sh @@ -1,11 +1,11 @@ #!/bin/bash -FN="GWASdata_1.20.0.tar.gz" +FN="GWASdata_1.22.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/experiment/src/contrib/GWASdata_1.20.0.tar.gz" - "https://bioarchive.galaxyproject.org/GWASdata_1.20.0.tar.gz" - "https://depot.galaxyproject.org/software/bioconductor-gwasdata/bioconductor-gwasdata_1.20.0_src_all.tar.gz" + "https://bioconductor.org/packages/3.9/data/experiment/src/contrib/GWASdata_1.22.0.tar.gz" + "https://bioarchive.galaxyproject.org/GWASdata_1.22.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-gwasdata/bioconductor-gwasdata_1.22.0_src_all.tar.gz" ) -MD5="6b7ab74910c712639fa896f6b19e2934" +MD5="4e1c2ce5dfcb6411e5b6d6690aeeb369" # Use a staging area in the conda dir rather than temp dirs, both to avoid # permission issues as well as to have things downloaded in a predictable @@ -16,7 +16,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-gwastools/meta.yaml b/recipes/bioconductor-gwastools/meta.yaml index 056210cb85df8..09d1a71d15aea 100644 --- a/recipes/bioconductor-gwastools/meta.yaml +++ b/recipes/bioconductor-gwastools/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.28.0" %} +{% set version = "1.30.0" %} {% set name = "GWASTools" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: e37216b340d24ffb378566279397852a + md5: 6f97345ccabcee4ef4fbc4308bfdad16 build: number: 0 rpaths: @@ -20,10 +20,10 @@ build: # Suggests: ncdf4, GWASdata, BiocGenerics, RUnit, Biostrings, GenomicRanges, IRanges, SNPRelate, snpStats, S4Vectors, VariantAnnotation requirements: host: - - 'bioconductor-biobase >=2.42.0,<2.43.0' - - 'bioconductor-dnacopy >=1.56.0,<1.57.0' - - 'bioconductor-gdsfmt >=1.18.0,<1.19.0' - - 'bioconductor-quantsmooth >=1.48.0,<1.49.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' + - 'bioconductor-dnacopy >=1.58.0,<1.59.0' + - 'bioconductor-gdsfmt >=1.20.0,<1.21.0' + - 'bioconductor-quantsmooth >=1.50.0,<1.51.0' - r-base - r-dbi - r-gwasexacthw @@ -33,10 +33,10 @@ requirements: - r-sandwich - r-survival run: - - 'bioconductor-biobase >=2.42.0,<2.43.0' - - 'bioconductor-dnacopy >=1.56.0,<1.57.0' - - 'bioconductor-gdsfmt >=1.18.0,<1.19.0' - - 'bioconductor-quantsmooth >=1.48.0,<1.49.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' + - 'bioconductor-dnacopy >=1.58.0,<1.59.0' + - 'bioconductor-gdsfmt >=1.20.0,<1.21.0' + - 'bioconductor-quantsmooth >=1.50.0,<1.51.0' - r-base - r-dbi - r-gwasexacthw diff --git a/recipes/bioconductor-gwasurvivr/meta.yaml b/recipes/bioconductor-gwasurvivr/meta.yaml index 31ba885653b01..5740b2ada82cb 100644 --- a/recipes/bioconductor-gwasurvivr/meta.yaml +++ b/recipes/bioconductor-gwasurvivr/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.0.0" %} +{% set version = "1.2.0" %} {% set name = "gwasurvivr" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,9 +10,9 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 0ac5d680b32b6c05cd5774b9691580bd + md5: 4903756809691e97955b79d0f185aa1f build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ @@ -20,18 +20,18 @@ build: # Suggests: BiocStyle, knitr, rmarkdown requirements: host: - - 'bioconductor-gwastools >=1.28.0,<1.29.0' - - 'bioconductor-snprelate >=1.16.0,<1.17.0' - - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' - - 'bioconductor-variantannotation >=1.28.0,<1.29.0' + - 'bioconductor-gwastools >=1.30.0,<1.31.0' + - 'bioconductor-snprelate >=1.18.0,<1.19.0' + - 'bioconductor-summarizedexperiment >=1.14.0,<1.15.0' + - 'bioconductor-variantannotation >=1.30.0,<1.31.0' - r-base - r-matrixstats - r-survival run: - - 'bioconductor-gwastools >=1.28.0,<1.29.0' - - 'bioconductor-snprelate >=1.16.0,<1.17.0' - - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' - - 'bioconductor-variantannotation >=1.28.0,<1.29.0' + - 'bioconductor-gwastools >=1.30.0,<1.31.0' + - 'bioconductor-snprelate >=1.18.0,<1.19.0' + - 'bioconductor-summarizedexperiment >=1.14.0,<1.15.0' + - 'bioconductor-variantannotation >=1.30.0,<1.31.0' - r-base - r-matrixstats - r-survival diff --git a/recipes/bioconductor-h10kcod.db/meta.yaml b/recipes/bioconductor-h10kcod.db/meta.yaml index 6b8a19a1dcb53..20ee9880ea60b 100644 --- a/recipes/bioconductor-h10kcod.db/meta.yaml +++ b/recipes/bioconductor-h10kcod.db/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.4.0" %} {% set name = "h10kcod.db" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -12,7 +12,7 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: a555739cea229f286953c3297c145e9c build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ @@ -20,14 +20,14 @@ build: # Suggests: annotate, RUnit requirements: host: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' - - 'bioconductor-org.hs.eg.db >=3.7.0,<3.8.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' + - 'bioconductor-org.hs.eg.db >=3.8.0,<3.9.0' - r-base run: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' - - 'bioconductor-org.hs.eg.db >=3.7.0,<3.8.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' + - 'bioconductor-org.hs.eg.db >=3.8.0,<3.9.0' - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-h10kcod.db/post-link.sh b/recipes/bioconductor-h10kcod.db/post-link.sh index ba6e431eb3155..434786251e1c4 100644 --- a/recipes/bioconductor-h10kcod.db/post-link.sh +++ b/recipes/bioconductor-h10kcod.db/post-link.sh @@ -1,9 +1,10 @@ #!/bin/bash FN="h10kcod.db_3.4.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/h10kcod.db_3.4.0.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/h10kcod.db_3.4.0.tar.gz" "https://bioarchive.galaxyproject.org/h10kcod.db_3.4.0.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-h10kcod.db/bioconductor-h10kcod.db_3.4.0_src_all.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-h10kcod.db/bioconductor-h10kcod.db_3.4.0_src_all.tar.gz" ) MD5="a555739cea229f286953c3297c145e9c" @@ -16,7 +17,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-h20kcod.db/meta.yaml b/recipes/bioconductor-h20kcod.db/meta.yaml index 311c2bd019deb..95900259f9f71 100644 --- a/recipes/bioconductor-h20kcod.db/meta.yaml +++ b/recipes/bioconductor-h20kcod.db/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.4.0" %} {% set name = "h20kcod.db" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -12,7 +12,7 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 3647facb272f58424f4c94ef92e8ee45 build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ @@ -20,14 +20,14 @@ build: # Suggests: annotate, RUnit requirements: host: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' - - 'bioconductor-org.hs.eg.db >=3.7.0,<3.8.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' + - 'bioconductor-org.hs.eg.db >=3.8.0,<3.9.0' - r-base run: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' - - 'bioconductor-org.hs.eg.db >=3.7.0,<3.8.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' + - 'bioconductor-org.hs.eg.db >=3.8.0,<3.9.0' - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-h20kcod.db/post-link.sh b/recipes/bioconductor-h20kcod.db/post-link.sh index 1abaa82214930..f8989bc2cb3ea 100644 --- a/recipes/bioconductor-h20kcod.db/post-link.sh +++ b/recipes/bioconductor-h20kcod.db/post-link.sh @@ -1,9 +1,10 @@ #!/bin/bash FN="h20kcod.db_3.4.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/h20kcod.db_3.4.0.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/h20kcod.db_3.4.0.tar.gz" "https://bioarchive.galaxyproject.org/h20kcod.db_3.4.0.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-h20kcod.db/bioconductor-h20kcod.db_3.4.0_src_all.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-h20kcod.db/bioconductor-h20kcod.db_3.4.0_src_all.tar.gz" ) MD5="3647facb272f58424f4c94ef92e8ee45" @@ -16,7 +17,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-h5vc/meta.yaml b/recipes/bioconductor-h5vc/meta.yaml index ac47fe485d691..d5ba7d1dd357c 100644 --- a/recipes/bioconductor-h5vc/meta.yaml +++ b/recipes/bioconductor-h5vc/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "2.16.0" %} +{% set version = "2.18.0" %} {% set name = "h5vc" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: eb32bc8bba6b5a375da0738e0b28c392 + md5: 7e2c123b13cf7d854810bb8e47c93e8a build: number: 0 rpaths: @@ -19,15 +19,16 @@ build: # Suggests: knitr, locfit, BSgenome.Hsapiens.UCSC.hg19, biomaRt, BSgenome.Hsapiens.NCBI.GRCh38, RUnit, BiocGenerics requirements: host: - - 'bioconductor-biocparallel >=1.16.0,<1.17.0' - - 'bioconductor-biostrings >=2.50.0,<2.51.0' - - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' - - 'bioconductor-genomicranges >=1.34.0,<1.35.0' - - 'bioconductor-h5vcdata >=2.2.0,<2.3.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-rhdf5 >=2.26.0,<2.27.0' - - 'bioconductor-rsamtools >=1.34.0,<1.35.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-biocparallel >=1.18.0,<1.19.0' + - 'bioconductor-biostrings >=2.52.0,<2.53.0' + - 'bioconductor-genomeinfodb >=1.20.0,<1.21.0' + - 'bioconductor-genomicranges >=1.36.0,<1.37.0' + - 'bioconductor-h5vcdata >=2.4.0,<2.5.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-rhdf5 >=2.28.0,<2.29.0' + - 'bioconductor-rhtslib >=1.16.0,<1.17.0' + - 'bioconductor-rsamtools >=2.0.0,<2.1.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' - r-abind - r-base - r-batchjobs @@ -35,15 +36,16 @@ requirements: - r-gridextra - r-reshape run: - - 'bioconductor-biocparallel >=1.16.0,<1.17.0' - - 'bioconductor-biostrings >=2.50.0,<2.51.0' - - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' - - 'bioconductor-genomicranges >=1.34.0,<1.35.0' - - 'bioconductor-h5vcdata >=2.2.0,<2.3.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-rhdf5 >=2.26.0,<2.27.0' - - 'bioconductor-rsamtools >=1.34.0,<1.35.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-biocparallel >=1.18.0,<1.19.0' + - 'bioconductor-biostrings >=2.52.0,<2.53.0' + - 'bioconductor-genomeinfodb >=1.20.0,<1.21.0' + - 'bioconductor-genomicranges >=1.36.0,<1.37.0' + - 'bioconductor-h5vcdata >=2.4.0,<2.5.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-rhdf5 >=2.28.0,<2.29.0' + - 'bioconductor-rhtslib >=1.16.0,<1.17.0' + - 'bioconductor-rsamtools >=2.0.0,<2.1.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' - r-abind - r-base - r-batchjobs diff --git a/recipes/bioconductor-h5vcdata/meta.yaml b/recipes/bioconductor-h5vcdata/meta.yaml index 955d5c0a49126..e4cc241e9dae1 100644 --- a/recipes/bioconductor-h5vcdata/meta.yaml +++ b/recipes/bioconductor-h5vcdata/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "2.2.0" %} +{% set version = "2.4.0" %} {% set name = "h5vcData" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: dafde62ac2fd221e41398ba6b3d6ccc2 + md5: cd3b929b2cde6716aa26ffd790f350da build: number: 0 rpaths: @@ -23,7 +23,7 @@ requirements: - r-base run: - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-h5vcdata/post-link.sh b/recipes/bioconductor-h5vcdata/post-link.sh index a40bf2bc1dc41..2cece8d586fde 100644 --- a/recipes/bioconductor-h5vcdata/post-link.sh +++ b/recipes/bioconductor-h5vcdata/post-link.sh @@ -1,11 +1,11 @@ #!/bin/bash -FN="h5vcData_2.2.0.tar.gz" +FN="h5vcData_2.4.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/experiment/src/contrib/h5vcData_2.2.0.tar.gz" - "https://bioarchive.galaxyproject.org/h5vcData_2.2.0.tar.gz" - "https://depot.galaxyproject.org/software/bioconductor-h5vcdata/bioconductor-h5vcdata_2.2.0_src_all.tar.gz" + "https://bioconductor.org/packages/3.9/data/experiment/src/contrib/h5vcData_2.4.0.tar.gz" + "https://bioarchive.galaxyproject.org/h5vcData_2.4.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-h5vcdata/bioconductor-h5vcdata_2.4.0_src_all.tar.gz" ) -MD5="dafde62ac2fd221e41398ba6b3d6ccc2" +MD5="cd3b929b2cde6716aa26ffd790f350da" # Use a staging area in the conda dir rather than temp dirs, both to avoid # permission issues as well as to have things downloaded in a predictable @@ -16,7 +16,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-hapfabia/meta.yaml b/recipes/bioconductor-hapfabia/meta.yaml index f56720413d01f..bef86b5387f66 100644 --- a/recipes/bioconductor-hapfabia/meta.yaml +++ b/recipes/bioconductor-hapfabia/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.24.0" %} +{% set version = "1.26.0" %} {% set name = "hapFabia" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,20 +10,20 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: acb38ecfda83a4ce592621b4fa13583c + md5: a63686618465f59c0545d0b36c51f238 build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ requirements: host: - - 'bioconductor-biobase >=2.42.0,<2.43.0' - - 'bioconductor-fabia >=2.28.0,<2.29.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' + - 'bioconductor-fabia >=2.30.0,<2.31.0' - r-base run: - - 'bioconductor-biobase >=2.42.0,<2.43.0' - - 'bioconductor-fabia >=2.28.0,<2.29.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' + - 'bioconductor-fabia >=2.30.0,<2.31.0' - r-base build: - {{ compiler('c') }} diff --git a/recipes/bioconductor-hapmap100khind/meta.yaml b/recipes/bioconductor-hapmap100khind/meta.yaml index d5c168ea556f9..cd8d675b95d9f 100644 --- a/recipes/bioconductor-hapmap100khind/meta.yaml +++ b/recipes/bioconductor-hapmap100khind/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.24.0" %} +{% set version = "1.26.0" %} {% set name = "hapmap100khind" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 41f5b3455328c928df5b6ae2d81e7c8b + md5: a5072491e91e762e1ec95fe998413f77 build: number: 0 rpaths: @@ -23,7 +23,7 @@ requirements: - r-base run: - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-hapmap100khind/post-link.sh b/recipes/bioconductor-hapmap100khind/post-link.sh index 619467b249cd0..07e4fa2242bac 100644 --- a/recipes/bioconductor-hapmap100khind/post-link.sh +++ b/recipes/bioconductor-hapmap100khind/post-link.sh @@ -1,11 +1,11 @@ #!/bin/bash -FN="hapmap100khind_1.24.0.tar.gz" +FN="hapmap100khind_1.26.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/experiment/src/contrib/hapmap100khind_1.24.0.tar.gz" - "https://bioarchive.galaxyproject.org/hapmap100khind_1.24.0.tar.gz" - "https://depot.galaxyproject.org/software/bioconductor-hapmap100khind/bioconductor-hapmap100khind_1.24.0_src_all.tar.gz" + "https://bioconductor.org/packages/3.9/data/experiment/src/contrib/hapmap100khind_1.26.0.tar.gz" + "https://bioarchive.galaxyproject.org/hapmap100khind_1.26.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-hapmap100khind/bioconductor-hapmap100khind_1.26.0_src_all.tar.gz" ) -MD5="41f5b3455328c928df5b6ae2d81e7c8b" +MD5="a5072491e91e762e1ec95fe998413f77" # Use a staging area in the conda dir rather than temp dirs, both to avoid # permission issues as well as to have things downloaded in a predictable @@ -16,7 +16,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-hapmap100kxba/meta.yaml b/recipes/bioconductor-hapmap100kxba/meta.yaml index 9a276dae13bcb..50b5e6e2ef567 100644 --- a/recipes/bioconductor-hapmap100kxba/meta.yaml +++ b/recipes/bioconductor-hapmap100kxba/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.24.0" %} +{% set version = "1.26.0" %} {% set name = "hapmap100kxba" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: a1d77e1d940c42e5b253d8517a29f414 + md5: 11ec72b847b929a9697461cb7143ecc1 build: number: 0 rpaths: @@ -23,7 +23,7 @@ requirements: - r-base run: - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-hapmap100kxba/post-link.sh b/recipes/bioconductor-hapmap100kxba/post-link.sh index f364bdf1da0b2..1fc0a8c7a6e24 100644 --- a/recipes/bioconductor-hapmap100kxba/post-link.sh +++ b/recipes/bioconductor-hapmap100kxba/post-link.sh @@ -1,11 +1,11 @@ #!/bin/bash -FN="hapmap100kxba_1.24.0.tar.gz" +FN="hapmap100kxba_1.26.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/experiment/src/contrib/hapmap100kxba_1.24.0.tar.gz" - "https://bioarchive.galaxyproject.org/hapmap100kxba_1.24.0.tar.gz" - "https://depot.galaxyproject.org/software/bioconductor-hapmap100kxba/bioconductor-hapmap100kxba_1.24.0_src_all.tar.gz" + "https://bioconductor.org/packages/3.9/data/experiment/src/contrib/hapmap100kxba_1.26.0.tar.gz" + "https://bioarchive.galaxyproject.org/hapmap100kxba_1.26.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-hapmap100kxba/bioconductor-hapmap100kxba_1.26.0_src_all.tar.gz" ) -MD5="a1d77e1d940c42e5b253d8517a29f414" +MD5="11ec72b847b929a9697461cb7143ecc1" # Use a staging area in the conda dir rather than temp dirs, both to avoid # permission issues as well as to have things downloaded in a predictable @@ -16,7 +16,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-hapmap370k/meta.yaml b/recipes/bioconductor-hapmap370k/meta.yaml index 7519e144a5a8e..d9dc9c910c6af 100644 --- a/recipes/bioconductor-hapmap370k/meta.yaml +++ b/recipes/bioconductor-hapmap370k/meta.yaml @@ -1,6 +1,6 @@ {% set version = "1.0.1" %} {% set name = "hapmap370k" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -12,7 +12,7 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 569556341a45da799372aaf1012be72e build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ @@ -23,7 +23,7 @@ requirements: - r-base run: - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-hapmap370k/post-link.sh b/recipes/bioconductor-hapmap370k/post-link.sh index 80834d45d096f..ef62790cfa35f 100644 --- a/recipes/bioconductor-hapmap370k/post-link.sh +++ b/recipes/bioconductor-hapmap370k/post-link.sh @@ -1,9 +1,10 @@ #!/bin/bash FN="hapmap370k_1.0.1.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/hapmap370k_1.0.1.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/hapmap370k_1.0.1.tar.gz" "https://bioarchive.galaxyproject.org/hapmap370k_1.0.1.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-hapmap370k/bioconductor-hapmap370k_1.0.1_src_all.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-hapmap370k/bioconductor-hapmap370k_1.0.1_src_all.tar.gz" ) MD5="569556341a45da799372aaf1012be72e" @@ -16,7 +17,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-hapmap500knsp/meta.yaml b/recipes/bioconductor-hapmap500knsp/meta.yaml index 3a5d299eba8f3..f4624fadd0967 100644 --- a/recipes/bioconductor-hapmap500knsp/meta.yaml +++ b/recipes/bioconductor-hapmap500knsp/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.24.0" %} +{% set version = "1.26.0" %} {% set name = "hapmap500knsp" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 6a1ab68e668feec8e7388dbbd4308252 + md5: c78f3012d3aee6bcfe793a7f14cdac6d build: number: 0 rpaths: @@ -23,7 +23,7 @@ requirements: - r-base run: - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-hapmap500knsp/post-link.sh b/recipes/bioconductor-hapmap500knsp/post-link.sh index 4d5b1128e8e69..b9531c5050153 100644 --- a/recipes/bioconductor-hapmap500knsp/post-link.sh +++ b/recipes/bioconductor-hapmap500knsp/post-link.sh @@ -1,11 +1,11 @@ #!/bin/bash -FN="hapmap500knsp_1.24.0.tar.gz" +FN="hapmap500knsp_1.26.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/experiment/src/contrib/hapmap500knsp_1.24.0.tar.gz" - "https://bioarchive.galaxyproject.org/hapmap500knsp_1.24.0.tar.gz" - "https://depot.galaxyproject.org/software/bioconductor-hapmap500knsp/bioconductor-hapmap500knsp_1.24.0_src_all.tar.gz" + "https://bioconductor.org/packages/3.9/data/experiment/src/contrib/hapmap500knsp_1.26.0.tar.gz" + "https://bioarchive.galaxyproject.org/hapmap500knsp_1.26.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-hapmap500knsp/bioconductor-hapmap500knsp_1.26.0_src_all.tar.gz" ) -MD5="6a1ab68e668feec8e7388dbbd4308252" +MD5="c78f3012d3aee6bcfe793a7f14cdac6d" # Use a staging area in the conda dir rather than temp dirs, both to avoid # permission issues as well as to have things downloaded in a predictable @@ -16,7 +16,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-hapmap500ksty/meta.yaml b/recipes/bioconductor-hapmap500ksty/meta.yaml index 3840fe07119ca..8e8c231b0602d 100644 --- a/recipes/bioconductor-hapmap500ksty/meta.yaml +++ b/recipes/bioconductor-hapmap500ksty/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.24.0" %} +{% set version = "1.26.0" %} {% set name = "hapmap500ksty" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: b33d5168b902765a63c25a6f2dae66af + md5: c9c6bd3acf4e2ab7e7beb7ad6a9dbb8f build: number: 0 rpaths: @@ -23,7 +23,7 @@ requirements: - r-base run: - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-hapmap500ksty/post-link.sh b/recipes/bioconductor-hapmap500ksty/post-link.sh index 703ea68535d61..acc67c21fecde 100644 --- a/recipes/bioconductor-hapmap500ksty/post-link.sh +++ b/recipes/bioconductor-hapmap500ksty/post-link.sh @@ -1,11 +1,11 @@ #!/bin/bash -FN="hapmap500ksty_1.24.0.tar.gz" +FN="hapmap500ksty_1.26.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/experiment/src/contrib/hapmap500ksty_1.24.0.tar.gz" - "https://bioarchive.galaxyproject.org/hapmap500ksty_1.24.0.tar.gz" - "https://depot.galaxyproject.org/software/bioconductor-hapmap500ksty/bioconductor-hapmap500ksty_1.24.0_src_all.tar.gz" + "https://bioconductor.org/packages/3.9/data/experiment/src/contrib/hapmap500ksty_1.26.0.tar.gz" + "https://bioarchive.galaxyproject.org/hapmap500ksty_1.26.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-hapmap500ksty/bioconductor-hapmap500ksty_1.26.0_src_all.tar.gz" ) -MD5="b33d5168b902765a63c25a6f2dae66af" +MD5="c9c6bd3acf4e2ab7e7beb7ad6a9dbb8f" # Use a staging area in the conda dir rather than temp dirs, both to avoid # permission issues as well as to have things downloaded in a predictable @@ -16,7 +16,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-hapmapsnp5/meta.yaml b/recipes/bioconductor-hapmapsnp5/meta.yaml index b0e88eb647892..6ba56c04140aa 100644 --- a/recipes/bioconductor-hapmapsnp5/meta.yaml +++ b/recipes/bioconductor-hapmapsnp5/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.24.0" %} +{% set version = "1.26.0" %} {% set name = "hapmapsnp5" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 518ce21d478eb25e29ed81256154e6fe + md5: 0ca43c40b0ef668b56edefa059dead89 build: number: 0 rpaths: @@ -23,7 +23,7 @@ requirements: - r-base run: - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-hapmapsnp5/post-link.sh b/recipes/bioconductor-hapmapsnp5/post-link.sh index 57e9d1c90e23f..53787d9039f0f 100644 --- a/recipes/bioconductor-hapmapsnp5/post-link.sh +++ b/recipes/bioconductor-hapmapsnp5/post-link.sh @@ -1,11 +1,11 @@ #!/bin/bash -FN="hapmapsnp5_1.24.0.tar.gz" +FN="hapmapsnp5_1.26.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/experiment/src/contrib/hapmapsnp5_1.24.0.tar.gz" - "https://bioarchive.galaxyproject.org/hapmapsnp5_1.24.0.tar.gz" - "https://depot.galaxyproject.org/software/bioconductor-hapmapsnp5/bioconductor-hapmapsnp5_1.24.0_src_all.tar.gz" + "https://bioconductor.org/packages/3.9/data/experiment/src/contrib/hapmapsnp5_1.26.0.tar.gz" + "https://bioarchive.galaxyproject.org/hapmapsnp5_1.26.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-hapmapsnp5/bioconductor-hapmapsnp5_1.26.0_src_all.tar.gz" ) -MD5="518ce21d478eb25e29ed81256154e6fe" +MD5="0ca43c40b0ef668b56edefa059dead89" # Use a staging area in the conda dir rather than temp dirs, both to avoid # permission issues as well as to have things downloaded in a predictable @@ -16,7 +16,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-hapmapsnp6/meta.yaml b/recipes/bioconductor-hapmapsnp6/meta.yaml index 3839692a18ed4..d2720f7a743c7 100644 --- a/recipes/bioconductor-hapmapsnp6/meta.yaml +++ b/recipes/bioconductor-hapmapsnp6/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.24.0" %} +{% set version = "1.26.0" %} {% set name = "hapmapsnp6" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 2d6a0cd7f337c99834d143215d74e787 + md5: df63dbabc0405f8f09ca76aecd6077b8 build: number: 0 rpaths: @@ -23,7 +23,7 @@ requirements: - r-base run: - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-hapmapsnp6/post-link.sh b/recipes/bioconductor-hapmapsnp6/post-link.sh index b9b29e242e5a0..87e3c80e1f98d 100644 --- a/recipes/bioconductor-hapmapsnp6/post-link.sh +++ b/recipes/bioconductor-hapmapsnp6/post-link.sh @@ -1,11 +1,11 @@ #!/bin/bash -FN="hapmapsnp6_1.24.0.tar.gz" +FN="hapmapsnp6_1.26.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/experiment/src/contrib/hapmapsnp6_1.24.0.tar.gz" - "https://bioarchive.galaxyproject.org/hapmapsnp6_1.24.0.tar.gz" - "https://depot.galaxyproject.org/software/bioconductor-hapmapsnp6/bioconductor-hapmapsnp6_1.24.0_src_all.tar.gz" + "https://bioconductor.org/packages/3.9/data/experiment/src/contrib/hapmapsnp6_1.26.0.tar.gz" + "https://bioarchive.galaxyproject.org/hapmapsnp6_1.26.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-hapmapsnp6/bioconductor-hapmapsnp6_1.26.0_src_all.tar.gz" ) -MD5="2d6a0cd7f337c99834d143215d74e787" +MD5="df63dbabc0405f8f09ca76aecd6077b8" # Use a staging area in the conda dir rather than temp dirs, both to avoid # permission issues as well as to have things downloaded in a predictable @@ -16,7 +16,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-harbchip/meta.yaml b/recipes/bioconductor-harbchip/meta.yaml index f543b485b637d..e454d946ef47a 100644 --- a/recipes/bioconductor-harbchip/meta.yaml +++ b/recipes/bioconductor-harbchip/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.20.0" %} +{% set version = "1.22.0" %} {% set name = "harbChIP" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 2dedda8ec8b79f7cd73648090853a31a + md5: 8b019087317d308012e39effa61094d7 build: number: 0 rpaths: @@ -19,16 +19,16 @@ build: noarch: generic requirements: host: - - 'bioconductor-biobase >=2.42.0,<2.43.0' - - 'bioconductor-biostrings >=2.50.0,<2.51.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' + - 'bioconductor-biostrings >=2.52.0,<2.53.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' - r-base run: - - 'bioconductor-biobase >=2.42.0,<2.43.0' - - 'bioconductor-biostrings >=2.50.0,<2.51.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' + - 'bioconductor-biostrings >=2.52.0,<2.53.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-harbchip/post-link.sh b/recipes/bioconductor-harbchip/post-link.sh index df3db69385dc5..f79b89f0c40ab 100644 --- a/recipes/bioconductor-harbchip/post-link.sh +++ b/recipes/bioconductor-harbchip/post-link.sh @@ -1,11 +1,11 @@ #!/bin/bash -FN="harbChIP_1.20.0.tar.gz" +FN="harbChIP_1.22.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/experiment/src/contrib/harbChIP_1.20.0.tar.gz" - "https://bioarchive.galaxyproject.org/harbChIP_1.20.0.tar.gz" - "https://depot.galaxyproject.org/software/bioconductor-harbchip/bioconductor-harbchip_1.20.0_src_all.tar.gz" + "https://bioconductor.org/packages/3.9/data/experiment/src/contrib/harbChIP_1.22.0.tar.gz" + "https://bioarchive.galaxyproject.org/harbChIP_1.22.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-harbchip/bioconductor-harbchip_1.22.0_src_all.tar.gz" ) -MD5="2dedda8ec8b79f7cd73648090853a31a" +MD5="8b019087317d308012e39effa61094d7" # Use a staging area in the conda dir rather than temp dirs, both to avoid # permission issues as well as to have things downloaded in a predictable @@ -16,7 +16,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-harman/meta.yaml b/recipes/bioconductor-harman/meta.yaml index 4646a05819a16..48c0525518381 100644 --- a/recipes/bioconductor-harman/meta.yaml +++ b/recipes/bioconductor-harman/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.10.0" %} +{% set version = "1.12.0" %} {% set name = "Harman" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: d93baf47bf61f0f0fb45d0a06e0e797a + md5: 52cf3b3f74e74865d98703cb842681aa build: number: 0 rpaths: diff --git a/recipes/bioconductor-harmandata/meta.yaml b/recipes/bioconductor-harmandata/meta.yaml index 8d0f532d842e8..e41a8df09b8fd 100644 --- a/recipes/bioconductor-harmandata/meta.yaml +++ b/recipes/bioconductor-harmandata/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.10.0" %} +{% set version = "1.12.0" %} {% set name = "HarmanData" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 527bf6823b7a6135e7c04b0031c8c486 + md5: e556ea2db6907201425241a1251c4149 build: number: 0 rpaths: @@ -23,7 +23,7 @@ requirements: - r-base run: - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-harmandata/post-link.sh b/recipes/bioconductor-harmandata/post-link.sh index 34b56f0f21f43..bec9c3d7f096d 100644 --- a/recipes/bioconductor-harmandata/post-link.sh +++ b/recipes/bioconductor-harmandata/post-link.sh @@ -1,11 +1,11 @@ #!/bin/bash -FN="HarmanData_1.10.0.tar.gz" +FN="HarmanData_1.12.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/experiment/src/contrib/HarmanData_1.10.0.tar.gz" - "https://bioarchive.galaxyproject.org/HarmanData_1.10.0.tar.gz" - "https://depot.galaxyproject.org/software/bioconductor-harmandata/bioconductor-harmandata_1.10.0_src_all.tar.gz" + "https://bioconductor.org/packages/3.9/data/experiment/src/contrib/HarmanData_1.12.0.tar.gz" + "https://bioarchive.galaxyproject.org/HarmanData_1.12.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-harmandata/bioconductor-harmandata_1.12.0_src_all.tar.gz" ) -MD5="527bf6823b7a6135e7c04b0031c8c486" +MD5="e556ea2db6907201425241a1251c4149" # Use a staging area in the conda dir rather than temp dirs, both to avoid # permission issues as well as to have things downloaded in a predictable @@ -16,7 +16,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-harmonizedtcgadata/meta.yaml b/recipes/bioconductor-harmonizedtcgadata/meta.yaml index 0dbfbe1131337..e0ac3b27527e3 100644 --- a/recipes/bioconductor-harmonizedtcgadata/meta.yaml +++ b/recipes/bioconductor-harmonizedtcgadata/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.4.0" %} +{% set version = "1.6.0" %} {% set name = "HarmonizedTCGAData" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 064823184770359197455c835096eacb + md5: 90382d0b019354adb9ec7253737a1a5b build: number: 0 rpaths: @@ -20,12 +20,12 @@ build: # Suggests: AnnotationHub, knitr, rmarkdown, igraph, survival, ANF, stats, testthat requirements: host: - - 'bioconductor-experimenthub >=1.8.0,<1.9.0' + - 'bioconductor-experimenthub >=1.10.0,<1.11.0' - r-base run: - - 'bioconductor-experimenthub >=1.8.0,<1.9.0' + - 'bioconductor-experimenthub >=1.10.0,<1.11.0' - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-harmonizedtcgadata/post-link.sh b/recipes/bioconductor-harmonizedtcgadata/post-link.sh index 699358eed7cc5..72dace4128e8c 100644 --- a/recipes/bioconductor-harmonizedtcgadata/post-link.sh +++ b/recipes/bioconductor-harmonizedtcgadata/post-link.sh @@ -1,11 +1,11 @@ #!/bin/bash -FN="HarmonizedTCGAData_1.4.0.tar.gz" +FN="HarmonizedTCGAData_1.6.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/experiment/src/contrib/HarmonizedTCGAData_1.4.0.tar.gz" - "https://bioarchive.galaxyproject.org/HarmonizedTCGAData_1.4.0.tar.gz" - "https://depot.galaxyproject.org/software/bioconductor-harmonizedtcgadata/bioconductor-harmonizedtcgadata_1.4.0_src_all.tar.gz" + "https://bioconductor.org/packages/3.9/data/experiment/src/contrib/HarmonizedTCGAData_1.6.0.tar.gz" + "https://bioarchive.galaxyproject.org/HarmonizedTCGAData_1.6.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-harmonizedtcgadata/bioconductor-harmonizedtcgadata_1.6.0_src_all.tar.gz" ) -MD5="064823184770359197455c835096eacb" +MD5="90382d0b019354adb9ec7253737a1a5b" # Use a staging area in the conda dir rather than temp dirs, both to avoid # permission issues as well as to have things downloaded in a predictable @@ -16,7 +16,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-harshlight/meta.yaml b/recipes/bioconductor-harshlight/meta.yaml index 76d45f5a4d222..c4074476a0676 100644 --- a/recipes/bioconductor-harshlight/meta.yaml +++ b/recipes/bioconductor-harshlight/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.54.0" %} +{% set version = "1.56.0" %} {% set name = "Harshlight" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 001fce5a89c331b48513365b01adceb5 + md5: fd903a7f83459d6bf07f5ee37b2b606e build: number: 0 rpaths: @@ -18,14 +18,14 @@ build: - lib/ requirements: host: - - 'bioconductor-affy >=1.60.0,<1.61.0' - - 'bioconductor-altcdfenvs >=2.44.0,<2.45.0' - - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-affy >=1.62.0,<1.63.0' + - 'bioconductor-altcdfenvs >=2.46.0,<2.47.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' - r-base run: - - 'bioconductor-affy >=1.60.0,<1.61.0' - - 'bioconductor-altcdfenvs >=2.44.0,<2.45.0' - - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-affy >=1.62.0,<1.63.0' + - 'bioconductor-altcdfenvs >=2.46.0,<2.47.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' - r-base build: - {{ compiler('c') }} diff --git a/recipes/bioconductor-hcabrowser/build.sh b/recipes/bioconductor-hcabrowser/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-hcabrowser/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-hcabrowser/meta.yaml b/recipes/bioconductor-hcabrowser/meta.yaml new file mode 100644 index 0000000000000..8bbce04fcc437 --- /dev/null +++ b/recipes/bioconductor-hcabrowser/meta.yaml @@ -0,0 +1,59 @@ +{% set version = "1.0.0" %} +{% set name = "HCABrowser" %} +{% set bioc = "3.9" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: d8001d23d6f8fb7c2f812eda0120ed19 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: BiocStyle, knitr, rmarkdown, testthat +requirements: + host: + - 'bioconductor-biocfilecache >=1.8.0,<1.9.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' + - r-base + - r-dplyr + - r-googleauthr + - r-httr + - r-jsonlite + - r-plyr + - r-readr + - r-rlang + - r-stringr + - r-tibble + - r-tidygraph + - r-tidyr + run: + - 'bioconductor-biocfilecache >=1.8.0,<1.9.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' + - r-base + - r-dplyr + - r-googleauthr + - r-httr + - r-jsonlite + - r-plyr + - r-readr + - r-rlang + - r-stringr + - r-tibble + - r-tidygraph + - r-tidyr +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'Search, browse, reference, and download resources from the Human Cell Atlas data portal. Development of this package is supported through funds from the Chan / Zuckerberg initiative.' + diff --git a/recipes/bioconductor-hcadata/meta.yaml b/recipes/bioconductor-hcadata/meta.yaml new file mode 100644 index 0000000000000..a7a805cc10f0e --- /dev/null +++ b/recipes/bioconductor-hcadata/meta.yaml @@ -0,0 +1,42 @@ +{% set version = "1.0.0" %} +{% set name = "HCAData" %} +{% set bioc = "3.9" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: 1a28dbab85f7d88dc4d525dbdb7f6757 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: knitr, rmarkdown, BiocStyle, scran (>= 1.11.4), scater, igraph, iSEE, testthat +requirements: + host: + - 'bioconductor-annotationhub >=2.16.0,<2.17.0' + - 'bioconductor-experimenthub >=1.10.0,<1.11.0' + - 'bioconductor-hdf5array >=1.12.0,<1.13.0' + - 'bioconductor-singlecellexperiment >=1.6.0,<1.7.0' + - r-base + run: + - 'bioconductor-annotationhub >=2.16.0,<2.17.0' + - 'bioconductor-experimenthub >=1.10.0,<1.11.0' + - 'bioconductor-hdf5array >=1.12.0,<1.13.0' + - 'bioconductor-singlecellexperiment >=1.6.0,<1.7.0' + - r-base + - curl +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html' + license: 'MIT + file LICENSE' + summary: 'This package allows a direct access to the dataset generated by the Human Cell Atlas project for further processing in R and Bioconductor, in the comfortable format of SingleCellExperiment objects (available in other formats here: http://preview.data.humancellatlas.org/).' + diff --git a/recipes/bioconductor-hcadata/post-link.sh b/recipes/bioconductor-hcadata/post-link.sh new file mode 100644 index 0000000000000..d49c5478671ef --- /dev/null +++ b/recipes/bioconductor-hcadata/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="HCAData_1.0.0.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.9/data/experiment/src/contrib/HCAData_1.0.0.tar.gz" + "https://bioarchive.galaxyproject.org/HCAData_1.0.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-hcadata/bioconductor-hcadata_1.0.0_src_all.tar.gz" +) +MD5="1a28dbab85f7d88dc4d525dbdb7f6757" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + curl $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-hcadata/pre-unlink.sh b/recipes/bioconductor-hcadata/pre-unlink.sh new file mode 100644 index 0000000000000..ba1c71de6f78a --- /dev/null +++ b/recipes/bioconductor-hcadata/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ HCAData diff --git a/recipes/bioconductor-hcg110.db/meta.yaml b/recipes/bioconductor-hcg110.db/meta.yaml index a942dcd5db612..879cb2893bc57 100644 --- a/recipes/bioconductor-hcg110.db/meta.yaml +++ b/recipes/bioconductor-hcg110.db/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.2.3" %} {% set name = "hcg110.db" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -12,7 +12,7 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: eaba09d7e88bb913fd18f4e8fb72760b build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ @@ -20,14 +20,14 @@ build: # Suggests: DBI, annotate, RUnit requirements: host: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' - - 'bioconductor-org.hs.eg.db >=3.7.0,<3.8.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' + - 'bioconductor-org.hs.eg.db >=3.8.0,<3.9.0' - r-base run: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' - - 'bioconductor-org.hs.eg.db >=3.7.0,<3.8.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' + - 'bioconductor-org.hs.eg.db >=3.8.0,<3.9.0' - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-hcg110.db/post-link.sh b/recipes/bioconductor-hcg110.db/post-link.sh index a24675cd72d0f..8600ce5e705e8 100644 --- a/recipes/bioconductor-hcg110.db/post-link.sh +++ b/recipes/bioconductor-hcg110.db/post-link.sh @@ -1,9 +1,10 @@ #!/bin/bash FN="hcg110.db_3.2.3.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/hcg110.db_3.2.3.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/hcg110.db_3.2.3.tar.gz" "https://bioarchive.galaxyproject.org/hcg110.db_3.2.3.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-hcg110.db/bioconductor-hcg110.db_3.2.3_src_all.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-hcg110.db/bioconductor-hcg110.db_3.2.3_src_all.tar.gz" ) MD5="eaba09d7e88bb913fd18f4e8fb72760b" @@ -16,7 +17,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-hcg110cdf/meta.yaml b/recipes/bioconductor-hcg110cdf/meta.yaml index e6b5f49f6a236..4d6cb7a00a5d4 100644 --- a/recipes/bioconductor-hcg110cdf/meta.yaml +++ b/recipes/bioconductor-hcg110cdf/meta.yaml @@ -1,6 +1,6 @@ {% set version = "2.18.0" %} {% set name = "hcg110cdf" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -12,19 +12,19 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: b53167876217ddb301204719da23eafc build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' - r-base run: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-hcg110cdf/post-link.sh b/recipes/bioconductor-hcg110cdf/post-link.sh index bf76d5ea69451..4d38643aef8e4 100644 --- a/recipes/bioconductor-hcg110cdf/post-link.sh +++ b/recipes/bioconductor-hcg110cdf/post-link.sh @@ -1,9 +1,10 @@ #!/bin/bash FN="hcg110cdf_2.18.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/hcg110cdf_2.18.0.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/hcg110cdf_2.18.0.tar.gz" "https://bioarchive.galaxyproject.org/hcg110cdf_2.18.0.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-hcg110cdf/bioconductor-hcg110cdf_2.18.0_src_all.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-hcg110cdf/bioconductor-hcg110cdf_2.18.0_src_all.tar.gz" ) MD5="b53167876217ddb301204719da23eafc" @@ -16,7 +17,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-hcg110probe/meta.yaml b/recipes/bioconductor-hcg110probe/meta.yaml index 7926b07ad427b..f05eaa16db855 100644 --- a/recipes/bioconductor-hcg110probe/meta.yaml +++ b/recipes/bioconductor-hcg110probe/meta.yaml @@ -1,6 +1,6 @@ {% set version = "2.18.0" %} {% set name = "hcg110probe" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -12,19 +12,19 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 51af8d6a7090ea7c5fe630dcea68bfb3 build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' - r-base run: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-hcg110probe/post-link.sh b/recipes/bioconductor-hcg110probe/post-link.sh index ddc19382b9f5e..d2b4ead34bb81 100644 --- a/recipes/bioconductor-hcg110probe/post-link.sh +++ b/recipes/bioconductor-hcg110probe/post-link.sh @@ -1,9 +1,10 @@ #!/bin/bash FN="hcg110probe_2.18.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/hcg110probe_2.18.0.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/hcg110probe_2.18.0.tar.gz" "https://bioarchive.galaxyproject.org/hcg110probe_2.18.0.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-hcg110probe/bioconductor-hcg110probe_2.18.0_src_all.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-hcg110probe/bioconductor-hcg110probe_2.18.0_src_all.tar.gz" ) MD5="51af8d6a7090ea7c5fe630dcea68bfb3" @@ -16,7 +17,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-hd2013sgi/meta.yaml b/recipes/bioconductor-hd2013sgi/meta.yaml index f4406aa4489f0..63399d9d547bd 100644 --- a/recipes/bioconductor-hd2013sgi/meta.yaml +++ b/recipes/bioconductor-hd2013sgi/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.22.0" %} +{% set version = "1.24.0" %} {% set name = "HD2013SGI" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: e67f8f961700314d6ba0326dfebb0e3b + md5: bc5df4cfc33cf00def4c05aa6f6d78c9 build: number: 0 rpaths: @@ -21,26 +21,26 @@ build: # SystemRequirements: GNU make requirements: host: - - 'bioconductor-ebimage >=4.24.0,<4.25.0' - - 'bioconductor-geneplotter >=1.60.0,<1.61.0' - - 'bioconductor-limma >=3.38.0,<3.39.0' - - 'bioconductor-splots >=1.48.0,<1.49.0' + - 'bioconductor-ebimage >=4.26.0,<4.27.0' + - 'bioconductor-geneplotter >=1.62.0,<1.63.0' + - 'bioconductor-limma >=3.40.0,<3.41.0' + - 'bioconductor-splots >=1.50.0,<1.51.0' - r-base - r-gplots - r-lsd - r-rcolorbrewer - r-vcd run: - - 'bioconductor-ebimage >=4.24.0,<4.25.0' - - 'bioconductor-geneplotter >=1.60.0,<1.61.0' - - 'bioconductor-limma >=3.38.0,<3.39.0' - - 'bioconductor-splots >=1.48.0,<1.49.0' + - 'bioconductor-ebimage >=4.26.0,<4.27.0' + - 'bioconductor-geneplotter >=1.62.0,<1.63.0' + - 'bioconductor-limma >=3.40.0,<3.41.0' + - 'bioconductor-splots >=1.50.0,<1.51.0' - r-base - r-gplots - r-lsd - r-rcolorbrewer - r-vcd - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-hd2013sgi/post-link.sh b/recipes/bioconductor-hd2013sgi/post-link.sh index 3d0380bb26f2a..ae838e3479cfc 100644 --- a/recipes/bioconductor-hd2013sgi/post-link.sh +++ b/recipes/bioconductor-hd2013sgi/post-link.sh @@ -1,11 +1,11 @@ #!/bin/bash -FN="HD2013SGI_1.22.0.tar.gz" +FN="HD2013SGI_1.24.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/experiment/src/contrib/HD2013SGI_1.22.0.tar.gz" - "https://bioarchive.galaxyproject.org/HD2013SGI_1.22.0.tar.gz" - "https://depot.galaxyproject.org/software/bioconductor-hd2013sgi/bioconductor-hd2013sgi_1.22.0_src_all.tar.gz" + "https://bioconductor.org/packages/3.9/data/experiment/src/contrib/HD2013SGI_1.24.0.tar.gz" + "https://bioarchive.galaxyproject.org/HD2013SGI_1.24.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-hd2013sgi/bioconductor-hd2013sgi_1.24.0_src_all.tar.gz" ) -MD5="e67f8f961700314d6ba0326dfebb0e3b" +MD5="bc5df4cfc33cf00def4c05aa6f6d78c9" # Use a staging area in the conda dir rather than temp dirs, both to avoid # permission issues as well as to have things downloaded in a predictable @@ -16,7 +16,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-hdcytodata/meta.yaml b/recipes/bioconductor-hdcytodata/meta.yaml index 26505e6aee0c0..fffc98c53111d 100644 --- a/recipes/bioconductor-hdcytodata/meta.yaml +++ b/recipes/bioconductor-hdcytodata/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.2.1" %} +{% set version = "1.4.0" %} {% set name = "HDCytoData" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,31 +10,31 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 052694707ec8c44941417dc44e112d5a + md5: 7e6294543c192c0a089c6eb1c6c406ce build: number: 0 rpaths: - lib/R/lib/ - lib/ noarch: generic -# Suggests: BiocStyle, knitr, rmarkdown, FlowSOM, Rtsne, ggplot2 +# Suggests: BiocStyle, knitr, rmarkdown requirements: host: - - 'bioconductor-experimenthub >=1.8.0,<1.9.0' - - 'bioconductor-flowcore >=1.48.0,<1.49.0' - - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' + - 'bioconductor-experimenthub >=1.10.0,<1.11.0' + - 'bioconductor-flowcore >=1.50.0,<1.51.0' + - 'bioconductor-summarizedexperiment >=1.14.0,<1.15.0' - r-base run: - - 'bioconductor-experimenthub >=1.8.0,<1.9.0' - - 'bioconductor-flowcore >=1.48.0,<1.49.0' - - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' + - 'bioconductor-experimenthub >=1.10.0,<1.11.0' + - 'bioconductor-flowcore >=1.50.0,<1.51.0' + - 'bioconductor-summarizedexperiment >=1.14.0,<1.15.0' - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' about: home: 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html' license: 'MIT + file LICENSE' - summary: 'Data package containing a set of high-dimensional cytometry datasets saved in SummarizedExperiment and flowSet Bioconductor object formats, including row and column metadata describing samples, cell populations (clusters), and protein markers.' + summary: 'Data package containing a collection of high-dimensional cytometry benchmark datasets saved in SummarizedExperiment and flowSet Bioconductor object formats, including row and column metadata describing samples, cell populations (clusters), and protein markers.' diff --git a/recipes/bioconductor-hdcytodata/post-link.sh b/recipes/bioconductor-hdcytodata/post-link.sh index bbed9f230a3d8..a06d6ffa0a028 100644 --- a/recipes/bioconductor-hdcytodata/post-link.sh +++ b/recipes/bioconductor-hdcytodata/post-link.sh @@ -1,11 +1,11 @@ #!/bin/bash -FN="HDCytoData_1.2.1.tar.gz" +FN="HDCytoData_1.4.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/experiment/src/contrib/HDCytoData_1.2.1.tar.gz" - "https://bioarchive.galaxyproject.org/HDCytoData_1.2.1.tar.gz" - "https://depot.galaxyproject.org/software/bioconductor-hdcytodata/bioconductor-hdcytodata_1.2.1_src_all.tar.gz" + "https://bioconductor.org/packages/3.9/data/experiment/src/contrib/HDCytoData_1.4.0.tar.gz" + "https://bioarchive.galaxyproject.org/HDCytoData_1.4.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-hdcytodata/bioconductor-hdcytodata_1.4.0_src_all.tar.gz" ) -MD5="052694707ec8c44941417dc44e112d5a" +MD5="7e6294543c192c0a089c6eb1c6c406ce" # Use a staging area in the conda dir rather than temp dirs, both to avoid # permission issues as well as to have things downloaded in a predictable @@ -16,7 +16,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-hdf5array/meta.yaml b/recipes/bioconductor-hdf5array/meta.yaml index 32033eb1aca37..c7960c76861c1 100644 --- a/recipes/bioconductor-hdf5array/meta.yaml +++ b/recipes/bioconductor-hdf5array/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.10.1" %} +{% set version = "1.12.0" %} {% set name = "HDF5Array" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,29 +10,33 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 8364b79376541c14faea8f90d97be4a4 + md5: 9672128c2746cb7170b63f1a58d1d7cf build: number: 0 rpaths: - lib/R/lib/ - lib/ - noarch: generic -# Suggests: h5vcData, SummarizedExperiment (>= 1.9.6), GenomicRanges, ExperimentHub, BiocParallel, BiocStyle +# Suggests: h5vcData, SummarizedExperiment (>= 1.9.6), GenomicRanges, ExperimentHub, TENxBrainData, BiocParallel, GenomicFeatures, BiocStyle requirements: host: - - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' - - 'bioconductor-delayedarray >=0.8.0,<0.9.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-rhdf5 >=2.26.0,<2.27.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-biocgenerics >=0.30.0,<0.31.0' + - 'bioconductor-delayedarray >=0.10.0,<0.11.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-rhdf5 >=2.28.0,<2.29.0' + - 'bioconductor-rhdf5lib >=1.6.0,<1.7.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' - r-base run: - - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' - - 'bioconductor-delayedarray >=0.8.0,<0.9.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-rhdf5 >=2.26.0,<2.27.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-biocgenerics >=0.30.0,<0.31.0' + - 'bioconductor-delayedarray >=0.10.0,<0.11.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-rhdf5 >=2.28.0,<2.29.0' + - 'bioconductor-rhdf5lib >=1.6.0,<1.7.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' - r-base + build: + - {{ compiler('c') }} + - make test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-hdtd/meta.yaml b/recipes/bioconductor-hdtd/meta.yaml index 09b295f76a669..2687fa6b2457e 100644 --- a/recipes/bioconductor-hdtd/meta.yaml +++ b/recipes/bioconductor-hdtd/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.16.0" %} +{% set version = "1.18.0" %} {% set name = "HDTD" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: e4763c7b65d7e166c2f1d04aece51437 + md5: 96e4ebd46143fc76f1a8fd2f91978c14 build: number: 0 rpaths: @@ -26,12 +26,10 @@ requirements: - r-base - 'r-rcpp >=0.12.13' - r-rcpparmadillo - - llvm-openmp # [osx] build: - {{ compiler('c') }} - {{ compiler('cxx') }} - make - - llvm-openmp # [osx] test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-healthyflowdata/meta.yaml b/recipes/bioconductor-healthyflowdata/meta.yaml index f53e7f9f09826..315e205a4da36 100644 --- a/recipes/bioconductor-healthyflowdata/meta.yaml +++ b/recipes/bioconductor-healthyflowdata/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.20.0" %} +{% set version = "1.22.0" %} {% set name = "healthyFlowData" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: b8581160bd5bfcc2d539dd7c15b6015b + md5: e68c9638bbe2a477a0d8cf2b99d7fd3c build: number: 0 rpaths: @@ -19,12 +19,12 @@ build: noarch: generic requirements: host: - - 'bioconductor-flowcore >=1.48.0,<1.49.0' + - 'bioconductor-flowcore >=1.50.0,<1.51.0' - r-base run: - - 'bioconductor-flowcore >=1.48.0,<1.49.0' + - 'bioconductor-flowcore >=1.50.0,<1.51.0' - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-healthyflowdata/post-link.sh b/recipes/bioconductor-healthyflowdata/post-link.sh index f85ad89c65493..dc27e1b2b22da 100644 --- a/recipes/bioconductor-healthyflowdata/post-link.sh +++ b/recipes/bioconductor-healthyflowdata/post-link.sh @@ -1,11 +1,11 @@ #!/bin/bash -FN="healthyFlowData_1.20.0.tar.gz" +FN="healthyFlowData_1.22.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/experiment/src/contrib/healthyFlowData_1.20.0.tar.gz" - "https://bioarchive.galaxyproject.org/healthyFlowData_1.20.0.tar.gz" - "https://depot.galaxyproject.org/software/bioconductor-healthyflowdata/bioconductor-healthyflowdata_1.20.0_src_all.tar.gz" + "https://bioconductor.org/packages/3.9/data/experiment/src/contrib/healthyFlowData_1.22.0.tar.gz" + "https://bioarchive.galaxyproject.org/healthyFlowData_1.22.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-healthyflowdata/bioconductor-healthyflowdata_1.22.0_src_all.tar.gz" ) -MD5="b8581160bd5bfcc2d539dd7c15b6015b" +MD5="e68c9638bbe2a477a0d8cf2b99d7fd3c" # Use a staging area in the conda dir rather than temp dirs, both to avoid # permission issues as well as to have things downloaded in a predictable @@ -16,7 +16,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-heatmaps/meta.yaml b/recipes/bioconductor-heatmaps/meta.yaml index 14bc650fb4ea6..08adc4ffbad9b 100644 --- a/recipes/bioconductor-heatmaps/meta.yaml +++ b/recipes/bioconductor-heatmaps/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.6.0" %} +{% set version = "1.8.0" %} {% set name = "heatmaps" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: fc9f322f10602a84bcea0fe147003763 + md5: 3f929be2441b272387c5a7e59289cc47 build: number: 0 rpaths: @@ -20,24 +20,24 @@ build: # Suggests: BSgenome.Drerio.UCSC.danRer7, knitr, rmarkdown, testthat requirements: host: - - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' - - 'bioconductor-biostrings >=2.50.0,<2.51.0' - - 'bioconductor-ebimage >=4.24.0,<4.25.0' - - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' - - 'bioconductor-genomicranges >=1.34.0,<1.35.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-biocgenerics >=0.30.0,<0.31.0' + - 'bioconductor-biostrings >=2.52.0,<2.53.0' + - 'bioconductor-ebimage >=4.26.0,<4.27.0' + - 'bioconductor-genomeinfodb >=1.20.0,<1.21.0' + - 'bioconductor-genomicranges >=1.36.0,<1.37.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' - r-base - r-kernsmooth - r-matrix - r-plotrix - r-rcolorbrewer run: - - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' - - 'bioconductor-biostrings >=2.50.0,<2.51.0' - - 'bioconductor-ebimage >=4.24.0,<4.25.0' - - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' - - 'bioconductor-genomicranges >=1.34.0,<1.35.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-biocgenerics >=0.30.0,<0.31.0' + - 'bioconductor-biostrings >=2.52.0,<2.53.0' + - 'bioconductor-ebimage >=4.26.0,<4.27.0' + - 'bioconductor-genomeinfodb >=1.20.0,<1.21.0' + - 'bioconductor-genomicranges >=1.36.0,<1.37.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' - r-base - r-kernsmooth - r-matrix diff --git a/recipes/bioconductor-heatplus/meta.yaml b/recipes/bioconductor-heatplus/meta.yaml index 7d5d5d8af3a5e..b0f018dff8927 100644 --- a/recipes/bioconductor-heatplus/meta.yaml +++ b/recipes/bioconductor-heatplus/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "2.28.0" %} +{% set version = "2.30.0" %} {% set name = "Heatplus" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 20b3fb9d045f7ca40aa14fd4c9cef45c + md5: f2b40b768decb8a280ab1d5bb4212d14 build: number: 0 rpaths: diff --git a/recipes/bioconductor-heebodata/meta.yaml b/recipes/bioconductor-heebodata/meta.yaml index 8262d888237f8..f83392a22ee77 100644 --- a/recipes/bioconductor-heebodata/meta.yaml +++ b/recipes/bioconductor-heebodata/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.20.0" %} +{% set version = "1.22.0" %} {% set name = "HEEBOdata" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 637405f7b381653f36c87414a2902907 + md5: 76163c616e6f8e975962b0b0ad45da7f build: number: 0 rpaths: @@ -22,7 +22,7 @@ requirements: - r-base run: - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-heebodata/post-link.sh b/recipes/bioconductor-heebodata/post-link.sh index 72c71d6a37ad5..6e140e6f3e567 100644 --- a/recipes/bioconductor-heebodata/post-link.sh +++ b/recipes/bioconductor-heebodata/post-link.sh @@ -1,11 +1,11 @@ #!/bin/bash -FN="HEEBOdata_1.20.0.tar.gz" +FN="HEEBOdata_1.22.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/experiment/src/contrib/HEEBOdata_1.20.0.tar.gz" - "https://bioarchive.galaxyproject.org/HEEBOdata_1.20.0.tar.gz" - "https://depot.galaxyproject.org/software/bioconductor-heebodata/bioconductor-heebodata_1.20.0_src_all.tar.gz" + "https://bioconductor.org/packages/3.9/data/experiment/src/contrib/HEEBOdata_1.22.0.tar.gz" + "https://bioarchive.galaxyproject.org/HEEBOdata_1.22.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-heebodata/bioconductor-heebodata_1.22.0_src_all.tar.gz" ) -MD5="637405f7b381653f36c87414a2902907" +MD5="76163c616e6f8e975962b0b0ad45da7f" # Use a staging area in the conda dir rather than temp dirs, both to avoid # permission issues as well as to have things downloaded in a predictable @@ -16,7 +16,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-helloranges/meta.yaml b/recipes/bioconductor-helloranges/meta.yaml index 23ad765b56bec..02500bb27dc3f 100644 --- a/recipes/bioconductor-helloranges/meta.yaml +++ b/recipes/bioconductor-helloranges/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.8.0" %} +{% set version = "1.10.0" %} {% set name = "HelloRanges" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: ff03ab06cd4a7cf29704657f16a06fd8 + md5: 2162f8502e0051913184575fbed4ac7b build: number: 0 rpaths: @@ -20,35 +20,35 @@ build: # Suggests: HelloRangesData, BiocStyle requirements: host: - - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' - - 'bioconductor-biostrings >=2.50.0,<2.51.0' - - 'bioconductor-bsgenome >=1.50.0,<1.51.0' - - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' - - 'bioconductor-genomicalignments >=1.18.0,<1.19.0' - - 'bioconductor-genomicfeatures >=1.34.0,<1.35.0' - - 'bioconductor-genomicranges >=1.34.0,<1.35.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-rsamtools >=1.34.0,<1.35.0' - - 'bioconductor-rtracklayer >=1.42.0,<1.43.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' - - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' - - 'bioconductor-variantannotation >=1.28.0,<1.29.0' + - 'bioconductor-biocgenerics >=0.30.0,<0.31.0' + - 'bioconductor-biostrings >=2.52.0,<2.53.0' + - 'bioconductor-bsgenome >=1.52.0,<1.53.0' + - 'bioconductor-genomeinfodb >=1.20.0,<1.21.0' + - 'bioconductor-genomicalignments >=1.20.0,<1.21.0' + - 'bioconductor-genomicfeatures >=1.36.0,<1.37.0' + - 'bioconductor-genomicranges >=1.36.0,<1.37.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-rsamtools >=2.0.0,<2.1.0' + - 'bioconductor-rtracklayer >=1.44.0,<1.45.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' + - 'bioconductor-summarizedexperiment >=1.14.0,<1.15.0' + - 'bioconductor-variantannotation >=1.30.0,<1.31.0' - r-base - r-docopt run: - - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' - - 'bioconductor-biostrings >=2.50.0,<2.51.0' - - 'bioconductor-bsgenome >=1.50.0,<1.51.0' - - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' - - 'bioconductor-genomicalignments >=1.18.0,<1.19.0' - - 'bioconductor-genomicfeatures >=1.34.0,<1.35.0' - - 'bioconductor-genomicranges >=1.34.0,<1.35.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-rsamtools >=1.34.0,<1.35.0' - - 'bioconductor-rtracklayer >=1.42.0,<1.43.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' - - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' - - 'bioconductor-variantannotation >=1.28.0,<1.29.0' + - 'bioconductor-biocgenerics >=0.30.0,<0.31.0' + - 'bioconductor-biostrings >=2.52.0,<2.53.0' + - 'bioconductor-bsgenome >=1.52.0,<1.53.0' + - 'bioconductor-genomeinfodb >=1.20.0,<1.21.0' + - 'bioconductor-genomicalignments >=1.20.0,<1.21.0' + - 'bioconductor-genomicfeatures >=1.36.0,<1.37.0' + - 'bioconductor-genomicranges >=1.36.0,<1.37.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-rsamtools >=2.0.0,<2.1.0' + - 'bioconductor-rtracklayer >=1.44.0,<1.45.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' + - 'bioconductor-summarizedexperiment >=1.14.0,<1.15.0' + - 'bioconductor-variantannotation >=1.30.0,<1.31.0' - r-base - r-docopt test: diff --git a/recipes/bioconductor-hellorangesdata/meta.yaml b/recipes/bioconductor-hellorangesdata/meta.yaml index cfbb96c9b6b67..8b6da806fd8dc 100644 --- a/recipes/bioconductor-hellorangesdata/meta.yaml +++ b/recipes/bioconductor-hellorangesdata/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.8.0" %} +{% set version = "1.10.0" %} {% set name = "HelloRangesData" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 544429f8fe98d0ec98dd22061944d673 + md5: 25607b151c01f459bf0673a7a1fe6ea7 build: number: 0 rpaths: @@ -23,7 +23,7 @@ requirements: - r-base run: - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-hellorangesdata/post-link.sh b/recipes/bioconductor-hellorangesdata/post-link.sh index afe0244d385e6..5ace22c99e9aa 100644 --- a/recipes/bioconductor-hellorangesdata/post-link.sh +++ b/recipes/bioconductor-hellorangesdata/post-link.sh @@ -1,11 +1,11 @@ #!/bin/bash -FN="HelloRangesData_1.8.0.tar.gz" +FN="HelloRangesData_1.10.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/experiment/src/contrib/HelloRangesData_1.8.0.tar.gz" - "https://bioarchive.galaxyproject.org/HelloRangesData_1.8.0.tar.gz" - "https://depot.galaxyproject.org/software/bioconductor-hellorangesdata/bioconductor-hellorangesdata_1.8.0_src_all.tar.gz" + "https://bioconductor.org/packages/3.9/data/experiment/src/contrib/HelloRangesData_1.10.0.tar.gz" + "https://bioarchive.galaxyproject.org/HelloRangesData_1.10.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-hellorangesdata/bioconductor-hellorangesdata_1.10.0_src_all.tar.gz" ) -MD5="544429f8fe98d0ec98dd22061944d673" +MD5="25607b151c01f459bf0673a7a1fe6ea7" # Use a staging area in the conda dir rather than temp dirs, both to avoid # permission issues as well as to have things downloaded in a predictable @@ -16,7 +16,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-help/meta.yaml b/recipes/bioconductor-help/meta.yaml index 87e296c2eff0e..9c89b2028498d 100644 --- a/recipes/bioconductor-help/meta.yaml +++ b/recipes/bioconductor-help/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.40.0" %} +{% set version = "1.42.0" %} {% set name = "HELP" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,19 +10,19 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: e91bbeed8854a990d4c6ae520eed86df + md5: 779de524a7e41ec6fcdc7fe2f45e252b build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ noarch: generic requirements: host: - - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' - r-base run: - - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' - r-base test: commands: diff --git a/recipes/bioconductor-hem/meta.yaml b/recipes/bioconductor-hem/meta.yaml index f196729144b43..2900c484aad39 100644 --- a/recipes/bioconductor-hem/meta.yaml +++ b/recipes/bioconductor-hem/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.54.0" %} +{% set version = "1.56.0" %} {% set name = "HEM" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: d2d002ac97b8d515dc6b5676329209fa + md5: 8ac3fc2efa22e3d98e544b79834d337d build: number: 0 rpaths: @@ -18,10 +18,10 @@ build: - lib/ requirements: host: - - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' - r-base run: - - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' - r-base build: - {{ compiler('c') }} diff --git a/recipes/bioconductor-hgfocus.db/meta.yaml b/recipes/bioconductor-hgfocus.db/meta.yaml index 68d95b6208729..432c8a8b22920 100644 --- a/recipes/bioconductor-hgfocus.db/meta.yaml +++ b/recipes/bioconductor-hgfocus.db/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.2.3" %} {% set name = "hgfocus.db" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -12,7 +12,7 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 7fb2bb82975ff21d075d3c8ce6f8162a build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ @@ -20,14 +20,14 @@ build: # Suggests: DBI, annotate, RUnit requirements: host: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' - - 'bioconductor-org.hs.eg.db >=3.7.0,<3.8.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' + - 'bioconductor-org.hs.eg.db >=3.8.0,<3.9.0' - r-base run: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' - - 'bioconductor-org.hs.eg.db >=3.7.0,<3.8.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' + - 'bioconductor-org.hs.eg.db >=3.8.0,<3.9.0' - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-hgfocus.db/post-link.sh b/recipes/bioconductor-hgfocus.db/post-link.sh index 68f3797476b12..3994e4673fd1d 100644 --- a/recipes/bioconductor-hgfocus.db/post-link.sh +++ b/recipes/bioconductor-hgfocus.db/post-link.sh @@ -1,9 +1,10 @@ #!/bin/bash FN="hgfocus.db_3.2.3.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/hgfocus.db_3.2.3.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/hgfocus.db_3.2.3.tar.gz" "https://bioarchive.galaxyproject.org/hgfocus.db_3.2.3.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-hgfocus.db/bioconductor-hgfocus.db_3.2.3_src_all.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-hgfocus.db/bioconductor-hgfocus.db_3.2.3_src_all.tar.gz" ) MD5="7fb2bb82975ff21d075d3c8ce6f8162a" @@ -16,7 +17,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-hgfocuscdf/meta.yaml b/recipes/bioconductor-hgfocuscdf/meta.yaml index 73676002c4710..981af01bf86b8 100644 --- a/recipes/bioconductor-hgfocuscdf/meta.yaml +++ b/recipes/bioconductor-hgfocuscdf/meta.yaml @@ -1,6 +1,6 @@ {% set version = "2.18.0" %} {% set name = "hgfocuscdf" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -12,19 +12,19 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 9883e53bfd9ddb9ad5f3a9c2e47bbd2c build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' - r-base run: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-hgfocuscdf/post-link.sh b/recipes/bioconductor-hgfocuscdf/post-link.sh index cb0e564fa6f93..26ef61185da10 100644 --- a/recipes/bioconductor-hgfocuscdf/post-link.sh +++ b/recipes/bioconductor-hgfocuscdf/post-link.sh @@ -1,9 +1,10 @@ #!/bin/bash FN="hgfocuscdf_2.18.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/hgfocuscdf_2.18.0.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/hgfocuscdf_2.18.0.tar.gz" "https://bioarchive.galaxyproject.org/hgfocuscdf_2.18.0.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-hgfocuscdf/bioconductor-hgfocuscdf_2.18.0_src_all.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-hgfocuscdf/bioconductor-hgfocuscdf_2.18.0_src_all.tar.gz" ) MD5="9883e53bfd9ddb9ad5f3a9c2e47bbd2c" @@ -16,7 +17,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-hgfocusprobe/meta.yaml b/recipes/bioconductor-hgfocusprobe/meta.yaml index d1aed4a8eed82..6319f23b895de 100644 --- a/recipes/bioconductor-hgfocusprobe/meta.yaml +++ b/recipes/bioconductor-hgfocusprobe/meta.yaml @@ -1,6 +1,6 @@ {% set version = "2.18.0" %} {% set name = "hgfocusprobe" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -12,19 +12,19 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 0a399ed276b89e3d80946b6cbbf167b4 build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' - r-base run: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-hgfocusprobe/post-link.sh b/recipes/bioconductor-hgfocusprobe/post-link.sh index 45c46d333d084..5828d8bbc4b76 100644 --- a/recipes/bioconductor-hgfocusprobe/post-link.sh +++ b/recipes/bioconductor-hgfocusprobe/post-link.sh @@ -1,9 +1,10 @@ #!/bin/bash FN="hgfocusprobe_2.18.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/hgfocusprobe_2.18.0.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/hgfocusprobe_2.18.0.tar.gz" "https://bioarchive.galaxyproject.org/hgfocusprobe_2.18.0.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-hgfocusprobe/bioconductor-hgfocusprobe_2.18.0_src_all.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-hgfocusprobe/bioconductor-hgfocusprobe_2.18.0_src_all.tar.gz" ) MD5="0a399ed276b89e3d80946b6cbbf167b4" @@ -16,7 +17,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-hgu133a.db/meta.yaml b/recipes/bioconductor-hgu133a.db/meta.yaml index 23f16b2732959..c28917467fcbe 100644 --- a/recipes/bioconductor-hgu133a.db/meta.yaml +++ b/recipes/bioconductor-hgu133a.db/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.2.3" %} {% set name = "hgu133a.db" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -12,7 +12,7 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: ce0397160fe78a92671e492a22542a79 build: - number: 4 + number: 5 rpaths: - lib/R/lib/ - lib/ @@ -20,14 +20,14 @@ build: # Suggests: DBI, annotate, RUnit requirements: host: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' - - 'bioconductor-org.hs.eg.db >=3.7.0,<3.8.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' + - 'bioconductor-org.hs.eg.db >=3.8.0,<3.9.0' - r-base run: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' - - 'bioconductor-org.hs.eg.db >=3.7.0,<3.8.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' + - 'bioconductor-org.hs.eg.db >=3.8.0,<3.9.0' - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-hgu133a.db/post-link.sh b/recipes/bioconductor-hgu133a.db/post-link.sh index b4cdf6e2fdcfe..8ce287a3d99e5 100644 --- a/recipes/bioconductor-hgu133a.db/post-link.sh +++ b/recipes/bioconductor-hgu133a.db/post-link.sh @@ -1,7 +1,7 @@ #!/bin/bash FN="hgu133a.db_3.2.3.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/hgu133a.db_3.2.3.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/hgu133a.db_3.2.3.tar.gz" "https://bioarchive.galaxyproject.org/hgu133a.db_3.2.3.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-hgu133a.db/bioconductor-hgu133a.db_3.2.3_src_all.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-hgu133a.db/bioconductor-hgu133a.db_3.2.3_src_all.tar.gz" @@ -17,7 +17,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-hgu133a2.db/meta.yaml b/recipes/bioconductor-hgu133a2.db/meta.yaml index 198a611bbf4de..9043739f751a7 100644 --- a/recipes/bioconductor-hgu133a2.db/meta.yaml +++ b/recipes/bioconductor-hgu133a2.db/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.2.3" %} {% set name = "hgu133a2.db" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -12,7 +12,7 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 15cad9bc3f5ef6fca5300638a9c8bb86 build: - number: 3 + number: 4 rpaths: - lib/R/lib/ - lib/ @@ -20,14 +20,14 @@ build: # Suggests: DBI, annotate, RUnit requirements: host: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' - - 'bioconductor-org.hs.eg.db >=3.7.0,<3.8.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' + - 'bioconductor-org.hs.eg.db >=3.8.0,<3.9.0' - r-base run: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' - - 'bioconductor-org.hs.eg.db >=3.7.0,<3.8.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' + - 'bioconductor-org.hs.eg.db >=3.8.0,<3.9.0' - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-hgu133a2.db/post-link.sh b/recipes/bioconductor-hgu133a2.db/post-link.sh index 9eb31dbf8fc5a..af365ce839907 100644 --- a/recipes/bioconductor-hgu133a2.db/post-link.sh +++ b/recipes/bioconductor-hgu133a2.db/post-link.sh @@ -1,7 +1,7 @@ #!/bin/bash FN="hgu133a2.db_3.2.3.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/hgu133a2.db_3.2.3.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/hgu133a2.db_3.2.3.tar.gz" "https://bioarchive.galaxyproject.org/hgu133a2.db_3.2.3.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-hgu133a2.db/bioconductor-hgu133a2.db_3.2.3_src_all.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-hgu133a2.db/bioconductor-hgu133a2.db_3.2.3_src_all.tar.gz" @@ -17,7 +17,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-hgu133a2cdf/meta.yaml b/recipes/bioconductor-hgu133a2cdf/meta.yaml index 6698433bdec62..0851ef6e8c06d 100644 --- a/recipes/bioconductor-hgu133a2cdf/meta.yaml +++ b/recipes/bioconductor-hgu133a2cdf/meta.yaml @@ -1,6 +1,6 @@ {% set version = "2.18.0" %} {% set name = "hgu133a2cdf" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -12,19 +12,19 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 566bc70f0bb94a376bf88f191a2f067e build: - number: 1 + number: 2 rpaths: - lib/R/lib/ - lib/ noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' - r-base run: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-hgu133a2cdf/post-link.sh b/recipes/bioconductor-hgu133a2cdf/post-link.sh index 85381f3207e38..7f568f8801900 100644 --- a/recipes/bioconductor-hgu133a2cdf/post-link.sh +++ b/recipes/bioconductor-hgu133a2cdf/post-link.sh @@ -1,9 +1,10 @@ #!/bin/bash FN="hgu133a2cdf_2.18.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/hgu133a2cdf_2.18.0.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/hgu133a2cdf_2.18.0.tar.gz" "https://bioarchive.galaxyproject.org/hgu133a2cdf_2.18.0.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-hgu133a2cdf/bioconductor-hgu133a2cdf_2.18.0_src_all.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-hgu133a2cdf/bioconductor-hgu133a2cdf_2.18.0_src_all.tar.gz" ) MD5="566bc70f0bb94a376bf88f191a2f067e" @@ -16,7 +17,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-hgu133a2frmavecs/meta.yaml b/recipes/bioconductor-hgu133a2frmavecs/meta.yaml index 7d438aa8ade78..3dc2f917cf193 100644 --- a/recipes/bioconductor-hgu133a2frmavecs/meta.yaml +++ b/recipes/bioconductor-hgu133a2frmavecs/meta.yaml @@ -1,6 +1,6 @@ {% set version = "1.2.0" %} {% set name = "hgu133a2frmavecs" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -12,7 +12,7 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 4bf8cf5cbaf288ce0a9618d764c87044 build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ @@ -22,7 +22,7 @@ requirements: - r-base run: - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-hgu133a2frmavecs/post-link.sh b/recipes/bioconductor-hgu133a2frmavecs/post-link.sh index d70f4b6cfadef..602be314f787a 100644 --- a/recipes/bioconductor-hgu133a2frmavecs/post-link.sh +++ b/recipes/bioconductor-hgu133a2frmavecs/post-link.sh @@ -1,9 +1,10 @@ #!/bin/bash FN="hgu133a2frmavecs_1.2.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/hgu133a2frmavecs_1.2.0.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/hgu133a2frmavecs_1.2.0.tar.gz" "https://bioarchive.galaxyproject.org/hgu133a2frmavecs_1.2.0.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-hgu133a2frmavecs/bioconductor-hgu133a2frmavecs_1.2.0_src_all.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-hgu133a2frmavecs/bioconductor-hgu133a2frmavecs_1.2.0_src_all.tar.gz" ) MD5="4bf8cf5cbaf288ce0a9618d764c87044" @@ -16,7 +17,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-hgu133a2probe/meta.yaml b/recipes/bioconductor-hgu133a2probe/meta.yaml index 888e8bb7f6942..eb9c5db2f2c71 100644 --- a/recipes/bioconductor-hgu133a2probe/meta.yaml +++ b/recipes/bioconductor-hgu133a2probe/meta.yaml @@ -1,6 +1,6 @@ {% set version = "2.18.0" %} {% set name = "hgu133a2probe" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -12,19 +12,19 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 736b43cfc37a297ccc0d30cb75fcc95a build: - number: 1 + number: 2 rpaths: - lib/R/lib/ - lib/ noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' - r-base run: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-hgu133a2probe/post-link.sh b/recipes/bioconductor-hgu133a2probe/post-link.sh index 4e1c45878877e..b76d20ba4ab6c 100644 --- a/recipes/bioconductor-hgu133a2probe/post-link.sh +++ b/recipes/bioconductor-hgu133a2probe/post-link.sh @@ -1,9 +1,10 @@ #!/bin/bash FN="hgu133a2probe_2.18.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/hgu133a2probe_2.18.0.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/hgu133a2probe_2.18.0.tar.gz" "https://bioarchive.galaxyproject.org/hgu133a2probe_2.18.0.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-hgu133a2probe/bioconductor-hgu133a2probe_2.18.0_src_all.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-hgu133a2probe/bioconductor-hgu133a2probe_2.18.0_src_all.tar.gz" ) MD5="736b43cfc37a297ccc0d30cb75fcc95a" @@ -16,7 +17,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-hgu133abarcodevecs/meta.yaml b/recipes/bioconductor-hgu133abarcodevecs/meta.yaml index 8f5e886b3ae5a..74ba35b2598b7 100644 --- a/recipes/bioconductor-hgu133abarcodevecs/meta.yaml +++ b/recipes/bioconductor-hgu133abarcodevecs/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.20.0" %} +{% set version = "1.22.0" %} {% set name = "hgu133abarcodevecs" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: b32e4538a860079a21da485ffc31fbb9 + md5: c3a80fbd654d19c76355f818e4e19b24 build: number: 0 rpaths: @@ -22,7 +22,7 @@ requirements: - r-base run: - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-hgu133abarcodevecs/post-link.sh b/recipes/bioconductor-hgu133abarcodevecs/post-link.sh index c25774c005786..4700e66f0db63 100644 --- a/recipes/bioconductor-hgu133abarcodevecs/post-link.sh +++ b/recipes/bioconductor-hgu133abarcodevecs/post-link.sh @@ -1,11 +1,11 @@ #!/bin/bash -FN="hgu133abarcodevecs_1.20.0.tar.gz" +FN="hgu133abarcodevecs_1.22.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/experiment/src/contrib/hgu133abarcodevecs_1.20.0.tar.gz" - "https://bioarchive.galaxyproject.org/hgu133abarcodevecs_1.20.0.tar.gz" - "https://depot.galaxyproject.org/software/bioconductor-hgu133abarcodevecs/bioconductor-hgu133abarcodevecs_1.20.0_src_all.tar.gz" + "https://bioconductor.org/packages/3.9/data/experiment/src/contrib/hgu133abarcodevecs_1.22.0.tar.gz" + "https://bioarchive.galaxyproject.org/hgu133abarcodevecs_1.22.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-hgu133abarcodevecs/bioconductor-hgu133abarcodevecs_1.22.0_src_all.tar.gz" ) -MD5="b32e4538a860079a21da485ffc31fbb9" +MD5="c3a80fbd654d19c76355f818e4e19b24" # Use a staging area in the conda dir rather than temp dirs, both to avoid # permission issues as well as to have things downloaded in a predictable @@ -16,7 +16,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-hgu133acdf/meta.yaml b/recipes/bioconductor-hgu133acdf/meta.yaml index fedc14d9ecc6d..34c31a3f12c69 100644 --- a/recipes/bioconductor-hgu133acdf/meta.yaml +++ b/recipes/bioconductor-hgu133acdf/meta.yaml @@ -1,6 +1,6 @@ {% set version = "2.18.0" %} {% set name = "hgu133acdf" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -12,19 +12,19 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: d3e0e22b2d3943d26c94e7c01b91035c build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' - r-base run: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-hgu133acdf/post-link.sh b/recipes/bioconductor-hgu133acdf/post-link.sh index c78e1fafe2133..c8cb3d53a4e99 100644 --- a/recipes/bioconductor-hgu133acdf/post-link.sh +++ b/recipes/bioconductor-hgu133acdf/post-link.sh @@ -1,9 +1,10 @@ #!/bin/bash FN="hgu133acdf_2.18.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/hgu133acdf_2.18.0.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/hgu133acdf_2.18.0.tar.gz" "https://bioarchive.galaxyproject.org/hgu133acdf_2.18.0.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-hgu133acdf/bioconductor-hgu133acdf_2.18.0_src_all.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-hgu133acdf/bioconductor-hgu133acdf_2.18.0_src_all.tar.gz" ) MD5="d3e0e22b2d3943d26c94e7c01b91035c" @@ -16,7 +17,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-hgu133afrmavecs/meta.yaml b/recipes/bioconductor-hgu133afrmavecs/meta.yaml index 5c3975c11bb27..e3bcf86fd36c1 100644 --- a/recipes/bioconductor-hgu133afrmavecs/meta.yaml +++ b/recipes/bioconductor-hgu133afrmavecs/meta.yaml @@ -1,6 +1,6 @@ {% set version = "1.5.0" %} {% set name = "hgu133afrmavecs" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -12,7 +12,7 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 85034ab02491f5b3699d210cef50812d build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ @@ -22,7 +22,7 @@ requirements: - r-base run: - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-hgu133afrmavecs/post-link.sh b/recipes/bioconductor-hgu133afrmavecs/post-link.sh index b68622250e322..c17bda1f134e7 100644 --- a/recipes/bioconductor-hgu133afrmavecs/post-link.sh +++ b/recipes/bioconductor-hgu133afrmavecs/post-link.sh @@ -1,9 +1,10 @@ #!/bin/bash FN="hgu133afrmavecs_1.5.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/hgu133afrmavecs_1.5.0.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/hgu133afrmavecs_1.5.0.tar.gz" "https://bioarchive.galaxyproject.org/hgu133afrmavecs_1.5.0.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-hgu133afrmavecs/bioconductor-hgu133afrmavecs_1.5.0_src_all.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-hgu133afrmavecs/bioconductor-hgu133afrmavecs_1.5.0_src_all.tar.gz" ) MD5="85034ab02491f5b3699d210cef50812d" @@ -16,7 +17,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-hgu133aprobe/meta.yaml b/recipes/bioconductor-hgu133aprobe/meta.yaml index e94723b576637..67a6acc73e8cf 100644 --- a/recipes/bioconductor-hgu133aprobe/meta.yaml +++ b/recipes/bioconductor-hgu133aprobe/meta.yaml @@ -1,6 +1,6 @@ {% set version = "2.18.0" %} {% set name = "hgu133aprobe" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -12,19 +12,19 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 76cd9c54b0a8a0240dbb0fc758959d62 build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' - r-base run: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-hgu133aprobe/post-link.sh b/recipes/bioconductor-hgu133aprobe/post-link.sh index 0c0d0621da8a1..9ce61c28c83b2 100644 --- a/recipes/bioconductor-hgu133aprobe/post-link.sh +++ b/recipes/bioconductor-hgu133aprobe/post-link.sh @@ -1,9 +1,10 @@ #!/bin/bash FN="hgu133aprobe_2.18.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/hgu133aprobe_2.18.0.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/hgu133aprobe_2.18.0.tar.gz" "https://bioarchive.galaxyproject.org/hgu133aprobe_2.18.0.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-hgu133aprobe/bioconductor-hgu133aprobe_2.18.0_src_all.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-hgu133aprobe/bioconductor-hgu133aprobe_2.18.0_src_all.tar.gz" ) MD5="76cd9c54b0a8a0240dbb0fc758959d62" @@ -16,7 +17,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-hgu133atagcdf/meta.yaml b/recipes/bioconductor-hgu133atagcdf/meta.yaml index 57b2395658fa7..83498b5cdaff3 100644 --- a/recipes/bioconductor-hgu133atagcdf/meta.yaml +++ b/recipes/bioconductor-hgu133atagcdf/meta.yaml @@ -1,6 +1,6 @@ {% set version = "2.18.0" %} {% set name = "hgu133atagcdf" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -12,19 +12,19 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 01f8809e0deb5b83f3f0decec881a1d8 build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' - r-base run: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-hgu133atagcdf/post-link.sh b/recipes/bioconductor-hgu133atagcdf/post-link.sh index 37321aa43bcd1..ff0d25d1c2314 100644 --- a/recipes/bioconductor-hgu133atagcdf/post-link.sh +++ b/recipes/bioconductor-hgu133atagcdf/post-link.sh @@ -1,9 +1,10 @@ #!/bin/bash FN="hgu133atagcdf_2.18.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/hgu133atagcdf_2.18.0.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/hgu133atagcdf_2.18.0.tar.gz" "https://bioarchive.galaxyproject.org/hgu133atagcdf_2.18.0.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-hgu133atagcdf/bioconductor-hgu133atagcdf_2.18.0_src_all.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-hgu133atagcdf/bioconductor-hgu133atagcdf_2.18.0_src_all.tar.gz" ) MD5="01f8809e0deb5b83f3f0decec881a1d8" @@ -16,7 +17,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-hgu133atagprobe/meta.yaml b/recipes/bioconductor-hgu133atagprobe/meta.yaml index 1bb71ac0e3bf6..49d95f01b1ebf 100644 --- a/recipes/bioconductor-hgu133atagprobe/meta.yaml +++ b/recipes/bioconductor-hgu133atagprobe/meta.yaml @@ -1,6 +1,6 @@ {% set version = "2.18.0" %} {% set name = "hgu133atagprobe" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -12,19 +12,19 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 97aeaf9ac9450369cf030581b8ec5a53 build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' - r-base run: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-hgu133atagprobe/post-link.sh b/recipes/bioconductor-hgu133atagprobe/post-link.sh index 7c3ac7aa6e33d..aeb1a422a01f7 100644 --- a/recipes/bioconductor-hgu133atagprobe/post-link.sh +++ b/recipes/bioconductor-hgu133atagprobe/post-link.sh @@ -1,9 +1,10 @@ #!/bin/bash FN="hgu133atagprobe_2.18.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/hgu133atagprobe_2.18.0.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/hgu133atagprobe_2.18.0.tar.gz" "https://bioarchive.galaxyproject.org/hgu133atagprobe_2.18.0.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-hgu133atagprobe/bioconductor-hgu133atagprobe_2.18.0_src_all.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-hgu133atagprobe/bioconductor-hgu133atagprobe_2.18.0_src_all.tar.gz" ) MD5="97aeaf9ac9450369cf030581b8ec5a53" @@ -16,7 +17,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-hgu133b.db/meta.yaml b/recipes/bioconductor-hgu133b.db/meta.yaml index 5f5c4e4147de5..bf835df4dfa1e 100644 --- a/recipes/bioconductor-hgu133b.db/meta.yaml +++ b/recipes/bioconductor-hgu133b.db/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.2.3" %} {% set name = "hgu133b.db" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -12,7 +12,7 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 3e7c3fa57703d21d4a7624a45d921b24 build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ @@ -20,14 +20,14 @@ build: # Suggests: DBI, annotate, RUnit requirements: host: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' - - 'bioconductor-org.hs.eg.db >=3.7.0,<3.8.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' + - 'bioconductor-org.hs.eg.db >=3.8.0,<3.9.0' - r-base run: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' - - 'bioconductor-org.hs.eg.db >=3.7.0,<3.8.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' + - 'bioconductor-org.hs.eg.db >=3.8.0,<3.9.0' - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-hgu133b.db/post-link.sh b/recipes/bioconductor-hgu133b.db/post-link.sh index ffea8dbfdcbe7..5dc9fecc28988 100644 --- a/recipes/bioconductor-hgu133b.db/post-link.sh +++ b/recipes/bioconductor-hgu133b.db/post-link.sh @@ -1,9 +1,10 @@ #!/bin/bash FN="hgu133b.db_3.2.3.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/hgu133b.db_3.2.3.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/hgu133b.db_3.2.3.tar.gz" "https://bioarchive.galaxyproject.org/hgu133b.db_3.2.3.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-hgu133b.db/bioconductor-hgu133b.db_3.2.3_src_all.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-hgu133b.db/bioconductor-hgu133b.db_3.2.3_src_all.tar.gz" ) MD5="3e7c3fa57703d21d4a7624a45d921b24" @@ -16,7 +17,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-hgu133bcdf/meta.yaml b/recipes/bioconductor-hgu133bcdf/meta.yaml index efa521158302f..3d5d6f8cb90d7 100644 --- a/recipes/bioconductor-hgu133bcdf/meta.yaml +++ b/recipes/bioconductor-hgu133bcdf/meta.yaml @@ -1,6 +1,6 @@ {% set version = "2.18.0" %} {% set name = "hgu133bcdf" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -12,19 +12,19 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 649aaa5e6275be6ee4d24d80ca390ea5 build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' - r-base run: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-hgu133bcdf/post-link.sh b/recipes/bioconductor-hgu133bcdf/post-link.sh index 6bc36da9e77e0..e6256597e5c2b 100644 --- a/recipes/bioconductor-hgu133bcdf/post-link.sh +++ b/recipes/bioconductor-hgu133bcdf/post-link.sh @@ -1,9 +1,10 @@ #!/bin/bash FN="hgu133bcdf_2.18.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/hgu133bcdf_2.18.0.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/hgu133bcdf_2.18.0.tar.gz" "https://bioarchive.galaxyproject.org/hgu133bcdf_2.18.0.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-hgu133bcdf/bioconductor-hgu133bcdf_2.18.0_src_all.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-hgu133bcdf/bioconductor-hgu133bcdf_2.18.0_src_all.tar.gz" ) MD5="649aaa5e6275be6ee4d24d80ca390ea5" @@ -16,7 +17,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-hgu133bprobe/meta.yaml b/recipes/bioconductor-hgu133bprobe/meta.yaml index ac3f8a25e9bdf..6249d8f376531 100644 --- a/recipes/bioconductor-hgu133bprobe/meta.yaml +++ b/recipes/bioconductor-hgu133bprobe/meta.yaml @@ -1,6 +1,6 @@ {% set version = "2.18.0" %} {% set name = "hgu133bprobe" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -12,19 +12,19 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 203750510e51450e1267e08c241151c4 build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' - r-base run: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-hgu133bprobe/post-link.sh b/recipes/bioconductor-hgu133bprobe/post-link.sh index 6b99e2000f0af..75c574588c943 100644 --- a/recipes/bioconductor-hgu133bprobe/post-link.sh +++ b/recipes/bioconductor-hgu133bprobe/post-link.sh @@ -1,9 +1,10 @@ #!/bin/bash FN="hgu133bprobe_2.18.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/hgu133bprobe_2.18.0.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/hgu133bprobe_2.18.0.tar.gz" "https://bioarchive.galaxyproject.org/hgu133bprobe_2.18.0.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-hgu133bprobe/bioconductor-hgu133bprobe_2.18.0_src_all.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-hgu133bprobe/bioconductor-hgu133bprobe_2.18.0_src_all.tar.gz" ) MD5="203750510e51450e1267e08c241151c4" @@ -16,7 +17,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-hgu133plus2.db/meta.yaml b/recipes/bioconductor-hgu133plus2.db/meta.yaml index 7e6a068a43ca0..8f9a9a25c7f6d 100644 --- a/recipes/bioconductor-hgu133plus2.db/meta.yaml +++ b/recipes/bioconductor-hgu133plus2.db/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.2.3" %} {% set name = "hgu133plus2.db" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -12,7 +12,7 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 45a376b6092da75907b9e73bbd90e5bf build: - number: 4 + number: 5 rpaths: - lib/R/lib/ - lib/ @@ -20,14 +20,14 @@ build: # Suggests: DBI, annotate, RUnit requirements: host: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' - - 'bioconductor-org.hs.eg.db >=3.7.0,<3.8.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' + - 'bioconductor-org.hs.eg.db >=3.8.0,<3.9.0' - r-base run: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' - - 'bioconductor-org.hs.eg.db >=3.7.0,<3.8.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' + - 'bioconductor-org.hs.eg.db >=3.8.0,<3.9.0' - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-hgu133plus2.db/post-link.sh b/recipes/bioconductor-hgu133plus2.db/post-link.sh index 77d92f5877c73..246eff64ade3f 100644 --- a/recipes/bioconductor-hgu133plus2.db/post-link.sh +++ b/recipes/bioconductor-hgu133plus2.db/post-link.sh @@ -1,7 +1,7 @@ #!/bin/bash FN="hgu133plus2.db_3.2.3.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/hgu133plus2.db_3.2.3.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/hgu133plus2.db_3.2.3.tar.gz" "https://bioarchive.galaxyproject.org/hgu133plus2.db_3.2.3.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-hgu133plus2.db/bioconductor-hgu133plus2.db_3.2.3_src_all.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-hgu133plus2.db/bioconductor-hgu133plus2.db_3.2.3_src_all.tar.gz" @@ -17,7 +17,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-hgu133plus2barcodevecs/meta.yaml b/recipes/bioconductor-hgu133plus2barcodevecs/meta.yaml index f486c4221622f..1043e8dd43430 100644 --- a/recipes/bioconductor-hgu133plus2barcodevecs/meta.yaml +++ b/recipes/bioconductor-hgu133plus2barcodevecs/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.20.0" %} +{% set version = "1.22.0" %} {% set name = "hgu133plus2barcodevecs" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 638f4fcd029bb5b3d07a2c3b79ffa3f9 + md5: 48c436478b8b6da87385b0d4f8d3e205 build: number: 0 rpaths: @@ -22,7 +22,7 @@ requirements: - r-base run: - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-hgu133plus2barcodevecs/post-link.sh b/recipes/bioconductor-hgu133plus2barcodevecs/post-link.sh index e505f350f501e..eb47399a1c345 100644 --- a/recipes/bioconductor-hgu133plus2barcodevecs/post-link.sh +++ b/recipes/bioconductor-hgu133plus2barcodevecs/post-link.sh @@ -1,11 +1,11 @@ #!/bin/bash -FN="hgu133plus2barcodevecs_1.20.0.tar.gz" +FN="hgu133plus2barcodevecs_1.22.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/experiment/src/contrib/hgu133plus2barcodevecs_1.20.0.tar.gz" - "https://bioarchive.galaxyproject.org/hgu133plus2barcodevecs_1.20.0.tar.gz" - "https://depot.galaxyproject.org/software/bioconductor-hgu133plus2barcodevecs/bioconductor-hgu133plus2barcodevecs_1.20.0_src_all.tar.gz" + "https://bioconductor.org/packages/3.9/data/experiment/src/contrib/hgu133plus2barcodevecs_1.22.0.tar.gz" + "https://bioarchive.galaxyproject.org/hgu133plus2barcodevecs_1.22.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-hgu133plus2barcodevecs/bioconductor-hgu133plus2barcodevecs_1.22.0_src_all.tar.gz" ) -MD5="638f4fcd029bb5b3d07a2c3b79ffa3f9" +MD5="48c436478b8b6da87385b0d4f8d3e205" # Use a staging area in the conda dir rather than temp dirs, both to avoid # permission issues as well as to have things downloaded in a predictable @@ -16,7 +16,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-hgu133plus2cdf/meta.yaml b/recipes/bioconductor-hgu133plus2cdf/meta.yaml index 5ae13a90fff27..e6b9b1de2fb8d 100644 --- a/recipes/bioconductor-hgu133plus2cdf/meta.yaml +++ b/recipes/bioconductor-hgu133plus2cdf/meta.yaml @@ -1,6 +1,6 @@ {% set version = "2.18.0" %} {% set name = "hgu133plus2cdf" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -12,19 +12,19 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 284fef2f0b777d7b53451538ddd53de3 build: - number: 1 + number: 2 rpaths: - lib/R/lib/ - lib/ noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' - r-base run: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-hgu133plus2cdf/post-link.sh b/recipes/bioconductor-hgu133plus2cdf/post-link.sh index 2ef6564bd2c0d..e7730f7529988 100644 --- a/recipes/bioconductor-hgu133plus2cdf/post-link.sh +++ b/recipes/bioconductor-hgu133plus2cdf/post-link.sh @@ -1,9 +1,10 @@ #!/bin/bash FN="hgu133plus2cdf_2.18.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/hgu133plus2cdf_2.18.0.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/hgu133plus2cdf_2.18.0.tar.gz" "https://bioarchive.galaxyproject.org/hgu133plus2cdf_2.18.0.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-hgu133plus2cdf/bioconductor-hgu133plus2cdf_2.18.0_src_all.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-hgu133plus2cdf/bioconductor-hgu133plus2cdf_2.18.0_src_all.tar.gz" ) MD5="284fef2f0b777d7b53451538ddd53de3" @@ -16,7 +17,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-hgu133plus2cellscore/meta.yaml b/recipes/bioconductor-hgu133plus2cellscore/meta.yaml index b5cec8370fe00..84bd8fa766b40 100644 --- a/recipes/bioconductor-hgu133plus2cellscore/meta.yaml +++ b/recipes/bioconductor-hgu133plus2cellscore/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.2.0" %} +{% set version = "1.4.0" %} {% set name = "hgu133plus2CellScore" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 354194eddcc3f67ac375b08422007602 + md5: db5ad2756c518d14e1f2ed55e3794d16 build: number: 0 rpaths: @@ -20,12 +20,12 @@ build: # Suggests: knitr requirements: host: - - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' - r-base run: - - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-hgu133plus2cellscore/post-link.sh b/recipes/bioconductor-hgu133plus2cellscore/post-link.sh index 2e4683f16db8b..b2f226759c46b 100644 --- a/recipes/bioconductor-hgu133plus2cellscore/post-link.sh +++ b/recipes/bioconductor-hgu133plus2cellscore/post-link.sh @@ -1,11 +1,11 @@ #!/bin/bash -FN="hgu133plus2CellScore_1.2.0.tar.gz" +FN="hgu133plus2CellScore_1.4.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/experiment/src/contrib/hgu133plus2CellScore_1.2.0.tar.gz" - "https://bioarchive.galaxyproject.org/hgu133plus2CellScore_1.2.0.tar.gz" - "https://depot.galaxyproject.org/software/bioconductor-hgu133plus2cellscore/bioconductor-hgu133plus2cellscore_1.2.0_src_all.tar.gz" + "https://bioconductor.org/packages/3.9/data/experiment/src/contrib/hgu133plus2CellScore_1.4.0.tar.gz" + "https://bioarchive.galaxyproject.org/hgu133plus2CellScore_1.4.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-hgu133plus2cellscore/bioconductor-hgu133plus2cellscore_1.4.0_src_all.tar.gz" ) -MD5="354194eddcc3f67ac375b08422007602" +MD5="db5ad2756c518d14e1f2ed55e3794d16" # Use a staging area in the conda dir rather than temp dirs, both to avoid # permission issues as well as to have things downloaded in a predictable @@ -16,7 +16,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-hgu133plus2frmavecs/meta.yaml b/recipes/bioconductor-hgu133plus2frmavecs/meta.yaml index 0e76aa1829eb4..5f7616d2552bf 100644 --- a/recipes/bioconductor-hgu133plus2frmavecs/meta.yaml +++ b/recipes/bioconductor-hgu133plus2frmavecs/meta.yaml @@ -1,6 +1,6 @@ {% set version = "1.5.0" %} {% set name = "hgu133plus2frmavecs" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -12,7 +12,7 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: a4781cbcccc1ee17dfd16259f1c7bebc build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ @@ -22,7 +22,7 @@ requirements: - r-base run: - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-hgu133plus2frmavecs/post-link.sh b/recipes/bioconductor-hgu133plus2frmavecs/post-link.sh index 42f0febf0fa10..881e4cb0cad2f 100644 --- a/recipes/bioconductor-hgu133plus2frmavecs/post-link.sh +++ b/recipes/bioconductor-hgu133plus2frmavecs/post-link.sh @@ -1,9 +1,10 @@ #!/bin/bash FN="hgu133plus2frmavecs_1.5.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/hgu133plus2frmavecs_1.5.0.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/hgu133plus2frmavecs_1.5.0.tar.gz" "https://bioarchive.galaxyproject.org/hgu133plus2frmavecs_1.5.0.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-hgu133plus2frmavecs/bioconductor-hgu133plus2frmavecs_1.5.0_src_all.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-hgu133plus2frmavecs/bioconductor-hgu133plus2frmavecs_1.5.0_src_all.tar.gz" ) MD5="a4781cbcccc1ee17dfd16259f1c7bebc" @@ -16,7 +17,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-hgu133plus2probe/meta.yaml b/recipes/bioconductor-hgu133plus2probe/meta.yaml index 3b782bac87614..2dbdb0cb26d2f 100644 --- a/recipes/bioconductor-hgu133plus2probe/meta.yaml +++ b/recipes/bioconductor-hgu133plus2probe/meta.yaml @@ -1,6 +1,6 @@ {% set version = "2.18.0" %} {% set name = "hgu133plus2probe" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -12,19 +12,19 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 7a244787a0269bc72732ac3d830f34dd build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' - r-base run: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-hgu133plus2probe/post-link.sh b/recipes/bioconductor-hgu133plus2probe/post-link.sh index 8cfd65258b5ef..da033a15b302e 100644 --- a/recipes/bioconductor-hgu133plus2probe/post-link.sh +++ b/recipes/bioconductor-hgu133plus2probe/post-link.sh @@ -1,9 +1,10 @@ #!/bin/bash FN="hgu133plus2probe_2.18.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/hgu133plus2probe_2.18.0.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/hgu133plus2probe_2.18.0.tar.gz" "https://bioarchive.galaxyproject.org/hgu133plus2probe_2.18.0.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-hgu133plus2probe/bioconductor-hgu133plus2probe_2.18.0_src_all.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-hgu133plus2probe/bioconductor-hgu133plus2probe_2.18.0_src_all.tar.gz" ) MD5="7a244787a0269bc72732ac3d830f34dd" @@ -16,7 +17,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-hgu219.db/meta.yaml b/recipes/bioconductor-hgu219.db/meta.yaml index 33c546ffc5c6b..10443f05db367 100644 --- a/recipes/bioconductor-hgu219.db/meta.yaml +++ b/recipes/bioconductor-hgu219.db/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.2.3" %} {% set name = "hgu219.db" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -12,7 +12,7 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: a4a0fd2ac170a75d8b17618615fcd7a0 build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ @@ -20,14 +20,14 @@ build: # Suggests: DBI, annotate, RUnit requirements: host: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' - - 'bioconductor-org.hs.eg.db >=3.7.0,<3.8.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' + - 'bioconductor-org.hs.eg.db >=3.8.0,<3.9.0' - r-base run: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' - - 'bioconductor-org.hs.eg.db >=3.7.0,<3.8.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' + - 'bioconductor-org.hs.eg.db >=3.8.0,<3.9.0' - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-hgu219.db/post-link.sh b/recipes/bioconductor-hgu219.db/post-link.sh index 6e0d3f12c17a1..1efcbfed296d7 100644 --- a/recipes/bioconductor-hgu219.db/post-link.sh +++ b/recipes/bioconductor-hgu219.db/post-link.sh @@ -1,9 +1,10 @@ #!/bin/bash FN="hgu219.db_3.2.3.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/hgu219.db_3.2.3.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/hgu219.db_3.2.3.tar.gz" "https://bioarchive.galaxyproject.org/hgu219.db_3.2.3.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-hgu219.db/bioconductor-hgu219.db_3.2.3_src_all.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-hgu219.db/bioconductor-hgu219.db_3.2.3_src_all.tar.gz" ) MD5="a4a0fd2ac170a75d8b17618615fcd7a0" @@ -16,7 +17,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-hgu219cdf/meta.yaml b/recipes/bioconductor-hgu219cdf/meta.yaml index a04736e216f6d..cc00fcaf1ed1d 100644 --- a/recipes/bioconductor-hgu219cdf/meta.yaml +++ b/recipes/bioconductor-hgu219cdf/meta.yaml @@ -1,6 +1,6 @@ {% set version = "2.18.0" %} {% set name = "hgu219cdf" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -12,19 +12,19 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 157a4280a9de960902260ab18f678949 build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' - r-base run: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-hgu219cdf/post-link.sh b/recipes/bioconductor-hgu219cdf/post-link.sh index 7a7b1e893ce0e..a3ce704821d84 100644 --- a/recipes/bioconductor-hgu219cdf/post-link.sh +++ b/recipes/bioconductor-hgu219cdf/post-link.sh @@ -1,9 +1,10 @@ #!/bin/bash FN="hgu219cdf_2.18.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/hgu219cdf_2.18.0.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/hgu219cdf_2.18.0.tar.gz" "https://bioarchive.galaxyproject.org/hgu219cdf_2.18.0.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-hgu219cdf/bioconductor-hgu219cdf_2.18.0_src_all.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-hgu219cdf/bioconductor-hgu219cdf_2.18.0_src_all.tar.gz" ) MD5="157a4280a9de960902260ab18f678949" @@ -16,7 +17,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-hgu219probe/meta.yaml b/recipes/bioconductor-hgu219probe/meta.yaml index b42e348bc9519..dc65881e5b271 100644 --- a/recipes/bioconductor-hgu219probe/meta.yaml +++ b/recipes/bioconductor-hgu219probe/meta.yaml @@ -1,6 +1,6 @@ {% set version = "2.18.0" %} {% set name = "hgu219probe" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -12,19 +12,19 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: c5bb2f7b2e0f8fa89e6a30befaee6497 build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' - r-base run: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-hgu219probe/post-link.sh b/recipes/bioconductor-hgu219probe/post-link.sh index 47745a1cf31cd..545283661a1db 100644 --- a/recipes/bioconductor-hgu219probe/post-link.sh +++ b/recipes/bioconductor-hgu219probe/post-link.sh @@ -1,9 +1,10 @@ #!/bin/bash FN="hgu219probe_2.18.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/hgu219probe_2.18.0.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/hgu219probe_2.18.0.tar.gz" "https://bioarchive.galaxyproject.org/hgu219probe_2.18.0.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-hgu219probe/bioconductor-hgu219probe_2.18.0_src_all.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-hgu219probe/bioconductor-hgu219probe_2.18.0_src_all.tar.gz" ) MD5="c5bb2f7b2e0f8fa89e6a30befaee6497" @@ -16,7 +17,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-hgu2beta7/meta.yaml b/recipes/bioconductor-hgu2beta7/meta.yaml index ce65b5ba5caae..d927ad5e5ceca 100644 --- a/recipes/bioconductor-hgu2beta7/meta.yaml +++ b/recipes/bioconductor-hgu2beta7/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.22.0" %} +{% set version = "1.24.0" %} {% set name = "hgu2beta7" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 66fe43b6e1b602122964c9026dc9a660 + md5: 26d4ad63ca4429968dbdd8d981436c13 build: number: 0 rpaths: @@ -22,7 +22,7 @@ requirements: - r-base run: - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-hgu2beta7/post-link.sh b/recipes/bioconductor-hgu2beta7/post-link.sh index fbb30749e69d8..785ce7e4f7833 100644 --- a/recipes/bioconductor-hgu2beta7/post-link.sh +++ b/recipes/bioconductor-hgu2beta7/post-link.sh @@ -1,11 +1,11 @@ #!/bin/bash -FN="hgu2beta7_1.22.0.tar.gz" +FN="hgu2beta7_1.24.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/experiment/src/contrib/hgu2beta7_1.22.0.tar.gz" - "https://bioarchive.galaxyproject.org/hgu2beta7_1.22.0.tar.gz" - "https://depot.galaxyproject.org/software/bioconductor-hgu2beta7/bioconductor-hgu2beta7_1.22.0_src_all.tar.gz" + "https://bioconductor.org/packages/3.9/data/experiment/src/contrib/hgu2beta7_1.24.0.tar.gz" + "https://bioarchive.galaxyproject.org/hgu2beta7_1.24.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-hgu2beta7/bioconductor-hgu2beta7_1.24.0_src_all.tar.gz" ) -MD5="66fe43b6e1b602122964c9026dc9a660" +MD5="26d4ad63ca4429968dbdd8d981436c13" # Use a staging area in the conda dir rather than temp dirs, both to avoid # permission issues as well as to have things downloaded in a predictable @@ -16,7 +16,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-hgu95a.db/meta.yaml b/recipes/bioconductor-hgu95a.db/meta.yaml index fc79c9284690d..22a9e068eba98 100644 --- a/recipes/bioconductor-hgu95a.db/meta.yaml +++ b/recipes/bioconductor-hgu95a.db/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.2.3" %} {% set name = "hgu95a.db" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -12,7 +12,7 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: e509dd32292601d81af8aa61ec782ca7 build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ @@ -20,14 +20,14 @@ build: # Suggests: DBI, annotate, RUnit requirements: host: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' - - 'bioconductor-org.hs.eg.db >=3.7.0,<3.8.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' + - 'bioconductor-org.hs.eg.db >=3.8.0,<3.9.0' - r-base run: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' - - 'bioconductor-org.hs.eg.db >=3.7.0,<3.8.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' + - 'bioconductor-org.hs.eg.db >=3.8.0,<3.9.0' - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-hgu95a.db/post-link.sh b/recipes/bioconductor-hgu95a.db/post-link.sh index ffdee503dfde8..4c044625d6c31 100644 --- a/recipes/bioconductor-hgu95a.db/post-link.sh +++ b/recipes/bioconductor-hgu95a.db/post-link.sh @@ -1,9 +1,10 @@ #!/bin/bash FN="hgu95a.db_3.2.3.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/hgu95a.db_3.2.3.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/hgu95a.db_3.2.3.tar.gz" "https://bioarchive.galaxyproject.org/hgu95a.db_3.2.3.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-hgu95a.db/bioconductor-hgu95a.db_3.2.3_src_all.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-hgu95a.db/bioconductor-hgu95a.db_3.2.3_src_all.tar.gz" ) MD5="e509dd32292601d81af8aa61ec782ca7" @@ -16,7 +17,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-hgu95acdf/meta.yaml b/recipes/bioconductor-hgu95acdf/meta.yaml index 51ca4b15e7026..67121a654aabf 100644 --- a/recipes/bioconductor-hgu95acdf/meta.yaml +++ b/recipes/bioconductor-hgu95acdf/meta.yaml @@ -1,6 +1,6 @@ {% set version = "2.18.0" %} {% set name = "hgu95acdf" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -12,19 +12,19 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: afc999d77b1532154d45911ad15a5897 build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' - r-base run: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-hgu95acdf/post-link.sh b/recipes/bioconductor-hgu95acdf/post-link.sh index f0ff2131b842b..9da764f6ffd37 100644 --- a/recipes/bioconductor-hgu95acdf/post-link.sh +++ b/recipes/bioconductor-hgu95acdf/post-link.sh @@ -1,9 +1,10 @@ #!/bin/bash FN="hgu95acdf_2.18.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/hgu95acdf_2.18.0.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/hgu95acdf_2.18.0.tar.gz" "https://bioarchive.galaxyproject.org/hgu95acdf_2.18.0.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-hgu95acdf/bioconductor-hgu95acdf_2.18.0_src_all.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-hgu95acdf/bioconductor-hgu95acdf_2.18.0_src_all.tar.gz" ) MD5="afc999d77b1532154d45911ad15a5897" @@ -16,7 +17,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-hgu95aprobe/meta.yaml b/recipes/bioconductor-hgu95aprobe/meta.yaml index 0894785612641..83580c93f08fc 100644 --- a/recipes/bioconductor-hgu95aprobe/meta.yaml +++ b/recipes/bioconductor-hgu95aprobe/meta.yaml @@ -1,6 +1,6 @@ {% set version = "2.18.0" %} {% set name = "hgu95aprobe" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -12,19 +12,19 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 67d94ecdc1889acc19dafd19d26700a2 build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' - r-base run: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-hgu95aprobe/post-link.sh b/recipes/bioconductor-hgu95aprobe/post-link.sh index 781cc5229197d..5949f307e58d0 100644 --- a/recipes/bioconductor-hgu95aprobe/post-link.sh +++ b/recipes/bioconductor-hgu95aprobe/post-link.sh @@ -1,9 +1,10 @@ #!/bin/bash FN="hgu95aprobe_2.18.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/hgu95aprobe_2.18.0.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/hgu95aprobe_2.18.0.tar.gz" "https://bioarchive.galaxyproject.org/hgu95aprobe_2.18.0.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-hgu95aprobe/bioconductor-hgu95aprobe_2.18.0_src_all.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-hgu95aprobe/bioconductor-hgu95aprobe_2.18.0_src_all.tar.gz" ) MD5="67d94ecdc1889acc19dafd19d26700a2" @@ -16,7 +17,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-hgu95av2.db/meta.yaml b/recipes/bioconductor-hgu95av2.db/meta.yaml index 8d68fc38bf99b..b5dd767997dd2 100644 --- a/recipes/bioconductor-hgu95av2.db/meta.yaml +++ b/recipes/bioconductor-hgu95av2.db/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.2.3" %} {% set name = "hgu95av2.db" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -12,7 +12,7 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: a0ee1ba7f115a1504ca89619a0bc56dd build: - number: 3 + number: 4 rpaths: - lib/R/lib/ - lib/ @@ -20,14 +20,14 @@ build: # Suggests: DBI, annotate, RUnit requirements: host: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' - - 'bioconductor-org.hs.eg.db >=3.7.0,<3.8.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' + - 'bioconductor-org.hs.eg.db >=3.8.0,<3.9.0' - r-base run: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' - - 'bioconductor-org.hs.eg.db >=3.7.0,<3.8.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' + - 'bioconductor-org.hs.eg.db >=3.8.0,<3.9.0' - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-hgu95av2.db/post-link.sh b/recipes/bioconductor-hgu95av2.db/post-link.sh index f8e1f0de85dff..a82f43e1d1ec3 100644 --- a/recipes/bioconductor-hgu95av2.db/post-link.sh +++ b/recipes/bioconductor-hgu95av2.db/post-link.sh @@ -1,7 +1,7 @@ #!/bin/bash FN="hgu95av2.db_3.2.3.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/hgu95av2.db_3.2.3.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/hgu95av2.db_3.2.3.tar.gz" "https://bioarchive.galaxyproject.org/hgu95av2.db_3.2.3.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-hgu95av2.db/bioconductor-hgu95av2.db_3.2.3_src_all.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-hgu95av2.db/bioconductor-hgu95av2.db_3.2.3_src_all.tar.gz" @@ -17,7 +17,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-hgu95av2/meta.yaml b/recipes/bioconductor-hgu95av2/meta.yaml index df87105dfd118..c6e7386147232 100644 --- a/recipes/bioconductor-hgu95av2/meta.yaml +++ b/recipes/bioconductor-hgu95av2/meta.yaml @@ -1,6 +1,6 @@ {% set version = "2.2.0" %} {% set name = "hgu95av2" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -12,7 +12,7 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: b92585c0f43e91bd1abd234b9465a6a7 build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ @@ -22,7 +22,7 @@ requirements: - r-base run: - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-hgu95av2/post-link.sh b/recipes/bioconductor-hgu95av2/post-link.sh index b027a27e7477b..7e416406631df 100644 --- a/recipes/bioconductor-hgu95av2/post-link.sh +++ b/recipes/bioconductor-hgu95av2/post-link.sh @@ -1,9 +1,10 @@ #!/bin/bash FN="hgu95av2_2.2.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/hgu95av2_2.2.0.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/hgu95av2_2.2.0.tar.gz" "https://bioarchive.galaxyproject.org/hgu95av2_2.2.0.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-hgu95av2/bioconductor-hgu95av2_2.2.0_src_all.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-hgu95av2/bioconductor-hgu95av2_2.2.0_src_all.tar.gz" ) MD5="b92585c0f43e91bd1abd234b9465a6a7" @@ -16,7 +17,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-hgu95av2cdf/meta.yaml b/recipes/bioconductor-hgu95av2cdf/meta.yaml index 2dd366ea3584d..7c6760486583c 100644 --- a/recipes/bioconductor-hgu95av2cdf/meta.yaml +++ b/recipes/bioconductor-hgu95av2cdf/meta.yaml @@ -1,6 +1,6 @@ {% set version = "2.18.0" %} {% set name = "hgu95av2cdf" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -12,19 +12,19 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 026bae2f76433593f75ca6c79bc9a9d0 build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' - r-base run: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-hgu95av2cdf/post-link.sh b/recipes/bioconductor-hgu95av2cdf/post-link.sh index 0aa7f29b39e09..7bb40d62922f1 100644 --- a/recipes/bioconductor-hgu95av2cdf/post-link.sh +++ b/recipes/bioconductor-hgu95av2cdf/post-link.sh @@ -1,9 +1,10 @@ #!/bin/bash FN="hgu95av2cdf_2.18.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/hgu95av2cdf_2.18.0.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/hgu95av2cdf_2.18.0.tar.gz" "https://bioarchive.galaxyproject.org/hgu95av2cdf_2.18.0.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-hgu95av2cdf/bioconductor-hgu95av2cdf_2.18.0_src_all.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-hgu95av2cdf/bioconductor-hgu95av2cdf_2.18.0_src_all.tar.gz" ) MD5="026bae2f76433593f75ca6c79bc9a9d0" @@ -16,7 +17,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-hgu95av2probe/meta.yaml b/recipes/bioconductor-hgu95av2probe/meta.yaml index 357d23999dbda..602e9356e7ad4 100644 --- a/recipes/bioconductor-hgu95av2probe/meta.yaml +++ b/recipes/bioconductor-hgu95av2probe/meta.yaml @@ -1,6 +1,6 @@ {% set version = "2.18.0" %} {% set name = "hgu95av2probe" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -12,19 +12,19 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: d3efb56f7e7a264b633fac787a5a2b95 build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' - r-base run: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-hgu95av2probe/post-link.sh b/recipes/bioconductor-hgu95av2probe/post-link.sh index c2eb80031eb64..74bb80c4c3b3a 100644 --- a/recipes/bioconductor-hgu95av2probe/post-link.sh +++ b/recipes/bioconductor-hgu95av2probe/post-link.sh @@ -1,9 +1,10 @@ #!/bin/bash FN="hgu95av2probe_2.18.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/hgu95av2probe_2.18.0.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/hgu95av2probe_2.18.0.tar.gz" "https://bioarchive.galaxyproject.org/hgu95av2probe_2.18.0.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-hgu95av2probe/bioconductor-hgu95av2probe_2.18.0_src_all.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-hgu95av2probe/bioconductor-hgu95av2probe_2.18.0_src_all.tar.gz" ) MD5="d3efb56f7e7a264b633fac787a5a2b95" @@ -16,7 +17,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-hgu95b.db/meta.yaml b/recipes/bioconductor-hgu95b.db/meta.yaml index 2457ac4002295..34349d9151f8b 100644 --- a/recipes/bioconductor-hgu95b.db/meta.yaml +++ b/recipes/bioconductor-hgu95b.db/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.2.3" %} {% set name = "hgu95b.db" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -12,7 +12,7 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: c532e54fd7087f1b1cce0c1e61ae1c16 build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ @@ -20,14 +20,14 @@ build: # Suggests: DBI, annotate, RUnit requirements: host: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' - - 'bioconductor-org.hs.eg.db >=3.7.0,<3.8.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' + - 'bioconductor-org.hs.eg.db >=3.8.0,<3.9.0' - r-base run: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' - - 'bioconductor-org.hs.eg.db >=3.7.0,<3.8.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' + - 'bioconductor-org.hs.eg.db >=3.8.0,<3.9.0' - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-hgu95b.db/post-link.sh b/recipes/bioconductor-hgu95b.db/post-link.sh index 23ea569b20c19..e936e2c6c4a44 100644 --- a/recipes/bioconductor-hgu95b.db/post-link.sh +++ b/recipes/bioconductor-hgu95b.db/post-link.sh @@ -1,9 +1,10 @@ #!/bin/bash FN="hgu95b.db_3.2.3.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/hgu95b.db_3.2.3.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/hgu95b.db_3.2.3.tar.gz" "https://bioarchive.galaxyproject.org/hgu95b.db_3.2.3.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-hgu95b.db/bioconductor-hgu95b.db_3.2.3_src_all.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-hgu95b.db/bioconductor-hgu95b.db_3.2.3_src_all.tar.gz" ) MD5="c532e54fd7087f1b1cce0c1e61ae1c16" @@ -16,7 +17,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-hgu95bcdf/meta.yaml b/recipes/bioconductor-hgu95bcdf/meta.yaml index 134321e0a5665..b5f6297031a07 100644 --- a/recipes/bioconductor-hgu95bcdf/meta.yaml +++ b/recipes/bioconductor-hgu95bcdf/meta.yaml @@ -1,6 +1,6 @@ {% set version = "2.18.0" %} {% set name = "hgu95bcdf" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -12,19 +12,19 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: e6e56b7a107bb2df25b3c25a8191385d build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' - r-base run: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-hgu95bcdf/post-link.sh b/recipes/bioconductor-hgu95bcdf/post-link.sh index ac47f078abf73..50f163f9450e1 100644 --- a/recipes/bioconductor-hgu95bcdf/post-link.sh +++ b/recipes/bioconductor-hgu95bcdf/post-link.sh @@ -1,9 +1,10 @@ #!/bin/bash FN="hgu95bcdf_2.18.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/hgu95bcdf_2.18.0.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/hgu95bcdf_2.18.0.tar.gz" "https://bioarchive.galaxyproject.org/hgu95bcdf_2.18.0.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-hgu95bcdf/bioconductor-hgu95bcdf_2.18.0_src_all.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-hgu95bcdf/bioconductor-hgu95bcdf_2.18.0_src_all.tar.gz" ) MD5="e6e56b7a107bb2df25b3c25a8191385d" @@ -16,7 +17,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-hgu95bprobe/meta.yaml b/recipes/bioconductor-hgu95bprobe/meta.yaml index a2cab30e0e15e..935a30f80b112 100644 --- a/recipes/bioconductor-hgu95bprobe/meta.yaml +++ b/recipes/bioconductor-hgu95bprobe/meta.yaml @@ -1,6 +1,6 @@ {% set version = "2.18.0" %} {% set name = "hgu95bprobe" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -12,19 +12,19 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 60dcb57fd402dc24d53ef9390c893cfc build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' - r-base run: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-hgu95bprobe/post-link.sh b/recipes/bioconductor-hgu95bprobe/post-link.sh index c11144c32d5c0..3ee4741a883f5 100644 --- a/recipes/bioconductor-hgu95bprobe/post-link.sh +++ b/recipes/bioconductor-hgu95bprobe/post-link.sh @@ -1,9 +1,10 @@ #!/bin/bash FN="hgu95bprobe_2.18.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/hgu95bprobe_2.18.0.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/hgu95bprobe_2.18.0.tar.gz" "https://bioarchive.galaxyproject.org/hgu95bprobe_2.18.0.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-hgu95bprobe/bioconductor-hgu95bprobe_2.18.0_src_all.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-hgu95bprobe/bioconductor-hgu95bprobe_2.18.0_src_all.tar.gz" ) MD5="60dcb57fd402dc24d53ef9390c893cfc" @@ -16,7 +17,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-hgu95c.db/meta.yaml b/recipes/bioconductor-hgu95c.db/meta.yaml index 16ca6ee86075a..3bd1c3a791597 100644 --- a/recipes/bioconductor-hgu95c.db/meta.yaml +++ b/recipes/bioconductor-hgu95c.db/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.2.3" %} {% set name = "hgu95c.db" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -12,7 +12,7 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 273595199acfafe4c50182916c9893ca build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ @@ -20,14 +20,14 @@ build: # Suggests: DBI, annotate, RUnit requirements: host: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' - - 'bioconductor-org.hs.eg.db >=3.7.0,<3.8.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' + - 'bioconductor-org.hs.eg.db >=3.8.0,<3.9.0' - r-base run: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' - - 'bioconductor-org.hs.eg.db >=3.7.0,<3.8.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' + - 'bioconductor-org.hs.eg.db >=3.8.0,<3.9.0' - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-hgu95c.db/post-link.sh b/recipes/bioconductor-hgu95c.db/post-link.sh index 36522464748ca..349e689e5b4f1 100644 --- a/recipes/bioconductor-hgu95c.db/post-link.sh +++ b/recipes/bioconductor-hgu95c.db/post-link.sh @@ -1,9 +1,10 @@ #!/bin/bash FN="hgu95c.db_3.2.3.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/hgu95c.db_3.2.3.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/hgu95c.db_3.2.3.tar.gz" "https://bioarchive.galaxyproject.org/hgu95c.db_3.2.3.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-hgu95c.db/bioconductor-hgu95c.db_3.2.3_src_all.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-hgu95c.db/bioconductor-hgu95c.db_3.2.3_src_all.tar.gz" ) MD5="273595199acfafe4c50182916c9893ca" @@ -16,7 +17,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-hgu95ccdf/meta.yaml b/recipes/bioconductor-hgu95ccdf/meta.yaml index 52683b8e05c7e..3f20f06c0fa33 100644 --- a/recipes/bioconductor-hgu95ccdf/meta.yaml +++ b/recipes/bioconductor-hgu95ccdf/meta.yaml @@ -1,6 +1,6 @@ {% set version = "2.18.0" %} {% set name = "hgu95ccdf" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -12,19 +12,19 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 976151eac05c320aec7a24397a6b5806 build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' - r-base run: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-hgu95ccdf/post-link.sh b/recipes/bioconductor-hgu95ccdf/post-link.sh index acfe3b381336c..de5605e2842dd 100644 --- a/recipes/bioconductor-hgu95ccdf/post-link.sh +++ b/recipes/bioconductor-hgu95ccdf/post-link.sh @@ -1,9 +1,10 @@ #!/bin/bash FN="hgu95ccdf_2.18.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/hgu95ccdf_2.18.0.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/hgu95ccdf_2.18.0.tar.gz" "https://bioarchive.galaxyproject.org/hgu95ccdf_2.18.0.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-hgu95ccdf/bioconductor-hgu95ccdf_2.18.0_src_all.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-hgu95ccdf/bioconductor-hgu95ccdf_2.18.0_src_all.tar.gz" ) MD5="976151eac05c320aec7a24397a6b5806" @@ -16,7 +17,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-hgu95cprobe/meta.yaml b/recipes/bioconductor-hgu95cprobe/meta.yaml index 2cad6e52a8376..8212820b083aa 100644 --- a/recipes/bioconductor-hgu95cprobe/meta.yaml +++ b/recipes/bioconductor-hgu95cprobe/meta.yaml @@ -1,6 +1,6 @@ {% set version = "2.18.0" %} {% set name = "hgu95cprobe" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -12,19 +12,19 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 3fe935a52c70105dc7a214174c946455 build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' - r-base run: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-hgu95cprobe/post-link.sh b/recipes/bioconductor-hgu95cprobe/post-link.sh index 6c72c2cfe35b2..24481366da8cb 100644 --- a/recipes/bioconductor-hgu95cprobe/post-link.sh +++ b/recipes/bioconductor-hgu95cprobe/post-link.sh @@ -1,9 +1,10 @@ #!/bin/bash FN="hgu95cprobe_2.18.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/hgu95cprobe_2.18.0.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/hgu95cprobe_2.18.0.tar.gz" "https://bioarchive.galaxyproject.org/hgu95cprobe_2.18.0.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-hgu95cprobe/bioconductor-hgu95cprobe_2.18.0_src_all.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-hgu95cprobe/bioconductor-hgu95cprobe_2.18.0_src_all.tar.gz" ) MD5="3fe935a52c70105dc7a214174c946455" @@ -16,7 +17,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-hgu95d.db/meta.yaml b/recipes/bioconductor-hgu95d.db/meta.yaml index 4f90320f19780..67e588496db2d 100644 --- a/recipes/bioconductor-hgu95d.db/meta.yaml +++ b/recipes/bioconductor-hgu95d.db/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.2.3" %} {% set name = "hgu95d.db" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -12,7 +12,7 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: e56da8022bb88c1cd495ea516eae6613 build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ @@ -20,14 +20,14 @@ build: # Suggests: DBI, annotate, RUnit requirements: host: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' - - 'bioconductor-org.hs.eg.db >=3.7.0,<3.8.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' + - 'bioconductor-org.hs.eg.db >=3.8.0,<3.9.0' - r-base run: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' - - 'bioconductor-org.hs.eg.db >=3.7.0,<3.8.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' + - 'bioconductor-org.hs.eg.db >=3.8.0,<3.9.0' - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-hgu95d.db/post-link.sh b/recipes/bioconductor-hgu95d.db/post-link.sh index ce756fc368adb..32c056cb48fef 100644 --- a/recipes/bioconductor-hgu95d.db/post-link.sh +++ b/recipes/bioconductor-hgu95d.db/post-link.sh @@ -1,9 +1,10 @@ #!/bin/bash FN="hgu95d.db_3.2.3.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/hgu95d.db_3.2.3.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/hgu95d.db_3.2.3.tar.gz" "https://bioarchive.galaxyproject.org/hgu95d.db_3.2.3.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-hgu95d.db/bioconductor-hgu95d.db_3.2.3_src_all.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-hgu95d.db/bioconductor-hgu95d.db_3.2.3_src_all.tar.gz" ) MD5="e56da8022bb88c1cd495ea516eae6613" @@ -16,7 +17,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-hgu95dcdf/meta.yaml b/recipes/bioconductor-hgu95dcdf/meta.yaml index fcc0cfc6a3aa6..74a2b2847faa3 100644 --- a/recipes/bioconductor-hgu95dcdf/meta.yaml +++ b/recipes/bioconductor-hgu95dcdf/meta.yaml @@ -1,6 +1,6 @@ {% set version = "2.18.0" %} {% set name = "hgu95dcdf" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -12,19 +12,19 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 36e11ff001b1bec3f34ba7c93132ad6f build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' - r-base run: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-hgu95dcdf/post-link.sh b/recipes/bioconductor-hgu95dcdf/post-link.sh index 7abd799673d67..a1ba83239027b 100644 --- a/recipes/bioconductor-hgu95dcdf/post-link.sh +++ b/recipes/bioconductor-hgu95dcdf/post-link.sh @@ -1,9 +1,10 @@ #!/bin/bash FN="hgu95dcdf_2.18.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/hgu95dcdf_2.18.0.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/hgu95dcdf_2.18.0.tar.gz" "https://bioarchive.galaxyproject.org/hgu95dcdf_2.18.0.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-hgu95dcdf/bioconductor-hgu95dcdf_2.18.0_src_all.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-hgu95dcdf/bioconductor-hgu95dcdf_2.18.0_src_all.tar.gz" ) MD5="36e11ff001b1bec3f34ba7c93132ad6f" @@ -16,7 +17,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-hgu95dprobe/meta.yaml b/recipes/bioconductor-hgu95dprobe/meta.yaml index 0104d46e15936..82e645661f0f9 100644 --- a/recipes/bioconductor-hgu95dprobe/meta.yaml +++ b/recipes/bioconductor-hgu95dprobe/meta.yaml @@ -1,6 +1,6 @@ {% set version = "2.18.0" %} {% set name = "hgu95dprobe" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -12,19 +12,19 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 165ce5029f49fc515b9ee0e6a6a29cb5 build: - number: 1 + number: 2 rpaths: - lib/R/lib/ - lib/ noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' - r-base run: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-hgu95dprobe/post-link.sh b/recipes/bioconductor-hgu95dprobe/post-link.sh index d2186f470e988..92b2226f17422 100644 --- a/recipes/bioconductor-hgu95dprobe/post-link.sh +++ b/recipes/bioconductor-hgu95dprobe/post-link.sh @@ -1,9 +1,10 @@ #!/bin/bash FN="hgu95dprobe_2.18.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/hgu95dprobe_2.18.0.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/hgu95dprobe_2.18.0.tar.gz" "https://bioarchive.galaxyproject.org/hgu95dprobe_2.18.0.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-hgu95dprobe/bioconductor-hgu95dprobe_2.18.0_src_all.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-hgu95dprobe/bioconductor-hgu95dprobe_2.18.0_src_all.tar.gz" ) MD5="165ce5029f49fc515b9ee0e6a6a29cb5" @@ -16,7 +17,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-hgu95e.db/meta.yaml b/recipes/bioconductor-hgu95e.db/meta.yaml index 2ea4a0b5d664a..9e278b04edb17 100644 --- a/recipes/bioconductor-hgu95e.db/meta.yaml +++ b/recipes/bioconductor-hgu95e.db/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.2.3" %} {% set name = "hgu95e.db" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -12,7 +12,7 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 18bbf38f91172616a7f78e63e85630e5 build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ @@ -20,14 +20,14 @@ build: # Suggests: DBI, annotate, RUnit requirements: host: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' - - 'bioconductor-org.hs.eg.db >=3.7.0,<3.8.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' + - 'bioconductor-org.hs.eg.db >=3.8.0,<3.9.0' - r-base run: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' - - 'bioconductor-org.hs.eg.db >=3.7.0,<3.8.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' + - 'bioconductor-org.hs.eg.db >=3.8.0,<3.9.0' - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-hgu95e.db/post-link.sh b/recipes/bioconductor-hgu95e.db/post-link.sh index 28952b0d58bf0..0de3a4efd27d7 100644 --- a/recipes/bioconductor-hgu95e.db/post-link.sh +++ b/recipes/bioconductor-hgu95e.db/post-link.sh @@ -1,9 +1,10 @@ #!/bin/bash FN="hgu95e.db_3.2.3.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/hgu95e.db_3.2.3.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/hgu95e.db_3.2.3.tar.gz" "https://bioarchive.galaxyproject.org/hgu95e.db_3.2.3.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-hgu95e.db/bioconductor-hgu95e.db_3.2.3_src_all.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-hgu95e.db/bioconductor-hgu95e.db_3.2.3_src_all.tar.gz" ) MD5="18bbf38f91172616a7f78e63e85630e5" @@ -16,7 +17,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-hgu95ecdf/meta.yaml b/recipes/bioconductor-hgu95ecdf/meta.yaml index d352448a2348b..013683f094fe0 100644 --- a/recipes/bioconductor-hgu95ecdf/meta.yaml +++ b/recipes/bioconductor-hgu95ecdf/meta.yaml @@ -1,6 +1,6 @@ {% set version = "2.18.0" %} {% set name = "hgu95ecdf" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -12,19 +12,19 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: fa27cfff62a38fc51640d797bd628105 build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' - r-base run: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-hgu95ecdf/post-link.sh b/recipes/bioconductor-hgu95ecdf/post-link.sh index 8420b9812c883..95401a7a5190e 100644 --- a/recipes/bioconductor-hgu95ecdf/post-link.sh +++ b/recipes/bioconductor-hgu95ecdf/post-link.sh @@ -1,9 +1,10 @@ #!/bin/bash FN="hgu95ecdf_2.18.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/hgu95ecdf_2.18.0.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/hgu95ecdf_2.18.0.tar.gz" "https://bioarchive.galaxyproject.org/hgu95ecdf_2.18.0.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-hgu95ecdf/bioconductor-hgu95ecdf_2.18.0_src_all.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-hgu95ecdf/bioconductor-hgu95ecdf_2.18.0_src_all.tar.gz" ) MD5="fa27cfff62a38fc51640d797bd628105" @@ -16,7 +17,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-hgu95eprobe/meta.yaml b/recipes/bioconductor-hgu95eprobe/meta.yaml index a4deb05bc5d40..13eba9f98f2c9 100644 --- a/recipes/bioconductor-hgu95eprobe/meta.yaml +++ b/recipes/bioconductor-hgu95eprobe/meta.yaml @@ -1,6 +1,6 @@ {% set version = "2.18.0" %} {% set name = "hgu95eprobe" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -12,19 +12,19 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 9e5407ab80c5bbb4065484be0b9c6191 build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' - r-base run: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-hgu95eprobe/post-link.sh b/recipes/bioconductor-hgu95eprobe/post-link.sh index 816a40afa83a7..a7ed400ba8c1d 100644 --- a/recipes/bioconductor-hgu95eprobe/post-link.sh +++ b/recipes/bioconductor-hgu95eprobe/post-link.sh @@ -1,9 +1,10 @@ #!/bin/bash FN="hgu95eprobe_2.18.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/hgu95eprobe_2.18.0.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/hgu95eprobe_2.18.0.tar.gz" "https://bioarchive.galaxyproject.org/hgu95eprobe_2.18.0.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-hgu95eprobe/bioconductor-hgu95eprobe_2.18.0_src_all.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-hgu95eprobe/bioconductor-hgu95eprobe_2.18.0_src_all.tar.gz" ) MD5="9e5407ab80c5bbb4065484be0b9c6191" @@ -16,7 +17,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-hguatlas13k.db/meta.yaml b/recipes/bioconductor-hguatlas13k.db/meta.yaml index 9f57c5f2bad27..9e09d5623147b 100644 --- a/recipes/bioconductor-hguatlas13k.db/meta.yaml +++ b/recipes/bioconductor-hguatlas13k.db/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.2.3" %} {% set name = "hguatlas13k.db" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -12,7 +12,7 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: ab9ffe1a1de44c0f938129f193e7fb63 build: - number: 1 + number: 2 rpaths: - lib/R/lib/ - lib/ @@ -20,14 +20,14 @@ build: # Suggests: DBI, annotate, RUnit requirements: host: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' - - 'bioconductor-org.hs.eg.db >=3.7.0,<3.8.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' + - 'bioconductor-org.hs.eg.db >=3.8.0,<3.9.0' - r-base run: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' - - 'bioconductor-org.hs.eg.db >=3.7.0,<3.8.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' + - 'bioconductor-org.hs.eg.db >=3.8.0,<3.9.0' - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-hguatlas13k.db/post-link.sh b/recipes/bioconductor-hguatlas13k.db/post-link.sh index 6399329cff633..631d105e3552b 100644 --- a/recipes/bioconductor-hguatlas13k.db/post-link.sh +++ b/recipes/bioconductor-hguatlas13k.db/post-link.sh @@ -1,9 +1,10 @@ #!/bin/bash FN="hguatlas13k.db_3.2.3.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/hguatlas13k.db_3.2.3.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/hguatlas13k.db_3.2.3.tar.gz" "https://bioarchive.galaxyproject.org/hguatlas13k.db_3.2.3.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-hguatlas13k.db/bioconductor-hguatlas13k.db_3.2.3_src_all.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-hguatlas13k.db/bioconductor-hguatlas13k.db_3.2.3_src_all.tar.gz" ) MD5="ab9ffe1a1de44c0f938129f193e7fb63" @@ -16,7 +17,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-hgubeta7.db/meta.yaml b/recipes/bioconductor-hgubeta7.db/meta.yaml index 6d285ad63348a..688b6e7bbd6e3 100644 --- a/recipes/bioconductor-hgubeta7.db/meta.yaml +++ b/recipes/bioconductor-hgubeta7.db/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.2.3" %} {% set name = "hgubeta7.db" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -12,7 +12,7 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 1b8b065f95d2089985f59f22dcabc824 build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ @@ -20,14 +20,14 @@ build: # Suggests: DBI, annotate, RUnit requirements: host: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' - - 'bioconductor-org.hs.eg.db >=3.7.0,<3.8.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' + - 'bioconductor-org.hs.eg.db >=3.8.0,<3.9.0' - r-base run: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' - - 'bioconductor-org.hs.eg.db >=3.7.0,<3.8.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' + - 'bioconductor-org.hs.eg.db >=3.8.0,<3.9.0' - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-hgubeta7.db/post-link.sh b/recipes/bioconductor-hgubeta7.db/post-link.sh index 6c2a8aafa4528..dfd00125f58e0 100644 --- a/recipes/bioconductor-hgubeta7.db/post-link.sh +++ b/recipes/bioconductor-hgubeta7.db/post-link.sh @@ -1,9 +1,10 @@ #!/bin/bash FN="hgubeta7.db_3.2.3.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/hgubeta7.db_3.2.3.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/hgubeta7.db_3.2.3.tar.gz" "https://bioarchive.galaxyproject.org/hgubeta7.db_3.2.3.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-hgubeta7.db/bioconductor-hgubeta7.db_3.2.3_src_all.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-hgubeta7.db/bioconductor-hgubeta7.db_3.2.3_src_all.tar.gz" ) MD5="1b8b065f95d2089985f59f22dcabc824" @@ -16,7 +17,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-hgudkfz31.db/meta.yaml b/recipes/bioconductor-hgudkfz31.db/meta.yaml index 0b351a983c07a..37dc2a8dc655d 100644 --- a/recipes/bioconductor-hgudkfz31.db/meta.yaml +++ b/recipes/bioconductor-hgudkfz31.db/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.2.3" %} {% set name = "hguDKFZ31.db" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -12,7 +12,7 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' md5: fa3ba493cebdac4253dea8fe5d58452b build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ @@ -20,14 +20,14 @@ build: # Suggests: DBI, annotate, RUnit requirements: host: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' - - 'bioconductor-org.hs.eg.db >=3.7.0,<3.8.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' + - 'bioconductor-org.hs.eg.db >=3.8.0,<3.9.0' - r-base run: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' - - 'bioconductor-org.hs.eg.db >=3.7.0,<3.8.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' + - 'bioconductor-org.hs.eg.db >=3.8.0,<3.9.0' - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-hgudkfz31.db/post-link.sh b/recipes/bioconductor-hgudkfz31.db/post-link.sh index 43950bde2d58b..888a3d1a24d83 100644 --- a/recipes/bioconductor-hgudkfz31.db/post-link.sh +++ b/recipes/bioconductor-hgudkfz31.db/post-link.sh @@ -1,9 +1,10 @@ #!/bin/bash FN="hguDKFZ31.db_3.2.3.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/hguDKFZ31.db_3.2.3.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/hguDKFZ31.db_3.2.3.tar.gz" "https://bioarchive.galaxyproject.org/hguDKFZ31.db_3.2.3.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-hgudkfz31.db/bioconductor-hgudkfz31.db_3.2.3_src_all.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-hgudkfz31.db/bioconductor-hgudkfz31.db_3.2.3_src_all.tar.gz" ) MD5="fa3ba493cebdac4253dea8fe5d58452b" @@ -16,7 +17,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-hgug4100a.db/meta.yaml b/recipes/bioconductor-hgug4100a.db/meta.yaml index d16d6d2ba041e..4e2b286e18421 100644 --- a/recipes/bioconductor-hgug4100a.db/meta.yaml +++ b/recipes/bioconductor-hgug4100a.db/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.2.3" %} {% set name = "hgug4100a.db" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -12,7 +12,7 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: b7856928278a77d71f963410ea4f2376 build: - number: 1 + number: 2 rpaths: - lib/R/lib/ - lib/ @@ -20,14 +20,14 @@ build: # Suggests: DBI, annotate, RUnit requirements: host: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' - - 'bioconductor-org.hs.eg.db >=3.7.0,<3.8.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' + - 'bioconductor-org.hs.eg.db >=3.8.0,<3.9.0' - r-base run: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' - - 'bioconductor-org.hs.eg.db >=3.7.0,<3.8.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' + - 'bioconductor-org.hs.eg.db >=3.8.0,<3.9.0' - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-hgug4100a.db/post-link.sh b/recipes/bioconductor-hgug4100a.db/post-link.sh index 6b11ae1fb769e..4c8d16babd118 100644 --- a/recipes/bioconductor-hgug4100a.db/post-link.sh +++ b/recipes/bioconductor-hgug4100a.db/post-link.sh @@ -1,9 +1,10 @@ #!/bin/bash FN="hgug4100a.db_3.2.3.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/hgug4100a.db_3.2.3.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/hgug4100a.db_3.2.3.tar.gz" "https://bioarchive.galaxyproject.org/hgug4100a.db_3.2.3.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-hgug4100a.db/bioconductor-hgug4100a.db_3.2.3_src_all.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-hgug4100a.db/bioconductor-hgug4100a.db_3.2.3_src_all.tar.gz" ) MD5="b7856928278a77d71f963410ea4f2376" @@ -16,7 +17,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-hgug4101a.db/meta.yaml b/recipes/bioconductor-hgug4101a.db/meta.yaml index c9dfcaea266d2..1db5cfc8f3e1b 100644 --- a/recipes/bioconductor-hgug4101a.db/meta.yaml +++ b/recipes/bioconductor-hgug4101a.db/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.2.3" %} {% set name = "hgug4101a.db" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -12,7 +12,7 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: e4731217efbffd05d3ee7eec68ce0aa0 build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ @@ -20,14 +20,14 @@ build: # Suggests: DBI, annotate, RUnit requirements: host: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' - - 'bioconductor-org.hs.eg.db >=3.7.0,<3.8.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' + - 'bioconductor-org.hs.eg.db >=3.8.0,<3.9.0' - r-base run: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' - - 'bioconductor-org.hs.eg.db >=3.7.0,<3.8.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' + - 'bioconductor-org.hs.eg.db >=3.8.0,<3.9.0' - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-hgug4101a.db/post-link.sh b/recipes/bioconductor-hgug4101a.db/post-link.sh index 0310926412d00..6259ee61cc6fb 100644 --- a/recipes/bioconductor-hgug4101a.db/post-link.sh +++ b/recipes/bioconductor-hgug4101a.db/post-link.sh @@ -1,9 +1,10 @@ #!/bin/bash FN="hgug4101a.db_3.2.3.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/hgug4101a.db_3.2.3.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/hgug4101a.db_3.2.3.tar.gz" "https://bioarchive.galaxyproject.org/hgug4101a.db_3.2.3.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-hgug4101a.db/bioconductor-hgug4101a.db_3.2.3_src_all.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-hgug4101a.db/bioconductor-hgug4101a.db_3.2.3_src_all.tar.gz" ) MD5="e4731217efbffd05d3ee7eec68ce0aa0" @@ -16,7 +17,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-hgug4110b.db/meta.yaml b/recipes/bioconductor-hgug4110b.db/meta.yaml index 13abbaaf20551..8f8a176e3a82b 100644 --- a/recipes/bioconductor-hgug4110b.db/meta.yaml +++ b/recipes/bioconductor-hgug4110b.db/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.2.3" %} {% set name = "hgug4110b.db" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -12,7 +12,7 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: a9edcdbc121f22d4dec335a64598ff0e build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ @@ -20,14 +20,14 @@ build: # Suggests: DBI, annotate, RUnit requirements: host: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' - - 'bioconductor-org.hs.eg.db >=3.7.0,<3.8.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' + - 'bioconductor-org.hs.eg.db >=3.8.0,<3.9.0' - r-base run: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' - - 'bioconductor-org.hs.eg.db >=3.7.0,<3.8.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' + - 'bioconductor-org.hs.eg.db >=3.8.0,<3.9.0' - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-hgug4110b.db/post-link.sh b/recipes/bioconductor-hgug4110b.db/post-link.sh index e7badc58fbadc..574ea8b3f1593 100644 --- a/recipes/bioconductor-hgug4110b.db/post-link.sh +++ b/recipes/bioconductor-hgug4110b.db/post-link.sh @@ -1,9 +1,10 @@ #!/bin/bash FN="hgug4110b.db_3.2.3.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/hgug4110b.db_3.2.3.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/hgug4110b.db_3.2.3.tar.gz" "https://bioarchive.galaxyproject.org/hgug4110b.db_3.2.3.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-hgug4110b.db/bioconductor-hgug4110b.db_3.2.3_src_all.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-hgug4110b.db/bioconductor-hgug4110b.db_3.2.3_src_all.tar.gz" ) MD5="a9edcdbc121f22d4dec335a64598ff0e" @@ -16,7 +17,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-hgug4111a.db/meta.yaml b/recipes/bioconductor-hgug4111a.db/meta.yaml index eb01bf8f85b54..8020d3e54fa9f 100644 --- a/recipes/bioconductor-hgug4111a.db/meta.yaml +++ b/recipes/bioconductor-hgug4111a.db/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.2.3" %} {% set name = "hgug4111a.db" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -12,7 +12,7 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: a5f2c3b463915fa1ab0ca21e6b0f5840 build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ @@ -20,14 +20,14 @@ build: # Suggests: DBI, annotate, RUnit requirements: host: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' - - 'bioconductor-org.hs.eg.db >=3.7.0,<3.8.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' + - 'bioconductor-org.hs.eg.db >=3.8.0,<3.9.0' - r-base run: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' - - 'bioconductor-org.hs.eg.db >=3.7.0,<3.8.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' + - 'bioconductor-org.hs.eg.db >=3.8.0,<3.9.0' - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-hgug4111a.db/post-link.sh b/recipes/bioconductor-hgug4111a.db/post-link.sh index abaa4960b043b..bdcebefcf677b 100644 --- a/recipes/bioconductor-hgug4111a.db/post-link.sh +++ b/recipes/bioconductor-hgug4111a.db/post-link.sh @@ -1,9 +1,10 @@ #!/bin/bash FN="hgug4111a.db_3.2.3.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/hgug4111a.db_3.2.3.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/hgug4111a.db_3.2.3.tar.gz" "https://bioarchive.galaxyproject.org/hgug4111a.db_3.2.3.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-hgug4111a.db/bioconductor-hgug4111a.db_3.2.3_src_all.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-hgug4111a.db/bioconductor-hgug4111a.db_3.2.3_src_all.tar.gz" ) MD5="a5f2c3b463915fa1ab0ca21e6b0f5840" @@ -16,7 +17,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-hgug4112a.db/meta.yaml b/recipes/bioconductor-hgug4112a.db/meta.yaml index 52216aaef8948..bc84ac833ce0c 100644 --- a/recipes/bioconductor-hgug4112a.db/meta.yaml +++ b/recipes/bioconductor-hgug4112a.db/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.2.3" %} {% set name = "hgug4112a.db" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -12,7 +12,7 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 67ecf8c887e2ebe1941cc51d0f5fb468 build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ @@ -20,14 +20,14 @@ build: # Suggests: DBI, annotate, RUnit requirements: host: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' - - 'bioconductor-org.hs.eg.db >=3.7.0,<3.8.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' + - 'bioconductor-org.hs.eg.db >=3.8.0,<3.9.0' - r-base run: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' - - 'bioconductor-org.hs.eg.db >=3.7.0,<3.8.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' + - 'bioconductor-org.hs.eg.db >=3.8.0,<3.9.0' - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-hgug4112a.db/post-link.sh b/recipes/bioconductor-hgug4112a.db/post-link.sh index c17bc4f92c38a..e169e913533a1 100644 --- a/recipes/bioconductor-hgug4112a.db/post-link.sh +++ b/recipes/bioconductor-hgug4112a.db/post-link.sh @@ -1,9 +1,10 @@ #!/bin/bash FN="hgug4112a.db_3.2.3.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/hgug4112a.db_3.2.3.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/hgug4112a.db_3.2.3.tar.gz" "https://bioarchive.galaxyproject.org/hgug4112a.db_3.2.3.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-hgug4112a.db/bioconductor-hgug4112a.db_3.2.3_src_all.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-hgug4112a.db/bioconductor-hgug4112a.db_3.2.3_src_all.tar.gz" ) MD5="67ecf8c887e2ebe1941cc51d0f5fb468" @@ -16,7 +17,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-hgug4845a.db/meta.yaml b/recipes/bioconductor-hgug4845a.db/meta.yaml index d1a16438a16cf..ebb43b9510d9c 100644 --- a/recipes/bioconductor-hgug4845a.db/meta.yaml +++ b/recipes/bioconductor-hgug4845a.db/meta.yaml @@ -1,6 +1,6 @@ {% set version = "0.0.3" %} {% set name = "hgug4845a.db" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -12,7 +12,7 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 46133d7bcb6d8c24c026304e8ddd150d build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ @@ -20,14 +20,14 @@ build: # Suggests: annotate requirements: host: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' - - 'bioconductor-org.hs.eg.db >=3.7.0,<3.8.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' + - 'bioconductor-org.hs.eg.db >=3.8.0,<3.9.0' - r-base run: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' - - 'bioconductor-org.hs.eg.db >=3.7.0,<3.8.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' + - 'bioconductor-org.hs.eg.db >=3.8.0,<3.9.0' - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-hgug4845a.db/post-link.sh b/recipes/bioconductor-hgug4845a.db/post-link.sh index 0f3460429d6ad..d6021bcdd5315 100644 --- a/recipes/bioconductor-hgug4845a.db/post-link.sh +++ b/recipes/bioconductor-hgug4845a.db/post-link.sh @@ -1,9 +1,10 @@ #!/bin/bash FN="hgug4845a.db_0.0.3.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/hgug4845a.db_0.0.3.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/hgug4845a.db_0.0.3.tar.gz" "https://bioarchive.galaxyproject.org/hgug4845a.db_0.0.3.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-hgug4845a.db/bioconductor-hgug4845a.db_0.0.3_src_all.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-hgug4845a.db/bioconductor-hgug4845a.db_0.0.3_src_all.tar.gz" ) MD5="46133d7bcb6d8c24c026304e8ddd150d" @@ -16,7 +17,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-hguqiagenv3.db/meta.yaml b/recipes/bioconductor-hguqiagenv3.db/meta.yaml index 15501e5faf010..54476fe653a04 100644 --- a/recipes/bioconductor-hguqiagenv3.db/meta.yaml +++ b/recipes/bioconductor-hguqiagenv3.db/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.2.3" %} {% set name = "hguqiagenv3.db" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -12,7 +12,7 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 91ebb82e773ff799befdb8921b38e90e build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ @@ -20,14 +20,14 @@ build: # Suggests: DBI, annotate, RUnit requirements: host: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' - - 'bioconductor-org.hs.eg.db >=3.7.0,<3.8.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' + - 'bioconductor-org.hs.eg.db >=3.8.0,<3.9.0' - r-base run: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' - - 'bioconductor-org.hs.eg.db >=3.7.0,<3.8.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' + - 'bioconductor-org.hs.eg.db >=3.8.0,<3.9.0' - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-hguqiagenv3.db/post-link.sh b/recipes/bioconductor-hguqiagenv3.db/post-link.sh index 1ed51e4385205..de5279f2e8662 100644 --- a/recipes/bioconductor-hguqiagenv3.db/post-link.sh +++ b/recipes/bioconductor-hguqiagenv3.db/post-link.sh @@ -1,9 +1,10 @@ #!/bin/bash FN="hguqiagenv3.db_3.2.3.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/hguqiagenv3.db_3.2.3.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/hguqiagenv3.db_3.2.3.tar.gz" "https://bioarchive.galaxyproject.org/hguqiagenv3.db_3.2.3.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-hguqiagenv3.db/bioconductor-hguqiagenv3.db_3.2.3_src_all.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-hguqiagenv3.db/bioconductor-hguqiagenv3.db_3.2.3_src_all.tar.gz" ) MD5="91ebb82e773ff799befdb8921b38e90e" @@ -16,7 +17,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-hi16cod.db/meta.yaml b/recipes/bioconductor-hi16cod.db/meta.yaml index accc37338f0f4..b2d204e88826e 100644 --- a/recipes/bioconductor-hi16cod.db/meta.yaml +++ b/recipes/bioconductor-hi16cod.db/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.4.0" %} {% set name = "hi16cod.db" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -12,7 +12,7 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: abdc77937e8d37fa5468691376ceb6a5 build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ @@ -20,14 +20,14 @@ build: # Suggests: annotate, RUnit requirements: host: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' - - 'bioconductor-org.hs.eg.db >=3.7.0,<3.8.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' + - 'bioconductor-org.hs.eg.db >=3.8.0,<3.9.0' - r-base run: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' - - 'bioconductor-org.hs.eg.db >=3.7.0,<3.8.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' + - 'bioconductor-org.hs.eg.db >=3.8.0,<3.9.0' - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-hi16cod.db/post-link.sh b/recipes/bioconductor-hi16cod.db/post-link.sh index 9dc588fe66dd9..329519036490d 100644 --- a/recipes/bioconductor-hi16cod.db/post-link.sh +++ b/recipes/bioconductor-hi16cod.db/post-link.sh @@ -1,9 +1,10 @@ #!/bin/bash FN="hi16cod.db_3.4.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/hi16cod.db_3.4.0.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/hi16cod.db_3.4.0.tar.gz" "https://bioarchive.galaxyproject.org/hi16cod.db_3.4.0.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-hi16cod.db/bioconductor-hi16cod.db_3.4.0_src_all.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-hi16cod.db/bioconductor-hi16cod.db_3.4.0_src_all.tar.gz" ) MD5="abdc77937e8d37fa5468691376ceb6a5" @@ -16,7 +17,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-hiannotator/meta.yaml b/recipes/bioconductor-hiannotator/meta.yaml index 89c3d3975d068..3c86ba9d04f05 100644 --- a/recipes/bioconductor-hiannotator/meta.yaml +++ b/recipes/bioconductor-hiannotator/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.16.0" %} +{% set version = "1.18.0" %} {% set name = "hiAnnotator" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 708f87c006a43e2d4626012d67f9423b + md5: 5e82f0d2242854d2462903c158f78b0c build: number: 0 rpaths: @@ -20,9 +20,9 @@ build: # Suggests: knitr, doParallel, testthat, BiocGenerics requirements: host: - - 'bioconductor-bsgenome >=1.50.0,<1.51.0' - - 'bioconductor-genomicranges >=1.34.0,<1.35.0' - - 'bioconductor-rtracklayer >=1.42.0,<1.43.0' + - 'bioconductor-bsgenome >=1.52.0,<1.53.0' + - 'bioconductor-genomicranges >=1.36.0,<1.37.0' + - 'bioconductor-rtracklayer >=1.44.0,<1.45.0' - r-base - r-dplyr - r-foreach @@ -30,9 +30,9 @@ requirements: - r-iterators - r-scales run: - - 'bioconductor-bsgenome >=1.50.0,<1.51.0' - - 'bioconductor-genomicranges >=1.34.0,<1.35.0' - - 'bioconductor-rtracklayer >=1.42.0,<1.43.0' + - 'bioconductor-bsgenome >=1.52.0,<1.53.0' + - 'bioconductor-genomicranges >=1.36.0,<1.37.0' + - 'bioconductor-rtracklayer >=1.44.0,<1.45.0' - r-base - r-dplyr - r-foreach diff --git a/recipes/bioconductor-hibag/meta.yaml b/recipes/bioconductor-hibag/meta.yaml index d15b8c49ab5c8..07e1dfc91263d 100644 --- a/recipes/bioconductor-hibag/meta.yaml +++ b/recipes/bioconductor-hibag/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.18.1" %} +{% set version = "1.20.0" %} {% set name = "HIBAG" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: a1ba0ae738fdd4bac94f1e44b6710ce0 + md5: 726af2e377f5adb21cbceeadfc75e7d4 build: number: 0 rpaths: diff --git a/recipes/bioconductor-hicbricks/meta.yaml b/recipes/bioconductor-hicbricks/meta.yaml index eef7227b0f66e..4af156ed7a084 100644 --- a/recipes/bioconductor-hicbricks/meta.yaml +++ b/recipes/bioconductor-hicbricks/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.0.0" %} +{% set version = "1.2.0" %} {% set name = "HiCBricks" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,47 +10,44 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 00c648457572e0c06e09e1abe2cc7c96 + md5: 3b982b5180601d94f1d5d0dfb4e96665 build: number: 0 rpaths: - lib/R/lib/ - lib/ noarch: generic +# Suggests: BiocStyle, knitr, rmarkdown requirements: host: - - 'bioconductor-biocfilecache >=1.6.0,<1.7.0' - - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' - - 'bioconductor-genomicranges >=1.34.0,<1.35.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-rhdf5 >=2.26.0,<2.27.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-genomeinfodb >=1.20.0,<1.21.0' + - 'bioconductor-genomicranges >=1.36.0,<1.37.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-rhdf5 >=2.28.0,<2.29.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' - r-base - r-curl - r-data.table - r-digest - r-ggplot2 - r-r6 - - r-rappdirs - r-rcolorbrewer - r-reshape2 - r-scales - r-stringr - r-viridis run: - - 'bioconductor-biocfilecache >=1.6.0,<1.7.0' - - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' - - 'bioconductor-genomicranges >=1.34.0,<1.35.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-rhdf5 >=2.26.0,<2.27.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-genomeinfodb >=1.20.0,<1.21.0' + - 'bioconductor-genomicranges >=1.36.0,<1.37.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-rhdf5 >=2.28.0,<2.29.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' - r-base - r-curl - r-data.table - r-digest - r-ggplot2 - r-r6 - - r-rappdirs - r-rcolorbrewer - r-reshape2 - r-scales diff --git a/recipes/bioconductor-hiccompare/meta.yaml b/recipes/bioconductor-hiccompare/meta.yaml index c88d5613388b1..dd31c8a19bbdb 100644 --- a/recipes/bioconductor-hiccompare/meta.yaml +++ b/recipes/bioconductor-hiccompare/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.4.0" %} +{% set version = "1.6.0" %} {% set name = "HiCcompare" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 76d89712dadfae982a63327c74a4a2d4 + md5: 89f5a317b6381160c2ef31d6b2d8c553 build: number: 0 rpaths: @@ -20,12 +20,12 @@ build: # Suggests: knitr, rmarkdown, testthat, multiHiCcompare requirements: host: - - 'bioconductor-biocparallel >=1.16.0,<1.17.0' - - 'bioconductor-genomicranges >=1.34.0,<1.35.0' - - 'bioconductor-interactionset >=1.10.0,<1.11.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-qdnaseq >=1.18.0,<1.19.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-biocparallel >=1.18.0,<1.19.0' + - 'bioconductor-genomicranges >=1.36.0,<1.37.0' + - 'bioconductor-interactionset >=1.12.0,<1.13.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-qdnaseq >=1.20.0,<1.21.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' - r-base - r-data.table - r-dplyr @@ -36,12 +36,12 @@ requirements: - r-mgcv - r-pheatmap run: - - 'bioconductor-biocparallel >=1.16.0,<1.17.0' - - 'bioconductor-genomicranges >=1.34.0,<1.35.0' - - 'bioconductor-interactionset >=1.10.0,<1.11.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-qdnaseq >=1.18.0,<1.19.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-biocparallel >=1.18.0,<1.19.0' + - 'bioconductor-genomicranges >=1.36.0,<1.37.0' + - 'bioconductor-interactionset >=1.12.0,<1.13.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-qdnaseq >=1.20.0,<1.21.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' - r-base - r-data.table - r-dplyr diff --git a/recipes/bioconductor-hicdatahumanimr90/meta.yaml b/recipes/bioconductor-hicdatahumanimr90/meta.yaml index d088841be12b9..9dcc2ca3282ab 100644 --- a/recipes/bioconductor-hicdatahumanimr90/meta.yaml +++ b/recipes/bioconductor-hicdatahumanimr90/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.2.0" %} +{% set version = "1.4.0" %} {% set name = "HiCDataHumanIMR90" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: cdf34ec2f78ce9a1482efbea622d81e0 + md5: d7687765d6d2bee5988b52c927a1c6c3 build: number: 0 rpaths: @@ -23,7 +23,7 @@ requirements: - r-base run: - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-hicdatahumanimr90/post-link.sh b/recipes/bioconductor-hicdatahumanimr90/post-link.sh index 2950ce18e7d6e..3f8f287609327 100644 --- a/recipes/bioconductor-hicdatahumanimr90/post-link.sh +++ b/recipes/bioconductor-hicdatahumanimr90/post-link.sh @@ -1,11 +1,11 @@ #!/bin/bash -FN="HiCDataHumanIMR90_1.2.0.tar.gz" +FN="HiCDataHumanIMR90_1.4.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/experiment/src/contrib/HiCDataHumanIMR90_1.2.0.tar.gz" - "https://bioarchive.galaxyproject.org/HiCDataHumanIMR90_1.2.0.tar.gz" - "https://depot.galaxyproject.org/software/bioconductor-hicdatahumanimr90/bioconductor-hicdatahumanimr90_1.2.0_src_all.tar.gz" + "https://bioconductor.org/packages/3.9/data/experiment/src/contrib/HiCDataHumanIMR90_1.4.0.tar.gz" + "https://bioarchive.galaxyproject.org/HiCDataHumanIMR90_1.4.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-hicdatahumanimr90/bioconductor-hicdatahumanimr90_1.4.0_src_all.tar.gz" ) -MD5="cdf34ec2f78ce9a1482efbea622d81e0" +MD5="d7687765d6d2bee5988b52c927a1c6c3" # Use a staging area in the conda dir rather than temp dirs, both to avoid # permission issues as well as to have things downloaded in a predictable @@ -16,7 +16,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-hicdatalymphoblast/meta.yaml b/recipes/bioconductor-hicdatalymphoblast/meta.yaml index d90da48d0a2ab..bbc8d62aa590c 100644 --- a/recipes/bioconductor-hicdatalymphoblast/meta.yaml +++ b/recipes/bioconductor-hicdatalymphoblast/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.18.0" %} +{% set version = "1.20.0" %} {% set name = "HiCDataLymphoblast" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 55d001daefcf400a6f3474a4a6859c6e + md5: 6b12b6d3851d638acdab1a15a9225b92 build: number: 0 rpaths: @@ -23,7 +23,7 @@ requirements: - r-base run: - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-hicdatalymphoblast/post-link.sh b/recipes/bioconductor-hicdatalymphoblast/post-link.sh index ee256d7faf5e3..7e186e4d91dcd 100644 --- a/recipes/bioconductor-hicdatalymphoblast/post-link.sh +++ b/recipes/bioconductor-hicdatalymphoblast/post-link.sh @@ -1,11 +1,11 @@ #!/bin/bash -FN="HiCDataLymphoblast_1.18.0.tar.gz" +FN="HiCDataLymphoblast_1.20.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/experiment/src/contrib/HiCDataLymphoblast_1.18.0.tar.gz" - "https://bioarchive.galaxyproject.org/HiCDataLymphoblast_1.18.0.tar.gz" - "https://depot.galaxyproject.org/software/bioconductor-hicdatalymphoblast/bioconductor-hicdatalymphoblast_1.18.0_src_all.tar.gz" + "https://bioconductor.org/packages/3.9/data/experiment/src/contrib/HiCDataLymphoblast_1.20.0.tar.gz" + "https://bioarchive.galaxyproject.org/HiCDataLymphoblast_1.20.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-hicdatalymphoblast/bioconductor-hicdatalymphoblast_1.20.0_src_all.tar.gz" ) -MD5="55d001daefcf400a6f3474a4a6859c6e" +MD5="6b12b6d3851d638acdab1a15a9225b92" # Use a staging area in the conda dir rather than temp dirs, both to avoid # permission issues as well as to have things downloaded in a predictable @@ -16,7 +16,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-hicrep/meta.yaml b/recipes/bioconductor-hicrep/meta.yaml index 5644dc92ec46c..0e17aa99fed9d 100644 --- a/recipes/bioconductor-hicrep/meta.yaml +++ b/recipes/bioconductor-hicrep/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.6.0" %} +{% set version = "1.8.0" %} {% set name = "hicrep" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 451cb0aae520cb05dca1b5766b9a8bd6 + md5: 8eb8f8a4541cfd57b3dbdb43e83dafac build: number: 0 rpaths: diff --git a/recipes/bioconductor-hiergwas/meta.yaml b/recipes/bioconductor-hiergwas/meta.yaml index 92e937c4340bb..65ebe02734136 100644 --- a/recipes/bioconductor-hiergwas/meta.yaml +++ b/recipes/bioconductor-hiergwas/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.12.0" %} +{% set version = "1.14.0" %} {% set name = "hierGWAS" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,9 +10,9 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 161b52663e1b82379b6d2a876d74d33a + md5: 517560970b191c05a63c080c2abe8956 build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ diff --git a/recipes/bioconductor-hierinf/meta.yaml b/recipes/bioconductor-hierinf/meta.yaml index 782ac313ab810..6d3b0aa26e22b 100644 --- a/recipes/bioconductor-hierinf/meta.yaml +++ b/recipes/bioconductor-hierinf/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.0.0" %} +{% set version = "1.2.0" %} {% set name = "hierinf" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: f42529167e8ea2fd49e7290a6c4431d1 + md5: 4c22ae972ff46a7b71014120383c3cf9 build: number: 0 rpaths: diff --git a/recipes/bioconductor-hiiragi2013/meta.yaml b/recipes/bioconductor-hiiragi2013/meta.yaml index eca3181ea23f6..b6026cf9627c6 100644 --- a/recipes/bioconductor-hiiragi2013/meta.yaml +++ b/recipes/bioconductor-hiiragi2013/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.18.0" %} +{% set version = "1.20.0" %} {% set name = "Hiiragi2013" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 0e1fdc481e61f2612f88120f4d7cbdff + md5: c8382abd59d8f36b4ab89b63d0a7a438 build: number: 0 rpaths: @@ -20,11 +20,11 @@ build: # Suggests: ArrayExpress, BiocStyle requirements: host: - - 'bioconductor-affy >=1.60.0,<1.61.0' - - 'bioconductor-biobase >=2.42.0,<2.43.0' - - 'bioconductor-genefilter >=1.64.0,<1.65.0' - - 'bioconductor-geneplotter >=1.60.0,<1.61.0' - - 'bioconductor-keggrest >=1.22.0,<1.23.0' + - 'bioconductor-affy >=1.62.0,<1.63.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' + - 'bioconductor-genefilter >=1.66.0,<1.67.0' + - 'bioconductor-geneplotter >=1.62.0,<1.63.0' + - 'bioconductor-keggrest >=1.24.0,<1.25.0' - 'bioconductor-mouse4302.db >=3.2.0,<3.3.0' - r-base - r-boot @@ -38,11 +38,11 @@ requirements: - r-rcolorbrewer - r-xtable run: - - 'bioconductor-affy >=1.60.0,<1.61.0' - - 'bioconductor-biobase >=2.42.0,<2.43.0' - - 'bioconductor-genefilter >=1.64.0,<1.65.0' - - 'bioconductor-geneplotter >=1.60.0,<1.61.0' - - 'bioconductor-keggrest >=1.22.0,<1.23.0' + - 'bioconductor-affy >=1.62.0,<1.63.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' + - 'bioconductor-genefilter >=1.66.0,<1.67.0' + - 'bioconductor-geneplotter >=1.62.0,<1.63.0' + - 'bioconductor-keggrest >=1.24.0,<1.25.0' - 'bioconductor-mouse4302.db >=3.2.0,<3.3.0' - r-base - r-boot @@ -55,7 +55,7 @@ requirements: - r-mass - r-rcolorbrewer - r-xtable - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-hiiragi2013/post-link.sh b/recipes/bioconductor-hiiragi2013/post-link.sh index 5b9f50f482abc..da562979bac34 100644 --- a/recipes/bioconductor-hiiragi2013/post-link.sh +++ b/recipes/bioconductor-hiiragi2013/post-link.sh @@ -1,11 +1,11 @@ #!/bin/bash -FN="Hiiragi2013_1.18.0.tar.gz" +FN="Hiiragi2013_1.20.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/experiment/src/contrib/Hiiragi2013_1.18.0.tar.gz" - "https://bioarchive.galaxyproject.org/Hiiragi2013_1.18.0.tar.gz" - "https://depot.galaxyproject.org/software/bioconductor-hiiragi2013/bioconductor-hiiragi2013_1.18.0_src_all.tar.gz" + "https://bioconductor.org/packages/3.9/data/experiment/src/contrib/Hiiragi2013_1.20.0.tar.gz" + "https://bioarchive.galaxyproject.org/Hiiragi2013_1.20.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-hiiragi2013/bioconductor-hiiragi2013_1.20.0_src_all.tar.gz" ) -MD5="0e1fdc481e61f2612f88120f4d7cbdff" +MD5="c8382abd59d8f36b4ab89b63d0a7a438" # Use a staging area in the conda dir rather than temp dirs, both to avoid # permission issues as well as to have things downloaded in a predictable @@ -16,7 +16,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-hilbertcurve/meta.yaml b/recipes/bioconductor-hilbertcurve/meta.yaml index 1f53f802f572a..246e9b5e474bd 100644 --- a/recipes/bioconductor-hilbertcurve/meta.yaml +++ b/recipes/bioconductor-hilbertcurve/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.12.0" %} +{% set version = "1.14.0" %} {% set name = "HilbertCurve" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,29 +10,31 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: ba470369553e2da65efa8ca89a886146 + md5: 0f13456bc1c6c31c6d12556d7a4d756f build: number: 0 rpaths: - lib/R/lib/ - lib/ noarch: generic -# Suggests: knitr, testthat (>= 1.0.0), ComplexHeatmap (>= 1.13.2), markdown, RColorBrewer, RCurl, GetoptLong +# Suggests: knitr, testthat (>= 1.0.0), ComplexHeatmap (>= 1.99.0), markdown, RColorBrewer, RCurl, GetoptLong requirements: host: - - 'bioconductor-genomicranges >=1.34.0,<1.35.0' - - 'bioconductor-hilbertvis >=1.40.0,<1.41.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-genomicranges >=1.36.0,<1.37.0' + - 'bioconductor-hilbertvis >=1.42.0,<1.43.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' - r-base - 'r-circlize >=0.3.3' - r-png + - r-polylabelr run: - - 'bioconductor-genomicranges >=1.34.0,<1.35.0' - - 'bioconductor-hilbertvis >=1.40.0,<1.41.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-genomicranges >=1.36.0,<1.37.0' + - 'bioconductor-hilbertvis >=1.42.0,<1.43.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' - r-base - 'r-circlize >=0.3.3' - r-png + - r-polylabelr test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-hilbertvis/meta.yaml b/recipes/bioconductor-hilbertvis/meta.yaml index 42fba76a7e484..32531b980ee8a 100644 --- a/recipes/bioconductor-hilbertvis/meta.yaml +++ b/recipes/bioconductor-hilbertvis/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.40.0" %} +{% set version = "1.42.0" %} {% set name = "HilbertVis" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,9 +10,9 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: c7f99d6848ef995298d264b0e8996f1f + md5: b944cceadff5086688b47e2b5141b7dc build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ diff --git a/recipes/bioconductor-hilbertvisgui/meta.yaml b/recipes/bioconductor-hilbertvisgui/meta.yaml index 3ca0f32720787..f7596bf107b33 100644 --- a/recipes/bioconductor-hilbertvisgui/meta.yaml +++ b/recipes/bioconductor-hilbertvisgui/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.40.0" %} +{% set version = "1.42.0" %} {% set name = "HilbertVisGUI" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: c57941da89777104f1818f25aefd8c5f + md5: 267f2b6f362c492e5452fc3ee14e2ee4 build: number: 0 rpaths: @@ -20,19 +20,17 @@ build: # SystemRequirements: gtkmm-2.4, GNU make requirements: host: - - 'bioconductor-hilbertvis >=1.40.0,<1.41.0' + - 'bioconductor-hilbertvis >=1.42.0,<1.43.0' - r-base - - {{ cdt('gtkmm24-devel') }} + - {{ cdt("gtkmm24") }} run: - - 'bioconductor-hilbertvis >=1.40.0,<1.41.0' + - 'bioconductor-hilbertvis >=1.42.0,<1.43.0' - r-base - - {{ cdt('gtkmm24-devel') }} build: - {{ compiler('c') }} - {{ compiler('cxx') }} - automake - make - - pkg-config test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-hipathia/meta.yaml b/recipes/bioconductor-hipathia/meta.yaml index d73a70b23b1c1..556f9e59ce2bd 100644 --- a/recipes/bioconductor-hipathia/meta.yaml +++ b/recipes/bioconductor-hipathia/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.3.1" %} +{% set version = "2.0.0" %} {% set name = "hipathia" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: e8681aea4045ac2646eceb21ef411bae + md5: f7a13083f09722dba0d15cfea6fc3c8f build: number: 0 rpaths: @@ -20,26 +20,26 @@ build: # Suggests: BiocStyle, knitr, rmarkdown, testthat requirements: host: - - 'bioconductor-annotationhub >=2.14.0,<2.15.0' - - 'bioconductor-delayedarray >=0.8.0,<0.9.0' - - 'bioconductor-limma >=3.38.0,<3.39.0' - - 'bioconductor-multiassayexperiment >=1.8.0,<1.9.0' - - 'bioconductor-preprocesscore >=1.44.0,<1.45.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' - - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' + - 'bioconductor-annotationhub >=2.16.0,<2.17.0' + - 'bioconductor-delayedarray >=0.10.0,<0.11.0' + - 'bioconductor-limma >=3.40.0,<3.41.0' + - 'bioconductor-multiassayexperiment >=1.10.0,<1.11.0' + - 'bioconductor-preprocesscore >=1.46.0,<1.47.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' + - 'bioconductor-summarizedexperiment >=1.14.0,<1.15.0' - r-base - r-coin - 'r-igraph >=1.0.1' - r-matrixstats - r-servr run: - - 'bioconductor-annotationhub >=2.14.0,<2.15.0' - - 'bioconductor-delayedarray >=0.8.0,<0.9.0' - - 'bioconductor-limma >=3.38.0,<3.39.0' - - 'bioconductor-multiassayexperiment >=1.8.0,<1.9.0' - - 'bioconductor-preprocesscore >=1.44.0,<1.45.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' - - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' + - 'bioconductor-annotationhub >=2.16.0,<2.17.0' + - 'bioconductor-delayedarray >=0.10.0,<0.11.0' + - 'bioconductor-limma >=3.40.0,<3.41.0' + - 'bioconductor-multiassayexperiment >=1.10.0,<1.11.0' + - 'bioconductor-preprocesscore >=1.46.0,<1.47.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' + - 'bioconductor-summarizedexperiment >=1.14.0,<1.15.0' - r-base - r-coin - 'r-igraph >=1.0.1' diff --git a/recipes/bioconductor-hireadsprocessor/meta.yaml b/recipes/bioconductor-hireadsprocessor/meta.yaml index 8f7ebc997e77c..d4cdf020d21ab 100644 --- a/recipes/bioconductor-hireadsprocessor/meta.yaml +++ b/recipes/bioconductor-hireadsprocessor/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.18.0" %} +{% set version = "1.19.0" %} {% set name = "hiReadsProcessor" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 8dbd21ace9a68bf4f83bd337b8531f61 + md5: b73e50b02447211af7a7586757d3eb92 build: number: 0 rpaths: @@ -21,25 +21,25 @@ build: # SystemRequirements: BLAT, UCSC hg18 in 2bit format for BLAT requirements: host: - - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' - - 'bioconductor-biocparallel >=1.16.0,<1.17.0' - - 'bioconductor-biostrings >=2.50.0,<2.51.0' - - 'bioconductor-genomicalignments >=1.18.0,<1.19.0' - - 'bioconductor-genomicranges >=1.34.0,<1.35.0' - - 'bioconductor-hiannotator >=1.16.0,<1.17.0' - - 'bioconductor-rsffreader >=0.30.0,<0.31.0' + - 'bioconductor-biocgenerics >=0.30.0,<0.31.0' + - 'bioconductor-biocparallel >=1.18.0,<1.19.0' + - 'bioconductor-biostrings >=2.52.0,<2.53.0' + - 'bioconductor-genomicalignments >=1.20.0,<1.21.0' + - 'bioconductor-genomicranges >=1.36.0,<1.37.0' + - 'bioconductor-hiannotator >=1.18.0,<1.19.0' + - 'bioconductor-rsffreader >=0.32.0,<0.33.0' - r-base - r-dplyr - r-readxl - r-soniclength run: - - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' - - 'bioconductor-biocparallel >=1.16.0,<1.17.0' - - 'bioconductor-biostrings >=2.50.0,<2.51.0' - - 'bioconductor-genomicalignments >=1.18.0,<1.19.0' - - 'bioconductor-genomicranges >=1.34.0,<1.35.0' - - 'bioconductor-hiannotator >=1.16.0,<1.17.0' - - 'bioconductor-rsffreader >=0.30.0,<0.31.0' + - 'bioconductor-biocgenerics >=0.30.0,<0.31.0' + - 'bioconductor-biocparallel >=1.18.0,<1.19.0' + - 'bioconductor-biostrings >=2.52.0,<2.53.0' + - 'bioconductor-genomicalignments >=1.20.0,<1.21.0' + - 'bioconductor-genomicranges >=1.36.0,<1.37.0' + - 'bioconductor-hiannotator >=1.18.0,<1.19.0' + - 'bioconductor-rsffreader >=0.32.0,<0.33.0' - r-base - r-dplyr - r-readxl diff --git a/recipes/bioconductor-hireewas/meta.yaml b/recipes/bioconductor-hireewas/meta.yaml index 6c9c661f10b54..e7291c1a2d000 100644 --- a/recipes/bioconductor-hireewas/meta.yaml +++ b/recipes/bioconductor-hireewas/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.0.2" %} +{% set version = "1.2.0" %} {% set name = "HIREewas" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: af011790e1dd234cbd7df579cb6f5fba + md5: a885a8f029685d397a5572c26f02d054 build: number: 0 rpaths: diff --git a/recipes/bioconductor-hitc/meta.yaml b/recipes/bioconductor-hitc/meta.yaml index 4af803a64c060..efdd4e51daf33 100644 --- a/recipes/bioconductor-hitc/meta.yaml +++ b/recipes/bioconductor-hitc/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.26.0" %} +{% set version = "1.28.0" %} {% set name = "HiTC" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: eb493286bde0c875cc990d458b6b532d + md5: 80af3724d38ab86abf8f7e0eb0fb1649 build: number: 0 rpaths: @@ -20,20 +20,20 @@ build: # Suggests: BiocStyle, HiCDataHumanIMR90 requirements: host: - - 'bioconductor-biostrings >=2.50.0,<2.51.0' - - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' - - 'bioconductor-genomicranges >=1.34.0,<1.35.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-rtracklayer >=1.42.0,<1.43.0' + - 'bioconductor-biostrings >=2.52.0,<2.53.0' + - 'bioconductor-genomeinfodb >=1.20.0,<1.21.0' + - 'bioconductor-genomicranges >=1.36.0,<1.37.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-rtracklayer >=1.44.0,<1.45.0' - r-base - r-matrix - r-rcolorbrewer run: - - 'bioconductor-biostrings >=2.50.0,<2.51.0' - - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' - - 'bioconductor-genomicranges >=1.34.0,<1.35.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-rtracklayer >=1.42.0,<1.43.0' + - 'bioconductor-biostrings >=2.52.0,<2.53.0' + - 'bioconductor-genomeinfodb >=1.20.0,<1.21.0' + - 'bioconductor-genomicranges >=1.36.0,<1.37.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-rtracklayer >=1.44.0,<1.45.0' - r-base - r-matrix - r-rcolorbrewer diff --git a/recipes/bioconductor-hivcdnavantwout03/meta.yaml b/recipes/bioconductor-hivcdnavantwout03/meta.yaml index 13406acb38ea8..c6617249ac76e 100644 --- a/recipes/bioconductor-hivcdnavantwout03/meta.yaml +++ b/recipes/bioconductor-hivcdnavantwout03/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.22.0" %} +{% set version = "1.24.0" %} {% set name = "HIVcDNAvantWout03" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: e6bf73521bce0a019338afdbb9bbef30 + md5: 3978039dba5000fa5456c7fac8082002 build: number: 0 rpaths: @@ -22,7 +22,7 @@ requirements: - r-base run: - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-hivcdnavantwout03/post-link.sh b/recipes/bioconductor-hivcdnavantwout03/post-link.sh index 1da2b8e1acef1..3248677f6208f 100644 --- a/recipes/bioconductor-hivcdnavantwout03/post-link.sh +++ b/recipes/bioconductor-hivcdnavantwout03/post-link.sh @@ -1,11 +1,11 @@ #!/bin/bash -FN="HIVcDNAvantWout03_1.22.0.tar.gz" +FN="HIVcDNAvantWout03_1.24.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/experiment/src/contrib/HIVcDNAvantWout03_1.22.0.tar.gz" - "https://bioarchive.galaxyproject.org/HIVcDNAvantWout03_1.22.0.tar.gz" - "https://depot.galaxyproject.org/software/bioconductor-hivcdnavantwout03/bioconductor-hivcdnavantwout03_1.22.0_src_all.tar.gz" + "https://bioconductor.org/packages/3.9/data/experiment/src/contrib/HIVcDNAvantWout03_1.24.0.tar.gz" + "https://bioarchive.galaxyproject.org/HIVcDNAvantWout03_1.24.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-hivcdnavantwout03/bioconductor-hivcdnavantwout03_1.24.0_src_all.tar.gz" ) -MD5="e6bf73521bce0a019338afdbb9bbef30" +MD5="3978039dba5000fa5456c7fac8082002" # Use a staging area in the conda dir rather than temp dirs, both to avoid # permission issues as well as to have things downloaded in a predictable @@ -16,7 +16,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-hivprtplus2cdf/meta.yaml b/recipes/bioconductor-hivprtplus2cdf/meta.yaml index 5101d3b88c126..fa84cde769617 100644 --- a/recipes/bioconductor-hivprtplus2cdf/meta.yaml +++ b/recipes/bioconductor-hivprtplus2cdf/meta.yaml @@ -1,6 +1,6 @@ {% set version = "2.18.0" %} {% set name = "hivprtplus2cdf" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -12,19 +12,19 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 143d9c2f5f328786bae7bb8dc4daf261 build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' - r-base run: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-hivprtplus2cdf/post-link.sh b/recipes/bioconductor-hivprtplus2cdf/post-link.sh index 0b03c0276b47b..a4c2d5ddac191 100644 --- a/recipes/bioconductor-hivprtplus2cdf/post-link.sh +++ b/recipes/bioconductor-hivprtplus2cdf/post-link.sh @@ -1,9 +1,10 @@ #!/bin/bash FN="hivprtplus2cdf_2.18.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/hivprtplus2cdf_2.18.0.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/hivprtplus2cdf_2.18.0.tar.gz" "https://bioarchive.galaxyproject.org/hivprtplus2cdf_2.18.0.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-hivprtplus2cdf/bioconductor-hivprtplus2cdf_2.18.0_src_all.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-hivprtplus2cdf/bioconductor-hivprtplus2cdf_2.18.0_src_all.tar.gz" ) MD5="143d9c2f5f328786bae7bb8dc4daf261" @@ -16,7 +17,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-hmdbquery/meta.yaml b/recipes/bioconductor-hmdbquery/meta.yaml index c9542ac05b626..a5282a8b5ba44 100644 --- a/recipes/bioconductor-hmdbquery/meta.yaml +++ b/recipes/bioconductor-hmdbquery/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.2.0" %} +{% set version = "1.4.0" %} {% set name = "hmdbQuery" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 146f2e50a7a23ec70e559d88066f3615 + md5: 07e6442e9fa2d86e879df03d9472b6fe build: number: 0 rpaths: @@ -20,11 +20,11 @@ build: # Suggests: knitr, annotate, gwascat, testthat requirements: host: - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' - r-base - r-xml run: - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' - r-base - r-xml test: diff --git a/recipes/bioconductor-hmmcopy/meta.yaml b/recipes/bioconductor-hmmcopy/meta.yaml index c51f791cf816d..2423dea914ae1 100644 --- a/recipes/bioconductor-hmmcopy/meta.yaml +++ b/recipes/bioconductor-hmmcopy/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.24.0" %} +{% set version = "1.26.0" %} {% set name = "HMMcopy" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: b9a3c1f7f7ac714bacc10a09afaa9664 + md5: e18ef3f2af6b9d913c127002b9ca729b build: number: 0 rpaths: @@ -18,12 +18,12 @@ build: - lib/ requirements: host: - - 'bioconductor-geneplotter >=1.60.0,<1.61.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-geneplotter >=1.62.0,<1.63.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' - r-base run: - - 'bioconductor-geneplotter >=1.60.0,<1.61.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-geneplotter >=1.62.0,<1.63.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' - r-base build: - {{ compiler('c') }} diff --git a/recipes/bioconductor-hmp16sdata/meta.yaml b/recipes/bioconductor-hmp16sdata/meta.yaml index 9b10893279370..f697f707416f9 100644 --- a/recipes/bioconductor-hmp16sdata/meta.yaml +++ b/recipes/bioconductor-hmp16sdata/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.2.0" %} +{% set version = "1.3.2" %} {% set name = "HMP16SData" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,9 +10,9 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: d0369085597560d872684b5846833ee3 + md5: af1f24921e331d20bb1181483588a36d build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ @@ -20,10 +20,10 @@ build: # Suggests: Biobase, BiocCheck, BiocManager, BiocStyle, circlize, covr, cowplot, curatedMetagenomicData, dendextend, devtools, ggplot2, gridExtra, haven, phyloseq, rmarkdown, roxygen2, stats, testthat requirements: host: - - 'bioconductor-annotationhub >=2.14.0,<2.15.0' - - 'bioconductor-experimenthub >=1.8.0,<1.9.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' - - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' + - 'bioconductor-annotationhub >=2.16.0,<2.17.0' + - 'bioconductor-experimenthub >=1.10.0,<1.11.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' + - 'bioconductor-summarizedexperiment >=1.14.0,<1.15.0' - r-assertthat - r-base - r-dplyr @@ -33,10 +33,10 @@ requirements: - r-readr - r-tibble run: - - 'bioconductor-annotationhub >=2.14.0,<2.15.0' - - 'bioconductor-experimenthub >=1.8.0,<1.9.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' - - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' + - 'bioconductor-annotationhub >=2.16.0,<2.17.0' + - 'bioconductor-experimenthub >=1.10.0,<1.11.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' + - 'bioconductor-summarizedexperiment >=1.14.0,<1.15.0' - r-assertthat - r-base - r-dplyr @@ -45,7 +45,7 @@ requirements: - r-magrittr - r-readr - r-tibble - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-hmp16sdata/post-link.sh b/recipes/bioconductor-hmp16sdata/post-link.sh index c2daa2c2cb56f..d3aa1de38712a 100644 --- a/recipes/bioconductor-hmp16sdata/post-link.sh +++ b/recipes/bioconductor-hmp16sdata/post-link.sh @@ -1,11 +1,11 @@ #!/bin/bash -FN="HMP16SData_1.2.0.tar.gz" +FN="HMP16SData_1.3.2.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/experiment/src/contrib/HMP16SData_1.2.0.tar.gz" - "https://bioarchive.galaxyproject.org/HMP16SData_1.2.0.tar.gz" - "https://depot.galaxyproject.org/software/bioconductor-hmp16sdata/bioconductor-hmp16sdata_1.2.0_src_all.tar.gz" + "https://bioconductor.org/packages/3.9/data/experiment/src/contrib/HMP16SData_1.3.2.tar.gz" + "https://bioarchive.galaxyproject.org/HMP16SData_1.3.2.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-hmp16sdata/bioconductor-hmp16sdata_1.3.2_src_all.tar.gz" ) -MD5="d0369085597560d872684b5846833ee3" +MD5="af1f24921e331d20bb1181483588a36d" # Use a staging area in the conda dir rather than temp dirs, both to avoid # permission issues as well as to have things downloaded in a predictable @@ -16,7 +16,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-hmyrib36/meta.yaml b/recipes/bioconductor-hmyrib36/meta.yaml index cb7fdbac21188..b1b20bda1b29d 100644 --- a/recipes/bioconductor-hmyrib36/meta.yaml +++ b/recipes/bioconductor-hmyrib36/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.18.0" %} +{% set version = "1.20.0" %} {% set name = "hmyriB36" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: b5674b509a47b85c82b4173b4a13e5f1 + md5: e08284e8555bcedcdbdb4b1aa677b748 build: number: 0 rpaths: @@ -20,14 +20,14 @@ build: # Suggests: GGtools, illuminaHumanv1.db requirements: host: - - 'bioconductor-biobase >=2.42.0,<2.43.0' - - 'bioconductor-ggbase >=3.44.0,<3.45.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' + - 'bioconductor-ggbase >=3.46.0,<3.47.0' - r-base run: - - 'bioconductor-biobase >=2.42.0,<2.43.0' - - 'bioconductor-ggbase >=3.44.0,<3.45.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' + - 'bioconductor-ggbase >=3.46.0,<3.47.0' - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-hmyrib36/post-link.sh b/recipes/bioconductor-hmyrib36/post-link.sh index 0b9dcb8e77e99..6447498c8c9af 100644 --- a/recipes/bioconductor-hmyrib36/post-link.sh +++ b/recipes/bioconductor-hmyrib36/post-link.sh @@ -1,11 +1,11 @@ #!/bin/bash -FN="hmyriB36_1.18.0.tar.gz" +FN="hmyriB36_1.20.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/experiment/src/contrib/hmyriB36_1.18.0.tar.gz" - "https://bioarchive.galaxyproject.org/hmyriB36_1.18.0.tar.gz" - "https://depot.galaxyproject.org/software/bioconductor-hmyrib36/bioconductor-hmyrib36_1.18.0_src_all.tar.gz" + "https://bioconductor.org/packages/3.9/data/experiment/src/contrib/hmyriB36_1.20.0.tar.gz" + "https://bioarchive.galaxyproject.org/hmyriB36_1.20.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-hmyrib36/bioconductor-hmyrib36_1.20.0_src_all.tar.gz" ) -MD5="b5674b509a47b85c82b4173b4a13e5f1" +MD5="e08284e8555bcedcdbdb4b1aa677b748" # Use a staging area in the conda dir rather than temp dirs, both to avoid # permission issues as well as to have things downloaded in a predictable @@ -16,7 +16,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-hom.at.inp.db/meta.yaml b/recipes/bioconductor-hom.at.inp.db/meta.yaml index acad8a02df274..7977d4e1bf7a0 100644 --- a/recipes/bioconductor-hom.at.inp.db/meta.yaml +++ b/recipes/bioconductor-hom.at.inp.db/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.1.2" %} {% set name = "hom.At.inp.db" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -12,19 +12,19 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' md5: 9d96d343202848e129b96e5e234bd269 build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' - r-base run: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-hom.at.inp.db/post-link.sh b/recipes/bioconductor-hom.at.inp.db/post-link.sh index 93ae5b8811712..14f9c1a6ee5e6 100644 --- a/recipes/bioconductor-hom.at.inp.db/post-link.sh +++ b/recipes/bioconductor-hom.at.inp.db/post-link.sh @@ -1,9 +1,10 @@ #!/bin/bash FN="hom.At.inp.db_3.1.2.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/hom.At.inp.db_3.1.2.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/hom.At.inp.db_3.1.2.tar.gz" "https://bioarchive.galaxyproject.org/hom.At.inp.db_3.1.2.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-hom.at.inp.db/bioconductor-hom.at.inp.db_3.1.2_src_all.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-hom.at.inp.db/bioconductor-hom.at.inp.db_3.1.2_src_all.tar.gz" ) MD5="9d96d343202848e129b96e5e234bd269" @@ -16,7 +17,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-hom.ce.inp.db/meta.yaml b/recipes/bioconductor-hom.ce.inp.db/meta.yaml index de889e0ccfedd..a45fddc2659ad 100644 --- a/recipes/bioconductor-hom.ce.inp.db/meta.yaml +++ b/recipes/bioconductor-hom.ce.inp.db/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.1.2" %} {% set name = "hom.Ce.inp.db" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -12,19 +12,19 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' md5: 914b04390edfc06466fddd3bab1a5806 build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' - r-base run: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-hom.ce.inp.db/post-link.sh b/recipes/bioconductor-hom.ce.inp.db/post-link.sh index 1c2ecb9e36ff8..67efb82401687 100644 --- a/recipes/bioconductor-hom.ce.inp.db/post-link.sh +++ b/recipes/bioconductor-hom.ce.inp.db/post-link.sh @@ -1,9 +1,10 @@ #!/bin/bash FN="hom.Ce.inp.db_3.1.2.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/hom.Ce.inp.db_3.1.2.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/hom.Ce.inp.db_3.1.2.tar.gz" "https://bioarchive.galaxyproject.org/hom.Ce.inp.db_3.1.2.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-hom.ce.inp.db/bioconductor-hom.ce.inp.db_3.1.2_src_all.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-hom.ce.inp.db/bioconductor-hom.ce.inp.db_3.1.2_src_all.tar.gz" ) MD5="914b04390edfc06466fddd3bab1a5806" @@ -16,7 +17,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-hom.dm.inp.db/meta.yaml b/recipes/bioconductor-hom.dm.inp.db/meta.yaml index 00acca0678104..3858d54b6fdb2 100644 --- a/recipes/bioconductor-hom.dm.inp.db/meta.yaml +++ b/recipes/bioconductor-hom.dm.inp.db/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.1.2" %} {% set name = "hom.Dm.inp.db" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -12,19 +12,19 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' md5: 24599bd0267b6b6f83d9a27d42d72221 build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' - r-base run: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-hom.dm.inp.db/post-link.sh b/recipes/bioconductor-hom.dm.inp.db/post-link.sh index 30b0a6c8ec447..6ce71d105c989 100644 --- a/recipes/bioconductor-hom.dm.inp.db/post-link.sh +++ b/recipes/bioconductor-hom.dm.inp.db/post-link.sh @@ -1,9 +1,10 @@ #!/bin/bash FN="hom.Dm.inp.db_3.1.2.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/hom.Dm.inp.db_3.1.2.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/hom.Dm.inp.db_3.1.2.tar.gz" "https://bioarchive.galaxyproject.org/hom.Dm.inp.db_3.1.2.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-hom.dm.inp.db/bioconductor-hom.dm.inp.db_3.1.2_src_all.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-hom.dm.inp.db/bioconductor-hom.dm.inp.db_3.1.2_src_all.tar.gz" ) MD5="24599bd0267b6b6f83d9a27d42d72221" @@ -16,7 +17,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-hom.dr.inp.db/meta.yaml b/recipes/bioconductor-hom.dr.inp.db/meta.yaml index 44b71d458c41f..8b53c80b988f6 100644 --- a/recipes/bioconductor-hom.dr.inp.db/meta.yaml +++ b/recipes/bioconductor-hom.dr.inp.db/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.1.2" %} {% set name = "hom.Dr.inp.db" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -12,19 +12,19 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' md5: d3e588cb6116354605a024ed3e7f5c4e build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' - r-base run: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-hom.dr.inp.db/post-link.sh b/recipes/bioconductor-hom.dr.inp.db/post-link.sh index ef366eb43829c..db3e9b550e51b 100644 --- a/recipes/bioconductor-hom.dr.inp.db/post-link.sh +++ b/recipes/bioconductor-hom.dr.inp.db/post-link.sh @@ -1,9 +1,10 @@ #!/bin/bash FN="hom.Dr.inp.db_3.1.2.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/hom.Dr.inp.db_3.1.2.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/hom.Dr.inp.db_3.1.2.tar.gz" "https://bioarchive.galaxyproject.org/hom.Dr.inp.db_3.1.2.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-hom.dr.inp.db/bioconductor-hom.dr.inp.db_3.1.2_src_all.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-hom.dr.inp.db/bioconductor-hom.dr.inp.db_3.1.2_src_all.tar.gz" ) MD5="d3e588cb6116354605a024ed3e7f5c4e" @@ -16,7 +17,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-hom.hs.inp.db/meta.yaml b/recipes/bioconductor-hom.hs.inp.db/meta.yaml index 5f7cdb21bd5c1..73b10332e81a1 100644 --- a/recipes/bioconductor-hom.hs.inp.db/meta.yaml +++ b/recipes/bioconductor-hom.hs.inp.db/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.1.2" %} {% set name = "hom.Hs.inp.db" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -12,19 +12,19 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' md5: b0708148e9c6656527e004fbaf80c05c build: - number: 5 + number: 6 rpaths: - lib/R/lib/ - lib/ noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' - r-base run: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-hom.hs.inp.db/post-link.sh b/recipes/bioconductor-hom.hs.inp.db/post-link.sh index e5527be05352b..c0187c9132c63 100644 --- a/recipes/bioconductor-hom.hs.inp.db/post-link.sh +++ b/recipes/bioconductor-hom.hs.inp.db/post-link.sh @@ -1,7 +1,7 @@ #!/bin/bash FN="hom.Hs.inp.db_3.1.2.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/hom.Hs.inp.db_3.1.2.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/hom.Hs.inp.db_3.1.2.tar.gz" "https://bioarchive.galaxyproject.org/hom.Hs.inp.db_3.1.2.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-hom.hs.inp.db/bioconductor-hom.hs.inp.db_3.1.2_src_all.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-hom.hs.inp.db/bioconductor-hom.hs.inp.db_3.1.2_src_all.tar.gz" @@ -17,7 +17,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-hom.mm.inp.db/meta.yaml b/recipes/bioconductor-hom.mm.inp.db/meta.yaml index 6cbcd6927d1df..eb2c910298d8b 100644 --- a/recipes/bioconductor-hom.mm.inp.db/meta.yaml +++ b/recipes/bioconductor-hom.mm.inp.db/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.1.2" %} {% set name = "hom.Mm.inp.db" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -12,19 +12,19 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' md5: 27d49db64f3f6049210456121f33d6c0 build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' - r-base run: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-hom.mm.inp.db/post-link.sh b/recipes/bioconductor-hom.mm.inp.db/post-link.sh index 1158c9512e897..7be405f77b908 100644 --- a/recipes/bioconductor-hom.mm.inp.db/post-link.sh +++ b/recipes/bioconductor-hom.mm.inp.db/post-link.sh @@ -1,9 +1,10 @@ #!/bin/bash FN="hom.Mm.inp.db_3.1.2.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/hom.Mm.inp.db_3.1.2.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/hom.Mm.inp.db_3.1.2.tar.gz" "https://bioarchive.galaxyproject.org/hom.Mm.inp.db_3.1.2.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-hom.mm.inp.db/bioconductor-hom.mm.inp.db_3.1.2_src_all.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-hom.mm.inp.db/bioconductor-hom.mm.inp.db_3.1.2_src_all.tar.gz" ) MD5="27d49db64f3f6049210456121f33d6c0" @@ -16,7 +17,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-hom.rn.inp.db/meta.yaml b/recipes/bioconductor-hom.rn.inp.db/meta.yaml index d2da3dfe43fd9..64bacdf68c7b4 100644 --- a/recipes/bioconductor-hom.rn.inp.db/meta.yaml +++ b/recipes/bioconductor-hom.rn.inp.db/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.1.2" %} {% set name = "hom.Rn.inp.db" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -12,19 +12,19 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' md5: 17cf02b55681712da40405ffcd81ea5b build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' - r-base run: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-hom.rn.inp.db/post-link.sh b/recipes/bioconductor-hom.rn.inp.db/post-link.sh index 93272cbe64129..5e95d647c6007 100644 --- a/recipes/bioconductor-hom.rn.inp.db/post-link.sh +++ b/recipes/bioconductor-hom.rn.inp.db/post-link.sh @@ -1,9 +1,10 @@ #!/bin/bash FN="hom.Rn.inp.db_3.1.2.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/hom.Rn.inp.db_3.1.2.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/hom.Rn.inp.db_3.1.2.tar.gz" "https://bioarchive.galaxyproject.org/hom.Rn.inp.db_3.1.2.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-hom.rn.inp.db/bioconductor-hom.rn.inp.db_3.1.2_src_all.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-hom.rn.inp.db/bioconductor-hom.rn.inp.db_3.1.2_src_all.tar.gz" ) MD5="17cf02b55681712da40405ffcd81ea5b" @@ -16,7 +17,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-hom.sc.inp.db/meta.yaml b/recipes/bioconductor-hom.sc.inp.db/meta.yaml index 16a9f5d5b3d68..b6b04e4793b48 100644 --- a/recipes/bioconductor-hom.sc.inp.db/meta.yaml +++ b/recipes/bioconductor-hom.sc.inp.db/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.1.2" %} {% set name = "hom.Sc.inp.db" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -12,19 +12,19 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' md5: e3f58421e9067e8109e3e077b0109511 build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' - r-base run: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-hom.sc.inp.db/post-link.sh b/recipes/bioconductor-hom.sc.inp.db/post-link.sh index 43bc2d9046e02..de950c2e282f6 100644 --- a/recipes/bioconductor-hom.sc.inp.db/post-link.sh +++ b/recipes/bioconductor-hom.sc.inp.db/post-link.sh @@ -1,9 +1,10 @@ #!/bin/bash FN="hom.Sc.inp.db_3.1.2.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/hom.Sc.inp.db_3.1.2.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/hom.Sc.inp.db_3.1.2.tar.gz" "https://bioarchive.galaxyproject.org/hom.Sc.inp.db_3.1.2.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-hom.sc.inp.db/bioconductor-hom.sc.inp.db_3.1.2_src_all.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-hom.sc.inp.db/bioconductor-hom.sc.inp.db_3.1.2_src_all.tar.gz" ) MD5="e3f58421e9067e8109e3e077b0109511" @@ -16,7 +17,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-homo.sapiens/meta.yaml b/recipes/bioconductor-homo.sapiens/meta.yaml index 5c1e57e4f3f18..06c4447904d0d 100644 --- a/recipes/bioconductor-homo.sapiens/meta.yaml +++ b/recipes/bioconductor-homo.sapiens/meta.yaml @@ -1,6 +1,6 @@ {% set version = "1.3.1" %} {% set name = "Homo.sapiens" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -12,29 +12,29 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' md5: 653b60cfcdaefd171729115cd629b585 build: - number: 4 + number: 5 rpaths: - lib/R/lib/ - lib/ noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' - - 'bioconductor-genomicfeatures >=1.34.0,<1.35.0' - - 'bioconductor-go.db >=3.7.0,<3.8.0' - - 'bioconductor-org.hs.eg.db >=3.7.0,<3.8.0' - - 'bioconductor-organismdbi >=1.24.0,<1.25.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' + - 'bioconductor-genomicfeatures >=1.36.0,<1.37.0' + - 'bioconductor-go.db >=3.8.0,<3.9.0' + - 'bioconductor-org.hs.eg.db >=3.8.0,<3.9.0' + - 'bioconductor-organismdbi >=1.26.0,<1.27.0' - 'bioconductor-txdb.hsapiens.ucsc.hg19.knowngene >=3.2.0,<3.3.0' - r-base run: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' - - 'bioconductor-genomicfeatures >=1.34.0,<1.35.0' - - 'bioconductor-go.db >=3.7.0,<3.8.0' - - 'bioconductor-org.hs.eg.db >=3.7.0,<3.8.0' - - 'bioconductor-organismdbi >=1.24.0,<1.25.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' + - 'bioconductor-genomicfeatures >=1.36.0,<1.37.0' + - 'bioconductor-go.db >=3.8.0,<3.9.0' + - 'bioconductor-org.hs.eg.db >=3.8.0,<3.9.0' + - 'bioconductor-organismdbi >=1.26.0,<1.27.0' - 'bioconductor-txdb.hsapiens.ucsc.hg19.knowngene >=3.2.0,<3.3.0' - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-homo.sapiens/post-link.sh b/recipes/bioconductor-homo.sapiens/post-link.sh index 64b4ec891c6ea..e24dc8056d78b 100644 --- a/recipes/bioconductor-homo.sapiens/post-link.sh +++ b/recipes/bioconductor-homo.sapiens/post-link.sh @@ -1,7 +1,7 @@ #!/bin/bash FN="Homo.sapiens_1.3.1.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/Homo.sapiens_1.3.1.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/Homo.sapiens_1.3.1.tar.gz" "https://bioarchive.galaxyproject.org/Homo.sapiens_1.3.1.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-homo.sapiens/bioconductor-homo.sapiens_1.3.1_src_all.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-homo.sapiens/bioconductor-homo.sapiens_1.3.1_src_all.tar.gz" @@ -17,7 +17,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-hopach/meta.yaml b/recipes/bioconductor-hopach/meta.yaml index 568eb61392808..989ea7bfb0031 100644 --- a/recipes/bioconductor-hopach/meta.yaml +++ b/recipes/bioconductor-hopach/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "2.42.0" %} +{% set version = "2.44.0" %} {% set name = "hopach" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 35465e16c6f9f85363b0e00701eb5e52 + md5: a38ccfbd7bd30f6258d05248aea93788 build: number: 0 rpaths: @@ -18,13 +18,13 @@ build: - lib/ requirements: host: - - 'bioconductor-biobase >=2.42.0,<2.43.0' - - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' + - 'bioconductor-biocgenerics >=0.30.0,<0.31.0' - r-base - r-cluster run: - - 'bioconductor-biobase >=2.42.0,<2.43.0' - - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' + - 'bioconductor-biocgenerics >=0.30.0,<0.31.0' - r-base - r-cluster build: diff --git a/recipes/bioconductor-hpaanalyze/meta.yaml b/recipes/bioconductor-hpaanalyze/meta.yaml index 1f865d5b9b3e2..99c29c57ea1d0 100644 --- a/recipes/bioconductor-hpaanalyze/meta.yaml +++ b/recipes/bioconductor-hpaanalyze/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.0.0" %} +{% set version = "1.2.0" %} {% set name = "HPAanalyze" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 211c3fa0f4c721603e9c913f2723bbf5 + md5: a9b46d0c9adc901e15595ec3e0416312 build: number: 0 rpaths: @@ -20,30 +20,30 @@ build: # Suggests: knitr, rmarkdown, devtools, BiocStyle requirements: host: - - 'bioconductor-hpar >=1.24.0,<1.25.0' + - 'bioconductor-hpar >=1.26.0,<1.27.0' - r-base - r-cowplot - r-dplyr - r-ggplot2 - r-magrittr + - r-openxlsx - r-readr - r-reshape2 - r-tibble - r-tidyr - - r-xlconnect - r-xml2 run: - - 'bioconductor-hpar >=1.24.0,<1.25.0' + - 'bioconductor-hpar >=1.26.0,<1.27.0' - r-base - r-cowplot - r-dplyr - r-ggplot2 - r-magrittr + - r-openxlsx - r-readr - r-reshape2 - r-tibble - r-tidyr - - r-xlconnect - r-xml2 test: commands: diff --git a/recipes/bioconductor-hpannot/meta.yaml b/recipes/bioconductor-hpannot/meta.yaml new file mode 100644 index 0000000000000..d36254df7d99b --- /dev/null +++ b/recipes/bioconductor-hpannot/meta.yaml @@ -0,0 +1,34 @@ +{% set version = "1.0.1" %} +{% set name = "hpAnnot" %} +{% set bioc = "3.9" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: 7a1254a1d184b1a065f5f24d266cebdc +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: BiocStyle, knitr, rmarkdown +requirements: + host: + - r-base + run: + - r-base + - curl +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + license: GPL-2 + summary: 'Package containing example and annotation data for Hipathia package. Hipathia is a method for the computation of signal transduction along signaling pathways from transcriptomic data. The method is based on an iterative algorithm which is able to compute the signal intensity passing through the nodes of a network by taking into account the level of expression of each gene and the intensity of the signal arriving to it. It also provides a new approach to functional analysis allowing to compute the signal arriving to the functions annotated to each pathway. Hipathia depends on this package to be functional.' + diff --git a/recipes/bioconductor-hpannot/post-link.sh b/recipes/bioconductor-hpannot/post-link.sh new file mode 100644 index 0000000000000..22dd97b538f66 --- /dev/null +++ b/recipes/bioconductor-hpannot/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="hpAnnot_1.0.1.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/hpAnnot_1.0.1.tar.gz" + "https://bioarchive.galaxyproject.org/hpAnnot_1.0.1.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-hpannot/bioconductor-hpannot_1.0.1_src_all.tar.gz" +) +MD5="7a1254a1d184b1a065f5f24d266cebdc" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + curl $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-hpannot/pre-unlink.sh b/recipes/bioconductor-hpannot/pre-unlink.sh new file mode 100644 index 0000000000000..17c95070eaeef --- /dev/null +++ b/recipes/bioconductor-hpannot/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ hpAnnot diff --git a/recipes/bioconductor-hpar/meta.yaml b/recipes/bioconductor-hpar/meta.yaml index 25fbfff925304..cba2db58a93a6 100644 --- a/recipes/bioconductor-hpar/meta.yaml +++ b/recipes/bioconductor-hpar/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.24.0" %} +{% set version = "1.26.0" %} {% set name = "hpar" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: d424723a0f21b8ad24e7280040c4cea7 + md5: c4c17d1b40dd4a13e17a570ebae93480 build: number: 0 rpaths: diff --git a/recipes/bioconductor-hs25kresogen.db/meta.yaml b/recipes/bioconductor-hs25kresogen.db/meta.yaml index 829a383d20624..668a0f2b1ce1c 100644 --- a/recipes/bioconductor-hs25kresogen.db/meta.yaml +++ b/recipes/bioconductor-hs25kresogen.db/meta.yaml @@ -1,6 +1,6 @@ {% set version = "2.5.0" %} {% set name = "hs25kresogen.db" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -12,7 +12,7 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: a3800d072ce0e5f6f5d8299538b99cca build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ @@ -20,14 +20,14 @@ build: # Suggests: annotate requirements: host: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' - - 'bioconductor-org.hs.eg.db >=3.7.0,<3.8.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' + - 'bioconductor-org.hs.eg.db >=3.8.0,<3.9.0' - r-base run: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' - - 'bioconductor-org.hs.eg.db >=3.7.0,<3.8.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' + - 'bioconductor-org.hs.eg.db >=3.8.0,<3.9.0' - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-hs25kresogen.db/post-link.sh b/recipes/bioconductor-hs25kresogen.db/post-link.sh index 12649cd85a127..5e4d2cfdfdd70 100644 --- a/recipes/bioconductor-hs25kresogen.db/post-link.sh +++ b/recipes/bioconductor-hs25kresogen.db/post-link.sh @@ -1,9 +1,10 @@ #!/bin/bash FN="hs25kresogen.db_2.5.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/hs25kresogen.db_2.5.0.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/hs25kresogen.db_2.5.0.tar.gz" "https://bioarchive.galaxyproject.org/hs25kresogen.db_2.5.0.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-hs25kresogen.db/bioconductor-hs25kresogen.db_2.5.0_src_all.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-hs25kresogen.db/bioconductor-hs25kresogen.db_2.5.0_src_all.tar.gz" ) MD5="a3800d072ce0e5f6f5d8299538b99cca" @@ -16,7 +17,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-hs6ug171.db/meta.yaml b/recipes/bioconductor-hs6ug171.db/meta.yaml index 1bda954b909a3..c30c7a918a28f 100644 --- a/recipes/bioconductor-hs6ug171.db/meta.yaml +++ b/recipes/bioconductor-hs6ug171.db/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.2.3" %} {% set name = "Hs6UG171.db" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -12,7 +12,7 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' md5: 7aaf8a2441941f70247275c93735ed3b build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ @@ -20,14 +20,14 @@ build: # Suggests: DBI, annotate, RUnit requirements: host: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' - - 'bioconductor-org.hs.eg.db >=3.7.0,<3.8.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' + - 'bioconductor-org.hs.eg.db >=3.8.0,<3.9.0' - r-base run: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' - - 'bioconductor-org.hs.eg.db >=3.7.0,<3.8.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' + - 'bioconductor-org.hs.eg.db >=3.8.0,<3.9.0' - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-hs6ug171.db/post-link.sh b/recipes/bioconductor-hs6ug171.db/post-link.sh index 871c7837a170e..eb05dd9cbc910 100644 --- a/recipes/bioconductor-hs6ug171.db/post-link.sh +++ b/recipes/bioconductor-hs6ug171.db/post-link.sh @@ -1,9 +1,10 @@ #!/bin/bash FN="Hs6UG171.db_3.2.3.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/Hs6UG171.db_3.2.3.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/Hs6UG171.db_3.2.3.tar.gz" "https://bioarchive.galaxyproject.org/Hs6UG171.db_3.2.3.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-hs6ug171.db/bioconductor-hs6ug171.db_3.2.3_src_all.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-hs6ug171.db/bioconductor-hs6ug171.db_3.2.3_src_all.tar.gz" ) MD5="7aaf8a2441941f70247275c93735ed3b" @@ -16,7 +17,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-hsagilentdesign026652.db/meta.yaml b/recipes/bioconductor-hsagilentdesign026652.db/meta.yaml index 295d4513785f5..2124675f72b50 100644 --- a/recipes/bioconductor-hsagilentdesign026652.db/meta.yaml +++ b/recipes/bioconductor-hsagilentdesign026652.db/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.2.3" %} {% set name = "HsAgilentDesign026652.db" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -12,7 +12,7 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' md5: dcd2c748bf9d7c002611cd5cf2ff38c0 build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ @@ -20,14 +20,14 @@ build: # Suggests: DBI, annotate, RUnit requirements: host: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' - - 'bioconductor-org.hs.eg.db >=3.7.0,<3.8.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' + - 'bioconductor-org.hs.eg.db >=3.8.0,<3.9.0' - r-base run: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' - - 'bioconductor-org.hs.eg.db >=3.7.0,<3.8.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' + - 'bioconductor-org.hs.eg.db >=3.8.0,<3.9.0' - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-hsagilentdesign026652.db/post-link.sh b/recipes/bioconductor-hsagilentdesign026652.db/post-link.sh index 2788bafa958a6..761d8369afc99 100644 --- a/recipes/bioconductor-hsagilentdesign026652.db/post-link.sh +++ b/recipes/bioconductor-hsagilentdesign026652.db/post-link.sh @@ -1,9 +1,10 @@ #!/bin/bash FN="HsAgilentDesign026652.db_3.2.3.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/HsAgilentDesign026652.db_3.2.3.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/HsAgilentDesign026652.db_3.2.3.tar.gz" "https://bioarchive.galaxyproject.org/HsAgilentDesign026652.db_3.2.3.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-hsagilentdesign026652.db/bioconductor-hsagilentdesign026652.db_3.2.3_src_all.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-hsagilentdesign026652.db/bioconductor-hsagilentdesign026652.db_3.2.3_src_all.tar.gz" ) MD5="dcd2c748bf9d7c002611cd5cf2ff38c0" @@ -16,7 +17,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-hsmmsinglecell/meta.yaml b/recipes/bioconductor-hsmmsinglecell/meta.yaml index f6cc524d44ade..22e9b306951f4 100644 --- a/recipes/bioconductor-hsmmsinglecell/meta.yaml +++ b/recipes/bioconductor-hsmmsinglecell/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.2.0" %} +{% set version = "1.4.0" %} {% set name = "HSMMSingleCell" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 13554a8eacb310fd9af3900ba9ce68b9 + md5: 8ee141b0de4637baf95d871cb0ff163b build: number: 0 rpaths: @@ -22,7 +22,7 @@ requirements: - r-base run: - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-hsmmsinglecell/post-link.sh b/recipes/bioconductor-hsmmsinglecell/post-link.sh index 467be71f23881..591fac6e4dc86 100644 --- a/recipes/bioconductor-hsmmsinglecell/post-link.sh +++ b/recipes/bioconductor-hsmmsinglecell/post-link.sh @@ -1,11 +1,11 @@ #!/bin/bash -FN="HSMMSingleCell_1.2.0.tar.gz" +FN="HSMMSingleCell_1.4.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/experiment/src/contrib/HSMMSingleCell_1.2.0.tar.gz" - "https://bioarchive.galaxyproject.org/HSMMSingleCell_1.2.0.tar.gz" - "https://depot.galaxyproject.org/software/bioconductor-hsmmsinglecell/bioconductor-hsmmsinglecell_1.2.0_src_all.tar.gz" + "https://bioconductor.org/packages/3.9/data/experiment/src/contrib/HSMMSingleCell_1.4.0.tar.gz" + "https://bioarchive.galaxyproject.org/HSMMSingleCell_1.4.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-hsmmsinglecell/bioconductor-hsmmsinglecell_1.4.0_src_all.tar.gz" ) -MD5="13554a8eacb310fd9af3900ba9ce68b9" +MD5="8ee141b0de4637baf95d871cb0ff163b" # Use a staging area in the conda dir rather than temp dirs, both to avoid # permission issues as well as to have things downloaded in a predictable @@ -16,7 +16,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-hspec/meta.yaml b/recipes/bioconductor-hspec/meta.yaml index f49d7cd5ec90e..3703b81594872 100644 --- a/recipes/bioconductor-hspec/meta.yaml +++ b/recipes/bioconductor-hspec/meta.yaml @@ -1,6 +1,6 @@ {% set version = "0.99.1" %} {% set name = "Hspec" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -12,19 +12,19 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' md5: 0ade3e3147c8f0086e9be2312cccdfeb build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' - r-base run: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-hspec/post-link.sh b/recipes/bioconductor-hspec/post-link.sh index 92328dc7d37ab..aa3d85bea0030 100644 --- a/recipes/bioconductor-hspec/post-link.sh +++ b/recipes/bioconductor-hspec/post-link.sh @@ -1,9 +1,10 @@ #!/bin/bash FN="Hspec_0.99.1.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/Hspec_0.99.1.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/Hspec_0.99.1.tar.gz" "https://bioarchive.galaxyproject.org/Hspec_0.99.1.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-hspec/bioconductor-hspec_0.99.1_src_all.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-hspec/bioconductor-hspec_0.99.1_src_all.tar.gz" ) MD5="0ade3e3147c8f0086e9be2312cccdfeb" @@ -16,7 +17,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-hspeccdf/meta.yaml b/recipes/bioconductor-hspeccdf/meta.yaml index e466a0c141ab5..b67a199b314c3 100644 --- a/recipes/bioconductor-hspeccdf/meta.yaml +++ b/recipes/bioconductor-hspeccdf/meta.yaml @@ -1,6 +1,6 @@ {% set version = "0.99.1" %} {% set name = "hspeccdf" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -12,19 +12,19 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 89f81adf91094710558ce6aec79fc7fd build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' - r-base run: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-hspeccdf/post-link.sh b/recipes/bioconductor-hspeccdf/post-link.sh index d3d7381d00016..127c09457ece3 100644 --- a/recipes/bioconductor-hspeccdf/post-link.sh +++ b/recipes/bioconductor-hspeccdf/post-link.sh @@ -1,9 +1,10 @@ #!/bin/bash FN="hspeccdf_0.99.1.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/hspeccdf_0.99.1.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/hspeccdf_0.99.1.tar.gz" "https://bioarchive.galaxyproject.org/hspeccdf_0.99.1.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-hspeccdf/bioconductor-hspeccdf_0.99.1_src_all.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-hspeccdf/bioconductor-hspeccdf_0.99.1_src_all.tar.gz" ) MD5="89f81adf91094710558ce6aec79fc7fd" @@ -16,7 +17,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-hta20probeset.db/meta.yaml b/recipes/bioconductor-hta20probeset.db/meta.yaml index 6c520fdaf3f5f..aa748fa1573c3 100644 --- a/recipes/bioconductor-hta20probeset.db/meta.yaml +++ b/recipes/bioconductor-hta20probeset.db/meta.yaml @@ -1,6 +1,6 @@ {% set version = "8.7.0" %} {% set name = "hta20probeset.db" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -12,7 +12,7 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: d2123b0ecd324626b06a920f947a114e build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ @@ -20,14 +20,14 @@ build: # Suggests: DBI, annotate, RUnit requirements: host: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' - - 'bioconductor-org.hs.eg.db >=3.7.0,<3.8.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' + - 'bioconductor-org.hs.eg.db >=3.8.0,<3.9.0' - r-base run: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' - - 'bioconductor-org.hs.eg.db >=3.7.0,<3.8.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' + - 'bioconductor-org.hs.eg.db >=3.8.0,<3.9.0' - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-hta20probeset.db/post-link.sh b/recipes/bioconductor-hta20probeset.db/post-link.sh index d1348bcad7416..749e88eafb9af 100644 --- a/recipes/bioconductor-hta20probeset.db/post-link.sh +++ b/recipes/bioconductor-hta20probeset.db/post-link.sh @@ -1,9 +1,10 @@ #!/bin/bash FN="hta20probeset.db_8.7.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/hta20probeset.db_8.7.0.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/hta20probeset.db_8.7.0.tar.gz" "https://bioarchive.galaxyproject.org/hta20probeset.db_8.7.0.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-hta20probeset.db/bioconductor-hta20probeset.db_8.7.0_src_all.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-hta20probeset.db/bioconductor-hta20probeset.db_8.7.0_src_all.tar.gz" ) MD5="d2123b0ecd324626b06a920f947a114e" @@ -16,7 +17,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-hta20transcriptcluster.db/meta.yaml b/recipes/bioconductor-hta20transcriptcluster.db/meta.yaml index 924c80d4ef466..b68fb4d54889b 100644 --- a/recipes/bioconductor-hta20transcriptcluster.db/meta.yaml +++ b/recipes/bioconductor-hta20transcriptcluster.db/meta.yaml @@ -1,6 +1,6 @@ {% set version = "8.7.0" %} {% set name = "hta20transcriptcluster.db" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -12,7 +12,7 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: c7cdfe80bf2f7aa86fa3caff6da0c34c build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ @@ -20,14 +20,14 @@ build: # Suggests: DBI, annotate, RUnit requirements: host: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' - - 'bioconductor-org.hs.eg.db >=3.7.0,<3.8.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' + - 'bioconductor-org.hs.eg.db >=3.8.0,<3.9.0' - r-base run: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' - - 'bioconductor-org.hs.eg.db >=3.7.0,<3.8.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' + - 'bioconductor-org.hs.eg.db >=3.8.0,<3.9.0' - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-hta20transcriptcluster.db/post-link.sh b/recipes/bioconductor-hta20transcriptcluster.db/post-link.sh index 8a6c137e6f3ae..5aff2146a334b 100644 --- a/recipes/bioconductor-hta20transcriptcluster.db/post-link.sh +++ b/recipes/bioconductor-hta20transcriptcluster.db/post-link.sh @@ -1,9 +1,10 @@ #!/bin/bash FN="hta20transcriptcluster.db_8.7.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/hta20transcriptcluster.db_8.7.0.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/hta20transcriptcluster.db_8.7.0.tar.gz" "https://bioarchive.galaxyproject.org/hta20transcriptcluster.db_8.7.0.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-hta20transcriptcluster.db/bioconductor-hta20transcriptcluster.db_8.7.0_src_all.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-hta20transcriptcluster.db/bioconductor-hta20transcriptcluster.db_8.7.0_src_all.tar.gz" ) MD5="c7cdfe80bf2f7aa86fa3caff6da0c34c" @@ -16,7 +17,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-hthgu133a.db/meta.yaml b/recipes/bioconductor-hthgu133a.db/meta.yaml index 40e3cd9d2a284..a58481e7d7291 100644 --- a/recipes/bioconductor-hthgu133a.db/meta.yaml +++ b/recipes/bioconductor-hthgu133a.db/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.2.3" %} {% set name = "hthgu133a.db" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -12,7 +12,7 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: df8c18dcb8d0adfb6f7a9306cbe9b162 build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ @@ -20,14 +20,14 @@ build: # Suggests: DBI, annotate, RUnit requirements: host: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' - - 'bioconductor-org.hs.eg.db >=3.7.0,<3.8.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' + - 'bioconductor-org.hs.eg.db >=3.8.0,<3.9.0' - r-base run: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' - - 'bioconductor-org.hs.eg.db >=3.7.0,<3.8.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' + - 'bioconductor-org.hs.eg.db >=3.8.0,<3.9.0' - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-hthgu133a.db/post-link.sh b/recipes/bioconductor-hthgu133a.db/post-link.sh index d4c076e83efc8..8867aee83430e 100644 --- a/recipes/bioconductor-hthgu133a.db/post-link.sh +++ b/recipes/bioconductor-hthgu133a.db/post-link.sh @@ -1,9 +1,10 @@ #!/bin/bash FN="hthgu133a.db_3.2.3.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/hthgu133a.db_3.2.3.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/hthgu133a.db_3.2.3.tar.gz" "https://bioarchive.galaxyproject.org/hthgu133a.db_3.2.3.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-hthgu133a.db/bioconductor-hthgu133a.db_3.2.3_src_all.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-hthgu133a.db/bioconductor-hthgu133a.db_3.2.3_src_all.tar.gz" ) MD5="df8c18dcb8d0adfb6f7a9306cbe9b162" @@ -16,7 +17,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-hthgu133acdf/meta.yaml b/recipes/bioconductor-hthgu133acdf/meta.yaml index ca3b1465c40c3..e880e96e4adbe 100644 --- a/recipes/bioconductor-hthgu133acdf/meta.yaml +++ b/recipes/bioconductor-hthgu133acdf/meta.yaml @@ -1,6 +1,6 @@ {% set version = "2.18.0" %} {% set name = "hthgu133acdf" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -12,19 +12,19 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: b92e543867f1f0c08bfa9299e123d608 build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' - r-base run: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-hthgu133acdf/post-link.sh b/recipes/bioconductor-hthgu133acdf/post-link.sh index b582fa902c99d..178c20beed0ad 100644 --- a/recipes/bioconductor-hthgu133acdf/post-link.sh +++ b/recipes/bioconductor-hthgu133acdf/post-link.sh @@ -1,9 +1,10 @@ #!/bin/bash FN="hthgu133acdf_2.18.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/hthgu133acdf_2.18.0.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/hthgu133acdf_2.18.0.tar.gz" "https://bioarchive.galaxyproject.org/hthgu133acdf_2.18.0.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-hthgu133acdf/bioconductor-hthgu133acdf_2.18.0_src_all.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-hthgu133acdf/bioconductor-hthgu133acdf_2.18.0_src_all.tar.gz" ) MD5="b92e543867f1f0c08bfa9299e123d608" @@ -16,7 +17,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-hthgu133afrmavecs/meta.yaml b/recipes/bioconductor-hthgu133afrmavecs/meta.yaml index 06768a388af1c..d51529116b1d2 100644 --- a/recipes/bioconductor-hthgu133afrmavecs/meta.yaml +++ b/recipes/bioconductor-hthgu133afrmavecs/meta.yaml @@ -1,6 +1,6 @@ {% set version = "1.3.0" %} {% set name = "hthgu133afrmavecs" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -12,7 +12,7 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: be3f3d67a94dca3b080c184fba5ff6d8 build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ @@ -22,7 +22,7 @@ requirements: - r-base run: - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-hthgu133afrmavecs/post-link.sh b/recipes/bioconductor-hthgu133afrmavecs/post-link.sh index dbc26d673cbc4..88b7b69d138fa 100644 --- a/recipes/bioconductor-hthgu133afrmavecs/post-link.sh +++ b/recipes/bioconductor-hthgu133afrmavecs/post-link.sh @@ -1,9 +1,10 @@ #!/bin/bash FN="hthgu133afrmavecs_1.3.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/hthgu133afrmavecs_1.3.0.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/hthgu133afrmavecs_1.3.0.tar.gz" "https://bioarchive.galaxyproject.org/hthgu133afrmavecs_1.3.0.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-hthgu133afrmavecs/bioconductor-hthgu133afrmavecs_1.3.0_src_all.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-hthgu133afrmavecs/bioconductor-hthgu133afrmavecs_1.3.0_src_all.tar.gz" ) MD5="be3f3d67a94dca3b080c184fba5ff6d8" @@ -16,7 +17,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-hthgu133aprobe/meta.yaml b/recipes/bioconductor-hthgu133aprobe/meta.yaml index a7752647e80a2..5489ff8a6b073 100644 --- a/recipes/bioconductor-hthgu133aprobe/meta.yaml +++ b/recipes/bioconductor-hthgu133aprobe/meta.yaml @@ -1,6 +1,6 @@ {% set version = "2.18.0" %} {% set name = "hthgu133aprobe" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -12,19 +12,19 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: cdc17ea670719f055ee75bea1415c754 build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' - r-base run: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-hthgu133aprobe/post-link.sh b/recipes/bioconductor-hthgu133aprobe/post-link.sh index cf01b9fab6df4..fb8b467015040 100644 --- a/recipes/bioconductor-hthgu133aprobe/post-link.sh +++ b/recipes/bioconductor-hthgu133aprobe/post-link.sh @@ -1,9 +1,10 @@ #!/bin/bash FN="hthgu133aprobe_2.18.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/hthgu133aprobe_2.18.0.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/hthgu133aprobe_2.18.0.tar.gz" "https://bioarchive.galaxyproject.org/hthgu133aprobe_2.18.0.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-hthgu133aprobe/bioconductor-hthgu133aprobe_2.18.0_src_all.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-hthgu133aprobe/bioconductor-hthgu133aprobe_2.18.0_src_all.tar.gz" ) MD5="cdc17ea670719f055ee75bea1415c754" @@ -16,7 +17,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-hthgu133b.db/meta.yaml b/recipes/bioconductor-hthgu133b.db/meta.yaml index 8da72f6244661..d2bf6540803bd 100644 --- a/recipes/bioconductor-hthgu133b.db/meta.yaml +++ b/recipes/bioconductor-hthgu133b.db/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.2.3" %} {% set name = "hthgu133b.db" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -12,7 +12,7 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: a6dfceb47a306ec5365d8376dbb036c7 build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ @@ -20,14 +20,14 @@ build: # Suggests: DBI, annotate, RUnit requirements: host: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' - - 'bioconductor-org.hs.eg.db >=3.7.0,<3.8.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' + - 'bioconductor-org.hs.eg.db >=3.8.0,<3.9.0' - r-base run: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' - - 'bioconductor-org.hs.eg.db >=3.7.0,<3.8.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' + - 'bioconductor-org.hs.eg.db >=3.8.0,<3.9.0' - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-hthgu133b.db/post-link.sh b/recipes/bioconductor-hthgu133b.db/post-link.sh index 3a789e7ed3e49..d472d55f48cf4 100644 --- a/recipes/bioconductor-hthgu133b.db/post-link.sh +++ b/recipes/bioconductor-hthgu133b.db/post-link.sh @@ -1,9 +1,10 @@ #!/bin/bash FN="hthgu133b.db_3.2.3.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/hthgu133b.db_3.2.3.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/hthgu133b.db_3.2.3.tar.gz" "https://bioarchive.galaxyproject.org/hthgu133b.db_3.2.3.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-hthgu133b.db/bioconductor-hthgu133b.db_3.2.3_src_all.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-hthgu133b.db/bioconductor-hthgu133b.db_3.2.3_src_all.tar.gz" ) MD5="a6dfceb47a306ec5365d8376dbb036c7" @@ -16,7 +17,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-hthgu133bcdf/meta.yaml b/recipes/bioconductor-hthgu133bcdf/meta.yaml index 650d08e935c97..57c64805ed04b 100644 --- a/recipes/bioconductor-hthgu133bcdf/meta.yaml +++ b/recipes/bioconductor-hthgu133bcdf/meta.yaml @@ -1,6 +1,6 @@ {% set version = "2.18.0" %} {% set name = "hthgu133bcdf" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -12,19 +12,19 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 935ae53fb168d9c7890d71020ef4c366 build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' - r-base run: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-hthgu133bcdf/post-link.sh b/recipes/bioconductor-hthgu133bcdf/post-link.sh index 2b664ba0318fa..a443e0379051c 100644 --- a/recipes/bioconductor-hthgu133bcdf/post-link.sh +++ b/recipes/bioconductor-hthgu133bcdf/post-link.sh @@ -1,9 +1,10 @@ #!/bin/bash FN="hthgu133bcdf_2.18.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/hthgu133bcdf_2.18.0.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/hthgu133bcdf_2.18.0.tar.gz" "https://bioarchive.galaxyproject.org/hthgu133bcdf_2.18.0.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-hthgu133bcdf/bioconductor-hthgu133bcdf_2.18.0_src_all.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-hthgu133bcdf/bioconductor-hthgu133bcdf_2.18.0_src_all.tar.gz" ) MD5="935ae53fb168d9c7890d71020ef4c366" @@ -16,7 +17,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-hthgu133bprobe/meta.yaml b/recipes/bioconductor-hthgu133bprobe/meta.yaml index 58b6e1df0c01c..e0a3978b2875b 100644 --- a/recipes/bioconductor-hthgu133bprobe/meta.yaml +++ b/recipes/bioconductor-hthgu133bprobe/meta.yaml @@ -1,6 +1,6 @@ {% set version = "2.18.0" %} {% set name = "hthgu133bprobe" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -12,19 +12,19 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 8a2e306638a81fdec3b10a014c04c6b9 build: - number: 1 + number: 2 rpaths: - lib/R/lib/ - lib/ noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' - r-base run: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-hthgu133bprobe/post-link.sh b/recipes/bioconductor-hthgu133bprobe/post-link.sh index fdd57d7e64421..68199b8199b78 100644 --- a/recipes/bioconductor-hthgu133bprobe/post-link.sh +++ b/recipes/bioconductor-hthgu133bprobe/post-link.sh @@ -1,9 +1,10 @@ #!/bin/bash FN="hthgu133bprobe_2.18.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/hthgu133bprobe_2.18.0.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/hthgu133bprobe_2.18.0.tar.gz" "https://bioarchive.galaxyproject.org/hthgu133bprobe_2.18.0.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-hthgu133bprobe/bioconductor-hthgu133bprobe_2.18.0_src_all.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-hthgu133bprobe/bioconductor-hthgu133bprobe_2.18.0_src_all.tar.gz" ) MD5="8a2e306638a81fdec3b10a014c04c6b9" @@ -16,7 +17,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-hthgu133pluspmcdf/meta.yaml b/recipes/bioconductor-hthgu133pluspmcdf/meta.yaml index 809defa19deb1..b1227f5601495 100644 --- a/recipes/bioconductor-hthgu133pluspmcdf/meta.yaml +++ b/recipes/bioconductor-hthgu133pluspmcdf/meta.yaml @@ -1,6 +1,6 @@ {% set version = "2.18.0" %} {% set name = "hthgu133pluspmcdf" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -12,19 +12,19 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 56d15101d59decac7811caa15b349a9c build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' - r-base run: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-hthgu133pluspmcdf/post-link.sh b/recipes/bioconductor-hthgu133pluspmcdf/post-link.sh index 5ea0f46ae7d0f..1a63eceaaa961 100644 --- a/recipes/bioconductor-hthgu133pluspmcdf/post-link.sh +++ b/recipes/bioconductor-hthgu133pluspmcdf/post-link.sh @@ -1,9 +1,10 @@ #!/bin/bash FN="hthgu133pluspmcdf_2.18.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/hthgu133pluspmcdf_2.18.0.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/hthgu133pluspmcdf_2.18.0.tar.gz" "https://bioarchive.galaxyproject.org/hthgu133pluspmcdf_2.18.0.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-hthgu133pluspmcdf/bioconductor-hthgu133pluspmcdf_2.18.0_src_all.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-hthgu133pluspmcdf/bioconductor-hthgu133pluspmcdf_2.18.0_src_all.tar.gz" ) MD5="56d15101d59decac7811caa15b349a9c" @@ -16,7 +17,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-hthgu133pluspmprobe/meta.yaml b/recipes/bioconductor-hthgu133pluspmprobe/meta.yaml index 2a8e2ff08ca14..b4b29053714f6 100644 --- a/recipes/bioconductor-hthgu133pluspmprobe/meta.yaml +++ b/recipes/bioconductor-hthgu133pluspmprobe/meta.yaml @@ -1,6 +1,6 @@ {% set version = "2.18.0" %} {% set name = "hthgu133pluspmprobe" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -12,19 +12,19 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 74713e822a689007892d0eb92dbd456b build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' - r-base run: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-hthgu133pluspmprobe/post-link.sh b/recipes/bioconductor-hthgu133pluspmprobe/post-link.sh index ab4bc051075f8..4681022230518 100644 --- a/recipes/bioconductor-hthgu133pluspmprobe/post-link.sh +++ b/recipes/bioconductor-hthgu133pluspmprobe/post-link.sh @@ -1,9 +1,10 @@ #!/bin/bash FN="hthgu133pluspmprobe_2.18.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/hthgu133pluspmprobe_2.18.0.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/hthgu133pluspmprobe_2.18.0.tar.gz" "https://bioarchive.galaxyproject.org/hthgu133pluspmprobe_2.18.0.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-hthgu133pluspmprobe/bioconductor-hthgu133pluspmprobe_2.18.0_src_all.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-hthgu133pluspmprobe/bioconductor-hthgu133pluspmprobe_2.18.0_src_all.tar.gz" ) MD5="74713e822a689007892d0eb92dbd456b" @@ -16,7 +17,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-htmg430acdf/meta.yaml b/recipes/bioconductor-htmg430acdf/meta.yaml index eb204849efeb7..86d80f02e3caa 100644 --- a/recipes/bioconductor-htmg430acdf/meta.yaml +++ b/recipes/bioconductor-htmg430acdf/meta.yaml @@ -1,6 +1,6 @@ {% set version = "2.18.0" %} {% set name = "htmg430acdf" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -12,19 +12,19 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: aef7a3c3af7d2624ee6fc6f2d22472e2 build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' - r-base run: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-htmg430acdf/post-link.sh b/recipes/bioconductor-htmg430acdf/post-link.sh index b485226a75ffe..b4d433497cd14 100644 --- a/recipes/bioconductor-htmg430acdf/post-link.sh +++ b/recipes/bioconductor-htmg430acdf/post-link.sh @@ -1,9 +1,10 @@ #!/bin/bash FN="htmg430acdf_2.18.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/htmg430acdf_2.18.0.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/htmg430acdf_2.18.0.tar.gz" "https://bioarchive.galaxyproject.org/htmg430acdf_2.18.0.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-htmg430acdf/bioconductor-htmg430acdf_2.18.0_src_all.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-htmg430acdf/bioconductor-htmg430acdf_2.18.0_src_all.tar.gz" ) MD5="aef7a3c3af7d2624ee6fc6f2d22472e2" @@ -16,7 +17,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-htmg430aprobe/meta.yaml b/recipes/bioconductor-htmg430aprobe/meta.yaml index e0187372c652d..a80e460c160c1 100644 --- a/recipes/bioconductor-htmg430aprobe/meta.yaml +++ b/recipes/bioconductor-htmg430aprobe/meta.yaml @@ -1,6 +1,6 @@ {% set version = "2.18.0" %} {% set name = "htmg430aprobe" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -12,19 +12,19 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: e50cc49b8887b6ef8ee1152ec12d5010 build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' - r-base run: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-htmg430aprobe/post-link.sh b/recipes/bioconductor-htmg430aprobe/post-link.sh index 9724848bc1db2..bd5fdc4779bf2 100644 --- a/recipes/bioconductor-htmg430aprobe/post-link.sh +++ b/recipes/bioconductor-htmg430aprobe/post-link.sh @@ -1,9 +1,10 @@ #!/bin/bash FN="htmg430aprobe_2.18.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/htmg430aprobe_2.18.0.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/htmg430aprobe_2.18.0.tar.gz" "https://bioarchive.galaxyproject.org/htmg430aprobe_2.18.0.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-htmg430aprobe/bioconductor-htmg430aprobe_2.18.0_src_all.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-htmg430aprobe/bioconductor-htmg430aprobe_2.18.0_src_all.tar.gz" ) MD5="e50cc49b8887b6ef8ee1152ec12d5010" @@ -16,7 +17,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-htmg430bcdf/meta.yaml b/recipes/bioconductor-htmg430bcdf/meta.yaml index a4885eac8ce36..568023f6b2f6f 100644 --- a/recipes/bioconductor-htmg430bcdf/meta.yaml +++ b/recipes/bioconductor-htmg430bcdf/meta.yaml @@ -1,6 +1,6 @@ {% set version = "2.18.0" %} {% set name = "htmg430bcdf" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -12,19 +12,19 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 53cc1408504a5f07b5655aa46b969157 build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' - r-base run: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-htmg430bcdf/post-link.sh b/recipes/bioconductor-htmg430bcdf/post-link.sh index 20c2519e577b5..e39170ea15cf7 100644 --- a/recipes/bioconductor-htmg430bcdf/post-link.sh +++ b/recipes/bioconductor-htmg430bcdf/post-link.sh @@ -1,9 +1,10 @@ #!/bin/bash FN="htmg430bcdf_2.18.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/htmg430bcdf_2.18.0.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/htmg430bcdf_2.18.0.tar.gz" "https://bioarchive.galaxyproject.org/htmg430bcdf_2.18.0.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-htmg430bcdf/bioconductor-htmg430bcdf_2.18.0_src_all.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-htmg430bcdf/bioconductor-htmg430bcdf_2.18.0_src_all.tar.gz" ) MD5="53cc1408504a5f07b5655aa46b969157" @@ -16,7 +17,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-htmg430bprobe/meta.yaml b/recipes/bioconductor-htmg430bprobe/meta.yaml index 098d4151c678b..197a6f7708e95 100644 --- a/recipes/bioconductor-htmg430bprobe/meta.yaml +++ b/recipes/bioconductor-htmg430bprobe/meta.yaml @@ -1,6 +1,6 @@ {% set version = "2.18.0" %} {% set name = "htmg430bprobe" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -12,19 +12,19 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: f0e3eb56925d786762dee0c2dc82b530 build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' - r-base run: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-htmg430bprobe/post-link.sh b/recipes/bioconductor-htmg430bprobe/post-link.sh index ae8265e80e969..121d0f8cbb86a 100644 --- a/recipes/bioconductor-htmg430bprobe/post-link.sh +++ b/recipes/bioconductor-htmg430bprobe/post-link.sh @@ -1,9 +1,10 @@ #!/bin/bash FN="htmg430bprobe_2.18.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/htmg430bprobe_2.18.0.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/htmg430bprobe_2.18.0.tar.gz" "https://bioarchive.galaxyproject.org/htmg430bprobe_2.18.0.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-htmg430bprobe/bioconductor-htmg430bprobe_2.18.0_src_all.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-htmg430bprobe/bioconductor-htmg430bprobe_2.18.0_src_all.tar.gz" ) MD5="f0e3eb56925d786762dee0c2dc82b530" @@ -16,7 +17,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-htmg430pmcdf/meta.yaml b/recipes/bioconductor-htmg430pmcdf/meta.yaml index 82b68340a08a6..f47a47db644aa 100644 --- a/recipes/bioconductor-htmg430pmcdf/meta.yaml +++ b/recipes/bioconductor-htmg430pmcdf/meta.yaml @@ -1,6 +1,6 @@ {% set version = "2.18.0" %} {% set name = "htmg430pmcdf" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -12,19 +12,19 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 016a54b47adbbed7db989787646a0084 build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' - r-base run: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-htmg430pmcdf/post-link.sh b/recipes/bioconductor-htmg430pmcdf/post-link.sh index df7e368434c5d..d4655c1b6e540 100644 --- a/recipes/bioconductor-htmg430pmcdf/post-link.sh +++ b/recipes/bioconductor-htmg430pmcdf/post-link.sh @@ -1,9 +1,10 @@ #!/bin/bash FN="htmg430pmcdf_2.18.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/htmg430pmcdf_2.18.0.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/htmg430pmcdf_2.18.0.tar.gz" "https://bioarchive.galaxyproject.org/htmg430pmcdf_2.18.0.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-htmg430pmcdf/bioconductor-htmg430pmcdf_2.18.0_src_all.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-htmg430pmcdf/bioconductor-htmg430pmcdf_2.18.0_src_all.tar.gz" ) MD5="016a54b47adbbed7db989787646a0084" @@ -16,7 +17,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-htmg430pmprobe/meta.yaml b/recipes/bioconductor-htmg430pmprobe/meta.yaml index 374374e4068b4..1341d9e6650ce 100644 --- a/recipes/bioconductor-htmg430pmprobe/meta.yaml +++ b/recipes/bioconductor-htmg430pmprobe/meta.yaml @@ -1,6 +1,6 @@ {% set version = "2.18.0" %} {% set name = "htmg430pmprobe" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -12,19 +12,19 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: f0e053fcc0ca4b5f8c539fc0a3fcb076 build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' - r-base run: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-htmg430pmprobe/post-link.sh b/recipes/bioconductor-htmg430pmprobe/post-link.sh index 0e4b6483c19cf..5a602808913fd 100644 --- a/recipes/bioconductor-htmg430pmprobe/post-link.sh +++ b/recipes/bioconductor-htmg430pmprobe/post-link.sh @@ -1,9 +1,10 @@ #!/bin/bash FN="htmg430pmprobe_2.18.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/htmg430pmprobe_2.18.0.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/htmg430pmprobe_2.18.0.tar.gz" "https://bioarchive.galaxyproject.org/htmg430pmprobe_2.18.0.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-htmg430pmprobe/bioconductor-htmg430pmprobe_2.18.0_src_all.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-htmg430pmprobe/bioconductor-htmg430pmprobe_2.18.0_src_all.tar.gz" ) MD5="f0e053fcc0ca4b5f8c539fc0a3fcb076" @@ -16,7 +17,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-htqpcr/meta.yaml b/recipes/bioconductor-htqpcr/meta.yaml index 3be074a46fc0b..ee3ab0ef7c6eb 100644 --- a/recipes/bioconductor-htqpcr/meta.yaml +++ b/recipes/bioconductor-htqpcr/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.36.0" %} +{% set version = "1.38.0" %} {% set name = "HTqPCR" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 6b49cf2e293bb387f20845b568bfc20b + md5: cbef56085d20388836c255a4db656852 build: number: 0 rpaths: @@ -20,16 +20,16 @@ build: # Suggests: statmod requirements: host: - - 'bioconductor-affy >=1.60.0,<1.61.0' - - 'bioconductor-biobase >=2.42.0,<2.43.0' - - 'bioconductor-limma >=3.38.0,<3.39.0' + - 'bioconductor-affy >=1.62.0,<1.63.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' + - 'bioconductor-limma >=3.40.0,<3.41.0' - r-base - r-gplots - r-rcolorbrewer run: - - 'bioconductor-affy >=1.60.0,<1.61.0' - - 'bioconductor-biobase >=2.42.0,<2.43.0' - - 'bioconductor-limma >=3.38.0,<3.39.0' + - 'bioconductor-affy >=1.62.0,<1.63.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' + - 'bioconductor-limma >=3.40.0,<3.41.0' - r-base - r-gplots - r-rcolorbrewer diff --git a/recipes/bioconductor-htrat230pmcdf/meta.yaml b/recipes/bioconductor-htrat230pmcdf/meta.yaml index 0ee9efe725887..da34afe1da5d4 100644 --- a/recipes/bioconductor-htrat230pmcdf/meta.yaml +++ b/recipes/bioconductor-htrat230pmcdf/meta.yaml @@ -1,6 +1,6 @@ {% set version = "2.18.0" %} {% set name = "htrat230pmcdf" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -12,19 +12,19 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: c6683d16e8aacccd326f7a7eebb79b98 build: - number: 1 + number: 2 rpaths: - lib/R/lib/ - lib/ noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' - r-base run: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-htrat230pmcdf/post-link.sh b/recipes/bioconductor-htrat230pmcdf/post-link.sh index a06a8143abd04..7465201d67b18 100644 --- a/recipes/bioconductor-htrat230pmcdf/post-link.sh +++ b/recipes/bioconductor-htrat230pmcdf/post-link.sh @@ -1,9 +1,10 @@ #!/bin/bash FN="htrat230pmcdf_2.18.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/htrat230pmcdf_2.18.0.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/htrat230pmcdf_2.18.0.tar.gz" "https://bioarchive.galaxyproject.org/htrat230pmcdf_2.18.0.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-htrat230pmcdf/bioconductor-htrat230pmcdf_2.18.0_src_all.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-htrat230pmcdf/bioconductor-htrat230pmcdf_2.18.0_src_all.tar.gz" ) MD5="c6683d16e8aacccd326f7a7eebb79b98" @@ -16,7 +17,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-htrat230pmprobe/meta.yaml b/recipes/bioconductor-htrat230pmprobe/meta.yaml index 813779eea32ff..94c8bd848a520 100644 --- a/recipes/bioconductor-htrat230pmprobe/meta.yaml +++ b/recipes/bioconductor-htrat230pmprobe/meta.yaml @@ -1,6 +1,6 @@ {% set version = "2.18.0" %} {% set name = "htrat230pmprobe" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -12,19 +12,19 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: e4deeca2dc406367ac4a347e370267cf build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' - r-base run: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-htrat230pmprobe/post-link.sh b/recipes/bioconductor-htrat230pmprobe/post-link.sh index e7ac0e6982ada..8994cf60847d1 100644 --- a/recipes/bioconductor-htrat230pmprobe/post-link.sh +++ b/recipes/bioconductor-htrat230pmprobe/post-link.sh @@ -1,9 +1,10 @@ #!/bin/bash FN="htrat230pmprobe_2.18.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/htrat230pmprobe_2.18.0.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/htrat230pmprobe_2.18.0.tar.gz" "https://bioarchive.galaxyproject.org/htrat230pmprobe_2.18.0.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-htrat230pmprobe/bioconductor-htrat230pmprobe_2.18.0_src_all.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-htrat230pmprobe/bioconductor-htrat230pmprobe_2.18.0_src_all.tar.gz" ) MD5="e4deeca2dc406367ac4a347e370267cf" @@ -16,7 +17,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-htratfocuscdf/meta.yaml b/recipes/bioconductor-htratfocuscdf/meta.yaml index 8c422b7d1da79..8aad0476d6e8b 100644 --- a/recipes/bioconductor-htratfocuscdf/meta.yaml +++ b/recipes/bioconductor-htratfocuscdf/meta.yaml @@ -1,6 +1,6 @@ {% set version = "2.18.0" %} {% set name = "htratfocuscdf" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -12,19 +12,19 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 04b4952f7d8b607a7eb0f779c08c57dc build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' - r-base run: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-htratfocuscdf/post-link.sh b/recipes/bioconductor-htratfocuscdf/post-link.sh index 76c08fab70b7c..4f61fe8e9f267 100644 --- a/recipes/bioconductor-htratfocuscdf/post-link.sh +++ b/recipes/bioconductor-htratfocuscdf/post-link.sh @@ -1,9 +1,10 @@ #!/bin/bash FN="htratfocuscdf_2.18.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/htratfocuscdf_2.18.0.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/htratfocuscdf_2.18.0.tar.gz" "https://bioarchive.galaxyproject.org/htratfocuscdf_2.18.0.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-htratfocuscdf/bioconductor-htratfocuscdf_2.18.0_src_all.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-htratfocuscdf/bioconductor-htratfocuscdf_2.18.0_src_all.tar.gz" ) MD5="04b4952f7d8b607a7eb0f779c08c57dc" @@ -16,7 +17,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-htratfocusprobe/meta.yaml b/recipes/bioconductor-htratfocusprobe/meta.yaml index 11173b6a688c5..788476fe1615b 100644 --- a/recipes/bioconductor-htratfocusprobe/meta.yaml +++ b/recipes/bioconductor-htratfocusprobe/meta.yaml @@ -1,6 +1,6 @@ {% set version = "2.18.0" %} {% set name = "htratfocusprobe" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -12,19 +12,19 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 26a0963d8aff314a4a1f2c47e9147a8a build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' - r-base run: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-htratfocusprobe/post-link.sh b/recipes/bioconductor-htratfocusprobe/post-link.sh index b6f93ef3d94bb..4747ae5265b09 100644 --- a/recipes/bioconductor-htratfocusprobe/post-link.sh +++ b/recipes/bioconductor-htratfocusprobe/post-link.sh @@ -1,9 +1,10 @@ #!/bin/bash FN="htratfocusprobe_2.18.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/htratfocusprobe_2.18.0.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/htratfocusprobe_2.18.0.tar.gz" "https://bioarchive.galaxyproject.org/htratfocusprobe_2.18.0.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-htratfocusprobe/bioconductor-htratfocusprobe_2.18.0_src_all.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-htratfocusprobe/bioconductor-htratfocusprobe_2.18.0_src_all.tar.gz" ) MD5="26a0963d8aff314a4a1f2c47e9147a8a" @@ -16,7 +17,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-htsanalyzer/meta.yaml b/recipes/bioconductor-htsanalyzer/meta.yaml index 40338081c3381..d641ffc5d7cf0 100644 --- a/recipes/bioconductor-htsanalyzer/meta.yaml +++ b/recipes/bioconductor-htsanalyzer/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "2.34.0" %} +{% set version = "2.36.0" %} {% set name = "HTSanalyzeR" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 29d69fa45e56724f4586828c74dbe748 + md5: b9f2093f422cb35e3f3fe2f4730ae15f build: number: 0 rpaths: @@ -20,23 +20,23 @@ build: # Suggests: KEGG.db, GO.db, org.Dm.eg.db, GOstats, org.Ce.eg.db, org.Mm.eg.db, org.Rn.eg.db, org.Hs.eg.db, snow requirements: host: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' - - 'bioconductor-biomart >=2.38.0,<2.39.0' - - 'bioconductor-bionet >=1.42.0,<1.43.0' - - 'bioconductor-cellhts2 >=2.46.0,<2.47.0' - - 'bioconductor-graph >=1.60.0,<1.61.0' - - 'bioconductor-gseabase >=1.44.0,<1.45.0' - - 'bioconductor-rankprod >=3.8.0,<3.9.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' + - 'bioconductor-biomart >=2.40.0,<2.41.0' + - 'bioconductor-bionet >=1.44.0,<1.45.0' + - 'bioconductor-cellhts2 >=2.48.0,<2.49.0' + - 'bioconductor-graph >=1.62.0,<1.63.0' + - 'bioconductor-gseabase >=1.46.0,<1.47.0' + - 'bioconductor-rankprod >=3.10.0,<3.11.0' - r-base - r-igraph run: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' - - 'bioconductor-biomart >=2.38.0,<2.39.0' - - 'bioconductor-bionet >=1.42.0,<1.43.0' - - 'bioconductor-cellhts2 >=2.46.0,<2.47.0' - - 'bioconductor-graph >=1.60.0,<1.61.0' - - 'bioconductor-gseabase >=1.44.0,<1.45.0' - - 'bioconductor-rankprod >=3.8.0,<3.9.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' + - 'bioconductor-biomart >=2.40.0,<2.41.0' + - 'bioconductor-bionet >=1.44.0,<1.45.0' + - 'bioconductor-cellhts2 >=2.48.0,<2.49.0' + - 'bioconductor-graph >=1.62.0,<1.63.0' + - 'bioconductor-gseabase >=1.46.0,<1.47.0' + - 'bioconductor-rankprod >=3.10.0,<3.11.0' - r-base - r-igraph test: diff --git a/recipes/bioconductor-htseqgenie/meta.yaml b/recipes/bioconductor-htseqgenie/meta.yaml index 101be05bb4de3..1051139ed7839 100644 --- a/recipes/bioconductor-htseqgenie/meta.yaml +++ b/recipes/bioconductor-htseqgenie/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "4.12.0" %} +{% set version = "4.14.0" %} {% set name = "HTSeqGenie" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 7e4ef25284d34c49ec0c01d8502f4622 + md5: d46082df22d3f967a24751a34d62a293 build: number: 0 rpaths: @@ -20,44 +20,44 @@ build: # Suggests: TxDb.Hsapiens.UCSC.hg19.knownGene, LungCancerLines, org.Hs.eg.db requirements: host: - - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' - - 'bioconductor-biocparallel >=1.16.0,<1.17.0' - - 'bioconductor-biostrings >=2.50.0,<2.51.0' - - 'bioconductor-chipseq >=1.32.0,<1.33.0' - - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' - - 'bioconductor-genomicalignments >=1.18.0,<1.19.0' - - 'bioconductor-genomicfeatures >=1.34.0,<1.35.0' - - 'bioconductor-genomicranges >=1.34.0,<1.35.0' - - 'bioconductor-gmapr >=1.24.0,<1.25.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-rsamtools >=1.34.0,<1.35.0' - - 'bioconductor-rtracklayer >=1.42.0,<1.43.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' - - 'bioconductor-shortread >=1.40.0,<1.41.0' - - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' - - 'bioconductor-variantannotation >=1.28.0,<1.29.0' - - 'bioconductor-varianttools >=1.24.0,<1.25.0' + - 'bioconductor-biocgenerics >=0.30.0,<0.31.0' + - 'bioconductor-biocparallel >=1.18.0,<1.19.0' + - 'bioconductor-biostrings >=2.52.0,<2.53.0' + - 'bioconductor-chipseq >=1.34.0,<1.35.0' + - 'bioconductor-genomeinfodb >=1.20.0,<1.21.0' + - 'bioconductor-genomicalignments >=1.20.0,<1.21.0' + - 'bioconductor-genomicfeatures >=1.36.0,<1.37.0' + - 'bioconductor-genomicranges >=1.36.0,<1.37.0' + - 'bioconductor-gmapr >=1.26.0,<1.27.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-rsamtools >=2.0.0,<2.1.0' + - 'bioconductor-rtracklayer >=1.44.0,<1.45.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' + - 'bioconductor-shortread >=1.42.0,<1.43.0' + - 'bioconductor-summarizedexperiment >=1.14.0,<1.15.0' + - 'bioconductor-variantannotation >=1.30.0,<1.31.0' + - 'bioconductor-varianttools >=1.26.0,<1.27.0' - r-base - 'r-cairo >=1.5.5' - 'r-hwriter >=1.3.0' run: - - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' - - 'bioconductor-biocparallel >=1.16.0,<1.17.0' - - 'bioconductor-biostrings >=2.50.0,<2.51.0' - - 'bioconductor-chipseq >=1.32.0,<1.33.0' - - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' - - 'bioconductor-genomicalignments >=1.18.0,<1.19.0' - - 'bioconductor-genomicfeatures >=1.34.0,<1.35.0' - - 'bioconductor-genomicranges >=1.34.0,<1.35.0' - - 'bioconductor-gmapr >=1.24.0,<1.25.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-rsamtools >=1.34.0,<1.35.0' - - 'bioconductor-rtracklayer >=1.42.0,<1.43.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' - - 'bioconductor-shortread >=1.40.0,<1.41.0' - - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' - - 'bioconductor-variantannotation >=1.28.0,<1.29.0' - - 'bioconductor-varianttools >=1.24.0,<1.25.0' + - 'bioconductor-biocgenerics >=0.30.0,<0.31.0' + - 'bioconductor-biocparallel >=1.18.0,<1.19.0' + - 'bioconductor-biostrings >=2.52.0,<2.53.0' + - 'bioconductor-chipseq >=1.34.0,<1.35.0' + - 'bioconductor-genomeinfodb >=1.20.0,<1.21.0' + - 'bioconductor-genomicalignments >=1.20.0,<1.21.0' + - 'bioconductor-genomicfeatures >=1.36.0,<1.37.0' + - 'bioconductor-genomicranges >=1.36.0,<1.37.0' + - 'bioconductor-gmapr >=1.26.0,<1.27.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-rsamtools >=2.0.0,<2.1.0' + - 'bioconductor-rtracklayer >=1.44.0,<1.45.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' + - 'bioconductor-shortread >=1.42.0,<1.43.0' + - 'bioconductor-summarizedexperiment >=1.14.0,<1.15.0' + - 'bioconductor-variantannotation >=1.30.0,<1.31.0' + - 'bioconductor-varianttools >=1.26.0,<1.27.0' - r-base - 'r-cairo >=1.5.5' - 'r-hwriter >=1.3.0' diff --git a/recipes/bioconductor-htseqtools/meta.yaml b/recipes/bioconductor-htseqtools/meta.yaml index a4236d59b6fce..e20bd51f89f3c 100644 --- a/recipes/bioconductor-htseqtools/meta.yaml +++ b/recipes/bioconductor-htseqtools/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.30.0" %} +{% set version = "1.31.0" %} {% set name = "htSeqTools" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: e62c9dd3fa250ff61a92ee38400b23b8 + md5: 67c17cf06f81100c8d00c6e62abb7a56 build: number: 0 rpaths: @@ -19,23 +19,23 @@ build: noarch: generic requirements: host: - - 'bioconductor-biobase >=2.42.0,<2.43.0' - - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' - - 'bioconductor-bsgenome >=1.50.0,<1.51.0' - - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' - - 'bioconductor-genomicranges >=1.34.0,<1.35.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' + - 'bioconductor-biocgenerics >=0.30.0,<0.31.0' + - 'bioconductor-bsgenome >=1.52.0,<1.53.0' + - 'bioconductor-genomeinfodb >=1.20.0,<1.21.0' + - 'bioconductor-genomicranges >=1.36.0,<1.37.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' - r-base - r-mass run: - - 'bioconductor-biobase >=2.42.0,<2.43.0' - - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' - - 'bioconductor-bsgenome >=1.50.0,<1.51.0' - - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' - - 'bioconductor-genomicranges >=1.34.0,<1.35.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' + - 'bioconductor-biocgenerics >=0.30.0,<0.31.0' + - 'bioconductor-bsgenome >=1.52.0,<1.53.0' + - 'bioconductor-genomeinfodb >=1.20.0,<1.21.0' + - 'bioconductor-genomicranges >=1.36.0,<1.37.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' - r-base - r-mass test: diff --git a/recipes/bioconductor-htsfilter/meta.yaml b/recipes/bioconductor-htsfilter/meta.yaml index e2cf63d8cc4c2..ffa2155e44ddf 100644 --- a/recipes/bioconductor-htsfilter/meta.yaml +++ b/recipes/bioconductor-htsfilter/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.22.1" %} +{% set version = "1.24.0" %} {% set name = "HTSFilter" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 1a853603bd830413cee7db2f034d9148 + md5: 81e0bf6630e03003acf58479e7a2dff1 build: number: 0 rpaths: @@ -20,18 +20,18 @@ build: # Suggests: EDASeq (>= 2.1.4), BiocStyle, testthat requirements: host: - - 'bioconductor-biobase >=2.42.0,<2.43.0' - - 'bioconductor-biocparallel >=1.16.0,<1.17.0' - - 'bioconductor-deseq >=1.34.0,<1.35.0' - - 'bioconductor-deseq2 >=1.22.0,<1.23.0' - - 'bioconductor-edger >=3.24.0,<3.25.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' + - 'bioconductor-biocparallel >=1.18.0,<1.19.0' + - 'bioconductor-deseq >=1.36.0,<1.37.0' + - 'bioconductor-deseq2 >=1.24.0,<1.25.0' + - 'bioconductor-edger >=3.26.0,<3.27.0' - r-base run: - - 'bioconductor-biobase >=2.42.0,<2.43.0' - - 'bioconductor-biocparallel >=1.16.0,<1.17.0' - - 'bioconductor-deseq >=1.34.0,<1.35.0' - - 'bioconductor-deseq2 >=1.22.0,<1.23.0' - - 'bioconductor-edger >=3.24.0,<3.25.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' + - 'bioconductor-biocparallel >=1.18.0,<1.19.0' + - 'bioconductor-deseq >=1.36.0,<1.37.0' + - 'bioconductor-deseq2 >=1.24.0,<1.25.0' + - 'bioconductor-edger >=3.26.0,<3.27.0' - r-base test: commands: diff --git a/recipes/bioconductor-hu35ksuba.db/meta.yaml b/recipes/bioconductor-hu35ksuba.db/meta.yaml index 5cb1d4690004f..04eefb355a67e 100644 --- a/recipes/bioconductor-hu35ksuba.db/meta.yaml +++ b/recipes/bioconductor-hu35ksuba.db/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.2.3" %} {% set name = "hu35ksuba.db" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -12,7 +12,7 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: eef6de6790e904d0b63a3ec8faba2962 build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ @@ -20,14 +20,14 @@ build: # Suggests: DBI, annotate, RUnit requirements: host: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' - - 'bioconductor-org.hs.eg.db >=3.7.0,<3.8.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' + - 'bioconductor-org.hs.eg.db >=3.8.0,<3.9.0' - r-base run: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' - - 'bioconductor-org.hs.eg.db >=3.7.0,<3.8.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' + - 'bioconductor-org.hs.eg.db >=3.8.0,<3.9.0' - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-hu35ksuba.db/post-link.sh b/recipes/bioconductor-hu35ksuba.db/post-link.sh index 3e53f149c4d6d..50f91753e51d2 100644 --- a/recipes/bioconductor-hu35ksuba.db/post-link.sh +++ b/recipes/bioconductor-hu35ksuba.db/post-link.sh @@ -1,9 +1,10 @@ #!/bin/bash FN="hu35ksuba.db_3.2.3.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/hu35ksuba.db_3.2.3.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/hu35ksuba.db_3.2.3.tar.gz" "https://bioarchive.galaxyproject.org/hu35ksuba.db_3.2.3.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-hu35ksuba.db/bioconductor-hu35ksuba.db_3.2.3_src_all.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-hu35ksuba.db/bioconductor-hu35ksuba.db_3.2.3_src_all.tar.gz" ) MD5="eef6de6790e904d0b63a3ec8faba2962" @@ -16,7 +17,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-hu35ksubacdf/meta.yaml b/recipes/bioconductor-hu35ksubacdf/meta.yaml index d2679d898000d..5170ddd8669fd 100644 --- a/recipes/bioconductor-hu35ksubacdf/meta.yaml +++ b/recipes/bioconductor-hu35ksubacdf/meta.yaml @@ -1,6 +1,6 @@ {% set version = "2.18.0" %} {% set name = "hu35ksubacdf" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -12,19 +12,19 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: c8b82c4755eb62818ca0dbf22de5d25e build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' - r-base run: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-hu35ksubacdf/post-link.sh b/recipes/bioconductor-hu35ksubacdf/post-link.sh index 649ce0d4a73cc..6cf3bcdcfd666 100644 --- a/recipes/bioconductor-hu35ksubacdf/post-link.sh +++ b/recipes/bioconductor-hu35ksubacdf/post-link.sh @@ -1,9 +1,10 @@ #!/bin/bash FN="hu35ksubacdf_2.18.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/hu35ksubacdf_2.18.0.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/hu35ksubacdf_2.18.0.tar.gz" "https://bioarchive.galaxyproject.org/hu35ksubacdf_2.18.0.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-hu35ksubacdf/bioconductor-hu35ksubacdf_2.18.0_src_all.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-hu35ksubacdf/bioconductor-hu35ksubacdf_2.18.0_src_all.tar.gz" ) MD5="c8b82c4755eb62818ca0dbf22de5d25e" @@ -16,7 +17,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-hu35ksubaprobe/meta.yaml b/recipes/bioconductor-hu35ksubaprobe/meta.yaml index 2546e7e12281a..e45563099cd75 100644 --- a/recipes/bioconductor-hu35ksubaprobe/meta.yaml +++ b/recipes/bioconductor-hu35ksubaprobe/meta.yaml @@ -1,6 +1,6 @@ {% set version = "2.18.0" %} {% set name = "hu35ksubaprobe" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -12,19 +12,19 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 49bd19ec3b6404211f2e410e473fa644 build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' - r-base run: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-hu35ksubaprobe/post-link.sh b/recipes/bioconductor-hu35ksubaprobe/post-link.sh index 0576a32f18cf3..b72b8330d13fe 100644 --- a/recipes/bioconductor-hu35ksubaprobe/post-link.sh +++ b/recipes/bioconductor-hu35ksubaprobe/post-link.sh @@ -1,9 +1,10 @@ #!/bin/bash FN="hu35ksubaprobe_2.18.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/hu35ksubaprobe_2.18.0.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/hu35ksubaprobe_2.18.0.tar.gz" "https://bioarchive.galaxyproject.org/hu35ksubaprobe_2.18.0.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-hu35ksubaprobe/bioconductor-hu35ksubaprobe_2.18.0_src_all.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-hu35ksubaprobe/bioconductor-hu35ksubaprobe_2.18.0_src_all.tar.gz" ) MD5="49bd19ec3b6404211f2e410e473fa644" @@ -16,7 +17,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-hu35ksubb.db/meta.yaml b/recipes/bioconductor-hu35ksubb.db/meta.yaml index 1c9e56d1e5b32..ea5681249e142 100644 --- a/recipes/bioconductor-hu35ksubb.db/meta.yaml +++ b/recipes/bioconductor-hu35ksubb.db/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.2.3" %} {% set name = "hu35ksubb.db" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -12,7 +12,7 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: b49fc7bda2b0879d1be1ac0061a7ea98 build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ @@ -20,14 +20,14 @@ build: # Suggests: DBI, annotate, RUnit requirements: host: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' - - 'bioconductor-org.hs.eg.db >=3.7.0,<3.8.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' + - 'bioconductor-org.hs.eg.db >=3.8.0,<3.9.0' - r-base run: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' - - 'bioconductor-org.hs.eg.db >=3.7.0,<3.8.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' + - 'bioconductor-org.hs.eg.db >=3.8.0,<3.9.0' - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-hu35ksubb.db/post-link.sh b/recipes/bioconductor-hu35ksubb.db/post-link.sh index 8ce724fdf457f..900f6b1cf5908 100644 --- a/recipes/bioconductor-hu35ksubb.db/post-link.sh +++ b/recipes/bioconductor-hu35ksubb.db/post-link.sh @@ -1,9 +1,10 @@ #!/bin/bash FN="hu35ksubb.db_3.2.3.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/hu35ksubb.db_3.2.3.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/hu35ksubb.db_3.2.3.tar.gz" "https://bioarchive.galaxyproject.org/hu35ksubb.db_3.2.3.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-hu35ksubb.db/bioconductor-hu35ksubb.db_3.2.3_src_all.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-hu35ksubb.db/bioconductor-hu35ksubb.db_3.2.3_src_all.tar.gz" ) MD5="b49fc7bda2b0879d1be1ac0061a7ea98" @@ -16,7 +17,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-hu35ksubbcdf/meta.yaml b/recipes/bioconductor-hu35ksubbcdf/meta.yaml index 56cfe616d4da8..482eb4d96a6d1 100644 --- a/recipes/bioconductor-hu35ksubbcdf/meta.yaml +++ b/recipes/bioconductor-hu35ksubbcdf/meta.yaml @@ -1,6 +1,6 @@ {% set version = "2.18.0" %} {% set name = "hu35ksubbcdf" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -12,19 +12,19 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: d873b6c521e926b331f799baf10a4e13 build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' - r-base run: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-hu35ksubbcdf/post-link.sh b/recipes/bioconductor-hu35ksubbcdf/post-link.sh index fe0640ed70d26..fdc546d747419 100644 --- a/recipes/bioconductor-hu35ksubbcdf/post-link.sh +++ b/recipes/bioconductor-hu35ksubbcdf/post-link.sh @@ -1,9 +1,10 @@ #!/bin/bash FN="hu35ksubbcdf_2.18.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/hu35ksubbcdf_2.18.0.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/hu35ksubbcdf_2.18.0.tar.gz" "https://bioarchive.galaxyproject.org/hu35ksubbcdf_2.18.0.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-hu35ksubbcdf/bioconductor-hu35ksubbcdf_2.18.0_src_all.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-hu35ksubbcdf/bioconductor-hu35ksubbcdf_2.18.0_src_all.tar.gz" ) MD5="d873b6c521e926b331f799baf10a4e13" @@ -16,7 +17,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-hu35ksubbprobe/meta.yaml b/recipes/bioconductor-hu35ksubbprobe/meta.yaml index 725a53a556e6a..2bcc9da599fef 100644 --- a/recipes/bioconductor-hu35ksubbprobe/meta.yaml +++ b/recipes/bioconductor-hu35ksubbprobe/meta.yaml @@ -1,6 +1,6 @@ {% set version = "2.18.0" %} {% set name = "hu35ksubbprobe" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -12,19 +12,19 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 0a63051d0faf38a56f17d5865cbed9b1 build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' - r-base run: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-hu35ksubbprobe/post-link.sh b/recipes/bioconductor-hu35ksubbprobe/post-link.sh index 890681497c673..dc6efffa12a46 100644 --- a/recipes/bioconductor-hu35ksubbprobe/post-link.sh +++ b/recipes/bioconductor-hu35ksubbprobe/post-link.sh @@ -1,9 +1,10 @@ #!/bin/bash FN="hu35ksubbprobe_2.18.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/hu35ksubbprobe_2.18.0.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/hu35ksubbprobe_2.18.0.tar.gz" "https://bioarchive.galaxyproject.org/hu35ksubbprobe_2.18.0.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-hu35ksubbprobe/bioconductor-hu35ksubbprobe_2.18.0_src_all.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-hu35ksubbprobe/bioconductor-hu35ksubbprobe_2.18.0_src_all.tar.gz" ) MD5="0a63051d0faf38a56f17d5865cbed9b1" @@ -16,7 +17,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-hu35ksubc.db/meta.yaml b/recipes/bioconductor-hu35ksubc.db/meta.yaml index ebb4e1b835abc..38c89c6f73c22 100644 --- a/recipes/bioconductor-hu35ksubc.db/meta.yaml +++ b/recipes/bioconductor-hu35ksubc.db/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.2.3" %} {% set name = "hu35ksubc.db" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -12,7 +12,7 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: f3c215dc2ddbab7ddcdbf015495f87b3 build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ @@ -20,14 +20,14 @@ build: # Suggests: DBI, annotate, RUnit requirements: host: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' - - 'bioconductor-org.hs.eg.db >=3.7.0,<3.8.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' + - 'bioconductor-org.hs.eg.db >=3.8.0,<3.9.0' - r-base run: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' - - 'bioconductor-org.hs.eg.db >=3.7.0,<3.8.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' + - 'bioconductor-org.hs.eg.db >=3.8.0,<3.9.0' - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-hu35ksubc.db/post-link.sh b/recipes/bioconductor-hu35ksubc.db/post-link.sh index 814126788be8a..7cc7786a05108 100644 --- a/recipes/bioconductor-hu35ksubc.db/post-link.sh +++ b/recipes/bioconductor-hu35ksubc.db/post-link.sh @@ -1,9 +1,10 @@ #!/bin/bash FN="hu35ksubc.db_3.2.3.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/hu35ksubc.db_3.2.3.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/hu35ksubc.db_3.2.3.tar.gz" "https://bioarchive.galaxyproject.org/hu35ksubc.db_3.2.3.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-hu35ksubc.db/bioconductor-hu35ksubc.db_3.2.3_src_all.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-hu35ksubc.db/bioconductor-hu35ksubc.db_3.2.3_src_all.tar.gz" ) MD5="f3c215dc2ddbab7ddcdbf015495f87b3" @@ -16,7 +17,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-hu35ksubccdf/meta.yaml b/recipes/bioconductor-hu35ksubccdf/meta.yaml index 9f96cf6ba8556..cd2821d9f86e2 100644 --- a/recipes/bioconductor-hu35ksubccdf/meta.yaml +++ b/recipes/bioconductor-hu35ksubccdf/meta.yaml @@ -1,6 +1,6 @@ {% set version = "2.18.0" %} {% set name = "hu35ksubccdf" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -12,19 +12,19 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: de96e69680c5f8747c99d170272d7c3c build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' - r-base run: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-hu35ksubccdf/post-link.sh b/recipes/bioconductor-hu35ksubccdf/post-link.sh index b7f7adce1f279..7d4d77c6c2369 100644 --- a/recipes/bioconductor-hu35ksubccdf/post-link.sh +++ b/recipes/bioconductor-hu35ksubccdf/post-link.sh @@ -1,9 +1,10 @@ #!/bin/bash FN="hu35ksubccdf_2.18.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/hu35ksubccdf_2.18.0.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/hu35ksubccdf_2.18.0.tar.gz" "https://bioarchive.galaxyproject.org/hu35ksubccdf_2.18.0.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-hu35ksubccdf/bioconductor-hu35ksubccdf_2.18.0_src_all.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-hu35ksubccdf/bioconductor-hu35ksubccdf_2.18.0_src_all.tar.gz" ) MD5="de96e69680c5f8747c99d170272d7c3c" @@ -16,7 +17,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-hu35ksubcprobe/meta.yaml b/recipes/bioconductor-hu35ksubcprobe/meta.yaml index d2bcf4a019640..74e46696a0807 100644 --- a/recipes/bioconductor-hu35ksubcprobe/meta.yaml +++ b/recipes/bioconductor-hu35ksubcprobe/meta.yaml @@ -1,6 +1,6 @@ {% set version = "2.18.0" %} {% set name = "hu35ksubcprobe" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -12,19 +12,19 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: b10453ea061b09172192bd21baa9083d build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' - r-base run: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-hu35ksubcprobe/post-link.sh b/recipes/bioconductor-hu35ksubcprobe/post-link.sh index 95ccbcaa70f03..5078226e7b10f 100644 --- a/recipes/bioconductor-hu35ksubcprobe/post-link.sh +++ b/recipes/bioconductor-hu35ksubcprobe/post-link.sh @@ -1,9 +1,10 @@ #!/bin/bash FN="hu35ksubcprobe_2.18.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/hu35ksubcprobe_2.18.0.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/hu35ksubcprobe_2.18.0.tar.gz" "https://bioarchive.galaxyproject.org/hu35ksubcprobe_2.18.0.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-hu35ksubcprobe/bioconductor-hu35ksubcprobe_2.18.0_src_all.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-hu35ksubcprobe/bioconductor-hu35ksubcprobe_2.18.0_src_all.tar.gz" ) MD5="b10453ea061b09172192bd21baa9083d" @@ -16,7 +17,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-hu35ksubd.db/meta.yaml b/recipes/bioconductor-hu35ksubd.db/meta.yaml index dfdc4007ceac0..22d7c80ebe0ee 100644 --- a/recipes/bioconductor-hu35ksubd.db/meta.yaml +++ b/recipes/bioconductor-hu35ksubd.db/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.2.3" %} {% set name = "hu35ksubd.db" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -12,7 +12,7 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 9b8f09012d27c7b41e0d20321d83a625 build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ @@ -20,14 +20,14 @@ build: # Suggests: DBI, annotate, RUnit requirements: host: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' - - 'bioconductor-org.hs.eg.db >=3.7.0,<3.8.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' + - 'bioconductor-org.hs.eg.db >=3.8.0,<3.9.0' - r-base run: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' - - 'bioconductor-org.hs.eg.db >=3.7.0,<3.8.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' + - 'bioconductor-org.hs.eg.db >=3.8.0,<3.9.0' - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-hu35ksubd.db/post-link.sh b/recipes/bioconductor-hu35ksubd.db/post-link.sh index 61e06db03d603..ce05a9c58be73 100644 --- a/recipes/bioconductor-hu35ksubd.db/post-link.sh +++ b/recipes/bioconductor-hu35ksubd.db/post-link.sh @@ -1,9 +1,10 @@ #!/bin/bash FN="hu35ksubd.db_3.2.3.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/hu35ksubd.db_3.2.3.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/hu35ksubd.db_3.2.3.tar.gz" "https://bioarchive.galaxyproject.org/hu35ksubd.db_3.2.3.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-hu35ksubd.db/bioconductor-hu35ksubd.db_3.2.3_src_all.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-hu35ksubd.db/bioconductor-hu35ksubd.db_3.2.3_src_all.tar.gz" ) MD5="9b8f09012d27c7b41e0d20321d83a625" @@ -16,7 +17,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-hu35ksubdcdf/meta.yaml b/recipes/bioconductor-hu35ksubdcdf/meta.yaml index 6a0664ebebf79..1622258bb154d 100644 --- a/recipes/bioconductor-hu35ksubdcdf/meta.yaml +++ b/recipes/bioconductor-hu35ksubdcdf/meta.yaml @@ -1,6 +1,6 @@ {% set version = "2.18.0" %} {% set name = "hu35ksubdcdf" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -12,19 +12,19 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 6f6423426969f306fb0d5171e75b5380 build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' - r-base run: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-hu35ksubdcdf/post-link.sh b/recipes/bioconductor-hu35ksubdcdf/post-link.sh index 30c64240813da..9b2a3d1d30afa 100644 --- a/recipes/bioconductor-hu35ksubdcdf/post-link.sh +++ b/recipes/bioconductor-hu35ksubdcdf/post-link.sh @@ -1,9 +1,10 @@ #!/bin/bash FN="hu35ksubdcdf_2.18.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/hu35ksubdcdf_2.18.0.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/hu35ksubdcdf_2.18.0.tar.gz" "https://bioarchive.galaxyproject.org/hu35ksubdcdf_2.18.0.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-hu35ksubdcdf/bioconductor-hu35ksubdcdf_2.18.0_src_all.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-hu35ksubdcdf/bioconductor-hu35ksubdcdf_2.18.0_src_all.tar.gz" ) MD5="6f6423426969f306fb0d5171e75b5380" @@ -16,7 +17,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-hu35ksubdprobe/meta.yaml b/recipes/bioconductor-hu35ksubdprobe/meta.yaml index 310407e598b66..1bc55d73f07ef 100644 --- a/recipes/bioconductor-hu35ksubdprobe/meta.yaml +++ b/recipes/bioconductor-hu35ksubdprobe/meta.yaml @@ -1,6 +1,6 @@ {% set version = "2.18.0" %} {% set name = "hu35ksubdprobe" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -12,19 +12,19 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 430a9b8ccd646d8cb06e6c1d750eec23 build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' - r-base run: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-hu35ksubdprobe/post-link.sh b/recipes/bioconductor-hu35ksubdprobe/post-link.sh index c753393abbdcd..dc7ce942cf376 100644 --- a/recipes/bioconductor-hu35ksubdprobe/post-link.sh +++ b/recipes/bioconductor-hu35ksubdprobe/post-link.sh @@ -1,9 +1,10 @@ #!/bin/bash FN="hu35ksubdprobe_2.18.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/hu35ksubdprobe_2.18.0.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/hu35ksubdprobe_2.18.0.tar.gz" "https://bioarchive.galaxyproject.org/hu35ksubdprobe_2.18.0.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-hu35ksubdprobe/bioconductor-hu35ksubdprobe_2.18.0_src_all.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-hu35ksubdprobe/bioconductor-hu35ksubdprobe_2.18.0_src_all.tar.gz" ) MD5="430a9b8ccd646d8cb06e6c1d750eec23" @@ -16,7 +17,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-hu6800.db/meta.yaml b/recipes/bioconductor-hu6800.db/meta.yaml index 1ad8da797731e..1b723983beb81 100644 --- a/recipes/bioconductor-hu6800.db/meta.yaml +++ b/recipes/bioconductor-hu6800.db/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.2.3" %} {% set name = "hu6800.db" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -12,7 +12,7 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 7783c1539639aec9d3d736e38b4f028c build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ @@ -20,14 +20,14 @@ build: # Suggests: DBI, annotate, RUnit requirements: host: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' - - 'bioconductor-org.hs.eg.db >=3.7.0,<3.8.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' + - 'bioconductor-org.hs.eg.db >=3.8.0,<3.9.0' - r-base run: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' - - 'bioconductor-org.hs.eg.db >=3.7.0,<3.8.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' + - 'bioconductor-org.hs.eg.db >=3.8.0,<3.9.0' - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-hu6800.db/post-link.sh b/recipes/bioconductor-hu6800.db/post-link.sh index 33ac218e91abb..a94a4e2383e99 100644 --- a/recipes/bioconductor-hu6800.db/post-link.sh +++ b/recipes/bioconductor-hu6800.db/post-link.sh @@ -1,9 +1,10 @@ #!/bin/bash FN="hu6800.db_3.2.3.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/hu6800.db_3.2.3.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/hu6800.db_3.2.3.tar.gz" "https://bioarchive.galaxyproject.org/hu6800.db_3.2.3.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-hu6800.db/bioconductor-hu6800.db_3.2.3_src_all.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-hu6800.db/bioconductor-hu6800.db_3.2.3_src_all.tar.gz" ) MD5="7783c1539639aec9d3d736e38b4f028c" @@ -16,7 +17,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-hu6800cdf/meta.yaml b/recipes/bioconductor-hu6800cdf/meta.yaml index b1bae16a7485f..c4df2138c8a91 100644 --- a/recipes/bioconductor-hu6800cdf/meta.yaml +++ b/recipes/bioconductor-hu6800cdf/meta.yaml @@ -1,6 +1,6 @@ {% set version = "2.18.0" %} {% set name = "hu6800cdf" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -12,19 +12,19 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: fa2b2ab8f3aba517c63ad2e65873d2f0 build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' - r-base run: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-hu6800cdf/post-link.sh b/recipes/bioconductor-hu6800cdf/post-link.sh index 1e9ce7333bc18..62fb7a934ce16 100644 --- a/recipes/bioconductor-hu6800cdf/post-link.sh +++ b/recipes/bioconductor-hu6800cdf/post-link.sh @@ -1,9 +1,10 @@ #!/bin/bash FN="hu6800cdf_2.18.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/hu6800cdf_2.18.0.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/hu6800cdf_2.18.0.tar.gz" "https://bioarchive.galaxyproject.org/hu6800cdf_2.18.0.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-hu6800cdf/bioconductor-hu6800cdf_2.18.0_src_all.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-hu6800cdf/bioconductor-hu6800cdf_2.18.0_src_all.tar.gz" ) MD5="fa2b2ab8f3aba517c63ad2e65873d2f0" @@ -16,7 +17,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-hu6800probe/meta.yaml b/recipes/bioconductor-hu6800probe/meta.yaml index 2785838d967f9..c25c40f7bd23e 100644 --- a/recipes/bioconductor-hu6800probe/meta.yaml +++ b/recipes/bioconductor-hu6800probe/meta.yaml @@ -1,6 +1,6 @@ {% set version = "2.18.0" %} {% set name = "hu6800probe" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -12,19 +12,19 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 7a2383bd870cbc0628c210174e911250 build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' - r-base run: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-hu6800probe/post-link.sh b/recipes/bioconductor-hu6800probe/post-link.sh index b7a1d066298c9..f3005ed09b508 100644 --- a/recipes/bioconductor-hu6800probe/post-link.sh +++ b/recipes/bioconductor-hu6800probe/post-link.sh @@ -1,9 +1,10 @@ #!/bin/bash FN="hu6800probe_2.18.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/hu6800probe_2.18.0.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/hu6800probe_2.18.0.tar.gz" "https://bioarchive.galaxyproject.org/hu6800probe_2.18.0.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-hu6800probe/bioconductor-hu6800probe_2.18.0_src_all.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-hu6800probe/bioconductor-hu6800probe_2.18.0_src_all.tar.gz" ) MD5="7a2383bd870cbc0628c210174e911250" @@ -16,7 +17,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-hu6800subacdf/meta.yaml b/recipes/bioconductor-hu6800subacdf/meta.yaml index b0fe73828933a..6916e94adcc87 100644 --- a/recipes/bioconductor-hu6800subacdf/meta.yaml +++ b/recipes/bioconductor-hu6800subacdf/meta.yaml @@ -1,6 +1,6 @@ {% set version = "2.18.0" %} {% set name = "hu6800subacdf" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -12,19 +12,19 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 9e8ec301e066e400564976cd9750297e build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' - r-base run: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-hu6800subacdf/post-link.sh b/recipes/bioconductor-hu6800subacdf/post-link.sh index 17eeaf0bf0e17..e6f16bc78fa0b 100644 --- a/recipes/bioconductor-hu6800subacdf/post-link.sh +++ b/recipes/bioconductor-hu6800subacdf/post-link.sh @@ -1,9 +1,10 @@ #!/bin/bash FN="hu6800subacdf_2.18.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/hu6800subacdf_2.18.0.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/hu6800subacdf_2.18.0.tar.gz" "https://bioarchive.galaxyproject.org/hu6800subacdf_2.18.0.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-hu6800subacdf/bioconductor-hu6800subacdf_2.18.0_src_all.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-hu6800subacdf/bioconductor-hu6800subacdf_2.18.0_src_all.tar.gz" ) MD5="9e8ec301e066e400564976cd9750297e" @@ -16,7 +17,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-hu6800subbcdf/meta.yaml b/recipes/bioconductor-hu6800subbcdf/meta.yaml index f3ed189d2168a..bdc3b54e82ca6 100644 --- a/recipes/bioconductor-hu6800subbcdf/meta.yaml +++ b/recipes/bioconductor-hu6800subbcdf/meta.yaml @@ -1,6 +1,6 @@ {% set version = "2.18.0" %} {% set name = "hu6800subbcdf" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -12,19 +12,19 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 529aad5e4e73594c8cb66274d7e4adc5 build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' - r-base run: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-hu6800subbcdf/post-link.sh b/recipes/bioconductor-hu6800subbcdf/post-link.sh index 78a9c7db436b2..19186358e0a10 100644 --- a/recipes/bioconductor-hu6800subbcdf/post-link.sh +++ b/recipes/bioconductor-hu6800subbcdf/post-link.sh @@ -1,9 +1,10 @@ #!/bin/bash FN="hu6800subbcdf_2.18.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/hu6800subbcdf_2.18.0.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/hu6800subbcdf_2.18.0.tar.gz" "https://bioarchive.galaxyproject.org/hu6800subbcdf_2.18.0.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-hu6800subbcdf/bioconductor-hu6800subbcdf_2.18.0_src_all.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-hu6800subbcdf/bioconductor-hu6800subbcdf_2.18.0_src_all.tar.gz" ) MD5="529aad5e4e73594c8cb66274d7e4adc5" @@ -16,7 +17,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-hu6800subccdf/meta.yaml b/recipes/bioconductor-hu6800subccdf/meta.yaml index 5291dcd8b4171..4df494b2a1bbf 100644 --- a/recipes/bioconductor-hu6800subccdf/meta.yaml +++ b/recipes/bioconductor-hu6800subccdf/meta.yaml @@ -1,6 +1,6 @@ {% set version = "2.18.0" %} {% set name = "hu6800subccdf" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -12,19 +12,19 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 020fe3a6bdf44efbde15432b968433e8 build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' - r-base run: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-hu6800subccdf/post-link.sh b/recipes/bioconductor-hu6800subccdf/post-link.sh index 398ed39c5c183..277cf28b15670 100644 --- a/recipes/bioconductor-hu6800subccdf/post-link.sh +++ b/recipes/bioconductor-hu6800subccdf/post-link.sh @@ -1,9 +1,10 @@ #!/bin/bash FN="hu6800subccdf_2.18.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/hu6800subccdf_2.18.0.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/hu6800subccdf_2.18.0.tar.gz" "https://bioarchive.galaxyproject.org/hu6800subccdf_2.18.0.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-hu6800subccdf/bioconductor-hu6800subccdf_2.18.0_src_all.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-hu6800subccdf/bioconductor-hu6800subccdf_2.18.0_src_all.tar.gz" ) MD5="020fe3a6bdf44efbde15432b968433e8" @@ -16,7 +17,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-hu6800subdcdf/meta.yaml b/recipes/bioconductor-hu6800subdcdf/meta.yaml index 84b7a517966ef..c291a458050f5 100644 --- a/recipes/bioconductor-hu6800subdcdf/meta.yaml +++ b/recipes/bioconductor-hu6800subdcdf/meta.yaml @@ -1,6 +1,6 @@ {% set version = "2.18.0" %} {% set name = "hu6800subdcdf" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -12,19 +12,19 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 7966c21babb23e18cca4faafc8720f0a build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' - r-base run: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-hu6800subdcdf/post-link.sh b/recipes/bioconductor-hu6800subdcdf/post-link.sh index d44375860876c..fee5dd45fab5c 100644 --- a/recipes/bioconductor-hu6800subdcdf/post-link.sh +++ b/recipes/bioconductor-hu6800subdcdf/post-link.sh @@ -1,9 +1,10 @@ #!/bin/bash FN="hu6800subdcdf_2.18.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/hu6800subdcdf_2.18.0.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/hu6800subdcdf_2.18.0.tar.gz" "https://bioarchive.galaxyproject.org/hu6800subdcdf_2.18.0.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-hu6800subdcdf/bioconductor-hu6800subdcdf_2.18.0_src_all.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-hu6800subdcdf/bioconductor-hu6800subdcdf_2.18.0_src_all.tar.gz" ) MD5="7966c21babb23e18cca4faafc8720f0a" @@ -16,7 +17,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-huex.1.0.st.v2frmavecs/meta.yaml b/recipes/bioconductor-huex.1.0.st.v2frmavecs/meta.yaml index 7582f6bfbcd13..d7e49faf3f74c 100644 --- a/recipes/bioconductor-huex.1.0.st.v2frmavecs/meta.yaml +++ b/recipes/bioconductor-huex.1.0.st.v2frmavecs/meta.yaml @@ -1,6 +1,6 @@ {% set version = "1.1.0" %} {% set name = "huex.1.0.st.v2frmavecs" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -12,7 +12,7 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 982935d07b526ff555790e309fe4147e build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ @@ -22,7 +22,7 @@ requirements: - r-base run: - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-huex.1.0.st.v2frmavecs/post-link.sh b/recipes/bioconductor-huex.1.0.st.v2frmavecs/post-link.sh index 838cbc805e61a..e04572744797c 100644 --- a/recipes/bioconductor-huex.1.0.st.v2frmavecs/post-link.sh +++ b/recipes/bioconductor-huex.1.0.st.v2frmavecs/post-link.sh @@ -1,9 +1,10 @@ #!/bin/bash FN="huex.1.0.st.v2frmavecs_1.1.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/huex.1.0.st.v2frmavecs_1.1.0.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/huex.1.0.st.v2frmavecs_1.1.0.tar.gz" "https://bioarchive.galaxyproject.org/huex.1.0.st.v2frmavecs_1.1.0.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-huex.1.0.st.v2frmavecs/bioconductor-huex.1.0.st.v2frmavecs_1.1.0_src_all.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-huex.1.0.st.v2frmavecs/bioconductor-huex.1.0.st.v2frmavecs_1.1.0_src_all.tar.gz" ) MD5="982935d07b526ff555790e309fe4147e" @@ -16,7 +17,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-huex10stprobeset.db/meta.yaml b/recipes/bioconductor-huex10stprobeset.db/meta.yaml index a436499c3ed1a..35d16b0c80600 100644 --- a/recipes/bioconductor-huex10stprobeset.db/meta.yaml +++ b/recipes/bioconductor-huex10stprobeset.db/meta.yaml @@ -1,6 +1,6 @@ {% set version = "8.7.0" %} {% set name = "huex10stprobeset.db" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -12,7 +12,7 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 52cf39820872de4ac5529aa1192328b5 build: - number: 1 + number: 2 rpaths: - lib/R/lib/ - lib/ @@ -20,14 +20,14 @@ build: # Suggests: DBI, annotate, RUnit requirements: host: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' - - 'bioconductor-org.hs.eg.db >=3.7.0,<3.8.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' + - 'bioconductor-org.hs.eg.db >=3.8.0,<3.9.0' - r-base run: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' - - 'bioconductor-org.hs.eg.db >=3.7.0,<3.8.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' + - 'bioconductor-org.hs.eg.db >=3.8.0,<3.9.0' - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-huex10stprobeset.db/post-link.sh b/recipes/bioconductor-huex10stprobeset.db/post-link.sh index 740f0f83686da..ec1effebdf397 100644 --- a/recipes/bioconductor-huex10stprobeset.db/post-link.sh +++ b/recipes/bioconductor-huex10stprobeset.db/post-link.sh @@ -1,9 +1,10 @@ #!/bin/bash FN="huex10stprobeset.db_8.7.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/huex10stprobeset.db_8.7.0.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/huex10stprobeset.db_8.7.0.tar.gz" "https://bioarchive.galaxyproject.org/huex10stprobeset.db_8.7.0.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-huex10stprobeset.db/bioconductor-huex10stprobeset.db_8.7.0_src_all.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-huex10stprobeset.db/bioconductor-huex10stprobeset.db_8.7.0_src_all.tar.gz" ) MD5="52cf39820872de4ac5529aa1192328b5" @@ -16,7 +17,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-huex10sttranscriptcluster.db/meta.yaml b/recipes/bioconductor-huex10sttranscriptcluster.db/meta.yaml index 832a4fc48bb8e..6719e6041a28f 100644 --- a/recipes/bioconductor-huex10sttranscriptcluster.db/meta.yaml +++ b/recipes/bioconductor-huex10sttranscriptcluster.db/meta.yaml @@ -1,6 +1,6 @@ {% set version = "8.7.0" %} {% set name = "huex10sttranscriptcluster.db" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -12,7 +12,7 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 7fb762002b5792c64ccafbd7bacf92a4 build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ @@ -20,14 +20,14 @@ build: # Suggests: DBI, annotate, RUnit requirements: host: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' - - 'bioconductor-org.hs.eg.db >=3.7.0,<3.8.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' + - 'bioconductor-org.hs.eg.db >=3.8.0,<3.9.0' - r-base run: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' - - 'bioconductor-org.hs.eg.db >=3.7.0,<3.8.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' + - 'bioconductor-org.hs.eg.db >=3.8.0,<3.9.0' - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-huex10sttranscriptcluster.db/post-link.sh b/recipes/bioconductor-huex10sttranscriptcluster.db/post-link.sh index 5f18eace0a560..e2b74843b1467 100644 --- a/recipes/bioconductor-huex10sttranscriptcluster.db/post-link.sh +++ b/recipes/bioconductor-huex10sttranscriptcluster.db/post-link.sh @@ -1,9 +1,10 @@ #!/bin/bash FN="huex10sttranscriptcluster.db_8.7.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/huex10sttranscriptcluster.db_8.7.0.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/huex10sttranscriptcluster.db_8.7.0.tar.gz" "https://bioarchive.galaxyproject.org/huex10sttranscriptcluster.db_8.7.0.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-huex10sttranscriptcluster.db/bioconductor-huex10sttranscriptcluster.db_8.7.0_src_all.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-huex10sttranscriptcluster.db/bioconductor-huex10sttranscriptcluster.db_8.7.0_src_all.tar.gz" ) MD5="7fb762002b5792c64ccafbd7bacf92a4" @@ -16,7 +17,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-huexexonprobesetlocation/meta.yaml b/recipes/bioconductor-huexexonprobesetlocation/meta.yaml index 4b096e121b7b5..8a66cad788db1 100644 --- a/recipes/bioconductor-huexexonprobesetlocation/meta.yaml +++ b/recipes/bioconductor-huexexonprobesetlocation/meta.yaml @@ -1,6 +1,6 @@ {% set version = "1.15.0" %} {% set name = "HuExExonProbesetLocation" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -12,19 +12,19 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' md5: 11bf1b88d9e90711b4064497f611da4f build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' - r-base run: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-huexexonprobesetlocation/post-link.sh b/recipes/bioconductor-huexexonprobesetlocation/post-link.sh index c679be39ecaac..695fe2c82f7c9 100644 --- a/recipes/bioconductor-huexexonprobesetlocation/post-link.sh +++ b/recipes/bioconductor-huexexonprobesetlocation/post-link.sh @@ -1,9 +1,10 @@ #!/bin/bash FN="HuExExonProbesetLocation_1.15.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/HuExExonProbesetLocation_1.15.0.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/HuExExonProbesetLocation_1.15.0.tar.gz" "https://bioarchive.galaxyproject.org/HuExExonProbesetLocation_1.15.0.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-huexexonprobesetlocation/bioconductor-huexexonprobesetlocation_1.15.0_src_all.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-huexexonprobesetlocation/bioconductor-huexexonprobesetlocation_1.15.0_src_all.tar.gz" ) MD5="11bf1b88d9e90711b4064497f611da4f" @@ -16,7 +17,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-huexexonprobesetlocationhg18/meta.yaml b/recipes/bioconductor-huexexonprobesetlocationhg18/meta.yaml index 692d104786df3..b9298bc18150b 100644 --- a/recipes/bioconductor-huexexonprobesetlocationhg18/meta.yaml +++ b/recipes/bioconductor-huexexonprobesetlocationhg18/meta.yaml @@ -1,6 +1,6 @@ {% set version = "0.0.2" %} {% set name = "HuExExonProbesetLocationHg18" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -12,19 +12,19 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' md5: bb00b7f5e4db2b04dca5951aa6bd073e build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' - r-base run: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-huexexonprobesetlocationhg18/post-link.sh b/recipes/bioconductor-huexexonprobesetlocationhg18/post-link.sh index 21b3015a4040b..90d0829752677 100644 --- a/recipes/bioconductor-huexexonprobesetlocationhg18/post-link.sh +++ b/recipes/bioconductor-huexexonprobesetlocationhg18/post-link.sh @@ -1,9 +1,10 @@ #!/bin/bash FN="HuExExonProbesetLocationHg18_0.0.2.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/HuExExonProbesetLocationHg18_0.0.2.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/HuExExonProbesetLocationHg18_0.0.2.tar.gz" "https://bioarchive.galaxyproject.org/HuExExonProbesetLocationHg18_0.0.2.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-huexexonprobesetlocationhg18/bioconductor-huexexonprobesetlocationhg18_0.0.2_src_all.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-huexexonprobesetlocationhg18/bioconductor-huexexonprobesetlocationhg18_0.0.2_src_all.tar.gz" ) MD5="bb00b7f5e4db2b04dca5951aa6bd073e" @@ -16,7 +17,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-huexexonprobesetlocationhg19/meta.yaml b/recipes/bioconductor-huexexonprobesetlocationhg19/meta.yaml index c844b6205656d..09ca335c33def 100644 --- a/recipes/bioconductor-huexexonprobesetlocationhg19/meta.yaml +++ b/recipes/bioconductor-huexexonprobesetlocationhg19/meta.yaml @@ -1,6 +1,6 @@ {% set version = "0.0.3" %} {% set name = "HuExExonProbesetLocationHg19" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -12,19 +12,19 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' md5: 1a3843c95c82dc71a043d902961ba33a build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' - r-base run: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-huexexonprobesetlocationhg19/post-link.sh b/recipes/bioconductor-huexexonprobesetlocationhg19/post-link.sh index 5574f462d0508..ba93fc950a64b 100644 --- a/recipes/bioconductor-huexexonprobesetlocationhg19/post-link.sh +++ b/recipes/bioconductor-huexexonprobesetlocationhg19/post-link.sh @@ -1,9 +1,10 @@ #!/bin/bash FN="HuExExonProbesetLocationHg19_0.0.3.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/HuExExonProbesetLocationHg19_0.0.3.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/HuExExonProbesetLocationHg19_0.0.3.tar.gz" "https://bioarchive.galaxyproject.org/HuExExonProbesetLocationHg19_0.0.3.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-huexexonprobesetlocationhg19/bioconductor-huexexonprobesetlocationhg19_0.0.3_src_all.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-huexexonprobesetlocationhg19/bioconductor-huexexonprobesetlocationhg19_0.0.3_src_all.tar.gz" ) MD5="1a3843c95c82dc71a043d902961ba33a" @@ -16,7 +17,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-hugene.1.0.st.v1frmavecs/meta.yaml b/recipes/bioconductor-hugene.1.0.st.v1frmavecs/meta.yaml index 8c395885680de..3b0a111b19c1c 100644 --- a/recipes/bioconductor-hugene.1.0.st.v1frmavecs/meta.yaml +++ b/recipes/bioconductor-hugene.1.0.st.v1frmavecs/meta.yaml @@ -1,6 +1,6 @@ {% set version = "1.1.0" %} {% set name = "hugene.1.0.st.v1frmavecs" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -12,7 +12,7 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 711a69e6fa6dd3737a90615222416dfc build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ @@ -22,7 +22,7 @@ requirements: - r-base run: - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-hugene.1.0.st.v1frmavecs/post-link.sh b/recipes/bioconductor-hugene.1.0.st.v1frmavecs/post-link.sh index fcb874a4b59dc..64888d985f242 100644 --- a/recipes/bioconductor-hugene.1.0.st.v1frmavecs/post-link.sh +++ b/recipes/bioconductor-hugene.1.0.st.v1frmavecs/post-link.sh @@ -1,9 +1,10 @@ #!/bin/bash FN="hugene.1.0.st.v1frmavecs_1.1.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/hugene.1.0.st.v1frmavecs_1.1.0.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/hugene.1.0.st.v1frmavecs_1.1.0.tar.gz" "https://bioarchive.galaxyproject.org/hugene.1.0.st.v1frmavecs_1.1.0.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-hugene.1.0.st.v1frmavecs/bioconductor-hugene.1.0.st.v1frmavecs_1.1.0_src_all.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-hugene.1.0.st.v1frmavecs/bioconductor-hugene.1.0.st.v1frmavecs_1.1.0_src_all.tar.gz" ) MD5="711a69e6fa6dd3737a90615222416dfc" @@ -16,7 +17,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-hugene10stprobeset.db/meta.yaml b/recipes/bioconductor-hugene10stprobeset.db/meta.yaml index d9f9ce18286fa..f1662525d40b8 100644 --- a/recipes/bioconductor-hugene10stprobeset.db/meta.yaml +++ b/recipes/bioconductor-hugene10stprobeset.db/meta.yaml @@ -1,6 +1,6 @@ {% set version = "8.7.0" %} {% set name = "hugene10stprobeset.db" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -12,7 +12,7 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 8c138a26b4aa0391edd69ef6abed3247 build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ @@ -20,14 +20,14 @@ build: # Suggests: DBI, annotate, RUnit requirements: host: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' - - 'bioconductor-org.hs.eg.db >=3.7.0,<3.8.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' + - 'bioconductor-org.hs.eg.db >=3.8.0,<3.9.0' - r-base run: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' - - 'bioconductor-org.hs.eg.db >=3.7.0,<3.8.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' + - 'bioconductor-org.hs.eg.db >=3.8.0,<3.9.0' - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-hugene10stprobeset.db/post-link.sh b/recipes/bioconductor-hugene10stprobeset.db/post-link.sh index 841660800995e..1c72cc4db1c9f 100644 --- a/recipes/bioconductor-hugene10stprobeset.db/post-link.sh +++ b/recipes/bioconductor-hugene10stprobeset.db/post-link.sh @@ -1,9 +1,10 @@ #!/bin/bash FN="hugene10stprobeset.db_8.7.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/hugene10stprobeset.db_8.7.0.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/hugene10stprobeset.db_8.7.0.tar.gz" "https://bioarchive.galaxyproject.org/hugene10stprobeset.db_8.7.0.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-hugene10stprobeset.db/bioconductor-hugene10stprobeset.db_8.7.0_src_all.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-hugene10stprobeset.db/bioconductor-hugene10stprobeset.db_8.7.0_src_all.tar.gz" ) MD5="8c138a26b4aa0391edd69ef6abed3247" @@ -16,7 +17,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-hugene10sttranscriptcluster.db/meta.yaml b/recipes/bioconductor-hugene10sttranscriptcluster.db/meta.yaml index e079583c1957e..47ca2ba952078 100644 --- a/recipes/bioconductor-hugene10sttranscriptcluster.db/meta.yaml +++ b/recipes/bioconductor-hugene10sttranscriptcluster.db/meta.yaml @@ -1,6 +1,6 @@ {% set version = "8.7.0" %} {% set name = "hugene10sttranscriptcluster.db" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -12,7 +12,7 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: d38c7a0fb26410d420e72c6aacf622ad build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ @@ -20,14 +20,14 @@ build: # Suggests: DBI, annotate, RUnit requirements: host: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' - - 'bioconductor-org.hs.eg.db >=3.7.0,<3.8.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' + - 'bioconductor-org.hs.eg.db >=3.8.0,<3.9.0' - r-base run: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' - - 'bioconductor-org.hs.eg.db >=3.7.0,<3.8.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' + - 'bioconductor-org.hs.eg.db >=3.8.0,<3.9.0' - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-hugene10sttranscriptcluster.db/post-link.sh b/recipes/bioconductor-hugene10sttranscriptcluster.db/post-link.sh index c6a1614582e54..7cc2de321fab2 100644 --- a/recipes/bioconductor-hugene10sttranscriptcluster.db/post-link.sh +++ b/recipes/bioconductor-hugene10sttranscriptcluster.db/post-link.sh @@ -1,9 +1,10 @@ #!/bin/bash FN="hugene10sttranscriptcluster.db_8.7.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/hugene10sttranscriptcluster.db_8.7.0.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/hugene10sttranscriptcluster.db_8.7.0.tar.gz" "https://bioarchive.galaxyproject.org/hugene10sttranscriptcluster.db_8.7.0.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-hugene10sttranscriptcluster.db/bioconductor-hugene10sttranscriptcluster.db_8.7.0_src_all.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-hugene10sttranscriptcluster.db/bioconductor-hugene10sttranscriptcluster.db_8.7.0_src_all.tar.gz" ) MD5="d38c7a0fb26410d420e72c6aacf622ad" @@ -16,7 +17,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-hugene10stv1cdf/meta.yaml b/recipes/bioconductor-hugene10stv1cdf/meta.yaml index 9382986852961..c6a6398f695e3 100644 --- a/recipes/bioconductor-hugene10stv1cdf/meta.yaml +++ b/recipes/bioconductor-hugene10stv1cdf/meta.yaml @@ -1,6 +1,6 @@ {% set version = "2.18.0" %} {% set name = "hugene10stv1cdf" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -12,19 +12,19 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: f1fb1c7076ac40b9e709f18e645d6181 build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' - r-base run: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-hugene10stv1cdf/post-link.sh b/recipes/bioconductor-hugene10stv1cdf/post-link.sh index 8e3598454058b..c187fb7723ac0 100644 --- a/recipes/bioconductor-hugene10stv1cdf/post-link.sh +++ b/recipes/bioconductor-hugene10stv1cdf/post-link.sh @@ -1,9 +1,10 @@ #!/bin/bash FN="hugene10stv1cdf_2.18.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/hugene10stv1cdf_2.18.0.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/hugene10stv1cdf_2.18.0.tar.gz" "https://bioarchive.galaxyproject.org/hugene10stv1cdf_2.18.0.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-hugene10stv1cdf/bioconductor-hugene10stv1cdf_2.18.0_src_all.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-hugene10stv1cdf/bioconductor-hugene10stv1cdf_2.18.0_src_all.tar.gz" ) MD5="f1fb1c7076ac40b9e709f18e645d6181" @@ -16,7 +17,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-hugene10stv1probe/meta.yaml b/recipes/bioconductor-hugene10stv1probe/meta.yaml index 5745a6c2c8007..cb7cd614e7a51 100644 --- a/recipes/bioconductor-hugene10stv1probe/meta.yaml +++ b/recipes/bioconductor-hugene10stv1probe/meta.yaml @@ -1,6 +1,6 @@ {% set version = "2.18.0" %} {% set name = "hugene10stv1probe" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -12,19 +12,19 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 6ed3c17dd026acf008658a5994044c62 build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' - r-base run: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-hugene10stv1probe/post-link.sh b/recipes/bioconductor-hugene10stv1probe/post-link.sh index 6b97c38911d93..7d7b30677edb3 100644 --- a/recipes/bioconductor-hugene10stv1probe/post-link.sh +++ b/recipes/bioconductor-hugene10stv1probe/post-link.sh @@ -1,9 +1,10 @@ #!/bin/bash FN="hugene10stv1probe_2.18.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/hugene10stv1probe_2.18.0.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/hugene10stv1probe_2.18.0.tar.gz" "https://bioarchive.galaxyproject.org/hugene10stv1probe_2.18.0.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-hugene10stv1probe/bioconductor-hugene10stv1probe_2.18.0_src_all.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-hugene10stv1probe/bioconductor-hugene10stv1probe_2.18.0_src_all.tar.gz" ) MD5="6ed3c17dd026acf008658a5994044c62" @@ -16,7 +17,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-hugene11stprobeset.db/meta.yaml b/recipes/bioconductor-hugene11stprobeset.db/meta.yaml index a983289653101..3c4cb0c1ad466 100644 --- a/recipes/bioconductor-hugene11stprobeset.db/meta.yaml +++ b/recipes/bioconductor-hugene11stprobeset.db/meta.yaml @@ -1,6 +1,6 @@ {% set version = "8.7.0" %} {% set name = "hugene11stprobeset.db" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -12,7 +12,7 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 315c1dff0ba5240c6c5432d0dcc11eb1 build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ @@ -20,14 +20,14 @@ build: # Suggests: DBI, annotate, RUnit requirements: host: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' - - 'bioconductor-org.hs.eg.db >=3.7.0,<3.8.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' + - 'bioconductor-org.hs.eg.db >=3.8.0,<3.9.0' - r-base run: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' - - 'bioconductor-org.hs.eg.db >=3.7.0,<3.8.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' + - 'bioconductor-org.hs.eg.db >=3.8.0,<3.9.0' - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-hugene11stprobeset.db/post-link.sh b/recipes/bioconductor-hugene11stprobeset.db/post-link.sh index 5917c1a8504f4..35e909a10a1bc 100644 --- a/recipes/bioconductor-hugene11stprobeset.db/post-link.sh +++ b/recipes/bioconductor-hugene11stprobeset.db/post-link.sh @@ -1,9 +1,10 @@ #!/bin/bash FN="hugene11stprobeset.db_8.7.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/hugene11stprobeset.db_8.7.0.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/hugene11stprobeset.db_8.7.0.tar.gz" "https://bioarchive.galaxyproject.org/hugene11stprobeset.db_8.7.0.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-hugene11stprobeset.db/bioconductor-hugene11stprobeset.db_8.7.0_src_all.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-hugene11stprobeset.db/bioconductor-hugene11stprobeset.db_8.7.0_src_all.tar.gz" ) MD5="315c1dff0ba5240c6c5432d0dcc11eb1" @@ -16,7 +17,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-hugene11sttranscriptcluster.db/meta.yaml b/recipes/bioconductor-hugene11sttranscriptcluster.db/meta.yaml index 00b6123e7166d..93e2a7d09259a 100644 --- a/recipes/bioconductor-hugene11sttranscriptcluster.db/meta.yaml +++ b/recipes/bioconductor-hugene11sttranscriptcluster.db/meta.yaml @@ -1,6 +1,6 @@ {% set version = "8.7.0" %} {% set name = "hugene11sttranscriptcluster.db" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -12,7 +12,7 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 0d366281eac2cba4b1fcfbe48596975a build: - number: 1 + number: 2 rpaths: - lib/R/lib/ - lib/ @@ -20,14 +20,14 @@ build: # Suggests: DBI, annotate, RUnit requirements: host: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' - - 'bioconductor-org.hs.eg.db >=3.7.0,<3.8.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' + - 'bioconductor-org.hs.eg.db >=3.8.0,<3.9.0' - r-base run: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' - - 'bioconductor-org.hs.eg.db >=3.7.0,<3.8.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' + - 'bioconductor-org.hs.eg.db >=3.8.0,<3.9.0' - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-hugene11sttranscriptcluster.db/post-link.sh b/recipes/bioconductor-hugene11sttranscriptcluster.db/post-link.sh index 691aeccc0f017..fedc787219937 100644 --- a/recipes/bioconductor-hugene11sttranscriptcluster.db/post-link.sh +++ b/recipes/bioconductor-hugene11sttranscriptcluster.db/post-link.sh @@ -1,9 +1,10 @@ #!/bin/bash FN="hugene11sttranscriptcluster.db_8.7.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/hugene11sttranscriptcluster.db_8.7.0.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/hugene11sttranscriptcluster.db_8.7.0.tar.gz" "https://bioarchive.galaxyproject.org/hugene11sttranscriptcluster.db_8.7.0.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-hugene11sttranscriptcluster.db/bioconductor-hugene11sttranscriptcluster.db_8.7.0_src_all.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-hugene11sttranscriptcluster.db/bioconductor-hugene11sttranscriptcluster.db_8.7.0_src_all.tar.gz" ) MD5="0d366281eac2cba4b1fcfbe48596975a" @@ -16,7 +17,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-hugene20stprobeset.db/meta.yaml b/recipes/bioconductor-hugene20stprobeset.db/meta.yaml index 00ead16f1383f..73ffbea64e04b 100644 --- a/recipes/bioconductor-hugene20stprobeset.db/meta.yaml +++ b/recipes/bioconductor-hugene20stprobeset.db/meta.yaml @@ -1,6 +1,6 @@ {% set version = "8.7.0" %} {% set name = "hugene20stprobeset.db" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -12,7 +12,7 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 17e599fe0f885f17de29a6174324054d build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ @@ -20,14 +20,14 @@ build: # Suggests: DBI, annotate, RUnit requirements: host: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' - - 'bioconductor-org.hs.eg.db >=3.7.0,<3.8.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' + - 'bioconductor-org.hs.eg.db >=3.8.0,<3.9.0' - r-base run: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' - - 'bioconductor-org.hs.eg.db >=3.7.0,<3.8.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' + - 'bioconductor-org.hs.eg.db >=3.8.0,<3.9.0' - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-hugene20stprobeset.db/post-link.sh b/recipes/bioconductor-hugene20stprobeset.db/post-link.sh index e52dd27da0589..554a2d79fb6af 100644 --- a/recipes/bioconductor-hugene20stprobeset.db/post-link.sh +++ b/recipes/bioconductor-hugene20stprobeset.db/post-link.sh @@ -1,9 +1,10 @@ #!/bin/bash FN="hugene20stprobeset.db_8.7.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/hugene20stprobeset.db_8.7.0.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/hugene20stprobeset.db_8.7.0.tar.gz" "https://bioarchive.galaxyproject.org/hugene20stprobeset.db_8.7.0.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-hugene20stprobeset.db/bioconductor-hugene20stprobeset.db_8.7.0_src_all.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-hugene20stprobeset.db/bioconductor-hugene20stprobeset.db_8.7.0_src_all.tar.gz" ) MD5="17e599fe0f885f17de29a6174324054d" @@ -16,7 +17,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-hugene20sttranscriptcluster.db/meta.yaml b/recipes/bioconductor-hugene20sttranscriptcluster.db/meta.yaml index ca5f6e1e25dca..df9ef34cd02c8 100644 --- a/recipes/bioconductor-hugene20sttranscriptcluster.db/meta.yaml +++ b/recipes/bioconductor-hugene20sttranscriptcluster.db/meta.yaml @@ -1,6 +1,6 @@ {% set version = "8.7.0" %} {% set name = "hugene20sttranscriptcluster.db" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -12,7 +12,7 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 85b23453d8e7c6c92673deaa7a82e51e build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ @@ -20,14 +20,14 @@ build: # Suggests: DBI, annotate, RUnit requirements: host: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' - - 'bioconductor-org.hs.eg.db >=3.7.0,<3.8.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' + - 'bioconductor-org.hs.eg.db >=3.8.0,<3.9.0' - r-base run: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' - - 'bioconductor-org.hs.eg.db >=3.7.0,<3.8.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' + - 'bioconductor-org.hs.eg.db >=3.8.0,<3.9.0' - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-hugene20sttranscriptcluster.db/post-link.sh b/recipes/bioconductor-hugene20sttranscriptcluster.db/post-link.sh index 993b4c34b82e3..df3060b478374 100644 --- a/recipes/bioconductor-hugene20sttranscriptcluster.db/post-link.sh +++ b/recipes/bioconductor-hugene20sttranscriptcluster.db/post-link.sh @@ -1,9 +1,10 @@ #!/bin/bash FN="hugene20sttranscriptcluster.db_8.7.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/hugene20sttranscriptcluster.db_8.7.0.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/hugene20sttranscriptcluster.db_8.7.0.tar.gz" "https://bioarchive.galaxyproject.org/hugene20sttranscriptcluster.db_8.7.0.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-hugene20sttranscriptcluster.db/bioconductor-hugene20sttranscriptcluster.db_8.7.0_src_all.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-hugene20sttranscriptcluster.db/bioconductor-hugene20sttranscriptcluster.db_8.7.0_src_all.tar.gz" ) MD5="85b23453d8e7c6c92673deaa7a82e51e" @@ -16,7 +17,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-hugene21stprobeset.db/meta.yaml b/recipes/bioconductor-hugene21stprobeset.db/meta.yaml index 886142c6167fa..6da6a21a8143c 100644 --- a/recipes/bioconductor-hugene21stprobeset.db/meta.yaml +++ b/recipes/bioconductor-hugene21stprobeset.db/meta.yaml @@ -1,6 +1,6 @@ {% set version = "8.7.0" %} {% set name = "hugene21stprobeset.db" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -12,7 +12,7 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: ad101fb652b87da23d17547268019bb8 build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ @@ -20,14 +20,14 @@ build: # Suggests: DBI, annotate, RUnit requirements: host: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' - - 'bioconductor-org.hs.eg.db >=3.7.0,<3.8.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' + - 'bioconductor-org.hs.eg.db >=3.8.0,<3.9.0' - r-base run: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' - - 'bioconductor-org.hs.eg.db >=3.7.0,<3.8.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' + - 'bioconductor-org.hs.eg.db >=3.8.0,<3.9.0' - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-hugene21stprobeset.db/post-link.sh b/recipes/bioconductor-hugene21stprobeset.db/post-link.sh index b8f5b85770420..d38946fa7d356 100644 --- a/recipes/bioconductor-hugene21stprobeset.db/post-link.sh +++ b/recipes/bioconductor-hugene21stprobeset.db/post-link.sh @@ -1,9 +1,10 @@ #!/bin/bash FN="hugene21stprobeset.db_8.7.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/hugene21stprobeset.db_8.7.0.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/hugene21stprobeset.db_8.7.0.tar.gz" "https://bioarchive.galaxyproject.org/hugene21stprobeset.db_8.7.0.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-hugene21stprobeset.db/bioconductor-hugene21stprobeset.db_8.7.0_src_all.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-hugene21stprobeset.db/bioconductor-hugene21stprobeset.db_8.7.0_src_all.tar.gz" ) MD5="ad101fb652b87da23d17547268019bb8" @@ -16,7 +17,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-hugene21sttranscriptcluster.db/meta.yaml b/recipes/bioconductor-hugene21sttranscriptcluster.db/meta.yaml index 5170d241edeeb..cd2a167391ca5 100644 --- a/recipes/bioconductor-hugene21sttranscriptcluster.db/meta.yaml +++ b/recipes/bioconductor-hugene21sttranscriptcluster.db/meta.yaml @@ -1,6 +1,6 @@ {% set version = "8.7.0" %} {% set name = "hugene21sttranscriptcluster.db" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -12,7 +12,7 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 7d4d913f3e48f3eab45e036323d223b5 build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ @@ -20,14 +20,14 @@ build: # Suggests: DBI, annotate, RUnit requirements: host: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' - - 'bioconductor-org.hs.eg.db >=3.7.0,<3.8.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' + - 'bioconductor-org.hs.eg.db >=3.8.0,<3.9.0' - r-base run: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' - - 'bioconductor-org.hs.eg.db >=3.7.0,<3.8.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' + - 'bioconductor-org.hs.eg.db >=3.8.0,<3.9.0' - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-hugene21sttranscriptcluster.db/post-link.sh b/recipes/bioconductor-hugene21sttranscriptcluster.db/post-link.sh index 60f703ac2c110..e7d80c5508eee 100644 --- a/recipes/bioconductor-hugene21sttranscriptcluster.db/post-link.sh +++ b/recipes/bioconductor-hugene21sttranscriptcluster.db/post-link.sh @@ -1,9 +1,10 @@ #!/bin/bash FN="hugene21sttranscriptcluster.db_8.7.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/hugene21sttranscriptcluster.db_8.7.0.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/hugene21sttranscriptcluster.db_8.7.0.tar.gz" "https://bioarchive.galaxyproject.org/hugene21sttranscriptcluster.db_8.7.0.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-hugene21sttranscriptcluster.db/bioconductor-hugene21sttranscriptcluster.db_8.7.0_src_all.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-hugene21sttranscriptcluster.db/bioconductor-hugene21sttranscriptcluster.db_8.7.0_src_all.tar.gz" ) MD5="7d4d913f3e48f3eab45e036323d223b5" @@ -16,7 +17,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-human.db0/meta.yaml b/recipes/bioconductor-human.db0/meta.yaml index f52462c189d18..854b150526876 100644 --- a/recipes/bioconductor-human.db0/meta.yaml +++ b/recipes/bioconductor-human.db0/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "3.7.1" %} +{% set version = "3.8.2" %} {% set name = "human.db0" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: e34a53909394d8987f03e57345ab91f5 + md5: b150cae85c2594ebb694fa1996895ac0 build: number: 0 rpaths: @@ -19,12 +19,12 @@ build: noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' - r-base run: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-human.db0/post-link.sh b/recipes/bioconductor-human.db0/post-link.sh index ee678d0251862..c0e1b85c89583 100644 --- a/recipes/bioconductor-human.db0/post-link.sh +++ b/recipes/bioconductor-human.db0/post-link.sh @@ -1,11 +1,11 @@ #!/bin/bash -FN="human.db0_3.7.1.tar.gz" +FN="human.db0_3.8.2.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/human.db0_3.7.1.tar.gz" - "https://bioarchive.galaxyproject.org/human.db0_3.7.1.tar.gz" - "https://depot.galaxyproject.org/software/bioconductor-human.db0/bioconductor-human.db0_3.7.1_src_all.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/human.db0_3.8.2.tar.gz" + "https://bioarchive.galaxyproject.org/human.db0_3.8.2.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-human.db0/bioconductor-human.db0_3.8.2_src_all.tar.gz" ) -MD5="e34a53909394d8987f03e57345ab91f5" +MD5="b150cae85c2594ebb694fa1996895ac0" # Use a staging area in the conda dir rather than temp dirs, both to avoid # permission issues as well as to have things downloaded in a predictable @@ -16,7 +16,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-human1mduov3bcrlmm/meta.yaml b/recipes/bioconductor-human1mduov3bcrlmm/meta.yaml index 6f8c43fcdfcbe..4f520946bea50 100644 --- a/recipes/bioconductor-human1mduov3bcrlmm/meta.yaml +++ b/recipes/bioconductor-human1mduov3bcrlmm/meta.yaml @@ -1,6 +1,6 @@ {% set version = "1.0.4" %} {% set name = "human1mduov3bCrlmm" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -12,7 +12,7 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' md5: 0ff9f1e8bcc6348d6777bbb982ae0325 build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ @@ -22,7 +22,7 @@ requirements: - r-base run: - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-human1mduov3bcrlmm/post-link.sh b/recipes/bioconductor-human1mduov3bcrlmm/post-link.sh index e518af4ec4607..f21cb754cff6f 100644 --- a/recipes/bioconductor-human1mduov3bcrlmm/post-link.sh +++ b/recipes/bioconductor-human1mduov3bcrlmm/post-link.sh @@ -1,9 +1,10 @@ #!/bin/bash FN="human1mduov3bCrlmm_1.0.4.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/human1mduov3bCrlmm_1.0.4.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/human1mduov3bCrlmm_1.0.4.tar.gz" "https://bioarchive.galaxyproject.org/human1mduov3bCrlmm_1.0.4.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-human1mduov3bcrlmm/bioconductor-human1mduov3bcrlmm_1.0.4_src_all.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-human1mduov3bcrlmm/bioconductor-human1mduov3bcrlmm_1.0.4_src_all.tar.gz" ) MD5="0ff9f1e8bcc6348d6777bbb982ae0325" @@ -16,7 +17,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-human1mv1ccrlmm/meta.yaml b/recipes/bioconductor-human1mv1ccrlmm/meta.yaml index 639095433b5a1..a4c3f8d392c55 100644 --- a/recipes/bioconductor-human1mv1ccrlmm/meta.yaml +++ b/recipes/bioconductor-human1mv1ccrlmm/meta.yaml @@ -1,6 +1,6 @@ {% set version = "1.0.3" %} {% set name = "human1mv1cCrlmm" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -12,7 +12,7 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' md5: b9f638c7b0ede50cb070f1bae85eb4dc build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ @@ -22,7 +22,7 @@ requirements: - r-base run: - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-human1mv1ccrlmm/post-link.sh b/recipes/bioconductor-human1mv1ccrlmm/post-link.sh index 31a25eee41212..b8876831ca661 100644 --- a/recipes/bioconductor-human1mv1ccrlmm/post-link.sh +++ b/recipes/bioconductor-human1mv1ccrlmm/post-link.sh @@ -1,9 +1,10 @@ #!/bin/bash FN="human1mv1cCrlmm_1.0.3.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/human1mv1cCrlmm_1.0.3.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/human1mv1cCrlmm_1.0.3.tar.gz" "https://bioarchive.galaxyproject.org/human1mv1cCrlmm_1.0.3.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-human1mv1ccrlmm/bioconductor-human1mv1ccrlmm_1.0.3_src_all.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-human1mv1ccrlmm/bioconductor-human1mv1ccrlmm_1.0.3_src_all.tar.gz" ) MD5="b9f638c7b0ede50cb070f1bae85eb4dc" @@ -16,7 +17,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-human370quadv3ccrlmm/meta.yaml b/recipes/bioconductor-human370quadv3ccrlmm/meta.yaml index 53d20512e80b1..30c30f76ee59e 100644 --- a/recipes/bioconductor-human370quadv3ccrlmm/meta.yaml +++ b/recipes/bioconductor-human370quadv3ccrlmm/meta.yaml @@ -1,6 +1,6 @@ {% set version = "1.0.3" %} {% set name = "human370quadv3cCrlmm" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -12,7 +12,7 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' md5: 33c3ccc3793ed95647418b746a5177f9 build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ @@ -22,7 +22,7 @@ requirements: - r-base run: - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-human370quadv3ccrlmm/post-link.sh b/recipes/bioconductor-human370quadv3ccrlmm/post-link.sh index cd0816350a5d0..77192410adf49 100644 --- a/recipes/bioconductor-human370quadv3ccrlmm/post-link.sh +++ b/recipes/bioconductor-human370quadv3ccrlmm/post-link.sh @@ -1,9 +1,10 @@ #!/bin/bash FN="human370quadv3cCrlmm_1.0.3.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/human370quadv3cCrlmm_1.0.3.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/human370quadv3cCrlmm_1.0.3.tar.gz" "https://bioarchive.galaxyproject.org/human370quadv3cCrlmm_1.0.3.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-human370quadv3ccrlmm/bioconductor-human370quadv3ccrlmm_1.0.3_src_all.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-human370quadv3ccrlmm/bioconductor-human370quadv3ccrlmm_1.0.3_src_all.tar.gz" ) MD5="33c3ccc3793ed95647418b746a5177f9" @@ -16,7 +17,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-human370v1ccrlmm/meta.yaml b/recipes/bioconductor-human370v1ccrlmm/meta.yaml index 25913a5b016b1..49aa59e8c3b0c 100644 --- a/recipes/bioconductor-human370v1ccrlmm/meta.yaml +++ b/recipes/bioconductor-human370v1ccrlmm/meta.yaml @@ -1,6 +1,6 @@ {% set version = "1.0.2" %} {% set name = "human370v1cCrlmm" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -12,7 +12,7 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' md5: 9ec4192f533faee2b14484de02548075 build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ @@ -22,7 +22,7 @@ requirements: - r-base run: - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-human370v1ccrlmm/post-link.sh b/recipes/bioconductor-human370v1ccrlmm/post-link.sh index 18d0d73426068..46fb5a82b513f 100644 --- a/recipes/bioconductor-human370v1ccrlmm/post-link.sh +++ b/recipes/bioconductor-human370v1ccrlmm/post-link.sh @@ -1,9 +1,10 @@ #!/bin/bash FN="human370v1cCrlmm_1.0.2.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/human370v1cCrlmm_1.0.2.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/human370v1cCrlmm_1.0.2.tar.gz" "https://bioarchive.galaxyproject.org/human370v1cCrlmm_1.0.2.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-human370v1ccrlmm/bioconductor-human370v1ccrlmm_1.0.2_src_all.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-human370v1ccrlmm/bioconductor-human370v1ccrlmm_1.0.2_src_all.tar.gz" ) MD5="9ec4192f533faee2b14484de02548075" @@ -16,7 +17,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-human550v3bcrlmm/meta.yaml b/recipes/bioconductor-human550v3bcrlmm/meta.yaml index 320d2654e202e..c349eb9b2da6f 100644 --- a/recipes/bioconductor-human550v3bcrlmm/meta.yaml +++ b/recipes/bioconductor-human550v3bcrlmm/meta.yaml @@ -1,6 +1,6 @@ {% set version = "1.0.4" %} {% set name = "human550v3bCrlmm" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -12,7 +12,7 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' md5: 20e6b008fab5e1084354c87ad50d18a8 build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ @@ -22,7 +22,7 @@ requirements: - r-base run: - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-human550v3bcrlmm/post-link.sh b/recipes/bioconductor-human550v3bcrlmm/post-link.sh index 6d1d215b76df5..0f979dfe973aa 100644 --- a/recipes/bioconductor-human550v3bcrlmm/post-link.sh +++ b/recipes/bioconductor-human550v3bcrlmm/post-link.sh @@ -1,9 +1,10 @@ #!/bin/bash FN="human550v3bCrlmm_1.0.4.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/human550v3bCrlmm_1.0.4.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/human550v3bCrlmm_1.0.4.tar.gz" "https://bioarchive.galaxyproject.org/human550v3bCrlmm_1.0.4.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-human550v3bcrlmm/bioconductor-human550v3bcrlmm_1.0.4_src_all.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-human550v3bcrlmm/bioconductor-human550v3bcrlmm_1.0.4_src_all.tar.gz" ) MD5="20e6b008fab5e1084354c87ad50d18a8" @@ -16,7 +17,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-human610quadv1bcrlmm/meta.yaml b/recipes/bioconductor-human610quadv1bcrlmm/meta.yaml index 5966f0123cbce..b696357fcdddb 100644 --- a/recipes/bioconductor-human610quadv1bcrlmm/meta.yaml +++ b/recipes/bioconductor-human610quadv1bcrlmm/meta.yaml @@ -1,6 +1,6 @@ {% set version = "1.0.3" %} {% set name = "human610quadv1bCrlmm" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -12,7 +12,7 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' md5: 609cf09410774e084ee6a3286652bb1a build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ @@ -22,7 +22,7 @@ requirements: - r-base run: - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-human610quadv1bcrlmm/post-link.sh b/recipes/bioconductor-human610quadv1bcrlmm/post-link.sh index 471605a515a7e..c4decdd3d06bb 100644 --- a/recipes/bioconductor-human610quadv1bcrlmm/post-link.sh +++ b/recipes/bioconductor-human610quadv1bcrlmm/post-link.sh @@ -1,9 +1,10 @@ #!/bin/bash FN="human610quadv1bCrlmm_1.0.3.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/human610quadv1bCrlmm_1.0.3.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/human610quadv1bCrlmm_1.0.3.tar.gz" "https://bioarchive.galaxyproject.org/human610quadv1bCrlmm_1.0.3.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-human610quadv1bcrlmm/bioconductor-human610quadv1bcrlmm_1.0.3_src_all.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-human610quadv1bcrlmm/bioconductor-human610quadv1bcrlmm_1.0.3_src_all.tar.gz" ) MD5="609cf09410774e084ee6a3286652bb1a" @@ -16,7 +17,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-human650v3acrlmm/meta.yaml b/recipes/bioconductor-human650v3acrlmm/meta.yaml index ae0766acf461e..1a336e9ff0bbf 100644 --- a/recipes/bioconductor-human650v3acrlmm/meta.yaml +++ b/recipes/bioconductor-human650v3acrlmm/meta.yaml @@ -1,6 +1,6 @@ {% set version = "1.0.3" %} {% set name = "human650v3aCrlmm" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -12,7 +12,7 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' md5: 4b0de367ccc0f7499dcffe21ef1893c2 build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ @@ -22,7 +22,7 @@ requirements: - r-base run: - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-human650v3acrlmm/post-link.sh b/recipes/bioconductor-human650v3acrlmm/post-link.sh index c1d785c012602..c5707a6095aee 100644 --- a/recipes/bioconductor-human650v3acrlmm/post-link.sh +++ b/recipes/bioconductor-human650v3acrlmm/post-link.sh @@ -1,9 +1,10 @@ #!/bin/bash FN="human650v3aCrlmm_1.0.3.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/human650v3aCrlmm_1.0.3.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/human650v3aCrlmm_1.0.3.tar.gz" "https://bioarchive.galaxyproject.org/human650v3aCrlmm_1.0.3.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-human650v3acrlmm/bioconductor-human650v3acrlmm_1.0.3_src_all.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-human650v3acrlmm/bioconductor-human650v3acrlmm_1.0.3_src_all.tar.gz" ) MD5="4b0de367ccc0f7499dcffe21ef1893c2" @@ -16,7 +17,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-human660quadv1acrlmm/meta.yaml b/recipes/bioconductor-human660quadv1acrlmm/meta.yaml index d668d2c7ad048..b2cddb6d0e9e4 100644 --- a/recipes/bioconductor-human660quadv1acrlmm/meta.yaml +++ b/recipes/bioconductor-human660quadv1acrlmm/meta.yaml @@ -1,6 +1,6 @@ {% set version = "1.0.3" %} {% set name = "human660quadv1aCrlmm" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -12,7 +12,7 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' md5: 5fd2d94a462e150c888f13c5c0975c36 build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ @@ -22,7 +22,7 @@ requirements: - r-base run: - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-human660quadv1acrlmm/post-link.sh b/recipes/bioconductor-human660quadv1acrlmm/post-link.sh index 99899f2226e1a..170262770689b 100644 --- a/recipes/bioconductor-human660quadv1acrlmm/post-link.sh +++ b/recipes/bioconductor-human660quadv1acrlmm/post-link.sh @@ -1,9 +1,10 @@ #!/bin/bash FN="human660quadv1aCrlmm_1.0.3.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/human660quadv1aCrlmm_1.0.3.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/human660quadv1aCrlmm_1.0.3.tar.gz" "https://bioarchive.galaxyproject.org/human660quadv1aCrlmm_1.0.3.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-human660quadv1acrlmm/bioconductor-human660quadv1acrlmm_1.0.3_src_all.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-human660quadv1acrlmm/bioconductor-human660quadv1acrlmm_1.0.3_src_all.tar.gz" ) MD5="5fd2d94a462e150c888f13c5c0975c36" @@ -16,7 +17,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-humanaffydata/meta.yaml b/recipes/bioconductor-humanaffydata/meta.yaml index 71a0c0253f13d..03d8176edefbb 100644 --- a/recipes/bioconductor-humanaffydata/meta.yaml +++ b/recipes/bioconductor-humanaffydata/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.8.0" %} +{% set version = "1.10.0" %} {% set name = "HumanAffyData" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: dfe3425fce62815fdd066bd003bfb4d5 + md5: d013a2b88fb9a47ff7cd962099c6fd28 build: number: 0 rpaths: @@ -20,14 +20,14 @@ build: # Suggests: BiocStyle requirements: host: - - 'bioconductor-biobase >=2.42.0,<2.43.0' - - 'bioconductor-experimenthub >=1.8.0,<1.9.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' + - 'bioconductor-experimenthub >=1.10.0,<1.11.0' - r-base run: - - 'bioconductor-biobase >=2.42.0,<2.43.0' - - 'bioconductor-experimenthub >=1.8.0,<1.9.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' + - 'bioconductor-experimenthub >=1.10.0,<1.11.0' - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-humanaffydata/post-link.sh b/recipes/bioconductor-humanaffydata/post-link.sh index 09de247d325bb..a1389d26ff4c4 100644 --- a/recipes/bioconductor-humanaffydata/post-link.sh +++ b/recipes/bioconductor-humanaffydata/post-link.sh @@ -1,11 +1,11 @@ #!/bin/bash -FN="HumanAffyData_1.8.0.tar.gz" +FN="HumanAffyData_1.10.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/experiment/src/contrib/HumanAffyData_1.8.0.tar.gz" - "https://bioarchive.galaxyproject.org/HumanAffyData_1.8.0.tar.gz" - "https://depot.galaxyproject.org/software/bioconductor-humanaffydata/bioconductor-humanaffydata_1.8.0_src_all.tar.gz" + "https://bioconductor.org/packages/3.9/data/experiment/src/contrib/HumanAffyData_1.10.0.tar.gz" + "https://bioarchive.galaxyproject.org/HumanAffyData_1.10.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-humanaffydata/bioconductor-humanaffydata_1.10.0_src_all.tar.gz" ) -MD5="dfe3425fce62815fdd066bd003bfb4d5" +MD5="d013a2b88fb9a47ff7cd962099c6fd28" # Use a staging area in the conda dir rather than temp dirs, both to avoid # permission issues as well as to have things downloaded in a predictable @@ -16,7 +16,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-humanchrloc/meta.yaml b/recipes/bioconductor-humanchrloc/meta.yaml index 15a7bd98eee31..0ef1ad097ae5a 100644 --- a/recipes/bioconductor-humanchrloc/meta.yaml +++ b/recipes/bioconductor-humanchrloc/meta.yaml @@ -1,6 +1,6 @@ {% set version = "2.1.6" %} {% set name = "humanCHRLOC" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -12,7 +12,7 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' md5: 113450c0822000c9b4e8a0141cf4b819 build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ @@ -22,7 +22,7 @@ requirements: - r-base run: - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-humanchrloc/post-link.sh b/recipes/bioconductor-humanchrloc/post-link.sh index b5e4f2cbe5e79..b6b715ee5c8b7 100644 --- a/recipes/bioconductor-humanchrloc/post-link.sh +++ b/recipes/bioconductor-humanchrloc/post-link.sh @@ -1,9 +1,10 @@ #!/bin/bash FN="humanCHRLOC_2.1.6.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/humanCHRLOC_2.1.6.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/humanCHRLOC_2.1.6.tar.gz" "https://bioarchive.galaxyproject.org/humanCHRLOC_2.1.6.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-humanchrloc/bioconductor-humanchrloc_2.1.6_src_all.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-humanchrloc/bioconductor-humanchrloc_2.1.6_src_all.tar.gz" ) MD5="113450c0822000c9b4e8a0141cf4b819" @@ -16,7 +17,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-humancytosnp12v2p1hcrlmm/meta.yaml b/recipes/bioconductor-humancytosnp12v2p1hcrlmm/meta.yaml index 32430d9c4ca84..9d742278759ca 100644 --- a/recipes/bioconductor-humancytosnp12v2p1hcrlmm/meta.yaml +++ b/recipes/bioconductor-humancytosnp12v2p1hcrlmm/meta.yaml @@ -1,6 +1,6 @@ {% set version = "1.0.1" %} {% set name = "humancytosnp12v2p1hCrlmm" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -12,7 +12,7 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' md5: edf80245ddb28afb9fbaa6668187bf3a build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ @@ -22,7 +22,7 @@ requirements: - r-base run: - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-humancytosnp12v2p1hcrlmm/post-link.sh b/recipes/bioconductor-humancytosnp12v2p1hcrlmm/post-link.sh index 32ca50f70c929..ad2a3930d5642 100644 --- a/recipes/bioconductor-humancytosnp12v2p1hcrlmm/post-link.sh +++ b/recipes/bioconductor-humancytosnp12v2p1hcrlmm/post-link.sh @@ -1,9 +1,10 @@ #!/bin/bash FN="humancytosnp12v2p1hCrlmm_1.0.1.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/humancytosnp12v2p1hCrlmm_1.0.1.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/humancytosnp12v2p1hCrlmm_1.0.1.tar.gz" "https://bioarchive.galaxyproject.org/humancytosnp12v2p1hCrlmm_1.0.1.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-humancytosnp12v2p1hcrlmm/bioconductor-humancytosnp12v2p1hcrlmm_1.0.1_src_all.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-humancytosnp12v2p1hcrlmm/bioconductor-humancytosnp12v2p1hcrlmm_1.0.1_src_all.tar.gz" ) MD5="edf80245ddb28afb9fbaa6668187bf3a" @@ -16,7 +17,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-humanomni1quadv1bcrlmm/meta.yaml b/recipes/bioconductor-humanomni1quadv1bcrlmm/meta.yaml index 92395b4249dc4..e980b6992ab66 100644 --- a/recipes/bioconductor-humanomni1quadv1bcrlmm/meta.yaml +++ b/recipes/bioconductor-humanomni1quadv1bcrlmm/meta.yaml @@ -1,6 +1,6 @@ {% set version = "1.0.3" %} {% set name = "humanomni1quadv1bCrlmm" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -12,7 +12,7 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' md5: e81b2603f37d4cda3f28cd69a7296a23 build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ @@ -22,7 +22,7 @@ requirements: - r-base run: - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-humanomni1quadv1bcrlmm/post-link.sh b/recipes/bioconductor-humanomni1quadv1bcrlmm/post-link.sh index 2683ea367ee42..9700e74320e4c 100644 --- a/recipes/bioconductor-humanomni1quadv1bcrlmm/post-link.sh +++ b/recipes/bioconductor-humanomni1quadv1bcrlmm/post-link.sh @@ -1,9 +1,10 @@ #!/bin/bash FN="humanomni1quadv1bCrlmm_1.0.3.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/humanomni1quadv1bCrlmm_1.0.3.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/humanomni1quadv1bCrlmm_1.0.3.tar.gz" "https://bioarchive.galaxyproject.org/humanomni1quadv1bCrlmm_1.0.3.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-humanomni1quadv1bcrlmm/bioconductor-humanomni1quadv1bcrlmm_1.0.3_src_all.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-humanomni1quadv1bcrlmm/bioconductor-humanomni1quadv1bcrlmm_1.0.3_src_all.tar.gz" ) MD5="e81b2603f37d4cda3f28cd69a7296a23" @@ -16,7 +17,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-humanomni25quadv1bcrlmm/meta.yaml b/recipes/bioconductor-humanomni25quadv1bcrlmm/meta.yaml index 683e2ecd110f7..694522881c4eb 100644 --- a/recipes/bioconductor-humanomni25quadv1bcrlmm/meta.yaml +++ b/recipes/bioconductor-humanomni25quadv1bcrlmm/meta.yaml @@ -1,6 +1,6 @@ {% set version = "1.0.2" %} {% set name = "humanomni25quadv1bCrlmm" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -12,7 +12,7 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' md5: 2ee1fa7bf712d7f81a167079c975d49f build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ @@ -22,7 +22,7 @@ requirements: - r-base run: - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-humanomni25quadv1bcrlmm/post-link.sh b/recipes/bioconductor-humanomni25quadv1bcrlmm/post-link.sh index dd604ca05dd13..d87cdc4c49402 100644 --- a/recipes/bioconductor-humanomni25quadv1bcrlmm/post-link.sh +++ b/recipes/bioconductor-humanomni25quadv1bcrlmm/post-link.sh @@ -1,9 +1,10 @@ #!/bin/bash FN="humanomni25quadv1bCrlmm_1.0.2.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/humanomni25quadv1bCrlmm_1.0.2.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/humanomni25quadv1bCrlmm_1.0.2.tar.gz" "https://bioarchive.galaxyproject.org/humanomni25quadv1bCrlmm_1.0.2.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-humanomni25quadv1bcrlmm/bioconductor-humanomni25quadv1bcrlmm_1.0.2_src_all.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-humanomni25quadv1bcrlmm/bioconductor-humanomni25quadv1bcrlmm_1.0.2_src_all.tar.gz" ) MD5="2ee1fa7bf712d7f81a167079c975d49f" @@ -16,7 +17,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-humanomni5quadv1bcrlmm/meta.yaml b/recipes/bioconductor-humanomni5quadv1bcrlmm/meta.yaml index 57393d552fad5..103fbd1c4c050 100644 --- a/recipes/bioconductor-humanomni5quadv1bcrlmm/meta.yaml +++ b/recipes/bioconductor-humanomni5quadv1bcrlmm/meta.yaml @@ -1,6 +1,6 @@ {% set version = "1.0.0" %} {% set name = "humanomni5quadv1bCrlmm" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -12,7 +12,7 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' md5: 3ac4d6867c3d5590a6308d6edff0912b build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ @@ -22,7 +22,7 @@ requirements: - r-base run: - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-humanomni5quadv1bcrlmm/post-link.sh b/recipes/bioconductor-humanomni5quadv1bcrlmm/post-link.sh index 63ae406e36b5d..d18a1205e7930 100644 --- a/recipes/bioconductor-humanomni5quadv1bcrlmm/post-link.sh +++ b/recipes/bioconductor-humanomni5quadv1bcrlmm/post-link.sh @@ -1,9 +1,10 @@ #!/bin/bash FN="humanomni5quadv1bCrlmm_1.0.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/humanomni5quadv1bCrlmm_1.0.0.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/humanomni5quadv1bCrlmm_1.0.0.tar.gz" "https://bioarchive.galaxyproject.org/humanomni5quadv1bCrlmm_1.0.0.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-humanomni5quadv1bcrlmm/bioconductor-humanomni5quadv1bcrlmm_1.0.0_src_all.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-humanomni5quadv1bcrlmm/bioconductor-humanomni5quadv1bcrlmm_1.0.0_src_all.tar.gz" ) MD5="3ac4d6867c3d5590a6308d6edff0912b" @@ -16,7 +17,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-humanomniexpress12v1bcrlmm/meta.yaml b/recipes/bioconductor-humanomniexpress12v1bcrlmm/meta.yaml index d8c5b4dd12cd9..35920c1cba561 100644 --- a/recipes/bioconductor-humanomniexpress12v1bcrlmm/meta.yaml +++ b/recipes/bioconductor-humanomniexpress12v1bcrlmm/meta.yaml @@ -1,6 +1,6 @@ {% set version = "1.0.1" %} {% set name = "humanomniexpress12v1bCrlmm" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -12,7 +12,7 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' md5: abdb730fc230db669e588e024ee7624b build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ @@ -22,7 +22,7 @@ requirements: - r-base run: - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-humanomniexpress12v1bcrlmm/post-link.sh b/recipes/bioconductor-humanomniexpress12v1bcrlmm/post-link.sh index b232aec3bfa92..8a9decdd61371 100644 --- a/recipes/bioconductor-humanomniexpress12v1bcrlmm/post-link.sh +++ b/recipes/bioconductor-humanomniexpress12v1bcrlmm/post-link.sh @@ -1,9 +1,10 @@ #!/bin/bash FN="humanomniexpress12v1bCrlmm_1.0.1.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/humanomniexpress12v1bCrlmm_1.0.1.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/humanomniexpress12v1bCrlmm_1.0.1.tar.gz" "https://bioarchive.galaxyproject.org/humanomniexpress12v1bCrlmm_1.0.1.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-humanomniexpress12v1bcrlmm/bioconductor-humanomniexpress12v1bcrlmm_1.0.1_src_all.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-humanomniexpress12v1bcrlmm/bioconductor-humanomniexpress12v1bcrlmm_1.0.1_src_all.tar.gz" ) MD5="abdb730fc230db669e588e024ee7624b" @@ -16,7 +17,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-humanstemcell/meta.yaml b/recipes/bioconductor-humanstemcell/meta.yaml index 894f7e1532d08..1ae2875a122ef 100644 --- a/recipes/bioconductor-humanstemcell/meta.yaml +++ b/recipes/bioconductor-humanstemcell/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "0.22.0" %} +{% set version = "0.24.0" %} {% set name = "humanStemCell" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 9c51c8672331f6416b56f0224b5e7494 + md5: c4dd3efd3d8f2024250bf8f0f0610e1b build: number: 0 rpaths: @@ -19,14 +19,14 @@ build: noarch: generic requirements: host: - - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' - 'bioconductor-hgu133plus2.db >=3.2.0,<3.3.0' - r-base run: - - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' - 'bioconductor-hgu133plus2.db >=3.2.0,<3.3.0' - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-humanstemcell/post-link.sh b/recipes/bioconductor-humanstemcell/post-link.sh index c215c2bba704f..f601515bcddce 100644 --- a/recipes/bioconductor-humanstemcell/post-link.sh +++ b/recipes/bioconductor-humanstemcell/post-link.sh @@ -1,11 +1,11 @@ #!/bin/bash -FN="humanStemCell_0.22.0.tar.gz" +FN="humanStemCell_0.24.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/experiment/src/contrib/humanStemCell_0.22.0.tar.gz" - "https://bioarchive.galaxyproject.org/humanStemCell_0.22.0.tar.gz" - "https://depot.galaxyproject.org/software/bioconductor-humanstemcell/bioconductor-humanstemcell_0.22.0_src_all.tar.gz" + "https://bioconductor.org/packages/3.9/data/experiment/src/contrib/humanStemCell_0.24.0.tar.gz" + "https://bioarchive.galaxyproject.org/humanStemCell_0.24.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-humanstemcell/bioconductor-humanstemcell_0.24.0_src_all.tar.gz" ) -MD5="9c51c8672331f6416b56f0224b5e7494" +MD5="c4dd3efd3d8f2024250bf8f0f0610e1b" # Use a staging area in the conda dir rather than temp dirs, both to avoid # permission issues as well as to have things downloaded in a predictable @@ -16,7 +16,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-humantranscriptomecompendium/build.sh b/recipes/bioconductor-humantranscriptomecompendium/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-humantranscriptomecompendium/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-humantranscriptomecompendium/meta.yaml b/recipes/bioconductor-humantranscriptomecompendium/meta.yaml new file mode 100644 index 0000000000000..874626018a17e --- /dev/null +++ b/recipes/bioconductor-humantranscriptomecompendium/meta.yaml @@ -0,0 +1,41 @@ +{% set version = "1.0.0" %} +{% set name = "HumanTranscriptomeCompendium" %} +{% set bioc = "3.9" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: 57b35d328e6a5a859ef4f27552f98955 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: knitr, BiocStyle, beeswarm, tximportData, DT, tximport, dplyr, magrittr, BiocFileCache, testthat +requirements: + host: + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' + - 'bioconductor-ssrch >=1.0.0,<1.1.0' + - 'bioconductor-summarizedexperiment >=1.14.0,<1.15.0' + - r-base + - r-shiny + run: + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' + - 'bioconductor-ssrch >=1.0.0,<1.1.0' + - 'bioconductor-summarizedexperiment >=1.14.0,<1.15.0' + - r-base + - r-shiny +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'Provide tools for working with a compendium of human transcriptome sequences (originally htxcomp).' + diff --git a/recipes/bioconductor-huo22.db/meta.yaml b/recipes/bioconductor-huo22.db/meta.yaml index 85a08ebd8f0d6..d53d07a7a61f3 100644 --- a/recipes/bioconductor-huo22.db/meta.yaml +++ b/recipes/bioconductor-huo22.db/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.2.3" %} {% set name = "HuO22.db" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -12,7 +12,7 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' md5: ddabf6c01f94c1dfd6ab35b40852828a build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ @@ -20,14 +20,14 @@ build: # Suggests: DBI, annotate, RUnit requirements: host: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' - - 'bioconductor-org.hs.eg.db >=3.7.0,<3.8.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' + - 'bioconductor-org.hs.eg.db >=3.8.0,<3.9.0' - r-base run: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' - - 'bioconductor-org.hs.eg.db >=3.7.0,<3.8.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' + - 'bioconductor-org.hs.eg.db >=3.8.0,<3.9.0' - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-huo22.db/post-link.sh b/recipes/bioconductor-huo22.db/post-link.sh index 0db267ca18a94..a952bfd80ba55 100644 --- a/recipes/bioconductor-huo22.db/post-link.sh +++ b/recipes/bioconductor-huo22.db/post-link.sh @@ -1,9 +1,10 @@ #!/bin/bash FN="HuO22.db_3.2.3.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/HuO22.db_3.2.3.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/HuO22.db_3.2.3.tar.gz" "https://bioarchive.galaxyproject.org/HuO22.db_3.2.3.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-huo22.db/bioconductor-huo22.db_3.2.3_src_all.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-huo22.db/bioconductor-huo22.db_3.2.3_src_all.tar.gz" ) MD5="ddabf6c01f94c1dfd6ab35b40852828a" @@ -16,7 +17,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-hwgcod.db/meta.yaml b/recipes/bioconductor-hwgcod.db/meta.yaml index c26f4d9f8cf51..f771438e6eae0 100644 --- a/recipes/bioconductor-hwgcod.db/meta.yaml +++ b/recipes/bioconductor-hwgcod.db/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.4.0" %} {% set name = "hwgcod.db" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -12,7 +12,7 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: a46bf1a242853bbab26351a11b18030a build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ @@ -20,14 +20,14 @@ build: # Suggests: annotate, RUnit requirements: host: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' - - 'bioconductor-org.hs.eg.db >=3.7.0,<3.8.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' + - 'bioconductor-org.hs.eg.db >=3.8.0,<3.9.0' - r-base run: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' - - 'bioconductor-org.hs.eg.db >=3.7.0,<3.8.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' + - 'bioconductor-org.hs.eg.db >=3.8.0,<3.9.0' - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-hwgcod.db/post-link.sh b/recipes/bioconductor-hwgcod.db/post-link.sh index 4c399353cef52..a9a3fcbc82873 100644 --- a/recipes/bioconductor-hwgcod.db/post-link.sh +++ b/recipes/bioconductor-hwgcod.db/post-link.sh @@ -1,9 +1,10 @@ #!/bin/bash FN="hwgcod.db_3.4.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/hwgcod.db_3.4.0.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/hwgcod.db_3.4.0.tar.gz" "https://bioarchive.galaxyproject.org/hwgcod.db_3.4.0.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-hwgcod.db/bioconductor-hwgcod.db_3.4.0_src_all.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-hwgcod.db/bioconductor-hwgcod.db_3.4.0_src_all.tar.gz" ) MD5="a46bf1a242853bbab26351a11b18030a" @@ -16,7 +17,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-hybridmtest/meta.yaml b/recipes/bioconductor-hybridmtest/meta.yaml index 644a3b5662700..61ec349295fcc 100644 --- a/recipes/bioconductor-hybridmtest/meta.yaml +++ b/recipes/bioconductor-hybridmtest/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.26.0" %} +{% set version = "1.28.0" %} {% set name = "HybridMTest" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 37e8b32af15775b684fd95f27b08a29c + md5: 2adb9c6540ab27cedb4faa03e4583ac9 build: number: 0 rpaths: @@ -19,13 +19,13 @@ build: noarch: generic requirements: host: - - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' - r-base - r-fdrtool - r-mass - r-survival run: - - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' - r-base - r-fdrtool - r-mass diff --git a/recipes/bioconductor-hyper/build.sh b/recipes/bioconductor-hyper/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-hyper/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-hyper/meta.yaml b/recipes/bioconductor-hyper/meta.yaml new file mode 100644 index 0000000000000..7ed9cb14184e9 --- /dev/null +++ b/recipes/bioconductor-hyper/meta.yaml @@ -0,0 +1,45 @@ +{% set version = "1.00.0" %} +{% set name = "hypeR" %} +{% set bioc = "3.9" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: 4f570fff06ca8963acdc11a0b8a3650b +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: devtools, testthat, knitr, httr +requirements: + host: + - r-base + - r-dplyr + - r-dt + - r-magrittr + - r-msigdbr + - r-openxlsx + - r-plotly + run: + - r-base + - r-dplyr + - r-dt + - r-magrittr + - r-msigdbr + - r-openxlsx + - r-plotly +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: 'GPL-3 + file LICENSE' + summary: 'Geneset enrichment analysis based on hyper-geometric test.' + diff --git a/recipes/bioconductor-hyperdraw/meta.yaml b/recipes/bioconductor-hyperdraw/meta.yaml index 6afe94a0a5d56..365ff7d2eeeee 100644 --- a/recipes/bioconductor-hyperdraw/meta.yaml +++ b/recipes/bioconductor-hyperdraw/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.34.0" %} +{% set version = "1.36.0" %} {% set name = "hyperdraw" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 585067dc2db3c0ccf3d69733092811c8 + md5: bee18ff39dabc8070d4158ab8744d35e build: number: 0 rpaths: @@ -20,15 +20,17 @@ build: # SystemRequirements: graphviz requirements: host: - - 'bioconductor-graph >=1.60.0,<1.61.0' - - 'bioconductor-hypergraph >=1.54.0,<1.55.0' - - 'bioconductor-rgraphviz >=2.26.0,<2.27.0' + - 'bioconductor-graph >=1.62.0,<1.63.0' + - 'bioconductor-hypergraph >=1.56.0,<1.57.0' + - 'bioconductor-rgraphviz >=2.28.0,<2.29.0' - r-base + - graphviz run: - - 'bioconductor-graph >=1.60.0,<1.61.0' - - 'bioconductor-hypergraph >=1.54.0,<1.55.0' - - 'bioconductor-rgraphviz >=2.26.0,<2.27.0' + - 'bioconductor-graph >=1.62.0,<1.63.0' + - 'bioconductor-hypergraph >=1.56.0,<1.57.0' + - 'bioconductor-rgraphviz >=2.28.0,<2.29.0' - r-base + - graphviz test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-hypergraph/meta.yaml b/recipes/bioconductor-hypergraph/meta.yaml index bad3a341ab0c5..bd62b74e2234f 100644 --- a/recipes/bioconductor-hypergraph/meta.yaml +++ b/recipes/bioconductor-hypergraph/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.54.0" %} +{% set version = "1.56.0" %} {% set name = "hypergraph" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,9 +10,9 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: f26b3809c03897878b51a9f9e7fd11a1 + md5: 1be01b3c5187c8683d98db1d2562b3eb build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ @@ -20,10 +20,10 @@ build: # Suggests: BiocGenerics, RUnit requirements: host: - - 'bioconductor-graph >=1.60.0,<1.61.0' + - 'bioconductor-graph >=1.62.0,<1.63.0' - r-base run: - - 'bioconductor-graph >=1.60.0,<1.61.0' + - 'bioconductor-graph >=1.62.0,<1.63.0' - r-base test: commands: diff --git a/recipes/bioconductor-iaseq/meta.yaml b/recipes/bioconductor-iaseq/meta.yaml index 748bf51a2dac0..ac509318fd3ca 100644 --- a/recipes/bioconductor-iaseq/meta.yaml +++ b/recipes/bioconductor-iaseq/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.26.1" %} +{% set version = "1.28.0" %} {% set name = "iASeq" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 42f397bcc34329c812ef8d7c46cd774a + md5: c075e378b12b5200ad884c08a9350651 build: number: 0 rpaths: diff --git a/recipes/bioconductor-iasva/meta.yaml b/recipes/bioconductor-iasva/meta.yaml index 7ed350accb157..5af586a1fd975 100644 --- a/recipes/bioconductor-iasva/meta.yaml +++ b/recipes/bioconductor-iasva/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.0.0" %} +{% set version = "1.2.0" %} {% set name = "iasva" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 2e7572ca526ebf0b88442e25908ed305 + md5: 35ce6227d603e3cd72c02473af7e8a5b build: number: 0 rpaths: @@ -20,14 +20,14 @@ build: # Suggests: knitr, testthat, rmarkdown, sva, Rtsne, pheatmap, corrplot, DescTools, RColorBrewer requirements: host: - - 'bioconductor-biocparallel >=1.16.0,<1.17.0' - - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' + - 'bioconductor-biocparallel >=1.18.0,<1.19.0' + - 'bioconductor-summarizedexperiment >=1.14.0,<1.15.0' - r-base - r-cluster - r-irlba run: - - 'bioconductor-biocparallel >=1.16.0,<1.17.0' - - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' + - 'bioconductor-biocparallel >=1.18.0,<1.19.0' + - 'bioconductor-summarizedexperiment >=1.14.0,<1.15.0' - r-base - r-cluster - r-irlba diff --git a/recipes/bioconductor-ibbig/meta.yaml b/recipes/bioconductor-ibbig/meta.yaml index 13deb6e5be674..d3d3496a40711 100644 --- a/recipes/bioconductor-ibbig/meta.yaml +++ b/recipes/bioconductor-ibbig/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.26.0" %} +{% set version = "1.28.0" %} {% set name = "iBBiG" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: a8d9db691a24a412fd0e1bbbd10e635b + md5: a8c422a7147d66279038caa3afbd353b build: number: 0 rpaths: diff --git a/recipes/bioconductor-ibh/meta.yaml b/recipes/bioconductor-ibh/meta.yaml index 6c78dcd5fc07b..a105c7d3d5b4a 100644 --- a/recipes/bioconductor-ibh/meta.yaml +++ b/recipes/bioconductor-ibh/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.30.0" %} +{% set version = "1.32.0" %} {% set name = "ibh" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 2f9f043d554d46a1ce0146c3b59d556a + md5: d647de7adf78295460f5242db08080d6 build: number: 0 rpaths: @@ -20,10 +20,10 @@ build: # Suggests: yeastCC, stats requirements: host: - - 'bioconductor-simpintlists >=1.18.0,<1.19.0' + - 'bioconductor-simpintlists >=1.20.0,<1.21.0' - r-base run: - - 'bioconductor-simpintlists >=1.18.0,<1.19.0' + - 'bioconductor-simpintlists >=1.20.0,<1.21.0' - r-base test: commands: diff --git a/recipes/bioconductor-ibmq/meta.yaml b/recipes/bioconductor-ibmq/meta.yaml index 013a257a0062f..3631d527caff5 100644 --- a/recipes/bioconductor-ibmq/meta.yaml +++ b/recipes/bioconductor-ibmq/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.22.0" %} +{% set version = "1.24.0" %} {% set name = "iBMQ" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 18f8a0260516df35cf64a3dc6d8cf403 + md5: d578e07476692cef041d52c6e55c7a94 build: number: 0 rpaths: @@ -19,21 +19,21 @@ build: # SystemRequirements: GSL and OpenMP requirements: host: - - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' - r-base - 'r-ggplot2 >=0.9.2' - gsl run: - - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' - r-base - 'r-ggplot2 >=0.9.2' - gsl - llvm-openmp # [osx] build: - {{ compiler('c') }} + - llvm-openmp # [osx] - automake - make - - llvm-openmp # [osx] test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-icare/meta.yaml b/recipes/bioconductor-icare/meta.yaml index d25c1006cbe09..261f14101d6e2 100644 --- a/recipes/bioconductor-icare/meta.yaml +++ b/recipes/bioconductor-icare/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.10.3" %} +{% set version = "1.12.0" %} {% set name = "iCARE" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 1c0bd342ec42f95b64b8ffe717abac8b + md5: c919f4b68a344684f824fee6cc3cf899 build: number: 0 rpaths: diff --git a/recipes/bioconductor-icens/meta.yaml b/recipes/bioconductor-icens/meta.yaml index 6598ebcaab361..ef4fb50a73188 100644 --- a/recipes/bioconductor-icens/meta.yaml +++ b/recipes/bioconductor-icens/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.54.0" %} +{% set version = "1.56.0" %} {% set name = "Icens" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 6b85482eca0f13261be84bae8285c419 + md5: 5678e335cfd93285441e49987a9c6896 build: number: 0 rpaths: diff --git a/recipes/bioconductor-icetea/meta.yaml b/recipes/bioconductor-icetea/meta.yaml index 1fa24f86176f6..31501e9c7293f 100644 --- a/recipes/bioconductor-icetea/meta.yaml +++ b/recipes/bioconductor-icetea/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.0.0" %} +{% set version = "1.2.0" %} {% set name = "icetea" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 0c4660744294e5b10e06637c30e7962f + md5: 0e9cc78eaa1af347642bf79736f01f42 build: number: 0 rpaths: @@ -20,43 +20,45 @@ build: # Suggests: knitr, rmarkdown, Rsubread (>= 1.29.0), testthat requirements: host: - - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' - - 'bioconductor-biocparallel >=1.16.0,<1.17.0' - - 'bioconductor-biostrings >=2.50.0,<2.51.0' - - 'bioconductor-csaw >=1.16.0,<1.17.0' - - 'bioconductor-edger >=3.24.0,<3.25.0' - - 'bioconductor-genomicalignments >=1.18.0,<1.19.0' - - 'bioconductor-genomicfeatures >=1.34.0,<1.35.0' - - 'bioconductor-genomicranges >=1.34.0,<1.35.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-limma >=3.38.0,<3.39.0' - - 'bioconductor-rsamtools >=1.34.0,<1.35.0' - - 'bioconductor-rtracklayer >=1.42.0,<1.43.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' - - 'bioconductor-shortread >=1.40.0,<1.41.0' - - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' + - 'bioconductor-biocgenerics >=0.30.0,<0.31.0' + - 'bioconductor-biocparallel >=1.18.0,<1.19.0' + - 'bioconductor-biostrings >=2.52.0,<2.53.0' + - 'bioconductor-csaw >=1.18.0,<1.19.0' + - 'bioconductor-deseq2 >=1.24.0,<1.25.0' + - 'bioconductor-edger >=3.26.0,<3.27.0' + - 'bioconductor-genomicalignments >=1.20.0,<1.21.0' + - 'bioconductor-genomicfeatures >=1.36.0,<1.37.0' + - 'bioconductor-genomicranges >=1.36.0,<1.37.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-limma >=3.40.0,<3.41.0' + - 'bioconductor-rsamtools >=2.0.0,<2.1.0' + - 'bioconductor-rtracklayer >=1.44.0,<1.45.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' + - 'bioconductor-shortread >=1.42.0,<1.43.0' + - 'bioconductor-summarizedexperiment >=1.14.0,<1.15.0' - 'bioconductor-txdb.dmelanogaster.ucsc.dm6.ensgene >=3.4.0,<3.5.0' - - 'bioconductor-variantannotation >=1.28.0,<1.29.0' + - 'bioconductor-variantannotation >=1.30.0,<1.31.0' - r-base - r-ggplot2 run: - - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' - - 'bioconductor-biocparallel >=1.16.0,<1.17.0' - - 'bioconductor-biostrings >=2.50.0,<2.51.0' - - 'bioconductor-csaw >=1.16.0,<1.17.0' - - 'bioconductor-edger >=3.24.0,<3.25.0' - - 'bioconductor-genomicalignments >=1.18.0,<1.19.0' - - 'bioconductor-genomicfeatures >=1.34.0,<1.35.0' - - 'bioconductor-genomicranges >=1.34.0,<1.35.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-limma >=3.38.0,<3.39.0' - - 'bioconductor-rsamtools >=1.34.0,<1.35.0' - - 'bioconductor-rtracklayer >=1.42.0,<1.43.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' - - 'bioconductor-shortread >=1.40.0,<1.41.0' - - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' + - 'bioconductor-biocgenerics >=0.30.0,<0.31.0' + - 'bioconductor-biocparallel >=1.18.0,<1.19.0' + - 'bioconductor-biostrings >=2.52.0,<2.53.0' + - 'bioconductor-csaw >=1.18.0,<1.19.0' + - 'bioconductor-deseq2 >=1.24.0,<1.25.0' + - 'bioconductor-edger >=3.26.0,<3.27.0' + - 'bioconductor-genomicalignments >=1.20.0,<1.21.0' + - 'bioconductor-genomicfeatures >=1.36.0,<1.37.0' + - 'bioconductor-genomicranges >=1.36.0,<1.37.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-limma >=3.40.0,<3.41.0' + - 'bioconductor-rsamtools >=2.0.0,<2.1.0' + - 'bioconductor-rtracklayer >=1.44.0,<1.45.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' + - 'bioconductor-shortread >=1.42.0,<1.43.0' + - 'bioconductor-summarizedexperiment >=1.14.0,<1.15.0' - 'bioconductor-txdb.dmelanogaster.ucsc.dm6.ensgene >=3.4.0,<3.5.0' - - 'bioconductor-variantannotation >=1.28.0,<1.29.0' + - 'bioconductor-variantannotation >=1.30.0,<1.31.0' - r-base - r-ggplot2 test: diff --git a/recipes/bioconductor-icheck/meta.yaml b/recipes/bioconductor-icheck/meta.yaml index a47510000e3f0..ce16fb5d9cc14 100644 --- a/recipes/bioconductor-icheck/meta.yaml +++ b/recipes/bioconductor-icheck/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.12.0" %} +{% set version = "1.14.0" %} {% set name = "iCheck" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: e13b3395b8c803eb0f0f12b16ef9c9f8 + md5: 11e302f09eccac2f8ac6a5c774c9df7d build: number: 0 rpaths: @@ -19,12 +19,12 @@ build: noarch: generic requirements: host: - - 'bioconductor-affy >=1.60.0,<1.61.0' - - 'bioconductor-biobase >=2.42.0,<2.43.0' - - 'bioconductor-geneselectmmd >=2.26.0,<2.27.0' - - 'bioconductor-limma >=3.38.0,<3.39.0' - - 'bioconductor-lumi >=2.34.0,<2.35.0' - - 'bioconductor-preprocesscore >=1.44.0,<1.45.0' + - 'bioconductor-affy >=1.62.0,<1.63.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' + - 'bioconductor-geneselectmmd >=2.28.0,<2.29.0' + - 'bioconductor-limma >=3.40.0,<3.41.0' + - 'bioconductor-lumi >=2.36.0,<2.37.0' + - 'bioconductor-preprocesscore >=1.46.0,<1.47.0' - r-base - r-gplots - r-lmtest @@ -33,12 +33,12 @@ requirements: - r-rgl - r-scatterplot3d run: - - 'bioconductor-affy >=1.60.0,<1.61.0' - - 'bioconductor-biobase >=2.42.0,<2.43.0' - - 'bioconductor-geneselectmmd >=2.26.0,<2.27.0' - - 'bioconductor-limma >=3.38.0,<3.39.0' - - 'bioconductor-lumi >=2.34.0,<2.35.0' - - 'bioconductor-preprocesscore >=1.44.0,<1.45.0' + - 'bioconductor-affy >=1.62.0,<1.63.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' + - 'bioconductor-geneselectmmd >=2.28.0,<2.29.0' + - 'bioconductor-limma >=3.40.0,<3.41.0' + - 'bioconductor-lumi >=2.36.0,<2.37.0' + - 'bioconductor-preprocesscore >=1.46.0,<1.47.0' - r-base - r-gplots - r-lmtest @@ -46,17 +46,14 @@ requirements: - r-randomforest - r-rgl - r-scatterplot3d - test: commands: - '$R -e "library(''{{ name }}'')"' - about: home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: 'GPL (>= 2)' summary: 'QC pipeline and data analysis tools for high-dimensional Illumina mRNA expression data.' - extra: container: - # needed for libGL.so.1 - extended-base: true + extended-base: true + diff --git a/recipes/bioconductor-ichip/meta.yaml b/recipes/bioconductor-ichip/meta.yaml index dff1c5d3566b8..91a60f0afea4c 100644 --- a/recipes/bioconductor-ichip/meta.yaml +++ b/recipes/bioconductor-ichip/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.36.0" %} +{% set version = "1.38.0" %} {% set name = "iChip" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: db251b763a1f7693401bcb60141bef87 + md5: c9a7577c9aa5e5deeb81cc7d75c92158 build: number: 0 rpaths: @@ -18,10 +18,10 @@ build: - lib/ requirements: host: - - 'bioconductor-limma >=3.38.0,<3.39.0' + - 'bioconductor-limma >=3.40.0,<3.41.0' - r-base run: - - 'bioconductor-limma >=3.38.0,<3.39.0' + - 'bioconductor-limma >=3.40.0,<3.41.0' - r-base build: - {{ compiler('c') }} diff --git a/recipes/bioconductor-iclusterplus/meta.yaml b/recipes/bioconductor-iclusterplus/meta.yaml index 81acd6732ffb0..baf94ddcb7bda 100644 --- a/recipes/bioconductor-iclusterplus/meta.yaml +++ b/recipes/bioconductor-iclusterplus/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.18.0" %} +{% set version = "1.20.0" %} {% set name = "iClusterPlus" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 651bb943711a5b111ac411d248784f84 + md5: eaa03f67d33b21acc645d6da575e8cbc build: number: 0 rpaths: diff --git a/recipes/bioconductor-icnv/meta.yaml b/recipes/bioconductor-icnv/meta.yaml index d7350ce228bec..d65c8af0a70f6 100644 --- a/recipes/bioconductor-icnv/meta.yaml +++ b/recipes/bioconductor-icnv/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.2.1" %} +{% set version = "1.4.0" %} {% set name = "iCNV" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 8ac7190ed5a50ed053f107ea0a6d55e2 + md5: 6bcbd715cf66112e385017113c0053ce build: number: 0 rpaths: @@ -20,7 +20,7 @@ build: # Suggests: knitr, rmarkdown, WES.1KG.WUGSC requirements: host: - - 'bioconductor-codex >=1.14.0,<1.15.0' + - 'bioconductor-codex >=1.16.0,<1.17.0' - r-base - r-data.table - r-dplyr @@ -30,7 +30,7 @@ requirements: - r-tidyr - r-truncnorm run: - - 'bioconductor-codex >=1.14.0,<1.15.0' + - 'bioconductor-codex >=1.16.0,<1.17.0' - r-base - r-data.table - r-dplyr diff --git a/recipes/bioconductor-icobra/meta.yaml b/recipes/bioconductor-icobra/meta.yaml index f19558833aef2..7fee84fb0d3d9 100644 --- a/recipes/bioconductor-icobra/meta.yaml +++ b/recipes/bioconductor-icobra/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.10.0" %} +{% set version = "1.12.0" %} {% set name = "iCOBRA" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 144995f01f0fd56500c6d211ae072a31 + md5: ad14d6d8f8c46e9fc4ad287e2817fde0 build: number: 0 rpaths: @@ -20,7 +20,7 @@ build: # Suggests: knitr, testthat requirements: host: - - 'bioconductor-limma >=3.38.0,<3.39.0' + - 'bioconductor-limma >=3.40.0,<3.41.0' - r-base - r-dplyr - r-dt @@ -33,7 +33,7 @@ requirements: - r-shinydashboard - r-upsetr run: - - 'bioconductor-limma >=3.38.0,<3.39.0' + - 'bioconductor-limma >=3.40.0,<3.41.0' - r-base - r-dplyr - r-dt diff --git a/recipes/bioconductor-ideal/meta.yaml b/recipes/bioconductor-ideal/meta.yaml index 2f4aa8929b063..206ddb4f33d9e 100644 --- a/recipes/bioconductor-ideal/meta.yaml +++ b/recipes/bioconductor-ideal/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.6.0" %} +{% set version = "1.8.0" %} {% set name = "ideal" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 33ff8c3c3257c04588768124494540da + md5: 2b1e74e31daa2cf05ec42f4a92fefe6b build: number: 0 rpaths: @@ -20,25 +20,27 @@ build: # Suggests: testthat, BiocStyle, airway, org.Hs.eg.db, TxDb.Hsapiens.UCSC.hg38.knownGene, DEFormats, edgeR requirements: host: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' - - 'bioconductor-biocparallel >=1.16.0,<1.17.0' - - 'bioconductor-deseq2 >=1.22.0,<1.23.0' - - 'bioconductor-genomicranges >=1.34.0,<1.35.0' - - 'bioconductor-go.db >=3.7.0,<3.8.0' - - 'bioconductor-goseq >=1.34.0,<1.35.0' - - 'bioconductor-gostats >=2.48.0,<2.49.0' - - 'bioconductor-ihw >=1.10.0,<1.11.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-limma >=3.38.0,<3.39.0' - - 'bioconductor-pcaexplorer >=2.8.0,<2.9.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' - - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' - - 'bioconductor-topgo >=2.34.0,<2.35.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' + - 'bioconductor-biocparallel >=1.18.0,<1.19.0' + - 'bioconductor-deseq2 >=1.24.0,<1.25.0' + - 'bioconductor-genomicranges >=1.36.0,<1.37.0' + - 'bioconductor-go.db >=3.8.0,<3.9.0' + - 'bioconductor-goseq >=1.36.0,<1.37.0' + - 'bioconductor-gostats >=2.50.0,<2.51.0' + - 'bioconductor-ihw >=1.12.0,<1.13.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-limma >=3.40.0,<3.41.0' + - 'bioconductor-pcaexplorer >=2.10.0,<2.11.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' + - 'bioconductor-summarizedexperiment >=1.14.0,<1.15.0' + - 'bioconductor-topgo >=2.36.0,<2.37.0' - r-base + - r-base64enc - r-d3heatmap - r-dplyr - r-dt - 'r-ggplot2 >=2.0.0' + - r-ggrepel - r-gplots - r-knitr - r-pheatmap @@ -52,25 +54,27 @@ requirements: - r-stringr - r-upsetr run: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' - - 'bioconductor-biocparallel >=1.16.0,<1.17.0' - - 'bioconductor-deseq2 >=1.22.0,<1.23.0' - - 'bioconductor-genomicranges >=1.34.0,<1.35.0' - - 'bioconductor-go.db >=3.7.0,<3.8.0' - - 'bioconductor-goseq >=1.34.0,<1.35.0' - - 'bioconductor-gostats >=2.48.0,<2.49.0' - - 'bioconductor-ihw >=1.10.0,<1.11.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-limma >=3.38.0,<3.39.0' - - 'bioconductor-pcaexplorer >=2.8.0,<2.9.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' - - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' - - 'bioconductor-topgo >=2.34.0,<2.35.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' + - 'bioconductor-biocparallel >=1.18.0,<1.19.0' + - 'bioconductor-deseq2 >=1.24.0,<1.25.0' + - 'bioconductor-genomicranges >=1.36.0,<1.37.0' + - 'bioconductor-go.db >=3.8.0,<3.9.0' + - 'bioconductor-goseq >=1.36.0,<1.37.0' + - 'bioconductor-gostats >=2.50.0,<2.51.0' + - 'bioconductor-ihw >=1.12.0,<1.13.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-limma >=3.40.0,<3.41.0' + - 'bioconductor-pcaexplorer >=2.10.0,<2.11.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' + - 'bioconductor-summarizedexperiment >=1.14.0,<1.15.0' + - 'bioconductor-topgo >=2.36.0,<2.37.0' - r-base + - r-base64enc - r-d3heatmap - r-dplyr - r-dt - 'r-ggplot2 >=2.0.0' + - r-ggrepel - r-gplots - r-knitr - r-pheatmap diff --git a/recipes/bioconductor-ideoviz/meta.yaml b/recipes/bioconductor-ideoviz/meta.yaml index 20223a99ed3df..57a0772fe245c 100644 --- a/recipes/bioconductor-ideoviz/meta.yaml +++ b/recipes/bioconductor-ideoviz/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.18.0" %} +{% set version = "1.20.0" %} {% set name = "IdeoViz" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 9dc076de1e7d704ef8f359bc184c1b84 + md5: 34b57513cb86906e68de69fa85af6904 build: number: 0 rpaths: @@ -19,19 +19,19 @@ build: noarch: generic requirements: host: - - 'bioconductor-biobase >=2.42.0,<2.43.0' - - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' - - 'bioconductor-genomicranges >=1.34.0,<1.35.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-rtracklayer >=1.42.0,<1.43.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' + - 'bioconductor-genomeinfodb >=1.20.0,<1.21.0' + - 'bioconductor-genomicranges >=1.36.0,<1.37.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-rtracklayer >=1.44.0,<1.45.0' - r-base - r-rcolorbrewer run: - - 'bioconductor-biobase >=2.42.0,<2.43.0' - - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' - - 'bioconductor-genomicranges >=1.34.0,<1.35.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-rtracklayer >=1.42.0,<1.43.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' + - 'bioconductor-genomeinfodb >=1.20.0,<1.21.0' + - 'bioconductor-genomicranges >=1.36.0,<1.37.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-rtracklayer >=1.44.0,<1.45.0' - r-base - r-rcolorbrewer test: diff --git a/recipes/bioconductor-idiogram/meta.yaml b/recipes/bioconductor-idiogram/meta.yaml index bb3d221fe364d..42f57b18e41e8 100644 --- a/recipes/bioconductor-idiogram/meta.yaml +++ b/recipes/bioconductor-idiogram/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.58.0" %} +{% set version = "1.60.0" %} {% set name = "idiogram" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: d066bd7ee141691de135e4b6a5aebdda + md5: 2de17d1e45f463dc6fb1d54fde8b8520 build: number: 0 rpaths: @@ -20,13 +20,13 @@ build: # Suggests: hu6800.db, hgu95av2.db, golubEsets requirements: host: - - 'bioconductor-annotate >=1.60.0,<1.61.0' - - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-annotate >=1.62.0,<1.63.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' - r-base - r-plotrix run: - - 'bioconductor-annotate >=1.60.0,<1.61.0' - - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-annotate >=1.62.0,<1.63.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' - r-base - r-plotrix test: diff --git a/recipes/bioconductor-idmappinganalysis/meta.yaml b/recipes/bioconductor-idmappinganalysis/meta.yaml index 63b5a92f02c84..4efc3ca442f35 100644 --- a/recipes/bioconductor-idmappinganalysis/meta.yaml +++ b/recipes/bioconductor-idmappinganalysis/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.26.0" %} +{% set version = "1.28.0" %} {% set name = "IdMappingAnalysis" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 3c8890afd6e21106448dc0d3bc8b4d50 + md5: 86f495894ba88140d217d1a26c492171 build: number: 0 rpaths: @@ -19,7 +19,7 @@ build: noarch: generic requirements: host: - - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' - r-base - r-boot - r-mclust @@ -27,7 +27,7 @@ requirements: - r-rchoicedialogs - r-rcolorbrewer run: - - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' - r-base - r-boot - r-mclust diff --git a/recipes/bioconductor-idmappingretrieval/meta.yaml b/recipes/bioconductor-idmappingretrieval/meta.yaml index a72ebccf2f476..486ec4e339138 100644 --- a/recipes/bioconductor-idmappingretrieval/meta.yaml +++ b/recipes/bioconductor-idmappingretrieval/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.30.0" %} +{% set version = "1.32.0" %} {% set name = "IdMappingRetrieval" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 7da2fe9ac3cf79adc91f06e3a343cf86 + md5: 227712f71934cd713feb497ceacb2849 build: number: 0 rpaths: @@ -19,9 +19,9 @@ build: noarch: generic requirements: host: - - 'bioconductor-affycompatible >=1.42.0,<1.43.0' - - 'bioconductor-biomart >=2.38.0,<2.39.0' - - 'bioconductor-envisionquery >=1.30.0,<1.31.0' + - 'bioconductor-affycompatible >=1.44.0,<1.45.0' + - 'bioconductor-biomart >=2.40.0,<2.41.0' + - 'bioconductor-envisionquery >=1.32.0,<1.33.0' - r-base - r-r.methodss3 - r-r.oo @@ -29,9 +29,9 @@ requirements: - r-rcurl - r-xml run: - - 'bioconductor-affycompatible >=1.42.0,<1.43.0' - - 'bioconductor-biomart >=2.38.0,<2.39.0' - - 'bioconductor-envisionquery >=1.30.0,<1.31.0' + - 'bioconductor-affycompatible >=1.44.0,<1.45.0' + - 'bioconductor-biomart >=2.40.0,<2.41.0' + - 'bioconductor-envisionquery >=1.32.0,<1.33.0' - r-base - r-r.methodss3 - r-r.oo diff --git a/recipes/bioconductor-igc/meta.yaml b/recipes/bioconductor-igc/meta.yaml index 68c56a26cda44..d9c3407795842 100644 --- a/recipes/bioconductor-igc/meta.yaml +++ b/recipes/bioconductor-igc/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.12.0" %} +{% set version = "1.14.0" %} {% set name = "iGC" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 1914525e82325febd676e0700ec780e9 + md5: ec8a4c87e5d4db0f99530f45062fc34f build: number: 0 rpaths: diff --git a/recipes/bioconductor-igvr/meta.yaml b/recipes/bioconductor-igvr/meta.yaml index 9beb8b4aa0501..3d661d45b00bd 100644 --- a/recipes/bioconductor-igvr/meta.yaml +++ b/recipes/bioconductor-igvr/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.2.0" %} +{% set version = "1.4.0" %} {% set name = "igvR" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 9e2eac0566ea2b2810e66375f24c9917 + md5: 40f1f3d7da5dd3bde91bcf550d964bec build: number: 0 rpaths: @@ -20,19 +20,21 @@ build: # Suggests: RUnit, BiocStyle, knitr, rmarkdown requirements: host: - - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' - - 'bioconductor-browserviz >=2.4.0,<2.5.0' - - 'bioconductor-genomicranges >=1.34.0,<1.35.0' - - 'bioconductor-rtracklayer >=1.42.0,<1.43.0' - - 'bioconductor-variantannotation >=1.28.0,<1.29.0' + - 'bioconductor-biocgenerics >=0.30.0,<0.31.0' + - 'bioconductor-browserviz >=2.6.0,<2.7.0' + - 'bioconductor-genomicalignments >=1.20.0,<1.21.0' + - 'bioconductor-genomicranges >=1.36.0,<1.37.0' + - 'bioconductor-rtracklayer >=1.44.0,<1.45.0' + - 'bioconductor-variantannotation >=1.30.0,<1.31.0' - r-base - r-httpuv run: - - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' - - 'bioconductor-browserviz >=2.4.0,<2.5.0' - - 'bioconductor-genomicranges >=1.34.0,<1.35.0' - - 'bioconductor-rtracklayer >=1.42.0,<1.43.0' - - 'bioconductor-variantannotation >=1.28.0,<1.29.0' + - 'bioconductor-biocgenerics >=0.30.0,<0.31.0' + - 'bioconductor-browserviz >=2.6.0,<2.7.0' + - 'bioconductor-genomicalignments >=1.20.0,<1.21.0' + - 'bioconductor-genomicranges >=1.36.0,<1.37.0' + - 'bioconductor-rtracklayer >=1.44.0,<1.45.0' + - 'bioconductor-variantannotation >=1.30.0,<1.31.0' - r-base - r-httpuv test: diff --git a/recipes/bioconductor-ihw/meta.yaml b/recipes/bioconductor-ihw/meta.yaml index 31a60af43dd8f..190ff842d1eb8 100644 --- a/recipes/bioconductor-ihw/meta.yaml +++ b/recipes/bioconductor-ihw/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.10.1" %} +{% set version = "1.12.0" %} {% set name = "IHW" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: 36052906fa56082a6cf181f36e8a99d56b23bbc87d4cb571f1438a89a8569883 + md5: 6a4b581a105d27072db9cb26a332de6e build: number: 0 rpaths: @@ -20,14 +20,14 @@ build: # Suggests: ggplot2, dplyr, gridExtra, scales, DESeq2, airway, testthat, Matrix, BiocStyle, knitr, rmarkdown, devtools requirements: host: - - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' - - 'bioconductor-lpsymphony >=1.10.0,<1.11.0' + - 'bioconductor-biocgenerics >=0.30.0,<0.31.0' + - 'bioconductor-lpsymphony >=1.12.0,<1.13.0' - r-base - r-fdrtool - r-slam run: - - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' - - 'bioconductor-lpsymphony >=1.10.0,<1.11.0' + - 'bioconductor-biocgenerics >=0.30.0,<0.31.0' + - 'bioconductor-lpsymphony >=1.12.0,<1.13.0' - r-base - r-fdrtool - r-slam diff --git a/recipes/bioconductor-ihwpaper/meta.yaml b/recipes/bioconductor-ihwpaper/meta.yaml index 487797b375f0b..dc269791ce630 100644 --- a/recipes/bioconductor-ihwpaper/meta.yaml +++ b/recipes/bioconductor-ihwpaper/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.10.0" %} +{% set version = "1.12.0" %} {% set name = "IHWpaper" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 941b62cdbd35bd8c0327712b47963bf2 + md5: e697c090241b0d3437827f2f375a4fcf build: number: 0 rpaths: @@ -19,14 +19,14 @@ build: # Suggests: testthat, RColorBrewer, wesanderson, scales, gridExtra, BiocStyle, knitr, rmarkdown, airway, pasilla, DESeq, locfdr, tidyr, ggbio, latex2exp requirements: host: - - 'bioconductor-biobase >=2.42.0,<2.43.0' - - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' - - 'bioconductor-biocparallel >=1.16.0,<1.17.0' - - 'bioconductor-deseq2 >=1.22.0,<1.23.0' - - 'bioconductor-genefilter >=1.64.0,<1.65.0' - - 'bioconductor-ihw >=1.10.0,<1.11.0' - - 'bioconductor-qvalue >=2.14.0,<2.15.0' - - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' + - 'bioconductor-biocgenerics >=0.30.0,<0.31.0' + - 'bioconductor-biocparallel >=1.18.0,<1.19.0' + - 'bioconductor-deseq2 >=1.24.0,<1.25.0' + - 'bioconductor-genefilter >=1.66.0,<1.67.0' + - 'bioconductor-ihw >=1.12.0,<1.13.0' + - 'bioconductor-qvalue >=2.16.0,<2.17.0' + - 'bioconductor-summarizedexperiment >=1.14.0,<1.15.0' - r-base - r-cowplot - r-dplyr @@ -34,21 +34,21 @@ requirements: - r-ggplot2 - r-rcpp run: - - 'bioconductor-biobase >=2.42.0,<2.43.0' - - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' - - 'bioconductor-biocparallel >=1.16.0,<1.17.0' - - 'bioconductor-deseq2 >=1.22.0,<1.23.0' - - 'bioconductor-genefilter >=1.64.0,<1.65.0' - - 'bioconductor-ihw >=1.10.0,<1.11.0' - - 'bioconductor-qvalue >=2.14.0,<2.15.0' - - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' + - 'bioconductor-biocgenerics >=0.30.0,<0.31.0' + - 'bioconductor-biocparallel >=1.18.0,<1.19.0' + - 'bioconductor-deseq2 >=1.24.0,<1.25.0' + - 'bioconductor-genefilter >=1.66.0,<1.67.0' + - 'bioconductor-ihw >=1.12.0,<1.13.0' + - 'bioconductor-qvalue >=2.16.0,<2.17.0' + - 'bioconductor-summarizedexperiment >=1.14.0,<1.15.0' - r-base - r-cowplot - r-dplyr - r-fdrtool - r-ggplot2 - r-rcpp - - wget + - curl build: - {{ compiler('c') }} - {{ compiler('cxx') }} diff --git a/recipes/bioconductor-ihwpaper/post-link.sh b/recipes/bioconductor-ihwpaper/post-link.sh index 94a844f1b8312..ac06a6452315b 100644 --- a/recipes/bioconductor-ihwpaper/post-link.sh +++ b/recipes/bioconductor-ihwpaper/post-link.sh @@ -1,11 +1,11 @@ #!/bin/bash -FN="IHWpaper_1.10.0.tar.gz" +FN="IHWpaper_1.12.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/experiment/src/contrib/IHWpaper_1.10.0.tar.gz" - "https://bioarchive.galaxyproject.org/IHWpaper_1.10.0.tar.gz" - "https://depot.galaxyproject.org/software/bioconductor-ihwpaper/bioconductor-ihwpaper_1.10.0_src_all.tar.gz" + "https://bioconductor.org/packages/3.9/data/experiment/src/contrib/IHWpaper_1.12.0.tar.gz" + "https://bioarchive.galaxyproject.org/IHWpaper_1.12.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-ihwpaper/bioconductor-ihwpaper_1.12.0_src_all.tar.gz" ) -MD5="941b62cdbd35bd8c0327712b47963bf2" +MD5="e697c090241b0d3437827f2f375a4fcf" # Use a staging area in the conda dir rather than temp dirs, both to avoid # permission issues as well as to have things downloaded in a predictable @@ -16,7 +16,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-illumina450probevariants.db/meta.yaml b/recipes/bioconductor-illumina450probevariants.db/meta.yaml index b0048d21320b8..72368825bf810 100644 --- a/recipes/bioconductor-illumina450probevariants.db/meta.yaml +++ b/recipes/bioconductor-illumina450probevariants.db/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.18.0" %} +{% set version = "1.20.0" %} {% set name = "Illumina450ProbeVariants.db" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: f1a96cc966c6de6c687ad024efdc6551 + md5: 248d5c2f16cab95dafd3af53acd1b05f build: number: 0 rpaths: @@ -22,7 +22,7 @@ requirements: - r-base run: - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-illumina450probevariants.db/post-link.sh b/recipes/bioconductor-illumina450probevariants.db/post-link.sh index 78a598fb80dd8..40b1eaa78f90d 100644 --- a/recipes/bioconductor-illumina450probevariants.db/post-link.sh +++ b/recipes/bioconductor-illumina450probevariants.db/post-link.sh @@ -1,11 +1,11 @@ #!/bin/bash -FN="Illumina450ProbeVariants.db_1.18.0.tar.gz" +FN="Illumina450ProbeVariants.db_1.20.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/experiment/src/contrib/Illumina450ProbeVariants.db_1.18.0.tar.gz" - "https://bioarchive.galaxyproject.org/Illumina450ProbeVariants.db_1.18.0.tar.gz" - "https://depot.galaxyproject.org/software/bioconductor-illumina450probevariants.db/bioconductor-illumina450probevariants.db_1.18.0_src_all.tar.gz" + "https://bioconductor.org/packages/3.9/data/experiment/src/contrib/Illumina450ProbeVariants.db_1.20.0.tar.gz" + "https://bioarchive.galaxyproject.org/Illumina450ProbeVariants.db_1.20.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-illumina450probevariants.db/bioconductor-illumina450probevariants.db_1.20.0_src_all.tar.gz" ) -MD5="f1a96cc966c6de6c687ad024efdc6551" +MD5="248d5c2f16cab95dafd3af53acd1b05f" # Use a staging area in the conda dir rather than temp dirs, both to avoid # permission issues as well as to have things downloaded in a predictable @@ -16,7 +16,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-illuminadatatestfiles/meta.yaml b/recipes/bioconductor-illuminadatatestfiles/meta.yaml index 2bfc13b3beb1e..f4d079ae0708a 100644 --- a/recipes/bioconductor-illuminadatatestfiles/meta.yaml +++ b/recipes/bioconductor-illuminadatatestfiles/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.20.0" %} +{% set version = "1.22.0" %} {% set name = "IlluminaDataTestFiles" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 4038cc1acc8bcd01c8b18d1de6ff1ffd + md5: 546621b97e6be804d7e9db2262d4469e build: number: 0 rpaths: @@ -22,7 +22,7 @@ requirements: - r-base run: - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-illuminadatatestfiles/post-link.sh b/recipes/bioconductor-illuminadatatestfiles/post-link.sh index 8b88a3f1d1a79..261c188646bfe 100644 --- a/recipes/bioconductor-illuminadatatestfiles/post-link.sh +++ b/recipes/bioconductor-illuminadatatestfiles/post-link.sh @@ -1,11 +1,11 @@ #!/bin/bash -FN="IlluminaDataTestFiles_1.20.0.tar.gz" +FN="IlluminaDataTestFiles_1.22.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/experiment/src/contrib/IlluminaDataTestFiles_1.20.0.tar.gz" - "https://bioarchive.galaxyproject.org/IlluminaDataTestFiles_1.20.0.tar.gz" - "https://depot.galaxyproject.org/software/bioconductor-illuminadatatestfiles/bioconductor-illuminadatatestfiles_1.20.0_src_all.tar.gz" + "https://bioconductor.org/packages/3.9/data/experiment/src/contrib/IlluminaDataTestFiles_1.22.0.tar.gz" + "https://bioarchive.galaxyproject.org/IlluminaDataTestFiles_1.22.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-illuminadatatestfiles/bioconductor-illuminadatatestfiles_1.22.0_src_all.tar.gz" ) -MD5="4038cc1acc8bcd01c8b18d1de6ff1ffd" +MD5="546621b97e6be804d7e9db2262d4469e" # Use a staging area in the conda dir rather than temp dirs, both to avoid # permission issues as well as to have things downloaded in a predictable @@ -16,7 +16,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-illuminahumanmethylation27k.db/meta.yaml b/recipes/bioconductor-illuminahumanmethylation27k.db/meta.yaml index 482eb31d6aa8c..d170132ea9b6b 100644 --- a/recipes/bioconductor-illuminahumanmethylation27k.db/meta.yaml +++ b/recipes/bioconductor-illuminahumanmethylation27k.db/meta.yaml @@ -1,6 +1,6 @@ {% set version = "1.4.8" %} {% set name = "IlluminaHumanMethylation27k.db" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -12,7 +12,7 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' md5: 70586bda9db01d598723bb439c315367 build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ @@ -20,14 +20,14 @@ build: # Suggests: annotate requirements: host: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' - - 'bioconductor-org.hs.eg.db >=3.7.0,<3.8.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' + - 'bioconductor-org.hs.eg.db >=3.8.0,<3.9.0' - r-base run: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' - - 'bioconductor-org.hs.eg.db >=3.7.0,<3.8.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' + - 'bioconductor-org.hs.eg.db >=3.8.0,<3.9.0' - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-illuminahumanmethylation27k.db/post-link.sh b/recipes/bioconductor-illuminahumanmethylation27k.db/post-link.sh index f77b2518f7dc3..c77a26debcb44 100644 --- a/recipes/bioconductor-illuminahumanmethylation27k.db/post-link.sh +++ b/recipes/bioconductor-illuminahumanmethylation27k.db/post-link.sh @@ -1,9 +1,10 @@ #!/bin/bash FN="IlluminaHumanMethylation27k.db_1.4.8.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/IlluminaHumanMethylation27k.db_1.4.8.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/IlluminaHumanMethylation27k.db_1.4.8.tar.gz" "https://bioarchive.galaxyproject.org/IlluminaHumanMethylation27k.db_1.4.8.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-illuminahumanmethylation27k.db/bioconductor-illuminahumanmethylation27k.db_1.4.8_src_all.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-illuminahumanmethylation27k.db/bioconductor-illuminahumanmethylation27k.db_1.4.8_src_all.tar.gz" ) MD5="70586bda9db01d598723bb439c315367" @@ -16,7 +17,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-illuminahumanmethylation27kanno.ilmn12.hg19/meta.yaml b/recipes/bioconductor-illuminahumanmethylation27kanno.ilmn12.hg19/meta.yaml index 383e5030151d9..5bf6d59262eaf 100644 --- a/recipes/bioconductor-illuminahumanmethylation27kanno.ilmn12.hg19/meta.yaml +++ b/recipes/bioconductor-illuminahumanmethylation27kanno.ilmn12.hg19/meta.yaml @@ -1,6 +1,6 @@ {% set version = "0.6.0" %} {% set name = "IlluminaHumanMethylation27kanno.ilmn12.hg19" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -12,19 +12,19 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' md5: 765851336506120467c2e3cc6beef7ed build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ noarch: generic requirements: host: - - 'bioconductor-minfi >=1.28.0,<1.29.0' + - 'bioconductor-minfi >=1.30.0,<1.31.0' - r-base run: - - 'bioconductor-minfi >=1.28.0,<1.29.0' + - 'bioconductor-minfi >=1.30.0,<1.31.0' - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-illuminahumanmethylation27kanno.ilmn12.hg19/post-link.sh b/recipes/bioconductor-illuminahumanmethylation27kanno.ilmn12.hg19/post-link.sh index 7fab5c103af01..e8b33cf2c7b25 100644 --- a/recipes/bioconductor-illuminahumanmethylation27kanno.ilmn12.hg19/post-link.sh +++ b/recipes/bioconductor-illuminahumanmethylation27kanno.ilmn12.hg19/post-link.sh @@ -1,9 +1,10 @@ #!/bin/bash FN="IlluminaHumanMethylation27kanno.ilmn12.hg19_0.6.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/IlluminaHumanMethylation27kanno.ilmn12.hg19_0.6.0.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/IlluminaHumanMethylation27kanno.ilmn12.hg19_0.6.0.tar.gz" "https://bioarchive.galaxyproject.org/IlluminaHumanMethylation27kanno.ilmn12.hg19_0.6.0.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-illuminahumanmethylation27kanno.ilmn12.hg19/bioconductor-illuminahumanmethylation27kanno.ilmn12.hg19_0.6.0_src_all.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-illuminahumanmethylation27kanno.ilmn12.hg19/bioconductor-illuminahumanmethylation27kanno.ilmn12.hg19_0.6.0_src_all.tar.gz" ) MD5="765851336506120467c2e3cc6beef7ed" @@ -16,7 +17,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-illuminahumanmethylation27kmanifest/meta.yaml b/recipes/bioconductor-illuminahumanmethylation27kmanifest/meta.yaml index 81c8a4e138fbb..dbc5b18dd179c 100644 --- a/recipes/bioconductor-illuminahumanmethylation27kmanifest/meta.yaml +++ b/recipes/bioconductor-illuminahumanmethylation27kmanifest/meta.yaml @@ -1,6 +1,6 @@ {% set version = "0.4.0" %} {% set name = "IlluminaHumanMethylation27kmanifest" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -12,19 +12,19 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' md5: c4cdda637dccf85f193342c7262b02a6 build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ noarch: generic requirements: host: - - 'bioconductor-minfi >=1.28.0,<1.29.0' + - 'bioconductor-minfi >=1.30.0,<1.31.0' - r-base run: - - 'bioconductor-minfi >=1.28.0,<1.29.0' + - 'bioconductor-minfi >=1.30.0,<1.31.0' - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-illuminahumanmethylation27kmanifest/post-link.sh b/recipes/bioconductor-illuminahumanmethylation27kmanifest/post-link.sh index 8448c496ed3f5..aa89f9a900314 100644 --- a/recipes/bioconductor-illuminahumanmethylation27kmanifest/post-link.sh +++ b/recipes/bioconductor-illuminahumanmethylation27kmanifest/post-link.sh @@ -1,9 +1,10 @@ #!/bin/bash FN="IlluminaHumanMethylation27kmanifest_0.4.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/IlluminaHumanMethylation27kmanifest_0.4.0.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/IlluminaHumanMethylation27kmanifest_0.4.0.tar.gz" "https://bioarchive.galaxyproject.org/IlluminaHumanMethylation27kmanifest_0.4.0.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-illuminahumanmethylation27kmanifest/bioconductor-illuminahumanmethylation27kmanifest_0.4.0_src_all.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-illuminahumanmethylation27kmanifest/bioconductor-illuminahumanmethylation27kmanifest_0.4.0_src_all.tar.gz" ) MD5="c4cdda637dccf85f193342c7262b02a6" @@ -16,7 +17,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-illuminahumanmethylation450kanno.ilmn12.hg19/meta.yaml b/recipes/bioconductor-illuminahumanmethylation450kanno.ilmn12.hg19/meta.yaml index b4fcfb7a86d04..151abc70a7b13 100644 --- a/recipes/bioconductor-illuminahumanmethylation450kanno.ilmn12.hg19/meta.yaml +++ b/recipes/bioconductor-illuminahumanmethylation450kanno.ilmn12.hg19/meta.yaml @@ -1,6 +1,6 @@ {% set version = "0.6.0" %} {% set name = "IlluminaHumanMethylation450kanno.ilmn12.hg19" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -12,19 +12,19 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' md5: 2f569646ca8adc49863224b1cd076a79 build: - number: 5 + number: 6 rpaths: - lib/R/lib/ - lib/ noarch: generic requirements: host: - - 'bioconductor-minfi >=1.28.0,<1.29.0' + - 'bioconductor-minfi >=1.30.0,<1.31.0' - r-base run: - - 'bioconductor-minfi >=1.28.0,<1.29.0' + - 'bioconductor-minfi >=1.30.0,<1.31.0' - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-illuminahumanmethylation450kanno.ilmn12.hg19/post-link.sh b/recipes/bioconductor-illuminahumanmethylation450kanno.ilmn12.hg19/post-link.sh index 1e55d9061ba88..ce076b7b81c3a 100644 --- a/recipes/bioconductor-illuminahumanmethylation450kanno.ilmn12.hg19/post-link.sh +++ b/recipes/bioconductor-illuminahumanmethylation450kanno.ilmn12.hg19/post-link.sh @@ -1,7 +1,7 @@ #!/bin/bash FN="IlluminaHumanMethylation450kanno.ilmn12.hg19_0.6.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/IlluminaHumanMethylation450kanno.ilmn12.hg19_0.6.0.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/IlluminaHumanMethylation450kanno.ilmn12.hg19_0.6.0.tar.gz" "https://bioarchive.galaxyproject.org/IlluminaHumanMethylation450kanno.ilmn12.hg19_0.6.0.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-illuminahumanmethylation450kanno.ilmn12.hg19/bioconductor-illuminahumanmethylation450kanno.ilmn12.hg19_0.6.0_src_all.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-illuminahumanmethylation450kanno.ilmn12.hg19/bioconductor-illuminahumanmethylation450kanno.ilmn12.hg19_0.6.0_src_all.tar.gz" @@ -17,7 +17,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-illuminahumanmethylation450kmanifest/meta.yaml b/recipes/bioconductor-illuminahumanmethylation450kmanifest/meta.yaml index 09eeb4dbba1fd..78628288dccae 100644 --- a/recipes/bioconductor-illuminahumanmethylation450kmanifest/meta.yaml +++ b/recipes/bioconductor-illuminahumanmethylation450kmanifest/meta.yaml @@ -1,6 +1,6 @@ {% set version = "0.4.0" %} {% set name = "IlluminaHumanMethylation450kmanifest" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -12,19 +12,19 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' md5: 664d1f5a3892974334faa26757269509 build: - number: 4 + number: 5 rpaths: - lib/R/lib/ - lib/ noarch: generic requirements: host: - - 'bioconductor-minfi >=1.28.0,<1.29.0' + - 'bioconductor-minfi >=1.30.0,<1.31.0' - r-base run: - - 'bioconductor-minfi >=1.28.0,<1.29.0' + - 'bioconductor-minfi >=1.30.0,<1.31.0' - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-illuminahumanmethylation450kmanifest/post-link.sh b/recipes/bioconductor-illuminahumanmethylation450kmanifest/post-link.sh index b5cff1b1e535d..98fdf76a8b4df 100644 --- a/recipes/bioconductor-illuminahumanmethylation450kmanifest/post-link.sh +++ b/recipes/bioconductor-illuminahumanmethylation450kmanifest/post-link.sh @@ -1,7 +1,7 @@ #!/bin/bash FN="IlluminaHumanMethylation450kmanifest_0.4.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/IlluminaHumanMethylation450kmanifest_0.4.0.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/IlluminaHumanMethylation450kmanifest_0.4.0.tar.gz" "https://bioarchive.galaxyproject.org/IlluminaHumanMethylation450kmanifest_0.4.0.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-illuminahumanmethylation450kmanifest/bioconductor-illuminahumanmethylation450kmanifest_0.4.0_src_all.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-illuminahumanmethylation450kmanifest/bioconductor-illuminahumanmethylation450kmanifest_0.4.0_src_all.tar.gz" @@ -17,7 +17,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-illuminahumanmethylation450kprobe/meta.yaml b/recipes/bioconductor-illuminahumanmethylation450kprobe/meta.yaml index ffc364ef5f939..9e8dd47bad330 100644 --- a/recipes/bioconductor-illuminahumanmethylation450kprobe/meta.yaml +++ b/recipes/bioconductor-illuminahumanmethylation450kprobe/meta.yaml @@ -1,6 +1,6 @@ {% set version = "2.0.6" %} {% set name = "IlluminaHumanMethylation450kprobe" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -12,19 +12,19 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' md5: 84c31861fcbaddbf2a9c500b8d8d767d build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' - r-base run: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-illuminahumanmethylation450kprobe/post-link.sh b/recipes/bioconductor-illuminahumanmethylation450kprobe/post-link.sh index 92c4d47a92126..f29be6169a909 100644 --- a/recipes/bioconductor-illuminahumanmethylation450kprobe/post-link.sh +++ b/recipes/bioconductor-illuminahumanmethylation450kprobe/post-link.sh @@ -1,9 +1,10 @@ #!/bin/bash FN="IlluminaHumanMethylation450kprobe_2.0.6.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/IlluminaHumanMethylation450kprobe_2.0.6.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/IlluminaHumanMethylation450kprobe_2.0.6.tar.gz" "https://bioarchive.galaxyproject.org/IlluminaHumanMethylation450kprobe_2.0.6.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-illuminahumanmethylation450kprobe/bioconductor-illuminahumanmethylation450kprobe_2.0.6_src_all.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-illuminahumanmethylation450kprobe/bioconductor-illuminahumanmethylation450kprobe_2.0.6_src_all.tar.gz" ) MD5="84c31861fcbaddbf2a9c500b8d8d767d" @@ -16,7 +17,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-illuminahumanmethylationepicanno.ilm10b2.hg19/meta.yaml b/recipes/bioconductor-illuminahumanmethylationepicanno.ilm10b2.hg19/meta.yaml index 60d058c48725b..ac01bfbe8f117 100644 --- a/recipes/bioconductor-illuminahumanmethylationepicanno.ilm10b2.hg19/meta.yaml +++ b/recipes/bioconductor-illuminahumanmethylationepicanno.ilm10b2.hg19/meta.yaml @@ -1,6 +1,6 @@ {% set version = "0.6.0" %} {% set name = "IlluminaHumanMethylationEPICanno.ilm10b2.hg19" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -12,19 +12,19 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' md5: 6a8e2398a0f930aa7828a1412fb21e88 build: - number: 3 + number: 4 rpaths: - lib/R/lib/ - lib/ noarch: generic requirements: host: - - 'bioconductor-minfi >=1.28.0,<1.29.0' + - 'bioconductor-minfi >=1.30.0,<1.31.0' - r-base run: - - 'bioconductor-minfi >=1.28.0,<1.29.0' + - 'bioconductor-minfi >=1.30.0,<1.31.0' - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-illuminahumanmethylationepicanno.ilm10b2.hg19/post-link.sh b/recipes/bioconductor-illuminahumanmethylationepicanno.ilm10b2.hg19/post-link.sh index 66a13f17b4b27..54fe5e8b3b041 100644 --- a/recipes/bioconductor-illuminahumanmethylationepicanno.ilm10b2.hg19/post-link.sh +++ b/recipes/bioconductor-illuminahumanmethylationepicanno.ilm10b2.hg19/post-link.sh @@ -1,7 +1,7 @@ #!/bin/bash FN="IlluminaHumanMethylationEPICanno.ilm10b2.hg19_0.6.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/IlluminaHumanMethylationEPICanno.ilm10b2.hg19_0.6.0.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/IlluminaHumanMethylationEPICanno.ilm10b2.hg19_0.6.0.tar.gz" "https://bioarchive.galaxyproject.org/IlluminaHumanMethylationEPICanno.ilm10b2.hg19_0.6.0.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-illuminahumanmethylationepicanno.ilm10b2.hg19/bioconductor-illuminahumanmethylationepicanno.ilm10b2.hg19_0.6.0_src_all.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-illuminahumanmethylationepicanno.ilm10b2.hg19/bioconductor-illuminahumanmethylationepicanno.ilm10b2.hg19_0.6.0_src_all.tar.gz" @@ -17,7 +17,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-illuminahumanmethylationepicanno.ilm10b3.hg19/meta.yaml b/recipes/bioconductor-illuminahumanmethylationepicanno.ilm10b3.hg19/meta.yaml index 6ec157eac18aa..7ef4aeff18c33 100644 --- a/recipes/bioconductor-illuminahumanmethylationepicanno.ilm10b3.hg19/meta.yaml +++ b/recipes/bioconductor-illuminahumanmethylationepicanno.ilm10b3.hg19/meta.yaml @@ -1,6 +1,6 @@ {% set version = "0.6.0" %} {% set name = "IlluminaHumanMethylationEPICanno.ilm10b3.hg19" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -12,19 +12,19 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' md5: 2dac8e889486386eaea1bb7ce1beea2e build: - number: 3 + number: 4 rpaths: - lib/R/lib/ - lib/ noarch: generic requirements: host: - - 'bioconductor-minfi >=1.28.0,<1.29.0' + - 'bioconductor-minfi >=1.30.0,<1.31.0' - r-base run: - - 'bioconductor-minfi >=1.28.0,<1.29.0' + - 'bioconductor-minfi >=1.30.0,<1.31.0' - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-illuminahumanmethylationepicanno.ilm10b3.hg19/post-link.sh b/recipes/bioconductor-illuminahumanmethylationepicanno.ilm10b3.hg19/post-link.sh index aadbcfde1e02a..1ce96cd3d747e 100644 --- a/recipes/bioconductor-illuminahumanmethylationepicanno.ilm10b3.hg19/post-link.sh +++ b/recipes/bioconductor-illuminahumanmethylationepicanno.ilm10b3.hg19/post-link.sh @@ -1,7 +1,7 @@ #!/bin/bash FN="IlluminaHumanMethylationEPICanno.ilm10b3.hg19_0.6.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/IlluminaHumanMethylationEPICanno.ilm10b3.hg19_0.6.0.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/IlluminaHumanMethylationEPICanno.ilm10b3.hg19_0.6.0.tar.gz" "https://bioarchive.galaxyproject.org/IlluminaHumanMethylationEPICanno.ilm10b3.hg19_0.6.0.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-illuminahumanmethylationepicanno.ilm10b3.hg19/bioconductor-illuminahumanmethylationepicanno.ilm10b3.hg19_0.6.0_src_all.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-illuminahumanmethylationepicanno.ilm10b3.hg19/bioconductor-illuminahumanmethylationepicanno.ilm10b3.hg19_0.6.0_src_all.tar.gz" @@ -17,7 +17,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-illuminahumanmethylationepicanno.ilm10b4.hg19/meta.yaml b/recipes/bioconductor-illuminahumanmethylationepicanno.ilm10b4.hg19/meta.yaml index cfcd41c62696d..0424f42f968a3 100644 --- a/recipes/bioconductor-illuminahumanmethylationepicanno.ilm10b4.hg19/meta.yaml +++ b/recipes/bioconductor-illuminahumanmethylationepicanno.ilm10b4.hg19/meta.yaml @@ -1,6 +1,6 @@ {% set version = "0.6.0" %} {% set name = "IlluminaHumanMethylationEPICanno.ilm10b4.hg19" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -12,19 +12,19 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' md5: 2d0c05917bcbf9ba1e354380d4e17a77 build: - number: 3 + number: 4 rpaths: - lib/R/lib/ - lib/ noarch: generic requirements: host: - - 'bioconductor-minfi >=1.28.0,<1.29.0' + - 'bioconductor-minfi >=1.30.0,<1.31.0' - r-base run: - - 'bioconductor-minfi >=1.28.0,<1.29.0' + - 'bioconductor-minfi >=1.30.0,<1.31.0' - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-illuminahumanmethylationepicanno.ilm10b4.hg19/post-link.sh b/recipes/bioconductor-illuminahumanmethylationepicanno.ilm10b4.hg19/post-link.sh index d105dc46d6d84..9a3ad126e142b 100644 --- a/recipes/bioconductor-illuminahumanmethylationepicanno.ilm10b4.hg19/post-link.sh +++ b/recipes/bioconductor-illuminahumanmethylationepicanno.ilm10b4.hg19/post-link.sh @@ -1,7 +1,7 @@ #!/bin/bash FN="IlluminaHumanMethylationEPICanno.ilm10b4.hg19_0.6.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/IlluminaHumanMethylationEPICanno.ilm10b4.hg19_0.6.0.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/IlluminaHumanMethylationEPICanno.ilm10b4.hg19_0.6.0.tar.gz" "https://bioarchive.galaxyproject.org/IlluminaHumanMethylationEPICanno.ilm10b4.hg19_0.6.0.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-illuminahumanmethylationepicanno.ilm10b4.hg19/bioconductor-illuminahumanmethylationepicanno.ilm10b4.hg19_0.6.0_src_all.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-illuminahumanmethylationepicanno.ilm10b4.hg19/bioconductor-illuminahumanmethylationepicanno.ilm10b4.hg19_0.6.0_src_all.tar.gz" @@ -17,7 +17,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-illuminahumanmethylationepicmanifest/meta.yaml b/recipes/bioconductor-illuminahumanmethylationepicmanifest/meta.yaml index 34db3248ebf45..21810fe87cbde 100644 --- a/recipes/bioconductor-illuminahumanmethylationepicmanifest/meta.yaml +++ b/recipes/bioconductor-illuminahumanmethylationepicmanifest/meta.yaml @@ -1,6 +1,6 @@ {% set version = "0.3.0" %} {% set name = "IlluminaHumanMethylationEPICmanifest" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -12,19 +12,19 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' md5: c6b0268de177badfe0b8184002da7e16 build: - number: 3 + number: 4 rpaths: - lib/R/lib/ - lib/ noarch: generic requirements: host: - - 'bioconductor-minfi >=1.28.0,<1.29.0' + - 'bioconductor-minfi >=1.30.0,<1.31.0' - r-base run: - - 'bioconductor-minfi >=1.28.0,<1.29.0' + - 'bioconductor-minfi >=1.30.0,<1.31.0' - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-illuminahumanmethylationepicmanifest/post-link.sh b/recipes/bioconductor-illuminahumanmethylationepicmanifest/post-link.sh index 8bc687b1951c0..1c7eec6605dba 100644 --- a/recipes/bioconductor-illuminahumanmethylationepicmanifest/post-link.sh +++ b/recipes/bioconductor-illuminahumanmethylationepicmanifest/post-link.sh @@ -1,7 +1,7 @@ #!/bin/bash FN="IlluminaHumanMethylationEPICmanifest_0.3.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/IlluminaHumanMethylationEPICmanifest_0.3.0.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/IlluminaHumanMethylationEPICmanifest_0.3.0.tar.gz" "https://bioarchive.galaxyproject.org/IlluminaHumanMethylationEPICmanifest_0.3.0.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-illuminahumanmethylationepicmanifest/bioconductor-illuminahumanmethylationepicmanifest_0.3.0_src_all.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-illuminahumanmethylationepicmanifest/bioconductor-illuminahumanmethylationepicmanifest_0.3.0_src_all.tar.gz" @@ -17,7 +17,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-illuminahumanv1.db/meta.yaml b/recipes/bioconductor-illuminahumanv1.db/meta.yaml index 8834351218b83..ab6ef6065e12d 100644 --- a/recipes/bioconductor-illuminahumanv1.db/meta.yaml +++ b/recipes/bioconductor-illuminahumanv1.db/meta.yaml @@ -1,6 +1,6 @@ {% set version = "1.26.0" %} {% set name = "illuminaHumanv1.db" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -12,7 +12,7 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' md5: 2c362256b7be2861b8bf6e0d1fe46786 build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ @@ -20,14 +20,14 @@ build: # Suggests: annotate, RUnit requirements: host: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' - - 'bioconductor-org.hs.eg.db >=3.7.0,<3.8.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' + - 'bioconductor-org.hs.eg.db >=3.8.0,<3.9.0' - r-base run: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' - - 'bioconductor-org.hs.eg.db >=3.7.0,<3.8.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' + - 'bioconductor-org.hs.eg.db >=3.8.0,<3.9.0' - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-illuminahumanv1.db/post-link.sh b/recipes/bioconductor-illuminahumanv1.db/post-link.sh index a83022aa3b15b..56524a6465af3 100644 --- a/recipes/bioconductor-illuminahumanv1.db/post-link.sh +++ b/recipes/bioconductor-illuminahumanv1.db/post-link.sh @@ -1,9 +1,10 @@ #!/bin/bash FN="illuminaHumanv1.db_1.26.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/illuminaHumanv1.db_1.26.0.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/illuminaHumanv1.db_1.26.0.tar.gz" "https://bioarchive.galaxyproject.org/illuminaHumanv1.db_1.26.0.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-illuminahumanv1.db/bioconductor-illuminahumanv1.db_1.26.0_src_all.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-illuminahumanv1.db/bioconductor-illuminahumanv1.db_1.26.0_src_all.tar.gz" ) MD5="2c362256b7be2861b8bf6e0d1fe46786" @@ -16,7 +17,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-illuminahumanv2.db/meta.yaml b/recipes/bioconductor-illuminahumanv2.db/meta.yaml index c2a0d079f84ab..0c735a470b026 100644 --- a/recipes/bioconductor-illuminahumanv2.db/meta.yaml +++ b/recipes/bioconductor-illuminahumanv2.db/meta.yaml @@ -1,6 +1,6 @@ {% set version = "1.26.0" %} {% set name = "illuminaHumanv2.db" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -12,7 +12,7 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' md5: 006de5f671a9a68fb27a6b6bce39c555 build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ @@ -20,14 +20,14 @@ build: # Suggests: annotate, RUnit requirements: host: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' - - 'bioconductor-org.hs.eg.db >=3.7.0,<3.8.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' + - 'bioconductor-org.hs.eg.db >=3.8.0,<3.9.0' - r-base run: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' - - 'bioconductor-org.hs.eg.db >=3.7.0,<3.8.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' + - 'bioconductor-org.hs.eg.db >=3.8.0,<3.9.0' - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-illuminahumanv2.db/post-link.sh b/recipes/bioconductor-illuminahumanv2.db/post-link.sh index 79dec2a0ead37..d73ba97d28d4c 100644 --- a/recipes/bioconductor-illuminahumanv2.db/post-link.sh +++ b/recipes/bioconductor-illuminahumanv2.db/post-link.sh @@ -1,9 +1,10 @@ #!/bin/bash FN="illuminaHumanv2.db_1.26.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/illuminaHumanv2.db_1.26.0.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/illuminaHumanv2.db_1.26.0.tar.gz" "https://bioarchive.galaxyproject.org/illuminaHumanv2.db_1.26.0.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-illuminahumanv2.db/bioconductor-illuminahumanv2.db_1.26.0_src_all.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-illuminahumanv2.db/bioconductor-illuminahumanv2.db_1.26.0_src_all.tar.gz" ) MD5="006de5f671a9a68fb27a6b6bce39c555" @@ -16,7 +17,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-illuminahumanv2beadid.db/meta.yaml b/recipes/bioconductor-illuminahumanv2beadid.db/meta.yaml index fde117dea0e93..3af5d5d874006 100644 --- a/recipes/bioconductor-illuminahumanv2beadid.db/meta.yaml +++ b/recipes/bioconductor-illuminahumanv2beadid.db/meta.yaml @@ -1,6 +1,6 @@ {% set version = "1.8.0" %} {% set name = "illuminaHumanv2BeadID.db" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -12,7 +12,7 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' md5: b5a2b2deaa9a9b245a141043e7bc5270 build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ @@ -20,14 +20,14 @@ build: # Suggests: annotate requirements: host: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' - - 'bioconductor-org.hs.eg.db >=3.7.0,<3.8.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' + - 'bioconductor-org.hs.eg.db >=3.8.0,<3.9.0' - r-base run: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' - - 'bioconductor-org.hs.eg.db >=3.7.0,<3.8.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' + - 'bioconductor-org.hs.eg.db >=3.8.0,<3.9.0' - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-illuminahumanv2beadid.db/post-link.sh b/recipes/bioconductor-illuminahumanv2beadid.db/post-link.sh index 606074b49e8d7..6aadc3dcbe21b 100644 --- a/recipes/bioconductor-illuminahumanv2beadid.db/post-link.sh +++ b/recipes/bioconductor-illuminahumanv2beadid.db/post-link.sh @@ -1,9 +1,10 @@ #!/bin/bash FN="illuminaHumanv2BeadID.db_1.8.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/illuminaHumanv2BeadID.db_1.8.0.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/illuminaHumanv2BeadID.db_1.8.0.tar.gz" "https://bioarchive.galaxyproject.org/illuminaHumanv2BeadID.db_1.8.0.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-illuminahumanv2beadid.db/bioconductor-illuminahumanv2beadid.db_1.8.0_src_all.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-illuminahumanv2beadid.db/bioconductor-illuminahumanv2beadid.db_1.8.0_src_all.tar.gz" ) MD5="b5a2b2deaa9a9b245a141043e7bc5270" @@ -16,7 +17,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-illuminahumanv3.db/meta.yaml b/recipes/bioconductor-illuminahumanv3.db/meta.yaml index cec8c296b4a01..59d763c72e984 100644 --- a/recipes/bioconductor-illuminahumanv3.db/meta.yaml +++ b/recipes/bioconductor-illuminahumanv3.db/meta.yaml @@ -1,6 +1,6 @@ {% set version = "1.26.0" %} {% set name = "illuminaHumanv3.db" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -12,7 +12,7 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' md5: 7d9e7534f0b60f0e3e7473e545ef373d build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ @@ -20,14 +20,14 @@ build: # Suggests: annotate, RUnit requirements: host: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' - - 'bioconductor-org.hs.eg.db >=3.7.0,<3.8.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' + - 'bioconductor-org.hs.eg.db >=3.8.0,<3.9.0' - r-base run: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' - - 'bioconductor-org.hs.eg.db >=3.7.0,<3.8.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' + - 'bioconductor-org.hs.eg.db >=3.8.0,<3.9.0' - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-illuminahumanv3.db/post-link.sh b/recipes/bioconductor-illuminahumanv3.db/post-link.sh index 2b00a6e75a4ed..1b9f397f5f9e5 100644 --- a/recipes/bioconductor-illuminahumanv3.db/post-link.sh +++ b/recipes/bioconductor-illuminahumanv3.db/post-link.sh @@ -1,9 +1,10 @@ #!/bin/bash FN="illuminaHumanv3.db_1.26.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/illuminaHumanv3.db_1.26.0.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/illuminaHumanv3.db_1.26.0.tar.gz" "https://bioarchive.galaxyproject.org/illuminaHumanv3.db_1.26.0.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-illuminahumanv3.db/bioconductor-illuminahumanv3.db_1.26.0_src_all.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-illuminahumanv3.db/bioconductor-illuminahumanv3.db_1.26.0_src_all.tar.gz" ) MD5="7d9e7534f0b60f0e3e7473e545ef373d" @@ -16,7 +17,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-illuminahumanv4.db/meta.yaml b/recipes/bioconductor-illuminahumanv4.db/meta.yaml index 6093d254597fd..52893d2d4f085 100644 --- a/recipes/bioconductor-illuminahumanv4.db/meta.yaml +++ b/recipes/bioconductor-illuminahumanv4.db/meta.yaml @@ -1,6 +1,6 @@ {% set version = "1.26.0" %} {% set name = "illuminaHumanv4.db" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -12,7 +12,7 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' md5: 42d554559ac0106dc71317ffaf466421 build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ @@ -20,14 +20,14 @@ build: # Suggests: annotate, RUnit requirements: host: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' - - 'bioconductor-org.hs.eg.db >=3.7.0,<3.8.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' + - 'bioconductor-org.hs.eg.db >=3.8.0,<3.9.0' - r-base run: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' - - 'bioconductor-org.hs.eg.db >=3.7.0,<3.8.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' + - 'bioconductor-org.hs.eg.db >=3.8.0,<3.9.0' - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-illuminahumanv4.db/post-link.sh b/recipes/bioconductor-illuminahumanv4.db/post-link.sh index 0b0f34ab2ebd1..acd98e21fa25d 100644 --- a/recipes/bioconductor-illuminahumanv4.db/post-link.sh +++ b/recipes/bioconductor-illuminahumanv4.db/post-link.sh @@ -1,9 +1,10 @@ #!/bin/bash FN="illuminaHumanv4.db_1.26.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/illuminaHumanv4.db_1.26.0.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/illuminaHumanv4.db_1.26.0.tar.gz" "https://bioarchive.galaxyproject.org/illuminaHumanv4.db_1.26.0.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-illuminahumanv4.db/bioconductor-illuminahumanv4.db_1.26.0_src_all.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-illuminahumanv4.db/bioconductor-illuminahumanv4.db_1.26.0_src_all.tar.gz" ) MD5="42d554559ac0106dc71317ffaf466421" @@ -16,7 +17,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-illuminahumanwgdaslv3.db/meta.yaml b/recipes/bioconductor-illuminahumanwgdaslv3.db/meta.yaml index 2a671acc880f4..3f2436ab070b0 100644 --- a/recipes/bioconductor-illuminahumanwgdaslv3.db/meta.yaml +++ b/recipes/bioconductor-illuminahumanwgdaslv3.db/meta.yaml @@ -1,6 +1,6 @@ {% set version = "1.26.0" %} {% set name = "illuminaHumanWGDASLv3.db" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -12,7 +12,7 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' md5: 32e8e24555c16f6d0148438d4a841ab8 build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ @@ -20,14 +20,14 @@ build: # Suggests: annotate, RUnit requirements: host: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' - - 'bioconductor-org.hs.eg.db >=3.7.0,<3.8.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' + - 'bioconductor-org.hs.eg.db >=3.8.0,<3.9.0' - r-base run: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' - - 'bioconductor-org.hs.eg.db >=3.7.0,<3.8.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' + - 'bioconductor-org.hs.eg.db >=3.8.0,<3.9.0' - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-illuminahumanwgdaslv3.db/post-link.sh b/recipes/bioconductor-illuminahumanwgdaslv3.db/post-link.sh index 42e1c474cf816..09e7fef7fed3f 100644 --- a/recipes/bioconductor-illuminahumanwgdaslv3.db/post-link.sh +++ b/recipes/bioconductor-illuminahumanwgdaslv3.db/post-link.sh @@ -1,9 +1,10 @@ #!/bin/bash FN="illuminaHumanWGDASLv3.db_1.26.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/illuminaHumanWGDASLv3.db_1.26.0.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/illuminaHumanWGDASLv3.db_1.26.0.tar.gz" "https://bioarchive.galaxyproject.org/illuminaHumanWGDASLv3.db_1.26.0.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-illuminahumanwgdaslv3.db/bioconductor-illuminahumanwgdaslv3.db_1.26.0_src_all.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-illuminahumanwgdaslv3.db/bioconductor-illuminahumanwgdaslv3.db_1.26.0_src_all.tar.gz" ) MD5="32e8e24555c16f6d0148438d4a841ab8" @@ -16,7 +17,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-illuminahumanwgdaslv4.db/meta.yaml b/recipes/bioconductor-illuminahumanwgdaslv4.db/meta.yaml index 20f067eca038a..2fef68db325e8 100644 --- a/recipes/bioconductor-illuminahumanwgdaslv4.db/meta.yaml +++ b/recipes/bioconductor-illuminahumanwgdaslv4.db/meta.yaml @@ -1,6 +1,6 @@ {% set version = "1.26.0" %} {% set name = "illuminaHumanWGDASLv4.db" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -12,7 +12,7 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' md5: 4cc1f192de838f2b6c1b148706d354ca build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ @@ -20,14 +20,14 @@ build: # Suggests: annotate, RUnit requirements: host: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' - - 'bioconductor-org.hs.eg.db >=3.7.0,<3.8.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' + - 'bioconductor-org.hs.eg.db >=3.8.0,<3.9.0' - r-base run: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' - - 'bioconductor-org.hs.eg.db >=3.7.0,<3.8.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' + - 'bioconductor-org.hs.eg.db >=3.8.0,<3.9.0' - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-illuminahumanwgdaslv4.db/post-link.sh b/recipes/bioconductor-illuminahumanwgdaslv4.db/post-link.sh index 7dd1cf86e09d5..804ab99fe1d15 100644 --- a/recipes/bioconductor-illuminahumanwgdaslv4.db/post-link.sh +++ b/recipes/bioconductor-illuminahumanwgdaslv4.db/post-link.sh @@ -1,9 +1,10 @@ #!/bin/bash FN="illuminaHumanWGDASLv4.db_1.26.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/illuminaHumanWGDASLv4.db_1.26.0.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/illuminaHumanWGDASLv4.db_1.26.0.tar.gz" "https://bioarchive.galaxyproject.org/illuminaHumanWGDASLv4.db_1.26.0.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-illuminahumanwgdaslv4.db/bioconductor-illuminahumanwgdaslv4.db_1.26.0_src_all.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-illuminahumanwgdaslv4.db/bioconductor-illuminahumanwgdaslv4.db_1.26.0_src_all.tar.gz" ) MD5="4cc1f192de838f2b6c1b148706d354ca" @@ -16,7 +17,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-illuminaio/meta.yaml b/recipes/bioconductor-illuminaio/meta.yaml index 62a60b19d02e0..d93a3a76666a1 100644 --- a/recipes/bioconductor-illuminaio/meta.yaml +++ b/recipes/bioconductor-illuminaio/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "0.24.0" %} +{% set version = "0.26.0" %} {% set name = "illuminaio" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 739638c3a278019ba705240fb8818a65 + md5: bfcf25ce8fe6d149909e61885527b966 build: number: 0 rpaths: diff --git a/recipes/bioconductor-illuminamousev1.db/meta.yaml b/recipes/bioconductor-illuminamousev1.db/meta.yaml index b34f8c9032046..ca3281ea81674 100644 --- a/recipes/bioconductor-illuminamousev1.db/meta.yaml +++ b/recipes/bioconductor-illuminamousev1.db/meta.yaml @@ -1,6 +1,6 @@ {% set version = "1.26.0" %} {% set name = "illuminaMousev1.db" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -12,7 +12,7 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' md5: 13818c3b9acabe75550492bbe638fc05 build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ @@ -20,14 +20,14 @@ build: # Suggests: annotate, RUnit requirements: host: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' - - 'bioconductor-org.mm.eg.db >=3.7.0,<3.8.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' + - 'bioconductor-org.mm.eg.db >=3.8.0,<3.9.0' - r-base run: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' - - 'bioconductor-org.mm.eg.db >=3.7.0,<3.8.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' + - 'bioconductor-org.mm.eg.db >=3.8.0,<3.9.0' - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-illuminamousev1.db/post-link.sh b/recipes/bioconductor-illuminamousev1.db/post-link.sh index 05602c2702dc9..3d13fc31d64d9 100644 --- a/recipes/bioconductor-illuminamousev1.db/post-link.sh +++ b/recipes/bioconductor-illuminamousev1.db/post-link.sh @@ -1,9 +1,10 @@ #!/bin/bash FN="illuminaMousev1.db_1.26.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/illuminaMousev1.db_1.26.0.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/illuminaMousev1.db_1.26.0.tar.gz" "https://bioarchive.galaxyproject.org/illuminaMousev1.db_1.26.0.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-illuminamousev1.db/bioconductor-illuminamousev1.db_1.26.0_src_all.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-illuminamousev1.db/bioconductor-illuminamousev1.db_1.26.0_src_all.tar.gz" ) MD5="13818c3b9acabe75550492bbe638fc05" @@ -16,7 +17,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-illuminamousev1p1.db/meta.yaml b/recipes/bioconductor-illuminamousev1p1.db/meta.yaml index 219bd7086290e..823098b679ee2 100644 --- a/recipes/bioconductor-illuminamousev1p1.db/meta.yaml +++ b/recipes/bioconductor-illuminamousev1p1.db/meta.yaml @@ -1,6 +1,6 @@ {% set version = "1.26.0" %} {% set name = "illuminaMousev1p1.db" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -12,7 +12,7 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' md5: f6a4af01480a6f8d1d2d9b9b64a2b073 build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ @@ -20,14 +20,14 @@ build: # Suggests: annotate, RUnit requirements: host: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' - - 'bioconductor-org.mm.eg.db >=3.7.0,<3.8.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' + - 'bioconductor-org.mm.eg.db >=3.8.0,<3.9.0' - r-base run: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' - - 'bioconductor-org.mm.eg.db >=3.7.0,<3.8.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' + - 'bioconductor-org.mm.eg.db >=3.8.0,<3.9.0' - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-illuminamousev1p1.db/post-link.sh b/recipes/bioconductor-illuminamousev1p1.db/post-link.sh index 011e3158b850b..dbd4b29b3cb1c 100644 --- a/recipes/bioconductor-illuminamousev1p1.db/post-link.sh +++ b/recipes/bioconductor-illuminamousev1p1.db/post-link.sh @@ -1,9 +1,10 @@ #!/bin/bash FN="illuminaMousev1p1.db_1.26.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/illuminaMousev1p1.db_1.26.0.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/illuminaMousev1p1.db_1.26.0.tar.gz" "https://bioarchive.galaxyproject.org/illuminaMousev1p1.db_1.26.0.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-illuminamousev1p1.db/bioconductor-illuminamousev1p1.db_1.26.0_src_all.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-illuminamousev1p1.db/bioconductor-illuminamousev1p1.db_1.26.0_src_all.tar.gz" ) MD5="f6a4af01480a6f8d1d2d9b9b64a2b073" @@ -16,7 +17,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-illuminamousev2.db/meta.yaml b/recipes/bioconductor-illuminamousev2.db/meta.yaml index 919e2315a124e..ffedcd79a7cda 100644 --- a/recipes/bioconductor-illuminamousev2.db/meta.yaml +++ b/recipes/bioconductor-illuminamousev2.db/meta.yaml @@ -1,6 +1,6 @@ {% set version = "1.26.0" %} {% set name = "illuminaMousev2.db" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -12,7 +12,7 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' md5: fba228a71f264f976d8cdb035861974d build: - number: 5 + number: 6 rpaths: - lib/R/lib/ - lib/ @@ -20,14 +20,14 @@ build: # Suggests: annotate, RUnit requirements: host: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' - - 'bioconductor-org.mm.eg.db >=3.7.0,<3.8.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' + - 'bioconductor-org.mm.eg.db >=3.8.0,<3.9.0' - r-base run: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' - - 'bioconductor-org.mm.eg.db >=3.7.0,<3.8.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' + - 'bioconductor-org.mm.eg.db >=3.8.0,<3.9.0' - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-illuminamousev2.db/post-link.sh b/recipes/bioconductor-illuminamousev2.db/post-link.sh index 231bf226d946f..9130abfc5d02e 100644 --- a/recipes/bioconductor-illuminamousev2.db/post-link.sh +++ b/recipes/bioconductor-illuminamousev2.db/post-link.sh @@ -1,7 +1,7 @@ #!/bin/bash FN="illuminaMousev2.db_1.26.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/illuminaMousev2.db_1.26.0.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/illuminaMousev2.db_1.26.0.tar.gz" "https://bioarchive.galaxyproject.org/illuminaMousev2.db_1.26.0.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-illuminamousev2.db/bioconductor-illuminamousev2.db_1.26.0_src_all.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-illuminamousev2.db/bioconductor-illuminamousev2.db_1.26.0_src_all.tar.gz" @@ -17,7 +17,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-illuminaratv1.db/meta.yaml b/recipes/bioconductor-illuminaratv1.db/meta.yaml index b13e0b6dc8397..23d99fa32180d 100644 --- a/recipes/bioconductor-illuminaratv1.db/meta.yaml +++ b/recipes/bioconductor-illuminaratv1.db/meta.yaml @@ -1,6 +1,6 @@ {% set version = "1.26.0" %} {% set name = "illuminaRatv1.db" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -12,7 +12,7 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' md5: 5de2324d7b96c0cdb3301ef269341aa8 build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ @@ -20,14 +20,14 @@ build: # Suggests: annotate, RUnit requirements: host: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' - - 'bioconductor-org.rn.eg.db >=3.7.0,<3.8.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' + - 'bioconductor-org.rn.eg.db >=3.8.0,<3.9.0' - r-base run: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' - - 'bioconductor-org.rn.eg.db >=3.7.0,<3.8.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' + - 'bioconductor-org.rn.eg.db >=3.8.0,<3.9.0' - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-illuminaratv1.db/post-link.sh b/recipes/bioconductor-illuminaratv1.db/post-link.sh index 670ed09d90e03..5284d240ecd22 100644 --- a/recipes/bioconductor-illuminaratv1.db/post-link.sh +++ b/recipes/bioconductor-illuminaratv1.db/post-link.sh @@ -1,9 +1,10 @@ #!/bin/bash FN="illuminaRatv1.db_1.26.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/illuminaRatv1.db_1.26.0.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/illuminaRatv1.db_1.26.0.tar.gz" "https://bioarchive.galaxyproject.org/illuminaRatv1.db_1.26.0.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-illuminaratv1.db/bioconductor-illuminaratv1.db_1.26.0_src_all.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-illuminaratv1.db/bioconductor-illuminaratv1.db_1.26.0_src_all.tar.gz" ) MD5="5de2324d7b96c0cdb3301ef269341aa8" @@ -16,7 +17,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-imagehts/meta.yaml b/recipes/bioconductor-imagehts/meta.yaml index 9f2669b4d5a83..4c141c5ca5702 100644 --- a/recipes/bioconductor-imagehts/meta.yaml +++ b/recipes/bioconductor-imagehts/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.32.0" %} +{% set version = "1.34.0" %} {% set name = "imageHTS" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 19f67d974501ad1563397cb4d465ef2f + md5: a2a6b427bd861f6f0e13b46f3c6bd6d3 build: number: 0 rpaths: @@ -20,18 +20,18 @@ build: # Suggests: BiocStyle, MASS requirements: host: - - 'bioconductor-biobase >=2.42.0,<2.43.0' - - 'bioconductor-cellhts2 >=2.46.0,<2.47.0' - - 'bioconductor-ebimage >=4.24.0,<4.25.0' - - 'bioconductor-vsn >=3.50.0,<3.51.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' + - 'bioconductor-cellhts2 >=2.48.0,<2.49.0' + - 'bioconductor-ebimage >=4.26.0,<4.27.0' + - 'bioconductor-vsn >=3.52.0,<3.53.0' - r-base - r-e1071 - r-hwriter run: - - 'bioconductor-biobase >=2.42.0,<2.43.0' - - 'bioconductor-cellhts2 >=2.46.0,<2.47.0' - - 'bioconductor-ebimage >=4.24.0,<4.25.0' - - 'bioconductor-vsn >=3.50.0,<3.51.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' + - 'bioconductor-cellhts2 >=2.48.0,<2.49.0' + - 'bioconductor-ebimage >=4.26.0,<4.27.0' + - 'bioconductor-vsn >=3.52.0,<3.53.0' - r-base - r-e1071 - r-hwriter diff --git a/recipes/bioconductor-imas/meta.yaml b/recipes/bioconductor-imas/meta.yaml index 7984c70352a28..394b2a791df8e 100644 --- a/recipes/bioconductor-imas/meta.yaml +++ b/recipes/bioconductor-imas/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.6.0" %} +{% set version = "1.8.0" %} {% set name = "IMAS" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 58867e3f9d00eb28cd7368186e3cebb4 + md5: 2bbe62f67811961074d499b7927f7465 build: number: 0 rpaths: @@ -20,17 +20,17 @@ build: # Suggests: BiocStyle, RUnit requirements: host: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' - - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' - - 'bioconductor-biocparallel >=1.16.0,<1.17.0' - - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' - - 'bioconductor-genomicalignments >=1.18.0,<1.19.0' - - 'bioconductor-genomicfeatures >=1.34.0,<1.35.0' - - 'bioconductor-genomicranges >=1.34.0,<1.35.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-ivas >=2.2.0,<2.3.0' - - 'bioconductor-rsamtools >=1.34.0,<1.35.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' + - 'bioconductor-biocgenerics >=0.30.0,<0.31.0' + - 'bioconductor-biocparallel >=1.18.0,<1.19.0' + - 'bioconductor-genomeinfodb >=1.20.0,<1.21.0' + - 'bioconductor-genomicalignments >=1.20.0,<1.21.0' + - 'bioconductor-genomicfeatures >=1.36.0,<1.37.0' + - 'bioconductor-genomicranges >=1.36.0,<1.37.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-ivas >=2.4.0,<2.5.0' + - 'bioconductor-rsamtools >=2.0.0,<2.1.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' - r-base - r-doparallel - r-foreach @@ -42,17 +42,17 @@ requirements: - r-matrix - r-survival run: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' - - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' - - 'bioconductor-biocparallel >=1.16.0,<1.17.0' - - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' - - 'bioconductor-genomicalignments >=1.18.0,<1.19.0' - - 'bioconductor-genomicfeatures >=1.34.0,<1.35.0' - - 'bioconductor-genomicranges >=1.34.0,<1.35.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-ivas >=2.2.0,<2.3.0' - - 'bioconductor-rsamtools >=1.34.0,<1.35.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' + - 'bioconductor-biocgenerics >=0.30.0,<0.31.0' + - 'bioconductor-biocparallel >=1.18.0,<1.19.0' + - 'bioconductor-genomeinfodb >=1.20.0,<1.21.0' + - 'bioconductor-genomicalignments >=1.20.0,<1.21.0' + - 'bioconductor-genomicfeatures >=1.36.0,<1.37.0' + - 'bioconductor-genomicranges >=1.36.0,<1.37.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-ivas >=2.4.0,<2.5.0' + - 'bioconductor-rsamtools >=2.0.0,<2.1.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' - r-base - r-doparallel - r-foreach diff --git a/recipes/bioconductor-imetagene/meta.yaml b/recipes/bioconductor-imetagene/meta.yaml index c09c264448034..4c98f735c9ead 100644 --- a/recipes/bioconductor-imetagene/meta.yaml +++ b/recipes/bioconductor-imetagene/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.12.0" %} +{% set version = "1.14.0" %} {% set name = "Imetagene" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 2e924c04928d481ee78f0fdf35f51eeb + md5: 079bec706473caf6d5b36a0ecadbf963 build: number: 0 rpaths: @@ -20,7 +20,7 @@ build: # Suggests: knitr, BiocStyle, rmarkdown requirements: host: - - 'bioconductor-metagene >=2.14.0,<2.15.0' + - 'bioconductor-metagene >=2.16.0,<2.17.0' - r-base - r-d3heatmap - r-ggplot2 @@ -29,7 +29,7 @@ requirements: - r-shinyfiles - r-shinythemes run: - - 'bioconductor-metagene >=2.14.0,<2.15.0' + - 'bioconductor-metagene >=2.16.0,<2.17.0' - r-base - r-d3heatmap - r-ggplot2 diff --git a/recipes/bioconductor-imman/meta.yaml b/recipes/bioconductor-imman/meta.yaml index 9643ad2649c6c..61e688ef79ece 100644 --- a/recipes/bioconductor-imman/meta.yaml +++ b/recipes/bioconductor-imman/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.2.0" %} +{% set version = "1.4.0" %} {% set name = "IMMAN" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: cd457c7494ce1cb6339920531190bb73 + md5: 0d83a0ca90c511709dc5f03f97a07d49 build: number: 0 rpaths: @@ -20,16 +20,14 @@ build: # Suggests: knitr, rmarkdown, testthat requirements: host: - - 'bioconductor-biocfilecache >=1.6.0,<1.7.0' - - 'bioconductor-biostrings >=2.50.0,<2.51.0' - - 'bioconductor-stringdb >=1.22.0,<1.23.0' + - 'bioconductor-biostrings >=2.52.0,<2.53.0' + - 'bioconductor-stringdb >=1.24.0,<1.25.0' - r-base - r-igraph - r-seqinr run: - - 'bioconductor-biocfilecache >=1.6.0,<1.7.0' - - 'bioconductor-biostrings >=2.50.0,<2.51.0' - - 'bioconductor-stringdb >=1.22.0,<1.23.0' + - 'bioconductor-biostrings >=2.52.0,<2.53.0' + - 'bioconductor-stringdb >=1.24.0,<1.25.0' - r-base - r-igraph - r-seqinr diff --git a/recipes/bioconductor-immunespacer/meta.yaml b/recipes/bioconductor-immunespacer/meta.yaml index 2c458c1ff6c62..b1ef593e17ecc 100644 --- a/recipes/bioconductor-immunespacer/meta.yaml +++ b/recipes/bioconductor-immunespacer/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.10.5" %} +{% set version = "1.12.0" %} {% set name = "ImmuneSpaceR" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: f313e9577b1005c444698f6a20a1bc91b5376f4f2f19c666194102da37724596 + md5: ac83d473e77b4b7d705faf9b1bae332f build: number: 0 rpaths: @@ -20,44 +20,42 @@ build: # Suggests: knitr, testthat requirements: host: - - 'bioconductor-biobase >=2.42.0,<2.43.0' - - 'bioconductor-preprocesscore >=1.44.0,<1.45.0' - - 'bioconductor-flowcore' - - 'bioconductor-flowworkspace' + - 'bioconductor-biobase >=2.44.0,<2.45.0' + - 'bioconductor-flowcore >=1.50.0,<1.51.0' + - 'bioconductor-flowworkspace >=3.32.0,<3.33.0' + - 'bioconductor-preprocesscore >=1.46.0,<1.47.0' - r-base - r-curl - r-data.table + - r-digest - r-ggplot2 - r-gplots - - r-gtools - 'r-heatmaply >=0.7.0' - r-httr + - r-jsonlite - r-pheatmap - r-plotly - r-r6 - - r-reshape2 - - r-rjson - 'r-rlabkey >=2.1.136' - r-rmarkdown - r-scales run: - - 'bioconductor-biobase >=2.42.0,<2.43.0' - - 'bioconductor-preprocesscore >=1.44.0,<1.45.0' - - 'bioconductor-flowcore' - - 'bioconductor-flowworkspace' + - 'bioconductor-biobase >=2.44.0,<2.45.0' + - 'bioconductor-flowcore >=1.50.0,<1.51.0' + - 'bioconductor-flowworkspace >=3.32.0,<3.33.0' + - 'bioconductor-preprocesscore >=1.46.0,<1.47.0' - r-base - r-curl - r-data.table + - r-digest - r-ggplot2 - r-gplots - - r-gtools - 'r-heatmaply >=0.7.0' - r-httr + - r-jsonlite - r-pheatmap - r-plotly - r-r6 - - r-reshape2 - - r-rjson - 'r-rlabkey >=2.1.136' - r-rmarkdown - r-scales diff --git a/recipes/bioconductor-immunoclust/meta.yaml b/recipes/bioconductor-immunoclust/meta.yaml index afcaef7720ae2..a9d94e3689c9c 100644 --- a/recipes/bioconductor-immunoclust/meta.yaml +++ b/recipes/bioconductor-immunoclust/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.14.1" %} +{% set version = "1.16.0" %} {% set name = "immunoClust" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: de57ef8eaee13ab9a1c3dd9bbea5f857 + md5: 75cb645cc6c100e4899d21444fa92c85 build: number: 0 rpaths: @@ -19,17 +19,13 @@ build: # Suggests: BiocStyle requirements: host: - - 'bioconductor-flowcore >=1.48.0,<1.49.0' + - 'bioconductor-flowcore >=1.50.0,<1.51.0' - r-base - r-lattice - - openblas - - gsl run: - - 'bioconductor-flowcore >=1.48.0,<1.49.0' + - 'bioconductor-flowcore >=1.50.0,<1.51.0' - r-base - r-lattice - - openblas - - gsl build: - {{ compiler('c') }} - {{ compiler('cxx') }} diff --git a/recipes/bioconductor-impcdata/meta.yaml b/recipes/bioconductor-impcdata/meta.yaml index 7189435c00ed6..fca0af926366e 100644 --- a/recipes/bioconductor-impcdata/meta.yaml +++ b/recipes/bioconductor-impcdata/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.18.0" %} +{% set version = "1.20.0" %} {% set name = "IMPCdata" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 7a7078db25def7231965af0a6604b598 + md5: 10a82494a1fc776a715f32bf010d6fcb build: number: 0 rpaths: diff --git a/recipes/bioconductor-impulsede/meta.yaml b/recipes/bioconductor-impulsede/meta.yaml index 5f0a248e692ed..00e7c0d4fc0eb 100644 --- a/recipes/bioconductor-impulsede/meta.yaml +++ b/recipes/bioconductor-impulsede/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.8.0" %} +{% set version = "1.10.0" %} {% set name = "ImpulseDE" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 99b95fd2df1ea360f4555129a1d845bb + md5: d3fc8f7a9a204922e9b52a91bb2ae113 build: number: 0 rpaths: diff --git a/recipes/bioconductor-impulsede2/meta.yaml b/recipes/bioconductor-impulsede2/meta.yaml index 9d058fb8ac49b..66320d128c99e 100644 --- a/recipes/bioconductor-impulsede2/meta.yaml +++ b/recipes/bioconductor-impulsede2/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.6.0" %} +{% set version = "1.8.0" %} {% set name = "ImpulseDE2" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 1ab384e936b22d4bd426369da18e6e8b + md5: d5c0703064c18d87df62b888b81d2569 build: number: 0 rpaths: @@ -19,12 +19,12 @@ build: noarch: generic requirements: host: - - 'bioconductor-biobase >=2.42.0,<2.43.0' - - 'bioconductor-biocparallel >=1.16.0,<1.17.0' - - 'bioconductor-complexheatmap >=1.20.0,<1.21.0' - - 'bioconductor-deseq2 >=1.22.0,<1.23.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' - - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' + - 'bioconductor-biocparallel >=1.18.0,<1.19.0' + - 'bioconductor-complexheatmap >=2.0.0,<2.1.0' + - 'bioconductor-deseq2 >=1.24.0,<1.25.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' + - 'bioconductor-summarizedexperiment >=1.14.0,<1.15.0' - r-base - r-circlize - r-cowplot @@ -32,12 +32,12 @@ requirements: - r-knitr - r-matrix run: - - 'bioconductor-biobase >=2.42.0,<2.43.0' - - 'bioconductor-biocparallel >=1.16.0,<1.17.0' - - 'bioconductor-complexheatmap >=1.20.0,<1.21.0' - - 'bioconductor-deseq2 >=1.22.0,<1.23.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' - - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' + - 'bioconductor-biocparallel >=1.18.0,<1.19.0' + - 'bioconductor-complexheatmap >=2.0.0,<2.1.0' + - 'bioconductor-deseq2 >=1.24.0,<1.25.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' + - 'bioconductor-summarizedexperiment >=1.14.0,<1.15.0' - r-base - r-circlize - r-cowplot diff --git a/recipes/bioconductor-impute/meta.yaml b/recipes/bioconductor-impute/meta.yaml index 857e82695a348..c38d2086a2a6c 100644 --- a/recipes/bioconductor-impute/meta.yaml +++ b/recipes/bioconductor-impute/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.56.0" %} +{% set version = "1.58.0" %} {% set name = "impute" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: f9e8aa154a5e8069fe4cc12c61355e63 + md5: a2cd42f981e6f84c3d8dd43589cdf8ec build: number: 0 rpaths: diff --git a/recipes/bioconductor-indac.db/meta.yaml b/recipes/bioconductor-indac.db/meta.yaml index 0aafd3f7f8f94..9d2f09c9737f4 100644 --- a/recipes/bioconductor-indac.db/meta.yaml +++ b/recipes/bioconductor-indac.db/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.2.3" %} {% set name = "indac.db" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -12,7 +12,7 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: cba72edcf7278033151e0eac077d8ff8 build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ @@ -20,14 +20,14 @@ build: # Suggests: DBI, annotate, RUnit requirements: host: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' - - 'bioconductor-org.dm.eg.db >=3.7.0,<3.8.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' + - 'bioconductor-org.dm.eg.db >=3.8.0,<3.9.0' - r-base run: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' - - 'bioconductor-org.dm.eg.db >=3.7.0,<3.8.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' + - 'bioconductor-org.dm.eg.db >=3.8.0,<3.9.0' - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-indac.db/post-link.sh b/recipes/bioconductor-indac.db/post-link.sh index a6f24806aa4dd..ddb0a08f2fdb8 100644 --- a/recipes/bioconductor-indac.db/post-link.sh +++ b/recipes/bioconductor-indac.db/post-link.sh @@ -1,9 +1,10 @@ #!/bin/bash FN="indac.db_3.2.3.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/indac.db_3.2.3.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/indac.db_3.2.3.tar.gz" "https://bioarchive.galaxyproject.org/indac.db_3.2.3.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-indac.db/bioconductor-indac.db_3.2.3_src_all.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-indac.db/bioconductor-indac.db_3.2.3_src_all.tar.gz" ) MD5="cba72edcf7278033151e0eac077d8ff8" @@ -16,7 +17,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-indeed/meta.yaml b/recipes/bioconductor-indeed/meta.yaml index 0619da4a4f7d8..4e81490b4cd0c 100644 --- a/recipes/bioconductor-indeed/meta.yaml +++ b/recipes/bioconductor-indeed/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.0.1" %} +{% set version = "1.2.0" %} {% set name = "INDEED" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: d7292e9c864bf73b2f3c4ecad7b459aa + md5: 2dfab78fbd3675f6b52145078dd60c03 build: number: 0 rpaths: diff --git a/recipes/bioconductor-infercnv/build.sh b/recipes/bioconductor-infercnv/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-infercnv/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-infercnv/meta.yaml b/recipes/bioconductor-infercnv/meta.yaml new file mode 100644 index 0000000000000..67b21e3d77383 --- /dev/null +++ b/recipes/bioconductor-infercnv/meta.yaml @@ -0,0 +1,86 @@ +{% set version = "1.0.0" %} +{% set name = "infercnv" %} +{% set bioc = "3.9" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + md5: c5b74cb8bed015e8d34749f59b1c4f4f +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: BiocStyle, knitr, rmarkdown, testthat +# SystemRequirements: JAGS 4.x.y +requirements: + host: + - 'bioconductor-biocgenerics >=0.30.0,<0.31.0' + - 'bioconductor-edger >=3.26.0,<3.27.0' + - 'bioconductor-singlecellexperiment >=1.6.0,<1.7.0' + - 'bioconductor-summarizedexperiment >=1.14.0,<1.15.0' + - r-ape + - r-argparse + - r-base + - r-catools + - r-coda + - r-coin + - r-doparallel + - r-dplyr + - r-fastcluster + - r-fitdistrplus + - r-foreach + - r-futile.logger + - r-future + - r-ggplot2 + - r-gplots + - r-gridextra + - r-hiddenmarkov + - r-matrix + - r-rcolorbrewer + - r-reshape + - r-rjags + - r-tidyr + - jags 4 + run: + - 'bioconductor-biocgenerics >=0.30.0,<0.31.0' + - 'bioconductor-edger >=3.26.0,<3.27.0' + - 'bioconductor-singlecellexperiment >=1.6.0,<1.7.0' + - 'bioconductor-summarizedexperiment >=1.14.0,<1.15.0' + - r-ape + - r-argparse + - r-base + - r-catools + - r-coda + - r-coin + - r-doparallel + - r-dplyr + - r-fastcluster + - r-fitdistrplus + - r-foreach + - r-futile.logger + - r-future + - r-ggplot2 + - r-gplots + - r-gridextra + - r-hiddenmarkov + - r-matrix + - r-rcolorbrewer + - r-reshape + - r-rjags + - r-tidyr + - jags 4 +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: 'BSD_3_clause + file LICENSE' + summary: 'Using single-cell RNA-Seq expression to visualize CNV in cells.' + diff --git a/recipes/bioconductor-inpas/meta.yaml b/recipes/bioconductor-inpas/meta.yaml index bbb0bf0d914b2..3b64952a54129 100644 --- a/recipes/bioconductor-inpas/meta.yaml +++ b/recipes/bioconductor-inpas/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.14.1" %} +{% set version = "1.16.0" %} {% set name = "InPAS" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: ec41c3f0144286126e8edecb617fd2ee + md5: ee79cfafe7ecf4a91e030071945f4fb8 build: number: 0 rpaths: @@ -20,36 +20,36 @@ build: # Suggests: RUnit, BiocGenerics, BiocStyle, BSgenome.Hsapiens.UCSC.hg19, BSgenome.Mmusculus.UCSC.mm10, org.Hs.eg.db, org.Mm.eg.db, TxDb.Hsapiens.UCSC.hg19.knownGene, TxDb.Mmusculus.UCSC.mm10.knownGene, rtracklayer, knitr requirements: host: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' - - 'bioconductor-biobase >=2.42.0,<2.43.0' - - 'bioconductor-biocparallel >=1.16.0,<1.17.0' - - 'bioconductor-bsgenome >=1.50.0,<1.51.0' - - 'bioconductor-cleanupdtseq >=1.20.0,<1.21.0' - - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' - - 'bioconductor-genomicfeatures >=1.34.0,<1.35.0' - - 'bioconductor-genomicranges >=1.34.0,<1.35.0' - - 'bioconductor-gviz >=1.26.0,<1.27.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-limma >=3.38.0,<3.39.0' - - 'bioconductor-preprocesscore >=1.44.0,<1.45.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' + - 'bioconductor-biocparallel >=1.18.0,<1.19.0' + - 'bioconductor-bsgenome >=1.52.0,<1.53.0' + - 'bioconductor-cleanupdtseq >=1.22.0,<1.23.0' + - 'bioconductor-genomeinfodb >=1.20.0,<1.21.0' + - 'bioconductor-genomicfeatures >=1.36.0,<1.37.0' + - 'bioconductor-genomicranges >=1.36.0,<1.37.0' + - 'bioconductor-gviz >=1.28.0,<1.29.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-limma >=3.40.0,<3.41.0' + - 'bioconductor-preprocesscore >=1.46.0,<1.47.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' - r-base - r-depmixs4 - r-seqinr run: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' - - 'bioconductor-biobase >=2.42.0,<2.43.0' - - 'bioconductor-biocparallel >=1.16.0,<1.17.0' - - 'bioconductor-bsgenome >=1.50.0,<1.51.0' - - 'bioconductor-cleanupdtseq >=1.20.0,<1.21.0' - - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' - - 'bioconductor-genomicfeatures >=1.34.0,<1.35.0' - - 'bioconductor-genomicranges >=1.34.0,<1.35.0' - - 'bioconductor-gviz >=1.26.0,<1.27.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-limma >=3.38.0,<3.39.0' - - 'bioconductor-preprocesscore >=1.44.0,<1.45.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' + - 'bioconductor-biocparallel >=1.18.0,<1.19.0' + - 'bioconductor-bsgenome >=1.52.0,<1.53.0' + - 'bioconductor-cleanupdtseq >=1.22.0,<1.23.0' + - 'bioconductor-genomeinfodb >=1.20.0,<1.21.0' + - 'bioconductor-genomicfeatures >=1.36.0,<1.37.0' + - 'bioconductor-genomicranges >=1.36.0,<1.37.0' + - 'bioconductor-gviz >=1.28.0,<1.29.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-limma >=3.40.0,<3.41.0' + - 'bioconductor-preprocesscore >=1.46.0,<1.47.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' - r-base - r-depmixs4 - r-seqinr diff --git a/recipes/bioconductor-inpower/meta.yaml b/recipes/bioconductor-inpower/meta.yaml index b63149150c6b1..77bdb663d2216 100644 --- a/recipes/bioconductor-inpower/meta.yaml +++ b/recipes/bioconductor-inpower/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.18.0" %} +{% set version = "1.20.0" %} {% set name = "INPower" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: be5f4b9a24bea8cb1b0942152d79f49c + md5: f2956f51c54c958ef26f6e5fb5514053 build: number: 0 rpaths: diff --git a/recipes/bioconductor-inspect/meta.yaml b/recipes/bioconductor-inspect/meta.yaml index 35c5d8fabf759..cc483b1cfa09f 100644 --- a/recipes/bioconductor-inspect/meta.yaml +++ b/recipes/bioconductor-inspect/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.12.0" %} +{% set version = "1.14.0" %} {% set name = "INSPEcT" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,52 +10,62 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: fe9fe90244776aac0fe97a065eb29614 + md5: b7c4434d8f6346e3b3751eb8a7bd50f7 build: number: 0 rpaths: - lib/R/lib/ - lib/ noarch: generic -# Suggests: BiocStyle, knitr, TxDb.Mmusculus.UCSC.mm9.knownGene +# Suggests: BiocStyle, knitr requirements: host: - - 'bioconductor-biobase >=2.42.0,<2.43.0' - - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' - - 'bioconductor-biocparallel >=1.16.0,<1.17.0' - - 'bioconductor-genomicalignments >=1.18.0,<1.19.0' - - 'bioconductor-genomicfeatures >=1.34.0,<1.35.0' - - 'bioconductor-genomicranges >=1.34.0,<1.35.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-preprocesscore >=1.44.0,<1.45.0' - - 'bioconductor-rsamtools >=1.34.0,<1.35.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' + - 'bioconductor-biocgenerics >=0.30.0,<0.31.0' + - 'bioconductor-biocparallel >=1.18.0,<1.19.0' + - 'bioconductor-deseq2 >=1.24.0,<1.25.0' + - 'bioconductor-genomicalignments >=1.20.0,<1.21.0' + - 'bioconductor-genomicfeatures >=1.36.0,<1.37.0' + - 'bioconductor-genomicranges >=1.36.0,<1.37.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-plgem >=1.56.0,<1.57.0' + - 'bioconductor-preprocesscore >=1.46.0,<1.47.0' + - 'bioconductor-rsamtools >=2.0.0,<2.1.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' + - 'bioconductor-summarizedexperiment >=1.14.0,<1.15.0' + - 'bioconductor-txdb.mmusculus.ucsc.mm9.knowngene >=3.2.0,<3.3.0' - r-base - r-desolve - r-proc - r-rootsolve + - r-shiny run: - - 'bioconductor-biobase >=2.42.0,<2.43.0' - - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' - - 'bioconductor-biocparallel >=1.16.0,<1.17.0' - - 'bioconductor-genomicalignments >=1.18.0,<1.19.0' - - 'bioconductor-genomicfeatures >=1.34.0,<1.35.0' - - 'bioconductor-genomicranges >=1.34.0,<1.35.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-preprocesscore >=1.44.0,<1.45.0' - - 'bioconductor-rsamtools >=1.34.0,<1.35.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' + - 'bioconductor-biocgenerics >=0.30.0,<0.31.0' + - 'bioconductor-biocparallel >=1.18.0,<1.19.0' + - 'bioconductor-deseq2 >=1.24.0,<1.25.0' + - 'bioconductor-genomicalignments >=1.20.0,<1.21.0' + - 'bioconductor-genomicfeatures >=1.36.0,<1.37.0' + - 'bioconductor-genomicranges >=1.36.0,<1.37.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-plgem >=1.56.0,<1.57.0' + - 'bioconductor-preprocesscore >=1.46.0,<1.47.0' + - 'bioconductor-rsamtools >=2.0.0,<2.1.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' + - 'bioconductor-summarizedexperiment >=1.14.0,<1.15.0' + - 'bioconductor-txdb.mmusculus.ucsc.mm9.knowngene >=3.2.0,<3.3.0' - r-base - r-desolve - r-proc - r-rootsolve + - r-shiny test: commands: - '$R -e "library(''{{ name }}'')"' about: home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: GPL-2 - summary: 'INSPEcT (INference of Synthesis, Processing and dEgradation rates in Time-Course experiments) analyses 4sU-seq and RNA-seq time-course data in order to evaluate synthesis, processing and degradation rates and asses via modeling the rates that determines changes in mature mRNA levels.' + summary: 'INSPEcT (INference of Synthesis, Processing and dEgradation rates from Transcriptomic data) RNA-seq data in time-course experiments or different conditions, with or without the support of nascent RNA data.' extra: identifiers: - biotools:inspect diff --git a/recipes/bioconductor-intad/meta.yaml b/recipes/bioconductor-intad/meta.yaml index e68d1eb71130d..941d9f0fdfc9b 100644 --- a/recipes/bioconductor-intad/meta.yaml +++ b/recipes/bioconductor-intad/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.2.1" %} +{% set version = "1.4.0" %} {% set name = "InTAD" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: f08c0f6c34ad5b82c3dbea9a5c3afd81 + md5: 629fffc8ce328eb60cfa3c52cc9b2907 build: number: 0 rpaths: @@ -20,29 +20,29 @@ build: # Suggests: testthat, BiocStyle, knitr, rmarkdown requirements: host: - - 'bioconductor-biobase >=2.42.0,<2.43.0' - - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' - - 'bioconductor-genomicranges >=1.34.0,<1.35.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-multiassayexperiment >=1.8.0,<1.9.0' - - 'bioconductor-qvalue >=2.14.0,<2.15.0' - - 'bioconductor-rtracklayer >=1.42.0,<1.43.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' - - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' + - 'bioconductor-biocgenerics >=0.30.0,<0.31.0' + - 'bioconductor-genomicranges >=1.36.0,<1.37.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-multiassayexperiment >=1.10.0,<1.11.0' + - 'bioconductor-qvalue >=2.16.0,<2.17.0' + - 'bioconductor-rtracklayer >=1.44.0,<1.45.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' + - 'bioconductor-summarizedexperiment >=1.14.0,<1.15.0' - r-base - r-ggplot2 - r-ggpubr - r-mclust run: - - 'bioconductor-biobase >=2.42.0,<2.43.0' - - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' - - 'bioconductor-genomicranges >=1.34.0,<1.35.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-multiassayexperiment >=1.8.0,<1.9.0' - - 'bioconductor-qvalue >=2.14.0,<2.15.0' - - 'bioconductor-rtracklayer >=1.42.0,<1.43.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' - - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' + - 'bioconductor-biocgenerics >=0.30.0,<0.31.0' + - 'bioconductor-genomicranges >=1.36.0,<1.37.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-multiassayexperiment >=1.10.0,<1.11.0' + - 'bioconductor-qvalue >=2.16.0,<2.17.0' + - 'bioconductor-rtracklayer >=1.44.0,<1.45.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' + - 'bioconductor-summarizedexperiment >=1.14.0,<1.15.0' - r-base - r-ggplot2 - r-ggpubr diff --git a/recipes/bioconductor-intansv/meta.yaml b/recipes/bioconductor-intansv/meta.yaml index 48cd8bb0e011b..6fdca452ad6c8 100644 --- a/recipes/bioconductor-intansv/meta.yaml +++ b/recipes/bioconductor-intansv/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.22.0" %} +{% set version = "1.24.0" %} {% set name = "intansv" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 1286b959d63fb61017de3f1244738a42 + md5: 9e7fea98fb594a592249a9c8d7aadb8f build: number: 0 rpaths: @@ -19,17 +19,17 @@ build: noarch: generic requirements: host: - - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' - - 'bioconductor-genomicranges >=1.34.0,<1.35.0' - - 'bioconductor-ggbio >=1.30.0,<1.31.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-biocgenerics >=0.30.0,<0.31.0' + - 'bioconductor-genomicranges >=1.36.0,<1.37.0' + - 'bioconductor-ggbio >=1.32.0,<1.33.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' - r-base - r-plyr run: - - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' - - 'bioconductor-genomicranges >=1.34.0,<1.35.0' - - 'bioconductor-ggbio >=1.30.0,<1.31.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-biocgenerics >=0.30.0,<0.31.0' + - 'bioconductor-genomicranges >=1.36.0,<1.37.0' + - 'bioconductor-ggbio >=1.32.0,<1.33.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' - r-base - r-plyr test: diff --git a/recipes/bioconductor-interactionset/meta.yaml b/recipes/bioconductor-interactionset/meta.yaml index 81fba2f2f0cf3..437801d5fb651 100644 --- a/recipes/bioconductor-interactionset/meta.yaml +++ b/recipes/bioconductor-interactionset/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.10.0" %} +{% set version = "1.12.0" %} {% set name = "InteractionSet" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 9aa7ddaaad56bef6685c95ae3950141a + md5: 07e6970639ef0dbd8a73837560b37d61 build: number: 0 rpaths: @@ -20,22 +20,22 @@ build: # SystemRequirements: C++11 requirements: host: - - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' - - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' - - 'bioconductor-genomicranges >=1.34.0,<1.35.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' - - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' + - 'bioconductor-biocgenerics >=0.30.0,<0.31.0' + - 'bioconductor-genomeinfodb >=1.20.0,<1.21.0' + - 'bioconductor-genomicranges >=1.36.0,<1.37.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' + - 'bioconductor-summarizedexperiment >=1.14.0,<1.15.0' - r-base - r-matrix - r-rcpp run: - - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' - - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' - - 'bioconductor-genomicranges >=1.34.0,<1.35.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' - - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' + - 'bioconductor-biocgenerics >=0.30.0,<0.31.0' + - 'bioconductor-genomeinfodb >=1.20.0,<1.21.0' + - 'bioconductor-genomicranges >=1.36.0,<1.37.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' + - 'bioconductor-summarizedexperiment >=1.14.0,<1.15.0' - r-base - r-matrix - r-rcpp diff --git a/recipes/bioconductor-interactivedisplay/meta.yaml b/recipes/bioconductor-interactivedisplay/meta.yaml index 3fcb3d918d0aa..5580d2cdeb99c 100644 --- a/recipes/bioconductor-interactivedisplay/meta.yaml +++ b/recipes/bioconductor-interactivedisplay/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.20.0" %} +{% set version = "1.22.0" %} {% set name = "interactiveDisplay" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 34c2b077ccf7ef2b8048e802cb499e32 + md5: 9f41ae1b1f2663388f320e616e6f1c86 build: number: 0 rpaths: @@ -20,10 +20,10 @@ build: # Suggests: RUnit, hgu95av2.db, knitr, GenomicRanges, SummarizedExperiment, GOstats, ggbio, GO.db, Gviz, rtracklayer, metagenomeSeq, gplots, vegan, Biobase requirements: host: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' - - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' - - 'bioconductor-category >=2.48.0,<2.49.0' - - 'bioconductor-interactivedisplaybase >=1.20.0,<1.21.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' + - 'bioconductor-biocgenerics >=0.30.0,<0.31.0' + - 'bioconductor-category >=2.50.0,<2.51.0' + - 'bioconductor-interactivedisplaybase >=1.22.0,<1.23.0' - r-base - r-ggplot2 - r-gridsvg @@ -33,10 +33,10 @@ requirements: - r-shiny - r-xml run: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' - - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' - - 'bioconductor-category >=2.48.0,<2.49.0' - - 'bioconductor-interactivedisplaybase >=1.20.0,<1.21.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' + - 'bioconductor-biocgenerics >=0.30.0,<0.31.0' + - 'bioconductor-category >=2.50.0,<2.51.0' + - 'bioconductor-interactivedisplaybase >=1.22.0,<1.23.0' - r-base - r-ggplot2 - r-gridsvg diff --git a/recipes/bioconductor-interactivedisplaybase/meta.yaml b/recipes/bioconductor-interactivedisplaybase/meta.yaml index 5868f126584a9..b021c79289375 100644 --- a/recipes/bioconductor-interactivedisplaybase/meta.yaml +++ b/recipes/bioconductor-interactivedisplaybase/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.20.0" %} +{% set version = "1.22.0" %} {% set name = "interactiveDisplayBase" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 9fde04ff11ca32a7c8d7a5e59e10efae + md5: 69e4cf7831b72ac47f40df36c2db1ddb build: number: 0 rpaths: @@ -20,11 +20,11 @@ build: # Suggests: knitr requirements: host: - - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' + - 'bioconductor-biocgenerics >=0.30.0,<0.31.0' - r-base - r-shiny run: - - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' + - 'bioconductor-biocgenerics >=0.30.0,<0.31.0' - r-base - r-shiny test: diff --git a/recipes/bioconductor-interest/meta.yaml b/recipes/bioconductor-interest/meta.yaml index be0f0dea12df4..df8560e573df4 100644 --- a/recipes/bioconductor-interest/meta.yaml +++ b/recipes/bioconductor-interest/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.6.1" %} +{% set version = "1.8.0" %} {% set name = "IntEREst" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 3af0d22cde14690b2e71d4ca3da6a53e + md5: 9b3f4c58a0efe17843478e5bc800486e build: number: 0 rpaths: @@ -20,39 +20,39 @@ build: # Suggests: clinfun, knitr, BSgenome.Hsapiens.UCSC.hg19 requirements: host: - - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' - - 'bioconductor-biocparallel >=1.16.0,<1.17.0' - - 'bioconductor-biostrings >=2.50.0,<2.51.0' - - 'bioconductor-deseq2 >=1.22.0,<1.23.0' - - 'bioconductor-dexseq >=1.28.0,<1.29.0' - - 'bioconductor-edger >=3.24.0,<3.25.0' - - 'bioconductor-genomicalignments >=1.18.0,<1.19.0' - - 'bioconductor-genomicfeatures >=1.34.0,<1.35.0' - - 'bioconductor-genomicranges >=1.34.0,<1.35.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-rsamtools >=1.34.0,<1.35.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' - - 'bioconductor-seqlogo >=1.48.0,<1.49.0' - - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' + - 'bioconductor-biocgenerics >=0.30.0,<0.31.0' + - 'bioconductor-biocparallel >=1.18.0,<1.19.0' + - 'bioconductor-biostrings >=2.52.0,<2.53.0' + - 'bioconductor-deseq2 >=1.24.0,<1.25.0' + - 'bioconductor-dexseq >=1.30.0,<1.31.0' + - 'bioconductor-edger >=3.26.0,<3.27.0' + - 'bioconductor-genomicalignments >=1.20.0,<1.21.0' + - 'bioconductor-genomicfeatures >=1.36.0,<1.37.0' + - 'bioconductor-genomicranges >=1.36.0,<1.37.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-rsamtools >=2.0.0,<2.1.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' + - 'bioconductor-seqlogo >=1.50.0,<1.51.0' + - 'bioconductor-summarizedexperiment >=1.14.0,<1.15.0' - r-base - r-dbi - r-rmysql - r-seqinr run: - - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' - - 'bioconductor-biocparallel >=1.16.0,<1.17.0' - - 'bioconductor-biostrings >=2.50.0,<2.51.0' - - 'bioconductor-deseq2 >=1.22.0,<1.23.0' - - 'bioconductor-dexseq >=1.28.0,<1.29.0' - - 'bioconductor-edger >=3.24.0,<3.25.0' - - 'bioconductor-genomicalignments >=1.18.0,<1.19.0' - - 'bioconductor-genomicfeatures >=1.34.0,<1.35.0' - - 'bioconductor-genomicranges >=1.34.0,<1.35.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-rsamtools >=1.34.0,<1.35.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' - - 'bioconductor-seqlogo >=1.48.0,<1.49.0' - - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' + - 'bioconductor-biocgenerics >=0.30.0,<0.31.0' + - 'bioconductor-biocparallel >=1.18.0,<1.19.0' + - 'bioconductor-biostrings >=2.52.0,<2.53.0' + - 'bioconductor-deseq2 >=1.24.0,<1.25.0' + - 'bioconductor-dexseq >=1.30.0,<1.31.0' + - 'bioconductor-edger >=3.26.0,<3.27.0' + - 'bioconductor-genomicalignments >=1.20.0,<1.21.0' + - 'bioconductor-genomicfeatures >=1.36.0,<1.37.0' + - 'bioconductor-genomicranges >=1.36.0,<1.37.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-rsamtools >=2.0.0,<2.1.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' + - 'bioconductor-seqlogo >=1.50.0,<1.51.0' + - 'bioconductor-summarizedexperiment >=1.14.0,<1.15.0' - r-base - r-dbi - r-rmysql diff --git a/recipes/bioconductor-interminer/meta.yaml b/recipes/bioconductor-interminer/meta.yaml index 17b7fe5aee2fa..0f2f89dffa0c9 100644 --- a/recipes/bioconductor-interminer/meta.yaml +++ b/recipes/bioconductor-interminer/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.4.1" %} +{% set version = "1.6.0" %} {% set name = "InterMineR" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 8b0b9de68ba80994ea1a0a7a6d90ee36 + md5: 9be486c5d330e6818f9373621381893d build: number: 0 rpaths: @@ -20,11 +20,11 @@ build: # Suggests: BiocStyle, Gviz, knitr, rmarkdown, GeneAnswers, GO.db, org.Hs.eg.db requirements: host: - - 'bioconductor-biostrings >=2.50.0,<2.51.0' - - 'bioconductor-genomicranges >=1.34.0,<1.35.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' - - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' + - 'bioconductor-biostrings >=2.52.0,<2.53.0' + - 'bioconductor-genomicranges >=1.36.0,<1.37.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' + - 'bioconductor-summarizedexperiment >=1.14.0,<1.15.0' - r-base - r-httr - r-igraph @@ -34,11 +34,11 @@ requirements: - r-xml - r-xml2 run: - - 'bioconductor-biostrings >=2.50.0,<2.51.0' - - 'bioconductor-genomicranges >=1.34.0,<1.35.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' - - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' + - 'bioconductor-biostrings >=2.52.0,<2.53.0' + - 'bioconductor-genomicranges >=1.36.0,<1.37.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' + - 'bioconductor-summarizedexperiment >=1.14.0,<1.15.0' - r-base - r-httr - r-igraph diff --git a/recipes/bioconductor-intramirexplorer/meta.yaml b/recipes/bioconductor-intramirexplorer/meta.yaml index 01ce683f22b42..a710a01f746a1 100644 --- a/recipes/bioconductor-intramirexplorer/meta.yaml +++ b/recipes/bioconductor-intramirexplorer/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.4.0" %} +{% set version = "1.6.0" %} {% set name = "IntramiRExploreR" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 9dacefac5bab443f1f1e9fb9327c02c0 + md5: 2afcd5b9e14a10fef5cf8f4c9cfcbd3f build: number: 0 rpaths: @@ -20,12 +20,12 @@ build: # Suggests: RDAVIDWebService, gProfileR, topGO, KEGGprofile, org.Dm.eg.db, rmarkdown, testthat requirements: host: - - 'bioconductor-fgnet >=3.16.0,<3.17.0' + - 'bioconductor-fgnet >=3.18.0,<3.19.0' - r-base - 'r-igraph >=1.0.1' - 'r-knitr >=1.12.3' run: - - 'bioconductor-fgnet >=3.16.0,<3.17.0' + - 'bioconductor-fgnet >=3.18.0,<3.19.0' - r-base - 'r-igraph >=1.0.1' - 'r-knitr >=1.12.3' diff --git a/recipes/bioconductor-inversion/meta.yaml b/recipes/bioconductor-inversion/meta.yaml index 34c46e70e474c..f0a527253ce4e 100644 --- a/recipes/bioconductor-inversion/meta.yaml +++ b/recipes/bioconductor-inversion/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.30.0" %} +{% set version = "1.32.0" %} {% set name = "inveRsion" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: a412874157e3ce4f3c4ecea6fe37318f + md5: 8baae537f75d3a562e69b34a66def929 build: number: 0 rpaths: diff --git a/recipes/bioconductor-ioniser/meta.yaml b/recipes/bioconductor-ioniser/meta.yaml index bc7b99544562f..f2e1ed37cb715 100644 --- a/recipes/bioconductor-ioniser/meta.yaml +++ b/recipes/bioconductor-ioniser/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "2.6.0" %} +{% set version = "2.8.0" %} {% set name = "IONiseR" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 61e911d51f0caa89932208c837ab6342 + md5: 59bcb7f086b55f1551a88c2fb0542535 build: number: 0 rpaths: @@ -20,12 +20,12 @@ build: # Suggests: BiocStyle, knitr, rmarkdown, gridExtra, testthat, minionSummaryData requirements: host: - - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' - - 'bioconductor-biocparallel >=1.16.0,<1.17.0' - - 'bioconductor-biostrings >=2.50.0,<2.51.0' - - 'bioconductor-rhdf5 >=2.26.0,<2.27.0' - - 'bioconductor-shortread >=1.40.0,<1.41.0' - - 'bioconductor-xvector >=0.22.0,<0.23.0' + - 'bioconductor-biocgenerics >=0.30.0,<0.31.0' + - 'bioconductor-biocparallel >=1.18.0,<1.19.0' + - 'bioconductor-biostrings >=2.52.0,<2.53.0' + - 'bioconductor-rhdf5 >=2.28.0,<2.29.0' + - 'bioconductor-shortread >=1.42.0,<1.43.0' + - 'bioconductor-xvector >=0.24.0,<0.25.0' - r-base - r-bit64 - r-dplyr @@ -35,12 +35,12 @@ requirements: - r-tibble - r-tidyr run: - - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' - - 'bioconductor-biocparallel >=1.16.0,<1.17.0' - - 'bioconductor-biostrings >=2.50.0,<2.51.0' - - 'bioconductor-rhdf5 >=2.26.0,<2.27.0' - - 'bioconductor-shortread >=1.40.0,<1.41.0' - - 'bioconductor-xvector >=0.22.0,<0.23.0' + - 'bioconductor-biocgenerics >=0.30.0,<0.31.0' + - 'bioconductor-biocparallel >=1.18.0,<1.19.0' + - 'bioconductor-biostrings >=2.52.0,<2.53.0' + - 'bioconductor-rhdf5 >=2.28.0,<2.29.0' + - 'bioconductor-shortread >=1.42.0,<1.43.0' + - 'bioconductor-xvector >=0.24.0,<0.25.0' - r-base - r-bit64 - r-dplyr diff --git a/recipes/bioconductor-ipac/meta.yaml b/recipes/bioconductor-ipac/meta.yaml index 457a458f837c4..1dd3dc6a0614e 100644 --- a/recipes/bioconductor-ipac/meta.yaml +++ b/recipes/bioconductor-ipac/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.26.0" %} +{% set version = "1.28.0" %} {% set name = "iPAC" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,23 +10,23 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 11d1424c3e0f5f1d56e7a97e038d5c08 + md5: 1fdc1f29676fbb941f029d10b87044d2 build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ noarch: generic requirements: host: - - 'bioconductor-biostrings >=2.50.0,<2.51.0' - - 'bioconductor-multtest >=2.38.0,<2.39.0' + - 'bioconductor-biostrings >=2.52.0,<2.53.0' + - 'bioconductor-multtest >=2.40.0,<2.41.0' - r-base - r-gdata - r-scatterplot3d run: - - 'bioconductor-biostrings >=2.50.0,<2.51.0' - - 'bioconductor-multtest >=2.38.0,<2.39.0' + - 'bioconductor-biostrings >=2.52.0,<2.53.0' + - 'bioconductor-multtest >=2.40.0,<2.41.0' - r-base - r-gdata - r-scatterplot3d diff --git a/recipes/bioconductor-ipddb/meta.yaml b/recipes/bioconductor-ipddb/meta.yaml index 6fd289d8ff754..b286882dd00d4 100644 --- a/recipes/bioconductor-ipddb/meta.yaml +++ b/recipes/bioconductor-ipddb/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.0.0" %} +{% set version = "1.2.0" %} {% set name = "ipdDb" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 2fb18bc886d7261c082f6aef486d862f + md5: d9255c8440a60b0dff66aaf02291e498 build: number: 0 rpaths: @@ -20,21 +20,21 @@ build: # Suggests: knitr, rmarkdown, testthat requirements: host: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' - - 'bioconductor-annotationhub >=2.14.0,<2.15.0' - - 'bioconductor-biostrings >=2.50.0,<2.51.0' - - 'bioconductor-genomicranges >=1.34.0,<1.35.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' + - 'bioconductor-annotationhub >=2.16.0,<2.17.0' + - 'bioconductor-biostrings >=2.52.0,<2.53.0' + - 'bioconductor-genomicranges >=1.36.0,<1.37.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' - r-assertthat - r-base - r-dbi - r-rsqlite run: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' - - 'bioconductor-annotationhub >=2.14.0,<2.15.0' - - 'bioconductor-biostrings >=2.50.0,<2.51.0' - - 'bioconductor-genomicranges >=1.34.0,<1.35.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' + - 'bioconductor-annotationhub >=2.16.0,<2.17.0' + - 'bioconductor-biostrings >=2.52.0,<2.53.0' + - 'bioconductor-genomicranges >=1.36.0,<1.37.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' - r-assertthat - r-base - r-dbi diff --git a/recipes/bioconductor-ipo/meta.yaml b/recipes/bioconductor-ipo/meta.yaml index 6e2d0014df328..6c3ad74472a4b 100644 --- a/recipes/bioconductor-ipo/meta.yaml +++ b/recipes/bioconductor-ipo/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.8.1" %} +{% set version = "1.10.0" %} {% set name = "IPO" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,9 +10,9 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 92f90da2968bdfe08a9683f1e032ebaa + md5: dc27b55b709bae8e44e74d442792bcd8 build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ @@ -20,15 +20,15 @@ build: # Suggests: RUnit, BiocGenerics, msdata, mtbls2, faahKO, knitr requirements: host: - - 'bioconductor-biocparallel >=1.16.0,<1.17.0' - - 'bioconductor-camera >=1.38.0,<1.39.0' - - 'bioconductor-xcms >=3.4.0,<3.5.0' + - 'bioconductor-biocparallel >=1.18.0,<1.19.0' + - 'bioconductor-camera >=1.40.0,<1.41.0' + - 'bioconductor-xcms >=3.6.0,<3.7.0' - r-base - r-rsm run: - - 'bioconductor-biocparallel >=1.16.0,<1.17.0' - - 'bioconductor-camera >=1.38.0,<1.39.0' - - 'bioconductor-xcms >=3.4.0,<3.5.0' + - 'bioconductor-biocparallel >=1.18.0,<1.19.0' + - 'bioconductor-camera >=1.40.0,<1.41.0' + - 'bioconductor-xcms >=3.6.0,<3.7.0' - r-base - r-rsm test: diff --git a/recipes/bioconductor-ippd/meta.yaml b/recipes/bioconductor-ippd/meta.yaml index a66bcc5ba0f7d..dc4384aa858fb 100644 --- a/recipes/bioconductor-ippd/meta.yaml +++ b/recipes/bioconductor-ippd/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.30.0" %} +{% set version = "1.32.0" %} {% set name = "IPPD" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: ae63fe883f60495d5f67784e28e11a6f + md5: 8945de40830ddf1cf423a7ebacd346e7 build: number: 0 rpaths: diff --git a/recipes/bioconductor-iranges/meta.yaml b/recipes/bioconductor-iranges/meta.yaml index 27f8976c11d75..4b4b1958decfc 100644 --- a/recipes/bioconductor-iranges/meta.yaml +++ b/recipes/bioconductor-iranges/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "2.16.0" %} +{% set version = "2.18.0" %} {% set name = "IRanges" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: f37fa0b9438adf9af358844bf1f87c02 + md5: 3d00ac5aba67be591e3433abeb3c355d build: number: 0 rpaths: @@ -19,12 +19,12 @@ build: # Suggests: XVector, GenomicRanges, Rsamtools, GenomicAlignments, GenomicFeatures, BSgenome.Celegans.UCSC.ce2, pasillaBamSubset, RUnit, BiocStyle requirements: host: - - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-biocgenerics >=0.30.0,<0.31.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' - r-base run: - - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-biocgenerics >=0.30.0,<0.31.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' - r-base build: - {{ compiler('c') }} diff --git a/recipes/bioconductor-isee/meta.yaml b/recipes/bioconductor-isee/meta.yaml index c5c073becd436..42be2b04d4a4e 100644 --- a/recipes/bioconductor-isee/meta.yaml +++ b/recipes/bioconductor-isee/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.2.0" %} +{% set version = "1.4.0" %} {% set name = "iSEE" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 170e94a6acf704baad9742320af6c599 + md5: 09c890984d49ca15e67da9c23b40bc28 build: number: 0 rpaths: @@ -20,11 +20,11 @@ build: # Suggests: testthat, BiocStyle, knitr, rmarkdown, scRNAseq, scater, DelayedArray (>= 0.7.44), Rtsne, irlba, RColorBrewer, viridis, org.Mm.eg.db, htmltools requirements: host: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' - - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' - - 'bioconductor-singlecellexperiment >=1.4.0,<1.5.0' - - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' + - 'bioconductor-biocgenerics >=0.30.0,<0.31.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' + - 'bioconductor-singlecellexperiment >=1.6.0,<1.7.0' + - 'bioconductor-summarizedexperiment >=1.14.0,<1.15.0' - r-base - r-colourpicker - r-cowplot @@ -44,11 +44,11 @@ requirements: - r-vipor - r-viridislite run: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' - - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' - - 'bioconductor-singlecellexperiment >=1.4.0,<1.5.0' - - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' + - 'bioconductor-biocgenerics >=0.30.0,<0.31.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' + - 'bioconductor-singlecellexperiment >=1.6.0,<1.7.0' + - 'bioconductor-summarizedexperiment >=1.14.0,<1.15.0' - r-base - r-colourpicker - r-cowplot diff --git a/recipes/bioconductor-iseq/meta.yaml b/recipes/bioconductor-iseq/meta.yaml index e7d06b9bffc19..975442577447a 100644 --- a/recipes/bioconductor-iseq/meta.yaml +++ b/recipes/bioconductor-iseq/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.34.0" %} +{% set version = "1.36.0" %} {% set name = "iSeq" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 2059cc665dc0cd50aa204f216a64d332 + md5: 34fcf377d00fe05b4fb3fd030c73f960 build: number: 0 rpaths: diff --git a/recipes/bioconductor-isobar/meta.yaml b/recipes/bioconductor-isobar/meta.yaml index 4da91515ee213..61282d43c42d3 100644 --- a/recipes/bioconductor-isobar/meta.yaml +++ b/recipes/bioconductor-isobar/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.28.0" %} +{% set version = "1.30.0" %} {% set name = "isobar" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 68833968f99c12527e9923447b075d79 + md5: b7ee8950caf1433708ff8ac6b95260d9 build: number: 0 rpaths: @@ -20,15 +20,15 @@ build: # Suggests: MSnbase, OrgMassSpecR, XML, RJSONIO, Hmisc, gplots, RColorBrewer, gridExtra, limma, boot, DBI, MASS requirements: host: - - 'bioconductor-biobase >=2.42.0,<2.43.0' - - 'bioconductor-biomart >=2.38.0,<2.39.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' + - 'bioconductor-biomart >=2.40.0,<2.41.0' - r-base - r-distr - r-ggplot2 - r-plyr run: - - 'bioconductor-biobase >=2.42.0,<2.43.0' - - 'bioconductor-biomart >=2.38.0,<2.39.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' + - 'bioconductor-biomart >=2.40.0,<2.41.0' - r-base - r-distr - r-ggplot2 diff --git a/recipes/bioconductor-isocorrector/meta.yaml b/recipes/bioconductor-isocorrector/meta.yaml index b13fc108ad1f4..1f422c53a7851 100644 --- a/recipes/bioconductor-isocorrector/meta.yaml +++ b/recipes/bioconductor-isocorrector/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.0.5" %} +{% set version = "1.2.0" %} {% set name = "IsoCorrectoR" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 3f06be0cf58841751ea3031be9d33fe5 + md5: b4d5822280558aff3624199032462d2a build: number: 0 rpaths: diff --git a/recipes/bioconductor-isocorrectorgui/build.sh b/recipes/bioconductor-isocorrectorgui/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-isocorrectorgui/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-isocorrectorgui/meta.yaml b/recipes/bioconductor-isocorrectorgui/meta.yaml new file mode 100644 index 0000000000000..ea2f3b4ae9a86 --- /dev/null +++ b/recipes/bioconductor-isocorrectorgui/meta.yaml @@ -0,0 +1,39 @@ +{% set version = "1.0.0" %} +{% set name = "IsoCorrectoRGUI" %} +{% set bioc = "3.9" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: 711d12a341ba39a55603fba3aa4c6161 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: knitr, rmarkdown, testthat +requirements: + host: + - 'bioconductor-isocorrector >=1.2.0,<1.3.0' + - r-base + - r-readxl + - r-tcltk2 + run: + - 'bioconductor-isocorrector >=1.2.0,<1.3.0' + - r-base + - r-readxl + - r-tcltk2 +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: GPL-3 + summary: 'IsoCorrectoRGUI is a Graphical User Interface for the IsoCorrectoR package. IsoCorrectoR performs the correction of mass spectrometry data from stable isotope labeling/tracing metabolomics experiments with regard to natural isotope abundance and tracer impurity. Data from both MS and MS/MS measurements can be corrected (with any tracer isotope: 13C, 15N, 18O...), as well as high resolution MS data from multiple-tracer experiments (e.g. 13C and 15N used simultaneously).' + diff --git a/recipes/bioconductor-isoformswitchanalyzer/meta.yaml b/recipes/bioconductor-isoformswitchanalyzer/meta.yaml index a6326460b614c..b0e768c2408a3 100644 --- a/recipes/bioconductor-isoformswitchanalyzer/meta.yaml +++ b/recipes/bioconductor-isoformswitchanalyzer/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.4.0" %} +{% set version = "1.6.0" %} {% set name = "IsoformSwitchAnalyzeR" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: a4b45dc8dc2a54692d8a27ba67568d16 + md5: 7dd5e98185805f3db37b5721a227a9bb build: number: 0 rpaths: @@ -19,17 +19,18 @@ build: # Suggests: knitr, BSgenome.Hsapiens.UCSC.hg19, cummeRbund requirements: host: - - 'bioconductor-biostrings >=2.50.0,<2.51.0' - - 'bioconductor-bsgenome >=1.50.0,<1.51.0' - - 'bioconductor-dexseq >=1.28.0,<1.29.0' - - 'bioconductor-drimseq >=1.10.0,<1.11.0' - - 'bioconductor-edger >=3.24.0,<3.25.0' - - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' - - 'bioconductor-genomicranges >=1.34.0,<1.35.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-limma >=3.38.0,<3.39.0' - - 'bioconductor-rtracklayer >=1.42.0,<1.43.0' - - 'bioconductor-tximport >=1.10.0,<1.11.0' + - 'bioconductor-biostrings >=2.52.0,<2.53.0' + - 'bioconductor-bsgenome >=1.52.0,<1.53.0' + - 'bioconductor-dexseq >=1.30.0,<1.31.0' + - 'bioconductor-drimseq >=1.12.0,<1.13.0' + - 'bioconductor-edger >=3.26.0,<3.27.0' + - 'bioconductor-genomeinfodb >=1.20.0,<1.21.0' + - 'bioconductor-genomicranges >=1.36.0,<1.37.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-limma >=3.40.0,<3.41.0' + - 'bioconductor-rtracklayer >=1.44.0,<1.45.0' + - 'bioconductor-tximport >=1.12.0,<1.13.0' + - 'bioconductor-xvector >=0.24.0,<0.25.0' - r-base - r-dbi - r-dplyr @@ -44,17 +45,18 @@ requirements: - r-stringr - r-venndiagram run: - - 'bioconductor-biostrings >=2.50.0,<2.51.0' - - 'bioconductor-bsgenome >=1.50.0,<1.51.0' - - 'bioconductor-dexseq >=1.28.0,<1.29.0' - - 'bioconductor-drimseq >=1.10.0,<1.11.0' - - 'bioconductor-edger >=3.24.0,<3.25.0' - - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' - - 'bioconductor-genomicranges >=1.34.0,<1.35.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-limma >=3.38.0,<3.39.0' - - 'bioconductor-rtracklayer >=1.42.0,<1.43.0' - - 'bioconductor-tximport >=1.10.0,<1.11.0' + - 'bioconductor-biostrings >=2.52.0,<2.53.0' + - 'bioconductor-bsgenome >=1.52.0,<1.53.0' + - 'bioconductor-dexseq >=1.30.0,<1.31.0' + - 'bioconductor-drimseq >=1.12.0,<1.13.0' + - 'bioconductor-edger >=3.26.0,<3.27.0' + - 'bioconductor-genomeinfodb >=1.20.0,<1.21.0' + - 'bioconductor-genomicranges >=1.36.0,<1.37.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-limma >=3.40.0,<3.41.0' + - 'bioconductor-rtracklayer >=1.44.0,<1.45.0' + - 'bioconductor-tximport >=1.12.0,<1.13.0' + - 'bioconductor-xvector >=0.24.0,<0.25.0' - r-base - r-dbi - r-dplyr @@ -77,7 +79,7 @@ test: about: home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: 'GPL (>= 2)' - summary: 'IsoformSwitchAnalyzeR enables identification and analysis of alternative splicing and isoform switches with predicted functional consequences (such as gain/loss of protein domains etc) from quantification by Kallisto, Salmon, Cufflinks/Cuffdiff, RSEM etc.' + summary: 'IsoformSwitchAnalyzeR enables identification and analysis of alternative splicing and isoform switches with predicted functional consequences (e.g. gain/loss of protein domains etc.) from quantification by Kallisto, Salmon, Cufflinks/Cuffdiff, RSEM etc.' extra: identifiers: - biotools:IsoformSwitchAnalyzeR diff --git a/recipes/bioconductor-isogenegui/meta.yaml b/recipes/bioconductor-isogenegui/meta.yaml index 573310b2a5656..6cc0f5e9816bb 100644 --- a/recipes/bioconductor-isogenegui/meta.yaml +++ b/recipes/bioconductor-isogenegui/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "2.18.0" %} +{% set version = "2.20.0" %} {% set name = "IsoGeneGUI" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 872514812096a9484b45f0c86cd63911 + md5: a14a8953f9c3cc6c45c5d22d0a9c0345 build: number: 0 rpaths: @@ -19,9 +19,9 @@ build: # Suggests: RUnit requirements: host: - - 'bioconductor-biobase >=2.42.0,<2.43.0' - - 'bioconductor-geneplotter >=1.60.0,<1.61.0' - - 'bioconductor-multtest >=2.38.0,<2.39.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' + - 'bioconductor-geneplotter >=1.62.0,<1.63.0' + - 'bioconductor-multtest >=2.40.0,<2.41.0' - r-base - r-ff - r-goric @@ -37,9 +37,9 @@ requirements: - r-tkrplot - r-xlsx run: - - 'bioconductor-biobase >=2.42.0,<2.43.0' - - 'bioconductor-geneplotter >=1.60.0,<1.61.0' - - 'bioconductor-multtest >=2.38.0,<2.39.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' + - 'bioconductor-geneplotter >=1.62.0,<1.63.0' + - 'bioconductor-multtest >=2.40.0,<2.41.0' - r-base - r-ff - r-goric diff --git a/recipes/bioconductor-isolde/meta.yaml b/recipes/bioconductor-isolde/meta.yaml index f0c03bc1912a1..cd2956fabb3c0 100644 --- a/recipes/bioconductor-isolde/meta.yaml +++ b/recipes/bioconductor-isolde/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.10.1" %} +{% set version = "1.12.0" %} {% set name = "ISoLDE" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 415ea14c55b22b24737f4d7fba82e4c2 + md5: 276c0974c5b41c30d6838ecb3a9c4432 build: number: 0 rpaths: @@ -21,11 +21,9 @@ requirements: - r-base run: - r-base - - llvm-openmp # [osx] build: - {{ compiler('c') }} - make - - llvm-openmp # [osx] test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-isomirs/meta.yaml b/recipes/bioconductor-isomirs/meta.yaml index 178f298c8f366..b737ca78f8d28 100644 --- a/recipes/bioconductor-isomirs/meta.yaml +++ b/recipes/bioconductor-isomirs/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.10.0" %} +{% set version = "1.12.0" %} {% set name = "isomiRs" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: e7add4edfd77ebeee4faeedb961b8204 + md5: b4aed94aabd853358bfee3e7110766ab build: number: 0 rpaths: @@ -20,18 +20,19 @@ build: # Suggests: knitr, org.Mm.eg.db, targetscan.Hs.eg.db, pheatmap, BiocStyle, testthat requirements: host: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' - - 'bioconductor-biobase >=2.42.0,<2.43.0' - - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' - - 'bioconductor-degreport >=1.18.0,<1.19.0' - - 'bioconductor-deseq2 >=1.22.0,<1.23.0' - - 'bioconductor-genomicranges >=1.34.0,<1.35.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-limma >=3.38.0,<3.39.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' - - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' + - 'bioconductor-biocgenerics >=0.30.0,<0.31.0' + - 'bioconductor-degreport >=1.20.0,<1.21.0' + - 'bioconductor-deseq2 >=1.24.0,<1.25.0' + - 'bioconductor-genomicranges >=1.36.0,<1.37.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-limma >=3.40.0,<3.41.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' + - 'bioconductor-summarizedexperiment >=1.14.0,<1.15.0' - r-assertive.sets - r-base + - r-broom - r-cluster - r-cowplot - r-discriminer @@ -45,21 +46,23 @@ requirements: - r-readr - r-reshape - r-rlang + - r-stringr - r-tibble - r-tidyr run: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' - - 'bioconductor-biobase >=2.42.0,<2.43.0' - - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' - - 'bioconductor-degreport >=1.18.0,<1.19.0' - - 'bioconductor-deseq2 >=1.22.0,<1.23.0' - - 'bioconductor-genomicranges >=1.34.0,<1.35.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-limma >=3.38.0,<3.39.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' - - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' + - 'bioconductor-biocgenerics >=0.30.0,<0.31.0' + - 'bioconductor-degreport >=1.20.0,<1.21.0' + - 'bioconductor-deseq2 >=1.24.0,<1.25.0' + - 'bioconductor-genomicranges >=1.36.0,<1.37.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-limma >=3.40.0,<3.41.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' + - 'bioconductor-summarizedexperiment >=1.14.0,<1.15.0' - r-assertive.sets - r-base + - r-broom - r-cluster - r-cowplot - r-discriminer @@ -73,6 +76,7 @@ requirements: - r-readr - r-reshape - r-rlang + - r-stringr - r-tibble - r-tidyr test: diff --git a/recipes/bioconductor-italics/meta.yaml b/recipes/bioconductor-italics/meta.yaml index cab14240d0d3b..0ce24c5e94847 100644 --- a/recipes/bioconductor-italics/meta.yaml +++ b/recipes/bioconductor-italics/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "2.42.0" %} +{% set version = "2.44.0" %} {% set name = "ITALICS" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: ff61276d7d7957d1d43f81a3c44c143c + md5: e6f57ef7c5bbe5ed02dd9cb61250f250 build: number: 0 rpaths: @@ -20,20 +20,20 @@ build: # Suggests: pd.mapping50k.hind240, pd.mapping250k.sty, pd.mapping250k.nsp requirements: host: - - 'bioconductor-affxparser >=1.54.0,<1.55.0' - - 'bioconductor-glad >=2.46.0,<2.47.0' - - 'bioconductor-italicsdata >=2.20.0,<2.21.0' - - 'bioconductor-oligo >=1.46.0,<1.47.0' - - 'bioconductor-oligoclasses >=1.44.0,<1.45.0' + - 'bioconductor-affxparser >=1.56.0,<1.57.0' + - 'bioconductor-glad >=2.48.0,<2.49.0' + - 'bioconductor-italicsdata >=2.22.0,<2.23.0' + - 'bioconductor-oligo >=1.48.0,<1.49.0' + - 'bioconductor-oligoclasses >=1.46.0,<1.47.0' - 'bioconductor-pd.mapping50k.xba240 >=3.12.0,<3.13.0' - r-base - r-dbi run: - - 'bioconductor-affxparser >=1.54.0,<1.55.0' - - 'bioconductor-glad >=2.46.0,<2.47.0' - - 'bioconductor-italicsdata >=2.20.0,<2.21.0' - - 'bioconductor-oligo >=1.46.0,<1.47.0' - - 'bioconductor-oligoclasses >=1.44.0,<1.45.0' + - 'bioconductor-affxparser >=1.56.0,<1.57.0' + - 'bioconductor-glad >=2.48.0,<2.49.0' + - 'bioconductor-italicsdata >=2.22.0,<2.23.0' + - 'bioconductor-oligo >=1.48.0,<1.49.0' + - 'bioconductor-oligoclasses >=1.46.0,<1.47.0' - 'bioconductor-pd.mapping50k.xba240 >=3.12.0,<3.13.0' - r-base - r-dbi diff --git a/recipes/bioconductor-italicsdata/meta.yaml b/recipes/bioconductor-italicsdata/meta.yaml index 3b5c427bc0a58..930b8e4e4403a 100644 --- a/recipes/bioconductor-italicsdata/meta.yaml +++ b/recipes/bioconductor-italicsdata/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "2.20.0" %} +{% set version = "2.22.0" %} {% set name = "ITALICSData" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: a6efafe837fc28cafd205d8acfc3a94a + md5: 20e86e82a58cd3beddddf7ebd31f649b build: number: 0 rpaths: @@ -22,7 +22,7 @@ requirements: - r-base run: - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-italicsdata/post-link.sh b/recipes/bioconductor-italicsdata/post-link.sh index 6d0f84a1977df..35ffdeb6fccf8 100644 --- a/recipes/bioconductor-italicsdata/post-link.sh +++ b/recipes/bioconductor-italicsdata/post-link.sh @@ -1,11 +1,11 @@ #!/bin/bash -FN="ITALICSData_2.20.0.tar.gz" +FN="ITALICSData_2.22.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/experiment/src/contrib/ITALICSData_2.20.0.tar.gz" - "https://bioarchive.galaxyproject.org/ITALICSData_2.20.0.tar.gz" - "https://depot.galaxyproject.org/software/bioconductor-italicsdata/bioconductor-italicsdata_2.20.0_src_all.tar.gz" + "https://bioconductor.org/packages/3.9/data/experiment/src/contrib/ITALICSData_2.22.0.tar.gz" + "https://bioarchive.galaxyproject.org/ITALICSData_2.22.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-italicsdata/bioconductor-italicsdata_2.22.0_src_all.tar.gz" ) -MD5="a6efafe837fc28cafd205d8acfc3a94a" +MD5="20e86e82a58cd3beddddf7ebd31f649b" # Use a staging area in the conda dir rather than temp dirs, both to avoid # permission issues as well as to have things downloaded in a predictable @@ -16,7 +16,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-iterativebma/meta.yaml b/recipes/bioconductor-iterativebma/meta.yaml index 32a215e673c12..51a83d1996eb2 100644 --- a/recipes/bioconductor-iterativebma/meta.yaml +++ b/recipes/bioconductor-iterativebma/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.40.0" %} +{% set version = "1.42.0" %} {% set name = "iterativeBMA" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 7ceea6bdeb99f7b8ff5b46f8e938b860 + md5: c26210dc91288d115df41cc61354a7d4 build: number: 0 rpaths: @@ -19,12 +19,12 @@ build: noarch: generic requirements: host: - - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' - r-base - r-bma - r-leaps run: - - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' - r-base - r-bma - r-leaps diff --git a/recipes/bioconductor-iterativebmasurv/meta.yaml b/recipes/bioconductor-iterativebmasurv/meta.yaml index dc2d58d47c8a6..48b028538b799 100644 --- a/recipes/bioconductor-iterativebmasurv/meta.yaml +++ b/recipes/bioconductor-iterativebmasurv/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.40.0" %} +{% set version = "1.42.0" %} {% set name = "iterativeBMAsurv" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 0260494ff7be19fe0716230c2162fb09 + md5: aaa6fc21790a7635efadeed3a38844dc build: number: 0 rpaths: diff --git a/recipes/bioconductor-iterclust/meta.yaml b/recipes/bioconductor-iterclust/meta.yaml index 2091ef569c571..a8c379eda74e4 100644 --- a/recipes/bioconductor-iterclust/meta.yaml +++ b/recipes/bioconductor-iterclust/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.4.0" %} +{% set version = "1.6.0" %} {% set name = "iterClust" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 9d834de783d4ec4af9b9ead22236616b + md5: 70ac9c78685bb43b679b7ff045973b48 build: number: 0 rpaths: @@ -20,11 +20,11 @@ build: # Suggests: tsne, bcellViper requirements: host: - - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' - r-base - r-cluster run: - - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' - r-base - r-cluster test: diff --git a/recipes/bioconductor-iteremoval/meta.yaml b/recipes/bioconductor-iteremoval/meta.yaml index a8aa232d20122..32653ef8f1ce7 100644 --- a/recipes/bioconductor-iteremoval/meta.yaml +++ b/recipes/bioconductor-iteremoval/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.2.0" %} +{% set version = "1.4.0" %} {% set name = "iteremoval" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: eb105f0df6dd4e19a8683152705c6348 + md5: c46186d3425702960b2a52b9abf95e7d build: number: 0 rpaths: @@ -20,14 +20,14 @@ build: # Suggests: testthat, knitr requirements: host: - - 'bioconductor-genomicranges >=1.34.0,<1.35.0' - - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' + - 'bioconductor-genomicranges >=1.36.0,<1.37.0' + - 'bioconductor-summarizedexperiment >=1.14.0,<1.15.0' - r-base - 'r-ggplot2 >=2.2.1' - r-magrittr run: - - 'bioconductor-genomicranges >=1.34.0,<1.35.0' - - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' + - 'bioconductor-genomicranges >=1.36.0,<1.37.0' + - 'bioconductor-summarizedexperiment >=1.14.0,<1.15.0' - r-base - 'r-ggplot2 >=2.2.1' - r-magrittr diff --git a/recipes/bioconductor-ivas/meta.yaml b/recipes/bioconductor-ivas/meta.yaml index 18ce08f05c299..99a4e06b7cb33 100644 --- a/recipes/bioconductor-ivas/meta.yaml +++ b/recipes/bioconductor-ivas/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "2.2.0" %} +{% set version = "2.4.0" %} {% set name = "IVAS" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: deffefe8491728061122ab65714e3730 + md5: f47596c3dd0e30e36ffd95202598ffb5 build: number: 0 rpaths: @@ -20,15 +20,15 @@ build: # Suggests: BiocStyle requirements: host: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' - - 'bioconductor-biobase >=2.42.0,<2.43.0' - - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' - - 'bioconductor-biocparallel >=1.16.0,<1.17.0' - - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' - - 'bioconductor-genomicfeatures >=1.34.0,<1.35.0' - - 'bioconductor-genomicranges >=1.34.0,<1.35.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' + - 'bioconductor-biocgenerics >=0.30.0,<0.31.0' + - 'bioconductor-biocparallel >=1.18.0,<1.19.0' + - 'bioconductor-genomeinfodb >=1.20.0,<1.21.0' + - 'bioconductor-genomicfeatures >=1.36.0,<1.37.0' + - 'bioconductor-genomicranges >=1.36.0,<1.37.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' - r-base - r-doparallel - r-foreach @@ -37,15 +37,15 @@ requirements: - r-lme4 - r-matrix run: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' - - 'bioconductor-biobase >=2.42.0,<2.43.0' - - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' - - 'bioconductor-biocparallel >=1.16.0,<1.17.0' - - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' - - 'bioconductor-genomicfeatures >=1.34.0,<1.35.0' - - 'bioconductor-genomicranges >=1.34.0,<1.35.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' + - 'bioconductor-biocgenerics >=0.30.0,<0.31.0' + - 'bioconductor-biocparallel >=1.18.0,<1.19.0' + - 'bioconductor-genomeinfodb >=1.20.0,<1.21.0' + - 'bioconductor-genomicfeatures >=1.36.0,<1.37.0' + - 'bioconductor-genomicranges >=1.36.0,<1.37.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' - r-base - r-doparallel - r-foreach diff --git a/recipes/bioconductor-ivygapse/meta.yaml b/recipes/bioconductor-ivygapse/meta.yaml index c2b158a933472..e2e8a13aa0e9c 100644 --- a/recipes/bioconductor-ivygapse/meta.yaml +++ b/recipes/bioconductor-ivygapse/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.4.0" %} +{% set version = "1.6.0" %} {% set name = "ivygapSE" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,9 +10,9 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: e40c121410d8cd59555a1860e69c7e02 + md5: d65a1bbbb18590ab5d4511c32db0b219 build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ @@ -20,8 +20,8 @@ build: # Suggests: knitr, png, limma, grid, DT, randomForest, digest, testthat requirements: host: - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' - - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' + - 'bioconductor-summarizedexperiment >=1.14.0,<1.15.0' - r-base - r-ggplot2 - r-hwriter @@ -31,8 +31,8 @@ requirements: - r-survminer - r-upsetr run: - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' - - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' + - 'bioconductor-summarizedexperiment >=1.14.0,<1.15.0' - r-base - r-ggplot2 - r-hwriter diff --git a/recipes/bioconductor-iwtomics/meta.yaml b/recipes/bioconductor-iwtomics/meta.yaml index e83d182ef7467..53a7a0a8c61fe 100644 --- a/recipes/bioconductor-iwtomics/meta.yaml +++ b/recipes/bioconductor-iwtomics/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.6.0" %} +{% set version = "1.8.0" %} {% set name = "IWTomics" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 41ae9142f344cc1b42205ffe20758cec + md5: 83f139dee1677f2058729a33253ff7af build: number: 0 rpaths: @@ -20,17 +20,17 @@ build: # Suggests: knitr requirements: host: - - 'bioconductor-genomicranges >=1.34.0,<1.35.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-genomicranges >=1.36.0,<1.37.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' - r-base - r-fda - r-gtable - r-kernsmooth run: - - 'bioconductor-genomicranges >=1.34.0,<1.35.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-genomicranges >=1.36.0,<1.37.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' - r-base - r-fda - r-gtable diff --git a/recipes/bioconductor-iyer517/meta.yaml b/recipes/bioconductor-iyer517/meta.yaml index c4f940a21b5f2..2af8c3b0a78d0 100644 --- a/recipes/bioconductor-iyer517/meta.yaml +++ b/recipes/bioconductor-iyer517/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.24.0" %} +{% set version = "1.26.0" %} {% set name = "Iyer517" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: db3def2128ea25dabad86019961b2126 + md5: 22360bdd418629479e66c15026f99c7b build: number: 0 rpaths: @@ -19,12 +19,12 @@ build: noarch: generic requirements: host: - - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' - r-base run: - - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-iyer517/post-link.sh b/recipes/bioconductor-iyer517/post-link.sh index edffbd7b6b1df..7a95b835058ed 100644 --- a/recipes/bioconductor-iyer517/post-link.sh +++ b/recipes/bioconductor-iyer517/post-link.sh @@ -1,11 +1,11 @@ #!/bin/bash -FN="Iyer517_1.24.0.tar.gz" +FN="Iyer517_1.26.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/experiment/src/contrib/Iyer517_1.24.0.tar.gz" - "https://bioarchive.galaxyproject.org/Iyer517_1.24.0.tar.gz" - "https://depot.galaxyproject.org/software/bioconductor-iyer517/bioconductor-iyer517_1.24.0_src_all.tar.gz" + "https://bioconductor.org/packages/3.9/data/experiment/src/contrib/Iyer517_1.26.0.tar.gz" + "https://bioarchive.galaxyproject.org/Iyer517_1.26.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-iyer517/bioconductor-iyer517_1.26.0_src_all.tar.gz" ) -MD5="db3def2128ea25dabad86019961b2126" +MD5="22360bdd418629479e66c15026f99c7b" # Use a staging area in the conda dir rather than temp dirs, both to avoid # permission issues as well as to have things downloaded in a predictable @@ -16,7 +16,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-jaspar2014/meta.yaml b/recipes/bioconductor-jaspar2014/meta.yaml index c1cf0bcc3adee..26e2c2b4ec05f 100644 --- a/recipes/bioconductor-jaspar2014/meta.yaml +++ b/recipes/bioconductor-jaspar2014/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.18.0" %} +{% set version = "1.20.0" %} {% set name = "JASPAR2014" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 4b68fc946528a33446e29411731e9097 + md5: 4e907b35b06421d73433cc13987ddb9a build: number: 0 rpaths: @@ -19,12 +19,12 @@ build: noarch: generic requirements: host: - - 'bioconductor-biostrings >=2.50.0,<2.51.0' + - 'bioconductor-biostrings >=2.52.0,<2.53.0' - r-base run: - - 'bioconductor-biostrings >=2.50.0,<2.51.0' + - 'bioconductor-biostrings >=2.52.0,<2.53.0' - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-jaspar2014/post-link.sh b/recipes/bioconductor-jaspar2014/post-link.sh index 7716947c49769..c2734d02a5548 100644 --- a/recipes/bioconductor-jaspar2014/post-link.sh +++ b/recipes/bioconductor-jaspar2014/post-link.sh @@ -1,11 +1,11 @@ #!/bin/bash -FN="JASPAR2014_1.18.0.tar.gz" +FN="JASPAR2014_1.20.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/experiment/src/contrib/JASPAR2014_1.18.0.tar.gz" - "https://bioarchive.galaxyproject.org/JASPAR2014_1.18.0.tar.gz" - "https://depot.galaxyproject.org/software/bioconductor-jaspar2014/bioconductor-jaspar2014_1.18.0_src_all.tar.gz" + "https://bioconductor.org/packages/3.9/data/experiment/src/contrib/JASPAR2014_1.20.0.tar.gz" + "https://bioarchive.galaxyproject.org/JASPAR2014_1.20.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-jaspar2014/bioconductor-jaspar2014_1.20.0_src_all.tar.gz" ) -MD5="4b68fc946528a33446e29411731e9097" +MD5="4e907b35b06421d73433cc13987ddb9a" # Use a staging area in the conda dir rather than temp dirs, both to avoid # permission issues as well as to have things downloaded in a predictable @@ -16,7 +16,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-jaspar2016/meta.yaml b/recipes/bioconductor-jaspar2016/meta.yaml index feb88c584cebc..94feda1156e7b 100644 --- a/recipes/bioconductor-jaspar2016/meta.yaml +++ b/recipes/bioconductor-jaspar2016/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.10.0" %} +{% set version = "1.12.0" %} {% set name = "JASPAR2016" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 3dc95f750e4a98dfb227a4c3de6ce501 + md5: 010a850897534622a73f91dedb64dc4e build: number: 0 rpaths: @@ -22,7 +22,7 @@ requirements: - r-base run: - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-jaspar2016/post-link.sh b/recipes/bioconductor-jaspar2016/post-link.sh index d357124e150ee..fff3805a391e7 100644 --- a/recipes/bioconductor-jaspar2016/post-link.sh +++ b/recipes/bioconductor-jaspar2016/post-link.sh @@ -1,11 +1,11 @@ #!/bin/bash -FN="JASPAR2016_1.10.0.tar.gz" +FN="JASPAR2016_1.12.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/experiment/src/contrib/JASPAR2016_1.10.0.tar.gz" - "https://bioarchive.galaxyproject.org/JASPAR2016_1.10.0.tar.gz" - "https://depot.galaxyproject.org/software/bioconductor-jaspar2016/bioconductor-jaspar2016_1.10.0_src_all.tar.gz" + "https://bioconductor.org/packages/3.9/data/experiment/src/contrib/JASPAR2016_1.12.0.tar.gz" + "https://bioarchive.galaxyproject.org/JASPAR2016_1.12.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-jaspar2016/bioconductor-jaspar2016_1.12.0_src_all.tar.gz" ) -MD5="3dc95f750e4a98dfb227a4c3de6ce501" +MD5="010a850897534622a73f91dedb64dc4e" # Use a staging area in the conda dir rather than temp dirs, both to avoid # permission issues as well as to have things downloaded in a predictable @@ -16,7 +16,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-jaspar2018/meta.yaml b/recipes/bioconductor-jaspar2018/meta.yaml index afa19f52742e6..2293305ca3545 100644 --- a/recipes/bioconductor-jaspar2018/meta.yaml +++ b/recipes/bioconductor-jaspar2018/meta.yaml @@ -1,6 +1,6 @@ {% set version = "1.1.1" %} {% set name = "JASPAR2018" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -12,7 +12,7 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' md5: d91fce6ea0dc9fa6a3be6ebc05c1af5d build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ @@ -23,7 +23,7 @@ requirements: - r-base run: - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-jaspar2018/post-link.sh b/recipes/bioconductor-jaspar2018/post-link.sh index 2f4175df6b840..bc8e2be5f3250 100755 --- a/recipes/bioconductor-jaspar2018/post-link.sh +++ b/recipes/bioconductor-jaspar2018/post-link.sh @@ -1,9 +1,10 @@ #!/bin/bash FN="JASPAR2018_1.1.1.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/JASPAR2018_1.1.1.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/JASPAR2018_1.1.1.tar.gz" "https://bioarchive.galaxyproject.org/JASPAR2018_1.1.1.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-jaspar2018/bioconductor-jaspar2018_1.1.1_src_all.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-jaspar2018/bioconductor-jaspar2018_1.1.1_src_all.tar.gz" ) MD5="d91fce6ea0dc9fa6a3be6ebc05c1af5d" @@ -16,7 +17,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-jazaerimetadata.db/meta.yaml b/recipes/bioconductor-jazaerimetadata.db/meta.yaml index 4f1cfc35ffc19..14fb81944fc70 100644 --- a/recipes/bioconductor-jazaerimetadata.db/meta.yaml +++ b/recipes/bioconductor-jazaerimetadata.db/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.2.3" %} {% set name = "JazaeriMetaData.db" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -12,7 +12,7 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' md5: 3a154a74ac2acebe3471b039c9d9a4dc build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ @@ -20,14 +20,14 @@ build: # Suggests: DBI, annotate, RUnit requirements: host: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' - - 'bioconductor-org.hs.eg.db >=3.7.0,<3.8.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' + - 'bioconductor-org.hs.eg.db >=3.8.0,<3.9.0' - r-base run: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' - - 'bioconductor-org.hs.eg.db >=3.7.0,<3.8.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' + - 'bioconductor-org.hs.eg.db >=3.8.0,<3.9.0' - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-jazaerimetadata.db/post-link.sh b/recipes/bioconductor-jazaerimetadata.db/post-link.sh index b44bbf4a4aff3..007901eac2291 100644 --- a/recipes/bioconductor-jazaerimetadata.db/post-link.sh +++ b/recipes/bioconductor-jazaerimetadata.db/post-link.sh @@ -1,9 +1,10 @@ #!/bin/bash FN="JazaeriMetaData.db_3.2.3.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/JazaeriMetaData.db_3.2.3.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/JazaeriMetaData.db_3.2.3.tar.gz" "https://bioarchive.galaxyproject.org/JazaeriMetaData.db_3.2.3.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-jazaerimetadata.db/bioconductor-jazaerimetadata.db_3.2.3_src_all.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-jazaerimetadata.db/bioconductor-jazaerimetadata.db_3.2.3_src_all.tar.gz" ) MD5="3a154a74ac2acebe3471b039c9d9a4dc" @@ -16,7 +17,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-jctseqdata/meta.yaml b/recipes/bioconductor-jctseqdata/meta.yaml index bde4c340cd71e..fd484086cc841 100644 --- a/recipes/bioconductor-jctseqdata/meta.yaml +++ b/recipes/bioconductor-jctseqdata/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.12.0" %} +{% set version = "1.14.0" %} {% set name = "JctSeqData" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 76da9f6116c1a71cbb2244c7dd5c32a2 + md5: 26cbe5468815dbc5bb9d0e86c90cb88d build: number: 0 rpaths: @@ -23,7 +23,7 @@ requirements: - r-base run: - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-jctseqdata/post-link.sh b/recipes/bioconductor-jctseqdata/post-link.sh index def3b1fa8c182..db99eb992108a 100644 --- a/recipes/bioconductor-jctseqdata/post-link.sh +++ b/recipes/bioconductor-jctseqdata/post-link.sh @@ -1,11 +1,11 @@ #!/bin/bash -FN="JctSeqData_1.12.0.tar.gz" +FN="JctSeqData_1.14.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/experiment/src/contrib/JctSeqData_1.12.0.tar.gz" - "https://bioarchive.galaxyproject.org/JctSeqData_1.12.0.tar.gz" - "https://depot.galaxyproject.org/software/bioconductor-jctseqdata/bioconductor-jctseqdata_1.12.0_src_all.tar.gz" + "https://bioconductor.org/packages/3.9/data/experiment/src/contrib/JctSeqData_1.14.0.tar.gz" + "https://bioarchive.galaxyproject.org/JctSeqData_1.14.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-jctseqdata/bioconductor-jctseqdata_1.14.0_src_all.tar.gz" ) -MD5="76da9f6116c1a71cbb2244c7dd5c32a2" +MD5="26cbe5468815dbc5bb9d0e86c90cb88d" # Use a staging area in the conda dir rather than temp dirs, both to avoid # permission issues as well as to have things downloaded in a predictable @@ -16,7 +16,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-joda/meta.yaml b/recipes/bioconductor-joda/meta.yaml index 250e5e6f240fd..2eea7d148633d 100644 --- a/recipes/bioconductor-joda/meta.yaml +++ b/recipes/bioconductor-joda/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.30.0" %} +{% set version = "1.32.0" %} {% set name = "joda" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 40973ebc5b8862fca57737b9a04128a6 + md5: dd636d646cd32887e7482c3d33790873 build: number: 0 rpaths: @@ -19,11 +19,11 @@ build: noarch: generic requirements: host: - - 'bioconductor-rbgl >=1.58.0,<1.59.0' + - 'bioconductor-rbgl >=1.60.0,<1.61.0' - r-base - r-bgmm run: - - 'bioconductor-rbgl >=1.58.0,<1.59.0' + - 'bioconductor-rbgl >=1.60.0,<1.61.0' - r-base - r-bgmm test: diff --git a/recipes/bioconductor-junctionseq/meta.yaml b/recipes/bioconductor-junctionseq/meta.yaml index 9a78d1311238a..264eeb48af632 100644 --- a/recipes/bioconductor-junctionseq/meta.yaml +++ b/recipes/bioconductor-junctionseq/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.12.0" %} +{% set version = "1.14.0" %} {% set name = "JunctionSeq" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: baea765c524a275d35f74fb752cf0239 + md5: c86ceab0a76520077f0faaadeb246c90 build: number: 0 rpaths: @@ -19,16 +19,16 @@ build: # Suggests: MASS, knitr, JctSeqData, BiocStyle requirements: host: - - 'bioconductor-biobase >=2.42.0,<2.43.0' - - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' - - 'bioconductor-biocparallel >=1.16.0,<1.17.0' - - 'bioconductor-deseq2 >=1.22.0,<1.23.0' - - 'bioconductor-genefilter >=1.64.0,<1.65.0' - - 'bioconductor-geneplotter >=1.60.0,<1.61.0' - - 'bioconductor-genomicranges >=1.34.0,<1.35.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' - - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' + - 'bioconductor-biocgenerics >=0.30.0,<0.31.0' + - 'bioconductor-biocparallel >=1.18.0,<1.19.0' + - 'bioconductor-deseq2 >=1.24.0,<1.25.0' + - 'bioconductor-genefilter >=1.66.0,<1.67.0' + - 'bioconductor-geneplotter >=1.62.0,<1.63.0' + - 'bioconductor-genomicranges >=1.36.0,<1.37.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' + - 'bioconductor-summarizedexperiment >=1.14.0,<1.15.0' - r-base - r-hmisc - r-locfit @@ -38,16 +38,16 @@ requirements: - r-statmod - r-stringr run: - - 'bioconductor-biobase >=2.42.0,<2.43.0' - - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' - - 'bioconductor-biocparallel >=1.16.0,<1.17.0' - - 'bioconductor-deseq2 >=1.22.0,<1.23.0' - - 'bioconductor-genefilter >=1.64.0,<1.65.0' - - 'bioconductor-geneplotter >=1.60.0,<1.61.0' - - 'bioconductor-genomicranges >=1.34.0,<1.35.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' - - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' + - 'bioconductor-biocgenerics >=0.30.0,<0.31.0' + - 'bioconductor-biocparallel >=1.18.0,<1.19.0' + - 'bioconductor-deseq2 >=1.24.0,<1.25.0' + - 'bioconductor-genefilter >=1.66.0,<1.67.0' + - 'bioconductor-geneplotter >=1.62.0,<1.63.0' + - 'bioconductor-genomicranges >=1.36.0,<1.37.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' + - 'bioconductor-summarizedexperiment >=1.14.0,<1.15.0' - r-base - r-hmisc - r-locfit diff --git a/recipes/bioconductor-karyoploter/meta.yaml b/recipes/bioconductor-karyoploter/meta.yaml index fc2dc444661b8..f94c525e1cc9f 100644 --- a/recipes/bioconductor-karyoploter/meta.yaml +++ b/recipes/bioconductor-karyoploter/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.8.5" %} +{% set version = "1.10.0" %} {% set name = "karyoploteR" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,41 +10,43 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: 3364baf622b0fb1e91bf402c27bba96c2648eb0d52408865191cc80cb9851d03 + md5: b773f86a0f6e6fc3f1350b1d4e86e134 build: number: 0 rpaths: - lib/R/lib/ - lib/ noarch: generic -# Suggests: BiocStyle, knitr, testthat, magrittr, BSgenome.Hsapiens.UCSC.hg19, TxDb.Hsapiens.UCSC.hg19.knownGene, pasillaBamSubset +# Suggests: BiocStyle, knitr, testthat, magrittr, BSgenome.Hsapiens.UCSC.hg19, TxDb.Hsapiens.UCSC.hg19.knownGene, TxDb.Mmusculus.UCSC.mm10.knownGene, org.Hs.eg.db, org.Mm.eg.db, pasillaBamSubset requirements: host: - - 'bioconductor-bamsignals >=1.14.0,<1.15.0' - - 'bioconductor-biovizbase >=1.30.0,<1.31.0' - - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' - - 'bioconductor-genomicfeatures >=1.34.0,<1.35.0' - - 'bioconductor-genomicranges >=1.34.0,<1.35.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-regioner >=1.14.0,<1.15.0' - - 'bioconductor-rsamtools >=1.34.0,<1.35.0' - - 'bioconductor-rtracklayer >=1.42.0,<1.43.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' + - 'bioconductor-bamsignals >=1.16.0,<1.17.0' + - 'bioconductor-biovizbase >=1.32.0,<1.33.0' + - 'bioconductor-genomeinfodb >=1.20.0,<1.21.0' + - 'bioconductor-genomicfeatures >=1.36.0,<1.37.0' + - 'bioconductor-genomicranges >=1.36.0,<1.37.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-regioner >=1.16.0,<1.17.0' + - 'bioconductor-rsamtools >=2.0.0,<2.1.0' + - 'bioconductor-rtracklayer >=1.44.0,<1.45.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' - r-base - r-bezier - r-digest - r-memoise run: - - 'bioconductor-bamsignals >=1.14.0,<1.15.0' - - 'bioconductor-biovizbase >=1.30.0,<1.31.0' - - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' - - 'bioconductor-genomicfeatures >=1.34.0,<1.35.0' - - 'bioconductor-genomicranges >=1.34.0,<1.35.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-regioner >=1.14.0,<1.15.0' - - 'bioconductor-rsamtools >=1.34.0,<1.35.0' - - 'bioconductor-rtracklayer >=1.42.0,<1.43.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' + - 'bioconductor-bamsignals >=1.16.0,<1.17.0' + - 'bioconductor-biovizbase >=1.32.0,<1.33.0' + - 'bioconductor-genomeinfodb >=1.20.0,<1.21.0' + - 'bioconductor-genomicfeatures >=1.36.0,<1.37.0' + - 'bioconductor-genomicranges >=1.36.0,<1.37.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-regioner >=1.16.0,<1.17.0' + - 'bioconductor-rsamtools >=2.0.0,<2.1.0' + - 'bioconductor-rtracklayer >=1.44.0,<1.45.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' - r-base - r-bezier - r-digest diff --git a/recipes/bioconductor-kcsmart/meta.yaml b/recipes/bioconductor-kcsmart/meta.yaml index a483554d26771..53f40b49c681e 100644 --- a/recipes/bioconductor-kcsmart/meta.yaml +++ b/recipes/bioconductor-kcsmart/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "2.40.0" %} +{% set version = "2.42.0" %} {% set name = "KCsmart" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 8f57fd4003e5da98c7cd7749ac054e70 + md5: 35a417f9b9b31b4564cc1e471d4e5755 build: number: 0 rpaths: @@ -19,15 +19,15 @@ build: noarch: generic requirements: host: - - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' - - 'bioconductor-multtest >=2.38.0,<2.39.0' - - 'bioconductor-siggenes >=1.56.0,<1.57.0' + - 'bioconductor-biocgenerics >=0.30.0,<0.31.0' + - 'bioconductor-multtest >=2.40.0,<2.41.0' + - 'bioconductor-siggenes >=1.58.0,<1.59.0' - r-base - r-kernsmooth run: - - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' - - 'bioconductor-multtest >=2.38.0,<2.39.0' - - 'bioconductor-siggenes >=1.56.0,<1.57.0' + - 'bioconductor-biocgenerics >=0.30.0,<0.31.0' + - 'bioconductor-multtest >=2.40.0,<2.41.0' + - 'bioconductor-siggenes >=1.58.0,<1.59.0' - r-base - r-kernsmooth test: diff --git a/recipes/bioconductor-kebabs/meta.yaml b/recipes/bioconductor-kebabs/meta.yaml index e99f711799d98..db1bc73ea98ab 100644 --- a/recipes/bioconductor-kebabs/meta.yaml +++ b/recipes/bioconductor-kebabs/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.16.0" %} +{% set version = "1.18.0" %} {% set name = "kebabs" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 219c50a9e26b4adfd9e23c8fb3684bc6 + md5: 1ae029f6e3b610712443e5782250d37f build: number: 0 rpaths: @@ -19,10 +19,10 @@ build: # Suggests: SparseM, Biobase, BiocGenerics, knitr requirements: host: - - 'bioconductor-biostrings >=2.50.0,<2.51.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' - - 'bioconductor-xvector >=0.22.0,<0.23.0' + - 'bioconductor-biostrings >=2.52.0,<2.53.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' + - 'bioconductor-xvector >=0.24.0,<0.25.0' - r-apcluster - r-base - r-e1071 @@ -31,10 +31,10 @@ requirements: - r-matrix - 'r-rcpp >=0.11.2' run: - - 'bioconductor-biostrings >=2.50.0,<2.51.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' - - 'bioconductor-xvector >=0.22.0,<0.23.0' + - 'bioconductor-biostrings >=2.52.0,<2.53.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' + - 'bioconductor-xvector >=0.24.0,<0.25.0' - r-apcluster - r-base - r-e1071 diff --git a/recipes/bioconductor-kegg.db/meta.yaml b/recipes/bioconductor-kegg.db/meta.yaml index bc16b3dede543..e5077c88532a7 100644 --- a/recipes/bioconductor-kegg.db/meta.yaml +++ b/recipes/bioconductor-kegg.db/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.2.3" %} {% set name = "KEGG.db" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -12,7 +12,7 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' md5: 023ac22f57063627c2e62d1ae5e011b0 build: - number: 5 + number: 6 rpaths: - lib/R/lib/ - lib/ @@ -20,12 +20,12 @@ build: # Suggests: DBI requirements: host: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' - r-base run: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-kegg.db/post-link.sh b/recipes/bioconductor-kegg.db/post-link.sh index a7620544568ec..810f3710862cd 100644 --- a/recipes/bioconductor-kegg.db/post-link.sh +++ b/recipes/bioconductor-kegg.db/post-link.sh @@ -1,7 +1,7 @@ #!/bin/bash FN="KEGG.db_3.2.3.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/KEGG.db_3.2.3.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/KEGG.db_3.2.3.tar.gz" "https://bioarchive.galaxyproject.org/KEGG.db_3.2.3.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-kegg.db/bioconductor-kegg.db_3.2.3_src_all.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-kegg.db/bioconductor-kegg.db_3.2.3_src_all.tar.gz" @@ -17,7 +17,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-keggandmetacoredzpathwaysgeo/meta.yaml b/recipes/bioconductor-keggandmetacoredzpathwaysgeo/meta.yaml index 19aca1c673133..e3689fa23307a 100644 --- a/recipes/bioconductor-keggandmetacoredzpathwaysgeo/meta.yaml +++ b/recipes/bioconductor-keggandmetacoredzpathwaysgeo/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.2.0" %} +{% set version = "1.4.0" %} {% set name = "KEGGandMetacoreDzPathwaysGEO" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: da545248fec755e65427c118cd8d518d + md5: 7d61c7d151e5cb9b955199a4b184a761 build: number: 0 rpaths: @@ -19,14 +19,14 @@ build: noarch: generic requirements: host: - - 'bioconductor-biobase >=2.42.0,<2.43.0' - - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' + - 'bioconductor-biocgenerics >=0.30.0,<0.31.0' - r-base run: - - 'bioconductor-biobase >=2.42.0,<2.43.0' - - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' + - 'bioconductor-biocgenerics >=0.30.0,<0.31.0' - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-keggandmetacoredzpathwaysgeo/post-link.sh b/recipes/bioconductor-keggandmetacoredzpathwaysgeo/post-link.sh index c89436feb0f6e..92b30a6dbe365 100644 --- a/recipes/bioconductor-keggandmetacoredzpathwaysgeo/post-link.sh +++ b/recipes/bioconductor-keggandmetacoredzpathwaysgeo/post-link.sh @@ -1,11 +1,11 @@ #!/bin/bash -FN="KEGGandMetacoreDzPathwaysGEO_1.2.0.tar.gz" +FN="KEGGandMetacoreDzPathwaysGEO_1.4.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/experiment/src/contrib/KEGGandMetacoreDzPathwaysGEO_1.2.0.tar.gz" - "https://bioarchive.galaxyproject.org/KEGGandMetacoreDzPathwaysGEO_1.2.0.tar.gz" - "https://depot.galaxyproject.org/software/bioconductor-keggandmetacoredzpathwaysgeo/bioconductor-keggandmetacoredzpathwaysgeo_1.2.0_src_all.tar.gz" + "https://bioconductor.org/packages/3.9/data/experiment/src/contrib/KEGGandMetacoreDzPathwaysGEO_1.4.0.tar.gz" + "https://bioarchive.galaxyproject.org/KEGGandMetacoreDzPathwaysGEO_1.4.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-keggandmetacoredzpathwaysgeo/bioconductor-keggandmetacoredzpathwaysgeo_1.4.0_src_all.tar.gz" ) -MD5="da545248fec755e65427c118cd8d518d" +MD5="7d61c7d151e5cb9b955199a4b184a761" # Use a staging area in the conda dir rather than temp dirs, both to avoid # permission issues as well as to have things downloaded in a predictable @@ -16,7 +16,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-keggdzpathwaysgeo/meta.yaml b/recipes/bioconductor-keggdzpathwaysgeo/meta.yaml index 0a158c67ed50d..e11674803e212 100644 --- a/recipes/bioconductor-keggdzpathwaysgeo/meta.yaml +++ b/recipes/bioconductor-keggdzpathwaysgeo/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.20.0" %} +{% set version = "1.22.0" %} {% set name = "KEGGdzPathwaysGEO" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 773a71a68a75a39fc631776efb73e7dc + md5: 89a8755fa8639a60b631b1f72336e98f build: number: 0 rpaths: @@ -19,14 +19,14 @@ build: noarch: generic requirements: host: - - 'bioconductor-biobase >=2.42.0,<2.43.0' - - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' + - 'bioconductor-biocgenerics >=0.30.0,<0.31.0' - r-base run: - - 'bioconductor-biobase >=2.42.0,<2.43.0' - - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' + - 'bioconductor-biocgenerics >=0.30.0,<0.31.0' - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-keggdzpathwaysgeo/post-link.sh b/recipes/bioconductor-keggdzpathwaysgeo/post-link.sh index ece2ced785bd9..0d67fc87c4666 100644 --- a/recipes/bioconductor-keggdzpathwaysgeo/post-link.sh +++ b/recipes/bioconductor-keggdzpathwaysgeo/post-link.sh @@ -1,11 +1,11 @@ #!/bin/bash -FN="KEGGdzPathwaysGEO_1.20.0.tar.gz" +FN="KEGGdzPathwaysGEO_1.22.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/experiment/src/contrib/KEGGdzPathwaysGEO_1.20.0.tar.gz" - "https://bioarchive.galaxyproject.org/KEGGdzPathwaysGEO_1.20.0.tar.gz" - "https://depot.galaxyproject.org/software/bioconductor-keggdzpathwaysgeo/bioconductor-keggdzpathwaysgeo_1.20.0_src_all.tar.gz" + "https://bioconductor.org/packages/3.9/data/experiment/src/contrib/KEGGdzPathwaysGEO_1.22.0.tar.gz" + "https://bioarchive.galaxyproject.org/KEGGdzPathwaysGEO_1.22.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-keggdzpathwaysgeo/bioconductor-keggdzpathwaysgeo_1.22.0_src_all.tar.gz" ) -MD5="773a71a68a75a39fc631776efb73e7dc" +MD5="89a8755fa8639a60b631b1f72336e98f" # Use a staging area in the conda dir rather than temp dirs, both to avoid # permission issues as well as to have things downloaded in a predictable @@ -16,7 +16,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-kegggraph/meta.yaml b/recipes/bioconductor-kegggraph/meta.yaml index 527445dd033ed..b79fe590f4ba4 100644 --- a/recipes/bioconductor-kegggraph/meta.yaml +++ b/recipes/bioconductor-kegggraph/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.42.0" %} +{% set version = "1.44.0" %} {% set name = "KEGGgraph" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,22 +10,24 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 6299732316aed3d57a74c3750b1ab43c + md5: e298c4cd0727be85b994ce6d55b231b1 build: number: 0 rpaths: - lib/R/lib/ - lib/ noarch: generic -# Suggests: Rgraphviz, RBGL, RUnit, RColorBrewer, KEGG.db, org.Hs.eg.db, hgu133plus2.db, SPIA +# Suggests: Rgraphviz, RBGL, testthat, RColorBrewer, KEGG.db, org.Hs.eg.db, hgu133plus2.db, SPIA requirements: host: - - 'bioconductor-graph >=1.60.0,<1.61.0' + - 'bioconductor-graph >=1.62.0,<1.63.0' - r-base + - r-rcurl - 'r-xml >=2.3-0' run: - - 'bioconductor-graph >=1.60.0,<1.61.0' + - 'bioconductor-graph >=1.62.0,<1.63.0' - r-base + - r-rcurl - 'r-xml >=2.3-0' test: commands: diff --git a/recipes/bioconductor-kegglincs/meta.yaml b/recipes/bioconductor-kegglincs/meta.yaml index 89b0b7415e620..3e3ffa0d64881 100644 --- a/recipes/bioconductor-kegglincs/meta.yaml +++ b/recipes/bioconductor-kegglincs/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.8.0" %} +{% set version = "1.10.0" %} {% set name = "KEGGlincs" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 563a47dca90ab2a1999f27257ad8a4bc + md5: 36bea9619be4db9dcb06b96fd1e3412e build: number: 0 rpaths: @@ -21,12 +21,12 @@ build: # SystemRequirements: Cytoscape (>= 3.3.0), Java (>= 8) requirements: host: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' - 'bioconductor-hgu133a.db >=3.2.0,<3.3.0' - - 'bioconductor-kegggraph >=1.42.0,<1.43.0' - - 'bioconductor-keggrest >=1.22.0,<1.23.0' - - 'bioconductor-kodata >=1.8.0,<1.9.0' - - 'bioconductor-org.hs.eg.db >=3.7.0,<3.8.0' + - 'bioconductor-kegggraph >=1.44.0,<1.45.0' + - 'bioconductor-keggrest >=1.24.0,<1.25.0' + - 'bioconductor-kodata >=1.10.0,<1.11.0' + - 'bioconductor-org.hs.eg.db >=3.8.0,<3.9.0' - r-base - r-gtools - r-httr @@ -34,13 +34,15 @@ requirements: - r-plyr - r-rjsonio - r-xml + - cytoscape >=3.3.0 + - openjdk 8.* run: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' - 'bioconductor-hgu133a.db >=3.2.0,<3.3.0' - - 'bioconductor-kegggraph >=1.42.0,<1.43.0' - - 'bioconductor-keggrest >=1.22.0,<1.23.0' - - 'bioconductor-kodata >=1.8.0,<1.9.0' - - 'bioconductor-org.hs.eg.db >=3.7.0,<3.8.0' + - 'bioconductor-kegggraph >=1.44.0,<1.45.0' + - 'bioconductor-keggrest >=1.24.0,<1.25.0' + - 'bioconductor-kodata >=1.10.0,<1.11.0' + - 'bioconductor-org.hs.eg.db >=3.8.0,<3.9.0' - r-base - r-gtools - r-httr @@ -48,6 +50,8 @@ requirements: - r-plyr - r-rjsonio - r-xml + - cytoscape >=3.3.0 + - openjdk 8.* test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-keggorthology/meta.yaml b/recipes/bioconductor-keggorthology/meta.yaml index ce369fb59c205..be5bf136a557b 100644 --- a/recipes/bioconductor-keggorthology/meta.yaml +++ b/recipes/bioconductor-keggorthology/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "2.34.0" %} +{% set version = "2.36.0" %} {% set name = "keggorthology" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 62ca96db218f39f0168b022ccf63fcce + md5: a469c9ebfc6aa734e7ff0a370a76ea76 build: number: 0 rpaths: @@ -20,14 +20,14 @@ build: # Suggests: RBGL,ALL requirements: host: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' - - 'bioconductor-graph >=1.60.0,<1.61.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' + - 'bioconductor-graph >=1.62.0,<1.63.0' - 'bioconductor-hgu95av2.db >=3.2.0,<3.3.0' - r-base - r-dbi run: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' - - 'bioconductor-graph >=1.60.0,<1.61.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' + - 'bioconductor-graph >=1.62.0,<1.63.0' - 'bioconductor-hgu95av2.db >=3.2.0,<3.3.0' - r-base - r-dbi diff --git a/recipes/bioconductor-keggprofile/meta.yaml b/recipes/bioconductor-keggprofile/meta.yaml index 05cacb898013a..eb61d89179609 100644 --- a/recipes/bioconductor-keggprofile/meta.yaml +++ b/recipes/bioconductor-keggprofile/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.24.0" %} +{% set version = "1.26.0" %} {% set name = "KEGGprofile" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 94f3b5f4687557760207e432fba9c2e9 + md5: 91deb781c85b4721d458507ead2a49d4 build: number: 0 rpaths: @@ -19,20 +19,20 @@ build: noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' - - 'bioconductor-biomart >=2.38.0,<2.39.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' + - 'bioconductor-biomart >=2.40.0,<2.41.0' - 'bioconductor-kegg.db >=3.2.0,<3.3.0' - - 'bioconductor-keggrest >=1.22.0,<1.23.0' + - 'bioconductor-keggrest >=1.24.0,<1.25.0' - r-base - r-png - r-rcurl - r-teachingdemos - r-xml run: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' - - 'bioconductor-biomart >=2.38.0,<2.39.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' + - 'bioconductor-biomart >=2.40.0,<2.41.0' - 'bioconductor-kegg.db >=3.2.0,<3.3.0' - - 'bioconductor-keggrest >=1.22.0,<1.23.0' + - 'bioconductor-keggrest >=1.24.0,<1.25.0' - r-base - r-png - r-rcurl diff --git a/recipes/bioconductor-keggrest/meta.yaml b/recipes/bioconductor-keggrest/meta.yaml index a171fa01c9056..68dc8b6d95ae9 100644 --- a/recipes/bioconductor-keggrest/meta.yaml +++ b/recipes/bioconductor-keggrest/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.22.0" %} +{% set version = "1.24.0" %} {% set name = "KEGGREST" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: a261af7eef51941349a3ff93d4b4e28b + md5: 92afe9765a580a1c947fb6d5467c9eb7 build: number: 0 rpaths: @@ -20,12 +20,12 @@ build: # Suggests: RUnit, BiocGenerics, knitr requirements: host: - - 'bioconductor-biostrings >=2.50.0,<2.51.0' + - 'bioconductor-biostrings >=2.52.0,<2.53.0' - r-base - r-httr - r-png run: - - 'bioconductor-biostrings >=2.50.0,<2.51.0' + - 'bioconductor-biostrings >=2.52.0,<2.53.0' - r-base - r-httr - r-png diff --git a/recipes/bioconductor-kidpack/meta.yaml b/recipes/bioconductor-kidpack/meta.yaml index 258d489fc8226..53d5a0ec9168f 100644 --- a/recipes/bioconductor-kidpack/meta.yaml +++ b/recipes/bioconductor-kidpack/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.24.0" %} +{% set version = "1.26.0" %} {% set name = "kidpack" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 322beb70d039afe48c7107df1a498bc4 + md5: 380a3108979f90114e23c9756fb10bd0 build: number: 0 rpaths: @@ -19,12 +19,12 @@ build: noarch: generic requirements: host: - - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' - r-base run: - - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-kidpack/post-link.sh b/recipes/bioconductor-kidpack/post-link.sh index f30e762da9b94..6ea5af25a64af 100644 --- a/recipes/bioconductor-kidpack/post-link.sh +++ b/recipes/bioconductor-kidpack/post-link.sh @@ -1,11 +1,11 @@ #!/bin/bash -FN="kidpack_1.24.0.tar.gz" +FN="kidpack_1.26.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/experiment/src/contrib/kidpack_1.24.0.tar.gz" - "https://bioarchive.galaxyproject.org/kidpack_1.24.0.tar.gz" - "https://depot.galaxyproject.org/software/bioconductor-kidpack/bioconductor-kidpack_1.24.0_src_all.tar.gz" + "https://bioconductor.org/packages/3.9/data/experiment/src/contrib/kidpack_1.26.0.tar.gz" + "https://bioarchive.galaxyproject.org/kidpack_1.26.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-kidpack/bioconductor-kidpack_1.26.0_src_all.tar.gz" ) -MD5="322beb70d039afe48c7107df1a498bc4" +MD5="380a3108979f90114e23c9756fb10bd0" # Use a staging area in the conda dir rather than temp dirs, both to avoid # permission issues as well as to have things downloaded in a predictable @@ -16,7 +16,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-kimod/meta.yaml b/recipes/bioconductor-kimod/meta.yaml index ca073f0952834..3b9f33bb12a91 100644 --- a/recipes/bioconductor-kimod/meta.yaml +++ b/recipes/bioconductor-kimod/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.10.0" %} +{% set version = "1.12.0" %} {% set name = "kimod" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 3320975d680f42063eced2de930fe779 + md5: f5352633a9d77335245869357ea08738 build: number: 0 rpaths: @@ -19,11 +19,11 @@ build: noarch: generic requirements: host: - - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' - r-base - r-cluster run: - - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' - r-base - r-cluster test: diff --git a/recipes/bioconductor-kinswingr/meta.yaml b/recipes/bioconductor-kinswingr/meta.yaml index daa7cad17dde6..8d95fca484042 100644 --- a/recipes/bioconductor-kinswingr/meta.yaml +++ b/recipes/bioconductor-kinswingr/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.0.3" %} +{% set version = "1.2.0" %} {% set name = "KinSwingR" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 2fdf011f7c6e01a7283be53eadfec809 + md5: b0df202538b540f80dfc3ce1df2d5efa build: number: 0 rpaths: @@ -20,12 +20,12 @@ build: # Suggests: knitr, rmarkdown requirements: host: - - 'bioconductor-biocparallel >=1.16.0,<1.17.0' + - 'bioconductor-biocparallel >=1.18.0,<1.19.0' - r-base - r-data.table - r-sqldf run: - - 'bioconductor-biocparallel >=1.16.0,<1.17.0' + - 'bioconductor-biocparallel >=1.18.0,<1.19.0' - r-base - r-data.table - r-sqldf diff --git a/recipes/bioconductor-kissde/meta.yaml b/recipes/bioconductor-kissde/meta.yaml index bc8a6b7823662..42751197c284a 100644 --- a/recipes/bioconductor-kissde/meta.yaml +++ b/recipes/bioconductor-kissde/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.2.0" %} +{% set version = "1.4.0" %} {% set name = "kissDE" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: a68a4d0b79ff6681ae24ccd879f5caba + md5: 46b4f2ecba916fb54ee06357be23a29c build: number: 0 rpaths: @@ -20,9 +20,9 @@ build: # Suggests: BiocStyle, testthat requirements: host: - - 'bioconductor-biobase >=2.42.0,<2.43.0' - - 'bioconductor-deseq2 >=1.22.0,<1.23.0' - - 'bioconductor-dss >=2.30.0,<2.31.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' + - 'bioconductor-deseq2 >=1.24.0,<1.25.0' + - 'bioconductor-dss >=2.32.0,<2.33.0' - r-aod - r-base - r-doparallel @@ -31,9 +31,9 @@ requirements: - r-gplots - r-matrixstats run: - - 'bioconductor-biobase >=2.42.0,<2.43.0' - - 'bioconductor-deseq2 >=1.22.0,<1.23.0' - - 'bioconductor-dss >=2.30.0,<2.31.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' + - 'bioconductor-deseq2 >=1.24.0,<1.25.0' + - 'bioconductor-dss >=2.32.0,<2.33.0' - r-aod - r-base - r-doparallel diff --git a/recipes/bioconductor-kodata/meta.yaml b/recipes/bioconductor-kodata/meta.yaml index 13d6095fa60b0..a53e2d8655a89 100644 --- a/recipes/bioconductor-kodata/meta.yaml +++ b/recipes/bioconductor-kodata/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.8.0" %} +{% set version = "1.10.0" %} {% set name = "KOdata" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: e5ea569cc1a24a77599835327a104962 + md5: 4decbccf4763a957a56256bf026fd955 build: number: 0 rpaths: @@ -22,7 +22,7 @@ requirements: - r-base run: - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-kodata/post-link.sh b/recipes/bioconductor-kodata/post-link.sh index e2585228793e4..3c2cceb3fe1cf 100644 --- a/recipes/bioconductor-kodata/post-link.sh +++ b/recipes/bioconductor-kodata/post-link.sh @@ -1,11 +1,11 @@ #!/bin/bash -FN="KOdata_1.8.0.tar.gz" +FN="KOdata_1.10.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/experiment/src/contrib/KOdata_1.8.0.tar.gz" - "https://bioarchive.galaxyproject.org/KOdata_1.8.0.tar.gz" - "https://depot.galaxyproject.org/software/bioconductor-kodata/bioconductor-kodata_1.8.0_src_all.tar.gz" + "https://bioconductor.org/packages/3.9/data/experiment/src/contrib/KOdata_1.10.0.tar.gz" + "https://bioarchive.galaxyproject.org/KOdata_1.10.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-kodata/bioconductor-kodata_1.10.0_src_all.tar.gz" ) -MD5="e5ea569cc1a24a77599835327a104962" +MD5="4decbccf4763a957a56256bf026fd955" # Use a staging area in the conda dir rather than temp dirs, both to avoid # permission issues as well as to have things downloaded in a predictable @@ -16,7 +16,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-lapmix/meta.yaml b/recipes/bioconductor-lapmix/meta.yaml index b5993e2c52498..9e31235847e82 100644 --- a/recipes/bioconductor-lapmix/meta.yaml +++ b/recipes/bioconductor-lapmix/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.48.0" %} +{% set version = "1.50.0" %} {% set name = "lapmix" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: c923e2cecb461a0f5eda9c6c1e79b1f8 + md5: c651cdd30ef812c669b2b06561292126 build: number: 0 rpaths: @@ -19,10 +19,10 @@ build: noarch: generic requirements: host: - - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' - r-base run: - - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' - r-base test: commands: diff --git a/recipes/bioconductor-lapointe.db/meta.yaml b/recipes/bioconductor-lapointe.db/meta.yaml index f4574df9c4737..a141813dd36b5 100644 --- a/recipes/bioconductor-lapointe.db/meta.yaml +++ b/recipes/bioconductor-lapointe.db/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.2.3" %} {% set name = "LAPOINTE.db" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -12,7 +12,7 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' md5: 434b25ad7411201d8be6bb1a0463b387 build: - number: 1 + number: 2 rpaths: - lib/R/lib/ - lib/ @@ -20,14 +20,14 @@ build: # Suggests: DBI, annotate, RUnit requirements: host: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' - - 'bioconductor-org.hs.eg.db >=3.7.0,<3.8.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' + - 'bioconductor-org.hs.eg.db >=3.8.0,<3.9.0' - r-base run: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' - - 'bioconductor-org.hs.eg.db >=3.7.0,<3.8.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' + - 'bioconductor-org.hs.eg.db >=3.8.0,<3.9.0' - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-lapointe.db/post-link.sh b/recipes/bioconductor-lapointe.db/post-link.sh index 6e4d4ba91a1d3..67508f02cc57e 100644 --- a/recipes/bioconductor-lapointe.db/post-link.sh +++ b/recipes/bioconductor-lapointe.db/post-link.sh @@ -1,9 +1,10 @@ #!/bin/bash FN="LAPOINTE.db_3.2.3.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/LAPOINTE.db_3.2.3.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/LAPOINTE.db_3.2.3.tar.gz" "https://bioarchive.galaxyproject.org/LAPOINTE.db_3.2.3.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-lapointe.db/bioconductor-lapointe.db_3.2.3_src_all.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-lapointe.db/bioconductor-lapointe.db_3.2.3_src_all.tar.gz" ) MD5="434b25ad7411201d8be6bb1a0463b387" @@ -16,7 +17,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-lbe/meta.yaml b/recipes/bioconductor-lbe/meta.yaml index 2c98a80edc9f1..53afacd4de19a 100644 --- a/recipes/bioconductor-lbe/meta.yaml +++ b/recipes/bioconductor-lbe/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.50.0" %} +{% set version = "1.52.0" %} {% set name = "LBE" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: fe7324956ca41278f4c97e74910242bd + md5: b202a9fa83581c2ced9eda1b4878cedb build: number: 0 rpaths: diff --git a/recipes/bioconductor-ldblock/meta.yaml b/recipes/bioconductor-ldblock/meta.yaml index 3577e9127f876..0393ea5d26872 100644 --- a/recipes/bioconductor-ldblock/meta.yaml +++ b/recipes/bioconductor-ldblock/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.12.0" %} +{% set version = "1.14.0" %} {% set name = "ldblock" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: d9097bcd8ed27b87d49e01b1e17917c5 + md5: d67febd9e2a3b7117ab236bb253826ba build: number: 0 rpaths: @@ -20,27 +20,27 @@ build: # Suggests: RUnit, BiocGenerics, knitr requirements: host: - - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' - - 'bioconductor-erma >=0.14.0,<0.15.0' - - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' - - 'bioconductor-genomicfiles >=1.18.0,<1.19.0' - - 'bioconductor-go.db >=3.7.0,<3.8.0' - - 'bioconductor-homo.sapiens >=1.3.0,<1.4.0' - - 'bioconductor-rsamtools >=1.34.0,<1.35.0' - - 'bioconductor-snpstats >=1.32.0,<1.33.0' - - 'bioconductor-variantannotation >=1.28.0,<1.29.0' + - 'bioconductor-biocgenerics >=0.30.0,<0.31.0' + - 'bioconductor-erma >=1.0.0,<1.1.0' + - 'bioconductor-genomeinfodb >=1.20.0,<1.21.0' + - 'bioconductor-genomicfiles >=1.20.0,<1.21.0' + - 'bioconductor-go.db >=3.8.0,<3.9.0' + - 'bioconductor-homo.sapiens >=1.4.0,<1.5.0' + - 'bioconductor-rsamtools >=2.0.0,<2.1.0' + - 'bioconductor-snpstats >=1.34.0,<1.35.0' + - 'bioconductor-variantannotation >=1.30.0,<1.31.0' - r-base - r-matrix run: - - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' - - 'bioconductor-erma >=0.14.0,<0.15.0' - - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' - - 'bioconductor-genomicfiles >=1.18.0,<1.19.0' - - 'bioconductor-go.db >=3.7.0,<3.8.0' - - 'bioconductor-homo.sapiens >=1.3.0,<1.4.0' - - 'bioconductor-rsamtools >=1.34.0,<1.35.0' - - 'bioconductor-snpstats >=1.32.0,<1.33.0' - - 'bioconductor-variantannotation >=1.28.0,<1.29.0' + - 'bioconductor-biocgenerics >=0.30.0,<0.31.0' + - 'bioconductor-erma >=1.0.0,<1.1.0' + - 'bioconductor-genomeinfodb >=1.20.0,<1.21.0' + - 'bioconductor-genomicfiles >=1.20.0,<1.21.0' + - 'bioconductor-go.db >=3.8.0,<3.9.0' + - 'bioconductor-homo.sapiens >=1.4.0,<1.5.0' + - 'bioconductor-rsamtools >=2.0.0,<2.1.0' + - 'bioconductor-snpstats >=1.34.0,<1.35.0' + - 'bioconductor-variantannotation >=1.30.0,<1.31.0' - r-base - r-matrix test: diff --git a/recipes/bioconductor-lea/meta.yaml b/recipes/bioconductor-lea/meta.yaml index 78ed685fd0d73..38a24adc4a1a1 100644 --- a/recipes/bioconductor-lea/meta.yaml +++ b/recipes/bioconductor-lea/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "2.4.0" %} +{% set version = "2.6.0" %} {% set name = "LEA" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 09abcae8ba7f52591c344deec4c62867 + md5: a20d7c2992d2218b872b637768cd24a1 build: number: 0 rpaths: diff --git a/recipes/bioconductor-ledpred/meta.yaml b/recipes/bioconductor-ledpred/meta.yaml index e1c7b71e1c537..4164e8e08dae6 100644 --- a/recipes/bioconductor-ledpred/meta.yaml +++ b/recipes/bioconductor-ledpred/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.16.0" %} +{% set version = "1.18.0" %} {% set name = "LedPred" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 689b1b8c2a3248119bd8f8c4c6f16c77 + md5: a8c110446d86b622593f1326c4757d3c build: number: 0 rpaths: diff --git a/recipes/bioconductor-leebamviews/meta.yaml b/recipes/bioconductor-leebamviews/meta.yaml index 8c83e025a0fd5..0aa44b53f0cdf 100644 --- a/recipes/bioconductor-leebamviews/meta.yaml +++ b/recipes/bioconductor-leebamviews/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.18.0" %} +{% set version = "1.20.0" %} {% set name = "leeBamViews" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 0ef787cb317db2a29797f2b72a513c60 + md5: 6e912f317ff209d059e12093b2816993 build: number: 0 rpaths: @@ -20,20 +20,20 @@ build: # Suggests: GenomeGraphs, biomaRt, org.Sc.sgd.db, edgeR requirements: host: - - 'bioconductor-biobase >=2.42.0,<2.43.0' - - 'bioconductor-bsgenome >=1.50.0,<1.51.0' - - 'bioconductor-genomicalignments >=1.18.0,<1.19.0' - - 'bioconductor-genomicranges >=1.34.0,<1.35.0' - - 'bioconductor-rsamtools >=1.34.0,<1.35.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' + - 'bioconductor-bsgenome >=1.52.0,<1.53.0' + - 'bioconductor-genomicalignments >=1.20.0,<1.21.0' + - 'bioconductor-genomicranges >=1.36.0,<1.37.0' + - 'bioconductor-rsamtools >=2.0.0,<2.1.0' - r-base run: - - 'bioconductor-biobase >=2.42.0,<2.43.0' - - 'bioconductor-bsgenome >=1.50.0,<1.51.0' - - 'bioconductor-genomicalignments >=1.18.0,<1.19.0' - - 'bioconductor-genomicranges >=1.34.0,<1.35.0' - - 'bioconductor-rsamtools >=1.34.0,<1.35.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' + - 'bioconductor-bsgenome >=1.52.0,<1.53.0' + - 'bioconductor-genomicalignments >=1.20.0,<1.21.0' + - 'bioconductor-genomicranges >=1.36.0,<1.37.0' + - 'bioconductor-rsamtools >=2.0.0,<2.1.0' - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-leebamviews/post-link.sh b/recipes/bioconductor-leebamviews/post-link.sh index ca748e3d760b0..92041f9528f15 100644 --- a/recipes/bioconductor-leebamviews/post-link.sh +++ b/recipes/bioconductor-leebamviews/post-link.sh @@ -1,11 +1,11 @@ #!/bin/bash -FN="leeBamViews_1.18.0.tar.gz" +FN="leeBamViews_1.20.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/experiment/src/contrib/leeBamViews_1.18.0.tar.gz" - "https://bioarchive.galaxyproject.org/leeBamViews_1.18.0.tar.gz" - "https://depot.galaxyproject.org/software/bioconductor-leebamviews/bioconductor-leebamviews_1.18.0_src_all.tar.gz" + "https://bioconductor.org/packages/3.9/data/experiment/src/contrib/leeBamViews_1.20.0.tar.gz" + "https://bioarchive.galaxyproject.org/leeBamViews_1.20.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-leebamviews/bioconductor-leebamviews_1.20.0_src_all.tar.gz" ) -MD5="0ef787cb317db2a29797f2b72a513c60" +MD5="6e912f317ff209d059e12093b2816993" # Use a staging area in the conda dir rather than temp dirs, both to avoid # permission issues as well as to have things downloaded in a predictable @@ -16,7 +16,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-les/meta.yaml b/recipes/bioconductor-les/meta.yaml index faa82b0edb9a1..f3aa61a03f4bd 100644 --- a/recipes/bioconductor-les/meta.yaml +++ b/recipes/bioconductor-les/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.32.0" %} +{% set version = "1.34.0" %} {% set name = "les" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: d1f865bfb6b23e1d6dc272b84ca3c8d7 + md5: 674dc44527723d71cfeccb035f328b1b build: number: 0 rpaths: diff --git a/recipes/bioconductor-leukemiaseset/meta.yaml b/recipes/bioconductor-leukemiaseset/meta.yaml index 05198a36074d9..479697fee9de4 100644 --- a/recipes/bioconductor-leukemiaseset/meta.yaml +++ b/recipes/bioconductor-leukemiaseset/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.18.0" %} +{% set version = "1.20.0" %} {% set name = "leukemiasEset" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 266d9f40a851b36ce15025356ed08a72 + md5: d8ae541fe7fb33d22bff4cbf35d73a2c build: number: 0 rpaths: @@ -19,12 +19,12 @@ build: noarch: generic requirements: host: - - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' - r-base run: - - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-leukemiaseset/post-link.sh b/recipes/bioconductor-leukemiaseset/post-link.sh index ed7ad9f0a000f..1d0a9b9006469 100644 --- a/recipes/bioconductor-leukemiaseset/post-link.sh +++ b/recipes/bioconductor-leukemiaseset/post-link.sh @@ -1,11 +1,11 @@ #!/bin/bash -FN="leukemiasEset_1.18.0.tar.gz" +FN="leukemiasEset_1.20.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/experiment/src/contrib/leukemiasEset_1.18.0.tar.gz" - "https://bioarchive.galaxyproject.org/leukemiasEset_1.18.0.tar.gz" - "https://depot.galaxyproject.org/software/bioconductor-leukemiaseset/bioconductor-leukemiaseset_1.18.0_src_all.tar.gz" + "https://bioconductor.org/packages/3.9/data/experiment/src/contrib/leukemiasEset_1.20.0.tar.gz" + "https://bioarchive.galaxyproject.org/leukemiasEset_1.20.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-leukemiaseset/bioconductor-leukemiaseset_1.20.0_src_all.tar.gz" ) -MD5="266d9f40a851b36ce15025356ed08a72" +MD5="d8ae541fe7fb33d22bff4cbf35d73a2c" # Use a staging area in the conda dir rather than temp dirs, both to avoid # permission issues as well as to have things downloaded in a predictable @@ -16,7 +16,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-levi/meta.yaml b/recipes/bioconductor-levi/meta.yaml index 4ff914801dff0..de74a84021153 100644 --- a/recipes/bioconductor-levi/meta.yaml +++ b/recipes/bioconductor-levi/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.0.0" %} +{% set version = "1.2.0" %} {% set name = "levi" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 816a51b096ed10aa182443879db1c581 + md5: 0540fd445269f0f76b769c52390cad03 build: number: 0 rpaths: diff --git a/recipes/bioconductor-lfa/meta.yaml b/recipes/bioconductor-lfa/meta.yaml index 318bf315e2880..b72454ee47323 100644 --- a/recipes/bioconductor-lfa/meta.yaml +++ b/recipes/bioconductor-lfa/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.12.0" %} +{% set version = "1.14.0" %} {% set name = "lfa" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 0d6d80f6ebb2ff5c3fc03d7255c2d4e5 + md5: 8ffc04644ae46e129d8f9c28094b67c1 build: number: 0 rpaths: diff --git a/recipes/bioconductor-liebermanaidenhic2009/meta.yaml b/recipes/bioconductor-liebermanaidenhic2009/meta.yaml index 94d0a649062e9..b9ec022f2e750 100644 --- a/recipes/bioconductor-liebermanaidenhic2009/meta.yaml +++ b/recipes/bioconductor-liebermanaidenhic2009/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "0.20.0" %} +{% set version = "0.22.0" %} {% set name = "LiebermanAidenHiC2009" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 94eef9564f0209911a15142129efd9d0 + md5: f5bbf8ccf81d37918ff8ab7d55d8c5cc build: number: 0 rpaths: @@ -19,14 +19,14 @@ build: noarch: generic requirements: host: - - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' - r-base - r-kernsmooth run: - - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' - r-base - r-kernsmooth - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-liebermanaidenhic2009/post-link.sh b/recipes/bioconductor-liebermanaidenhic2009/post-link.sh index b6eb699daaca8..bb6dab7171528 100644 --- a/recipes/bioconductor-liebermanaidenhic2009/post-link.sh +++ b/recipes/bioconductor-liebermanaidenhic2009/post-link.sh @@ -1,11 +1,11 @@ #!/bin/bash -FN="LiebermanAidenHiC2009_0.20.0.tar.gz" +FN="LiebermanAidenHiC2009_0.22.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/experiment/src/contrib/LiebermanAidenHiC2009_0.20.0.tar.gz" - "https://bioarchive.galaxyproject.org/LiebermanAidenHiC2009_0.20.0.tar.gz" - "https://depot.galaxyproject.org/software/bioconductor-liebermanaidenhic2009/bioconductor-liebermanaidenhic2009_0.20.0_src_all.tar.gz" + "https://bioconductor.org/packages/3.9/data/experiment/src/contrib/LiebermanAidenHiC2009_0.22.0.tar.gz" + "https://bioarchive.galaxyproject.org/LiebermanAidenHiC2009_0.22.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-liebermanaidenhic2009/bioconductor-liebermanaidenhic2009_0.22.0_src_all.tar.gz" ) -MD5="94eef9564f0209911a15142129efd9d0" +MD5="f5bbf8ccf81d37918ff8ab7d55d8c5cc" # Use a staging area in the conda dir rather than temp dirs, both to avoid # permission issues as well as to have things downloaded in a predictable @@ -16,7 +16,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-limma/meta.yaml b/recipes/bioconductor-limma/meta.yaml index 7afab488223ff..c5959ce797c60 100644 --- a/recipes/bioconductor-limma/meta.yaml +++ b/recipes/bioconductor-limma/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "3.38.3" %} +{% set version = "3.40.0" %} {% set name = "limma" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 71d46ed99a9c5267645c6ad5c6bec64b + md5: e0f515b4bf85f94de2a8922da7b213a3 build: number: 0 rpaths: diff --git a/recipes/bioconductor-limmagui/meta.yaml b/recipes/bioconductor-limmagui/meta.yaml index e64331cb628f4..d8f831be913ec 100644 --- a/recipes/bioconductor-limmagui/meta.yaml +++ b/recipes/bioconductor-limmagui/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.58.0" %} +{% set version = "1.60.0" %} {% set name = "limmaGUI" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 294967acdf8df9dfe9242d09ba53b527 + md5: da7cbfa9ead2ea122e7c1a4e4f048933 build: number: 0 rpaths: @@ -19,13 +19,13 @@ build: noarch: generic requirements: host: - - 'bioconductor-limma >=3.38.0,<3.39.0' + - 'bioconductor-limma >=3.40.0,<3.41.0' - r-base - r-r2html - r-tkrplot - r-xtable run: - - 'bioconductor-limma >=3.38.0,<3.39.0' + - 'bioconductor-limma >=3.40.0,<3.41.0' - r-base - r-r2html - r-tkrplot diff --git a/recipes/bioconductor-linc/meta.yaml b/recipes/bioconductor-linc/meta.yaml index de436585ff083..fb49b3366313e 100644 --- a/recipes/bioconductor-linc/meta.yaml +++ b/recipes/bioconductor-linc/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.10.0" %} +{% set version = "1.12.0" %} {% set name = "LINC" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 29086a9caad42adcd346b9efa078457e + md5: 5b3d4f07c51e87efa8b1894f69cfd085 build: number: 0 rpaths: @@ -19,13 +19,13 @@ build: # Suggests: RUnit, BiocGenerics, knitr, biomaRt requirements: host: - - 'bioconductor-biobase >=2.42.0,<2.43.0' - - 'bioconductor-clusterprofiler >=3.10.0,<3.11.0' - - 'bioconductor-dose >=3.8.0,<3.9.0' - - 'bioconductor-ggtree >=1.14.0,<1.15.0' - - 'bioconductor-org.hs.eg.db >=3.7.0,<3.8.0' - - 'bioconductor-reactomepa >=1.26.0,<1.27.0' - - 'bioconductor-sva >=3.30.0,<3.31.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' + - 'bioconductor-clusterprofiler >=3.12.0,<3.13.0' + - 'bioconductor-dose >=3.10.0,<3.11.0' + - 'bioconductor-ggtree >=1.16.0,<1.17.0' + - 'bioconductor-org.hs.eg.db >=3.8.0,<3.9.0' + - 'bioconductor-reactomepa >=1.28.0,<1.29.0' + - 'bioconductor-sva >=3.32.0,<3.33.0' - r-ape - r-base - r-ggplot2 @@ -34,13 +34,13 @@ requirements: - 'r-rcpp >=0.11.0' - r-reshape2 run: - - 'bioconductor-biobase >=2.42.0,<2.43.0' - - 'bioconductor-clusterprofiler >=3.10.0,<3.11.0' - - 'bioconductor-dose >=3.8.0,<3.9.0' - - 'bioconductor-ggtree >=1.14.0,<1.15.0' - - 'bioconductor-org.hs.eg.db >=3.7.0,<3.8.0' - - 'bioconductor-reactomepa >=1.26.0,<1.27.0' - - 'bioconductor-sva >=3.30.0,<3.31.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' + - 'bioconductor-clusterprofiler >=3.12.0,<3.13.0' + - 'bioconductor-dose >=3.10.0,<3.11.0' + - 'bioconductor-ggtree >=1.16.0,<1.17.0' + - 'bioconductor-org.hs.eg.db >=3.8.0,<3.9.0' + - 'bioconductor-reactomepa >=1.28.0,<1.29.0' + - 'bioconductor-sva >=3.32.0,<3.33.0' - r-ape - r-base - r-ggplot2 diff --git a/recipes/bioconductor-lineagepulse/meta.yaml b/recipes/bioconductor-lineagepulse/meta.yaml index 94053c8cc5638..dbb71b4f41613 100644 --- a/recipes/bioconductor-lineagepulse/meta.yaml +++ b/recipes/bioconductor-lineagepulse/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.2.0" %} +{% set version = "1.4.0" %} {% set name = "LineagePulse" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 9271369de31f071054199e8dd0781c57 + md5: 4284019bc000d29688f6141de4a5c344 build: number: 0 rpaths: @@ -19,10 +19,10 @@ build: noarch: generic requirements: host: - - 'bioconductor-biocparallel >=1.16.0,<1.17.0' - - 'bioconductor-complexheatmap >=1.20.0,<1.21.0' - - 'bioconductor-singlecellexperiment >=1.4.0,<1.5.0' - - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' + - 'bioconductor-biocparallel >=1.18.0,<1.19.0' + - 'bioconductor-complexheatmap >=2.0.0,<2.1.0' + - 'bioconductor-singlecellexperiment >=1.6.0,<1.7.0' + - 'bioconductor-summarizedexperiment >=1.14.0,<1.15.0' - r-base - r-circlize - r-ggplot2 @@ -31,10 +31,10 @@ requirements: - r-matrix - r-rcolorbrewer run: - - 'bioconductor-biocparallel >=1.16.0,<1.17.0' - - 'bioconductor-complexheatmap >=1.20.0,<1.21.0' - - 'bioconductor-singlecellexperiment >=1.4.0,<1.5.0' - - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' + - 'bioconductor-biocparallel >=1.18.0,<1.19.0' + - 'bioconductor-complexheatmap >=2.0.0,<2.1.0' + - 'bioconductor-singlecellexperiment >=1.6.0,<1.7.0' + - 'bioconductor-summarizedexperiment >=1.14.0,<1.15.0' - r-base - r-circlize - r-ggplot2 diff --git a/recipes/bioconductor-linnorm/meta.yaml b/recipes/bioconductor-linnorm/meta.yaml index 37db4fe32391b..b89356693c9b7 100644 --- a/recipes/bioconductor-linnorm/meta.yaml +++ b/recipes/bioconductor-linnorm/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "2.6.1" %} +{% set version = "2.8.0" %} {% set name = "Linnorm" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: e6aef6bd899b47ffdc83c95f844508e08f8d8470760fdd31750910364b45f3e1 + md5: f7a2a4de6993c6351ae07f7d70370deb build: number: 0 rpaths: @@ -19,7 +19,7 @@ build: # Suggests: BiocStyle, knitr, rmarkdown, gplots, RColorBrewer, moments, testthat requirements: host: - - 'bioconductor-limma >=3.38.0,<3.39.0' + - 'bioconductor-limma >=3.40.0,<3.41.0' - r-amap - r-apcluster - r-base @@ -39,7 +39,7 @@ requirements: - r-vegan - r-zoo run: - - 'bioconductor-limma >=3.38.0,<3.39.0' + - 'bioconductor-limma >=3.40.0,<3.41.0' - r-amap - r-apcluster - r-base @@ -68,5 +68,5 @@ test: about: home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: 'MIT + file LICENSE' - summary: 'Linnorm is an R package for the analysis of RNA-seq, scRNA-seq, ChIP-seq count data or any large scale count data. It transforms such datasets for parametric tests. In addition to the transformtion function (Linnorm), the following pipelines are implemented: 1. Library size/Batch effect normalization (Linnorm.Norm), 2. Cell subpopluation analysis and visualization using t-SNE or PCA K-means clustering or Hierarchical clustering (Linnorm.tSNE, Linnorm.PCA, Linnorm.HClust), 3. Differential expression analysis or differential peak detection using limma (Linnorm.limma), 4. Highly variable gene discovery and visualization (Linnorm.HVar), 5. Gene correlation network analysis and visualization (Linnorm.Cor), 6. Stable gene selection for scRNA-seq data; for users without or do not want to rely on spike-in genes (Linnorm.SGenes). 7. Data imputation. (under development) (Linnorm.DataImput). Linnorm can work with raw count, CPM, RPKM, FPKM and TPM. Additionally, the RnaXSim function is included for simulating RNA-seq data for the evaluation of DEG analysis methods.' + summary: 'Linnorm is an R package for the analysis of RNA-seq, scRNA-seq, ChIP-seq count data or any large scale count data. It normalizes and performs variance-stabilizing transformation on such datasets. In addition to the transformtion function (Linnorm), the following pipelines are implemented: 1. Library size/Batch effect normalization (Linnorm.Norm), 2. Cell subpopluation analysis and visualization using t-SNE or PCA K-means clustering or Hierarchical clustering (Linnorm.tSNE, Linnorm.PCA, Linnorm.HClust), 3. Differential expression analysis or differential peak detection using limma (Linnorm.limma), 4. Highly variable gene discovery and visualization (Linnorm.HVar), 5. Gene correlation network analysis and visualization (Linnorm.Cor), 6. Stable gene selection for scRNA-seq data; for users without or do not want to rely on spike-in genes (Linnorm.SGenes). 7. Data imputation. (under development) (Linnorm.DataImput). Linnorm can work with raw count, CPM, RPKM, FPKM and TPM. Additionally, the RnaXSim function is included for simulating RNA-seq data for the evaluation of DEG analysis methods.' diff --git a/recipes/bioconductor-lipidr/build.sh b/recipes/bioconductor-lipidr/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-lipidr/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-lipidr/meta.yaml b/recipes/bioconductor-lipidr/meta.yaml new file mode 100644 index 0000000000000..40e9cf19d7dca --- /dev/null +++ b/recipes/bioconductor-lipidr/meta.yaml @@ -0,0 +1,55 @@ +{% set version = "1.0.0" %} +{% set name = "lipidr" %} +{% set bioc = "3.9" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + md5: a827e4309c6d3751f78e194bd2b4668d +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: knitr, rmarkdown, BiocStyle, ggrepel, plotly, covr, spelling +requirements: + host: + - 'bioconductor-fgsea >=1.10.0,<1.11.0' + - 'bioconductor-limma >=3.40.0,<3.41.0' + - 'bioconductor-ropls >=1.16.0,<1.17.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' + - 'bioconductor-summarizedexperiment >=1.14.0,<1.15.0' + - r-base + - r-dplyr + - r-forcats + - r-ggplot2 + - r-magrittr + - r-rlang + - r-tidyr + run: + - 'bioconductor-fgsea >=1.10.0,<1.11.0' + - 'bioconductor-limma >=3.40.0,<3.41.0' + - 'bioconductor-ropls >=1.16.0,<1.17.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' + - 'bioconductor-summarizedexperiment >=1.14.0,<1.15.0' + - r-base + - r-dplyr + - r-forcats + - r-ggplot2 + - r-magrittr + - r-rlang + - r-tidyr +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: 'MIT + file LICENSE' + summary: 'lipidr an easy-to-use R package implementing a complete workflow for downstream analysis of lipidomics data. lipidr parses results exported from Skyline directly into R, allowing integration into current analysis frameworks. lipidr allows data inspection, normalization, univariate and multivariate analysis, displaying informative visualizations. lipidr also implements a novel Lipid Set Enrichment Analysis (LSEA), harnessing molecular information such as lipid class, chain length and unsaturation.' + diff --git a/recipes/bioconductor-liquidassociation/meta.yaml b/recipes/bioconductor-liquidassociation/meta.yaml index 8479f03eb2248..ae56b07d14f85 100644 --- a/recipes/bioconductor-liquidassociation/meta.yaml +++ b/recipes/bioconductor-liquidassociation/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.36.0" %} +{% set version = "1.38.0" %} {% set name = "LiquidAssociation" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 0c5372f29db62136b3797b29b3debe18 + md5: 8ff9e0913456b720c8366e01ec419d48 build: number: 0 rpaths: @@ -19,15 +19,15 @@ build: noarch: generic requirements: host: - - 'bioconductor-biobase >=2.42.0,<2.43.0' - - 'bioconductor-org.sc.sgd.db >=3.7.0,<3.8.0' - - 'bioconductor-yeastcc >=1.22.0,<1.23.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' + - 'bioconductor-org.sc.sgd.db >=3.8.0,<3.9.0' + - 'bioconductor-yeastcc >=1.24.0,<1.25.0' - r-base - r-geepack run: - - 'bioconductor-biobase >=2.42.0,<2.43.0' - - 'bioconductor-org.sc.sgd.db >=3.7.0,<3.8.0' - - 'bioconductor-yeastcc >=1.22.0,<1.23.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' + - 'bioconductor-org.sc.sgd.db >=3.8.0,<3.9.0' + - 'bioconductor-yeastcc >=1.24.0,<1.25.0' - r-base - r-geepack test: diff --git a/recipes/bioconductor-listeretalbsseq/meta.yaml b/recipes/bioconductor-listeretalbsseq/meta.yaml index ee0733cfec077..8c8ad02bc82e7 100644 --- a/recipes/bioconductor-listeretalbsseq/meta.yaml +++ b/recipes/bioconductor-listeretalbsseq/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.14.0" %} +{% set version = "1.16.0" %} {% set name = "ListerEtAlBSseq" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,9 +10,9 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: c36fbf6d20c087f6591c9c39174878cb + md5: 65a04e46b826417c971c461fa1599ba2 build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ @@ -20,12 +20,12 @@ build: # Suggests: BSgenome.Hsapiens.UCSC.hg18 requirements: host: - - 'bioconductor-methylpipe >=1.16.0,<1.17.0' + - 'bioconductor-methylpipe >=1.18.0,<1.19.0' - r-base run: - - 'bioconductor-methylpipe >=1.16.0,<1.17.0' + - 'bioconductor-methylpipe >=1.18.0,<1.19.0' - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-listeretalbsseq/post-link.sh b/recipes/bioconductor-listeretalbsseq/post-link.sh index e4d791ab0e81e..f0e265d908e45 100644 --- a/recipes/bioconductor-listeretalbsseq/post-link.sh +++ b/recipes/bioconductor-listeretalbsseq/post-link.sh @@ -1,11 +1,11 @@ #!/bin/bash -FN="ListerEtAlBSseq_1.14.0.tar.gz" +FN="ListerEtAlBSseq_1.16.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/experiment/src/contrib/ListerEtAlBSseq_1.14.0.tar.gz" - "https://bioarchive.galaxyproject.org/ListerEtAlBSseq_1.14.0.tar.gz" - "https://depot.galaxyproject.org/software/bioconductor-listeretalbsseq/bioconductor-listeretalbsseq_1.14.0_src_all.tar.gz" + "https://bioconductor.org/packages/3.9/data/experiment/src/contrib/ListerEtAlBSseq_1.16.0.tar.gz" + "https://bioarchive.galaxyproject.org/ListerEtAlBSseq_1.16.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-listeretalbsseq/bioconductor-listeretalbsseq_1.16.0_src_all.tar.gz" ) -MD5="c36fbf6d20c087f6591c9c39174878cb" +MD5="65a04e46b826417c971c461fa1599ba2" # Use a staging area in the conda dir rather than temp dirs, both to avoid # permission issues as well as to have things downloaded in a predictable @@ -16,7 +16,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-lmdme/meta.yaml b/recipes/bioconductor-lmdme/meta.yaml index 72aa95c4b4eeb..c06eed41717de 100644 --- a/recipes/bioconductor-lmdme/meta.yaml +++ b/recipes/bioconductor-lmdme/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.24.0" %} +{% set version = "1.26.0" %} {% set name = "lmdme" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: d84c1a13e28adbb587d9006cff7938db + md5: 546f6d67cd946e4d9d81632e2214ee41 build: number: 0 rpaths: @@ -19,13 +19,13 @@ build: noarch: generic requirements: host: - - 'bioconductor-limma >=3.38.0,<3.39.0' - - 'bioconductor-stemhypoxia >=1.18.0,<1.19.0' + - 'bioconductor-limma >=3.40.0,<3.41.0' + - 'bioconductor-stemhypoxia >=1.20.0,<1.21.0' - r-base - r-pls run: - - 'bioconductor-limma >=3.38.0,<3.39.0' - - 'bioconductor-stemhypoxia >=1.18.0,<1.19.0' + - 'bioconductor-limma >=3.40.0,<3.41.0' + - 'bioconductor-stemhypoxia >=1.20.0,<1.21.0' - r-base - r-pls test: diff --git a/recipes/bioconductor-lmgene/meta.yaml b/recipes/bioconductor-lmgene/meta.yaml index 87b6bd7f1d91f..46ad37ab86341 100644 --- a/recipes/bioconductor-lmgene/meta.yaml +++ b/recipes/bioconductor-lmgene/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "2.38.0" %} +{% set version = "2.40.0" %} {% set name = "LMGene" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,9 +10,9 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 1d5e6672bd23b4c523568b712545643c + md5: 0073afa14740274f430c190c90ae3f2b build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ @@ -20,15 +20,15 @@ build: # Suggests: affydata requirements: host: - - 'bioconductor-affy >=1.60.0,<1.61.0' - - 'bioconductor-biobase >=2.42.0,<2.43.0' - - 'bioconductor-multtest >=2.38.0,<2.39.0' + - 'bioconductor-affy >=1.62.0,<1.63.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' + - 'bioconductor-multtest >=2.40.0,<2.41.0' - r-base - r-survival run: - - 'bioconductor-affy >=1.60.0,<1.61.0' - - 'bioconductor-biobase >=2.42.0,<2.43.0' - - 'bioconductor-multtest >=2.38.0,<2.39.0' + - 'bioconductor-affy >=1.62.0,<1.63.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' + - 'bioconductor-multtest >=2.40.0,<2.41.0' - r-base - r-survival test: diff --git a/recipes/bioconductor-lobstahs/meta.yaml b/recipes/bioconductor-lobstahs/meta.yaml index bc8938ee20b40..8d3c1ed5df471 100644 --- a/recipes/bioconductor-lobstahs/meta.yaml +++ b/recipes/bioconductor-lobstahs/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.8.1" %} +{% set version = "1.10.0" %} {% set name = "LOBSTAHS" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 1acf4da2bb8e0d50fc8c96bd9499b2f2 + md5: 4153540588b21a7939bcd124d4b01ed7 build: number: 0 rpaths: @@ -20,12 +20,12 @@ build: # Suggests: PtH2O2lipids, knitr, rmarkdown requirements: host: - - 'bioconductor-camera >=1.38.0,<1.39.0' - - 'bioconductor-xcms >=3.4.0,<3.5.0' + - 'bioconductor-camera >=1.40.0,<1.41.0' + - 'bioconductor-xcms >=3.6.0,<3.7.0' - r-base run: - - 'bioconductor-camera >=1.38.0,<1.39.0' - - 'bioconductor-xcms >=3.4.0,<3.5.0' + - 'bioconductor-camera >=1.40.0,<1.41.0' + - 'bioconductor-xcms >=3.6.0,<3.7.0' - r-base test: commands: diff --git a/recipes/bioconductor-loci2path/meta.yaml b/recipes/bioconductor-loci2path/meta.yaml index 49df7b6f51834..55a2ff99fb8d5 100644 --- a/recipes/bioconductor-loci2path/meta.yaml +++ b/recipes/bioconductor-loci2path/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.2.0" %} +{% set version = "1.4.0" %} {% set name = "loci2path" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,9 +10,9 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 90e463d21339295ec91413e52911e733 + md5: a887d9af75e7ab94335dd7335f3048f2 build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ @@ -20,18 +20,18 @@ build: # Suggests: BiocStyle, knitr, rmarkdown requirements: host: - - 'bioconductor-biocparallel >=1.16.0,<1.17.0' - - 'bioconductor-genomicranges >=1.34.0,<1.35.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-biocparallel >=1.18.0,<1.19.0' + - 'bioconductor-genomicranges >=1.36.0,<1.37.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' - r-base - r-data.table - r-pheatmap - r-rcolorbrewer - r-wordcloud run: - - 'bioconductor-biocparallel >=1.16.0,<1.17.0' - - 'bioconductor-genomicranges >=1.34.0,<1.35.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-biocparallel >=1.18.0,<1.19.0' + - 'bioconductor-genomicranges >=1.36.0,<1.37.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' - r-base - r-data.table - r-pheatmap diff --git a/recipes/bioconductor-logicfs/meta.yaml b/recipes/bioconductor-logicfs/meta.yaml index 8a923b36e1af9..6a8b56150731d 100644 --- a/recipes/bioconductor-logicfs/meta.yaml +++ b/recipes/bioconductor-logicfs/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "2.2.0" %} +{% set version = "2.4.0" %} {% set name = "logicFS" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: c938e0a3bb72e81baeb62791e8cbd6d9 + md5: a63b247f856912abb2fe160c3d3b7039 build: number: 0 rpaths: diff --git a/recipes/bioconductor-logitt/meta.yaml b/recipes/bioconductor-logitt/meta.yaml index 6032b4f052366..e340da12c2681 100644 --- a/recipes/bioconductor-logitt/meta.yaml +++ b/recipes/bioconductor-logitt/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.40.0" %} +{% set version = "1.42.0" %} {% set name = "logitT" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: b84aee3b9e43a884c6119562b543a9f2 + md5: 26d824e6c1b564e3e6ad3d86f8765124 build: number: 0 rpaths: @@ -19,10 +19,10 @@ build: # Suggests: SpikeInSubset requirements: host: - - 'bioconductor-affy >=1.60.0,<1.61.0' + - 'bioconductor-affy >=1.62.0,<1.63.0' - r-base run: - - 'bioconductor-affy >=1.60.0,<1.61.0' + - 'bioconductor-affy >=1.62.0,<1.63.0' - r-base build: - {{ compiler('c') }} diff --git a/recipes/bioconductor-logolas/meta.yaml b/recipes/bioconductor-logolas/meta.yaml index 0505ab4e0bd5e..413ddb1b105b6 100644 --- a/recipes/bioconductor-logolas/meta.yaml +++ b/recipes/bioconductor-logolas/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.6.0" %} +{% set version = "1.8.0" %} {% set name = "Logolas" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 3aacdce238af176577fbf05161b54325 + md5: 72af8e4603d85cfe4c8c2e63bcdface6 build: number: 0 rpaths: @@ -20,14 +20,14 @@ build: # Suggests: knitr, rmarkdown, BiocStyle, Biobase, devtools, xtable, gridExtra, RColorBrewer, seqLogo, ggseqlogo requirements: host: - - 'bioconductor-biostrings >=2.50.0,<2.51.0' + - 'bioconductor-biostrings >=2.52.0,<2.53.0' - r-base - r-ggplot2 - r-gridbase - r-laplacesdemon - r-squarem run: - - 'bioconductor-biostrings >=2.50.0,<2.51.0' + - 'bioconductor-biostrings >=2.52.0,<2.53.0' - r-base - r-ggplot2 - r-gridbase diff --git a/recipes/bioconductor-lol/meta.yaml b/recipes/bioconductor-lol/meta.yaml index 0d0957a4ef61b..2d201cdc36976 100644 --- a/recipes/bioconductor-lol/meta.yaml +++ b/recipes/bioconductor-lol/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.30.0" %} +{% set version = "1.32.0" %} {% set name = "lol" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 9339f2a964b2d4470286d87eaaba88cb + md5: 5454962e90b5ded1b75a52788f8ddb31 build: number: 0 rpaths: diff --git a/recipes/bioconductor-lola/meta.yaml b/recipes/bioconductor-lola/meta.yaml index 3e18406faecd2..4ea545de220f2 100644 --- a/recipes/bioconductor-lola/meta.yaml +++ b/recipes/bioconductor-lola/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.12.0" %} +{% set version = "1.14.0" %} {% set name = "LOLA" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: e57b955b1d44900a375fce04c3217d1f + md5: c058753a3f86f5cecef272313d90f6b1 build: number: 0 rpaths: @@ -20,18 +20,18 @@ build: # Suggests: parallel, testthat, knitr, BiocStyle, rmarkdown requirements: host: - - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' - - 'bioconductor-genomicranges >=1.34.0,<1.35.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-biocgenerics >=0.30.0,<0.31.0' + - 'bioconductor-genomicranges >=1.36.0,<1.37.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' - r-base - r-data.table - r-reshape2 run: - - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' - - 'bioconductor-genomicranges >=1.34.0,<1.35.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-biocgenerics >=0.30.0,<0.31.0' + - 'bioconductor-genomicranges >=1.36.0,<1.37.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' - r-base - r-data.table - r-reshape2 diff --git a/recipes/bioconductor-loomexperiment/meta.yaml b/recipes/bioconductor-loomexperiment/meta.yaml index 8396a235ce8cf..2a8fd6cf7e096 100644 --- a/recipes/bioconductor-loomexperiment/meta.yaml +++ b/recipes/bioconductor-loomexperiment/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.0.1" %} +{% set version = "1.2.0" %} {% set name = "LoomExperiment" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 332c0891e383c84ae4a4c7cf92cd9727 + md5: a06d4541c1ab40fc8dd322308a3ea0d7 build: number: 0 rpaths: @@ -20,24 +20,24 @@ build: # Suggests: testthat, BiocStyle, knitr requirements: host: - - 'bioconductor-delayedarray >=0.8.0,<0.9.0' - - 'bioconductor-genomicranges >=1.34.0,<1.35.0' - - 'bioconductor-hdf5array >=1.10.0,<1.11.0' - - 'bioconductor-rhdf5 >=2.26.0,<2.27.0' - - 'bioconductor-rtracklayer >=1.42.0,<1.43.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' - - 'bioconductor-singlecellexperiment >=1.4.0,<1.5.0' - - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' + - 'bioconductor-delayedarray >=0.10.0,<0.11.0' + - 'bioconductor-genomicranges >=1.36.0,<1.37.0' + - 'bioconductor-hdf5array >=1.12.0,<1.13.0' + - 'bioconductor-rhdf5 >=2.28.0,<2.29.0' + - 'bioconductor-rtracklayer >=1.44.0,<1.45.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' + - 'bioconductor-singlecellexperiment >=1.6.0,<1.7.0' + - 'bioconductor-summarizedexperiment >=1.14.0,<1.15.0' - r-base run: - - 'bioconductor-delayedarray >=0.8.0,<0.9.0' - - 'bioconductor-genomicranges >=1.34.0,<1.35.0' - - 'bioconductor-hdf5array >=1.10.0,<1.11.0' - - 'bioconductor-rhdf5 >=2.26.0,<2.27.0' - - 'bioconductor-rtracklayer >=1.42.0,<1.43.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' - - 'bioconductor-singlecellexperiment >=1.4.0,<1.5.0' - - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' + - 'bioconductor-delayedarray >=0.10.0,<0.11.0' + - 'bioconductor-genomicranges >=1.36.0,<1.37.0' + - 'bioconductor-hdf5array >=1.12.0,<1.13.0' + - 'bioconductor-rhdf5 >=2.28.0,<2.29.0' + - 'bioconductor-rtracklayer >=1.44.0,<1.45.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' + - 'bioconductor-singlecellexperiment >=1.6.0,<1.7.0' + - 'bioconductor-summarizedexperiment >=1.14.0,<1.15.0' - r-base test: commands: diff --git a/recipes/bioconductor-lowmaca/meta.yaml b/recipes/bioconductor-lowmaca/meta.yaml index 30fb94fe94e7f..ce10df0111e6f 100644 --- a/recipes/bioconductor-lowmaca/meta.yaml +++ b/recipes/bioconductor-lowmaca/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.12.0" %} +{% set version = "1.14.0" %} {% set name = "LowMACA" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 08f3aa079582ae9129e9e5b82ba1687a + md5: 91e15e0134043b52a8e1780e67ccfe15 build: number: 0 rpaths: @@ -21,29 +21,37 @@ build: # SystemRequirements: clustalo, gs, perl requirements: host: - - 'bioconductor-biocparallel >=1.16.0,<1.17.0' - - 'bioconductor-biostrings >=2.50.0,<2.51.0' - - 'bioconductor-lowmacaannotation >=0.99.0,<0.100.0' - - 'bioconductor-motifstack >=1.26.0,<1.27.0' + - 'bioconductor-biocparallel >=1.18.0,<1.19.0' + - 'bioconductor-biostrings >=2.52.0,<2.53.0' + - 'bioconductor-lowmacaannotation >=1.0.0,<1.1.0' + - 'bioconductor-motifstack >=1.28.0,<1.29.0' - r-base - r-cgdsr - r-data.table + - r-gridbase - r-httr - r-rcolorbrewer - r-reshape2 - r-stringr + - clustalo + - ghostscript + - perl run: - - 'bioconductor-biocparallel >=1.16.0,<1.17.0' - - 'bioconductor-biostrings >=2.50.0,<2.51.0' - - 'bioconductor-lowmacaannotation >=0.99.0,<0.100.0' - - 'bioconductor-motifstack >=1.26.0,<1.27.0' + - 'bioconductor-biocparallel >=1.18.0,<1.19.0' + - 'bioconductor-biostrings >=2.52.0,<2.53.0' + - 'bioconductor-lowmacaannotation >=1.0.0,<1.1.0' + - 'bioconductor-motifstack >=1.28.0,<1.29.0' - r-base - r-cgdsr - r-data.table + - r-gridbase - r-httr - r-rcolorbrewer - r-reshape2 - r-stringr + - clustalo + - ghostscript + - perl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-lowmacaannotation/meta.yaml b/recipes/bioconductor-lowmacaannotation/meta.yaml index affdac27630a2..5d34daaea2402 100644 --- a/recipes/bioconductor-lowmacaannotation/meta.yaml +++ b/recipes/bioconductor-lowmacaannotation/meta.yaml @@ -1,6 +1,6 @@ {% set version = "0.99.3" %} {% set name = "LowMACAAnnotation" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -12,7 +12,7 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' md5: 9e0d3fe7f30fe48aef9c4387eb5bacfa build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ @@ -23,7 +23,7 @@ requirements: - r-base run: - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-lowmacaannotation/post-link.sh b/recipes/bioconductor-lowmacaannotation/post-link.sh index 619f1e4ca11de..c738be01a3a18 100644 --- a/recipes/bioconductor-lowmacaannotation/post-link.sh +++ b/recipes/bioconductor-lowmacaannotation/post-link.sh @@ -1,9 +1,10 @@ #!/bin/bash FN="LowMACAAnnotation_0.99.3.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/LowMACAAnnotation_0.99.3.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/LowMACAAnnotation_0.99.3.tar.gz" "https://bioarchive.galaxyproject.org/LowMACAAnnotation_0.99.3.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-lowmacaannotation/bioconductor-lowmacaannotation_0.99.3_src_all.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-lowmacaannotation/bioconductor-lowmacaannotation_0.99.3_src_all.tar.gz" ) MD5="9e0d3fe7f30fe48aef9c4387eb5bacfa" @@ -16,7 +17,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-lpe/meta.yaml b/recipes/bioconductor-lpe/meta.yaml index e87219cd01e1e..9d9e819caa7fe 100644 --- a/recipes/bioconductor-lpe/meta.yaml +++ b/recipes/bioconductor-lpe/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.56.0" %} +{% set version = "1.58.0" %} {% set name = "LPE" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 7ddf8da425759856e5c6071ec4762b6a + md5: 1771e59d10976d6bc23c35a5b919c8fb build: number: 0 rpaths: diff --git a/recipes/bioconductor-lpeadj/meta.yaml b/recipes/bioconductor-lpeadj/meta.yaml index 3099fb43c137a..46561d52235c6 100644 --- a/recipes/bioconductor-lpeadj/meta.yaml +++ b/recipes/bioconductor-lpeadj/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.42.0" %} +{% set version = "1.44.0" %} {% set name = "LPEadj" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: a50c028087f227ddee20391e296bc199 + md5: 399c100e5653af8e3a44a40690d85961 build: number: 0 rpaths: @@ -19,10 +19,10 @@ build: noarch: generic requirements: host: - - 'bioconductor-lpe >=1.56.0,<1.57.0' + - 'bioconductor-lpe >=1.58.0,<1.59.0' - r-base run: - - 'bioconductor-lpe >=1.56.0,<1.57.0' + - 'bioconductor-lpe >=1.58.0,<1.59.0' - r-base test: commands: diff --git a/recipes/bioconductor-lpnet/meta.yaml b/recipes/bioconductor-lpnet/meta.yaml index 5c573da5724c9..1b23cf21d5697 100644 --- a/recipes/bioconductor-lpnet/meta.yaml +++ b/recipes/bioconductor-lpnet/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "2.14.0" %} +{% set version = "2.16.0" %} {% set name = "lpNet" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 80548ee68471e1474411ea5d691d205b + md5: 3c07b7d48480cc94e895140d38ac0767 build: number: 0 rpaths: @@ -19,11 +19,11 @@ build: noarch: generic requirements: host: - - 'bioconductor-nem >=2.56.0,<2.57.0' + - 'bioconductor-nem >=2.58.0,<2.59.0' - r-base - r-lpsolve run: - - 'bioconductor-nem >=2.56.0,<2.57.0' + - 'bioconductor-nem >=2.58.0,<2.59.0' - r-base - r-lpsolve test: diff --git a/recipes/bioconductor-lpsymphony/meta.yaml b/recipes/bioconductor-lpsymphony/meta.yaml index f7045da8d94da..d0963fb5fe61e 100644 --- a/recipes/bioconductor-lpsymphony/meta.yaml +++ b/recipes/bioconductor-lpsymphony/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.10.0" %} +{% set version = "1.12.0" %} {% set name = "lpsymphony" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: ef6e41c4c16fa4ba123f2095618eff4b + md5: acce764137f7f9a82443decd693b5efb build: number: 0 rpaths: diff --git a/recipes/bioconductor-lrbase.rno.eg.db/meta.yaml b/recipes/bioconductor-lrbase.rno.eg.db/meta.yaml index 5c586e84e824c..cea5903cd5b14 100644 --- a/recipes/bioconductor-lrbase.rno.eg.db/meta.yaml +++ b/recipes/bioconductor-lrbase.rno.eg.db/meta.yaml @@ -1,18 +1,17 @@ {% set version = "1.0.0" %} {% set name = "LRBase.Rno.eg.db" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' md5: 7b2e0f64dfbbfa91d07bdd7a580ac9a7 build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ @@ -20,11 +19,11 @@ build: # Suggests: RUnit, BiocGenerics requirements: host: - - 'bioconductor-lrbasedbi >=1.0.0,<1.1.0' + - 'bioconductor-lrbasedbi >=1.2.0,<1.3.0' - r-base - r-rsqlite run: - - 'bioconductor-lrbasedbi >=1.0.0,<1.1.0' + - 'bioconductor-lrbasedbi >=1.2.0,<1.3.0' - r-base - r-rsqlite - curl diff --git a/recipes/bioconductor-lrbase.rno.eg.db/post-link.sh b/recipes/bioconductor-lrbase.rno.eg.db/post-link.sh index f1fec90be4024..3ea4b3cca3588 100644 --- a/recipes/bioconductor-lrbase.rno.eg.db/post-link.sh +++ b/recipes/bioconductor-lrbase.rno.eg.db/post-link.sh @@ -1,9 +1,9 @@ #!/bin/bash -FN="LRBase.Rno.eg.db_1.0.0.tar.gz" +FN="bioconductor-lrbase.rno.eg.db_1.0.0_src_all.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/LRBase.Rno.eg.db_1.0.0.tar.gz" "https://bioarchive.galaxyproject.org/LRBase.Rno.eg.db_1.0.0.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-lrbase.rno.eg.db/bioconductor-lrbase.rno.eg.db_1.0.0_src_all.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-lrbase.rno.eg.db/bioconductor-lrbase.rno.eg.db_1.0.0_src_all.tar.gz" ) MD5="7b2e0f64dfbbfa91d07bdd7a580ac9a7" diff --git a/recipes/bioconductor-lrbasedbi/meta.yaml b/recipes/bioconductor-lrbasedbi/meta.yaml index c84d8aeba59e0..12647b057ef2b 100644 --- a/recipes/bioconductor-lrbasedbi/meta.yaml +++ b/recipes/bioconductor-lrbasedbi/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.0.0" %} +{% set version = "1.2.0" %} {% set name = "LRBaseDbi" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: f983eacbbe7593cfae1996944d5f4710 + md5: 6ea76caccdee3afc0765ace6a3ee6370 build: number: 0 rpaths: @@ -20,14 +20,14 @@ build: # Suggests: RUnit, BiocGenerics, BiocStyle requirements: host: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' - - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' - r-base - r-dbi - r-rsqlite run: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' - - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' - r-base - r-dbi - r-rsqlite diff --git a/recipes/bioconductor-lumi/meta.yaml b/recipes/bioconductor-lumi/meta.yaml index 8b3e33a4ad4d5..59571f855c5e8 100644 --- a/recipes/bioconductor-lumi/meta.yaml +++ b/recipes/bioconductor-lumi/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "2.34.0" %} +{% set version = "2.36.0" %} {% set name = "lumi" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 8d2ae23d6b7c8021a10020c0f42baa71 + md5: cb0925407710d86cc84f39ff5f971fe9 build: number: 0 rpaths: @@ -20,14 +20,14 @@ build: # Suggests: beadarray, limma, vsn, lumiBarnes, lumiHumanAll.db, lumiHumanIDMapping, genefilter, RColorBrewer requirements: host: - - 'bioconductor-affy >=1.60.0,<1.61.0' - - 'bioconductor-annotate >=1.60.0,<1.61.0' - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' - - 'bioconductor-biobase >=2.42.0,<2.43.0' - - 'bioconductor-genomicfeatures >=1.34.0,<1.35.0' - - 'bioconductor-genomicranges >=1.34.0,<1.35.0' - - 'bioconductor-methylumi >=2.28.0,<2.29.0' - - 'bioconductor-preprocesscore >=1.44.0,<1.45.0' + - 'bioconductor-affy >=1.62.0,<1.63.0' + - 'bioconductor-annotate >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' + - 'bioconductor-genomicfeatures >=1.36.0,<1.37.0' + - 'bioconductor-genomicranges >=1.36.0,<1.37.0' + - 'bioconductor-methylumi >=2.30.0,<2.31.0' + - 'bioconductor-preprocesscore >=1.46.0,<1.47.0' - r-base - r-dbi - r-kernsmooth @@ -37,14 +37,14 @@ requirements: - r-nleqslv - r-rsqlite run: - - 'bioconductor-affy >=1.60.0,<1.61.0' - - 'bioconductor-annotate >=1.60.0,<1.61.0' - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' - - 'bioconductor-biobase >=2.42.0,<2.43.0' - - 'bioconductor-genomicfeatures >=1.34.0,<1.35.0' - - 'bioconductor-genomicranges >=1.34.0,<1.35.0' - - 'bioconductor-methylumi >=2.28.0,<2.29.0' - - 'bioconductor-preprocesscore >=1.44.0,<1.45.0' + - 'bioconductor-affy >=1.62.0,<1.63.0' + - 'bioconductor-annotate >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' + - 'bioconductor-genomicfeatures >=1.36.0,<1.37.0' + - 'bioconductor-genomicranges >=1.36.0,<1.37.0' + - 'bioconductor-methylumi >=2.30.0,<2.31.0' + - 'bioconductor-preprocesscore >=1.46.0,<1.47.0' - r-base - r-dbi - r-kernsmooth diff --git a/recipes/bioconductor-lumibarnes/meta.yaml b/recipes/bioconductor-lumibarnes/meta.yaml index 71467219403d9..352e35f996059 100644 --- a/recipes/bioconductor-lumibarnes/meta.yaml +++ b/recipes/bioconductor-lumibarnes/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.22.0" %} +{% set version = "1.24.0" %} {% set name = "lumiBarnes" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 1bd89b6adf74489e3e5a23434809ebac + md5: b611fcdaf9f3f878f2122a2a67fe946a build: number: 0 rpaths: @@ -19,14 +19,14 @@ build: noarch: generic requirements: host: - - 'bioconductor-biobase >=2.42.0,<2.43.0' - - 'bioconductor-lumi >=2.34.0,<2.35.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' + - 'bioconductor-lumi >=2.36.0,<2.37.0' - r-base run: - - 'bioconductor-biobase >=2.42.0,<2.43.0' - - 'bioconductor-lumi >=2.34.0,<2.35.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' + - 'bioconductor-lumi >=2.36.0,<2.37.0' - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-lumibarnes/post-link.sh b/recipes/bioconductor-lumibarnes/post-link.sh index 62c77e5d0dc5c..27f00281d12d4 100644 --- a/recipes/bioconductor-lumibarnes/post-link.sh +++ b/recipes/bioconductor-lumibarnes/post-link.sh @@ -1,11 +1,11 @@ #!/bin/bash -FN="lumiBarnes_1.22.0.tar.gz" +FN="lumiBarnes_1.24.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/experiment/src/contrib/lumiBarnes_1.22.0.tar.gz" - "https://bioarchive.galaxyproject.org/lumiBarnes_1.22.0.tar.gz" - "https://depot.galaxyproject.org/software/bioconductor-lumibarnes/bioconductor-lumibarnes_1.22.0_src_all.tar.gz" + "https://bioconductor.org/packages/3.9/data/experiment/src/contrib/lumiBarnes_1.24.0.tar.gz" + "https://bioarchive.galaxyproject.org/lumiBarnes_1.24.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-lumibarnes/bioconductor-lumibarnes_1.24.0_src_all.tar.gz" ) -MD5="1bd89b6adf74489e3e5a23434809ebac" +MD5="b611fcdaf9f3f878f2122a2a67fe946a" # Use a staging area in the conda dir rather than temp dirs, both to avoid # permission issues as well as to have things downloaded in a predictable @@ -16,7 +16,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-lumihumanall.db/meta.yaml b/recipes/bioconductor-lumihumanall.db/meta.yaml index 9ac4d4ca75ecb..7c6ce634d746c 100644 --- a/recipes/bioconductor-lumihumanall.db/meta.yaml +++ b/recipes/bioconductor-lumihumanall.db/meta.yaml @@ -1,6 +1,6 @@ {% set version = "1.22.0" %} {% set name = "lumiHumanAll.db" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -12,7 +12,7 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' md5: ce7e219b50833ceab203f0bbfb11d917 build: - number: 3 + number: 4 rpaths: - lib/R/lib/ - lib/ @@ -20,14 +20,14 @@ build: # Suggests: annotate, RUnit requirements: host: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' - - 'bioconductor-org.hs.eg.db >=3.7.0,<3.8.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' + - 'bioconductor-org.hs.eg.db >=3.8.0,<3.9.0' - r-base run: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' - - 'bioconductor-org.hs.eg.db >=3.7.0,<3.8.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' + - 'bioconductor-org.hs.eg.db >=3.8.0,<3.9.0' - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-lumihumanall.db/post-link.sh b/recipes/bioconductor-lumihumanall.db/post-link.sh index 5fbab6559da22..1ebe1a63f86d0 100644 --- a/recipes/bioconductor-lumihumanall.db/post-link.sh +++ b/recipes/bioconductor-lumihumanall.db/post-link.sh @@ -1,7 +1,7 @@ #!/bin/bash FN="lumiHumanAll.db_1.22.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/lumiHumanAll.db_1.22.0.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/lumiHumanAll.db_1.22.0.tar.gz" "https://bioarchive.galaxyproject.org/lumiHumanAll.db_1.22.0.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-lumihumanall.db/bioconductor-lumihumanall.db_1.22.0_src_all.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-lumihumanall.db/bioconductor-lumihumanall.db_1.22.0_src_all.tar.gz" @@ -17,7 +17,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-lumihumanidmapping/meta.yaml b/recipes/bioconductor-lumihumanidmapping/meta.yaml index 5ad3b9e521868..1259647d56017 100644 --- a/recipes/bioconductor-lumihumanidmapping/meta.yaml +++ b/recipes/bioconductor-lumihumanidmapping/meta.yaml @@ -1,6 +1,6 @@ {% set version = "1.10.1" %} {% set name = "lumiHumanIDMapping" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -12,23 +12,23 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' md5: 007e5aa2f1596cc08d888ba6dce7148a build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' - - 'bioconductor-lumi >=2.34.0,<2.35.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' + - 'bioconductor-lumi >=2.36.0,<2.37.0' - r-base - r-dbi run: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' - - 'bioconductor-lumi >=2.34.0,<2.35.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' + - 'bioconductor-lumi >=2.36.0,<2.37.0' - r-base - r-dbi - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-lumihumanidmapping/post-link.sh b/recipes/bioconductor-lumihumanidmapping/post-link.sh index c6673542f4497..6a46c5fbc81b8 100644 --- a/recipes/bioconductor-lumihumanidmapping/post-link.sh +++ b/recipes/bioconductor-lumihumanidmapping/post-link.sh @@ -1,9 +1,10 @@ #!/bin/bash FN="lumiHumanIDMapping_1.10.1.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/lumiHumanIDMapping_1.10.1.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/lumiHumanIDMapping_1.10.1.tar.gz" "https://bioarchive.galaxyproject.org/lumiHumanIDMapping_1.10.1.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-lumihumanidmapping/bioconductor-lumihumanidmapping_1.10.1_src_all.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-lumihumanidmapping/bioconductor-lumihumanidmapping_1.10.1_src_all.tar.gz" ) MD5="007e5aa2f1596cc08d888ba6dce7148a" @@ -16,7 +17,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-lumimouseall.db/meta.yaml b/recipes/bioconductor-lumimouseall.db/meta.yaml index 8fca36d5e5926..663505b563e0b 100644 --- a/recipes/bioconductor-lumimouseall.db/meta.yaml +++ b/recipes/bioconductor-lumimouseall.db/meta.yaml @@ -1,6 +1,6 @@ {% set version = "1.22.0" %} {% set name = "lumiMouseAll.db" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -12,7 +12,7 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' md5: 6f12330377aaddc83bfa9c37477b999e build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ @@ -20,14 +20,14 @@ build: # Suggests: annotate, RUnit requirements: host: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' - - 'bioconductor-org.mm.eg.db >=3.7.0,<3.8.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' + - 'bioconductor-org.mm.eg.db >=3.8.0,<3.9.0' - r-base run: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' - - 'bioconductor-org.mm.eg.db >=3.7.0,<3.8.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' + - 'bioconductor-org.mm.eg.db >=3.8.0,<3.9.0' - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-lumimouseall.db/post-link.sh b/recipes/bioconductor-lumimouseall.db/post-link.sh index bfb76a9c44502..48d8c351d46b2 100644 --- a/recipes/bioconductor-lumimouseall.db/post-link.sh +++ b/recipes/bioconductor-lumimouseall.db/post-link.sh @@ -1,9 +1,10 @@ #!/bin/bash FN="lumiMouseAll.db_1.22.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/lumiMouseAll.db_1.22.0.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/lumiMouseAll.db_1.22.0.tar.gz" "https://bioarchive.galaxyproject.org/lumiMouseAll.db_1.22.0.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-lumimouseall.db/bioconductor-lumimouseall.db_1.22.0_src_all.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-lumimouseall.db/bioconductor-lumimouseall.db_1.22.0_src_all.tar.gz" ) MD5="6f12330377aaddc83bfa9c37477b999e" @@ -16,7 +17,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-lumimouseidmapping/meta.yaml b/recipes/bioconductor-lumimouseidmapping/meta.yaml index 36d5353e288b7..9e3cd1011de7e 100644 --- a/recipes/bioconductor-lumimouseidmapping/meta.yaml +++ b/recipes/bioconductor-lumimouseidmapping/meta.yaml @@ -1,6 +1,6 @@ {% set version = "1.10.0" %} {% set name = "lumiMouseIDMapping" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -12,21 +12,21 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' md5: 305aba80ebf6ef4c26899302ea9e50e8 build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' - - 'bioconductor-lumi >=2.34.0,<2.35.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' + - 'bioconductor-lumi >=2.36.0,<2.37.0' - r-base run: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' - - 'bioconductor-lumi >=2.34.0,<2.35.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' + - 'bioconductor-lumi >=2.36.0,<2.37.0' - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-lumimouseidmapping/post-link.sh b/recipes/bioconductor-lumimouseidmapping/post-link.sh index 514f72be8bfe8..1004a43ff3f76 100644 --- a/recipes/bioconductor-lumimouseidmapping/post-link.sh +++ b/recipes/bioconductor-lumimouseidmapping/post-link.sh @@ -1,9 +1,10 @@ #!/bin/bash FN="lumiMouseIDMapping_1.10.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/lumiMouseIDMapping_1.10.0.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/lumiMouseIDMapping_1.10.0.tar.gz" "https://bioarchive.galaxyproject.org/lumiMouseIDMapping_1.10.0.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-lumimouseidmapping/bioconductor-lumimouseidmapping_1.10.0_src_all.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-lumimouseidmapping/bioconductor-lumimouseidmapping_1.10.0_src_all.tar.gz" ) MD5="305aba80ebf6ef4c26899302ea9e50e8" @@ -16,7 +17,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-lumiratall.db/meta.yaml b/recipes/bioconductor-lumiratall.db/meta.yaml index 47dd0c3e3e389..96002e0d2f0f8 100644 --- a/recipes/bioconductor-lumiratall.db/meta.yaml +++ b/recipes/bioconductor-lumiratall.db/meta.yaml @@ -1,6 +1,6 @@ {% set version = "1.22.0" %} {% set name = "lumiRatAll.db" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -12,7 +12,7 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' md5: 65027624574d5e33f18b0a54a54f4be9 build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ @@ -20,14 +20,14 @@ build: # Suggests: annotate, RUnit requirements: host: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' - - 'bioconductor-org.rn.eg.db >=3.7.0,<3.8.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' + - 'bioconductor-org.rn.eg.db >=3.8.0,<3.9.0' - r-base run: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' - - 'bioconductor-org.rn.eg.db >=3.7.0,<3.8.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' + - 'bioconductor-org.rn.eg.db >=3.8.0,<3.9.0' - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-lumiratall.db/post-link.sh b/recipes/bioconductor-lumiratall.db/post-link.sh index f9151c2b88b09..a351322c929ef 100644 --- a/recipes/bioconductor-lumiratall.db/post-link.sh +++ b/recipes/bioconductor-lumiratall.db/post-link.sh @@ -1,9 +1,10 @@ #!/bin/bash FN="lumiRatAll.db_1.22.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/lumiRatAll.db_1.22.0.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/lumiRatAll.db_1.22.0.tar.gz" "https://bioarchive.galaxyproject.org/lumiRatAll.db_1.22.0.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-lumiratall.db/bioconductor-lumiratall.db_1.22.0_src_all.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-lumiratall.db/bioconductor-lumiratall.db_1.22.0_src_all.tar.gz" ) MD5="65027624574d5e33f18b0a54a54f4be9" @@ -16,7 +17,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-lumiratidmapping/meta.yaml b/recipes/bioconductor-lumiratidmapping/meta.yaml index d45ec08fef71a..a9e561916d2aa 100644 --- a/recipes/bioconductor-lumiratidmapping/meta.yaml +++ b/recipes/bioconductor-lumiratidmapping/meta.yaml @@ -1,6 +1,6 @@ {% set version = "1.10.0" %} {% set name = "lumiRatIDMapping" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -12,21 +12,21 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' md5: 1122fc25e3fff62678bed36f9d7b5709 build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' - - 'bioconductor-lumi >=2.34.0,<2.35.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' + - 'bioconductor-lumi >=2.36.0,<2.37.0' - r-base run: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' - - 'bioconductor-lumi >=2.34.0,<2.35.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' + - 'bioconductor-lumi >=2.36.0,<2.37.0' - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-lumiratidmapping/post-link.sh b/recipes/bioconductor-lumiratidmapping/post-link.sh index 2f7df5f1431e2..959cfa0cc85a1 100644 --- a/recipes/bioconductor-lumiratidmapping/post-link.sh +++ b/recipes/bioconductor-lumiratidmapping/post-link.sh @@ -1,9 +1,10 @@ #!/bin/bash FN="lumiRatIDMapping_1.10.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/lumiRatIDMapping_1.10.0.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/lumiRatIDMapping_1.10.0.tar.gz" "https://bioarchive.galaxyproject.org/lumiRatIDMapping_1.10.0.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-lumiratidmapping/bioconductor-lumiratidmapping_1.10.0_src_all.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-lumiratidmapping/bioconductor-lumiratidmapping_1.10.0_src_all.tar.gz" ) MD5="1122fc25e3fff62678bed36f9d7b5709" @@ -16,7 +17,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-lungcanceracvssccgeo/meta.yaml b/recipes/bioconductor-lungcanceracvssccgeo/meta.yaml index efac6d3a93f0e..846ca91c550ac 100644 --- a/recipes/bioconductor-lungcanceracvssccgeo/meta.yaml +++ b/recipes/bioconductor-lungcanceracvssccgeo/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.18.0" %} +{% set version = "1.20.0" %} {% set name = "LungCancerACvsSCCGEO" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: de4f81552f2a5f3484bd43cb1e089c76 + md5: 4a61ccf290a9409dc3126805139c4577 build: number: 0 rpaths: @@ -22,7 +22,7 @@ requirements: - r-base run: - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-lungcanceracvssccgeo/post-link.sh b/recipes/bioconductor-lungcanceracvssccgeo/post-link.sh index a9883af6679a5..03dfa6620ea89 100644 --- a/recipes/bioconductor-lungcanceracvssccgeo/post-link.sh +++ b/recipes/bioconductor-lungcanceracvssccgeo/post-link.sh @@ -1,11 +1,11 @@ #!/bin/bash -FN="LungCancerACvsSCCGEO_1.18.0.tar.gz" +FN="LungCancerACvsSCCGEO_1.20.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/experiment/src/contrib/LungCancerACvsSCCGEO_1.18.0.tar.gz" - "https://bioarchive.galaxyproject.org/LungCancerACvsSCCGEO_1.18.0.tar.gz" - "https://depot.galaxyproject.org/software/bioconductor-lungcanceracvssccgeo/bioconductor-lungcanceracvssccgeo_1.18.0_src_all.tar.gz" + "https://bioconductor.org/packages/3.9/data/experiment/src/contrib/LungCancerACvsSCCGEO_1.20.0.tar.gz" + "https://bioarchive.galaxyproject.org/LungCancerACvsSCCGEO_1.20.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-lungcanceracvssccgeo/bioconductor-lungcanceracvssccgeo_1.20.0_src_all.tar.gz" ) -MD5="de4f81552f2a5f3484bd43cb1e089c76" +MD5="4a61ccf290a9409dc3126805139c4577" # Use a staging area in the conda dir rather than temp dirs, both to avoid # permission issues as well as to have things downloaded in a predictable @@ -16,7 +16,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-lungcancerlines/meta.yaml b/recipes/bioconductor-lungcancerlines/meta.yaml index d2ce005293402..1d6b7394e82ab 100644 --- a/recipes/bioconductor-lungcancerlines/meta.yaml +++ b/recipes/bioconductor-lungcancerlines/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "0.20.0" %} +{% set version = "0.22.0" %} {% set name = "LungCancerLines" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 05943d693a693d21d910d70e7fa2e6b3 + md5: 96f8ced18a07cd538b51bd1d9bf5f50a build: number: 0 rpaths: @@ -19,12 +19,12 @@ build: noarch: generic requirements: host: - - 'bioconductor-rsamtools >=1.34.0,<1.35.0' + - 'bioconductor-rsamtools >=2.0.0,<2.1.0' - r-base run: - - 'bioconductor-rsamtools >=1.34.0,<1.35.0' + - 'bioconductor-rsamtools >=2.0.0,<2.1.0' - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-lungcancerlines/post-link.sh b/recipes/bioconductor-lungcancerlines/post-link.sh index ef19b1715bdf3..116d97f0ef957 100644 --- a/recipes/bioconductor-lungcancerlines/post-link.sh +++ b/recipes/bioconductor-lungcancerlines/post-link.sh @@ -1,11 +1,11 @@ #!/bin/bash -FN="LungCancerLines_0.20.0.tar.gz" +FN="LungCancerLines_0.22.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/experiment/src/contrib/LungCancerLines_0.20.0.tar.gz" - "https://bioarchive.galaxyproject.org/LungCancerLines_0.20.0.tar.gz" - "https://depot.galaxyproject.org/software/bioconductor-lungcancerlines/bioconductor-lungcancerlines_0.20.0_src_all.tar.gz" + "https://bioconductor.org/packages/3.9/data/experiment/src/contrib/LungCancerLines_0.22.0.tar.gz" + "https://bioarchive.galaxyproject.org/LungCancerLines_0.22.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-lungcancerlines/bioconductor-lungcancerlines_0.22.0_src_all.tar.gz" ) -MD5="05943d693a693d21d910d70e7fa2e6b3" +MD5="96f8ced18a07cd538b51bd1d9bf5f50a" # Use a staging area in the conda dir rather than temp dirs, both to avoid # permission issues as well as to have things downloaded in a predictable @@ -16,7 +16,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-lungexpression/meta.yaml b/recipes/bioconductor-lungexpression/meta.yaml index 8f9e05bc6eef6..71704f22a015d 100644 --- a/recipes/bioconductor-lungexpression/meta.yaml +++ b/recipes/bioconductor-lungexpression/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "0.20.0" %} +{% set version = "0.22.0" %} {% set name = "lungExpression" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: ddf0673ccf961ceb1875ac92d104f512 + md5: ca0abb60a770427af34dbe8f5498effc build: number: 0 rpaths: @@ -19,12 +19,12 @@ build: noarch: generic requirements: host: - - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' - r-base run: - - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-lungexpression/post-link.sh b/recipes/bioconductor-lungexpression/post-link.sh index 719a362508c77..2507147a3b176 100644 --- a/recipes/bioconductor-lungexpression/post-link.sh +++ b/recipes/bioconductor-lungexpression/post-link.sh @@ -1,11 +1,11 @@ #!/bin/bash -FN="lungExpression_0.20.0.tar.gz" +FN="lungExpression_0.22.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/experiment/src/contrib/lungExpression_0.20.0.tar.gz" - "https://bioarchive.galaxyproject.org/lungExpression_0.20.0.tar.gz" - "https://depot.galaxyproject.org/software/bioconductor-lungexpression/bioconductor-lungexpression_0.20.0_src_all.tar.gz" + "https://bioconductor.org/packages/3.9/data/experiment/src/contrib/lungExpression_0.22.0.tar.gz" + "https://bioarchive.galaxyproject.org/lungExpression_0.22.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-lungexpression/bioconductor-lungexpression_0.22.0_src_all.tar.gz" ) -MD5="ddf0673ccf961ceb1875ac92d104f512" +MD5="ca0abb60a770427af34dbe8f5498effc" # Use a staging area in the conda dir rather than temp dirs, both to avoid # permission issues as well as to have things downloaded in a predictable @@ -16,7 +16,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-lvsmirna/meta.yaml b/recipes/bioconductor-lvsmirna/meta.yaml index c9cfce638a078..1e281d7baf06b 100644 --- a/recipes/bioconductor-lvsmirna/meta.yaml +++ b/recipes/bioconductor-lvsmirna/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.32.0" %} +{% set version = "1.34.0" %} {% set name = "LVSmiRNA" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 970f3c4e6fb62c5d9dcf870a700288ae + md5: 6e6961cde4bccf6e492cfe3283c2b490 build: number: 0 rpaths: @@ -18,23 +18,23 @@ build: - lib/ requirements: host: - - 'bioconductor-affy >=1.60.0,<1.61.0' - - 'bioconductor-biobase >=2.42.0,<2.43.0' - - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' - - 'bioconductor-limma >=3.38.0,<3.39.0' - - 'bioconductor-vsn >=3.50.0,<3.51.0' - - 'bioconductor-zlibbioc >=1.28.0,<1.29.0' + - 'bioconductor-affy >=1.62.0,<1.63.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' + - 'bioconductor-biocgenerics >=0.30.0,<0.31.0' + - 'bioconductor-limma >=3.40.0,<3.41.0' + - 'bioconductor-vsn >=3.52.0,<3.53.0' + - 'bioconductor-zlibbioc >=1.30.0,<1.31.0' - r-base - r-mass - r-quantreg - r-sparsem run: - - 'bioconductor-affy >=1.60.0,<1.61.0' - - 'bioconductor-biobase >=2.42.0,<2.43.0' - - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' - - 'bioconductor-limma >=3.38.0,<3.39.0' - - 'bioconductor-vsn >=3.50.0,<3.51.0' - - 'bioconductor-zlibbioc >=1.28.0,<1.29.0' + - 'bioconductor-affy >=1.62.0,<1.63.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' + - 'bioconductor-biocgenerics >=0.30.0,<0.31.0' + - 'bioconductor-limma >=3.40.0,<3.41.0' + - 'bioconductor-vsn >=3.52.0,<3.53.0' + - 'bioconductor-zlibbioc >=1.30.0,<1.31.0' - r-base - r-mass - r-quantreg diff --git a/recipes/bioconductor-lydata/meta.yaml b/recipes/bioconductor-lydata/meta.yaml index be2209bf45d84..8efd1852e9696 100644 --- a/recipes/bioconductor-lydata/meta.yaml +++ b/recipes/bioconductor-lydata/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.8.0" %} +{% set version = "1.10.0" %} {% set name = "lydata" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: d64eba72812c41d245f9972c33d71226 + md5: ddb7b13ac19ac940d615d9cb7ff14770 build: number: 0 rpaths: @@ -22,7 +22,7 @@ requirements: - r-base run: - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-lydata/post-link.sh b/recipes/bioconductor-lydata/post-link.sh index c210ac6e66a05..af49d42fb182f 100644 --- a/recipes/bioconductor-lydata/post-link.sh +++ b/recipes/bioconductor-lydata/post-link.sh @@ -1,11 +1,11 @@ #!/bin/bash -FN="lydata_1.8.0.tar.gz" +FN="lydata_1.10.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/experiment/src/contrib/lydata_1.8.0.tar.gz" - "https://bioarchive.galaxyproject.org/lydata_1.8.0.tar.gz" - "https://depot.galaxyproject.org/software/bioconductor-lydata/bioconductor-lydata_1.8.0_src_all.tar.gz" + "https://bioconductor.org/packages/3.9/data/experiment/src/contrib/lydata_1.10.0.tar.gz" + "https://bioarchive.galaxyproject.org/lydata_1.10.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-lydata/bioconductor-lydata_1.10.0_src_all.tar.gz" ) -MD5="d64eba72812c41d245f9972c33d71226" +MD5="ddb7b13ac19ac940d615d9cb7ff14770" # Use a staging area in the conda dir rather than temp dirs, both to avoid # permission issues as well as to have things downloaded in a predictable @@ -16,7 +16,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-lymphoseq/meta.yaml b/recipes/bioconductor-lymphoseq/meta.yaml index 96457d24d5916..3436e7bd6814b 100644 --- a/recipes/bioconductor-lymphoseq/meta.yaml +++ b/recipes/bioconductor-lymphoseq/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.10.0" %} +{% set version = "1.12.0" %} {% set name = "LymphoSeq" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 1b5c24b3df8523d37d12cae3fdfe4a33 + md5: 8f0f2ee5a5a72794136a79e4ee8ecc98 build: number: 0 rpaths: @@ -20,10 +20,10 @@ build: # Suggests: knitr, pheatmap, wordcloud, rmarkdown requirements: host: - - 'bioconductor-biostrings >=2.50.0,<2.51.0' - - 'bioconductor-ggtree >=1.14.0,<1.15.0' - - 'bioconductor-lymphoseqdb >=0.99.0,<0.100.0' - - 'bioconductor-msa >=1.14.0,<1.15.0' + - 'bioconductor-biostrings >=2.52.0,<2.53.0' + - 'bioconductor-ggtree >=1.16.0,<1.17.0' + - 'bioconductor-lymphoseqdb >=1.0.0,<1.1.0' + - 'bioconductor-msa >=1.16.0,<1.17.0' - r-base - r-circlize - r-data.table @@ -38,10 +38,10 @@ requirements: - r-upsetr - r-venndiagram run: - - 'bioconductor-biostrings >=2.50.0,<2.51.0' - - 'bioconductor-ggtree >=1.14.0,<1.15.0' - - 'bioconductor-lymphoseqdb >=0.99.0,<0.100.0' - - 'bioconductor-msa >=1.14.0,<1.15.0' + - 'bioconductor-biostrings >=2.52.0,<2.53.0' + - 'bioconductor-ggtree >=1.16.0,<1.17.0' + - 'bioconductor-lymphoseqdb >=1.0.0,<1.1.0' + - 'bioconductor-msa >=1.16.0,<1.17.0' - r-base - r-circlize - r-data.table diff --git a/recipes/bioconductor-lymphoseqdb/meta.yaml b/recipes/bioconductor-lymphoseqdb/meta.yaml index ea2c11b74fdbf..264490cc25ab2 100644 --- a/recipes/bioconductor-lymphoseqdb/meta.yaml +++ b/recipes/bioconductor-lymphoseqdb/meta.yaml @@ -1,6 +1,6 @@ {% set version = "0.99.2" %} {% set name = "LymphoSeqDB" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -12,7 +12,7 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' md5: 22fc0dc2439ef497982a5ffddda1e418 build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ @@ -22,7 +22,7 @@ requirements: - r-base run: - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-lymphoseqdb/post-link.sh b/recipes/bioconductor-lymphoseqdb/post-link.sh index 17d02fe94bf9c..01057e3dee964 100644 --- a/recipes/bioconductor-lymphoseqdb/post-link.sh +++ b/recipes/bioconductor-lymphoseqdb/post-link.sh @@ -1,9 +1,10 @@ #!/bin/bash FN="LymphoSeqDB_0.99.2.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/LymphoSeqDB_0.99.2.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/LymphoSeqDB_0.99.2.tar.gz" "https://bioarchive.galaxyproject.org/LymphoSeqDB_0.99.2.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-lymphoseqdb/bioconductor-lymphoseqdb_0.99.2_src_all.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-lymphoseqdb/bioconductor-lymphoseqdb_0.99.2_src_all.tar.gz" ) MD5="22fc0dc2439ef497982a5ffddda1e418" @@ -16,7 +17,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-m10kcod.db/meta.yaml b/recipes/bioconductor-m10kcod.db/meta.yaml index 497ac5dba9bb0..ea2bc42faae2a 100644 --- a/recipes/bioconductor-m10kcod.db/meta.yaml +++ b/recipes/bioconductor-m10kcod.db/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.4.0" %} {% set name = "m10kcod.db" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -12,7 +12,7 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 04811628e4b37cd6d24e0b2a17d79ab8 build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ @@ -20,14 +20,14 @@ build: # Suggests: annotate, RUnit requirements: host: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' - - 'bioconductor-org.mm.eg.db >=3.7.0,<3.8.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' + - 'bioconductor-org.mm.eg.db >=3.8.0,<3.9.0' - r-base run: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' - - 'bioconductor-org.mm.eg.db >=3.7.0,<3.8.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' + - 'bioconductor-org.mm.eg.db >=3.8.0,<3.9.0' - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-m10kcod.db/post-link.sh b/recipes/bioconductor-m10kcod.db/post-link.sh index b1f800c37f600..e1af72ce42d3b 100644 --- a/recipes/bioconductor-m10kcod.db/post-link.sh +++ b/recipes/bioconductor-m10kcod.db/post-link.sh @@ -1,9 +1,10 @@ #!/bin/bash FN="m10kcod.db_3.4.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/m10kcod.db_3.4.0.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/m10kcod.db_3.4.0.tar.gz" "https://bioarchive.galaxyproject.org/m10kcod.db_3.4.0.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-m10kcod.db/bioconductor-m10kcod.db_3.4.0_src_all.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-m10kcod.db/bioconductor-m10kcod.db_3.4.0_src_all.tar.gz" ) MD5="04811628e4b37cd6d24e0b2a17d79ab8" @@ -16,7 +17,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-m20kcod.db/meta.yaml b/recipes/bioconductor-m20kcod.db/meta.yaml index ec8aa27e87561..f224557dc2a13 100644 --- a/recipes/bioconductor-m20kcod.db/meta.yaml +++ b/recipes/bioconductor-m20kcod.db/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.4.0" %} {% set name = "m20kcod.db" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -12,7 +12,7 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: f2f734fb41e1ae4e949abf09687733bf build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ @@ -20,14 +20,14 @@ build: # Suggests: annotate, RUnit requirements: host: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' - - 'bioconductor-org.mm.eg.db >=3.7.0,<3.8.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' + - 'bioconductor-org.mm.eg.db >=3.8.0,<3.9.0' - r-base run: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' - - 'bioconductor-org.mm.eg.db >=3.7.0,<3.8.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' + - 'bioconductor-org.mm.eg.db >=3.8.0,<3.9.0' - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-m20kcod.db/post-link.sh b/recipes/bioconductor-m20kcod.db/post-link.sh index 1d8b00641ee4a..da817a5aac65d 100644 --- a/recipes/bioconductor-m20kcod.db/post-link.sh +++ b/recipes/bioconductor-m20kcod.db/post-link.sh @@ -1,9 +1,10 @@ #!/bin/bash FN="m20kcod.db_3.4.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/m20kcod.db_3.4.0.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/m20kcod.db_3.4.0.tar.gz" "https://bioarchive.galaxyproject.org/m20kcod.db_3.4.0.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-m20kcod.db/bioconductor-m20kcod.db_3.4.0_src_all.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-m20kcod.db/bioconductor-m20kcod.db_3.4.0_src_all.tar.gz" ) MD5="f2f734fb41e1ae4e949abf09687733bf" @@ -16,7 +17,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-m3c/meta.yaml b/recipes/bioconductor-m3c/meta.yaml index e8b471c55072c..465371e14ddad 100644 --- a/recipes/bioconductor-m3c/meta.yaml +++ b/recipes/bioconductor-m3c/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.4.1" %} +{% set version = "1.6.0" %} {% set name = "M3C" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 77c756f2e0df9460a72956e7f7b8b542 + md5: f23daab52c79f49bafba10a97f6bed97 build: number: 0 rpaths: @@ -22,6 +22,7 @@ requirements: host: - r-base - r-cluster + - r-corpcor - r-dendextend - r-doparallel - r-dosnow @@ -34,9 +35,11 @@ requirements: - r-rtsne - r-sigclust - r-survival + - r-umap run: - r-base - r-cluster + - r-corpcor - r-dendextend - r-doparallel - r-dosnow @@ -49,13 +52,14 @@ requirements: - r-rtsne - r-sigclust - r-survival + - r-umap test: commands: - '$R -e "library(''{{ name }}'')"' about: home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: AGPL-3 - summary: 'Genome-wide data is used to stratify large complex datasets into classes using class discovery algorithms. A widely applied technique is consensus clustering, however; the approach is prone to overfitting and false positives. These issues arise from not considering reference distributions while selecting the number of classes (K). As a solution, we developed Monte Carlo reference-based consensus clustering (M3C). M3C uses a multi-core enabled Monte Carlo simulation to generate null distributions along the range of K which are used to select its value. Using a reference, that maintains the correlation structure of the input features, eliminates the limitations of consensus clustering. M3C uses the Relative Cluster Stability Index (RCSI) and p values to decide on the value of K and reject the null hypothesis, K=1. M3C can also quantify structural relationships between clusters, and uses spectral clustering to deal with non-Gaussian and complex structures. M3C can automatically analyse biological or clinical data with respect to the discovered classes.' + summary: 'M3C is a consensus clustering algorithm that uses a Monte Carlo simulation to eliminate overfitting and can reject the null hypothesis K=1.' extra: parent_recipe: name: bioconductor-m3c diff --git a/recipes/bioconductor-m3d/meta.yaml b/recipes/bioconductor-m3d/meta.yaml index ae50696f110a2..ea7fc8b604e62 100644 --- a/recipes/bioconductor-m3d/meta.yaml +++ b/recipes/bioconductor-m3d/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.16.0" %} +{% set version = "1.18.0" %} {% set name = "M3D" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 77b8592c2b95342c0d27f10277002627 + md5: 68024daf277220047ac158ce60b1f461 build: number: 0 rpaths: @@ -19,21 +19,21 @@ build: # Suggests: BiocStyle, knitr, testthat requirements: host: - - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' - - 'bioconductor-biseq >=1.22.0,<1.23.0' - - 'bioconductor-genomicranges >=1.34.0,<1.35.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' - - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' + - 'bioconductor-biocgenerics >=0.30.0,<0.31.0' + - 'bioconductor-biseq >=1.24.0,<1.25.0' + - 'bioconductor-genomicranges >=1.36.0,<1.37.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' + - 'bioconductor-summarizedexperiment >=1.14.0,<1.15.0' - r-base - r-rcpp run: - - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' - - 'bioconductor-biseq >=1.22.0,<1.23.0' - - 'bioconductor-genomicranges >=1.34.0,<1.35.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' - - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' + - 'bioconductor-biocgenerics >=0.30.0,<0.31.0' + - 'bioconductor-biseq >=1.24.0,<1.25.0' + - 'bioconductor-genomicranges >=1.36.0,<1.37.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' + - 'bioconductor-summarizedexperiment >=1.14.0,<1.15.0' - r-base - r-rcpp build: diff --git a/recipes/bioconductor-m3dexampledata/meta.yaml b/recipes/bioconductor-m3dexampledata/meta.yaml index d2adadca69a85..b38adec8a1e1a 100644 --- a/recipes/bioconductor-m3dexampledata/meta.yaml +++ b/recipes/bioconductor-m3dexampledata/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.8.0" %} +{% set version = "1.10.0" %} {% set name = "M3DExampleData" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 13f405ac3714731aff20afbab68db3f6 + md5: ddaac0734044e83b21ecf67eb3532eb7 build: number: 0 rpaths: @@ -22,7 +22,7 @@ requirements: - r-base run: - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-m3dexampledata/post-link.sh b/recipes/bioconductor-m3dexampledata/post-link.sh index 05df3f8cafbf3..d2fddd33ac997 100644 --- a/recipes/bioconductor-m3dexampledata/post-link.sh +++ b/recipes/bioconductor-m3dexampledata/post-link.sh @@ -1,11 +1,11 @@ #!/bin/bash -FN="M3DExampleData_1.8.0.tar.gz" +FN="M3DExampleData_1.10.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/experiment/src/contrib/M3DExampleData_1.8.0.tar.gz" - "https://bioarchive.galaxyproject.org/M3DExampleData_1.8.0.tar.gz" - "https://depot.galaxyproject.org/software/bioconductor-m3dexampledata/bioconductor-m3dexampledata_1.8.0_src_all.tar.gz" + "https://bioconductor.org/packages/3.9/data/experiment/src/contrib/M3DExampleData_1.10.0.tar.gz" + "https://bioarchive.galaxyproject.org/M3DExampleData_1.10.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-m3dexampledata/bioconductor-m3dexampledata_1.10.0_src_all.tar.gz" ) -MD5="13f405ac3714731aff20afbab68db3f6" +MD5="ddaac0734044e83b21ecf67eb3532eb7" # Use a staging area in the conda dir rather than temp dirs, both to avoid # permission issues as well as to have things downloaded in a predictable @@ -16,7 +16,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-m3drop/meta.yaml b/recipes/bioconductor-m3drop/meta.yaml index 3bac0bf0e5734..913be110d2876 100644 --- a/recipes/bioconductor-m3drop/meta.yaml +++ b/recipes/bioconductor-m3drop/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.8.1" %} +{% set version = "1.10.0" %} {% set name = "M3Drop" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,28 +10,38 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 6dc5e92a9ab6f512b94d362d100c170f + md5: 9683152b6e21fa7f3078e84619bff56b build: number: 0 rpaths: - lib/R/lib/ - lib/ noarch: generic -# Suggests: ROCR, knitr, M3DExampleData +# Suggests: ROCR, knitr, M3DExampleData, scater, SingleCellExperiment, monocle, Seurat, Biobase requirements: host: - r-base - r-bbmle - r-gplots + - r-hmisc + - r-irlba + - r-matrix + - r-matrixstats - r-numderiv - r-rcolorbrewer + - r-reldist - r-statmod run: - r-base - r-bbmle - r-gplots + - r-hmisc + - r-irlba + - r-matrix + - r-matrixstats - r-numderiv - r-rcolorbrewer + - r-reldist - r-statmod test: commands: diff --git a/recipes/bioconductor-maanova/meta.yaml b/recipes/bioconductor-maanova/meta.yaml index 5bb581904a787..679abb608128d 100644 --- a/recipes/bioconductor-maanova/meta.yaml +++ b/recipes/bioconductor-maanova/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.52.0" %} +{% set version = "1.54.0" %} {% set name = "maanova" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 98d914299500ad6464eabd0244389b4a + md5: 5e95bee8b96e44435ec6d3d482ee2ceb build: number: 0 rpaths: @@ -19,10 +19,10 @@ build: # Suggests: qvalue, snow requirements: host: - - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' - r-base run: - - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' - r-base build: - {{ compiler('c') }} diff --git a/recipes/bioconductor-macat/meta.yaml b/recipes/bioconductor-macat/meta.yaml index 58483bb30a5b4..535182c14efaa 100644 --- a/recipes/bioconductor-macat/meta.yaml +++ b/recipes/bioconductor-macat/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.56.0" %} +{% set version = "1.58.0" %} {% set name = "macat" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: de0e3159813ba422b6ad6ff8e24776f4 + md5: f6f33205bbc943513b0ad8bcfcf1acfb build: number: 0 rpaths: @@ -20,12 +20,12 @@ build: # Suggests: hgu95av2.db, stjudem requirements: host: - - 'bioconductor-annotate >=1.60.0,<1.61.0' - - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-annotate >=1.62.0,<1.63.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' - r-base run: - - 'bioconductor-annotate >=1.60.0,<1.61.0' - - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-annotate >=1.62.0,<1.63.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' - r-base test: commands: diff --git a/recipes/bioconductor-macorrplot/meta.yaml b/recipes/bioconductor-macorrplot/meta.yaml index 6513655044b87..7e8bf08773572 100644 --- a/recipes/bioconductor-macorrplot/meta.yaml +++ b/recipes/bioconductor-macorrplot/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.52.0" %} +{% set version = "1.54.0" %} {% set name = "maCorrPlot" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 2cdfe3ac5b1ab5504522a96ce8fab1b3 + md5: e7a012e07292b0a09b4ab3b781d7e609 build: number: 0 rpaths: diff --git a/recipes/bioconductor-macpet/meta.yaml b/recipes/bioconductor-macpet/meta.yaml index cf1747b4f6273..5f9dd10ae4714 100644 --- a/recipes/bioconductor-macpet/meta.yaml +++ b/recipes/bioconductor-macpet/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.2.0" %} +{% set version = "1.4.0" %} {% set name = "MACPET" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,63 +10,61 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 30f1bd24dfd02ee23e5b41c72147f57d + md5: 194312a63083aaf1fe4333ecab11fd12 build: number: 0 rpaths: - lib/R/lib/ - lib/ -# Suggests: ggplot2 (>= 3.0.0), igraph (>= 1.2.1), rmarkdown (>= 1.10), reshape2 (>= 1.4.3), BiocStyle (>= 2.8.2) +# Suggests: ggplot2 (>= 3.1.0), igraph (>= 1.2.4), rmarkdown (>= 1.12), reshape2 (>= 1.4.3), BiocStyle (>= 2.11.0) # SystemRequirements: C++11 requirements: host: - - 'bioconductor-biocparallel >=1.16.0,<1.17.0' - - 'bioconductor-biostrings >=2.50.0,<2.51.0' - - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' - - 'bioconductor-genomicalignments >=1.18.0,<1.19.0' - - 'bioconductor-genomicranges >=1.34.0,<1.35.0' - - 'bioconductor-geoquery >=2.50.0,<2.51.0' - - 'bioconductor-interactionset >=1.10.0,<1.11.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-rbowtie >=1.22.0,<1.23.0' - - 'bioconductor-rsamtools >=1.34.0,<1.35.0' - - 'bioconductor-rtracklayer >=1.42.0,<1.43.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' - - 'bioconductor-shortread >=1.40.0,<1.41.0' + - 'bioconductor-biocparallel >=1.18.0,<1.19.0' + - 'bioconductor-biostrings >=2.52.0,<2.53.0' + - 'bioconductor-genomeinfodb >=1.20.0,<1.21.0' + - 'bioconductor-genomicalignments >=1.20.0,<1.21.0' + - 'bioconductor-genomicranges >=1.36.0,<1.37.0' + - 'bioconductor-geoquery >=2.52.0,<2.53.0' + - 'bioconductor-interactionset >=1.12.0,<1.13.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-rbowtie >=1.24.0,<1.25.0' + - 'bioconductor-rsamtools >=2.0.0,<2.1.0' + - 'bioconductor-rtracklayer >=1.44.0,<1.45.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' + - 'bioconductor-shortread >=1.42.0,<1.43.0' - r-base - 'r-bh >=1.66.0.1' - 'r-bigmemory >=4.5.33' - 'r-futile.logger >=1.4.3' - 'r-gtools >=3.8.1' - 'r-intervals >=0.15.1' - - 'r-knitr >=1.20' + - 'r-knitr >=1.22' - 'r-plyr >=1.8.4' - - 'r-rbamtools >=2.16.11' - - 'r-rcpp >=0.12.17' + - 'r-rcpp >=1.0.1' run: - - 'bioconductor-biocparallel >=1.16.0,<1.17.0' - - 'bioconductor-biostrings >=2.50.0,<2.51.0' - - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' - - 'bioconductor-genomicalignments >=1.18.0,<1.19.0' - - 'bioconductor-genomicranges >=1.34.0,<1.35.0' - - 'bioconductor-geoquery >=2.50.0,<2.51.0' - - 'bioconductor-interactionset >=1.10.0,<1.11.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-rbowtie >=1.22.0,<1.23.0' - - 'bioconductor-rsamtools >=1.34.0,<1.35.0' - - 'bioconductor-rtracklayer >=1.42.0,<1.43.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' - - 'bioconductor-shortread >=1.40.0,<1.41.0' + - 'bioconductor-biocparallel >=1.18.0,<1.19.0' + - 'bioconductor-biostrings >=2.52.0,<2.53.0' + - 'bioconductor-genomeinfodb >=1.20.0,<1.21.0' + - 'bioconductor-genomicalignments >=1.20.0,<1.21.0' + - 'bioconductor-genomicranges >=1.36.0,<1.37.0' + - 'bioconductor-geoquery >=2.52.0,<2.53.0' + - 'bioconductor-interactionset >=1.12.0,<1.13.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-rbowtie >=1.24.0,<1.25.0' + - 'bioconductor-rsamtools >=2.0.0,<2.1.0' + - 'bioconductor-rtracklayer >=1.44.0,<1.45.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' + - 'bioconductor-shortread >=1.42.0,<1.43.0' - r-base - 'r-bh >=1.66.0.1' - 'r-bigmemory >=4.5.33' - 'r-futile.logger >=1.4.3' - 'r-gtools >=3.8.1' - 'r-intervals >=0.15.1' - - 'r-knitr >=1.20' + - 'r-knitr >=1.22' - 'r-plyr >=1.8.4' - - 'r-rbamtools >=2.16.11' - - 'r-rcpp >=0.12.17' + - 'r-rcpp >=1.0.1' build: - {{ compiler('c') }} - {{ compiler('cxx') }} diff --git a/recipes/bioconductor-macrophage/meta.yaml b/recipes/bioconductor-macrophage/meta.yaml new file mode 100644 index 0000000000000..b63f6187b89e0 --- /dev/null +++ b/recipes/bioconductor-macrophage/meta.yaml @@ -0,0 +1,34 @@ +{% set version = "1.0.0" %} +{% set name = "macrophage" %} +{% set bioc = "3.9" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + md5: 323708aa316444965821e5662ef2ee7d +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: knitr +requirements: + host: + - r-base + run: + - r-base + - curl +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html' + license: 'GPL (>= 2)' + summary: 'This package provides the output of running Salmon on a set of 24 RNA-seq samples from Alasoo, et al. "Shared genetic effects on chromatin and gene expression indicate a role for enhancer priming in immune response", published in Nature Genetics, January 2018. For details on version numbers and how the samples were processed see the package vignette.' + diff --git a/recipes/bioconductor-macrophage/post-link.sh b/recipes/bioconductor-macrophage/post-link.sh new file mode 100644 index 0000000000000..d2da2cced8e9f --- /dev/null +++ b/recipes/bioconductor-macrophage/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="macrophage_1.0.0.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.9/data/experiment/src/contrib/macrophage_1.0.0.tar.gz" + "https://bioarchive.galaxyproject.org/macrophage_1.0.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-macrophage/bioconductor-macrophage_1.0.0_src_all.tar.gz" +) +MD5="323708aa316444965821e5662ef2ee7d" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + curl $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-macrophage/pre-unlink.sh b/recipes/bioconductor-macrophage/pre-unlink.sh new file mode 100644 index 0000000000000..cfc9e89ad1f85 --- /dev/null +++ b/recipes/bioconductor-macrophage/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ macrophage diff --git a/recipes/bioconductor-made4/meta.yaml b/recipes/bioconductor-made4/meta.yaml index 6246825bb4202..17f0682197c93 100644 --- a/recipes/bioconductor-made4/meta.yaml +++ b/recipes/bioconductor-made4/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.56.0" %} +{% set version = "1.58.0" %} {% set name = "made4" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: b93783edb8e0c0de6df719e01b79ebfe + md5: 00c2a89c91fb59c1ee485cd754d8f538 build: number: 0 rpaths: diff --git a/recipes/bioconductor-madseq/meta.yaml b/recipes/bioconductor-madseq/meta.yaml index c89abe2196896..1bbbbea3ae9a0 100644 --- a/recipes/bioconductor-madseq/meta.yaml +++ b/recipes/bioconductor-madseq/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.8.0" %} +{% set version = "1.10.0" %} {% set name = "MADSEQ" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 4ca89b5fc53ad2b4b6806b37991fa2ab + md5: 7e62d154cf3cf3b0e18dd3987918ff47 build: number: 0 rpaths: @@ -20,40 +20,40 @@ build: # Suggests: knitr requirements: host: - - 'bioconductor-biostrings >=2.50.0,<2.51.0' - - 'bioconductor-bsgenome >=1.50.0,<1.51.0' + - 'bioconductor-biostrings >=2.52.0,<2.53.0' + - 'bioconductor-bsgenome >=1.52.0,<1.53.0' - 'bioconductor-bsgenome.hsapiens.ucsc.hg19 >=1.4.0,<1.5.0' - - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' - - 'bioconductor-genomicalignments >=1.18.0,<1.19.0' - - 'bioconductor-genomicranges >=1.34.0,<1.35.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-preprocesscore >=1.44.0,<1.45.0' - - 'bioconductor-rsamtools >=1.34.0,<1.35.0' - - 'bioconductor-rtracklayer >=1.42.0,<1.43.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' - - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' - - 'bioconductor-variantannotation >=1.28.0,<1.29.0' - - 'bioconductor-zlibbioc >=1.28.0,<1.29.0' + - 'bioconductor-genomeinfodb >=1.20.0,<1.21.0' + - 'bioconductor-genomicalignments >=1.20.0,<1.21.0' + - 'bioconductor-genomicranges >=1.36.0,<1.37.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-preprocesscore >=1.46.0,<1.47.0' + - 'bioconductor-rsamtools >=2.0.0,<2.1.0' + - 'bioconductor-rtracklayer >=1.44.0,<1.45.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' + - 'bioconductor-summarizedexperiment >=1.14.0,<1.15.0' + - 'bioconductor-variantannotation >=1.30.0,<1.31.0' + - 'bioconductor-zlibbioc >=1.30.0,<1.31.0' - r-base - r-coda - 'r-rjags >=4-6' - r-vcfr - r-vgam run: - - 'bioconductor-biostrings >=2.50.0,<2.51.0' - - 'bioconductor-bsgenome >=1.50.0,<1.51.0' + - 'bioconductor-biostrings >=2.52.0,<2.53.0' + - 'bioconductor-bsgenome >=1.52.0,<1.53.0' - 'bioconductor-bsgenome.hsapiens.ucsc.hg19 >=1.4.0,<1.5.0' - - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' - - 'bioconductor-genomicalignments >=1.18.0,<1.19.0' - - 'bioconductor-genomicranges >=1.34.0,<1.35.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-preprocesscore >=1.44.0,<1.45.0' - - 'bioconductor-rsamtools >=1.34.0,<1.35.0' - - 'bioconductor-rtracklayer >=1.42.0,<1.43.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' - - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' - - 'bioconductor-variantannotation >=1.28.0,<1.29.0' - - 'bioconductor-zlibbioc >=1.28.0,<1.29.0' + - 'bioconductor-genomeinfodb >=1.20.0,<1.21.0' + - 'bioconductor-genomicalignments >=1.20.0,<1.21.0' + - 'bioconductor-genomicranges >=1.36.0,<1.37.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-preprocesscore >=1.46.0,<1.47.0' + - 'bioconductor-rsamtools >=2.0.0,<2.1.0' + - 'bioconductor-rtracklayer >=1.44.0,<1.45.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' + - 'bioconductor-summarizedexperiment >=1.14.0,<1.15.0' + - 'bioconductor-variantannotation >=1.30.0,<1.31.0' + - 'bioconductor-zlibbioc >=1.30.0,<1.31.0' - r-base - r-coda - 'r-rjags >=4-6' diff --git a/recipes/bioconductor-mafdb.1kgenomes.phase1.grch38/meta.yaml b/recipes/bioconductor-mafdb.1kgenomes.phase1.grch38/meta.yaml index b1326c553d3e3..fa4e8dd039917 100644 --- a/recipes/bioconductor-mafdb.1kgenomes.phase1.grch38/meta.yaml +++ b/recipes/bioconductor-mafdb.1kgenomes.phase1.grch38/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.7.0" %} {% set name = "MafDb.1Kgenomes.phase1.GRCh38" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -12,7 +12,7 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' md5: 793705d2a4a4a80a770b436c0df52add build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ @@ -20,22 +20,22 @@ build: # Suggests: SNPlocs.Hsapiens.dbSNP149.GRCh38 requirements: host: - - 'bioconductor-bsgenome >=1.50.0,<1.51.0' - - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' - - 'bioconductor-genomicranges >=1.34.0,<1.35.0' - - 'bioconductor-genomicscores >=1.6.0,<1.7.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-bsgenome >=1.52.0,<1.53.0' + - 'bioconductor-genomeinfodb >=1.20.0,<1.21.0' + - 'bioconductor-genomicranges >=1.36.0,<1.37.0' + - 'bioconductor-genomicscores >=1.8.0,<1.9.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' - r-base run: - - 'bioconductor-bsgenome >=1.50.0,<1.51.0' - - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' - - 'bioconductor-genomicranges >=1.34.0,<1.35.0' - - 'bioconductor-genomicscores >=1.6.0,<1.7.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-bsgenome >=1.52.0,<1.53.0' + - 'bioconductor-genomeinfodb >=1.20.0,<1.21.0' + - 'bioconductor-genomicranges >=1.36.0,<1.37.0' + - 'bioconductor-genomicscores >=1.8.0,<1.9.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-mafdb.1kgenomes.phase1.grch38/post-link.sh b/recipes/bioconductor-mafdb.1kgenomes.phase1.grch38/post-link.sh index 78a8a04f1fb26..c6ac448bef8cc 100644 --- a/recipes/bioconductor-mafdb.1kgenomes.phase1.grch38/post-link.sh +++ b/recipes/bioconductor-mafdb.1kgenomes.phase1.grch38/post-link.sh @@ -1,9 +1,10 @@ #!/bin/bash FN="MafDb.1Kgenomes.phase1.GRCh38_3.7.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/MafDb.1Kgenomes.phase1.GRCh38_3.7.0.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/MafDb.1Kgenomes.phase1.GRCh38_3.7.0.tar.gz" "https://bioarchive.galaxyproject.org/MafDb.1Kgenomes.phase1.GRCh38_3.7.0.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-mafdb.1kgenomes.phase1.grch38/bioconductor-mafdb.1kgenomes.phase1.grch38_3.7.0_src_all.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-mafdb.1kgenomes.phase1.grch38/bioconductor-mafdb.1kgenomes.phase1.grch38_3.7.0_src_all.tar.gz" ) MD5="793705d2a4a4a80a770b436c0df52add" @@ -16,7 +17,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-mafdb.1kgenomes.phase1.hs37d5/meta.yaml b/recipes/bioconductor-mafdb.1kgenomes.phase1.hs37d5/meta.yaml index f3c4c299dead7..a7d55a28bf9d3 100644 --- a/recipes/bioconductor-mafdb.1kgenomes.phase1.hs37d5/meta.yaml +++ b/recipes/bioconductor-mafdb.1kgenomes.phase1.hs37d5/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.7.1" %} {% set name = "MafDb.1Kgenomes.phase1.hs37d5" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -12,7 +12,7 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' md5: a13d138f00d0f38642f1dfc6cc705050 build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ @@ -20,22 +20,22 @@ build: # Suggests: SNPlocs.Hsapiens.dbSNP144.GRCh37 requirements: host: - - 'bioconductor-bsgenome >=1.50.0,<1.51.0' - - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' - - 'bioconductor-genomicranges >=1.34.0,<1.35.0' - - 'bioconductor-genomicscores >=1.6.0,<1.7.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-bsgenome >=1.52.0,<1.53.0' + - 'bioconductor-genomeinfodb >=1.20.0,<1.21.0' + - 'bioconductor-genomicranges >=1.36.0,<1.37.0' + - 'bioconductor-genomicscores >=1.8.0,<1.9.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' - r-base run: - - 'bioconductor-bsgenome >=1.50.0,<1.51.0' - - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' - - 'bioconductor-genomicranges >=1.34.0,<1.35.0' - - 'bioconductor-genomicscores >=1.6.0,<1.7.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-bsgenome >=1.52.0,<1.53.0' + - 'bioconductor-genomeinfodb >=1.20.0,<1.21.0' + - 'bioconductor-genomicranges >=1.36.0,<1.37.0' + - 'bioconductor-genomicscores >=1.8.0,<1.9.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-mafdb.1kgenomes.phase1.hs37d5/post-link.sh b/recipes/bioconductor-mafdb.1kgenomes.phase1.hs37d5/post-link.sh index 97efcf0908fb2..5174c68e69597 100644 --- a/recipes/bioconductor-mafdb.1kgenomes.phase1.hs37d5/post-link.sh +++ b/recipes/bioconductor-mafdb.1kgenomes.phase1.hs37d5/post-link.sh @@ -1,9 +1,10 @@ #!/bin/bash FN="MafDb.1Kgenomes.phase1.hs37d5_3.7.1.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/MafDb.1Kgenomes.phase1.hs37d5_3.7.1.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/MafDb.1Kgenomes.phase1.hs37d5_3.7.1.tar.gz" "https://bioarchive.galaxyproject.org/MafDb.1Kgenomes.phase1.hs37d5_3.7.1.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-mafdb.1kgenomes.phase1.hs37d5/bioconductor-mafdb.1kgenomes.phase1.hs37d5_3.7.1_src_all.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-mafdb.1kgenomes.phase1.hs37d5/bioconductor-mafdb.1kgenomes.phase1.hs37d5_3.7.1_src_all.tar.gz" ) MD5="a13d138f00d0f38642f1dfc6cc705050" @@ -16,7 +17,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-mafdb.1kgenomes.phase3.grch38/meta.yaml b/recipes/bioconductor-mafdb.1kgenomes.phase3.grch38/meta.yaml index cf087727df80e..1a63b1fdacaf0 100644 --- a/recipes/bioconductor-mafdb.1kgenomes.phase3.grch38/meta.yaml +++ b/recipes/bioconductor-mafdb.1kgenomes.phase3.grch38/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.7.0" %} {% set name = "MafDb.1Kgenomes.phase3.GRCh38" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -12,7 +12,7 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' md5: 062f9d00e3f0650806520cf39f3f9dac build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ @@ -20,22 +20,22 @@ build: # Suggests: SNPlocs.Hsapiens.dbSNP149.GRCh38 requirements: host: - - 'bioconductor-bsgenome >=1.50.0,<1.51.0' - - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' - - 'bioconductor-genomicranges >=1.34.0,<1.35.0' - - 'bioconductor-genomicscores >=1.6.0,<1.7.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-bsgenome >=1.52.0,<1.53.0' + - 'bioconductor-genomeinfodb >=1.20.0,<1.21.0' + - 'bioconductor-genomicranges >=1.36.0,<1.37.0' + - 'bioconductor-genomicscores >=1.8.0,<1.9.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' - r-base run: - - 'bioconductor-bsgenome >=1.50.0,<1.51.0' - - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' - - 'bioconductor-genomicranges >=1.34.0,<1.35.0' - - 'bioconductor-genomicscores >=1.6.0,<1.7.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-bsgenome >=1.52.0,<1.53.0' + - 'bioconductor-genomeinfodb >=1.20.0,<1.21.0' + - 'bioconductor-genomicranges >=1.36.0,<1.37.0' + - 'bioconductor-genomicscores >=1.8.0,<1.9.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-mafdb.1kgenomes.phase3.grch38/post-link.sh b/recipes/bioconductor-mafdb.1kgenomes.phase3.grch38/post-link.sh index 3aad34029a32a..5f6016cd3028f 100644 --- a/recipes/bioconductor-mafdb.1kgenomes.phase3.grch38/post-link.sh +++ b/recipes/bioconductor-mafdb.1kgenomes.phase3.grch38/post-link.sh @@ -1,9 +1,10 @@ #!/bin/bash FN="MafDb.1Kgenomes.phase3.GRCh38_3.7.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/MafDb.1Kgenomes.phase3.GRCh38_3.7.0.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/MafDb.1Kgenomes.phase3.GRCh38_3.7.0.tar.gz" "https://bioarchive.galaxyproject.org/MafDb.1Kgenomes.phase3.GRCh38_3.7.0.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-mafdb.1kgenomes.phase3.grch38/bioconductor-mafdb.1kgenomes.phase3.grch38_3.7.0_src_all.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-mafdb.1kgenomes.phase3.grch38/bioconductor-mafdb.1kgenomes.phase3.grch38_3.7.0_src_all.tar.gz" ) MD5="062f9d00e3f0650806520cf39f3f9dac" @@ -16,7 +17,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-mafdb.1kgenomes.phase3.hs37d5/meta.yaml b/recipes/bioconductor-mafdb.1kgenomes.phase3.hs37d5/meta.yaml index 02c08fa54f4c8..018d616101c37 100644 --- a/recipes/bioconductor-mafdb.1kgenomes.phase3.hs37d5/meta.yaml +++ b/recipes/bioconductor-mafdb.1kgenomes.phase3.hs37d5/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.7.0" %} {% set name = "MafDb.1Kgenomes.phase3.hs37d5" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -12,7 +12,7 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' md5: a659554d3056e019b4f3a179e9628a2d build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ @@ -20,22 +20,22 @@ build: # Suggests: SNPlocs.Hsapiens.dbSNP144.GRCh37 requirements: host: - - 'bioconductor-bsgenome >=1.50.0,<1.51.0' - - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' - - 'bioconductor-genomicranges >=1.34.0,<1.35.0' - - 'bioconductor-genomicscores >=1.6.0,<1.7.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-bsgenome >=1.52.0,<1.53.0' + - 'bioconductor-genomeinfodb >=1.20.0,<1.21.0' + - 'bioconductor-genomicranges >=1.36.0,<1.37.0' + - 'bioconductor-genomicscores >=1.8.0,<1.9.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' - r-base run: - - 'bioconductor-bsgenome >=1.50.0,<1.51.0' - - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' - - 'bioconductor-genomicranges >=1.34.0,<1.35.0' - - 'bioconductor-genomicscores >=1.6.0,<1.7.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-bsgenome >=1.52.0,<1.53.0' + - 'bioconductor-genomeinfodb >=1.20.0,<1.21.0' + - 'bioconductor-genomicranges >=1.36.0,<1.37.0' + - 'bioconductor-genomicscores >=1.8.0,<1.9.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-mafdb.1kgenomes.phase3.hs37d5/post-link.sh b/recipes/bioconductor-mafdb.1kgenomes.phase3.hs37d5/post-link.sh index 2d89a25e964e2..952e81b8c5f5e 100644 --- a/recipes/bioconductor-mafdb.1kgenomes.phase3.hs37d5/post-link.sh +++ b/recipes/bioconductor-mafdb.1kgenomes.phase3.hs37d5/post-link.sh @@ -1,9 +1,10 @@ #!/bin/bash FN="MafDb.1Kgenomes.phase3.hs37d5_3.7.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/MafDb.1Kgenomes.phase3.hs37d5_3.7.0.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/MafDb.1Kgenomes.phase3.hs37d5_3.7.0.tar.gz" "https://bioarchive.galaxyproject.org/MafDb.1Kgenomes.phase3.hs37d5_3.7.0.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-mafdb.1kgenomes.phase3.hs37d5/bioconductor-mafdb.1kgenomes.phase3.hs37d5_3.7.0_src_all.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-mafdb.1kgenomes.phase3.hs37d5/bioconductor-mafdb.1kgenomes.phase3.hs37d5_3.7.0_src_all.tar.gz" ) MD5="a659554d3056e019b4f3a179e9628a2d" @@ -16,7 +17,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-mafdb.esp6500si.v2.ssa137.grch38/meta.yaml b/recipes/bioconductor-mafdb.esp6500si.v2.ssa137.grch38/meta.yaml index ce080210afff5..3150e86873da1 100644 --- a/recipes/bioconductor-mafdb.esp6500si.v2.ssa137.grch38/meta.yaml +++ b/recipes/bioconductor-mafdb.esp6500si.v2.ssa137.grch38/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.7.0" %} {% set name = "MafDb.ESP6500SI.V2.SSA137.GRCh38" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -12,7 +12,7 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' md5: 5c6afa001de76b91bc685c5c4b002b05 build: - number: 1 + number: 2 rpaths: - lib/R/lib/ - lib/ @@ -20,22 +20,22 @@ build: # Suggests: SNPlocs.Hsapiens.dbSNP149.GRCh38 requirements: host: - - 'bioconductor-bsgenome >=1.50.0,<1.51.0' - - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' - - 'bioconductor-genomicranges >=1.34.0,<1.35.0' - - 'bioconductor-genomicscores >=1.6.0,<1.7.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-bsgenome >=1.52.0,<1.53.0' + - 'bioconductor-genomeinfodb >=1.20.0,<1.21.0' + - 'bioconductor-genomicranges >=1.36.0,<1.37.0' + - 'bioconductor-genomicscores >=1.8.0,<1.9.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' - r-base run: - - 'bioconductor-bsgenome >=1.50.0,<1.51.0' - - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' - - 'bioconductor-genomicranges >=1.34.0,<1.35.0' - - 'bioconductor-genomicscores >=1.6.0,<1.7.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-bsgenome >=1.52.0,<1.53.0' + - 'bioconductor-genomeinfodb >=1.20.0,<1.21.0' + - 'bioconductor-genomicranges >=1.36.0,<1.37.0' + - 'bioconductor-genomicscores >=1.8.0,<1.9.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-mafdb.esp6500si.v2.ssa137.grch38/post-link.sh b/recipes/bioconductor-mafdb.esp6500si.v2.ssa137.grch38/post-link.sh index c8e2a66de4eda..ed82c48c5640d 100644 --- a/recipes/bioconductor-mafdb.esp6500si.v2.ssa137.grch38/post-link.sh +++ b/recipes/bioconductor-mafdb.esp6500si.v2.ssa137.grch38/post-link.sh @@ -1,9 +1,10 @@ #!/bin/bash FN="MafDb.ESP6500SI.V2.SSA137.GRCh38_3.7.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/MafDb.ESP6500SI.V2.SSA137.GRCh38_3.7.0.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/MafDb.ESP6500SI.V2.SSA137.GRCh38_3.7.0.tar.gz" "https://bioarchive.galaxyproject.org/MafDb.ESP6500SI.V2.SSA137.GRCh38_3.7.0.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-mafdb.esp6500si.v2.ssa137.grch38/bioconductor-mafdb.esp6500si.v2.ssa137.grch38_3.7.0_src_all.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-mafdb.esp6500si.v2.ssa137.grch38/bioconductor-mafdb.esp6500si.v2.ssa137.grch38_3.7.0_src_all.tar.gz" ) MD5="5c6afa001de76b91bc685c5c4b002b05" @@ -16,7 +17,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-mafdb.esp6500si.v2.ssa137.hs37d5/meta.yaml b/recipes/bioconductor-mafdb.esp6500si.v2.ssa137.hs37d5/meta.yaml index db8c74131ca73..3eda5fd1da6a9 100644 --- a/recipes/bioconductor-mafdb.esp6500si.v2.ssa137.hs37d5/meta.yaml +++ b/recipes/bioconductor-mafdb.esp6500si.v2.ssa137.hs37d5/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.7.0" %} {% set name = "MafDb.ESP6500SI.V2.SSA137.hs37d5" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -12,7 +12,7 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' md5: 6ae9642f33195aca7c84240a8642eb8a build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ @@ -20,22 +20,22 @@ build: # Suggests: SNPlocs.Hsapiens.dbSNP144.GRCh37 requirements: host: - - 'bioconductor-bsgenome >=1.50.0,<1.51.0' - - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' - - 'bioconductor-genomicranges >=1.34.0,<1.35.0' - - 'bioconductor-genomicscores >=1.6.0,<1.7.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-bsgenome >=1.52.0,<1.53.0' + - 'bioconductor-genomeinfodb >=1.20.0,<1.21.0' + - 'bioconductor-genomicranges >=1.36.0,<1.37.0' + - 'bioconductor-genomicscores >=1.8.0,<1.9.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' - r-base run: - - 'bioconductor-bsgenome >=1.50.0,<1.51.0' - - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' - - 'bioconductor-genomicranges >=1.34.0,<1.35.0' - - 'bioconductor-genomicscores >=1.6.0,<1.7.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-bsgenome >=1.52.0,<1.53.0' + - 'bioconductor-genomeinfodb >=1.20.0,<1.21.0' + - 'bioconductor-genomicranges >=1.36.0,<1.37.0' + - 'bioconductor-genomicscores >=1.8.0,<1.9.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-mafdb.esp6500si.v2.ssa137.hs37d5/post-link.sh b/recipes/bioconductor-mafdb.esp6500si.v2.ssa137.hs37d5/post-link.sh index 0eab40f5ccec3..402ebf49ca569 100644 --- a/recipes/bioconductor-mafdb.esp6500si.v2.ssa137.hs37d5/post-link.sh +++ b/recipes/bioconductor-mafdb.esp6500si.v2.ssa137.hs37d5/post-link.sh @@ -1,9 +1,10 @@ #!/bin/bash FN="MafDb.ESP6500SI.V2.SSA137.hs37d5_3.7.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/MafDb.ESP6500SI.V2.SSA137.hs37d5_3.7.0.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/MafDb.ESP6500SI.V2.SSA137.hs37d5_3.7.0.tar.gz" "https://bioarchive.galaxyproject.org/MafDb.ESP6500SI.V2.SSA137.hs37d5_3.7.0.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-mafdb.esp6500si.v2.ssa137.hs37d5/bioconductor-mafdb.esp6500si.v2.ssa137.hs37d5_3.7.0_src_all.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-mafdb.esp6500si.v2.ssa137.hs37d5/bioconductor-mafdb.esp6500si.v2.ssa137.hs37d5_3.7.0_src_all.tar.gz" ) MD5="6ae9642f33195aca7c84240a8642eb8a" @@ -16,7 +17,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-mafdb.exac.r1.0.grch38/meta.yaml b/recipes/bioconductor-mafdb.exac.r1.0.grch38/meta.yaml index 6f4d3fe786a23..73e301e55dd08 100644 --- a/recipes/bioconductor-mafdb.exac.r1.0.grch38/meta.yaml +++ b/recipes/bioconductor-mafdb.exac.r1.0.grch38/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.7.0" %} {% set name = "MafDb.ExAC.r1.0.GRCh38" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -12,7 +12,7 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' md5: ab8ee4f77c84ecb0f8954f9cec199ef4 build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ @@ -20,22 +20,22 @@ build: # Suggests: SNPlocs.Hsapiens.dbSNP149.GRCh38 requirements: host: - - 'bioconductor-bsgenome >=1.50.0,<1.51.0' - - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' - - 'bioconductor-genomicranges >=1.34.0,<1.35.0' - - 'bioconductor-genomicscores >=1.6.0,<1.7.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-bsgenome >=1.52.0,<1.53.0' + - 'bioconductor-genomeinfodb >=1.20.0,<1.21.0' + - 'bioconductor-genomicranges >=1.36.0,<1.37.0' + - 'bioconductor-genomicscores >=1.8.0,<1.9.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' - r-base run: - - 'bioconductor-bsgenome >=1.50.0,<1.51.0' - - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' - - 'bioconductor-genomicranges >=1.34.0,<1.35.0' - - 'bioconductor-genomicscores >=1.6.0,<1.7.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-bsgenome >=1.52.0,<1.53.0' + - 'bioconductor-genomeinfodb >=1.20.0,<1.21.0' + - 'bioconductor-genomicranges >=1.36.0,<1.37.0' + - 'bioconductor-genomicscores >=1.8.0,<1.9.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-mafdb.exac.r1.0.grch38/post-link.sh b/recipes/bioconductor-mafdb.exac.r1.0.grch38/post-link.sh index d565105e88035..114190cb4f6c2 100644 --- a/recipes/bioconductor-mafdb.exac.r1.0.grch38/post-link.sh +++ b/recipes/bioconductor-mafdb.exac.r1.0.grch38/post-link.sh @@ -1,9 +1,10 @@ #!/bin/bash FN="MafDb.ExAC.r1.0.GRCh38_3.7.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/MafDb.ExAC.r1.0.GRCh38_3.7.0.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/MafDb.ExAC.r1.0.GRCh38_3.7.0.tar.gz" "https://bioarchive.galaxyproject.org/MafDb.ExAC.r1.0.GRCh38_3.7.0.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-mafdb.exac.r1.0.grch38/bioconductor-mafdb.exac.r1.0.grch38_3.7.0_src_all.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-mafdb.exac.r1.0.grch38/bioconductor-mafdb.exac.r1.0.grch38_3.7.0_src_all.tar.gz" ) MD5="ab8ee4f77c84ecb0f8954f9cec199ef4" @@ -16,7 +17,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-mafdb.exac.r1.0.hs37d5/meta.yaml b/recipes/bioconductor-mafdb.exac.r1.0.hs37d5/meta.yaml index c54c9ada1ad6e..117474de62500 100644 --- a/recipes/bioconductor-mafdb.exac.r1.0.hs37d5/meta.yaml +++ b/recipes/bioconductor-mafdb.exac.r1.0.hs37d5/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.7.0" %} {% set name = "MafDb.ExAC.r1.0.hs37d5" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -12,7 +12,7 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' md5: a4d494d62a02d808248a058e82e353fa build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ @@ -20,22 +20,22 @@ build: # Suggests: SNPlocs.Hsapiens.dbSNP144.GRCh37 requirements: host: - - 'bioconductor-bsgenome >=1.50.0,<1.51.0' - - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' - - 'bioconductor-genomicranges >=1.34.0,<1.35.0' - - 'bioconductor-genomicscores >=1.6.0,<1.7.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-bsgenome >=1.52.0,<1.53.0' + - 'bioconductor-genomeinfodb >=1.20.0,<1.21.0' + - 'bioconductor-genomicranges >=1.36.0,<1.37.0' + - 'bioconductor-genomicscores >=1.8.0,<1.9.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' - r-base run: - - 'bioconductor-bsgenome >=1.50.0,<1.51.0' - - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' - - 'bioconductor-genomicranges >=1.34.0,<1.35.0' - - 'bioconductor-genomicscores >=1.6.0,<1.7.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-bsgenome >=1.52.0,<1.53.0' + - 'bioconductor-genomeinfodb >=1.20.0,<1.21.0' + - 'bioconductor-genomicranges >=1.36.0,<1.37.0' + - 'bioconductor-genomicscores >=1.8.0,<1.9.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-mafdb.exac.r1.0.hs37d5/post-link.sh b/recipes/bioconductor-mafdb.exac.r1.0.hs37d5/post-link.sh index d14346cd09d0e..6558ca57064b4 100644 --- a/recipes/bioconductor-mafdb.exac.r1.0.hs37d5/post-link.sh +++ b/recipes/bioconductor-mafdb.exac.r1.0.hs37d5/post-link.sh @@ -1,9 +1,10 @@ #!/bin/bash FN="MafDb.ExAC.r1.0.hs37d5_3.7.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/MafDb.ExAC.r1.0.hs37d5_3.7.0.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/MafDb.ExAC.r1.0.hs37d5_3.7.0.tar.gz" "https://bioarchive.galaxyproject.org/MafDb.ExAC.r1.0.hs37d5_3.7.0.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-mafdb.exac.r1.0.hs37d5/bioconductor-mafdb.exac.r1.0.hs37d5_3.7.0_src_all.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-mafdb.exac.r1.0.hs37d5/bioconductor-mafdb.exac.r1.0.hs37d5_3.7.0_src_all.tar.gz" ) MD5="a4d494d62a02d808248a058e82e353fa" @@ -16,7 +17,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-mafdb.exac.r1.0.nontcga.grch38/meta.yaml b/recipes/bioconductor-mafdb.exac.r1.0.nontcga.grch38/meta.yaml index 900d73f75d4ee..94502dcf5f3bf 100644 --- a/recipes/bioconductor-mafdb.exac.r1.0.nontcga.grch38/meta.yaml +++ b/recipes/bioconductor-mafdb.exac.r1.0.nontcga.grch38/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.7.0" %} {% set name = "MafDb.ExAC.r1.0.nonTCGA.GRCh38" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -12,7 +12,7 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' md5: 3826e2d43f9b5cc614dec3ca1059b582 build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ @@ -20,22 +20,22 @@ build: # Suggests: SNPlocs.Hsapiens.dbSNP149.GRCh38 requirements: host: - - 'bioconductor-bsgenome >=1.50.0,<1.51.0' - - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' - - 'bioconductor-genomicranges >=1.34.0,<1.35.0' - - 'bioconductor-genomicscores >=1.6.0,<1.7.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-bsgenome >=1.52.0,<1.53.0' + - 'bioconductor-genomeinfodb >=1.20.0,<1.21.0' + - 'bioconductor-genomicranges >=1.36.0,<1.37.0' + - 'bioconductor-genomicscores >=1.8.0,<1.9.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' - r-base run: - - 'bioconductor-bsgenome >=1.50.0,<1.51.0' - - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' - - 'bioconductor-genomicranges >=1.34.0,<1.35.0' - - 'bioconductor-genomicscores >=1.6.0,<1.7.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-bsgenome >=1.52.0,<1.53.0' + - 'bioconductor-genomeinfodb >=1.20.0,<1.21.0' + - 'bioconductor-genomicranges >=1.36.0,<1.37.0' + - 'bioconductor-genomicscores >=1.8.0,<1.9.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-mafdb.exac.r1.0.nontcga.grch38/post-link.sh b/recipes/bioconductor-mafdb.exac.r1.0.nontcga.grch38/post-link.sh index 1ff36e50f7a34..40156447549cd 100644 --- a/recipes/bioconductor-mafdb.exac.r1.0.nontcga.grch38/post-link.sh +++ b/recipes/bioconductor-mafdb.exac.r1.0.nontcga.grch38/post-link.sh @@ -1,9 +1,10 @@ #!/bin/bash FN="MafDb.ExAC.r1.0.nonTCGA.GRCh38_3.7.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/MafDb.ExAC.r1.0.nonTCGA.GRCh38_3.7.0.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/MafDb.ExAC.r1.0.nonTCGA.GRCh38_3.7.0.tar.gz" "https://bioarchive.galaxyproject.org/MafDb.ExAC.r1.0.nonTCGA.GRCh38_3.7.0.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-mafdb.exac.r1.0.nontcga.grch38/bioconductor-mafdb.exac.r1.0.nontcga.grch38_3.7.0_src_all.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-mafdb.exac.r1.0.nontcga.grch38/bioconductor-mafdb.exac.r1.0.nontcga.grch38_3.7.0_src_all.tar.gz" ) MD5="3826e2d43f9b5cc614dec3ca1059b582" @@ -16,7 +17,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-mafdb.exac.r1.0.nontcga.hs37d5/meta.yaml b/recipes/bioconductor-mafdb.exac.r1.0.nontcga.hs37d5/meta.yaml index 2ff61d4d283e8..19bddacf80394 100644 --- a/recipes/bioconductor-mafdb.exac.r1.0.nontcga.hs37d5/meta.yaml +++ b/recipes/bioconductor-mafdb.exac.r1.0.nontcga.hs37d5/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.7.0" %} {% set name = "MafDb.ExAC.r1.0.nonTCGA.hs37d5" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -12,7 +12,7 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' md5: f557aba8027c87df7bc0cac088b7eaa2 build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ @@ -20,22 +20,22 @@ build: # Suggests: SNPlocs.Hsapiens.dbSNP144.GRCh37 requirements: host: - - 'bioconductor-bsgenome >=1.50.0,<1.51.0' - - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' - - 'bioconductor-genomicranges >=1.34.0,<1.35.0' - - 'bioconductor-genomicscores >=1.6.0,<1.7.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-bsgenome >=1.52.0,<1.53.0' + - 'bioconductor-genomeinfodb >=1.20.0,<1.21.0' + - 'bioconductor-genomicranges >=1.36.0,<1.37.0' + - 'bioconductor-genomicscores >=1.8.0,<1.9.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' - r-base run: - - 'bioconductor-bsgenome >=1.50.0,<1.51.0' - - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' - - 'bioconductor-genomicranges >=1.34.0,<1.35.0' - - 'bioconductor-genomicscores >=1.6.0,<1.7.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-bsgenome >=1.52.0,<1.53.0' + - 'bioconductor-genomeinfodb >=1.20.0,<1.21.0' + - 'bioconductor-genomicranges >=1.36.0,<1.37.0' + - 'bioconductor-genomicscores >=1.8.0,<1.9.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-mafdb.exac.r1.0.nontcga.hs37d5/post-link.sh b/recipes/bioconductor-mafdb.exac.r1.0.nontcga.hs37d5/post-link.sh index c6c6a4be1b294..78a6929d6b6dc 100644 --- a/recipes/bioconductor-mafdb.exac.r1.0.nontcga.hs37d5/post-link.sh +++ b/recipes/bioconductor-mafdb.exac.r1.0.nontcga.hs37d5/post-link.sh @@ -1,9 +1,10 @@ #!/bin/bash FN="MafDb.ExAC.r1.0.nonTCGA.hs37d5_3.7.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/MafDb.ExAC.r1.0.nonTCGA.hs37d5_3.7.0.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/MafDb.ExAC.r1.0.nonTCGA.hs37d5_3.7.0.tar.gz" "https://bioarchive.galaxyproject.org/MafDb.ExAC.r1.0.nonTCGA.hs37d5_3.7.0.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-mafdb.exac.r1.0.nontcga.hs37d5/bioconductor-mafdb.exac.r1.0.nontcga.hs37d5_3.7.0_src_all.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-mafdb.exac.r1.0.nontcga.hs37d5/bioconductor-mafdb.exac.r1.0.nontcga.hs37d5_3.7.0_src_all.tar.gz" ) MD5="f557aba8027c87df7bc0cac088b7eaa2" @@ -16,7 +17,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-mafdb.gnomad.r2.0.1.grch38/meta.yaml b/recipes/bioconductor-mafdb.gnomad.r2.0.1.grch38/meta.yaml index df33fdd7425a5..0d5bfa49e0057 100644 --- a/recipes/bioconductor-mafdb.gnomad.r2.0.1.grch38/meta.yaml +++ b/recipes/bioconductor-mafdb.gnomad.r2.0.1.grch38/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "3.7.0" %} +{% set version = "3.9.0" %} {% set name = "MafDb.gnomAD.r2.0.1.GRCh38" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 735178d5c746753c81acfb3023007ac2 + md5: b20f9a0e1cc202c8ac9ee70e503ebada build: number: 0 rpaths: @@ -20,22 +20,22 @@ build: # Suggests: SNPlocs.Hsapiens.dbSNP149.GRCh38 requirements: host: - - 'bioconductor-bsgenome >=1.50.0,<1.51.0' - - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' - - 'bioconductor-genomicranges >=1.34.0,<1.35.0' - - 'bioconductor-genomicscores >=1.6.0,<1.7.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-bsgenome >=1.52.0,<1.53.0' + - 'bioconductor-genomeinfodb >=1.20.0,<1.21.0' + - 'bioconductor-genomicranges >=1.36.0,<1.37.0' + - 'bioconductor-genomicscores >=1.8.0,<1.9.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' - r-base run: - - 'bioconductor-bsgenome >=1.50.0,<1.51.0' - - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' - - 'bioconductor-genomicranges >=1.34.0,<1.35.0' - - 'bioconductor-genomicscores >=1.6.0,<1.7.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-bsgenome >=1.52.0,<1.53.0' + - 'bioconductor-genomeinfodb >=1.20.0,<1.21.0' + - 'bioconductor-genomicranges >=1.36.0,<1.37.0' + - 'bioconductor-genomicscores >=1.8.0,<1.9.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-mafdb.gnomad.r2.0.1.grch38/post-link.sh b/recipes/bioconductor-mafdb.gnomad.r2.0.1.grch38/post-link.sh index bed6a7ef28ac7..424af211b431c 100644 --- a/recipes/bioconductor-mafdb.gnomad.r2.0.1.grch38/post-link.sh +++ b/recipes/bioconductor-mafdb.gnomad.r2.0.1.grch38/post-link.sh @@ -1,11 +1,11 @@ #!/bin/bash -FN="MafDb.gnomAD.r2.0.1.GRCh38_3.7.0.tar.gz" +FN="MafDb.gnomAD.r2.0.1.GRCh38_3.9.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/MafDb.gnomAD.r2.0.1.GRCh38_3.7.0.tar.gz" - "https://bioarchive.galaxyproject.org/MafDb.gnomAD.r2.0.1.GRCh38_3.7.0.tar.gz" - "https://depot.galaxyproject.org/software/bioconductor-mafdb.gnomad.r2.0.1.grch38/bioconductor-mafdb.gnomad.r2.0.1.grch38_3.7.0_src_all.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/MafDb.gnomAD.r2.0.1.GRCh38_3.9.0.tar.gz" + "https://bioarchive.galaxyproject.org/MafDb.gnomAD.r2.0.1.GRCh38_3.9.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-mafdb.gnomad.r2.0.1.grch38/bioconductor-mafdb.gnomad.r2.0.1.grch38_3.9.0_src_all.tar.gz" ) -MD5="735178d5c746753c81acfb3023007ac2" +MD5="b20f9a0e1cc202c8ac9ee70e503ebada" # Use a staging area in the conda dir rather than temp dirs, both to avoid # permission issues as well as to have things downloaded in a predictable @@ -16,7 +16,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-mafdb.gnomad.r2.1.grch38/meta.yaml b/recipes/bioconductor-mafdb.gnomad.r2.1.grch38/meta.yaml new file mode 100644 index 0000000000000..bd8edaa2acaca --- /dev/null +++ b/recipes/bioconductor-mafdb.gnomad.r2.1.grch38/meta.yaml @@ -0,0 +1,46 @@ +{% set version = "3.9.0" %} +{% set name = "MafDb.gnomAD.r2.1.GRCh38" %} +{% set bioc = "3.9" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: 867371efca8b4904f648ccb1e030213c +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: SNPlocs.Hsapiens.dbSNP149.GRCh38 +requirements: + host: + - 'bioconductor-bsgenome >=1.52.0,<1.53.0' + - 'bioconductor-genomeinfodb >=1.20.0,<1.21.0' + - 'bioconductor-genomicranges >=1.36.0,<1.37.0' + - 'bioconductor-genomicscores >=1.8.0,<1.9.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' + - r-base + run: + - 'bioconductor-bsgenome >=1.52.0,<1.53.0' + - 'bioconductor-genomeinfodb >=1.20.0,<1.21.0' + - 'bioconductor-genomicranges >=1.36.0,<1.37.0' + - 'bioconductor-genomicscores >=1.8.0,<1.9.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' + - r-base + - curl +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'Store minor allele frequency data from the Genome Aggregation Database (gnomAD release 2.1) for the human genome version GRCh38.' + diff --git a/recipes/bioconductor-mafdb.gnomad.r2.1.grch38/post-link.sh b/recipes/bioconductor-mafdb.gnomad.r2.1.grch38/post-link.sh new file mode 100644 index 0000000000000..f7aa85e591160 --- /dev/null +++ b/recipes/bioconductor-mafdb.gnomad.r2.1.grch38/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="MafDb.gnomAD.r2.1.GRCh38_3.9.0.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/MafDb.gnomAD.r2.1.GRCh38_3.9.0.tar.gz" + "https://bioarchive.galaxyproject.org/MafDb.gnomAD.r2.1.GRCh38_3.9.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-mafdb.gnomad.r2.1.grch38/bioconductor-mafdb.gnomad.r2.1.grch38_3.9.0_src_all.tar.gz" +) +MD5="867371efca8b4904f648ccb1e030213c" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + curl $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-mafdb.gnomad.r2.1.grch38/pre-unlink.sh b/recipes/bioconductor-mafdb.gnomad.r2.1.grch38/pre-unlink.sh new file mode 100644 index 0000000000000..5f92e7c6b30e1 --- /dev/null +++ b/recipes/bioconductor-mafdb.gnomad.r2.1.grch38/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ MafDb.gnomAD.r2.1.GRCh38 diff --git a/recipes/bioconductor-mafdb.gnomad.r2.1.hs37d5/meta.yaml b/recipes/bioconductor-mafdb.gnomad.r2.1.hs37d5/meta.yaml index 8011934870c93..7b76fa5c0ef91 100644 --- a/recipes/bioconductor-mafdb.gnomad.r2.1.hs37d5/meta.yaml +++ b/recipes/bioconductor-mafdb.gnomad.r2.1.hs37d5/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.8.0" %} {% set name = "MafDb.gnomAD.r2.1.hs37d5" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -12,7 +12,7 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' md5: fd068f564166d58bb18ebd380f6e431e build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ @@ -20,22 +20,22 @@ build: # Suggests: SNPlocs.Hsapiens.dbSNP144.GRCh37 requirements: host: - - 'bioconductor-bsgenome >=1.50.0,<1.51.0' - - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' - - 'bioconductor-genomicranges >=1.34.0,<1.35.0' - - 'bioconductor-genomicscores >=1.6.0,<1.7.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-bsgenome >=1.52.0,<1.53.0' + - 'bioconductor-genomeinfodb >=1.20.0,<1.21.0' + - 'bioconductor-genomicranges >=1.36.0,<1.37.0' + - 'bioconductor-genomicscores >=1.8.0,<1.9.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' - r-base run: - - 'bioconductor-bsgenome >=1.50.0,<1.51.0' - - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' - - 'bioconductor-genomicranges >=1.34.0,<1.35.0' - - 'bioconductor-genomicscores >=1.6.0,<1.7.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-bsgenome >=1.52.0,<1.53.0' + - 'bioconductor-genomeinfodb >=1.20.0,<1.21.0' + - 'bioconductor-genomicranges >=1.36.0,<1.37.0' + - 'bioconductor-genomicscores >=1.8.0,<1.9.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-mafdb.gnomad.r2.1.hs37d5/post-link.sh b/recipes/bioconductor-mafdb.gnomad.r2.1.hs37d5/post-link.sh index 6f18fedac9dec..2545399f76cf6 100644 --- a/recipes/bioconductor-mafdb.gnomad.r2.1.hs37d5/post-link.sh +++ b/recipes/bioconductor-mafdb.gnomad.r2.1.hs37d5/post-link.sh @@ -1,9 +1,10 @@ #!/bin/bash FN="MafDb.gnomAD.r2.1.hs37d5_3.8.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/MafDb.gnomAD.r2.1.hs37d5_3.8.0.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/MafDb.gnomAD.r2.1.hs37d5_3.8.0.tar.gz" "https://bioarchive.galaxyproject.org/MafDb.gnomAD.r2.1.hs37d5_3.8.0.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-mafdb.gnomad.r2.1.hs37d5/bioconductor-mafdb.gnomad.r2.1.hs37d5_3.8.0_src_all.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-mafdb.gnomad.r2.1.hs37d5/bioconductor-mafdb.gnomad.r2.1.hs37d5_3.8.0_src_all.tar.gz" ) MD5="fd068f564166d58bb18ebd380f6e431e" @@ -16,7 +17,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-mafdb.gnomadex.r2.0.1.grch38/meta.yaml b/recipes/bioconductor-mafdb.gnomadex.r2.0.1.grch38/meta.yaml index 9a634d31fde5e..e92e70e5aa1bf 100644 --- a/recipes/bioconductor-mafdb.gnomadex.r2.0.1.grch38/meta.yaml +++ b/recipes/bioconductor-mafdb.gnomadex.r2.0.1.grch38/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "3.7.0" %} +{% set version = "3.9.0" %} {% set name = "MafDb.gnomADex.r2.0.1.GRCh38" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 95070dc7a5d707d63dbb6ae51ad0e68b + md5: dde927145675571aae324af3db7fe7be build: number: 0 rpaths: @@ -20,22 +20,22 @@ build: # Suggests: SNPlocs.Hsapiens.dbSNP149.GRCh38 requirements: host: - - 'bioconductor-bsgenome >=1.50.0,<1.51.0' - - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' - - 'bioconductor-genomicranges >=1.34.0,<1.35.0' - - 'bioconductor-genomicscores >=1.6.0,<1.7.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-bsgenome >=1.52.0,<1.53.0' + - 'bioconductor-genomeinfodb >=1.20.0,<1.21.0' + - 'bioconductor-genomicranges >=1.36.0,<1.37.0' + - 'bioconductor-genomicscores >=1.8.0,<1.9.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' - r-base run: - - 'bioconductor-bsgenome >=1.50.0,<1.51.0' - - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' - - 'bioconductor-genomicranges >=1.34.0,<1.35.0' - - 'bioconductor-genomicscores >=1.6.0,<1.7.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-bsgenome >=1.52.0,<1.53.0' + - 'bioconductor-genomeinfodb >=1.20.0,<1.21.0' + - 'bioconductor-genomicranges >=1.36.0,<1.37.0' + - 'bioconductor-genomicscores >=1.8.0,<1.9.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-mafdb.gnomadex.r2.0.1.grch38/post-link.sh b/recipes/bioconductor-mafdb.gnomadex.r2.0.1.grch38/post-link.sh index 5e61e9a48c3db..27705ed76fc9f 100644 --- a/recipes/bioconductor-mafdb.gnomadex.r2.0.1.grch38/post-link.sh +++ b/recipes/bioconductor-mafdb.gnomadex.r2.0.1.grch38/post-link.sh @@ -1,11 +1,11 @@ #!/bin/bash -FN="MafDb.gnomADex.r2.0.1.GRCh38_3.7.0.tar.gz" +FN="MafDb.gnomADex.r2.0.1.GRCh38_3.9.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/MafDb.gnomADex.r2.0.1.GRCh38_3.7.0.tar.gz" - "https://bioarchive.galaxyproject.org/MafDb.gnomADex.r2.0.1.GRCh38_3.7.0.tar.gz" - "https://depot.galaxyproject.org/software/bioconductor-mafdb.gnomadex.r2.0.1.grch38/bioconductor-mafdb.gnomadex.r2.0.1.grch38_3.7.0_src_all.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/MafDb.gnomADex.r2.0.1.GRCh38_3.9.0.tar.gz" + "https://bioarchive.galaxyproject.org/MafDb.gnomADex.r2.0.1.GRCh38_3.9.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-mafdb.gnomadex.r2.0.1.grch38/bioconductor-mafdb.gnomadex.r2.0.1.grch38_3.9.0_src_all.tar.gz" ) -MD5="95070dc7a5d707d63dbb6ae51ad0e68b" +MD5="dde927145675571aae324af3db7fe7be" # Use a staging area in the conda dir rather than temp dirs, both to avoid # permission issues as well as to have things downloaded in a predictable @@ -16,7 +16,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-mafdb.gnomadex.r2.1.grch38/meta.yaml b/recipes/bioconductor-mafdb.gnomadex.r2.1.grch38/meta.yaml new file mode 100644 index 0000000000000..91cb81e861acd --- /dev/null +++ b/recipes/bioconductor-mafdb.gnomadex.r2.1.grch38/meta.yaml @@ -0,0 +1,46 @@ +{% set version = "3.9.0" %} +{% set name = "MafDb.gnomADex.r2.1.GRCh38" %} +{% set bioc = "3.9" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: 16c0b79554bd5fc0b4942bba5eca1db2 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: SNPlocs.Hsapiens.dbSNP149.GRCh38 +requirements: + host: + - 'bioconductor-bsgenome >=1.52.0,<1.53.0' + - 'bioconductor-genomeinfodb >=1.20.0,<1.21.0' + - 'bioconductor-genomicranges >=1.36.0,<1.37.0' + - 'bioconductor-genomicscores >=1.8.0,<1.9.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' + - r-base + run: + - 'bioconductor-bsgenome >=1.52.0,<1.53.0' + - 'bioconductor-genomeinfodb >=1.20.0,<1.21.0' + - 'bioconductor-genomicranges >=1.36.0,<1.37.0' + - 'bioconductor-genomicscores >=1.8.0,<1.9.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' + - r-base + - curl +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'Store minor allele frequency data from the Genome Aggregation Database (gnomAD exomes release 2.1) for the human genome version GRCh38.' + diff --git a/recipes/bioconductor-mafdb.gnomadex.r2.1.grch38/post-link.sh b/recipes/bioconductor-mafdb.gnomadex.r2.1.grch38/post-link.sh new file mode 100644 index 0000000000000..b054010d220f3 --- /dev/null +++ b/recipes/bioconductor-mafdb.gnomadex.r2.1.grch38/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="MafDb.gnomADex.r2.1.GRCh38_3.9.0.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/MafDb.gnomADex.r2.1.GRCh38_3.9.0.tar.gz" + "https://bioarchive.galaxyproject.org/MafDb.gnomADex.r2.1.GRCh38_3.9.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-mafdb.gnomadex.r2.1.grch38/bioconductor-mafdb.gnomadex.r2.1.grch38_3.9.0_src_all.tar.gz" +) +MD5="16c0b79554bd5fc0b4942bba5eca1db2" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + curl $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-mafdb.gnomadex.r2.1.grch38/pre-unlink.sh b/recipes/bioconductor-mafdb.gnomadex.r2.1.grch38/pre-unlink.sh new file mode 100644 index 0000000000000..ec5c3432de750 --- /dev/null +++ b/recipes/bioconductor-mafdb.gnomadex.r2.1.grch38/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ MafDb.gnomADex.r2.1.GRCh38 diff --git a/recipes/bioconductor-mafdb.gnomadex.r2.1.hs37d5/meta.yaml b/recipes/bioconductor-mafdb.gnomadex.r2.1.hs37d5/meta.yaml index f22bceb16d329..4234342d90cf1 100644 --- a/recipes/bioconductor-mafdb.gnomadex.r2.1.hs37d5/meta.yaml +++ b/recipes/bioconductor-mafdb.gnomadex.r2.1.hs37d5/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.8.0" %} {% set name = "MafDb.gnomADex.r2.1.hs37d5" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -12,7 +12,7 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' md5: 46272d8c1d0d811cf6471a7a6edd1ba2 build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ @@ -20,22 +20,22 @@ build: # Suggests: SNPlocs.Hsapiens.dbSNP144.GRCh37 requirements: host: - - 'bioconductor-bsgenome >=1.50.0,<1.51.0' - - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' - - 'bioconductor-genomicranges >=1.34.0,<1.35.0' - - 'bioconductor-genomicscores >=1.6.0,<1.7.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-bsgenome >=1.52.0,<1.53.0' + - 'bioconductor-genomeinfodb >=1.20.0,<1.21.0' + - 'bioconductor-genomicranges >=1.36.0,<1.37.0' + - 'bioconductor-genomicscores >=1.8.0,<1.9.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' - r-base run: - - 'bioconductor-bsgenome >=1.50.0,<1.51.0' - - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' - - 'bioconductor-genomicranges >=1.34.0,<1.35.0' - - 'bioconductor-genomicscores >=1.6.0,<1.7.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-bsgenome >=1.52.0,<1.53.0' + - 'bioconductor-genomeinfodb >=1.20.0,<1.21.0' + - 'bioconductor-genomicranges >=1.36.0,<1.37.0' + - 'bioconductor-genomicscores >=1.8.0,<1.9.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-mafdb.gnomadex.r2.1.hs37d5/post-link.sh b/recipes/bioconductor-mafdb.gnomadex.r2.1.hs37d5/post-link.sh index 62033d67ebb27..bd5e6929a56d7 100644 --- a/recipes/bioconductor-mafdb.gnomadex.r2.1.hs37d5/post-link.sh +++ b/recipes/bioconductor-mafdb.gnomadex.r2.1.hs37d5/post-link.sh @@ -1,9 +1,10 @@ #!/bin/bash FN="MafDb.gnomADex.r2.1.hs37d5_3.8.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/MafDb.gnomADex.r2.1.hs37d5_3.8.0.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/MafDb.gnomADex.r2.1.hs37d5_3.8.0.tar.gz" "https://bioarchive.galaxyproject.org/MafDb.gnomADex.r2.1.hs37d5_3.8.0.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-mafdb.gnomadex.r2.1.hs37d5/bioconductor-mafdb.gnomadex.r2.1.hs37d5_3.8.0_src_all.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-mafdb.gnomadex.r2.1.hs37d5/bioconductor-mafdb.gnomadex.r2.1.hs37d5_3.8.0_src_all.tar.gz" ) MD5="46272d8c1d0d811cf6471a7a6edd1ba2" @@ -16,7 +17,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-mafdb.topmed.freeze5.hg19/meta.yaml b/recipes/bioconductor-mafdb.topmed.freeze5.hg19/meta.yaml index bc632baa894cd..243d6f34d08d0 100644 --- a/recipes/bioconductor-mafdb.topmed.freeze5.hg19/meta.yaml +++ b/recipes/bioconductor-mafdb.topmed.freeze5.hg19/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "3.7.1" %} +{% set version = "3.9.0" %} {% set name = "MafDb.TOPMed.freeze5.hg19" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: efa58223437a23aa77a4da3d0ae4aa90 + md5: 0606168d9e2764402a83042d57e6a87a build: number: 0 rpaths: @@ -20,22 +20,22 @@ build: # Suggests: SNPlocs.Hsapiens.dbSNP144.GRCh37 requirements: host: - - 'bioconductor-bsgenome >=1.50.0,<1.51.0' - - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' - - 'bioconductor-genomicranges >=1.34.0,<1.35.0' - - 'bioconductor-genomicscores >=1.6.0,<1.7.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-bsgenome >=1.52.0,<1.53.0' + - 'bioconductor-genomeinfodb >=1.20.0,<1.21.0' + - 'bioconductor-genomicranges >=1.36.0,<1.37.0' + - 'bioconductor-genomicscores >=1.8.0,<1.9.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' - r-base run: - - 'bioconductor-bsgenome >=1.50.0,<1.51.0' - - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' - - 'bioconductor-genomicranges >=1.34.0,<1.35.0' - - 'bioconductor-genomicscores >=1.6.0,<1.7.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-bsgenome >=1.52.0,<1.53.0' + - 'bioconductor-genomeinfodb >=1.20.0,<1.21.0' + - 'bioconductor-genomicranges >=1.36.0,<1.37.0' + - 'bioconductor-genomicscores >=1.8.0,<1.9.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-mafdb.topmed.freeze5.hg19/post-link.sh b/recipes/bioconductor-mafdb.topmed.freeze5.hg19/post-link.sh index f0caf9817e546..ed9c300227858 100644 --- a/recipes/bioconductor-mafdb.topmed.freeze5.hg19/post-link.sh +++ b/recipes/bioconductor-mafdb.topmed.freeze5.hg19/post-link.sh @@ -1,11 +1,11 @@ #!/bin/bash -FN="MafDb.TOPMed.freeze5.hg19_3.7.1.tar.gz" +FN="MafDb.TOPMed.freeze5.hg19_3.9.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/MafDb.TOPMed.freeze5.hg19_3.7.1.tar.gz" - "https://bioarchive.galaxyproject.org/MafDb.TOPMed.freeze5.hg19_3.7.1.tar.gz" - "https://depot.galaxyproject.org/software/bioconductor-mafdb.topmed.freeze5.hg19/bioconductor-mafdb.topmed.freeze5.hg19_3.7.1_src_all.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/MafDb.TOPMed.freeze5.hg19_3.9.0.tar.gz" + "https://bioarchive.galaxyproject.org/MafDb.TOPMed.freeze5.hg19_3.9.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-mafdb.topmed.freeze5.hg19/bioconductor-mafdb.topmed.freeze5.hg19_3.9.0_src_all.tar.gz" ) -MD5="efa58223437a23aa77a4da3d0ae4aa90" +MD5="0606168d9e2764402a83042d57e6a87a" # Use a staging area in the conda dir rather than temp dirs, both to avoid # permission issues as well as to have things downloaded in a predictable @@ -16,7 +16,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-mafdb.topmed.freeze5.hg38/meta.yaml b/recipes/bioconductor-mafdb.topmed.freeze5.hg38/meta.yaml index 6e4bc5d27aff3..a640744815d87 100644 --- a/recipes/bioconductor-mafdb.topmed.freeze5.hg38/meta.yaml +++ b/recipes/bioconductor-mafdb.topmed.freeze5.hg38/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "3.7.1" %} +{% set version = "3.9.0" %} {% set name = "MafDb.TOPMed.freeze5.hg38" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 9d47a5c4e2f94f243c426e4701f6b74a + md5: b7522cfd7c3cd5266a0b7762ef5ba157 build: number: 0 rpaths: @@ -20,22 +20,22 @@ build: # Suggests: SNPlocs.Hsapiens.dbSNP149.GRCh38 requirements: host: - - 'bioconductor-bsgenome >=1.50.0,<1.51.0' - - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' - - 'bioconductor-genomicranges >=1.34.0,<1.35.0' - - 'bioconductor-genomicscores >=1.6.0,<1.7.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-bsgenome >=1.52.0,<1.53.0' + - 'bioconductor-genomeinfodb >=1.20.0,<1.21.0' + - 'bioconductor-genomicranges >=1.36.0,<1.37.0' + - 'bioconductor-genomicscores >=1.8.0,<1.9.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' - r-base run: - - 'bioconductor-bsgenome >=1.50.0,<1.51.0' - - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' - - 'bioconductor-genomicranges >=1.34.0,<1.35.0' - - 'bioconductor-genomicscores >=1.6.0,<1.7.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-bsgenome >=1.52.0,<1.53.0' + - 'bioconductor-genomeinfodb >=1.20.0,<1.21.0' + - 'bioconductor-genomicranges >=1.36.0,<1.37.0' + - 'bioconductor-genomicscores >=1.8.0,<1.9.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-mafdb.topmed.freeze5.hg38/post-link.sh b/recipes/bioconductor-mafdb.topmed.freeze5.hg38/post-link.sh index 7aa46ed82bb79..870332296bc70 100644 --- a/recipes/bioconductor-mafdb.topmed.freeze5.hg38/post-link.sh +++ b/recipes/bioconductor-mafdb.topmed.freeze5.hg38/post-link.sh @@ -1,11 +1,11 @@ #!/bin/bash -FN="MafDb.TOPMed.freeze5.hg38_3.7.1.tar.gz" +FN="MafDb.TOPMed.freeze5.hg38_3.9.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/MafDb.TOPMed.freeze5.hg38_3.7.1.tar.gz" - "https://bioarchive.galaxyproject.org/MafDb.TOPMed.freeze5.hg38_3.7.1.tar.gz" - "https://depot.galaxyproject.org/software/bioconductor-mafdb.topmed.freeze5.hg38/bioconductor-mafdb.topmed.freeze5.hg38_3.7.1_src_all.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/MafDb.TOPMed.freeze5.hg38_3.9.0.tar.gz" + "https://bioarchive.galaxyproject.org/MafDb.TOPMed.freeze5.hg38_3.9.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-mafdb.topmed.freeze5.hg38/bioconductor-mafdb.topmed.freeze5.hg38_3.9.0_src_all.tar.gz" ) -MD5="9d47a5c4e2f94f243c426e4701f6b74a" +MD5="b7522cfd7c3cd5266a0b7762ef5ba157" # Use a staging area in the conda dir rather than temp dirs, both to avoid # permission issues as well as to have things downloaded in a predictable @@ -16,7 +16,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-maftools/meta.yaml b/recipes/bioconductor-maftools/meta.yaml index af47a5d8177a3..354374b15fd84 100644 --- a/recipes/bioconductor-maftools/meta.yaml +++ b/recipes/bioconductor-maftools/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.8.0" %} +{% set version = "2.0.0" %} {% set name = "maftools" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,47 +10,29 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 5e5bd8c517982b1d835d07081632c2ab + md5: 5267d82afbeb9a7a1e4b7ba6b893fb72 build: number: 0 rpaths: - lib/R/lib/ - lib/ noarch: generic -# Suggests: knitr, rmarkdown +# Suggests: knitr, rmarkdown, BSgenome, Biostrings, mclust, rjson requirements: host: - - 'bioconductor-biostrings >=2.50.0,<2.51.0' - - 'bioconductor-bsgenome >=1.50.0,<1.51.0' - - 'bioconductor-complexheatmap >=1.20.0,<1.21.0' - r-base - r-cometexacttest - - r-cowplot - r-data.table - - 'r-ggplot2 >=2.0' - - r-ggrepel - - r-gridextra - - r-mclust - r-nmf - r-rcolorbrewer - - r-rjson - r-survival - r-wordcloud run: - - 'bioconductor-biostrings >=2.50.0,<2.51.0' - - 'bioconductor-bsgenome >=1.50.0,<1.51.0' - - 'bioconductor-complexheatmap >=1.20.0,<1.21.0' - r-base - r-cometexacttest - - r-cowplot - r-data.table - - 'r-ggplot2 >=2.0' - - r-ggrepel - - r-gridextra - - r-mclust - r-nmf - r-rcolorbrewer - - r-rjson - r-survival - r-wordcloud test: diff --git a/recipes/bioconductor-mageckflute/meta.yaml b/recipes/bioconductor-mageckflute/meta.yaml index c915008b34174..5fdc88bd4327b 100644 --- a/recipes/bioconductor-mageckflute/meta.yaml +++ b/recipes/bioconductor-mageckflute/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.2.3" %} +{% set version = "1.4.0" %} {% set name = "MAGeCKFlute" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 783deb6c1ff79461eacbb9016488283f + md5: 509658918962fbc8209d5199f640c8c4 build: number: 0 rpaths: @@ -20,12 +20,12 @@ build: # Suggests: knitr, rmarkdown, BiocStyle, org.Mm.eg.db requirements: host: - - 'bioconductor-biomart >=2.38.0,<2.39.0' - - 'bioconductor-bladderbatch >=1.20.0,<1.21.0' - - 'bioconductor-clusterprofiler >=3.10.0,<3.11.0' - - 'bioconductor-dose >=3.8.0,<3.9.0' - - 'bioconductor-pathview >=1.22.0,<1.23.0' - - 'bioconductor-sva >=3.30.0,<3.31.0' + - 'bioconductor-biomart >=2.40.0,<2.41.0' + - 'bioconductor-bladderbatch >=1.22.0,<1.23.0' + - 'bioconductor-clusterprofiler >=3.12.0,<3.13.0' + - 'bioconductor-dose >=3.10.0,<3.11.0' + - 'bioconductor-pathview >=1.24.0,<1.25.0' + - 'bioconductor-sva >=3.32.0,<3.33.0' - r-base - r-data.table - r-ggextra @@ -36,12 +36,12 @@ requirements: - r-pheatmap - r-png run: - - 'bioconductor-biomart >=2.38.0,<2.39.0' - - 'bioconductor-bladderbatch >=1.20.0,<1.21.0' - - 'bioconductor-clusterprofiler >=3.10.0,<3.11.0' - - 'bioconductor-dose >=3.8.0,<3.9.0' - - 'bioconductor-pathview >=1.22.0,<1.23.0' - - 'bioconductor-sva >=3.30.0,<3.31.0' + - 'bioconductor-biomart >=2.40.0,<2.41.0' + - 'bioconductor-bladderbatch >=1.22.0,<1.23.0' + - 'bioconductor-clusterprofiler >=3.12.0,<3.13.0' + - 'bioconductor-dose >=3.10.0,<3.11.0' + - 'bioconductor-pathview >=1.24.0,<1.25.0' + - 'bioconductor-sva >=3.32.0,<3.33.0' - r-base - r-data.table - r-ggextra diff --git a/recipes/bioconductor-maigespack/meta.yaml b/recipes/bioconductor-maigespack/meta.yaml index 8afed60dcd3ab..69ee8239cea69 100644 --- a/recipes/bioconductor-maigespack/meta.yaml +++ b/recipes/bioconductor-maigespack/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.46.0" %} +{% set version = "1.48.0" %} {% set name = "maigesPack" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 98e206be973a22e3f190a1a3fc044acc + md5: bd7b7b4a8952913853d1f25c342f671b build: number: 0 rpaths: @@ -19,16 +19,16 @@ build: # Suggests: amap, annotate, class, e1071, MASS, multtest, OLIN, R2HTML, rgl, som requirements: host: - - 'bioconductor-convert >=1.58.0,<1.59.0' - - 'bioconductor-graph >=1.60.0,<1.61.0' - - 'bioconductor-limma >=3.38.0,<3.39.0' - - 'bioconductor-marray >=1.60.0,<1.61.0' + - 'bioconductor-convert >=1.60.0,<1.61.0' + - 'bioconductor-graph >=1.62.0,<1.63.0' + - 'bioconductor-limma >=3.40.0,<3.41.0' + - 'bioconductor-marray >=1.62.0,<1.63.0' - r-base run: - - 'bioconductor-convert >=1.58.0,<1.59.0' - - 'bioconductor-graph >=1.60.0,<1.61.0' - - 'bioconductor-limma >=3.38.0,<3.39.0' - - 'bioconductor-marray >=1.60.0,<1.61.0' + - 'bioconductor-convert >=1.60.0,<1.61.0' + - 'bioconductor-graph >=1.62.0,<1.63.0' + - 'bioconductor-limma >=3.40.0,<3.41.0' + - 'bioconductor-marray >=1.62.0,<1.63.0' - r-base build: - {{ compiler('c') }} diff --git a/recipes/bioconductor-mait/meta.yaml b/recipes/bioconductor-mait/meta.yaml index 972b4862dd8f6..93ad061c729bb 100644 --- a/recipes/bioconductor-mait/meta.yaml +++ b/recipes/bioconductor-mait/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.16.1" %} +{% set version = "1.18.0" %} {% set name = "MAIT" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,17 +10,17 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 1408eff274fb1b85fc403e9e27bfd785 + md5: ebad68909a67b2224649a8ec8583d38c build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ # Suggests: faahKO requirements: host: - - 'bioconductor-camera >=1.38.0,<1.39.0' - - 'bioconductor-xcms >=3.4.0,<3.5.0' + - 'bioconductor-camera >=1.40.0,<1.41.0' + - 'bioconductor-xcms >=3.6.0,<3.7.0' - r-agricolae - r-base - r-caret @@ -32,8 +32,8 @@ requirements: - r-plsgenomics - r-rcpp run: - - 'bioconductor-camera >=1.38.0,<1.39.0' - - 'bioconductor-xcms >=3.4.0,<3.5.0' + - 'bioconductor-camera >=1.40.0,<1.41.0' + - 'bioconductor-xcms >=3.6.0,<3.7.0' - r-agricolae - r-base - r-caret diff --git a/recipes/bioconductor-maizecdf/meta.yaml b/recipes/bioconductor-maizecdf/meta.yaml index 47b078e1775dd..4670a91d64fb7 100644 --- a/recipes/bioconductor-maizecdf/meta.yaml +++ b/recipes/bioconductor-maizecdf/meta.yaml @@ -1,6 +1,6 @@ {% set version = "2.18.0" %} {% set name = "maizecdf" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -12,19 +12,19 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: f9dec9e46688d96daf1e07d4e815afb4 build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' - r-base run: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-maizecdf/post-link.sh b/recipes/bioconductor-maizecdf/post-link.sh index 451ea3f66dac3..523242271a310 100644 --- a/recipes/bioconductor-maizecdf/post-link.sh +++ b/recipes/bioconductor-maizecdf/post-link.sh @@ -1,9 +1,10 @@ #!/bin/bash FN="maizecdf_2.18.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/maizecdf_2.18.0.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/maizecdf_2.18.0.tar.gz" "https://bioarchive.galaxyproject.org/maizecdf_2.18.0.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-maizecdf/bioconductor-maizecdf_2.18.0_src_all.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-maizecdf/bioconductor-maizecdf_2.18.0_src_all.tar.gz" ) MD5="f9dec9e46688d96daf1e07d4e815afb4" @@ -16,7 +17,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-maizeprobe/meta.yaml b/recipes/bioconductor-maizeprobe/meta.yaml index f77009dd337a2..9b7c5ca35c263 100644 --- a/recipes/bioconductor-maizeprobe/meta.yaml +++ b/recipes/bioconductor-maizeprobe/meta.yaml @@ -1,6 +1,6 @@ {% set version = "2.18.0" %} {% set name = "maizeprobe" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -12,19 +12,19 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: ef7ba47de2346b3552621263399c05d1 build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' - r-base run: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-maizeprobe/post-link.sh b/recipes/bioconductor-maizeprobe/post-link.sh index 4d518932db798..293440d922c8b 100644 --- a/recipes/bioconductor-maizeprobe/post-link.sh +++ b/recipes/bioconductor-maizeprobe/post-link.sh @@ -1,9 +1,10 @@ #!/bin/bash FN="maizeprobe_2.18.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/maizeprobe_2.18.0.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/maizeprobe_2.18.0.tar.gz" "https://bioarchive.galaxyproject.org/maizeprobe_2.18.0.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-maizeprobe/bioconductor-maizeprobe_2.18.0_src_all.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-maizeprobe/bioconductor-maizeprobe_2.18.0_src_all.tar.gz" ) MD5="ef7ba47de2346b3552621263399c05d1" @@ -16,7 +17,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-makecdfenv/meta.yaml b/recipes/bioconductor-makecdfenv/meta.yaml index 9f6600a8951e1..9cc243a1ad266 100644 --- a/recipes/bioconductor-makecdfenv/meta.yaml +++ b/recipes/bioconductor-makecdfenv/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.58.0" %} +{% set version = "1.60.0" %} {% set name = "makecdfenv" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 4f1ba6b03964861e6553e52ff5c9cfb3 + md5: 79ef6ba4960a32d7691d7428a58aa89b build: number: 0 rpaths: @@ -18,16 +18,16 @@ build: - lib/ requirements: host: - - 'bioconductor-affy >=1.60.0,<1.61.0' - - 'bioconductor-affyio >=1.52.0,<1.53.0' - - 'bioconductor-biobase >=2.42.0,<2.43.0' - - 'bioconductor-zlibbioc >=1.28.0,<1.29.0' + - 'bioconductor-affy >=1.62.0,<1.63.0' + - 'bioconductor-affyio >=1.54.0,<1.55.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' + - 'bioconductor-zlibbioc >=1.30.0,<1.31.0' - r-base run: - - 'bioconductor-affy >=1.60.0,<1.61.0' - - 'bioconductor-affyio >=1.52.0,<1.53.0' - - 'bioconductor-biobase >=2.42.0,<2.43.0' - - 'bioconductor-zlibbioc >=1.28.0,<1.29.0' + - 'bioconductor-affy >=1.62.0,<1.63.0' + - 'bioconductor-affyio >=1.54.0,<1.55.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' + - 'bioconductor-zlibbioc >=1.30.0,<1.31.0' - r-base build: - {{ compiler('c') }} diff --git a/recipes/bioconductor-malaria.db0/meta.yaml b/recipes/bioconductor-malaria.db0/meta.yaml index 0be373a4b1d62..a5168b258f64b 100644 --- a/recipes/bioconductor-malaria.db0/meta.yaml +++ b/recipes/bioconductor-malaria.db0/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "3.7.1" %} +{% set version = "3.8.2" %} {% set name = "malaria.db0" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,21 +10,21 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 217e4954b728ef55cdb913960d34c63a + md5: c6028e87fd7d4c72656a4f865d43e81a build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' - r-base run: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-malaria.db0/post-link.sh b/recipes/bioconductor-malaria.db0/post-link.sh index 9544599fc59d8..4c31c5e55348f 100644 --- a/recipes/bioconductor-malaria.db0/post-link.sh +++ b/recipes/bioconductor-malaria.db0/post-link.sh @@ -1,11 +1,11 @@ #!/bin/bash -FN="malaria.db0_3.7.1.tar.gz" +FN="malaria.db0_3.8.2.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/malaria.db0_3.7.1.tar.gz" - "https://bioarchive.galaxyproject.org/malaria.db0_3.7.1.tar.gz" - "https://depot.galaxyproject.org/software/bioconductor-malaria.db0/bioconductor-malaria.db0_3.7.1_src_all.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/malaria.db0_3.8.2.tar.gz" + "https://bioarchive.galaxyproject.org/malaria.db0_3.8.2.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-malaria.db0/bioconductor-malaria.db0_3.8.2_src_all.tar.gz" ) -MD5="217e4954b728ef55cdb913960d34c63a" +MD5="c6028e87fd7d4c72656a4f865d43e81a" # Use a staging area in the conda dir rather than temp dirs, both to avoid # permission issues as well as to have things downloaded in a predictable @@ -16,7 +16,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-mammaprintdata/meta.yaml b/recipes/bioconductor-mammaprintdata/meta.yaml index a0bf21f6a89e3..93d30a0496002 100644 --- a/recipes/bioconductor-mammaprintdata/meta.yaml +++ b/recipes/bioconductor-mammaprintdata/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.18.0" %} +{% set version = "1.20.0" %} {% set name = "mammaPrintData" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 8bf8e8805b3af4953469a353d305c74c + md5: 12cc4c98823e833df14c94a612bddad9 build: number: 0 rpaths: @@ -23,7 +23,7 @@ requirements: - r-base run: - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-mammaprintdata/post-link.sh b/recipes/bioconductor-mammaprintdata/post-link.sh index b1c680319582e..29acb2afc1521 100644 --- a/recipes/bioconductor-mammaprintdata/post-link.sh +++ b/recipes/bioconductor-mammaprintdata/post-link.sh @@ -1,11 +1,11 @@ #!/bin/bash -FN="mammaPrintData_1.18.0.tar.gz" +FN="mammaPrintData_1.20.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/experiment/src/contrib/mammaPrintData_1.18.0.tar.gz" - "https://bioarchive.galaxyproject.org/mammaPrintData_1.18.0.tar.gz" - "https://depot.galaxyproject.org/software/bioconductor-mammaprintdata/bioconductor-mammaprintdata_1.18.0_src_all.tar.gz" + "https://bioconductor.org/packages/3.9/data/experiment/src/contrib/mammaPrintData_1.20.0.tar.gz" + "https://bioarchive.galaxyproject.org/mammaPrintData_1.20.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-mammaprintdata/bioconductor-mammaprintdata_1.20.0_src_all.tar.gz" ) -MD5="8bf8e8805b3af4953469a353d305c74c" +MD5="12cc4c98823e833df14c94a612bddad9" # Use a staging area in the conda dir rather than temp dirs, both to avoid # permission issues as well as to have things downloaded in a predictable @@ -16,7 +16,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-manor/meta.yaml b/recipes/bioconductor-manor/meta.yaml index c64217b6ca74f..ef57a514f6d40 100644 --- a/recipes/bioconductor-manor/meta.yaml +++ b/recipes/bioconductor-manor/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.54.0" %} +{% set version = "1.56.0" %} {% set name = "MANOR" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: f06fe382abee16e0de2e65e43419d59f + md5: fa54da1038acb0b053315892539d8dd0 build: number: 0 rpaths: @@ -18,10 +18,10 @@ build: - lib/ requirements: host: - - 'bioconductor-glad >=2.46.0,<2.47.0' + - 'bioconductor-glad >=2.48.0,<2.49.0' - r-base run: - - 'bioconductor-glad >=2.46.0,<2.47.0' + - 'bioconductor-glad >=2.48.0,<2.49.0' - r-base build: - {{ compiler('c') }} diff --git a/recipes/bioconductor-manta/meta.yaml b/recipes/bioconductor-manta/meta.yaml index 5df7c66b4a7ca..abec78d789dac 100644 --- a/recipes/bioconductor-manta/meta.yaml +++ b/recipes/bioconductor-manta/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.28.1" %} +{% set version = "1.30.0" %} {% set name = "manta" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - sha256: c51f9b49f7ee8b401610f44d00f6c14250162c3124d25844c5190612fd80fc53 + md5: 0ceb88d84dff7742d4dcc6cc53e5ef2c build: number: 0 rpaths: @@ -20,12 +20,12 @@ build: # Suggests: RSQLite, plotrix requirements: host: - - 'bioconductor-edger >=3.24.0,<3.25.0' + - 'bioconductor-edger >=3.26.0,<3.27.0' - r-base - 'r-caroline >=0.6.6' - r-hmisc run: - - 'bioconductor-edger >=3.24.0,<3.25.0' + - 'bioconductor-edger >=3.26.0,<3.27.0' - r-base - 'r-caroline >=0.6.6' - r-hmisc diff --git a/recipes/bioconductor-mantelcorr/meta.yaml b/recipes/bioconductor-mantelcorr/meta.yaml index d05ae4c49b83d..f3f792d3cec26 100644 --- a/recipes/bioconductor-mantelcorr/meta.yaml +++ b/recipes/bioconductor-mantelcorr/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.52.0" %} +{% set version = "1.54.0" %} {% set name = "MantelCorr" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 8de0637aa10324d7ff3d37ca1ec4f7d5 + md5: dd59c2cb7112102a25e153f10432ea6e build: number: 0 rpaths: diff --git a/recipes/bioconductor-mapkl/build.sh b/recipes/bioconductor-mapkl/build.sh index bdc283dd1fc08..c1d13421f5f1e 100644 --- a/recipes/bioconductor-mapkl/build.sh +++ b/recipes/bioconductor-mapkl/build.sh @@ -1,14 +1,11 @@ #!/bin/bash - mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION mkdir -p ~/.R - echo -e "CC=$CC FC=$FC CXX=$CXX CXX98=$CXX CXX11=$CXX CXX14=$CXX" > ~/.R/Makevars - -$R CMD INSTALL --build . +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-mapkl/meta.yaml b/recipes/bioconductor-mapkl/meta.yaml index 94a9aea8fd85d..8ad91efa2a358 100644 --- a/recipes/bioconductor-mapkl/meta.yaml +++ b/recipes/bioconductor-mapkl/meta.yaml @@ -1,35 +1,30 @@ -{% set version = "1.12.0" %} +{% set version = "1.13.0" %} {% set name = "mAPKL" %} -{% set bioc = "3.8" %} -{% set sha256 = "49d260aebe0f1df3d663d033f245aeec8dfb7311579cfb1535a79d9fd9ede8ae" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' - source: url: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: {{ sha256 }} - + md5: e5763a6bb545a2f2cbc99b732717ada7 build: number: 0 rpaths: - lib/R/lib/ - lib/ - # r-clustersim is not available for osx because of X11 issues - skip: True # [osx] - + noarch: generic # Suggests: BiocStyle, knitr, mAPKLData, hgu133plus2.db, RUnit, BiocGenerics requirements: host: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' - - 'bioconductor-biobase >=2.42.0,<2.43.0' - - 'bioconductor-limma >=3.38.0,<3.39.0' - - 'bioconductor-multtest >=2.38.0,<2.39.0' - - 'bioconductor-reactome.db >=1.66.0,<1.67.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' + - 'bioconductor-limma >=3.40.0,<3.41.0' + - 'bioconductor-multtest >=2.40.0,<2.41.0' + - 'bioconductor-reactome.db >=1.68.0,<1.69.0' - r-apcluster - r-base - r-clustersim @@ -37,29 +32,25 @@ requirements: - r-igraph - r-parmigene run: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' - - 'bioconductor-biobase >=2.42.0,<2.43.0' - - 'bioconductor-limma >=3.38.0,<3.39.0' - - 'bioconductor-multtest >=2.38.0,<2.39.0' - - 'bioconductor-reactome.db >=1.66.0,<1.67.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' + - 'bioconductor-limma >=3.40.0,<3.41.0' + - 'bioconductor-multtest >=2.40.0,<2.41.0' + - 'bioconductor-reactome.db >=1.68.0,<1.69.0' - r-apcluster - r-base - r-clustersim - r-e1071 - r-igraph - r-parmigene - test: commands: - '$R -e "library(''{{ name }}'')"' - about: home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: 'GPL (>= 2)' - license_family: GPL - summary: 'We proposie a hybrid FS method (mAP-KL), which combines multiple hypothesis testing and affinity propagation (AP)-clustering algorithm along with the Krzanowski & Lai cluster quality index, to select a small yet informative subset of genes.' - -# libGL.so.1 dependency + summary: 'We propose a hybrid FS method (mAP-KL), which combines multiple hypothesis testing and affinity propagation (AP)-clustering algorithm along with the Krzanowski & Lai cluster quality index, to select a small yet informative subset of genes.' extra: container: - extended-base: True + extended-base: true + diff --git a/recipes/bioconductor-mapkldata/meta.yaml b/recipes/bioconductor-mapkldata/meta.yaml index abc5d454f7bf2..2177acb72155a 100644 --- a/recipes/bioconductor-mapkldata/meta.yaml +++ b/recipes/bioconductor-mapkldata/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.14.0" %} +{% set version = "1.16.0" %} {% set name = "mAPKLData" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 6d044355ab9473e4e724918a054df95c + md5: 9a0bc0eb61a441595cbe17308a2c7d7c build: number: 0 rpaths: @@ -23,7 +23,7 @@ requirements: - r-base run: - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-mapkldata/post-link.sh b/recipes/bioconductor-mapkldata/post-link.sh index 6dca6e70ecd97..03c56d84e8c3d 100644 --- a/recipes/bioconductor-mapkldata/post-link.sh +++ b/recipes/bioconductor-mapkldata/post-link.sh @@ -1,11 +1,11 @@ #!/bin/bash -FN="mAPKLData_1.14.0.tar.gz" +FN="mAPKLData_1.16.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/experiment/src/contrib/mAPKLData_1.14.0.tar.gz" - "https://bioarchive.galaxyproject.org/mAPKLData_1.14.0.tar.gz" - "https://depot.galaxyproject.org/software/bioconductor-mapkldata/bioconductor-mapkldata_1.14.0_src_all.tar.gz" + "https://bioconductor.org/packages/3.9/data/experiment/src/contrib/mAPKLData_1.16.0.tar.gz" + "https://bioarchive.galaxyproject.org/mAPKLData_1.16.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-mapkldata/bioconductor-mapkldata_1.16.0_src_all.tar.gz" ) -MD5="6d044355ab9473e4e724918a054df95c" +MD5="9a0bc0eb61a441595cbe17308a2c7d7c" # Use a staging area in the conda dir rather than temp dirs, both to avoid # permission issues as well as to have things downloaded in a predictable @@ -16,7 +16,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-mapredictdsc/meta.yaml b/recipes/bioconductor-mapredictdsc/meta.yaml index 168126504742d..ce238c33c6bc7 100644 --- a/recipes/bioconductor-mapredictdsc/meta.yaml +++ b/recipes/bioconductor-mapredictdsc/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.20.0" %} +{% set version = "1.22.0" %} {% set name = "maPredictDSC" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 58b9e88d3fdbb667047c967923367f82 + md5: 2d5cd443eb8639b69b8421686a834a79 build: number: 0 rpaths: @@ -20,13 +20,13 @@ build: # Suggests: parallel requirements: host: - - 'bioconductor-affy >=1.60.0,<1.61.0' - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' - - 'bioconductor-gcrma >=2.54.0,<2.55.0' + - 'bioconductor-affy >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' + - 'bioconductor-gcrma >=2.56.0,<2.57.0' - 'bioconductor-hgu133plus2.db >=3.2.0,<3.3.0' - - 'bioconductor-limma >=3.38.0,<3.39.0' - - 'bioconductor-lungcanceracvssccgeo >=1.18.0,<1.19.0' - - 'bioconductor-roc >=1.58.0,<1.59.0' + - 'bioconductor-limma >=3.40.0,<3.41.0' + - 'bioconductor-lungcanceracvssccgeo >=1.20.0,<1.21.0' + - 'bioconductor-roc >=1.60.0,<1.61.0' - r-base - r-caret - r-class @@ -34,13 +34,13 @@ requirements: - r-mass - r-rocr run: - - 'bioconductor-affy >=1.60.0,<1.61.0' - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' - - 'bioconductor-gcrma >=2.54.0,<2.55.0' + - 'bioconductor-affy >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' + - 'bioconductor-gcrma >=2.56.0,<2.57.0' - 'bioconductor-hgu133plus2.db >=3.2.0,<3.3.0' - - 'bioconductor-limma >=3.38.0,<3.39.0' - - 'bioconductor-lungcanceracvssccgeo >=1.18.0,<1.19.0' - - 'bioconductor-roc >=1.58.0,<1.59.0' + - 'bioconductor-limma >=3.40.0,<3.41.0' + - 'bioconductor-lungcanceracvssccgeo >=1.20.0,<1.21.0' + - 'bioconductor-roc >=1.60.0,<1.61.0' - r-base - r-caret - r-class diff --git a/recipes/bioconductor-mapscape/meta.yaml b/recipes/bioconductor-mapscape/meta.yaml index aead67191d8cb..f320ccce33a37 100644 --- a/recipes/bioconductor-mapscape/meta.yaml +++ b/recipes/bioconductor-mapscape/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.6.0" %} +{% set version = "1.8.0" %} {% set name = "mapscape" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: b0155ab540b77d549bf9d403b384e24a + md5: c9408c2837e9ddeacfcf9f676b4589d4 build: number: 0 rpaths: diff --git a/recipes/bioconductor-maqcexpression4plex/meta.yaml b/recipes/bioconductor-maqcexpression4plex/meta.yaml index ecca167818302..e72a2a8037f25 100644 --- a/recipes/bioconductor-maqcexpression4plex/meta.yaml +++ b/recipes/bioconductor-maqcexpression4plex/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.26.0" %} +{% set version = "1.28.0" %} {% set name = "maqcExpression4plex" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 3ce8a0a849ae354153897db598f86fab + md5: fa9ecd1de4f0ee49935ea8620c3605e2 build: number: 0 rpaths: @@ -23,7 +23,7 @@ requirements: - r-base run: - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-maqcexpression4plex/post-link.sh b/recipes/bioconductor-maqcexpression4plex/post-link.sh index 244463616f6a9..a8af52a79173d 100644 --- a/recipes/bioconductor-maqcexpression4plex/post-link.sh +++ b/recipes/bioconductor-maqcexpression4plex/post-link.sh @@ -1,11 +1,11 @@ #!/bin/bash -FN="maqcExpression4plex_1.26.0.tar.gz" +FN="maqcExpression4plex_1.28.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/experiment/src/contrib/maqcExpression4plex_1.26.0.tar.gz" - "https://bioarchive.galaxyproject.org/maqcExpression4plex_1.26.0.tar.gz" - "https://depot.galaxyproject.org/software/bioconductor-maqcexpression4plex/bioconductor-maqcexpression4plex_1.26.0_src_all.tar.gz" + "https://bioconductor.org/packages/3.9/data/experiment/src/contrib/maqcExpression4plex_1.28.0.tar.gz" + "https://bioarchive.galaxyproject.org/maqcExpression4plex_1.28.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-maqcexpression4plex/bioconductor-maqcexpression4plex_1.28.0_src_all.tar.gz" ) -MD5="3ce8a0a849ae354153897db598f86fab" +MD5="fa9ecd1de4f0ee49935ea8620c3605e2" # Use a staging area in the conda dir rather than temp dirs, both to avoid # permission issues as well as to have things downloaded in a predictable @@ -16,7 +16,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-maqcsubset/meta.yaml b/recipes/bioconductor-maqcsubset/meta.yaml index 763c126638ee2..844cc24131d93 100644 --- a/recipes/bioconductor-maqcsubset/meta.yaml +++ b/recipes/bioconductor-maqcsubset/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.20.0" %} +{% set version = "1.22.0" %} {% set name = "MAQCsubset" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: e8b9ec1c5c7aec22ebe396f03e5088ad + md5: 97b078cd701d3c46e2ad4342570b7e51 build: number: 0 rpaths: @@ -20,16 +20,16 @@ build: # Suggests: genefilter, codelink requirements: host: - - 'bioconductor-affy >=1.60.0,<1.61.0' - - 'bioconductor-biobase >=2.42.0,<2.43.0' - - 'bioconductor-lumi >=2.34.0,<2.35.0' + - 'bioconductor-affy >=1.62.0,<1.63.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' + - 'bioconductor-lumi >=2.36.0,<2.37.0' - r-base run: - - 'bioconductor-affy >=1.60.0,<1.61.0' - - 'bioconductor-biobase >=2.42.0,<2.43.0' - - 'bioconductor-lumi >=2.34.0,<2.35.0' + - 'bioconductor-affy >=1.62.0,<1.63.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' + - 'bioconductor-lumi >=2.36.0,<2.37.0' - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-maqcsubset/post-link.sh b/recipes/bioconductor-maqcsubset/post-link.sh index 95c431ca92220..36d1aa151bb76 100644 --- a/recipes/bioconductor-maqcsubset/post-link.sh +++ b/recipes/bioconductor-maqcsubset/post-link.sh @@ -1,11 +1,11 @@ #!/bin/bash -FN="MAQCsubset_1.20.0.tar.gz" +FN="MAQCsubset_1.22.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/experiment/src/contrib/MAQCsubset_1.20.0.tar.gz" - "https://bioarchive.galaxyproject.org/MAQCsubset_1.20.0.tar.gz" - "https://depot.galaxyproject.org/software/bioconductor-maqcsubset/bioconductor-maqcsubset_1.20.0_src_all.tar.gz" + "https://bioconductor.org/packages/3.9/data/experiment/src/contrib/MAQCsubset_1.22.0.tar.gz" + "https://bioarchive.galaxyproject.org/MAQCsubset_1.22.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-maqcsubset/bioconductor-maqcsubset_1.22.0_src_all.tar.gz" ) -MD5="e8b9ec1c5c7aec22ebe396f03e5088ad" +MD5="97b078cd701d3c46e2ad4342570b7e51" # Use a staging area in the conda dir rather than temp dirs, both to avoid # permission issues as well as to have things downloaded in a predictable @@ -16,7 +16,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-maqcsubsetafx/meta.yaml b/recipes/bioconductor-maqcsubsetafx/meta.yaml index 79ae6106fc51a..d89cc6ab25425 100644 --- a/recipes/bioconductor-maqcsubsetafx/meta.yaml +++ b/recipes/bioconductor-maqcsubsetafx/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.20.0" %} +{% set version = "1.22.0" %} {% set name = "MAQCsubsetAFX" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,23 +10,23 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 9463855db7431adda8bd920b13a090b2 + md5: c361d50c4fa96fe0fb4a8fa47f5b1522 build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ noarch: generic requirements: host: - - 'bioconductor-affy >=1.60.0,<1.61.0' - - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-affy >=1.62.0,<1.63.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' - r-base run: - - 'bioconductor-affy >=1.60.0,<1.61.0' - - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-affy >=1.62.0,<1.63.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-maqcsubsetafx/post-link.sh b/recipes/bioconductor-maqcsubsetafx/post-link.sh index 29314ceca6865..5e1a015c7d1a8 100644 --- a/recipes/bioconductor-maqcsubsetafx/post-link.sh +++ b/recipes/bioconductor-maqcsubsetafx/post-link.sh @@ -1,11 +1,11 @@ #!/bin/bash -FN="MAQCsubsetAFX_1.20.0.tar.gz" +FN="MAQCsubsetAFX_1.22.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/experiment/src/contrib/MAQCsubsetAFX_1.20.0.tar.gz" - "https://bioarchive.galaxyproject.org/MAQCsubsetAFX_1.20.0.tar.gz" - "https://depot.galaxyproject.org/software/bioconductor-maqcsubsetafx/bioconductor-maqcsubsetafx_1.20.0_src_all.tar.gz" + "https://bioconductor.org/packages/3.9/data/experiment/src/contrib/MAQCsubsetAFX_1.22.0.tar.gz" + "https://bioarchive.galaxyproject.org/MAQCsubsetAFX_1.22.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-maqcsubsetafx/bioconductor-maqcsubsetafx_1.22.0_src_all.tar.gz" ) -MD5="9463855db7431adda8bd920b13a090b2" +MD5="c361d50c4fa96fe0fb4a8fa47f5b1522" # Use a staging area in the conda dir rather than temp dirs, both to avoid # permission issues as well as to have things downloaded in a predictable @@ -16,7 +16,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-maqcsubsetilm/meta.yaml b/recipes/bioconductor-maqcsubsetilm/meta.yaml index 2b640b1887fef..ead3b5b04af99 100644 --- a/recipes/bioconductor-maqcsubsetilm/meta.yaml +++ b/recipes/bioconductor-maqcsubsetilm/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.20.0" %} +{% set version = "1.22.0" %} {% set name = "MAQCsubsetILM" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 92c3de4c8a84a1ef6f3ef994f9a627f3 + md5: 29ec94614e117e09ca659d61b071618b build: number: 0 rpaths: @@ -19,14 +19,14 @@ build: noarch: generic requirements: host: - - 'bioconductor-biobase >=2.42.0,<2.43.0' - - 'bioconductor-lumi >=2.34.0,<2.35.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' + - 'bioconductor-lumi >=2.36.0,<2.37.0' - r-base run: - - 'bioconductor-biobase >=2.42.0,<2.43.0' - - 'bioconductor-lumi >=2.34.0,<2.35.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' + - 'bioconductor-lumi >=2.36.0,<2.37.0' - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-maqcsubsetilm/post-link.sh b/recipes/bioconductor-maqcsubsetilm/post-link.sh index d27ac910087c9..81a28bce9d6c3 100644 --- a/recipes/bioconductor-maqcsubsetilm/post-link.sh +++ b/recipes/bioconductor-maqcsubsetilm/post-link.sh @@ -1,11 +1,11 @@ #!/bin/bash -FN="MAQCsubsetILM_1.20.0.tar.gz" +FN="MAQCsubsetILM_1.22.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/experiment/src/contrib/MAQCsubsetILM_1.20.0.tar.gz" - "https://bioarchive.galaxyproject.org/MAQCsubsetILM_1.20.0.tar.gz" - "https://depot.galaxyproject.org/software/bioconductor-maqcsubsetilm/bioconductor-maqcsubsetilm_1.20.0_src_all.tar.gz" + "https://bioconductor.org/packages/3.9/data/experiment/src/contrib/MAQCsubsetILM_1.22.0.tar.gz" + "https://bioarchive.galaxyproject.org/MAQCsubsetILM_1.22.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-maqcsubsetilm/bioconductor-maqcsubsetilm_1.22.0_src_all.tar.gz" ) -MD5="92c3de4c8a84a1ef6f3ef994f9a627f3" +MD5="29ec94614e117e09ca659d61b071618b" # Use a staging area in the conda dir rather than temp dirs, both to avoid # permission issues as well as to have things downloaded in a predictable @@ -16,7 +16,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-marray/meta.yaml b/recipes/bioconductor-marray/meta.yaml index 107230766964e..9eaefbb3c3d46 100644 --- a/recipes/bioconductor-marray/meta.yaml +++ b/recipes/bioconductor-marray/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.60.0" %} +{% set version = "1.62.0" %} {% set name = "marray" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,9 +10,9 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 9620bb609afca132e43100410100b934 + md5: d2628eb19ca37a181402798dc8543ec9 build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ @@ -20,10 +20,10 @@ build: # Suggests: tkWidgets requirements: host: - - 'bioconductor-limma >=3.38.0,<3.39.0' + - 'bioconductor-limma >=3.40.0,<3.41.0' - r-base run: - - 'bioconductor-limma >=3.38.0,<3.39.0' + - 'bioconductor-limma >=3.40.0,<3.41.0' - r-base test: commands: diff --git a/recipes/bioconductor-martini/meta.yaml b/recipes/bioconductor-martini/meta.yaml index 160a7a558c8a2..92414d514373d 100644 --- a/recipes/bioconductor-martini/meta.yaml +++ b/recipes/bioconductor-martini/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.2.0" %} +{% set version = "1.4.0" %} {% set name = "martini" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: a700575374a986a0013bff3b1e08a134 + md5: 55b0a9fc5a85e9499c83db57640c0472 build: number: 0 rpaths: @@ -19,28 +19,27 @@ build: # Suggests: biomaRt (>= 2.34.1), httr (>= 1.2.1), IRanges (>= 2.8.2), knitr, testthat, tidyverse, rmarkdown requirements: host: - - 'bioconductor-rgin >=1.2.0,<1.3.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' - - 'bioconductor-snpstats >=1.32.0,<1.33.0' + - 'bioconductor-rgin >=1.4.0,<1.5.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' + - 'bioconductor-snpstats >=1.34.0,<1.35.0' - r-base - 'r-igraph >=1.0.1' - r-matrix - 'r-rcpp >=0.12.8' - - 'r-rcppeigen >=0.3.3.3.0' + - 'r-rcppeigen >=0.3.3.5.0' run: - - 'bioconductor-rgin >=1.2.0,<1.3.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' - - 'bioconductor-snpstats >=1.32.0,<1.33.0' + - 'bioconductor-rgin >=1.4.0,<1.5.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' + - 'bioconductor-snpstats >=1.34.0,<1.35.0' - r-base - 'r-igraph >=1.0.1' - r-matrix - 'r-rcpp >=0.12.8' - - 'r-rcppeigen >=0.3.3.3.0' + - 'r-rcppeigen >=0.3.3.5.0' build: - {{ compiler('c') }} - {{ compiler('cxx') }} - make - - llvm-openmp # [osx] test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-maser/meta.yaml b/recipes/bioconductor-maser/meta.yaml index 12494367ab8b3..43aaa40dd112e 100644 --- a/recipes/bioconductor-maser/meta.yaml +++ b/recipes/bioconductor-maser/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.0.0" %} +{% set version = "1.2.0" %} {% set name = "maser" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 3736c02b9c3b7db33c31da8fa9e72eea + md5: faf35d96da67a1559eb6c9eb65b34280 build: number: 0 rpaths: @@ -20,12 +20,12 @@ build: # Suggests: testthat, knitr, rmarkdown, BiocStyle, AnnotationHub requirements: host: - - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' - - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' - - 'bioconductor-genomicranges >=1.34.0,<1.35.0' - - 'bioconductor-gviz >=1.26.0,<1.27.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-rtracklayer >=1.42.0,<1.43.0' + - 'bioconductor-biocgenerics >=0.30.0,<0.31.0' + - 'bioconductor-genomeinfodb >=1.20.0,<1.21.0' + - 'bioconductor-genomicranges >=1.36.0,<1.37.0' + - 'bioconductor-gviz >=1.28.0,<1.29.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-rtracklayer >=1.44.0,<1.45.0' - r-base - r-data.table - r-dplyr @@ -33,12 +33,12 @@ requirements: - r-ggplot2 - r-reshape2 run: - - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' - - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' - - 'bioconductor-genomicranges >=1.34.0,<1.35.0' - - 'bioconductor-gviz >=1.26.0,<1.27.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-rtracklayer >=1.42.0,<1.43.0' + - 'bioconductor-biocgenerics >=0.30.0,<0.31.0' + - 'bioconductor-genomeinfodb >=1.20.0,<1.21.0' + - 'bioconductor-genomicranges >=1.36.0,<1.37.0' + - 'bioconductor-gviz >=1.28.0,<1.29.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-rtracklayer >=1.44.0,<1.45.0' - r-base - r-data.table - r-dplyr @@ -51,5 +51,5 @@ test: about: home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: 'MIT + file LICENSE' - summary: 'This package provides functionalities for analysis, annotation and visualizaton of alternative splicing events.' + summary: 'This package provides functionalities for downstream analysis, annotation and visualizaton of alternative splicing events generated by rMATS.' diff --git a/recipes/bioconductor-masigpro/meta.yaml b/recipes/bioconductor-masigpro/meta.yaml index 34f56320bc9bf..75eeaa6e11daf 100644 --- a/recipes/bioconductor-masigpro/meta.yaml +++ b/recipes/bioconductor-masigpro/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.54.0" %} +{% set version = "1.56.0" %} {% set name = "maSigPro" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 4a642f18b31d99eee5b5d7dcd7b54b8e + md5: 0b3ed0e8fd063fbf6700d64d2300082a build: number: 0 rpaths: @@ -19,13 +19,13 @@ build: noarch: generic requirements: host: - - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' - r-base - r-mass - r-mclust - r-venn run: - - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' - r-base - r-mass - r-mclust diff --git a/recipes/bioconductor-maskbad/meta.yaml b/recipes/bioconductor-maskbad/meta.yaml index 36318da926a7d..fbbc8e9bed30d 100644 --- a/recipes/bioconductor-maskbad/meta.yaml +++ b/recipes/bioconductor-maskbad/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.26.0" %} +{% set version = "1.28.0" %} {% set name = "maskBAD" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: f4729f51911770bb1448510b43e5e479 + md5: 908a121329b4d59a384fb44921547c5c build: number: 0 rpaths: @@ -20,12 +20,12 @@ build: # Suggests: hgu95av2probe, hgu95av2cdf requirements: host: - - 'bioconductor-affy >=1.60.0,<1.61.0' - - 'bioconductor-gcrma >=2.54.0,<2.55.0' + - 'bioconductor-affy >=1.62.0,<1.63.0' + - 'bioconductor-gcrma >=2.56.0,<2.57.0' - r-base run: - - 'bioconductor-affy >=1.60.0,<1.61.0' - - 'bioconductor-gcrma >=2.54.0,<2.55.0' + - 'bioconductor-affy >=1.62.0,<1.63.0' + - 'bioconductor-gcrma >=2.56.0,<2.57.0' - r-base test: commands: diff --git a/recipes/bioconductor-massarray/meta.yaml b/recipes/bioconductor-massarray/meta.yaml index c51440b7a7321..f74eb0c40d8cb 100644 --- a/recipes/bioconductor-massarray/meta.yaml +++ b/recipes/bioconductor-massarray/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.34.1" %} +{% set version = "1.36.0" %} {% set name = "MassArray" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 4285277c93fb350d5b9ad3c1afb551ec + md5: 9bcb895ad4c9c4e7100d65de88baf906 build: number: 0 rpaths: diff --git a/recipes/bioconductor-massir/meta.yaml b/recipes/bioconductor-massir/meta.yaml index 0e6920ec6676f..b5b8801a52a5b 100644 --- a/recipes/bioconductor-massir/meta.yaml +++ b/recipes/bioconductor-massir/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.18.0" %} +{% set version = "1.20.0" %} {% set name = "massiR" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 155d85624615ff8b2a8dfc5614a8cc78 + md5: f5a3d0d1e7f63a5da7bd5dc4d7bfbbdd build: number: 0 rpaths: @@ -20,13 +20,13 @@ build: # Suggests: biomaRt, RUnit, BiocGenerics requirements: host: - - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' - r-base - r-cluster - r-diptest - r-gplots run: - - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' - r-base - r-cluster - r-diptest diff --git a/recipes/bioconductor-massspecwavelet/meta.yaml b/recipes/bioconductor-massspecwavelet/meta.yaml index eaa2df978a4c3..a9101b4c7bb18 100644 --- a/recipes/bioconductor-massspecwavelet/meta.yaml +++ b/recipes/bioconductor-massspecwavelet/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.48.1" %} +{% set version = "1.50.0" %} {% set name = "MassSpecWavelet" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: 7fb2619b242475d3dfa7ad39e38af3c74aa108e647f84633386599a1902999f5 + md5: 6715f272814bb903e02be64a15d18a0c build: number: 0 rpaths: diff --git a/recipes/bioconductor-mast/meta.yaml b/recipes/bioconductor-mast/meta.yaml index 69c27a2b52816..ccb9596dcbe50 100644 --- a/recipes/bioconductor-mast/meta.yaml +++ b/recipes/bioconductor-mast/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.8.1" %} +{% set version = "1.10.0" %} {% set name = "MAST" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 2aff93e37d44268b59c52e6f6323e3a2 + md5: 6095a6cedbe585761fbb1c8df4ce9ea6 build: number: 0 rpaths: @@ -20,13 +20,14 @@ build: # Suggests: knitr, rmarkdown, testthat, lme4(>= 1.0), roxygen2(> 4.0.0), numDeriv, car, gdata, lattice, GGally, GSEABase, NMF, TxDb.Hsapiens.UCSC.hg19.knownGene, rsvd, limma, RColorBrewer, BiocStyle, scater requirements: host: - - 'bioconductor-biobase >=2.42.0,<2.43.0' - - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' - - 'bioconductor-singlecellexperiment >=1.4.0,<1.5.0' - - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' + - 'bioconductor-biocgenerics >=0.30.0,<0.31.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' + - 'bioconductor-singlecellexperiment >=1.6.0,<1.7.0' + - 'bioconductor-summarizedexperiment >=1.14.0,<1.15.0' - r-abind - r-base + - r-blme - r-data.table - r-ggplot2 - r-plyr @@ -34,13 +35,14 @@ requirements: - r-reshape2 - r-stringr run: - - 'bioconductor-biobase >=2.42.0,<2.43.0' - - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' - - 'bioconductor-singlecellexperiment >=1.4.0,<1.5.0' - - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' + - 'bioconductor-biocgenerics >=0.30.0,<0.31.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' + - 'bioconductor-singlecellexperiment >=1.6.0,<1.7.0' + - 'bioconductor-summarizedexperiment >=1.14.0,<1.15.0' - r-abind - r-base + - r-blme - r-data.table - r-ggplot2 - r-plyr diff --git a/recipes/bioconductor-matchbox/meta.yaml b/recipes/bioconductor-matchbox/meta.yaml index 9e02c85f8458a..803bd8bc72be2 100644 --- a/recipes/bioconductor-matchbox/meta.yaml +++ b/recipes/bioconductor-matchbox/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.24.0" %} +{% set version = "1.26.0" %} {% set name = "matchBox" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 96cde96f3ff554796874b2a7cc27bdb9 + md5: cb3a8fdbf40e1dc8d26533bb1fd6a7f8 build: number: 0 rpaths: diff --git a/recipes/bioconductor-matrixrider/meta.yaml b/recipes/bioconductor-matrixrider/meta.yaml index 7b42cfb9e760e..6aa2a4f87a6aa 100644 --- a/recipes/bioconductor-matrixrider/meta.yaml +++ b/recipes/bioconductor-matrixrider/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.14.0" %} +{% set version = "1.16.0" %} {% set name = "MatrixRider" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,27 +10,27 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 96fe9ae1dd48d87fae7b56afd0c4808e + md5: 7f85bfa32fc6a25b3b6987e8a3f064fa build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ # Suggests: RUnit, BiocGenerics, BiocStyle, JASPAR2014 requirements: host: - - 'bioconductor-biostrings >=2.50.0,<2.51.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' - - 'bioconductor-tfbstools >=1.20.0,<1.21.0' - - 'bioconductor-xvector >=0.22.0,<0.23.0' + - 'bioconductor-biostrings >=2.52.0,<2.53.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' + - 'bioconductor-tfbstools >=1.22.0,<1.23.0' + - 'bioconductor-xvector >=0.24.0,<0.25.0' - r-base run: - - 'bioconductor-biostrings >=2.50.0,<2.51.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' - - 'bioconductor-tfbstools >=1.20.0,<1.21.0' - - 'bioconductor-xvector >=0.22.0,<0.23.0' + - 'bioconductor-biostrings >=2.52.0,<2.53.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' + - 'bioconductor-tfbstools >=1.22.0,<1.23.0' + - 'bioconductor-xvector >=0.24.0,<0.25.0' - r-base build: - {{ compiler('c') }} diff --git a/recipes/bioconductor-matter/meta.yaml b/recipes/bioconductor-matter/meta.yaml index 76bfb260feb82..a202a3a390a2a 100644 --- a/recipes/bioconductor-matter/meta.yaml +++ b/recipes/bioconductor-matter/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.8.3" %} +{% set version = "1.10.0" %} {% set name = "matter" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - sha256: 957f0dd34830f51c53f6c661721ea5d7537d73ef4403a1142a442232017d1a0e + md5: 80c2d4693acc88b40867e100e4ade2dd build: number: 0 rpaths: @@ -19,13 +19,15 @@ build: # Suggests: BiocStyle, testthat requirements: host: - - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' + - 'bioconductor-biocgenerics >=0.30.0,<0.31.0' + - 'bioconductor-biocparallel >=1.18.0,<1.19.0' - r-base - r-biglm - r-digest - r-irlba run: - - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' + - 'bioconductor-biocgenerics >=0.30.0,<0.31.0' + - 'bioconductor-biocparallel >=1.18.0,<1.19.0' - r-base - r-biglm - r-digest diff --git a/recipes/bioconductor-maxcontrastprojection/meta.yaml b/recipes/bioconductor-maxcontrastprojection/meta.yaml index 28a4d7a5275f5..ba6f382151844 100644 --- a/recipes/bioconductor-maxcontrastprojection/meta.yaml +++ b/recipes/bioconductor-maxcontrastprojection/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.6.1" %} +{% set version = "1.8.0" %} {% set name = "MaxContrastProjection" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: ba20c5a9763a663bc0361ac116dcfe164b7e7d1be60c09ee4e8a9597d0c26a80 + md5: a4636912f434c1ec7ecfe24743e77a06 build: number: 0 rpaths: @@ -21,10 +21,10 @@ build: # SystemRequirements: GNU make requirements: host: - - 'bioconductor-ebimage >=4.24.0,<4.25.0' + - 'bioconductor-ebimage >=4.26.0,<4.27.0' - r-base run: - - 'bioconductor-ebimage >=4.24.0,<4.25.0' + - 'bioconductor-ebimage >=4.26.0,<4.27.0' - r-base test: commands: diff --git a/recipes/bioconductor-mbamethyl/meta.yaml b/recipes/bioconductor-mbamethyl/meta.yaml index c6ec254015721..a95e2621bfc26 100644 --- a/recipes/bioconductor-mbamethyl/meta.yaml +++ b/recipes/bioconductor-mbamethyl/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.16.0" %} +{% set version = "1.18.0" %} {% set name = "MBAmethyl" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 6299112309d19ef270d439e7a23ee3ae + md5: 46b488829917ef5750391463877be1ab build: number: 0 rpaths: diff --git a/recipes/bioconductor-mbased/meta.yaml b/recipes/bioconductor-mbased/meta.yaml index 586fcb6f38f8c..f248c919d3efa 100644 --- a/recipes/bioconductor-mbased/meta.yaml +++ b/recipes/bioconductor-mbased/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.16.0" %} +{% set version = "1.18.0" %} {% set name = "MBASED" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 503273be8ad6f478d004d993d9f1c054 + md5: 992a08870864f79fa226791b969c3b8b build: number: 0 rpaths: @@ -20,17 +20,17 @@ build: # Suggests: BiocStyle requirements: host: - - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' - - 'bioconductor-biocparallel >=1.16.0,<1.17.0' - - 'bioconductor-genomicranges >=1.34.0,<1.35.0' - - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' + - 'bioconductor-biocgenerics >=0.30.0,<0.31.0' + - 'bioconductor-biocparallel >=1.18.0,<1.19.0' + - 'bioconductor-genomicranges >=1.36.0,<1.37.0' + - 'bioconductor-summarizedexperiment >=1.14.0,<1.15.0' - r-base - r-runit run: - - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' - - 'bioconductor-biocparallel >=1.16.0,<1.17.0' - - 'bioconductor-genomicranges >=1.34.0,<1.35.0' - - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' + - 'bioconductor-biocgenerics >=0.30.0,<0.31.0' + - 'bioconductor-biocparallel >=1.18.0,<1.19.0' + - 'bioconductor-genomicranges >=1.36.0,<1.37.0' + - 'bioconductor-summarizedexperiment >=1.14.0,<1.15.0' - r-base - r-runit test: diff --git a/recipes/bioconductor-mbcb/meta.yaml b/recipes/bioconductor-mbcb/meta.yaml index 783e6f3d583b7..2b83c96099c63 100644 --- a/recipes/bioconductor-mbcb/meta.yaml +++ b/recipes/bioconductor-mbcb/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.36.0" %} +{% set version = "1.38.0" %} {% set name = "MBCB" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,20 +10,20 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 21bf4710d8291d63d7c6615b73000955 + md5: fa2a4736e30c0df5d78602349fda7852 build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ noarch: generic requirements: host: - - 'bioconductor-preprocesscore >=1.44.0,<1.45.0' + - 'bioconductor-preprocesscore >=1.46.0,<1.47.0' - r-base - r-tcltk2 run: - - 'bioconductor-preprocesscore >=1.44.0,<1.45.0' + - 'bioconductor-preprocesscore >=1.46.0,<1.47.0' - r-base - r-tcltk2 test: diff --git a/recipes/bioconductor-mbkmeans/build.sh b/recipes/bioconductor-mbkmeans/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-mbkmeans/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-mbkmeans/meta.yaml b/recipes/bioconductor-mbkmeans/meta.yaml new file mode 100644 index 0000000000000..7823b81a8c469 --- /dev/null +++ b/recipes/bioconductor-mbkmeans/meta.yaml @@ -0,0 +1,57 @@ +{% set version = "1.0.0" %} +{% set name = "mbkmeans" %} +{% set bioc = "3.9" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + md5: d48afe30bbd4b7fc336a4e3021442e73 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ +# Suggests: beachmat, HDF5Array, Rhdf5lib, BiocStyle, TENxPBMCData, scater, DelayedMatrixStats, knitr, testthat +# SystemRequirements: C++11 +requirements: + host: + - 'bioconductor-beachmat >=2.0.0,<2.1.0' + - 'bioconductor-delayedarray >=0.10.0,<0.11.0' + - 'bioconductor-rhdf5lib >=1.6.0,<1.7.0' + - 'bioconductor-singlecellexperiment >=1.6.0,<1.7.0' + - 'bioconductor-summarizedexperiment >=1.14.0,<1.15.0' + - r-base + - r-benchmarkme + - r-clusterr + - r-matrix + - r-rcpp + - 'r-rcpparmadillo >=0.7.2' + run: + - 'bioconductor-beachmat >=2.0.0,<2.1.0' + - 'bioconductor-delayedarray >=0.10.0,<0.11.0' + - 'bioconductor-rhdf5lib >=1.6.0,<1.7.0' + - 'bioconductor-singlecellexperiment >=1.6.0,<1.7.0' + - 'bioconductor-summarizedexperiment >=1.14.0,<1.15.0' + - r-base + - r-benchmarkme + - r-clusterr + - r-matrix + - r-rcpp + - 'r-rcpparmadillo >=0.7.2' + build: + - {{ compiler('c') }} + - {{ compiler('cxx') }} + - make +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: 'MIT + file LICENSE' + summary: 'Implements the mini-batch k-means algorithm for large datasets, including support for on-disk data representation.' + diff --git a/recipes/bioconductor-mbpcr/meta.yaml b/recipes/bioconductor-mbpcr/meta.yaml index 0bdbee69663ba..e24e7b5601ca9 100644 --- a/recipes/bioconductor-mbpcr/meta.yaml +++ b/recipes/bioconductor-mbpcr/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.36.0" %} +{% set version = "1.38.0" %} {% set name = "mBPCR" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: b429a42900934745c81407e4116c9f54 + md5: c7a90c7e1527258452c9793cb06532ab build: number: 0 rpaths: @@ -20,14 +20,14 @@ build: # Suggests: xtable requirements: host: - - 'bioconductor-biobase >=2.42.0,<2.43.0' - - 'bioconductor-oligoclasses >=1.44.0,<1.45.0' - - 'bioconductor-snpchip >=2.28.0,<2.29.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' + - 'bioconductor-oligoclasses >=1.46.0,<1.47.0' + - 'bioconductor-snpchip >=2.30.0,<2.31.0' - r-base run: - - 'bioconductor-biobase >=2.42.0,<2.43.0' - - 'bioconductor-oligoclasses >=1.44.0,<1.45.0' - - 'bioconductor-snpchip >=2.28.0,<2.29.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' + - 'bioconductor-oligoclasses >=1.46.0,<1.47.0' + - 'bioconductor-snpchip >=2.30.0,<2.31.0' - r-base test: commands: diff --git a/recipes/bioconductor-mbttest/meta.yaml b/recipes/bioconductor-mbttest/meta.yaml index c7ca11121081e..b76aacf2e1d5a 100644 --- a/recipes/bioconductor-mbttest/meta.yaml +++ b/recipes/bioconductor-mbttest/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.10.0" %} +{% set version = "1.12.0" %} {% set name = "MBttest" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: e7f88536245d563302be0374bcdf8009 + md5: d65acd60c9194c071d70909738d8363c build: number: 0 rpaths: diff --git a/recipes/bioconductor-mcagui/meta.yaml b/recipes/bioconductor-mcagui/meta.yaml index 76643d1372d11..64ba74ba0388b 100644 --- a/recipes/bioconductor-mcagui/meta.yaml +++ b/recipes/bioconductor-mcagui/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.30.0" %} +{% set version = "1.32.0" %} {% set name = "mcaGUI" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 8375e8dda6d5515700a95ab587d07c2f + md5: 1b55ca169ec63abfd1a4ca454cbbd8a7 build: number: 0 rpaths: @@ -19,7 +19,7 @@ build: noarch: generic requirements: host: - - 'bioconductor-otubase >=1.32.0,<1.33.0' + - 'bioconductor-otubase >=1.34.0,<1.35.0' - r-base - r-bpca - r-foreign @@ -30,7 +30,7 @@ requirements: - r-proto - r-vegan run: - - 'bioconductor-otubase >=1.32.0,<1.33.0' + - 'bioconductor-otubase >=1.34.0,<1.35.0' - r-base - r-bpca - r-foreign diff --git a/recipes/bioconductor-mcbiclust/meta.yaml b/recipes/bioconductor-mcbiclust/meta.yaml index d6f5b2afbda35..af73d0f40bd5a 100644 --- a/recipes/bioconductor-mcbiclust/meta.yaml +++ b/recipes/bioconductor-mcbiclust/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.6.0" %} +{% set version = "1.8.0" %} {% set name = "MCbiclust" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 16b7342f3ac123ba54e0efc7df2ba492 + md5: 48e7603efa86b31fff7a2a9d50cf5b78 build: number: 0 rpaths: @@ -20,10 +20,10 @@ build: # Suggests: gplots, knitr, rmarkdown, BiocStyle, gProfileR, MASS, dplyr, pander, devtools, testthat, GSVA requirements: host: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' - - 'bioconductor-biocparallel >=1.16.0,<1.17.0' - - 'bioconductor-go.db >=3.7.0,<3.8.0' - - 'bioconductor-org.hs.eg.db >=3.7.0,<3.8.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' + - 'bioconductor-biocparallel >=1.18.0,<1.19.0' + - 'bioconductor-go.db >=3.8.0,<3.9.0' + - 'bioconductor-org.hs.eg.db >=3.8.0,<3.9.0' - r-base - r-cluster - r-ggally @@ -31,10 +31,10 @@ requirements: - r-scales - r-wgcna run: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' - - 'bioconductor-biocparallel >=1.16.0,<1.17.0' - - 'bioconductor-go.db >=3.7.0,<3.8.0' - - 'bioconductor-org.hs.eg.db >=3.7.0,<3.8.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' + - 'bioconductor-biocparallel >=1.18.0,<1.19.0' + - 'bioconductor-go.db >=3.8.0,<3.9.0' + - 'bioconductor-org.hs.eg.db >=3.8.0,<3.9.0' - r-base - r-cluster - r-ggally diff --git a/recipes/bioconductor-mcrestimate/meta.yaml b/recipes/bioconductor-mcrestimate/meta.yaml index 54cd5ff2db504..9f01c39ac9892 100644 --- a/recipes/bioconductor-mcrestimate/meta.yaml +++ b/recipes/bioconductor-mcrestimate/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "2.38.0" %} +{% set version = "2.40.0" %} {% set name = "MCRestimate" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: f72686ef3ef87989030a376fec562d0f + md5: a76acf3b63978eb5a1cf9c99540c5d19 build: number: 0 rpaths: @@ -20,16 +20,16 @@ build: # Suggests: xtable (>= 1.2-1), ROC (>= 1.8.0), genefilter (>= 1.12.0), gpls (>= 1.6.0) requirements: host: - - 'bioconductor-biobase >=2.42.0,<2.43.0' - - 'bioconductor-golubesets >=1.24.0,<1.25.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' + - 'bioconductor-golubesets >=1.26.0,<1.27.0' - r-base - 'r-e1071 >=1.5-12' - 'r-pamr >=1.22' - 'r-randomforest >=3.9-6' - 'r-rcolorbrewer >=0.1-3' run: - - 'bioconductor-biobase >=2.42.0,<2.43.0' - - 'bioconductor-golubesets >=1.24.0,<1.25.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' + - 'bioconductor-golubesets >=1.26.0,<1.27.0' - r-base - 'r-e1071 >=1.5-12' - 'r-pamr >=1.22' diff --git a/recipes/bioconductor-mcsea/meta.yaml b/recipes/bioconductor-mcsea/meta.yaml index 13c4b41cf4fcb..b32e3b73fda50 100644 --- a/recipes/bioconductor-mcsea/meta.yaml +++ b/recipes/bioconductor-mcsea/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.2.0" %} +{% set version = "1.4.0" %} {% set name = "mCSEA" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,39 +10,41 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 1511621e7aa960674da610667a7ea6e8 + md5: 7a9cabd1953c0e519ee9efe5fa6476d0 build: number: 0 rpaths: - lib/R/lib/ - lib/ noarch: generic -# Suggests: Biobase, BiocGenerics, BiocStyle, knitr, leukemiasEset, rmarkdown, RUnit +# Suggests: Biobase, BiocGenerics, BiocStyle, FlowSorted.Blood.450k, knitr, leukemiasEset, minfi, minfiData, rmarkdown, RUnit requirements: host: - - 'bioconductor-fgsea >=1.8.0,<1.9.0' - - 'bioconductor-genomicfeatures >=1.34.0,<1.35.0' - - 'bioconductor-genomicranges >=1.34.0,<1.35.0' - - 'bioconductor-gviz >=1.26.0,<1.27.0' - - 'bioconductor-homo.sapiens >=1.3.0,<1.4.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-limma >=3.38.0,<3.39.0' - - 'bioconductor-mcseadata >=1.2.0,<1.3.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' - - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' + - 'bioconductor-biomart >=2.40.0,<2.41.0' + - 'bioconductor-fgsea >=1.10.0,<1.11.0' + - 'bioconductor-genomicfeatures >=1.36.0,<1.37.0' + - 'bioconductor-genomicranges >=1.36.0,<1.37.0' + - 'bioconductor-gviz >=1.28.0,<1.29.0' + - 'bioconductor-homo.sapiens >=1.4.0,<1.5.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-limma >=3.40.0,<3.41.0' + - 'bioconductor-mcseadata >=1.4.0,<1.5.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' + - 'bioconductor-summarizedexperiment >=1.14.0,<1.15.0' - r-base - r-ggplot2 run: - - 'bioconductor-fgsea >=1.8.0,<1.9.0' - - 'bioconductor-genomicfeatures >=1.34.0,<1.35.0' - - 'bioconductor-genomicranges >=1.34.0,<1.35.0' - - 'bioconductor-gviz >=1.26.0,<1.27.0' - - 'bioconductor-homo.sapiens >=1.3.0,<1.4.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-limma >=3.38.0,<3.39.0' - - 'bioconductor-mcseadata >=1.2.0,<1.3.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' - - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' + - 'bioconductor-biomart >=2.40.0,<2.41.0' + - 'bioconductor-fgsea >=1.10.0,<1.11.0' + - 'bioconductor-genomicfeatures >=1.36.0,<1.37.0' + - 'bioconductor-genomicranges >=1.36.0,<1.37.0' + - 'bioconductor-gviz >=1.28.0,<1.29.0' + - 'bioconductor-homo.sapiens >=1.4.0,<1.5.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-limma >=3.40.0,<3.41.0' + - 'bioconductor-mcseadata >=1.4.0,<1.5.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' + - 'bioconductor-summarizedexperiment >=1.14.0,<1.15.0' - r-base - r-ggplot2 test: diff --git a/recipes/bioconductor-mcseadata/meta.yaml b/recipes/bioconductor-mcseadata/meta.yaml index 48b233cec7373..c29cb7840b787 100644 --- a/recipes/bioconductor-mcseadata/meta.yaml +++ b/recipes/bioconductor-mcseadata/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.2.0" %} +{% set version = "1.4.0" %} {% set name = "mCSEAdata" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 45eb34bc0dcb1414abbd892e3d4f70ec + md5: 2ababb1156ca58b2075b8a78841f2d7b build: number: 0 rpaths: @@ -23,7 +23,7 @@ requirements: - r-base run: - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-mcseadata/post-link.sh b/recipes/bioconductor-mcseadata/post-link.sh index c022f8111626e..249905aa32088 100644 --- a/recipes/bioconductor-mcseadata/post-link.sh +++ b/recipes/bioconductor-mcseadata/post-link.sh @@ -1,11 +1,11 @@ #!/bin/bash -FN="mCSEAdata_1.2.0.tar.gz" +FN="mCSEAdata_1.4.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/experiment/src/contrib/mCSEAdata_1.2.0.tar.gz" - "https://bioarchive.galaxyproject.org/mCSEAdata_1.2.0.tar.gz" - "https://depot.galaxyproject.org/software/bioconductor-mcseadata/bioconductor-mcseadata_1.2.0_src_all.tar.gz" + "https://bioconductor.org/packages/3.9/data/experiment/src/contrib/mCSEAdata_1.4.0.tar.gz" + "https://bioarchive.galaxyproject.org/mCSEAdata_1.4.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-mcseadata/bioconductor-mcseadata_1.4.0_src_all.tar.gz" ) -MD5="45eb34bc0dcb1414abbd892e3d4f70ec" +MD5="2ababb1156ca58b2075b8a78841f2d7b" # Use a staging area in the conda dir rather than temp dirs, both to avoid # permission issues as well as to have things downloaded in a predictable @@ -16,7 +16,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-mcsurvdata/meta.yaml b/recipes/bioconductor-mcsurvdata/meta.yaml index 567c03b60d1ed..4550819e33736 100644 --- a/recipes/bioconductor-mcsurvdata/meta.yaml +++ b/recipes/bioconductor-mcsurvdata/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.0.0" %} +{% set version = "1.2.0" %} {% set name = "mcsurvdata" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,9 +10,9 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: b58022a7e2590ccf7b3a38d4587d7f50 + md5: 3e2204677f27ed5f9a47551a24963bdd build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ @@ -20,16 +20,16 @@ build: # Suggests: knitr requirements: host: - - 'bioconductor-annotationhub >=2.14.0,<2.15.0' - - 'bioconductor-biobase >=2.42.0,<2.43.0' - - 'bioconductor-experimenthub >=1.8.0,<1.9.0' + - 'bioconductor-annotationhub >=2.16.0,<2.17.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' + - 'bioconductor-experimenthub >=1.10.0,<1.11.0' - r-base run: - - 'bioconductor-annotationhub >=2.14.0,<2.15.0' - - 'bioconductor-biobase >=2.42.0,<2.43.0' - - 'bioconductor-experimenthub >=1.8.0,<1.9.0' + - 'bioconductor-annotationhub >=2.16.0,<2.17.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' + - 'bioconductor-experimenthub >=1.10.0,<1.11.0' - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-mcsurvdata/post-link.sh b/recipes/bioconductor-mcsurvdata/post-link.sh index 55b2ecc2d32c2..5b7189d731431 100644 --- a/recipes/bioconductor-mcsurvdata/post-link.sh +++ b/recipes/bioconductor-mcsurvdata/post-link.sh @@ -1,11 +1,11 @@ #!/bin/bash -FN="mcsurvdata_1.0.0.tar.gz" +FN="mcsurvdata_1.2.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/experiment/src/contrib/mcsurvdata_1.0.0.tar.gz" - "https://bioarchive.galaxyproject.org/mcsurvdata_1.0.0.tar.gz" - "https://depot.galaxyproject.org/software/bioconductor-mcsurvdata/bioconductor-mcsurvdata_1.0.0_src_all.tar.gz" + "https://bioconductor.org/packages/3.9/data/experiment/src/contrib/mcsurvdata_1.2.0.tar.gz" + "https://bioarchive.galaxyproject.org/mcsurvdata_1.2.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-mcsurvdata/bioconductor-mcsurvdata_1.2.0_src_all.tar.gz" ) -MD5="b58022a7e2590ccf7b3a38d4587d7f50" +MD5="3e2204677f27ed5f9a47551a24963bdd" # Use a staging area in the conda dir rather than temp dirs, both to avoid # permission issues as well as to have things downloaded in a predictable @@ -16,7 +16,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-mdgsa/meta.yaml b/recipes/bioconductor-mdgsa/meta.yaml index 41586f5c203cf..c58bff72c6fea 100644 --- a/recipes/bioconductor-mdgsa/meta.yaml +++ b/recipes/bioconductor-mdgsa/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.14.0" %} +{% set version = "1.16.0" %} {% set name = "mdgsa" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 28668e2ddf14e96380fbe1961c10e357 + md5: d2c1c33f82b90c3c12dfa048b879d6aa build: number: 0 rpaths: @@ -20,16 +20,16 @@ build: # Suggests: BiocStyle, knitr, rmarkdown, limma, ALL, hgu95av2.db, RUnit, BiocGenerics requirements: host: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' - - 'bioconductor-go.db >=3.7.0,<3.8.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' + - 'bioconductor-go.db >=3.8.0,<3.9.0' - 'bioconductor-kegg.db >=3.2.0,<3.3.0' - r-base - r-cluster - r-dbi - r-matrix run: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' - - 'bioconductor-go.db >=3.7.0,<3.8.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' + - 'bioconductor-go.db >=3.8.0,<3.9.0' - 'bioconductor-kegg.db >=3.2.0,<3.3.0' - r-base - r-cluster diff --git a/recipes/bioconductor-mdp/meta.yaml b/recipes/bioconductor-mdp/meta.yaml index 24b4c42b92c4f..a993dd2eb1e72 100644 --- a/recipes/bioconductor-mdp/meta.yaml +++ b/recipes/bioconductor-mdp/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.2.0" %} +{% set version = "1.4.0" %} {% set name = "mdp" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 51954cabceb7d8de92fe7b889a2da705 + md5: 251498b10ed231066befda17a853a5b9 build: number: 0 rpaths: @@ -22,9 +22,11 @@ requirements: host: - r-base - r-ggplot2 + - r-gridextra run: - r-base - r-ggplot2 + - r-gridextra test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-mdqc/meta.yaml b/recipes/bioconductor-mdqc/meta.yaml index 8bf7a07e195bb..76761713664c7 100644 --- a/recipes/bioconductor-mdqc/meta.yaml +++ b/recipes/bioconductor-mdqc/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.44.0" %} +{% set version = "1.46.0" %} {% set name = "mdqc" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: d82132337f2ad3520bf49b73cb29c6f8 + md5: 79dff4086686e27cc40bec33c13475b2 build: number: 0 rpaths: diff --git a/recipes/bioconductor-mdts/meta.yaml b/recipes/bioconductor-mdts/meta.yaml index 7869cb39a5303..e7e64925634ae 100644 --- a/recipes/bioconductor-mdts/meta.yaml +++ b/recipes/bioconductor-mdts/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.2.0" %} +{% set version = "1.4.0" %} {% set name = "MDTS" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 509a06e8a0f6897ed1edb83f5687b479 + md5: 0e8eb9fb588b9952a92ce0dd081b70fc build: number: 0 rpaths: @@ -20,21 +20,21 @@ build: # Suggests: testthat, knitr requirements: host: - - 'bioconductor-biostrings >=2.50.0,<2.51.0' - - 'bioconductor-dnacopy >=1.56.0,<1.57.0' - - 'bioconductor-genomicalignments >=1.18.0,<1.19.0' - - 'bioconductor-genomicranges >=1.34.0,<1.35.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-rsamtools >=1.34.0,<1.35.0' + - 'bioconductor-biostrings >=2.52.0,<2.53.0' + - 'bioconductor-dnacopy >=1.58.0,<1.59.0' + - 'bioconductor-genomicalignments >=1.20.0,<1.21.0' + - 'bioconductor-genomicranges >=1.36.0,<1.37.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-rsamtools >=2.0.0,<2.1.0' - r-base - r-stringr run: - - 'bioconductor-biostrings >=2.50.0,<2.51.0' - - 'bioconductor-dnacopy >=1.56.0,<1.57.0' - - 'bioconductor-genomicalignments >=1.18.0,<1.19.0' - - 'bioconductor-genomicranges >=1.34.0,<1.35.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-rsamtools >=1.34.0,<1.35.0' + - 'bioconductor-biostrings >=2.52.0,<2.53.0' + - 'bioconductor-dnacopy >=1.58.0,<1.59.0' + - 'bioconductor-genomicalignments >=1.20.0,<1.21.0' + - 'bioconductor-genomicranges >=1.36.0,<1.37.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-rsamtools >=2.0.0,<2.1.0' - r-base - r-stringr test: diff --git a/recipes/bioconductor-meal/meta.yaml b/recipes/bioconductor-meal/meta.yaml index 15c35deb1f867..1d642842e7b7d 100644 --- a/recipes/bioconductor-meal/meta.yaml +++ b/recipes/bioconductor-meal/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.12.0" %} +{% set version = "1.14.0" %} {% set name = "MEAL" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: fa53c8e7918242e6fadea0f6c9894496 + md5: f1d54fb22bf6fe39a3fbc7674e7d6372 build: number: 0 rpaths: @@ -20,18 +20,18 @@ build: # Suggests: testthat, IlluminaHumanMethylationEPICanno.ilm10b2.hg19, IlluminaHumanMethylation450kanno.ilmn12.hg19, knitr, minfiData, BiocStyle, rmarkdown, brgedata requirements: host: - - 'bioconductor-biobase >=2.42.0,<2.43.0' - - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' - - 'bioconductor-dmrcate >=1.18.0,<1.19.0' - - 'bioconductor-genomicranges >=1.34.0,<1.35.0' - - 'bioconductor-gviz >=1.26.0,<1.27.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-limma >=3.38.0,<3.39.0' - - 'bioconductor-minfi >=1.28.0,<1.29.0' - - 'bioconductor-missmethyl >=1.16.0,<1.17.0' - - 'bioconductor-multidataset >=1.10.0,<1.11.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' - - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' + - 'bioconductor-biocgenerics >=0.30.0,<0.31.0' + - 'bioconductor-dmrcate >=1.20.0,<1.21.0' + - 'bioconductor-genomicranges >=1.36.0,<1.37.0' + - 'bioconductor-gviz >=1.28.0,<1.29.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-limma >=3.40.0,<3.41.0' + - 'bioconductor-minfi >=1.30.0,<1.31.0' + - 'bioconductor-missmethyl >=1.18.0,<1.19.0' + - 'bioconductor-multidataset >=1.12.0,<1.13.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' + - 'bioconductor-summarizedexperiment >=1.14.0,<1.15.0' - r-base - 'r-ggplot2 >=2.0.0' - r-isva @@ -40,18 +40,18 @@ requirements: - r-smartsva - r-vegan run: - - 'bioconductor-biobase >=2.42.0,<2.43.0' - - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' - - 'bioconductor-dmrcate >=1.18.0,<1.19.0' - - 'bioconductor-genomicranges >=1.34.0,<1.35.0' - - 'bioconductor-gviz >=1.26.0,<1.27.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-limma >=3.38.0,<3.39.0' - - 'bioconductor-minfi >=1.28.0,<1.29.0' - - 'bioconductor-missmethyl >=1.16.0,<1.17.0' - - 'bioconductor-multidataset >=1.10.0,<1.11.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' - - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' + - 'bioconductor-biocgenerics >=0.30.0,<0.31.0' + - 'bioconductor-dmrcate >=1.20.0,<1.21.0' + - 'bioconductor-genomicranges >=1.36.0,<1.37.0' + - 'bioconductor-gviz >=1.28.0,<1.29.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-limma >=3.40.0,<3.41.0' + - 'bioconductor-minfi >=1.30.0,<1.31.0' + - 'bioconductor-missmethyl >=1.18.0,<1.19.0' + - 'bioconductor-multidataset >=1.12.0,<1.13.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' + - 'bioconductor-summarizedexperiment >=1.14.0,<1.15.0' - r-base - 'r-ggplot2 >=2.0.0' - r-isva diff --git a/recipes/bioconductor-measurementerror.cor/meta.yaml b/recipes/bioconductor-measurementerror.cor/meta.yaml index af177793b3873..c7097e62dd965 100644 --- a/recipes/bioconductor-measurementerror.cor/meta.yaml +++ b/recipes/bioconductor-measurementerror.cor/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.54.0" %} +{% set version = "1.56.0" %} {% set name = "MeasurementError.cor" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: fca8d3daecf480356153659e0a0c1e74 + md5: 5a2fbc85ddce4e114407282ba1289d7a build: number: 0 rpaths: diff --git a/recipes/bioconductor-medicagocdf/meta.yaml b/recipes/bioconductor-medicagocdf/meta.yaml index 2bcf7256dc864..7088c01c62962 100644 --- a/recipes/bioconductor-medicagocdf/meta.yaml +++ b/recipes/bioconductor-medicagocdf/meta.yaml @@ -1,6 +1,6 @@ {% set version = "2.18.0" %} {% set name = "medicagocdf" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -12,19 +12,19 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 1fbb2e4c070344d18e65f1b3993867db build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' - r-base run: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-medicagocdf/post-link.sh b/recipes/bioconductor-medicagocdf/post-link.sh index 498fab6c724cf..b8e55bb096b30 100644 --- a/recipes/bioconductor-medicagocdf/post-link.sh +++ b/recipes/bioconductor-medicagocdf/post-link.sh @@ -1,9 +1,10 @@ #!/bin/bash FN="medicagocdf_2.18.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/medicagocdf_2.18.0.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/medicagocdf_2.18.0.tar.gz" "https://bioarchive.galaxyproject.org/medicagocdf_2.18.0.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-medicagocdf/bioconductor-medicagocdf_2.18.0_src_all.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-medicagocdf/bioconductor-medicagocdf_2.18.0_src_all.tar.gz" ) MD5="1fbb2e4c070344d18e65f1b3993867db" @@ -16,7 +17,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-medicagoprobe/meta.yaml b/recipes/bioconductor-medicagoprobe/meta.yaml index b9a14995a4a65..420ef4e77402e 100644 --- a/recipes/bioconductor-medicagoprobe/meta.yaml +++ b/recipes/bioconductor-medicagoprobe/meta.yaml @@ -1,6 +1,6 @@ {% set version = "2.18.0" %} {% set name = "medicagoprobe" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -12,19 +12,19 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 83b9887ad2ed26c704b0ca7115e5838d build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' - r-base run: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-medicagoprobe/post-link.sh b/recipes/bioconductor-medicagoprobe/post-link.sh index 2baf145f7f87b..9241d0094c5c8 100644 --- a/recipes/bioconductor-medicagoprobe/post-link.sh +++ b/recipes/bioconductor-medicagoprobe/post-link.sh @@ -1,9 +1,10 @@ #!/bin/bash FN="medicagoprobe_2.18.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/medicagoprobe_2.18.0.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/medicagoprobe_2.18.0.tar.gz" "https://bioarchive.galaxyproject.org/medicagoprobe_2.18.0.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-medicagoprobe/bioconductor-medicagoprobe_2.18.0_src_all.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-medicagoprobe/bioconductor-medicagoprobe_2.18.0_src_all.tar.gz" ) MD5="83b9887ad2ed26c704b0ca7115e5838d" @@ -16,7 +17,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-medips/meta.yaml b/recipes/bioconductor-medips/meta.yaml index 2d8385a1f2737..cded5c3397988 100644 --- a/recipes/bioconductor-medips/meta.yaml +++ b/recipes/bioconductor-medips/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.34.0" %} +{% set version = "1.36.0" %} {% set name = "MEDIPS" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 20d8d11b858c8912edff6d11917faa5c + md5: 91aa3cc0532aa4d5778c256eea57e8de build: number: 0 rpaths: @@ -20,29 +20,29 @@ build: # Suggests: BSgenome.Hsapiens.UCSC.hg19, MEDIPSData, BiocStyle requirements: host: - - 'bioconductor-biomart >=2.38.0,<2.39.0' - - 'bioconductor-biostrings >=2.50.0,<2.51.0' - - 'bioconductor-bsgenome >=1.50.0,<1.51.0' - - 'bioconductor-dnacopy >=1.56.0,<1.57.0' - - 'bioconductor-edger >=3.24.0,<3.25.0' - - 'bioconductor-genomicranges >=1.34.0,<1.35.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-preprocesscore >=1.44.0,<1.45.0' - - 'bioconductor-rsamtools >=1.34.0,<1.35.0' - - 'bioconductor-rtracklayer >=1.42.0,<1.43.0' + - 'bioconductor-biomart >=2.40.0,<2.41.0' + - 'bioconductor-biostrings >=2.52.0,<2.53.0' + - 'bioconductor-bsgenome >=1.52.0,<1.53.0' + - 'bioconductor-dnacopy >=1.58.0,<1.59.0' + - 'bioconductor-edger >=3.26.0,<3.27.0' + - 'bioconductor-genomicranges >=1.36.0,<1.37.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-preprocesscore >=1.46.0,<1.47.0' + - 'bioconductor-rsamtools >=2.0.0,<2.1.0' + - 'bioconductor-rtracklayer >=1.44.0,<1.45.0' - r-base - r-gtools run: - - 'bioconductor-biomart >=2.38.0,<2.39.0' - - 'bioconductor-biostrings >=2.50.0,<2.51.0' - - 'bioconductor-bsgenome >=1.50.0,<1.51.0' - - 'bioconductor-dnacopy >=1.56.0,<1.57.0' - - 'bioconductor-edger >=3.24.0,<3.25.0' - - 'bioconductor-genomicranges >=1.34.0,<1.35.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-preprocesscore >=1.44.0,<1.45.0' - - 'bioconductor-rsamtools >=1.34.0,<1.35.0' - - 'bioconductor-rtracklayer >=1.42.0,<1.43.0' + - 'bioconductor-biomart >=2.40.0,<2.41.0' + - 'bioconductor-biostrings >=2.52.0,<2.53.0' + - 'bioconductor-bsgenome >=1.52.0,<1.53.0' + - 'bioconductor-dnacopy >=1.58.0,<1.59.0' + - 'bioconductor-edger >=3.26.0,<3.27.0' + - 'bioconductor-genomicranges >=1.36.0,<1.37.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-preprocesscore >=1.46.0,<1.47.0' + - 'bioconductor-rsamtools >=2.0.0,<2.1.0' + - 'bioconductor-rtracklayer >=1.44.0,<1.45.0' - r-base - r-gtools test: diff --git a/recipes/bioconductor-medipsdata/meta.yaml b/recipes/bioconductor-medipsdata/meta.yaml index 0d91901836195..84105a00ab43f 100644 --- a/recipes/bioconductor-medipsdata/meta.yaml +++ b/recipes/bioconductor-medipsdata/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.18.0" %} +{% set version = "1.20.0" %} {% set name = "MEDIPSData" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 80c0076eae9f53aeda545a4e2716ab69 + md5: 1f78f8ed24c8c17f2ceb8847a7b05ec1 build: number: 0 rpaths: @@ -22,7 +22,7 @@ requirements: - r-base run: - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-medipsdata/post-link.sh b/recipes/bioconductor-medipsdata/post-link.sh index 8096af1f47262..8be0d2f0d15ce 100644 --- a/recipes/bioconductor-medipsdata/post-link.sh +++ b/recipes/bioconductor-medipsdata/post-link.sh @@ -1,11 +1,11 @@ #!/bin/bash -FN="MEDIPSData_1.18.0.tar.gz" +FN="MEDIPSData_1.20.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/experiment/src/contrib/MEDIPSData_1.18.0.tar.gz" - "https://bioarchive.galaxyproject.org/MEDIPSData_1.18.0.tar.gz" - "https://depot.galaxyproject.org/software/bioconductor-medipsdata/bioconductor-medipsdata_1.18.0_src_all.tar.gz" + "https://bioconductor.org/packages/3.9/data/experiment/src/contrib/MEDIPSData_1.20.0.tar.gz" + "https://bioarchive.galaxyproject.org/MEDIPSData_1.20.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-medipsdata/bioconductor-medipsdata_1.20.0_src_all.tar.gz" ) -MD5="80c0076eae9f53aeda545a4e2716ab69" +MD5="1f78f8ed24c8c17f2ceb8847a7b05ec1" # Use a staging area in the conda dir rather than temp dirs, both to avoid # permission issues as well as to have things downloaded in a predictable @@ -16,7 +16,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-medme/meta.yaml b/recipes/bioconductor-medme/meta.yaml index a13d5a1e9e558..984b07f1ff4ee 100644 --- a/recipes/bioconductor-medme/meta.yaml +++ b/recipes/bioconductor-medme/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.42.0" %} +{% set version = "1.44.0" %} {% set name = "MEDME" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: a77cb873abc5ef82394b847801debb3a + md5: 62985b7b4ebe51262d25380963c26d4a build: number: 0 rpaths: @@ -19,12 +19,12 @@ build: # Suggests: BSgenome.Hsapiens.UCSC.hg18, BSgenome.Mmusculus.UCSC.mm9 requirements: host: - - 'bioconductor-biostrings >=2.50.0,<2.51.0' + - 'bioconductor-biostrings >=2.52.0,<2.53.0' - r-base - r-drc - r-mass run: - - 'bioconductor-biostrings >=2.50.0,<2.51.0' + - 'bioconductor-biostrings >=2.52.0,<2.53.0' - r-base - r-drc - r-mass diff --git a/recipes/bioconductor-meebodata/meta.yaml b/recipes/bioconductor-meebodata/meta.yaml index b9125d8bed339..f6078a3cc6ef9 100644 --- a/recipes/bioconductor-meebodata/meta.yaml +++ b/recipes/bioconductor-meebodata/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.20.0" %} +{% set version = "1.22.0" %} {% set name = "MEEBOdata" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 6f406364f10353a1a634a4d726c66a22 + md5: 95cc758068d87d1b741390a5e0b5a30c build: number: 0 rpaths: @@ -22,7 +22,7 @@ requirements: - r-base run: - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-meebodata/post-link.sh b/recipes/bioconductor-meebodata/post-link.sh index 57c69c607fe50..acc9a15d40215 100644 --- a/recipes/bioconductor-meebodata/post-link.sh +++ b/recipes/bioconductor-meebodata/post-link.sh @@ -1,11 +1,11 @@ #!/bin/bash -FN="MEEBOdata_1.20.0.tar.gz" +FN="MEEBOdata_1.22.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/experiment/src/contrib/MEEBOdata_1.20.0.tar.gz" - "https://bioarchive.galaxyproject.org/MEEBOdata_1.20.0.tar.gz" - "https://depot.galaxyproject.org/software/bioconductor-meebodata/bioconductor-meebodata_1.20.0_src_all.tar.gz" + "https://bioconductor.org/packages/3.9/data/experiment/src/contrib/MEEBOdata_1.22.0.tar.gz" + "https://bioarchive.galaxyproject.org/MEEBOdata_1.22.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-meebodata/bioconductor-meebodata_1.22.0_src_all.tar.gz" ) -MD5="6f406364f10353a1a634a4d726c66a22" +MD5="95cc758068d87d1b741390a5e0b5a30c" # Use a staging area in the conda dir rather than temp dirs, both to avoid # permission issues as well as to have things downloaded in a predictable @@ -16,7 +16,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-meigor/meta.yaml b/recipes/bioconductor-meigor/meta.yaml index 85d48333fe30b..a685c248888d6 100644 --- a/recipes/bioconductor-meigor/meta.yaml +++ b/recipes/bioconductor-meigor/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.16.0" %} +{% set version = "1.18.0" %} {% set name = "MEIGOR" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 3ebe8603dbf28a32751dc0e048d0b2c1 + md5: 7f8232f8bc699168903b7f124bd890eb build: number: 0 rpaths: @@ -20,13 +20,13 @@ build: # Suggests: CellNOptR requirements: host: - - 'bioconductor-cnorode >=1.24.0,<1.25.0' + - 'bioconductor-cnorode >=1.26.0,<1.27.0' - r-base - r-desolve - r-rsolnp - r-snowfall run: - - 'bioconductor-cnorode >=1.24.0,<1.25.0' + - 'bioconductor-cnorode >=1.26.0,<1.27.0' - r-base - r-desolve - r-rsolnp diff --git a/recipes/bioconductor-melissa/build.sh b/recipes/bioconductor-melissa/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-melissa/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-melissa/meta.yaml b/recipes/bioconductor-melissa/meta.yaml new file mode 100644 index 0000000000000..194357fc70109 --- /dev/null +++ b/recipes/bioconductor-melissa/meta.yaml @@ -0,0 +1,65 @@ +{% set version = "1.0.0" %} +{% set name = "Melissa" %} +{% set bioc = "3.9" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: 1c43fd1e2d6fd481079f43eac08c5483 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: testthat, knitr, rmarkdown +requirements: + host: + - 'bioconductor-biocstyle >=2.12.0,<2.13.0' + - 'bioconductor-bprmeth >=1.10.0,<1.11.0' + - 'bioconductor-genomicranges >=1.36.0,<1.37.0' + - r-assertthat + - r-base + - r-clues + - r-cowplot + - r-data.table + - r-doparallel + - r-foreach + - r-ggplot2 + - r-magrittr + - r-matrixcalc + - r-mcmcpack + - r-mvtnorm + - r-rocr + - r-truncnorm + run: + - 'bioconductor-biocstyle >=2.12.0,<2.13.0' + - 'bioconductor-bprmeth >=1.10.0,<1.11.0' + - 'bioconductor-genomicranges >=1.36.0,<1.37.0' + - r-assertthat + - r-base + - r-clues + - r-cowplot + - r-data.table + - r-doparallel + - r-foreach + - r-ggplot2 + - r-magrittr + - r-matrixcalc + - r-mcmcpack + - r-mvtnorm + - r-rocr + - r-truncnorm +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: 'GPL-3 | file LICENSE' + summary: 'Melissa is a Baysian probabilistic model for jointly clustering and imputing single cell methylomes. This is done by taking into account local correlations via a Generalised Linear Model approach and global similarities using a mixture modelling approach.' + diff --git a/recipes/bioconductor-mergemaid/meta.yaml b/recipes/bioconductor-mergemaid/meta.yaml index 66c1dbc7dde4f..80cc5b3eddd00 100644 --- a/recipes/bioconductor-mergemaid/meta.yaml +++ b/recipes/bioconductor-mergemaid/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "2.54.0" %} +{% set version = "2.56.0" %} {% set name = "MergeMaid" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 11c316392b5fb033937ab626cc4a1054 + md5: 85560308a14870e7e571a1a517830836 build: number: 0 rpaths: @@ -19,12 +19,12 @@ build: noarch: generic requirements: host: - - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' - r-base - r-mass - r-survival run: - - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' - r-base - r-mass - r-survival diff --git a/recipes/bioconductor-mergeomics/meta.yaml b/recipes/bioconductor-mergeomics/meta.yaml index 707061a2b257f..c6dfeff4cb542 100644 --- a/recipes/bioconductor-mergeomics/meta.yaml +++ b/recipes/bioconductor-mergeomics/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.10.0" %} +{% set version = "1.12.0" %} {% set name = "Mergeomics" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 042173c4efb0b75209df2bf35cbf70d6 + md5: b199d231ce140214caac7667f3142dad build: number: 0 rpaths: diff --git a/recipes/bioconductor-mesh.aca.eg.db/meta.yaml b/recipes/bioconductor-mesh.aca.eg.db/meta.yaml index f2d989a44e661..f9398abce0271 100644 --- a/recipes/bioconductor-mesh.aca.eg.db/meta.yaml +++ b/recipes/bioconductor-mesh.aca.eg.db/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.11.0" %} +{% set version = "1.12.0" %} {% set name = "MeSH.Aca.eg.db" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 9ccbcbec0fe189c42c94ee382a4f91e9 + md5: 5e2a81ebf27098b81e4ed973301b2caa build: number: 0 rpaths: @@ -20,12 +20,12 @@ build: # Suggests: RUnit, BiocGenerics requirements: host: - - 'bioconductor-meshdbi >=1.18.0,<1.19.0' + - 'bioconductor-meshdbi >=1.20.0,<1.21.0' - r-base run: - - 'bioconductor-meshdbi >=1.18.0,<1.19.0' + - 'bioconductor-meshdbi >=1.20.0,<1.21.0' - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-mesh.aca.eg.db/post-link.sh b/recipes/bioconductor-mesh.aca.eg.db/post-link.sh index 253d81a4ff07f..36d667fdfe753 100644 --- a/recipes/bioconductor-mesh.aca.eg.db/post-link.sh +++ b/recipes/bioconductor-mesh.aca.eg.db/post-link.sh @@ -1,11 +1,11 @@ #!/bin/bash -FN="MeSH.Aca.eg.db_1.11.0.tar.gz" +FN="MeSH.Aca.eg.db_1.12.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/MeSH.Aca.eg.db_1.11.0.tar.gz" - "https://bioarchive.galaxyproject.org/MeSH.Aca.eg.db_1.11.0.tar.gz" - "https://depot.galaxyproject.org/software/bioconductor-mesh.aca.eg.db/bioconductor-mesh.aca.eg.db_1.11.0_src_all.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/MeSH.Aca.eg.db_1.12.0.tar.gz" + "https://bioarchive.galaxyproject.org/MeSH.Aca.eg.db_1.12.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-mesh.aca.eg.db/bioconductor-mesh.aca.eg.db_1.12.0_src_all.tar.gz" ) -MD5="9ccbcbec0fe189c42c94ee382a4f91e9" +MD5="5e2a81ebf27098b81e4ed973301b2caa" # Use a staging area in the conda dir rather than temp dirs, both to avoid # permission issues as well as to have things downloaded in a predictable @@ -16,7 +16,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-mesh.aga.pest.eg.db/meta.yaml b/recipes/bioconductor-mesh.aga.pest.eg.db/meta.yaml index bed17797dc65a..a4d73c3ab227c 100644 --- a/recipes/bioconductor-mesh.aga.pest.eg.db/meta.yaml +++ b/recipes/bioconductor-mesh.aga.pest.eg.db/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.11.0" %} +{% set version = "1.12.0" %} {% set name = "MeSH.Aga.PEST.eg.db" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: a4743af6866821a43a0dca3b32ddb5a5 + md5: 55d9c4c29db06de62d39143b2de46dbd build: number: 0 rpaths: @@ -20,12 +20,12 @@ build: # Suggests: RUnit, BiocGenerics requirements: host: - - 'bioconductor-meshdbi >=1.18.0,<1.19.0' + - 'bioconductor-meshdbi >=1.20.0,<1.21.0' - r-base run: - - 'bioconductor-meshdbi >=1.18.0,<1.19.0' + - 'bioconductor-meshdbi >=1.20.0,<1.21.0' - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-mesh.aga.pest.eg.db/post-link.sh b/recipes/bioconductor-mesh.aga.pest.eg.db/post-link.sh index 5141ce98b1df4..388b62f5b1f63 100644 --- a/recipes/bioconductor-mesh.aga.pest.eg.db/post-link.sh +++ b/recipes/bioconductor-mesh.aga.pest.eg.db/post-link.sh @@ -1,11 +1,11 @@ #!/bin/bash -FN="MeSH.Aga.PEST.eg.db_1.11.0.tar.gz" +FN="MeSH.Aga.PEST.eg.db_1.12.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/MeSH.Aga.PEST.eg.db_1.11.0.tar.gz" - "https://bioarchive.galaxyproject.org/MeSH.Aga.PEST.eg.db_1.11.0.tar.gz" - "https://depot.galaxyproject.org/software/bioconductor-mesh.aga.pest.eg.db/bioconductor-mesh.aga.pest.eg.db_1.11.0_src_all.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/MeSH.Aga.PEST.eg.db_1.12.0.tar.gz" + "https://bioarchive.galaxyproject.org/MeSH.Aga.PEST.eg.db_1.12.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-mesh.aga.pest.eg.db/bioconductor-mesh.aga.pest.eg.db_1.12.0_src_all.tar.gz" ) -MD5="a4743af6866821a43a0dca3b32ddb5a5" +MD5="55d9c4c29db06de62d39143b2de46dbd" # Use a staging area in the conda dir rather than temp dirs, both to avoid # permission issues as well as to have things downloaded in a predictable @@ -16,7 +16,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-mesh.ame.eg.db/meta.yaml b/recipes/bioconductor-mesh.ame.eg.db/meta.yaml index fc0ab677503f9..93c5b47667649 100644 --- a/recipes/bioconductor-mesh.ame.eg.db/meta.yaml +++ b/recipes/bioconductor-mesh.ame.eg.db/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.11.0" %} +{% set version = "1.12.0" %} {% set name = "MeSH.Ame.eg.db" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: caac4a2dbb385e12508b9b783301a108 + md5: 77f92103ca5a4cc50d4faea41acf6e5d build: number: 0 rpaths: @@ -20,12 +20,12 @@ build: # Suggests: RUnit, BiocGenerics requirements: host: - - 'bioconductor-meshdbi >=1.18.0,<1.19.0' + - 'bioconductor-meshdbi >=1.20.0,<1.21.0' - r-base run: - - 'bioconductor-meshdbi >=1.18.0,<1.19.0' + - 'bioconductor-meshdbi >=1.20.0,<1.21.0' - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-mesh.ame.eg.db/post-link.sh b/recipes/bioconductor-mesh.ame.eg.db/post-link.sh index e38db8ad8d0ca..b602f87beab33 100644 --- a/recipes/bioconductor-mesh.ame.eg.db/post-link.sh +++ b/recipes/bioconductor-mesh.ame.eg.db/post-link.sh @@ -1,11 +1,11 @@ #!/bin/bash -FN="MeSH.Ame.eg.db_1.11.0.tar.gz" +FN="MeSH.Ame.eg.db_1.12.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/MeSH.Ame.eg.db_1.11.0.tar.gz" - "https://bioarchive.galaxyproject.org/MeSH.Ame.eg.db_1.11.0.tar.gz" - "https://depot.galaxyproject.org/software/bioconductor-mesh.ame.eg.db/bioconductor-mesh.ame.eg.db_1.11.0_src_all.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/MeSH.Ame.eg.db_1.12.0.tar.gz" + "https://bioarchive.galaxyproject.org/MeSH.Ame.eg.db_1.12.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-mesh.ame.eg.db/bioconductor-mesh.ame.eg.db_1.12.0_src_all.tar.gz" ) -MD5="caac4a2dbb385e12508b9b783301a108" +MD5="77f92103ca5a4cc50d4faea41acf6e5d" # Use a staging area in the conda dir rather than temp dirs, both to avoid # permission issues as well as to have things downloaded in a predictable @@ -16,7 +16,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-mesh.aml.eg.db/meta.yaml b/recipes/bioconductor-mesh.aml.eg.db/meta.yaml index 6ef712f202b21..f1821d9e73bbf 100644 --- a/recipes/bioconductor-mesh.aml.eg.db/meta.yaml +++ b/recipes/bioconductor-mesh.aml.eg.db/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.11.0" %} +{% set version = "1.12.0" %} {% set name = "MeSH.Aml.eg.db" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 0d4213a8c23de5feaea66f809b4cfe5f + md5: d6b7340f71e068a815aec178367a4963 build: number: 0 rpaths: @@ -20,12 +20,12 @@ build: # Suggests: RUnit, BiocGenerics requirements: host: - - 'bioconductor-meshdbi >=1.18.0,<1.19.0' + - 'bioconductor-meshdbi >=1.20.0,<1.21.0' - r-base run: - - 'bioconductor-meshdbi >=1.18.0,<1.19.0' + - 'bioconductor-meshdbi >=1.20.0,<1.21.0' - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-mesh.aml.eg.db/post-link.sh b/recipes/bioconductor-mesh.aml.eg.db/post-link.sh index 759b15c6e6d21..8241bdc380e70 100644 --- a/recipes/bioconductor-mesh.aml.eg.db/post-link.sh +++ b/recipes/bioconductor-mesh.aml.eg.db/post-link.sh @@ -1,11 +1,11 @@ #!/bin/bash -FN="MeSH.Aml.eg.db_1.11.0.tar.gz" +FN="MeSH.Aml.eg.db_1.12.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/MeSH.Aml.eg.db_1.11.0.tar.gz" - "https://bioarchive.galaxyproject.org/MeSH.Aml.eg.db_1.11.0.tar.gz" - "https://depot.galaxyproject.org/software/bioconductor-mesh.aml.eg.db/bioconductor-mesh.aml.eg.db_1.11.0_src_all.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/MeSH.Aml.eg.db_1.12.0.tar.gz" + "https://bioarchive.galaxyproject.org/MeSH.Aml.eg.db_1.12.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-mesh.aml.eg.db/bioconductor-mesh.aml.eg.db_1.12.0_src_all.tar.gz" ) -MD5="0d4213a8c23de5feaea66f809b4cfe5f" +MD5="d6b7340f71e068a815aec178367a4963" # Use a staging area in the conda dir rather than temp dirs, both to avoid # permission issues as well as to have things downloaded in a predictable @@ -16,7 +16,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-mesh.ana.eg.db/meta.yaml b/recipes/bioconductor-mesh.ana.eg.db/meta.yaml index 2d98afe433160..ded12263aef65 100644 --- a/recipes/bioconductor-mesh.ana.eg.db/meta.yaml +++ b/recipes/bioconductor-mesh.ana.eg.db/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.11.0" %} +{% set version = "1.12.0" %} {% set name = "MeSH.Ana.eg.db" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 3d146c598a66e6e40081517169bda1e0 + md5: 32877b98b506fea152de79ddd580442e build: number: 0 rpaths: @@ -20,12 +20,12 @@ build: # Suggests: RUnit, BiocGenerics requirements: host: - - 'bioconductor-meshdbi >=1.18.0,<1.19.0' + - 'bioconductor-meshdbi >=1.20.0,<1.21.0' - r-base run: - - 'bioconductor-meshdbi >=1.18.0,<1.19.0' + - 'bioconductor-meshdbi >=1.20.0,<1.21.0' - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-mesh.ana.eg.db/post-link.sh b/recipes/bioconductor-mesh.ana.eg.db/post-link.sh index 16ee1b23e937f..2e1456d8f5c48 100644 --- a/recipes/bioconductor-mesh.ana.eg.db/post-link.sh +++ b/recipes/bioconductor-mesh.ana.eg.db/post-link.sh @@ -1,11 +1,11 @@ #!/bin/bash -FN="MeSH.Ana.eg.db_1.11.0.tar.gz" +FN="MeSH.Ana.eg.db_1.12.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/MeSH.Ana.eg.db_1.11.0.tar.gz" - "https://bioarchive.galaxyproject.org/MeSH.Ana.eg.db_1.11.0.tar.gz" - "https://depot.galaxyproject.org/software/bioconductor-mesh.ana.eg.db/bioconductor-mesh.ana.eg.db_1.11.0_src_all.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/MeSH.Ana.eg.db_1.12.0.tar.gz" + "https://bioarchive.galaxyproject.org/MeSH.Ana.eg.db_1.12.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-mesh.ana.eg.db/bioconductor-mesh.ana.eg.db_1.12.0_src_all.tar.gz" ) -MD5="3d146c598a66e6e40081517169bda1e0" +MD5="32877b98b506fea152de79ddd580442e" # Use a staging area in the conda dir rather than temp dirs, both to avoid # permission issues as well as to have things downloaded in a predictable @@ -16,7 +16,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-mesh.ani.fgsc.eg.db/meta.yaml b/recipes/bioconductor-mesh.ani.fgsc.eg.db/meta.yaml index 5e55e3525b2cd..aa805b457cddc 100644 --- a/recipes/bioconductor-mesh.ani.fgsc.eg.db/meta.yaml +++ b/recipes/bioconductor-mesh.ani.fgsc.eg.db/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.11.0" %} +{% set version = "1.12.0" %} {% set name = "MeSH.Ani.FGSC.eg.db" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 719ef69619c7ff3e69eb14ac01777450 + md5: f1d9c0e500981f4b7df7dc67e9c59d89 build: number: 0 rpaths: @@ -20,12 +20,12 @@ build: # Suggests: RUnit, BiocGenerics requirements: host: - - 'bioconductor-meshdbi >=1.18.0,<1.19.0' + - 'bioconductor-meshdbi >=1.20.0,<1.21.0' - r-base run: - - 'bioconductor-meshdbi >=1.18.0,<1.19.0' + - 'bioconductor-meshdbi >=1.20.0,<1.21.0' - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-mesh.ani.fgsc.eg.db/post-link.sh b/recipes/bioconductor-mesh.ani.fgsc.eg.db/post-link.sh index 52a7f377f8bfa..0e11dd99ed9a9 100644 --- a/recipes/bioconductor-mesh.ani.fgsc.eg.db/post-link.sh +++ b/recipes/bioconductor-mesh.ani.fgsc.eg.db/post-link.sh @@ -1,11 +1,11 @@ #!/bin/bash -FN="MeSH.Ani.FGSC.eg.db_1.11.0.tar.gz" +FN="MeSH.Ani.FGSC.eg.db_1.12.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/MeSH.Ani.FGSC.eg.db_1.11.0.tar.gz" - "https://bioarchive.galaxyproject.org/MeSH.Ani.FGSC.eg.db_1.11.0.tar.gz" - "https://depot.galaxyproject.org/software/bioconductor-mesh.ani.fgsc.eg.db/bioconductor-mesh.ani.fgsc.eg.db_1.11.0_src_all.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/MeSH.Ani.FGSC.eg.db_1.12.0.tar.gz" + "https://bioarchive.galaxyproject.org/MeSH.Ani.FGSC.eg.db_1.12.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-mesh.ani.fgsc.eg.db/bioconductor-mesh.ani.fgsc.eg.db_1.12.0_src_all.tar.gz" ) -MD5="719ef69619c7ff3e69eb14ac01777450" +MD5="f1d9c0e500981f4b7df7dc67e9c59d89" # Use a staging area in the conda dir rather than temp dirs, both to avoid # permission issues as well as to have things downloaded in a predictable @@ -16,7 +16,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-mesh.aor.db/meta.yaml b/recipes/bioconductor-mesh.aor.db/meta.yaml index 1a1dc8318ddcd..0d66ad9d5223b 100644 --- a/recipes/bioconductor-mesh.aor.db/meta.yaml +++ b/recipes/bioconductor-mesh.aor.db/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.11.0" %} +{% set version = "1.12.0" %} {% set name = "MeSH.AOR.db" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 1f10237a8a9140ee1f6da72ca1308427 + md5: ed748fe3fab893d25073a2ce14a8820f build: number: 0 rpaths: @@ -20,12 +20,12 @@ build: # Suggests: RUnit, BiocGenerics requirements: host: - - 'bioconductor-meshdbi >=1.18.0,<1.19.0' + - 'bioconductor-meshdbi >=1.20.0,<1.21.0' - r-base run: - - 'bioconductor-meshdbi >=1.18.0,<1.19.0' + - 'bioconductor-meshdbi >=1.20.0,<1.21.0' - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-mesh.aor.db/post-link.sh b/recipes/bioconductor-mesh.aor.db/post-link.sh index 47c5e3143895b..fb597f41c2e86 100644 --- a/recipes/bioconductor-mesh.aor.db/post-link.sh +++ b/recipes/bioconductor-mesh.aor.db/post-link.sh @@ -1,11 +1,11 @@ #!/bin/bash -FN="MeSH.AOR.db_1.11.0.tar.gz" +FN="MeSH.AOR.db_1.12.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/MeSH.AOR.db_1.11.0.tar.gz" - "https://bioarchive.galaxyproject.org/MeSH.AOR.db_1.11.0.tar.gz" - "https://depot.galaxyproject.org/software/bioconductor-mesh.aor.db/bioconductor-mesh.aor.db_1.11.0_src_all.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/MeSH.AOR.db_1.12.0.tar.gz" + "https://bioarchive.galaxyproject.org/MeSH.AOR.db_1.12.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-mesh.aor.db/bioconductor-mesh.aor.db_1.12.0_src_all.tar.gz" ) -MD5="1f10237a8a9140ee1f6da72ca1308427" +MD5="ed748fe3fab893d25073a2ce14a8820f" # Use a staging area in the conda dir rather than temp dirs, both to avoid # permission issues as well as to have things downloaded in a predictable @@ -16,7 +16,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-mesh.ath.eg.db/meta.yaml b/recipes/bioconductor-mesh.ath.eg.db/meta.yaml index abd54b28a5c0b..be42be1fd8616 100644 --- a/recipes/bioconductor-mesh.ath.eg.db/meta.yaml +++ b/recipes/bioconductor-mesh.ath.eg.db/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.11.0" %} +{% set version = "1.12.0" %} {% set name = "MeSH.Ath.eg.db" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 73520c331ee0fd50fb21b62dc8b81e0f + md5: b051c34b72cccb24d822e1e4aa53ec52 build: number: 0 rpaths: @@ -20,12 +20,12 @@ build: # Suggests: RUnit, BiocGenerics requirements: host: - - 'bioconductor-meshdbi >=1.18.0,<1.19.0' + - 'bioconductor-meshdbi >=1.20.0,<1.21.0' - r-base run: - - 'bioconductor-meshdbi >=1.18.0,<1.19.0' + - 'bioconductor-meshdbi >=1.20.0,<1.21.0' - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-mesh.ath.eg.db/post-link.sh b/recipes/bioconductor-mesh.ath.eg.db/post-link.sh index d3afe0409b789..f13ae0d9ee410 100644 --- a/recipes/bioconductor-mesh.ath.eg.db/post-link.sh +++ b/recipes/bioconductor-mesh.ath.eg.db/post-link.sh @@ -1,11 +1,11 @@ #!/bin/bash -FN="MeSH.Ath.eg.db_1.11.0.tar.gz" +FN="MeSH.Ath.eg.db_1.12.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/MeSH.Ath.eg.db_1.11.0.tar.gz" - "https://bioarchive.galaxyproject.org/MeSH.Ath.eg.db_1.11.0.tar.gz" - "https://depot.galaxyproject.org/software/bioconductor-mesh.ath.eg.db/bioconductor-mesh.ath.eg.db_1.11.0_src_all.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/MeSH.Ath.eg.db_1.12.0.tar.gz" + "https://bioarchive.galaxyproject.org/MeSH.Ath.eg.db_1.12.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-mesh.ath.eg.db/bioconductor-mesh.ath.eg.db_1.12.0_src_all.tar.gz" ) -MD5="73520c331ee0fd50fb21b62dc8b81e0f" +MD5="b051c34b72cccb24d822e1e4aa53ec52" # Use a staging area in the conda dir rather than temp dirs, both to avoid # permission issues as well as to have things downloaded in a predictable @@ -16,7 +16,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-mesh.bfl.eg.db/meta.yaml b/recipes/bioconductor-mesh.bfl.eg.db/meta.yaml index 7d478380c9bc2..8ae8e11bcca21 100644 --- a/recipes/bioconductor-mesh.bfl.eg.db/meta.yaml +++ b/recipes/bioconductor-mesh.bfl.eg.db/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.11.0" %} +{% set version = "1.12.0" %} {% set name = "MeSH.Bfl.eg.db" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: e3d17146970aba917ffa2e75a4b61668 + md5: e587f2b53c1ce51bcf241ee4c7a978a9 build: number: 0 rpaths: @@ -20,12 +20,12 @@ build: # Suggests: RUnit, BiocGenerics requirements: host: - - 'bioconductor-meshdbi >=1.18.0,<1.19.0' + - 'bioconductor-meshdbi >=1.20.0,<1.21.0' - r-base run: - - 'bioconductor-meshdbi >=1.18.0,<1.19.0' + - 'bioconductor-meshdbi >=1.20.0,<1.21.0' - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-mesh.bfl.eg.db/post-link.sh b/recipes/bioconductor-mesh.bfl.eg.db/post-link.sh index a1944e9d34b50..2ddaa492aa84b 100644 --- a/recipes/bioconductor-mesh.bfl.eg.db/post-link.sh +++ b/recipes/bioconductor-mesh.bfl.eg.db/post-link.sh @@ -1,11 +1,11 @@ #!/bin/bash -FN="MeSH.Bfl.eg.db_1.11.0.tar.gz" +FN="MeSH.Bfl.eg.db_1.12.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/MeSH.Bfl.eg.db_1.11.0.tar.gz" - "https://bioarchive.galaxyproject.org/MeSH.Bfl.eg.db_1.11.0.tar.gz" - "https://depot.galaxyproject.org/software/bioconductor-mesh.bfl.eg.db/bioconductor-mesh.bfl.eg.db_1.11.0_src_all.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/MeSH.Bfl.eg.db_1.12.0.tar.gz" + "https://bioarchive.galaxyproject.org/MeSH.Bfl.eg.db_1.12.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-mesh.bfl.eg.db/bioconductor-mesh.bfl.eg.db_1.12.0_src_all.tar.gz" ) -MD5="e3d17146970aba917ffa2e75a4b61668" +MD5="e587f2b53c1ce51bcf241ee4c7a978a9" # Use a staging area in the conda dir rather than temp dirs, both to avoid # permission issues as well as to have things downloaded in a predictable @@ -16,7 +16,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-mesh.bsu.168.eg.db/meta.yaml b/recipes/bioconductor-mesh.bsu.168.eg.db/meta.yaml index c4a9431679d4b..1335a3cdfb5b5 100644 --- a/recipes/bioconductor-mesh.bsu.168.eg.db/meta.yaml +++ b/recipes/bioconductor-mesh.bsu.168.eg.db/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.11.0" %} +{% set version = "1.12.0" %} {% set name = "MeSH.Bsu.168.eg.db" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: a65d23890cee17d4c2eff1e4a8d39714 + md5: 89464279a892e7faab76f91a086b3fa4 build: number: 0 rpaths: @@ -20,12 +20,12 @@ build: # Suggests: RUnit, BiocGenerics requirements: host: - - 'bioconductor-meshdbi >=1.18.0,<1.19.0' + - 'bioconductor-meshdbi >=1.20.0,<1.21.0' - r-base run: - - 'bioconductor-meshdbi >=1.18.0,<1.19.0' + - 'bioconductor-meshdbi >=1.20.0,<1.21.0' - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-mesh.bsu.168.eg.db/post-link.sh b/recipes/bioconductor-mesh.bsu.168.eg.db/post-link.sh index 0b036154e6c3d..a1e5bde8232f3 100644 --- a/recipes/bioconductor-mesh.bsu.168.eg.db/post-link.sh +++ b/recipes/bioconductor-mesh.bsu.168.eg.db/post-link.sh @@ -1,11 +1,11 @@ #!/bin/bash -FN="MeSH.Bsu.168.eg.db_1.11.0.tar.gz" +FN="MeSH.Bsu.168.eg.db_1.12.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/MeSH.Bsu.168.eg.db_1.11.0.tar.gz" - "https://bioarchive.galaxyproject.org/MeSH.Bsu.168.eg.db_1.11.0.tar.gz" - "https://depot.galaxyproject.org/software/bioconductor-mesh.bsu.168.eg.db/bioconductor-mesh.bsu.168.eg.db_1.11.0_src_all.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/MeSH.Bsu.168.eg.db_1.12.0.tar.gz" + "https://bioarchive.galaxyproject.org/MeSH.Bsu.168.eg.db_1.12.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-mesh.bsu.168.eg.db/bioconductor-mesh.bsu.168.eg.db_1.12.0_src_all.tar.gz" ) -MD5="a65d23890cee17d4c2eff1e4a8d39714" +MD5="89464279a892e7faab76f91a086b3fa4" # Use a staging area in the conda dir rather than temp dirs, both to avoid # permission issues as well as to have things downloaded in a predictable @@ -16,7 +16,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-mesh.bta.eg.db/meta.yaml b/recipes/bioconductor-mesh.bta.eg.db/meta.yaml index a115407306393..879547f234c15 100644 --- a/recipes/bioconductor-mesh.bta.eg.db/meta.yaml +++ b/recipes/bioconductor-mesh.bta.eg.db/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.11.0" %} +{% set version = "1.12.0" %} {% set name = "MeSH.Bta.eg.db" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 8ed09310cb68d0b8ea7e075c669c69cf + md5: 1b6213dfe7731258b867fbe8ede5e592 build: number: 0 rpaths: @@ -20,12 +20,12 @@ build: # Suggests: RUnit, BiocGenerics requirements: host: - - 'bioconductor-meshdbi >=1.18.0,<1.19.0' + - 'bioconductor-meshdbi >=1.20.0,<1.21.0' - r-base run: - - 'bioconductor-meshdbi >=1.18.0,<1.19.0' + - 'bioconductor-meshdbi >=1.20.0,<1.21.0' - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-mesh.bta.eg.db/post-link.sh b/recipes/bioconductor-mesh.bta.eg.db/post-link.sh index 054ffdd5b37bf..3e98e69ae09df 100644 --- a/recipes/bioconductor-mesh.bta.eg.db/post-link.sh +++ b/recipes/bioconductor-mesh.bta.eg.db/post-link.sh @@ -1,11 +1,11 @@ #!/bin/bash -FN="MeSH.Bta.eg.db_1.11.0.tar.gz" +FN="MeSH.Bta.eg.db_1.12.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/MeSH.Bta.eg.db_1.11.0.tar.gz" - "https://bioarchive.galaxyproject.org/MeSH.Bta.eg.db_1.11.0.tar.gz" - "https://depot.galaxyproject.org/software/bioconductor-mesh.bta.eg.db/bioconductor-mesh.bta.eg.db_1.11.0_src_all.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/MeSH.Bta.eg.db_1.12.0.tar.gz" + "https://bioarchive.galaxyproject.org/MeSH.Bta.eg.db_1.12.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-mesh.bta.eg.db/bioconductor-mesh.bta.eg.db_1.12.0_src_all.tar.gz" ) -MD5="8ed09310cb68d0b8ea7e075c669c69cf" +MD5="1b6213dfe7731258b867fbe8ede5e592" # Use a staging area in the conda dir rather than temp dirs, both to avoid # permission issues as well as to have things downloaded in a predictable @@ -16,7 +16,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-mesh.cal.sc5314.eg.db/meta.yaml b/recipes/bioconductor-mesh.cal.sc5314.eg.db/meta.yaml index 777b8513b6f35..6ff711ee86012 100644 --- a/recipes/bioconductor-mesh.cal.sc5314.eg.db/meta.yaml +++ b/recipes/bioconductor-mesh.cal.sc5314.eg.db/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.11.0" %} +{% set version = "1.12.0" %} {% set name = "MeSH.Cal.SC5314.eg.db" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: abe3f60190131f0a2a65e7408b829fbd + md5: 011b57f3115f1809dfd3af611c430734 build: number: 0 rpaths: @@ -20,12 +20,12 @@ build: # Suggests: RUnit, BiocGenerics requirements: host: - - 'bioconductor-meshdbi >=1.18.0,<1.19.0' + - 'bioconductor-meshdbi >=1.20.0,<1.21.0' - r-base run: - - 'bioconductor-meshdbi >=1.18.0,<1.19.0' + - 'bioconductor-meshdbi >=1.20.0,<1.21.0' - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-mesh.cal.sc5314.eg.db/post-link.sh b/recipes/bioconductor-mesh.cal.sc5314.eg.db/post-link.sh index f8602e85d0e15..1e7f33268902d 100644 --- a/recipes/bioconductor-mesh.cal.sc5314.eg.db/post-link.sh +++ b/recipes/bioconductor-mesh.cal.sc5314.eg.db/post-link.sh @@ -1,11 +1,11 @@ #!/bin/bash -FN="MeSH.Cal.SC5314.eg.db_1.11.0.tar.gz" +FN="MeSH.Cal.SC5314.eg.db_1.12.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/MeSH.Cal.SC5314.eg.db_1.11.0.tar.gz" - "https://bioarchive.galaxyproject.org/MeSH.Cal.SC5314.eg.db_1.11.0.tar.gz" - "https://depot.galaxyproject.org/software/bioconductor-mesh.cal.sc5314.eg.db/bioconductor-mesh.cal.sc5314.eg.db_1.11.0_src_all.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/MeSH.Cal.SC5314.eg.db_1.12.0.tar.gz" + "https://bioarchive.galaxyproject.org/MeSH.Cal.SC5314.eg.db_1.12.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-mesh.cal.sc5314.eg.db/bioconductor-mesh.cal.sc5314.eg.db_1.12.0_src_all.tar.gz" ) -MD5="abe3f60190131f0a2a65e7408b829fbd" +MD5="011b57f3115f1809dfd3af611c430734" # Use a staging area in the conda dir rather than temp dirs, both to avoid # permission issues as well as to have things downloaded in a predictable @@ -16,7 +16,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-mesh.cbr.eg.db/meta.yaml b/recipes/bioconductor-mesh.cbr.eg.db/meta.yaml index 0d5cdb7fc37d5..fffe558d3ec00 100644 --- a/recipes/bioconductor-mesh.cbr.eg.db/meta.yaml +++ b/recipes/bioconductor-mesh.cbr.eg.db/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.11.0" %} +{% set version = "1.12.0" %} {% set name = "MeSH.Cbr.eg.db" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: f7376562bb5b90f71142bc6430e39c6d + md5: ea955abefc52da00ec50e395e3285692 build: number: 0 rpaths: @@ -20,12 +20,12 @@ build: # Suggests: RUnit, BiocGenerics requirements: host: - - 'bioconductor-meshdbi >=1.18.0,<1.19.0' + - 'bioconductor-meshdbi >=1.20.0,<1.21.0' - r-base run: - - 'bioconductor-meshdbi >=1.18.0,<1.19.0' + - 'bioconductor-meshdbi >=1.20.0,<1.21.0' - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-mesh.cbr.eg.db/post-link.sh b/recipes/bioconductor-mesh.cbr.eg.db/post-link.sh index 738f2d5c77ebc..70e27b45eeb6f 100644 --- a/recipes/bioconductor-mesh.cbr.eg.db/post-link.sh +++ b/recipes/bioconductor-mesh.cbr.eg.db/post-link.sh @@ -1,11 +1,11 @@ #!/bin/bash -FN="MeSH.Cbr.eg.db_1.11.0.tar.gz" +FN="MeSH.Cbr.eg.db_1.12.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/MeSH.Cbr.eg.db_1.11.0.tar.gz" - "https://bioarchive.galaxyproject.org/MeSH.Cbr.eg.db_1.11.0.tar.gz" - "https://depot.galaxyproject.org/software/bioconductor-mesh.cbr.eg.db/bioconductor-mesh.cbr.eg.db_1.11.0_src_all.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/MeSH.Cbr.eg.db_1.12.0.tar.gz" + "https://bioarchive.galaxyproject.org/MeSH.Cbr.eg.db_1.12.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-mesh.cbr.eg.db/bioconductor-mesh.cbr.eg.db_1.12.0_src_all.tar.gz" ) -MD5="f7376562bb5b90f71142bc6430e39c6d" +MD5="ea955abefc52da00ec50e395e3285692" # Use a staging area in the conda dir rather than temp dirs, both to avoid # permission issues as well as to have things downloaded in a predictable @@ -16,7 +16,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-mesh.cel.eg.db/meta.yaml b/recipes/bioconductor-mesh.cel.eg.db/meta.yaml index f9f7e1cbab73f..86954223e9d1b 100644 --- a/recipes/bioconductor-mesh.cel.eg.db/meta.yaml +++ b/recipes/bioconductor-mesh.cel.eg.db/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.11.0" %} +{% set version = "1.12.0" %} {% set name = "MeSH.Cel.eg.db" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 40395428c53ccc5bed4a5720f13c1126 + md5: 3f373ac2b09e5049b85a9702fc64a957 build: number: 0 rpaths: @@ -20,12 +20,12 @@ build: # Suggests: RUnit, BiocGenerics requirements: host: - - 'bioconductor-meshdbi >=1.18.0,<1.19.0' + - 'bioconductor-meshdbi >=1.20.0,<1.21.0' - r-base run: - - 'bioconductor-meshdbi >=1.18.0,<1.19.0' + - 'bioconductor-meshdbi >=1.20.0,<1.21.0' - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-mesh.cel.eg.db/post-link.sh b/recipes/bioconductor-mesh.cel.eg.db/post-link.sh index 31c2ca7fda244..ee9591f8e0ed7 100644 --- a/recipes/bioconductor-mesh.cel.eg.db/post-link.sh +++ b/recipes/bioconductor-mesh.cel.eg.db/post-link.sh @@ -1,11 +1,11 @@ #!/bin/bash -FN="MeSH.Cel.eg.db_1.11.0.tar.gz" +FN="MeSH.Cel.eg.db_1.12.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/MeSH.Cel.eg.db_1.11.0.tar.gz" - "https://bioarchive.galaxyproject.org/MeSH.Cel.eg.db_1.11.0.tar.gz" - "https://depot.galaxyproject.org/software/bioconductor-mesh.cel.eg.db/bioconductor-mesh.cel.eg.db_1.11.0_src_all.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/MeSH.Cel.eg.db_1.12.0.tar.gz" + "https://bioarchive.galaxyproject.org/MeSH.Cel.eg.db_1.12.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-mesh.cel.eg.db/bioconductor-mesh.cel.eg.db_1.12.0_src_all.tar.gz" ) -MD5="40395428c53ccc5bed4a5720f13c1126" +MD5="3f373ac2b09e5049b85a9702fc64a957" # Use a staging area in the conda dir rather than temp dirs, both to avoid # permission issues as well as to have things downloaded in a predictable @@ -16,7 +16,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-mesh.cfa.eg.db/meta.yaml b/recipes/bioconductor-mesh.cfa.eg.db/meta.yaml index 75196d6ae9273..73b94a8ac9dac 100644 --- a/recipes/bioconductor-mesh.cfa.eg.db/meta.yaml +++ b/recipes/bioconductor-mesh.cfa.eg.db/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.11.0" %} +{% set version = "1.12.0" %} {% set name = "MeSH.Cfa.eg.db" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 1a51d80a9c253fdc7037a4a4d23f7429 + md5: ec99f0c24e61b6c39335bbb2faf4ca3d build: number: 0 rpaths: @@ -20,12 +20,12 @@ build: # Suggests: RUnit, BiocGenerics requirements: host: - - 'bioconductor-meshdbi >=1.18.0,<1.19.0' + - 'bioconductor-meshdbi >=1.20.0,<1.21.0' - r-base run: - - 'bioconductor-meshdbi >=1.18.0,<1.19.0' + - 'bioconductor-meshdbi >=1.20.0,<1.21.0' - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-mesh.cfa.eg.db/post-link.sh b/recipes/bioconductor-mesh.cfa.eg.db/post-link.sh index 578c5f564a89c..5f9c6f96a872b 100644 --- a/recipes/bioconductor-mesh.cfa.eg.db/post-link.sh +++ b/recipes/bioconductor-mesh.cfa.eg.db/post-link.sh @@ -1,11 +1,11 @@ #!/bin/bash -FN="MeSH.Cfa.eg.db_1.11.0.tar.gz" +FN="MeSH.Cfa.eg.db_1.12.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/MeSH.Cfa.eg.db_1.11.0.tar.gz" - "https://bioarchive.galaxyproject.org/MeSH.Cfa.eg.db_1.11.0.tar.gz" - "https://depot.galaxyproject.org/software/bioconductor-mesh.cfa.eg.db/bioconductor-mesh.cfa.eg.db_1.11.0_src_all.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/MeSH.Cfa.eg.db_1.12.0.tar.gz" + "https://bioarchive.galaxyproject.org/MeSH.Cfa.eg.db_1.12.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-mesh.cfa.eg.db/bioconductor-mesh.cfa.eg.db_1.12.0_src_all.tar.gz" ) -MD5="1a51d80a9c253fdc7037a4a4d23f7429" +MD5="ec99f0c24e61b6c39335bbb2faf4ca3d" # Use a staging area in the conda dir rather than temp dirs, both to avoid # permission issues as well as to have things downloaded in a predictable @@ -16,7 +16,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-mesh.cin.eg.db/meta.yaml b/recipes/bioconductor-mesh.cin.eg.db/meta.yaml index 35bd2bd234bb9..5d6c63dc3f1a5 100644 --- a/recipes/bioconductor-mesh.cin.eg.db/meta.yaml +++ b/recipes/bioconductor-mesh.cin.eg.db/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.11.0" %} +{% set version = "1.12.0" %} {% set name = "MeSH.Cin.eg.db" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: d3eee14d64663fdc86f9e1f8964341b9 + md5: 89b55b0ecb065acd391242d1d23136b2 build: number: 0 rpaths: @@ -20,12 +20,12 @@ build: # Suggests: RUnit, BiocGenerics requirements: host: - - 'bioconductor-meshdbi >=1.18.0,<1.19.0' + - 'bioconductor-meshdbi >=1.20.0,<1.21.0' - r-base run: - - 'bioconductor-meshdbi >=1.18.0,<1.19.0' + - 'bioconductor-meshdbi >=1.20.0,<1.21.0' - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-mesh.cin.eg.db/post-link.sh b/recipes/bioconductor-mesh.cin.eg.db/post-link.sh index 6c41fdad037bd..1f23513b314e1 100644 --- a/recipes/bioconductor-mesh.cin.eg.db/post-link.sh +++ b/recipes/bioconductor-mesh.cin.eg.db/post-link.sh @@ -1,11 +1,11 @@ #!/bin/bash -FN="MeSH.Cin.eg.db_1.11.0.tar.gz" +FN="MeSH.Cin.eg.db_1.12.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/MeSH.Cin.eg.db_1.11.0.tar.gz" - "https://bioarchive.galaxyproject.org/MeSH.Cin.eg.db_1.11.0.tar.gz" - "https://depot.galaxyproject.org/software/bioconductor-mesh.cin.eg.db/bioconductor-mesh.cin.eg.db_1.11.0_src_all.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/MeSH.Cin.eg.db_1.12.0.tar.gz" + "https://bioarchive.galaxyproject.org/MeSH.Cin.eg.db_1.12.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-mesh.cin.eg.db/bioconductor-mesh.cin.eg.db_1.12.0_src_all.tar.gz" ) -MD5="d3eee14d64663fdc86f9e1f8964341b9" +MD5="89b55b0ecb065acd391242d1d23136b2" # Use a staging area in the conda dir rather than temp dirs, both to avoid # permission issues as well as to have things downloaded in a predictable @@ -16,7 +16,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-mesh.cja.eg.db/meta.yaml b/recipes/bioconductor-mesh.cja.eg.db/meta.yaml index f4f5f20ede484..251a6e0bdad0a 100644 --- a/recipes/bioconductor-mesh.cja.eg.db/meta.yaml +++ b/recipes/bioconductor-mesh.cja.eg.db/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.11.0" %} +{% set version = "1.12.0" %} {% set name = "MeSH.Cja.eg.db" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 202f330085d91903e587263de9e3f0c0 + md5: 2182ecdced26c7705696f9c2453d7c24 build: number: 0 rpaths: @@ -20,12 +20,12 @@ build: # Suggests: RUnit, BiocGenerics requirements: host: - - 'bioconductor-meshdbi >=1.18.0,<1.19.0' + - 'bioconductor-meshdbi >=1.20.0,<1.21.0' - r-base run: - - 'bioconductor-meshdbi >=1.18.0,<1.19.0' + - 'bioconductor-meshdbi >=1.20.0,<1.21.0' - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-mesh.cja.eg.db/post-link.sh b/recipes/bioconductor-mesh.cja.eg.db/post-link.sh index 3fc96dade47cb..975f013597def 100644 --- a/recipes/bioconductor-mesh.cja.eg.db/post-link.sh +++ b/recipes/bioconductor-mesh.cja.eg.db/post-link.sh @@ -1,11 +1,11 @@ #!/bin/bash -FN="MeSH.Cja.eg.db_1.11.0.tar.gz" +FN="MeSH.Cja.eg.db_1.12.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/MeSH.Cja.eg.db_1.11.0.tar.gz" - "https://bioarchive.galaxyproject.org/MeSH.Cja.eg.db_1.11.0.tar.gz" - "https://depot.galaxyproject.org/software/bioconductor-mesh.cja.eg.db/bioconductor-mesh.cja.eg.db_1.11.0_src_all.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/MeSH.Cja.eg.db_1.12.0.tar.gz" + "https://bioarchive.galaxyproject.org/MeSH.Cja.eg.db_1.12.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-mesh.cja.eg.db/bioconductor-mesh.cja.eg.db_1.12.0_src_all.tar.gz" ) -MD5="202f330085d91903e587263de9e3f0c0" +MD5="2182ecdced26c7705696f9c2453d7c24" # Use a staging area in the conda dir rather than temp dirs, both to avoid # permission issues as well as to have things downloaded in a predictable @@ -16,7 +16,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-mesh.cpo.eg.db/meta.yaml b/recipes/bioconductor-mesh.cpo.eg.db/meta.yaml index 920485cc7a3a4..506934b3f5e73 100644 --- a/recipes/bioconductor-mesh.cpo.eg.db/meta.yaml +++ b/recipes/bioconductor-mesh.cpo.eg.db/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.11.0" %} +{% set version = "1.12.0" %} {% set name = "MeSH.Cpo.eg.db" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: e2dc546ff799e5a99f0a521e682d62fa + md5: 8d2f3999d655a72c3775080651944333 build: number: 0 rpaths: @@ -20,12 +20,12 @@ build: # Suggests: RUnit, BiocGenerics requirements: host: - - 'bioconductor-meshdbi >=1.18.0,<1.19.0' + - 'bioconductor-meshdbi >=1.20.0,<1.21.0' - r-base run: - - 'bioconductor-meshdbi >=1.18.0,<1.19.0' + - 'bioconductor-meshdbi >=1.20.0,<1.21.0' - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-mesh.cpo.eg.db/post-link.sh b/recipes/bioconductor-mesh.cpo.eg.db/post-link.sh index c498b9beeea6a..aa9177d652563 100644 --- a/recipes/bioconductor-mesh.cpo.eg.db/post-link.sh +++ b/recipes/bioconductor-mesh.cpo.eg.db/post-link.sh @@ -1,11 +1,11 @@ #!/bin/bash -FN="MeSH.Cpo.eg.db_1.11.0.tar.gz" +FN="MeSH.Cpo.eg.db_1.12.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/MeSH.Cpo.eg.db_1.11.0.tar.gz" - "https://bioarchive.galaxyproject.org/MeSH.Cpo.eg.db_1.11.0.tar.gz" - "https://depot.galaxyproject.org/software/bioconductor-mesh.cpo.eg.db/bioconductor-mesh.cpo.eg.db_1.11.0_src_all.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/MeSH.Cpo.eg.db_1.12.0.tar.gz" + "https://bioarchive.galaxyproject.org/MeSH.Cpo.eg.db_1.12.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-mesh.cpo.eg.db/bioconductor-mesh.cpo.eg.db_1.12.0_src_all.tar.gz" ) -MD5="e2dc546ff799e5a99f0a521e682d62fa" +MD5="8d2f3999d655a72c3775080651944333" # Use a staging area in the conda dir rather than temp dirs, both to avoid # permission issues as well as to have things downloaded in a predictable @@ -16,7 +16,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-mesh.cre.eg.db/meta.yaml b/recipes/bioconductor-mesh.cre.eg.db/meta.yaml index 3e4e6e6e2f254..7415458429ba0 100644 --- a/recipes/bioconductor-mesh.cre.eg.db/meta.yaml +++ b/recipes/bioconductor-mesh.cre.eg.db/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.11.0" %} +{% set version = "1.12.0" %} {% set name = "MeSH.Cre.eg.db" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 9f1aa5546a1f7b2164c92ad0262d5f5f + md5: 34a3c416c910bfbdde1febc66fcf8a02 build: number: 0 rpaths: @@ -20,12 +20,12 @@ build: # Suggests: RUnit, BiocGenerics requirements: host: - - 'bioconductor-meshdbi >=1.18.0,<1.19.0' + - 'bioconductor-meshdbi >=1.20.0,<1.21.0' - r-base run: - - 'bioconductor-meshdbi >=1.18.0,<1.19.0' + - 'bioconductor-meshdbi >=1.20.0,<1.21.0' - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-mesh.cre.eg.db/post-link.sh b/recipes/bioconductor-mesh.cre.eg.db/post-link.sh index 798e307c0a05d..9eb869bc2a1cb 100644 --- a/recipes/bioconductor-mesh.cre.eg.db/post-link.sh +++ b/recipes/bioconductor-mesh.cre.eg.db/post-link.sh @@ -1,11 +1,11 @@ #!/bin/bash -FN="MeSH.Cre.eg.db_1.11.0.tar.gz" +FN="MeSH.Cre.eg.db_1.12.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/MeSH.Cre.eg.db_1.11.0.tar.gz" - "https://bioarchive.galaxyproject.org/MeSH.Cre.eg.db_1.11.0.tar.gz" - "https://depot.galaxyproject.org/software/bioconductor-mesh.cre.eg.db/bioconductor-mesh.cre.eg.db_1.11.0_src_all.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/MeSH.Cre.eg.db_1.12.0.tar.gz" + "https://bioarchive.galaxyproject.org/MeSH.Cre.eg.db_1.12.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-mesh.cre.eg.db/bioconductor-mesh.cre.eg.db_1.12.0_src_all.tar.gz" ) -MD5="9f1aa5546a1f7b2164c92ad0262d5f5f" +MD5="34a3c416c910bfbdde1febc66fcf8a02" # Use a staging area in the conda dir rather than temp dirs, both to avoid # permission issues as well as to have things downloaded in a predictable @@ -16,7 +16,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-mesh.dan.eg.db/meta.yaml b/recipes/bioconductor-mesh.dan.eg.db/meta.yaml index 892ff68e2aa91..83605718c9bb9 100644 --- a/recipes/bioconductor-mesh.dan.eg.db/meta.yaml +++ b/recipes/bioconductor-mesh.dan.eg.db/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.11.0" %} +{% set version = "1.12.0" %} {% set name = "MeSH.Dan.eg.db" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 06ceff65e0124447a748a20c90034f1f + md5: bac1907757c826866d96ea6a6f0290e7 build: number: 0 rpaths: @@ -20,12 +20,12 @@ build: # Suggests: RUnit, BiocGenerics requirements: host: - - 'bioconductor-meshdbi >=1.18.0,<1.19.0' + - 'bioconductor-meshdbi >=1.20.0,<1.21.0' - r-base run: - - 'bioconductor-meshdbi >=1.18.0,<1.19.0' + - 'bioconductor-meshdbi >=1.20.0,<1.21.0' - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-mesh.dan.eg.db/post-link.sh b/recipes/bioconductor-mesh.dan.eg.db/post-link.sh index 049c4f8899f2c..8bee837d570e0 100644 --- a/recipes/bioconductor-mesh.dan.eg.db/post-link.sh +++ b/recipes/bioconductor-mesh.dan.eg.db/post-link.sh @@ -1,11 +1,11 @@ #!/bin/bash -FN="MeSH.Dan.eg.db_1.11.0.tar.gz" +FN="MeSH.Dan.eg.db_1.12.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/MeSH.Dan.eg.db_1.11.0.tar.gz" - "https://bioarchive.galaxyproject.org/MeSH.Dan.eg.db_1.11.0.tar.gz" - "https://depot.galaxyproject.org/software/bioconductor-mesh.dan.eg.db/bioconductor-mesh.dan.eg.db_1.11.0_src_all.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/MeSH.Dan.eg.db_1.12.0.tar.gz" + "https://bioarchive.galaxyproject.org/MeSH.Dan.eg.db_1.12.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-mesh.dan.eg.db/bioconductor-mesh.dan.eg.db_1.12.0_src_all.tar.gz" ) -MD5="06ceff65e0124447a748a20c90034f1f" +MD5="bac1907757c826866d96ea6a6f0290e7" # Use a staging area in the conda dir rather than temp dirs, both to avoid # permission issues as well as to have things downloaded in a predictable @@ -16,7 +16,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-mesh.db/meta.yaml b/recipes/bioconductor-mesh.db/meta.yaml index d5a610d4e5242..a30dd9158df30 100644 --- a/recipes/bioconductor-mesh.db/meta.yaml +++ b/recipes/bioconductor-mesh.db/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.11.0" %} +{% set version = "1.12.0" %} {% set name = "MeSH.db" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: c6b74bfc2623be738b9ac6ed981f8810 + md5: d4e468c076c3e7548f24a8a569c9e087 build: number: 0 rpaths: @@ -20,12 +20,12 @@ build: # Suggests: RUnit, BiocGenerics requirements: host: - - 'bioconductor-meshdbi >=1.18.0,<1.19.0' + - 'bioconductor-meshdbi >=1.20.0,<1.21.0' - r-base run: - - 'bioconductor-meshdbi >=1.18.0,<1.19.0' + - 'bioconductor-meshdbi >=1.20.0,<1.21.0' - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-mesh.db/post-link.sh b/recipes/bioconductor-mesh.db/post-link.sh index a3b5b92a936bc..2d515b14bcb98 100644 --- a/recipes/bioconductor-mesh.db/post-link.sh +++ b/recipes/bioconductor-mesh.db/post-link.sh @@ -1,11 +1,11 @@ #!/bin/bash -FN="MeSH.db_1.11.0.tar.gz" +FN="MeSH.db_1.12.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/MeSH.db_1.11.0.tar.gz" - "https://bioarchive.galaxyproject.org/MeSH.db_1.11.0.tar.gz" - "https://depot.galaxyproject.org/software/bioconductor-mesh.db/bioconductor-mesh.db_1.11.0_src_all.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/MeSH.db_1.12.0.tar.gz" + "https://bioarchive.galaxyproject.org/MeSH.db_1.12.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-mesh.db/bioconductor-mesh.db_1.12.0_src_all.tar.gz" ) -MD5="c6b74bfc2623be738b9ac6ed981f8810" +MD5="d4e468c076c3e7548f24a8a569c9e087" # Use a staging area in the conda dir rather than temp dirs, both to avoid # permission issues as well as to have things downloaded in a predictable @@ -16,7 +16,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-mesh.dda.3937.eg.db/meta.yaml b/recipes/bioconductor-mesh.dda.3937.eg.db/meta.yaml index c4da70c823471..e6650a00f6e24 100644 --- a/recipes/bioconductor-mesh.dda.3937.eg.db/meta.yaml +++ b/recipes/bioconductor-mesh.dda.3937.eg.db/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.11.0" %} +{% set version = "1.12.0" %} {% set name = "MeSH.Dda.3937.eg.db" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: fa6921643753b56290fefb57274a59be + md5: 5480a4fde51d0aaf3d33628fcd0c08bd build: number: 0 rpaths: @@ -20,12 +20,12 @@ build: # Suggests: RUnit, BiocGenerics requirements: host: - - 'bioconductor-meshdbi >=1.18.0,<1.19.0' + - 'bioconductor-meshdbi >=1.20.0,<1.21.0' - r-base run: - - 'bioconductor-meshdbi >=1.18.0,<1.19.0' + - 'bioconductor-meshdbi >=1.20.0,<1.21.0' - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-mesh.dda.3937.eg.db/post-link.sh b/recipes/bioconductor-mesh.dda.3937.eg.db/post-link.sh index 60fd411cacc62..4a4f8126fb655 100644 --- a/recipes/bioconductor-mesh.dda.3937.eg.db/post-link.sh +++ b/recipes/bioconductor-mesh.dda.3937.eg.db/post-link.sh @@ -1,11 +1,11 @@ #!/bin/bash -FN="MeSH.Dda.3937.eg.db_1.11.0.tar.gz" +FN="MeSH.Dda.3937.eg.db_1.12.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/MeSH.Dda.3937.eg.db_1.11.0.tar.gz" - "https://bioarchive.galaxyproject.org/MeSH.Dda.3937.eg.db_1.11.0.tar.gz" - "https://depot.galaxyproject.org/software/bioconductor-mesh.dda.3937.eg.db/bioconductor-mesh.dda.3937.eg.db_1.11.0_src_all.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/MeSH.Dda.3937.eg.db_1.12.0.tar.gz" + "https://bioarchive.galaxyproject.org/MeSH.Dda.3937.eg.db_1.12.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-mesh.dda.3937.eg.db/bioconductor-mesh.dda.3937.eg.db_1.12.0_src_all.tar.gz" ) -MD5="fa6921643753b56290fefb57274a59be" +MD5="5480a4fde51d0aaf3d33628fcd0c08bd" # Use a staging area in the conda dir rather than temp dirs, both to avoid # permission issues as well as to have things downloaded in a predictable @@ -16,7 +16,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-mesh.ddi.ax4.eg.db/meta.yaml b/recipes/bioconductor-mesh.ddi.ax4.eg.db/meta.yaml index 606a7d8508ac6..794944bb999ee 100644 --- a/recipes/bioconductor-mesh.ddi.ax4.eg.db/meta.yaml +++ b/recipes/bioconductor-mesh.ddi.ax4.eg.db/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.11.0" %} +{% set version = "1.12.0" %} {% set name = "MeSH.Ddi.AX4.eg.db" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: f16d5ae80376c352f770a6ace7ca5c78 + md5: 69e13d6fc6e627ae014dcc8813ab5e9a build: number: 0 rpaths: @@ -20,12 +20,12 @@ build: # Suggests: RUnit, BiocGenerics requirements: host: - - 'bioconductor-meshdbi >=1.18.0,<1.19.0' + - 'bioconductor-meshdbi >=1.20.0,<1.21.0' - r-base run: - - 'bioconductor-meshdbi >=1.18.0,<1.19.0' + - 'bioconductor-meshdbi >=1.20.0,<1.21.0' - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-mesh.ddi.ax4.eg.db/post-link.sh b/recipes/bioconductor-mesh.ddi.ax4.eg.db/post-link.sh index ff7478efb0112..7d903b6c307f1 100644 --- a/recipes/bioconductor-mesh.ddi.ax4.eg.db/post-link.sh +++ b/recipes/bioconductor-mesh.ddi.ax4.eg.db/post-link.sh @@ -1,11 +1,11 @@ #!/bin/bash -FN="MeSH.Ddi.AX4.eg.db_1.11.0.tar.gz" +FN="MeSH.Ddi.AX4.eg.db_1.12.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/MeSH.Ddi.AX4.eg.db_1.11.0.tar.gz" - "https://bioarchive.galaxyproject.org/MeSH.Ddi.AX4.eg.db_1.11.0.tar.gz" - "https://depot.galaxyproject.org/software/bioconductor-mesh.ddi.ax4.eg.db/bioconductor-mesh.ddi.ax4.eg.db_1.11.0_src_all.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/MeSH.Ddi.AX4.eg.db_1.12.0.tar.gz" + "https://bioarchive.galaxyproject.org/MeSH.Ddi.AX4.eg.db_1.12.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-mesh.ddi.ax4.eg.db/bioconductor-mesh.ddi.ax4.eg.db_1.12.0_src_all.tar.gz" ) -MD5="f16d5ae80376c352f770a6ace7ca5c78" +MD5="69e13d6fc6e627ae014dcc8813ab5e9a" # Use a staging area in the conda dir rather than temp dirs, both to avoid # permission issues as well as to have things downloaded in a predictable @@ -16,7 +16,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-mesh.der.eg.db/meta.yaml b/recipes/bioconductor-mesh.der.eg.db/meta.yaml index 0ff9384570578..88b0e6d054de2 100644 --- a/recipes/bioconductor-mesh.der.eg.db/meta.yaml +++ b/recipes/bioconductor-mesh.der.eg.db/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.11.0" %} +{% set version = "1.12.0" %} {% set name = "MeSH.Der.eg.db" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 6e983cc8b9eea0dfa80d34d1dcc427f3 + md5: f45c156f0b1c80404a365c0fa72b40d1 build: number: 0 rpaths: @@ -20,12 +20,12 @@ build: # Suggests: RUnit, BiocGenerics requirements: host: - - 'bioconductor-meshdbi >=1.18.0,<1.19.0' + - 'bioconductor-meshdbi >=1.20.0,<1.21.0' - r-base run: - - 'bioconductor-meshdbi >=1.18.0,<1.19.0' + - 'bioconductor-meshdbi >=1.20.0,<1.21.0' - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-mesh.der.eg.db/post-link.sh b/recipes/bioconductor-mesh.der.eg.db/post-link.sh index a9401798130c5..1f33e4524677b 100644 --- a/recipes/bioconductor-mesh.der.eg.db/post-link.sh +++ b/recipes/bioconductor-mesh.der.eg.db/post-link.sh @@ -1,11 +1,11 @@ #!/bin/bash -FN="MeSH.Der.eg.db_1.11.0.tar.gz" +FN="MeSH.Der.eg.db_1.12.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/MeSH.Der.eg.db_1.11.0.tar.gz" - "https://bioarchive.galaxyproject.org/MeSH.Der.eg.db_1.11.0.tar.gz" - "https://depot.galaxyproject.org/software/bioconductor-mesh.der.eg.db/bioconductor-mesh.der.eg.db_1.11.0_src_all.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/MeSH.Der.eg.db_1.12.0.tar.gz" + "https://bioarchive.galaxyproject.org/MeSH.Der.eg.db_1.12.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-mesh.der.eg.db/bioconductor-mesh.der.eg.db_1.12.0_src_all.tar.gz" ) -MD5="6e983cc8b9eea0dfa80d34d1dcc427f3" +MD5="f45c156f0b1c80404a365c0fa72b40d1" # Use a staging area in the conda dir rather than temp dirs, both to avoid # permission issues as well as to have things downloaded in a predictable @@ -16,7 +16,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-mesh.dgr.eg.db/meta.yaml b/recipes/bioconductor-mesh.dgr.eg.db/meta.yaml index d9ce9492c5cd0..46be7b4a4f85e 100644 --- a/recipes/bioconductor-mesh.dgr.eg.db/meta.yaml +++ b/recipes/bioconductor-mesh.dgr.eg.db/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.11.0" %} +{% set version = "1.12.0" %} {% set name = "MeSH.Dgr.eg.db" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: af40bdddd4d0d2596b085605734ba4d3 + md5: 5c897dd84151aac1251479dc95813d19 build: number: 0 rpaths: @@ -20,12 +20,12 @@ build: # Suggests: RUnit, BiocGenerics requirements: host: - - 'bioconductor-meshdbi >=1.18.0,<1.19.0' + - 'bioconductor-meshdbi >=1.20.0,<1.21.0' - r-base run: - - 'bioconductor-meshdbi >=1.18.0,<1.19.0' + - 'bioconductor-meshdbi >=1.20.0,<1.21.0' - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-mesh.dgr.eg.db/post-link.sh b/recipes/bioconductor-mesh.dgr.eg.db/post-link.sh index 10e18b03a8280..d395fa341fe97 100644 --- a/recipes/bioconductor-mesh.dgr.eg.db/post-link.sh +++ b/recipes/bioconductor-mesh.dgr.eg.db/post-link.sh @@ -1,11 +1,11 @@ #!/bin/bash -FN="MeSH.Dgr.eg.db_1.11.0.tar.gz" +FN="MeSH.Dgr.eg.db_1.12.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/MeSH.Dgr.eg.db_1.11.0.tar.gz" - "https://bioarchive.galaxyproject.org/MeSH.Dgr.eg.db_1.11.0.tar.gz" - "https://depot.galaxyproject.org/software/bioconductor-mesh.dgr.eg.db/bioconductor-mesh.dgr.eg.db_1.11.0_src_all.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/MeSH.Dgr.eg.db_1.12.0.tar.gz" + "https://bioarchive.galaxyproject.org/MeSH.Dgr.eg.db_1.12.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-mesh.dgr.eg.db/bioconductor-mesh.dgr.eg.db_1.12.0_src_all.tar.gz" ) -MD5="af40bdddd4d0d2596b085605734ba4d3" +MD5="5c897dd84151aac1251479dc95813d19" # Use a staging area in the conda dir rather than temp dirs, both to avoid # permission issues as well as to have things downloaded in a predictable @@ -16,7 +16,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-mesh.dme.eg.db/meta.yaml b/recipes/bioconductor-mesh.dme.eg.db/meta.yaml index 1898226eeb2de..415c70582c333 100644 --- a/recipes/bioconductor-mesh.dme.eg.db/meta.yaml +++ b/recipes/bioconductor-mesh.dme.eg.db/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.11.0" %} +{% set version = "1.12.0" %} {% set name = "MeSH.Dme.eg.db" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: b9f1b8e5882366a3362fe861a7f366e6 + md5: 24b5a3cb6e8a5ad695d6282ac852475f build: number: 0 rpaths: @@ -20,12 +20,12 @@ build: # Suggests: RUnit, BiocGenerics requirements: host: - - 'bioconductor-meshdbi >=1.18.0,<1.19.0' + - 'bioconductor-meshdbi >=1.20.0,<1.21.0' - r-base run: - - 'bioconductor-meshdbi >=1.18.0,<1.19.0' + - 'bioconductor-meshdbi >=1.20.0,<1.21.0' - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-mesh.dme.eg.db/post-link.sh b/recipes/bioconductor-mesh.dme.eg.db/post-link.sh index 820f1608c7fbf..9c7dc41a9e0e1 100644 --- a/recipes/bioconductor-mesh.dme.eg.db/post-link.sh +++ b/recipes/bioconductor-mesh.dme.eg.db/post-link.sh @@ -1,11 +1,11 @@ #!/bin/bash -FN="MeSH.Dme.eg.db_1.11.0.tar.gz" +FN="MeSH.Dme.eg.db_1.12.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/MeSH.Dme.eg.db_1.11.0.tar.gz" - "https://bioarchive.galaxyproject.org/MeSH.Dme.eg.db_1.11.0.tar.gz" - "https://depot.galaxyproject.org/software/bioconductor-mesh.dme.eg.db/bioconductor-mesh.dme.eg.db_1.11.0_src_all.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/MeSH.Dme.eg.db_1.12.0.tar.gz" + "https://bioarchive.galaxyproject.org/MeSH.Dme.eg.db_1.12.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-mesh.dme.eg.db/bioconductor-mesh.dme.eg.db_1.12.0_src_all.tar.gz" ) -MD5="b9f1b8e5882366a3362fe861a7f366e6" +MD5="24b5a3cb6e8a5ad695d6282ac852475f" # Use a staging area in the conda dir rather than temp dirs, both to avoid # permission issues as well as to have things downloaded in a predictable @@ -16,7 +16,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-mesh.dmo.eg.db/meta.yaml b/recipes/bioconductor-mesh.dmo.eg.db/meta.yaml index e49625f33c1af..b6469251a8cda 100644 --- a/recipes/bioconductor-mesh.dmo.eg.db/meta.yaml +++ b/recipes/bioconductor-mesh.dmo.eg.db/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.11.0" %} +{% set version = "1.12.0" %} {% set name = "MeSH.Dmo.eg.db" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: e5267e6a3961a67f289b3f58e484a508 + md5: 89c488b437d119d4120b8e0709df5ed0 build: number: 0 rpaths: @@ -20,12 +20,12 @@ build: # Suggests: RUnit, BiocGenerics requirements: host: - - 'bioconductor-meshdbi >=1.18.0,<1.19.0' + - 'bioconductor-meshdbi >=1.20.0,<1.21.0' - r-base run: - - 'bioconductor-meshdbi >=1.18.0,<1.19.0' + - 'bioconductor-meshdbi >=1.20.0,<1.21.0' - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-mesh.dmo.eg.db/post-link.sh b/recipes/bioconductor-mesh.dmo.eg.db/post-link.sh index 71faacbab346c..494afb9de29a7 100644 --- a/recipes/bioconductor-mesh.dmo.eg.db/post-link.sh +++ b/recipes/bioconductor-mesh.dmo.eg.db/post-link.sh @@ -1,11 +1,11 @@ #!/bin/bash -FN="MeSH.Dmo.eg.db_1.11.0.tar.gz" +FN="MeSH.Dmo.eg.db_1.12.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/MeSH.Dmo.eg.db_1.11.0.tar.gz" - "https://bioarchive.galaxyproject.org/MeSH.Dmo.eg.db_1.11.0.tar.gz" - "https://depot.galaxyproject.org/software/bioconductor-mesh.dmo.eg.db/bioconductor-mesh.dmo.eg.db_1.11.0_src_all.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/MeSH.Dmo.eg.db_1.12.0.tar.gz" + "https://bioarchive.galaxyproject.org/MeSH.Dmo.eg.db_1.12.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-mesh.dmo.eg.db/bioconductor-mesh.dmo.eg.db_1.12.0_src_all.tar.gz" ) -MD5="e5267e6a3961a67f289b3f58e484a508" +MD5="89c488b437d119d4120b8e0709df5ed0" # Use a staging area in the conda dir rather than temp dirs, both to avoid # permission issues as well as to have things downloaded in a predictable @@ -16,7 +16,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-mesh.dpe.eg.db/meta.yaml b/recipes/bioconductor-mesh.dpe.eg.db/meta.yaml index bf4ad8be08607..0150e7c8397b3 100644 --- a/recipes/bioconductor-mesh.dpe.eg.db/meta.yaml +++ b/recipes/bioconductor-mesh.dpe.eg.db/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.11.0" %} +{% set version = "1.12.0" %} {% set name = "MeSH.Dpe.eg.db" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 89bc6448d7420b8808260bbd2fce5c6a + md5: 269bdc39765da0193b19ce6b408ceb3a build: number: 0 rpaths: @@ -20,12 +20,12 @@ build: # Suggests: RUnit, BiocGenerics requirements: host: - - 'bioconductor-meshdbi >=1.18.0,<1.19.0' + - 'bioconductor-meshdbi >=1.20.0,<1.21.0' - r-base run: - - 'bioconductor-meshdbi >=1.18.0,<1.19.0' + - 'bioconductor-meshdbi >=1.20.0,<1.21.0' - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-mesh.dpe.eg.db/post-link.sh b/recipes/bioconductor-mesh.dpe.eg.db/post-link.sh index 38a032961b4c0..12c1dd1efa889 100644 --- a/recipes/bioconductor-mesh.dpe.eg.db/post-link.sh +++ b/recipes/bioconductor-mesh.dpe.eg.db/post-link.sh @@ -1,11 +1,11 @@ #!/bin/bash -FN="MeSH.Dpe.eg.db_1.11.0.tar.gz" +FN="MeSH.Dpe.eg.db_1.12.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/MeSH.Dpe.eg.db_1.11.0.tar.gz" - "https://bioarchive.galaxyproject.org/MeSH.Dpe.eg.db_1.11.0.tar.gz" - "https://depot.galaxyproject.org/software/bioconductor-mesh.dpe.eg.db/bioconductor-mesh.dpe.eg.db_1.11.0_src_all.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/MeSH.Dpe.eg.db_1.12.0.tar.gz" + "https://bioarchive.galaxyproject.org/MeSH.Dpe.eg.db_1.12.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-mesh.dpe.eg.db/bioconductor-mesh.dpe.eg.db_1.12.0_src_all.tar.gz" ) -MD5="89bc6448d7420b8808260bbd2fce5c6a" +MD5="269bdc39765da0193b19ce6b408ceb3a" # Use a staging area in the conda dir rather than temp dirs, both to avoid # permission issues as well as to have things downloaded in a predictable @@ -16,7 +16,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-mesh.dre.eg.db/meta.yaml b/recipes/bioconductor-mesh.dre.eg.db/meta.yaml index 41a8305740b78..792c985505370 100644 --- a/recipes/bioconductor-mesh.dre.eg.db/meta.yaml +++ b/recipes/bioconductor-mesh.dre.eg.db/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.11.0" %} +{% set version = "1.12.0" %} {% set name = "MeSH.Dre.eg.db" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 4776847a50cbd8afe46626f3c3437b45 + md5: 89700462b20d1077637a5ea827e41dce build: number: 0 rpaths: @@ -20,12 +20,12 @@ build: # Suggests: RUnit, BiocGenerics requirements: host: - - 'bioconductor-meshdbi >=1.18.0,<1.19.0' + - 'bioconductor-meshdbi >=1.20.0,<1.21.0' - r-base run: - - 'bioconductor-meshdbi >=1.18.0,<1.19.0' + - 'bioconductor-meshdbi >=1.20.0,<1.21.0' - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-mesh.dre.eg.db/post-link.sh b/recipes/bioconductor-mesh.dre.eg.db/post-link.sh index f94885bb5ff8d..60f14299eff92 100644 --- a/recipes/bioconductor-mesh.dre.eg.db/post-link.sh +++ b/recipes/bioconductor-mesh.dre.eg.db/post-link.sh @@ -1,11 +1,11 @@ #!/bin/bash -FN="MeSH.Dre.eg.db_1.11.0.tar.gz" +FN="MeSH.Dre.eg.db_1.12.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/MeSH.Dre.eg.db_1.11.0.tar.gz" - "https://bioarchive.galaxyproject.org/MeSH.Dre.eg.db_1.11.0.tar.gz" - "https://depot.galaxyproject.org/software/bioconductor-mesh.dre.eg.db/bioconductor-mesh.dre.eg.db_1.11.0_src_all.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/MeSH.Dre.eg.db_1.12.0.tar.gz" + "https://bioarchive.galaxyproject.org/MeSH.Dre.eg.db_1.12.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-mesh.dre.eg.db/bioconductor-mesh.dre.eg.db_1.12.0_src_all.tar.gz" ) -MD5="4776847a50cbd8afe46626f3c3437b45" +MD5="89700462b20d1077637a5ea827e41dce" # Use a staging area in the conda dir rather than temp dirs, both to avoid # permission issues as well as to have things downloaded in a predictable @@ -16,7 +16,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-mesh.dse.eg.db/meta.yaml b/recipes/bioconductor-mesh.dse.eg.db/meta.yaml index 56396c7c7cf69..f52c7781c9bca 100644 --- a/recipes/bioconductor-mesh.dse.eg.db/meta.yaml +++ b/recipes/bioconductor-mesh.dse.eg.db/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.11.0" %} +{% set version = "1.12.0" %} {% set name = "MeSH.Dse.eg.db" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 583f5f954ed715f511317f9dc424b9d4 + md5: 8276661907001767b21ace678385713d build: number: 0 rpaths: @@ -20,12 +20,12 @@ build: # Suggests: RUnit, BiocGenerics requirements: host: - - 'bioconductor-meshdbi >=1.18.0,<1.19.0' + - 'bioconductor-meshdbi >=1.20.0,<1.21.0' - r-base run: - - 'bioconductor-meshdbi >=1.18.0,<1.19.0' + - 'bioconductor-meshdbi >=1.20.0,<1.21.0' - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-mesh.dse.eg.db/post-link.sh b/recipes/bioconductor-mesh.dse.eg.db/post-link.sh index b3cfccb2128ca..8e6b49595ca18 100644 --- a/recipes/bioconductor-mesh.dse.eg.db/post-link.sh +++ b/recipes/bioconductor-mesh.dse.eg.db/post-link.sh @@ -1,11 +1,11 @@ #!/bin/bash -FN="MeSH.Dse.eg.db_1.11.0.tar.gz" +FN="MeSH.Dse.eg.db_1.12.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/MeSH.Dse.eg.db_1.11.0.tar.gz" - "https://bioarchive.galaxyproject.org/MeSH.Dse.eg.db_1.11.0.tar.gz" - "https://depot.galaxyproject.org/software/bioconductor-mesh.dse.eg.db/bioconductor-mesh.dse.eg.db_1.11.0_src_all.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/MeSH.Dse.eg.db_1.12.0.tar.gz" + "https://bioarchive.galaxyproject.org/MeSH.Dse.eg.db_1.12.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-mesh.dse.eg.db/bioconductor-mesh.dse.eg.db_1.12.0_src_all.tar.gz" ) -MD5="583f5f954ed715f511317f9dc424b9d4" +MD5="8276661907001767b21ace678385713d" # Use a staging area in the conda dir rather than temp dirs, both to avoid # permission issues as well as to have things downloaded in a predictable @@ -16,7 +16,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-mesh.dsi.eg.db/meta.yaml b/recipes/bioconductor-mesh.dsi.eg.db/meta.yaml index 2efafb2462a53..e5dee4b7fbdff 100644 --- a/recipes/bioconductor-mesh.dsi.eg.db/meta.yaml +++ b/recipes/bioconductor-mesh.dsi.eg.db/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.11.0" %} +{% set version = "1.12.0" %} {% set name = "MeSH.Dsi.eg.db" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: cf96a96c3f2f869956b7c02d68b0dbbd + md5: 6b5be7ed0d482654995818d5a4d40acf build: number: 0 rpaths: @@ -20,12 +20,12 @@ build: # Suggests: RUnit, BiocGenerics requirements: host: - - 'bioconductor-meshdbi >=1.18.0,<1.19.0' + - 'bioconductor-meshdbi >=1.20.0,<1.21.0' - r-base run: - - 'bioconductor-meshdbi >=1.18.0,<1.19.0' + - 'bioconductor-meshdbi >=1.20.0,<1.21.0' - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-mesh.dsi.eg.db/post-link.sh b/recipes/bioconductor-mesh.dsi.eg.db/post-link.sh index d41ad8c49f28e..0c7d4784ea58c 100644 --- a/recipes/bioconductor-mesh.dsi.eg.db/post-link.sh +++ b/recipes/bioconductor-mesh.dsi.eg.db/post-link.sh @@ -1,11 +1,11 @@ #!/bin/bash -FN="MeSH.Dsi.eg.db_1.11.0.tar.gz" +FN="MeSH.Dsi.eg.db_1.12.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/MeSH.Dsi.eg.db_1.11.0.tar.gz" - "https://bioarchive.galaxyproject.org/MeSH.Dsi.eg.db_1.11.0.tar.gz" - "https://depot.galaxyproject.org/software/bioconductor-mesh.dsi.eg.db/bioconductor-mesh.dsi.eg.db_1.11.0_src_all.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/MeSH.Dsi.eg.db_1.12.0.tar.gz" + "https://bioarchive.galaxyproject.org/MeSH.Dsi.eg.db_1.12.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-mesh.dsi.eg.db/bioconductor-mesh.dsi.eg.db_1.12.0_src_all.tar.gz" ) -MD5="cf96a96c3f2f869956b7c02d68b0dbbd" +MD5="6b5be7ed0d482654995818d5a4d40acf" # Use a staging area in the conda dir rather than temp dirs, both to avoid # permission issues as well as to have things downloaded in a predictable @@ -16,7 +16,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-mesh.dvi.eg.db/meta.yaml b/recipes/bioconductor-mesh.dvi.eg.db/meta.yaml index 7972264a0f260..62866c0edb85f 100644 --- a/recipes/bioconductor-mesh.dvi.eg.db/meta.yaml +++ b/recipes/bioconductor-mesh.dvi.eg.db/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.11.0" %} +{% set version = "1.12.0" %} {% set name = "MeSH.Dvi.eg.db" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: e26b6b84d33832c1d2b19c5406bd4ddf + md5: d3ffd23cb6c89270b7919cccb922d57c build: number: 0 rpaths: @@ -20,12 +20,12 @@ build: # Suggests: RUnit, BiocGenerics requirements: host: - - 'bioconductor-meshdbi >=1.18.0,<1.19.0' + - 'bioconductor-meshdbi >=1.20.0,<1.21.0' - r-base run: - - 'bioconductor-meshdbi >=1.18.0,<1.19.0' + - 'bioconductor-meshdbi >=1.20.0,<1.21.0' - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-mesh.dvi.eg.db/post-link.sh b/recipes/bioconductor-mesh.dvi.eg.db/post-link.sh index 5b9e6e3b25459..9cfe8d0f8b04c 100644 --- a/recipes/bioconductor-mesh.dvi.eg.db/post-link.sh +++ b/recipes/bioconductor-mesh.dvi.eg.db/post-link.sh @@ -1,11 +1,11 @@ #!/bin/bash -FN="MeSH.Dvi.eg.db_1.11.0.tar.gz" +FN="MeSH.Dvi.eg.db_1.12.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/MeSH.Dvi.eg.db_1.11.0.tar.gz" - "https://bioarchive.galaxyproject.org/MeSH.Dvi.eg.db_1.11.0.tar.gz" - "https://depot.galaxyproject.org/software/bioconductor-mesh.dvi.eg.db/bioconductor-mesh.dvi.eg.db_1.11.0_src_all.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/MeSH.Dvi.eg.db_1.12.0.tar.gz" + "https://bioarchive.galaxyproject.org/MeSH.Dvi.eg.db_1.12.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-mesh.dvi.eg.db/bioconductor-mesh.dvi.eg.db_1.12.0_src_all.tar.gz" ) -MD5="e26b6b84d33832c1d2b19c5406bd4ddf" +MD5="d3ffd23cb6c89270b7919cccb922d57c" # Use a staging area in the conda dir rather than temp dirs, both to avoid # permission issues as well as to have things downloaded in a predictable @@ -16,7 +16,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-mesh.dya.eg.db/meta.yaml b/recipes/bioconductor-mesh.dya.eg.db/meta.yaml index 400868bf282ca..201d1d8d8c8fb 100644 --- a/recipes/bioconductor-mesh.dya.eg.db/meta.yaml +++ b/recipes/bioconductor-mesh.dya.eg.db/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.11.0" %} +{% set version = "1.12.0" %} {% set name = "MeSH.Dya.eg.db" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 2407944d8054f00a17cf922d7bdf58b6 + md5: a86aa0e7de6cd626aa26ce681988a7ef build: number: 0 rpaths: @@ -20,12 +20,12 @@ build: # Suggests: RUnit, BiocGenerics requirements: host: - - 'bioconductor-meshdbi >=1.18.0,<1.19.0' + - 'bioconductor-meshdbi >=1.20.0,<1.21.0' - r-base run: - - 'bioconductor-meshdbi >=1.18.0,<1.19.0' + - 'bioconductor-meshdbi >=1.20.0,<1.21.0' - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-mesh.dya.eg.db/post-link.sh b/recipes/bioconductor-mesh.dya.eg.db/post-link.sh index e929a5495a2ce..c09148f91fef2 100644 --- a/recipes/bioconductor-mesh.dya.eg.db/post-link.sh +++ b/recipes/bioconductor-mesh.dya.eg.db/post-link.sh @@ -1,11 +1,11 @@ #!/bin/bash -FN="MeSH.Dya.eg.db_1.11.0.tar.gz" +FN="MeSH.Dya.eg.db_1.12.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/MeSH.Dya.eg.db_1.11.0.tar.gz" - "https://bioarchive.galaxyproject.org/MeSH.Dya.eg.db_1.11.0.tar.gz" - "https://depot.galaxyproject.org/software/bioconductor-mesh.dya.eg.db/bioconductor-mesh.dya.eg.db_1.11.0_src_all.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/MeSH.Dya.eg.db_1.12.0.tar.gz" + "https://bioarchive.galaxyproject.org/MeSH.Dya.eg.db_1.12.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-mesh.dya.eg.db/bioconductor-mesh.dya.eg.db_1.12.0_src_all.tar.gz" ) -MD5="2407944d8054f00a17cf922d7bdf58b6" +MD5="a86aa0e7de6cd626aa26ce681988a7ef" # Use a staging area in the conda dir rather than temp dirs, both to avoid # permission issues as well as to have things downloaded in a predictable @@ -16,7 +16,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-mesh.eco.55989.eg.db/meta.yaml b/recipes/bioconductor-mesh.eco.55989.eg.db/meta.yaml index 124dfdbc9e380..f94636e0bfebe 100644 --- a/recipes/bioconductor-mesh.eco.55989.eg.db/meta.yaml +++ b/recipes/bioconductor-mesh.eco.55989.eg.db/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.11.0" %} +{% set version = "1.12.0" %} {% set name = "MeSH.Eco.55989.eg.db" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 89c5cff5ae86667b6a515f1314e28ce5 + md5: 5ce7bf538a544393e0a1f20447905f6e build: number: 0 rpaths: @@ -20,12 +20,12 @@ build: # Suggests: RUnit, BiocGenerics requirements: host: - - 'bioconductor-meshdbi >=1.18.0,<1.19.0' + - 'bioconductor-meshdbi >=1.20.0,<1.21.0' - r-base run: - - 'bioconductor-meshdbi >=1.18.0,<1.19.0' + - 'bioconductor-meshdbi >=1.20.0,<1.21.0' - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-mesh.eco.55989.eg.db/post-link.sh b/recipes/bioconductor-mesh.eco.55989.eg.db/post-link.sh index e01046dd0a460..77b3ce008da9c 100644 --- a/recipes/bioconductor-mesh.eco.55989.eg.db/post-link.sh +++ b/recipes/bioconductor-mesh.eco.55989.eg.db/post-link.sh @@ -1,11 +1,11 @@ #!/bin/bash -FN="MeSH.Eco.55989.eg.db_1.11.0.tar.gz" +FN="MeSH.Eco.55989.eg.db_1.12.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/MeSH.Eco.55989.eg.db_1.11.0.tar.gz" - "https://bioarchive.galaxyproject.org/MeSH.Eco.55989.eg.db_1.11.0.tar.gz" - "https://depot.galaxyproject.org/software/bioconductor-mesh.eco.55989.eg.db/bioconductor-mesh.eco.55989.eg.db_1.11.0_src_all.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/MeSH.Eco.55989.eg.db_1.12.0.tar.gz" + "https://bioarchive.galaxyproject.org/MeSH.Eco.55989.eg.db_1.12.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-mesh.eco.55989.eg.db/bioconductor-mesh.eco.55989.eg.db_1.12.0_src_all.tar.gz" ) -MD5="89c5cff5ae86667b6a515f1314e28ce5" +MD5="5ce7bf538a544393e0a1f20447905f6e" # Use a staging area in the conda dir rather than temp dirs, both to avoid # permission issues as well as to have things downloaded in a predictable @@ -16,7 +16,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-mesh.eco.ed1a.eg.db/meta.yaml b/recipes/bioconductor-mesh.eco.ed1a.eg.db/meta.yaml index 57426719a6ff0..5ccf0a3cea45c 100644 --- a/recipes/bioconductor-mesh.eco.ed1a.eg.db/meta.yaml +++ b/recipes/bioconductor-mesh.eco.ed1a.eg.db/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.11.0" %} +{% set version = "1.12.0" %} {% set name = "MeSH.Eco.ED1a.eg.db" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 48e7ade0744cc673ddddadbe55967ad3 + md5: 03e3d6d633bf57b80aeb866091ccebb5 build: number: 0 rpaths: @@ -20,12 +20,12 @@ build: # Suggests: RUnit, BiocGenerics requirements: host: - - 'bioconductor-meshdbi >=1.18.0,<1.19.0' + - 'bioconductor-meshdbi >=1.20.0,<1.21.0' - r-base run: - - 'bioconductor-meshdbi >=1.18.0,<1.19.0' + - 'bioconductor-meshdbi >=1.20.0,<1.21.0' - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-mesh.eco.ed1a.eg.db/post-link.sh b/recipes/bioconductor-mesh.eco.ed1a.eg.db/post-link.sh index b7ed21ec8fa08..1e38147374fa6 100644 --- a/recipes/bioconductor-mesh.eco.ed1a.eg.db/post-link.sh +++ b/recipes/bioconductor-mesh.eco.ed1a.eg.db/post-link.sh @@ -1,11 +1,11 @@ #!/bin/bash -FN="MeSH.Eco.ED1a.eg.db_1.11.0.tar.gz" +FN="MeSH.Eco.ED1a.eg.db_1.12.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/MeSH.Eco.ED1a.eg.db_1.11.0.tar.gz" - "https://bioarchive.galaxyproject.org/MeSH.Eco.ED1a.eg.db_1.11.0.tar.gz" - "https://depot.galaxyproject.org/software/bioconductor-mesh.eco.ed1a.eg.db/bioconductor-mesh.eco.ed1a.eg.db_1.11.0_src_all.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/MeSH.Eco.ED1a.eg.db_1.12.0.tar.gz" + "https://bioarchive.galaxyproject.org/MeSH.Eco.ED1a.eg.db_1.12.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-mesh.eco.ed1a.eg.db/bioconductor-mesh.eco.ed1a.eg.db_1.12.0_src_all.tar.gz" ) -MD5="48e7ade0744cc673ddddadbe55967ad3" +MD5="03e3d6d633bf57b80aeb866091ccebb5" # Use a staging area in the conda dir rather than temp dirs, both to avoid # permission issues as well as to have things downloaded in a predictable @@ -16,7 +16,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-mesh.eco.iai39.eg.db/meta.yaml b/recipes/bioconductor-mesh.eco.iai39.eg.db/meta.yaml index cf53d4024a3a0..e21485baf794d 100644 --- a/recipes/bioconductor-mesh.eco.iai39.eg.db/meta.yaml +++ b/recipes/bioconductor-mesh.eco.iai39.eg.db/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.11.0" %} +{% set version = "1.12.0" %} {% set name = "MeSH.Eco.IAI39.eg.db" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: ba2f514da060d4315d09567829a78d3a + md5: a08c7a3a0e24d574f230ccaa0fe077f2 build: number: 0 rpaths: @@ -20,12 +20,12 @@ build: # Suggests: RUnit, BiocGenerics requirements: host: - - 'bioconductor-meshdbi >=1.18.0,<1.19.0' + - 'bioconductor-meshdbi >=1.20.0,<1.21.0' - r-base run: - - 'bioconductor-meshdbi >=1.18.0,<1.19.0' + - 'bioconductor-meshdbi >=1.20.0,<1.21.0' - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-mesh.eco.iai39.eg.db/post-link.sh b/recipes/bioconductor-mesh.eco.iai39.eg.db/post-link.sh index cf1828f8f85b8..8de8c6f2bbb36 100644 --- a/recipes/bioconductor-mesh.eco.iai39.eg.db/post-link.sh +++ b/recipes/bioconductor-mesh.eco.iai39.eg.db/post-link.sh @@ -1,11 +1,11 @@ #!/bin/bash -FN="MeSH.Eco.IAI39.eg.db_1.11.0.tar.gz" +FN="MeSH.Eco.IAI39.eg.db_1.12.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/MeSH.Eco.IAI39.eg.db_1.11.0.tar.gz" - "https://bioarchive.galaxyproject.org/MeSH.Eco.IAI39.eg.db_1.11.0.tar.gz" - "https://depot.galaxyproject.org/software/bioconductor-mesh.eco.iai39.eg.db/bioconductor-mesh.eco.iai39.eg.db_1.11.0_src_all.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/MeSH.Eco.IAI39.eg.db_1.12.0.tar.gz" + "https://bioarchive.galaxyproject.org/MeSH.Eco.IAI39.eg.db_1.12.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-mesh.eco.iai39.eg.db/bioconductor-mesh.eco.iai39.eg.db_1.12.0_src_all.tar.gz" ) -MD5="ba2f514da060d4315d09567829a78d3a" +MD5="a08c7a3a0e24d574f230ccaa0fe077f2" # Use a staging area in the conda dir rather than temp dirs, both to avoid # permission issues as well as to have things downloaded in a predictable @@ -16,7 +16,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-mesh.eco.k12.mg1655.eg.db/meta.yaml b/recipes/bioconductor-mesh.eco.k12.mg1655.eg.db/meta.yaml index ddbcd76c3c021..997db9628f557 100644 --- a/recipes/bioconductor-mesh.eco.k12.mg1655.eg.db/meta.yaml +++ b/recipes/bioconductor-mesh.eco.k12.mg1655.eg.db/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.11.0" %} +{% set version = "1.12.0" %} {% set name = "MeSH.Eco.K12.MG1655.eg.db" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: d0f3c397bbe677efa0e4cfebc6e6eead + md5: 06187eebaa4970a42afc08a050e37c5b build: number: 0 rpaths: @@ -20,12 +20,12 @@ build: # Suggests: RUnit, BiocGenerics requirements: host: - - 'bioconductor-meshdbi >=1.18.0,<1.19.0' + - 'bioconductor-meshdbi >=1.20.0,<1.21.0' - r-base run: - - 'bioconductor-meshdbi >=1.18.0,<1.19.0' + - 'bioconductor-meshdbi >=1.20.0,<1.21.0' - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-mesh.eco.k12.mg1655.eg.db/post-link.sh b/recipes/bioconductor-mesh.eco.k12.mg1655.eg.db/post-link.sh index 748c583d55531..9b4d2c27653f9 100644 --- a/recipes/bioconductor-mesh.eco.k12.mg1655.eg.db/post-link.sh +++ b/recipes/bioconductor-mesh.eco.k12.mg1655.eg.db/post-link.sh @@ -1,11 +1,11 @@ #!/bin/bash -FN="MeSH.Eco.K12.MG1655.eg.db_1.11.0.tar.gz" +FN="MeSH.Eco.K12.MG1655.eg.db_1.12.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/MeSH.Eco.K12.MG1655.eg.db_1.11.0.tar.gz" - "https://bioarchive.galaxyproject.org/MeSH.Eco.K12.MG1655.eg.db_1.11.0.tar.gz" - "https://depot.galaxyproject.org/software/bioconductor-mesh.eco.k12.mg1655.eg.db/bioconductor-mesh.eco.k12.mg1655.eg.db_1.11.0_src_all.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/MeSH.Eco.K12.MG1655.eg.db_1.12.0.tar.gz" + "https://bioarchive.galaxyproject.org/MeSH.Eco.K12.MG1655.eg.db_1.12.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-mesh.eco.k12.mg1655.eg.db/bioconductor-mesh.eco.k12.mg1655.eg.db_1.12.0_src_all.tar.gz" ) -MD5="d0f3c397bbe677efa0e4cfebc6e6eead" +MD5="06187eebaa4970a42afc08a050e37c5b" # Use a staging area in the conda dir rather than temp dirs, both to avoid # permission issues as well as to have things downloaded in a predictable @@ -16,7 +16,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-mesh.eco.o157.h7.sakai.eg.db/meta.yaml b/recipes/bioconductor-mesh.eco.o157.h7.sakai.eg.db/meta.yaml index fc72de194e578..07eb576b6d4e8 100644 --- a/recipes/bioconductor-mesh.eco.o157.h7.sakai.eg.db/meta.yaml +++ b/recipes/bioconductor-mesh.eco.o157.h7.sakai.eg.db/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.11.0" %} +{% set version = "1.12.0" %} {% set name = "MeSH.Eco.O157.H7.Sakai.eg.db" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 80d4f81563edbdf16da37e6e67cd2e04 + md5: 2104ca21e2956dd186a0b15a0de27c08 build: number: 0 rpaths: @@ -20,12 +20,12 @@ build: # Suggests: RUnit, BiocGenerics requirements: host: - - 'bioconductor-meshdbi >=1.18.0,<1.19.0' + - 'bioconductor-meshdbi >=1.20.0,<1.21.0' - r-base run: - - 'bioconductor-meshdbi >=1.18.0,<1.19.0' + - 'bioconductor-meshdbi >=1.20.0,<1.21.0' - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-mesh.eco.o157.h7.sakai.eg.db/post-link.sh b/recipes/bioconductor-mesh.eco.o157.h7.sakai.eg.db/post-link.sh index 2c491a1886a71..ade1d1b09fefd 100644 --- a/recipes/bioconductor-mesh.eco.o157.h7.sakai.eg.db/post-link.sh +++ b/recipes/bioconductor-mesh.eco.o157.h7.sakai.eg.db/post-link.sh @@ -1,11 +1,11 @@ #!/bin/bash -FN="MeSH.Eco.O157.H7.Sakai.eg.db_1.11.0.tar.gz" +FN="MeSH.Eco.O157.H7.Sakai.eg.db_1.12.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/MeSH.Eco.O157.H7.Sakai.eg.db_1.11.0.tar.gz" - "https://bioarchive.galaxyproject.org/MeSH.Eco.O157.H7.Sakai.eg.db_1.11.0.tar.gz" - "https://depot.galaxyproject.org/software/bioconductor-mesh.eco.o157.h7.sakai.eg.db/bioconductor-mesh.eco.o157.h7.sakai.eg.db_1.11.0_src_all.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/MeSH.Eco.O157.H7.Sakai.eg.db_1.12.0.tar.gz" + "https://bioarchive.galaxyproject.org/MeSH.Eco.O157.H7.Sakai.eg.db_1.12.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-mesh.eco.o157.h7.sakai.eg.db/bioconductor-mesh.eco.o157.h7.sakai.eg.db_1.12.0_src_all.tar.gz" ) -MD5="80d4f81563edbdf16da37e6e67cd2e04" +MD5="2104ca21e2956dd186a0b15a0de27c08" # Use a staging area in the conda dir rather than temp dirs, both to avoid # permission issues as well as to have things downloaded in a predictable @@ -16,7 +16,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-mesh.eco.umn026.eg.db/meta.yaml b/recipes/bioconductor-mesh.eco.umn026.eg.db/meta.yaml index 9e4336987a168..e79b6c4dbc077 100644 --- a/recipes/bioconductor-mesh.eco.umn026.eg.db/meta.yaml +++ b/recipes/bioconductor-mesh.eco.umn026.eg.db/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.11.0" %} +{% set version = "1.12.0" %} {% set name = "MeSH.Eco.UMN026.eg.db" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 557a999dfe0e422cf01efd2ba9735450 + md5: 7d85896ef685ed1e603c8e3726c075c9 build: number: 0 rpaths: @@ -20,12 +20,12 @@ build: # Suggests: RUnit, BiocGenerics requirements: host: - - 'bioconductor-meshdbi >=1.18.0,<1.19.0' + - 'bioconductor-meshdbi >=1.20.0,<1.21.0' - r-base run: - - 'bioconductor-meshdbi >=1.18.0,<1.19.0' + - 'bioconductor-meshdbi >=1.20.0,<1.21.0' - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-mesh.eco.umn026.eg.db/post-link.sh b/recipes/bioconductor-mesh.eco.umn026.eg.db/post-link.sh index 62bf265f0ca51..36679f9fd4c9b 100644 --- a/recipes/bioconductor-mesh.eco.umn026.eg.db/post-link.sh +++ b/recipes/bioconductor-mesh.eco.umn026.eg.db/post-link.sh @@ -1,11 +1,11 @@ #!/bin/bash -FN="MeSH.Eco.UMN026.eg.db_1.11.0.tar.gz" +FN="MeSH.Eco.UMN026.eg.db_1.12.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/MeSH.Eco.UMN026.eg.db_1.11.0.tar.gz" - "https://bioarchive.galaxyproject.org/MeSH.Eco.UMN026.eg.db_1.11.0.tar.gz" - "https://depot.galaxyproject.org/software/bioconductor-mesh.eco.umn026.eg.db/bioconductor-mesh.eco.umn026.eg.db_1.11.0_src_all.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/MeSH.Eco.UMN026.eg.db_1.12.0.tar.gz" + "https://bioarchive.galaxyproject.org/MeSH.Eco.UMN026.eg.db_1.12.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-mesh.eco.umn026.eg.db/bioconductor-mesh.eco.umn026.eg.db_1.12.0_src_all.tar.gz" ) -MD5="557a999dfe0e422cf01efd2ba9735450" +MD5="7d85896ef685ed1e603c8e3726c075c9" # Use a staging area in the conda dir rather than temp dirs, both to avoid # permission issues as well as to have things downloaded in a predictable @@ -16,7 +16,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-mesh.eqc.eg.db/meta.yaml b/recipes/bioconductor-mesh.eqc.eg.db/meta.yaml index 844349aabc7d6..7c36d54dd22f3 100644 --- a/recipes/bioconductor-mesh.eqc.eg.db/meta.yaml +++ b/recipes/bioconductor-mesh.eqc.eg.db/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.11.0" %} +{% set version = "1.12.0" %} {% set name = "MeSH.Eqc.eg.db" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 16c88a92bc3f91d93cffed92f420f92f + md5: 93f8af406857db4cd7684fb08feaea28 build: number: 0 rpaths: @@ -20,12 +20,12 @@ build: # Suggests: RUnit, BiocGenerics requirements: host: - - 'bioconductor-meshdbi >=1.18.0,<1.19.0' + - 'bioconductor-meshdbi >=1.20.0,<1.21.0' - r-base run: - - 'bioconductor-meshdbi >=1.18.0,<1.19.0' + - 'bioconductor-meshdbi >=1.20.0,<1.21.0' - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-mesh.eqc.eg.db/post-link.sh b/recipes/bioconductor-mesh.eqc.eg.db/post-link.sh index 50a610c1890fc..1942dd1c4faeb 100644 --- a/recipes/bioconductor-mesh.eqc.eg.db/post-link.sh +++ b/recipes/bioconductor-mesh.eqc.eg.db/post-link.sh @@ -1,11 +1,11 @@ #!/bin/bash -FN="MeSH.Eqc.eg.db_1.11.0.tar.gz" +FN="MeSH.Eqc.eg.db_1.12.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/MeSH.Eqc.eg.db_1.11.0.tar.gz" - "https://bioarchive.galaxyproject.org/MeSH.Eqc.eg.db_1.11.0.tar.gz" - "https://depot.galaxyproject.org/software/bioconductor-mesh.eqc.eg.db/bioconductor-mesh.eqc.eg.db_1.11.0_src_all.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/MeSH.Eqc.eg.db_1.12.0.tar.gz" + "https://bioarchive.galaxyproject.org/MeSH.Eqc.eg.db_1.12.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-mesh.eqc.eg.db/bioconductor-mesh.eqc.eg.db_1.12.0_src_all.tar.gz" ) -MD5="16c88a92bc3f91d93cffed92f420f92f" +MD5="93f8af406857db4cd7684fb08feaea28" # Use a staging area in the conda dir rather than temp dirs, both to avoid # permission issues as well as to have things downloaded in a predictable @@ -16,7 +16,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-mesh.gga.eg.db/meta.yaml b/recipes/bioconductor-mesh.gga.eg.db/meta.yaml index 46c0d2973577f..4643196d5568c 100644 --- a/recipes/bioconductor-mesh.gga.eg.db/meta.yaml +++ b/recipes/bioconductor-mesh.gga.eg.db/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.11.0" %} +{% set version = "1.12.0" %} {% set name = "MeSH.Gga.eg.db" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 7fc1e66d6029ba8b6c615265b3ce9de0 + md5: d95eac3889b634882499ab9a341aed74 build: number: 0 rpaths: @@ -20,12 +20,12 @@ build: # Suggests: RUnit, BiocGenerics requirements: host: - - 'bioconductor-meshdbi >=1.18.0,<1.19.0' + - 'bioconductor-meshdbi >=1.20.0,<1.21.0' - r-base run: - - 'bioconductor-meshdbi >=1.18.0,<1.19.0' + - 'bioconductor-meshdbi >=1.20.0,<1.21.0' - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-mesh.gga.eg.db/post-link.sh b/recipes/bioconductor-mesh.gga.eg.db/post-link.sh index 72a6936bc1aef..17f9fb2474f4e 100644 --- a/recipes/bioconductor-mesh.gga.eg.db/post-link.sh +++ b/recipes/bioconductor-mesh.gga.eg.db/post-link.sh @@ -1,11 +1,11 @@ #!/bin/bash -FN="MeSH.Gga.eg.db_1.11.0.tar.gz" +FN="MeSH.Gga.eg.db_1.12.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/MeSH.Gga.eg.db_1.11.0.tar.gz" - "https://bioarchive.galaxyproject.org/MeSH.Gga.eg.db_1.11.0.tar.gz" - "https://depot.galaxyproject.org/software/bioconductor-mesh.gga.eg.db/bioconductor-mesh.gga.eg.db_1.11.0_src_all.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/MeSH.Gga.eg.db_1.12.0.tar.gz" + "https://bioarchive.galaxyproject.org/MeSH.Gga.eg.db_1.12.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-mesh.gga.eg.db/bioconductor-mesh.gga.eg.db_1.12.0_src_all.tar.gz" ) -MD5="7fc1e66d6029ba8b6c615265b3ce9de0" +MD5="d95eac3889b634882499ab9a341aed74" # Use a staging area in the conda dir rather than temp dirs, both to avoid # permission issues as well as to have things downloaded in a predictable @@ -16,7 +16,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-mesh.gma.eg.db/meta.yaml b/recipes/bioconductor-mesh.gma.eg.db/meta.yaml index 8e0443ec705fb..81216016094a0 100644 --- a/recipes/bioconductor-mesh.gma.eg.db/meta.yaml +++ b/recipes/bioconductor-mesh.gma.eg.db/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.11.0" %} +{% set version = "1.12.0" %} {% set name = "MeSH.Gma.eg.db" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 4ea83c4f59c36cd57129650b97902776 + md5: 2e9f6010abcbdae5138d90a6feb0b614 build: number: 0 rpaths: @@ -20,12 +20,12 @@ build: # Suggests: RUnit, BiocGenerics requirements: host: - - 'bioconductor-meshdbi >=1.18.0,<1.19.0' + - 'bioconductor-meshdbi >=1.20.0,<1.21.0' - r-base run: - - 'bioconductor-meshdbi >=1.18.0,<1.19.0' + - 'bioconductor-meshdbi >=1.20.0,<1.21.0' - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-mesh.gma.eg.db/post-link.sh b/recipes/bioconductor-mesh.gma.eg.db/post-link.sh index 58b07098ba39f..28b73eec25a2f 100644 --- a/recipes/bioconductor-mesh.gma.eg.db/post-link.sh +++ b/recipes/bioconductor-mesh.gma.eg.db/post-link.sh @@ -1,11 +1,11 @@ #!/bin/bash -FN="MeSH.Gma.eg.db_1.11.0.tar.gz" +FN="MeSH.Gma.eg.db_1.12.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/MeSH.Gma.eg.db_1.11.0.tar.gz" - "https://bioarchive.galaxyproject.org/MeSH.Gma.eg.db_1.11.0.tar.gz" - "https://depot.galaxyproject.org/software/bioconductor-mesh.gma.eg.db/bioconductor-mesh.gma.eg.db_1.11.0_src_all.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/MeSH.Gma.eg.db_1.12.0.tar.gz" + "https://bioarchive.galaxyproject.org/MeSH.Gma.eg.db_1.12.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-mesh.gma.eg.db/bioconductor-mesh.gma.eg.db_1.12.0_src_all.tar.gz" ) -MD5="4ea83c4f59c36cd57129650b97902776" +MD5="2e9f6010abcbdae5138d90a6feb0b614" # Use a staging area in the conda dir rather than temp dirs, both to avoid # permission issues as well as to have things downloaded in a predictable @@ -16,7 +16,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-mesh.hsa.eg.db/meta.yaml b/recipes/bioconductor-mesh.hsa.eg.db/meta.yaml index 77e7f4eddcebd..03e4dd87b84cf 100644 --- a/recipes/bioconductor-mesh.hsa.eg.db/meta.yaml +++ b/recipes/bioconductor-mesh.hsa.eg.db/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.11.0" %} +{% set version = "1.12.0" %} {% set name = "MeSH.Hsa.eg.db" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: ca0da5b6e8cf66b6b796fe64cf7a1a66 + md5: 6f501a99a6f8dee9d14290897f5b0051 build: number: 0 rpaths: @@ -20,12 +20,12 @@ build: # Suggests: RUnit, BiocGenerics requirements: host: - - 'bioconductor-meshdbi >=1.18.0,<1.19.0' + - 'bioconductor-meshdbi >=1.20.0,<1.21.0' - r-base run: - - 'bioconductor-meshdbi >=1.18.0,<1.19.0' + - 'bioconductor-meshdbi >=1.20.0,<1.21.0' - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-mesh.hsa.eg.db/post-link.sh b/recipes/bioconductor-mesh.hsa.eg.db/post-link.sh index b792187370f0a..2fc66c7b2c316 100644 --- a/recipes/bioconductor-mesh.hsa.eg.db/post-link.sh +++ b/recipes/bioconductor-mesh.hsa.eg.db/post-link.sh @@ -1,11 +1,11 @@ #!/bin/bash -FN="MeSH.Hsa.eg.db_1.11.0.tar.gz" +FN="MeSH.Hsa.eg.db_1.12.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/MeSH.Hsa.eg.db_1.11.0.tar.gz" - "https://bioarchive.galaxyproject.org/MeSH.Hsa.eg.db_1.11.0.tar.gz" - "https://depot.galaxyproject.org/software/bioconductor-mesh.hsa.eg.db/bioconductor-mesh.hsa.eg.db_1.11.0_src_all.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/MeSH.Hsa.eg.db_1.12.0.tar.gz" + "https://bioarchive.galaxyproject.org/MeSH.Hsa.eg.db_1.12.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-mesh.hsa.eg.db/bioconductor-mesh.hsa.eg.db_1.12.0_src_all.tar.gz" ) -MD5="ca0da5b6e8cf66b6b796fe64cf7a1a66" +MD5="6f501a99a6f8dee9d14290897f5b0051" # Use a staging area in the conda dir rather than temp dirs, both to avoid # permission issues as well as to have things downloaded in a predictable @@ -16,7 +16,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-mesh.laf.eg.db/meta.yaml b/recipes/bioconductor-mesh.laf.eg.db/meta.yaml index 71356d030401e..0b57e3a87addf 100644 --- a/recipes/bioconductor-mesh.laf.eg.db/meta.yaml +++ b/recipes/bioconductor-mesh.laf.eg.db/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.11.0" %} +{% set version = "1.12.0" %} {% set name = "MeSH.Laf.eg.db" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 9fd4415f7d81a0158923d6e9bb582dd8 + md5: 309db1c0bfabafdf67dd7d8bd923a4bb build: number: 0 rpaths: @@ -20,12 +20,12 @@ build: # Suggests: RUnit, BiocGenerics requirements: host: - - 'bioconductor-meshdbi >=1.18.0,<1.19.0' + - 'bioconductor-meshdbi >=1.20.0,<1.21.0' - r-base run: - - 'bioconductor-meshdbi >=1.18.0,<1.19.0' + - 'bioconductor-meshdbi >=1.20.0,<1.21.0' - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-mesh.laf.eg.db/post-link.sh b/recipes/bioconductor-mesh.laf.eg.db/post-link.sh index 571ef095c7502..017c32f0f8ef6 100644 --- a/recipes/bioconductor-mesh.laf.eg.db/post-link.sh +++ b/recipes/bioconductor-mesh.laf.eg.db/post-link.sh @@ -1,11 +1,11 @@ #!/bin/bash -FN="MeSH.Laf.eg.db_1.11.0.tar.gz" +FN="MeSH.Laf.eg.db_1.12.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/MeSH.Laf.eg.db_1.11.0.tar.gz" - "https://bioarchive.galaxyproject.org/MeSH.Laf.eg.db_1.11.0.tar.gz" - "https://depot.galaxyproject.org/software/bioconductor-mesh.laf.eg.db/bioconductor-mesh.laf.eg.db_1.11.0_src_all.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/MeSH.Laf.eg.db_1.12.0.tar.gz" + "https://bioarchive.galaxyproject.org/MeSH.Laf.eg.db_1.12.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-mesh.laf.eg.db/bioconductor-mesh.laf.eg.db_1.12.0_src_all.tar.gz" ) -MD5="9fd4415f7d81a0158923d6e9bb582dd8" +MD5="309db1c0bfabafdf67dd7d8bd923a4bb" # Use a staging area in the conda dir rather than temp dirs, both to avoid # permission issues as well as to have things downloaded in a predictable @@ -16,7 +16,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-mesh.lma.eg.db/meta.yaml b/recipes/bioconductor-mesh.lma.eg.db/meta.yaml index c33087f91d482..58f68dbb96e63 100644 --- a/recipes/bioconductor-mesh.lma.eg.db/meta.yaml +++ b/recipes/bioconductor-mesh.lma.eg.db/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.11.0" %} +{% set version = "1.12.0" %} {% set name = "MeSH.Lma.eg.db" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,9 +10,9 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 196be5e739ac7537272bc5511196cd4b + md5: 721401ba48afbb7607bbeed319201dd6 build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ @@ -20,12 +20,12 @@ build: # Suggests: RUnit, BiocGenerics requirements: host: - - 'bioconductor-meshdbi >=1.18.0,<1.19.0' + - 'bioconductor-meshdbi >=1.20.0,<1.21.0' - r-base run: - - 'bioconductor-meshdbi >=1.18.0,<1.19.0' + - 'bioconductor-meshdbi >=1.20.0,<1.21.0' - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-mesh.lma.eg.db/post-link.sh b/recipes/bioconductor-mesh.lma.eg.db/post-link.sh index d0410e9ce4c99..5745becf14692 100644 --- a/recipes/bioconductor-mesh.lma.eg.db/post-link.sh +++ b/recipes/bioconductor-mesh.lma.eg.db/post-link.sh @@ -1,11 +1,11 @@ #!/bin/bash -FN="MeSH.Lma.eg.db_1.11.0.tar.gz" +FN="MeSH.Lma.eg.db_1.12.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/MeSH.Lma.eg.db_1.11.0.tar.gz" - "https://bioarchive.galaxyproject.org/MeSH.Lma.eg.db_1.11.0.tar.gz" - "https://depot.galaxyproject.org/software/bioconductor-mesh.lma.eg.db/bioconductor-mesh.lma.eg.db_1.11.0_src_all.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/MeSH.Lma.eg.db_1.12.0.tar.gz" + "https://bioarchive.galaxyproject.org/MeSH.Lma.eg.db_1.12.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-mesh.lma.eg.db/bioconductor-mesh.lma.eg.db_1.12.0_src_all.tar.gz" ) -MD5="196be5e739ac7537272bc5511196cd4b" +MD5="721401ba48afbb7607bbeed319201dd6" # Use a staging area in the conda dir rather than temp dirs, both to avoid # permission issues as well as to have things downloaded in a predictable @@ -16,7 +16,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-mesh.mdo.eg.db/meta.yaml b/recipes/bioconductor-mesh.mdo.eg.db/meta.yaml index 4d47db6aeb4fd..5ee59098226e9 100644 --- a/recipes/bioconductor-mesh.mdo.eg.db/meta.yaml +++ b/recipes/bioconductor-mesh.mdo.eg.db/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.11.0" %} +{% set version = "1.12.0" %} {% set name = "MeSH.Mdo.eg.db" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,9 +10,9 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: ac78f04e3d382e622e8f711b304299d5 + md5: 56deff651c2d15ec96a0afc329ab6bb1 build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ @@ -20,12 +20,12 @@ build: # Suggests: RUnit, BiocGenerics requirements: host: - - 'bioconductor-meshdbi >=1.18.0,<1.19.0' + - 'bioconductor-meshdbi >=1.20.0,<1.21.0' - r-base run: - - 'bioconductor-meshdbi >=1.18.0,<1.19.0' + - 'bioconductor-meshdbi >=1.20.0,<1.21.0' - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-mesh.mdo.eg.db/post-link.sh b/recipes/bioconductor-mesh.mdo.eg.db/post-link.sh index 29f65c5c8529e..28ac959f35f28 100644 --- a/recipes/bioconductor-mesh.mdo.eg.db/post-link.sh +++ b/recipes/bioconductor-mesh.mdo.eg.db/post-link.sh @@ -1,11 +1,11 @@ #!/bin/bash -FN="MeSH.Mdo.eg.db_1.11.0.tar.gz" +FN="MeSH.Mdo.eg.db_1.12.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/MeSH.Mdo.eg.db_1.11.0.tar.gz" - "https://bioarchive.galaxyproject.org/MeSH.Mdo.eg.db_1.11.0.tar.gz" - "https://depot.galaxyproject.org/software/bioconductor-mesh.mdo.eg.db/bioconductor-mesh.mdo.eg.db_1.11.0_src_all.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/MeSH.Mdo.eg.db_1.12.0.tar.gz" + "https://bioarchive.galaxyproject.org/MeSH.Mdo.eg.db_1.12.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-mesh.mdo.eg.db/bioconductor-mesh.mdo.eg.db_1.12.0_src_all.tar.gz" ) -MD5="ac78f04e3d382e622e8f711b304299d5" +MD5="56deff651c2d15ec96a0afc329ab6bb1" # Use a staging area in the conda dir rather than temp dirs, both to avoid # permission issues as well as to have things downloaded in a predictable @@ -16,7 +16,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-mesh.mes.eg.db/meta.yaml b/recipes/bioconductor-mesh.mes.eg.db/meta.yaml index 5f8611e8af930..562c38a788bec 100644 --- a/recipes/bioconductor-mesh.mes.eg.db/meta.yaml +++ b/recipes/bioconductor-mesh.mes.eg.db/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.11.0" %} +{% set version = "1.12.0" %} {% set name = "MeSH.Mes.eg.db" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 79ddb75c5d270505271411f89ac3a5d2 + md5: 4c65242716fb7aa5d5968a2d91307530 build: number: 0 rpaths: @@ -20,12 +20,12 @@ build: # Suggests: RUnit, BiocGenerics requirements: host: - - 'bioconductor-meshdbi >=1.18.0,<1.19.0' + - 'bioconductor-meshdbi >=1.20.0,<1.21.0' - r-base run: - - 'bioconductor-meshdbi >=1.18.0,<1.19.0' + - 'bioconductor-meshdbi >=1.20.0,<1.21.0' - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-mesh.mes.eg.db/post-link.sh b/recipes/bioconductor-mesh.mes.eg.db/post-link.sh index ab4440cea524f..506320d5e1439 100644 --- a/recipes/bioconductor-mesh.mes.eg.db/post-link.sh +++ b/recipes/bioconductor-mesh.mes.eg.db/post-link.sh @@ -1,11 +1,11 @@ #!/bin/bash -FN="MeSH.Mes.eg.db_1.11.0.tar.gz" +FN="MeSH.Mes.eg.db_1.12.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/MeSH.Mes.eg.db_1.11.0.tar.gz" - "https://bioarchive.galaxyproject.org/MeSH.Mes.eg.db_1.11.0.tar.gz" - "https://depot.galaxyproject.org/software/bioconductor-mesh.mes.eg.db/bioconductor-mesh.mes.eg.db_1.11.0_src_all.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/MeSH.Mes.eg.db_1.12.0.tar.gz" + "https://bioarchive.galaxyproject.org/MeSH.Mes.eg.db_1.12.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-mesh.mes.eg.db/bioconductor-mesh.mes.eg.db_1.12.0_src_all.tar.gz" ) -MD5="79ddb75c5d270505271411f89ac3a5d2" +MD5="4c65242716fb7aa5d5968a2d91307530" # Use a staging area in the conda dir rather than temp dirs, both to avoid # permission issues as well as to have things downloaded in a predictable @@ -16,7 +16,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-mesh.mga.eg.db/meta.yaml b/recipes/bioconductor-mesh.mga.eg.db/meta.yaml index 1acb7a9a9db26..99ac004e755f6 100644 --- a/recipes/bioconductor-mesh.mga.eg.db/meta.yaml +++ b/recipes/bioconductor-mesh.mga.eg.db/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.11.0" %} +{% set version = "1.12.0" %} {% set name = "MeSH.Mga.eg.db" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 8052f93acc2adbec71a2759e41302b73 + md5: 659315d8b301c67a59412bd4f0727f1b build: number: 0 rpaths: @@ -20,12 +20,12 @@ build: # Suggests: RUnit, BiocGenerics requirements: host: - - 'bioconductor-meshdbi >=1.18.0,<1.19.0' + - 'bioconductor-meshdbi >=1.20.0,<1.21.0' - r-base run: - - 'bioconductor-meshdbi >=1.18.0,<1.19.0' + - 'bioconductor-meshdbi >=1.20.0,<1.21.0' - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-mesh.mga.eg.db/post-link.sh b/recipes/bioconductor-mesh.mga.eg.db/post-link.sh index 3b37019c1a3be..cfd15b3b6a3aa 100644 --- a/recipes/bioconductor-mesh.mga.eg.db/post-link.sh +++ b/recipes/bioconductor-mesh.mga.eg.db/post-link.sh @@ -1,11 +1,11 @@ #!/bin/bash -FN="MeSH.Mga.eg.db_1.11.0.tar.gz" +FN="MeSH.Mga.eg.db_1.12.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/MeSH.Mga.eg.db_1.11.0.tar.gz" - "https://bioarchive.galaxyproject.org/MeSH.Mga.eg.db_1.11.0.tar.gz" - "https://depot.galaxyproject.org/software/bioconductor-mesh.mga.eg.db/bioconductor-mesh.mga.eg.db_1.11.0_src_all.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/MeSH.Mga.eg.db_1.12.0.tar.gz" + "https://bioarchive.galaxyproject.org/MeSH.Mga.eg.db_1.12.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-mesh.mga.eg.db/bioconductor-mesh.mga.eg.db_1.12.0_src_all.tar.gz" ) -MD5="8052f93acc2adbec71a2759e41302b73" +MD5="659315d8b301c67a59412bd4f0727f1b" # Use a staging area in the conda dir rather than temp dirs, both to avoid # permission issues as well as to have things downloaded in a predictable @@ -16,7 +16,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-mesh.miy.eg.db/meta.yaml b/recipes/bioconductor-mesh.miy.eg.db/meta.yaml index 09245ee79d01d..a2534683b718c 100644 --- a/recipes/bioconductor-mesh.miy.eg.db/meta.yaml +++ b/recipes/bioconductor-mesh.miy.eg.db/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.11.0" %} +{% set version = "1.12.0" %} {% set name = "MeSH.Miy.eg.db" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 0940dec688bc7d05a45d4167affb05cc + md5: 522b6f0a257ff520c419c8d22969502c build: number: 0 rpaths: @@ -20,12 +20,12 @@ build: # Suggests: RUnit, BiocGenerics requirements: host: - - 'bioconductor-meshdbi >=1.18.0,<1.19.0' + - 'bioconductor-meshdbi >=1.20.0,<1.21.0' - r-base run: - - 'bioconductor-meshdbi >=1.18.0,<1.19.0' + - 'bioconductor-meshdbi >=1.20.0,<1.21.0' - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-mesh.miy.eg.db/post-link.sh b/recipes/bioconductor-mesh.miy.eg.db/post-link.sh index fefc147e71087..3c5c032c13eba 100644 --- a/recipes/bioconductor-mesh.miy.eg.db/post-link.sh +++ b/recipes/bioconductor-mesh.miy.eg.db/post-link.sh @@ -1,11 +1,11 @@ #!/bin/bash -FN="MeSH.Miy.eg.db_1.11.0.tar.gz" +FN="MeSH.Miy.eg.db_1.12.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/MeSH.Miy.eg.db_1.11.0.tar.gz" - "https://bioarchive.galaxyproject.org/MeSH.Miy.eg.db_1.11.0.tar.gz" - "https://depot.galaxyproject.org/software/bioconductor-mesh.miy.eg.db/bioconductor-mesh.miy.eg.db_1.11.0_src_all.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/MeSH.Miy.eg.db_1.12.0.tar.gz" + "https://bioarchive.galaxyproject.org/MeSH.Miy.eg.db_1.12.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-mesh.miy.eg.db/bioconductor-mesh.miy.eg.db_1.12.0_src_all.tar.gz" ) -MD5="0940dec688bc7d05a45d4167affb05cc" +MD5="522b6f0a257ff520c419c8d22969502c" # Use a staging area in the conda dir rather than temp dirs, both to avoid # permission issues as well as to have things downloaded in a predictable @@ -16,7 +16,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-mesh.mml.eg.db/meta.yaml b/recipes/bioconductor-mesh.mml.eg.db/meta.yaml index 66ac8e55f5f3d..3b188a2ddfa04 100644 --- a/recipes/bioconductor-mesh.mml.eg.db/meta.yaml +++ b/recipes/bioconductor-mesh.mml.eg.db/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.11.0" %} +{% set version = "1.12.0" %} {% set name = "MeSH.Mml.eg.db" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: ace49003b51dac2903cd6d52984a69f7 + md5: a7cd43e9541c7b836118358b9165cbf5 build: number: 0 rpaths: @@ -20,12 +20,12 @@ build: # Suggests: RUnit, BiocGenerics requirements: host: - - 'bioconductor-meshdbi >=1.18.0,<1.19.0' + - 'bioconductor-meshdbi >=1.20.0,<1.21.0' - r-base run: - - 'bioconductor-meshdbi >=1.18.0,<1.19.0' + - 'bioconductor-meshdbi >=1.20.0,<1.21.0' - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-mesh.mml.eg.db/post-link.sh b/recipes/bioconductor-mesh.mml.eg.db/post-link.sh index 940ede69a52c7..ad9d21d3939fe 100644 --- a/recipes/bioconductor-mesh.mml.eg.db/post-link.sh +++ b/recipes/bioconductor-mesh.mml.eg.db/post-link.sh @@ -1,11 +1,11 @@ #!/bin/bash -FN="MeSH.Mml.eg.db_1.11.0.tar.gz" +FN="MeSH.Mml.eg.db_1.12.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/MeSH.Mml.eg.db_1.11.0.tar.gz" - "https://bioarchive.galaxyproject.org/MeSH.Mml.eg.db_1.11.0.tar.gz" - "https://depot.galaxyproject.org/software/bioconductor-mesh.mml.eg.db/bioconductor-mesh.mml.eg.db_1.11.0_src_all.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/MeSH.Mml.eg.db_1.12.0.tar.gz" + "https://bioarchive.galaxyproject.org/MeSH.Mml.eg.db_1.12.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-mesh.mml.eg.db/bioconductor-mesh.mml.eg.db_1.12.0_src_all.tar.gz" ) -MD5="ace49003b51dac2903cd6d52984a69f7" +MD5="a7cd43e9541c7b836118358b9165cbf5" # Use a staging area in the conda dir rather than temp dirs, both to avoid # permission issues as well as to have things downloaded in a predictable @@ -16,7 +16,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-mesh.mmu.eg.db/meta.yaml b/recipes/bioconductor-mesh.mmu.eg.db/meta.yaml index 80cd8cd7bf874..2385d27741fe5 100644 --- a/recipes/bioconductor-mesh.mmu.eg.db/meta.yaml +++ b/recipes/bioconductor-mesh.mmu.eg.db/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.11.0" %} +{% set version = "1.12.0" %} {% set name = "MeSH.Mmu.eg.db" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: da945297c55815c252c935f913564dd9 + md5: 6a74e15d6f326ea1a59a9ac8dc40a35f build: number: 0 rpaths: @@ -20,12 +20,12 @@ build: # Suggests: RUnit, BiocGenerics requirements: host: - - 'bioconductor-meshdbi >=1.18.0,<1.19.0' + - 'bioconductor-meshdbi >=1.20.0,<1.21.0' - r-base run: - - 'bioconductor-meshdbi >=1.18.0,<1.19.0' + - 'bioconductor-meshdbi >=1.20.0,<1.21.0' - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-mesh.mmu.eg.db/post-link.sh b/recipes/bioconductor-mesh.mmu.eg.db/post-link.sh index 290e8b73b4b05..c9f1682a39912 100644 --- a/recipes/bioconductor-mesh.mmu.eg.db/post-link.sh +++ b/recipes/bioconductor-mesh.mmu.eg.db/post-link.sh @@ -1,11 +1,11 @@ #!/bin/bash -FN="MeSH.Mmu.eg.db_1.11.0.tar.gz" +FN="MeSH.Mmu.eg.db_1.12.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/MeSH.Mmu.eg.db_1.11.0.tar.gz" - "https://bioarchive.galaxyproject.org/MeSH.Mmu.eg.db_1.11.0.tar.gz" - "https://depot.galaxyproject.org/software/bioconductor-mesh.mmu.eg.db/bioconductor-mesh.mmu.eg.db_1.11.0_src_all.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/MeSH.Mmu.eg.db_1.12.0.tar.gz" + "https://bioarchive.galaxyproject.org/MeSH.Mmu.eg.db_1.12.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-mesh.mmu.eg.db/bioconductor-mesh.mmu.eg.db_1.12.0_src_all.tar.gz" ) -MD5="da945297c55815c252c935f913564dd9" +MD5="6a74e15d6f326ea1a59a9ac8dc40a35f" # Use a staging area in the conda dir rather than temp dirs, both to avoid # permission issues as well as to have things downloaded in a predictable @@ -16,7 +16,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-mesh.mtr.eg.db/meta.yaml b/recipes/bioconductor-mesh.mtr.eg.db/meta.yaml index 836882486dc0c..5608cb449b8f3 100644 --- a/recipes/bioconductor-mesh.mtr.eg.db/meta.yaml +++ b/recipes/bioconductor-mesh.mtr.eg.db/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.11.0" %} +{% set version = "1.12.0" %} {% set name = "MeSH.Mtr.eg.db" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: c255db3b10a80bab983401965723419e + md5: daf79961fe978d2b48c13dc3a3ba6725 build: number: 0 rpaths: @@ -20,12 +20,12 @@ build: # Suggests: RUnit, BiocGenerics requirements: host: - - 'bioconductor-meshdbi >=1.18.0,<1.19.0' + - 'bioconductor-meshdbi >=1.20.0,<1.21.0' - r-base run: - - 'bioconductor-meshdbi >=1.18.0,<1.19.0' + - 'bioconductor-meshdbi >=1.20.0,<1.21.0' - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-mesh.mtr.eg.db/post-link.sh b/recipes/bioconductor-mesh.mtr.eg.db/post-link.sh index 31805e0c1ae72..94fec3430d0a9 100644 --- a/recipes/bioconductor-mesh.mtr.eg.db/post-link.sh +++ b/recipes/bioconductor-mesh.mtr.eg.db/post-link.sh @@ -1,11 +1,11 @@ #!/bin/bash -FN="MeSH.Mtr.eg.db_1.11.0.tar.gz" +FN="MeSH.Mtr.eg.db_1.12.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/MeSH.Mtr.eg.db_1.11.0.tar.gz" - "https://bioarchive.galaxyproject.org/MeSH.Mtr.eg.db_1.11.0.tar.gz" - "https://depot.galaxyproject.org/software/bioconductor-mesh.mtr.eg.db/bioconductor-mesh.mtr.eg.db_1.11.0_src_all.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/MeSH.Mtr.eg.db_1.12.0.tar.gz" + "https://bioarchive.galaxyproject.org/MeSH.Mtr.eg.db_1.12.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-mesh.mtr.eg.db/bioconductor-mesh.mtr.eg.db_1.12.0_src_all.tar.gz" ) -MD5="c255db3b10a80bab983401965723419e" +MD5="daf79961fe978d2b48c13dc3a3ba6725" # Use a staging area in the conda dir rather than temp dirs, both to avoid # permission issues as well as to have things downloaded in a predictable @@ -16,7 +16,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-mesh.nle.eg.db/meta.yaml b/recipes/bioconductor-mesh.nle.eg.db/meta.yaml index 213f2d3d1eef0..149ee06f76436 100644 --- a/recipes/bioconductor-mesh.nle.eg.db/meta.yaml +++ b/recipes/bioconductor-mesh.nle.eg.db/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.11.0" %} +{% set version = "1.12.0" %} {% set name = "MeSH.Nle.eg.db" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,9 +10,9 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 27b9882d18e1a078f65a58fba142dbcb + md5: 669f9d933f499d2ef95d14c1e35e6d60 build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ @@ -20,12 +20,12 @@ build: # Suggests: RUnit, BiocGenerics requirements: host: - - 'bioconductor-meshdbi >=1.18.0,<1.19.0' + - 'bioconductor-meshdbi >=1.20.0,<1.21.0' - r-base run: - - 'bioconductor-meshdbi >=1.18.0,<1.19.0' + - 'bioconductor-meshdbi >=1.20.0,<1.21.0' - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-mesh.nle.eg.db/post-link.sh b/recipes/bioconductor-mesh.nle.eg.db/post-link.sh index b32c327324c98..0f56e73b5b9bc 100644 --- a/recipes/bioconductor-mesh.nle.eg.db/post-link.sh +++ b/recipes/bioconductor-mesh.nle.eg.db/post-link.sh @@ -1,11 +1,11 @@ #!/bin/bash -FN="MeSH.Nle.eg.db_1.11.0.tar.gz" +FN="MeSH.Nle.eg.db_1.12.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/MeSH.Nle.eg.db_1.11.0.tar.gz" - "https://bioarchive.galaxyproject.org/MeSH.Nle.eg.db_1.11.0.tar.gz" - "https://depot.galaxyproject.org/software/bioconductor-mesh.nle.eg.db/bioconductor-mesh.nle.eg.db_1.11.0_src_all.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/MeSH.Nle.eg.db_1.12.0.tar.gz" + "https://bioarchive.galaxyproject.org/MeSH.Nle.eg.db_1.12.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-mesh.nle.eg.db/bioconductor-mesh.nle.eg.db_1.12.0_src_all.tar.gz" ) -MD5="27b9882d18e1a078f65a58fba142dbcb" +MD5="669f9d933f499d2ef95d14c1e35e6d60" # Use a staging area in the conda dir rather than temp dirs, both to avoid # permission issues as well as to have things downloaded in a predictable @@ -16,7 +16,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-mesh.oan.eg.db/meta.yaml b/recipes/bioconductor-mesh.oan.eg.db/meta.yaml index 79c208b902a01..7ce69c9f444e4 100644 --- a/recipes/bioconductor-mesh.oan.eg.db/meta.yaml +++ b/recipes/bioconductor-mesh.oan.eg.db/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.11.0" %} +{% set version = "1.12.0" %} {% set name = "MeSH.Oan.eg.db" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 18dbb385493d99c5b1b61e297afca5bc + md5: ecec08fc3217a3115b90b7ee25542181 build: number: 0 rpaths: @@ -20,12 +20,12 @@ build: # Suggests: RUnit, BiocGenerics requirements: host: - - 'bioconductor-meshdbi >=1.18.0,<1.19.0' + - 'bioconductor-meshdbi >=1.20.0,<1.21.0' - r-base run: - - 'bioconductor-meshdbi >=1.18.0,<1.19.0' + - 'bioconductor-meshdbi >=1.20.0,<1.21.0' - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-mesh.oan.eg.db/post-link.sh b/recipes/bioconductor-mesh.oan.eg.db/post-link.sh index 93745716a0a40..47030913c9da5 100644 --- a/recipes/bioconductor-mesh.oan.eg.db/post-link.sh +++ b/recipes/bioconductor-mesh.oan.eg.db/post-link.sh @@ -1,11 +1,11 @@ #!/bin/bash -FN="MeSH.Oan.eg.db_1.11.0.tar.gz" +FN="MeSH.Oan.eg.db_1.12.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/MeSH.Oan.eg.db_1.11.0.tar.gz" - "https://bioarchive.galaxyproject.org/MeSH.Oan.eg.db_1.11.0.tar.gz" - "https://depot.galaxyproject.org/software/bioconductor-mesh.oan.eg.db/bioconductor-mesh.oan.eg.db_1.11.0_src_all.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/MeSH.Oan.eg.db_1.12.0.tar.gz" + "https://bioarchive.galaxyproject.org/MeSH.Oan.eg.db_1.12.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-mesh.oan.eg.db/bioconductor-mesh.oan.eg.db_1.12.0_src_all.tar.gz" ) -MD5="18dbb385493d99c5b1b61e297afca5bc" +MD5="ecec08fc3217a3115b90b7ee25542181" # Use a staging area in the conda dir rather than temp dirs, both to avoid # permission issues as well as to have things downloaded in a predictable @@ -16,7 +16,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-mesh.ocu.eg.db/meta.yaml b/recipes/bioconductor-mesh.ocu.eg.db/meta.yaml index 0c00407b09bfa..d59b5a5ecf1d4 100644 --- a/recipes/bioconductor-mesh.ocu.eg.db/meta.yaml +++ b/recipes/bioconductor-mesh.ocu.eg.db/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.11.0" %} +{% set version = "1.12.0" %} {% set name = "MeSH.Ocu.eg.db" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 3c01c62fe2154b4bde7f261f6d549206 + md5: dde3bb54635e7d29ce36442f765a4a4e build: number: 0 rpaths: @@ -20,12 +20,12 @@ build: # Suggests: RUnit, BiocGenerics requirements: host: - - 'bioconductor-meshdbi >=1.18.0,<1.19.0' + - 'bioconductor-meshdbi >=1.20.0,<1.21.0' - r-base run: - - 'bioconductor-meshdbi >=1.18.0,<1.19.0' + - 'bioconductor-meshdbi >=1.20.0,<1.21.0' - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-mesh.ocu.eg.db/post-link.sh b/recipes/bioconductor-mesh.ocu.eg.db/post-link.sh index 93ceb0f56a9b1..4f263f58b5746 100644 --- a/recipes/bioconductor-mesh.ocu.eg.db/post-link.sh +++ b/recipes/bioconductor-mesh.ocu.eg.db/post-link.sh @@ -1,11 +1,11 @@ #!/bin/bash -FN="MeSH.Ocu.eg.db_1.11.0.tar.gz" +FN="MeSH.Ocu.eg.db_1.12.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/MeSH.Ocu.eg.db_1.11.0.tar.gz" - "https://bioarchive.galaxyproject.org/MeSH.Ocu.eg.db_1.11.0.tar.gz" - "https://depot.galaxyproject.org/software/bioconductor-mesh.ocu.eg.db/bioconductor-mesh.ocu.eg.db_1.11.0_src_all.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/MeSH.Ocu.eg.db_1.12.0.tar.gz" + "https://bioarchive.galaxyproject.org/MeSH.Ocu.eg.db_1.12.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-mesh.ocu.eg.db/bioconductor-mesh.ocu.eg.db_1.12.0_src_all.tar.gz" ) -MD5="3c01c62fe2154b4bde7f261f6d549206" +MD5="dde3bb54635e7d29ce36442f765a4a4e" # Use a staging area in the conda dir rather than temp dirs, both to avoid # permission issues as well as to have things downloaded in a predictable @@ -16,7 +16,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-mesh.oni.eg.db/meta.yaml b/recipes/bioconductor-mesh.oni.eg.db/meta.yaml index 2457b38b61b06..2e8df1d3531fd 100644 --- a/recipes/bioconductor-mesh.oni.eg.db/meta.yaml +++ b/recipes/bioconductor-mesh.oni.eg.db/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.11.0" %} +{% set version = "1.12.0" %} {% set name = "MeSH.Oni.eg.db" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 4ffafa6e1d30aef16245f01cffaea20a + md5: 1e60d2f6c0db960a61acac0edc115165 build: number: 0 rpaths: @@ -20,12 +20,12 @@ build: # Suggests: RUnit, BiocGenerics requirements: host: - - 'bioconductor-meshdbi >=1.18.0,<1.19.0' + - 'bioconductor-meshdbi >=1.20.0,<1.21.0' - r-base run: - - 'bioconductor-meshdbi >=1.18.0,<1.19.0' + - 'bioconductor-meshdbi >=1.20.0,<1.21.0' - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-mesh.oni.eg.db/post-link.sh b/recipes/bioconductor-mesh.oni.eg.db/post-link.sh index 550d51b2c0f9d..13a88b38ae19f 100644 --- a/recipes/bioconductor-mesh.oni.eg.db/post-link.sh +++ b/recipes/bioconductor-mesh.oni.eg.db/post-link.sh @@ -1,11 +1,11 @@ #!/bin/bash -FN="MeSH.Oni.eg.db_1.11.0.tar.gz" +FN="MeSH.Oni.eg.db_1.12.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/MeSH.Oni.eg.db_1.11.0.tar.gz" - "https://bioarchive.galaxyproject.org/MeSH.Oni.eg.db_1.11.0.tar.gz" - "https://depot.galaxyproject.org/software/bioconductor-mesh.oni.eg.db/bioconductor-mesh.oni.eg.db_1.11.0_src_all.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/MeSH.Oni.eg.db_1.12.0.tar.gz" + "https://bioarchive.galaxyproject.org/MeSH.Oni.eg.db_1.12.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-mesh.oni.eg.db/bioconductor-mesh.oni.eg.db_1.12.0_src_all.tar.gz" ) -MD5="4ffafa6e1d30aef16245f01cffaea20a" +MD5="1e60d2f6c0db960a61acac0edc115165" # Use a staging area in the conda dir rather than temp dirs, both to avoid # permission issues as well as to have things downloaded in a predictable @@ -16,7 +16,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-mesh.osa.eg.db/meta.yaml b/recipes/bioconductor-mesh.osa.eg.db/meta.yaml index d954655f64d7a..7f2d8127d20df 100644 --- a/recipes/bioconductor-mesh.osa.eg.db/meta.yaml +++ b/recipes/bioconductor-mesh.osa.eg.db/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.11.0" %} +{% set version = "1.12.0" %} {% set name = "MeSH.Osa.eg.db" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 89027273281c37a56cb0c53123c3ac86 + md5: 8b4f81cd17b23186cedd32cc171a0317 build: number: 0 rpaths: @@ -20,12 +20,12 @@ build: # Suggests: RUnit, BiocGenerics requirements: host: - - 'bioconductor-meshdbi >=1.18.0,<1.19.0' + - 'bioconductor-meshdbi >=1.20.0,<1.21.0' - r-base run: - - 'bioconductor-meshdbi >=1.18.0,<1.19.0' + - 'bioconductor-meshdbi >=1.20.0,<1.21.0' - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-mesh.osa.eg.db/post-link.sh b/recipes/bioconductor-mesh.osa.eg.db/post-link.sh index cd83fb298e6f8..7872ccc3324bf 100644 --- a/recipes/bioconductor-mesh.osa.eg.db/post-link.sh +++ b/recipes/bioconductor-mesh.osa.eg.db/post-link.sh @@ -1,11 +1,11 @@ #!/bin/bash -FN="MeSH.Osa.eg.db_1.11.0.tar.gz" +FN="MeSH.Osa.eg.db_1.12.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/MeSH.Osa.eg.db_1.11.0.tar.gz" - "https://bioarchive.galaxyproject.org/MeSH.Osa.eg.db_1.11.0.tar.gz" - "https://depot.galaxyproject.org/software/bioconductor-mesh.osa.eg.db/bioconductor-mesh.osa.eg.db_1.11.0_src_all.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/MeSH.Osa.eg.db_1.12.0.tar.gz" + "https://bioarchive.galaxyproject.org/MeSH.Osa.eg.db_1.12.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-mesh.osa.eg.db/bioconductor-mesh.osa.eg.db_1.12.0_src_all.tar.gz" ) -MD5="89027273281c37a56cb0c53123c3ac86" +MD5="8b4f81cd17b23186cedd32cc171a0317" # Use a staging area in the conda dir rather than temp dirs, both to avoid # permission issues as well as to have things downloaded in a predictable @@ -16,7 +16,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-mesh.pab.eg.db/meta.yaml b/recipes/bioconductor-mesh.pab.eg.db/meta.yaml index f0f2856ea527e..10e9b87641137 100644 --- a/recipes/bioconductor-mesh.pab.eg.db/meta.yaml +++ b/recipes/bioconductor-mesh.pab.eg.db/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.11.0" %} +{% set version = "1.12.0" %} {% set name = "MeSH.Pab.eg.db" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,9 +10,9 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: b156e5aab93facda91f391d174968450 + md5: 05e1649d5a99c21de690b75f52217bce build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ @@ -20,12 +20,12 @@ build: # Suggests: RUnit, BiocGenerics requirements: host: - - 'bioconductor-meshdbi >=1.18.0,<1.19.0' + - 'bioconductor-meshdbi >=1.20.0,<1.21.0' - r-base run: - - 'bioconductor-meshdbi >=1.18.0,<1.19.0' + - 'bioconductor-meshdbi >=1.20.0,<1.21.0' - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-mesh.pab.eg.db/post-link.sh b/recipes/bioconductor-mesh.pab.eg.db/post-link.sh index 1c810c130327d..35fa62b1b38ec 100644 --- a/recipes/bioconductor-mesh.pab.eg.db/post-link.sh +++ b/recipes/bioconductor-mesh.pab.eg.db/post-link.sh @@ -1,11 +1,11 @@ #!/bin/bash -FN="MeSH.Pab.eg.db_1.11.0.tar.gz" +FN="MeSH.Pab.eg.db_1.12.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/MeSH.Pab.eg.db_1.11.0.tar.gz" - "https://bioarchive.galaxyproject.org/MeSH.Pab.eg.db_1.11.0.tar.gz" - "https://depot.galaxyproject.org/software/bioconductor-mesh.pab.eg.db/bioconductor-mesh.pab.eg.db_1.11.0_src_all.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/MeSH.Pab.eg.db_1.12.0.tar.gz" + "https://bioarchive.galaxyproject.org/MeSH.Pab.eg.db_1.12.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-mesh.pab.eg.db/bioconductor-mesh.pab.eg.db_1.12.0_src_all.tar.gz" ) -MD5="b156e5aab93facda91f391d174968450" +MD5="05e1649d5a99c21de690b75f52217bce" # Use a staging area in the conda dir rather than temp dirs, both to avoid # permission issues as well as to have things downloaded in a predictable @@ -16,7 +16,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-mesh.pae.pao1.eg.db/meta.yaml b/recipes/bioconductor-mesh.pae.pao1.eg.db/meta.yaml index ed5b2397e1aff..ea1e5093c71e3 100644 --- a/recipes/bioconductor-mesh.pae.pao1.eg.db/meta.yaml +++ b/recipes/bioconductor-mesh.pae.pao1.eg.db/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.11.0" %} +{% set version = "1.12.0" %} {% set name = "MeSH.Pae.PAO1.eg.db" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 281b4562470d51760d4e0d039229a09d + md5: aba001fa355b5dcfc3aee1fbd99a2db5 build: number: 0 rpaths: @@ -20,12 +20,12 @@ build: # Suggests: RUnit, BiocGenerics requirements: host: - - 'bioconductor-meshdbi >=1.18.0,<1.19.0' + - 'bioconductor-meshdbi >=1.20.0,<1.21.0' - r-base run: - - 'bioconductor-meshdbi >=1.18.0,<1.19.0' + - 'bioconductor-meshdbi >=1.20.0,<1.21.0' - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-mesh.pae.pao1.eg.db/post-link.sh b/recipes/bioconductor-mesh.pae.pao1.eg.db/post-link.sh index 35d3c84cf5eaa..db096db973d97 100644 --- a/recipes/bioconductor-mesh.pae.pao1.eg.db/post-link.sh +++ b/recipes/bioconductor-mesh.pae.pao1.eg.db/post-link.sh @@ -1,11 +1,11 @@ #!/bin/bash -FN="MeSH.Pae.PAO1.eg.db_1.11.0.tar.gz" +FN="MeSH.Pae.PAO1.eg.db_1.12.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/MeSH.Pae.PAO1.eg.db_1.11.0.tar.gz" - "https://bioarchive.galaxyproject.org/MeSH.Pae.PAO1.eg.db_1.11.0.tar.gz" - "https://depot.galaxyproject.org/software/bioconductor-mesh.pae.pao1.eg.db/bioconductor-mesh.pae.pao1.eg.db_1.11.0_src_all.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/MeSH.Pae.PAO1.eg.db_1.12.0.tar.gz" + "https://bioarchive.galaxyproject.org/MeSH.Pae.PAO1.eg.db_1.12.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-mesh.pae.pao1.eg.db/bioconductor-mesh.pae.pao1.eg.db_1.12.0_src_all.tar.gz" ) -MD5="281b4562470d51760d4e0d039229a09d" +MD5="aba001fa355b5dcfc3aee1fbd99a2db5" # Use a staging area in the conda dir rather than temp dirs, both to avoid # permission issues as well as to have things downloaded in a predictable @@ -16,7 +16,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-mesh.pcr.db/meta.yaml b/recipes/bioconductor-mesh.pcr.db/meta.yaml index 828e51e886b86..fe163ab3ffb00 100644 --- a/recipes/bioconductor-mesh.pcr.db/meta.yaml +++ b/recipes/bioconductor-mesh.pcr.db/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.11.0" %} +{% set version = "1.12.0" %} {% set name = "MeSH.PCR.db" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 9783b11c1f930c575a7a1cd62050484d + md5: 4926de52ba0a431d445b50c8e0d9e2aa build: number: 0 rpaths: @@ -20,12 +20,12 @@ build: # Suggests: RUnit, BiocGenerics requirements: host: - - 'bioconductor-meshdbi >=1.18.0,<1.19.0' + - 'bioconductor-meshdbi >=1.20.0,<1.21.0' - r-base run: - - 'bioconductor-meshdbi >=1.18.0,<1.19.0' + - 'bioconductor-meshdbi >=1.20.0,<1.21.0' - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-mesh.pcr.db/post-link.sh b/recipes/bioconductor-mesh.pcr.db/post-link.sh index 951a099cf1741..4b0500e2de4a5 100644 --- a/recipes/bioconductor-mesh.pcr.db/post-link.sh +++ b/recipes/bioconductor-mesh.pcr.db/post-link.sh @@ -1,11 +1,11 @@ #!/bin/bash -FN="MeSH.PCR.db_1.11.0.tar.gz" +FN="MeSH.PCR.db_1.12.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/MeSH.PCR.db_1.11.0.tar.gz" - "https://bioarchive.galaxyproject.org/MeSH.PCR.db_1.11.0.tar.gz" - "https://depot.galaxyproject.org/software/bioconductor-mesh.pcr.db/bioconductor-mesh.pcr.db_1.11.0_src_all.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/MeSH.PCR.db_1.12.0.tar.gz" + "https://bioarchive.galaxyproject.org/MeSH.PCR.db_1.12.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-mesh.pcr.db/bioconductor-mesh.pcr.db_1.12.0_src_all.tar.gz" ) -MD5="9783b11c1f930c575a7a1cd62050484d" +MD5="4926de52ba0a431d445b50c8e0d9e2aa" # Use a staging area in the conda dir rather than temp dirs, both to avoid # permission issues as well as to have things downloaded in a predictable @@ -16,7 +16,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-mesh.pfa.3d7.eg.db/meta.yaml b/recipes/bioconductor-mesh.pfa.3d7.eg.db/meta.yaml index 3bf7c5d933fa6..c1bc5289a385b 100644 --- a/recipes/bioconductor-mesh.pfa.3d7.eg.db/meta.yaml +++ b/recipes/bioconductor-mesh.pfa.3d7.eg.db/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.11.0" %} +{% set version = "1.12.0" %} {% set name = "MeSH.Pfa.3D7.eg.db" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 749aa5c6f52653c81258acb10b4c1e7a + md5: d961776f4f0327b3225501536f72c5c1 build: number: 0 rpaths: @@ -20,12 +20,12 @@ build: # Suggests: RUnit, BiocGenerics requirements: host: - - 'bioconductor-meshdbi >=1.18.0,<1.19.0' + - 'bioconductor-meshdbi >=1.20.0,<1.21.0' - r-base run: - - 'bioconductor-meshdbi >=1.18.0,<1.19.0' + - 'bioconductor-meshdbi >=1.20.0,<1.21.0' - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-mesh.pfa.3d7.eg.db/post-link.sh b/recipes/bioconductor-mesh.pfa.3d7.eg.db/post-link.sh index 09a8d29b59b87..2c19bcedbca2c 100644 --- a/recipes/bioconductor-mesh.pfa.3d7.eg.db/post-link.sh +++ b/recipes/bioconductor-mesh.pfa.3d7.eg.db/post-link.sh @@ -1,11 +1,11 @@ #!/bin/bash -FN="MeSH.Pfa.3D7.eg.db_1.11.0.tar.gz" +FN="MeSH.Pfa.3D7.eg.db_1.12.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/MeSH.Pfa.3D7.eg.db_1.11.0.tar.gz" - "https://bioarchive.galaxyproject.org/MeSH.Pfa.3D7.eg.db_1.11.0.tar.gz" - "https://depot.galaxyproject.org/software/bioconductor-mesh.pfa.3d7.eg.db/bioconductor-mesh.pfa.3d7.eg.db_1.11.0_src_all.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/MeSH.Pfa.3D7.eg.db_1.12.0.tar.gz" + "https://bioarchive.galaxyproject.org/MeSH.Pfa.3D7.eg.db_1.12.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-mesh.pfa.3d7.eg.db/bioconductor-mesh.pfa.3d7.eg.db_1.12.0_src_all.tar.gz" ) -MD5="749aa5c6f52653c81258acb10b4c1e7a" +MD5="d961776f4f0327b3225501536f72c5c1" # Use a staging area in the conda dir rather than temp dirs, both to avoid # permission issues as well as to have things downloaded in a predictable @@ -16,7 +16,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-mesh.pto.eg.db/meta.yaml b/recipes/bioconductor-mesh.pto.eg.db/meta.yaml index daa9eb079e35c..3fbad320dc510 100644 --- a/recipes/bioconductor-mesh.pto.eg.db/meta.yaml +++ b/recipes/bioconductor-mesh.pto.eg.db/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.11.0" %} +{% set version = "1.12.0" %} {% set name = "MeSH.Pto.eg.db" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,9 +10,9 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 0448b207fbf726ff6f62ef739864aa2d + md5: f1fe6e6cfae85bc91012c4c2f412574f build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ @@ -20,12 +20,12 @@ build: # Suggests: RUnit, BiocGenerics requirements: host: - - 'bioconductor-meshdbi >=1.18.0,<1.19.0' + - 'bioconductor-meshdbi >=1.20.0,<1.21.0' - r-base run: - - 'bioconductor-meshdbi >=1.18.0,<1.19.0' + - 'bioconductor-meshdbi >=1.20.0,<1.21.0' - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-mesh.pto.eg.db/post-link.sh b/recipes/bioconductor-mesh.pto.eg.db/post-link.sh index dab4a4c03fd32..88b07b7892a6f 100644 --- a/recipes/bioconductor-mesh.pto.eg.db/post-link.sh +++ b/recipes/bioconductor-mesh.pto.eg.db/post-link.sh @@ -1,11 +1,11 @@ #!/bin/bash -FN="MeSH.Pto.eg.db_1.11.0.tar.gz" +FN="MeSH.Pto.eg.db_1.12.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/MeSH.Pto.eg.db_1.11.0.tar.gz" - "https://bioarchive.galaxyproject.org/MeSH.Pto.eg.db_1.11.0.tar.gz" - "https://depot.galaxyproject.org/software/bioconductor-mesh.pto.eg.db/bioconductor-mesh.pto.eg.db_1.11.0_src_all.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/MeSH.Pto.eg.db_1.12.0.tar.gz" + "https://bioarchive.galaxyproject.org/MeSH.Pto.eg.db_1.12.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-mesh.pto.eg.db/bioconductor-mesh.pto.eg.db_1.12.0_src_all.tar.gz" ) -MD5="0448b207fbf726ff6f62ef739864aa2d" +MD5="f1fe6e6cfae85bc91012c4c2f412574f" # Use a staging area in the conda dir rather than temp dirs, both to avoid # permission issues as well as to have things downloaded in a predictable @@ -16,7 +16,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-mesh.ptr.eg.db/meta.yaml b/recipes/bioconductor-mesh.ptr.eg.db/meta.yaml index 525fb823043ec..b654e823386fb 100644 --- a/recipes/bioconductor-mesh.ptr.eg.db/meta.yaml +++ b/recipes/bioconductor-mesh.ptr.eg.db/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.11.0" %} +{% set version = "1.12.0" %} {% set name = "MeSH.Ptr.eg.db" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,9 +10,9 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: b497c8bfc04f1a2101c498100dbd9f0f + md5: 89378cdf2ec173927c6b13ff3a7773be build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ @@ -20,12 +20,12 @@ build: # Suggests: RUnit, BiocGenerics requirements: host: - - 'bioconductor-meshdbi >=1.18.0,<1.19.0' + - 'bioconductor-meshdbi >=1.20.0,<1.21.0' - r-base run: - - 'bioconductor-meshdbi >=1.18.0,<1.19.0' + - 'bioconductor-meshdbi >=1.20.0,<1.21.0' - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-mesh.ptr.eg.db/post-link.sh b/recipes/bioconductor-mesh.ptr.eg.db/post-link.sh index 2fe9c70039395..29ee7414cf4f9 100644 --- a/recipes/bioconductor-mesh.ptr.eg.db/post-link.sh +++ b/recipes/bioconductor-mesh.ptr.eg.db/post-link.sh @@ -1,11 +1,11 @@ #!/bin/bash -FN="MeSH.Ptr.eg.db_1.11.0.tar.gz" +FN="MeSH.Ptr.eg.db_1.12.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/MeSH.Ptr.eg.db_1.11.0.tar.gz" - "https://bioarchive.galaxyproject.org/MeSH.Ptr.eg.db_1.11.0.tar.gz" - "https://depot.galaxyproject.org/software/bioconductor-mesh.ptr.eg.db/bioconductor-mesh.ptr.eg.db_1.11.0_src_all.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/MeSH.Ptr.eg.db_1.12.0.tar.gz" + "https://bioarchive.galaxyproject.org/MeSH.Ptr.eg.db_1.12.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-mesh.ptr.eg.db/bioconductor-mesh.ptr.eg.db_1.12.0_src_all.tar.gz" ) -MD5="b497c8bfc04f1a2101c498100dbd9f0f" +MD5="89378cdf2ec173927c6b13ff3a7773be" # Use a staging area in the conda dir rather than temp dirs, both to avoid # permission issues as well as to have things downloaded in a predictable @@ -16,7 +16,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-mesh.rno.eg.db/meta.yaml b/recipes/bioconductor-mesh.rno.eg.db/meta.yaml index 0934cfdf3c851..ff9e6f5a06d6d 100644 --- a/recipes/bioconductor-mesh.rno.eg.db/meta.yaml +++ b/recipes/bioconductor-mesh.rno.eg.db/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.11.0" %} +{% set version = "1.12.0" %} {% set name = "MeSH.Rno.eg.db" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: b821144643cc233cca92148617566b31 + md5: f1af7cf2392bf2f1f12dd24018abedd0 build: number: 0 rpaths: @@ -20,12 +20,12 @@ build: # Suggests: RUnit, BiocGenerics requirements: host: - - 'bioconductor-meshdbi >=1.18.0,<1.19.0' + - 'bioconductor-meshdbi >=1.20.0,<1.21.0' - r-base run: - - 'bioconductor-meshdbi >=1.18.0,<1.19.0' + - 'bioconductor-meshdbi >=1.20.0,<1.21.0' - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-mesh.rno.eg.db/post-link.sh b/recipes/bioconductor-mesh.rno.eg.db/post-link.sh index 9c2940f3eb214..e1587b6d024bd 100644 --- a/recipes/bioconductor-mesh.rno.eg.db/post-link.sh +++ b/recipes/bioconductor-mesh.rno.eg.db/post-link.sh @@ -1,11 +1,11 @@ #!/bin/bash -FN="MeSH.Rno.eg.db_1.11.0.tar.gz" +FN="MeSH.Rno.eg.db_1.12.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/MeSH.Rno.eg.db_1.11.0.tar.gz" - "https://bioarchive.galaxyproject.org/MeSH.Rno.eg.db_1.11.0.tar.gz" - "https://depot.galaxyproject.org/software/bioconductor-mesh.rno.eg.db/bioconductor-mesh.rno.eg.db_1.11.0_src_all.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/MeSH.Rno.eg.db_1.12.0.tar.gz" + "https://bioarchive.galaxyproject.org/MeSH.Rno.eg.db_1.12.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-mesh.rno.eg.db/bioconductor-mesh.rno.eg.db_1.12.0_src_all.tar.gz" ) -MD5="b821144643cc233cca92148617566b31" +MD5="f1af7cf2392bf2f1f12dd24018abedd0" # Use a staging area in the conda dir rather than temp dirs, both to avoid # permission issues as well as to have things downloaded in a predictable @@ -16,7 +16,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-mesh.sce.s288c.eg.db/meta.yaml b/recipes/bioconductor-mesh.sce.s288c.eg.db/meta.yaml index c9abead0aadab..d4f27f4d9072c 100644 --- a/recipes/bioconductor-mesh.sce.s288c.eg.db/meta.yaml +++ b/recipes/bioconductor-mesh.sce.s288c.eg.db/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.11.0" %} +{% set version = "1.12.0" %} {% set name = "MeSH.Sce.S288c.eg.db" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 4db271c6a1df2c4e438ca4405f4bf8ce + md5: 04c21f9e0331a3ac3daac4b6157df5bb build: number: 0 rpaths: @@ -20,12 +20,12 @@ build: # Suggests: RUnit, BiocGenerics requirements: host: - - 'bioconductor-meshdbi >=1.18.0,<1.19.0' + - 'bioconductor-meshdbi >=1.20.0,<1.21.0' - r-base run: - - 'bioconductor-meshdbi >=1.18.0,<1.19.0' + - 'bioconductor-meshdbi >=1.20.0,<1.21.0' - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-mesh.sce.s288c.eg.db/post-link.sh b/recipes/bioconductor-mesh.sce.s288c.eg.db/post-link.sh index dbd809204f616..c5baa80bd66cf 100644 --- a/recipes/bioconductor-mesh.sce.s288c.eg.db/post-link.sh +++ b/recipes/bioconductor-mesh.sce.s288c.eg.db/post-link.sh @@ -1,11 +1,11 @@ #!/bin/bash -FN="MeSH.Sce.S288c.eg.db_1.11.0.tar.gz" +FN="MeSH.Sce.S288c.eg.db_1.12.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/MeSH.Sce.S288c.eg.db_1.11.0.tar.gz" - "https://bioarchive.galaxyproject.org/MeSH.Sce.S288c.eg.db_1.11.0.tar.gz" - "https://depot.galaxyproject.org/software/bioconductor-mesh.sce.s288c.eg.db/bioconductor-mesh.sce.s288c.eg.db_1.11.0_src_all.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/MeSH.Sce.S288c.eg.db_1.12.0.tar.gz" + "https://bioarchive.galaxyproject.org/MeSH.Sce.S288c.eg.db_1.12.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-mesh.sce.s288c.eg.db/bioconductor-mesh.sce.s288c.eg.db_1.12.0_src_all.tar.gz" ) -MD5="4db271c6a1df2c4e438ca4405f4bf8ce" +MD5="04c21f9e0331a3ac3daac4b6157df5bb" # Use a staging area in the conda dir rather than temp dirs, both to avoid # permission issues as well as to have things downloaded in a predictable @@ -16,7 +16,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-mesh.sco.a32.eg.db/meta.yaml b/recipes/bioconductor-mesh.sco.a32.eg.db/meta.yaml index 219b0f3c28945..2f38be2f28cc3 100644 --- a/recipes/bioconductor-mesh.sco.a32.eg.db/meta.yaml +++ b/recipes/bioconductor-mesh.sco.a32.eg.db/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.11.0" %} +{% set version = "1.12.0" %} {% set name = "MeSH.Sco.A32.eg.db" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,9 +10,9 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: a89a8bf1179059f69eeb32ba0dfff796 + md5: fb3a9481651a8c21f0a019c83eee2de2 build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ @@ -20,12 +20,12 @@ build: # Suggests: RUnit, BiocGenerics requirements: host: - - 'bioconductor-meshdbi >=1.18.0,<1.19.0' + - 'bioconductor-meshdbi >=1.20.0,<1.21.0' - r-base run: - - 'bioconductor-meshdbi >=1.18.0,<1.19.0' + - 'bioconductor-meshdbi >=1.20.0,<1.21.0' - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-mesh.sco.a32.eg.db/post-link.sh b/recipes/bioconductor-mesh.sco.a32.eg.db/post-link.sh index d90b9b675522c..1fe3af74a22ec 100644 --- a/recipes/bioconductor-mesh.sco.a32.eg.db/post-link.sh +++ b/recipes/bioconductor-mesh.sco.a32.eg.db/post-link.sh @@ -1,11 +1,11 @@ #!/bin/bash -FN="MeSH.Sco.A32.eg.db_1.11.0.tar.gz" +FN="MeSH.Sco.A32.eg.db_1.12.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/MeSH.Sco.A32.eg.db_1.11.0.tar.gz" - "https://bioarchive.galaxyproject.org/MeSH.Sco.A32.eg.db_1.11.0.tar.gz" - "https://depot.galaxyproject.org/software/bioconductor-mesh.sco.a32.eg.db/bioconductor-mesh.sco.a32.eg.db_1.11.0_src_all.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/MeSH.Sco.A32.eg.db_1.12.0.tar.gz" + "https://bioarchive.galaxyproject.org/MeSH.Sco.A32.eg.db_1.12.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-mesh.sco.a32.eg.db/bioconductor-mesh.sco.a32.eg.db_1.12.0_src_all.tar.gz" ) -MD5="a89a8bf1179059f69eeb32ba0dfff796" +MD5="fb3a9481651a8c21f0a019c83eee2de2" # Use a staging area in the conda dir rather than temp dirs, both to avoid # permission issues as well as to have things downloaded in a predictable @@ -16,7 +16,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-mesh.sil.eg.db/meta.yaml b/recipes/bioconductor-mesh.sil.eg.db/meta.yaml index 0051845e602a2..984ac0f563b87 100644 --- a/recipes/bioconductor-mesh.sil.eg.db/meta.yaml +++ b/recipes/bioconductor-mesh.sil.eg.db/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.11.0" %} +{% set version = "1.12.0" %} {% set name = "MeSH.Sil.eg.db" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 2fd601ed25adfdd2412d9c723a2f72d5 + md5: fd31b4ca3919da597e1f49ef6e94c81f build: number: 0 rpaths: @@ -20,12 +20,12 @@ build: # Suggests: RUnit, BiocGenerics requirements: host: - - 'bioconductor-meshdbi >=1.18.0,<1.19.0' + - 'bioconductor-meshdbi >=1.20.0,<1.21.0' - r-base run: - - 'bioconductor-meshdbi >=1.18.0,<1.19.0' + - 'bioconductor-meshdbi >=1.20.0,<1.21.0' - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-mesh.sil.eg.db/post-link.sh b/recipes/bioconductor-mesh.sil.eg.db/post-link.sh index d514d9a5a8ba9..f72c2ee663a7b 100644 --- a/recipes/bioconductor-mesh.sil.eg.db/post-link.sh +++ b/recipes/bioconductor-mesh.sil.eg.db/post-link.sh @@ -1,11 +1,11 @@ #!/bin/bash -FN="MeSH.Sil.eg.db_1.11.0.tar.gz" +FN="MeSH.Sil.eg.db_1.12.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/MeSH.Sil.eg.db_1.11.0.tar.gz" - "https://bioarchive.galaxyproject.org/MeSH.Sil.eg.db_1.11.0.tar.gz" - "https://depot.galaxyproject.org/software/bioconductor-mesh.sil.eg.db/bioconductor-mesh.sil.eg.db_1.11.0_src_all.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/MeSH.Sil.eg.db_1.12.0.tar.gz" + "https://bioarchive.galaxyproject.org/MeSH.Sil.eg.db_1.12.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-mesh.sil.eg.db/bioconductor-mesh.sil.eg.db_1.12.0_src_all.tar.gz" ) -MD5="2fd601ed25adfdd2412d9c723a2f72d5" +MD5="fd31b4ca3919da597e1f49ef6e94c81f" # Use a staging area in the conda dir rather than temp dirs, both to avoid # permission issues as well as to have things downloaded in a predictable @@ -16,7 +16,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-mesh.spu.eg.db/meta.yaml b/recipes/bioconductor-mesh.spu.eg.db/meta.yaml index 1553a85f7adc4..5aff2dd668b60 100644 --- a/recipes/bioconductor-mesh.spu.eg.db/meta.yaml +++ b/recipes/bioconductor-mesh.spu.eg.db/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.11.0" %} +{% set version = "1.12.0" %} {% set name = "MeSH.Spu.eg.db" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,9 +10,9 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 6f0c6530bbd904a55c1a34fb61ccfd61 + md5: 0c4afe697c0807f98c7654a380165fb6 build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ @@ -20,12 +20,12 @@ build: # Suggests: RUnit, BiocGenerics requirements: host: - - 'bioconductor-meshdbi >=1.18.0,<1.19.0' + - 'bioconductor-meshdbi >=1.20.0,<1.21.0' - r-base run: - - 'bioconductor-meshdbi >=1.18.0,<1.19.0' + - 'bioconductor-meshdbi >=1.20.0,<1.21.0' - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-mesh.spu.eg.db/post-link.sh b/recipes/bioconductor-mesh.spu.eg.db/post-link.sh index 92f7b891cecc8..2aa1a53344c30 100644 --- a/recipes/bioconductor-mesh.spu.eg.db/post-link.sh +++ b/recipes/bioconductor-mesh.spu.eg.db/post-link.sh @@ -1,11 +1,11 @@ #!/bin/bash -FN="MeSH.Spu.eg.db_1.11.0.tar.gz" +FN="MeSH.Spu.eg.db_1.12.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/MeSH.Spu.eg.db_1.11.0.tar.gz" - "https://bioarchive.galaxyproject.org/MeSH.Spu.eg.db_1.11.0.tar.gz" - "https://depot.galaxyproject.org/software/bioconductor-mesh.spu.eg.db/bioconductor-mesh.spu.eg.db_1.11.0_src_all.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/MeSH.Spu.eg.db_1.12.0.tar.gz" + "https://bioarchive.galaxyproject.org/MeSH.Spu.eg.db_1.12.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-mesh.spu.eg.db/bioconductor-mesh.spu.eg.db_1.12.0_src_all.tar.gz" ) -MD5="6f0c6530bbd904a55c1a34fb61ccfd61" +MD5="0c4afe697c0807f98c7654a380165fb6" # Use a staging area in the conda dir rather than temp dirs, both to avoid # permission issues as well as to have things downloaded in a predictable @@ -16,7 +16,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-mesh.ssc.eg.db/meta.yaml b/recipes/bioconductor-mesh.ssc.eg.db/meta.yaml index 42413888a5fbd..cb08af1f8a32a 100644 --- a/recipes/bioconductor-mesh.ssc.eg.db/meta.yaml +++ b/recipes/bioconductor-mesh.ssc.eg.db/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.11.0" %} +{% set version = "1.12.0" %} {% set name = "MeSH.Ssc.eg.db" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 8641af272a45c721a9cbd9c229776de5 + md5: c402e9dffa1060d299977ecf77c95e31 build: number: 0 rpaths: @@ -20,12 +20,12 @@ build: # Suggests: RUnit, BiocGenerics requirements: host: - - 'bioconductor-meshdbi >=1.18.0,<1.19.0' + - 'bioconductor-meshdbi >=1.20.0,<1.21.0' - r-base run: - - 'bioconductor-meshdbi >=1.18.0,<1.19.0' + - 'bioconductor-meshdbi >=1.20.0,<1.21.0' - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-mesh.ssc.eg.db/post-link.sh b/recipes/bioconductor-mesh.ssc.eg.db/post-link.sh index ab2e93c4ab684..db5277aabd72f 100644 --- a/recipes/bioconductor-mesh.ssc.eg.db/post-link.sh +++ b/recipes/bioconductor-mesh.ssc.eg.db/post-link.sh @@ -1,11 +1,11 @@ #!/bin/bash -FN="MeSH.Ssc.eg.db_1.11.0.tar.gz" +FN="MeSH.Ssc.eg.db_1.12.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/MeSH.Ssc.eg.db_1.11.0.tar.gz" - "https://bioarchive.galaxyproject.org/MeSH.Ssc.eg.db_1.11.0.tar.gz" - "https://depot.galaxyproject.org/software/bioconductor-mesh.ssc.eg.db/bioconductor-mesh.ssc.eg.db_1.11.0_src_all.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/MeSH.Ssc.eg.db_1.12.0.tar.gz" + "https://bioarchive.galaxyproject.org/MeSH.Ssc.eg.db_1.12.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-mesh.ssc.eg.db/bioconductor-mesh.ssc.eg.db_1.12.0_src_all.tar.gz" ) -MD5="8641af272a45c721a9cbd9c229776de5" +MD5="c402e9dffa1060d299977ecf77c95e31" # Use a staging area in the conda dir rather than temp dirs, both to avoid # permission issues as well as to have things downloaded in a predictable @@ -16,7 +16,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-mesh.syn.eg.db/meta.yaml b/recipes/bioconductor-mesh.syn.eg.db/meta.yaml index f85e557d1b141..cfccfcd92cc66 100644 --- a/recipes/bioconductor-mesh.syn.eg.db/meta.yaml +++ b/recipes/bioconductor-mesh.syn.eg.db/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.11.0" %} +{% set version = "1.12.0" %} {% set name = "MeSH.Syn.eg.db" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: ec4df33cef0022929018947d66c0e024 + md5: be1717480eabc1ace26196d2608c39f5 build: number: 0 rpaths: @@ -20,12 +20,12 @@ build: # Suggests: RUnit, BiocGenerics requirements: host: - - 'bioconductor-meshdbi >=1.18.0,<1.19.0' + - 'bioconductor-meshdbi >=1.20.0,<1.21.0' - r-base run: - - 'bioconductor-meshdbi >=1.18.0,<1.19.0' + - 'bioconductor-meshdbi >=1.20.0,<1.21.0' - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-mesh.syn.eg.db/post-link.sh b/recipes/bioconductor-mesh.syn.eg.db/post-link.sh index 14f5b8218368e..5bbf6307f3ea5 100644 --- a/recipes/bioconductor-mesh.syn.eg.db/post-link.sh +++ b/recipes/bioconductor-mesh.syn.eg.db/post-link.sh @@ -1,11 +1,11 @@ #!/bin/bash -FN="MeSH.Syn.eg.db_1.11.0.tar.gz" +FN="MeSH.Syn.eg.db_1.12.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/MeSH.Syn.eg.db_1.11.0.tar.gz" - "https://bioarchive.galaxyproject.org/MeSH.Syn.eg.db_1.11.0.tar.gz" - "https://depot.galaxyproject.org/software/bioconductor-mesh.syn.eg.db/bioconductor-mesh.syn.eg.db_1.11.0_src_all.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/MeSH.Syn.eg.db_1.12.0.tar.gz" + "https://bioarchive.galaxyproject.org/MeSH.Syn.eg.db_1.12.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-mesh.syn.eg.db/bioconductor-mesh.syn.eg.db_1.12.0_src_all.tar.gz" ) -MD5="ec4df33cef0022929018947d66c0e024" +MD5="be1717480eabc1ace26196d2608c39f5" # Use a staging area in the conda dir rather than temp dirs, both to avoid # permission issues as well as to have things downloaded in a predictable @@ -16,7 +16,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-mesh.tbr.9274.eg.db/meta.yaml b/recipes/bioconductor-mesh.tbr.9274.eg.db/meta.yaml index 3d2c4a009b3b8..4549da4e030df 100644 --- a/recipes/bioconductor-mesh.tbr.9274.eg.db/meta.yaml +++ b/recipes/bioconductor-mesh.tbr.9274.eg.db/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.11.0" %} +{% set version = "1.12.0" %} {% set name = "MeSH.Tbr.9274.eg.db" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 9465b3f70608a6f5363ede1c075aa1f1 + md5: 0736c3869de19755b03c7b9849c560f1 build: number: 0 rpaths: @@ -20,12 +20,12 @@ build: # Suggests: RUnit, BiocGenerics requirements: host: - - 'bioconductor-meshdbi >=1.18.0,<1.19.0' + - 'bioconductor-meshdbi >=1.20.0,<1.21.0' - r-base run: - - 'bioconductor-meshdbi >=1.18.0,<1.19.0' + - 'bioconductor-meshdbi >=1.20.0,<1.21.0' - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-mesh.tbr.9274.eg.db/post-link.sh b/recipes/bioconductor-mesh.tbr.9274.eg.db/post-link.sh index 534f6685c803f..6f38e91639c4c 100644 --- a/recipes/bioconductor-mesh.tbr.9274.eg.db/post-link.sh +++ b/recipes/bioconductor-mesh.tbr.9274.eg.db/post-link.sh @@ -1,11 +1,11 @@ #!/bin/bash -FN="MeSH.Tbr.9274.eg.db_1.11.0.tar.gz" +FN="MeSH.Tbr.9274.eg.db_1.12.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/MeSH.Tbr.9274.eg.db_1.11.0.tar.gz" - "https://bioarchive.galaxyproject.org/MeSH.Tbr.9274.eg.db_1.11.0.tar.gz" - "https://depot.galaxyproject.org/software/bioconductor-mesh.tbr.9274.eg.db/bioconductor-mesh.tbr.9274.eg.db_1.11.0_src_all.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/MeSH.Tbr.9274.eg.db_1.12.0.tar.gz" + "https://bioarchive.galaxyproject.org/MeSH.Tbr.9274.eg.db_1.12.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-mesh.tbr.9274.eg.db/bioconductor-mesh.tbr.9274.eg.db_1.12.0_src_all.tar.gz" ) -MD5="9465b3f70608a6f5363ede1c075aa1f1" +MD5="0736c3869de19755b03c7b9849c560f1" # Use a staging area in the conda dir rather than temp dirs, both to avoid # permission issues as well as to have things downloaded in a predictable @@ -16,7 +16,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-mesh.tgo.me49.eg.db/meta.yaml b/recipes/bioconductor-mesh.tgo.me49.eg.db/meta.yaml index 3f9ab81b476e6..96c6f7a598316 100644 --- a/recipes/bioconductor-mesh.tgo.me49.eg.db/meta.yaml +++ b/recipes/bioconductor-mesh.tgo.me49.eg.db/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.11.0" %} +{% set version = "1.12.0" %} {% set name = "MeSH.Tgo.ME49.eg.db" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 437d5be6e97f4b2cc2cee1972e3be115 + md5: ef6c6bb69bb039dc3174a3a02e12156f build: number: 0 rpaths: @@ -20,12 +20,12 @@ build: # Suggests: RUnit, BiocGenerics requirements: host: - - 'bioconductor-meshdbi >=1.18.0,<1.19.0' + - 'bioconductor-meshdbi >=1.20.0,<1.21.0' - r-base run: - - 'bioconductor-meshdbi >=1.18.0,<1.19.0' + - 'bioconductor-meshdbi >=1.20.0,<1.21.0' - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-mesh.tgo.me49.eg.db/post-link.sh b/recipes/bioconductor-mesh.tgo.me49.eg.db/post-link.sh index 7b0de41fc077e..2785fcb4012e9 100644 --- a/recipes/bioconductor-mesh.tgo.me49.eg.db/post-link.sh +++ b/recipes/bioconductor-mesh.tgo.me49.eg.db/post-link.sh @@ -1,11 +1,11 @@ #!/bin/bash -FN="MeSH.Tgo.ME49.eg.db_1.11.0.tar.gz" +FN="MeSH.Tgo.ME49.eg.db_1.12.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/MeSH.Tgo.ME49.eg.db_1.11.0.tar.gz" - "https://bioarchive.galaxyproject.org/MeSH.Tgo.ME49.eg.db_1.11.0.tar.gz" - "https://depot.galaxyproject.org/software/bioconductor-mesh.tgo.me49.eg.db/bioconductor-mesh.tgo.me49.eg.db_1.11.0_src_all.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/MeSH.Tgo.ME49.eg.db_1.12.0.tar.gz" + "https://bioarchive.galaxyproject.org/MeSH.Tgo.ME49.eg.db_1.12.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-mesh.tgo.me49.eg.db/bioconductor-mesh.tgo.me49.eg.db_1.12.0_src_all.tar.gz" ) -MD5="437d5be6e97f4b2cc2cee1972e3be115" +MD5="ef6c6bb69bb039dc3174a3a02e12156f" # Use a staging area in the conda dir rather than temp dirs, both to avoid # permission issues as well as to have things downloaded in a predictable @@ -16,7 +16,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-mesh.tgu.eg.db/meta.yaml b/recipes/bioconductor-mesh.tgu.eg.db/meta.yaml index 7fd95b34ad556..93c83b21135be 100644 --- a/recipes/bioconductor-mesh.tgu.eg.db/meta.yaml +++ b/recipes/bioconductor-mesh.tgu.eg.db/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.11.0" %} +{% set version = "1.12.0" %} {% set name = "MeSH.Tgu.eg.db" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: b75f668b61550b675aa3fdd3d556a935 + md5: 632ef7433017f0e48ca67da3c49f7939 build: number: 0 rpaths: @@ -20,12 +20,12 @@ build: # Suggests: RUnit, BiocGenerics requirements: host: - - 'bioconductor-meshdbi >=1.18.0,<1.19.0' + - 'bioconductor-meshdbi >=1.20.0,<1.21.0' - r-base run: - - 'bioconductor-meshdbi >=1.18.0,<1.19.0' + - 'bioconductor-meshdbi >=1.20.0,<1.21.0' - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-mesh.tgu.eg.db/post-link.sh b/recipes/bioconductor-mesh.tgu.eg.db/post-link.sh index b0549e1be73f3..26715b73841d7 100644 --- a/recipes/bioconductor-mesh.tgu.eg.db/post-link.sh +++ b/recipes/bioconductor-mesh.tgu.eg.db/post-link.sh @@ -1,11 +1,11 @@ #!/bin/bash -FN="MeSH.Tgu.eg.db_1.11.0.tar.gz" +FN="MeSH.Tgu.eg.db_1.12.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/MeSH.Tgu.eg.db_1.11.0.tar.gz" - "https://bioarchive.galaxyproject.org/MeSH.Tgu.eg.db_1.11.0.tar.gz" - "https://depot.galaxyproject.org/software/bioconductor-mesh.tgu.eg.db/bioconductor-mesh.tgu.eg.db_1.11.0_src_all.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/MeSH.Tgu.eg.db_1.12.0.tar.gz" + "https://bioarchive.galaxyproject.org/MeSH.Tgu.eg.db_1.12.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-mesh.tgu.eg.db/bioconductor-mesh.tgu.eg.db_1.12.0_src_all.tar.gz" ) -MD5="b75f668b61550b675aa3fdd3d556a935" +MD5="632ef7433017f0e48ca67da3c49f7939" # Use a staging area in the conda dir rather than temp dirs, both to avoid # permission issues as well as to have things downloaded in a predictable @@ -16,7 +16,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-mesh.vvi.eg.db/meta.yaml b/recipes/bioconductor-mesh.vvi.eg.db/meta.yaml index 9d34619d08fe5..2091020e998b5 100644 --- a/recipes/bioconductor-mesh.vvi.eg.db/meta.yaml +++ b/recipes/bioconductor-mesh.vvi.eg.db/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.11.0" %} +{% set version = "1.12.0" %} {% set name = "MeSH.Vvi.eg.db" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,9 +10,9 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: fdf974109135d9569d7d2c280f71716c + md5: 4d24b9a2d581e5d5afc86f939db963b1 build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ @@ -20,12 +20,12 @@ build: # Suggests: RUnit, BiocGenerics requirements: host: - - 'bioconductor-meshdbi >=1.18.0,<1.19.0' + - 'bioconductor-meshdbi >=1.20.0,<1.21.0' - r-base run: - - 'bioconductor-meshdbi >=1.18.0,<1.19.0' + - 'bioconductor-meshdbi >=1.20.0,<1.21.0' - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-mesh.vvi.eg.db/post-link.sh b/recipes/bioconductor-mesh.vvi.eg.db/post-link.sh index 847ae005673a3..5c0e4a7c72367 100644 --- a/recipes/bioconductor-mesh.vvi.eg.db/post-link.sh +++ b/recipes/bioconductor-mesh.vvi.eg.db/post-link.sh @@ -1,11 +1,11 @@ #!/bin/bash -FN="MeSH.Vvi.eg.db_1.11.0.tar.gz" +FN="MeSH.Vvi.eg.db_1.12.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/MeSH.Vvi.eg.db_1.11.0.tar.gz" - "https://bioarchive.galaxyproject.org/MeSH.Vvi.eg.db_1.11.0.tar.gz" - "https://depot.galaxyproject.org/software/bioconductor-mesh.vvi.eg.db/bioconductor-mesh.vvi.eg.db_1.11.0_src_all.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/MeSH.Vvi.eg.db_1.12.0.tar.gz" + "https://bioarchive.galaxyproject.org/MeSH.Vvi.eg.db_1.12.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-mesh.vvi.eg.db/bioconductor-mesh.vvi.eg.db_1.12.0_src_all.tar.gz" ) -MD5="fdf974109135d9569d7d2c280f71716c" +MD5="4d24b9a2d581e5d5afc86f939db963b1" # Use a staging area in the conda dir rather than temp dirs, both to avoid # permission issues as well as to have things downloaded in a predictable @@ -16,7 +16,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-mesh.xla.eg.db/meta.yaml b/recipes/bioconductor-mesh.xla.eg.db/meta.yaml index b24e121242d1e..9a616b0065194 100644 --- a/recipes/bioconductor-mesh.xla.eg.db/meta.yaml +++ b/recipes/bioconductor-mesh.xla.eg.db/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.11.0" %} +{% set version = "1.12.0" %} {% set name = "MeSH.Xla.eg.db" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 624c4086857259bb0f77e588a9ee4eb3 + md5: c2ca106352ddfe896e2079037a67d0ee build: number: 0 rpaths: @@ -20,12 +20,12 @@ build: # Suggests: RUnit, BiocGenerics requirements: host: - - 'bioconductor-meshdbi >=1.18.0,<1.19.0' + - 'bioconductor-meshdbi >=1.20.0,<1.21.0' - r-base run: - - 'bioconductor-meshdbi >=1.18.0,<1.19.0' + - 'bioconductor-meshdbi >=1.20.0,<1.21.0' - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-mesh.xla.eg.db/post-link.sh b/recipes/bioconductor-mesh.xla.eg.db/post-link.sh index 82bc34b741bd4..713ebd583909c 100644 --- a/recipes/bioconductor-mesh.xla.eg.db/post-link.sh +++ b/recipes/bioconductor-mesh.xla.eg.db/post-link.sh @@ -1,11 +1,11 @@ #!/bin/bash -FN="MeSH.Xla.eg.db_1.11.0.tar.gz" +FN="MeSH.Xla.eg.db_1.12.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/MeSH.Xla.eg.db_1.11.0.tar.gz" - "https://bioarchive.galaxyproject.org/MeSH.Xla.eg.db_1.11.0.tar.gz" - "https://depot.galaxyproject.org/software/bioconductor-mesh.xla.eg.db/bioconductor-mesh.xla.eg.db_1.11.0_src_all.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/MeSH.Xla.eg.db_1.12.0.tar.gz" + "https://bioarchive.galaxyproject.org/MeSH.Xla.eg.db_1.12.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-mesh.xla.eg.db/bioconductor-mesh.xla.eg.db_1.12.0_src_all.tar.gz" ) -MD5="624c4086857259bb0f77e588a9ee4eb3" +MD5="c2ca106352ddfe896e2079037a67d0ee" # Use a staging area in the conda dir rather than temp dirs, both to avoid # permission issues as well as to have things downloaded in a predictable @@ -16,7 +16,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-mesh.xtr.eg.db/meta.yaml b/recipes/bioconductor-mesh.xtr.eg.db/meta.yaml index c326785ccaa42..fd9ec72e35bb0 100644 --- a/recipes/bioconductor-mesh.xtr.eg.db/meta.yaml +++ b/recipes/bioconductor-mesh.xtr.eg.db/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.11.0" %} +{% set version = "1.12.0" %} {% set name = "MeSH.Xtr.eg.db" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 1b49f5370146697faef0d8ae965f7e29 + md5: aec288e916f0702d95b0d113d06c1a14 build: number: 0 rpaths: @@ -20,12 +20,12 @@ build: # Suggests: RUnit, BiocGenerics requirements: host: - - 'bioconductor-meshdbi >=1.18.0,<1.19.0' + - 'bioconductor-meshdbi >=1.20.0,<1.21.0' - r-base run: - - 'bioconductor-meshdbi >=1.18.0,<1.19.0' + - 'bioconductor-meshdbi >=1.20.0,<1.21.0' - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-mesh.xtr.eg.db/post-link.sh b/recipes/bioconductor-mesh.xtr.eg.db/post-link.sh index f58171f1e1e36..784de683023ce 100644 --- a/recipes/bioconductor-mesh.xtr.eg.db/post-link.sh +++ b/recipes/bioconductor-mesh.xtr.eg.db/post-link.sh @@ -1,11 +1,11 @@ #!/bin/bash -FN="MeSH.Xtr.eg.db_1.11.0.tar.gz" +FN="MeSH.Xtr.eg.db_1.12.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/MeSH.Xtr.eg.db_1.11.0.tar.gz" - "https://bioarchive.galaxyproject.org/MeSH.Xtr.eg.db_1.11.0.tar.gz" - "https://depot.galaxyproject.org/software/bioconductor-mesh.xtr.eg.db/bioconductor-mesh.xtr.eg.db_1.11.0_src_all.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/MeSH.Xtr.eg.db_1.12.0.tar.gz" + "https://bioarchive.galaxyproject.org/MeSH.Xtr.eg.db_1.12.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-mesh.xtr.eg.db/bioconductor-mesh.xtr.eg.db_1.12.0_src_all.tar.gz" ) -MD5="1b49f5370146697faef0d8ae965f7e29" +MD5="aec288e916f0702d95b0d113d06c1a14" # Use a staging area in the conda dir rather than temp dirs, both to avoid # permission issues as well as to have things downloaded in a predictable @@ -16,7 +16,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-mesh.zma.eg.db/meta.yaml b/recipes/bioconductor-mesh.zma.eg.db/meta.yaml index 6a5d4be8108e2..9550e0b7f363b 100644 --- a/recipes/bioconductor-mesh.zma.eg.db/meta.yaml +++ b/recipes/bioconductor-mesh.zma.eg.db/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.11.0" %} +{% set version = "1.12.0" %} {% set name = "MeSH.Zma.eg.db" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: f15886b139eac087d5c183f8643f4c5d + md5: 6fae1bfade2e7144d9be54d50725cd89 build: number: 0 rpaths: @@ -20,12 +20,12 @@ build: # Suggests: RUnit, BiocGenerics requirements: host: - - 'bioconductor-meshdbi >=1.18.0,<1.19.0' + - 'bioconductor-meshdbi >=1.20.0,<1.21.0' - r-base run: - - 'bioconductor-meshdbi >=1.18.0,<1.19.0' + - 'bioconductor-meshdbi >=1.20.0,<1.21.0' - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-mesh.zma.eg.db/post-link.sh b/recipes/bioconductor-mesh.zma.eg.db/post-link.sh index a4ce4cd0dc214..f806c68302872 100644 --- a/recipes/bioconductor-mesh.zma.eg.db/post-link.sh +++ b/recipes/bioconductor-mesh.zma.eg.db/post-link.sh @@ -1,11 +1,11 @@ #!/bin/bash -FN="MeSH.Zma.eg.db_1.11.0.tar.gz" +FN="MeSH.Zma.eg.db_1.12.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/MeSH.Zma.eg.db_1.11.0.tar.gz" - "https://bioarchive.galaxyproject.org/MeSH.Zma.eg.db_1.11.0.tar.gz" - "https://depot.galaxyproject.org/software/bioconductor-mesh.zma.eg.db/bioconductor-mesh.zma.eg.db_1.11.0_src_all.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/MeSH.Zma.eg.db_1.12.0.tar.gz" + "https://bioarchive.galaxyproject.org/MeSH.Zma.eg.db_1.12.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-mesh.zma.eg.db/bioconductor-mesh.zma.eg.db_1.12.0_src_all.tar.gz" ) -MD5="f15886b139eac087d5c183f8643f4c5d" +MD5="6fae1bfade2e7144d9be54d50725cd89" # Use a staging area in the conda dir rather than temp dirs, both to avoid # permission issues as well as to have things downloaded in a predictable @@ -16,7 +16,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-meshdbi/meta.yaml b/recipes/bioconductor-meshdbi/meta.yaml index 7dfc8426142d3..183adf24c83fa 100644 --- a/recipes/bioconductor-meshdbi/meta.yaml +++ b/recipes/bioconductor-meshdbi/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.18.0" %} +{% set version = "1.20.0" %} {% set name = "MeSHDbi" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 0a8007f98154bf5d6dc7399938c4c143 + md5: 8e5ddfc622ed4f0ea2380222996695f1 build: number: 0 rpaths: @@ -20,15 +20,15 @@ build: # Suggests: RUnit requirements: host: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' - - 'bioconductor-biobase >=2.42.0,<2.43.0' - - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' + - 'bioconductor-biocgenerics >=0.30.0,<0.31.0' - r-base - r-rsqlite run: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' - - 'bioconductor-biobase >=2.42.0,<2.43.0' - - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' + - 'bioconductor-biocgenerics >=0.30.0,<0.31.0' - r-base - r-rsqlite test: diff --git a/recipes/bioconductor-meshes/meta.yaml b/recipes/bioconductor-meshes/meta.yaml index 81ec30f6b0a8d..5eca952c930fc 100644 --- a/recipes/bioconductor-meshes/meta.yaml +++ b/recipes/bioconductor-meshes/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.8.0" %} +{% set version = "1.10.0" %} {% set name = "meshes" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 82fde49d4067c7941020d0da49df8f1d + md5: fee72009cb9fd04feef89fe26f569dc7 build: number: 0 rpaths: @@ -20,19 +20,19 @@ build: # Suggests: knitr, MeSH.Cel.eg.db, MeSH.Hsa.eg.db, prettydoc requirements: host: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' - - 'bioconductor-dose >=3.8.0,<3.9.0' - - 'bioconductor-enrichplot >=1.2.0,<1.3.0' - - 'bioconductor-gosemsim >=2.8.0,<2.9.0' - - 'bioconductor-mesh.db >=1.11.0,<1.12.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' + - 'bioconductor-dose >=3.10.0,<3.11.0' + - 'bioconductor-enrichplot >=1.4.0,<1.5.0' + - 'bioconductor-gosemsim >=2.10.0,<2.11.0' + - 'bioconductor-mesh.db >=1.12.0,<1.13.0' - r-base - r-rvcheck run: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' - - 'bioconductor-dose >=3.8.0,<3.9.0' - - 'bioconductor-enrichplot >=1.2.0,<1.3.0' - - 'bioconductor-gosemsim >=2.8.0,<2.9.0' - - 'bioconductor-mesh.db >=1.11.0,<1.12.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' + - 'bioconductor-dose >=3.10.0,<3.11.0' + - 'bioconductor-enrichplot >=1.4.0,<1.5.0' + - 'bioconductor-gosemsim >=2.10.0,<2.11.0' + - 'bioconductor-mesh.db >=1.12.0,<1.13.0' - r-base - r-rvcheck test: diff --git a/recipes/bioconductor-meshr/meta.yaml b/recipes/bioconductor-meshr/meta.yaml index 9241b2f5afcbb..bd9b3ca7c9884 100644 --- a/recipes/bioconductor-meshr/meta.yaml +++ b/recipes/bioconductor-meshr/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.18.0" %} +{% set version = "1.20.0" %} {% set name = "meshr" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,45 +10,45 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 2949ce68968d8e93325b2e4081038246 + md5: 14b9bd13f8dedc691b578adc0be88b04 build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ noarch: generic requirements: host: - - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' - - 'bioconductor-category >=2.48.0,<2.49.0' - - 'bioconductor-cummerbund >=2.24.0,<2.25.0' - - 'bioconductor-mesh.aca.eg.db >=1.11.0,<1.12.0' - - 'bioconductor-mesh.aor.db >=1.11.0,<1.12.0' - - 'bioconductor-mesh.bsu.168.eg.db >=1.11.0,<1.12.0' - - 'bioconductor-mesh.db >=1.11.0,<1.12.0' - - 'bioconductor-mesh.hsa.eg.db >=1.11.0,<1.12.0' - - 'bioconductor-mesh.pcr.db >=1.11.0,<1.12.0' - - 'bioconductor-mesh.syn.eg.db >=1.11.0,<1.12.0' - - 'bioconductor-meshdbi >=1.18.0,<1.19.0' - - 'bioconductor-org.hs.eg.db >=3.7.0,<3.8.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-biocgenerics >=0.30.0,<0.31.0' + - 'bioconductor-category >=2.50.0,<2.51.0' + - 'bioconductor-cummerbund >=2.26.0,<2.27.0' + - 'bioconductor-mesh.aca.eg.db >=1.12.0,<1.13.0' + - 'bioconductor-mesh.aor.db >=1.12.0,<1.13.0' + - 'bioconductor-mesh.bsu.168.eg.db >=1.12.0,<1.13.0' + - 'bioconductor-mesh.db >=1.12.0,<1.13.0' + - 'bioconductor-mesh.hsa.eg.db >=1.12.0,<1.13.0' + - 'bioconductor-mesh.pcr.db >=1.12.0,<1.13.0' + - 'bioconductor-mesh.syn.eg.db >=1.12.0,<1.13.0' + - 'bioconductor-meshdbi >=1.20.0,<1.21.0' + - 'bioconductor-org.hs.eg.db >=3.8.0,<3.9.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' - r-base - r-fdrtool - r-rsqlite run: - - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' - - 'bioconductor-category >=2.48.0,<2.49.0' - - 'bioconductor-cummerbund >=2.24.0,<2.25.0' - - 'bioconductor-mesh.aca.eg.db >=1.11.0,<1.12.0' - - 'bioconductor-mesh.aor.db >=1.11.0,<1.12.0' - - 'bioconductor-mesh.bsu.168.eg.db >=1.11.0,<1.12.0' - - 'bioconductor-mesh.db >=1.11.0,<1.12.0' - - 'bioconductor-mesh.hsa.eg.db >=1.11.0,<1.12.0' - - 'bioconductor-mesh.pcr.db >=1.11.0,<1.12.0' - - 'bioconductor-mesh.syn.eg.db >=1.11.0,<1.12.0' - - 'bioconductor-meshdbi >=1.18.0,<1.19.0' - - 'bioconductor-org.hs.eg.db >=3.7.0,<3.8.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-biocgenerics >=0.30.0,<0.31.0' + - 'bioconductor-category >=2.50.0,<2.51.0' + - 'bioconductor-cummerbund >=2.26.0,<2.27.0' + - 'bioconductor-mesh.aca.eg.db >=1.12.0,<1.13.0' + - 'bioconductor-mesh.aor.db >=1.12.0,<1.13.0' + - 'bioconductor-mesh.bsu.168.eg.db >=1.12.0,<1.13.0' + - 'bioconductor-mesh.db >=1.12.0,<1.13.0' + - 'bioconductor-mesh.hsa.eg.db >=1.12.0,<1.13.0' + - 'bioconductor-mesh.pcr.db >=1.12.0,<1.13.0' + - 'bioconductor-mesh.syn.eg.db >=1.12.0,<1.13.0' + - 'bioconductor-meshdbi >=1.20.0,<1.21.0' + - 'bioconductor-org.hs.eg.db >=3.8.0,<3.9.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' - r-base - r-fdrtool - r-rsqlite diff --git a/recipes/bioconductor-messina/meta.yaml b/recipes/bioconductor-messina/meta.yaml index 80c4eee637924..8eb765b17e52f 100644 --- a/recipes/bioconductor-messina/meta.yaml +++ b/recipes/bioconductor-messina/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.18.0" %} +{% set version = "1.20.0" %} {% set name = "messina" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 9e461e240fdb0e98fb3eac38288e5014 + md5: bfd3714601dfff75a4dd9be6c8a7a5d4 build: number: 0 rpaths: diff --git a/recipes/bioconductor-metaarray/meta.yaml b/recipes/bioconductor-metaarray/meta.yaml index 7a4e75b29745c..cbca6b7bcfad6 100644 --- a/recipes/bioconductor-metaarray/meta.yaml +++ b/recipes/bioconductor-metaarray/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.60.0" %} +{% set version = "1.62.0" %} {% set name = "metaArray" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,20 +10,20 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: e6157bb8e824426a8762f4b0779f3eb8 + md5: 083da57aabf27d356e0de1b8cbab1320 build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ requirements: host: - - 'bioconductor-biobase >=2.42.0,<2.43.0' - - 'bioconductor-mergemaid >=2.54.0,<2.55.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' + - 'bioconductor-mergemaid >=2.56.0,<2.57.0' - r-base run: - - 'bioconductor-biobase >=2.42.0,<2.43.0' - - 'bioconductor-mergemaid >=2.54.0,<2.55.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' + - 'bioconductor-mergemaid >=2.56.0,<2.57.0' - r-base build: - {{ compiler('c') }} diff --git a/recipes/bioconductor-metab/build.sh b/recipes/bioconductor-metab/build.sh index 5ea71a1203cac..c1d13421f5f1e 100644 --- a/recipes/bioconductor-metab/build.sh +++ b/recipes/bioconductor-metab/build.sh @@ -8,4 +8,4 @@ CXX=$CXX CXX98=$CXX CXX11=$CXX CXX14=$CXX" > ~/.R/Makevars -$R CMD INSTALL --build . +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-metab/meta.yaml b/recipes/bioconductor-metab/meta.yaml index fd913199f4198..e8d4e48522fa7 100644 --- a/recipes/bioconductor-metab/meta.yaml +++ b/recipes/bioconductor-metab/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.16.1" %} +{% set version = "1.18.0" %} {% set name = "Metab" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 96f5fdfd612c7a2c52e89ac3d3a7f0c0 + md5: 72560743a678a57eb3a634be599a72fd build: number: 0 rpaths: @@ -20,12 +20,12 @@ build: # Suggests: RUnit, BiocGenerics requirements: host: - - 'bioconductor-xcms >=3.4.0,<3.5.0' + - 'bioconductor-xcms >=3.6.0,<3.7.0' - r-base - r-pander - r-svdialogs run: - - 'bioconductor-xcms >=3.4.0,<3.5.0' + - 'bioconductor-xcms >=3.6.0,<3.7.0' - r-base - r-pander - r-svdialogs diff --git a/recipes/bioconductor-metabomxtr/meta.yaml b/recipes/bioconductor-metabomxtr/meta.yaml index 44a410465aba7..a9e220b01b017 100644 --- a/recipes/bioconductor-metabomxtr/meta.yaml +++ b/recipes/bioconductor-metabomxtr/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.16.1" %} +{% set version = "1.18.0" %} {% set name = "metabomxtr" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - sha256: 8c1e0fce07d18c254a4f46e9edc43af5f26e897265f787eba2270ee55f84e1db + md5: 9d9d01919c3c1a6862df51f84037f152 build: number: 0 rpaths: @@ -20,18 +20,18 @@ build: # Suggests: xtable, reshape2 requirements: host: - - 'bioconductor-biobase >=2.42.0,<2.43.0' - - 'bioconductor-biocparallel >=1.16.0,<1.17.0' - - 'bioconductor-multtest >=2.38.0,<2.39.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' + - 'bioconductor-biocparallel >=1.18.0,<1.19.0' + - 'bioconductor-multtest >=2.40.0,<2.41.0' - r-base - r-formula - r-ggplot2 - r-optimx - r-plyr run: - - 'bioconductor-biobase >=2.42.0,<2.43.0' - - 'bioconductor-biocparallel >=1.16.0,<1.17.0' - - 'bioconductor-multtest >=2.38.0,<2.39.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' + - 'bioconductor-biocparallel >=1.18.0,<1.19.0' + - 'bioconductor-multtest >=2.40.0,<2.41.0' - r-base - r-formula - r-ggplot2 diff --git a/recipes/bioconductor-metabosignal/meta.yaml b/recipes/bioconductor-metabosignal/meta.yaml index 4380d8a95e8c3..d5c6bb87496a0 100644 --- a/recipes/bioconductor-metabosignal/meta.yaml +++ b/recipes/bioconductor-metabosignal/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.12.0" %} +{% set version = "1.14.0" %} {% set name = "MetaboSignal" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: cde3fdfabbe4271392c9c5a5b6b0827f + md5: 0871a575a25e669e1419961747e5ad3f build: number: 0 rpaths: @@ -20,28 +20,28 @@ build: # Suggests: RUnit, BiocGenerics, knitr, BiocStyle, rmarkdown requirements: host: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' - - 'bioconductor-biomart >=2.38.0,<2.39.0' - - 'bioconductor-ensdb.hsapiens.v75 >=2.99.0,<2.100.0' - - 'bioconductor-hpar >=1.24.0,<1.25.0' - - 'bioconductor-kegggraph >=1.42.0,<1.43.0' - - 'bioconductor-keggrest >=1.22.0,<1.23.0' - - 'bioconductor-mwastools >=1.6.0,<1.7.0' - - 'bioconductor-mygene >=1.18.0,<1.19.0' - - 'bioconductor-org.hs.eg.db >=3.7.0,<3.8.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' + - 'bioconductor-biomart >=2.40.0,<2.41.0' + - 'bioconductor-ensdb.hsapiens.v75 >=3.0.0,<3.1.0' + - 'bioconductor-hpar >=1.26.0,<1.27.0' + - 'bioconductor-kegggraph >=1.44.0,<1.45.0' + - 'bioconductor-keggrest >=1.24.0,<1.25.0' + - 'bioconductor-mwastools >=1.8.0,<1.9.0' + - 'bioconductor-mygene >=1.20.0,<1.21.0' + - 'bioconductor-org.hs.eg.db >=3.8.0,<3.9.0' - r-base - r-igraph - r-rcurl run: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' - - 'bioconductor-biomart >=2.38.0,<2.39.0' - - 'bioconductor-ensdb.hsapiens.v75 >=2.99.0,<2.100.0' - - 'bioconductor-hpar >=1.24.0,<1.25.0' - - 'bioconductor-kegggraph >=1.42.0,<1.43.0' - - 'bioconductor-keggrest >=1.22.0,<1.23.0' - - 'bioconductor-mwastools >=1.6.0,<1.7.0' - - 'bioconductor-mygene >=1.18.0,<1.19.0' - - 'bioconductor-org.hs.eg.db >=3.7.0,<3.8.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' + - 'bioconductor-biomart >=2.40.0,<2.41.0' + - 'bioconductor-ensdb.hsapiens.v75 >=3.0.0,<3.1.0' + - 'bioconductor-hpar >=1.26.0,<1.27.0' + - 'bioconductor-kegggraph >=1.44.0,<1.45.0' + - 'bioconductor-keggrest >=1.24.0,<1.25.0' + - 'bioconductor-mwastools >=1.8.0,<1.9.0' + - 'bioconductor-mygene >=1.20.0,<1.21.0' + - 'bioconductor-org.hs.eg.db >=3.8.0,<3.9.0' - r-base - r-igraph - r-rcurl diff --git a/recipes/bioconductor-metacca/meta.yaml b/recipes/bioconductor-metacca/meta.yaml index 9bbbae46c74e8..ec71bdc8129f4 100644 --- a/recipes/bioconductor-metacca/meta.yaml +++ b/recipes/bioconductor-metacca/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.10.0" %} +{% set version = "1.12.0" %} {% set name = "metaCCA" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 50c6cad7861b8a8c9d42e5ee6cba4a4f + md5: 02cd0b7e8ba5bf167a3313dd8397e03b build: number: 0 rpaths: diff --git a/recipes/bioconductor-metacyto/meta.yaml b/recipes/bioconductor-metacyto/meta.yaml index 57fbd9fe848f8..a54fca9a4d698 100644 --- a/recipes/bioconductor-metacyto/meta.yaml +++ b/recipes/bioconductor-metacyto/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.4.1" %} +{% set version = "1.6.0" %} {% set name = "MetaCyto" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 72f59f04fc721b26517bc2968210f410 + md5: 38315a7bc63f03a7f2fdf63a04671134 build: number: 0 rpaths: @@ -20,8 +20,8 @@ build: # Suggests: knitr, dplyr requirements: host: - - 'bioconductor-flowcore >=1.48.0,<1.49.0' - - 'bioconductor-flowsom >=1.14.0,<1.15.0' + - 'bioconductor-flowcore >=1.50.0,<1.51.0' + - 'bioconductor-flowsom >=1.16.0,<1.17.0' - r-base - r-cluster - r-fastcluster @@ -29,8 +29,8 @@ requirements: - r-metafor - 'r-tidyr >=0.7' run: - - 'bioconductor-flowcore >=1.48.0,<1.49.0' - - 'bioconductor-flowsom >=1.14.0,<1.15.0' + - 'bioconductor-flowcore >=1.50.0,<1.51.0' + - 'bioconductor-flowsom >=1.16.0,<1.17.0' - r-base - r-cluster - r-fastcluster diff --git a/recipes/bioconductor-metagene/meta.yaml b/recipes/bioconductor-metagene/meta.yaml index 13a33b99f14d6..d07aadd3cbeb2 100644 --- a/recipes/bioconductor-metagene/meta.yaml +++ b/recipes/bioconductor-metagene/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "2.14.0" %} +{% set version = "2.16.0" %} {% set name = "metagene" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 5a33016df96518252fa9483efbea65f8 + md5: dad27037a0cf662f0db8b1ebbe83f3c8 build: number: 0 rpaths: @@ -20,17 +20,17 @@ build: # Suggests: BiocGenerics, similaRpeak, RUnit, knitr, BiocStyle, rmarkdown, similaRpeak requirements: host: - - 'bioconductor-biocparallel >=1.16.0,<1.17.0' - - 'bioconductor-dbchip >=1.26.0,<1.27.0' - - 'bioconductor-ensdb.hsapiens.v86 >=2.99.0,<2.100.0' - - 'bioconductor-ensembldb >=2.6.0,<2.7.0' - - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' - - 'bioconductor-genomicalignments >=1.18.0,<1.19.0' - - 'bioconductor-genomicfeatures >=1.34.0,<1.35.0' - - 'bioconductor-genomicranges >=1.34.0,<1.35.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-rsamtools >=1.34.0,<1.35.0' - - 'bioconductor-rtracklayer >=1.42.0,<1.43.0' + - 'bioconductor-biocparallel >=1.18.0,<1.19.0' + - 'bioconductor-dbchip >=1.28.0,<1.29.0' + - 'bioconductor-ensdb.hsapiens.v86 >=3.0.0,<3.1.0' + - 'bioconductor-ensembldb >=2.8.0,<2.9.0' + - 'bioconductor-genomeinfodb >=1.20.0,<1.21.0' + - 'bioconductor-genomicalignments >=1.20.0,<1.21.0' + - 'bioconductor-genomicfeatures >=1.36.0,<1.37.0' + - 'bioconductor-genomicranges >=1.36.0,<1.37.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-rsamtools >=2.0.0,<2.1.0' + - 'bioconductor-rtracklayer >=1.44.0,<1.45.0' - r-base - r-data.table - r-ggplot2 @@ -42,17 +42,17 @@ requirements: - 'r-r6 >=2.0' - r-stringr run: - - 'bioconductor-biocparallel >=1.16.0,<1.17.0' - - 'bioconductor-dbchip >=1.26.0,<1.27.0' - - 'bioconductor-ensdb.hsapiens.v86 >=2.99.0,<2.100.0' - - 'bioconductor-ensembldb >=2.6.0,<2.7.0' - - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' - - 'bioconductor-genomicalignments >=1.18.0,<1.19.0' - - 'bioconductor-genomicfeatures >=1.34.0,<1.35.0' - - 'bioconductor-genomicranges >=1.34.0,<1.35.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-rsamtools >=1.34.0,<1.35.0' - - 'bioconductor-rtracklayer >=1.42.0,<1.43.0' + - 'bioconductor-biocparallel >=1.18.0,<1.19.0' + - 'bioconductor-dbchip >=1.28.0,<1.29.0' + - 'bioconductor-ensdb.hsapiens.v86 >=3.0.0,<3.1.0' + - 'bioconductor-ensembldb >=2.8.0,<2.9.0' + - 'bioconductor-genomeinfodb >=1.20.0,<1.21.0' + - 'bioconductor-genomicalignments >=1.20.0,<1.21.0' + - 'bioconductor-genomicfeatures >=1.36.0,<1.37.0' + - 'bioconductor-genomicranges >=1.36.0,<1.37.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-rsamtools >=2.0.0,<2.1.0' + - 'bioconductor-rtracklayer >=1.44.0,<1.45.0' - r-base - r-data.table - r-ggplot2 diff --git a/recipes/bioconductor-metagene2/build.sh b/recipes/bioconductor-metagene2/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-metagene2/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-metagene2/meta.yaml b/recipes/bioconductor-metagene2/meta.yaml new file mode 100644 index 0000000000000..cf2c056050eca --- /dev/null +++ b/recipes/bioconductor-metagene2/meta.yaml @@ -0,0 +1,61 @@ +{% set version = "1.0.0" %} +{% set name = "metagene2" %} +{% set bioc = "3.9" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + md5: 381dbccb0c6a7b747e5261115f1970cd +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: BiocGenerics, RUnit, knitr, BiocStyle, rmarkdown +requirements: + host: + - 'bioconductor-biocparallel >=1.18.0,<1.19.0' + - 'bioconductor-dbchip >=1.28.0,<1.29.0' + - 'bioconductor-genomeinfodb >=1.20.0,<1.21.0' + - 'bioconductor-genomicalignments >=1.20.0,<1.21.0' + - 'bioconductor-genomicranges >=1.36.0,<1.37.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-rsamtools >=2.0.0,<2.1.0' + - 'bioconductor-rtracklayer >=1.44.0,<1.45.0' + - r-base + - r-data.table + - r-dplyr + - r-ggplot2 + - r-magrittr + - r-purrr + - 'r-r6 >=2.0' + run: + - 'bioconductor-biocparallel >=1.18.0,<1.19.0' + - 'bioconductor-dbchip >=1.28.0,<1.29.0' + - 'bioconductor-genomeinfodb >=1.20.0,<1.21.0' + - 'bioconductor-genomicalignments >=1.20.0,<1.21.0' + - 'bioconductor-genomicranges >=1.36.0,<1.37.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-rsamtools >=2.0.0,<2.1.0' + - 'bioconductor-rtracklayer >=1.44.0,<1.45.0' + - r-base + - r-data.table + - r-dplyr + - r-ggplot2 + - r-magrittr + - r-purrr + - 'r-r6 >=2.0' +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'This package produces metagene plots to compare coverages of sequencing experiments at selected groups of genomic regions. It can be used for such analyses as assessing the binding of DNA-interacting proteins at promoter regions or surveying antisense transcription over the length of a gene. The metagene2 package can manage all aspects of the analysis, from normalization of coverages to plot facetting according to experimental metadata. Bootstraping analysis is used to provide confidence intervals of per-sample mean coverages.' + diff --git a/recipes/bioconductor-metagenomefeatures/meta.yaml b/recipes/bioconductor-metagenomefeatures/meta.yaml index c6336316eb7fc..c13cdb6b77f97 100644 --- a/recipes/bioconductor-metagenomefeatures/meta.yaml +++ b/recipes/bioconductor-metagenomefeatures/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "2.2.0" %} +{% set version = "2.4.0" %} {% set name = "metagenomeFeatures" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,20 +10,20 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 751c0d0ab00c437e3b87e2c068f83f39 + md5: 1c3987396555e229b181613b022514d2 build: number: 0 rpaths: - lib/R/lib/ - lib/ noarch: generic -# Suggests: knitr (>= 1.11), testthat (>= 0.10.0), rmarkdown (>= 1.3), tidyverse (>= 1.2.1), devtools (>= 1.13.5), ggtree(>= 1.8.2) +# Suggests: knitr (>= 1.11), testthat (>= 0.10.0), rmarkdown (>= 1.3), devtools (>= 1.13.5), ggtree(>= 1.8.2), BiocStyle (>= 2.8.2), phyloseq (>= 1.24.2), forcats (>= 0.3.0), ggplot2 (>= 3.0.0) requirements: host: - - 'bioconductor-biobase >=2.42.0,<2.43.0' - - 'bioconductor-biostrings >=2.50.0,<2.51.0' - - 'bioconductor-decipher >=2.10.0,<2.11.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' + - 'bioconductor-biostrings >=2.52.0,<2.53.0' + - 'bioconductor-decipher >=2.12.0,<2.13.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' - 'r-ape >=3.5' - r-base - 'r-dbplyr >=1.0.0' @@ -31,14 +31,13 @@ requirements: - 'r-lattice >=0.20.33' - 'r-lazyeval >=0.1.10' - 'r-magrittr >=1.5' - - 'r-purrr >=0.2.2' - 'r-rsqlite >=1.0.0' - 'r-stringr >=1.0.0' run: - - 'bioconductor-biobase >=2.42.0,<2.43.0' - - 'bioconductor-biostrings >=2.50.0,<2.51.0' - - 'bioconductor-decipher >=2.10.0,<2.11.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' + - 'bioconductor-biostrings >=2.52.0,<2.53.0' + - 'bioconductor-decipher >=2.12.0,<2.13.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' - 'r-ape >=3.5' - r-base - 'r-dbplyr >=1.0.0' @@ -46,7 +45,6 @@ requirements: - 'r-lattice >=0.20.33' - 'r-lazyeval >=0.1.10' - 'r-magrittr >=1.5' - - 'r-purrr >=0.2.2' - 'r-rsqlite >=1.0.0' - 'r-stringr >=1.0.0' test: diff --git a/recipes/bioconductor-metagenomeseq/meta.yaml b/recipes/bioconductor-metagenomeseq/meta.yaml index 84d7cf3af1d61..7bc019fe663ac 100644 --- a/recipes/bioconductor-metagenomeseq/meta.yaml +++ b/recipes/bioconductor-metagenomeseq/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.24.1" %} +{% set version = "1.26.0" %} {% set name = "metagenomeSeq" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: e8785142935fd01357c1a27f182768bdc43e1f2607100ef7e975cf4ae34e4b7f + md5: bf7742b3561fbf9fd63ffc76ba8388f5 build: number: 0 rpaths: @@ -20,8 +20,10 @@ build: # Suggests: annotate, BiocGenerics, biomformat, knitr, gss, testthat (>= 0.8), vegan, interactiveDisplay requirements: host: - - 'bioconductor-biobase >=2.42.0,<2.43.0' - - 'bioconductor-limma >=3.38.0,<3.39.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' + - 'bioconductor-ihw >=1.12.0,<1.13.0' + - 'bioconductor-limma >=3.40.0,<3.41.0' + - 'bioconductor-wrench >=1.2.0,<1.3.0' - r-base - r-foreach - r-glmnet @@ -30,8 +32,10 @@ requirements: - r-matrixstats - r-rcolorbrewer run: - - 'bioconductor-biobase >=2.42.0,<2.43.0' - - 'bioconductor-limma >=3.38.0,<3.39.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' + - 'bioconductor-ihw >=1.12.0,<1.13.0' + - 'bioconductor-limma >=3.40.0,<3.41.0' + - 'bioconductor-wrench >=1.2.0,<1.3.0' - r-base - r-foreach - r-glmnet diff --git a/recipes/bioconductor-metagxbreast/meta.yaml b/recipes/bioconductor-metagxbreast/meta.yaml index 02457e3758156..19a2d06fad3ce 100644 --- a/recipes/bioconductor-metagxbreast/meta.yaml +++ b/recipes/bioconductor-metagxbreast/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.2.0" %} +{% set version = "1.4.0" %} {% set name = "MetaGxBreast" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 1157831dd3b4e2b789b5833c1586b7a6 + md5: ebc1b88b0cbc809a6ee615a618ae9e87 build: number: 0 rpaths: @@ -20,20 +20,22 @@ build: # Suggests: testthat, xtable requirements: host: - - 'bioconductor-annotationhub >=2.14.0,<2.15.0' - - 'bioconductor-biobase >=2.42.0,<2.43.0' - - 'bioconductor-experimenthub >=1.8.0,<1.9.0' - - 'bioconductor-impute >=1.56.0,<1.57.0' + - 'bioconductor-annotationhub >=2.16.0,<2.17.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' + - 'bioconductor-experimenthub >=1.10.0,<1.11.0' + - 'bioconductor-impute >=1.58.0,<1.59.0' + - 'bioconductor-summarizedexperiment >=1.14.0,<1.15.0' - r-base - r-lattice run: - - 'bioconductor-annotationhub >=2.14.0,<2.15.0' - - 'bioconductor-biobase >=2.42.0,<2.43.0' - - 'bioconductor-experimenthub >=1.8.0,<1.9.0' - - 'bioconductor-impute >=1.56.0,<1.57.0' + - 'bioconductor-annotationhub >=2.16.0,<2.17.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' + - 'bioconductor-experimenthub >=1.10.0,<1.11.0' + - 'bioconductor-impute >=1.58.0,<1.59.0' + - 'bioconductor-summarizedexperiment >=1.14.0,<1.15.0' - r-base - r-lattice - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-metagxbreast/post-link.sh b/recipes/bioconductor-metagxbreast/post-link.sh index 819dd8ea34b6d..f6c7ff84acad7 100644 --- a/recipes/bioconductor-metagxbreast/post-link.sh +++ b/recipes/bioconductor-metagxbreast/post-link.sh @@ -1,11 +1,11 @@ #!/bin/bash -FN="MetaGxBreast_1.2.0.tar.gz" +FN="MetaGxBreast_1.4.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/experiment/src/contrib/MetaGxBreast_1.2.0.tar.gz" - "https://bioarchive.galaxyproject.org/MetaGxBreast_1.2.0.tar.gz" - "https://depot.galaxyproject.org/software/bioconductor-metagxbreast/bioconductor-metagxbreast_1.2.0_src_all.tar.gz" + "https://bioconductor.org/packages/3.9/data/experiment/src/contrib/MetaGxBreast_1.4.0.tar.gz" + "https://bioarchive.galaxyproject.org/MetaGxBreast_1.4.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-metagxbreast/bioconductor-metagxbreast_1.4.0_src_all.tar.gz" ) -MD5="1157831dd3b4e2b789b5833c1586b7a6" +MD5="ebc1b88b0cbc809a6ee615a618ae9e87" # Use a staging area in the conda dir rather than temp dirs, both to avoid # permission issues as well as to have things downloaded in a predictable @@ -16,7 +16,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-metagxovarian/meta.yaml b/recipes/bioconductor-metagxovarian/meta.yaml index 16c37921b28db..fb10d83e532bc 100644 --- a/recipes/bioconductor-metagxovarian/meta.yaml +++ b/recipes/bioconductor-metagxovarian/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.2.0" %} +{% set version = "1.4.0" %} {% set name = "MetaGxOvarian" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: fc131f6eb1d2c6317560da14ff12c06d + md5: 19c08da41e05075e9498397490027658 build: number: 0 rpaths: @@ -20,20 +20,22 @@ build: # Suggests: testthat, xtable requirements: host: - - 'bioconductor-annotationhub >=2.14.0,<2.15.0' - - 'bioconductor-biobase >=2.42.0,<2.43.0' - - 'bioconductor-experimenthub >=1.8.0,<1.9.0' - - 'bioconductor-impute >=1.56.0,<1.57.0' + - 'bioconductor-annotationhub >=2.16.0,<2.17.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' + - 'bioconductor-experimenthub >=1.10.0,<1.11.0' + - 'bioconductor-impute >=1.58.0,<1.59.0' + - 'bioconductor-summarizedexperiment >=1.14.0,<1.15.0' - r-base - r-lattice run: - - 'bioconductor-annotationhub >=2.14.0,<2.15.0' - - 'bioconductor-biobase >=2.42.0,<2.43.0' - - 'bioconductor-experimenthub >=1.8.0,<1.9.0' - - 'bioconductor-impute >=1.56.0,<1.57.0' + - 'bioconductor-annotationhub >=2.16.0,<2.17.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' + - 'bioconductor-experimenthub >=1.10.0,<1.11.0' + - 'bioconductor-impute >=1.58.0,<1.59.0' + - 'bioconductor-summarizedexperiment >=1.14.0,<1.15.0' - r-base - r-lattice - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-metagxovarian/post-link.sh b/recipes/bioconductor-metagxovarian/post-link.sh index 0a3daf8cf07a0..20ef91fc7c699 100644 --- a/recipes/bioconductor-metagxovarian/post-link.sh +++ b/recipes/bioconductor-metagxovarian/post-link.sh @@ -1,11 +1,11 @@ #!/bin/bash -FN="MetaGxOvarian_1.2.0.tar.gz" +FN="MetaGxOvarian_1.4.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/experiment/src/contrib/MetaGxOvarian_1.2.0.tar.gz" - "https://bioarchive.galaxyproject.org/MetaGxOvarian_1.2.0.tar.gz" - "https://depot.galaxyproject.org/software/bioconductor-metagxovarian/bioconductor-metagxovarian_1.2.0_src_all.tar.gz" + "https://bioconductor.org/packages/3.9/data/experiment/src/contrib/MetaGxOvarian_1.4.0.tar.gz" + "https://bioarchive.galaxyproject.org/MetaGxOvarian_1.4.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-metagxovarian/bioconductor-metagxovarian_1.4.0_src_all.tar.gz" ) -MD5="fc131f6eb1d2c6317560da14ff12c06d" +MD5="19c08da41e05075e9498397490027658" # Use a staging area in the conda dir rather than temp dirs, both to avoid # permission issues as well as to have things downloaded in a predictable @@ -16,7 +16,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-metagxpancreas/meta.yaml b/recipes/bioconductor-metagxpancreas/meta.yaml index d929faf294d2a..db2ef0b18a07b 100644 --- a/recipes/bioconductor-metagxpancreas/meta.yaml +++ b/recipes/bioconductor-metagxpancreas/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.2.0" %} +{% set version = "1.4.0" %} {% set name = "MetaGxPancreas" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 974a7f5e6f82070585bdc35cc843ccea + md5: 8c87608964940fa1f28b5713c6588414 build: number: 0 rpaths: @@ -20,20 +20,22 @@ build: # Suggests: testthat, xtable requirements: host: - - 'bioconductor-annotationhub >=2.14.0,<2.15.0' - - 'bioconductor-biobase >=2.42.0,<2.43.0' - - 'bioconductor-experimenthub >=1.8.0,<1.9.0' - - 'bioconductor-impute >=1.56.0,<1.57.0' + - 'bioconductor-annotationhub >=2.16.0,<2.17.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' + - 'bioconductor-experimenthub >=1.10.0,<1.11.0' + - 'bioconductor-impute >=1.58.0,<1.59.0' + - 'bioconductor-summarizedexperiment >=1.14.0,<1.15.0' - r-base - r-lattice run: - - 'bioconductor-annotationhub >=2.14.0,<2.15.0' - - 'bioconductor-biobase >=2.42.0,<2.43.0' - - 'bioconductor-experimenthub >=1.8.0,<1.9.0' - - 'bioconductor-impute >=1.56.0,<1.57.0' + - 'bioconductor-annotationhub >=2.16.0,<2.17.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' + - 'bioconductor-experimenthub >=1.10.0,<1.11.0' + - 'bioconductor-impute >=1.58.0,<1.59.0' + - 'bioconductor-summarizedexperiment >=1.14.0,<1.15.0' - r-base - r-lattice - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-metagxpancreas/post-link.sh b/recipes/bioconductor-metagxpancreas/post-link.sh index 21aab26b9027a..aab54d1b4c847 100644 --- a/recipes/bioconductor-metagxpancreas/post-link.sh +++ b/recipes/bioconductor-metagxpancreas/post-link.sh @@ -1,11 +1,11 @@ #!/bin/bash -FN="MetaGxPancreas_1.2.0.tar.gz" +FN="MetaGxPancreas_1.4.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/experiment/src/contrib/MetaGxPancreas_1.2.0.tar.gz" - "https://bioarchive.galaxyproject.org/MetaGxPancreas_1.2.0.tar.gz" - "https://depot.galaxyproject.org/software/bioconductor-metagxpancreas/bioconductor-metagxpancreas_1.2.0_src_all.tar.gz" + "https://bioconductor.org/packages/3.9/data/experiment/src/contrib/MetaGxPancreas_1.4.0.tar.gz" + "https://bioarchive.galaxyproject.org/MetaGxPancreas_1.4.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-metagxpancreas/bioconductor-metagxpancreas_1.4.0_src_all.tar.gz" ) -MD5="974a7f5e6f82070585bdc35cc843ccea" +MD5="8c87608964940fa1f28b5713c6588414" # Use a staging area in the conda dir rather than temp dirs, both to avoid # permission issues as well as to have things downloaded in a predictable @@ -16,7 +16,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-metahdep/meta.yaml b/recipes/bioconductor-metahdep/meta.yaml index 24f27d92ca270..4199040068496 100644 --- a/recipes/bioconductor-metahdep/meta.yaml +++ b/recipes/bioconductor-metahdep/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.40.0" %} +{% set version = "1.42.0" %} {% set name = "metahdep" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 1ec5c00ecd70c4a2989f0ef02ae1e868 + md5: 53978153bca3e1c0eeb53c335c52ece8 build: number: 0 rpaths: diff --git a/recipes/bioconductor-metams/meta.yaml b/recipes/bioconductor-metams/meta.yaml index b75e7325523ec..a43456e7a003d 100644 --- a/recipes/bioconductor-metams/meta.yaml +++ b/recipes/bioconductor-metams/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.18.1" %} +{% set version = "1.20.0" %} {% set name = "metaMS" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 01f703155939aae7470e303f6a722cee + md5: d8fe444714c4b37bd55b105fb733dbe6 build: number: 0 rpaths: @@ -20,16 +20,16 @@ build: # Suggests: metaMSdata, RUnit requirements: host: - - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' - - 'bioconductor-camera >=1.38.0,<1.39.0' - - 'bioconductor-xcms >=3.4.0,<3.5.0' + - 'bioconductor-biocgenerics >=0.30.0,<0.31.0' + - 'bioconductor-camera >=1.40.0,<1.41.0' + - 'bioconductor-xcms >=3.6.0,<3.7.0' - r-base - r-matrix - r-robustbase run: - - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' - - 'bioconductor-camera >=1.38.0,<1.39.0' - - 'bioconductor-xcms >=3.4.0,<3.5.0' + - 'bioconductor-biocgenerics >=0.30.0,<0.31.0' + - 'bioconductor-camera >=1.40.0,<1.41.0' + - 'bioconductor-xcms >=3.6.0,<3.7.0' - r-base - r-matrix - r-robustbase diff --git a/recipes/bioconductor-metamsdata/meta.yaml b/recipes/bioconductor-metamsdata/meta.yaml index 4734a887f56a5..10ab77671c2fe 100644 --- a/recipes/bioconductor-metamsdata/meta.yaml +++ b/recipes/bioconductor-metamsdata/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.18.0" %} +{% set version = "1.20.0" %} {% set name = "metaMSdata" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: c2755dd8852d556ae98deb6d06d355af + md5: 60703c7f827a3e2f1ca0abe3afa39d5b build: number: 0 rpaths: @@ -22,7 +22,7 @@ requirements: - r-base run: - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-metamsdata/post-link.sh b/recipes/bioconductor-metamsdata/post-link.sh index ee1e7a247348d..6ba64fbab3332 100644 --- a/recipes/bioconductor-metamsdata/post-link.sh +++ b/recipes/bioconductor-metamsdata/post-link.sh @@ -1,11 +1,11 @@ #!/bin/bash -FN="metaMSdata_1.18.0.tar.gz" +FN="metaMSdata_1.20.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/experiment/src/contrib/metaMSdata_1.18.0.tar.gz" - "https://bioarchive.galaxyproject.org/metaMSdata_1.18.0.tar.gz" - "https://depot.galaxyproject.org/software/bioconductor-metamsdata/bioconductor-metamsdata_1.18.0_src_all.tar.gz" + "https://bioconductor.org/packages/3.9/data/experiment/src/contrib/metaMSdata_1.20.0.tar.gz" + "https://bioarchive.galaxyproject.org/metaMSdata_1.20.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-metamsdata/bioconductor-metamsdata_1.20.0_src_all.tar.gz" ) -MD5="c2755dd8852d556ae98deb6d06d355af" +MD5="60703c7f827a3e2f1ca0abe3afa39d5b" # Use a staging area in the conda dir rather than temp dirs, both to avoid # permission issues as well as to have things downloaded in a predictable @@ -16,7 +16,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-metaneighbor/meta.yaml b/recipes/bioconductor-metaneighbor/meta.yaml index 8ec51b14f57aa..a9ad215b663fe 100644 --- a/recipes/bioconductor-metaneighbor/meta.yaml +++ b/recipes/bioconductor-metaneighbor/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.2.0" %} +{% set version = "1.4.0" %} {% set name = "MetaNeighbor" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,27 +10,38 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: cdfa4ea9e41f76e1cd208d5dbcb182d9 + md5: a56fc917c62d35882e3cda1aa7132759 build: number: 0 rpaths: - lib/R/lib/ - lib/ - noarch: generic # Suggests: knitr (>= 1.17), rmarkdown (>= 1.6), testthat (>= 1.0.2) requirements: host: - - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' + - 'bioconductor-genomicranges >=1.36.0,<1.37.0' + - 'bioconductor-summarizedexperiment >=1.14.0,<1.15.0' - r-base - 'r-beanplot >=1.2' - 'r-gplots >=3.0.1' + - 'r-matrix >=1.2' + - 'r-matrixstats >=0.54' - 'r-rcolorbrewer >=1.1' + - r-rcpp run: - - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' + - 'bioconductor-genomicranges >=1.36.0,<1.37.0' + - 'bioconductor-summarizedexperiment >=1.14.0,<1.15.0' - r-base - 'r-beanplot >=1.2' - 'r-gplots >=3.0.1' + - 'r-matrix >=1.2' + - 'r-matrixstats >=0.54' - 'r-rcolorbrewer >=1.1' + - r-rcpp + build: + - {{ compiler('c') }} + - {{ compiler('cxx') }} + - make test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-metaseq/meta.yaml b/recipes/bioconductor-metaseq/meta.yaml index 1df553df8f1f6..23d0a46242bac 100644 --- a/recipes/bioconductor-metaseq/meta.yaml +++ b/recipes/bioconductor-metaseq/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.22.1" %} +{% set version = "1.24.0" %} {% set name = "metaSeq" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 524028c02437bc7f07237cf2a83f727f + md5: 9849976f5f3130155bcc317d002c50a6 build: number: 0 rpaths: @@ -18,12 +18,12 @@ build: - lib/ requirements: host: - - 'bioconductor-noiseq >=2.26.0,<2.27.0' + - 'bioconductor-noiseq >=2.28.0,<2.29.0' - r-base - r-rcpp - r-snow run: - - 'bioconductor-noiseq >=2.26.0,<2.27.0' + - 'bioconductor-noiseq >=2.28.0,<2.29.0' - r-base - r-rcpp - r-snow diff --git a/recipes/bioconductor-metaseqr/meta.yaml b/recipes/bioconductor-metaseqr/meta.yaml index f6396cd320ae4..dbefe39037eaa 100644 --- a/recipes/bioconductor-metaseqr/meta.yaml +++ b/recipes/bioconductor-metaseqr/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.22.1" %} +{% set version = "1.24.0" %} {% set name = "metaseqR" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 68442083a54f6e92703baa04477846de + md5: c6754c642aa149667090c8b30c96d915 build: number: 0 rpaths: @@ -20,15 +20,15 @@ build: # Suggests: BiocGenerics, GenomicRanges, rtracklayer, Rsamtools, survcomp, VennDiagram, knitr, zoo, RUnit, BiocManager, BSgenome, RSQLite requirements: host: - - 'bioconductor-bayseq >=2.16.0,<2.17.0' - - 'bioconductor-biomart >=2.38.0,<2.39.0' - - 'bioconductor-deseq >=1.34.0,<1.35.0' - - 'bioconductor-edaseq >=2.16.0,<2.17.0' - - 'bioconductor-edger >=3.24.0,<3.25.0' - - 'bioconductor-limma >=3.38.0,<3.39.0' - - 'bioconductor-noiseq >=2.26.0,<2.27.0' - - 'bioconductor-qvalue >=2.14.0,<2.15.0' - - 'bioconductor-vsn >=3.50.0,<3.51.0' + - 'bioconductor-bayseq >=2.18.0,<2.19.0' + - 'bioconductor-biomart >=2.40.0,<2.41.0' + - 'bioconductor-deseq >=1.36.0,<1.37.0' + - 'bioconductor-edaseq >=2.18.0,<2.19.0' + - 'bioconductor-edger >=3.26.0,<3.27.0' + - 'bioconductor-limma >=3.40.0,<3.41.0' + - 'bioconductor-noiseq >=2.28.0,<2.29.0' + - 'bioconductor-qvalue >=2.16.0,<2.17.0' + - 'bioconductor-vsn >=3.52.0,<3.53.0' - r-base - r-brew - r-corrplot @@ -37,15 +37,15 @@ requirements: - r-nbpseq - r-rjson run: - - 'bioconductor-bayseq >=2.16.0,<2.17.0' - - 'bioconductor-biomart >=2.38.0,<2.39.0' - - 'bioconductor-deseq >=1.34.0,<1.35.0' - - 'bioconductor-edaseq >=2.16.0,<2.17.0' - - 'bioconductor-edger >=3.24.0,<3.25.0' - - 'bioconductor-limma >=3.38.0,<3.39.0' - - 'bioconductor-noiseq >=2.26.0,<2.27.0' - - 'bioconductor-qvalue >=2.14.0,<2.15.0' - - 'bioconductor-vsn >=3.50.0,<3.51.0' + - 'bioconductor-bayseq >=2.18.0,<2.19.0' + - 'bioconductor-biomart >=2.40.0,<2.41.0' + - 'bioconductor-deseq >=1.36.0,<1.37.0' + - 'bioconductor-edaseq >=2.18.0,<2.19.0' + - 'bioconductor-edger >=3.26.0,<3.27.0' + - 'bioconductor-limma >=3.40.0,<3.41.0' + - 'bioconductor-noiseq >=2.28.0,<2.29.0' + - 'bioconductor-qvalue >=2.16.0,<2.17.0' + - 'bioconductor-vsn >=3.52.0,<3.53.0' - r-base - r-brew - r-corrplot diff --git a/recipes/bioconductor-metavizr/meta.yaml b/recipes/bioconductor-metavizr/meta.yaml index 07853c4c3b549..a272f43fdcda4 100644 --- a/recipes/bioconductor-metavizr/meta.yaml +++ b/recipes/bioconductor-metavizr/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.6.1" %} +{% set version = "1.8.0" %} {% set name = "metavizr" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: a9f2fa64aa45b79c822c284ae5205d1c + md5: 454f7b0bed4f0f936f91f8f92e6f8340 build: number: 0 rpaths: @@ -20,28 +20,28 @@ build: # Suggests: knitr, BiocStyle, matrixStats, msd16s (>= 0.109.1), etec16s, testthat, gss, curatedMetagenomicData requirements: host: - - 'bioconductor-biobase >=2.42.0,<2.43.0' - - 'bioconductor-epivizr >=2.12.0,<2.13.0' - - 'bioconductor-epivizrdata >=1.10.0,<1.11.0' - - 'bioconductor-epivizrserver >=1.10.0,<1.11.0' - - 'bioconductor-epivizrstandalone >=1.10.0,<1.11.0' - - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' - - 'bioconductor-metagenomeseq >=1.24.0,<1.25.0' - - 'bioconductor-phyloseq >=1.26.0,<1.27.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' + - 'bioconductor-epivizr >=2.14.0,<2.15.0' + - 'bioconductor-epivizrdata >=1.12.0,<1.13.0' + - 'bioconductor-epivizrserver >=1.12.0,<1.13.0' + - 'bioconductor-epivizrstandalone >=1.12.0,<1.13.0' + - 'bioconductor-genomeinfodb >=1.20.0,<1.21.0' + - 'bioconductor-metagenomeseq >=1.26.0,<1.27.0' + - 'bioconductor-phyloseq >=1.28.0,<1.29.0' - r-base - r-data.table - r-digest - r-httr - r-vegan run: - - 'bioconductor-biobase >=2.42.0,<2.43.0' - - 'bioconductor-epivizr >=2.12.0,<2.13.0' - - 'bioconductor-epivizrdata >=1.10.0,<1.11.0' - - 'bioconductor-epivizrserver >=1.10.0,<1.11.0' - - 'bioconductor-epivizrstandalone >=1.10.0,<1.11.0' - - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' - - 'bioconductor-metagenomeseq >=1.24.0,<1.25.0' - - 'bioconductor-phyloseq >=1.26.0,<1.27.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' + - 'bioconductor-epivizr >=2.14.0,<2.15.0' + - 'bioconductor-epivizrdata >=1.12.0,<1.13.0' + - 'bioconductor-epivizrserver >=1.12.0,<1.13.0' + - 'bioconductor-epivizrstandalone >=1.12.0,<1.13.0' + - 'bioconductor-genomeinfodb >=1.20.0,<1.21.0' + - 'bioconductor-metagenomeseq >=1.26.0,<1.27.0' + - 'bioconductor-phyloseq >=1.28.0,<1.29.0' - r-base - r-data.table - r-digest diff --git a/recipes/bioconductor-metcirc/meta.yaml b/recipes/bioconductor-metcirc/meta.yaml index b47c8c1d8e804..5adf9f11fc921 100644 --- a/recipes/bioconductor-metcirc/meta.yaml +++ b/recipes/bioconductor-metcirc/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.12.1" %} +{% set version = "1.14.0" %} {% set name = "MetCirc" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 2bc0310c41d407d8d94188648f7e582a + md5: e4bdd5d5bf79760717004e0e768dc6fd build: number: 0 rpaths: diff --git a/recipes/bioconductor-methimpute/meta.yaml b/recipes/bioconductor-methimpute/meta.yaml index 8bb66702e5485..00b6dd32addd0 100644 --- a/recipes/bioconductor-methimpute/meta.yaml +++ b/recipes/bioconductor-methimpute/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.4.1" %} +{% set version = "1.6.0" %} {% set name = "methimpute" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: c63f19357ed780b1cb2cc16eecf61524 + md5: 8c2fce21cbc830cae5b9d64526c6b569 build: number: 0 rpaths: @@ -19,10 +19,10 @@ build: # Suggests: knitr, BiocStyle requirements: host: - - 'bioconductor-biostrings >=2.50.0,<2.51.0' - - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' - - 'bioconductor-genomicranges >=1.34.0,<1.35.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-biostrings >=2.52.0,<2.53.0' + - 'bioconductor-genomeinfodb >=1.20.0,<1.21.0' + - 'bioconductor-genomicranges >=1.36.0,<1.37.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' - r-base - r-data.table - r-ggplot2 @@ -30,10 +30,10 @@ requirements: - 'r-rcpp >=0.12.4.5' - r-reshape2 run: - - 'bioconductor-biostrings >=2.50.0,<2.51.0' - - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' - - 'bioconductor-genomicranges >=1.34.0,<1.35.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-biostrings >=2.52.0,<2.53.0' + - 'bioconductor-genomeinfodb >=1.20.0,<1.21.0' + - 'bioconductor-genomicranges >=1.36.0,<1.37.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' - r-base - r-data.table - r-ggplot2 @@ -44,7 +44,6 @@ requirements: - {{ compiler('c') }} - {{ compiler('cxx') }} - make - - llvm-openmp # [osx] test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-methinheritsim/meta.yaml b/recipes/bioconductor-methinheritsim/meta.yaml index 644696f844b4f..5f2454e5192eb 100644 --- a/recipes/bioconductor-methinheritsim/meta.yaml +++ b/recipes/bioconductor-methinheritsim/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.4.1" %} +{% set version = "1.6.0" %} {% set name = "methInheritSim" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 70da35403445ef588556718166474bc0 + md5: 33436a108f37f5e549a03e6612dc89d0 build: number: 0 rpaths: @@ -20,21 +20,21 @@ build: # Suggests: BiocStyle, knitr, rmarkdown, RUnit, methylInheritance requirements: host: - - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' - - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' - - 'bioconductor-genomicranges >=1.34.0,<1.35.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-methylkit >=1.8.0,<1.9.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-biocgenerics >=0.30.0,<0.31.0' + - 'bioconductor-genomeinfodb >=1.20.0,<1.21.0' + - 'bioconductor-genomicranges >=1.36.0,<1.37.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-methylkit >=1.10.0,<1.11.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' - r-base - r-msm run: - - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' - - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' - - 'bioconductor-genomicranges >=1.34.0,<1.35.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-methylkit >=1.8.0,<1.9.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-biocgenerics >=0.30.0,<0.31.0' + - 'bioconductor-genomeinfodb >=1.20.0,<1.21.0' + - 'bioconductor-genomicranges >=1.36.0,<1.37.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-methylkit >=1.10.0,<1.11.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' - r-base - r-msm test: diff --git a/recipes/bioconductor-methped/meta.yaml b/recipes/bioconductor-methped/meta.yaml index 53ddaa704406e..3ad2c9a008155 100644 --- a/recipes/bioconductor-methped/meta.yaml +++ b/recipes/bioconductor-methped/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.10.1" %} +{% set version = "1.12.0" %} {% set name = "MethPed" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: 16eb24c7bfeaac33d04055fd99011b8c2650dd97bcd322aff3172e714f279eed + md5: 772eab7137db1e2a13f07fefcb3f0366 build: number: 0 rpaths: @@ -20,11 +20,11 @@ build: # Suggests: BiocStyle, knitr, markdown, impute requirements: host: - - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' - r-base - r-randomforest run: - - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' - r-base - r-randomforest test: diff --git a/recipes/bioconductor-methtargetedngs/meta.yaml b/recipes/bioconductor-methtargetedngs/meta.yaml index b9cfbb9ff32ec..e9f68187800d0 100644 --- a/recipes/bioconductor-methtargetedngs/meta.yaml +++ b/recipes/bioconductor-methtargetedngs/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.14.0" %} +{% set version = "1.16.0" %} {% set name = "MethTargetedNGS" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: ade70d7cd180adfcc0cbb28eec6345ef + md5: 560df7085ab23e24f4cbd039a2c5a7c3 build: number: 0 rpaths: @@ -20,17 +20,19 @@ build: # SystemRequirements: HMMER3 requirements: host: - - 'bioconductor-biostrings >=2.50.0,<2.51.0' + - 'bioconductor-biostrings >=2.52.0,<2.53.0' - r-base - r-gplots - r-seqinr - r-stringr + - hmmer run: - - 'bioconductor-biostrings >=2.50.0,<2.51.0' + - 'bioconductor-biostrings >=2.52.0,<2.53.0' - r-base - r-gplots - r-seqinr - r-stringr + - hmmer test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-methvisual/meta.yaml b/recipes/bioconductor-methvisual/meta.yaml index c4ae956f52d5b..691d53d3017b6 100644 --- a/recipes/bioconductor-methvisual/meta.yaml +++ b/recipes/bioconductor-methvisual/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.34.0" %} +{% set version = "1.36.0" %} {% set name = "methVisual" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,17 +10,17 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: ec537978bc45ab9ada43c3b429825362 + md5: 4b4766fc35ffaa8929472d59000dd7d1 build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ noarch: generic requirements: host: - - 'bioconductor-biostrings >=2.50.0,<2.51.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-biostrings >=2.52.0,<2.53.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' - r-base - r-ca - r-gridbase @@ -28,8 +28,8 @@ requirements: - r-plotrix - r-sqldf run: - - 'bioconductor-biostrings >=2.50.0,<2.51.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-biostrings >=2.52.0,<2.53.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' - r-base - r-ca - r-gridbase diff --git a/recipes/bioconductor-methyanalysis/meta.yaml b/recipes/bioconductor-methyanalysis/meta.yaml index dc6de15927ea3..c7e8ab911b420 100644 --- a/recipes/bioconductor-methyanalysis/meta.yaml +++ b/recipes/bioconductor-methyanalysis/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.24.0" %} +{% set version = "1.26.0" %} {% set name = "methyAnalysis" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 3075fef8d84c73154ba460e1390106af + md5: 8a5dd849c1286e568fe64cbe9ffbf339 build: number: 0 rpaths: @@ -20,44 +20,44 @@ build: # Suggests: FDb.InfiniumMethylation.hg19, TxDb.Hsapiens.UCSC.hg19.knownGene requirements: host: - - 'bioconductor-annotate >=1.60.0,<1.61.0' - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' - - 'bioconductor-biobase >=2.42.0,<2.43.0' - - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' - - 'bioconductor-biomart >=2.38.0,<2.39.0' - - 'bioconductor-genefilter >=1.64.0,<1.65.0' - - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' - - 'bioconductor-genomicfeatures >=1.34.0,<1.35.0' - - 'bioconductor-genomicranges >=1.34.0,<1.35.0' - - 'bioconductor-genoset >=1.38.0,<1.39.0' - - 'bioconductor-gviz >=1.26.0,<1.27.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-lumi >=2.34.0,<2.35.0' - - 'bioconductor-methylumi >=2.28.0,<2.29.0' - - 'bioconductor-org.hs.eg.db >=3.7.0,<3.8.0' - - 'bioconductor-rtracklayer >=1.42.0,<1.43.0' - - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' - - 'bioconductor-variantannotation >=1.28.0,<1.29.0' + - 'bioconductor-annotate >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' + - 'bioconductor-biocgenerics >=0.30.0,<0.31.0' + - 'bioconductor-biomart >=2.40.0,<2.41.0' + - 'bioconductor-genefilter >=1.66.0,<1.67.0' + - 'bioconductor-genomeinfodb >=1.20.0,<1.21.0' + - 'bioconductor-genomicfeatures >=1.36.0,<1.37.0' + - 'bioconductor-genomicranges >=1.36.0,<1.37.0' + - 'bioconductor-genoset >=1.40.0,<1.41.0' + - 'bioconductor-gviz >=1.28.0,<1.29.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-lumi >=2.36.0,<2.37.0' + - 'bioconductor-methylumi >=2.30.0,<2.31.0' + - 'bioconductor-org.hs.eg.db >=3.8.0,<3.9.0' + - 'bioconductor-rtracklayer >=1.44.0,<1.45.0' + - 'bioconductor-summarizedexperiment >=1.14.0,<1.15.0' + - 'bioconductor-variantannotation >=1.30.0,<1.31.0' - r-base run: - - 'bioconductor-annotate >=1.60.0,<1.61.0' - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' - - 'bioconductor-biobase >=2.42.0,<2.43.0' - - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' - - 'bioconductor-biomart >=2.38.0,<2.39.0' - - 'bioconductor-genefilter >=1.64.0,<1.65.0' - - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' - - 'bioconductor-genomicfeatures >=1.34.0,<1.35.0' - - 'bioconductor-genomicranges >=1.34.0,<1.35.0' - - 'bioconductor-genoset >=1.38.0,<1.39.0' - - 'bioconductor-gviz >=1.26.0,<1.27.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-lumi >=2.34.0,<2.35.0' - - 'bioconductor-methylumi >=2.28.0,<2.29.0' - - 'bioconductor-org.hs.eg.db >=3.7.0,<3.8.0' - - 'bioconductor-rtracklayer >=1.42.0,<1.43.0' - - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' - - 'bioconductor-variantannotation >=1.28.0,<1.29.0' + - 'bioconductor-annotate >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' + - 'bioconductor-biocgenerics >=0.30.0,<0.31.0' + - 'bioconductor-biomart >=2.40.0,<2.41.0' + - 'bioconductor-genefilter >=1.66.0,<1.67.0' + - 'bioconductor-genomeinfodb >=1.20.0,<1.21.0' + - 'bioconductor-genomicfeatures >=1.36.0,<1.37.0' + - 'bioconductor-genomicranges >=1.36.0,<1.37.0' + - 'bioconductor-genoset >=1.40.0,<1.41.0' + - 'bioconductor-gviz >=1.28.0,<1.29.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-lumi >=2.36.0,<2.37.0' + - 'bioconductor-methylumi >=2.30.0,<2.31.0' + - 'bioconductor-org.hs.eg.db >=3.8.0,<3.9.0' + - 'bioconductor-rtracklayer >=1.44.0,<1.45.0' + - 'bioconductor-summarizedexperiment >=1.14.0,<1.15.0' + - 'bioconductor-variantannotation >=1.30.0,<1.31.0' - r-base test: commands: diff --git a/recipes/bioconductor-methylaid/meta.yaml b/recipes/bioconductor-methylaid/meta.yaml index d721c75925542..b419616b0cae9 100644 --- a/recipes/bioconductor-methylaid/meta.yaml +++ b/recipes/bioconductor-methylaid/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.16.0" %} +{% set version = "1.18.0" %} {% set name = "MethylAid" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: c654109f11f3e32cf050cee84dbb956f + md5: e9f8c4e6f49241bfb5ff9f0464ff6470 build: number: 0 rpaths: @@ -20,11 +20,11 @@ build: # Suggests: BiocStyle, knitr, MethylAidData, minfiData, minfiDataEPIC, RUnit requirements: host: - - 'bioconductor-biobase >=2.42.0,<2.43.0' - - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' - - 'bioconductor-biocparallel >=1.16.0,<1.17.0' - - 'bioconductor-minfi >=1.28.0,<1.29.0' - - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' + - 'bioconductor-biocgenerics >=0.30.0,<0.31.0' + - 'bioconductor-biocparallel >=1.18.0,<1.19.0' + - 'bioconductor-minfi >=1.30.0,<1.31.0' + - 'bioconductor-summarizedexperiment >=1.14.0,<1.15.0' - r-base - r-ggplot2 - r-gridbase @@ -33,11 +33,11 @@ requirements: - r-rcolorbrewer - r-shiny run: - - 'bioconductor-biobase >=2.42.0,<2.43.0' - - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' - - 'bioconductor-biocparallel >=1.16.0,<1.17.0' - - 'bioconductor-minfi >=1.28.0,<1.29.0' - - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' + - 'bioconductor-biocgenerics >=0.30.0,<0.31.0' + - 'bioconductor-biocparallel >=1.18.0,<1.19.0' + - 'bioconductor-minfi >=1.30.0,<1.31.0' + - 'bioconductor-summarizedexperiment >=1.14.0,<1.15.0' - r-base - r-ggplot2 - r-gridbase diff --git a/recipes/bioconductor-methylaiddata/meta.yaml b/recipes/bioconductor-methylaiddata/meta.yaml index 9086ad93a5f85..74f4d654c038c 100644 --- a/recipes/bioconductor-methylaiddata/meta.yaml +++ b/recipes/bioconductor-methylaiddata/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.14.0" %} +{% set version = "1.16.0" %} {% set name = "MethylAidData" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: b7445efd87e21834a9a35e92bae6bbad + md5: 2ceb994d8b7cc00b2a7ccf2e4af60579 build: number: 0 rpaths: @@ -20,12 +20,12 @@ build: # Suggests: BiocParallel, BiocStyle, knitr, minfiData, minfiDataEPIC requirements: host: - - 'bioconductor-methylaid >=1.16.0,<1.17.0' + - 'bioconductor-methylaid >=1.18.0,<1.19.0' - r-base run: - - 'bioconductor-methylaid >=1.16.0,<1.17.0' + - 'bioconductor-methylaid >=1.18.0,<1.19.0' - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-methylaiddata/post-link.sh b/recipes/bioconductor-methylaiddata/post-link.sh index 1da5185e259de..22e077c3c870b 100644 --- a/recipes/bioconductor-methylaiddata/post-link.sh +++ b/recipes/bioconductor-methylaiddata/post-link.sh @@ -1,11 +1,11 @@ #!/bin/bash -FN="MethylAidData_1.14.0.tar.gz" +FN="MethylAidData_1.16.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/experiment/src/contrib/MethylAidData_1.14.0.tar.gz" - "https://bioarchive.galaxyproject.org/MethylAidData_1.14.0.tar.gz" - "https://depot.galaxyproject.org/software/bioconductor-methylaiddata/bioconductor-methylaiddata_1.14.0_src_all.tar.gz" + "https://bioconductor.org/packages/3.9/data/experiment/src/contrib/MethylAidData_1.16.0.tar.gz" + "https://bioarchive.galaxyproject.org/MethylAidData_1.16.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-methylaiddata/bioconductor-methylaiddata_1.16.0_src_all.tar.gz" ) -MD5="b7445efd87e21834a9a35e92bae6bbad" +MD5="2ceb994d8b7cc00b2a7ccf2e4af60579" # Use a staging area in the conda dir rather than temp dirs, both to avoid # permission issues as well as to have things downloaded in a predictable @@ -16,7 +16,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-methylgsa/meta.yaml b/recipes/bioconductor-methylgsa/meta.yaml index 07a1b5ebc4ff6..0b21a2144b81a 100644 --- a/recipes/bioconductor-methylgsa/meta.yaml +++ b/recipes/bioconductor-methylgsa/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.0.2" %} +{% set version = "1.2.0" %} {% set name = "methylGSA" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 70e7765f6a6e518a9e512e5595b82596 + md5: ee584f38de4f84c0c2c8e73d7a7e2fec build: number: 0 rpaths: @@ -20,27 +20,29 @@ build: # Suggests: knitr, rmarkdown, testthat, enrichplot requirements: host: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' - - 'bioconductor-clusterprofiler >=3.10.0,<3.11.0' - - 'bioconductor-go.db >=3.7.0,<3.8.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' + - 'bioconductor-biocparallel >=1.18.0,<1.19.0' + - 'bioconductor-clusterprofiler >=3.12.0,<3.13.0' + - 'bioconductor-go.db >=3.8.0,<3.9.0' - 'bioconductor-illuminahumanmethylation450kanno.ilmn12.hg19 >=0.6.0,<0.7.0' - 'bioconductor-illuminahumanmethylationepicanno.ilm10b2.hg19 >=0.6.0,<0.7.0' - - 'bioconductor-missmethyl >=1.16.0,<1.17.0' - - 'bioconductor-org.hs.eg.db >=3.7.0,<3.8.0' - - 'bioconductor-reactome.db >=1.66.0,<1.67.0' + - 'bioconductor-missmethyl >=1.18.0,<1.19.0' + - 'bioconductor-org.hs.eg.db >=3.8.0,<3.9.0' + - 'bioconductor-reactome.db >=1.68.0,<1.69.0' - r-base - r-ggplot2 - r-robustrankaggreg - r-stringr run: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' - - 'bioconductor-clusterprofiler >=3.10.0,<3.11.0' - - 'bioconductor-go.db >=3.7.0,<3.8.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' + - 'bioconductor-biocparallel >=1.18.0,<1.19.0' + - 'bioconductor-clusterprofiler >=3.12.0,<3.13.0' + - 'bioconductor-go.db >=3.8.0,<3.9.0' - 'bioconductor-illuminahumanmethylation450kanno.ilmn12.hg19 >=0.6.0,<0.7.0' - 'bioconductor-illuminahumanmethylationepicanno.ilm10b2.hg19 >=0.6.0,<0.7.0' - - 'bioconductor-missmethyl >=1.16.0,<1.17.0' - - 'bioconductor-org.hs.eg.db >=3.7.0,<3.8.0' - - 'bioconductor-reactome.db >=1.66.0,<1.67.0' + - 'bioconductor-missmethyl >=1.18.0,<1.19.0' + - 'bioconductor-org.hs.eg.db >=3.8.0,<3.9.0' + - 'bioconductor-reactome.db >=1.68.0,<1.69.0' - r-base - r-ggplot2 - r-robustrankaggreg diff --git a/recipes/bioconductor-methylinheritance/meta.yaml b/recipes/bioconductor-methylinheritance/meta.yaml index 622927c611b01..f38ebcec1be40 100644 --- a/recipes/bioconductor-methylinheritance/meta.yaml +++ b/recipes/bioconductor-methylinheritance/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.6.1" %} +{% set version = "1.8.0" %} {% set name = "methylInheritance" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 21df16eb1d54500c0e3b1f7de6405a1d + md5: 37d08eb046e151e8acc867eaab557275 build: number: 0 rpaths: @@ -20,21 +20,21 @@ build: # Suggests: BiocStyle, BiocGenerics, knitr, rmarkdown, RUnit, methInheritSim requirements: host: - - 'bioconductor-biocparallel >=1.16.0,<1.17.0' - - 'bioconductor-genomicranges >=1.34.0,<1.35.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-methylkit >=1.8.0,<1.9.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-biocparallel >=1.18.0,<1.19.0' + - 'bioconductor-genomicranges >=1.36.0,<1.37.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-methylkit >=1.10.0,<1.11.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' - r-base - r-ggplot2 - r-gridextra - r-rebus run: - - 'bioconductor-biocparallel >=1.16.0,<1.17.0' - - 'bioconductor-genomicranges >=1.34.0,<1.35.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-methylkit >=1.8.0,<1.9.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-biocparallel >=1.18.0,<1.19.0' + - 'bioconductor-genomicranges >=1.36.0,<1.37.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-methylkit >=1.10.0,<1.11.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' - r-base - r-ggplot2 - r-gridextra diff --git a/recipes/bioconductor-methylkit/meta.yaml b/recipes/bioconductor-methylkit/meta.yaml index f94856b4e03ae..389a2cf9b90bc 100644 --- a/recipes/bioconductor-methylkit/meta.yaml +++ b/recipes/bioconductor-methylkit/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.8.1" %} +{% set version = "1.10.0" %} {% set name = "methylKit" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: ce147e59306bc117dffbeea24518e169 + md5: a06456112ec7e30a1429d877edf44d32 build: number: 0 rpaths: @@ -19,43 +19,45 @@ build: # Suggests: testthat,knitr, rmarkdown, genomation, BiocManager requirements: host: - - 'bioconductor-fastseg >=1.28.0,<1.29.0' - - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' - - 'bioconductor-genomicranges >=1.34.0,<1.35.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-limma >=3.38.0,<3.39.0' - - 'bioconductor-qvalue >=2.14.0,<2.15.0' - - 'bioconductor-rhtslib >=1.14.0,<1.15.0' - - 'bioconductor-rsamtools >=1.34.0,<1.35.0' - - 'bioconductor-rtracklayer >=1.42.0,<1.43.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' - - 'bioconductor-zlibbioc >=1.28.0,<1.29.0' + - 'bioconductor-fastseg >=1.30.0,<1.31.0' + - 'bioconductor-genomeinfodb >=1.20.0,<1.21.0' + - 'bioconductor-genomicranges >=1.36.0,<1.37.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-limma >=3.40.0,<3.41.0' + - 'bioconductor-qvalue >=2.16.0,<2.17.0' + - 'bioconductor-rhtslib >=1.16.0,<1.17.0' + - 'bioconductor-rsamtools >=2.0.0,<2.1.0' + - 'bioconductor-rtracklayer >=1.44.0,<1.45.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' + - 'bioconductor-zlibbioc >=1.30.0,<1.31.0' - r-base - 'r-data.table >=1.9.6' - r-emdbook - r-gtools - r-kernsmooth - r-mclust + - r-mgcv - r-r.utils - r-rcpp run: - - 'bioconductor-fastseg >=1.28.0,<1.29.0' - - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' - - 'bioconductor-genomicranges >=1.34.0,<1.35.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-limma >=3.38.0,<3.39.0' - - 'bioconductor-qvalue >=2.14.0,<2.15.0' - - 'bioconductor-rhtslib >=1.14.0,<1.15.0' - - 'bioconductor-rsamtools >=1.34.0,<1.35.0' - - 'bioconductor-rtracklayer >=1.42.0,<1.43.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' - - 'bioconductor-zlibbioc >=1.28.0,<1.29.0' + - 'bioconductor-fastseg >=1.30.0,<1.31.0' + - 'bioconductor-genomeinfodb >=1.20.0,<1.21.0' + - 'bioconductor-genomicranges >=1.36.0,<1.37.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-limma >=3.40.0,<3.41.0' + - 'bioconductor-qvalue >=2.16.0,<2.17.0' + - 'bioconductor-rhtslib >=1.16.0,<1.17.0' + - 'bioconductor-rsamtools >=2.0.0,<2.1.0' + - 'bioconductor-rtracklayer >=1.44.0,<1.45.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' + - 'bioconductor-zlibbioc >=1.30.0,<1.31.0' - r-base - 'r-data.table >=1.9.6' - r-emdbook - r-gtools - r-kernsmooth - r-mclust + - r-mgcv - r-r.utils - r-rcpp build: @@ -68,7 +70,7 @@ test: about: home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: Artistic-2.0 - summary: 'methylKit is an R package for DNA methylation analysis and annotation from high-throughput bisulfite sequencing. The package is designed to deal with sequencing data from RRBS and its variants, but also target-capture methods and whole genome bisulfite sequencing. It also has functions to analyze base-pair resolution 5hmC data from experimental protocols such as oxBS-Seq and TAB-Seq. Perl is needed to read SAM files only.' + summary: 'methylKit is an R package for DNA methylation analysis and annotation from high-throughput bisulfite sequencing. The package is designed to deal with sequencing data from RRBS and its variants, but also target-capture methods and whole genome bisulfite sequencing. It also has functions to analyze base-pair resolution 5hmC data from experimental protocols such as oxBS-Seq and TAB-Seq. Methylation calling can be performed directly from Bismark aligned BAM files.' extra: identifiers: - biotools:methylkit diff --git a/recipes/bioconductor-methylmix/meta.yaml b/recipes/bioconductor-methylmix/meta.yaml index 7899e6e513ea6..cd6fd08b0dc9a 100644 --- a/recipes/bioconductor-methylmix/meta.yaml +++ b/recipes/bioconductor-methylmix/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "2.12.0" %} +{% set version = "2.14.0" %} {% set name = "MethylMix" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: e894baa2827b774cc07acc38faa8d6d2 + md5: 9a3202f240fc625c7f68f8659cba3382 build: number: 0 rpaths: @@ -20,8 +20,8 @@ build: # Suggests: BiocStyle, doParallel, testthat, knitr, rmarkdown requirements: host: - - 'bioconductor-impute >=1.56.0,<1.57.0' - - 'bioconductor-limma >=3.38.0,<3.39.0' + - 'bioconductor-impute >=1.58.0,<1.59.0' + - 'bioconductor-limma >=3.40.0,<3.41.0' - r-base - r-data.table - r-digest @@ -32,8 +32,8 @@ requirements: - r-rcurl - r-rpmm run: - - 'bioconductor-impute >=1.56.0,<1.57.0' - - 'bioconductor-limma >=3.38.0,<3.39.0' + - 'bioconductor-impute >=1.58.0,<1.59.0' + - 'bioconductor-limma >=3.40.0,<3.41.0' - r-base - r-data.table - r-digest diff --git a/recipes/bioconductor-methylmnm/meta.yaml b/recipes/bioconductor-methylmnm/meta.yaml index 8fe29eb0741b0..557df320095e1 100644 --- a/recipes/bioconductor-methylmnm/meta.yaml +++ b/recipes/bioconductor-methylmnm/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.20.0" %} +{% set version = "1.22.0" %} {% set name = "methylMnM" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 595ea0397f953ec93b06932e0e724dd4 + md5: c6e10d64eef549b55d4447db0264f60d build: number: 0 rpaths: @@ -18,11 +18,11 @@ build: - lib/ requirements: host: - - 'bioconductor-edger >=3.24.0,<3.25.0' + - 'bioconductor-edger >=3.26.0,<3.27.0' - r-base - r-statmod run: - - 'bioconductor-edger >=3.24.0,<3.25.0' + - 'bioconductor-edger >=3.26.0,<3.27.0' - r-base - r-statmod build: diff --git a/recipes/bioconductor-methylpipe/meta.yaml b/recipes/bioconductor-methylpipe/meta.yaml index 5aea45bd3151c..0808068aeea79 100644 --- a/recipes/bioconductor-methylpipe/meta.yaml +++ b/recipes/bioconductor-methylpipe/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.16.0" %} +{% set version = "1.18.0" %} {% set name = "methylPipe" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 0174e17c1fbcf664052973c8be3f5c79 + md5: e671d3ee89cf1a770cf8ac13b919c284 build: number: 0 rpaths: @@ -19,32 +19,32 @@ build: # Suggests: BSgenome.Hsapiens.UCSC.hg18, TxDb.Hsapiens.UCSC.hg18.knownGene, knitr, MethylSeekR requirements: host: - - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' - - 'bioconductor-biostrings >=2.50.0,<2.51.0' - - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' - - 'bioconductor-genomicalignments >=1.18.0,<1.19.0' - - 'bioconductor-genomicranges >=1.34.0,<1.35.0' - - 'bioconductor-gviz >=1.26.0,<1.27.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-marray >=1.60.0,<1.61.0' - - 'bioconductor-rsamtools >=1.34.0,<1.35.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' - - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' + - 'bioconductor-biocgenerics >=0.30.0,<0.31.0' + - 'bioconductor-biostrings >=2.52.0,<2.53.0' + - 'bioconductor-genomeinfodb >=1.20.0,<1.21.0' + - 'bioconductor-genomicalignments >=1.20.0,<1.21.0' + - 'bioconductor-genomicranges >=1.36.0,<1.37.0' + - 'bioconductor-gviz >=1.28.0,<1.29.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-marray >=1.62.0,<1.63.0' + - 'bioconductor-rsamtools >=2.0.0,<2.1.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' + - 'bioconductor-summarizedexperiment >=1.14.0,<1.15.0' - r-base - r-data.table - r-gplots run: - - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' - - 'bioconductor-biostrings >=2.50.0,<2.51.0' - - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' - - 'bioconductor-genomicalignments >=1.18.0,<1.19.0' - - 'bioconductor-genomicranges >=1.34.0,<1.35.0' - - 'bioconductor-gviz >=1.26.0,<1.27.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-marray >=1.60.0,<1.61.0' - - 'bioconductor-rsamtools >=1.34.0,<1.35.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' - - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' + - 'bioconductor-biocgenerics >=0.30.0,<0.31.0' + - 'bioconductor-biostrings >=2.52.0,<2.53.0' + - 'bioconductor-genomeinfodb >=1.20.0,<1.21.0' + - 'bioconductor-genomicalignments >=1.20.0,<1.21.0' + - 'bioconductor-genomicranges >=1.36.0,<1.37.0' + - 'bioconductor-gviz >=1.28.0,<1.29.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-marray >=1.62.0,<1.63.0' + - 'bioconductor-rsamtools >=2.0.0,<2.1.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' + - 'bioconductor-summarizedexperiment >=1.14.0,<1.15.0' - r-base - r-data.table - r-gplots diff --git a/recipes/bioconductor-methylseekr/meta.yaml b/recipes/bioconductor-methylseekr/meta.yaml index 2574538e269c6..7fe88386d923b 100644 --- a/recipes/bioconductor-methylseekr/meta.yaml +++ b/recipes/bioconductor-methylseekr/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.22.0" %} +{% set version = "1.24.0" %} {% set name = "MethylSeekR" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,9 +10,9 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 19080118abe4bf6ba3aed35b2643764b + md5: 0dcc61e0699c68e56893d16c2d2230ff build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ @@ -20,19 +20,19 @@ build: # Suggests: BSgenome.Hsapiens.UCSC.hg18 requirements: host: - - 'bioconductor-bsgenome >=1.50.0,<1.51.0' - - 'bioconductor-geneplotter >=1.60.0,<1.61.0' - - 'bioconductor-genomicranges >=1.34.0,<1.35.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-rtracklayer >=1.42.0,<1.43.0' + - 'bioconductor-bsgenome >=1.52.0,<1.53.0' + - 'bioconductor-geneplotter >=1.62.0,<1.63.0' + - 'bioconductor-genomicranges >=1.36.0,<1.37.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-rtracklayer >=1.44.0,<1.45.0' - r-base - 'r-mhsmm >=0.4.4' run: - - 'bioconductor-bsgenome >=1.50.0,<1.51.0' - - 'bioconductor-geneplotter >=1.60.0,<1.61.0' - - 'bioconductor-genomicranges >=1.34.0,<1.35.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-rtracklayer >=1.42.0,<1.43.0' + - 'bioconductor-bsgenome >=1.52.0,<1.53.0' + - 'bioconductor-geneplotter >=1.62.0,<1.63.0' + - 'bioconductor-genomicranges >=1.36.0,<1.37.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-rtracklayer >=1.44.0,<1.45.0' - r-base - 'r-mhsmm >=0.4.4' test: diff --git a/recipes/bioconductor-methylumi/meta.yaml b/recipes/bioconductor-methylumi/meta.yaml index 285ab12014b43..ca1c129b27fb1 100644 --- a/recipes/bioconductor-methylumi/meta.yaml +++ b/recipes/bioconductor-methylumi/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "2.28.0" %} +{% set version = "2.30.0" %} {% set name = "methylumi" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: f1a2ca6160d851c6db5797cf4636058e + md5: e5e8dd104dba330867bb8b3c3a78922a build: number: 0 rpaths: @@ -20,19 +20,19 @@ build: # Suggests: lumi, lattice, limma, xtable, SQN, MASS, matrixStats, parallel, rtracklayer, Biostrings, methyAnalysis, TCGAMethylation450k, IlluminaHumanMethylation450kanno.ilmn12.hg19, FDb.InfiniumMethylation.hg18 (>= 2.2.0), Homo.sapiens, knitr requirements: host: - - 'bioconductor-annotate >=1.60.0,<1.61.0' - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' - - 'bioconductor-biobase >=2.42.0,<2.43.0' - - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' + - 'bioconductor-annotate >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' + - 'bioconductor-biocgenerics >=0.30.0,<0.31.0' - 'bioconductor-fdb.infiniummethylation.hg19 >=2.2.0,<2.3.0' - - 'bioconductor-genefilter >=1.64.0,<1.65.0' - - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' - - 'bioconductor-genomicranges >=1.34.0,<1.35.0' - - 'bioconductor-illuminaio >=0.24.0,<0.25.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-minfi >=1.28.0,<1.29.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' - - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' + - 'bioconductor-genefilter >=1.66.0,<1.67.0' + - 'bioconductor-genomeinfodb >=1.20.0,<1.21.0' + - 'bioconductor-genomicranges >=1.36.0,<1.37.0' + - 'bioconductor-illuminaio >=0.26.0,<0.27.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-minfi >=1.30.0,<1.31.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' + - 'bioconductor-summarizedexperiment >=1.14.0,<1.15.0' - r-base - r-ggplot2 - r-lattice @@ -40,19 +40,19 @@ requirements: - r-reshape2 - r-scales run: - - 'bioconductor-annotate >=1.60.0,<1.61.0' - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' - - 'bioconductor-biobase >=2.42.0,<2.43.0' - - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' + - 'bioconductor-annotate >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' + - 'bioconductor-biocgenerics >=0.30.0,<0.31.0' - 'bioconductor-fdb.infiniummethylation.hg19 >=2.2.0,<2.3.0' - - 'bioconductor-genefilter >=1.64.0,<1.65.0' - - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' - - 'bioconductor-genomicranges >=1.34.0,<1.35.0' - - 'bioconductor-illuminaio >=0.24.0,<0.25.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-minfi >=1.28.0,<1.29.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' - - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' + - 'bioconductor-genefilter >=1.66.0,<1.67.0' + - 'bioconductor-genomeinfodb >=1.20.0,<1.21.0' + - 'bioconductor-genomicranges >=1.36.0,<1.37.0' + - 'bioconductor-illuminaio >=0.26.0,<0.27.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-minfi >=1.30.0,<1.31.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' + - 'bioconductor-summarizedexperiment >=1.14.0,<1.15.0' - r-base - r-ggplot2 - r-lattice diff --git a/recipes/bioconductor-methyvim/meta.yaml b/recipes/bioconductor-methyvim/meta.yaml index fe8982b5580c3..9e1befddb43df 100644 --- a/recipes/bioconductor-methyvim/meta.yaml +++ b/recipes/bioconductor-methyvim/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.4.0" %} +{% set version = "1.6.0" %} {% set name = "methyvim" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: c8c7263ae8d200c1780273158bfda8fb + md5: 8a62c97ee32462f27dec7a8b7f868b73 build: number: 0 rpaths: @@ -20,15 +20,15 @@ build: # Suggests: testthat, knitr, rmarkdown, BiocStyle, SuperLearner, earth, nnet, gam, arm, snow, parallel, BatchJobs, minfiData, methyvimData requirements: host: - - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' - - 'bioconductor-biocparallel >=1.16.0,<1.17.0' - - 'bioconductor-bumphunter >=1.24.0,<1.25.0' - - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-limma >=3.38.0,<3.39.0' - - 'bioconductor-minfi >=1.28.0,<1.29.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' - - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' + - 'bioconductor-biocgenerics >=0.30.0,<0.31.0' + - 'bioconductor-biocparallel >=1.18.0,<1.19.0' + - 'bioconductor-bumphunter >=1.26.0,<1.27.0' + - 'bioconductor-genomeinfodb >=1.20.0,<1.21.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-limma >=3.40.0,<3.41.0' + - 'bioconductor-minfi >=1.30.0,<1.31.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' + - 'bioconductor-summarizedexperiment >=1.14.0,<1.15.0' - r-base - r-cluster - r-dofuture @@ -41,15 +41,15 @@ requirements: - r-superheat - r-tmle run: - - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' - - 'bioconductor-biocparallel >=1.16.0,<1.17.0' - - 'bioconductor-bumphunter >=1.24.0,<1.25.0' - - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-limma >=3.38.0,<3.39.0' - - 'bioconductor-minfi >=1.28.0,<1.29.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' - - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' + - 'bioconductor-biocgenerics >=0.30.0,<0.31.0' + - 'bioconductor-biocparallel >=1.18.0,<1.19.0' + - 'bioconductor-bumphunter >=1.26.0,<1.27.0' + - 'bioconductor-genomeinfodb >=1.20.0,<1.21.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-limma >=3.40.0,<3.41.0' + - 'bioconductor-minfi >=1.30.0,<1.31.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' + - 'bioconductor-summarizedexperiment >=1.14.0,<1.15.0' - r-base - r-cluster - r-dofuture diff --git a/recipes/bioconductor-methyvimdata/meta.yaml b/recipes/bioconductor-methyvimdata/meta.yaml index b204fed4bd36c..5a23bc5fa6c40 100644 --- a/recipes/bioconductor-methyvimdata/meta.yaml +++ b/recipes/bioconductor-methyvimdata/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.4.0" %} +{% set version = "1.6.0" %} {% set name = "methyvimData" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 2d04580044269f4e9f1f904aed11ff6f + md5: a4c9dd38473186f1632b57e21a3ef671 build: number: 0 rpaths: @@ -20,12 +20,12 @@ build: # Suggests: Biobase, BiocStyle, SummarizedExperiment, knitr, rmarkdown requirements: host: - - 'bioconductor-minfi >=1.28.0,<1.29.0' + - 'bioconductor-minfi >=1.30.0,<1.31.0' - r-base run: - - 'bioconductor-minfi >=1.28.0,<1.29.0' + - 'bioconductor-minfi >=1.30.0,<1.31.0' - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-methyvimdata/post-link.sh b/recipes/bioconductor-methyvimdata/post-link.sh index b88aa59ae16e3..b141094c51c63 100644 --- a/recipes/bioconductor-methyvimdata/post-link.sh +++ b/recipes/bioconductor-methyvimdata/post-link.sh @@ -1,11 +1,11 @@ #!/bin/bash -FN="methyvimData_1.4.0.tar.gz" +FN="methyvimData_1.6.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/experiment/src/contrib/methyvimData_1.4.0.tar.gz" - "https://bioarchive.galaxyproject.org/methyvimData_1.4.0.tar.gz" - "https://depot.galaxyproject.org/software/bioconductor-methyvimdata/bioconductor-methyvimdata_1.4.0_src_all.tar.gz" + "https://bioconductor.org/packages/3.9/data/experiment/src/contrib/methyvimData_1.6.0.tar.gz" + "https://bioarchive.galaxyproject.org/methyvimData_1.6.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-methyvimdata/bioconductor-methyvimdata_1.6.0_src_all.tar.gz" ) -MD5="2d04580044269f4e9f1f904aed11ff6f" +MD5="a4c9dd38473186f1632b57e21a3ef671" # Use a staging area in the conda dir rather than temp dirs, both to avoid # permission issues as well as to have things downloaded in a predictable @@ -16,7 +16,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-metid/meta.yaml b/recipes/bioconductor-metid/meta.yaml index 7cbd25413f1a3..85e865f72932e 100644 --- a/recipes/bioconductor-metid/meta.yaml +++ b/recipes/bioconductor-metid/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.0.0" %} +{% set version = "1.2.0" %} {% set name = "MetID" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: c5b7dea163a632b9626c4b3db70334bf + md5: 706e4dfefc5c60903c0248a9aeaf4272 build: number: 0 rpaths: @@ -20,14 +20,14 @@ build: # Suggests: knitr (>= 1.19), rmarkdown (>= 1.8) requirements: host: - - 'bioconductor-chemminer >=3.34.0,<3.35.0' + - 'bioconductor-chemminer >=3.36.0,<3.37.0' - r-base - 'r-devtools >=1.13.0' - 'r-igraph >=1.2.1' - 'r-matrix >=1.2-12' - 'r-stringr >=1.3.0' run: - - 'bioconductor-chemminer >=3.34.0,<3.35.0' + - 'bioconductor-chemminer >=3.36.0,<3.37.0' - r-base - 'r-devtools >=1.13.0' - 'r-igraph >=1.2.1' diff --git a/recipes/bioconductor-metnet/meta.yaml b/recipes/bioconductor-metnet/meta.yaml index ede817e93b557..b8bbfb7ac045f 100644 --- a/recipes/bioconductor-metnet/meta.yaml +++ b/recipes/bioconductor-metnet/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.0.0" %} +{% set version = "1.2.0" %} {% set name = "MetNet" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 6f9840eca47a1f6485e581fbde8da864 + md5: d3e06137d7f3e5d6aaca1891002998cb build: number: 0 rpaths: @@ -20,7 +20,7 @@ build: # Suggests: BiocGenerics (>= 0.24.0), BiocStyle (>= 2.6.1), igraph (>= 1.1.2), knitr (>= 1.11) requirements: host: - - 'bioconductor-biocparallel >=1.16.0,<1.17.0' + - 'bioconductor-biocparallel >=1.18.0,<1.19.0' - r-base - 'r-bnlearn >=4.3' - 'r-mpmi >=0.42' @@ -31,7 +31,7 @@ requirements: - 'r-stabs >=0.6' - 'r-wgcna >=1.61' run: - - 'bioconductor-biocparallel >=1.16.0,<1.17.0' + - 'bioconductor-biocparallel >=1.18.0,<1.19.0' - r-base - 'r-bnlearn >=4.3' - 'r-mpmi >=0.42' diff --git a/recipes/bioconductor-mfa/meta.yaml b/recipes/bioconductor-mfa/meta.yaml index ab76ee4bfd4f6..45e7c825bacf4 100644 --- a/recipes/bioconductor-mfa/meta.yaml +++ b/recipes/bioconductor-mfa/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.4.1" %} +{% set version = "1.6.0" %} {% set name = "mfa" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - sha256: a75f8428c668bc5dad2be1163472b3580513a41994395b64a4c3dc69e2a4114e + md5: 314a4a4488fe8701cbe57b5d0b0879f6 build: number: 0 rpaths: @@ -19,7 +19,7 @@ build: # Suggests: knitr, rmarkdown, BiocStyle, testthat requirements: host: - - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' - r-base - r-coda - r-dplyr @@ -31,7 +31,7 @@ requirements: - r-rcpp - r-tibble run: - - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' - r-base - r-coda - r-dplyr diff --git a/recipes/bioconductor-mfuzz/meta.yaml b/recipes/bioconductor-mfuzz/meta.yaml index fcc6a82d9e290..045df805a6244 100644 --- a/recipes/bioconductor-mfuzz/meta.yaml +++ b/recipes/bioconductor-mfuzz/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "2.42.0" %} +{% set version = "2.44.0" %} {% set name = "Mfuzz" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: e994e57b660e1e59335de41f82762d58 + md5: 6e1c8d489ab1865140d579655cf696f2 build: number: 0 rpaths: @@ -20,13 +20,13 @@ build: # Suggests: marray requirements: host: - - 'bioconductor-biobase >=2.42.0,<2.43.0' - - 'bioconductor-tkwidgets >=1.60.0,<1.61.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' + - 'bioconductor-tkwidgets >=1.62.0,<1.63.0' - r-base - r-e1071 run: - - 'bioconductor-biobase >=2.42.0,<2.43.0' - - 'bioconductor-tkwidgets >=1.60.0,<1.61.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' + - 'bioconductor-tkwidgets >=1.62.0,<1.63.0' - r-base - r-e1071 test: diff --git a/recipes/bioconductor-mgfm/meta.yaml b/recipes/bioconductor-mgfm/meta.yaml index bc5a1c5f6c42d..96b11a26d7bb1 100644 --- a/recipes/bioconductor-mgfm/meta.yaml +++ b/recipes/bioconductor-mgfm/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.16.0" %} +{% set version = "1.18.0" %} {% set name = "MGFM" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 4c546557bee46a59290c4900403f7edf + md5: a59528c30e469dda4121cf7dbcb277e4 build: number: 0 rpaths: @@ -20,12 +20,12 @@ build: # Suggests: hgu133a.db requirements: host: - - 'bioconductor-annotate >=1.60.0,<1.61.0' - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-annotate >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' - r-base run: - - 'bioconductor-annotate >=1.60.0,<1.61.0' - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-annotate >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' - r-base test: commands: diff --git a/recipes/bioconductor-mgfr/meta.yaml b/recipes/bioconductor-mgfr/meta.yaml index c83898101b689..1a4a045c27232 100644 --- a/recipes/bioconductor-mgfr/meta.yaml +++ b/recipes/bioconductor-mgfr/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.8.0" %} +{% set version = "1.10.0" %} {% set name = "MGFR" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 53e276e661120a9237e382c5da01d8d3 + md5: f699f6c45ad738977582580b637dbff4 build: number: 0 rpaths: @@ -19,12 +19,12 @@ build: noarch: generic requirements: host: - - 'bioconductor-annotate >=1.60.0,<1.61.0' - - 'bioconductor-biomart >=2.38.0,<2.39.0' + - 'bioconductor-annotate >=1.62.0,<1.63.0' + - 'bioconductor-biomart >=2.40.0,<2.41.0' - r-base run: - - 'bioconductor-annotate >=1.60.0,<1.61.0' - - 'bioconductor-biomart >=2.38.0,<2.39.0' + - 'bioconductor-annotate >=1.62.0,<1.63.0' + - 'bioconductor-biomart >=2.40.0,<2.41.0' - r-base test: commands: diff --git a/recipes/bioconductor-mgsa/meta.yaml b/recipes/bioconductor-mgsa/meta.yaml index a1cba90c5f9cf..86734c580e35f 100644 --- a/recipes/bioconductor-mgsa/meta.yaml +++ b/recipes/bioconductor-mgsa/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.30.0" %} +{% set version = "1.32.0" %} {% set name = "mgsa" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 273187423f0ea752f7d0e31aa3def023 + md5: 2ac224cf9bb013adc8ede543a950c658 build: number: 0 rpaths: diff --git a/recipes/bioconductor-mgu74a.db/meta.yaml b/recipes/bioconductor-mgu74a.db/meta.yaml index f09cf8dd554aa..a0f1a01a94b19 100644 --- a/recipes/bioconductor-mgu74a.db/meta.yaml +++ b/recipes/bioconductor-mgu74a.db/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.2.3" %} {% set name = "mgu74a.db" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -12,7 +12,7 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: b746929f272a811061cf03040ec5ea3b build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ @@ -20,14 +20,14 @@ build: # Suggests: DBI, annotate, RUnit requirements: host: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' - - 'bioconductor-org.mm.eg.db >=3.7.0,<3.8.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' + - 'bioconductor-org.mm.eg.db >=3.8.0,<3.9.0' - r-base run: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' - - 'bioconductor-org.mm.eg.db >=3.7.0,<3.8.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' + - 'bioconductor-org.mm.eg.db >=3.8.0,<3.9.0' - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-mgu74a.db/post-link.sh b/recipes/bioconductor-mgu74a.db/post-link.sh index 7887cb4633b7e..e1ac5dc52721d 100644 --- a/recipes/bioconductor-mgu74a.db/post-link.sh +++ b/recipes/bioconductor-mgu74a.db/post-link.sh @@ -1,9 +1,10 @@ #!/bin/bash FN="mgu74a.db_3.2.3.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/mgu74a.db_3.2.3.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/mgu74a.db_3.2.3.tar.gz" "https://bioarchive.galaxyproject.org/mgu74a.db_3.2.3.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-mgu74a.db/bioconductor-mgu74a.db_3.2.3_src_all.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-mgu74a.db/bioconductor-mgu74a.db_3.2.3_src_all.tar.gz" ) MD5="b746929f272a811061cf03040ec5ea3b" @@ -16,7 +17,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-mgu74acdf/meta.yaml b/recipes/bioconductor-mgu74acdf/meta.yaml index 3ecd4436473ac..55f5f35fc9213 100644 --- a/recipes/bioconductor-mgu74acdf/meta.yaml +++ b/recipes/bioconductor-mgu74acdf/meta.yaml @@ -1,6 +1,6 @@ {% set version = "2.18.0" %} {% set name = "mgu74acdf" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -12,19 +12,19 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: ed6e86398e51c7b0ddca4431797ecbc0 build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' - r-base run: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-mgu74acdf/post-link.sh b/recipes/bioconductor-mgu74acdf/post-link.sh index 9daecb6bb66d0..6d816e4487b4a 100644 --- a/recipes/bioconductor-mgu74acdf/post-link.sh +++ b/recipes/bioconductor-mgu74acdf/post-link.sh @@ -1,9 +1,10 @@ #!/bin/bash FN="mgu74acdf_2.18.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/mgu74acdf_2.18.0.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/mgu74acdf_2.18.0.tar.gz" "https://bioarchive.galaxyproject.org/mgu74acdf_2.18.0.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-mgu74acdf/bioconductor-mgu74acdf_2.18.0_src_all.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-mgu74acdf/bioconductor-mgu74acdf_2.18.0_src_all.tar.gz" ) MD5="ed6e86398e51c7b0ddca4431797ecbc0" @@ -16,7 +17,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-mgu74aprobe/meta.yaml b/recipes/bioconductor-mgu74aprobe/meta.yaml index 292e9774d7f0e..1cf7ba8d32d82 100644 --- a/recipes/bioconductor-mgu74aprobe/meta.yaml +++ b/recipes/bioconductor-mgu74aprobe/meta.yaml @@ -1,6 +1,6 @@ {% set version = "2.18.0" %} {% set name = "mgu74aprobe" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -12,19 +12,19 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 7fea6d44856203e6293e0cd9fe1ad066 build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' - r-base run: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-mgu74aprobe/post-link.sh b/recipes/bioconductor-mgu74aprobe/post-link.sh index c60592c1ac828..e529025d029fe 100644 --- a/recipes/bioconductor-mgu74aprobe/post-link.sh +++ b/recipes/bioconductor-mgu74aprobe/post-link.sh @@ -1,9 +1,10 @@ #!/bin/bash FN="mgu74aprobe_2.18.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/mgu74aprobe_2.18.0.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/mgu74aprobe_2.18.0.tar.gz" "https://bioarchive.galaxyproject.org/mgu74aprobe_2.18.0.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-mgu74aprobe/bioconductor-mgu74aprobe_2.18.0_src_all.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-mgu74aprobe/bioconductor-mgu74aprobe_2.18.0_src_all.tar.gz" ) MD5="7fea6d44856203e6293e0cd9fe1ad066" @@ -16,7 +17,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-mgu74av2.db/meta.yaml b/recipes/bioconductor-mgu74av2.db/meta.yaml index 10a81e7eb53a4..e42b3c2978e90 100644 --- a/recipes/bioconductor-mgu74av2.db/meta.yaml +++ b/recipes/bioconductor-mgu74av2.db/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.2.3" %} {% set name = "mgu74av2.db" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -12,7 +12,7 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: ca637dece483fe0a0f752e4fa013d389 build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ @@ -20,14 +20,14 @@ build: # Suggests: DBI, annotate, RUnit requirements: host: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' - - 'bioconductor-org.mm.eg.db >=3.7.0,<3.8.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' + - 'bioconductor-org.mm.eg.db >=3.8.0,<3.9.0' - r-base run: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' - - 'bioconductor-org.mm.eg.db >=3.7.0,<3.8.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' + - 'bioconductor-org.mm.eg.db >=3.8.0,<3.9.0' - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-mgu74av2.db/post-link.sh b/recipes/bioconductor-mgu74av2.db/post-link.sh index c960acd2da7dc..360d943a565cd 100644 --- a/recipes/bioconductor-mgu74av2.db/post-link.sh +++ b/recipes/bioconductor-mgu74av2.db/post-link.sh @@ -1,9 +1,10 @@ #!/bin/bash FN="mgu74av2.db_3.2.3.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/mgu74av2.db_3.2.3.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/mgu74av2.db_3.2.3.tar.gz" "https://bioarchive.galaxyproject.org/mgu74av2.db_3.2.3.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-mgu74av2.db/bioconductor-mgu74av2.db_3.2.3_src_all.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-mgu74av2.db/bioconductor-mgu74av2.db_3.2.3_src_all.tar.gz" ) MD5="ca637dece483fe0a0f752e4fa013d389" @@ -16,7 +17,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-mgu74av2cdf/meta.yaml b/recipes/bioconductor-mgu74av2cdf/meta.yaml index 1da559ec84bd7..b282ec238c3a9 100644 --- a/recipes/bioconductor-mgu74av2cdf/meta.yaml +++ b/recipes/bioconductor-mgu74av2cdf/meta.yaml @@ -1,6 +1,6 @@ {% set version = "2.18.0" %} {% set name = "mgu74av2cdf" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -12,19 +12,19 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 35e2abb9fbfd68d90dc32a2faae00c95 build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' - r-base run: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-mgu74av2cdf/post-link.sh b/recipes/bioconductor-mgu74av2cdf/post-link.sh index 5983908152195..0ff13c1356f2e 100644 --- a/recipes/bioconductor-mgu74av2cdf/post-link.sh +++ b/recipes/bioconductor-mgu74av2cdf/post-link.sh @@ -1,9 +1,10 @@ #!/bin/bash FN="mgu74av2cdf_2.18.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/mgu74av2cdf_2.18.0.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/mgu74av2cdf_2.18.0.tar.gz" "https://bioarchive.galaxyproject.org/mgu74av2cdf_2.18.0.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-mgu74av2cdf/bioconductor-mgu74av2cdf_2.18.0_src_all.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-mgu74av2cdf/bioconductor-mgu74av2cdf_2.18.0_src_all.tar.gz" ) MD5="35e2abb9fbfd68d90dc32a2faae00c95" @@ -16,7 +17,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-mgu74av2probe/meta.yaml b/recipes/bioconductor-mgu74av2probe/meta.yaml index c48e73cc91b2d..d51124fa42a1e 100644 --- a/recipes/bioconductor-mgu74av2probe/meta.yaml +++ b/recipes/bioconductor-mgu74av2probe/meta.yaml @@ -1,6 +1,6 @@ {% set version = "2.18.0" %} {% set name = "mgu74av2probe" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -12,19 +12,19 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: ac540b0e26b14a411740233b02d3e11c build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' - r-base run: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-mgu74av2probe/post-link.sh b/recipes/bioconductor-mgu74av2probe/post-link.sh index 22c3db98e7990..907db24b1a720 100644 --- a/recipes/bioconductor-mgu74av2probe/post-link.sh +++ b/recipes/bioconductor-mgu74av2probe/post-link.sh @@ -1,9 +1,10 @@ #!/bin/bash FN="mgu74av2probe_2.18.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/mgu74av2probe_2.18.0.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/mgu74av2probe_2.18.0.tar.gz" "https://bioarchive.galaxyproject.org/mgu74av2probe_2.18.0.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-mgu74av2probe/bioconductor-mgu74av2probe_2.18.0_src_all.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-mgu74av2probe/bioconductor-mgu74av2probe_2.18.0_src_all.tar.gz" ) MD5="ac540b0e26b14a411740233b02d3e11c" @@ -16,7 +17,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-mgu74b.db/meta.yaml b/recipes/bioconductor-mgu74b.db/meta.yaml index a6007d9bf3cc3..94eb507c7c795 100644 --- a/recipes/bioconductor-mgu74b.db/meta.yaml +++ b/recipes/bioconductor-mgu74b.db/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.2.3" %} {% set name = "mgu74b.db" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -12,7 +12,7 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 9d019b194a64ec8c915514019896708e build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ @@ -20,14 +20,14 @@ build: # Suggests: DBI, annotate, RUnit requirements: host: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' - - 'bioconductor-org.mm.eg.db >=3.7.0,<3.8.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' + - 'bioconductor-org.mm.eg.db >=3.8.0,<3.9.0' - r-base run: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' - - 'bioconductor-org.mm.eg.db >=3.7.0,<3.8.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' + - 'bioconductor-org.mm.eg.db >=3.8.0,<3.9.0' - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-mgu74b.db/post-link.sh b/recipes/bioconductor-mgu74b.db/post-link.sh index a13a8bd413ad4..b56e98cf1c4bf 100644 --- a/recipes/bioconductor-mgu74b.db/post-link.sh +++ b/recipes/bioconductor-mgu74b.db/post-link.sh @@ -1,9 +1,10 @@ #!/bin/bash FN="mgu74b.db_3.2.3.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/mgu74b.db_3.2.3.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/mgu74b.db_3.2.3.tar.gz" "https://bioarchive.galaxyproject.org/mgu74b.db_3.2.3.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-mgu74b.db/bioconductor-mgu74b.db_3.2.3_src_all.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-mgu74b.db/bioconductor-mgu74b.db_3.2.3_src_all.tar.gz" ) MD5="9d019b194a64ec8c915514019896708e" @@ -16,7 +17,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-mgu74bcdf/meta.yaml b/recipes/bioconductor-mgu74bcdf/meta.yaml index 1a0097b7b9ed7..6ba27082c7e22 100644 --- a/recipes/bioconductor-mgu74bcdf/meta.yaml +++ b/recipes/bioconductor-mgu74bcdf/meta.yaml @@ -1,6 +1,6 @@ {% set version = "2.18.0" %} {% set name = "mgu74bcdf" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -12,19 +12,19 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: a1f0f98f29d34a421622447252113e1e build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' - r-base run: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-mgu74bcdf/post-link.sh b/recipes/bioconductor-mgu74bcdf/post-link.sh index 9e2adf9c0d53b..8cfae6f0e9795 100644 --- a/recipes/bioconductor-mgu74bcdf/post-link.sh +++ b/recipes/bioconductor-mgu74bcdf/post-link.sh @@ -1,9 +1,10 @@ #!/bin/bash FN="mgu74bcdf_2.18.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/mgu74bcdf_2.18.0.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/mgu74bcdf_2.18.0.tar.gz" "https://bioarchive.galaxyproject.org/mgu74bcdf_2.18.0.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-mgu74bcdf/bioconductor-mgu74bcdf_2.18.0_src_all.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-mgu74bcdf/bioconductor-mgu74bcdf_2.18.0_src_all.tar.gz" ) MD5="a1f0f98f29d34a421622447252113e1e" @@ -16,7 +17,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-mgu74bprobe/meta.yaml b/recipes/bioconductor-mgu74bprobe/meta.yaml index 6925c6a876ab1..1b766fc1a0810 100644 --- a/recipes/bioconductor-mgu74bprobe/meta.yaml +++ b/recipes/bioconductor-mgu74bprobe/meta.yaml @@ -1,6 +1,6 @@ {% set version = "2.18.0" %} {% set name = "mgu74bprobe" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -12,19 +12,19 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 224d606e6fc87592d387dbaabe5cd353 build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' - r-base run: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-mgu74bprobe/post-link.sh b/recipes/bioconductor-mgu74bprobe/post-link.sh index a3ea38f1a3258..ff2a8bcb2b7e7 100644 --- a/recipes/bioconductor-mgu74bprobe/post-link.sh +++ b/recipes/bioconductor-mgu74bprobe/post-link.sh @@ -1,9 +1,10 @@ #!/bin/bash FN="mgu74bprobe_2.18.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/mgu74bprobe_2.18.0.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/mgu74bprobe_2.18.0.tar.gz" "https://bioarchive.galaxyproject.org/mgu74bprobe_2.18.0.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-mgu74bprobe/bioconductor-mgu74bprobe_2.18.0_src_all.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-mgu74bprobe/bioconductor-mgu74bprobe_2.18.0_src_all.tar.gz" ) MD5="224d606e6fc87592d387dbaabe5cd353" @@ -16,7 +17,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-mgu74bv2.db/meta.yaml b/recipes/bioconductor-mgu74bv2.db/meta.yaml index 7dbbcdb391f34..a679d93fbda8d 100644 --- a/recipes/bioconductor-mgu74bv2.db/meta.yaml +++ b/recipes/bioconductor-mgu74bv2.db/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.2.3" %} {% set name = "mgu74bv2.db" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -12,7 +12,7 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: dfc729955539aa0a2a852745a515d413 build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ @@ -20,14 +20,14 @@ build: # Suggests: DBI, annotate, RUnit requirements: host: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' - - 'bioconductor-org.mm.eg.db >=3.7.0,<3.8.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' + - 'bioconductor-org.mm.eg.db >=3.8.0,<3.9.0' - r-base run: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' - - 'bioconductor-org.mm.eg.db >=3.7.0,<3.8.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' + - 'bioconductor-org.mm.eg.db >=3.8.0,<3.9.0' - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-mgu74bv2.db/post-link.sh b/recipes/bioconductor-mgu74bv2.db/post-link.sh index edd912987907f..ceffca675b302 100644 --- a/recipes/bioconductor-mgu74bv2.db/post-link.sh +++ b/recipes/bioconductor-mgu74bv2.db/post-link.sh @@ -1,9 +1,10 @@ #!/bin/bash FN="mgu74bv2.db_3.2.3.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/mgu74bv2.db_3.2.3.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/mgu74bv2.db_3.2.3.tar.gz" "https://bioarchive.galaxyproject.org/mgu74bv2.db_3.2.3.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-mgu74bv2.db/bioconductor-mgu74bv2.db_3.2.3_src_all.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-mgu74bv2.db/bioconductor-mgu74bv2.db_3.2.3_src_all.tar.gz" ) MD5="dfc729955539aa0a2a852745a515d413" @@ -16,7 +17,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-mgu74bv2cdf/meta.yaml b/recipes/bioconductor-mgu74bv2cdf/meta.yaml index 23ec9644f50d6..966653a0ad1ac 100644 --- a/recipes/bioconductor-mgu74bv2cdf/meta.yaml +++ b/recipes/bioconductor-mgu74bv2cdf/meta.yaml @@ -1,6 +1,6 @@ {% set version = "2.18.0" %} {% set name = "mgu74bv2cdf" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -12,19 +12,19 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 45c48d11af03633dc10f8682b7ad74c5 build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' - r-base run: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-mgu74bv2cdf/post-link.sh b/recipes/bioconductor-mgu74bv2cdf/post-link.sh index 0823bf2b39cef..425da44b15c2d 100644 --- a/recipes/bioconductor-mgu74bv2cdf/post-link.sh +++ b/recipes/bioconductor-mgu74bv2cdf/post-link.sh @@ -1,9 +1,10 @@ #!/bin/bash FN="mgu74bv2cdf_2.18.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/mgu74bv2cdf_2.18.0.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/mgu74bv2cdf_2.18.0.tar.gz" "https://bioarchive.galaxyproject.org/mgu74bv2cdf_2.18.0.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-mgu74bv2cdf/bioconductor-mgu74bv2cdf_2.18.0_src_all.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-mgu74bv2cdf/bioconductor-mgu74bv2cdf_2.18.0_src_all.tar.gz" ) MD5="45c48d11af03633dc10f8682b7ad74c5" @@ -16,7 +17,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-mgu74bv2probe/meta.yaml b/recipes/bioconductor-mgu74bv2probe/meta.yaml index ba67aa5ce8b20..0166658d6a187 100644 --- a/recipes/bioconductor-mgu74bv2probe/meta.yaml +++ b/recipes/bioconductor-mgu74bv2probe/meta.yaml @@ -1,6 +1,6 @@ {% set version = "2.18.0" %} {% set name = "mgu74bv2probe" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -12,19 +12,19 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: f6a12f88ea3c43a3e885c7e9b3fd03d2 build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' - r-base run: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-mgu74bv2probe/post-link.sh b/recipes/bioconductor-mgu74bv2probe/post-link.sh index 87d047de5a680..689c31fac608c 100644 --- a/recipes/bioconductor-mgu74bv2probe/post-link.sh +++ b/recipes/bioconductor-mgu74bv2probe/post-link.sh @@ -1,9 +1,10 @@ #!/bin/bash FN="mgu74bv2probe_2.18.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/mgu74bv2probe_2.18.0.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/mgu74bv2probe_2.18.0.tar.gz" "https://bioarchive.galaxyproject.org/mgu74bv2probe_2.18.0.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-mgu74bv2probe/bioconductor-mgu74bv2probe_2.18.0_src_all.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-mgu74bv2probe/bioconductor-mgu74bv2probe_2.18.0_src_all.tar.gz" ) MD5="f6a12f88ea3c43a3e885c7e9b3fd03d2" @@ -16,7 +17,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-mgu74c.db/meta.yaml b/recipes/bioconductor-mgu74c.db/meta.yaml index 5f0fd33f27739..ec77c28c698de 100644 --- a/recipes/bioconductor-mgu74c.db/meta.yaml +++ b/recipes/bioconductor-mgu74c.db/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.2.3" %} {% set name = "mgu74c.db" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -12,7 +12,7 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: a92c9ac08ce2f543b016268948178776 build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ @@ -20,14 +20,14 @@ build: # Suggests: DBI, annotate, RUnit requirements: host: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' - - 'bioconductor-org.mm.eg.db >=3.7.0,<3.8.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' + - 'bioconductor-org.mm.eg.db >=3.8.0,<3.9.0' - r-base run: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' - - 'bioconductor-org.mm.eg.db >=3.7.0,<3.8.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' + - 'bioconductor-org.mm.eg.db >=3.8.0,<3.9.0' - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-mgu74c.db/post-link.sh b/recipes/bioconductor-mgu74c.db/post-link.sh index a1e0e9d773cde..fb089f8ddd1f0 100644 --- a/recipes/bioconductor-mgu74c.db/post-link.sh +++ b/recipes/bioconductor-mgu74c.db/post-link.sh @@ -1,9 +1,10 @@ #!/bin/bash FN="mgu74c.db_3.2.3.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/mgu74c.db_3.2.3.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/mgu74c.db_3.2.3.tar.gz" "https://bioarchive.galaxyproject.org/mgu74c.db_3.2.3.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-mgu74c.db/bioconductor-mgu74c.db_3.2.3_src_all.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-mgu74c.db/bioconductor-mgu74c.db_3.2.3_src_all.tar.gz" ) MD5="a92c9ac08ce2f543b016268948178776" @@ -16,7 +17,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-mgu74ccdf/meta.yaml b/recipes/bioconductor-mgu74ccdf/meta.yaml index 6f5a23a0712d9..d2e416e7b4492 100644 --- a/recipes/bioconductor-mgu74ccdf/meta.yaml +++ b/recipes/bioconductor-mgu74ccdf/meta.yaml @@ -1,6 +1,6 @@ {% set version = "2.18.0" %} {% set name = "mgu74ccdf" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -12,19 +12,19 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 172e626b0e3072edc65c4efff35fe998 build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' - r-base run: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-mgu74ccdf/post-link.sh b/recipes/bioconductor-mgu74ccdf/post-link.sh index 3ae3ca619dce0..546811efd7aa1 100644 --- a/recipes/bioconductor-mgu74ccdf/post-link.sh +++ b/recipes/bioconductor-mgu74ccdf/post-link.sh @@ -1,9 +1,10 @@ #!/bin/bash FN="mgu74ccdf_2.18.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/mgu74ccdf_2.18.0.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/mgu74ccdf_2.18.0.tar.gz" "https://bioarchive.galaxyproject.org/mgu74ccdf_2.18.0.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-mgu74ccdf/bioconductor-mgu74ccdf_2.18.0_src_all.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-mgu74ccdf/bioconductor-mgu74ccdf_2.18.0_src_all.tar.gz" ) MD5="172e626b0e3072edc65c4efff35fe998" @@ -16,7 +17,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-mgu74cprobe/meta.yaml b/recipes/bioconductor-mgu74cprobe/meta.yaml index 94b9efc32a04e..a7e12d840d948 100644 --- a/recipes/bioconductor-mgu74cprobe/meta.yaml +++ b/recipes/bioconductor-mgu74cprobe/meta.yaml @@ -1,6 +1,6 @@ {% set version = "2.18.0" %} {% set name = "mgu74cprobe" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -12,19 +12,19 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 186992992708f0071fd552ef92b9e25c build: - number: 1 + number: 2 rpaths: - lib/R/lib/ - lib/ noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' - r-base run: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-mgu74cprobe/post-link.sh b/recipes/bioconductor-mgu74cprobe/post-link.sh index 4c8a42f8041f8..d7f7fa0e763c0 100644 --- a/recipes/bioconductor-mgu74cprobe/post-link.sh +++ b/recipes/bioconductor-mgu74cprobe/post-link.sh @@ -1,9 +1,10 @@ #!/bin/bash FN="mgu74cprobe_2.18.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/mgu74cprobe_2.18.0.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/mgu74cprobe_2.18.0.tar.gz" "https://bioarchive.galaxyproject.org/mgu74cprobe_2.18.0.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-mgu74cprobe/bioconductor-mgu74cprobe_2.18.0_src_all.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-mgu74cprobe/bioconductor-mgu74cprobe_2.18.0_src_all.tar.gz" ) MD5="186992992708f0071fd552ef92b9e25c" @@ -16,7 +17,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-mgu74cv2.db/meta.yaml b/recipes/bioconductor-mgu74cv2.db/meta.yaml index a70207ef0e9bc..2bf4ae5f508fc 100644 --- a/recipes/bioconductor-mgu74cv2.db/meta.yaml +++ b/recipes/bioconductor-mgu74cv2.db/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.2.3" %} {% set name = "mgu74cv2.db" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -12,7 +12,7 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 3f9ebd44f6dc4b23c009afa95afeb638 build: - number: 1 + number: 2 rpaths: - lib/R/lib/ - lib/ @@ -20,14 +20,14 @@ build: # Suggests: DBI, annotate, RUnit requirements: host: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' - - 'bioconductor-org.mm.eg.db >=3.7.0,<3.8.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' + - 'bioconductor-org.mm.eg.db >=3.8.0,<3.9.0' - r-base run: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' - - 'bioconductor-org.mm.eg.db >=3.7.0,<3.8.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' + - 'bioconductor-org.mm.eg.db >=3.8.0,<3.9.0' - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-mgu74cv2.db/post-link.sh b/recipes/bioconductor-mgu74cv2.db/post-link.sh index 9d7c8fa665efd..da44e363382a0 100644 --- a/recipes/bioconductor-mgu74cv2.db/post-link.sh +++ b/recipes/bioconductor-mgu74cv2.db/post-link.sh @@ -1,9 +1,10 @@ #!/bin/bash FN="mgu74cv2.db_3.2.3.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/mgu74cv2.db_3.2.3.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/mgu74cv2.db_3.2.3.tar.gz" "https://bioarchive.galaxyproject.org/mgu74cv2.db_3.2.3.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-mgu74cv2.db/bioconductor-mgu74cv2.db_3.2.3_src_all.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-mgu74cv2.db/bioconductor-mgu74cv2.db_3.2.3_src_all.tar.gz" ) MD5="3f9ebd44f6dc4b23c009afa95afeb638" @@ -16,7 +17,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-mgu74cv2cdf/meta.yaml b/recipes/bioconductor-mgu74cv2cdf/meta.yaml index 703b915762597..19381eb1d9d4d 100644 --- a/recipes/bioconductor-mgu74cv2cdf/meta.yaml +++ b/recipes/bioconductor-mgu74cv2cdf/meta.yaml @@ -1,6 +1,6 @@ {% set version = "2.18.0" %} {% set name = "mgu74cv2cdf" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -12,19 +12,19 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 9ef62b4b28f97770859db24393a07ed5 build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' - r-base run: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-mgu74cv2cdf/post-link.sh b/recipes/bioconductor-mgu74cv2cdf/post-link.sh index fcd77d0612e80..24c535589e13f 100644 --- a/recipes/bioconductor-mgu74cv2cdf/post-link.sh +++ b/recipes/bioconductor-mgu74cv2cdf/post-link.sh @@ -1,9 +1,10 @@ #!/bin/bash FN="mgu74cv2cdf_2.18.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/mgu74cv2cdf_2.18.0.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/mgu74cv2cdf_2.18.0.tar.gz" "https://bioarchive.galaxyproject.org/mgu74cv2cdf_2.18.0.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-mgu74cv2cdf/bioconductor-mgu74cv2cdf_2.18.0_src_all.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-mgu74cv2cdf/bioconductor-mgu74cv2cdf_2.18.0_src_all.tar.gz" ) MD5="9ef62b4b28f97770859db24393a07ed5" @@ -16,7 +17,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-mgu74cv2probe/meta.yaml b/recipes/bioconductor-mgu74cv2probe/meta.yaml index 660e327c3edd9..9e89e142b3d91 100644 --- a/recipes/bioconductor-mgu74cv2probe/meta.yaml +++ b/recipes/bioconductor-mgu74cv2probe/meta.yaml @@ -1,6 +1,6 @@ {% set version = "2.18.0" %} {% set name = "mgu74cv2probe" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -12,19 +12,19 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 0373496c817a1c1a153114047cfa7c5b build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' - r-base run: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-mgu74cv2probe/post-link.sh b/recipes/bioconductor-mgu74cv2probe/post-link.sh index 78d7874916b66..1ad698169fffd 100644 --- a/recipes/bioconductor-mgu74cv2probe/post-link.sh +++ b/recipes/bioconductor-mgu74cv2probe/post-link.sh @@ -1,9 +1,10 @@ #!/bin/bash FN="mgu74cv2probe_2.18.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/mgu74cv2probe_2.18.0.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/mgu74cv2probe_2.18.0.tar.gz" "https://bioarchive.galaxyproject.org/mgu74cv2probe_2.18.0.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-mgu74cv2probe/bioconductor-mgu74cv2probe_2.18.0_src_all.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-mgu74cv2probe/bioconductor-mgu74cv2probe_2.18.0_src_all.tar.gz" ) MD5="0373496c817a1c1a153114047cfa7c5b" @@ -16,7 +17,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-mguatlas5k.db/meta.yaml b/recipes/bioconductor-mguatlas5k.db/meta.yaml index 5cb50746b57e8..ec5f8a8099557 100644 --- a/recipes/bioconductor-mguatlas5k.db/meta.yaml +++ b/recipes/bioconductor-mguatlas5k.db/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.2.3" %} {% set name = "mguatlas5k.db" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -12,7 +12,7 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 826093fe7228c08962aff36ad89af28e build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ @@ -20,14 +20,14 @@ build: # Suggests: DBI, annotate, RUnit requirements: host: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' - - 'bioconductor-org.mm.eg.db >=3.7.0,<3.8.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' + - 'bioconductor-org.mm.eg.db >=3.8.0,<3.9.0' - r-base run: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' - - 'bioconductor-org.mm.eg.db >=3.7.0,<3.8.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' + - 'bioconductor-org.mm.eg.db >=3.8.0,<3.9.0' - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-mguatlas5k.db/post-link.sh b/recipes/bioconductor-mguatlas5k.db/post-link.sh index 173e8ca8ae172..cd3eed68b857b 100644 --- a/recipes/bioconductor-mguatlas5k.db/post-link.sh +++ b/recipes/bioconductor-mguatlas5k.db/post-link.sh @@ -1,9 +1,10 @@ #!/bin/bash FN="mguatlas5k.db_3.2.3.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/mguatlas5k.db_3.2.3.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/mguatlas5k.db_3.2.3.tar.gz" "https://bioarchive.galaxyproject.org/mguatlas5k.db_3.2.3.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-mguatlas5k.db/bioconductor-mguatlas5k.db_3.2.3_src_all.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-mguatlas5k.db/bioconductor-mguatlas5k.db_3.2.3_src_all.tar.gz" ) MD5="826093fe7228c08962aff36ad89af28e" @@ -16,7 +17,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-mgug4104a.db/meta.yaml b/recipes/bioconductor-mgug4104a.db/meta.yaml index 6322154f7a890..fec2c1dcf76bf 100644 --- a/recipes/bioconductor-mgug4104a.db/meta.yaml +++ b/recipes/bioconductor-mgug4104a.db/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.2.3" %} {% set name = "mgug4104a.db" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -12,7 +12,7 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 7b1cef094a226257cd657ed8d61e9ef1 build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ @@ -20,14 +20,14 @@ build: # Suggests: DBI, annotate, RUnit requirements: host: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' - - 'bioconductor-org.mm.eg.db >=3.7.0,<3.8.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' + - 'bioconductor-org.mm.eg.db >=3.8.0,<3.9.0' - r-base run: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' - - 'bioconductor-org.mm.eg.db >=3.7.0,<3.8.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' + - 'bioconductor-org.mm.eg.db >=3.8.0,<3.9.0' - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-mgug4104a.db/post-link.sh b/recipes/bioconductor-mgug4104a.db/post-link.sh index 0c221ff3dfd7f..429ac4d60669a 100644 --- a/recipes/bioconductor-mgug4104a.db/post-link.sh +++ b/recipes/bioconductor-mgug4104a.db/post-link.sh @@ -1,9 +1,10 @@ #!/bin/bash FN="mgug4104a.db_3.2.3.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/mgug4104a.db_3.2.3.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/mgug4104a.db_3.2.3.tar.gz" "https://bioarchive.galaxyproject.org/mgug4104a.db_3.2.3.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-mgug4104a.db/bioconductor-mgug4104a.db_3.2.3_src_all.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-mgug4104a.db/bioconductor-mgug4104a.db_3.2.3_src_all.tar.gz" ) MD5="7b1cef094a226257cd657ed8d61e9ef1" @@ -16,7 +17,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-mgug4120a.db/meta.yaml b/recipes/bioconductor-mgug4120a.db/meta.yaml index 26dbe381760c1..b180efbbef1fb 100644 --- a/recipes/bioconductor-mgug4120a.db/meta.yaml +++ b/recipes/bioconductor-mgug4120a.db/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.2.3" %} {% set name = "mgug4120a.db" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -12,7 +12,7 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: bb57e8b2efe3d038ec2a0ace0313a4e7 build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ @@ -20,14 +20,14 @@ build: # Suggests: DBI, annotate, RUnit requirements: host: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' - - 'bioconductor-org.mm.eg.db >=3.7.0,<3.8.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' + - 'bioconductor-org.mm.eg.db >=3.8.0,<3.9.0' - r-base run: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' - - 'bioconductor-org.mm.eg.db >=3.7.0,<3.8.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' + - 'bioconductor-org.mm.eg.db >=3.8.0,<3.9.0' - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-mgug4120a.db/post-link.sh b/recipes/bioconductor-mgug4120a.db/post-link.sh index b77cb2f742364..09fab9a225d58 100644 --- a/recipes/bioconductor-mgug4120a.db/post-link.sh +++ b/recipes/bioconductor-mgug4120a.db/post-link.sh @@ -1,9 +1,10 @@ #!/bin/bash FN="mgug4120a.db_3.2.3.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/mgug4120a.db_3.2.3.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/mgug4120a.db_3.2.3.tar.gz" "https://bioarchive.galaxyproject.org/mgug4120a.db_3.2.3.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-mgug4120a.db/bioconductor-mgug4120a.db_3.2.3_src_all.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-mgug4120a.db/bioconductor-mgug4120a.db_3.2.3_src_all.tar.gz" ) MD5="bb57e8b2efe3d038ec2a0ace0313a4e7" @@ -16,7 +17,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-mgug4121a.db/meta.yaml b/recipes/bioconductor-mgug4121a.db/meta.yaml index c7de07c755351..c30a4b5d63736 100644 --- a/recipes/bioconductor-mgug4121a.db/meta.yaml +++ b/recipes/bioconductor-mgug4121a.db/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.2.3" %} {% set name = "mgug4121a.db" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -12,7 +12,7 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 6b5cc321d5175356c383b91e30e120b7 build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ @@ -20,14 +20,14 @@ build: # Suggests: DBI, annotate, RUnit requirements: host: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' - - 'bioconductor-org.mm.eg.db >=3.7.0,<3.8.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' + - 'bioconductor-org.mm.eg.db >=3.8.0,<3.9.0' - r-base run: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' - - 'bioconductor-org.mm.eg.db >=3.7.0,<3.8.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' + - 'bioconductor-org.mm.eg.db >=3.8.0,<3.9.0' - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-mgug4121a.db/post-link.sh b/recipes/bioconductor-mgug4121a.db/post-link.sh index e9d5fb12fbfe8..ff75de219cce0 100644 --- a/recipes/bioconductor-mgug4121a.db/post-link.sh +++ b/recipes/bioconductor-mgug4121a.db/post-link.sh @@ -1,9 +1,10 @@ #!/bin/bash FN="mgug4121a.db_3.2.3.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/mgug4121a.db_3.2.3.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/mgug4121a.db_3.2.3.tar.gz" "https://bioarchive.galaxyproject.org/mgug4121a.db_3.2.3.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-mgug4121a.db/bioconductor-mgug4121a.db_3.2.3_src_all.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-mgug4121a.db/bioconductor-mgug4121a.db_3.2.3_src_all.tar.gz" ) MD5="6b5cc321d5175356c383b91e30e120b7" @@ -16,7 +17,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-mgug4122a.db/meta.yaml b/recipes/bioconductor-mgug4122a.db/meta.yaml index 97cb40089f656..419aededf8350 100644 --- a/recipes/bioconductor-mgug4122a.db/meta.yaml +++ b/recipes/bioconductor-mgug4122a.db/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.2.3" %} {% set name = "mgug4122a.db" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -12,7 +12,7 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 5fcdce909ac1c0ccbf06bf6411f6fe52 build: - number: 5 + number: 6 rpaths: - lib/R/lib/ - lib/ @@ -20,14 +20,14 @@ build: # Suggests: DBI, annotate, RUnit requirements: host: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' - - 'bioconductor-org.mm.eg.db >=3.7.0,<3.8.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' + - 'bioconductor-org.mm.eg.db >=3.8.0,<3.9.0' - r-base run: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' - - 'bioconductor-org.mm.eg.db >=3.7.0,<3.8.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' + - 'bioconductor-org.mm.eg.db >=3.8.0,<3.9.0' - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-mgug4122a.db/post-link.sh b/recipes/bioconductor-mgug4122a.db/post-link.sh index 5cda8d3fe83dc..0813c92614e91 100644 --- a/recipes/bioconductor-mgug4122a.db/post-link.sh +++ b/recipes/bioconductor-mgug4122a.db/post-link.sh @@ -1,7 +1,7 @@ #!/bin/bash FN="mgug4122a.db_3.2.3.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/mgug4122a.db_3.2.3.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/mgug4122a.db_3.2.3.tar.gz" "https://bioarchive.galaxyproject.org/mgug4122a.db_3.2.3.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-mgug4122a.db/bioconductor-mgug4122a.db_3.2.3_src_all.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-mgug4122a.db/bioconductor-mgug4122a.db_3.2.3_src_all.tar.gz" @@ -17,7 +17,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-mi16cod.db/meta.yaml b/recipes/bioconductor-mi16cod.db/meta.yaml index 54991a513c612..92ebef0a1f762 100644 --- a/recipes/bioconductor-mi16cod.db/meta.yaml +++ b/recipes/bioconductor-mi16cod.db/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.4.0" %} {% set name = "mi16cod.db" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -12,7 +12,7 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: f3a8e6f45ce5c298c1b1c5b32bf2630c build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ @@ -20,14 +20,14 @@ build: # Suggests: annotate, RUnit requirements: host: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' - - 'bioconductor-org.mm.eg.db >=3.7.0,<3.8.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' + - 'bioconductor-org.mm.eg.db >=3.8.0,<3.9.0' - r-base run: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' - - 'bioconductor-org.mm.eg.db >=3.7.0,<3.8.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' + - 'bioconductor-org.mm.eg.db >=3.8.0,<3.9.0' - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-mi16cod.db/post-link.sh b/recipes/bioconductor-mi16cod.db/post-link.sh index 03e21373676a1..3a9c0f98701ea 100644 --- a/recipes/bioconductor-mi16cod.db/post-link.sh +++ b/recipes/bioconductor-mi16cod.db/post-link.sh @@ -1,9 +1,10 @@ #!/bin/bash FN="mi16cod.db_3.4.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/mi16cod.db_3.4.0.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/mi16cod.db_3.4.0.tar.gz" "https://bioarchive.galaxyproject.org/mi16cod.db_3.4.0.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-mi16cod.db/bioconductor-mi16cod.db_3.4.0_src_all.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-mi16cod.db/bioconductor-mi16cod.db_3.4.0_src_all.tar.gz" ) MD5="f3a8e6f45ce5c298c1b1c5b32bf2630c" @@ -16,7 +17,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-michip/meta.yaml b/recipes/bioconductor-michip/meta.yaml index 95776537fb8ba..acb8804ef6632 100644 --- a/recipes/bioconductor-michip/meta.yaml +++ b/recipes/bioconductor-michip/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.36.0" %} +{% set version = "1.38.0" %} {% set name = "MiChip" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: b64b0ae539c74dcf5d71610ffce198a2 + md5: 6c43bb98c9ed2508386b44e5980c519b build: number: 0 rpaths: @@ -19,10 +19,10 @@ build: noarch: generic requirements: host: - - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' - r-base run: - - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' - r-base test: commands: diff --git a/recipes/bioconductor-microbiome/meta.yaml b/recipes/bioconductor-microbiome/meta.yaml index fd773cb792e8f..7b031e1c01502 100644 --- a/recipes/bioconductor-microbiome/meta.yaml +++ b/recipes/bioconductor-microbiome/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.4.2" %} +{% set version = "1.6.0" %} {% set name = "microbiome" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: faf9cbb6d7ae71b815ead3c8448cde2a + md5: 2f87ce1db908d6621fd4bfc97b8c6225 build: number: 0 rpaths: @@ -20,19 +20,23 @@ build: # Suggests: BiocGenerics, BiocStyle, Cairo, knitcitations, knitr, rmarkdown, testthat requirements: host: - - 'bioconductor-phyloseq >=1.26.0,<1.27.0' + - 'bioconductor-phyloseq >=1.28.0,<1.29.0' - r-base - r-dplyr - r-ggplot2 - r-reshape2 + - r-rtsne + - r-scales - r-tidyr - r-vegan run: - - 'bioconductor-phyloseq >=1.26.0,<1.27.0' + - 'bioconductor-phyloseq >=1.28.0,<1.29.0' - r-base - r-dplyr - r-ggplot2 - r-reshape2 + - r-rtsne + - r-scales - r-tidyr - r-vegan test: diff --git a/recipes/bioconductor-microrna/meta.yaml b/recipes/bioconductor-microrna/meta.yaml index 229f8a5129c78..3ad2c3daba0de 100644 --- a/recipes/bioconductor-microrna/meta.yaml +++ b/recipes/bioconductor-microrna/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.40.0" %} +{% set version = "1.42.0" %} {% set name = "microRNA" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 2ee23e69a38f498c578d6721d97dc985 + md5: 14fbaf24634fc9b16f8a05ed579f43eb build: number: 0 rpaths: @@ -18,10 +18,10 @@ build: - lib/ requirements: host: - - 'bioconductor-biostrings >=2.50.0,<2.51.0' + - 'bioconductor-biostrings >=2.52.0,<2.53.0' - r-base run: - - 'bioconductor-biostrings >=2.50.0,<2.51.0' + - 'bioconductor-biostrings >=2.52.0,<2.53.0' - r-base build: - {{ compiler('c') }} diff --git a/recipes/bioconductor-micrornaome/meta.yaml b/recipes/bioconductor-micrornaome/meta.yaml index 01b5708939cb8..476e70c41a138 100644 --- a/recipes/bioconductor-micrornaome/meta.yaml +++ b/recipes/bioconductor-micrornaome/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.4.0" %} +{% set version = "1.6.0" %} {% set name = "microRNAome" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: bae32fb7fe64c2d23b0ac8d5d5574a1a + md5: ac73eb0ae684ab92a99aaf4618878bcc build: number: 0 rpaths: @@ -20,12 +20,12 @@ build: # Suggests: BiocGenerics, RUnit requirements: host: - - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' + - 'bioconductor-summarizedexperiment >=1.14.0,<1.15.0' - r-base run: - - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' + - 'bioconductor-summarizedexperiment >=1.14.0,<1.15.0' - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-micrornaome/post-link.sh b/recipes/bioconductor-micrornaome/post-link.sh index a5169ee2ac333..4eb60b9732657 100644 --- a/recipes/bioconductor-micrornaome/post-link.sh +++ b/recipes/bioconductor-micrornaome/post-link.sh @@ -1,11 +1,11 @@ #!/bin/bash -FN="microRNAome_1.4.0.tar.gz" +FN="microRNAome_1.6.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/experiment/src/contrib/microRNAome_1.4.0.tar.gz" - "https://bioarchive.galaxyproject.org/microRNAome_1.4.0.tar.gz" - "https://depot.galaxyproject.org/software/bioconductor-micrornaome/bioconductor-micrornaome_1.4.0_src_all.tar.gz" + "https://bioconductor.org/packages/3.9/data/experiment/src/contrib/microRNAome_1.6.0.tar.gz" + "https://bioarchive.galaxyproject.org/microRNAome_1.6.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-micrornaome/bioconductor-micrornaome_1.6.0_src_all.tar.gz" ) -MD5="bae32fb7fe64c2d23b0ac8d5d5574a1a" +MD5="ac73eb0ae684ab92a99aaf4618878bcc" # Use a staging area in the conda dir rather than temp dirs, both to avoid # permission issues as well as to have things downloaded in a predictable @@ -16,7 +16,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-migsa/meta.yaml b/recipes/bioconductor-migsa/meta.yaml index 87409dc9776d6..642128ad6bf5b 100644 --- a/recipes/bioconductor-migsa/meta.yaml +++ b/recipes/bioconductor-migsa/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.6.0" %} +{% set version = "1.8.0" %} {% set name = "MIGSA" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,29 +10,29 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 0db3f4f96d22c45fbc237fdeeb59aa5e + md5: 4635b1037713c025a5a76962cc95c25a build: number: 0 rpaths: - lib/R/lib/ - lib/ noarch: generic -# Suggests: breastCancerMAINZ, breastCancerNKI, breastCancerTRANSBIG, breastCancerUNT, breastCancerUPP, breastCancerVDX, mGSZ, pbcmc, MIGSAdata +# Suggests: breastCancerMAINZ, breastCancerNKI, breastCancerTRANSBIG, breastCancerUNT, breastCancerUPP, breastCancerVDX, mGSZ, MIGSAdata requirements: host: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' - - 'bioconductor-biobase >=2.42.0,<2.43.0' - - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' - - 'bioconductor-biocparallel >=1.16.0,<1.17.0' - - 'bioconductor-edger >=3.24.0,<3.25.0' - - 'bioconductor-go.db >=3.7.0,<3.8.0' - - 'bioconductor-gostats >=2.48.0,<2.49.0' - - 'bioconductor-graph >=1.60.0,<1.61.0' - - 'bioconductor-gseabase >=1.44.0,<1.45.0' - - 'bioconductor-limma >=3.38.0,<3.39.0' - - 'bioconductor-org.hs.eg.db >=3.7.0,<3.8.0' - - 'bioconductor-rbgl >=1.58.0,<1.59.0' - - 'bioconductor-rgraphviz >=2.26.0,<2.27.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' + - 'bioconductor-biocgenerics >=0.30.0,<0.31.0' + - 'bioconductor-biocparallel >=1.18.0,<1.19.0' + - 'bioconductor-edger >=3.26.0,<3.27.0' + - 'bioconductor-go.db >=3.8.0,<3.9.0' + - 'bioconductor-gostats >=2.50.0,<2.51.0' + - 'bioconductor-graph >=1.62.0,<1.63.0' + - 'bioconductor-gseabase >=1.46.0,<1.47.0' + - 'bioconductor-limma >=3.40.0,<3.41.0' + - 'bioconductor-org.hs.eg.db >=3.8.0,<3.9.0' + - 'bioconductor-rbgl >=1.60.0,<1.61.0' + - 'bioconductor-rgraphviz >=2.28.0,<2.29.0' - r-base - r-data.table - r-futile.logger @@ -44,19 +44,19 @@ requirements: - r-rjsonio - r-vegan run: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' - - 'bioconductor-biobase >=2.42.0,<2.43.0' - - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' - - 'bioconductor-biocparallel >=1.16.0,<1.17.0' - - 'bioconductor-edger >=3.24.0,<3.25.0' - - 'bioconductor-go.db >=3.7.0,<3.8.0' - - 'bioconductor-gostats >=2.48.0,<2.49.0' - - 'bioconductor-graph >=1.60.0,<1.61.0' - - 'bioconductor-gseabase >=1.44.0,<1.45.0' - - 'bioconductor-limma >=3.38.0,<3.39.0' - - 'bioconductor-org.hs.eg.db >=3.7.0,<3.8.0' - - 'bioconductor-rbgl >=1.58.0,<1.59.0' - - 'bioconductor-rgraphviz >=2.26.0,<2.27.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' + - 'bioconductor-biocgenerics >=0.30.0,<0.31.0' + - 'bioconductor-biocparallel >=1.18.0,<1.19.0' + - 'bioconductor-edger >=3.26.0,<3.27.0' + - 'bioconductor-go.db >=3.8.0,<3.9.0' + - 'bioconductor-gostats >=2.50.0,<2.51.0' + - 'bioconductor-graph >=1.62.0,<1.63.0' + - 'bioconductor-gseabase >=1.46.0,<1.47.0' + - 'bioconductor-limma >=3.40.0,<3.41.0' + - 'bioconductor-org.hs.eg.db >=3.8.0,<3.9.0' + - 'bioconductor-rbgl >=1.60.0,<1.61.0' + - 'bioconductor-rgraphviz >=2.28.0,<2.29.0' - r-base - r-data.table - r-futile.logger diff --git a/recipes/bioconductor-migsadata/meta.yaml b/recipes/bioconductor-migsadata/meta.yaml index 5b30220f65294..9f31d528d894b 100644 --- a/recipes/bioconductor-migsadata/meta.yaml +++ b/recipes/bioconductor-migsadata/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.6.0" %} +{% set version = "1.8.0" %} {% set name = "MIGSAdata" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: a9d6b8af543c349a1955dc93934b487b + md5: c510924ea1ebf2892f33b16b3fd21473 build: number: 0 rpaths: @@ -23,7 +23,7 @@ requirements: - r-base run: - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-migsadata/post-link.sh b/recipes/bioconductor-migsadata/post-link.sh index 23938e3617496..845e446c92074 100644 --- a/recipes/bioconductor-migsadata/post-link.sh +++ b/recipes/bioconductor-migsadata/post-link.sh @@ -1,11 +1,11 @@ #!/bin/bash -FN="MIGSAdata_1.6.0.tar.gz" +FN="MIGSAdata_1.8.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/experiment/src/contrib/MIGSAdata_1.6.0.tar.gz" - "https://bioarchive.galaxyproject.org/MIGSAdata_1.6.0.tar.gz" - "https://depot.galaxyproject.org/software/bioconductor-migsadata/bioconductor-migsadata_1.6.0_src_all.tar.gz" + "https://bioconductor.org/packages/3.9/data/experiment/src/contrib/MIGSAdata_1.8.0.tar.gz" + "https://bioarchive.galaxyproject.org/MIGSAdata_1.8.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-migsadata/bioconductor-migsadata_1.8.0_src_all.tar.gz" ) -MD5="a9d6b8af543c349a1955dc93934b487b" +MD5="c510924ea1ebf2892f33b16b3fd21473" # Use a staging area in the conda dir rather than temp dirs, both to avoid # permission issues as well as to have things downloaded in a predictable @@ -16,7 +16,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-mimager/meta.yaml b/recipes/bioconductor-mimager/meta.yaml index 0c06e3eb66f8b..2b15cb3351089 100644 --- a/recipes/bioconductor-mimager/meta.yaml +++ b/recipes/bioconductor-mimager/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.6.0" %} +{% set version = "1.8.0" %} {% set name = "mimager" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 15abbaac41f80515ccbc4fda98e409a9 + md5: 44be4c0b62ff306350b691c2518863bb build: number: 0 rpaths: @@ -20,27 +20,27 @@ build: # Suggests: knitr, rmarkdown, BiocStyle, testthat, lintr, Matrix, abind, affydata, hgu95av2cdf, oligoData, pd.hugene.1.0.st.v1 requirements: host: - - 'bioconductor-affy >=1.60.0,<1.61.0' - - 'bioconductor-affyplm >=1.58.0,<1.59.0' - - 'bioconductor-biobase >=2.42.0,<2.43.0' - - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' - - 'bioconductor-oligo >=1.46.0,<1.47.0' - - 'bioconductor-oligoclasses >=1.44.0,<1.45.0' - - 'bioconductor-preprocesscore >=1.44.0,<1.45.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-affy >=1.62.0,<1.63.0' + - 'bioconductor-affyplm >=1.60.0,<1.61.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' + - 'bioconductor-biocgenerics >=0.30.0,<0.31.0' + - 'bioconductor-oligo >=1.48.0,<1.49.0' + - 'bioconductor-oligoclasses >=1.46.0,<1.47.0' + - 'bioconductor-preprocesscore >=1.46.0,<1.47.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' - r-base - r-dbi - r-gtable - r-scales run: - - 'bioconductor-affy >=1.60.0,<1.61.0' - - 'bioconductor-affyplm >=1.58.0,<1.59.0' - - 'bioconductor-biobase >=2.42.0,<2.43.0' - - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' - - 'bioconductor-oligo >=1.46.0,<1.47.0' - - 'bioconductor-oligoclasses >=1.44.0,<1.45.0' - - 'bioconductor-preprocesscore >=1.44.0,<1.45.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-affy >=1.62.0,<1.63.0' + - 'bioconductor-affyplm >=1.60.0,<1.61.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' + - 'bioconductor-biocgenerics >=0.30.0,<0.31.0' + - 'bioconductor-oligo >=1.48.0,<1.49.0' + - 'bioconductor-oligoclasses >=1.46.0,<1.47.0' + - 'bioconductor-preprocesscore >=1.46.0,<1.47.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' - r-base - r-dbi - r-gtable diff --git a/recipes/bioconductor-mimosa/meta.yaml b/recipes/bioconductor-mimosa/meta.yaml index b278f86371cc6..6b0e57e6e1390 100644 --- a/recipes/bioconductor-mimosa/meta.yaml +++ b/recipes/bioconductor-mimosa/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.20.1" %} +{% set version = "1.22.0" %} {% set name = "MIMOSA" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 1d92a6dd8cee028f10c198bd80692890 + md5: e835f0461ae09de0d4a554cc4a5b8b57 build: number: 0 rpaths: @@ -19,7 +19,7 @@ build: # Suggests: parallel, knitr requirements: host: - - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' - r-base - r-coda - r-data.table @@ -36,7 +36,7 @@ requirements: - r-scales - r-testthat run: - - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' - r-base - r-coda - r-data.table diff --git a/recipes/bioconductor-mineica/meta.yaml b/recipes/bioconductor-mineica/meta.yaml index 0c89b46c5febd..d706eb269d49e 100644 --- a/recipes/bioconductor-mineica/meta.yaml +++ b/recipes/bioconductor-mineica/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.22.0" %} +{% set version = "1.24.0" %} {% set name = "MineICA" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 0580f82c0a418930e9246cacb625dc93 + md5: 912b6bf849378551e84ceeda342e31d0 build: number: 0 rpaths: @@ -20,17 +20,17 @@ build: # Suggests: biomaRt, GOstats, cluster, hgu133a.db, mclust, igraph, breastCancerMAINZ, breastCancerTRANSBIG, breastCancerUPP, breastCancerVDX requirements: host: - - 'bioconductor-annotate >=1.60.0,<1.61.0' - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' - - 'bioconductor-biobase >=2.42.0,<2.43.0' - - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' - - 'bioconductor-biomart >=2.38.0,<2.39.0' - - 'bioconductor-gostats >=2.48.0,<2.49.0' - - 'bioconductor-graph >=1.60.0,<1.61.0' - - 'bioconductor-lumi >=2.34.0,<2.35.0' + - 'bioconductor-annotate >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' + - 'bioconductor-biocgenerics >=0.30.0,<0.31.0' + - 'bioconductor-biomart >=2.40.0,<2.41.0' + - 'bioconductor-gostats >=2.50.0,<2.51.0' + - 'bioconductor-graph >=1.62.0,<1.63.0' + - 'bioconductor-lumi >=2.36.0,<2.37.0' - 'bioconductor-lumihumanall.db >=1.22.0,<1.23.0' - - 'bioconductor-marray >=1.60.0,<1.61.0' - - 'bioconductor-rgraphviz >=2.26.0,<2.27.0' + - 'bioconductor-marray >=1.62.0,<1.63.0' + - 'bioconductor-rgraphviz >=2.28.0,<2.29.0' - r-base - r-cluster - r-colorspace @@ -48,17 +48,17 @@ requirements: - r-scales - r-xtable run: - - 'bioconductor-annotate >=1.60.0,<1.61.0' - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' - - 'bioconductor-biobase >=2.42.0,<2.43.0' - - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' - - 'bioconductor-biomart >=2.38.0,<2.39.0' - - 'bioconductor-gostats >=2.48.0,<2.49.0' - - 'bioconductor-graph >=1.60.0,<1.61.0' - - 'bioconductor-lumi >=2.34.0,<2.35.0' + - 'bioconductor-annotate >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' + - 'bioconductor-biocgenerics >=0.30.0,<0.31.0' + - 'bioconductor-biomart >=2.40.0,<2.41.0' + - 'bioconductor-gostats >=2.50.0,<2.51.0' + - 'bioconductor-graph >=1.62.0,<1.63.0' + - 'bioconductor-lumi >=2.36.0,<2.37.0' - 'bioconductor-lumihumanall.db >=1.22.0,<1.23.0' - - 'bioconductor-marray >=1.60.0,<1.61.0' - - 'bioconductor-rgraphviz >=2.26.0,<2.27.0' + - 'bioconductor-marray >=1.62.0,<1.63.0' + - 'bioconductor-rgraphviz >=2.28.0,<2.29.0' - r-base - r-cluster - r-colorspace diff --git a/recipes/bioconductor-minet/meta.yaml b/recipes/bioconductor-minet/meta.yaml index 68e2b5a5dc65b..05d1df4fa9f15 100644 --- a/recipes/bioconductor-minet/meta.yaml +++ b/recipes/bioconductor-minet/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "3.40.0" %} +{% set version = "3.42.0" %} {% set name = "minet" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: cfe31fbcec7dfc321436f468487dd842 + md5: 7b93b37bf615c6b55b51095c04d626b8 build: number: 0 rpaths: diff --git a/recipes/bioconductor-minfi/meta.yaml b/recipes/bioconductor-minfi/meta.yaml index 9bd56a0386347..7e92d13a0e05c 100644 --- a/recipes/bioconductor-minfi/meta.yaml +++ b/recipes/bioconductor-minfi/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.28.0" %} +{% set version = "1.30.0" %} {% set name = "minfi" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 5db8544bddf740588efc96a00e7c1b7c + md5: dacb09fcdb430b4ceb5d60ff816332a7 build: number: 0 rpaths: @@ -20,25 +20,25 @@ build: # Suggests: IlluminaHumanMethylation450kmanifest (>= 0.2.0), IlluminaHumanMethylation450kanno.ilmn12.hg19 (>= 0.2.1), minfiData (>= 0.18.0), minfiDataEPIC, FlowSorted.Blood.450k (>= 1.0.1), RUnit, digest, BiocStyle, knitr, rmarkdown, tools requirements: host: - - 'bioconductor-biobase >=2.42.0,<2.43.0' - - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' - - 'bioconductor-biocparallel >=1.16.0,<1.17.0' - - 'bioconductor-biostrings >=2.50.0,<2.51.0' - - 'bioconductor-bumphunter >=1.24.0,<1.25.0' - - 'bioconductor-delayedarray >=0.8.0,<0.9.0' - - 'bioconductor-delayedmatrixstats >=1.4.0,<1.5.0' - - 'bioconductor-genefilter >=1.64.0,<1.65.0' - - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' - - 'bioconductor-genomicranges >=1.34.0,<1.35.0' - - 'bioconductor-geoquery >=2.50.0,<2.51.0' - - 'bioconductor-hdf5array >=1.10.0,<1.11.0' - - 'bioconductor-illuminaio >=0.24.0,<0.25.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-limma >=3.38.0,<3.39.0' - - 'bioconductor-preprocesscore >=1.44.0,<1.45.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' - - 'bioconductor-siggenes >=1.56.0,<1.57.0' - - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' + - 'bioconductor-biocgenerics >=0.30.0,<0.31.0' + - 'bioconductor-biocparallel >=1.18.0,<1.19.0' + - 'bioconductor-biostrings >=2.52.0,<2.53.0' + - 'bioconductor-bumphunter >=1.26.0,<1.27.0' + - 'bioconductor-delayedarray >=0.10.0,<0.11.0' + - 'bioconductor-delayedmatrixstats >=1.6.0,<1.7.0' + - 'bioconductor-genefilter >=1.66.0,<1.67.0' + - 'bioconductor-genomeinfodb >=1.20.0,<1.21.0' + - 'bioconductor-genomicranges >=1.36.0,<1.37.0' + - 'bioconductor-geoquery >=2.52.0,<2.53.0' + - 'bioconductor-hdf5array >=1.12.0,<1.13.0' + - 'bioconductor-illuminaio >=0.26.0,<0.27.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-limma >=3.40.0,<3.41.0' + - 'bioconductor-preprocesscore >=1.46.0,<1.47.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' + - 'bioconductor-siggenes >=1.58.0,<1.59.0' + - 'bioconductor-summarizedexperiment >=1.14.0,<1.15.0' - r-base - r-beanplot - r-data.table @@ -51,25 +51,25 @@ requirements: - r-rcolorbrewer - r-reshape run: - - 'bioconductor-biobase >=2.42.0,<2.43.0' - - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' - - 'bioconductor-biocparallel >=1.16.0,<1.17.0' - - 'bioconductor-biostrings >=2.50.0,<2.51.0' - - 'bioconductor-bumphunter >=1.24.0,<1.25.0' - - 'bioconductor-delayedarray >=0.8.0,<0.9.0' - - 'bioconductor-delayedmatrixstats >=1.4.0,<1.5.0' - - 'bioconductor-genefilter >=1.64.0,<1.65.0' - - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' - - 'bioconductor-genomicranges >=1.34.0,<1.35.0' - - 'bioconductor-geoquery >=2.50.0,<2.51.0' - - 'bioconductor-hdf5array >=1.10.0,<1.11.0' - - 'bioconductor-illuminaio >=0.24.0,<0.25.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-limma >=3.38.0,<3.39.0' - - 'bioconductor-preprocesscore >=1.44.0,<1.45.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' - - 'bioconductor-siggenes >=1.56.0,<1.57.0' - - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' + - 'bioconductor-biocgenerics >=0.30.0,<0.31.0' + - 'bioconductor-biocparallel >=1.18.0,<1.19.0' + - 'bioconductor-biostrings >=2.52.0,<2.53.0' + - 'bioconductor-bumphunter >=1.26.0,<1.27.0' + - 'bioconductor-delayedarray >=0.10.0,<0.11.0' + - 'bioconductor-delayedmatrixstats >=1.6.0,<1.7.0' + - 'bioconductor-genefilter >=1.66.0,<1.67.0' + - 'bioconductor-genomeinfodb >=1.20.0,<1.21.0' + - 'bioconductor-genomicranges >=1.36.0,<1.37.0' + - 'bioconductor-geoquery >=2.52.0,<2.53.0' + - 'bioconductor-hdf5array >=1.12.0,<1.13.0' + - 'bioconductor-illuminaio >=0.26.0,<0.27.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-limma >=3.40.0,<3.41.0' + - 'bioconductor-preprocesscore >=1.46.0,<1.47.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' + - 'bioconductor-siggenes >=1.58.0,<1.59.0' + - 'bioconductor-summarizedexperiment >=1.14.0,<1.15.0' - r-base - r-beanplot - r-data.table diff --git a/recipes/bioconductor-minfidata/meta.yaml b/recipes/bioconductor-minfidata/meta.yaml index 6cc7fb8dbf3da..a62fa5e14df7e 100644 --- a/recipes/bioconductor-minfidata/meta.yaml +++ b/recipes/bioconductor-minfidata/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "0.28.0" %} +{% set version = "0.30.0" %} {% set name = "minfiData" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,9 +10,9 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 40cafa6a33fdc318ced42d538a27b98d + md5: 91b5668c839ed8fcca5ea36439c46473 build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ @@ -21,14 +21,14 @@ requirements: host: - 'bioconductor-illuminahumanmethylation450kanno.ilmn12.hg19 >=0.6.0,<0.7.0' - 'bioconductor-illuminahumanmethylation450kmanifest >=0.4.0,<0.5.0' - - 'bioconductor-minfi >=1.28.0,<1.29.0' + - 'bioconductor-minfi >=1.30.0,<1.31.0' - r-base run: - 'bioconductor-illuminahumanmethylation450kanno.ilmn12.hg19 >=0.6.0,<0.7.0' - 'bioconductor-illuminahumanmethylation450kmanifest >=0.4.0,<0.5.0' - - 'bioconductor-minfi >=1.28.0,<1.29.0' + - 'bioconductor-minfi >=1.30.0,<1.31.0' - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-minfidata/post-link.sh b/recipes/bioconductor-minfidata/post-link.sh index ce5ceda20246c..2a156b8d236a2 100644 --- a/recipes/bioconductor-minfidata/post-link.sh +++ b/recipes/bioconductor-minfidata/post-link.sh @@ -1,11 +1,11 @@ #!/bin/bash -FN="minfiData_0.28.0.tar.gz" +FN="minfiData_0.30.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/experiment/src/contrib/minfiData_0.28.0.tar.gz" - "https://bioarchive.galaxyproject.org/minfiData_0.28.0.tar.gz" - "https://depot.galaxyproject.org/software/bioconductor-minfidata/bioconductor-minfidata_0.28.0_src_all.tar.gz" + "https://bioconductor.org/packages/3.9/data/experiment/src/contrib/minfiData_0.30.0.tar.gz" + "https://bioarchive.galaxyproject.org/minfiData_0.30.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-minfidata/bioconductor-minfidata_0.30.0_src_all.tar.gz" ) -MD5="40cafa6a33fdc318ced42d538a27b98d" +MD5="91b5668c839ed8fcca5ea36439c46473" # Use a staging area in the conda dir rather than temp dirs, both to avoid # permission issues as well as to have things downloaded in a predictable @@ -16,7 +16,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-minfidataepic/meta.yaml b/recipes/bioconductor-minfidataepic/meta.yaml index dd3c96c94c9c8..831547a61c050 100644 --- a/recipes/bioconductor-minfidataepic/meta.yaml +++ b/recipes/bioconductor-minfidataepic/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.8.0" %} +{% set version = "1.10.0" %} {% set name = "minfiDataEPIC" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 92cb1d44c458f6d61d7893e7288a1589 + md5: 3a7541b38950d9ca5cdff14c8b721e31 build: number: 0 rpaths: @@ -20,15 +20,15 @@ build: requirements: host: - 'bioconductor-illuminahumanmethylationepicanno.ilm10b2.hg19 >=0.6.0,<0.7.0' - - 'bioconductor-illuminahumanmethylationepicmanifest >=0.3.0,<0.4.0' - - 'bioconductor-minfi >=1.28.0,<1.29.0' + - 'bioconductor-illuminahumanmethylationepicmanifest >=0.4.0,<0.5.0' + - 'bioconductor-minfi >=1.30.0,<1.31.0' - r-base run: - 'bioconductor-illuminahumanmethylationepicanno.ilm10b2.hg19 >=0.6.0,<0.7.0' - - 'bioconductor-illuminahumanmethylationepicmanifest >=0.3.0,<0.4.0' - - 'bioconductor-minfi >=1.28.0,<1.29.0' + - 'bioconductor-illuminahumanmethylationepicmanifest >=0.4.0,<0.5.0' + - 'bioconductor-minfi >=1.30.0,<1.31.0' - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-minfidataepic/post-link.sh b/recipes/bioconductor-minfidataepic/post-link.sh index 09f6fe0407137..a53c5ecd9448d 100644 --- a/recipes/bioconductor-minfidataepic/post-link.sh +++ b/recipes/bioconductor-minfidataepic/post-link.sh @@ -1,11 +1,11 @@ #!/bin/bash -FN="minfiDataEPIC_1.8.0.tar.gz" +FN="minfiDataEPIC_1.10.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/experiment/src/contrib/minfiDataEPIC_1.8.0.tar.gz" - "https://bioarchive.galaxyproject.org/minfiDataEPIC_1.8.0.tar.gz" - "https://depot.galaxyproject.org/software/bioconductor-minfidataepic/bioconductor-minfidataepic_1.8.0_src_all.tar.gz" + "https://bioconductor.org/packages/3.9/data/experiment/src/contrib/minfiDataEPIC_1.10.0.tar.gz" + "https://bioarchive.galaxyproject.org/minfiDataEPIC_1.10.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-minfidataepic/bioconductor-minfidataepic_1.10.0_src_all.tar.gz" ) -MD5="92cb1d44c458f6d61d7893e7288a1589" +MD5="3a7541b38950d9ca5cdff14c8b721e31" # Use a staging area in the conda dir rather than temp dirs, both to avoid # permission issues as well as to have things downloaded in a predictable @@ -16,7 +16,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-minimumdistance/meta.yaml b/recipes/bioconductor-minimumdistance/meta.yaml index 0ba4538456823..1c55c4701d426 100644 --- a/recipes/bioconductor-minimumdistance/meta.yaml +++ b/recipes/bioconductor-minimumdistance/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.26.0" %} +{% set version = "1.28.0" %} {% set name = "MinimumDistance" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,9 +10,9 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 94c0e99960d55c5416e88f76a65bc021 + md5: f22446874922f48dd65b7530c1fda2b0 build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ @@ -20,16 +20,16 @@ build: # Suggests: human610quadv1bCrlmm (>= 1.0.3), BSgenome.Hsapiens.UCSC.hg18, BSgenome.Hsapiens.UCSC.hg19, SNPchip, RUnit requirements: host: - - 'bioconductor-biobase >=2.42.0,<2.43.0' - - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' - - 'bioconductor-dnacopy >=1.56.0,<1.57.0' - - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' - - 'bioconductor-genomicranges >=1.34.0,<1.35.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-oligoclasses >=1.44.0,<1.45.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' - - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' - - 'bioconductor-vanillaice >=1.44.0,<1.45.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' + - 'bioconductor-biocgenerics >=0.30.0,<0.31.0' + - 'bioconductor-dnacopy >=1.58.0,<1.59.0' + - 'bioconductor-genomeinfodb >=1.20.0,<1.21.0' + - 'bioconductor-genomicranges >=1.36.0,<1.37.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-oligoclasses >=1.46.0,<1.47.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' + - 'bioconductor-summarizedexperiment >=1.14.0,<1.15.0' + - 'bioconductor-vanillaice >=1.46.0,<1.47.0' - r-base - r-data.table - r-ff @@ -37,16 +37,16 @@ requirements: - r-lattice - r-matrixstats run: - - 'bioconductor-biobase >=2.42.0,<2.43.0' - - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' - - 'bioconductor-dnacopy >=1.56.0,<1.57.0' - - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' - - 'bioconductor-genomicranges >=1.34.0,<1.35.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-oligoclasses >=1.44.0,<1.45.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' - - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' - - 'bioconductor-vanillaice >=1.44.0,<1.45.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' + - 'bioconductor-biocgenerics >=0.30.0,<0.31.0' + - 'bioconductor-dnacopy >=1.58.0,<1.59.0' + - 'bioconductor-genomeinfodb >=1.20.0,<1.21.0' + - 'bioconductor-genomicranges >=1.36.0,<1.37.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-oligoclasses >=1.46.0,<1.47.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' + - 'bioconductor-summarizedexperiment >=1.14.0,<1.15.0' + - 'bioconductor-vanillaice >=1.46.0,<1.47.0' - r-base - r-data.table - r-ff diff --git a/recipes/bioconductor-minionsummarydata/meta.yaml b/recipes/bioconductor-minionsummarydata/meta.yaml index 531cbdd60deda..6ec888b067502 100644 --- a/recipes/bioconductor-minionsummarydata/meta.yaml +++ b/recipes/bioconductor-minionsummarydata/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.12.0" %} +{% set version = "1.14.0" %} {% set name = "minionSummaryData" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 4e3db62e383ae1e28af148fadaf23a40 + md5: b5009bbbc5b2a0fa5e71180dd18a6a7b build: number: 0 rpaths: @@ -23,7 +23,7 @@ requirements: - r-base run: - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-minionsummarydata/post-link.sh b/recipes/bioconductor-minionsummarydata/post-link.sh index 55c4b8fb3b46a..92b648ddd7a5f 100644 --- a/recipes/bioconductor-minionsummarydata/post-link.sh +++ b/recipes/bioconductor-minionsummarydata/post-link.sh @@ -1,11 +1,11 @@ #!/bin/bash -FN="minionSummaryData_1.12.0.tar.gz" +FN="minionSummaryData_1.14.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/experiment/src/contrib/minionSummaryData_1.12.0.tar.gz" - "https://bioarchive.galaxyproject.org/minionSummaryData_1.12.0.tar.gz" - "https://depot.galaxyproject.org/software/bioconductor-minionsummarydata/bioconductor-minionsummarydata_1.12.0_src_all.tar.gz" + "https://bioconductor.org/packages/3.9/data/experiment/src/contrib/minionSummaryData_1.14.0.tar.gz" + "https://bioarchive.galaxyproject.org/minionSummaryData_1.14.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-minionsummarydata/bioconductor-minionsummarydata_1.14.0_src_all.tar.gz" ) -MD5="4e3db62e383ae1e28af148fadaf23a40" +MD5="b5009bbbc5b2a0fa5e71180dd18a6a7b" # Use a staging area in the conda dir rather than temp dirs, both to avoid # permission issues as well as to have things downloaded in a predictable @@ -16,7 +16,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-mipp/meta.yaml b/recipes/bioconductor-mipp/meta.yaml index aadf3a03ca62b..7eede4539081c 100644 --- a/recipes/bioconductor-mipp/meta.yaml +++ b/recipes/bioconductor-mipp/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.54.0" %} +{% set version = "1.56.0" %} {% set name = "MiPP" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 44dbca699e0c65714e8fa3c1375205c3 + md5: 394a2e8f00d6eec273ab9ab6915a5b0b build: number: 0 rpaths: @@ -19,12 +19,12 @@ build: noarch: generic requirements: host: - - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' - r-base - r-e1071 - r-mass run: - - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' - r-base - r-e1071 - r-mass diff --git a/recipes/bioconductor-mira/meta.yaml b/recipes/bioconductor-mira/meta.yaml index e017ad3664d4e..7a02e2cd41216 100644 --- a/recipes/bioconductor-mira/meta.yaml +++ b/recipes/bioconductor-mira/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.4.0" %} +{% set version = "1.6.0" %} {% set name = "MIRA" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 02bb707ed5364f77a096150ec6735ae0 + md5: 9f9204d9c3afd2c8e0dddd4a82f17853 build: number: 0 rpaths: @@ -20,22 +20,22 @@ build: # Suggests: knitr, parallel, testthat, BiocStyle, rmarkdown, AnnotationHub, LOLA requirements: host: - - 'bioconductor-biobase >=2.42.0,<2.43.0' - - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' - - 'bioconductor-bsseq >=1.18.0,<1.19.0' - - 'bioconductor-genomicranges >=1.34.0,<1.35.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' + - 'bioconductor-biocgenerics >=0.30.0,<0.31.0' + - 'bioconductor-bsseq >=1.20.0,<1.21.0' + - 'bioconductor-genomicranges >=1.36.0,<1.37.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' - r-base - r-data.table - r-ggplot2 run: - - 'bioconductor-biobase >=2.42.0,<2.43.0' - - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' - - 'bioconductor-bsseq >=1.18.0,<1.19.0' - - 'bioconductor-genomicranges >=1.34.0,<1.35.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' + - 'bioconductor-biocgenerics >=0.30.0,<0.31.0' + - 'bioconductor-bsseq >=1.20.0,<1.21.0' + - 'bioconductor-genomicranges >=1.36.0,<1.37.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' - r-base - r-data.table - r-ggplot2 diff --git a/recipes/bioconductor-mirage/meta.yaml b/recipes/bioconductor-mirage/meta.yaml index 8275c79479e09..c671842db5361 100644 --- a/recipes/bioconductor-mirage/meta.yaml +++ b/recipes/bioconductor-mirage/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.24.1" %} +{% set version = "1.26.0" %} {% set name = "MiRaGE" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: c3f99de0be7f849a9794ca0f584fc7faa0b560248accd81894deba49e40153c9 + md5: 0aa3af0ddc085eee4d4470de1ca2404b build: number: 0 rpaths: @@ -20,17 +20,17 @@ build: # Suggests: seqinr (>= 3.0.7), biomaRt (>= 2.19.1), GenomicFeatures (>= 1.15.4), Biostrings (>= 2.31.3), BSgenome.Hsapiens.UCSC.hg19, BSgenome.Mmusculus.UCSC.mm10, miRNATarget, humanStemCell, IRanges, GenomicRanges (>= 1.8.3), BSgenome, beadarrayExampleData requirements: host: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' - - 'bioconductor-biobase >=2.42.0,<2.43.0' - - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' + - 'bioconductor-biocgenerics >=0.30.0,<0.31.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' - r-base - r-biocmanager run: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' - - 'bioconductor-biobase >=2.42.0,<2.43.0' - - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' + - 'bioconductor-biocgenerics >=0.30.0,<0.31.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' - r-base - r-biocmanager test: diff --git a/recipes/bioconductor-mirbase.db/meta.yaml b/recipes/bioconductor-mirbase.db/meta.yaml index e8ec09b37e9ad..4f4293233c8fe 100644 --- a/recipes/bioconductor-mirbase.db/meta.yaml +++ b/recipes/bioconductor-mirbase.db/meta.yaml @@ -1,6 +1,6 @@ {% set version = "1.2.0" %} {% set name = "mirbase.db" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -12,19 +12,19 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 316bc12cee8c2dd9240b7fc30cd1619e build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' - r-base run: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-mirbase.db/post-link.sh b/recipes/bioconductor-mirbase.db/post-link.sh index 5ce988916ffd8..5555f8dd463f9 100644 --- a/recipes/bioconductor-mirbase.db/post-link.sh +++ b/recipes/bioconductor-mirbase.db/post-link.sh @@ -1,9 +1,10 @@ #!/bin/bash FN="mirbase.db_1.2.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/mirbase.db_1.2.0.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/mirbase.db_1.2.0.tar.gz" "https://bioarchive.galaxyproject.org/mirbase.db_1.2.0.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-mirbase.db/bioconductor-mirbase.db_1.2.0_src_all.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-mirbase.db/bioconductor-mirbase.db_1.2.0_src_all.tar.gz" ) MD5="316bc12cee8c2dd9240b7fc30cd1619e" @@ -16,7 +17,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-mirbaseconverter/meta.yaml b/recipes/bioconductor-mirbaseconverter/meta.yaml index 687cd5ff7311e..c35a9cc9ded92 100644 --- a/recipes/bioconductor-mirbaseconverter/meta.yaml +++ b/recipes/bioconductor-mirbaseconverter/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.6.0" %} +{% set version = "1.8.0" %} {% set name = "miRBaseConverter" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 4333ef90ec81266289f19a0857a614a5 + md5: 068113b3bb53e38fd5311719df6895d9 build: number: 0 rpaths: diff --git a/recipes/bioconductor-mirbaseversions.db/meta.yaml b/recipes/bioconductor-mirbaseversions.db/meta.yaml index 49eb5c6abd5cb..54effffcca374 100644 --- a/recipes/bioconductor-mirbaseversions.db/meta.yaml +++ b/recipes/bioconductor-mirbaseversions.db/meta.yaml @@ -1,6 +1,6 @@ {% set version = "1.1.0" %} {% set name = "miRBaseVersions.db" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -12,7 +12,7 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' md5: 9944ab7a474f84a40100c56298f9cb77 build: - number: 1 + number: 2 rpaths: - lib/R/lib/ - lib/ @@ -20,18 +20,18 @@ build: # Suggests: testthat, knitr, rmarkdown, annotate requirements: host: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' - r-base - r-dbi - r-gtools - r-rsqlite run: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' - r-base - r-dbi - r-gtools - r-rsqlite - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-mirbaseversions.db/post-link.sh b/recipes/bioconductor-mirbaseversions.db/post-link.sh index f32dff43924f9..d8772df5fcf5d 100644 --- a/recipes/bioconductor-mirbaseversions.db/post-link.sh +++ b/recipes/bioconductor-mirbaseversions.db/post-link.sh @@ -1,7 +1,7 @@ #!/bin/bash FN="miRBaseVersions.db_1.1.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/miRBaseVersions.db_1.1.0.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/miRBaseVersions.db_1.1.0.tar.gz" "https://bioarchive.galaxyproject.org/miRBaseVersions.db_1.1.0.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-mirbaseversions.db/bioconductor-mirbaseversions.db_1.1.0_src_all.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-mirbaseversions.db/bioconductor-mirbaseversions.db_1.1.0_src_all.tar.gz" @@ -17,7 +17,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-mircomp/meta.yaml b/recipes/bioconductor-mircomp/meta.yaml index 1d8f4b5109300..d2228b95ef042 100644 --- a/recipes/bioconductor-mircomp/meta.yaml +++ b/recipes/bioconductor-mircomp/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.12.0" %} +{% set version = "1.14.0" %} {% set name = "miRcomp" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 776c9e34a4c9d963f2588068c8438170 + md5: 1de52795a9179f5a582f06f640d37b63 build: number: 0 rpaths: @@ -20,13 +20,13 @@ build: # Suggests: BiocStyle, knitr, rmarkdown, RUnit, BiocGenerics, shiny requirements: host: - - 'bioconductor-biobase >=2.42.0,<2.43.0' - - 'bioconductor-mircompdata >=1.12.0,<1.13.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' + - 'bioconductor-mircompdata >=1.14.0,<1.15.0' - r-base - r-kernsmooth run: - - 'bioconductor-biobase >=2.42.0,<2.43.0' - - 'bioconductor-mircompdata >=1.12.0,<1.13.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' + - 'bioconductor-mircompdata >=1.14.0,<1.15.0' - r-base - r-kernsmooth test: diff --git a/recipes/bioconductor-mircompdata/meta.yaml b/recipes/bioconductor-mircompdata/meta.yaml index 64b451416c3cb..4a4f0d8559a9c 100644 --- a/recipes/bioconductor-mircompdata/meta.yaml +++ b/recipes/bioconductor-mircompdata/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.12.0" %} +{% set version = "1.14.0" %} {% set name = "miRcompData" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 2b86aeb9ff05f956dbaa0f7dd132cbc4 + md5: 30e555c141406e16ec2a98a71fb9dfb3 build: number: 0 rpaths: @@ -22,7 +22,7 @@ requirements: - r-base run: - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-mircompdata/post-link.sh b/recipes/bioconductor-mircompdata/post-link.sh index 8fa5ee554c358..3434520022815 100644 --- a/recipes/bioconductor-mircompdata/post-link.sh +++ b/recipes/bioconductor-mircompdata/post-link.sh @@ -1,11 +1,11 @@ #!/bin/bash -FN="miRcompData_1.12.0.tar.gz" +FN="miRcompData_1.14.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/experiment/src/contrib/miRcompData_1.12.0.tar.gz" - "https://bioarchive.galaxyproject.org/miRcompData_1.12.0.tar.gz" - "https://depot.galaxyproject.org/software/bioconductor-mircompdata/bioconductor-mircompdata_1.12.0_src_all.tar.gz" + "https://bioconductor.org/packages/3.9/data/experiment/src/contrib/miRcompData_1.14.0.tar.gz" + "https://bioarchive.galaxyproject.org/miRcompData_1.14.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-mircompdata/bioconductor-mircompdata_1.14.0_src_all.tar.gz" ) -MD5="2b86aeb9ff05f956dbaa0f7dd132cbc4" +MD5="30e555c141406e16ec2a98a71fb9dfb3" # Use a staging area in the conda dir rather than temp dirs, both to avoid # permission issues as well as to have things downloaded in a predictable @@ -16,7 +16,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-mirintegrator/meta.yaml b/recipes/bioconductor-mirintegrator/meta.yaml index aa899e50b4945..9132061fb17d2 100644 --- a/recipes/bioconductor-mirintegrator/meta.yaml +++ b/recipes/bioconductor-mirintegrator/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.12.0" %} +{% set version = "1.14.0" %} {% set name = "mirIntegrator" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: c89d486120b4e814ee43c8268a64e7d8 + md5: a25c9b60b0e10b2cc870f6ac5ba87118 build: number: 0 rpaths: @@ -20,19 +20,19 @@ build: # Suggests: RUnit, BiocGenerics requirements: host: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' - - 'bioconductor-graph >=1.60.0,<1.61.0' - - 'bioconductor-org.hs.eg.db >=3.7.0,<3.8.0' - - 'bioconductor-rgraphviz >=2.26.0,<2.27.0' - - 'bioconductor-rontotools >=2.10.0,<2.11.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' + - 'bioconductor-graph >=1.62.0,<1.63.0' + - 'bioconductor-org.hs.eg.db >=3.8.0,<3.9.0' + - 'bioconductor-rgraphviz >=2.28.0,<2.29.0' + - 'bioconductor-rontotools >=2.12.0,<2.13.0' - r-base - r-ggplot2 run: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' - - 'bioconductor-graph >=1.60.0,<1.61.0' - - 'bioconductor-org.hs.eg.db >=3.7.0,<3.8.0' - - 'bioconductor-rgraphviz >=2.26.0,<2.27.0' - - 'bioconductor-rontotools >=2.10.0,<2.11.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' + - 'bioconductor-graph >=1.62.0,<1.63.0' + - 'bioconductor-org.hs.eg.db >=3.8.0,<3.9.0' + - 'bioconductor-rgraphviz >=2.28.0,<2.29.0' + - 'bioconductor-rontotools >=2.12.0,<2.13.0' - r-base - r-ggplot2 test: diff --git a/recipes/bioconductor-mirlab/meta.yaml b/recipes/bioconductor-mirlab/meta.yaml index 58d4f2db1e5e1..24eb4e2d82656 100644 --- a/recipes/bioconductor-mirlab/meta.yaml +++ b/recipes/bioconductor-mirlab/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.12.0" %} +{% set version = "1.14.0" %} {% set name = "miRLAB" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 0ff8f05e5b21897eb8a29bf4f4b93ea9 + md5: 0f9533b1c1d4d19d3c88d8d122a919bd build: number: 0 rpaths: @@ -20,15 +20,15 @@ build: # Suggests: knitr,BiocGenerics, AnnotationDbi,RUnit requirements: host: - - 'bioconductor-category >=2.48.0,<2.49.0' - - 'bioconductor-ctc >=1.56.0,<1.57.0' - - 'bioconductor-gostats >=2.48.0,<2.49.0' - - 'bioconductor-impute >=1.56.0,<1.57.0' - - 'bioconductor-limma >=3.38.0,<3.39.0' - - 'bioconductor-org.hs.eg.db >=3.7.0,<3.8.0' - - 'bioconductor-roleswitch >=1.20.0,<1.21.0' - - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' - - 'bioconductor-tcgabiolinks >=2.10.0,<2.11.0' + - 'bioconductor-category >=2.50.0,<2.51.0' + - 'bioconductor-ctc >=1.58.0,<1.59.0' + - 'bioconductor-gostats >=2.50.0,<2.51.0' + - 'bioconductor-impute >=1.58.0,<1.59.0' + - 'bioconductor-limma >=3.40.0,<3.41.0' + - 'bioconductor-org.hs.eg.db >=3.8.0,<3.9.0' + - 'bioconductor-roleswitch >=1.22.0,<1.23.0' + - 'bioconductor-summarizedexperiment >=1.14.0,<1.15.0' + - 'bioconductor-tcgabiolinks >=2.12.0,<2.13.0' - r-base - r-dplyr - r-energy @@ -43,15 +43,15 @@ requirements: - r-rcurl - r-stringr run: - - 'bioconductor-category >=2.48.0,<2.49.0' - - 'bioconductor-ctc >=1.56.0,<1.57.0' - - 'bioconductor-gostats >=2.48.0,<2.49.0' - - 'bioconductor-impute >=1.56.0,<1.57.0' - - 'bioconductor-limma >=3.38.0,<3.39.0' - - 'bioconductor-org.hs.eg.db >=3.7.0,<3.8.0' - - 'bioconductor-roleswitch >=1.20.0,<1.21.0' - - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' - - 'bioconductor-tcgabiolinks >=2.10.0,<2.11.0' + - 'bioconductor-category >=2.50.0,<2.51.0' + - 'bioconductor-ctc >=1.58.0,<1.59.0' + - 'bioconductor-gostats >=2.50.0,<2.51.0' + - 'bioconductor-impute >=1.58.0,<1.59.0' + - 'bioconductor-limma >=3.40.0,<3.41.0' + - 'bioconductor-org.hs.eg.db >=3.8.0,<3.9.0' + - 'bioconductor-roleswitch >=1.22.0,<1.23.0' + - 'bioconductor-summarizedexperiment >=1.14.0,<1.15.0' + - 'bioconductor-tcgabiolinks >=2.12.0,<2.13.0' - r-base - r-dplyr - r-energy diff --git a/recipes/bioconductor-mirmine/meta.yaml b/recipes/bioconductor-mirmine/meta.yaml index dc58d6835d768..5d366122d76fa 100644 --- a/recipes/bioconductor-mirmine/meta.yaml +++ b/recipes/bioconductor-mirmine/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.4.0" %} +{% set version = "1.6.0" %} {% set name = "miRmine" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 2936f1b79cedb5ec7b30eda3374a3b1a + md5: db116d76b70324451da0adf8db57b280 build: number: 0 rpaths: @@ -20,10 +20,10 @@ build: # Suggests: BiocStyle, knitr, rmarkdown, DESeq2 requirements: host: - - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' + - 'bioconductor-summarizedexperiment >=1.14.0,<1.15.0' - r-base run: - - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' + - 'bioconductor-summarizedexperiment >=1.14.0,<1.15.0' - r-base test: commands: diff --git a/recipes/bioconductor-mirna102xgaincdf/meta.yaml b/recipes/bioconductor-mirna102xgaincdf/meta.yaml index d9f6796e420db..eb476e0a534ff 100644 --- a/recipes/bioconductor-mirna102xgaincdf/meta.yaml +++ b/recipes/bioconductor-mirna102xgaincdf/meta.yaml @@ -1,6 +1,6 @@ {% set version = "2.18.0" %} {% set name = "mirna102xgaincdf" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -12,19 +12,19 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 9091a45c2ac15c2de0263743ab334f97 build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' - r-base run: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-mirna102xgaincdf/post-link.sh b/recipes/bioconductor-mirna102xgaincdf/post-link.sh index 9c75a47fbcade..40b879cb27e0d 100644 --- a/recipes/bioconductor-mirna102xgaincdf/post-link.sh +++ b/recipes/bioconductor-mirna102xgaincdf/post-link.sh @@ -1,9 +1,10 @@ #!/bin/bash FN="mirna102xgaincdf_2.18.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/mirna102xgaincdf_2.18.0.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/mirna102xgaincdf_2.18.0.tar.gz" "https://bioarchive.galaxyproject.org/mirna102xgaincdf_2.18.0.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-mirna102xgaincdf/bioconductor-mirna102xgaincdf_2.18.0_src_all.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-mirna102xgaincdf/bioconductor-mirna102xgaincdf_2.18.0_src_all.tar.gz" ) MD5="9091a45c2ac15c2de0263743ab334f97" @@ -16,7 +17,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-mirna10cdf/meta.yaml b/recipes/bioconductor-mirna10cdf/meta.yaml index e1fa03d3d447d..fe9519c2251b2 100644 --- a/recipes/bioconductor-mirna10cdf/meta.yaml +++ b/recipes/bioconductor-mirna10cdf/meta.yaml @@ -1,6 +1,6 @@ {% set version = "2.18.0" %} {% set name = "mirna10cdf" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -12,19 +12,19 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 814da2a2e298e132f4db0b2e8ab814be build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' - r-base run: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-mirna10cdf/post-link.sh b/recipes/bioconductor-mirna10cdf/post-link.sh index 8d9e0e7c09aa0..fd07e76a1aeb3 100644 --- a/recipes/bioconductor-mirna10cdf/post-link.sh +++ b/recipes/bioconductor-mirna10cdf/post-link.sh @@ -1,9 +1,10 @@ #!/bin/bash FN="mirna10cdf_2.18.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/mirna10cdf_2.18.0.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/mirna10cdf_2.18.0.tar.gz" "https://bioarchive.galaxyproject.org/mirna10cdf_2.18.0.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-mirna10cdf/bioconductor-mirna10cdf_2.18.0_src_all.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-mirna10cdf/bioconductor-mirna10cdf_2.18.0_src_all.tar.gz" ) MD5="814da2a2e298e132f4db0b2e8ab814be" @@ -16,7 +17,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-mirna10probe/meta.yaml b/recipes/bioconductor-mirna10probe/meta.yaml index 34b2628d554fd..9fd5fafa2d779 100644 --- a/recipes/bioconductor-mirna10probe/meta.yaml +++ b/recipes/bioconductor-mirna10probe/meta.yaml @@ -1,6 +1,6 @@ {% set version = "2.18.0" %} {% set name = "mirna10probe" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -12,19 +12,19 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 8bfa6cdfeee1c563b4881214bd5d4ce1 build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' - r-base run: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-mirna10probe/post-link.sh b/recipes/bioconductor-mirna10probe/post-link.sh index b03f1e170b613..add15d2b61d16 100644 --- a/recipes/bioconductor-mirna10probe/post-link.sh +++ b/recipes/bioconductor-mirna10probe/post-link.sh @@ -1,9 +1,10 @@ #!/bin/bash FN="mirna10probe_2.18.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/mirna10probe_2.18.0.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/mirna10probe_2.18.0.tar.gz" "https://bioarchive.galaxyproject.org/mirna10probe_2.18.0.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-mirna10probe/bioconductor-mirna10probe_2.18.0_src_all.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-mirna10probe/bioconductor-mirna10probe_2.18.0_src_all.tar.gz" ) MD5="8bfa6cdfeee1c563b4881214bd5d4ce1" @@ -16,7 +17,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-mirna20cdf/meta.yaml b/recipes/bioconductor-mirna20cdf/meta.yaml index 29c93823b7725..6ee762be40b4c 100644 --- a/recipes/bioconductor-mirna20cdf/meta.yaml +++ b/recipes/bioconductor-mirna20cdf/meta.yaml @@ -1,6 +1,6 @@ {% set version = "2.18.0" %} {% set name = "mirna20cdf" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -12,19 +12,19 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 56f7807673ff108427ae7f6bdf85ae1c build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' - r-base run: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-mirna20cdf/post-link.sh b/recipes/bioconductor-mirna20cdf/post-link.sh index 0fc5c0a174ec0..9ba3b2945e132 100644 --- a/recipes/bioconductor-mirna20cdf/post-link.sh +++ b/recipes/bioconductor-mirna20cdf/post-link.sh @@ -1,9 +1,10 @@ #!/bin/bash FN="mirna20cdf_2.18.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/mirna20cdf_2.18.0.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/mirna20cdf_2.18.0.tar.gz" "https://bioarchive.galaxyproject.org/mirna20cdf_2.18.0.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-mirna20cdf/bioconductor-mirna20cdf_2.18.0_src_all.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-mirna20cdf/bioconductor-mirna20cdf_2.18.0_src_all.tar.gz" ) MD5="56f7807673ff108427ae7f6bdf85ae1c" @@ -16,7 +17,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-mirnameconverter/meta.yaml b/recipes/bioconductor-mirnameconverter/meta.yaml index 2daa44a0437d3..af4aafc8da4f3 100644 --- a/recipes/bioconductor-mirnameconverter/meta.yaml +++ b/recipes/bioconductor-mirnameconverter/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.10.0" %} +{% set version = "1.12.0" %} {% set name = "miRNAmeConverter" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: fe9206b632ea3f12bd7d4d20e7d65db6 + md5: 677abb97b5124109ab30fe667414039f build: number: 0 rpaths: @@ -20,14 +20,14 @@ build: # Suggests: methods, testthat, knitr, rmarkdown requirements: host: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' - - 'bioconductor-mirbaseversions.db >=1.1.0,<1.2.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' + - 'bioconductor-mirbaseversions.db >=1.2.0,<1.3.0' - r-base - r-dbi - r-reshape2 run: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' - - 'bioconductor-mirbaseversions.db >=1.1.0,<1.2.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' + - 'bioconductor-mirbaseversions.db >=1.2.0,<1.3.0' - r-base - r-dbi - r-reshape2 diff --git a/recipes/bioconductor-mirnapath/meta.yaml b/recipes/bioconductor-mirnapath/meta.yaml index f4aa2c6204f77..fabd597167b0c 100644 --- a/recipes/bioconductor-mirnapath/meta.yaml +++ b/recipes/bioconductor-mirnapath/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.42.0" %} +{% set version = "1.44.0" %} {% set name = "miRNApath" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: a7abdc36034d7ef47f5946a42bf72ff6 + md5: 61d82ff92e3b7025d776598e719eb647 build: number: 0 rpaths: diff --git a/recipes/bioconductor-mirnatap.db/meta.yaml b/recipes/bioconductor-mirnatap.db/meta.yaml index 665720bb1672c..4a9fd4dd21b67 100644 --- a/recipes/bioconductor-mirnatap.db/meta.yaml +++ b/recipes/bioconductor-mirnatap.db/meta.yaml @@ -1,6 +1,6 @@ {% set version = "0.99.10" %} {% set name = "miRNAtap.db" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -12,25 +12,25 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' md5: 48010280b68d6f1ddbff3b374132ce0a build: - number: 3 + number: 4 rpaths: - lib/R/lib/ - lib/ noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' - - 'bioconductor-mirnatap >=1.16.0,<1.17.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' + - 'bioconductor-mirnatap >=1.18.0,<1.19.0' - r-base - r-dbi - r-rsqlite run: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' - - 'bioconductor-mirnatap >=1.16.0,<1.17.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' + - 'bioconductor-mirnatap >=1.18.0,<1.19.0' - r-base - r-dbi - r-rsqlite - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-mirnatap.db/post-link.sh b/recipes/bioconductor-mirnatap.db/post-link.sh index d36d6707719bc..d5c58543ac8b6 100644 --- a/recipes/bioconductor-mirnatap.db/post-link.sh +++ b/recipes/bioconductor-mirnatap.db/post-link.sh @@ -1,7 +1,7 @@ #!/bin/bash FN="miRNAtap.db_0.99.10.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/miRNAtap.db_0.99.10.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/miRNAtap.db_0.99.10.tar.gz" "https://bioarchive.galaxyproject.org/miRNAtap.db_0.99.10.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-mirnatap.db/bioconductor-mirnatap.db_0.99.10_src_all.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-mirnatap.db/bioconductor-mirnatap.db_0.99.10_src_all.tar.gz" @@ -17,7 +17,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-mirnatap/meta.yaml b/recipes/bioconductor-mirnatap/meta.yaml index 61ff7b16f064a..03316d230d284 100644 --- a/recipes/bioconductor-mirnatap/meta.yaml +++ b/recipes/bioconductor-mirnatap/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.16.0" %} +{% set version = "1.18.0" %} {% set name = "miRNAtap" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: a56e2fa7cabbdeba36042c08fab11890 + md5: 8fe90803d5bec9678d94e761e384d2f4 build: number: 0 rpaths: @@ -20,7 +20,7 @@ build: # Suggests: topGO, org.Hs.eg.db, miRNAtap.db, testthat requirements: host: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' - r-base - r-dbi - r-plyr @@ -28,7 +28,7 @@ requirements: - r-sqldf - r-stringr run: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' - r-base - r-dbi - r-plyr diff --git a/recipes/bioconductor-mirnatarget/meta.yaml b/recipes/bioconductor-mirnatarget/meta.yaml index 79661ab1d6df8..7cfc557d4ce2f 100644 --- a/recipes/bioconductor-mirnatarget/meta.yaml +++ b/recipes/bioconductor-mirnatarget/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.20.0" %} +{% set version = "1.22.0" %} {% set name = "miRNATarget" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: ccb859ec474b6235e9d5deb41c955dda + md5: f53ec633f1b577134140f432f0af82db build: number: 0 rpaths: @@ -19,12 +19,12 @@ build: noarch: generic requirements: host: - - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' - r-base run: - - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-mirnatarget/post-link.sh b/recipes/bioconductor-mirnatarget/post-link.sh index f32cfd16b0c1b..945cfde1bc52f 100644 --- a/recipes/bioconductor-mirnatarget/post-link.sh +++ b/recipes/bioconductor-mirnatarget/post-link.sh @@ -1,11 +1,11 @@ #!/bin/bash -FN="miRNATarget_1.20.0.tar.gz" +FN="miRNATarget_1.22.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/experiment/src/contrib/miRNATarget_1.20.0.tar.gz" - "https://bioarchive.galaxyproject.org/miRNATarget_1.20.0.tar.gz" - "https://depot.galaxyproject.org/software/bioconductor-mirnatarget/bioconductor-mirnatarget_1.20.0_src_all.tar.gz" + "https://bioconductor.org/packages/3.9/data/experiment/src/contrib/miRNATarget_1.22.0.tar.gz" + "https://bioarchive.galaxyproject.org/miRNATarget_1.22.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-mirnatarget/bioconductor-mirnatarget_1.22.0_src_all.tar.gz" ) -MD5="ccb859ec474b6235e9d5deb41c955dda" +MD5="f53ec633f1b577134140f432f0af82db" # Use a staging area in the conda dir rather than temp dirs, both to avoid # permission issues as well as to have things downloaded in a predictable @@ -16,7 +16,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-mirsm/meta.yaml b/recipes/bioconductor-mirsm/meta.yaml index bcbc13eb3f5f0..14e5f5517df9e 100644 --- a/recipes/bioconductor-mirsm/meta.yaml +++ b/recipes/bioconductor-mirsm/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.0.0" %} +{% set version = "1.2.0" %} {% set name = "miRSM" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,27 +10,29 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: b3a0717a35ca8d1c1edde44aaee7a27c + md5: 6bd3d592afb3071db1e99948458d0a41 build: number: 0 rpaths: - lib/R/lib/ - lib/ -# Suggests: BiocStyle, knitr, rmarkdown, testthat, org.Hs.eg.db +# Suggests: BiocStyle, knitr, rmarkdown, testthat requirements: host: - - 'bioconductor-bicare >=1.40.0,<1.41.0' - - 'bioconductor-biobase >=2.42.0,<2.43.0' - - 'bioconductor-fabia >=2.28.0,<2.29.0' - - 'bioconductor-gseabase >=1.44.0,<1.45.0' - - 'bioconductor-ibbig >=1.26.0,<1.27.0' - - 'bioconductor-mirsponge >=1.8.0,<1.9.0' - - 'bioconductor-rqubic >=1.28.0,<1.29.0' - - 'bioconductor-runibic >=1.4.0,<1.5.0' - - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' + - 'bioconductor-bicare >=1.42.0,<1.43.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' + - 'bioconductor-fabia >=2.30.0,<2.31.0' + - 'bioconductor-gseabase >=1.46.0,<1.47.0' + - 'bioconductor-ibbig >=1.28.0,<1.29.0' + - 'bioconductor-mirsponger >=1.10.0,<1.11.0' + - 'bioconductor-org.hs.eg.db >=3.8.0,<3.9.0' + - 'bioconductor-rqubic >=1.30.0,<1.31.0' + - 'bioconductor-runibic >=1.6.0,<1.7.0' + - 'bioconductor-summarizedexperiment >=1.14.0,<1.15.0' - r-base - r-bibitr - r-biclust + - r-dbscan - r-dynamictreecut - r-flashclust - r-gfa @@ -38,24 +40,30 @@ requirements: - r-isa2 - r-linkcomm - r-mcl + - r-mclust - r-nmf - r-pma + - r-ppclust - r-rcpp - r-s4vd + - r-sombrero + - r-subspace - r-wgcna run: - - 'bioconductor-bicare >=1.40.0,<1.41.0' - - 'bioconductor-biobase >=2.42.0,<2.43.0' - - 'bioconductor-fabia >=2.28.0,<2.29.0' - - 'bioconductor-gseabase >=1.44.0,<1.45.0' - - 'bioconductor-ibbig >=1.26.0,<1.27.0' - - 'bioconductor-mirsponge >=1.8.0,<1.9.0' - - 'bioconductor-rqubic >=1.28.0,<1.29.0' - - 'bioconductor-runibic >=1.4.0,<1.5.0' - - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' + - 'bioconductor-bicare >=1.42.0,<1.43.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' + - 'bioconductor-fabia >=2.30.0,<2.31.0' + - 'bioconductor-gseabase >=1.46.0,<1.47.0' + - 'bioconductor-ibbig >=1.28.0,<1.29.0' + - 'bioconductor-mirsponger >=1.10.0,<1.11.0' + - 'bioconductor-org.hs.eg.db >=3.8.0,<3.9.0' + - 'bioconductor-rqubic >=1.30.0,<1.31.0' + - 'bioconductor-runibic >=1.6.0,<1.7.0' + - 'bioconductor-summarizedexperiment >=1.14.0,<1.15.0' - r-base - r-bibitr - r-biclust + - r-dbscan - r-dynamictreecut - r-flashclust - r-gfa @@ -63,10 +71,14 @@ requirements: - r-isa2 - r-linkcomm - r-mcl + - r-mclust - r-nmf - r-pma + - r-ppclust - r-rcpp - r-s4vd + - r-sombrero + - r-subspace - r-wgcna build: - {{ compiler('c') }} diff --git a/recipes/bioconductor-mirsponge/meta.yaml b/recipes/bioconductor-mirsponge/meta.yaml index 190bc851a3d6c..b97bf4ac72b6a 100644 --- a/recipes/bioconductor-mirsponge/meta.yaml +++ b/recipes/bioconductor-mirsponge/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.8.0" %} +{% set version = "1.10.0" %} {% set name = "miRsponge" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,18 +10,19 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 559435233adf8708b41cebf0fbb786e1 + md5: 55cba888afbd7ad39a0661a38600012e build: number: 0 rpaths: - lib/R/lib/ - lib/ -# Suggests: BiocStyle, knitr, rmarkdown, testthat, org.Hs.eg.db +# Suggests: BiocStyle, knitr, rmarkdown, testthat requirements: host: - - 'bioconductor-clusterprofiler >=3.10.0,<3.11.0' - - 'bioconductor-dose >=3.8.0,<3.9.0' - - 'bioconductor-reactomepa >=1.26.0,<1.27.0' + - 'bioconductor-clusterprofiler >=3.12.0,<3.13.0' + - 'bioconductor-dose >=3.10.0,<3.11.0' + - 'bioconductor-org.hs.eg.db >=3.8.0,<3.9.0' + - 'bioconductor-reactomepa >=1.28.0,<1.29.0' - r-base - r-corpcor - r-igraph @@ -31,9 +32,10 @@ requirements: - r-survival - r-varhandle run: - - 'bioconductor-clusterprofiler >=3.10.0,<3.11.0' - - 'bioconductor-dose >=3.8.0,<3.9.0' - - 'bioconductor-reactomepa >=1.26.0,<1.27.0' + - 'bioconductor-clusterprofiler >=3.12.0,<3.13.0' + - 'bioconductor-dose >=3.10.0,<3.11.0' + - 'bioconductor-org.hs.eg.db >=3.8.0,<3.9.0' + - 'bioconductor-reactomepa >=1.28.0,<1.29.0' - r-base - r-corpcor - r-igraph @@ -52,5 +54,5 @@ test: about: home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: GPL-3 - summary: 'This package provides several functions to study miRNA sponge (also called ceRNA or miRNA decoy), including popular methods for identifying miRNA sponge interactions, and the integrative method to integrate miRNA sponge interactions from different methods, as well as the functions to validate miRNA sponge interactions, and infer miRNA sponge modules, conduct enrichment analysis of modules, and conduct survival analysis of modules.' + summary: 'The name of the miRsponge package has been changed into "miRspongeR". Future updates will be seen in the miRspongeR package (http://bioconductor.org/packages/miRspongeR/). This package provides several functions to study miRNA sponge (also called ceRNA or miRNA decoy), including popular methods for identifying miRNA sponge interactions, and the integrative method to integrate miRNA sponge interactions from different methods, as well as the functions to validate miRNA sponge interactions, and infer miRNA sponge modules, conduct enrichment analysis of modules, and conduct survival analysis of modules.' diff --git a/recipes/bioconductor-mirsponger/build.sh b/recipes/bioconductor-mirsponger/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-mirsponger/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-mirsponger/meta.yaml b/recipes/bioconductor-mirsponger/meta.yaml new file mode 100644 index 0000000000000..45d06afffc67e --- /dev/null +++ b/recipes/bioconductor-mirsponger/meta.yaml @@ -0,0 +1,58 @@ +{% set version = "1.10.0" %} +{% set name = "miRspongeR" %} +{% set bioc = "3.9" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: c959ca897a5dffa0fd7be57052580ef6 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ +# Suggests: BiocStyle, knitr, rmarkdown, testthat +requirements: + host: + - 'bioconductor-clusterprofiler >=3.12.0,<3.13.0' + - 'bioconductor-dose >=3.10.0,<3.11.0' + - 'bioconductor-org.hs.eg.db >=3.8.0,<3.9.0' + - 'bioconductor-reactomepa >=1.28.0,<1.29.0' + - r-base + - r-corpcor + - r-igraph + - r-linkcomm + - r-mcl + - r-rcpp + - r-survival + - r-varhandle + run: + - 'bioconductor-clusterprofiler >=3.12.0,<3.13.0' + - 'bioconductor-dose >=3.10.0,<3.11.0' + - 'bioconductor-org.hs.eg.db >=3.8.0,<3.9.0' + - 'bioconductor-reactomepa >=1.28.0,<1.29.0' + - r-base + - r-corpcor + - r-igraph + - r-linkcomm + - r-mcl + - r-rcpp + - r-survival + - r-varhandle + build: + - {{ compiler('c') }} + - {{ compiler('cxx') }} + - make +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: GPL-3 + summary: 'This package provides several functions to study miRNA sponge (also called ceRNA or miRNA decoy), including popular methods for identifying miRNA sponge interactions, and the integrative method to integrate miRNA sponge interactions from different methods, as well as the functions to validate miRNA sponge interactions, and infer miRNA sponge modules, conduct enrichment analysis of modules, and conduct survival analysis of modules.' + diff --git a/recipes/bioconductor-mirsynergy/meta.yaml b/recipes/bioconductor-mirsynergy/meta.yaml index 084d3d8cfab10..9799298ec3093 100644 --- a/recipes/bioconductor-mirsynergy/meta.yaml +++ b/recipes/bioconductor-mirsynergy/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.18.0" %} +{% set version = "1.20.0" %} {% set name = "Mirsynergy" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 59cb823d731e6970bc39bbee925bb6f3 + md5: 3acbca5e8024960a4a5cf8d2c85c656b build: number: 0 rpaths: diff --git a/recipes/bioconductor-missmethyl/meta.yaml b/recipes/bioconductor-missmethyl/meta.yaml index cc1174d6ce723..ced1631987d97 100644 --- a/recipes/bioconductor-missmethyl/meta.yaml +++ b/recipes/bioconductor-missmethyl/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.16.0" %} +{% set version = "1.18.0" %} {% set name = "missMethyl" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: d18a07d4783273dabcefecbb86ceee77 + md5: 3c31671ca90e5b59d28e99894fee1e8f build: number: 0 rpaths: @@ -20,32 +20,32 @@ build: # Suggests: minfiData, BiocStyle, knitr, rmarkdown, edgeR, tweeDEseqCountData requirements: host: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' - - 'bioconductor-go.db >=3.7.0,<3.8.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' + - 'bioconductor-go.db >=3.8.0,<3.9.0' - 'bioconductor-illuminahumanmethylation450kanno.ilmn12.hg19 >=0.6.0,<0.7.0' - 'bioconductor-illuminahumanmethylation450kmanifest >=0.4.0,<0.5.0' - 'bioconductor-illuminahumanmethylationepicanno.ilm10b4.hg19 >=0.6.0,<0.7.0' - - 'bioconductor-illuminahumanmethylationepicmanifest >=0.3.0,<0.4.0' - - 'bioconductor-limma >=3.38.0,<3.39.0' - - 'bioconductor-methylumi >=2.28.0,<2.29.0' - - 'bioconductor-minfi >=1.28.0,<1.29.0' - - 'bioconductor-org.hs.eg.db >=3.7.0,<3.8.0' + - 'bioconductor-illuminahumanmethylationepicmanifest >=0.4.0,<0.5.0' + - 'bioconductor-limma >=3.40.0,<3.41.0' + - 'bioconductor-methylumi >=2.30.0,<2.31.0' + - 'bioconductor-minfi >=1.30.0,<1.31.0' + - 'bioconductor-org.hs.eg.db >=3.8.0,<3.9.0' - r-base - r-biasedurn - r-ruv - r-statmod - r-stringr run: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' - - 'bioconductor-go.db >=3.7.0,<3.8.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' + - 'bioconductor-go.db >=3.8.0,<3.9.0' - 'bioconductor-illuminahumanmethylation450kanno.ilmn12.hg19 >=0.6.0,<0.7.0' - 'bioconductor-illuminahumanmethylation450kmanifest >=0.4.0,<0.5.0' - 'bioconductor-illuminahumanmethylationepicanno.ilm10b4.hg19 >=0.6.0,<0.7.0' - - 'bioconductor-illuminahumanmethylationepicmanifest >=0.3.0,<0.4.0' - - 'bioconductor-limma >=3.38.0,<3.39.0' - - 'bioconductor-methylumi >=2.28.0,<2.29.0' - - 'bioconductor-minfi >=1.28.0,<1.29.0' - - 'bioconductor-org.hs.eg.db >=3.7.0,<3.8.0' + - 'bioconductor-illuminahumanmethylationepicmanifest >=0.4.0,<0.5.0' + - 'bioconductor-limma >=3.40.0,<3.41.0' + - 'bioconductor-methylumi >=2.30.0,<2.31.0' + - 'bioconductor-minfi >=1.30.0,<1.31.0' + - 'bioconductor-org.hs.eg.db >=3.8.0,<3.9.0' - r-base - r-biasedurn - r-ruv diff --git a/recipes/bioconductor-missrows/meta.yaml b/recipes/bioconductor-missrows/meta.yaml index 4cad6bee28a77..e46c86187bbb9 100644 --- a/recipes/bioconductor-missrows/meta.yaml +++ b/recipes/bioconductor-missrows/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.2.0" %} +{% set version = "1.4.0" %} {% set name = "missRows" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: ffdf5f3c103e7749bacded4b44aa7762 + md5: b6495bc10db157bf9e04d3130d360c99 build: number: 0 rpaths: @@ -20,15 +20,15 @@ build: # Suggests: BiocStyle, knitr, testthat requirements: host: - - 'bioconductor-multiassayexperiment >=1.8.0,<1.9.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-multiassayexperiment >=1.10.0,<1.11.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' - r-base - r-ggplot2 - r-gtools - r-plyr run: - - 'bioconductor-multiassayexperiment >=1.8.0,<1.9.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-multiassayexperiment >=1.10.0,<1.11.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' - r-base - r-ggplot2 - r-gtools diff --git a/recipes/bioconductor-mitoode/meta.yaml b/recipes/bioconductor-mitoode/meta.yaml index 0e8da4be7dd66..b14018c91abb9 100644 --- a/recipes/bioconductor-mitoode/meta.yaml +++ b/recipes/bioconductor-mitoode/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.20.1" %} +{% set version = "1.22.0" %} {% set name = "mitoODE" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: bae4fa58550a6de1e57956d17cb69ffb + md5: 99ecb4b674edcc0a17849d5b62105635 build: number: 0 rpaths: @@ -19,13 +19,13 @@ build: # SystemRequirements: requirements: host: - - 'bioconductor-mitoodedata >=1.18.0,<1.19.0' + - 'bioconductor-mitoodedata >=1.20.0,<1.21.0' - r-base - r-kernsmooth - r-mass - r-minpack.lm run: - - 'bioconductor-mitoodedata >=1.18.0,<1.19.0' + - 'bioconductor-mitoodedata >=1.20.0,<1.21.0' - r-base - r-kernsmooth - r-mass diff --git a/recipes/bioconductor-mitoodedata/meta.yaml b/recipes/bioconductor-mitoodedata/meta.yaml index e193b03e3dfb8..24704a46deee3 100644 --- a/recipes/bioconductor-mitoodedata/meta.yaml +++ b/recipes/bioconductor-mitoodedata/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.18.0" %} +{% set version = "1.20.0" %} {% set name = "mitoODEdata" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 2b4cf1081b1509c750a63a16a9ec3fc9 + md5: c306352e4f966d2f508a2b18ab299207 build: number: 0 rpaths: @@ -23,7 +23,7 @@ requirements: - r-base run: - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-mitoodedata/post-link.sh b/recipes/bioconductor-mitoodedata/post-link.sh index f0449371816fa..6ed398306b8a0 100644 --- a/recipes/bioconductor-mitoodedata/post-link.sh +++ b/recipes/bioconductor-mitoodedata/post-link.sh @@ -1,11 +1,11 @@ #!/bin/bash -FN="mitoODEdata_1.18.0.tar.gz" +FN="mitoODEdata_1.20.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/experiment/src/contrib/mitoODEdata_1.18.0.tar.gz" - "https://bioarchive.galaxyproject.org/mitoODEdata_1.18.0.tar.gz" - "https://depot.galaxyproject.org/software/bioconductor-mitoodedata/bioconductor-mitoodedata_1.18.0_src_all.tar.gz" + "https://bioconductor.org/packages/3.9/data/experiment/src/contrib/mitoODEdata_1.20.0.tar.gz" + "https://bioarchive.galaxyproject.org/mitoODEdata_1.20.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-mitoodedata/bioconductor-mitoodedata_1.20.0_src_all.tar.gz" ) -MD5="2b4cf1081b1509c750a63a16a9ec3fc9" +MD5="c306352e4f966d2f508a2b18ab299207" # Use a staging area in the conda dir rather than temp dirs, both to avoid # permission issues as well as to have things downloaded in a predictable @@ -16,7 +16,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-mixomics/meta.yaml b/recipes/bioconductor-mixomics/meta.yaml index dbd94611d4ba6..2f23a4b84bda5 100644 --- a/recipes/bioconductor-mixomics/meta.yaml +++ b/recipes/bioconductor-mixomics/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "6.6.2" %} +{% set version = "6.8.0" %} {% set name = "mixOmics" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: 95dbe96dd7f30742e12193da72e75f740e648b8e5fe2c8f6d31575db671cb802 + md5: 1bf9c089a85fd248901764d978ff59e2 build: number: 0 rpaths: diff --git a/recipes/bioconductor-mlinterfaces/meta.yaml b/recipes/bioconductor-mlinterfaces/meta.yaml index a117b2c56bd5e..86a66da9aa108 100644 --- a/recipes/bioconductor-mlinterfaces/meta.yaml +++ b/recipes/bioconductor-mlinterfaces/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.62.0" %} +{% set version = "1.64.0" %} {% set name = "MLInterfaces" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 0375d370e1cd5ad27b392bf8528efa93 + md5: 20a7b8da9ea5a3ad999edd44626aac59 build: number: 0 rpaths: @@ -20,10 +20,10 @@ build: # Suggests: class, e1071, ipred, randomForest, gpls, pamr, nnet, ALL, hgu95av2.db, som, hu6800.db, lattice, caret (>= 5.07), golubEsets, ada, keggorthology, kernlab, mboost, party requirements: host: - - 'bioconductor-annotate >=1.60.0,<1.61.0' - - 'bioconductor-biobase >=2.42.0,<2.43.0' - - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' - - 'bioconductor-genefilter >=1.64.0,<1.65.0' + - 'bioconductor-annotate >=1.62.0,<1.63.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' + - 'bioconductor-biocgenerics >=0.30.0,<0.31.0' + - 'bioconductor-genefilter >=1.66.0,<1.67.0' - r-base - r-cluster - r-fpc @@ -41,10 +41,10 @@ requirements: - r-shiny - 'r-threejs >=0.2.2' run: - - 'bioconductor-annotate >=1.60.0,<1.61.0' - - 'bioconductor-biobase >=2.42.0,<2.43.0' - - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' - - 'bioconductor-genefilter >=1.64.0,<1.65.0' + - 'bioconductor-annotate >=1.62.0,<1.63.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' + - 'bioconductor-biocgenerics >=0.30.0,<0.31.0' + - 'bioconductor-genefilter >=1.66.0,<1.67.0' - r-base - r-cluster - r-fpc diff --git a/recipes/bioconductor-mlm4omics/build.sh b/recipes/bioconductor-mlm4omics/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-mlm4omics/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-mlm4omics/meta.yaml b/recipes/bioconductor-mlm4omics/meta.yaml new file mode 100644 index 0000000000000..1cbca27162343 --- /dev/null +++ b/recipes/bioconductor-mlm4omics/meta.yaml @@ -0,0 +1,55 @@ +{% set version = "1.2.0" %} +{% set name = "mlm4omics" %} +{% set bioc = "3.9" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + md5: 5df4309116903f2eb7418e7fb783fd8e +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ +# Suggests: testthat, BiocStyle, knitr, rmarkdown, roxygen2 (>= 5.0.0) +# SystemRequirements: GNU make +requirements: + host: + - r-base + - 'r-bh >=1.66.0-1' + - r-ggplot2 + - r-mass + - r-matrix + - 'r-rcpp >=0.12.17' + - 'r-rcppeigen >=0.3.3.4.0' + - 'r-rstan >=2.17.3' + - 'r-rstantools >=1.5.0' + - 'r-stanheaders >=2.17.2' + run: + - r-base + - 'r-bh >=1.66.0-1' + - r-ggplot2 + - r-mass + - r-matrix + - 'r-rcpp >=0.12.17' + - 'r-rcppeigen >=0.3.3.4.0' + - 'r-rstan >=2.17.3' + - 'r-rstantools >=1.5.0' + - 'r-stanheaders >=2.17.2' + build: + - {{ compiler('c') }} + - {{ compiler('cxx') }} + - make +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: GPL-3 + summary: 'To conduct Bayesian inference regression for responses with multilevel explanatory variables and missing values; It uses function from ''Stan'', a software to implement posterior sampling using Hamiltonian MC and its variation Non-U-Turn algorithms. It implements the posterior sampling of regression coefficients from the multilevel regression models. The package has two main functions to handle not-missing-at-random missing responses and left-censored with not-missing-at random responses. The purpose is to provide a similar format as the other R regression functions but using ''Stan'' models.' + diff --git a/recipes/bioconductor-mlp/meta.yaml b/recipes/bioconductor-mlp/meta.yaml index 374c9aac26989..ab17749326c4a 100644 --- a/recipes/bioconductor-mlp/meta.yaml +++ b/recipes/bioconductor-mlp/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.30.0" %} +{% set version = "1.32.0" %} {% set name = "MLP" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: aa60c8428853779c635788ea6e600255 + md5: 0f025c2156526df2dd6c926f3f9b7820 build: number: 0 rpaths: @@ -20,8 +20,8 @@ build: # Suggests: GO.db, org.Hs.eg.db, org.Mm.eg.db, org.Rn.eg.db, org.Cf.eg.db, KEGG.db, annotate, Rgraphviz, GOstats, limma, mouse4302.db, reactome.db requirements: host: - - 'bioconductor-affy >=1.60.0,<1.61.0' - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-affy >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' - r-base - r-gdata - r-gmodels @@ -29,8 +29,8 @@ requirements: - r-gtools - r-plotrix run: - - 'bioconductor-affy >=1.60.0,<1.61.0' - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-affy >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' - r-base - r-gdata - r-gmodels diff --git a/recipes/bioconductor-mlseq/meta.yaml b/recipes/bioconductor-mlseq/meta.yaml index 1eb504281fd97..a626f03c4eabe 100644 --- a/recipes/bioconductor-mlseq/meta.yaml +++ b/recipes/bioconductor-mlseq/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "2.0.0" %} +{% set version = "2.2.1" %} {% set name = "MLSeq" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 8f9f9f5111af5496b8c8f3cb0ea5f8db + md5: 692c6c7c6042f25c428681642f36dfe7 build: number: 0 rpaths: @@ -20,12 +20,12 @@ build: # Suggests: knitr, testthat, BiocStyle, VennDiagram, pamr requirements: host: - - 'bioconductor-biobase >=2.42.0,<2.43.0' - - 'bioconductor-deseq2 >=1.22.0,<1.23.0' - - 'bioconductor-edger >=3.24.0,<3.25.0' - - 'bioconductor-limma >=3.38.0,<3.39.0' - - 'bioconductor-sseq >=1.20.0,<1.21.0' - - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' + - 'bioconductor-deseq2 >=1.24.0,<1.25.0' + - 'bioconductor-edger >=3.26.0,<3.27.0' + - 'bioconductor-limma >=3.40.0,<3.41.0' + - 'bioconductor-sseq >=1.22.0,<1.23.0' + - 'bioconductor-summarizedexperiment >=1.14.0,<1.15.0' - r-base - r-caret - r-foreach @@ -33,12 +33,12 @@ requirements: - r-plyr - r-xtable run: - - 'bioconductor-biobase >=2.42.0,<2.43.0' - - 'bioconductor-deseq2 >=1.22.0,<1.23.0' - - 'bioconductor-edger >=3.24.0,<3.25.0' - - 'bioconductor-limma >=3.38.0,<3.39.0' - - 'bioconductor-sseq >=1.20.0,<1.21.0' - - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' + - 'bioconductor-deseq2 >=1.24.0,<1.25.0' + - 'bioconductor-edger >=3.26.0,<3.27.0' + - 'bioconductor-limma >=3.40.0,<3.41.0' + - 'bioconductor-sseq >=1.22.0,<1.23.0' + - 'bioconductor-summarizedexperiment >=1.14.0,<1.15.0' - r-base - r-caret - r-foreach diff --git a/recipes/bioconductor-mm24kresogen.db/meta.yaml b/recipes/bioconductor-mm24kresogen.db/meta.yaml index 1cdea13147bc5..00536e3f758f0 100644 --- a/recipes/bioconductor-mm24kresogen.db/meta.yaml +++ b/recipes/bioconductor-mm24kresogen.db/meta.yaml @@ -1,6 +1,6 @@ {% set version = "2.5.0" %} {% set name = "mm24kresogen.db" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -12,7 +12,7 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 437f5d4bc225ee500af1ecc2d4da472b build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ @@ -20,14 +20,14 @@ build: # Suggests: annotate requirements: host: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' - - 'bioconductor-org.mm.eg.db >=3.7.0,<3.8.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' + - 'bioconductor-org.mm.eg.db >=3.8.0,<3.9.0' - r-base run: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' - - 'bioconductor-org.mm.eg.db >=3.7.0,<3.8.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' + - 'bioconductor-org.mm.eg.db >=3.8.0,<3.9.0' - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-mm24kresogen.db/post-link.sh b/recipes/bioconductor-mm24kresogen.db/post-link.sh index 14d210937114d..0636a6d623cd7 100644 --- a/recipes/bioconductor-mm24kresogen.db/post-link.sh +++ b/recipes/bioconductor-mm24kresogen.db/post-link.sh @@ -1,9 +1,10 @@ #!/bin/bash FN="mm24kresogen.db_2.5.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/mm24kresogen.db_2.5.0.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/mm24kresogen.db_2.5.0.tar.gz" "https://bioarchive.galaxyproject.org/mm24kresogen.db_2.5.0.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-mm24kresogen.db/bioconductor-mm24kresogen.db_2.5.0_src_all.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-mm24kresogen.db/bioconductor-mm24kresogen.db_2.5.0_src_all.tar.gz" ) MD5="437f5d4bc225ee500af1ecc2d4da472b" @@ -16,7 +17,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-mmagilentdesign026655.db/meta.yaml b/recipes/bioconductor-mmagilentdesign026655.db/meta.yaml index 3bfeff3e4e5ca..bcad399b0fa41 100644 --- a/recipes/bioconductor-mmagilentdesign026655.db/meta.yaml +++ b/recipes/bioconductor-mmagilentdesign026655.db/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.2.3" %} {% set name = "MmAgilentDesign026655.db" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -12,7 +12,7 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' md5: 7ef619bd2c74f22ea4f3c2b2c4131fe9 build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ @@ -20,14 +20,14 @@ build: # Suggests: DBI, annotate, RUnit requirements: host: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' - - 'bioconductor-org.mm.eg.db >=3.7.0,<3.8.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' + - 'bioconductor-org.mm.eg.db >=3.8.0,<3.9.0' - r-base run: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' - - 'bioconductor-org.mm.eg.db >=3.7.0,<3.8.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' + - 'bioconductor-org.mm.eg.db >=3.8.0,<3.9.0' - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-mmagilentdesign026655.db/post-link.sh b/recipes/bioconductor-mmagilentdesign026655.db/post-link.sh index adc9172431c2d..3fe0e894b42d4 100644 --- a/recipes/bioconductor-mmagilentdesign026655.db/post-link.sh +++ b/recipes/bioconductor-mmagilentdesign026655.db/post-link.sh @@ -1,9 +1,10 @@ #!/bin/bash FN="MmAgilentDesign026655.db_3.2.3.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/MmAgilentDesign026655.db_3.2.3.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/MmAgilentDesign026655.db_3.2.3.tar.gz" "https://bioarchive.galaxyproject.org/MmAgilentDesign026655.db_3.2.3.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-mmagilentdesign026655.db/bioconductor-mmagilentdesign026655.db_3.2.3_src_all.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-mmagilentdesign026655.db/bioconductor-mmagilentdesign026655.db_3.2.3_src_all.tar.gz" ) MD5="7ef619bd2c74f22ea4f3c2b2c4131fe9" @@ -16,7 +17,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-mmdiff2/meta.yaml b/recipes/bioconductor-mmdiff2/meta.yaml index cbd878d02bfb4..d60705e55cad3 100644 --- a/recipes/bioconductor-mmdiff2/meta.yaml +++ b/recipes/bioconductor-mmdiff2/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.10.0" %} +{% set version = "1.12.0" %} {% set name = "MMDiff2" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: e13ca07c7dea4123eb3cb08be914edef + md5: 79ca696eca801944858d690fba6f6468 build: number: 0 rpaths: @@ -20,24 +20,24 @@ build: # Suggests: MMDiffBamSubset, MotifDb, knitr, BiocStyle, BSgenome.Mmusculus.UCSC.mm9 requirements: host: - - 'bioconductor-biobase >=2.42.0,<2.43.0' - - 'bioconductor-biostrings >=2.50.0,<2.51.0' - - 'bioconductor-bsgenome >=1.50.0,<1.51.0' - - 'bioconductor-genomicranges >=1.34.0,<1.35.0' - - 'bioconductor-rsamtools >=1.34.0,<1.35.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' + - 'bioconductor-biostrings >=2.52.0,<2.53.0' + - 'bioconductor-bsgenome >=1.52.0,<1.53.0' + - 'bioconductor-genomicranges >=1.36.0,<1.37.0' + - 'bioconductor-rsamtools >=2.0.0,<2.1.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' - r-base - r-ggplot2 - r-locfit - r-rcolorbrewer - r-shiny run: - - 'bioconductor-biobase >=2.42.0,<2.43.0' - - 'bioconductor-biostrings >=2.50.0,<2.51.0' - - 'bioconductor-bsgenome >=1.50.0,<1.51.0' - - 'bioconductor-genomicranges >=1.34.0,<1.35.0' - - 'bioconductor-rsamtools >=1.34.0,<1.35.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' + - 'bioconductor-biostrings >=2.52.0,<2.53.0' + - 'bioconductor-bsgenome >=1.52.0,<1.53.0' + - 'bioconductor-genomicranges >=1.36.0,<1.37.0' + - 'bioconductor-rsamtools >=2.0.0,<2.1.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' - r-base - r-ggplot2 - r-locfit diff --git a/recipes/bioconductor-mmdiffbamsubset/meta.yaml b/recipes/bioconductor-mmdiffbamsubset/meta.yaml index d443a483a323b..395e2bb4d9e89 100644 --- a/recipes/bioconductor-mmdiffbamsubset/meta.yaml +++ b/recipes/bioconductor-mmdiffbamsubset/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.18.0" %} +{% set version = "1.20.0" %} {% set name = "MMDiffBamSubset" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 28e6a879bd736040d44de460c7e582aa + md5: a4db104aef49d0178d476f3539d5f218 build: number: 0 rpaths: @@ -23,7 +23,7 @@ requirements: - r-base run: - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-mmdiffbamsubset/post-link.sh b/recipes/bioconductor-mmdiffbamsubset/post-link.sh index 3360054b8f984..cb9040e00f61b 100644 --- a/recipes/bioconductor-mmdiffbamsubset/post-link.sh +++ b/recipes/bioconductor-mmdiffbamsubset/post-link.sh @@ -1,11 +1,11 @@ #!/bin/bash -FN="MMDiffBamSubset_1.18.0.tar.gz" +FN="MMDiffBamSubset_1.20.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/experiment/src/contrib/MMDiffBamSubset_1.18.0.tar.gz" - "https://bioarchive.galaxyproject.org/MMDiffBamSubset_1.18.0.tar.gz" - "https://depot.galaxyproject.org/software/bioconductor-mmdiffbamsubset/bioconductor-mmdiffbamsubset_1.18.0_src_all.tar.gz" + "https://bioconductor.org/packages/3.9/data/experiment/src/contrib/MMDiffBamSubset_1.20.0.tar.gz" + "https://bioarchive.galaxyproject.org/MMDiffBamSubset_1.20.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-mmdiffbamsubset/bioconductor-mmdiffbamsubset_1.20.0_src_all.tar.gz" ) -MD5="28e6a879bd736040d44de460c7e582aa" +MD5="a4db104aef49d0178d476f3539d5f218" # Use a staging area in the conda dir rather than temp dirs, both to avoid # permission issues as well as to have things downloaded in a predictable @@ -16,7 +16,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-mmpalatemirna/meta.yaml b/recipes/bioconductor-mmpalatemirna/meta.yaml index 31bafecf016bd..aa6a09bf28957 100644 --- a/recipes/bioconductor-mmpalatemirna/meta.yaml +++ b/recipes/bioconductor-mmpalatemirna/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.32.0" %} +{% set version = "1.34.0" %} {% set name = "MmPalateMiRNA" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: f4d32e709429b59908cea3fd1ef9e70b + md5: f86647e1b79b46ede2ace3a46e7e1109 build: number: 0 rpaths: @@ -20,17 +20,17 @@ build: # Suggests: GOstats, graph, Category, org.Mm.eg.db, microRNA, targetscan.Mm.eg.db, RSQLite, DBI, AnnotationDbi, clValid, class, cluster, multtest, RColorBrewer, latticeExtra requirements: host: - - 'bioconductor-biobase >=2.42.0,<2.43.0' - - 'bioconductor-limma >=3.38.0,<3.39.0' - - 'bioconductor-vsn >=3.50.0,<3.51.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' + - 'bioconductor-limma >=3.40.0,<3.41.0' + - 'bioconductor-vsn >=3.52.0,<3.53.0' - r-base - r-lattice - r-statmod - r-xtable run: - - 'bioconductor-biobase >=2.42.0,<2.43.0' - - 'bioconductor-limma >=3.38.0,<3.39.0' - - 'bioconductor-vsn >=3.50.0,<3.51.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' + - 'bioconductor-limma >=3.40.0,<3.41.0' + - 'bioconductor-vsn >=3.52.0,<3.53.0' - r-base - r-lattice - r-statmod diff --git a/recipes/bioconductor-mnem/build.sh b/recipes/bioconductor-mnem/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-mnem/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-mnem/meta.yaml b/recipes/bioconductor-mnem/meta.yaml new file mode 100644 index 0000000000000..a386599eecb8c --- /dev/null +++ b/recipes/bioconductor-mnem/meta.yaml @@ -0,0 +1,66 @@ +{% set version = "1.0.0" %} +{% set name = "mnem" %} +{% set bioc = "3.9" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + md5: c15128027e81bc349db30c15c64ce477 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ +# Suggests: knitr, devtools, rmarkdown, BiocGenerics, RUnit +requirements: + host: + - 'bioconductor-epinem >=1.8.0,<1.9.0' + - 'bioconductor-graph >=1.62.0,<1.63.0' + - 'bioconductor-linnorm >=2.8.0,<2.9.0' + - 'bioconductor-nem >=2.58.0,<2.59.0' + - 'bioconductor-rgraphviz >=2.28.0,<2.29.0' + - r-base + - r-cluster + - r-data.table + - r-flexclust + - r-lattice + - r-matrixstats + - r-naturalsort + - r-rcpp + - r-rcppeigen + - r-snowfall + - r-tsne + run: + - 'bioconductor-epinem >=1.8.0,<1.9.0' + - 'bioconductor-graph >=1.62.0,<1.63.0' + - 'bioconductor-linnorm >=2.8.0,<2.9.0' + - 'bioconductor-nem >=2.58.0,<2.59.0' + - 'bioconductor-rgraphviz >=2.28.0,<2.29.0' + - r-base + - r-cluster + - r-data.table + - r-flexclust + - r-lattice + - r-matrixstats + - r-naturalsort + - r-rcpp + - r-rcppeigen + - r-snowfall + - r-tsne + build: + - {{ compiler('c') }} + - {{ compiler('cxx') }} + - make +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: GPL-3 + summary: 'Mixture Nested Effects Models (mnem) is an extension of Nested Effects Models and allows for the analysis of single cell perturbation data provided by methods like Perturb-Seq (Dixit et al., 2016) or Crop-Seq (Datlinger et al., 2017). In those experiments each of many cells is perturbed by a knock-down of a specific gene, i.e. several cells are perturbed by a knock-down of gene A, several by a knock-down of gene B, ... and so forth. The observed read-out has to be multi-trait and in the case of the Perturb-/Crop-Seq gene are expression profiles for each cell. mnem uses a mixture model to simultaneously cluster the cell population into k clusters and and infer k networks causally linking the perturbed genes for each cluster. The mixture components are inferred via an expectation maximization algorithm.' + diff --git a/recipes/bioconductor-moda/meta.yaml b/recipes/bioconductor-moda/meta.yaml index 5887d637af86d..dd7728ff88d59 100644 --- a/recipes/bioconductor-moda/meta.yaml +++ b/recipes/bioconductor-moda/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.8.0" %} +{% set version = "1.10.0" %} {% set name = "MODA" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 50ed2605dabd7656e45804206fcafc6f + md5: 8aea3d81a6f5c87f07d12c96f70cee15 build: number: 0 rpaths: @@ -20,7 +20,7 @@ build: # Suggests: BiocStyle, knitr, rmarkdown requirements: host: - - 'bioconductor-amountain >=1.8.0,<1.9.0' + - 'bioconductor-amountain >=1.10.0,<1.11.0' - r-base - r-cluster - r-dynamictreecut @@ -28,7 +28,7 @@ requirements: - r-rcolorbrewer - r-wgcna run: - - 'bioconductor-amountain >=1.8.0,<1.9.0' + - 'bioconductor-amountain >=1.10.0,<1.11.0' - r-base - r-cluster - r-dynamictreecut diff --git a/recipes/bioconductor-modstrings/build.sh b/recipes/bioconductor-modstrings/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-modstrings/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-modstrings/meta.yaml b/recipes/bioconductor-modstrings/meta.yaml new file mode 100644 index 0000000000000..3add6f17c73f1 --- /dev/null +++ b/recipes/bioconductor-modstrings/meta.yaml @@ -0,0 +1,51 @@ +{% set version = "1.0.0" %} +{% set name = "Modstrings" %} +{% set bioc = "3.9" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: 3c1ce4bf65e827c9fb4385f3aaffd84d +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: BiocStyle, knitr, rmarkdown, testthat, usethis, sessioninfo +requirements: + host: + - 'bioconductor-biocgenerics >=0.30.0,<0.31.0' + - 'bioconductor-biostrings >=2.52.0,<2.53.0' + - 'bioconductor-genomicranges >=1.36.0,<1.37.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' + - 'bioconductor-xvector >=0.24.0,<0.25.0' + - r-assertive + - r-base + - r-stringi + - r-stringr + run: + - 'bioconductor-biocgenerics >=0.30.0,<0.31.0' + - 'bioconductor-biostrings >=2.52.0,<2.53.0' + - 'bioconductor-genomicranges >=1.36.0,<1.37.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' + - 'bioconductor-xvector >=0.24.0,<0.25.0' + - r-assertive + - r-base + - r-stringi + - r-stringr +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'Representing nucleotide modifications in a nucleotide sequence is usually done via special characters from a number of sources. This represents a challenge to work with in R and the Biostrings package. The Modstrings package implements this functionallity for RNA and DNA sequences containing modified nucleotides by translating the character internally in order to work with the infrastructure of the Biostrings package. For this the ModRNAString and ModDNAString classes and derivates and functions to construct and modify these objects despite the encoding issues are implemenented. In addition the conversion from sequences to list like location information (and the reverse operation) is implemented as well.' + diff --git a/recipes/bioconductor-moe430a.db/meta.yaml b/recipes/bioconductor-moe430a.db/meta.yaml index ed01ed0a31a51..e663ac0b051b8 100644 --- a/recipes/bioconductor-moe430a.db/meta.yaml +++ b/recipes/bioconductor-moe430a.db/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.2.3" %} {% set name = "moe430a.db" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -12,7 +12,7 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: c95b12e1954943ccc347ae57794e1c19 build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ @@ -20,14 +20,14 @@ build: # Suggests: DBI, annotate, RUnit requirements: host: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' - - 'bioconductor-org.mm.eg.db >=3.7.0,<3.8.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' + - 'bioconductor-org.mm.eg.db >=3.8.0,<3.9.0' - r-base run: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' - - 'bioconductor-org.mm.eg.db >=3.7.0,<3.8.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' + - 'bioconductor-org.mm.eg.db >=3.8.0,<3.9.0' - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-moe430a.db/post-link.sh b/recipes/bioconductor-moe430a.db/post-link.sh index 0ff71a18492aa..d51fb186461da 100644 --- a/recipes/bioconductor-moe430a.db/post-link.sh +++ b/recipes/bioconductor-moe430a.db/post-link.sh @@ -1,9 +1,10 @@ #!/bin/bash FN="moe430a.db_3.2.3.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/moe430a.db_3.2.3.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/moe430a.db_3.2.3.tar.gz" "https://bioarchive.galaxyproject.org/moe430a.db_3.2.3.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-moe430a.db/bioconductor-moe430a.db_3.2.3_src_all.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-moe430a.db/bioconductor-moe430a.db_3.2.3_src_all.tar.gz" ) MD5="c95b12e1954943ccc347ae57794e1c19" @@ -16,7 +17,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-moe430acdf/meta.yaml b/recipes/bioconductor-moe430acdf/meta.yaml index 74b8dc8468938..a5242e47aa388 100644 --- a/recipes/bioconductor-moe430acdf/meta.yaml +++ b/recipes/bioconductor-moe430acdf/meta.yaml @@ -1,6 +1,6 @@ {% set version = "2.18.0" %} {% set name = "moe430acdf" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -12,19 +12,19 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: b03f1295fc483f0d782a4615e8ca0137 build: - number: 1 + number: 2 rpaths: - lib/R/lib/ - lib/ noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' - r-base run: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-moe430acdf/post-link.sh b/recipes/bioconductor-moe430acdf/post-link.sh index ae6a77da243fc..b55b39cf44fbe 100644 --- a/recipes/bioconductor-moe430acdf/post-link.sh +++ b/recipes/bioconductor-moe430acdf/post-link.sh @@ -1,9 +1,10 @@ #!/bin/bash FN="moe430acdf_2.18.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/moe430acdf_2.18.0.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/moe430acdf_2.18.0.tar.gz" "https://bioarchive.galaxyproject.org/moe430acdf_2.18.0.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-moe430acdf/bioconductor-moe430acdf_2.18.0_src_all.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-moe430acdf/bioconductor-moe430acdf_2.18.0_src_all.tar.gz" ) MD5="b03f1295fc483f0d782a4615e8ca0137" @@ -16,7 +17,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-moe430aprobe/meta.yaml b/recipes/bioconductor-moe430aprobe/meta.yaml index 0bd56d3d6aae8..413bc60b054e7 100644 --- a/recipes/bioconductor-moe430aprobe/meta.yaml +++ b/recipes/bioconductor-moe430aprobe/meta.yaml @@ -1,6 +1,6 @@ {% set version = "2.18.0" %} {% set name = "moe430aprobe" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -12,19 +12,19 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 0aa83189d04599a65211d1a2f0a51c8f build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' - r-base run: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-moe430aprobe/post-link.sh b/recipes/bioconductor-moe430aprobe/post-link.sh index 2a7c1d83f6cea..d3ac47dfd4ad9 100644 --- a/recipes/bioconductor-moe430aprobe/post-link.sh +++ b/recipes/bioconductor-moe430aprobe/post-link.sh @@ -1,9 +1,10 @@ #!/bin/bash FN="moe430aprobe_2.18.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/moe430aprobe_2.18.0.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/moe430aprobe_2.18.0.tar.gz" "https://bioarchive.galaxyproject.org/moe430aprobe_2.18.0.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-moe430aprobe/bioconductor-moe430aprobe_2.18.0_src_all.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-moe430aprobe/bioconductor-moe430aprobe_2.18.0_src_all.tar.gz" ) MD5="0aa83189d04599a65211d1a2f0a51c8f" @@ -16,7 +17,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-moe430b.db/meta.yaml b/recipes/bioconductor-moe430b.db/meta.yaml index 575c14639750e..5d8d91d89978d 100644 --- a/recipes/bioconductor-moe430b.db/meta.yaml +++ b/recipes/bioconductor-moe430b.db/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.2.3" %} {% set name = "moe430b.db" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -12,7 +12,7 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 74027eafdb3815a8310e84ade3a43dff build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ @@ -20,14 +20,14 @@ build: # Suggests: DBI, annotate, RUnit requirements: host: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' - - 'bioconductor-org.mm.eg.db >=3.7.0,<3.8.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' + - 'bioconductor-org.mm.eg.db >=3.8.0,<3.9.0' - r-base run: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' - - 'bioconductor-org.mm.eg.db >=3.7.0,<3.8.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' + - 'bioconductor-org.mm.eg.db >=3.8.0,<3.9.0' - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-moe430b.db/post-link.sh b/recipes/bioconductor-moe430b.db/post-link.sh index 857b193382bc6..4702f5ee78ece 100644 --- a/recipes/bioconductor-moe430b.db/post-link.sh +++ b/recipes/bioconductor-moe430b.db/post-link.sh @@ -1,9 +1,10 @@ #!/bin/bash FN="moe430b.db_3.2.3.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/moe430b.db_3.2.3.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/moe430b.db_3.2.3.tar.gz" "https://bioarchive.galaxyproject.org/moe430b.db_3.2.3.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-moe430b.db/bioconductor-moe430b.db_3.2.3_src_all.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-moe430b.db/bioconductor-moe430b.db_3.2.3_src_all.tar.gz" ) MD5="74027eafdb3815a8310e84ade3a43dff" @@ -16,7 +17,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-moe430bcdf/meta.yaml b/recipes/bioconductor-moe430bcdf/meta.yaml index 8e7aa427baa3a..c945b04478bc4 100644 --- a/recipes/bioconductor-moe430bcdf/meta.yaml +++ b/recipes/bioconductor-moe430bcdf/meta.yaml @@ -1,6 +1,6 @@ {% set version = "2.18.0" %} {% set name = "moe430bcdf" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -12,19 +12,19 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: b7112dcf8ccfe4e079ca67ff62046f2e build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' - r-base run: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-moe430bcdf/post-link.sh b/recipes/bioconductor-moe430bcdf/post-link.sh index 0d9bdc8c844e1..665cfd9f65667 100644 --- a/recipes/bioconductor-moe430bcdf/post-link.sh +++ b/recipes/bioconductor-moe430bcdf/post-link.sh @@ -1,9 +1,10 @@ #!/bin/bash FN="moe430bcdf_2.18.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/moe430bcdf_2.18.0.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/moe430bcdf_2.18.0.tar.gz" "https://bioarchive.galaxyproject.org/moe430bcdf_2.18.0.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-moe430bcdf/bioconductor-moe430bcdf_2.18.0_src_all.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-moe430bcdf/bioconductor-moe430bcdf_2.18.0_src_all.tar.gz" ) MD5="b7112dcf8ccfe4e079ca67ff62046f2e" @@ -16,7 +17,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-moe430bprobe/meta.yaml b/recipes/bioconductor-moe430bprobe/meta.yaml index 52d92ff84f957..c82448fe5e29c 100644 --- a/recipes/bioconductor-moe430bprobe/meta.yaml +++ b/recipes/bioconductor-moe430bprobe/meta.yaml @@ -1,6 +1,6 @@ {% set version = "2.18.0" %} {% set name = "moe430bprobe" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -12,19 +12,19 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 1368e6f4225babe7a693ccd39a3a436a build: - number: 1 + number: 2 rpaths: - lib/R/lib/ - lib/ noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' - r-base run: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-moe430bprobe/post-link.sh b/recipes/bioconductor-moe430bprobe/post-link.sh index 957490e625ae2..5bf43745391e6 100644 --- a/recipes/bioconductor-moe430bprobe/post-link.sh +++ b/recipes/bioconductor-moe430bprobe/post-link.sh @@ -1,9 +1,10 @@ #!/bin/bash FN="moe430bprobe_2.18.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/moe430bprobe_2.18.0.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/moe430bprobe_2.18.0.tar.gz" "https://bioarchive.galaxyproject.org/moe430bprobe_2.18.0.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-moe430bprobe/bioconductor-moe430bprobe_2.18.0_src_all.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-moe430bprobe/bioconductor-moe430bprobe_2.18.0_src_all.tar.gz" ) MD5="1368e6f4225babe7a693ccd39a3a436a" @@ -16,7 +17,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-moex10stprobeset.db/meta.yaml b/recipes/bioconductor-moex10stprobeset.db/meta.yaml index 0a52728df75ea..0060efff8a9a0 100644 --- a/recipes/bioconductor-moex10stprobeset.db/meta.yaml +++ b/recipes/bioconductor-moex10stprobeset.db/meta.yaml @@ -1,6 +1,6 @@ {% set version = "8.7.0" %} {% set name = "moex10stprobeset.db" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -12,7 +12,7 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 1464d765c3db1bf50a6eb115ae30c74c build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ @@ -20,14 +20,14 @@ build: # Suggests: DBI, annotate, RUnit requirements: host: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' - - 'bioconductor-org.mm.eg.db >=3.7.0,<3.8.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' + - 'bioconductor-org.mm.eg.db >=3.8.0,<3.9.0' - r-base run: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' - - 'bioconductor-org.mm.eg.db >=3.7.0,<3.8.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' + - 'bioconductor-org.mm.eg.db >=3.8.0,<3.9.0' - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-moex10stprobeset.db/post-link.sh b/recipes/bioconductor-moex10stprobeset.db/post-link.sh index a366f8d83335d..f61168203593b 100644 --- a/recipes/bioconductor-moex10stprobeset.db/post-link.sh +++ b/recipes/bioconductor-moex10stprobeset.db/post-link.sh @@ -1,9 +1,10 @@ #!/bin/bash FN="moex10stprobeset.db_8.7.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/moex10stprobeset.db_8.7.0.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/moex10stprobeset.db_8.7.0.tar.gz" "https://bioarchive.galaxyproject.org/moex10stprobeset.db_8.7.0.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-moex10stprobeset.db/bioconductor-moex10stprobeset.db_8.7.0_src_all.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-moex10stprobeset.db/bioconductor-moex10stprobeset.db_8.7.0_src_all.tar.gz" ) MD5="1464d765c3db1bf50a6eb115ae30c74c" @@ -16,7 +17,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-moex10sttranscriptcluster.db/meta.yaml b/recipes/bioconductor-moex10sttranscriptcluster.db/meta.yaml index 7a90adec78582..f64258a1ded03 100644 --- a/recipes/bioconductor-moex10sttranscriptcluster.db/meta.yaml +++ b/recipes/bioconductor-moex10sttranscriptcluster.db/meta.yaml @@ -1,6 +1,6 @@ {% set version = "8.7.0" %} {% set name = "moex10sttranscriptcluster.db" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -12,7 +12,7 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 67253f6ab5cb335049139951ca8064bd build: - number: 1 + number: 2 rpaths: - lib/R/lib/ - lib/ @@ -20,14 +20,14 @@ build: # Suggests: DBI, annotate, RUnit requirements: host: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' - - 'bioconductor-org.mm.eg.db >=3.7.0,<3.8.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' + - 'bioconductor-org.mm.eg.db >=3.8.0,<3.9.0' - r-base run: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' - - 'bioconductor-org.mm.eg.db >=3.7.0,<3.8.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' + - 'bioconductor-org.mm.eg.db >=3.8.0,<3.9.0' - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-moex10sttranscriptcluster.db/post-link.sh b/recipes/bioconductor-moex10sttranscriptcluster.db/post-link.sh index b9289050a3fee..b84f9ff8fa261 100644 --- a/recipes/bioconductor-moex10sttranscriptcluster.db/post-link.sh +++ b/recipes/bioconductor-moex10sttranscriptcluster.db/post-link.sh @@ -1,9 +1,10 @@ #!/bin/bash FN="moex10sttranscriptcluster.db_8.7.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/moex10sttranscriptcluster.db_8.7.0.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/moex10sttranscriptcluster.db_8.7.0.tar.gz" "https://bioarchive.galaxyproject.org/moex10sttranscriptcluster.db_8.7.0.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-moex10sttranscriptcluster.db/bioconductor-moex10sttranscriptcluster.db_8.7.0_src_all.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-moex10sttranscriptcluster.db/bioconductor-moex10sttranscriptcluster.db_8.7.0_src_all.tar.gz" ) MD5="67253f6ab5cb335049139951ca8064bd" @@ -16,7 +17,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-moexexonprobesetlocation/meta.yaml b/recipes/bioconductor-moexexonprobesetlocation/meta.yaml index f8fca38a14224..51a2afa5ef5ee 100644 --- a/recipes/bioconductor-moexexonprobesetlocation/meta.yaml +++ b/recipes/bioconductor-moexexonprobesetlocation/meta.yaml @@ -1,6 +1,6 @@ {% set version = "1.15.0" %} {% set name = "MoExExonProbesetLocation" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -12,19 +12,19 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' md5: 07eea205fce2a8cf4585fa7e71fb0057 build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' - r-base run: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-moexexonprobesetlocation/post-link.sh b/recipes/bioconductor-moexexonprobesetlocation/post-link.sh index b38f5a397f078..dc80f5a5db0f7 100644 --- a/recipes/bioconductor-moexexonprobesetlocation/post-link.sh +++ b/recipes/bioconductor-moexexonprobesetlocation/post-link.sh @@ -1,9 +1,10 @@ #!/bin/bash FN="MoExExonProbesetLocation_1.15.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/MoExExonProbesetLocation_1.15.0.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/MoExExonProbesetLocation_1.15.0.tar.gz" "https://bioarchive.galaxyproject.org/MoExExonProbesetLocation_1.15.0.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-moexexonprobesetlocation/bioconductor-moexexonprobesetlocation_1.15.0_src_all.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-moexexonprobesetlocation/bioconductor-moexexonprobesetlocation_1.15.0_src_all.tar.gz" ) MD5="07eea205fce2a8cf4585fa7e71fb0057" @@ -16,7 +17,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-mofa/build.sh b/recipes/bioconductor-mofa/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-mofa/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-mofa/meta.yaml b/recipes/bioconductor-mofa/meta.yaml new file mode 100644 index 0000000000000..b563d0d34a1d3 --- /dev/null +++ b/recipes/bioconductor-mofa/meta.yaml @@ -0,0 +1,82 @@ +{% set version = "1.0.0" %} +{% set name = "MOFA" %} +{% set bioc = "3.9" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: a117c49e792026198df1770613e3761c +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: knitr, MOFAdata +# SystemRequirements: Python (>=2.7.0), numpy, pandas, h5py, scipy, sklearn, mofapy +requirements: + host: + - 'bioconductor-biobase >=2.44.0,<2.45.0' + - 'bioconductor-multiassayexperiment >=1.10.0,<1.11.0' + - 'bioconductor-rhdf5 >=2.28.0,<2.29.0' + - r-base + - r-corrplot + - r-cowplot + - r-doparallel + - r-dplyr + - r-foreach + - r-ggally + - r-ggbeeswarm + - r-ggplot2 + - r-ggrepel + - r-pheatmap + - r-rcolorbrewer + - r-reshape2 + - r-reticulate + - r-scales + - python + - numpy + - pandas + - h5py + - scipy + - sklearn + - mofapy + run: + - 'bioconductor-biobase >=2.44.0,<2.45.0' + - 'bioconductor-multiassayexperiment >=1.10.0,<1.11.0' + - 'bioconductor-rhdf5 >=2.28.0,<2.29.0' + - r-base + - r-corrplot + - r-cowplot + - r-doparallel + - r-dplyr + - r-foreach + - r-ggally + - r-ggbeeswarm + - r-ggplot2 + - r-ggrepel + - r-pheatmap + - r-rcolorbrewer + - r-reshape2 + - r-reticulate + - r-scales + - python + - numpy + - pandas + - h5py + - scipy + - sklearn + - mofapy +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: 'LGPL-3 | file LICENSE' + summary: 'Multi-Omics Factor Analysis: an unsupervised framework for the integration of multi-omics data sets.' + diff --git a/recipes/bioconductor-mofadata/meta.yaml b/recipes/bioconductor-mofadata/meta.yaml new file mode 100644 index 0000000000000..931942f94d12c --- /dev/null +++ b/recipes/bioconductor-mofadata/meta.yaml @@ -0,0 +1,34 @@ +{% set version = "1.0.0" %} +{% set name = "MOFAdata" %} +{% set bioc = "3.9" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: d6487d6a88855eff8711a5af287bbb2d +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: knitr, MultiAssayExperiment +requirements: + host: + - r-base + run: + - r-base + - curl +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html' + license: LGPL-3 + summary: 'A collection of datasets to accompany the R package MOFA and illustrate running and analysing MOFA models.' + diff --git a/recipes/bioconductor-mofadata/post-link.sh b/recipes/bioconductor-mofadata/post-link.sh new file mode 100644 index 0000000000000..761d8fe340fde --- /dev/null +++ b/recipes/bioconductor-mofadata/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="MOFAdata_1.0.0.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.9/data/experiment/src/contrib/MOFAdata_1.0.0.tar.gz" + "https://bioarchive.galaxyproject.org/MOFAdata_1.0.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-mofadata/bioconductor-mofadata_1.0.0_src_all.tar.gz" +) +MD5="d6487d6a88855eff8711a5af287bbb2d" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + curl $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-mofadata/pre-unlink.sh b/recipes/bioconductor-mofadata/pre-unlink.sh new file mode 100644 index 0000000000000..5190d9440fbe4 --- /dev/null +++ b/recipes/bioconductor-mofadata/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ MOFAdata diff --git a/recipes/bioconductor-mogene.1.0.st.v1frmavecs/meta.yaml b/recipes/bioconductor-mogene.1.0.st.v1frmavecs/meta.yaml index 3c5009663dbb5..dfd923519d797 100644 --- a/recipes/bioconductor-mogene.1.0.st.v1frmavecs/meta.yaml +++ b/recipes/bioconductor-mogene.1.0.st.v1frmavecs/meta.yaml @@ -1,6 +1,6 @@ {% set version = "1.1.0" %} {% set name = "mogene.1.0.st.v1frmavecs" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -12,7 +12,7 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: b46f76903d0f19b85e8fa30347813ff5 build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ @@ -22,7 +22,7 @@ requirements: - r-base run: - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-mogene.1.0.st.v1frmavecs/post-link.sh b/recipes/bioconductor-mogene.1.0.st.v1frmavecs/post-link.sh index 3684e28ad6c61..230827d59ed52 100644 --- a/recipes/bioconductor-mogene.1.0.st.v1frmavecs/post-link.sh +++ b/recipes/bioconductor-mogene.1.0.st.v1frmavecs/post-link.sh @@ -1,9 +1,10 @@ #!/bin/bash FN="mogene.1.0.st.v1frmavecs_1.1.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/mogene.1.0.st.v1frmavecs_1.1.0.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/mogene.1.0.st.v1frmavecs_1.1.0.tar.gz" "https://bioarchive.galaxyproject.org/mogene.1.0.st.v1frmavecs_1.1.0.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-mogene.1.0.st.v1frmavecs/bioconductor-mogene.1.0.st.v1frmavecs_1.1.0_src_all.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-mogene.1.0.st.v1frmavecs/bioconductor-mogene.1.0.st.v1frmavecs_1.1.0_src_all.tar.gz" ) MD5="b46f76903d0f19b85e8fa30347813ff5" @@ -16,7 +17,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-mogene10stprobeset.db/meta.yaml b/recipes/bioconductor-mogene10stprobeset.db/meta.yaml index 274bc5a722cbb..337bd78979011 100644 --- a/recipes/bioconductor-mogene10stprobeset.db/meta.yaml +++ b/recipes/bioconductor-mogene10stprobeset.db/meta.yaml @@ -1,6 +1,6 @@ {% set version = "8.7.0" %} {% set name = "mogene10stprobeset.db" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -12,7 +12,7 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: f4859f71d1314d19ead1c4fe20c04e4b build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ @@ -20,14 +20,14 @@ build: # Suggests: DBI, annotate, RUnit requirements: host: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' - - 'bioconductor-org.mm.eg.db >=3.7.0,<3.8.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' + - 'bioconductor-org.mm.eg.db >=3.8.0,<3.9.0' - r-base run: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' - - 'bioconductor-org.mm.eg.db >=3.7.0,<3.8.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' + - 'bioconductor-org.mm.eg.db >=3.8.0,<3.9.0' - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-mogene10stprobeset.db/post-link.sh b/recipes/bioconductor-mogene10stprobeset.db/post-link.sh index 7650d00d4447c..a9229ad6aa72d 100644 --- a/recipes/bioconductor-mogene10stprobeset.db/post-link.sh +++ b/recipes/bioconductor-mogene10stprobeset.db/post-link.sh @@ -1,9 +1,10 @@ #!/bin/bash FN="mogene10stprobeset.db_8.7.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/mogene10stprobeset.db_8.7.0.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/mogene10stprobeset.db_8.7.0.tar.gz" "https://bioarchive.galaxyproject.org/mogene10stprobeset.db_8.7.0.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-mogene10stprobeset.db/bioconductor-mogene10stprobeset.db_8.7.0_src_all.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-mogene10stprobeset.db/bioconductor-mogene10stprobeset.db_8.7.0_src_all.tar.gz" ) MD5="f4859f71d1314d19ead1c4fe20c04e4b" @@ -16,7 +17,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-mogene10sttranscriptcluster.db/meta.yaml b/recipes/bioconductor-mogene10sttranscriptcluster.db/meta.yaml index ef1707ed6fefa..b46093ada4f8a 100644 --- a/recipes/bioconductor-mogene10sttranscriptcluster.db/meta.yaml +++ b/recipes/bioconductor-mogene10sttranscriptcluster.db/meta.yaml @@ -1,6 +1,6 @@ {% set version = "8.7.0" %} {% set name = "mogene10sttranscriptcluster.db" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -12,7 +12,7 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 84966d4986d62c859f61f2725c7b20ea build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ @@ -20,14 +20,14 @@ build: # Suggests: DBI, annotate, RUnit requirements: host: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' - - 'bioconductor-org.mm.eg.db >=3.7.0,<3.8.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' + - 'bioconductor-org.mm.eg.db >=3.8.0,<3.9.0' - r-base run: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' - - 'bioconductor-org.mm.eg.db >=3.7.0,<3.8.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' + - 'bioconductor-org.mm.eg.db >=3.8.0,<3.9.0' - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-mogene10sttranscriptcluster.db/post-link.sh b/recipes/bioconductor-mogene10sttranscriptcluster.db/post-link.sh index c340dda60bcae..d909e0bd0c390 100644 --- a/recipes/bioconductor-mogene10sttranscriptcluster.db/post-link.sh +++ b/recipes/bioconductor-mogene10sttranscriptcluster.db/post-link.sh @@ -1,9 +1,10 @@ #!/bin/bash FN="mogene10sttranscriptcluster.db_8.7.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/mogene10sttranscriptcluster.db_8.7.0.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/mogene10sttranscriptcluster.db_8.7.0.tar.gz" "https://bioarchive.galaxyproject.org/mogene10sttranscriptcluster.db_8.7.0.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-mogene10sttranscriptcluster.db/bioconductor-mogene10sttranscriptcluster.db_8.7.0_src_all.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-mogene10sttranscriptcluster.db/bioconductor-mogene10sttranscriptcluster.db_8.7.0_src_all.tar.gz" ) MD5="84966d4986d62c859f61f2725c7b20ea" @@ -16,7 +17,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-mogene10stv1cdf/meta.yaml b/recipes/bioconductor-mogene10stv1cdf/meta.yaml index 43e697ef43c98..04d8e95239922 100644 --- a/recipes/bioconductor-mogene10stv1cdf/meta.yaml +++ b/recipes/bioconductor-mogene10stv1cdf/meta.yaml @@ -1,6 +1,6 @@ {% set version = "2.18.0" %} {% set name = "mogene10stv1cdf" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -12,19 +12,19 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 9c0271f5d6493290fc47f041a8c3f925 build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' - r-base run: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-mogene10stv1cdf/post-link.sh b/recipes/bioconductor-mogene10stv1cdf/post-link.sh index 2c36e501df7a3..3683bc0b278ef 100644 --- a/recipes/bioconductor-mogene10stv1cdf/post-link.sh +++ b/recipes/bioconductor-mogene10stv1cdf/post-link.sh @@ -1,9 +1,10 @@ #!/bin/bash FN="mogene10stv1cdf_2.18.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/mogene10stv1cdf_2.18.0.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/mogene10stv1cdf_2.18.0.tar.gz" "https://bioarchive.galaxyproject.org/mogene10stv1cdf_2.18.0.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-mogene10stv1cdf/bioconductor-mogene10stv1cdf_2.18.0_src_all.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-mogene10stv1cdf/bioconductor-mogene10stv1cdf_2.18.0_src_all.tar.gz" ) MD5="9c0271f5d6493290fc47f041a8c3f925" @@ -16,7 +17,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-mogene10stv1probe/meta.yaml b/recipes/bioconductor-mogene10stv1probe/meta.yaml index a659c360b2d4b..821439abceb64 100644 --- a/recipes/bioconductor-mogene10stv1probe/meta.yaml +++ b/recipes/bioconductor-mogene10stv1probe/meta.yaml @@ -1,6 +1,6 @@ {% set version = "2.18.0" %} {% set name = "mogene10stv1probe" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -12,19 +12,19 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 63cba1e2a0edee9f201267057fddb0fa build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' - r-base run: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-mogene10stv1probe/post-link.sh b/recipes/bioconductor-mogene10stv1probe/post-link.sh index 1c02997b9e805..2f1299aef1047 100644 --- a/recipes/bioconductor-mogene10stv1probe/post-link.sh +++ b/recipes/bioconductor-mogene10stv1probe/post-link.sh @@ -1,9 +1,10 @@ #!/bin/bash FN="mogene10stv1probe_2.18.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/mogene10stv1probe_2.18.0.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/mogene10stv1probe_2.18.0.tar.gz" "https://bioarchive.galaxyproject.org/mogene10stv1probe_2.18.0.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-mogene10stv1probe/bioconductor-mogene10stv1probe_2.18.0_src_all.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-mogene10stv1probe/bioconductor-mogene10stv1probe_2.18.0_src_all.tar.gz" ) MD5="63cba1e2a0edee9f201267057fddb0fa" @@ -16,7 +17,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-mogene11stprobeset.db/meta.yaml b/recipes/bioconductor-mogene11stprobeset.db/meta.yaml index a4e13d1307583..179511eb22d1c 100644 --- a/recipes/bioconductor-mogene11stprobeset.db/meta.yaml +++ b/recipes/bioconductor-mogene11stprobeset.db/meta.yaml @@ -1,6 +1,6 @@ {% set version = "8.7.0" %} {% set name = "mogene11stprobeset.db" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -12,7 +12,7 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 9bfdd5ede041282555dca8a6a75e7579 build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ @@ -20,14 +20,14 @@ build: # Suggests: DBI, annotate, RUnit requirements: host: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' - - 'bioconductor-org.mm.eg.db >=3.7.0,<3.8.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' + - 'bioconductor-org.mm.eg.db >=3.8.0,<3.9.0' - r-base run: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' - - 'bioconductor-org.mm.eg.db >=3.7.0,<3.8.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' + - 'bioconductor-org.mm.eg.db >=3.8.0,<3.9.0' - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-mogene11stprobeset.db/post-link.sh b/recipes/bioconductor-mogene11stprobeset.db/post-link.sh index 62866bb96ceea..077e7467fb5c0 100644 --- a/recipes/bioconductor-mogene11stprobeset.db/post-link.sh +++ b/recipes/bioconductor-mogene11stprobeset.db/post-link.sh @@ -1,9 +1,10 @@ #!/bin/bash FN="mogene11stprobeset.db_8.7.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/mogene11stprobeset.db_8.7.0.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/mogene11stprobeset.db_8.7.0.tar.gz" "https://bioarchive.galaxyproject.org/mogene11stprobeset.db_8.7.0.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-mogene11stprobeset.db/bioconductor-mogene11stprobeset.db_8.7.0_src_all.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-mogene11stprobeset.db/bioconductor-mogene11stprobeset.db_8.7.0_src_all.tar.gz" ) MD5="9bfdd5ede041282555dca8a6a75e7579" @@ -16,7 +17,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-mogene11sttranscriptcluster.db/meta.yaml b/recipes/bioconductor-mogene11sttranscriptcluster.db/meta.yaml index c9d8a7ff8a892..a5712d47ed6ab 100644 --- a/recipes/bioconductor-mogene11sttranscriptcluster.db/meta.yaml +++ b/recipes/bioconductor-mogene11sttranscriptcluster.db/meta.yaml @@ -1,6 +1,6 @@ {% set version = "8.7.0" %} {% set name = "mogene11sttranscriptcluster.db" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -12,7 +12,7 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: a3bc3ed82534b5a53bdba583f7a403c7 build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ @@ -20,14 +20,14 @@ build: # Suggests: DBI, annotate, RUnit requirements: host: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' - - 'bioconductor-org.mm.eg.db >=3.7.0,<3.8.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' + - 'bioconductor-org.mm.eg.db >=3.8.0,<3.9.0' - r-base run: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' - - 'bioconductor-org.mm.eg.db >=3.7.0,<3.8.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' + - 'bioconductor-org.mm.eg.db >=3.8.0,<3.9.0' - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-mogene11sttranscriptcluster.db/post-link.sh b/recipes/bioconductor-mogene11sttranscriptcluster.db/post-link.sh index a55407be9622c..640893154b70b 100644 --- a/recipes/bioconductor-mogene11sttranscriptcluster.db/post-link.sh +++ b/recipes/bioconductor-mogene11sttranscriptcluster.db/post-link.sh @@ -1,9 +1,10 @@ #!/bin/bash FN="mogene11sttranscriptcluster.db_8.7.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/mogene11sttranscriptcluster.db_8.7.0.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/mogene11sttranscriptcluster.db_8.7.0.tar.gz" "https://bioarchive.galaxyproject.org/mogene11sttranscriptcluster.db_8.7.0.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-mogene11sttranscriptcluster.db/bioconductor-mogene11sttranscriptcluster.db_8.7.0_src_all.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-mogene11sttranscriptcluster.db/bioconductor-mogene11sttranscriptcluster.db_8.7.0_src_all.tar.gz" ) MD5="a3bc3ed82534b5a53bdba583f7a403c7" @@ -16,7 +17,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-mogene20stprobeset.db/meta.yaml b/recipes/bioconductor-mogene20stprobeset.db/meta.yaml index 5ce6158da6890..6f4a5d48bb040 100644 --- a/recipes/bioconductor-mogene20stprobeset.db/meta.yaml +++ b/recipes/bioconductor-mogene20stprobeset.db/meta.yaml @@ -1,6 +1,6 @@ {% set version = "8.7.0" %} {% set name = "mogene20stprobeset.db" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -12,7 +12,7 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 228a1172930e05806cd8b184b326b556 build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ @@ -20,14 +20,14 @@ build: # Suggests: DBI, annotate, RUnit requirements: host: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' - - 'bioconductor-org.mm.eg.db >=3.7.0,<3.8.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' + - 'bioconductor-org.mm.eg.db >=3.8.0,<3.9.0' - r-base run: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' - - 'bioconductor-org.mm.eg.db >=3.7.0,<3.8.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' + - 'bioconductor-org.mm.eg.db >=3.8.0,<3.9.0' - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-mogene20stprobeset.db/post-link.sh b/recipes/bioconductor-mogene20stprobeset.db/post-link.sh index 6c3efd4b63b04..de888f8a0fb4d 100644 --- a/recipes/bioconductor-mogene20stprobeset.db/post-link.sh +++ b/recipes/bioconductor-mogene20stprobeset.db/post-link.sh @@ -1,9 +1,10 @@ #!/bin/bash FN="mogene20stprobeset.db_8.7.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/mogene20stprobeset.db_8.7.0.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/mogene20stprobeset.db_8.7.0.tar.gz" "https://bioarchive.galaxyproject.org/mogene20stprobeset.db_8.7.0.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-mogene20stprobeset.db/bioconductor-mogene20stprobeset.db_8.7.0_src_all.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-mogene20stprobeset.db/bioconductor-mogene20stprobeset.db_8.7.0_src_all.tar.gz" ) MD5="228a1172930e05806cd8b184b326b556" @@ -16,7 +17,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-mogene20sttranscriptcluster.db/meta.yaml b/recipes/bioconductor-mogene20sttranscriptcluster.db/meta.yaml index bfaa41e68fb94..9e3f5f54d6f25 100644 --- a/recipes/bioconductor-mogene20sttranscriptcluster.db/meta.yaml +++ b/recipes/bioconductor-mogene20sttranscriptcluster.db/meta.yaml @@ -1,6 +1,6 @@ {% set version = "8.7.0" %} {% set name = "mogene20sttranscriptcluster.db" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -12,7 +12,7 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: c3c6f08d15d9cd3fe850860de0a06213 build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ @@ -20,14 +20,14 @@ build: # Suggests: DBI, annotate, RUnit requirements: host: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' - - 'bioconductor-org.mm.eg.db >=3.7.0,<3.8.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' + - 'bioconductor-org.mm.eg.db >=3.8.0,<3.9.0' - r-base run: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' - - 'bioconductor-org.mm.eg.db >=3.7.0,<3.8.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' + - 'bioconductor-org.mm.eg.db >=3.8.0,<3.9.0' - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-mogene20sttranscriptcluster.db/post-link.sh b/recipes/bioconductor-mogene20sttranscriptcluster.db/post-link.sh index 8187d6f49d1c4..dbfa78cda4289 100644 --- a/recipes/bioconductor-mogene20sttranscriptcluster.db/post-link.sh +++ b/recipes/bioconductor-mogene20sttranscriptcluster.db/post-link.sh @@ -1,9 +1,10 @@ #!/bin/bash FN="mogene20sttranscriptcluster.db_8.7.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/mogene20sttranscriptcluster.db_8.7.0.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/mogene20sttranscriptcluster.db_8.7.0.tar.gz" "https://bioarchive.galaxyproject.org/mogene20sttranscriptcluster.db_8.7.0.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-mogene20sttranscriptcluster.db/bioconductor-mogene20sttranscriptcluster.db_8.7.0_src_all.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-mogene20sttranscriptcluster.db/bioconductor-mogene20sttranscriptcluster.db_8.7.0_src_all.tar.gz" ) MD5="c3c6f08d15d9cd3fe850860de0a06213" @@ -16,7 +17,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-mogene21stprobeset.db/meta.yaml b/recipes/bioconductor-mogene21stprobeset.db/meta.yaml index b7cd40fd39b23..61a11dc2e3b1e 100644 --- a/recipes/bioconductor-mogene21stprobeset.db/meta.yaml +++ b/recipes/bioconductor-mogene21stprobeset.db/meta.yaml @@ -1,6 +1,6 @@ {% set version = "8.7.0" %} {% set name = "mogene21stprobeset.db" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -12,7 +12,7 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 34c2b435725e7dcd29c3d921453216dc build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ @@ -20,14 +20,14 @@ build: # Suggests: DBI, annotate, RUnit requirements: host: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' - - 'bioconductor-org.mm.eg.db >=3.7.0,<3.8.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' + - 'bioconductor-org.mm.eg.db >=3.8.0,<3.9.0' - r-base run: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' - - 'bioconductor-org.mm.eg.db >=3.7.0,<3.8.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' + - 'bioconductor-org.mm.eg.db >=3.8.0,<3.9.0' - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-mogene21stprobeset.db/post-link.sh b/recipes/bioconductor-mogene21stprobeset.db/post-link.sh index 6896396fde4d0..ac14a204b5582 100644 --- a/recipes/bioconductor-mogene21stprobeset.db/post-link.sh +++ b/recipes/bioconductor-mogene21stprobeset.db/post-link.sh @@ -1,9 +1,10 @@ #!/bin/bash FN="mogene21stprobeset.db_8.7.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/mogene21stprobeset.db_8.7.0.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/mogene21stprobeset.db_8.7.0.tar.gz" "https://bioarchive.galaxyproject.org/mogene21stprobeset.db_8.7.0.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-mogene21stprobeset.db/bioconductor-mogene21stprobeset.db_8.7.0_src_all.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-mogene21stprobeset.db/bioconductor-mogene21stprobeset.db_8.7.0_src_all.tar.gz" ) MD5="34c2b435725e7dcd29c3d921453216dc" @@ -16,7 +17,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-mogene21sttranscriptcluster.db/meta.yaml b/recipes/bioconductor-mogene21sttranscriptcluster.db/meta.yaml index bafcec46d09d4..d6ba7d28531a2 100644 --- a/recipes/bioconductor-mogene21sttranscriptcluster.db/meta.yaml +++ b/recipes/bioconductor-mogene21sttranscriptcluster.db/meta.yaml @@ -1,6 +1,6 @@ {% set version = "8.7.0" %} {% set name = "mogene21sttranscriptcluster.db" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -12,7 +12,7 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 0f131b607470652724d7b22ae2af1c7a build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ @@ -20,14 +20,14 @@ build: # Suggests: DBI, annotate, RUnit requirements: host: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' - - 'bioconductor-org.mm.eg.db >=3.7.0,<3.8.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' + - 'bioconductor-org.mm.eg.db >=3.8.0,<3.9.0' - r-base run: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' - - 'bioconductor-org.mm.eg.db >=3.7.0,<3.8.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' + - 'bioconductor-org.mm.eg.db >=3.8.0,<3.9.0' - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-mogene21sttranscriptcluster.db/post-link.sh b/recipes/bioconductor-mogene21sttranscriptcluster.db/post-link.sh index d9c50941f8116..cb03adadd68bb 100644 --- a/recipes/bioconductor-mogene21sttranscriptcluster.db/post-link.sh +++ b/recipes/bioconductor-mogene21sttranscriptcluster.db/post-link.sh @@ -1,9 +1,10 @@ #!/bin/bash FN="mogene21sttranscriptcluster.db_8.7.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/mogene21sttranscriptcluster.db_8.7.0.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/mogene21sttranscriptcluster.db_8.7.0.tar.gz" "https://bioarchive.galaxyproject.org/mogene21sttranscriptcluster.db_8.7.0.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-mogene21sttranscriptcluster.db/bioconductor-mogene21sttranscriptcluster.db_8.7.0_src_all.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-mogene21sttranscriptcluster.db/bioconductor-mogene21sttranscriptcluster.db_8.7.0_src_all.tar.gz" ) MD5="0f131b607470652724d7b22ae2af1c7a" @@ -16,7 +17,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-mogsa/meta.yaml b/recipes/bioconductor-mogsa/meta.yaml index 47d3e696737a6..9aa704aace017 100644 --- a/recipes/bioconductor-mogsa/meta.yaml +++ b/recipes/bioconductor-mogsa/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.16.0" %} +{% set version = "1.17.5" %} {% set name = "mogsa" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,32 +10,32 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 8cf09a49ac7d52e667f40ab2e5d2922c + md5: 64e223e6393c7db286b6a87874b4647c build: number: 0 rpaths: - lib/R/lib/ - lib/ noarch: generic -# Suggests: BiocStyle, knitr +# Suggests: BiocStyle, knitr, org.Hs.eg.db requirements: host: - - 'bioconductor-biobase >=2.42.0,<2.43.0' - - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' - - 'bioconductor-genefilter >=1.64.0,<1.65.0' - - 'bioconductor-graphite >=1.28.0,<1.29.0' - - 'bioconductor-gseabase >=1.44.0,<1.45.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' + - 'bioconductor-biocgenerics >=0.30.0,<0.31.0' + - 'bioconductor-genefilter >=1.66.0,<1.67.0' + - 'bioconductor-graphite >=1.30.0,<1.31.0' + - 'bioconductor-gseabase >=1.46.0,<1.47.0' - r-base - r-cluster - r-corpcor - r-gplots - r-svd run: - - 'bioconductor-biobase >=2.42.0,<2.43.0' - - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' - - 'bioconductor-genefilter >=1.64.0,<1.65.0' - - 'bioconductor-graphite >=1.28.0,<1.29.0' - - 'bioconductor-gseabase >=1.44.0,<1.45.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' + - 'bioconductor-biocgenerics >=0.30.0,<0.31.0' + - 'bioconductor-genefilter >=1.66.0,<1.67.0' + - 'bioconductor-graphite >=1.30.0,<1.31.0' + - 'bioconductor-gseabase >=1.46.0,<1.47.0' - r-base - r-cluster - r-corpcor diff --git a/recipes/bioconductor-monocle/meta.yaml b/recipes/bioconductor-monocle/meta.yaml index 5a08fe6b87657..86140b91cc470 100644 --- a/recipes/bioconductor-monocle/meta.yaml +++ b/recipes/bioconductor-monocle/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "2.10.0" %} +{% set version = "2.12.0" %} {% set name = "monocle" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: bc85ee520d81832a181fe01680558997 + md5: d56a4b34d746a190c68fcb54d4c0dab7 build: number: 0 rpaths: @@ -19,11 +19,11 @@ build: # Suggests: destiny, Hmisc, knitr, Seurat, scater, testthat requirements: host: - - 'bioconductor-biobase >=2.42.0,<2.43.0' - - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' - - 'bioconductor-biocviews >=1.50.0,<1.51.0' - - 'bioconductor-hsmmsinglecell >=1.2.0,<1.3.0' - - 'bioconductor-limma >=3.38.0,<3.39.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' + - 'bioconductor-biocgenerics >=0.30.0,<0.31.0' + - 'bioconductor-biocviews >=1.52.0,<1.53.0' + - 'bioconductor-hsmmsinglecell >=1.4.0,<1.5.0' + - 'bioconductor-limma >=3.40.0,<3.41.0' - r-base - r-cluster - r-combinat @@ -51,11 +51,11 @@ requirements: - 'r-vgam >=1.0-6' - r-viridis run: - - 'bioconductor-biobase >=2.42.0,<2.43.0' - - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' - - 'bioconductor-biocviews >=1.50.0,<1.51.0' - - 'bioconductor-hsmmsinglecell >=1.2.0,<1.3.0' - - 'bioconductor-limma >=3.38.0,<3.39.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' + - 'bioconductor-biocgenerics >=0.30.0,<0.31.0' + - 'bioconductor-biocviews >=1.52.0,<1.53.0' + - 'bioconductor-hsmmsinglecell >=1.4.0,<1.5.0' + - 'bioconductor-limma >=3.40.0,<3.41.0' - r-base - r-cluster - r-combinat diff --git a/recipes/bioconductor-moonlightr/meta.yaml b/recipes/bioconductor-moonlightr/meta.yaml index 40b84b2232285..4ef9501810a89 100644 --- a/recipes/bioconductor-moonlightr/meta.yaml +++ b/recipes/bioconductor-moonlightr/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.8.0" %} +{% set version = "1.9.0" %} {% set name = "MoonlightR" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: ee7e9a7914dd2f526db0f189785be525 + md5: b611552e9e00c271a50d757aef81b93f build: number: 0 rpaths: @@ -20,13 +20,13 @@ build: # Suggests: BiocStyle, knitr, rmarkdown, testthat, devtools, roxygen2, png requirements: host: - - 'bioconductor-biobase >=2.42.0,<2.43.0' - - 'bioconductor-clusterprofiler >=3.10.0,<3.11.0' - - 'bioconductor-dose >=3.8.0,<3.9.0' - - 'bioconductor-geoquery >=2.50.0,<2.51.0' - - 'bioconductor-limma >=3.38.0,<3.39.0' - - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' - - 'bioconductor-tcgabiolinks >=2.10.0,<2.11.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' + - 'bioconductor-clusterprofiler >=3.12.0,<3.13.0' + - 'bioconductor-dose >=3.10.0,<3.11.0' + - 'bioconductor-geoquery >=2.52.0,<2.53.0' + - 'bioconductor-limma >=3.40.0,<3.41.0' + - 'bioconductor-summarizedexperiment >=1.14.0,<1.15.0' + - 'bioconductor-tcgabiolinks >=2.12.0,<2.13.0' - r-base - r-circlize - r-doparallel @@ -38,13 +38,13 @@ requirements: - r-rcolorbrewer - r-rismed run: - - 'bioconductor-biobase >=2.42.0,<2.43.0' - - 'bioconductor-clusterprofiler >=3.10.0,<3.11.0' - - 'bioconductor-dose >=3.8.0,<3.9.0' - - 'bioconductor-geoquery >=2.50.0,<2.51.0' - - 'bioconductor-limma >=3.38.0,<3.39.0' - - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' - - 'bioconductor-tcgabiolinks >=2.10.0,<2.11.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' + - 'bioconductor-clusterprofiler >=3.12.0,<3.13.0' + - 'bioconductor-dose >=3.10.0,<3.11.0' + - 'bioconductor-geoquery >=2.52.0,<2.53.0' + - 'bioconductor-limma >=3.40.0,<3.41.0' + - 'bioconductor-summarizedexperiment >=1.14.0,<1.15.0' + - 'bioconductor-tcgabiolinks >=2.12.0,<2.13.0' - r-base - r-circlize - r-doparallel @@ -62,8 +62,7 @@ about: home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: 'GPL (>= 3)' summary: 'Motivation: The understanding of cancer mechanism requires the identification of genes playing a role in the development of the pathology and the characterization of their role (notably oncogenes and tumor suppressors). Results: We present an R/bioconductor package called MoonlightR which returns a list of candidate driver genes for specific cancer types on the basis of TCGA expression data. The method first infers gene regulatory networks and then carries out a functional enrichment analysis (FEA) (implementing an upstream regulator analysis, URA) to score the importance of well-known biological processes with respect to the studied cancer type. Eventually, by means of random forests, MoonlightR predicts two specific roles for the candidate driver genes: i) tumor suppressor genes (TSGs) and ii) oncogenes (OCGs). As a consequence, this methodology does not only identify genes playing a dual role (e.g. TSG in one cancer type and OCG in another) but also helps in elucidating the biological processes underlying their specific roles. In particular, MoonlightR can be used to discover OCGs and TSGs in the same cancer type. This may help in answering the question whether some genes change role between early stages (I, II) and late stages (III, IV) in breast cancer. In the future, this analysis could be useful to determine the causes of different resistances to chemotherapeutic treatments.' - extra: container: - # needed for libGL.so.1 - extended-base: true + extended-base: true + diff --git a/recipes/bioconductor-mops/meta.yaml b/recipes/bioconductor-mops/meta.yaml index 6d6543867a486..2846f24e8ce58 100644 --- a/recipes/bioconductor-mops/meta.yaml +++ b/recipes/bioconductor-mops/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.16.0" %} +{% set version = "1.18.0" %} {% set name = "MoPS" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 45c3777290bc95c462428fcc28aa18e0 + md5: 475aff991362cea8669041b4a8252c3e build: number: 0 rpaths: @@ -19,10 +19,10 @@ build: noarch: generic requirements: host: - - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' - r-base run: - - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' - r-base test: commands: diff --git a/recipes/bioconductor-mosaics/meta.yaml b/recipes/bioconductor-mosaics/meta.yaml index 07bf38ea897aa..831e83874d636 100644 --- a/recipes/bioconductor-mosaics/meta.yaml +++ b/recipes/bioconductor-mosaics/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "2.20.0" %} +{% set version = "2.22.0" %} {% set name = "mosaics" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 9e40d17d91730001365219582cd223fc + md5: 91e1ae361b6c172d27f265e44b54609e build: number: 0 rpaths: @@ -20,27 +20,29 @@ build: # SystemRequirements: Perl requirements: host: - - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' - - 'bioconductor-genomicalignments >=1.18.0,<1.19.0' - - 'bioconductor-genomicranges >=1.34.0,<1.35.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-rsamtools >=1.34.0,<1.35.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-genomeinfodb >=1.20.0,<1.21.0' + - 'bioconductor-genomicalignments >=1.20.0,<1.21.0' + - 'bioconductor-genomicranges >=1.36.0,<1.37.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-rsamtools >=2.0.0,<2.1.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' - r-base - r-lattice - r-mass - r-rcpp + - perl run: - - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' - - 'bioconductor-genomicalignments >=1.18.0,<1.19.0' - - 'bioconductor-genomicranges >=1.34.0,<1.35.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-rsamtools >=1.34.0,<1.35.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-genomeinfodb >=1.20.0,<1.21.0' + - 'bioconductor-genomicalignments >=1.20.0,<1.21.0' + - 'bioconductor-genomicranges >=1.36.0,<1.37.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-rsamtools >=2.0.0,<2.1.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' - r-base - r-lattice - r-mass - r-rcpp + - perl build: - {{ compiler('c') }} - {{ compiler('cxx') }} diff --git a/recipes/bioconductor-mosaicsexample/meta.yaml b/recipes/bioconductor-mosaicsexample/meta.yaml index e737ef7933a2c..b6952a62cc035 100644 --- a/recipes/bioconductor-mosaicsexample/meta.yaml +++ b/recipes/bioconductor-mosaicsexample/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.20.0" %} +{% set version = "1.22.0" %} {% set name = "mosaicsExample" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 5f16c9ddafc0db17641a7c8dde96a62b + md5: c87a905df5b38287895aff9adb2c8406 build: number: 0 rpaths: @@ -22,7 +22,7 @@ requirements: - r-base run: - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-mosaicsexample/post-link.sh b/recipes/bioconductor-mosaicsexample/post-link.sh index 96ba22aba647f..c158495987d46 100644 --- a/recipes/bioconductor-mosaicsexample/post-link.sh +++ b/recipes/bioconductor-mosaicsexample/post-link.sh @@ -1,11 +1,11 @@ #!/bin/bash -FN="mosaicsExample_1.20.0.tar.gz" +FN="mosaicsExample_1.22.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/experiment/src/contrib/mosaicsExample_1.20.0.tar.gz" - "https://bioarchive.galaxyproject.org/mosaicsExample_1.20.0.tar.gz" - "https://depot.galaxyproject.org/software/bioconductor-mosaicsexample/bioconductor-mosaicsexample_1.20.0_src_all.tar.gz" + "https://bioconductor.org/packages/3.9/data/experiment/src/contrib/mosaicsExample_1.22.0.tar.gz" + "https://bioarchive.galaxyproject.org/mosaicsExample_1.22.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-mosaicsexample/bioconductor-mosaicsexample_1.22.0_src_all.tar.gz" ) -MD5="5f16c9ddafc0db17641a7c8dde96a62b" +MD5="c87a905df5b38287895aff9adb2c8406" # Use a staging area in the conda dir rather than temp dirs, both to avoid # permission issues as well as to have things downloaded in a predictable @@ -16,7 +16,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-motifbreakr/meta.yaml b/recipes/bioconductor-motifbreakr/meta.yaml index 9729c1ac90b37..573eeaa0cb4b3 100644 --- a/recipes/bioconductor-motifbreakr/meta.yaml +++ b/recipes/bioconductor-motifbreakr/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.12.0" %} +{% set version = "1.14.0" %} {% set name = "motifbreakR" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: f4acb1d102a78b4ca2bb951366e5cace + md5: 3dd9087f717dc73dff5223aea9cde251 build: number: 0 rpaths: @@ -20,38 +20,40 @@ build: # Suggests: BSgenome.Hsapiens.UCSC.hg19, SNPlocs.Hsapiens.dbSNP.20120608, SNPlocs.Hsapiens.dbSNP142.GRCh37, knitr, rmarkdown, BSgenome.Drerio.UCSC.danRer7, BiocStyle requirements: host: - - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' - - 'bioconductor-biocparallel >=1.16.0,<1.17.0' - - 'bioconductor-biostrings >=2.50.0,<2.51.0' - - 'bioconductor-bsgenome >=1.50.0,<1.51.0' - - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' - - 'bioconductor-genomicranges >=1.34.0,<1.35.0' - - 'bioconductor-gviz >=1.26.0,<1.27.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-motifdb >=1.24.0,<1.25.0' - - 'bioconductor-motifstack >=1.26.0,<1.27.0' - - 'bioconductor-rtracklayer >=1.42.0,<1.43.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' - - 'bioconductor-variantannotation >=1.28.0,<1.29.0' + - 'bioconductor-biocgenerics >=0.30.0,<0.31.0' + - 'bioconductor-biocparallel >=1.18.0,<1.19.0' + - 'bioconductor-biostrings >=2.52.0,<2.53.0' + - 'bioconductor-bsgenome >=1.52.0,<1.53.0' + - 'bioconductor-genomeinfodb >=1.20.0,<1.21.0' + - 'bioconductor-genomicranges >=1.36.0,<1.37.0' + - 'bioconductor-gviz >=1.28.0,<1.29.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-motifdb >=1.26.0,<1.27.0' + - 'bioconductor-motifstack >=1.28.0,<1.29.0' + - 'bioconductor-rtracklayer >=1.44.0,<1.45.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' + - 'bioconductor-summarizedexperiment >=1.14.0,<1.15.0' + - 'bioconductor-variantannotation >=1.30.0,<1.31.0' - r-base - r-grimport - r-matrixstats - r-stringr - r-tfmpvalue run: - - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' - - 'bioconductor-biocparallel >=1.16.0,<1.17.0' - - 'bioconductor-biostrings >=2.50.0,<2.51.0' - - 'bioconductor-bsgenome >=1.50.0,<1.51.0' - - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' - - 'bioconductor-genomicranges >=1.34.0,<1.35.0' - - 'bioconductor-gviz >=1.26.0,<1.27.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-motifdb >=1.24.0,<1.25.0' - - 'bioconductor-motifstack >=1.26.0,<1.27.0' - - 'bioconductor-rtracklayer >=1.42.0,<1.43.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' - - 'bioconductor-variantannotation >=1.28.0,<1.29.0' + - 'bioconductor-biocgenerics >=0.30.0,<0.31.0' + - 'bioconductor-biocparallel >=1.18.0,<1.19.0' + - 'bioconductor-biostrings >=2.52.0,<2.53.0' + - 'bioconductor-bsgenome >=1.52.0,<1.53.0' + - 'bioconductor-genomeinfodb >=1.20.0,<1.21.0' + - 'bioconductor-genomicranges >=1.36.0,<1.37.0' + - 'bioconductor-gviz >=1.28.0,<1.29.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-motifdb >=1.26.0,<1.27.0' + - 'bioconductor-motifstack >=1.28.0,<1.29.0' + - 'bioconductor-rtracklayer >=1.44.0,<1.45.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' + - 'bioconductor-summarizedexperiment >=1.14.0,<1.15.0' + - 'bioconductor-variantannotation >=1.30.0,<1.31.0' - r-base - r-grimport - r-matrixstats diff --git a/recipes/bioconductor-motifcounter/meta.yaml b/recipes/bioconductor-motifcounter/meta.yaml index f33a193b376eb..9d21bbf6a0b52 100644 --- a/recipes/bioconductor-motifcounter/meta.yaml +++ b/recipes/bioconductor-motifcounter/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.6.0" %} +{% set version = "1.8.0" %} {% set name = "motifcounter" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 17980f892c118972ea93583cd449328d + md5: b2423266714b75836a8250ebb1a3a0a6 build: number: 0 rpaths: @@ -19,15 +19,14 @@ build: # Suggests: knitr, rmarkdown, testthat, MotifDb, seqLogo, prettydoc requirements: host: - - 'bioconductor-biostrings >=2.50.0,<2.51.0' + - 'bioconductor-biostrings >=2.52.0,<2.53.0' - r-base run: - - 'bioconductor-biostrings >=2.50.0,<2.51.0' + - 'bioconductor-biostrings >=2.52.0,<2.53.0' - r-base build: - {{ compiler('c') }} - make - - llvm-openmp # [osx] test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-motifdb/meta.yaml b/recipes/bioconductor-motifdb/meta.yaml index 42049622bdd72..d198c3844681d 100644 --- a/recipes/bioconductor-motifdb/meta.yaml +++ b/recipes/bioconductor-motifdb/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.24.1" %} +{% set version = "1.26.0" %} {% set name = "MotifDb" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 0e4f0a765443f27fa97aa8c26ba18331 + md5: a67c80f80fe5a4c3e4c6f6c56c1fc5cc build: number: 0 rpaths: @@ -20,19 +20,19 @@ build: # Suggests: RUnit requirements: host: - - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' - - 'bioconductor-biostrings >=2.50.0,<2.51.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-rtracklayer >=1.42.0,<1.43.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-biocgenerics >=0.30.0,<0.31.0' + - 'bioconductor-biostrings >=2.52.0,<2.53.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-rtracklayer >=1.44.0,<1.45.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' - r-base - r-splitstackshape run: - - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' - - 'bioconductor-biostrings >=2.50.0,<2.51.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-rtracklayer >=1.42.0,<1.43.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-biocgenerics >=0.30.0,<0.31.0' + - 'bioconductor-biostrings >=2.52.0,<2.53.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-rtracklayer >=1.44.0,<1.45.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' - r-base - r-splitstackshape test: diff --git a/recipes/bioconductor-motifmatchr/meta.yaml b/recipes/bioconductor-motifmatchr/meta.yaml index dd72988110474..85eed71f58bf0 100644 --- a/recipes/bioconductor-motifmatchr/meta.yaml +++ b/recipes/bioconductor-motifmatchr/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.4.0" %} +{% set version = "1.6.0" %} {% set name = "motifmatchr" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 81b108d831a4e6084991dadd868f779a + md5: e8538782c56a4cae9ff880a8bcc8ec3d build: number: 0 rpaths: @@ -20,29 +20,29 @@ build: # SystemRequirements: C++11 requirements: host: - - 'bioconductor-biostrings >=2.50.0,<2.51.0' - - 'bioconductor-bsgenome >=1.50.0,<1.51.0' - - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' - - 'bioconductor-genomicranges >=1.34.0,<1.35.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-rsamtools >=1.34.0,<1.35.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' - - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' - - 'bioconductor-tfbstools >=1.20.0,<1.21.0' + - 'bioconductor-biostrings >=2.52.0,<2.53.0' + - 'bioconductor-bsgenome >=1.52.0,<1.53.0' + - 'bioconductor-genomeinfodb >=1.20.0,<1.21.0' + - 'bioconductor-genomicranges >=1.36.0,<1.37.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-rsamtools >=2.0.0,<2.1.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' + - 'bioconductor-summarizedexperiment >=1.14.0,<1.15.0' + - 'bioconductor-tfbstools >=1.22.0,<1.23.0' - r-base - r-matrix - r-rcpp - r-rcpparmadillo run: - - 'bioconductor-biostrings >=2.50.0,<2.51.0' - - 'bioconductor-bsgenome >=1.50.0,<1.51.0' - - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' - - 'bioconductor-genomicranges >=1.34.0,<1.35.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-rsamtools >=1.34.0,<1.35.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' - - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' - - 'bioconductor-tfbstools >=1.20.0,<1.21.0' + - 'bioconductor-biostrings >=2.52.0,<2.53.0' + - 'bioconductor-bsgenome >=1.52.0,<1.53.0' + - 'bioconductor-genomeinfodb >=1.20.0,<1.21.0' + - 'bioconductor-genomicranges >=1.36.0,<1.37.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-rsamtools >=2.0.0,<2.1.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' + - 'bioconductor-summarizedexperiment >=1.14.0,<1.15.0' + - 'bioconductor-tfbstools >=1.22.0,<1.23.0' - r-base - r-matrix - r-rcpp diff --git a/recipes/bioconductor-motifrg/meta.yaml b/recipes/bioconductor-motifrg/meta.yaml index b28b0e488463f..cceca36411bf2 100644 --- a/recipes/bioconductor-motifrg/meta.yaml +++ b/recipes/bioconductor-motifrg/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.26.0" %} +{% set version = "1.28.0" %} {% set name = "motifRG" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 6e6636d8724438f812dd372a28196722 + md5: c6f8456a1449bf9101aed4ce783e682a build: number: 0 rpaths: @@ -19,20 +19,20 @@ build: noarch: generic requirements: host: - - 'bioconductor-biostrings >=2.50.0,<2.51.0' - - 'bioconductor-bsgenome >=1.50.0,<1.51.0' + - 'bioconductor-biostrings >=2.52.0,<2.53.0' + - 'bioconductor-bsgenome >=1.52.0,<1.53.0' - 'bioconductor-bsgenome.hsapiens.ucsc.hg19 >=1.4.0,<1.5.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-seqlogo >=1.48.0,<1.49.0' - - 'bioconductor-xvector >=0.22.0,<0.23.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-seqlogo >=1.50.0,<1.51.0' + - 'bioconductor-xvector >=0.24.0,<0.25.0' - r-base run: - - 'bioconductor-biostrings >=2.50.0,<2.51.0' - - 'bioconductor-bsgenome >=1.50.0,<1.51.0' + - 'bioconductor-biostrings >=2.52.0,<2.53.0' + - 'bioconductor-bsgenome >=1.52.0,<1.53.0' - 'bioconductor-bsgenome.hsapiens.ucsc.hg19 >=1.4.0,<1.5.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-seqlogo >=1.48.0,<1.49.0' - - 'bioconductor-xvector >=0.22.0,<0.23.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-seqlogo >=1.50.0,<1.51.0' + - 'bioconductor-xvector >=0.24.0,<0.25.0' - r-base test: commands: diff --git a/recipes/bioconductor-motifstack/meta.yaml b/recipes/bioconductor-motifstack/meta.yaml index 38ae6b3faf1d1..dfafafe2dcadb 100644 --- a/recipes/bioconductor-motifstack/meta.yaml +++ b/recipes/bioconductor-motifstack/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.26.0" %} +{% set version = "1.28.0" %} {% set name = "motifStack" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,9 +10,9 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 1ae29bba676e9d9f4d6c43430266946d + md5: 91fbdf0016d23504079d5eb6511cebee build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ @@ -20,20 +20,20 @@ build: # Suggests: RUnit, BiocGenerics, MotifDb, RColorBrewer, BiocStyle, knitr requirements: host: - - 'bioconductor-biostrings >=2.50.0,<2.51.0' - - 'bioconductor-motiv >=1.38.0,<1.39.0' + - 'bioconductor-biostrings >=2.52.0,<2.53.0' + - 'bioconductor-motiv >=1.40.0,<1.41.0' - r-ade4 - r-base - - r-grimport + - r-grimport2 - r-htmlwidgets - r-scales - r-xml run: - - 'bioconductor-biostrings >=2.50.0,<2.51.0' - - 'bioconductor-motiv >=1.38.0,<1.39.0' + - 'bioconductor-biostrings >=2.52.0,<2.53.0' + - 'bioconductor-motiv >=1.40.0,<1.41.0' - r-ade4 - r-base - - r-grimport + - r-grimport2 - r-htmlwidgets - r-scales - r-xml diff --git a/recipes/bioconductor-motiv/meta.yaml b/recipes/bioconductor-motiv/meta.yaml index fca353c4a4bc8..f1e75bc93f715 100644 --- a/recipes/bioconductor-motiv/meta.yaml +++ b/recipes/bioconductor-motiv/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.38.0" %} +{% set version = "1.40.0" %} {% set name = "MotIV" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 513e9e6da9a911fc4d5b23c48b06c5d2 + md5: f8a64bac15749b7e95f5169c52080c53 build: number: 0 rpaths: @@ -20,24 +20,23 @@ build: # SystemRequirements: GNU Scientific Library >= 1.6 (http://www.gnu.org/software/gsl/) requirements: host: - - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' - - 'bioconductor-biostrings >=2.50.0,<2.51.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-rgadem >=2.30.0,<2.31.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-biocgenerics >=0.30.0,<0.31.0' + - 'bioconductor-biostrings >=2.52.0,<2.53.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-rgadem >=2.32.0,<2.33.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' - r-base - r-lattice - gsl run: - - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' - - 'bioconductor-biostrings >=2.50.0,<2.51.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-rgadem >=2.30.0,<2.31.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-biocgenerics >=0.30.0,<0.31.0' + - 'bioconductor-biostrings >=2.52.0,<2.53.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-rgadem >=2.32.0,<2.33.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' - r-base - r-lattice - gsl - - openblas build: - {{ compiler('c') }} - {{ compiler('cxx') }} diff --git a/recipes/bioconductor-mouse.db0/meta.yaml b/recipes/bioconductor-mouse.db0/meta.yaml index 57be6bab80414..d151d969dc254 100644 --- a/recipes/bioconductor-mouse.db0/meta.yaml +++ b/recipes/bioconductor-mouse.db0/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "3.7.1" %} +{% set version = "3.8.2" %} {% set name = "mouse.db0" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 01237a7808395a578f72063603b6db98 + md5: 1927a435523cfdf1a94b67a674fdfce5 build: number: 0 rpaths: @@ -19,12 +19,12 @@ build: noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' - r-base run: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-mouse.db0/post-link.sh b/recipes/bioconductor-mouse.db0/post-link.sh index e2584ea7c7c19..4e63c782f8578 100644 --- a/recipes/bioconductor-mouse.db0/post-link.sh +++ b/recipes/bioconductor-mouse.db0/post-link.sh @@ -1,11 +1,11 @@ #!/bin/bash -FN="mouse.db0_3.7.1.tar.gz" +FN="mouse.db0_3.8.2.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/mouse.db0_3.7.1.tar.gz" - "https://bioarchive.galaxyproject.org/mouse.db0_3.7.1.tar.gz" - "https://depot.galaxyproject.org/software/bioconductor-mouse.db0/bioconductor-mouse.db0_3.7.1_src_all.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/mouse.db0_3.8.2.tar.gz" + "https://bioarchive.galaxyproject.org/mouse.db0_3.8.2.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-mouse.db0/bioconductor-mouse.db0_3.8.2_src_all.tar.gz" ) -MD5="01237a7808395a578f72063603b6db98" +MD5="1927a435523cfdf1a94b67a674fdfce5" # Use a staging area in the conda dir rather than temp dirs, both to avoid # permission issues as well as to have things downloaded in a predictable @@ -16,7 +16,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-mouse4302.db/meta.yaml b/recipes/bioconductor-mouse4302.db/meta.yaml index f0709c398fa4e..3019d93ce383a 100644 --- a/recipes/bioconductor-mouse4302.db/meta.yaml +++ b/recipes/bioconductor-mouse4302.db/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.2.3" %} {% set name = "mouse4302.db" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -12,7 +12,7 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: f959fad0072a265d04a8851db1deed74 build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ @@ -20,14 +20,14 @@ build: # Suggests: DBI, annotate, RUnit requirements: host: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' - - 'bioconductor-org.mm.eg.db >=3.7.0,<3.8.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' + - 'bioconductor-org.mm.eg.db >=3.8.0,<3.9.0' - r-base run: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' - - 'bioconductor-org.mm.eg.db >=3.7.0,<3.8.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' + - 'bioconductor-org.mm.eg.db >=3.8.0,<3.9.0' - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-mouse4302.db/post-link.sh b/recipes/bioconductor-mouse4302.db/post-link.sh index 0852b25a0754a..08317a0a61f21 100644 --- a/recipes/bioconductor-mouse4302.db/post-link.sh +++ b/recipes/bioconductor-mouse4302.db/post-link.sh @@ -1,9 +1,10 @@ #!/bin/bash FN="mouse4302.db_3.2.3.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/mouse4302.db_3.2.3.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/mouse4302.db_3.2.3.tar.gz" "https://bioarchive.galaxyproject.org/mouse4302.db_3.2.3.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-mouse4302.db/bioconductor-mouse4302.db_3.2.3_src_all.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-mouse4302.db/bioconductor-mouse4302.db_3.2.3_src_all.tar.gz" ) MD5="f959fad0072a265d04a8851db1deed74" @@ -16,7 +17,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-mouse4302barcodevecs/meta.yaml b/recipes/bioconductor-mouse4302barcodevecs/meta.yaml index 93d3882df8639..b4679920a31f3 100644 --- a/recipes/bioconductor-mouse4302barcodevecs/meta.yaml +++ b/recipes/bioconductor-mouse4302barcodevecs/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.20.0" %} +{% set version = "1.22.0" %} {% set name = "mouse4302barcodevecs" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 01aade84e4b3b235cfe37e825c8fe171 + md5: 8d80293e4fa8d95431c9e1ccba298433 build: number: 0 rpaths: @@ -22,7 +22,7 @@ requirements: - r-base run: - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-mouse4302barcodevecs/post-link.sh b/recipes/bioconductor-mouse4302barcodevecs/post-link.sh index e80b116aeb639..2235c32cd2673 100644 --- a/recipes/bioconductor-mouse4302barcodevecs/post-link.sh +++ b/recipes/bioconductor-mouse4302barcodevecs/post-link.sh @@ -1,11 +1,11 @@ #!/bin/bash -FN="mouse4302barcodevecs_1.20.0.tar.gz" +FN="mouse4302barcodevecs_1.22.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/experiment/src/contrib/mouse4302barcodevecs_1.20.0.tar.gz" - "https://bioarchive.galaxyproject.org/mouse4302barcodevecs_1.20.0.tar.gz" - "https://depot.galaxyproject.org/software/bioconductor-mouse4302barcodevecs/bioconductor-mouse4302barcodevecs_1.20.0_src_all.tar.gz" + "https://bioconductor.org/packages/3.9/data/experiment/src/contrib/mouse4302barcodevecs_1.22.0.tar.gz" + "https://bioarchive.galaxyproject.org/mouse4302barcodevecs_1.22.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-mouse4302barcodevecs/bioconductor-mouse4302barcodevecs_1.22.0_src_all.tar.gz" ) -MD5="01aade84e4b3b235cfe37e825c8fe171" +MD5="8d80293e4fa8d95431c9e1ccba298433" # Use a staging area in the conda dir rather than temp dirs, both to avoid # permission issues as well as to have things downloaded in a predictable @@ -16,7 +16,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-mouse4302cdf/meta.yaml b/recipes/bioconductor-mouse4302cdf/meta.yaml index fcee012a14516..5ca6290ec18d0 100644 --- a/recipes/bioconductor-mouse4302cdf/meta.yaml +++ b/recipes/bioconductor-mouse4302cdf/meta.yaml @@ -1,6 +1,6 @@ {% set version = "2.18.0" %} {% set name = "mouse4302cdf" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -12,19 +12,19 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: bda3463613f958de35c58777db05cec2 build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' - r-base run: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-mouse4302cdf/post-link.sh b/recipes/bioconductor-mouse4302cdf/post-link.sh index 99eeee2fd894e..da876cf5d9fd0 100644 --- a/recipes/bioconductor-mouse4302cdf/post-link.sh +++ b/recipes/bioconductor-mouse4302cdf/post-link.sh @@ -1,9 +1,10 @@ #!/bin/bash FN="mouse4302cdf_2.18.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/mouse4302cdf_2.18.0.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/mouse4302cdf_2.18.0.tar.gz" "https://bioarchive.galaxyproject.org/mouse4302cdf_2.18.0.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-mouse4302cdf/bioconductor-mouse4302cdf_2.18.0_src_all.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-mouse4302cdf/bioconductor-mouse4302cdf_2.18.0_src_all.tar.gz" ) MD5="bda3463613f958de35c58777db05cec2" @@ -16,7 +17,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-mouse4302frmavecs/meta.yaml b/recipes/bioconductor-mouse4302frmavecs/meta.yaml index d835d5bdc5f64..f622f08eab143 100644 --- a/recipes/bioconductor-mouse4302frmavecs/meta.yaml +++ b/recipes/bioconductor-mouse4302frmavecs/meta.yaml @@ -1,6 +1,6 @@ {% set version = "1.5.0" %} {% set name = "mouse4302frmavecs" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -12,7 +12,7 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: ec144b381abbe54d696356c1c124e372 build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ @@ -22,7 +22,7 @@ requirements: - r-base run: - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-mouse4302frmavecs/post-link.sh b/recipes/bioconductor-mouse4302frmavecs/post-link.sh index 863d0f7c6916d..a9ca57bac3aaf 100644 --- a/recipes/bioconductor-mouse4302frmavecs/post-link.sh +++ b/recipes/bioconductor-mouse4302frmavecs/post-link.sh @@ -1,9 +1,10 @@ #!/bin/bash FN="mouse4302frmavecs_1.5.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/mouse4302frmavecs_1.5.0.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/mouse4302frmavecs_1.5.0.tar.gz" "https://bioarchive.galaxyproject.org/mouse4302frmavecs_1.5.0.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-mouse4302frmavecs/bioconductor-mouse4302frmavecs_1.5.0_src_all.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-mouse4302frmavecs/bioconductor-mouse4302frmavecs_1.5.0_src_all.tar.gz" ) MD5="ec144b381abbe54d696356c1c124e372" @@ -16,7 +17,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-mouse4302probe/meta.yaml b/recipes/bioconductor-mouse4302probe/meta.yaml index 39d73c6a03754..b525389dc0a09 100644 --- a/recipes/bioconductor-mouse4302probe/meta.yaml +++ b/recipes/bioconductor-mouse4302probe/meta.yaml @@ -1,6 +1,6 @@ {% set version = "2.18.0" %} {% set name = "mouse4302probe" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -12,19 +12,19 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 7116787a7db241a545e79e419a8cfa0d build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' - r-base run: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-mouse4302probe/post-link.sh b/recipes/bioconductor-mouse4302probe/post-link.sh index bd069e23bc491..7e7789e9b69f1 100644 --- a/recipes/bioconductor-mouse4302probe/post-link.sh +++ b/recipes/bioconductor-mouse4302probe/post-link.sh @@ -1,9 +1,10 @@ #!/bin/bash FN="mouse4302probe_2.18.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/mouse4302probe_2.18.0.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/mouse4302probe_2.18.0.tar.gz" "https://bioarchive.galaxyproject.org/mouse4302probe_2.18.0.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-mouse4302probe/bioconductor-mouse4302probe_2.18.0_src_all.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-mouse4302probe/bioconductor-mouse4302probe_2.18.0_src_all.tar.gz" ) MD5="7116787a7db241a545e79e419a8cfa0d" @@ -16,7 +17,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-mouse430a2.db/meta.yaml b/recipes/bioconductor-mouse430a2.db/meta.yaml index 7640d865e93f7..2800ade47d142 100644 --- a/recipes/bioconductor-mouse430a2.db/meta.yaml +++ b/recipes/bioconductor-mouse430a2.db/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.2.3" %} {% set name = "mouse430a2.db" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -12,7 +12,7 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 4700ba9bf151277334af4fef9020a197 build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ @@ -20,14 +20,14 @@ build: # Suggests: DBI, annotate, RUnit requirements: host: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' - - 'bioconductor-org.mm.eg.db >=3.7.0,<3.8.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' + - 'bioconductor-org.mm.eg.db >=3.8.0,<3.9.0' - r-base run: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' - - 'bioconductor-org.mm.eg.db >=3.7.0,<3.8.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' + - 'bioconductor-org.mm.eg.db >=3.8.0,<3.9.0' - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-mouse430a2.db/post-link.sh b/recipes/bioconductor-mouse430a2.db/post-link.sh index 73befef803f09..b554bbb1e9a51 100644 --- a/recipes/bioconductor-mouse430a2.db/post-link.sh +++ b/recipes/bioconductor-mouse430a2.db/post-link.sh @@ -1,9 +1,10 @@ #!/bin/bash FN="mouse430a2.db_3.2.3.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/mouse430a2.db_3.2.3.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/mouse430a2.db_3.2.3.tar.gz" "https://bioarchive.galaxyproject.org/mouse430a2.db_3.2.3.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-mouse430a2.db/bioconductor-mouse430a2.db_3.2.3_src_all.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-mouse430a2.db/bioconductor-mouse430a2.db_3.2.3_src_all.tar.gz" ) MD5="4700ba9bf151277334af4fef9020a197" @@ -16,7 +17,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-mouse430a2cdf/meta.yaml b/recipes/bioconductor-mouse430a2cdf/meta.yaml index 6a80d567e9a3c..4150eb806663f 100644 --- a/recipes/bioconductor-mouse430a2cdf/meta.yaml +++ b/recipes/bioconductor-mouse430a2cdf/meta.yaml @@ -1,6 +1,6 @@ {% set version = "2.18.0" %} {% set name = "mouse430a2cdf" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -12,19 +12,19 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 1114c0415d1200bc21ad205e0830b075 build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' - r-base run: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-mouse430a2cdf/post-link.sh b/recipes/bioconductor-mouse430a2cdf/post-link.sh index 7378333ea0cf3..1b5083628577f 100644 --- a/recipes/bioconductor-mouse430a2cdf/post-link.sh +++ b/recipes/bioconductor-mouse430a2cdf/post-link.sh @@ -1,9 +1,10 @@ #!/bin/bash FN="mouse430a2cdf_2.18.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/mouse430a2cdf_2.18.0.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/mouse430a2cdf_2.18.0.tar.gz" "https://bioarchive.galaxyproject.org/mouse430a2cdf_2.18.0.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-mouse430a2cdf/bioconductor-mouse430a2cdf_2.18.0_src_all.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-mouse430a2cdf/bioconductor-mouse430a2cdf_2.18.0_src_all.tar.gz" ) MD5="1114c0415d1200bc21ad205e0830b075" @@ -16,7 +17,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-mouse430a2frmavecs/meta.yaml b/recipes/bioconductor-mouse430a2frmavecs/meta.yaml index d42e4af88070d..f374e9ab4f1d1 100644 --- a/recipes/bioconductor-mouse430a2frmavecs/meta.yaml +++ b/recipes/bioconductor-mouse430a2frmavecs/meta.yaml @@ -1,6 +1,6 @@ {% set version = "1.3.0" %} {% set name = "mouse430a2frmavecs" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -12,7 +12,7 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 3bcb8de9182bbb8de5d560748eafa0cc build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ @@ -22,7 +22,7 @@ requirements: - r-base run: - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-mouse430a2frmavecs/post-link.sh b/recipes/bioconductor-mouse430a2frmavecs/post-link.sh index e64b1d7800a14..5a3efb72aa3f3 100644 --- a/recipes/bioconductor-mouse430a2frmavecs/post-link.sh +++ b/recipes/bioconductor-mouse430a2frmavecs/post-link.sh @@ -1,9 +1,10 @@ #!/bin/bash FN="mouse430a2frmavecs_1.3.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/mouse430a2frmavecs_1.3.0.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/mouse430a2frmavecs_1.3.0.tar.gz" "https://bioarchive.galaxyproject.org/mouse430a2frmavecs_1.3.0.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-mouse430a2frmavecs/bioconductor-mouse430a2frmavecs_1.3.0_src_all.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-mouse430a2frmavecs/bioconductor-mouse430a2frmavecs_1.3.0_src_all.tar.gz" ) MD5="3bcb8de9182bbb8de5d560748eafa0cc" @@ -16,7 +17,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-mouse430a2probe/meta.yaml b/recipes/bioconductor-mouse430a2probe/meta.yaml index 43d2d0da46697..ec7a90b6c616c 100644 --- a/recipes/bioconductor-mouse430a2probe/meta.yaml +++ b/recipes/bioconductor-mouse430a2probe/meta.yaml @@ -1,6 +1,6 @@ {% set version = "2.18.0" %} {% set name = "mouse430a2probe" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -12,19 +12,19 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: bb3c34477d4fcf03a539772011118795 build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' - r-base run: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-mouse430a2probe/post-link.sh b/recipes/bioconductor-mouse430a2probe/post-link.sh index e61da4a643010..e3404116a92b2 100644 --- a/recipes/bioconductor-mouse430a2probe/post-link.sh +++ b/recipes/bioconductor-mouse430a2probe/post-link.sh @@ -1,9 +1,10 @@ #!/bin/bash FN="mouse430a2probe_2.18.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/mouse430a2probe_2.18.0.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/mouse430a2probe_2.18.0.tar.gz" "https://bioarchive.galaxyproject.org/mouse430a2probe_2.18.0.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-mouse430a2probe/bioconductor-mouse430a2probe_2.18.0_src_all.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-mouse430a2probe/bioconductor-mouse430a2probe_2.18.0_src_all.tar.gz" ) MD5="bb3c34477d4fcf03a539772011118795" @@ -16,7 +17,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-mousechrloc/meta.yaml b/recipes/bioconductor-mousechrloc/meta.yaml index cc36c7e3cd185..8924522d43f55 100644 --- a/recipes/bioconductor-mousechrloc/meta.yaml +++ b/recipes/bioconductor-mousechrloc/meta.yaml @@ -1,6 +1,6 @@ {% set version = "2.1.6" %} {% set name = "mouseCHRLOC" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -12,7 +12,7 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' md5: 0b81d7391e628cc355af4de3c5585a5f build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ @@ -22,7 +22,7 @@ requirements: - r-base run: - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-mousechrloc/post-link.sh b/recipes/bioconductor-mousechrloc/post-link.sh index 28548d0e18029..540a9d76ccdc7 100644 --- a/recipes/bioconductor-mousechrloc/post-link.sh +++ b/recipes/bioconductor-mousechrloc/post-link.sh @@ -1,9 +1,10 @@ #!/bin/bash FN="mouseCHRLOC_2.1.6.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/mouseCHRLOC_2.1.6.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/mouseCHRLOC_2.1.6.tar.gz" "https://bioarchive.galaxyproject.org/mouseCHRLOC_2.1.6.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-mousechrloc/bioconductor-mousechrloc_2.1.6_src_all.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-mousechrloc/bioconductor-mousechrloc_2.1.6_src_all.tar.gz" ) MD5="0b81d7391e628cc355af4de3c5585a5f" @@ -16,7 +17,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-mpedbarray.db/meta.yaml b/recipes/bioconductor-mpedbarray.db/meta.yaml index a2fbdacb9b27a..beb616291dd66 100644 --- a/recipes/bioconductor-mpedbarray.db/meta.yaml +++ b/recipes/bioconductor-mpedbarray.db/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.2.3" %} {% set name = "mpedbarray.db" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -12,7 +12,7 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 7bcd1fee1554b6f8844c9bf30b7db4ef build: - number: 1 + number: 2 rpaths: - lib/R/lib/ - lib/ @@ -20,14 +20,14 @@ build: # Suggests: DBI, annotate, RUnit requirements: host: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' - - 'bioconductor-org.mm.eg.db >=3.7.0,<3.8.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' + - 'bioconductor-org.mm.eg.db >=3.8.0,<3.9.0' - r-base run: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' - - 'bioconductor-org.mm.eg.db >=3.7.0,<3.8.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' + - 'bioconductor-org.mm.eg.db >=3.8.0,<3.9.0' - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-mpedbarray.db/post-link.sh b/recipes/bioconductor-mpedbarray.db/post-link.sh index bf5ef0a66b6d2..cc6ade80f1a56 100644 --- a/recipes/bioconductor-mpedbarray.db/post-link.sh +++ b/recipes/bioconductor-mpedbarray.db/post-link.sh @@ -1,9 +1,10 @@ #!/bin/bash FN="mpedbarray.db_3.2.3.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/mpedbarray.db_3.2.3.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/mpedbarray.db_3.2.3.tar.gz" "https://bioarchive.galaxyproject.org/mpedbarray.db_3.2.3.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-mpedbarray.db/bioconductor-mpedbarray.db_3.2.3_src_all.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-mpedbarray.db/bioconductor-mpedbarray.db_3.2.3_src_all.tar.gz" ) MD5="7bcd1fee1554b6f8844c9bf30b7db4ef" @@ -16,7 +17,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-mpfe/meta.yaml b/recipes/bioconductor-mpfe/meta.yaml index 102cd3d3f6feb..f891d02081636 100644 --- a/recipes/bioconductor-mpfe/meta.yaml +++ b/recipes/bioconductor-mpfe/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.18.0" %} +{% set version = "1.20.0" %} {% set name = "MPFE" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 92ff1513ce4265b001b14cf66c945c7d + md5: 3969c31ce3bb273790779fdc1be3287a build: number: 0 rpaths: diff --git a/recipes/bioconductor-mpra/meta.yaml b/recipes/bioconductor-mpra/meta.yaml index 2f7a95ec0896e..373962bacc429 100644 --- a/recipes/bioconductor-mpra/meta.yaml +++ b/recipes/bioconductor-mpra/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.4.1" %} +{% set version = "1.6.0" %} {% set name = "mpra" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: b0422b285ab02e09f2f90544ce57a1d9 + md5: 9d8851deeb9c912a5d31773f7d0a967e build: number: 0 rpaths: @@ -20,18 +20,18 @@ build: # Suggests: BiocStyle, knitr, rmarkdown, RUnit requirements: host: - - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' - - 'bioconductor-limma >=3.38.0,<3.39.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' - - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' + - 'bioconductor-biocgenerics >=0.30.0,<0.31.0' + - 'bioconductor-limma >=3.40.0,<3.41.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' + - 'bioconductor-summarizedexperiment >=1.14.0,<1.15.0' - r-base - r-scales - r-statmod run: - - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' - - 'bioconductor-limma >=3.38.0,<3.39.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' - - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' + - 'bioconductor-biocgenerics >=0.30.0,<0.31.0' + - 'bioconductor-limma >=3.40.0,<3.41.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' + - 'bioconductor-summarizedexperiment >=1.14.0,<1.15.0' - r-base - r-scales - r-statmod diff --git a/recipes/bioconductor-mpranalyze/meta.yaml b/recipes/bioconductor-mpranalyze/meta.yaml index 4d498fb3e69d8..a8eebafea2da7 100644 --- a/recipes/bioconductor-mpranalyze/meta.yaml +++ b/recipes/bioconductor-mpranalyze/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.0.0" %} +{% set version = "1.2.0" %} {% set name = "MPRAnalyze" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 541246cf352908065896374ab33e6957 + md5: b75748825f109b1050c03ed043f9fe8c build: number: 0 rpaths: @@ -20,13 +20,13 @@ build: # Suggests: knitr requirements: host: - - 'bioconductor-biocparallel >=1.16.0,<1.17.0' - - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' + - 'bioconductor-biocparallel >=1.18.0,<1.19.0' + - 'bioconductor-summarizedexperiment >=1.14.0,<1.15.0' - r-base - r-progress run: - - 'bioconductor-biocparallel >=1.16.0,<1.17.0' - - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' + - 'bioconductor-biocparallel >=1.18.0,<1.19.0' + - 'bioconductor-summarizedexperiment >=1.14.0,<1.15.0' - r-base - r-progress test: diff --git a/recipes/bioconductor-msa/meta.yaml b/recipes/bioconductor-msa/meta.yaml index ea34c454942a7..3f3483255cdc9 100644 --- a/recipes/bioconductor-msa/meta.yaml +++ b/recipes/bioconductor-msa/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.14.0" %} +{% set version = "1.16.0" %} {% set name = "msa" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 65b7ca9155681b6bb247565c249918e3 + md5: 420454bb8b4b80059f3370245f73a55e build: number: 0 rpaths: @@ -20,17 +20,17 @@ build: # SystemRequirements: GNU make requirements: host: - - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' - - 'bioconductor-biostrings >=2.50.0,<2.51.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-biocgenerics >=0.30.0,<0.31.0' + - 'bioconductor-biostrings >=2.52.0,<2.53.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' - r-base - 'r-rcpp >=0.11.1' run: - - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' - - 'bioconductor-biostrings >=2.50.0,<2.51.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-biocgenerics >=0.30.0,<0.31.0' + - 'bioconductor-biostrings >=2.52.0,<2.53.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' - r-base - 'r-rcpp >=0.11.1' build: diff --git a/recipes/bioconductor-msd16s/meta.yaml b/recipes/bioconductor-msd16s/meta.yaml index 4a5078a3b2e1e..e201a8669d7b5 100644 --- a/recipes/bioconductor-msd16s/meta.yaml +++ b/recipes/bioconductor-msd16s/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.2.0" %} +{% set version = "1.4.0" %} {% set name = "msd16s" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 1c717466a3154de3717810a24aa2620f + md5: c6671e141bf8abb9df5fa623a5702fcb build: number: 0 rpaths: @@ -19,14 +19,14 @@ build: noarch: generic requirements: host: - - 'bioconductor-biobase >=2.42.0,<2.43.0' - - 'bioconductor-metagenomeseq >=1.24.0,<1.25.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' + - 'bioconductor-metagenomeseq >=1.26.0,<1.27.0' - r-base run: - - 'bioconductor-biobase >=2.42.0,<2.43.0' - - 'bioconductor-metagenomeseq >=1.24.0,<1.25.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' + - 'bioconductor-metagenomeseq >=1.26.0,<1.27.0' - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-msd16s/post-link.sh b/recipes/bioconductor-msd16s/post-link.sh index 39eb513b68779..7882c24010599 100644 --- a/recipes/bioconductor-msd16s/post-link.sh +++ b/recipes/bioconductor-msd16s/post-link.sh @@ -1,11 +1,11 @@ #!/bin/bash -FN="msd16s_1.2.0.tar.gz" +FN="msd16s_1.4.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/experiment/src/contrib/msd16s_1.2.0.tar.gz" - "https://bioarchive.galaxyproject.org/msd16s_1.2.0.tar.gz" - "https://depot.galaxyproject.org/software/bioconductor-msd16s/bioconductor-msd16s_1.2.0_src_all.tar.gz" + "https://bioconductor.org/packages/3.9/data/experiment/src/contrib/msd16s_1.4.0.tar.gz" + "https://bioarchive.galaxyproject.org/msd16s_1.4.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-msd16s/bioconductor-msd16s_1.4.0_src_all.tar.gz" ) -MD5="1c717466a3154de3717810a24aa2620f" +MD5="c6671e141bf8abb9df5fa623a5702fcb" # Use a staging area in the conda dir rather than temp dirs, both to avoid # permission issues as well as to have things downloaded in a predictable @@ -16,7 +16,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-msdata/meta.yaml b/recipes/bioconductor-msdata/meta.yaml index d11ca6817686d..8a89cca91eee8 100644 --- a/recipes/bioconductor-msdata/meta.yaml +++ b/recipes/bioconductor-msdata/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "0.22.0" %} +{% set version = "0.24.0" %} {% set name = "msdata" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: a0a63e124df97fca391c7ae458439dad + md5: 94f80d707b61b87c498cdb7f2a40ffbb build: number: 0 rpaths: @@ -23,7 +23,7 @@ requirements: - r-base run: - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-msdata/post-link.sh b/recipes/bioconductor-msdata/post-link.sh index 544240642a162..2ec5778055392 100644 --- a/recipes/bioconductor-msdata/post-link.sh +++ b/recipes/bioconductor-msdata/post-link.sh @@ -1,11 +1,11 @@ #!/bin/bash -FN="msdata_0.22.0.tar.gz" +FN="msdata_0.24.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/experiment/src/contrib/msdata_0.22.0.tar.gz" - "https://bioarchive.galaxyproject.org/msdata_0.22.0.tar.gz" - "https://depot.galaxyproject.org/software/bioconductor-msdata/bioconductor-msdata_0.22.0_src_all.tar.gz" + "https://bioconductor.org/packages/3.9/data/experiment/src/contrib/msdata_0.24.0.tar.gz" + "https://bioarchive.galaxyproject.org/msdata_0.24.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-msdata/bioconductor-msdata_0.24.0_src_all.tar.gz" ) -MD5="a0a63e124df97fca391c7ae458439dad" +MD5="94f80d707b61b87c498cdb7f2a40ffbb" # Use a staging area in the conda dir rather than temp dirs, both to avoid # permission issues as well as to have things downloaded in a predictable @@ -16,7 +16,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-msgbsr/meta.yaml b/recipes/bioconductor-msgbsr/meta.yaml index 471765203c1f7..f5588150bc39b 100644 --- a/recipes/bioconductor-msgbsr/meta.yaml +++ b/recipes/bioconductor-msgbsr/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.6.0" %} +{% set version = "1.8.0" %} {% set name = "msgbsR" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: b9c5908b8e17e076243823c0f265940e + md5: f69feed2ab2a4927775f9c0eb6d3c029 build: number: 0 rpaths: @@ -20,35 +20,35 @@ build: # Suggests: roxygen2, BSgenome.Rnorvegicus.UCSC.rn6 requirements: host: - - 'bioconductor-bsgenome >=1.50.0,<1.51.0' - - 'bioconductor-easyrnaseq >=2.18.0,<2.19.0' - - 'bioconductor-edger >=3.24.0,<3.25.0' - - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' - - 'bioconductor-genomicalignments >=1.18.0,<1.19.0' - - 'bioconductor-genomicfeatures >=1.34.0,<1.35.0' - - 'bioconductor-genomicranges >=1.34.0,<1.35.0' - - 'bioconductor-ggbio >=1.30.0,<1.31.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-rsamtools >=1.34.0,<1.35.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' - - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' + - 'bioconductor-bsgenome >=1.52.0,<1.53.0' + - 'bioconductor-easyrnaseq >=2.20.0,<2.21.0' + - 'bioconductor-edger >=3.26.0,<3.27.0' + - 'bioconductor-genomeinfodb >=1.20.0,<1.21.0' + - 'bioconductor-genomicalignments >=1.20.0,<1.21.0' + - 'bioconductor-genomicfeatures >=1.36.0,<1.37.0' + - 'bioconductor-genomicranges >=1.36.0,<1.37.0' + - 'bioconductor-ggbio >=1.32.0,<1.33.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-rsamtools >=2.0.0,<2.1.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' + - 'bioconductor-summarizedexperiment >=1.14.0,<1.15.0' - r-base - r-ggplot2 - r-plyr - r-r.utils run: - - 'bioconductor-bsgenome >=1.50.0,<1.51.0' - - 'bioconductor-easyrnaseq >=2.18.0,<2.19.0' - - 'bioconductor-edger >=3.24.0,<3.25.0' - - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' - - 'bioconductor-genomicalignments >=1.18.0,<1.19.0' - - 'bioconductor-genomicfeatures >=1.34.0,<1.35.0' - - 'bioconductor-genomicranges >=1.34.0,<1.35.0' - - 'bioconductor-ggbio >=1.30.0,<1.31.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-rsamtools >=1.34.0,<1.35.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' - - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' + - 'bioconductor-bsgenome >=1.52.0,<1.53.0' + - 'bioconductor-easyrnaseq >=2.20.0,<2.21.0' + - 'bioconductor-edger >=3.26.0,<3.27.0' + - 'bioconductor-genomeinfodb >=1.20.0,<1.21.0' + - 'bioconductor-genomicalignments >=1.20.0,<1.21.0' + - 'bioconductor-genomicfeatures >=1.36.0,<1.37.0' + - 'bioconductor-genomicranges >=1.36.0,<1.37.0' + - 'bioconductor-ggbio >=1.32.0,<1.33.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-rsamtools >=2.0.0,<2.1.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' + - 'bioconductor-summarizedexperiment >=1.14.0,<1.15.0' - r-base - r-ggplot2 - r-plyr diff --git a/recipes/bioconductor-msgfgui/build.sh b/recipes/bioconductor-msgfgui/build.sh index 4a709afbd7ab4..c1d13421f5f1e 100644 --- a/recipes/bioconductor-msgfgui/build.sh +++ b/recipes/bioconductor-msgfgui/build.sh @@ -1,11 +1,11 @@ - #!/bin/bash - mv DESCRIPTION DESCRIPTION.old - grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION - mkdir -p ~/.R - echo -e "CC=$CC +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC FC=$FC -$CXX=$CXX +CXX=$CXX CXX98=$CXX CXX11=$CXX CXX14=$CXX" > ~/.R/Makevars - $R CMD INSTALL --build . \ No newline at end of file +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-msgfgui/meta.yaml b/recipes/bioconductor-msgfgui/meta.yaml index 1dc73ef28374c..454b7b29d94f0 100644 --- a/recipes/bioconductor-msgfgui/meta.yaml +++ b/recipes/bioconductor-msgfgui/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.16.1" %} +{% set version = "1.18.0" %} {% set name = "MSGFgui" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 4f7ca4e38b57cdeb850d92769e9450df + md5: 8ff04d21ba7710e2ee76534fc6915d6b build: number: 0 rpaths: @@ -20,17 +20,17 @@ build: # Suggests: knitr, testthat requirements: host: - - 'bioconductor-msgfplus >=1.16.0,<1.17.0' - - 'bioconductor-mzid >=1.20.0,<1.21.0' - - 'bioconductor-mzr >=2.16.0,<2.17.0' + - 'bioconductor-msgfplus >=1.18.0,<1.19.0' + - 'bioconductor-mzid >=1.22.0,<1.23.0' + - 'bioconductor-mzr >=2.18.0,<2.19.0' - r-base - r-shiny - 'r-shinyfiles >=0.4.0' - r-xlsx run: - - 'bioconductor-msgfplus >=1.16.0,<1.17.0' - - 'bioconductor-mzid >=1.20.0,<1.21.0' - - 'bioconductor-mzr >=2.16.0,<2.17.0' + - 'bioconductor-msgfplus >=1.18.0,<1.19.0' + - 'bioconductor-mzid >=1.22.0,<1.23.0' + - 'bioconductor-mzr >=2.18.0,<2.19.0' - r-base - r-shiny - 'r-shinyfiles >=0.4.0' diff --git a/recipes/bioconductor-msgfplus/build.sh b/recipes/bioconductor-msgfplus/build.sh index 5ea71a1203cac..c1d13421f5f1e 100644 --- a/recipes/bioconductor-msgfplus/build.sh +++ b/recipes/bioconductor-msgfplus/build.sh @@ -8,4 +8,4 @@ CXX=$CXX CXX98=$CXX CXX11=$CXX CXX14=$CXX" > ~/.R/Makevars -$R CMD INSTALL --build . +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-msgfplus/meta.yaml b/recipes/bioconductor-msgfplus/meta.yaml index 07d3e4fa40b2c..5d8434aa37e0b 100644 --- a/recipes/bioconductor-msgfplus/meta.yaml +++ b/recipes/bioconductor-msgfplus/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.16.1" %} +{% set version = "1.18.0" %} {% set name = "MSGFplus" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,9 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 7e4934f61b71a759f7c9dadfd3398990 - patches: - - patch + md5: d05568404d2517ffef6c498d6b559d53 build: number: 0 rpaths: @@ -23,17 +21,15 @@ build: # SystemRequirements: Java (>= 1.7) requirements: host: - - 'bioconductor-mzid >=1.20.0,<1.21.0' - - 'bioconductor-protgenerics >=1.14.0,<1.15.0' + - 'bioconductor-mzid >=1.22.0,<1.23.0' + - 'bioconductor-protgenerics >=1.16.0,<1.17.0' - r-base - - r-stringr - - openjdk + - openjdk 8.* run: - - 'bioconductor-mzid >=1.20.0,<1.21.0' - - 'bioconductor-protgenerics >=1.14.0,<1.15.0' + - 'bioconductor-mzid >=1.22.0,<1.23.0' + - 'bioconductor-protgenerics >=1.16.0,<1.17.0' - r-base - - r-stringr - - openjdk + - openjdk 8.* test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-msmb/meta.yaml b/recipes/bioconductor-msmb/meta.yaml new file mode 100644 index 0000000000000..039d2d002d938 --- /dev/null +++ b/recipes/bioconductor-msmb/meta.yaml @@ -0,0 +1,34 @@ +{% set version = "1.2.0" %} +{% set name = "MSMB" %} +{% set bioc = "3.9" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: 8898fad9df534a2d3de0af0c74a5dfc5 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: knitr, BiocStyle +requirements: + host: + - r-base + run: + - r-base + - curl +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html' + license: LGPL + summary: 'Data sets for the book ''Modern Statistics for Modern Biology'', S.P. Holmes and W. Huber.' + diff --git a/recipes/bioconductor-msmb/post-link.sh b/recipes/bioconductor-msmb/post-link.sh new file mode 100644 index 0000000000000..0992c33a4ab43 --- /dev/null +++ b/recipes/bioconductor-msmb/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="MSMB_1.2.0.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.9/data/experiment/src/contrib/MSMB_1.2.0.tar.gz" + "https://bioarchive.galaxyproject.org/MSMB_1.2.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-msmb/bioconductor-msmb_1.2.0_src_all.tar.gz" +) +MD5="8898fad9df534a2d3de0af0c74a5dfc5" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + curl $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-msmb/pre-unlink.sh b/recipes/bioconductor-msmb/pre-unlink.sh new file mode 100644 index 0000000000000..1ad7945ba0e69 --- /dev/null +++ b/recipes/bioconductor-msmb/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ MSMB diff --git a/recipes/bioconductor-msmseda/meta.yaml b/recipes/bioconductor-msmseda/meta.yaml index 95d7bb4568111..b65e231a32e6c 100644 --- a/recipes/bioconductor-msmseda/meta.yaml +++ b/recipes/bioconductor-msmseda/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.20.0" %} +{% set version = "1.22.0" %} {% set name = "msmsEDA" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: ee7217c0d5ab5172234cf644ff61dad4 + md5: aa3ccb1fd5a87df729da090d5ee9b7f4 build: number: 0 rpaths: @@ -19,13 +19,13 @@ build: noarch: generic requirements: host: - - 'bioconductor-msnbase >=2.8.0,<2.9.0' + - 'bioconductor-msnbase >=2.10.0,<2.11.0' - r-base - r-gplots - r-mass - r-rcolorbrewer run: - - 'bioconductor-msnbase >=2.8.0,<2.9.0' + - 'bioconductor-msnbase >=2.10.0,<2.11.0' - r-base - r-gplots - r-mass diff --git a/recipes/bioconductor-msmstests/meta.yaml b/recipes/bioconductor-msmstests/meta.yaml index 01061c5c4306c..4ddf88c08cc6a 100644 --- a/recipes/bioconductor-msmstests/meta.yaml +++ b/recipes/bioconductor-msmstests/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.20.1" %} +{% set version = "1.22.0" %} {% set name = "msmsTests" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 2b38c323def13d0e97cc178d25ffa300 + md5: cbc1d71ad96f24c31683d8f2a4518d15 build: number: 0 rpaths: @@ -19,16 +19,16 @@ build: noarch: generic requirements: host: - - 'bioconductor-edger >=3.24.0,<3.25.0' - - 'bioconductor-msmseda >=1.20.0,<1.21.0' - - 'bioconductor-msnbase >=2.8.0,<2.9.0' - - 'bioconductor-qvalue >=2.14.0,<2.15.0' + - 'bioconductor-edger >=3.26.0,<3.27.0' + - 'bioconductor-msmseda >=1.22.0,<1.23.0' + - 'bioconductor-msnbase >=2.10.0,<2.11.0' + - 'bioconductor-qvalue >=2.16.0,<2.17.0' - r-base run: - - 'bioconductor-edger >=3.24.0,<3.25.0' - - 'bioconductor-msmseda >=1.20.0,<1.21.0' - - 'bioconductor-msnbase >=2.8.0,<2.9.0' - - 'bioconductor-qvalue >=2.14.0,<2.15.0' + - 'bioconductor-edger >=3.26.0,<3.27.0' + - 'bioconductor-msmseda >=1.22.0,<1.23.0' + - 'bioconductor-msnbase >=2.10.0,<2.11.0' + - 'bioconductor-qvalue >=2.16.0,<2.17.0' - r-base test: commands: diff --git a/recipes/bioconductor-msnbase/meta.yaml b/recipes/bioconductor-msnbase/meta.yaml index 82fe152133455..91a1ae2304e76 100644 --- a/recipes/bioconductor-msnbase/meta.yaml +++ b/recipes/bioconductor-msnbase/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "2.8.3" %} +{% set version = "2.10.0" %} {% set name = "MSnbase" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: 22917bc7b6c0babb4251f374dff48553f7868c7eebbb4257bdcec2ebd76981ce + md5: d34329ccde067334a4a729ae0d72dee5 build: number: 0 rpaths: @@ -19,19 +19,19 @@ build: # Suggests: testthat, pryr, gridExtra, microbenchmark, zoo, knitr (>= 1.1.0), rols, Rdisop, pRoloc, pRolocdata (>= 1.7.1), msdata (>= 0.19.3), roxygen2, rgl, rpx, AnnotationHub, BiocStyle (>= 2.5.19), rmarkdown, imputeLCMD, norm, gplots, shiny, magrittr, SummarizedExperiment requirements: host: - - 'bioconductor-affy >=1.60.0,<1.61.0' - - 'bioconductor-biobase >=2.42.0,<2.43.0' - - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' - - 'bioconductor-biocparallel >=1.16.0,<1.17.0' - - 'bioconductor-impute >=1.56.0,<1.57.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-mzid >=1.20.0,<1.21.0' - - 'bioconductor-mzr >=2.16.0,<2.17.0' - - 'bioconductor-pcamethods >=1.74.0,<1.75.0' - - 'bioconductor-preprocesscore >=1.44.0,<1.45.0' - - 'bioconductor-protgenerics >=1.14.0,<1.15.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' - - 'bioconductor-vsn >=3.50.0,<3.51.0' + - 'bioconductor-affy >=1.62.0,<1.63.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' + - 'bioconductor-biocgenerics >=0.30.0,<0.31.0' + - 'bioconductor-biocparallel >=1.18.0,<1.19.0' + - 'bioconductor-impute >=1.58.0,<1.59.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-mzid >=1.22.0,<1.23.0' + - 'bioconductor-mzr >=2.18.0,<2.19.0' + - 'bioconductor-pcamethods >=1.76.0,<1.77.0' + - 'bioconductor-preprocesscore >=1.46.0,<1.47.0' + - 'bioconductor-protgenerics >=1.16.0,<1.17.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' + - 'bioconductor-vsn >=3.52.0,<3.53.0' - r-base - r-digest - r-ggplot2 @@ -43,19 +43,19 @@ requirements: - r-scales - r-xml run: - - 'bioconductor-affy >=1.60.0,<1.61.0' - - 'bioconductor-biobase >=2.42.0,<2.43.0' - - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' - - 'bioconductor-biocparallel >=1.16.0,<1.17.0' - - 'bioconductor-impute >=1.56.0,<1.57.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-mzid >=1.20.0,<1.21.0' - - 'bioconductor-mzr >=2.16.0,<2.17.0' - - 'bioconductor-pcamethods >=1.74.0,<1.75.0' - - 'bioconductor-preprocesscore >=1.44.0,<1.45.0' - - 'bioconductor-protgenerics >=1.14.0,<1.15.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' - - 'bioconductor-vsn >=3.50.0,<3.51.0' + - 'bioconductor-affy >=1.62.0,<1.63.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' + - 'bioconductor-biocgenerics >=0.30.0,<0.31.0' + - 'bioconductor-biocparallel >=1.18.0,<1.19.0' + - 'bioconductor-impute >=1.58.0,<1.59.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-mzid >=1.22.0,<1.23.0' + - 'bioconductor-mzr >=2.18.0,<2.19.0' + - 'bioconductor-pcamethods >=1.76.0,<1.77.0' + - 'bioconductor-preprocesscore >=1.46.0,<1.47.0' + - 'bioconductor-protgenerics >=1.16.0,<1.17.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' + - 'bioconductor-vsn >=3.52.0,<3.53.0' - r-base - r-digest - r-ggplot2 diff --git a/recipes/bioconductor-msnid/meta.yaml b/recipes/bioconductor-msnid/meta.yaml index 6f4d0c82cc893..c0b379d502b1f 100644 --- a/recipes/bioconductor-msnid/meta.yaml +++ b/recipes/bioconductor-msnid/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.16.1" %} +{% set version = "1.18.0" %} {% set name = "MSnID" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 6ed6ba769c2e517b3bda627fa3f759ee + md5: a6c34153f93ba9c3120ca6df1e38deec build: number: 0 rpaths: @@ -19,11 +19,11 @@ build: # Suggests: BiocStyle, msmsTests, ggplot2, RUnit, BiocGenerics requirements: host: - - 'bioconductor-biobase >=2.42.0,<2.43.0' - - 'bioconductor-msnbase >=2.8.0,<2.9.0' - - 'bioconductor-mzid >=1.20.0,<1.21.0' - - 'bioconductor-mzr >=2.16.0,<2.17.0' - - 'bioconductor-protgenerics >=1.14.0,<1.15.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' + - 'bioconductor-msnbase >=2.10.0,<2.11.0' + - 'bioconductor-mzid >=1.22.0,<1.23.0' + - 'bioconductor-mzr >=2.18.0,<2.19.0' + - 'bioconductor-protgenerics >=1.16.0,<1.17.0' - r-base - r-data.table - r-doparallel @@ -34,11 +34,11 @@ requirements: - r-rcpp - r-reshape2 run: - - 'bioconductor-biobase >=2.42.0,<2.43.0' - - 'bioconductor-msnbase >=2.8.0,<2.9.0' - - 'bioconductor-mzid >=1.20.0,<1.21.0' - - 'bioconductor-mzr >=2.16.0,<2.17.0' - - 'bioconductor-protgenerics >=1.14.0,<1.15.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' + - 'bioconductor-msnbase >=2.10.0,<2.11.0' + - 'bioconductor-mzid >=1.22.0,<1.23.0' + - 'bioconductor-mzr >=2.18.0,<2.19.0' + - 'bioconductor-protgenerics >=1.16.0,<1.17.0' - r-base - r-data.table - r-doparallel diff --git a/recipes/bioconductor-mspurity/meta.yaml b/recipes/bioconductor-mspurity/meta.yaml index 8e0100e630cda..0efa2d95609eb 100644 --- a/recipes/bioconductor-mspurity/meta.yaml +++ b/recipes/bioconductor-mspurity/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.8.0" %} +{% set version = "1.10.0" %} {% set name = "msPurity" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 3074b76fb2b1feb6057eefb1f0d08375 + md5: 3c75ae8d5c3437d5193646273b393b3c build: number: 0 rpaths: @@ -19,31 +19,43 @@ build: # Suggests: testthat, xcms, BiocStyle, knitr, rmarkdown, msPurityData, CAMERA requirements: host: - - 'bioconductor-mzr >=2.16.0,<2.17.0' + - 'bioconductor-keggrest >=1.24.0,<1.25.0' + - 'bioconductor-mzr >=2.18.0,<2.19.0' - r-base - r-dbi + - r-dbplyr - r-dosnow + - r-dplyr - r-fastcluster - r-foreach - r-ggplot2 + - r-jsonlite + - r-magrittr - r-plyr - r-rcpp - r-reshape2 - r-rsqlite - r-stringr + - r-uuid run: - - 'bioconductor-mzr >=2.16.0,<2.17.0' + - 'bioconductor-keggrest >=1.24.0,<1.25.0' + - 'bioconductor-mzr >=2.18.0,<2.19.0' - r-base - r-dbi + - r-dbplyr - r-dosnow + - r-dplyr - r-fastcluster - r-foreach - r-ggplot2 + - r-jsonlite + - r-magrittr - r-plyr - r-rcpp - r-reshape2 - r-rsqlite - r-stringr + - r-uuid build: - {{ compiler('c') }} - {{ compiler('cxx') }} @@ -53,7 +65,7 @@ test: about: home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: 'GPL (>= 2)' - summary: 'Assess the contribution of the targeted precursor in fragmentation acquired or anticipated isolation windows using a metric called "precursor purity". Also provides simple processing steps (averaging, filtering, blank subtraction, etc) for DI-MS data. Works for both LC-MS(/MS) and DI-MS(/MS) data. Spectral matching of fragmentation spectra can also be run against a SQLite database of library spectra.' + summary: 'msPurity R package was developed to: 1) Assess the spectral quality of fragmentation spectra by evaluating the "precursor ion purity". 2) Process fragmentation spectra. 3) Perform spectral matching. What is precursor ion purity? -What we call "Precursor ion purity" is a measure of the contribution of a selected precursor peak in an isolation window used for fragmentation. The simple calculation involves dividing the intensity of the selected precursor peak by the total intensity of the isolation window. When assessing MS/MS spectra this calculation is done before and after the MS/MS scan of interest and the purity is interpolated at the recorded time of the MS/MS acquisition. Additionally, isotopic peaks can be removed, low abundance peaks are removed that are thought to have limited contribution to the resulting MS/MS spectra and the isolation efficiency of the mass spectrometer can be used to normalise the intensities used for the calculation.' extra: identifiers: - biotools:mspurity diff --git a/recipes/bioconductor-mspuritydata/meta.yaml b/recipes/bioconductor-mspuritydata/meta.yaml index 99058fedf2f10..6a48b6b83c46d 100644 --- a/recipes/bioconductor-mspuritydata/meta.yaml +++ b/recipes/bioconductor-mspuritydata/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.10.0" %} +{% set version = "1.12.0" %} {% set name = "msPurityData" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 4425b2e32df130a6cdd51cf1647ed17a + md5: ae6f756fe49c343dac284309d67b26ac build: number: 0 rpaths: @@ -23,7 +23,7 @@ requirements: - r-base run: - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-mspuritydata/post-link.sh b/recipes/bioconductor-mspuritydata/post-link.sh index ca72bc030662a..04ffd5dd6ae67 100644 --- a/recipes/bioconductor-mspuritydata/post-link.sh +++ b/recipes/bioconductor-mspuritydata/post-link.sh @@ -1,11 +1,11 @@ #!/bin/bash -FN="msPurityData_1.10.0.tar.gz" +FN="msPurityData_1.12.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/experiment/src/contrib/msPurityData_1.10.0.tar.gz" - "https://bioarchive.galaxyproject.org/msPurityData_1.10.0.tar.gz" - "https://depot.galaxyproject.org/software/bioconductor-mspuritydata/bioconductor-mspuritydata_1.10.0_src_all.tar.gz" + "https://bioconductor.org/packages/3.9/data/experiment/src/contrib/msPurityData_1.12.0.tar.gz" + "https://bioarchive.galaxyproject.org/msPurityData_1.12.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-mspuritydata/bioconductor-mspuritydata_1.12.0_src_all.tar.gz" ) -MD5="4425b2e32df130a6cdd51cf1647ed17a" +MD5="ae6f756fe49c343dac284309d67b26ac" # Use a staging area in the conda dir rather than temp dirs, both to avoid # permission issues as well as to have things downloaded in a predictable @@ -16,7 +16,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-msqc1/meta.yaml b/recipes/bioconductor-msqc1/meta.yaml index fc57bba2f17f8..2ab461f66c8d1 100644 --- a/recipes/bioconductor-msqc1/meta.yaml +++ b/recipes/bioconductor-msqc1/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.10.0" %} +{% set version = "1.12.0" %} {% set name = "msqc1" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 9c2ac1fa46c8e7b1baa7e503c5c8d3b3 + md5: ceb2ef3c5998e786e3bc8233b0d2724f build: number: 0 rpaths: @@ -25,7 +25,7 @@ requirements: run: - r-base - r-lattice - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-msqc1/post-link.sh b/recipes/bioconductor-msqc1/post-link.sh index f3bb24d3734dc..28e844927e98f 100644 --- a/recipes/bioconductor-msqc1/post-link.sh +++ b/recipes/bioconductor-msqc1/post-link.sh @@ -1,11 +1,11 @@ #!/bin/bash -FN="msqc1_1.10.0.tar.gz" +FN="msqc1_1.12.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/experiment/src/contrib/msqc1_1.10.0.tar.gz" - "https://bioarchive.galaxyproject.org/msqc1_1.10.0.tar.gz" - "https://depot.galaxyproject.org/software/bioconductor-msqc1/bioconductor-msqc1_1.10.0_src_all.tar.gz" + "https://bioconductor.org/packages/3.9/data/experiment/src/contrib/msqc1_1.12.0.tar.gz" + "https://bioarchive.galaxyproject.org/msqc1_1.12.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-msqc1/bioconductor-msqc1_1.12.0_src_all.tar.gz" ) -MD5="9c2ac1fa46c8e7b1baa7e503c5c8d3b3" +MD5="ceb2ef3c5998e786e3bc8233b0d2724f" # Use a staging area in the conda dir rather than temp dirs, both to avoid # permission issues as well as to have things downloaded in a predictable @@ -16,7 +16,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-msstats/meta.yaml b/recipes/bioconductor-msstats/meta.yaml index 9486253893e51..c94ce8446e95e 100644 --- a/recipes/bioconductor-msstats/meta.yaml +++ b/recipes/bioconductor-msstats/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "3.14.1" %} +{% set version = "3.16.0" %} {% set name = "MSstats" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: ea3ae8006b39aa5e0662ea6b270b9653 + md5: 7622d57810ca63c20b224a69b4b62f19 build: number: 0 rpaths: @@ -20,10 +20,11 @@ build: # Suggests: BiocStyle, knitr, rmarkdown, MSstatsBioData requirements: host: - - 'bioconductor-limma >=3.38.0,<3.39.0' - - 'bioconductor-marray >=1.60.0,<1.61.0' - - 'bioconductor-preprocesscore >=1.44.0,<1.45.0' + - 'bioconductor-limma >=3.40.0,<3.41.0' + - 'bioconductor-marray >=1.62.0,<1.63.0' + - 'bioconductor-preprocesscore >=1.46.0,<1.47.0' - r-base + - r-broom - r-data.table - r-dosnow - r-dplyr @@ -34,17 +35,20 @@ requirements: - r-lme4 - r-mass - r-minpack.lm + - r-purrr - r-randomforest - r-reshape2 - r-snow + - r-statmod - r-stringr - r-survival - r-tidyr run: - - 'bioconductor-limma >=3.38.0,<3.39.0' - - 'bioconductor-marray >=1.60.0,<1.61.0' - - 'bioconductor-preprocesscore >=1.44.0,<1.45.0' + - 'bioconductor-limma >=3.40.0,<3.41.0' + - 'bioconductor-marray >=1.62.0,<1.63.0' + - 'bioconductor-preprocesscore >=1.46.0,<1.47.0' - r-base + - r-broom - r-data.table - r-dosnow - r-dplyr @@ -55,9 +59,11 @@ requirements: - r-lme4 - r-mass - r-minpack.lm + - r-purrr - r-randomforest - r-reshape2 - r-snow + - r-statmod - r-stringr - r-survival - r-tidyr diff --git a/recipes/bioconductor-msstatsbiodata/meta.yaml b/recipes/bioconductor-msstatsbiodata/meta.yaml index 19f9ff21fbc5e..a58bbd11f4580 100644 --- a/recipes/bioconductor-msstatsbiodata/meta.yaml +++ b/recipes/bioconductor-msstatsbiodata/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.4.0" %} +{% set version = "1.6.0" %} {% set name = "MSstatsBioData" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: d6b9978157012351f0fea33b1c678296 + md5: a0a04b89a7eaee9c85a630483b296a0c build: number: 0 rpaths: @@ -23,7 +23,7 @@ requirements: - r-base run: - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-msstatsbiodata/post-link.sh b/recipes/bioconductor-msstatsbiodata/post-link.sh index 86d438d785dd8..a5adbdb16ed93 100644 --- a/recipes/bioconductor-msstatsbiodata/post-link.sh +++ b/recipes/bioconductor-msstatsbiodata/post-link.sh @@ -1,11 +1,11 @@ #!/bin/bash -FN="MSstatsBioData_1.4.0.tar.gz" +FN="MSstatsBioData_1.6.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/experiment/src/contrib/MSstatsBioData_1.4.0.tar.gz" - "https://bioarchive.galaxyproject.org/MSstatsBioData_1.4.0.tar.gz" - "https://depot.galaxyproject.org/software/bioconductor-msstatsbiodata/bioconductor-msstatsbiodata_1.4.0_src_all.tar.gz" + "https://bioconductor.org/packages/3.9/data/experiment/src/contrib/MSstatsBioData_1.6.0.tar.gz" + "https://bioarchive.galaxyproject.org/MSstatsBioData_1.6.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-msstatsbiodata/bioconductor-msstatsbiodata_1.6.0_src_all.tar.gz" ) -MD5="d6b9978157012351f0fea33b1c678296" +MD5="a0a04b89a7eaee9c85a630483b296a0c" # Use a staging area in the conda dir rather than temp dirs, both to avoid # permission issues as well as to have things downloaded in a predictable @@ -16,7 +16,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-msstatsqc/build.sh b/recipes/bioconductor-msstatsqc/build.sh index 4a709afbd7ab4..c1d13421f5f1e 100644 --- a/recipes/bioconductor-msstatsqc/build.sh +++ b/recipes/bioconductor-msstatsqc/build.sh @@ -1,11 +1,11 @@ - #!/bin/bash - mv DESCRIPTION DESCRIPTION.old - grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION - mkdir -p ~/.R - echo -e "CC=$CC +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC FC=$FC -$CXX=$CXX +CXX=$CXX CXX98=$CXX CXX11=$CXX CXX14=$CXX" > ~/.R/Makevars - $R CMD INSTALL --build . \ No newline at end of file +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-msstatsqc/meta.yaml b/recipes/bioconductor-msstatsqc/meta.yaml index 74fe29c44533e..8fc9cec788f9d 100644 --- a/recipes/bioconductor-msstatsqc/meta.yaml +++ b/recipes/bioconductor-msstatsqc/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "2.0.1" %} +{% set version = "2.2.0" %} {% set name = "MSstatsQC" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: d9b69e724760fafae32e00e8c0d544fb + md5: e73a4941dde9b2893295400a2a5a46fb build: number: 0 rpaths: @@ -20,8 +20,8 @@ build: # Suggests: knitr,rmarkdown, testthat, RforProteomics requirements: host: - - 'bioconductor-msnbase >=2.8.0,<2.9.0' - - 'bioconductor-qcmetrics >=1.20.0,<1.21.0' + - 'bioconductor-msnbase >=2.10.0,<2.11.0' + - 'bioconductor-qcmetrics >=1.22.0,<1.23.0' - r-base - r-dplyr - r-ggextra @@ -29,8 +29,8 @@ requirements: - r-plotly - r-recordlinkage run: - - 'bioconductor-msnbase >=2.8.0,<2.9.0' - - 'bioconductor-qcmetrics >=1.20.0,<1.21.0' + - 'bioconductor-msnbase >=2.10.0,<2.11.0' + - 'bioconductor-qcmetrics >=1.22.0,<1.23.0' - r-base - r-dplyr - r-ggextra diff --git a/recipes/bioconductor-msstatsqcgui/build.sh b/recipes/bioconductor-msstatsqcgui/build.sh index d4be2beab962b..c1d13421f5f1e 100644 --- a/recipes/bioconductor-msstatsqcgui/build.sh +++ b/recipes/bioconductor-msstatsqcgui/build.sh @@ -4,8 +4,8 @@ grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION mkdir -p ~/.R echo -e "CC=$CC FC=$FC -$CXX=$CXX +CXX=$CXX CXX98=$CXX CXX11=$CXX CXX14=$CXX" > ~/.R/Makevars -$R CMD INSTALL --build . +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-msstatsqcgui/meta.yaml b/recipes/bioconductor-msstatsqcgui/meta.yaml index 5fb6f823f32f4..7632ff2146f4d 100644 --- a/recipes/bioconductor-msstatsqcgui/meta.yaml +++ b/recipes/bioconductor-msstatsqcgui/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.2.1" %} +{% set version = "1.4.0" %} {% set name = "MSstatsQCgui" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: d666317e4fc2bb1e71da65368d997f83 + md5: f1b035376687e76ad64bacf1d269f15b build: number: 0 rpaths: @@ -20,7 +20,7 @@ build: # Suggests: knitr requirements: host: - - 'bioconductor-msstatsqc >=2.0.0,<2.1.0' + - 'bioconductor-msstatsqc >=2.2.0,<2.3.0' - r-base - r-dplyr - r-ggextra @@ -29,7 +29,7 @@ requirements: - r-recordlinkage - r-shiny run: - - 'bioconductor-msstatsqc >=2.0.0,<2.1.0' + - 'bioconductor-msstatsqc >=2.2.0,<2.3.0' - r-base - r-dplyr - r-ggextra diff --git a/recipes/bioconductor-msstatstmt/meta.yaml b/recipes/bioconductor-msstatstmt/meta.yaml index a926ba6722d6c..3974eba0ae689 100644 --- a/recipes/bioconductor-msstatstmt/meta.yaml +++ b/recipes/bioconductor-msstatstmt/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.1.2" %} +{% set version = "1.2.1" %} {% set name = "MSstatsTMT" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: 390f82058a247b1e92dd5f5887b0a50c86527610fab4da3e93d9314a231e5c29 + md5: 18c6b877b211c95e9a0e3e189d7eab73 build: number: 0 rpaths: @@ -20,8 +20,8 @@ build: # Suggests: BiocStyle, knitr, rmarkdown, testthat requirements: host: - - 'bioconductor-limma >=3.38.0,<3.39.0' - - 'bioconductor-msstats >=3.14.0,<3.15.0' + - 'bioconductor-limma >=3.40.0,<3.41.0' + - 'bioconductor-msstats >=3.16.0,<3.17.0' - r-base - r-data.table - r-dplyr @@ -30,10 +30,11 @@ requirements: - r-matrixstats - r-nlme - r-reshape2 + - r-statmod - r-tidyr run: - - 'bioconductor-limma >=3.38.0,<3.39.0' - - 'bioconductor-msstats >=3.14.0,<3.15.0' + - 'bioconductor-limma >=3.40.0,<3.41.0' + - 'bioconductor-msstats >=3.16.0,<3.17.0' - r-base - r-data.table - r-dplyr @@ -42,6 +43,7 @@ requirements: - r-matrixstats - r-nlme - r-reshape2 + - r-statmod - r-tidyr test: commands: diff --git a/recipes/bioconductor-mta10probeset.db/meta.yaml b/recipes/bioconductor-mta10probeset.db/meta.yaml index c699afe260d7c..e74e1fc9d82ff 100644 --- a/recipes/bioconductor-mta10probeset.db/meta.yaml +++ b/recipes/bioconductor-mta10probeset.db/meta.yaml @@ -1,6 +1,6 @@ {% set version = "8.7.0" %} {% set name = "mta10probeset.db" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -12,7 +12,7 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 80ca03d68b6c9dd51d50122039b2d8ba build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ @@ -20,14 +20,14 @@ build: # Suggests: DBI, annotate, RUnit requirements: host: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' - - 'bioconductor-org.mm.eg.db >=3.7.0,<3.8.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' + - 'bioconductor-org.mm.eg.db >=3.8.0,<3.9.0' - r-base run: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' - - 'bioconductor-org.mm.eg.db >=3.7.0,<3.8.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' + - 'bioconductor-org.mm.eg.db >=3.8.0,<3.9.0' - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-mta10probeset.db/post-link.sh b/recipes/bioconductor-mta10probeset.db/post-link.sh index d673a9f5c5012..6836f7259278c 100644 --- a/recipes/bioconductor-mta10probeset.db/post-link.sh +++ b/recipes/bioconductor-mta10probeset.db/post-link.sh @@ -1,9 +1,10 @@ #!/bin/bash FN="mta10probeset.db_8.7.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/mta10probeset.db_8.7.0.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/mta10probeset.db_8.7.0.tar.gz" "https://bioarchive.galaxyproject.org/mta10probeset.db_8.7.0.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-mta10probeset.db/bioconductor-mta10probeset.db_8.7.0_src_all.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-mta10probeset.db/bioconductor-mta10probeset.db_8.7.0_src_all.tar.gz" ) MD5="80ca03d68b6c9dd51d50122039b2d8ba" @@ -16,7 +17,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-mta10transcriptcluster.db/meta.yaml b/recipes/bioconductor-mta10transcriptcluster.db/meta.yaml index 688f5e77a0d88..002db766797ca 100644 --- a/recipes/bioconductor-mta10transcriptcluster.db/meta.yaml +++ b/recipes/bioconductor-mta10transcriptcluster.db/meta.yaml @@ -1,6 +1,6 @@ {% set version = "8.7.0" %} {% set name = "mta10transcriptcluster.db" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -12,7 +12,7 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 04cb3bf18fafd5bef3c4444d32df8bd0 build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ @@ -20,14 +20,14 @@ build: # Suggests: DBI, annotate, RUnit requirements: host: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' - - 'bioconductor-org.mm.eg.db >=3.7.0,<3.8.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' + - 'bioconductor-org.mm.eg.db >=3.8.0,<3.9.0' - r-base run: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' - - 'bioconductor-org.mm.eg.db >=3.7.0,<3.8.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' + - 'bioconductor-org.mm.eg.db >=3.8.0,<3.9.0' - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-mta10transcriptcluster.db/post-link.sh b/recipes/bioconductor-mta10transcriptcluster.db/post-link.sh index a96d57ac4a345..664e4f9c1a73c 100644 --- a/recipes/bioconductor-mta10transcriptcluster.db/post-link.sh +++ b/recipes/bioconductor-mta10transcriptcluster.db/post-link.sh @@ -1,9 +1,10 @@ #!/bin/bash FN="mta10transcriptcluster.db_8.7.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/mta10transcriptcluster.db_8.7.0.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/mta10transcriptcluster.db_8.7.0.tar.gz" "https://bioarchive.galaxyproject.org/mta10transcriptcluster.db_8.7.0.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-mta10transcriptcluster.db/bioconductor-mta10transcriptcluster.db_8.7.0_src_all.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-mta10transcriptcluster.db/bioconductor-mta10transcriptcluster.db_8.7.0_src_all.tar.gz" ) MD5="04cb3bf18fafd5bef3c4444d32df8bd0" @@ -16,7 +17,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-mtbls2/meta.yaml b/recipes/bioconductor-mtbls2/meta.yaml index 13fb95a1f81be..35a3f547726a2 100644 --- a/recipes/bioconductor-mtbls2/meta.yaml +++ b/recipes/bioconductor-mtbls2/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.12.0" %} +{% set version = "1.14.0" %} {% set name = "mtbls2" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: d5fee1a7b0b6c8511edb2f540f59997d + md5: c6b95b76c7aa21672c277100dbf75f19 build: number: 0 rpaths: @@ -23,7 +23,7 @@ requirements: - r-base run: - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-mtbls2/post-link.sh b/recipes/bioconductor-mtbls2/post-link.sh index 465aa5074d393..e6b2c3ff94f9f 100644 --- a/recipes/bioconductor-mtbls2/post-link.sh +++ b/recipes/bioconductor-mtbls2/post-link.sh @@ -1,11 +1,11 @@ #!/bin/bash -FN="mtbls2_1.12.0.tar.gz" +FN="mtbls2_1.14.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/experiment/src/contrib/mtbls2_1.12.0.tar.gz" - "https://bioarchive.galaxyproject.org/mtbls2_1.12.0.tar.gz" - "https://depot.galaxyproject.org/software/bioconductor-mtbls2/bioconductor-mtbls2_1.12.0_src_all.tar.gz" + "https://bioconductor.org/packages/3.9/data/experiment/src/contrib/mtbls2_1.14.0.tar.gz" + "https://bioarchive.galaxyproject.org/mtbls2_1.14.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-mtbls2/bioconductor-mtbls2_1.14.0_src_all.tar.gz" ) -MD5="d5fee1a7b0b6c8511edb2f540f59997d" +MD5="c6b95b76c7aa21672c277100dbf75f19" # Use a staging area in the conda dir rather than temp dirs, both to avoid # permission issues as well as to have things downloaded in a predictable @@ -16,7 +16,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-mtseeker/meta.yaml b/recipes/bioconductor-mtseeker/meta.yaml index 4069c6a2952d9..62a13ff2712b5 100644 --- a/recipes/bioconductor-mtseeker/meta.yaml +++ b/recipes/bioconductor-mtseeker/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.0.6" %} +{% set version = "1.2.0" %} {% set name = "MTseeker" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 32712fee3db29edecc7b398e555850f1 + md5: e58ce97bc0d80e4200e8830fd9d6bf1b build: number: 0 rpaths: @@ -20,44 +20,44 @@ build: # Suggests: MTseekerData, BiocStyle, rmarkdown, ggthemes, ggplot2, pkgdown, knitr, rsvg requirements: host: - - 'bioconductor-biobase >=2.42.0,<2.43.0' - - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' - - 'bioconductor-biostrings >=2.50.0,<2.51.0' - - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' - - 'bioconductor-genomicalignments >=1.18.0,<1.19.0' - - 'bioconductor-genomicfeatures >=1.34.0,<1.35.0' - - 'bioconductor-genomicranges >=1.34.0,<1.35.0' - - 'bioconductor-gmapr >=1.24.0,<1.25.0' - - 'bioconductor-homo.sapiens >=1.3.0,<1.4.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-rsamtools >=1.34.0,<1.35.0' - - 'bioconductor-rtracklayer >=1.42.0,<1.43.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' - - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' - - 'bioconductor-variantannotation >=1.28.0,<1.29.0' - - 'bioconductor-varianttools >=1.24.0,<1.25.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' + - 'bioconductor-biocgenerics >=0.30.0,<0.31.0' + - 'bioconductor-biostrings >=2.52.0,<2.53.0' + - 'bioconductor-genomeinfodb >=1.20.0,<1.21.0' + - 'bioconductor-genomicalignments >=1.20.0,<1.21.0' + - 'bioconductor-genomicfeatures >=1.36.0,<1.37.0' + - 'bioconductor-genomicranges >=1.36.0,<1.37.0' + - 'bioconductor-gmapr >=1.26.0,<1.27.0' + - 'bioconductor-homo.sapiens >=1.4.0,<1.5.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-rsamtools >=2.0.0,<2.1.0' + - 'bioconductor-rtracklayer >=1.44.0,<1.45.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' + - 'bioconductor-summarizedexperiment >=1.14.0,<1.15.0' + - 'bioconductor-variantannotation >=1.30.0,<1.31.0' + - 'bioconductor-varianttools >=1.26.0,<1.27.0' - r-base - r-circlize - r-jsonlite - r-viridis - r-xml2 run: - - 'bioconductor-biobase >=2.42.0,<2.43.0' - - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' - - 'bioconductor-biostrings >=2.50.0,<2.51.0' - - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' - - 'bioconductor-genomicalignments >=1.18.0,<1.19.0' - - 'bioconductor-genomicfeatures >=1.34.0,<1.35.0' - - 'bioconductor-genomicranges >=1.34.0,<1.35.0' - - 'bioconductor-gmapr >=1.24.0,<1.25.0' - - 'bioconductor-homo.sapiens >=1.3.0,<1.4.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-rsamtools >=1.34.0,<1.35.0' - - 'bioconductor-rtracklayer >=1.42.0,<1.43.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' - - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' - - 'bioconductor-variantannotation >=1.28.0,<1.29.0' - - 'bioconductor-varianttools >=1.24.0,<1.25.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' + - 'bioconductor-biocgenerics >=0.30.0,<0.31.0' + - 'bioconductor-biostrings >=2.52.0,<2.53.0' + - 'bioconductor-genomeinfodb >=1.20.0,<1.21.0' + - 'bioconductor-genomicalignments >=1.20.0,<1.21.0' + - 'bioconductor-genomicfeatures >=1.36.0,<1.37.0' + - 'bioconductor-genomicranges >=1.36.0,<1.37.0' + - 'bioconductor-gmapr >=1.26.0,<1.27.0' + - 'bioconductor-homo.sapiens >=1.4.0,<1.5.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-rsamtools >=2.0.0,<2.1.0' + - 'bioconductor-rtracklayer >=1.44.0,<1.45.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' + - 'bioconductor-summarizedexperiment >=1.14.0,<1.15.0' + - 'bioconductor-variantannotation >=1.30.0,<1.31.0' + - 'bioconductor-varianttools >=1.26.0,<1.27.0' - r-base - r-circlize - r-jsonlite diff --git a/recipes/bioconductor-mtseekerdata/meta.yaml b/recipes/bioconductor-mtseekerdata/meta.yaml index 45d42b269e65d..4e31a06d177ee 100644 --- a/recipes/bioconductor-mtseekerdata/meta.yaml +++ b/recipes/bioconductor-mtseekerdata/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.0.0" %} +{% set version = "1.2.0" %} {% set name = "MTseekerData" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: f5271cbb8d617a4fb35b794def24e72a + md5: f36216a2c91f9d02efbca8071367edc1 build: number: 0 rpaths: @@ -20,24 +20,24 @@ build: # Suggests: gmapR, xml2, rtracklayer requirements: host: - - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' - - 'bioconductor-genomicfeatures >=1.34.0,<1.35.0' - - 'bioconductor-genomicranges >=1.34.0,<1.35.0' - - 'bioconductor-homo.sapiens >=1.3.0,<1.4.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-mtseeker >=1.0.0,<1.1.0' - - 'bioconductor-variantannotation >=1.28.0,<1.29.0' + - 'bioconductor-genomeinfodb >=1.20.0,<1.21.0' + - 'bioconductor-genomicfeatures >=1.36.0,<1.37.0' + - 'bioconductor-genomicranges >=1.36.0,<1.37.0' + - 'bioconductor-homo.sapiens >=1.4.0,<1.5.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-mtseeker >=1.2.0,<1.3.0' + - 'bioconductor-variantannotation >=1.30.0,<1.31.0' - r-base run: - - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' - - 'bioconductor-genomicfeatures >=1.34.0,<1.35.0' - - 'bioconductor-genomicranges >=1.34.0,<1.35.0' - - 'bioconductor-homo.sapiens >=1.3.0,<1.4.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-mtseeker >=1.0.0,<1.1.0' - - 'bioconductor-variantannotation >=1.28.0,<1.29.0' + - 'bioconductor-genomeinfodb >=1.20.0,<1.21.0' + - 'bioconductor-genomicfeatures >=1.36.0,<1.37.0' + - 'bioconductor-genomicranges >=1.36.0,<1.37.0' + - 'bioconductor-homo.sapiens >=1.4.0,<1.5.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-mtseeker >=1.2.0,<1.3.0' + - 'bioconductor-variantannotation >=1.30.0,<1.31.0' - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-mtseekerdata/post-link.sh b/recipes/bioconductor-mtseekerdata/post-link.sh index 0321a9ba5bcfc..80a5895da78b3 100644 --- a/recipes/bioconductor-mtseekerdata/post-link.sh +++ b/recipes/bioconductor-mtseekerdata/post-link.sh @@ -1,11 +1,11 @@ #!/bin/bash -FN="MTseekerData_1.0.0.tar.gz" +FN="MTseekerData_1.2.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/experiment/src/contrib/MTseekerData_1.0.0.tar.gz" - "https://bioarchive.galaxyproject.org/MTseekerData_1.0.0.tar.gz" - "https://depot.galaxyproject.org/software/bioconductor-mtseekerdata/bioconductor-mtseekerdata_1.0.0_src_all.tar.gz" + "https://bioconductor.org/packages/3.9/data/experiment/src/contrib/MTseekerData_1.2.0.tar.gz" + "https://bioarchive.galaxyproject.org/MTseekerData_1.2.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-mtseekerdata/bioconductor-mtseekerdata_1.2.0_src_all.tar.gz" ) -MD5="f5271cbb8d617a4fb35b794def24e72a" +MD5="f36216a2c91f9d02efbca8071367edc1" # Use a staging area in the conda dir rather than temp dirs, both to avoid # permission issues as well as to have things downloaded in a predictable @@ -16,7 +16,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-mu11ksuba.db/meta.yaml b/recipes/bioconductor-mu11ksuba.db/meta.yaml index b71bc9de7e322..b2e9f0ea279fb 100644 --- a/recipes/bioconductor-mu11ksuba.db/meta.yaml +++ b/recipes/bioconductor-mu11ksuba.db/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.2.3" %} {% set name = "mu11ksuba.db" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -12,7 +12,7 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 2ed9098b7efa45430488d4c9f8df0750 build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ @@ -20,14 +20,14 @@ build: # Suggests: DBI, annotate, RUnit requirements: host: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' - - 'bioconductor-org.mm.eg.db >=3.7.0,<3.8.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' + - 'bioconductor-org.mm.eg.db >=3.8.0,<3.9.0' - r-base run: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' - - 'bioconductor-org.mm.eg.db >=3.7.0,<3.8.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' + - 'bioconductor-org.mm.eg.db >=3.8.0,<3.9.0' - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-mu11ksuba.db/post-link.sh b/recipes/bioconductor-mu11ksuba.db/post-link.sh index bb44543ae3955..21aa8df78e893 100644 --- a/recipes/bioconductor-mu11ksuba.db/post-link.sh +++ b/recipes/bioconductor-mu11ksuba.db/post-link.sh @@ -1,9 +1,10 @@ #!/bin/bash FN="mu11ksuba.db_3.2.3.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/mu11ksuba.db_3.2.3.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/mu11ksuba.db_3.2.3.tar.gz" "https://bioarchive.galaxyproject.org/mu11ksuba.db_3.2.3.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-mu11ksuba.db/bioconductor-mu11ksuba.db_3.2.3_src_all.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-mu11ksuba.db/bioconductor-mu11ksuba.db_3.2.3_src_all.tar.gz" ) MD5="2ed9098b7efa45430488d4c9f8df0750" @@ -16,7 +17,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-mu11ksubacdf/meta.yaml b/recipes/bioconductor-mu11ksubacdf/meta.yaml index 6ccda93ce9b3b..6ea9d9af9e663 100644 --- a/recipes/bioconductor-mu11ksubacdf/meta.yaml +++ b/recipes/bioconductor-mu11ksubacdf/meta.yaml @@ -1,6 +1,6 @@ {% set version = "2.18.0" %} {% set name = "mu11ksubacdf" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -12,19 +12,19 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 52fb8ac56435775022fb62f40efafd22 build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' - r-base run: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-mu11ksubacdf/post-link.sh b/recipes/bioconductor-mu11ksubacdf/post-link.sh index 40a8fa1b958a1..d49cad4cd1fdc 100644 --- a/recipes/bioconductor-mu11ksubacdf/post-link.sh +++ b/recipes/bioconductor-mu11ksubacdf/post-link.sh @@ -1,9 +1,10 @@ #!/bin/bash FN="mu11ksubacdf_2.18.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/mu11ksubacdf_2.18.0.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/mu11ksubacdf_2.18.0.tar.gz" "https://bioarchive.galaxyproject.org/mu11ksubacdf_2.18.0.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-mu11ksubacdf/bioconductor-mu11ksubacdf_2.18.0_src_all.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-mu11ksubacdf/bioconductor-mu11ksubacdf_2.18.0_src_all.tar.gz" ) MD5="52fb8ac56435775022fb62f40efafd22" @@ -16,7 +17,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-mu11ksubaprobe/meta.yaml b/recipes/bioconductor-mu11ksubaprobe/meta.yaml index abbadff19ee6c..ce9adf3189dfd 100644 --- a/recipes/bioconductor-mu11ksubaprobe/meta.yaml +++ b/recipes/bioconductor-mu11ksubaprobe/meta.yaml @@ -1,6 +1,6 @@ {% set version = "2.18.0" %} {% set name = "mu11ksubaprobe" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -12,19 +12,19 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 813cd0750cca6ff0cfb696b83286177e build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' - r-base run: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-mu11ksubaprobe/post-link.sh b/recipes/bioconductor-mu11ksubaprobe/post-link.sh index 52dbdf4d29ecc..ccd1f972a7332 100644 --- a/recipes/bioconductor-mu11ksubaprobe/post-link.sh +++ b/recipes/bioconductor-mu11ksubaprobe/post-link.sh @@ -1,9 +1,10 @@ #!/bin/bash FN="mu11ksubaprobe_2.18.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/mu11ksubaprobe_2.18.0.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/mu11ksubaprobe_2.18.0.tar.gz" "https://bioarchive.galaxyproject.org/mu11ksubaprobe_2.18.0.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-mu11ksubaprobe/bioconductor-mu11ksubaprobe_2.18.0_src_all.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-mu11ksubaprobe/bioconductor-mu11ksubaprobe_2.18.0_src_all.tar.gz" ) MD5="813cd0750cca6ff0cfb696b83286177e" @@ -16,7 +17,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-mu11ksubb.db/meta.yaml b/recipes/bioconductor-mu11ksubb.db/meta.yaml index 0db8583818e79..89dd8506633ec 100644 --- a/recipes/bioconductor-mu11ksubb.db/meta.yaml +++ b/recipes/bioconductor-mu11ksubb.db/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.2.3" %} {% set name = "mu11ksubb.db" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -12,7 +12,7 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 44bde347574efd353ae89f41c06ccf76 build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ @@ -20,14 +20,14 @@ build: # Suggests: DBI, annotate, RUnit requirements: host: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' - - 'bioconductor-org.mm.eg.db >=3.7.0,<3.8.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' + - 'bioconductor-org.mm.eg.db >=3.8.0,<3.9.0' - r-base run: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' - - 'bioconductor-org.mm.eg.db >=3.7.0,<3.8.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' + - 'bioconductor-org.mm.eg.db >=3.8.0,<3.9.0' - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-mu11ksubb.db/post-link.sh b/recipes/bioconductor-mu11ksubb.db/post-link.sh index c01b37610c145..b11366e30be2e 100644 --- a/recipes/bioconductor-mu11ksubb.db/post-link.sh +++ b/recipes/bioconductor-mu11ksubb.db/post-link.sh @@ -1,9 +1,10 @@ #!/bin/bash FN="mu11ksubb.db_3.2.3.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/mu11ksubb.db_3.2.3.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/mu11ksubb.db_3.2.3.tar.gz" "https://bioarchive.galaxyproject.org/mu11ksubb.db_3.2.3.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-mu11ksubb.db/bioconductor-mu11ksubb.db_3.2.3_src_all.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-mu11ksubb.db/bioconductor-mu11ksubb.db_3.2.3_src_all.tar.gz" ) MD5="44bde347574efd353ae89f41c06ccf76" @@ -16,7 +17,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-mu11ksubbcdf/meta.yaml b/recipes/bioconductor-mu11ksubbcdf/meta.yaml index 22f084d0fff32..8a1f7f22fcdbf 100644 --- a/recipes/bioconductor-mu11ksubbcdf/meta.yaml +++ b/recipes/bioconductor-mu11ksubbcdf/meta.yaml @@ -1,6 +1,6 @@ {% set version = "2.18.0" %} {% set name = "mu11ksubbcdf" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -12,19 +12,19 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: f9691ea74e19dfe57bf6cca6ed396947 build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' - r-base run: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-mu11ksubbcdf/post-link.sh b/recipes/bioconductor-mu11ksubbcdf/post-link.sh index ff17bc6af04e3..bf530e5b01379 100644 --- a/recipes/bioconductor-mu11ksubbcdf/post-link.sh +++ b/recipes/bioconductor-mu11ksubbcdf/post-link.sh @@ -1,9 +1,10 @@ #!/bin/bash FN="mu11ksubbcdf_2.18.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/mu11ksubbcdf_2.18.0.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/mu11ksubbcdf_2.18.0.tar.gz" "https://bioarchive.galaxyproject.org/mu11ksubbcdf_2.18.0.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-mu11ksubbcdf/bioconductor-mu11ksubbcdf_2.18.0_src_all.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-mu11ksubbcdf/bioconductor-mu11ksubbcdf_2.18.0_src_all.tar.gz" ) MD5="f9691ea74e19dfe57bf6cca6ed396947" @@ -16,7 +17,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-mu11ksubbprobe/meta.yaml b/recipes/bioconductor-mu11ksubbprobe/meta.yaml index 46df0e0f551ae..8a9b898d10924 100644 --- a/recipes/bioconductor-mu11ksubbprobe/meta.yaml +++ b/recipes/bioconductor-mu11ksubbprobe/meta.yaml @@ -1,6 +1,6 @@ {% set version = "2.18.0" %} {% set name = "mu11ksubbprobe" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -12,19 +12,19 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 28d162e18e4e16e3c6db47195d2ea0ac build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' - r-base run: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-mu11ksubbprobe/post-link.sh b/recipes/bioconductor-mu11ksubbprobe/post-link.sh index fecda913ffa46..396a016d7a3f2 100644 --- a/recipes/bioconductor-mu11ksubbprobe/post-link.sh +++ b/recipes/bioconductor-mu11ksubbprobe/post-link.sh @@ -1,9 +1,10 @@ #!/bin/bash FN="mu11ksubbprobe_2.18.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/mu11ksubbprobe_2.18.0.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/mu11ksubbprobe_2.18.0.tar.gz" "https://bioarchive.galaxyproject.org/mu11ksubbprobe_2.18.0.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-mu11ksubbprobe/bioconductor-mu11ksubbprobe_2.18.0_src_all.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-mu11ksubbprobe/bioconductor-mu11ksubbprobe_2.18.0_src_all.tar.gz" ) MD5="28d162e18e4e16e3c6db47195d2ea0ac" @@ -16,7 +17,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-mu15v1.db/meta.yaml b/recipes/bioconductor-mu15v1.db/meta.yaml index f7cbe3c383b7f..ee83fef898030 100644 --- a/recipes/bioconductor-mu15v1.db/meta.yaml +++ b/recipes/bioconductor-mu15v1.db/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.2.3" %} {% set name = "Mu15v1.db" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -12,7 +12,7 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' md5: e9297b5fe223b046bc65dc6ea0b4376d build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ @@ -20,14 +20,14 @@ build: # Suggests: DBI, annotate, RUnit requirements: host: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' - - 'bioconductor-org.mm.eg.db >=3.7.0,<3.8.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' + - 'bioconductor-org.mm.eg.db >=3.8.0,<3.9.0' - r-base run: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' - - 'bioconductor-org.mm.eg.db >=3.7.0,<3.8.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' + - 'bioconductor-org.mm.eg.db >=3.8.0,<3.9.0' - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-mu15v1.db/post-link.sh b/recipes/bioconductor-mu15v1.db/post-link.sh index c95fa4f398763..52046010b7070 100644 --- a/recipes/bioconductor-mu15v1.db/post-link.sh +++ b/recipes/bioconductor-mu15v1.db/post-link.sh @@ -1,9 +1,10 @@ #!/bin/bash FN="Mu15v1.db_3.2.3.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/Mu15v1.db_3.2.3.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/Mu15v1.db_3.2.3.tar.gz" "https://bioarchive.galaxyproject.org/Mu15v1.db_3.2.3.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-mu15v1.db/bioconductor-mu15v1.db_3.2.3_src_all.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-mu15v1.db/bioconductor-mu15v1.db_3.2.3_src_all.tar.gz" ) MD5="e9297b5fe223b046bc65dc6ea0b4376d" @@ -16,7 +17,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-mu19ksuba.db/meta.yaml b/recipes/bioconductor-mu19ksuba.db/meta.yaml index 0825a74f872cd..0e11c197a34c6 100644 --- a/recipes/bioconductor-mu19ksuba.db/meta.yaml +++ b/recipes/bioconductor-mu19ksuba.db/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.2.3" %} {% set name = "mu19ksuba.db" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -12,7 +12,7 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 668c92eb1b9e2367c5a69dc8d0498cca build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ @@ -20,14 +20,14 @@ build: # Suggests: DBI, annotate, RUnit requirements: host: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' - - 'bioconductor-org.mm.eg.db >=3.7.0,<3.8.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' + - 'bioconductor-org.mm.eg.db >=3.8.0,<3.9.0' - r-base run: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' - - 'bioconductor-org.mm.eg.db >=3.7.0,<3.8.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' + - 'bioconductor-org.mm.eg.db >=3.8.0,<3.9.0' - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-mu19ksuba.db/post-link.sh b/recipes/bioconductor-mu19ksuba.db/post-link.sh index 11d20d3a86d16..2619d9e2ca1d2 100644 --- a/recipes/bioconductor-mu19ksuba.db/post-link.sh +++ b/recipes/bioconductor-mu19ksuba.db/post-link.sh @@ -1,9 +1,10 @@ #!/bin/bash FN="mu19ksuba.db_3.2.3.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/mu19ksuba.db_3.2.3.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/mu19ksuba.db_3.2.3.tar.gz" "https://bioarchive.galaxyproject.org/mu19ksuba.db_3.2.3.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-mu19ksuba.db/bioconductor-mu19ksuba.db_3.2.3_src_all.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-mu19ksuba.db/bioconductor-mu19ksuba.db_3.2.3_src_all.tar.gz" ) MD5="668c92eb1b9e2367c5a69dc8d0498cca" @@ -16,7 +17,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-mu19ksubacdf/meta.yaml b/recipes/bioconductor-mu19ksubacdf/meta.yaml index 5785479903c07..446e99f9e1679 100644 --- a/recipes/bioconductor-mu19ksubacdf/meta.yaml +++ b/recipes/bioconductor-mu19ksubacdf/meta.yaml @@ -1,6 +1,6 @@ {% set version = "2.18.0" %} {% set name = "mu19ksubacdf" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -12,19 +12,19 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 83a9e7a3bac665b655786e66dbd77848 build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' - r-base run: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-mu19ksubacdf/post-link.sh b/recipes/bioconductor-mu19ksubacdf/post-link.sh index 6ba6dc32afcf3..d30391e3ab17a 100644 --- a/recipes/bioconductor-mu19ksubacdf/post-link.sh +++ b/recipes/bioconductor-mu19ksubacdf/post-link.sh @@ -1,9 +1,10 @@ #!/bin/bash FN="mu19ksubacdf_2.18.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/mu19ksubacdf_2.18.0.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/mu19ksubacdf_2.18.0.tar.gz" "https://bioarchive.galaxyproject.org/mu19ksubacdf_2.18.0.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-mu19ksubacdf/bioconductor-mu19ksubacdf_2.18.0_src_all.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-mu19ksubacdf/bioconductor-mu19ksubacdf_2.18.0_src_all.tar.gz" ) MD5="83a9e7a3bac665b655786e66dbd77848" @@ -16,7 +17,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-mu19ksubb.db/meta.yaml b/recipes/bioconductor-mu19ksubb.db/meta.yaml index 3915f7dce8eb7..7fac564b7c77d 100644 --- a/recipes/bioconductor-mu19ksubb.db/meta.yaml +++ b/recipes/bioconductor-mu19ksubb.db/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.2.3" %} {% set name = "mu19ksubb.db" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -12,7 +12,7 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 54ffae3e05d9fd79caadf51954473b93 build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ @@ -20,14 +20,14 @@ build: # Suggests: DBI, annotate, RUnit requirements: host: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' - - 'bioconductor-org.mm.eg.db >=3.7.0,<3.8.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' + - 'bioconductor-org.mm.eg.db >=3.8.0,<3.9.0' - r-base run: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' - - 'bioconductor-org.mm.eg.db >=3.7.0,<3.8.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' + - 'bioconductor-org.mm.eg.db >=3.8.0,<3.9.0' - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-mu19ksubb.db/post-link.sh b/recipes/bioconductor-mu19ksubb.db/post-link.sh index b838768053646..89d53ad1b3332 100644 --- a/recipes/bioconductor-mu19ksubb.db/post-link.sh +++ b/recipes/bioconductor-mu19ksubb.db/post-link.sh @@ -1,9 +1,10 @@ #!/bin/bash FN="mu19ksubb.db_3.2.3.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/mu19ksubb.db_3.2.3.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/mu19ksubb.db_3.2.3.tar.gz" "https://bioarchive.galaxyproject.org/mu19ksubb.db_3.2.3.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-mu19ksubb.db/bioconductor-mu19ksubb.db_3.2.3_src_all.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-mu19ksubb.db/bioconductor-mu19ksubb.db_3.2.3_src_all.tar.gz" ) MD5="54ffae3e05d9fd79caadf51954473b93" @@ -16,7 +17,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-mu19ksubbcdf/meta.yaml b/recipes/bioconductor-mu19ksubbcdf/meta.yaml index 41602cc41749e..47282f6f9ba69 100644 --- a/recipes/bioconductor-mu19ksubbcdf/meta.yaml +++ b/recipes/bioconductor-mu19ksubbcdf/meta.yaml @@ -1,6 +1,6 @@ {% set version = "2.18.0" %} {% set name = "mu19ksubbcdf" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -12,19 +12,19 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 35e5ebcb4cb51950a85c1e3622bb39f0 build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' - r-base run: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-mu19ksubbcdf/post-link.sh b/recipes/bioconductor-mu19ksubbcdf/post-link.sh index 0196a17c07402..1d38ce950977d 100644 --- a/recipes/bioconductor-mu19ksubbcdf/post-link.sh +++ b/recipes/bioconductor-mu19ksubbcdf/post-link.sh @@ -1,9 +1,10 @@ #!/bin/bash FN="mu19ksubbcdf_2.18.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/mu19ksubbcdf_2.18.0.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/mu19ksubbcdf_2.18.0.tar.gz" "https://bioarchive.galaxyproject.org/mu19ksubbcdf_2.18.0.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-mu19ksubbcdf/bioconductor-mu19ksubbcdf_2.18.0_src_all.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-mu19ksubbcdf/bioconductor-mu19ksubbcdf_2.18.0_src_all.tar.gz" ) MD5="35e5ebcb4cb51950a85c1e3622bb39f0" @@ -16,7 +17,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-mu19ksubc.db/meta.yaml b/recipes/bioconductor-mu19ksubc.db/meta.yaml index 401061ac74a50..4b26c678a1ec8 100644 --- a/recipes/bioconductor-mu19ksubc.db/meta.yaml +++ b/recipes/bioconductor-mu19ksubc.db/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.2.3" %} {% set name = "mu19ksubc.db" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -12,7 +12,7 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 0cb0abb16337b8acc9dd365f5225856c build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ @@ -20,14 +20,14 @@ build: # Suggests: DBI, annotate, RUnit requirements: host: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' - - 'bioconductor-org.mm.eg.db >=3.7.0,<3.8.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' + - 'bioconductor-org.mm.eg.db >=3.8.0,<3.9.0' - r-base run: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' - - 'bioconductor-org.mm.eg.db >=3.7.0,<3.8.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' + - 'bioconductor-org.mm.eg.db >=3.8.0,<3.9.0' - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-mu19ksubc.db/post-link.sh b/recipes/bioconductor-mu19ksubc.db/post-link.sh index 60b5e13d6973a..9d32c5aa0dade 100644 --- a/recipes/bioconductor-mu19ksubc.db/post-link.sh +++ b/recipes/bioconductor-mu19ksubc.db/post-link.sh @@ -1,9 +1,10 @@ #!/bin/bash FN="mu19ksubc.db_3.2.3.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/mu19ksubc.db_3.2.3.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/mu19ksubc.db_3.2.3.tar.gz" "https://bioarchive.galaxyproject.org/mu19ksubc.db_3.2.3.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-mu19ksubc.db/bioconductor-mu19ksubc.db_3.2.3_src_all.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-mu19ksubc.db/bioconductor-mu19ksubc.db_3.2.3_src_all.tar.gz" ) MD5="0cb0abb16337b8acc9dd365f5225856c" @@ -16,7 +17,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-mu19ksubccdf/meta.yaml b/recipes/bioconductor-mu19ksubccdf/meta.yaml index ec2a46f586ddf..137d7f8ffaa41 100644 --- a/recipes/bioconductor-mu19ksubccdf/meta.yaml +++ b/recipes/bioconductor-mu19ksubccdf/meta.yaml @@ -1,6 +1,6 @@ {% set version = "2.18.0" %} {% set name = "mu19ksubccdf" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -12,19 +12,19 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: e53ef2716f88022e5e41e2cd857fc2a3 build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' - r-base run: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-mu19ksubccdf/post-link.sh b/recipes/bioconductor-mu19ksubccdf/post-link.sh index fd12c362e9932..b0680abf19a99 100644 --- a/recipes/bioconductor-mu19ksubccdf/post-link.sh +++ b/recipes/bioconductor-mu19ksubccdf/post-link.sh @@ -1,9 +1,10 @@ #!/bin/bash FN="mu19ksubccdf_2.18.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/mu19ksubccdf_2.18.0.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/mu19ksubccdf_2.18.0.tar.gz" "https://bioarchive.galaxyproject.org/mu19ksubccdf_2.18.0.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-mu19ksubccdf/bioconductor-mu19ksubccdf_2.18.0_src_all.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-mu19ksubccdf/bioconductor-mu19ksubccdf_2.18.0_src_all.tar.gz" ) MD5="e53ef2716f88022e5e41e2cd857fc2a3" @@ -16,7 +17,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-mu22v3.db/meta.yaml b/recipes/bioconductor-mu22v3.db/meta.yaml index 1337ee591df6a..f0c24df0d90d1 100644 --- a/recipes/bioconductor-mu22v3.db/meta.yaml +++ b/recipes/bioconductor-mu22v3.db/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.2.3" %} {% set name = "Mu22v3.db" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -12,7 +12,7 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' md5: 44aaebe909be9b0108256194c55cf6fb build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ @@ -20,14 +20,14 @@ build: # Suggests: DBI, annotate, RUnit requirements: host: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' - - 'bioconductor-org.mm.eg.db >=3.7.0,<3.8.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' + - 'bioconductor-org.mm.eg.db >=3.8.0,<3.9.0' - r-base run: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' - - 'bioconductor-org.mm.eg.db >=3.7.0,<3.8.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' + - 'bioconductor-org.mm.eg.db >=3.8.0,<3.9.0' - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-mu22v3.db/post-link.sh b/recipes/bioconductor-mu22v3.db/post-link.sh index f2e531eb850d4..d7c9dad25229b 100644 --- a/recipes/bioconductor-mu22v3.db/post-link.sh +++ b/recipes/bioconductor-mu22v3.db/post-link.sh @@ -1,9 +1,10 @@ #!/bin/bash FN="Mu22v3.db_3.2.3.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/Mu22v3.db_3.2.3.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/Mu22v3.db_3.2.3.tar.gz" "https://bioarchive.galaxyproject.org/Mu22v3.db_3.2.3.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-mu22v3.db/bioconductor-mu22v3.db_3.2.3_src_all.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-mu22v3.db/bioconductor-mu22v3.db_3.2.3_src_all.tar.gz" ) MD5="44aaebe909be9b0108256194c55cf6fb" @@ -16,7 +17,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-mu6500subacdf/meta.yaml b/recipes/bioconductor-mu6500subacdf/meta.yaml index 807ab229d3cfe..0530c212a3457 100644 --- a/recipes/bioconductor-mu6500subacdf/meta.yaml +++ b/recipes/bioconductor-mu6500subacdf/meta.yaml @@ -1,6 +1,6 @@ {% set version = "2.18.0" %} {% set name = "mu6500subacdf" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -12,19 +12,19 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: e72152fc4bae307e3858160e018b7f92 build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' - r-base run: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-mu6500subacdf/post-link.sh b/recipes/bioconductor-mu6500subacdf/post-link.sh index c4349060f3bcf..2929d09358dd0 100644 --- a/recipes/bioconductor-mu6500subacdf/post-link.sh +++ b/recipes/bioconductor-mu6500subacdf/post-link.sh @@ -1,9 +1,10 @@ #!/bin/bash FN="mu6500subacdf_2.18.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/mu6500subacdf_2.18.0.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/mu6500subacdf_2.18.0.tar.gz" "https://bioarchive.galaxyproject.org/mu6500subacdf_2.18.0.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-mu6500subacdf/bioconductor-mu6500subacdf_2.18.0_src_all.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-mu6500subacdf/bioconductor-mu6500subacdf_2.18.0_src_all.tar.gz" ) MD5="e72152fc4bae307e3858160e018b7f92" @@ -16,7 +17,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-mu6500subbcdf/meta.yaml b/recipes/bioconductor-mu6500subbcdf/meta.yaml index 4d7dfdf64999d..fe15741e4594f 100644 --- a/recipes/bioconductor-mu6500subbcdf/meta.yaml +++ b/recipes/bioconductor-mu6500subbcdf/meta.yaml @@ -1,6 +1,6 @@ {% set version = "2.18.0" %} {% set name = "mu6500subbcdf" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -12,19 +12,19 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 5000bea2a018b4b6ec05cda111438bc1 build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' - r-base run: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-mu6500subbcdf/post-link.sh b/recipes/bioconductor-mu6500subbcdf/post-link.sh index 0b44f226e2ba2..453396ac623c9 100644 --- a/recipes/bioconductor-mu6500subbcdf/post-link.sh +++ b/recipes/bioconductor-mu6500subbcdf/post-link.sh @@ -1,9 +1,10 @@ #!/bin/bash FN="mu6500subbcdf_2.18.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/mu6500subbcdf_2.18.0.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/mu6500subbcdf_2.18.0.tar.gz" "https://bioarchive.galaxyproject.org/mu6500subbcdf_2.18.0.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-mu6500subbcdf/bioconductor-mu6500subbcdf_2.18.0_src_all.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-mu6500subbcdf/bioconductor-mu6500subbcdf_2.18.0_src_all.tar.gz" ) MD5="5000bea2a018b4b6ec05cda111438bc1" @@ -16,7 +17,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-mu6500subccdf/meta.yaml b/recipes/bioconductor-mu6500subccdf/meta.yaml index 8eb1988a22edb..9a46592a31729 100644 --- a/recipes/bioconductor-mu6500subccdf/meta.yaml +++ b/recipes/bioconductor-mu6500subccdf/meta.yaml @@ -1,6 +1,6 @@ {% set version = "2.18.0" %} {% set name = "mu6500subccdf" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -12,19 +12,19 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: c7cbbe6c70a0a3ae11600ad6c0e540c1 build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' - r-base run: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-mu6500subccdf/post-link.sh b/recipes/bioconductor-mu6500subccdf/post-link.sh index 27881cd4c4d77..947de1c93b90c 100644 --- a/recipes/bioconductor-mu6500subccdf/post-link.sh +++ b/recipes/bioconductor-mu6500subccdf/post-link.sh @@ -1,9 +1,10 @@ #!/bin/bash FN="mu6500subccdf_2.18.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/mu6500subccdf_2.18.0.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/mu6500subccdf_2.18.0.tar.gz" "https://bioarchive.galaxyproject.org/mu6500subccdf_2.18.0.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-mu6500subccdf/bioconductor-mu6500subccdf_2.18.0_src_all.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-mu6500subccdf/bioconductor-mu6500subccdf_2.18.0_src_all.tar.gz" ) MD5="c7cbbe6c70a0a3ae11600ad6c0e540c1" @@ -16,7 +17,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-mu6500subdcdf/meta.yaml b/recipes/bioconductor-mu6500subdcdf/meta.yaml index d44b8a0512dc9..7d7ffe4590032 100644 --- a/recipes/bioconductor-mu6500subdcdf/meta.yaml +++ b/recipes/bioconductor-mu6500subdcdf/meta.yaml @@ -1,6 +1,6 @@ {% set version = "2.18.0" %} {% set name = "mu6500subdcdf" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -12,19 +12,19 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: a614674e8bc60fefd8520dd25d45f8d0 build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' - r-base run: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-mu6500subdcdf/post-link.sh b/recipes/bioconductor-mu6500subdcdf/post-link.sh index 2cfb719da7c45..e97cd2ff15652 100644 --- a/recipes/bioconductor-mu6500subdcdf/post-link.sh +++ b/recipes/bioconductor-mu6500subdcdf/post-link.sh @@ -1,9 +1,10 @@ #!/bin/bash FN="mu6500subdcdf_2.18.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/mu6500subdcdf_2.18.0.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/mu6500subdcdf_2.18.0.tar.gz" "https://bioarchive.galaxyproject.org/mu6500subdcdf_2.18.0.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-mu6500subdcdf/bioconductor-mu6500subdcdf_2.18.0_src_all.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-mu6500subdcdf/bioconductor-mu6500subdcdf_2.18.0_src_all.tar.gz" ) MD5="a614674e8bc60fefd8520dd25d45f8d0" @@ -16,7 +17,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-mugaexampledata/meta.yaml b/recipes/bioconductor-mugaexampledata/meta.yaml index e304cd33ae9c5..dbb029c9c9947 100644 --- a/recipes/bioconductor-mugaexampledata/meta.yaml +++ b/recipes/bioconductor-mugaexampledata/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.2.0" %} +{% set version = "1.4.0" %} {% set name = "MUGAExampleData" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 66132942d0d409057570d914ec435e39 + md5: 307ef40b4459572843bf422be2dc998b build: number: 0 rpaths: @@ -22,7 +22,7 @@ requirements: - r-base run: - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-mugaexampledata/post-link.sh b/recipes/bioconductor-mugaexampledata/post-link.sh index b22b8d0c57c5b..3319790a4d7f9 100644 --- a/recipes/bioconductor-mugaexampledata/post-link.sh +++ b/recipes/bioconductor-mugaexampledata/post-link.sh @@ -1,11 +1,11 @@ #!/bin/bash -FN="MUGAExampleData_1.2.0.tar.gz" +FN="MUGAExampleData_1.4.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/experiment/src/contrib/MUGAExampleData_1.2.0.tar.gz" - "https://bioarchive.galaxyproject.org/MUGAExampleData_1.2.0.tar.gz" - "https://depot.galaxyproject.org/software/bioconductor-mugaexampledata/bioconductor-mugaexampledata_1.2.0_src_all.tar.gz" + "https://bioconductor.org/packages/3.9/data/experiment/src/contrib/MUGAExampleData_1.4.0.tar.gz" + "https://bioarchive.galaxyproject.org/MUGAExampleData_1.4.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-mugaexampledata/bioconductor-mugaexampledata_1.4.0_src_all.tar.gz" ) -MD5="66132942d0d409057570d914ec435e39" +MD5="307ef40b4459572843bf422be2dc998b" # Use a staging area in the conda dir rather than temp dirs, both to avoid # permission issues as well as to have things downloaded in a predictable @@ -16,7 +16,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-mulcom/meta.yaml b/recipes/bioconductor-mulcom/meta.yaml index 05b8c934904a5..b69a72cf4169c 100644 --- a/recipes/bioconductor-mulcom/meta.yaml +++ b/recipes/bioconductor-mulcom/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.32.0" %} +{% set version = "1.33.0" %} {% set name = "Mulcom" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 10bd7bcd1965c6f95c7d5a5c110d9c49 + md5: 210fbbf76aae7912a33b7a95a6d86314 build: number: 0 rpaths: @@ -18,11 +18,11 @@ build: - lib/ requirements: host: - - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' - r-base - r-fields run: - - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' - r-base - r-fields build: diff --git a/recipes/bioconductor-mulder2012/meta.yaml b/recipes/bioconductor-mulder2012/meta.yaml index 4886d0c732887..73e344480b364 100644 --- a/recipes/bioconductor-mulder2012/meta.yaml +++ b/recipes/bioconductor-mulder2012/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "0.22.0" %} +{% set version = "0.24.0" %} {% set name = "Mulder2012" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 4c3890e75f415c4978187fb416586b1b + md5: cf1ccb7133defdc49f889dfe9efabbf4 build: number: 0 rpaths: @@ -20,26 +20,26 @@ build: # Suggests: snow requirements: host: - - 'bioconductor-htsanalyzer >=2.34.0,<2.35.0' + - 'bioconductor-htsanalyzer >=2.36.0,<2.37.0' - 'bioconductor-kegg.db >=3.2.0,<3.3.0' - - 'bioconductor-org.hs.eg.db >=3.7.0,<3.8.0' - - 'bioconductor-panr >=1.28.0,<1.29.0' - - 'bioconductor-reder >=1.30.0,<1.31.0' + - 'bioconductor-org.hs.eg.db >=3.8.0,<3.9.0' + - 'bioconductor-panr >=1.30.0,<1.31.0' + - 'bioconductor-reder >=1.32.0,<1.33.0' - r-base - r-igraph - r-mass - r-pvclust run: - - 'bioconductor-htsanalyzer >=2.34.0,<2.35.0' + - 'bioconductor-htsanalyzer >=2.36.0,<2.37.0' - 'bioconductor-kegg.db >=3.2.0,<3.3.0' - - 'bioconductor-org.hs.eg.db >=3.7.0,<3.8.0' - - 'bioconductor-panr >=1.28.0,<1.29.0' - - 'bioconductor-reder >=1.30.0,<1.31.0' + - 'bioconductor-org.hs.eg.db >=3.8.0,<3.9.0' + - 'bioconductor-panr >=1.30.0,<1.31.0' + - 'bioconductor-reder >=1.32.0,<1.33.0' - r-base - r-igraph - r-mass - r-pvclust - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-mulder2012/post-link.sh b/recipes/bioconductor-mulder2012/post-link.sh index a99bcc19cfb11..36748308f4e7e 100644 --- a/recipes/bioconductor-mulder2012/post-link.sh +++ b/recipes/bioconductor-mulder2012/post-link.sh @@ -1,11 +1,11 @@ #!/bin/bash -FN="Mulder2012_0.22.0.tar.gz" +FN="Mulder2012_0.24.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/experiment/src/contrib/Mulder2012_0.22.0.tar.gz" - "https://bioarchive.galaxyproject.org/Mulder2012_0.22.0.tar.gz" - "https://depot.galaxyproject.org/software/bioconductor-mulder2012/bioconductor-mulder2012_0.22.0_src_all.tar.gz" + "https://bioconductor.org/packages/3.9/data/experiment/src/contrib/Mulder2012_0.24.0.tar.gz" + "https://bioarchive.galaxyproject.org/Mulder2012_0.24.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-mulder2012/bioconductor-mulder2012_0.24.0_src_all.tar.gz" ) -MD5="4c3890e75f415c4978187fb416586b1b" +MD5="cf1ccb7133defdc49f889dfe9efabbf4" # Use a staging area in the conda dir rather than temp dirs, both to avoid # permission issues as well as to have things downloaded in a predictable @@ -16,7 +16,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-multiassayexperiment/meta.yaml b/recipes/bioconductor-multiassayexperiment/meta.yaml index 153aab776fe4b..2757301c1dce5 100644 --- a/recipes/bioconductor-multiassayexperiment/meta.yaml +++ b/recipes/bioconductor-multiassayexperiment/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.8.1" %} +{% set version = "1.10.0" %} {% set name = "MultiAssayExperiment" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 5ee305237b41fa6b1b7af703bdea464a + md5: df8cc8809c7657adb497cc963ff90cf6 build: number: 0 rpaths: @@ -20,21 +20,21 @@ build: # Suggests: BiocStyle, testthat, knitr, rmarkdown, R.rsp, HDF5Array, RaggedExperiment, UpSetR, survival, survminer requirements: host: - - 'bioconductor-biobase >=2.42.0,<2.43.0' - - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' - - 'bioconductor-genomicranges >=1.34.0,<1.35.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' - - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' + - 'bioconductor-biocgenerics >=0.30.0,<0.31.0' + - 'bioconductor-genomicranges >=1.36.0,<1.37.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' + - 'bioconductor-summarizedexperiment >=1.14.0,<1.15.0' - r-base - r-tidyr run: - - 'bioconductor-biobase >=2.42.0,<2.43.0' - - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' - - 'bioconductor-genomicranges >=1.34.0,<1.35.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' - - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' + - 'bioconductor-biocgenerics >=0.30.0,<0.31.0' + - 'bioconductor-genomicranges >=1.36.0,<1.37.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' + - 'bioconductor-summarizedexperiment >=1.14.0,<1.15.0' - r-base - r-tidyr test: diff --git a/recipes/bioconductor-multiclust/meta.yaml b/recipes/bioconductor-multiclust/meta.yaml index 6b3d7f321b1e2..d2e1ab1503d96 100644 --- a/recipes/bioconductor-multiclust/meta.yaml +++ b/recipes/bioconductor-multiclust/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.12.0" %} +{% set version = "1.14.0" %} {% set name = "multiClust" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: bd8c78d8df3588f2f1cce8b43d17bdcc + md5: 0419d9b762cbf770200af0d422ffc92a build: number: 0 rpaths: @@ -20,7 +20,7 @@ build: # Suggests: knitr, gplots, RUnit, BiocGenerics, preprocessCore, Biobase, GEOquery requirements: host: - - 'bioconductor-ctc >=1.56.0,<1.57.0' + - 'bioconductor-ctc >=1.58.0,<1.59.0' - r-amap - r-base - r-cluster @@ -28,7 +28,7 @@ requirements: - r-mclust - r-survival run: - - 'bioconductor-ctc >=1.56.0,<1.57.0' + - 'bioconductor-ctc >=1.58.0,<1.59.0' - r-amap - r-base - r-cluster diff --git a/recipes/bioconductor-multidataset/meta.yaml b/recipes/bioconductor-multidataset/meta.yaml index 9465635b4ae00..2a89a04a3e55f 100644 --- a/recipes/bioconductor-multidataset/meta.yaml +++ b/recipes/bioconductor-multidataset/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.10.0" %} +{% set version = "1.12.0" %} {% set name = "MultiDataSet" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: c16950d938bd000b1ba441a751320ed4 + md5: 29d5353058ddf3b0be75aec607c05d7a build: number: 0 rpaths: @@ -20,25 +20,25 @@ build: # Suggests: brgedata, minfi, minfiData, knitr, rmarkdown, testthat, omicade4, iClusterPlus, GEOquery, MultiAssayExperiment, BiocStyle, RaggedExperiment requirements: host: - - 'bioconductor-biobase >=2.42.0,<2.43.0' - - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' - - 'bioconductor-genomicranges >=1.34.0,<1.35.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-limma >=3.38.0,<3.39.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' - - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' + - 'bioconductor-biocgenerics >=0.30.0,<0.31.0' + - 'bioconductor-genomicranges >=1.36.0,<1.37.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-limma >=3.40.0,<3.41.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' + - 'bioconductor-summarizedexperiment >=1.14.0,<1.15.0' - r-base - r-ggplot2 - r-ggrepel - r-qqman run: - - 'bioconductor-biobase >=2.42.0,<2.43.0' - - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' - - 'bioconductor-genomicranges >=1.34.0,<1.35.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-limma >=3.38.0,<3.39.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' - - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' + - 'bioconductor-biocgenerics >=0.30.0,<0.31.0' + - 'bioconductor-genomicranges >=1.36.0,<1.37.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-limma >=3.40.0,<3.41.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' + - 'bioconductor-summarizedexperiment >=1.14.0,<1.15.0' - r-base - r-ggplot2 - r-ggrepel diff --git a/recipes/bioconductor-multihiccompare/meta.yaml b/recipes/bioconductor-multihiccompare/meta.yaml index 9002a80064d3e..1af62e52cca4d 100644 --- a/recipes/bioconductor-multihiccompare/meta.yaml +++ b/recipes/bioconductor-multihiccompare/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.0.0" %} +{% set version = "1.2.0" %} {% set name = "multiHiCcompare" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,9 +10,9 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: c33ece7658baba97e8012e67ab1495ae + md5: 4030c762379a976b95076872876bf659 build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ @@ -20,13 +20,13 @@ build: # Suggests: knitr, rmarkdown, testthat, BiocStyle requirements: host: - - 'bioconductor-biocparallel >=1.16.0,<1.17.0' - - 'bioconductor-blma >=1.6.0,<1.7.0' - - 'bioconductor-edger >=3.24.0,<3.25.0' - - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' + - 'bioconductor-biocparallel >=1.18.0,<1.19.0' + - 'bioconductor-blma >=1.8.0,<1.9.0' + - 'bioconductor-edger >=3.26.0,<3.27.0' + - 'bioconductor-genomeinfodb >=1.20.0,<1.21.0' - 'bioconductor-genomeinfodbdata >=1.2.0,<1.3.0' - - 'bioconductor-genomicranges >=1.34.0,<1.35.0' - - 'bioconductor-hiccompare >=1.4.0,<1.5.0' + - 'bioconductor-genomicranges >=1.36.0,<1.37.0' + - 'bioconductor-hiccompare >=1.6.0,<1.7.0' - r-base - r-data.table - r-dplyr @@ -35,13 +35,13 @@ requirements: - r-pheatmap - r-qqman run: - - 'bioconductor-biocparallel >=1.16.0,<1.17.0' - - 'bioconductor-blma >=1.6.0,<1.7.0' - - 'bioconductor-edger >=3.24.0,<3.25.0' - - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' + - 'bioconductor-biocparallel >=1.18.0,<1.19.0' + - 'bioconductor-blma >=1.8.0,<1.9.0' + - 'bioconductor-edger >=3.26.0,<3.27.0' + - 'bioconductor-genomeinfodb >=1.20.0,<1.21.0' - 'bioconductor-genomeinfodbdata >=1.2.0,<1.3.0' - - 'bioconductor-genomicranges >=1.34.0,<1.35.0' - - 'bioconductor-hiccompare >=1.4.0,<1.5.0' + - 'bioconductor-genomicranges >=1.36.0,<1.37.0' + - 'bioconductor-hiccompare >=1.6.0,<1.7.0' - r-base - r-data.table - r-dplyr diff --git a/recipes/bioconductor-multimed/meta.yaml b/recipes/bioconductor-multimed/meta.yaml index 4549d44bd58ab..867e79202e9a4 100644 --- a/recipes/bioconductor-multimed/meta.yaml +++ b/recipes/bioconductor-multimed/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "2.4.0" %} +{% set version = "2.6.0" %} {% set name = "MultiMed" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 53df4140afc3b479077ff254370b89af + md5: d9ee95935c15445833065ac51918fd4d build: number: 0 rpaths: diff --git a/recipes/bioconductor-multimir/meta.yaml b/recipes/bioconductor-multimir/meta.yaml index 090f357d20c25..bc988d1ff0d6e 100644 --- a/recipes/bioconductor-multimir/meta.yaml +++ b/recipes/bioconductor-multimir/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.4.0" %} +{% set version = "1.6.0" %} {% set name = "multiMiR" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,9 +10,9 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 26ca39b201e466a51cdf18d73d243930 + md5: be190b22f4424ab912609f7b5bbcedac build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ @@ -20,8 +20,8 @@ build: # Suggests: BiocStyle, edgeR, knitr, rmarkdown, testthat (>= 1.0.2) requirements: host: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' - - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' + - 'bioconductor-biocgenerics >=0.30.0,<0.31.0' - r-base - r-dplyr - 'r-purrr >=0.2.2' @@ -29,8 +29,8 @@ requirements: - 'r-tibble >=1.2' - r-xml run: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' - - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' + - 'bioconductor-biocgenerics >=0.30.0,<0.31.0' - r-base - r-dplyr - 'r-purrr >=0.2.2' diff --git a/recipes/bioconductor-multiomicsviz/meta.yaml b/recipes/bioconductor-multiomicsviz/meta.yaml index 0c8b936937237..4ce5b232753eb 100644 --- a/recipes/bioconductor-multiomicsviz/meta.yaml +++ b/recipes/bioconductor-multiomicsviz/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.6.0" %} +{% set version = "1.8.0" %} {% set name = "multiOmicsViz" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 1fb971e30027eab84bb48dd7552a11a4 + md5: 27efea72517daffda09ad491d7781341 build: number: 0 rpaths: @@ -20,12 +20,12 @@ build: # Suggests: BiocGenerics requirements: host: - - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' + - 'bioconductor-summarizedexperiment >=1.14.0,<1.15.0' - r-base - r-doparallel - r-foreach run: - - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' + - 'bioconductor-summarizedexperiment >=1.14.0,<1.15.0' - r-base - r-doparallel - r-foreach diff --git a/recipes/bioconductor-multiscan/meta.yaml b/recipes/bioconductor-multiscan/meta.yaml index cb3229ce8e839..1a9867f0596b1 100644 --- a/recipes/bioconductor-multiscan/meta.yaml +++ b/recipes/bioconductor-multiscan/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.42.0" %} +{% set version = "1.44.0" %} {% set name = "multiscan" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: f30405ccb188b9d543f7e32c4c1c1b61 + md5: 55c6835dbb636b628ea63f5ec1f7bbe8 build: number: 0 rpaths: @@ -18,10 +18,10 @@ build: - lib/ requirements: host: - - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' - r-base run: - - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' - r-base build: - {{ compiler('c') }} diff --git a/recipes/bioconductor-multtest/meta.yaml b/recipes/bioconductor-multtest/meta.yaml index ad075725eed32..cec673c6427ae 100644 --- a/recipes/bioconductor-multtest/meta.yaml +++ b/recipes/bioconductor-multtest/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "2.38.0" %} +{% set version = "2.40.0" %} {% set name = "multtest" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 8d72610b6a4266100d65cb49fca11158 + md5: 9a61cd841ac53057c3019f016535d785 build: number: 0 rpaths: @@ -19,14 +19,14 @@ build: # Suggests: snow requirements: host: - - 'bioconductor-biobase >=2.42.0,<2.43.0' - - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' + - 'bioconductor-biocgenerics >=0.30.0,<0.31.0' - r-base - r-mass - r-survival run: - - 'bioconductor-biobase >=2.42.0,<2.43.0' - - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' + - 'bioconductor-biocgenerics >=0.30.0,<0.31.0' - r-base - r-mass - r-survival diff --git a/recipes/bioconductor-mus.musculus/meta.yaml b/recipes/bioconductor-mus.musculus/meta.yaml index b439af49a307d..f8fa0c2ac4d32 100644 --- a/recipes/bioconductor-mus.musculus/meta.yaml +++ b/recipes/bioconductor-mus.musculus/meta.yaml @@ -1,6 +1,6 @@ {% set version = "1.3.1" %} {% set name = "Mus.musculus" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -12,29 +12,29 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' md5: 1b8defe64c2dd308a88d1ac7a4ce04b9 build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' - - 'bioconductor-genomicfeatures >=1.34.0,<1.35.0' - - 'bioconductor-go.db >=3.7.0,<3.8.0' - - 'bioconductor-org.mm.eg.db >=3.7.0,<3.8.0' - - 'bioconductor-organismdbi >=1.24.0,<1.25.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' + - 'bioconductor-genomicfeatures >=1.36.0,<1.37.0' + - 'bioconductor-go.db >=3.8.0,<3.9.0' + - 'bioconductor-org.mm.eg.db >=3.8.0,<3.9.0' + - 'bioconductor-organismdbi >=1.26.0,<1.27.0' - 'bioconductor-txdb.mmusculus.ucsc.mm10.knowngene >=3.4.0,<3.5.0' - r-base run: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' - - 'bioconductor-genomicfeatures >=1.34.0,<1.35.0' - - 'bioconductor-go.db >=3.7.0,<3.8.0' - - 'bioconductor-org.mm.eg.db >=3.7.0,<3.8.0' - - 'bioconductor-organismdbi >=1.24.0,<1.25.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' + - 'bioconductor-genomicfeatures >=1.36.0,<1.37.0' + - 'bioconductor-go.db >=3.8.0,<3.9.0' + - 'bioconductor-org.mm.eg.db >=3.8.0,<3.9.0' + - 'bioconductor-organismdbi >=1.26.0,<1.27.0' - 'bioconductor-txdb.mmusculus.ucsc.mm10.knowngene >=3.4.0,<3.5.0' - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-mus.musculus/post-link.sh b/recipes/bioconductor-mus.musculus/post-link.sh index 7e34203e64761..a32fef31e060b 100644 --- a/recipes/bioconductor-mus.musculus/post-link.sh +++ b/recipes/bioconductor-mus.musculus/post-link.sh @@ -1,9 +1,10 @@ #!/bin/bash FN="Mus.musculus_1.3.1.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/Mus.musculus_1.3.1.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/Mus.musculus_1.3.1.tar.gz" "https://bioarchive.galaxyproject.org/Mus.musculus_1.3.1.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-mus.musculus/bioconductor-mus.musculus_1.3.1_src_all.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-mus.musculus/bioconductor-mus.musculus_1.3.1_src_all.tar.gz" ) MD5="1b8defe64c2dd308a88d1ac7a4ce04b9" @@ -16,7 +17,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-muscle/meta.yaml b/recipes/bioconductor-muscle/meta.yaml index 1fe1d6ee0af77..8b7f424749bbb 100644 --- a/recipes/bioconductor-muscle/meta.yaml +++ b/recipes/bioconductor-muscle/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "3.24.0" %} +{% set version = "3.26.0" %} {% set name = "muscle" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 3fe18a5e6501d11231663070b783e744 + md5: bd068ea9ecafda73dc59d95186c23cd0 build: number: 0 rpaths: @@ -18,10 +18,10 @@ build: - lib/ requirements: host: - - 'bioconductor-biostrings >=2.50.0,<2.51.0' + - 'bioconductor-biostrings >=2.52.0,<2.53.0' - r-base run: - - 'bioconductor-biostrings >=2.50.0,<2.51.0' + - 'bioconductor-biostrings >=2.52.0,<2.53.0' - r-base build: - {{ compiler('c') }} diff --git a/recipes/bioconductor-mutationalpatterns/meta.yaml b/recipes/bioconductor-mutationalpatterns/meta.yaml index 2d78ef1f1fe4c..8633c717d7093 100644 --- a/recipes/bioconductor-mutationalpatterns/meta.yaml +++ b/recipes/bioconductor-mutationalpatterns/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.8.0" %} +{% set version = "1.10.0" %} {% set name = "MutationalPatterns" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 9ce25a78720c4904d5b951f9d37b901a + md5: 25087f2b88a9828eef9b62ba6245275a build: number: 0 rpaths: @@ -20,14 +20,14 @@ build: # Suggests: BSgenome (>= 1.40.0), BSgenome.Hsapiens.1000genomes.hs37d5 (>= 0.99.1), BSgenome.Hsapiens.UCSC.hg19 (>= 1.4.0), BiocStyle (>= 2.0.3), TxDb.Hsapiens.UCSC.hg19.knownGene (>= 3.2.2), biomaRt (>= 2.28.0), gridExtra (>= 2.2.1), rtracklayer (>= 1.32.2), testthat requirements: host: - - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' - - 'bioconductor-biostrings >=2.50.0,<2.51.0' - - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' - - 'bioconductor-genomicranges >=1.34.0,<1.35.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' - - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' - - 'bioconductor-variantannotation >=1.28.0,<1.29.0' + - 'bioconductor-biocgenerics >=0.30.0,<0.31.0' + - 'bioconductor-biostrings >=2.52.0,<2.53.0' + - 'bioconductor-genomeinfodb >=1.20.0,<1.21.0' + - 'bioconductor-genomicranges >=1.36.0,<1.37.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' + - 'bioconductor-summarizedexperiment >=1.14.0,<1.15.0' + - 'bioconductor-variantannotation >=1.30.0,<1.31.0' - r-base - 'r-cowplot >=0.9.2' - 'r-ggdendro >=0.1-20' @@ -37,14 +37,14 @@ requirements: - 'r-pracma >=1.8.8' - 'r-reshape2 >=1.4.1' run: - - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' - - 'bioconductor-biostrings >=2.50.0,<2.51.0' - - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' - - 'bioconductor-genomicranges >=1.34.0,<1.35.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' - - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' - - 'bioconductor-variantannotation >=1.28.0,<1.29.0' + - 'bioconductor-biocgenerics >=0.30.0,<0.31.0' + - 'bioconductor-biostrings >=2.52.0,<2.53.0' + - 'bioconductor-genomeinfodb >=1.20.0,<1.21.0' + - 'bioconductor-genomicranges >=1.36.0,<1.37.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' + - 'bioconductor-summarizedexperiment >=1.14.0,<1.15.0' + - 'bioconductor-variantannotation >=1.30.0,<1.31.0' - r-base - 'r-cowplot >=0.9.2' - 'r-ggdendro >=0.1-20' diff --git a/recipes/bioconductor-mvcclass/meta.yaml b/recipes/bioconductor-mvcclass/meta.yaml index bc0f40dfc8dbe..8860d395ac014 100644 --- a/recipes/bioconductor-mvcclass/meta.yaml +++ b/recipes/bioconductor-mvcclass/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.56.0" %} +{% set version = "1.58.0" %} {% set name = "MVCClass" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 7bcceaf0251bfe3b06c2ff5bd6d95e80 + md5: ee30a4d2a083afcff0e7b9c3bd3e7fe6 build: number: 0 rpaths: diff --git a/recipes/bioconductor-mvoutdata/meta.yaml b/recipes/bioconductor-mvoutdata/meta.yaml index 63be83e51c17a..58956485884bd 100644 --- a/recipes/bioconductor-mvoutdata/meta.yaml +++ b/recipes/bioconductor-mvoutdata/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.18.0" %} +{% set version = "1.20.0" %} {% set name = "mvoutData" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 8927221feca30eeac834f6b88ab2d83b + md5: dee1616c6e51610b038b7df786676238 build: number: 0 rpaths: @@ -19,16 +19,16 @@ build: noarch: generic requirements: host: - - 'bioconductor-affy >=1.60.0,<1.61.0' - - 'bioconductor-biobase >=2.42.0,<2.43.0' - - 'bioconductor-lumi >=2.34.0,<2.35.0' + - 'bioconductor-affy >=1.62.0,<1.63.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' + - 'bioconductor-lumi >=2.36.0,<2.37.0' - r-base run: - - 'bioconductor-affy >=1.60.0,<1.61.0' - - 'bioconductor-biobase >=2.42.0,<2.43.0' - - 'bioconductor-lumi >=2.34.0,<2.35.0' + - 'bioconductor-affy >=1.62.0,<1.63.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' + - 'bioconductor-lumi >=2.36.0,<2.37.0' - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-mvoutdata/post-link.sh b/recipes/bioconductor-mvoutdata/post-link.sh index cddd4b27e724a..2b95f4d1794e7 100644 --- a/recipes/bioconductor-mvoutdata/post-link.sh +++ b/recipes/bioconductor-mvoutdata/post-link.sh @@ -1,11 +1,11 @@ #!/bin/bash -FN="mvoutData_1.18.0.tar.gz" +FN="mvoutData_1.20.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/experiment/src/contrib/mvoutData_1.18.0.tar.gz" - "https://bioarchive.galaxyproject.org/mvoutData_1.18.0.tar.gz" - "https://depot.galaxyproject.org/software/bioconductor-mvoutdata/bioconductor-mvoutdata_1.18.0_src_all.tar.gz" + "https://bioconductor.org/packages/3.9/data/experiment/src/contrib/mvoutData_1.20.0.tar.gz" + "https://bioarchive.galaxyproject.org/mvoutData_1.20.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-mvoutdata/bioconductor-mvoutdata_1.20.0_src_all.tar.gz" ) -MD5="8927221feca30eeac834f6b88ab2d83b" +MD5="dee1616c6e51610b038b7df786676238" # Use a staging area in the conda dir rather than temp dirs, both to avoid # permission issues as well as to have things downloaded in a predictable @@ -16,7 +16,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-mwastools/meta.yaml b/recipes/bioconductor-mwastools/meta.yaml index b17e8c6f818f7..b945f81d1a4cf 100644 --- a/recipes/bioconductor-mwastools/meta.yaml +++ b/recipes/bioconductor-mwastools/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.6.0" %} +{% set version = "1.8.0" %} {% set name = "MWASTools" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 9cc4188f3ca64ea0f6161c11876fe795 + md5: 6682a0abac0f768907754383a22bd954 build: number: 0 rpaths: @@ -20,11 +20,11 @@ build: # Suggests: RUnit, BiocGenerics, knitr, BiocStyle, rmarkdown requirements: host: - - 'bioconductor-complexheatmap >=1.20.0,<1.21.0' - - 'bioconductor-kegggraph >=1.42.0,<1.43.0' - - 'bioconductor-keggrest >=1.22.0,<1.23.0' - - 'bioconductor-qvalue >=2.14.0,<2.15.0' - - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' + - 'bioconductor-complexheatmap >=2.0.0,<2.1.0' + - 'bioconductor-kegggraph >=1.44.0,<1.45.0' + - 'bioconductor-keggrest >=1.24.0,<1.25.0' + - 'bioconductor-qvalue >=2.16.0,<2.17.0' + - 'bioconductor-summarizedexperiment >=1.14.0,<1.15.0' - r-base - r-boot - r-car @@ -35,11 +35,11 @@ requirements: - r-ppcor - r-rcurl run: - - 'bioconductor-complexheatmap >=1.20.0,<1.21.0' - - 'bioconductor-kegggraph >=1.42.0,<1.43.0' - - 'bioconductor-keggrest >=1.22.0,<1.23.0' - - 'bioconductor-qvalue >=2.14.0,<2.15.0' - - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' + - 'bioconductor-complexheatmap >=2.0.0,<2.1.0' + - 'bioconductor-kegggraph >=1.44.0,<1.45.0' + - 'bioconductor-keggrest >=1.24.0,<1.25.0' + - 'bioconductor-qvalue >=2.16.0,<2.17.0' + - 'bioconductor-summarizedexperiment >=1.14.0,<1.15.0' - r-base - r-boot - r-car diff --git a/recipes/bioconductor-mwgcod.db/meta.yaml b/recipes/bioconductor-mwgcod.db/meta.yaml index 29602703ce11e..b63a58a3b8388 100644 --- a/recipes/bioconductor-mwgcod.db/meta.yaml +++ b/recipes/bioconductor-mwgcod.db/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.4.0" %} {% set name = "mwgcod.db" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -12,7 +12,7 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 3d6e2af6b05d6e07a212c043dc9d37c4 build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ @@ -20,14 +20,14 @@ build: # Suggests: annotate, RUnit requirements: host: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' - - 'bioconductor-org.mm.eg.db >=3.7.0,<3.8.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' + - 'bioconductor-org.mm.eg.db >=3.8.0,<3.9.0' - r-base run: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' - - 'bioconductor-org.mm.eg.db >=3.7.0,<3.8.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' + - 'bioconductor-org.mm.eg.db >=3.8.0,<3.9.0' - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-mwgcod.db/post-link.sh b/recipes/bioconductor-mwgcod.db/post-link.sh index 0fce1669cc165..7ca6a82120309 100644 --- a/recipes/bioconductor-mwgcod.db/post-link.sh +++ b/recipes/bioconductor-mwgcod.db/post-link.sh @@ -1,9 +1,10 @@ #!/bin/bash FN="mwgcod.db_3.4.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/mwgcod.db_3.4.0.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/mwgcod.db_3.4.0.tar.gz" "https://bioarchive.galaxyproject.org/mwgcod.db_3.4.0.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-mwgcod.db/bioconductor-mwgcod.db_3.4.0_src_all.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-mwgcod.db/bioconductor-mwgcod.db_3.4.0_src_all.tar.gz" ) MD5="3d6e2af6b05d6e07a212c043dc9d37c4" @@ -16,7 +17,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-mygene/meta.yaml b/recipes/bioconductor-mygene/meta.yaml index 984f1430b0663..62debe95b45b1 100644 --- a/recipes/bioconductor-mygene/meta.yaml +++ b/recipes/bioconductor-mygene/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.18.0" %} +{% set version = "1.20.0" %} {% set name = "mygene" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 3a0f8aff0ef5eef0df7ed072ef98b771 + md5: 0b83f62d78a6c3dca0bfd49c4b4a2abc build: number: 0 rpaths: @@ -20,8 +20,8 @@ build: # Suggests: BiocStyle requirements: host: - - 'bioconductor-genomicfeatures >=1.34.0,<1.35.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-genomicfeatures >=1.36.0,<1.37.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' - r-base - r-hmisc - 'r-httr >=0.3' @@ -29,8 +29,8 @@ requirements: - r-plyr - r-sqldf run: - - 'bioconductor-genomicfeatures >=1.34.0,<1.35.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-genomicfeatures >=1.36.0,<1.37.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' - r-base - r-hmisc - 'r-httr >=0.3' diff --git a/recipes/bioconductor-myvariant/meta.yaml b/recipes/bioconductor-myvariant/meta.yaml index 13e2ca00f237b..676708d44de85 100644 --- a/recipes/bioconductor-myvariant/meta.yaml +++ b/recipes/bioconductor-myvariant/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.12.0" %} +{% set version = "1.14.0" %} {% set name = "myvariant" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,9 +10,9 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 186efbf26d9009e544d8874bb3f5778e + md5: 3fd2a1cd530340e48ed29d1b6a0282fc build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ @@ -20,9 +20,9 @@ build: # Suggests: BiocStyle requirements: host: - - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' - - 'bioconductor-variantannotation >=1.28.0,<1.29.0' + - 'bioconductor-genomeinfodb >=1.20.0,<1.21.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' + - 'bioconductor-variantannotation >=1.30.0,<1.31.0' - r-base - r-hmisc - r-httr @@ -30,9 +30,9 @@ requirements: - r-magrittr - r-plyr run: - - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' - - 'bioconductor-variantannotation >=1.28.0,<1.29.0' + - 'bioconductor-genomeinfodb >=1.20.0,<1.21.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' + - 'bioconductor-variantannotation >=1.30.0,<1.31.0' - r-base - r-hmisc - r-httr diff --git a/recipes/bioconductor-mzid/meta.yaml b/recipes/bioconductor-mzid/meta.yaml index 860960d18bdd5..811c89d94b87f 100644 --- a/recipes/bioconductor-mzid/meta.yaml +++ b/recipes/bioconductor-mzid/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.20.1" %} +{% set version = "1.22.0" %} {% set name = "mzID" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: 0cb43c04d30fd469379648f018d0897a643fbc28660af9cf9b83e7dbdb22cd97 + md5: d3b509c2903fedb8bbd5498b7b619159 build: number: 0 rpaths: @@ -20,7 +20,7 @@ build: # Suggests: knitr, testthat requirements: host: - - 'bioconductor-protgenerics >=1.14.0,<1.15.0' + - 'bioconductor-protgenerics >=1.16.0,<1.17.0' - r-base - r-doparallel - r-foreach @@ -28,7 +28,7 @@ requirements: - r-plyr - r-xml run: - - 'bioconductor-protgenerics >=1.14.0,<1.15.0' + - 'bioconductor-protgenerics >=1.16.0,<1.17.0' - r-base - r-doparallel - r-foreach diff --git a/recipes/bioconductor-mzr/meta.yaml b/recipes/bioconductor-mzr/meta.yaml index 4058e8b7e4517..2ccb1210800ca 100644 --- a/recipes/bioconductor-mzr/meta.yaml +++ b/recipes/bioconductor-mzr/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "2.16.2" %} +{% set version = "2.18.0" %} {% set name = "mzR" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: 768f559ee349833d26514800a0a9b30785e4cb49de302935046da6423f2ad6a5 + md5: 0d04f2321954557784e8080983a7d0e6 build: number: 0 rpaths: @@ -20,20 +20,20 @@ build: # SystemRequirements: C++11, GNU make requirements: host: - - 'bioconductor-biobase >=2.42.0,<2.43.0' - - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' - - 'bioconductor-protgenerics >=1.14.0,<1.15.0' - - 'bioconductor-rhdf5lib >=1.4.0,<1.5.0' - - 'bioconductor-zlibbioc >=1.28.0,<1.29.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' + - 'bioconductor-biocgenerics >=0.30.0,<0.31.0' + - 'bioconductor-protgenerics >=1.16.0,<1.17.0' + - 'bioconductor-rhdf5lib >=1.6.0,<1.7.0' + - 'bioconductor-zlibbioc >=1.30.0,<1.31.0' - r-base - r-ncdf4 - 'r-rcpp >=0.10.1' run: - - 'bioconductor-biobase >=2.42.0,<2.43.0' - - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' - - 'bioconductor-protgenerics >=1.14.0,<1.15.0' - - 'bioconductor-rhdf5lib >=1.4.0,<1.5.0' - - 'bioconductor-zlibbioc >=1.28.0,<1.29.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' + - 'bioconductor-biocgenerics >=0.30.0,<0.31.0' + - 'bioconductor-protgenerics >=1.16.0,<1.17.0' + - 'bioconductor-rhdf5lib >=1.6.0,<1.7.0' + - 'bioconductor-zlibbioc >=1.30.0,<1.31.0' - r-base - r-ncdf4 - 'r-rcpp >=0.10.1' diff --git a/recipes/bioconductor-nadfinder/meta.yaml b/recipes/bioconductor-nadfinder/meta.yaml index fda00cfbbacd5..5b59593debd27 100644 --- a/recipes/bioconductor-nadfinder/meta.yaml +++ b/recipes/bioconductor-nadfinder/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.6.0" %} +{% set version = "1.8.0" %} {% set name = "NADfinder" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: b34fd2ba65777d26f1012cef1411888b + md5: c04d0d9e049f2c075f6299fbdc14c03b build: number: 0 rpaths: @@ -20,46 +20,44 @@ build: # Suggests: RUnit, BiocStyle, knitr, BSgenome.Mmusculus.UCSC.mm10, testthat, BiocManager requirements: host: - - 'bioconductor-atacseqqc >=1.6.0,<1.7.0' - - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' - - 'bioconductor-csaw >=1.16.0,<1.17.0' - - 'bioconductor-empiricalbrownsmethod >=1.10.0,<1.11.0' - - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' - - 'bioconductor-genomicalignments >=1.18.0,<1.19.0' - - 'bioconductor-genomicranges >=1.34.0,<1.35.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-limma >=3.38.0,<3.39.0' - - 'bioconductor-rsamtools >=1.34.0,<1.35.0' - - 'bioconductor-rtracklayer >=1.42.0,<1.43.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' - - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' - - 'bioconductor-trackviewer >=1.18.0,<1.19.0' + - 'bioconductor-atacseqqc >=1.8.0,<1.9.0' + - 'bioconductor-biocgenerics >=0.30.0,<0.31.0' + - 'bioconductor-csaw >=1.18.0,<1.19.0' + - 'bioconductor-empiricalbrownsmethod >=1.12.0,<1.13.0' + - 'bioconductor-genomeinfodb >=1.20.0,<1.21.0' + - 'bioconductor-genomicalignments >=1.20.0,<1.21.0' + - 'bioconductor-genomicranges >=1.36.0,<1.37.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-limma >=3.40.0,<3.41.0' + - 'bioconductor-rsamtools >=2.0.0,<2.1.0' + - 'bioconductor-rtracklayer >=1.44.0,<1.45.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' + - 'bioconductor-summarizedexperiment >=1.14.0,<1.15.0' + - 'bioconductor-trackviewer >=1.20.0,<1.21.0' - r-base - r-baseline - r-corrplot - r-metap - - r-rbamtools - r-signal run: - - 'bioconductor-atacseqqc >=1.6.0,<1.7.0' - - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' - - 'bioconductor-csaw >=1.16.0,<1.17.0' - - 'bioconductor-empiricalbrownsmethod >=1.10.0,<1.11.0' - - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' - - 'bioconductor-genomicalignments >=1.18.0,<1.19.0' - - 'bioconductor-genomicranges >=1.34.0,<1.35.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-limma >=3.38.0,<3.39.0' - - 'bioconductor-rsamtools >=1.34.0,<1.35.0' - - 'bioconductor-rtracklayer >=1.42.0,<1.43.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' - - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' - - 'bioconductor-trackviewer >=1.18.0,<1.19.0' + - 'bioconductor-atacseqqc >=1.8.0,<1.9.0' + - 'bioconductor-biocgenerics >=0.30.0,<0.31.0' + - 'bioconductor-csaw >=1.18.0,<1.19.0' + - 'bioconductor-empiricalbrownsmethod >=1.12.0,<1.13.0' + - 'bioconductor-genomeinfodb >=1.20.0,<1.21.0' + - 'bioconductor-genomicalignments >=1.20.0,<1.21.0' + - 'bioconductor-genomicranges >=1.36.0,<1.37.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-limma >=3.40.0,<3.41.0' + - 'bioconductor-rsamtools >=2.0.0,<2.1.0' + - 'bioconductor-rtracklayer >=1.44.0,<1.45.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' + - 'bioconductor-summarizedexperiment >=1.14.0,<1.15.0' + - 'bioconductor-trackviewer >=1.20.0,<1.21.0' - r-base - r-baseline - r-corrplot - r-metap - - r-rbamtools - r-signal test: commands: diff --git a/recipes/bioconductor-nanostringdiff/meta.yaml b/recipes/bioconductor-nanostringdiff/meta.yaml index 233b314550dbc..db39de58ad855 100644 --- a/recipes/bioconductor-nanostringdiff/meta.yaml +++ b/recipes/bioconductor-nanostringdiff/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.12.0" %} +{% set version = "1.14.0" %} {% set name = "NanoStringDiff" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: a651308ff607d0b38673ad2849dcd81b + md5: 4e7839ffa608368251d100a3177bd495 build: number: 0 rpaths: @@ -19,12 +19,12 @@ build: # Suggests: testthat, BiocStyle requirements: host: - - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' - r-base - r-matrixstats - r-rcpp run: - - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' - r-base - r-matrixstats - r-rcpp diff --git a/recipes/bioconductor-nanostringqcpro/meta.yaml b/recipes/bioconductor-nanostringqcpro/meta.yaml index 1bbf30e7c0e84..1817122f5de41 100644 --- a/recipes/bioconductor-nanostringqcpro/meta.yaml +++ b/recipes/bioconductor-nanostringqcpro/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.14.0" %} +{% set version = "1.16.0" %} {% set name = "NanoStringQCPro" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 40009524e65ceb0fca927bfbda64acd0 + md5: a2bf9ee2b3bdfc8baa6e60b24465811d build: number: 0 rpaths: @@ -20,18 +20,18 @@ build: # Suggests: roxygen2 (>= 4.0.1), testthat, BiocStyle, knitr, rmarkdown requirements: host: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' - - 'bioconductor-biobase >=2.42.0,<2.43.0' - - 'bioconductor-org.hs.eg.db >=3.7.0,<3.8.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' + - 'bioconductor-org.hs.eg.db >=3.8.0,<3.9.0' - r-base - 'r-knitr >=1.12' - 'r-nmf >=0.20.5' - 'r-png >=0.1-7' - 'r-rcolorbrewer >=1.0-5' run: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' - - 'bioconductor-biobase >=2.42.0,<2.43.0' - - 'bioconductor-org.hs.eg.db >=3.7.0,<3.8.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' + - 'bioconductor-org.hs.eg.db >=3.8.0,<3.9.0' - r-base - 'r-knitr >=1.12' - 'r-nmf >=0.20.5' diff --git a/recipes/bioconductor-nanotator/build.sh b/recipes/bioconductor-nanotator/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-nanotator/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-nanotator/meta.yaml b/recipes/bioconductor-nanotator/meta.yaml new file mode 100644 index 0000000000000..adb2f265da1ef --- /dev/null +++ b/recipes/bioconductor-nanotator/meta.yaml @@ -0,0 +1,53 @@ +{% set version = "1.0.0" %} +{% set name = "nanotatoR" %} +{% set bioc = "3.9" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: fc74467fa96a2c4329e8494eb6caf9ea +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: rmarkdown, yaml +requirements: + host: + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' + - 'bioconductor-org.hs.eg.db >=3.8.0,<3.9.0' + - 'bioconductor-rtracklayer >=1.44.0,<1.45.0' + - r-base + - 'r-hash >=2.2.6' + - r-httr + - r-knitr + - 'r-openxlsx >=4.0.17' + - 'r-rentrez >=1.1.0' + - r-stringr + - r-testthat + run: + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' + - 'bioconductor-org.hs.eg.db >=3.8.0,<3.9.0' + - 'bioconductor-rtracklayer >=1.44.0,<1.45.0' + - r-base + - 'r-hash >=2.2.6' + - r-httr + - r-knitr + - 'r-openxlsx >=4.0.17' + - 'r-rentrez >=1.1.0' + - r-stringr + - r-testthat +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: 'file LICENSE' + summary: 'Whole genome sequencing (WGS) has successfully been used to identify single-nucleotide variants (SNV), small insertions and deletions and, more recently, small copy number variants. However, due to utilization of short reads, it is not well suited for identification of structural variants (SV) and the majority of SV calling tools having high false positive and negative rates.Optical next-generation mapping (NGM) utilizes long fluorescently labeled native-state DNA molecules for de novo genome assembly to overcome the limitations of WGS. NGM allows for a significant increase in SV detection capability. However, accuracy of SV annotation is highly important for variant classification and filtration to determine pathogenicity.Here we create a new tool in R, for SV annotation, including population frequency and gene function and expression, using publicly available datasets. We use DGV (Database of Genomic Variants), to calculate the population frequency of the SVs identified by the Bionano SVCaller in the NGM dataset of a cohort of 50 undiagnosed patients with a variety of phenotypes. The new annotation tool, nanotatoR, also calculates the internal frequency of SVs, which could be beneficial in identification of potential false positive or common calls. The software creates a primary gene list (PG) from NCBI databases based on patient phenotype and compares the list to the set of genes overlapping the patient’s SVs generated by SVCaller, providing analysts with an easy way to identify variants affecting genes in the PG. The output is given in an Excel file format, which is subdivided into multiple sheets based on SV type. Users then have a choice to filter SVs using the provided annotation for identification of inherited, de novo or rare variants. nanotatoR provides integrated annotation and the expression patterns to enable users to identify potential pathogenic SVs with greater precision and faster turnaround times.' + diff --git a/recipes/bioconductor-nanotubes/meta.yaml b/recipes/bioconductor-nanotubes/meta.yaml new file mode 100644 index 0000000000000..90893f82daea5 --- /dev/null +++ b/recipes/bioconductor-nanotubes/meta.yaml @@ -0,0 +1,34 @@ +{% set version = "1.0.0" %} +{% set name = "nanotubes" %} +{% set bioc = "3.9" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + md5: 6f54f293086643f47c81eea20f55f165 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: knitr, rmarkdown, BiocStyle, GenomicRanges, rtracklayer, CAGEfightR +requirements: + host: + - r-base + run: + - r-base + - curl +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html' + license: GPL-3 + summary: 'Cap Analysis of Gene Expression (CAGE) data from "Identification of Gene Transcription Start Sites and Enhancers Responding to Pulmonary Carbon Nanotube Exposure in Vivo" by Bornholdt et al. supplied as CAGE Transcription Start Sites (CTSSs).' + diff --git a/recipes/bioconductor-nanotubes/post-link.sh b/recipes/bioconductor-nanotubes/post-link.sh new file mode 100644 index 0000000000000..d4be505b1ec0a --- /dev/null +++ b/recipes/bioconductor-nanotubes/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="nanotubes_1.0.0.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.9/data/experiment/src/contrib/nanotubes_1.0.0.tar.gz" + "https://bioarchive.galaxyproject.org/nanotubes_1.0.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-nanotubes/bioconductor-nanotubes_1.0.0_src_all.tar.gz" +) +MD5="6f54f293086643f47c81eea20f55f165" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + curl $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-nanotubes/pre-unlink.sh b/recipes/bioconductor-nanotubes/pre-unlink.sh new file mode 100644 index 0000000000000..8b38582ce35ee --- /dev/null +++ b/recipes/bioconductor-nanotubes/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ nanotubes diff --git a/recipes/bioconductor-narrowpeaks/meta.yaml b/recipes/bioconductor-narrowpeaks/meta.yaml index 04e6e6fccc8b5..8d9f2588b97ac 100644 --- a/recipes/bioconductor-narrowpeaks/meta.yaml +++ b/recipes/bioconductor-narrowpeaks/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.26.0" %} +{% set version = "1.28.0" %} {% set name = "NarrowPeaks" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 31857409c4a4c04e695e58839670127e + md5: 5964cd4667e6bb6dafba34e392a6b835 build: number: 0 rpaths: @@ -19,22 +19,22 @@ build: # Suggests: rtracklayer, BiocStyle, GenomicRanges, CSAR requirements: host: - - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' - - 'bioconductor-csar >=1.34.0,<1.35.0' - - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' - - 'bioconductor-genomicranges >=1.34.0,<1.35.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-biocgenerics >=0.30.0,<0.31.0' + - 'bioconductor-csar >=1.36.0,<1.37.0' + - 'bioconductor-genomeinfodb >=1.20.0,<1.21.0' + - 'bioconductor-genomicranges >=1.36.0,<1.37.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' - r-base - r-fda - r-icsnp run: - - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' - - 'bioconductor-csar >=1.34.0,<1.35.0' - - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' - - 'bioconductor-genomicranges >=1.34.0,<1.35.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-biocgenerics >=0.30.0,<0.31.0' + - 'bioconductor-csar >=1.36.0,<1.37.0' + - 'bioconductor-genomeinfodb >=1.20.0,<1.21.0' + - 'bioconductor-genomicranges >=1.36.0,<1.37.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' - r-base - r-fda - r-icsnp diff --git a/recipes/bioconductor-nbamseq/build.sh b/recipes/bioconductor-nbamseq/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-nbamseq/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-nbamseq/meta.yaml b/recipes/bioconductor-nbamseq/meta.yaml new file mode 100644 index 0000000000000..a5cf71700f255 --- /dev/null +++ b/recipes/bioconductor-nbamseq/meta.yaml @@ -0,0 +1,45 @@ +{% set version = "1.0.0" %} +{% set name = "NBAMSeq" %} +{% set bioc = "3.9" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: 7d3149d0936dee0b074c613e4363f64c +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: knitr, rmarkdown, testthat, ggplot2 +requirements: + host: + - 'bioconductor-biocparallel >=1.18.0,<1.19.0' + - 'bioconductor-deseq2 >=1.24.0,<1.25.0' + - 'bioconductor-genefilter >=1.66.0,<1.67.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' + - 'bioconductor-summarizedexperiment >=1.14.0,<1.15.0' + - r-base + - 'r-mgcv >=1.8-24' + run: + - 'bioconductor-biocparallel >=1.18.0,<1.19.0' + - 'bioconductor-deseq2 >=1.24.0,<1.25.0' + - 'bioconductor-genefilter >=1.66.0,<1.67.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' + - 'bioconductor-summarizedexperiment >=1.14.0,<1.15.0' + - r-base + - 'r-mgcv >=1.8-24' +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: GPL-2 + summary: 'High-throughput sequencing experiments followed by differential expression analysis is a widely used approach to detect genomic biomarkers. A fundamental step in differential expression analysis is to model the association between gene counts and covariates of interest. NBAMSeq a flexible statistical model based on the generalized additive model and allows for information sharing across genes in variance estimation.' + diff --git a/recipes/bioconductor-nbsplice/meta.yaml b/recipes/bioconductor-nbsplice/meta.yaml index d5e37b2c661f2..7c20ec386068e 100644 --- a/recipes/bioconductor-nbsplice/meta.yaml +++ b/recipes/bioconductor-nbsplice/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.0.6" %} +{% set version = "1.2.0" %} {% set name = "NBSplice" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: 895403df894e834fbce65c5082bd984c291049ebc5609767850f137be46554d9 + md5: 497fa5cb8bfe4c1be5f6e4712c3e8ce3 build: number: 0 rpaths: @@ -20,8 +20,8 @@ build: # Suggests: knitr, RUnit, BiocGenerics requirements: host: - - 'bioconductor-biocparallel >=1.16.0,<1.17.0' - - 'bioconductor-edger >=3.24.0,<3.25.0' + - 'bioconductor-biocparallel >=1.18.0,<1.19.0' + - 'bioconductor-edger >=3.26.0,<3.27.0' - r-base - r-car - r-ggplot2 @@ -29,8 +29,8 @@ requirements: - r-mppa - r-reshape2 run: - - 'bioconductor-biocparallel >=1.16.0,<1.17.0' - - 'bioconductor-edger >=3.24.0,<3.25.0' + - 'bioconductor-biocparallel >=1.18.0,<1.19.0' + - 'bioconductor-edger >=3.26.0,<3.27.0' - r-base - r-car - r-ggplot2 diff --git a/recipes/bioconductor-ncdfflow/meta.yaml b/recipes/bioconductor-ncdfflow/meta.yaml index 02842c7dc8b02..819730a86850c 100644 --- a/recipes/bioconductor-ncdfflow/meta.yaml +++ b/recipes/bioconductor-ncdfflow/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "2.28.1" %} +{% set version = "2.30.0" %} {% set name = "ncdfFlow" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: 2e2161e8360e7ec54a3069af969299be57ec5c078aba2e38e2f49a6f91724bd9 + md5: 9ebbdc3deecbb3ecf369719d36b2e96c build: number: 0 rpaths: @@ -19,23 +19,23 @@ build: # Suggests: testthat,parallel requirements: host: - - 'bioconductor-biobase >=2.42.0,<2.43.0' - - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' - - 'bioconductor-flowcore >=1.48.0,<1.49.0' - - 'bioconductor-flowviz >=1.46.0,<1.47.0' - - 'bioconductor-rhdf5lib >=1.4.0,<1.5.0' - - 'bioconductor-zlibbioc >=1.28.0,<1.29.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' + - 'bioconductor-biocgenerics >=0.30.0,<0.31.0' + - 'bioconductor-flowcore >=1.50.0,<1.51.0' + - 'bioconductor-flowviz >=1.48.0,<1.49.0' + - 'bioconductor-rhdf5lib >=1.6.0,<1.7.0' + - 'bioconductor-zlibbioc >=1.30.0,<1.31.0' - r-base - r-bh - r-rcpp - r-rcpparmadillo run: - - 'bioconductor-biobase >=2.42.0,<2.43.0' - - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' - - 'bioconductor-flowcore >=1.48.0,<1.49.0' - - 'bioconductor-flowviz >=1.46.0,<1.47.0' - - 'bioconductor-rhdf5lib >=1.4.0,<1.5.0' - - 'bioconductor-zlibbioc >=1.28.0,<1.29.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' + - 'bioconductor-biocgenerics >=0.30.0,<0.31.0' + - 'bioconductor-flowcore >=1.50.0,<1.51.0' + - 'bioconductor-flowviz >=1.48.0,<1.49.0' + - 'bioconductor-rhdf5lib >=1.6.0,<1.7.0' + - 'bioconductor-zlibbioc >=1.30.0,<1.31.0' - r-base - r-bh - r-rcpp diff --git a/recipes/bioconductor-ncigraph/meta.yaml b/recipes/bioconductor-ncigraph/meta.yaml index dce511bd3234e..1019d24c749bd 100644 --- a/recipes/bioconductor-ncigraph/meta.yaml +++ b/recipes/bioconductor-ncigraph/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.30.0" %} +{% set version = "1.32.0" %} {% set name = "NCIgraph" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,9 +10,9 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: d43797d5c080c69cfd2ac24545dec3a1 + md5: 0bcb95b9449cc4451fcf113b5f1a3b10 build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ @@ -20,17 +20,17 @@ build: # Suggests: Rgraphviz requirements: host: - - 'bioconductor-graph >=1.60.0,<1.61.0' - - 'bioconductor-kegggraph >=1.42.0,<1.43.0' - - 'bioconductor-rbgl >=1.58.0,<1.59.0' - - 'bioconductor-rcy3 >=2.2.0,<2.3.0' + - 'bioconductor-graph >=1.62.0,<1.63.0' + - 'bioconductor-kegggraph >=1.44.0,<1.45.0' + - 'bioconductor-rbgl >=1.60.0,<1.61.0' + - 'bioconductor-rcy3 >=2.4.0,<2.5.0' - r-base - r-r.methodss3 run: - - 'bioconductor-graph >=1.60.0,<1.61.0' - - 'bioconductor-kegggraph >=1.42.0,<1.43.0' - - 'bioconductor-rbgl >=1.58.0,<1.59.0' - - 'bioconductor-rcy3 >=2.2.0,<2.3.0' + - 'bioconductor-graph >=1.62.0,<1.63.0' + - 'bioconductor-kegggraph >=1.44.0,<1.45.0' + - 'bioconductor-rbgl >=1.60.0,<1.61.0' + - 'bioconductor-rcy3 >=2.4.0,<2.5.0' - r-base - r-r.methodss3 test: diff --git a/recipes/bioconductor-ncigraphdata/meta.yaml b/recipes/bioconductor-ncigraphdata/meta.yaml index 7638fe543b200..61bc1c0b0e892 100644 --- a/recipes/bioconductor-ncigraphdata/meta.yaml +++ b/recipes/bioconductor-ncigraphdata/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.18.0" %} +{% set version = "1.20.0" %} {% set name = "NCIgraphData" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: fc2723da5d02c9f6baa7d05054f912a1 + md5: b69030f40d2818cbd1c004d33403a653 build: number: 0 rpaths: @@ -23,7 +23,7 @@ requirements: - r-base run: - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-ncigraphdata/post-link.sh b/recipes/bioconductor-ncigraphdata/post-link.sh index dd96ed39f5837..12ee87a47b8b1 100644 --- a/recipes/bioconductor-ncigraphdata/post-link.sh +++ b/recipes/bioconductor-ncigraphdata/post-link.sh @@ -1,11 +1,11 @@ #!/bin/bash -FN="NCIgraphData_1.18.0.tar.gz" +FN="NCIgraphData_1.20.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/experiment/src/contrib/NCIgraphData_1.18.0.tar.gz" - "https://bioarchive.galaxyproject.org/NCIgraphData_1.18.0.tar.gz" - "https://depot.galaxyproject.org/software/bioconductor-ncigraphdata/bioconductor-ncigraphdata_1.18.0_src_all.tar.gz" + "https://bioconductor.org/packages/3.9/data/experiment/src/contrib/NCIgraphData_1.20.0.tar.gz" + "https://bioarchive.galaxyproject.org/NCIgraphData_1.20.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-ncigraphdata/bioconductor-ncigraphdata_1.20.0_src_all.tar.gz" ) -MD5="fc2723da5d02c9f6baa7d05054f912a1" +MD5="b69030f40d2818cbd1c004d33403a653" # Use a staging area in the conda dir rather than temp dirs, both to avoid # permission issues as well as to have things downloaded in a predictable @@ -16,7 +16,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-ndexr/meta.yaml b/recipes/bioconductor-ndexr/meta.yaml index 70d6788d72352..8ad0188ff7d8b 100644 --- a/recipes/bioconductor-ndexr/meta.yaml +++ b/recipes/bioconductor-ndexr/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.4.0" %} +{% set version = "1.6.0" %} {% set name = "ndexr" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 3028152656c2a2b5361713bfc713a6ed + md5: 5162ec97e81196a65a256f1f78783baf build: number: 0 rpaths: diff --git a/recipes/bioconductor-neighbornet/meta.yaml b/recipes/bioconductor-neighbornet/meta.yaml index a49fa46145989..0d9e5ff611a57 100644 --- a/recipes/bioconductor-neighbornet/meta.yaml +++ b/recipes/bioconductor-neighbornet/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.0.0" %} +{% set version = "1.2.0" %} {% set name = "NeighborNet" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,19 +10,19 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: a3341ae47afcce8284786132a3bdf393 + md5: 678c606cc75df11a475c99688a809b11 build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ noarch: generic requirements: host: - - 'bioconductor-graph >=1.60.0,<1.61.0' + - 'bioconductor-graph >=1.62.0,<1.63.0' - r-base run: - - 'bioconductor-graph >=1.60.0,<1.61.0' + - 'bioconductor-graph >=1.62.0,<1.63.0' - r-base test: commands: diff --git a/recipes/bioconductor-nem/meta.yaml b/recipes/bioconductor-nem/meta.yaml index de476bb3cb19a..894c08370b3e3 100644 --- a/recipes/bioconductor-nem/meta.yaml +++ b/recipes/bioconductor-nem/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "2.56.0" %} +{% set version = "2.58.0" %} {% set name = "nem" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 0f3029446be3426d2e2ea986073e0122 + md5: 26c590b60db3f910b797964eba70b38d build: number: 0 rpaths: @@ -19,10 +19,10 @@ build: # Suggests: Biobase (>= 1.10) requirements: host: - - 'bioconductor-graph >=1.60.0,<1.61.0' - - 'bioconductor-limma >=3.38.0,<3.39.0' - - 'bioconductor-rbgl >=1.58.0,<1.59.0' - - 'bioconductor-rgraphviz >=2.26.0,<2.27.0' + - 'bioconductor-graph >=1.62.0,<1.63.0' + - 'bioconductor-limma >=3.40.0,<3.41.0' + - 'bioconductor-rbgl >=1.60.0,<1.61.0' + - 'bioconductor-rgraphviz >=2.28.0,<2.29.0' - r-base - r-boot - r-e1071 @@ -30,10 +30,10 @@ requirements: - r-rcolorbrewer - r-statmod run: - - 'bioconductor-graph >=1.60.0,<1.61.0' - - 'bioconductor-limma >=3.38.0,<3.39.0' - - 'bioconductor-rbgl >=1.58.0,<1.59.0' - - 'bioconductor-rgraphviz >=2.26.0,<2.27.0' + - 'bioconductor-graph >=1.62.0,<1.63.0' + - 'bioconductor-limma >=3.40.0,<3.41.0' + - 'bioconductor-rbgl >=1.60.0,<1.61.0' + - 'bioconductor-rgraphviz >=2.28.0,<2.29.0' - r-base - r-boot - r-e1071 diff --git a/recipes/bioconductor-nestlink/meta.yaml b/recipes/bioconductor-nestlink/meta.yaml new file mode 100644 index 0000000000000..5b5d29f3908e7 --- /dev/null +++ b/recipes/bioconductor-nestlink/meta.yaml @@ -0,0 +1,46 @@ +{% set version = "1.0.0" %} +{% set name = "NestLink" %} +{% set bioc = "3.9" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: f71e0add07a81dd57fb97103af33762f +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: BiocStyle (>= 2.2.0), DT, ggplot2, knitr, rmarkdown, testthat, specL, lattice, scales +requirements: + host: + - 'bioconductor-annotationhub >=2.16.0,<2.17.0' + - 'bioconductor-biostrings >=2.52.0,<2.53.0' + - 'bioconductor-experimenthub >=1.10.0,<1.11.0' + - 'bioconductor-shortread >=1.42.0,<1.43.0' + - r-base + - 'r-gplots >=3.0.0' + - 'r-protviz >=0.4.0' + run: + - 'bioconductor-annotationhub >=2.16.0,<2.17.0' + - 'bioconductor-biostrings >=2.52.0,<2.53.0' + - 'bioconductor-experimenthub >=1.10.0,<1.11.0' + - 'bioconductor-shortread >=1.42.0,<1.43.0' + - r-base + - 'r-gplots >=3.0.0' + - 'r-protviz >=0.4.0' + - curl +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html' + license: GPL + summary: 'Provides next-generation sequencing (NGS) and mass spectrometry (MS) sample data, code snippets and replication material used for developing NestLink. The NestLink approach is a protein binder selection and identification technology able to biophysically characterize thousands of library members at once without handling individual clones at any stage of the process. Data were acquired on NGS and MS platforms at the Functional Genomics Center Zurich.' + diff --git a/recipes/bioconductor-nestlink/post-link.sh b/recipes/bioconductor-nestlink/post-link.sh new file mode 100644 index 0000000000000..f1c1975ebd0ff --- /dev/null +++ b/recipes/bioconductor-nestlink/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="NestLink_1.0.0.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.9/data/experiment/src/contrib/NestLink_1.0.0.tar.gz" + "https://bioarchive.galaxyproject.org/NestLink_1.0.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-nestlink/bioconductor-nestlink_1.0.0_src_all.tar.gz" +) +MD5="f71e0add07a81dd57fb97103af33762f" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + curl $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-nestlink/pre-unlink.sh b/recipes/bioconductor-nestlink/pre-unlink.sh new file mode 100644 index 0000000000000..d0cc64f146420 --- /dev/null +++ b/recipes/bioconductor-nestlink/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ NestLink diff --git a/recipes/bioconductor-netbenchmark/meta.yaml b/recipes/bioconductor-netbenchmark/meta.yaml index 6d45634d20837..f44e6f0175877 100644 --- a/recipes/bioconductor-netbenchmark/meta.yaml +++ b/recipes/bioconductor-netbenchmark/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.14.0" %} +{% set version = "1.16.0" %} {% set name = "netbenchmark" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 3d0c34121a30be63e0fc2837c021f253 + md5: a1b4608795a70e022d26aa7c5c34a6d2 build: number: 0 rpaths: @@ -19,9 +19,9 @@ build: # Suggests: RUnit, BiocGenerics, knitr, graph requirements: host: - - 'bioconductor-genie3 >=1.4.0,<1.5.0' - - 'bioconductor-grndata >=1.14.0,<1.15.0' - - 'bioconductor-minet >=3.40.0,<3.41.0' + - 'bioconductor-genie3 >=1.6.0,<1.7.0' + - 'bioconductor-grndata >=1.16.0,<1.17.0' + - 'bioconductor-minet >=3.42.0,<3.43.0' - r-base - r-c3net - r-corpcor @@ -32,9 +32,9 @@ requirements: - r-pracma - 'r-rcpp >=0.11.0' run: - - 'bioconductor-genie3 >=1.4.0,<1.5.0' - - 'bioconductor-grndata >=1.14.0,<1.15.0' - - 'bioconductor-minet >=3.40.0,<3.41.0' + - 'bioconductor-genie3 >=1.6.0,<1.7.0' + - 'bioconductor-grndata >=1.16.0,<1.17.0' + - 'bioconductor-minet >=3.42.0,<3.43.0' - r-base - r-c3net - r-corpcor diff --git a/recipes/bioconductor-netbiov/meta.yaml b/recipes/bioconductor-netbiov/meta.yaml index 60d7c4ccd14a4..81cdb9e813907 100644 --- a/recipes/bioconductor-netbiov/meta.yaml +++ b/recipes/bioconductor-netbiov/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.16.0" %} +{% set version = "1.18.0" %} {% set name = "netbiov" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 41e9eece65723f5328ca9f15ffce01b9 + md5: ccc0ab1d17b66fabdfa2ea927353e361 build: number: 0 rpaths: diff --git a/recipes/bioconductor-netboost/build.sh b/recipes/bioconductor-netboost/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-netboost/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-netboost/meta.yaml b/recipes/bioconductor-netboost/meta.yaml new file mode 100644 index 0000000000000..ede8859641c3e --- /dev/null +++ b/recipes/bioconductor-netboost/meta.yaml @@ -0,0 +1,54 @@ +{% set version = "1.0.0" %} +{% set name = "netboost" %} +{% set bioc = "3.9" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + md5: eca9de5dc79b990dbac1e08f0716492d +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ +# Suggests: knitr +# SystemRequirements: GNU make, Bash, Perl, Gzip +requirements: + host: + - 'bioconductor-impute >=1.58.0,<1.59.0' + - r-base + - r-colorspace + - r-dynamictreecut + - r-r.utils + - r-rcpp + - r-rcppparallel + - r-wgcna + - perl + run: + - 'bioconductor-impute >=1.58.0,<1.59.0' + - r-base + - r-colorspace + - r-dynamictreecut + - r-r.utils + - r-rcpp + - r-rcppparallel + - r-wgcna + - perl + build: + - {{ compiler('c') }} + - {{ compiler('cxx') }} + - automake + - make +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: GPL-3 + summary: 'Boosting supported network analysis for high-dimensional omics applications. This package comes bundled with the MC-UPGMA clustering package by Yaniv Loewenstein.' + diff --git a/recipes/bioconductor-nethet/meta.yaml b/recipes/bioconductor-nethet/meta.yaml index 46453697aa2da..bd98d6e18da17 100644 --- a/recipes/bioconductor-nethet/meta.yaml +++ b/recipes/bioconductor-nethet/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.14.0" %} +{% set version = "1.15.0" %} {% set name = "nethet" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: de7f46b2f5c400fde16c3954ebc9ff1b + md5: 9bed54881788cf300de6032684c993bf build: number: 0 rpaths: @@ -19,8 +19,8 @@ build: # Suggests: knitr, xtable, BiocStyle requirements: host: - - 'bioconductor-limma >=3.38.0,<3.39.0' - - 'bioconductor-multtest >=2.38.0,<2.39.0' + - 'bioconductor-limma >=3.40.0,<3.41.0' + - 'bioconductor-multtest >=2.40.0,<2.41.0' - r-base - r-compquadform - r-genenet @@ -36,8 +36,8 @@ requirements: - r-network - r-parcor run: - - 'bioconductor-limma >=3.38.0,<3.39.0' - - 'bioconductor-multtest >=2.38.0,<2.39.0' + - 'bioconductor-limma >=3.40.0,<3.41.0' + - 'bioconductor-multtest >=2.40.0,<2.41.0' - r-base - r-compquadform - r-genenet diff --git a/recipes/bioconductor-netpathminer/meta.yaml b/recipes/bioconductor-netpathminer/meta.yaml index 335f8db3313e5..63795ee686f69 100644 --- a/recipes/bioconductor-netpathminer/meta.yaml +++ b/recipes/bioconductor-netpathminer/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.18.0" %} +{% set version = "1.20.0" %} {% set name = "NetPathMiner" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,21 +10,26 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: a7126fcb4431a1f78cb8e4742ae70635 + md5: b5229cee01ad66180ee86c8a50ee9d03 build: number: 0 + skip: True # [osx] rpaths: - lib/R/lib/ - lib/ -# Suggests: rBiopaxParser (>= 2.1), RCurl, graph +# Suggests: rBiopaxParser (>= 2.1), RCurl, graph, knitr, rmarkdown, BiocStyle # SystemRequirements: libxml2, libSBML (>= 5.5) requirements: host: - r-base - 'r-igraph >=1.0' + - libxml2 + - libsbml >=5.5 run: - r-base - 'r-igraph >=1.0' + - libxml2 + - libsbml >=5.5 build: - {{ compiler('c') }} - {{ compiler('cxx') }} diff --git a/recipes/bioconductor-netprior/meta.yaml b/recipes/bioconductor-netprior/meta.yaml index 77cbd13a58d07..e7400140ba4a5 100644 --- a/recipes/bioconductor-netprior/meta.yaml +++ b/recipes/bioconductor-netprior/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.8.1" %} +{% set version = "1.10.0" %} {% set name = "netprioR" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 3078ae2243153e998aabc88e6ac119aa + md5: a09b310b2afd257aa263df687c15e0c4 build: number: 0 rpaths: diff --git a/recipes/bioconductor-netreg/meta.yaml b/recipes/bioconductor-netreg/meta.yaml index f186ebd818c73..5e10320715bc1 100644 --- a/recipes/bioconductor-netreg/meta.yaml +++ b/recipes/bioconductor-netreg/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.6.0" %} +{% set version = "1.8.0" %} {% set name = "netReg" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 8f3db56ff84e07615627658da1c40bff + md5: 3577e49e7a74fac264e70a907d4834c9 build: number: 0 rpaths: diff --git a/recipes/bioconductor-netresponse/meta.yaml b/recipes/bioconductor-netresponse/meta.yaml index 9e59b062950a2..9b2008671ede6 100644 --- a/recipes/bioconductor-netresponse/meta.yaml +++ b/recipes/bioconductor-netresponse/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.42.0" %} +{% set version = "1.44.0" %} {% set name = "netresponse" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 6f7b9e38c87012015f0bb9ba8f53b718 + md5: c0ad8cb4cdef69e676af176c72cf9cac build: number: 0 rpaths: @@ -18,10 +18,10 @@ build: - lib/ requirements: host: - - 'bioconductor-graph >=1.60.0,<1.61.0' - - 'bioconductor-minet >=3.40.0,<3.41.0' - - 'bioconductor-qvalue >=2.14.0,<2.15.0' - - 'bioconductor-rgraphviz >=2.26.0,<2.27.0' + - 'bioconductor-graph >=1.62.0,<1.63.0' + - 'bioconductor-minet >=3.42.0,<3.43.0' + - 'bioconductor-qvalue >=2.16.0,<2.17.0' + - 'bioconductor-rgraphviz >=2.28.0,<2.29.0' - r-base - r-dmt - r-ggplot2 @@ -31,10 +31,10 @@ requirements: - r-rcolorbrewer - r-reshape2 run: - - 'bioconductor-graph >=1.60.0,<1.61.0' - - 'bioconductor-minet >=3.40.0,<3.41.0' - - 'bioconductor-qvalue >=2.14.0,<2.15.0' - - 'bioconductor-rgraphviz >=2.26.0,<2.27.0' + - 'bioconductor-graph >=1.62.0,<1.63.0' + - 'bioconductor-minet >=3.42.0,<3.43.0' + - 'bioconductor-qvalue >=2.16.0,<2.17.0' + - 'bioconductor-rgraphviz >=2.28.0,<2.29.0' - r-base - r-dmt - r-ggplot2 diff --git a/recipes/bioconductor-netsam/meta.yaml b/recipes/bioconductor-netsam/meta.yaml index 37ca3df031f8c..e192e431f0b8c 100644 --- a/recipes/bioconductor-netsam/meta.yaml +++ b/recipes/bioconductor-netsam/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.22.0" %} +{% set version = "1.24.0" %} {% set name = "NetSAM" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 38f4ae15c77a17e4b2774fc0b6ce9e8d + md5: ab2e72fd048e17cd4f19366c2851c433 build: number: 0 rpaths: @@ -20,12 +20,12 @@ build: # Suggests: RUnit, BiocGenerics requirements: host: - - 'bioconductor-graph >=1.60.0,<1.61.0' + - 'bioconductor-graph >=1.62.0,<1.63.0' - r-base - 'r-igraph >=0.6-1' - 'r-seriation >=1.0-6' run: - - 'bioconductor-graph >=1.60.0,<1.61.0' + - 'bioconductor-graph >=1.62.0,<1.63.0' - r-base - 'r-igraph >=0.6-1' - 'r-seriation >=1.0-6' diff --git a/recipes/bioconductor-netsmooth/meta.yaml b/recipes/bioconductor-netsmooth/meta.yaml index 4715258930e6f..dd51788d4d2f3 100644 --- a/recipes/bioconductor-netsmooth/meta.yaml +++ b/recipes/bioconductor-netsmooth/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.2.0" %} +{% set version = "1.4.0" %} {% set name = "netSmooth" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,9 +10,9 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 30774513e8fa21902cc5d68b92e4ca54 + md5: c53bbdefc35f6169ed76bf30ad1cf686 build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ @@ -20,20 +20,24 @@ build: # Suggests: knitr, testthat, Rtsne, biomaRt, igraph, STRINGdb, NMI, pheatmap, ggplot2, BiocStyle, rmarkdown, BiocParallel requirements: host: - - 'bioconductor-clusterexperiment >=2.2.0,<2.3.0' - - 'bioconductor-scater >=1.10.0,<1.11.0' - - 'bioconductor-singlecellexperiment >=1.4.0,<1.5.0' - - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' + - 'bioconductor-clusterexperiment >=2.4.0,<2.5.0' + - 'bioconductor-delayedarray >=0.10.0,<0.11.0' + - 'bioconductor-hdf5array >=1.12.0,<1.13.0' + - 'bioconductor-scater >=1.12.0,<1.13.0' + - 'bioconductor-singlecellexperiment >=1.6.0,<1.7.0' + - 'bioconductor-summarizedexperiment >=1.14.0,<1.15.0' - r-base - r-cluster - r-data.table - r-entropy - r-matrix run: - - 'bioconductor-clusterexperiment >=2.2.0,<2.3.0' - - 'bioconductor-scater >=1.10.0,<1.11.0' - - 'bioconductor-singlecellexperiment >=1.4.0,<1.5.0' - - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' + - 'bioconductor-clusterexperiment >=2.4.0,<2.5.0' + - 'bioconductor-delayedarray >=0.10.0,<0.11.0' + - 'bioconductor-hdf5array >=1.12.0,<1.13.0' + - 'bioconductor-scater >=1.12.0,<1.13.0' + - 'bioconductor-singlecellexperiment >=1.6.0,<1.7.0' + - 'bioconductor-summarizedexperiment >=1.14.0,<1.15.0' - r-base - r-cluster - r-data.table diff --git a/recipes/bioconductor-networkbma/meta.yaml b/recipes/bioconductor-networkbma/meta.yaml index aa640aa89e0b9..708bb69110db2 100644 --- a/recipes/bioconductor-networkbma/meta.yaml +++ b/recipes/bioconductor-networkbma/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "2.22.0" %} +{% set version = "2.24.0" %} {% set name = "networkBMA" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 44c5d02a7bd54f626209644786f8a5d4 + md5: c4412287f245abd27fad8563da668e11 build: number: 0 rpaths: @@ -26,6 +26,7 @@ requirements: - 'r-rcpp >=0.10.3' - 'r-rcpparmadillo >=0.3.810.2' - 'r-rcppeigen >=0.3.1.2.1' + - liblapack run: - r-base - r-bh @@ -34,6 +35,7 @@ requirements: - 'r-rcpp >=0.10.3' - 'r-rcpparmadillo >=0.3.810.2' - 'r-rcppeigen >=0.3.1.2.1' + - liblapack build: - {{ compiler('c') }} - {{ compiler('cxx') }} diff --git a/recipes/bioconductor-neve2006/meta.yaml b/recipes/bioconductor-neve2006/meta.yaml index 1ae36fe02bc52..6c267c9c7222d 100644 --- a/recipes/bioconductor-neve2006/meta.yaml +++ b/recipes/bioconductor-neve2006/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "0.20.0" %} +{% set version = "0.22.0" %} {% set name = "Neve2006" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: b20d24255cdccb1d06f070bc60879d28 + md5: 1649911c89a1d20393bd58b3376e622d build: number: 0 rpaths: @@ -19,16 +19,16 @@ build: noarch: generic requirements: host: - - 'bioconductor-annotate >=1.60.0,<1.61.0' - - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-annotate >=1.62.0,<1.63.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' - 'bioconductor-hgu133a.db >=3.2.0,<3.3.0' - r-base run: - - 'bioconductor-annotate >=1.60.0,<1.61.0' - - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-annotate >=1.62.0,<1.63.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' - 'bioconductor-hgu133a.db >=3.2.0,<3.3.0' - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-neve2006/post-link.sh b/recipes/bioconductor-neve2006/post-link.sh index 7f42d040d3f5d..16106854d2605 100644 --- a/recipes/bioconductor-neve2006/post-link.sh +++ b/recipes/bioconductor-neve2006/post-link.sh @@ -1,11 +1,11 @@ #!/bin/bash -FN="Neve2006_0.20.0.tar.gz" +FN="Neve2006_0.22.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/experiment/src/contrib/Neve2006_0.20.0.tar.gz" - "https://bioarchive.galaxyproject.org/Neve2006_0.20.0.tar.gz" - "https://depot.galaxyproject.org/software/bioconductor-neve2006/bioconductor-neve2006_0.20.0_src_all.tar.gz" + "https://bioconductor.org/packages/3.9/data/experiment/src/contrib/Neve2006_0.22.0.tar.gz" + "https://bioarchive.galaxyproject.org/Neve2006_0.22.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-neve2006/bioconductor-neve2006_0.22.0_src_all.tar.gz" ) -MD5="b20d24255cdccb1d06f070bc60879d28" +MD5="1649911c89a1d20393bd58b3376e622d" # Use a staging area in the conda dir rather than temp dirs, both to avoid # permission issues as well as to have things downloaded in a predictable @@ -16,7 +16,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-ngscopy/meta.yaml b/recipes/bioconductor-ngscopy/meta.yaml index 1006286262a38..b71fa8c30c56d 100644 --- a/recipes/bioconductor-ngscopy/meta.yaml +++ b/recipes/bioconductor-ngscopy/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.16.1" %} +{% set version = "1.17.1" %} {% set name = "NGScopy" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 031942d8487ccaa4d6144a4f721c9035 + md5: b8b9721f675895d17f74e4a40db36eb2 build: number: 0 rpaths: diff --git a/recipes/bioconductor-ngscopydata/meta.yaml b/recipes/bioconductor-ngscopydata/meta.yaml index 3db076f159366..c534416a4af23 100644 --- a/recipes/bioconductor-ngscopydata/meta.yaml +++ b/recipes/bioconductor-ngscopydata/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.2.0" %} +{% set version = "1.4.0" %} {% set name = "NGScopyData" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 5a873e124972f000b294486fd2512c12 + md5: a1ad1b18cdab0cb0f60674d0482e3e6b build: number: 0 rpaths: @@ -22,7 +22,7 @@ requirements: - r-base run: - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-ngscopydata/post-link.sh b/recipes/bioconductor-ngscopydata/post-link.sh index ff06cc0f9990b..19c5b77e6b1af 100644 --- a/recipes/bioconductor-ngscopydata/post-link.sh +++ b/recipes/bioconductor-ngscopydata/post-link.sh @@ -1,11 +1,11 @@ #!/bin/bash -FN="NGScopyData_1.2.0.tar.gz" +FN="NGScopyData_1.4.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/experiment/src/contrib/NGScopyData_1.2.0.tar.gz" - "https://bioarchive.galaxyproject.org/NGScopyData_1.2.0.tar.gz" - "https://depot.galaxyproject.org/software/bioconductor-ngscopydata/bioconductor-ngscopydata_1.2.0_src_all.tar.gz" + "https://bioconductor.org/packages/3.9/data/experiment/src/contrib/NGScopyData_1.4.0.tar.gz" + "https://bioarchive.galaxyproject.org/NGScopyData_1.4.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-ngscopydata/bioconductor-ngscopydata_1.4.0_src_all.tar.gz" ) -MD5="5a873e124972f000b294486fd2512c12" +MD5="a1ad1b18cdab0cb0f60674d0482e3e6b" # Use a staging area in the conda dir rather than temp dirs, both to avoid # permission issues as well as to have things downloaded in a predictable @@ -16,7 +16,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-ngsreports/build.sh b/recipes/bioconductor-ngsreports/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-ngsreports/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-ngsreports/meta.yaml b/recipes/bioconductor-ngsreports/meta.yaml new file mode 100644 index 0000000000000..c47b082aaa3c8 --- /dev/null +++ b/recipes/bioconductor-ngsreports/meta.yaml @@ -0,0 +1,77 @@ +{% set version = "1.0.0" %} +{% set name = "ngsReports" %} +{% set bioc = "3.9" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: 275e9a8d91e3a30bbd0362450d9a8cf4 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: BiocStyle, Cairo, knitr, pander, testthat +requirements: + host: + - 'bioconductor-biocgenerics >=0.30.0,<0.31.0' + - 'bioconductor-biostrings >=2.52.0,<2.53.0' + - 'bioconductor-rsamtools >=2.0.0,<2.1.0' + - 'bioconductor-shortread >=1.42.0,<1.43.0' + - 'bioconductor-xvector >=0.24.0,<0.25.0' + - r-base + - r-checkmate + - 'r-dplyr >=0.7.5' + - r-ggdendro + - r-ggplot2 + - r-lubridate + - r-plotly + - r-readr + - r-reshape2 + - r-rmarkdown + - r-scales + - r-stringr + - 'r-tibble >=1.3.1' + - r-tidyr + - 'r-tidyselect >=0.2.3' + - r-truncnorm + - r-viridislite + - r-zoo + run: + - 'bioconductor-biocgenerics >=0.30.0,<0.31.0' + - 'bioconductor-biostrings >=2.52.0,<2.53.0' + - 'bioconductor-rsamtools >=2.0.0,<2.1.0' + - 'bioconductor-shortread >=1.42.0,<1.43.0' + - 'bioconductor-xvector >=0.24.0,<0.25.0' + - r-base + - r-checkmate + - 'r-dplyr >=0.7.5' + - r-ggdendro + - r-ggplot2 + - r-lubridate + - r-plotly + - r-readr + - r-reshape2 + - r-rmarkdown + - r-scales + - r-stringr + - 'r-tibble >=1.3.1' + - r-tidyr + - 'r-tidyselect >=0.2.3' + - r-truncnorm + - r-viridislite + - r-zoo +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: 'LGPL (>= 3)' + summary: 'This package provides methods and object classes for parsing FastQC reports and output summaries from other NGS tools into R, as well as visualising the data loaded from these files.' + diff --git a/recipes/bioconductor-nnnorm/meta.yaml b/recipes/bioconductor-nnnorm/meta.yaml index 807b8d6761478..04f8e19438808 100644 --- a/recipes/bioconductor-nnnorm/meta.yaml +++ b/recipes/bioconductor-nnnorm/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "2.46.0" %} +{% set version = "2.48.0" %} {% set name = "nnNorm" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: f9f516d28deb61db8d90266ed1adce97 + md5: a1dd8fef52c92c47e1bc17ca0fe5c823 build: number: 0 rpaths: @@ -19,11 +19,11 @@ build: noarch: generic requirements: host: - - 'bioconductor-marray >=1.60.0,<1.61.0' + - 'bioconductor-marray >=1.62.0,<1.63.0' - r-base - r-nnet run: - - 'bioconductor-marray >=1.60.0,<1.61.0' + - 'bioconductor-marray >=1.62.0,<1.63.0' - r-base - r-nnet test: diff --git a/recipes/bioconductor-noiseq/meta.yaml b/recipes/bioconductor-noiseq/meta.yaml index bd668629e5b22..43cd21601bfd7 100644 --- a/recipes/bioconductor-noiseq/meta.yaml +++ b/recipes/bioconductor-noiseq/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "2.26.1" %} +{% set version = "2.28.0" %} {% set name = "NOISeq" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: 56632baa984d5fda7d14acf033ec397edd5b6eab238123c8a772d1e65384d0f3 + md5: 2211009273dbb9def27fab7612bf5ee7 build: number: 0 rpaths: @@ -19,11 +19,11 @@ build: noarch: generic requirements: host: - - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' - r-base - 'r-matrix >=1.2' run: - - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' - r-base - 'r-matrix >=1.2' test: diff --git a/recipes/bioconductor-nondetects/meta.yaml b/recipes/bioconductor-nondetects/meta.yaml index b3584d8886461..b5cef1f763961 100644 --- a/recipes/bioconductor-nondetects/meta.yaml +++ b/recipes/bioconductor-nondetects/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "2.12.0" %} +{% set version = "2.14.0" %} {% set name = "nondetects" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 38eb1814c20ef744c713f59b42707d47 + md5: 6ed082936ef8d168c1bb04cb44def8df build: number: 0 rpaths: @@ -20,16 +20,16 @@ build: # Suggests: knitr, rmarkdown, BiocStyle (>= 1.0.0), RUnit, BiocGenerics (>= 0.8.0) requirements: host: - - 'bioconductor-biobase >=2.42.0,<2.43.0' - - 'bioconductor-htqpcr >=1.36.0,<1.37.0' - - 'bioconductor-limma >=3.38.0,<3.39.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' + - 'bioconductor-htqpcr >=1.38.0,<1.39.0' + - 'bioconductor-limma >=3.40.0,<3.41.0' - r-arm - r-base - r-mvtnorm run: - - 'bioconductor-biobase >=2.42.0,<2.43.0' - - 'bioconductor-htqpcr >=1.36.0,<1.37.0' - - 'bioconductor-limma >=3.38.0,<3.39.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' + - 'bioconductor-htqpcr >=1.38.0,<1.39.0' + - 'bioconductor-limma >=3.40.0,<3.41.0' - r-arm - r-base - r-mvtnorm diff --git a/recipes/bioconductor-normalize450k/meta.yaml b/recipes/bioconductor-normalize450k/meta.yaml index ee1e8fbd3f36d..baf7e9812ab96 100644 --- a/recipes/bioconductor-normalize450k/meta.yaml +++ b/recipes/bioconductor-normalize450k/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.10.0" %} +{% set version = "1.12.0" %} {% set name = "normalize450K" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 0a46946dedab5b5e7ae7f269aedd7664 + md5: 28b62cd9b5c4cf1b1e2b02e9043e35fa build: number: 0 rpaths: @@ -19,13 +19,13 @@ build: noarch: generic requirements: host: - - 'bioconductor-biobase >=2.42.0,<2.43.0' - - 'bioconductor-illuminaio >=0.24.0,<0.25.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' + - 'bioconductor-illuminaio >=0.26.0,<0.27.0' - r-base - r-quadprog run: - - 'bioconductor-biobase >=2.42.0,<2.43.0' - - 'bioconductor-illuminaio >=0.24.0,<0.25.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' + - 'bioconductor-illuminaio >=0.26.0,<0.27.0' - r-base - r-quadprog test: diff --git a/recipes/bioconductor-normalyzerde/meta.yaml b/recipes/bioconductor-normalyzerde/meta.yaml index 5e7a1d5274b87..824cff6938067 100644 --- a/recipes/bioconductor-normalyzerde/meta.yaml +++ b/recipes/bioconductor-normalyzerde/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.0.0" %} +{% set version = "1.2.0" %} {% set name = "NormalyzerDE" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,38 +10,40 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: e1ce8d162271f6aa58b181ea8135dfd8 + md5: 670b920cccf0189ef5a6ad4a6bce3988 build: number: 0 rpaths: - lib/R/lib/ - lib/ noarch: generic -# Suggests: knitr, testthat, rmarkdown, roxygen2, hexbin +# Suggests: knitr, testthat, rmarkdown, roxygen2, hexbin, BiocStyle requirements: host: - - 'bioconductor-biobase >=2.42.0,<2.43.0' - - 'bioconductor-limma >=3.38.0,<3.39.0' - - 'bioconductor-preprocesscore >=1.44.0,<1.45.0' - - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' - - 'bioconductor-vsn >=3.50.0,<3.51.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' + - 'bioconductor-limma >=3.40.0,<3.41.0' + - 'bioconductor-preprocesscore >=1.46.0,<1.47.0' + - 'bioconductor-summarizedexperiment >=1.14.0,<1.15.0' + - 'bioconductor-vsn >=3.52.0,<3.53.0' - r-ape - r-base - r-car + - r-ggforce - r-ggplot2 - r-mass - r-matrixstats - r-raster - r-rcmdrmisc run: - - 'bioconductor-biobase >=2.42.0,<2.43.0' - - 'bioconductor-limma >=3.38.0,<3.39.0' - - 'bioconductor-preprocesscore >=1.44.0,<1.45.0' - - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' - - 'bioconductor-vsn >=3.50.0,<3.51.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' + - 'bioconductor-limma >=3.40.0,<3.41.0' + - 'bioconductor-preprocesscore >=1.46.0,<1.47.0' + - 'bioconductor-summarizedexperiment >=1.14.0,<1.15.0' + - 'bioconductor-vsn >=3.52.0,<3.53.0' - r-ape - r-base - r-car + - r-ggforce - r-ggplot2 - r-mass - r-matrixstats diff --git a/recipes/bioconductor-normqpcr/meta.yaml b/recipes/bioconductor-normqpcr/meta.yaml index f2ea3517b2077..b06a5b60467b3 100644 --- a/recipes/bioconductor-normqpcr/meta.yaml +++ b/recipes/bioconductor-normqpcr/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.28.0" %} +{% set version = "1.30.0" %} {% set name = "NormqPCR" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: b1753d4e090d39b0d490eb14ff5d47c3 + md5: 9851470e31655277db61d1a4e42b965e build: number: 0 rpaths: @@ -19,14 +19,14 @@ build: noarch: generic requirements: host: - - 'bioconductor-biobase >=2.42.0,<2.43.0' - - 'bioconductor-readqpcr >=1.28.0,<1.29.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' + - 'bioconductor-readqpcr >=1.30.0,<1.31.0' - r-base - r-qpcr - r-rcolorbrewer run: - - 'bioconductor-biobase >=2.42.0,<2.43.0' - - 'bioconductor-readqpcr >=1.28.0,<1.29.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' + - 'bioconductor-readqpcr >=1.30.0,<1.31.0' - r-base - r-qpcr - r-rcolorbrewer @@ -37,8 +37,7 @@ about: home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: LGPL-3 summary: 'Functions for the selection of optimal reference genes and the normalisation of real-time quantitative PCR data.' - extra: container: - # rgl extended-base: true + diff --git a/recipes/bioconductor-normr/meta.yaml b/recipes/bioconductor-normr/meta.yaml index b2af3d0b864e2..00845243d0058 100644 --- a/recipes/bioconductor-normr/meta.yaml +++ b/recipes/bioconductor-normr/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.8.0" %} +{% set version = "1.10.0" %} {% set name = "normr" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: b809094a96f2751f7562dfa70759b690 + md5: d7a14e44272acd117020c25ebfccfd08 build: number: 0 rpaths: @@ -20,28 +20,27 @@ build: # SystemRequirements: C++11 requirements: host: - - 'bioconductor-bamsignals >=1.14.0,<1.15.0' - - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' - - 'bioconductor-genomicranges >=1.34.0,<1.35.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-qvalue >=2.14.0,<2.15.0' - - 'bioconductor-rtracklayer >=1.42.0,<1.43.0' + - 'bioconductor-bamsignals >=1.16.0,<1.17.0' + - 'bioconductor-genomeinfodb >=1.20.0,<1.21.0' + - 'bioconductor-genomicranges >=1.36.0,<1.37.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-qvalue >=2.16.0,<2.17.0' + - 'bioconductor-rtracklayer >=1.44.0,<1.45.0' - r-base - 'r-rcpp >=0.11' run: - - 'bioconductor-bamsignals >=1.14.0,<1.15.0' - - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' - - 'bioconductor-genomicranges >=1.34.0,<1.35.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-qvalue >=2.14.0,<2.15.0' - - 'bioconductor-rtracklayer >=1.42.0,<1.43.0' + - 'bioconductor-bamsignals >=1.16.0,<1.17.0' + - 'bioconductor-genomeinfodb >=1.20.0,<1.21.0' + - 'bioconductor-genomicranges >=1.36.0,<1.37.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-qvalue >=2.16.0,<2.17.0' + - 'bioconductor-rtracklayer >=1.44.0,<1.45.0' - r-base - 'r-rcpp >=0.11' build: - {{ compiler('c') }} - {{ compiler('cxx') }} - make - - llvm-openmp # [osx] test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-norway981.db/meta.yaml b/recipes/bioconductor-norway981.db/meta.yaml index 2329354595ba6..9955b0b1d5f4f 100644 --- a/recipes/bioconductor-norway981.db/meta.yaml +++ b/recipes/bioconductor-norway981.db/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.2.3" %} {% set name = "Norway981.db" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -12,7 +12,7 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' md5: 85367390919bba9018438585e59fbb87 build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ @@ -20,14 +20,14 @@ build: # Suggests: DBI, annotate, RUnit requirements: host: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' - - 'bioconductor-org.hs.eg.db >=3.7.0,<3.8.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' + - 'bioconductor-org.hs.eg.db >=3.8.0,<3.9.0' - r-base run: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' - - 'bioconductor-org.hs.eg.db >=3.7.0,<3.8.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' + - 'bioconductor-org.hs.eg.db >=3.8.0,<3.9.0' - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-norway981.db/post-link.sh b/recipes/bioconductor-norway981.db/post-link.sh index 33f8c337b5aaf..503c5fbd6cf7b 100644 --- a/recipes/bioconductor-norway981.db/post-link.sh +++ b/recipes/bioconductor-norway981.db/post-link.sh @@ -1,9 +1,10 @@ #!/bin/bash FN="Norway981.db_3.2.3.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/Norway981.db_3.2.3.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/Norway981.db_3.2.3.tar.gz" "https://bioarchive.galaxyproject.org/Norway981.db_3.2.3.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-norway981.db/bioconductor-norway981.db_3.2.3_src_all.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-norway981.db/bioconductor-norway981.db_3.2.3_src_all.tar.gz" ) MD5="85367390919bba9018438585e59fbb87" @@ -16,7 +17,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-npgsea/meta.yaml b/recipes/bioconductor-npgsea/meta.yaml index 8a3ab763e235d..bb1a8eca5f732 100644 --- a/recipes/bioconductor-npgsea/meta.yaml +++ b/recipes/bioconductor-npgsea/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.18.0" %} +{% set version = "1.20.0" %} {% set name = "npGSEA" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 6cb8b32d6c6c22ce37e259a411912495 + md5: e52fe0ffeaaa40b3e988dd4550f99052 build: number: 0 rpaths: @@ -20,14 +20,14 @@ build: # Suggests: ALL, genefilter, limma, hgu95av2.db, ReportingTools, BiocStyle requirements: host: - - 'bioconductor-biobase >=2.42.0,<2.43.0' - - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' - - 'bioconductor-gseabase >=1.44.0,<1.45.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' + - 'bioconductor-biocgenerics >=0.30.0,<0.31.0' + - 'bioconductor-gseabase >=1.46.0,<1.47.0' - r-base run: - - 'bioconductor-biobase >=2.42.0,<2.43.0' - - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' - - 'bioconductor-gseabase >=1.44.0,<1.45.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' + - 'bioconductor-biocgenerics >=0.30.0,<0.31.0' + - 'bioconductor-gseabase >=1.46.0,<1.47.0' - r-base test: commands: diff --git a/recipes/bioconductor-ntw/meta.yaml b/recipes/bioconductor-ntw/meta.yaml index 4416605459695..4e0e052f49d12 100644 --- a/recipes/bioconductor-ntw/meta.yaml +++ b/recipes/bioconductor-ntw/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.32.0" %} +{% set version = "1.34.0" %} {% set name = "NTW" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 68f21a43a4f188db6c040831e7385b10 + md5: e76680fac1736cf1e010febd204d5300 build: number: 0 rpaths: diff --git a/recipes/bioconductor-nucleosim/meta.yaml b/recipes/bioconductor-nucleosim/meta.yaml index 7879f514e54de..4d375791d1e3c 100644 --- a/recipes/bioconductor-nucleosim/meta.yaml +++ b/recipes/bioconductor-nucleosim/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.10.0" %} +{% set version = "1.12.0" %} {% set name = "nucleoSim" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 29ba1741cbd3ec9feee1a274523abc2f + md5: a7c5dacf53ecce0dd78991928b9656c5 build: number: 0 rpaths: @@ -20,12 +20,12 @@ build: # Suggests: BiocStyle, BiocGenerics, knitr, rmarkdown, RUnit requirements: host: - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' - r-base run: - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' - r-base test: commands: diff --git a/recipes/bioconductor-nucler/meta.yaml b/recipes/bioconductor-nucler/meta.yaml index 147355f992817..68443d59adb55 100644 --- a/recipes/bioconductor-nucler/meta.yaml +++ b/recipes/bioconductor-nucler/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "2.14.0" %} +{% set version = "2.16.0" %} {% set name = "nucleR" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 076a8f41e0d540563418f0874b2f3590 + md5: 03152cac4449fffd5ebda5bc4f2fa849 build: number: 0 rpaths: @@ -20,29 +20,29 @@ build: # Suggests: Starr, BiocStyle, knitr, rmarkdown, testthat requirements: host: - - 'bioconductor-biobase >=2.42.0,<2.43.0' - - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' - - 'bioconductor-biostrings >=2.50.0,<2.51.0' - - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' - - 'bioconductor-genomicranges >=1.34.0,<1.35.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-rsamtools >=1.34.0,<1.35.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' - - 'bioconductor-shortread >=1.40.0,<1.41.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' + - 'bioconductor-biocgenerics >=0.30.0,<0.31.0' + - 'bioconductor-biostrings >=2.52.0,<2.53.0' + - 'bioconductor-genomeinfodb >=1.20.0,<1.21.0' + - 'bioconductor-genomicranges >=1.36.0,<1.37.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-rsamtools >=2.0.0,<2.1.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' + - 'bioconductor-shortread >=1.42.0,<1.43.0' - r-base - r-dplyr - r-ggplot2 - r-magrittr run: - - 'bioconductor-biobase >=2.42.0,<2.43.0' - - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' - - 'bioconductor-biostrings >=2.50.0,<2.51.0' - - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' - - 'bioconductor-genomicranges >=1.34.0,<1.35.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-rsamtools >=1.34.0,<1.35.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' - - 'bioconductor-shortread >=1.40.0,<1.41.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' + - 'bioconductor-biocgenerics >=0.30.0,<0.31.0' + - 'bioconductor-biostrings >=2.52.0,<2.53.0' + - 'bioconductor-genomeinfodb >=1.20.0,<1.21.0' + - 'bioconductor-genomicranges >=1.36.0,<1.37.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-rsamtools >=2.0.0,<2.1.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' + - 'bioconductor-shortread >=1.42.0,<1.43.0' - r-base - r-dplyr - r-ggplot2 diff --git a/recipes/bioconductor-nucpos/meta.yaml b/recipes/bioconductor-nucpos/meta.yaml index 5e56b119e7a0e..91af9c3eb8c5f 100644 --- a/recipes/bioconductor-nucpos/meta.yaml +++ b/recipes/bioconductor-nucpos/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.0.1" %} +{% set version = "1.2.0" %} {% set name = "nuCpos" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 6ccdb6f4d22329dcde145b703cc56974 + md5: 8ae37dce2a611262d22eb1fe3c7dfb15 build: number: 0 rpaths: diff --git a/recipes/bioconductor-nugohs1a520180.db/meta.yaml b/recipes/bioconductor-nugohs1a520180.db/meta.yaml index daab94f21138b..596eea68e62f9 100644 --- a/recipes/bioconductor-nugohs1a520180.db/meta.yaml +++ b/recipes/bioconductor-nugohs1a520180.db/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.4.0" %} {% set name = "nugohs1a520180.db" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -12,7 +12,7 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: f83701b35b07e69e1ad503b546bb5eaf build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ @@ -20,14 +20,14 @@ build: # Suggests: annotate, RUnit requirements: host: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' - - 'bioconductor-org.hs.eg.db >=3.7.0,<3.8.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' + - 'bioconductor-org.hs.eg.db >=3.8.0,<3.9.0' - r-base run: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' - - 'bioconductor-org.hs.eg.db >=3.7.0,<3.8.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' + - 'bioconductor-org.hs.eg.db >=3.8.0,<3.9.0' - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-nugohs1a520180.db/post-link.sh b/recipes/bioconductor-nugohs1a520180.db/post-link.sh index 85ed043f449db..0a07613c39be8 100644 --- a/recipes/bioconductor-nugohs1a520180.db/post-link.sh +++ b/recipes/bioconductor-nugohs1a520180.db/post-link.sh @@ -1,9 +1,10 @@ #!/bin/bash FN="nugohs1a520180.db_3.4.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/nugohs1a520180.db_3.4.0.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/nugohs1a520180.db_3.4.0.tar.gz" "https://bioarchive.galaxyproject.org/nugohs1a520180.db_3.4.0.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-nugohs1a520180.db/bioconductor-nugohs1a520180.db_3.4.0_src_all.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-nugohs1a520180.db/bioconductor-nugohs1a520180.db_3.4.0_src_all.tar.gz" ) MD5="f83701b35b07e69e1ad503b546bb5eaf" @@ -16,7 +17,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-nugohs1a520180cdf/meta.yaml b/recipes/bioconductor-nugohs1a520180cdf/meta.yaml index 0f34f7b793e3f..130452d0f1a55 100644 --- a/recipes/bioconductor-nugohs1a520180cdf/meta.yaml +++ b/recipes/bioconductor-nugohs1a520180cdf/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.4.0" %} {% set name = "nugohs1a520180cdf" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -12,19 +12,19 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: aa152658a4a801cc0edb552a98aee841 build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' - r-base run: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-nugohs1a520180cdf/post-link.sh b/recipes/bioconductor-nugohs1a520180cdf/post-link.sh index 3bac5f680930e..15e9d9e1fa342 100644 --- a/recipes/bioconductor-nugohs1a520180cdf/post-link.sh +++ b/recipes/bioconductor-nugohs1a520180cdf/post-link.sh @@ -1,9 +1,10 @@ #!/bin/bash FN="nugohs1a520180cdf_3.4.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/nugohs1a520180cdf_3.4.0.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/nugohs1a520180cdf_3.4.0.tar.gz" "https://bioarchive.galaxyproject.org/nugohs1a520180cdf_3.4.0.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-nugohs1a520180cdf/bioconductor-nugohs1a520180cdf_3.4.0_src_all.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-nugohs1a520180cdf/bioconductor-nugohs1a520180cdf_3.4.0_src_all.tar.gz" ) MD5="aa152658a4a801cc0edb552a98aee841" @@ -16,7 +17,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-nugohs1a520180probe/meta.yaml b/recipes/bioconductor-nugohs1a520180probe/meta.yaml index 270127b234506..e3ba86650aa1b 100644 --- a/recipes/bioconductor-nugohs1a520180probe/meta.yaml +++ b/recipes/bioconductor-nugohs1a520180probe/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.4.0" %} {% set name = "nugohs1a520180probe" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -12,19 +12,19 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 6acf20ac4a799eaae97d0a64426d6ac3 build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' - r-base run: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-nugohs1a520180probe/post-link.sh b/recipes/bioconductor-nugohs1a520180probe/post-link.sh index 14feef1997906..08fca467ed4c3 100644 --- a/recipes/bioconductor-nugohs1a520180probe/post-link.sh +++ b/recipes/bioconductor-nugohs1a520180probe/post-link.sh @@ -1,9 +1,10 @@ #!/bin/bash FN="nugohs1a520180probe_3.4.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/nugohs1a520180probe_3.4.0.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/nugohs1a520180probe_3.4.0.tar.gz" "https://bioarchive.galaxyproject.org/nugohs1a520180probe_3.4.0.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-nugohs1a520180probe/bioconductor-nugohs1a520180probe_3.4.0_src_all.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-nugohs1a520180probe/bioconductor-nugohs1a520180probe_3.4.0_src_all.tar.gz" ) MD5="6acf20ac4a799eaae97d0a64426d6ac3" @@ -16,7 +17,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-nugomm1a520177.db/meta.yaml b/recipes/bioconductor-nugomm1a520177.db/meta.yaml index 8330d945e9f44..30f1cd9e61644 100644 --- a/recipes/bioconductor-nugomm1a520177.db/meta.yaml +++ b/recipes/bioconductor-nugomm1a520177.db/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.4.0" %} {% set name = "nugomm1a520177.db" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -12,7 +12,7 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 99f69ea2cbb80a79bedee99e3d726e50 build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ @@ -20,14 +20,14 @@ build: # Suggests: annotate, RUnit requirements: host: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' - - 'bioconductor-org.mm.eg.db >=3.7.0,<3.8.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' + - 'bioconductor-org.mm.eg.db >=3.8.0,<3.9.0' - r-base run: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' - - 'bioconductor-org.mm.eg.db >=3.7.0,<3.8.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' + - 'bioconductor-org.mm.eg.db >=3.8.0,<3.9.0' - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-nugomm1a520177.db/post-link.sh b/recipes/bioconductor-nugomm1a520177.db/post-link.sh index cf84b41742f3f..0b9a2ea251af5 100644 --- a/recipes/bioconductor-nugomm1a520177.db/post-link.sh +++ b/recipes/bioconductor-nugomm1a520177.db/post-link.sh @@ -1,9 +1,10 @@ #!/bin/bash FN="nugomm1a520177.db_3.4.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/nugomm1a520177.db_3.4.0.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/nugomm1a520177.db_3.4.0.tar.gz" "https://bioarchive.galaxyproject.org/nugomm1a520177.db_3.4.0.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-nugomm1a520177.db/bioconductor-nugomm1a520177.db_3.4.0_src_all.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-nugomm1a520177.db/bioconductor-nugomm1a520177.db_3.4.0_src_all.tar.gz" ) MD5="99f69ea2cbb80a79bedee99e3d726e50" @@ -16,7 +17,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-nugomm1a520177cdf/meta.yaml b/recipes/bioconductor-nugomm1a520177cdf/meta.yaml index 709265f1f3771..d86d5a0903d24 100644 --- a/recipes/bioconductor-nugomm1a520177cdf/meta.yaml +++ b/recipes/bioconductor-nugomm1a520177cdf/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.4.0" %} {% set name = "nugomm1a520177cdf" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -12,19 +12,19 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: fc60c2018580decaea30f09de55142fb build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' - r-base run: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-nugomm1a520177cdf/post-link.sh b/recipes/bioconductor-nugomm1a520177cdf/post-link.sh index 61e45ccfdd064..a08841809a610 100644 --- a/recipes/bioconductor-nugomm1a520177cdf/post-link.sh +++ b/recipes/bioconductor-nugomm1a520177cdf/post-link.sh @@ -1,9 +1,10 @@ #!/bin/bash FN="nugomm1a520177cdf_3.4.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/nugomm1a520177cdf_3.4.0.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/nugomm1a520177cdf_3.4.0.tar.gz" "https://bioarchive.galaxyproject.org/nugomm1a520177cdf_3.4.0.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-nugomm1a520177cdf/bioconductor-nugomm1a520177cdf_3.4.0_src_all.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-nugomm1a520177cdf/bioconductor-nugomm1a520177cdf_3.4.0_src_all.tar.gz" ) MD5="fc60c2018580decaea30f09de55142fb" @@ -16,7 +17,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-nugomm1a520177probe/meta.yaml b/recipes/bioconductor-nugomm1a520177probe/meta.yaml index 0a3c9479520d0..8e0f5712d77c5 100644 --- a/recipes/bioconductor-nugomm1a520177probe/meta.yaml +++ b/recipes/bioconductor-nugomm1a520177probe/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.4.0" %} {% set name = "nugomm1a520177probe" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -12,19 +12,19 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 7fa974389ad2be6ebda8810496221a9b build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' - r-base run: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-nugomm1a520177probe/post-link.sh b/recipes/bioconductor-nugomm1a520177probe/post-link.sh index 798dff26d5c81..e72fa101610f4 100644 --- a/recipes/bioconductor-nugomm1a520177probe/post-link.sh +++ b/recipes/bioconductor-nugomm1a520177probe/post-link.sh @@ -1,9 +1,10 @@ #!/bin/bash FN="nugomm1a520177probe_3.4.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/nugomm1a520177probe_3.4.0.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/nugomm1a520177probe_3.4.0.tar.gz" "https://bioarchive.galaxyproject.org/nugomm1a520177probe_3.4.0.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-nugomm1a520177probe/bioconductor-nugomm1a520177probe_3.4.0_src_all.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-nugomm1a520177probe/bioconductor-nugomm1a520177probe_3.4.0_src_all.tar.gz" ) MD5="7fa974389ad2be6ebda8810496221a9b" @@ -16,7 +17,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-nupop/meta.yaml b/recipes/bioconductor-nupop/meta.yaml index 02e9195d889f4..9fb52e99d44cc 100644 --- a/recipes/bioconductor-nupop/meta.yaml +++ b/recipes/bioconductor-nupop/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.32.0" %} +{% set version = "1.34.0" %} {% set name = "NuPoP" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 4770138a010896a75cfedbde935bc816 + md5: 2f2469ea1cc2c7a36a3ebe6abc8cfe28 build: number: 0 rpaths: diff --git a/recipes/bioconductor-occugene/meta.yaml b/recipes/bioconductor-occugene/meta.yaml index 35c68a95c9589..cc7d7b82ac627 100644 --- a/recipes/bioconductor-occugene/meta.yaml +++ b/recipes/bioconductor-occugene/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.42.0" %} +{% set version = "1.44.0" %} {% set name = "occugene" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: c294febad5ded94b6e0f1223beac3b78 + md5: f962202fd42a1aa9933fe50bacbdef7d build: number: 0 rpaths: diff --git a/recipes/bioconductor-ocplus/meta.yaml b/recipes/bioconductor-ocplus/meta.yaml index 4e70e2c90bbb6..497f245616261 100644 --- a/recipes/bioconductor-ocplus/meta.yaml +++ b/recipes/bioconductor-ocplus/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.56.0" %} +{% set version = "1.58.0" %} {% set name = "OCplus" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 318784b120a74c9a49abecfdeb6d0891 + md5: 67aa4e3c2f906fb79a70714819df5e13 build: number: 0 rpaths: @@ -19,11 +19,11 @@ build: noarch: generic requirements: host: - - 'bioconductor-multtest >=2.38.0,<2.39.0' + - 'bioconductor-multtest >=2.40.0,<2.41.0' - r-akima - r-base run: - - 'bioconductor-multtest >=2.38.0,<2.39.0' + - 'bioconductor-multtest >=2.40.0,<2.41.0' - r-akima - r-base test: diff --git a/recipes/bioconductor-oct4/meta.yaml b/recipes/bioconductor-oct4/meta.yaml new file mode 100644 index 0000000000000..bf88c80942d32 --- /dev/null +++ b/recipes/bioconductor-oct4/meta.yaml @@ -0,0 +1,34 @@ +{% set version = "1.0.0" %} +{% set name = "oct4" %} +{% set bioc = "3.9" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + md5: 4258694f3a51f0723ee90a5cdc241d03 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: knitr +requirements: + host: + - r-base + run: + - r-base + - curl +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html' + license: 'GPL (>= 2)' + summary: 'This package provides the output of running Salmon on a set of 12 RNA-seq samples from King & Klose, "The pioneer factor OCT4 requires the chromatin remodeller BRG1 to support gene regulatory element function in mouse embryonic stem cells", published in eLIFE, March 2017. For details on version numbers and how the samples were processed see the package vignette.' + diff --git a/recipes/bioconductor-oct4/post-link.sh b/recipes/bioconductor-oct4/post-link.sh new file mode 100644 index 0000000000000..c75291f6124b4 --- /dev/null +++ b/recipes/bioconductor-oct4/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="oct4_1.0.0.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.9/data/experiment/src/contrib/oct4_1.0.0.tar.gz" + "https://bioarchive.galaxyproject.org/oct4_1.0.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-oct4/bioconductor-oct4_1.0.0_src_all.tar.gz" +) +MD5="4258694f3a51f0723ee90a5cdc241d03" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + curl $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-oct4/pre-unlink.sh b/recipes/bioconductor-oct4/pre-unlink.sh new file mode 100644 index 0000000000000..1e9b75c4e8560 --- /dev/null +++ b/recipes/bioconductor-oct4/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ oct4 diff --git a/recipes/bioconductor-odseq/meta.yaml b/recipes/bioconductor-odseq/meta.yaml index 62b19ede042bb..4192733c9f598 100644 --- a/recipes/bioconductor-odseq/meta.yaml +++ b/recipes/bioconductor-odseq/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.10.0" %} +{% set version = "1.12.0" %} {% set name = "odseq" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 18974dd1cc6085e325565b9a4f01e635 + md5: 7b25fb80682d5695daa2562bafa1987d build: number: 0 rpaths: @@ -20,13 +20,13 @@ build: # Suggests: knitr(>= 1.11) requirements: host: - - 'bioconductor-kebabs >=1.16.0,<1.17.0' - - 'bioconductor-msa >=1.14.0,<1.15.0' + - 'bioconductor-kebabs >=1.18.0,<1.19.0' + - 'bioconductor-msa >=1.16.0,<1.17.0' - r-base - 'r-mclust >=5.1' run: - - 'bioconductor-kebabs >=1.16.0,<1.17.0' - - 'bioconductor-msa >=1.14.0,<1.15.0' + - 'bioconductor-kebabs >=1.18.0,<1.19.0' + - 'bioconductor-msa >=1.16.0,<1.17.0' - r-base - 'r-mclust >=5.1' test: diff --git a/recipes/bioconductor-ogsa/meta.yaml b/recipes/bioconductor-ogsa/meta.yaml index 7a378cf39df2c..531c8c7666aac 100644 --- a/recipes/bioconductor-ogsa/meta.yaml +++ b/recipes/bioconductor-ogsa/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.12.0" %} +{% set version = "1.14.0" %} {% set name = "OGSA" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 3e46b50f76f97e0da3c912e661bd5e12 + md5: ea8ef4b05643bef784d87d23ffa04d50 build: number: 0 rpaths: @@ -19,13 +19,13 @@ build: noarch: generic requirements: host: - - 'bioconductor-biobase >=2.42.0,<2.43.0' - - 'bioconductor-limma >=3.38.0,<3.39.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' + - 'bioconductor-limma >=3.40.0,<3.41.0' - r-base - 'r-gplots >=2.8.0' run: - - 'bioconductor-biobase >=2.42.0,<2.43.0' - - 'bioconductor-limma >=3.38.0,<3.39.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' + - 'bioconductor-limma >=3.40.0,<3.41.0' - r-base - 'r-gplots >=2.8.0' test: diff --git a/recipes/bioconductor-oligo/meta.yaml b/recipes/bioconductor-oligo/meta.yaml index df50408444dfb..05afcd143c083 100644 --- a/recipes/bioconductor-oligo/meta.yaml +++ b/recipes/bioconductor-oligo/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.46.0" %} +{% set version = "1.48.0" %} {% set name = "oligo" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: a3ecdc244b8f0b20408c7251c13cc0ca + md5: d0d6c5b97dfe4ab1811da5c58d3cad1b build: number: 0 rpaths: @@ -19,27 +19,27 @@ build: # Suggests: BSgenome.Hsapiens.UCSC.hg18, hapmap100kxba, pd.hg.u95av2, pd.mapping50k.xba240, pd.huex.1.0.st.v2, pd.hg18.60mer.expr, pd.hugene.1.0.st.v1, maqcExpression4plex, genefilter, limma, RColorBrewer, oligoData, BiocStyle, knitr, RUnit, biomaRt, AnnotationDbi, GenomeGraphs, RCurl, ACME, biomaRt, AnnotationDbi, GenomeGraphs, RCurl requirements: host: - - 'bioconductor-affxparser >=1.54.0,<1.55.0' - - 'bioconductor-affyio >=1.52.0,<1.53.0' - - 'bioconductor-biobase >=2.42.0,<2.43.0' - - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' - - 'bioconductor-biostrings >=2.50.0,<2.51.0' - - 'bioconductor-oligoclasses >=1.44.0,<1.45.0' - - 'bioconductor-preprocesscore >=1.44.0,<1.45.0' - - 'bioconductor-zlibbioc >=1.28.0,<1.29.0' + - 'bioconductor-affxparser >=1.56.0,<1.57.0' + - 'bioconductor-affyio >=1.54.0,<1.55.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' + - 'bioconductor-biocgenerics >=0.30.0,<0.31.0' + - 'bioconductor-biostrings >=2.52.0,<2.53.0' + - 'bioconductor-oligoclasses >=1.46.0,<1.47.0' + - 'bioconductor-preprocesscore >=1.46.0,<1.47.0' + - 'bioconductor-zlibbioc >=1.30.0,<1.31.0' - r-base - 'r-dbi >=0.3.1' - r-ff - 'r-rsqlite >=1.0.0' run: - - 'bioconductor-affxparser >=1.54.0,<1.55.0' - - 'bioconductor-affyio >=1.52.0,<1.53.0' - - 'bioconductor-biobase >=2.42.0,<2.43.0' - - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' - - 'bioconductor-biostrings >=2.50.0,<2.51.0' - - 'bioconductor-oligoclasses >=1.44.0,<1.45.0' - - 'bioconductor-preprocesscore >=1.44.0,<1.45.0' - - 'bioconductor-zlibbioc >=1.28.0,<1.29.0' + - 'bioconductor-affxparser >=1.56.0,<1.57.0' + - 'bioconductor-affyio >=1.54.0,<1.55.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' + - 'bioconductor-biocgenerics >=0.30.0,<0.31.0' + - 'bioconductor-biostrings >=2.52.0,<2.53.0' + - 'bioconductor-oligoclasses >=1.46.0,<1.47.0' + - 'bioconductor-preprocesscore >=1.46.0,<1.47.0' + - 'bioconductor-zlibbioc >=1.30.0,<1.31.0' - r-base - 'r-dbi >=0.3.1' - r-ff diff --git a/recipes/bioconductor-oligoclasses/meta.yaml b/recipes/bioconductor-oligoclasses/meta.yaml index acef8e6c452ac..28fd4a0051b5d 100644 --- a/recipes/bioconductor-oligoclasses/meta.yaml +++ b/recipes/bioconductor-oligoclasses/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.44.0" %} +{% set version = "1.46.0" %} {% set name = "oligoClasses" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: c58277928932218857e89afeeffc7aa9 + md5: f7ddb837c47f2126caea204d7cf0deb5 build: number: 0 rpaths: @@ -20,14 +20,14 @@ build: # Suggests: hapmapsnp5, hapmapsnp6, pd.genomewidesnp.6, pd.genomewidesnp.5, pd.mapping50k.hind240, pd.mapping50k.xba240, pd.mapping250k.sty, pd.mapping250k.nsp, genomewidesnp6Crlmm (>= 1.0.7), genomewidesnp5Crlmm (>= 1.0.6), RUnit, human370v1cCrlmm, SNPchip, VanillaICE, crlmm requirements: host: - - 'bioconductor-affyio >=1.52.0,<1.53.0' - - 'bioconductor-biobase >=2.42.0,<2.43.0' - - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' - - 'bioconductor-biostrings >=2.50.0,<2.51.0' - - 'bioconductor-genomicranges >=1.34.0,<1.35.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' - - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' + - 'bioconductor-affyio >=1.54.0,<1.55.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' + - 'bioconductor-biocgenerics >=0.30.0,<0.31.0' + - 'bioconductor-biostrings >=2.52.0,<2.53.0' + - 'bioconductor-genomicranges >=1.36.0,<1.37.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' + - 'bioconductor-summarizedexperiment >=1.14.0,<1.15.0' - r-base - r-biocmanager - r-dbi @@ -35,14 +35,14 @@ requirements: - r-foreach - r-rsqlite run: - - 'bioconductor-affyio >=1.52.0,<1.53.0' - - 'bioconductor-biobase >=2.42.0,<2.43.0' - - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' - - 'bioconductor-biostrings >=2.50.0,<2.51.0' - - 'bioconductor-genomicranges >=1.34.0,<1.35.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' - - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' + - 'bioconductor-affyio >=1.54.0,<1.55.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' + - 'bioconductor-biocgenerics >=0.30.0,<0.31.0' + - 'bioconductor-biostrings >=2.52.0,<2.53.0' + - 'bioconductor-genomicranges >=1.36.0,<1.37.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' + - 'bioconductor-summarizedexperiment >=1.14.0,<1.15.0' - r-base - r-biocmanager - r-dbi diff --git a/recipes/bioconductor-oligodata/meta.yaml b/recipes/bioconductor-oligodata/meta.yaml index 9a4853479a6e2..8f81b0d6c3f44 100644 --- a/recipes/bioconductor-oligodata/meta.yaml +++ b/recipes/bioconductor-oligodata/meta.yaml @@ -1,6 +1,6 @@ {% set version = "1.8.0" %} {% set name = "oligoData" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -12,7 +12,7 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' md5: 9625cfd4b31bb575c4029a0632a7ee12 build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ @@ -20,12 +20,12 @@ build: # Suggests: pd.hg.u95av2, pd.huex.1.0.st.v2, pd.mapping50k.xba240, pd.hg18.60mer.expr, pd.2006.07.18.hg18.refseq.promoter, pd.hugene.1.0.st.v1 requirements: host: - - 'bioconductor-oligo >=1.46.0,<1.47.0' + - 'bioconductor-oligo >=1.48.0,<1.49.0' - r-base run: - - 'bioconductor-oligo >=1.46.0,<1.47.0' + - 'bioconductor-oligo >=1.48.0,<1.49.0' - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-oligodata/post-link.sh b/recipes/bioconductor-oligodata/post-link.sh index d911d5e768893..1c9a3719ac6f9 100644 --- a/recipes/bioconductor-oligodata/post-link.sh +++ b/recipes/bioconductor-oligodata/post-link.sh @@ -1,9 +1,10 @@ #!/bin/bash FN="oligoData_1.8.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/oligoData_1.8.0.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/oligoData_1.8.0.tar.gz" "https://bioarchive.galaxyproject.org/oligoData_1.8.0.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-oligodata/bioconductor-oligodata_1.8.0_src_all.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-oligodata/bioconductor-oligodata_1.8.0_src_all.tar.gz" ) MD5="9625cfd4b31bb575c4029a0632a7ee12" @@ -16,7 +17,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-olin/meta.yaml b/recipes/bioconductor-olin/meta.yaml index 69a0a23a61cd4..0fec1dd3d24a4 100644 --- a/recipes/bioconductor-olin/meta.yaml +++ b/recipes/bioconductor-olin/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.60.0" %} +{% set version = "1.62.0" %} {% set name = "OLIN" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 8c56f4b27a4c0fd7d3554d7153ba260b + md5: 3853f23caccdf30142ec1c85b4d9a47b build: number: 0 rpaths: @@ -20,13 +20,13 @@ build: # Suggests: convert requirements: host: - - 'bioconductor-limma >=3.38.0,<3.39.0' - - 'bioconductor-marray >=1.60.0,<1.61.0' + - 'bioconductor-limma >=3.40.0,<3.41.0' + - 'bioconductor-marray >=1.62.0,<1.63.0' - r-base - r-locfit run: - - 'bioconductor-limma >=3.38.0,<3.39.0' - - 'bioconductor-marray >=1.60.0,<1.61.0' + - 'bioconductor-limma >=3.40.0,<3.41.0' + - 'bioconductor-marray >=1.62.0,<1.63.0' - r-base - r-locfit test: diff --git a/recipes/bioconductor-olingui/meta.yaml b/recipes/bioconductor-olingui/meta.yaml index dc379c3b825ba..6f71c3fe5d376 100644 --- a/recipes/bioconductor-olingui/meta.yaml +++ b/recipes/bioconductor-olingui/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.56.0" %} +{% set version = "1.58.0" %} {% set name = "OLINgui" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: d80fde109f35a28abd65089848537969 + md5: de501564169222861b7036ba2516ad07 build: number: 0 rpaths: @@ -19,16 +19,16 @@ build: noarch: generic requirements: host: - - 'bioconductor-marray >=1.60.0,<1.61.0' - - 'bioconductor-olin >=1.60.0,<1.61.0' - - 'bioconductor-tkwidgets >=1.60.0,<1.61.0' - - 'bioconductor-widgettools >=1.60.0,<1.61.0' + - 'bioconductor-marray >=1.62.0,<1.63.0' + - 'bioconductor-olin >=1.62.0,<1.63.0' + - 'bioconductor-tkwidgets >=1.62.0,<1.63.0' + - 'bioconductor-widgettools >=1.62.0,<1.63.0' - r-base run: - - 'bioconductor-marray >=1.60.0,<1.61.0' - - 'bioconductor-olin >=1.60.0,<1.61.0' - - 'bioconductor-tkwidgets >=1.60.0,<1.61.0' - - 'bioconductor-widgettools >=1.60.0,<1.61.0' + - 'bioconductor-marray >=1.62.0,<1.63.0' + - 'bioconductor-olin >=1.62.0,<1.63.0' + - 'bioconductor-tkwidgets >=1.62.0,<1.63.0' + - 'bioconductor-widgettools >=1.62.0,<1.63.0' - r-base test: commands: diff --git a/recipes/bioconductor-omadb/meta.yaml b/recipes/bioconductor-omadb/meta.yaml index aaffe7996b59d..2e8175e8b1a67 100644 --- a/recipes/bioconductor-omadb/meta.yaml +++ b/recipes/bioconductor-omadb/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.2.0" %} +{% set version = "2.0.0" %} {% set name = "OmaDB" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 60387eba231f92262948624be804cc12 + md5: 04d5c2a7123cc04e31e0a3c4c0f8eac2 build: number: 0 rpaths: @@ -20,20 +20,20 @@ build: # Suggests: knitr, rmarkdown, testthat requirements: host: - - 'bioconductor-biostrings >=2.50.0,<2.51.0' - - 'bioconductor-genomicranges >=1.34.0,<1.35.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-topgo >=2.34.0,<2.35.0' + - 'bioconductor-biostrings >=2.52.0,<2.53.0' + - 'bioconductor-genomicranges >=1.36.0,<1.37.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-topgo >=2.36.0,<2.37.0' - r-ape - r-base - 'r-httr >=1.2.1' - r-jsonlite - 'r-plyr >=1.8.4' run: - - 'bioconductor-biostrings >=2.50.0,<2.51.0' - - 'bioconductor-genomicranges >=1.34.0,<1.35.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-topgo >=2.34.0,<2.35.0' + - 'bioconductor-biostrings >=2.52.0,<2.53.0' + - 'bioconductor-genomicranges >=1.36.0,<1.37.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-topgo >=2.36.0,<2.37.0' - r-ape - r-base - 'r-httr >=1.2.1' @@ -44,6 +44,6 @@ test: - '$R -e "library(''{{ name }}'')"' about: home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: GPL-2 + license: GPL-3 summary: 'A package for the orthology prediction data download from OMA database.' diff --git a/recipes/bioconductor-omicade4/meta.yaml b/recipes/bioconductor-omicade4/meta.yaml index e1320ccfaa3a3..0081efbf54d65 100644 --- a/recipes/bioconductor-omicade4/meta.yaml +++ b/recipes/bioconductor-omicade4/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.22.0" %} +{% set version = "1.24.0" %} {% set name = "omicade4" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 5a5e6def3842ea64955d6f4004c01ca0 + md5: fd3f9e91dd3b5fbd13dd938232348e50 build: number: 0 rpaths: @@ -20,11 +20,11 @@ build: # Suggests: BiocStyle requirements: host: - - 'bioconductor-made4 >=1.56.0,<1.57.0' + - 'bioconductor-made4 >=1.58.0,<1.59.0' - r-ade4 - r-base run: - - 'bioconductor-made4 >=1.56.0,<1.57.0' + - 'bioconductor-made4 >=1.58.0,<1.59.0' - r-ade4 - r-base test: diff --git a/recipes/bioconductor-omiccircos/meta.yaml b/recipes/bioconductor-omiccircos/meta.yaml index f8e8393bcb042..877c72345ff52 100644 --- a/recipes/bioconductor-omiccircos/meta.yaml +++ b/recipes/bioconductor-omiccircos/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.20.0" %} +{% set version = "1.22.0" %} {% set name = "OmicCircos" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 6f138f977152b3f86101ae451fc9368d + md5: 9d3312b4108c9266549045b04bbdba88 build: number: 0 rpaths: @@ -19,10 +19,10 @@ build: noarch: generic requirements: host: - - 'bioconductor-genomicranges >=1.34.0,<1.35.0' + - 'bioconductor-genomicranges >=1.36.0,<1.37.0' - r-base run: - - 'bioconductor-genomicranges >=1.34.0,<1.35.0' + - 'bioconductor-genomicranges >=1.36.0,<1.37.0' - r-base test: commands: diff --git a/recipes/bioconductor-omicplotr/meta.yaml b/recipes/bioconductor-omicplotr/meta.yaml index 08bf7516af493..6753e2e3c5006 100644 --- a/recipes/bioconductor-omicplotr/meta.yaml +++ b/recipes/bioconductor-omicplotr/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.2.0" %} +{% set version = "1.4.0" %} {% set name = "omicplotR" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 90b98aa96f0ed392ab2fc92c038ee9f8 + md5: 3ab083839f9b7efdfd632b9204eb7288 build: number: 0 rpaths: @@ -19,7 +19,7 @@ build: noarch: generic requirements: host: - - 'bioconductor-aldex2 >=1.14.0,<1.15.0' + - 'bioconductor-aldex2 >=1.16.0,<1.17.0' - r-base - r-compositions - r-knitr @@ -29,7 +29,7 @@ requirements: - r-vegan - r-zcompositions run: - - 'bioconductor-aldex2 >=1.14.0,<1.15.0' + - 'bioconductor-aldex2 >=1.16.0,<1.17.0' - r-base - r-compositions - r-knitr diff --git a/recipes/bioconductor-omicrexposome/meta.yaml b/recipes/bioconductor-omicrexposome/meta.yaml index c97ddcbb4e6ec..6cb3b9dd93ebb 100644 --- a/recipes/bioconductor-omicrexposome/meta.yaml +++ b/recipes/bioconductor-omicrexposome/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.4.0" %} +{% set version = "1.6.0" %} {% set name = "omicRexposome" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 84a97bc40482e4ac0b1bf9524b0d30a5 + md5: b6f376d1a54b397d8ae243ecdfe6142b build: number: 0 rpaths: @@ -20,13 +20,13 @@ build: # Suggests: BiocStyle, knitr, rmarkdown, snpStats, brgedata requirements: host: - - 'bioconductor-biobase >=2.42.0,<2.43.0' - - 'bioconductor-limma >=3.38.0,<3.39.0' - - 'bioconductor-multidataset >=1.10.0,<1.11.0' - - 'bioconductor-omicade4 >=1.22.0,<1.23.0' - - 'bioconductor-rexposome >=1.4.0,<1.5.0' - - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' - - 'bioconductor-sva >=3.30.0,<3.31.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' + - 'bioconductor-limma >=3.40.0,<3.41.0' + - 'bioconductor-multidataset >=1.12.0,<1.13.0' + - 'bioconductor-omicade4 >=1.24.0,<1.25.0' + - 'bioconductor-rexposome >=1.6.0,<1.7.0' + - 'bioconductor-summarizedexperiment >=1.14.0,<1.15.0' + - 'bioconductor-sva >=3.32.0,<3.33.0' - r-base - r-ggplot2 - r-ggrepel @@ -36,13 +36,13 @@ requirements: - r-smartsva - r-stringr run: - - 'bioconductor-biobase >=2.42.0,<2.43.0' - - 'bioconductor-limma >=3.38.0,<3.39.0' - - 'bioconductor-multidataset >=1.10.0,<1.11.0' - - 'bioconductor-omicade4 >=1.22.0,<1.23.0' - - 'bioconductor-rexposome >=1.4.0,<1.5.0' - - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' - - 'bioconductor-sva >=3.30.0,<3.31.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' + - 'bioconductor-limma >=3.40.0,<3.41.0' + - 'bioconductor-multidataset >=1.12.0,<1.13.0' + - 'bioconductor-omicade4 >=1.24.0,<1.25.0' + - 'bioconductor-rexposome >=1.6.0,<1.7.0' + - 'bioconductor-summarizedexperiment >=1.14.0,<1.15.0' + - 'bioconductor-sva >=3.32.0,<3.33.0' - r-base - r-ggplot2 - r-ggrepel diff --git a/recipes/bioconductor-omicslonda/build.sh b/recipes/bioconductor-omicslonda/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-omicslonda/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-omicslonda/meta.yaml b/recipes/bioconductor-omicslonda/meta.yaml new file mode 100644 index 0000000000000..552cf99513c1a --- /dev/null +++ b/recipes/bioconductor-omicslonda/meta.yaml @@ -0,0 +1,49 @@ +{% set version = "1.0.0" %} +{% set name = "OmicsLonDA" %} +{% set bioc = "3.9" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: f67896a0ef0785819dc9642850235b15 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: knitr, rmarkdown, testthat, devtools, BiocManager +requirements: + host: + - 'bioconductor-biocgenerics >=0.30.0,<0.31.0' + - 'bioconductor-biocparallel >=1.18.0,<1.19.0' + - 'bioconductor-summarizedexperiment >=1.14.0,<1.15.0' + - r-base + - r-ggplot2 + - r-gss + - r-plyr + - r-pracma + - r-zoo + run: + - 'bioconductor-biocgenerics >=0.30.0,<0.31.0' + - 'bioconductor-biocparallel >=1.18.0,<1.19.0' + - 'bioconductor-summarizedexperiment >=1.14.0,<1.15.0' + - r-base + - r-ggplot2 + - r-gss + - r-plyr + - r-pracma + - r-zoo +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: 'MIT + file LICENSE' + summary: 'Statistical method that provides robust identification of time intervals where omics features (such as proteomics, lipidomics, metabolomics, transcriptomics, microbiome, as well as physiological parameters captured by wearable sensors such as heart rhythm, body temperature, and activity level) are significantly different between groups.' + diff --git a/recipes/bioconductor-omicsmarker/meta.yaml b/recipes/bioconductor-omicsmarker/meta.yaml index ee498290a5a21..9799ec570532e 100644 --- a/recipes/bioconductor-omicsmarker/meta.yaml +++ b/recipes/bioconductor-omicsmarker/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.14.0" %} +{% set version = "1.16.0" %} {% set name = "OmicsMarkeR" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 10593af3dcc1bdf37ac363bf3956af43 + md5: 9c82a60dce4f945966d2ba6fd761ecb3 build: number: 0 rpaths: diff --git a/recipes/bioconductor-omicspca/meta.yaml b/recipes/bioconductor-omicspca/meta.yaml index 643d3346f53d5..63ca059318d7d 100644 --- a/recipes/bioconductor-omicspca/meta.yaml +++ b/recipes/bioconductor-omicspca/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.0.1" %} +{% set version = "1.2.0" %} {% set name = "OMICsPCA" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: fe7ca779103cbd3414d8d5b6bd4ad022 + md5: e69ae22e13ed95a9060126f90b5ecbd0 build: number: 0 rpaths: @@ -20,12 +20,12 @@ build: # Suggests: knitr, RUnit, BiocGenerics requirements: host: - - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' - - 'bioconductor-helloranges >=1.8.0,<1.9.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-multiassayexperiment >=1.8.0,<1.9.0' - - 'bioconductor-omicspcadata >=1.0.0,<1.1.0' - - 'bioconductor-rtracklayer >=1.42.0,<1.43.0' + - 'bioconductor-genomeinfodb >=1.20.0,<1.21.0' + - 'bioconductor-helloranges >=1.10.0,<1.11.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-multiassayexperiment >=1.10.0,<1.11.0' + - 'bioconductor-omicspcadata >=1.2.0,<1.3.0' + - 'bioconductor-rtracklayer >=1.44.0,<1.45.0' - r-base - r-cluster - r-clvalid @@ -47,12 +47,12 @@ requirements: - r-rmarkdown - r-tidyr run: - - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' - - 'bioconductor-helloranges >=1.8.0,<1.9.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-multiassayexperiment >=1.8.0,<1.9.0' - - 'bioconductor-omicspcadata >=1.0.0,<1.1.0' - - 'bioconductor-rtracklayer >=1.42.0,<1.43.0' + - 'bioconductor-genomeinfodb >=1.20.0,<1.21.0' + - 'bioconductor-helloranges >=1.10.0,<1.11.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-multiassayexperiment >=1.10.0,<1.11.0' + - 'bioconductor-omicspcadata >=1.2.0,<1.3.0' + - 'bioconductor-rtracklayer >=1.44.0,<1.45.0' - r-base - r-cluster - r-clvalid diff --git a/recipes/bioconductor-omicspcadata/meta.yaml b/recipes/bioconductor-omicspcadata/meta.yaml index 142c6f8133679..4416386c265e4 100644 --- a/recipes/bioconductor-omicspcadata/meta.yaml +++ b/recipes/bioconductor-omicspcadata/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.0.0" %} +{% set version = "1.2.0" %} {% set name = "OMICsPCAdata" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: aec265a048e822143e27ad37dbde1c38 + md5: 8edbe12b716d34eb42783e0b327582bf build: number: 0 rpaths: @@ -20,12 +20,12 @@ build: # Suggests: knitr, kableExtra, rmarkdown requirements: host: - - 'bioconductor-multiassayexperiment >=1.8.0,<1.9.0' + - 'bioconductor-multiassayexperiment >=1.10.0,<1.11.0' - r-base run: - - 'bioconductor-multiassayexperiment >=1.8.0,<1.9.0' + - 'bioconductor-multiassayexperiment >=1.10.0,<1.11.0' - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-omicspcadata/post-link.sh b/recipes/bioconductor-omicspcadata/post-link.sh index 305cbbe3b5ed5..5c0afcb91e7aa 100644 --- a/recipes/bioconductor-omicspcadata/post-link.sh +++ b/recipes/bioconductor-omicspcadata/post-link.sh @@ -1,11 +1,11 @@ #!/bin/bash -FN="OMICsPCAdata_1.0.0.tar.gz" +FN="OMICsPCAdata_1.2.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/experiment/src/contrib/OMICsPCAdata_1.0.0.tar.gz" - "https://bioarchive.galaxyproject.org/OMICsPCAdata_1.0.0.tar.gz" - "https://depot.galaxyproject.org/software/bioconductor-omicspcadata/bioconductor-omicspcadata_1.0.0_src_all.tar.gz" + "https://bioconductor.org/packages/3.9/data/experiment/src/contrib/OMICsPCAdata_1.2.0.tar.gz" + "https://bioarchive.galaxyproject.org/OMICsPCAdata_1.2.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-omicspcadata/bioconductor-omicspcadata_1.2.0_src_all.tar.gz" ) -MD5="aec265a048e822143e27ad37dbde1c38" +MD5="8edbe12b716d34eb42783e0b327582bf" # Use a staging area in the conda dir rather than temp dirs, both to avoid # permission issues as well as to have things downloaded in a predictable @@ -16,7 +16,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-omicsprint/meta.yaml b/recipes/bioconductor-omicsprint/meta.yaml index 81e609104129c..d37831e225f73 100644 --- a/recipes/bioconductor-omicsprint/meta.yaml +++ b/recipes/bioconductor-omicsprint/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.2.1" %} +{% set version = "1.4.0" %} {% set name = "omicsPrint" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 50236bbbb3b86de54afb81de6ea0aee5 + md5: 2021c5dae6aac2e7d35b1ddafe15135c build: number: 0 rpaths: @@ -20,16 +20,16 @@ build: # Suggests: BiocStyle, knitr, rmarkdown, testthat, GEOquery, VariantAnnotation, Rsamtools, BiocParallel, GenomicRanges, FDb.InfiniumMethylation.hg19, snpStats requirements: host: - - 'bioconductor-multiassayexperiment >=1.8.0,<1.9.0' - - 'bioconductor-raggedexperiment >=1.6.0,<1.7.0' - - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' + - 'bioconductor-multiassayexperiment >=1.10.0,<1.11.0' + - 'bioconductor-raggedexperiment >=1.8.0,<1.9.0' + - 'bioconductor-summarizedexperiment >=1.14.0,<1.15.0' - r-base - r-mass - r-matrixstats run: - - 'bioconductor-multiassayexperiment >=1.8.0,<1.9.0' - - 'bioconductor-raggedexperiment >=1.6.0,<1.7.0' - - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' + - 'bioconductor-multiassayexperiment >=1.10.0,<1.11.0' + - 'bioconductor-raggedexperiment >=1.8.0,<1.9.0' + - 'bioconductor-summarizedexperiment >=1.14.0,<1.15.0' - r-base - r-mass - r-matrixstats diff --git a/recipes/bioconductor-onassis/meta.yaml b/recipes/bioconductor-onassis/meta.yaml index 94e3a2a2f53c7..06742399b9f08 100644 --- a/recipes/bioconductor-onassis/meta.yaml +++ b/recipes/bioconductor-onassis/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.4.5" %} +{% set version = "1.6.0" %} {% set name = "Onassis" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 89a0e8751411bc21806a3159112bc2b8 + md5: 49ba45c496aa91382326605371c0022d build: number: 0 rpaths: @@ -21,9 +21,9 @@ build: # SystemRequirements: Java (>= 1.8) requirements: host: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' - - 'bioconductor-geometadb >=1.44.0,<1.45.0' - - 'bioconductor-onassisjavalibs >=1.4.0,<1.5.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' + - 'bioconductor-geometadb >=1.46.0,<1.47.0' + - 'bioconductor-onassisjavalibs >=1.6.0,<1.7.0' - r-base - r-data.table - r-dt @@ -32,9 +32,9 @@ requirements: - r-rjava - r-rsqlite run: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' - - 'bioconductor-geometadb >=1.44.0,<1.45.0' - - 'bioconductor-onassisjavalibs >=1.4.0,<1.5.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' + - 'bioconductor-geometadb >=1.46.0,<1.47.0' + - 'bioconductor-onassisjavalibs >=1.6.0,<1.7.0' - r-base - r-data.table - r-dt diff --git a/recipes/bioconductor-onassisjavalibs/meta.yaml b/recipes/bioconductor-onassisjavalibs/meta.yaml index bd450781fb8e1..ddaebe9b6e7ac 100644 --- a/recipes/bioconductor-onassisjavalibs/meta.yaml +++ b/recipes/bioconductor-onassisjavalibs/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.4.2" %} +{% set version = "1.6.0" %} {% set name = "OnassisJavaLibs" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 06e52b38a80a47e6b340cc0365e47554 + md5: ec733ed33c8932261fc34adaad85d038 build: number: 0 rpaths: @@ -26,7 +26,7 @@ requirements: run: - r-base - r-rjava - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-onassisjavalibs/post-link.sh b/recipes/bioconductor-onassisjavalibs/post-link.sh index d42ae05d9a199..09422c138da4a 100644 --- a/recipes/bioconductor-onassisjavalibs/post-link.sh +++ b/recipes/bioconductor-onassisjavalibs/post-link.sh @@ -1,11 +1,11 @@ #!/bin/bash -FN="OnassisJavaLibs_1.4.2.tar.gz" +FN="OnassisJavaLibs_1.6.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/experiment/src/contrib/OnassisJavaLibs_1.4.2.tar.gz" - "https://bioarchive.galaxyproject.org/OnassisJavaLibs_1.4.2.tar.gz" - "https://depot.galaxyproject.org/software/bioconductor-onassisjavalibs/bioconductor-onassisjavalibs_1.4.2_src_all.tar.gz" + "https://bioconductor.org/packages/3.9/data/experiment/src/contrib/OnassisJavaLibs_1.6.0.tar.gz" + "https://bioarchive.galaxyproject.org/OnassisJavaLibs_1.6.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-onassisjavalibs/bioconductor-onassisjavalibs_1.6.0_src_all.tar.gz" ) -MD5="06e52b38a80a47e6b340cc0365e47554" +MD5="ec733ed33c8932261fc34adaad85d038" # Use a staging area in the conda dir rather than temp dirs, both to avoid # permission issues as well as to have things downloaded in a predictable @@ -16,7 +16,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-oncomix/meta.yaml b/recipes/bioconductor-oncomix/meta.yaml index fab012e181e6f..905ea0644e178 100644 --- a/recipes/bioconductor-oncomix/meta.yaml +++ b/recipes/bioconductor-oncomix/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.4.0" %} +{% set version = "1.6.0" %} {% set name = "oncomix" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 24f731f87764297454ff5a4a9357f994 + md5: dc2814bcbc50ab49ba1b907cddb72e40 build: number: 0 rpaths: @@ -20,14 +20,14 @@ build: # Suggests: knitr, rmarkdown, testthat, RMySQL requirements: host: - - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' + - 'bioconductor-summarizedexperiment >=1.14.0,<1.15.0' - r-base - r-ggplot2 - r-ggrepel - r-mclust - r-rcolorbrewer run: - - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' + - 'bioconductor-summarizedexperiment >=1.14.0,<1.15.0' - r-base - r-ggplot2 - r-ggrepel diff --git a/recipes/bioconductor-oncoscore/meta.yaml b/recipes/bioconductor-oncoscore/meta.yaml index 5a8d3261d8164..c6c4d288e1922 100644 --- a/recipes/bioconductor-oncoscore/meta.yaml +++ b/recipes/bioconductor-oncoscore/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.10.0" %} +{% set version = "1.12.0" %} {% set name = "OncoScore" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 2037b880068e7ce59e92d799f28a9c4d + md5: bdf73cdd63364222c25bc2da53f68684 build: number: 0 rpaths: @@ -20,10 +20,10 @@ build: # Suggests: BiocGenerics, BiocStyle, knitr, testthat, requirements: host: - - 'bioconductor-biomart >=2.38.0,<2.39.0' + - 'bioconductor-biomart >=2.40.0,<2.41.0' - r-base run: - - 'bioconductor-biomart >=2.38.0,<2.39.0' + - 'bioconductor-biomart >=2.40.0,<2.41.0' - r-base test: commands: diff --git a/recipes/bioconductor-oncosimulr/meta.yaml b/recipes/bioconductor-oncosimulr/meta.yaml index c94d14aaae409..2be8c45bc61cb 100644 --- a/recipes/bioconductor-oncosimulr/meta.yaml +++ b/recipes/bioconductor-oncosimulr/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "2.12.0" %} +{% set version = "2.14.0" %} {% set name = "OncoSimulR" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 44f9be22a9965fe0389aad902c2d08d0 + md5: ad7ec9aa5aa85b0e0c961a23adf441ab build: number: 0 rpaths: @@ -19,9 +19,9 @@ build: # Suggests: BiocStyle, knitr, Oncotree, testthat (>= 1.0.0), rmarkdown, bookdown, pander requirements: host: - - 'bioconductor-graph >=1.60.0,<1.61.0' - - 'bioconductor-nem >=2.56.0,<2.57.0' - - 'bioconductor-rgraphviz >=2.26.0,<2.27.0' + - 'bioconductor-graph >=1.62.0,<1.63.0' + - 'bioconductor-nem >=2.58.0,<2.59.0' + - 'bioconductor-rgraphviz >=2.28.0,<2.29.0' - r-base - r-car - r-data.table @@ -34,9 +34,9 @@ requirements: - 'r-rcpp >=0.12.4' - r-smatr run: - - 'bioconductor-graph >=1.60.0,<1.61.0' - - 'bioconductor-nem >=2.56.0,<2.57.0' - - 'bioconductor-rgraphviz >=2.26.0,<2.27.0' + - 'bioconductor-graph >=1.62.0,<1.63.0' + - 'bioconductor-nem >=2.58.0,<2.59.0' + - 'bioconductor-rgraphviz >=2.28.0,<2.29.0' - r-base - r-car - r-data.table @@ -58,7 +58,7 @@ test: about: home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: 'GPL (>= 3)' - summary: 'Functions for forward population genetic simulation in asexual populations, with special focus on cancer progression. Fitness can be an arbitrary function of genetic interactions between multiple genes or modules of genes, including epistasis, order restrictions in mutation accumulation, and order effects. Mutation rates can differ between genes, and we can include mutator/antimutator genes (to model mutator phenotypes). Simulations use continuous-time models and can include driver and passenger genes and modules. Also included are functions for: simulating random DAGs of the type found in Oncogenetic Tress, Conjunctive Bayesian Networks, and other tumor progression models; plotting and sampling from single or multiple realizations of the simulations, including single-cell sampling; plotting the parent-child relationships of the clones; generating random fitness landscapes (Rough Mount Fuji, House of Cards, and additive models) and plotting them.' + summary: 'Functions for forward population genetic simulation in asexual populations, with special focus on cancer progression. Fitness can be an arbitrary function of genetic interactions between multiple genes or modules of genes, including epistasis, order restrictions in mutation accumulation, and order effects. Mutation rates can differ between genes, and we can include mutator/antimutator genes (to model mutator phenotypes). Simulations use continuous-time models and can include driver and passenger genes and modules. Also included are functions for: simulating random DAGs of the type found in Oncogenetic Trees, Conjunctive Bayesian Networks, and other cancer progression models; plotting and sampling from single or multiple realizations of the simulations, including single-cell sampling; plotting the parent-child relationships of the clones; generating random fitness landscapes (Rough Mount Fuji, House of Cards, and additive models) and plotting them.' extra: identifiers: - biotools:oncosimulr diff --git a/recipes/bioconductor-onesense/meta.yaml b/recipes/bioconductor-onesense/meta.yaml index 288eb659f698a..7344a4f931ef8 100644 --- a/recipes/bioconductor-onesense/meta.yaml +++ b/recipes/bioconductor-onesense/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.4.0" %} +{% set version = "1.6.0" %} {% set name = "oneSENSE" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 2bf3f4b39f72aab46b8a59d1475a0057 + md5: 54a7031cad9942f3de0ced671a2e7c5c build: number: 0 rpaths: @@ -20,7 +20,7 @@ build: # Suggests: knitr, rmarkdown requirements: host: - - 'bioconductor-flowcore >=1.48.0,<1.49.0' + - 'bioconductor-flowcore >=1.50.0,<1.51.0' - r-base - r-gplots - r-plotly @@ -30,7 +30,7 @@ requirements: - r-shinyfiles - r-webshot run: - - 'bioconductor-flowcore >=1.48.0,<1.49.0' + - 'bioconductor-flowcore >=1.50.0,<1.51.0' - r-base - r-gplots - r-plotly diff --git a/recipes/bioconductor-onlinefdr/meta.yaml b/recipes/bioconductor-onlinefdr/meta.yaml index 4dd94fe4fc2cb..0c16b722e4ee1 100644 --- a/recipes/bioconductor-onlinefdr/meta.yaml +++ b/recipes/bioconductor-onlinefdr/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.0.0" %} +{% set version = "1.2.0" %} {% set name = "onlineFDR" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 0f6c5c4dc344739ada4dc4be60aea0a5 + md5: 8c0cc1ff5c7853c657c14a291fa3c130 build: number: 0 rpaths: @@ -29,5 +29,5 @@ test: about: home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: GPL-3 - summary: 'This package allows users to control the false discovery rate for online hypothesis testing, where hypotheses arrive sequentially in a stream, as presented by Javanmard and Montanari (2015, 2018). In this framework, a null hypothesis is rejected based only on the previous decisions, as the future p-values and the number of hypotheses to be tested are unknown.' + summary: 'This package allows users to control the false discovery rate for online hypothesis testing, where hypotheses arrive sequentially in a stream, as presented by Javanmard and Montanari (2015, 2018) and Ramdas et al. (2017). In this framework, a null hypothesis is rejected based only on the previous decisions, as the future p-values and the number of hypotheses to be tested are unknown.' diff --git a/recipes/bioconductor-ontoproc/meta.yaml b/recipes/bioconductor-ontoproc/meta.yaml index 5cf1ab6e4b240..894c32adcca3d 100644 --- a/recipes/bioconductor-ontoproc/meta.yaml +++ b/recipes/bioconductor-ontoproc/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.4.0" %} +{% set version = "1.6.0" %} {% set name = "ontoProc" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 6c923d964ffaa80eff31fb0049e554ef + md5: 1339c7f7b63ecf3a629765e8ba2c5a1a build: number: 0 rpaths: @@ -20,18 +20,28 @@ build: # Suggests: knitr, org.Hs.eg.db, org.Mm.eg.db, testthat, BiocStyle requirements: host: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' - - 'bioconductor-biobase >=2.42.0,<2.43.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' + - 'bioconductor-graph >=1.62.0,<1.63.0' + - 'bioconductor-rgraphviz >=2.28.0,<2.29.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' - r-base + - r-dplyr + - r-magrittr - r-ontologyindex + - r-ontologyplot - r-shiny run: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' - - 'bioconductor-biobase >=2.42.0,<2.43.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' + - 'bioconductor-graph >=1.62.0,<1.63.0' + - 'bioconductor-rgraphviz >=2.28.0,<2.29.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' - r-base + - r-dplyr + - r-magrittr - r-ontologyindex + - r-ontologyplot - r-shiny test: commands: diff --git a/recipes/bioconductor-opencyto/meta.yaml b/recipes/bioconductor-opencyto/meta.yaml index 641a5df05c97c..eb0c9a096c2c2 100644 --- a/recipes/bioconductor-opencyto/meta.yaml +++ b/recipes/bioconductor-opencyto/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.20.1" %} +{% set version = "1.22.0" %} {% set name = "openCyto" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,25 +10,25 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: dbf8ed0437f362f3949f1c7180b836a7 + md5: 8ef329fcc5a35b0d0dc888d04503c78d build: number: 0 rpaths: - lib/R/lib/ - lib/ -# Suggests: flowWorkspaceData, knitr, testthat, utils, tools, parallel, ggcyto +# Suggests: flowWorkspaceData, knitr, testthat, utils, tools, parallel, ggcyto, CytoML requirements: host: - - 'bioconductor-biobase >=2.42.0,<2.43.0' - - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' - - 'bioconductor-flowclust >=3.20.0,<3.21.0' - - 'bioconductor-flowcore >=1.48.0,<1.49.0' - - 'bioconductor-flowstats >=3.40.0,<3.41.0' - - 'bioconductor-flowviz >=1.46.0,<1.47.0' - - 'bioconductor-flowworkspace >=3.30.0,<3.31.0' - - 'bioconductor-graph >=1.60.0,<1.61.0' - - 'bioconductor-ncdfflow >=2.28.0,<2.29.0' - - 'bioconductor-rbgl >=1.58.0,<1.59.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' + - 'bioconductor-biocgenerics >=0.30.0,<0.31.0' + - 'bioconductor-flowclust >=3.22.0,<3.23.0' + - 'bioconductor-flowcore >=1.50.0,<1.51.0' + - 'bioconductor-flowstats >=3.42.0,<3.43.0' + - 'bioconductor-flowviz >=1.48.0,<1.49.0' + - 'bioconductor-flowworkspace >=3.32.0,<3.33.0' + - 'bioconductor-graph >=1.62.0,<1.63.0' + - 'bioconductor-ncdfflow >=2.30.0,<2.31.0' + - 'bioconductor-rbgl >=1.60.0,<1.61.0' - r-base - r-clue - r-data.table @@ -42,16 +42,16 @@ requirements: - r-rcpp - r-rrcov run: - - 'bioconductor-biobase >=2.42.0,<2.43.0' - - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' - - 'bioconductor-flowclust >=3.20.0,<3.21.0' - - 'bioconductor-flowcore >=1.48.0,<1.49.0' - - 'bioconductor-flowstats >=3.40.0,<3.41.0' - - 'bioconductor-flowviz >=1.46.0,<1.47.0' - - 'bioconductor-flowworkspace >=3.30.0,<3.31.0' - - 'bioconductor-graph >=1.60.0,<1.61.0' - - 'bioconductor-ncdfflow >=2.28.0,<2.29.0' - - 'bioconductor-rbgl >=1.58.0,<1.59.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' + - 'bioconductor-biocgenerics >=0.30.0,<0.31.0' + - 'bioconductor-flowclust >=3.22.0,<3.23.0' + - 'bioconductor-flowcore >=1.50.0,<1.51.0' + - 'bioconductor-flowstats >=3.42.0,<3.43.0' + - 'bioconductor-flowviz >=1.48.0,<1.49.0' + - 'bioconductor-flowworkspace >=3.32.0,<3.33.0' + - 'bioconductor-graph >=1.62.0,<1.63.0' + - 'bioconductor-ncdfflow >=2.30.0,<2.31.0' + - 'bioconductor-rbgl >=1.60.0,<1.61.0' - r-base - r-clue - r-data.table diff --git a/recipes/bioconductor-openprimer/meta.yaml b/recipes/bioconductor-openprimer/meta.yaml index 15d6b04217c8e..f5cddaa652cfa 100644 --- a/recipes/bioconductor-openprimer/meta.yaml +++ b/recipes/bioconductor-openprimer/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.4.1" %} +{% set version = "1.6.0" %} {% set name = "openPrimeR" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: a1bc7c07f1486703b09f7f291737fe84 + md5: a46cb62bd821bd0381698fa8d3adf64c build: number: 0 rpaths: @@ -21,12 +21,12 @@ build: # SystemRequirements: MAFFT (>= 7.305), OligoArrayAux (>= 3.8), ViennaRNA (>= 2.4.1), MELTING (>= 5.1.1), Pandoc (>= 1.12.3) requirements: host: - - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' - - 'bioconductor-biostrings >=2.50.0,<2.51.0' - - 'bioconductor-decipher >=2.10.0,<2.11.0' - - 'bioconductor-genomicranges >=1.34.0,<1.35.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-biocgenerics >=0.30.0,<0.31.0' + - 'bioconductor-biostrings >=2.52.0,<2.53.0' + - 'bioconductor-decipher >=2.12.0,<2.13.0' + - 'bioconductor-genomicranges >=1.36.0,<1.37.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' - 'r-ape >=3.5' - r-base - 'r-digest >=0.6.9' @@ -50,13 +50,18 @@ requirements: - 'r-tinytex >=0.5' - 'r-uniqtag >=1.0' - 'r-xml >=3.98-1.4' + - mafft >=7.305 + - oligoarrayaux >=3.8 + - viennarna >=2.4.1 + - melting >=5.1.1 + - pandoc run: - - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' - - 'bioconductor-biostrings >=2.50.0,<2.51.0' - - 'bioconductor-decipher >=2.10.0,<2.11.0' - - 'bioconductor-genomicranges >=1.34.0,<1.35.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-biocgenerics >=0.30.0,<0.31.0' + - 'bioconductor-biostrings >=2.52.0,<2.53.0' + - 'bioconductor-decipher >=2.12.0,<2.13.0' + - 'bioconductor-genomicranges >=1.36.0,<1.37.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' - 'r-ape >=3.5' - r-base - 'r-digest >=0.6.9' @@ -80,6 +85,11 @@ requirements: - 'r-tinytex >=0.5' - 'r-uniqtag >=1.0' - 'r-xml >=3.98-1.4' + - mafft >=7.305 + - oligoarrayaux >=3.8 + - viennarna >=2.4.1 + - melting >=5.1.1 + - pandoc test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-openprimerui/meta.yaml b/recipes/bioconductor-openprimerui/meta.yaml index da3fd3492c617..c1adb4950372b 100644 --- a/recipes/bioconductor-openprimerui/meta.yaml +++ b/recipes/bioconductor-openprimerui/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.4.1" %} +{% set version = "1.6.0" %} {% set name = "openPrimeRui" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 9c68b6e58d4425b89b2e45289a83878d + md5: 64ce3b33f1750ddd769caa1f01686597 build: number: 0 rpaths: @@ -20,7 +20,7 @@ build: # Suggests: knitr (>= 1.13) requirements: host: - - 'bioconductor-openprimer >=1.4.0,<1.5.0' + - 'bioconductor-openprimer >=1.6.0,<1.7.0' - r-base - 'r-dt >=0.2' - 'r-rmarkdown >=1.0' @@ -28,7 +28,7 @@ requirements: - 'r-shinybs >=0.61' - 'r-shinyjs >=0.9' run: - - 'bioconductor-openprimer >=1.4.0,<1.5.0' + - 'bioconductor-openprimer >=1.6.0,<1.7.0' - r-base - 'r-dt >=0.2' - 'r-rmarkdown >=1.0' diff --git a/recipes/bioconductor-operonhumanv3.db/meta.yaml b/recipes/bioconductor-operonhumanv3.db/meta.yaml index a5f2f55a6b589..b15023a135372 100644 --- a/recipes/bioconductor-operonhumanv3.db/meta.yaml +++ b/recipes/bioconductor-operonhumanv3.db/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.2.3" %} {% set name = "OperonHumanV3.db" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -12,7 +12,7 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' md5: 648da5d4d63c6c8327f6035ee09f2b65 build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ @@ -20,14 +20,14 @@ build: # Suggests: DBI, annotate, RUnit requirements: host: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' - - 'bioconductor-org.hs.eg.db >=3.7.0,<3.8.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' + - 'bioconductor-org.hs.eg.db >=3.8.0,<3.9.0' - r-base run: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' - - 'bioconductor-org.hs.eg.db >=3.7.0,<3.8.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' + - 'bioconductor-org.hs.eg.db >=3.8.0,<3.9.0' - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-operonhumanv3.db/post-link.sh b/recipes/bioconductor-operonhumanv3.db/post-link.sh index d963aaf9105e7..4e3ac2ed0c0ce 100644 --- a/recipes/bioconductor-operonhumanv3.db/post-link.sh +++ b/recipes/bioconductor-operonhumanv3.db/post-link.sh @@ -1,9 +1,10 @@ #!/bin/bash FN="OperonHumanV3.db_3.2.3.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/OperonHumanV3.db_3.2.3.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/OperonHumanV3.db_3.2.3.tar.gz" "https://bioarchive.galaxyproject.org/OperonHumanV3.db_3.2.3.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-operonhumanv3.db/bioconductor-operonhumanv3.db_3.2.3_src_all.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-operonhumanv3.db/bioconductor-operonhumanv3.db_3.2.3_src_all.tar.gz" ) MD5="648da5d4d63c6c8327f6035ee09f2b65" @@ -16,7 +17,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-opossom/meta.yaml b/recipes/bioconductor-opossom/meta.yaml index b7c3e7d70e813..09fca7bc3d642 100644 --- a/recipes/bioconductor-opossom/meta.yaml +++ b/recipes/bioconductor-opossom/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "2.0.0" %} +{% set version = "2.2.0" %} {% set name = "oposSOM" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: b313fe4f7305c8e1c1bcc5738e6924ff + md5: b92d8034deb4e699e0da43859bc42378 build: number: 0 rpaths: @@ -18,8 +18,8 @@ build: - lib/ requirements: host: - - 'bioconductor-biobase >=2.42.0,<2.43.0' - - 'bioconductor-biomart >=2.38.0,<2.39.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' + - 'bioconductor-biomart >=2.40.0,<2.41.0' - r-ape - r-base - r-fastica @@ -31,8 +31,8 @@ requirements: - r-scatterplot3d - r-tsne run: - - 'bioconductor-biobase >=2.42.0,<2.43.0' - - 'bioconductor-biomart >=2.38.0,<2.39.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' + - 'bioconductor-biomart >=2.40.0,<2.41.0' - r-ape - r-base - r-fastica diff --git a/recipes/bioconductor-oppar/meta.yaml b/recipes/bioconductor-oppar/meta.yaml index 794ef8208da8e..62c24e5d632aa 100644 --- a/recipes/bioconductor-oppar/meta.yaml +++ b/recipes/bioconductor-oppar/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.10.0" %} +{% set version = "1.12.0" %} {% set name = "oppar" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 03de1726e43965f7622a81ccfc411f4d + md5: c2cdab3611fa027800da04b13fc75da6 build: number: 0 rpaths: @@ -19,14 +19,14 @@ build: # Suggests: knitr, rmarkdown, limma, org.Hs.eg.db, GO.db, snow, parallel requirements: host: - - 'bioconductor-biobase >=2.42.0,<2.43.0' - - 'bioconductor-gseabase >=1.44.0,<1.45.0' - - 'bioconductor-gsva >=1.30.0,<1.31.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' + - 'bioconductor-gseabase >=1.46.0,<1.47.0' + - 'bioconductor-gsva >=1.32.0,<1.33.0' - r-base run: - - 'bioconductor-biobase >=2.42.0,<2.43.0' - - 'bioconductor-gseabase >=1.44.0,<1.45.0' - - 'bioconductor-gsva >=1.30.0,<1.31.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' + - 'bioconductor-gseabase >=1.46.0,<1.47.0' + - 'bioconductor-gsva >=1.32.0,<1.33.0' - r-base build: - {{ compiler('c') }} diff --git a/recipes/bioconductor-opweight/meta.yaml b/recipes/bioconductor-opweight/meta.yaml index 84244cf5ca039..c33c6413ecf1c 100644 --- a/recipes/bioconductor-opweight/meta.yaml +++ b/recipes/bioconductor-opweight/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.4.1" %} +{% set version = "1.6.0" %} {% set name = "OPWeight" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: bbcfe34abd0d51932ee518982a1a575a243ad934c64bf471bbf2a8bb4955bc03 + md5: 4472bf693a02a5fc0225ab8c6a741881 build: number: 0 rpaths: @@ -20,12 +20,12 @@ build: # Suggests: airway, BiocStyle, cowplot, DESeq2, devtools, ggplot2, gridExtra, knitr, Matrix, rmarkdown, scales, testthat requirements: host: - - 'bioconductor-qvalue >=2.14.0,<2.15.0' + - 'bioconductor-qvalue >=2.16.0,<2.17.0' - r-base - r-mass - r-tibble run: - - 'bioconductor-qvalue >=2.14.0,<2.15.0' + - 'bioconductor-qvalue >=2.16.0,<2.17.0' - r-base - r-mass - r-tibble diff --git a/recipes/bioconductor-orderedlist/meta.yaml b/recipes/bioconductor-orderedlist/meta.yaml index 68c9ef485381f..59c049d59eaec 100644 --- a/recipes/bioconductor-orderedlist/meta.yaml +++ b/recipes/bioconductor-orderedlist/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.54.0" %} +{% set version = "1.56.0" %} {% set name = "OrderedList" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,21 +10,21 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 6bd1c5786a4c4d6aec16c91f6c481984 + md5: 80f6759e6648c53a1979233a4dd0a7b4 build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ noarch: generic requirements: host: - - 'bioconductor-biobase >=2.42.0,<2.43.0' - - 'bioconductor-twilight >=1.58.0,<1.59.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' + - 'bioconductor-twilight >=1.60.0,<1.61.0' - r-base run: - - 'bioconductor-biobase >=2.42.0,<2.43.0' - - 'bioconductor-twilight >=1.58.0,<1.59.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' + - 'bioconductor-twilight >=1.60.0,<1.61.0' - r-base test: commands: diff --git a/recipes/bioconductor-orfik/meta.yaml b/recipes/bioconductor-orfik/meta.yaml index 36fbc32d5db5f..e145f9e45b594 100644 --- a/recipes/bioconductor-orfik/meta.yaml +++ b/recipes/bioconductor-orfik/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.2.0" %} +{% set version = "1.4.0" %} {% set name = "ORFik" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,42 +10,46 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 9892e6673964b186680c6a39e5f97873 + md5: 339394a4aacc9be399307306bb24d501 build: number: 0 rpaths: - lib/R/lib/ - lib/ -# Suggests: testthat, rmarkdown, knitr, BiocStyle, BSgenome, BSgenome.Hsapiens.UCSC.hg19, ggplot2 (>= 2.2.1) +# Suggests: testthat, rmarkdown, knitr, BiocStyle, BSgenome, BSgenome.Hsapiens.UCSC.hg19 requirements: host: - - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' - - 'bioconductor-biostrings >=2.50.0,<2.51.0' - - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' - - 'bioconductor-genomicalignments >=1.18.0,<1.19.0' - - 'bioconductor-genomicfeatures >=1.34.0,<1.35.0' - - 'bioconductor-genomicranges >=1.34.0,<1.35.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-rsamtools >=1.34.0,<1.35.0' - - 'bioconductor-rtracklayer >=1.42.0,<1.43.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' + - 'bioconductor-biocgenerics >=0.30.0,<0.31.0' + - 'bioconductor-biostrings >=2.52.0,<2.53.0' + - 'bioconductor-genomeinfodb >=1.20.0,<1.21.0' + - 'bioconductor-genomicalignments >=1.20.0,<1.21.0' + - 'bioconductor-genomicfeatures >=1.36.0,<1.37.0' + - 'bioconductor-genomicranges >=1.36.0,<1.37.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-rsamtools >=2.0.0,<2.1.0' + - 'bioconductor-rtracklayer >=1.44.0,<1.45.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' - r-base - - 'r-data.table >=1.10.4-3' - - 'r-rcpp >=0.12.16' + - 'r-data.table >=1.11.8' + - 'r-ggplot2 >=2.2.1' + - 'r-rcpp >=1.0.0' run: - - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' - - 'bioconductor-biostrings >=2.50.0,<2.51.0' - - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' - - 'bioconductor-genomicalignments >=1.18.0,<1.19.0' - - 'bioconductor-genomicfeatures >=1.34.0,<1.35.0' - - 'bioconductor-genomicranges >=1.34.0,<1.35.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-rsamtools >=1.34.0,<1.35.0' - - 'bioconductor-rtracklayer >=1.42.0,<1.43.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' + - 'bioconductor-biocgenerics >=0.30.0,<0.31.0' + - 'bioconductor-biostrings >=2.52.0,<2.53.0' + - 'bioconductor-genomeinfodb >=1.20.0,<1.21.0' + - 'bioconductor-genomicalignments >=1.20.0,<1.21.0' + - 'bioconductor-genomicfeatures >=1.36.0,<1.37.0' + - 'bioconductor-genomicranges >=1.36.0,<1.37.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-rsamtools >=2.0.0,<2.1.0' + - 'bioconductor-rtracklayer >=1.44.0,<1.45.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' - r-base - - 'r-data.table >=1.10.4-3' - - 'r-rcpp >=0.12.16' + - 'r-data.table >=1.11.8' + - 'r-ggplot2 >=2.2.1' + - 'r-rcpp >=1.0.0' build: - {{ compiler('c') }} - {{ compiler('cxx') }} @@ -56,5 +60,5 @@ test: about: home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: 'MIT + file LICENSE' - summary: 'Tools for manipulation of RiboSeq, RNASeq and CageSeq data. ORFik is extremely fast through use of C, data.table and GenomicRanges. Package allows to reassign starts of the transcripts with the use of CageSeq data, automatic shifting of RiboSeq reads, finding of Open Reading Frames for the whole genomes and many more.' + summary: 'Tools for manipulation of RiboSeq, RNASeq and CageSeq data. ORFik is extremely fast through use of C, data.table and GenomicRanges. Package allows to reassign starts of the transcripts with the use of CageSeq data, automatic shifting of RiboSeq reads, finding of Open Reading Frames for whole genomes and much more.' diff --git a/recipes/bioconductor-org.ag.eg.db/meta.yaml b/recipes/bioconductor-org.ag.eg.db/meta.yaml index 033c23d3766bf..3cbc1cbec596c 100644 --- a/recipes/bioconductor-org.ag.eg.db/meta.yaml +++ b/recipes/bioconductor-org.ag.eg.db/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "3.7.0" %} +{% set version = "3.8.2" %} {% set name = "org.Ag.eg.db" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 29ff8024311fc6e9dab0ac508aa25093 + md5: 12c692e93ad991dfd783cde907e753bb build: number: 0 rpaths: @@ -20,12 +20,12 @@ build: # Suggests: DBI, annotate, RUnit requirements: host: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' - r-base run: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-org.ag.eg.db/post-link.sh b/recipes/bioconductor-org.ag.eg.db/post-link.sh index f6e3ba8c3343b..bbebc3ec1ca2d 100644 --- a/recipes/bioconductor-org.ag.eg.db/post-link.sh +++ b/recipes/bioconductor-org.ag.eg.db/post-link.sh @@ -1,11 +1,11 @@ #!/bin/bash -FN="org.Ag.eg.db_3.7.0.tar.gz" +FN="org.Ag.eg.db_3.8.2.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/org.Ag.eg.db_3.7.0.tar.gz" - "https://bioarchive.galaxyproject.org/org.Ag.eg.db_3.7.0.tar.gz" - "https://depot.galaxyproject.org/software/bioconductor-org.ag.eg.db/bioconductor-org.ag.eg.db_3.7.0_src_all.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/org.Ag.eg.db_3.8.2.tar.gz" + "https://bioarchive.galaxyproject.org/org.Ag.eg.db_3.8.2.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-org.ag.eg.db/bioconductor-org.ag.eg.db_3.8.2_src_all.tar.gz" ) -MD5="29ff8024311fc6e9dab0ac508aa25093" +MD5="12c692e93ad991dfd783cde907e753bb" # Use a staging area in the conda dir rather than temp dirs, both to avoid # permission issues as well as to have things downloaded in a predictable @@ -16,7 +16,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-org.at.tair.db/meta.yaml b/recipes/bioconductor-org.at.tair.db/meta.yaml index e6e52a348ceea..3747bef5f4c9c 100644 --- a/recipes/bioconductor-org.at.tair.db/meta.yaml +++ b/recipes/bioconductor-org.at.tair.db/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "3.7.0" %} +{% set version = "3.8.2" %} {% set name = "org.At.tair.db" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 31ee4b1608601ad431d3baf1693c485d + md5: e3efecf164d207eba2fec62cb167f9b9 build: number: 0 rpaths: @@ -20,12 +20,12 @@ build: # Suggests: DBI, annotate, RUnit requirements: host: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' - r-base run: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-org.at.tair.db/post-link.sh b/recipes/bioconductor-org.at.tair.db/post-link.sh index 091e1c6486ff5..8e4f406274f96 100644 --- a/recipes/bioconductor-org.at.tair.db/post-link.sh +++ b/recipes/bioconductor-org.at.tair.db/post-link.sh @@ -1,11 +1,11 @@ #!/bin/bash -FN="org.At.tair.db_3.7.0.tar.gz" +FN="org.At.tair.db_3.8.2.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/org.At.tair.db_3.7.0.tar.gz" - "https://bioarchive.galaxyproject.org/org.At.tair.db_3.7.0.tar.gz" - "https://depot.galaxyproject.org/software/bioconductor-org.at.tair.db/bioconductor-org.at.tair.db_3.7.0_src_all.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/org.At.tair.db_3.8.2.tar.gz" + "https://bioarchive.galaxyproject.org/org.At.tair.db_3.8.2.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-org.at.tair.db/bioconductor-org.at.tair.db_3.8.2_src_all.tar.gz" ) -MD5="31ee4b1608601ad431d3baf1693c485d" +MD5="e3efecf164d207eba2fec62cb167f9b9" # Use a staging area in the conda dir rather than temp dirs, both to avoid # permission issues as well as to have things downloaded in a predictable @@ -16,7 +16,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-org.bt.eg.db/meta.yaml b/recipes/bioconductor-org.bt.eg.db/meta.yaml index d33d0c131cca5..4c6dc3b4fee7a 100644 --- a/recipes/bioconductor-org.bt.eg.db/meta.yaml +++ b/recipes/bioconductor-org.bt.eg.db/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "3.7.0" %} +{% set version = "3.8.2" %} {% set name = "org.Bt.eg.db" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 04acb6baf4ea87f5643604afc38994d9 + md5: dd66082b68fe1993058086b74be713e2 build: number: 0 rpaths: @@ -20,12 +20,12 @@ build: # Suggests: DBI, annotate, RUnit requirements: host: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' - r-base run: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-org.bt.eg.db/post-link.sh b/recipes/bioconductor-org.bt.eg.db/post-link.sh index 3fac1bcd5b882..2e833a3c7a880 100644 --- a/recipes/bioconductor-org.bt.eg.db/post-link.sh +++ b/recipes/bioconductor-org.bt.eg.db/post-link.sh @@ -1,11 +1,11 @@ #!/bin/bash -FN="org.Bt.eg.db_3.7.0.tar.gz" +FN="org.Bt.eg.db_3.8.2.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/org.Bt.eg.db_3.7.0.tar.gz" - "https://bioarchive.galaxyproject.org/org.Bt.eg.db_3.7.0.tar.gz" - "https://depot.galaxyproject.org/software/bioconductor-org.bt.eg.db/bioconductor-org.bt.eg.db_3.7.0_src_all.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/org.Bt.eg.db_3.8.2.tar.gz" + "https://bioarchive.galaxyproject.org/org.Bt.eg.db_3.8.2.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-org.bt.eg.db/bioconductor-org.bt.eg.db_3.8.2_src_all.tar.gz" ) -MD5="04acb6baf4ea87f5643604afc38994d9" +MD5="dd66082b68fe1993058086b74be713e2" # Use a staging area in the conda dir rather than temp dirs, both to avoid # permission issues as well as to have things downloaded in a predictable @@ -16,7 +16,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-org.ce.eg.db/meta.yaml b/recipes/bioconductor-org.ce.eg.db/meta.yaml index 91a2b14fdda4a..45b841b31028b 100644 --- a/recipes/bioconductor-org.ce.eg.db/meta.yaml +++ b/recipes/bioconductor-org.ce.eg.db/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "3.7.0" %} +{% set version = "3.8.2" %} {% set name = "org.Ce.eg.db" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: fd97efab38b5106699a913440f5ebd10 + md5: 8d60c5d14fa63b6b4bbaee3b65611136 build: number: 0 rpaths: @@ -20,12 +20,12 @@ build: # Suggests: DBI, annotate, RUnit requirements: host: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' - r-base run: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-org.ce.eg.db/post-link.sh b/recipes/bioconductor-org.ce.eg.db/post-link.sh index b249790a061ce..a2fb60831c434 100644 --- a/recipes/bioconductor-org.ce.eg.db/post-link.sh +++ b/recipes/bioconductor-org.ce.eg.db/post-link.sh @@ -1,11 +1,11 @@ #!/bin/bash -FN="org.Ce.eg.db_3.7.0.tar.gz" +FN="org.Ce.eg.db_3.8.2.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/org.Ce.eg.db_3.7.0.tar.gz" - "https://bioarchive.galaxyproject.org/org.Ce.eg.db_3.7.0.tar.gz" - "https://depot.galaxyproject.org/software/bioconductor-org.ce.eg.db/bioconductor-org.ce.eg.db_3.7.0_src_all.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/org.Ce.eg.db_3.8.2.tar.gz" + "https://bioarchive.galaxyproject.org/org.Ce.eg.db_3.8.2.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-org.ce.eg.db/bioconductor-org.ce.eg.db_3.8.2_src_all.tar.gz" ) -MD5="fd97efab38b5106699a913440f5ebd10" +MD5="8d60c5d14fa63b6b4bbaee3b65611136" # Use a staging area in the conda dir rather than temp dirs, both to avoid # permission issues as well as to have things downloaded in a predictable @@ -16,7 +16,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-org.cf.eg.db/meta.yaml b/recipes/bioconductor-org.cf.eg.db/meta.yaml index 7e47623969f87..bc1009f706263 100644 --- a/recipes/bioconductor-org.cf.eg.db/meta.yaml +++ b/recipes/bioconductor-org.cf.eg.db/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "3.7.0" %} +{% set version = "3.8.2" %} {% set name = "org.Cf.eg.db" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 7be91e9255dc1db7ab8231040c1bf973 + md5: b2529f280240e86ff4fd9e3f6ceacbc8 build: number: 0 rpaths: @@ -20,12 +20,12 @@ build: # Suggests: DBI, annotate, RUnit requirements: host: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' - r-base run: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-org.cf.eg.db/post-link.sh b/recipes/bioconductor-org.cf.eg.db/post-link.sh index df80df8384913..cd3590278df2e 100644 --- a/recipes/bioconductor-org.cf.eg.db/post-link.sh +++ b/recipes/bioconductor-org.cf.eg.db/post-link.sh @@ -1,11 +1,11 @@ #!/bin/bash -FN="org.Cf.eg.db_3.7.0.tar.gz" +FN="org.Cf.eg.db_3.8.2.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/org.Cf.eg.db_3.7.0.tar.gz" - "https://bioarchive.galaxyproject.org/org.Cf.eg.db_3.7.0.tar.gz" - "https://depot.galaxyproject.org/software/bioconductor-org.cf.eg.db/bioconductor-org.cf.eg.db_3.7.0_src_all.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/org.Cf.eg.db_3.8.2.tar.gz" + "https://bioarchive.galaxyproject.org/org.Cf.eg.db_3.8.2.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-org.cf.eg.db/bioconductor-org.cf.eg.db_3.8.2_src_all.tar.gz" ) -MD5="7be91e9255dc1db7ab8231040c1bf973" +MD5="b2529f280240e86ff4fd9e3f6ceacbc8" # Use a staging area in the conda dir rather than temp dirs, both to avoid # permission issues as well as to have things downloaded in a predictable @@ -16,7 +16,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-org.dm.eg.db/meta.yaml b/recipes/bioconductor-org.dm.eg.db/meta.yaml index 63620059347f0..7d972b0b17baa 100644 --- a/recipes/bioconductor-org.dm.eg.db/meta.yaml +++ b/recipes/bioconductor-org.dm.eg.db/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "3.7.0" %} +{% set version = "3.8.2" %} {% set name = "org.Dm.eg.db" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,9 +10,9 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 8b1f0d67805df142418829c440796566 + md5: 4df4da07ee0e0bb367cf91bf2f5c3909 build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ @@ -20,12 +20,12 @@ build: # Suggests: DBI, annotate, RUnit requirements: host: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' - r-base run: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-org.dm.eg.db/post-link.sh b/recipes/bioconductor-org.dm.eg.db/post-link.sh index f8344fd154fff..92f40a6500ebe 100644 --- a/recipes/bioconductor-org.dm.eg.db/post-link.sh +++ b/recipes/bioconductor-org.dm.eg.db/post-link.sh @@ -1,11 +1,11 @@ #!/bin/bash -FN="org.Dm.eg.db_3.7.0.tar.gz" +FN="org.Dm.eg.db_3.8.2.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/org.Dm.eg.db_3.7.0.tar.gz" - "https://bioarchive.galaxyproject.org/org.Dm.eg.db_3.7.0.tar.gz" - "https://depot.galaxyproject.org/software/bioconductor-org.dm.eg.db/bioconductor-org.dm.eg.db_3.7.0_src_all.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/org.Dm.eg.db_3.8.2.tar.gz" + "https://bioarchive.galaxyproject.org/org.Dm.eg.db_3.8.2.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-org.dm.eg.db/bioconductor-org.dm.eg.db_3.8.2_src_all.tar.gz" ) -MD5="8b1f0d67805df142418829c440796566" +MD5="4df4da07ee0e0bb367cf91bf2f5c3909" # Use a staging area in the conda dir rather than temp dirs, both to avoid # permission issues as well as to have things downloaded in a predictable @@ -16,7 +16,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-org.dr.eg.db/meta.yaml b/recipes/bioconductor-org.dr.eg.db/meta.yaml index 6ad8ec9d9e347..dd0a2e48b133a 100644 --- a/recipes/bioconductor-org.dr.eg.db/meta.yaml +++ b/recipes/bioconductor-org.dr.eg.db/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "3.7.0" %} +{% set version = "3.8.2" %} {% set name = "org.Dr.eg.db" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,9 +10,9 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 0e0c2337494c3175f0bb09341e45a2a0 + md5: 3426287b8ba7d41fbb5c0a8c6f6b2276 build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ @@ -20,12 +20,12 @@ build: # Suggests: DBI, annotate, RUnit requirements: host: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' - r-base run: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-org.dr.eg.db/post-link.sh b/recipes/bioconductor-org.dr.eg.db/post-link.sh index a989b171d9e05..1a75f7b9364f1 100644 --- a/recipes/bioconductor-org.dr.eg.db/post-link.sh +++ b/recipes/bioconductor-org.dr.eg.db/post-link.sh @@ -1,11 +1,11 @@ #!/bin/bash -FN="org.Dr.eg.db_3.7.0.tar.gz" +FN="org.Dr.eg.db_3.8.2.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/org.Dr.eg.db_3.7.0.tar.gz" - "https://bioarchive.galaxyproject.org/org.Dr.eg.db_3.7.0.tar.gz" - "https://depot.galaxyproject.org/software/bioconductor-org.dr.eg.db/bioconductor-org.dr.eg.db_3.7.0_src_all.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/org.Dr.eg.db_3.8.2.tar.gz" + "https://bioarchive.galaxyproject.org/org.Dr.eg.db_3.8.2.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-org.dr.eg.db/bioconductor-org.dr.eg.db_3.8.2_src_all.tar.gz" ) -MD5="0e0c2337494c3175f0bb09341e45a2a0" +MD5="3426287b8ba7d41fbb5c0a8c6f6b2276" # Use a staging area in the conda dir rather than temp dirs, both to avoid # permission issues as well as to have things downloaded in a predictable @@ -16,7 +16,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-org.eck12.eg.db/meta.yaml b/recipes/bioconductor-org.eck12.eg.db/meta.yaml index f9663ba1d723c..f954277c6ca1e 100644 --- a/recipes/bioconductor-org.eck12.eg.db/meta.yaml +++ b/recipes/bioconductor-org.eck12.eg.db/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "3.7.0" %} +{% set version = "3.8.2" %} {% set name = "org.EcK12.eg.db" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: ed681d12efeabaa6104895ddf8697b65 + md5: ab6ed04e6c51571fc754f90bf21861a2 build: number: 0 rpaths: @@ -20,12 +20,12 @@ build: # Suggests: DBI, annotate, RUnit requirements: host: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' - r-base run: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-org.eck12.eg.db/post-link.sh b/recipes/bioconductor-org.eck12.eg.db/post-link.sh index 40c7e8393f758..7038f208738fc 100644 --- a/recipes/bioconductor-org.eck12.eg.db/post-link.sh +++ b/recipes/bioconductor-org.eck12.eg.db/post-link.sh @@ -1,11 +1,11 @@ #!/bin/bash -FN="org.EcK12.eg.db_3.7.0.tar.gz" +FN="org.EcK12.eg.db_3.8.2.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/org.EcK12.eg.db_3.7.0.tar.gz" - "https://bioarchive.galaxyproject.org/org.EcK12.eg.db_3.7.0.tar.gz" - "https://depot.galaxyproject.org/software/bioconductor-org.eck12.eg.db/bioconductor-org.eck12.eg.db_3.7.0_src_all.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/org.EcK12.eg.db_3.8.2.tar.gz" + "https://bioarchive.galaxyproject.org/org.EcK12.eg.db_3.8.2.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-org.eck12.eg.db/bioconductor-org.eck12.eg.db_3.8.2_src_all.tar.gz" ) -MD5="ed681d12efeabaa6104895ddf8697b65" +MD5="ab6ed04e6c51571fc754f90bf21861a2" # Use a staging area in the conda dir rather than temp dirs, both to avoid # permission issues as well as to have things downloaded in a predictable @@ -16,7 +16,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-org.ecsakai.eg.db/meta.yaml b/recipes/bioconductor-org.ecsakai.eg.db/meta.yaml index 99530d9970532..1a1195fbd6ffc 100644 --- a/recipes/bioconductor-org.ecsakai.eg.db/meta.yaml +++ b/recipes/bioconductor-org.ecsakai.eg.db/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "3.7.0" %} +{% set version = "3.8.2" %} {% set name = "org.EcSakai.eg.db" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: c03bf25879cee8d40a3362d8bb4a7ced + md5: 006ead1a2f9f27ad61d79709b1a7bf68 build: number: 0 rpaths: @@ -20,12 +20,12 @@ build: # Suggests: DBI, annotate, RUnit requirements: host: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' - r-base run: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-org.ecsakai.eg.db/post-link.sh b/recipes/bioconductor-org.ecsakai.eg.db/post-link.sh index 20edb54a39dd9..56171876ac22e 100644 --- a/recipes/bioconductor-org.ecsakai.eg.db/post-link.sh +++ b/recipes/bioconductor-org.ecsakai.eg.db/post-link.sh @@ -1,11 +1,11 @@ #!/bin/bash -FN="org.EcSakai.eg.db_3.7.0.tar.gz" +FN="org.EcSakai.eg.db_3.8.2.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/org.EcSakai.eg.db_3.7.0.tar.gz" - "https://bioarchive.galaxyproject.org/org.EcSakai.eg.db_3.7.0.tar.gz" - "https://depot.galaxyproject.org/software/bioconductor-org.ecsakai.eg.db/bioconductor-org.ecsakai.eg.db_3.7.0_src_all.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/org.EcSakai.eg.db_3.8.2.tar.gz" + "https://bioarchive.galaxyproject.org/org.EcSakai.eg.db_3.8.2.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-org.ecsakai.eg.db/bioconductor-org.ecsakai.eg.db_3.8.2_src_all.tar.gz" ) -MD5="c03bf25879cee8d40a3362d8bb4a7ced" +MD5="006ead1a2f9f27ad61d79709b1a7bf68" # Use a staging area in the conda dir rather than temp dirs, both to avoid # permission issues as well as to have things downloaded in a predictable @@ -16,7 +16,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-org.gg.eg.db/meta.yaml b/recipes/bioconductor-org.gg.eg.db/meta.yaml index 1b570aaf8a40c..a4d87c96b8bf3 100644 --- a/recipes/bioconductor-org.gg.eg.db/meta.yaml +++ b/recipes/bioconductor-org.gg.eg.db/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "3.7.0" %} +{% set version = "3.8.2" %} {% set name = "org.Gg.eg.db" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 341bd6dcd6fc11ca7519a06b478dc9c1 + md5: 01c0e59d398059d547d45b4998e0959a build: number: 0 rpaths: @@ -20,12 +20,12 @@ build: # Suggests: DBI, annotate, RUnit requirements: host: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' - r-base run: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-org.gg.eg.db/post-link.sh b/recipes/bioconductor-org.gg.eg.db/post-link.sh index b82e464d0189e..be0d4513ad02a 100644 --- a/recipes/bioconductor-org.gg.eg.db/post-link.sh +++ b/recipes/bioconductor-org.gg.eg.db/post-link.sh @@ -1,11 +1,11 @@ #!/bin/bash -FN="org.Gg.eg.db_3.7.0.tar.gz" +FN="org.Gg.eg.db_3.8.2.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/org.Gg.eg.db_3.7.0.tar.gz" - "https://bioarchive.galaxyproject.org/org.Gg.eg.db_3.7.0.tar.gz" - "https://depot.galaxyproject.org/software/bioconductor-org.gg.eg.db/bioconductor-org.gg.eg.db_3.7.0_src_all.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/org.Gg.eg.db_3.8.2.tar.gz" + "https://bioarchive.galaxyproject.org/org.Gg.eg.db_3.8.2.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-org.gg.eg.db/bioconductor-org.gg.eg.db_3.8.2_src_all.tar.gz" ) -MD5="341bd6dcd6fc11ca7519a06b478dc9c1" +MD5="01c0e59d398059d547d45b4998e0959a" # Use a staging area in the conda dir rather than temp dirs, both to avoid # permission issues as well as to have things downloaded in a predictable @@ -16,7 +16,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-org.hs.eg.db/meta.yaml b/recipes/bioconductor-org.hs.eg.db/meta.yaml index d5df7b38ac4d4..24e53c3bba0f0 100644 --- a/recipes/bioconductor-org.hs.eg.db/meta.yaml +++ b/recipes/bioconductor-org.hs.eg.db/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "3.7.0" %} +{% set version = "3.8.2" %} {% set name = "org.Hs.eg.db" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: cfa2c28b70a64cbec969b42e993ff5de + md5: 79de4b2d1cb26b303a9a4d286d6dd766 build: number: 0 rpaths: @@ -20,12 +20,12 @@ build: # Suggests: DBI, annotate, RUnit requirements: host: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' - r-base run: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-org.hs.eg.db/post-link.sh b/recipes/bioconductor-org.hs.eg.db/post-link.sh index 0c4e620d21279..c047c7ffb96a9 100644 --- a/recipes/bioconductor-org.hs.eg.db/post-link.sh +++ b/recipes/bioconductor-org.hs.eg.db/post-link.sh @@ -1,11 +1,11 @@ #!/bin/bash -FN="org.Hs.eg.db_3.7.0.tar.gz" +FN="org.Hs.eg.db_3.8.2.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/org.Hs.eg.db_3.7.0.tar.gz" - "https://bioarchive.galaxyproject.org/org.Hs.eg.db_3.7.0.tar.gz" - "https://depot.galaxyproject.org/software/bioconductor-org.hs.eg.db/bioconductor-org.hs.eg.db_3.7.0_src_all.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/org.Hs.eg.db_3.8.2.tar.gz" + "https://bioarchive.galaxyproject.org/org.Hs.eg.db_3.8.2.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-org.hs.eg.db/bioconductor-org.hs.eg.db_3.8.2_src_all.tar.gz" ) -MD5="cfa2c28b70a64cbec969b42e993ff5de" +MD5="79de4b2d1cb26b303a9a4d286d6dd766" # Use a staging area in the conda dir rather than temp dirs, both to avoid # permission issues as well as to have things downloaded in a predictable @@ -16,7 +16,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-org.mm.eg.db/meta.yaml b/recipes/bioconductor-org.mm.eg.db/meta.yaml index db9b73ca6c713..7aafa3254e79c 100644 --- a/recipes/bioconductor-org.mm.eg.db/meta.yaml +++ b/recipes/bioconductor-org.mm.eg.db/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "3.7.0" %} +{% set version = "3.8.2" %} {% set name = "org.Mm.eg.db" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: fcb8cc04ab5918c38c91ab77aeab0ad8 + md5: 6a8c0350bcdbcfa8ef904c83d18bce3f build: number: 0 rpaths: @@ -20,12 +20,12 @@ build: # Suggests: DBI, annotate, RUnit requirements: host: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' - r-base run: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-org.mm.eg.db/post-link.sh b/recipes/bioconductor-org.mm.eg.db/post-link.sh index 3328cfa1923c3..d968e33661358 100644 --- a/recipes/bioconductor-org.mm.eg.db/post-link.sh +++ b/recipes/bioconductor-org.mm.eg.db/post-link.sh @@ -1,11 +1,11 @@ #!/bin/bash -FN="org.Mm.eg.db_3.7.0.tar.gz" +FN="org.Mm.eg.db_3.8.2.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/org.Mm.eg.db_3.7.0.tar.gz" - "https://bioarchive.galaxyproject.org/org.Mm.eg.db_3.7.0.tar.gz" - "https://depot.galaxyproject.org/software/bioconductor-org.mm.eg.db/bioconductor-org.mm.eg.db_3.7.0_src_all.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/org.Mm.eg.db_3.8.2.tar.gz" + "https://bioarchive.galaxyproject.org/org.Mm.eg.db_3.8.2.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-org.mm.eg.db/bioconductor-org.mm.eg.db_3.8.2_src_all.tar.gz" ) -MD5="fcb8cc04ab5918c38c91ab77aeab0ad8" +MD5="6a8c0350bcdbcfa8ef904c83d18bce3f" # Use a staging area in the conda dir rather than temp dirs, both to avoid # permission issues as well as to have things downloaded in a predictable @@ -16,7 +16,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-org.mmu.eg.db/meta.yaml b/recipes/bioconductor-org.mmu.eg.db/meta.yaml index 0f08b9b4548ff..98c7c66e1a3ba 100644 --- a/recipes/bioconductor-org.mmu.eg.db/meta.yaml +++ b/recipes/bioconductor-org.mmu.eg.db/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "3.7.0" %} +{% set version = "3.8.2" %} {% set name = "org.Mmu.eg.db" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 02540628677b237dd3800faf6325aaf6 + md5: 23ca43a82c03c50004eb237c1989bac5 build: number: 0 rpaths: @@ -20,12 +20,12 @@ build: # Suggests: DBI, annotate, RUnit requirements: host: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' - r-base run: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-org.mmu.eg.db/post-link.sh b/recipes/bioconductor-org.mmu.eg.db/post-link.sh index 6bf545b5b5d9f..b7535b4783f8f 100644 --- a/recipes/bioconductor-org.mmu.eg.db/post-link.sh +++ b/recipes/bioconductor-org.mmu.eg.db/post-link.sh @@ -1,11 +1,11 @@ #!/bin/bash -FN="org.Mmu.eg.db_3.7.0.tar.gz" +FN="org.Mmu.eg.db_3.8.2.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/org.Mmu.eg.db_3.7.0.tar.gz" - "https://bioarchive.galaxyproject.org/org.Mmu.eg.db_3.7.0.tar.gz" - "https://depot.galaxyproject.org/software/bioconductor-org.mmu.eg.db/bioconductor-org.mmu.eg.db_3.7.0_src_all.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/org.Mmu.eg.db_3.8.2.tar.gz" + "https://bioarchive.galaxyproject.org/org.Mmu.eg.db_3.8.2.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-org.mmu.eg.db/bioconductor-org.mmu.eg.db_3.8.2_src_all.tar.gz" ) -MD5="02540628677b237dd3800faf6325aaf6" +MD5="23ca43a82c03c50004eb237c1989bac5" # Use a staging area in the conda dir rather than temp dirs, both to avoid # permission issues as well as to have things downloaded in a predictable @@ -16,7 +16,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-org.pf.plasmo.db/meta.yaml b/recipes/bioconductor-org.pf.plasmo.db/meta.yaml index 24b7af438375e..9f53867cc506a 100644 --- a/recipes/bioconductor-org.pf.plasmo.db/meta.yaml +++ b/recipes/bioconductor-org.pf.plasmo.db/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "3.7.0" %} +{% set version = "3.8.2" %} {% set name = "org.Pf.plasmo.db" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: ec01cc690e01acb3af144a44b5ee2f5b + md5: 5ae4ea5101f16c79f5b7ad6b8717a5d0 build: number: 0 rpaths: @@ -20,12 +20,12 @@ build: # Suggests: DBI, annotate, RUnit requirements: host: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' - r-base run: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-org.pf.plasmo.db/post-link.sh b/recipes/bioconductor-org.pf.plasmo.db/post-link.sh index b40d07d654d52..a319cfd27a0b3 100644 --- a/recipes/bioconductor-org.pf.plasmo.db/post-link.sh +++ b/recipes/bioconductor-org.pf.plasmo.db/post-link.sh @@ -1,11 +1,11 @@ #!/bin/bash -FN="org.Pf.plasmo.db_3.7.0.tar.gz" +FN="org.Pf.plasmo.db_3.8.2.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/org.Pf.plasmo.db_3.7.0.tar.gz" - "https://bioarchive.galaxyproject.org/org.Pf.plasmo.db_3.7.0.tar.gz" - "https://depot.galaxyproject.org/software/bioconductor-org.pf.plasmo.db/bioconductor-org.pf.plasmo.db_3.7.0_src_all.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/org.Pf.plasmo.db_3.8.2.tar.gz" + "https://bioarchive.galaxyproject.org/org.Pf.plasmo.db_3.8.2.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-org.pf.plasmo.db/bioconductor-org.pf.plasmo.db_3.8.2_src_all.tar.gz" ) -MD5="ec01cc690e01acb3af144a44b5ee2f5b" +MD5="5ae4ea5101f16c79f5b7ad6b8717a5d0" # Use a staging area in the conda dir rather than temp dirs, both to avoid # permission issues as well as to have things downloaded in a predictable @@ -16,7 +16,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-org.pt.eg.db/meta.yaml b/recipes/bioconductor-org.pt.eg.db/meta.yaml index fc7c4ab993330..0946f58f27977 100644 --- a/recipes/bioconductor-org.pt.eg.db/meta.yaml +++ b/recipes/bioconductor-org.pt.eg.db/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "3.7.0" %} +{% set version = "3.8.2" %} {% set name = "org.Pt.eg.db" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 302ef39a2501087cc252a0b3afb48135 + md5: 6a9c57b4b41612569c8d2d1ca0a077e6 build: number: 0 rpaths: @@ -20,12 +20,12 @@ build: # Suggests: DBI, annotate, RUnit requirements: host: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' - r-base run: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-org.pt.eg.db/post-link.sh b/recipes/bioconductor-org.pt.eg.db/post-link.sh index f4cc1a4255907..1743b1dca0cd2 100644 --- a/recipes/bioconductor-org.pt.eg.db/post-link.sh +++ b/recipes/bioconductor-org.pt.eg.db/post-link.sh @@ -1,11 +1,11 @@ #!/bin/bash -FN="org.Pt.eg.db_3.7.0.tar.gz" +FN="org.Pt.eg.db_3.8.2.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/org.Pt.eg.db_3.7.0.tar.gz" - "https://bioarchive.galaxyproject.org/org.Pt.eg.db_3.7.0.tar.gz" - "https://depot.galaxyproject.org/software/bioconductor-org.pt.eg.db/bioconductor-org.pt.eg.db_3.7.0_src_all.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/org.Pt.eg.db_3.8.2.tar.gz" + "https://bioarchive.galaxyproject.org/org.Pt.eg.db_3.8.2.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-org.pt.eg.db/bioconductor-org.pt.eg.db_3.8.2_src_all.tar.gz" ) -MD5="302ef39a2501087cc252a0b3afb48135" +MD5="6a9c57b4b41612569c8d2d1ca0a077e6" # Use a staging area in the conda dir rather than temp dirs, both to avoid # permission issues as well as to have things downloaded in a predictable @@ -16,7 +16,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-org.rn.eg.db/meta.yaml b/recipes/bioconductor-org.rn.eg.db/meta.yaml index 8aa185303a5aa..db10a9ca028cc 100644 --- a/recipes/bioconductor-org.rn.eg.db/meta.yaml +++ b/recipes/bioconductor-org.rn.eg.db/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "3.7.0" %} +{% set version = "3.8.2" %} {% set name = "org.Rn.eg.db" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 62ddd7b20549e4c3aa455377f0efa17a + md5: e53247d4a84bcc5a11c6479e565dc16f build: number: 0 rpaths: @@ -20,12 +20,12 @@ build: # Suggests: DBI, annotate, RUnit requirements: host: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' - r-base run: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-org.rn.eg.db/post-link.sh b/recipes/bioconductor-org.rn.eg.db/post-link.sh index 21e0d4bef49e9..9838ded89c5db 100644 --- a/recipes/bioconductor-org.rn.eg.db/post-link.sh +++ b/recipes/bioconductor-org.rn.eg.db/post-link.sh @@ -1,11 +1,11 @@ #!/bin/bash -FN="org.Rn.eg.db_3.7.0.tar.gz" +FN="org.Rn.eg.db_3.8.2.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/org.Rn.eg.db_3.7.0.tar.gz" - "https://bioarchive.galaxyproject.org/org.Rn.eg.db_3.7.0.tar.gz" - "https://depot.galaxyproject.org/software/bioconductor-org.rn.eg.db/bioconductor-org.rn.eg.db_3.7.0_src_all.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/org.Rn.eg.db_3.8.2.tar.gz" + "https://bioarchive.galaxyproject.org/org.Rn.eg.db_3.8.2.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-org.rn.eg.db/bioconductor-org.rn.eg.db_3.8.2_src_all.tar.gz" ) -MD5="62ddd7b20549e4c3aa455377f0efa17a" +MD5="e53247d4a84bcc5a11c6479e565dc16f" # Use a staging area in the conda dir rather than temp dirs, both to avoid # permission issues as well as to have things downloaded in a predictable @@ -16,7 +16,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-org.sc.sgd.db/meta.yaml b/recipes/bioconductor-org.sc.sgd.db/meta.yaml index 57db8617ab408..a8b84c182c37e 100644 --- a/recipes/bioconductor-org.sc.sgd.db/meta.yaml +++ b/recipes/bioconductor-org.sc.sgd.db/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "3.7.0" %} +{% set version = "3.8.2" %} {% set name = "org.Sc.sgd.db" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: ab71de66c00d1abc7941768408eb8e80 + md5: 386e853c14191f8845fc0237aad0d0db build: number: 0 rpaths: @@ -20,12 +20,12 @@ build: # Suggests: DBI, annotate, RUnit requirements: host: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' - r-base run: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-org.sc.sgd.db/post-link.sh b/recipes/bioconductor-org.sc.sgd.db/post-link.sh index abec8fb534d9e..9d92d721c9db1 100644 --- a/recipes/bioconductor-org.sc.sgd.db/post-link.sh +++ b/recipes/bioconductor-org.sc.sgd.db/post-link.sh @@ -1,11 +1,11 @@ #!/bin/bash -FN="org.Sc.sgd.db_3.7.0.tar.gz" +FN="org.Sc.sgd.db_3.8.2.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/org.Sc.sgd.db_3.7.0.tar.gz" - "https://bioarchive.galaxyproject.org/org.Sc.sgd.db_3.7.0.tar.gz" - "https://depot.galaxyproject.org/software/bioconductor-org.sc.sgd.db/bioconductor-org.sc.sgd.db_3.7.0_src_all.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/org.Sc.sgd.db_3.8.2.tar.gz" + "https://bioarchive.galaxyproject.org/org.Sc.sgd.db_3.8.2.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-org.sc.sgd.db/bioconductor-org.sc.sgd.db_3.8.2_src_all.tar.gz" ) -MD5="ab71de66c00d1abc7941768408eb8e80" +MD5="386e853c14191f8845fc0237aad0d0db" # Use a staging area in the conda dir rather than temp dirs, both to avoid # permission issues as well as to have things downloaded in a predictable @@ -16,7 +16,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-org.ss.eg.db/meta.yaml b/recipes/bioconductor-org.ss.eg.db/meta.yaml index ad3a2bffec69d..18627b1a6b577 100644 --- a/recipes/bioconductor-org.ss.eg.db/meta.yaml +++ b/recipes/bioconductor-org.ss.eg.db/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "3.7.0" %} +{% set version = "3.8.2" %} {% set name = "org.Ss.eg.db" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 9186f97704df0af8b485be518be405cc + md5: 8a177d13bc1a02df2edec3a017d62e2c build: number: 0 rpaths: @@ -20,12 +20,12 @@ build: # Suggests: DBI, annotate, RUnit requirements: host: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' - r-base run: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-org.ss.eg.db/post-link.sh b/recipes/bioconductor-org.ss.eg.db/post-link.sh index 6eb61c0dfab6b..c373ba5bf6131 100644 --- a/recipes/bioconductor-org.ss.eg.db/post-link.sh +++ b/recipes/bioconductor-org.ss.eg.db/post-link.sh @@ -1,11 +1,11 @@ #!/bin/bash -FN="org.Ss.eg.db_3.7.0.tar.gz" +FN="org.Ss.eg.db_3.8.2.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/org.Ss.eg.db_3.7.0.tar.gz" - "https://bioarchive.galaxyproject.org/org.Ss.eg.db_3.7.0.tar.gz" - "https://depot.galaxyproject.org/software/bioconductor-org.ss.eg.db/bioconductor-org.ss.eg.db_3.7.0_src_all.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/org.Ss.eg.db_3.8.2.tar.gz" + "https://bioarchive.galaxyproject.org/org.Ss.eg.db_3.8.2.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-org.ss.eg.db/bioconductor-org.ss.eg.db_3.8.2_src_all.tar.gz" ) -MD5="9186f97704df0af8b485be518be405cc" +MD5="8a177d13bc1a02df2edec3a017d62e2c" # Use a staging area in the conda dir rather than temp dirs, both to avoid # permission issues as well as to have things downloaded in a predictable @@ -16,7 +16,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-org.xl.eg.db/meta.yaml b/recipes/bioconductor-org.xl.eg.db/meta.yaml index 82e5d8f9d0b32..dd773f9ff9039 100644 --- a/recipes/bioconductor-org.xl.eg.db/meta.yaml +++ b/recipes/bioconductor-org.xl.eg.db/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "3.7.0" %} +{% set version = "3.8.2" %} {% set name = "org.Xl.eg.db" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,9 +10,9 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 2459dc4156660821213b1086bd9bcbcf + md5: 7161e10c46295930372f0febb2e36829 build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ @@ -20,12 +20,12 @@ build: # Suggests: DBI, annotate, RUnit requirements: host: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' - r-base run: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-org.xl.eg.db/post-link.sh b/recipes/bioconductor-org.xl.eg.db/post-link.sh index d74c6132abff7..e18e4dda3baa0 100644 --- a/recipes/bioconductor-org.xl.eg.db/post-link.sh +++ b/recipes/bioconductor-org.xl.eg.db/post-link.sh @@ -1,11 +1,11 @@ #!/bin/bash -FN="org.Xl.eg.db_3.7.0.tar.gz" +FN="org.Xl.eg.db_3.8.2.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/org.Xl.eg.db_3.7.0.tar.gz" - "https://bioarchive.galaxyproject.org/org.Xl.eg.db_3.7.0.tar.gz" - "https://depot.galaxyproject.org/software/bioconductor-org.xl.eg.db/bioconductor-org.xl.eg.db_3.7.0_src_all.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/org.Xl.eg.db_3.8.2.tar.gz" + "https://bioarchive.galaxyproject.org/org.Xl.eg.db_3.8.2.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-org.xl.eg.db/bioconductor-org.xl.eg.db_3.8.2_src_all.tar.gz" ) -MD5="2459dc4156660821213b1086bd9bcbcf" +MD5="7161e10c46295930372f0febb2e36829" # Use a staging area in the conda dir rather than temp dirs, both to avoid # permission issues as well as to have things downloaded in a predictable @@ -16,7 +16,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-organism.dplyr/meta.yaml b/recipes/bioconductor-organism.dplyr/meta.yaml index 19b7f5b4f0987..1ea6cddb43cd3 100644 --- a/recipes/bioconductor-organism.dplyr/meta.yaml +++ b/recipes/bioconductor-organism.dplyr/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.10.0" %} +{% set version = "1.11.2" %} {% set name = "Organism.dplyr" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 2852cd417e6f66dea89e0c4dbb7cd9d4 + md5: d56512695734db7fd6ecdefa0e3e606c build: number: 0 rpaths: @@ -20,28 +20,28 @@ build: # Suggests: org.Hs.eg.db, TxDb.Hsapiens.UCSC.hg38.knownGene, org.Mm.eg.db, TxDb.Mmusculus.UCSC.mm10.ensGene, testthat, knitr, rmarkdown, BiocStyle, ggplot2 requirements: host: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' - - 'bioconductor-annotationfilter >=1.6.0,<1.7.0' - - 'bioconductor-biocfilecache >=1.6.0,<1.7.0' - - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' - - 'bioconductor-genomicfeatures >=1.34.0,<1.35.0' - - 'bioconductor-genomicranges >=1.34.0,<1.35.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' + - 'bioconductor-annotationfilter >=1.8.0,<1.9.0' + - 'bioconductor-biocfilecache >=1.8.0,<1.9.0' + - 'bioconductor-genomeinfodb >=1.20.0,<1.21.0' + - 'bioconductor-genomicfeatures >=1.36.0,<1.37.0' + - 'bioconductor-genomicranges >=1.36.0,<1.37.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' - r-base - r-dbi - r-dbplyr - 'r-dplyr >=0.7.0' - r-rsqlite run: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' - - 'bioconductor-annotationfilter >=1.6.0,<1.7.0' - - 'bioconductor-biocfilecache >=1.6.0,<1.7.0' - - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' - - 'bioconductor-genomicfeatures >=1.34.0,<1.35.0' - - 'bioconductor-genomicranges >=1.34.0,<1.35.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' + - 'bioconductor-annotationfilter >=1.8.0,<1.9.0' + - 'bioconductor-biocfilecache >=1.8.0,<1.9.0' + - 'bioconductor-genomeinfodb >=1.20.0,<1.21.0' + - 'bioconductor-genomicfeatures >=1.36.0,<1.37.0' + - 'bioconductor-genomicranges >=1.36.0,<1.37.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' - r-base - r-dbi - r-dbplyr diff --git a/recipes/bioconductor-organismdbi/meta.yaml b/recipes/bioconductor-organismdbi/meta.yaml index f1052ae9d7834..61805096f9006 100644 --- a/recipes/bioconductor-organismdbi/meta.yaml +++ b/recipes/bioconductor-organismdbi/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.24.0" %} +{% set version = "1.26.0" %} {% set name = "OrganismDbi" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 5b61c03153b43c626fbdbbd1780e7652 + md5: c0f1638c0a1fe72f968933fd0877c3a9 build: number: 0 rpaths: @@ -20,28 +20,28 @@ build: # Suggests: Homo.sapiens, Rattus.norvegicus, BSgenome.Hsapiens.UCSC.hg19, AnnotationHub, FDb.UCSC.tRNAs, rtracklayer, biomaRt, RUnit, RMariaDB requirements: host: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' - - 'bioconductor-biobase >=2.42.0,<2.43.0' - - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' - - 'bioconductor-genomicfeatures >=1.34.0,<1.35.0' - - 'bioconductor-genomicranges >=1.34.0,<1.35.0' - - 'bioconductor-graph >=1.60.0,<1.61.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-rbgl >=1.58.0,<1.59.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' + - 'bioconductor-biocgenerics >=0.30.0,<0.31.0' + - 'bioconductor-genomicfeatures >=1.36.0,<1.37.0' + - 'bioconductor-genomicranges >=1.36.0,<1.37.0' + - 'bioconductor-graph >=1.62.0,<1.63.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-rbgl >=1.60.0,<1.61.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' - r-base - r-biocmanager - r-dbi run: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' - - 'bioconductor-biobase >=2.42.0,<2.43.0' - - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' - - 'bioconductor-genomicfeatures >=1.34.0,<1.35.0' - - 'bioconductor-genomicranges >=1.34.0,<1.35.0' - - 'bioconductor-graph >=1.60.0,<1.61.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-rbgl >=1.58.0,<1.59.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' + - 'bioconductor-biocgenerics >=0.30.0,<0.31.0' + - 'bioconductor-genomicfeatures >=1.36.0,<1.37.0' + - 'bioconductor-genomicranges >=1.36.0,<1.37.0' + - 'bioconductor-graph >=1.62.0,<1.63.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-rbgl >=1.60.0,<1.61.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' - r-base - r-biocmanager - r-dbi diff --git a/recipes/bioconductor-osat/meta.yaml b/recipes/bioconductor-osat/meta.yaml index a28d244e56eba..2078532ec8490 100644 --- a/recipes/bioconductor-osat/meta.yaml +++ b/recipes/bioconductor-osat/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.30.0" %} +{% set version = "1.32.0" %} {% set name = "OSAT" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 25da0a3ebe891d2149a22612d0e2884e + md5: d3f00e9577e4ec4149a4f5f568d7ad4e build: number: 0 rpaths: diff --git a/recipes/bioconductor-oscope/meta.yaml b/recipes/bioconductor-oscope/meta.yaml index 85db9e06d7d33..0c5896630c320 100644 --- a/recipes/bioconductor-oscope/meta.yaml +++ b/recipes/bioconductor-oscope/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.12.1" %} +{% set version = "1.14.0" %} {% set name = "Oscope" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: e5ec1b4537f1a5f32c0d3831938f70cf407e4d7ed486c8d0357c23fe838bad37 + md5: 25588131ddda3404c7e1c1674c9f486c build: number: 0 rpaths: @@ -20,14 +20,14 @@ build: # Suggests: BiocStyle requirements: host: - - 'bioconductor-biocparallel >=1.16.0,<1.17.0' - - 'bioconductor-ebseq >=1.22.0,<1.23.0' + - 'bioconductor-biocparallel >=1.18.0,<1.19.0' + - 'bioconductor-ebseq >=1.24.0,<1.25.0' - r-base - r-cluster - r-testthat run: - - 'bioconductor-biocparallel >=1.16.0,<1.17.0' - - 'bioconductor-ebseq >=1.22.0,<1.23.0' + - 'bioconductor-biocparallel >=1.18.0,<1.19.0' + - 'bioconductor-ebseq >=1.24.0,<1.25.0' - r-base - r-cluster - r-testthat diff --git a/recipes/bioconductor-otubase/meta.yaml b/recipes/bioconductor-otubase/meta.yaml index 9105d2a7b4e1a..b0e2eab5c33ed 100644 --- a/recipes/bioconductor-otubase/meta.yaml +++ b/recipes/bioconductor-otubase/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.32.0" %} +{% set version = "1.34.0" %} {% set name = "OTUbase" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 1d7602393bcbe0d127f647249cf9a0e9 + md5: cb91122e96e990e5975138ff36d21c7f build: number: 0 rpaths: @@ -19,19 +19,19 @@ build: noarch: generic requirements: host: - - 'bioconductor-biobase >=2.42.0,<2.43.0' - - 'bioconductor-biostrings >=2.50.0,<2.51.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' - - 'bioconductor-shortread >=1.40.0,<1.41.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' + - 'bioconductor-biostrings >=2.52.0,<2.53.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' + - 'bioconductor-shortread >=1.42.0,<1.43.0' - r-base - r-vegan run: - - 'bioconductor-biobase >=2.42.0,<2.43.0' - - 'bioconductor-biostrings >=2.50.0,<2.51.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' - - 'bioconductor-shortread >=1.40.0,<1.41.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' + - 'bioconductor-biostrings >=2.52.0,<2.53.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' + - 'bioconductor-shortread >=1.42.0,<1.43.0' - r-base - r-vegan test: diff --git a/recipes/bioconductor-outlierd/meta.yaml b/recipes/bioconductor-outlierd/meta.yaml index 10d0eaa51dd41..523812bcaf6e6 100644 --- a/recipes/bioconductor-outlierd/meta.yaml +++ b/recipes/bioconductor-outlierd/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.46.0" %} +{% set version = "1.48.0" %} {% set name = "OutlierD" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: faccbb13610392cf250252e1d03498f5 + md5: 44a6e07c906fa063969f5544505ca011 build: number: 0 rpaths: @@ -19,11 +19,11 @@ build: noarch: generic requirements: host: - - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' - r-base - r-quantreg run: - - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' - r-base - r-quantreg test: diff --git a/recipes/bioconductor-outrider/meta.yaml b/recipes/bioconductor-outrider/meta.yaml index de7da1b5de66d..b5ea64103eb1c 100644 --- a/recipes/bioconductor-outrider/meta.yaml +++ b/recipes/bioconductor-outrider/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.0.2" %} +{% set version = "1.2.0" %} {% set name = "OUTRIDER" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 6a8eea904c51ca4fa9acf23a93cb6fa3 + md5: 2de375148f4a0c65158b4e852bbca080 build: number: 0 rpaths: @@ -19,16 +19,16 @@ build: # Suggests: testthat, knitr, rmarkdown, BiocStyle, TxDb.Hsapiens.UCSC.hg19.knownGene, org.Hs.eg.db, RMySQL, AnnotationDbi, beeswarm, covr requirements: host: - - 'bioconductor-biobase >=2.42.0,<2.43.0' - - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' - - 'bioconductor-biocparallel >=1.16.0,<1.17.0' - - 'bioconductor-deseq2 >=1.22.0,<1.23.0' - - 'bioconductor-genomicfeatures >=1.34.0,<1.35.0' - - 'bioconductor-genomicranges >=1.34.0,<1.35.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-pcamethods >=1.74.0,<1.75.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' - - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' + - 'bioconductor-biocgenerics >=0.30.0,<0.31.0' + - 'bioconductor-biocparallel >=1.18.0,<1.19.0' + - 'bioconductor-deseq2 >=1.24.0,<1.25.0' + - 'bioconductor-genomicfeatures >=1.36.0,<1.37.0' + - 'bioconductor-genomicranges >=1.36.0,<1.37.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-pcamethods >=1.76.0,<1.77.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' + - 'bioconductor-summarizedexperiment >=1.14.0,<1.15.0' - r-base - r-bbmisc - r-data.table @@ -45,16 +45,16 @@ requirements: - r-reticulate - r-scales run: - - 'bioconductor-biobase >=2.42.0,<2.43.0' - - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' - - 'bioconductor-biocparallel >=1.16.0,<1.17.0' - - 'bioconductor-deseq2 >=1.22.0,<1.23.0' - - 'bioconductor-genomicfeatures >=1.34.0,<1.35.0' - - 'bioconductor-genomicranges >=1.34.0,<1.35.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-pcamethods >=1.74.0,<1.75.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' - - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' + - 'bioconductor-biocgenerics >=0.30.0,<0.31.0' + - 'bioconductor-biocparallel >=1.18.0,<1.19.0' + - 'bioconductor-deseq2 >=1.24.0,<1.25.0' + - 'bioconductor-genomicfeatures >=1.36.0,<1.37.0' + - 'bioconductor-genomicranges >=1.36.0,<1.37.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-pcamethods >=1.76.0,<1.77.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' + - 'bioconductor-summarizedexperiment >=1.14.0,<1.15.0' - r-base - r-bbmisc - r-data.table @@ -74,7 +74,6 @@ requirements: - {{ compiler('c') }} - {{ compiler('cxx') }} - make - - llvm-openmp # [osx] test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-oveseg/build.sh b/recipes/bioconductor-oveseg/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-oveseg/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-oveseg/meta.yaml b/recipes/bioconductor-oveseg/meta.yaml new file mode 100644 index 0000000000000..4515f35613cdd --- /dev/null +++ b/recipes/bioconductor-oveseg/meta.yaml @@ -0,0 +1,47 @@ +{% set version = "1.0.0" %} +{% set name = "OVESEG" %} +{% set bioc = "3.9" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: 046a686ab8c0f5679692f8899b8a8c25 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ +# Suggests: knitr, rmarkdown, BiocStyle, testthat, ggplot2, gridExtra, grid, reshape2, scales +# SystemRequirements: C++11 +requirements: + host: + - 'bioconductor-biocparallel >=1.18.0,<1.19.0' + - 'bioconductor-limma >=3.40.0,<3.41.0' + - 'bioconductor-summarizedexperiment >=1.14.0,<1.15.0' + - r-base + - r-fdrtool + - r-rcpp + run: + - 'bioconductor-biocparallel >=1.18.0,<1.19.0' + - 'bioconductor-limma >=3.40.0,<3.41.0' + - 'bioconductor-summarizedexperiment >=1.14.0,<1.15.0' + - r-base + - r-fdrtool + - r-rcpp + build: + - {{ compiler('c') }} + - {{ compiler('cxx') }} + - make +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: GPL-2 + summary: 'An R package for multiple-group comparison to detect tissue/cell-specific marker genes among subtypes. It provides functions to compute OVESEG-test statistics, derive component weights in the mixture null distribution model and estimate p-values from weightedly aggregated permutations. Obtained posterior probabilities of component null hypotheses can also portrait all kinds of upregulation patterns among subtypes.' + diff --git a/recipes/bioconductor-paa/meta.yaml b/recipes/bioconductor-paa/meta.yaml index 76b9a9ebf862b..8ce564d49c03a 100644 --- a/recipes/bioconductor-paa/meta.yaml +++ b/recipes/bioconductor-paa/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.16.0" %} +{% set version = "1.18.0" %} {% set name = "PAA" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 0452cfe09ff503b2cde95e81feafe9d5 + md5: 88bae0739cd3c1eb902e07a2ae2a2d10 build: number: 0 rpaths: @@ -20,8 +20,8 @@ build: # SystemRequirements: C++ software package Random Jungle requirements: host: - - 'bioconductor-limma >=3.38.0,<3.39.0' - - 'bioconductor-sva >=3.30.0,<3.31.0' + - 'bioconductor-limma >=3.40.0,<3.41.0' + - 'bioconductor-sva >=3.32.0,<3.33.0' - r-base - r-e1071 - r-gplots @@ -31,9 +31,10 @@ requirements: - r-randomforest - 'r-rcpp >=0.11.6' - r-rocr + - random-jungle run: - - 'bioconductor-limma >=3.38.0,<3.39.0' - - 'bioconductor-sva >=3.30.0,<3.31.0' + - 'bioconductor-limma >=3.40.0,<3.41.0' + - 'bioconductor-sva >=3.32.0,<3.33.0' - r-base - r-e1071 - r-gplots @@ -43,6 +44,7 @@ requirements: - r-randomforest - 'r-rcpp >=0.11.6' - r-rocr + - random-jungle build: - {{ compiler('c') }} - {{ compiler('cxx') }} diff --git a/recipes/bioconductor-padog/meta.yaml b/recipes/bioconductor-padog/meta.yaml index 3a4ad3a96350a..a7fd1f5368814 100644 --- a/recipes/bioconductor-padog/meta.yaml +++ b/recipes/bioconductor-padog/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.24.0" %} +{% set version = "1.26.0" %} {% set name = "PADOG" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 56431caee5cc198ddfdd7f93646d72d9 + md5: b3d4cf132c70bf0ce99691aabcf0ea3e build: number: 0 rpaths: @@ -20,26 +20,26 @@ build: # Suggests: doParallel, parallel requirements: host: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' - - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' - 'bioconductor-hgu133a.db >=3.2.0,<3.3.0' - 'bioconductor-hgu133plus2.db >=3.2.0,<3.3.0' - 'bioconductor-kegg.db >=3.2.0,<3.3.0' - - 'bioconductor-keggdzpathwaysgeo >=1.20.0,<1.21.0' - - 'bioconductor-limma >=3.38.0,<3.39.0' + - 'bioconductor-keggdzpathwaysgeo >=1.22.0,<1.23.0' + - 'bioconductor-limma >=3.40.0,<3.41.0' - r-base - r-dorng - r-foreach - r-gsa - r-nlme run: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' - - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' - 'bioconductor-hgu133a.db >=3.2.0,<3.3.0' - 'bioconductor-hgu133plus2.db >=3.2.0,<3.3.0' - 'bioconductor-kegg.db >=3.2.0,<3.3.0' - - 'bioconductor-keggdzpathwaysgeo >=1.20.0,<1.21.0' - - 'bioconductor-limma >=3.38.0,<3.39.0' + - 'bioconductor-keggdzpathwaysgeo >=1.22.0,<1.23.0' + - 'bioconductor-limma >=3.40.0,<3.41.0' - r-base - r-dorng - r-foreach diff --git a/recipes/bioconductor-paeg1acdf/meta.yaml b/recipes/bioconductor-paeg1acdf/meta.yaml index b2db35e597fbb..bb54451eba5c7 100644 --- a/recipes/bioconductor-paeg1acdf/meta.yaml +++ b/recipes/bioconductor-paeg1acdf/meta.yaml @@ -1,6 +1,6 @@ {% set version = "2.18.0" %} {% set name = "paeg1acdf" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -12,19 +12,19 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 73af974112051db0f715518393e84726 build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' - r-base run: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-paeg1acdf/post-link.sh b/recipes/bioconductor-paeg1acdf/post-link.sh index 72f469324e8d0..b0df43325a6ae 100644 --- a/recipes/bioconductor-paeg1acdf/post-link.sh +++ b/recipes/bioconductor-paeg1acdf/post-link.sh @@ -1,9 +1,10 @@ #!/bin/bash FN="paeg1acdf_2.18.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/paeg1acdf_2.18.0.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/paeg1acdf_2.18.0.tar.gz" "https://bioarchive.galaxyproject.org/paeg1acdf_2.18.0.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-paeg1acdf/bioconductor-paeg1acdf_2.18.0_src_all.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-paeg1acdf/bioconductor-paeg1acdf_2.18.0_src_all.tar.gz" ) MD5="73af974112051db0f715518393e84726" @@ -16,7 +17,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-paeg1aprobe/meta.yaml b/recipes/bioconductor-paeg1aprobe/meta.yaml index a9e19eaa9666b..fbba4a8c48153 100644 --- a/recipes/bioconductor-paeg1aprobe/meta.yaml +++ b/recipes/bioconductor-paeg1aprobe/meta.yaml @@ -1,6 +1,6 @@ {% set version = "2.18.0" %} {% set name = "paeg1aprobe" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -12,19 +12,19 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 493fa1fc7b92a78c8114b65038113c42 build: - number: 1 + number: 2 rpaths: - lib/R/lib/ - lib/ noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' - r-base run: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-paeg1aprobe/post-link.sh b/recipes/bioconductor-paeg1aprobe/post-link.sh index 2a76e15fc73f1..b29a7af74f808 100644 --- a/recipes/bioconductor-paeg1aprobe/post-link.sh +++ b/recipes/bioconductor-paeg1aprobe/post-link.sh @@ -1,9 +1,10 @@ #!/bin/bash FN="paeg1aprobe_2.18.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/paeg1aprobe_2.18.0.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/paeg1aprobe_2.18.0.tar.gz" "https://bioarchive.galaxyproject.org/paeg1aprobe_2.18.0.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-paeg1aprobe/bioconductor-paeg1aprobe_2.18.0_src_all.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-paeg1aprobe/bioconductor-paeg1aprobe_2.18.0_src_all.tar.gz" ) MD5="493fa1fc7b92a78c8114b65038113c42" @@ -16,7 +17,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-pairadise/build.sh b/recipes/bioconductor-pairadise/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-pairadise/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-pairadise/meta.yaml b/recipes/bioconductor-pairadise/meta.yaml new file mode 100644 index 0000000000000..03dcdd320d4f6 --- /dev/null +++ b/recipes/bioconductor-pairadise/meta.yaml @@ -0,0 +1,43 @@ +{% set version = "1.0.0" %} +{% set name = "PAIRADISE" %} +{% set bioc = "3.9" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: d394254a019c201f6b9bc6e5490bd29c +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: testthat, knitr, rmarkdown, BiocStyle +requirements: + host: + - 'bioconductor-biocparallel >=1.18.0,<1.19.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' + - 'bioconductor-summarizedexperiment >=1.14.0,<1.15.0' + - r-abind + - r-base + - r-nloptr + run: + - 'bioconductor-biocparallel >=1.18.0,<1.19.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' + - 'bioconductor-summarizedexperiment >=1.14.0,<1.15.0' + - r-abind + - r-base + - r-nloptr +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: 'MIT + file LICENSE' + summary: 'This package implements the PAIRADISE procedure for detecting differential isoform expression between matched replicates in paired RNA-Seq data.' + diff --git a/recipes/bioconductor-paircompviz/meta.yaml b/recipes/bioconductor-paircompviz/meta.yaml index ced485bde86cc..d21c9d368e387 100644 --- a/recipes/bioconductor-paircompviz/meta.yaml +++ b/recipes/bioconductor-paircompviz/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.20.0" %} +{% set version = "1.22.0" %} {% set name = "paircompviz" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: c2b68b9feed3ae0a7b15ad87e72465d6 + md5: b52ac2a27612f5ea60289601fac42af3 build: number: 0 rpaths: @@ -20,10 +20,10 @@ build: # Suggests: multcomp, reshape, rpart, plyr, xtable requirements: host: - - 'bioconductor-rgraphviz >=2.26.0,<2.27.0' + - 'bioconductor-rgraphviz >=2.28.0,<2.29.0' - r-base run: - - 'bioconductor-rgraphviz >=2.26.0,<2.27.0' + - 'bioconductor-rgraphviz >=2.28.0,<2.29.0' - r-base test: commands: diff --git a/recipes/bioconductor-pandar/meta.yaml b/recipes/bioconductor-pandar/meta.yaml index d785f58427337..c78303828dac5 100644 --- a/recipes/bioconductor-pandar/meta.yaml +++ b/recipes/bioconductor-pandar/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.14.0" %} +{% set version = "1.16.0" %} {% set name = "pandaR" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: adba12e16232b6d5443a2877e53ad90b + md5: dc76ba50e9307fd00be88cfc5a8eae54 build: number: 0 rpaths: @@ -20,8 +20,8 @@ build: # Suggests: knitr requirements: host: - - 'bioconductor-biobase >=2.42.0,<2.43.0' - - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' + - 'bioconductor-biocgenerics >=0.30.0,<0.31.0' - r-base - r-ggplot2 - r-hexbin @@ -31,8 +31,8 @@ requirements: - r-reshape - r-runit run: - - 'bioconductor-biobase >=2.42.0,<2.43.0' - - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' + - 'bioconductor-biocgenerics >=0.30.0,<0.31.0' - r-base - r-ggplot2 - r-hexbin diff --git a/recipes/bioconductor-panelcn.mops/meta.yaml b/recipes/bioconductor-panelcn.mops/meta.yaml index e5f3d92fe7703..b57a8cab1f7ac 100644 --- a/recipes/bioconductor-panelcn.mops/meta.yaml +++ b/recipes/bioconductor-panelcn.mops/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.4.0" %} +{% set version = "1.6.0" %} {% set name = "panelcn.mops" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 974ec0d14c6d3a3d8bca8c3f5140e718 + md5: 98a51f428f49f6b3148f7523a253189f build: number: 0 rpaths: @@ -20,20 +20,20 @@ build: # Suggests: knitr, rmarkdown, RUnit, BiocGenerics requirements: host: - - 'bioconductor-cn.mops >=1.28.0,<1.29.0' - - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' - - 'bioconductor-genomicranges >=1.34.0,<1.35.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-rsamtools >=1.34.0,<1.35.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-cn.mops >=1.30.0,<1.31.0' + - 'bioconductor-genomeinfodb >=1.20.0,<1.21.0' + - 'bioconductor-genomicranges >=1.36.0,<1.37.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-rsamtools >=2.0.0,<2.1.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' - r-base run: - - 'bioconductor-cn.mops >=1.28.0,<1.29.0' - - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' - - 'bioconductor-genomicranges >=1.34.0,<1.35.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-rsamtools >=1.34.0,<1.35.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-cn.mops >=1.30.0,<1.31.0' + - 'bioconductor-genomeinfodb >=1.20.0,<1.21.0' + - 'bioconductor-genomicranges >=1.36.0,<1.37.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-rsamtools >=2.0.0,<2.1.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' - r-base test: commands: diff --git a/recipes/bioconductor-panp/meta.yaml b/recipes/bioconductor-panp/meta.yaml index d9905ecba3994..191b92ab4933d 100644 --- a/recipes/bioconductor-panp/meta.yaml +++ b/recipes/bioconductor-panp/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.52.0" %} +{% set version = "1.54.0" %} {% set name = "panp" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: ce35790cd1d330942a3266e4c391d380 + md5: 9f78631585e785d969cbc4f2035a2083 build: number: 0 rpaths: @@ -20,12 +20,12 @@ build: # Suggests: gcrma requirements: host: - - 'bioconductor-affy >=1.60.0,<1.61.0' - - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-affy >=1.62.0,<1.63.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' - r-base run: - - 'bioconductor-affy >=1.60.0,<1.61.0' - - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-affy >=1.62.0,<1.63.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' - r-base test: commands: diff --git a/recipes/bioconductor-panr/meta.yaml b/recipes/bioconductor-panr/meta.yaml index cd36a4aded38a..66be4e390bfcf 100644 --- a/recipes/bioconductor-panr/meta.yaml +++ b/recipes/bioconductor-panr/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.28.1" %} +{% set version = "1.30.0" %} {% set name = "PANR" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: eeb904229161bcf7adf5cf5fbf7e482d + md5: 0a7ad116627065730fe5473064cd5f81 build: number: 0 rpaths: @@ -20,13 +20,13 @@ build: # Suggests: snow requirements: host: - - 'bioconductor-reder >=1.30.0,<1.31.0' + - 'bioconductor-reder >=1.32.0,<1.33.0' - r-base - r-igraph - r-mass - r-pvclust run: - - 'bioconductor-reder >=1.30.0,<1.31.0' + - 'bioconductor-reder >=1.32.0,<1.33.0' - r-base - r-igraph - r-mass diff --git a/recipes/bioconductor-panther.db/meta.yaml b/recipes/bioconductor-panther.db/meta.yaml index 74b2c273c15ce..9e15f337ce33b 100644 --- a/recipes/bioconductor-panther.db/meta.yaml +++ b/recipes/bioconductor-panther.db/meta.yaml @@ -1,6 +1,6 @@ {% set version = "1.0.4" %} {% set name = "PANTHER.db" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -12,7 +12,7 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' md5: bfd7362a4823bd3fda1bfab8e5b7908e build: - number: 3 + number: 4 rpaths: - lib/R/lib/ - lib/ @@ -20,14 +20,14 @@ build: # Suggests: RUnit,knitr,BiocStyle requirements: host: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' - r-base - r-rsqlite run: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' - r-base - r-rsqlite - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-panther.db/post-link.sh b/recipes/bioconductor-panther.db/post-link.sh index 1d24ae9984ebe..81af9cccd73ee 100644 --- a/recipes/bioconductor-panther.db/post-link.sh +++ b/recipes/bioconductor-panther.db/post-link.sh @@ -1,7 +1,7 @@ #!/bin/bash FN="PANTHER.db_1.0.4.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/PANTHER.db_1.0.4.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/PANTHER.db_1.0.4.tar.gz" "https://bioarchive.galaxyproject.org/PANTHER.db_1.0.4.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-panther.db/bioconductor-panther.db_1.0.4_src_all.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-panther.db/bioconductor-panther.db_1.0.4_src_all.tar.gz" @@ -17,7 +17,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-panvizgenerator/meta.yaml b/recipes/bioconductor-panvizgenerator/meta.yaml index b4ad27990dbda..aab47e7307030 100644 --- a/recipes/bioconductor-panvizgenerator/meta.yaml +++ b/recipes/bioconductor-panvizgenerator/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.10.0" %} +{% set version = "1.12.0" %} {% set name = "PanVizGenerator" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: d4415d9cb3e2e6c4e46abfe7e5cf601e + md5: 68fb5e9658c0cc6fab0a3eb8aea62fec build: number: 0 rpaths: @@ -20,15 +20,15 @@ build: # Suggests: BiocStyle, knitr, rmarkdown, testthat, digest requirements: host: - - 'bioconductor-findmyfriends >=1.12.0,<1.13.0' - - 'bioconductor-pcamethods >=1.74.0,<1.75.0' + - 'bioconductor-findmyfriends >=1.14.0,<1.15.0' + - 'bioconductor-pcamethods >=1.76.0,<1.77.0' - r-base - r-igraph - r-jsonlite - r-shiny run: - - 'bioconductor-findmyfriends >=1.12.0,<1.13.0' - - 'bioconductor-pcamethods >=1.74.0,<1.75.0' + - 'bioconductor-findmyfriends >=1.14.0,<1.15.0' + - 'bioconductor-pcamethods >=1.76.0,<1.77.0' - r-base - r-igraph - r-jsonlite diff --git a/recipes/bioconductor-papi/meta.yaml b/recipes/bioconductor-papi/meta.yaml index 503c87dcede6c..2b9eb36a5f474 100644 --- a/recipes/bioconductor-papi/meta.yaml +++ b/recipes/bioconductor-papi/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.22.0" %} +{% set version = "1.24.0" %} {% set name = "PAPi" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 118ecbaf4baea52351cba63b518b9176 + md5: 196bdffd32b72380c9e610b615c765ae build: number: 0 rpaths: @@ -19,11 +19,11 @@ build: noarch: generic requirements: host: - - 'bioconductor-keggrest >=1.22.0,<1.23.0' + - 'bioconductor-keggrest >=1.24.0,<1.25.0' - r-base - r-svdialogs run: - - 'bioconductor-keggrest >=1.22.0,<1.23.0' + - 'bioconductor-keggrest >=1.24.0,<1.25.0' - r-base - r-svdialogs test: diff --git a/recipes/bioconductor-parathyroidse/meta.yaml b/recipes/bioconductor-parathyroidse/meta.yaml index fe5fad1600ee2..6b7886b0c3cd7 100644 --- a/recipes/bioconductor-parathyroidse/meta.yaml +++ b/recipes/bioconductor-parathyroidse/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.20.0" %} +{% set version = "1.22.0" %} {% set name = "parathyroidSE" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 3a64ecf796315fd4b7b86173612b586e + md5: f0afc965e91000f48da3b5bb7b141b1f build: number: 0 rpaths: @@ -20,12 +20,12 @@ build: # Suggests: Rsamtools, GenomicAlignments, GEOquery, SRAdb, GenomicFeatures, BiocStyle requirements: host: - - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' + - 'bioconductor-summarizedexperiment >=1.14.0,<1.15.0' - r-base run: - - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' + - 'bioconductor-summarizedexperiment >=1.14.0,<1.15.0' - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-parathyroidse/post-link.sh b/recipes/bioconductor-parathyroidse/post-link.sh index d078938102406..7d68f0a704d69 100644 --- a/recipes/bioconductor-parathyroidse/post-link.sh +++ b/recipes/bioconductor-parathyroidse/post-link.sh @@ -1,11 +1,11 @@ #!/bin/bash -FN="parathyroidSE_1.20.0.tar.gz" +FN="parathyroidSE_1.22.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/experiment/src/contrib/parathyroidSE_1.20.0.tar.gz" - "https://bioarchive.galaxyproject.org/parathyroidSE_1.20.0.tar.gz" - "https://depot.galaxyproject.org/software/bioconductor-parathyroidse/bioconductor-parathyroidse_1.20.0_src_all.tar.gz" + "https://bioconductor.org/packages/3.9/data/experiment/src/contrib/parathyroidSE_1.22.0.tar.gz" + "https://bioarchive.galaxyproject.org/parathyroidSE_1.22.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-parathyroidse/bioconductor-parathyroidse_1.22.0_src_all.tar.gz" ) -MD5="3a64ecf796315fd4b7b86173612b586e" +MD5="f0afc965e91000f48da3b5bb7b141b1f" # Use a staging area in the conda dir rather than temp dirs, both to avoid # permission issues as well as to have things downloaded in a predictable @@ -16,7 +16,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-parglms/meta.yaml b/recipes/bioconductor-parglms/meta.yaml index b03b6a19c9332..71f0f3d6c7110 100644 --- a/recipes/bioconductor-parglms/meta.yaml +++ b/recipes/bioconductor-parglms/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.14.0" %} +{% set version = "1.16.0" %} {% set name = "parglms" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,23 +10,23 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 61af77bc2927d500ecba6c0427cd8d68 + md5: 0494730840ec5e71ff1a444532edfc65 build: number: 0 rpaths: - lib/R/lib/ - lib/ noarch: generic -# Suggests: RUnit, sandwich, MASS, knitr +# Suggests: RUnit, sandwich, MASS, knitr, GenomeInfoDb, GenomicRanges, gQTLBase, gQTLstats, geuvStore2, gwascat, BiocStyle requirements: host: - - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' + - 'bioconductor-biocgenerics >=0.30.0,<0.31.0' - r-base - r-batchjobs - r-doparallel - r-foreach run: - - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' + - 'bioconductor-biocgenerics >=0.30.0,<0.31.0' - r-base - r-batchjobs - r-doparallel diff --git a/recipes/bioconductor-parody/meta.yaml b/recipes/bioconductor-parody/meta.yaml index b52f3a574c909..c890092489543 100644 --- a/recipes/bioconductor-parody/meta.yaml +++ b/recipes/bioconductor-parody/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.40.0" %} +{% set version = "1.42.0" %} {% set name = "parody" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 7fed47b92aa3019bc677948bcd13cde6 + md5: d3707ed299e935718c26f52a37fb2d00 build: number: 0 rpaths: diff --git a/recipes/bioconductor-partheenmetadata.db/meta.yaml b/recipes/bioconductor-partheenmetadata.db/meta.yaml index 3c056e53e1885..ac1b7d54bcf97 100644 --- a/recipes/bioconductor-partheenmetadata.db/meta.yaml +++ b/recipes/bioconductor-partheenmetadata.db/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.2.3" %} {% set name = "PartheenMetaData.db" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -12,7 +12,7 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' md5: 1c9fd27e13a341b9aba9a235a67ce978 build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ @@ -20,14 +20,14 @@ build: # Suggests: DBI, annotate, RUnit requirements: host: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' - - 'bioconductor-org.hs.eg.db >=3.7.0,<3.8.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' + - 'bioconductor-org.hs.eg.db >=3.8.0,<3.9.0' - r-base run: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' - - 'bioconductor-org.hs.eg.db >=3.7.0,<3.8.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' + - 'bioconductor-org.hs.eg.db >=3.8.0,<3.9.0' - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-partheenmetadata.db/post-link.sh b/recipes/bioconductor-partheenmetadata.db/post-link.sh index ed961d9d8a46a..095c4a1317334 100644 --- a/recipes/bioconductor-partheenmetadata.db/post-link.sh +++ b/recipes/bioconductor-partheenmetadata.db/post-link.sh @@ -1,9 +1,10 @@ #!/bin/bash FN="PartheenMetaData.db_3.2.3.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/PartheenMetaData.db_3.2.3.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/PartheenMetaData.db_3.2.3.tar.gz" "https://bioarchive.galaxyproject.org/PartheenMetaData.db_3.2.3.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-partheenmetadata.db/bioconductor-partheenmetadata.db_3.2.3_src_all.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-partheenmetadata.db/bioconductor-partheenmetadata.db_3.2.3_src_all.tar.gz" ) MD5="1c9fd27e13a341b9aba9a235a67ce978" @@ -16,7 +17,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-pasilla/meta.yaml b/recipes/bioconductor-pasilla/meta.yaml index 8b3169ea7d131..e62c61ba96095 100644 --- a/recipes/bioconductor-pasilla/meta.yaml +++ b/recipes/bioconductor-pasilla/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.10.0" %} +{% set version = "1.12.0" %} {% set name = "pasilla" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 88ad1534662b8442e6d7a61cd0bb40dc + md5: 0bd04b62ac21a38cb820a74c4bd42534 build: number: 0 rpaths: @@ -23,7 +23,7 @@ requirements: - r-base run: - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-pasilla/post-link.sh b/recipes/bioconductor-pasilla/post-link.sh index 3206ebf59151a..6a95484b69855 100644 --- a/recipes/bioconductor-pasilla/post-link.sh +++ b/recipes/bioconductor-pasilla/post-link.sh @@ -1,11 +1,11 @@ #!/bin/bash -FN="pasilla_1.10.0.tar.gz" +FN="pasilla_1.12.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/experiment/src/contrib/pasilla_1.10.0.tar.gz" - "https://bioarchive.galaxyproject.org/pasilla_1.10.0.tar.gz" - "https://depot.galaxyproject.org/software/bioconductor-pasilla/bioconductor-pasilla_1.10.0_src_all.tar.gz" + "https://bioconductor.org/packages/3.9/data/experiment/src/contrib/pasilla_1.12.0.tar.gz" + "https://bioarchive.galaxyproject.org/pasilla_1.12.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-pasilla/bioconductor-pasilla_1.12.0_src_all.tar.gz" ) -MD5="88ad1534662b8442e6d7a61cd0bb40dc" +MD5="0bd04b62ac21a38cb820a74c4bd42534" # Use a staging area in the conda dir rather than temp dirs, both to avoid # permission issues as well as to have things downloaded in a predictable @@ -16,7 +16,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-pasillabamsubset/meta.yaml b/recipes/bioconductor-pasillabamsubset/meta.yaml index 4ddce1c20e4c2..cd8f396c08f5e 100644 --- a/recipes/bioconductor-pasillabamsubset/meta.yaml +++ b/recipes/bioconductor-pasillabamsubset/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "0.20.0" %} +{% set version = "0.22.0" %} {% set name = "pasillaBamSubset" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: a418f3d054320e023b3c533c5df9a20a + md5: a941d288f2aa572abce323159e473271 build: number: 0 rpaths: @@ -23,7 +23,7 @@ requirements: - r-base run: - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-pasillabamsubset/post-link.sh b/recipes/bioconductor-pasillabamsubset/post-link.sh index b42804ef48bd1..9ce659deedfe8 100644 --- a/recipes/bioconductor-pasillabamsubset/post-link.sh +++ b/recipes/bioconductor-pasillabamsubset/post-link.sh @@ -1,11 +1,11 @@ #!/bin/bash -FN="pasillaBamSubset_0.20.0.tar.gz" +FN="pasillaBamSubset_0.22.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/experiment/src/contrib/pasillaBamSubset_0.20.0.tar.gz" - "https://bioarchive.galaxyproject.org/pasillaBamSubset_0.20.0.tar.gz" - "https://depot.galaxyproject.org/software/bioconductor-pasillabamsubset/bioconductor-pasillabamsubset_0.20.0_src_all.tar.gz" + "https://bioconductor.org/packages/3.9/data/experiment/src/contrib/pasillaBamSubset_0.22.0.tar.gz" + "https://bioarchive.galaxyproject.org/pasillaBamSubset_0.22.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-pasillabamsubset/bioconductor-pasillabamsubset_0.22.0_src_all.tar.gz" ) -MD5="a418f3d054320e023b3c533c5df9a20a" +MD5="a941d288f2aa572abce323159e473271" # Use a staging area in the conda dir rather than temp dirs, both to avoid # permission issues as well as to have things downloaded in a predictable @@ -16,7 +16,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-pasillatranscriptexpr/meta.yaml b/recipes/bioconductor-pasillatranscriptexpr/meta.yaml index 1c11897d8650e..80c63172f8011 100644 --- a/recipes/bioconductor-pasillatranscriptexpr/meta.yaml +++ b/recipes/bioconductor-pasillatranscriptexpr/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.10.0" %} +{% set version = "1.12.0" %} {% set name = "PasillaTranscriptExpr" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: dd8a68bb858f26a8a675895b7aaf4467 + md5: faceed94f7269a49ff908400b7aab192 build: number: 0 rpaths: @@ -23,7 +23,7 @@ requirements: - r-base run: - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-pasillatranscriptexpr/post-link.sh b/recipes/bioconductor-pasillatranscriptexpr/post-link.sh index 9a0d50eee8401..f5e113f2bd80f 100644 --- a/recipes/bioconductor-pasillatranscriptexpr/post-link.sh +++ b/recipes/bioconductor-pasillatranscriptexpr/post-link.sh @@ -1,11 +1,11 @@ #!/bin/bash -FN="PasillaTranscriptExpr_1.10.0.tar.gz" +FN="PasillaTranscriptExpr_1.12.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/experiment/src/contrib/PasillaTranscriptExpr_1.10.0.tar.gz" - "https://bioarchive.galaxyproject.org/PasillaTranscriptExpr_1.10.0.tar.gz" - "https://depot.galaxyproject.org/software/bioconductor-pasillatranscriptexpr/bioconductor-pasillatranscriptexpr_1.10.0_src_all.tar.gz" + "https://bioconductor.org/packages/3.9/data/experiment/src/contrib/PasillaTranscriptExpr_1.12.0.tar.gz" + "https://bioarchive.galaxyproject.org/PasillaTranscriptExpr_1.12.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-pasillatranscriptexpr/bioconductor-pasillatranscriptexpr_1.12.0_src_all.tar.gz" ) -MD5="dd8a68bb858f26a8a675895b7aaf4467" +MD5="faceed94f7269a49ff908400b7aab192" # Use a staging area in the conda dir rather than temp dirs, both to avoid # permission issues as well as to have things downloaded in a predictable @@ -16,7 +16,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-past/build.sh b/recipes/bioconductor-past/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-past/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-past/meta.yaml b/recipes/bioconductor-past/meta.yaml new file mode 100644 index 0000000000000..29e0a07abf1f7 --- /dev/null +++ b/recipes/bioconductor-past/meta.yaml @@ -0,0 +1,49 @@ +{% set version = "1.0.0" %} +{% set name = "PAST" %} +{% set bioc = "3.9" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: 3c6515bb913a54463b8c597aef5fbda4 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: knitr, rmarkdown +requirements: + host: + - 'bioconductor-qvalue >=2.16.0,<2.17.0' + - 'bioconductor-rtracklayer >=1.44.0,<1.45.0' + - r-base + - r-doparallel + - r-dplyr + - r-foreach + - r-ggplot2 + - r-iterators + - r-rlang + run: + - 'bioconductor-qvalue >=2.16.0,<2.17.0' + - 'bioconductor-rtracklayer >=1.44.0,<1.45.0' + - r-base + - r-doparallel + - r-dplyr + - r-foreach + - r-ggplot2 + - r-iterators + - r-rlang +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: 'GPL (>=3)' + summary: 'PAST takes GWAS output and assigns SNPs to genes, uses those genes to find pathways associated with the genes, and plots pathways based on significance. Implements methods for reading GWAS input data, finding genes associated with SNPs, calculating enrichment score and significance of pathways, and plotting pathways.' + diff --git a/recipes/bioconductor-path2ppi/meta.yaml b/recipes/bioconductor-path2ppi/meta.yaml index 1d985f164aede..cdef730f8e350 100644 --- a/recipes/bioconductor-path2ppi/meta.yaml +++ b/recipes/bioconductor-path2ppi/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.12.0" %} +{% set version = "1.14.0" %} {% set name = "Path2PPI" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: fa0f1aa93584b7a1d724309e6f8b60c4 + md5: fb9995b5286c70abba1ec04d9331358d build: number: 0 rpaths: diff --git a/recipes/bioconductor-pathifier/meta.yaml b/recipes/bioconductor-pathifier/meta.yaml index aaa2feac6aa10..255544fba664e 100644 --- a/recipes/bioconductor-pathifier/meta.yaml +++ b/recipes/bioconductor-pathifier/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.20.0" %} +{% set version = "1.22.0" %} {% set name = "pathifier" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,9 +10,9 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: a3c03fc2a9686179902658a4e3d02946 + md5: 58df0dff57cf54fd9a4cd0f21f13157b build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ diff --git a/recipes/bioconductor-pathnet/meta.yaml b/recipes/bioconductor-pathnet/meta.yaml index b4bd6fff988be..ee06ed9b5f77e 100644 --- a/recipes/bioconductor-pathnet/meta.yaml +++ b/recipes/bioconductor-pathnet/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.22.0" %} +{% set version = "1.23.0" %} {% set name = "PathNet" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: b7ba6c5f1e0cec5a3b1d5c820345b02a + md5: 8379b86eac97f490fe40f90d7dcae045 build: number: 0 rpaths: diff --git a/recipes/bioconductor-pathnetdata/meta.yaml b/recipes/bioconductor-pathnetdata/meta.yaml index 5d48436e4f880..a49c103a85b46 100644 --- a/recipes/bioconductor-pathnetdata/meta.yaml +++ b/recipes/bioconductor-pathnetdata/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.18.0" %} +{% set version = "1.20.0" %} {% set name = "PathNetData" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: baad9f77b8914d21f84963e3b19f67ed + md5: 2001039db08246bf7daef431935a2ef6 build: number: 0 rpaths: @@ -22,7 +22,7 @@ requirements: - r-base run: - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-pathnetdata/post-link.sh b/recipes/bioconductor-pathnetdata/post-link.sh index 49f82e32a03a6..0568d0497d1ef 100644 --- a/recipes/bioconductor-pathnetdata/post-link.sh +++ b/recipes/bioconductor-pathnetdata/post-link.sh @@ -1,11 +1,11 @@ #!/bin/bash -FN="PathNetData_1.18.0.tar.gz" +FN="PathNetData_1.20.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/experiment/src/contrib/PathNetData_1.18.0.tar.gz" - "https://bioarchive.galaxyproject.org/PathNetData_1.18.0.tar.gz" - "https://depot.galaxyproject.org/software/bioconductor-pathnetdata/bioconductor-pathnetdata_1.18.0_src_all.tar.gz" + "https://bioconductor.org/packages/3.9/data/experiment/src/contrib/PathNetData_1.20.0.tar.gz" + "https://bioarchive.galaxyproject.org/PathNetData_1.20.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-pathnetdata/bioconductor-pathnetdata_1.20.0_src_all.tar.gz" ) -MD5="baad9f77b8914d21f84963e3b19f67ed" +MD5="2001039db08246bf7daef431935a2ef6" # Use a staging area in the conda dir rather than temp dirs, both to avoid # permission issues as well as to have things downloaded in a predictable @@ -16,7 +16,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-pathostat/meta.yaml b/recipes/bioconductor-pathostat/meta.yaml index 6210339c749e9..48ed96bd2835c 100644 --- a/recipes/bioconductor-pathostat/meta.yaml +++ b/recipes/bioconductor-pathostat/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.8.4" %} +{% set version = "1.10.0" %} {% set name = "PathoStat" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 385833d81ba649fab612821f5f0fad55 + md5: 39aa70d559ca8ed7159ea9fefeab67db build: number: 0 rpaths: @@ -20,12 +20,12 @@ build: # Suggests: rmarkdown, testthat requirements: host: - - 'bioconductor-biocstyle >=2.10.0,<2.11.0' - - 'bioconductor-complexheatmap >=1.20.0,<1.21.0' - - 'bioconductor-deseq2 >=1.22.0,<1.23.0' - - 'bioconductor-edger >=3.24.0,<3.25.0' - - 'bioconductor-limma >=3.38.0,<3.39.0' - - 'bioconductor-phyloseq >=1.26.0,<1.27.0' + - 'bioconductor-biocstyle >=2.12.0,<2.13.0' + - 'bioconductor-complexheatmap >=2.0.0,<2.1.0' + - 'bioconductor-deseq2 >=1.24.0,<1.25.0' + - 'bioconductor-edger >=3.26.0,<3.27.0' + - 'bioconductor-limma >=3.40.0,<3.41.0' + - 'bioconductor-phyloseq >=1.28.0,<1.29.0' - r-ape - r-base - r-corpcor @@ -51,12 +51,12 @@ requirements: - r-webshot - r-xml run: - - 'bioconductor-biocstyle >=2.10.0,<2.11.0' - - 'bioconductor-complexheatmap >=1.20.0,<1.21.0' - - 'bioconductor-deseq2 >=1.22.0,<1.23.0' - - 'bioconductor-edger >=3.24.0,<3.25.0' - - 'bioconductor-limma >=3.38.0,<3.39.0' - - 'bioconductor-phyloseq >=1.26.0,<1.27.0' + - 'bioconductor-biocstyle >=2.12.0,<2.13.0' + - 'bioconductor-complexheatmap >=2.0.0,<2.1.0' + - 'bioconductor-deseq2 >=1.24.0,<1.25.0' + - 'bioconductor-edger >=3.26.0,<3.27.0' + - 'bioconductor-limma >=3.40.0,<3.41.0' + - 'bioconductor-phyloseq >=1.28.0,<1.29.0' - r-ape - r-base - r-corpcor diff --git a/recipes/bioconductor-pathprint/meta.yaml b/recipes/bioconductor-pathprint/meta.yaml index f7b0a8544209c..a1699c329b56b 100644 --- a/recipes/bioconductor-pathprint/meta.yaml +++ b/recipes/bioconductor-pathprint/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.12.0" %} +{% set version = "1.14.0" %} {% set name = "pathprint" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 4fa4f3fecafee2af2d62766f6affa9fa + md5: f78e3b730d7c273fea0d23ad7c350461 build: number: 0 rpaths: diff --git a/recipes/bioconductor-pathprintgeodata/meta.yaml b/recipes/bioconductor-pathprintgeodata/meta.yaml index 8bb2c5a056a94..5b210989cf718 100644 --- a/recipes/bioconductor-pathprintgeodata/meta.yaml +++ b/recipes/bioconductor-pathprintgeodata/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.12.0" %} +{% set version = "1.14.0" %} {% set name = "pathprintGEOData" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: ad2f10bec6bb16df90e3e9ad1e193563 + md5: a7237e62dda8f356c41d35e50fef33e8 build: number: 0 rpaths: @@ -23,7 +23,7 @@ requirements: - r-base run: - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-pathprintgeodata/post-link.sh b/recipes/bioconductor-pathprintgeodata/post-link.sh index 582c94b134d86..2e7f85b268240 100644 --- a/recipes/bioconductor-pathprintgeodata/post-link.sh +++ b/recipes/bioconductor-pathprintgeodata/post-link.sh @@ -1,11 +1,11 @@ #!/bin/bash -FN="pathprintGEOData_1.12.0.tar.gz" +FN="pathprintGEOData_1.14.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/experiment/src/contrib/pathprintGEOData_1.12.0.tar.gz" - "https://bioarchive.galaxyproject.org/pathprintGEOData_1.12.0.tar.gz" - "https://depot.galaxyproject.org/software/bioconductor-pathprintgeodata/bioconductor-pathprintgeodata_1.12.0_src_all.tar.gz" + "https://bioconductor.org/packages/3.9/data/experiment/src/contrib/pathprintGEOData_1.14.0.tar.gz" + "https://bioarchive.galaxyproject.org/pathprintGEOData_1.14.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-pathprintgeodata/bioconductor-pathprintgeodata_1.14.0_src_all.tar.gz" ) -MD5="ad2f10bec6bb16df90e3e9ad1e193563" +MD5="a7237e62dda8f356c41d35e50fef33e8" # Use a staging area in the conda dir rather than temp dirs, both to avoid # permission issues as well as to have things downloaded in a predictable @@ -16,7 +16,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-pathrender/meta.yaml b/recipes/bioconductor-pathrender/meta.yaml index 3dc5825cf9802..df23da862496c 100644 --- a/recipes/bioconductor-pathrender/meta.yaml +++ b/recipes/bioconductor-pathrender/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.50.0" %} +{% set version = "1.52.0" %} {% set name = "pathRender" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 91a194d410a75cfcd81136ccce3496e7 + md5: 74527eae51dd579c3d27e1c8c15d6932 build: number: 0 rpaths: @@ -20,17 +20,17 @@ build: # Suggests: ALL, hgu95av2.db requirements: host: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' - - 'bioconductor-cmap >=1.15.0,<1.16.0' - - 'bioconductor-graph >=1.60.0,<1.61.0' - - 'bioconductor-rgraphviz >=2.26.0,<2.27.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' + - 'bioconductor-cmap >=1.16.0,<1.17.0' + - 'bioconductor-graph >=1.62.0,<1.63.0' + - 'bioconductor-rgraphviz >=2.28.0,<2.29.0' - r-base - r-rcolorbrewer run: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' - - 'bioconductor-cmap >=1.15.0,<1.16.0' - - 'bioconductor-graph >=1.60.0,<1.61.0' - - 'bioconductor-rgraphviz >=2.26.0,<2.27.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' + - 'bioconductor-cmap >=1.16.0,<1.17.0' + - 'bioconductor-graph >=1.62.0,<1.63.0' + - 'bioconductor-rgraphviz >=2.28.0,<2.29.0' - r-base - r-rcolorbrewer test: diff --git a/recipes/bioconductor-pathvar/meta.yaml b/recipes/bioconductor-pathvar/meta.yaml index 46d799cca0508..7d3fd71d53358 100644 --- a/recipes/bioconductor-pathvar/meta.yaml +++ b/recipes/bioconductor-pathvar/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.12.0" %} +{% set version = "1.14.0" %} {% set name = "pathVar" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 6a0e4fc15f3b005a5d188b3242149420 + md5: bb2379f993f3a1fa95240838df6b739e build: number: 0 rpaths: diff --git a/recipes/bioconductor-pathview/meta.yaml b/recipes/bioconductor-pathview/meta.yaml index d46b16e2dee60..531f881830061 100644 --- a/recipes/bioconductor-pathview/meta.yaml +++ b/recipes/bioconductor-pathview/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.22.0" %} +{% set version = "1.24.0" %} {% set name = "pathview" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: e11c9047d1053c360d828e5312684f39 + md5: 9b6dd193eb8566c7991ca16a95913f45 build: number: 0 rpaths: @@ -20,22 +20,22 @@ build: # Suggests: gage, org.Mm.eg.db, RUnit, BiocGenerics requirements: host: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' - - 'bioconductor-graph >=1.60.0,<1.61.0' - - 'bioconductor-kegggraph >=1.42.0,<1.43.0' - - 'bioconductor-keggrest >=1.22.0,<1.23.0' - - 'bioconductor-org.hs.eg.db >=3.7.0,<3.8.0' - - 'bioconductor-rgraphviz >=2.26.0,<2.27.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' + - 'bioconductor-graph >=1.62.0,<1.63.0' + - 'bioconductor-kegggraph >=1.44.0,<1.45.0' + - 'bioconductor-keggrest >=1.24.0,<1.25.0' + - 'bioconductor-org.hs.eg.db >=3.8.0,<3.9.0' + - 'bioconductor-rgraphviz >=2.28.0,<2.29.0' - r-base - r-png - r-xml run: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' - - 'bioconductor-graph >=1.60.0,<1.61.0' - - 'bioconductor-kegggraph >=1.42.0,<1.43.0' - - 'bioconductor-keggrest >=1.22.0,<1.23.0' - - 'bioconductor-org.hs.eg.db >=3.7.0,<3.8.0' - - 'bioconductor-rgraphviz >=2.26.0,<2.27.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' + - 'bioconductor-graph >=1.62.0,<1.63.0' + - 'bioconductor-kegggraph >=1.44.0,<1.45.0' + - 'bioconductor-keggrest >=1.24.0,<1.25.0' + - 'bioconductor-org.hs.eg.db >=3.8.0,<3.9.0' + - 'bioconductor-rgraphviz >=2.28.0,<2.29.0' - r-base - r-png - r-xml diff --git a/recipes/bioconductor-pathwaypca/build.sh b/recipes/bioconductor-pathwaypca/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-pathwaypca/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-pathwaypca/meta.yaml b/recipes/bioconductor-pathwaypca/meta.yaml new file mode 100644 index 0000000000000..3209178d51b67 --- /dev/null +++ b/recipes/bioconductor-pathwaypca/meta.yaml @@ -0,0 +1,37 @@ +{% set version = "1.0.0" %} +{% set name = "pathwayPCA" %} +{% set bioc = "3.9" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: d71f4103f7a8b57c8c57c05e616587dd +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: airway, circlize, grDevices, knitr, RCurl, reshape2, rmarkdown, SummarizedExperiment, survminer, testthat, tidyverse +requirements: + host: + - r-base + - r-lars + - r-survival + run: + - r-base + - r-lars + - r-survival +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: GPL-3 + summary: 'Apply the Supervised PCA and Adaptive, Elastic-Net, Sparse PCA methods to extract principal components from each pathway. Use these pathway- specific principal components as the design matrix relating the response to each pathway. Return the model fit statistic p-values, and adjust these values for False Discovery Rate. Return a data frame of the pathways sorted by their adjusted p-values. This package has corresponding vignettes hosted in the ''''User Guides'''' page of , and the website for the development information is hosted at .' + diff --git a/recipes/bioconductor-pathwaysplice/meta.yaml b/recipes/bioconductor-pathwaysplice/meta.yaml index b53be9e5274f6..9d34bd9f169f3 100644 --- a/recipes/bioconductor-pathwaysplice/meta.yaml +++ b/recipes/bioconductor-pathwaysplice/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.6.0" %} +{% set version = "1.8.0" %} {% set name = "PathwaySplice" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 5f7e8982f76c5513f7194ed91beef545 + md5: 039776737311855f25e984c72c6bebaa build: number: 0 rpaths: @@ -20,22 +20,22 @@ build: # Suggests: testthat, knitr, rmarkdown requirements: host: - - 'bioconductor-annotate >=1.60.0,<1.61.0' - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' - - 'bioconductor-annotationhub >=2.14.0,<2.15.0' - - 'bioconductor-biobase >=2.42.0,<2.43.0' - - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' - - 'bioconductor-dose >=3.8.0,<3.9.0' - - 'bioconductor-enrichmentbrowser >=2.12.0,<2.13.0' - - 'bioconductor-ensembldb >=2.6.0,<2.7.0' - - 'bioconductor-genelendatabase >=1.18.0,<1.19.0' - - 'bioconductor-go.db >=3.7.0,<3.8.0' - - 'bioconductor-goseq >=1.34.0,<1.35.0' - - 'bioconductor-junctionseq >=1.12.0,<1.13.0' - - 'bioconductor-keggrest >=1.22.0,<1.23.0' - - 'bioconductor-org.hs.eg.db >=3.7.0,<3.8.0' - - 'bioconductor-org.mm.eg.db >=3.7.0,<3.8.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-annotate >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' + - 'bioconductor-annotationhub >=2.16.0,<2.17.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' + - 'bioconductor-biocgenerics >=0.30.0,<0.31.0' + - 'bioconductor-dose >=3.10.0,<3.11.0' + - 'bioconductor-enrichmentbrowser >=2.14.0,<2.15.0' + - 'bioconductor-ensembldb >=2.8.0,<2.9.0' + - 'bioconductor-genelendatabase >=1.20.0,<1.21.0' + - 'bioconductor-go.db >=3.8.0,<3.9.0' + - 'bioconductor-goseq >=1.36.0,<1.37.0' + - 'bioconductor-junctionseq >=1.14.0,<1.15.0' + - 'bioconductor-keggrest >=1.24.0,<1.25.0' + - 'bioconductor-org.hs.eg.db >=3.8.0,<3.9.0' + - 'bioconductor-org.mm.eg.db >=3.8.0,<3.9.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' - r-base - r-biasedurn - r-dplyr @@ -52,22 +52,22 @@ requirements: - r-venndiagram - r-webshot run: - - 'bioconductor-annotate >=1.60.0,<1.61.0' - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' - - 'bioconductor-annotationhub >=2.14.0,<2.15.0' - - 'bioconductor-biobase >=2.42.0,<2.43.0' - - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' - - 'bioconductor-dose >=3.8.0,<3.9.0' - - 'bioconductor-enrichmentbrowser >=2.12.0,<2.13.0' - - 'bioconductor-ensembldb >=2.6.0,<2.7.0' - - 'bioconductor-genelendatabase >=1.18.0,<1.19.0' - - 'bioconductor-go.db >=3.7.0,<3.8.0' - - 'bioconductor-goseq >=1.34.0,<1.35.0' - - 'bioconductor-junctionseq >=1.12.0,<1.13.0' - - 'bioconductor-keggrest >=1.22.0,<1.23.0' - - 'bioconductor-org.hs.eg.db >=3.7.0,<3.8.0' - - 'bioconductor-org.mm.eg.db >=3.7.0,<3.8.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-annotate >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' + - 'bioconductor-annotationhub >=2.16.0,<2.17.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' + - 'bioconductor-biocgenerics >=0.30.0,<0.31.0' + - 'bioconductor-dose >=3.10.0,<3.11.0' + - 'bioconductor-enrichmentbrowser >=2.14.0,<2.15.0' + - 'bioconductor-ensembldb >=2.8.0,<2.9.0' + - 'bioconductor-genelendatabase >=1.20.0,<1.21.0' + - 'bioconductor-go.db >=3.8.0,<3.9.0' + - 'bioconductor-goseq >=1.36.0,<1.37.0' + - 'bioconductor-junctionseq >=1.14.0,<1.15.0' + - 'bioconductor-keggrest >=1.24.0,<1.25.0' + - 'bioconductor-org.hs.eg.db >=3.8.0,<3.9.0' + - 'bioconductor-org.mm.eg.db >=3.8.0,<3.9.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' - r-base - r-biasedurn - r-dplyr diff --git a/recipes/bioconductor-paxtoolsr/meta.yaml b/recipes/bioconductor-paxtoolsr/meta.yaml index 589efcb21308b..78c557414431d 100644 --- a/recipes/bioconductor-paxtoolsr/meta.yaml +++ b/recipes/bioconductor-paxtoolsr/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.16.0" %} +{% set version = "1.18.0" %} {% set name = "paxtoolsr" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 8394eb60eeaee13886d8934e67581e7d + md5: 3652a8dd52b4f53044e378ad85457550 build: number: 0 rpaths: diff --git a/recipes/bioconductor-pbase/meta.yaml b/recipes/bioconductor-pbase/meta.yaml index ca21299f08d39..1de93c9bfe820 100644 --- a/recipes/bioconductor-pbase/meta.yaml +++ b/recipes/bioconductor-pbase/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "0.22.1" %} +{% set version = "0.24.0" %} {% set name = "Pbase" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: d4af30b3cf547b82b29d5b6853745661 + md5: 76e54fdaedbffd9c9fd04a08529b0519 build: number: 0 rpaths: @@ -19,43 +19,43 @@ build: # Suggests: testthat (>= 0.8), ggplot2, BSgenome.Hsapiens.NCBI.GRCh38, TxDb.Hsapiens.UCSC.hg38.knownGene, AnnotationHub, knitr, rmarkdown, BiocStyle, EnsDb.Hsapiens.v86 (>= 2.0.0) requirements: host: - - 'bioconductor-annotationfilter >=1.6.0,<1.7.0' - - 'bioconductor-biobase >=2.42.0,<2.43.0' - - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' - - 'bioconductor-biocparallel >=1.16.0,<1.17.0' - - 'bioconductor-biomart >=2.38.0,<2.39.0' - - 'bioconductor-biostrings >=2.50.0,<2.51.0' - - 'bioconductor-cleaver >=1.20.0,<1.21.0' - - 'bioconductor-ensembldb >=2.6.0,<2.7.0' - - 'bioconductor-genomicranges >=1.34.0,<1.35.0' - - 'bioconductor-gviz >=1.26.0,<1.27.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-msnbase >=2.8.0,<2.9.0' - - 'bioconductor-mzid >=1.20.0,<1.21.0' - - 'bioconductor-mzr >=2.16.0,<2.17.0' - - 'bioconductor-pviz >=1.16.0,<1.17.0' - - 'bioconductor-rtracklayer >=1.42.0,<1.43.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-annotationfilter >=1.8.0,<1.9.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' + - 'bioconductor-biocgenerics >=0.30.0,<0.31.0' + - 'bioconductor-biocparallel >=1.18.0,<1.19.0' + - 'bioconductor-biomart >=2.40.0,<2.41.0' + - 'bioconductor-biostrings >=2.52.0,<2.53.0' + - 'bioconductor-cleaver >=1.22.0,<1.23.0' + - 'bioconductor-ensembldb >=2.8.0,<2.9.0' + - 'bioconductor-genomicranges >=1.36.0,<1.37.0' + - 'bioconductor-gviz >=1.28.0,<1.29.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-msnbase >=2.10.0,<2.11.0' + - 'bioconductor-mzid >=1.22.0,<1.23.0' + - 'bioconductor-mzr >=2.18.0,<2.19.0' + - 'bioconductor-pviz >=1.18.0,<1.19.0' + - 'bioconductor-rtracklayer >=1.44.0,<1.45.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' - r-base - r-rcpp run: - - 'bioconductor-annotationfilter >=1.6.0,<1.7.0' - - 'bioconductor-biobase >=2.42.0,<2.43.0' - - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' - - 'bioconductor-biocparallel >=1.16.0,<1.17.0' - - 'bioconductor-biomart >=2.38.0,<2.39.0' - - 'bioconductor-biostrings >=2.50.0,<2.51.0' - - 'bioconductor-cleaver >=1.20.0,<1.21.0' - - 'bioconductor-ensembldb >=2.6.0,<2.7.0' - - 'bioconductor-genomicranges >=1.34.0,<1.35.0' - - 'bioconductor-gviz >=1.26.0,<1.27.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-msnbase >=2.8.0,<2.9.0' - - 'bioconductor-mzid >=1.20.0,<1.21.0' - - 'bioconductor-mzr >=2.16.0,<2.17.0' - - 'bioconductor-pviz >=1.16.0,<1.17.0' - - 'bioconductor-rtracklayer >=1.42.0,<1.43.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-annotationfilter >=1.8.0,<1.9.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' + - 'bioconductor-biocgenerics >=0.30.0,<0.31.0' + - 'bioconductor-biocparallel >=1.18.0,<1.19.0' + - 'bioconductor-biomart >=2.40.0,<2.41.0' + - 'bioconductor-biostrings >=2.52.0,<2.53.0' + - 'bioconductor-cleaver >=1.22.0,<1.23.0' + - 'bioconductor-ensembldb >=2.8.0,<2.9.0' + - 'bioconductor-genomicranges >=1.36.0,<1.37.0' + - 'bioconductor-gviz >=1.28.0,<1.29.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-msnbase >=2.10.0,<2.11.0' + - 'bioconductor-mzid >=1.22.0,<1.23.0' + - 'bioconductor-mzr >=2.18.0,<2.19.0' + - 'bioconductor-pviz >=1.18.0,<1.19.0' + - 'bioconductor-rtracklayer >=1.44.0,<1.45.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' - r-base - r-rcpp build: diff --git a/recipes/bioconductor-pcaexplorer/meta.yaml b/recipes/bioconductor-pcaexplorer/meta.yaml index 46d59f859c4bf..0e1cbb747580e 100644 --- a/recipes/bioconductor-pcaexplorer/meta.yaml +++ b/recipes/bioconductor-pcaexplorer/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "2.8.0" %} +{% set version = "2.10.0" %} {% set name = "pcaExplorer" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,29 +10,30 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: dd19f6f70e9b1cc4a09ec19d725bc2ca + md5: 21e405e483d86636c37046d8d7dcea8d build: number: 0 rpaths: - lib/R/lib/ - lib/ noarch: generic -# Suggests: testthat, BiocStyle, airway, org.Hs.eg.db +# Suggests: testthat, BiocStyle, airway, org.Hs.eg.db, htmltools requirements: host: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' - - 'bioconductor-biomart >=2.38.0,<2.39.0' - - 'bioconductor-deseq2 >=1.22.0,<1.23.0' - - 'bioconductor-genefilter >=1.64.0,<1.65.0' - - 'bioconductor-genomicranges >=1.34.0,<1.35.0' - - 'bioconductor-go.db >=3.7.0,<3.8.0' - - 'bioconductor-gostats >=2.48.0,<2.49.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-limma >=3.38.0,<3.39.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' - - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' - - 'bioconductor-topgo >=2.34.0,<2.35.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' + - 'bioconductor-biomart >=2.40.0,<2.41.0' + - 'bioconductor-deseq2 >=1.24.0,<1.25.0' + - 'bioconductor-genefilter >=1.66.0,<1.67.0' + - 'bioconductor-genomicranges >=1.36.0,<1.37.0' + - 'bioconductor-go.db >=3.8.0,<3.9.0' + - 'bioconductor-gostats >=2.50.0,<2.51.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-limma >=3.40.0,<3.41.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' + - 'bioconductor-summarizedexperiment >=1.14.0,<1.15.0' + - 'bioconductor-topgo >=2.36.0,<2.37.0' - r-base + - r-base64enc - r-d3heatmap - r-dt - 'r-ggplot2 >=2.0.0' @@ -50,19 +51,20 @@ requirements: - r-threejs - r-tidyr run: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' - - 'bioconductor-biomart >=2.38.0,<2.39.0' - - 'bioconductor-deseq2 >=1.22.0,<1.23.0' - - 'bioconductor-genefilter >=1.64.0,<1.65.0' - - 'bioconductor-genomicranges >=1.34.0,<1.35.0' - - 'bioconductor-go.db >=3.7.0,<3.8.0' - - 'bioconductor-gostats >=2.48.0,<2.49.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-limma >=3.38.0,<3.39.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' - - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' - - 'bioconductor-topgo >=2.34.0,<2.35.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' + - 'bioconductor-biomart >=2.40.0,<2.41.0' + - 'bioconductor-deseq2 >=1.24.0,<1.25.0' + - 'bioconductor-genefilter >=1.66.0,<1.67.0' + - 'bioconductor-genomicranges >=1.36.0,<1.37.0' + - 'bioconductor-go.db >=3.8.0,<3.9.0' + - 'bioconductor-gostats >=2.50.0,<2.51.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-limma >=3.40.0,<3.41.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' + - 'bioconductor-summarizedexperiment >=1.14.0,<1.15.0' + - 'bioconductor-topgo >=2.36.0,<2.37.0' - r-base + - r-base64enc - r-d3heatmap - r-dt - 'r-ggplot2 >=2.0.0' diff --git a/recipes/bioconductor-pcagopromoter.hs.hg19/meta.yaml b/recipes/bioconductor-pcagopromoter.hs.hg19/meta.yaml index 44a88b2b48ca9..e7fa55393d1dd 100644 --- a/recipes/bioconductor-pcagopromoter.hs.hg19/meta.yaml +++ b/recipes/bioconductor-pcagopromoter.hs.hg19/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.18.0" %} +{% set version = "1.20.0" %} {% set name = "pcaGoPromoter.Hs.hg19" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 4cc30df25e7ebdcfda9a818e51a58a5d + md5: 74341bab4a5971398732071dad1898b0 build: number: 0 rpaths: @@ -22,7 +22,7 @@ requirements: - r-base run: - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-pcagopromoter.hs.hg19/post-link.sh b/recipes/bioconductor-pcagopromoter.hs.hg19/post-link.sh index d5e7b80871515..39b37c4fdeda4 100644 --- a/recipes/bioconductor-pcagopromoter.hs.hg19/post-link.sh +++ b/recipes/bioconductor-pcagopromoter.hs.hg19/post-link.sh @@ -1,11 +1,11 @@ #!/bin/bash -FN="pcaGoPromoter.Hs.hg19_1.18.0.tar.gz" +FN="pcaGoPromoter.Hs.hg19_1.20.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/experiment/src/contrib/pcaGoPromoter.Hs.hg19_1.18.0.tar.gz" - "https://bioarchive.galaxyproject.org/pcaGoPromoter.Hs.hg19_1.18.0.tar.gz" - "https://depot.galaxyproject.org/software/bioconductor-pcagopromoter.hs.hg19/bioconductor-pcagopromoter.hs.hg19_1.18.0_src_all.tar.gz" + "https://bioconductor.org/packages/3.9/data/experiment/src/contrib/pcaGoPromoter.Hs.hg19_1.20.0.tar.gz" + "https://bioarchive.galaxyproject.org/pcaGoPromoter.Hs.hg19_1.20.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-pcagopromoter.hs.hg19/bioconductor-pcagopromoter.hs.hg19_1.20.0_src_all.tar.gz" ) -MD5="4cc30df25e7ebdcfda9a818e51a58a5d" +MD5="74341bab4a5971398732071dad1898b0" # Use a staging area in the conda dir rather than temp dirs, both to avoid # permission issues as well as to have things downloaded in a predictable @@ -16,7 +16,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-pcagopromoter.mm.mm9/meta.yaml b/recipes/bioconductor-pcagopromoter.mm.mm9/meta.yaml index c1e13d279fea4..dc397ace0614b 100644 --- a/recipes/bioconductor-pcagopromoter.mm.mm9/meta.yaml +++ b/recipes/bioconductor-pcagopromoter.mm.mm9/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.18.0" %} +{% set version = "1.20.0" %} {% set name = "pcaGoPromoter.Mm.mm9" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 33379deaeaa464ca75ad1b86a737c8dd + md5: cdcf550e2a810757e4f0fdd661c0e1a9 build: number: 0 rpaths: @@ -22,7 +22,7 @@ requirements: - r-base run: - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-pcagopromoter.mm.mm9/post-link.sh b/recipes/bioconductor-pcagopromoter.mm.mm9/post-link.sh index 468977784b6c9..709cc7999b1fb 100644 --- a/recipes/bioconductor-pcagopromoter.mm.mm9/post-link.sh +++ b/recipes/bioconductor-pcagopromoter.mm.mm9/post-link.sh @@ -1,11 +1,11 @@ #!/bin/bash -FN="pcaGoPromoter.Mm.mm9_1.18.0.tar.gz" +FN="pcaGoPromoter.Mm.mm9_1.20.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/experiment/src/contrib/pcaGoPromoter.Mm.mm9_1.18.0.tar.gz" - "https://bioarchive.galaxyproject.org/pcaGoPromoter.Mm.mm9_1.18.0.tar.gz" - "https://depot.galaxyproject.org/software/bioconductor-pcagopromoter.mm.mm9/bioconductor-pcagopromoter.mm.mm9_1.18.0_src_all.tar.gz" + "https://bioconductor.org/packages/3.9/data/experiment/src/contrib/pcaGoPromoter.Mm.mm9_1.20.0.tar.gz" + "https://bioarchive.galaxyproject.org/pcaGoPromoter.Mm.mm9_1.20.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-pcagopromoter.mm.mm9/bioconductor-pcagopromoter.mm.mm9_1.20.0_src_all.tar.gz" ) -MD5="33379deaeaa464ca75ad1b86a737c8dd" +MD5="cdcf550e2a810757e4f0fdd661c0e1a9" # Use a staging area in the conda dir rather than temp dirs, both to avoid # permission issues as well as to have things downloaded in a predictable @@ -16,7 +16,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-pcagopromoter.rn.rn4/meta.yaml b/recipes/bioconductor-pcagopromoter.rn.rn4/meta.yaml index 27a42bf27dc26..2d745ee4c2c87 100644 --- a/recipes/bioconductor-pcagopromoter.rn.rn4/meta.yaml +++ b/recipes/bioconductor-pcagopromoter.rn.rn4/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.18.0" %} +{% set version = "1.20.0" %} {% set name = "pcaGoPromoter.Rn.rn4" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 8d3ddf814343009ddddecc7082f971c5 + md5: 0ed2f9e355f461739739ac1d67bbce29 build: number: 0 rpaths: @@ -22,7 +22,7 @@ requirements: - r-base run: - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-pcagopromoter.rn.rn4/post-link.sh b/recipes/bioconductor-pcagopromoter.rn.rn4/post-link.sh index da56d49bcce68..7213356096725 100644 --- a/recipes/bioconductor-pcagopromoter.rn.rn4/post-link.sh +++ b/recipes/bioconductor-pcagopromoter.rn.rn4/post-link.sh @@ -1,11 +1,11 @@ #!/bin/bash -FN="pcaGoPromoter.Rn.rn4_1.18.0.tar.gz" +FN="pcaGoPromoter.Rn.rn4_1.20.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/experiment/src/contrib/pcaGoPromoter.Rn.rn4_1.18.0.tar.gz" - "https://bioarchive.galaxyproject.org/pcaGoPromoter.Rn.rn4_1.18.0.tar.gz" - "https://depot.galaxyproject.org/software/bioconductor-pcagopromoter.rn.rn4/bioconductor-pcagopromoter.rn.rn4_1.18.0_src_all.tar.gz" + "https://bioconductor.org/packages/3.9/data/experiment/src/contrib/pcaGoPromoter.Rn.rn4_1.20.0.tar.gz" + "https://bioarchive.galaxyproject.org/pcaGoPromoter.Rn.rn4_1.20.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-pcagopromoter.rn.rn4/bioconductor-pcagopromoter.rn.rn4_1.20.0_src_all.tar.gz" ) -MD5="8d3ddf814343009ddddecc7082f971c5" +MD5="0ed2f9e355f461739739ac1d67bbce29" # Use a staging area in the conda dir rather than temp dirs, both to avoid # permission issues as well as to have things downloaded in a predictable @@ -16,7 +16,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-pcagopromoter/meta.yaml b/recipes/bioconductor-pcagopromoter/meta.yaml index 1b21df4afe96a..ef52abdc75110 100644 --- a/recipes/bioconductor-pcagopromoter/meta.yaml +++ b/recipes/bioconductor-pcagopromoter/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.26.0" %} +{% set version = "1.28.0" %} {% set name = "pcaGoPromoter" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 4e977c7652ab79cdbc1f34bb9f2e69e0 + md5: da4aa4bf501174c978b6f2718e2d32ae build: number: 0 rpaths: @@ -20,13 +20,13 @@ build: # Suggests: Rgraphviz, GO.db, hgu133plus2.db, mouse4302.db, rat2302.db, hugene10sttranscriptcluster.db, mogene10sttranscriptcluster.db, pcaGoPromoter.Hs.hg19, pcaGoPromoter.Mm.mm9, pcaGoPromoter.Rn.rn4, serumStimulation, parallel requirements: host: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' - - 'bioconductor-biostrings >=2.50.0,<2.51.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' + - 'bioconductor-biostrings >=2.52.0,<2.53.0' - r-base - r-ellipse run: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' - - 'bioconductor-biostrings >=2.50.0,<2.51.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' + - 'bioconductor-biostrings >=2.52.0,<2.53.0' - r-base - r-ellipse test: diff --git a/recipes/bioconductor-pcamethods/meta.yaml b/recipes/bioconductor-pcamethods/meta.yaml index 4e7e44b982aa2..75ab52042095a 100644 --- a/recipes/bioconductor-pcamethods/meta.yaml +++ b/recipes/bioconductor-pcamethods/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.74.0" %} +{% set version = "1.76.0" %} {% set name = "pcaMethods" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 6a9c216fb47845695f034c5a8d76a804 + md5: 999fb2811e2fff2da737fa969cf809fd build: number: 0 rpaths: @@ -20,14 +20,14 @@ build: # SystemRequirements: Rcpp requirements: host: - - 'bioconductor-biobase >=2.42.0,<2.43.0' - - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' + - 'bioconductor-biocgenerics >=0.30.0,<0.31.0' - r-base - r-mass - 'r-rcpp >=0.11.3' run: - - 'bioconductor-biobase >=2.42.0,<2.43.0' - - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' + - 'bioconductor-biocgenerics >=0.30.0,<0.31.0' - r-base - r-mass - 'r-rcpp >=0.11.3' diff --git a/recipes/bioconductor-pcan/meta.yaml b/recipes/bioconductor-pcan/meta.yaml index f8d372eda7cc9..c50350e04e43f 100644 --- a/recipes/bioconductor-pcan/meta.yaml +++ b/recipes/bioconductor-pcan/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.10.0" %} +{% set version = "1.12.0" %} {% set name = "PCAN" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 07f2255c8748a0a112ff3870d63e63ed + md5: f1232cbd6da8413cc00d752f91521c1b build: number: 0 rpaths: @@ -20,10 +20,10 @@ build: # Suggests: BiocStyle, knitr, rmarkdown, reactome.db, STRINGdb requirements: host: - - 'bioconductor-biocparallel >=1.16.0,<1.17.0' + - 'bioconductor-biocparallel >=1.18.0,<1.19.0' - r-base run: - - 'bioconductor-biocparallel >=1.16.0,<1.17.0' + - 'bioconductor-biocparallel >=1.18.0,<1.19.0' - r-base test: commands: diff --git a/recipes/bioconductor-pcatools/build.sh b/recipes/bioconductor-pcatools/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-pcatools/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-pcatools/meta.yaml b/recipes/bioconductor-pcatools/meta.yaml new file mode 100644 index 0000000000000..5a7fb520e4c9d --- /dev/null +++ b/recipes/bioconductor-pcatools/meta.yaml @@ -0,0 +1,43 @@ +{% set version = "1.0.0" %} +{% set name = "PCAtools" %} +{% set bioc = "3.9" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: 6ef2bff3637161a072efc798a8fb2af9 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: RUnit, BiocGenerics, knitr, Biobase, GEOquery, biomaRt, ggplotify +requirements: + host: + - r-base + - r-cowplot + - r-ggplot2 + - r-ggrepel + - r-lattice + - r-reshape2 + run: + - r-base + - r-cowplot + - r-ggplot2 + - r-ggrepel + - r-lattice + - r-reshape2 +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: GPL-3 + summary: 'Principal Components Analysis (PCA) is a very powerful technique that has wide applicability in data science, bioinformatics, and further afield. It was initially developed to analyse large volumes of data in order to tease out the differences/relationships between the logical entities being analysed. It extracts the fundamental structure of the data without the need to build any model to represent it. This ''summary'' of the data is arrived at through a process of reduction that can transform the large number of variables into a lesser number that are uncorrelated, i.e., the principal components, whilst at the same time being capable of easy interpretation on the original data.' + diff --git a/recipes/bioconductor-pchicdata/meta.yaml b/recipes/bioconductor-pchicdata/meta.yaml index 0207c513f4aff..cba43d99013cc 100644 --- a/recipes/bioconductor-pchicdata/meta.yaml +++ b/recipes/bioconductor-pchicdata/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.10.0" %} +{% set version = "1.12.0" %} {% set name = "PCHiCdata" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 8e3da1443273ed288b35b8fd0cdf1d1d + md5: 18936bf2c0bf4b12b969b6bf8141773a build: number: 0 rpaths: @@ -20,12 +20,12 @@ build: # Suggests: testthat, BiocStyle, knitr requirements: host: - - 'bioconductor-chicago >=1.10.0,<1.11.0' + - 'bioconductor-chicago >=1.12.0,<1.13.0' - r-base run: - - 'bioconductor-chicago >=1.10.0,<1.11.0' + - 'bioconductor-chicago >=1.12.0,<1.13.0' - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-pchicdata/post-link.sh b/recipes/bioconductor-pchicdata/post-link.sh index 2bef2d25f70c0..0012ef3494102 100644 --- a/recipes/bioconductor-pchicdata/post-link.sh +++ b/recipes/bioconductor-pchicdata/post-link.sh @@ -1,11 +1,11 @@ #!/bin/bash -FN="PCHiCdata_1.10.0.tar.gz" +FN="PCHiCdata_1.12.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/experiment/src/contrib/PCHiCdata_1.10.0.tar.gz" - "https://bioarchive.galaxyproject.org/PCHiCdata_1.10.0.tar.gz" - "https://depot.galaxyproject.org/software/bioconductor-pchicdata/bioconductor-pchicdata_1.10.0_src_all.tar.gz" + "https://bioconductor.org/packages/3.9/data/experiment/src/contrib/PCHiCdata_1.12.0.tar.gz" + "https://bioarchive.galaxyproject.org/PCHiCdata_1.12.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-pchicdata/bioconductor-pchicdata_1.12.0_src_all.tar.gz" ) -MD5="8e3da1443273ed288b35b8fd0cdf1d1d" +MD5="18936bf2c0bf4b12b969b6bf8141773a" # Use a staging area in the conda dir rather than temp dirs, both to avoid # permission issues as well as to have things downloaded in a predictable @@ -16,7 +16,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-pcot2/meta.yaml b/recipes/bioconductor-pcot2/meta.yaml index 6c043f1799c65..60ce8ce0578d4 100644 --- a/recipes/bioconductor-pcot2/meta.yaml +++ b/recipes/bioconductor-pcot2/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.50.0" %} +{% set version = "1.52.0" %} {% set name = "pcot2" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: aa57791e2f80a012910aba04f449bf80 + md5: 140130ec124351e324200761b14f98d0 build: number: 0 rpaths: @@ -20,11 +20,11 @@ build: # Suggests: multtest, hu6800.db, KEGG.db, mvtnorm requirements: host: - - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' - r-amap - r-base run: - - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' - r-amap - r-base test: diff --git a/recipes/bioconductor-pcpheno/meta.yaml b/recipes/bioconductor-pcpheno/meta.yaml index c252adf4b43eb..c25d628e1e05b 100644 --- a/recipes/bioconductor-pcpheno/meta.yaml +++ b/recipes/bioconductor-pcpheno/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.44.0" %} +{% set version = "1.46.0" %} {% set name = "PCpheno" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 145f9f7d83b7405cb42e5949fae540e2 + md5: 9d57cab88fccbf8ec5ff40dcb0923125 build: number: 0 rpaths: @@ -20,32 +20,32 @@ build: # Suggests: KEGG.db, GO.db, org.Sc.sgd.db requirements: host: - - 'bioconductor-annotate >=1.60.0,<1.61.0' - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' - - 'bioconductor-biobase >=2.42.0,<2.43.0' - - 'bioconductor-category >=2.48.0,<2.49.0' - - 'bioconductor-go.db >=3.7.0,<3.8.0' - - 'bioconductor-graph >=1.60.0,<1.61.0' - - 'bioconductor-gseabase >=1.44.0,<1.45.0' + - 'bioconductor-annotate >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' + - 'bioconductor-category >=2.50.0,<2.51.0' + - 'bioconductor-go.db >=3.8.0,<3.9.0' + - 'bioconductor-graph >=1.62.0,<1.63.0' + - 'bioconductor-gseabase >=1.46.0,<1.47.0' - 'bioconductor-kegg.db >=3.2.0,<3.3.0' - - 'bioconductor-ppidata >=0.20.0,<0.21.0' - - 'bioconductor-ppistats >=1.48.0,<1.49.0' - - 'bioconductor-scisi >=1.54.0,<1.55.0' - - 'bioconductor-slgi >=1.42.0,<1.43.0' + - 'bioconductor-ppidata >=0.22.0,<0.23.0' + - 'bioconductor-ppistats >=1.50.0,<1.51.0' + - 'bioconductor-scisi >=1.56.0,<1.57.0' + - 'bioconductor-slgi >=1.44.0,<1.45.0' - r-base run: - - 'bioconductor-annotate >=1.60.0,<1.61.0' - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' - - 'bioconductor-biobase >=2.42.0,<2.43.0' - - 'bioconductor-category >=2.48.0,<2.49.0' - - 'bioconductor-go.db >=3.7.0,<3.8.0' - - 'bioconductor-graph >=1.60.0,<1.61.0' - - 'bioconductor-gseabase >=1.44.0,<1.45.0' + - 'bioconductor-annotate >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' + - 'bioconductor-category >=2.50.0,<2.51.0' + - 'bioconductor-go.db >=3.8.0,<3.9.0' + - 'bioconductor-graph >=1.62.0,<1.63.0' + - 'bioconductor-gseabase >=1.46.0,<1.47.0' - 'bioconductor-kegg.db >=3.2.0,<3.3.0' - - 'bioconductor-ppidata >=0.20.0,<0.21.0' - - 'bioconductor-ppistats >=1.48.0,<1.49.0' - - 'bioconductor-scisi >=1.54.0,<1.55.0' - - 'bioconductor-slgi >=1.42.0,<1.43.0' + - 'bioconductor-ppidata >=0.22.0,<0.23.0' + - 'bioconductor-ppistats >=1.50.0,<1.51.0' + - 'bioconductor-scisi >=1.56.0,<1.57.0' + - 'bioconductor-slgi >=1.44.0,<1.45.0' - r-base test: commands: diff --git a/recipes/bioconductor-pcxn/meta.yaml b/recipes/bioconductor-pcxn/meta.yaml index c197a164dec83..c748535363d65 100644 --- a/recipes/bioconductor-pcxn/meta.yaml +++ b/recipes/bioconductor-pcxn/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "2.4.0" %} +{% set version = "2.6.0" %} {% set name = "pcxn" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 3945e77826c7917f07557d39f5d7af19 + md5: 7354db0c5ff6dfe33eba1ca08d943360 build: number: 0 rpaths: @@ -20,11 +20,11 @@ build: # Suggests: igraph, annotate, org.Hs.eg.db requirements: host: - - 'bioconductor-pcxndata >=2.4.0,<2.5.0' + - 'bioconductor-pcxndata >=2.6.0,<2.7.0' - r-base - r-pheatmap run: - - 'bioconductor-pcxndata >=2.4.0,<2.5.0' + - 'bioconductor-pcxndata >=2.6.0,<2.7.0' - r-base - r-pheatmap test: diff --git a/recipes/bioconductor-pcxndata/meta.yaml b/recipes/bioconductor-pcxndata/meta.yaml index af51782dc3961..7ec87bf9336c0 100644 --- a/recipes/bioconductor-pcxndata/meta.yaml +++ b/recipes/bioconductor-pcxndata/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "2.4.0" %} +{% set version = "2.6.0" %} {% set name = "pcxnData" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: b5c348c5e4f36193ef30afef989fdc49 + md5: 49ae7b9155cd6680c186180c03869e7f build: number: 0 rpaths: @@ -23,7 +23,7 @@ requirements: - r-base run: - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-pcxndata/post-link.sh b/recipes/bioconductor-pcxndata/post-link.sh index 7b6caddf8403b..5750c7a00c942 100644 --- a/recipes/bioconductor-pcxndata/post-link.sh +++ b/recipes/bioconductor-pcxndata/post-link.sh @@ -1,11 +1,11 @@ #!/bin/bash -FN="pcxnData_2.4.0.tar.gz" +FN="pcxnData_2.6.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/experiment/src/contrib/pcxnData_2.4.0.tar.gz" - "https://bioarchive.galaxyproject.org/pcxnData_2.4.0.tar.gz" - "https://depot.galaxyproject.org/software/bioconductor-pcxndata/bioconductor-pcxndata_2.4.0_src_all.tar.gz" + "https://bioconductor.org/packages/3.9/data/experiment/src/contrib/pcxnData_2.6.0.tar.gz" + "https://bioarchive.galaxyproject.org/pcxnData_2.6.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-pcxndata/bioconductor-pcxndata_2.6.0_src_all.tar.gz" ) -MD5="b5c348c5e4f36193ef30afef989fdc49" +MD5="49ae7b9155cd6680c186180c03869e7f" # Use a staging area in the conda dir rather than temp dirs, both to avoid # permission issues as well as to have things downloaded in a predictable @@ -16,7 +16,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-pd.081229.hg18.promoter.medip.hx1/meta.yaml b/recipes/bioconductor-pd.081229.hg18.promoter.medip.hx1/meta.yaml index afd3959f107df..2929fb78b45ae 100644 --- a/recipes/bioconductor-pd.081229.hg18.promoter.medip.hx1/meta.yaml +++ b/recipes/bioconductor-pd.081229.hg18.promoter.medip.hx1/meta.yaml @@ -1,6 +1,6 @@ {% set version = "0.99.4" %} {% set name = "pd.081229.hg18.promoter.medip.hx1" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -12,29 +12,29 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: f3c240fa0d4503e94047be5ee323856b build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ noarch: generic requirements: host: - - 'bioconductor-biostrings >=2.50.0,<2.51.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-oligo >=1.46.0,<1.47.0' - - 'bioconductor-oligoclasses >=1.44.0,<1.45.0' + - 'bioconductor-biostrings >=2.52.0,<2.53.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-oligo >=1.48.0,<1.49.0' + - 'bioconductor-oligoclasses >=1.46.0,<1.47.0' - r-base - r-dbi - 'r-rsqlite >=0.7-1' run: - - 'bioconductor-biostrings >=2.50.0,<2.51.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-oligo >=1.46.0,<1.47.0' - - 'bioconductor-oligoclasses >=1.44.0,<1.45.0' + - 'bioconductor-biostrings >=2.52.0,<2.53.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-oligo >=1.48.0,<1.49.0' + - 'bioconductor-oligoclasses >=1.46.0,<1.47.0' - r-base - r-dbi - 'r-rsqlite >=0.7-1' - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-pd.081229.hg18.promoter.medip.hx1/post-link.sh b/recipes/bioconductor-pd.081229.hg18.promoter.medip.hx1/post-link.sh index a97e49c395d65..68735396d8c54 100644 --- a/recipes/bioconductor-pd.081229.hg18.promoter.medip.hx1/post-link.sh +++ b/recipes/bioconductor-pd.081229.hg18.promoter.medip.hx1/post-link.sh @@ -1,9 +1,10 @@ #!/bin/bash FN="pd.081229.hg18.promoter.medip.hx1_0.99.4.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/pd.081229.hg18.promoter.medip.hx1_0.99.4.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/pd.081229.hg18.promoter.medip.hx1_0.99.4.tar.gz" "https://bioarchive.galaxyproject.org/pd.081229.hg18.promoter.medip.hx1_0.99.4.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-pd.081229.hg18.promoter.medip.hx1/bioconductor-pd.081229.hg18.promoter.medip.hx1_0.99.4_src_all.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-pd.081229.hg18.promoter.medip.hx1/bioconductor-pd.081229.hg18.promoter.medip.hx1_0.99.4_src_all.tar.gz" ) MD5="f3c240fa0d4503e94047be5ee323856b" @@ -16,7 +17,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-pd.2006.07.18.hg18.refseq.promoter/meta.yaml b/recipes/bioconductor-pd.2006.07.18.hg18.refseq.promoter/meta.yaml index dc253cdc85c9a..20321f6e7dac7 100644 --- a/recipes/bioconductor-pd.2006.07.18.hg18.refseq.promoter/meta.yaml +++ b/recipes/bioconductor-pd.2006.07.18.hg18.refseq.promoter/meta.yaml @@ -1,6 +1,6 @@ {% set version = "1.8.1" %} {% set name = "pd.2006.07.18.hg18.refseq.promoter" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -12,29 +12,29 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 00838332d75b82d212078a9957f495df build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ noarch: generic requirements: host: - - 'bioconductor-biostrings >=2.50.0,<2.51.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-oligo >=1.46.0,<1.47.0' - - 'bioconductor-oligoclasses >=1.44.0,<1.45.0' + - 'bioconductor-biostrings >=2.52.0,<2.53.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-oligo >=1.48.0,<1.49.0' + - 'bioconductor-oligoclasses >=1.46.0,<1.47.0' - r-base - r-dbi - 'r-rsqlite >=0.11.1' run: - - 'bioconductor-biostrings >=2.50.0,<2.51.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-oligo >=1.46.0,<1.47.0' - - 'bioconductor-oligoclasses >=1.44.0,<1.45.0' + - 'bioconductor-biostrings >=2.52.0,<2.53.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-oligo >=1.48.0,<1.49.0' + - 'bioconductor-oligoclasses >=1.46.0,<1.47.0' - r-base - r-dbi - 'r-rsqlite >=0.11.1' - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-pd.2006.07.18.hg18.refseq.promoter/post-link.sh b/recipes/bioconductor-pd.2006.07.18.hg18.refseq.promoter/post-link.sh index a9a4cae8b2b5e..54c8165413c9c 100644 --- a/recipes/bioconductor-pd.2006.07.18.hg18.refseq.promoter/post-link.sh +++ b/recipes/bioconductor-pd.2006.07.18.hg18.refseq.promoter/post-link.sh @@ -1,9 +1,10 @@ #!/bin/bash FN="pd.2006.07.18.hg18.refseq.promoter_1.8.1.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/pd.2006.07.18.hg18.refseq.promoter_1.8.1.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/pd.2006.07.18.hg18.refseq.promoter_1.8.1.tar.gz" "https://bioarchive.galaxyproject.org/pd.2006.07.18.hg18.refseq.promoter_1.8.1.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-pd.2006.07.18.hg18.refseq.promoter/bioconductor-pd.2006.07.18.hg18.refseq.promoter_1.8.1_src_all.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-pd.2006.07.18.hg18.refseq.promoter/bioconductor-pd.2006.07.18.hg18.refseq.promoter_1.8.1_src_all.tar.gz" ) MD5="00838332d75b82d212078a9957f495df" @@ -16,7 +17,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-pd.2006.07.18.mm8.refseq.promoter/meta.yaml b/recipes/bioconductor-pd.2006.07.18.mm8.refseq.promoter/meta.yaml index 7fcf628c1b03e..8872712551415 100644 --- a/recipes/bioconductor-pd.2006.07.18.mm8.refseq.promoter/meta.yaml +++ b/recipes/bioconductor-pd.2006.07.18.mm8.refseq.promoter/meta.yaml @@ -1,6 +1,6 @@ {% set version = "0.99.3" %} {% set name = "pd.2006.07.18.mm8.refseq.promoter" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -12,29 +12,29 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 084b0a6759fd96d1bc775dd4c66c42b0 build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ noarch: generic requirements: host: - - 'bioconductor-biostrings >=2.50.0,<2.51.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-oligo >=1.46.0,<1.47.0' - - 'bioconductor-oligoclasses >=1.44.0,<1.45.0' + - 'bioconductor-biostrings >=2.52.0,<2.53.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-oligo >=1.48.0,<1.49.0' + - 'bioconductor-oligoclasses >=1.46.0,<1.47.0' - r-base - r-dbi - 'r-rsqlite >=0.7-1' run: - - 'bioconductor-biostrings >=2.50.0,<2.51.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-oligo >=1.46.0,<1.47.0' - - 'bioconductor-oligoclasses >=1.44.0,<1.45.0' + - 'bioconductor-biostrings >=2.52.0,<2.53.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-oligo >=1.48.0,<1.49.0' + - 'bioconductor-oligoclasses >=1.46.0,<1.47.0' - r-base - r-dbi - 'r-rsqlite >=0.7-1' - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-pd.2006.07.18.mm8.refseq.promoter/post-link.sh b/recipes/bioconductor-pd.2006.07.18.mm8.refseq.promoter/post-link.sh index 7a8f98f7a8306..f64168d37b0e9 100644 --- a/recipes/bioconductor-pd.2006.07.18.mm8.refseq.promoter/post-link.sh +++ b/recipes/bioconductor-pd.2006.07.18.mm8.refseq.promoter/post-link.sh @@ -1,9 +1,10 @@ #!/bin/bash FN="pd.2006.07.18.mm8.refseq.promoter_0.99.3.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/pd.2006.07.18.mm8.refseq.promoter_0.99.3.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/pd.2006.07.18.mm8.refseq.promoter_0.99.3.tar.gz" "https://bioarchive.galaxyproject.org/pd.2006.07.18.mm8.refseq.promoter_0.99.3.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-pd.2006.07.18.mm8.refseq.promoter/bioconductor-pd.2006.07.18.mm8.refseq.promoter_0.99.3_src_all.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-pd.2006.07.18.mm8.refseq.promoter/bioconductor-pd.2006.07.18.mm8.refseq.promoter_0.99.3_src_all.tar.gz" ) MD5="084b0a6759fd96d1bc775dd4c66c42b0" @@ -16,7 +17,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-pd.2006.10.31.rn34.refseq.promoter/meta.yaml b/recipes/bioconductor-pd.2006.10.31.rn34.refseq.promoter/meta.yaml index 5e1b85e231cef..6c39431c219b4 100644 --- a/recipes/bioconductor-pd.2006.10.31.rn34.refseq.promoter/meta.yaml +++ b/recipes/bioconductor-pd.2006.10.31.rn34.refseq.promoter/meta.yaml @@ -1,6 +1,6 @@ {% set version = "0.99.3" %} {% set name = "pd.2006.10.31.rn34.refseq.promoter" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -12,29 +12,29 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: ab5bb767ad29b213e5a969a5fc51ee7d build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ noarch: generic requirements: host: - - 'bioconductor-biostrings >=2.50.0,<2.51.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-oligo >=1.46.0,<1.47.0' - - 'bioconductor-oligoclasses >=1.44.0,<1.45.0' + - 'bioconductor-biostrings >=2.52.0,<2.53.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-oligo >=1.48.0,<1.49.0' + - 'bioconductor-oligoclasses >=1.46.0,<1.47.0' - r-base - r-dbi - 'r-rsqlite >=0.7-1' run: - - 'bioconductor-biostrings >=2.50.0,<2.51.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-oligo >=1.46.0,<1.47.0' - - 'bioconductor-oligoclasses >=1.44.0,<1.45.0' + - 'bioconductor-biostrings >=2.52.0,<2.53.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-oligo >=1.48.0,<1.49.0' + - 'bioconductor-oligoclasses >=1.46.0,<1.47.0' - r-base - r-dbi - 'r-rsqlite >=0.7-1' - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-pd.2006.10.31.rn34.refseq.promoter/post-link.sh b/recipes/bioconductor-pd.2006.10.31.rn34.refseq.promoter/post-link.sh index 0e2e8d679287c..bc798db2626f7 100644 --- a/recipes/bioconductor-pd.2006.10.31.rn34.refseq.promoter/post-link.sh +++ b/recipes/bioconductor-pd.2006.10.31.rn34.refseq.promoter/post-link.sh @@ -1,9 +1,10 @@ #!/bin/bash FN="pd.2006.10.31.rn34.refseq.promoter_0.99.3.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/pd.2006.10.31.rn34.refseq.promoter_0.99.3.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/pd.2006.10.31.rn34.refseq.promoter_0.99.3.tar.gz" "https://bioarchive.galaxyproject.org/pd.2006.10.31.rn34.refseq.promoter_0.99.3.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-pd.2006.10.31.rn34.refseq.promoter/bioconductor-pd.2006.10.31.rn34.refseq.promoter_0.99.3_src_all.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-pd.2006.10.31.rn34.refseq.promoter/bioconductor-pd.2006.10.31.rn34.refseq.promoter_0.99.3_src_all.tar.gz" ) MD5="ab5bb767ad29b213e5a969a5fc51ee7d" @@ -16,7 +17,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-pd.ag/meta.yaml b/recipes/bioconductor-pd.ag/meta.yaml index 6fa58b284314f..8586ccf72cadc 100644 --- a/recipes/bioconductor-pd.ag/meta.yaml +++ b/recipes/bioconductor-pd.ag/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.12.0" %} {% set name = "pd.ag" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -12,31 +12,31 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 21fb288536568ff010ad4847b671f9d6 build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ noarch: generic requirements: host: - - 'bioconductor-biostrings >=2.50.0,<2.51.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-oligo >=1.46.0,<1.47.0' - - 'bioconductor-oligoclasses >=1.44.0,<1.45.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-biostrings >=2.52.0,<2.53.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-oligo >=1.48.0,<1.49.0' + - 'bioconductor-oligoclasses >=1.46.0,<1.47.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' run: - - 'bioconductor-biostrings >=2.50.0,<2.51.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-oligo >=1.46.0,<1.47.0' - - 'bioconductor-oligoclasses >=1.44.0,<1.45.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-biostrings >=2.52.0,<2.53.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-oligo >=1.48.0,<1.49.0' + - 'bioconductor-oligoclasses >=1.46.0,<1.47.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-pd.ag/post-link.sh b/recipes/bioconductor-pd.ag/post-link.sh index cfbe50a58e4a7..7b87835af73ac 100644 --- a/recipes/bioconductor-pd.ag/post-link.sh +++ b/recipes/bioconductor-pd.ag/post-link.sh @@ -1,9 +1,10 @@ #!/bin/bash FN="pd.ag_3.12.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/pd.ag_3.12.0.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/pd.ag_3.12.0.tar.gz" "https://bioarchive.galaxyproject.org/pd.ag_3.12.0.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-pd.ag/bioconductor-pd.ag_3.12.0_src_all.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-pd.ag/bioconductor-pd.ag_3.12.0_src_all.tar.gz" ) MD5="21fb288536568ff010ad4847b671f9d6" @@ -16,7 +17,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-pd.aragene.1.0.st/meta.yaml b/recipes/bioconductor-pd.aragene.1.0.st/meta.yaml index e2f53d9fa8a9b..49047496dcc03 100644 --- a/recipes/bioconductor-pd.aragene.1.0.st/meta.yaml +++ b/recipes/bioconductor-pd.aragene.1.0.st/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.12.0" %} {% set name = "pd.aragene.1.0.st" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -12,31 +12,31 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: ff87a0793fd4b713c4a45b6c1d4a4977 build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ noarch: generic requirements: host: - - 'bioconductor-biostrings >=2.50.0,<2.51.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-oligo >=1.46.0,<1.47.0' - - 'bioconductor-oligoclasses >=1.44.0,<1.45.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-biostrings >=2.52.0,<2.53.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-oligo >=1.48.0,<1.49.0' + - 'bioconductor-oligoclasses >=1.46.0,<1.47.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' run: - - 'bioconductor-biostrings >=2.50.0,<2.51.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-oligo >=1.46.0,<1.47.0' - - 'bioconductor-oligoclasses >=1.44.0,<1.45.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-biostrings >=2.52.0,<2.53.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-oligo >=1.48.0,<1.49.0' + - 'bioconductor-oligoclasses >=1.46.0,<1.47.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-pd.aragene.1.0.st/post-link.sh b/recipes/bioconductor-pd.aragene.1.0.st/post-link.sh index 1e1e430c19a22..34829c4cc929a 100644 --- a/recipes/bioconductor-pd.aragene.1.0.st/post-link.sh +++ b/recipes/bioconductor-pd.aragene.1.0.st/post-link.sh @@ -1,9 +1,10 @@ #!/bin/bash FN="pd.aragene.1.0.st_3.12.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/pd.aragene.1.0.st_3.12.0.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/pd.aragene.1.0.st_3.12.0.tar.gz" "https://bioarchive.galaxyproject.org/pd.aragene.1.0.st_3.12.0.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-pd.aragene.1.0.st/bioconductor-pd.aragene.1.0.st_3.12.0_src_all.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-pd.aragene.1.0.st/bioconductor-pd.aragene.1.0.st_3.12.0_src_all.tar.gz" ) MD5="ff87a0793fd4b713c4a45b6c1d4a4977" @@ -16,7 +17,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-pd.aragene.1.1.st/meta.yaml b/recipes/bioconductor-pd.aragene.1.1.st/meta.yaml index 1c20130332728..68fde787a40b1 100644 --- a/recipes/bioconductor-pd.aragene.1.1.st/meta.yaml +++ b/recipes/bioconductor-pd.aragene.1.1.st/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.12.0" %} {% set name = "pd.aragene.1.1.st" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -12,31 +12,31 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 828ad790eb2495e396d7fcd9bcbf9133 build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ noarch: generic requirements: host: - - 'bioconductor-biostrings >=2.50.0,<2.51.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-oligo >=1.46.0,<1.47.0' - - 'bioconductor-oligoclasses >=1.44.0,<1.45.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-biostrings >=2.52.0,<2.53.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-oligo >=1.48.0,<1.49.0' + - 'bioconductor-oligoclasses >=1.46.0,<1.47.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' run: - - 'bioconductor-biostrings >=2.50.0,<2.51.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-oligo >=1.46.0,<1.47.0' - - 'bioconductor-oligoclasses >=1.44.0,<1.45.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-biostrings >=2.52.0,<2.53.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-oligo >=1.48.0,<1.49.0' + - 'bioconductor-oligoclasses >=1.46.0,<1.47.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-pd.aragene.1.1.st/post-link.sh b/recipes/bioconductor-pd.aragene.1.1.st/post-link.sh index 60cd0ad3dd936..6b0cf097ba90a 100644 --- a/recipes/bioconductor-pd.aragene.1.1.st/post-link.sh +++ b/recipes/bioconductor-pd.aragene.1.1.st/post-link.sh @@ -1,9 +1,10 @@ #!/bin/bash FN="pd.aragene.1.1.st_3.12.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/pd.aragene.1.1.st_3.12.0.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/pd.aragene.1.1.st_3.12.0.tar.gz" "https://bioarchive.galaxyproject.org/pd.aragene.1.1.st_3.12.0.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-pd.aragene.1.1.st/bioconductor-pd.aragene.1.1.st_3.12.0_src_all.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-pd.aragene.1.1.st/bioconductor-pd.aragene.1.1.st_3.12.0_src_all.tar.gz" ) MD5="828ad790eb2495e396d7fcd9bcbf9133" @@ -16,7 +17,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-pd.atdschip.tiling/meta.yaml b/recipes/bioconductor-pd.atdschip.tiling/meta.yaml index 147db876a8d13..420afe7b12ef6 100644 --- a/recipes/bioconductor-pd.atdschip.tiling/meta.yaml +++ b/recipes/bioconductor-pd.atdschip.tiling/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "0.20.0" %} +{% set version = "0.22.0" %} {% set name = "pd.atdschip.tiling" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,33 +10,33 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 4e8b33dcee82491454fb2954983fab60 + md5: 00f43b23dba09ecca0ff49cf28c013e9 build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ noarch: generic requirements: host: - - 'bioconductor-biostrings >=2.50.0,<2.51.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-oligo >=1.46.0,<1.47.0' - - 'bioconductor-oligoclasses >=1.44.0,<1.45.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-biostrings >=2.52.0,<2.53.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-oligo >=1.48.0,<1.49.0' + - 'bioconductor-oligoclasses >=1.46.0,<1.47.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' - r-base - r-dbi - 'r-rsqlite >=0.10.0' run: - - 'bioconductor-biostrings >=2.50.0,<2.51.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-oligo >=1.46.0,<1.47.0' - - 'bioconductor-oligoclasses >=1.44.0,<1.45.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-biostrings >=2.52.0,<2.53.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-oligo >=1.48.0,<1.49.0' + - 'bioconductor-oligoclasses >=1.46.0,<1.47.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' - r-base - r-dbi - 'r-rsqlite >=0.10.0' - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-pd.atdschip.tiling/post-link.sh b/recipes/bioconductor-pd.atdschip.tiling/post-link.sh index 541cfc4ee9997..d2a00e1bfa7f0 100644 --- a/recipes/bioconductor-pd.atdschip.tiling/post-link.sh +++ b/recipes/bioconductor-pd.atdschip.tiling/post-link.sh @@ -1,11 +1,11 @@ #!/bin/bash -FN="pd.atdschip.tiling_0.20.0.tar.gz" +FN="pd.atdschip.tiling_0.22.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/experiment/src/contrib/pd.atdschip.tiling_0.20.0.tar.gz" - "https://bioarchive.galaxyproject.org/pd.atdschip.tiling_0.20.0.tar.gz" - "https://depot.galaxyproject.org/software/bioconductor-pd.atdschip.tiling/bioconductor-pd.atdschip.tiling_0.20.0_src_all.tar.gz" + "https://bioconductor.org/packages/3.9/data/experiment/src/contrib/pd.atdschip.tiling_0.22.0.tar.gz" + "https://bioarchive.galaxyproject.org/pd.atdschip.tiling_0.22.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-pd.atdschip.tiling/bioconductor-pd.atdschip.tiling_0.22.0_src_all.tar.gz" ) -MD5="4e8b33dcee82491454fb2954983fab60" +MD5="00f43b23dba09ecca0ff49cf28c013e9" # Use a staging area in the conda dir rather than temp dirs, both to avoid # permission issues as well as to have things downloaded in a predictable @@ -16,7 +16,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-pd.ath1.121501/meta.yaml b/recipes/bioconductor-pd.ath1.121501/meta.yaml index ea30ac5c3bfbd..13924b04a2efc 100644 --- a/recipes/bioconductor-pd.ath1.121501/meta.yaml +++ b/recipes/bioconductor-pd.ath1.121501/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.12.0" %} {% set name = "pd.ath1.121501" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -12,31 +12,31 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: d7ed8640f0deac552e0083a091e72a72 build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ noarch: generic requirements: host: - - 'bioconductor-biostrings >=2.50.0,<2.51.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-oligo >=1.46.0,<1.47.0' - - 'bioconductor-oligoclasses >=1.44.0,<1.45.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-biostrings >=2.52.0,<2.53.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-oligo >=1.48.0,<1.49.0' + - 'bioconductor-oligoclasses >=1.46.0,<1.47.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' run: - - 'bioconductor-biostrings >=2.50.0,<2.51.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-oligo >=1.46.0,<1.47.0' - - 'bioconductor-oligoclasses >=1.44.0,<1.45.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-biostrings >=2.52.0,<2.53.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-oligo >=1.48.0,<1.49.0' + - 'bioconductor-oligoclasses >=1.46.0,<1.47.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-pd.ath1.121501/post-link.sh b/recipes/bioconductor-pd.ath1.121501/post-link.sh index b477843bccb4c..624f77912486d 100644 --- a/recipes/bioconductor-pd.ath1.121501/post-link.sh +++ b/recipes/bioconductor-pd.ath1.121501/post-link.sh @@ -1,9 +1,10 @@ #!/bin/bash FN="pd.ath1.121501_3.12.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/pd.ath1.121501_3.12.0.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/pd.ath1.121501_3.12.0.tar.gz" "https://bioarchive.galaxyproject.org/pd.ath1.121501_3.12.0.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-pd.ath1.121501/bioconductor-pd.ath1.121501_3.12.0_src_all.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-pd.ath1.121501/bioconductor-pd.ath1.121501_3.12.0_src_all.tar.gz" ) MD5="d7ed8640f0deac552e0083a091e72a72" @@ -16,7 +17,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-pd.barley1/meta.yaml b/recipes/bioconductor-pd.barley1/meta.yaml index b5474e854377c..e0f370d4d4795 100644 --- a/recipes/bioconductor-pd.barley1/meta.yaml +++ b/recipes/bioconductor-pd.barley1/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.12.0" %} {% set name = "pd.barley1" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -12,31 +12,31 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: b8d11f5ad42e75f7a91931b46d449c1a build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ noarch: generic requirements: host: - - 'bioconductor-biostrings >=2.50.0,<2.51.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-oligo >=1.46.0,<1.47.0' - - 'bioconductor-oligoclasses >=1.44.0,<1.45.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-biostrings >=2.52.0,<2.53.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-oligo >=1.48.0,<1.49.0' + - 'bioconductor-oligoclasses >=1.46.0,<1.47.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' run: - - 'bioconductor-biostrings >=2.50.0,<2.51.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-oligo >=1.46.0,<1.47.0' - - 'bioconductor-oligoclasses >=1.44.0,<1.45.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-biostrings >=2.52.0,<2.53.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-oligo >=1.48.0,<1.49.0' + - 'bioconductor-oligoclasses >=1.46.0,<1.47.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-pd.barley1/post-link.sh b/recipes/bioconductor-pd.barley1/post-link.sh index 6131b0b8f131b..6e2394807b2f5 100644 --- a/recipes/bioconductor-pd.barley1/post-link.sh +++ b/recipes/bioconductor-pd.barley1/post-link.sh @@ -1,9 +1,10 @@ #!/bin/bash FN="pd.barley1_3.12.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/pd.barley1_3.12.0.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/pd.barley1_3.12.0.tar.gz" "https://bioarchive.galaxyproject.org/pd.barley1_3.12.0.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-pd.barley1/bioconductor-pd.barley1_3.12.0_src_all.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-pd.barley1/bioconductor-pd.barley1_3.12.0_src_all.tar.gz" ) MD5="b8d11f5ad42e75f7a91931b46d449c1a" @@ -16,7 +17,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-pd.bovgene.1.0.st/meta.yaml b/recipes/bioconductor-pd.bovgene.1.0.st/meta.yaml index ecf92461a2dfa..aa194381d0518 100644 --- a/recipes/bioconductor-pd.bovgene.1.0.st/meta.yaml +++ b/recipes/bioconductor-pd.bovgene.1.0.st/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.12.0" %} {% set name = "pd.bovgene.1.0.st" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -12,31 +12,31 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 6e9747d13aee7825722562ccc49ad35f build: - number: 1 + number: 2 rpaths: - lib/R/lib/ - lib/ noarch: generic requirements: host: - - 'bioconductor-biostrings >=2.50.0,<2.51.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-oligo >=1.46.0,<1.47.0' - - 'bioconductor-oligoclasses >=1.44.0,<1.45.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-biostrings >=2.52.0,<2.53.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-oligo >=1.48.0,<1.49.0' + - 'bioconductor-oligoclasses >=1.46.0,<1.47.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' run: - - 'bioconductor-biostrings >=2.50.0,<2.51.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-oligo >=1.46.0,<1.47.0' - - 'bioconductor-oligoclasses >=1.44.0,<1.45.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-biostrings >=2.52.0,<2.53.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-oligo >=1.48.0,<1.49.0' + - 'bioconductor-oligoclasses >=1.46.0,<1.47.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-pd.bovgene.1.0.st/post-link.sh b/recipes/bioconductor-pd.bovgene.1.0.st/post-link.sh index a40737e3f522f..600fd17646e0d 100644 --- a/recipes/bioconductor-pd.bovgene.1.0.st/post-link.sh +++ b/recipes/bioconductor-pd.bovgene.1.0.st/post-link.sh @@ -1,9 +1,10 @@ #!/bin/bash FN="pd.bovgene.1.0.st_3.12.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/pd.bovgene.1.0.st_3.12.0.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/pd.bovgene.1.0.st_3.12.0.tar.gz" "https://bioarchive.galaxyproject.org/pd.bovgene.1.0.st_3.12.0.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-pd.bovgene.1.0.st/bioconductor-pd.bovgene.1.0.st_3.12.0_src_all.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-pd.bovgene.1.0.st/bioconductor-pd.bovgene.1.0.st_3.12.0_src_all.tar.gz" ) MD5="6e9747d13aee7825722562ccc49ad35f" @@ -16,7 +17,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-pd.bovgene.1.1.st/meta.yaml b/recipes/bioconductor-pd.bovgene.1.1.st/meta.yaml index fb0f79bfdc981..7d24c9f98b242 100644 --- a/recipes/bioconductor-pd.bovgene.1.1.st/meta.yaml +++ b/recipes/bioconductor-pd.bovgene.1.1.st/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.12.0" %} {% set name = "pd.bovgene.1.1.st" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -12,31 +12,31 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 342246c0a76755fcca458cd723b3e98e build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ noarch: generic requirements: host: - - 'bioconductor-biostrings >=2.50.0,<2.51.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-oligo >=1.46.0,<1.47.0' - - 'bioconductor-oligoclasses >=1.44.0,<1.45.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-biostrings >=2.52.0,<2.53.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-oligo >=1.48.0,<1.49.0' + - 'bioconductor-oligoclasses >=1.46.0,<1.47.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' run: - - 'bioconductor-biostrings >=2.50.0,<2.51.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-oligo >=1.46.0,<1.47.0' - - 'bioconductor-oligoclasses >=1.44.0,<1.45.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-biostrings >=2.52.0,<2.53.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-oligo >=1.48.0,<1.49.0' + - 'bioconductor-oligoclasses >=1.46.0,<1.47.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-pd.bovgene.1.1.st/post-link.sh b/recipes/bioconductor-pd.bovgene.1.1.st/post-link.sh index 3252f7266567e..cfeab6b71ad64 100644 --- a/recipes/bioconductor-pd.bovgene.1.1.st/post-link.sh +++ b/recipes/bioconductor-pd.bovgene.1.1.st/post-link.sh @@ -1,9 +1,10 @@ #!/bin/bash FN="pd.bovgene.1.1.st_3.12.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/pd.bovgene.1.1.st_3.12.0.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/pd.bovgene.1.1.st_3.12.0.tar.gz" "https://bioarchive.galaxyproject.org/pd.bovgene.1.1.st_3.12.0.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-pd.bovgene.1.1.st/bioconductor-pd.bovgene.1.1.st_3.12.0_src_all.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-pd.bovgene.1.1.st/bioconductor-pd.bovgene.1.1.st_3.12.0_src_all.tar.gz" ) MD5="342246c0a76755fcca458cd723b3e98e" @@ -16,7 +17,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-pd.bovine/meta.yaml b/recipes/bioconductor-pd.bovine/meta.yaml index f59f5bb25b11e..1db0936cb8140 100644 --- a/recipes/bioconductor-pd.bovine/meta.yaml +++ b/recipes/bioconductor-pd.bovine/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.12.0" %} {% set name = "pd.bovine" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -12,31 +12,31 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 6c7026dba53b54b547b1f1e135d043b3 build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ noarch: generic requirements: host: - - 'bioconductor-biostrings >=2.50.0,<2.51.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-oligo >=1.46.0,<1.47.0' - - 'bioconductor-oligoclasses >=1.44.0,<1.45.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-biostrings >=2.52.0,<2.53.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-oligo >=1.48.0,<1.49.0' + - 'bioconductor-oligoclasses >=1.46.0,<1.47.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' run: - - 'bioconductor-biostrings >=2.50.0,<2.51.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-oligo >=1.46.0,<1.47.0' - - 'bioconductor-oligoclasses >=1.44.0,<1.45.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-biostrings >=2.52.0,<2.53.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-oligo >=1.48.0,<1.49.0' + - 'bioconductor-oligoclasses >=1.46.0,<1.47.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-pd.bovine/post-link.sh b/recipes/bioconductor-pd.bovine/post-link.sh index c3ecdb3d4d996..f377126923ec9 100644 --- a/recipes/bioconductor-pd.bovine/post-link.sh +++ b/recipes/bioconductor-pd.bovine/post-link.sh @@ -1,9 +1,10 @@ #!/bin/bash FN="pd.bovine_3.12.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/pd.bovine_3.12.0.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/pd.bovine_3.12.0.tar.gz" "https://bioarchive.galaxyproject.org/pd.bovine_3.12.0.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-pd.bovine/bioconductor-pd.bovine_3.12.0_src_all.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-pd.bovine/bioconductor-pd.bovine_3.12.0_src_all.tar.gz" ) MD5="6c7026dba53b54b547b1f1e135d043b3" @@ -16,7 +17,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-pd.bsubtilis/meta.yaml b/recipes/bioconductor-pd.bsubtilis/meta.yaml index f7f4a21a6a514..02474e6fc15e0 100644 --- a/recipes/bioconductor-pd.bsubtilis/meta.yaml +++ b/recipes/bioconductor-pd.bsubtilis/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.12.0" %} {% set name = "pd.bsubtilis" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -12,31 +12,31 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 2261d8b0ec178beb432d71eafd90ec9a build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ noarch: generic requirements: host: - - 'bioconductor-biostrings >=2.50.0,<2.51.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-oligo >=1.46.0,<1.47.0' - - 'bioconductor-oligoclasses >=1.44.0,<1.45.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-biostrings >=2.52.0,<2.53.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-oligo >=1.48.0,<1.49.0' + - 'bioconductor-oligoclasses >=1.46.0,<1.47.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' run: - - 'bioconductor-biostrings >=2.50.0,<2.51.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-oligo >=1.46.0,<1.47.0' - - 'bioconductor-oligoclasses >=1.44.0,<1.45.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-biostrings >=2.52.0,<2.53.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-oligo >=1.48.0,<1.49.0' + - 'bioconductor-oligoclasses >=1.46.0,<1.47.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-pd.bsubtilis/post-link.sh b/recipes/bioconductor-pd.bsubtilis/post-link.sh index 4b54ebd9a4914..caca8cc07ba29 100644 --- a/recipes/bioconductor-pd.bsubtilis/post-link.sh +++ b/recipes/bioconductor-pd.bsubtilis/post-link.sh @@ -1,9 +1,10 @@ #!/bin/bash FN="pd.bsubtilis_3.12.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/pd.bsubtilis_3.12.0.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/pd.bsubtilis_3.12.0.tar.gz" "https://bioarchive.galaxyproject.org/pd.bsubtilis_3.12.0.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-pd.bsubtilis/bioconductor-pd.bsubtilis_3.12.0_src_all.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-pd.bsubtilis/bioconductor-pd.bsubtilis_3.12.0_src_all.tar.gz" ) MD5="2261d8b0ec178beb432d71eafd90ec9a" @@ -16,7 +17,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-pd.cangene.1.0.st/meta.yaml b/recipes/bioconductor-pd.cangene.1.0.st/meta.yaml index a4d9804405d91..d525119b0e613 100644 --- a/recipes/bioconductor-pd.cangene.1.0.st/meta.yaml +++ b/recipes/bioconductor-pd.cangene.1.0.st/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.12.0" %} {% set name = "pd.cangene.1.0.st" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -12,31 +12,31 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 0a39d6378193e3f7d31a7210f6766eaf build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ noarch: generic requirements: host: - - 'bioconductor-biostrings >=2.50.0,<2.51.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-oligo >=1.46.0,<1.47.0' - - 'bioconductor-oligoclasses >=1.44.0,<1.45.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-biostrings >=2.52.0,<2.53.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-oligo >=1.48.0,<1.49.0' + - 'bioconductor-oligoclasses >=1.46.0,<1.47.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' run: - - 'bioconductor-biostrings >=2.50.0,<2.51.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-oligo >=1.46.0,<1.47.0' - - 'bioconductor-oligoclasses >=1.44.0,<1.45.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-biostrings >=2.52.0,<2.53.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-oligo >=1.48.0,<1.49.0' + - 'bioconductor-oligoclasses >=1.46.0,<1.47.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-pd.cangene.1.0.st/post-link.sh b/recipes/bioconductor-pd.cangene.1.0.st/post-link.sh index 123e44e3148ba..0300911f5a8c8 100644 --- a/recipes/bioconductor-pd.cangene.1.0.st/post-link.sh +++ b/recipes/bioconductor-pd.cangene.1.0.st/post-link.sh @@ -1,9 +1,10 @@ #!/bin/bash FN="pd.cangene.1.0.st_3.12.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/pd.cangene.1.0.st_3.12.0.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/pd.cangene.1.0.st_3.12.0.tar.gz" "https://bioarchive.galaxyproject.org/pd.cangene.1.0.st_3.12.0.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-pd.cangene.1.0.st/bioconductor-pd.cangene.1.0.st_3.12.0_src_all.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-pd.cangene.1.0.st/bioconductor-pd.cangene.1.0.st_3.12.0_src_all.tar.gz" ) MD5="0a39d6378193e3f7d31a7210f6766eaf" @@ -16,7 +17,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-pd.cangene.1.1.st/meta.yaml b/recipes/bioconductor-pd.cangene.1.1.st/meta.yaml index 37dda7d173e73..ccc81ff26d976 100644 --- a/recipes/bioconductor-pd.cangene.1.1.st/meta.yaml +++ b/recipes/bioconductor-pd.cangene.1.1.st/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.12.0" %} {% set name = "pd.cangene.1.1.st" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -12,31 +12,31 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 946074601e7bee72f3b3dd6ae6b3bc33 build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ noarch: generic requirements: host: - - 'bioconductor-biostrings >=2.50.0,<2.51.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-oligo >=1.46.0,<1.47.0' - - 'bioconductor-oligoclasses >=1.44.0,<1.45.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-biostrings >=2.52.0,<2.53.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-oligo >=1.48.0,<1.49.0' + - 'bioconductor-oligoclasses >=1.46.0,<1.47.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' run: - - 'bioconductor-biostrings >=2.50.0,<2.51.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-oligo >=1.46.0,<1.47.0' - - 'bioconductor-oligoclasses >=1.44.0,<1.45.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-biostrings >=2.52.0,<2.53.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-oligo >=1.48.0,<1.49.0' + - 'bioconductor-oligoclasses >=1.46.0,<1.47.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-pd.cangene.1.1.st/post-link.sh b/recipes/bioconductor-pd.cangene.1.1.st/post-link.sh index e4ed2b3049373..15021ba815efc 100644 --- a/recipes/bioconductor-pd.cangene.1.1.st/post-link.sh +++ b/recipes/bioconductor-pd.cangene.1.1.st/post-link.sh @@ -1,9 +1,10 @@ #!/bin/bash FN="pd.cangene.1.1.st_3.12.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/pd.cangene.1.1.st_3.12.0.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/pd.cangene.1.1.st_3.12.0.tar.gz" "https://bioarchive.galaxyproject.org/pd.cangene.1.1.st_3.12.0.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-pd.cangene.1.1.st/bioconductor-pd.cangene.1.1.st_3.12.0_src_all.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-pd.cangene.1.1.st/bioconductor-pd.cangene.1.1.st_3.12.0_src_all.tar.gz" ) MD5="946074601e7bee72f3b3dd6ae6b3bc33" @@ -16,7 +17,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-pd.canine.2/meta.yaml b/recipes/bioconductor-pd.canine.2/meta.yaml index 0df7c79a2a4e7..523613a1c82fe 100644 --- a/recipes/bioconductor-pd.canine.2/meta.yaml +++ b/recipes/bioconductor-pd.canine.2/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.12.0" %} {% set name = "pd.canine.2" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -12,31 +12,31 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: bc918d1953a3c7ac7168b60a53405a93 build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ noarch: generic requirements: host: - - 'bioconductor-biostrings >=2.50.0,<2.51.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-oligo >=1.46.0,<1.47.0' - - 'bioconductor-oligoclasses >=1.44.0,<1.45.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-biostrings >=2.52.0,<2.53.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-oligo >=1.48.0,<1.49.0' + - 'bioconductor-oligoclasses >=1.46.0,<1.47.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' run: - - 'bioconductor-biostrings >=2.50.0,<2.51.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-oligo >=1.46.0,<1.47.0' - - 'bioconductor-oligoclasses >=1.44.0,<1.45.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-biostrings >=2.52.0,<2.53.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-oligo >=1.48.0,<1.49.0' + - 'bioconductor-oligoclasses >=1.46.0,<1.47.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-pd.canine.2/post-link.sh b/recipes/bioconductor-pd.canine.2/post-link.sh index 63cedc9a36867..10f324e57c555 100644 --- a/recipes/bioconductor-pd.canine.2/post-link.sh +++ b/recipes/bioconductor-pd.canine.2/post-link.sh @@ -1,9 +1,10 @@ #!/bin/bash FN="pd.canine.2_3.12.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/pd.canine.2_3.12.0.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/pd.canine.2_3.12.0.tar.gz" "https://bioarchive.galaxyproject.org/pd.canine.2_3.12.0.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-pd.canine.2/bioconductor-pd.canine.2_3.12.0_src_all.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-pd.canine.2/bioconductor-pd.canine.2_3.12.0_src_all.tar.gz" ) MD5="bc918d1953a3c7ac7168b60a53405a93" @@ -16,7 +17,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-pd.canine/meta.yaml b/recipes/bioconductor-pd.canine/meta.yaml index 17ca6704ea069..82eeb879b99f1 100644 --- a/recipes/bioconductor-pd.canine/meta.yaml +++ b/recipes/bioconductor-pd.canine/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.12.0" %} {% set name = "pd.canine" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -12,31 +12,31 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 5b40fe9e40d0b7f36d338e413d121ba7 build: - number: 1 + number: 2 rpaths: - lib/R/lib/ - lib/ noarch: generic requirements: host: - - 'bioconductor-biostrings >=2.50.0,<2.51.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-oligo >=1.46.0,<1.47.0' - - 'bioconductor-oligoclasses >=1.44.0,<1.45.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-biostrings >=2.52.0,<2.53.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-oligo >=1.48.0,<1.49.0' + - 'bioconductor-oligoclasses >=1.46.0,<1.47.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' run: - - 'bioconductor-biostrings >=2.50.0,<2.51.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-oligo >=1.46.0,<1.47.0' - - 'bioconductor-oligoclasses >=1.44.0,<1.45.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-biostrings >=2.52.0,<2.53.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-oligo >=1.48.0,<1.49.0' + - 'bioconductor-oligoclasses >=1.46.0,<1.47.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-pd.canine/post-link.sh b/recipes/bioconductor-pd.canine/post-link.sh index e818fc076d2f4..9b612f7442fdd 100644 --- a/recipes/bioconductor-pd.canine/post-link.sh +++ b/recipes/bioconductor-pd.canine/post-link.sh @@ -1,9 +1,10 @@ #!/bin/bash FN="pd.canine_3.12.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/pd.canine_3.12.0.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/pd.canine_3.12.0.tar.gz" "https://bioarchive.galaxyproject.org/pd.canine_3.12.0.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-pd.canine/bioconductor-pd.canine_3.12.0_src_all.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-pd.canine/bioconductor-pd.canine_3.12.0_src_all.tar.gz" ) MD5="5b40fe9e40d0b7f36d338e413d121ba7" @@ -16,7 +17,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-pd.celegans/meta.yaml b/recipes/bioconductor-pd.celegans/meta.yaml index 17cf2f64068de..b3b9f9cc75069 100644 --- a/recipes/bioconductor-pd.celegans/meta.yaml +++ b/recipes/bioconductor-pd.celegans/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.12.0" %} {% set name = "pd.celegans" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -12,31 +12,31 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: b90ea2e071522bb340c103a1c8270205 build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ noarch: generic requirements: host: - - 'bioconductor-biostrings >=2.50.0,<2.51.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-oligo >=1.46.0,<1.47.0' - - 'bioconductor-oligoclasses >=1.44.0,<1.45.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-biostrings >=2.52.0,<2.53.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-oligo >=1.48.0,<1.49.0' + - 'bioconductor-oligoclasses >=1.46.0,<1.47.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' run: - - 'bioconductor-biostrings >=2.50.0,<2.51.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-oligo >=1.46.0,<1.47.0' - - 'bioconductor-oligoclasses >=1.44.0,<1.45.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-biostrings >=2.52.0,<2.53.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-oligo >=1.48.0,<1.49.0' + - 'bioconductor-oligoclasses >=1.46.0,<1.47.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-pd.celegans/post-link.sh b/recipes/bioconductor-pd.celegans/post-link.sh index 3ba6718567f3f..710047f41d30b 100644 --- a/recipes/bioconductor-pd.celegans/post-link.sh +++ b/recipes/bioconductor-pd.celegans/post-link.sh @@ -1,9 +1,10 @@ #!/bin/bash FN="pd.celegans_3.12.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/pd.celegans_3.12.0.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/pd.celegans_3.12.0.tar.gz" "https://bioarchive.galaxyproject.org/pd.celegans_3.12.0.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-pd.celegans/bioconductor-pd.celegans_3.12.0_src_all.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-pd.celegans/bioconductor-pd.celegans_3.12.0_src_all.tar.gz" ) MD5="b90ea2e071522bb340c103a1c8270205" @@ -16,7 +17,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-pd.charm.hg18.example/meta.yaml b/recipes/bioconductor-pd.charm.hg18.example/meta.yaml index 8350d307c75af..15f5710dd131c 100644 --- a/recipes/bioconductor-pd.charm.hg18.example/meta.yaml +++ b/recipes/bioconductor-pd.charm.hg18.example/meta.yaml @@ -1,6 +1,6 @@ {% set version = "0.99.4" %} {% set name = "pd.charm.hg18.example" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -12,29 +12,29 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: e201d4281a23c202f57bae1135e226b4 build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ noarch: generic requirements: host: - - 'bioconductor-biostrings >=2.50.0,<2.51.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-oligo >=1.46.0,<1.47.0' - - 'bioconductor-oligoclasses >=1.44.0,<1.45.0' + - 'bioconductor-biostrings >=2.52.0,<2.53.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-oligo >=1.48.0,<1.49.0' + - 'bioconductor-oligoclasses >=1.46.0,<1.47.0' - r-base - r-dbi - 'r-rsqlite >=0.7-1' run: - - 'bioconductor-biostrings >=2.50.0,<2.51.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-oligo >=1.46.0,<1.47.0' - - 'bioconductor-oligoclasses >=1.44.0,<1.45.0' + - 'bioconductor-biostrings >=2.52.0,<2.53.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-oligo >=1.48.0,<1.49.0' + - 'bioconductor-oligoclasses >=1.46.0,<1.47.0' - r-base - r-dbi - 'r-rsqlite >=0.7-1' - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-pd.charm.hg18.example/post-link.sh b/recipes/bioconductor-pd.charm.hg18.example/post-link.sh index 3899ce0b754c7..21bc5d8e7eed7 100644 --- a/recipes/bioconductor-pd.charm.hg18.example/post-link.sh +++ b/recipes/bioconductor-pd.charm.hg18.example/post-link.sh @@ -1,9 +1,10 @@ #!/bin/bash FN="pd.charm.hg18.example_0.99.4.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/pd.charm.hg18.example_0.99.4.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/pd.charm.hg18.example_0.99.4.tar.gz" "https://bioarchive.galaxyproject.org/pd.charm.hg18.example_0.99.4.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-pd.charm.hg18.example/bioconductor-pd.charm.hg18.example_0.99.4_src_all.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-pd.charm.hg18.example/bioconductor-pd.charm.hg18.example_0.99.4_src_all.tar.gz" ) MD5="e201d4281a23c202f57bae1135e226b4" @@ -16,7 +17,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-pd.chicken/meta.yaml b/recipes/bioconductor-pd.chicken/meta.yaml index 83ebac8bf942b..d22677202f4d5 100644 --- a/recipes/bioconductor-pd.chicken/meta.yaml +++ b/recipes/bioconductor-pd.chicken/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.12.0" %} {% set name = "pd.chicken" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -12,31 +12,31 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: af79b6d0910621910e72ea374499e5eb build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ noarch: generic requirements: host: - - 'bioconductor-biostrings >=2.50.0,<2.51.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-oligo >=1.46.0,<1.47.0' - - 'bioconductor-oligoclasses >=1.44.0,<1.45.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-biostrings >=2.52.0,<2.53.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-oligo >=1.48.0,<1.49.0' + - 'bioconductor-oligoclasses >=1.46.0,<1.47.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' run: - - 'bioconductor-biostrings >=2.50.0,<2.51.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-oligo >=1.46.0,<1.47.0' - - 'bioconductor-oligoclasses >=1.44.0,<1.45.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-biostrings >=2.52.0,<2.53.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-oligo >=1.48.0,<1.49.0' + - 'bioconductor-oligoclasses >=1.46.0,<1.47.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-pd.chicken/post-link.sh b/recipes/bioconductor-pd.chicken/post-link.sh index 8553edad6657b..0a1c761345725 100644 --- a/recipes/bioconductor-pd.chicken/post-link.sh +++ b/recipes/bioconductor-pd.chicken/post-link.sh @@ -1,9 +1,10 @@ #!/bin/bash FN="pd.chicken_3.12.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/pd.chicken_3.12.0.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/pd.chicken_3.12.0.tar.gz" "https://bioarchive.galaxyproject.org/pd.chicken_3.12.0.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-pd.chicken/bioconductor-pd.chicken_3.12.0_src_all.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-pd.chicken/bioconductor-pd.chicken_3.12.0_src_all.tar.gz" ) MD5="af79b6d0910621910e72ea374499e5eb" @@ -16,7 +17,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-pd.chigene.1.0.st/meta.yaml b/recipes/bioconductor-pd.chigene.1.0.st/meta.yaml index 3483dfba62d97..92006451eb783 100644 --- a/recipes/bioconductor-pd.chigene.1.0.st/meta.yaml +++ b/recipes/bioconductor-pd.chigene.1.0.st/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.12.0" %} {% set name = "pd.chigene.1.0.st" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -12,31 +12,31 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: e37cb047678fabb1801109d4efd16773 build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ noarch: generic requirements: host: - - 'bioconductor-biostrings >=2.50.0,<2.51.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-oligo >=1.46.0,<1.47.0' - - 'bioconductor-oligoclasses >=1.44.0,<1.45.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-biostrings >=2.52.0,<2.53.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-oligo >=1.48.0,<1.49.0' + - 'bioconductor-oligoclasses >=1.46.0,<1.47.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' run: - - 'bioconductor-biostrings >=2.50.0,<2.51.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-oligo >=1.46.0,<1.47.0' - - 'bioconductor-oligoclasses >=1.44.0,<1.45.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-biostrings >=2.52.0,<2.53.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-oligo >=1.48.0,<1.49.0' + - 'bioconductor-oligoclasses >=1.46.0,<1.47.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-pd.chigene.1.0.st/post-link.sh b/recipes/bioconductor-pd.chigene.1.0.st/post-link.sh index b08755291502d..0e2cc29393474 100644 --- a/recipes/bioconductor-pd.chigene.1.0.st/post-link.sh +++ b/recipes/bioconductor-pd.chigene.1.0.st/post-link.sh @@ -1,9 +1,10 @@ #!/bin/bash FN="pd.chigene.1.0.st_3.12.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/pd.chigene.1.0.st_3.12.0.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/pd.chigene.1.0.st_3.12.0.tar.gz" "https://bioarchive.galaxyproject.org/pd.chigene.1.0.st_3.12.0.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-pd.chigene.1.0.st/bioconductor-pd.chigene.1.0.st_3.12.0_src_all.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-pd.chigene.1.0.st/bioconductor-pd.chigene.1.0.st_3.12.0_src_all.tar.gz" ) MD5="e37cb047678fabb1801109d4efd16773" @@ -16,7 +17,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-pd.chigene.1.1.st/meta.yaml b/recipes/bioconductor-pd.chigene.1.1.st/meta.yaml index b4123160acea7..c7563766adbc8 100644 --- a/recipes/bioconductor-pd.chigene.1.1.st/meta.yaml +++ b/recipes/bioconductor-pd.chigene.1.1.st/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.12.0" %} {% set name = "pd.chigene.1.1.st" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -12,31 +12,31 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: bec602b45961607f5a4571977d54e015 build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ noarch: generic requirements: host: - - 'bioconductor-biostrings >=2.50.0,<2.51.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-oligo >=1.46.0,<1.47.0' - - 'bioconductor-oligoclasses >=1.44.0,<1.45.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-biostrings >=2.52.0,<2.53.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-oligo >=1.48.0,<1.49.0' + - 'bioconductor-oligoclasses >=1.46.0,<1.47.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' run: - - 'bioconductor-biostrings >=2.50.0,<2.51.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-oligo >=1.46.0,<1.47.0' - - 'bioconductor-oligoclasses >=1.44.0,<1.45.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-biostrings >=2.52.0,<2.53.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-oligo >=1.48.0,<1.49.0' + - 'bioconductor-oligoclasses >=1.46.0,<1.47.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-pd.chigene.1.1.st/post-link.sh b/recipes/bioconductor-pd.chigene.1.1.st/post-link.sh index b6a57f582b114..07f55fe821a0a 100644 --- a/recipes/bioconductor-pd.chigene.1.1.st/post-link.sh +++ b/recipes/bioconductor-pd.chigene.1.1.st/post-link.sh @@ -1,9 +1,10 @@ #!/bin/bash FN="pd.chigene.1.1.st_3.12.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/pd.chigene.1.1.st_3.12.0.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/pd.chigene.1.1.st_3.12.0.tar.gz" "https://bioarchive.galaxyproject.org/pd.chigene.1.1.st_3.12.0.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-pd.chigene.1.1.st/bioconductor-pd.chigene.1.1.st_3.12.0_src_all.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-pd.chigene.1.1.st/bioconductor-pd.chigene.1.1.st_3.12.0_src_all.tar.gz" ) MD5="bec602b45961607f5a4571977d54e015" @@ -16,7 +17,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-pd.chogene.2.0.st/meta.yaml b/recipes/bioconductor-pd.chogene.2.0.st/meta.yaml index 0a62763efd2c4..42f4c13727275 100644 --- a/recipes/bioconductor-pd.chogene.2.0.st/meta.yaml +++ b/recipes/bioconductor-pd.chogene.2.0.st/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.12.0" %} {% set name = "pd.chogene.2.0.st" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -12,31 +12,31 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 641718e3d172838185a200bac3d32433 build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ noarch: generic requirements: host: - - 'bioconductor-biostrings >=2.50.0,<2.51.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-oligo >=1.46.0,<1.47.0' - - 'bioconductor-oligoclasses >=1.44.0,<1.45.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-biostrings >=2.52.0,<2.53.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-oligo >=1.48.0,<1.49.0' + - 'bioconductor-oligoclasses >=1.46.0,<1.47.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' run: - - 'bioconductor-biostrings >=2.50.0,<2.51.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-oligo >=1.46.0,<1.47.0' - - 'bioconductor-oligoclasses >=1.44.0,<1.45.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-biostrings >=2.52.0,<2.53.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-oligo >=1.48.0,<1.49.0' + - 'bioconductor-oligoclasses >=1.46.0,<1.47.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-pd.chogene.2.0.st/post-link.sh b/recipes/bioconductor-pd.chogene.2.0.st/post-link.sh index 57a7516fad3a2..edde47ae54838 100644 --- a/recipes/bioconductor-pd.chogene.2.0.st/post-link.sh +++ b/recipes/bioconductor-pd.chogene.2.0.st/post-link.sh @@ -1,9 +1,10 @@ #!/bin/bash FN="pd.chogene.2.0.st_3.12.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/pd.chogene.2.0.st_3.12.0.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/pd.chogene.2.0.st_3.12.0.tar.gz" "https://bioarchive.galaxyproject.org/pd.chogene.2.0.st_3.12.0.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-pd.chogene.2.0.st/bioconductor-pd.chogene.2.0.st_3.12.0_src_all.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-pd.chogene.2.0.st/bioconductor-pd.chogene.2.0.st_3.12.0_src_all.tar.gz" ) MD5="641718e3d172838185a200bac3d32433" @@ -16,7 +17,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-pd.chogene.2.1.st/meta.yaml b/recipes/bioconductor-pd.chogene.2.1.st/meta.yaml index 5131123b0501c..2f3bac0f67e73 100644 --- a/recipes/bioconductor-pd.chogene.2.1.st/meta.yaml +++ b/recipes/bioconductor-pd.chogene.2.1.st/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.12.0" %} {% set name = "pd.chogene.2.1.st" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -12,31 +12,31 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: ed25825e58a514cdde70b961bce9b4d7 build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ noarch: generic requirements: host: - - 'bioconductor-biostrings >=2.50.0,<2.51.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-oligo >=1.46.0,<1.47.0' - - 'bioconductor-oligoclasses >=1.44.0,<1.45.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-biostrings >=2.52.0,<2.53.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-oligo >=1.48.0,<1.49.0' + - 'bioconductor-oligoclasses >=1.46.0,<1.47.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' run: - - 'bioconductor-biostrings >=2.50.0,<2.51.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-oligo >=1.46.0,<1.47.0' - - 'bioconductor-oligoclasses >=1.44.0,<1.45.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-biostrings >=2.52.0,<2.53.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-oligo >=1.48.0,<1.49.0' + - 'bioconductor-oligoclasses >=1.46.0,<1.47.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-pd.chogene.2.1.st/post-link.sh b/recipes/bioconductor-pd.chogene.2.1.st/post-link.sh index 266636f0809ca..aad8115a00e68 100644 --- a/recipes/bioconductor-pd.chogene.2.1.st/post-link.sh +++ b/recipes/bioconductor-pd.chogene.2.1.st/post-link.sh @@ -1,9 +1,10 @@ #!/bin/bash FN="pd.chogene.2.1.st_3.12.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/pd.chogene.2.1.st_3.12.0.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/pd.chogene.2.1.st_3.12.0.tar.gz" "https://bioarchive.galaxyproject.org/pd.chogene.2.1.st_3.12.0.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-pd.chogene.2.1.st/bioconductor-pd.chogene.2.1.st_3.12.0_src_all.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-pd.chogene.2.1.st/bioconductor-pd.chogene.2.1.st_3.12.0_src_all.tar.gz" ) MD5="ed25825e58a514cdde70b961bce9b4d7" @@ -16,7 +17,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-pd.citrus/meta.yaml b/recipes/bioconductor-pd.citrus/meta.yaml index f483b8d9c3067..6e52eab5e0f7e 100644 --- a/recipes/bioconductor-pd.citrus/meta.yaml +++ b/recipes/bioconductor-pd.citrus/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.12.0" %} {% set name = "pd.citrus" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -12,31 +12,31 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: dee9b3298b84e7dd5152f48ad449b15a build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ noarch: generic requirements: host: - - 'bioconductor-biostrings >=2.50.0,<2.51.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-oligo >=1.46.0,<1.47.0' - - 'bioconductor-oligoclasses >=1.44.0,<1.45.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-biostrings >=2.52.0,<2.53.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-oligo >=1.48.0,<1.49.0' + - 'bioconductor-oligoclasses >=1.46.0,<1.47.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' run: - - 'bioconductor-biostrings >=2.50.0,<2.51.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-oligo >=1.46.0,<1.47.0' - - 'bioconductor-oligoclasses >=1.44.0,<1.45.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-biostrings >=2.52.0,<2.53.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-oligo >=1.48.0,<1.49.0' + - 'bioconductor-oligoclasses >=1.46.0,<1.47.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-pd.citrus/post-link.sh b/recipes/bioconductor-pd.citrus/post-link.sh index 46f0e2e7d2bc4..45c4aec45e017 100644 --- a/recipes/bioconductor-pd.citrus/post-link.sh +++ b/recipes/bioconductor-pd.citrus/post-link.sh @@ -1,9 +1,10 @@ #!/bin/bash FN="pd.citrus_3.12.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/pd.citrus_3.12.0.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/pd.citrus_3.12.0.tar.gz" "https://bioarchive.galaxyproject.org/pd.citrus_3.12.0.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-pd.citrus/bioconductor-pd.citrus_3.12.0_src_all.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-pd.citrus/bioconductor-pd.citrus_3.12.0_src_all.tar.gz" ) MD5="dee9b3298b84e7dd5152f48ad449b15a" @@ -16,7 +17,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-pd.clariom.d.human/meta.yaml b/recipes/bioconductor-pd.clariom.d.human/meta.yaml index ea5ee3c88bab4..cc5dad07c1b49 100644 --- a/recipes/bioconductor-pd.clariom.d.human/meta.yaml +++ b/recipes/bioconductor-pd.clariom.d.human/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.14.1" %} {% set name = "pd.clariom.d.human" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -12,31 +12,31 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 9d3505af53cc7c99980f29c527f0f37d build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ noarch: generic requirements: host: - - 'bioconductor-biostrings >=2.50.0,<2.51.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-oligo >=1.46.0,<1.47.0' - - 'bioconductor-oligoclasses >=1.44.0,<1.45.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-biostrings >=2.52.0,<2.53.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-oligo >=1.48.0,<1.49.0' + - 'bioconductor-oligoclasses >=1.46.0,<1.47.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' run: - - 'bioconductor-biostrings >=2.50.0,<2.51.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-oligo >=1.46.0,<1.47.0' - - 'bioconductor-oligoclasses >=1.44.0,<1.45.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-biostrings >=2.52.0,<2.53.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-oligo >=1.48.0,<1.49.0' + - 'bioconductor-oligoclasses >=1.46.0,<1.47.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-pd.clariom.d.human/post-link.sh b/recipes/bioconductor-pd.clariom.d.human/post-link.sh index eb290145c606e..f92a745369f62 100644 --- a/recipes/bioconductor-pd.clariom.d.human/post-link.sh +++ b/recipes/bioconductor-pd.clariom.d.human/post-link.sh @@ -1,9 +1,10 @@ #!/bin/bash FN="pd.clariom.d.human_3.14.1.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/pd.clariom.d.human_3.14.1.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/pd.clariom.d.human_3.14.1.tar.gz" "https://bioarchive.galaxyproject.org/pd.clariom.d.human_3.14.1.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-pd.clariom.d.human/bioconductor-pd.clariom.d.human_3.14.1_src_all.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-pd.clariom.d.human/bioconductor-pd.clariom.d.human_3.14.1_src_all.tar.gz" ) MD5="9d3505af53cc7c99980f29c527f0f37d" @@ -16,7 +17,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-pd.clariom.s.human.ht/meta.yaml b/recipes/bioconductor-pd.clariom.s.human.ht/meta.yaml index 84d15b4917bbb..772c9cded2e48 100644 --- a/recipes/bioconductor-pd.clariom.s.human.ht/meta.yaml +++ b/recipes/bioconductor-pd.clariom.s.human.ht/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.14.1" %} {% set name = "pd.clariom.s.human.ht" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -12,31 +12,31 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 90f910bea1b1aeb550a3f1bdd91d1a06 build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ noarch: generic requirements: host: - - 'bioconductor-biostrings >=2.50.0,<2.51.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-oligo >=1.46.0,<1.47.0' - - 'bioconductor-oligoclasses >=1.44.0,<1.45.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-biostrings >=2.52.0,<2.53.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-oligo >=1.48.0,<1.49.0' + - 'bioconductor-oligoclasses >=1.46.0,<1.47.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' run: - - 'bioconductor-biostrings >=2.50.0,<2.51.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-oligo >=1.46.0,<1.47.0' - - 'bioconductor-oligoclasses >=1.44.0,<1.45.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-biostrings >=2.52.0,<2.53.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-oligo >=1.48.0,<1.49.0' + - 'bioconductor-oligoclasses >=1.46.0,<1.47.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-pd.clariom.s.human.ht/post-link.sh b/recipes/bioconductor-pd.clariom.s.human.ht/post-link.sh index 89cfd9968a5db..999e9efa7b4d8 100644 --- a/recipes/bioconductor-pd.clariom.s.human.ht/post-link.sh +++ b/recipes/bioconductor-pd.clariom.s.human.ht/post-link.sh @@ -1,9 +1,10 @@ #!/bin/bash FN="pd.clariom.s.human.ht_3.14.1.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/pd.clariom.s.human.ht_3.14.1.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/pd.clariom.s.human.ht_3.14.1.tar.gz" "https://bioarchive.galaxyproject.org/pd.clariom.s.human.ht_3.14.1.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-pd.clariom.s.human.ht/bioconductor-pd.clariom.s.human.ht_3.14.1_src_all.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-pd.clariom.s.human.ht/bioconductor-pd.clariom.s.human.ht_3.14.1_src_all.tar.gz" ) MD5="90f910bea1b1aeb550a3f1bdd91d1a06" @@ -16,7 +17,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-pd.clariom.s.human/meta.yaml b/recipes/bioconductor-pd.clariom.s.human/meta.yaml index 18652019a287e..63a8864e953b9 100644 --- a/recipes/bioconductor-pd.clariom.s.human/meta.yaml +++ b/recipes/bioconductor-pd.clariom.s.human/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.14.1" %} {% set name = "pd.clariom.s.human" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -12,31 +12,31 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 797afe8a6a8041453a34ced3cce34884 build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ noarch: generic requirements: host: - - 'bioconductor-biostrings >=2.50.0,<2.51.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-oligo >=1.46.0,<1.47.0' - - 'bioconductor-oligoclasses >=1.44.0,<1.45.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-biostrings >=2.52.0,<2.53.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-oligo >=1.48.0,<1.49.0' + - 'bioconductor-oligoclasses >=1.46.0,<1.47.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' run: - - 'bioconductor-biostrings >=2.50.0,<2.51.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-oligo >=1.46.0,<1.47.0' - - 'bioconductor-oligoclasses >=1.44.0,<1.45.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-biostrings >=2.52.0,<2.53.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-oligo >=1.48.0,<1.49.0' + - 'bioconductor-oligoclasses >=1.46.0,<1.47.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-pd.clariom.s.human/post-link.sh b/recipes/bioconductor-pd.clariom.s.human/post-link.sh index ff48c5e4f1fe2..f33ed99fe4b5e 100644 --- a/recipes/bioconductor-pd.clariom.s.human/post-link.sh +++ b/recipes/bioconductor-pd.clariom.s.human/post-link.sh @@ -1,9 +1,10 @@ #!/bin/bash FN="pd.clariom.s.human_3.14.1.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/pd.clariom.s.human_3.14.1.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/pd.clariom.s.human_3.14.1.tar.gz" "https://bioarchive.galaxyproject.org/pd.clariom.s.human_3.14.1.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-pd.clariom.s.human/bioconductor-pd.clariom.s.human_3.14.1_src_all.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-pd.clariom.s.human/bioconductor-pd.clariom.s.human_3.14.1_src_all.tar.gz" ) MD5="797afe8a6a8041453a34ced3cce34884" @@ -16,7 +17,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-pd.clariom.s.mouse.ht/meta.yaml b/recipes/bioconductor-pd.clariom.s.mouse.ht/meta.yaml index 0bb1e39afa69b..64cc73f260a95 100644 --- a/recipes/bioconductor-pd.clariom.s.mouse.ht/meta.yaml +++ b/recipes/bioconductor-pd.clariom.s.mouse.ht/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.14.1" %} {% set name = "pd.clariom.s.mouse.ht" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -12,31 +12,31 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 9cb6f77cf9666a0d54e1eacb904fd57c build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ noarch: generic requirements: host: - - 'bioconductor-biostrings >=2.50.0,<2.51.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-oligo >=1.46.0,<1.47.0' - - 'bioconductor-oligoclasses >=1.44.0,<1.45.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-biostrings >=2.52.0,<2.53.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-oligo >=1.48.0,<1.49.0' + - 'bioconductor-oligoclasses >=1.46.0,<1.47.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' run: - - 'bioconductor-biostrings >=2.50.0,<2.51.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-oligo >=1.46.0,<1.47.0' - - 'bioconductor-oligoclasses >=1.44.0,<1.45.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-biostrings >=2.52.0,<2.53.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-oligo >=1.48.0,<1.49.0' + - 'bioconductor-oligoclasses >=1.46.0,<1.47.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-pd.clariom.s.mouse.ht/post-link.sh b/recipes/bioconductor-pd.clariom.s.mouse.ht/post-link.sh index 3880ba9a16daf..4d5f06358a489 100644 --- a/recipes/bioconductor-pd.clariom.s.mouse.ht/post-link.sh +++ b/recipes/bioconductor-pd.clariom.s.mouse.ht/post-link.sh @@ -1,9 +1,10 @@ #!/bin/bash FN="pd.clariom.s.mouse.ht_3.14.1.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/pd.clariom.s.mouse.ht_3.14.1.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/pd.clariom.s.mouse.ht_3.14.1.tar.gz" "https://bioarchive.galaxyproject.org/pd.clariom.s.mouse.ht_3.14.1.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-pd.clariom.s.mouse.ht/bioconductor-pd.clariom.s.mouse.ht_3.14.1_src_all.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-pd.clariom.s.mouse.ht/bioconductor-pd.clariom.s.mouse.ht_3.14.1_src_all.tar.gz" ) MD5="9cb6f77cf9666a0d54e1eacb904fd57c" @@ -16,7 +17,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-pd.clariom.s.mouse/meta.yaml b/recipes/bioconductor-pd.clariom.s.mouse/meta.yaml index 05510e9f3d4dd..f9a258eb32e20 100644 --- a/recipes/bioconductor-pd.clariom.s.mouse/meta.yaml +++ b/recipes/bioconductor-pd.clariom.s.mouse/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.14.1" %} {% set name = "pd.clariom.s.mouse" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -12,31 +12,31 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: e3e4ce2b22a78faf525dd6c0c0b2a42d build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ noarch: generic requirements: host: - - 'bioconductor-biostrings >=2.50.0,<2.51.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-oligo >=1.46.0,<1.47.0' - - 'bioconductor-oligoclasses >=1.44.0,<1.45.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-biostrings >=2.52.0,<2.53.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-oligo >=1.48.0,<1.49.0' + - 'bioconductor-oligoclasses >=1.46.0,<1.47.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' run: - - 'bioconductor-biostrings >=2.50.0,<2.51.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-oligo >=1.46.0,<1.47.0' - - 'bioconductor-oligoclasses >=1.44.0,<1.45.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-biostrings >=2.52.0,<2.53.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-oligo >=1.48.0,<1.49.0' + - 'bioconductor-oligoclasses >=1.46.0,<1.47.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-pd.clariom.s.mouse/post-link.sh b/recipes/bioconductor-pd.clariom.s.mouse/post-link.sh index 21bcc2011163a..f8d9569781ea8 100644 --- a/recipes/bioconductor-pd.clariom.s.mouse/post-link.sh +++ b/recipes/bioconductor-pd.clariom.s.mouse/post-link.sh @@ -1,9 +1,10 @@ #!/bin/bash FN="pd.clariom.s.mouse_3.14.1.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/pd.clariom.s.mouse_3.14.1.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/pd.clariom.s.mouse_3.14.1.tar.gz" "https://bioarchive.galaxyproject.org/pd.clariom.s.mouse_3.14.1.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-pd.clariom.s.mouse/bioconductor-pd.clariom.s.mouse_3.14.1_src_all.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-pd.clariom.s.mouse/bioconductor-pd.clariom.s.mouse_3.14.1_src_all.tar.gz" ) MD5="e3e4ce2b22a78faf525dd6c0c0b2a42d" @@ -16,7 +17,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-pd.clariom.s.rat.ht/meta.yaml b/recipes/bioconductor-pd.clariom.s.rat.ht/meta.yaml index 60fb604a31b06..19a50bd8cf934 100644 --- a/recipes/bioconductor-pd.clariom.s.rat.ht/meta.yaml +++ b/recipes/bioconductor-pd.clariom.s.rat.ht/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.14.1" %} {% set name = "pd.clariom.s.rat.ht" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -12,31 +12,31 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: be901eb9e8830f3e5bedf154189a3743 build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ noarch: generic requirements: host: - - 'bioconductor-biostrings >=2.50.0,<2.51.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-oligo >=1.46.0,<1.47.0' - - 'bioconductor-oligoclasses >=1.44.0,<1.45.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-biostrings >=2.52.0,<2.53.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-oligo >=1.48.0,<1.49.0' + - 'bioconductor-oligoclasses >=1.46.0,<1.47.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' run: - - 'bioconductor-biostrings >=2.50.0,<2.51.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-oligo >=1.46.0,<1.47.0' - - 'bioconductor-oligoclasses >=1.44.0,<1.45.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-biostrings >=2.52.0,<2.53.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-oligo >=1.48.0,<1.49.0' + - 'bioconductor-oligoclasses >=1.46.0,<1.47.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-pd.clariom.s.rat.ht/post-link.sh b/recipes/bioconductor-pd.clariom.s.rat.ht/post-link.sh index 1887053fd7dac..e419977a7c7ac 100644 --- a/recipes/bioconductor-pd.clariom.s.rat.ht/post-link.sh +++ b/recipes/bioconductor-pd.clariom.s.rat.ht/post-link.sh @@ -1,9 +1,10 @@ #!/bin/bash FN="pd.clariom.s.rat.ht_3.14.1.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/pd.clariom.s.rat.ht_3.14.1.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/pd.clariom.s.rat.ht_3.14.1.tar.gz" "https://bioarchive.galaxyproject.org/pd.clariom.s.rat.ht_3.14.1.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-pd.clariom.s.rat.ht/bioconductor-pd.clariom.s.rat.ht_3.14.1_src_all.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-pd.clariom.s.rat.ht/bioconductor-pd.clariom.s.rat.ht_3.14.1_src_all.tar.gz" ) MD5="be901eb9e8830f3e5bedf154189a3743" @@ -16,7 +17,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-pd.clariom.s.rat/meta.yaml b/recipes/bioconductor-pd.clariom.s.rat/meta.yaml index dd432e9a4ae29..1a458bbecdc14 100644 --- a/recipes/bioconductor-pd.clariom.s.rat/meta.yaml +++ b/recipes/bioconductor-pd.clariom.s.rat/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.14.1" %} {% set name = "pd.clariom.s.rat" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -12,31 +12,31 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: be464b3eaea8eb8bdbcca6047fce4dea build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ noarch: generic requirements: host: - - 'bioconductor-biostrings >=2.50.0,<2.51.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-oligo >=1.46.0,<1.47.0' - - 'bioconductor-oligoclasses >=1.44.0,<1.45.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-biostrings >=2.52.0,<2.53.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-oligo >=1.48.0,<1.49.0' + - 'bioconductor-oligoclasses >=1.46.0,<1.47.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' run: - - 'bioconductor-biostrings >=2.50.0,<2.51.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-oligo >=1.46.0,<1.47.0' - - 'bioconductor-oligoclasses >=1.44.0,<1.45.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-biostrings >=2.52.0,<2.53.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-oligo >=1.48.0,<1.49.0' + - 'bioconductor-oligoclasses >=1.46.0,<1.47.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-pd.clariom.s.rat/post-link.sh b/recipes/bioconductor-pd.clariom.s.rat/post-link.sh index e817dad8b19ae..5bc4fe41f73f0 100644 --- a/recipes/bioconductor-pd.clariom.s.rat/post-link.sh +++ b/recipes/bioconductor-pd.clariom.s.rat/post-link.sh @@ -1,9 +1,10 @@ #!/bin/bash FN="pd.clariom.s.rat_3.14.1.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/pd.clariom.s.rat_3.14.1.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/pd.clariom.s.rat_3.14.1.tar.gz" "https://bioarchive.galaxyproject.org/pd.clariom.s.rat_3.14.1.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-pd.clariom.s.rat/bioconductor-pd.clariom.s.rat_3.14.1_src_all.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-pd.clariom.s.rat/bioconductor-pd.clariom.s.rat_3.14.1_src_all.tar.gz" ) MD5="be464b3eaea8eb8bdbcca6047fce4dea" @@ -16,7 +17,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-pd.cotton/meta.yaml b/recipes/bioconductor-pd.cotton/meta.yaml index 0d24b4d76f1b2..daa074aff1160 100644 --- a/recipes/bioconductor-pd.cotton/meta.yaml +++ b/recipes/bioconductor-pd.cotton/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.12.0" %} {% set name = "pd.cotton" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -12,31 +12,31 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 78c408902bcefb8c695119767534b393 build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ noarch: generic requirements: host: - - 'bioconductor-biostrings >=2.50.0,<2.51.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-oligo >=1.46.0,<1.47.0' - - 'bioconductor-oligoclasses >=1.44.0,<1.45.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-biostrings >=2.52.0,<2.53.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-oligo >=1.48.0,<1.49.0' + - 'bioconductor-oligoclasses >=1.46.0,<1.47.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' run: - - 'bioconductor-biostrings >=2.50.0,<2.51.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-oligo >=1.46.0,<1.47.0' - - 'bioconductor-oligoclasses >=1.44.0,<1.45.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-biostrings >=2.52.0,<2.53.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-oligo >=1.48.0,<1.49.0' + - 'bioconductor-oligoclasses >=1.46.0,<1.47.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-pd.cotton/post-link.sh b/recipes/bioconductor-pd.cotton/post-link.sh index 1dea45c247502..410c5ece3809f 100644 --- a/recipes/bioconductor-pd.cotton/post-link.sh +++ b/recipes/bioconductor-pd.cotton/post-link.sh @@ -1,9 +1,10 @@ #!/bin/bash FN="pd.cotton_3.12.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/pd.cotton_3.12.0.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/pd.cotton_3.12.0.tar.gz" "https://bioarchive.galaxyproject.org/pd.cotton_3.12.0.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-pd.cotton/bioconductor-pd.cotton_3.12.0_src_all.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-pd.cotton/bioconductor-pd.cotton_3.12.0_src_all.tar.gz" ) MD5="78c408902bcefb8c695119767534b393" @@ -16,7 +17,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-pd.cyngene.1.0.st/meta.yaml b/recipes/bioconductor-pd.cyngene.1.0.st/meta.yaml index e664de6b79cf3..485e87b1a91b6 100644 --- a/recipes/bioconductor-pd.cyngene.1.0.st/meta.yaml +++ b/recipes/bioconductor-pd.cyngene.1.0.st/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.12.0" %} {% set name = "pd.cyngene.1.0.st" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -12,31 +12,31 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 784fac6cc92a0fe46dae32c9b737812a build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ noarch: generic requirements: host: - - 'bioconductor-biostrings >=2.50.0,<2.51.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-oligo >=1.46.0,<1.47.0' - - 'bioconductor-oligoclasses >=1.44.0,<1.45.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-biostrings >=2.52.0,<2.53.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-oligo >=1.48.0,<1.49.0' + - 'bioconductor-oligoclasses >=1.46.0,<1.47.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' run: - - 'bioconductor-biostrings >=2.50.0,<2.51.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-oligo >=1.46.0,<1.47.0' - - 'bioconductor-oligoclasses >=1.44.0,<1.45.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-biostrings >=2.52.0,<2.53.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-oligo >=1.48.0,<1.49.0' + - 'bioconductor-oligoclasses >=1.46.0,<1.47.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-pd.cyngene.1.0.st/post-link.sh b/recipes/bioconductor-pd.cyngene.1.0.st/post-link.sh index 27fee7fe4f45a..3f8d7921cd367 100644 --- a/recipes/bioconductor-pd.cyngene.1.0.st/post-link.sh +++ b/recipes/bioconductor-pd.cyngene.1.0.st/post-link.sh @@ -1,9 +1,10 @@ #!/bin/bash FN="pd.cyngene.1.0.st_3.12.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/pd.cyngene.1.0.st_3.12.0.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/pd.cyngene.1.0.st_3.12.0.tar.gz" "https://bioarchive.galaxyproject.org/pd.cyngene.1.0.st_3.12.0.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-pd.cyngene.1.0.st/bioconductor-pd.cyngene.1.0.st_3.12.0_src_all.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-pd.cyngene.1.0.st/bioconductor-pd.cyngene.1.0.st_3.12.0_src_all.tar.gz" ) MD5="784fac6cc92a0fe46dae32c9b737812a" @@ -16,7 +17,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-pd.cyngene.1.1.st/meta.yaml b/recipes/bioconductor-pd.cyngene.1.1.st/meta.yaml index 9da5ef3f1911e..803e084847fa2 100644 --- a/recipes/bioconductor-pd.cyngene.1.1.st/meta.yaml +++ b/recipes/bioconductor-pd.cyngene.1.1.st/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.12.0" %} {% set name = "pd.cyngene.1.1.st" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -12,31 +12,31 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: a6217267e3e08a15f70c600918c7d4f6 build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ noarch: generic requirements: host: - - 'bioconductor-biostrings >=2.50.0,<2.51.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-oligo >=1.46.0,<1.47.0' - - 'bioconductor-oligoclasses >=1.44.0,<1.45.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-biostrings >=2.52.0,<2.53.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-oligo >=1.48.0,<1.49.0' + - 'bioconductor-oligoclasses >=1.46.0,<1.47.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' run: - - 'bioconductor-biostrings >=2.50.0,<2.51.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-oligo >=1.46.0,<1.47.0' - - 'bioconductor-oligoclasses >=1.44.0,<1.45.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-biostrings >=2.52.0,<2.53.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-oligo >=1.48.0,<1.49.0' + - 'bioconductor-oligoclasses >=1.46.0,<1.47.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-pd.cyngene.1.1.st/post-link.sh b/recipes/bioconductor-pd.cyngene.1.1.st/post-link.sh index ec1fcdea905da..570562bbfefe4 100644 --- a/recipes/bioconductor-pd.cyngene.1.1.st/post-link.sh +++ b/recipes/bioconductor-pd.cyngene.1.1.st/post-link.sh @@ -1,9 +1,10 @@ #!/bin/bash FN="pd.cyngene.1.1.st_3.12.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/pd.cyngene.1.1.st_3.12.0.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/pd.cyngene.1.1.st_3.12.0.tar.gz" "https://bioarchive.galaxyproject.org/pd.cyngene.1.1.st_3.12.0.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-pd.cyngene.1.1.st/bioconductor-pd.cyngene.1.1.st_3.12.0_src_all.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-pd.cyngene.1.1.st/bioconductor-pd.cyngene.1.1.st_3.12.0_src_all.tar.gz" ) MD5="a6217267e3e08a15f70c600918c7d4f6" @@ -16,7 +17,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-pd.cyrgene.1.0.st/meta.yaml b/recipes/bioconductor-pd.cyrgene.1.0.st/meta.yaml index 2fc72014bb125..efba5476a88e0 100644 --- a/recipes/bioconductor-pd.cyrgene.1.0.st/meta.yaml +++ b/recipes/bioconductor-pd.cyrgene.1.0.st/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.12.0" %} {% set name = "pd.cyrgene.1.0.st" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -12,31 +12,31 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 63228c07d3d16d6c62e9c0e83f10a855 build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ noarch: generic requirements: host: - - 'bioconductor-biostrings >=2.50.0,<2.51.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-oligo >=1.46.0,<1.47.0' - - 'bioconductor-oligoclasses >=1.44.0,<1.45.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-biostrings >=2.52.0,<2.53.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-oligo >=1.48.0,<1.49.0' + - 'bioconductor-oligoclasses >=1.46.0,<1.47.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' run: - - 'bioconductor-biostrings >=2.50.0,<2.51.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-oligo >=1.46.0,<1.47.0' - - 'bioconductor-oligoclasses >=1.44.0,<1.45.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-biostrings >=2.52.0,<2.53.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-oligo >=1.48.0,<1.49.0' + - 'bioconductor-oligoclasses >=1.46.0,<1.47.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-pd.cyrgene.1.0.st/post-link.sh b/recipes/bioconductor-pd.cyrgene.1.0.st/post-link.sh index b1fd50f92c43a..1514c7c40e9f8 100644 --- a/recipes/bioconductor-pd.cyrgene.1.0.st/post-link.sh +++ b/recipes/bioconductor-pd.cyrgene.1.0.st/post-link.sh @@ -1,9 +1,10 @@ #!/bin/bash FN="pd.cyrgene.1.0.st_3.12.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/pd.cyrgene.1.0.st_3.12.0.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/pd.cyrgene.1.0.st_3.12.0.tar.gz" "https://bioarchive.galaxyproject.org/pd.cyrgene.1.0.st_3.12.0.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-pd.cyrgene.1.0.st/bioconductor-pd.cyrgene.1.0.st_3.12.0_src_all.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-pd.cyrgene.1.0.st/bioconductor-pd.cyrgene.1.0.st_3.12.0_src_all.tar.gz" ) MD5="63228c07d3d16d6c62e9c0e83f10a855" @@ -16,7 +17,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-pd.cyrgene.1.1.st/meta.yaml b/recipes/bioconductor-pd.cyrgene.1.1.st/meta.yaml index 48417e813630c..9adfd2f6067dd 100644 --- a/recipes/bioconductor-pd.cyrgene.1.1.st/meta.yaml +++ b/recipes/bioconductor-pd.cyrgene.1.1.st/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.12.0" %} {% set name = "pd.cyrgene.1.1.st" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -12,31 +12,31 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: dbe3bb580b96aaddcc597de45159320d build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ noarch: generic requirements: host: - - 'bioconductor-biostrings >=2.50.0,<2.51.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-oligo >=1.46.0,<1.47.0' - - 'bioconductor-oligoclasses >=1.44.0,<1.45.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-biostrings >=2.52.0,<2.53.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-oligo >=1.48.0,<1.49.0' + - 'bioconductor-oligoclasses >=1.46.0,<1.47.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' run: - - 'bioconductor-biostrings >=2.50.0,<2.51.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-oligo >=1.46.0,<1.47.0' - - 'bioconductor-oligoclasses >=1.44.0,<1.45.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-biostrings >=2.52.0,<2.53.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-oligo >=1.48.0,<1.49.0' + - 'bioconductor-oligoclasses >=1.46.0,<1.47.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-pd.cyrgene.1.1.st/post-link.sh b/recipes/bioconductor-pd.cyrgene.1.1.st/post-link.sh index e656b3b1acc05..47d6d1ce9990e 100644 --- a/recipes/bioconductor-pd.cyrgene.1.1.st/post-link.sh +++ b/recipes/bioconductor-pd.cyrgene.1.1.st/post-link.sh @@ -1,9 +1,10 @@ #!/bin/bash FN="pd.cyrgene.1.1.st_3.12.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/pd.cyrgene.1.1.st_3.12.0.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/pd.cyrgene.1.1.st_3.12.0.tar.gz" "https://bioarchive.galaxyproject.org/pd.cyrgene.1.1.st_3.12.0.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-pd.cyrgene.1.1.st/bioconductor-pd.cyrgene.1.1.st_3.12.0_src_all.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-pd.cyrgene.1.1.st/bioconductor-pd.cyrgene.1.1.st_3.12.0_src_all.tar.gz" ) MD5="dbe3bb580b96aaddcc597de45159320d" @@ -16,7 +17,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-pd.cytogenetics.array/meta.yaml b/recipes/bioconductor-pd.cytogenetics.array/meta.yaml index 99936587debd1..e5f4f92cdc613 100644 --- a/recipes/bioconductor-pd.cytogenetics.array/meta.yaml +++ b/recipes/bioconductor-pd.cytogenetics.array/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.12.0" %} {% set name = "pd.cytogenetics.array" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -12,31 +12,31 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 8c359ff56a9a558d370dc9a6a54218e0 build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ noarch: generic requirements: host: - - 'bioconductor-biostrings >=2.50.0,<2.51.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-oligo >=1.46.0,<1.47.0' - - 'bioconductor-oligoclasses >=1.44.0,<1.45.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-biostrings >=2.52.0,<2.53.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-oligo >=1.48.0,<1.49.0' + - 'bioconductor-oligoclasses >=1.46.0,<1.47.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' run: - - 'bioconductor-biostrings >=2.50.0,<2.51.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-oligo >=1.46.0,<1.47.0' - - 'bioconductor-oligoclasses >=1.44.0,<1.45.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-biostrings >=2.52.0,<2.53.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-oligo >=1.48.0,<1.49.0' + - 'bioconductor-oligoclasses >=1.46.0,<1.47.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-pd.cytogenetics.array/post-link.sh b/recipes/bioconductor-pd.cytogenetics.array/post-link.sh index 831860ad70750..06607247ee3e6 100644 --- a/recipes/bioconductor-pd.cytogenetics.array/post-link.sh +++ b/recipes/bioconductor-pd.cytogenetics.array/post-link.sh @@ -1,9 +1,10 @@ #!/bin/bash FN="pd.cytogenetics.array_3.12.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/pd.cytogenetics.array_3.12.0.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/pd.cytogenetics.array_3.12.0.tar.gz" "https://bioarchive.galaxyproject.org/pd.cytogenetics.array_3.12.0.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-pd.cytogenetics.array/bioconductor-pd.cytogenetics.array_3.12.0_src_all.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-pd.cytogenetics.array/bioconductor-pd.cytogenetics.array_3.12.0_src_all.tar.gz" ) MD5="8c359ff56a9a558d370dc9a6a54218e0" @@ -16,7 +17,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-pd.drogene.1.0.st/meta.yaml b/recipes/bioconductor-pd.drogene.1.0.st/meta.yaml index bf953109a6f50..f12f37e4dffc1 100644 --- a/recipes/bioconductor-pd.drogene.1.0.st/meta.yaml +++ b/recipes/bioconductor-pd.drogene.1.0.st/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.12.0" %} {% set name = "pd.drogene.1.0.st" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -12,31 +12,31 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 67f92a97a5b78a95693edfdd32b67e93 build: - number: 1 + number: 2 rpaths: - lib/R/lib/ - lib/ noarch: generic requirements: host: - - 'bioconductor-biostrings >=2.50.0,<2.51.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-oligo >=1.46.0,<1.47.0' - - 'bioconductor-oligoclasses >=1.44.0,<1.45.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-biostrings >=2.52.0,<2.53.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-oligo >=1.48.0,<1.49.0' + - 'bioconductor-oligoclasses >=1.46.0,<1.47.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' run: - - 'bioconductor-biostrings >=2.50.0,<2.51.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-oligo >=1.46.0,<1.47.0' - - 'bioconductor-oligoclasses >=1.44.0,<1.45.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-biostrings >=2.52.0,<2.53.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-oligo >=1.48.0,<1.49.0' + - 'bioconductor-oligoclasses >=1.46.0,<1.47.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-pd.drogene.1.0.st/post-link.sh b/recipes/bioconductor-pd.drogene.1.0.st/post-link.sh index e6aba7fd5c973..862d140ebe5df 100644 --- a/recipes/bioconductor-pd.drogene.1.0.st/post-link.sh +++ b/recipes/bioconductor-pd.drogene.1.0.st/post-link.sh @@ -1,9 +1,10 @@ #!/bin/bash FN="pd.drogene.1.0.st_3.12.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/pd.drogene.1.0.st_3.12.0.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/pd.drogene.1.0.st_3.12.0.tar.gz" "https://bioarchive.galaxyproject.org/pd.drogene.1.0.st_3.12.0.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-pd.drogene.1.0.st/bioconductor-pd.drogene.1.0.st_3.12.0_src_all.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-pd.drogene.1.0.st/bioconductor-pd.drogene.1.0.st_3.12.0_src_all.tar.gz" ) MD5="67f92a97a5b78a95693edfdd32b67e93" @@ -16,7 +17,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-pd.drogene.1.1.st/meta.yaml b/recipes/bioconductor-pd.drogene.1.1.st/meta.yaml index 84a1aa8ee8c82..4ebfafd1ae43d 100644 --- a/recipes/bioconductor-pd.drogene.1.1.st/meta.yaml +++ b/recipes/bioconductor-pd.drogene.1.1.st/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.12.0" %} {% set name = "pd.drogene.1.1.st" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -12,31 +12,31 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 5c63236ea91390d49dbabea63a48f0a2 build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ noarch: generic requirements: host: - - 'bioconductor-biostrings >=2.50.0,<2.51.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-oligo >=1.46.0,<1.47.0' - - 'bioconductor-oligoclasses >=1.44.0,<1.45.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-biostrings >=2.52.0,<2.53.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-oligo >=1.48.0,<1.49.0' + - 'bioconductor-oligoclasses >=1.46.0,<1.47.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' run: - - 'bioconductor-biostrings >=2.50.0,<2.51.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-oligo >=1.46.0,<1.47.0' - - 'bioconductor-oligoclasses >=1.44.0,<1.45.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-biostrings >=2.52.0,<2.53.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-oligo >=1.48.0,<1.49.0' + - 'bioconductor-oligoclasses >=1.46.0,<1.47.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-pd.drogene.1.1.st/post-link.sh b/recipes/bioconductor-pd.drogene.1.1.st/post-link.sh index 06600c1985315..8cad3f91df7c6 100644 --- a/recipes/bioconductor-pd.drogene.1.1.st/post-link.sh +++ b/recipes/bioconductor-pd.drogene.1.1.st/post-link.sh @@ -1,9 +1,10 @@ #!/bin/bash FN="pd.drogene.1.1.st_3.12.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/pd.drogene.1.1.st_3.12.0.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/pd.drogene.1.1.st_3.12.0.tar.gz" "https://bioarchive.galaxyproject.org/pd.drogene.1.1.st_3.12.0.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-pd.drogene.1.1.st/bioconductor-pd.drogene.1.1.st_3.12.0_src_all.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-pd.drogene.1.1.st/bioconductor-pd.drogene.1.1.st_3.12.0_src_all.tar.gz" ) MD5="5c63236ea91390d49dbabea63a48f0a2" @@ -16,7 +17,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-pd.drosgenome1/meta.yaml b/recipes/bioconductor-pd.drosgenome1/meta.yaml index 8f92379750aab..7fc2f126c390e 100644 --- a/recipes/bioconductor-pd.drosgenome1/meta.yaml +++ b/recipes/bioconductor-pd.drosgenome1/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.12.0" %} {% set name = "pd.drosgenome1" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -12,31 +12,31 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 59c1a37a7d6a43fc70ff8756bf1195ef build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ noarch: generic requirements: host: - - 'bioconductor-biostrings >=2.50.0,<2.51.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-oligo >=1.46.0,<1.47.0' - - 'bioconductor-oligoclasses >=1.44.0,<1.45.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-biostrings >=2.52.0,<2.53.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-oligo >=1.48.0,<1.49.0' + - 'bioconductor-oligoclasses >=1.46.0,<1.47.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' run: - - 'bioconductor-biostrings >=2.50.0,<2.51.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-oligo >=1.46.0,<1.47.0' - - 'bioconductor-oligoclasses >=1.44.0,<1.45.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-biostrings >=2.52.0,<2.53.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-oligo >=1.48.0,<1.49.0' + - 'bioconductor-oligoclasses >=1.46.0,<1.47.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-pd.drosgenome1/post-link.sh b/recipes/bioconductor-pd.drosgenome1/post-link.sh index 8cb838a5ebf40..44491252b4505 100644 --- a/recipes/bioconductor-pd.drosgenome1/post-link.sh +++ b/recipes/bioconductor-pd.drosgenome1/post-link.sh @@ -1,9 +1,10 @@ #!/bin/bash FN="pd.drosgenome1_3.12.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/pd.drosgenome1_3.12.0.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/pd.drosgenome1_3.12.0.tar.gz" "https://bioarchive.galaxyproject.org/pd.drosgenome1_3.12.0.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-pd.drosgenome1/bioconductor-pd.drosgenome1_3.12.0_src_all.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-pd.drosgenome1/bioconductor-pd.drosgenome1_3.12.0_src_all.tar.gz" ) MD5="59c1a37a7d6a43fc70ff8756bf1195ef" @@ -16,7 +17,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-pd.drosophila.2/meta.yaml b/recipes/bioconductor-pd.drosophila.2/meta.yaml index 532ef5e05999b..5b0c0dae14fb3 100644 --- a/recipes/bioconductor-pd.drosophila.2/meta.yaml +++ b/recipes/bioconductor-pd.drosophila.2/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.12.0" %} {% set name = "pd.drosophila.2" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -12,31 +12,31 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: ddb821e35e722af8dcf0807c6da4fac1 build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ noarch: generic requirements: host: - - 'bioconductor-biostrings >=2.50.0,<2.51.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-oligo >=1.46.0,<1.47.0' - - 'bioconductor-oligoclasses >=1.44.0,<1.45.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-biostrings >=2.52.0,<2.53.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-oligo >=1.48.0,<1.49.0' + - 'bioconductor-oligoclasses >=1.46.0,<1.47.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' run: - - 'bioconductor-biostrings >=2.50.0,<2.51.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-oligo >=1.46.0,<1.47.0' - - 'bioconductor-oligoclasses >=1.44.0,<1.45.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-biostrings >=2.52.0,<2.53.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-oligo >=1.48.0,<1.49.0' + - 'bioconductor-oligoclasses >=1.46.0,<1.47.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-pd.drosophila.2/post-link.sh b/recipes/bioconductor-pd.drosophila.2/post-link.sh index 1df4b0a76f7b9..a9447e8aef10e 100644 --- a/recipes/bioconductor-pd.drosophila.2/post-link.sh +++ b/recipes/bioconductor-pd.drosophila.2/post-link.sh @@ -1,9 +1,10 @@ #!/bin/bash FN="pd.drosophila.2_3.12.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/pd.drosophila.2_3.12.0.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/pd.drosophila.2_3.12.0.tar.gz" "https://bioarchive.galaxyproject.org/pd.drosophila.2_3.12.0.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-pd.drosophila.2/bioconductor-pd.drosophila.2_3.12.0_src_all.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-pd.drosophila.2/bioconductor-pd.drosophila.2_3.12.0_src_all.tar.gz" ) MD5="ddb821e35e722af8dcf0807c6da4fac1" @@ -16,7 +17,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-pd.e.coli.2/meta.yaml b/recipes/bioconductor-pd.e.coli.2/meta.yaml index 01e07e69f1525..f04dde9460e68 100644 --- a/recipes/bioconductor-pd.e.coli.2/meta.yaml +++ b/recipes/bioconductor-pd.e.coli.2/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.12.0" %} {% set name = "pd.e.coli.2" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -12,31 +12,31 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 9176faa60a0c252a815b2a74d2f63dd4 build: - number: 1 + number: 2 rpaths: - lib/R/lib/ - lib/ noarch: generic requirements: host: - - 'bioconductor-biostrings >=2.50.0,<2.51.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-oligo >=1.46.0,<1.47.0' - - 'bioconductor-oligoclasses >=1.44.0,<1.45.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-biostrings >=2.52.0,<2.53.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-oligo >=1.48.0,<1.49.0' + - 'bioconductor-oligoclasses >=1.46.0,<1.47.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' run: - - 'bioconductor-biostrings >=2.50.0,<2.51.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-oligo >=1.46.0,<1.47.0' - - 'bioconductor-oligoclasses >=1.44.0,<1.45.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-biostrings >=2.52.0,<2.53.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-oligo >=1.48.0,<1.49.0' + - 'bioconductor-oligoclasses >=1.46.0,<1.47.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-pd.e.coli.2/post-link.sh b/recipes/bioconductor-pd.e.coli.2/post-link.sh index 2200e5e2443a1..b2242587f8b8f 100644 --- a/recipes/bioconductor-pd.e.coli.2/post-link.sh +++ b/recipes/bioconductor-pd.e.coli.2/post-link.sh @@ -1,9 +1,10 @@ #!/bin/bash FN="pd.e.coli.2_3.12.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/pd.e.coli.2_3.12.0.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/pd.e.coli.2_3.12.0.tar.gz" "https://bioarchive.galaxyproject.org/pd.e.coli.2_3.12.0.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-pd.e.coli.2/bioconductor-pd.e.coli.2_3.12.0_src_all.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-pd.e.coli.2/bioconductor-pd.e.coli.2_3.12.0_src_all.tar.gz" ) MD5="9176faa60a0c252a815b2a74d2f63dd4" @@ -16,7 +17,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-pd.ecoli.asv2/meta.yaml b/recipes/bioconductor-pd.ecoli.asv2/meta.yaml index 1c514227b35f3..6ff4b909082d8 100644 --- a/recipes/bioconductor-pd.ecoli.asv2/meta.yaml +++ b/recipes/bioconductor-pd.ecoli.asv2/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.12.0" %} {% set name = "pd.ecoli.asv2" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -12,31 +12,31 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: d789ddf5a178a9a50c5587ee3ab294a4 build: - number: 1 + number: 2 rpaths: - lib/R/lib/ - lib/ noarch: generic requirements: host: - - 'bioconductor-biostrings >=2.50.0,<2.51.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-oligo >=1.46.0,<1.47.0' - - 'bioconductor-oligoclasses >=1.44.0,<1.45.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-biostrings >=2.52.0,<2.53.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-oligo >=1.48.0,<1.49.0' + - 'bioconductor-oligoclasses >=1.46.0,<1.47.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' run: - - 'bioconductor-biostrings >=2.50.0,<2.51.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-oligo >=1.46.0,<1.47.0' - - 'bioconductor-oligoclasses >=1.44.0,<1.45.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-biostrings >=2.52.0,<2.53.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-oligo >=1.48.0,<1.49.0' + - 'bioconductor-oligoclasses >=1.46.0,<1.47.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-pd.ecoli.asv2/post-link.sh b/recipes/bioconductor-pd.ecoli.asv2/post-link.sh index 0fd3583bcd5ee..bd2274f6123a8 100644 --- a/recipes/bioconductor-pd.ecoli.asv2/post-link.sh +++ b/recipes/bioconductor-pd.ecoli.asv2/post-link.sh @@ -1,9 +1,10 @@ #!/bin/bash FN="pd.ecoli.asv2_3.12.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/pd.ecoli.asv2_3.12.0.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/pd.ecoli.asv2_3.12.0.tar.gz" "https://bioarchive.galaxyproject.org/pd.ecoli.asv2_3.12.0.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-pd.ecoli.asv2/bioconductor-pd.ecoli.asv2_3.12.0_src_all.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-pd.ecoli.asv2/bioconductor-pd.ecoli.asv2_3.12.0_src_all.tar.gz" ) MD5="d789ddf5a178a9a50c5587ee3ab294a4" @@ -16,7 +17,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-pd.ecoli/meta.yaml b/recipes/bioconductor-pd.ecoli/meta.yaml index 5df2ad1927929..25708769c12c9 100644 --- a/recipes/bioconductor-pd.ecoli/meta.yaml +++ b/recipes/bioconductor-pd.ecoli/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.12.0" %} {% set name = "pd.ecoli" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -12,31 +12,31 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 077e91b2567a32780305f0fb6b126fe9 build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ noarch: generic requirements: host: - - 'bioconductor-biostrings >=2.50.0,<2.51.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-oligo >=1.46.0,<1.47.0' - - 'bioconductor-oligoclasses >=1.44.0,<1.45.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-biostrings >=2.52.0,<2.53.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-oligo >=1.48.0,<1.49.0' + - 'bioconductor-oligoclasses >=1.46.0,<1.47.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' run: - - 'bioconductor-biostrings >=2.50.0,<2.51.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-oligo >=1.46.0,<1.47.0' - - 'bioconductor-oligoclasses >=1.44.0,<1.45.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-biostrings >=2.52.0,<2.53.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-oligo >=1.48.0,<1.49.0' + - 'bioconductor-oligoclasses >=1.46.0,<1.47.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-pd.ecoli/post-link.sh b/recipes/bioconductor-pd.ecoli/post-link.sh index 6c965575707d7..d0d5a4d58f526 100644 --- a/recipes/bioconductor-pd.ecoli/post-link.sh +++ b/recipes/bioconductor-pd.ecoli/post-link.sh @@ -1,9 +1,10 @@ #!/bin/bash FN="pd.ecoli_3.12.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/pd.ecoli_3.12.0.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/pd.ecoli_3.12.0.tar.gz" "https://bioarchive.galaxyproject.org/pd.ecoli_3.12.0.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-pd.ecoli/bioconductor-pd.ecoli_3.12.0_src_all.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-pd.ecoli/bioconductor-pd.ecoli_3.12.0_src_all.tar.gz" ) MD5="077e91b2567a32780305f0fb6b126fe9" @@ -16,7 +17,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-pd.elegene.1.0.st/meta.yaml b/recipes/bioconductor-pd.elegene.1.0.st/meta.yaml index 73b38012c45aa..1e0febf6935d6 100644 --- a/recipes/bioconductor-pd.elegene.1.0.st/meta.yaml +++ b/recipes/bioconductor-pd.elegene.1.0.st/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.12.0" %} {% set name = "pd.elegene.1.0.st" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -12,31 +12,31 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: b6110c58d5964703c7117e5e0668c901 build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ noarch: generic requirements: host: - - 'bioconductor-biostrings >=2.50.0,<2.51.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-oligo >=1.46.0,<1.47.0' - - 'bioconductor-oligoclasses >=1.44.0,<1.45.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-biostrings >=2.52.0,<2.53.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-oligo >=1.48.0,<1.49.0' + - 'bioconductor-oligoclasses >=1.46.0,<1.47.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' run: - - 'bioconductor-biostrings >=2.50.0,<2.51.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-oligo >=1.46.0,<1.47.0' - - 'bioconductor-oligoclasses >=1.44.0,<1.45.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-biostrings >=2.52.0,<2.53.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-oligo >=1.48.0,<1.49.0' + - 'bioconductor-oligoclasses >=1.46.0,<1.47.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-pd.elegene.1.0.st/post-link.sh b/recipes/bioconductor-pd.elegene.1.0.st/post-link.sh index f43b260f75e59..cf5492b3c7cf6 100644 --- a/recipes/bioconductor-pd.elegene.1.0.st/post-link.sh +++ b/recipes/bioconductor-pd.elegene.1.0.st/post-link.sh @@ -1,9 +1,10 @@ #!/bin/bash FN="pd.elegene.1.0.st_3.12.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/pd.elegene.1.0.st_3.12.0.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/pd.elegene.1.0.st_3.12.0.tar.gz" "https://bioarchive.galaxyproject.org/pd.elegene.1.0.st_3.12.0.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-pd.elegene.1.0.st/bioconductor-pd.elegene.1.0.st_3.12.0_src_all.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-pd.elegene.1.0.st/bioconductor-pd.elegene.1.0.st_3.12.0_src_all.tar.gz" ) MD5="b6110c58d5964703c7117e5e0668c901" @@ -16,7 +17,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-pd.elegene.1.1.st/meta.yaml b/recipes/bioconductor-pd.elegene.1.1.st/meta.yaml index 84e7b1a37ba53..9d4c3b8d7b06d 100644 --- a/recipes/bioconductor-pd.elegene.1.1.st/meta.yaml +++ b/recipes/bioconductor-pd.elegene.1.1.st/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.12.0" %} {% set name = "pd.elegene.1.1.st" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -12,31 +12,31 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 1dbe166ea347a5a7e240db925d2081c7 build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ noarch: generic requirements: host: - - 'bioconductor-biostrings >=2.50.0,<2.51.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-oligo >=1.46.0,<1.47.0' - - 'bioconductor-oligoclasses >=1.44.0,<1.45.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-biostrings >=2.52.0,<2.53.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-oligo >=1.48.0,<1.49.0' + - 'bioconductor-oligoclasses >=1.46.0,<1.47.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' run: - - 'bioconductor-biostrings >=2.50.0,<2.51.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-oligo >=1.46.0,<1.47.0' - - 'bioconductor-oligoclasses >=1.44.0,<1.45.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-biostrings >=2.52.0,<2.53.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-oligo >=1.48.0,<1.49.0' + - 'bioconductor-oligoclasses >=1.46.0,<1.47.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-pd.elegene.1.1.st/post-link.sh b/recipes/bioconductor-pd.elegene.1.1.st/post-link.sh index 5a7a686c1639e..c443ac5c06a0a 100644 --- a/recipes/bioconductor-pd.elegene.1.1.st/post-link.sh +++ b/recipes/bioconductor-pd.elegene.1.1.st/post-link.sh @@ -1,9 +1,10 @@ #!/bin/bash FN="pd.elegene.1.1.st_3.12.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/pd.elegene.1.1.st_3.12.0.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/pd.elegene.1.1.st_3.12.0.tar.gz" "https://bioarchive.galaxyproject.org/pd.elegene.1.1.st_3.12.0.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-pd.elegene.1.1.st/bioconductor-pd.elegene.1.1.st_3.12.0_src_all.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-pd.elegene.1.1.st/bioconductor-pd.elegene.1.1.st_3.12.0_src_all.tar.gz" ) MD5="1dbe166ea347a5a7e240db925d2081c7" @@ -16,7 +17,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-pd.equgene.1.0.st/meta.yaml b/recipes/bioconductor-pd.equgene.1.0.st/meta.yaml index 2ce1c9c7caea3..e214dd887d957 100644 --- a/recipes/bioconductor-pd.equgene.1.0.st/meta.yaml +++ b/recipes/bioconductor-pd.equgene.1.0.st/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.12.0" %} {% set name = "pd.equgene.1.0.st" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -12,31 +12,31 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 3448f36fdb899f04702be37ffab4c4c7 build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ noarch: generic requirements: host: - - 'bioconductor-biostrings >=2.50.0,<2.51.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-oligo >=1.46.0,<1.47.0' - - 'bioconductor-oligoclasses >=1.44.0,<1.45.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-biostrings >=2.52.0,<2.53.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-oligo >=1.48.0,<1.49.0' + - 'bioconductor-oligoclasses >=1.46.0,<1.47.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' run: - - 'bioconductor-biostrings >=2.50.0,<2.51.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-oligo >=1.46.0,<1.47.0' - - 'bioconductor-oligoclasses >=1.44.0,<1.45.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-biostrings >=2.52.0,<2.53.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-oligo >=1.48.0,<1.49.0' + - 'bioconductor-oligoclasses >=1.46.0,<1.47.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-pd.equgene.1.0.st/post-link.sh b/recipes/bioconductor-pd.equgene.1.0.st/post-link.sh index 7a4502a6b4c8b..537edf5e07383 100644 --- a/recipes/bioconductor-pd.equgene.1.0.st/post-link.sh +++ b/recipes/bioconductor-pd.equgene.1.0.st/post-link.sh @@ -1,9 +1,10 @@ #!/bin/bash FN="pd.equgene.1.0.st_3.12.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/pd.equgene.1.0.st_3.12.0.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/pd.equgene.1.0.st_3.12.0.tar.gz" "https://bioarchive.galaxyproject.org/pd.equgene.1.0.st_3.12.0.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-pd.equgene.1.0.st/bioconductor-pd.equgene.1.0.st_3.12.0_src_all.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-pd.equgene.1.0.st/bioconductor-pd.equgene.1.0.st_3.12.0_src_all.tar.gz" ) MD5="3448f36fdb899f04702be37ffab4c4c7" @@ -16,7 +17,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-pd.equgene.1.1.st/meta.yaml b/recipes/bioconductor-pd.equgene.1.1.st/meta.yaml index 84bdbe4e0fc01..388aab23529e8 100644 --- a/recipes/bioconductor-pd.equgene.1.1.st/meta.yaml +++ b/recipes/bioconductor-pd.equgene.1.1.st/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.12.0" %} {% set name = "pd.equgene.1.1.st" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -12,31 +12,31 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: bed32525513ce25f14d433ce805e7d6c build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ noarch: generic requirements: host: - - 'bioconductor-biostrings >=2.50.0,<2.51.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-oligo >=1.46.0,<1.47.0' - - 'bioconductor-oligoclasses >=1.44.0,<1.45.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-biostrings >=2.52.0,<2.53.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-oligo >=1.48.0,<1.49.0' + - 'bioconductor-oligoclasses >=1.46.0,<1.47.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' run: - - 'bioconductor-biostrings >=2.50.0,<2.51.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-oligo >=1.46.0,<1.47.0' - - 'bioconductor-oligoclasses >=1.44.0,<1.45.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-biostrings >=2.52.0,<2.53.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-oligo >=1.48.0,<1.49.0' + - 'bioconductor-oligoclasses >=1.46.0,<1.47.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-pd.equgene.1.1.st/post-link.sh b/recipes/bioconductor-pd.equgene.1.1.st/post-link.sh index db87d4d745e85..66b4e739a81ae 100644 --- a/recipes/bioconductor-pd.equgene.1.1.st/post-link.sh +++ b/recipes/bioconductor-pd.equgene.1.1.st/post-link.sh @@ -1,9 +1,10 @@ #!/bin/bash FN="pd.equgene.1.1.st_3.12.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/pd.equgene.1.1.st_3.12.0.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/pd.equgene.1.1.st_3.12.0.tar.gz" "https://bioarchive.galaxyproject.org/pd.equgene.1.1.st_3.12.0.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-pd.equgene.1.1.st/bioconductor-pd.equgene.1.1.st_3.12.0_src_all.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-pd.equgene.1.1.st/bioconductor-pd.equgene.1.1.st_3.12.0_src_all.tar.gz" ) MD5="bed32525513ce25f14d433ce805e7d6c" @@ -16,7 +17,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-pd.feinberg.hg18.me.hx1/meta.yaml b/recipes/bioconductor-pd.feinberg.hg18.me.hx1/meta.yaml index f096ba5520db5..f4fc5a5c6a7ed 100644 --- a/recipes/bioconductor-pd.feinberg.hg18.me.hx1/meta.yaml +++ b/recipes/bioconductor-pd.feinberg.hg18.me.hx1/meta.yaml @@ -1,6 +1,6 @@ {% set version = "0.99.3" %} {% set name = "pd.feinberg.hg18.me.hx1" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -12,29 +12,29 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: b6eeaf79671bab6f597965009516ce57 build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ noarch: generic requirements: host: - - 'bioconductor-biostrings >=2.50.0,<2.51.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-oligo >=1.46.0,<1.47.0' - - 'bioconductor-oligoclasses >=1.44.0,<1.45.0' + - 'bioconductor-biostrings >=2.52.0,<2.53.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-oligo >=1.48.0,<1.49.0' + - 'bioconductor-oligoclasses >=1.46.0,<1.47.0' - r-base - r-dbi - 'r-rsqlite >=0.7-1' run: - - 'bioconductor-biostrings >=2.50.0,<2.51.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-oligo >=1.46.0,<1.47.0' - - 'bioconductor-oligoclasses >=1.44.0,<1.45.0' + - 'bioconductor-biostrings >=2.52.0,<2.53.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-oligo >=1.48.0,<1.49.0' + - 'bioconductor-oligoclasses >=1.46.0,<1.47.0' - r-base - r-dbi - 'r-rsqlite >=0.7-1' - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-pd.feinberg.hg18.me.hx1/post-link.sh b/recipes/bioconductor-pd.feinberg.hg18.me.hx1/post-link.sh index c87c99640012f..748f60849684d 100644 --- a/recipes/bioconductor-pd.feinberg.hg18.me.hx1/post-link.sh +++ b/recipes/bioconductor-pd.feinberg.hg18.me.hx1/post-link.sh @@ -1,9 +1,10 @@ #!/bin/bash FN="pd.feinberg.hg18.me.hx1_0.99.3.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/pd.feinberg.hg18.me.hx1_0.99.3.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/pd.feinberg.hg18.me.hx1_0.99.3.tar.gz" "https://bioarchive.galaxyproject.org/pd.feinberg.hg18.me.hx1_0.99.3.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-pd.feinberg.hg18.me.hx1/bioconductor-pd.feinberg.hg18.me.hx1_0.99.3_src_all.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-pd.feinberg.hg18.me.hx1/bioconductor-pd.feinberg.hg18.me.hx1_0.99.3_src_all.tar.gz" ) MD5="b6eeaf79671bab6f597965009516ce57" @@ -16,7 +17,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-pd.feinberg.mm8.me.hx1/meta.yaml b/recipes/bioconductor-pd.feinberg.mm8.me.hx1/meta.yaml index e2a6a6fc7e6e9..99d7727fa51dd 100644 --- a/recipes/bioconductor-pd.feinberg.mm8.me.hx1/meta.yaml +++ b/recipes/bioconductor-pd.feinberg.mm8.me.hx1/meta.yaml @@ -1,6 +1,6 @@ {% set version = "0.99.3" %} {% set name = "pd.feinberg.mm8.me.hx1" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -12,29 +12,29 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 7332102b69fc9ee087f52d3cdc311d00 build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ noarch: generic requirements: host: - - 'bioconductor-biostrings >=2.50.0,<2.51.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-oligo >=1.46.0,<1.47.0' - - 'bioconductor-oligoclasses >=1.44.0,<1.45.0' + - 'bioconductor-biostrings >=2.52.0,<2.53.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-oligo >=1.48.0,<1.49.0' + - 'bioconductor-oligoclasses >=1.46.0,<1.47.0' - r-base - r-dbi - 'r-rsqlite >=0.7-1' run: - - 'bioconductor-biostrings >=2.50.0,<2.51.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-oligo >=1.46.0,<1.47.0' - - 'bioconductor-oligoclasses >=1.44.0,<1.45.0' + - 'bioconductor-biostrings >=2.52.0,<2.53.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-oligo >=1.48.0,<1.49.0' + - 'bioconductor-oligoclasses >=1.46.0,<1.47.0' - r-base - r-dbi - 'r-rsqlite >=0.7-1' - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-pd.feinberg.mm8.me.hx1/post-link.sh b/recipes/bioconductor-pd.feinberg.mm8.me.hx1/post-link.sh index 280587ed11eaf..e3cd9b57a193f 100644 --- a/recipes/bioconductor-pd.feinberg.mm8.me.hx1/post-link.sh +++ b/recipes/bioconductor-pd.feinberg.mm8.me.hx1/post-link.sh @@ -1,9 +1,10 @@ #!/bin/bash FN="pd.feinberg.mm8.me.hx1_0.99.3.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/pd.feinberg.mm8.me.hx1_0.99.3.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/pd.feinberg.mm8.me.hx1_0.99.3.tar.gz" "https://bioarchive.galaxyproject.org/pd.feinberg.mm8.me.hx1_0.99.3.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-pd.feinberg.mm8.me.hx1/bioconductor-pd.feinberg.mm8.me.hx1_0.99.3_src_all.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-pd.feinberg.mm8.me.hx1/bioconductor-pd.feinberg.mm8.me.hx1_0.99.3_src_all.tar.gz" ) MD5="7332102b69fc9ee087f52d3cdc311d00" @@ -16,7 +17,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-pd.felgene.1.0.st/meta.yaml b/recipes/bioconductor-pd.felgene.1.0.st/meta.yaml index d39e3885d27ad..e5f113841fd41 100644 --- a/recipes/bioconductor-pd.felgene.1.0.st/meta.yaml +++ b/recipes/bioconductor-pd.felgene.1.0.st/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.12.0" %} {% set name = "pd.felgene.1.0.st" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -12,31 +12,31 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: b7ac0a5cbde5f248aac5d0a7422bd88d build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ noarch: generic requirements: host: - - 'bioconductor-biostrings >=2.50.0,<2.51.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-oligo >=1.46.0,<1.47.0' - - 'bioconductor-oligoclasses >=1.44.0,<1.45.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-biostrings >=2.52.0,<2.53.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-oligo >=1.48.0,<1.49.0' + - 'bioconductor-oligoclasses >=1.46.0,<1.47.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' run: - - 'bioconductor-biostrings >=2.50.0,<2.51.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-oligo >=1.46.0,<1.47.0' - - 'bioconductor-oligoclasses >=1.44.0,<1.45.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-biostrings >=2.52.0,<2.53.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-oligo >=1.48.0,<1.49.0' + - 'bioconductor-oligoclasses >=1.46.0,<1.47.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-pd.felgene.1.0.st/post-link.sh b/recipes/bioconductor-pd.felgene.1.0.st/post-link.sh index f03580f8ecaf9..8d788b81e812e 100644 --- a/recipes/bioconductor-pd.felgene.1.0.st/post-link.sh +++ b/recipes/bioconductor-pd.felgene.1.0.st/post-link.sh @@ -1,9 +1,10 @@ #!/bin/bash FN="pd.felgene.1.0.st_3.12.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/pd.felgene.1.0.st_3.12.0.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/pd.felgene.1.0.st_3.12.0.tar.gz" "https://bioarchive.galaxyproject.org/pd.felgene.1.0.st_3.12.0.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-pd.felgene.1.0.st/bioconductor-pd.felgene.1.0.st_3.12.0_src_all.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-pd.felgene.1.0.st/bioconductor-pd.felgene.1.0.st_3.12.0_src_all.tar.gz" ) MD5="b7ac0a5cbde5f248aac5d0a7422bd88d" @@ -16,7 +17,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-pd.felgene.1.1.st/meta.yaml b/recipes/bioconductor-pd.felgene.1.1.st/meta.yaml index 5309cae021ad0..dfcf5039f39f7 100644 --- a/recipes/bioconductor-pd.felgene.1.1.st/meta.yaml +++ b/recipes/bioconductor-pd.felgene.1.1.st/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.12.0" %} {% set name = "pd.felgene.1.1.st" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -12,31 +12,31 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 734807a7f3608f6c44c76df7eee04c99 build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ noarch: generic requirements: host: - - 'bioconductor-biostrings >=2.50.0,<2.51.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-oligo >=1.46.0,<1.47.0' - - 'bioconductor-oligoclasses >=1.44.0,<1.45.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-biostrings >=2.52.0,<2.53.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-oligo >=1.48.0,<1.49.0' + - 'bioconductor-oligoclasses >=1.46.0,<1.47.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' run: - - 'bioconductor-biostrings >=2.50.0,<2.51.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-oligo >=1.46.0,<1.47.0' - - 'bioconductor-oligoclasses >=1.44.0,<1.45.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-biostrings >=2.52.0,<2.53.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-oligo >=1.48.0,<1.49.0' + - 'bioconductor-oligoclasses >=1.46.0,<1.47.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-pd.felgene.1.1.st/post-link.sh b/recipes/bioconductor-pd.felgene.1.1.st/post-link.sh index 54221bf99ce9d..681361ebce300 100644 --- a/recipes/bioconductor-pd.felgene.1.1.st/post-link.sh +++ b/recipes/bioconductor-pd.felgene.1.1.st/post-link.sh @@ -1,9 +1,10 @@ #!/bin/bash FN="pd.felgene.1.1.st_3.12.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/pd.felgene.1.1.st_3.12.0.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/pd.felgene.1.1.st_3.12.0.tar.gz" "https://bioarchive.galaxyproject.org/pd.felgene.1.1.st_3.12.0.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-pd.felgene.1.1.st/bioconductor-pd.felgene.1.1.st_3.12.0_src_all.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-pd.felgene.1.1.st/bioconductor-pd.felgene.1.1.st_3.12.0_src_all.tar.gz" ) MD5="734807a7f3608f6c44c76df7eee04c99" @@ -16,7 +17,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-pd.fingene.1.0.st/meta.yaml b/recipes/bioconductor-pd.fingene.1.0.st/meta.yaml index 7d7f124e88b7f..4b6b8b4d5fc5d 100644 --- a/recipes/bioconductor-pd.fingene.1.0.st/meta.yaml +++ b/recipes/bioconductor-pd.fingene.1.0.st/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.12.0" %} {% set name = "pd.fingene.1.0.st" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -12,31 +12,31 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: b79e4f8a52cad3b62e32401bbe74603d build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ noarch: generic requirements: host: - - 'bioconductor-biostrings >=2.50.0,<2.51.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-oligo >=1.46.0,<1.47.0' - - 'bioconductor-oligoclasses >=1.44.0,<1.45.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-biostrings >=2.52.0,<2.53.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-oligo >=1.48.0,<1.49.0' + - 'bioconductor-oligoclasses >=1.46.0,<1.47.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' run: - - 'bioconductor-biostrings >=2.50.0,<2.51.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-oligo >=1.46.0,<1.47.0' - - 'bioconductor-oligoclasses >=1.44.0,<1.45.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-biostrings >=2.52.0,<2.53.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-oligo >=1.48.0,<1.49.0' + - 'bioconductor-oligoclasses >=1.46.0,<1.47.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-pd.fingene.1.0.st/post-link.sh b/recipes/bioconductor-pd.fingene.1.0.st/post-link.sh index 3eaab1bffc31b..5a25edb60f745 100644 --- a/recipes/bioconductor-pd.fingene.1.0.st/post-link.sh +++ b/recipes/bioconductor-pd.fingene.1.0.st/post-link.sh @@ -1,9 +1,10 @@ #!/bin/bash FN="pd.fingene.1.0.st_3.12.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/pd.fingene.1.0.st_3.12.0.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/pd.fingene.1.0.st_3.12.0.tar.gz" "https://bioarchive.galaxyproject.org/pd.fingene.1.0.st_3.12.0.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-pd.fingene.1.0.st/bioconductor-pd.fingene.1.0.st_3.12.0_src_all.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-pd.fingene.1.0.st/bioconductor-pd.fingene.1.0.st_3.12.0_src_all.tar.gz" ) MD5="b79e4f8a52cad3b62e32401bbe74603d" @@ -16,7 +17,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-pd.fingene.1.1.st/meta.yaml b/recipes/bioconductor-pd.fingene.1.1.st/meta.yaml index 6675c46159c45..f4a42c2697e1d 100644 --- a/recipes/bioconductor-pd.fingene.1.1.st/meta.yaml +++ b/recipes/bioconductor-pd.fingene.1.1.st/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.12.0" %} {% set name = "pd.fingene.1.1.st" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -12,31 +12,31 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 29030b14a0e8f8073874fb694a8c0c09 build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ noarch: generic requirements: host: - - 'bioconductor-biostrings >=2.50.0,<2.51.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-oligo >=1.46.0,<1.47.0' - - 'bioconductor-oligoclasses >=1.44.0,<1.45.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-biostrings >=2.52.0,<2.53.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-oligo >=1.48.0,<1.49.0' + - 'bioconductor-oligoclasses >=1.46.0,<1.47.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' run: - - 'bioconductor-biostrings >=2.50.0,<2.51.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-oligo >=1.46.0,<1.47.0' - - 'bioconductor-oligoclasses >=1.44.0,<1.45.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-biostrings >=2.52.0,<2.53.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-oligo >=1.48.0,<1.49.0' + - 'bioconductor-oligoclasses >=1.46.0,<1.47.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-pd.fingene.1.1.st/post-link.sh b/recipes/bioconductor-pd.fingene.1.1.st/post-link.sh index f372ffd255515..869092089b545 100644 --- a/recipes/bioconductor-pd.fingene.1.1.st/post-link.sh +++ b/recipes/bioconductor-pd.fingene.1.1.st/post-link.sh @@ -1,9 +1,10 @@ #!/bin/bash FN="pd.fingene.1.1.st_3.12.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/pd.fingene.1.1.st_3.12.0.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/pd.fingene.1.1.st_3.12.0.tar.gz" "https://bioarchive.galaxyproject.org/pd.fingene.1.1.st_3.12.0.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-pd.fingene.1.1.st/bioconductor-pd.fingene.1.1.st_3.12.0_src_all.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-pd.fingene.1.1.st/bioconductor-pd.fingene.1.1.st_3.12.0_src_all.tar.gz" ) MD5="29030b14a0e8f8073874fb694a8c0c09" @@ -16,7 +17,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-pd.genomewidesnp.5/meta.yaml b/recipes/bioconductor-pd.genomewidesnp.5/meta.yaml index e0ca4764fa82f..13617f386e211 100644 --- a/recipes/bioconductor-pd.genomewidesnp.5/meta.yaml +++ b/recipes/bioconductor-pd.genomewidesnp.5/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.14.1" %} {% set name = "pd.genomewidesnp.5" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -12,31 +12,31 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: d02255c861e82fca6a7445ada0c69e5d build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ noarch: generic requirements: host: - - 'bioconductor-biostrings >=2.50.0,<2.51.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-oligo >=1.46.0,<1.47.0' - - 'bioconductor-oligoclasses >=1.44.0,<1.45.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-biostrings >=2.52.0,<2.53.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-oligo >=1.48.0,<1.49.0' + - 'bioconductor-oligoclasses >=1.46.0,<1.47.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' run: - - 'bioconductor-biostrings >=2.50.0,<2.51.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-oligo >=1.46.0,<1.47.0' - - 'bioconductor-oligoclasses >=1.44.0,<1.45.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-biostrings >=2.52.0,<2.53.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-oligo >=1.48.0,<1.49.0' + - 'bioconductor-oligoclasses >=1.46.0,<1.47.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-pd.genomewidesnp.5/post-link.sh b/recipes/bioconductor-pd.genomewidesnp.5/post-link.sh index c375c3508fecc..b8e09448fe94d 100644 --- a/recipes/bioconductor-pd.genomewidesnp.5/post-link.sh +++ b/recipes/bioconductor-pd.genomewidesnp.5/post-link.sh @@ -1,9 +1,10 @@ #!/bin/bash FN="pd.genomewidesnp.5_3.14.1.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/pd.genomewidesnp.5_3.14.1.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/pd.genomewidesnp.5_3.14.1.tar.gz" "https://bioarchive.galaxyproject.org/pd.genomewidesnp.5_3.14.1.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-pd.genomewidesnp.5/bioconductor-pd.genomewidesnp.5_3.14.1_src_all.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-pd.genomewidesnp.5/bioconductor-pd.genomewidesnp.5_3.14.1_src_all.tar.gz" ) MD5="d02255c861e82fca6a7445ada0c69e5d" @@ -16,7 +17,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-pd.genomewidesnp.6/meta.yaml b/recipes/bioconductor-pd.genomewidesnp.6/meta.yaml index 31d01a87aa181..d18015d415c47 100644 --- a/recipes/bioconductor-pd.genomewidesnp.6/meta.yaml +++ b/recipes/bioconductor-pd.genomewidesnp.6/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.14.1" %} {% set name = "pd.genomewidesnp.6" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -12,31 +12,31 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 6e5369234e251c763f4f6c0220fbcb0c build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ noarch: generic requirements: host: - - 'bioconductor-biostrings >=2.50.0,<2.51.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-oligo >=1.46.0,<1.47.0' - - 'bioconductor-oligoclasses >=1.44.0,<1.45.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-biostrings >=2.52.0,<2.53.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-oligo >=1.48.0,<1.49.0' + - 'bioconductor-oligoclasses >=1.46.0,<1.47.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' run: - - 'bioconductor-biostrings >=2.50.0,<2.51.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-oligo >=1.46.0,<1.47.0' - - 'bioconductor-oligoclasses >=1.44.0,<1.45.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-biostrings >=2.52.0,<2.53.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-oligo >=1.48.0,<1.49.0' + - 'bioconductor-oligoclasses >=1.46.0,<1.47.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-pd.genomewidesnp.6/post-link.sh b/recipes/bioconductor-pd.genomewidesnp.6/post-link.sh index 0102fa0221f65..c47733d7781bd 100644 --- a/recipes/bioconductor-pd.genomewidesnp.6/post-link.sh +++ b/recipes/bioconductor-pd.genomewidesnp.6/post-link.sh @@ -1,9 +1,10 @@ #!/bin/bash FN="pd.genomewidesnp.6_3.14.1.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/pd.genomewidesnp.6_3.14.1.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/pd.genomewidesnp.6_3.14.1.tar.gz" "https://bioarchive.galaxyproject.org/pd.genomewidesnp.6_3.14.1.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-pd.genomewidesnp.6/bioconductor-pd.genomewidesnp.6_3.14.1_src_all.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-pd.genomewidesnp.6/bioconductor-pd.genomewidesnp.6_3.14.1_src_all.tar.gz" ) MD5="6e5369234e251c763f4f6c0220fbcb0c" @@ -16,7 +17,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-pd.guigene.1.0.st/meta.yaml b/recipes/bioconductor-pd.guigene.1.0.st/meta.yaml index 70a23e632291d..5e25e5485ab86 100644 --- a/recipes/bioconductor-pd.guigene.1.0.st/meta.yaml +++ b/recipes/bioconductor-pd.guigene.1.0.st/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.12.0" %} {% set name = "pd.guigene.1.0.st" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -12,31 +12,31 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 29fe31499931836af72ddd0c7d06acfa build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ noarch: generic requirements: host: - - 'bioconductor-biostrings >=2.50.0,<2.51.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-oligo >=1.46.0,<1.47.0' - - 'bioconductor-oligoclasses >=1.44.0,<1.45.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-biostrings >=2.52.0,<2.53.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-oligo >=1.48.0,<1.49.0' + - 'bioconductor-oligoclasses >=1.46.0,<1.47.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' run: - - 'bioconductor-biostrings >=2.50.0,<2.51.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-oligo >=1.46.0,<1.47.0' - - 'bioconductor-oligoclasses >=1.44.0,<1.45.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-biostrings >=2.52.0,<2.53.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-oligo >=1.48.0,<1.49.0' + - 'bioconductor-oligoclasses >=1.46.0,<1.47.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-pd.guigene.1.0.st/post-link.sh b/recipes/bioconductor-pd.guigene.1.0.st/post-link.sh index 3d4f555fa42ba..f4d2c817555a4 100644 --- a/recipes/bioconductor-pd.guigene.1.0.st/post-link.sh +++ b/recipes/bioconductor-pd.guigene.1.0.st/post-link.sh @@ -1,9 +1,10 @@ #!/bin/bash FN="pd.guigene.1.0.st_3.12.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/pd.guigene.1.0.st_3.12.0.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/pd.guigene.1.0.st_3.12.0.tar.gz" "https://bioarchive.galaxyproject.org/pd.guigene.1.0.st_3.12.0.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-pd.guigene.1.0.st/bioconductor-pd.guigene.1.0.st_3.12.0_src_all.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-pd.guigene.1.0.st/bioconductor-pd.guigene.1.0.st_3.12.0_src_all.tar.gz" ) MD5="29fe31499931836af72ddd0c7d06acfa" @@ -16,7 +17,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-pd.guigene.1.1.st/meta.yaml b/recipes/bioconductor-pd.guigene.1.1.st/meta.yaml index b41b1b441ca0f..951d66cff5879 100644 --- a/recipes/bioconductor-pd.guigene.1.1.st/meta.yaml +++ b/recipes/bioconductor-pd.guigene.1.1.st/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.12.0" %} {% set name = "pd.guigene.1.1.st" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -12,31 +12,31 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: aa3e0389c596a3676322104de5ad2358 build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ noarch: generic requirements: host: - - 'bioconductor-biostrings >=2.50.0,<2.51.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-oligo >=1.46.0,<1.47.0' - - 'bioconductor-oligoclasses >=1.44.0,<1.45.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-biostrings >=2.52.0,<2.53.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-oligo >=1.48.0,<1.49.0' + - 'bioconductor-oligoclasses >=1.46.0,<1.47.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' run: - - 'bioconductor-biostrings >=2.50.0,<2.51.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-oligo >=1.46.0,<1.47.0' - - 'bioconductor-oligoclasses >=1.44.0,<1.45.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-biostrings >=2.52.0,<2.53.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-oligo >=1.48.0,<1.49.0' + - 'bioconductor-oligoclasses >=1.46.0,<1.47.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-pd.guigene.1.1.st/post-link.sh b/recipes/bioconductor-pd.guigene.1.1.st/post-link.sh index ffa298288dd39..a057d7bcefc6a 100644 --- a/recipes/bioconductor-pd.guigene.1.1.st/post-link.sh +++ b/recipes/bioconductor-pd.guigene.1.1.st/post-link.sh @@ -1,9 +1,10 @@ #!/bin/bash FN="pd.guigene.1.1.st_3.12.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/pd.guigene.1.1.st_3.12.0.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/pd.guigene.1.1.st_3.12.0.tar.gz" "https://bioarchive.galaxyproject.org/pd.guigene.1.1.st_3.12.0.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-pd.guigene.1.1.st/bioconductor-pd.guigene.1.1.st_3.12.0_src_all.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-pd.guigene.1.1.st/bioconductor-pd.guigene.1.1.st_3.12.0_src_all.tar.gz" ) MD5="aa3e0389c596a3676322104de5ad2358" @@ -16,7 +17,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-pd.hc.g110/meta.yaml b/recipes/bioconductor-pd.hc.g110/meta.yaml index bcf46a6f68877..8e7464f638384 100644 --- a/recipes/bioconductor-pd.hc.g110/meta.yaml +++ b/recipes/bioconductor-pd.hc.g110/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.12.0" %} {% set name = "pd.hc.g110" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -12,31 +12,31 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 5c5418c588ed28e2fa088c7952c48b91 build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ noarch: generic requirements: host: - - 'bioconductor-biostrings >=2.50.0,<2.51.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-oligo >=1.46.0,<1.47.0' - - 'bioconductor-oligoclasses >=1.44.0,<1.45.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-biostrings >=2.52.0,<2.53.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-oligo >=1.48.0,<1.49.0' + - 'bioconductor-oligoclasses >=1.46.0,<1.47.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' run: - - 'bioconductor-biostrings >=2.50.0,<2.51.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-oligo >=1.46.0,<1.47.0' - - 'bioconductor-oligoclasses >=1.44.0,<1.45.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-biostrings >=2.52.0,<2.53.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-oligo >=1.48.0,<1.49.0' + - 'bioconductor-oligoclasses >=1.46.0,<1.47.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-pd.hc.g110/post-link.sh b/recipes/bioconductor-pd.hc.g110/post-link.sh index 9137af9411e05..f8b3cfc54aa71 100644 --- a/recipes/bioconductor-pd.hc.g110/post-link.sh +++ b/recipes/bioconductor-pd.hc.g110/post-link.sh @@ -1,9 +1,10 @@ #!/bin/bash FN="pd.hc.g110_3.12.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/pd.hc.g110_3.12.0.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/pd.hc.g110_3.12.0.tar.gz" "https://bioarchive.galaxyproject.org/pd.hc.g110_3.12.0.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-pd.hc.g110/bioconductor-pd.hc.g110_3.12.0_src_all.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-pd.hc.g110/bioconductor-pd.hc.g110_3.12.0_src_all.tar.gz" ) MD5="5c5418c588ed28e2fa088c7952c48b91" @@ -16,7 +17,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-pd.hg.focus/meta.yaml b/recipes/bioconductor-pd.hg.focus/meta.yaml index d8f0a81a7cf85..e0c8d1d55040b 100644 --- a/recipes/bioconductor-pd.hg.focus/meta.yaml +++ b/recipes/bioconductor-pd.hg.focus/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.12.0" %} {% set name = "pd.hg.focus" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -12,31 +12,31 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: a89f344ae7ff8061a8e7968f155f4bcf build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ noarch: generic requirements: host: - - 'bioconductor-biostrings >=2.50.0,<2.51.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-oligo >=1.46.0,<1.47.0' - - 'bioconductor-oligoclasses >=1.44.0,<1.45.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-biostrings >=2.52.0,<2.53.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-oligo >=1.48.0,<1.49.0' + - 'bioconductor-oligoclasses >=1.46.0,<1.47.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' run: - - 'bioconductor-biostrings >=2.50.0,<2.51.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-oligo >=1.46.0,<1.47.0' - - 'bioconductor-oligoclasses >=1.44.0,<1.45.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-biostrings >=2.52.0,<2.53.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-oligo >=1.48.0,<1.49.0' + - 'bioconductor-oligoclasses >=1.46.0,<1.47.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-pd.hg.focus/post-link.sh b/recipes/bioconductor-pd.hg.focus/post-link.sh index b459c1c819b82..599efe00bc669 100644 --- a/recipes/bioconductor-pd.hg.focus/post-link.sh +++ b/recipes/bioconductor-pd.hg.focus/post-link.sh @@ -1,9 +1,10 @@ #!/bin/bash FN="pd.hg.focus_3.12.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/pd.hg.focus_3.12.0.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/pd.hg.focus_3.12.0.tar.gz" "https://bioarchive.galaxyproject.org/pd.hg.focus_3.12.0.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-pd.hg.focus/bioconductor-pd.hg.focus_3.12.0_src_all.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-pd.hg.focus/bioconductor-pd.hg.focus_3.12.0_src_all.tar.gz" ) MD5="a89f344ae7ff8061a8e7968f155f4bcf" @@ -16,7 +17,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-pd.hg.u133.plus.2/meta.yaml b/recipes/bioconductor-pd.hg.u133.plus.2/meta.yaml index 78adae80ac122..3d76d1ba680dc 100644 --- a/recipes/bioconductor-pd.hg.u133.plus.2/meta.yaml +++ b/recipes/bioconductor-pd.hg.u133.plus.2/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.12.0" %} {% set name = "pd.hg.u133.plus.2" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -12,31 +12,31 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 8a87aa63c04e84266962bdde5226c06c build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ noarch: generic requirements: host: - - 'bioconductor-biostrings >=2.50.0,<2.51.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-oligo >=1.46.0,<1.47.0' - - 'bioconductor-oligoclasses >=1.44.0,<1.45.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-biostrings >=2.52.0,<2.53.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-oligo >=1.48.0,<1.49.0' + - 'bioconductor-oligoclasses >=1.46.0,<1.47.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' run: - - 'bioconductor-biostrings >=2.50.0,<2.51.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-oligo >=1.46.0,<1.47.0' - - 'bioconductor-oligoclasses >=1.44.0,<1.45.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-biostrings >=2.52.0,<2.53.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-oligo >=1.48.0,<1.49.0' + - 'bioconductor-oligoclasses >=1.46.0,<1.47.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-pd.hg.u133.plus.2/post-link.sh b/recipes/bioconductor-pd.hg.u133.plus.2/post-link.sh index a25d5c7815f34..39b99206e1686 100644 --- a/recipes/bioconductor-pd.hg.u133.plus.2/post-link.sh +++ b/recipes/bioconductor-pd.hg.u133.plus.2/post-link.sh @@ -1,9 +1,10 @@ #!/bin/bash FN="pd.hg.u133.plus.2_3.12.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/pd.hg.u133.plus.2_3.12.0.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/pd.hg.u133.plus.2_3.12.0.tar.gz" "https://bioarchive.galaxyproject.org/pd.hg.u133.plus.2_3.12.0.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-pd.hg.u133.plus.2/bioconductor-pd.hg.u133.plus.2_3.12.0_src_all.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-pd.hg.u133.plus.2/bioconductor-pd.hg.u133.plus.2_3.12.0_src_all.tar.gz" ) MD5="8a87aa63c04e84266962bdde5226c06c" @@ -16,7 +17,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-pd.hg.u133a.2/meta.yaml b/recipes/bioconductor-pd.hg.u133a.2/meta.yaml index 671580261d468..d236cb61a9abc 100644 --- a/recipes/bioconductor-pd.hg.u133a.2/meta.yaml +++ b/recipes/bioconductor-pd.hg.u133a.2/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.12.0" %} {% set name = "pd.hg.u133a.2" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -12,31 +12,31 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: a7941473bf081831fad4f4412023d9ee build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ noarch: generic requirements: host: - - 'bioconductor-biostrings >=2.50.0,<2.51.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-oligo >=1.46.0,<1.47.0' - - 'bioconductor-oligoclasses >=1.44.0,<1.45.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-biostrings >=2.52.0,<2.53.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-oligo >=1.48.0,<1.49.0' + - 'bioconductor-oligoclasses >=1.46.0,<1.47.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' run: - - 'bioconductor-biostrings >=2.50.0,<2.51.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-oligo >=1.46.0,<1.47.0' - - 'bioconductor-oligoclasses >=1.44.0,<1.45.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-biostrings >=2.52.0,<2.53.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-oligo >=1.48.0,<1.49.0' + - 'bioconductor-oligoclasses >=1.46.0,<1.47.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-pd.hg.u133a.2/post-link.sh b/recipes/bioconductor-pd.hg.u133a.2/post-link.sh index f9948b8a72d3f..3f09f45c6e6cc 100644 --- a/recipes/bioconductor-pd.hg.u133a.2/post-link.sh +++ b/recipes/bioconductor-pd.hg.u133a.2/post-link.sh @@ -1,9 +1,10 @@ #!/bin/bash FN="pd.hg.u133a.2_3.12.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/pd.hg.u133a.2_3.12.0.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/pd.hg.u133a.2_3.12.0.tar.gz" "https://bioarchive.galaxyproject.org/pd.hg.u133a.2_3.12.0.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-pd.hg.u133a.2/bioconductor-pd.hg.u133a.2_3.12.0_src_all.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-pd.hg.u133a.2/bioconductor-pd.hg.u133a.2_3.12.0_src_all.tar.gz" ) MD5="a7941473bf081831fad4f4412023d9ee" @@ -16,7 +17,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-pd.hg.u133a.tag/meta.yaml b/recipes/bioconductor-pd.hg.u133a.tag/meta.yaml index 3ae9c2cc9d075..73e53d6f7135d 100644 --- a/recipes/bioconductor-pd.hg.u133a.tag/meta.yaml +++ b/recipes/bioconductor-pd.hg.u133a.tag/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.12.0" %} {% set name = "pd.hg.u133a.tag" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -12,31 +12,31 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: e090383098d6e1062b290889fba065d5 build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ noarch: generic requirements: host: - - 'bioconductor-biostrings >=2.50.0,<2.51.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-oligo >=1.46.0,<1.47.0' - - 'bioconductor-oligoclasses >=1.44.0,<1.45.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-biostrings >=2.52.0,<2.53.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-oligo >=1.48.0,<1.49.0' + - 'bioconductor-oligoclasses >=1.46.0,<1.47.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' run: - - 'bioconductor-biostrings >=2.50.0,<2.51.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-oligo >=1.46.0,<1.47.0' - - 'bioconductor-oligoclasses >=1.44.0,<1.45.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-biostrings >=2.52.0,<2.53.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-oligo >=1.48.0,<1.49.0' + - 'bioconductor-oligoclasses >=1.46.0,<1.47.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-pd.hg.u133a.tag/post-link.sh b/recipes/bioconductor-pd.hg.u133a.tag/post-link.sh index f79e46beee695..5cdb98dc8fa5c 100644 --- a/recipes/bioconductor-pd.hg.u133a.tag/post-link.sh +++ b/recipes/bioconductor-pd.hg.u133a.tag/post-link.sh @@ -1,9 +1,10 @@ #!/bin/bash FN="pd.hg.u133a.tag_3.12.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/pd.hg.u133a.tag_3.12.0.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/pd.hg.u133a.tag_3.12.0.tar.gz" "https://bioarchive.galaxyproject.org/pd.hg.u133a.tag_3.12.0.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-pd.hg.u133a.tag/bioconductor-pd.hg.u133a.tag_3.12.0_src_all.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-pd.hg.u133a.tag/bioconductor-pd.hg.u133a.tag_3.12.0_src_all.tar.gz" ) MD5="e090383098d6e1062b290889fba065d5" @@ -16,7 +17,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-pd.hg.u133a/meta.yaml b/recipes/bioconductor-pd.hg.u133a/meta.yaml index 0c3b21de43fa9..6d6611e79f1b4 100644 --- a/recipes/bioconductor-pd.hg.u133a/meta.yaml +++ b/recipes/bioconductor-pd.hg.u133a/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.12.0" %} {% set name = "pd.hg.u133a" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -12,31 +12,31 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 05b4521f65ab294a5040a0c60198d22c build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ noarch: generic requirements: host: - - 'bioconductor-biostrings >=2.50.0,<2.51.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-oligo >=1.46.0,<1.47.0' - - 'bioconductor-oligoclasses >=1.44.0,<1.45.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-biostrings >=2.52.0,<2.53.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-oligo >=1.48.0,<1.49.0' + - 'bioconductor-oligoclasses >=1.46.0,<1.47.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' run: - - 'bioconductor-biostrings >=2.50.0,<2.51.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-oligo >=1.46.0,<1.47.0' - - 'bioconductor-oligoclasses >=1.44.0,<1.45.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-biostrings >=2.52.0,<2.53.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-oligo >=1.48.0,<1.49.0' + - 'bioconductor-oligoclasses >=1.46.0,<1.47.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-pd.hg.u133a/post-link.sh b/recipes/bioconductor-pd.hg.u133a/post-link.sh index cb30da469c283..3cc7238966ead 100644 --- a/recipes/bioconductor-pd.hg.u133a/post-link.sh +++ b/recipes/bioconductor-pd.hg.u133a/post-link.sh @@ -1,9 +1,10 @@ #!/bin/bash FN="pd.hg.u133a_3.12.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/pd.hg.u133a_3.12.0.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/pd.hg.u133a_3.12.0.tar.gz" "https://bioarchive.galaxyproject.org/pd.hg.u133a_3.12.0.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-pd.hg.u133a/bioconductor-pd.hg.u133a_3.12.0_src_all.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-pd.hg.u133a/bioconductor-pd.hg.u133a_3.12.0_src_all.tar.gz" ) MD5="05b4521f65ab294a5040a0c60198d22c" @@ -16,7 +17,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-pd.hg.u133b/meta.yaml b/recipes/bioconductor-pd.hg.u133b/meta.yaml index e583674f2c5a7..33ec153e85dcf 100644 --- a/recipes/bioconductor-pd.hg.u133b/meta.yaml +++ b/recipes/bioconductor-pd.hg.u133b/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.12.0" %} {% set name = "pd.hg.u133b" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -12,31 +12,31 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: c5eac82ad7480571b9f2b442b4a8faa6 build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ noarch: generic requirements: host: - - 'bioconductor-biostrings >=2.50.0,<2.51.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-oligo >=1.46.0,<1.47.0' - - 'bioconductor-oligoclasses >=1.44.0,<1.45.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-biostrings >=2.52.0,<2.53.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-oligo >=1.48.0,<1.49.0' + - 'bioconductor-oligoclasses >=1.46.0,<1.47.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' run: - - 'bioconductor-biostrings >=2.50.0,<2.51.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-oligo >=1.46.0,<1.47.0' - - 'bioconductor-oligoclasses >=1.44.0,<1.45.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-biostrings >=2.52.0,<2.53.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-oligo >=1.48.0,<1.49.0' + - 'bioconductor-oligoclasses >=1.46.0,<1.47.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-pd.hg.u133b/post-link.sh b/recipes/bioconductor-pd.hg.u133b/post-link.sh index 9d3f10b09a49c..2016c623185c2 100644 --- a/recipes/bioconductor-pd.hg.u133b/post-link.sh +++ b/recipes/bioconductor-pd.hg.u133b/post-link.sh @@ -1,9 +1,10 @@ #!/bin/bash FN="pd.hg.u133b_3.12.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/pd.hg.u133b_3.12.0.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/pd.hg.u133b_3.12.0.tar.gz" "https://bioarchive.galaxyproject.org/pd.hg.u133b_3.12.0.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-pd.hg.u133b/bioconductor-pd.hg.u133b_3.12.0_src_all.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-pd.hg.u133b/bioconductor-pd.hg.u133b_3.12.0_src_all.tar.gz" ) MD5="c5eac82ad7480571b9f2b442b4a8faa6" @@ -16,7 +17,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-pd.hg.u219/meta.yaml b/recipes/bioconductor-pd.hg.u219/meta.yaml index 71afd04fa8078..b8d2eaa140551 100644 --- a/recipes/bioconductor-pd.hg.u219/meta.yaml +++ b/recipes/bioconductor-pd.hg.u219/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.12.0" %} {% set name = "pd.hg.u219" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -12,31 +12,31 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: dab073d315af47ff3001c72a6d1e7972 build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ noarch: generic requirements: host: - - 'bioconductor-biostrings >=2.50.0,<2.51.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-oligo >=1.46.0,<1.47.0' - - 'bioconductor-oligoclasses >=1.44.0,<1.45.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-biostrings >=2.52.0,<2.53.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-oligo >=1.48.0,<1.49.0' + - 'bioconductor-oligoclasses >=1.46.0,<1.47.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' run: - - 'bioconductor-biostrings >=2.50.0,<2.51.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-oligo >=1.46.0,<1.47.0' - - 'bioconductor-oligoclasses >=1.44.0,<1.45.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-biostrings >=2.52.0,<2.53.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-oligo >=1.48.0,<1.49.0' + - 'bioconductor-oligoclasses >=1.46.0,<1.47.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-pd.hg.u219/post-link.sh b/recipes/bioconductor-pd.hg.u219/post-link.sh index 568dc042368e9..fc7055109e251 100644 --- a/recipes/bioconductor-pd.hg.u219/post-link.sh +++ b/recipes/bioconductor-pd.hg.u219/post-link.sh @@ -1,9 +1,10 @@ #!/bin/bash FN="pd.hg.u219_3.12.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/pd.hg.u219_3.12.0.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/pd.hg.u219_3.12.0.tar.gz" "https://bioarchive.galaxyproject.org/pd.hg.u219_3.12.0.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-pd.hg.u219/bioconductor-pd.hg.u219_3.12.0_src_all.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-pd.hg.u219/bioconductor-pd.hg.u219_3.12.0_src_all.tar.gz" ) MD5="dab073d315af47ff3001c72a6d1e7972" @@ -16,7 +17,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-pd.hg.u95a/meta.yaml b/recipes/bioconductor-pd.hg.u95a/meta.yaml index a0e7b7a5a45f8..5d30d18c7ee51 100644 --- a/recipes/bioconductor-pd.hg.u95a/meta.yaml +++ b/recipes/bioconductor-pd.hg.u95a/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.12.0" %} {% set name = "pd.hg.u95a" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -12,31 +12,31 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: a9ad7d6a085e0e3ed7623902e7810da0 build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ noarch: generic requirements: host: - - 'bioconductor-biostrings >=2.50.0,<2.51.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-oligo >=1.46.0,<1.47.0' - - 'bioconductor-oligoclasses >=1.44.0,<1.45.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-biostrings >=2.52.0,<2.53.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-oligo >=1.48.0,<1.49.0' + - 'bioconductor-oligoclasses >=1.46.0,<1.47.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' run: - - 'bioconductor-biostrings >=2.50.0,<2.51.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-oligo >=1.46.0,<1.47.0' - - 'bioconductor-oligoclasses >=1.44.0,<1.45.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-biostrings >=2.52.0,<2.53.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-oligo >=1.48.0,<1.49.0' + - 'bioconductor-oligoclasses >=1.46.0,<1.47.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-pd.hg.u95a/post-link.sh b/recipes/bioconductor-pd.hg.u95a/post-link.sh index b7b663d097dd3..7c81fb12c48a5 100644 --- a/recipes/bioconductor-pd.hg.u95a/post-link.sh +++ b/recipes/bioconductor-pd.hg.u95a/post-link.sh @@ -1,9 +1,10 @@ #!/bin/bash FN="pd.hg.u95a_3.12.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/pd.hg.u95a_3.12.0.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/pd.hg.u95a_3.12.0.tar.gz" "https://bioarchive.galaxyproject.org/pd.hg.u95a_3.12.0.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-pd.hg.u95a/bioconductor-pd.hg.u95a_3.12.0_src_all.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-pd.hg.u95a/bioconductor-pd.hg.u95a_3.12.0_src_all.tar.gz" ) MD5="a9ad7d6a085e0e3ed7623902e7810da0" @@ -16,7 +17,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-pd.hg.u95av2/meta.yaml b/recipes/bioconductor-pd.hg.u95av2/meta.yaml index cab257d09afad..cd58f3d753d6e 100644 --- a/recipes/bioconductor-pd.hg.u95av2/meta.yaml +++ b/recipes/bioconductor-pd.hg.u95av2/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.12.0" %} {% set name = "pd.hg.u95av2" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -12,31 +12,31 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 3a4182b529bc07ec91277a95b1462468 build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ noarch: generic requirements: host: - - 'bioconductor-biostrings >=2.50.0,<2.51.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-oligo >=1.46.0,<1.47.0' - - 'bioconductor-oligoclasses >=1.44.0,<1.45.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-biostrings >=2.52.0,<2.53.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-oligo >=1.48.0,<1.49.0' + - 'bioconductor-oligoclasses >=1.46.0,<1.47.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' run: - - 'bioconductor-biostrings >=2.50.0,<2.51.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-oligo >=1.46.0,<1.47.0' - - 'bioconductor-oligoclasses >=1.44.0,<1.45.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-biostrings >=2.52.0,<2.53.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-oligo >=1.48.0,<1.49.0' + - 'bioconductor-oligoclasses >=1.46.0,<1.47.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-pd.hg.u95av2/post-link.sh b/recipes/bioconductor-pd.hg.u95av2/post-link.sh index 9e7d9913d7b5b..0eaddc01d341e 100644 --- a/recipes/bioconductor-pd.hg.u95av2/post-link.sh +++ b/recipes/bioconductor-pd.hg.u95av2/post-link.sh @@ -1,9 +1,10 @@ #!/bin/bash FN="pd.hg.u95av2_3.12.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/pd.hg.u95av2_3.12.0.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/pd.hg.u95av2_3.12.0.tar.gz" "https://bioarchive.galaxyproject.org/pd.hg.u95av2_3.12.0.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-pd.hg.u95av2/bioconductor-pd.hg.u95av2_3.12.0_src_all.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-pd.hg.u95av2/bioconductor-pd.hg.u95av2_3.12.0_src_all.tar.gz" ) MD5="3a4182b529bc07ec91277a95b1462468" @@ -16,7 +17,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-pd.hg.u95b/meta.yaml b/recipes/bioconductor-pd.hg.u95b/meta.yaml index a8b20f16bfcee..68991168757f2 100644 --- a/recipes/bioconductor-pd.hg.u95b/meta.yaml +++ b/recipes/bioconductor-pd.hg.u95b/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.12.0" %} {% set name = "pd.hg.u95b" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -12,31 +12,31 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: a7f10f91e920e191c5009fac8ca79c24 build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ noarch: generic requirements: host: - - 'bioconductor-biostrings >=2.50.0,<2.51.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-oligo >=1.46.0,<1.47.0' - - 'bioconductor-oligoclasses >=1.44.0,<1.45.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-biostrings >=2.52.0,<2.53.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-oligo >=1.48.0,<1.49.0' + - 'bioconductor-oligoclasses >=1.46.0,<1.47.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' run: - - 'bioconductor-biostrings >=2.50.0,<2.51.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-oligo >=1.46.0,<1.47.0' - - 'bioconductor-oligoclasses >=1.44.0,<1.45.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-biostrings >=2.52.0,<2.53.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-oligo >=1.48.0,<1.49.0' + - 'bioconductor-oligoclasses >=1.46.0,<1.47.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-pd.hg.u95b/post-link.sh b/recipes/bioconductor-pd.hg.u95b/post-link.sh index 31329bba8a115..ae7dd6f24b5f3 100644 --- a/recipes/bioconductor-pd.hg.u95b/post-link.sh +++ b/recipes/bioconductor-pd.hg.u95b/post-link.sh @@ -1,9 +1,10 @@ #!/bin/bash FN="pd.hg.u95b_3.12.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/pd.hg.u95b_3.12.0.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/pd.hg.u95b_3.12.0.tar.gz" "https://bioarchive.galaxyproject.org/pd.hg.u95b_3.12.0.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-pd.hg.u95b/bioconductor-pd.hg.u95b_3.12.0_src_all.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-pd.hg.u95b/bioconductor-pd.hg.u95b_3.12.0_src_all.tar.gz" ) MD5="a7f10f91e920e191c5009fac8ca79c24" @@ -16,7 +17,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-pd.hg.u95c/meta.yaml b/recipes/bioconductor-pd.hg.u95c/meta.yaml index 1197616ee4bf0..22c9a11d4950c 100644 --- a/recipes/bioconductor-pd.hg.u95c/meta.yaml +++ b/recipes/bioconductor-pd.hg.u95c/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.12.0" %} {% set name = "pd.hg.u95c" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -12,31 +12,31 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 85655bf7a9ecd7aaa867e05899c5e3e4 build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ noarch: generic requirements: host: - - 'bioconductor-biostrings >=2.50.0,<2.51.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-oligo >=1.46.0,<1.47.0' - - 'bioconductor-oligoclasses >=1.44.0,<1.45.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-biostrings >=2.52.0,<2.53.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-oligo >=1.48.0,<1.49.0' + - 'bioconductor-oligoclasses >=1.46.0,<1.47.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' run: - - 'bioconductor-biostrings >=2.50.0,<2.51.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-oligo >=1.46.0,<1.47.0' - - 'bioconductor-oligoclasses >=1.44.0,<1.45.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-biostrings >=2.52.0,<2.53.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-oligo >=1.48.0,<1.49.0' + - 'bioconductor-oligoclasses >=1.46.0,<1.47.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-pd.hg.u95c/post-link.sh b/recipes/bioconductor-pd.hg.u95c/post-link.sh index 37f08145fbbbf..877f1c38551a2 100644 --- a/recipes/bioconductor-pd.hg.u95c/post-link.sh +++ b/recipes/bioconductor-pd.hg.u95c/post-link.sh @@ -1,9 +1,10 @@ #!/bin/bash FN="pd.hg.u95c_3.12.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/pd.hg.u95c_3.12.0.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/pd.hg.u95c_3.12.0.tar.gz" "https://bioarchive.galaxyproject.org/pd.hg.u95c_3.12.0.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-pd.hg.u95c/bioconductor-pd.hg.u95c_3.12.0_src_all.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-pd.hg.u95c/bioconductor-pd.hg.u95c_3.12.0_src_all.tar.gz" ) MD5="85655bf7a9ecd7aaa867e05899c5e3e4" @@ -16,7 +17,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-pd.hg.u95d/meta.yaml b/recipes/bioconductor-pd.hg.u95d/meta.yaml index 854904b189322..c7d29da79e788 100644 --- a/recipes/bioconductor-pd.hg.u95d/meta.yaml +++ b/recipes/bioconductor-pd.hg.u95d/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.12.0" %} {% set name = "pd.hg.u95d" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -12,31 +12,31 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 946701ecfc9cccb46aaeb57a4d6fe1c5 build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ noarch: generic requirements: host: - - 'bioconductor-biostrings >=2.50.0,<2.51.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-oligo >=1.46.0,<1.47.0' - - 'bioconductor-oligoclasses >=1.44.0,<1.45.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-biostrings >=2.52.0,<2.53.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-oligo >=1.48.0,<1.49.0' + - 'bioconductor-oligoclasses >=1.46.0,<1.47.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' run: - - 'bioconductor-biostrings >=2.50.0,<2.51.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-oligo >=1.46.0,<1.47.0' - - 'bioconductor-oligoclasses >=1.44.0,<1.45.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-biostrings >=2.52.0,<2.53.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-oligo >=1.48.0,<1.49.0' + - 'bioconductor-oligoclasses >=1.46.0,<1.47.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-pd.hg.u95d/post-link.sh b/recipes/bioconductor-pd.hg.u95d/post-link.sh index 4481a3b1e83f0..c4d05cd7beaf0 100644 --- a/recipes/bioconductor-pd.hg.u95d/post-link.sh +++ b/recipes/bioconductor-pd.hg.u95d/post-link.sh @@ -1,9 +1,10 @@ #!/bin/bash FN="pd.hg.u95d_3.12.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/pd.hg.u95d_3.12.0.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/pd.hg.u95d_3.12.0.tar.gz" "https://bioarchive.galaxyproject.org/pd.hg.u95d_3.12.0.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-pd.hg.u95d/bioconductor-pd.hg.u95d_3.12.0_src_all.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-pd.hg.u95d/bioconductor-pd.hg.u95d_3.12.0_src_all.tar.gz" ) MD5="946701ecfc9cccb46aaeb57a4d6fe1c5" @@ -16,7 +17,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-pd.hg.u95e/meta.yaml b/recipes/bioconductor-pd.hg.u95e/meta.yaml index ca1efd9e89962..a526d5f585ba5 100644 --- a/recipes/bioconductor-pd.hg.u95e/meta.yaml +++ b/recipes/bioconductor-pd.hg.u95e/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.12.0" %} {% set name = "pd.hg.u95e" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -12,31 +12,31 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 9295e2fd1b4be6ff58477ea5a5de45ee build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ noarch: generic requirements: host: - - 'bioconductor-biostrings >=2.50.0,<2.51.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-oligo >=1.46.0,<1.47.0' - - 'bioconductor-oligoclasses >=1.44.0,<1.45.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-biostrings >=2.52.0,<2.53.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-oligo >=1.48.0,<1.49.0' + - 'bioconductor-oligoclasses >=1.46.0,<1.47.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' run: - - 'bioconductor-biostrings >=2.50.0,<2.51.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-oligo >=1.46.0,<1.47.0' - - 'bioconductor-oligoclasses >=1.44.0,<1.45.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-biostrings >=2.52.0,<2.53.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-oligo >=1.48.0,<1.49.0' + - 'bioconductor-oligoclasses >=1.46.0,<1.47.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-pd.hg.u95e/post-link.sh b/recipes/bioconductor-pd.hg.u95e/post-link.sh index 0cc7e31503076..e4aa0c7ed60ea 100644 --- a/recipes/bioconductor-pd.hg.u95e/post-link.sh +++ b/recipes/bioconductor-pd.hg.u95e/post-link.sh @@ -1,9 +1,10 @@ #!/bin/bash FN="pd.hg.u95e_3.12.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/pd.hg.u95e_3.12.0.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/pd.hg.u95e_3.12.0.tar.gz" "https://bioarchive.galaxyproject.org/pd.hg.u95e_3.12.0.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-pd.hg.u95e/bioconductor-pd.hg.u95e_3.12.0_src_all.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-pd.hg.u95e/bioconductor-pd.hg.u95e_3.12.0_src_all.tar.gz" ) MD5="9295e2fd1b4be6ff58477ea5a5de45ee" @@ -16,7 +17,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-pd.hg18.60mer.expr/meta.yaml b/recipes/bioconductor-pd.hg18.60mer.expr/meta.yaml index 1c90f86056a36..60fe60596e1bd 100644 --- a/recipes/bioconductor-pd.hg18.60mer.expr/meta.yaml +++ b/recipes/bioconductor-pd.hg18.60mer.expr/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.12.0" %} {% set name = "pd.hg18.60mer.expr" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -12,31 +12,31 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: ee8d3813f74edce4e796933aa63999fb build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ noarch: generic requirements: host: - - 'bioconductor-biostrings >=2.50.0,<2.51.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-oligo >=1.46.0,<1.47.0' - - 'bioconductor-oligoclasses >=1.44.0,<1.45.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-biostrings >=2.52.0,<2.53.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-oligo >=1.48.0,<1.49.0' + - 'bioconductor-oligoclasses >=1.46.0,<1.47.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' run: - - 'bioconductor-biostrings >=2.50.0,<2.51.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-oligo >=1.46.0,<1.47.0' - - 'bioconductor-oligoclasses >=1.44.0,<1.45.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-biostrings >=2.52.0,<2.53.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-oligo >=1.48.0,<1.49.0' + - 'bioconductor-oligoclasses >=1.46.0,<1.47.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-pd.hg18.60mer.expr/post-link.sh b/recipes/bioconductor-pd.hg18.60mer.expr/post-link.sh index 3921c9d1a6f2a..55824b93a0a6a 100644 --- a/recipes/bioconductor-pd.hg18.60mer.expr/post-link.sh +++ b/recipes/bioconductor-pd.hg18.60mer.expr/post-link.sh @@ -1,9 +1,10 @@ #!/bin/bash FN="pd.hg18.60mer.expr_3.12.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/pd.hg18.60mer.expr_3.12.0.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/pd.hg18.60mer.expr_3.12.0.tar.gz" "https://bioarchive.galaxyproject.org/pd.hg18.60mer.expr_3.12.0.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-pd.hg18.60mer.expr/bioconductor-pd.hg18.60mer.expr_3.12.0_src_all.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-pd.hg18.60mer.expr/bioconductor-pd.hg18.60mer.expr_3.12.0_src_all.tar.gz" ) MD5="ee8d3813f74edce4e796933aa63999fb" @@ -16,7 +17,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-pd.ht.hg.u133.plus.pm/meta.yaml b/recipes/bioconductor-pd.ht.hg.u133.plus.pm/meta.yaml index be2bbe27053b3..a5d8d9d676752 100644 --- a/recipes/bioconductor-pd.ht.hg.u133.plus.pm/meta.yaml +++ b/recipes/bioconductor-pd.ht.hg.u133.plus.pm/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.12.0" %} {% set name = "pd.ht.hg.u133.plus.pm" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -12,31 +12,31 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 5b1c3dd0ab3f8b21154982c197512a7c build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ noarch: generic requirements: host: - - 'bioconductor-biostrings >=2.50.0,<2.51.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-oligo >=1.46.0,<1.47.0' - - 'bioconductor-oligoclasses >=1.44.0,<1.45.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-biostrings >=2.52.0,<2.53.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-oligo >=1.48.0,<1.49.0' + - 'bioconductor-oligoclasses >=1.46.0,<1.47.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' run: - - 'bioconductor-biostrings >=2.50.0,<2.51.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-oligo >=1.46.0,<1.47.0' - - 'bioconductor-oligoclasses >=1.44.0,<1.45.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-biostrings >=2.52.0,<2.53.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-oligo >=1.48.0,<1.49.0' + - 'bioconductor-oligoclasses >=1.46.0,<1.47.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-pd.ht.hg.u133.plus.pm/post-link.sh b/recipes/bioconductor-pd.ht.hg.u133.plus.pm/post-link.sh index cd9e2bfda9a6f..1c09dd34b2ff7 100644 --- a/recipes/bioconductor-pd.ht.hg.u133.plus.pm/post-link.sh +++ b/recipes/bioconductor-pd.ht.hg.u133.plus.pm/post-link.sh @@ -1,9 +1,10 @@ #!/bin/bash FN="pd.ht.hg.u133.plus.pm_3.12.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/pd.ht.hg.u133.plus.pm_3.12.0.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/pd.ht.hg.u133.plus.pm_3.12.0.tar.gz" "https://bioarchive.galaxyproject.org/pd.ht.hg.u133.plus.pm_3.12.0.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-pd.ht.hg.u133.plus.pm/bioconductor-pd.ht.hg.u133.plus.pm_3.12.0_src_all.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-pd.ht.hg.u133.plus.pm/bioconductor-pd.ht.hg.u133.plus.pm_3.12.0_src_all.tar.gz" ) MD5="5b1c3dd0ab3f8b21154982c197512a7c" @@ -16,7 +17,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-pd.ht.hg.u133a/meta.yaml b/recipes/bioconductor-pd.ht.hg.u133a/meta.yaml index 1f30b170f4240..5e1133d4ead2a 100644 --- a/recipes/bioconductor-pd.ht.hg.u133a/meta.yaml +++ b/recipes/bioconductor-pd.ht.hg.u133a/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.12.0" %} {% set name = "pd.ht.hg.u133a" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -12,31 +12,31 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 80a82f43083f95e1e9f5e2e2da2e288e build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ noarch: generic requirements: host: - - 'bioconductor-biostrings >=2.50.0,<2.51.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-oligo >=1.46.0,<1.47.0' - - 'bioconductor-oligoclasses >=1.44.0,<1.45.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-biostrings >=2.52.0,<2.53.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-oligo >=1.48.0,<1.49.0' + - 'bioconductor-oligoclasses >=1.46.0,<1.47.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' run: - - 'bioconductor-biostrings >=2.50.0,<2.51.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-oligo >=1.46.0,<1.47.0' - - 'bioconductor-oligoclasses >=1.44.0,<1.45.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-biostrings >=2.52.0,<2.53.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-oligo >=1.48.0,<1.49.0' + - 'bioconductor-oligoclasses >=1.46.0,<1.47.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-pd.ht.hg.u133a/post-link.sh b/recipes/bioconductor-pd.ht.hg.u133a/post-link.sh index c15cfd5c6df0b..1b0355dd4c286 100644 --- a/recipes/bioconductor-pd.ht.hg.u133a/post-link.sh +++ b/recipes/bioconductor-pd.ht.hg.u133a/post-link.sh @@ -1,9 +1,10 @@ #!/bin/bash FN="pd.ht.hg.u133a_3.12.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/pd.ht.hg.u133a_3.12.0.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/pd.ht.hg.u133a_3.12.0.tar.gz" "https://bioarchive.galaxyproject.org/pd.ht.hg.u133a_3.12.0.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-pd.ht.hg.u133a/bioconductor-pd.ht.hg.u133a_3.12.0_src_all.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-pd.ht.hg.u133a/bioconductor-pd.ht.hg.u133a_3.12.0_src_all.tar.gz" ) MD5="80a82f43083f95e1e9f5e2e2da2e288e" @@ -16,7 +17,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-pd.ht.mg.430a/meta.yaml b/recipes/bioconductor-pd.ht.mg.430a/meta.yaml index 7fef8da9d1497..abea6162c9ea5 100644 --- a/recipes/bioconductor-pd.ht.mg.430a/meta.yaml +++ b/recipes/bioconductor-pd.ht.mg.430a/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.12.0" %} {% set name = "pd.ht.mg.430a" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -12,31 +12,31 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 65ea4fae22d21ad70998ba3ea034dcc0 build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ noarch: generic requirements: host: - - 'bioconductor-biostrings >=2.50.0,<2.51.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-oligo >=1.46.0,<1.47.0' - - 'bioconductor-oligoclasses >=1.44.0,<1.45.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-biostrings >=2.52.0,<2.53.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-oligo >=1.48.0,<1.49.0' + - 'bioconductor-oligoclasses >=1.46.0,<1.47.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' run: - - 'bioconductor-biostrings >=2.50.0,<2.51.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-oligo >=1.46.0,<1.47.0' - - 'bioconductor-oligoclasses >=1.44.0,<1.45.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-biostrings >=2.52.0,<2.53.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-oligo >=1.48.0,<1.49.0' + - 'bioconductor-oligoclasses >=1.46.0,<1.47.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-pd.ht.mg.430a/post-link.sh b/recipes/bioconductor-pd.ht.mg.430a/post-link.sh index fb26eeb510fde..fe8ad0735a024 100644 --- a/recipes/bioconductor-pd.ht.mg.430a/post-link.sh +++ b/recipes/bioconductor-pd.ht.mg.430a/post-link.sh @@ -1,9 +1,10 @@ #!/bin/bash FN="pd.ht.mg.430a_3.12.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/pd.ht.mg.430a_3.12.0.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/pd.ht.mg.430a_3.12.0.tar.gz" "https://bioarchive.galaxyproject.org/pd.ht.mg.430a_3.12.0.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-pd.ht.mg.430a/bioconductor-pd.ht.mg.430a_3.12.0_src_all.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-pd.ht.mg.430a/bioconductor-pd.ht.mg.430a_3.12.0_src_all.tar.gz" ) MD5="65ea4fae22d21ad70998ba3ea034dcc0" @@ -16,7 +17,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-pd.hta.2.0/meta.yaml b/recipes/bioconductor-pd.hta.2.0/meta.yaml index 22fd2e74bbc83..9b91329f998be 100644 --- a/recipes/bioconductor-pd.hta.2.0/meta.yaml +++ b/recipes/bioconductor-pd.hta.2.0/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.12.2" %} {% set name = "pd.hta.2.0" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -12,31 +12,31 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 8e13f85ece49c38da73eaf7b2247f5f0 build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ noarch: generic requirements: host: - - 'bioconductor-biostrings >=2.50.0,<2.51.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-oligo >=1.46.0,<1.47.0' - - 'bioconductor-oligoclasses >=1.44.0,<1.45.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-biostrings >=2.52.0,<2.53.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-oligo >=1.48.0,<1.49.0' + - 'bioconductor-oligoclasses >=1.46.0,<1.47.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' run: - - 'bioconductor-biostrings >=2.50.0,<2.51.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-oligo >=1.46.0,<1.47.0' - - 'bioconductor-oligoclasses >=1.44.0,<1.45.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-biostrings >=2.52.0,<2.53.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-oligo >=1.48.0,<1.49.0' + - 'bioconductor-oligoclasses >=1.46.0,<1.47.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-pd.hta.2.0/post-link.sh b/recipes/bioconductor-pd.hta.2.0/post-link.sh index f344df59892aa..d39302f0a4c21 100644 --- a/recipes/bioconductor-pd.hta.2.0/post-link.sh +++ b/recipes/bioconductor-pd.hta.2.0/post-link.sh @@ -1,9 +1,10 @@ #!/bin/bash FN="pd.hta.2.0_3.12.2.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/pd.hta.2.0_3.12.2.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/pd.hta.2.0_3.12.2.tar.gz" "https://bioarchive.galaxyproject.org/pd.hta.2.0_3.12.2.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-pd.hta.2.0/bioconductor-pd.hta.2.0_3.12.2_src_all.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-pd.hta.2.0/bioconductor-pd.hta.2.0_3.12.2_src_all.tar.gz" ) MD5="8e13f85ece49c38da73eaf7b2247f5f0" @@ -16,7 +17,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-pd.hu6800/meta.yaml b/recipes/bioconductor-pd.hu6800/meta.yaml index 1f61fa9012872..951de974bb597 100644 --- a/recipes/bioconductor-pd.hu6800/meta.yaml +++ b/recipes/bioconductor-pd.hu6800/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.12.0" %} {% set name = "pd.hu6800" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -12,31 +12,31 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 9a3a3edde6d6f31b9e90dc32aa68875d build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ noarch: generic requirements: host: - - 'bioconductor-biostrings >=2.50.0,<2.51.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-oligo >=1.46.0,<1.47.0' - - 'bioconductor-oligoclasses >=1.44.0,<1.45.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-biostrings >=2.52.0,<2.53.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-oligo >=1.48.0,<1.49.0' + - 'bioconductor-oligoclasses >=1.46.0,<1.47.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' run: - - 'bioconductor-biostrings >=2.50.0,<2.51.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-oligo >=1.46.0,<1.47.0' - - 'bioconductor-oligoclasses >=1.44.0,<1.45.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-biostrings >=2.52.0,<2.53.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-oligo >=1.48.0,<1.49.0' + - 'bioconductor-oligoclasses >=1.46.0,<1.47.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-pd.hu6800/post-link.sh b/recipes/bioconductor-pd.hu6800/post-link.sh index 804544b0486c9..2546aae678894 100644 --- a/recipes/bioconductor-pd.hu6800/post-link.sh +++ b/recipes/bioconductor-pd.hu6800/post-link.sh @@ -1,9 +1,10 @@ #!/bin/bash FN="pd.hu6800_3.12.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/pd.hu6800_3.12.0.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/pd.hu6800_3.12.0.tar.gz" "https://bioarchive.galaxyproject.org/pd.hu6800_3.12.0.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-pd.hu6800/bioconductor-pd.hu6800_3.12.0_src_all.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-pd.hu6800/bioconductor-pd.hu6800_3.12.0_src_all.tar.gz" ) MD5="9a3a3edde6d6f31b9e90dc32aa68875d" @@ -16,7 +17,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-pd.huex.1.0.st.v2/meta.yaml b/recipes/bioconductor-pd.huex.1.0.st.v2/meta.yaml index c7c78ec2b31ac..a833a5dc67aae 100644 --- a/recipes/bioconductor-pd.huex.1.0.st.v2/meta.yaml +++ b/recipes/bioconductor-pd.huex.1.0.st.v2/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.14.1" %} {% set name = "pd.huex.1.0.st.v2" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -12,31 +12,31 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: f4c4836c53447890b75b012efbdef3e9 build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ noarch: generic requirements: host: - - 'bioconductor-biostrings >=2.50.0,<2.51.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-oligo >=1.46.0,<1.47.0' - - 'bioconductor-oligoclasses >=1.44.0,<1.45.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-biostrings >=2.52.0,<2.53.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-oligo >=1.48.0,<1.49.0' + - 'bioconductor-oligoclasses >=1.46.0,<1.47.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' run: - - 'bioconductor-biostrings >=2.50.0,<2.51.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-oligo >=1.46.0,<1.47.0' - - 'bioconductor-oligoclasses >=1.44.0,<1.45.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-biostrings >=2.52.0,<2.53.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-oligo >=1.48.0,<1.49.0' + - 'bioconductor-oligoclasses >=1.46.0,<1.47.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-pd.huex.1.0.st.v2/post-link.sh b/recipes/bioconductor-pd.huex.1.0.st.v2/post-link.sh index 23d37dc1adba3..cc6bbd355057b 100644 --- a/recipes/bioconductor-pd.huex.1.0.st.v2/post-link.sh +++ b/recipes/bioconductor-pd.huex.1.0.st.v2/post-link.sh @@ -1,9 +1,10 @@ #!/bin/bash FN="pd.huex.1.0.st.v2_3.14.1.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/pd.huex.1.0.st.v2_3.14.1.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/pd.huex.1.0.st.v2_3.14.1.tar.gz" "https://bioarchive.galaxyproject.org/pd.huex.1.0.st.v2_3.14.1.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-pd.huex.1.0.st.v2/bioconductor-pd.huex.1.0.st.v2_3.14.1_src_all.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-pd.huex.1.0.st.v2/bioconductor-pd.huex.1.0.st.v2_3.14.1_src_all.tar.gz" ) MD5="f4c4836c53447890b75b012efbdef3e9" @@ -16,7 +17,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-pd.hugene.1.0.st.v1/meta.yaml b/recipes/bioconductor-pd.hugene.1.0.st.v1/meta.yaml index 9f01db74671ee..47ca9f5b3b3fb 100644 --- a/recipes/bioconductor-pd.hugene.1.0.st.v1/meta.yaml +++ b/recipes/bioconductor-pd.hugene.1.0.st.v1/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.14.1" %} {% set name = "pd.hugene.1.0.st.v1" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -12,31 +12,31 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 8cb24c351aee5bf216180e4b19742506 build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ noarch: generic requirements: host: - - 'bioconductor-biostrings >=2.50.0,<2.51.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-oligo >=1.46.0,<1.47.0' - - 'bioconductor-oligoclasses >=1.44.0,<1.45.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-biostrings >=2.52.0,<2.53.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-oligo >=1.48.0,<1.49.0' + - 'bioconductor-oligoclasses >=1.46.0,<1.47.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' run: - - 'bioconductor-biostrings >=2.50.0,<2.51.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-oligo >=1.46.0,<1.47.0' - - 'bioconductor-oligoclasses >=1.44.0,<1.45.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-biostrings >=2.52.0,<2.53.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-oligo >=1.48.0,<1.49.0' + - 'bioconductor-oligoclasses >=1.46.0,<1.47.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-pd.hugene.1.0.st.v1/post-link.sh b/recipes/bioconductor-pd.hugene.1.0.st.v1/post-link.sh index c58169067d1e4..8b934296c97b7 100644 --- a/recipes/bioconductor-pd.hugene.1.0.st.v1/post-link.sh +++ b/recipes/bioconductor-pd.hugene.1.0.st.v1/post-link.sh @@ -1,9 +1,10 @@ #!/bin/bash FN="pd.hugene.1.0.st.v1_3.14.1.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/pd.hugene.1.0.st.v1_3.14.1.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/pd.hugene.1.0.st.v1_3.14.1.tar.gz" "https://bioarchive.galaxyproject.org/pd.hugene.1.0.st.v1_3.14.1.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-pd.hugene.1.0.st.v1/bioconductor-pd.hugene.1.0.st.v1_3.14.1_src_all.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-pd.hugene.1.0.st.v1/bioconductor-pd.hugene.1.0.st.v1_3.14.1_src_all.tar.gz" ) MD5="8cb24c351aee5bf216180e4b19742506" @@ -16,7 +17,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-pd.hugene.1.1.st.v1/meta.yaml b/recipes/bioconductor-pd.hugene.1.1.st.v1/meta.yaml index b875ae4b67337..ede869a42b1c8 100644 --- a/recipes/bioconductor-pd.hugene.1.1.st.v1/meta.yaml +++ b/recipes/bioconductor-pd.hugene.1.1.st.v1/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.14.1" %} {% set name = "pd.hugene.1.1.st.v1" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -12,31 +12,31 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 7a17ee4f7d258792be1d21be7d03deb0 build: - number: 1 + number: 2 rpaths: - lib/R/lib/ - lib/ noarch: generic requirements: host: - - 'bioconductor-biostrings >=2.50.0,<2.51.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-oligo >=1.46.0,<1.47.0' - - 'bioconductor-oligoclasses >=1.44.0,<1.45.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-biostrings >=2.52.0,<2.53.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-oligo >=1.48.0,<1.49.0' + - 'bioconductor-oligoclasses >=1.46.0,<1.47.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' run: - - 'bioconductor-biostrings >=2.50.0,<2.51.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-oligo >=1.46.0,<1.47.0' - - 'bioconductor-oligoclasses >=1.44.0,<1.45.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-biostrings >=2.52.0,<2.53.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-oligo >=1.48.0,<1.49.0' + - 'bioconductor-oligoclasses >=1.46.0,<1.47.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-pd.hugene.1.1.st.v1/post-link.sh b/recipes/bioconductor-pd.hugene.1.1.st.v1/post-link.sh index a474fb42bbf0e..f6fc9d14df6e4 100644 --- a/recipes/bioconductor-pd.hugene.1.1.st.v1/post-link.sh +++ b/recipes/bioconductor-pd.hugene.1.1.st.v1/post-link.sh @@ -1,9 +1,10 @@ #!/bin/bash FN="pd.hugene.1.1.st.v1_3.14.1.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/pd.hugene.1.1.st.v1_3.14.1.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/pd.hugene.1.1.st.v1_3.14.1.tar.gz" "https://bioarchive.galaxyproject.org/pd.hugene.1.1.st.v1_3.14.1.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-pd.hugene.1.1.st.v1/bioconductor-pd.hugene.1.1.st.v1_3.14.1_src_all.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-pd.hugene.1.1.st.v1/bioconductor-pd.hugene.1.1.st.v1_3.14.1_src_all.tar.gz" ) MD5="7a17ee4f7d258792be1d21be7d03deb0" @@ -16,7 +17,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-pd.hugene.2.0.st/meta.yaml b/recipes/bioconductor-pd.hugene.2.0.st/meta.yaml index 45a8dd6e0abdb..177992d64913d 100644 --- a/recipes/bioconductor-pd.hugene.2.0.st/meta.yaml +++ b/recipes/bioconductor-pd.hugene.2.0.st/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.14.1" %} {% set name = "pd.hugene.2.0.st" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -12,31 +12,31 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: e484209aa0c2a839c3445d91c1a799ce build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ noarch: generic requirements: host: - - 'bioconductor-biostrings >=2.50.0,<2.51.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-oligo >=1.46.0,<1.47.0' - - 'bioconductor-oligoclasses >=1.44.0,<1.45.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-biostrings >=2.52.0,<2.53.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-oligo >=1.48.0,<1.49.0' + - 'bioconductor-oligoclasses >=1.46.0,<1.47.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' run: - - 'bioconductor-biostrings >=2.50.0,<2.51.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-oligo >=1.46.0,<1.47.0' - - 'bioconductor-oligoclasses >=1.44.0,<1.45.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-biostrings >=2.52.0,<2.53.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-oligo >=1.48.0,<1.49.0' + - 'bioconductor-oligoclasses >=1.46.0,<1.47.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-pd.hugene.2.0.st/post-link.sh b/recipes/bioconductor-pd.hugene.2.0.st/post-link.sh index 4ef0d6c6405c8..1aba4bce9d07f 100644 --- a/recipes/bioconductor-pd.hugene.2.0.st/post-link.sh +++ b/recipes/bioconductor-pd.hugene.2.0.st/post-link.sh @@ -1,9 +1,10 @@ #!/bin/bash FN="pd.hugene.2.0.st_3.14.1.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/pd.hugene.2.0.st_3.14.1.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/pd.hugene.2.0.st_3.14.1.tar.gz" "https://bioarchive.galaxyproject.org/pd.hugene.2.0.st_3.14.1.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-pd.hugene.2.0.st/bioconductor-pd.hugene.2.0.st_3.14.1_src_all.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-pd.hugene.2.0.st/bioconductor-pd.hugene.2.0.st_3.14.1_src_all.tar.gz" ) MD5="e484209aa0c2a839c3445d91c1a799ce" @@ -16,7 +17,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-pd.hugene.2.1.st/meta.yaml b/recipes/bioconductor-pd.hugene.2.1.st/meta.yaml index 3c469087ecb8f..1d1a8f7ebffe8 100644 --- a/recipes/bioconductor-pd.hugene.2.1.st/meta.yaml +++ b/recipes/bioconductor-pd.hugene.2.1.st/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.14.1" %} {% set name = "pd.hugene.2.1.st" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -12,31 +12,31 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 164227f10b87f87059e4ae27b40f5238 build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ noarch: generic requirements: host: - - 'bioconductor-biostrings >=2.50.0,<2.51.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-oligo >=1.46.0,<1.47.0' - - 'bioconductor-oligoclasses >=1.44.0,<1.45.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-biostrings >=2.52.0,<2.53.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-oligo >=1.48.0,<1.49.0' + - 'bioconductor-oligoclasses >=1.46.0,<1.47.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' run: - - 'bioconductor-biostrings >=2.50.0,<2.51.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-oligo >=1.46.0,<1.47.0' - - 'bioconductor-oligoclasses >=1.44.0,<1.45.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-biostrings >=2.52.0,<2.53.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-oligo >=1.48.0,<1.49.0' + - 'bioconductor-oligoclasses >=1.46.0,<1.47.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-pd.hugene.2.1.st/post-link.sh b/recipes/bioconductor-pd.hugene.2.1.st/post-link.sh index 22b5fe3db8493..751a384a873f3 100644 --- a/recipes/bioconductor-pd.hugene.2.1.st/post-link.sh +++ b/recipes/bioconductor-pd.hugene.2.1.st/post-link.sh @@ -1,9 +1,10 @@ #!/bin/bash FN="pd.hugene.2.1.st_3.14.1.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/pd.hugene.2.1.st_3.14.1.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/pd.hugene.2.1.st_3.14.1.tar.gz" "https://bioarchive.galaxyproject.org/pd.hugene.2.1.st_3.14.1.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-pd.hugene.2.1.st/bioconductor-pd.hugene.2.1.st_3.14.1_src_all.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-pd.hugene.2.1.st/bioconductor-pd.hugene.2.1.st_3.14.1_src_all.tar.gz" ) MD5="164227f10b87f87059e4ae27b40f5238" @@ -16,7 +17,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-pd.maize/meta.yaml b/recipes/bioconductor-pd.maize/meta.yaml index b023717c7fdb4..1a73d306ae326 100644 --- a/recipes/bioconductor-pd.maize/meta.yaml +++ b/recipes/bioconductor-pd.maize/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.12.0" %} {% set name = "pd.maize" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -12,31 +12,31 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: a1689518c8525d3dfa97e870f90b7a7b build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ noarch: generic requirements: host: - - 'bioconductor-biostrings >=2.50.0,<2.51.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-oligo >=1.46.0,<1.47.0' - - 'bioconductor-oligoclasses >=1.44.0,<1.45.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-biostrings >=2.52.0,<2.53.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-oligo >=1.48.0,<1.49.0' + - 'bioconductor-oligoclasses >=1.46.0,<1.47.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' run: - - 'bioconductor-biostrings >=2.50.0,<2.51.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-oligo >=1.46.0,<1.47.0' - - 'bioconductor-oligoclasses >=1.44.0,<1.45.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-biostrings >=2.52.0,<2.53.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-oligo >=1.48.0,<1.49.0' + - 'bioconductor-oligoclasses >=1.46.0,<1.47.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-pd.maize/post-link.sh b/recipes/bioconductor-pd.maize/post-link.sh index af49bbd2cbd2c..f4b66e217e187 100644 --- a/recipes/bioconductor-pd.maize/post-link.sh +++ b/recipes/bioconductor-pd.maize/post-link.sh @@ -1,9 +1,10 @@ #!/bin/bash FN="pd.maize_3.12.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/pd.maize_3.12.0.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/pd.maize_3.12.0.tar.gz" "https://bioarchive.galaxyproject.org/pd.maize_3.12.0.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-pd.maize/bioconductor-pd.maize_3.12.0_src_all.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-pd.maize/bioconductor-pd.maize_3.12.0_src_all.tar.gz" ) MD5="a1689518c8525d3dfa97e870f90b7a7b" @@ -16,7 +17,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-pd.mapping250k.nsp/meta.yaml b/recipes/bioconductor-pd.mapping250k.nsp/meta.yaml index 04c36cec81448..265125f1a6d61 100644 --- a/recipes/bioconductor-pd.mapping250k.nsp/meta.yaml +++ b/recipes/bioconductor-pd.mapping250k.nsp/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.12.0" %} {% set name = "pd.mapping250k.nsp" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -12,31 +12,31 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 2786d00e1d621a9c415a599b4afe838b build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ noarch: generic requirements: host: - - 'bioconductor-biostrings >=2.50.0,<2.51.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-oligo >=1.46.0,<1.47.0' - - 'bioconductor-oligoclasses >=1.44.0,<1.45.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-biostrings >=2.52.0,<2.53.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-oligo >=1.48.0,<1.49.0' + - 'bioconductor-oligoclasses >=1.46.0,<1.47.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' run: - - 'bioconductor-biostrings >=2.50.0,<2.51.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-oligo >=1.46.0,<1.47.0' - - 'bioconductor-oligoclasses >=1.44.0,<1.45.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-biostrings >=2.52.0,<2.53.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-oligo >=1.48.0,<1.49.0' + - 'bioconductor-oligoclasses >=1.46.0,<1.47.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-pd.mapping250k.nsp/post-link.sh b/recipes/bioconductor-pd.mapping250k.nsp/post-link.sh index 0919d44f63b4a..2a7061fe0fb30 100644 --- a/recipes/bioconductor-pd.mapping250k.nsp/post-link.sh +++ b/recipes/bioconductor-pd.mapping250k.nsp/post-link.sh @@ -1,9 +1,10 @@ #!/bin/bash FN="pd.mapping250k.nsp_3.12.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/pd.mapping250k.nsp_3.12.0.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/pd.mapping250k.nsp_3.12.0.tar.gz" "https://bioarchive.galaxyproject.org/pd.mapping250k.nsp_3.12.0.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-pd.mapping250k.nsp/bioconductor-pd.mapping250k.nsp_3.12.0_src_all.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-pd.mapping250k.nsp/bioconductor-pd.mapping250k.nsp_3.12.0_src_all.tar.gz" ) MD5="2786d00e1d621a9c415a599b4afe838b" @@ -16,7 +17,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-pd.mapping250k.sty/meta.yaml b/recipes/bioconductor-pd.mapping250k.sty/meta.yaml index b6538eae6d40e..2c39a06472920 100644 --- a/recipes/bioconductor-pd.mapping250k.sty/meta.yaml +++ b/recipes/bioconductor-pd.mapping250k.sty/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.12.0" %} {% set name = "pd.mapping250k.sty" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -12,31 +12,31 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 0db5992855eaf9b8f61f8bc2e57ef347 build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ noarch: generic requirements: host: - - 'bioconductor-biostrings >=2.50.0,<2.51.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-oligo >=1.46.0,<1.47.0' - - 'bioconductor-oligoclasses >=1.44.0,<1.45.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-biostrings >=2.52.0,<2.53.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-oligo >=1.48.0,<1.49.0' + - 'bioconductor-oligoclasses >=1.46.0,<1.47.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' run: - - 'bioconductor-biostrings >=2.50.0,<2.51.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-oligo >=1.46.0,<1.47.0' - - 'bioconductor-oligoclasses >=1.44.0,<1.45.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-biostrings >=2.52.0,<2.53.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-oligo >=1.48.0,<1.49.0' + - 'bioconductor-oligoclasses >=1.46.0,<1.47.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-pd.mapping250k.sty/post-link.sh b/recipes/bioconductor-pd.mapping250k.sty/post-link.sh index dd68cb1b2fc42..f4d373b5ac36d 100644 --- a/recipes/bioconductor-pd.mapping250k.sty/post-link.sh +++ b/recipes/bioconductor-pd.mapping250k.sty/post-link.sh @@ -1,9 +1,10 @@ #!/bin/bash FN="pd.mapping250k.sty_3.12.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/pd.mapping250k.sty_3.12.0.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/pd.mapping250k.sty_3.12.0.tar.gz" "https://bioarchive.galaxyproject.org/pd.mapping250k.sty_3.12.0.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-pd.mapping250k.sty/bioconductor-pd.mapping250k.sty_3.12.0_src_all.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-pd.mapping250k.sty/bioconductor-pd.mapping250k.sty_3.12.0_src_all.tar.gz" ) MD5="0db5992855eaf9b8f61f8bc2e57ef347" @@ -16,7 +17,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-pd.mapping50k.hind240/meta.yaml b/recipes/bioconductor-pd.mapping50k.hind240/meta.yaml index a20f1c299ae2e..37c2c58d44cb9 100644 --- a/recipes/bioconductor-pd.mapping50k.hind240/meta.yaml +++ b/recipes/bioconductor-pd.mapping50k.hind240/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.12.0" %} {% set name = "pd.mapping50k.hind240" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -12,31 +12,31 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 83615dcb01eb381f0c69e07504809094 build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ noarch: generic requirements: host: - - 'bioconductor-biostrings >=2.50.0,<2.51.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-oligo >=1.46.0,<1.47.0' - - 'bioconductor-oligoclasses >=1.44.0,<1.45.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-biostrings >=2.52.0,<2.53.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-oligo >=1.48.0,<1.49.0' + - 'bioconductor-oligoclasses >=1.46.0,<1.47.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' run: - - 'bioconductor-biostrings >=2.50.0,<2.51.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-oligo >=1.46.0,<1.47.0' - - 'bioconductor-oligoclasses >=1.44.0,<1.45.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-biostrings >=2.52.0,<2.53.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-oligo >=1.48.0,<1.49.0' + - 'bioconductor-oligoclasses >=1.46.0,<1.47.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-pd.mapping50k.hind240/post-link.sh b/recipes/bioconductor-pd.mapping50k.hind240/post-link.sh index 85866da94c21e..d16e735686c6b 100644 --- a/recipes/bioconductor-pd.mapping50k.hind240/post-link.sh +++ b/recipes/bioconductor-pd.mapping50k.hind240/post-link.sh @@ -1,9 +1,10 @@ #!/bin/bash FN="pd.mapping50k.hind240_3.12.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/pd.mapping50k.hind240_3.12.0.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/pd.mapping50k.hind240_3.12.0.tar.gz" "https://bioarchive.galaxyproject.org/pd.mapping50k.hind240_3.12.0.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-pd.mapping50k.hind240/bioconductor-pd.mapping50k.hind240_3.12.0_src_all.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-pd.mapping50k.hind240/bioconductor-pd.mapping50k.hind240_3.12.0_src_all.tar.gz" ) MD5="83615dcb01eb381f0c69e07504809094" @@ -16,7 +17,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-pd.mapping50k.xba240/meta.yaml b/recipes/bioconductor-pd.mapping50k.xba240/meta.yaml index 2af765f8663e5..c916d5327b108 100644 --- a/recipes/bioconductor-pd.mapping50k.xba240/meta.yaml +++ b/recipes/bioconductor-pd.mapping50k.xba240/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.12.0" %} {% set name = "pd.mapping50k.xba240" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -12,31 +12,31 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: eb0f9250fe0d7b590ca9938fee88f2e7 build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ noarch: generic requirements: host: - - 'bioconductor-biostrings >=2.50.0,<2.51.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-oligo >=1.46.0,<1.47.0' - - 'bioconductor-oligoclasses >=1.44.0,<1.45.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-biostrings >=2.52.0,<2.53.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-oligo >=1.48.0,<1.49.0' + - 'bioconductor-oligoclasses >=1.46.0,<1.47.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' run: - - 'bioconductor-biostrings >=2.50.0,<2.51.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-oligo >=1.46.0,<1.47.0' - - 'bioconductor-oligoclasses >=1.44.0,<1.45.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-biostrings >=2.52.0,<2.53.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-oligo >=1.48.0,<1.49.0' + - 'bioconductor-oligoclasses >=1.46.0,<1.47.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-pd.mapping50k.xba240/post-link.sh b/recipes/bioconductor-pd.mapping50k.xba240/post-link.sh index fc37c8c7f2f64..9311332d85934 100644 --- a/recipes/bioconductor-pd.mapping50k.xba240/post-link.sh +++ b/recipes/bioconductor-pd.mapping50k.xba240/post-link.sh @@ -1,9 +1,10 @@ #!/bin/bash FN="pd.mapping50k.xba240_3.12.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/pd.mapping50k.xba240_3.12.0.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/pd.mapping50k.xba240_3.12.0.tar.gz" "https://bioarchive.galaxyproject.org/pd.mapping50k.xba240_3.12.0.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-pd.mapping50k.xba240/bioconductor-pd.mapping50k.xba240_3.12.0_src_all.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-pd.mapping50k.xba240/bioconductor-pd.mapping50k.xba240_3.12.0_src_all.tar.gz" ) MD5="eb0f9250fe0d7b590ca9938fee88f2e7" @@ -16,7 +17,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-pd.margene.1.0.st/meta.yaml b/recipes/bioconductor-pd.margene.1.0.st/meta.yaml index 418f148f0ede8..732fd3842c15a 100644 --- a/recipes/bioconductor-pd.margene.1.0.st/meta.yaml +++ b/recipes/bioconductor-pd.margene.1.0.st/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.12.0" %} {% set name = "pd.margene.1.0.st" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -12,31 +12,31 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: f670b192e4b453f13bb7cae154b5de42 build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ noarch: generic requirements: host: - - 'bioconductor-biostrings >=2.50.0,<2.51.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-oligo >=1.46.0,<1.47.0' - - 'bioconductor-oligoclasses >=1.44.0,<1.45.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-biostrings >=2.52.0,<2.53.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-oligo >=1.48.0,<1.49.0' + - 'bioconductor-oligoclasses >=1.46.0,<1.47.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' run: - - 'bioconductor-biostrings >=2.50.0,<2.51.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-oligo >=1.46.0,<1.47.0' - - 'bioconductor-oligoclasses >=1.44.0,<1.45.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-biostrings >=2.52.0,<2.53.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-oligo >=1.48.0,<1.49.0' + - 'bioconductor-oligoclasses >=1.46.0,<1.47.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-pd.margene.1.0.st/post-link.sh b/recipes/bioconductor-pd.margene.1.0.st/post-link.sh index ece1638b37566..b92465895f08b 100644 --- a/recipes/bioconductor-pd.margene.1.0.st/post-link.sh +++ b/recipes/bioconductor-pd.margene.1.0.st/post-link.sh @@ -1,9 +1,10 @@ #!/bin/bash FN="pd.margene.1.0.st_3.12.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/pd.margene.1.0.st_3.12.0.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/pd.margene.1.0.st_3.12.0.tar.gz" "https://bioarchive.galaxyproject.org/pd.margene.1.0.st_3.12.0.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-pd.margene.1.0.st/bioconductor-pd.margene.1.0.st_3.12.0_src_all.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-pd.margene.1.0.st/bioconductor-pd.margene.1.0.st_3.12.0_src_all.tar.gz" ) MD5="f670b192e4b453f13bb7cae154b5de42" @@ -16,7 +17,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-pd.margene.1.1.st/meta.yaml b/recipes/bioconductor-pd.margene.1.1.st/meta.yaml index be6c3a466e56f..93e98f5948781 100644 --- a/recipes/bioconductor-pd.margene.1.1.st/meta.yaml +++ b/recipes/bioconductor-pd.margene.1.1.st/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.12.0" %} {% set name = "pd.margene.1.1.st" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -12,31 +12,31 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: efd71aeb9c5ab36c2ddeccf9cb66ddec build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ noarch: generic requirements: host: - - 'bioconductor-biostrings >=2.50.0,<2.51.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-oligo >=1.46.0,<1.47.0' - - 'bioconductor-oligoclasses >=1.44.0,<1.45.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-biostrings >=2.52.0,<2.53.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-oligo >=1.48.0,<1.49.0' + - 'bioconductor-oligoclasses >=1.46.0,<1.47.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' run: - - 'bioconductor-biostrings >=2.50.0,<2.51.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-oligo >=1.46.0,<1.47.0' - - 'bioconductor-oligoclasses >=1.44.0,<1.45.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-biostrings >=2.52.0,<2.53.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-oligo >=1.48.0,<1.49.0' + - 'bioconductor-oligoclasses >=1.46.0,<1.47.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-pd.margene.1.1.st/post-link.sh b/recipes/bioconductor-pd.margene.1.1.st/post-link.sh index 61578f865a0ea..2a2e21048e1f4 100644 --- a/recipes/bioconductor-pd.margene.1.1.st/post-link.sh +++ b/recipes/bioconductor-pd.margene.1.1.st/post-link.sh @@ -1,9 +1,10 @@ #!/bin/bash FN="pd.margene.1.1.st_3.12.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/pd.margene.1.1.st_3.12.0.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/pd.margene.1.1.st_3.12.0.tar.gz" "https://bioarchive.galaxyproject.org/pd.margene.1.1.st_3.12.0.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-pd.margene.1.1.st/bioconductor-pd.margene.1.1.st_3.12.0_src_all.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-pd.margene.1.1.st/bioconductor-pd.margene.1.1.st_3.12.0_src_all.tar.gz" ) MD5="efd71aeb9c5ab36c2ddeccf9cb66ddec" @@ -16,7 +17,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-pd.medgene.1.0.st/meta.yaml b/recipes/bioconductor-pd.medgene.1.0.st/meta.yaml index 0f915d68abbd9..c2fcc4ba9e73a 100644 --- a/recipes/bioconductor-pd.medgene.1.0.st/meta.yaml +++ b/recipes/bioconductor-pd.medgene.1.0.st/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.12.0" %} {% set name = "pd.medgene.1.0.st" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -12,31 +12,31 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 2a0048ccd5310ec5c45bb691f3c25885 build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ noarch: generic requirements: host: - - 'bioconductor-biostrings >=2.50.0,<2.51.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-oligo >=1.46.0,<1.47.0' - - 'bioconductor-oligoclasses >=1.44.0,<1.45.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-biostrings >=2.52.0,<2.53.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-oligo >=1.48.0,<1.49.0' + - 'bioconductor-oligoclasses >=1.46.0,<1.47.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' run: - - 'bioconductor-biostrings >=2.50.0,<2.51.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-oligo >=1.46.0,<1.47.0' - - 'bioconductor-oligoclasses >=1.44.0,<1.45.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-biostrings >=2.52.0,<2.53.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-oligo >=1.48.0,<1.49.0' + - 'bioconductor-oligoclasses >=1.46.0,<1.47.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-pd.medgene.1.0.st/post-link.sh b/recipes/bioconductor-pd.medgene.1.0.st/post-link.sh index c3f35fe410253..c2b05f7b4aa14 100644 --- a/recipes/bioconductor-pd.medgene.1.0.st/post-link.sh +++ b/recipes/bioconductor-pd.medgene.1.0.st/post-link.sh @@ -1,9 +1,10 @@ #!/bin/bash FN="pd.medgene.1.0.st_3.12.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/pd.medgene.1.0.st_3.12.0.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/pd.medgene.1.0.st_3.12.0.tar.gz" "https://bioarchive.galaxyproject.org/pd.medgene.1.0.st_3.12.0.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-pd.medgene.1.0.st/bioconductor-pd.medgene.1.0.st_3.12.0_src_all.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-pd.medgene.1.0.st/bioconductor-pd.medgene.1.0.st_3.12.0_src_all.tar.gz" ) MD5="2a0048ccd5310ec5c45bb691f3c25885" @@ -16,7 +17,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-pd.medgene.1.1.st/meta.yaml b/recipes/bioconductor-pd.medgene.1.1.st/meta.yaml index afd6294028a17..5ff5f0ab2ea2c 100644 --- a/recipes/bioconductor-pd.medgene.1.1.st/meta.yaml +++ b/recipes/bioconductor-pd.medgene.1.1.st/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.12.0" %} {% set name = "pd.medgene.1.1.st" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -12,31 +12,31 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: d96894cfea509734af62110311100142 build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ noarch: generic requirements: host: - - 'bioconductor-biostrings >=2.50.0,<2.51.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-oligo >=1.46.0,<1.47.0' - - 'bioconductor-oligoclasses >=1.44.0,<1.45.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-biostrings >=2.52.0,<2.53.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-oligo >=1.48.0,<1.49.0' + - 'bioconductor-oligoclasses >=1.46.0,<1.47.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' run: - - 'bioconductor-biostrings >=2.50.0,<2.51.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-oligo >=1.46.0,<1.47.0' - - 'bioconductor-oligoclasses >=1.44.0,<1.45.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-biostrings >=2.52.0,<2.53.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-oligo >=1.48.0,<1.49.0' + - 'bioconductor-oligoclasses >=1.46.0,<1.47.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-pd.medgene.1.1.st/post-link.sh b/recipes/bioconductor-pd.medgene.1.1.st/post-link.sh index b53d4d2b555af..2acfa0d4e68cb 100644 --- a/recipes/bioconductor-pd.medgene.1.1.st/post-link.sh +++ b/recipes/bioconductor-pd.medgene.1.1.st/post-link.sh @@ -1,9 +1,10 @@ #!/bin/bash FN="pd.medgene.1.1.st_3.12.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/pd.medgene.1.1.st_3.12.0.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/pd.medgene.1.1.st_3.12.0.tar.gz" "https://bioarchive.galaxyproject.org/pd.medgene.1.1.st_3.12.0.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-pd.medgene.1.1.st/bioconductor-pd.medgene.1.1.st_3.12.0_src_all.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-pd.medgene.1.1.st/bioconductor-pd.medgene.1.1.st_3.12.0_src_all.tar.gz" ) MD5="d96894cfea509734af62110311100142" @@ -16,7 +17,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-pd.medicago/meta.yaml b/recipes/bioconductor-pd.medicago/meta.yaml index b12eb1cebd578..45690d79f6ec3 100644 --- a/recipes/bioconductor-pd.medicago/meta.yaml +++ b/recipes/bioconductor-pd.medicago/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.12.0" %} {% set name = "pd.medicago" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -12,31 +12,31 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 0e3f00777919374619a9dc8244167068 build: - number: 1 + number: 2 rpaths: - lib/R/lib/ - lib/ noarch: generic requirements: host: - - 'bioconductor-biostrings >=2.50.0,<2.51.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-oligo >=1.46.0,<1.47.0' - - 'bioconductor-oligoclasses >=1.44.0,<1.45.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-biostrings >=2.52.0,<2.53.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-oligo >=1.48.0,<1.49.0' + - 'bioconductor-oligoclasses >=1.46.0,<1.47.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' run: - - 'bioconductor-biostrings >=2.50.0,<2.51.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-oligo >=1.46.0,<1.47.0' - - 'bioconductor-oligoclasses >=1.44.0,<1.45.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-biostrings >=2.52.0,<2.53.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-oligo >=1.48.0,<1.49.0' + - 'bioconductor-oligoclasses >=1.46.0,<1.47.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-pd.medicago/post-link.sh b/recipes/bioconductor-pd.medicago/post-link.sh index 7792f916f1355..8a26abe69742b 100644 --- a/recipes/bioconductor-pd.medicago/post-link.sh +++ b/recipes/bioconductor-pd.medicago/post-link.sh @@ -1,9 +1,10 @@ #!/bin/bash FN="pd.medicago_3.12.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/pd.medicago_3.12.0.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/pd.medicago_3.12.0.tar.gz" "https://bioarchive.galaxyproject.org/pd.medicago_3.12.0.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-pd.medicago/bioconductor-pd.medicago_3.12.0_src_all.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-pd.medicago/bioconductor-pd.medicago_3.12.0_src_all.tar.gz" ) MD5="0e3f00777919374619a9dc8244167068" @@ -16,7 +17,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-pd.mg.u74a/meta.yaml b/recipes/bioconductor-pd.mg.u74a/meta.yaml index 932b8798fe557..75881b76817e2 100644 --- a/recipes/bioconductor-pd.mg.u74a/meta.yaml +++ b/recipes/bioconductor-pd.mg.u74a/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.12.0" %} {% set name = "pd.mg.u74a" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -12,31 +12,31 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: a855c7d2b80e9b8f9bbc1a3f83aca799 build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ noarch: generic requirements: host: - - 'bioconductor-biostrings >=2.50.0,<2.51.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-oligo >=1.46.0,<1.47.0' - - 'bioconductor-oligoclasses >=1.44.0,<1.45.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-biostrings >=2.52.0,<2.53.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-oligo >=1.48.0,<1.49.0' + - 'bioconductor-oligoclasses >=1.46.0,<1.47.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' run: - - 'bioconductor-biostrings >=2.50.0,<2.51.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-oligo >=1.46.0,<1.47.0' - - 'bioconductor-oligoclasses >=1.44.0,<1.45.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-biostrings >=2.52.0,<2.53.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-oligo >=1.48.0,<1.49.0' + - 'bioconductor-oligoclasses >=1.46.0,<1.47.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-pd.mg.u74a/post-link.sh b/recipes/bioconductor-pd.mg.u74a/post-link.sh index b339624cb27ec..aa0c93763ea56 100644 --- a/recipes/bioconductor-pd.mg.u74a/post-link.sh +++ b/recipes/bioconductor-pd.mg.u74a/post-link.sh @@ -1,9 +1,10 @@ #!/bin/bash FN="pd.mg.u74a_3.12.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/pd.mg.u74a_3.12.0.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/pd.mg.u74a_3.12.0.tar.gz" "https://bioarchive.galaxyproject.org/pd.mg.u74a_3.12.0.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-pd.mg.u74a/bioconductor-pd.mg.u74a_3.12.0_src_all.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-pd.mg.u74a/bioconductor-pd.mg.u74a_3.12.0_src_all.tar.gz" ) MD5="a855c7d2b80e9b8f9bbc1a3f83aca799" @@ -16,7 +17,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-pd.mg.u74av2/meta.yaml b/recipes/bioconductor-pd.mg.u74av2/meta.yaml index 4ac48a298231b..df19fe5f7c0bc 100644 --- a/recipes/bioconductor-pd.mg.u74av2/meta.yaml +++ b/recipes/bioconductor-pd.mg.u74av2/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.12.0" %} {% set name = "pd.mg.u74av2" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -12,31 +12,31 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 01c6e4da9c2ad0f1939482284dd5b421 build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ noarch: generic requirements: host: - - 'bioconductor-biostrings >=2.50.0,<2.51.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-oligo >=1.46.0,<1.47.0' - - 'bioconductor-oligoclasses >=1.44.0,<1.45.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-biostrings >=2.52.0,<2.53.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-oligo >=1.48.0,<1.49.0' + - 'bioconductor-oligoclasses >=1.46.0,<1.47.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' run: - - 'bioconductor-biostrings >=2.50.0,<2.51.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-oligo >=1.46.0,<1.47.0' - - 'bioconductor-oligoclasses >=1.44.0,<1.45.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-biostrings >=2.52.0,<2.53.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-oligo >=1.48.0,<1.49.0' + - 'bioconductor-oligoclasses >=1.46.0,<1.47.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-pd.mg.u74av2/post-link.sh b/recipes/bioconductor-pd.mg.u74av2/post-link.sh index be3e7994073e8..890b5c6904691 100644 --- a/recipes/bioconductor-pd.mg.u74av2/post-link.sh +++ b/recipes/bioconductor-pd.mg.u74av2/post-link.sh @@ -1,9 +1,10 @@ #!/bin/bash FN="pd.mg.u74av2_3.12.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/pd.mg.u74av2_3.12.0.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/pd.mg.u74av2_3.12.0.tar.gz" "https://bioarchive.galaxyproject.org/pd.mg.u74av2_3.12.0.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-pd.mg.u74av2/bioconductor-pd.mg.u74av2_3.12.0_src_all.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-pd.mg.u74av2/bioconductor-pd.mg.u74av2_3.12.0_src_all.tar.gz" ) MD5="01c6e4da9c2ad0f1939482284dd5b421" @@ -16,7 +17,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-pd.mg.u74b/meta.yaml b/recipes/bioconductor-pd.mg.u74b/meta.yaml index 5222e0cfeda99..7d9d5cb7960bf 100644 --- a/recipes/bioconductor-pd.mg.u74b/meta.yaml +++ b/recipes/bioconductor-pd.mg.u74b/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.12.0" %} {% set name = "pd.mg.u74b" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -12,31 +12,31 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 47bb81abaceba6dfaab3e0987f28706c build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ noarch: generic requirements: host: - - 'bioconductor-biostrings >=2.50.0,<2.51.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-oligo >=1.46.0,<1.47.0' - - 'bioconductor-oligoclasses >=1.44.0,<1.45.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-biostrings >=2.52.0,<2.53.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-oligo >=1.48.0,<1.49.0' + - 'bioconductor-oligoclasses >=1.46.0,<1.47.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' run: - - 'bioconductor-biostrings >=2.50.0,<2.51.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-oligo >=1.46.0,<1.47.0' - - 'bioconductor-oligoclasses >=1.44.0,<1.45.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-biostrings >=2.52.0,<2.53.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-oligo >=1.48.0,<1.49.0' + - 'bioconductor-oligoclasses >=1.46.0,<1.47.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-pd.mg.u74b/post-link.sh b/recipes/bioconductor-pd.mg.u74b/post-link.sh index 810c4114af8ee..6605bb649d5b3 100644 --- a/recipes/bioconductor-pd.mg.u74b/post-link.sh +++ b/recipes/bioconductor-pd.mg.u74b/post-link.sh @@ -1,9 +1,10 @@ #!/bin/bash FN="pd.mg.u74b_3.12.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/pd.mg.u74b_3.12.0.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/pd.mg.u74b_3.12.0.tar.gz" "https://bioarchive.galaxyproject.org/pd.mg.u74b_3.12.0.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-pd.mg.u74b/bioconductor-pd.mg.u74b_3.12.0_src_all.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-pd.mg.u74b/bioconductor-pd.mg.u74b_3.12.0_src_all.tar.gz" ) MD5="47bb81abaceba6dfaab3e0987f28706c" @@ -16,7 +17,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-pd.mg.u74bv2/meta.yaml b/recipes/bioconductor-pd.mg.u74bv2/meta.yaml index d4699ca43ace6..bc8262f9b5ad4 100644 --- a/recipes/bioconductor-pd.mg.u74bv2/meta.yaml +++ b/recipes/bioconductor-pd.mg.u74bv2/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.12.0" %} {% set name = "pd.mg.u74bv2" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -12,31 +12,31 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: dbb6cd5b16bd5cafbf654744bc2d5c5c build: - number: 1 + number: 2 rpaths: - lib/R/lib/ - lib/ noarch: generic requirements: host: - - 'bioconductor-biostrings >=2.50.0,<2.51.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-oligo >=1.46.0,<1.47.0' - - 'bioconductor-oligoclasses >=1.44.0,<1.45.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-biostrings >=2.52.0,<2.53.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-oligo >=1.48.0,<1.49.0' + - 'bioconductor-oligoclasses >=1.46.0,<1.47.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' run: - - 'bioconductor-biostrings >=2.50.0,<2.51.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-oligo >=1.46.0,<1.47.0' - - 'bioconductor-oligoclasses >=1.44.0,<1.45.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-biostrings >=2.52.0,<2.53.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-oligo >=1.48.0,<1.49.0' + - 'bioconductor-oligoclasses >=1.46.0,<1.47.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-pd.mg.u74bv2/post-link.sh b/recipes/bioconductor-pd.mg.u74bv2/post-link.sh index 67c7398120e56..92fb547cb8639 100644 --- a/recipes/bioconductor-pd.mg.u74bv2/post-link.sh +++ b/recipes/bioconductor-pd.mg.u74bv2/post-link.sh @@ -1,9 +1,10 @@ #!/bin/bash FN="pd.mg.u74bv2_3.12.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/pd.mg.u74bv2_3.12.0.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/pd.mg.u74bv2_3.12.0.tar.gz" "https://bioarchive.galaxyproject.org/pd.mg.u74bv2_3.12.0.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-pd.mg.u74bv2/bioconductor-pd.mg.u74bv2_3.12.0_src_all.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-pd.mg.u74bv2/bioconductor-pd.mg.u74bv2_3.12.0_src_all.tar.gz" ) MD5="dbb6cd5b16bd5cafbf654744bc2d5c5c" @@ -16,7 +17,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-pd.mg.u74c/meta.yaml b/recipes/bioconductor-pd.mg.u74c/meta.yaml index a53f367ca6a64..22db99658c4df 100644 --- a/recipes/bioconductor-pd.mg.u74c/meta.yaml +++ b/recipes/bioconductor-pd.mg.u74c/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.12.0" %} {% set name = "pd.mg.u74c" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -12,31 +12,31 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 01f10eae99481f03d1d5a6a2c2f01733 build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ noarch: generic requirements: host: - - 'bioconductor-biostrings >=2.50.0,<2.51.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-oligo >=1.46.0,<1.47.0' - - 'bioconductor-oligoclasses >=1.44.0,<1.45.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-biostrings >=2.52.0,<2.53.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-oligo >=1.48.0,<1.49.0' + - 'bioconductor-oligoclasses >=1.46.0,<1.47.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' run: - - 'bioconductor-biostrings >=2.50.0,<2.51.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-oligo >=1.46.0,<1.47.0' - - 'bioconductor-oligoclasses >=1.44.0,<1.45.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-biostrings >=2.52.0,<2.53.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-oligo >=1.48.0,<1.49.0' + - 'bioconductor-oligoclasses >=1.46.0,<1.47.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-pd.mg.u74c/post-link.sh b/recipes/bioconductor-pd.mg.u74c/post-link.sh index 0d9ab5aa829a8..035d32cb61f5b 100644 --- a/recipes/bioconductor-pd.mg.u74c/post-link.sh +++ b/recipes/bioconductor-pd.mg.u74c/post-link.sh @@ -1,9 +1,10 @@ #!/bin/bash FN="pd.mg.u74c_3.12.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/pd.mg.u74c_3.12.0.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/pd.mg.u74c_3.12.0.tar.gz" "https://bioarchive.galaxyproject.org/pd.mg.u74c_3.12.0.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-pd.mg.u74c/bioconductor-pd.mg.u74c_3.12.0_src_all.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-pd.mg.u74c/bioconductor-pd.mg.u74c_3.12.0_src_all.tar.gz" ) MD5="01f10eae99481f03d1d5a6a2c2f01733" @@ -16,7 +17,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-pd.mg.u74cv2/meta.yaml b/recipes/bioconductor-pd.mg.u74cv2/meta.yaml index 5db33c5231782..d7ee676862cd9 100644 --- a/recipes/bioconductor-pd.mg.u74cv2/meta.yaml +++ b/recipes/bioconductor-pd.mg.u74cv2/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.12.0" %} {% set name = "pd.mg.u74cv2" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -12,31 +12,31 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: b60943b90b95a24fcf93f8c245fd88be build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ noarch: generic requirements: host: - - 'bioconductor-biostrings >=2.50.0,<2.51.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-oligo >=1.46.0,<1.47.0' - - 'bioconductor-oligoclasses >=1.44.0,<1.45.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-biostrings >=2.52.0,<2.53.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-oligo >=1.48.0,<1.49.0' + - 'bioconductor-oligoclasses >=1.46.0,<1.47.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' run: - - 'bioconductor-biostrings >=2.50.0,<2.51.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-oligo >=1.46.0,<1.47.0' - - 'bioconductor-oligoclasses >=1.44.0,<1.45.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-biostrings >=2.52.0,<2.53.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-oligo >=1.48.0,<1.49.0' + - 'bioconductor-oligoclasses >=1.46.0,<1.47.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-pd.mg.u74cv2/post-link.sh b/recipes/bioconductor-pd.mg.u74cv2/post-link.sh index bdf367a6701b0..44a7b40a1e7ca 100644 --- a/recipes/bioconductor-pd.mg.u74cv2/post-link.sh +++ b/recipes/bioconductor-pd.mg.u74cv2/post-link.sh @@ -1,9 +1,10 @@ #!/bin/bash FN="pd.mg.u74cv2_3.12.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/pd.mg.u74cv2_3.12.0.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/pd.mg.u74cv2_3.12.0.tar.gz" "https://bioarchive.galaxyproject.org/pd.mg.u74cv2_3.12.0.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-pd.mg.u74cv2/bioconductor-pd.mg.u74cv2_3.12.0_src_all.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-pd.mg.u74cv2/bioconductor-pd.mg.u74cv2_3.12.0_src_all.tar.gz" ) MD5="b60943b90b95a24fcf93f8c245fd88be" @@ -16,7 +17,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-pd.mirna.1.0/meta.yaml b/recipes/bioconductor-pd.mirna.1.0/meta.yaml index fbaf0a3953983..89ee7e3c2c677 100644 --- a/recipes/bioconductor-pd.mirna.1.0/meta.yaml +++ b/recipes/bioconductor-pd.mirna.1.0/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.12.0" %} {% set name = "pd.mirna.1.0" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -12,31 +12,31 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 8dfeb82a9da6d6f73e5fb716a2867a34 build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ noarch: generic requirements: host: - - 'bioconductor-biostrings >=2.50.0,<2.51.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-oligo >=1.46.0,<1.47.0' - - 'bioconductor-oligoclasses >=1.44.0,<1.45.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-biostrings >=2.52.0,<2.53.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-oligo >=1.48.0,<1.49.0' + - 'bioconductor-oligoclasses >=1.46.0,<1.47.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' run: - - 'bioconductor-biostrings >=2.50.0,<2.51.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-oligo >=1.46.0,<1.47.0' - - 'bioconductor-oligoclasses >=1.44.0,<1.45.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-biostrings >=2.52.0,<2.53.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-oligo >=1.48.0,<1.49.0' + - 'bioconductor-oligoclasses >=1.46.0,<1.47.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-pd.mirna.1.0/post-link.sh b/recipes/bioconductor-pd.mirna.1.0/post-link.sh index 6c0b22f2eedb1..358e90f4147ab 100644 --- a/recipes/bioconductor-pd.mirna.1.0/post-link.sh +++ b/recipes/bioconductor-pd.mirna.1.0/post-link.sh @@ -1,9 +1,10 @@ #!/bin/bash FN="pd.mirna.1.0_3.12.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/pd.mirna.1.0_3.12.0.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/pd.mirna.1.0_3.12.0.tar.gz" "https://bioarchive.galaxyproject.org/pd.mirna.1.0_3.12.0.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-pd.mirna.1.0/bioconductor-pd.mirna.1.0_3.12.0_src_all.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-pd.mirna.1.0/bioconductor-pd.mirna.1.0_3.12.0_src_all.tar.gz" ) MD5="8dfeb82a9da6d6f73e5fb716a2867a34" @@ -16,7 +17,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-pd.mirna.2.0/meta.yaml b/recipes/bioconductor-pd.mirna.2.0/meta.yaml index 5a2ba95b1f343..463b5427dd1fb 100644 --- a/recipes/bioconductor-pd.mirna.2.0/meta.yaml +++ b/recipes/bioconductor-pd.mirna.2.0/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.12.0" %} {% set name = "pd.mirna.2.0" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -12,31 +12,31 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: aab53cbc62fbd7727ca0303aeb1dca13 build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ noarch: generic requirements: host: - - 'bioconductor-biostrings >=2.50.0,<2.51.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-oligo >=1.46.0,<1.47.0' - - 'bioconductor-oligoclasses >=1.44.0,<1.45.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-biostrings >=2.52.0,<2.53.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-oligo >=1.48.0,<1.49.0' + - 'bioconductor-oligoclasses >=1.46.0,<1.47.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' run: - - 'bioconductor-biostrings >=2.50.0,<2.51.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-oligo >=1.46.0,<1.47.0' - - 'bioconductor-oligoclasses >=1.44.0,<1.45.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-biostrings >=2.52.0,<2.53.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-oligo >=1.48.0,<1.49.0' + - 'bioconductor-oligoclasses >=1.46.0,<1.47.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-pd.mirna.2.0/post-link.sh b/recipes/bioconductor-pd.mirna.2.0/post-link.sh index c621a45ce9712..425869a8eeb2e 100644 --- a/recipes/bioconductor-pd.mirna.2.0/post-link.sh +++ b/recipes/bioconductor-pd.mirna.2.0/post-link.sh @@ -1,9 +1,10 @@ #!/bin/bash FN="pd.mirna.2.0_3.12.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/pd.mirna.2.0_3.12.0.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/pd.mirna.2.0_3.12.0.tar.gz" "https://bioarchive.galaxyproject.org/pd.mirna.2.0_3.12.0.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-pd.mirna.2.0/bioconductor-pd.mirna.2.0_3.12.0_src_all.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-pd.mirna.2.0/bioconductor-pd.mirna.2.0_3.12.0_src_all.tar.gz" ) MD5="aab53cbc62fbd7727ca0303aeb1dca13" @@ -16,7 +17,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-pd.mirna.3.0/meta.yaml b/recipes/bioconductor-pd.mirna.3.0/meta.yaml index 198938b3fcf7d..4abc5bddc3c78 100644 --- a/recipes/bioconductor-pd.mirna.3.0/meta.yaml +++ b/recipes/bioconductor-pd.mirna.3.0/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.12.0" %} {% set name = "pd.mirna.3.0" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -12,31 +12,31 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 1265f1969c618b3b5121e6a77ba57009 build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ noarch: generic requirements: host: - - 'bioconductor-biostrings >=2.50.0,<2.51.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-oligo >=1.46.0,<1.47.0' - - 'bioconductor-oligoclasses >=1.44.0,<1.45.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-biostrings >=2.52.0,<2.53.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-oligo >=1.48.0,<1.49.0' + - 'bioconductor-oligoclasses >=1.46.0,<1.47.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' run: - - 'bioconductor-biostrings >=2.50.0,<2.51.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-oligo >=1.46.0,<1.47.0' - - 'bioconductor-oligoclasses >=1.44.0,<1.45.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-biostrings >=2.52.0,<2.53.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-oligo >=1.48.0,<1.49.0' + - 'bioconductor-oligoclasses >=1.46.0,<1.47.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-pd.mirna.3.0/post-link.sh b/recipes/bioconductor-pd.mirna.3.0/post-link.sh index 085739a23bf46..abdd507eaf039 100644 --- a/recipes/bioconductor-pd.mirna.3.0/post-link.sh +++ b/recipes/bioconductor-pd.mirna.3.0/post-link.sh @@ -1,9 +1,10 @@ #!/bin/bash FN="pd.mirna.3.0_3.12.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/pd.mirna.3.0_3.12.0.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/pd.mirna.3.0_3.12.0.tar.gz" "https://bioarchive.galaxyproject.org/pd.mirna.3.0_3.12.0.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-pd.mirna.3.0/bioconductor-pd.mirna.3.0_3.12.0_src_all.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-pd.mirna.3.0/bioconductor-pd.mirna.3.0_3.12.0_src_all.tar.gz" ) MD5="1265f1969c618b3b5121e6a77ba57009" @@ -16,7 +17,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-pd.mirna.3.1/meta.yaml b/recipes/bioconductor-pd.mirna.3.1/meta.yaml index b9d0f495c2ab3..b94a56d295263 100644 --- a/recipes/bioconductor-pd.mirna.3.1/meta.yaml +++ b/recipes/bioconductor-pd.mirna.3.1/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.8.1" %} {% set name = "pd.mirna.3.1" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -12,29 +12,29 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 296b3584ee5e9416c9018353d3e29c6c build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ noarch: generic requirements: host: - - 'bioconductor-biostrings >=2.50.0,<2.51.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-oligo >=1.46.0,<1.47.0' - - 'bioconductor-oligoclasses >=1.44.0,<1.45.0' + - 'bioconductor-biostrings >=2.52.0,<2.53.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-oligo >=1.48.0,<1.49.0' + - 'bioconductor-oligoclasses >=1.46.0,<1.47.0' - r-base - r-dbi - 'r-rsqlite >=0.11.1' run: - - 'bioconductor-biostrings >=2.50.0,<2.51.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-oligo >=1.46.0,<1.47.0' - - 'bioconductor-oligoclasses >=1.44.0,<1.45.0' + - 'bioconductor-biostrings >=2.52.0,<2.53.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-oligo >=1.48.0,<1.49.0' + - 'bioconductor-oligoclasses >=1.46.0,<1.47.0' - r-base - r-dbi - 'r-rsqlite >=0.11.1' - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-pd.mirna.3.1/post-link.sh b/recipes/bioconductor-pd.mirna.3.1/post-link.sh index 557d67ff2d640..38d3c3720a8a0 100644 --- a/recipes/bioconductor-pd.mirna.3.1/post-link.sh +++ b/recipes/bioconductor-pd.mirna.3.1/post-link.sh @@ -1,9 +1,10 @@ #!/bin/bash FN="pd.mirna.3.1_3.8.1.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/pd.mirna.3.1_3.8.1.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/pd.mirna.3.1_3.8.1.tar.gz" "https://bioarchive.galaxyproject.org/pd.mirna.3.1_3.8.1.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-pd.mirna.3.1/bioconductor-pd.mirna.3.1_3.8.1_src_all.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-pd.mirna.3.1/bioconductor-pd.mirna.3.1_3.8.1_src_all.tar.gz" ) MD5="296b3584ee5e9416c9018353d3e29c6c" @@ -16,7 +17,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-pd.mirna.4.0/meta.yaml b/recipes/bioconductor-pd.mirna.4.0/meta.yaml index 19e6ddfdcd07b..33eff9a274866 100644 --- a/recipes/bioconductor-pd.mirna.4.0/meta.yaml +++ b/recipes/bioconductor-pd.mirna.4.0/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.12.0" %} {% set name = "pd.mirna.4.0" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -12,31 +12,31 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: cae1a18c02aaa20a2f05172103e9d938 build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ noarch: generic requirements: host: - - 'bioconductor-biostrings >=2.50.0,<2.51.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-oligo >=1.46.0,<1.47.0' - - 'bioconductor-oligoclasses >=1.44.0,<1.45.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-biostrings >=2.52.0,<2.53.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-oligo >=1.48.0,<1.49.0' + - 'bioconductor-oligoclasses >=1.46.0,<1.47.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' run: - - 'bioconductor-biostrings >=2.50.0,<2.51.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-oligo >=1.46.0,<1.47.0' - - 'bioconductor-oligoclasses >=1.44.0,<1.45.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-biostrings >=2.52.0,<2.53.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-oligo >=1.48.0,<1.49.0' + - 'bioconductor-oligoclasses >=1.46.0,<1.47.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-pd.mirna.4.0/post-link.sh b/recipes/bioconductor-pd.mirna.4.0/post-link.sh index 910d53d8cda5c..d7a64dbfa76d6 100644 --- a/recipes/bioconductor-pd.mirna.4.0/post-link.sh +++ b/recipes/bioconductor-pd.mirna.4.0/post-link.sh @@ -1,9 +1,10 @@ #!/bin/bash FN="pd.mirna.4.0_3.12.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/pd.mirna.4.0_3.12.0.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/pd.mirna.4.0_3.12.0.tar.gz" "https://bioarchive.galaxyproject.org/pd.mirna.4.0_3.12.0.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-pd.mirna.4.0/bioconductor-pd.mirna.4.0_3.12.0_src_all.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-pd.mirna.4.0/bioconductor-pd.mirna.4.0_3.12.0_src_all.tar.gz" ) MD5="cae1a18c02aaa20a2f05172103e9d938" @@ -16,7 +17,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-pd.moe430a/meta.yaml b/recipes/bioconductor-pd.moe430a/meta.yaml index da54059410b55..680816727302c 100644 --- a/recipes/bioconductor-pd.moe430a/meta.yaml +++ b/recipes/bioconductor-pd.moe430a/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.12.0" %} {% set name = "pd.moe430a" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -12,31 +12,31 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: f9a7cb62140e42c2a82177548a1c73fb build: - number: 1 + number: 2 rpaths: - lib/R/lib/ - lib/ noarch: generic requirements: host: - - 'bioconductor-biostrings >=2.50.0,<2.51.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-oligo >=1.46.0,<1.47.0' - - 'bioconductor-oligoclasses >=1.44.0,<1.45.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-biostrings >=2.52.0,<2.53.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-oligo >=1.48.0,<1.49.0' + - 'bioconductor-oligoclasses >=1.46.0,<1.47.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' run: - - 'bioconductor-biostrings >=2.50.0,<2.51.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-oligo >=1.46.0,<1.47.0' - - 'bioconductor-oligoclasses >=1.44.0,<1.45.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-biostrings >=2.52.0,<2.53.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-oligo >=1.48.0,<1.49.0' + - 'bioconductor-oligoclasses >=1.46.0,<1.47.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-pd.moe430a/post-link.sh b/recipes/bioconductor-pd.moe430a/post-link.sh index 5904b6d4634f3..ddc1e5fc77ebf 100644 --- a/recipes/bioconductor-pd.moe430a/post-link.sh +++ b/recipes/bioconductor-pd.moe430a/post-link.sh @@ -1,9 +1,10 @@ #!/bin/bash FN="pd.moe430a_3.12.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/pd.moe430a_3.12.0.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/pd.moe430a_3.12.0.tar.gz" "https://bioarchive.galaxyproject.org/pd.moe430a_3.12.0.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-pd.moe430a/bioconductor-pd.moe430a_3.12.0_src_all.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-pd.moe430a/bioconductor-pd.moe430a_3.12.0_src_all.tar.gz" ) MD5="f9a7cb62140e42c2a82177548a1c73fb" @@ -16,7 +17,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-pd.moe430b/meta.yaml b/recipes/bioconductor-pd.moe430b/meta.yaml index 16e03b2be047d..7726989da8cab 100644 --- a/recipes/bioconductor-pd.moe430b/meta.yaml +++ b/recipes/bioconductor-pd.moe430b/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.12.0" %} {% set name = "pd.moe430b" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -12,31 +12,31 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: c19d2ee5e7e87703cf73afa33a5f3156 build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ noarch: generic requirements: host: - - 'bioconductor-biostrings >=2.50.0,<2.51.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-oligo >=1.46.0,<1.47.0' - - 'bioconductor-oligoclasses >=1.44.0,<1.45.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-biostrings >=2.52.0,<2.53.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-oligo >=1.48.0,<1.49.0' + - 'bioconductor-oligoclasses >=1.46.0,<1.47.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' run: - - 'bioconductor-biostrings >=2.50.0,<2.51.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-oligo >=1.46.0,<1.47.0' - - 'bioconductor-oligoclasses >=1.44.0,<1.45.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-biostrings >=2.52.0,<2.53.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-oligo >=1.48.0,<1.49.0' + - 'bioconductor-oligoclasses >=1.46.0,<1.47.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-pd.moe430b/post-link.sh b/recipes/bioconductor-pd.moe430b/post-link.sh index e5c1d9176a24f..3068955aa0e39 100644 --- a/recipes/bioconductor-pd.moe430b/post-link.sh +++ b/recipes/bioconductor-pd.moe430b/post-link.sh @@ -1,9 +1,10 @@ #!/bin/bash FN="pd.moe430b_3.12.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/pd.moe430b_3.12.0.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/pd.moe430b_3.12.0.tar.gz" "https://bioarchive.galaxyproject.org/pd.moe430b_3.12.0.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-pd.moe430b/bioconductor-pd.moe430b_3.12.0_src_all.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-pd.moe430b/bioconductor-pd.moe430b_3.12.0_src_all.tar.gz" ) MD5="c19d2ee5e7e87703cf73afa33a5f3156" @@ -16,7 +17,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-pd.moex.1.0.st.v1/meta.yaml b/recipes/bioconductor-pd.moex.1.0.st.v1/meta.yaml index 87152ed202bf5..ea11601f9f4c2 100644 --- a/recipes/bioconductor-pd.moex.1.0.st.v1/meta.yaml +++ b/recipes/bioconductor-pd.moex.1.0.st.v1/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.14.1" %} {% set name = "pd.moex.1.0.st.v1" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -12,31 +12,31 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 57427e63b2d44258c12d796eada1897b build: - number: 1 + number: 2 rpaths: - lib/R/lib/ - lib/ noarch: generic requirements: host: - - 'bioconductor-biostrings >=2.50.0,<2.51.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-oligo >=1.46.0,<1.47.0' - - 'bioconductor-oligoclasses >=1.44.0,<1.45.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-biostrings >=2.52.0,<2.53.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-oligo >=1.48.0,<1.49.0' + - 'bioconductor-oligoclasses >=1.46.0,<1.47.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' run: - - 'bioconductor-biostrings >=2.50.0,<2.51.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-oligo >=1.46.0,<1.47.0' - - 'bioconductor-oligoclasses >=1.44.0,<1.45.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-biostrings >=2.52.0,<2.53.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-oligo >=1.48.0,<1.49.0' + - 'bioconductor-oligoclasses >=1.46.0,<1.47.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-pd.moex.1.0.st.v1/post-link.sh b/recipes/bioconductor-pd.moex.1.0.st.v1/post-link.sh index 01b472f139f86..1efdf7543a631 100644 --- a/recipes/bioconductor-pd.moex.1.0.st.v1/post-link.sh +++ b/recipes/bioconductor-pd.moex.1.0.st.v1/post-link.sh @@ -1,9 +1,10 @@ #!/bin/bash FN="pd.moex.1.0.st.v1_3.14.1.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/pd.moex.1.0.st.v1_3.14.1.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/pd.moex.1.0.st.v1_3.14.1.tar.gz" "https://bioarchive.galaxyproject.org/pd.moex.1.0.st.v1_3.14.1.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-pd.moex.1.0.st.v1/bioconductor-pd.moex.1.0.st.v1_3.14.1_src_all.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-pd.moex.1.0.st.v1/bioconductor-pd.moex.1.0.st.v1_3.14.1_src_all.tar.gz" ) MD5="57427e63b2d44258c12d796eada1897b" @@ -16,7 +17,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-pd.mogene.1.0.st.v1/meta.yaml b/recipes/bioconductor-pd.mogene.1.0.st.v1/meta.yaml index 118dd521ebd39..eb70a556dd8f4 100644 --- a/recipes/bioconductor-pd.mogene.1.0.st.v1/meta.yaml +++ b/recipes/bioconductor-pd.mogene.1.0.st.v1/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.14.1" %} {% set name = "pd.mogene.1.0.st.v1" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -12,31 +12,31 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: c3767385af3b9a120c777adb6d6e3364 build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ noarch: generic requirements: host: - - 'bioconductor-biostrings >=2.50.0,<2.51.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-oligo >=1.46.0,<1.47.0' - - 'bioconductor-oligoclasses >=1.44.0,<1.45.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-biostrings >=2.52.0,<2.53.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-oligo >=1.48.0,<1.49.0' + - 'bioconductor-oligoclasses >=1.46.0,<1.47.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' run: - - 'bioconductor-biostrings >=2.50.0,<2.51.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-oligo >=1.46.0,<1.47.0' - - 'bioconductor-oligoclasses >=1.44.0,<1.45.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-biostrings >=2.52.0,<2.53.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-oligo >=1.48.0,<1.49.0' + - 'bioconductor-oligoclasses >=1.46.0,<1.47.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-pd.mogene.1.0.st.v1/post-link.sh b/recipes/bioconductor-pd.mogene.1.0.st.v1/post-link.sh index e78faef855e72..ce4e57048e50e 100644 --- a/recipes/bioconductor-pd.mogene.1.0.st.v1/post-link.sh +++ b/recipes/bioconductor-pd.mogene.1.0.st.v1/post-link.sh @@ -1,9 +1,10 @@ #!/bin/bash FN="pd.mogene.1.0.st.v1_3.14.1.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/pd.mogene.1.0.st.v1_3.14.1.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/pd.mogene.1.0.st.v1_3.14.1.tar.gz" "https://bioarchive.galaxyproject.org/pd.mogene.1.0.st.v1_3.14.1.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-pd.mogene.1.0.st.v1/bioconductor-pd.mogene.1.0.st.v1_3.14.1_src_all.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-pd.mogene.1.0.st.v1/bioconductor-pd.mogene.1.0.st.v1_3.14.1_src_all.tar.gz" ) MD5="c3767385af3b9a120c777adb6d6e3364" @@ -16,7 +17,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-pd.mogene.1.1.st.v1/meta.yaml b/recipes/bioconductor-pd.mogene.1.1.st.v1/meta.yaml index a33a141573bc5..3a15e52102906 100644 --- a/recipes/bioconductor-pd.mogene.1.1.st.v1/meta.yaml +++ b/recipes/bioconductor-pd.mogene.1.1.st.v1/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.14.1" %} {% set name = "pd.mogene.1.1.st.v1" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -12,31 +12,31 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 3d6c5d29e4d8a0b0152e109b68f82c37 build: - number: 1 + number: 2 rpaths: - lib/R/lib/ - lib/ noarch: generic requirements: host: - - 'bioconductor-biostrings >=2.50.0,<2.51.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-oligo >=1.46.0,<1.47.0' - - 'bioconductor-oligoclasses >=1.44.0,<1.45.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-biostrings >=2.52.0,<2.53.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-oligo >=1.48.0,<1.49.0' + - 'bioconductor-oligoclasses >=1.46.0,<1.47.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' run: - - 'bioconductor-biostrings >=2.50.0,<2.51.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-oligo >=1.46.0,<1.47.0' - - 'bioconductor-oligoclasses >=1.44.0,<1.45.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-biostrings >=2.52.0,<2.53.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-oligo >=1.48.0,<1.49.0' + - 'bioconductor-oligoclasses >=1.46.0,<1.47.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-pd.mogene.1.1.st.v1/post-link.sh b/recipes/bioconductor-pd.mogene.1.1.st.v1/post-link.sh index a55e6aef3c943..016022ebfe94b 100644 --- a/recipes/bioconductor-pd.mogene.1.1.st.v1/post-link.sh +++ b/recipes/bioconductor-pd.mogene.1.1.st.v1/post-link.sh @@ -1,9 +1,10 @@ #!/bin/bash FN="pd.mogene.1.1.st.v1_3.14.1.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/pd.mogene.1.1.st.v1_3.14.1.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/pd.mogene.1.1.st.v1_3.14.1.tar.gz" "https://bioarchive.galaxyproject.org/pd.mogene.1.1.st.v1_3.14.1.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-pd.mogene.1.1.st.v1/bioconductor-pd.mogene.1.1.st.v1_3.14.1_src_all.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-pd.mogene.1.1.st.v1/bioconductor-pd.mogene.1.1.st.v1_3.14.1_src_all.tar.gz" ) MD5="3d6c5d29e4d8a0b0152e109b68f82c37" @@ -16,7 +17,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-pd.mogene.2.0.st/meta.yaml b/recipes/bioconductor-pd.mogene.2.0.st/meta.yaml index 9266d76840128..8a1f8117a155c 100644 --- a/recipes/bioconductor-pd.mogene.2.0.st/meta.yaml +++ b/recipes/bioconductor-pd.mogene.2.0.st/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.14.1" %} {% set name = "pd.mogene.2.0.st" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -12,31 +12,31 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 71326d6bd85de02490171696f923d053 build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ noarch: generic requirements: host: - - 'bioconductor-biostrings >=2.50.0,<2.51.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-oligo >=1.46.0,<1.47.0' - - 'bioconductor-oligoclasses >=1.44.0,<1.45.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-biostrings >=2.52.0,<2.53.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-oligo >=1.48.0,<1.49.0' + - 'bioconductor-oligoclasses >=1.46.0,<1.47.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' run: - - 'bioconductor-biostrings >=2.50.0,<2.51.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-oligo >=1.46.0,<1.47.0' - - 'bioconductor-oligoclasses >=1.44.0,<1.45.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-biostrings >=2.52.0,<2.53.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-oligo >=1.48.0,<1.49.0' + - 'bioconductor-oligoclasses >=1.46.0,<1.47.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-pd.mogene.2.0.st/post-link.sh b/recipes/bioconductor-pd.mogene.2.0.st/post-link.sh index 8c0457f0f5cb9..fcf9b22379144 100644 --- a/recipes/bioconductor-pd.mogene.2.0.st/post-link.sh +++ b/recipes/bioconductor-pd.mogene.2.0.st/post-link.sh @@ -1,9 +1,10 @@ #!/bin/bash FN="pd.mogene.2.0.st_3.14.1.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/pd.mogene.2.0.st_3.14.1.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/pd.mogene.2.0.st_3.14.1.tar.gz" "https://bioarchive.galaxyproject.org/pd.mogene.2.0.st_3.14.1.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-pd.mogene.2.0.st/bioconductor-pd.mogene.2.0.st_3.14.1_src_all.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-pd.mogene.2.0.st/bioconductor-pd.mogene.2.0.st_3.14.1_src_all.tar.gz" ) MD5="71326d6bd85de02490171696f923d053" @@ -16,7 +17,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-pd.mogene.2.1.st/meta.yaml b/recipes/bioconductor-pd.mogene.2.1.st/meta.yaml index 4ae0c5ef48ee4..3227841b626d0 100644 --- a/recipes/bioconductor-pd.mogene.2.1.st/meta.yaml +++ b/recipes/bioconductor-pd.mogene.2.1.st/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.14.1" %} {% set name = "pd.mogene.2.1.st" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -12,31 +12,31 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 2c7fc5644eae98359cb945ff16d072a2 build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ noarch: generic requirements: host: - - 'bioconductor-biostrings >=2.50.0,<2.51.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-oligo >=1.46.0,<1.47.0' - - 'bioconductor-oligoclasses >=1.44.0,<1.45.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-biostrings >=2.52.0,<2.53.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-oligo >=1.48.0,<1.49.0' + - 'bioconductor-oligoclasses >=1.46.0,<1.47.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' run: - - 'bioconductor-biostrings >=2.50.0,<2.51.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-oligo >=1.46.0,<1.47.0' - - 'bioconductor-oligoclasses >=1.44.0,<1.45.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-biostrings >=2.52.0,<2.53.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-oligo >=1.48.0,<1.49.0' + - 'bioconductor-oligoclasses >=1.46.0,<1.47.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-pd.mogene.2.1.st/post-link.sh b/recipes/bioconductor-pd.mogene.2.1.st/post-link.sh index 5cf42e83de2fc..502f231be5f80 100644 --- a/recipes/bioconductor-pd.mogene.2.1.st/post-link.sh +++ b/recipes/bioconductor-pd.mogene.2.1.st/post-link.sh @@ -1,9 +1,10 @@ #!/bin/bash FN="pd.mogene.2.1.st_3.14.1.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/pd.mogene.2.1.st_3.14.1.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/pd.mogene.2.1.st_3.14.1.tar.gz" "https://bioarchive.galaxyproject.org/pd.mogene.2.1.st_3.14.1.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-pd.mogene.2.1.st/bioconductor-pd.mogene.2.1.st_3.14.1_src_all.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-pd.mogene.2.1.st/bioconductor-pd.mogene.2.1.st_3.14.1_src_all.tar.gz" ) MD5="2c7fc5644eae98359cb945ff16d072a2" @@ -16,7 +17,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-pd.mouse430.2/meta.yaml b/recipes/bioconductor-pd.mouse430.2/meta.yaml index c1f7e8ef7cee3..73f9fd51f1c48 100644 --- a/recipes/bioconductor-pd.mouse430.2/meta.yaml +++ b/recipes/bioconductor-pd.mouse430.2/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.12.0" %} {% set name = "pd.mouse430.2" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -12,31 +12,31 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 7f37397a57b06d15101ef86fa6242ca4 build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ noarch: generic requirements: host: - - 'bioconductor-biostrings >=2.50.0,<2.51.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-oligo >=1.46.0,<1.47.0' - - 'bioconductor-oligoclasses >=1.44.0,<1.45.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-biostrings >=2.52.0,<2.53.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-oligo >=1.48.0,<1.49.0' + - 'bioconductor-oligoclasses >=1.46.0,<1.47.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' run: - - 'bioconductor-biostrings >=2.50.0,<2.51.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-oligo >=1.46.0,<1.47.0' - - 'bioconductor-oligoclasses >=1.44.0,<1.45.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-biostrings >=2.52.0,<2.53.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-oligo >=1.48.0,<1.49.0' + - 'bioconductor-oligoclasses >=1.46.0,<1.47.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-pd.mouse430.2/post-link.sh b/recipes/bioconductor-pd.mouse430.2/post-link.sh index c0e23c2942155..a90f84c134e7e 100644 --- a/recipes/bioconductor-pd.mouse430.2/post-link.sh +++ b/recipes/bioconductor-pd.mouse430.2/post-link.sh @@ -1,9 +1,10 @@ #!/bin/bash FN="pd.mouse430.2_3.12.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/pd.mouse430.2_3.12.0.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/pd.mouse430.2_3.12.0.tar.gz" "https://bioarchive.galaxyproject.org/pd.mouse430.2_3.12.0.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-pd.mouse430.2/bioconductor-pd.mouse430.2_3.12.0_src_all.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-pd.mouse430.2/bioconductor-pd.mouse430.2_3.12.0_src_all.tar.gz" ) MD5="7f37397a57b06d15101ef86fa6242ca4" @@ -16,7 +17,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-pd.mouse430a.2/meta.yaml b/recipes/bioconductor-pd.mouse430a.2/meta.yaml index 5efa51f441a3f..f674aebea6606 100644 --- a/recipes/bioconductor-pd.mouse430a.2/meta.yaml +++ b/recipes/bioconductor-pd.mouse430a.2/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.12.0" %} {% set name = "pd.mouse430a.2" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -12,31 +12,31 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 0c28f564a1fa23f59c936d42c156796d build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ noarch: generic requirements: host: - - 'bioconductor-biostrings >=2.50.0,<2.51.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-oligo >=1.46.0,<1.47.0' - - 'bioconductor-oligoclasses >=1.44.0,<1.45.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-biostrings >=2.52.0,<2.53.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-oligo >=1.48.0,<1.49.0' + - 'bioconductor-oligoclasses >=1.46.0,<1.47.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' run: - - 'bioconductor-biostrings >=2.50.0,<2.51.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-oligo >=1.46.0,<1.47.0' - - 'bioconductor-oligoclasses >=1.44.0,<1.45.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-biostrings >=2.52.0,<2.53.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-oligo >=1.48.0,<1.49.0' + - 'bioconductor-oligoclasses >=1.46.0,<1.47.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-pd.mouse430a.2/post-link.sh b/recipes/bioconductor-pd.mouse430a.2/post-link.sh index 08adb1187962e..e3f22fcf90322 100644 --- a/recipes/bioconductor-pd.mouse430a.2/post-link.sh +++ b/recipes/bioconductor-pd.mouse430a.2/post-link.sh @@ -1,9 +1,10 @@ #!/bin/bash FN="pd.mouse430a.2_3.12.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/pd.mouse430a.2_3.12.0.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/pd.mouse430a.2_3.12.0.tar.gz" "https://bioarchive.galaxyproject.org/pd.mouse430a.2_3.12.0.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-pd.mouse430a.2/bioconductor-pd.mouse430a.2_3.12.0_src_all.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-pd.mouse430a.2/bioconductor-pd.mouse430a.2_3.12.0_src_all.tar.gz" ) MD5="0c28f564a1fa23f59c936d42c156796d" @@ -16,7 +17,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-pd.mta.1.0/meta.yaml b/recipes/bioconductor-pd.mta.1.0/meta.yaml index 4cc68033ac38b..f6d7d098f6c77 100644 --- a/recipes/bioconductor-pd.mta.1.0/meta.yaml +++ b/recipes/bioconductor-pd.mta.1.0/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.12.0" %} {% set name = "pd.mta.1.0" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -12,31 +12,31 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 0f737b4f1f1353733e56e2df637f554b build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ noarch: generic requirements: host: - - 'bioconductor-biostrings >=2.50.0,<2.51.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-oligo >=1.46.0,<1.47.0' - - 'bioconductor-oligoclasses >=1.44.0,<1.45.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-biostrings >=2.52.0,<2.53.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-oligo >=1.48.0,<1.49.0' + - 'bioconductor-oligoclasses >=1.46.0,<1.47.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' run: - - 'bioconductor-biostrings >=2.50.0,<2.51.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-oligo >=1.46.0,<1.47.0' - - 'bioconductor-oligoclasses >=1.44.0,<1.45.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-biostrings >=2.52.0,<2.53.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-oligo >=1.48.0,<1.49.0' + - 'bioconductor-oligoclasses >=1.46.0,<1.47.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-pd.mta.1.0/post-link.sh b/recipes/bioconductor-pd.mta.1.0/post-link.sh index d7bb9fe6f4352..6a7ec9c61e346 100644 --- a/recipes/bioconductor-pd.mta.1.0/post-link.sh +++ b/recipes/bioconductor-pd.mta.1.0/post-link.sh @@ -1,9 +1,10 @@ #!/bin/bash FN="pd.mta.1.0_3.12.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/pd.mta.1.0_3.12.0.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/pd.mta.1.0_3.12.0.tar.gz" "https://bioarchive.galaxyproject.org/pd.mta.1.0_3.12.0.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-pd.mta.1.0/bioconductor-pd.mta.1.0_3.12.0_src_all.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-pd.mta.1.0/bioconductor-pd.mta.1.0_3.12.0_src_all.tar.gz" ) MD5="0f737b4f1f1353733e56e2df637f554b" @@ -16,7 +17,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-pd.mu11ksuba/meta.yaml b/recipes/bioconductor-pd.mu11ksuba/meta.yaml index 1813fad5bfa3f..eb49e8344da13 100644 --- a/recipes/bioconductor-pd.mu11ksuba/meta.yaml +++ b/recipes/bioconductor-pd.mu11ksuba/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.12.0" %} {% set name = "pd.mu11ksuba" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -12,31 +12,31 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 56be58b3f444ccb9572dc4c3882964b2 build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ noarch: generic requirements: host: - - 'bioconductor-biostrings >=2.50.0,<2.51.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-oligo >=1.46.0,<1.47.0' - - 'bioconductor-oligoclasses >=1.44.0,<1.45.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-biostrings >=2.52.0,<2.53.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-oligo >=1.48.0,<1.49.0' + - 'bioconductor-oligoclasses >=1.46.0,<1.47.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' run: - - 'bioconductor-biostrings >=2.50.0,<2.51.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-oligo >=1.46.0,<1.47.0' - - 'bioconductor-oligoclasses >=1.44.0,<1.45.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-biostrings >=2.52.0,<2.53.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-oligo >=1.48.0,<1.49.0' + - 'bioconductor-oligoclasses >=1.46.0,<1.47.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-pd.mu11ksuba/post-link.sh b/recipes/bioconductor-pd.mu11ksuba/post-link.sh index bc09886823b82..3569fd0bd07a6 100644 --- a/recipes/bioconductor-pd.mu11ksuba/post-link.sh +++ b/recipes/bioconductor-pd.mu11ksuba/post-link.sh @@ -1,9 +1,10 @@ #!/bin/bash FN="pd.mu11ksuba_3.12.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/pd.mu11ksuba_3.12.0.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/pd.mu11ksuba_3.12.0.tar.gz" "https://bioarchive.galaxyproject.org/pd.mu11ksuba_3.12.0.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-pd.mu11ksuba/bioconductor-pd.mu11ksuba_3.12.0_src_all.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-pd.mu11ksuba/bioconductor-pd.mu11ksuba_3.12.0_src_all.tar.gz" ) MD5="56be58b3f444ccb9572dc4c3882964b2" @@ -16,7 +17,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-pd.mu11ksubb/meta.yaml b/recipes/bioconductor-pd.mu11ksubb/meta.yaml index 5f04ea5c23082..66d202cb81841 100644 --- a/recipes/bioconductor-pd.mu11ksubb/meta.yaml +++ b/recipes/bioconductor-pd.mu11ksubb/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.12.0" %} {% set name = "pd.mu11ksubb" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -12,31 +12,31 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: c45b0ebe777b99cec38499826cc1b457 build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ noarch: generic requirements: host: - - 'bioconductor-biostrings >=2.50.0,<2.51.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-oligo >=1.46.0,<1.47.0' - - 'bioconductor-oligoclasses >=1.44.0,<1.45.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-biostrings >=2.52.0,<2.53.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-oligo >=1.48.0,<1.49.0' + - 'bioconductor-oligoclasses >=1.46.0,<1.47.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' run: - - 'bioconductor-biostrings >=2.50.0,<2.51.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-oligo >=1.46.0,<1.47.0' - - 'bioconductor-oligoclasses >=1.44.0,<1.45.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-biostrings >=2.52.0,<2.53.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-oligo >=1.48.0,<1.49.0' + - 'bioconductor-oligoclasses >=1.46.0,<1.47.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-pd.mu11ksubb/post-link.sh b/recipes/bioconductor-pd.mu11ksubb/post-link.sh index 59bfa000e0a0d..25264397fd9e0 100644 --- a/recipes/bioconductor-pd.mu11ksubb/post-link.sh +++ b/recipes/bioconductor-pd.mu11ksubb/post-link.sh @@ -1,9 +1,10 @@ #!/bin/bash FN="pd.mu11ksubb_3.12.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/pd.mu11ksubb_3.12.0.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/pd.mu11ksubb_3.12.0.tar.gz" "https://bioarchive.galaxyproject.org/pd.mu11ksubb_3.12.0.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-pd.mu11ksubb/bioconductor-pd.mu11ksubb_3.12.0_src_all.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-pd.mu11ksubb/bioconductor-pd.mu11ksubb_3.12.0_src_all.tar.gz" ) MD5="c45b0ebe777b99cec38499826cc1b457" @@ -16,7 +17,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-pd.nugo.hs1a520180/meta.yaml b/recipes/bioconductor-pd.nugo.hs1a520180/meta.yaml index e221357173936..182d5760f20ff 100644 --- a/recipes/bioconductor-pd.nugo.hs1a520180/meta.yaml +++ b/recipes/bioconductor-pd.nugo.hs1a520180/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.4.0" %} {% set name = "pd.nugo.hs1a520180" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -12,31 +12,31 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 88a836472f0f9aab2e1d54e4bad7d6af build: - number: 1 + number: 2 rpaths: - lib/R/lib/ - lib/ noarch: generic requirements: host: - - 'bioconductor-biostrings >=2.50.0,<2.51.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-oligo >=1.46.0,<1.47.0' - - 'bioconductor-oligoclasses >=1.44.0,<1.45.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-biostrings >=2.52.0,<2.53.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-oligo >=1.48.0,<1.49.0' + - 'bioconductor-oligoclasses >=1.46.0,<1.47.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' run: - - 'bioconductor-biostrings >=2.50.0,<2.51.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-oligo >=1.46.0,<1.47.0' - - 'bioconductor-oligoclasses >=1.44.0,<1.45.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-biostrings >=2.52.0,<2.53.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-oligo >=1.48.0,<1.49.0' + - 'bioconductor-oligoclasses >=1.46.0,<1.47.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-pd.nugo.hs1a520180/post-link.sh b/recipes/bioconductor-pd.nugo.hs1a520180/post-link.sh index 0ab9093b71c05..2aae255d6a56e 100644 --- a/recipes/bioconductor-pd.nugo.hs1a520180/post-link.sh +++ b/recipes/bioconductor-pd.nugo.hs1a520180/post-link.sh @@ -1,9 +1,10 @@ #!/bin/bash FN="pd.nugo.hs1a520180_3.4.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/pd.nugo.hs1a520180_3.4.0.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/pd.nugo.hs1a520180_3.4.0.tar.gz" "https://bioarchive.galaxyproject.org/pd.nugo.hs1a520180_3.4.0.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-pd.nugo.hs1a520180/bioconductor-pd.nugo.hs1a520180_3.4.0_src_all.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-pd.nugo.hs1a520180/bioconductor-pd.nugo.hs1a520180_3.4.0_src_all.tar.gz" ) MD5="88a836472f0f9aab2e1d54e4bad7d6af" @@ -16,7 +17,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-pd.nugo.mm1a520177/meta.yaml b/recipes/bioconductor-pd.nugo.mm1a520177/meta.yaml index 4e9d7cf7d3f4e..238ea5d8a0eb4 100644 --- a/recipes/bioconductor-pd.nugo.mm1a520177/meta.yaml +++ b/recipes/bioconductor-pd.nugo.mm1a520177/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.4.0" %} {% set name = "pd.nugo.mm1a520177" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -12,31 +12,31 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 5cd64895eaddaf4cae1c48db9468c079 build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ noarch: generic requirements: host: - - 'bioconductor-biostrings >=2.50.0,<2.51.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-oligo >=1.46.0,<1.47.0' - - 'bioconductor-oligoclasses >=1.44.0,<1.45.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-biostrings >=2.52.0,<2.53.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-oligo >=1.48.0,<1.49.0' + - 'bioconductor-oligoclasses >=1.46.0,<1.47.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' run: - - 'bioconductor-biostrings >=2.50.0,<2.51.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-oligo >=1.46.0,<1.47.0' - - 'bioconductor-oligoclasses >=1.44.0,<1.45.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-biostrings >=2.52.0,<2.53.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-oligo >=1.48.0,<1.49.0' + - 'bioconductor-oligoclasses >=1.46.0,<1.47.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-pd.nugo.mm1a520177/post-link.sh b/recipes/bioconductor-pd.nugo.mm1a520177/post-link.sh index 40a3fe068d44f..1ebc53dd83099 100644 --- a/recipes/bioconductor-pd.nugo.mm1a520177/post-link.sh +++ b/recipes/bioconductor-pd.nugo.mm1a520177/post-link.sh @@ -1,9 +1,10 @@ #!/bin/bash FN="pd.nugo.mm1a520177_3.4.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/pd.nugo.mm1a520177_3.4.0.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/pd.nugo.mm1a520177_3.4.0.tar.gz" "https://bioarchive.galaxyproject.org/pd.nugo.mm1a520177_3.4.0.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-pd.nugo.mm1a520177/bioconductor-pd.nugo.mm1a520177_3.4.0_src_all.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-pd.nugo.mm1a520177/bioconductor-pd.nugo.mm1a520177_3.4.0_src_all.tar.gz" ) MD5="5cd64895eaddaf4cae1c48db9468c079" @@ -16,7 +17,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-pd.ovigene.1.0.st/meta.yaml b/recipes/bioconductor-pd.ovigene.1.0.st/meta.yaml index 4626ef43efed3..39cbf8461819c 100644 --- a/recipes/bioconductor-pd.ovigene.1.0.st/meta.yaml +++ b/recipes/bioconductor-pd.ovigene.1.0.st/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.12.0" %} {% set name = "pd.ovigene.1.0.st" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -12,31 +12,31 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 88cfedfe10dd357539305051a69d31a1 build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ noarch: generic requirements: host: - - 'bioconductor-biostrings >=2.50.0,<2.51.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-oligo >=1.46.0,<1.47.0' - - 'bioconductor-oligoclasses >=1.44.0,<1.45.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-biostrings >=2.52.0,<2.53.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-oligo >=1.48.0,<1.49.0' + - 'bioconductor-oligoclasses >=1.46.0,<1.47.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' run: - - 'bioconductor-biostrings >=2.50.0,<2.51.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-oligo >=1.46.0,<1.47.0' - - 'bioconductor-oligoclasses >=1.44.0,<1.45.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-biostrings >=2.52.0,<2.53.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-oligo >=1.48.0,<1.49.0' + - 'bioconductor-oligoclasses >=1.46.0,<1.47.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-pd.ovigene.1.0.st/post-link.sh b/recipes/bioconductor-pd.ovigene.1.0.st/post-link.sh index 36b5a01b46781..224b44481194c 100644 --- a/recipes/bioconductor-pd.ovigene.1.0.st/post-link.sh +++ b/recipes/bioconductor-pd.ovigene.1.0.st/post-link.sh @@ -1,9 +1,10 @@ #!/bin/bash FN="pd.ovigene.1.0.st_3.12.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/pd.ovigene.1.0.st_3.12.0.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/pd.ovigene.1.0.st_3.12.0.tar.gz" "https://bioarchive.galaxyproject.org/pd.ovigene.1.0.st_3.12.0.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-pd.ovigene.1.0.st/bioconductor-pd.ovigene.1.0.st_3.12.0_src_all.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-pd.ovigene.1.0.st/bioconductor-pd.ovigene.1.0.st_3.12.0_src_all.tar.gz" ) MD5="88cfedfe10dd357539305051a69d31a1" @@ -16,7 +17,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-pd.ovigene.1.1.st/meta.yaml b/recipes/bioconductor-pd.ovigene.1.1.st/meta.yaml index d8ca32c874ca9..374890cf4f83c 100644 --- a/recipes/bioconductor-pd.ovigene.1.1.st/meta.yaml +++ b/recipes/bioconductor-pd.ovigene.1.1.st/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.12.0" %} {% set name = "pd.ovigene.1.1.st" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -12,31 +12,31 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: d6158cacd32a1892975fddd8dc8bb3f2 build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ noarch: generic requirements: host: - - 'bioconductor-biostrings >=2.50.0,<2.51.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-oligo >=1.46.0,<1.47.0' - - 'bioconductor-oligoclasses >=1.44.0,<1.45.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-biostrings >=2.52.0,<2.53.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-oligo >=1.48.0,<1.49.0' + - 'bioconductor-oligoclasses >=1.46.0,<1.47.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' run: - - 'bioconductor-biostrings >=2.50.0,<2.51.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-oligo >=1.46.0,<1.47.0' - - 'bioconductor-oligoclasses >=1.44.0,<1.45.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-biostrings >=2.52.0,<2.53.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-oligo >=1.48.0,<1.49.0' + - 'bioconductor-oligoclasses >=1.46.0,<1.47.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-pd.ovigene.1.1.st/post-link.sh b/recipes/bioconductor-pd.ovigene.1.1.st/post-link.sh index 73944815fb6b7..6351db91cf377 100644 --- a/recipes/bioconductor-pd.ovigene.1.1.st/post-link.sh +++ b/recipes/bioconductor-pd.ovigene.1.1.st/post-link.sh @@ -1,9 +1,10 @@ #!/bin/bash FN="pd.ovigene.1.1.st_3.12.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/pd.ovigene.1.1.st_3.12.0.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/pd.ovigene.1.1.st_3.12.0.tar.gz" "https://bioarchive.galaxyproject.org/pd.ovigene.1.1.st_3.12.0.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-pd.ovigene.1.1.st/bioconductor-pd.ovigene.1.1.st_3.12.0_src_all.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-pd.ovigene.1.1.st/bioconductor-pd.ovigene.1.1.st_3.12.0_src_all.tar.gz" ) MD5="d6158cacd32a1892975fddd8dc8bb3f2" @@ -16,7 +17,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-pd.pae.g1a/meta.yaml b/recipes/bioconductor-pd.pae.g1a/meta.yaml index 3dc92fdfa84a9..beb8fd027bf39 100644 --- a/recipes/bioconductor-pd.pae.g1a/meta.yaml +++ b/recipes/bioconductor-pd.pae.g1a/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.12.0" %} {% set name = "pd.pae.g1a" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -12,31 +12,31 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: d96462eb35c63b30772bccae2a27a8cd build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ noarch: generic requirements: host: - - 'bioconductor-biostrings >=2.50.0,<2.51.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-oligo >=1.46.0,<1.47.0' - - 'bioconductor-oligoclasses >=1.44.0,<1.45.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-biostrings >=2.52.0,<2.53.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-oligo >=1.48.0,<1.49.0' + - 'bioconductor-oligoclasses >=1.46.0,<1.47.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' run: - - 'bioconductor-biostrings >=2.50.0,<2.51.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-oligo >=1.46.0,<1.47.0' - - 'bioconductor-oligoclasses >=1.44.0,<1.45.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-biostrings >=2.52.0,<2.53.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-oligo >=1.48.0,<1.49.0' + - 'bioconductor-oligoclasses >=1.46.0,<1.47.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-pd.pae.g1a/post-link.sh b/recipes/bioconductor-pd.pae.g1a/post-link.sh index d95e014b5a3d0..86de75fa9a3c8 100644 --- a/recipes/bioconductor-pd.pae.g1a/post-link.sh +++ b/recipes/bioconductor-pd.pae.g1a/post-link.sh @@ -1,9 +1,10 @@ #!/bin/bash FN="pd.pae.g1a_3.12.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/pd.pae.g1a_3.12.0.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/pd.pae.g1a_3.12.0.tar.gz" "https://bioarchive.galaxyproject.org/pd.pae.g1a_3.12.0.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-pd.pae.g1a/bioconductor-pd.pae.g1a_3.12.0_src_all.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-pd.pae.g1a/bioconductor-pd.pae.g1a_3.12.0_src_all.tar.gz" ) MD5="d96462eb35c63b30772bccae2a27a8cd" @@ -16,7 +17,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-pd.plasmodium.anopheles/meta.yaml b/recipes/bioconductor-pd.plasmodium.anopheles/meta.yaml index 0d72c4b87af78..9db914d6a0ef4 100644 --- a/recipes/bioconductor-pd.plasmodium.anopheles/meta.yaml +++ b/recipes/bioconductor-pd.plasmodium.anopheles/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.12.0" %} {% set name = "pd.plasmodium.anopheles" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -12,31 +12,31 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: ae55b1451ceaed951f68213c0433f3d0 build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ noarch: generic requirements: host: - - 'bioconductor-biostrings >=2.50.0,<2.51.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-oligo >=1.46.0,<1.47.0' - - 'bioconductor-oligoclasses >=1.44.0,<1.45.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-biostrings >=2.52.0,<2.53.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-oligo >=1.48.0,<1.49.0' + - 'bioconductor-oligoclasses >=1.46.0,<1.47.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' run: - - 'bioconductor-biostrings >=2.50.0,<2.51.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-oligo >=1.46.0,<1.47.0' - - 'bioconductor-oligoclasses >=1.44.0,<1.45.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-biostrings >=2.52.0,<2.53.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-oligo >=1.48.0,<1.49.0' + - 'bioconductor-oligoclasses >=1.46.0,<1.47.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-pd.plasmodium.anopheles/post-link.sh b/recipes/bioconductor-pd.plasmodium.anopheles/post-link.sh index 1b0416d2e97a5..3528d0b6bc550 100644 --- a/recipes/bioconductor-pd.plasmodium.anopheles/post-link.sh +++ b/recipes/bioconductor-pd.plasmodium.anopheles/post-link.sh @@ -1,9 +1,10 @@ #!/bin/bash FN="pd.plasmodium.anopheles_3.12.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/pd.plasmodium.anopheles_3.12.0.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/pd.plasmodium.anopheles_3.12.0.tar.gz" "https://bioarchive.galaxyproject.org/pd.plasmodium.anopheles_3.12.0.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-pd.plasmodium.anopheles/bioconductor-pd.plasmodium.anopheles_3.12.0_src_all.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-pd.plasmodium.anopheles/bioconductor-pd.plasmodium.anopheles_3.12.0_src_all.tar.gz" ) MD5="ae55b1451ceaed951f68213c0433f3d0" @@ -16,7 +17,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-pd.poplar/meta.yaml b/recipes/bioconductor-pd.poplar/meta.yaml index ea17481d19759..6ad3de0e624b3 100644 --- a/recipes/bioconductor-pd.poplar/meta.yaml +++ b/recipes/bioconductor-pd.poplar/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.12.0" %} {% set name = "pd.poplar" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -12,31 +12,31 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 9c33b7528e5a47654aeacf61b71058a8 build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ noarch: generic requirements: host: - - 'bioconductor-biostrings >=2.50.0,<2.51.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-oligo >=1.46.0,<1.47.0' - - 'bioconductor-oligoclasses >=1.44.0,<1.45.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-biostrings >=2.52.0,<2.53.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-oligo >=1.48.0,<1.49.0' + - 'bioconductor-oligoclasses >=1.46.0,<1.47.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' run: - - 'bioconductor-biostrings >=2.50.0,<2.51.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-oligo >=1.46.0,<1.47.0' - - 'bioconductor-oligoclasses >=1.44.0,<1.45.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-biostrings >=2.52.0,<2.53.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-oligo >=1.48.0,<1.49.0' + - 'bioconductor-oligoclasses >=1.46.0,<1.47.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-pd.poplar/post-link.sh b/recipes/bioconductor-pd.poplar/post-link.sh index e312b76ac2e30..2e2a931da75e0 100644 --- a/recipes/bioconductor-pd.poplar/post-link.sh +++ b/recipes/bioconductor-pd.poplar/post-link.sh @@ -1,9 +1,10 @@ #!/bin/bash FN="pd.poplar_3.12.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/pd.poplar_3.12.0.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/pd.poplar_3.12.0.tar.gz" "https://bioarchive.galaxyproject.org/pd.poplar_3.12.0.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-pd.poplar/bioconductor-pd.poplar_3.12.0_src_all.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-pd.poplar/bioconductor-pd.poplar_3.12.0_src_all.tar.gz" ) MD5="9c33b7528e5a47654aeacf61b71058a8" @@ -16,7 +17,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-pd.porcine/meta.yaml b/recipes/bioconductor-pd.porcine/meta.yaml index 298b44ccf9970..6ad0cd2a0c162 100644 --- a/recipes/bioconductor-pd.porcine/meta.yaml +++ b/recipes/bioconductor-pd.porcine/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.12.0" %} {% set name = "pd.porcine" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -12,31 +12,31 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 5df404babadb1d6faef73e249c819a72 build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ noarch: generic requirements: host: - - 'bioconductor-biostrings >=2.50.0,<2.51.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-oligo >=1.46.0,<1.47.0' - - 'bioconductor-oligoclasses >=1.44.0,<1.45.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-biostrings >=2.52.0,<2.53.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-oligo >=1.48.0,<1.49.0' + - 'bioconductor-oligoclasses >=1.46.0,<1.47.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' run: - - 'bioconductor-biostrings >=2.50.0,<2.51.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-oligo >=1.46.0,<1.47.0' - - 'bioconductor-oligoclasses >=1.44.0,<1.45.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-biostrings >=2.52.0,<2.53.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-oligo >=1.48.0,<1.49.0' + - 'bioconductor-oligoclasses >=1.46.0,<1.47.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-pd.porcine/post-link.sh b/recipes/bioconductor-pd.porcine/post-link.sh index f46533e1d4001..89b362b9e3ca2 100644 --- a/recipes/bioconductor-pd.porcine/post-link.sh +++ b/recipes/bioconductor-pd.porcine/post-link.sh @@ -1,9 +1,10 @@ #!/bin/bash FN="pd.porcine_3.12.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/pd.porcine_3.12.0.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/pd.porcine_3.12.0.tar.gz" "https://bioarchive.galaxyproject.org/pd.porcine_3.12.0.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-pd.porcine/bioconductor-pd.porcine_3.12.0_src_all.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-pd.porcine/bioconductor-pd.porcine_3.12.0_src_all.tar.gz" ) MD5="5df404babadb1d6faef73e249c819a72" @@ -16,7 +17,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-pd.porgene.1.0.st/meta.yaml b/recipes/bioconductor-pd.porgene.1.0.st/meta.yaml index 34c1c5cc82dc5..0ac081ca61ed4 100644 --- a/recipes/bioconductor-pd.porgene.1.0.st/meta.yaml +++ b/recipes/bioconductor-pd.porgene.1.0.st/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.12.0" %} {% set name = "pd.porgene.1.0.st" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -12,31 +12,31 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 203fc56b0e2904fa7063c4a325e038f1 build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ noarch: generic requirements: host: - - 'bioconductor-biostrings >=2.50.0,<2.51.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-oligo >=1.46.0,<1.47.0' - - 'bioconductor-oligoclasses >=1.44.0,<1.45.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-biostrings >=2.52.0,<2.53.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-oligo >=1.48.0,<1.49.0' + - 'bioconductor-oligoclasses >=1.46.0,<1.47.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' run: - - 'bioconductor-biostrings >=2.50.0,<2.51.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-oligo >=1.46.0,<1.47.0' - - 'bioconductor-oligoclasses >=1.44.0,<1.45.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-biostrings >=2.52.0,<2.53.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-oligo >=1.48.0,<1.49.0' + - 'bioconductor-oligoclasses >=1.46.0,<1.47.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-pd.porgene.1.0.st/post-link.sh b/recipes/bioconductor-pd.porgene.1.0.st/post-link.sh index 8e2d4a333becd..d7e922bb06862 100644 --- a/recipes/bioconductor-pd.porgene.1.0.st/post-link.sh +++ b/recipes/bioconductor-pd.porgene.1.0.st/post-link.sh @@ -1,9 +1,10 @@ #!/bin/bash FN="pd.porgene.1.0.st_3.12.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/pd.porgene.1.0.st_3.12.0.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/pd.porgene.1.0.st_3.12.0.tar.gz" "https://bioarchive.galaxyproject.org/pd.porgene.1.0.st_3.12.0.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-pd.porgene.1.0.st/bioconductor-pd.porgene.1.0.st_3.12.0_src_all.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-pd.porgene.1.0.st/bioconductor-pd.porgene.1.0.st_3.12.0_src_all.tar.gz" ) MD5="203fc56b0e2904fa7063c4a325e038f1" @@ -16,7 +17,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-pd.porgene.1.1.st/meta.yaml b/recipes/bioconductor-pd.porgene.1.1.st/meta.yaml index 762ee9eff28a8..a51a3a6381224 100644 --- a/recipes/bioconductor-pd.porgene.1.1.st/meta.yaml +++ b/recipes/bioconductor-pd.porgene.1.1.st/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.12.0" %} {% set name = "pd.porgene.1.1.st" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -12,31 +12,31 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 3a31d325861925a7428241207c461a1d build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ noarch: generic requirements: host: - - 'bioconductor-biostrings >=2.50.0,<2.51.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-oligo >=1.46.0,<1.47.0' - - 'bioconductor-oligoclasses >=1.44.0,<1.45.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-biostrings >=2.52.0,<2.53.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-oligo >=1.48.0,<1.49.0' + - 'bioconductor-oligoclasses >=1.46.0,<1.47.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' run: - - 'bioconductor-biostrings >=2.50.0,<2.51.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-oligo >=1.46.0,<1.47.0' - - 'bioconductor-oligoclasses >=1.44.0,<1.45.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-biostrings >=2.52.0,<2.53.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-oligo >=1.48.0,<1.49.0' + - 'bioconductor-oligoclasses >=1.46.0,<1.47.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-pd.porgene.1.1.st/post-link.sh b/recipes/bioconductor-pd.porgene.1.1.st/post-link.sh index 259b6afddf79b..ca810800d1f40 100644 --- a/recipes/bioconductor-pd.porgene.1.1.st/post-link.sh +++ b/recipes/bioconductor-pd.porgene.1.1.st/post-link.sh @@ -1,9 +1,10 @@ #!/bin/bash FN="pd.porgene.1.1.st_3.12.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/pd.porgene.1.1.st_3.12.0.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/pd.porgene.1.1.st_3.12.0.tar.gz" "https://bioarchive.galaxyproject.org/pd.porgene.1.1.st_3.12.0.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-pd.porgene.1.1.st/bioconductor-pd.porgene.1.1.st_3.12.0_src_all.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-pd.porgene.1.1.st/bioconductor-pd.porgene.1.1.st_3.12.0_src_all.tar.gz" ) MD5="3a31d325861925a7428241207c461a1d" @@ -16,7 +17,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-pd.rabgene.1.0.st/meta.yaml b/recipes/bioconductor-pd.rabgene.1.0.st/meta.yaml index 1add7d7362342..1d7ff6261f671 100644 --- a/recipes/bioconductor-pd.rabgene.1.0.st/meta.yaml +++ b/recipes/bioconductor-pd.rabgene.1.0.st/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.12.0" %} {% set name = "pd.rabgene.1.0.st" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -12,31 +12,31 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 7f1e33f4767a4c4653bdaff2b79989a0 build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ noarch: generic requirements: host: - - 'bioconductor-biostrings >=2.50.0,<2.51.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-oligo >=1.46.0,<1.47.0' - - 'bioconductor-oligoclasses >=1.44.0,<1.45.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-biostrings >=2.52.0,<2.53.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-oligo >=1.48.0,<1.49.0' + - 'bioconductor-oligoclasses >=1.46.0,<1.47.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' run: - - 'bioconductor-biostrings >=2.50.0,<2.51.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-oligo >=1.46.0,<1.47.0' - - 'bioconductor-oligoclasses >=1.44.0,<1.45.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-biostrings >=2.52.0,<2.53.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-oligo >=1.48.0,<1.49.0' + - 'bioconductor-oligoclasses >=1.46.0,<1.47.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-pd.rabgene.1.0.st/post-link.sh b/recipes/bioconductor-pd.rabgene.1.0.st/post-link.sh index 5c1066d6e2c47..da3951c7d53f2 100644 --- a/recipes/bioconductor-pd.rabgene.1.0.st/post-link.sh +++ b/recipes/bioconductor-pd.rabgene.1.0.st/post-link.sh @@ -1,9 +1,10 @@ #!/bin/bash FN="pd.rabgene.1.0.st_3.12.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/pd.rabgene.1.0.st_3.12.0.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/pd.rabgene.1.0.st_3.12.0.tar.gz" "https://bioarchive.galaxyproject.org/pd.rabgene.1.0.st_3.12.0.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-pd.rabgene.1.0.st/bioconductor-pd.rabgene.1.0.st_3.12.0_src_all.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-pd.rabgene.1.0.st/bioconductor-pd.rabgene.1.0.st_3.12.0_src_all.tar.gz" ) MD5="7f1e33f4767a4c4653bdaff2b79989a0" @@ -16,7 +17,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-pd.rabgene.1.1.st/meta.yaml b/recipes/bioconductor-pd.rabgene.1.1.st/meta.yaml index dc1075fb37315..dbcb17933d072 100644 --- a/recipes/bioconductor-pd.rabgene.1.1.st/meta.yaml +++ b/recipes/bioconductor-pd.rabgene.1.1.st/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.12.0" %} {% set name = "pd.rabgene.1.1.st" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -12,31 +12,31 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 2492695661309f5e6628612685460ee5 build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ noarch: generic requirements: host: - - 'bioconductor-biostrings >=2.50.0,<2.51.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-oligo >=1.46.0,<1.47.0' - - 'bioconductor-oligoclasses >=1.44.0,<1.45.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-biostrings >=2.52.0,<2.53.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-oligo >=1.48.0,<1.49.0' + - 'bioconductor-oligoclasses >=1.46.0,<1.47.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' run: - - 'bioconductor-biostrings >=2.50.0,<2.51.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-oligo >=1.46.0,<1.47.0' - - 'bioconductor-oligoclasses >=1.44.0,<1.45.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-biostrings >=2.52.0,<2.53.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-oligo >=1.48.0,<1.49.0' + - 'bioconductor-oligoclasses >=1.46.0,<1.47.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-pd.rabgene.1.1.st/post-link.sh b/recipes/bioconductor-pd.rabgene.1.1.st/post-link.sh index 6de544b2644d5..df33ee512cdc7 100644 --- a/recipes/bioconductor-pd.rabgene.1.1.st/post-link.sh +++ b/recipes/bioconductor-pd.rabgene.1.1.st/post-link.sh @@ -1,9 +1,10 @@ #!/bin/bash FN="pd.rabgene.1.1.st_3.12.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/pd.rabgene.1.1.st_3.12.0.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/pd.rabgene.1.1.st_3.12.0.tar.gz" "https://bioarchive.galaxyproject.org/pd.rabgene.1.1.st_3.12.0.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-pd.rabgene.1.1.st/bioconductor-pd.rabgene.1.1.st_3.12.0_src_all.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-pd.rabgene.1.1.st/bioconductor-pd.rabgene.1.1.st_3.12.0_src_all.tar.gz" ) MD5="2492695661309f5e6628612685460ee5" @@ -16,7 +17,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-pd.rae230a/meta.yaml b/recipes/bioconductor-pd.rae230a/meta.yaml index 693724c087a3e..231b670305943 100644 --- a/recipes/bioconductor-pd.rae230a/meta.yaml +++ b/recipes/bioconductor-pd.rae230a/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.12.0" %} {% set name = "pd.rae230a" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -12,31 +12,31 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: fa4a1c29d3457b1db82b1010c5f72412 build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ noarch: generic requirements: host: - - 'bioconductor-biostrings >=2.50.0,<2.51.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-oligo >=1.46.0,<1.47.0' - - 'bioconductor-oligoclasses >=1.44.0,<1.45.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-biostrings >=2.52.0,<2.53.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-oligo >=1.48.0,<1.49.0' + - 'bioconductor-oligoclasses >=1.46.0,<1.47.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' run: - - 'bioconductor-biostrings >=2.50.0,<2.51.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-oligo >=1.46.0,<1.47.0' - - 'bioconductor-oligoclasses >=1.44.0,<1.45.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-biostrings >=2.52.0,<2.53.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-oligo >=1.48.0,<1.49.0' + - 'bioconductor-oligoclasses >=1.46.0,<1.47.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-pd.rae230a/post-link.sh b/recipes/bioconductor-pd.rae230a/post-link.sh index 9890ffc859cf5..0422dfc058742 100644 --- a/recipes/bioconductor-pd.rae230a/post-link.sh +++ b/recipes/bioconductor-pd.rae230a/post-link.sh @@ -1,9 +1,10 @@ #!/bin/bash FN="pd.rae230a_3.12.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/pd.rae230a_3.12.0.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/pd.rae230a_3.12.0.tar.gz" "https://bioarchive.galaxyproject.org/pd.rae230a_3.12.0.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-pd.rae230a/bioconductor-pd.rae230a_3.12.0_src_all.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-pd.rae230a/bioconductor-pd.rae230a_3.12.0_src_all.tar.gz" ) MD5="fa4a1c29d3457b1db82b1010c5f72412" @@ -16,7 +17,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-pd.rae230b/meta.yaml b/recipes/bioconductor-pd.rae230b/meta.yaml index 8cc778f198afa..9cd21e6912e91 100644 --- a/recipes/bioconductor-pd.rae230b/meta.yaml +++ b/recipes/bioconductor-pd.rae230b/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.12.0" %} {% set name = "pd.rae230b" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -12,31 +12,31 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 10e2e70bb7538119127cd65f636f93b6 build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ noarch: generic requirements: host: - - 'bioconductor-biostrings >=2.50.0,<2.51.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-oligo >=1.46.0,<1.47.0' - - 'bioconductor-oligoclasses >=1.44.0,<1.45.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-biostrings >=2.52.0,<2.53.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-oligo >=1.48.0,<1.49.0' + - 'bioconductor-oligoclasses >=1.46.0,<1.47.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' run: - - 'bioconductor-biostrings >=2.50.0,<2.51.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-oligo >=1.46.0,<1.47.0' - - 'bioconductor-oligoclasses >=1.44.0,<1.45.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-biostrings >=2.52.0,<2.53.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-oligo >=1.48.0,<1.49.0' + - 'bioconductor-oligoclasses >=1.46.0,<1.47.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-pd.rae230b/post-link.sh b/recipes/bioconductor-pd.rae230b/post-link.sh index 15d2035239b82..dd6c295dd66c5 100644 --- a/recipes/bioconductor-pd.rae230b/post-link.sh +++ b/recipes/bioconductor-pd.rae230b/post-link.sh @@ -1,9 +1,10 @@ #!/bin/bash FN="pd.rae230b_3.12.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/pd.rae230b_3.12.0.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/pd.rae230b_3.12.0.tar.gz" "https://bioarchive.galaxyproject.org/pd.rae230b_3.12.0.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-pd.rae230b/bioconductor-pd.rae230b_3.12.0_src_all.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-pd.rae230b/bioconductor-pd.rae230b_3.12.0_src_all.tar.gz" ) MD5="10e2e70bb7538119127cd65f636f93b6" @@ -16,7 +17,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-pd.raex.1.0.st.v1/meta.yaml b/recipes/bioconductor-pd.raex.1.0.st.v1/meta.yaml index a402c2d258b37..844c439cb5f85 100644 --- a/recipes/bioconductor-pd.raex.1.0.st.v1/meta.yaml +++ b/recipes/bioconductor-pd.raex.1.0.st.v1/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.14.1" %} {% set name = "pd.raex.1.0.st.v1" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -12,31 +12,31 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: e2160b549f63ffcc9222d88d82d4d393 build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ noarch: generic requirements: host: - - 'bioconductor-biostrings >=2.50.0,<2.51.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-oligo >=1.46.0,<1.47.0' - - 'bioconductor-oligoclasses >=1.44.0,<1.45.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-biostrings >=2.52.0,<2.53.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-oligo >=1.48.0,<1.49.0' + - 'bioconductor-oligoclasses >=1.46.0,<1.47.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' run: - - 'bioconductor-biostrings >=2.50.0,<2.51.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-oligo >=1.46.0,<1.47.0' - - 'bioconductor-oligoclasses >=1.44.0,<1.45.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-biostrings >=2.52.0,<2.53.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-oligo >=1.48.0,<1.49.0' + - 'bioconductor-oligoclasses >=1.46.0,<1.47.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-pd.raex.1.0.st.v1/post-link.sh b/recipes/bioconductor-pd.raex.1.0.st.v1/post-link.sh index 2d1bfbbd97b7a..87ed4dea50543 100644 --- a/recipes/bioconductor-pd.raex.1.0.st.v1/post-link.sh +++ b/recipes/bioconductor-pd.raex.1.0.st.v1/post-link.sh @@ -1,9 +1,10 @@ #!/bin/bash FN="pd.raex.1.0.st.v1_3.14.1.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/pd.raex.1.0.st.v1_3.14.1.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/pd.raex.1.0.st.v1_3.14.1.tar.gz" "https://bioarchive.galaxyproject.org/pd.raex.1.0.st.v1_3.14.1.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-pd.raex.1.0.st.v1/bioconductor-pd.raex.1.0.st.v1_3.14.1_src_all.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-pd.raex.1.0.st.v1/bioconductor-pd.raex.1.0.st.v1_3.14.1_src_all.tar.gz" ) MD5="e2160b549f63ffcc9222d88d82d4d393" @@ -16,7 +17,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-pd.ragene.1.0.st.v1/meta.yaml b/recipes/bioconductor-pd.ragene.1.0.st.v1/meta.yaml index abb26f7641121..39dcad3480d99 100644 --- a/recipes/bioconductor-pd.ragene.1.0.st.v1/meta.yaml +++ b/recipes/bioconductor-pd.ragene.1.0.st.v1/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.14.1" %} {% set name = "pd.ragene.1.0.st.v1" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -12,31 +12,31 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 122cb69603e705218d01d70f48e90cad build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ noarch: generic requirements: host: - - 'bioconductor-biostrings >=2.50.0,<2.51.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-oligo >=1.46.0,<1.47.0' - - 'bioconductor-oligoclasses >=1.44.0,<1.45.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-biostrings >=2.52.0,<2.53.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-oligo >=1.48.0,<1.49.0' + - 'bioconductor-oligoclasses >=1.46.0,<1.47.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' run: - - 'bioconductor-biostrings >=2.50.0,<2.51.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-oligo >=1.46.0,<1.47.0' - - 'bioconductor-oligoclasses >=1.44.0,<1.45.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-biostrings >=2.52.0,<2.53.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-oligo >=1.48.0,<1.49.0' + - 'bioconductor-oligoclasses >=1.46.0,<1.47.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-pd.ragene.1.0.st.v1/post-link.sh b/recipes/bioconductor-pd.ragene.1.0.st.v1/post-link.sh index 2dff263cadfb0..411d2193c077a 100644 --- a/recipes/bioconductor-pd.ragene.1.0.st.v1/post-link.sh +++ b/recipes/bioconductor-pd.ragene.1.0.st.v1/post-link.sh @@ -1,9 +1,10 @@ #!/bin/bash FN="pd.ragene.1.0.st.v1_3.14.1.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/pd.ragene.1.0.st.v1_3.14.1.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/pd.ragene.1.0.st.v1_3.14.1.tar.gz" "https://bioarchive.galaxyproject.org/pd.ragene.1.0.st.v1_3.14.1.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-pd.ragene.1.0.st.v1/bioconductor-pd.ragene.1.0.st.v1_3.14.1_src_all.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-pd.ragene.1.0.st.v1/bioconductor-pd.ragene.1.0.st.v1_3.14.1_src_all.tar.gz" ) MD5="122cb69603e705218d01d70f48e90cad" @@ -16,7 +17,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-pd.ragene.1.1.st.v1/meta.yaml b/recipes/bioconductor-pd.ragene.1.1.st.v1/meta.yaml index ab471f8b814c8..77278cc7bd1ec 100644 --- a/recipes/bioconductor-pd.ragene.1.1.st.v1/meta.yaml +++ b/recipes/bioconductor-pd.ragene.1.1.st.v1/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.14.1" %} {% set name = "pd.ragene.1.1.st.v1" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -12,31 +12,31 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 7301ab6472849395ccb800c39807e969 build: - number: 1 + number: 2 rpaths: - lib/R/lib/ - lib/ noarch: generic requirements: host: - - 'bioconductor-biostrings >=2.50.0,<2.51.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-oligo >=1.46.0,<1.47.0' - - 'bioconductor-oligoclasses >=1.44.0,<1.45.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-biostrings >=2.52.0,<2.53.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-oligo >=1.48.0,<1.49.0' + - 'bioconductor-oligoclasses >=1.46.0,<1.47.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' run: - - 'bioconductor-biostrings >=2.50.0,<2.51.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-oligo >=1.46.0,<1.47.0' - - 'bioconductor-oligoclasses >=1.44.0,<1.45.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-biostrings >=2.52.0,<2.53.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-oligo >=1.48.0,<1.49.0' + - 'bioconductor-oligoclasses >=1.46.0,<1.47.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-pd.ragene.1.1.st.v1/post-link.sh b/recipes/bioconductor-pd.ragene.1.1.st.v1/post-link.sh index 54d407613f244..e1a8261ee4820 100644 --- a/recipes/bioconductor-pd.ragene.1.1.st.v1/post-link.sh +++ b/recipes/bioconductor-pd.ragene.1.1.st.v1/post-link.sh @@ -1,9 +1,10 @@ #!/bin/bash FN="pd.ragene.1.1.st.v1_3.14.1.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/pd.ragene.1.1.st.v1_3.14.1.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/pd.ragene.1.1.st.v1_3.14.1.tar.gz" "https://bioarchive.galaxyproject.org/pd.ragene.1.1.st.v1_3.14.1.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-pd.ragene.1.1.st.v1/bioconductor-pd.ragene.1.1.st.v1_3.14.1_src_all.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-pd.ragene.1.1.st.v1/bioconductor-pd.ragene.1.1.st.v1_3.14.1_src_all.tar.gz" ) MD5="7301ab6472849395ccb800c39807e969" @@ -16,7 +17,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-pd.ragene.2.0.st/meta.yaml b/recipes/bioconductor-pd.ragene.2.0.st/meta.yaml index 0fbfb7dca5215..2446f9a867a26 100644 --- a/recipes/bioconductor-pd.ragene.2.0.st/meta.yaml +++ b/recipes/bioconductor-pd.ragene.2.0.st/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.14.1" %} {% set name = "pd.ragene.2.0.st" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -12,31 +12,31 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 37157b09f009fef368b54e47711c313b build: - number: 1 + number: 2 rpaths: - lib/R/lib/ - lib/ noarch: generic requirements: host: - - 'bioconductor-biostrings >=2.50.0,<2.51.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-oligo >=1.46.0,<1.47.0' - - 'bioconductor-oligoclasses >=1.44.0,<1.45.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-biostrings >=2.52.0,<2.53.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-oligo >=1.48.0,<1.49.0' + - 'bioconductor-oligoclasses >=1.46.0,<1.47.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' run: - - 'bioconductor-biostrings >=2.50.0,<2.51.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-oligo >=1.46.0,<1.47.0' - - 'bioconductor-oligoclasses >=1.44.0,<1.45.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-biostrings >=2.52.0,<2.53.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-oligo >=1.48.0,<1.49.0' + - 'bioconductor-oligoclasses >=1.46.0,<1.47.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-pd.ragene.2.0.st/post-link.sh b/recipes/bioconductor-pd.ragene.2.0.st/post-link.sh index de1980207e6ad..4ef8b89ab3733 100644 --- a/recipes/bioconductor-pd.ragene.2.0.st/post-link.sh +++ b/recipes/bioconductor-pd.ragene.2.0.st/post-link.sh @@ -1,9 +1,10 @@ #!/bin/bash FN="pd.ragene.2.0.st_3.14.1.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/pd.ragene.2.0.st_3.14.1.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/pd.ragene.2.0.st_3.14.1.tar.gz" "https://bioarchive.galaxyproject.org/pd.ragene.2.0.st_3.14.1.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-pd.ragene.2.0.st/bioconductor-pd.ragene.2.0.st_3.14.1_src_all.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-pd.ragene.2.0.st/bioconductor-pd.ragene.2.0.st_3.14.1_src_all.tar.gz" ) MD5="37157b09f009fef368b54e47711c313b" @@ -16,7 +17,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-pd.ragene.2.1.st/meta.yaml b/recipes/bioconductor-pd.ragene.2.1.st/meta.yaml index f541a6e0b6036..13d93ce1212c1 100644 --- a/recipes/bioconductor-pd.ragene.2.1.st/meta.yaml +++ b/recipes/bioconductor-pd.ragene.2.1.st/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.14.1" %} {% set name = "pd.ragene.2.1.st" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -12,31 +12,31 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 53adfa5ff2c7e466da83b807dbc7b237 build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ noarch: generic requirements: host: - - 'bioconductor-biostrings >=2.50.0,<2.51.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-oligo >=1.46.0,<1.47.0' - - 'bioconductor-oligoclasses >=1.44.0,<1.45.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-biostrings >=2.52.0,<2.53.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-oligo >=1.48.0,<1.49.0' + - 'bioconductor-oligoclasses >=1.46.0,<1.47.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' run: - - 'bioconductor-biostrings >=2.50.0,<2.51.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-oligo >=1.46.0,<1.47.0' - - 'bioconductor-oligoclasses >=1.44.0,<1.45.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-biostrings >=2.52.0,<2.53.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-oligo >=1.48.0,<1.49.0' + - 'bioconductor-oligoclasses >=1.46.0,<1.47.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-pd.ragene.2.1.st/post-link.sh b/recipes/bioconductor-pd.ragene.2.1.st/post-link.sh index e1f72d156d6a3..02e87aa691c0b 100644 --- a/recipes/bioconductor-pd.ragene.2.1.st/post-link.sh +++ b/recipes/bioconductor-pd.ragene.2.1.st/post-link.sh @@ -1,9 +1,10 @@ #!/bin/bash FN="pd.ragene.2.1.st_3.14.1.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/pd.ragene.2.1.st_3.14.1.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/pd.ragene.2.1.st_3.14.1.tar.gz" "https://bioarchive.galaxyproject.org/pd.ragene.2.1.st_3.14.1.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-pd.ragene.2.1.st/bioconductor-pd.ragene.2.1.st_3.14.1_src_all.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-pd.ragene.2.1.st/bioconductor-pd.ragene.2.1.st_3.14.1_src_all.tar.gz" ) MD5="53adfa5ff2c7e466da83b807dbc7b237" @@ -16,7 +17,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-pd.rat230.2/meta.yaml b/recipes/bioconductor-pd.rat230.2/meta.yaml index 4ab1361705c55..81dfdd6761a20 100644 --- a/recipes/bioconductor-pd.rat230.2/meta.yaml +++ b/recipes/bioconductor-pd.rat230.2/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.12.0" %} {% set name = "pd.rat230.2" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -12,31 +12,31 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 286b1a7868ef6c795ebeb6dd8a5d5920 build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ noarch: generic requirements: host: - - 'bioconductor-biostrings >=2.50.0,<2.51.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-oligo >=1.46.0,<1.47.0' - - 'bioconductor-oligoclasses >=1.44.0,<1.45.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-biostrings >=2.52.0,<2.53.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-oligo >=1.48.0,<1.49.0' + - 'bioconductor-oligoclasses >=1.46.0,<1.47.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' run: - - 'bioconductor-biostrings >=2.50.0,<2.51.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-oligo >=1.46.0,<1.47.0' - - 'bioconductor-oligoclasses >=1.44.0,<1.45.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-biostrings >=2.52.0,<2.53.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-oligo >=1.48.0,<1.49.0' + - 'bioconductor-oligoclasses >=1.46.0,<1.47.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-pd.rat230.2/post-link.sh b/recipes/bioconductor-pd.rat230.2/post-link.sh index cbd826be87d39..1981b91043303 100644 --- a/recipes/bioconductor-pd.rat230.2/post-link.sh +++ b/recipes/bioconductor-pd.rat230.2/post-link.sh @@ -1,9 +1,10 @@ #!/bin/bash FN="pd.rat230.2_3.12.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/pd.rat230.2_3.12.0.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/pd.rat230.2_3.12.0.tar.gz" "https://bioarchive.galaxyproject.org/pd.rat230.2_3.12.0.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-pd.rat230.2/bioconductor-pd.rat230.2_3.12.0_src_all.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-pd.rat230.2/bioconductor-pd.rat230.2_3.12.0_src_all.tar.gz" ) MD5="286b1a7868ef6c795ebeb6dd8a5d5920" @@ -16,7 +17,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-pd.rcngene.1.0.st/meta.yaml b/recipes/bioconductor-pd.rcngene.1.0.st/meta.yaml index ee73766158a5a..8a4513486d345 100644 --- a/recipes/bioconductor-pd.rcngene.1.0.st/meta.yaml +++ b/recipes/bioconductor-pd.rcngene.1.0.st/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.12.0" %} {% set name = "pd.rcngene.1.0.st" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -12,31 +12,31 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 9c7c5ef4d4f5ed92d9130d77a99a0685 build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ noarch: generic requirements: host: - - 'bioconductor-biostrings >=2.50.0,<2.51.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-oligo >=1.46.0,<1.47.0' - - 'bioconductor-oligoclasses >=1.44.0,<1.45.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-biostrings >=2.52.0,<2.53.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-oligo >=1.48.0,<1.49.0' + - 'bioconductor-oligoclasses >=1.46.0,<1.47.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' run: - - 'bioconductor-biostrings >=2.50.0,<2.51.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-oligo >=1.46.0,<1.47.0' - - 'bioconductor-oligoclasses >=1.44.0,<1.45.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-biostrings >=2.52.0,<2.53.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-oligo >=1.48.0,<1.49.0' + - 'bioconductor-oligoclasses >=1.46.0,<1.47.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-pd.rcngene.1.0.st/post-link.sh b/recipes/bioconductor-pd.rcngene.1.0.st/post-link.sh index 7abc8c8915f5d..2251661398b7b 100644 --- a/recipes/bioconductor-pd.rcngene.1.0.st/post-link.sh +++ b/recipes/bioconductor-pd.rcngene.1.0.st/post-link.sh @@ -1,9 +1,10 @@ #!/bin/bash FN="pd.rcngene.1.0.st_3.12.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/pd.rcngene.1.0.st_3.12.0.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/pd.rcngene.1.0.st_3.12.0.tar.gz" "https://bioarchive.galaxyproject.org/pd.rcngene.1.0.st_3.12.0.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-pd.rcngene.1.0.st/bioconductor-pd.rcngene.1.0.st_3.12.0_src_all.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-pd.rcngene.1.0.st/bioconductor-pd.rcngene.1.0.st_3.12.0_src_all.tar.gz" ) MD5="9c7c5ef4d4f5ed92d9130d77a99a0685" @@ -16,7 +17,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-pd.rcngene.1.1.st/meta.yaml b/recipes/bioconductor-pd.rcngene.1.1.st/meta.yaml index db27f8f57e0b8..687539c44c92e 100644 --- a/recipes/bioconductor-pd.rcngene.1.1.st/meta.yaml +++ b/recipes/bioconductor-pd.rcngene.1.1.st/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.12.0" %} {% set name = "pd.rcngene.1.1.st" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -12,31 +12,31 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 9781549447d90b5423e820fff5cc6273 build: - number: 1 + number: 2 rpaths: - lib/R/lib/ - lib/ noarch: generic requirements: host: - - 'bioconductor-biostrings >=2.50.0,<2.51.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-oligo >=1.46.0,<1.47.0' - - 'bioconductor-oligoclasses >=1.44.0,<1.45.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-biostrings >=2.52.0,<2.53.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-oligo >=1.48.0,<1.49.0' + - 'bioconductor-oligoclasses >=1.46.0,<1.47.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' run: - - 'bioconductor-biostrings >=2.50.0,<2.51.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-oligo >=1.46.0,<1.47.0' - - 'bioconductor-oligoclasses >=1.44.0,<1.45.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-biostrings >=2.52.0,<2.53.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-oligo >=1.48.0,<1.49.0' + - 'bioconductor-oligoclasses >=1.46.0,<1.47.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-pd.rcngene.1.1.st/post-link.sh b/recipes/bioconductor-pd.rcngene.1.1.st/post-link.sh index f43c70696ada1..5c16f7c3a7e61 100644 --- a/recipes/bioconductor-pd.rcngene.1.1.st/post-link.sh +++ b/recipes/bioconductor-pd.rcngene.1.1.st/post-link.sh @@ -1,9 +1,10 @@ #!/bin/bash FN="pd.rcngene.1.1.st_3.12.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/pd.rcngene.1.1.st_3.12.0.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/pd.rcngene.1.1.st_3.12.0.tar.gz" "https://bioarchive.galaxyproject.org/pd.rcngene.1.1.st_3.12.0.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-pd.rcngene.1.1.st/bioconductor-pd.rcngene.1.1.st_3.12.0_src_all.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-pd.rcngene.1.1.st/bioconductor-pd.rcngene.1.1.st_3.12.0_src_all.tar.gz" ) MD5="9781549447d90b5423e820fff5cc6273" @@ -16,7 +17,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-pd.rg.u34a/meta.yaml b/recipes/bioconductor-pd.rg.u34a/meta.yaml index 849e610981ed7..199c3c8cf9258 100644 --- a/recipes/bioconductor-pd.rg.u34a/meta.yaml +++ b/recipes/bioconductor-pd.rg.u34a/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.12.0" %} {% set name = "pd.rg.u34a" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -12,31 +12,31 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: ac3a6cc203dabb8faab85b97f1a7ae3c build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ noarch: generic requirements: host: - - 'bioconductor-biostrings >=2.50.0,<2.51.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-oligo >=1.46.0,<1.47.0' - - 'bioconductor-oligoclasses >=1.44.0,<1.45.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-biostrings >=2.52.0,<2.53.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-oligo >=1.48.0,<1.49.0' + - 'bioconductor-oligoclasses >=1.46.0,<1.47.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' run: - - 'bioconductor-biostrings >=2.50.0,<2.51.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-oligo >=1.46.0,<1.47.0' - - 'bioconductor-oligoclasses >=1.44.0,<1.45.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-biostrings >=2.52.0,<2.53.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-oligo >=1.48.0,<1.49.0' + - 'bioconductor-oligoclasses >=1.46.0,<1.47.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-pd.rg.u34a/post-link.sh b/recipes/bioconductor-pd.rg.u34a/post-link.sh index 8dd25d5de44f2..8e1f3fa6f9825 100644 --- a/recipes/bioconductor-pd.rg.u34a/post-link.sh +++ b/recipes/bioconductor-pd.rg.u34a/post-link.sh @@ -1,9 +1,10 @@ #!/bin/bash FN="pd.rg.u34a_3.12.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/pd.rg.u34a_3.12.0.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/pd.rg.u34a_3.12.0.tar.gz" "https://bioarchive.galaxyproject.org/pd.rg.u34a_3.12.0.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-pd.rg.u34a/bioconductor-pd.rg.u34a_3.12.0_src_all.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-pd.rg.u34a/bioconductor-pd.rg.u34a_3.12.0_src_all.tar.gz" ) MD5="ac3a6cc203dabb8faab85b97f1a7ae3c" @@ -16,7 +17,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-pd.rg.u34b/meta.yaml b/recipes/bioconductor-pd.rg.u34b/meta.yaml index 7f9fc6818b199..6c2a5a4821c1a 100644 --- a/recipes/bioconductor-pd.rg.u34b/meta.yaml +++ b/recipes/bioconductor-pd.rg.u34b/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.12.0" %} {% set name = "pd.rg.u34b" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -12,31 +12,31 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 757966b66795d388c7169816d31977ad build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ noarch: generic requirements: host: - - 'bioconductor-biostrings >=2.50.0,<2.51.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-oligo >=1.46.0,<1.47.0' - - 'bioconductor-oligoclasses >=1.44.0,<1.45.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-biostrings >=2.52.0,<2.53.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-oligo >=1.48.0,<1.49.0' + - 'bioconductor-oligoclasses >=1.46.0,<1.47.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' run: - - 'bioconductor-biostrings >=2.50.0,<2.51.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-oligo >=1.46.0,<1.47.0' - - 'bioconductor-oligoclasses >=1.44.0,<1.45.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-biostrings >=2.52.0,<2.53.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-oligo >=1.48.0,<1.49.0' + - 'bioconductor-oligoclasses >=1.46.0,<1.47.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-pd.rg.u34b/post-link.sh b/recipes/bioconductor-pd.rg.u34b/post-link.sh index adc9803bda966..b2c01607d1854 100644 --- a/recipes/bioconductor-pd.rg.u34b/post-link.sh +++ b/recipes/bioconductor-pd.rg.u34b/post-link.sh @@ -1,9 +1,10 @@ #!/bin/bash FN="pd.rg.u34b_3.12.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/pd.rg.u34b_3.12.0.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/pd.rg.u34b_3.12.0.tar.gz" "https://bioarchive.galaxyproject.org/pd.rg.u34b_3.12.0.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-pd.rg.u34b/bioconductor-pd.rg.u34b_3.12.0_src_all.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-pd.rg.u34b/bioconductor-pd.rg.u34b_3.12.0_src_all.tar.gz" ) MD5="757966b66795d388c7169816d31977ad" @@ -16,7 +17,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-pd.rg.u34c/meta.yaml b/recipes/bioconductor-pd.rg.u34c/meta.yaml index 6c89b0ad42db4..2c497c1c4c2b2 100644 --- a/recipes/bioconductor-pd.rg.u34c/meta.yaml +++ b/recipes/bioconductor-pd.rg.u34c/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.12.0" %} {% set name = "pd.rg.u34c" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -12,31 +12,31 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: bc9cb7b208972ac2901235bdabdee5b2 build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ noarch: generic requirements: host: - - 'bioconductor-biostrings >=2.50.0,<2.51.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-oligo >=1.46.0,<1.47.0' - - 'bioconductor-oligoclasses >=1.44.0,<1.45.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-biostrings >=2.52.0,<2.53.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-oligo >=1.48.0,<1.49.0' + - 'bioconductor-oligoclasses >=1.46.0,<1.47.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' run: - - 'bioconductor-biostrings >=2.50.0,<2.51.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-oligo >=1.46.0,<1.47.0' - - 'bioconductor-oligoclasses >=1.44.0,<1.45.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-biostrings >=2.52.0,<2.53.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-oligo >=1.48.0,<1.49.0' + - 'bioconductor-oligoclasses >=1.46.0,<1.47.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-pd.rg.u34c/post-link.sh b/recipes/bioconductor-pd.rg.u34c/post-link.sh index b7be3908cb2bf..a1dc920605536 100644 --- a/recipes/bioconductor-pd.rg.u34c/post-link.sh +++ b/recipes/bioconductor-pd.rg.u34c/post-link.sh @@ -1,9 +1,10 @@ #!/bin/bash FN="pd.rg.u34c_3.12.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/pd.rg.u34c_3.12.0.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/pd.rg.u34c_3.12.0.tar.gz" "https://bioarchive.galaxyproject.org/pd.rg.u34c_3.12.0.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-pd.rg.u34c/bioconductor-pd.rg.u34c_3.12.0_src_all.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-pd.rg.u34c/bioconductor-pd.rg.u34c_3.12.0_src_all.tar.gz" ) MD5="bc9cb7b208972ac2901235bdabdee5b2" @@ -16,7 +17,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-pd.rhegene.1.0.st/meta.yaml b/recipes/bioconductor-pd.rhegene.1.0.st/meta.yaml index c9907fcbafdd9..bd4fdd03864cc 100644 --- a/recipes/bioconductor-pd.rhegene.1.0.st/meta.yaml +++ b/recipes/bioconductor-pd.rhegene.1.0.st/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.12.0" %} {% set name = "pd.rhegene.1.0.st" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -12,31 +12,31 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 6469add6928e663529df4df98fcdd7a8 build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ noarch: generic requirements: host: - - 'bioconductor-biostrings >=2.50.0,<2.51.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-oligo >=1.46.0,<1.47.0' - - 'bioconductor-oligoclasses >=1.44.0,<1.45.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-biostrings >=2.52.0,<2.53.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-oligo >=1.48.0,<1.49.0' + - 'bioconductor-oligoclasses >=1.46.0,<1.47.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' run: - - 'bioconductor-biostrings >=2.50.0,<2.51.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-oligo >=1.46.0,<1.47.0' - - 'bioconductor-oligoclasses >=1.44.0,<1.45.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-biostrings >=2.52.0,<2.53.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-oligo >=1.48.0,<1.49.0' + - 'bioconductor-oligoclasses >=1.46.0,<1.47.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-pd.rhegene.1.0.st/post-link.sh b/recipes/bioconductor-pd.rhegene.1.0.st/post-link.sh index e44422059d24a..0445d13b552cf 100644 --- a/recipes/bioconductor-pd.rhegene.1.0.st/post-link.sh +++ b/recipes/bioconductor-pd.rhegene.1.0.st/post-link.sh @@ -1,9 +1,10 @@ #!/bin/bash FN="pd.rhegene.1.0.st_3.12.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/pd.rhegene.1.0.st_3.12.0.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/pd.rhegene.1.0.st_3.12.0.tar.gz" "https://bioarchive.galaxyproject.org/pd.rhegene.1.0.st_3.12.0.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-pd.rhegene.1.0.st/bioconductor-pd.rhegene.1.0.st_3.12.0_src_all.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-pd.rhegene.1.0.st/bioconductor-pd.rhegene.1.0.st_3.12.0_src_all.tar.gz" ) MD5="6469add6928e663529df4df98fcdd7a8" @@ -16,7 +17,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-pd.rhegene.1.1.st/meta.yaml b/recipes/bioconductor-pd.rhegene.1.1.st/meta.yaml index 28d58fd1c675c..26fdc1aa11919 100644 --- a/recipes/bioconductor-pd.rhegene.1.1.st/meta.yaml +++ b/recipes/bioconductor-pd.rhegene.1.1.st/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.12.0" %} {% set name = "pd.rhegene.1.1.st" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -12,31 +12,31 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 4f63424ab52283a95731767dce6623cd build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ noarch: generic requirements: host: - - 'bioconductor-biostrings >=2.50.0,<2.51.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-oligo >=1.46.0,<1.47.0' - - 'bioconductor-oligoclasses >=1.44.0,<1.45.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-biostrings >=2.52.0,<2.53.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-oligo >=1.48.0,<1.49.0' + - 'bioconductor-oligoclasses >=1.46.0,<1.47.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' run: - - 'bioconductor-biostrings >=2.50.0,<2.51.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-oligo >=1.46.0,<1.47.0' - - 'bioconductor-oligoclasses >=1.44.0,<1.45.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-biostrings >=2.52.0,<2.53.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-oligo >=1.48.0,<1.49.0' + - 'bioconductor-oligoclasses >=1.46.0,<1.47.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-pd.rhegene.1.1.st/post-link.sh b/recipes/bioconductor-pd.rhegene.1.1.st/post-link.sh index 44c1bd5e13eb4..f777bd6324e84 100644 --- a/recipes/bioconductor-pd.rhegene.1.1.st/post-link.sh +++ b/recipes/bioconductor-pd.rhegene.1.1.st/post-link.sh @@ -1,9 +1,10 @@ #!/bin/bash FN="pd.rhegene.1.1.st_3.12.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/pd.rhegene.1.1.st_3.12.0.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/pd.rhegene.1.1.st_3.12.0.tar.gz" "https://bioarchive.galaxyproject.org/pd.rhegene.1.1.st_3.12.0.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-pd.rhegene.1.1.st/bioconductor-pd.rhegene.1.1.st_3.12.0_src_all.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-pd.rhegene.1.1.st/bioconductor-pd.rhegene.1.1.st_3.12.0_src_all.tar.gz" ) MD5="4f63424ab52283a95731767dce6623cd" @@ -16,7 +17,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-pd.rhesus/meta.yaml b/recipes/bioconductor-pd.rhesus/meta.yaml index 808950302c055..544f40d04b0b1 100644 --- a/recipes/bioconductor-pd.rhesus/meta.yaml +++ b/recipes/bioconductor-pd.rhesus/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.12.0" %} {% set name = "pd.rhesus" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -12,31 +12,31 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 51efcfe1384ac956ff93bf0530965054 build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ noarch: generic requirements: host: - - 'bioconductor-biostrings >=2.50.0,<2.51.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-oligo >=1.46.0,<1.47.0' - - 'bioconductor-oligoclasses >=1.44.0,<1.45.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-biostrings >=2.52.0,<2.53.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-oligo >=1.48.0,<1.49.0' + - 'bioconductor-oligoclasses >=1.46.0,<1.47.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' run: - - 'bioconductor-biostrings >=2.50.0,<2.51.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-oligo >=1.46.0,<1.47.0' - - 'bioconductor-oligoclasses >=1.44.0,<1.45.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-biostrings >=2.52.0,<2.53.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-oligo >=1.48.0,<1.49.0' + - 'bioconductor-oligoclasses >=1.46.0,<1.47.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-pd.rhesus/post-link.sh b/recipes/bioconductor-pd.rhesus/post-link.sh index aff35e4f01495..308cd2df4ef2d 100644 --- a/recipes/bioconductor-pd.rhesus/post-link.sh +++ b/recipes/bioconductor-pd.rhesus/post-link.sh @@ -1,9 +1,10 @@ #!/bin/bash FN="pd.rhesus_3.12.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/pd.rhesus_3.12.0.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/pd.rhesus_3.12.0.tar.gz" "https://bioarchive.galaxyproject.org/pd.rhesus_3.12.0.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-pd.rhesus/bioconductor-pd.rhesus_3.12.0_src_all.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-pd.rhesus/bioconductor-pd.rhesus_3.12.0_src_all.tar.gz" ) MD5="51efcfe1384ac956ff93bf0530965054" @@ -16,7 +17,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-pd.rice/meta.yaml b/recipes/bioconductor-pd.rice/meta.yaml index 2af44cf17a7d4..b3f0ccee299ef 100644 --- a/recipes/bioconductor-pd.rice/meta.yaml +++ b/recipes/bioconductor-pd.rice/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.12.0" %} {% set name = "pd.rice" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -12,31 +12,31 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 9c456981b3d0b99a96ac6c71e3eb7c8a build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ noarch: generic requirements: host: - - 'bioconductor-biostrings >=2.50.0,<2.51.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-oligo >=1.46.0,<1.47.0' - - 'bioconductor-oligoclasses >=1.44.0,<1.45.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-biostrings >=2.52.0,<2.53.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-oligo >=1.48.0,<1.49.0' + - 'bioconductor-oligoclasses >=1.46.0,<1.47.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' run: - - 'bioconductor-biostrings >=2.50.0,<2.51.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-oligo >=1.46.0,<1.47.0' - - 'bioconductor-oligoclasses >=1.44.0,<1.45.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-biostrings >=2.52.0,<2.53.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-oligo >=1.48.0,<1.49.0' + - 'bioconductor-oligoclasses >=1.46.0,<1.47.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-pd.rice/post-link.sh b/recipes/bioconductor-pd.rice/post-link.sh index 93be3e525b029..f207654c093f9 100644 --- a/recipes/bioconductor-pd.rice/post-link.sh +++ b/recipes/bioconductor-pd.rice/post-link.sh @@ -1,9 +1,10 @@ #!/bin/bash FN="pd.rice_3.12.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/pd.rice_3.12.0.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/pd.rice_3.12.0.tar.gz" "https://bioarchive.galaxyproject.org/pd.rice_3.12.0.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-pd.rice/bioconductor-pd.rice_3.12.0_src_all.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-pd.rice/bioconductor-pd.rice_3.12.0_src_all.tar.gz" ) MD5="9c456981b3d0b99a96ac6c71e3eb7c8a" @@ -16,7 +17,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-pd.rjpgene.1.0.st/meta.yaml b/recipes/bioconductor-pd.rjpgene.1.0.st/meta.yaml index d5778e24116b9..feb648b548308 100644 --- a/recipes/bioconductor-pd.rjpgene.1.0.st/meta.yaml +++ b/recipes/bioconductor-pd.rjpgene.1.0.st/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.12.0" %} {% set name = "pd.rjpgene.1.0.st" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -12,31 +12,31 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 066f5dbacc1110e42ce4d457ad3b9306 build: - number: 1 + number: 2 rpaths: - lib/R/lib/ - lib/ noarch: generic requirements: host: - - 'bioconductor-biostrings >=2.50.0,<2.51.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-oligo >=1.46.0,<1.47.0' - - 'bioconductor-oligoclasses >=1.44.0,<1.45.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-biostrings >=2.52.0,<2.53.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-oligo >=1.48.0,<1.49.0' + - 'bioconductor-oligoclasses >=1.46.0,<1.47.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' run: - - 'bioconductor-biostrings >=2.50.0,<2.51.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-oligo >=1.46.0,<1.47.0' - - 'bioconductor-oligoclasses >=1.44.0,<1.45.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-biostrings >=2.52.0,<2.53.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-oligo >=1.48.0,<1.49.0' + - 'bioconductor-oligoclasses >=1.46.0,<1.47.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-pd.rjpgene.1.0.st/post-link.sh b/recipes/bioconductor-pd.rjpgene.1.0.st/post-link.sh index e4c1e667cc79d..e56857685b87f 100644 --- a/recipes/bioconductor-pd.rjpgene.1.0.st/post-link.sh +++ b/recipes/bioconductor-pd.rjpgene.1.0.st/post-link.sh @@ -1,9 +1,10 @@ #!/bin/bash FN="pd.rjpgene.1.0.st_3.12.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/pd.rjpgene.1.0.st_3.12.0.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/pd.rjpgene.1.0.st_3.12.0.tar.gz" "https://bioarchive.galaxyproject.org/pd.rjpgene.1.0.st_3.12.0.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-pd.rjpgene.1.0.st/bioconductor-pd.rjpgene.1.0.st_3.12.0_src_all.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-pd.rjpgene.1.0.st/bioconductor-pd.rjpgene.1.0.st_3.12.0_src_all.tar.gz" ) MD5="066f5dbacc1110e42ce4d457ad3b9306" @@ -16,7 +17,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-pd.rjpgene.1.1.st/meta.yaml b/recipes/bioconductor-pd.rjpgene.1.1.st/meta.yaml index 3e3f56eb9f463..c2d410c530792 100644 --- a/recipes/bioconductor-pd.rjpgene.1.1.st/meta.yaml +++ b/recipes/bioconductor-pd.rjpgene.1.1.st/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.12.0" %} {% set name = "pd.rjpgene.1.1.st" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -12,31 +12,31 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 265503774b15e0f4e71ac53a276a80f2 build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ noarch: generic requirements: host: - - 'bioconductor-biostrings >=2.50.0,<2.51.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-oligo >=1.46.0,<1.47.0' - - 'bioconductor-oligoclasses >=1.44.0,<1.45.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-biostrings >=2.52.0,<2.53.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-oligo >=1.48.0,<1.49.0' + - 'bioconductor-oligoclasses >=1.46.0,<1.47.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' run: - - 'bioconductor-biostrings >=2.50.0,<2.51.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-oligo >=1.46.0,<1.47.0' - - 'bioconductor-oligoclasses >=1.44.0,<1.45.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-biostrings >=2.52.0,<2.53.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-oligo >=1.48.0,<1.49.0' + - 'bioconductor-oligoclasses >=1.46.0,<1.47.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-pd.rjpgene.1.1.st/post-link.sh b/recipes/bioconductor-pd.rjpgene.1.1.st/post-link.sh index c09a977871521..1caacf2cf8cae 100644 --- a/recipes/bioconductor-pd.rjpgene.1.1.st/post-link.sh +++ b/recipes/bioconductor-pd.rjpgene.1.1.st/post-link.sh @@ -1,9 +1,10 @@ #!/bin/bash FN="pd.rjpgene.1.1.st_3.12.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/pd.rjpgene.1.1.st_3.12.0.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/pd.rjpgene.1.1.st_3.12.0.tar.gz" "https://bioarchive.galaxyproject.org/pd.rjpgene.1.1.st_3.12.0.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-pd.rjpgene.1.1.st/bioconductor-pd.rjpgene.1.1.st_3.12.0_src_all.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-pd.rjpgene.1.1.st/bioconductor-pd.rjpgene.1.1.st_3.12.0_src_all.tar.gz" ) MD5="265503774b15e0f4e71ac53a276a80f2" @@ -16,7 +17,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-pd.rn.u34/meta.yaml b/recipes/bioconductor-pd.rn.u34/meta.yaml index a7fd5de75dc3c..c1d2b5e332954 100644 --- a/recipes/bioconductor-pd.rn.u34/meta.yaml +++ b/recipes/bioconductor-pd.rn.u34/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.12.0" %} {% set name = "pd.rn.u34" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -12,31 +12,31 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 1728c547f1383bffab330796505119ec build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ noarch: generic requirements: host: - - 'bioconductor-biostrings >=2.50.0,<2.51.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-oligo >=1.46.0,<1.47.0' - - 'bioconductor-oligoclasses >=1.44.0,<1.45.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-biostrings >=2.52.0,<2.53.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-oligo >=1.48.0,<1.49.0' + - 'bioconductor-oligoclasses >=1.46.0,<1.47.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' run: - - 'bioconductor-biostrings >=2.50.0,<2.51.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-oligo >=1.46.0,<1.47.0' - - 'bioconductor-oligoclasses >=1.44.0,<1.45.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-biostrings >=2.52.0,<2.53.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-oligo >=1.48.0,<1.49.0' + - 'bioconductor-oligoclasses >=1.46.0,<1.47.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-pd.rn.u34/post-link.sh b/recipes/bioconductor-pd.rn.u34/post-link.sh index 1c9920cb6d093..1086f4115a539 100644 --- a/recipes/bioconductor-pd.rn.u34/post-link.sh +++ b/recipes/bioconductor-pd.rn.u34/post-link.sh @@ -1,9 +1,10 @@ #!/bin/bash FN="pd.rn.u34_3.12.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/pd.rn.u34_3.12.0.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/pd.rn.u34_3.12.0.tar.gz" "https://bioarchive.galaxyproject.org/pd.rn.u34_3.12.0.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-pd.rn.u34/bioconductor-pd.rn.u34_3.12.0_src_all.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-pd.rn.u34/bioconductor-pd.rn.u34_3.12.0_src_all.tar.gz" ) MD5="1728c547f1383bffab330796505119ec" @@ -16,7 +17,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-pd.rta.1.0/meta.yaml b/recipes/bioconductor-pd.rta.1.0/meta.yaml index a0418e6bf4499..ef49bfa25851a 100644 --- a/recipes/bioconductor-pd.rta.1.0/meta.yaml +++ b/recipes/bioconductor-pd.rta.1.0/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.12.2" %} {% set name = "pd.rta.1.0" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -12,31 +12,31 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 90752a892a103c7fe4cd6c86e61a61db build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ noarch: generic requirements: host: - - 'bioconductor-biostrings >=2.50.0,<2.51.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-oligo >=1.46.0,<1.47.0' - - 'bioconductor-oligoclasses >=1.44.0,<1.45.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-biostrings >=2.52.0,<2.53.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-oligo >=1.48.0,<1.49.0' + - 'bioconductor-oligoclasses >=1.46.0,<1.47.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' run: - - 'bioconductor-biostrings >=2.50.0,<2.51.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-oligo >=1.46.0,<1.47.0' - - 'bioconductor-oligoclasses >=1.44.0,<1.45.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-biostrings >=2.52.0,<2.53.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-oligo >=1.48.0,<1.49.0' + - 'bioconductor-oligoclasses >=1.46.0,<1.47.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-pd.rta.1.0/post-link.sh b/recipes/bioconductor-pd.rta.1.0/post-link.sh index 013a09f092237..1611882af4f93 100644 --- a/recipes/bioconductor-pd.rta.1.0/post-link.sh +++ b/recipes/bioconductor-pd.rta.1.0/post-link.sh @@ -1,9 +1,10 @@ #!/bin/bash FN="pd.rta.1.0_3.12.2.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/pd.rta.1.0_3.12.2.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/pd.rta.1.0_3.12.2.tar.gz" "https://bioarchive.galaxyproject.org/pd.rta.1.0_3.12.2.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-pd.rta.1.0/bioconductor-pd.rta.1.0_3.12.2_src_all.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-pd.rta.1.0/bioconductor-pd.rta.1.0_3.12.2_src_all.tar.gz" ) MD5="90752a892a103c7fe4cd6c86e61a61db" @@ -16,7 +17,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-pd.rusgene.1.0.st/meta.yaml b/recipes/bioconductor-pd.rusgene.1.0.st/meta.yaml index f0f99b78f0634..6f80424ebd7b3 100644 --- a/recipes/bioconductor-pd.rusgene.1.0.st/meta.yaml +++ b/recipes/bioconductor-pd.rusgene.1.0.st/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.12.0" %} {% set name = "pd.rusgene.1.0.st" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -12,31 +12,31 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 0b9b00fee58ef211e041395052344483 build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ noarch: generic requirements: host: - - 'bioconductor-biostrings >=2.50.0,<2.51.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-oligo >=1.46.0,<1.47.0' - - 'bioconductor-oligoclasses >=1.44.0,<1.45.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-biostrings >=2.52.0,<2.53.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-oligo >=1.48.0,<1.49.0' + - 'bioconductor-oligoclasses >=1.46.0,<1.47.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' run: - - 'bioconductor-biostrings >=2.50.0,<2.51.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-oligo >=1.46.0,<1.47.0' - - 'bioconductor-oligoclasses >=1.44.0,<1.45.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-biostrings >=2.52.0,<2.53.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-oligo >=1.48.0,<1.49.0' + - 'bioconductor-oligoclasses >=1.46.0,<1.47.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-pd.rusgene.1.0.st/post-link.sh b/recipes/bioconductor-pd.rusgene.1.0.st/post-link.sh index 7a192701bce8a..2aef4871f3fee 100644 --- a/recipes/bioconductor-pd.rusgene.1.0.st/post-link.sh +++ b/recipes/bioconductor-pd.rusgene.1.0.st/post-link.sh @@ -1,9 +1,10 @@ #!/bin/bash FN="pd.rusgene.1.0.st_3.12.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/pd.rusgene.1.0.st_3.12.0.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/pd.rusgene.1.0.st_3.12.0.tar.gz" "https://bioarchive.galaxyproject.org/pd.rusgene.1.0.st_3.12.0.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-pd.rusgene.1.0.st/bioconductor-pd.rusgene.1.0.st_3.12.0_src_all.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-pd.rusgene.1.0.st/bioconductor-pd.rusgene.1.0.st_3.12.0_src_all.tar.gz" ) MD5="0b9b00fee58ef211e041395052344483" @@ -16,7 +17,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-pd.rusgene.1.1.st/meta.yaml b/recipes/bioconductor-pd.rusgene.1.1.st/meta.yaml index 4513e18f66d31..750d1ff78f620 100644 --- a/recipes/bioconductor-pd.rusgene.1.1.st/meta.yaml +++ b/recipes/bioconductor-pd.rusgene.1.1.st/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.12.0" %} {% set name = "pd.rusgene.1.1.st" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -12,31 +12,31 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 228837c2de4a4b106806cb7f384564fa build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ noarch: generic requirements: host: - - 'bioconductor-biostrings >=2.50.0,<2.51.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-oligo >=1.46.0,<1.47.0' - - 'bioconductor-oligoclasses >=1.44.0,<1.45.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-biostrings >=2.52.0,<2.53.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-oligo >=1.48.0,<1.49.0' + - 'bioconductor-oligoclasses >=1.46.0,<1.47.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' run: - - 'bioconductor-biostrings >=2.50.0,<2.51.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-oligo >=1.46.0,<1.47.0' - - 'bioconductor-oligoclasses >=1.44.0,<1.45.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-biostrings >=2.52.0,<2.53.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-oligo >=1.48.0,<1.49.0' + - 'bioconductor-oligoclasses >=1.46.0,<1.47.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-pd.rusgene.1.1.st/post-link.sh b/recipes/bioconductor-pd.rusgene.1.1.st/post-link.sh index 29b4dd017bf4e..1bc8031c833f4 100644 --- a/recipes/bioconductor-pd.rusgene.1.1.st/post-link.sh +++ b/recipes/bioconductor-pd.rusgene.1.1.st/post-link.sh @@ -1,9 +1,10 @@ #!/bin/bash FN="pd.rusgene.1.1.st_3.12.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/pd.rusgene.1.1.st_3.12.0.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/pd.rusgene.1.1.st_3.12.0.tar.gz" "https://bioarchive.galaxyproject.org/pd.rusgene.1.1.st_3.12.0.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-pd.rusgene.1.1.st/bioconductor-pd.rusgene.1.1.st_3.12.0_src_all.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-pd.rusgene.1.1.st/bioconductor-pd.rusgene.1.1.st_3.12.0_src_all.tar.gz" ) MD5="228837c2de4a4b106806cb7f384564fa" @@ -16,7 +17,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-pd.s.aureus/meta.yaml b/recipes/bioconductor-pd.s.aureus/meta.yaml index 6ed7021b4a477..a139ad89450f7 100644 --- a/recipes/bioconductor-pd.s.aureus/meta.yaml +++ b/recipes/bioconductor-pd.s.aureus/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.12.0" %} {% set name = "pd.s.aureus" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -12,31 +12,31 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: f173ae6e4316aaa2eafbde92d5868a5a build: - number: 1 + number: 2 rpaths: - lib/R/lib/ - lib/ noarch: generic requirements: host: - - 'bioconductor-biostrings >=2.50.0,<2.51.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-oligo >=1.46.0,<1.47.0' - - 'bioconductor-oligoclasses >=1.44.0,<1.45.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-biostrings >=2.52.0,<2.53.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-oligo >=1.48.0,<1.49.0' + - 'bioconductor-oligoclasses >=1.46.0,<1.47.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' run: - - 'bioconductor-biostrings >=2.50.0,<2.51.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-oligo >=1.46.0,<1.47.0' - - 'bioconductor-oligoclasses >=1.44.0,<1.45.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-biostrings >=2.52.0,<2.53.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-oligo >=1.48.0,<1.49.0' + - 'bioconductor-oligoclasses >=1.46.0,<1.47.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-pd.s.aureus/post-link.sh b/recipes/bioconductor-pd.s.aureus/post-link.sh index 8ad18e28ccca6..5345e683bed25 100644 --- a/recipes/bioconductor-pd.s.aureus/post-link.sh +++ b/recipes/bioconductor-pd.s.aureus/post-link.sh @@ -1,9 +1,10 @@ #!/bin/bash FN="pd.s.aureus_3.12.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/pd.s.aureus_3.12.0.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/pd.s.aureus_3.12.0.tar.gz" "https://bioarchive.galaxyproject.org/pd.s.aureus_3.12.0.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-pd.s.aureus/bioconductor-pd.s.aureus_3.12.0_src_all.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-pd.s.aureus/bioconductor-pd.s.aureus_3.12.0_src_all.tar.gz" ) MD5="f173ae6e4316aaa2eafbde92d5868a5a" @@ -16,7 +17,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-pd.soybean/meta.yaml b/recipes/bioconductor-pd.soybean/meta.yaml index 3455db067e1c8..647327fd61c93 100644 --- a/recipes/bioconductor-pd.soybean/meta.yaml +++ b/recipes/bioconductor-pd.soybean/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.12.0" %} {% set name = "pd.soybean" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -12,31 +12,31 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 6dbe167be9d40c1d9096485afb4525f0 build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ noarch: generic requirements: host: - - 'bioconductor-biostrings >=2.50.0,<2.51.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-oligo >=1.46.0,<1.47.0' - - 'bioconductor-oligoclasses >=1.44.0,<1.45.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-biostrings >=2.52.0,<2.53.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-oligo >=1.48.0,<1.49.0' + - 'bioconductor-oligoclasses >=1.46.0,<1.47.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' run: - - 'bioconductor-biostrings >=2.50.0,<2.51.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-oligo >=1.46.0,<1.47.0' - - 'bioconductor-oligoclasses >=1.44.0,<1.45.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-biostrings >=2.52.0,<2.53.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-oligo >=1.48.0,<1.49.0' + - 'bioconductor-oligoclasses >=1.46.0,<1.47.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-pd.soybean/post-link.sh b/recipes/bioconductor-pd.soybean/post-link.sh index a6d22d34e6336..1ba5547db8e57 100644 --- a/recipes/bioconductor-pd.soybean/post-link.sh +++ b/recipes/bioconductor-pd.soybean/post-link.sh @@ -1,9 +1,10 @@ #!/bin/bash FN="pd.soybean_3.12.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/pd.soybean_3.12.0.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/pd.soybean_3.12.0.tar.gz" "https://bioarchive.galaxyproject.org/pd.soybean_3.12.0.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-pd.soybean/bioconductor-pd.soybean_3.12.0_src_all.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-pd.soybean/bioconductor-pd.soybean_3.12.0_src_all.tar.gz" ) MD5="6dbe167be9d40c1d9096485afb4525f0" @@ -16,7 +17,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-pd.soygene.1.0.st/meta.yaml b/recipes/bioconductor-pd.soygene.1.0.st/meta.yaml index bc932a8cef225..42227891425b8 100644 --- a/recipes/bioconductor-pd.soygene.1.0.st/meta.yaml +++ b/recipes/bioconductor-pd.soygene.1.0.st/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.12.0" %} {% set name = "pd.soygene.1.0.st" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -12,31 +12,31 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: b264df0648ec35d04f91e0ef8e26ac95 build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ noarch: generic requirements: host: - - 'bioconductor-biostrings >=2.50.0,<2.51.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-oligo >=1.46.0,<1.47.0' - - 'bioconductor-oligoclasses >=1.44.0,<1.45.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-biostrings >=2.52.0,<2.53.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-oligo >=1.48.0,<1.49.0' + - 'bioconductor-oligoclasses >=1.46.0,<1.47.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' run: - - 'bioconductor-biostrings >=2.50.0,<2.51.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-oligo >=1.46.0,<1.47.0' - - 'bioconductor-oligoclasses >=1.44.0,<1.45.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-biostrings >=2.52.0,<2.53.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-oligo >=1.48.0,<1.49.0' + - 'bioconductor-oligoclasses >=1.46.0,<1.47.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-pd.soygene.1.0.st/post-link.sh b/recipes/bioconductor-pd.soygene.1.0.st/post-link.sh index f470e1244acee..a47cb2dbf9582 100644 --- a/recipes/bioconductor-pd.soygene.1.0.st/post-link.sh +++ b/recipes/bioconductor-pd.soygene.1.0.st/post-link.sh @@ -1,9 +1,10 @@ #!/bin/bash FN="pd.soygene.1.0.st_3.12.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/pd.soygene.1.0.st_3.12.0.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/pd.soygene.1.0.st_3.12.0.tar.gz" "https://bioarchive.galaxyproject.org/pd.soygene.1.0.st_3.12.0.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-pd.soygene.1.0.st/bioconductor-pd.soygene.1.0.st_3.12.0_src_all.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-pd.soygene.1.0.st/bioconductor-pd.soygene.1.0.st_3.12.0_src_all.tar.gz" ) MD5="b264df0648ec35d04f91e0ef8e26ac95" @@ -16,7 +17,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-pd.soygene.1.1.st/meta.yaml b/recipes/bioconductor-pd.soygene.1.1.st/meta.yaml index 9d88114b187ba..d8d01bc252a08 100644 --- a/recipes/bioconductor-pd.soygene.1.1.st/meta.yaml +++ b/recipes/bioconductor-pd.soygene.1.1.st/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.12.0" %} {% set name = "pd.soygene.1.1.st" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -12,31 +12,31 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 4a911a4a4b5de927fe6239e500a2993f build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ noarch: generic requirements: host: - - 'bioconductor-biostrings >=2.50.0,<2.51.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-oligo >=1.46.0,<1.47.0' - - 'bioconductor-oligoclasses >=1.44.0,<1.45.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-biostrings >=2.52.0,<2.53.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-oligo >=1.48.0,<1.49.0' + - 'bioconductor-oligoclasses >=1.46.0,<1.47.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' run: - - 'bioconductor-biostrings >=2.50.0,<2.51.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-oligo >=1.46.0,<1.47.0' - - 'bioconductor-oligoclasses >=1.44.0,<1.45.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-biostrings >=2.52.0,<2.53.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-oligo >=1.48.0,<1.49.0' + - 'bioconductor-oligoclasses >=1.46.0,<1.47.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-pd.soygene.1.1.st/post-link.sh b/recipes/bioconductor-pd.soygene.1.1.st/post-link.sh index bb2b8935bd98e..46daf544940b8 100644 --- a/recipes/bioconductor-pd.soygene.1.1.st/post-link.sh +++ b/recipes/bioconductor-pd.soygene.1.1.st/post-link.sh @@ -1,9 +1,10 @@ #!/bin/bash FN="pd.soygene.1.1.st_3.12.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/pd.soygene.1.1.st_3.12.0.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/pd.soygene.1.1.st_3.12.0.tar.gz" "https://bioarchive.galaxyproject.org/pd.soygene.1.1.st_3.12.0.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-pd.soygene.1.1.st/bioconductor-pd.soygene.1.1.st_3.12.0_src_all.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-pd.soygene.1.1.st/bioconductor-pd.soygene.1.1.st_3.12.0_src_all.tar.gz" ) MD5="4a911a4a4b5de927fe6239e500a2993f" @@ -16,7 +17,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-pd.sugar.cane/meta.yaml b/recipes/bioconductor-pd.sugar.cane/meta.yaml index 41fc8801affa5..c4136beac1260 100644 --- a/recipes/bioconductor-pd.sugar.cane/meta.yaml +++ b/recipes/bioconductor-pd.sugar.cane/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.12.0" %} {% set name = "pd.sugar.cane" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -12,31 +12,31 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: bd7eb8b1a1c9ac77359358a5347330fb build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ noarch: generic requirements: host: - - 'bioconductor-biostrings >=2.50.0,<2.51.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-oligo >=1.46.0,<1.47.0' - - 'bioconductor-oligoclasses >=1.44.0,<1.45.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-biostrings >=2.52.0,<2.53.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-oligo >=1.48.0,<1.49.0' + - 'bioconductor-oligoclasses >=1.46.0,<1.47.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' run: - - 'bioconductor-biostrings >=2.50.0,<2.51.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-oligo >=1.46.0,<1.47.0' - - 'bioconductor-oligoclasses >=1.44.0,<1.45.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-biostrings >=2.52.0,<2.53.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-oligo >=1.48.0,<1.49.0' + - 'bioconductor-oligoclasses >=1.46.0,<1.47.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-pd.sugar.cane/post-link.sh b/recipes/bioconductor-pd.sugar.cane/post-link.sh index e63846ab1c367..dd46972725d26 100644 --- a/recipes/bioconductor-pd.sugar.cane/post-link.sh +++ b/recipes/bioconductor-pd.sugar.cane/post-link.sh @@ -1,9 +1,10 @@ #!/bin/bash FN="pd.sugar.cane_3.12.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/pd.sugar.cane_3.12.0.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/pd.sugar.cane_3.12.0.tar.gz" "https://bioarchive.galaxyproject.org/pd.sugar.cane_3.12.0.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-pd.sugar.cane/bioconductor-pd.sugar.cane_3.12.0_src_all.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-pd.sugar.cane/bioconductor-pd.sugar.cane_3.12.0_src_all.tar.gz" ) MD5="bd7eb8b1a1c9ac77359358a5347330fb" @@ -16,7 +17,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-pd.tomato/meta.yaml b/recipes/bioconductor-pd.tomato/meta.yaml index be349c4cc439d..0d20aa0128631 100644 --- a/recipes/bioconductor-pd.tomato/meta.yaml +++ b/recipes/bioconductor-pd.tomato/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.12.0" %} {% set name = "pd.tomato" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -12,31 +12,31 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: ce78f6ee43d72e017608413dd4d50580 build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ noarch: generic requirements: host: - - 'bioconductor-biostrings >=2.50.0,<2.51.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-oligo >=1.46.0,<1.47.0' - - 'bioconductor-oligoclasses >=1.44.0,<1.45.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-biostrings >=2.52.0,<2.53.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-oligo >=1.48.0,<1.49.0' + - 'bioconductor-oligoclasses >=1.46.0,<1.47.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' run: - - 'bioconductor-biostrings >=2.50.0,<2.51.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-oligo >=1.46.0,<1.47.0' - - 'bioconductor-oligoclasses >=1.44.0,<1.45.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-biostrings >=2.52.0,<2.53.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-oligo >=1.48.0,<1.49.0' + - 'bioconductor-oligoclasses >=1.46.0,<1.47.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-pd.tomato/post-link.sh b/recipes/bioconductor-pd.tomato/post-link.sh index 59a43d012ec00..0e3b76e7eb263 100644 --- a/recipes/bioconductor-pd.tomato/post-link.sh +++ b/recipes/bioconductor-pd.tomato/post-link.sh @@ -1,9 +1,10 @@ #!/bin/bash FN="pd.tomato_3.12.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/pd.tomato_3.12.0.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/pd.tomato_3.12.0.tar.gz" "https://bioarchive.galaxyproject.org/pd.tomato_3.12.0.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-pd.tomato/bioconductor-pd.tomato_3.12.0_src_all.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-pd.tomato/bioconductor-pd.tomato_3.12.0_src_all.tar.gz" ) MD5="ce78f6ee43d72e017608413dd4d50580" @@ -16,7 +17,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-pd.u133.x3p/meta.yaml b/recipes/bioconductor-pd.u133.x3p/meta.yaml index 13b6eb026c29c..cff64dcf99e60 100644 --- a/recipes/bioconductor-pd.u133.x3p/meta.yaml +++ b/recipes/bioconductor-pd.u133.x3p/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.12.0" %} {% set name = "pd.u133.x3p" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -12,31 +12,31 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: e3f343e32273667f851e26d7b8a7a5db build: - number: 1 + number: 2 rpaths: - lib/R/lib/ - lib/ noarch: generic requirements: host: - - 'bioconductor-biostrings >=2.50.0,<2.51.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-oligo >=1.46.0,<1.47.0' - - 'bioconductor-oligoclasses >=1.44.0,<1.45.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-biostrings >=2.52.0,<2.53.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-oligo >=1.48.0,<1.49.0' + - 'bioconductor-oligoclasses >=1.46.0,<1.47.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' run: - - 'bioconductor-biostrings >=2.50.0,<2.51.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-oligo >=1.46.0,<1.47.0' - - 'bioconductor-oligoclasses >=1.44.0,<1.45.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-biostrings >=2.52.0,<2.53.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-oligo >=1.48.0,<1.49.0' + - 'bioconductor-oligoclasses >=1.46.0,<1.47.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-pd.u133.x3p/post-link.sh b/recipes/bioconductor-pd.u133.x3p/post-link.sh index c7e2a713a2220..7689dbe3ae5be 100644 --- a/recipes/bioconductor-pd.u133.x3p/post-link.sh +++ b/recipes/bioconductor-pd.u133.x3p/post-link.sh @@ -1,9 +1,10 @@ #!/bin/bash FN="pd.u133.x3p_3.12.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/pd.u133.x3p_3.12.0.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/pd.u133.x3p_3.12.0.tar.gz" "https://bioarchive.galaxyproject.org/pd.u133.x3p_3.12.0.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-pd.u133.x3p/bioconductor-pd.u133.x3p_3.12.0_src_all.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-pd.u133.x3p/bioconductor-pd.u133.x3p_3.12.0_src_all.tar.gz" ) MD5="e3f343e32273667f851e26d7b8a7a5db" @@ -16,7 +17,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-pd.vitis.vinifera/meta.yaml b/recipes/bioconductor-pd.vitis.vinifera/meta.yaml index 121fcd62ead73..8b97f4c0d0b72 100644 --- a/recipes/bioconductor-pd.vitis.vinifera/meta.yaml +++ b/recipes/bioconductor-pd.vitis.vinifera/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.12.0" %} {% set name = "pd.vitis.vinifera" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -12,31 +12,31 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 104a8ac33a9baa25a61f953679795696 build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ noarch: generic requirements: host: - - 'bioconductor-biostrings >=2.50.0,<2.51.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-oligo >=1.46.0,<1.47.0' - - 'bioconductor-oligoclasses >=1.44.0,<1.45.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-biostrings >=2.52.0,<2.53.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-oligo >=1.48.0,<1.49.0' + - 'bioconductor-oligoclasses >=1.46.0,<1.47.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' run: - - 'bioconductor-biostrings >=2.50.0,<2.51.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-oligo >=1.46.0,<1.47.0' - - 'bioconductor-oligoclasses >=1.44.0,<1.45.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-biostrings >=2.52.0,<2.53.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-oligo >=1.48.0,<1.49.0' + - 'bioconductor-oligoclasses >=1.46.0,<1.47.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-pd.vitis.vinifera/post-link.sh b/recipes/bioconductor-pd.vitis.vinifera/post-link.sh index 7bdc1562f6f75..d1d7947b8d40f 100644 --- a/recipes/bioconductor-pd.vitis.vinifera/post-link.sh +++ b/recipes/bioconductor-pd.vitis.vinifera/post-link.sh @@ -1,9 +1,10 @@ #!/bin/bash FN="pd.vitis.vinifera_3.12.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/pd.vitis.vinifera_3.12.0.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/pd.vitis.vinifera_3.12.0.tar.gz" "https://bioarchive.galaxyproject.org/pd.vitis.vinifera_3.12.0.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-pd.vitis.vinifera/bioconductor-pd.vitis.vinifera_3.12.0_src_all.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-pd.vitis.vinifera/bioconductor-pd.vitis.vinifera_3.12.0_src_all.tar.gz" ) MD5="104a8ac33a9baa25a61f953679795696" @@ -16,7 +17,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-pd.wheat/meta.yaml b/recipes/bioconductor-pd.wheat/meta.yaml index 4697694543a0b..7e5dde54ee908 100644 --- a/recipes/bioconductor-pd.wheat/meta.yaml +++ b/recipes/bioconductor-pd.wheat/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.12.0" %} {% set name = "pd.wheat" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -12,31 +12,31 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 38a7183c8d3b874cf62391a9e9169bb9 build: - number: 1 + number: 2 rpaths: - lib/R/lib/ - lib/ noarch: generic requirements: host: - - 'bioconductor-biostrings >=2.50.0,<2.51.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-oligo >=1.46.0,<1.47.0' - - 'bioconductor-oligoclasses >=1.44.0,<1.45.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-biostrings >=2.52.0,<2.53.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-oligo >=1.48.0,<1.49.0' + - 'bioconductor-oligoclasses >=1.46.0,<1.47.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' run: - - 'bioconductor-biostrings >=2.50.0,<2.51.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-oligo >=1.46.0,<1.47.0' - - 'bioconductor-oligoclasses >=1.44.0,<1.45.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-biostrings >=2.52.0,<2.53.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-oligo >=1.48.0,<1.49.0' + - 'bioconductor-oligoclasses >=1.46.0,<1.47.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-pd.wheat/post-link.sh b/recipes/bioconductor-pd.wheat/post-link.sh index 9d5b91253068d..57fd545524acb 100644 --- a/recipes/bioconductor-pd.wheat/post-link.sh +++ b/recipes/bioconductor-pd.wheat/post-link.sh @@ -1,9 +1,10 @@ #!/bin/bash FN="pd.wheat_3.12.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/pd.wheat_3.12.0.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/pd.wheat_3.12.0.tar.gz" "https://bioarchive.galaxyproject.org/pd.wheat_3.12.0.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-pd.wheat/bioconductor-pd.wheat_3.12.0_src_all.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-pd.wheat/bioconductor-pd.wheat_3.12.0_src_all.tar.gz" ) MD5="38a7183c8d3b874cf62391a9e9169bb9" @@ -16,7 +17,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-pd.x.laevis.2/meta.yaml b/recipes/bioconductor-pd.x.laevis.2/meta.yaml index 8cd5317c6b0be..1bc470eb93b5c 100644 --- a/recipes/bioconductor-pd.x.laevis.2/meta.yaml +++ b/recipes/bioconductor-pd.x.laevis.2/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.12.0" %} {% set name = "pd.x.laevis.2" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -12,31 +12,31 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 32416957e3cdc11ad4dbfcd9141ff113 build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ noarch: generic requirements: host: - - 'bioconductor-biostrings >=2.50.0,<2.51.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-oligo >=1.46.0,<1.47.0' - - 'bioconductor-oligoclasses >=1.44.0,<1.45.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-biostrings >=2.52.0,<2.53.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-oligo >=1.48.0,<1.49.0' + - 'bioconductor-oligoclasses >=1.46.0,<1.47.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' run: - - 'bioconductor-biostrings >=2.50.0,<2.51.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-oligo >=1.46.0,<1.47.0' - - 'bioconductor-oligoclasses >=1.44.0,<1.45.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-biostrings >=2.52.0,<2.53.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-oligo >=1.48.0,<1.49.0' + - 'bioconductor-oligoclasses >=1.46.0,<1.47.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-pd.x.laevis.2/post-link.sh b/recipes/bioconductor-pd.x.laevis.2/post-link.sh index 314748e1db2ff..1ea7983f1492d 100644 --- a/recipes/bioconductor-pd.x.laevis.2/post-link.sh +++ b/recipes/bioconductor-pd.x.laevis.2/post-link.sh @@ -1,9 +1,10 @@ #!/bin/bash FN="pd.x.laevis.2_3.12.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/pd.x.laevis.2_3.12.0.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/pd.x.laevis.2_3.12.0.tar.gz" "https://bioarchive.galaxyproject.org/pd.x.laevis.2_3.12.0.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-pd.x.laevis.2/bioconductor-pd.x.laevis.2_3.12.0_src_all.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-pd.x.laevis.2/bioconductor-pd.x.laevis.2_3.12.0_src_all.tar.gz" ) MD5="32416957e3cdc11ad4dbfcd9141ff113" @@ -16,7 +17,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-pd.x.tropicalis/meta.yaml b/recipes/bioconductor-pd.x.tropicalis/meta.yaml index 9a76ae659c39b..6ee82938608f1 100644 --- a/recipes/bioconductor-pd.x.tropicalis/meta.yaml +++ b/recipes/bioconductor-pd.x.tropicalis/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.12.0" %} {% set name = "pd.x.tropicalis" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -12,31 +12,31 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 79a4de91831e4b0153495e12b9c6e8d3 build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ noarch: generic requirements: host: - - 'bioconductor-biostrings >=2.50.0,<2.51.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-oligo >=1.46.0,<1.47.0' - - 'bioconductor-oligoclasses >=1.44.0,<1.45.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-biostrings >=2.52.0,<2.53.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-oligo >=1.48.0,<1.49.0' + - 'bioconductor-oligoclasses >=1.46.0,<1.47.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' run: - - 'bioconductor-biostrings >=2.50.0,<2.51.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-oligo >=1.46.0,<1.47.0' - - 'bioconductor-oligoclasses >=1.44.0,<1.45.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-biostrings >=2.52.0,<2.53.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-oligo >=1.48.0,<1.49.0' + - 'bioconductor-oligoclasses >=1.46.0,<1.47.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-pd.x.tropicalis/post-link.sh b/recipes/bioconductor-pd.x.tropicalis/post-link.sh index 033c2aba64140..4ae3f76fe2d4a 100644 --- a/recipes/bioconductor-pd.x.tropicalis/post-link.sh +++ b/recipes/bioconductor-pd.x.tropicalis/post-link.sh @@ -1,9 +1,10 @@ #!/bin/bash FN="pd.x.tropicalis_3.12.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/pd.x.tropicalis_3.12.0.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/pd.x.tropicalis_3.12.0.tar.gz" "https://bioarchive.galaxyproject.org/pd.x.tropicalis_3.12.0.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-pd.x.tropicalis/bioconductor-pd.x.tropicalis_3.12.0_src_all.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-pd.x.tropicalis/bioconductor-pd.x.tropicalis_3.12.0_src_all.tar.gz" ) MD5="79a4de91831e4b0153495e12b9c6e8d3" @@ -16,7 +17,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-pd.xenopus.laevis/meta.yaml b/recipes/bioconductor-pd.xenopus.laevis/meta.yaml index 53654ca08bc0c..a2dded70c1e1b 100644 --- a/recipes/bioconductor-pd.xenopus.laevis/meta.yaml +++ b/recipes/bioconductor-pd.xenopus.laevis/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.12.0" %} {% set name = "pd.xenopus.laevis" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -12,31 +12,31 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 6d5c2c9e8e3891770b1c6e9dcd823c0d build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ noarch: generic requirements: host: - - 'bioconductor-biostrings >=2.50.0,<2.51.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-oligo >=1.46.0,<1.47.0' - - 'bioconductor-oligoclasses >=1.44.0,<1.45.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-biostrings >=2.52.0,<2.53.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-oligo >=1.48.0,<1.49.0' + - 'bioconductor-oligoclasses >=1.46.0,<1.47.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' run: - - 'bioconductor-biostrings >=2.50.0,<2.51.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-oligo >=1.46.0,<1.47.0' - - 'bioconductor-oligoclasses >=1.44.0,<1.45.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-biostrings >=2.52.0,<2.53.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-oligo >=1.48.0,<1.49.0' + - 'bioconductor-oligoclasses >=1.46.0,<1.47.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-pd.xenopus.laevis/post-link.sh b/recipes/bioconductor-pd.xenopus.laevis/post-link.sh index 12e5b07b39af8..d6dd3855944a9 100644 --- a/recipes/bioconductor-pd.xenopus.laevis/post-link.sh +++ b/recipes/bioconductor-pd.xenopus.laevis/post-link.sh @@ -1,9 +1,10 @@ #!/bin/bash FN="pd.xenopus.laevis_3.12.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/pd.xenopus.laevis_3.12.0.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/pd.xenopus.laevis_3.12.0.tar.gz" "https://bioarchive.galaxyproject.org/pd.xenopus.laevis_3.12.0.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-pd.xenopus.laevis/bioconductor-pd.xenopus.laevis_3.12.0_src_all.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-pd.xenopus.laevis/bioconductor-pd.xenopus.laevis_3.12.0_src_all.tar.gz" ) MD5="6d5c2c9e8e3891770b1c6e9dcd823c0d" @@ -16,7 +17,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-pd.yeast.2/meta.yaml b/recipes/bioconductor-pd.yeast.2/meta.yaml index e2fb06e7b8471..1217c843c5d1e 100644 --- a/recipes/bioconductor-pd.yeast.2/meta.yaml +++ b/recipes/bioconductor-pd.yeast.2/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.12.0" %} {% set name = "pd.yeast.2" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -12,31 +12,31 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 780f5139ee9cda46c9e38122538ce129 build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ noarch: generic requirements: host: - - 'bioconductor-biostrings >=2.50.0,<2.51.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-oligo >=1.46.0,<1.47.0' - - 'bioconductor-oligoclasses >=1.44.0,<1.45.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-biostrings >=2.52.0,<2.53.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-oligo >=1.48.0,<1.49.0' + - 'bioconductor-oligoclasses >=1.46.0,<1.47.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' run: - - 'bioconductor-biostrings >=2.50.0,<2.51.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-oligo >=1.46.0,<1.47.0' - - 'bioconductor-oligoclasses >=1.44.0,<1.45.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-biostrings >=2.52.0,<2.53.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-oligo >=1.48.0,<1.49.0' + - 'bioconductor-oligoclasses >=1.46.0,<1.47.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-pd.yeast.2/post-link.sh b/recipes/bioconductor-pd.yeast.2/post-link.sh index ab7a742336b8b..bd37ca58922eb 100644 --- a/recipes/bioconductor-pd.yeast.2/post-link.sh +++ b/recipes/bioconductor-pd.yeast.2/post-link.sh @@ -1,9 +1,10 @@ #!/bin/bash FN="pd.yeast.2_3.12.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/pd.yeast.2_3.12.0.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/pd.yeast.2_3.12.0.tar.gz" "https://bioarchive.galaxyproject.org/pd.yeast.2_3.12.0.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-pd.yeast.2/bioconductor-pd.yeast.2_3.12.0_src_all.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-pd.yeast.2/bioconductor-pd.yeast.2_3.12.0_src_all.tar.gz" ) MD5="780f5139ee9cda46c9e38122538ce129" @@ -16,7 +17,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-pd.yg.s98/meta.yaml b/recipes/bioconductor-pd.yg.s98/meta.yaml index ca4801af96ddc..2ebecd1c9a955 100644 --- a/recipes/bioconductor-pd.yg.s98/meta.yaml +++ b/recipes/bioconductor-pd.yg.s98/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.12.0" %} {% set name = "pd.yg.s98" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -12,31 +12,31 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: caec3e8f29918f078b2dc7c76f4a74e2 build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ noarch: generic requirements: host: - - 'bioconductor-biostrings >=2.50.0,<2.51.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-oligo >=1.46.0,<1.47.0' - - 'bioconductor-oligoclasses >=1.44.0,<1.45.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-biostrings >=2.52.0,<2.53.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-oligo >=1.48.0,<1.49.0' + - 'bioconductor-oligoclasses >=1.46.0,<1.47.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' run: - - 'bioconductor-biostrings >=2.50.0,<2.51.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-oligo >=1.46.0,<1.47.0' - - 'bioconductor-oligoclasses >=1.44.0,<1.45.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-biostrings >=2.52.0,<2.53.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-oligo >=1.48.0,<1.49.0' + - 'bioconductor-oligoclasses >=1.46.0,<1.47.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-pd.yg.s98/post-link.sh b/recipes/bioconductor-pd.yg.s98/post-link.sh index bbcce2c024fab..901ff80ecece4 100644 --- a/recipes/bioconductor-pd.yg.s98/post-link.sh +++ b/recipes/bioconductor-pd.yg.s98/post-link.sh @@ -1,9 +1,10 @@ #!/bin/bash FN="pd.yg.s98_3.12.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/pd.yg.s98_3.12.0.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/pd.yg.s98_3.12.0.tar.gz" "https://bioarchive.galaxyproject.org/pd.yg.s98_3.12.0.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-pd.yg.s98/bioconductor-pd.yg.s98_3.12.0_src_all.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-pd.yg.s98/bioconductor-pd.yg.s98_3.12.0_src_all.tar.gz" ) MD5="caec3e8f29918f078b2dc7c76f4a74e2" @@ -16,7 +17,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-pd.zebgene.1.0.st/meta.yaml b/recipes/bioconductor-pd.zebgene.1.0.st/meta.yaml index 177a43e329723..f7d381dec47a4 100644 --- a/recipes/bioconductor-pd.zebgene.1.0.st/meta.yaml +++ b/recipes/bioconductor-pd.zebgene.1.0.st/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.12.0" %} {% set name = "pd.zebgene.1.0.st" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -12,31 +12,31 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 54fcf757b8069e95dd7e2f3ff74ae050 build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ noarch: generic requirements: host: - - 'bioconductor-biostrings >=2.50.0,<2.51.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-oligo >=1.46.0,<1.47.0' - - 'bioconductor-oligoclasses >=1.44.0,<1.45.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-biostrings >=2.52.0,<2.53.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-oligo >=1.48.0,<1.49.0' + - 'bioconductor-oligoclasses >=1.46.0,<1.47.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' run: - - 'bioconductor-biostrings >=2.50.0,<2.51.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-oligo >=1.46.0,<1.47.0' - - 'bioconductor-oligoclasses >=1.44.0,<1.45.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-biostrings >=2.52.0,<2.53.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-oligo >=1.48.0,<1.49.0' + - 'bioconductor-oligoclasses >=1.46.0,<1.47.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-pd.zebgene.1.0.st/post-link.sh b/recipes/bioconductor-pd.zebgene.1.0.st/post-link.sh index f217b96288308..7a203bd96afae 100644 --- a/recipes/bioconductor-pd.zebgene.1.0.st/post-link.sh +++ b/recipes/bioconductor-pd.zebgene.1.0.st/post-link.sh @@ -1,9 +1,10 @@ #!/bin/bash FN="pd.zebgene.1.0.st_3.12.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/pd.zebgene.1.0.st_3.12.0.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/pd.zebgene.1.0.st_3.12.0.tar.gz" "https://bioarchive.galaxyproject.org/pd.zebgene.1.0.st_3.12.0.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-pd.zebgene.1.0.st/bioconductor-pd.zebgene.1.0.st_3.12.0_src_all.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-pd.zebgene.1.0.st/bioconductor-pd.zebgene.1.0.st_3.12.0_src_all.tar.gz" ) MD5="54fcf757b8069e95dd7e2f3ff74ae050" @@ -16,7 +17,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-pd.zebgene.1.1.st/meta.yaml b/recipes/bioconductor-pd.zebgene.1.1.st/meta.yaml index 672e50eb86340..dd24a601647ff 100644 --- a/recipes/bioconductor-pd.zebgene.1.1.st/meta.yaml +++ b/recipes/bioconductor-pd.zebgene.1.1.st/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.12.0" %} {% set name = "pd.zebgene.1.1.st" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -12,31 +12,31 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: d87028cd9024bc33be518635cf2f48fc build: - number: 1 + number: 2 rpaths: - lib/R/lib/ - lib/ noarch: generic requirements: host: - - 'bioconductor-biostrings >=2.50.0,<2.51.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-oligo >=1.46.0,<1.47.0' - - 'bioconductor-oligoclasses >=1.44.0,<1.45.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-biostrings >=2.52.0,<2.53.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-oligo >=1.48.0,<1.49.0' + - 'bioconductor-oligoclasses >=1.46.0,<1.47.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' run: - - 'bioconductor-biostrings >=2.50.0,<2.51.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-oligo >=1.46.0,<1.47.0' - - 'bioconductor-oligoclasses >=1.44.0,<1.45.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-biostrings >=2.52.0,<2.53.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-oligo >=1.48.0,<1.49.0' + - 'bioconductor-oligoclasses >=1.46.0,<1.47.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-pd.zebgene.1.1.st/post-link.sh b/recipes/bioconductor-pd.zebgene.1.1.st/post-link.sh index c18a403206093..a80a81ab16cd2 100644 --- a/recipes/bioconductor-pd.zebgene.1.1.st/post-link.sh +++ b/recipes/bioconductor-pd.zebgene.1.1.st/post-link.sh @@ -1,9 +1,10 @@ #!/bin/bash FN="pd.zebgene.1.1.st_3.12.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/pd.zebgene.1.1.st_3.12.0.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/pd.zebgene.1.1.st_3.12.0.tar.gz" "https://bioarchive.galaxyproject.org/pd.zebgene.1.1.st_3.12.0.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-pd.zebgene.1.1.st/bioconductor-pd.zebgene.1.1.st_3.12.0_src_all.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-pd.zebgene.1.1.st/bioconductor-pd.zebgene.1.1.st_3.12.0_src_all.tar.gz" ) MD5="d87028cd9024bc33be518635cf2f48fc" @@ -16,7 +17,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-pd.zebrafish/meta.yaml b/recipes/bioconductor-pd.zebrafish/meta.yaml index 975546614d4b0..2f8865fcc8417 100644 --- a/recipes/bioconductor-pd.zebrafish/meta.yaml +++ b/recipes/bioconductor-pd.zebrafish/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.12.0" %} {% set name = "pd.zebrafish" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -12,31 +12,31 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 101f09a9d9304d1d8fbcc7f4812897b1 build: - number: 1 + number: 2 rpaths: - lib/R/lib/ - lib/ noarch: generic requirements: host: - - 'bioconductor-biostrings >=2.50.0,<2.51.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-oligo >=1.46.0,<1.47.0' - - 'bioconductor-oligoclasses >=1.44.0,<1.45.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-biostrings >=2.52.0,<2.53.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-oligo >=1.48.0,<1.49.0' + - 'bioconductor-oligoclasses >=1.46.0,<1.47.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' run: - - 'bioconductor-biostrings >=2.50.0,<2.51.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-oligo >=1.46.0,<1.47.0' - - 'bioconductor-oligoclasses >=1.44.0,<1.45.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-biostrings >=2.52.0,<2.53.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-oligo >=1.48.0,<1.49.0' + - 'bioconductor-oligoclasses >=1.46.0,<1.47.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-pd.zebrafish/post-link.sh b/recipes/bioconductor-pd.zebrafish/post-link.sh index 8c0d249d03995..07c9e42ff6ada 100644 --- a/recipes/bioconductor-pd.zebrafish/post-link.sh +++ b/recipes/bioconductor-pd.zebrafish/post-link.sh @@ -1,9 +1,10 @@ #!/bin/bash FN="pd.zebrafish_3.12.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/pd.zebrafish_3.12.0.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/pd.zebrafish_3.12.0.tar.gz" "https://bioarchive.galaxyproject.org/pd.zebrafish_3.12.0.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-pd.zebrafish/bioconductor-pd.zebrafish_3.12.0_src_all.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-pd.zebrafish/bioconductor-pd.zebrafish_3.12.0_src_all.tar.gz" ) MD5="101f09a9d9304d1d8fbcc7f4812897b1" @@ -16,7 +17,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-pdinfobuilder/meta.yaml b/recipes/bioconductor-pdinfobuilder/meta.yaml index c6f8cd11105eb..3e514d729071e 100644 --- a/recipes/bioconductor-pdinfobuilder/meta.yaml +++ b/recipes/bioconductor-pdinfobuilder/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.46.0" %} +{% set version = "1.48.0" %} {% set name = "pdInfoBuilder" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 11f99f8aa61c41052f80979136449ca7 + md5: 49c010d594178513df2396a1a0b69fb2 build: number: 0 rpaths: @@ -18,26 +18,26 @@ build: - lib/ requirements: host: - - 'bioconductor-affxparser >=1.54.0,<1.55.0' - - 'bioconductor-biobase >=2.42.0,<2.43.0' - - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' - - 'bioconductor-biostrings >=2.50.0,<2.51.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-oligo >=1.46.0,<1.47.0' - - 'bioconductor-oligoclasses >=1.44.0,<1.45.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-affxparser >=1.56.0,<1.57.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' + - 'bioconductor-biocgenerics >=0.30.0,<0.31.0' + - 'bioconductor-biostrings >=2.52.0,<2.53.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-oligo >=1.48.0,<1.49.0' + - 'bioconductor-oligoclasses >=1.46.0,<1.47.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' run: - - 'bioconductor-affxparser >=1.54.0,<1.55.0' - - 'bioconductor-biobase >=2.42.0,<2.43.0' - - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' - - 'bioconductor-biostrings >=2.50.0,<2.51.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-oligo >=1.46.0,<1.47.0' - - 'bioconductor-oligoclasses >=1.44.0,<1.45.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-affxparser >=1.56.0,<1.57.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' + - 'bioconductor-biocgenerics >=0.30.0,<0.31.0' + - 'bioconductor-biostrings >=2.52.0,<2.53.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-oligo >=1.48.0,<1.49.0' + - 'bioconductor-oligoclasses >=1.46.0,<1.47.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' diff --git a/recipes/bioconductor-peca/meta.yaml b/recipes/bioconductor-peca/meta.yaml index b3ed613696253..fecee38093256 100644 --- a/recipes/bioconductor-peca/meta.yaml +++ b/recipes/bioconductor-peca/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.18.0" %} +{% set version = "1.20.0" %} {% set name = "PECA" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 0403c0ac60f05fb12d20f3c186e0c140 + md5: b0a710433143e3c8529b31953dd75096 build: number: 0 rpaths: @@ -20,20 +20,20 @@ build: # Suggests: SpikeIn requirements: host: - - 'bioconductor-affy >=1.60.0,<1.61.0' - - 'bioconductor-genefilter >=1.64.0,<1.65.0' - - 'bioconductor-limma >=3.38.0,<3.39.0' - - 'bioconductor-preprocesscore >=1.44.0,<1.45.0' - - 'bioconductor-rots >=1.10.0,<1.11.0' + - 'bioconductor-affy >=1.62.0,<1.63.0' + - 'bioconductor-genefilter >=1.66.0,<1.67.0' + - 'bioconductor-limma >=3.40.0,<3.41.0' + - 'bioconductor-preprocesscore >=1.46.0,<1.47.0' + - 'bioconductor-rots >=1.12.0,<1.13.0' - r-aroma.affymetrix - r-aroma.core - r-base run: - - 'bioconductor-affy >=1.60.0,<1.61.0' - - 'bioconductor-genefilter >=1.64.0,<1.65.0' - - 'bioconductor-limma >=3.38.0,<3.39.0' - - 'bioconductor-preprocesscore >=1.44.0,<1.45.0' - - 'bioconductor-rots >=1.10.0,<1.11.0' + - 'bioconductor-affy >=1.62.0,<1.63.0' + - 'bioconductor-genefilter >=1.66.0,<1.67.0' + - 'bioconductor-limma >=3.40.0,<3.41.0' + - 'bioconductor-preprocesscore >=1.46.0,<1.47.0' + - 'bioconductor-rots >=1.12.0,<1.13.0' - r-aroma.affymetrix - r-aroma.core - r-base diff --git a/recipes/bioconductor-pedbarrayv10.db/meta.yaml b/recipes/bioconductor-pedbarrayv10.db/meta.yaml index f6379720bc6de..2b12844a8aa72 100644 --- a/recipes/bioconductor-pedbarrayv10.db/meta.yaml +++ b/recipes/bioconductor-pedbarrayv10.db/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.2.3" %} {% set name = "pedbarrayv10.db" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -12,7 +12,7 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 25acc3bfee229015ecca1c7d688e5168 build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ @@ -20,14 +20,14 @@ build: # Suggests: DBI, annotate, RUnit requirements: host: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' - - 'bioconductor-org.hs.eg.db >=3.7.0,<3.8.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' + - 'bioconductor-org.hs.eg.db >=3.8.0,<3.9.0' - r-base run: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' - - 'bioconductor-org.hs.eg.db >=3.7.0,<3.8.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' + - 'bioconductor-org.hs.eg.db >=3.8.0,<3.9.0' - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-pedbarrayv10.db/post-link.sh b/recipes/bioconductor-pedbarrayv10.db/post-link.sh index e1f720830c869..3867484ef9bcc 100644 --- a/recipes/bioconductor-pedbarrayv10.db/post-link.sh +++ b/recipes/bioconductor-pedbarrayv10.db/post-link.sh @@ -1,9 +1,10 @@ #!/bin/bash FN="pedbarrayv10.db_3.2.3.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/pedbarrayv10.db_3.2.3.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/pedbarrayv10.db_3.2.3.tar.gz" "https://bioarchive.galaxyproject.org/pedbarrayv10.db_3.2.3.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-pedbarrayv10.db/bioconductor-pedbarrayv10.db_3.2.3_src_all.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-pedbarrayv10.db/bioconductor-pedbarrayv10.db_3.2.3_src_all.tar.gz" ) MD5="25acc3bfee229015ecca1c7d688e5168" @@ -16,7 +17,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-pedbarrayv9.db/meta.yaml b/recipes/bioconductor-pedbarrayv9.db/meta.yaml index 9ffa2202f5cf0..b9ec635cc852e 100644 --- a/recipes/bioconductor-pedbarrayv9.db/meta.yaml +++ b/recipes/bioconductor-pedbarrayv9.db/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.2.3" %} {% set name = "pedbarrayv9.db" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -12,7 +12,7 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: da4b2f9c0a672e0c9ee53f017bacaff7 build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ @@ -20,14 +20,14 @@ build: # Suggests: DBI, annotate, RUnit requirements: host: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' - - 'bioconductor-org.hs.eg.db >=3.7.0,<3.8.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' + - 'bioconductor-org.hs.eg.db >=3.8.0,<3.9.0' - r-base run: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' - - 'bioconductor-org.hs.eg.db >=3.7.0,<3.8.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' + - 'bioconductor-org.hs.eg.db >=3.8.0,<3.9.0' - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-pedbarrayv9.db/post-link.sh b/recipes/bioconductor-pedbarrayv9.db/post-link.sh index 1e9c2ffa4b060..e5e51fe98938e 100644 --- a/recipes/bioconductor-pedbarrayv9.db/post-link.sh +++ b/recipes/bioconductor-pedbarrayv9.db/post-link.sh @@ -1,9 +1,10 @@ #!/bin/bash FN="pedbarrayv9.db_3.2.3.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/pedbarrayv9.db_3.2.3.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/pedbarrayv9.db_3.2.3.tar.gz" "https://bioarchive.galaxyproject.org/pedbarrayv9.db_3.2.3.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-pedbarrayv9.db/bioconductor-pedbarrayv9.db_3.2.3_src_all.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-pedbarrayv9.db/bioconductor-pedbarrayv9.db_3.2.3_src_all.tar.gz" ) MD5="da4b2f9c0a672e0c9ee53f017bacaff7" @@ -16,7 +17,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-pepdat/meta.yaml b/recipes/bioconductor-pepdat/meta.yaml index 9e98dbf7bd463..588727af6cee7 100644 --- a/recipes/bioconductor-pepdat/meta.yaml +++ b/recipes/bioconductor-pepdat/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.2.0" %} +{% set version = "1.4.0" %} {% set name = "pepDat" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 6348dfe04bb83e78df150d7f67fb3e03 + md5: c72c91f64f3099c7ac03fe30244a4a9d build: number: 0 rpaths: @@ -20,12 +20,12 @@ build: # Suggests: knitr requirements: host: - - 'bioconductor-genomicranges >=1.34.0,<1.35.0' + - 'bioconductor-genomicranges >=1.36.0,<1.37.0' - r-base run: - - 'bioconductor-genomicranges >=1.34.0,<1.35.0' + - 'bioconductor-genomicranges >=1.36.0,<1.37.0' - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-pepdat/post-link.sh b/recipes/bioconductor-pepdat/post-link.sh index 563fe1ea0e559..c7ab78c0747aa 100644 --- a/recipes/bioconductor-pepdat/post-link.sh +++ b/recipes/bioconductor-pepdat/post-link.sh @@ -1,11 +1,11 @@ #!/bin/bash -FN="pepDat_1.2.0.tar.gz" +FN="pepDat_1.4.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/experiment/src/contrib/pepDat_1.2.0.tar.gz" - "https://bioarchive.galaxyproject.org/pepDat_1.2.0.tar.gz" - "https://depot.galaxyproject.org/software/bioconductor-pepdat/bioconductor-pepdat_1.2.0_src_all.tar.gz" + "https://bioconductor.org/packages/3.9/data/experiment/src/contrib/pepDat_1.4.0.tar.gz" + "https://bioarchive.galaxyproject.org/pepDat_1.4.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-pepdat/bioconductor-pepdat_1.4.0_src_all.tar.gz" ) -MD5="6348dfe04bb83e78df150d7f67fb3e03" +MD5="c72c91f64f3099c7ac03fe30244a4a9d" # Use a staging area in the conda dir rather than temp dirs, both to avoid # permission issues as well as to have things downloaded in a predictable @@ -16,7 +16,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-pepsnmr/meta.yaml b/recipes/bioconductor-pepsnmr/meta.yaml index c95594739aa02..2bef4b5123ba2 100644 --- a/recipes/bioconductor-pepsnmr/meta.yaml +++ b/recipes/bioconductor-pepsnmr/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.0.1" %} +{% set version = "1.2.0" %} {% set name = "PepsNMR" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 7c24032f0d642d8d5965d0f60f9d1cf8 + md5: 4b0d8a295ca2dc9bfe5ec4a6e9befd9f build: number: 0 rpaths: diff --git a/recipes/bioconductor-pepsnmrdata/meta.yaml b/recipes/bioconductor-pepsnmrdata/meta.yaml index f782f0ffbbff4..d354c9b0dfbb3 100644 --- a/recipes/bioconductor-pepsnmrdata/meta.yaml +++ b/recipes/bioconductor-pepsnmrdata/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.0.0" %} +{% set version = "1.2.0" %} {% set name = "PepsNMRData" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: ef7f2931dab1c82cb13f7b1af8bfd91f + md5: 4426ad09c50010889fece7df54bf184d build: number: 0 rpaths: @@ -23,7 +23,7 @@ requirements: - r-base run: - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-pepsnmrdata/post-link.sh b/recipes/bioconductor-pepsnmrdata/post-link.sh index cc029a12c3e5c..1d206dca92bd6 100644 --- a/recipes/bioconductor-pepsnmrdata/post-link.sh +++ b/recipes/bioconductor-pepsnmrdata/post-link.sh @@ -1,11 +1,11 @@ #!/bin/bash -FN="PepsNMRData_1.0.0.tar.gz" +FN="PepsNMRData_1.2.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/experiment/src/contrib/PepsNMRData_1.0.0.tar.gz" - "https://bioarchive.galaxyproject.org/PepsNMRData_1.0.0.tar.gz" - "https://depot.galaxyproject.org/software/bioconductor-pepsnmrdata/bioconductor-pepsnmrdata_1.0.0_src_all.tar.gz" + "https://bioconductor.org/packages/3.9/data/experiment/src/contrib/PepsNMRData_1.2.0.tar.gz" + "https://bioarchive.galaxyproject.org/PepsNMRData_1.2.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-pepsnmrdata/bioconductor-pepsnmrdata_1.2.0_src_all.tar.gz" ) -MD5="ef7f2931dab1c82cb13f7b1af8bfd91f" +MD5="4426ad09c50010889fece7df54bf184d" # Use a staging area in the conda dir rather than temp dirs, both to avoid # permission issues as well as to have things downloaded in a predictable @@ -16,7 +16,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-pepstat/meta.yaml b/recipes/bioconductor-pepstat/meta.yaml index a0122ed4519ff..0002934d68cb8 100644 --- a/recipes/bioconductor-pepstat/meta.yaml +++ b/recipes/bioconductor-pepstat/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.16.0" %} +{% set version = "1.18.0" %} {% set name = "pepStat" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: c232a1a342e9683a99da75bc419d5f71 + md5: e78ab9a2f6eb8002061befa6ff303c68 build: number: 0 rpaths: @@ -20,20 +20,20 @@ build: # Suggests: pepDat, Pviz, knitr, shiny requirements: host: - - 'bioconductor-biobase >=2.42.0,<2.43.0' - - 'bioconductor-genomicranges >=1.34.0,<1.35.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-limma >=3.38.0,<3.39.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' + - 'bioconductor-genomicranges >=1.36.0,<1.37.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-limma >=3.40.0,<3.41.0' - r-base - r-data.table - r-fields - r-ggplot2 - r-plyr run: - - 'bioconductor-biobase >=2.42.0,<2.43.0' - - 'bioconductor-genomicranges >=1.34.0,<1.35.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-limma >=3.38.0,<3.39.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' + - 'bioconductor-genomicranges >=1.36.0,<1.37.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-limma >=3.40.0,<3.41.0' - r-base - r-data.table - r-fields diff --git a/recipes/bioconductor-pepxmltab/meta.yaml b/recipes/bioconductor-pepxmltab/meta.yaml index 9ee888dba97b7..6242f81f06d8f 100644 --- a/recipes/bioconductor-pepxmltab/meta.yaml +++ b/recipes/bioconductor-pepxmltab/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.16.1" %} +{% set version = "1.18.0" %} {% set name = "pepXMLTab" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: c8a8a4e4efb1434b03f3f10eb0f47821 + md5: 602907c5343bbd61c7b0692fe5ad9202 build: number: 0 rpaths: diff --git a/recipes/bioconductor-perturbatr/meta.yaml b/recipes/bioconductor-perturbatr/meta.yaml index abd700a482fb1..7af0b7b6e859a 100644 --- a/recipes/bioconductor-perturbatr/meta.yaml +++ b/recipes/bioconductor-perturbatr/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.2.1" %} +{% set version = "1.4.0" %} {% set name = "perturbatr" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: fa76f0549fd75d023d2c5c231453cdee + md5: dcc3d7550c1dd7cfdd7d36e972ffc36d build: number: 0 rpaths: diff --git a/recipes/bioconductor-pfam.db/meta.yaml b/recipes/bioconductor-pfam.db/meta.yaml index 22f829432db80..ac0998956b8b3 100644 --- a/recipes/bioconductor-pfam.db/meta.yaml +++ b/recipes/bioconductor-pfam.db/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "3.7.0" %} +{% set version = "3.8.2" %} {% set name = "PFAM.db" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 4d7be786ff8dcff586998dc8fea9cf04 + md5: 5439ecd3a3caf591e77ffcd01e70dea5 build: number: 0 rpaths: @@ -20,12 +20,12 @@ build: # Suggests: DBI requirements: host: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' - r-base run: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-pfam.db/post-link.sh b/recipes/bioconductor-pfam.db/post-link.sh index 85bd62d0b2943..1753291590f9b 100644 --- a/recipes/bioconductor-pfam.db/post-link.sh +++ b/recipes/bioconductor-pfam.db/post-link.sh @@ -1,11 +1,11 @@ #!/bin/bash -FN="PFAM.db_3.7.0.tar.gz" +FN="PFAM.db_3.8.2.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/PFAM.db_3.7.0.tar.gz" - "https://bioarchive.galaxyproject.org/PFAM.db_3.7.0.tar.gz" - "https://depot.galaxyproject.org/software/bioconductor-pfam.db/bioconductor-pfam.db_3.7.0_src_all.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/PFAM.db_3.8.2.tar.gz" + "https://bioarchive.galaxyproject.org/PFAM.db_3.8.2.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-pfam.db/bioconductor-pfam.db_3.8.2_src_all.tar.gz" ) -MD5="4d7be786ff8dcff586998dc8fea9cf04" +MD5="5439ecd3a3caf591e77ffcd01e70dea5" # Use a staging area in the conda dir rather than temp dirs, both to avoid # permission issues as well as to have things downloaded in a predictable @@ -16,7 +16,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-pga/meta.yaml b/recipes/bioconductor-pga/meta.yaml index 586dcb9bc1a57..89911f3905186 100644 --- a/recipes/bioconductor-pga/meta.yaml +++ b/recipes/bioconductor-pga/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.12.1" %} +{% set version = "1.14.0" %} {% set name = "PGA" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 9d81a4174770180665ff1d6e06fc45ae + md5: b2a21d6f3de2c4b7472feffcc39067fa build: number: 0 rpaths: @@ -20,18 +20,18 @@ build: # Suggests: RMariaDB, BSgenome.Hsapiens.UCSC.hg19, RUnit, BiocGenerics, BiocStyle, knitr, R.utils requirements: host: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' - - 'bioconductor-biomart >=2.38.0,<2.39.0' - - 'bioconductor-biostrings >=2.50.0,<2.51.0' - - 'bioconductor-customprodb >=1.22.0,<1.23.0' - - 'bioconductor-genomicfeatures >=1.34.0,<1.35.0' - - 'bioconductor-genomicranges >=1.34.0,<1.35.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-rsamtools >=1.34.0,<1.35.0' - - 'bioconductor-rtandem >=1.22.0,<1.23.0' - - 'bioconductor-rtracklayer >=1.42.0,<1.43.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' - - 'bioconductor-variantannotation >=1.28.0,<1.29.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' + - 'bioconductor-biomart >=2.40.0,<2.41.0' + - 'bioconductor-biostrings >=2.52.0,<2.53.0' + - 'bioconductor-customprodb >=1.24.0,<1.25.0' + - 'bioconductor-genomicfeatures >=1.36.0,<1.37.0' + - 'bioconductor-genomicranges >=1.36.0,<1.37.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-rsamtools >=2.0.0,<2.1.0' + - 'bioconductor-rtandem >=1.24.0,<1.25.0' + - 'bioconductor-rtracklayer >=1.44.0,<1.45.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' + - 'bioconductor-variantannotation >=1.30.0,<1.31.0' - r-base - r-data.table - r-ggplot2 @@ -41,18 +41,18 @@ requirements: - r-rsqlite - r-stringr run: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' - - 'bioconductor-biomart >=2.38.0,<2.39.0' - - 'bioconductor-biostrings >=2.50.0,<2.51.0' - - 'bioconductor-customprodb >=1.22.0,<1.23.0' - - 'bioconductor-genomicfeatures >=1.34.0,<1.35.0' - - 'bioconductor-genomicranges >=1.34.0,<1.35.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-rsamtools >=1.34.0,<1.35.0' - - 'bioconductor-rtandem >=1.22.0,<1.23.0' - - 'bioconductor-rtracklayer >=1.42.0,<1.43.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' - - 'bioconductor-variantannotation >=1.28.0,<1.29.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' + - 'bioconductor-biomart >=2.40.0,<2.41.0' + - 'bioconductor-biostrings >=2.52.0,<2.53.0' + - 'bioconductor-customprodb >=1.24.0,<1.25.0' + - 'bioconductor-genomicfeatures >=1.36.0,<1.37.0' + - 'bioconductor-genomicranges >=1.36.0,<1.37.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-rsamtools >=2.0.0,<2.1.0' + - 'bioconductor-rtandem >=1.24.0,<1.25.0' + - 'bioconductor-rtracklayer >=1.44.0,<1.45.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' + - 'bioconductor-variantannotation >=1.30.0,<1.31.0' - r-base - r-data.table - r-ggplot2 diff --git a/recipes/bioconductor-pgca/meta.yaml b/recipes/bioconductor-pgca/meta.yaml index 9809b4d4b63ae..3d448c5f28ed6 100644 --- a/recipes/bioconductor-pgca/meta.yaml +++ b/recipes/bioconductor-pgca/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.6.1" %} +{% set version = "1.8.0" %} {% set name = "pgca" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 6d8bbcb59439c8d9294610f678d070bf + md5: 0294ac9de15c3e72b20f63e3dfa2ea46 build: number: 0 rpaths: diff --git a/recipes/bioconductor-pgsea/meta.yaml b/recipes/bioconductor-pgsea/meta.yaml index bdb6bec05995a..1d00c97c02e6d 100644 --- a/recipes/bioconductor-pgsea/meta.yaml +++ b/recipes/bioconductor-pgsea/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.56.0" %} +{% set version = "1.58.0" %} {% set name = "PGSEA" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 59661093e4e69ad9cb79b2f1243da19e + md5: 93b85788807b8e3a877613edb930b59d build: number: 0 rpaths: @@ -20,17 +20,17 @@ build: # Suggests: GSEABase, GEOquery, org.Hs.eg.db, hgu95av2.db, limma requirements: host: - - 'bioconductor-annaffy >=1.54.0,<1.55.0' - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' - - 'bioconductor-biobase >=2.42.0,<2.43.0' - - 'bioconductor-go.db >=3.7.0,<3.8.0' + - 'bioconductor-annaffy >=1.56.0,<1.57.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' + - 'bioconductor-go.db >=3.8.0,<3.9.0' - 'bioconductor-kegg.db >=3.2.0,<3.3.0' - r-base run: - - 'bioconductor-annaffy >=1.54.0,<1.55.0' - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' - - 'bioconductor-biobase >=2.42.0,<2.43.0' - - 'bioconductor-go.db >=3.7.0,<3.8.0' + - 'bioconductor-annaffy >=1.56.0,<1.57.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' + - 'bioconductor-go.db >=3.8.0,<3.9.0' - 'bioconductor-kegg.db >=3.2.0,<3.3.0' - r-base test: diff --git a/recipes/bioconductor-phantasus/meta.yaml b/recipes/bioconductor-phantasus/meta.yaml index 3271f29a9b2d4..22c9612d257b1 100644 --- a/recipes/bioconductor-phantasus/meta.yaml +++ b/recipes/bioconductor-phantasus/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.2.1" %} +{% set version = "1.4.0" %} {% set name = "phantasus" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 990d22722534910c8d036c0d78ba4692 + md5: 7baaeca928110d421ce44d191994569e build: number: 0 rpaths: @@ -20,11 +20,12 @@ build: # Suggests: testthat, BiocStyle, knitr, rmarkdown, data.table requirements: host: - - 'bioconductor-biobase >=2.42.0,<2.43.0' - - 'bioconductor-fgsea >=1.8.0,<1.9.0' - - 'bioconductor-geoquery >=2.50.0,<2.51.0' - - 'bioconductor-limma >=3.38.0,<3.39.0' - - 'bioconductor-rhdf5 >=2.26.0,<2.27.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' + - 'bioconductor-fgsea >=1.10.0,<1.11.0' + - 'bioconductor-geoquery >=2.52.0,<2.53.0' + - 'bioconductor-limma >=3.40.0,<3.41.0' + - 'bioconductor-rhdf5 >=2.28.0,<2.29.0' - r-assertthat - r-base - r-ccapp @@ -44,11 +45,12 @@ requirements: - r-stringr - r-svglite run: - - 'bioconductor-biobase >=2.42.0,<2.43.0' - - 'bioconductor-fgsea >=1.8.0,<1.9.0' - - 'bioconductor-geoquery >=2.50.0,<2.51.0' - - 'bioconductor-limma >=3.38.0,<3.39.0' - - 'bioconductor-rhdf5 >=2.26.0,<2.27.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' + - 'bioconductor-fgsea >=1.10.0,<1.11.0' + - 'bioconductor-geoquery >=2.52.0,<2.53.0' + - 'bioconductor-limma >=3.40.0,<3.41.0' + - 'bioconductor-rhdf5 >=2.28.0,<2.29.0' - r-assertthat - r-base - r-ccapp diff --git a/recipes/bioconductor-pharmacogx/meta.yaml b/recipes/bioconductor-pharmacogx/meta.yaml index 59c68d93e5f9c..4dc222a58a8e8 100644 --- a/recipes/bioconductor-pharmacogx/meta.yaml +++ b/recipes/bioconductor-pharmacogx/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.12.0" %} +{% set version = "1.14.0" %} {% set name = "PharmacoGx" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: bd3a5c92c8622f561b3c1cd6fe35e21b + md5: 2bad8919504392b6a04212b16d7e2e2a build: number: 0 rpaths: @@ -20,8 +20,8 @@ build: # Suggests: xtable, testthat requirements: host: - - 'bioconductor-biobase >=2.42.0,<2.43.0' - - 'bioconductor-piano >=1.22.0,<1.23.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' + - 'bioconductor-piano >=2.0.0,<2.1.0' - r-base - r-catools - r-downloader @@ -30,8 +30,8 @@ requirements: - r-rcolorbrewer - r-reshape2 run: - - 'bioconductor-biobase >=2.42.0,<2.43.0' - - 'bioconductor-piano >=1.22.0,<1.23.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' + - 'bioconductor-piano >=2.0.0,<2.1.0' - r-base - r-catools - r-downloader diff --git a/recipes/bioconductor-phastcons100way.ucsc.hg19/meta.yaml b/recipes/bioconductor-phastcons100way.ucsc.hg19/meta.yaml index 805ed66a26848..97c94935fcadd 100644 --- a/recipes/bioconductor-phastcons100way.ucsc.hg19/meta.yaml +++ b/recipes/bioconductor-phastcons100way.ucsc.hg19/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.7.2" %} {% set name = "phastCons100way.UCSC.hg19" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -12,29 +12,29 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' md5: 65aa706a567f7e328dbba0095f995cf1 build: - number: 2 + number: 3 rpaths: - lib/R/lib/ - lib/ noarch: generic requirements: host: - - 'bioconductor-bsgenome >=1.50.0,<1.51.0' - - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' - - 'bioconductor-genomicranges >=1.34.0,<1.35.0' - - 'bioconductor-genomicscores >=1.6.0,<1.7.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-bsgenome >=1.52.0,<1.53.0' + - 'bioconductor-genomeinfodb >=1.20.0,<1.21.0' + - 'bioconductor-genomicranges >=1.36.0,<1.37.0' + - 'bioconductor-genomicscores >=1.8.0,<1.9.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' - r-base run: - - 'bioconductor-bsgenome >=1.50.0,<1.51.0' - - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' - - 'bioconductor-genomicranges >=1.34.0,<1.35.0' - - 'bioconductor-genomicscores >=1.6.0,<1.7.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-bsgenome >=1.52.0,<1.53.0' + - 'bioconductor-genomeinfodb >=1.20.0,<1.21.0' + - 'bioconductor-genomicranges >=1.36.0,<1.37.0' + - 'bioconductor-genomicscores >=1.8.0,<1.9.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-phastcons100way.ucsc.hg19/post-link.sh b/recipes/bioconductor-phastcons100way.ucsc.hg19/post-link.sh index 14b405c87ef61..a7b80666189cc 100644 --- a/recipes/bioconductor-phastcons100way.ucsc.hg19/post-link.sh +++ b/recipes/bioconductor-phastcons100way.ucsc.hg19/post-link.sh @@ -1,7 +1,7 @@ #!/bin/bash FN="phastCons100way.UCSC.hg19_3.7.2.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/phastCons100way.UCSC.hg19_3.7.2.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/phastCons100way.UCSC.hg19_3.7.2.tar.gz" "https://bioarchive.galaxyproject.org/phastCons100way.UCSC.hg19_3.7.2.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-phastcons100way.ucsc.hg19/bioconductor-phastcons100way.ucsc.hg19_3.7.2_src_all.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-phastcons100way.ucsc.hg19/bioconductor-phastcons100way.ucsc.hg19_3.7.2_src_all.tar.gz" @@ -17,7 +17,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-phastcons100way.ucsc.hg38/meta.yaml b/recipes/bioconductor-phastcons100way.ucsc.hg38/meta.yaml index e98a973830ada..29d5534ddc348 100644 --- a/recipes/bioconductor-phastcons100way.ucsc.hg38/meta.yaml +++ b/recipes/bioconductor-phastcons100way.ucsc.hg38/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.7.1" %} {% set name = "phastCons100way.UCSC.hg38" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -12,29 +12,29 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' md5: 878c757f9270b3410d11e4e4a4213c8e build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ noarch: generic requirements: host: - - 'bioconductor-bsgenome >=1.50.0,<1.51.0' - - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' - - 'bioconductor-genomicranges >=1.34.0,<1.35.0' - - 'bioconductor-genomicscores >=1.6.0,<1.7.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-bsgenome >=1.52.0,<1.53.0' + - 'bioconductor-genomeinfodb >=1.20.0,<1.21.0' + - 'bioconductor-genomicranges >=1.36.0,<1.37.0' + - 'bioconductor-genomicscores >=1.8.0,<1.9.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' - r-base run: - - 'bioconductor-bsgenome >=1.50.0,<1.51.0' - - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' - - 'bioconductor-genomicranges >=1.34.0,<1.35.0' - - 'bioconductor-genomicscores >=1.6.0,<1.7.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-bsgenome >=1.52.0,<1.53.0' + - 'bioconductor-genomeinfodb >=1.20.0,<1.21.0' + - 'bioconductor-genomicranges >=1.36.0,<1.37.0' + - 'bioconductor-genomicscores >=1.8.0,<1.9.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-phastcons100way.ucsc.hg38/post-link.sh b/recipes/bioconductor-phastcons100way.ucsc.hg38/post-link.sh index 1eaf5fc2742b9..da6e37a97353b 100644 --- a/recipes/bioconductor-phastcons100way.ucsc.hg38/post-link.sh +++ b/recipes/bioconductor-phastcons100way.ucsc.hg38/post-link.sh @@ -1,9 +1,10 @@ #!/bin/bash FN="phastCons100way.UCSC.hg38_3.7.1.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/phastCons100way.UCSC.hg38_3.7.1.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/phastCons100way.UCSC.hg38_3.7.1.tar.gz" "https://bioarchive.galaxyproject.org/phastCons100way.UCSC.hg38_3.7.1.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-phastcons100way.ucsc.hg38/bioconductor-phastcons100way.ucsc.hg38_3.7.1_src_all.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-phastcons100way.ucsc.hg38/bioconductor-phastcons100way.ucsc.hg38_3.7.1_src_all.tar.gz" ) MD5="878c757f9270b3410d11e4e4a4213c8e" @@ -16,7 +17,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-phastcons7way.ucsc.hg38/meta.yaml b/recipes/bioconductor-phastcons7way.ucsc.hg38/meta.yaml index b2ffcbf010e7a..63d1bd8faa1f9 100644 --- a/recipes/bioconductor-phastcons7way.ucsc.hg38/meta.yaml +++ b/recipes/bioconductor-phastcons7way.ucsc.hg38/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.7.1" %} {% set name = "phastCons7way.UCSC.hg38" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -12,29 +12,29 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' md5: c2d87446b022c166c1c325ea2aef521d build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ noarch: generic requirements: host: - - 'bioconductor-bsgenome >=1.50.0,<1.51.0' - - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' - - 'bioconductor-genomicranges >=1.34.0,<1.35.0' - - 'bioconductor-genomicscores >=1.6.0,<1.7.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-bsgenome >=1.52.0,<1.53.0' + - 'bioconductor-genomeinfodb >=1.20.0,<1.21.0' + - 'bioconductor-genomicranges >=1.36.0,<1.37.0' + - 'bioconductor-genomicscores >=1.8.0,<1.9.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' - r-base run: - - 'bioconductor-bsgenome >=1.50.0,<1.51.0' - - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' - - 'bioconductor-genomicranges >=1.34.0,<1.35.0' - - 'bioconductor-genomicscores >=1.6.0,<1.7.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-bsgenome >=1.52.0,<1.53.0' + - 'bioconductor-genomeinfodb >=1.20.0,<1.21.0' + - 'bioconductor-genomicranges >=1.36.0,<1.37.0' + - 'bioconductor-genomicscores >=1.8.0,<1.9.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-phastcons7way.ucsc.hg38/post-link.sh b/recipes/bioconductor-phastcons7way.ucsc.hg38/post-link.sh index 1fcf36d1951f8..cafc55b03d58f 100644 --- a/recipes/bioconductor-phastcons7way.ucsc.hg38/post-link.sh +++ b/recipes/bioconductor-phastcons7way.ucsc.hg38/post-link.sh @@ -1,9 +1,10 @@ #!/bin/bash FN="phastCons7way.UCSC.hg38_3.7.1.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/phastCons7way.UCSC.hg38_3.7.1.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/phastCons7way.UCSC.hg38_3.7.1.tar.gz" "https://bioarchive.galaxyproject.org/phastCons7way.UCSC.hg38_3.7.1.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-phastcons7way.ucsc.hg38/bioconductor-phastcons7way.ucsc.hg38_3.7.1_src_all.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-phastcons7way.ucsc.hg38/bioconductor-phastcons7way.ucsc.hg38_3.7.1_src_all.tar.gz" ) MD5="c2d87446b022c166c1c325ea2aef521d" @@ -16,7 +17,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-phemd/build.sh b/recipes/bioconductor-phemd/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-phemd/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-phemd/meta.yaml b/recipes/bioconductor-phemd/meta.yaml new file mode 100644 index 0000000000000..91ad87e4cb336 --- /dev/null +++ b/recipes/bioconductor-phemd/meta.yaml @@ -0,0 +1,75 @@ +{% set version = "1.0.0" %} +{% set name = "phemd" %} +{% set bioc = "3.9" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + md5: 47b7e165094e371907496edda51706b8 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: knitr +requirements: + host: + - 'bioconductor-biobase >=2.44.0,<2.45.0' + - 'bioconductor-biocgenerics >=0.30.0,<0.31.0' + - 'bioconductor-destiny >=2.14.0,<2.15.0' + - 'bioconductor-monocle >=2.12.0,<2.13.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' + - 'bioconductor-singlecellexperiment >=1.6.0,<1.7.0' + - 'bioconductor-summarizedexperiment >=1.14.0,<1.15.0' + - r-base + - r-cluster + - r-cowplot + - r-ggplot2 + - r-igraph + - r-maptree + - r-pheatmap + - r-pracma + - r-rann + - r-rcolorbrewer + - r-rtsne + - r-scatterplot3d + - r-seurat + - r-transport + - r-vgam + run: + - 'bioconductor-biobase >=2.44.0,<2.45.0' + - 'bioconductor-biocgenerics >=0.30.0,<0.31.0' + - 'bioconductor-destiny >=2.14.0,<2.15.0' + - 'bioconductor-monocle >=2.12.0,<2.13.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' + - 'bioconductor-singlecellexperiment >=1.6.0,<1.7.0' + - 'bioconductor-summarizedexperiment >=1.14.0,<1.15.0' + - r-base + - r-cluster + - r-cowplot + - r-ggplot2 + - r-igraph + - r-maptree + - r-pheatmap + - r-pracma + - r-rann + - r-rcolorbrewer + - r-rtsne + - r-scatterplot3d + - r-seurat + - r-transport + - r-vgam +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: GPL-2 + summary: 'Package for comparing and generating a low-dimensional embedding of multiple single-cell samples.' + diff --git a/recipes/bioconductor-phenopath/meta.yaml b/recipes/bioconductor-phenopath/meta.yaml index 80f98a39da934..14127153380a4 100644 --- a/recipes/bioconductor-phenopath/meta.yaml +++ b/recipes/bioconductor-phenopath/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.6.0" %} +{% set version = "1.8.0" %} {% set name = "phenopath" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 212dfa7aecc32424ce587400cad72b1b + md5: 85a6e099b86c2fa0a42f319fbc937ae8 build: number: 0 rpaths: @@ -19,7 +19,7 @@ build: # Suggests: knitr, rmarkdown, forcats, testthat, BiocStyle, SingleCellExperiment requirements: host: - - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' + - 'bioconductor-summarizedexperiment >=1.14.0,<1.15.0' - r-base - r-dplyr - r-ggplot2 @@ -27,7 +27,7 @@ requirements: - r-tibble - r-tidyr run: - - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' + - 'bioconductor-summarizedexperiment >=1.14.0,<1.15.0' - r-base - r-dplyr - r-ggplot2 diff --git a/recipes/bioconductor-phenotest/meta.yaml b/recipes/bioconductor-phenotest/meta.yaml index 608f9b0ae5228..4cb58568c45eb 100644 --- a/recipes/bioconductor-phenotest/meta.yaml +++ b/recipes/bioconductor-phenotest/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.30.0" %} +{% set version = "1.32.0" %} {% set name = "phenoTest" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 448ca78e9eca883a0f9801e31a0e4336 + md5: 61f3a068e4988e693f6f2858030b0d02 build: number: 0 rpaths: @@ -20,19 +20,19 @@ build: # Suggests: GSEABase, KEGG.db, GO.db requirements: host: - - 'bioconductor-annotate >=1.60.0,<1.61.0' - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' - - 'bioconductor-biobase >=2.42.0,<2.43.0' - - 'bioconductor-biomart >=2.38.0,<2.39.0' - - 'bioconductor-category >=2.48.0,<2.49.0' - - 'bioconductor-genefilter >=1.64.0,<1.65.0' - - 'bioconductor-gseabase >=1.44.0,<1.45.0' - - 'bioconductor-heatplus >=2.28.0,<2.29.0' + - 'bioconductor-annotate >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' + - 'bioconductor-biomart >=2.40.0,<2.41.0' + - 'bioconductor-category >=2.50.0,<2.51.0' + - 'bioconductor-genefilter >=1.66.0,<1.67.0' + - 'bioconductor-gseabase >=1.46.0,<1.47.0' + - 'bioconductor-heatplus >=2.30.0,<2.31.0' - 'bioconductor-hgu133a.db >=3.2.0,<3.3.0' - - 'bioconductor-hopach >=2.42.0,<2.43.0' - - 'bioconductor-htsanalyzer >=2.34.0,<2.35.0' - - 'bioconductor-limma >=3.38.0,<3.39.0' - - 'bioconductor-snpchip >=2.28.0,<2.29.0' + - 'bioconductor-hopach >=2.44.0,<2.45.0' + - 'bioconductor-htsanalyzer >=2.36.0,<2.37.0' + - 'bioconductor-limma >=3.40.0,<3.41.0' + - 'bioconductor-snpchip >=2.30.0,<2.31.0' - r-base - r-bma - r-ellipse @@ -43,19 +43,19 @@ requirements: - r-survival - r-xtable run: - - 'bioconductor-annotate >=1.60.0,<1.61.0' - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' - - 'bioconductor-biobase >=2.42.0,<2.43.0' - - 'bioconductor-biomart >=2.38.0,<2.39.0' - - 'bioconductor-category >=2.48.0,<2.49.0' - - 'bioconductor-genefilter >=1.64.0,<1.65.0' - - 'bioconductor-gseabase >=1.44.0,<1.45.0' - - 'bioconductor-heatplus >=2.28.0,<2.29.0' + - 'bioconductor-annotate >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' + - 'bioconductor-biomart >=2.40.0,<2.41.0' + - 'bioconductor-category >=2.50.0,<2.51.0' + - 'bioconductor-genefilter >=1.66.0,<1.67.0' + - 'bioconductor-gseabase >=1.46.0,<1.47.0' + - 'bioconductor-heatplus >=2.30.0,<2.31.0' - 'bioconductor-hgu133a.db >=3.2.0,<3.3.0' - - 'bioconductor-hopach >=2.42.0,<2.43.0' - - 'bioconductor-htsanalyzer >=2.34.0,<2.35.0' - - 'bioconductor-limma >=3.38.0,<3.39.0' - - 'bioconductor-snpchip >=2.28.0,<2.29.0' + - 'bioconductor-hopach >=2.44.0,<2.45.0' + - 'bioconductor-htsanalyzer >=2.36.0,<2.37.0' + - 'bioconductor-limma >=3.40.0,<3.41.0' + - 'bioconductor-snpchip >=2.30.0,<2.31.0' - r-base - r-bma - r-ellipse diff --git a/recipes/bioconductor-phenstat/meta.yaml b/recipes/bioconductor-phenstat/meta.yaml index b0cbf6a6cdec0..10cb127c4cbfb 100644 --- a/recipes/bioconductor-phenstat/meta.yaml +++ b/recipes/bioconductor-phenstat/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "2.18.1" %} +{% set version = "2.20.0" %} {% set name = "PhenStat" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,18 +10,17 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: a51b583a8083c2dfa8359a84f0e9e6a162a11b662d2e3b13fcfe91c5c80c00bb + md5: 5e0b89ce0beb4ae23f694ea2a1dc4a87 build: number: 0 rpaths: - lib/R/lib/ - lib/ + noarch: generic # Suggests: RUnit, BiocGenerics requirements: - build: - - {{ compiler('fortran') }} host: - - 'bioconductor-graph >=1.60.0,<1.61.0' + - 'bioconductor-graph >=1.62.0,<1.63.0' - r-base - r-car - r-corrplot @@ -37,7 +36,7 @@ requirements: - r-reshape - r-smoothwin run: - - 'bioconductor-graph >=1.60.0,<1.61.0' + - 'bioconductor-graph >=1.62.0,<1.63.0' - r-base - r-car - r-corrplot diff --git a/recipes/bioconductor-philr/meta.yaml b/recipes/bioconductor-philr/meta.yaml index a27b39a5dd41c..84687060e093f 100644 --- a/recipes/bioconductor-philr/meta.yaml +++ b/recipes/bioconductor-philr/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.8.1" %} +{% set version = "1.10.0" %} {% set name = "philr" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: bd10f494d79b06f27cdca4388feafbb5 + md5: 4cfeb72bb1273b6d476807548970517e build: number: 0 rpaths: @@ -20,14 +20,14 @@ build: # Suggests: testthat, knitr, rmarkdown, BiocStyle, phyloseq, glmnet, dplyr requirements: host: - - 'bioconductor-ggtree >=1.14.0,<1.15.0' + - 'bioconductor-ggtree >=1.16.0,<1.17.0' - r-ape - r-base - r-ggplot2 - r-phangorn - r-tidyr run: - - 'bioconductor-ggtree >=1.14.0,<1.15.0' + - 'bioconductor-ggtree >=1.16.0,<1.17.0' - r-ape - r-base - r-ggplot2 diff --git a/recipes/bioconductor-phosphonormalizer/meta.yaml b/recipes/bioconductor-phosphonormalizer/meta.yaml index 9ce40608185b1..dfd66362f2d93 100644 --- a/recipes/bioconductor-phosphonormalizer/meta.yaml +++ b/recipes/bioconductor-phosphonormalizer/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.6.0" %} +{% set version = "1.8.0" %} {% set name = "phosphonormalizer" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: c2476b36059d282f900701bc4982e9fb + md5: cb886d2ef9235727c1ceeb53324493de build: number: 0 rpaths: diff --git a/recipes/bioconductor-phyloseq/meta.yaml b/recipes/bioconductor-phyloseq/meta.yaml index d400417b7a67a..62de6ea1039e1 100644 --- a/recipes/bioconductor-phyloseq/meta.yaml +++ b/recipes/bioconductor-phyloseq/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.26.1" %} +{% set version = "1.28.0" %} {% set name = "phyloseq" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,21 +10,21 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - sha256: fcea94a1d59b022764fd0d44839ecb038f6b58128b896e7a7102c16ca40c578d + md5: e335968eb4f632162cb6a177117c8cf0 build: number: 0 rpaths: - lib/R/lib/ - lib/ noarch: generic -# Suggests: BiocStyle (>= 2.4), DESeq2 (>= 1.16.1), genefilter (>= 1.58), knitr (>= 1.16), metagenomeSeq (>= 1.14), rmarkdown (>= 1.6), testthat (>= 1.0.2) +# Suggests: BiocStyle (>= 2.4), DESeq2 (>= 1.16.1), genefilter (>= 1.58), knitr (>= 1.16), magrittr (>= 1.5), metagenomeSeq (>= 1.14), rmarkdown (>= 1.6), testthat (>= 1.0.2) requirements: host: - - 'bioconductor-biobase >=2.42.0,<2.43.0' - - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' - - 'bioconductor-biomformat >=1.10.0,<1.11.0' - - 'bioconductor-biostrings >=2.50.0,<2.51.0' - - 'bioconductor-multtest >=2.38.0,<2.39.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' + - 'bioconductor-biocgenerics >=0.30.0,<0.31.0' + - 'bioconductor-biomformat >=1.12.0,<1.13.0' + - 'bioconductor-biostrings >=2.52.0,<2.53.0' + - 'bioconductor-multtest >=2.40.0,<2.41.0' - 'r-ade4 >=1.7.4' - 'r-ape >=5.0' - r-base @@ -38,11 +38,11 @@ requirements: - 'r-scales >=0.4.0' - 'r-vegan >=2.5' run: - - 'bioconductor-biobase >=2.42.0,<2.43.0' - - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' - - 'bioconductor-biomformat >=1.10.0,<1.11.0' - - 'bioconductor-biostrings >=2.50.0,<2.51.0' - - 'bioconductor-multtest >=2.38.0,<2.39.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' + - 'bioconductor-biocgenerics >=0.30.0,<0.31.0' + - 'bioconductor-biomformat >=1.12.0,<1.13.0' + - 'bioconductor-biostrings >=2.52.0,<2.53.0' + - 'bioconductor-multtest >=2.40.0,<2.41.0' - 'r-ade4 >=1.7.4' - 'r-ape >=5.0' - r-base diff --git a/recipes/bioconductor-pi/meta.yaml b/recipes/bioconductor-pi/meta.yaml index 4a2559d3390a3..c3cb78be1b2b8 100644 --- a/recipes/bioconductor-pi/meta.yaml +++ b/recipes/bioconductor-pi/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.10.0" %} +{% set version = "1.12.0" %} {% set name = "Pi" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,21 +10,21 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 2fc7306e9555e44f153cf1b2b48802e2 + md5: 5d4c183ea18ca8fb9483a0c78f753d79 build: number: 0 rpaths: - lib/R/lib/ - lib/ noarch: generic -# Suggests: foreach, doParallel, BiocStyle, knitr, rmarkdown, png, GGally, gridExtra, ExpressionAtlas, ggforce, fgsea, pathview, tidyr +# Suggests: foreach, doParallel, BiocStyle, knitr, rmarkdown, png, GGally, gridExtra, ExpressionAtlas, ggforce, fgsea, pathview, tidyr, dplyr requirements: host: - - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' - - 'bioconductor-genomicranges >=1.34.0,<1.35.0' - - 'bioconductor-ggbio >=1.30.0,<1.31.0' - - 'bioconductor-gviz >=1.26.0,<1.27.0' - - 'bioconductor-suprahex >=1.20.0,<1.21.0' + - 'bioconductor-genomeinfodb >=1.20.0,<1.21.0' + - 'bioconductor-genomicranges >=1.36.0,<1.37.0' + - 'bioconductor-ggbio >=1.32.0,<1.33.0' + - 'bioconductor-gviz >=1.28.0,<1.29.0' + - 'bioconductor-suprahex >=1.22.0,<1.23.0' - r-base - r-caret - r-dnet @@ -33,7 +33,6 @@ requirements: - r-glmnet - r-igraph - r-lattice - - r-mass - r-matrix - r-plot3d - r-randomforest @@ -41,11 +40,11 @@ requirements: - r-scales - r-xgr run: - - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' - - 'bioconductor-genomicranges >=1.34.0,<1.35.0' - - 'bioconductor-ggbio >=1.30.0,<1.31.0' - - 'bioconductor-gviz >=1.26.0,<1.27.0' - - 'bioconductor-suprahex >=1.20.0,<1.21.0' + - 'bioconductor-genomeinfodb >=1.20.0,<1.21.0' + - 'bioconductor-genomicranges >=1.36.0,<1.37.0' + - 'bioconductor-ggbio >=1.32.0,<1.33.0' + - 'bioconductor-gviz >=1.28.0,<1.29.0' + - 'bioconductor-suprahex >=1.22.0,<1.23.0' - r-base - r-caret - r-dnet @@ -54,7 +53,6 @@ requirements: - r-glmnet - r-igraph - r-lattice - - r-mass - r-matrix - r-plot3d - r-randomforest diff --git a/recipes/bioconductor-piano/meta.yaml b/recipes/bioconductor-piano/meta.yaml index 1dc3f6533c707..a9012df2d46f4 100644 --- a/recipes/bioconductor-piano/meta.yaml +++ b/recipes/bioconductor-piano/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.22.0" %} +{% set version = "2.0.0" %} {% set name = "piano" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,33 +10,47 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: ddf4cefb13b149cbac5ee9ecec0ffbc8 + md5: 4df05c2b7c9e67fc07a50f3abd268845 build: number: 0 rpaths: - lib/R/lib/ - lib/ noarch: generic -# Suggests: yeast2.db, rsbml, plotrix, limma, affy, plier, affyPLM, gtools, biomaRt, snowfall, AnnotationDbi +# Suggests: yeast2.db, rsbml, plotrix, limma, affy, plier, affyPLM, gtools, biomaRt, snowfall, AnnotationDbi, knitr, rmarkdown, BiocStyle requirements: host: - - 'bioconductor-biobase >=2.42.0,<2.43.0' - - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' - - 'bioconductor-fgsea >=1.8.0,<1.9.0' - - 'bioconductor-marray >=1.60.0,<1.61.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' + - 'bioconductor-biocgenerics >=0.30.0,<0.31.0' + - 'bioconductor-fgsea >=1.10.0,<1.11.0' + - 'bioconductor-marray >=1.62.0,<1.63.0' - r-base + - r-dt - r-gplots + - r-htmlwidgets - r-igraph - r-relations + - r-scales + - r-shiny + - r-shinydashboard + - r-shinyjs + - r-visnetwork run: - - 'bioconductor-biobase >=2.42.0,<2.43.0' - - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' - - 'bioconductor-fgsea >=1.8.0,<1.9.0' - - 'bioconductor-marray >=1.60.0,<1.61.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' + - 'bioconductor-biocgenerics >=0.30.0,<0.31.0' + - 'bioconductor-fgsea >=1.10.0,<1.11.0' + - 'bioconductor-marray >=1.62.0,<1.63.0' - r-base + - r-dt - r-gplots + - r-htmlwidgets - r-igraph - r-relations + - r-scales + - r-shiny + - r-shinydashboard + - r-shinyjs + - r-visnetwork test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-pickgene/meta.yaml b/recipes/bioconductor-pickgene/meta.yaml index 9c5f8a8a4f301..4b36bc03d8694 100644 --- a/recipes/bioconductor-pickgene/meta.yaml +++ b/recipes/bioconductor-pickgene/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.54.0" %} +{% set version = "1.56.0" %} {% set name = "pickgene" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 8c766281cb3b997e869fb2afe3ab0a03 + md5: 3e07394aaa3cf494b93d00b7307bda59 build: number: 0 rpaths: diff --git a/recipes/bioconductor-pics/meta.yaml b/recipes/bioconductor-pics/meta.yaml index aa808cc1d1bc9..8d4b861f9e905 100644 --- a/recipes/bioconductor-pics/meta.yaml +++ b/recipes/bioconductor-pics/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "2.26.0" %} +{% set version = "2.28.0" %} {% set name = "PICS" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 37aad6428e79e861d9e42d519aa133e5 + md5: e0ebcad166db4df73d197dc69be40893 build: number: 0 rpaths: @@ -20,24 +20,23 @@ build: # SystemRequirements: GSL (GNU Scientific Library) requirements: host: - - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' - - 'bioconductor-genomicalignments >=1.18.0,<1.19.0' - - 'bioconductor-genomicranges >=1.34.0,<1.35.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-rsamtools >=1.34.0,<1.35.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-biocgenerics >=0.30.0,<0.31.0' + - 'bioconductor-genomicalignments >=1.20.0,<1.21.0' + - 'bioconductor-genomicranges >=1.36.0,<1.37.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-rsamtools >=2.0.0,<2.1.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' - r-base - gsl - - openblas run: - - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' - - 'bioconductor-genomicalignments >=1.18.0,<1.19.0' - - 'bioconductor-genomicranges >=1.34.0,<1.35.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-rsamtools >=1.34.0,<1.35.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-biocgenerics >=0.30.0,<0.31.0' + - 'bioconductor-genomicalignments >=1.20.0,<1.21.0' + - 'bioconductor-genomicranges >=1.36.0,<1.37.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-rsamtools >=2.0.0,<2.1.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' - r-base - - openblas + - gsl build: - {{ compiler('c') }} - automake diff --git a/recipes/bioconductor-pig.db0/meta.yaml b/recipes/bioconductor-pig.db0/meta.yaml index 9d6619519106b..89a91bb5adeac 100644 --- a/recipes/bioconductor-pig.db0/meta.yaml +++ b/recipes/bioconductor-pig.db0/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "3.7.1" %} +{% set version = "3.8.2" %} {% set name = "pig.db0" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 7c8a8945b98ad5bca03e2765046664f6 + md5: e3109e7efd1a29387f318a62e8b6892c build: number: 0 rpaths: @@ -19,12 +19,12 @@ build: noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' - r-base run: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-pig.db0/post-link.sh b/recipes/bioconductor-pig.db0/post-link.sh index 2d252c3ee3a92..c8119b7134dd8 100644 --- a/recipes/bioconductor-pig.db0/post-link.sh +++ b/recipes/bioconductor-pig.db0/post-link.sh @@ -1,11 +1,11 @@ #!/bin/bash -FN="pig.db0_3.7.1.tar.gz" +FN="pig.db0_3.8.2.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/pig.db0_3.7.1.tar.gz" - "https://bioarchive.galaxyproject.org/pig.db0_3.7.1.tar.gz" - "https://depot.galaxyproject.org/software/bioconductor-pig.db0/bioconductor-pig.db0_3.7.1_src_all.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/pig.db0_3.8.2.tar.gz" + "https://bioarchive.galaxyproject.org/pig.db0_3.8.2.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-pig.db0/bioconductor-pig.db0_3.8.2_src_all.tar.gz" ) -MD5="7c8a8945b98ad5bca03e2765046664f6" +MD5="e3109e7efd1a29387f318a62e8b6892c" # Use a staging area in the conda dir rather than temp dirs, both to avoid # permission issues as well as to have things downloaded in a predictable @@ -16,7 +16,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-pigengene/meta.yaml b/recipes/bioconductor-pigengene/meta.yaml index 4260d8358473a..8deb171f33cc6 100644 --- a/recipes/bioconductor-pigengene/meta.yaml +++ b/recipes/bioconductor-pigengene/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.8.0" %} +{% set version = "1.10.0" %} {% set name = "Pigengene" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,23 +10,23 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 9a1b55edd6fa640512ed44c536f1ea18 + md5: 08665f7c9021ef0176f685b864986b92 build: number: 0 rpaths: - lib/R/lib/ - lib/ noarch: generic -# Suggests: org.Hs.eg.db, org.Mm.eg.db, biomaRt (>= 2.30.0), knitr, BiocStyle, AnnotationDbi, energy +# Suggests: org.Hs.eg.db (>= 3.7.0), org.Mm.eg.db (>= 3.7.0), biomaRt (>= 2.30.0), knitr, BiocStyle, AnnotationDbi, energy requirements: host: - - 'bioconductor-go.db >=3.7.0,<3.8.0' - - 'bioconductor-graph >=1.60.0,<1.61.0' - - 'bioconductor-impute >=1.56.0,<1.57.0' - - 'bioconductor-preprocesscore >=1.44.0,<1.45.0' - - 'bioconductor-rgraphviz >=2.26.0,<2.27.0' + - 'bioconductor-go.db >=3.8.0,<3.9.0' + - 'bioconductor-graph >=1.62.0,<1.63.0' + - 'bioconductor-impute >=1.58.0,<1.59.0' + - 'bioconductor-preprocesscore >=1.46.0,<1.47.0' + - 'bioconductor-rgraphviz >=2.28.0,<2.29.0' - r-base - - r-bnlearn + - 'r-bnlearn >=4.4.1' - 'r-c50 >=0.1.2' - r-mass - r-matrixstats @@ -34,13 +34,13 @@ requirements: - 'r-pheatmap >=1.0.8' - r-wgcna run: - - 'bioconductor-go.db >=3.7.0,<3.8.0' - - 'bioconductor-graph >=1.60.0,<1.61.0' - - 'bioconductor-impute >=1.56.0,<1.57.0' - - 'bioconductor-preprocesscore >=1.44.0,<1.45.0' - - 'bioconductor-rgraphviz >=2.26.0,<2.27.0' + - 'bioconductor-go.db >=3.8.0,<3.9.0' + - 'bioconductor-graph >=1.62.0,<1.63.0' + - 'bioconductor-impute >=1.58.0,<1.59.0' + - 'bioconductor-preprocesscore >=1.46.0,<1.47.0' + - 'bioconductor-rgraphviz >=2.28.0,<2.29.0' - r-base - - r-bnlearn + - 'r-bnlearn >=4.4.1' - 'r-c50 >=0.1.2' - r-mass - r-matrixstats diff --git a/recipes/bioconductor-ping/meta.yaml b/recipes/bioconductor-ping/meta.yaml index a3df4b84c11d1..20376e9ab4ebf 100644 --- a/recipes/bioconductor-ping/meta.yaml +++ b/recipes/bioconductor-ping/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "2.26.0" %} +{% set version = "2.28.0" %} {% set name = "PING" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: d7d3a4467e3c8ea97ff0099a4e31285c + md5: 26cf6d98525f5454eb6aad179efb0063 build: number: 0 rpaths: @@ -19,25 +19,25 @@ build: # Suggests: parallel, ShortRead, rtracklayer requirements: host: - - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' - - 'bioconductor-bsgenome >=1.50.0,<1.51.0' - - 'bioconductor-chipseq >=1.32.0,<1.33.0' - - 'bioconductor-genomicranges >=1.34.0,<1.35.0' - - 'bioconductor-gviz >=1.26.0,<1.27.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-pics >=2.26.0,<2.27.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-biocgenerics >=0.30.0,<0.31.0' + - 'bioconductor-bsgenome >=1.52.0,<1.53.0' + - 'bioconductor-chipseq >=1.34.0,<1.35.0' + - 'bioconductor-genomicranges >=1.36.0,<1.37.0' + - 'bioconductor-gviz >=1.28.0,<1.29.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-pics >=2.28.0,<2.29.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' - r-base - r-fda run: - - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' - - 'bioconductor-bsgenome >=1.50.0,<1.51.0' - - 'bioconductor-chipseq >=1.32.0,<1.33.0' - - 'bioconductor-genomicranges >=1.34.0,<1.35.0' - - 'bioconductor-gviz >=1.26.0,<1.27.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-pics >=2.26.0,<2.27.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-biocgenerics >=0.30.0,<0.31.0' + - 'bioconductor-bsgenome >=1.52.0,<1.53.0' + - 'bioconductor-chipseq >=1.34.0,<1.35.0' + - 'bioconductor-genomicranges >=1.36.0,<1.37.0' + - 'bioconductor-gviz >=1.28.0,<1.29.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-pics >=2.28.0,<2.29.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' - r-base - r-fda build: diff --git a/recipes/bioconductor-pint/meta.yaml b/recipes/bioconductor-pint/meta.yaml index c67ffbc547847..a9624056736d4 100644 --- a/recipes/bioconductor-pint/meta.yaml +++ b/recipes/bioconductor-pint/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.32.0" %} +{% set version = "1.34.0" %} {% set name = "pint" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 52094d95be76e9b7eb15f0c1f826f4fe + md5: be40bec1406b1a9a9c2d208e7277a2d4 build: number: 0 rpaths: diff --git a/recipes/bioconductor-pipeframe/build.sh b/recipes/bioconductor-pipeframe/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-pipeframe/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-pipeframe/meta.yaml b/recipes/bioconductor-pipeframe/meta.yaml new file mode 100644 index 0000000000000..d8b639314bb85 --- /dev/null +++ b/recipes/bioconductor-pipeframe/meta.yaml @@ -0,0 +1,45 @@ +{% set version = "1.0.0" %} +{% set name = "pipeFrame" %} +{% set bioc = "3.9" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: bc92296ebc9ad5fb1438ee41a753d1e3 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: BiocManager, knitr, rtracklayer, testthat +requirements: + host: + - 'bioconductor-biostrings >=2.52.0,<2.53.0' + - 'bioconductor-bsgenome >=1.52.0,<1.53.0' + - 'bioconductor-genomeinfodb >=1.20.0,<1.21.0' + - r-base + - r-digest + - r-magrittr + - r-visnetwork + run: + - 'bioconductor-biostrings >=2.52.0,<2.53.0' + - 'bioconductor-bsgenome >=1.52.0,<1.53.0' + - 'bioconductor-genomeinfodb >=1.20.0,<1.21.0' + - r-base + - r-digest + - r-magrittr + - r-visnetwork +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: GPL-3 + summary: 'pipeFrame is an R package for building a componentized bioinformatics pipeline. Each step in this pipeline is wrapped in the framework, so the connection among steps is created seamlessly and automatically. Users could focus more on fine-tuning arguments rather than spending a lot of time on transforming file format, passing task outputs to task inputs or installing the dependencies. Componentized step elements can be customized into other new pipelines flexibly as well. This pipeline can be split into several important functional steps, so it is much easier for users to understand the complex arguments from each step rather than parameter combination from the whole pipeline. At the same time, componentized pipeline can restart at the breakpoint and avoid rerunning the whole pipeline, which may save a lot of time for users on pipeline tuning or such issues as power off or process other interrupts.' + diff --git a/recipes/bioconductor-pkgdeptools/meta.yaml b/recipes/bioconductor-pkgdeptools/meta.yaml index 2b60a54456583..2fa777099284a 100644 --- a/recipes/bioconductor-pkgdeptools/meta.yaml +++ b/recipes/bioconductor-pkgdeptools/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.48.0" %} +{% set version = "1.50.0" %} {% set name = "pkgDepTools" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 9b7ac81bcf76d15218c6044b6620a931 + md5: a94aca53e28b9b9f8f3835295c17aa12 build: number: 0 rpaths: @@ -20,12 +20,12 @@ build: # Suggests: Biobase, Rgraphviz, RCurl, BiocManager requirements: host: - - 'bioconductor-graph >=1.60.0,<1.61.0' - - 'bioconductor-rbgl >=1.58.0,<1.59.0' + - 'bioconductor-graph >=1.62.0,<1.63.0' + - 'bioconductor-rbgl >=1.60.0,<1.61.0' - r-base run: - - 'bioconductor-graph >=1.60.0,<1.61.0' - - 'bioconductor-rbgl >=1.58.0,<1.59.0' + - 'bioconductor-graph >=1.62.0,<1.63.0' + - 'bioconductor-rbgl >=1.60.0,<1.61.0' - r-base test: commands: diff --git a/recipes/bioconductor-plasfia/meta.yaml b/recipes/bioconductor-plasfia/meta.yaml index 47cde4a0e5f8c..b18172c77d02b 100644 --- a/recipes/bioconductor-plasfia/meta.yaml +++ b/recipes/bioconductor-plasfia/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.10.0" %} +{% set version = "1.12.0" %} {% set name = "plasFIA" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 9eecc8e69adc6fae52eb4eac6d18de51 + md5: 047cd501ce813df543a0e502d20cbbc5 build: number: 0 rpaths: @@ -19,12 +19,12 @@ build: noarch: generic requirements: host: - - 'bioconductor-profia >=1.8.0,<1.9.0' + - 'bioconductor-profia >=1.10.0,<1.11.0' - r-base run: - - 'bioconductor-profia >=1.8.0,<1.9.0' + - 'bioconductor-profia >=1.10.0,<1.11.0' - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-plasfia/post-link.sh b/recipes/bioconductor-plasfia/post-link.sh index 5315a0ca02e4b..b7cf578ed14d5 100644 --- a/recipes/bioconductor-plasfia/post-link.sh +++ b/recipes/bioconductor-plasfia/post-link.sh @@ -1,11 +1,11 @@ #!/bin/bash -FN="plasFIA_1.10.0.tar.gz" +FN="plasFIA_1.12.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/experiment/src/contrib/plasFIA_1.10.0.tar.gz" - "https://bioarchive.galaxyproject.org/plasFIA_1.10.0.tar.gz" - "https://depot.galaxyproject.org/software/bioconductor-plasfia/bioconductor-plasfia_1.10.0_src_all.tar.gz" + "https://bioconductor.org/packages/3.9/data/experiment/src/contrib/plasFIA_1.12.0.tar.gz" + "https://bioarchive.galaxyproject.org/plasFIA_1.12.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-plasfia/bioconductor-plasfia_1.12.0_src_all.tar.gz" ) -MD5="9eecc8e69adc6fae52eb4eac6d18de51" +MD5="047cd501ce813df543a0e502d20cbbc5" # Use a staging area in the conda dir rather than temp dirs, both to avoid # permission issues as well as to have things downloaded in a predictable @@ -16,7 +16,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-plasmodiumanophelescdf/meta.yaml b/recipes/bioconductor-plasmodiumanophelescdf/meta.yaml index f30d70b0bbb3d..2d3b2a1d81453 100644 --- a/recipes/bioconductor-plasmodiumanophelescdf/meta.yaml +++ b/recipes/bioconductor-plasmodiumanophelescdf/meta.yaml @@ -1,6 +1,6 @@ {% set version = "2.18.0" %} {% set name = "plasmodiumanophelescdf" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -12,19 +12,19 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 54c5c326977d6358c40cacf34cb2aca2 build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' - r-base run: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-plasmodiumanophelescdf/post-link.sh b/recipes/bioconductor-plasmodiumanophelescdf/post-link.sh index 5d374f9983fe3..c8f061c11fca9 100644 --- a/recipes/bioconductor-plasmodiumanophelescdf/post-link.sh +++ b/recipes/bioconductor-plasmodiumanophelescdf/post-link.sh @@ -1,9 +1,10 @@ #!/bin/bash FN="plasmodiumanophelescdf_2.18.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/plasmodiumanophelescdf_2.18.0.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/plasmodiumanophelescdf_2.18.0.tar.gz" "https://bioarchive.galaxyproject.org/plasmodiumanophelescdf_2.18.0.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-plasmodiumanophelescdf/bioconductor-plasmodiumanophelescdf_2.18.0_src_all.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-plasmodiumanophelescdf/bioconductor-plasmodiumanophelescdf_2.18.0_src_all.tar.gz" ) MD5="54c5c326977d6358c40cacf34cb2aca2" @@ -16,7 +17,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-plasmodiumanophelesprobe/meta.yaml b/recipes/bioconductor-plasmodiumanophelesprobe/meta.yaml index 35c8f5ff22899..e21fba5302f75 100644 --- a/recipes/bioconductor-plasmodiumanophelesprobe/meta.yaml +++ b/recipes/bioconductor-plasmodiumanophelesprobe/meta.yaml @@ -1,6 +1,6 @@ {% set version = "2.18.0" %} {% set name = "plasmodiumanophelesprobe" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -12,19 +12,19 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 281683dab923168c2eedb7b08c528935 build: - number: 1 + number: 2 rpaths: - lib/R/lib/ - lib/ noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' - r-base run: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-plasmodiumanophelesprobe/post-link.sh b/recipes/bioconductor-plasmodiumanophelesprobe/post-link.sh index 0e09baf0a87b4..63c57c1df5186 100644 --- a/recipes/bioconductor-plasmodiumanophelesprobe/post-link.sh +++ b/recipes/bioconductor-plasmodiumanophelesprobe/post-link.sh @@ -1,9 +1,10 @@ #!/bin/bash FN="plasmodiumanophelesprobe_2.18.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/plasmodiumanophelesprobe_2.18.0.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/plasmodiumanophelesprobe_2.18.0.tar.gz" "https://bioarchive.galaxyproject.org/plasmodiumanophelesprobe_2.18.0.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-plasmodiumanophelesprobe/bioconductor-plasmodiumanophelesprobe_2.18.0_src_all.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-plasmodiumanophelesprobe/bioconductor-plasmodiumanophelesprobe_2.18.0_src_all.tar.gz" ) MD5="281683dab923168c2eedb7b08c528935" @@ -16,7 +17,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-platecore/meta.yaml b/recipes/bioconductor-platecore/meta.yaml index 51dd9b5320327..e6cf955508c0f 100644 --- a/recipes/bioconductor-platecore/meta.yaml +++ b/recipes/bioconductor-platecore/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.40.1" %} +{% set version = "1.41.1" %} {% set name = "plateCore" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 59e976ddf32e8638605cf80e898752d7 + md5: 06081e7ebf7b8136766ba03420f1a2da build: number: 0 rpaths: @@ -20,20 +20,20 @@ build: # Suggests: gplots requirements: host: - - 'bioconductor-biobase >=2.42.0,<2.43.0' - - 'bioconductor-flowcore >=1.48.0,<1.49.0' - - 'bioconductor-flowstats >=3.40.0,<3.41.0' - - 'bioconductor-flowviz >=1.46.0,<1.47.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' + - 'bioconductor-flowcore >=1.50.0,<1.51.0' + - 'bioconductor-flowstats >=3.42.0,<3.43.0' + - 'bioconductor-flowviz >=1.48.0,<1.49.0' - r-base - r-lattice - r-latticeextra - r-mass - r-robustbase run: - - 'bioconductor-biobase >=2.42.0,<2.43.0' - - 'bioconductor-flowcore >=1.48.0,<1.49.0' - - 'bioconductor-flowstats >=3.40.0,<3.41.0' - - 'bioconductor-flowviz >=1.46.0,<1.47.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' + - 'bioconductor-flowcore >=1.50.0,<1.51.0' + - 'bioconductor-flowstats >=3.42.0,<3.43.0' + - 'bioconductor-flowviz >=1.48.0,<1.49.0' - r-base - r-lattice - r-latticeextra diff --git a/recipes/bioconductor-plethy/meta.yaml b/recipes/bioconductor-plethy/meta.yaml index 46b3fa0e8860c..81dec4fecef42 100644 --- a/recipes/bioconductor-plethy/meta.yaml +++ b/recipes/bioconductor-plethy/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.20.0" %} +{% set version = "1.22.0" %} {% set name = "plethy" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: cfaa49593a30cf99fe842236a8b34583 + md5: 602fa867af93cc7b3635b972b4aa16e9 build: number: 0 rpaths: @@ -20,11 +20,11 @@ build: # Suggests: RUnit, BiocStyle requirements: host: - - 'bioconductor-biobase >=2.42.0,<2.43.0' - - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' - - 'bioconductor-streamer >=1.28.0,<1.29.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' + - 'bioconductor-biocgenerics >=0.30.0,<0.31.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' + - 'bioconductor-streamer >=1.30.0,<1.31.0' - r-base - 'r-dbi >=0.5-1' - r-ggplot2 @@ -33,11 +33,11 @@ requirements: - r-reshape2 - 'r-rsqlite >=1.1' run: - - 'bioconductor-biobase >=2.42.0,<2.43.0' - - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' - - 'bioconductor-streamer >=1.28.0,<1.29.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' + - 'bioconductor-biocgenerics >=0.30.0,<0.31.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' + - 'bioconductor-streamer >=1.30.0,<1.31.0' - r-base - 'r-dbi >=0.5-1' - r-ggplot2 diff --git a/recipes/bioconductor-plgem/meta.yaml b/recipes/bioconductor-plgem/meta.yaml index d164fe28bf46a..78fe78c3b7c48 100644 --- a/recipes/bioconductor-plgem/meta.yaml +++ b/recipes/bioconductor-plgem/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.54.1" %} +{% set version = "1.56.0" %} {% set name = "plgem" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - sha256: ef6b737f392792927a1e1a1cacaf7fcbe4336898993be44bede88ed5ca30608c + md5: 790c2aa391353fcfe65940c349b1f31e build: number: 0 rpaths: @@ -19,11 +19,11 @@ build: noarch: generic requirements: host: - - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' - r-base - r-mass run: - - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' - r-base - r-mass test: diff --git a/recipes/bioconductor-plier/meta.yaml b/recipes/bioconductor-plier/meta.yaml index fe3c52b554480..57ead2f283252 100644 --- a/recipes/bioconductor-plier/meta.yaml +++ b/recipes/bioconductor-plier/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.52.0" %} +{% set version = "1.54.0" %} {% set name = "plier" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 878f9d104165863bb2779f78af70f559 + md5: cccc4742ee3ce9dfcd187b955cd91b16 build: number: 0 rpaths: @@ -18,12 +18,12 @@ build: - lib/ requirements: host: - - 'bioconductor-affy >=1.60.0,<1.61.0' - - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-affy >=1.62.0,<1.63.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' - r-base run: - - 'bioconductor-affy >=1.60.0,<1.61.0' - - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-affy >=1.62.0,<1.63.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' - r-base build: - {{ compiler('c') }} diff --git a/recipes/bioconductor-plotgrouper/meta.yaml b/recipes/bioconductor-plotgrouper/meta.yaml index cd54c64bf4eb7..8d5ae56dba87c 100644 --- a/recipes/bioconductor-plotgrouper/meta.yaml +++ b/recipes/bioconductor-plotgrouper/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.0.1" %} +{% set version = "1.2.0" %} {% set name = "plotGrouper" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: acacc62ceda98794cedee778f8c6a416 + md5: a6c7449cf43ca43eea040a1288c1432d build: number: 0 rpaths: diff --git a/recipes/bioconductor-plpe/meta.yaml b/recipes/bioconductor-plpe/meta.yaml index 465dd190b21a3..1bb1ee5e7136c 100644 --- a/recipes/bioconductor-plpe/meta.yaml +++ b/recipes/bioconductor-plpe/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.42.0" %} +{% set version = "1.44.0" %} {% set name = "PLPE" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: e14a72c1493694cf9270d6b3f8c7888c + md5: d2deab4a268dc342757b63a8d4645700 build: number: 0 rpaths: @@ -19,13 +19,13 @@ build: noarch: generic requirements: host: - - 'bioconductor-biobase >=2.42.0,<2.43.0' - - 'bioconductor-lpe >=1.56.0,<1.57.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' + - 'bioconductor-lpe >=1.58.0,<1.59.0' - r-base - r-mass run: - - 'bioconductor-biobase >=2.42.0,<2.43.0' - - 'bioconductor-lpe >=1.56.0,<1.57.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' + - 'bioconductor-lpe >=1.58.0,<1.59.0' - r-base - r-mass test: diff --git a/recipes/bioconductor-plrs/meta.yaml b/recipes/bioconductor-plrs/meta.yaml index 608e1acf494e2..bd3094ca726db 100644 --- a/recipes/bioconductor-plrs/meta.yaml +++ b/recipes/bioconductor-plrs/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.22.0" %} +{% set version = "1.24.0" %} {% set name = "plrs" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 41bf5ad9dc49a153c0fcb4ddfa4b5e44 + md5: 8b386b7ca4465d74f79d9e67002c6f2a build: number: 0 rpaths: @@ -20,19 +20,19 @@ build: # Suggests: mvtnorm, methods requirements: host: - - 'bioconductor-biobase >=2.42.0,<2.43.0' - - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' - - 'bioconductor-cghbase >=1.42.0,<1.43.0' - - 'bioconductor-marray >=1.60.0,<1.61.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' + - 'bioconductor-biocgenerics >=0.30.0,<0.31.0' + - 'bioconductor-cghbase >=1.44.0,<1.45.0' + - 'bioconductor-marray >=1.62.0,<1.63.0' - r-base - r-ic.infer - r-quadprog - r-rcsdp run: - - 'bioconductor-biobase >=2.42.0,<2.43.0' - - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' - - 'bioconductor-cghbase >=1.42.0,<1.43.0' - - 'bioconductor-marray >=1.60.0,<1.61.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' + - 'bioconductor-biocgenerics >=0.30.0,<0.31.0' + - 'bioconductor-cghbase >=1.44.0,<1.45.0' + - 'bioconductor-marray >=1.62.0,<1.63.0' - r-base - r-ic.infer - r-quadprog diff --git a/recipes/bioconductor-plw/meta.yaml b/recipes/bioconductor-plw/meta.yaml index 101e26a5073bd..00385ae43e542 100644 --- a/recipes/bioconductor-plw/meta.yaml +++ b/recipes/bioconductor-plw/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.42.0" %} +{% set version = "1.44.0" %} {% set name = "plw" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: dc4109cd98ee3817f3ab6b5308f13680 + md5: 9817b3abce8d6597da3ce7584cb04807 build: number: 0 rpaths: @@ -19,11 +19,11 @@ build: # Suggests: limma requirements: host: - - 'bioconductor-affy >=1.60.0,<1.61.0' + - 'bioconductor-affy >=1.62.0,<1.63.0' - r-base - r-mass run: - - 'bioconductor-affy >=1.60.0,<1.61.0' + - 'bioconductor-affy >=1.62.0,<1.63.0' - r-base - r-mass build: diff --git a/recipes/bioconductor-plyranges/meta.yaml b/recipes/bioconductor-plyranges/meta.yaml index bb740cb6003ed..1ba2fec15578a 100644 --- a/recipes/bioconductor-plyranges/meta.yaml +++ b/recipes/bioconductor-plyranges/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.2.0" %} +{% set version = "1.4.0" %} {% set name = "plyranges" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 7f6a2b20360203ca9fb94f75e10e0c17 + md5: 99a06a134e19605640d09c4b5cfb1210 build: number: 0 rpaths: @@ -20,14 +20,14 @@ build: # Suggests: knitr, BiocStyle, rmarkdown, testthat, ggplot2, HelloRanges, HelloRangesData, BSgenome.Hsapiens.UCSC.hg19, pasillaBamSubset, covr requirements: host: - - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' - - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' - - 'bioconductor-genomicalignments >=1.18.0,<1.19.0' - - 'bioconductor-genomicranges >=1.34.0,<1.35.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-rsamtools >=1.34.0,<1.35.0' - - 'bioconductor-rtracklayer >=1.42.0,<1.43.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-biocgenerics >=0.30.0,<0.31.0' + - 'bioconductor-genomeinfodb >=1.20.0,<1.21.0' + - 'bioconductor-genomicalignments >=1.20.0,<1.21.0' + - 'bioconductor-genomicranges >=1.36.0,<1.37.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-rsamtools >=2.0.0,<2.1.0' + - 'bioconductor-rtracklayer >=1.44.0,<1.45.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' - r-base - r-dplyr - r-magrittr @@ -35,14 +35,14 @@ requirements: - r-tidyr - r-tidyselect run: - - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' - - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' - - 'bioconductor-genomicalignments >=1.18.0,<1.19.0' - - 'bioconductor-genomicranges >=1.34.0,<1.35.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-rsamtools >=1.34.0,<1.35.0' - - 'bioconductor-rtracklayer >=1.42.0,<1.43.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-biocgenerics >=0.30.0,<0.31.0' + - 'bioconductor-genomeinfodb >=1.20.0,<1.21.0' + - 'bioconductor-genomicalignments >=1.20.0,<1.21.0' + - 'bioconductor-genomicranges >=1.36.0,<1.37.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-rsamtools >=2.0.0,<2.1.0' + - 'bioconductor-rtracklayer >=1.44.0,<1.45.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' - r-base - r-dplyr - r-magrittr diff --git a/recipes/bioconductor-pmm/meta.yaml b/recipes/bioconductor-pmm/meta.yaml index caf671906ac4d..dd4ff222532ef 100644 --- a/recipes/bioconductor-pmm/meta.yaml +++ b/recipes/bioconductor-pmm/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.14.0" %} +{% set version = "1.16.0" %} {% set name = "pmm" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 62c7a8f094a67345c7f968665c5da863 + md5: cfed0aed28aaae52afda91973a26487a build: number: 0 rpaths: diff --git a/recipes/bioconductor-pocrcannotation.db/meta.yaml b/recipes/bioconductor-pocrcannotation.db/meta.yaml index 35340caf36adb..aeed8b01cbeaa 100644 --- a/recipes/bioconductor-pocrcannotation.db/meta.yaml +++ b/recipes/bioconductor-pocrcannotation.db/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.2.3" %} {% set name = "POCRCannotation.db" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -12,7 +12,7 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' md5: da1d4dacc5fffb9c5dfea55649974aa5 build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ @@ -20,14 +20,14 @@ build: # Suggests: DBI, annotate, RUnit requirements: host: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' - - 'bioconductor-org.hs.eg.db >=3.7.0,<3.8.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' + - 'bioconductor-org.hs.eg.db >=3.8.0,<3.9.0' - r-base run: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' - - 'bioconductor-org.hs.eg.db >=3.7.0,<3.8.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' + - 'bioconductor-org.hs.eg.db >=3.8.0,<3.9.0' - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-pocrcannotation.db/post-link.sh b/recipes/bioconductor-pocrcannotation.db/post-link.sh index b4da8d9706211..cd28faa958aa4 100644 --- a/recipes/bioconductor-pocrcannotation.db/post-link.sh +++ b/recipes/bioconductor-pocrcannotation.db/post-link.sh @@ -1,9 +1,10 @@ #!/bin/bash FN="POCRCannotation.db_3.2.3.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/POCRCannotation.db_3.2.3.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/POCRCannotation.db_3.2.3.tar.gz" "https://bioarchive.galaxyproject.org/POCRCannotation.db_3.2.3.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-pocrcannotation.db/bioconductor-pocrcannotation.db_3.2.3_src_all.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-pocrcannotation.db/bioconductor-pocrcannotation.db_3.2.3_src_all.tar.gz" ) MD5="da1d4dacc5fffb9c5dfea55649974aa5" @@ -16,7 +17,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-podkat/meta.yaml b/recipes/bioconductor-podkat/meta.yaml index 018e2a01bb617..448850dcb1f78 100644 --- a/recipes/bioconductor-podkat/meta.yaml +++ b/recipes/bioconductor-podkat/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.14.0" %} +{% set version = "1.16.0" %} {% set name = "podkat" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,35 +10,37 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: bf4f038d282695aaab44b9f08dd840ed + md5: 679979f4046c4e43e81d953f250091fb build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ # Suggests: BSgenome.Hsapiens.UCSC.hg38.masked, TxDb.Hsapiens.UCSC.hg38.knownGene, BSgenome.Mmusculus.UCSC.mm10.masked, GWASTools (>= 1.13.24), VariantAnnotation, SummarizedExperiment, knitr requirements: host: - - 'bioconductor-biobase >=2.42.0,<2.43.0' - - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' - - 'bioconductor-biostrings >=2.50.0,<2.51.0' - - 'bioconductor-bsgenome >=1.50.0,<1.51.0' - - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' - - 'bioconductor-genomicranges >=1.34.0,<1.35.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-rsamtools >=1.34.0,<1.35.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' + - 'bioconductor-biocgenerics >=0.30.0,<0.31.0' + - 'bioconductor-biostrings >=2.52.0,<2.53.0' + - 'bioconductor-bsgenome >=1.52.0,<1.53.0' + - 'bioconductor-genomeinfodb >=1.20.0,<1.21.0' + - 'bioconductor-genomicranges >=1.36.0,<1.37.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-rhtslib >=1.16.0,<1.17.0' + - 'bioconductor-rsamtools >=2.0.0,<2.1.0' - r-base - r-matrix - 'r-rcpp >=0.11.1' run: - - 'bioconductor-biobase >=2.42.0,<2.43.0' - - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' - - 'bioconductor-biostrings >=2.50.0,<2.51.0' - - 'bioconductor-bsgenome >=1.50.0,<1.51.0' - - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' - - 'bioconductor-genomicranges >=1.34.0,<1.35.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-rsamtools >=1.34.0,<1.35.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' + - 'bioconductor-biocgenerics >=0.30.0,<0.31.0' + - 'bioconductor-biostrings >=2.52.0,<2.53.0' + - 'bioconductor-bsgenome >=1.52.0,<1.53.0' + - 'bioconductor-genomeinfodb >=1.20.0,<1.21.0' + - 'bioconductor-genomicranges >=1.36.0,<1.37.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-rhtslib >=1.16.0,<1.17.0' + - 'bioconductor-rsamtools >=2.0.0,<2.1.0' - r-base - r-matrix - 'r-rcpp >=0.11.1' diff --git a/recipes/bioconductor-pogos/meta.yaml b/recipes/bioconductor-pogos/meta.yaml index be9a12180a8c5..1681111a7d861 100644 --- a/recipes/bioconductor-pogos/meta.yaml +++ b/recipes/bioconductor-pogos/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.2.0" %} +{% set version = "1.4.0" %} {% set name = "pogos" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 7b05b4af8e7b91f52c22e25ba834ec4e + md5: c5c65f17d311d12b7c8725f16ae7941d build: number: 0 rpaths: @@ -20,16 +20,16 @@ build: # Suggests: knitr, DT, ontologyPlot, testthat requirements: host: - - 'bioconductor-ontoproc >=1.4.0,<1.5.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-ontoproc >=1.6.0,<1.7.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' - r-base - r-ggplot2 - 'r-httr >=1.3.1' - 'r-rjson >=0.2.15' - r-shiny run: - - 'bioconductor-ontoproc >=1.4.0,<1.5.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-ontoproc >=1.6.0,<1.7.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' - r-base - r-ggplot2 - 'r-httr >=1.3.1' diff --git a/recipes/bioconductor-polyester/meta.yaml b/recipes/bioconductor-polyester/meta.yaml index 0850fca717bcd..4df6a3f0e01af 100644 --- a/recipes/bioconductor-polyester/meta.yaml +++ b/recipes/bioconductor-polyester/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.18.0" %} +{% set version = "1.20.0" %} {% set name = "polyester" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: c7a2bb655890a4fa6f80eae248d10d94 + md5: 7e80f66d0d4d869281a4ad04764594b9 build: number: 0 rpaths: @@ -20,19 +20,19 @@ build: # Suggests: knitr, ballgown requirements: host: - - 'bioconductor-biostrings >=2.50.0,<2.51.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-limma >=3.38.0,<3.39.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' - - 'bioconductor-zlibbioc >=1.28.0,<1.29.0' + - 'bioconductor-biostrings >=2.52.0,<2.53.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-limma >=3.40.0,<3.41.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' + - 'bioconductor-zlibbioc >=1.30.0,<1.31.0' - r-base - r-logspline run: - - 'bioconductor-biostrings >=2.50.0,<2.51.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-limma >=3.38.0,<3.39.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' - - 'bioconductor-zlibbioc >=1.28.0,<1.29.0' + - 'bioconductor-biostrings >=2.52.0,<2.53.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-limma >=3.40.0,<3.41.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' + - 'bioconductor-zlibbioc >=1.30.0,<1.31.0' - r-base - r-logspline test: diff --git a/recipes/bioconductor-polyfit/meta.yaml b/recipes/bioconductor-polyfit/meta.yaml index 0d92e15ab786e..398c9522b9184 100644 --- a/recipes/bioconductor-polyfit/meta.yaml +++ b/recipes/bioconductor-polyfit/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.16.1" %} +{% set version = "1.18.0" %} {% set name = "Polyfit" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 3bf6fc9eb02104686f15f1360a05d43b + md5: 34ca445df2af6dcabf24929bd126a6d2 build: number: 0 rpaths: @@ -20,10 +20,10 @@ build: # Suggests: BiocStyle requirements: host: - - 'bioconductor-deseq >=1.34.0,<1.35.0' + - 'bioconductor-deseq >=1.36.0,<1.37.0' - r-base run: - - 'bioconductor-deseq >=1.34.0,<1.35.0' + - 'bioconductor-deseq >=1.36.0,<1.37.0' - r-base test: commands: diff --git a/recipes/bioconductor-polyphen.hsapiens.dbsnp131/meta.yaml b/recipes/bioconductor-polyphen.hsapiens.dbsnp131/meta.yaml index 115229308ecf5..5e8deaa2db11f 100644 --- a/recipes/bioconductor-polyphen.hsapiens.dbsnp131/meta.yaml +++ b/recipes/bioconductor-polyphen.hsapiens.dbsnp131/meta.yaml @@ -1,6 +1,6 @@ {% set version = "1.0.2" %} {% set name = "PolyPhen.Hsapiens.dbSNP131" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -12,23 +12,23 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' md5: 763e9cd4afd97b36f7e659f5454ef61f build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' - - 'bioconductor-variantannotation >=1.28.0,<1.29.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' + - 'bioconductor-variantannotation >=1.30.0,<1.31.0' - r-base - 'r-rsqlite >=0.11.0' run: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' - - 'bioconductor-variantannotation >=1.28.0,<1.29.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' + - 'bioconductor-variantannotation >=1.30.0,<1.31.0' - r-base - 'r-rsqlite >=0.11.0' - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-polyphen.hsapiens.dbsnp131/post-link.sh b/recipes/bioconductor-polyphen.hsapiens.dbsnp131/post-link.sh index 07c62534645ac..bf2c2eab7a46a 100644 --- a/recipes/bioconductor-polyphen.hsapiens.dbsnp131/post-link.sh +++ b/recipes/bioconductor-polyphen.hsapiens.dbsnp131/post-link.sh @@ -1,9 +1,10 @@ #!/bin/bash FN="PolyPhen.Hsapiens.dbSNP131_1.0.2.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/PolyPhen.Hsapiens.dbSNP131_1.0.2.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/PolyPhen.Hsapiens.dbSNP131_1.0.2.tar.gz" "https://bioarchive.galaxyproject.org/PolyPhen.Hsapiens.dbSNP131_1.0.2.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-polyphen.hsapiens.dbsnp131/bioconductor-polyphen.hsapiens.dbsnp131_1.0.2_src_all.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-polyphen.hsapiens.dbsnp131/bioconductor-polyphen.hsapiens.dbsnp131_1.0.2_src_all.tar.gz" ) MD5="763e9cd4afd97b36f7e659f5454ef61f" @@ -16,7 +17,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-poplarcdf/meta.yaml b/recipes/bioconductor-poplarcdf/meta.yaml index c89157967a51c..4cd5a194b0541 100644 --- a/recipes/bioconductor-poplarcdf/meta.yaml +++ b/recipes/bioconductor-poplarcdf/meta.yaml @@ -1,6 +1,6 @@ {% set version = "2.18.0" %} {% set name = "poplarcdf" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -12,19 +12,19 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 556e7f8f6f76436552d8044ef29279cb build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' - r-base run: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-poplarcdf/post-link.sh b/recipes/bioconductor-poplarcdf/post-link.sh index d91f5d7294c9d..1c8e1c7ff000a 100644 --- a/recipes/bioconductor-poplarcdf/post-link.sh +++ b/recipes/bioconductor-poplarcdf/post-link.sh @@ -1,9 +1,10 @@ #!/bin/bash FN="poplarcdf_2.18.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/poplarcdf_2.18.0.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/poplarcdf_2.18.0.tar.gz" "https://bioarchive.galaxyproject.org/poplarcdf_2.18.0.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-poplarcdf/bioconductor-poplarcdf_2.18.0_src_all.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-poplarcdf/bioconductor-poplarcdf_2.18.0_src_all.tar.gz" ) MD5="556e7f8f6f76436552d8044ef29279cb" @@ -16,7 +17,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-poplarprobe/meta.yaml b/recipes/bioconductor-poplarprobe/meta.yaml index ae477aad7926c..2c0780be8efab 100644 --- a/recipes/bioconductor-poplarprobe/meta.yaml +++ b/recipes/bioconductor-poplarprobe/meta.yaml @@ -1,6 +1,6 @@ {% set version = "2.18.0" %} {% set name = "poplarprobe" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -12,19 +12,19 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 87a608cd86084a06973a88e9b51f799a build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' - r-base run: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-poplarprobe/post-link.sh b/recipes/bioconductor-poplarprobe/post-link.sh index 930cd2a4b8708..27af95185bdee 100644 --- a/recipes/bioconductor-poplarprobe/post-link.sh +++ b/recipes/bioconductor-poplarprobe/post-link.sh @@ -1,9 +1,10 @@ #!/bin/bash FN="poplarprobe_2.18.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/poplarprobe_2.18.0.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/poplarprobe_2.18.0.tar.gz" "https://bioarchive.galaxyproject.org/poplarprobe_2.18.0.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-poplarprobe/bioconductor-poplarprobe_2.18.0_src_all.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-poplarprobe/bioconductor-poplarprobe_2.18.0_src_all.tar.gz" ) MD5="87a608cd86084a06973a88e9b51f799a" @@ -16,7 +17,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-porcine.db/meta.yaml b/recipes/bioconductor-porcine.db/meta.yaml index 0b9dced0fb3d0..95dd8436890a7 100644 --- a/recipes/bioconductor-porcine.db/meta.yaml +++ b/recipes/bioconductor-porcine.db/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.2.3" %} {% set name = "porcine.db" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -12,7 +12,7 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: a90a6ad39b7fda3f30c23ab315201317 build: - number: 1 + number: 2 rpaths: - lib/R/lib/ - lib/ @@ -20,14 +20,14 @@ build: # Suggests: DBI, annotate, RUnit requirements: host: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' - - 'bioconductor-org.ss.eg.db >=3.7.0,<3.8.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' + - 'bioconductor-org.ss.eg.db >=3.8.0,<3.9.0' - r-base run: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' - - 'bioconductor-org.ss.eg.db >=3.7.0,<3.8.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' + - 'bioconductor-org.ss.eg.db >=3.8.0,<3.9.0' - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-porcine.db/post-link.sh b/recipes/bioconductor-porcine.db/post-link.sh index 25e305b0bb4ec..d220a761ffb74 100644 --- a/recipes/bioconductor-porcine.db/post-link.sh +++ b/recipes/bioconductor-porcine.db/post-link.sh @@ -1,9 +1,10 @@ #!/bin/bash FN="porcine.db_3.2.3.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/porcine.db_3.2.3.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/porcine.db_3.2.3.tar.gz" "https://bioarchive.galaxyproject.org/porcine.db_3.2.3.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-porcine.db/bioconductor-porcine.db_3.2.3_src_all.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-porcine.db/bioconductor-porcine.db_3.2.3_src_all.tar.gz" ) MD5="a90a6ad39b7fda3f30c23ab315201317" @@ -16,7 +17,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-porcinecdf/meta.yaml b/recipes/bioconductor-porcinecdf/meta.yaml index e96719cdc09a2..c87d4c62e76c7 100644 --- a/recipes/bioconductor-porcinecdf/meta.yaml +++ b/recipes/bioconductor-porcinecdf/meta.yaml @@ -1,6 +1,6 @@ {% set version = "2.18.0" %} {% set name = "porcinecdf" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -12,19 +12,19 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 32a60b93829c06a935895fab0a469228 build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' - r-base run: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-porcinecdf/post-link.sh b/recipes/bioconductor-porcinecdf/post-link.sh index a0eeb623c2d61..1886075d1b449 100644 --- a/recipes/bioconductor-porcinecdf/post-link.sh +++ b/recipes/bioconductor-porcinecdf/post-link.sh @@ -1,9 +1,10 @@ #!/bin/bash FN="porcinecdf_2.18.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/porcinecdf_2.18.0.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/porcinecdf_2.18.0.tar.gz" "https://bioarchive.galaxyproject.org/porcinecdf_2.18.0.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-porcinecdf/bioconductor-porcinecdf_2.18.0_src_all.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-porcinecdf/bioconductor-porcinecdf_2.18.0_src_all.tar.gz" ) MD5="32a60b93829c06a935895fab0a469228" @@ -16,7 +17,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-porcineprobe/meta.yaml b/recipes/bioconductor-porcineprobe/meta.yaml index b63af99eba402..1025ea15cd928 100644 --- a/recipes/bioconductor-porcineprobe/meta.yaml +++ b/recipes/bioconductor-porcineprobe/meta.yaml @@ -1,6 +1,6 @@ {% set version = "2.18.0" %} {% set name = "porcineprobe" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -12,19 +12,19 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 5ac483b6329a012d4c9954e3dee8869e build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' - r-base run: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-porcineprobe/post-link.sh b/recipes/bioconductor-porcineprobe/post-link.sh index a36f598eadf82..7cb02d227b61a 100644 --- a/recipes/bioconductor-porcineprobe/post-link.sh +++ b/recipes/bioconductor-porcineprobe/post-link.sh @@ -1,9 +1,10 @@ #!/bin/bash FN="porcineprobe_2.18.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/porcineprobe_2.18.0.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/porcineprobe_2.18.0.tar.gz" "https://bioarchive.galaxyproject.org/porcineprobe_2.18.0.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-porcineprobe/bioconductor-porcineprobe_2.18.0_src_all.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-porcineprobe/bioconductor-porcineprobe_2.18.0_src_all.tar.gz" ) MD5="5ac483b6329a012d4c9954e3dee8869e" @@ -16,7 +17,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-post/meta.yaml b/recipes/bioconductor-post/meta.yaml index bb09bd4b65c4c..a380b97a9200f 100644 --- a/recipes/bioconductor-post/meta.yaml +++ b/recipes/bioconductor-post/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.6.0" %} +{% set version = "1.8.0" %} {% set name = "POST" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 53dc1ab5813de6f37505e96d2dd29c5c + md5: c46f4319e91a8ac8655003ed8ff437bc build: number: 0 rpaths: @@ -19,15 +19,15 @@ build: noarch: generic requirements: host: - - 'bioconductor-biobase >=2.42.0,<2.43.0' - - 'bioconductor-gseabase >=1.44.0,<1.45.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' + - 'bioconductor-gseabase >=1.46.0,<1.47.0' - r-base - r-compquadform - r-matrix - r-survival run: - - 'bioconductor-biobase >=2.42.0,<2.43.0' - - 'bioconductor-gseabase >=1.44.0,<1.45.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' + - 'bioconductor-gseabase >=1.46.0,<1.47.0' - r-base - r-compquadform - r-matrix diff --git a/recipes/bioconductor-potra/build.sh b/recipes/bioconductor-potra/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-potra/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-potra/meta.yaml b/recipes/bioconductor-potra/meta.yaml new file mode 100644 index 0000000000000..b7d968da450fb --- /dev/null +++ b/recipes/bioconductor-potra/meta.yaml @@ -0,0 +1,43 @@ +{% set version = "1.0.0" %} +{% set name = "PoTRA" %} +{% set bioc = "3.9" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: 28dd409c781102ceb5ea0088be879397 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: BiocStyle, knitr, rmarkdown, colr, metap, repmis +requirements: + host: + - 'bioconductor-biocgenerics >=0.30.0,<0.31.0' + - 'bioconductor-graph >=1.62.0,<1.63.0' + - 'bioconductor-graphite >=1.30.0,<1.31.0' + - 'bioconductor-org.hs.eg.db >=3.8.0,<3.9.0' + - r-base + - r-igraph + run: + - 'bioconductor-biocgenerics >=0.30.0,<0.31.0' + - 'bioconductor-graph >=1.62.0,<1.63.0' + - 'bioconductor-graphite >=1.30.0,<1.31.0' + - 'bioconductor-org.hs.eg.db >=3.8.0,<3.9.0' + - r-base + - r-igraph +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: LGPL + summary: 'The PoTRA analysis is based on topological ranks of genes in biological pathways. PoTRA can be used to detect pathways involved in disease (Li, Liu & Dinu, 2018). We use PageRank to measure the relative topological ranks of genes in each biological pathway, then select hub genes for each pathway, and use Fishers Exact test to determine if the number of hub genes in each pathway is altered from normal to cancer (Li, Liu & Dinu, 2018). Alternatively, if the distribution of topological ranks of gene in a pathway is altered between normal and cancer, this pathway might also be involved in cancer (Li, Liu & Dinu, 2018). Hence, we use the Kolmogorov–Smirnov test to detect pathways that have an altered distribution of topological ranks of genes between two phenotypes (Li, Liu & Dinu, 2018). PoTRA can be used with the KEGG, Biocarta, Reactome, NCI, SMPDB and PharmGKB databases from the devel graphite library.' + diff --git a/recipes/bioconductor-powerexplorer/meta.yaml b/recipes/bioconductor-powerexplorer/meta.yaml index 1be9fe88b6c6b..24e00acfd45c6 100644 --- a/recipes/bioconductor-powerexplorer/meta.yaml +++ b/recipes/bioconductor-powerexplorer/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.2.2" %} +{% set version = "1.4.0" %} {% set name = "PowerExplorer" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 8de67e18b225337478a5bde3e510a4b4 + md5: 9327ee552a02d059fa9f4efe1d0a816e build: number: 0 rpaths: @@ -20,26 +20,26 @@ build: # Suggests: knitr, rmarkdown requirements: host: - - 'bioconductor-biobase >=2.42.0,<2.43.0' - - 'bioconductor-biocparallel >=1.16.0,<1.17.0' - - 'bioconductor-deseq2 >=1.22.0,<1.23.0' - - 'bioconductor-rots >=1.10.0,<1.11.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' - - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' - - 'bioconductor-vsn >=3.50.0,<3.51.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' + - 'bioconductor-biocparallel >=1.18.0,<1.19.0' + - 'bioconductor-deseq2 >=1.24.0,<1.25.0' + - 'bioconductor-rots >=1.12.0,<1.13.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' + - 'bioconductor-summarizedexperiment >=1.14.0,<1.15.0' + - 'bioconductor-vsn >=3.52.0,<3.53.0' - r-base - r-data.table - r-ggplot2 - r-gridextra - r-mass run: - - 'bioconductor-biobase >=2.42.0,<2.43.0' - - 'bioconductor-biocparallel >=1.16.0,<1.17.0' - - 'bioconductor-deseq2 >=1.22.0,<1.23.0' - - 'bioconductor-rots >=1.10.0,<1.11.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' - - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' - - 'bioconductor-vsn >=3.50.0,<3.51.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' + - 'bioconductor-biocparallel >=1.18.0,<1.19.0' + - 'bioconductor-deseq2 >=1.24.0,<1.25.0' + - 'bioconductor-rots >=1.12.0,<1.13.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' + - 'bioconductor-summarizedexperiment >=1.14.0,<1.15.0' + - 'bioconductor-vsn >=3.52.0,<3.53.0' - r-base - r-data.table - r-ggplot2 diff --git a/recipes/bioconductor-powertcr/meta.yaml b/recipes/bioconductor-powertcr/meta.yaml index 63bfbca2fee38..7246a8cfb42cc 100644 --- a/recipes/bioconductor-powertcr/meta.yaml +++ b/recipes/bioconductor-powertcr/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.2.0" %} +{% set version = "1.4.0" %} {% set name = "powerTCR" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: e355b3691f1b481999f271edce674a87 + md5: ad42fe5c1066c24b604c06bc70370584 build: number: 0 rpaths: diff --git a/recipes/bioconductor-ppidata/meta.yaml b/recipes/bioconductor-ppidata/meta.yaml index 69cf0836331fb..4e35481fe6c13 100644 --- a/recipes/bioconductor-ppidata/meta.yaml +++ b/recipes/bioconductor-ppidata/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "0.20.0" %} +{% set version = "0.22.0" %} {% set name = "ppiData" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: eff4cead7fba4a8443cb3c3426391bb0 + md5: 93d6dce530ee9a0d3ed886ae0e53b909 build: number: 0 rpaths: @@ -20,14 +20,14 @@ build: # Suggests: org.Sc.sgd.db, ppiStats requirements: host: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' - - 'bioconductor-graph >=1.60.0,<1.61.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' + - 'bioconductor-graph >=1.62.0,<1.63.0' - r-base run: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' - - 'bioconductor-graph >=1.60.0,<1.61.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' + - 'bioconductor-graph >=1.62.0,<1.63.0' - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-ppidata/post-link.sh b/recipes/bioconductor-ppidata/post-link.sh index 40c1a1c281b3d..3280ce57a3071 100644 --- a/recipes/bioconductor-ppidata/post-link.sh +++ b/recipes/bioconductor-ppidata/post-link.sh @@ -1,11 +1,11 @@ #!/bin/bash -FN="ppiData_0.20.0.tar.gz" +FN="ppiData_0.22.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/experiment/src/contrib/ppiData_0.20.0.tar.gz" - "https://bioarchive.galaxyproject.org/ppiData_0.20.0.tar.gz" - "https://depot.galaxyproject.org/software/bioconductor-ppidata/bioconductor-ppidata_0.20.0_src_all.tar.gz" + "https://bioconductor.org/packages/3.9/data/experiment/src/contrib/ppiData_0.22.0.tar.gz" + "https://bioarchive.galaxyproject.org/ppiData_0.22.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-ppidata/bioconductor-ppidata_0.22.0_src_all.tar.gz" ) -MD5="eff4cead7fba4a8443cb3c3426391bb0" +MD5="93d6dce530ee9a0d3ed886ae0e53b909" # Use a staging area in the conda dir rather than temp dirs, both to avoid # permission issues as well as to have things downloaded in a predictable @@ -16,7 +16,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-ppinfer/meta.yaml b/recipes/bioconductor-ppinfer/meta.yaml index 0d58d73af8c1a..c19c2496d5e86 100644 --- a/recipes/bioconductor-ppinfer/meta.yaml +++ b/recipes/bioconductor-ppinfer/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.8.1" %} +{% set version = "1.10.0" %} {% set name = "PPInfer" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,29 +10,28 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 3f431c624b08318fd0ef332a6ae63e1a + md5: c9394e3414d3dd3f12878b6513c77a42 build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ noarch: generic -# Suggests: testthat requirements: host: - - 'bioconductor-biomart >=2.38.0,<2.39.0' - - 'bioconductor-fgsea >=1.8.0,<1.9.0' - - 'bioconductor-stringdb >=1.22.0,<1.23.0' - - 'bioconductor-yeastexpdata >=0.28.0,<0.29.0' + - 'bioconductor-biomart >=2.40.0,<2.41.0' + - 'bioconductor-fgsea >=1.10.0,<1.11.0' + - 'bioconductor-stringdb >=1.24.0,<1.25.0' + - 'bioconductor-yeastexpdata >=0.30.0,<0.31.0' - r-base - r-ggplot2 - r-igraph - r-kernlab run: - - 'bioconductor-biomart >=2.38.0,<2.39.0' - - 'bioconductor-fgsea >=1.8.0,<1.9.0' - - 'bioconductor-stringdb >=1.22.0,<1.23.0' - - 'bioconductor-yeastexpdata >=0.28.0,<0.29.0' + - 'bioconductor-biomart >=2.40.0,<2.41.0' + - 'bioconductor-fgsea >=1.10.0,<1.11.0' + - 'bioconductor-stringdb >=1.24.0,<1.25.0' + - 'bioconductor-yeastexpdata >=0.30.0,<0.31.0' - r-base - r-ggplot2 - r-igraph diff --git a/recipes/bioconductor-ppistats/meta.yaml b/recipes/bioconductor-ppistats/meta.yaml index e1e62c4eaeb10..432690b7523a5 100644 --- a/recipes/bioconductor-ppistats/meta.yaml +++ b/recipes/bioconductor-ppistats/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.48.0" %} +{% set version = "1.50.0" %} {% set name = "ppiStats" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 143b0f3a760c921de1444f04cea91c98 + md5: 3e33c457efd15516f13d7f8144e76709 build: number: 0 rpaths: @@ -20,20 +20,20 @@ build: # Suggests: yeastExpData, xtable requirements: host: - - 'bioconductor-biobase >=2.42.0,<2.43.0' - - 'bioconductor-category >=2.48.0,<2.49.0' - - 'bioconductor-graph >=1.60.0,<1.61.0' - - 'bioconductor-ppidata >=0.20.0,<0.21.0' - - 'bioconductor-scisi >=1.54.0,<1.55.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' + - 'bioconductor-category >=2.50.0,<2.51.0' + - 'bioconductor-graph >=1.62.0,<1.63.0' + - 'bioconductor-ppidata >=0.22.0,<0.23.0' + - 'bioconductor-scisi >=1.56.0,<1.57.0' - r-base - r-lattice - r-rcolorbrewer run: - - 'bioconductor-biobase >=2.42.0,<2.43.0' - - 'bioconductor-category >=2.48.0,<2.49.0' - - 'bioconductor-graph >=1.60.0,<1.61.0' - - 'bioconductor-ppidata >=0.20.0,<0.21.0' - - 'bioconductor-scisi >=1.54.0,<1.55.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' + - 'bioconductor-category >=2.50.0,<2.51.0' + - 'bioconductor-graph >=1.62.0,<1.63.0' + - 'bioconductor-ppidata >=0.22.0,<0.23.0' + - 'bioconductor-scisi >=1.56.0,<1.57.0' - r-base - r-lattice - r-rcolorbrewer diff --git a/recipes/bioconductor-pqsfinder/meta.yaml b/recipes/bioconductor-pqsfinder/meta.yaml index 0bc788735e7f8..71ca4df501662 100644 --- a/recipes/bioconductor-pqsfinder/meta.yaml +++ b/recipes/bioconductor-pqsfinder/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.10.0" %} +{% set version = "2.0.0" %} {% set name = "pqsfinder" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: ad81bbb70003e7a96e2eb916b19e81d3 + md5: f9f28704585bad9683e2ce87c531d902 build: number: 0 rpaths: @@ -20,20 +20,20 @@ build: # SystemRequirements: GNU make, C++11 requirements: host: - - 'bioconductor-biostrings >=2.50.0,<2.51.0' - - 'bioconductor-genomicranges >=1.34.0,<1.35.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-biostrings >=2.52.0,<2.53.0' + - 'bioconductor-genomicranges >=1.36.0,<1.37.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' - r-base - - 'r-bh >=1.66.0' + - 'r-bh >=1.69.0' - 'r-rcpp >=0.12.3' run: - - 'bioconductor-biostrings >=2.50.0,<2.51.0' - - 'bioconductor-genomicranges >=1.34.0,<1.35.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-biostrings >=2.52.0,<2.53.0' + - 'bioconductor-genomicranges >=1.36.0,<1.37.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' - r-base - - 'r-bh >=1.66.0' + - 'r-bh >=1.69.0' - 'r-rcpp >=0.12.3' build: - {{ compiler('c') }} @@ -45,7 +45,7 @@ test: about: home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: 'BSD_2_clause + file LICENSE' - summary: 'The main functionality of this package is to detect DNA sequence patterns that are likely to fold into an intramolecular G-quadruplex (G4). Unlike many other approaches, this package is able to detect sequences responsible for G4s folded from imperfect G-runs containing bulges or mismatches and as such is more sensitive than competing algorithms.' + summary: 'Pqsfinder detects DNA sequence patterns that are likely to fold into an intramolecular G-quadruplex (G4). Unlike many other approaches, pqsfinder is able to detect G4s folded from imperfect G-runs containing bulges or mismatches or G4s having long loops. Pqsfinder also assigns an integer score to each hit that was fitted on G4 sequencing data and corresponds to expected stability of the folded G4.' extra: identifiers: - biotools:pqsfinder diff --git a/recipes/bioconductor-prada/meta.yaml b/recipes/bioconductor-prada/meta.yaml index b7792186a45a0..58ccd0d6eaf28 100644 --- a/recipes/bioconductor-prada/meta.yaml +++ b/recipes/bioconductor-prada/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.58.1" %} +{% set version = "1.60.0" %} {% set name = "prada" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - sha256: da4495fed6f41f167a828c95782060b94e19f7445a4b3b1ccb71fba5a9f55a41 + md5: bdb750f5fd7eee86f2189acc886dc394 build: number: 0 rpaths: @@ -19,15 +19,15 @@ build: # Suggests: cellHTS2, tcltk requirements: host: - - 'bioconductor-biobase >=2.42.0,<2.43.0' - - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' + - 'bioconductor-biocgenerics >=0.30.0,<0.31.0' - r-base - r-mass - r-rcolorbrewer - r-rrcov run: - - 'bioconductor-biobase >=2.42.0,<2.43.0' - - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' + - 'bioconductor-biocgenerics >=0.30.0,<0.31.0' - r-base - r-mass - r-rcolorbrewer diff --git a/recipes/bioconductor-pram/build.sh b/recipes/bioconductor-pram/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-pram/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-pram/meta.yaml b/recipes/bioconductor-pram/meta.yaml new file mode 100644 index 0000000000000..cee83c397b539 --- /dev/null +++ b/recipes/bioconductor-pram/meta.yaml @@ -0,0 +1,53 @@ +{% set version = "1.0.0" %} +{% set name = "pram" %} +{% set bioc = "3.9" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + md5: bb7c3664804776014818ec6c3c14187b +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: testthat, BiocStyle, knitr, rmarkdown +requirements: + host: + - 'bioconductor-biocgenerics >=0.30.0,<0.31.0' + - 'bioconductor-biocparallel >=1.18.0,<1.19.0' + - 'bioconductor-genomeinfodb >=1.20.0,<1.21.0' + - 'bioconductor-genomicalignments >=1.20.0,<1.21.0' + - 'bioconductor-genomicranges >=1.36.0,<1.37.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-rsamtools >=2.0.0,<2.1.0' + - 'bioconductor-rtracklayer >=1.44.0,<1.45.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' + - r-base + - 'r-data.table >=1.11.8' + run: + - 'bioconductor-biocgenerics >=0.30.0,<0.31.0' + - 'bioconductor-biocparallel >=1.18.0,<1.19.0' + - 'bioconductor-genomeinfodb >=1.20.0,<1.21.0' + - 'bioconductor-genomicalignments >=1.20.0,<1.21.0' + - 'bioconductor-genomicranges >=1.36.0,<1.37.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-rsamtools >=2.0.0,<2.1.0' + - 'bioconductor-rtracklayer >=1.44.0,<1.45.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' + - r-base + - 'r-data.table >=1.11.8' +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: 'GPL (>= 3)' + summary: 'Publicly available RNA-seq data is routinely used for retrospective analysis to elucidate new biology. Novel transcript discovery enabled by large collections of RNA-seq datasets has emerged as one of such analysis. To increase the power of transcript discovery from large collections of RNA-seq datasets, we developed a new R package named Pooling RNA-seq and Assembling Models (PRAM), which builds transcript models in intergenic regions from pooled RNA-seq datasets. This package includes functions for defining intergenic regions, extracting and pooling related RNA-seq alignments, predicting, selected, and evaluating transcript models.' + diff --git a/recipes/bioconductor-prebs/meta.yaml b/recipes/bioconductor-prebs/meta.yaml index 2f5ffc805d019..52591cc93a514 100644 --- a/recipes/bioconductor-prebs/meta.yaml +++ b/recipes/bioconductor-prebs/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.22.0" %} +{% set version = "1.24.0" %} {% set name = "prebs" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 339b874803bc26c3d5f72c75174bf155 + md5: c71c6d8ff29857fbdfd7ccd9e8986313 build: number: 0 rpaths: @@ -20,24 +20,24 @@ build: # Suggests: prebsdata, hgu133plus2cdf, hgu133plus2probe requirements: host: - - 'bioconductor-affy >=1.60.0,<1.61.0' - - 'bioconductor-biobase >=2.42.0,<2.43.0' - - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' - - 'bioconductor-genomicalignments >=1.18.0,<1.19.0' - - 'bioconductor-genomicranges >=1.34.0,<1.35.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-rpa >=1.38.0,<1.39.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-affy >=1.62.0,<1.63.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' + - 'bioconductor-genomeinfodb >=1.20.0,<1.21.0' + - 'bioconductor-genomicalignments >=1.20.0,<1.21.0' + - 'bioconductor-genomicranges >=1.36.0,<1.37.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-rpa >=1.40.0,<1.41.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' - r-base run: - - 'bioconductor-affy >=1.60.0,<1.61.0' - - 'bioconductor-biobase >=2.42.0,<2.43.0' - - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' - - 'bioconductor-genomicalignments >=1.18.0,<1.19.0' - - 'bioconductor-genomicranges >=1.34.0,<1.35.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-rpa >=1.38.0,<1.39.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-affy >=1.62.0,<1.63.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' + - 'bioconductor-genomeinfodb >=1.20.0,<1.21.0' + - 'bioconductor-genomicalignments >=1.20.0,<1.21.0' + - 'bioconductor-genomicranges >=1.36.0,<1.37.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-rpa >=1.40.0,<1.41.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' - r-base test: commands: diff --git a/recipes/bioconductor-prebsdata/meta.yaml b/recipes/bioconductor-prebsdata/meta.yaml index d135499c74a77..bcbcd522d3029 100644 --- a/recipes/bioconductor-prebsdata/meta.yaml +++ b/recipes/bioconductor-prebsdata/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.18.0" %} +{% set version = "1.20.0" %} {% set name = "prebsdata" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: ddb000d474c089466ab15aa67b44cdfa + md5: fd5ede83923d6157b6303b81d058678f build: number: 0 rpaths: @@ -22,7 +22,7 @@ requirements: - r-base run: - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-prebsdata/post-link.sh b/recipes/bioconductor-prebsdata/post-link.sh index 2973fed125299..f8e8e15fcbed3 100644 --- a/recipes/bioconductor-prebsdata/post-link.sh +++ b/recipes/bioconductor-prebsdata/post-link.sh @@ -1,11 +1,11 @@ #!/bin/bash -FN="prebsdata_1.18.0.tar.gz" +FN="prebsdata_1.20.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/experiment/src/contrib/prebsdata_1.18.0.tar.gz" - "https://bioarchive.galaxyproject.org/prebsdata_1.18.0.tar.gz" - "https://depot.galaxyproject.org/software/bioconductor-prebsdata/bioconductor-prebsdata_1.18.0_src_all.tar.gz" + "https://bioconductor.org/packages/3.9/data/experiment/src/contrib/prebsdata_1.20.0.tar.gz" + "https://bioarchive.galaxyproject.org/prebsdata_1.20.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-prebsdata/bioconductor-prebsdata_1.20.0_src_all.tar.gz" ) -MD5="ddb000d474c089466ab15aa67b44cdfa" +MD5="fd5ede83923d6157b6303b81d058678f" # Use a staging area in the conda dir rather than temp dirs, both to avoid # permission issues as well as to have things downloaded in a predictable @@ -16,7 +16,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-precisiontrialdrawer/build.sh b/recipes/bioconductor-precisiontrialdrawer/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-precisiontrialdrawer/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-precisiontrialdrawer/meta.yaml b/recipes/bioconductor-precisiontrialdrawer/meta.yaml new file mode 100644 index 0000000000000..896af83a6d423 --- /dev/null +++ b/recipes/bioconductor-precisiontrialdrawer/meta.yaml @@ -0,0 +1,79 @@ +{% set version = "1.0.0" %} +{% set name = "PrecisionTrialDrawer" %} +{% set bioc = "3.9" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: 322e6b3ee76359734f1e6a1f9ad1da1a +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: BiocStyle, knitr, rmarkdown, dplyr +requirements: + host: + - 'bioconductor-biocparallel >=1.18.0,<1.19.0' + - 'bioconductor-biomart >=2.40.0,<2.41.0' + - 'bioconductor-genomicranges >=1.36.0,<1.37.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-lowmacaannotation >=1.0.0,<1.1.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' + - r-base + - r-brglm + - r-cgdsr + - r-data.table + - r-dt + - r-ggplot2 + - r-ggrepel + - r-googlevis + - r-httr + - r-jsonlite + - r-magrittr + - r-matrixstats + - r-rcolorbrewer + - r-reshape2 + - r-shiny + - r-shinybs + - r-stringr + - r-xml + run: + - 'bioconductor-biocparallel >=1.18.0,<1.19.0' + - 'bioconductor-biomart >=2.40.0,<2.41.0' + - 'bioconductor-genomicranges >=1.36.0,<1.37.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-lowmacaannotation >=1.0.0,<1.1.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' + - r-base + - r-brglm + - r-cgdsr + - r-data.table + - r-dt + - r-ggplot2 + - r-ggrepel + - r-googlevis + - r-httr + - r-jsonlite + - r-magrittr + - r-matrixstats + - r-rcolorbrewer + - r-reshape2 + - r-shiny + - r-shinybs + - r-stringr + - r-xml +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: GPL-3 + summary: 'A suite of methods to design umbrella and basket trials for preision oncology.' + diff --git a/recipes/bioconductor-preda/meta.yaml b/recipes/bioconductor-preda/meta.yaml index b757008f8cad4..1dbc9f89c6829 100644 --- a/recipes/bioconductor-preda/meta.yaml +++ b/recipes/bioconductor-preda/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.28.0" %} +{% set version = "1.30.0" %} {% set name = "PREDA" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 4bb593ea42c1bf03653cadffd9202aa4 + md5: df5582ae2251f2f67890132053c1104e build: number: 0 rpaths: @@ -20,15 +20,15 @@ build: # Suggests: quantsmooth, qvalue, limma, caTools, affy, PREDAsampledata requirements: host: - - 'bioconductor-annotate >=1.60.0,<1.61.0' - - 'bioconductor-biobase >=2.42.0,<2.43.0' - - 'bioconductor-multtest >=2.38.0,<2.39.0' + - 'bioconductor-annotate >=1.62.0,<1.63.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' + - 'bioconductor-multtest >=2.40.0,<2.41.0' - r-base - 'r-lokern >=1.0.9' run: - - 'bioconductor-annotate >=1.60.0,<1.61.0' - - 'bioconductor-biobase >=2.42.0,<2.43.0' - - 'bioconductor-multtest >=2.38.0,<2.39.0' + - 'bioconductor-annotate >=1.62.0,<1.63.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' + - 'bioconductor-multtest >=2.40.0,<2.41.0' - r-base - 'r-lokern >=1.0.9' test: diff --git a/recipes/bioconductor-predasampledata/meta.yaml b/recipes/bioconductor-predasampledata/meta.yaml index 243b4635db246..cad97904d2a47 100644 --- a/recipes/bioconductor-predasampledata/meta.yaml +++ b/recipes/bioconductor-predasampledata/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "0.22.0" %} +{% set version = "0.24.0" %} {% set name = "PREDAsampledata" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: f8850b39d6ecfc64fe4cc26f6e305751 + md5: b8ad6ccaa9332b95fe1c17172c39e4d7 build: number: 0 rpaths: @@ -20,18 +20,18 @@ build: # Suggests: hgu133plus2.db, hgu133plus2cdf requirements: host: - - 'bioconductor-affy >=1.60.0,<1.61.0' - - 'bioconductor-annotate >=1.60.0,<1.61.0' - - 'bioconductor-biobase >=2.42.0,<2.43.0' - - 'bioconductor-preda >=1.28.0,<1.29.0' + - 'bioconductor-affy >=1.62.0,<1.63.0' + - 'bioconductor-annotate >=1.62.0,<1.63.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' + - 'bioconductor-preda >=1.30.0,<1.31.0' - r-base run: - - 'bioconductor-affy >=1.60.0,<1.61.0' - - 'bioconductor-annotate >=1.60.0,<1.61.0' - - 'bioconductor-biobase >=2.42.0,<2.43.0' - - 'bioconductor-preda >=1.28.0,<1.29.0' + - 'bioconductor-affy >=1.62.0,<1.63.0' + - 'bioconductor-annotate >=1.62.0,<1.63.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' + - 'bioconductor-preda >=1.30.0,<1.31.0' - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-predasampledata/post-link.sh b/recipes/bioconductor-predasampledata/post-link.sh index 1b8569971c49c..a6be6a8c612a1 100644 --- a/recipes/bioconductor-predasampledata/post-link.sh +++ b/recipes/bioconductor-predasampledata/post-link.sh @@ -1,11 +1,11 @@ #!/bin/bash -FN="PREDAsampledata_0.22.0.tar.gz" +FN="PREDAsampledata_0.24.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/experiment/src/contrib/PREDAsampledata_0.22.0.tar.gz" - "https://bioarchive.galaxyproject.org/PREDAsampledata_0.22.0.tar.gz" - "https://depot.galaxyproject.org/software/bioconductor-predasampledata/bioconductor-predasampledata_0.22.0_src_all.tar.gz" + "https://bioconductor.org/packages/3.9/data/experiment/src/contrib/PREDAsampledata_0.24.0.tar.gz" + "https://bioarchive.galaxyproject.org/PREDAsampledata_0.24.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-predasampledata/bioconductor-predasampledata_0.24.0_src_all.tar.gz" ) -MD5="f8850b39d6ecfc64fe4cc26f6e305751" +MD5="b8ad6ccaa9332b95fe1c17172c39e4d7" # Use a staging area in the conda dir rather than temp dirs, both to avoid # permission issues as well as to have things downloaded in a predictable @@ -16,7 +16,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-predictionet/meta.yaml b/recipes/bioconductor-predictionet/meta.yaml index 156b2258d45a0..e104cba6ee99d 100644 --- a/recipes/bioconductor-predictionet/meta.yaml +++ b/recipes/bioconductor-predictionet/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.28.0" %} +{% set version = "1.30.0" %} {% set name = "predictionet" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: d95f178dcf079e1c8c9d0a2462fba591 + md5: 38a12700b0f4e71deaecacb35555b12c build: number: 0 rpaths: @@ -19,14 +19,14 @@ build: # Suggests: network, minet, knitr requirements: host: - - 'bioconductor-rbgl >=1.58.0,<1.59.0' + - 'bioconductor-rbgl >=1.60.0,<1.61.0' - r-base - r-catnet - r-igraph - r-mass - r-penalized run: - - 'bioconductor-rbgl >=1.58.0,<1.59.0' + - 'bioconductor-rbgl >=1.60.0,<1.61.0' - r-base - r-catnet - r-igraph diff --git a/recipes/bioconductor-preprocesscore/meta.yaml b/recipes/bioconductor-preprocesscore/meta.yaml index c307a09dc9013..f3f22e2a81d7b 100644 --- a/recipes/bioconductor-preprocesscore/meta.yaml +++ b/recipes/bioconductor-preprocesscore/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.44.0" %} +{% set version = "1.46.0" %} {% set name = "preprocessCore" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 973ffdd342f2443573ca0fe558fb0cdc + md5: 898d22c5820f39234dd575ae4f46631f build: number: 0 rpaths: diff --git a/recipes/bioconductor-primeviewcdf/meta.yaml b/recipes/bioconductor-primeviewcdf/meta.yaml index c7bd21a48e60a..6e35709f9e666 100644 --- a/recipes/bioconductor-primeviewcdf/meta.yaml +++ b/recipes/bioconductor-primeviewcdf/meta.yaml @@ -1,6 +1,6 @@ {% set version = "2.18.0" %} {% set name = "primeviewcdf" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -12,19 +12,19 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 71e39a59a5907e9b8a8dba58d36eee50 build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' - r-base run: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-primeviewcdf/post-link.sh b/recipes/bioconductor-primeviewcdf/post-link.sh index 4d88dbacba130..3b20798a5a0a0 100644 --- a/recipes/bioconductor-primeviewcdf/post-link.sh +++ b/recipes/bioconductor-primeviewcdf/post-link.sh @@ -1,9 +1,10 @@ #!/bin/bash FN="primeviewcdf_2.18.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/primeviewcdf_2.18.0.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/primeviewcdf_2.18.0.tar.gz" "https://bioarchive.galaxyproject.org/primeviewcdf_2.18.0.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-primeviewcdf/bioconductor-primeviewcdf_2.18.0_src_all.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-primeviewcdf/bioconductor-primeviewcdf_2.18.0_src_all.tar.gz" ) MD5="71e39a59a5907e9b8a8dba58d36eee50" @@ -16,7 +17,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-primeviewprobe/meta.yaml b/recipes/bioconductor-primeviewprobe/meta.yaml index fb57e540993f6..19f95777a7e84 100644 --- a/recipes/bioconductor-primeviewprobe/meta.yaml +++ b/recipes/bioconductor-primeviewprobe/meta.yaml @@ -1,6 +1,6 @@ {% set version = "2.18.0" %} {% set name = "primeviewprobe" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -12,19 +12,19 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 87cc56a8da4fb742ab1558ce1d3d26cc build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' - r-base run: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-primeviewprobe/post-link.sh b/recipes/bioconductor-primeviewprobe/post-link.sh index 1d63723c36a4e..2aeb7a11b2225 100644 --- a/recipes/bioconductor-primeviewprobe/post-link.sh +++ b/recipes/bioconductor-primeviewprobe/post-link.sh @@ -1,9 +1,10 @@ #!/bin/bash FN="primeviewprobe_2.18.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/primeviewprobe_2.18.0.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/primeviewprobe_2.18.0.tar.gz" "https://bioarchive.galaxyproject.org/primeviewprobe_2.18.0.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-primeviewprobe/bioconductor-primeviewprobe_2.18.0_src_all.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-primeviewprobe/bioconductor-primeviewprobe_2.18.0_src_all.tar.gz" ) MD5="87cc56a8da4fb742ab1558ce1d3d26cc" @@ -16,7 +17,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-primirtss/meta.yaml b/recipes/bioconductor-primirtss/meta.yaml index 0eb3c626d6821..629b10cbcab12 100644 --- a/recipes/bioconductor-primirtss/meta.yaml +++ b/recipes/bioconductor-primirtss/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.0.1" %} +{% set version = "1.2.0" %} {% set name = "primirTSS" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 766668da1afd9328500d67924f8f8522 + md5: d01f813dec836a5a410b486e9957186f build: number: 0 rpaths: @@ -20,18 +20,18 @@ build: # Suggests: knitr, rmarkdown requirements: host: - - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' - - 'bioconductor-biostrings >=2.50.0,<2.51.0' + - 'bioconductor-biocgenerics >=0.30.0,<0.31.0' + - 'bioconductor-biostrings >=2.52.0,<2.53.0' - 'bioconductor-bsgenome.hsapiens.ucsc.hg38 >=1.4.0,<1.5.0' - - 'bioconductor-genomicranges >=1.34.0,<1.35.0' - - 'bioconductor-genomicscores >=1.6.0,<1.7.0' - - 'bioconductor-gviz >=1.26.0,<1.27.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-jaspar2018 >=1.1.0,<1.2.0' - - 'bioconductor-phastcons100way.ucsc.hg38 >=3.7.0,<3.8.0' - - 'bioconductor-rtracklayer >=1.42.0,<1.43.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' - - 'bioconductor-tfbstools >=1.20.0,<1.21.0' + - 'bioconductor-genomicranges >=1.36.0,<1.37.0' + - 'bioconductor-genomicscores >=1.8.0,<1.9.0' + - 'bioconductor-gviz >=1.28.0,<1.29.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-jaspar2018 >=1.2.0,<1.3.0' + - 'bioconductor-phastcons100way.ucsc.hg38 >=3.8.0,<3.9.0' + - 'bioconductor-rtracklayer >=1.44.0,<1.45.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' + - 'bioconductor-tfbstools >=1.22.0,<1.23.0' - r-base - 'r-dplyr >=0.7.6' - 'r-purrr >=0.2.5' @@ -41,18 +41,18 @@ requirements: - 'r-tibble >=1.4.2' - 'r-tidyr >=0.8.1' run: - - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' - - 'bioconductor-biostrings >=2.50.0,<2.51.0' + - 'bioconductor-biocgenerics >=0.30.0,<0.31.0' + - 'bioconductor-biostrings >=2.52.0,<2.53.0' - 'bioconductor-bsgenome.hsapiens.ucsc.hg38 >=1.4.0,<1.5.0' - - 'bioconductor-genomicranges >=1.34.0,<1.35.0' - - 'bioconductor-genomicscores >=1.6.0,<1.7.0' - - 'bioconductor-gviz >=1.26.0,<1.27.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-jaspar2018 >=1.1.0,<1.2.0' - - 'bioconductor-phastcons100way.ucsc.hg38 >=3.7.0,<3.8.0' - - 'bioconductor-rtracklayer >=1.42.0,<1.43.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' - - 'bioconductor-tfbstools >=1.20.0,<1.21.0' + - 'bioconductor-genomicranges >=1.36.0,<1.37.0' + - 'bioconductor-genomicscores >=1.8.0,<1.9.0' + - 'bioconductor-gviz >=1.28.0,<1.29.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-jaspar2018 >=1.2.0,<1.3.0' + - 'bioconductor-phastcons100way.ucsc.hg38 >=3.8.0,<3.9.0' + - 'bioconductor-rtracklayer >=1.44.0,<1.45.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' + - 'bioconductor-tfbstools >=1.22.0,<1.23.0' - r-base - 'r-dplyr >=0.7.6' - 'r-purrr >=0.2.5' diff --git a/recipes/bioconductor-prince/build.sh b/recipes/bioconductor-prince/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-prince/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-prince/meta.yaml b/recipes/bioconductor-prince/meta.yaml new file mode 100644 index 0000000000000..a4f37f42b63b8 --- /dev/null +++ b/recipes/bioconductor-prince/meta.yaml @@ -0,0 +1,65 @@ +{% set version = "1.0.0" %} +{% set name = "PrInCE" %} +{% set bioc = "3.9" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: 33b3a94e8da1142de863250abd031484 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: BiocStyle, knitr, rmarkdown +requirements: + host: + - 'bioconductor-biobase >=2.44.0,<2.45.0' + - 'bioconductor-msnbase >=2.10.0,<2.11.0' + - r-base + - 'r-dplyr >=0.7.4' + - 'r-forecast >=8.2' + - 'r-hmisc >=4.0' + - 'r-liblinear >=2.10-8' + - 'r-magrittr >=1.5' + - 'r-naivebayes >=0.9.1' + - 'r-progress >=1.1.2' + - 'r-purrr >=0.2.4' + - 'r-ranger >=0.8.0' + - 'r-rdpack >=0.7' + - 'r-robustbase >=0.92-7' + - 'r-speedglm >=0.3-2' + - 'r-tester >=0.1.7' + - 'r-tidyr >=0.7.2' + run: + - 'bioconductor-biobase >=2.44.0,<2.45.0' + - 'bioconductor-msnbase >=2.10.0,<2.11.0' + - r-base + - 'r-dplyr >=0.7.4' + - 'r-forecast >=8.2' + - 'r-hmisc >=4.0' + - 'r-liblinear >=2.10-8' + - 'r-magrittr >=1.5' + - 'r-naivebayes >=0.9.1' + - 'r-progress >=1.1.2' + - 'r-purrr >=0.2.4' + - 'r-ranger >=0.8.0' + - 'r-rdpack >=0.7' + - 'r-robustbase >=0.92-7' + - 'r-speedglm >=0.3-2' + - 'r-tester >=0.1.7' + - 'r-tidyr >=0.7.2' +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: 'GPL-3 + file LICENSE' + summary: 'PrInCE (Predicting Interactomes from Co-Elution) uses a naive Bayes classifier trained on dataset-derived features to recover protein-protein interactions from co-elution chromatogram profiles. This package contains the R implementation of PrInCE.' + diff --git a/recipes/bioconductor-prize/meta.yaml b/recipes/bioconductor-prize/meta.yaml index 2acb318159ae8..d14063f136d0c 100644 --- a/recipes/bioconductor-prize/meta.yaml +++ b/recipes/bioconductor-prize/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.12.1" %} +{% set version = "1.14.0" %} {% set name = "Prize" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 06e1d7184b6e71370bb2784b9c94e615 + md5: e9227d878c72a4eb9b1a2757566f0755 build: number: 0 rpaths: diff --git a/recipes/bioconductor-probamr/meta.yaml b/recipes/bioconductor-probamr/meta.yaml index 59852d0bb5991..480106fc11ef5 100644 --- a/recipes/bioconductor-probamr/meta.yaml +++ b/recipes/bioconductor-probamr/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.16.0" %} +{% set version = "1.18.0" %} {% set name = "proBAMr" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: cb59e471a54b77323e3d8aa981f253b4 + md5: e6c06b72cd2b79acefe5811234f8b0d4 build: number: 0 rpaths: @@ -20,20 +20,20 @@ build: # Suggests: RUnit, BiocGenerics requirements: host: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' - - 'bioconductor-biostrings >=2.50.0,<2.51.0' - - 'bioconductor-genomicfeatures >=1.34.0,<1.35.0' - - 'bioconductor-genomicranges >=1.34.0,<1.35.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-rtracklayer >=1.42.0,<1.43.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' + - 'bioconductor-biostrings >=2.52.0,<2.53.0' + - 'bioconductor-genomicfeatures >=1.36.0,<1.37.0' + - 'bioconductor-genomicranges >=1.36.0,<1.37.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-rtracklayer >=1.44.0,<1.45.0' - r-base run: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' - - 'bioconductor-biostrings >=2.50.0,<2.51.0' - - 'bioconductor-genomicfeatures >=1.34.0,<1.35.0' - - 'bioconductor-genomicranges >=1.34.0,<1.35.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-rtracklayer >=1.42.0,<1.43.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' + - 'bioconductor-biostrings >=2.52.0,<2.53.0' + - 'bioconductor-genomicfeatures >=1.36.0,<1.37.0' + - 'bioconductor-genomicranges >=1.36.0,<1.37.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-rtracklayer >=1.44.0,<1.45.0' - r-base test: commands: diff --git a/recipes/bioconductor-probatch/build.sh b/recipes/bioconductor-probatch/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-probatch/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-probatch/meta.yaml b/recipes/bioconductor-probatch/meta.yaml new file mode 100644 index 0000000000000..0915beb3c19aa --- /dev/null +++ b/recipes/bioconductor-probatch/meta.yaml @@ -0,0 +1,81 @@ +{% set version = "1.0.0" %} +{% set name = "proBatch" %} +{% set bioc = "3.9" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: 44e29aaeccc43d5683608c7a5acb32ea +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: knitr, rmarkdown, devtools, roxygen2, testthat +requirements: + host: + - 'bioconductor-biobase >=2.44.0,<2.45.0' + - 'bioconductor-preprocesscore >=1.46.0,<1.47.0' + - 'bioconductor-pvca >=1.24.0,<1.25.0' + - 'bioconductor-sva >=3.32.0,<3.33.0' + - r-base + - r-corrplot + - r-data.table + - r-dplyr + - r-ggfortify + - r-ggplot2 + - r-lazyeval + - r-lubridate + - r-magrittr + - r-pheatmap + - r-purrr + - r-rcolorbrewer + - r-readr + - r-reshape2 + - r-rlang + - r-scales + - r-tibble + - r-tidyr + - r-viridis + - r-wesanderson + - r-wgcna + run: + - 'bioconductor-biobase >=2.44.0,<2.45.0' + - 'bioconductor-preprocesscore >=1.46.0,<1.47.0' + - 'bioconductor-pvca >=1.24.0,<1.25.0' + - 'bioconductor-sva >=3.32.0,<3.33.0' + - r-base + - r-corrplot + - r-data.table + - r-dplyr + - r-ggfortify + - r-ggplot2 + - r-lazyeval + - r-lubridate + - r-magrittr + - r-pheatmap + - r-purrr + - r-rcolorbrewer + - r-readr + - r-reshape2 + - r-rlang + - r-scales + - r-tibble + - r-tidyr + - r-viridis + - r-wesanderson + - r-wgcna +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: GPL-3 + summary: 'The proBatch package facilitates batch effects analysis and correction in high-thoughput experiments. It was developed primarily for mass-spectrometry proteomics (DIA/SWATH), but could also be applicable to most omic data with minor adaptations. The package contains functions for diagnostics (proteome/genome-wide and feature-level), correction (normalization and batch effects correction) and quality control. Non-linear fitting based approaches were also included to deal with complex, mass spectrometry-specific signal drifts.' + diff --git a/recipes/bioconductor-process/meta.yaml b/recipes/bioconductor-process/meta.yaml index cbf8122b1ff0a..eb54aefe73cd4 100644 --- a/recipes/bioconductor-process/meta.yaml +++ b/recipes/bioconductor-process/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.58.1" %} +{% set version = "1.60.0" %} {% set name = "PROcess" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: a5b428d7ac389fb7f808711e6012b880 + md5: 491d0d87b6f78d90fb63e97754e31e21 build: number: 0 rpaths: @@ -19,10 +19,10 @@ build: noarch: generic requirements: host: - - 'bioconductor-icens >=1.54.0,<1.55.0' + - 'bioconductor-icens >=1.56.0,<1.57.0' - r-base run: - - 'bioconductor-icens >=1.54.0,<1.55.0' + - 'bioconductor-icens >=1.56.0,<1.57.0' - r-base test: commands: diff --git a/recipes/bioconductor-procoil/meta.yaml b/recipes/bioconductor-procoil/meta.yaml index f7fae1f341037..1e4e10076ae40 100644 --- a/recipes/bioconductor-procoil/meta.yaml +++ b/recipes/bioconductor-procoil/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "2.10.0" %} +{% set version = "2.12.0" %} {% set name = "procoil" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 270f49603fd44f3062e45a3af865959a + md5: 728915d86c49b2a50f60bc7b44f5fa2c build: number: 0 rpaths: @@ -20,14 +20,14 @@ build: # Suggests: knitr requirements: host: - - 'bioconductor-biostrings >=2.50.0,<2.51.0' - - 'bioconductor-kebabs >=1.16.0,<1.17.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-biostrings >=2.52.0,<2.53.0' + - 'bioconductor-kebabs >=1.18.0,<1.19.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' - r-base run: - - 'bioconductor-biostrings >=2.50.0,<2.51.0' - - 'bioconductor-kebabs >=1.16.0,<1.17.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-biostrings >=2.52.0,<2.53.0' + - 'bioconductor-kebabs >=1.18.0,<1.19.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' - r-base test: commands: diff --git a/recipes/bioconductor-prodata/meta.yaml b/recipes/bioconductor-prodata/meta.yaml index cca6ef858e145..7529fa8345b23 100644 --- a/recipes/bioconductor-prodata/meta.yaml +++ b/recipes/bioconductor-prodata/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.20.0" %} +{% set version = "1.22.0" %} {% set name = "ProData" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 3c3b90d81fe5c686b86ea33d8d4c15e8 + md5: 1f8da0ea4c4c1ec424901ab1e4246b48 build: number: 0 rpaths: @@ -19,12 +19,12 @@ build: noarch: generic requirements: host: - - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' - r-base run: - - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-prodata/post-link.sh b/recipes/bioconductor-prodata/post-link.sh index 36f2d7e580d73..9e26667bf2db6 100644 --- a/recipes/bioconductor-prodata/post-link.sh +++ b/recipes/bioconductor-prodata/post-link.sh @@ -1,11 +1,11 @@ #!/bin/bash -FN="ProData_1.20.0.tar.gz" +FN="ProData_1.22.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/experiment/src/contrib/ProData_1.20.0.tar.gz" - "https://bioarchive.galaxyproject.org/ProData_1.20.0.tar.gz" - "https://depot.galaxyproject.org/software/bioconductor-prodata/bioconductor-prodata_1.20.0_src_all.tar.gz" + "https://bioconductor.org/packages/3.9/data/experiment/src/contrib/ProData_1.22.0.tar.gz" + "https://bioarchive.galaxyproject.org/ProData_1.22.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-prodata/bioconductor-prodata_1.22.0_src_all.tar.gz" ) -MD5="3c3b90d81fe5c686b86ea33d8d4c15e8" +MD5="1f8da0ea4c4c1ec424901ab1e4246b48" # Use a staging area in the conda dir rather than temp dirs, both to avoid # permission issues as well as to have things downloaded in a predictable @@ -16,7 +16,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-profia/meta.yaml b/recipes/bioconductor-profia/meta.yaml index db7dca59c7139..8ad4b4f51ccee 100644 --- a/recipes/bioconductor-profia/meta.yaml +++ b/recipes/bioconductor-profia/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.8.1" %} +{% set version = "1.10.0" %} {% set name = "proFIA" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 1b956906a15daabb5dee28cc520d1aa4 + md5: dbd75f01b57a3e7dd6116f621d4a4cfa build: number: 0 rpaths: @@ -19,19 +19,19 @@ build: # Suggests: BiocGenerics, plasFIA, knitr, requirements: host: - - 'bioconductor-biobase >=2.42.0,<2.43.0' - - 'bioconductor-biocparallel >=1.16.0,<1.17.0' - - 'bioconductor-ropls >=1.14.0,<1.15.0' - - 'bioconductor-xcms >=3.4.0,<3.5.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' + - 'bioconductor-biocparallel >=1.18.0,<1.19.0' + - 'bioconductor-ropls >=1.16.0,<1.17.0' + - 'bioconductor-xcms >=3.6.0,<3.7.0' - r-base - r-minpack.lm - r-missforest - r-pracma run: - - 'bioconductor-biobase >=2.42.0,<2.43.0' - - 'bioconductor-biocparallel >=1.16.0,<1.17.0' - - 'bioconductor-ropls >=1.14.0,<1.15.0' - - 'bioconductor-xcms >=3.4.0,<3.5.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' + - 'bioconductor-biocparallel >=1.18.0,<1.19.0' + - 'bioconductor-ropls >=1.16.0,<1.17.0' + - 'bioconductor-xcms >=3.6.0,<3.7.0' - r-base - r-minpack.lm - r-missforest diff --git a/recipes/bioconductor-profileplyr/build.sh b/recipes/bioconductor-profileplyr/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-profileplyr/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-profileplyr/meta.yaml b/recipes/bioconductor-profileplyr/meta.yaml new file mode 100644 index 0000000000000..f88a04417ab12 --- /dev/null +++ b/recipes/bioconductor-profileplyr/meta.yaml @@ -0,0 +1,87 @@ +{% set version = "1.0.0" %} +{% set name = "profileplyr" %} +{% set bioc = "3.9" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + md5: 7f625ec51b41263e161afae241575bc4 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: BiocStyle, testthat, knitr, rmarkdown, png, Rsamtools, ggplot2 +requirements: + host: + - 'bioconductor-biocgenerics >=0.30.0,<0.31.0' + - 'bioconductor-biocparallel >=1.18.0,<1.19.0' + - 'bioconductor-chipseeker >=1.20.0,<1.21.0' + - 'bioconductor-complexheatmap >=2.0.0,<2.1.0' + - 'bioconductor-enrichedheatmap >=1.14.0,<1.15.0' + - 'bioconductor-genomeinfodb >=1.20.0,<1.21.0' + - 'bioconductor-genomicfeatures >=1.36.0,<1.37.0' + - 'bioconductor-genomicranges >=1.36.0,<1.37.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-org.hs.eg.db >=3.8.0,<3.9.0' + - 'bioconductor-org.mm.eg.db >=3.8.0,<3.9.0' + - 'bioconductor-rgreat >=1.16.0,<1.17.0' + - 'bioconductor-rtracklayer >=1.44.0,<1.45.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' + - 'bioconductor-soggi >=1.16.0,<1.17.0' + - 'bioconductor-summarizedexperiment >=1.14.0,<1.15.0' + - 'bioconductor-txdb.hsapiens.ucsc.hg19.knowngene >=3.2.0,<3.3.0' + - 'bioconductor-txdb.hsapiens.ucsc.hg38.knowngene >=3.4.0,<3.5.0' + - 'bioconductor-txdb.mmusculus.ucsc.mm10.knowngene >=3.4.0,<3.5.0' + - 'bioconductor-txdb.mmusculus.ucsc.mm9.knowngene >=3.2.0,<3.3.0' + - r-base + - r-circlize + - r-dplyr + - r-magrittr + - r-pheatmap + - r-r.utils + - r-rjson + - r-tidyr + run: + - 'bioconductor-biocgenerics >=0.30.0,<0.31.0' + - 'bioconductor-biocparallel >=1.18.0,<1.19.0' + - 'bioconductor-chipseeker >=1.20.0,<1.21.0' + - 'bioconductor-complexheatmap >=2.0.0,<2.1.0' + - 'bioconductor-enrichedheatmap >=1.14.0,<1.15.0' + - 'bioconductor-genomeinfodb >=1.20.0,<1.21.0' + - 'bioconductor-genomicfeatures >=1.36.0,<1.37.0' + - 'bioconductor-genomicranges >=1.36.0,<1.37.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-org.hs.eg.db >=3.8.0,<3.9.0' + - 'bioconductor-org.mm.eg.db >=3.8.0,<3.9.0' + - 'bioconductor-rgreat >=1.16.0,<1.17.0' + - 'bioconductor-rtracklayer >=1.44.0,<1.45.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' + - 'bioconductor-soggi >=1.16.0,<1.17.0' + - 'bioconductor-summarizedexperiment >=1.14.0,<1.15.0' + - 'bioconductor-txdb.hsapiens.ucsc.hg19.knowngene >=3.2.0,<3.3.0' + - 'bioconductor-txdb.hsapiens.ucsc.hg38.knowngene >=3.4.0,<3.5.0' + - 'bioconductor-txdb.mmusculus.ucsc.mm10.knowngene >=3.4.0,<3.5.0' + - 'bioconductor-txdb.mmusculus.ucsc.mm9.knowngene >=3.2.0,<3.3.0' + - r-base + - r-circlize + - r-dplyr + - r-magrittr + - r-pheatmap + - r-r.utils + - r-rjson + - r-tidyr +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: 'GPL (>= 3)' + summary: 'Quick and straighforward visualization of read signal over genomic intervals is key for generating hypotheses from sequencing data sets (e.g. ChIP-seq, ATAC-seq, bisulfite/methyl-seq). Many tools both inside and outside of R and Bioconductor are available to explore these types of data, and they typically start with a bigWig or BAM file and end with some representation of the signal (e.g. heatmap). profileplyr leverages many Bioconductor tools to allow for both flexibility and additional functionality in workflows that end with visualization of the read signal.' + diff --git a/recipes/bioconductor-profilescoredist/meta.yaml b/recipes/bioconductor-profilescoredist/meta.yaml index bd7dadf5fae7f..09b5ec5dfcd20 100644 --- a/recipes/bioconductor-profilescoredist/meta.yaml +++ b/recipes/bioconductor-profilescoredist/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.10.0" %} +{% set version = "1.12.0" %} {% set name = "profileScoreDist" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: c1043816d33dad80676d2e4b4b675a82 + md5: a188b68fbaee0c0d2f85da954c5ae4e6 build: number: 0 rpaths: @@ -19,11 +19,11 @@ build: # Suggests: BiocStyle, knitr, MotifDb requirements: host: - - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' + - 'bioconductor-biocgenerics >=0.30.0,<0.31.0' - r-base - r-rcpp run: - - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' + - 'bioconductor-biocgenerics >=0.30.0,<0.31.0' - r-base - r-rcpp build: diff --git a/recipes/bioconductor-progeny/meta.yaml b/recipes/bioconductor-progeny/meta.yaml index 28ac037e8aa1f..8ba6f185f90a9 100644 --- a/recipes/bioconductor-progeny/meta.yaml +++ b/recipes/bioconductor-progeny/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.4.1" %} +{% set version = "1.6.0" %} {% set name = "progeny" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - sha256: 67de43d7c4c4147e5326b751c53a1da60814bb571f45f57996058cf8574ee00b + md5: e0365039dc839c386095ce036ebf39d6 build: number: 0 rpaths: @@ -20,10 +20,10 @@ build: # Suggests: airway, biomaRt, BiocFileCache, broom, DESeq2, dplyr, knitr, readr, readxl requirements: host: - - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' - r-base run: - - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' - r-base test: commands: diff --git a/recipes/bioconductor-projectr/build.sh b/recipes/bioconductor-projectr/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-projectr/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-projectr/meta.yaml b/recipes/bioconductor-projectr/meta.yaml new file mode 100644 index 0000000000000..30abe41e05de1 --- /dev/null +++ b/recipes/bioconductor-projectr/meta.yaml @@ -0,0 +1,43 @@ +{% set version = "1.0.0" %} +{% set name = "projectR" %} +{% set bioc = "3.9" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: d483de0763d074a224b9189620ad65a8 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: BiocStyle, gridExtra, grid, testthat, devtools, knitr, rmarkdown, ComplexHeatmap, viridis, ggplot2 +requirements: + host: + - 'bioconductor-cogaps >=3.4.0,<3.5.0' + - 'bioconductor-limma >=3.40.0,<3.41.0' + - r-base + - r-cluster + - r-nmf + - r-rocr + run: + - 'bioconductor-cogaps >=3.4.0,<3.5.0' + - 'bioconductor-limma >=3.40.0,<3.41.0' + - r-base + - r-cluster + - r-nmf + - r-rocr +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: 'GPL (==2)' + summary: 'Functions for the projection of data into the spaces defined by PCA, CoGAPS, NMF, correlation, and clustering.' + diff --git a/recipes/bioconductor-proloc/meta.yaml b/recipes/bioconductor-proloc/meta.yaml index 2baa73ea17ded..6db0d37b4fdbb 100644 --- a/recipes/bioconductor-proloc/meta.yaml +++ b/recipes/bioconductor-proloc/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.22.1" %} +{% set version = "1.24.0" %} {% set name = "pRoloc" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,21 +10,21 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 6a37b5fbf55fef04d7e6c044b90d4c2f + md5: a4215d6b672595d3471574956597ac2e build: number: 0 rpaths: - lib/R/lib/ - lib/ -# Suggests: testthat, rmarkdown, pRolocdata (>= 1.9.4), roxygen2, synapter, xtable, rgl, BiocStyle (>= 2.5.19), hpar (>= 1.15.3), dplyr, GO.db, AnnotationDbi, Rtsne (>= 0.13), nipals +# Suggests: testthat, rmarkdown, pRolocdata (>= 1.9.4), roxygen2, synapter, xtable, rgl, BiocStyle (>= 2.5.19), hpar (>= 1.15.3), dplyr, GO.db, AnnotationDbi, Rtsne (>= 0.13), nipals, reshape requirements: host: - - 'bioconductor-biobase >=2.42.0,<2.43.0' - - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' - - 'bioconductor-biocparallel >=1.16.0,<1.17.0' - - 'bioconductor-biomart >=2.38.0,<2.39.0' - - 'bioconductor-mlinterfaces >=1.62.0,<1.63.0' - - 'bioconductor-msnbase >=2.8.0,<2.9.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' + - 'bioconductor-biocgenerics >=0.30.0,<0.31.0' + - 'bioconductor-biocparallel >=1.18.0,<1.19.0' + - 'bioconductor-biomart >=2.40.0,<2.41.0' + - 'bioconductor-mlinterfaces >=1.64.0,<1.65.0' + - 'bioconductor-msnbase >=2.10.0,<2.11.0' - r-base - r-caret - r-class @@ -53,12 +53,12 @@ requirements: - r-sampling - r-scales run: - - 'bioconductor-biobase >=2.42.0,<2.43.0' - - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' - - 'bioconductor-biocparallel >=1.16.0,<1.17.0' - - 'bioconductor-biomart >=2.38.0,<2.39.0' - - 'bioconductor-mlinterfaces >=1.62.0,<1.63.0' - - 'bioconductor-msnbase >=2.8.0,<2.9.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' + - 'bioconductor-biocgenerics >=0.30.0,<0.31.0' + - 'bioconductor-biocparallel >=1.18.0,<1.19.0' + - 'bioconductor-biomart >=2.40.0,<2.41.0' + - 'bioconductor-mlinterfaces >=1.64.0,<1.65.0' + - 'bioconductor-msnbase >=2.10.0,<2.11.0' - r-base - r-caret - r-class diff --git a/recipes/bioconductor-prolocdata/meta.yaml b/recipes/bioconductor-prolocdata/meta.yaml index 4637e9a6f0c9d..feb38641ab4cc 100644 --- a/recipes/bioconductor-prolocdata/meta.yaml +++ b/recipes/bioconductor-prolocdata/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.20.0" %} +{% set version = "1.22.0" %} {% set name = "pRolocdata" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: a251f615e1307eb3129875b823c2ed22 + md5: 1234945e2ea61bb519cdfa9d1e712b63 build: number: 0 rpaths: @@ -20,14 +20,14 @@ build: # Suggests: pRoloc (>= 1.13.8), testthat requirements: host: - - 'bioconductor-biobase >=2.42.0,<2.43.0' - - 'bioconductor-msnbase >=2.8.0,<2.9.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' + - 'bioconductor-msnbase >=2.10.0,<2.11.0' - r-base run: - - 'bioconductor-biobase >=2.42.0,<2.43.0' - - 'bioconductor-msnbase >=2.8.0,<2.9.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' + - 'bioconductor-msnbase >=2.10.0,<2.11.0' - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-prolocdata/post-link.sh b/recipes/bioconductor-prolocdata/post-link.sh index 3bbb38c4fa3aa..a0bd5d3c2647d 100644 --- a/recipes/bioconductor-prolocdata/post-link.sh +++ b/recipes/bioconductor-prolocdata/post-link.sh @@ -1,11 +1,11 @@ #!/bin/bash -FN="pRolocdata_1.20.0.tar.gz" +FN="pRolocdata_1.22.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/experiment/src/contrib/pRolocdata_1.20.0.tar.gz" - "https://bioarchive.galaxyproject.org/pRolocdata_1.20.0.tar.gz" - "https://depot.galaxyproject.org/software/bioconductor-prolocdata/bioconductor-prolocdata_1.20.0_src_all.tar.gz" + "https://bioconductor.org/packages/3.9/data/experiment/src/contrib/pRolocdata_1.22.0.tar.gz" + "https://bioarchive.galaxyproject.org/pRolocdata_1.22.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-prolocdata/bioconductor-prolocdata_1.22.0_src_all.tar.gz" ) -MD5="a251f615e1307eb3129875b823c2ed22" +MD5="1234945e2ea61bb519cdfa9d1e712b63" # Use a staging area in the conda dir rather than temp dirs, both to avoid # permission issues as well as to have things downloaded in a predictable @@ -16,7 +16,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-prolocgui/meta.yaml b/recipes/bioconductor-prolocgui/meta.yaml index 7e9b93437bb5f..08c86e29cf7d7 100644 --- a/recipes/bioconductor-prolocgui/meta.yaml +++ b/recipes/bioconductor-prolocgui/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.16.0" %} +{% set version = "1.18.0" %} {% set name = "pRolocGUI" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 00b70d7e6c984f287bfbff80c165e87f + md5: b399020af3773548f3e8e4a4375058ec build: number: 0 rpaths: @@ -20,9 +20,9 @@ build: # Suggests: pRolocdata, knitr, BiocStyle (>= 2.5.19), rmarkdown requirements: host: - - 'bioconductor-biobase >=2.42.0,<2.43.0' - - 'bioconductor-msnbase >=2.8.0,<2.9.0' - - 'bioconductor-proloc >=1.22.0,<1.23.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' + - 'bioconductor-msnbase >=2.10.0,<2.11.0' + - 'bioconductor-proloc >=1.24.0,<1.25.0' - r-base - r-dplyr - 'r-dt >=0.1.40' @@ -30,9 +30,9 @@ requirements: - r-scales - 'r-shiny >=0.9.1' run: - - 'bioconductor-biobase >=2.42.0,<2.43.0' - - 'bioconductor-msnbase >=2.8.0,<2.9.0' - - 'bioconductor-proloc >=1.22.0,<1.23.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' + - 'bioconductor-msnbase >=2.10.0,<2.11.0' + - 'bioconductor-proloc >=1.24.0,<1.25.0' - r-base - r-dplyr - 'r-dt >=0.1.40' diff --git a/recipes/bioconductor-promise/meta.yaml b/recipes/bioconductor-promise/meta.yaml index 9b3780be4d262..30a330ab2abb4 100644 --- a/recipes/bioconductor-promise/meta.yaml +++ b/recipes/bioconductor-promise/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.34.0" %} +{% set version = "1.36.0" %} {% set name = "PROMISE" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 1551860b6a6c1cb1e2e1c2eca0188269 + md5: deab13ebe8ec088e9585aa2291557a4b build: number: 0 rpaths: @@ -19,12 +19,12 @@ build: noarch: generic requirements: host: - - 'bioconductor-biobase >=2.42.0,<2.43.0' - - 'bioconductor-gseabase >=1.44.0,<1.45.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' + - 'bioconductor-gseabase >=1.46.0,<1.47.0' - r-base run: - - 'bioconductor-biobase >=2.42.0,<2.43.0' - - 'bioconductor-gseabase >=1.44.0,<1.45.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' + - 'bioconductor-gseabase >=1.46.0,<1.47.0' - r-base test: commands: diff --git a/recipes/bioconductor-proper/meta.yaml b/recipes/bioconductor-proper/meta.yaml index 945d865c02c3b..975b613486ee6 100644 --- a/recipes/bioconductor-proper/meta.yaml +++ b/recipes/bioconductor-proper/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.14.1" %} +{% set version = "1.16.0" %} {% set name = "PROPER" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 0c319501b8950f1968169b99f843db64 + md5: f1e52dedad4eca5991a82a7f828ddc18 build: number: 0 rpaths: @@ -20,10 +20,10 @@ build: # Suggests: BiocStyle,DESeq,DSS,knitr requirements: host: - - 'bioconductor-edger >=3.24.0,<3.25.0' + - 'bioconductor-edger >=3.26.0,<3.27.0' - r-base run: - - 'bioconductor-edger >=3.24.0,<3.25.0' + - 'bioconductor-edger >=3.26.0,<3.27.0' - r-base test: commands: diff --git a/recipes/bioconductor-props/meta.yaml b/recipes/bioconductor-props/meta.yaml index 9840ef878d91d..73eb7f0801982 100644 --- a/recipes/bioconductor-props/meta.yaml +++ b/recipes/bioconductor-props/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.4.0" %} +{% set version = "1.6.0" %} {% set name = "PROPS" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: e52f805ee22719f72202aa8768657455 + md5: 6883deadd0520221e162f777a595af90 build: number: 0 rpaths: @@ -20,14 +20,14 @@ build: # Suggests: knitr, rmarkdown requirements: host: - - 'bioconductor-biobase >=2.42.0,<2.43.0' - - 'bioconductor-sva >=3.30.0,<3.31.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' + - 'bioconductor-sva >=3.32.0,<3.33.0' - r-base - r-bnlearn - r-reshape2 run: - - 'bioconductor-biobase >=2.42.0,<2.43.0' - - 'bioconductor-sva >=3.30.0,<3.31.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' + - 'bioconductor-sva >=3.32.0,<3.33.0' - r-base - r-bnlearn - r-reshape2 diff --git a/recipes/bioconductor-prostar/meta.yaml b/recipes/bioconductor-prostar/meta.yaml index 4b6d47905d005..aac91a80242b5 100644 --- a/recipes/bioconductor-prostar/meta.yaml +++ b/recipes/bioconductor-prostar/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.14.8" %} +{% set version = "1.16.0" %} {% set name = "Prostar" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 013d81f17cd080a4491b1b49cb6f5968 + md5: 8b2769defdfd70762bd6ce3204625b5c build: number: 0 rpaths: @@ -20,8 +20,8 @@ build: # Suggests: BiocStyle, testthat requirements: host: - - 'bioconductor-dapar >=1.14.0,<1.15.0' - - 'bioconductor-dapardata >=1.12.0,<1.13.0' + - 'bioconductor-dapar >=1.16.0,<1.17.0' + - 'bioconductor-dapardata >=1.14.0,<1.15.0' - r-base - r-biocmanager - r-colourpicker @@ -47,8 +47,8 @@ requirements: - r-webshot - r-xml run: - - 'bioconductor-dapar >=1.14.0,<1.15.0' - - 'bioconductor-dapardata >=1.12.0,<1.13.0' + - 'bioconductor-dapar >=1.16.0,<1.17.0' + - 'bioconductor-dapardata >=1.14.0,<1.15.0' - r-base - r-biocmanager - r-colourpicker diff --git a/recipes/bioconductor-prostatecancercamcap/meta.yaml b/recipes/bioconductor-prostatecancercamcap/meta.yaml index d122cb979e28d..ffcb995de53d0 100644 --- a/recipes/bioconductor-prostatecancercamcap/meta.yaml +++ b/recipes/bioconductor-prostatecancercamcap/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.10.0" %} +{% set version = "1.12.0" %} {% set name = "prostateCancerCamcap" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: bd8f6f0d10eaeebeb45ec56d911ee8d3 + md5: 2f595f639b4adeb9a7a9c7ac8326840e build: number: 0 rpaths: @@ -20,12 +20,12 @@ build: # Suggests: GEOquery requirements: host: - - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' - r-base run: - - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-prostatecancercamcap/post-link.sh b/recipes/bioconductor-prostatecancercamcap/post-link.sh index 573236d860378..51243700aeecb 100644 --- a/recipes/bioconductor-prostatecancercamcap/post-link.sh +++ b/recipes/bioconductor-prostatecancercamcap/post-link.sh @@ -1,11 +1,11 @@ #!/bin/bash -FN="prostateCancerCamcap_1.10.0.tar.gz" +FN="prostateCancerCamcap_1.12.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/experiment/src/contrib/prostateCancerCamcap_1.10.0.tar.gz" - "https://bioarchive.galaxyproject.org/prostateCancerCamcap_1.10.0.tar.gz" - "https://depot.galaxyproject.org/software/bioconductor-prostatecancercamcap/bioconductor-prostatecancercamcap_1.10.0_src_all.tar.gz" + "https://bioconductor.org/packages/3.9/data/experiment/src/contrib/prostateCancerCamcap_1.12.0.tar.gz" + "https://bioarchive.galaxyproject.org/prostateCancerCamcap_1.12.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-prostatecancercamcap/bioconductor-prostatecancercamcap_1.12.0_src_all.tar.gz" ) -MD5="bd8f6f0d10eaeebeb45ec56d911ee8d3" +MD5="2f595f639b4adeb9a7a9c7ac8326840e" # Use a staging area in the conda dir rather than temp dirs, both to avoid # permission issues as well as to have things downloaded in a predictable @@ -16,7 +16,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-prostatecancergrasso/meta.yaml b/recipes/bioconductor-prostatecancergrasso/meta.yaml index 4abf92a20e8a0..c85859dee9e8f 100644 --- a/recipes/bioconductor-prostatecancergrasso/meta.yaml +++ b/recipes/bioconductor-prostatecancergrasso/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.10.0" %} +{% set version = "1.12.0" %} {% set name = "prostateCancerGrasso" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 91b4dadaaa9d775625c625dc7763b6bd + md5: 6bf3e5b205d0f15bd2ffb93d87029a16 build: number: 0 rpaths: @@ -20,12 +20,12 @@ build: # Suggests: GEOquery requirements: host: - - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' - r-base run: - - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-prostatecancergrasso/post-link.sh b/recipes/bioconductor-prostatecancergrasso/post-link.sh index cfe865f958b94..2602f09c046f7 100644 --- a/recipes/bioconductor-prostatecancergrasso/post-link.sh +++ b/recipes/bioconductor-prostatecancergrasso/post-link.sh @@ -1,11 +1,11 @@ #!/bin/bash -FN="prostateCancerGrasso_1.10.0.tar.gz" +FN="prostateCancerGrasso_1.12.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/experiment/src/contrib/prostateCancerGrasso_1.10.0.tar.gz" - "https://bioarchive.galaxyproject.org/prostateCancerGrasso_1.10.0.tar.gz" - "https://depot.galaxyproject.org/software/bioconductor-prostatecancergrasso/bioconductor-prostatecancergrasso_1.10.0_src_all.tar.gz" + "https://bioconductor.org/packages/3.9/data/experiment/src/contrib/prostateCancerGrasso_1.12.0.tar.gz" + "https://bioarchive.galaxyproject.org/prostateCancerGrasso_1.12.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-prostatecancergrasso/bioconductor-prostatecancergrasso_1.12.0_src_all.tar.gz" ) -MD5="91b4dadaaa9d775625c625dc7763b6bd" +MD5="6bf3e5b205d0f15bd2ffb93d87029a16" # Use a staging area in the conda dir rather than temp dirs, both to avoid # permission issues as well as to have things downloaded in a predictable @@ -16,7 +16,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-prostatecancerstockholm/meta.yaml b/recipes/bioconductor-prostatecancerstockholm/meta.yaml index 1752a84d6b842..2c8cc4c8e018d 100644 --- a/recipes/bioconductor-prostatecancerstockholm/meta.yaml +++ b/recipes/bioconductor-prostatecancerstockholm/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.10.0" %} +{% set version = "1.12.0" %} {% set name = "prostateCancerStockholm" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: e76e4cf258025b14950fa035662b7be5 + md5: b800030dbb59abf7e492e57b6d063b89 build: number: 0 rpaths: @@ -20,12 +20,12 @@ build: # Suggests: GEOquery requirements: host: - - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' - r-base run: - - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-prostatecancerstockholm/post-link.sh b/recipes/bioconductor-prostatecancerstockholm/post-link.sh index 3c3a8b66c9b77..efdb3965f2d9d 100644 --- a/recipes/bioconductor-prostatecancerstockholm/post-link.sh +++ b/recipes/bioconductor-prostatecancerstockholm/post-link.sh @@ -1,11 +1,11 @@ #!/bin/bash -FN="prostateCancerStockholm_1.10.0.tar.gz" +FN="prostateCancerStockholm_1.12.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/experiment/src/contrib/prostateCancerStockholm_1.10.0.tar.gz" - "https://bioarchive.galaxyproject.org/prostateCancerStockholm_1.10.0.tar.gz" - "https://depot.galaxyproject.org/software/bioconductor-prostatecancerstockholm/bioconductor-prostatecancerstockholm_1.10.0_src_all.tar.gz" + "https://bioconductor.org/packages/3.9/data/experiment/src/contrib/prostateCancerStockholm_1.12.0.tar.gz" + "https://bioarchive.galaxyproject.org/prostateCancerStockholm_1.12.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-prostatecancerstockholm/bioconductor-prostatecancerstockholm_1.12.0_src_all.tar.gz" ) -MD5="e76e4cf258025b14950fa035662b7be5" +MD5="b800030dbb59abf7e492e57b6d063b89" # Use a staging area in the conda dir rather than temp dirs, both to avoid # permission issues as well as to have things downloaded in a predictable @@ -16,7 +16,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-prostatecancertaylor/meta.yaml b/recipes/bioconductor-prostatecancertaylor/meta.yaml index 85b27b10bfc09..e4dfa47905548 100644 --- a/recipes/bioconductor-prostatecancertaylor/meta.yaml +++ b/recipes/bioconductor-prostatecancertaylor/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.10.0" %} +{% set version = "1.12.0" %} {% set name = "prostateCancerTaylor" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 17217ff2d4cfaa8ff50b4fb5b1da2bf1 + md5: b95fe8d4d6ecd8bfbaeba23a0d53c829 build: number: 0 rpaths: @@ -20,12 +20,12 @@ build: # Suggests: GEOquery, org.Hs.eg.db requirements: host: - - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' - r-base run: - - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-prostatecancertaylor/post-link.sh b/recipes/bioconductor-prostatecancertaylor/post-link.sh index bfe5ae9d02094..cc52fb1afdec0 100644 --- a/recipes/bioconductor-prostatecancertaylor/post-link.sh +++ b/recipes/bioconductor-prostatecancertaylor/post-link.sh @@ -1,11 +1,11 @@ #!/bin/bash -FN="prostateCancerTaylor_1.10.0.tar.gz" +FN="prostateCancerTaylor_1.12.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/experiment/src/contrib/prostateCancerTaylor_1.10.0.tar.gz" - "https://bioarchive.galaxyproject.org/prostateCancerTaylor_1.10.0.tar.gz" - "https://depot.galaxyproject.org/software/bioconductor-prostatecancertaylor/bioconductor-prostatecancertaylor_1.10.0_src_all.tar.gz" + "https://bioconductor.org/packages/3.9/data/experiment/src/contrib/prostateCancerTaylor_1.12.0.tar.gz" + "https://bioarchive.galaxyproject.org/prostateCancerTaylor_1.12.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-prostatecancertaylor/bioconductor-prostatecancertaylor_1.12.0_src_all.tar.gz" ) -MD5="17217ff2d4cfaa8ff50b4fb5b1da2bf1" +MD5="b95fe8d4d6ecd8bfbaeba23a0d53c829" # Use a staging area in the conda dir rather than temp dirs, both to avoid # permission issues as well as to have things downloaded in a predictable @@ -16,7 +16,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-prostatecancervarambally/meta.yaml b/recipes/bioconductor-prostatecancervarambally/meta.yaml index 790e4d859c926..d648e19b21070 100644 --- a/recipes/bioconductor-prostatecancervarambally/meta.yaml +++ b/recipes/bioconductor-prostatecancervarambally/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.10.0" %} +{% set version = "1.12.0" %} {% set name = "prostateCancerVarambally" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,9 +10,9 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: c35f1f99121183a4332dbbc56a3de36b + md5: 47ad7ca82845afe9830f4cb1ad3f27c5 build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ @@ -20,12 +20,12 @@ build: # Suggests: GEOquery requirements: host: - - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' - r-base run: - - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-prostatecancervarambally/post-link.sh b/recipes/bioconductor-prostatecancervarambally/post-link.sh index b1fd0d87f9f75..6e226027a9e1f 100644 --- a/recipes/bioconductor-prostatecancervarambally/post-link.sh +++ b/recipes/bioconductor-prostatecancervarambally/post-link.sh @@ -1,11 +1,11 @@ #!/bin/bash -FN="prostateCancerVarambally_1.10.0.tar.gz" +FN="prostateCancerVarambally_1.12.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/experiment/src/contrib/prostateCancerVarambally_1.10.0.tar.gz" - "https://bioarchive.galaxyproject.org/prostateCancerVarambally_1.10.0.tar.gz" - "https://depot.galaxyproject.org/software/bioconductor-prostatecancervarambally/bioconductor-prostatecancervarambally_1.10.0_src_all.tar.gz" + "https://bioconductor.org/packages/3.9/data/experiment/src/contrib/prostateCancerVarambally_1.12.0.tar.gz" + "https://bioarchive.galaxyproject.org/prostateCancerVarambally_1.12.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-prostatecancervarambally/bioconductor-prostatecancervarambally_1.12.0_src_all.tar.gz" ) -MD5="c35f1f99121183a4332dbbc56a3de36b" +MD5="47ad7ca82845afe9830f4cb1ad3f27c5" # Use a staging area in the conda dir rather than temp dirs, both to avoid # permission issues as well as to have things downloaded in a predictable @@ -16,7 +16,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-proteinprofiles/meta.yaml b/recipes/bioconductor-proteinprofiles/meta.yaml index c47bcd74b0a2c..ba1f10c9dff2b 100644 --- a/recipes/bioconductor-proteinprofiles/meta.yaml +++ b/recipes/bioconductor-proteinprofiles/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.22.0" %} +{% set version = "1.24.0" %} {% set name = "proteinProfiles" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: b6351027c4dfef576a396a03a053c864 + md5: 1fa0f4040fd773e2b93b140148d2158e build: number: 0 rpaths: diff --git a/recipes/bioconductor-proteomicsannotationhubdata/meta.yaml b/recipes/bioconductor-proteomicsannotationhubdata/meta.yaml index 602b4f127ea9f..ab0ee9e4ac259 100644 --- a/recipes/bioconductor-proteomicsannotationhubdata/meta.yaml +++ b/recipes/bioconductor-proteomicsannotationhubdata/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.12.0" %} +{% set version = "1.14.0" %} {% set name = "ProteomicsAnnotationHubData" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: afbe09761bee9c27606041a3bef95f08 + md5: 64ec92b50e7965a36c7097de7a946814 build: number: 0 rpaths: @@ -20,24 +20,24 @@ build: # Suggests: knitr, BiocStyle, rmarkdown, testthat requirements: host: - - 'bioconductor-annotationhub >=2.14.0,<2.15.0' - - 'bioconductor-annotationhubdata >=1.12.0,<1.13.0' - - 'bioconductor-biobase >=2.42.0,<2.43.0' - - 'bioconductor-biostrings >=2.50.0,<2.51.0' - - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' - - 'bioconductor-msnbase >=2.8.0,<2.9.0' - - 'bioconductor-mzr >=2.16.0,<2.17.0' + - 'bioconductor-annotationhub >=2.16.0,<2.17.0' + - 'bioconductor-annotationhubdata >=1.14.0,<1.15.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' + - 'bioconductor-biostrings >=2.52.0,<2.53.0' + - 'bioconductor-genomeinfodb >=1.20.0,<1.21.0' + - 'bioconductor-msnbase >=2.10.0,<2.11.0' + - 'bioconductor-mzr >=2.18.0,<2.19.0' - r-base - r-biocmanager - r-rcurl run: - - 'bioconductor-annotationhub >=2.14.0,<2.15.0' - - 'bioconductor-annotationhubdata >=1.12.0,<1.13.0' - - 'bioconductor-biobase >=2.42.0,<2.43.0' - - 'bioconductor-biostrings >=2.50.0,<2.51.0' - - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' - - 'bioconductor-msnbase >=2.8.0,<2.9.0' - - 'bioconductor-mzr >=2.16.0,<2.17.0' + - 'bioconductor-annotationhub >=2.16.0,<2.17.0' + - 'bioconductor-annotationhubdata >=1.14.0,<1.15.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' + - 'bioconductor-biostrings >=2.52.0,<2.53.0' + - 'bioconductor-genomeinfodb >=1.20.0,<1.21.0' + - 'bioconductor-msnbase >=2.10.0,<2.11.0' + - 'bioconductor-mzr >=2.18.0,<2.19.0' - r-base - r-biocmanager - r-rcurl diff --git a/recipes/bioconductor-proteomm/meta.yaml b/recipes/bioconductor-proteomm/meta.yaml index 7f6d364c7ac29..030eb36c384f7 100644 --- a/recipes/bioconductor-proteomm/meta.yaml +++ b/recipes/bioconductor-proteomm/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.0.0" %} +{% set version = "1.2.0" %} {% set name = "ProteoMM" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 0fbe0a6120951bd31424c327b5448c0e + md5: 39878649f2415502a7e23ec22f732fa6 build: number: 0 rpaths: @@ -20,7 +20,7 @@ build: # Suggests: BiocStyle, knitr, rmarkdown requirements: host: - - 'bioconductor-biomart >=2.38.0,<2.39.0' + - 'bioconductor-biomart >=2.40.0,<2.41.0' - r-base - r-gdata - r-ggplot2 @@ -28,7 +28,7 @@ requirements: - r-gtools - r-matrixstats run: - - 'bioconductor-biomart >=2.38.0,<2.39.0' + - 'bioconductor-biomart >=2.40.0,<2.41.0' - r-base - r-gdata - r-ggplot2 diff --git a/recipes/bioconductor-proteoqc/meta.yaml b/recipes/bioconductor-proteoqc/meta.yaml index 6c413bf6452ca..9199c960912f2 100644 --- a/recipes/bioconductor-proteoqc/meta.yaml +++ b/recipes/bioconductor-proteoqc/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.18.1" %} +{% set version = "1.20.0" %} {% set name = "proteoQC" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: d8b9baf4fbe7c1615a3afc90c4dfbce5 + md5: d4e2ae9b7a83e7ca71e5f416a8b44d55 build: number: 0 rpaths: @@ -20,9 +20,9 @@ build: # Suggests: RforProteomics, knitr, BiocStyle, R.utils, RUnit,BiocGenerics requirements: host: - - 'bioconductor-msnbase >=2.8.0,<2.9.0' - - 'bioconductor-rpx >=1.18.0,<1.19.0' - - 'bioconductor-rtandem >=1.22.0,<1.23.0' + - 'bioconductor-msnbase >=2.10.0,<2.11.0' + - 'bioconductor-rpx >=1.20.0,<1.21.0' + - 'bioconductor-rtandem >=1.24.0,<1.25.0' - r-base - r-dplyr - r-ggplot2 @@ -36,9 +36,9 @@ requirements: - r-venndiagram - r-xml run: - - 'bioconductor-msnbase >=2.8.0,<2.9.0' - - 'bioconductor-rpx >=1.18.0,<1.19.0' - - 'bioconductor-rtandem >=1.22.0,<1.23.0' + - 'bioconductor-msnbase >=2.10.0,<2.11.0' + - 'bioconductor-rpx >=1.20.0,<1.21.0' + - 'bioconductor-rtandem >=1.24.0,<1.25.0' - r-base - r-dplyr - r-ggplot2 diff --git a/recipes/bioconductor-protgenerics/meta.yaml b/recipes/bioconductor-protgenerics/meta.yaml index 4884d7bd6b99e..b0d5902e2be9b 100644 --- a/recipes/bioconductor-protgenerics/meta.yaml +++ b/recipes/bioconductor-protgenerics/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.14.0" %} +{% set version = "1.16.0" %} {% set name = "ProtGenerics" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 837d899bc08e3518bf11a892f6b95e50 + md5: e2315c50a88dfbfb1c3c9232bde4f6ce build: number: 0 rpaths: diff --git a/recipes/bioconductor-psea/meta.yaml b/recipes/bioconductor-psea/meta.yaml index c37d1b687676b..5f28b36cb5cc0 100644 --- a/recipes/bioconductor-psea/meta.yaml +++ b/recipes/bioconductor-psea/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.16.0" %} +{% set version = "1.18.0" %} {% set name = "PSEA" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 70a53aecf51323ffa3ed319f0983e175 + md5: c33029fffd8410028cf1e4cf81a2259d build: number: 0 rpaths: @@ -20,11 +20,11 @@ build: # Suggests: BiocStyle requirements: host: - - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' - r-base - r-mass run: - - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' - r-base - r-mass test: diff --git a/recipes/bioconductor-psichomics/meta.yaml b/recipes/bioconductor-psichomics/meta.yaml index 2f5f21e9f0dd0..a7c20cd537bbc 100644 --- a/recipes/bioconductor-psichomics/meta.yaml +++ b/recipes/bioconductor-psichomics/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.8.1" %} +{% set version = "1.10.0" %} {% set name = "psichomics" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 348aac50fd1626722ed857f8d1d7b679 + md5: 87befda8f17860edd8944d4a467ca9fc build: number: 0 rpaths: @@ -19,11 +19,13 @@ build: # Suggests: testthat, knitr, parallel, devtools, rmarkdown, gplots, covr, car, rstudioapi requirements: host: - - 'bioconductor-annotationhub >=2.14.0,<2.15.0' - - 'bioconductor-edger >=3.24.0,<3.25.0' - - 'bioconductor-limma >=3.38.0,<3.39.0' - - 'bioconductor-recount >=1.8.0,<1.9.0' - - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' + - 'bioconductor-annotationhub >=2.16.0,<2.17.0' + - 'bioconductor-edger >=3.26.0,<3.27.0' + - 'bioconductor-limma >=3.40.0,<3.41.0' + - 'bioconductor-org.hs.eg.db >=3.8.0,<3.9.0' + - 'bioconductor-recount >=1.10.0,<1.11.0' + - 'bioconductor-summarizedexperiment >=1.14.0,<1.15.0' - r-base - r-cluster - r-colourpicker @@ -44,6 +46,7 @@ requirements: - r-plyr - r-r.utils - 'r-rcpp >=0.12.14' + - r-reshape2 - 'r-shiny >=1.0.3' - r-shinybs - r-shinyjs @@ -52,11 +55,13 @@ requirements: - r-xml - r-xtable run: - - 'bioconductor-annotationhub >=2.14.0,<2.15.0' - - 'bioconductor-edger >=3.24.0,<3.25.0' - - 'bioconductor-limma >=3.38.0,<3.39.0' - - 'bioconductor-recount >=1.8.0,<1.9.0' - - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' + - 'bioconductor-annotationhub >=2.16.0,<2.17.0' + - 'bioconductor-edger >=3.26.0,<3.27.0' + - 'bioconductor-limma >=3.40.0,<3.41.0' + - 'bioconductor-org.hs.eg.db >=3.8.0,<3.9.0' + - 'bioconductor-recount >=1.10.0,<1.11.0' + - 'bioconductor-summarizedexperiment >=1.14.0,<1.15.0' - r-base - r-cluster - r-colourpicker @@ -77,6 +82,7 @@ requirements: - r-plyr - r-r.utils - 'r-rcpp >=0.12.14' + - r-reshape2 - 'r-shiny >=1.0.3' - r-shinybs - r-shinyjs diff --git a/recipes/bioconductor-psicquic/meta.yaml b/recipes/bioconductor-psicquic/meta.yaml index 7b28acbb1244b..130be0ebee2bc 100644 --- a/recipes/bioconductor-psicquic/meta.yaml +++ b/recipes/bioconductor-psicquic/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.20.0" %} +{% set version = "1.22.0" %} {% set name = "PSICQUIC" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,9 +10,9 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 019a4417247c16e5ebcdf22ffac1c77b + md5: e3a6c1993c6cfdd38d53f1ba627b154c build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ @@ -20,17 +20,17 @@ build: # Suggests: org.Hs.eg.db requirements: host: - - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' - - 'bioconductor-biomart >=2.38.0,<2.39.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-biocgenerics >=0.30.0,<0.31.0' + - 'bioconductor-biomart >=2.40.0,<2.41.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' - r-base - r-httr - r-plyr - r-rcurl run: - - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' - - 'bioconductor-biomart >=2.38.0,<2.39.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-biocgenerics >=0.30.0,<0.31.0' + - 'bioconductor-biomart >=2.40.0,<2.41.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' - r-base - r-httr - r-plyr diff --git a/recipes/bioconductor-psygenet2r/meta.yaml b/recipes/bioconductor-psygenet2r/meta.yaml index 98582e70fb369..fde3e83509e03 100644 --- a/recipes/bioconductor-psygenet2r/meta.yaml +++ b/recipes/bioconductor-psygenet2r/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.14.0" %} +{% set version = "1.16.0" %} {% set name = "psygenet2r" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: ad685186daa974d0b5e6b91e0cc7d0b8 + md5: d2c4b6390dd4574a02d4e6ccc50ee6b5 build: number: 0 rpaths: @@ -20,11 +20,11 @@ build: # Suggests: testthat, knitr requirements: host: - - 'bioconductor-bgeedb >=2.8.0,<2.9.0' - - 'bioconductor-biobase >=2.42.0,<2.43.0' - - 'bioconductor-biomart >=2.38.0,<2.39.0' - - 'bioconductor-go.db >=3.7.0,<3.8.0' - - 'bioconductor-topgo >=2.34.0,<2.35.0' + - 'bioconductor-bgeedb >=2.10.0,<2.11.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' + - 'bioconductor-biomart >=2.40.0,<2.41.0' + - 'bioconductor-go.db >=3.8.0,<3.9.0' + - 'bioconductor-topgo >=2.36.0,<2.37.0' - r-base - r-biocmanager - r-ggplot2 @@ -34,11 +34,11 @@ requirements: - r-reshape2 - r-stringr run: - - 'bioconductor-bgeedb >=2.8.0,<2.9.0' - - 'bioconductor-biobase >=2.42.0,<2.43.0' - - 'bioconductor-biomart >=2.38.0,<2.39.0' - - 'bioconductor-go.db >=3.7.0,<3.8.0' - - 'bioconductor-topgo >=2.34.0,<2.35.0' + - 'bioconductor-bgeedb >=2.10.0,<2.11.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' + - 'bioconductor-biomart >=2.40.0,<2.41.0' + - 'bioconductor-go.db >=3.8.0,<3.9.0' + - 'bioconductor-topgo >=2.36.0,<2.37.0' - r-base - r-biocmanager - r-ggplot2 diff --git a/recipes/bioconductor-pth2o2lipids/meta.yaml b/recipes/bioconductor-pth2o2lipids/meta.yaml index 72ffc249c294c..5371184049cbc 100644 --- a/recipes/bioconductor-pth2o2lipids/meta.yaml +++ b/recipes/bioconductor-pth2o2lipids/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.8.0" %} +{% set version = "1.10.0" %} {% set name = "PtH2O2lipids" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 4e581e8fef911bd546261ddc9c4f7cb7 + md5: ed9ec8732208f082981ca3ef9c8a1367 build: number: 0 rpaths: @@ -20,16 +20,16 @@ build: # Suggests: gplots, RColorBrewer, cluster, vegan, clustsig requirements: host: - - 'bioconductor-camera >=1.38.0,<1.39.0' - - 'bioconductor-lobstahs >=1.8.0,<1.9.0' - - 'bioconductor-xcms >=3.4.0,<3.5.0' + - 'bioconductor-camera >=1.40.0,<1.41.0' + - 'bioconductor-lobstahs >=1.10.0,<1.11.0' + - 'bioconductor-xcms >=3.6.0,<3.7.0' - r-base run: - - 'bioconductor-camera >=1.38.0,<1.39.0' - - 'bioconductor-lobstahs >=1.8.0,<1.9.0' - - 'bioconductor-xcms >=3.4.0,<3.5.0' + - 'bioconductor-camera >=1.40.0,<1.41.0' + - 'bioconductor-lobstahs >=1.10.0,<1.11.0' + - 'bioconductor-xcms >=3.6.0,<3.7.0' - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-pth2o2lipids/post-link.sh b/recipes/bioconductor-pth2o2lipids/post-link.sh index b55eb240d54d0..418c0cc111934 100644 --- a/recipes/bioconductor-pth2o2lipids/post-link.sh +++ b/recipes/bioconductor-pth2o2lipids/post-link.sh @@ -1,11 +1,11 @@ #!/bin/bash -FN="PtH2O2lipids_1.8.0.tar.gz" +FN="PtH2O2lipids_1.10.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/experiment/src/contrib/PtH2O2lipids_1.8.0.tar.gz" - "https://bioarchive.galaxyproject.org/PtH2O2lipids_1.8.0.tar.gz" - "https://depot.galaxyproject.org/software/bioconductor-pth2o2lipids/bioconductor-pth2o2lipids_1.8.0_src_all.tar.gz" + "https://bioconductor.org/packages/3.9/data/experiment/src/contrib/PtH2O2lipids_1.10.0.tar.gz" + "https://bioarchive.galaxyproject.org/PtH2O2lipids_1.10.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-pth2o2lipids/bioconductor-pth2o2lipids_1.10.0_src_all.tar.gz" ) -MD5="4e581e8fef911bd546261ddc9c4f7cb7" +MD5="ed9ec8732208f082981ca3ef9c8a1367" # Use a staging area in the conda dir rather than temp dirs, both to avoid # permission issues as well as to have things downloaded in a predictable @@ -16,7 +16,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-puma/meta.yaml b/recipes/bioconductor-puma/meta.yaml index a239dc9825488..5cd8f0e1cc8c5 100644 --- a/recipes/bioconductor-puma/meta.yaml +++ b/recipes/bioconductor-puma/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "3.24.0" %} +{% set version = "3.26.0" %} {% set name = "puma" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: c27be11118a5db7432f6b9cde9f06d5b + md5: 3f6c478de9518b82f635da32011d1455 build: number: 0 rpaths: @@ -19,19 +19,19 @@ build: # Suggests: pumadata, affydata, snow, limma, ROCR,annotate requirements: host: - - 'bioconductor-affy >=1.60.0,<1.61.0' - - 'bioconductor-affyio >=1.52.0,<1.53.0' - - 'bioconductor-biobase >=2.42.0,<2.43.0' - - 'bioconductor-oligo >=1.46.0,<1.47.0' - - 'bioconductor-oligoclasses >=1.44.0,<1.45.0' + - 'bioconductor-affy >=1.62.0,<1.63.0' + - 'bioconductor-affyio >=1.54.0,<1.55.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' + - 'bioconductor-oligo >=1.48.0,<1.49.0' + - 'bioconductor-oligoclasses >=1.46.0,<1.47.0' - r-base - r-mclust run: - - 'bioconductor-affy >=1.60.0,<1.61.0' - - 'bioconductor-affyio >=1.52.0,<1.53.0' - - 'bioconductor-biobase >=2.42.0,<2.43.0' - - 'bioconductor-oligo >=1.46.0,<1.47.0' - - 'bioconductor-oligoclasses >=1.44.0,<1.45.0' + - 'bioconductor-affy >=1.62.0,<1.63.0' + - 'bioconductor-affyio >=1.54.0,<1.55.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' + - 'bioconductor-oligo >=1.48.0,<1.49.0' + - 'bioconductor-oligoclasses >=1.46.0,<1.47.0' - r-base - r-mclust build: diff --git a/recipes/bioconductor-pumadata/meta.yaml b/recipes/bioconductor-pumadata/meta.yaml index c6afdbfa36c04..5f430cd265f0c 100644 --- a/recipes/bioconductor-pumadata/meta.yaml +++ b/recipes/bioconductor-pumadata/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "2.18.0" %} +{% set version = "2.20.0" %} {% set name = "pumadata" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: ec6c6ebbaa066139f26af9e175936484 + md5: bc4a7df5441823c28dfaa3c291750d5a build: number: 0 rpaths: @@ -19,18 +19,18 @@ build: noarch: generic requirements: host: - - 'bioconductor-affy >=1.60.0,<1.61.0' - - 'bioconductor-biobase >=2.42.0,<2.43.0' - - 'bioconductor-oligo >=1.46.0,<1.47.0' - - 'bioconductor-puma >=3.24.0,<3.25.0' + - 'bioconductor-affy >=1.62.0,<1.63.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' + - 'bioconductor-oligo >=1.48.0,<1.49.0' + - 'bioconductor-puma >=3.26.0,<3.27.0' - r-base run: - - 'bioconductor-affy >=1.60.0,<1.61.0' - - 'bioconductor-biobase >=2.42.0,<2.43.0' - - 'bioconductor-oligo >=1.46.0,<1.47.0' - - 'bioconductor-puma >=3.24.0,<3.25.0' + - 'bioconductor-affy >=1.62.0,<1.63.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' + - 'bioconductor-oligo >=1.48.0,<1.49.0' + - 'bioconductor-puma >=3.26.0,<3.27.0' - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-pumadata/post-link.sh b/recipes/bioconductor-pumadata/post-link.sh index 2f80f84f248c9..dcc3f4bcb343d 100644 --- a/recipes/bioconductor-pumadata/post-link.sh +++ b/recipes/bioconductor-pumadata/post-link.sh @@ -1,11 +1,11 @@ #!/bin/bash -FN="pumadata_2.18.0.tar.gz" +FN="pumadata_2.20.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/experiment/src/contrib/pumadata_2.18.0.tar.gz" - "https://bioarchive.galaxyproject.org/pumadata_2.18.0.tar.gz" - "https://depot.galaxyproject.org/software/bioconductor-pumadata/bioconductor-pumadata_2.18.0_src_all.tar.gz" + "https://bioconductor.org/packages/3.9/data/experiment/src/contrib/pumadata_2.20.0.tar.gz" + "https://bioarchive.galaxyproject.org/pumadata_2.20.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-pumadata/bioconductor-pumadata_2.20.0_src_all.tar.gz" ) -MD5="ec6c6ebbaa066139f26af9e175936484" +MD5="bc4a7df5441823c28dfaa3c291750d5a" # Use a staging area in the conda dir rather than temp dirs, both to avoid # permission issues as well as to have things downloaded in a predictable @@ -16,7 +16,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-purecn/meta.yaml b/recipes/bioconductor-purecn/meta.yaml index 6eeba1eacb465..aca01386f53fe 100644 --- a/recipes/bioconductor-purecn/meta.yaml +++ b/recipes/bioconductor-purecn/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.12.1" %} +{% set version = "1.14.0" %} {% set name = "PureCN" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,29 +10,29 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 9f30c118ba5234d2854f0b782a111e88 + md5: b24d437e23ed509a68a41e7fabe7eb51 build: number: 0 rpaths: - lib/R/lib/ - lib/ noarch: generic -# Suggests: PSCBS, BiocStyle, BiocParallel, knitr, optparse, TxDb.Hsapiens.UCSC.hg19.knownGene, org.Hs.eg.db, covr, testthat +# Suggests: PSCBS, copynumber, BiocStyle, BiocParallel, knitr, optparse, TxDb.Hsapiens.UCSC.hg19.knownGene, org.Hs.eg.db, covr, testthat requirements: host: - - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' - - 'bioconductor-biostrings >=2.50.0,<2.51.0' - - 'bioconductor-dnacopy >=1.56.0,<1.57.0' - - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' - - 'bioconductor-genomicfeatures >=1.34.0,<1.35.0' - - 'bioconductor-genomicranges >=1.34.0,<1.35.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-rhdf5 >=2.26.0,<2.27.0' - - 'bioconductor-rsamtools >=1.34.0,<1.35.0' - - 'bioconductor-rtracklayer >=1.42.0,<1.43.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' - - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' - - 'bioconductor-variantannotation >=1.28.0,<1.29.0' + - 'bioconductor-biocgenerics >=0.30.0,<0.31.0' + - 'bioconductor-biostrings >=2.52.0,<2.53.0' + - 'bioconductor-dnacopy >=1.58.0,<1.59.0' + - 'bioconductor-genomeinfodb >=1.20.0,<1.21.0' + - 'bioconductor-genomicfeatures >=1.36.0,<1.37.0' + - 'bioconductor-genomicranges >=1.36.0,<1.37.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-rhdf5 >=2.28.0,<2.29.0' + - 'bioconductor-rsamtools >=2.0.0,<2.1.0' + - 'bioconductor-rtracklayer >=1.44.0,<1.45.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' + - 'bioconductor-summarizedexperiment >=1.14.0,<1.15.0' + - 'bioconductor-variantannotation >=1.30.0,<1.31.0' - r-base - r-data.table - r-futile.logger @@ -42,19 +42,19 @@ requirements: - r-rcolorbrewer - r-vgam run: - - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' - - 'bioconductor-biostrings >=2.50.0,<2.51.0' - - 'bioconductor-dnacopy >=1.56.0,<1.57.0' - - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' - - 'bioconductor-genomicfeatures >=1.34.0,<1.35.0' - - 'bioconductor-genomicranges >=1.34.0,<1.35.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-rhdf5 >=2.26.0,<2.27.0' - - 'bioconductor-rsamtools >=1.34.0,<1.35.0' - - 'bioconductor-rtracklayer >=1.42.0,<1.43.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' - - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' - - 'bioconductor-variantannotation >=1.28.0,<1.29.0' + - 'bioconductor-biocgenerics >=0.30.0,<0.31.0' + - 'bioconductor-biostrings >=2.52.0,<2.53.0' + - 'bioconductor-dnacopy >=1.58.0,<1.59.0' + - 'bioconductor-genomeinfodb >=1.20.0,<1.21.0' + - 'bioconductor-genomicfeatures >=1.36.0,<1.37.0' + - 'bioconductor-genomicranges >=1.36.0,<1.37.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-rhdf5 >=2.28.0,<2.29.0' + - 'bioconductor-rsamtools >=2.0.0,<2.1.0' + - 'bioconductor-rtracklayer >=1.44.0,<1.45.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' + - 'bioconductor-summarizedexperiment >=1.14.0,<1.15.0' + - 'bioconductor-variantannotation >=1.30.0,<1.31.0' - r-base - r-data.table - r-futile.logger diff --git a/recipes/bioconductor-pvac/meta.yaml b/recipes/bioconductor-pvac/meta.yaml index 610677add7809..c872515e8e9e6 100644 --- a/recipes/bioconductor-pvac/meta.yaml +++ b/recipes/bioconductor-pvac/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.30.0" %} +{% set version = "1.32.0" %} {% set name = "pvac" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 2d1c05d44125333ae877c99001bcfa6b + md5: fe0195602ae0184096ea60fecc37be75 build: number: 0 rpaths: @@ -20,12 +20,12 @@ build: # Suggests: pbapply, affydata, ALLMLL, genefilter requirements: host: - - 'bioconductor-affy >=1.60.0,<1.61.0' - - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-affy >=1.62.0,<1.63.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' - r-base run: - - 'bioconductor-affy >=1.60.0,<1.61.0' - - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-affy >=1.62.0,<1.63.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' - r-base test: commands: diff --git a/recipes/bioconductor-pvca/meta.yaml b/recipes/bioconductor-pvca/meta.yaml index b713169bcee03..33f65ec5142a5 100644 --- a/recipes/bioconductor-pvca/meta.yaml +++ b/recipes/bioconductor-pvca/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.22.0" %} +{% set version = "1.24.0" %} {% set name = "pvca" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: d138f4edb7fa0c055c6f0abad5dac160 + md5: 5977112497ca22656df168911b6fcbc1 build: number: 0 rpaths: @@ -20,14 +20,14 @@ build: # Suggests: golubEsets requirements: host: - - 'bioconductor-biobase >=2.42.0,<2.43.0' - - 'bioconductor-vsn >=3.50.0,<3.51.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' + - 'bioconductor-vsn >=3.52.0,<3.53.0' - r-base - r-lme4 - r-matrix run: - - 'bioconductor-biobase >=2.42.0,<2.43.0' - - 'bioconductor-vsn >=3.50.0,<3.51.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' + - 'bioconductor-vsn >=3.52.0,<3.53.0' - r-base - r-lme4 - r-matrix diff --git a/recipes/bioconductor-pviz/meta.yaml b/recipes/bioconductor-pviz/meta.yaml index 12f24e101dacb..4d4289bcaa23b 100644 --- a/recipes/bioconductor-pviz/meta.yaml +++ b/recipes/bioconductor-pviz/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.16.0" %} +{% set version = "1.18.0" %} {% set name = "Pviz" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: f5bd670dee87e666b06e6e506d39c2e0 + md5: 699bc1eefaddda38bed03d0226c36ddd build: number: 0 rpaths: @@ -20,19 +20,19 @@ build: # Suggests: knitr, pepDat requirements: host: - - 'bioconductor-biostrings >=2.50.0,<2.51.0' - - 'bioconductor-biovizbase >=1.30.0,<1.31.0' - - 'bioconductor-genomicranges >=1.34.0,<1.35.0' - - 'bioconductor-gviz >=1.26.0,<1.27.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-biostrings >=2.52.0,<2.53.0' + - 'bioconductor-biovizbase >=1.32.0,<1.33.0' + - 'bioconductor-genomicranges >=1.36.0,<1.37.0' + - 'bioconductor-gviz >=1.28.0,<1.29.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' - r-base - r-data.table run: - - 'bioconductor-biostrings >=2.50.0,<2.51.0' - - 'bioconductor-biovizbase >=1.30.0,<1.31.0' - - 'bioconductor-genomicranges >=1.34.0,<1.35.0' - - 'bioconductor-gviz >=1.26.0,<1.27.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-biostrings >=2.52.0,<2.53.0' + - 'bioconductor-biovizbase >=1.32.0,<1.33.0' + - 'bioconductor-genomicranges >=1.36.0,<1.37.0' + - 'bioconductor-gviz >=1.28.0,<1.29.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' - r-base - r-data.table test: diff --git a/recipes/bioconductor-pwmenrich.dmelanogaster.background/meta.yaml b/recipes/bioconductor-pwmenrich.dmelanogaster.background/meta.yaml index 8c8e652a981ea..9b84e587442f0 100644 --- a/recipes/bioconductor-pwmenrich.dmelanogaster.background/meta.yaml +++ b/recipes/bioconductor-pwmenrich.dmelanogaster.background/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "4.16.0" %} +{% set version = "4.18.0" %} {% set name = "PWMEnrich.Dmelanogaster.background" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 265967f539c3da744389a1fb5a3f112a + md5: ccbaca13154018cdc8ab613a92b77d67 build: number: 0 rpaths: @@ -19,12 +19,12 @@ build: noarch: generic requirements: host: - - 'bioconductor-pwmenrich >=4.18.0,<4.19.0' + - 'bioconductor-pwmenrich >=4.20.0,<4.21.0' - r-base run: - - 'bioconductor-pwmenrich >=4.18.0,<4.19.0' + - 'bioconductor-pwmenrich >=4.20.0,<4.21.0' - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-pwmenrich.dmelanogaster.background/post-link.sh b/recipes/bioconductor-pwmenrich.dmelanogaster.background/post-link.sh index 2f8178363bd35..1f3e8b37d63fd 100644 --- a/recipes/bioconductor-pwmenrich.dmelanogaster.background/post-link.sh +++ b/recipes/bioconductor-pwmenrich.dmelanogaster.background/post-link.sh @@ -1,11 +1,11 @@ #!/bin/bash -FN="PWMEnrich.Dmelanogaster.background_4.16.0.tar.gz" +FN="PWMEnrich.Dmelanogaster.background_4.18.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/experiment/src/contrib/PWMEnrich.Dmelanogaster.background_4.16.0.tar.gz" - "https://bioarchive.galaxyproject.org/PWMEnrich.Dmelanogaster.background_4.16.0.tar.gz" - "https://depot.galaxyproject.org/software/bioconductor-pwmenrich.dmelanogaster.background/bioconductor-pwmenrich.dmelanogaster.background_4.16.0_src_all.tar.gz" + "https://bioconductor.org/packages/3.9/data/experiment/src/contrib/PWMEnrich.Dmelanogaster.background_4.18.0.tar.gz" + "https://bioarchive.galaxyproject.org/PWMEnrich.Dmelanogaster.background_4.18.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-pwmenrich.dmelanogaster.background/bioconductor-pwmenrich.dmelanogaster.background_4.18.0_src_all.tar.gz" ) -MD5="265967f539c3da744389a1fb5a3f112a" +MD5="ccbaca13154018cdc8ab613a92b77d67" # Use a staging area in the conda dir rather than temp dirs, both to avoid # permission issues as well as to have things downloaded in a predictable @@ -16,7 +16,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-pwmenrich.hsapiens.background/meta.yaml b/recipes/bioconductor-pwmenrich.hsapiens.background/meta.yaml index 58464b99c0078..7f73c3ada9c6c 100644 --- a/recipes/bioconductor-pwmenrich.hsapiens.background/meta.yaml +++ b/recipes/bioconductor-pwmenrich.hsapiens.background/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "4.16.0" %} +{% set version = "4.18.0" %} {% set name = "PWMEnrich.Hsapiens.background" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: bffb6a95c2c744fe3a430bbb758dc8e0 + md5: ddb7753fa5b296989688aa37ebb52a66 build: number: 0 rpaths: @@ -19,12 +19,12 @@ build: noarch: generic requirements: host: - - 'bioconductor-pwmenrich >=4.18.0,<4.19.0' + - 'bioconductor-pwmenrich >=4.20.0,<4.21.0' - r-base run: - - 'bioconductor-pwmenrich >=4.18.0,<4.19.0' + - 'bioconductor-pwmenrich >=4.20.0,<4.21.0' - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-pwmenrich.hsapiens.background/post-link.sh b/recipes/bioconductor-pwmenrich.hsapiens.background/post-link.sh index 08025fc168909..6c7d2f8b9c04a 100644 --- a/recipes/bioconductor-pwmenrich.hsapiens.background/post-link.sh +++ b/recipes/bioconductor-pwmenrich.hsapiens.background/post-link.sh @@ -1,11 +1,11 @@ #!/bin/bash -FN="PWMEnrich.Hsapiens.background_4.16.0.tar.gz" +FN="PWMEnrich.Hsapiens.background_4.18.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/experiment/src/contrib/PWMEnrich.Hsapiens.background_4.16.0.tar.gz" - "https://bioarchive.galaxyproject.org/PWMEnrich.Hsapiens.background_4.16.0.tar.gz" - "https://depot.galaxyproject.org/software/bioconductor-pwmenrich.hsapiens.background/bioconductor-pwmenrich.hsapiens.background_4.16.0_src_all.tar.gz" + "https://bioconductor.org/packages/3.9/data/experiment/src/contrib/PWMEnrich.Hsapiens.background_4.18.0.tar.gz" + "https://bioarchive.galaxyproject.org/PWMEnrich.Hsapiens.background_4.18.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-pwmenrich.hsapiens.background/bioconductor-pwmenrich.hsapiens.background_4.18.0_src_all.tar.gz" ) -MD5="bffb6a95c2c744fe3a430bbb758dc8e0" +MD5="ddb7753fa5b296989688aa37ebb52a66" # Use a staging area in the conda dir rather than temp dirs, both to avoid # permission issues as well as to have things downloaded in a predictable @@ -16,7 +16,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-pwmenrich.mmusculus.background/meta.yaml b/recipes/bioconductor-pwmenrich.mmusculus.background/meta.yaml index 457ff00ef6d28..0a3c34a853a0f 100644 --- a/recipes/bioconductor-pwmenrich.mmusculus.background/meta.yaml +++ b/recipes/bioconductor-pwmenrich.mmusculus.background/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "4.16.0" %} +{% set version = "4.18.0" %} {% set name = "PWMEnrich.Mmusculus.background" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: a26cdb4eb465daba22b3e13e4db1a86b + md5: d9cab0ba0958913a7cfaac48f615513a build: number: 0 rpaths: @@ -19,12 +19,12 @@ build: noarch: generic requirements: host: - - 'bioconductor-pwmenrich >=4.18.0,<4.19.0' + - 'bioconductor-pwmenrich >=4.20.0,<4.21.0' - r-base run: - - 'bioconductor-pwmenrich >=4.18.0,<4.19.0' + - 'bioconductor-pwmenrich >=4.20.0,<4.21.0' - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-pwmenrich.mmusculus.background/post-link.sh b/recipes/bioconductor-pwmenrich.mmusculus.background/post-link.sh index 9509089e3f0b7..e0e2cc6696abe 100644 --- a/recipes/bioconductor-pwmenrich.mmusculus.background/post-link.sh +++ b/recipes/bioconductor-pwmenrich.mmusculus.background/post-link.sh @@ -1,11 +1,11 @@ #!/bin/bash -FN="PWMEnrich.Mmusculus.background_4.16.0.tar.gz" +FN="PWMEnrich.Mmusculus.background_4.18.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/experiment/src/contrib/PWMEnrich.Mmusculus.background_4.16.0.tar.gz" - "https://bioarchive.galaxyproject.org/PWMEnrich.Mmusculus.background_4.16.0.tar.gz" - "https://depot.galaxyproject.org/software/bioconductor-pwmenrich.mmusculus.background/bioconductor-pwmenrich.mmusculus.background_4.16.0_src_all.tar.gz" + "https://bioconductor.org/packages/3.9/data/experiment/src/contrib/PWMEnrich.Mmusculus.background_4.18.0.tar.gz" + "https://bioarchive.galaxyproject.org/PWMEnrich.Mmusculus.background_4.18.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-pwmenrich.mmusculus.background/bioconductor-pwmenrich.mmusculus.background_4.18.0_src_all.tar.gz" ) -MD5="a26cdb4eb465daba22b3e13e4db1a86b" +MD5="d9cab0ba0958913a7cfaac48f615513a" # Use a staging area in the conda dir rather than temp dirs, both to avoid # permission issues as well as to have things downloaded in a predictable @@ -16,7 +16,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-pwmenrich/meta.yaml b/recipes/bioconductor-pwmenrich/meta.yaml index 9cfc62d587ff7..31efb3ca04557 100644 --- a/recipes/bioconductor-pwmenrich/meta.yaml +++ b/recipes/bioconductor-pwmenrich/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "4.18.0" %} +{% set version = "4.20.0" %} {% set name = "PWMEnrich" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: b04f4faa148db904e60269da8b987bd6 + md5: 4cf6c371eaf391c0c888b5aec6eeb739 build: number: 0 rpaths: @@ -20,16 +20,16 @@ build: # Suggests: MotifDb, BSgenome.Dmelanogaster.UCSC.dm3, PWMEnrich.Dmelanogaster.background, testthat, gtools, parallel, PWMEnrich.Hsapiens.background, PWMEnrich.Mmusculus.background, BiocStyle, knitr requirements: host: - - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' - - 'bioconductor-biostrings >=2.50.0,<2.51.0' - - 'bioconductor-seqlogo >=1.48.0,<1.49.0' + - 'bioconductor-biocgenerics >=0.30.0,<0.31.0' + - 'bioconductor-biostrings >=2.52.0,<2.53.0' + - 'bioconductor-seqlogo >=1.50.0,<1.51.0' - r-base - r-evd - r-gdata run: - - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' - - 'bioconductor-biostrings >=2.50.0,<2.51.0' - - 'bioconductor-seqlogo >=1.48.0,<1.49.0' + - 'bioconductor-biocgenerics >=0.30.0,<0.31.0' + - 'bioconductor-biostrings >=2.52.0,<2.53.0' + - 'bioconductor-seqlogo >=1.50.0,<1.51.0' - r-base - r-evd - r-gdata diff --git a/recipes/bioconductor-pwomics/meta.yaml b/recipes/bioconductor-pwomics/meta.yaml index 80b8d66154b57..fb50652836fd8 100644 --- a/recipes/bioconductor-pwomics/meta.yaml +++ b/recipes/bioconductor-pwomics/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.14.0" %} +{% set version = "1.16.0" %} {% set name = "pwOmics" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: e762db025a30377ad4908bb3191d20e8 + md5: b37d8682715801a50d85e8e06446a7bf build: number: 0 rpaths: @@ -20,29 +20,29 @@ build: # Suggests: ebdbNet, longitudinal, Mfuzz requirements: host: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' - - 'bioconductor-annotationhub >=2.14.0,<2.15.0' - - 'bioconductor-biobase >=2.42.0,<2.43.0' - - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' - - 'bioconductor-biomart >=2.38.0,<2.39.0' - - 'bioconductor-genomicranges >=1.34.0,<1.35.0' - - 'bioconductor-graph >=1.60.0,<1.61.0' - - 'bioconductor-rbiopaxparser >=2.22.0,<2.23.0' - - 'bioconductor-stringdb >=1.22.0,<1.23.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' + - 'bioconductor-annotationhub >=2.16.0,<2.17.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' + - 'bioconductor-biocgenerics >=0.30.0,<0.31.0' + - 'bioconductor-biomart >=2.40.0,<2.41.0' + - 'bioconductor-genomicranges >=1.36.0,<1.37.0' + - 'bioconductor-graph >=1.62.0,<1.63.0' + - 'bioconductor-rbiopaxparser >=2.24.0,<2.25.0' + - 'bioconductor-stringdb >=1.24.0,<1.25.0' - r-base - r-data.table - r-gplots - r-igraph run: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' - - 'bioconductor-annotationhub >=2.14.0,<2.15.0' - - 'bioconductor-biobase >=2.42.0,<2.43.0' - - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' - - 'bioconductor-biomart >=2.38.0,<2.39.0' - - 'bioconductor-genomicranges >=1.34.0,<1.35.0' - - 'bioconductor-graph >=1.60.0,<1.61.0' - - 'bioconductor-rbiopaxparser >=2.22.0,<2.23.0' - - 'bioconductor-stringdb >=1.22.0,<1.23.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' + - 'bioconductor-annotationhub >=2.16.0,<2.17.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' + - 'bioconductor-biocgenerics >=0.30.0,<0.31.0' + - 'bioconductor-biomart >=2.40.0,<2.41.0' + - 'bioconductor-genomicranges >=1.36.0,<1.37.0' + - 'bioconductor-graph >=1.62.0,<1.63.0' + - 'bioconductor-rbiopaxparser >=2.24.0,<2.25.0' + - 'bioconductor-stringdb >=1.24.0,<1.25.0' - r-base - r-data.table - r-gplots diff --git a/recipes/bioconductor-qckitfastq/build.sh b/recipes/bioconductor-qckitfastq/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-qckitfastq/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-qckitfastq/meta.yaml b/recipes/bioconductor-qckitfastq/meta.yaml new file mode 100644 index 0000000000000..2893a6e35526a --- /dev/null +++ b/recipes/bioconductor-qckitfastq/meta.yaml @@ -0,0 +1,57 @@ +{% set version = "1.0.0" %} +{% set name = "qckitfastq" %} +{% set bioc = "3.9" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + md5: a2bd110c0093a787ec56dc40fbc51cc3 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ +# Suggests: knitr, rmarkdown, kableExtra, testthat +# SystemRequirements: GNU make +requirements: + host: + - 'bioconductor-rseqan >=1.4.0,<1.5.0' + - 'bioconductor-seqtools >=1.18.0,<1.19.0' + - 'bioconductor-zlibbioc >=1.30.0,<1.31.0' + - r-base + - r-data.table + - r-dplyr + - r-ggplot2 + - r-magrittr + - r-rcpp + - r-reshape2 + - r-rlang + run: + - 'bioconductor-rseqan >=1.4.0,<1.5.0' + - 'bioconductor-seqtools >=1.18.0,<1.19.0' + - 'bioconductor-zlibbioc >=1.30.0,<1.31.0' + - r-base + - r-data.table + - r-dplyr + - r-ggplot2 + - r-magrittr + - r-rcpp + - r-reshape2 + - r-rlang + build: + - {{ compiler('c') }} + - {{ compiler('cxx') }} + - make +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'Assessment of FASTQ file format with multiple metrics including quality score, sequence content, overrepresented sequence and Kmers.' + diff --git a/recipes/bioconductor-qcmetrics/meta.yaml b/recipes/bioconductor-qcmetrics/meta.yaml index 089a1344a2595..5118aa1e9c7b5 100644 --- a/recipes/bioconductor-qcmetrics/meta.yaml +++ b/recipes/bioconductor-qcmetrics/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.20.1" %} +{% set version = "1.22.0" %} {% set name = "qcmetrics" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - sha256: fae72108fbc9a21ec3f2d07cdcf89f049e18212216d6b74755818e29ad88096c + md5: 58dc1a2e6afca43f5d883fdde8d1282b build: number: 0 rpaths: @@ -20,16 +20,16 @@ build: # Suggests: affy, MSnbase, ggplot2, lattice, yaqcaffy, MAQCsubsetAFX, RforProteomics, AnnotationDbi, mzR, hgu133plus2cdf, BiocStyle requirements: host: - - 'bioconductor-biobase >=2.42.0,<2.43.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' - r-base - r-knitr - r-nozzle.r1 - r-pander - r-xtable run: - - 'bioconductor-biobase >=2.42.0,<2.43.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' - r-base - r-knitr - r-nozzle.r1 diff --git a/recipes/bioconductor-qdnaseq.hg19/meta.yaml b/recipes/bioconductor-qdnaseq.hg19/meta.yaml index 84c4c58dcc7fb..f92f6b46b4262 100644 --- a/recipes/bioconductor-qdnaseq.hg19/meta.yaml +++ b/recipes/bioconductor-qdnaseq.hg19/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.12.0" %} +{% set version = "1.14.0" %} {% set name = "QDNAseq.hg19" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,21 +10,21 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 5644d966c2331d01df686107f85f0899 + md5: 18bb6347a3912c344deca9f2646087b4 build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ noarch: generic requirements: host: - - 'bioconductor-qdnaseq >=1.18.0,<1.19.0' + - 'bioconductor-qdnaseq >=1.20.0,<1.21.0' - r-base run: - - 'bioconductor-qdnaseq >=1.18.0,<1.19.0' + - 'bioconductor-qdnaseq >=1.20.0,<1.21.0' - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-qdnaseq.hg19/post-link.sh b/recipes/bioconductor-qdnaseq.hg19/post-link.sh index 6d5f3827ae74d..c2de38fe828bb 100644 --- a/recipes/bioconductor-qdnaseq.hg19/post-link.sh +++ b/recipes/bioconductor-qdnaseq.hg19/post-link.sh @@ -1,11 +1,11 @@ #!/bin/bash -FN="QDNAseq.hg19_1.12.0.tar.gz" +FN="QDNAseq.hg19_1.14.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/experiment/src/contrib/QDNAseq.hg19_1.12.0.tar.gz" - "https://bioarchive.galaxyproject.org/QDNAseq.hg19_1.12.0.tar.gz" - "https://depot.galaxyproject.org/software/bioconductor-qdnaseq.hg19/bioconductor-qdnaseq.hg19_1.12.0_src_all.tar.gz" + "https://bioconductor.org/packages/3.9/data/experiment/src/contrib/QDNAseq.hg19_1.14.0.tar.gz" + "https://bioarchive.galaxyproject.org/QDNAseq.hg19_1.14.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-qdnaseq.hg19/bioconductor-qdnaseq.hg19_1.14.0_src_all.tar.gz" ) -MD5="5644d966c2331d01df686107f85f0899" +MD5="18bb6347a3912c344deca9f2646087b4" # Use a staging area in the conda dir rather than temp dirs, both to avoid # permission issues as well as to have things downloaded in a predictable @@ -16,7 +16,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-qdnaseq.mm10/meta.yaml b/recipes/bioconductor-qdnaseq.mm10/meta.yaml index 05b00c08fd035..5f083d3e5638d 100644 --- a/recipes/bioconductor-qdnaseq.mm10/meta.yaml +++ b/recipes/bioconductor-qdnaseq.mm10/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.12.0" %} +{% set version = "1.14.0" %} {% set name = "QDNAseq.mm10" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 3557bc3a5f5820eb17d7a643730ed314 + md5: 6f2c864b3e8cba93980603dd0c5b215e build: number: 0 rpaths: @@ -19,12 +19,12 @@ build: noarch: generic requirements: host: - - 'bioconductor-qdnaseq >=1.18.0,<1.19.0' + - 'bioconductor-qdnaseq >=1.20.0,<1.21.0' - r-base run: - - 'bioconductor-qdnaseq >=1.18.0,<1.19.0' + - 'bioconductor-qdnaseq >=1.20.0,<1.21.0' - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-qdnaseq.mm10/post-link.sh b/recipes/bioconductor-qdnaseq.mm10/post-link.sh index 991ac13319d90..13ee0b66323c3 100644 --- a/recipes/bioconductor-qdnaseq.mm10/post-link.sh +++ b/recipes/bioconductor-qdnaseq.mm10/post-link.sh @@ -1,11 +1,11 @@ #!/bin/bash -FN="QDNAseq.mm10_1.12.0.tar.gz" +FN="QDNAseq.mm10_1.14.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/experiment/src/contrib/QDNAseq.mm10_1.12.0.tar.gz" - "https://bioarchive.galaxyproject.org/QDNAseq.mm10_1.12.0.tar.gz" - "https://depot.galaxyproject.org/software/bioconductor-qdnaseq.mm10/bioconductor-qdnaseq.mm10_1.12.0_src_all.tar.gz" + "https://bioconductor.org/packages/3.9/data/experiment/src/contrib/QDNAseq.mm10_1.14.0.tar.gz" + "https://bioarchive.galaxyproject.org/QDNAseq.mm10_1.14.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-qdnaseq.mm10/bioconductor-qdnaseq.mm10_1.14.0_src_all.tar.gz" ) -MD5="3557bc3a5f5820eb17d7a643730ed314" +MD5="6f2c864b3e8cba93980603dd0c5b215e" # Use a staging area in the conda dir rather than temp dirs, both to avoid # permission issues as well as to have things downloaded in a predictable @@ -16,7 +16,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-qdnaseq/meta.yaml b/recipes/bioconductor-qdnaseq/meta.yaml index 4a13346463ffb..afe4fcd96cd48 100644 --- a/recipes/bioconductor-qdnaseq/meta.yaml +++ b/recipes/bioconductor-qdnaseq/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.18.0" %} +{% set version = "1.20.0" %} {% set name = "QDNAseq" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: d25872be8df20f65786d1df51d79181b + md5: 9a6c7d92574ef0f22d4742de20100cfa build: number: 0 rpaths: @@ -20,26 +20,26 @@ build: # Suggests: BiocStyle (>= 1.8.0), BSgenome (>= 1.38.0), digest (>= 0.6.8), GenomeInfoDb (>= 1.6.0), future (>= 0.14.0), R.cache (>= 0.12.0) requirements: host: - - 'bioconductor-biobase >=2.42.0,<2.43.0' - - 'bioconductor-biocparallel >=1.16.0,<1.17.0' - - 'bioconductor-cghbase >=1.42.0,<1.43.0' - - 'bioconductor-cghcall >=2.44.0,<2.45.0' - - 'bioconductor-dnacopy >=1.56.0,<1.57.0' - - 'bioconductor-genomicranges >=1.34.0,<1.35.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-rsamtools >=1.34.0,<1.35.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' + - 'bioconductor-biocparallel >=1.18.0,<1.19.0' + - 'bioconductor-cghbase >=1.44.0,<1.45.0' + - 'bioconductor-cghcall >=2.46.0,<2.47.0' + - 'bioconductor-dnacopy >=1.58.0,<1.59.0' + - 'bioconductor-genomicranges >=1.36.0,<1.37.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-rsamtools >=2.0.0,<2.1.0' - r-base - 'r-matrixstats >=0.50.2' - 'r-r.utils >=2.3.0' run: - - 'bioconductor-biobase >=2.42.0,<2.43.0' - - 'bioconductor-biocparallel >=1.16.0,<1.17.0' - - 'bioconductor-cghbase >=1.42.0,<1.43.0' - - 'bioconductor-cghcall >=2.44.0,<2.45.0' - - 'bioconductor-dnacopy >=1.56.0,<1.57.0' - - 'bioconductor-genomicranges >=1.34.0,<1.35.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-rsamtools >=1.34.0,<1.35.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' + - 'bioconductor-biocparallel >=1.18.0,<1.19.0' + - 'bioconductor-cghbase >=1.44.0,<1.45.0' + - 'bioconductor-cghcall >=2.46.0,<2.47.0' + - 'bioconductor-dnacopy >=1.58.0,<1.59.0' + - 'bioconductor-genomicranges >=1.36.0,<1.37.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-rsamtools >=2.0.0,<2.1.0' - r-base - 'r-matrixstats >=0.50.2' - 'r-r.utils >=2.3.0' diff --git a/recipes/bioconductor-qpcrnorm/meta.yaml b/recipes/bioconductor-qpcrnorm/meta.yaml index ce6f11c13f703..ce1f047247e3c 100644 --- a/recipes/bioconductor-qpcrnorm/meta.yaml +++ b/recipes/bioconductor-qpcrnorm/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.40.0" %} +{% set version = "1.42.0" %} {% set name = "qpcrNorm" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,23 +10,23 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 16a79fad66a1af84d66805d099ba0c58 + md5: 49976aed28892f2c1e3c62c86f42d9e7 build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ noarch: generic requirements: host: - - 'bioconductor-affy >=1.60.0,<1.61.0' - - 'bioconductor-biobase >=2.42.0,<2.43.0' - - 'bioconductor-limma >=3.38.0,<3.39.0' + - 'bioconductor-affy >=1.62.0,<1.63.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' + - 'bioconductor-limma >=3.40.0,<3.41.0' - r-base run: - - 'bioconductor-affy >=1.60.0,<1.61.0' - - 'bioconductor-biobase >=2.42.0,<2.43.0' - - 'bioconductor-limma >=3.38.0,<3.39.0' + - 'bioconductor-affy >=1.62.0,<1.63.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' + - 'bioconductor-limma >=3.40.0,<3.41.0' - r-base test: commands: diff --git a/recipes/bioconductor-qpgraph/meta.yaml b/recipes/bioconductor-qpgraph/meta.yaml index 45a12101a0629..d704a800fedeb 100644 --- a/recipes/bioconductor-qpgraph/meta.yaml +++ b/recipes/bioconductor-qpgraph/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "2.16.0" %} +{% set version = "2.18.0" %} {% set name = "qpgraph" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: c31410ede77ec4bde909a2755488d2af + md5: 336334ed0593d42313616e0fd7800c48 build: number: 0 rpaths: @@ -19,33 +19,33 @@ build: # Suggests: RUnit, BiocGenerics, BiocStyle, genefilter, org.EcK12.eg.db, rlecuyer, snow, Category, GOstats requirements: host: - - 'bioconductor-annotate >=1.60.0,<1.61.0' - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' - - 'bioconductor-biobase >=2.42.0,<2.43.0' - - 'bioconductor-biocparallel >=1.16.0,<1.17.0' - - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' - - 'bioconductor-genomicfeatures >=1.34.0,<1.35.0' - - 'bioconductor-genomicranges >=1.34.0,<1.35.0' - - 'bioconductor-graph >=1.60.0,<1.61.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-rgraphviz >=2.26.0,<2.27.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-annotate >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' + - 'bioconductor-biocparallel >=1.18.0,<1.19.0' + - 'bioconductor-genomeinfodb >=1.20.0,<1.21.0' + - 'bioconductor-genomicfeatures >=1.36.0,<1.37.0' + - 'bioconductor-genomicranges >=1.36.0,<1.37.0' + - 'bioconductor-graph >=1.62.0,<1.63.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-rgraphviz >=2.28.0,<2.29.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' - r-base - 'r-matrix >=1.0' - r-mvtnorm - r-qtl run: - - 'bioconductor-annotate >=1.60.0,<1.61.0' - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' - - 'bioconductor-biobase >=2.42.0,<2.43.0' - - 'bioconductor-biocparallel >=1.16.0,<1.17.0' - - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' - - 'bioconductor-genomicfeatures >=1.34.0,<1.35.0' - - 'bioconductor-genomicranges >=1.34.0,<1.35.0' - - 'bioconductor-graph >=1.60.0,<1.61.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-rgraphviz >=2.26.0,<2.27.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-annotate >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' + - 'bioconductor-biocparallel >=1.18.0,<1.19.0' + - 'bioconductor-genomeinfodb >=1.20.0,<1.21.0' + - 'bioconductor-genomicfeatures >=1.36.0,<1.37.0' + - 'bioconductor-genomicranges >=1.36.0,<1.37.0' + - 'bioconductor-graph >=1.62.0,<1.63.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-rgraphviz >=2.28.0,<2.29.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' - r-base - 'r-matrix >=1.0' - r-mvtnorm diff --git a/recipes/bioconductor-qplexanalyzer/meta.yaml b/recipes/bioconductor-qplexanalyzer/meta.yaml index af01eab0b0479..d3fe3dd82a4bf 100644 --- a/recipes/bioconductor-qplexanalyzer/meta.yaml +++ b/recipes/bioconductor-qplexanalyzer/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.0.3" %} +{% set version = "1.2.0" %} {% set name = "qPLEXanalyzer" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: b93cc585ddb6cebe0b8a04c9cf615420 + md5: fc7302cc24a8bd83209303b4b3951950 build: number: 0 rpaths: @@ -20,14 +20,14 @@ build: # Suggests: UniProt.ws, knitr, qPLEXdata requirements: host: - - 'bioconductor-biobase >=2.42.0,<2.43.0' - - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' - - 'bioconductor-biostrings >=2.50.0,<2.51.0' - - 'bioconductor-genomicranges >=1.34.0,<1.35.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-limma >=3.38.0,<3.39.0' - - 'bioconductor-msnbase >=2.8.0,<2.9.0' - - 'bioconductor-preprocesscore >=1.44.0,<1.45.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' + - 'bioconductor-biocgenerics >=0.30.0,<0.31.0' + - 'bioconductor-biostrings >=2.52.0,<2.53.0' + - 'bioconductor-genomicranges >=1.36.0,<1.37.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-limma >=3.40.0,<3.41.0' + - 'bioconductor-msnbase >=2.10.0,<2.11.0' + - 'bioconductor-preprocesscore >=1.46.0,<1.47.0' - r-assertthat - r-base - r-dplyr @@ -41,14 +41,14 @@ requirements: - r-tibble - r-tidyr run: - - 'bioconductor-biobase >=2.42.0,<2.43.0' - - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' - - 'bioconductor-biostrings >=2.50.0,<2.51.0' - - 'bioconductor-genomicranges >=1.34.0,<1.35.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-limma >=3.38.0,<3.39.0' - - 'bioconductor-msnbase >=2.8.0,<2.9.0' - - 'bioconductor-preprocesscore >=1.44.0,<1.45.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' + - 'bioconductor-biocgenerics >=0.30.0,<0.31.0' + - 'bioconductor-biostrings >=2.52.0,<2.53.0' + - 'bioconductor-genomicranges >=1.36.0,<1.37.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-limma >=3.40.0,<3.41.0' + - 'bioconductor-msnbase >=2.10.0,<2.11.0' + - 'bioconductor-preprocesscore >=1.46.0,<1.47.0' - r-assertthat - r-base - r-dplyr diff --git a/recipes/bioconductor-qplexdata/meta.yaml b/recipes/bioconductor-qplexdata/meta.yaml index 6ae164b62a7fd..a93fda9949c17 100644 --- a/recipes/bioconductor-qplexdata/meta.yaml +++ b/recipes/bioconductor-qplexdata/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.0.1" %} +{% set version = "1.2.0" %} {% set name = "qPLEXdata" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 27c05de065b8225c34d8a99ac7ce1992 + md5: e60329bb0a7c25957e0504beb98dd1f8 build: number: 0 rpaths: @@ -19,18 +19,18 @@ build: noarch: generic requirements: host: - - 'bioconductor-msnbase >=2.8.0,<2.9.0' - - 'bioconductor-qplexanalyzer >=1.0.0,<1.1.0' + - 'bioconductor-msnbase >=2.10.0,<2.11.0' + - 'bioconductor-qplexanalyzer >=1.2.0,<1.3.0' - r-base - r-dplyr - r-knitr run: - - 'bioconductor-msnbase >=2.8.0,<2.9.0' - - 'bioconductor-qplexanalyzer >=1.0.0,<1.1.0' + - 'bioconductor-msnbase >=2.10.0,<2.11.0' + - 'bioconductor-qplexanalyzer >=1.2.0,<1.3.0' - r-base - r-dplyr - r-knitr - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-qplexdata/post-link.sh b/recipes/bioconductor-qplexdata/post-link.sh index 80d46e1644008..8f4ea0cba459c 100644 --- a/recipes/bioconductor-qplexdata/post-link.sh +++ b/recipes/bioconductor-qplexdata/post-link.sh @@ -1,11 +1,11 @@ #!/bin/bash -FN="qPLEXdata_1.0.1.tar.gz" +FN="qPLEXdata_1.2.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/experiment/src/contrib/qPLEXdata_1.0.1.tar.gz" - "https://bioarchive.galaxyproject.org/qPLEXdata_1.0.1.tar.gz" - "https://depot.galaxyproject.org/software/bioconductor-qplexdata/bioconductor-qplexdata_1.0.1_src_all.tar.gz" + "https://bioconductor.org/packages/3.9/data/experiment/src/contrib/qPLEXdata_1.2.0.tar.gz" + "https://bioarchive.galaxyproject.org/qPLEXdata_1.2.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-qplexdata/bioconductor-qplexdata_1.2.0_src_all.tar.gz" ) -MD5="27c05de065b8225c34d8a99ac7ce1992" +MD5="e60329bb0a7c25957e0504beb98dd1f8" # Use a staging area in the conda dir rather than temp dirs, both to avoid # permission issues as well as to have things downloaded in a predictable @@ -16,7 +16,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-qrqc/meta.yaml b/recipes/bioconductor-qrqc/meta.yaml index 548aca1ecd18e..6a1e9df628584 100644 --- a/recipes/bioconductor-qrqc/meta.yaml +++ b/recipes/bioconductor-qrqc/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.36.0" %} +{% set version = "1.38.0" %} {% set name = "qrqc" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: f6cafce11da089f3c97ce564659f07a4 + md5: d1614dbf5b895a83baf034fe49f1789a build: number: 0 rpaths: @@ -18,9 +18,9 @@ build: - lib/ requirements: host: - - 'bioconductor-biostrings >=2.50.0,<2.51.0' - - 'bioconductor-biovizbase >=1.30.0,<1.31.0' - - 'bioconductor-rsamtools >=1.34.0,<1.35.0' + - 'bioconductor-biostrings >=2.52.0,<2.53.0' + - 'bioconductor-biovizbase >=1.32.0,<1.33.0' + - 'bioconductor-rhtslib >=1.16.0,<1.17.0' - r-base - r-brew - r-ggplot2 @@ -29,9 +29,9 @@ requirements: - r-testthat - r-xtable run: - - 'bioconductor-biostrings >=2.50.0,<2.51.0' - - 'bioconductor-biovizbase >=1.30.0,<1.31.0' - - 'bioconductor-rsamtools >=1.34.0,<1.35.0' + - 'bioconductor-biostrings >=2.52.0,<2.53.0' + - 'bioconductor-biovizbase >=1.32.0,<1.33.0' + - 'bioconductor-rhtslib >=1.16.0,<1.17.0' - r-base - r-brew - r-ggplot2 diff --git a/recipes/bioconductor-qsea/meta.yaml b/recipes/bioconductor-qsea/meta.yaml index 9eaad569bac3f..27897e8158276 100644 --- a/recipes/bioconductor-qsea/meta.yaml +++ b/recipes/bioconductor-qsea/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.8.0" %} +{% set version = "1.10.0" %} {% set name = "qsea" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: c2a094a5f1c9135228c41eef8ac4f639 + md5: 0fae5fe514b3c766dd6df177706887a2 build: number: 0 rpaths: @@ -19,32 +19,32 @@ build: # Suggests: BSgenome.Hsapiens.UCSC.hg19, MEDIPSData, testthat, BiocStyle, knitr, rmarkdown, BiocManager requirements: host: - - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' - - 'bioconductor-biocparallel >=1.16.0,<1.17.0' - - 'bioconductor-biostrings >=2.50.0,<2.51.0' - - 'bioconductor-bsgenome >=1.50.0,<1.51.0' - - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' - - 'bioconductor-genomicranges >=1.34.0,<1.35.0' - - 'bioconductor-hmmcopy >=1.24.0,<1.25.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-limma >=3.38.0,<3.39.0' - - 'bioconductor-rsamtools >=1.34.0,<1.35.0' - - 'bioconductor-rtracklayer >=1.42.0,<1.43.0' + - 'bioconductor-biocgenerics >=0.30.0,<0.31.0' + - 'bioconductor-biocparallel >=1.18.0,<1.19.0' + - 'bioconductor-biostrings >=2.52.0,<2.53.0' + - 'bioconductor-bsgenome >=1.52.0,<1.53.0' + - 'bioconductor-genomeinfodb >=1.20.0,<1.21.0' + - 'bioconductor-genomicranges >=1.36.0,<1.37.0' + - 'bioconductor-hmmcopy >=1.26.0,<1.27.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-limma >=3.40.0,<3.41.0' + - 'bioconductor-rsamtools >=2.0.0,<2.1.0' + - 'bioconductor-rtracklayer >=1.44.0,<1.45.0' - r-base - r-gtools - r-zoo run: - - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' - - 'bioconductor-biocparallel >=1.16.0,<1.17.0' - - 'bioconductor-biostrings >=2.50.0,<2.51.0' - - 'bioconductor-bsgenome >=1.50.0,<1.51.0' - - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' - - 'bioconductor-genomicranges >=1.34.0,<1.35.0' - - 'bioconductor-hmmcopy >=1.24.0,<1.25.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-limma >=3.38.0,<3.39.0' - - 'bioconductor-rsamtools >=1.34.0,<1.35.0' - - 'bioconductor-rtracklayer >=1.42.0,<1.43.0' + - 'bioconductor-biocgenerics >=0.30.0,<0.31.0' + - 'bioconductor-biocparallel >=1.18.0,<1.19.0' + - 'bioconductor-biostrings >=2.52.0,<2.53.0' + - 'bioconductor-bsgenome >=1.52.0,<1.53.0' + - 'bioconductor-genomeinfodb >=1.20.0,<1.21.0' + - 'bioconductor-genomicranges >=1.36.0,<1.37.0' + - 'bioconductor-hmmcopy >=1.26.0,<1.27.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-limma >=3.40.0,<3.41.0' + - 'bioconductor-rsamtools >=2.0.0,<2.1.0' + - 'bioconductor-rtracklayer >=1.44.0,<1.45.0' - r-base - r-gtools - r-zoo diff --git a/recipes/bioconductor-qsmooth/build.sh b/recipes/bioconductor-qsmooth/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-qsmooth/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-qsmooth/meta.yaml b/recipes/bioconductor-qsmooth/meta.yaml new file mode 100644 index 0000000000000..082c71077315f --- /dev/null +++ b/recipes/bioconductor-qsmooth/meta.yaml @@ -0,0 +1,37 @@ +{% set version = "1.0.0" %} +{% set name = "qsmooth" %} +{% set bioc = "3.9" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + md5: d4e7613cae77fa6e53984260041a71d4 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: bodymapRat, quantro, knitr, rmarkdown, BiocStyle, testthat +requirements: + host: + - 'bioconductor-summarizedexperiment >=1.14.0,<1.15.0' + - 'bioconductor-sva >=3.32.0,<3.33.0' + - r-base + run: + - 'bioconductor-summarizedexperiment >=1.14.0,<1.15.0' + - 'bioconductor-sva >=3.32.0,<3.33.0' + - r-base +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: 'CC BY 4.0' + summary: 'Smooth quantile normalization is a generalization of quantile normalization, which is average of the two types of assumptions about the data generation process: quantile normalization and quantile normalization between groups.' + diff --git a/recipes/bioconductor-qsutils/meta.yaml b/recipes/bioconductor-qsutils/meta.yaml index bf2bc397fe697..43a5f67d76e3f 100644 --- a/recipes/bioconductor-qsutils/meta.yaml +++ b/recipes/bioconductor-qsutils/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.0.0" %} +{% set version = "1.2.0" %} {% set name = "QSutils" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 1dcee86cb9a096cdc552fb279ce8f094 + md5: 546493a7b9a5316616aa61281e3b4d36 build: number: 0 rpaths: @@ -20,14 +20,14 @@ build: # Suggests: BiocStyle, knitr, rmarkdown, ggplot2 requirements: host: - - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' - - 'bioconductor-biostrings >=2.50.0,<2.51.0' + - 'bioconductor-biocgenerics >=0.30.0,<0.31.0' + - 'bioconductor-biostrings >=2.52.0,<2.53.0' - r-ape - r-base - r-psych run: - - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' - - 'bioconductor-biostrings >=2.50.0,<2.51.0' + - 'bioconductor-biocgenerics >=0.30.0,<0.31.0' + - 'bioconductor-biostrings >=2.52.0,<2.53.0' - r-ape - r-base - r-psych diff --git a/recipes/bioconductor-qualifier/meta.yaml b/recipes/bioconductor-qualifier/meta.yaml index 3f3c36c7d2537..b4a9e8ba11d44 100644 --- a/recipes/bioconductor-qualifier/meta.yaml +++ b/recipes/bioconductor-qualifier/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.26.0" %} +{% set version = "1.28.0" %} {% set name = "QUALIFIER" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 30ff0cb2ff2920f6141547a9546c5cf1 + md5: 2c6692e2c10c358cc2caa8d0947c1620 build: number: 0 rpaths: @@ -20,11 +20,11 @@ build: # Suggests: RSVGTipsDevice, knitr requirements: host: - - 'bioconductor-biobase >=2.42.0,<2.43.0' - - 'bioconductor-flowcore >=1.48.0,<1.49.0' - - 'bioconductor-flowviz >=1.46.0,<1.47.0' - - 'bioconductor-flowworkspace >=3.30.0,<3.31.0' - - 'bioconductor-ncdfflow >=2.28.0,<2.29.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' + - 'bioconductor-flowcore >=1.50.0,<1.51.0' + - 'bioconductor-flowviz >=1.48.0,<1.49.0' + - 'bioconductor-flowworkspace >=3.32.0,<3.33.0' + - 'bioconductor-ncdfflow >=2.30.0,<2.31.0' - r-base - r-data.table - r-hwriter @@ -34,11 +34,11 @@ requirements: - r-reshape - r-xml run: - - 'bioconductor-biobase >=2.42.0,<2.43.0' - - 'bioconductor-flowcore >=1.48.0,<1.49.0' - - 'bioconductor-flowviz >=1.46.0,<1.47.0' - - 'bioconductor-flowworkspace >=3.30.0,<3.31.0' - - 'bioconductor-ncdfflow >=2.28.0,<2.29.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' + - 'bioconductor-flowcore >=1.50.0,<1.51.0' + - 'bioconductor-flowviz >=1.48.0,<1.49.0' + - 'bioconductor-flowworkspace >=3.32.0,<3.33.0' + - 'bioconductor-ncdfflow >=2.30.0,<2.31.0' - r-base - r-data.table - r-hwriter diff --git a/recipes/bioconductor-quantro/meta.yaml b/recipes/bioconductor-quantro/meta.yaml index 19b37effba879..56d111d5f02be 100644 --- a/recipes/bioconductor-quantro/meta.yaml +++ b/recipes/bioconductor-quantro/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.16.0" %} +{% set version = "1.18.0" %} {% set name = "quantro" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,9 +10,9 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: f7d79a596f7a2e9c965a1e341aeca26c + md5: c271662d585e8997b71f103a08dacf8a build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ @@ -20,8 +20,8 @@ build: # Suggests: knitr, RUnit, BiocGenerics, BiocStyle requirements: host: - - 'bioconductor-biobase >=2.42.0,<2.43.0' - - 'bioconductor-minfi >=1.28.0,<1.29.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' + - 'bioconductor-minfi >=1.30.0,<1.31.0' - r-base - r-doparallel - r-foreach @@ -29,8 +29,8 @@ requirements: - r-iterators - r-rcolorbrewer run: - - 'bioconductor-biobase >=2.42.0,<2.43.0' - - 'bioconductor-minfi >=1.28.0,<1.29.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' + - 'bioconductor-minfi >=1.30.0,<1.31.0' - r-base - r-doparallel - r-foreach diff --git a/recipes/bioconductor-quantsmooth/meta.yaml b/recipes/bioconductor-quantsmooth/meta.yaml index c09b5df117174..b4f0051c212ec 100644 --- a/recipes/bioconductor-quantsmooth/meta.yaml +++ b/recipes/bioconductor-quantsmooth/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.48.0" %} +{% set version = "1.50.0" %} {% set name = "quantsmooth" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 6617f7e9ad5b4d7f66a5eb214d6b7cee + md5: 06ba796cd1e44554ed3e62d234269d6b build: number: 0 rpaths: diff --git a/recipes/bioconductor-quartpac/meta.yaml b/recipes/bioconductor-quartpac/meta.yaml index ce935fe15b18a..8d05078319378 100644 --- a/recipes/bioconductor-quartpac/meta.yaml +++ b/recipes/bioconductor-quartpac/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.14.0" %} +{% set version = "1.16.0" %} {% set name = "QuartPAC" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: f423fa2cb29443befb977c06700a8dcf + md5: d47f56657de973251a31d1b66909329f build: number: 0 rpaths: @@ -20,15 +20,15 @@ build: # Suggests: RUnit, BiocGenerics, rgl requirements: host: - - 'bioconductor-graphpac >=1.24.0,<1.25.0' - - 'bioconductor-ipac >=1.26.0,<1.27.0' - - 'bioconductor-spacepac >=1.20.0,<1.21.0' + - 'bioconductor-graphpac >=1.26.0,<1.27.0' + - 'bioconductor-ipac >=1.28.0,<1.29.0' + - 'bioconductor-spacepac >=1.22.0,<1.23.0' - r-base - r-data.table run: - - 'bioconductor-graphpac >=1.24.0,<1.25.0' - - 'bioconductor-ipac >=1.26.0,<1.27.0' - - 'bioconductor-spacepac >=1.20.0,<1.21.0' + - 'bioconductor-graphpac >=1.26.0,<1.27.0' + - 'bioconductor-ipac >=1.28.0,<1.29.0' + - 'bioconductor-spacepac >=1.22.0,<1.23.0' - r-base - r-data.table test: diff --git a/recipes/bioconductor-quasr/meta.yaml b/recipes/bioconductor-quasr/meta.yaml index 01d83a41d6f73..27dd91453e9dc 100644 --- a/recipes/bioconductor-quasr/meta.yaml +++ b/recipes/bioconductor-quasr/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.22.1" %} +{% set version = "1.24.0" %} {% set name = "QuasR" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,52 +10,56 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 4add73c5e114233621711ace6c8d1e35 + md5: 30473891dbb03a0f54a05490f764737b build: number: 0 rpaths: - lib/R/lib/ - lib/ -# Suggests: Gviz, RUnit, BiocStyle, knitr, rmarkdown +# Suggests: Gviz, BiocStyle, knitr, rmarkdown, covr, testthat requirements: host: - - 'bioconductor-biobase >=2.42.0,<2.43.0' - - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' - - 'bioconductor-biocparallel >=1.16.0,<1.17.0' - - 'bioconductor-biostrings >=2.50.0,<2.51.0' - - 'bioconductor-bsgenome >=1.50.0,<1.51.0' - - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' - - 'bioconductor-genomicalignments >=1.18.0,<1.19.0' - - 'bioconductor-genomicfeatures >=1.34.0,<1.35.0' - - 'bioconductor-genomicfiles >=1.18.0,<1.19.0' - - 'bioconductor-genomicranges >=1.34.0,<1.35.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-rbowtie >=1.22.0,<1.23.0' - - 'bioconductor-rsamtools >=1.34.0,<1.35.0' - - 'bioconductor-rtracklayer >=1.42.0,<1.43.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' - - 'bioconductor-shortread >=1.40.0,<1.41.0' - - 'bioconductor-zlibbioc >=1.28.0,<1.29.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' + - 'bioconductor-biocgenerics >=0.30.0,<0.31.0' + - 'bioconductor-biocparallel >=1.18.0,<1.19.0' + - 'bioconductor-biostrings >=2.52.0,<2.53.0' + - 'bioconductor-bsgenome >=1.52.0,<1.53.0' + - 'bioconductor-genomeinfodb >=1.20.0,<1.21.0' + - 'bioconductor-genomicalignments >=1.20.0,<1.21.0' + - 'bioconductor-genomicfeatures >=1.36.0,<1.37.0' + - 'bioconductor-genomicfiles >=1.20.0,<1.21.0' + - 'bioconductor-genomicranges >=1.36.0,<1.37.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-rbowtie >=1.24.0,<1.25.0' + - 'bioconductor-rhisat2 >=1.0.0,<1.1.0' + - 'bioconductor-rhtslib >=1.16.0,<1.17.0' + - 'bioconductor-rsamtools >=2.0.0,<2.1.0' + - 'bioconductor-rtracklayer >=1.44.0,<1.45.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' + - 'bioconductor-shortread >=1.42.0,<1.43.0' - r-base - r-biocmanager run: - - 'bioconductor-biobase >=2.42.0,<2.43.0' - - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' - - 'bioconductor-biocparallel >=1.16.0,<1.17.0' - - 'bioconductor-biostrings >=2.50.0,<2.51.0' - - 'bioconductor-bsgenome >=1.50.0,<1.51.0' - - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' - - 'bioconductor-genomicalignments >=1.18.0,<1.19.0' - - 'bioconductor-genomicfeatures >=1.34.0,<1.35.0' - - 'bioconductor-genomicfiles >=1.18.0,<1.19.0' - - 'bioconductor-genomicranges >=1.34.0,<1.35.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-rbowtie >=1.22.0,<1.23.0' - - 'bioconductor-rsamtools >=1.34.0,<1.35.0' - - 'bioconductor-rtracklayer >=1.42.0,<1.43.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' - - 'bioconductor-shortread >=1.40.0,<1.41.0' - - 'bioconductor-zlibbioc >=1.28.0,<1.29.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' + - 'bioconductor-biocgenerics >=0.30.0,<0.31.0' + - 'bioconductor-biocparallel >=1.18.0,<1.19.0' + - 'bioconductor-biostrings >=2.52.0,<2.53.0' + - 'bioconductor-bsgenome >=1.52.0,<1.53.0' + - 'bioconductor-genomeinfodb >=1.20.0,<1.21.0' + - 'bioconductor-genomicalignments >=1.20.0,<1.21.0' + - 'bioconductor-genomicfeatures >=1.36.0,<1.37.0' + - 'bioconductor-genomicfiles >=1.20.0,<1.21.0' + - 'bioconductor-genomicranges >=1.36.0,<1.37.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-rbowtie >=1.24.0,<1.25.0' + - 'bioconductor-rhisat2 >=1.0.0,<1.1.0' + - 'bioconductor-rhtslib >=1.16.0,<1.17.0' + - 'bioconductor-rsamtools >=2.0.0,<2.1.0' + - 'bioconductor-rtracklayer >=1.44.0,<1.45.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' + - 'bioconductor-shortread >=1.42.0,<1.43.0' - r-base - r-biocmanager build: diff --git a/recipes/bioconductor-quaternaryprod/meta.yaml b/recipes/bioconductor-quaternaryprod/meta.yaml index 8c5b82ddbc372..f2ab2e8c4e949 100644 --- a/recipes/bioconductor-quaternaryprod/meta.yaml +++ b/recipes/bioconductor-quaternaryprod/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.16.0" %} +{% set version = "1.18.0" %} {% set name = "QuaternaryProd" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 47be657148eb3d8caa9db8d007f65c25 + md5: 1123375c16ab1573f3885096bf438f22 build: number: 0 rpaths: diff --git a/recipes/bioconductor-qubic/meta.yaml b/recipes/bioconductor-qubic/meta.yaml index 74f345e9e2db4..e676c62d11f5a 100644 --- a/recipes/bioconductor-qubic/meta.yaml +++ b/recipes/bioconductor-qubic/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.10.0" %} +{% set version = "1.12.0" %} {% set name = "QUBIC" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: ab39857fee893ea726e3d3d1392ee190 + md5: 62cc1d219fac17e3d73e77ecbfb1dc10 build: number: 0 rpaths: @@ -31,12 +31,10 @@ requirements: - r-matrix - 'r-rcpp >=0.11.0' - r-rcpparmadillo - - llvm-openmp # [osx] build: - {{ compiler('c') }} - {{ compiler('cxx') }} - make - - llvm-openmp # [osx] test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-qubicdata/meta.yaml b/recipes/bioconductor-qubicdata/meta.yaml index 8dac9db9e950d..4587679dc25ba 100644 --- a/recipes/bioconductor-qubicdata/meta.yaml +++ b/recipes/bioconductor-qubicdata/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.10.0" %} +{% set version = "1.12.0" %} {% set name = "QUBICdata" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 66ed9092477ac1c0ddf2b367d55682e1 + md5: db90386771c4b586cb2e466881e897d6 build: number: 0 rpaths: @@ -23,7 +23,7 @@ requirements: - r-base run: - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-qubicdata/post-link.sh b/recipes/bioconductor-qubicdata/post-link.sh index 6802402680e15..9ee5958f967de 100644 --- a/recipes/bioconductor-qubicdata/post-link.sh +++ b/recipes/bioconductor-qubicdata/post-link.sh @@ -1,11 +1,11 @@ #!/bin/bash -FN="QUBICdata_1.10.0.tar.gz" +FN="QUBICdata_1.12.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/experiment/src/contrib/QUBICdata_1.10.0.tar.gz" - "https://bioarchive.galaxyproject.org/QUBICdata_1.10.0.tar.gz" - "https://depot.galaxyproject.org/software/bioconductor-qubicdata/bioconductor-qubicdata_1.10.0_src_all.tar.gz" + "https://bioconductor.org/packages/3.9/data/experiment/src/contrib/QUBICdata_1.12.0.tar.gz" + "https://bioarchive.galaxyproject.org/QUBICdata_1.12.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-qubicdata/bioconductor-qubicdata_1.12.0_src_all.tar.gz" ) -MD5="66ed9092477ac1c0ddf2b367d55682e1" +MD5="db90386771c4b586cb2e466881e897d6" # Use a staging area in the conda dir rather than temp dirs, both to avoid # permission issues as well as to have things downloaded in a predictable @@ -16,7 +16,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-qusage/meta.yaml b/recipes/bioconductor-qusage/meta.yaml index 75159edb0d503..accde0a5d7ceb 100644 --- a/recipes/bioconductor-qusage/meta.yaml +++ b/recipes/bioconductor-qusage/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "2.16.1" %} +{% set version = "2.18.0" %} {% set name = "qusage" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - sha256: 2316d12285ff4776397f9846514df9c58da45e34e93659b55f3c5b239ba7bac9 + md5: 6ce81ce507c1b76c40a33058159813ee build: number: 0 rpaths: @@ -19,16 +19,16 @@ build: noarch: generic requirements: host: - - 'bioconductor-biobase >=2.42.0,<2.43.0' - - 'bioconductor-limma >=3.38.0,<3.39.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' + - 'bioconductor-limma >=3.40.0,<3.41.0' - r-base - - r-lsmeans + - r-emmeans - r-nlme run: - - 'bioconductor-biobase >=2.42.0,<2.43.0' - - 'bioconductor-limma >=3.38.0,<3.39.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' + - 'bioconductor-limma >=3.40.0,<3.41.0' - r-base - - r-lsmeans + - r-emmeans - r-nlme test: commands: diff --git a/recipes/bioconductor-qvalue/meta.yaml b/recipes/bioconductor-qvalue/meta.yaml index f6010e51cd335..6a5c40df0fe50 100644 --- a/recipes/bioconductor-qvalue/meta.yaml +++ b/recipes/bioconductor-qvalue/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "2.14.1" %} +{% set version = "2.16.0" %} {% set name = "qvalue" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - sha256: 4c7b86e6f00ac6cf8f9e1fbed8db808593de2d48555616b111b30a19eadfaa4f + md5: 2606ad06ad8b41c16fa5b6cc7a9f14ba build: number: 0 rpaths: diff --git a/recipes/bioconductor-r10kcod.db/meta.yaml b/recipes/bioconductor-r10kcod.db/meta.yaml index b4561e63b7fd8..077ecdf8c766f 100644 --- a/recipes/bioconductor-r10kcod.db/meta.yaml +++ b/recipes/bioconductor-r10kcod.db/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.4.0" %} {% set name = "r10kcod.db" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -12,7 +12,7 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 4a7a25fee64294cfb5adccaa6cf28772 build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ @@ -20,14 +20,14 @@ build: # Suggests: annotate, RUnit requirements: host: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' - - 'bioconductor-org.rn.eg.db >=3.7.0,<3.8.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' + - 'bioconductor-org.rn.eg.db >=3.8.0,<3.9.0' - r-base run: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' - - 'bioconductor-org.rn.eg.db >=3.7.0,<3.8.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' + - 'bioconductor-org.rn.eg.db >=3.8.0,<3.9.0' - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-r10kcod.db/post-link.sh b/recipes/bioconductor-r10kcod.db/post-link.sh index 986774e50c771..80322a6f87ad0 100644 --- a/recipes/bioconductor-r10kcod.db/post-link.sh +++ b/recipes/bioconductor-r10kcod.db/post-link.sh @@ -1,9 +1,10 @@ #!/bin/bash FN="r10kcod.db_3.4.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/r10kcod.db_3.4.0.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/r10kcod.db_3.4.0.tar.gz" "https://bioarchive.galaxyproject.org/r10kcod.db_3.4.0.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-r10kcod.db/bioconductor-r10kcod.db_3.4.0_src_all.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-r10kcod.db/bioconductor-r10kcod.db_3.4.0_src_all.tar.gz" ) MD5="4a7a25fee64294cfb5adccaa6cf28772" @@ -16,7 +17,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-r3cpet/meta.yaml b/recipes/bioconductor-r3cpet/meta.yaml index 7d7109198bcc5..2c87a1f2e69b6 100644 --- a/recipes/bioconductor-r3cpet/meta.yaml +++ b/recipes/bioconductor-r3cpet/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.14.0" %} +{% set version = "1.16.0" %} {% set name = "R3CPET" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: de75b6f33919464203ed7042c9fc5f6e + md5: 5d62ab7bf2c8e55bc2ed601855ce4d86 build: number: 0 rpaths: @@ -19,12 +19,12 @@ build: # Suggests: BiocStyle, knitr, TxDb.Hsapiens.UCSC.hg19.knownGene, biovizBase, biomaRt, AnnotationDbi, org.Hs.eg.db, shiny, ChIPpeakAnno requirements: host: - - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' - - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' - - 'bioconductor-genomicranges >=1.34.0,<1.35.0' - - 'bioconductor-ggbio >=1.30.0,<1.31.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-biocgenerics >=0.30.0,<0.31.0' + - 'bioconductor-genomeinfodb >=1.20.0,<1.21.0' + - 'bioconductor-genomicranges >=1.36.0,<1.37.0' + - 'bioconductor-ggbio >=1.32.0,<1.33.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' - r-base - r-clues - r-clvalid @@ -37,12 +37,12 @@ requirements: - r-rcurl - r-reshape2 run: - - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' - - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' - - 'bioconductor-genomicranges >=1.34.0,<1.35.0' - - 'bioconductor-ggbio >=1.30.0,<1.31.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-biocgenerics >=0.30.0,<0.31.0' + - 'bioconductor-genomeinfodb >=1.20.0,<1.21.0' + - 'bioconductor-genomicranges >=1.36.0,<1.37.0' + - 'bioconductor-ggbio >=1.32.0,<1.33.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' - r-base - r-clues - r-clvalid diff --git a/recipes/bioconductor-r3cseq/meta.yaml b/recipes/bioconductor-r3cseq/meta.yaml index 70ebd66a1ecd6..2b895cc9a595d 100644 --- a/recipes/bioconductor-r3cseq/meta.yaml +++ b/recipes/bioconductor-r3cseq/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.28.0" %} +{% set version = "1.30.0" %} {% set name = "r3Cseq" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: e900fcaf098fd698650694cf4f2b3dad + md5: b39e873a2ae7044574684b964168f7e0 build: number: 0 rpaths: @@ -20,26 +20,26 @@ build: # Suggests: BSgenome.Mmusculus.UCSC.mm9.masked, BSgenome.Mmusculus.UCSC.mm10.masked, BSgenome.Hsapiens.UCSC.hg18.masked, BSgenome.Hsapiens.UCSC.hg19.masked, BSgenome.Rnorvegicus.UCSC.rn5.masked requirements: host: - - 'bioconductor-biostrings >=2.50.0,<2.51.0' - - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' - - 'bioconductor-genomicranges >=1.34.0,<1.35.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-qvalue >=2.14.0,<2.15.0' - - 'bioconductor-rsamtools >=1.34.0,<1.35.0' - - 'bioconductor-rtracklayer >=1.42.0,<1.43.0' + - 'bioconductor-biostrings >=2.52.0,<2.53.0' + - 'bioconductor-genomeinfodb >=1.20.0,<1.21.0' + - 'bioconductor-genomicranges >=1.36.0,<1.37.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-qvalue >=2.16.0,<2.17.0' + - 'bioconductor-rsamtools >=2.0.0,<2.1.0' + - 'bioconductor-rtracklayer >=1.44.0,<1.45.0' - r-base - r-data.table - r-rcolorbrewer - r-sqldf - r-vgam run: - - 'bioconductor-biostrings >=2.50.0,<2.51.0' - - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' - - 'bioconductor-genomicranges >=1.34.0,<1.35.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-qvalue >=2.14.0,<2.15.0' - - 'bioconductor-rsamtools >=1.34.0,<1.35.0' - - 'bioconductor-rtracklayer >=1.42.0,<1.43.0' + - 'bioconductor-biostrings >=2.52.0,<2.53.0' + - 'bioconductor-genomeinfodb >=1.20.0,<1.21.0' + - 'bioconductor-genomicranges >=1.36.0,<1.37.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-qvalue >=2.16.0,<2.17.0' + - 'bioconductor-rsamtools >=2.0.0,<2.1.0' + - 'bioconductor-rtracklayer >=1.44.0,<1.45.0' - r-base - r-data.table - r-rcolorbrewer @@ -51,7 +51,7 @@ test: about: home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: GPL-3 - summary: 'This package is an implementation of data analysis for the long-range interactions from 3C-seq assay.' + summary: 'This package is used for the analysis of long-range chromatin interactions from 3C-seq assay.' extra: identifiers: - biotools:r3cseq diff --git a/recipes/bioconductor-r453plus1toolbox/meta.yaml b/recipes/bioconductor-r453plus1toolbox/meta.yaml index 39c2da66fa4d3..c65ef1f54f2c7 100644 --- a/recipes/bioconductor-r453plus1toolbox/meta.yaml +++ b/recipes/bioconductor-r453plus1toolbox/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.32.0" %} +{% set version = "1.34.0" %} {% set name = "R453Plus1Toolbox" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 4a5bb4fe4d331ca8c30ca120a0d8ea17 + md5: c13e0ea174443f8c59551b6797f15977 build: number: 0 rpaths: @@ -19,37 +19,37 @@ build: # Suggests: rtracklayer, BSgenome.Hsapiens.UCSC.hg19, BSgenome.Scerevisiae.UCSC.sacCer2 requirements: host: - - 'bioconductor-biobase >=2.42.0,<2.43.0' - - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' - - 'bioconductor-biomart >=2.38.0,<2.39.0' - - 'bioconductor-biostrings >=2.50.0,<2.51.0' - - 'bioconductor-bsgenome >=1.50.0,<1.51.0' - - 'bioconductor-genomicranges >=1.34.0,<1.35.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-rsamtools >=1.34.0,<1.35.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' - - 'bioconductor-shortread >=1.40.0,<1.41.0' - - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' - - 'bioconductor-variantannotation >=1.28.0,<1.29.0' - - 'bioconductor-xvector >=0.22.0,<0.23.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' + - 'bioconductor-biocgenerics >=0.30.0,<0.31.0' + - 'bioconductor-biomart >=2.40.0,<2.41.0' + - 'bioconductor-biostrings >=2.52.0,<2.53.0' + - 'bioconductor-bsgenome >=1.52.0,<1.53.0' + - 'bioconductor-genomicranges >=1.36.0,<1.37.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-rsamtools >=2.0.0,<2.1.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' + - 'bioconductor-shortread >=1.42.0,<1.43.0' + - 'bioconductor-summarizedexperiment >=1.14.0,<1.15.0' + - 'bioconductor-variantannotation >=1.30.0,<1.31.0' + - 'bioconductor-xvector >=0.24.0,<0.25.0' - r-base - r-r2html - r-teachingdemos - r-xtable run: - - 'bioconductor-biobase >=2.42.0,<2.43.0' - - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' - - 'bioconductor-biomart >=2.38.0,<2.39.0' - - 'bioconductor-biostrings >=2.50.0,<2.51.0' - - 'bioconductor-bsgenome >=1.50.0,<1.51.0' - - 'bioconductor-genomicranges >=1.34.0,<1.35.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-rsamtools >=1.34.0,<1.35.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' - - 'bioconductor-shortread >=1.40.0,<1.41.0' - - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' - - 'bioconductor-variantannotation >=1.28.0,<1.29.0' - - 'bioconductor-xvector >=0.22.0,<0.23.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' + - 'bioconductor-biocgenerics >=0.30.0,<0.31.0' + - 'bioconductor-biomart >=2.40.0,<2.41.0' + - 'bioconductor-biostrings >=2.52.0,<2.53.0' + - 'bioconductor-bsgenome >=1.52.0,<1.53.0' + - 'bioconductor-genomicranges >=1.36.0,<1.37.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-rsamtools >=2.0.0,<2.1.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' + - 'bioconductor-shortread >=1.42.0,<1.43.0' + - 'bioconductor-summarizedexperiment >=1.14.0,<1.15.0' + - 'bioconductor-variantannotation >=1.30.0,<1.31.0' + - 'bioconductor-xvector >=0.24.0,<0.25.0' - r-base - r-r2html - r-teachingdemos diff --git a/recipes/bioconductor-r4rna/meta.yaml b/recipes/bioconductor-r4rna/meta.yaml index b8a5ee2deb5a4..214f5b30cc68d 100644 --- a/recipes/bioconductor-r4rna/meta.yaml +++ b/recipes/bioconductor-r4rna/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.10.0" %} +{% set version = "1.12.0" %} {% set name = "R4RNA" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: e6c4cca4a785471fb80fbf9f3d66358e + md5: 4ce7f63eb631f73c6cb99ce4ef43c5e7 build: number: 0 rpaths: @@ -19,10 +19,10 @@ build: noarch: generic requirements: host: - - 'bioconductor-biostrings >=2.50.0,<2.51.0' + - 'bioconductor-biostrings >=2.52.0,<2.53.0' - r-base run: - - 'bioconductor-biostrings >=2.50.0,<2.51.0' + - 'bioconductor-biostrings >=2.52.0,<2.53.0' - r-base test: commands: diff --git a/recipes/bioconductor-rae230a.db/meta.yaml b/recipes/bioconductor-rae230a.db/meta.yaml index 1d989be598dd4..d5b65cb313086 100644 --- a/recipes/bioconductor-rae230a.db/meta.yaml +++ b/recipes/bioconductor-rae230a.db/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.2.3" %} {% set name = "rae230a.db" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -12,7 +12,7 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: fb9d6a02ce85cc521c0477a1a6f861f6 build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ @@ -20,14 +20,14 @@ build: # Suggests: DBI, annotate, RUnit requirements: host: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' - - 'bioconductor-org.rn.eg.db >=3.7.0,<3.8.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' + - 'bioconductor-org.rn.eg.db >=3.8.0,<3.9.0' - r-base run: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' - - 'bioconductor-org.rn.eg.db >=3.7.0,<3.8.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' + - 'bioconductor-org.rn.eg.db >=3.8.0,<3.9.0' - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-rae230a.db/post-link.sh b/recipes/bioconductor-rae230a.db/post-link.sh index 35a1153957d93..f90785c943e4f 100644 --- a/recipes/bioconductor-rae230a.db/post-link.sh +++ b/recipes/bioconductor-rae230a.db/post-link.sh @@ -1,9 +1,10 @@ #!/bin/bash FN="rae230a.db_3.2.3.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/rae230a.db_3.2.3.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/rae230a.db_3.2.3.tar.gz" "https://bioarchive.galaxyproject.org/rae230a.db_3.2.3.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-rae230a.db/bioconductor-rae230a.db_3.2.3_src_all.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-rae230a.db/bioconductor-rae230a.db_3.2.3_src_all.tar.gz" ) MD5="fb9d6a02ce85cc521c0477a1a6f861f6" @@ -16,7 +17,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-rae230acdf/meta.yaml b/recipes/bioconductor-rae230acdf/meta.yaml index 5f879845f3554..652499ea84032 100644 --- a/recipes/bioconductor-rae230acdf/meta.yaml +++ b/recipes/bioconductor-rae230acdf/meta.yaml @@ -1,6 +1,6 @@ {% set version = "2.18.0" %} {% set name = "rae230acdf" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -12,19 +12,19 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 6f2281124e1be164d5fd599e84f6adbc build: - number: 1 + number: 2 rpaths: - lib/R/lib/ - lib/ noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' - r-base run: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-rae230acdf/post-link.sh b/recipes/bioconductor-rae230acdf/post-link.sh index f23870faecc85..f64a9a7a3707d 100644 --- a/recipes/bioconductor-rae230acdf/post-link.sh +++ b/recipes/bioconductor-rae230acdf/post-link.sh @@ -1,9 +1,10 @@ #!/bin/bash FN="rae230acdf_2.18.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/rae230acdf_2.18.0.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/rae230acdf_2.18.0.tar.gz" "https://bioarchive.galaxyproject.org/rae230acdf_2.18.0.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-rae230acdf/bioconductor-rae230acdf_2.18.0_src_all.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-rae230acdf/bioconductor-rae230acdf_2.18.0_src_all.tar.gz" ) MD5="6f2281124e1be164d5fd599e84f6adbc" @@ -16,7 +17,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-rae230aprobe/meta.yaml b/recipes/bioconductor-rae230aprobe/meta.yaml index 1a846af66b330..949128c2a0770 100644 --- a/recipes/bioconductor-rae230aprobe/meta.yaml +++ b/recipes/bioconductor-rae230aprobe/meta.yaml @@ -1,6 +1,6 @@ {% set version = "2.18.0" %} {% set name = "rae230aprobe" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -12,19 +12,19 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 6f2d77e1d9c1e3afb96ef78b3202bb0b build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' - r-base run: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-rae230aprobe/post-link.sh b/recipes/bioconductor-rae230aprobe/post-link.sh index d826c1810d3d2..8afa6ca9d4f7f 100644 --- a/recipes/bioconductor-rae230aprobe/post-link.sh +++ b/recipes/bioconductor-rae230aprobe/post-link.sh @@ -1,9 +1,10 @@ #!/bin/bash FN="rae230aprobe_2.18.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/rae230aprobe_2.18.0.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/rae230aprobe_2.18.0.tar.gz" "https://bioarchive.galaxyproject.org/rae230aprobe_2.18.0.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-rae230aprobe/bioconductor-rae230aprobe_2.18.0_src_all.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-rae230aprobe/bioconductor-rae230aprobe_2.18.0_src_all.tar.gz" ) MD5="6f2d77e1d9c1e3afb96ef78b3202bb0b" @@ -16,7 +17,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-rae230b.db/meta.yaml b/recipes/bioconductor-rae230b.db/meta.yaml index e4f4984c0ca55..56c6deb285976 100644 --- a/recipes/bioconductor-rae230b.db/meta.yaml +++ b/recipes/bioconductor-rae230b.db/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.2.3" %} {% set name = "rae230b.db" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -12,7 +12,7 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 23fb8fd2cf3f178020db9b7f5692a28d build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ @@ -20,14 +20,14 @@ build: # Suggests: DBI, annotate, RUnit requirements: host: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' - - 'bioconductor-org.rn.eg.db >=3.7.0,<3.8.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' + - 'bioconductor-org.rn.eg.db >=3.8.0,<3.9.0' - r-base run: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' - - 'bioconductor-org.rn.eg.db >=3.7.0,<3.8.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' + - 'bioconductor-org.rn.eg.db >=3.8.0,<3.9.0' - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-rae230b.db/post-link.sh b/recipes/bioconductor-rae230b.db/post-link.sh index a6ad41c26083d..0e77864a4efc6 100644 --- a/recipes/bioconductor-rae230b.db/post-link.sh +++ b/recipes/bioconductor-rae230b.db/post-link.sh @@ -1,9 +1,10 @@ #!/bin/bash FN="rae230b.db_3.2.3.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/rae230b.db_3.2.3.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/rae230b.db_3.2.3.tar.gz" "https://bioarchive.galaxyproject.org/rae230b.db_3.2.3.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-rae230b.db/bioconductor-rae230b.db_3.2.3_src_all.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-rae230b.db/bioconductor-rae230b.db_3.2.3_src_all.tar.gz" ) MD5="23fb8fd2cf3f178020db9b7f5692a28d" @@ -16,7 +17,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-rae230bcdf/meta.yaml b/recipes/bioconductor-rae230bcdf/meta.yaml index 2014fe4270303..a27ec7ed8e775 100644 --- a/recipes/bioconductor-rae230bcdf/meta.yaml +++ b/recipes/bioconductor-rae230bcdf/meta.yaml @@ -1,6 +1,6 @@ {% set version = "2.18.0" %} {% set name = "rae230bcdf" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -12,19 +12,19 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: bd61c17402e9c04be1000c16e0356618 build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' - r-base run: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-rae230bcdf/post-link.sh b/recipes/bioconductor-rae230bcdf/post-link.sh index 5bb434c6827ad..a489f09ba595c 100644 --- a/recipes/bioconductor-rae230bcdf/post-link.sh +++ b/recipes/bioconductor-rae230bcdf/post-link.sh @@ -1,9 +1,10 @@ #!/bin/bash FN="rae230bcdf_2.18.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/rae230bcdf_2.18.0.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/rae230bcdf_2.18.0.tar.gz" "https://bioarchive.galaxyproject.org/rae230bcdf_2.18.0.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-rae230bcdf/bioconductor-rae230bcdf_2.18.0_src_all.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-rae230bcdf/bioconductor-rae230bcdf_2.18.0_src_all.tar.gz" ) MD5="bd61c17402e9c04be1000c16e0356618" @@ -16,7 +17,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-rae230bprobe/meta.yaml b/recipes/bioconductor-rae230bprobe/meta.yaml index 2ab69b63ae210..aa0350361002f 100644 --- a/recipes/bioconductor-rae230bprobe/meta.yaml +++ b/recipes/bioconductor-rae230bprobe/meta.yaml @@ -1,6 +1,6 @@ {% set version = "2.18.0" %} {% set name = "rae230bprobe" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -12,19 +12,19 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 7bdb3a07e1f00de8ff510a69bdac4c53 build: - number: 1 + number: 2 rpaths: - lib/R/lib/ - lib/ noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' - r-base run: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-rae230bprobe/post-link.sh b/recipes/bioconductor-rae230bprobe/post-link.sh index e280c29f60741..acc0a04ab0719 100644 --- a/recipes/bioconductor-rae230bprobe/post-link.sh +++ b/recipes/bioconductor-rae230bprobe/post-link.sh @@ -1,9 +1,10 @@ #!/bin/bash FN="rae230bprobe_2.18.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/rae230bprobe_2.18.0.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/rae230bprobe_2.18.0.tar.gz" "https://bioarchive.galaxyproject.org/rae230bprobe_2.18.0.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-rae230bprobe/bioconductor-rae230bprobe_2.18.0_src_all.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-rae230bprobe/bioconductor-rae230bprobe_2.18.0_src_all.tar.gz" ) MD5="7bdb3a07e1f00de8ff510a69bdac4c53" @@ -16,7 +17,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-raex10stprobeset.db/meta.yaml b/recipes/bioconductor-raex10stprobeset.db/meta.yaml index 83854f12a3323..97ea9c107dcf4 100644 --- a/recipes/bioconductor-raex10stprobeset.db/meta.yaml +++ b/recipes/bioconductor-raex10stprobeset.db/meta.yaml @@ -1,6 +1,6 @@ {% set version = "8.7.0" %} {% set name = "raex10stprobeset.db" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -12,7 +12,7 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 9cdc6abb3cf39eb7363fe74a0963c5b7 build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ @@ -20,14 +20,14 @@ build: # Suggests: DBI, annotate, RUnit requirements: host: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' - - 'bioconductor-org.rn.eg.db >=3.7.0,<3.8.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' + - 'bioconductor-org.rn.eg.db >=3.8.0,<3.9.0' - r-base run: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' - - 'bioconductor-org.rn.eg.db >=3.7.0,<3.8.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' + - 'bioconductor-org.rn.eg.db >=3.8.0,<3.9.0' - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-raex10stprobeset.db/post-link.sh b/recipes/bioconductor-raex10stprobeset.db/post-link.sh index a1b0e1a717bec..5749150e416cc 100644 --- a/recipes/bioconductor-raex10stprobeset.db/post-link.sh +++ b/recipes/bioconductor-raex10stprobeset.db/post-link.sh @@ -1,9 +1,10 @@ #!/bin/bash FN="raex10stprobeset.db_8.7.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/raex10stprobeset.db_8.7.0.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/raex10stprobeset.db_8.7.0.tar.gz" "https://bioarchive.galaxyproject.org/raex10stprobeset.db_8.7.0.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-raex10stprobeset.db/bioconductor-raex10stprobeset.db_8.7.0_src_all.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-raex10stprobeset.db/bioconductor-raex10stprobeset.db_8.7.0_src_all.tar.gz" ) MD5="9cdc6abb3cf39eb7363fe74a0963c5b7" @@ -16,7 +17,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-raex10sttranscriptcluster.db/meta.yaml b/recipes/bioconductor-raex10sttranscriptcluster.db/meta.yaml index b3972b4473d94..2ffc6d2464ed1 100644 --- a/recipes/bioconductor-raex10sttranscriptcluster.db/meta.yaml +++ b/recipes/bioconductor-raex10sttranscriptcluster.db/meta.yaml @@ -1,6 +1,6 @@ {% set version = "8.7.0" %} {% set name = "raex10sttranscriptcluster.db" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -12,7 +12,7 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 3eb2d97bfffb595e6b23550f4a27a8c3 build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ @@ -20,14 +20,14 @@ build: # Suggests: DBI, annotate, RUnit requirements: host: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' - - 'bioconductor-org.rn.eg.db >=3.7.0,<3.8.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' + - 'bioconductor-org.rn.eg.db >=3.8.0,<3.9.0' - r-base run: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' - - 'bioconductor-org.rn.eg.db >=3.7.0,<3.8.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' + - 'bioconductor-org.rn.eg.db >=3.8.0,<3.9.0' - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-raex10sttranscriptcluster.db/post-link.sh b/recipes/bioconductor-raex10sttranscriptcluster.db/post-link.sh index c69196a44ab5e..dd50ea69c9752 100644 --- a/recipes/bioconductor-raex10sttranscriptcluster.db/post-link.sh +++ b/recipes/bioconductor-raex10sttranscriptcluster.db/post-link.sh @@ -1,9 +1,10 @@ #!/bin/bash FN="raex10sttranscriptcluster.db_8.7.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/raex10sttranscriptcluster.db_8.7.0.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/raex10sttranscriptcluster.db_8.7.0.tar.gz" "https://bioarchive.galaxyproject.org/raex10sttranscriptcluster.db_8.7.0.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-raex10sttranscriptcluster.db/bioconductor-raex10sttranscriptcluster.db_8.7.0_src_all.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-raex10sttranscriptcluster.db/bioconductor-raex10sttranscriptcluster.db_8.7.0_src_all.tar.gz" ) MD5="3eb2d97bfffb595e6b23550f4a27a8c3" @@ -16,7 +17,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-raexexonprobesetlocation/meta.yaml b/recipes/bioconductor-raexexonprobesetlocation/meta.yaml index 8e55e2f5145d5..e8cf3ad8fa0bb 100644 --- a/recipes/bioconductor-raexexonprobesetlocation/meta.yaml +++ b/recipes/bioconductor-raexexonprobesetlocation/meta.yaml @@ -1,6 +1,6 @@ {% set version = "1.15.0" %} {% set name = "RaExExonProbesetLocation" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -12,19 +12,19 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' md5: d547bcd30685495283b32f0f86ecc79b build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' - r-base run: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-raexexonprobesetlocation/post-link.sh b/recipes/bioconductor-raexexonprobesetlocation/post-link.sh index e42205b196dde..6b2d78096b64c 100644 --- a/recipes/bioconductor-raexexonprobesetlocation/post-link.sh +++ b/recipes/bioconductor-raexexonprobesetlocation/post-link.sh @@ -1,9 +1,10 @@ #!/bin/bash FN="RaExExonProbesetLocation_1.15.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/RaExExonProbesetLocation_1.15.0.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/RaExExonProbesetLocation_1.15.0.tar.gz" "https://bioarchive.galaxyproject.org/RaExExonProbesetLocation_1.15.0.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-raexexonprobesetlocation/bioconductor-raexexonprobesetlocation_1.15.0_src_all.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-raexexonprobesetlocation/bioconductor-raexexonprobesetlocation_1.15.0_src_all.tar.gz" ) MD5="d547bcd30685495283b32f0f86ecc79b" @@ -16,7 +17,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-ragene10stprobeset.db/meta.yaml b/recipes/bioconductor-ragene10stprobeset.db/meta.yaml index 36986607d49b1..4ad75d9d5774d 100644 --- a/recipes/bioconductor-ragene10stprobeset.db/meta.yaml +++ b/recipes/bioconductor-ragene10stprobeset.db/meta.yaml @@ -1,6 +1,6 @@ {% set version = "8.7.0" %} {% set name = "ragene10stprobeset.db" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -12,7 +12,7 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 7338948d43b2200ca255aeb87cf99f3e build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ @@ -20,14 +20,14 @@ build: # Suggests: DBI, annotate, RUnit requirements: host: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' - - 'bioconductor-org.rn.eg.db >=3.7.0,<3.8.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' + - 'bioconductor-org.rn.eg.db >=3.8.0,<3.9.0' - r-base run: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' - - 'bioconductor-org.rn.eg.db >=3.7.0,<3.8.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' + - 'bioconductor-org.rn.eg.db >=3.8.0,<3.9.0' - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-ragene10stprobeset.db/post-link.sh b/recipes/bioconductor-ragene10stprobeset.db/post-link.sh index 7db691a1a7092..708242a260f38 100644 --- a/recipes/bioconductor-ragene10stprobeset.db/post-link.sh +++ b/recipes/bioconductor-ragene10stprobeset.db/post-link.sh @@ -1,9 +1,10 @@ #!/bin/bash FN="ragene10stprobeset.db_8.7.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/ragene10stprobeset.db_8.7.0.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/ragene10stprobeset.db_8.7.0.tar.gz" "https://bioarchive.galaxyproject.org/ragene10stprobeset.db_8.7.0.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-ragene10stprobeset.db/bioconductor-ragene10stprobeset.db_8.7.0_src_all.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-ragene10stprobeset.db/bioconductor-ragene10stprobeset.db_8.7.0_src_all.tar.gz" ) MD5="7338948d43b2200ca255aeb87cf99f3e" @@ -16,7 +17,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-ragene10sttranscriptcluster.db/meta.yaml b/recipes/bioconductor-ragene10sttranscriptcluster.db/meta.yaml index 5c26abfef3dac..a59a71fa66025 100644 --- a/recipes/bioconductor-ragene10sttranscriptcluster.db/meta.yaml +++ b/recipes/bioconductor-ragene10sttranscriptcluster.db/meta.yaml @@ -1,6 +1,6 @@ {% set version = "8.7.0" %} {% set name = "ragene10sttranscriptcluster.db" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -12,7 +12,7 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 2523540bab5f12e6e5c1e140c1663832 build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ @@ -20,14 +20,14 @@ build: # Suggests: DBI, annotate, RUnit requirements: host: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' - - 'bioconductor-org.rn.eg.db >=3.7.0,<3.8.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' + - 'bioconductor-org.rn.eg.db >=3.8.0,<3.9.0' - r-base run: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' - - 'bioconductor-org.rn.eg.db >=3.7.0,<3.8.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' + - 'bioconductor-org.rn.eg.db >=3.8.0,<3.9.0' - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-ragene10sttranscriptcluster.db/post-link.sh b/recipes/bioconductor-ragene10sttranscriptcluster.db/post-link.sh index 1f4d5e95e09c2..49570ec678c20 100644 --- a/recipes/bioconductor-ragene10sttranscriptcluster.db/post-link.sh +++ b/recipes/bioconductor-ragene10sttranscriptcluster.db/post-link.sh @@ -1,9 +1,10 @@ #!/bin/bash FN="ragene10sttranscriptcluster.db_8.7.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/ragene10sttranscriptcluster.db_8.7.0.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/ragene10sttranscriptcluster.db_8.7.0.tar.gz" "https://bioarchive.galaxyproject.org/ragene10sttranscriptcluster.db_8.7.0.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-ragene10sttranscriptcluster.db/bioconductor-ragene10sttranscriptcluster.db_8.7.0_src_all.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-ragene10sttranscriptcluster.db/bioconductor-ragene10sttranscriptcluster.db_8.7.0_src_all.tar.gz" ) MD5="2523540bab5f12e6e5c1e140c1663832" @@ -16,7 +17,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-ragene10stv1cdf/meta.yaml b/recipes/bioconductor-ragene10stv1cdf/meta.yaml index 532fc2b40020a..e42e4b9a6ce90 100644 --- a/recipes/bioconductor-ragene10stv1cdf/meta.yaml +++ b/recipes/bioconductor-ragene10stv1cdf/meta.yaml @@ -1,6 +1,6 @@ {% set version = "2.18.0" %} {% set name = "ragene10stv1cdf" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -12,19 +12,19 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: df696e9dbf5b3f2761b6a0a5914be058 build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' - r-base run: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-ragene10stv1cdf/post-link.sh b/recipes/bioconductor-ragene10stv1cdf/post-link.sh index 6c394ecfd9d4e..04b9de535bb4c 100644 --- a/recipes/bioconductor-ragene10stv1cdf/post-link.sh +++ b/recipes/bioconductor-ragene10stv1cdf/post-link.sh @@ -1,9 +1,10 @@ #!/bin/bash FN="ragene10stv1cdf_2.18.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/ragene10stv1cdf_2.18.0.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/ragene10stv1cdf_2.18.0.tar.gz" "https://bioarchive.galaxyproject.org/ragene10stv1cdf_2.18.0.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-ragene10stv1cdf/bioconductor-ragene10stv1cdf_2.18.0_src_all.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-ragene10stv1cdf/bioconductor-ragene10stv1cdf_2.18.0_src_all.tar.gz" ) MD5="df696e9dbf5b3f2761b6a0a5914be058" @@ -16,7 +17,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-ragene10stv1probe/meta.yaml b/recipes/bioconductor-ragene10stv1probe/meta.yaml index 1c86c67966c58..092fca9e8fc66 100644 --- a/recipes/bioconductor-ragene10stv1probe/meta.yaml +++ b/recipes/bioconductor-ragene10stv1probe/meta.yaml @@ -1,6 +1,6 @@ {% set version = "2.18.0" %} {% set name = "ragene10stv1probe" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -12,19 +12,19 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 94978b6efb075aacf31ccdc8000e40fa build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' - r-base run: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-ragene10stv1probe/post-link.sh b/recipes/bioconductor-ragene10stv1probe/post-link.sh index 959d40221fcdc..7abdf6abca46e 100644 --- a/recipes/bioconductor-ragene10stv1probe/post-link.sh +++ b/recipes/bioconductor-ragene10stv1probe/post-link.sh @@ -1,9 +1,10 @@ #!/bin/bash FN="ragene10stv1probe_2.18.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/ragene10stv1probe_2.18.0.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/ragene10stv1probe_2.18.0.tar.gz" "https://bioarchive.galaxyproject.org/ragene10stv1probe_2.18.0.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-ragene10stv1probe/bioconductor-ragene10stv1probe_2.18.0_src_all.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-ragene10stv1probe/bioconductor-ragene10stv1probe_2.18.0_src_all.tar.gz" ) MD5="94978b6efb075aacf31ccdc8000e40fa" @@ -16,7 +17,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-ragene11stprobeset.db/meta.yaml b/recipes/bioconductor-ragene11stprobeset.db/meta.yaml index 2efc31a7a2fc2..e76d7aff28b7c 100644 --- a/recipes/bioconductor-ragene11stprobeset.db/meta.yaml +++ b/recipes/bioconductor-ragene11stprobeset.db/meta.yaml @@ -1,6 +1,6 @@ {% set version = "8.7.0" %} {% set name = "ragene11stprobeset.db" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -12,7 +12,7 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 5ce8dfb793afc7307106f3d4872dfeb1 build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ @@ -20,14 +20,14 @@ build: # Suggests: DBI, annotate, RUnit requirements: host: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' - - 'bioconductor-org.rn.eg.db >=3.7.0,<3.8.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' + - 'bioconductor-org.rn.eg.db >=3.8.0,<3.9.0' - r-base run: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' - - 'bioconductor-org.rn.eg.db >=3.7.0,<3.8.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' + - 'bioconductor-org.rn.eg.db >=3.8.0,<3.9.0' - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-ragene11stprobeset.db/post-link.sh b/recipes/bioconductor-ragene11stprobeset.db/post-link.sh index ad9d2e606e770..92ae85c74d410 100644 --- a/recipes/bioconductor-ragene11stprobeset.db/post-link.sh +++ b/recipes/bioconductor-ragene11stprobeset.db/post-link.sh @@ -1,9 +1,10 @@ #!/bin/bash FN="ragene11stprobeset.db_8.7.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/ragene11stprobeset.db_8.7.0.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/ragene11stprobeset.db_8.7.0.tar.gz" "https://bioarchive.galaxyproject.org/ragene11stprobeset.db_8.7.0.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-ragene11stprobeset.db/bioconductor-ragene11stprobeset.db_8.7.0_src_all.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-ragene11stprobeset.db/bioconductor-ragene11stprobeset.db_8.7.0_src_all.tar.gz" ) MD5="5ce8dfb793afc7307106f3d4872dfeb1" @@ -16,7 +17,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-ragene11sttranscriptcluster.db/meta.yaml b/recipes/bioconductor-ragene11sttranscriptcluster.db/meta.yaml index 265411283f5b2..ca16e756087f4 100644 --- a/recipes/bioconductor-ragene11sttranscriptcluster.db/meta.yaml +++ b/recipes/bioconductor-ragene11sttranscriptcluster.db/meta.yaml @@ -1,6 +1,6 @@ {% set version = "8.7.0" %} {% set name = "ragene11sttranscriptcluster.db" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -12,7 +12,7 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 81a645c32105ffb4bfb45eb8bcf13855 build: - number: 1 + number: 2 rpaths: - lib/R/lib/ - lib/ @@ -20,14 +20,14 @@ build: # Suggests: DBI, annotate, RUnit requirements: host: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' - - 'bioconductor-org.rn.eg.db >=3.7.0,<3.8.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' + - 'bioconductor-org.rn.eg.db >=3.8.0,<3.9.0' - r-base run: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' - - 'bioconductor-org.rn.eg.db >=3.7.0,<3.8.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' + - 'bioconductor-org.rn.eg.db >=3.8.0,<3.9.0' - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-ragene11sttranscriptcluster.db/post-link.sh b/recipes/bioconductor-ragene11sttranscriptcluster.db/post-link.sh index afcd3d90b18f2..f86f89f75f335 100644 --- a/recipes/bioconductor-ragene11sttranscriptcluster.db/post-link.sh +++ b/recipes/bioconductor-ragene11sttranscriptcluster.db/post-link.sh @@ -1,9 +1,10 @@ #!/bin/bash FN="ragene11sttranscriptcluster.db_8.7.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/ragene11sttranscriptcluster.db_8.7.0.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/ragene11sttranscriptcluster.db_8.7.0.tar.gz" "https://bioarchive.galaxyproject.org/ragene11sttranscriptcluster.db_8.7.0.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-ragene11sttranscriptcluster.db/bioconductor-ragene11sttranscriptcluster.db_8.7.0_src_all.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-ragene11sttranscriptcluster.db/bioconductor-ragene11sttranscriptcluster.db_8.7.0_src_all.tar.gz" ) MD5="81a645c32105ffb4bfb45eb8bcf13855" @@ -16,7 +17,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-ragene20stprobeset.db/meta.yaml b/recipes/bioconductor-ragene20stprobeset.db/meta.yaml index 163aeb1174cdd..430ccddc5a2be 100644 --- a/recipes/bioconductor-ragene20stprobeset.db/meta.yaml +++ b/recipes/bioconductor-ragene20stprobeset.db/meta.yaml @@ -1,6 +1,6 @@ {% set version = "8.7.0" %} {% set name = "ragene20stprobeset.db" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -12,7 +12,7 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: dd4e8701fd716e8564da2581d52ce1db build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ @@ -20,14 +20,14 @@ build: # Suggests: DBI, annotate, RUnit requirements: host: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' - - 'bioconductor-org.rn.eg.db >=3.7.0,<3.8.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' + - 'bioconductor-org.rn.eg.db >=3.8.0,<3.9.0' - r-base run: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' - - 'bioconductor-org.rn.eg.db >=3.7.0,<3.8.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' + - 'bioconductor-org.rn.eg.db >=3.8.0,<3.9.0' - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-ragene20stprobeset.db/post-link.sh b/recipes/bioconductor-ragene20stprobeset.db/post-link.sh index dd8a7cd3e42da..16ae03f5b6127 100644 --- a/recipes/bioconductor-ragene20stprobeset.db/post-link.sh +++ b/recipes/bioconductor-ragene20stprobeset.db/post-link.sh @@ -1,9 +1,10 @@ #!/bin/bash FN="ragene20stprobeset.db_8.7.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/ragene20stprobeset.db_8.7.0.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/ragene20stprobeset.db_8.7.0.tar.gz" "https://bioarchive.galaxyproject.org/ragene20stprobeset.db_8.7.0.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-ragene20stprobeset.db/bioconductor-ragene20stprobeset.db_8.7.0_src_all.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-ragene20stprobeset.db/bioconductor-ragene20stprobeset.db_8.7.0_src_all.tar.gz" ) MD5="dd4e8701fd716e8564da2581d52ce1db" @@ -16,7 +17,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-ragene20sttranscriptcluster.db/meta.yaml b/recipes/bioconductor-ragene20sttranscriptcluster.db/meta.yaml index c748c9b50d549..680f206700923 100644 --- a/recipes/bioconductor-ragene20sttranscriptcluster.db/meta.yaml +++ b/recipes/bioconductor-ragene20sttranscriptcluster.db/meta.yaml @@ -1,6 +1,6 @@ {% set version = "8.7.0" %} {% set name = "ragene20sttranscriptcluster.db" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -12,7 +12,7 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 79693b35c3837f9e5fe7337ac3e86e1f build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ @@ -20,14 +20,14 @@ build: # Suggests: DBI, annotate, RUnit requirements: host: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' - - 'bioconductor-org.rn.eg.db >=3.7.0,<3.8.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' + - 'bioconductor-org.rn.eg.db >=3.8.0,<3.9.0' - r-base run: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' - - 'bioconductor-org.rn.eg.db >=3.7.0,<3.8.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' + - 'bioconductor-org.rn.eg.db >=3.8.0,<3.9.0' - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-ragene20sttranscriptcluster.db/post-link.sh b/recipes/bioconductor-ragene20sttranscriptcluster.db/post-link.sh index 221463d0b2328..42066648fe19e 100644 --- a/recipes/bioconductor-ragene20sttranscriptcluster.db/post-link.sh +++ b/recipes/bioconductor-ragene20sttranscriptcluster.db/post-link.sh @@ -1,9 +1,10 @@ #!/bin/bash FN="ragene20sttranscriptcluster.db_8.7.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/ragene20sttranscriptcluster.db_8.7.0.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/ragene20sttranscriptcluster.db_8.7.0.tar.gz" "https://bioarchive.galaxyproject.org/ragene20sttranscriptcluster.db_8.7.0.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-ragene20sttranscriptcluster.db/bioconductor-ragene20sttranscriptcluster.db_8.7.0_src_all.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-ragene20sttranscriptcluster.db/bioconductor-ragene20sttranscriptcluster.db_8.7.0_src_all.tar.gz" ) MD5="79693b35c3837f9e5fe7337ac3e86e1f" @@ -16,7 +17,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-ragene21stprobeset.db/meta.yaml b/recipes/bioconductor-ragene21stprobeset.db/meta.yaml index 55679f655ce19..7f62267877fbd 100644 --- a/recipes/bioconductor-ragene21stprobeset.db/meta.yaml +++ b/recipes/bioconductor-ragene21stprobeset.db/meta.yaml @@ -1,6 +1,6 @@ {% set version = "8.7.0" %} {% set name = "ragene21stprobeset.db" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -12,7 +12,7 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 9a2e1eb46277622a673eb3e11ca14aee build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ @@ -20,14 +20,14 @@ build: # Suggests: DBI, annotate, RUnit requirements: host: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' - - 'bioconductor-org.rn.eg.db >=3.7.0,<3.8.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' + - 'bioconductor-org.rn.eg.db >=3.8.0,<3.9.0' - r-base run: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' - - 'bioconductor-org.rn.eg.db >=3.7.0,<3.8.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' + - 'bioconductor-org.rn.eg.db >=3.8.0,<3.9.0' - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-ragene21stprobeset.db/post-link.sh b/recipes/bioconductor-ragene21stprobeset.db/post-link.sh index 4c592d8b1e55c..3568ace65249a 100644 --- a/recipes/bioconductor-ragene21stprobeset.db/post-link.sh +++ b/recipes/bioconductor-ragene21stprobeset.db/post-link.sh @@ -1,9 +1,10 @@ #!/bin/bash FN="ragene21stprobeset.db_8.7.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/ragene21stprobeset.db_8.7.0.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/ragene21stprobeset.db_8.7.0.tar.gz" "https://bioarchive.galaxyproject.org/ragene21stprobeset.db_8.7.0.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-ragene21stprobeset.db/bioconductor-ragene21stprobeset.db_8.7.0_src_all.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-ragene21stprobeset.db/bioconductor-ragene21stprobeset.db_8.7.0_src_all.tar.gz" ) MD5="9a2e1eb46277622a673eb3e11ca14aee" @@ -16,7 +17,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-ragene21sttranscriptcluster.db/meta.yaml b/recipes/bioconductor-ragene21sttranscriptcluster.db/meta.yaml index 5f575d48bf059..c357d5f88d13b 100644 --- a/recipes/bioconductor-ragene21sttranscriptcluster.db/meta.yaml +++ b/recipes/bioconductor-ragene21sttranscriptcluster.db/meta.yaml @@ -1,6 +1,6 @@ {% set version = "8.7.0" %} {% set name = "ragene21sttranscriptcluster.db" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -12,7 +12,7 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 45a0cfb35fc78ec28705024a8d091163 build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ @@ -20,14 +20,14 @@ build: # Suggests: DBI, annotate, RUnit requirements: host: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' - - 'bioconductor-org.rn.eg.db >=3.7.0,<3.8.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' + - 'bioconductor-org.rn.eg.db >=3.8.0,<3.9.0' - r-base run: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' - - 'bioconductor-org.rn.eg.db >=3.7.0,<3.8.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' + - 'bioconductor-org.rn.eg.db >=3.8.0,<3.9.0' - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-ragene21sttranscriptcluster.db/post-link.sh b/recipes/bioconductor-ragene21sttranscriptcluster.db/post-link.sh index c0aeade5e8a98..7ec5ab2947b79 100644 --- a/recipes/bioconductor-ragene21sttranscriptcluster.db/post-link.sh +++ b/recipes/bioconductor-ragene21sttranscriptcluster.db/post-link.sh @@ -1,9 +1,10 @@ #!/bin/bash FN="ragene21sttranscriptcluster.db_8.7.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/ragene21sttranscriptcluster.db_8.7.0.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/ragene21sttranscriptcluster.db_8.7.0.tar.gz" "https://bioarchive.galaxyproject.org/ragene21sttranscriptcluster.db_8.7.0.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-ragene21sttranscriptcluster.db/bioconductor-ragene21sttranscriptcluster.db_8.7.0_src_all.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-ragene21sttranscriptcluster.db/bioconductor-ragene21sttranscriptcluster.db_8.7.0_src_all.tar.gz" ) MD5="45a0cfb35fc78ec28705024a8d091163" @@ -16,7 +17,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-raggedexperiment/meta.yaml b/recipes/bioconductor-raggedexperiment/meta.yaml index 2a62441ece65f..802869057f7d0 100644 --- a/recipes/bioconductor-raggedexperiment/meta.yaml +++ b/recipes/bioconductor-raggedexperiment/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.6.0" %} +{% set version = "1.8.0" %} {% set name = "RaggedExperiment" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: a07596ff746251104b6c1ce3ddd933e2 + md5: 3fdea8716d8fde43aa363a97dafcd91f build: number: 0 rpaths: @@ -20,20 +20,20 @@ build: # Suggests: BiocStyle, knitr, testthat, MultiAssayExperiment requirements: host: - - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' - - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' - - 'bioconductor-genomicranges >=1.34.0,<1.35.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' - - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' + - 'bioconductor-biocgenerics >=0.30.0,<0.31.0' + - 'bioconductor-genomeinfodb >=1.20.0,<1.21.0' + - 'bioconductor-genomicranges >=1.36.0,<1.37.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' + - 'bioconductor-summarizedexperiment >=1.14.0,<1.15.0' - r-base run: - - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' - - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' - - 'bioconductor-genomicranges >=1.34.0,<1.35.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' - - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' + - 'bioconductor-biocgenerics >=0.30.0,<0.31.0' + - 'bioconductor-genomeinfodb >=1.20.0,<1.21.0' + - 'bioconductor-genomicranges >=1.36.0,<1.37.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' + - 'bioconductor-summarizedexperiment >=1.14.0,<1.15.0' - r-base test: commands: diff --git a/recipes/bioconductor-rain/meta.yaml b/recipes/bioconductor-rain/meta.yaml index 9c4a482051eb8..0ad5177d33bc7 100644 --- a/recipes/bioconductor-rain/meta.yaml +++ b/recipes/bioconductor-rain/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.16.0" %} +{% set version = "1.18.0" %} {% set name = "rain" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: f2ec7a42028c930beb3857c0e1292817 + md5: 65a71f22d50df3704c7d697a2e78dbfd build: number: 0 rpaths: @@ -20,11 +20,11 @@ build: # Suggests: lattice, BiocStyle requirements: host: - - 'bioconductor-multtest >=2.38.0,<2.39.0' + - 'bioconductor-multtest >=2.40.0,<2.41.0' - r-base - r-gmp run: - - 'bioconductor-multtest >=2.38.0,<2.39.0' + - 'bioconductor-multtest >=2.40.0,<2.41.0' - r-base - r-gmp test: diff --git a/recipes/bioconductor-rama/meta.yaml b/recipes/bioconductor-rama/meta.yaml index 184d299a55f2d..391d82a674c0e 100644 --- a/recipes/bioconductor-rama/meta.yaml +++ b/recipes/bioconductor-rama/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.56.0" %} +{% set version = "1.58.0" %} {% set name = "rama" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,9 +10,9 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 698c5d694e8e08c717ab7e0f7a6495d9 + md5: 09183bff22ae8499d8f99175f334c193 build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ diff --git a/recipes/bioconductor-ramwas/meta.yaml b/recipes/bioconductor-ramwas/meta.yaml index 9839b469e11b8..87a8b1593e9c1 100644 --- a/recipes/bioconductor-ramwas/meta.yaml +++ b/recipes/bioconductor-ramwas/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.6.0" %} +{% set version = "1.8.0" %} {% set name = "ramwas" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 63327d48803487a400eea7b0dcb09611 + md5: 1e3f7ddaa2171b7a1889ddb830d12712 build: number: 0 rpaths: @@ -19,22 +19,22 @@ build: # Suggests: knitr, rmarkdown, pander, BiocStyle, BSgenome.Ecoli.NCBI.20080805 requirements: host: - - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' - - 'bioconductor-biomart >=2.38.0,<2.39.0' - - 'bioconductor-biostrings >=2.50.0,<2.51.0' - - 'bioconductor-genomicalignments >=1.18.0,<1.19.0' - - 'bioconductor-rsamtools >=1.34.0,<1.35.0' + - 'bioconductor-biocgenerics >=0.30.0,<0.31.0' + - 'bioconductor-biomart >=2.40.0,<2.41.0' + - 'bioconductor-biostrings >=2.52.0,<2.53.0' + - 'bioconductor-genomicalignments >=1.20.0,<1.21.0' + - 'bioconductor-rsamtools >=2.0.0,<2.1.0' - r-base - r-digest - r-filematrix - r-glmnet - r-kernsmooth run: - - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' - - 'bioconductor-biomart >=2.38.0,<2.39.0' - - 'bioconductor-biostrings >=2.50.0,<2.51.0' - - 'bioconductor-genomicalignments >=1.18.0,<1.19.0' - - 'bioconductor-rsamtools >=1.34.0,<1.35.0' + - 'bioconductor-biocgenerics >=0.30.0,<0.31.0' + - 'bioconductor-biomart >=2.40.0,<2.41.0' + - 'bioconductor-biostrings >=2.52.0,<2.53.0' + - 'bioconductor-genomicalignments >=1.20.0,<1.21.0' + - 'bioconductor-rsamtools >=2.0.0,<2.1.0' - r-base - r-digest - r-filematrix diff --git a/recipes/bioconductor-randomwalkrestartmh/meta.yaml b/recipes/bioconductor-randomwalkrestartmh/meta.yaml index 4fd637f929c06..776fbc3bd1e58 100644 --- a/recipes/bioconductor-randomwalkrestartmh/meta.yaml +++ b/recipes/bioconductor-randomwalkrestartmh/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.2.0" %} +{% set version = "1.4.0" %} {% set name = "RandomWalkRestartMH" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 351404a67f4b115a3d24314cb60f9d20 + md5: 969cdbf1c3cac6c81e8c7a0d47e8ba13 build: number: 0 rpaths: diff --git a/recipes/bioconductor-randpack/meta.yaml b/recipes/bioconductor-randpack/meta.yaml index e06bc2b218bac..5849c957f551c 100644 --- a/recipes/bioconductor-randpack/meta.yaml +++ b/recipes/bioconductor-randpack/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.28.0" %} +{% set version = "1.30.0" %} {% set name = "randPack" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 92c6a0d2bee12aa5cc9fae2882ac72f1 + md5: 063a95e021d78fe49fc130d47493c892 build: number: 0 rpaths: @@ -19,10 +19,10 @@ build: noarch: generic requirements: host: - - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' - r-base run: - - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' - r-base test: commands: diff --git a/recipes/bioconductor-rankprod/meta.yaml b/recipes/bioconductor-rankprod/meta.yaml index 5207123a975b0..fc1a58da96fa5 100644 --- a/recipes/bioconductor-rankprod/meta.yaml +++ b/recipes/bioconductor-rankprod/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "3.8.0" %} +{% set version = "3.10.0" %} {% set name = "RankProd" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 86e2a46efa5edd1ad7ecaf7556b18208 + md5: 2df702820b143840f7a35de342f2aa92 build: number: 0 rpaths: diff --git a/recipes/bioconductor-rarevariantvis/meta.yaml b/recipes/bioconductor-rarevariantvis/meta.yaml index 6da8c4cb49ac2..2263c05fca442 100644 --- a/recipes/bioconductor-rarevariantvis/meta.yaml +++ b/recipes/bioconductor-rarevariantvis/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "2.10.0" %} +{% set version = "2.12.0" %} {% set name = "RareVariantVis" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 193cfc429d07fdf039d3e2edea0893ae + md5: 264c45546060173959e66bdce31ad53f build: number: 0 rpaths: @@ -20,36 +20,36 @@ build: # Suggests: knitr requirements: host: - - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' - - 'bioconductor-bsgenome >=1.50.0,<1.51.0' + - 'bioconductor-biocgenerics >=0.30.0,<0.31.0' + - 'bioconductor-bsgenome >=1.52.0,<1.53.0' - 'bioconductor-bsgenome.hsapiens.ucsc.hg19 >=1.4.0,<1.5.0' - - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' - - 'bioconductor-genomicfeatures >=1.34.0,<1.35.0' - - 'bioconductor-genomicranges >=1.34.0,<1.35.0' - - 'bioconductor-genomicscores >=1.6.0,<1.7.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-phastcons100way.ucsc.hg19 >=3.7.0,<3.8.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' - - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' + - 'bioconductor-genomeinfodb >=1.20.0,<1.21.0' + - 'bioconductor-genomicfeatures >=1.36.0,<1.37.0' + - 'bioconductor-genomicranges >=1.36.0,<1.37.0' + - 'bioconductor-genomicscores >=1.8.0,<1.9.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-phastcons100way.ucsc.hg19 >=3.8.0,<3.9.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' + - 'bioconductor-summarizedexperiment >=1.14.0,<1.15.0' - 'bioconductor-txdb.hsapiens.ucsc.hg19.knowngene >=3.2.0,<3.3.0' - - 'bioconductor-variantannotation >=1.28.0,<1.29.0' + - 'bioconductor-variantannotation >=1.30.0,<1.31.0' - r-base - r-googlevis - r-gtools run: - - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' - - 'bioconductor-bsgenome >=1.50.0,<1.51.0' + - 'bioconductor-biocgenerics >=0.30.0,<0.31.0' + - 'bioconductor-bsgenome >=1.52.0,<1.53.0' - 'bioconductor-bsgenome.hsapiens.ucsc.hg19 >=1.4.0,<1.5.0' - - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' - - 'bioconductor-genomicfeatures >=1.34.0,<1.35.0' - - 'bioconductor-genomicranges >=1.34.0,<1.35.0' - - 'bioconductor-genomicscores >=1.6.0,<1.7.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-phastcons100way.ucsc.hg19 >=3.7.0,<3.8.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' - - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' + - 'bioconductor-genomeinfodb >=1.20.0,<1.21.0' + - 'bioconductor-genomicfeatures >=1.36.0,<1.37.0' + - 'bioconductor-genomicranges >=1.36.0,<1.37.0' + - 'bioconductor-genomicscores >=1.8.0,<1.9.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-phastcons100way.ucsc.hg19 >=3.8.0,<3.9.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' + - 'bioconductor-summarizedexperiment >=1.14.0,<1.15.0' - 'bioconductor-txdb.hsapiens.ucsc.hg19.knowngene >=3.2.0,<3.3.0' - - 'bioconductor-variantannotation >=1.28.0,<1.29.0' + - 'bioconductor-variantannotation >=1.30.0,<1.31.0' - r-base - r-googlevis - r-gtools diff --git a/recipes/bioconductor-rariant/meta.yaml b/recipes/bioconductor-rariant/meta.yaml index 41f62dacb896c..b2aad87c29bab 100644 --- a/recipes/bioconductor-rariant/meta.yaml +++ b/recipes/bioconductor-rariant/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.18.0" %} +{% set version = "1.20.0" %} {% set name = "Rariant" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: cc3ad6548566082286949d086014730c + md5: 35bff83f4c34da31a2cbea4dfcfe2894 build: number: 0 rpaths: @@ -20,16 +20,16 @@ build: # Suggests: h5vcData, testthat, knitr, optparse, BSgenome.Hsapiens.UCSC.hg19 requirements: host: - - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' - - 'bioconductor-exomecopy >=1.28.0,<1.29.0' - - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' - - 'bioconductor-genomicranges >=1.34.0,<1.35.0' - - 'bioconductor-ggbio >=1.30.0,<1.31.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-rsamtools >=1.34.0,<1.35.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' - - 'bioconductor-somaticsignatures >=2.18.0,<2.19.0' - - 'bioconductor-variantannotation >=1.28.0,<1.29.0' + - 'bioconductor-biocgenerics >=0.30.0,<0.31.0' + - 'bioconductor-exomecopy >=1.30.0,<1.31.0' + - 'bioconductor-genomeinfodb >=1.20.0,<1.21.0' + - 'bioconductor-genomicranges >=1.36.0,<1.37.0' + - 'bioconductor-ggbio >=1.32.0,<1.33.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-rsamtools >=2.0.0,<2.1.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' + - 'bioconductor-somaticsignatures >=2.20.0,<2.21.0' + - 'bioconductor-variantannotation >=1.30.0,<1.31.0' - r-base - r-dplyr - r-ggplot2 @@ -37,16 +37,16 @@ requirements: - r-shiny - r-vgam run: - - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' - - 'bioconductor-exomecopy >=1.28.0,<1.29.0' - - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' - - 'bioconductor-genomicranges >=1.34.0,<1.35.0' - - 'bioconductor-ggbio >=1.30.0,<1.31.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-rsamtools >=1.34.0,<1.35.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' - - 'bioconductor-somaticsignatures >=2.18.0,<2.19.0' - - 'bioconductor-variantannotation >=1.28.0,<1.29.0' + - 'bioconductor-biocgenerics >=0.30.0,<0.31.0' + - 'bioconductor-exomecopy >=1.30.0,<1.31.0' + - 'bioconductor-genomeinfodb >=1.20.0,<1.21.0' + - 'bioconductor-genomicranges >=1.36.0,<1.37.0' + - 'bioconductor-ggbio >=1.32.0,<1.33.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-rsamtools >=2.0.0,<2.1.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' + - 'bioconductor-somaticsignatures >=2.20.0,<2.21.0' + - 'bioconductor-variantannotation >=1.30.0,<1.31.0' - r-base - r-dplyr - r-ggplot2 diff --git a/recipes/bioconductor-rat.db0/meta.yaml b/recipes/bioconductor-rat.db0/meta.yaml index a185a2d0a7c8a..e2c29ce3c2a3b 100644 --- a/recipes/bioconductor-rat.db0/meta.yaml +++ b/recipes/bioconductor-rat.db0/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "3.7.1" %} +{% set version = "3.8.2" %} {% set name = "rat.db0" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 356c5e1a7c24d7e3f1d6785c59af1016 + md5: 8095a030c23fddc14b56466dbf7d2b82 build: number: 0 rpaths: @@ -19,12 +19,12 @@ build: noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' - r-base run: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-rat.db0/post-link.sh b/recipes/bioconductor-rat.db0/post-link.sh index 96abc9b36c44e..e80fb0da6b38b 100644 --- a/recipes/bioconductor-rat.db0/post-link.sh +++ b/recipes/bioconductor-rat.db0/post-link.sh @@ -1,11 +1,11 @@ #!/bin/bash -FN="rat.db0_3.7.1.tar.gz" +FN="rat.db0_3.8.2.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/rat.db0_3.7.1.tar.gz" - "https://bioarchive.galaxyproject.org/rat.db0_3.7.1.tar.gz" - "https://depot.galaxyproject.org/software/bioconductor-rat.db0/bioconductor-rat.db0_3.7.1_src_all.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/rat.db0_3.8.2.tar.gz" + "https://bioarchive.galaxyproject.org/rat.db0_3.8.2.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-rat.db0/bioconductor-rat.db0_3.8.2_src_all.tar.gz" ) -MD5="356c5e1a7c24d7e3f1d6785c59af1016" +MD5="8095a030c23fddc14b56466dbf7d2b82" # Use a staging area in the conda dir rather than temp dirs, both to avoid # permission issues as well as to have things downloaded in a predictable @@ -16,7 +16,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-rat2302.db/meta.yaml b/recipes/bioconductor-rat2302.db/meta.yaml index 2481b77bcddb7..0a86249e8c843 100644 --- a/recipes/bioconductor-rat2302.db/meta.yaml +++ b/recipes/bioconductor-rat2302.db/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.2.3" %} {% set name = "rat2302.db" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -12,7 +12,7 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: bcd325ab88de497001867a7cae4501cc build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ @@ -20,14 +20,14 @@ build: # Suggests: DBI, annotate, RUnit requirements: host: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' - - 'bioconductor-org.rn.eg.db >=3.7.0,<3.8.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' + - 'bioconductor-org.rn.eg.db >=3.8.0,<3.9.0' - r-base run: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' - - 'bioconductor-org.rn.eg.db >=3.7.0,<3.8.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' + - 'bioconductor-org.rn.eg.db >=3.8.0,<3.9.0' - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-rat2302.db/post-link.sh b/recipes/bioconductor-rat2302.db/post-link.sh index 3da5b5189776d..acdaf2513b602 100644 --- a/recipes/bioconductor-rat2302.db/post-link.sh +++ b/recipes/bioconductor-rat2302.db/post-link.sh @@ -1,9 +1,10 @@ #!/bin/bash FN="rat2302.db_3.2.3.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/rat2302.db_3.2.3.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/rat2302.db_3.2.3.tar.gz" "https://bioarchive.galaxyproject.org/rat2302.db_3.2.3.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-rat2302.db/bioconductor-rat2302.db_3.2.3_src_all.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-rat2302.db/bioconductor-rat2302.db_3.2.3_src_all.tar.gz" ) MD5="bcd325ab88de497001867a7cae4501cc" @@ -16,7 +17,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-rat2302cdf/meta.yaml b/recipes/bioconductor-rat2302cdf/meta.yaml index a410d176714c1..76296d6adff6b 100644 --- a/recipes/bioconductor-rat2302cdf/meta.yaml +++ b/recipes/bioconductor-rat2302cdf/meta.yaml @@ -1,6 +1,6 @@ {% set version = "2.18.0" %} {% set name = "rat2302cdf" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -12,19 +12,19 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: a033730f79a11d45b4cd7e7c520f8052 build: - number: 1 + number: 2 rpaths: - lib/R/lib/ - lib/ noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' - r-base run: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-rat2302cdf/post-link.sh b/recipes/bioconductor-rat2302cdf/post-link.sh index 8e3c967cdc9a8..434e4f39e3556 100644 --- a/recipes/bioconductor-rat2302cdf/post-link.sh +++ b/recipes/bioconductor-rat2302cdf/post-link.sh @@ -1,9 +1,10 @@ #!/bin/bash FN="rat2302cdf_2.18.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/rat2302cdf_2.18.0.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/rat2302cdf_2.18.0.tar.gz" "https://bioarchive.galaxyproject.org/rat2302cdf_2.18.0.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-rat2302cdf/bioconductor-rat2302cdf_2.18.0_src_all.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-rat2302cdf/bioconductor-rat2302cdf_2.18.0_src_all.tar.gz" ) MD5="a033730f79a11d45b4cd7e7c520f8052" @@ -16,7 +17,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-rat2302frmavecs/meta.yaml b/recipes/bioconductor-rat2302frmavecs/meta.yaml new file mode 100644 index 0000000000000..ea53795a1e9ad --- /dev/null +++ b/recipes/bioconductor-rat2302frmavecs/meta.yaml @@ -0,0 +1,38 @@ +{% set version = "0.99.11" %} +{% set name = "rat2302frmavecs" %} +{% set bioc = "3.9" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + md5: 44d9f00c2f3806899c6605d1ba274066 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: BiocStyle, knitr, rmarkdown +requirements: + host: + - 'bioconductor-affy >=1.62.0,<1.63.0' + - 'bioconductor-frma >=1.36.0,<1.37.0' + - r-base + run: + - 'bioconductor-affy >=1.62.0,<1.63.0' + - 'bioconductor-frma >=1.36.0,<1.37.0' + - r-base + - curl +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + license: 'GPL (>= 2)' + summary: 'This package was created with the help of frmaTools version 1.24.0.' + diff --git a/recipes/bioconductor-rat2302frmavecs/post-link.sh b/recipes/bioconductor-rat2302frmavecs/post-link.sh new file mode 100644 index 0000000000000..4d7faeb27a133 --- /dev/null +++ b/recipes/bioconductor-rat2302frmavecs/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="rat2302frmavecs_0.99.11.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/rat2302frmavecs_0.99.11.tar.gz" + "https://bioarchive.galaxyproject.org/rat2302frmavecs_0.99.11.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-rat2302frmavecs/bioconductor-rat2302frmavecs_0.99.11_src_all.tar.gz" +) +MD5="44d9f00c2f3806899c6605d1ba274066" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + curl $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-rat2302frmavecs/pre-unlink.sh b/recipes/bioconductor-rat2302frmavecs/pre-unlink.sh new file mode 100644 index 0000000000000..ad2dbd3951ca8 --- /dev/null +++ b/recipes/bioconductor-rat2302frmavecs/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ rat2302frmavecs diff --git a/recipes/bioconductor-rat2302probe/meta.yaml b/recipes/bioconductor-rat2302probe/meta.yaml index e1d7e83abdf14..5e2b9e164391b 100644 --- a/recipes/bioconductor-rat2302probe/meta.yaml +++ b/recipes/bioconductor-rat2302probe/meta.yaml @@ -1,6 +1,6 @@ {% set version = "2.18.0" %} {% set name = "rat2302probe" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -12,19 +12,19 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: d1d9215e52b9e845cc4d7c902536e0d6 build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' - r-base run: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-rat2302probe/post-link.sh b/recipes/bioconductor-rat2302probe/post-link.sh index 3146429141a53..dd6aef334ded4 100644 --- a/recipes/bioconductor-rat2302probe/post-link.sh +++ b/recipes/bioconductor-rat2302probe/post-link.sh @@ -1,9 +1,10 @@ #!/bin/bash FN="rat2302probe_2.18.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/rat2302probe_2.18.0.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/rat2302probe_2.18.0.tar.gz" "https://bioarchive.galaxyproject.org/rat2302probe_2.18.0.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-rat2302probe/bioconductor-rat2302probe_2.18.0_src_all.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-rat2302probe/bioconductor-rat2302probe_2.18.0_src_all.tar.gz" ) MD5="d1d9215e52b9e845cc4d7c902536e0d6" @@ -16,7 +17,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-ratchrloc/meta.yaml b/recipes/bioconductor-ratchrloc/meta.yaml index 7612b172c684e..775f175c682f6 100644 --- a/recipes/bioconductor-ratchrloc/meta.yaml +++ b/recipes/bioconductor-ratchrloc/meta.yaml @@ -1,6 +1,6 @@ {% set version = "2.1.6" %} {% set name = "ratCHRLOC" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -12,7 +12,7 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' md5: 6fecff4821a5a47e3bd38a2ff78173d5 build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ @@ -22,7 +22,7 @@ requirements: - r-base run: - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-ratchrloc/post-link.sh b/recipes/bioconductor-ratchrloc/post-link.sh index 8f4441d3e9074..2f78295d737b5 100644 --- a/recipes/bioconductor-ratchrloc/post-link.sh +++ b/recipes/bioconductor-ratchrloc/post-link.sh @@ -1,9 +1,10 @@ #!/bin/bash FN="ratCHRLOC_2.1.6.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/ratCHRLOC_2.1.6.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/ratCHRLOC_2.1.6.tar.gz" "https://bioarchive.galaxyproject.org/ratCHRLOC_2.1.6.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-ratchrloc/bioconductor-ratchrloc_2.1.6_src_all.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-ratchrloc/bioconductor-ratchrloc_2.1.6_src_all.tar.gz" ) MD5="6fecff4821a5a47e3bd38a2ff78173d5" @@ -16,7 +17,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-rattoxfxcdf/meta.yaml b/recipes/bioconductor-rattoxfxcdf/meta.yaml index dd65a93a7708f..850eff019c75c 100644 --- a/recipes/bioconductor-rattoxfxcdf/meta.yaml +++ b/recipes/bioconductor-rattoxfxcdf/meta.yaml @@ -1,6 +1,6 @@ {% set version = "2.18.0" %} {% set name = "rattoxfxcdf" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -12,19 +12,19 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 912d0fa424615fcd92773ed174d5efdd build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' - r-base run: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-rattoxfxcdf/post-link.sh b/recipes/bioconductor-rattoxfxcdf/post-link.sh index 6aef9d95287bf..5721c47115c3c 100644 --- a/recipes/bioconductor-rattoxfxcdf/post-link.sh +++ b/recipes/bioconductor-rattoxfxcdf/post-link.sh @@ -1,9 +1,10 @@ #!/bin/bash FN="rattoxfxcdf_2.18.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/rattoxfxcdf_2.18.0.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/rattoxfxcdf_2.18.0.tar.gz" "https://bioarchive.galaxyproject.org/rattoxfxcdf_2.18.0.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-rattoxfxcdf/bioconductor-rattoxfxcdf_2.18.0_src_all.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-rattoxfxcdf/bioconductor-rattoxfxcdf_2.18.0_src_all.tar.gz" ) MD5="912d0fa424615fcd92773ed174d5efdd" @@ -16,7 +17,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-rattoxfxprobe/meta.yaml b/recipes/bioconductor-rattoxfxprobe/meta.yaml index 4c3d3a721f069..374649be026a2 100644 --- a/recipes/bioconductor-rattoxfxprobe/meta.yaml +++ b/recipes/bioconductor-rattoxfxprobe/meta.yaml @@ -1,6 +1,6 @@ {% set version = "2.18.0" %} {% set name = "rattoxfxprobe" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -12,19 +12,19 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 202791c72e8c956b9854fa4d9ba67a24 build: - number: 1 + number: 2 rpaths: - lib/R/lib/ - lib/ noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' - r-base run: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-rattoxfxprobe/post-link.sh b/recipes/bioconductor-rattoxfxprobe/post-link.sh index 5788be0de840c..697bc8ddf9b90 100644 --- a/recipes/bioconductor-rattoxfxprobe/post-link.sh +++ b/recipes/bioconductor-rattoxfxprobe/post-link.sh @@ -1,9 +1,10 @@ #!/bin/bash FN="rattoxfxprobe_2.18.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/rattoxfxprobe_2.18.0.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/rattoxfxprobe_2.18.0.tar.gz" "https://bioarchive.galaxyproject.org/rattoxfxprobe_2.18.0.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-rattoxfxprobe/bioconductor-rattoxfxprobe_2.18.0_src_all.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-rattoxfxprobe/bioconductor-rattoxfxprobe_2.18.0_src_all.tar.gz" ) MD5="202791c72e8c956b9854fa4d9ba67a24" @@ -16,7 +17,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-rattus.norvegicus/meta.yaml b/recipes/bioconductor-rattus.norvegicus/meta.yaml index 8a013fe1473a9..040ba9e13c935 100644 --- a/recipes/bioconductor-rattus.norvegicus/meta.yaml +++ b/recipes/bioconductor-rattus.norvegicus/meta.yaml @@ -1,6 +1,6 @@ {% set version = "1.3.1" %} {% set name = "Rattus.norvegicus" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -12,29 +12,29 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' md5: 5692fdeb0bc7f94e1db35f097cad99a9 build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' - - 'bioconductor-genomicfeatures >=1.34.0,<1.35.0' - - 'bioconductor-go.db >=3.7.0,<3.8.0' - - 'bioconductor-org.rn.eg.db >=3.7.0,<3.8.0' - - 'bioconductor-organismdbi >=1.24.0,<1.25.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' + - 'bioconductor-genomicfeatures >=1.36.0,<1.37.0' + - 'bioconductor-go.db >=3.8.0,<3.9.0' + - 'bioconductor-org.rn.eg.db >=3.8.0,<3.9.0' + - 'bioconductor-organismdbi >=1.26.0,<1.27.0' - 'bioconductor-txdb.rnorvegicus.ucsc.rn5.refgene >=3.4.0,<3.5.0' - r-base run: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' - - 'bioconductor-genomicfeatures >=1.34.0,<1.35.0' - - 'bioconductor-go.db >=3.7.0,<3.8.0' - - 'bioconductor-org.rn.eg.db >=3.7.0,<3.8.0' - - 'bioconductor-organismdbi >=1.24.0,<1.25.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' + - 'bioconductor-genomicfeatures >=1.36.0,<1.37.0' + - 'bioconductor-go.db >=3.8.0,<3.9.0' + - 'bioconductor-org.rn.eg.db >=3.8.0,<3.9.0' + - 'bioconductor-organismdbi >=1.26.0,<1.27.0' - 'bioconductor-txdb.rnorvegicus.ucsc.rn5.refgene >=3.4.0,<3.5.0' - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-rattus.norvegicus/post-link.sh b/recipes/bioconductor-rattus.norvegicus/post-link.sh index df34ef1ad5b70..2734053377667 100644 --- a/recipes/bioconductor-rattus.norvegicus/post-link.sh +++ b/recipes/bioconductor-rattus.norvegicus/post-link.sh @@ -1,9 +1,10 @@ #!/bin/bash FN="Rattus.norvegicus_1.3.1.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/Rattus.norvegicus_1.3.1.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/Rattus.norvegicus_1.3.1.tar.gz" "https://bioarchive.galaxyproject.org/Rattus.norvegicus_1.3.1.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-rattus.norvegicus/bioconductor-rattus.norvegicus_1.3.1_src_all.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-rattus.norvegicus/bioconductor-rattus.norvegicus_1.3.1_src_all.tar.gz" ) MD5="5692fdeb0bc7f94e1db35f097cad99a9" @@ -16,7 +17,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-rbcbook1/meta.yaml b/recipes/bioconductor-rbcbook1/meta.yaml index dfa0c44c5c887..fd6ed62432eb3 100644 --- a/recipes/bioconductor-rbcbook1/meta.yaml +++ b/recipes/bioconductor-rbcbook1/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.50.0" %} +{% set version = "1.52.0" %} {% set name = "RbcBook1" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: ab688a83dd3cb0dacea22caacd02c9cc + md5: d27a11f7a88414446ebca92f66665b5b build: number: 0 rpaths: @@ -19,13 +19,13 @@ build: noarch: generic requirements: host: - - 'bioconductor-biobase >=2.42.0,<2.43.0' - - 'bioconductor-graph >=1.60.0,<1.61.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' + - 'bioconductor-graph >=1.62.0,<1.63.0' - r-base - r-rpart run: - - 'bioconductor-biobase >=2.42.0,<2.43.0' - - 'bioconductor-graph >=1.60.0,<1.61.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' + - 'bioconductor-graph >=1.62.0,<1.63.0' - r-base - r-rpart test: diff --git a/recipes/bioconductor-rbgl/meta.yaml b/recipes/bioconductor-rbgl/meta.yaml index 63849f613e43d..4736bf352371b 100644 --- a/recipes/bioconductor-rbgl/meta.yaml +++ b/recipes/bioconductor-rbgl/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.58.2" %} +{% set version = "1.60.0" %} {% set name = "RBGL" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: d433421d6eb494020c7a49e7c73a1bb83aafb4b58be10fd811d7727d0f81166e + md5: 300bba134b21fa85d6b24efa5a0ec21c build: number: 0 rpaths: @@ -19,11 +19,13 @@ build: # Suggests: Rgraphviz, XML, RUnit, BiocGenerics requirements: host: - - 'bioconductor-graph >=1.60.0,<1.61.0' + - 'bioconductor-graph >=1.62.0,<1.63.0' - r-base + - r-bh run: - - 'bioconductor-graph >=1.60.0,<1.61.0' + - 'bioconductor-graph >=1.62.0,<1.63.0' - r-base + - r-bh build: - {{ compiler('c') }} - {{ compiler('cxx') }} diff --git a/recipes/bioconductor-rbioinf/meta.yaml b/recipes/bioconductor-rbioinf/meta.yaml index 903a40c044080..82b8ab13dfa43 100644 --- a/recipes/bioconductor-rbioinf/meta.yaml +++ b/recipes/bioconductor-rbioinf/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.42.0" %} +{% set version = "1.44.0" %} {% set name = "RBioinf" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: ccc0e1c81f86882eef47cef5b74b94d2 + md5: c157e29f804f8b12ec5771f2283f1850 build: number: 0 rpaths: @@ -19,10 +19,10 @@ build: # Suggests: Rgraphviz requirements: host: - - 'bioconductor-graph >=1.60.0,<1.61.0' + - 'bioconductor-graph >=1.62.0,<1.63.0' - r-base run: - - 'bioconductor-graph >=1.60.0,<1.61.0' + - 'bioconductor-graph >=1.62.0,<1.63.0' - r-base build: - {{ compiler('c') }} diff --git a/recipes/bioconductor-rbiopaxparser/meta.yaml b/recipes/bioconductor-rbiopaxparser/meta.yaml index d97f8820fe140..9624f088446f1 100644 --- a/recipes/bioconductor-rbiopaxparser/meta.yaml +++ b/recipes/bioconductor-rbiopaxparser/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "2.22.0" %} +{% set version = "2.24.0" %} {% set name = "rBiopaxParser" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,9 +10,9 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: d83ba9fc20daeefc0ec70a01a4a99c07 + md5: b8e64e8bcf94e7674e7b5bcda29cd06c build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ diff --git a/recipes/bioconductor-rbm/meta.yaml b/recipes/bioconductor-rbm/meta.yaml index 159c63c02b35b..a2dfd8cd5cba6 100644 --- a/recipes/bioconductor-rbm/meta.yaml +++ b/recipes/bioconductor-rbm/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.14.0" %} +{% set version = "1.16.0" %} {% set name = "RBM" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 3606f3c75a1198316189c26f7ea7ba85 + md5: ef9b3a8bb641fc13f7d536400f49dd64 build: number: 0 rpaths: @@ -19,12 +19,12 @@ build: noarch: generic requirements: host: - - 'bioconductor-limma >=3.38.0,<3.39.0' - - 'bioconductor-marray >=1.60.0,<1.61.0' + - 'bioconductor-limma >=3.40.0,<3.41.0' + - 'bioconductor-marray >=1.62.0,<1.63.0' - r-base run: - - 'bioconductor-limma >=3.38.0,<3.39.0' - - 'bioconductor-marray >=1.60.0,<1.61.0' + - 'bioconductor-limma >=3.40.0,<3.41.0' + - 'bioconductor-marray >=1.62.0,<1.63.0' - r-base test: commands: diff --git a/recipes/bioconductor-rbowtie/meta.yaml b/recipes/bioconductor-rbowtie/meta.yaml index 8be861b313c6e..34b7099d52c35 100644 --- a/recipes/bioconductor-rbowtie/meta.yaml +++ b/recipes/bioconductor-rbowtie/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.22.0" %} +{% set version = "1.24.0" %} {% set name = "Rbowtie" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 4c1a3ec981370710eb6d526043a31965 + md5: 6b2e05e40fda2c1f4d5671167fca5bf5 build: number: 0 rpaths: @@ -32,7 +32,7 @@ test: - '$R -e "library(''{{ name }}'')"' about: home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: 'Artistic-1.0 | file LICENSE' + license: 'Artistic-2.0 | file LICENSE' summary: 'This package provides an R wrapper around the popular bowtie short read aligner and around SpliceMap, a de novo splice junction discovery and alignment tool. The package is used by the QuasR bioconductor package. We recommend to use the QuasR package instead of using Rbowtie directly.' extra: identifiers: diff --git a/recipes/bioconductor-rbowtie2/build.sh b/recipes/bioconductor-rbowtie2/build.sh index 2d70ff7fa9ac7..9f9ee1efd6a6d 100644 --- a/recipes/bioconductor-rbowtie2/build.sh +++ b/recipes/bioconductor-rbowtie2/build.sh @@ -4,11 +4,10 @@ grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION mkdir -p ~/.R echo -e "CC=$CC FC=$FC +CFLAGS=$CFLAGS +CXXFLAGS=$CXXFLAGS CXX=$CXX CXX98=$CXX CXX11=$CXX CXX14=$CXX" > ~/.R/Makevars -export CXX_INCLUDE_PATH=${PREFIX}/include -export CPP_INCLUDE_PATH=${PREFIX}/include -export CPLUS_INCLUDE_PATH=${PREFIX}/include $R CMD INSTALL --build . diff --git a/recipes/bioconductor-rbowtie2/meta.yaml b/recipes/bioconductor-rbowtie2/meta.yaml index 42c5516b911c3..685df134d67ea 100644 --- a/recipes/bioconductor-rbowtie2/meta.yaml +++ b/recipes/bioconductor-rbowtie2/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.4.0" %} +{% set version = "1.6.0" %} {% set name = "Rbowtie2" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 8c6f2b4f4cf420132402458cc0431d96 + md5: f77a146308dcd3517165fec88262caa7 build: number: 0 rpaths: @@ -21,8 +21,10 @@ build: requirements: host: - r-base + - zlib run: - r-base + - zlib build: - {{ compiler('c') }} - {{ compiler('cxx') }} diff --git a/recipes/bioconductor-rbsurv/meta.yaml b/recipes/bioconductor-rbsurv/meta.yaml index 62c1d1f19ba06..e862aa15662cd 100644 --- a/recipes/bioconductor-rbsurv/meta.yaml +++ b/recipes/bioconductor-rbsurv/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "2.40.0" %} +{% set version = "2.42.0" %} {% set name = "rbsurv" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,20 +10,20 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 1e470e032da134db83ae929adb8ff66a + md5: 9e7d74ec22e1d4b835daa9eaea04f65c build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ noarch: generic requirements: host: - - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' - r-base - r-survival run: - - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' - r-base - r-survival test: diff --git a/recipes/bioconductor-rcade/meta.yaml b/recipes/bioconductor-rcade/meta.yaml index 10bac3bc37466..251519da6b35a 100644 --- a/recipes/bioconductor-rcade/meta.yaml +++ b/recipes/bioconductor-rcade/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.24.0" %} +{% set version = "1.26.0" %} {% set name = "Rcade" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 33e6f9f825b0dabf32897a4044af6f7f + md5: fdd9ad4b78ffed906437541c24fd7d86 build: number: 0 rpaths: @@ -20,24 +20,24 @@ build: # Suggests: limma, biomaRt, RUnit, BiocGenerics, BiocStyle requirements: host: - - 'bioconductor-bayseq >=2.16.0,<2.17.0' - - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' - - 'bioconductor-genomicalignments >=1.18.0,<1.19.0' - - 'bioconductor-genomicranges >=1.34.0,<1.35.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-rsamtools >=1.34.0,<1.35.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-bayseq >=2.18.0,<2.19.0' + - 'bioconductor-genomeinfodb >=1.20.0,<1.21.0' + - 'bioconductor-genomicalignments >=1.20.0,<1.21.0' + - 'bioconductor-genomicranges >=1.36.0,<1.37.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-rsamtools >=2.0.0,<2.1.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' - r-base - r-plotrix - r-rgl run: - - 'bioconductor-bayseq >=2.16.0,<2.17.0' - - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' - - 'bioconductor-genomicalignments >=1.18.0,<1.19.0' - - 'bioconductor-genomicranges >=1.34.0,<1.35.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-rsamtools >=1.34.0,<1.35.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-bayseq >=2.18.0,<2.19.0' + - 'bioconductor-genomeinfodb >=1.20.0,<1.21.0' + - 'bioconductor-genomicalignments >=1.20.0,<1.21.0' + - 'bioconductor-genomicranges >=1.36.0,<1.37.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-rsamtools >=2.0.0,<2.1.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' - r-base - r-plotrix - r-rgl @@ -48,8 +48,7 @@ about: home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: GPL-2 summary: 'Rcade (which stands for "R-based analysis of ChIP-seq And Differential Expression") is a tool for integrating ChIP-seq data with differential expression summary data, through a Bayesian framework. A key application is in identifing the genes targeted by a transcription factor of interest - that is, we collect genes that are associated with a ChIP-seq peak, and differential expression under some perturbation related to that TF.' - extra: container: - # needs libGL.so.1 extended-base: true + diff --git a/recipes/bioconductor-rcas/meta.yaml b/recipes/bioconductor-rcas/meta.yaml index 7f4671eeb6cee..959dc48d8a793 100644 --- a/recipes/bioconductor-rcas/meta.yaml +++ b/recipes/bioconductor-rcas/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.8.0" %} +{% set version = "1.10.0" %} {% set name = "RCAS" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 2146754031cbc929a628de63e7088388 + md5: b8fa7781aeab949d1e011fc71c1aa2c9 build: number: 0 rpaths: @@ -21,20 +21,20 @@ build: # SystemRequirements: pandoc (>= 1.12.3) requirements: host: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' - - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' - - 'bioconductor-biomart >=2.38.0,<2.39.0' - - 'bioconductor-biostrings >=2.50.0,<2.51.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' + - 'bioconductor-biocgenerics >=0.30.0,<0.31.0' + - 'bioconductor-biomart >=2.40.0,<2.41.0' + - 'bioconductor-biostrings >=2.52.0,<2.53.0' - 'bioconductor-bsgenome.hsapiens.ucsc.hg19 >=1.4.0,<1.5.0' - - 'bioconductor-genomation >=1.14.0,<1.15.0' - - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' - - 'bioconductor-genomicfeatures >=1.34.0,<1.35.0' - - 'bioconductor-genomicranges >=1.34.0,<1.35.0' - - 'bioconductor-motifrg >=1.26.0,<1.27.0' - - 'bioconductor-org.hs.eg.db >=3.7.0,<3.8.0' - - 'bioconductor-rtracklayer >=1.42.0,<1.43.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' - - 'bioconductor-topgo >=2.34.0,<2.35.0' + - 'bioconductor-genomation >=1.16.0,<1.17.0' + - 'bioconductor-genomeinfodb >=1.20.0,<1.21.0' + - 'bioconductor-genomicfeatures >=1.36.0,<1.37.0' + - 'bioconductor-genomicranges >=1.36.0,<1.37.0' + - 'bioconductor-motifrg >=1.28.0,<1.29.0' + - 'bioconductor-org.hs.eg.db >=3.8.0,<3.9.0' + - 'bioconductor-rtracklayer >=1.44.0,<1.45.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' + - 'bioconductor-topgo >=2.36.0,<2.37.0' - r-base - r-cowplot - r-data.table @@ -50,21 +50,22 @@ requirements: - r-proxy - 'r-rmarkdown >=0.9.5' - r-rsqlite + - pandoc run: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' - - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' - - 'bioconductor-biomart >=2.38.0,<2.39.0' - - 'bioconductor-biostrings >=2.50.0,<2.51.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' + - 'bioconductor-biocgenerics >=0.30.0,<0.31.0' + - 'bioconductor-biomart >=2.40.0,<2.41.0' + - 'bioconductor-biostrings >=2.52.0,<2.53.0' - 'bioconductor-bsgenome.hsapiens.ucsc.hg19 >=1.4.0,<1.5.0' - - 'bioconductor-genomation >=1.14.0,<1.15.0' - - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' - - 'bioconductor-genomicfeatures >=1.34.0,<1.35.0' - - 'bioconductor-genomicranges >=1.34.0,<1.35.0' - - 'bioconductor-motifrg >=1.26.0,<1.27.0' - - 'bioconductor-org.hs.eg.db >=3.7.0,<3.8.0' - - 'bioconductor-rtracklayer >=1.42.0,<1.43.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' - - 'bioconductor-topgo >=2.34.0,<2.35.0' + - 'bioconductor-genomation >=1.16.0,<1.17.0' + - 'bioconductor-genomeinfodb >=1.20.0,<1.21.0' + - 'bioconductor-genomicfeatures >=1.36.0,<1.37.0' + - 'bioconductor-genomicranges >=1.36.0,<1.37.0' + - 'bioconductor-motifrg >=1.28.0,<1.29.0' + - 'bioconductor-org.hs.eg.db >=3.8.0,<3.9.0' + - 'bioconductor-rtracklayer >=1.44.0,<1.45.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' + - 'bioconductor-topgo >=2.36.0,<2.37.0' - r-base - r-cowplot - r-data.table @@ -80,6 +81,7 @@ requirements: - r-proxy - 'r-rmarkdown >=0.9.5' - r-rsqlite + - pandoc test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-rcaspar/meta.yaml b/recipes/bioconductor-rcaspar/meta.yaml index 1911f4a19f275..74926e65eeebe 100644 --- a/recipes/bioconductor-rcaspar/meta.yaml +++ b/recipes/bioconductor-rcaspar/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.28.0" %} +{% set version = "1.30.0" %} {% set name = "RCASPAR" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: e479b18cfbc19c9ff633add554d85c2f + md5: 306067d091c8eb65e9a09bcef1a65b19 build: number: 0 rpaths: diff --git a/recipes/bioconductor-rcellminer/meta.yaml b/recipes/bioconductor-rcellminer/meta.yaml index 050ab39792704..63628cb66e6b8 100644 --- a/recipes/bioconductor-rcellminer/meta.yaml +++ b/recipes/bioconductor-rcellminer/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "2.4.0" %} +{% set version = "2.6.0" %} {% set name = "rcellminer" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: b4cc81cd0e95c5987a8bb9780abdf85c + md5: fabbb8cb40bd48d4722e3a31cdec57f5 build: number: 0 rpaths: @@ -20,8 +20,8 @@ build: # Suggests: knitr, RColorBrewer, sqldf, BiocGenerics, testthat, BiocStyle, jsonlite, d3heatmap, glmnet, foreach, doSNOW, parallel requirements: host: - - 'bioconductor-biobase >=2.42.0,<2.43.0' - - 'bioconductor-rcellminerdata >=2.4.0,<2.5.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' + - 'bioconductor-rcellminerdata >=2.6.0,<2.7.0' - r-base - r-fingerprint - r-ggplot2 @@ -30,8 +30,8 @@ requirements: - r-shiny - r-stringr run: - - 'bioconductor-biobase >=2.42.0,<2.43.0' - - 'bioconductor-rcellminerdata >=2.4.0,<2.5.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' + - 'bioconductor-rcellminerdata >=2.6.0,<2.7.0' - r-base - r-fingerprint - r-ggplot2 diff --git a/recipes/bioconductor-rcellminerdata/meta.yaml b/recipes/bioconductor-rcellminerdata/meta.yaml index 7bf2795c40198..07671f4d723fe 100644 --- a/recipes/bioconductor-rcellminerdata/meta.yaml +++ b/recipes/bioconductor-rcellminerdata/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "2.4.0" %} +{% set version = "2.6.0" %} {% set name = "rcellminerData" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 7259b2817b463847c17e2d6f1d85fe04 + md5: d45f5a4a645566548f7b472e787b710a build: number: 0 rpaths: @@ -20,12 +20,12 @@ build: # Suggests: knitr, testthat, BiocStyle, rcellminer requirements: host: - - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' - r-base run: - - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-rcellminerdata/post-link.sh b/recipes/bioconductor-rcellminerdata/post-link.sh index 22a0e5c20ba80..ee5b1414134b9 100644 --- a/recipes/bioconductor-rcellminerdata/post-link.sh +++ b/recipes/bioconductor-rcellminerdata/post-link.sh @@ -1,11 +1,11 @@ #!/bin/bash -FN="rcellminerData_2.4.0.tar.gz" +FN="rcellminerData_2.6.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/experiment/src/contrib/rcellminerData_2.4.0.tar.gz" - "https://bioarchive.galaxyproject.org/rcellminerData_2.4.0.tar.gz" - "https://depot.galaxyproject.org/software/bioconductor-rcellminerdata/bioconductor-rcellminerdata_2.4.0_src_all.tar.gz" + "https://bioconductor.org/packages/3.9/data/experiment/src/contrib/rcellminerData_2.6.0.tar.gz" + "https://bioarchive.galaxyproject.org/rcellminerData_2.6.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-rcellminerdata/bioconductor-rcellminerdata_2.6.0_src_all.tar.gz" ) -MD5="7259b2817b463847c17e2d6f1d85fe04" +MD5="d45f5a4a645566548f7b472e787b710a" # Use a staging area in the conda dir rather than temp dirs, both to avoid # permission issues as well as to have things downloaded in a predictable @@ -16,7 +16,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-rcgh/meta.yaml b/recipes/bioconductor-rcgh/meta.yaml index 00b942296defd..04e605bc7c0e1 100644 --- a/recipes/bioconductor-rcgh/meta.yaml +++ b/recipes/bioconductor-rcgh/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.12.0" %} +{% set version = "1.14.0" %} {% set name = "rCGH" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: eae2203e032108c2873331c9de08161e + md5: 522541f1b2847440b4f8b4507db575be build: number: 0 rpaths: @@ -20,16 +20,16 @@ build: # Suggests: BiocStyle, knitr, BiocGenerics, RUnit requirements: host: - - 'bioconductor-acgh >=1.60.0,<1.61.0' - - 'bioconductor-affy >=1.60.0,<1.61.0' - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' - - 'bioconductor-dnacopy >=1.56.0,<1.57.0' - - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' - - 'bioconductor-genomicfeatures >=1.34.0,<1.35.0' - - 'bioconductor-genomicranges >=1.34.0,<1.35.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-limma >=3.38.0,<3.39.0' - - 'bioconductor-org.hs.eg.db >=3.7.0,<3.8.0' + - 'bioconductor-acgh >=1.62.0,<1.63.0' + - 'bioconductor-affy >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' + - 'bioconductor-dnacopy >=1.58.0,<1.59.0' + - 'bioconductor-genomeinfodb >=1.20.0,<1.21.0' + - 'bioconductor-genomicfeatures >=1.36.0,<1.37.0' + - 'bioconductor-genomicranges >=1.36.0,<1.37.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-limma >=3.40.0,<3.41.0' + - 'bioconductor-org.hs.eg.db >=3.8.0,<3.9.0' - 'bioconductor-txdb.hsapiens.ucsc.hg18.knowngene >=3.2.0,<3.3.0' - 'bioconductor-txdb.hsapiens.ucsc.hg19.knowngene >=3.2.0,<3.3.0' - 'bioconductor-txdb.hsapiens.ucsc.hg38.knowngene >=3.4.0,<3.5.0' @@ -40,16 +40,16 @@ requirements: - r-plyr - 'r-shiny >=0.11.1' run: - - 'bioconductor-acgh >=1.60.0,<1.61.0' - - 'bioconductor-affy >=1.60.0,<1.61.0' - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' - - 'bioconductor-dnacopy >=1.56.0,<1.57.0' - - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' - - 'bioconductor-genomicfeatures >=1.34.0,<1.35.0' - - 'bioconductor-genomicranges >=1.34.0,<1.35.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-limma >=3.38.0,<3.39.0' - - 'bioconductor-org.hs.eg.db >=3.7.0,<3.8.0' + - 'bioconductor-acgh >=1.62.0,<1.63.0' + - 'bioconductor-affy >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' + - 'bioconductor-dnacopy >=1.58.0,<1.59.0' + - 'bioconductor-genomeinfodb >=1.20.0,<1.21.0' + - 'bioconductor-genomicfeatures >=1.36.0,<1.37.0' + - 'bioconductor-genomicranges >=1.36.0,<1.37.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-limma >=3.40.0,<3.41.0' + - 'bioconductor-org.hs.eg.db >=3.8.0,<3.9.0' - 'bioconductor-txdb.hsapiens.ucsc.hg18.knowngene >=3.2.0,<3.3.0' - 'bioconductor-txdb.hsapiens.ucsc.hg19.knowngene >=3.2.0,<3.3.0' - 'bioconductor-txdb.hsapiens.ucsc.hg38.knowngene >=3.4.0,<3.5.0' diff --git a/recipes/bioconductor-rchemcpp/meta.yaml b/recipes/bioconductor-rchemcpp/meta.yaml index 6a6cafcd9e5a2..41defd95e206e 100644 --- a/recipes/bioconductor-rchemcpp/meta.yaml +++ b/recipes/bioconductor-rchemcpp/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "2.20.1" %} +{% set version = "2.21.1" %} {% set name = "Rchemcpp" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: c20462911ab119a4f43c89ce23144ab2fa918f58d31a060650768722554f4b03 + md5: 7baa3710ac856f7b70b580e127f0aa0e build: number: 0 rpaths: @@ -20,11 +20,11 @@ build: # SystemRequirements: GNU make requirements: host: - - 'bioconductor-chemminer >=3.34.0,<3.35.0' + - 'bioconductor-chemminer >=3.36.0,<3.37.0' - r-base - 'r-rcpp >=0.11.1' run: - - 'bioconductor-chemminer >=3.34.0,<3.35.0' + - 'bioconductor-chemminer >=3.36.0,<3.37.0' - r-base - 'r-rcpp >=0.11.1' build: diff --git a/recipes/bioconductor-rchyoptimyx/meta.yaml b/recipes/bioconductor-rchyoptimyx/meta.yaml index 7503f19f19c3f..059b2392e235e 100644 --- a/recipes/bioconductor-rchyoptimyx/meta.yaml +++ b/recipes/bioconductor-rchyoptimyx/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "2.22.0" %} +{% set version = "2.24.0" %} {% set name = "RchyOptimyx" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,25 +10,24 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: da60b35d34e9ca50d24128210ea043cd + md5: 31073dc97f960a5b01c81c383bbe40e6 build: number: 0 - skip: True # [osx] rpaths: - lib/R/lib/ - lib/ # Suggests: flowCore requirements: host: - - 'bioconductor-flowtype >=2.20.0,<2.21.0' - - 'bioconductor-graph >=1.60.0,<1.61.0' - - 'bioconductor-rgraphviz >=2.26.0,<2.27.0' + - 'bioconductor-flowtype >=2.22.0,<2.23.0' + - 'bioconductor-graph >=1.62.0,<1.63.0' + - 'bioconductor-rgraphviz >=2.28.0,<2.29.0' - r-base - r-sfsmisc run: - - 'bioconductor-flowtype >=2.20.0,<2.21.0' - - 'bioconductor-graph >=1.60.0,<1.61.0' - - 'bioconductor-rgraphviz >=2.26.0,<2.27.0' + - 'bioconductor-flowtype >=2.22.0,<2.23.0' + - 'bioconductor-graph >=1.62.0,<1.63.0' + - 'bioconductor-rgraphviz >=2.28.0,<2.29.0' - r-base - r-sfsmisc build: @@ -42,7 +41,7 @@ about: home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: Artistic-2.0 summary: 'Constructs a hierarchy of cells using flow cytometry for maximization of an external variable (e.g., a clinical outcome or a cytokine response).' - extra: container: - extended-base: True + extended-base: true + diff --git a/recipes/bioconductor-rcistarget.hg19.motifdbs.cisbponly.500bp/meta.yaml b/recipes/bioconductor-rcistarget.hg19.motifdbs.cisbponly.500bp/meta.yaml index f8ce7287009e4..744375cea7b8b 100644 --- a/recipes/bioconductor-rcistarget.hg19.motifdbs.cisbponly.500bp/meta.yaml +++ b/recipes/bioconductor-rcistarget.hg19.motifdbs.cisbponly.500bp/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.2.0" %} +{% set version = "1.4.0" %} {% set name = "RcisTarget.hg19.motifDBs.cisbpOnly.500bp" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: a43b2fd762e2ea0d13283c4c7fa5221c + md5: 2558d0f1567d5e36b21cc109a030d844 build: number: 0 rpaths: @@ -24,7 +24,7 @@ requirements: run: - r-base - r-data.table - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-rcistarget.hg19.motifdbs.cisbponly.500bp/post-link.sh b/recipes/bioconductor-rcistarget.hg19.motifdbs.cisbponly.500bp/post-link.sh index 1ff243153d5bc..7660418e88a2c 100644 --- a/recipes/bioconductor-rcistarget.hg19.motifdbs.cisbponly.500bp/post-link.sh +++ b/recipes/bioconductor-rcistarget.hg19.motifdbs.cisbponly.500bp/post-link.sh @@ -1,11 +1,11 @@ #!/bin/bash -FN="RcisTarget.hg19.motifDBs.cisbpOnly.500bp_1.2.0.tar.gz" +FN="RcisTarget.hg19.motifDBs.cisbpOnly.500bp_1.4.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/experiment/src/contrib/RcisTarget.hg19.motifDBs.cisbpOnly.500bp_1.2.0.tar.gz" - "https://bioarchive.galaxyproject.org/RcisTarget.hg19.motifDBs.cisbpOnly.500bp_1.2.0.tar.gz" - "https://depot.galaxyproject.org/software/bioconductor-rcistarget.hg19.motifdbs.cisbponly.500bp/bioconductor-rcistarget.hg19.motifdbs.cisbponly.500bp_1.2.0_src_all.tar.gz" + "https://bioconductor.org/packages/3.9/data/experiment/src/contrib/RcisTarget.hg19.motifDBs.cisbpOnly.500bp_1.4.0.tar.gz" + "https://bioarchive.galaxyproject.org/RcisTarget.hg19.motifDBs.cisbpOnly.500bp_1.4.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-rcistarget.hg19.motifdbs.cisbponly.500bp/bioconductor-rcistarget.hg19.motifdbs.cisbponly.500bp_1.4.0_src_all.tar.gz" ) -MD5="a43b2fd762e2ea0d13283c4c7fa5221c" +MD5="2558d0f1567d5e36b21cc109a030d844" # Use a staging area in the conda dir rather than temp dirs, both to avoid # permission issues as well as to have things downloaded in a predictable @@ -16,7 +16,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-rcistarget/meta.yaml b/recipes/bioconductor-rcistarget/meta.yaml index d12e29237ea51..2c091baf70e7f 100644 --- a/recipes/bioconductor-rcistarget/meta.yaml +++ b/recipes/bioconductor-rcistarget/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.2.1" %} +{% set version = "1.4.0" %} {% set name = "RcisTarget" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 436ba541859959c23c23c925d11f7342 + md5: adc62e71ca1030c785f3c0e80a1a60c7 build: number: 0 rpaths: @@ -20,19 +20,19 @@ build: # Suggests: Biobase, BiocStyle, BiocParallel, doParallel, DT, foreach, igraph, knitr, RcisTarget.hg19.motifDBs.cisbpOnly.500bp, rmarkdown, testthat, visNetwork requirements: host: - - 'bioconductor-aucell >=1.4.0,<1.5.0' - - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' - - 'bioconductor-gseabase >=1.44.0,<1.45.0' - - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' + - 'bioconductor-aucell >=1.6.0,<1.7.0' + - 'bioconductor-biocgenerics >=0.30.0,<0.31.0' + - 'bioconductor-gseabase >=1.46.0,<1.47.0' + - 'bioconductor-summarizedexperiment >=1.14.0,<1.15.0' - r-base - r-data.table - r-feather - r-r.utils run: - - 'bioconductor-aucell >=1.4.0,<1.5.0' - - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' - - 'bioconductor-gseabase >=1.44.0,<1.45.0' - - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' + - 'bioconductor-aucell >=1.6.0,<1.7.0' + - 'bioconductor-biocgenerics >=0.30.0,<0.31.0' + - 'bioconductor-gseabase >=1.46.0,<1.47.0' + - 'bioconductor-summarizedexperiment >=1.14.0,<1.15.0' - r-base - r-data.table - r-feather diff --git a/recipes/bioconductor-rcm/build.sh b/recipes/bioconductor-rcm/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-rcm/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-rcm/meta.yaml b/recipes/bioconductor-rcm/meta.yaml new file mode 100644 index 0000000000000..c34abb4e129a2 --- /dev/null +++ b/recipes/bioconductor-rcm/meta.yaml @@ -0,0 +1,57 @@ +{% set version = "1.0.0" %} +{% set name = "RCM" %} +{% set bioc = "3.9" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: 8d34d630c361a2426ae5054ba7e536b1 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: knitr, rmarkdown, testthat +requirements: + host: + - 'bioconductor-edger >=3.26.0,<3.27.0' + - 'bioconductor-phyloseq >=1.28.0,<1.29.0' + - r-alabama + - r-base + - 'r-ggplot2 >=2.2.1.9000' + - r-mass + - r-nleqslv + - r-rcolorbrewer + - r-reshape2 + - r-tensor + - r-tseries + - r-vegan + - r-vgam + run: + - 'bioconductor-edger >=3.26.0,<3.27.0' + - 'bioconductor-phyloseq >=1.28.0,<1.29.0' + - r-alabama + - r-base + - 'r-ggplot2 >=2.2.1.9000' + - r-mass + - r-nleqslv + - r-rcolorbrewer + - r-reshape2 + - r-tensor + - r-tseries + - r-vegan + - r-vgam +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: GPL-2 + summary: 'Combine ideas of log-linear analysis of contingency table, flexible response function estimation and empirical Bayes dispersion estimation for explorative visualization of microbiome datasets. The package includes unconstrained as well as constrained analysis.' + diff --git a/recipes/bioconductor-rcpi/meta.yaml b/recipes/bioconductor-rcpi/meta.yaml index 6a5571a4f25eb..46eb1142dd60b 100644 --- a/recipes/bioconductor-rcpi/meta.yaml +++ b/recipes/bioconductor-rcpi/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.18.1" %} +{% set version = "1.20.0" %} {% set name = "Rcpi" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: ee46e5f6fe8d72cb137d8f2bbf37c7f9 + md5: 299a4ae1a053e56c720beb9a1a8055e9 build: number: 0 rpaths: @@ -20,10 +20,10 @@ build: # Suggests: knitr, rmarkdown, RUnit, BiocGenerics requirements: host: - - 'bioconductor-biostrings >=2.50.0,<2.51.0' - - 'bioconductor-chemminer >=3.34.0,<3.35.0' - - 'bioconductor-fmcsr >=1.24.0,<1.25.0' - - 'bioconductor-gosemsim >=2.8.0,<2.9.0' + - 'bioconductor-biostrings >=2.52.0,<2.53.0' + - 'bioconductor-chemminer >=3.36.0,<3.37.0' + - 'bioconductor-fmcsr >=1.26.0,<1.27.0' + - 'bioconductor-gosemsim >=2.10.0,<2.11.0' - r-base - r-doparallel - r-foreach @@ -31,10 +31,10 @@ requirements: - r-rcurl - r-rjson run: - - 'bioconductor-biostrings >=2.50.0,<2.51.0' - - 'bioconductor-chemminer >=3.34.0,<3.35.0' - - 'bioconductor-fmcsr >=1.24.0,<1.25.0' - - 'bioconductor-gosemsim >=2.8.0,<2.9.0' + - 'bioconductor-biostrings >=2.52.0,<2.53.0' + - 'bioconductor-chemminer >=3.36.0,<3.37.0' + - 'bioconductor-fmcsr >=1.26.0,<1.27.0' + - 'bioconductor-gosemsim >=2.10.0,<2.11.0' - r-base - r-doparallel - r-foreach diff --git a/recipes/bioconductor-rcwl/build.sh b/recipes/bioconductor-rcwl/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-rcwl/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-rcwl/meta.yaml b/recipes/bioconductor-rcwl/meta.yaml new file mode 100644 index 0000000000000..5d758fce63ee9 --- /dev/null +++ b/recipes/bioconductor-rcwl/meta.yaml @@ -0,0 +1,50 @@ +{% set version = "1.0.0" %} +{% set name = "Rcwl" %} +{% set bioc = "3.9" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: b028c8787f65de48c28ff1f31a46269b +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: testthat, knitr, rmarkdown +# SystemRequirements: python (>= 2.7), cwltool (>= 1.0.2018) +requirements: + host: + - 'bioconductor-biocparallel >=1.18.0,<1.19.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' + - r-base + - r-batchtools + - r-diagrammer + - r-shiny + - r-yaml + - python + - cwltool >=1.0.2018 + run: + - 'bioconductor-biocparallel >=1.18.0,<1.19.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' + - r-base + - r-batchtools + - r-diagrammer + - r-shiny + - r-yaml + - python + - cwltool >=1.0.2018 +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: 'GPL-2 | file LICENSE' + summary: 'The package can be a simple and user-friendly way to manage command line tools and build data analysis pipelines in R using Common Workflow Language (CWL).' + diff --git a/recipes/bioconductor-rcwlpipelines/build.sh b/recipes/bioconductor-rcwlpipelines/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-rcwlpipelines/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-rcwlpipelines/meta.yaml b/recipes/bioconductor-rcwlpipelines/meta.yaml new file mode 100644 index 0000000000000..8290d18af09d1 --- /dev/null +++ b/recipes/bioconductor-rcwlpipelines/meta.yaml @@ -0,0 +1,44 @@ +{% set version = "1.0.0" %} +{% set name = "RcwlPipelines" %} +{% set bioc = "3.9" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: 207f3342aa004b2b69ba8b1d45733dd9 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: testthat, knitr, rmarkdown +# SystemRequirements: nodejs +requirements: + host: + - 'bioconductor-biocfilecache >=1.8.0,<1.9.0' + - 'bioconductor-rcwl >=1.0.0,<1.1.0' + - r-base + - r-dplyr + - r-rappdirs + - nodejs + run: + - 'bioconductor-biocfilecache >=1.8.0,<1.9.0' + - 'bioconductor-rcwl >=1.0.0,<1.1.0' + - r-base + - r-dplyr + - r-rappdirs + - nodejs +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: GPL-2 + summary: 'A collection of Bioinformatics pipeline recipes based on Rcwl.' + diff --git a/recipes/bioconductor-rcy3/meta.yaml b/recipes/bioconductor-rcy3/meta.yaml index 4585a661ae7e7..c6b704646d995 100644 --- a/recipes/bioconductor-rcy3/meta.yaml +++ b/recipes/bioconductor-rcy3/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "2.2.9" %} +{% set version = "2.4.0" %} {% set name = "RCy3" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,34 +10,38 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: 9b819effebf5e58f7d8082ae6f28c0fbc2f39c0a38569c13cd2e2f011f1cc712 + md5: a1ac06fc9eaf9ec62b8485c5ab5c3b1b build: number: 0 rpaths: - lib/R/lib/ - lib/ noarch: generic -# Suggests: RUnit, RColorBrewer, BiocStyle, knitr, rmarkdown -# SystemRequirements: Cytoscape (>= 3.7.0), CyREST (>= 3.8.0) +# Suggests: RUnit, BiocStyle, knitr, rmarkdown +# SystemRequirements: Cytoscape (>= 3.7.1), CyREST (>= 3.8.0) requirements: host: - - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' - - 'bioconductor-graph >=1.60.0,<1.61.0' + - 'bioconductor-biocgenerics >=0.30.0,<0.31.0' + - 'bioconductor-graph >=1.62.0,<1.63.0' - r-base - r-httr - r-igraph + - r-r.utils - r-rjsonio - r-xml - - r-r.utils + - cytoscape >=3.7.1 + - cyrest >=3.8.0 run: - - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' - - 'bioconductor-graph >=1.60.0,<1.61.0' + - 'bioconductor-biocgenerics >=0.30.0,<0.31.0' + - 'bioconductor-graph >=1.62.0,<1.63.0' - r-base - r-httr - r-igraph + - r-r.utils - r-rjsonio - r-xml - - r-r.utils + - cytoscape >=3.7.1 + - cyrest >=3.8.0 test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-rcyjs/meta.yaml b/recipes/bioconductor-rcyjs/meta.yaml index e1416d9510b49..5c813790e92c9 100644 --- a/recipes/bioconductor-rcyjs/meta.yaml +++ b/recipes/bioconductor-rcyjs/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "2.4.0" %} +{% set version = "2.6.0" %} {% set name = "RCyjs" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 19c7f00c1017e0322bca3036a696fc66 + md5: b08a087c3857b27c5a97c92de29a2b98 build: number: 0 rpaths: @@ -20,19 +20,19 @@ build: # Suggests: RUnit, BiocStyle, RefNet, knitr, rmarkdown requirements: host: - - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' - - 'bioconductor-browserviz >=2.4.0,<2.5.0' - - 'bioconductor-graph >=1.60.0,<1.61.0' + - 'bioconductor-biocgenerics >=0.30.0,<0.31.0' + - 'bioconductor-browserviz >=2.6.0,<2.7.0' + - 'bioconductor-graph >=1.62.0,<1.63.0' - r-base - r-base64enc - - 'r-httpuv >=1.4.0' + - 'r-httpuv >=1.5.0' run: - - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' - - 'bioconductor-browserviz >=2.4.0,<2.5.0' - - 'bioconductor-graph >=1.60.0,<1.61.0' + - 'bioconductor-biocgenerics >=0.30.0,<0.31.0' + - 'bioconductor-browserviz >=2.6.0,<2.7.0' + - 'bioconductor-graph >=1.62.0,<1.63.0' - r-base - r-base64enc - - 'r-httpuv >=1.4.0' + - 'r-httpuv >=1.5.0' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-rcytoscape/meta.yaml b/recipes/bioconductor-rcytoscape/meta.yaml index 847862b22dc77..a3b0711f202ae 100644 --- a/recipes/bioconductor-rcytoscape/meta.yaml +++ b/recipes/bioconductor-rcytoscape/meta.yaml @@ -19,12 +19,12 @@ build: requirements: host: - bioconductor-biocgenerics - - 'bioconductor-graph >=1.31.0' + - 'bioconductor-graph >=1.32.0' - r-base - 'r-xmlrpc >=0.2.4' run: - bioconductor-biocgenerics - - 'bioconductor-graph >=1.31.0' + - 'bioconductor-graph >=1.32.0' - r-base - 'r-xmlrpc >=0.2.4' test: diff --git a/recipes/bioconductor-rdavidwebservice/meta.yaml b/recipes/bioconductor-rdavidwebservice/meta.yaml index afde7ac7c629d..20f6748a39787 100644 --- a/recipes/bioconductor-rdavidwebservice/meta.yaml +++ b/recipes/bioconductor-rdavidwebservice/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.20.0" %} +{% set version = "1.22.0" %} {% set name = "RDAVIDWebService" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 21a1209b7e43d5753dcf84a4590d06e7 + md5: 3b8b125d8f39ee1f0b017168127a8661 build: number: 0 rpaths: @@ -20,20 +20,20 @@ build: # Suggests: Rgraphviz requirements: host: - - 'bioconductor-category >=2.48.0,<2.49.0' - - 'bioconductor-go.db >=3.7.0,<3.8.0' - - 'bioconductor-gostats >=2.48.0,<2.49.0' - - 'bioconductor-graph >=1.60.0,<1.61.0' - - 'bioconductor-rbgl >=1.58.0,<1.59.0' + - 'bioconductor-category >=2.50.0,<2.51.0' + - 'bioconductor-go.db >=3.8.0,<3.9.0' + - 'bioconductor-gostats >=2.50.0,<2.51.0' + - 'bioconductor-graph >=1.62.0,<1.63.0' + - 'bioconductor-rbgl >=1.60.0,<1.61.0' - r-base - r-ggplot2 - r-rjava run: - - 'bioconductor-category >=2.48.0,<2.49.0' - - 'bioconductor-go.db >=3.7.0,<3.8.0' - - 'bioconductor-gostats >=2.48.0,<2.49.0' - - 'bioconductor-graph >=1.60.0,<1.61.0' - - 'bioconductor-rbgl >=1.58.0,<1.59.0' + - 'bioconductor-category >=2.50.0,<2.51.0' + - 'bioconductor-go.db >=3.8.0,<3.9.0' + - 'bioconductor-gostats >=2.50.0,<2.51.0' + - 'bioconductor-graph >=1.62.0,<1.63.0' + - 'bioconductor-rbgl >=1.60.0,<1.61.0' - r-base - r-ggplot2 - r-rjava diff --git a/recipes/bioconductor-rdgidb/meta.yaml b/recipes/bioconductor-rdgidb/meta.yaml index 60eccba952eeb..1cf839df198e0 100644 --- a/recipes/bioconductor-rdgidb/meta.yaml +++ b/recipes/bioconductor-rdgidb/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.8.0" %} +{% set version = "1.10.0" %} {% set name = "rDGIdb" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: b08e5cd64ac2af2f3fd05a7ec4472b1c + md5: e8ea9465dfeff48d4475c8375f2bc2c4 build: number: 0 rpaths: diff --git a/recipes/bioconductor-rdisop/meta.yaml b/recipes/bioconductor-rdisop/meta.yaml index d06de71777b26..8a978dbd0d593 100644 --- a/recipes/bioconductor-rdisop/meta.yaml +++ b/recipes/bioconductor-rdisop/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.42.1" %} +{% set version = "1.44.0" %} {% set name = "Rdisop" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 669585bc83dbc17643777baa37564444 + md5: 13e4b81c9b0e526c06e97789f32f9a40 build: number: 0 rpaths: @@ -22,11 +22,9 @@ requirements: host: - r-base - r-rcpp - - r-rcppclassic run: - r-base - r-rcpp - - r-rcppclassic build: - {{ compiler('c') }} - {{ compiler('cxx') }} diff --git a/recipes/bioconductor-rdrtoolbox/build.sh b/recipes/bioconductor-rdrtoolbox/build.sh index c1d13421f5f1e..068014183bd4e 100644 --- a/recipes/bioconductor-rdrtoolbox/build.sh +++ b/recipes/bioconductor-rdrtoolbox/build.sh @@ -1,4 +1,5 @@ #!/bin/bash +export LD_LIBRARY_PATH=${BUILD_PREFIX}/x86_64-conda_cos6-linux-gnu/sysroot/usr/lib64 mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION mkdir -p ~/.R @@ -8,4 +9,4 @@ CXX=$CXX CXX98=$CXX CXX11=$CXX CXX14=$CXX" > ~/.R/Makevars -$R CMD INSTALL --build . \ No newline at end of file +$R CMD INSTALL --build . diff --git a/recipes/bioconductor-rdrtoolbox/meta.yaml b/recipes/bioconductor-rdrtoolbox/meta.yaml index d2831a86f00bb..8bfc0f29537a8 100644 --- a/recipes/bioconductor-rdrtoolbox/meta.yaml +++ b/recipes/bioconductor-rdrtoolbox/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.32.0" %} +{% set version = "1.34.0" %} {% set name = "RDRToolbox" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 4878943bca03a276c3ad77772ae786cc + md5: 2b190cad4839dd6c06b6bca0cbe5996c build: number: 0 rpaths: @@ -19,6 +19,13 @@ build: noarch: generic # Suggests: golubEsets requirements: + build: + - {{ cdt('mesa-libgl-devel') }} + - {{ cdt('mesa-dri-drivers') }} + - {{ cdt('libselinux') }} + - {{ cdt('libxdamage') }} + - {{ cdt('libxxf86vm') }} + - {{ cdt('libxfixes') }} host: - r-base - r-mass @@ -29,13 +36,12 @@ requirements: - r-rgl test: commands: - - '$R -e "library(''{{ name }}'')"' + - LD_LIBRARY_PATH="${BUILD_PREFIX}/x86_64-conda_cos6-linux-gnu/sysroot/usr/lib64:/usr/lib/x86_64-linux-gnu/" $R -e "library('{{ name }}')" about: home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: 'GPL (>= 2)' summary: 'A package for nonlinear dimension reduction using the Isomap and LLE algorithm. It also includes a routine for computing the Davis-Bouldin-Index for cluster validation, a plotting tool and a data generator for microarray gene expression data and for the Swiss Roll dataset.' - extra: container: - # needed for libGL.so.1 extended-base: true + diff --git a/recipes/bioconductor-reactome.db/meta.yaml b/recipes/bioconductor-reactome.db/meta.yaml index 4d4818a1196bb..704ee50e04456 100644 --- a/recipes/bioconductor-reactome.db/meta.yaml +++ b/recipes/bioconductor-reactome.db/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.66.0" %} +{% set version = "1.68.0" %} {% set name = "reactome.db" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 986cbb0b2f951b57c682364213f5016e + md5: 281e47eea8f6bf72502843ad6a48dab0 build: number: 0 rpaths: @@ -20,12 +20,12 @@ build: # Suggests: RSQLite requirements: host: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' - r-base run: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-reactome.db/post-link.sh b/recipes/bioconductor-reactome.db/post-link.sh index 735e7cee27dea..9ad7c5e625eec 100644 --- a/recipes/bioconductor-reactome.db/post-link.sh +++ b/recipes/bioconductor-reactome.db/post-link.sh @@ -1,11 +1,11 @@ #!/bin/bash -FN="reactome.db_1.66.0.tar.gz" +FN="reactome.db_1.68.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/reactome.db_1.66.0.tar.gz" - "https://bioarchive.galaxyproject.org/reactome.db_1.66.0.tar.gz" - "https://depot.galaxyproject.org/software/bioconductor-reactome.db/bioconductor-reactome.db_1.66.0_src_all.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/reactome.db_1.68.0.tar.gz" + "https://bioarchive.galaxyproject.org/reactome.db_1.68.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-reactome.db/bioconductor-reactome.db_1.68.0_src_all.tar.gz" ) -MD5="986cbb0b2f951b57c682364213f5016e" +MD5="281e47eea8f6bf72502843ad6a48dab0" # Use a staging area in the conda dir rather than temp dirs, both to avoid # permission issues as well as to have things downloaded in a predictable @@ -16,7 +16,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-reactomepa/meta.yaml b/recipes/bioconductor-reactomepa/meta.yaml index 62b0a5f14473f..7c39eb0452125 100644 --- a/recipes/bioconductor-reactomepa/meta.yaml +++ b/recipes/bioconductor-reactomepa/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.26.0" %} +{% set version = "1.28.0" %} {% set name = "ReactomePA" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: b240608152ce98d954046ecd1e14ba7b + md5: 18193e4881138989bcd4333944982058 build: number: 0 rpaths: @@ -20,21 +20,21 @@ build: # Suggests: BiocStyle, clusterProfiler, knitr, org.Hs.eg.db, prettydoc, testthat requirements: host: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' - - 'bioconductor-dose >=3.8.0,<3.9.0' - - 'bioconductor-enrichplot >=1.2.0,<1.3.0' - - 'bioconductor-graphite >=1.28.0,<1.29.0' - - 'bioconductor-reactome.db >=1.66.0,<1.67.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' + - 'bioconductor-dose >=3.10.0,<3.11.0' + - 'bioconductor-enrichplot >=1.4.0,<1.5.0' + - 'bioconductor-graphite >=1.30.0,<1.31.0' + - 'bioconductor-reactome.db >=1.68.0,<1.69.0' - r-base - r-ggplot2 - r-ggraph - r-igraph run: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' - - 'bioconductor-dose >=3.8.0,<3.9.0' - - 'bioconductor-enrichplot >=1.2.0,<1.3.0' - - 'bioconductor-graphite >=1.28.0,<1.29.0' - - 'bioconductor-reactome.db >=1.66.0,<1.67.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' + - 'bioconductor-dose >=3.10.0,<3.11.0' + - 'bioconductor-enrichplot >=1.4.0,<1.5.0' + - 'bioconductor-graphite >=1.30.0,<1.31.0' + - 'bioconductor-reactome.db >=1.68.0,<1.69.0' - r-base - r-ggplot2 - r-ggraph diff --git a/recipes/bioconductor-readat/meta.yaml b/recipes/bioconductor-readat/meta.yaml index d79436b5f9486..e80a10c19aa11 100644 --- a/recipes/bioconductor-readat/meta.yaml +++ b/recipes/bioconductor-readat/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.8.0" %} +{% set version = "1.10.0" %} {% set name = "readat" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 5997fc86272923223432b715e16ba7be + md5: 8507f3bf56c2e3ac48cbe25e364a9c45 build: number: 0 rpaths: @@ -20,8 +20,8 @@ build: # Suggests: knitr, MSnbase, rmarkdown, withr requirements: host: - - 'bioconductor-biobase >=2.42.0,<2.43.0' - - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' + - 'bioconductor-summarizedexperiment >=1.14.0,<1.15.0' - 'r-assertive.base >=0.0-7' - 'r-assertive.files >=0.0-2' - 'r-assertive.numbers >=0.0-2' @@ -39,8 +39,8 @@ requirements: - 'r-testthat >=1.0.2' - 'r-tidyr >=0.6.2' run: - - 'bioconductor-biobase >=2.42.0,<2.43.0' - - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' + - 'bioconductor-summarizedexperiment >=1.14.0,<1.15.0' - 'r-assertive.base >=0.0-7' - 'r-assertive.files >=0.0-2' - 'r-assertive.numbers >=0.0-2' diff --git a/recipes/bioconductor-readqpcr/meta.yaml b/recipes/bioconductor-readqpcr/meta.yaml index fd5f2c733f927..4809cc7f32c0c 100644 --- a/recipes/bioconductor-readqpcr/meta.yaml +++ b/recipes/bioconductor-readqpcr/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.28.0" %} +{% set version = "1.30.0" %} {% set name = "ReadqPCR" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: dff61efd77bb86fb720acd7c63b32976 + md5: 086211aa45bcbff6dcfde3efe7bd781c build: number: 0 rpaths: @@ -20,10 +20,10 @@ build: # Suggests: qpcR requirements: host: - - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' - r-base run: - - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' - r-base test: commands: diff --git a/recipes/bioconductor-reb/meta.yaml b/recipes/bioconductor-reb/meta.yaml index 3fd3edf15047d..0f50c437a20ac 100644 --- a/recipes/bioconductor-reb/meta.yaml +++ b/recipes/bioconductor-reb/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.60.0" %} +{% set version = "1.62.0" %} {% set name = "reb" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: b4e0632e5c9173414286e0dba2af409a + md5: 207f4057530bd1b3ced23270a7a11925 build: number: 0 rpaths: @@ -18,12 +18,12 @@ build: - lib/ requirements: host: - - 'bioconductor-biobase >=2.42.0,<2.43.0' - - 'bioconductor-idiogram >=1.58.0,<1.59.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' + - 'bioconductor-idiogram >=1.60.0,<1.61.0' - r-base run: - - 'bioconductor-biobase >=2.42.0,<2.43.0' - - 'bioconductor-idiogram >=1.58.0,<1.59.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' + - 'bioconductor-idiogram >=1.60.0,<1.61.0' - r-base build: - {{ compiler('c') }} diff --git a/recipes/bioconductor-rebet/meta.yaml b/recipes/bioconductor-rebet/meta.yaml index 065ee7a92e0c0..6b1035482d196 100644 --- a/recipes/bioconductor-rebet/meta.yaml +++ b/recipes/bioconductor-rebet/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.0.0" %} +{% set version = "1.2.0" %} {% set name = "REBET" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: f48ce39437f7c86e3685d0426ba8083c + md5: 776e872bca2020d7cc861bfc798478b0 build: number: 0 rpaths: @@ -19,10 +19,10 @@ build: # Suggests: RUnit, BiocGenerics requirements: host: - - 'bioconductor-asset >=2.0.0,<2.1.0' + - 'bioconductor-asset >=2.2.0,<2.3.0' - r-base run: - - 'bioconductor-asset >=2.0.0,<2.1.0' + - 'bioconductor-asset >=2.2.0,<2.3.0' - r-base build: - {{ compiler('c') }} diff --git a/recipes/bioconductor-recount/meta.yaml b/recipes/bioconductor-recount/meta.yaml index b0a0f175f8e5e..482e396c6d7b3 100644 --- a/recipes/bioconductor-recount/meta.yaml +++ b/recipes/bioconductor-recount/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.8.1" %} +{% set version = "1.10.0" %} {% set name = "recount" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: b2277eb66cef0baf558f8b9a3fbc9d7e + md5: 7647fec40ba9684e08abdc9ec0d660ba build: number: 0 rpaths: @@ -20,29 +20,29 @@ build: # Suggests: AnnotationDbi, BiocManager, BiocStyle (>= 2.5.19), DESeq2, sessioninfo, EnsDb.Hsapiens.v79, GenomicFeatures, knitcitations, knitr (>= 1.6), org.Hs.eg.db, RefManageR, regionReport (>= 1.9.4), rmarkdown (>= 0.9.5), testthat requirements: host: - - 'bioconductor-biocparallel >=1.16.0,<1.17.0' - - 'bioconductor-derfinder >=1.16.0,<1.17.0' - - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' - - 'bioconductor-genomicranges >=1.34.0,<1.35.0' - - 'bioconductor-geoquery >=2.50.0,<2.51.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-rtracklayer >=1.42.0,<1.43.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' - - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' + - 'bioconductor-biocparallel >=1.18.0,<1.19.0' + - 'bioconductor-derfinder >=1.18.0,<1.19.0' + - 'bioconductor-genomeinfodb >=1.20.0,<1.21.0' + - 'bioconductor-genomicranges >=1.36.0,<1.37.0' + - 'bioconductor-geoquery >=2.52.0,<2.53.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-rtracklayer >=1.44.0,<1.45.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' + - 'bioconductor-summarizedexperiment >=1.14.0,<1.15.0' - r-base - r-downloader - r-rcurl - r-rentrez run: - - 'bioconductor-biocparallel >=1.16.0,<1.17.0' - - 'bioconductor-derfinder >=1.16.0,<1.17.0' - - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' - - 'bioconductor-genomicranges >=1.34.0,<1.35.0' - - 'bioconductor-geoquery >=2.50.0,<2.51.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-rtracklayer >=1.42.0,<1.43.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' - - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' + - 'bioconductor-biocparallel >=1.18.0,<1.19.0' + - 'bioconductor-derfinder >=1.18.0,<1.19.0' + - 'bioconductor-genomeinfodb >=1.20.0,<1.21.0' + - 'bioconductor-genomicranges >=1.36.0,<1.37.0' + - 'bioconductor-geoquery >=2.52.0,<2.53.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-rtracklayer >=1.44.0,<1.45.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' + - 'bioconductor-summarizedexperiment >=1.14.0,<1.15.0' - r-base - r-downloader - r-rcurl diff --git a/recipes/bioconductor-recoup/meta.yaml b/recipes/bioconductor-recoup/meta.yaml index a6b5275d96ec4..f58606403da2e 100644 --- a/recipes/bioconductor-recoup/meta.yaml +++ b/recipes/bioconductor-recoup/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.10.0" %} +{% set version = "1.12.0" %} {% set name = "recoup" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 01f46bb984f1c8a7370d9405565609d2 + md5: 3aae87e834e6ba51e39a16426611a8fc build: number: 0 rpaths: @@ -20,23 +20,23 @@ build: # Suggests: grid, GenomeInfoDb, Rsamtools, BiocStyle, knitr, rmarkdown, zoo, RUnit, BiocManager, BSgenome, RSQLite, RMySQL requirements: host: - - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' - - 'bioconductor-biomart >=2.38.0,<2.39.0' - - 'bioconductor-complexheatmap >=1.20.0,<1.21.0' - - 'bioconductor-genomicalignments >=1.18.0,<1.19.0' - - 'bioconductor-genomicranges >=1.34.0,<1.35.0' - - 'bioconductor-rtracklayer >=1.42.0,<1.43.0' + - 'bioconductor-biocgenerics >=0.30.0,<0.31.0' + - 'bioconductor-biomart >=2.40.0,<2.41.0' + - 'bioconductor-complexheatmap >=2.0.0,<2.1.0' + - 'bioconductor-genomicalignments >=1.20.0,<1.21.0' + - 'bioconductor-genomicranges >=1.36.0,<1.37.0' + - 'bioconductor-rtracklayer >=1.44.0,<1.45.0' - r-base - r-circlize - r-ggplot2 - r-plyr run: - - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' - - 'bioconductor-biomart >=2.38.0,<2.39.0' - - 'bioconductor-complexheatmap >=1.20.0,<1.21.0' - - 'bioconductor-genomicalignments >=1.18.0,<1.19.0' - - 'bioconductor-genomicranges >=1.34.0,<1.35.0' - - 'bioconductor-rtracklayer >=1.42.0,<1.43.0' + - 'bioconductor-biocgenerics >=0.30.0,<0.31.0' + - 'bioconductor-biomart >=2.40.0,<2.41.0' + - 'bioconductor-complexheatmap >=2.0.0,<2.1.0' + - 'bioconductor-genomicalignments >=1.20.0,<1.21.0' + - 'bioconductor-genomicranges >=1.36.0,<1.37.0' + - 'bioconductor-rtracklayer >=1.44.0,<1.45.0' - r-base - r-circlize - r-ggplot2 diff --git a/recipes/bioconductor-reder/meta.yaml b/recipes/bioconductor-reder/meta.yaml index 30c6f0c7aace6..671a8856fb6f4 100644 --- a/recipes/bioconductor-reder/meta.yaml +++ b/recipes/bioconductor-reder/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.30.0" %} +{% set version = "1.32.0" %} {% set name = "RedeR" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: feec78beaad4c43950605f9fb6af3f9d + md5: 429be5e96c997a1bb12c3080610f90c5 build: number: 0 rpaths: @@ -23,9 +23,11 @@ requirements: host: - r-base - r-igraph + - openjdk 8.* run: - r-base - r-igraph + - openjdk 8.* test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-redseq/meta.yaml b/recipes/bioconductor-redseq/meta.yaml index 807a5519ca735..32e613e2d604e 100644 --- a/recipes/bioconductor-redseq/meta.yaml +++ b/recipes/bioconductor-redseq/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.28.0" %} +{% set version = "1.30.0" %} {% set name = "REDseq" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 77974694af5810b7e9cbec3c126cc814 + md5: 28992addf8f0a83b68e7a3188cd5f442 build: number: 0 rpaths: @@ -19,24 +19,24 @@ build: noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' - - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' - - 'bioconductor-biostrings >=2.50.0,<2.51.0' - - 'bioconductor-bsgenome >=1.50.0,<1.51.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' + - 'bioconductor-biocgenerics >=0.30.0,<0.31.0' + - 'bioconductor-biostrings >=2.52.0,<2.53.0' + - 'bioconductor-bsgenome >=1.52.0,<1.53.0' - 'bioconductor-bsgenome.celegans.ucsc.ce2 >=1.4.0,<1.5.0' - - 'bioconductor-chippeakanno >=3.16.0,<3.17.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-multtest >=2.38.0,<2.39.0' + - 'bioconductor-chippeakanno >=3.18.0,<3.19.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-multtest >=2.40.0,<2.41.0' - r-base run: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' - - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' - - 'bioconductor-biostrings >=2.50.0,<2.51.0' - - 'bioconductor-bsgenome >=1.50.0,<1.51.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' + - 'bioconductor-biocgenerics >=0.30.0,<0.31.0' + - 'bioconductor-biostrings >=2.52.0,<2.53.0' + - 'bioconductor-bsgenome >=1.52.0,<1.53.0' - 'bioconductor-bsgenome.celegans.ucsc.ce2 >=1.4.0,<1.5.0' - - 'bioconductor-chippeakanno >=3.16.0,<3.17.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-multtest >=2.38.0,<2.39.0' + - 'bioconductor-chippeakanno >=3.18.0,<3.19.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-multtest >=2.40.0,<2.41.0' - r-base test: commands: diff --git a/recipes/bioconductor-refnet/meta.yaml b/recipes/bioconductor-refnet/meta.yaml index dc0baeb1b9d4f..fcfaaf6c232d1 100644 --- a/recipes/bioconductor-refnet/meta.yaml +++ b/recipes/bioconductor-refnet/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.18.0" %} +{% set version = "1.20.0" %} {% set name = "RefNet" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 5f543dd88c9275d0decf135bffa552dd + md5: fef9148fdfb0828b0d06d6e6ec1d210a build: number: 0 rpaths: @@ -20,18 +20,18 @@ build: # Suggests: RUnit, BiocStyle, org.Hs.eg.db requirements: host: - - 'bioconductor-annotationhub >=2.14.0,<2.15.0' - - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-psicquic >=1.20.0,<1.21.0' + - 'bioconductor-annotationhub >=2.16.0,<2.17.0' + - 'bioconductor-biocgenerics >=0.30.0,<0.31.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-psicquic >=1.22.0,<1.23.0' - r-base - r-rcurl - r-shiny run: - - 'bioconductor-annotationhub >=2.14.0,<2.15.0' - - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-psicquic >=1.20.0,<1.21.0' + - 'bioconductor-annotationhub >=2.16.0,<2.17.0' + - 'bioconductor-biocgenerics >=0.30.0,<0.31.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-psicquic >=1.22.0,<1.23.0' - r-base - r-rcurl - r-shiny diff --git a/recipes/bioconductor-refplus/meta.yaml b/recipes/bioconductor-refplus/meta.yaml index 8b54cee2d1f86..d2c11f064cc65 100644 --- a/recipes/bioconductor-refplus/meta.yaml +++ b/recipes/bioconductor-refplus/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.52.0" %} +{% set version = "1.54.0" %} {% set name = "RefPlus" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 1f3f27dfeccc81b91cef120849de5d1d + md5: d56a965cd314a7cb995c993c6512a6c3 build: number: 0 rpaths: @@ -20,16 +20,16 @@ build: # Suggests: affydata requirements: host: - - 'bioconductor-affy >=1.60.0,<1.61.0' - - 'bioconductor-affyplm >=1.58.0,<1.59.0' - - 'bioconductor-biobase >=2.42.0,<2.43.0' - - 'bioconductor-preprocesscore >=1.44.0,<1.45.0' + - 'bioconductor-affy >=1.62.0,<1.63.0' + - 'bioconductor-affyplm >=1.60.0,<1.61.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' + - 'bioconductor-preprocesscore >=1.46.0,<1.47.0' - r-base run: - - 'bioconductor-affy >=1.60.0,<1.61.0' - - 'bioconductor-affyplm >=1.58.0,<1.59.0' - - 'bioconductor-biobase >=2.42.0,<2.43.0' - - 'bioconductor-preprocesscore >=1.44.0,<1.45.0' + - 'bioconductor-affy >=1.62.0,<1.63.0' + - 'bioconductor-affyplm >=1.60.0,<1.61.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' + - 'bioconductor-preprocesscore >=1.46.0,<1.47.0' - r-base test: commands: diff --git a/recipes/bioconductor-regioner/meta.yaml b/recipes/bioconductor-regioner/meta.yaml index ae7d2b900b559..4048b67a96f90 100644 --- a/recipes/bioconductor-regioner/meta.yaml +++ b/recipes/bioconductor-regioner/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.14.0" %} +{% set version = "1.16.0" %} {% set name = "regioneR" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 526f133b01e3b43e3e1e72a1c34b4076 + md5: 866be8383faaeecd5b6f3faf5aceb4cd build: number: 0 rpaths: @@ -20,23 +20,23 @@ build: # Suggests: BiocStyle, knitr, BSgenome.Hsapiens.UCSC.hg19.masked, testthat requirements: host: - - 'bioconductor-biostrings >=2.50.0,<2.51.0' - - 'bioconductor-bsgenome >=1.50.0,<1.51.0' - - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' - - 'bioconductor-genomicranges >=1.34.0,<1.35.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-rtracklayer >=1.42.0,<1.43.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-biostrings >=2.52.0,<2.53.0' + - 'bioconductor-bsgenome >=1.52.0,<1.53.0' + - 'bioconductor-genomeinfodb >=1.20.0,<1.21.0' + - 'bioconductor-genomicranges >=1.36.0,<1.37.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-rtracklayer >=1.44.0,<1.45.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' - r-base - r-memoise run: - - 'bioconductor-biostrings >=2.50.0,<2.51.0' - - 'bioconductor-bsgenome >=1.50.0,<1.51.0' - - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' - - 'bioconductor-genomicranges >=1.34.0,<1.35.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-rtracklayer >=1.42.0,<1.43.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-biostrings >=2.52.0,<2.53.0' + - 'bioconductor-bsgenome >=1.52.0,<1.53.0' + - 'bioconductor-genomeinfodb >=1.20.0,<1.21.0' + - 'bioconductor-genomicranges >=1.36.0,<1.37.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-rtracklayer >=1.44.0,<1.45.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' - r-base - r-memoise test: diff --git a/recipes/bioconductor-regionreport/meta.yaml b/recipes/bioconductor-regionreport/meta.yaml index 2333b2cd421a6..efecf721d8515 100644 --- a/recipes/bioconductor-regionreport/meta.yaml +++ b/recipes/bioconductor-regionreport/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.16.1" %} +{% set version = "1.18.0" %} {% set name = "regionReport" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 52d87e72b67f0cbe611fbf647ccbff39 + md5: c2a1d5e7993c04d7783230f9f13ad1d9 build: number: 0 rpaths: @@ -20,14 +20,14 @@ build: # Suggests: BiocManager, biovizBase, bumphunter (>= 1.7.6), derfinderPlot (>= 1.3.2), sessioninfo, DT, DESeq, edgeR, ggbio (>= 1.13.13), ggplot2, grid, gridExtra, IRanges, mgcv, pasilla, pheatmap, RColorBrewer, TxDb.Hsapiens.UCSC.hg19.knownGene, whisker requirements: host: - - 'bioconductor-biocstyle >=2.10.0,<2.11.0' - - 'bioconductor-deformats >=1.10.0,<1.11.0' - - 'bioconductor-derfinder >=1.16.0,<1.17.0' - - 'bioconductor-deseq2 >=1.22.0,<1.23.0' - - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' - - 'bioconductor-genomicranges >=1.34.0,<1.35.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' - - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' + - 'bioconductor-biocstyle >=2.12.0,<2.13.0' + - 'bioconductor-deformats >=1.12.0,<1.13.0' + - 'bioconductor-derfinder >=1.18.0,<1.19.0' + - 'bioconductor-deseq2 >=1.24.0,<1.25.0' + - 'bioconductor-genomeinfodb >=1.20.0,<1.21.0' + - 'bioconductor-genomicranges >=1.36.0,<1.37.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' + - 'bioconductor-summarizedexperiment >=1.14.0,<1.15.0' - r-base - 'r-knitcitations >=1.0.1' - 'r-knitr >=1.6' @@ -35,14 +35,14 @@ requirements: - r-refmanager - 'r-rmarkdown >=0.9.5' run: - - 'bioconductor-biocstyle >=2.10.0,<2.11.0' - - 'bioconductor-deformats >=1.10.0,<1.11.0' - - 'bioconductor-derfinder >=1.16.0,<1.17.0' - - 'bioconductor-deseq2 >=1.22.0,<1.23.0' - - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' - - 'bioconductor-genomicranges >=1.34.0,<1.35.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' - - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' + - 'bioconductor-biocstyle >=2.12.0,<2.13.0' + - 'bioconductor-deformats >=1.12.0,<1.13.0' + - 'bioconductor-derfinder >=1.18.0,<1.19.0' + - 'bioconductor-deseq2 >=1.24.0,<1.25.0' + - 'bioconductor-genomeinfodb >=1.20.0,<1.21.0' + - 'bioconductor-genomicranges >=1.36.0,<1.37.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' + - 'bioconductor-summarizedexperiment >=1.14.0,<1.15.0' - r-base - 'r-knitcitations >=1.0.1' - 'r-knitr >=1.6' diff --git a/recipes/bioconductor-regparallel/meta.yaml b/recipes/bioconductor-regparallel/meta.yaml index 1e1defc858ade..8a9286f7bc7a1 100644 --- a/recipes/bioconductor-regparallel/meta.yaml +++ b/recipes/bioconductor-regparallel/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.0.0" %} +{% set version = "1.2.0" %} {% set name = "RegParallel" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: dbfebc547b8aaf83e060210498e8492a + md5: cebd94e58b4216cd3c14e4586d8761e1 build: number: 0 rpaths: @@ -39,7 +39,7 @@ requirements: - r-mass - r-stringr - r-survival - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-regparallel/post-link.sh b/recipes/bioconductor-regparallel/post-link.sh index 1a3d4b0b7b7d7..6d8f8ed3b782d 100644 --- a/recipes/bioconductor-regparallel/post-link.sh +++ b/recipes/bioconductor-regparallel/post-link.sh @@ -1,11 +1,11 @@ #!/bin/bash -FN="RegParallel_1.0.0.tar.gz" +FN="RegParallel_1.2.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/experiment/src/contrib/RegParallel_1.0.0.tar.gz" - "https://bioarchive.galaxyproject.org/RegParallel_1.0.0.tar.gz" - "https://depot.galaxyproject.org/software/bioconductor-regparallel/bioconductor-regparallel_1.0.0_src_all.tar.gz" + "https://bioconductor.org/packages/3.9/data/experiment/src/contrib/RegParallel_1.2.0.tar.gz" + "https://bioarchive.galaxyproject.org/RegParallel_1.2.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-regparallel/bioconductor-regparallel_1.2.0_src_all.tar.gz" ) -MD5="dbfebc547b8aaf83e060210498e8492a" +MD5="cebd94e58b4216cd3c14e4586d8761e1" # Use a staging area in the conda dir rather than temp dirs, both to avoid # permission issues as well as to have things downloaded in a predictable @@ -16,7 +16,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-regsplice/meta.yaml b/recipes/bioconductor-regsplice/meta.yaml index ad0f7064abc5a..cc3f59e68765f 100644 --- a/recipes/bioconductor-regsplice/meta.yaml +++ b/recipes/bioconductor-regsplice/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.8.0" %} +{% set version = "1.10.0" %} {% set name = "regsplice" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: b16a6d2c1bf9d695e268a1d515fe9230 + md5: 32b236f311812f449bd9bd81b0a2bd3c build: number: 0 rpaths: @@ -20,18 +20,18 @@ build: # Suggests: testthat, BiocStyle, knitr, rmarkdown requirements: host: - - 'bioconductor-edger >=3.24.0,<3.25.0' - - 'bioconductor-limma >=3.38.0,<3.39.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' - - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' + - 'bioconductor-edger >=3.26.0,<3.27.0' + - 'bioconductor-limma >=3.40.0,<3.41.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' + - 'bioconductor-summarizedexperiment >=1.14.0,<1.15.0' - r-base - r-glmnet - r-pbapply run: - - 'bioconductor-edger >=3.24.0,<3.25.0' - - 'bioconductor-limma >=3.38.0,<3.39.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' - - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' + - 'bioconductor-edger >=3.26.0,<3.27.0' + - 'bioconductor-limma >=3.40.0,<3.41.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' + - 'bioconductor-summarizedexperiment >=1.14.0,<1.15.0' - r-base - r-glmnet - r-pbapply diff --git a/recipes/bioconductor-remp/meta.yaml b/recipes/bioconductor-remp/meta.yaml index 971ae283565d6..2643cc507516c 100644 --- a/recipes/bioconductor-remp/meta.yaml +++ b/recipes/bioconductor-remp/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.6.1" %} +{% set version = "1.8.1" %} {% set name = "REMP" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 0905f19c4e54251951492aa785130231 + md5: 0a01ae2905bd2cfe7ad1f6474b55edf0 build: number: 0 rpaths: @@ -20,21 +20,21 @@ build: # Suggests: knitr, rmarkdown, minfiDataEPIC requirements: host: - - 'bioconductor-annotationhub >=2.14.0,<2.15.0' - - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' - - 'bioconductor-biocparallel >=1.16.0,<1.17.0' - - 'bioconductor-biostrings >=2.50.0,<2.51.0' - - 'bioconductor-bsgenome >=1.50.0,<1.51.0' + - 'bioconductor-annotationhub >=2.16.0,<2.17.0' + - 'bioconductor-biocgenerics >=0.30.0,<0.31.0' + - 'bioconductor-biocparallel >=1.18.0,<1.19.0' + - 'bioconductor-biostrings >=2.52.0,<2.53.0' + - 'bioconductor-bsgenome >=1.52.0,<1.53.0' - 'bioconductor-bsgenome.hsapiens.ucsc.hg19 >=1.4.0,<1.5.0' - - 'bioconductor-genomicranges >=1.34.0,<1.35.0' + - 'bioconductor-genomicranges >=1.36.0,<1.37.0' - 'bioconductor-illuminahumanmethylation450kanno.ilmn12.hg19 >=0.6.0,<0.7.0' - 'bioconductor-illuminahumanmethylationepicanno.ilm10b2.hg19 >=0.6.0,<0.7.0' - - 'bioconductor-impute >=1.56.0,<1.57.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-minfi >=1.28.0,<1.29.0' - - 'bioconductor-org.hs.eg.db >=3.7.0,<3.8.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' - - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' + - 'bioconductor-impute >=1.58.0,<1.59.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-minfi >=1.30.0,<1.31.0' + - 'bioconductor-org.hs.eg.db >=3.8.0,<3.9.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' + - 'bioconductor-summarizedexperiment >=1.14.0,<1.15.0' - r-base - r-caret - r-doparallel @@ -44,21 +44,21 @@ requirements: - r-ranger - r-settings run: - - 'bioconductor-annotationhub >=2.14.0,<2.15.0' - - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' - - 'bioconductor-biocparallel >=1.16.0,<1.17.0' - - 'bioconductor-biostrings >=2.50.0,<2.51.0' - - 'bioconductor-bsgenome >=1.50.0,<1.51.0' + - 'bioconductor-annotationhub >=2.16.0,<2.17.0' + - 'bioconductor-biocgenerics >=0.30.0,<0.31.0' + - 'bioconductor-biocparallel >=1.18.0,<1.19.0' + - 'bioconductor-biostrings >=2.52.0,<2.53.0' + - 'bioconductor-bsgenome >=1.52.0,<1.53.0' - 'bioconductor-bsgenome.hsapiens.ucsc.hg19 >=1.4.0,<1.5.0' - - 'bioconductor-genomicranges >=1.34.0,<1.35.0' + - 'bioconductor-genomicranges >=1.36.0,<1.37.0' - 'bioconductor-illuminahumanmethylation450kanno.ilmn12.hg19 >=0.6.0,<0.7.0' - 'bioconductor-illuminahumanmethylationepicanno.ilm10b2.hg19 >=0.6.0,<0.7.0' - - 'bioconductor-impute >=1.56.0,<1.57.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-minfi >=1.28.0,<1.29.0' - - 'bioconductor-org.hs.eg.db >=3.7.0,<3.8.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' - - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' + - 'bioconductor-impute >=1.58.0,<1.59.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-minfi >=1.30.0,<1.31.0' + - 'bioconductor-org.hs.eg.db >=3.8.0,<3.9.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' + - 'bioconductor-summarizedexperiment >=1.14.0,<1.15.0' - r-base - r-caret - r-doparallel diff --git a/recipes/bioconductor-repitools/meta.yaml b/recipes/bioconductor-repitools/meta.yaml index bf30bcf12acde..a8cbdb74bdf80 100644 --- a/recipes/bioconductor-repitools/meta.yaml +++ b/recipes/bioconductor-repitools/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.28.0" %} +{% set version = "1.30.0" %} {% set name = "Repitools" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 59c4e8b79e061909762b5e6d25f55510 + md5: be4217174c229d982e547851342de8d8 build: number: 0 rpaths: @@ -19,19 +19,19 @@ build: # Suggests: ShortRead, BSgenome.Hsapiens.UCSC.hg18 requirements: host: - - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' - - 'bioconductor-biostrings >=2.50.0,<2.51.0' - - 'bioconductor-bsgenome >=1.50.0,<1.51.0' - - 'bioconductor-dnacopy >=1.56.0,<1.57.0' - - 'bioconductor-edger >=3.24.0,<3.25.0' - - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' - - 'bioconductor-genomicalignments >=1.18.0,<1.19.0' - - 'bioconductor-genomicranges >=1.34.0,<1.35.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-ringo >=1.46.0,<1.47.0' - - 'bioconductor-rsamtools >=1.34.0,<1.35.0' - - 'bioconductor-rtracklayer >=1.42.0,<1.43.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-biocgenerics >=0.30.0,<0.31.0' + - 'bioconductor-biostrings >=2.52.0,<2.53.0' + - 'bioconductor-bsgenome >=1.52.0,<1.53.0' + - 'bioconductor-dnacopy >=1.58.0,<1.59.0' + - 'bioconductor-edger >=3.26.0,<3.27.0' + - 'bioconductor-genomeinfodb >=1.20.0,<1.21.0' + - 'bioconductor-genomicalignments >=1.20.0,<1.21.0' + - 'bioconductor-genomicranges >=1.36.0,<1.37.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-ringo >=1.48.0,<1.49.0' + - 'bioconductor-rsamtools >=2.0.0,<2.1.0' + - 'bioconductor-rtracklayer >=1.44.0,<1.45.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' - r-aroma.affymetrix - r-base - r-cluster @@ -40,19 +40,19 @@ requirements: - r-mass - r-rsolnp run: - - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' - - 'bioconductor-biostrings >=2.50.0,<2.51.0' - - 'bioconductor-bsgenome >=1.50.0,<1.51.0' - - 'bioconductor-dnacopy >=1.56.0,<1.57.0' - - 'bioconductor-edger >=3.24.0,<3.25.0' - - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' - - 'bioconductor-genomicalignments >=1.18.0,<1.19.0' - - 'bioconductor-genomicranges >=1.34.0,<1.35.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-ringo >=1.46.0,<1.47.0' - - 'bioconductor-rsamtools >=1.34.0,<1.35.0' - - 'bioconductor-rtracklayer >=1.42.0,<1.43.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-biocgenerics >=0.30.0,<0.31.0' + - 'bioconductor-biostrings >=2.52.0,<2.53.0' + - 'bioconductor-bsgenome >=1.52.0,<1.53.0' + - 'bioconductor-dnacopy >=1.58.0,<1.59.0' + - 'bioconductor-edger >=3.26.0,<3.27.0' + - 'bioconductor-genomeinfodb >=1.20.0,<1.21.0' + - 'bioconductor-genomicalignments >=1.20.0,<1.21.0' + - 'bioconductor-genomicranges >=1.36.0,<1.37.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-ringo >=1.48.0,<1.49.0' + - 'bioconductor-rsamtools >=2.0.0,<2.1.0' + - 'bioconductor-rtracklayer >=1.44.0,<1.45.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' - r-aroma.affymetrix - r-base - r-cluster diff --git a/recipes/bioconductor-reportingtools/meta.yaml b/recipes/bioconductor-reportingtools/meta.yaml index d9a47449ef8ff..8608dca6ea1b0 100644 --- a/recipes/bioconductor-reportingtools/meta.yaml +++ b/recipes/bioconductor-reportingtools/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "2.22.1" %} +{% set version = "2.24.0" %} {% set name = "ReportingTools" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 9f1b8a6037be14b4dc273334c6b57a58 + md5: 10cc6f059f95b306df1b1e3ddd7a788d build: number: 0 rpaths: @@ -20,19 +20,19 @@ build: # Suggests: RUnit, ALL, hgu95av2.db, org.Mm.eg.db, shiny, pasilla, org.Sc.sgd.db requirements: host: - - 'bioconductor-annotate >=1.60.0,<1.61.0' - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' - - 'bioconductor-biobase >=2.42.0,<2.43.0' - - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' - - 'bioconductor-category >=2.48.0,<2.49.0' - - 'bioconductor-deseq2 >=1.22.0,<1.23.0' - - 'bioconductor-edger >=3.24.0,<3.25.0' - - 'bioconductor-ggbio >=1.30.0,<1.31.0' - - 'bioconductor-gostats >=2.48.0,<2.49.0' - - 'bioconductor-gseabase >=1.44.0,<1.45.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-limma >=3.38.0,<3.39.0' - - 'bioconductor-pfam.db >=3.7.0,<3.8.0' + - 'bioconductor-annotate >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' + - 'bioconductor-biocgenerics >=0.30.0,<0.31.0' + - 'bioconductor-category >=2.50.0,<2.51.0' + - 'bioconductor-deseq2 >=1.24.0,<1.25.0' + - 'bioconductor-edger >=3.26.0,<3.27.0' + - 'bioconductor-ggbio >=1.32.0,<1.33.0' + - 'bioconductor-gostats >=2.50.0,<2.51.0' + - 'bioconductor-gseabase >=1.46.0,<1.47.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-limma >=3.40.0,<3.41.0' + - 'bioconductor-pfam.db >=3.8.0,<3.9.0' - r-base - r-ggplot2 - r-hwriter @@ -41,19 +41,19 @@ requirements: - r-r.utils - r-xml run: - - 'bioconductor-annotate >=1.60.0,<1.61.0' - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' - - 'bioconductor-biobase >=2.42.0,<2.43.0' - - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' - - 'bioconductor-category >=2.48.0,<2.49.0' - - 'bioconductor-deseq2 >=1.22.0,<1.23.0' - - 'bioconductor-edger >=3.24.0,<3.25.0' - - 'bioconductor-ggbio >=1.30.0,<1.31.0' - - 'bioconductor-gostats >=2.48.0,<2.49.0' - - 'bioconductor-gseabase >=1.44.0,<1.45.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-limma >=3.38.0,<3.39.0' - - 'bioconductor-pfam.db >=3.7.0,<3.8.0' + - 'bioconductor-annotate >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' + - 'bioconductor-biocgenerics >=0.30.0,<0.31.0' + - 'bioconductor-category >=2.50.0,<2.51.0' + - 'bioconductor-deseq2 >=1.24.0,<1.25.0' + - 'bioconductor-edger >=3.26.0,<3.27.0' + - 'bioconductor-ggbio >=1.32.0,<1.33.0' + - 'bioconductor-gostats >=2.50.0,<2.51.0' + - 'bioconductor-gseabase >=1.46.0,<1.47.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-limma >=3.40.0,<3.41.0' + - 'bioconductor-pfam.db >=3.8.0,<3.9.0' - r-base - r-ggplot2 - r-hwriter diff --git a/recipes/bioconductor-repviz/build.sh b/recipes/bioconductor-repviz/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-repviz/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-repviz/meta.yaml b/recipes/bioconductor-repviz/meta.yaml new file mode 100644 index 0000000000000..34571a160a69e --- /dev/null +++ b/recipes/bioconductor-repviz/meta.yaml @@ -0,0 +1,43 @@ +{% set version = "1.0.0" %} +{% set name = "RepViz" %} +{% set bioc = "3.9" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: d0c0a511327feb084f01ac4c22b56ae7 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: knitr, testthat +requirements: + host: + - 'bioconductor-biomart >=2.40.0,<2.41.0' + - 'bioconductor-genomicranges >=1.36.0,<1.37.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-rsamtools >=2.0.0,<2.1.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' + - r-base + run: + - 'bioconductor-biomart >=2.40.0,<2.41.0' + - 'bioconductor-genomicranges >=1.36.0,<1.37.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-rsamtools >=2.0.0,<2.1.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' + - r-base +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: GPL-3 + summary: 'RepViz enables the view of a genomic region in a simple and efficient way. RepViz allows simultaneous viewing of both intra- and intergroup variation in sequencing counts of the studied conditions, as well as their comparison to the output features (e.g. identified peaks) from user selected data analysis methods.The RepViz tool is primarily designed for chromatin data such as ChIP-seq and ATAC-seq, but can also be used with other sequencing data such as RNA-seq, or combinations of different types of genomic data.' + diff --git a/recipes/bioconductor-reqon/meta.yaml b/recipes/bioconductor-reqon/meta.yaml index 37249ec3ccbbc..92272f069639f 100644 --- a/recipes/bioconductor-reqon/meta.yaml +++ b/recipes/bioconductor-reqon/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.28.0" %} +{% set version = "1.30.0" %} {% set name = "ReQON" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 4e9e1fd5a4b1c189e039a97dff587ccb + md5: 3d26cf04e111979ca2b1e349c4256720 build: number: 0 rpaths: @@ -21,13 +21,13 @@ build: # SystemRequirements: Java version >= 1.6 requirements: host: - - 'bioconductor-rsamtools >=1.34.0,<1.35.0' - - 'bioconductor-seqbias >=1.30.0,<1.31.0' + - 'bioconductor-rsamtools >=2.0.0,<2.1.0' + - 'bioconductor-seqbias >=1.32.0,<1.33.0' - r-base - r-rjava run: - - 'bioconductor-rsamtools >=1.34.0,<1.35.0' - - 'bioconductor-seqbias >=1.30.0,<1.31.0' + - 'bioconductor-rsamtools >=2.0.0,<2.1.0' + - 'bioconductor-seqbias >=1.32.0,<1.33.0' - r-base - r-rjava test: diff --git a/recipes/bioconductor-restfulse/meta.yaml b/recipes/bioconductor-restfulse/meta.yaml index 23f15ed36f356..a77ac9b63d00e 100644 --- a/recipes/bioconductor-restfulse/meta.yaml +++ b/recipes/bioconductor-restfulse/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.4.0" %} +{% set version = "1.6.0" %} {% set name = "restfulSE" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,25 +10,25 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 71a91f399fd3f3cbfc5a7b2009c15696 + md5: ed78e68f9ff60490bed0ed16933bfc49 build: number: 0 rpaths: - lib/R/lib/ - lib/ noarch: generic -# Suggests: knitr, testthat, Rtsne, org.Mm.eg.db, org.Hs.eg.db, BiocStyle +# Suggests: knitr, testthat, Rtsne, org.Mm.eg.db, org.Hs.eg.db, BiocStyle, restfulSEData requirements: host: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' - - 'bioconductor-annotationhub >=2.14.0,<2.15.0' - - 'bioconductor-biobase >=2.42.0,<2.43.0' - - 'bioconductor-delayedarray >=0.8.0,<0.9.0' - - 'bioconductor-experimenthub >=1.8.0,<1.9.0' - - 'bioconductor-go.db >=3.7.0,<3.8.0' - - 'bioconductor-rhdf5client >=1.4.0,<1.5.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' - - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' + - 'bioconductor-annotationhub >=2.16.0,<2.17.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' + - 'bioconductor-delayedarray >=0.10.0,<0.11.0' + - 'bioconductor-experimenthub >=1.10.0,<1.11.0' + - 'bioconductor-go.db >=3.8.0,<3.9.0' + - 'bioconductor-rhdf5client >=1.6.0,<1.7.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' + - 'bioconductor-summarizedexperiment >=1.14.0,<1.15.0' - r-base - r-bigrquery - r-dbi @@ -37,15 +37,15 @@ requirements: - r-reshape2 - r-rlang run: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' - - 'bioconductor-annotationhub >=2.14.0,<2.15.0' - - 'bioconductor-biobase >=2.42.0,<2.43.0' - - 'bioconductor-delayedarray >=0.8.0,<0.9.0' - - 'bioconductor-experimenthub >=1.8.0,<1.9.0' - - 'bioconductor-go.db >=3.7.0,<3.8.0' - - 'bioconductor-rhdf5client >=1.4.0,<1.5.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' - - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' + - 'bioconductor-annotationhub >=2.16.0,<2.17.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' + - 'bioconductor-delayedarray >=0.10.0,<0.11.0' + - 'bioconductor-experimenthub >=1.10.0,<1.11.0' + - 'bioconductor-go.db >=3.8.0,<3.9.0' + - 'bioconductor-rhdf5client >=1.6.0,<1.7.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' + - 'bioconductor-summarizedexperiment >=1.14.0,<1.15.0' - r-base - r-bigrquery - r-dbi diff --git a/recipes/bioconductor-restfulsedata/meta.yaml b/recipes/bioconductor-restfulsedata/meta.yaml index 63b4b9345e411..050bc653bac2a 100644 --- a/recipes/bioconductor-restfulsedata/meta.yaml +++ b/recipes/bioconductor-restfulsedata/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.4.0" %} +{% set version = "1.6.0" %} {% set name = "restfulSEData" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: a4008a223e2c5417f8f164fb3b2d3752 + md5: b057b9fc07de16899fa3ef2879d06f33 build: number: 0 rpaths: @@ -20,14 +20,14 @@ build: # Suggests: knitr requirements: host: - - 'bioconductor-experimenthub >=1.8.0,<1.9.0' - - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' + - 'bioconductor-experimenthub >=1.10.0,<1.11.0' + - 'bioconductor-summarizedexperiment >=1.14.0,<1.15.0' - r-base run: - - 'bioconductor-experimenthub >=1.8.0,<1.9.0' - - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' + - 'bioconductor-experimenthub >=1.10.0,<1.11.0' + - 'bioconductor-summarizedexperiment >=1.14.0,<1.15.0' - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-restfulsedata/post-link.sh b/recipes/bioconductor-restfulsedata/post-link.sh index cf47f0955f61d..a7db2616265d8 100644 --- a/recipes/bioconductor-restfulsedata/post-link.sh +++ b/recipes/bioconductor-restfulsedata/post-link.sh @@ -1,11 +1,11 @@ #!/bin/bash -FN="restfulSEData_1.4.0.tar.gz" +FN="restfulSEData_1.6.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/experiment/src/contrib/restfulSEData_1.4.0.tar.gz" - "https://bioarchive.galaxyproject.org/restfulSEData_1.4.0.tar.gz" - "https://depot.galaxyproject.org/software/bioconductor-restfulsedata/bioconductor-restfulsedata_1.4.0_src_all.tar.gz" + "https://bioconductor.org/packages/3.9/data/experiment/src/contrib/restfulSEData_1.6.0.tar.gz" + "https://bioarchive.galaxyproject.org/restfulSEData_1.6.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-restfulsedata/bioconductor-restfulsedata_1.6.0_src_all.tar.gz" ) -MD5="a4008a223e2c5417f8f164fb3b2d3752" +MD5="b057b9fc07de16899fa3ef2879d06f33" # Use a staging area in the conda dir rather than temp dirs, both to avoid # permission issues as well as to have things downloaded in a predictable @@ -16,7 +16,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-rexposome/meta.yaml b/recipes/bioconductor-rexposome/meta.yaml index 0d0f27774ebab..1c665848c8f58 100644 --- a/recipes/bioconductor-rexposome/meta.yaml +++ b/recipes/bioconductor-rexposome/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.4.0" %} +{% set version = "1.6.0" %} {% set name = "rexposome" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 3ba602e53b72ac2e89c0206164a9f6df + md5: 6aa1e97a833510086fea68191f1f8c68 build: number: 0 rpaths: @@ -20,8 +20,8 @@ build: # Suggests: mclust, flexmix, testthat, BiocStyle, knitr, rmarkdown requirements: host: - - 'bioconductor-biobase >=2.42.0,<2.43.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' - r-base - r-circlize - r-corrplot @@ -43,8 +43,8 @@ requirements: - r-scatterplot3d - r-stringr run: - - 'bioconductor-biobase >=2.42.0,<2.43.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' - r-base - r-circlize - r-corrplot diff --git a/recipes/bioconductor-rforproteomics/meta.yaml b/recipes/bioconductor-rforproteomics/meta.yaml index 3df3f684c0071..bf9c722bb1647 100644 --- a/recipes/bioconductor-rforproteomics/meta.yaml +++ b/recipes/bioconductor-rforproteomics/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.20.0" %} +{% set version = "1.22.0" %} {% set name = "RforProteomics" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: c2df3edec11e6ebf57e0c7b7c19c3e14 + md5: b3512efa8224bd8069e638bae018384b build: number: 0 rpaths: @@ -20,20 +20,20 @@ build: # Suggests: AnnotationDbi, rpx, DT, knitr, rmarkdown, BiocStyle, mzR, xcms, msdata, isobar, MALDIquant (>= 1.12), MALDIquantForeign, readBrukerFlexData, rTANDEM, synapter, synapterdata, IPPD, Rdisop, OrgMassSpecR, SummarizedExperiment, BRAIN, rols, hpar, GO.db, org.Hs.eg.db, e1071, biomaRt, RColorBrewer, ggplot2, reshape2, xtable, lattice, mzID, pRoloc, pRolocdata, MSGFplus, MSGFgui, MSnID, msmsTests, msmsEDA, DEP, corrplot, beanplot, Heatplus, gplots, VennDiagram, protViz, genefilter, plotly, gridExtra, dplyr, lubridate requirements: host: - - 'bioconductor-biocviews >=1.50.0,<1.51.0' - - 'bioconductor-msnbase >=2.8.0,<2.9.0' + - 'bioconductor-biocviews >=1.52.0,<1.53.0' + - 'bioconductor-msnbase >=2.10.0,<2.11.0' - r-base - r-biocmanager - r-r.utils - r-shiny run: - - 'bioconductor-biocviews >=1.50.0,<1.51.0' - - 'bioconductor-msnbase >=2.8.0,<2.9.0' + - 'bioconductor-biocviews >=1.52.0,<1.53.0' + - 'bioconductor-msnbase >=2.10.0,<2.11.0' - r-base - r-biocmanager - r-r.utils - r-shiny - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-rforproteomics/post-link.sh b/recipes/bioconductor-rforproteomics/post-link.sh index 2afce6ddc2630..0d8852d5f4b31 100644 --- a/recipes/bioconductor-rforproteomics/post-link.sh +++ b/recipes/bioconductor-rforproteomics/post-link.sh @@ -1,11 +1,11 @@ #!/bin/bash -FN="RforProteomics_1.20.0.tar.gz" +FN="RforProteomics_1.22.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/experiment/src/contrib/RforProteomics_1.20.0.tar.gz" - "https://bioarchive.galaxyproject.org/RforProteomics_1.20.0.tar.gz" - "https://depot.galaxyproject.org/software/bioconductor-rforproteomics/bioconductor-rforproteomics_1.20.0_src_all.tar.gz" + "https://bioconductor.org/packages/3.9/data/experiment/src/contrib/RforProteomics_1.22.0.tar.gz" + "https://bioarchive.galaxyproject.org/RforProteomics_1.22.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-rforproteomics/bioconductor-rforproteomics_1.22.0_src_all.tar.gz" ) -MD5="c2df3edec11e6ebf57e0c7b7c19c3e14" +MD5="b3512efa8224bd8069e638bae018384b" # Use a staging area in the conda dir rather than temp dirs, both to avoid # permission issues as well as to have things downloaded in a predictable @@ -16,7 +16,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-rfpred/meta.yaml b/recipes/bioconductor-rfpred/meta.yaml index 15446b9b6fdb3..dab9bd3836acb 100644 --- a/recipes/bioconductor-rfpred/meta.yaml +++ b/recipes/bioconductor-rfpred/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.20.0" %} +{% set version = "1.22.0" %} {% set name = "rfPred" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 9d76d084ffbc2c95925accca4d39888b + md5: 42a8359f2e811af6d85b9944b07b6d26 build: number: 0 rpaths: @@ -19,15 +19,15 @@ build: # Suggests: BiocStyle requirements: host: - - 'bioconductor-genomicranges >=1.34.0,<1.35.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-rsamtools >=1.34.0,<1.35.0' + - 'bioconductor-genomicranges >=1.36.0,<1.37.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-rsamtools >=2.0.0,<2.1.0' - r-base - r-data.table run: - - 'bioconductor-genomicranges >=1.34.0,<1.35.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-rsamtools >=1.34.0,<1.35.0' + - 'bioconductor-genomicranges >=1.36.0,<1.37.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-rsamtools >=2.0.0,<2.1.0' - r-base - r-data.table build: diff --git a/recipes/bioconductor-rgadem/meta.yaml b/recipes/bioconductor-rgadem/meta.yaml index ba53a7e1c4ec0..57d3df34990d6 100644 --- a/recipes/bioconductor-rgadem/meta.yaml +++ b/recipes/bioconductor-rgadem/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "2.30.0" %} +{% set version = "2.32.0" %} {% set name = "rGADEM" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 6c91a120a1451994f8a92d7a61b55662 + md5: e74557572cacc6c9fee8f5112fdf3df6 build: number: 0 rpaths: @@ -19,16 +19,16 @@ build: # Suggests: BSgenome.Hsapiens.UCSC.hg19 requirements: host: - - 'bioconductor-biostrings >=2.50.0,<2.51.0' - - 'bioconductor-bsgenome >=1.50.0,<1.51.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-seqlogo >=1.48.0,<1.49.0' + - 'bioconductor-biostrings >=2.52.0,<2.53.0' + - 'bioconductor-bsgenome >=1.52.0,<1.53.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-seqlogo >=1.50.0,<1.51.0' - r-base run: - - 'bioconductor-biostrings >=2.50.0,<2.51.0' - - 'bioconductor-bsgenome >=1.50.0,<1.51.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-seqlogo >=1.48.0,<1.49.0' + - 'bioconductor-biostrings >=2.52.0,<2.53.0' + - 'bioconductor-bsgenome >=1.52.0,<1.53.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-seqlogo >=1.50.0,<1.51.0' - r-base build: - {{ compiler('c') }} diff --git a/recipes/bioconductor-rgalaxy/meta.yaml b/recipes/bioconductor-rgalaxy/meta.yaml index 84e9c60f8f4ca..b4a81ba048f61 100644 --- a/recipes/bioconductor-rgalaxy/meta.yaml +++ b/recipes/bioconductor-rgalaxy/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.26.0" %} +{% set version = "1.28.0" %} {% set name = "RGalaxy" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: b88c6f6f410d2f852096e69ebbe040d1 + md5: f6f4addc405440ff80b290bdbacfb468 build: number: 0 rpaths: @@ -20,15 +20,15 @@ build: # Suggests: RUnit, hgu95av2.db, AnnotationDbi, knitr, formatR, Rserve requirements: host: - - 'bioconductor-biobase >=2.42.0,<2.43.0' - - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' + - 'bioconductor-biocgenerics >=0.30.0,<0.31.0' - r-base - r-optparse - r-roxygen2 - r-xml run: - - 'bioconductor-biobase >=2.42.0,<2.43.0' - - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' + - 'bioconductor-biocgenerics >=0.30.0,<0.31.0' - r-base - r-optparse - r-roxygen2 diff --git a/recipes/bioconductor-rgin/meta.yaml b/recipes/bioconductor-rgin/meta.yaml index 942a7c061ed45..b966e3732d5cc 100644 --- a/recipes/bioconductor-rgin/meta.yaml +++ b/recipes/bioconductor-rgin/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.2.0" %} +{% set version = "1.4.0" %} {% set name = "Rgin" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 2d535bbeb2ba5810a0112f6c211a27a7 + md5: f67682923c47b4b278d728cf815f8a44 build: number: 0 rpaths: @@ -20,16 +20,14 @@ build: requirements: host: - r-base - - 'r-rcppeigen >=0.3.3.3.0' + - 'r-rcppeigen >=0.3.3.5.0' run: - r-base - - 'r-rcppeigen >=0.3.3.3.0' - - llvm-openmp # [osx] + - 'r-rcppeigen >=0.3.3.5.0' build: - {{ compiler('c') }} - {{ compiler('cxx') }} - make - - llvm-openmp # [osx] test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-rgmql/meta.yaml b/recipes/bioconductor-rgmql/meta.yaml index 173c170e72163..c48e4ff360e17 100644 --- a/recipes/bioconductor-rgmql/meta.yaml +++ b/recipes/bioconductor-rgmql/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.2.0" %} +{% set version = "1.4.0" %} {% set name = "RGMQL" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: ecee8f65b339090d4a4d9a0db3311424 + md5: f8dfc3cf424d23254cb855f1672d1141 build: number: 0 rpaths: @@ -20,11 +20,11 @@ build: # Suggests: BiocStyle, knitr, rmarkdown requirements: host: - - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' - - 'bioconductor-genomicranges >=1.34.0,<1.35.0' - - 'bioconductor-rgmqllib >=1.2.0,<1.3.0' - - 'bioconductor-rtracklayer >=1.42.0,<1.43.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-biocgenerics >=0.30.0,<0.31.0' + - 'bioconductor-genomicranges >=1.36.0,<1.37.0' + - 'bioconductor-rgmqllib >=1.4.0,<1.5.0' + - 'bioconductor-rtracklayer >=1.44.0,<1.45.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' - r-base - r-data.table - r-dplyr @@ -34,11 +34,11 @@ requirements: - r-rjava - r-xml2 run: - - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' - - 'bioconductor-genomicranges >=1.34.0,<1.35.0' - - 'bioconductor-rgmqllib >=1.2.0,<1.3.0' - - 'bioconductor-rtracklayer >=1.42.0,<1.43.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-biocgenerics >=0.30.0,<0.31.0' + - 'bioconductor-genomicranges >=1.36.0,<1.37.0' + - 'bioconductor-rgmqllib >=1.4.0,<1.5.0' + - 'bioconductor-rtracklayer >=1.44.0,<1.45.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' - r-base - r-data.table - r-dplyr diff --git a/recipes/bioconductor-rgmqllib/meta.yaml b/recipes/bioconductor-rgmqllib/meta.yaml index d3e820b9e22b5..d79fc34dddaf8 100644 --- a/recipes/bioconductor-rgmqllib/meta.yaml +++ b/recipes/bioconductor-rgmqllib/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.2.0" %} +{% set version = "1.4.0" %} {% set name = "RGMQLlib" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,9 +10,9 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 71eae8b46e7104c9733252c6162002f6 + md5: da01b2fe647643af1df9d3563c61f446 build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ @@ -23,7 +23,7 @@ requirements: - r-base run: - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-rgmqllib/post-link.sh b/recipes/bioconductor-rgmqllib/post-link.sh index a09d31b2f8db2..1db7979bca80b 100644 --- a/recipes/bioconductor-rgmqllib/post-link.sh +++ b/recipes/bioconductor-rgmqllib/post-link.sh @@ -1,11 +1,11 @@ #!/bin/bash -FN="RGMQLlib_1.2.0.tar.gz" +FN="RGMQLlib_1.4.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/experiment/src/contrib/RGMQLlib_1.2.0.tar.gz" - "https://bioarchive.galaxyproject.org/RGMQLlib_1.2.0.tar.gz" - "https://depot.galaxyproject.org/software/bioconductor-rgmqllib/bioconductor-rgmqllib_1.2.0_src_all.tar.gz" + "https://bioconductor.org/packages/3.9/data/experiment/src/contrib/RGMQLlib_1.4.0.tar.gz" + "https://bioarchive.galaxyproject.org/RGMQLlib_1.4.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-rgmqllib/bioconductor-rgmqllib_1.4.0_src_all.tar.gz" ) -MD5="71eae8b46e7104c9733252c6162002f6" +MD5="da01b2fe647643af1df9d3563c61f446" # Use a staging area in the conda dir rather than temp dirs, both to avoid # permission issues as well as to have things downloaded in a predictable @@ -16,7 +16,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-rgraph2js/meta.yaml b/recipes/bioconductor-rgraph2js/meta.yaml index 0fe766ef516b3..b60610d202f82 100644 --- a/recipes/bioconductor-rgraph2js/meta.yaml +++ b/recipes/bioconductor-rgraph2js/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.10.0" %} +{% set version = "1.12.0" %} {% set name = "RGraph2js" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: e407635c0ffbdb22152a1313025a8b4a + md5: fd88db04ecb5dbe766ee4e2d4bdac794 build: number: 0 rpaths: @@ -21,13 +21,13 @@ build: # SystemRequirements: jQuery, jQueryUI, qTip2, D3js and Raphael are required Javascript libraries made available via the online CDNJS service (http://cdnjs.cloudflare.com). requirements: host: - - 'bioconductor-graph >=1.60.0,<1.61.0' + - 'bioconductor-graph >=1.62.0,<1.63.0' - r-base - r-digest - r-rjson - r-whisker run: - - 'bioconductor-graph >=1.60.0,<1.61.0' + - 'bioconductor-graph >=1.62.0,<1.63.0' - r-base - r-digest - r-rjson diff --git a/recipes/bioconductor-rgraphviz/build.sh b/recipes/bioconductor-rgraphviz/build.sh index 5ea71a1203cac..c1d13421f5f1e 100644 --- a/recipes/bioconductor-rgraphviz/build.sh +++ b/recipes/bioconductor-rgraphviz/build.sh @@ -8,4 +8,4 @@ CXX=$CXX CXX98=$CXX CXX11=$CXX CXX14=$CXX" > ~/.R/Makevars -$R CMD INSTALL --build . +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-rgraphviz/meta.yaml b/recipes/bioconductor-rgraphviz/meta.yaml index 1e22329830d62..f56df72cb6c06 100644 --- a/recipes/bioconductor-rgraphviz/meta.yaml +++ b/recipes/bioconductor-rgraphviz/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "2.26.0" %} +{% set version = "2.28.0" %} {% set name = "Rgraphviz" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 148a37430c6f20d15b1564cb91796f00 + md5: 939f3939e3bed3a546143ed40f95e722 build: number: 0 rpaths: @@ -20,12 +20,11 @@ build: # SystemRequirements: optionally Graphviz (>= 2.16) requirements: host: - - 'bioconductor-graph >=1.60.0,<1.61.0' + - 'bioconductor-graph >=1.62.0,<1.63.0' - r-base run: - - 'bioconductor-graph >=1.60.0,<1.61.0' + - 'bioconductor-graph >=1.62.0,<1.63.0' - r-base - - graphviz build: - {{ compiler('c') }} - {{ compiler('cxx') }} diff --git a/recipes/bioconductor-rgreat/meta.yaml b/recipes/bioconductor-rgreat/meta.yaml index e60c21f2d70cd..3ca67d21c01aa 100644 --- a/recipes/bioconductor-rgreat/meta.yaml +++ b/recipes/bioconductor-rgreat/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.14.0" %} +{% set version = "1.16.0" %} {% set name = "rGREAT" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: c7e906676ad1d4ce133a2d285e10b053 + md5: 4c2fca6609f651d5206ce6d7c3cd0d89 build: number: 0 rpaths: @@ -20,15 +20,15 @@ build: # Suggests: testthat (>= 0.3), knitr, circlize requirements: host: - - 'bioconductor-genomicranges >=1.34.0,<1.35.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-genomicranges >=1.36.0,<1.37.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' - r-base - 'r-getoptlong >=0.0.9' - r-rcurl - r-rjson run: - - 'bioconductor-genomicranges >=1.34.0,<1.35.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-genomicranges >=1.36.0,<1.37.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' - r-base - 'r-getoptlong >=0.0.9' - r-rcurl diff --git a/recipes/bioconductor-rgsea/meta.yaml b/recipes/bioconductor-rgsea/meta.yaml index bd7bbf414c089..2db2e51b50a9f 100644 --- a/recipes/bioconductor-rgsea/meta.yaml +++ b/recipes/bioconductor-rgsea/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.16.0" %} +{% set version = "1.18.0" %} {% set name = "RGSEA" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,9 +10,9 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 7e45c90d4e1335e8fcc983f9a86e0ac0 + md5: e981c0f0c51104ee88b7ac9c89154ad6 build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ @@ -20,10 +20,10 @@ build: # Suggests: BiocStyle, GEOquery, knitr, RUnit requirements: host: - - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' + - 'bioconductor-biocgenerics >=0.30.0,<0.31.0' - r-base run: - - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' + - 'bioconductor-biocgenerics >=0.30.0,<0.31.0' - r-base test: commands: diff --git a/recipes/bioconductor-rgsepd/meta.yaml b/recipes/bioconductor-rgsepd/meta.yaml index 7fd5958a3ac78..4c2dac49391b8 100644 --- a/recipes/bioconductor-rgsepd/meta.yaml +++ b/recipes/bioconductor-rgsepd/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.14.0" %} +{% set version = "1.16.0" %} {% set name = "rgsepd" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 88a18b7f1243982774b8acfa3c3716f6 + md5: f42efca6296232068359728818cd0365 build: number: 0 rpaths: @@ -20,24 +20,24 @@ build: # Suggests: boot, tools, BiocGenerics, knitr, xtable requirements: host: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' - - 'bioconductor-biomart >=2.38.0,<2.39.0' - - 'bioconductor-deseq2 >=1.22.0,<1.23.0' - - 'bioconductor-go.db >=3.7.0,<3.8.0' - - 'bioconductor-goseq >=1.34.0,<1.35.0' - - 'bioconductor-org.hs.eg.db >=3.7.0,<3.8.0' - - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' + - 'bioconductor-biomart >=2.40.0,<2.41.0' + - 'bioconductor-deseq2 >=1.24.0,<1.25.0' + - 'bioconductor-go.db >=3.8.0,<3.9.0' + - 'bioconductor-goseq >=1.36.0,<1.37.0' + - 'bioconductor-org.hs.eg.db >=3.8.0,<3.9.0' + - 'bioconductor-summarizedexperiment >=1.14.0,<1.15.0' - r-base - r-gplots - r-hash run: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' - - 'bioconductor-biomart >=2.38.0,<2.39.0' - - 'bioconductor-deseq2 >=1.22.0,<1.23.0' - - 'bioconductor-go.db >=3.7.0,<3.8.0' - - 'bioconductor-goseq >=1.34.0,<1.35.0' - - 'bioconductor-org.hs.eg.db >=3.7.0,<3.8.0' - - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' + - 'bioconductor-biomart >=2.40.0,<2.41.0' + - 'bioconductor-deseq2 >=1.24.0,<1.25.0' + - 'bioconductor-go.db >=3.8.0,<3.9.0' + - 'bioconductor-goseq >=1.36.0,<1.37.0' + - 'bioconductor-org.hs.eg.db >=3.8.0,<3.9.0' + - 'bioconductor-summarizedexperiment >=1.14.0,<1.15.0' - r-base - r-gplots - r-hash @@ -47,7 +47,7 @@ test: about: home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: GPL-3 - summary: 'R/GSEPD is a bioinformatics package for R to help disambiguate transcriptome samples (a matrix of RNA-Seq counts at RefSeq IDs) by automating differential expression (with DESeq2), then gene set enrichment (with GOSeq), and finally a N-dimensional projection to quantify in which ways each sample is like either treatment group.' + summary: 'R/GSEPD is a bioinformatics package for R to help disambiguate transcriptome samples (a matrix of RNA-Seq counts at transcript IDs) by automating differential expression (with DESeq2), then gene set enrichment (with GOSeq), and finally a N-dimensional projection to quantify in which ways each sample is like either treatment group.' extra: identifiers: - biotools:rgsepd diff --git a/recipes/bioconductor-rgu34a.db/meta.yaml b/recipes/bioconductor-rgu34a.db/meta.yaml index 89d6e3e20b9e5..fea178dd10ca1 100644 --- a/recipes/bioconductor-rgu34a.db/meta.yaml +++ b/recipes/bioconductor-rgu34a.db/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.2.3" %} {% set name = "rgu34a.db" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -12,7 +12,7 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: b8e7fec45ef9e1423cda3171bb12e34c build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ @@ -20,14 +20,14 @@ build: # Suggests: DBI, annotate, RUnit requirements: host: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' - - 'bioconductor-org.rn.eg.db >=3.7.0,<3.8.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' + - 'bioconductor-org.rn.eg.db >=3.8.0,<3.9.0' - r-base run: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' - - 'bioconductor-org.rn.eg.db >=3.7.0,<3.8.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' + - 'bioconductor-org.rn.eg.db >=3.8.0,<3.9.0' - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-rgu34a.db/post-link.sh b/recipes/bioconductor-rgu34a.db/post-link.sh index 20b52fdb618c2..736eb867e924c 100644 --- a/recipes/bioconductor-rgu34a.db/post-link.sh +++ b/recipes/bioconductor-rgu34a.db/post-link.sh @@ -1,9 +1,10 @@ #!/bin/bash FN="rgu34a.db_3.2.3.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/rgu34a.db_3.2.3.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/rgu34a.db_3.2.3.tar.gz" "https://bioarchive.galaxyproject.org/rgu34a.db_3.2.3.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-rgu34a.db/bioconductor-rgu34a.db_3.2.3_src_all.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-rgu34a.db/bioconductor-rgu34a.db_3.2.3_src_all.tar.gz" ) MD5="b8e7fec45ef9e1423cda3171bb12e34c" @@ -16,7 +17,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-rgu34acdf/meta.yaml b/recipes/bioconductor-rgu34acdf/meta.yaml index f5bcef17f6831..0cb82328fc63d 100644 --- a/recipes/bioconductor-rgu34acdf/meta.yaml +++ b/recipes/bioconductor-rgu34acdf/meta.yaml @@ -1,6 +1,6 @@ {% set version = "2.18.0" %} {% set name = "rgu34acdf" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -12,19 +12,19 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: dcfa7ecce00e529f93809759ed837b8d build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' - r-base run: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-rgu34acdf/post-link.sh b/recipes/bioconductor-rgu34acdf/post-link.sh index d4cec3b060c3c..b99e66048cf3a 100644 --- a/recipes/bioconductor-rgu34acdf/post-link.sh +++ b/recipes/bioconductor-rgu34acdf/post-link.sh @@ -1,9 +1,10 @@ #!/bin/bash FN="rgu34acdf_2.18.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/rgu34acdf_2.18.0.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/rgu34acdf_2.18.0.tar.gz" "https://bioarchive.galaxyproject.org/rgu34acdf_2.18.0.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-rgu34acdf/bioconductor-rgu34acdf_2.18.0_src_all.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-rgu34acdf/bioconductor-rgu34acdf_2.18.0_src_all.tar.gz" ) MD5="dcfa7ecce00e529f93809759ed837b8d" @@ -16,7 +17,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-rgu34aprobe/meta.yaml b/recipes/bioconductor-rgu34aprobe/meta.yaml index 017a6d4b6fac8..c9330882cf6d1 100644 --- a/recipes/bioconductor-rgu34aprobe/meta.yaml +++ b/recipes/bioconductor-rgu34aprobe/meta.yaml @@ -1,6 +1,6 @@ {% set version = "2.18.0" %} {% set name = "rgu34aprobe" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -12,19 +12,19 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 902aee259a2894fa8713c4bf9266c0e2 build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' - r-base run: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-rgu34aprobe/post-link.sh b/recipes/bioconductor-rgu34aprobe/post-link.sh index cf60e0459e448..19f65c36f6811 100644 --- a/recipes/bioconductor-rgu34aprobe/post-link.sh +++ b/recipes/bioconductor-rgu34aprobe/post-link.sh @@ -1,9 +1,10 @@ #!/bin/bash FN="rgu34aprobe_2.18.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/rgu34aprobe_2.18.0.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/rgu34aprobe_2.18.0.tar.gz" "https://bioarchive.galaxyproject.org/rgu34aprobe_2.18.0.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-rgu34aprobe/bioconductor-rgu34aprobe_2.18.0_src_all.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-rgu34aprobe/bioconductor-rgu34aprobe_2.18.0_src_all.tar.gz" ) MD5="902aee259a2894fa8713c4bf9266c0e2" @@ -16,7 +17,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-rgu34b.db/meta.yaml b/recipes/bioconductor-rgu34b.db/meta.yaml index b51bc01826666..442e2e0e2dc55 100644 --- a/recipes/bioconductor-rgu34b.db/meta.yaml +++ b/recipes/bioconductor-rgu34b.db/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.2.3" %} {% set name = "rgu34b.db" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -12,7 +12,7 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: d2ad468820c1cfbe94297d423237f5bb build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ @@ -20,14 +20,14 @@ build: # Suggests: DBI, annotate, RUnit requirements: host: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' - - 'bioconductor-org.rn.eg.db >=3.7.0,<3.8.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' + - 'bioconductor-org.rn.eg.db >=3.8.0,<3.9.0' - r-base run: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' - - 'bioconductor-org.rn.eg.db >=3.7.0,<3.8.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' + - 'bioconductor-org.rn.eg.db >=3.8.0,<3.9.0' - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-rgu34b.db/post-link.sh b/recipes/bioconductor-rgu34b.db/post-link.sh index a3f3bac85f4c1..f14bb2df239b3 100644 --- a/recipes/bioconductor-rgu34b.db/post-link.sh +++ b/recipes/bioconductor-rgu34b.db/post-link.sh @@ -1,9 +1,10 @@ #!/bin/bash FN="rgu34b.db_3.2.3.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/rgu34b.db_3.2.3.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/rgu34b.db_3.2.3.tar.gz" "https://bioarchive.galaxyproject.org/rgu34b.db_3.2.3.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-rgu34b.db/bioconductor-rgu34b.db_3.2.3_src_all.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-rgu34b.db/bioconductor-rgu34b.db_3.2.3_src_all.tar.gz" ) MD5="d2ad468820c1cfbe94297d423237f5bb" @@ -16,7 +17,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-rgu34bcdf/meta.yaml b/recipes/bioconductor-rgu34bcdf/meta.yaml index 2395056e66a11..3c01646d05b31 100644 --- a/recipes/bioconductor-rgu34bcdf/meta.yaml +++ b/recipes/bioconductor-rgu34bcdf/meta.yaml @@ -1,6 +1,6 @@ {% set version = "2.18.0" %} {% set name = "rgu34bcdf" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -12,19 +12,19 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 428b3a39f0d8addd7d863539b8cda6ea build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' - r-base run: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-rgu34bcdf/post-link.sh b/recipes/bioconductor-rgu34bcdf/post-link.sh index 6b1a967eca3d1..e4740967f32e6 100644 --- a/recipes/bioconductor-rgu34bcdf/post-link.sh +++ b/recipes/bioconductor-rgu34bcdf/post-link.sh @@ -1,9 +1,10 @@ #!/bin/bash FN="rgu34bcdf_2.18.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/rgu34bcdf_2.18.0.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/rgu34bcdf_2.18.0.tar.gz" "https://bioarchive.galaxyproject.org/rgu34bcdf_2.18.0.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-rgu34bcdf/bioconductor-rgu34bcdf_2.18.0_src_all.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-rgu34bcdf/bioconductor-rgu34bcdf_2.18.0_src_all.tar.gz" ) MD5="428b3a39f0d8addd7d863539b8cda6ea" @@ -16,7 +17,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-rgu34bprobe/meta.yaml b/recipes/bioconductor-rgu34bprobe/meta.yaml index e0d2aff1aea67..0711b0b48acaf 100644 --- a/recipes/bioconductor-rgu34bprobe/meta.yaml +++ b/recipes/bioconductor-rgu34bprobe/meta.yaml @@ -1,6 +1,6 @@ {% set version = "2.18.0" %} {% set name = "rgu34bprobe" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -12,19 +12,19 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 2d6488309c5e54231a18e2ecf5608bb1 build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' - r-base run: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-rgu34bprobe/post-link.sh b/recipes/bioconductor-rgu34bprobe/post-link.sh index 8bc4e109e4215..9450045a38474 100644 --- a/recipes/bioconductor-rgu34bprobe/post-link.sh +++ b/recipes/bioconductor-rgu34bprobe/post-link.sh @@ -1,9 +1,10 @@ #!/bin/bash FN="rgu34bprobe_2.18.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/rgu34bprobe_2.18.0.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/rgu34bprobe_2.18.0.tar.gz" "https://bioarchive.galaxyproject.org/rgu34bprobe_2.18.0.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-rgu34bprobe/bioconductor-rgu34bprobe_2.18.0_src_all.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-rgu34bprobe/bioconductor-rgu34bprobe_2.18.0_src_all.tar.gz" ) MD5="2d6488309c5e54231a18e2ecf5608bb1" @@ -16,7 +17,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-rgu34c.db/meta.yaml b/recipes/bioconductor-rgu34c.db/meta.yaml index df1ae92bb9bff..d915e81e3da89 100644 --- a/recipes/bioconductor-rgu34c.db/meta.yaml +++ b/recipes/bioconductor-rgu34c.db/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.2.3" %} {% set name = "rgu34c.db" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -12,7 +12,7 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 59b66663b8d419599d48301661bfa2c3 build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ @@ -20,14 +20,14 @@ build: # Suggests: DBI, annotate, RUnit requirements: host: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' - - 'bioconductor-org.rn.eg.db >=3.7.0,<3.8.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' + - 'bioconductor-org.rn.eg.db >=3.8.0,<3.9.0' - r-base run: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' - - 'bioconductor-org.rn.eg.db >=3.7.0,<3.8.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' + - 'bioconductor-org.rn.eg.db >=3.8.0,<3.9.0' - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-rgu34c.db/post-link.sh b/recipes/bioconductor-rgu34c.db/post-link.sh index 97988923a70e5..2c40e5d4001b6 100644 --- a/recipes/bioconductor-rgu34c.db/post-link.sh +++ b/recipes/bioconductor-rgu34c.db/post-link.sh @@ -1,9 +1,10 @@ #!/bin/bash FN="rgu34c.db_3.2.3.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/rgu34c.db_3.2.3.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/rgu34c.db_3.2.3.tar.gz" "https://bioarchive.galaxyproject.org/rgu34c.db_3.2.3.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-rgu34c.db/bioconductor-rgu34c.db_3.2.3_src_all.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-rgu34c.db/bioconductor-rgu34c.db_3.2.3_src_all.tar.gz" ) MD5="59b66663b8d419599d48301661bfa2c3" @@ -16,7 +17,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-rgu34ccdf/meta.yaml b/recipes/bioconductor-rgu34ccdf/meta.yaml index 38103e88314a5..a90d9f91a692f 100644 --- a/recipes/bioconductor-rgu34ccdf/meta.yaml +++ b/recipes/bioconductor-rgu34ccdf/meta.yaml @@ -1,6 +1,6 @@ {% set version = "2.18.0" %} {% set name = "rgu34ccdf" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -12,19 +12,19 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 556a7130086004d26095594da31c6410 build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' - r-base run: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-rgu34ccdf/post-link.sh b/recipes/bioconductor-rgu34ccdf/post-link.sh index d02087f9bb019..f013f3824e490 100644 --- a/recipes/bioconductor-rgu34ccdf/post-link.sh +++ b/recipes/bioconductor-rgu34ccdf/post-link.sh @@ -1,9 +1,10 @@ #!/bin/bash FN="rgu34ccdf_2.18.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/rgu34ccdf_2.18.0.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/rgu34ccdf_2.18.0.tar.gz" "https://bioarchive.galaxyproject.org/rgu34ccdf_2.18.0.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-rgu34ccdf/bioconductor-rgu34ccdf_2.18.0_src_all.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-rgu34ccdf/bioconductor-rgu34ccdf_2.18.0_src_all.tar.gz" ) MD5="556a7130086004d26095594da31c6410" @@ -16,7 +17,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-rgu34cprobe/meta.yaml b/recipes/bioconductor-rgu34cprobe/meta.yaml index 4cd1904c9eba2..b85548f88b7dc 100644 --- a/recipes/bioconductor-rgu34cprobe/meta.yaml +++ b/recipes/bioconductor-rgu34cprobe/meta.yaml @@ -1,6 +1,6 @@ {% set version = "2.18.0" %} {% set name = "rgu34cprobe" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -12,19 +12,19 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: d1a6c433acd30b95fa7be89147105b74 build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' - r-base run: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-rgu34cprobe/post-link.sh b/recipes/bioconductor-rgu34cprobe/post-link.sh index 3e41e281ab3ba..f288f6ff605b9 100644 --- a/recipes/bioconductor-rgu34cprobe/post-link.sh +++ b/recipes/bioconductor-rgu34cprobe/post-link.sh @@ -1,9 +1,10 @@ #!/bin/bash FN="rgu34cprobe_2.18.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/rgu34cprobe_2.18.0.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/rgu34cprobe_2.18.0.tar.gz" "https://bioarchive.galaxyproject.org/rgu34cprobe_2.18.0.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-rgu34cprobe/bioconductor-rgu34cprobe_2.18.0_src_all.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-rgu34cprobe/bioconductor-rgu34cprobe_2.18.0_src_all.tar.gz" ) MD5="d1a6c433acd30b95fa7be89147105b74" @@ -16,7 +17,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-rguatlas4k.db/meta.yaml b/recipes/bioconductor-rguatlas4k.db/meta.yaml index 3b3cc1453fa50..bfd3a458c7e4f 100644 --- a/recipes/bioconductor-rguatlas4k.db/meta.yaml +++ b/recipes/bioconductor-rguatlas4k.db/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.2.3" %} {% set name = "rguatlas4k.db" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -12,7 +12,7 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 6a360676e08319ec5465c47c758110bd build: - number: 1 + number: 2 rpaths: - lib/R/lib/ - lib/ @@ -20,14 +20,14 @@ build: # Suggests: DBI, annotate, RUnit requirements: host: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' - - 'bioconductor-org.rn.eg.db >=3.7.0,<3.8.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' + - 'bioconductor-org.rn.eg.db >=3.8.0,<3.9.0' - r-base run: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' - - 'bioconductor-org.rn.eg.db >=3.7.0,<3.8.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' + - 'bioconductor-org.rn.eg.db >=3.8.0,<3.9.0' - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-rguatlas4k.db/post-link.sh b/recipes/bioconductor-rguatlas4k.db/post-link.sh index a6d1413d132fe..ede16db0d3802 100644 --- a/recipes/bioconductor-rguatlas4k.db/post-link.sh +++ b/recipes/bioconductor-rguatlas4k.db/post-link.sh @@ -1,9 +1,10 @@ #!/bin/bash FN="rguatlas4k.db_3.2.3.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/rguatlas4k.db_3.2.3.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/rguatlas4k.db_3.2.3.tar.gz" "https://bioarchive.galaxyproject.org/rguatlas4k.db_3.2.3.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-rguatlas4k.db/bioconductor-rguatlas4k.db_3.2.3_src_all.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-rguatlas4k.db/bioconductor-rguatlas4k.db_3.2.3_src_all.tar.gz" ) MD5="6a360676e08319ec5465c47c758110bd" @@ -16,7 +17,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-rgug4105a.db/meta.yaml b/recipes/bioconductor-rgug4105a.db/meta.yaml index 65ce9e572cd0f..f179ffa29a869 100644 --- a/recipes/bioconductor-rgug4105a.db/meta.yaml +++ b/recipes/bioconductor-rgug4105a.db/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.2.3" %} {% set name = "rgug4105a.db" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -12,7 +12,7 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 3ccf354083ae36a7ae687fb8209c4e5b build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ @@ -20,14 +20,14 @@ build: # Suggests: DBI, annotate, RUnit requirements: host: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' - - 'bioconductor-org.rn.eg.db >=3.7.0,<3.8.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' + - 'bioconductor-org.rn.eg.db >=3.8.0,<3.9.0' - r-base run: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' - - 'bioconductor-org.rn.eg.db >=3.7.0,<3.8.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' + - 'bioconductor-org.rn.eg.db >=3.8.0,<3.9.0' - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-rgug4105a.db/post-link.sh b/recipes/bioconductor-rgug4105a.db/post-link.sh index bc2be09f2757e..44bbdc0fbffb9 100644 --- a/recipes/bioconductor-rgug4105a.db/post-link.sh +++ b/recipes/bioconductor-rgug4105a.db/post-link.sh @@ -1,9 +1,10 @@ #!/bin/bash FN="rgug4105a.db_3.2.3.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/rgug4105a.db_3.2.3.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/rgug4105a.db_3.2.3.tar.gz" "https://bioarchive.galaxyproject.org/rgug4105a.db_3.2.3.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-rgug4105a.db/bioconductor-rgug4105a.db_3.2.3_src_all.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-rgug4105a.db/bioconductor-rgug4105a.db_3.2.3_src_all.tar.gz" ) MD5="3ccf354083ae36a7ae687fb8209c4e5b" @@ -16,7 +17,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-rgug4130a.db/meta.yaml b/recipes/bioconductor-rgug4130a.db/meta.yaml index 9f9be92b5032e..8da55cef21454 100644 --- a/recipes/bioconductor-rgug4130a.db/meta.yaml +++ b/recipes/bioconductor-rgug4130a.db/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.2.3" %} {% set name = "rgug4130a.db" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -12,7 +12,7 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 13643ac109aaf12590a5b6e379609b79 build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ @@ -20,14 +20,14 @@ build: # Suggests: DBI, annotate, RUnit requirements: host: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' - - 'bioconductor-org.rn.eg.db >=3.7.0,<3.8.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' + - 'bioconductor-org.rn.eg.db >=3.8.0,<3.9.0' - r-base run: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' - - 'bioconductor-org.rn.eg.db >=3.7.0,<3.8.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' + - 'bioconductor-org.rn.eg.db >=3.8.0,<3.9.0' - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-rgug4130a.db/post-link.sh b/recipes/bioconductor-rgug4130a.db/post-link.sh index a8ce3eb976c3d..a2c2857e4a275 100644 --- a/recipes/bioconductor-rgug4130a.db/post-link.sh +++ b/recipes/bioconductor-rgug4130a.db/post-link.sh @@ -1,9 +1,10 @@ #!/bin/bash FN="rgug4130a.db_3.2.3.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/rgug4130a.db_3.2.3.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/rgug4130a.db_3.2.3.tar.gz" "https://bioarchive.galaxyproject.org/rgug4130a.db_3.2.3.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-rgug4130a.db/bioconductor-rgug4130a.db_3.2.3_src_all.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-rgug4130a.db/bioconductor-rgug4130a.db_3.2.3_src_all.tar.gz" ) MD5="13643ac109aaf12590a5b6e379609b79" @@ -16,7 +17,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-rgug4131a.db/meta.yaml b/recipes/bioconductor-rgug4131a.db/meta.yaml index 41c6d13998a61..ecd31d6ecb2e2 100644 --- a/recipes/bioconductor-rgug4131a.db/meta.yaml +++ b/recipes/bioconductor-rgug4131a.db/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.2.3" %} {% set name = "rgug4131a.db" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -12,7 +12,7 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 1168d4906fb8ce60cbc0fa6cfa3b8ec6 build: - number: 1 + number: 2 rpaths: - lib/R/lib/ - lib/ @@ -20,14 +20,14 @@ build: # Suggests: DBI, annotate, RUnit requirements: host: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' - - 'bioconductor-org.rn.eg.db >=3.7.0,<3.8.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' + - 'bioconductor-org.rn.eg.db >=3.8.0,<3.9.0' - r-base run: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' - - 'bioconductor-org.rn.eg.db >=3.7.0,<3.8.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' + - 'bioconductor-org.rn.eg.db >=3.8.0,<3.9.0' - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-rgug4131a.db/post-link.sh b/recipes/bioconductor-rgug4131a.db/post-link.sh index c20034ba70469..cd61cb7d3e839 100644 --- a/recipes/bioconductor-rgug4131a.db/post-link.sh +++ b/recipes/bioconductor-rgug4131a.db/post-link.sh @@ -1,9 +1,10 @@ #!/bin/bash FN="rgug4131a.db_3.2.3.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/rgug4131a.db_3.2.3.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/rgug4131a.db_3.2.3.tar.gz" "https://bioarchive.galaxyproject.org/rgug4131a.db_3.2.3.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-rgug4131a.db/bioconductor-rgug4131a.db_3.2.3_src_all.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-rgug4131a.db/bioconductor-rgug4131a.db_3.2.3_src_all.tar.gz" ) MD5="1168d4906fb8ce60cbc0fa6cfa3b8ec6" @@ -16,7 +17,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-rhdf5/build.sh b/recipes/bioconductor-rhdf5/build.sh index 5372f710f826e..c1d13421f5f1e 100644 --- a/recipes/bioconductor-rhdf5/build.sh +++ b/recipes/bioconductor-rhdf5/build.sh @@ -7,6 +7,5 @@ FC=$FC CXX=$CXX CXX98=$CXX CXX11=$CXX -CXX14=$CXX -CFLAGS='-std=c99'" > ~/.R/Makevars -$R CMD INSTALL --build . +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-rhdf5/meta.yaml b/recipes/bioconductor-rhdf5/meta.yaml index e36ac031cef9d..83b3b92e5d6a7 100644 --- a/recipes/bioconductor-rhdf5/meta.yaml +++ b/recipes/bioconductor-rhdf5/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "2.26.2" %} +{% set version = "2.28.0" %} {% set name = "rhdf5" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,22 +10,20 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - sha256: 34f99cc588c989cd213d896b25e77de2f26c9ca7f79d405cf4bbf211e6e0f383 + md5: 7b4ac800b93750924391110fa7e93d60 build: - number: 2 + number: 0 rpaths: - lib/R/lib/ - lib/ -# Suggests: bit64, BiocStyle, knitr, rmarkdown, testthat +# Suggests: bit64, BiocStyle, knitr, rmarkdown, testthat, microbenchmark, dplyr, ggplot2 requirements: host: - - 'bioconductor-rhdf5lib >=1.4.3,<1.5.0' + - 'bioconductor-rhdf5lib >=1.6.0,<1.7.0' - r-base - - zlib run: - - 'bioconductor-rhdf5lib >=1.4.3,<1.5.0' + - 'bioconductor-rhdf5lib >=1.6.0,<1.7.0' - r-base - - zlib build: - {{ compiler('c') }} - {{ compiler('cxx') }} @@ -33,8 +31,6 @@ requirements: test: commands: - '$R -e "library(''{{ name }}'')"' - - 'curl https://raw.githubusercontent.com/pachterlab/sleuth/master/tests/testthat/small_test_data/kallisto/abundance.h5 -O; $R -e "library(rhdf5); h5errorHandling(type=''verbose''); quit(''no'', status=is.null(h5read(''abundance.h5'', ''bootstrap/bs0'')))"' - - 'curl https://www.huber.embl.de/users/msmith/h5ex_d_szip.h5 -O; $R -e "library(rhdf5); h5errorHandling(type=''verbose''); quit(''no'', status=is.null(h5read(''h5ex_d_szip.h5'', ''DS1'')))"' about: home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: Artistic-2.0 diff --git a/recipes/bioconductor-rhdf5client/meta.yaml b/recipes/bioconductor-rhdf5client/meta.yaml index 9b0b795c3ab0d..6104f0f2f638b 100644 --- a/recipes/bioconductor-rhdf5client/meta.yaml +++ b/recipes/bioconductor-rhdf5client/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.4.1" %} +{% set version = "1.6.0" %} {% set name = "rhdf5client" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - sha256: 1d4a59df2f2acfac8ba519d54dfacac14bb62d9c4120ce262f261fc57fe66ddd + md5: 52a82ed4f7216b08471cb7c0a51c69f6 build: number: 0 rpaths: @@ -19,15 +19,15 @@ build: # Suggests: knitr, testthat, BiocStyle, DT, reticulate requirements: host: - - 'bioconductor-delayedarray >=0.8.0,<0.9.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-delayedarray >=0.10.0,<0.11.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' - r-base - r-httr - r-r6 - r-rjson run: - - 'bioconductor-delayedarray >=0.8.0,<0.9.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-delayedarray >=0.10.0,<0.11.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' - r-base - r-httr - r-r6 diff --git a/recipes/bioconductor-rhdf5lib/build.sh b/recipes/bioconductor-rhdf5lib/build.sh index 8af1be8947252..c1d13421f5f1e 100644 --- a/recipes/bioconductor-rhdf5lib/build.sh +++ b/recipes/bioconductor-rhdf5lib/build.sh @@ -7,9 +7,5 @@ FC=$FC CXX=$CXX CXX98=$CXX CXX11=$CXX -CXX14=$CXX -LDFLAGS='-L$PREFIX/lib' -CPPFLAGS='-I$PREFIX/include' -PREFIX=$PREFIX" > ~/.R/Makevars - -$R CMD INSTALL --build . +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-rhdf5lib/meta.yaml b/recipes/bioconductor-rhdf5lib/meta.yaml index 098a62fe6f0dc..6063a962c78cd 100644 --- a/recipes/bioconductor-rhdf5lib/meta.yaml +++ b/recipes/bioconductor-rhdf5lib/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.4.3" %} +{% set version = "1.6.0" %} {% set name = "Rhdf5lib" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 79b9c0902ae67edbc6faa63143fc2a9d + md5: a669973a49d9f7f38d5a0b02635794d4 build: number: 0 rpaths: @@ -21,13 +21,10 @@ build: requirements: host: - r-base - - zlib run: - r-base - - zlib build: - {{ compiler('c') }} - - {{ compiler('fortran') }} - automake - make test: diff --git a/recipes/bioconductor-rhesus.db0/meta.yaml b/recipes/bioconductor-rhesus.db0/meta.yaml index 420e79f1bda21..c82292c50a162 100644 --- a/recipes/bioconductor-rhesus.db0/meta.yaml +++ b/recipes/bioconductor-rhesus.db0/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "3.7.1" %} +{% set version = "3.8.2" %} {% set name = "rhesus.db0" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: c93d15f3864b15368d896db0961b0b35 + md5: 48321e16fd44fa3db5975b1b918c9865 build: number: 0 rpaths: @@ -19,12 +19,12 @@ build: noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' - r-base run: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-rhesus.db0/post-link.sh b/recipes/bioconductor-rhesus.db0/post-link.sh index 86ff40bc912a4..c3d09845242c1 100644 --- a/recipes/bioconductor-rhesus.db0/post-link.sh +++ b/recipes/bioconductor-rhesus.db0/post-link.sh @@ -1,11 +1,11 @@ #!/bin/bash -FN="rhesus.db0_3.7.1.tar.gz" +FN="rhesus.db0_3.8.2.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/rhesus.db0_3.7.1.tar.gz" - "https://bioarchive.galaxyproject.org/rhesus.db0_3.7.1.tar.gz" - "https://depot.galaxyproject.org/software/bioconductor-rhesus.db0/bioconductor-rhesus.db0_3.7.1_src_all.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/rhesus.db0_3.8.2.tar.gz" + "https://bioarchive.galaxyproject.org/rhesus.db0_3.8.2.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-rhesus.db0/bioconductor-rhesus.db0_3.8.2_src_all.tar.gz" ) -MD5="c93d15f3864b15368d896db0961b0b35" +MD5="48321e16fd44fa3db5975b1b918c9865" # Use a staging area in the conda dir rather than temp dirs, both to avoid # permission issues as well as to have things downloaded in a predictable @@ -16,7 +16,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-rhesuscdf/meta.yaml b/recipes/bioconductor-rhesuscdf/meta.yaml index 5a074bf79b966..3c47997d27155 100644 --- a/recipes/bioconductor-rhesuscdf/meta.yaml +++ b/recipes/bioconductor-rhesuscdf/meta.yaml @@ -1,6 +1,6 @@ {% set version = "2.18.0" %} {% set name = "rhesuscdf" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -12,19 +12,19 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 994e16da5dd31bc2796d0da40aa2634f build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' - r-base run: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-rhesuscdf/post-link.sh b/recipes/bioconductor-rhesuscdf/post-link.sh index 1f77c9ec4e245..57a7df50e662d 100644 --- a/recipes/bioconductor-rhesuscdf/post-link.sh +++ b/recipes/bioconductor-rhesuscdf/post-link.sh @@ -1,9 +1,10 @@ #!/bin/bash FN="rhesuscdf_2.18.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/rhesuscdf_2.18.0.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/rhesuscdf_2.18.0.tar.gz" "https://bioarchive.galaxyproject.org/rhesuscdf_2.18.0.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-rhesuscdf/bioconductor-rhesuscdf_2.18.0_src_all.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-rhesuscdf/bioconductor-rhesuscdf_2.18.0_src_all.tar.gz" ) MD5="994e16da5dd31bc2796d0da40aa2634f" @@ -16,7 +17,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-rhesusprobe/meta.yaml b/recipes/bioconductor-rhesusprobe/meta.yaml index f9fd6da246bc5..f7b73dccec90a 100644 --- a/recipes/bioconductor-rhesusprobe/meta.yaml +++ b/recipes/bioconductor-rhesusprobe/meta.yaml @@ -1,6 +1,6 @@ {% set version = "2.18.0" %} {% set name = "rhesusprobe" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -12,19 +12,19 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 4169c1c997c4c08b027bc7489533e11e build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' - r-base run: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-rhesusprobe/post-link.sh b/recipes/bioconductor-rhesusprobe/post-link.sh index b7229a0358346..7a8c0837d107e 100644 --- a/recipes/bioconductor-rhesusprobe/post-link.sh +++ b/recipes/bioconductor-rhesusprobe/post-link.sh @@ -1,9 +1,10 @@ #!/bin/bash FN="rhesusprobe_2.18.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/rhesusprobe_2.18.0.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/rhesusprobe_2.18.0.tar.gz" "https://bioarchive.galaxyproject.org/rhesusprobe_2.18.0.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-rhesusprobe/bioconductor-rhesusprobe_2.18.0_src_all.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-rhesusprobe/bioconductor-rhesusprobe_2.18.0_src_all.tar.gz" ) MD5="4169c1c997c4c08b027bc7489533e11e" @@ -16,7 +17,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-rheumaticconditionwollbold/meta.yaml b/recipes/bioconductor-rheumaticconditionwollbold/meta.yaml index beb10caca7856..d6cad9a911dea 100644 --- a/recipes/bioconductor-rheumaticconditionwollbold/meta.yaml +++ b/recipes/bioconductor-rheumaticconditionwollbold/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.20.0" %} +{% set version = "1.22.0" %} {% set name = "rheumaticConditionWOLLBOLD" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 8e65dd2904480c3e37fa19cec75c15c9 + md5: b5d1fcb87c69694aaf7e3ceb24b15452 build: number: 0 rpaths: @@ -23,7 +23,7 @@ requirements: - r-base run: - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-rheumaticconditionwollbold/post-link.sh b/recipes/bioconductor-rheumaticconditionwollbold/post-link.sh index f834b9d124c82..b5c657b533a72 100644 --- a/recipes/bioconductor-rheumaticconditionwollbold/post-link.sh +++ b/recipes/bioconductor-rheumaticconditionwollbold/post-link.sh @@ -1,11 +1,11 @@ #!/bin/bash -FN="rheumaticConditionWOLLBOLD_1.20.0.tar.gz" +FN="rheumaticConditionWOLLBOLD_1.22.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/experiment/src/contrib/rheumaticConditionWOLLBOLD_1.20.0.tar.gz" - "https://bioarchive.galaxyproject.org/rheumaticConditionWOLLBOLD_1.20.0.tar.gz" - "https://depot.galaxyproject.org/software/bioconductor-rheumaticconditionwollbold/bioconductor-rheumaticconditionwollbold_1.20.0_src_all.tar.gz" + "https://bioconductor.org/packages/3.9/data/experiment/src/contrib/rheumaticConditionWOLLBOLD_1.22.0.tar.gz" + "https://bioarchive.galaxyproject.org/rheumaticConditionWOLLBOLD_1.22.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-rheumaticconditionwollbold/bioconductor-rheumaticconditionwollbold_1.22.0_src_all.tar.gz" ) -MD5="8e65dd2904480c3e37fa19cec75c15c9" +MD5="b5d1fcb87c69694aaf7e3ceb24b15452" # Use a staging area in the conda dir rather than temp dirs, both to avoid # permission issues as well as to have things downloaded in a predictable @@ -16,7 +16,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-rhisat2/build.sh b/recipes/bioconductor-rhisat2/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-rhisat2/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-rhisat2/meta.yaml b/recipes/bioconductor-rhisat2/meta.yaml new file mode 100644 index 0000000000000..fb4d7fd64f41f --- /dev/null +++ b/recipes/bioconductor-rhisat2/meta.yaml @@ -0,0 +1,43 @@ +{% set version = "1.0.0" %} +{% set name = "Rhisat2" %} +{% set bioc = "3.9" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: a495d34bd02a2225255f7e8046a1df27 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ +# Suggests: testthat, knitr, rmarkdown, BiocStyle +# SystemRequirements: GNU make +requirements: + host: + - 'bioconductor-genomicfeatures >=1.36.0,<1.37.0' + - 'bioconductor-genomicranges >=1.36.0,<1.37.0' + - 'bioconductor-sgseq >=1.18.0,<1.19.0' + - r-base + run: + - 'bioconductor-genomicfeatures >=1.36.0,<1.37.0' + - 'bioconductor-genomicranges >=1.36.0,<1.37.0' + - 'bioconductor-sgseq >=1.18.0,<1.19.0' + - r-base + build: + - {{ compiler('c') }} + - {{ compiler('cxx') }} + - make +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: GPL-3 + summary: 'An R interface to the HISAT2 spliced short-read aligner by Kim et al. (2015). The package contains wrapper functions to create a genome index and to perform the read alignment to the generated index.' + diff --git a/recipes/bioconductor-rhtslib/build.sh b/recipes/bioconductor-rhtslib/build.sh index b396b6896ced4..3f7e8934d1721 100644 --- a/recipes/bioconductor-rhtslib/build.sh +++ b/recipes/bioconductor-rhtslib/build.sh @@ -1,4 +1,6 @@ #!/bin/bash +export C_INCLUDE_PATH=${PREFIX}/include +export LD_LIBRARY_PATH=${PREFIX}/lib mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION mkdir -p ~/.R @@ -8,5 +10,7 @@ CXX=$CXX CXX98=$CXX CXX11=$CXX CXX14=$CXX" > ~/.R/Makevars -export C_INCLUDE_PATH="${PREFIX}/include" +pushd src/htslib-1.7 +make CC="${CC}" CFLAGS="${CFLAGS}" LDFLAGS="-L${PREFIX}/lib" +popd $R CMD INSTALL --build . diff --git a/recipes/bioconductor-rhtslib/meta.yaml b/recipes/bioconductor-rhtslib/meta.yaml index 3374d579cb5d3..75b202ae436db 100644 --- a/recipes/bioconductor-rhtslib/meta.yaml +++ b/recipes/bioconductor-rhtslib/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.14.1" %} +{% set version = "1.16.1" %} {% set name = "Rhtslib" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,9 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: d9c233bb1fa4c793cdb06ff74f89326606f687be79e839a8c30fbc32353adb8d - patches: - - patch + md5: b15beb320dcfd0b7653bcce0a0623899 build: number: 0 rpaths: @@ -21,16 +19,16 @@ build: # Suggests: BiocStyle, knitr requirements: host: - - 'bioconductor-zlibbioc >=1.28.0,<1.29.0' + - 'bioconductor-zlibbioc >=1.30.0,<1.31.0' - r-base - - zlib - xz + - zlib - bzip2 run: - - 'bioconductor-zlibbioc >=1.28.0,<1.29.0' + - 'bioconductor-zlibbioc >=1.30.0,<1.31.0' - r-base - - zlib - xz + - zlib - bzip2 build: - {{ compiler('c') }} diff --git a/recipes/bioconductor-rhvdm/meta.yaml b/recipes/bioconductor-rhvdm/meta.yaml index 44dce1f6c6b7a..08870469b8d73 100644 --- a/recipes/bioconductor-rhvdm/meta.yaml +++ b/recipes/bioconductor-rhvdm/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.48.0" %} +{% set version = "1.49.0" %} {% set name = "rHVDM" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 03b3afcc36d32af3e5f32f14cbbdf79a + md5: 30ac36983f2746d0d2ee2be4ee6ba55d build: number: 0 rpaths: @@ -19,14 +19,14 @@ build: noarch: generic requirements: host: - - 'bioconductor-affy >=1.60.0,<1.61.0' - - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-affy >=1.62.0,<1.63.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' - r-base - 'r-minpack.lm >=1.0-5' - 'r-r2html >=1.5' run: - - 'bioconductor-affy >=1.60.0,<1.61.0' - - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-affy >=1.62.0,<1.63.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' - r-base - 'r-minpack.lm >=1.0-5' - 'r-r2html >=1.5' diff --git a/recipes/bioconductor-ri16cod.db/meta.yaml b/recipes/bioconductor-ri16cod.db/meta.yaml index 18a532f2ddabb..82195cdd54d55 100644 --- a/recipes/bioconductor-ri16cod.db/meta.yaml +++ b/recipes/bioconductor-ri16cod.db/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.4.0" %} {% set name = "ri16cod.db" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -12,7 +12,7 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: cd01b429295fdbba21dbe566effacbdd build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ @@ -20,14 +20,14 @@ build: # Suggests: annotate, RUnit requirements: host: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' - - 'bioconductor-org.rn.eg.db >=3.7.0,<3.8.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' + - 'bioconductor-org.rn.eg.db >=3.8.0,<3.9.0' - r-base run: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' - - 'bioconductor-org.rn.eg.db >=3.7.0,<3.8.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' + - 'bioconductor-org.rn.eg.db >=3.8.0,<3.9.0' - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-ri16cod.db/post-link.sh b/recipes/bioconductor-ri16cod.db/post-link.sh index 62d920fe1c6b0..53f8336aa69c6 100644 --- a/recipes/bioconductor-ri16cod.db/post-link.sh +++ b/recipes/bioconductor-ri16cod.db/post-link.sh @@ -1,9 +1,10 @@ #!/bin/bash FN="ri16cod.db_3.4.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/ri16cod.db_3.4.0.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/ri16cod.db_3.4.0.tar.gz" "https://bioarchive.galaxyproject.org/ri16cod.db_3.4.0.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-ri16cod.db/bioconductor-ri16cod.db_3.4.0_src_all.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-ri16cod.db/bioconductor-ri16cod.db_3.4.0_src_all.tar.gz" ) MD5="cd01b429295fdbba21dbe566effacbdd" @@ -16,7 +17,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-riboprofiling/meta.yaml b/recipes/bioconductor-riboprofiling/meta.yaml index 386c4b16bdcad..da623cb7ce78b 100644 --- a/recipes/bioconductor-riboprofiling/meta.yaml +++ b/recipes/bioconductor-riboprofiling/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.12.0" %} +{% set version = "1.14.0" %} {% set name = "RiboProfiling" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,9 +10,9 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: bde2fcd441936a57773f4c14fe283ffe + md5: 30da7540d39e7c752c224c226322f6df build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ @@ -20,17 +20,17 @@ build: # Suggests: knitr, BiocStyle, TxDb.Hsapiens.UCSC.hg19.knownGene, BSgenome.Hsapiens.UCSC.hg19, testthat, SummarizedExperiment requirements: host: - - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' - - 'bioconductor-biostrings >=2.50.0,<2.51.0' - - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' - - 'bioconductor-genomicalignments >=1.18.0,<1.19.0' - - 'bioconductor-genomicfeatures >=1.34.0,<1.35.0' - - 'bioconductor-genomicranges >=1.34.0,<1.35.0' - - 'bioconductor-ggbio >=1.30.0,<1.31.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-rsamtools >=1.34.0,<1.35.0' - - 'bioconductor-rtracklayer >=1.42.0,<1.43.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-biocgenerics >=0.30.0,<0.31.0' + - 'bioconductor-biostrings >=2.52.0,<2.53.0' + - 'bioconductor-genomeinfodb >=1.20.0,<1.21.0' + - 'bioconductor-genomicalignments >=1.20.0,<1.21.0' + - 'bioconductor-genomicfeatures >=1.36.0,<1.37.0' + - 'bioconductor-genomicranges >=1.36.0,<1.37.0' + - 'bioconductor-ggbio >=1.32.0,<1.33.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-rsamtools >=2.0.0,<2.1.0' + - 'bioconductor-rtracklayer >=1.44.0,<1.45.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' - r-base - r-data.table - r-ggplot2 @@ -38,17 +38,17 @@ requirements: - r-reshape2 - r-sqldf run: - - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' - - 'bioconductor-biostrings >=2.50.0,<2.51.0' - - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' - - 'bioconductor-genomicalignments >=1.18.0,<1.19.0' - - 'bioconductor-genomicfeatures >=1.34.0,<1.35.0' - - 'bioconductor-genomicranges >=1.34.0,<1.35.0' - - 'bioconductor-ggbio >=1.30.0,<1.31.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-rsamtools >=1.34.0,<1.35.0' - - 'bioconductor-rtracklayer >=1.42.0,<1.43.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-biocgenerics >=0.30.0,<0.31.0' + - 'bioconductor-biostrings >=2.52.0,<2.53.0' + - 'bioconductor-genomeinfodb >=1.20.0,<1.21.0' + - 'bioconductor-genomicalignments >=1.20.0,<1.21.0' + - 'bioconductor-genomicfeatures >=1.36.0,<1.37.0' + - 'bioconductor-genomicranges >=1.36.0,<1.37.0' + - 'bioconductor-ggbio >=1.32.0,<1.33.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-rsamtools >=2.0.0,<2.1.0' + - 'bioconductor-rtracklayer >=1.44.0,<1.45.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' - r-base - r-data.table - r-ggplot2 diff --git a/recipes/bioconductor-riboseqr/meta.yaml b/recipes/bioconductor-riboseqr/meta.yaml index 746fc428d7d64..dc82ef398644c 100644 --- a/recipes/bioconductor-riboseqr/meta.yaml +++ b/recipes/bioconductor-riboseqr/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.16.0" %} +{% set version = "1.18.0" %} {% set name = "riboSeqR" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 48f5aad232a33ca5f3ab9766c1b246f2 + md5: 4e9c3e5e2eac839d8fc9fac1bac3b5b7 build: number: 0 rpaths: @@ -20,21 +20,21 @@ build: # Suggests: BiocStyle, RUnit, BiocGenerics requirements: host: - - 'bioconductor-bayseq >=2.16.0,<2.17.0' - - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' - - 'bioconductor-genomicranges >=1.34.0,<1.35.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-rsamtools >=1.34.0,<1.35.0' - - 'bioconductor-seqlogo >=1.48.0,<1.49.0' + - 'bioconductor-bayseq >=2.18.0,<2.19.0' + - 'bioconductor-genomeinfodb >=1.20.0,<1.21.0' + - 'bioconductor-genomicranges >=1.36.0,<1.37.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-rsamtools >=2.0.0,<2.1.0' + - 'bioconductor-seqlogo >=1.50.0,<1.51.0' - r-abind - r-base run: - - 'bioconductor-bayseq >=2.16.0,<2.17.0' - - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' - - 'bioconductor-genomicranges >=1.34.0,<1.35.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-rsamtools >=1.34.0,<1.35.0' - - 'bioconductor-seqlogo >=1.48.0,<1.49.0' + - 'bioconductor-bayseq >=2.18.0,<2.19.0' + - 'bioconductor-genomeinfodb >=1.20.0,<1.21.0' + - 'bioconductor-genomicranges >=1.36.0,<1.37.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-rsamtools >=2.0.0,<2.1.0' + - 'bioconductor-seqlogo >=1.50.0,<1.51.0' - r-abind - r-base test: diff --git a/recipes/bioconductor-ribosomaldatabaseproject11.5mgdb/meta.yaml b/recipes/bioconductor-ribosomaldatabaseproject11.5mgdb/meta.yaml index 8b81fc87b0bf3..81cdb69589996 100644 --- a/recipes/bioconductor-ribosomaldatabaseproject11.5mgdb/meta.yaml +++ b/recipes/bioconductor-ribosomaldatabaseproject11.5mgdb/meta.yaml @@ -1,6 +1,6 @@ {% set version = "1.00.0" %} {% set name = "ribosomaldatabaseproject11.5MgDb" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -12,19 +12,19 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' md5: b50b3dedc5ed906df4f335c80ad072cf build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ noarch: generic requirements: host: - - 'bioconductor-metagenomefeatures >=2.2.0,<2.3.0' + - 'bioconductor-metagenomefeatures >=2.4.0,<2.5.0' - r-base run: - - 'bioconductor-metagenomefeatures >=2.2.0,<2.3.0' + - 'bioconductor-metagenomefeatures >=2.4.0,<2.5.0' - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-ribosomaldatabaseproject11.5mgdb/post-link.sh b/recipes/bioconductor-ribosomaldatabaseproject11.5mgdb/post-link.sh index 792b40118d5e8..5615f5323cf01 100644 --- a/recipes/bioconductor-ribosomaldatabaseproject11.5mgdb/post-link.sh +++ b/recipes/bioconductor-ribosomaldatabaseproject11.5mgdb/post-link.sh @@ -1,9 +1,10 @@ #!/bin/bash FN="ribosomaldatabaseproject11.5MgDb_1.00.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/ribosomaldatabaseproject11.5MgDb_1.00.0.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/ribosomaldatabaseproject11.5MgDb_1.00.0.tar.gz" "https://bioarchive.galaxyproject.org/ribosomaldatabaseproject11.5MgDb_1.00.0.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-ribosomaldatabaseproject11.5mgdb/bioconductor-ribosomaldatabaseproject11.5mgdb_1.00.0_src_all.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-ribosomaldatabaseproject11.5mgdb/bioconductor-ribosomaldatabaseproject11.5mgdb_1.00.0_src_all.tar.gz" ) MD5="b50b3dedc5ed906df4f335c80ad072cf" @@ -16,7 +17,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-ricecdf/meta.yaml b/recipes/bioconductor-ricecdf/meta.yaml index fcdc6205c1dc6..7bd5b078c6669 100644 --- a/recipes/bioconductor-ricecdf/meta.yaml +++ b/recipes/bioconductor-ricecdf/meta.yaml @@ -1,6 +1,6 @@ {% set version = "2.18.0" %} {% set name = "ricecdf" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -12,19 +12,19 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 51db6f51f4adcfb7f4940d07668db8b8 build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' - r-base run: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-ricecdf/post-link.sh b/recipes/bioconductor-ricecdf/post-link.sh index a4a4cb0c0670d..20897b2022d19 100644 --- a/recipes/bioconductor-ricecdf/post-link.sh +++ b/recipes/bioconductor-ricecdf/post-link.sh @@ -1,9 +1,10 @@ #!/bin/bash FN="ricecdf_2.18.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/ricecdf_2.18.0.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/ricecdf_2.18.0.tar.gz" "https://bioarchive.galaxyproject.org/ricecdf_2.18.0.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-ricecdf/bioconductor-ricecdf_2.18.0_src_all.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-ricecdf/bioconductor-ricecdf_2.18.0_src_all.tar.gz" ) MD5="51db6f51f4adcfb7f4940d07668db8b8" @@ -16,7 +17,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-riceprobe/meta.yaml b/recipes/bioconductor-riceprobe/meta.yaml index 4732e479eff40..8e549733cb655 100644 --- a/recipes/bioconductor-riceprobe/meta.yaml +++ b/recipes/bioconductor-riceprobe/meta.yaml @@ -1,6 +1,6 @@ {% set version = "2.18.0" %} {% set name = "riceprobe" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -12,19 +12,19 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 2fac7746c343546cf30e6d54bc1e2019 build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' - r-base run: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-riceprobe/post-link.sh b/recipes/bioconductor-riceprobe/post-link.sh index 46c42cfcc9358..3cb9f2958cd2a 100644 --- a/recipes/bioconductor-riceprobe/post-link.sh +++ b/recipes/bioconductor-riceprobe/post-link.sh @@ -1,9 +1,10 @@ #!/bin/bash FN="riceprobe_2.18.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/riceprobe_2.18.0.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/riceprobe_2.18.0.tar.gz" "https://bioarchive.galaxyproject.org/riceprobe_2.18.0.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-riceprobe/bioconductor-riceprobe_2.18.0_src_all.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-riceprobe/bioconductor-riceprobe_2.18.0_src_all.tar.gz" ) MD5="2fac7746c343546cf30e6d54bc1e2019" @@ -16,7 +17,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-rimmport/meta.yaml b/recipes/bioconductor-rimmport/meta.yaml index e1f3272a3c205..cd87d6ad7365f 100644 --- a/recipes/bioconductor-rimmport/meta.yaml +++ b/recipes/bioconductor-rimmport/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.10.0" %} +{% set version = "1.12.0" %} {% set name = "RImmPort" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 6912d86ace8499a7be8bbcd2f2496ec5 + md5: 74e9aacd1917e4ea6b968bd30371db56 build: number: 0 rpaths: diff --git a/recipes/bioconductor-ringo/meta.yaml b/recipes/bioconductor-ringo/meta.yaml index cd1b5cd4ae841..56d4e2d376bc3 100644 --- a/recipes/bioconductor-ringo/meta.yaml +++ b/recipes/bioconductor-ringo/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.46.0" %} +{% set version = "1.48.0" %} {% set name = "Ringo" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 3436818ae4313f8dfab65d0db0e0b86f + md5: 905cfe4b4a6f9bf4bcfbdf0250c7cc0c build: number: 0 rpaths: @@ -19,21 +19,21 @@ build: # Suggests: rtracklayer (>= 1.3.1), mclust, topGO (>= 1.15.0) requirements: host: - - 'bioconductor-biobase >=2.42.0,<2.43.0' - - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' - - 'bioconductor-genefilter >=1.64.0,<1.65.0' - - 'bioconductor-limma >=3.38.0,<3.39.0' - - 'bioconductor-vsn >=3.50.0,<3.51.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' + - 'bioconductor-biocgenerics >=0.30.0,<0.31.0' + - 'bioconductor-genefilter >=1.66.0,<1.67.0' + - 'bioconductor-limma >=3.40.0,<3.41.0' + - 'bioconductor-vsn >=3.52.0,<3.53.0' - r-base - r-lattice - r-matrix - r-rcolorbrewer run: - - 'bioconductor-biobase >=2.42.0,<2.43.0' - - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' - - 'bioconductor-genefilter >=1.64.0,<1.65.0' - - 'bioconductor-limma >=3.38.0,<3.39.0' - - 'bioconductor-vsn >=3.50.0,<3.51.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' + - 'bioconductor-biocgenerics >=0.30.0,<0.31.0' + - 'bioconductor-genefilter >=1.66.0,<1.67.0' + - 'bioconductor-limma >=3.40.0,<3.41.0' + - 'bioconductor-vsn >=3.52.0,<3.53.0' - r-base - r-lattice - r-matrix diff --git a/recipes/bioconductor-ripseeker/meta.yaml b/recipes/bioconductor-ripseeker/meta.yaml index de32bbf146713..0f0f196e6cfb0 100644 --- a/recipes/bioconductor-ripseeker/meta.yaml +++ b/recipes/bioconductor-ripseeker/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.22.0" %} +{% set version = "1.24.0" %} {% set name = "RIPSeeker" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: ca82b8eb26b72bc28c55f133afcc7c2a + md5: f2b707b4fca1df7b241ef4b24a85fcb6 build: number: 0 rpaths: @@ -20,22 +20,22 @@ build: # Suggests: biomaRt, ChIPpeakAnno, parallel, GenomicFeatures requirements: host: - - 'bioconductor-genomicalignments >=1.18.0,<1.19.0' - - 'bioconductor-genomicranges >=1.34.0,<1.35.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-rsamtools >=1.34.0,<1.35.0' - - 'bioconductor-rtracklayer >=1.42.0,<1.43.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' - - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' + - 'bioconductor-genomicalignments >=1.20.0,<1.21.0' + - 'bioconductor-genomicranges >=1.36.0,<1.37.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-rsamtools >=2.0.0,<2.1.0' + - 'bioconductor-rtracklayer >=1.44.0,<1.45.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' + - 'bioconductor-summarizedexperiment >=1.14.0,<1.15.0' - r-base run: - - 'bioconductor-genomicalignments >=1.18.0,<1.19.0' - - 'bioconductor-genomicranges >=1.34.0,<1.35.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-rsamtools >=1.34.0,<1.35.0' - - 'bioconductor-rtracklayer >=1.42.0,<1.43.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' - - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' + - 'bioconductor-genomicalignments >=1.20.0,<1.21.0' + - 'bioconductor-genomicranges >=1.36.0,<1.37.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-rsamtools >=2.0.0,<2.1.0' + - 'bioconductor-rtracklayer >=1.44.0,<1.45.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' + - 'bioconductor-summarizedexperiment >=1.14.0,<1.15.0' - r-base test: commands: diff --git a/recipes/bioconductor-ripseekerdata/meta.yaml b/recipes/bioconductor-ripseekerdata/meta.yaml index 0740095a0058b..5a696bea8eef3 100644 --- a/recipes/bioconductor-ripseekerdata/meta.yaml +++ b/recipes/bioconductor-ripseekerdata/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.18.0" %} +{% set version = "1.20.0" %} {% set name = "RIPSeekerData" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: f81b8966e307327aeba0796f80f0e97a + md5: 5393a250ac8618929a6240d902c738d1 build: number: 0 rpaths: @@ -19,12 +19,12 @@ build: noarch: generic requirements: host: - - 'bioconductor-ripseeker >=1.22.0,<1.23.0' + - 'bioconductor-ripseeker >=1.24.0,<1.25.0' - r-base run: - - 'bioconductor-ripseeker >=1.22.0,<1.23.0' + - 'bioconductor-ripseeker >=1.24.0,<1.25.0' - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-ripseekerdata/post-link.sh b/recipes/bioconductor-ripseekerdata/post-link.sh index 3a13eb32f60c8..6b9c272238483 100644 --- a/recipes/bioconductor-ripseekerdata/post-link.sh +++ b/recipes/bioconductor-ripseekerdata/post-link.sh @@ -1,11 +1,11 @@ #!/bin/bash -FN="RIPSeekerData_1.18.0.tar.gz" +FN="RIPSeekerData_1.20.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/experiment/src/contrib/RIPSeekerData_1.18.0.tar.gz" - "https://bioarchive.galaxyproject.org/RIPSeekerData_1.18.0.tar.gz" - "https://depot.galaxyproject.org/software/bioconductor-ripseekerdata/bioconductor-ripseekerdata_1.18.0_src_all.tar.gz" + "https://bioconductor.org/packages/3.9/data/experiment/src/contrib/RIPSeekerData_1.20.0.tar.gz" + "https://bioarchive.galaxyproject.org/RIPSeekerData_1.20.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-ripseekerdata/bioconductor-ripseekerdata_1.20.0_src_all.tar.gz" ) -MD5="f81b8966e307327aeba0796f80f0e97a" +MD5="5393a250ac8618929a6240d902c738d1" # Use a staging area in the conda dir rather than temp dirs, both to avoid # permission issues as well as to have things downloaded in a predictable @@ -16,7 +16,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-risa/meta.yaml b/recipes/bioconductor-risa/meta.yaml index 2d5f7a031718b..e3ac635d5a54d 100644 --- a/recipes/bioconductor-risa/meta.yaml +++ b/recipes/bioconductor-risa/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.24.0" %} +{% set version = "1.26.0" %} {% set name = "Risa" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 7e0030432ea9e984265b3326e1cc08f9 + md5: cae993c23c4cf66321261b1115a18500 build: number: 0 rpaths: @@ -19,17 +19,17 @@ build: # Suggests: faahKO (>= 1.2.11) requirements: host: - - 'bioconductor-affy >=1.60.0,<1.61.0' - - 'bioconductor-biobase >=2.42.0,<2.43.0' - - 'bioconductor-biocviews >=1.50.0,<1.51.0' - - 'bioconductor-xcms >=3.4.0,<3.5.0' + - 'bioconductor-affy >=1.62.0,<1.63.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' + - 'bioconductor-biocviews >=1.52.0,<1.53.0' + - 'bioconductor-xcms >=3.6.0,<3.7.0' - r-base - 'r-rcpp >=0.9.13' run: - - 'bioconductor-affy >=1.60.0,<1.61.0' - - 'bioconductor-biobase >=2.42.0,<2.43.0' - - 'bioconductor-biocviews >=1.50.0,<1.51.0' - - 'bioconductor-xcms >=3.4.0,<3.5.0' + - 'bioconductor-affy >=1.62.0,<1.63.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' + - 'bioconductor-biocviews >=1.52.0,<1.53.0' + - 'bioconductor-xcms >=3.6.0,<3.7.0' - r-base - 'r-rcpp >=0.9.13' build: diff --git a/recipes/bioconductor-ritan/meta.yaml b/recipes/bioconductor-ritan/meta.yaml index ca903533941fb..91af2a016aa52 100644 --- a/recipes/bioconductor-ritan/meta.yaml +++ b/recipes/bioconductor-ritan/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.6.0" %} +{% set version = "1.8.0" %} {% set name = "RITAN" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,9 +10,9 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 922a970ba929bac0ecbc38e9f4496975 + md5: d9be8da5c38acb02332534452faf630c build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ @@ -20,9 +20,9 @@ build: # Suggests: rmarkdown requirements: host: - - 'bioconductor-bgeedb >=2.8.0,<2.9.0' - - 'bioconductor-ritandata >=1.6.0,<1.7.0' - - 'bioconductor-stringdb >=1.22.0,<1.23.0' + - 'bioconductor-bgeedb >=2.10.0,<2.11.0' + - 'bioconductor-ritandata >=1.8.0,<1.9.0' + - 'bioconductor-stringdb >=1.24.0,<1.25.0' - r-base - r-dynamictreecut - r-ggplot2 @@ -40,9 +40,9 @@ requirements: - r-reshape2 - r-sqldf run: - - 'bioconductor-bgeedb >=2.8.0,<2.9.0' - - 'bioconductor-ritandata >=1.6.0,<1.7.0' - - 'bioconductor-stringdb >=1.22.0,<1.23.0' + - 'bioconductor-bgeedb >=2.10.0,<2.11.0' + - 'bioconductor-ritandata >=1.8.0,<1.9.0' + - 'bioconductor-stringdb >=1.24.0,<1.25.0' - r-base - r-dynamictreecut - r-ggplot2 diff --git a/recipes/bioconductor-ritandata/meta.yaml b/recipes/bioconductor-ritandata/meta.yaml index 0a0b1accbb6a6..85e46028f66ed 100644 --- a/recipes/bioconductor-ritandata/meta.yaml +++ b/recipes/bioconductor-ritandata/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.6.0" %} +{% set version = "1.8.0" %} {% set name = "RITANdata" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 2cf6bf4546fd2e53d870202ba8b33ad3 + md5: 1e056a9bac392cc82d544af54324449e build: number: 0 rpaths: @@ -22,7 +22,7 @@ requirements: - r-base run: - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-ritandata/post-link.sh b/recipes/bioconductor-ritandata/post-link.sh index d2ae9b8cae120..c4b3047119765 100644 --- a/recipes/bioconductor-ritandata/post-link.sh +++ b/recipes/bioconductor-ritandata/post-link.sh @@ -1,11 +1,11 @@ #!/bin/bash -FN="RITANdata_1.6.0.tar.gz" +FN="RITANdata_1.8.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/experiment/src/contrib/RITANdata_1.6.0.tar.gz" - "https://bioarchive.galaxyproject.org/RITANdata_1.6.0.tar.gz" - "https://depot.galaxyproject.org/software/bioconductor-ritandata/bioconductor-ritandata_1.6.0_src_all.tar.gz" + "https://bioconductor.org/packages/3.9/data/experiment/src/contrib/RITANdata_1.8.0.tar.gz" + "https://bioarchive.galaxyproject.org/RITANdata_1.8.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-ritandata/bioconductor-ritandata_1.8.0_src_all.tar.gz" ) -MD5="2cf6bf4546fd2e53d870202ba8b33ad3" +MD5="1e056a9bac392cc82d544af54324449e" # Use a staging area in the conda dir rather than temp dirs, both to avoid # permission issues as well as to have things downloaded in a predictable @@ -16,7 +16,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-river/meta.yaml b/recipes/bioconductor-river/meta.yaml index e5c664f30297b..6cd0a9f07c756 100644 --- a/recipes/bioconductor-river/meta.yaml +++ b/recipes/bioconductor-river/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.6.0" %} +{% set version = "1.8.0" %} {% set name = "RIVER" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 1c71522aa5110c5e162019c2be4531ae + md5: 87b2517810b6bdad09d5cb027946a3fe build: number: 0 rpaths: @@ -20,13 +20,13 @@ build: # Suggests: BiocStyle, knitr, rmarkdown, testthat, devtools requirements: host: - - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' - r-base - r-ggplot2 - r-glmnet - r-proc run: - - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' - r-base - r-ggplot2 - r-glmnet diff --git a/recipes/bioconductor-rjmcmcnucleosomes/meta.yaml b/recipes/bioconductor-rjmcmcnucleosomes/meta.yaml index 70a707268bec1..3bb915348dbf9 100644 --- a/recipes/bioconductor-rjmcmcnucleosomes/meta.yaml +++ b/recipes/bioconductor-rjmcmcnucleosomes/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.6.0" %} +{% set version = "1.8.0" %} {% set name = "RJMCMCNucleosomes" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 969be4b78d5429790fe5921118ba8b7e + md5: 855eb918b7b4c78face174a2b7f4ede2 build: number: 0 rpaths: @@ -20,29 +20,25 @@ build: # SystemRequirements: Rcpp requirements: host: - - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' - - 'bioconductor-biocparallel >=1.16.0,<1.17.0' - - 'bioconductor-consensusseeker >=1.10.0,<1.11.0' - - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' - - 'bioconductor-genomicranges >=1.34.0,<1.35.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-biocgenerics >=0.30.0,<0.31.0' + - 'bioconductor-biocparallel >=1.18.0,<1.19.0' + - 'bioconductor-consensusseeker >=1.12.0,<1.13.0' + - 'bioconductor-genomeinfodb >=1.20.0,<1.21.0' + - 'bioconductor-genomicranges >=1.36.0,<1.37.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' - r-base - 'r-rcpp >=0.12.5' - - gsl - - openblas run: - - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' - - 'bioconductor-biocparallel >=1.16.0,<1.17.0' - - 'bioconductor-consensusseeker >=1.10.0,<1.11.0' - - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' - - 'bioconductor-genomicranges >=1.34.0,<1.35.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-biocgenerics >=0.30.0,<0.31.0' + - 'bioconductor-biocparallel >=1.18.0,<1.19.0' + - 'bioconductor-consensusseeker >=1.12.0,<1.13.0' + - 'bioconductor-genomeinfodb >=1.20.0,<1.21.0' + - 'bioconductor-genomicranges >=1.36.0,<1.37.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' - r-base - 'r-rcpp >=0.12.5' - - gsl - - openblas build: - {{ compiler('c') }} - {{ compiler('cxx') }} diff --git a/recipes/bioconductor-rlmm/meta.yaml b/recipes/bioconductor-rlmm/meta.yaml index 9e8d62277a8d9..6c7536297c0a9 100644 --- a/recipes/bioconductor-rlmm/meta.yaml +++ b/recipes/bioconductor-rlmm/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.44.0" %} +{% set version = "1.46.0" %} {% set name = "RLMM" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 8421a9bb66653cde951b58562ce7aaaf + md5: a3796e7da8e9a0dc62085026207c22ca build: number: 0 rpaths: diff --git a/recipes/bioconductor-rmagpie/meta.yaml b/recipes/bioconductor-rmagpie/meta.yaml index e402003d45893..66fa3b33c8172 100644 --- a/recipes/bioconductor-rmagpie/meta.yaml +++ b/recipes/bioconductor-rmagpie/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.38.0" %} +{% set version = "1.40.0" %} {% set name = "Rmagpie" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: dcc38ce1cc7a63089db512988d0e5611 + md5: 42d34c1f3fa1f5390b12488fe0c3da9a build: number: 0 rpaths: @@ -20,13 +20,13 @@ build: # Suggests: xtable requirements: host: - - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' - r-base - r-e1071 - r-kernlab - r-pamr run: - - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' - r-base - r-e1071 - r-kernlab diff --git a/recipes/bioconductor-rmassbank/meta.yaml b/recipes/bioconductor-rmassbank/meta.yaml index 48a201c0adf8a..b0339209f8a17 100644 --- a/recipes/bioconductor-rmassbank/meta.yaml +++ b/recipes/bioconductor-rmassbank/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "2.10.1" %} +{% set version = "2.12.0" %} {% set name = "RMassBank" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 47a3192d7b020db8dc92f01e42ecf0fa + md5: 9cadbd9a88b737eed282e0563f918b64 build: number: 0 rpaths: @@ -20,10 +20,10 @@ build: # SystemRequirements: OpenBabel requirements: host: - - 'bioconductor-biobase >=2.42.0,<2.43.0' - - 'bioconductor-msnbase >=2.8.0,<2.9.0' - - 'bioconductor-mzr >=2.16.0,<2.17.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' + - 'bioconductor-msnbase >=2.10.0,<2.11.0' + - 'bioconductor-mzr >=2.18.0,<2.19.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' - r-base - r-digest - r-httr @@ -35,10 +35,10 @@ requirements: - r-yaml - openbabel run: - - 'bioconductor-biobase >=2.42.0,<2.43.0' - - 'bioconductor-msnbase >=2.8.0,<2.9.0' - - 'bioconductor-mzr >=2.16.0,<2.17.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' + - 'bioconductor-msnbase >=2.10.0,<2.11.0' + - 'bioconductor-mzr >=2.18.0,<2.19.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' - r-base - r-digest - r-httr diff --git a/recipes/bioconductor-rmassbankdata/meta.yaml b/recipes/bioconductor-rmassbankdata/meta.yaml index 651eeb73af54d..0fa8a9344444d 100644 --- a/recipes/bioconductor-rmassbankdata/meta.yaml +++ b/recipes/bioconductor-rmassbankdata/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.20.0" %} +{% set version = "1.22.0" %} {% set name = "RMassBankData" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 46d74376c499336ed7d6f2abbad99b73 + md5: fc66ede0eb4d7ad10d96b38d2c1a212a build: number: 0 rpaths: @@ -23,7 +23,7 @@ requirements: - r-base run: - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-rmassbankdata/post-link.sh b/recipes/bioconductor-rmassbankdata/post-link.sh index 76e9155168170..763e2fbd95301 100644 --- a/recipes/bioconductor-rmassbankdata/post-link.sh +++ b/recipes/bioconductor-rmassbankdata/post-link.sh @@ -1,11 +1,11 @@ #!/bin/bash -FN="RMassBankData_1.20.0.tar.gz" +FN="RMassBankData_1.22.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/experiment/src/contrib/RMassBankData_1.20.0.tar.gz" - "https://bioarchive.galaxyproject.org/RMassBankData_1.20.0.tar.gz" - "https://depot.galaxyproject.org/software/bioconductor-rmassbankdata/bioconductor-rmassbankdata_1.20.0_src_all.tar.gz" + "https://bioconductor.org/packages/3.9/data/experiment/src/contrib/RMassBankData_1.22.0.tar.gz" + "https://bioarchive.galaxyproject.org/RMassBankData_1.22.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-rmassbankdata/bioconductor-rmassbankdata_1.22.0_src_all.tar.gz" ) -MD5="46d74376c499336ed7d6f2abbad99b73" +MD5="fc66ede0eb4d7ad10d96b38d2c1a212a" # Use a staging area in the conda dir rather than temp dirs, both to avoid # permission issues as well as to have things downloaded in a predictable @@ -16,7 +16,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-rmat/meta.yaml b/recipes/bioconductor-rmat/meta.yaml index 17988c984d77e..a6559056aca10 100644 --- a/recipes/bioconductor-rmat/meta.yaml +++ b/recipes/bioconductor-rmat/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "3.32.0" %} +{% set version = "3.33.0" %} {% set name = "rMAT" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: c37de71a14cb83a43f58db7c6ce5cbf2 + md5: 707db595db889f056a62d5802dc0e291 build: number: 0 rpaths: @@ -20,17 +20,17 @@ build: # SystemRequirements: GSL (GNU Scientific Library) requirements: host: - - 'bioconductor-affxparser >=1.54.0,<1.55.0' - - 'bioconductor-biobase >=2.42.0,<2.43.0' - - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-affxparser >=1.56.0,<1.57.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' + - 'bioconductor-biocgenerics >=0.30.0,<0.31.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' - r-base - gsl run: - - 'bioconductor-affxparser >=1.54.0,<1.55.0' - - 'bioconductor-biobase >=2.42.0,<2.43.0' - - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-affxparser >=1.56.0,<1.57.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' + - 'bioconductor-biocgenerics >=0.30.0,<0.31.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' - r-base - gsl build: diff --git a/recipes/bioconductor-rmelting/build.sh b/recipes/bioconductor-rmelting/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-rmelting/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-rmelting/meta.yaml b/recipes/bioconductor-rmelting/meta.yaml new file mode 100644 index 0000000000000..b0d546fb01a2b --- /dev/null +++ b/recipes/bioconductor-rmelting/meta.yaml @@ -0,0 +1,38 @@ +{% set version = "1.0.0" %} +{% set name = "rmelting" %} +{% set bioc = "3.9" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + md5: 169898a7e014553431e1adf202502a20 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: readxl, knitr, rmarkdown, reshape2, pander, testthat +# SystemRequirements: Java +requirements: + host: + - r-base + - r-rdpack + - 'r-rjava >=0.5-0' + run: + - r-base + - r-rdpack + - 'r-rjava >=0.5-0' +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: 'GPL-2 | GPL-3' + summary: 'R interface to the MELTING 5 program () to compute melting temperatures of nucleic acid duplexes along with other thermodynamic parameters.' + diff --git a/recipes/bioconductor-rmir.hs.mirna/meta.yaml b/recipes/bioconductor-rmir.hs.mirna/meta.yaml index 111e225f157a9..4be30325f1870 100644 --- a/recipes/bioconductor-rmir.hs.mirna/meta.yaml +++ b/recipes/bioconductor-rmir.hs.mirna/meta.yaml @@ -1,6 +1,6 @@ {% set version = "1.0.7" %} {% set name = "RmiR.Hs.miRNA" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -12,7 +12,7 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' md5: 4aedac188382447d9907d2617aa2e8e6 build: - number: 3 + number: 4 rpaths: - lib/R/lib/ - lib/ @@ -20,12 +20,12 @@ build: # Suggests: methods, hgug4112a.db requirements: host: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' - r-base run: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-rmir.hs.mirna/post-link.sh b/recipes/bioconductor-rmir.hs.mirna/post-link.sh index 342ed67ad7746..a024aa4f69991 100644 --- a/recipes/bioconductor-rmir.hs.mirna/post-link.sh +++ b/recipes/bioconductor-rmir.hs.mirna/post-link.sh @@ -1,7 +1,7 @@ #!/bin/bash FN="RmiR.Hs.miRNA_1.0.7.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/RmiR.Hs.miRNA_1.0.7.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/RmiR.Hs.miRNA_1.0.7.tar.gz" "https://bioarchive.galaxyproject.org/RmiR.Hs.miRNA_1.0.7.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-rmir.hs.mirna/bioconductor-rmir.hs.mirna_1.0.7_src_all.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-rmir.hs.mirna/bioconductor-rmir.hs.mirna_1.0.7_src_all.tar.gz" @@ -17,7 +17,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-rmir.hsa/meta.yaml b/recipes/bioconductor-rmir.hsa/meta.yaml index c3790a8942937..5e53c0ca58580 100644 --- a/recipes/bioconductor-rmir.hsa/meta.yaml +++ b/recipes/bioconductor-rmir.hsa/meta.yaml @@ -1,6 +1,6 @@ {% set version = "1.0.5" %} {% set name = "RmiR.hsa" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -12,7 +12,7 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' md5: f22a18d1a34d12f8fc4ba3daaf1379fd build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ @@ -20,12 +20,12 @@ build: # Suggests: methods, hgug4112a.db requirements: host: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' - r-base run: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-rmir.hsa/post-link.sh b/recipes/bioconductor-rmir.hsa/post-link.sh index 8a4983e94a4f4..880bd78763ec7 100644 --- a/recipes/bioconductor-rmir.hsa/post-link.sh +++ b/recipes/bioconductor-rmir.hsa/post-link.sh @@ -1,9 +1,10 @@ #!/bin/bash FN="RmiR.hsa_1.0.5.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/RmiR.hsa_1.0.5.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/RmiR.hsa_1.0.5.tar.gz" "https://bioarchive.galaxyproject.org/RmiR.hsa_1.0.5.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-rmir.hsa/bioconductor-rmir.hsa_1.0.5_src_all.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-rmir.hsa/bioconductor-rmir.hsa_1.0.5_src_all.tar.gz" ) MD5="f22a18d1a34d12f8fc4ba3daaf1379fd" @@ -16,7 +17,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-rmir/meta.yaml b/recipes/bioconductor-rmir/meta.yaml index 1b14333c1c8d0..797845f203345 100644 --- a/recipes/bioconductor-rmir/meta.yaml +++ b/recipes/bioconductor-rmir/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.38.0" %} +{% set version = "1.40.0" %} {% set name = "RmiR" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: f4320c1b98aa85b078b9b4c2c55ded07 + md5: 648f2070b121489b7d478d80cfe774a0 build: number: 0 rpaths: diff --git a/recipes/bioconductor-rmmquant/meta.yaml b/recipes/bioconductor-rmmquant/meta.yaml index 9e9b079aef065..1cff310ed7c74 100644 --- a/recipes/bioconductor-rmmquant/meta.yaml +++ b/recipes/bioconductor-rmmquant/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.0.0" %} +{% set version = "1.2.0" %} {% set name = "Rmmquant" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: c872cd62c9559b1d5c652be647d1ee5e + md5: 050e95348776d7b8b0b5bdfb08715b21 build: number: 0 rpaths: @@ -20,25 +20,25 @@ build: # SystemRequirements: C++11 requirements: host: - - 'bioconductor-biocstyle >=2.10.0,<2.11.0' - - 'bioconductor-deseq2 >=1.22.0,<1.23.0' - - 'bioconductor-genomicranges >=1.34.0,<1.35.0' - - 'bioconductor-org.mm.eg.db >=3.7.0,<3.8.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' - - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' - - 'bioconductor-tbx20bamsubset >=1.18.0,<1.19.0' + - 'bioconductor-biocstyle >=2.12.0,<2.13.0' + - 'bioconductor-deseq2 >=1.24.0,<1.25.0' + - 'bioconductor-genomicranges >=1.36.0,<1.37.0' + - 'bioconductor-org.mm.eg.db >=3.8.0,<3.9.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' + - 'bioconductor-summarizedexperiment >=1.14.0,<1.15.0' + - 'bioconductor-tbx20bamsubset >=1.20.0,<1.21.0' - 'bioconductor-txdb.mmusculus.ucsc.mm9.knowngene >=3.2.0,<3.3.0' - r-base - r-devtools - 'r-rcpp >=0.12.8' run: - - 'bioconductor-biocstyle >=2.10.0,<2.11.0' - - 'bioconductor-deseq2 >=1.22.0,<1.23.0' - - 'bioconductor-genomicranges >=1.34.0,<1.35.0' - - 'bioconductor-org.mm.eg.db >=3.7.0,<3.8.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' - - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' - - 'bioconductor-tbx20bamsubset >=1.18.0,<1.19.0' + - 'bioconductor-biocstyle >=2.12.0,<2.13.0' + - 'bioconductor-deseq2 >=1.24.0,<1.25.0' + - 'bioconductor-genomicranges >=1.36.0,<1.37.0' + - 'bioconductor-org.mm.eg.db >=3.8.0,<3.9.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' + - 'bioconductor-summarizedexperiment >=1.14.0,<1.15.0' + - 'bioconductor-tbx20bamsubset >=1.20.0,<1.21.0' - 'bioconductor-txdb.mmusculus.ucsc.mm9.knowngene >=3.2.0,<3.3.0' - r-base - r-devtools diff --git a/recipes/bioconductor-rnadecay/meta.yaml b/recipes/bioconductor-rnadecay/meta.yaml index 165263194094e..9a32dee35d77b 100644 --- a/recipes/bioconductor-rnadecay/meta.yaml +++ b/recipes/bioconductor-rnadecay/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.2.1" %} +{% set version = "1.4.0" %} {% set name = "RNAdecay" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 46409994305fd5f78320b67590641bb5 + md5: 7fe84f6a5edb236cf8dcd1a88f649155 build: number: 0 rpaths: diff --git a/recipes/bioconductor-rnagilentdesign028282.db/meta.yaml b/recipes/bioconductor-rnagilentdesign028282.db/meta.yaml index 46c2bc3b3e2db..731bfb2ec54d1 100644 --- a/recipes/bioconductor-rnagilentdesign028282.db/meta.yaml +++ b/recipes/bioconductor-rnagilentdesign028282.db/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.2.3" %} {% set name = "RnAgilentDesign028282.db" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -12,7 +12,7 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' md5: 72cafb0f7514a81f462acb3248e21aa9 build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ @@ -20,14 +20,14 @@ build: # Suggests: DBI, annotate, RUnit requirements: host: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' - - 'bioconductor-org.rn.eg.db >=3.7.0,<3.8.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' + - 'bioconductor-org.rn.eg.db >=3.8.0,<3.9.0' - r-base run: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' - - 'bioconductor-org.rn.eg.db >=3.7.0,<3.8.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' + - 'bioconductor-org.rn.eg.db >=3.8.0,<3.9.0' - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-rnagilentdesign028282.db/post-link.sh b/recipes/bioconductor-rnagilentdesign028282.db/post-link.sh index 2e7fbe7a5976e..5f1b4aeab6f13 100644 --- a/recipes/bioconductor-rnagilentdesign028282.db/post-link.sh +++ b/recipes/bioconductor-rnagilentdesign028282.db/post-link.sh @@ -1,9 +1,10 @@ #!/bin/bash FN="RnAgilentDesign028282.db_3.2.3.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/RnAgilentDesign028282.db_3.2.3.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/RnAgilentDesign028282.db_3.2.3.tar.gz" "https://bioarchive.galaxyproject.org/RnAgilentDesign028282.db_3.2.3.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-rnagilentdesign028282.db/bioconductor-rnagilentdesign028282.db_3.2.3_src_all.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-rnagilentdesign028282.db/bioconductor-rnagilentdesign028282.db_3.2.3_src_all.tar.gz" ) MD5="72cafb0f7514a81f462acb3248e21aa9" @@ -16,7 +17,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-rnainteract/meta.yaml b/recipes/bioconductor-rnainteract/meta.yaml index 8dca983042178..1ea383a0d496b 100644 --- a/recipes/bioconductor-rnainteract/meta.yaml +++ b/recipes/bioconductor-rnainteract/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.30.0" %} +{% set version = "1.32.0" %} {% set name = "RNAinteract" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: b9aaf6f1cbb298ce83184334f93c5a5d + md5: edc219a8b4c1af4ee194087c5e34bacf build: number: 0 rpaths: @@ -19,11 +19,11 @@ build: noarch: generic requirements: host: - - 'bioconductor-biobase >=2.42.0,<2.43.0' - - 'bioconductor-cellhts2 >=2.46.0,<2.47.0' - - 'bioconductor-geneplotter >=1.60.0,<1.61.0' - - 'bioconductor-limma >=3.38.0,<3.39.0' - - 'bioconductor-splots >=1.48.0,<1.49.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' + - 'bioconductor-cellhts2 >=2.48.0,<2.49.0' + - 'bioconductor-geneplotter >=1.62.0,<1.63.0' + - 'bioconductor-limma >=3.40.0,<3.41.0' + - 'bioconductor-splots >=1.50.0,<1.51.0' - r-abind - r-base - r-gplots @@ -35,11 +35,11 @@ requirements: - r-locfit - r-rcolorbrewer run: - - 'bioconductor-biobase >=2.42.0,<2.43.0' - - 'bioconductor-cellhts2 >=2.46.0,<2.47.0' - - 'bioconductor-geneplotter >=1.60.0,<1.61.0' - - 'bioconductor-limma >=3.38.0,<3.39.0' - - 'bioconductor-splots >=1.48.0,<1.49.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' + - 'bioconductor-cellhts2 >=2.48.0,<2.49.0' + - 'bioconductor-geneplotter >=1.62.0,<1.63.0' + - 'bioconductor-limma >=3.40.0,<3.41.0' + - 'bioconductor-splots >=1.50.0,<1.51.0' - r-abind - r-base - r-gplots diff --git a/recipes/bioconductor-rnainteractmapk/meta.yaml b/recipes/bioconductor-rnainteractmapk/meta.yaml index b156a4b79732c..832ca76e6b560 100644 --- a/recipes/bioconductor-rnainteractmapk/meta.yaml +++ b/recipes/bioconductor-rnainteractmapk/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.20.0" %} +{% set version = "1.22.0" %} {% set name = "RNAinteractMAPK" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 06d12d93a9a99709c6b5946fa4932486 + md5: d8ae6fcd34f94ad097f1948ccdefcc5e build: number: 0 rpaths: @@ -20,22 +20,22 @@ build: # Suggests: qvalue, lattice requirements: host: - - 'bioconductor-genefilter >=1.64.0,<1.65.0' - - 'bioconductor-rnainteract >=1.30.0,<1.31.0' + - 'bioconductor-genefilter >=1.66.0,<1.67.0' + - 'bioconductor-rnainteract >=1.32.0,<1.33.0' - r-base - r-fields - r-gdata - r-mass - r-sparselda run: - - 'bioconductor-genefilter >=1.64.0,<1.65.0' - - 'bioconductor-rnainteract >=1.30.0,<1.31.0' + - 'bioconductor-genefilter >=1.66.0,<1.67.0' + - 'bioconductor-rnainteract >=1.32.0,<1.33.0' - r-base - r-fields - r-gdata - r-mass - r-sparselda - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-rnainteractmapk/post-link.sh b/recipes/bioconductor-rnainteractmapk/post-link.sh index 246b206596d38..e4842698b4dec 100644 --- a/recipes/bioconductor-rnainteractmapk/post-link.sh +++ b/recipes/bioconductor-rnainteractmapk/post-link.sh @@ -1,11 +1,11 @@ #!/bin/bash -FN="RNAinteractMAPK_1.20.0.tar.gz" +FN="RNAinteractMAPK_1.22.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/experiment/src/contrib/RNAinteractMAPK_1.20.0.tar.gz" - "https://bioarchive.galaxyproject.org/RNAinteractMAPK_1.20.0.tar.gz" - "https://depot.galaxyproject.org/software/bioconductor-rnainteractmapk/bioconductor-rnainteractmapk_1.20.0_src_all.tar.gz" + "https://bioconductor.org/packages/3.9/data/experiment/src/contrib/RNAinteractMAPK_1.22.0.tar.gz" + "https://bioarchive.galaxyproject.org/RNAinteractMAPK_1.22.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-rnainteractmapk/bioconductor-rnainteractmapk_1.22.0_src_all.tar.gz" ) -MD5="06d12d93a9a99709c6b5946fa4932486" +MD5="d8ae6fcd34f94ad097f1948ccdefcc5e" # Use a staging area in the conda dir rather than temp dirs, both to avoid # permission issues as well as to have things downloaded in a predictable @@ -16,7 +16,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-rnaither/meta.yaml b/recipes/bioconductor-rnaither/meta.yaml index eefa0e0d77b87..eacb3354de4b1 100644 --- a/recipes/bioconductor-rnaither/meta.yaml +++ b/recipes/bioconductor-rnaither/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "2.30.0" %} +{% set version = "2.32.0" %} {% set name = "RNAither" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 0f8239609b46a02e35c85fb4e14aff89 + md5: 49c001354fe14669a8996adbd56f79ee build: number: 0 rpaths: @@ -19,23 +19,23 @@ build: noarch: generic requirements: host: - - 'bioconductor-biomart >=2.38.0,<2.39.0' - - 'bioconductor-geneplotter >=1.60.0,<1.61.0' - - 'bioconductor-limma >=3.38.0,<3.39.0' - - 'bioconductor-prada >=1.58.0,<1.59.0' - - 'bioconductor-rankprod >=3.8.0,<3.9.0' - - 'bioconductor-splots >=1.48.0,<1.49.0' - - 'bioconductor-topgo >=2.34.0,<2.35.0' + - 'bioconductor-biomart >=2.40.0,<2.41.0' + - 'bioconductor-geneplotter >=1.62.0,<1.63.0' + - 'bioconductor-limma >=3.40.0,<3.41.0' + - 'bioconductor-prada >=1.60.0,<1.61.0' + - 'bioconductor-rankprod >=3.10.0,<3.11.0' + - 'bioconductor-splots >=1.50.0,<1.51.0' + - 'bioconductor-topgo >=2.36.0,<2.37.0' - r-base - r-car run: - - 'bioconductor-biomart >=2.38.0,<2.39.0' - - 'bioconductor-geneplotter >=1.60.0,<1.61.0' - - 'bioconductor-limma >=3.38.0,<3.39.0' - - 'bioconductor-prada >=1.58.0,<1.59.0' - - 'bioconductor-rankprod >=3.8.0,<3.9.0' - - 'bioconductor-splots >=1.48.0,<1.49.0' - - 'bioconductor-topgo >=2.34.0,<2.35.0' + - 'bioconductor-biomart >=2.40.0,<2.41.0' + - 'bioconductor-geneplotter >=1.62.0,<1.63.0' + - 'bioconductor-limma >=3.40.0,<3.41.0' + - 'bioconductor-prada >=1.60.0,<1.61.0' + - 'bioconductor-rankprod >=3.10.0,<3.11.0' + - 'bioconductor-splots >=1.50.0,<1.51.0' + - 'bioconductor-topgo >=2.36.0,<2.37.0' - r-base - r-car test: diff --git a/recipes/bioconductor-rnaprobr/meta.yaml b/recipes/bioconductor-rnaprobr/meta.yaml index 1e5a928512de2..4e5853c626355 100644 --- a/recipes/bioconductor-rnaprobr/meta.yaml +++ b/recipes/bioconductor-rnaprobr/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.14.0" %} +{% set version = "1.16.0" %} {% set name = "RNAprobR" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 7c4c5ed21a3b2594fe094e7b75f053bc + md5: 4fd50c68767817514dfd3f24012ee68a build: number: 0 rpaths: @@ -20,27 +20,27 @@ build: # Suggests: BiocStyle requirements: host: - - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' - - 'bioconductor-biostrings >=2.50.0,<2.51.0' - - 'bioconductor-genomicalignments >=1.18.0,<1.19.0' - - 'bioconductor-genomicfeatures >=1.34.0,<1.35.0' - - 'bioconductor-genomicranges >=1.34.0,<1.35.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-rsamtools >=1.34.0,<1.35.0' - - 'bioconductor-rtracklayer >=1.42.0,<1.43.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-biocgenerics >=0.30.0,<0.31.0' + - 'bioconductor-biostrings >=2.52.0,<2.53.0' + - 'bioconductor-genomicalignments >=1.20.0,<1.21.0' + - 'bioconductor-genomicfeatures >=1.36.0,<1.37.0' + - 'bioconductor-genomicranges >=1.36.0,<1.37.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-rsamtools >=2.0.0,<2.1.0' + - 'bioconductor-rtracklayer >=1.44.0,<1.45.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' - r-base - 'r-plyr >=1.8.1' run: - - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' - - 'bioconductor-biostrings >=2.50.0,<2.51.0' - - 'bioconductor-genomicalignments >=1.18.0,<1.19.0' - - 'bioconductor-genomicfeatures >=1.34.0,<1.35.0' - - 'bioconductor-genomicranges >=1.34.0,<1.35.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-rsamtools >=1.34.0,<1.35.0' - - 'bioconductor-rtracklayer >=1.42.0,<1.43.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-biocgenerics >=0.30.0,<0.31.0' + - 'bioconductor-biostrings >=2.52.0,<2.53.0' + - 'bioconductor-genomicalignments >=1.20.0,<1.21.0' + - 'bioconductor-genomicfeatures >=1.36.0,<1.37.0' + - 'bioconductor-genomicranges >=1.36.0,<1.37.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-rsamtools >=2.0.0,<2.1.0' + - 'bioconductor-rtracklayer >=1.44.0,<1.45.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' - r-base - 'r-plyr >=1.8.1' test: diff --git a/recipes/bioconductor-rnaseqcomp/meta.yaml b/recipes/bioconductor-rnaseqcomp/meta.yaml index 4435f6c2f5377..03a99d44406c7 100644 --- a/recipes/bioconductor-rnaseqcomp/meta.yaml +++ b/recipes/bioconductor-rnaseqcomp/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.12.0" %} +{% set version = "1.14.0" %} {% set name = "rnaseqcomp" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 42917eebae09b1408fd29f6e929793bc + md5: 070446c7cfa966892b854ce6fdc4b6ab build: number: 0 rpaths: diff --git a/recipes/bioconductor-rnaseqdata.hnrnpc.bam.chr14/meta.yaml b/recipes/bioconductor-rnaseqdata.hnrnpc.bam.chr14/meta.yaml index 4c5f476868465..394e2918c7014 100644 --- a/recipes/bioconductor-rnaseqdata.hnrnpc.bam.chr14/meta.yaml +++ b/recipes/bioconductor-rnaseqdata.hnrnpc.bam.chr14/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "0.20.0" %} +{% set version = "0.22.0" %} {% set name = "RNAseqData.HNRNPC.bam.chr14" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,9 +10,9 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 936faad52a796dfc487f2d104bfb91bd + md5: 355b2ea49c593b0f4d0284d7c47f8686 build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ @@ -23,7 +23,7 @@ requirements: - r-base run: - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-rnaseqdata.hnrnpc.bam.chr14/post-link.sh b/recipes/bioconductor-rnaseqdata.hnrnpc.bam.chr14/post-link.sh index 07255ecd5ffd8..0bb074124ac20 100644 --- a/recipes/bioconductor-rnaseqdata.hnrnpc.bam.chr14/post-link.sh +++ b/recipes/bioconductor-rnaseqdata.hnrnpc.bam.chr14/post-link.sh @@ -1,11 +1,11 @@ #!/bin/bash -FN="RNAseqData.HNRNPC.bam.chr14_0.20.0.tar.gz" +FN="RNAseqData.HNRNPC.bam.chr14_0.22.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/experiment/src/contrib/RNAseqData.HNRNPC.bam.chr14_0.20.0.tar.gz" - "https://bioarchive.galaxyproject.org/RNAseqData.HNRNPC.bam.chr14_0.20.0.tar.gz" - "https://depot.galaxyproject.org/software/bioconductor-rnaseqdata.hnrnpc.bam.chr14/bioconductor-rnaseqdata.hnrnpc.bam.chr14_0.20.0_src_all.tar.gz" + "https://bioconductor.org/packages/3.9/data/experiment/src/contrib/RNAseqData.HNRNPC.bam.chr14_0.22.0.tar.gz" + "https://bioarchive.galaxyproject.org/RNAseqData.HNRNPC.bam.chr14_0.22.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-rnaseqdata.hnrnpc.bam.chr14/bioconductor-rnaseqdata.hnrnpc.bam.chr14_0.22.0_src_all.tar.gz" ) -MD5="936faad52a796dfc487f2d104bfb91bd" +MD5="355b2ea49c593b0f4d0284d7c47f8686" # Use a staging area in the conda dir rather than temp dirs, both to avoid # permission issues as well as to have things downloaded in a predictable @@ -16,7 +16,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-rnaseqmap/meta.yaml b/recipes/bioconductor-rnaseqmap/meta.yaml index cd3cf43b42161..93592a4ed0410 100644 --- a/recipes/bioconductor-rnaseqmap/meta.yaml +++ b/recipes/bioconductor-rnaseqmap/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "2.40.0" %} +{% set version = "2.42.0" %} {% set name = "rnaSeqMap" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: eb522f0cd8e74c18127295d42efe34fe + md5: 3534ea405fc475ddc1e002f7918f20f3 build: number: 0 rpaths: @@ -18,23 +18,23 @@ build: - lib/ requirements: host: - - 'bioconductor-biobase >=2.42.0,<2.43.0' - - 'bioconductor-deseq >=1.34.0,<1.35.0' - - 'bioconductor-edger >=3.24.0,<3.25.0' - - 'bioconductor-genomicalignments >=1.18.0,<1.19.0' - - 'bioconductor-genomicranges >=1.34.0,<1.35.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-rsamtools >=1.34.0,<1.35.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' + - 'bioconductor-deseq >=1.36.0,<1.37.0' + - 'bioconductor-edger >=3.26.0,<3.27.0' + - 'bioconductor-genomicalignments >=1.20.0,<1.21.0' + - 'bioconductor-genomicranges >=1.36.0,<1.37.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-rsamtools >=2.0.0,<2.1.0' - r-base - r-dbi run: - - 'bioconductor-biobase >=2.42.0,<2.43.0' - - 'bioconductor-deseq >=1.34.0,<1.35.0' - - 'bioconductor-edger >=3.24.0,<3.25.0' - - 'bioconductor-genomicalignments >=1.18.0,<1.19.0' - - 'bioconductor-genomicranges >=1.34.0,<1.35.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-rsamtools >=1.34.0,<1.35.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' + - 'bioconductor-deseq >=1.36.0,<1.37.0' + - 'bioconductor-edger >=3.26.0,<3.27.0' + - 'bioconductor-genomicalignments >=1.20.0,<1.21.0' + - 'bioconductor-genomicranges >=1.36.0,<1.37.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-rsamtools >=2.0.0,<2.1.0' - r-base - r-dbi build: diff --git a/recipes/bioconductor-rnaseqpower/meta.yaml b/recipes/bioconductor-rnaseqpower/meta.yaml index 6488b9dd2e7db..a25759e5884e8 100644 --- a/recipes/bioconductor-rnaseqpower/meta.yaml +++ b/recipes/bioconductor-rnaseqpower/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.22.1" %} +{% set version = "1.24.0" %} {% set name = "RNASeqPower" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 30691ae43fbcd92a8446ef972d6aad81 + md5: 128398a48bdc1d1cb763643a72e4725d build: number: 0 rpaths: diff --git a/recipes/bioconductor-rnaseqr/meta.yaml b/recipes/bioconductor-rnaseqr/meta.yaml index c674c0d422412..9a1664e5d1ecf 100644 --- a/recipes/bioconductor-rnaseqr/meta.yaml +++ b/recipes/bioconductor-rnaseqr/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.0.3" %} +{% set version = "1.2.0" %} {% set name = "RNASeqR" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 41ef8cfd67effa33cca28f4a353edbd8 + md5: e502bb689c1b44c013987e29600a0424 build: number: 0 rpaths: @@ -21,18 +21,18 @@ build: # SystemRequirements: RNASeqR only support Linux and macOS. Window is not supported. Python2 is highly recommended. If your machine is Python3, make sure '2to3' command is available. requirements: host: - - 'bioconductor-ballgown >=2.14.0,<2.15.0' - - 'bioconductor-biostrings >=2.50.0,<2.51.0' - - 'bioconductor-clusterprofiler >=3.10.0,<3.11.0' - - 'bioconductor-deseq2 >=1.22.0,<1.23.0' - - 'bioconductor-dose >=3.8.0,<3.9.0' - - 'bioconductor-edger >=3.24.0,<3.25.0' - - 'bioconductor-org.hs.eg.db >=3.7.0,<3.8.0' - - 'bioconductor-org.sc.sgd.db >=3.7.0,<3.8.0' - - 'bioconductor-pathview >=1.22.0,<1.23.0' - - 'bioconductor-rsamtools >=1.34.0,<1.35.0' - - 'bioconductor-systempiper >=1.16.0,<1.17.0' - - 'bioconductor-systempiperdata >=1.10.0,<1.11.0' + - 'bioconductor-ballgown >=2.16.0,<2.17.0' + - 'bioconductor-biostrings >=2.52.0,<2.53.0' + - 'bioconductor-clusterprofiler >=3.12.0,<3.13.0' + - 'bioconductor-deseq2 >=1.24.0,<1.25.0' + - 'bioconductor-dose >=3.10.0,<3.11.0' + - 'bioconductor-edger >=3.26.0,<3.27.0' + - 'bioconductor-org.hs.eg.db >=3.8.0,<3.9.0' + - 'bioconductor-org.sc.sgd.db >=3.8.0,<3.9.0' + - 'bioconductor-pathview >=1.24.0,<1.25.0' + - 'bioconductor-rsamtools >=2.0.0,<2.1.0' + - 'bioconductor-systempiper >=1.18.0,<1.19.0' + - 'bioconductor-systempiperdata >=1.12.0,<1.13.0' - r-base - r-corrplot - r-factoextra @@ -45,19 +45,20 @@ requirements: - r-reshape2 - r-reticulate - r-stringr + - python 2.7 run: - - 'bioconductor-ballgown >=2.14.0,<2.15.0' - - 'bioconductor-biostrings >=2.50.0,<2.51.0' - - 'bioconductor-clusterprofiler >=3.10.0,<3.11.0' - - 'bioconductor-deseq2 >=1.22.0,<1.23.0' - - 'bioconductor-dose >=3.8.0,<3.9.0' - - 'bioconductor-edger >=3.24.0,<3.25.0' - - 'bioconductor-org.hs.eg.db >=3.7.0,<3.8.0' - - 'bioconductor-org.sc.sgd.db >=3.7.0,<3.8.0' - - 'bioconductor-pathview >=1.22.0,<1.23.0' - - 'bioconductor-rsamtools >=1.34.0,<1.35.0' - - 'bioconductor-systempiper >=1.16.0,<1.17.0' - - 'bioconductor-systempiperdata >=1.10.0,<1.11.0' + - 'bioconductor-ballgown >=2.16.0,<2.17.0' + - 'bioconductor-biostrings >=2.52.0,<2.53.0' + - 'bioconductor-clusterprofiler >=3.12.0,<3.13.0' + - 'bioconductor-deseq2 >=1.24.0,<1.25.0' + - 'bioconductor-dose >=3.10.0,<3.11.0' + - 'bioconductor-edger >=3.26.0,<3.27.0' + - 'bioconductor-org.hs.eg.db >=3.8.0,<3.9.0' + - 'bioconductor-org.sc.sgd.db >=3.8.0,<3.9.0' + - 'bioconductor-pathview >=1.24.0,<1.25.0' + - 'bioconductor-rsamtools >=2.0.0,<2.1.0' + - 'bioconductor-systempiper >=1.18.0,<1.19.0' + - 'bioconductor-systempiperdata >=1.12.0,<1.13.0' - r-base - r-corrplot - r-factoextra @@ -70,6 +71,7 @@ requirements: - r-reshape2 - r-reticulate - r-stringr + - python 2.7 test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-rnaseqrdata/meta.yaml b/recipes/bioconductor-rnaseqrdata/meta.yaml index 995730a3f2964..0fe5dd550f870 100644 --- a/recipes/bioconductor-rnaseqrdata/meta.yaml +++ b/recipes/bioconductor-rnaseqrdata/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.0.0" %} +{% set version = "1.2.0" %} {% set name = "RNASeqRData" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: aac4f4cb75fd142b66b9e954ac2652e3 + md5: 48362fed1dbde122a713bc0c238b85ce build: number: 0 rpaths: @@ -23,7 +23,7 @@ requirements: - r-base run: - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-rnaseqrdata/post-link.sh b/recipes/bioconductor-rnaseqrdata/post-link.sh index 02180d718b314..af25880cf6f64 100644 --- a/recipes/bioconductor-rnaseqrdata/post-link.sh +++ b/recipes/bioconductor-rnaseqrdata/post-link.sh @@ -1,11 +1,11 @@ #!/bin/bash -FN="RNASeqRData_1.0.0.tar.gz" +FN="RNASeqRData_1.2.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/experiment/src/contrib/RNASeqRData_1.0.0.tar.gz" - "https://bioarchive.galaxyproject.org/RNASeqRData_1.0.0.tar.gz" - "https://depot.galaxyproject.org/software/bioconductor-rnaseqrdata/bioconductor-rnaseqrdata_1.0.0_src_all.tar.gz" + "https://bioconductor.org/packages/3.9/data/experiment/src/contrib/RNASeqRData_1.2.0.tar.gz" + "https://bioarchive.galaxyproject.org/RNASeqRData_1.2.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-rnaseqrdata/bioconductor-rnaseqrdata_1.2.0_src_all.tar.gz" ) -MD5="aac4f4cb75fd142b66b9e954ac2652e3" +MD5="48362fed1dbde122a713bc0c238b85ce" # Use a staging area in the conda dir rather than temp dirs, both to avoid # permission issues as well as to have things downloaded in a predictable @@ -16,7 +16,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-rnaseqsamplesize/meta.yaml b/recipes/bioconductor-rnaseqsamplesize/meta.yaml index 9adebc80ec02d..c0595cce21938 100644 --- a/recipes/bioconductor-rnaseqsamplesize/meta.yaml +++ b/recipes/bioconductor-rnaseqsamplesize/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.14.0" %} +{% set version = "1.16.0" %} {% set name = "RnaSeqSampleSize" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 1613200808429e5e11933e889b3a7221 + md5: 58a066d152246ca13c8436c1be1a17d9 build: number: 0 rpaths: @@ -19,19 +19,19 @@ build: # Suggests: BiocStyle, knitr requirements: host: - - 'bioconductor-biomart >=2.38.0,<2.39.0' - - 'bioconductor-edger >=3.24.0,<3.25.0' - - 'bioconductor-keggrest >=1.22.0,<1.23.0' - - 'bioconductor-rnaseqsamplesizedata >=1.14.0,<1.15.0' + - 'bioconductor-biomart >=2.40.0,<2.41.0' + - 'bioconductor-edger >=3.26.0,<3.27.0' + - 'bioconductor-keggrest >=1.24.0,<1.25.0' + - 'bioconductor-rnaseqsamplesizedata >=1.16.0,<1.17.0' - r-base - r-heatmap3 - r-matlab - 'r-rcpp >=0.11.2' run: - - 'bioconductor-biomart >=2.38.0,<2.39.0' - - 'bioconductor-edger >=3.24.0,<3.25.0' - - 'bioconductor-keggrest >=1.22.0,<1.23.0' - - 'bioconductor-rnaseqsamplesizedata >=1.14.0,<1.15.0' + - 'bioconductor-biomart >=2.40.0,<2.41.0' + - 'bioconductor-edger >=3.26.0,<3.27.0' + - 'bioconductor-keggrest >=1.24.0,<1.25.0' + - 'bioconductor-rnaseqsamplesizedata >=1.16.0,<1.17.0' - r-base - r-heatmap3 - r-matlab diff --git a/recipes/bioconductor-rnaseqsamplesizedata/meta.yaml b/recipes/bioconductor-rnaseqsamplesizedata/meta.yaml index cd8ed7b9d2df9..931ccdfe9eef7 100644 --- a/recipes/bioconductor-rnaseqsamplesizedata/meta.yaml +++ b/recipes/bioconductor-rnaseqsamplesizedata/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.14.0" %} +{% set version = "1.16.0" %} {% set name = "RnaSeqSampleSizeData" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: faba578ad3a43e5fb8a72961dc17eef6 + md5: b5807095357790233a3b0901e093d4e2 build: number: 0 rpaths: @@ -20,12 +20,12 @@ build: # Suggests: BiocStyle, knitr requirements: host: - - 'bioconductor-edger >=3.24.0,<3.25.0' + - 'bioconductor-edger >=3.26.0,<3.27.0' - r-base run: - - 'bioconductor-edger >=3.24.0,<3.25.0' + - 'bioconductor-edger >=3.26.0,<3.27.0' - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-rnaseqsamplesizedata/post-link.sh b/recipes/bioconductor-rnaseqsamplesizedata/post-link.sh index ea641788d603a..b78fac6dcc5fa 100644 --- a/recipes/bioconductor-rnaseqsamplesizedata/post-link.sh +++ b/recipes/bioconductor-rnaseqsamplesizedata/post-link.sh @@ -1,11 +1,11 @@ #!/bin/bash -FN="RnaSeqSampleSizeData_1.14.0.tar.gz" +FN="RnaSeqSampleSizeData_1.16.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/experiment/src/contrib/RnaSeqSampleSizeData_1.14.0.tar.gz" - "https://bioarchive.galaxyproject.org/RnaSeqSampleSizeData_1.14.0.tar.gz" - "https://depot.galaxyproject.org/software/bioconductor-rnaseqsamplesizedata/bioconductor-rnaseqsamplesizedata_1.14.0_src_all.tar.gz" + "https://bioconductor.org/packages/3.9/data/experiment/src/contrib/RnaSeqSampleSizeData_1.16.0.tar.gz" + "https://bioarchive.galaxyproject.org/RnaSeqSampleSizeData_1.16.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-rnaseqsamplesizedata/bioconductor-rnaseqsamplesizedata_1.16.0_src_all.tar.gz" ) -MD5="faba578ad3a43e5fb8a72961dc17eef6" +MD5="b5807095357790233a3b0901e093d4e2" # Use a staging area in the conda dir rather than temp dirs, both to avoid # permission issues as well as to have things downloaded in a predictable @@ -16,7 +16,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-rnbeads.hg19/meta.yaml b/recipes/bioconductor-rnbeads.hg19/meta.yaml index f855657a8e063..5531a68efe66a 100644 --- a/recipes/bioconductor-rnbeads.hg19/meta.yaml +++ b/recipes/bioconductor-rnbeads.hg19/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.14.0" %} +{% set version = "1.16.0" %} {% set name = "RnBeads.hg19" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,9 +10,9 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 4fc451cec743ae5482c90aa230bfbc05 + md5: 49124fe698070ac641edccd84738a403 build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ @@ -20,12 +20,12 @@ build: # Suggests: RnBeads requirements: host: - - 'bioconductor-genomicranges >=1.34.0,<1.35.0' + - 'bioconductor-genomicranges >=1.36.0,<1.37.0' - r-base run: - - 'bioconductor-genomicranges >=1.34.0,<1.35.0' + - 'bioconductor-genomicranges >=1.36.0,<1.37.0' - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-rnbeads.hg19/post-link.sh b/recipes/bioconductor-rnbeads.hg19/post-link.sh index e29edf50cf25e..63f038624a4bf 100644 --- a/recipes/bioconductor-rnbeads.hg19/post-link.sh +++ b/recipes/bioconductor-rnbeads.hg19/post-link.sh @@ -1,11 +1,11 @@ #!/bin/bash -FN="RnBeads.hg19_1.14.0.tar.gz" +FN="RnBeads.hg19_1.16.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/experiment/src/contrib/RnBeads.hg19_1.14.0.tar.gz" - "https://bioarchive.galaxyproject.org/RnBeads.hg19_1.14.0.tar.gz" - "https://depot.galaxyproject.org/software/bioconductor-rnbeads.hg19/bioconductor-rnbeads.hg19_1.14.0_src_all.tar.gz" + "https://bioconductor.org/packages/3.9/data/experiment/src/contrib/RnBeads.hg19_1.16.0.tar.gz" + "https://bioarchive.galaxyproject.org/RnBeads.hg19_1.16.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-rnbeads.hg19/bioconductor-rnbeads.hg19_1.16.0_src_all.tar.gz" ) -MD5="4fc451cec743ae5482c90aa230bfbc05" +MD5="49124fe698070ac641edccd84738a403" # Use a staging area in the conda dir rather than temp dirs, both to avoid # permission issues as well as to have things downloaded in a predictable @@ -16,7 +16,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-rnbeads.hg38/meta.yaml b/recipes/bioconductor-rnbeads.hg38/meta.yaml index d8d0825a87ec1..49de3a4ed0e79 100644 --- a/recipes/bioconductor-rnbeads.hg38/meta.yaml +++ b/recipes/bioconductor-rnbeads.hg38/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.14.0" %} +{% set version = "1.16.0" %} {% set name = "RnBeads.hg38" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 184f7387ab19409cbb5eee2cbe0da8df + md5: 1f69ca76421c139e33d51cd6257d61ec build: number: 0 rpaths: @@ -20,12 +20,12 @@ build: # Suggests: RnBeads requirements: host: - - 'bioconductor-genomicranges >=1.34.0,<1.35.0' + - 'bioconductor-genomicranges >=1.36.0,<1.37.0' - r-base run: - - 'bioconductor-genomicranges >=1.34.0,<1.35.0' + - 'bioconductor-genomicranges >=1.36.0,<1.37.0' - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-rnbeads.hg38/post-link.sh b/recipes/bioconductor-rnbeads.hg38/post-link.sh index d823284a02098..feff49ce74fab 100644 --- a/recipes/bioconductor-rnbeads.hg38/post-link.sh +++ b/recipes/bioconductor-rnbeads.hg38/post-link.sh @@ -1,11 +1,11 @@ #!/bin/bash -FN="RnBeads.hg38_1.14.0.tar.gz" +FN="RnBeads.hg38_1.16.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/experiment/src/contrib/RnBeads.hg38_1.14.0.tar.gz" - "https://bioarchive.galaxyproject.org/RnBeads.hg38_1.14.0.tar.gz" - "https://depot.galaxyproject.org/software/bioconductor-rnbeads.hg38/bioconductor-rnbeads.hg38_1.14.0_src_all.tar.gz" + "https://bioconductor.org/packages/3.9/data/experiment/src/contrib/RnBeads.hg38_1.16.0.tar.gz" + "https://bioarchive.galaxyproject.org/RnBeads.hg38_1.16.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-rnbeads.hg38/bioconductor-rnbeads.hg38_1.16.0_src_all.tar.gz" ) -MD5="184f7387ab19409cbb5eee2cbe0da8df" +MD5="1f69ca76421c139e33d51cd6257d61ec" # Use a staging area in the conda dir rather than temp dirs, both to avoid # permission issues as well as to have things downloaded in a predictable @@ -16,7 +16,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-rnbeads.mm10/meta.yaml b/recipes/bioconductor-rnbeads.mm10/meta.yaml index 709a14b4b07a5..fb885f5e188b7 100644 --- a/recipes/bioconductor-rnbeads.mm10/meta.yaml +++ b/recipes/bioconductor-rnbeads.mm10/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.14.0" %} +{% set version = "1.16.0" %} {% set name = "RnBeads.mm10" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 94634f0b5fcea83c3c35545a7f097251 + md5: bc59c0c33a16831ea8b9b55e17a9b3dc build: number: 0 rpaths: @@ -20,12 +20,12 @@ build: # Suggests: RnBeads requirements: host: - - 'bioconductor-genomicranges >=1.34.0,<1.35.0' + - 'bioconductor-genomicranges >=1.36.0,<1.37.0' - r-base run: - - 'bioconductor-genomicranges >=1.34.0,<1.35.0' + - 'bioconductor-genomicranges >=1.36.0,<1.37.0' - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-rnbeads.mm10/post-link.sh b/recipes/bioconductor-rnbeads.mm10/post-link.sh index 19e49e50e2af3..6c533dc6626d4 100644 --- a/recipes/bioconductor-rnbeads.mm10/post-link.sh +++ b/recipes/bioconductor-rnbeads.mm10/post-link.sh @@ -1,11 +1,11 @@ #!/bin/bash -FN="RnBeads.mm10_1.14.0.tar.gz" +FN="RnBeads.mm10_1.16.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/experiment/src/contrib/RnBeads.mm10_1.14.0.tar.gz" - "https://bioarchive.galaxyproject.org/RnBeads.mm10_1.14.0.tar.gz" - "https://depot.galaxyproject.org/software/bioconductor-rnbeads.mm10/bioconductor-rnbeads.mm10_1.14.0_src_all.tar.gz" + "https://bioconductor.org/packages/3.9/data/experiment/src/contrib/RnBeads.mm10_1.16.0.tar.gz" + "https://bioarchive.galaxyproject.org/RnBeads.mm10_1.16.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-rnbeads.mm10/bioconductor-rnbeads.mm10_1.16.0_src_all.tar.gz" ) -MD5="94634f0b5fcea83c3c35545a7f097251" +MD5="bc59c0c33a16831ea8b9b55e17a9b3dc" # Use a staging area in the conda dir rather than temp dirs, both to avoid # permission issues as well as to have things downloaded in a predictable @@ -16,7 +16,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-rnbeads.mm9/meta.yaml b/recipes/bioconductor-rnbeads.mm9/meta.yaml index c6a493b1be330..10d1b0f01d35b 100644 --- a/recipes/bioconductor-rnbeads.mm9/meta.yaml +++ b/recipes/bioconductor-rnbeads.mm9/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.14.0" %} +{% set version = "1.16.0" %} {% set name = "RnBeads.mm9" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 613c050b649b8ac4f8de05aff0df51ad + md5: bf09e958b0bbf362715e29f29f1f9089 build: number: 0 rpaths: @@ -20,12 +20,12 @@ build: # Suggests: RnBeads requirements: host: - - 'bioconductor-genomicranges >=1.34.0,<1.35.0' + - 'bioconductor-genomicranges >=1.36.0,<1.37.0' - r-base run: - - 'bioconductor-genomicranges >=1.34.0,<1.35.0' + - 'bioconductor-genomicranges >=1.36.0,<1.37.0' - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-rnbeads.mm9/post-link.sh b/recipes/bioconductor-rnbeads.mm9/post-link.sh index 86796faf87d3a..3c2fe052fa492 100644 --- a/recipes/bioconductor-rnbeads.mm9/post-link.sh +++ b/recipes/bioconductor-rnbeads.mm9/post-link.sh @@ -1,11 +1,11 @@ #!/bin/bash -FN="RnBeads.mm9_1.14.0.tar.gz" +FN="RnBeads.mm9_1.16.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/experiment/src/contrib/RnBeads.mm9_1.14.0.tar.gz" - "https://bioarchive.galaxyproject.org/RnBeads.mm9_1.14.0.tar.gz" - "https://depot.galaxyproject.org/software/bioconductor-rnbeads.mm9/bioconductor-rnbeads.mm9_1.14.0_src_all.tar.gz" + "https://bioconductor.org/packages/3.9/data/experiment/src/contrib/RnBeads.mm9_1.16.0.tar.gz" + "https://bioarchive.galaxyproject.org/RnBeads.mm9_1.16.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-rnbeads.mm9/bioconductor-rnbeads.mm9_1.16.0_src_all.tar.gz" ) -MD5="613c050b649b8ac4f8de05aff0df51ad" +MD5="bf09e958b0bbf362715e29f29f1f9089" # Use a staging area in the conda dir rather than temp dirs, both to avoid # permission issues as well as to have things downloaded in a predictable @@ -16,7 +16,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-rnbeads.rn5/meta.yaml b/recipes/bioconductor-rnbeads.rn5/meta.yaml index a22c8be62239f..442240fd51523 100644 --- a/recipes/bioconductor-rnbeads.rn5/meta.yaml +++ b/recipes/bioconductor-rnbeads.rn5/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.14.0" %} +{% set version = "1.16.0" %} {% set name = "RnBeads.rn5" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: f3a037e9bd35824a15ceaededed22b6d + md5: 1fa4dc52e604abd00c95bf29702eb9f2 build: number: 0 rpaths: @@ -20,12 +20,12 @@ build: # Suggests: RnBeads requirements: host: - - 'bioconductor-genomicranges >=1.34.0,<1.35.0' + - 'bioconductor-genomicranges >=1.36.0,<1.37.0' - r-base run: - - 'bioconductor-genomicranges >=1.34.0,<1.35.0' + - 'bioconductor-genomicranges >=1.36.0,<1.37.0' - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-rnbeads.rn5/post-link.sh b/recipes/bioconductor-rnbeads.rn5/post-link.sh index 2df2eecdf8467..89a610bcc5fd6 100644 --- a/recipes/bioconductor-rnbeads.rn5/post-link.sh +++ b/recipes/bioconductor-rnbeads.rn5/post-link.sh @@ -1,11 +1,11 @@ #!/bin/bash -FN="RnBeads.rn5_1.14.0.tar.gz" +FN="RnBeads.rn5_1.16.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/experiment/src/contrib/RnBeads.rn5_1.14.0.tar.gz" - "https://bioarchive.galaxyproject.org/RnBeads.rn5_1.14.0.tar.gz" - "https://depot.galaxyproject.org/software/bioconductor-rnbeads.rn5/bioconductor-rnbeads.rn5_1.14.0_src_all.tar.gz" + "https://bioconductor.org/packages/3.9/data/experiment/src/contrib/RnBeads.rn5_1.16.0.tar.gz" + "https://bioarchive.galaxyproject.org/RnBeads.rn5_1.16.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-rnbeads.rn5/bioconductor-rnbeads.rn5_1.16.0_src_all.tar.gz" ) -MD5="f3a037e9bd35824a15ceaededed22b6d" +MD5="1fa4dc52e604abd00c95bf29702eb9f2" # Use a staging area in the conda dir rather than temp dirs, both to avoid # permission issues as well as to have things downloaded in a predictable @@ -16,7 +16,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-rnbeads/meta.yaml b/recipes/bioconductor-rnbeads/meta.yaml index 51c22c7db73f1..2cc73ac9916fb 100644 --- a/recipes/bioconductor-rnbeads/meta.yaml +++ b/recipes/bioconductor-rnbeads/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "2.0.0" %} +{% set version = "2.2.0" %} {% set name = "RnBeads" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 41a307928bc110ab23d901037ac523e0 + md5: bbf902d71dbc1ff3140b69786eec53a8 build: number: 0 rpaths: @@ -20,13 +20,13 @@ build: # Suggests: Category, GOstats, Gviz, IlluminaHumanMethylation450kmanifest, RPMM, RefFreeEWAS, RnBeads.hg19, XML, annotate, biomaRt, foreach, doParallel, ggbio, isva, mclust, mgcv, minfi, nlme, org.Hs.eg.db, org.Mm.eg.db, org.Rn.eg.db, quadprog, rtracklayer, qvalue, sva, wateRmelon, wordcloud, qvalue, argparse, glmnet, GLAD, IlluminaHumanMethylation450kanno.ilmn12.hg19, scales, missMethyl, impute, shiny, shinyjs, plotrix, hexbin, RUnit requirements: host: - - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' - - 'bioconductor-genomicranges >=1.34.0,<1.35.0' - - 'bioconductor-illuminaio >=0.24.0,<0.25.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-limma >=3.38.0,<3.39.0' - - 'bioconductor-methylumi >=2.28.0,<2.29.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-biocgenerics >=0.30.0,<0.31.0' + - 'bioconductor-genomicranges >=1.36.0,<1.37.0' + - 'bioconductor-illuminaio >=0.26.0,<0.27.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-limma >=3.40.0,<3.41.0' + - 'bioconductor-methylumi >=2.30.0,<2.31.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' - r-base - r-cluster - r-ff @@ -38,13 +38,13 @@ requirements: - r-matrixstats - r-plyr run: - - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' - - 'bioconductor-genomicranges >=1.34.0,<1.35.0' - - 'bioconductor-illuminaio >=0.24.0,<0.25.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-limma >=3.38.0,<3.39.0' - - 'bioconductor-methylumi >=2.28.0,<2.29.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-biocgenerics >=0.30.0,<0.31.0' + - 'bioconductor-genomicranges >=1.36.0,<1.37.0' + - 'bioconductor-illuminaio >=0.26.0,<0.27.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-limma >=3.40.0,<3.41.0' + - 'bioconductor-methylumi >=2.30.0,<2.31.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' - r-base - r-cluster - r-ff diff --git a/recipes/bioconductor-rnits/meta.yaml b/recipes/bioconductor-rnits/meta.yaml index dc3eff3969cb2..1d1ccf2114879 100644 --- a/recipes/bioconductor-rnits/meta.yaml +++ b/recipes/bioconductor-rnits/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.16.0" %} +{% set version = "1.18.0" %} {% set name = "Rnits" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 47d6ced6ce9154da7718e97178123f13 + md5: f2dc9da60be5b567aa10ee868f420f76 build: number: 0 rpaths: @@ -20,21 +20,21 @@ build: # Suggests: BiocStyle, knitr, GEOquery, stringr requirements: host: - - 'bioconductor-affy >=1.60.0,<1.61.0' - - 'bioconductor-biobase >=2.42.0,<2.43.0' - - 'bioconductor-impute >=1.56.0,<1.57.0' - - 'bioconductor-limma >=3.38.0,<3.39.0' - - 'bioconductor-qvalue >=2.14.0,<2.15.0' + - 'bioconductor-affy >=1.62.0,<1.63.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' + - 'bioconductor-impute >=1.58.0,<1.59.0' + - 'bioconductor-limma >=3.40.0,<3.41.0' + - 'bioconductor-qvalue >=2.16.0,<2.17.0' - r-base - r-boot - r-ggplot2 - r-reshape2 run: - - 'bioconductor-affy >=1.60.0,<1.61.0' - - 'bioconductor-biobase >=2.42.0,<2.43.0' - - 'bioconductor-impute >=1.56.0,<1.57.0' - - 'bioconductor-limma >=3.38.0,<3.39.0' - - 'bioconductor-qvalue >=2.14.0,<2.15.0' + - 'bioconductor-affy >=1.62.0,<1.63.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' + - 'bioconductor-impute >=1.58.0,<1.59.0' + - 'bioconductor-limma >=3.40.0,<3.41.0' + - 'bioconductor-qvalue >=2.16.0,<2.17.0' - r-base - r-boot - r-ggplot2 @@ -45,7 +45,7 @@ test: about: home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: GPL-3 - summary: 'R/Bioconductor package for normalization, curve registration and inference in time course gene expression data' + summary: 'R/Bioconductor package for normalization, curve registration and inference in time course gene expression data.' extra: identifiers: - biotools:rnits diff --git a/recipes/bioconductor-rnu34.db/meta.yaml b/recipes/bioconductor-rnu34.db/meta.yaml index 73e694016d720..279c3d11627db 100644 --- a/recipes/bioconductor-rnu34.db/meta.yaml +++ b/recipes/bioconductor-rnu34.db/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.2.3" %} {% set name = "rnu34.db" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -12,7 +12,7 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: a95920bb41a2f78da82f419b245ad1a9 build: - number: 1 + number: 2 rpaths: - lib/R/lib/ - lib/ @@ -20,14 +20,14 @@ build: # Suggests: DBI, annotate, RUnit requirements: host: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' - - 'bioconductor-org.rn.eg.db >=3.7.0,<3.8.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' + - 'bioconductor-org.rn.eg.db >=3.8.0,<3.9.0' - r-base run: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' - - 'bioconductor-org.rn.eg.db >=3.7.0,<3.8.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' + - 'bioconductor-org.rn.eg.db >=3.8.0,<3.9.0' - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-rnu34.db/post-link.sh b/recipes/bioconductor-rnu34.db/post-link.sh index 2296d3a55b369..da5fd1646a944 100644 --- a/recipes/bioconductor-rnu34.db/post-link.sh +++ b/recipes/bioconductor-rnu34.db/post-link.sh @@ -1,9 +1,10 @@ #!/bin/bash FN="rnu34.db_3.2.3.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/rnu34.db_3.2.3.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/rnu34.db_3.2.3.tar.gz" "https://bioarchive.galaxyproject.org/rnu34.db_3.2.3.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-rnu34.db/bioconductor-rnu34.db_3.2.3_src_all.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-rnu34.db/bioconductor-rnu34.db_3.2.3_src_all.tar.gz" ) MD5="a95920bb41a2f78da82f419b245ad1a9" @@ -16,7 +17,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-rnu34cdf/meta.yaml b/recipes/bioconductor-rnu34cdf/meta.yaml index 5d96b63719319..25931a8ed44a7 100644 --- a/recipes/bioconductor-rnu34cdf/meta.yaml +++ b/recipes/bioconductor-rnu34cdf/meta.yaml @@ -1,6 +1,6 @@ {% set version = "2.18.0" %} {% set name = "rnu34cdf" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -12,19 +12,19 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 0f2564fc6ac89de4d779faf253f23ce3 build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' - r-base run: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-rnu34cdf/post-link.sh b/recipes/bioconductor-rnu34cdf/post-link.sh index 62d24968b6429..e27e5016650dd 100644 --- a/recipes/bioconductor-rnu34cdf/post-link.sh +++ b/recipes/bioconductor-rnu34cdf/post-link.sh @@ -1,9 +1,10 @@ #!/bin/bash FN="rnu34cdf_2.18.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/rnu34cdf_2.18.0.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/rnu34cdf_2.18.0.tar.gz" "https://bioarchive.galaxyproject.org/rnu34cdf_2.18.0.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-rnu34cdf/bioconductor-rnu34cdf_2.18.0_src_all.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-rnu34cdf/bioconductor-rnu34cdf_2.18.0_src_all.tar.gz" ) MD5="0f2564fc6ac89de4d779faf253f23ce3" @@ -16,7 +17,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-rnu34probe/meta.yaml b/recipes/bioconductor-rnu34probe/meta.yaml index ece982a658fc3..9a63669cf7c47 100644 --- a/recipes/bioconductor-rnu34probe/meta.yaml +++ b/recipes/bioconductor-rnu34probe/meta.yaml @@ -1,6 +1,6 @@ {% set version = "2.18.0" %} {% set name = "rnu34probe" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -12,19 +12,19 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: c5ef9793a437f2bf990f6e84d31da0de build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' - r-base run: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-rnu34probe/post-link.sh b/recipes/bioconductor-rnu34probe/post-link.sh index 08b0c99d8b4d8..244f2f5ffb9bb 100644 --- a/recipes/bioconductor-rnu34probe/post-link.sh +++ b/recipes/bioconductor-rnu34probe/post-link.sh @@ -1,9 +1,10 @@ #!/bin/bash FN="rnu34probe_2.18.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/rnu34probe_2.18.0.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/rnu34probe_2.18.0.tar.gz" "https://bioarchive.galaxyproject.org/rnu34probe_2.18.0.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-rnu34probe/bioconductor-rnu34probe_2.18.0_src_all.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-rnu34probe/bioconductor-rnu34probe_2.18.0_src_all.tar.gz" ) MD5="c5ef9793a437f2bf990f6e84d31da0de" @@ -16,7 +17,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-roar/meta.yaml b/recipes/bioconductor-roar/meta.yaml index 2a8399fe9a954..770c6f0069185 100644 --- a/recipes/bioconductor-roar/meta.yaml +++ b/recipes/bioconductor-roar/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.18.0" %} +{% set version = "1.20.0" %} {% set name = "roar" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: af18fe575adeb3d3cddeea46774d9a07 + md5: 92ef146820e62dc15b03d47103b7b842 build: number: 0 rpaths: @@ -20,24 +20,24 @@ build: # Suggests: RNAseqData.HNRNPC.bam.chr14, testthat requirements: host: - - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' - - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' - - 'bioconductor-genomicalignments >=1.18.0,<1.19.0' - - 'bioconductor-genomicranges >=1.34.0,<1.35.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-rtracklayer >=1.42.0,<1.43.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' - - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' + - 'bioconductor-biocgenerics >=0.30.0,<0.31.0' + - 'bioconductor-genomeinfodb >=1.20.0,<1.21.0' + - 'bioconductor-genomicalignments >=1.20.0,<1.21.0' + - 'bioconductor-genomicranges >=1.36.0,<1.37.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-rtracklayer >=1.44.0,<1.45.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' + - 'bioconductor-summarizedexperiment >=1.14.0,<1.15.0' - r-base run: - - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' - - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' - - 'bioconductor-genomicalignments >=1.18.0,<1.19.0' - - 'bioconductor-genomicranges >=1.34.0,<1.35.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-rtracklayer >=1.42.0,<1.43.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' - - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' + - 'bioconductor-biocgenerics >=0.30.0,<0.31.0' + - 'bioconductor-genomeinfodb >=1.20.0,<1.21.0' + - 'bioconductor-genomicalignments >=1.20.0,<1.21.0' + - 'bioconductor-genomicranges >=1.36.0,<1.37.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-rtracklayer >=1.44.0,<1.45.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' + - 'bioconductor-summarizedexperiment >=1.14.0,<1.15.0' - r-base test: commands: diff --git a/recipes/bioconductor-roberts2005annotation.db/meta.yaml b/recipes/bioconductor-roberts2005annotation.db/meta.yaml index 29bd2ed9c2934..1417c28073d30 100644 --- a/recipes/bioconductor-roberts2005annotation.db/meta.yaml +++ b/recipes/bioconductor-roberts2005annotation.db/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.2.3" %} {% set name = "Roberts2005Annotation.db" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -12,7 +12,7 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' md5: fb28aaf1a1e0c81cf936badc674b754a build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ @@ -20,14 +20,14 @@ build: # Suggests: DBI, annotate, RUnit requirements: host: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' - - 'bioconductor-org.hs.eg.db >=3.7.0,<3.8.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' + - 'bioconductor-org.hs.eg.db >=3.8.0,<3.9.0' - r-base run: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' - - 'bioconductor-org.hs.eg.db >=3.7.0,<3.8.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' + - 'bioconductor-org.hs.eg.db >=3.8.0,<3.9.0' - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-roberts2005annotation.db/post-link.sh b/recipes/bioconductor-roberts2005annotation.db/post-link.sh index 88fa85fbefe93..d70087f054a03 100644 --- a/recipes/bioconductor-roberts2005annotation.db/post-link.sh +++ b/recipes/bioconductor-roberts2005annotation.db/post-link.sh @@ -1,9 +1,10 @@ #!/bin/bash FN="Roberts2005Annotation.db_3.2.3.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/Roberts2005Annotation.db_3.2.3.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/Roberts2005Annotation.db_3.2.3.tar.gz" "https://bioarchive.galaxyproject.org/Roberts2005Annotation.db_3.2.3.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-roberts2005annotation.db/bioconductor-roberts2005annotation.db_3.2.3_src_all.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-roberts2005annotation.db/bioconductor-roberts2005annotation.db_3.2.3_src_all.tar.gz" ) MD5="fb28aaf1a1e0c81cf936badc674b754a" @@ -16,7 +17,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-roc/build.sh b/recipes/bioconductor-roc/build.sh index b23b57398f093..c1d13421f5f1e 100644 --- a/recipes/bioconductor-roc/build.sh +++ b/recipes/bioconductor-roc/build.sh @@ -1,11 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R echo -e "CC=$CC FC=$FC CXX=$CXX -CXXFLAGS=$CXXFLAGS CXX98=$CXX CXX11=$CXX -CXX14=$CXX" > src/Makevars -$R CMD INSTALL --build . +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-roc/meta.yaml b/recipes/bioconductor-roc/meta.yaml index 6cdca53ba90a5..b6fb58192083b 100644 --- a/recipes/bioconductor-roc/meta.yaml +++ b/recipes/bioconductor-roc/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.58.0" %} +{% set version = "1.60.0" %} {% set name = "ROC" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: d7a7d3f092af4fbba537c070c6f0efc0 + md5: e8b0381abdb97b4e05462c5aa9cb1b40 build: number: 0 rpaths: @@ -18,14 +18,14 @@ build: - lib/ # Suggests: Biobase requirements: - build: - - {{ compiler('c') }} - - {{ compiler('cxx') }} - - make host: - r-base run: - r-base + build: + - {{ compiler('c') }} + - {{ compiler('cxx') }} + - make test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-roleswitch/meta.yaml b/recipes/bioconductor-roleswitch/meta.yaml index 221b388ca3c04..0c2027001e2d8 100644 --- a/recipes/bioconductor-roleswitch/meta.yaml +++ b/recipes/bioconductor-roleswitch/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.20.0" %} +{% set version = "1.22.0" %} {% set name = "Roleswitch" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: e714b785159b4e22b1886d246a89adfc + md5: e5b8341739aaa57153f976065382980c build: number: 0 rpaths: @@ -20,20 +20,20 @@ build: # Suggests: ggplot2 requirements: host: - - 'bioconductor-biobase >=2.42.0,<2.43.0' - - 'bioconductor-biomart >=2.38.0,<2.39.0' - - 'bioconductor-biostrings >=2.50.0,<2.51.0' - - 'bioconductor-microrna >=1.40.0,<1.41.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' + - 'bioconductor-biomart >=2.40.0,<2.41.0' + - 'bioconductor-biostrings >=2.52.0,<2.53.0' + - 'bioconductor-microrna >=1.42.0,<1.43.0' - r-base - r-dbi - r-plotrix - r-pracma - r-reshape run: - - 'bioconductor-biobase >=2.42.0,<2.43.0' - - 'bioconductor-biomart >=2.38.0,<2.39.0' - - 'bioconductor-biostrings >=2.50.0,<2.51.0' - - 'bioconductor-microrna >=1.40.0,<1.41.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' + - 'bioconductor-biomart >=2.40.0,<2.41.0' + - 'bioconductor-biostrings >=2.52.0,<2.53.0' + - 'bioconductor-microrna >=1.42.0,<1.43.0' - r-base - r-dbi - r-plotrix diff --git a/recipes/bioconductor-rols/meta.yaml b/recipes/bioconductor-rols/meta.yaml index 60a8ded85cfbb..9f083d4be2ef9 100644 --- a/recipes/bioconductor-rols/meta.yaml +++ b/recipes/bioconductor-rols/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "2.10.1" %} +{% set version = "2.12.0" %} {% set name = "rols" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - sha256: 2b50d13510cf766a7e89c71be75f2833aba5950a7923bcee600de69e178f9809 + md5: 43920a7e240b734d4e4d16375cdae87f build: number: 0 rpaths: @@ -20,15 +20,15 @@ build: # Suggests: GO.db, knitr (>= 1.1.0), BiocStyle (>= 2.5.19), testthat, lubridate, DT, rmarkdown, requirements: host: - - 'bioconductor-biobase >=2.42.0,<2.43.0' - - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' + - 'bioconductor-biocgenerics >=0.30.0,<0.31.0' - r-base - r-httr - r-jsonlite - r-progress run: - - 'bioconductor-biobase >=2.42.0,<2.43.0' - - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' + - 'bioconductor-biocgenerics >=0.30.0,<0.31.0' - r-base - r-httr - r-jsonlite diff --git a/recipes/bioconductor-rontotools/meta.yaml b/recipes/bioconductor-rontotools/meta.yaml index 03f90a340f2d9..b19fc97ee9b39 100644 --- a/recipes/bioconductor-rontotools/meta.yaml +++ b/recipes/bioconductor-rontotools/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "2.10.0" %} +{% set version = "2.12.0" %} {% set name = "ROntoTools" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 75691c4b8aa9bf7bd9a948c2bd0d36e3 + md5: fbd173389451d2dba4d9cab0d6d0aa43 build: number: 0 rpaths: @@ -20,17 +20,17 @@ build: # Suggests: RUnit, BiocGenerics requirements: host: - - 'bioconductor-graph >=1.60.0,<1.61.0' - - 'bioconductor-kegggraph >=1.42.0,<1.43.0' - - 'bioconductor-keggrest >=1.22.0,<1.23.0' - - 'bioconductor-rgraphviz >=2.26.0,<2.27.0' + - 'bioconductor-graph >=1.62.0,<1.63.0' + - 'bioconductor-kegggraph >=1.44.0,<1.45.0' + - 'bioconductor-keggrest >=1.24.0,<1.25.0' + - 'bioconductor-rgraphviz >=2.28.0,<2.29.0' - r-base - r-boot run: - - 'bioconductor-graph >=1.60.0,<1.61.0' - - 'bioconductor-kegggraph >=1.42.0,<1.43.0' - - 'bioconductor-keggrest >=1.22.0,<1.23.0' - - 'bioconductor-rgraphviz >=2.26.0,<2.27.0' + - 'bioconductor-graph >=1.62.0,<1.63.0' + - 'bioconductor-kegggraph >=1.44.0,<1.45.0' + - 'bioconductor-keggrest >=1.24.0,<1.25.0' + - 'bioconductor-rgraphviz >=2.28.0,<2.29.0' - r-base - r-boot test: diff --git a/recipes/bioconductor-ropls/meta.yaml b/recipes/bioconductor-ropls/meta.yaml index 15934c7ce9fac..8d13824ffc080 100644 --- a/recipes/bioconductor-ropls/meta.yaml +++ b/recipes/bioconductor-ropls/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.14.1" %} +{% set version = "1.16.0" %} {% set name = "ropls" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,20 +10,20 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - sha256: 7be9ef97000f94cd15c382f1a84aaa289550aafd8e3ea6b5f5411256b14939bc + md5: 6f400551a42309cdab9516e3a3699310 build: number: 0 rpaths: - lib/R/lib/ - lib/ noarch: generic -# Suggests: BiocGenerics, BiocStyle, knitr, multtest, rmarkdown, RUnit +# Suggests: BiocGenerics, BiocStyle, knitr, multtest, rmarkdown, testthat requirements: host: - - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' - r-base run: - - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' - r-base test: commands: diff --git a/recipes/bioconductor-rots/meta.yaml b/recipes/bioconductor-rots/meta.yaml index e6b5d3ea35105..9adcb4eaa3d11 100644 --- a/recipes/bioconductor-rots/meta.yaml +++ b/recipes/bioconductor-rots/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.10.1" %} +{% set version = "1.12.0" %} {% set name = "ROTS" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: e6e9bfdd727d5c896135a451961e554eb8552336e578f7a362cbf743e67cafb4 + md5: 855cd21624ca96a2d869308321c15455 build: number: 0 rpaths: @@ -19,11 +19,11 @@ build: # Suggests: testthat requirements: host: - - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' - r-base - r-rcpp run: - - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' - r-base - r-rcpp build: diff --git a/recipes/bioconductor-rpa/meta.yaml b/recipes/bioconductor-rpa/meta.yaml index d7dc1837f315e..ab6210c9cfe01 100644 --- a/recipes/bioconductor-rpa/meta.yaml +++ b/recipes/bioconductor-rpa/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.38.0" %} +{% set version = "1.40.0" %} {% set name = "RPA" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,9 +10,9 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 7b2d727e06ee9202a906a384a1514c01 + md5: cdf4f68b4db2f44027ab8a2b64cd6fbc build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ @@ -20,14 +20,14 @@ build: # Suggests: affydata, knitr, parallel requirements: host: - - 'bioconductor-affy >=1.60.0,<1.61.0' - - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' - - 'bioconductor-phyloseq >=1.26.0,<1.27.0' + - 'bioconductor-affy >=1.62.0,<1.63.0' + - 'bioconductor-biocgenerics >=0.30.0,<0.31.0' + - 'bioconductor-phyloseq >=1.28.0,<1.29.0' - r-base run: - - 'bioconductor-affy >=1.60.0,<1.61.0' - - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' - - 'bioconductor-phyloseq >=1.26.0,<1.27.0' + - 'bioconductor-affy >=1.62.0,<1.63.0' + - 'bioconductor-biocgenerics >=0.30.0,<0.31.0' + - 'bioconductor-phyloseq >=1.28.0,<1.29.0' - r-base test: commands: diff --git a/recipes/bioconductor-rprotobuflib/meta.yaml b/recipes/bioconductor-rprotobuflib/meta.yaml index d89523946a37d..b776b0fe1551b 100644 --- a/recipes/bioconductor-rprotobuflib/meta.yaml +++ b/recipes/bioconductor-rprotobuflib/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.4.0" %} +{% set version = "1.6.0" %} {% set name = "RProtoBufLib" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 0aec534ff083127809f3313676f7b48e + md5: 051dff736a8a9472967af4ab7592eb75 build: number: 0 rpaths: diff --git a/recipes/bioconductor-rpsixml/meta.yaml b/recipes/bioconductor-rpsixml/meta.yaml index ee11f7c388873..6079a0dc8cdac 100644 --- a/recipes/bioconductor-rpsixml/meta.yaml +++ b/recipes/bioconductor-rpsixml/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "2.24.0" %} +{% set version = "2.26.0" %} {% set name = "RpsiXML" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 7be74bec83e9b9afd74726a08f9e435b + md5: d1e54d5af83439601aa072ed9cd9813a build: number: 0 rpaths: @@ -20,21 +20,21 @@ build: # Suggests: org.Hs.eg.db, org.Mm.eg.db, org.Dm.eg.db, org.Rn.eg.db, org.Sc.sgd.db,hom.Hs.inp.db, hom.Mm.inp.db, hom.Dm.inp.db, hom.Rn.inp.db, hom.Sc.inp.db,Rgraphviz, ppiStats, ScISI requirements: host: - - 'bioconductor-annotate >=1.60.0,<1.61.0' - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' - - 'bioconductor-biobase >=2.42.0,<2.43.0' - - 'bioconductor-graph >=1.60.0,<1.61.0' - - 'bioconductor-hypergraph >=1.54.0,<1.55.0' - - 'bioconductor-rbgl >=1.58.0,<1.59.0' + - 'bioconductor-annotate >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' + - 'bioconductor-graph >=1.62.0,<1.63.0' + - 'bioconductor-hypergraph >=1.56.0,<1.57.0' + - 'bioconductor-rbgl >=1.60.0,<1.61.0' - r-base - 'r-xml >=2.4.0' run: - - 'bioconductor-annotate >=1.60.0,<1.61.0' - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' - - 'bioconductor-biobase >=2.42.0,<2.43.0' - - 'bioconductor-graph >=1.60.0,<1.61.0' - - 'bioconductor-hypergraph >=1.54.0,<1.55.0' - - 'bioconductor-rbgl >=1.58.0,<1.59.0' + - 'bioconductor-annotate >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' + - 'bioconductor-graph >=1.62.0,<1.63.0' + - 'bioconductor-hypergraph >=1.56.0,<1.57.0' + - 'bioconductor-rbgl >=1.60.0,<1.61.0' - r-base - 'r-xml >=2.4.0' test: diff --git a/recipes/bioconductor-rpx/meta.yaml b/recipes/bioconductor-rpx/meta.yaml index d69494736fae7..5e29d59f2ddf4 100644 --- a/recipes/bioconductor-rpx/meta.yaml +++ b/recipes/bioconductor-rpx/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.18.1" %} +{% set version = "1.20.0" %} {% set name = "rpx" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - sha256: 3444cb90e07271d3b9114e49cb08a662e9ce797f426d19efd901829e39358993 + md5: 97d1e71c49b3cd2afeea2dd82b6cdfb8 build: number: 0 rpaths: diff --git a/recipes/bioconductor-rqc/meta.yaml b/recipes/bioconductor-rqc/meta.yaml index ebea1c4e87b88..343c1369f9b61 100644 --- a/recipes/bioconductor-rqc/meta.yaml +++ b/recipes/bioconductor-rqc/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.16.2" %} +{% set version = "1.18.0" %} {% set name = "Rqc" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 58558b854ed79b3950d6f83db6cbf554 + md5: 8179a6fd97cb7e253b3e9b0b4930213c build: number: 0 rpaths: @@ -19,19 +19,18 @@ build: # Suggests: testthat requirements: host: - - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' - - 'bioconductor-biocparallel >=1.16.0,<1.17.0' - - 'bioconductor-biocstyle >=2.10.0,<2.11.0' - - 'bioconductor-biostrings >=2.50.0,<2.51.0' - - 'bioconductor-biovizbase >=1.30.0,<1.31.0' - - 'bioconductor-genomicalignments >=1.18.0,<1.19.0' - - 'bioconductor-genomicfiles >=1.18.0,<1.19.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-rsamtools >=1.34.0,<1.35.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' - - 'bioconductor-shortread >=1.40.0,<1.41.0' + - 'bioconductor-biocgenerics >=0.30.0,<0.31.0' + - 'bioconductor-biocparallel >=1.18.0,<1.19.0' + - 'bioconductor-biocstyle >=2.12.0,<2.13.0' + - 'bioconductor-biostrings >=2.52.0,<2.53.0' + - 'bioconductor-biovizbase >=1.32.0,<1.33.0' + - 'bioconductor-genomicalignments >=1.20.0,<1.21.0' + - 'bioconductor-genomicfiles >=1.20.0,<1.21.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-rsamtools >=2.0.0,<2.1.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' + - 'bioconductor-shortread >=1.42.0,<1.43.0' - r-base - - r-digest - r-ggplot2 - 'r-knitr >=1.7' - r-markdown @@ -40,19 +39,18 @@ requirements: - r-reshape2 - r-shiny run: - - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' - - 'bioconductor-biocparallel >=1.16.0,<1.17.0' - - 'bioconductor-biocstyle >=2.10.0,<2.11.0' - - 'bioconductor-biostrings >=2.50.0,<2.51.0' - - 'bioconductor-biovizbase >=1.30.0,<1.31.0' - - 'bioconductor-genomicalignments >=1.18.0,<1.19.0' - - 'bioconductor-genomicfiles >=1.18.0,<1.19.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-rsamtools >=1.34.0,<1.35.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' - - 'bioconductor-shortread >=1.40.0,<1.41.0' + - 'bioconductor-biocgenerics >=0.30.0,<0.31.0' + - 'bioconductor-biocparallel >=1.18.0,<1.19.0' + - 'bioconductor-biocstyle >=2.12.0,<2.13.0' + - 'bioconductor-biostrings >=2.52.0,<2.53.0' + - 'bioconductor-biovizbase >=1.32.0,<1.33.0' + - 'bioconductor-genomicalignments >=1.20.0,<1.21.0' + - 'bioconductor-genomicfiles >=1.20.0,<1.21.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-rsamtools >=2.0.0,<2.1.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' + - 'bioconductor-shortread >=1.42.0,<1.43.0' - r-base - - r-digest - r-ggplot2 - 'r-knitr >=1.7' - r-markdown diff --git a/recipes/bioconductor-rqt/meta.yaml b/recipes/bioconductor-rqt/meta.yaml index 880c054b23c5c..089e8a79be38e 100644 --- a/recipes/bioconductor-rqt/meta.yaml +++ b/recipes/bioconductor-rqt/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.8.0" %} +{% set version = "1.10.0" %} {% set name = "rqt" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 7ce8c07744e2c70c68fb04ce7f7edab2 + md5: be2f07e3861cacc72175b7211849ba08 build: number: 0 rpaths: @@ -20,8 +20,8 @@ build: # Suggests: BiocStyle, knitr, rmarkdown requirements: host: - - 'bioconductor-ropls >=1.14.0,<1.15.0' - - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' + - 'bioconductor-ropls >=1.16.0,<1.17.0' + - 'bioconductor-summarizedexperiment >=1.14.0,<1.15.0' - r-base - r-car - r-compquadform @@ -31,8 +31,8 @@ requirements: - r-pls - r-runit run: - - 'bioconductor-ropls >=1.14.0,<1.15.0' - - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' + - 'bioconductor-ropls >=1.16.0,<1.17.0' + - 'bioconductor-summarizedexperiment >=1.14.0,<1.15.0' - r-base - r-car - r-compquadform diff --git a/recipes/bioconductor-rqubic/meta.yaml b/recipes/bioconductor-rqubic/meta.yaml index e77ccba944fda..3ae0c93775eb9 100644 --- a/recipes/bioconductor-rqubic/meta.yaml +++ b/recipes/bioconductor-rqubic/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.28.0" %} +{% set version = "1.30.0" %} {% set name = "rqubic" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 9a57a107dffeee5d00f42aaaeab6400c + md5: d76444400bdf99e353f4ff3ef6ce3597 build: number: 0 rpaths: @@ -19,13 +19,13 @@ build: # Suggests: RColorBrewer requirements: host: - - 'bioconductor-biobase >=2.42.0,<2.43.0' - - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' + - 'bioconductor-biocgenerics >=0.30.0,<0.31.0' - r-base - r-biclust run: - - 'bioconductor-biobase >=2.42.0,<2.43.0' - - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' + - 'bioconductor-biocgenerics >=0.30.0,<0.31.0' - r-base - r-biclust build: diff --git a/recipes/bioconductor-rrbsdata/meta.yaml b/recipes/bioconductor-rrbsdata/meta.yaml index 4d55287a61c61..3b041debc526c 100644 --- a/recipes/bioconductor-rrbsdata/meta.yaml +++ b/recipes/bioconductor-rrbsdata/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.2.0" %} +{% set version = "1.4.0" %} {% set name = "RRBSdata" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 0b5b0c9b0b5dba4129cc67482eb24e58 + md5: 53ac77ef644a80ac96da8a6b8ff1ae80 build: number: 0 rpaths: @@ -19,12 +19,12 @@ build: noarch: generic requirements: host: - - 'bioconductor-biseq >=1.22.0,<1.23.0' + - 'bioconductor-biseq >=1.24.0,<1.25.0' - r-base run: - - 'bioconductor-biseq >=1.22.0,<1.23.0' + - 'bioconductor-biseq >=1.24.0,<1.25.0' - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-rrbsdata/post-link.sh b/recipes/bioconductor-rrbsdata/post-link.sh index 4db532fa3745e..7e5229c7549b0 100644 --- a/recipes/bioconductor-rrbsdata/post-link.sh +++ b/recipes/bioconductor-rrbsdata/post-link.sh @@ -1,11 +1,11 @@ #!/bin/bash -FN="RRBSdata_1.2.0.tar.gz" +FN="RRBSdata_1.4.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/experiment/src/contrib/RRBSdata_1.2.0.tar.gz" - "https://bioarchive.galaxyproject.org/RRBSdata_1.2.0.tar.gz" - "https://depot.galaxyproject.org/software/bioconductor-rrbsdata/bioconductor-rrbsdata_1.2.0_src_all.tar.gz" + "https://bioconductor.org/packages/3.9/data/experiment/src/contrib/RRBSdata_1.4.0.tar.gz" + "https://bioarchive.galaxyproject.org/RRBSdata_1.4.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-rrbsdata/bioconductor-rrbsdata_1.4.0_src_all.tar.gz" ) -MD5="0b5b0c9b0b5dba4129cc67482eb24e58" +MD5="53ac77ef644a80ac96da8a6b8ff1ae80" # Use a staging area in the conda dir rather than temp dirs, both to avoid # permission issues as well as to have things downloaded in a predictable @@ -16,7 +16,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-rrdp/meta.yaml b/recipes/bioconductor-rrdp/meta.yaml index ebb942388e9e0..bd8cf3399f553 100644 --- a/recipes/bioconductor-rrdp/meta.yaml +++ b/recipes/bioconductor-rrdp/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.16.0" %} +{% set version = "1.18.0" %} {% set name = "rRDP" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 2a7b1489cb060197edd55b4a334d7cc3 + md5: 943c2acf0f62f3132d9e6a3f4c0301e5 build: number: 0 rpaths: @@ -21,11 +21,13 @@ build: # SystemRequirements: Java requirements: host: - - 'bioconductor-biostrings >=2.50.0,<2.51.0' + - 'bioconductor-biostrings >=2.52.0,<2.53.0' - r-base + - openjdk 8.* run: - - 'bioconductor-biostrings >=2.50.0,<2.51.0' + - 'bioconductor-biostrings >=2.52.0,<2.53.0' - r-base + - openjdk 8.* test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-rrdpdata/meta.yaml b/recipes/bioconductor-rrdpdata/meta.yaml index 4ba3f44b461e1..bfc5bcc09404c 100644 --- a/recipes/bioconductor-rrdpdata/meta.yaml +++ b/recipes/bioconductor-rrdpdata/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.2.0" %} +{% set version = "1.4.0" %} {% set name = "rRDPData" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 92bc7797510726832537d8aafdcb220d + md5: c86d4a780bd0a4c15addf5654bda6fc9 build: number: 0 rpaths: @@ -20,12 +20,12 @@ build: # SystemRequirements: Java requirements: host: - - 'bioconductor-rrdp >=1.16.0,<1.17.0' + - 'bioconductor-rrdp >=1.18.0,<1.19.0' - r-base run: - - 'bioconductor-rrdp >=1.16.0,<1.17.0' + - 'bioconductor-rrdp >=1.18.0,<1.19.0' - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-rrdpdata/post-link.sh b/recipes/bioconductor-rrdpdata/post-link.sh index 9e281ed4bd9e1..1569c0f9b34d6 100644 --- a/recipes/bioconductor-rrdpdata/post-link.sh +++ b/recipes/bioconductor-rrdpdata/post-link.sh @@ -1,11 +1,11 @@ #!/bin/bash -FN="rRDPData_1.2.0.tar.gz" +FN="rRDPData_1.4.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/experiment/src/contrib/rRDPData_1.2.0.tar.gz" - "https://bioarchive.galaxyproject.org/rRDPData_1.2.0.tar.gz" - "https://depot.galaxyproject.org/software/bioconductor-rrdpdata/bioconductor-rrdpdata_1.2.0_src_all.tar.gz" + "https://bioconductor.org/packages/3.9/data/experiment/src/contrib/rRDPData_1.4.0.tar.gz" + "https://bioarchive.galaxyproject.org/rRDPData_1.4.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-rrdpdata/bioconductor-rrdpdata_1.4.0_src_all.tar.gz" ) -MD5="92bc7797510726832537d8aafdcb220d" +MD5="c86d4a780bd0a4c15addf5654bda6fc9" # Use a staging area in the conda dir rather than temp dirs, both to avoid # permission issues as well as to have things downloaded in a predictable @@ -16,7 +16,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-rrho/meta.yaml b/recipes/bioconductor-rrho/meta.yaml index 7ea007dc9f375..7b7cf2a5bccd2 100644 --- a/recipes/bioconductor-rrho/meta.yaml +++ b/recipes/bioconductor-rrho/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.22.0" %} +{% set version = "1.24.0" %} {% set name = "RRHO" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 04b3d6a5bda498c229c22855b329bbb8 + md5: 7da61e5969e445ef71938c8e1f627276 build: number: 0 rpaths: diff --git a/recipes/bioconductor-rsamtools/meta.yaml b/recipes/bioconductor-rsamtools/meta.yaml index f84774d757f5f..f8551b4ecf249 100644 --- a/recipes/bioconductor-rsamtools/meta.yaml +++ b/recipes/bioconductor-rsamtools/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.34.0" %} +{% set version = "2.0.0" %} {% set name = "Rsamtools" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: cf950e0d0ff34e8464ac04a33aa86d9d + md5: e6bda2a7bdb2250ec991dd2966c31f3b build: number: 0 rpaths: @@ -19,27 +19,29 @@ build: # Suggests: GenomicAlignments, ShortRead (>= 1.19.10), GenomicFeatures, TxDb.Dmelanogaster.UCSC.dm3.ensGene, KEGG.db, TxDb.Hsapiens.UCSC.hg18.knownGene, RNAseqData.HNRNPC.bam.chr14, BSgenome.Hsapiens.UCSC.hg19, RUnit, BiocStyle requirements: host: - - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' - - 'bioconductor-biocparallel >=1.16.0,<1.17.0' - - 'bioconductor-biostrings >=2.50.0,<2.51.0' - - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' - - 'bioconductor-genomicranges >=1.34.0,<1.35.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' - - 'bioconductor-xvector >=0.22.0,<0.23.0' - - 'bioconductor-zlibbioc >=1.28.0,<1.29.0' + - 'bioconductor-biocgenerics >=0.30.0,<0.31.0' + - 'bioconductor-biocparallel >=1.18.0,<1.19.0' + - 'bioconductor-biostrings >=2.52.0,<2.53.0' + - 'bioconductor-genomeinfodb >=1.20.0,<1.21.0' + - 'bioconductor-genomicranges >=1.36.0,<1.37.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-rhtslib >=1.16.0,<1.17.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' + - 'bioconductor-xvector >=0.24.0,<0.25.0' + - 'bioconductor-zlibbioc >=1.30.0,<1.31.0' - r-base - r-bitops run: - - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' - - 'bioconductor-biocparallel >=1.16.0,<1.17.0' - - 'bioconductor-biostrings >=2.50.0,<2.51.0' - - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' - - 'bioconductor-genomicranges >=1.34.0,<1.35.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' - - 'bioconductor-xvector >=0.22.0,<0.23.0' - - 'bioconductor-zlibbioc >=1.28.0,<1.29.0' + - 'bioconductor-biocgenerics >=0.30.0,<0.31.0' + - 'bioconductor-biocparallel >=1.18.0,<1.19.0' + - 'bioconductor-biostrings >=2.52.0,<2.53.0' + - 'bioconductor-genomeinfodb >=1.20.0,<1.21.0' + - 'bioconductor-genomicranges >=1.36.0,<1.37.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-rhtslib >=1.16.0,<1.17.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' + - 'bioconductor-xvector >=0.24.0,<0.25.0' + - 'bioconductor-zlibbioc >=1.30.0,<1.31.0' - r-base - r-bitops build: @@ -52,7 +54,7 @@ test: about: home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: 'Artistic-2.0 | file LICENSE' - summary: 'This package provides an interface to the ''samtools'', ''bcftools'', and ''tabix'' utilities (see ''LICENCE'') for manipulating SAM (Sequence Alignment / Map), FASTA, binary variant call (BCF) and compressed indexed tab-delimited (tabix) files.' + summary: 'This package provides an interface to the ''samtools'', ''bcftools'', and ''tabix'' utilities for manipulating SAM (Sequence Alignment / Map), FASTA, binary variant call (BCF) and compressed indexed tab-delimited (tabix) files.' extra: identifiers: - biotools:rsamtools diff --git a/recipes/bioconductor-rsbml/meta.yaml b/recipes/bioconductor-rsbml/meta.yaml index ea540d05e4029..de44afd1bc1ac 100644 --- a/recipes/bioconductor-rsbml/meta.yaml +++ b/recipes/bioconductor-rsbml/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "2.40.0" %} +{% set version = "2.42.0" %} {% set name = "rsbml" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: c273ebb42e08542258b93904b3e132e4 + md5: 8a1462618926a032d37ad539386304bf build: number: 0 rpaths: @@ -19,15 +19,15 @@ build: # SystemRequirements: libsbml (==5.10.2) requirements: host: - - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' - - 'bioconductor-graph >=1.60.0,<1.61.0' + - 'bioconductor-biocgenerics >=0.30.0,<0.31.0' + - 'bioconductor-graph >=1.62.0,<1.63.0' - r-base - - python-libsbml + - libsbml 5.10.2 run: - - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' - - 'bioconductor-graph >=1.60.0,<1.61.0' + - 'bioconductor-biocgenerics >=0.30.0,<0.31.0' + - 'bioconductor-graph >=1.62.0,<1.63.0' - r-base - - python-libsbml + - libsbml 5.10.2 build: - {{ compiler('c') }} - {{ compiler('cxx') }} diff --git a/recipes/bioconductor-rscudo/build.sh b/recipes/bioconductor-rscudo/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-rscudo/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-rscudo/meta.yaml b/recipes/bioconductor-rscudo/meta.yaml new file mode 100644 index 0000000000000..25d2f5ebd0b05 --- /dev/null +++ b/recipes/bioconductor-rscudo/meta.yaml @@ -0,0 +1,45 @@ +{% set version = "1.0.0" %} +{% set name = "rScudo" %} +{% set bioc = "3.9" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: 12e0c91e5d423a7ec438ac459ded02b3 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: testthat, BiocStyle, knitr, rmarkdown, ALL, RCy3, caret, e1071, parallel, doParallel +requirements: + host: + - 'bioconductor-biobase >=2.44.0,<2.45.0' + - 'bioconductor-biocgenerics >=0.30.0,<0.31.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' + - 'bioconductor-summarizedexperiment >=1.14.0,<1.15.0' + - r-base + - r-igraph + - r-stringr + run: + - 'bioconductor-biobase >=2.44.0,<2.45.0' + - 'bioconductor-biocgenerics >=0.30.0,<0.31.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' + - 'bioconductor-summarizedexperiment >=1.14.0,<1.15.0' + - r-base + - r-igraph + - r-stringr +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: GPL-3 + summary: 'SCUDO (Signature-based Clustering for Diagnostic Purposes) is a rank-based method for the analysis of gene expression profiles for diagnostic and classification purposes. It is based on the identification of sample-specific gene signatures composed of the most up- and down-regulated genes for that sample. Starting from gene expression data, functions in this package identify sample-specific gene signatures and use them to build a graph of samples. In this graph samples are joined by edges if they have a similar expression profile, according to a pre-computed similarity matrix. The similarity between the expression profiles of two samples is computed using a method similar to GSEA. The graph of samples can then be used to perform community clustering or to perform supervised classification of samples in a testing set.' + diff --git a/recipes/bioconductor-rseqan/meta.yaml b/recipes/bioconductor-rseqan/meta.yaml index 744f144e8a4f6..b7310fb356221 100644 --- a/recipes/bioconductor-rseqan/meta.yaml +++ b/recipes/bioconductor-rseqan/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.2.0" %} +{% set version = "1.4.0" %} {% set name = "RSeqAn" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,24 +10,29 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 3ccf58bab71c87b4df1c300b4766d750 + md5: a758f8f9fd49a40baab1a0e875a0b33f build: number: 0 rpaths: - lib/R/lib/ - lib/ - noarch: generic -# Suggests: knitr, rmarkdown +# Suggests: knitr, rmarkdown, testthat requirements: host: - r-base + - r-rcpp run: - r-base + - r-rcpp + build: + - {{ compiler('c') }} + - {{ compiler('cxx') }} + - make test: commands: - '$R -e "library(''{{ name }}'')"' about: home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: 'BSD_3_clause + file LICENSE' - summary: 'Headers from the SeqAn C++ library for easy of usage in R.' + summary: 'Headers and some wrapper functions from the SeqAn C++ library for ease of usage in R.' diff --git a/recipes/bioconductor-rsffreader/meta.yaml b/recipes/bioconductor-rsffreader/meta.yaml index 87f77d8ed1dca..6b0c4770283a7 100644 --- a/recipes/bioconductor-rsffreader/meta.yaml +++ b/recipes/bioconductor-rsffreader/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "0.30.0" %} +{% set version = "0.31.0" %} {% set name = "rSFFreader" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: b3d8f6fb10462ef51867185257accc61 + md5: 3358439570e653a0993554a493c46025 build: number: 0 rpaths: @@ -19,18 +19,18 @@ build: # Suggests: xtable requirements: host: - - 'bioconductor-biostrings >=2.50.0,<2.51.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' - - 'bioconductor-shortread >=1.40.0,<1.41.0' - - 'bioconductor-xvector >=0.22.0,<0.23.0' + - 'bioconductor-biostrings >=2.52.0,<2.53.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' + - 'bioconductor-shortread >=1.42.0,<1.43.0' + - 'bioconductor-xvector >=0.24.0,<0.25.0' - r-base run: - - 'bioconductor-biostrings >=2.50.0,<2.51.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' - - 'bioconductor-shortread >=1.40.0,<1.41.0' - - 'bioconductor-xvector >=0.22.0,<0.23.0' + - 'bioconductor-biostrings >=2.52.0,<2.53.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' + - 'bioconductor-shortread >=1.42.0,<1.43.0' + - 'bioconductor-xvector >=0.24.0,<0.25.0' - r-base build: - {{ compiler('c') }} diff --git a/recipes/bioconductor-rsubread/meta.yaml b/recipes/bioconductor-rsubread/meta.yaml index dba4fbcf6c469..f6f3ae1165307 100644 --- a/recipes/bioconductor-rsubread/meta.yaml +++ b/recipes/bioconductor-rsubread/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.32.4" %} +{% set version = "1.34.0" %} {% set name = "Rsubread" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: 43aa5870f46c9c044f0f0eb5304deb67cf78efef3d214394165ffea3ee600fb4 + md5: 76783b46d5fabf661ac19f853fedec57 build: number: 0 rpaths: @@ -31,7 +31,7 @@ test: about: home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: GPL-3 - summary: 'Rsubread is a toolbox developed for the analyses of second and third generation sequencing data. It can be used for read mapping, read counting, SNP calling, structural variant detection and gene fusion discovery. It can be applied to all major sequencing techologies and is suitable for the analysis of both short and long reads.' + summary: 'Alignment, quantification and analysis of second and third generation sequencing data. Includes functionality for read mapping, read counting, SNP calling, structural variant detection and gene fusion discovery. Can be applied to all major sequencing techologies and to both short and long sequence reads.' extra: identifiers: - biotools:rsubread diff --git a/recipes/bioconductor-rsvsim/meta.yaml b/recipes/bioconductor-rsvsim/meta.yaml index 5e66c83a5e70b..feb0d3b9fd43c 100644 --- a/recipes/bioconductor-rsvsim/meta.yaml +++ b/recipes/bioconductor-rsvsim/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.22.0" %} +{% set version = "1.24.0" %} {% set name = "RSVSim" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 161be094cdccdb551c4e702d1c687b4b + md5: 6e49fea17a802712a961c19759ad5426 build: number: 0 rpaths: @@ -20,16 +20,16 @@ build: # Suggests: BSgenome.Hsapiens.UCSC.hg19, BSgenome.Hsapiens.UCSC.hg19.masked, MASS, rtracklayer requirements: host: - - 'bioconductor-biostrings >=2.50.0,<2.51.0' - - 'bioconductor-genomicranges >=1.34.0,<1.35.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-shortread >=1.40.0,<1.41.0' + - 'bioconductor-biostrings >=2.52.0,<2.53.0' + - 'bioconductor-genomicranges >=1.36.0,<1.37.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-shortread >=1.42.0,<1.43.0' - r-base run: - - 'bioconductor-biostrings >=2.50.0,<2.51.0' - - 'bioconductor-genomicranges >=1.34.0,<1.35.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-shortread >=1.40.0,<1.41.0' + - 'bioconductor-biostrings >=2.52.0,<2.53.0' + - 'bioconductor-genomicranges >=1.36.0,<1.37.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-shortread >=1.42.0,<1.43.0' - r-base test: commands: diff --git a/recipes/bioconductor-rta10probeset.db/meta.yaml b/recipes/bioconductor-rta10probeset.db/meta.yaml index 9b33e6b33e7ed..c000e8033b13d 100644 --- a/recipes/bioconductor-rta10probeset.db/meta.yaml +++ b/recipes/bioconductor-rta10probeset.db/meta.yaml @@ -1,6 +1,6 @@ {% set version = "8.7.0" %} {% set name = "rta10probeset.db" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -12,7 +12,7 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 62d35f5ac75a51c2ac91730fd681d031 build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ @@ -20,14 +20,14 @@ build: # Suggests: DBI, annotate, RUnit requirements: host: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' - - 'bioconductor-org.rn.eg.db >=3.7.0,<3.8.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' + - 'bioconductor-org.rn.eg.db >=3.8.0,<3.9.0' - r-base run: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' - - 'bioconductor-org.rn.eg.db >=3.7.0,<3.8.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' + - 'bioconductor-org.rn.eg.db >=3.8.0,<3.9.0' - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-rta10probeset.db/post-link.sh b/recipes/bioconductor-rta10probeset.db/post-link.sh index ead626c812a94..c332266449c3b 100644 --- a/recipes/bioconductor-rta10probeset.db/post-link.sh +++ b/recipes/bioconductor-rta10probeset.db/post-link.sh @@ -1,9 +1,10 @@ #!/bin/bash FN="rta10probeset.db_8.7.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/rta10probeset.db_8.7.0.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/rta10probeset.db_8.7.0.tar.gz" "https://bioarchive.galaxyproject.org/rta10probeset.db_8.7.0.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-rta10probeset.db/bioconductor-rta10probeset.db_8.7.0_src_all.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-rta10probeset.db/bioconductor-rta10probeset.db_8.7.0_src_all.tar.gz" ) MD5="62d35f5ac75a51c2ac91730fd681d031" @@ -16,7 +17,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-rta10transcriptcluster.db/meta.yaml b/recipes/bioconductor-rta10transcriptcluster.db/meta.yaml index b14c2eb5c1b73..7b8e27bd58c42 100644 --- a/recipes/bioconductor-rta10transcriptcluster.db/meta.yaml +++ b/recipes/bioconductor-rta10transcriptcluster.db/meta.yaml @@ -1,6 +1,6 @@ {% set version = "8.7.0" %} {% set name = "rta10transcriptcluster.db" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -12,7 +12,7 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: c6a854395aec7296ffb7d98534b112f7 build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ @@ -20,14 +20,14 @@ build: # Suggests: DBI, annotate, RUnit requirements: host: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' - - 'bioconductor-org.rn.eg.db >=3.7.0,<3.8.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' + - 'bioconductor-org.rn.eg.db >=3.8.0,<3.9.0' - r-base run: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' - - 'bioconductor-org.rn.eg.db >=3.7.0,<3.8.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' + - 'bioconductor-org.rn.eg.db >=3.8.0,<3.9.0' - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-rta10transcriptcluster.db/post-link.sh b/recipes/bioconductor-rta10transcriptcluster.db/post-link.sh index 1f826208f5173..2d8faab4bfe1b 100644 --- a/recipes/bioconductor-rta10transcriptcluster.db/post-link.sh +++ b/recipes/bioconductor-rta10transcriptcluster.db/post-link.sh @@ -1,9 +1,10 @@ #!/bin/bash FN="rta10transcriptcluster.db_8.7.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/rta10transcriptcluster.db_8.7.0.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/rta10transcriptcluster.db_8.7.0.tar.gz" "https://bioarchive.galaxyproject.org/rta10transcriptcluster.db_8.7.0.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-rta10transcriptcluster.db/bioconductor-rta10transcriptcluster.db_8.7.0_src_all.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-rta10transcriptcluster.db/bioconductor-rta10transcriptcluster.db_8.7.0_src_all.tar.gz" ) MD5="c6a854395aec7296ffb7d98534b112f7" @@ -16,7 +17,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-rtandem/meta.yaml b/recipes/bioconductor-rtandem/meta.yaml index 8c8e50dd36f5d..3b51d2a0839b5 100644 --- a/recipes/bioconductor-rtandem/meta.yaml +++ b/recipes/bioconductor-rtandem/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.22.1" %} +{% set version = "1.24.0" %} {% set name = "rTANDEM" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,9 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 3fd2dc74043c26e804771a32100d06e7 - patches: - - patch + md5: 44208a1e3fa4519631026eaaca1c6f06 build: number: 0 rpaths: diff --git a/recipes/bioconductor-rtca/meta.yaml b/recipes/bioconductor-rtca/meta.yaml index f01fd73605345..dbb5b884c9ddb 100644 --- a/recipes/bioconductor-rtca/meta.yaml +++ b/recipes/bioconductor-rtca/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.34.1" %} +{% set version = "1.36.0" %} {% set name = "RTCA" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: fcca6e0b88b6cc602611acdf30bb5da13763841c5fd4d811cd248766fc1d1342 + md5: fd9e6aa7833069a60b2bfeddf8071d19 build: number: 0 rpaths: @@ -20,12 +20,12 @@ build: # Suggests: xtable requirements: host: - - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' - r-base - r-gtools - r-rcolorbrewer run: - - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' - r-base - r-gtools - r-rcolorbrewer diff --git a/recipes/bioconductor-rtcga.clinical/meta.yaml b/recipes/bioconductor-rtcga.clinical/meta.yaml index adc7b2345cd93..6666c319f49cd 100644 --- a/recipes/bioconductor-rtcga.clinical/meta.yaml +++ b/recipes/bioconductor-rtcga.clinical/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "20151101.12.0" %} +{% set version = "20151101.14.0" %} {% set name = "RTCGA.clinical" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 8b41502e323b7992553be6850c754c40 + md5: 7d65d00fe077a509138e6234d9195cd3 build: number: 0 rpaths: @@ -20,12 +20,12 @@ build: # Suggests: knitr requirements: host: - - 'bioconductor-rtcga >=1.12.0,<1.13.0' + - 'bioconductor-rtcga >=1.14.0,<1.15.0' - r-base run: - - 'bioconductor-rtcga >=1.12.0,<1.13.0' + - 'bioconductor-rtcga >=1.14.0,<1.15.0' - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-rtcga.clinical/post-link.sh b/recipes/bioconductor-rtcga.clinical/post-link.sh index 561cd22d7d049..0ef2e456a01ff 100644 --- a/recipes/bioconductor-rtcga.clinical/post-link.sh +++ b/recipes/bioconductor-rtcga.clinical/post-link.sh @@ -1,11 +1,11 @@ #!/bin/bash -FN="RTCGA.clinical_20151101.12.0.tar.gz" +FN="RTCGA.clinical_20151101.14.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/experiment/src/contrib/RTCGA.clinical_20151101.12.0.tar.gz" - "https://bioarchive.galaxyproject.org/RTCGA.clinical_20151101.12.0.tar.gz" - "https://depot.galaxyproject.org/software/bioconductor-rtcga.clinical/bioconductor-rtcga.clinical_20151101.12.0_src_all.tar.gz" + "https://bioconductor.org/packages/3.9/data/experiment/src/contrib/RTCGA.clinical_20151101.14.0.tar.gz" + "https://bioarchive.galaxyproject.org/RTCGA.clinical_20151101.14.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-rtcga.clinical/bioconductor-rtcga.clinical_20151101.14.0_src_all.tar.gz" ) -MD5="8b41502e323b7992553be6850c754c40" +MD5="7d65d00fe077a509138e6234d9195cd3" # Use a staging area in the conda dir rather than temp dirs, both to avoid # permission issues as well as to have things downloaded in a predictable @@ -16,7 +16,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-rtcga.cnv/meta.yaml b/recipes/bioconductor-rtcga.cnv/meta.yaml index 38959272aced0..6b05b9a0aa904 100644 --- a/recipes/bioconductor-rtcga.cnv/meta.yaml +++ b/recipes/bioconductor-rtcga.cnv/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.10.0" %} +{% set version = "1.12.0" %} {% set name = "RTCGA.CNV" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 136f7ff44b65e7a2034e913694fbec9a + md5: 45de80778e2b1ff9334485bf4b86d268 build: number: 0 rpaths: @@ -20,12 +20,12 @@ build: # Suggests: knitr requirements: host: - - 'bioconductor-rtcga >=1.12.0,<1.13.0' + - 'bioconductor-rtcga >=1.14.0,<1.15.0' - r-base run: - - 'bioconductor-rtcga >=1.12.0,<1.13.0' + - 'bioconductor-rtcga >=1.14.0,<1.15.0' - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-rtcga.cnv/post-link.sh b/recipes/bioconductor-rtcga.cnv/post-link.sh index ba68cab617ba6..7f73c514104ae 100644 --- a/recipes/bioconductor-rtcga.cnv/post-link.sh +++ b/recipes/bioconductor-rtcga.cnv/post-link.sh @@ -1,11 +1,11 @@ #!/bin/bash -FN="RTCGA.CNV_1.10.0.tar.gz" +FN="RTCGA.CNV_1.12.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/experiment/src/contrib/RTCGA.CNV_1.10.0.tar.gz" - "https://bioarchive.galaxyproject.org/RTCGA.CNV_1.10.0.tar.gz" - "https://depot.galaxyproject.org/software/bioconductor-rtcga.cnv/bioconductor-rtcga.cnv_1.10.0_src_all.tar.gz" + "https://bioconductor.org/packages/3.9/data/experiment/src/contrib/RTCGA.CNV_1.12.0.tar.gz" + "https://bioarchive.galaxyproject.org/RTCGA.CNV_1.12.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-rtcga.cnv/bioconductor-rtcga.cnv_1.12.0_src_all.tar.gz" ) -MD5="136f7ff44b65e7a2034e913694fbec9a" +MD5="45de80778e2b1ff9334485bf4b86d268" # Use a staging area in the conda dir rather than temp dirs, both to avoid # permission issues as well as to have things downloaded in a predictable @@ -16,7 +16,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-rtcga.methylation/meta.yaml b/recipes/bioconductor-rtcga.methylation/meta.yaml index c0f6dbd5cf0c5..f521e3dcf1e64 100644 --- a/recipes/bioconductor-rtcga.methylation/meta.yaml +++ b/recipes/bioconductor-rtcga.methylation/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.10.0" %} +{% set version = "1.12.0" %} {% set name = "RTCGA.methylation" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 769045e7855bdfbafdb6477a419b72fc + md5: 39f7bae6e164ffe53315ddbf7ed3b168 build: number: 0 rpaths: @@ -20,12 +20,12 @@ build: # Suggests: knitr requirements: host: - - 'bioconductor-rtcga >=1.12.0,<1.13.0' + - 'bioconductor-rtcga >=1.14.0,<1.15.0' - r-base run: - - 'bioconductor-rtcga >=1.12.0,<1.13.0' + - 'bioconductor-rtcga >=1.14.0,<1.15.0' - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-rtcga.methylation/post-link.sh b/recipes/bioconductor-rtcga.methylation/post-link.sh index 3cf837d8374de..1bf2cf3231a76 100644 --- a/recipes/bioconductor-rtcga.methylation/post-link.sh +++ b/recipes/bioconductor-rtcga.methylation/post-link.sh @@ -1,11 +1,11 @@ #!/bin/bash -FN="RTCGA.methylation_1.10.0.tar.gz" +FN="RTCGA.methylation_1.12.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/experiment/src/contrib/RTCGA.methylation_1.10.0.tar.gz" - "https://bioarchive.galaxyproject.org/RTCGA.methylation_1.10.0.tar.gz" - "https://depot.galaxyproject.org/software/bioconductor-rtcga.methylation/bioconductor-rtcga.methylation_1.10.0_src_all.tar.gz" + "https://bioconductor.org/packages/3.9/data/experiment/src/contrib/RTCGA.methylation_1.12.0.tar.gz" + "https://bioarchive.galaxyproject.org/RTCGA.methylation_1.12.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-rtcga.methylation/bioconductor-rtcga.methylation_1.12.0_src_all.tar.gz" ) -MD5="769045e7855bdfbafdb6477a419b72fc" +MD5="39f7bae6e164ffe53315ddbf7ed3b168" # Use a staging area in the conda dir rather than temp dirs, both to avoid # permission issues as well as to have things downloaded in a predictable @@ -16,7 +16,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-rtcga.mirnaseq/meta.yaml b/recipes/bioconductor-rtcga.mirnaseq/meta.yaml index 01fd755e899a4..1e341188a8fb2 100644 --- a/recipes/bioconductor-rtcga.mirnaseq/meta.yaml +++ b/recipes/bioconductor-rtcga.mirnaseq/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.10.0" %} +{% set version = "1.12.0" %} {% set name = "RTCGA.miRNASeq" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 245f55ab458f95ce93485c2e108a7a81 + md5: 8b0c9b1c5fb35170ec999dc1875194a9 build: number: 0 rpaths: @@ -20,12 +20,12 @@ build: # Suggests: knitr requirements: host: - - 'bioconductor-rtcga >=1.12.0,<1.13.0' + - 'bioconductor-rtcga >=1.14.0,<1.15.0' - r-base run: - - 'bioconductor-rtcga >=1.12.0,<1.13.0' + - 'bioconductor-rtcga >=1.14.0,<1.15.0' - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-rtcga.mirnaseq/post-link.sh b/recipes/bioconductor-rtcga.mirnaseq/post-link.sh index 3f5590930ddd7..4d1de560e53a6 100644 --- a/recipes/bioconductor-rtcga.mirnaseq/post-link.sh +++ b/recipes/bioconductor-rtcga.mirnaseq/post-link.sh @@ -1,11 +1,11 @@ #!/bin/bash -FN="RTCGA.miRNASeq_1.10.0.tar.gz" +FN="RTCGA.miRNASeq_1.12.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/experiment/src/contrib/RTCGA.miRNASeq_1.10.0.tar.gz" - "https://bioarchive.galaxyproject.org/RTCGA.miRNASeq_1.10.0.tar.gz" - "https://depot.galaxyproject.org/software/bioconductor-rtcga.mirnaseq/bioconductor-rtcga.mirnaseq_1.10.0_src_all.tar.gz" + "https://bioconductor.org/packages/3.9/data/experiment/src/contrib/RTCGA.miRNASeq_1.12.0.tar.gz" + "https://bioarchive.galaxyproject.org/RTCGA.miRNASeq_1.12.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-rtcga.mirnaseq/bioconductor-rtcga.mirnaseq_1.12.0_src_all.tar.gz" ) -MD5="245f55ab458f95ce93485c2e108a7a81" +MD5="8b0c9b1c5fb35170ec999dc1875194a9" # Use a staging area in the conda dir rather than temp dirs, both to avoid # permission issues as well as to have things downloaded in a predictable @@ -16,7 +16,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-rtcga.mrna/meta.yaml b/recipes/bioconductor-rtcga.mrna/meta.yaml index 42d0fbd759e5c..6c9496bfff40c 100644 --- a/recipes/bioconductor-rtcga.mrna/meta.yaml +++ b/recipes/bioconductor-rtcga.mrna/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.10.0" %} +{% set version = "1.12.0" %} {% set name = "RTCGA.mRNA" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 7b8d58ede359d36512a5c838c23f0ce2 + md5: 87f5ceb10640bc62bf465e6d0137fd0e build: number: 0 rpaths: @@ -20,12 +20,12 @@ build: # Suggests: knitr requirements: host: - - 'bioconductor-rtcga >=1.12.0,<1.13.0' + - 'bioconductor-rtcga >=1.14.0,<1.15.0' - r-base run: - - 'bioconductor-rtcga >=1.12.0,<1.13.0' + - 'bioconductor-rtcga >=1.14.0,<1.15.0' - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-rtcga.mrna/post-link.sh b/recipes/bioconductor-rtcga.mrna/post-link.sh index bc1d5d5536aa6..ec12aea5260ec 100644 --- a/recipes/bioconductor-rtcga.mrna/post-link.sh +++ b/recipes/bioconductor-rtcga.mrna/post-link.sh @@ -1,11 +1,11 @@ #!/bin/bash -FN="RTCGA.mRNA_1.10.0.tar.gz" +FN="RTCGA.mRNA_1.12.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/experiment/src/contrib/RTCGA.mRNA_1.10.0.tar.gz" - "https://bioarchive.galaxyproject.org/RTCGA.mRNA_1.10.0.tar.gz" - "https://depot.galaxyproject.org/software/bioconductor-rtcga.mrna/bioconductor-rtcga.mrna_1.10.0_src_all.tar.gz" + "https://bioconductor.org/packages/3.9/data/experiment/src/contrib/RTCGA.mRNA_1.12.0.tar.gz" + "https://bioarchive.galaxyproject.org/RTCGA.mRNA_1.12.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-rtcga.mrna/bioconductor-rtcga.mrna_1.12.0_src_all.tar.gz" ) -MD5="7b8d58ede359d36512a5c838c23f0ce2" +MD5="87f5ceb10640bc62bf465e6d0137fd0e" # Use a staging area in the conda dir rather than temp dirs, both to avoid # permission issues as well as to have things downloaded in a predictable @@ -16,7 +16,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-rtcga.mutations/meta.yaml b/recipes/bioconductor-rtcga.mutations/meta.yaml index 9a2a71c63698d..0c4f6f021a702 100644 --- a/recipes/bioconductor-rtcga.mutations/meta.yaml +++ b/recipes/bioconductor-rtcga.mutations/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "20151101.12.0" %} +{% set version = "20151101.14.0" %} {% set name = "RTCGA.mutations" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 742f2540bf6458f5b74a670666c5510a + md5: cf3d79748430e6c9afc08dc1d28aa8a9 build: number: 0 rpaths: @@ -20,12 +20,12 @@ build: # Suggests: knitr requirements: host: - - 'bioconductor-rtcga >=1.12.0,<1.13.0' + - 'bioconductor-rtcga >=1.14.0,<1.15.0' - r-base run: - - 'bioconductor-rtcga >=1.12.0,<1.13.0' + - 'bioconductor-rtcga >=1.14.0,<1.15.0' - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-rtcga.mutations/post-link.sh b/recipes/bioconductor-rtcga.mutations/post-link.sh index 5f144571d89fc..81b4eefb93d4e 100644 --- a/recipes/bioconductor-rtcga.mutations/post-link.sh +++ b/recipes/bioconductor-rtcga.mutations/post-link.sh @@ -1,11 +1,11 @@ #!/bin/bash -FN="RTCGA.mutations_20151101.12.0.tar.gz" +FN="RTCGA.mutations_20151101.14.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/experiment/src/contrib/RTCGA.mutations_20151101.12.0.tar.gz" - "https://bioarchive.galaxyproject.org/RTCGA.mutations_20151101.12.0.tar.gz" - "https://depot.galaxyproject.org/software/bioconductor-rtcga.mutations/bioconductor-rtcga.mutations_20151101.12.0_src_all.tar.gz" + "https://bioconductor.org/packages/3.9/data/experiment/src/contrib/RTCGA.mutations_20151101.14.0.tar.gz" + "https://bioarchive.galaxyproject.org/RTCGA.mutations_20151101.14.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-rtcga.mutations/bioconductor-rtcga.mutations_20151101.14.0_src_all.tar.gz" ) -MD5="742f2540bf6458f5b74a670666c5510a" +MD5="cf3d79748430e6c9afc08dc1d28aa8a9" # Use a staging area in the conda dir rather than temp dirs, both to avoid # permission issues as well as to have things downloaded in a predictable @@ -16,7 +16,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-rtcga.pancan12/meta.yaml b/recipes/bioconductor-rtcga.pancan12/meta.yaml index c66b5e2aa1f71..a256c85c8ea54 100644 --- a/recipes/bioconductor-rtcga.pancan12/meta.yaml +++ b/recipes/bioconductor-rtcga.pancan12/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.10.0" %} +{% set version = "1.12.0" %} {% set name = "RTCGA.PANCAN12" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 182d4b50b5b54b364dcec350ee225320 + md5: d245828f779b7cf0ca7cf3263d700b15 build: number: 0 rpaths: @@ -20,12 +20,12 @@ build: # Suggests: knitr requirements: host: - - 'bioconductor-rtcga >=1.12.0,<1.13.0' + - 'bioconductor-rtcga >=1.14.0,<1.15.0' - r-base run: - - 'bioconductor-rtcga >=1.12.0,<1.13.0' + - 'bioconductor-rtcga >=1.14.0,<1.15.0' - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-rtcga.pancan12/post-link.sh b/recipes/bioconductor-rtcga.pancan12/post-link.sh index 41f2eec7a011b..bd77c1ca30e2a 100644 --- a/recipes/bioconductor-rtcga.pancan12/post-link.sh +++ b/recipes/bioconductor-rtcga.pancan12/post-link.sh @@ -1,11 +1,11 @@ #!/bin/bash -FN="RTCGA.PANCAN12_1.10.0.tar.gz" +FN="RTCGA.PANCAN12_1.12.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/experiment/src/contrib/RTCGA.PANCAN12_1.10.0.tar.gz" - "https://bioarchive.galaxyproject.org/RTCGA.PANCAN12_1.10.0.tar.gz" - "https://depot.galaxyproject.org/software/bioconductor-rtcga.pancan12/bioconductor-rtcga.pancan12_1.10.0_src_all.tar.gz" + "https://bioconductor.org/packages/3.9/data/experiment/src/contrib/RTCGA.PANCAN12_1.12.0.tar.gz" + "https://bioarchive.galaxyproject.org/RTCGA.PANCAN12_1.12.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-rtcga.pancan12/bioconductor-rtcga.pancan12_1.12.0_src_all.tar.gz" ) -MD5="182d4b50b5b54b364dcec350ee225320" +MD5="d245828f779b7cf0ca7cf3263d700b15" # Use a staging area in the conda dir rather than temp dirs, both to avoid # permission issues as well as to have things downloaded in a predictable @@ -16,7 +16,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-rtcga.rnaseq/meta.yaml b/recipes/bioconductor-rtcga.rnaseq/meta.yaml index fad57ca8b8f80..eb22adb0c0458 100644 --- a/recipes/bioconductor-rtcga.rnaseq/meta.yaml +++ b/recipes/bioconductor-rtcga.rnaseq/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "20151101.12.0" %} +{% set version = "20151101.14.0" %} {% set name = "RTCGA.rnaseq" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: bf1eb3e02b137d9ded0089bd3a2c4f38 + md5: 2a388fc3928cbbd967a5a7a742574a16 build: number: 0 rpaths: @@ -20,12 +20,12 @@ build: # Suggests: knitr requirements: host: - - 'bioconductor-rtcga >=1.12.0,<1.13.0' + - 'bioconductor-rtcga >=1.14.0,<1.15.0' - r-base run: - - 'bioconductor-rtcga >=1.12.0,<1.13.0' + - 'bioconductor-rtcga >=1.14.0,<1.15.0' - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-rtcga.rnaseq/post-link.sh b/recipes/bioconductor-rtcga.rnaseq/post-link.sh index 2e7b15fb7b4b0..bc2f3c52a176e 100644 --- a/recipes/bioconductor-rtcga.rnaseq/post-link.sh +++ b/recipes/bioconductor-rtcga.rnaseq/post-link.sh @@ -1,11 +1,11 @@ #!/bin/bash -FN="RTCGA.rnaseq_20151101.12.0.tar.gz" +FN="RTCGA.rnaseq_20151101.14.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/experiment/src/contrib/RTCGA.rnaseq_20151101.12.0.tar.gz" - "https://bioarchive.galaxyproject.org/RTCGA.rnaseq_20151101.12.0.tar.gz" - "https://depot.galaxyproject.org/software/bioconductor-rtcga.rnaseq/bioconductor-rtcga.rnaseq_20151101.12.0_src_all.tar.gz" + "https://bioconductor.org/packages/3.9/data/experiment/src/contrib/RTCGA.rnaseq_20151101.14.0.tar.gz" + "https://bioarchive.galaxyproject.org/RTCGA.rnaseq_20151101.14.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-rtcga.rnaseq/bioconductor-rtcga.rnaseq_20151101.14.0_src_all.tar.gz" ) -MD5="bf1eb3e02b137d9ded0089bd3a2c4f38" +MD5="2a388fc3928cbbd967a5a7a742574a16" # Use a staging area in the conda dir rather than temp dirs, both to avoid # permission issues as well as to have things downloaded in a predictable @@ -16,7 +16,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-rtcga.rppa/meta.yaml b/recipes/bioconductor-rtcga.rppa/meta.yaml index fe00f410d9928..2d405b1ea76b9 100644 --- a/recipes/bioconductor-rtcga.rppa/meta.yaml +++ b/recipes/bioconductor-rtcga.rppa/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.10.0" %} +{% set version = "1.12.0" %} {% set name = "RTCGA.RPPA" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 22570706e120890e3bc21225a910409b + md5: 0e74a091c00ddaabd10c8ccab0e38248 build: number: 0 rpaths: @@ -20,12 +20,12 @@ build: # Suggests: knitr requirements: host: - - 'bioconductor-rtcga >=1.12.0,<1.13.0' + - 'bioconductor-rtcga >=1.14.0,<1.15.0' - r-base run: - - 'bioconductor-rtcga >=1.12.0,<1.13.0' + - 'bioconductor-rtcga >=1.14.0,<1.15.0' - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-rtcga.rppa/post-link.sh b/recipes/bioconductor-rtcga.rppa/post-link.sh index cbb40d5127d95..110dc6131a189 100644 --- a/recipes/bioconductor-rtcga.rppa/post-link.sh +++ b/recipes/bioconductor-rtcga.rppa/post-link.sh @@ -1,11 +1,11 @@ #!/bin/bash -FN="RTCGA.RPPA_1.10.0.tar.gz" +FN="RTCGA.RPPA_1.12.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/experiment/src/contrib/RTCGA.RPPA_1.10.0.tar.gz" - "https://bioarchive.galaxyproject.org/RTCGA.RPPA_1.10.0.tar.gz" - "https://depot.galaxyproject.org/software/bioconductor-rtcga.rppa/bioconductor-rtcga.rppa_1.10.0_src_all.tar.gz" + "https://bioconductor.org/packages/3.9/data/experiment/src/contrib/RTCGA.RPPA_1.12.0.tar.gz" + "https://bioarchive.galaxyproject.org/RTCGA.RPPA_1.12.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-rtcga.rppa/bioconductor-rtcga.rppa_1.12.0_src_all.tar.gz" ) -MD5="22570706e120890e3bc21225a910409b" +MD5="0e74a091c00ddaabd10c8ccab0e38248" # Use a staging area in the conda dir rather than temp dirs, both to avoid # permission issues as well as to have things downloaded in a predictable @@ -16,7 +16,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-rtcga/meta.yaml b/recipes/bioconductor-rtcga/meta.yaml index 256892166bab7..1855cb7a47d38 100644 --- a/recipes/bioconductor-rtcga/meta.yaml +++ b/recipes/bioconductor-rtcga/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.12.1" %} +{% set version = "1.14.0" %} {% set name = "RTCGA" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 1f7114fe41af1f41baed69a17c0610f7 + md5: 197a319790d242d89d7c2a70eec3f209 build: number: 0 rpaths: diff --git a/recipes/bioconductor-rtcgatoolbox/meta.yaml b/recipes/bioconductor-rtcgatoolbox/meta.yaml index d38fc4a3d4bc5..152e1eda3847a 100644 --- a/recipes/bioconductor-rtcgatoolbox/meta.yaml +++ b/recipes/bioconductor-rtcgatoolbox/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "2.12.1" %} +{% set version = "2.14.0" %} {% set name = "RTCGAToolbox" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 9644f99d8dea390f69387baf45f5fb9a + md5: 012e8a4cbfb4a00a4828f81d516adf97 build: number: 0 rpaths: @@ -20,16 +20,16 @@ build: # Suggests: BiocStyle, Homo.sapiens, knitr, readr, rmarkdown requirements: host: - - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' - - 'bioconductor-delayedarray >=0.8.0,<0.9.0' - - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' - - 'bioconductor-genomicranges >=1.34.0,<1.35.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-limma >=3.38.0,<3.39.0' - - 'bioconductor-raggedexperiment >=1.6.0,<1.7.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' - - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' - - 'bioconductor-tcgautils >=1.2.0,<1.3.0' + - 'bioconductor-biocgenerics >=0.30.0,<0.31.0' + - 'bioconductor-delayedarray >=0.10.0,<0.11.0' + - 'bioconductor-genomeinfodb >=1.20.0,<1.21.0' + - 'bioconductor-genomicranges >=1.36.0,<1.37.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-limma >=3.40.0,<3.41.0' + - 'bioconductor-raggedexperiment >=1.8.0,<1.9.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' + - 'bioconductor-summarizedexperiment >=1.14.0,<1.15.0' + - 'bioconductor-tcgautils >=1.4.0,<1.5.0' - r-base - r-data.table - r-rcircos @@ -39,16 +39,16 @@ requirements: - r-survival - r-xml run: - - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' - - 'bioconductor-delayedarray >=0.8.0,<0.9.0' - - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' - - 'bioconductor-genomicranges >=1.34.0,<1.35.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-limma >=3.38.0,<3.39.0' - - 'bioconductor-raggedexperiment >=1.6.0,<1.7.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' - - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' - - 'bioconductor-tcgautils >=1.2.0,<1.3.0' + - 'bioconductor-biocgenerics >=0.30.0,<0.31.0' + - 'bioconductor-delayedarray >=0.10.0,<0.11.0' + - 'bioconductor-genomeinfodb >=1.20.0,<1.21.0' + - 'bioconductor-genomicranges >=1.36.0,<1.37.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-limma >=3.40.0,<3.41.0' + - 'bioconductor-raggedexperiment >=1.8.0,<1.9.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' + - 'bioconductor-summarizedexperiment >=1.14.0,<1.15.0' + - 'bioconductor-tcgautils >=1.4.0,<1.5.0' - r-base - r-data.table - r-rcircos diff --git a/recipes/bioconductor-rtn/meta.yaml b/recipes/bioconductor-rtn/meta.yaml index acf220d98cf2f..8c80073a41b79 100644 --- a/recipes/bioconductor-rtn/meta.yaml +++ b/recipes/bioconductor-rtn/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "2.6.3" %} +{% set version = "2.8.0" %} {% set name = "RTN" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: 856f2e02d2a2380649669cdc17d0014f428346a6105f401932d2271846bd1dbc + md5: ea763ba5e52bcf40fa29f0fd40cdc470 build: number: 0 rpaths: @@ -20,26 +20,26 @@ build: # Suggests: RUnit, BiocGenerics, BiocStyle, knitr, rmarkdown requirements: host: - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-limma >=3.38.0,<3.39.0' - - 'bioconductor-minet >=3.40.0,<3.41.0' - - 'bioconductor-reder >=1.30.0,<1.31.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' - - 'bioconductor-viper >=1.16.0,<1.17.0' - - 'bioconductor-summarizedexperiment' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-limma >=3.40.0,<3.41.0' + - 'bioconductor-minet >=3.42.0,<3.43.0' + - 'bioconductor-reder >=1.32.0,<1.33.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' + - 'bioconductor-summarizedexperiment >=1.14.0,<1.15.0' + - 'bioconductor-viper >=1.18.0,<1.19.0' - r-base - r-data.table - r-igraph - r-mixtools - r-snow run: - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-limma >=3.38.0,<3.39.0' - - 'bioconductor-minet >=3.40.0,<3.41.0' - - 'bioconductor-reder >=1.30.0,<1.31.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' - - 'bioconductor-viper >=1.16.0,<1.17.0' - - 'bioconductor-summarizedexperiment' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-limma >=3.40.0,<3.41.0' + - 'bioconductor-minet >=3.42.0,<3.43.0' + - 'bioconductor-reder >=1.32.0,<1.33.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' + - 'bioconductor-summarizedexperiment >=1.14.0,<1.15.0' + - 'bioconductor-viper >=1.18.0,<1.19.0' - r-base - r-data.table - r-igraph diff --git a/recipes/bioconductor-rtnduals/meta.yaml b/recipes/bioconductor-rtnduals/meta.yaml index 183af50df5cea..a88e608b39a8a 100644 --- a/recipes/bioconductor-rtnduals/meta.yaml +++ b/recipes/bioconductor-rtnduals/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.6.0" %} +{% set version = "1.8.0" %} {% set name = "RTNduals" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 302f0702b4b1e40a1b3128e3b53c1435 + md5: ddab05a413891707fc1277364d51f842 build: number: 0 rpaths: @@ -20,10 +20,10 @@ build: # Suggests: knitr, rmarkdown, BiocStyle, RUnit, BiocGenerics requirements: host: - - 'bioconductor-rtn >=2.6.0,<2.7.0' + - 'bioconductor-rtn >=2.8.0,<2.9.0' - r-base run: - - 'bioconductor-rtn >=2.6.0,<2.7.0' + - 'bioconductor-rtn >=2.8.0,<2.9.0' - r-base test: commands: diff --git a/recipes/bioconductor-rtnsurvival/meta.yaml b/recipes/bioconductor-rtnsurvival/meta.yaml index ffc2295550f71..e033598bea54f 100644 --- a/recipes/bioconductor-rtnsurvival/meta.yaml +++ b/recipes/bioconductor-rtnsurvival/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.6.0" %} +{% set version = "1.8.0" %} {% set name = "RTNsurvival" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,28 +10,36 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 917fa8f14be19050667e0e5c42c36c75 + md5: d39d0d714083d758d2e1391e6f22bac8 build: number: 0 rpaths: - lib/R/lib/ - lib/ noarch: generic -# Suggests: Fletcher2013b, pheatmap, knitr, rmarkdown, BiocStyle, RUnit, BiocGenerics +# Suggests: Fletcher2013b, knitr, rmarkdown, BiocStyle, RUnit, BiocGenerics requirements: host: - - 'bioconductor-rtn >=2.6.0,<2.7.0' - - 'bioconductor-rtnduals >=1.6.0,<1.7.0' - - 'bioconductor-viper >=1.16.0,<1.17.0' + - 'bioconductor-rtn >=2.8.0,<2.9.0' + - 'bioconductor-rtnduals >=1.8.0,<1.9.0' - r-base + - r-data.table + - r-dunn.test + - r-egg + - r-ggplot2 + - r-pheatmap - r-rcolorbrewer - r-scales - r-survival run: - - 'bioconductor-rtn >=2.6.0,<2.7.0' - - 'bioconductor-rtnduals >=1.6.0,<1.7.0' - - 'bioconductor-viper >=1.16.0,<1.17.0' + - 'bioconductor-rtn >=2.8.0,<2.9.0' + - 'bioconductor-rtnduals >=1.8.0,<1.9.0' - r-base + - r-data.table + - r-dunn.test + - r-egg + - r-ggplot2 + - r-pheatmap - r-rcolorbrewer - r-scales - r-survival diff --git a/recipes/bioconductor-rtopper/meta.yaml b/recipes/bioconductor-rtopper/meta.yaml index a3f0c55188fdc..1f955e67b8595 100644 --- a/recipes/bioconductor-rtopper/meta.yaml +++ b/recipes/bioconductor-rtopper/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.28.0" %} +{% set version = "1.30.0" %} {% set name = "RTopper" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 1248ca53c00dd4a687d62632bc75a1c5 + md5: e1c2eb8d873ba6524793846bae561bca build: number: 0 rpaths: @@ -20,14 +20,14 @@ build: # Suggests: limma, org.Hs.eg.db, KEGG.db, GO.db requirements: host: - - 'bioconductor-biobase >=2.42.0,<2.43.0' - - 'bioconductor-limma >=3.38.0,<3.39.0' - - 'bioconductor-multtest >=2.38.0,<2.39.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' + - 'bioconductor-limma >=3.40.0,<3.41.0' + - 'bioconductor-multtest >=2.40.0,<2.41.0' - r-base run: - - 'bioconductor-biobase >=2.42.0,<2.43.0' - - 'bioconductor-limma >=3.38.0,<3.39.0' - - 'bioconductor-multtest >=2.38.0,<2.39.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' + - 'bioconductor-limma >=3.40.0,<3.41.0' + - 'bioconductor-multtest >=2.40.0,<2.41.0' - r-base test: commands: diff --git a/recipes/bioconductor-rtracklayer/meta.yaml b/recipes/bioconductor-rtracklayer/meta.yaml index d6a49d7a7f852..8e1640c6b6320 100644 --- a/recipes/bioconductor-rtracklayer/meta.yaml +++ b/recipes/bioconductor-rtracklayer/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.42.1" %} +{% set version = "1.44.0" %} {% set name = "rtracklayer" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,44 +10,42 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: ed9836f8c2d85972edb8a89f0d454c95 + md5: d8f23a9769da7ea163f2cb32601bc256 build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ # Suggests: BSgenome (>= 1.33.4), humanStemCell, microRNA (>= 1.1.1), genefilter, limma, org.Hs.eg.db, hgu133plus2.db, GenomicFeatures, BSgenome.Hsapiens.UCSC.hg19, TxDb.Hsapiens.UCSC.hg19.knownGene, RUnit requirements: host: - - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' - - 'bioconductor-biostrings >=2.50.0,<2.51.0' - - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' - - 'bioconductor-genomicalignments >=1.18.0,<1.19.0' - - 'bioconductor-genomicranges >=1.34.0,<1.35.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-rsamtools >=1.34.0,<1.35.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' - - 'bioconductor-xvector >=0.22.0,<0.23.0' - - 'bioconductor-zlibbioc >=1.28.0,<1.29.0' + - 'bioconductor-biocgenerics >=0.30.0,<0.31.0' + - 'bioconductor-biostrings >=2.52.0,<2.53.0' + - 'bioconductor-genomeinfodb >=1.20.0,<1.21.0' + - 'bioconductor-genomicalignments >=1.20.0,<1.21.0' + - 'bioconductor-genomicranges >=1.36.0,<1.37.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-rsamtools >=2.0.0,<2.1.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' + - 'bioconductor-xvector >=0.24.0,<0.25.0' + - 'bioconductor-zlibbioc >=1.30.0,<1.31.0' - r-base - 'r-rcurl >=1.4-2' - 'r-xml >=1.98-0' - - openssl run: - - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' - - 'bioconductor-biostrings >=2.50.0,<2.51.0' - - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' - - 'bioconductor-genomicalignments >=1.18.0,<1.19.0' - - 'bioconductor-genomicranges >=1.34.0,<1.35.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-rsamtools >=1.34.0,<1.35.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' - - 'bioconductor-xvector >=0.22.0,<0.23.0' - - 'bioconductor-zlibbioc >=1.28.0,<1.29.0' + - 'bioconductor-biocgenerics >=0.30.0,<0.31.0' + - 'bioconductor-biostrings >=2.52.0,<2.53.0' + - 'bioconductor-genomeinfodb >=1.20.0,<1.21.0' + - 'bioconductor-genomicalignments >=1.20.0,<1.21.0' + - 'bioconductor-genomicranges >=1.36.0,<1.37.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-rsamtools >=2.0.0,<2.1.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' + - 'bioconductor-xvector >=0.24.0,<0.25.0' + - 'bioconductor-zlibbioc >=1.30.0,<1.31.0' - r-base - 'r-rcurl >=1.4-2' - 'r-xml >=1.98-0' - - openssl build: - {{ compiler('c') }} - automake diff --git a/recipes/bioconductor-rtreemix/meta.yaml b/recipes/bioconductor-rtreemix/meta.yaml index 32ffe8b26d82c..ff0aab65ee8a8 100644 --- a/recipes/bioconductor-rtreemix/meta.yaml +++ b/recipes/bioconductor-rtreemix/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.44.0" %} +{% set version = "1.46.0" %} {% set name = "Rtreemix" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 54dad4f9295a159b1358b3e09ab86f12 + md5: 8fd53d3b038779d64d0c79e458073794 build: number: 0 rpaths: @@ -19,13 +19,13 @@ build: # Suggests: Rgraphviz requirements: host: - - 'bioconductor-biobase >=2.42.0,<2.43.0' - - 'bioconductor-graph >=1.60.0,<1.61.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' + - 'bioconductor-graph >=1.62.0,<1.63.0' - r-base - r-hmisc run: - - 'bioconductor-biobase >=2.42.0,<2.43.0' - - 'bioconductor-graph >=1.60.0,<1.61.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' + - 'bioconductor-graph >=1.62.0,<1.63.0' - r-base - r-hmisc build: diff --git a/recipes/bioconductor-rtrm/meta.yaml b/recipes/bioconductor-rtrm/meta.yaml index 73d501b1404ac..b8b6cfcb16e59 100644 --- a/recipes/bioconductor-rtrm/meta.yaml +++ b/recipes/bioconductor-rtrm/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.20.0" %} +{% set version = "1.22.0" %} {% set name = "rTRM" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 2f3ca2f454102df0fb6790d11beb14e4 + md5: e58e2df0a7aa36fef947ec613787e6ff build: number: 0 rpaths: @@ -20,13 +20,13 @@ build: # Suggests: RUnit, BiocGenerics, MotifDb, graph, PWMEnrich, biomaRt, knitr, Biostrings, BSgenome.Mmusculus.UCSC.mm8.masked, org.Hs.eg.db, org.Mm.eg.db, ggplot2 requirements: host: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' - r-base - r-dbi - 'r-igraph >=1.0' - r-rsqlite run: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' - r-base - r-dbi - 'r-igraph >=1.0' diff --git a/recipes/bioconductor-rtrmui/meta.yaml b/recipes/bioconductor-rtrmui/meta.yaml index 90d882c11b273..18c2dd602a21e 100644 --- a/recipes/bioconductor-rtrmui/meta.yaml +++ b/recipes/bioconductor-rtrmui/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.20.0" %} +{% set version = "1.22.0" %} {% set name = "rTRMui" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,26 +10,26 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 1e0da9b0bbe347b9d4557d8dca91360f + md5: b68c48722a81e8e7538326a8d620bdb0 build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ noarch: generic requirements: host: - - 'bioconductor-motifdb >=1.24.0,<1.25.0' - - 'bioconductor-org.hs.eg.db >=3.7.0,<3.8.0' - - 'bioconductor-org.mm.eg.db >=3.7.0,<3.8.0' - - 'bioconductor-rtrm >=1.20.0,<1.21.0' + - 'bioconductor-motifdb >=1.26.0,<1.27.0' + - 'bioconductor-org.hs.eg.db >=3.8.0,<3.9.0' + - 'bioconductor-org.mm.eg.db >=3.8.0,<3.9.0' + - 'bioconductor-rtrm >=1.22.0,<1.23.0' - r-base - 'r-shiny >=0.9' run: - - 'bioconductor-motifdb >=1.24.0,<1.25.0' - - 'bioconductor-org.hs.eg.db >=3.7.0,<3.8.0' - - 'bioconductor-org.mm.eg.db >=3.7.0,<3.8.0' - - 'bioconductor-rtrm >=1.20.0,<1.21.0' + - 'bioconductor-motifdb >=1.26.0,<1.27.0' + - 'bioconductor-org.hs.eg.db >=3.8.0,<3.9.0' + - 'bioconductor-org.mm.eg.db >=3.8.0,<3.9.0' + - 'bioconductor-rtrm >=1.22.0,<1.23.0' - r-base - 'r-shiny >=0.9' test: diff --git a/recipes/bioconductor-rtu34.db/meta.yaml b/recipes/bioconductor-rtu34.db/meta.yaml index 86dca752a9579..c8fa9a229e8f6 100644 --- a/recipes/bioconductor-rtu34.db/meta.yaml +++ b/recipes/bioconductor-rtu34.db/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.2.3" %} {% set name = "rtu34.db" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -12,7 +12,7 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: c598b5caedc421e104e2e541f396d213 build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ @@ -20,14 +20,14 @@ build: # Suggests: DBI, annotate, RUnit requirements: host: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' - - 'bioconductor-org.rn.eg.db >=3.7.0,<3.8.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' + - 'bioconductor-org.rn.eg.db >=3.8.0,<3.9.0' - r-base run: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' - - 'bioconductor-org.rn.eg.db >=3.7.0,<3.8.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' + - 'bioconductor-org.rn.eg.db >=3.8.0,<3.9.0' - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-rtu34.db/post-link.sh b/recipes/bioconductor-rtu34.db/post-link.sh index aab924d2deb5c..0f6b1bf4d6204 100644 --- a/recipes/bioconductor-rtu34.db/post-link.sh +++ b/recipes/bioconductor-rtu34.db/post-link.sh @@ -1,9 +1,10 @@ #!/bin/bash FN="rtu34.db_3.2.3.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/rtu34.db_3.2.3.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/rtu34.db_3.2.3.tar.gz" "https://bioarchive.galaxyproject.org/rtu34.db_3.2.3.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-rtu34.db/bioconductor-rtu34.db_3.2.3_src_all.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-rtu34.db/bioconductor-rtu34.db_3.2.3_src_all.tar.gz" ) MD5="c598b5caedc421e104e2e541f396d213" @@ -16,7 +17,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-rtu34cdf/meta.yaml b/recipes/bioconductor-rtu34cdf/meta.yaml index 1cd357917115a..d0d244927500c 100644 --- a/recipes/bioconductor-rtu34cdf/meta.yaml +++ b/recipes/bioconductor-rtu34cdf/meta.yaml @@ -1,6 +1,6 @@ {% set version = "2.18.0" %} {% set name = "rtu34cdf" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -12,19 +12,19 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 317abfcca319d01eb14f16efa6d91da1 build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' - r-base run: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-rtu34cdf/post-link.sh b/recipes/bioconductor-rtu34cdf/post-link.sh index 837dbeaa79856..f2823a903e1b4 100644 --- a/recipes/bioconductor-rtu34cdf/post-link.sh +++ b/recipes/bioconductor-rtu34cdf/post-link.sh @@ -1,9 +1,10 @@ #!/bin/bash FN="rtu34cdf_2.18.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/rtu34cdf_2.18.0.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/rtu34cdf_2.18.0.tar.gz" "https://bioarchive.galaxyproject.org/rtu34cdf_2.18.0.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-rtu34cdf/bioconductor-rtu34cdf_2.18.0_src_all.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-rtu34cdf/bioconductor-rtu34cdf_2.18.0_src_all.tar.gz" ) MD5="317abfcca319d01eb14f16efa6d91da1" @@ -16,7 +17,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-rtu34probe/meta.yaml b/recipes/bioconductor-rtu34probe/meta.yaml index 662173d399bdd..361831409cf57 100644 --- a/recipes/bioconductor-rtu34probe/meta.yaml +++ b/recipes/bioconductor-rtu34probe/meta.yaml @@ -1,6 +1,6 @@ {% set version = "2.18.0" %} {% set name = "rtu34probe" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -12,19 +12,19 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 1778d857a61bf181b80b9fcf46ebd2c3 build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' - r-base run: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-rtu34probe/post-link.sh b/recipes/bioconductor-rtu34probe/post-link.sh index 4273b022bebc0..3782933abf7b6 100644 --- a/recipes/bioconductor-rtu34probe/post-link.sh +++ b/recipes/bioconductor-rtu34probe/post-link.sh @@ -1,9 +1,10 @@ #!/bin/bash FN="rtu34probe_2.18.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/rtu34probe_2.18.0.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/rtu34probe_2.18.0.tar.gz" "https://bioarchive.galaxyproject.org/rtu34probe_2.18.0.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-rtu34probe/bioconductor-rtu34probe_2.18.0_src_all.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-rtu34probe/bioconductor-rtu34probe_2.18.0_src_all.tar.gz" ) MD5="1778d857a61bf181b80b9fcf46ebd2c3" @@ -16,7 +17,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-runibic/meta.yaml b/recipes/bioconductor-runibic/meta.yaml index ef185957415ec..9cb3bdf66036b 100644 --- a/recipes/bioconductor-runibic/meta.yaml +++ b/recipes/bioconductor-runibic/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.4.0" %} +{% set version = "1.6.0" %} {% set name = "runibic" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: d0cedd151b4819370ba67bbde690ddf3 + md5: c8f01e6c053657c2965534977c011fd3 build: number: 0 rpaths: @@ -20,13 +20,13 @@ build: # SystemRequirements: C++11, GNU make requirements: host: - - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' + - 'bioconductor-summarizedexperiment >=1.14.0,<1.15.0' - r-base - r-biclust - 'r-rcpp >=0.12.12' - r-testthat run: - - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' + - 'bioconductor-summarizedexperiment >=1.14.0,<1.15.0' - r-base - r-biclust - 'r-rcpp >=0.12.12' @@ -35,7 +35,6 @@ requirements: - {{ compiler('c') }} - {{ compiler('cxx') }} - make - - llvm-openmp # [osx] test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-ruvcorr/meta.yaml b/recipes/bioconductor-ruvcorr/meta.yaml index 8982f86f1c943..a779e23c272cb 100644 --- a/recipes/bioconductor-ruvcorr/meta.yaml +++ b/recipes/bioconductor-ruvcorr/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.14.0" %} +{% set version = "1.16.0" %} {% set name = "RUVcorr" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 158715467d2a0cb8bc83af04bd6ea3b4 + md5: f6531125e9cdbe8b059809cca024282f build: number: 0 rpaths: @@ -20,8 +20,8 @@ build: # Suggests: knitr, BiocStyle, hgu133a2.db requirements: host: - - 'bioconductor-biocparallel >=1.16.0,<1.17.0' - - 'bioconductor-bladderbatch >=1.20.0,<1.21.0' + - 'bioconductor-biocparallel >=1.18.0,<1.19.0' + - 'bioconductor-bladderbatch >=1.22.0,<1.23.0' - r-base - r-corrplot - r-gridextra @@ -31,8 +31,8 @@ requirements: - r-reshape2 - r-snowfall run: - - 'bioconductor-biocparallel >=1.16.0,<1.17.0' - - 'bioconductor-bladderbatch >=1.20.0,<1.21.0' + - 'bioconductor-biocparallel >=1.18.0,<1.19.0' + - 'bioconductor-bladderbatch >=1.22.0,<1.23.0' - r-base - r-corrplot - r-gridextra diff --git a/recipes/bioconductor-ruvnormalize/meta.yaml b/recipes/bioconductor-ruvnormalize/meta.yaml index d6b64d051e2fb..1ec93a0381276 100644 --- a/recipes/bioconductor-ruvnormalize/meta.yaml +++ b/recipes/bioconductor-ruvnormalize/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.16.0" %} +{% set version = "1.18.0" %} {% set name = "RUVnormalize" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 167b64fcfec25e40893b0170df327ed1 + md5: 6dbb367a168bc1afdd02500678511afe build: number: 0 rpaths: @@ -19,12 +19,12 @@ build: noarch: generic requirements: host: - - 'bioconductor-biobase >=2.42.0,<2.43.0' - - 'bioconductor-ruvnormalizedata >=1.2.0,<1.3.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' + - 'bioconductor-ruvnormalizedata >=1.4.0,<1.5.0' - r-base run: - - 'bioconductor-biobase >=2.42.0,<2.43.0' - - 'bioconductor-ruvnormalizedata >=1.2.0,<1.3.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' + - 'bioconductor-ruvnormalizedata >=1.4.0,<1.5.0' - r-base test: commands: diff --git a/recipes/bioconductor-ruvnormalizedata/meta.yaml b/recipes/bioconductor-ruvnormalizedata/meta.yaml index a0267fc9e53b7..bc8c0a7cc63a7 100644 --- a/recipes/bioconductor-ruvnormalizedata/meta.yaml +++ b/recipes/bioconductor-ruvnormalizedata/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.2.0" %} +{% set version = "1.4.0" %} {% set name = "RUVnormalizeData" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 8c3859b5bf555e74be9d480d3ba9539b + md5: cf46437c54508c46e43c5679bdedf2b0 build: number: 0 rpaths: @@ -19,12 +19,12 @@ build: noarch: generic requirements: host: - - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' - r-base run: - - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-ruvnormalizedata/post-link.sh b/recipes/bioconductor-ruvnormalizedata/post-link.sh index 99dda191def72..eed2d16d5a9f7 100644 --- a/recipes/bioconductor-ruvnormalizedata/post-link.sh +++ b/recipes/bioconductor-ruvnormalizedata/post-link.sh @@ -1,11 +1,11 @@ #!/bin/bash -FN="RUVnormalizeData_1.2.0.tar.gz" +FN="RUVnormalizeData_1.4.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/experiment/src/contrib/RUVnormalizeData_1.2.0.tar.gz" - "https://bioarchive.galaxyproject.org/RUVnormalizeData_1.2.0.tar.gz" - "https://depot.galaxyproject.org/software/bioconductor-ruvnormalizedata/bioconductor-ruvnormalizedata_1.2.0_src_all.tar.gz" + "https://bioconductor.org/packages/3.9/data/experiment/src/contrib/RUVnormalizeData_1.4.0.tar.gz" + "https://bioarchive.galaxyproject.org/RUVnormalizeData_1.4.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-ruvnormalizedata/bioconductor-ruvnormalizedata_1.4.0_src_all.tar.gz" ) -MD5="8c3859b5bf555e74be9d480d3ba9539b" +MD5="cf46437c54508c46e43c5679bdedf2b0" # Use a staging area in the conda dir rather than temp dirs, both to avoid # permission issues as well as to have things downloaded in a predictable @@ -16,7 +16,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-ruvseq/meta.yaml b/recipes/bioconductor-ruvseq/meta.yaml index 4cd7ce9eb2b39..a0e75e548e844 100644 --- a/recipes/bioconductor-ruvseq/meta.yaml +++ b/recipes/bioconductor-ruvseq/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.16.0" %} +{% set version = "1.18.0" %} {% set name = "RUVSeq" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: ca4bcbee94ae08bc71253b2ab4b96253 + md5: bacf3b82eb0dfaf71deedde3f134197e build: number: 0 rpaths: @@ -20,15 +20,15 @@ build: # Suggests: BiocStyle, knitr, RColorBrewer, zebrafishRNASeq, DESeq2 requirements: host: - - 'bioconductor-biobase >=2.42.0,<2.43.0' - - 'bioconductor-edaseq >=2.16.0,<2.17.0' - - 'bioconductor-edger >=3.24.0,<3.25.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' + - 'bioconductor-edaseq >=2.18.0,<2.19.0' + - 'bioconductor-edger >=3.26.0,<3.27.0' - r-base - r-mass run: - - 'bioconductor-biobase >=2.42.0,<2.43.0' - - 'bioconductor-edaseq >=2.16.0,<2.17.0' - - 'bioconductor-edger >=3.24.0,<3.25.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' + - 'bioconductor-edaseq >=2.18.0,<2.19.0' + - 'bioconductor-edger >=3.26.0,<3.27.0' - r-base - r-mass test: diff --git a/recipes/bioconductor-rvs/meta.yaml b/recipes/bioconductor-rvs/meta.yaml index 5ab103063e35e..05d3ecb510de9 100644 --- a/recipes/bioconductor-rvs/meta.yaml +++ b/recipes/bioconductor-rvs/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.4.0" %} +{% set version = "1.6.0" %} {% set name = "RVS" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,23 +10,25 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 187862c0e1c2f0e21da5cb0012793d72 + md5: f291c45d810295d1c0807c8c15b04fab build: number: 0 rpaths: - lib/R/lib/ - lib/ noarch: generic -# Suggests: knitr, testthat, rmarkdown, BiocStyle +# Suggests: knitr, testthat, rmarkdown, BiocStyle, VariantAnnotation requirements: host: - - 'bioconductor-snpstats >=1.32.0,<1.33.0' + - 'bioconductor-snpstats >=1.34.0,<1.35.0' - r-base + - r-genlib - r-grain - r-kinship2 run: - - 'bioconductor-snpstats >=1.32.0,<1.33.0' + - 'bioconductor-snpstats >=1.34.0,<1.35.0' - r-base + - r-genlib - r-grain - r-kinship2 test: diff --git a/recipes/bioconductor-rwgcod.db/meta.yaml b/recipes/bioconductor-rwgcod.db/meta.yaml index ea63cb8f3147d..873ce92e949b5 100644 --- a/recipes/bioconductor-rwgcod.db/meta.yaml +++ b/recipes/bioconductor-rwgcod.db/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.4.0" %} {% set name = "rwgcod.db" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -12,7 +12,7 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: c8d2fa81b6f03c4ee629a0883431e5fd build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ @@ -20,14 +20,14 @@ build: # Suggests: annotate, RUnit requirements: host: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' - - 'bioconductor-org.rn.eg.db >=3.7.0,<3.8.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' + - 'bioconductor-org.rn.eg.db >=3.8.0,<3.9.0' - r-base run: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' - - 'bioconductor-org.rn.eg.db >=3.7.0,<3.8.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' + - 'bioconductor-org.rn.eg.db >=3.8.0,<3.9.0' - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-rwgcod.db/post-link.sh b/recipes/bioconductor-rwgcod.db/post-link.sh index 425f4a4fc3f44..ecc9d255f1261 100644 --- a/recipes/bioconductor-rwgcod.db/post-link.sh +++ b/recipes/bioconductor-rwgcod.db/post-link.sh @@ -1,9 +1,10 @@ #!/bin/bash FN="rwgcod.db_3.4.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/rwgcod.db_3.4.0.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/rwgcod.db_3.4.0.tar.gz" "https://bioarchive.galaxyproject.org/rwgcod.db_3.4.0.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-rwgcod.db/bioconductor-rwgcod.db_3.4.0_src_all.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-rwgcod.db/bioconductor-rwgcod.db_3.4.0_src_all.tar.gz" ) MD5="c8d2fa81b6f03c4ee629a0883431e5fd" @@ -16,7 +17,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-rwikipathways/meta.yaml b/recipes/bioconductor-rwikipathways/meta.yaml index 92727e87503ac..9a0306f03ae5e 100644 --- a/recipes/bioconductor-rwikipathways/meta.yaml +++ b/recipes/bioconductor-rwikipathways/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.2.0" %} +{% set version = "1.4.0" %} {% set name = "rWikiPathways" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 1c55c4213a1cd8da4a73083fa4f3c1b0 + md5: bab46f1a1f44222d92153de25d80308f build: number: 0 rpaths: @@ -24,11 +24,13 @@ requirements: - r-catools - r-httr - r-rjsonio + - r-xml run: - r-base - r-catools - r-httr - r-rjsonio + - r-xml test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-s4vectors/meta.yaml b/recipes/bioconductor-s4vectors/meta.yaml index f0370f7b15a2a..5826c1a1e47f8 100644 --- a/recipes/bioconductor-s4vectors/meta.yaml +++ b/recipes/bioconductor-s4vectors/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "0.20.1" %} +{% set version = "0.22.0" %} {% set name = "S4Vectors" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 688d781fb673cfb94e9f1c164be1e24e + md5: 95ceabaa2d81b1d5e3fdc1238789210e build: number: 0 rpaths: @@ -19,10 +19,10 @@ build: # Suggests: IRanges, GenomicRanges, SummarizedExperiment, Matrix, DelayedArray, ShortRead, graph, data.table, RUnit, BiocStyle requirements: host: - - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' + - 'bioconductor-biocgenerics >=0.30.0,<0.31.0' - r-base run: - - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' + - 'bioconductor-biocgenerics >=0.30.0,<0.31.0' - r-base build: - {{ compiler('c') }} diff --git a/recipes/bioconductor-safe/meta.yaml b/recipes/bioconductor-safe/meta.yaml index acfe58db50896..2529efb2fa29b 100644 --- a/recipes/bioconductor-safe/meta.yaml +++ b/recipes/bioconductor-safe/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "3.22.0" %} +{% set version = "3.24.0" %} {% set name = "safe" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 130b1a1220cb3703b2fc990ae2059378 + md5: 25aa7f520ac63c8278502724744081a5 build: number: 0 rpaths: @@ -20,13 +20,13 @@ build: # Suggests: GO.db, PFAM.db, reactome.db, hgu133a.db, breastCancerUPP, survival, foreach, doRNG, Rgraphviz, GOstats requirements: host: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' - - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' - r-base - r-sparsem run: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' - - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' - r-base - r-sparsem test: diff --git a/recipes/bioconductor-sagenhaft/meta.yaml b/recipes/bioconductor-sagenhaft/meta.yaml index 550b53bbb7ec4..062008d79ecca 100644 --- a/recipes/bioconductor-sagenhaft/meta.yaml +++ b/recipes/bioconductor-sagenhaft/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.52.0" %} +{% set version = "1.54.0" %} {% set name = "sagenhaft" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 582c5897ff5d4d7395a42f4655e33962 + md5: c7bc38a2be0fbefcaa1574b9eabc4e37 build: number: 0 rpaths: diff --git a/recipes/bioconductor-sagx/meta.yaml b/recipes/bioconductor-sagx/meta.yaml index 2a6ebb3cdfb54..da5b8505a9cdc 100644 --- a/recipes/bioconductor-sagx/meta.yaml +++ b/recipes/bioconductor-sagx/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.56.0" %} +{% set version = "1.58.0" %} {% set name = "SAGx" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 3b4d03837b6be876bd3969c8f0d2a04f + md5: 492ec5dae06e1ee6efd1727720220d18 build: number: 0 rpaths: @@ -19,12 +19,12 @@ build: # Suggests: KEGG.db, hu6800.db, MASS requirements: host: - - 'bioconductor-biobase >=2.42.0,<2.43.0' - - 'bioconductor-multtest >=2.38.0,<2.39.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' + - 'bioconductor-multtest >=2.40.0,<2.41.0' - r-base run: - - 'bioconductor-biobase >=2.42.0,<2.43.0' - - 'bioconductor-multtest >=2.38.0,<2.39.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' + - 'bioconductor-multtest >=2.40.0,<2.41.0' - r-base build: - {{ compiler('c') }} diff --git a/recipes/bioconductor-samexplorer/meta.yaml b/recipes/bioconductor-samexplorer/meta.yaml index cbbf100fb91fb..7a89e5f179ab2 100644 --- a/recipes/bioconductor-samexplorer/meta.yaml +++ b/recipes/bioconductor-samexplorer/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.6.1" %} +{% set version = "1.8.0" %} {% set name = "samExploreR" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: eda95a94e71706d054eeb5e63087084ad4f0deb326be20cc17e248a24193f861 + md5: b474822f7c070af3860e1d6099963b91 build: number: 0 rpaths: @@ -20,15 +20,15 @@ build: # Suggests: BiocStyle,RUnit,BiocGenerics,Matrix requirements: host: - - 'bioconductor-edger >=3.24.0,<3.25.0' - - 'bioconductor-rnaseqdata.hnrnpc.bam.chr14 >=0.20.0,<0.21.0' - - 'bioconductor-rsubread >=1.32.0,<1.33.0' + - 'bioconductor-edger >=3.26.0,<3.27.0' + - 'bioconductor-rnaseqdata.hnrnpc.bam.chr14 >=0.22.0,<0.23.0' + - 'bioconductor-rsubread >=1.34.0,<1.35.0' - r-base - r-ggplot2 run: - - 'bioconductor-edger >=3.24.0,<3.25.0' - - 'bioconductor-rnaseqdata.hnrnpc.bam.chr14 >=0.20.0,<0.21.0' - - 'bioconductor-rsubread >=1.32.0,<1.33.0' + - 'bioconductor-edger >=3.26.0,<3.27.0' + - 'bioconductor-rnaseqdata.hnrnpc.bam.chr14 >=0.22.0,<0.23.0' + - 'bioconductor-rsubread >=1.34.0,<1.35.0' - r-base - r-ggplot2 test: diff --git a/recipes/bioconductor-sampleclassifier/meta.yaml b/recipes/bioconductor-sampleclassifier/meta.yaml index baedfc96dfb4c..0be3a3dd64b68 100644 --- a/recipes/bioconductor-sampleclassifier/meta.yaml +++ b/recipes/bioconductor-sampleclassifier/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.6.0" %} +{% set version = "1.8.0" %} {% set name = "sampleClassifier" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 605d9bcc34512ef553d246c2168e79a3 + md5: 62a530a8913a194cd3d1ef7f597c0c30 build: number: 0 rpaths: @@ -20,16 +20,16 @@ build: # Suggests: sampleClassifierData, BiocStyle, hgu133a.db, hgu133plus2.db requirements: host: - - 'bioconductor-annotate >=1.60.0,<1.61.0' - - 'bioconductor-mgfm >=1.16.0,<1.17.0' - - 'bioconductor-mgfr >=1.8.0,<1.9.0' + - 'bioconductor-annotate >=1.62.0,<1.63.0' + - 'bioconductor-mgfm >=1.18.0,<1.19.0' + - 'bioconductor-mgfr >=1.10.0,<1.11.0' - r-base - r-e1071 - r-ggplot2 run: - - 'bioconductor-annotate >=1.60.0,<1.61.0' - - 'bioconductor-mgfm >=1.16.0,<1.17.0' - - 'bioconductor-mgfr >=1.8.0,<1.9.0' + - 'bioconductor-annotate >=1.62.0,<1.63.0' + - 'bioconductor-mgfm >=1.18.0,<1.19.0' + - 'bioconductor-mgfr >=1.10.0,<1.11.0' - r-base - r-e1071 - r-ggplot2 diff --git a/recipes/bioconductor-sampleclassifierdata/meta.yaml b/recipes/bioconductor-sampleclassifierdata/meta.yaml index 99f2a9d3eec97..26aacb0a666f3 100644 --- a/recipes/bioconductor-sampleclassifierdata/meta.yaml +++ b/recipes/bioconductor-sampleclassifierdata/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.6.0" %} +{% set version = "1.8.0" %} {% set name = "sampleClassifierData" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 82f2071bfa8b19d3909760e813dfa760 + md5: 6fcc9c1340d095ffb07ab865540dbe72 build: number: 0 rpaths: @@ -20,12 +20,12 @@ build: # Suggests: BiocStyle requirements: host: - - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' + - 'bioconductor-summarizedexperiment >=1.14.0,<1.15.0' - r-base run: - - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' + - 'bioconductor-summarizedexperiment >=1.14.0,<1.15.0' - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-sampleclassifierdata/post-link.sh b/recipes/bioconductor-sampleclassifierdata/post-link.sh index 7ae2155f81e6f..b1822e1c104d7 100644 --- a/recipes/bioconductor-sampleclassifierdata/post-link.sh +++ b/recipes/bioconductor-sampleclassifierdata/post-link.sh @@ -1,11 +1,11 @@ #!/bin/bash -FN="sampleClassifierData_1.6.0.tar.gz" +FN="sampleClassifierData_1.8.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/experiment/src/contrib/sampleClassifierData_1.6.0.tar.gz" - "https://bioarchive.galaxyproject.org/sampleClassifierData_1.6.0.tar.gz" - "https://depot.galaxyproject.org/software/bioconductor-sampleclassifierdata/bioconductor-sampleclassifierdata_1.6.0_src_all.tar.gz" + "https://bioconductor.org/packages/3.9/data/experiment/src/contrib/sampleClassifierData_1.8.0.tar.gz" + "https://bioarchive.galaxyproject.org/sampleClassifierData_1.8.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-sampleclassifierdata/bioconductor-sampleclassifierdata_1.8.0_src_all.tar.gz" ) -MD5="82f2071bfa8b19d3909760e813dfa760" +MD5="6fcc9c1340d095ffb07ab865540dbe72" # Use a staging area in the conda dir rather than temp dirs, both to avoid # permission issues as well as to have things downloaded in a predictable @@ -16,7 +16,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-samspectral/meta.yaml b/recipes/bioconductor-samspectral/meta.yaml index 6cdd463366c46..3ebbf7205f2e5 100644 --- a/recipes/bioconductor-samspectral/meta.yaml +++ b/recipes/bioconductor-samspectral/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.36.1" %} +{% set version = "1.38.0" %} {% set name = "SamSPECTRAL" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: 3db3d828dfc14466b2e08d4e8bf8505044e8aa34422736024b79870a82bdb5a6 + md5: 57b8e4af80ec16503f640076e448df6a build: number: 0 rpaths: diff --git a/recipes/bioconductor-sangerseqr/meta.yaml b/recipes/bioconductor-sangerseqr/meta.yaml index 75744f6956bee..f73180e8e1e4b 100644 --- a/recipes/bioconductor-sangerseqr/meta.yaml +++ b/recipes/bioconductor-sangerseqr/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.18.0" %} +{% set version = "1.20.0" %} {% set name = "sangerseqR" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: a9087a41aa05c312e686f3b5578f82ab + md5: 31264d633b121298f642ed7e79e366d1 build: number: 0 rpaths: @@ -20,11 +20,11 @@ build: # Suggests: BiocStyle, knitr, RUnit, BiocGenerics requirements: host: - - 'bioconductor-biostrings >=2.50.0,<2.51.0' + - 'bioconductor-biostrings >=2.52.0,<2.53.0' - r-base - r-shiny run: - - 'bioconductor-biostrings >=2.50.0,<2.51.0' + - 'bioconductor-biostrings >=2.52.0,<2.53.0' - r-base - r-shiny test: diff --git a/recipes/bioconductor-santa/meta.yaml b/recipes/bioconductor-santa/meta.yaml index d02582cd6d9eb..2801b5aaf5ffe 100644 --- a/recipes/bioconductor-santa/meta.yaml +++ b/recipes/bioconductor-santa/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "2.20.0" %} +{% set version = "2.22.0" %} {% set name = "SANTA" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 2d2c95468044819a5b1b41c4a563e636 + md5: 6ba9ce317557ad49c1147be11dc9024b build: number: 0 rpaths: diff --git a/recipes/bioconductor-sapfinder/meta.yaml b/recipes/bioconductor-sapfinder/meta.yaml index a591491606f11..b3af2d38bb153 100644 --- a/recipes/bioconductor-sapfinder/meta.yaml +++ b/recipes/bioconductor-sapfinder/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.20.1" %} +{% set version = "1.22.0" %} {% set name = "sapFinder" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 1d4171bf15a1a4b7eb67ef1154f37abe + md5: 6d6a661040edbe9d0adb12390988e71e build: number: 0 rpaths: @@ -19,12 +19,12 @@ build: # Suggests: RUnit, BiocGenerics, BiocStyle requirements: host: - - 'bioconductor-rtandem >=1.22.0,<1.23.0' + - 'bioconductor-rtandem >=1.24.0,<1.25.0' - r-base - r-pheatmap - 'r-rcpp >=0.10.6' run: - - 'bioconductor-rtandem >=1.22.0,<1.23.0' + - 'bioconductor-rtandem >=1.24.0,<1.25.0' - r-base - r-pheatmap - 'r-rcpp >=0.10.6' diff --git a/recipes/bioconductor-saureuscdf/meta.yaml b/recipes/bioconductor-saureuscdf/meta.yaml index fbaa3990fca91..1d193eb6bdb7c 100644 --- a/recipes/bioconductor-saureuscdf/meta.yaml +++ b/recipes/bioconductor-saureuscdf/meta.yaml @@ -1,6 +1,6 @@ {% set version = "2.18.0" %} {% set name = "saureuscdf" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -12,19 +12,19 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: d01883e4c3dd99f32012e6dbab8cdb8b build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' - r-base run: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-saureuscdf/post-link.sh b/recipes/bioconductor-saureuscdf/post-link.sh index fdb9e299da0b0..cadce2a772fb8 100644 --- a/recipes/bioconductor-saureuscdf/post-link.sh +++ b/recipes/bioconductor-saureuscdf/post-link.sh @@ -1,9 +1,10 @@ #!/bin/bash FN="saureuscdf_2.18.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/saureuscdf_2.18.0.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/saureuscdf_2.18.0.tar.gz" "https://bioarchive.galaxyproject.org/saureuscdf_2.18.0.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-saureuscdf/bioconductor-saureuscdf_2.18.0_src_all.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-saureuscdf/bioconductor-saureuscdf_2.18.0_src_all.tar.gz" ) MD5="d01883e4c3dd99f32012e6dbab8cdb8b" @@ -16,7 +17,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-saureusprobe/meta.yaml b/recipes/bioconductor-saureusprobe/meta.yaml index 5e571e26a8ad0..743e9badd7aed 100644 --- a/recipes/bioconductor-saureusprobe/meta.yaml +++ b/recipes/bioconductor-saureusprobe/meta.yaml @@ -1,6 +1,6 @@ {% set version = "2.18.0" %} {% set name = "saureusprobe" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -12,19 +12,19 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: eb4e91b10a536cbde4ecc08951ddf4d3 build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' - r-base run: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-saureusprobe/post-link.sh b/recipes/bioconductor-saureusprobe/post-link.sh index 2c4eeed869409..5b9db6a6d6101 100644 --- a/recipes/bioconductor-saureusprobe/post-link.sh +++ b/recipes/bioconductor-saureusprobe/post-link.sh @@ -1,9 +1,10 @@ #!/bin/bash FN="saureusprobe_2.18.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/saureusprobe_2.18.0.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/saureusprobe_2.18.0.tar.gz" "https://bioarchive.galaxyproject.org/saureusprobe_2.18.0.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-saureusprobe/bioconductor-saureusprobe_2.18.0_src_all.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-saureusprobe/bioconductor-saureusprobe_2.18.0_src_all.tar.gz" ) MD5="eb4e91b10a536cbde4ecc08951ddf4d3" @@ -16,7 +17,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-savr/meta.yaml b/recipes/bioconductor-savr/meta.yaml index 20e83c92f236a..6806fc07225bf 100644 --- a/recipes/bioconductor-savr/meta.yaml +++ b/recipes/bioconductor-savr/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.20.0" %} +{% set version = "1.22.0" %} {% set name = "savR" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 765521fb53c6b8ab25bbd2ff26efe67b + md5: 7baac100f53958464842eb9cd31d4759 build: number: 0 rpaths: diff --git a/recipes/bioconductor-sbmlr/meta.yaml b/recipes/bioconductor-sbmlr/meta.yaml index dfc6cb4940570..700e3ffc8556e 100644 --- a/recipes/bioconductor-sbmlr/meta.yaml +++ b/recipes/bioconductor-sbmlr/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.78.0" %} +{% set version = "1.80.0" %} {% set name = "SBMLR" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 8263d9957245263681e6349e13058a2c + md5: ff571f4e83243d39124016025836e7a3 build: number: 0 rpaths: diff --git a/recipes/bioconductor-sc3/meta.yaml b/recipes/bioconductor-sc3/meta.yaml index a1fef7e14801a..1979651e0f840 100644 --- a/recipes/bioconductor-sc3/meta.yaml +++ b/recipes/bioconductor-sc3/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.10.0" %} +{% set version = "1.12.0" %} {% set name = "SC3" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: a8a19e4da4d87fcc989a068aac8811c4 + md5: 198efa24f98a1c941fa8ad793d582e12 build: number: 0 rpaths: @@ -19,10 +19,10 @@ build: # Suggests: knitr, rmarkdown, mclust, scater requirements: host: - - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' - - 'bioconductor-singlecellexperiment >=1.4.0,<1.5.0' - - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' + - 'bioconductor-biocgenerics >=0.30.0,<0.31.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' + - 'bioconductor-singlecellexperiment >=1.6.0,<1.7.0' + - 'bioconductor-summarizedexperiment >=1.14.0,<1.15.0' - r-base - r-cluster - r-doparallel @@ -39,10 +39,10 @@ requirements: - r-shiny - r-writexls run: - - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' - - 'bioconductor-singlecellexperiment >=1.4.0,<1.5.0' - - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' + - 'bioconductor-biocgenerics >=0.30.0,<0.31.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' + - 'bioconductor-singlecellexperiment >=1.6.0,<1.7.0' + - 'bioconductor-summarizedexperiment >=1.14.0,<1.15.0' - r-base - r-cluster - r-doparallel diff --git a/recipes/bioconductor-scale4c/meta.yaml b/recipes/bioconductor-scale4c/meta.yaml index 62d102ba3507e..3cd14c07af0fe 100644 --- a/recipes/bioconductor-scale4c/meta.yaml +++ b/recipes/bioconductor-scale4c/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.4.0" %} +{% set version = "1.6.0" %} {% set name = "Scale4C" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 42129ff892946f7832161ae468afd8cf + md5: 12361c8ea9c3d72f3560fac83015a116 build: number: 0 rpaths: @@ -19,15 +19,15 @@ build: noarch: generic requirements: host: - - 'bioconductor-genomicranges >=1.34.0,<1.35.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' + - 'bioconductor-genomicranges >=1.36.0,<1.37.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-summarizedexperiment >=1.14.0,<1.15.0' - r-base - r-smoothie run: - - 'bioconductor-genomicranges >=1.34.0,<1.35.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' + - 'bioconductor-genomicranges >=1.36.0,<1.37.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-summarizedexperiment >=1.14.0,<1.15.0' - r-base - r-smoothie test: diff --git a/recipes/bioconductor-scalign/build.sh b/recipes/bioconductor-scalign/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-scalign/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-scalign/meta.yaml b/recipes/bioconductor-scalign/meta.yaml new file mode 100644 index 0000000000000..37af6719f14ea --- /dev/null +++ b/recipes/bioconductor-scalign/meta.yaml @@ -0,0 +1,54 @@ +{% set version = "1.0.0" %} +{% set name = "scAlign" %} +{% set bioc = "3.9" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: 08d737df935ad85a6b65cba882bf18f5 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: knitr, rmarkdown, testthat +# SystemRequirements: python (< 3.7), tensorflow +requirements: + host: + - 'bioconductor-singlecellexperiment >=1.6.0,<1.7.0' + - r-base + - r-fnn + - r-ggplot2 + - r-irlba + - r-purrr + - r-rtsne + - 'r-seurat >=2.3.4' + - r-tensorflow + - python <3.7 + - tensorflow + run: + - 'bioconductor-singlecellexperiment >=1.6.0,<1.7.0' + - r-base + - r-fnn + - r-ggplot2 + - r-irlba + - r-purrr + - r-rtsne + - 'r-seurat >=2.3.4' + - r-tensorflow + - python <3.7 + - tensorflow +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: GPL-3 + summary: 'An unsupervised deep learning method for data alignment, integration and estimation of per-cell differences in -omic data (e.g. gene expression) across datasets (conditions, tissues, species). See Johansen and Quon (2019) for more details.' + diff --git a/recipes/bioconductor-scan.upc/meta.yaml b/recipes/bioconductor-scan.upc/meta.yaml index a9e35773b1de4..1fec7a7b739c4 100644 --- a/recipes/bioconductor-scan.upc/meta.yaml +++ b/recipes/bioconductor-scan.upc/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "2.24.1" %} +{% set version = "2.26.0" %} {% set name = "SCAN.UPC" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 41c135cf7832a54404fbe1d060aa6eb3 + md5: 60fdbafce89a0c2eea88316bab3d2f4b build: number: 0 rpaths: @@ -20,26 +20,26 @@ build: # Suggests: pd.hg.u95a requirements: host: - - 'bioconductor-affy >=1.60.0,<1.61.0' - - 'bioconductor-affyio >=1.52.0,<1.53.0' - - 'bioconductor-biobase >=2.42.0,<2.43.0' - - 'bioconductor-biostrings >=2.50.0,<2.51.0' - - 'bioconductor-geoquery >=2.50.0,<2.51.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-oligo >=1.46.0,<1.47.0' - - 'bioconductor-sva >=3.30.0,<3.31.0' + - 'bioconductor-affy >=1.62.0,<1.63.0' + - 'bioconductor-affyio >=1.54.0,<1.55.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' + - 'bioconductor-biostrings >=2.52.0,<2.53.0' + - 'bioconductor-geoquery >=2.52.0,<2.53.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-oligo >=1.48.0,<1.49.0' + - 'bioconductor-sva >=3.32.0,<3.33.0' - r-base - r-foreach - r-mass run: - - 'bioconductor-affy >=1.60.0,<1.61.0' - - 'bioconductor-affyio >=1.52.0,<1.53.0' - - 'bioconductor-biobase >=2.42.0,<2.43.0' - - 'bioconductor-biostrings >=2.50.0,<2.51.0' - - 'bioconductor-geoquery >=2.50.0,<2.51.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-oligo >=1.46.0,<1.47.0' - - 'bioconductor-sva >=3.30.0,<3.31.0' + - 'bioconductor-affy >=1.62.0,<1.63.0' + - 'bioconductor-affyio >=1.54.0,<1.55.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' + - 'bioconductor-biostrings >=2.52.0,<2.53.0' + - 'bioconductor-geoquery >=2.52.0,<2.53.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-oligo >=1.48.0,<1.49.0' + - 'bioconductor-sva >=3.32.0,<3.33.0' - r-base - r-foreach - r-mass diff --git a/recipes/bioconductor-scater/meta.yaml b/recipes/bioconductor-scater/meta.yaml index 30f9462c46667..bb86e65d2e8b2 100644 --- a/recipes/bioconductor-scater/meta.yaml +++ b/recipes/bioconductor-scater/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.10.1" %} +{% set version = "1.12.0" %} {% set name = "scater" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,52 +10,50 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: faa6a6ab933d20c4ded77a10040b50ca + md5: de59145813bb9cf3668d6b8113413bbd build: number: 0 rpaths: - lib/R/lib/ - lib/ -# Suggests: BiocStyle, biomaRt, beachmat, cowplot, cluster, destiny, knitr, monocle, mvoutlier, rmarkdown, Rtsne, umap, testthat, magrittr, pheatmap, irlba, tximport, tximportData, tximeta, Biobase, limma +# Suggests: BiocStyle, biomaRt, beachmat, cowplot, destiny, knitr, mvoutlier, rmarkdown, Rtsne, uwot, testthat, magrittr, pheatmap, Biobase, limma # SystemRequirements: C++11 requirements: host: - - 'bioconductor-beachmat >=1.4.0,<1.5.0' - - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' - - 'bioconductor-biocparallel >=1.16.0,<1.17.0' - - 'bioconductor-delayedarray >=0.8.0,<0.9.0' - - 'bioconductor-delayedmatrixstats >=1.4.0,<1.5.0' - - 'bioconductor-rhdf5lib >=1.4.0,<1.5.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' - - 'bioconductor-singlecellexperiment >=1.4.0,<1.5.0' - - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' + - 'bioconductor-beachmat >=2.0.0,<2.1.0' + - 'bioconductor-biocgenerics >=0.30.0,<0.31.0' + - 'bioconductor-biocneighbors >=1.2.0,<1.3.0' + - 'bioconductor-biocparallel >=1.18.0,<1.19.0' + - 'bioconductor-biocsingular >=1.0.0,<1.1.0' + - 'bioconductor-delayedarray >=0.10.0,<0.11.0' + - 'bioconductor-delayedmatrixstats >=1.6.0,<1.7.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' + - 'bioconductor-singlecellexperiment >=1.6.0,<1.7.0' + - 'bioconductor-summarizedexperiment >=1.14.0,<1.15.0' - r-base - r-dplyr - r-ggbeeswarm - r-ggplot2 - r-matrix - - r-plyr - - 'r-rcpp >=0.12.14' - - r-reshape2 + - r-rcpp - r-viridis run: - - 'bioconductor-beachmat >=1.4.0,<1.5.0' - - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' - - 'bioconductor-biocparallel >=1.16.0,<1.17.0' - - 'bioconductor-delayedarray >=0.8.0,<0.9.0' - - 'bioconductor-delayedmatrixstats >=1.4.0,<1.5.0' - - 'bioconductor-rhdf5lib >=1.4.0,<1.5.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' - - 'bioconductor-singlecellexperiment >=1.4.0,<1.5.0' - - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' + - 'bioconductor-beachmat >=2.0.0,<2.1.0' + - 'bioconductor-biocgenerics >=0.30.0,<0.31.0' + - 'bioconductor-biocneighbors >=1.2.0,<1.3.0' + - 'bioconductor-biocparallel >=1.18.0,<1.19.0' + - 'bioconductor-biocsingular >=1.0.0,<1.1.0' + - 'bioconductor-delayedarray >=0.10.0,<0.11.0' + - 'bioconductor-delayedmatrixstats >=1.6.0,<1.7.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' + - 'bioconductor-singlecellexperiment >=1.6.0,<1.7.0' + - 'bioconductor-summarizedexperiment >=1.14.0,<1.15.0' - r-base - r-dplyr - r-ggbeeswarm - r-ggplot2 - r-matrix - - r-plyr - - 'r-rcpp >=0.12.14' - - r-reshape2 + - r-rcpp - r-viridis build: - {{ compiler('c') }} diff --git a/recipes/bioconductor-scbn/meta.yaml b/recipes/bioconductor-scbn/meta.yaml index 73525c7027996..0aa975e88b550 100644 --- a/recipes/bioconductor-scbn/meta.yaml +++ b/recipes/bioconductor-scbn/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.0.0" %} +{% set version = "1.2.0" %} {% set name = "SCBN" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 36f0eef432e32fd3a5aa9c63b0bf2dda + md5: 70393c9f4b1630bf8d79e103c06bc43c build: number: 0 rpaths: diff --git a/recipes/bioconductor-scdd/meta.yaml b/recipes/bioconductor-scdd/meta.yaml index 1dc70b6158dad..7c8d5706f11b2 100644 --- a/recipes/bioconductor-scdd/meta.yaml +++ b/recipes/bioconductor-scdd/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.6.0" %} +{% set version = "1.8.0" %} {% set name = "scDD" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 8fe3bae3220b1e02e04e58ba27e97d7a + md5: 68b1fb9761657eb28f9b90e796d2e92b build: number: 0 rpaths: @@ -20,12 +20,12 @@ build: # Suggests: BiocStyle, knitr, gridExtra requirements: host: - - 'bioconductor-biocparallel >=1.16.0,<1.17.0' - - 'bioconductor-ebseq >=1.22.0,<1.23.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' - - 'bioconductor-scran >=1.10.0,<1.11.0' - - 'bioconductor-singlecellexperiment >=1.4.0,<1.5.0' - - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' + - 'bioconductor-biocparallel >=1.18.0,<1.19.0' + - 'bioconductor-ebseq >=1.24.0,<1.25.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' + - 'bioconductor-scran >=1.12.0,<1.13.0' + - 'bioconductor-singlecellexperiment >=1.6.0,<1.7.0' + - 'bioconductor-summarizedexperiment >=1.14.0,<1.15.0' - r-arm - r-base - r-fields @@ -33,12 +33,12 @@ requirements: - r-mclust - r-outliers run: - - 'bioconductor-biocparallel >=1.16.0,<1.17.0' - - 'bioconductor-ebseq >=1.22.0,<1.23.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' - - 'bioconductor-scran >=1.10.0,<1.11.0' - - 'bioconductor-singlecellexperiment >=1.4.0,<1.5.0' - - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' + - 'bioconductor-biocparallel >=1.18.0,<1.19.0' + - 'bioconductor-ebseq >=1.24.0,<1.25.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' + - 'bioconductor-scran >=1.12.0,<1.13.0' + - 'bioconductor-singlecellexperiment >=1.6.0,<1.7.0' + - 'bioconductor-summarizedexperiment >=1.14.0,<1.15.0' - r-arm - r-base - r-fields diff --git a/recipes/bioconductor-scde/meta.yaml b/recipes/bioconductor-scde/meta.yaml index a290eb864143b..0c708eb847a4b 100644 --- a/recipes/bioconductor-scde/meta.yaml +++ b/recipes/bioconductor-scde/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "2.10.0" %} +{% set version = "2.12.0" %} {% set name = "scde" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: f856b5990653ffab946edf208040bcb4 + md5: 1bc7fdc7e95e1fe2c34684111e503668 build: number: 0 rpaths: @@ -19,9 +19,9 @@ build: # Suggests: knitr, cba, fastcluster, WGCNA, GO.db, org.Hs.eg.db, rmarkdown requirements: host: - - 'bioconductor-biocparallel >=1.16.0,<1.17.0' - - 'bioconductor-edger >=3.24.0,<3.25.0' - - 'bioconductor-pcamethods >=1.74.0,<1.75.0' + - 'bioconductor-biocparallel >=1.18.0,<1.19.0' + - 'bioconductor-edger >=3.26.0,<3.27.0' + - 'bioconductor-pcamethods >=1.76.0,<1.77.0' - r-base - r-cairo - r-extremes @@ -37,9 +37,9 @@ requirements: - r-rmtstat - r-rook run: - - 'bioconductor-biocparallel >=1.16.0,<1.17.0' - - 'bioconductor-edger >=3.24.0,<3.25.0' - - 'bioconductor-pcamethods >=1.74.0,<1.75.0' + - 'bioconductor-biocparallel >=1.18.0,<1.19.0' + - 'bioconductor-edger >=3.26.0,<3.27.0' + - 'bioconductor-pcamethods >=1.76.0,<1.77.0' - r-base - r-cairo - r-extremes diff --git a/recipes/bioconductor-scds/build.sh b/recipes/bioconductor-scds/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-scds/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-scds/meta.yaml b/recipes/bioconductor-scds/meta.yaml new file mode 100644 index 0000000000000..f34be70d6ec07 --- /dev/null +++ b/recipes/bioconductor-scds/meta.yaml @@ -0,0 +1,43 @@ +{% set version = "1.0.0" %} +{% set name = "scds" %} +{% set bioc = "3.9" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + md5: 3cbb33a493bb7e80601d4517d097571f +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: BiocStyle, knitr, rsvd, Rtsne, scater, cowplot +requirements: + host: + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' + - 'bioconductor-singlecellexperiment >=1.6.0,<1.7.0' + - 'bioconductor-summarizedexperiment >=1.14.0,<1.15.0' + - r-base + - r-matrix + - r-xgboost + run: + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' + - 'bioconductor-singlecellexperiment >=1.6.0,<1.7.0' + - 'bioconductor-summarizedexperiment >=1.14.0,<1.15.0' + - r-base + - r-matrix + - r-xgboost +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: 'MIT + file LICENSE' + summary: 'In single cell RNA sequencing (scRNA-seq) data combinations of cells are sometimes considered a single cell (doublets). The scds package provides methods to annotate doublets in scRNA-seq data computationally.' + diff --git a/recipes/bioconductor-scfeaturefilter/meta.yaml b/recipes/bioconductor-scfeaturefilter/meta.yaml index 473aada4efa11..7c937930638d7 100644 --- a/recipes/bioconductor-scfeaturefilter/meta.yaml +++ b/recipes/bioconductor-scfeaturefilter/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.2.1" %} +{% set version = "1.4.0" %} {% set name = "scFeatureFilter" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 8c1bfa91efbaa3bd6f6734bdc98cebdf + md5: 24ca2e4e62ed8d14aac28b73efe1c449 build: number: 0 rpaths: diff --git a/recipes/bioconductor-scfind/meta.yaml b/recipes/bioconductor-scfind/meta.yaml index 3f76200dc4c17..89d51985d58c5 100644 --- a/recipes/bioconductor-scfind/meta.yaml +++ b/recipes/bioconductor-scfind/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.4.0" %} +{% set version = "1.6.0" %} {% set name = "scfind" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: f29ed57914ffdecb38b856bd5ceede22 + md5: e258b0f73b91921b7c068431b09fa3db build: number: 0 rpaths: @@ -19,8 +19,8 @@ build: # Suggests: knitr, rmarkdown, testthat requirements: host: - - 'bioconductor-singlecellexperiment >=1.4.0,<1.5.0' - - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' + - 'bioconductor-singlecellexperiment >=1.6.0,<1.7.0' + - 'bioconductor-summarizedexperiment >=1.14.0,<1.15.0' - r-base - r-bit - r-dplyr @@ -28,8 +28,8 @@ requirements: - 'r-rcpp >=0.12.12' - r-reshape2 run: - - 'bioconductor-singlecellexperiment >=1.4.0,<1.5.0' - - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' + - 'bioconductor-singlecellexperiment >=1.6.0,<1.7.0' + - 'bioconductor-summarizedexperiment >=1.14.0,<1.15.0' - r-base - r-bit - r-dplyr diff --git a/recipes/bioconductor-scisi/meta.yaml b/recipes/bioconductor-scisi/meta.yaml index 0b48389be20e8..2cab1f9f9a8e7 100644 --- a/recipes/bioconductor-scisi/meta.yaml +++ b/recipes/bioconductor-scisi/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.54.0" %} +{% set version = "1.56.0" %} {% set name = "ScISI" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 88cc06d0227f9111004afc9da312fed3 + md5: 08db1fc90b15828040a6c7a997052f24 build: number: 0 rpaths: @@ -20,20 +20,20 @@ build: # Suggests: ppiData, xtable requirements: host: - - 'bioconductor-annotate >=1.60.0,<1.61.0' - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' - - 'bioconductor-apcomplex >=2.48.0,<2.49.0' - - 'bioconductor-go.db >=3.7.0,<3.8.0' - - 'bioconductor-org.sc.sgd.db >=3.7.0,<3.8.0' - - 'bioconductor-rpsixml >=2.24.0,<2.25.0' + - 'bioconductor-annotate >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' + - 'bioconductor-apcomplex >=2.50.0,<2.51.0' + - 'bioconductor-go.db >=3.8.0,<3.9.0' + - 'bioconductor-org.sc.sgd.db >=3.8.0,<3.9.0' + - 'bioconductor-rpsixml >=2.26.0,<2.27.0' - r-base run: - - 'bioconductor-annotate >=1.60.0,<1.61.0' - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' - - 'bioconductor-apcomplex >=2.48.0,<2.49.0' - - 'bioconductor-go.db >=3.7.0,<3.8.0' - - 'bioconductor-org.sc.sgd.db >=3.7.0,<3.8.0' - - 'bioconductor-rpsixml >=2.24.0,<2.25.0' + - 'bioconductor-annotate >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' + - 'bioconductor-apcomplex >=2.50.0,<2.51.0' + - 'bioconductor-go.db >=3.8.0,<3.9.0' + - 'bioconductor-org.sc.sgd.db >=3.8.0,<3.9.0' + - 'bioconductor-rpsixml >=2.26.0,<2.27.0' - r-base test: commands: diff --git a/recipes/bioconductor-sclcbam/meta.yaml b/recipes/bioconductor-sclcbam/meta.yaml index c2440a9be69d0..64d731b8a16c5 100644 --- a/recipes/bioconductor-sclcbam/meta.yaml +++ b/recipes/bioconductor-sclcbam/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.14.0" %} +{% set version = "1.16.0" %} {% set name = "SCLCBam" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: c9a6578784fd79568802485be95841f5 + md5: e3a0df322f55197c0f2edf05cb00e655 build: number: 0 rpaths: @@ -23,7 +23,7 @@ requirements: - r-base run: - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-sclcbam/post-link.sh b/recipes/bioconductor-sclcbam/post-link.sh index dcd6171ad5cea..e81fd049a731c 100644 --- a/recipes/bioconductor-sclcbam/post-link.sh +++ b/recipes/bioconductor-sclcbam/post-link.sh @@ -1,11 +1,11 @@ #!/bin/bash -FN="SCLCBam_1.14.0.tar.gz" +FN="SCLCBam_1.16.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/experiment/src/contrib/SCLCBam_1.14.0.tar.gz" - "https://bioarchive.galaxyproject.org/SCLCBam_1.14.0.tar.gz" - "https://depot.galaxyproject.org/software/bioconductor-sclcbam/bioconductor-sclcbam_1.14.0_src_all.tar.gz" + "https://bioconductor.org/packages/3.9/data/experiment/src/contrib/SCLCBam_1.16.0.tar.gz" + "https://bioarchive.galaxyproject.org/SCLCBam_1.16.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-sclcbam/bioconductor-sclcbam_1.16.0_src_all.tar.gz" ) -MD5="c9a6578784fd79568802485be95841f5" +MD5="e3a0df322f55197c0f2edf05cb00e655" # Use a staging area in the conda dir rather than temp dirs, both to avoid # permission issues as well as to have things downloaded in a predictable @@ -16,7 +16,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-scmap/meta.yaml b/recipes/bioconductor-scmap/meta.yaml index 8dbae085e7d5f..50b4b168f5c88 100644 --- a/recipes/bioconductor-scmap/meta.yaml +++ b/recipes/bioconductor-scmap/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.4.0" %} +{% set version = "1.6.0" %} {% set name = "scmap" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 766eeb1333304b3a0fc8ebac09901d6a + md5: fbfc24aaeecf65952e59e18f2c598db7 build: number: 0 rpaths: @@ -19,11 +19,11 @@ build: # Suggests: knitr, rmarkdown requirements: host: - - 'bioconductor-biobase >=2.42.0,<2.43.0' - - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' - - 'bioconductor-singlecellexperiment >=1.4.0,<1.5.0' - - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' + - 'bioconductor-biocgenerics >=0.30.0,<0.31.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' + - 'bioconductor-singlecellexperiment >=1.6.0,<1.7.0' + - 'bioconductor-summarizedexperiment >=1.14.0,<1.15.0' - r-base - r-dplyr - r-e1071 @@ -36,11 +36,11 @@ requirements: - r-rcpparmadillo - r-reshape2 run: - - 'bioconductor-biobase >=2.42.0,<2.43.0' - - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' - - 'bioconductor-singlecellexperiment >=1.4.0,<1.5.0' - - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' + - 'bioconductor-biocgenerics >=0.30.0,<0.31.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' + - 'bioconductor-singlecellexperiment >=1.6.0,<1.7.0' + - 'bioconductor-summarizedexperiment >=1.14.0,<1.15.0' - r-base - r-dplyr - r-e1071 diff --git a/recipes/bioconductor-scmerge/build.sh b/recipes/bioconductor-scmerge/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-scmerge/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-scmerge/meta.yaml b/recipes/bioconductor-scmerge/meta.yaml new file mode 100644 index 0000000000000..4c61b31b37a98 --- /dev/null +++ b/recipes/bioconductor-scmerge/meta.yaml @@ -0,0 +1,76 @@ +{% set version = "1.0.0" %} +{% set name = "scMerge" %} +{% set bioc = "3.9" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: 38fc29f95339fe69c968234be33ac4ee +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ +# Suggests: BiocStyle, covr, knitr, Matrix, rmarkdown, scales, scater, testthat +requirements: + host: + - 'bioconductor-biocparallel >=1.18.0,<1.19.0' + - 'bioconductor-m3drop >=1.10.0,<1.11.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' + - 'bioconductor-singlecellexperiment >=1.6.0,<1.7.0' + - 'bioconductor-summarizedexperiment >=1.14.0,<1.15.0' + - r-base + - r-cluster + - r-distr + - r-dosnow + - r-foreach + - r-igraph + - r-irlba + - r-iterators + - r-matrixstats + - r-pdist + - r-proxy + - 'r-rcpp >=0.12.18' + - 'r-rcppeigen >=0.3.3.4.0' + - r-rsvd + - r-ruv + - r-testthat + run: + - 'bioconductor-biocparallel >=1.18.0,<1.19.0' + - 'bioconductor-m3drop >=1.10.0,<1.11.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' + - 'bioconductor-singlecellexperiment >=1.6.0,<1.7.0' + - 'bioconductor-summarizedexperiment >=1.14.0,<1.15.0' + - r-base + - r-cluster + - r-distr + - r-dosnow + - r-foreach + - r-igraph + - r-irlba + - r-iterators + - r-matrixstats + - r-pdist + - r-proxy + - 'r-rcpp >=0.12.18' + - 'r-rcppeigen >=0.3.3.4.0' + - r-rsvd + - r-ruv + - r-testthat + build: + - {{ compiler('c') }} + - {{ compiler('cxx') }} + - make +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: GPL-3 + summary: 'Like all gene expression data, single-cell RNA-seq (scRNA-Seq) data suffers from batch effects and other unwanted variations that makes accurate biological interpretations difficult. The scMerge method leverages factor analysis, stably expressed genes (SEGs) and (pseudo-) replicates to remove unwanted variations and merge multiple scRNA-Seq data. This package contains all the necessary functions in the scMerge pipeline, including the identification of SEGs, replication-identification methods, and merging of scRNA-Seq data.' + diff --git a/recipes/bioconductor-scmeth/meta.yaml b/recipes/bioconductor-scmeth/meta.yaml index dbac708925cc1..bc245262dfdf0 100644 --- a/recipes/bioconductor-scmeth/meta.yaml +++ b/recipes/bioconductor-scmeth/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.2.1" %} +{% set version = "1.4.0" %} {% set name = "scmeth" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 3d53d9f2895ad6c888811c939e9b0207 + md5: 3842b6dbd7a08a3f2e2d780ac1278cdd build: number: 0 rpaths: @@ -20,32 +20,32 @@ build: # Suggests: BSgenome.Mmusculus.UCSC.mm10, BSgenome.Hsapiens.NCBI.GRCh38, TxDb.Hsapiens.UCSC.hg38.knownGene, org.Hs.eg.db, Biobase, BiocGenerics, ggplot2, ggthemes requirements: host: - - 'bioconductor-annotationhub >=2.14.0,<2.15.0' - - 'bioconductor-annotatr >=1.8.0,<1.9.0' - - 'bioconductor-biostrings >=2.50.0,<2.51.0' - - 'bioconductor-bsgenome >=1.50.0,<1.51.0' - - 'bioconductor-bsseq >=1.18.0,<1.19.0' - - 'bioconductor-delayedarray >=0.8.0,<0.9.0' - - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' - - 'bioconductor-genomicranges >=1.34.0,<1.35.0' - - 'bioconductor-hdf5array >=1.10.0,<1.11.0' - - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' + - 'bioconductor-annotationhub >=2.16.0,<2.17.0' + - 'bioconductor-annotatr >=1.10.0,<1.11.0' + - 'bioconductor-biostrings >=2.52.0,<2.53.0' + - 'bioconductor-bsgenome >=1.52.0,<1.53.0' + - 'bioconductor-bsseq >=1.20.0,<1.21.0' + - 'bioconductor-delayedarray >=0.10.0,<0.11.0' + - 'bioconductor-genomeinfodb >=1.20.0,<1.21.0' + - 'bioconductor-genomicranges >=1.36.0,<1.37.0' + - 'bioconductor-hdf5array >=1.12.0,<1.13.0' + - 'bioconductor-summarizedexperiment >=1.14.0,<1.15.0' - r-base - r-dt - r-knitr - r-reshape2 - r-rmarkdown run: - - 'bioconductor-annotationhub >=2.14.0,<2.15.0' - - 'bioconductor-annotatr >=1.8.0,<1.9.0' - - 'bioconductor-biostrings >=2.50.0,<2.51.0' - - 'bioconductor-bsgenome >=1.50.0,<1.51.0' - - 'bioconductor-bsseq >=1.18.0,<1.19.0' - - 'bioconductor-delayedarray >=0.8.0,<0.9.0' - - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' - - 'bioconductor-genomicranges >=1.34.0,<1.35.0' - - 'bioconductor-hdf5array >=1.10.0,<1.11.0' - - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' + - 'bioconductor-annotationhub >=2.16.0,<2.17.0' + - 'bioconductor-annotatr >=1.10.0,<1.11.0' + - 'bioconductor-biostrings >=2.52.0,<2.53.0' + - 'bioconductor-bsgenome >=1.52.0,<1.53.0' + - 'bioconductor-bsseq >=1.20.0,<1.21.0' + - 'bioconductor-delayedarray >=0.10.0,<0.11.0' + - 'bioconductor-genomeinfodb >=1.20.0,<1.21.0' + - 'bioconductor-genomicranges >=1.36.0,<1.37.0' + - 'bioconductor-hdf5array >=1.12.0,<1.13.0' + - 'bioconductor-summarizedexperiment >=1.14.0,<1.15.0' - r-base - r-dt - r-knitr diff --git a/recipes/bioconductor-scnorm/meta.yaml b/recipes/bioconductor-scnorm/meta.yaml index ee99a17abbba9..8ec942be08db9 100644 --- a/recipes/bioconductor-scnorm/meta.yaml +++ b/recipes/bioconductor-scnorm/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.4.3" %} +{% set version = "1.6.0" %} {% set name = "SCnorm" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 4a6f810e737c972d7722fed7f78f9eeb + md5: 03654c349ec319e48ba68c201858730e build: number: 0 rpaths: @@ -20,10 +20,10 @@ build: # Suggests: BiocStyle, knitr, rmarkdown, devtools requirements: host: - - 'bioconductor-biocparallel >=1.16.0,<1.17.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' - - 'bioconductor-singlecellexperiment >=1.4.0,<1.5.0' - - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' + - 'bioconductor-biocparallel >=1.18.0,<1.19.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' + - 'bioconductor-singlecellexperiment >=1.6.0,<1.7.0' + - 'bioconductor-summarizedexperiment >=1.14.0,<1.15.0' - r-base - r-cluster - r-data.table @@ -32,10 +32,10 @@ requirements: - r-moments - r-quantreg run: - - 'bioconductor-biocparallel >=1.16.0,<1.17.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' - - 'bioconductor-singlecellexperiment >=1.4.0,<1.5.0' - - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' + - 'bioconductor-biocparallel >=1.18.0,<1.19.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' + - 'bioconductor-singlecellexperiment >=1.6.0,<1.7.0' + - 'bioconductor-summarizedexperiment >=1.14.0,<1.15.0' - r-base - r-cluster - r-data.table diff --git a/recipes/bioconductor-scone/meta.yaml b/recipes/bioconductor-scone/meta.yaml index d1cb89b6e2dc5..ad67626188ddf 100644 --- a/recipes/bioconductor-scone/meta.yaml +++ b/recipes/bioconductor-scone/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.6.1" %} +{% set version = "1.8.0" %} {% set name = "scone" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 555e5a118ab8bcd2f13d125499094226 + md5: 0320a55f3d8bfedec227455ea94625e8 build: number: 0 rpaths: @@ -20,13 +20,13 @@ build: # Suggests: BiocStyle, DT, ggplot2, knitr, miniUI, NMF, plotly, reshape2, rmarkdown, scran, scRNAseq, shiny, testthat, visNetwork requirements: host: - - 'bioconductor-aroma.light >=3.12.0,<3.13.0' - - 'bioconductor-biocparallel >=1.16.0,<1.17.0' - - 'bioconductor-edger >=3.24.0,<3.25.0' - - 'bioconductor-limma >=3.38.0,<3.39.0' - - 'bioconductor-rhdf5 >=2.26.0,<2.27.0' - - 'bioconductor-ruvseq >=1.16.0,<1.17.0' - - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' + - 'bioconductor-aroma.light >=3.14.0,<3.15.0' + - 'bioconductor-biocparallel >=1.18.0,<1.19.0' + - 'bioconductor-edger >=3.26.0,<3.27.0' + - 'bioconductor-limma >=3.40.0,<3.41.0' + - 'bioconductor-rhdf5 >=2.28.0,<2.29.0' + - 'bioconductor-ruvseq >=1.18.0,<1.19.0' + - 'bioconductor-summarizedexperiment >=1.14.0,<1.15.0' - r-base - r-boot - r-class @@ -41,13 +41,13 @@ requirements: - r-rarpack - r-rcolorbrewer run: - - 'bioconductor-aroma.light >=3.12.0,<3.13.0' - - 'bioconductor-biocparallel >=1.16.0,<1.17.0' - - 'bioconductor-edger >=3.24.0,<3.25.0' - - 'bioconductor-limma >=3.38.0,<3.39.0' - - 'bioconductor-rhdf5 >=2.26.0,<2.27.0' - - 'bioconductor-ruvseq >=1.16.0,<1.17.0' - - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' + - 'bioconductor-aroma.light >=3.14.0,<3.15.0' + - 'bioconductor-biocparallel >=1.18.0,<1.19.0' + - 'bioconductor-edger >=3.26.0,<3.27.0' + - 'bioconductor-limma >=3.40.0,<3.41.0' + - 'bioconductor-rhdf5 >=2.28.0,<2.29.0' + - 'bioconductor-ruvseq >=1.18.0,<1.19.0' + - 'bioconductor-summarizedexperiment >=1.14.0,<1.15.0' - r-base - r-boot - r-class diff --git a/recipes/bioconductor-sconify/meta.yaml b/recipes/bioconductor-sconify/meta.yaml index 4662cf0113d4a..3d0e62cda6b8d 100644 --- a/recipes/bioconductor-sconify/meta.yaml +++ b/recipes/bioconductor-sconify/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.2.0" %} +{% set version = "1.4.0" %} {% set name = "Sconify" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 7dc1b90821623faf0bf978c1c27d27f5 + md5: e47d764c109c9805e7353c11958afe6e build: number: 0 rpaths: @@ -20,7 +20,7 @@ build: # Suggests: knitr, rmarkdown, testthat requirements: host: - - 'bioconductor-flowcore >=1.48.0,<1.49.0' + - 'bioconductor-flowcore >=1.50.0,<1.51.0' - r-base - r-dplyr - r-fnn @@ -30,7 +30,7 @@ requirements: - r-rtsne - r-tibble run: - - 'bioconductor-flowcore >=1.48.0,<1.49.0' + - 'bioconductor-flowcore >=1.50.0,<1.51.0' - r-base - r-dplyr - r-fnn diff --git a/recipes/bioconductor-scoreinvhap/meta.yaml b/recipes/bioconductor-scoreinvhap/meta.yaml index 78f2360e767b1..34581155423bb 100644 --- a/recipes/bioconductor-scoreinvhap/meta.yaml +++ b/recipes/bioconductor-scoreinvhap/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.4.0" %} +{% set version = "1.6.0" %} {% set name = "scoreInvHap" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 2ad194689a37b11ae8e50c00056c2e86 + md5: a2613081ec201c27e63afac172d80fa9 build: number: 0 rpaths: @@ -20,20 +20,20 @@ build: # Suggests: testthat, knitr, BiocStyle, rmarkdown requirements: host: - - 'bioconductor-biocparallel >=1.16.0,<1.17.0' - - 'bioconductor-biostrings >=2.50.0,<2.51.0' - - 'bioconductor-genomicranges >=1.34.0,<1.35.0' - - 'bioconductor-snpstats >=1.32.0,<1.33.0' - - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' - - 'bioconductor-variantannotation >=1.28.0,<1.29.0' + - 'bioconductor-biocparallel >=1.18.0,<1.19.0' + - 'bioconductor-biostrings >=2.52.0,<2.53.0' + - 'bioconductor-genomicranges >=1.36.0,<1.37.0' + - 'bioconductor-snpstats >=1.34.0,<1.35.0' + - 'bioconductor-summarizedexperiment >=1.14.0,<1.15.0' + - 'bioconductor-variantannotation >=1.30.0,<1.31.0' - r-base run: - - 'bioconductor-biocparallel >=1.16.0,<1.17.0' - - 'bioconductor-biostrings >=2.50.0,<2.51.0' - - 'bioconductor-genomicranges >=1.34.0,<1.35.0' - - 'bioconductor-snpstats >=1.32.0,<1.33.0' - - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' - - 'bioconductor-variantannotation >=1.28.0,<1.29.0' + - 'bioconductor-biocparallel >=1.18.0,<1.19.0' + - 'bioconductor-biostrings >=2.52.0,<2.53.0' + - 'bioconductor-genomicranges >=1.36.0,<1.37.0' + - 'bioconductor-snpstats >=1.34.0,<1.35.0' + - 'bioconductor-summarizedexperiment >=1.14.0,<1.15.0' + - 'bioconductor-variantannotation >=1.30.0,<1.31.0' - r-base test: commands: diff --git a/recipes/bioconductor-scpipe/meta.yaml b/recipes/bioconductor-scpipe/meta.yaml index 6c1a2e274c42d..5d53100957d03 100644 --- a/recipes/bioconductor-scpipe/meta.yaml +++ b/recipes/bioconductor-scpipe/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.4.1" %} +{% set version = "1.6.0" %} {% set name = "scPipe" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 6a4ef0adf5fcfc0e94db6b8caf6486ca + md5: 7b3a3482d6610048fcdc9156f44610dd build: number: 0 rpaths: @@ -19,18 +19,18 @@ build: # Suggests: Rsubread, knitr, rmarkdown, testthat requirements: host: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' - - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' - - 'bioconductor-biomart >=2.38.0,<2.39.0' - - 'bioconductor-genomicranges >=1.34.0,<1.35.0' - - 'bioconductor-org.hs.eg.db >=3.7.0,<3.8.0' - - 'bioconductor-org.mm.eg.db >=3.7.0,<3.8.0' - - 'bioconductor-rhtslib >=1.14.0,<1.15.0' - - 'bioconductor-rtracklayer >=1.42.0,<1.43.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' - - 'bioconductor-singlecellexperiment >=1.4.0,<1.5.0' - - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' - - 'bioconductor-zlibbioc >=1.28.0,<1.29.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' + - 'bioconductor-biocgenerics >=0.30.0,<0.31.0' + - 'bioconductor-biomart >=2.40.0,<2.41.0' + - 'bioconductor-genomicranges >=1.36.0,<1.37.0' + - 'bioconductor-org.hs.eg.db >=3.8.0,<3.9.0' + - 'bioconductor-org.mm.eg.db >=3.8.0,<3.9.0' + - 'bioconductor-rhtslib >=1.16.0,<1.17.0' + - 'bioconductor-rtracklayer >=1.44.0,<1.45.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' + - 'bioconductor-singlecellexperiment >=1.6.0,<1.7.0' + - 'bioconductor-summarizedexperiment >=1.14.0,<1.15.0' + - 'bioconductor-zlibbioc >=1.30.0,<1.31.0' - r-base - r-dplyr - r-ggally @@ -47,18 +47,18 @@ requirements: - r-stringr - r-testthat run: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' - - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' - - 'bioconductor-biomart >=2.38.0,<2.39.0' - - 'bioconductor-genomicranges >=1.34.0,<1.35.0' - - 'bioconductor-org.hs.eg.db >=3.7.0,<3.8.0' - - 'bioconductor-org.mm.eg.db >=3.7.0,<3.8.0' - - 'bioconductor-rhtslib >=1.14.0,<1.15.0' - - 'bioconductor-rtracklayer >=1.42.0,<1.43.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' - - 'bioconductor-singlecellexperiment >=1.4.0,<1.5.0' - - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' - - 'bioconductor-zlibbioc >=1.28.0,<1.29.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' + - 'bioconductor-biocgenerics >=0.30.0,<0.31.0' + - 'bioconductor-biomart >=2.40.0,<2.41.0' + - 'bioconductor-genomicranges >=1.36.0,<1.37.0' + - 'bioconductor-org.hs.eg.db >=3.8.0,<3.9.0' + - 'bioconductor-org.mm.eg.db >=3.8.0,<3.9.0' + - 'bioconductor-rhtslib >=1.16.0,<1.17.0' + - 'bioconductor-rtracklayer >=1.44.0,<1.45.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' + - 'bioconductor-singlecellexperiment >=1.6.0,<1.7.0' + - 'bioconductor-summarizedexperiment >=1.14.0,<1.15.0' + - 'bioconductor-zlibbioc >=1.30.0,<1.31.0' - r-base - r-dplyr - r-ggally diff --git a/recipes/bioconductor-scran/meta.yaml b/recipes/bioconductor-scran/meta.yaml index ff6ae819c0490..623f6ceee9483 100644 --- a/recipes/bioconductor-scran/meta.yaml +++ b/recipes/bioconductor-scran/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.10.1" %} +{% set version = "1.12.0" %} {% set name = "scran" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 9e3d89d750bc401907a7cef02154dea7 + md5: f41053591a02f6e35c902b9af6cc5efd build: number: 0 rpaths: @@ -20,40 +20,44 @@ build: # SystemRequirements: C++11 requirements: host: - - 'bioconductor-beachmat >=1.4.0,<1.5.0' - - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' - - 'bioconductor-biocneighbors >=1.0.0,<1.1.0' - - 'bioconductor-biocparallel >=1.16.0,<1.17.0' - - 'bioconductor-delayedarray >=0.8.0,<0.9.0' - - 'bioconductor-delayedmatrixstats >=1.4.0,<1.5.0' - - 'bioconductor-edger >=3.24.0,<3.25.0' - - 'bioconductor-limma >=3.38.0,<3.39.0' - - 'bioconductor-rhdf5lib >=1.4.0,<1.5.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' - - 'bioconductor-scater >=1.10.0,<1.11.0' - - 'bioconductor-singlecellexperiment >=1.4.0,<1.5.0' - - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' + - 'bioconductor-beachmat >=2.0.0,<2.1.0' + - 'bioconductor-biocgenerics >=0.30.0,<0.31.0' + - 'bioconductor-biocneighbors >=1.2.0,<1.3.0' + - 'bioconductor-biocparallel >=1.18.0,<1.19.0' + - 'bioconductor-biocsingular >=1.0.0,<1.1.0' + - 'bioconductor-delayedarray >=0.10.0,<0.11.0' + - 'bioconductor-delayedmatrixstats >=1.6.0,<1.7.0' + - 'bioconductor-edger >=3.26.0,<3.27.0' + - 'bioconductor-limma >=3.40.0,<3.41.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' + - 'bioconductor-scater >=1.12.0,<1.13.0' + - 'bioconductor-singlecellexperiment >=1.6.0,<1.7.0' + - 'bioconductor-summarizedexperiment >=1.14.0,<1.15.0' - r-base + - r-bh + - r-dqrng - r-dynamictreecut - r-igraph - r-matrix - 'r-rcpp >=0.12.14' - r-statmod run: - - 'bioconductor-beachmat >=1.4.0,<1.5.0' - - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' - - 'bioconductor-biocneighbors >=1.0.0,<1.1.0' - - 'bioconductor-biocparallel >=1.16.0,<1.17.0' - - 'bioconductor-delayedarray >=0.8.0,<0.9.0' - - 'bioconductor-delayedmatrixstats >=1.4.0,<1.5.0' - - 'bioconductor-edger >=3.24.0,<3.25.0' - - 'bioconductor-limma >=3.38.0,<3.39.0' - - 'bioconductor-rhdf5lib >=1.4.0,<1.5.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' - - 'bioconductor-scater >=1.10.0,<1.11.0' - - 'bioconductor-singlecellexperiment >=1.4.0,<1.5.0' - - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' + - 'bioconductor-beachmat >=2.0.0,<2.1.0' + - 'bioconductor-biocgenerics >=0.30.0,<0.31.0' + - 'bioconductor-biocneighbors >=1.2.0,<1.3.0' + - 'bioconductor-biocparallel >=1.18.0,<1.19.0' + - 'bioconductor-biocsingular >=1.0.0,<1.1.0' + - 'bioconductor-delayedarray >=0.10.0,<0.11.0' + - 'bioconductor-delayedmatrixstats >=1.6.0,<1.7.0' + - 'bioconductor-edger >=3.26.0,<3.27.0' + - 'bioconductor-limma >=3.40.0,<3.41.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' + - 'bioconductor-scater >=1.12.0,<1.13.0' + - 'bioconductor-singlecellexperiment >=1.6.0,<1.7.0' + - 'bioconductor-summarizedexperiment >=1.14.0,<1.15.0' - r-base + - r-bh + - r-dqrng - r-dynamictreecut - r-igraph - r-matrix diff --git a/recipes/bioconductor-screcover/build.sh b/recipes/bioconductor-screcover/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-screcover/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-screcover/meta.yaml b/recipes/bioconductor-screcover/meta.yaml new file mode 100644 index 0000000000000..70640d9f4a943 --- /dev/null +++ b/recipes/bioconductor-screcover/meta.yaml @@ -0,0 +1,61 @@ +{% set version = "1.0.0" %} +{% set name = "scRecover" %} +{% set bioc = "3.9" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: 8cbf4391ae6493e1a8cfd34f7f585592 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: knitr, rmarkdown, SingleCellExperiment, testthat +requirements: + host: + - 'bioconductor-biocparallel >=1.18.0,<1.19.0' + - r-base + - 'r-bbmle >=1.0.18' + - r-doparallel + - r-foreach + - 'r-gamlss >=4.4-0' + - r-kernlab + - 'r-mass >=7.3-45' + - 'r-matrix >=1.2-14' + - r-penalized + - 'r-preseqr >=4.0.0' + - 'r-pscl >=1.4.9' + - 'r-rmagic >=1.3.0' + - r-rsvd + - 'r-saver >=1.1.1' + run: + - 'bioconductor-biocparallel >=1.18.0,<1.19.0' + - r-base + - 'r-bbmle >=1.0.18' + - r-doparallel + - r-foreach + - 'r-gamlss >=4.4-0' + - r-kernlab + - 'r-mass >=7.3-45' + - 'r-matrix >=1.2-14' + - r-penalized + - 'r-preseqr >=4.0.0' + - 'r-pscl >=1.4.9' + - 'r-rmagic >=1.3.0' + - r-rsvd + - 'r-saver >=1.1.1' +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: GPL + summary: 'scRecover is an R package for imputation of single-cell RNA-seq (scRNA-seq) data. It will detect and impute dropout values in a scRNA-seq raw read counts matrix while keeping the real zeros unchanged, since there are both dropout zeros and real zeros in scRNA-seq data. By combination with scImpute, SAVER and MAGIC, scRecover not only detects dropout and real zeros at higher accuracy, but also improve the downstream clustering and visualization results.' + diff --git a/recipes/bioconductor-scrnaseq/meta.yaml b/recipes/bioconductor-scrnaseq/meta.yaml index 10ac81ced3700..28d51e2cf0724 100644 --- a/recipes/bioconductor-scrnaseq/meta.yaml +++ b/recipes/bioconductor-scrnaseq/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.8.0" %} +{% set version = "1.10.0" %} {% set name = "scRNAseq" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: fe0e002e82591d592eefbf687d46dc56 + md5: e9aded444d5781911c8678274f7abbbe build: number: 0 rpaths: @@ -20,12 +20,12 @@ build: # Suggests: BiocStyle, knitr, rmarkdown requirements: host: - - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' + - 'bioconductor-summarizedexperiment >=1.14.0,<1.15.0' - r-base run: - - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' + - 'bioconductor-summarizedexperiment >=1.14.0,<1.15.0' - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-scrnaseq/post-link.sh b/recipes/bioconductor-scrnaseq/post-link.sh index 863ca029ffcbe..4af1a7213e309 100644 --- a/recipes/bioconductor-scrnaseq/post-link.sh +++ b/recipes/bioconductor-scrnaseq/post-link.sh @@ -1,11 +1,11 @@ #!/bin/bash -FN="scRNAseq_1.8.0.tar.gz" +FN="scRNAseq_1.10.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/experiment/src/contrib/scRNAseq_1.8.0.tar.gz" - "https://bioarchive.galaxyproject.org/scRNAseq_1.8.0.tar.gz" - "https://depot.galaxyproject.org/software/bioconductor-scrnaseq/bioconductor-scrnaseq_1.8.0_src_all.tar.gz" + "https://bioconductor.org/packages/3.9/data/experiment/src/contrib/scRNAseq_1.10.0.tar.gz" + "https://bioarchive.galaxyproject.org/scRNAseq_1.10.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-scrnaseq/bioconductor-scrnaseq_1.10.0_src_all.tar.gz" ) -MD5="fe0e002e82591d592eefbf687d46dc56" +MD5="e9aded444d5781911c8678274f7abbbe" # Use a staging area in the conda dir rather than temp dirs, both to avoid # permission issues as well as to have things downloaded in a predictable @@ -16,7 +16,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-scruff/meta.yaml b/recipes/bioconductor-scruff/meta.yaml index 6bb28437fd286..936ca5fe236e8 100644 --- a/recipes/bioconductor-scruff/meta.yaml +++ b/recipes/bioconductor-scruff/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.0.1" %} +{% set version = "1.2.0" %} {% set name = "scruff" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,9 +10,9 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 32fcb7089073e8f44303048a54ac2059 + md5: 3733ec635baad765a1e5f05a07b4b918 build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ @@ -20,49 +20,49 @@ build: # Suggests: BiocStyle, knitr, rmarkdown, Rsubread, testthat requirements: host: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' - - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' - - 'bioconductor-biocparallel >=1.16.0,<1.17.0' - - 'bioconductor-biostrings >=2.50.0,<2.51.0' - - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' - - 'bioconductor-genomicalignments >=1.18.0,<1.19.0' - - 'bioconductor-genomicfeatures >=1.34.0,<1.35.0' - - 'bioconductor-genomicranges >=1.34.0,<1.35.0' - - 'bioconductor-ggbio >=1.30.0,<1.31.0' - - 'bioconductor-rsamtools >=1.34.0,<1.35.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' - - 'bioconductor-shortread >=1.40.0,<1.41.0' - - 'bioconductor-singlecellexperiment >=1.4.0,<1.5.0' - - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' + - 'bioconductor-biocgenerics >=0.30.0,<0.31.0' + - 'bioconductor-biocparallel >=1.18.0,<1.19.0' + - 'bioconductor-biostrings >=2.52.0,<2.53.0' + - 'bioconductor-genomeinfodb >=1.20.0,<1.21.0' + - 'bioconductor-genomicalignments >=1.20.0,<1.21.0' + - 'bioconductor-genomicfeatures >=1.36.0,<1.37.0' + - 'bioconductor-genomicranges >=1.36.0,<1.37.0' + - 'bioconductor-ggbio >=1.32.0,<1.33.0' + - 'bioconductor-rsamtools >=2.0.0,<2.1.0' + - 'bioconductor-rtracklayer >=1.44.0,<1.45.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' + - 'bioconductor-shortread >=1.42.0,<1.43.0' + - 'bioconductor-singlecellexperiment >=1.6.0,<1.7.0' + - 'bioconductor-summarizedexperiment >=1.14.0,<1.15.0' - r-base - r-data.table - r-ggplot2 - r-ggthemes - r-plyr - - r-refgenome - r-scales - r-stringdist run: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' - - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' - - 'bioconductor-biocparallel >=1.16.0,<1.17.0' - - 'bioconductor-biostrings >=2.50.0,<2.51.0' - - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' - - 'bioconductor-genomicalignments >=1.18.0,<1.19.0' - - 'bioconductor-genomicfeatures >=1.34.0,<1.35.0' - - 'bioconductor-genomicranges >=1.34.0,<1.35.0' - - 'bioconductor-ggbio >=1.30.0,<1.31.0' - - 'bioconductor-rsamtools >=1.34.0,<1.35.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' - - 'bioconductor-shortread >=1.40.0,<1.41.0' - - 'bioconductor-singlecellexperiment >=1.4.0,<1.5.0' - - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' + - 'bioconductor-biocgenerics >=0.30.0,<0.31.0' + - 'bioconductor-biocparallel >=1.18.0,<1.19.0' + - 'bioconductor-biostrings >=2.52.0,<2.53.0' + - 'bioconductor-genomeinfodb >=1.20.0,<1.21.0' + - 'bioconductor-genomicalignments >=1.20.0,<1.21.0' + - 'bioconductor-genomicfeatures >=1.36.0,<1.37.0' + - 'bioconductor-genomicranges >=1.36.0,<1.37.0' + - 'bioconductor-ggbio >=1.32.0,<1.33.0' + - 'bioconductor-rsamtools >=2.0.0,<2.1.0' + - 'bioconductor-rtracklayer >=1.44.0,<1.45.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' + - 'bioconductor-shortread >=1.42.0,<1.43.0' + - 'bioconductor-singlecellexperiment >=1.6.0,<1.7.0' + - 'bioconductor-summarizedexperiment >=1.14.0,<1.15.0' - r-base - r-data.table - r-ggplot2 - r-ggthemes - r-plyr - - r-refgenome - r-scales - r-stringdist test: diff --git a/recipes/bioconductor-scsr/meta.yaml b/recipes/bioconductor-scsr/meta.yaml index dc4a8031625c1..c4c7f81db79d1 100644 --- a/recipes/bioconductor-scsr/meta.yaml +++ b/recipes/bioconductor-scsr/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.18.0" %} +{% set version = "1.20.0" %} {% set name = "scsR" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 0f4b6a6a4da4a834cf90834a9d93f83b + md5: b6aa1d18d3ba19c7cf6b77052a550aad build: number: 0 rpaths: @@ -20,10 +20,10 @@ build: # Suggests: RUnit requirements: host: - - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' - - 'bioconductor-biostrings >=2.50.0,<2.51.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-stringdb >=1.22.0,<1.23.0' + - 'bioconductor-biocgenerics >=0.30.0,<0.31.0' + - 'bioconductor-biostrings >=2.52.0,<2.53.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-stringdb >=1.24.0,<1.25.0' - r-base - r-ggplot2 - r-hash @@ -31,10 +31,10 @@ requirements: - r-rcolorbrewer - r-sqldf run: - - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' - - 'bioconductor-biostrings >=2.50.0,<2.51.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-stringdb >=1.22.0,<1.23.0' + - 'bioconductor-biocgenerics >=0.30.0,<0.31.0' + - 'bioconductor-biostrings >=2.52.0,<2.53.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-stringdb >=1.24.0,<1.25.0' - r-base - r-ggplot2 - r-hash diff --git a/recipes/bioconductor-sctensor/build.sh b/recipes/bioconductor-sctensor/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-sctensor/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-sctensor/meta.yaml b/recipes/bioconductor-sctensor/meta.yaml new file mode 100644 index 0000000000000..444d2451bfe8c --- /dev/null +++ b/recipes/bioconductor-sctensor/meta.yaml @@ -0,0 +1,87 @@ +{% set version = "1.0.0" %} +{% set name = "scTensor" %} +{% set bioc = "3.9" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: e98fa149d49c2befcbc5d1b6be575041 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: testthat, LRBase.Hsa.eg.db, MeSH.Hsa.eg.db, LRBase.Mmu.eg.db, MeSH.Mmu.eg.db, LRBaseDbi +requirements: + host: + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' + - 'bioconductor-biocstyle >=2.12.0,<2.13.0' + - 'bioconductor-biomart >=2.40.0,<2.41.0' + - 'bioconductor-category >=2.50.0,<2.51.0' + - 'bioconductor-dose >=3.10.0,<3.11.0' + - 'bioconductor-gostats >=2.50.0,<2.51.0' + - 'bioconductor-meshdbi >=1.20.0,<1.21.0' + - 'bioconductor-meshr >=1.20.0,<1.21.0' + - 'bioconductor-reactome.db >=1.68.0,<1.69.0' + - 'bioconductor-reactomepa >=1.28.0,<1.29.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' + - 'bioconductor-singlecellexperiment >=1.6.0,<1.7.0' + - 'bioconductor-summarizedexperiment >=1.14.0,<1.15.0' + - r-abind + - r-base + - r-checkmate + - r-crayon + - r-heatmaply + - r-igraph + - r-knitr + - r-nntensor + - r-outliers + - r-plotly + - r-plotrix + - r-rmarkdown + - r-rsqlite + - r-rtensor + - r-tagcloud + run: + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' + - 'bioconductor-biocstyle >=2.12.0,<2.13.0' + - 'bioconductor-biomart >=2.40.0,<2.41.0' + - 'bioconductor-category >=2.50.0,<2.51.0' + - 'bioconductor-dose >=3.10.0,<3.11.0' + - 'bioconductor-gostats >=2.50.0,<2.51.0' + - 'bioconductor-meshdbi >=1.20.0,<1.21.0' + - 'bioconductor-meshr >=1.20.0,<1.21.0' + - 'bioconductor-reactome.db >=1.68.0,<1.69.0' + - 'bioconductor-reactomepa >=1.28.0,<1.29.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' + - 'bioconductor-singlecellexperiment >=1.6.0,<1.7.0' + - 'bioconductor-summarizedexperiment >=1.14.0,<1.15.0' + - r-abind + - r-base + - r-checkmate + - r-crayon + - r-heatmaply + - r-igraph + - r-knitr + - r-nntensor + - r-outliers + - r-plotly + - r-plotrix + - r-rmarkdown + - r-rsqlite + - r-rtensor + - r-tagcloud +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'The algorithm is based on the non-negative tucker decomposition (NTD) of nnTensor.' + diff --git a/recipes/bioconductor-sdams/meta.yaml b/recipes/bioconductor-sdams/meta.yaml index 634b3c06007ef..a81ce766a0032 100644 --- a/recipes/bioconductor-sdams/meta.yaml +++ b/recipes/bioconductor-sdams/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.2.0" %} +{% set version = "1.4.0" %} {% set name = "SDAMS" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 0eb7021f092abd2f4741bfec7bbe2315 + md5: 5d90e928e0187ec8d9f8f3a0013302f1 build: number: 0 rpaths: @@ -20,13 +20,13 @@ build: # Suggests: testthat requirements: host: - - 'bioconductor-qvalue >=2.14.0,<2.15.0' - - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' + - 'bioconductor-qvalue >=2.16.0,<2.17.0' + - 'bioconductor-summarizedexperiment >=1.14.0,<1.15.0' - r-base - r-trust run: - - 'bioconductor-qvalue >=2.14.0,<2.15.0' - - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' + - 'bioconductor-qvalue >=2.16.0,<2.17.0' + - 'bioconductor-summarizedexperiment >=1.14.0,<1.15.0' - r-base - r-trust test: diff --git a/recipes/bioconductor-segmentseq/meta.yaml b/recipes/bioconductor-segmentseq/meta.yaml index 04055a9f22cbe..4b7ef231f4e13 100644 --- a/recipes/bioconductor-segmentseq/meta.yaml +++ b/recipes/bioconductor-segmentseq/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "2.16.0" %} +{% set version = "2.18.0" %} {% set name = "segmentSeq" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: d824a0fa29add988a1ce56eb6fe3dcdb + md5: f02009d37d365688285d7ca6106e7d27 build: number: 0 rpaths: @@ -20,23 +20,23 @@ build: # Suggests: BiocStyle, BiocGenerics requirements: host: - - 'bioconductor-bayseq >=2.16.0,<2.17.0' - - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' - - 'bioconductor-genomicranges >=1.34.0,<1.35.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-rsamtools >=1.34.0,<1.35.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' - - 'bioconductor-shortread >=1.40.0,<1.41.0' + - 'bioconductor-bayseq >=2.18.0,<2.19.0' + - 'bioconductor-genomeinfodb >=1.20.0,<1.21.0' + - 'bioconductor-genomicranges >=1.36.0,<1.37.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-rsamtools >=2.0.0,<2.1.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' + - 'bioconductor-shortread >=1.42.0,<1.43.0' - r-abind - r-base run: - - 'bioconductor-bayseq >=2.16.0,<2.17.0' - - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' - - 'bioconductor-genomicranges >=1.34.0,<1.35.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-rsamtools >=1.34.0,<1.35.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' - - 'bioconductor-shortread >=1.40.0,<1.41.0' + - 'bioconductor-bayseq >=2.18.0,<2.19.0' + - 'bioconductor-genomeinfodb >=1.20.0,<1.21.0' + - 'bioconductor-genomicranges >=1.36.0,<1.37.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-rsamtools >=2.0.0,<2.1.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' + - 'bioconductor-shortread >=1.42.0,<1.43.0' - r-abind - r-base test: diff --git a/recipes/bioconductor-selex/meta.yaml b/recipes/bioconductor-selex/meta.yaml index ce54b40e55fd9..02076b6cfcd1d 100644 --- a/recipes/bioconductor-selex/meta.yaml +++ b/recipes/bioconductor-selex/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.14.0" %} +{% set version = "1.16.0" %} {% set name = "SELEX" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 50fc8dc5e8723d5c1d93f7e1b9140ca8 + md5: 94bd0e2afdff212e8f350f096e67b3c8 build: number: 0 rpaths: @@ -20,11 +20,11 @@ build: # SystemRequirements: Java (>= 1.5) requirements: host: - - 'bioconductor-biostrings >=2.50.0,<2.51.0' + - 'bioconductor-biostrings >=2.52.0,<2.53.0' - r-base - 'r-rjava >=0.5-0' run: - - 'bioconductor-biostrings >=2.50.0,<2.51.0' + - 'bioconductor-biostrings >=2.52.0,<2.53.0' - r-base - 'r-rjava >=0.5-0' test: diff --git a/recipes/bioconductor-semdist/meta.yaml b/recipes/bioconductor-semdist/meta.yaml index ba127d8951dcc..320172cdad122 100644 --- a/recipes/bioconductor-semdist/meta.yaml +++ b/recipes/bioconductor-semdist/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.16.0" %} +{% set version = "1.18.0" %} {% set name = "SemDist" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,9 +10,9 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: eab03908affcfa4650727b2d59de3a1e + md5: 9a7024a94ff4b88d11879bce11a2aaf3 build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ @@ -20,14 +20,14 @@ build: # Suggests: GOSemSim requirements: host: - - 'bioconductor-annotate >=1.60.0,<1.61.0' - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' - - 'bioconductor-go.db >=3.7.0,<3.8.0' + - 'bioconductor-annotate >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' + - 'bioconductor-go.db >=3.8.0,<3.9.0' - r-base run: - - 'bioconductor-annotate >=1.60.0,<1.61.0' - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' - - 'bioconductor-go.db >=3.7.0,<3.8.0' + - 'bioconductor-annotate >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' + - 'bioconductor-go.db >=3.8.0,<3.9.0' - r-base test: commands: diff --git a/recipes/bioconductor-semisup/meta.yaml b/recipes/bioconductor-semisup/meta.yaml index f657d25a4bc28..31c5ae0cf68db 100644 --- a/recipes/bioconductor-semisup/meta.yaml +++ b/recipes/bioconductor-semisup/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.6.0" %} +{% set version = "1.8.0" %} {% set name = "semisup" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,21 +10,19 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 7de301d6f0da4d2fb6c7b720c33d0801 + md5: 57a8dfe6011f2f46f1ca0960bd4309e7 build: number: 0 rpaths: - lib/R/lib/ - lib/ noarch: generic -# Suggests: knitr, testthat +# Suggests: knitr, testthat, SummarizedExperiment requirements: host: - - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' - r-base - r-vgam run: - - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' - r-base - r-vgam test: diff --git a/recipes/bioconductor-sepa/meta.yaml b/recipes/bioconductor-sepa/meta.yaml index d29d1056602d2..80bca946a3881 100644 --- a/recipes/bioconductor-sepa/meta.yaml +++ b/recipes/bioconductor-sepa/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.12.0" %} +{% set version = "1.13.0" %} {% set name = "SEPA" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 8e24d376c6932b319c7220271d2ac3d9 + md5: ad3202957761df88df45c4485fa1bfe8 build: number: 0 rpaths: @@ -20,18 +20,18 @@ build: # Suggests: knitr requirements: host: - - 'bioconductor-org.hs.eg.db >=3.7.0,<3.8.0' - - 'bioconductor-org.mm.eg.db >=3.7.0,<3.8.0' - - 'bioconductor-topgo >=2.34.0,<2.35.0' + - 'bioconductor-org.hs.eg.db >=3.8.0,<3.9.0' + - 'bioconductor-org.mm.eg.db >=3.8.0,<3.9.0' + - 'bioconductor-topgo >=2.36.0,<2.37.0' - r-base - r-ggplot2 - r-reshape2 - r-segmented - r-shiny run: - - 'bioconductor-org.hs.eg.db >=3.7.0,<3.8.0' - - 'bioconductor-org.mm.eg.db >=3.7.0,<3.8.0' - - 'bioconductor-topgo >=2.34.0,<2.35.0' + - 'bioconductor-org.hs.eg.db >=3.8.0,<3.9.0' + - 'bioconductor-org.mm.eg.db >=3.8.0,<3.9.0' + - 'bioconductor-topgo >=2.36.0,<2.37.0' - r-base - r-ggplot2 - r-reshape2 diff --git a/recipes/bioconductor-sepira/meta.yaml b/recipes/bioconductor-sepira/meta.yaml index 47c95a16975c8..f2db7e7f3e998 100644 --- a/recipes/bioconductor-sepira/meta.yaml +++ b/recipes/bioconductor-sepira/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.2.0" %} +{% set version = "1.4.0" %} {% set name = "SEPIRA" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 9c692e31570fd41c696bb62f2f48b45e + md5: fc977e6b55303e47f0ff69b5ea8a85fa build: number: 0 rpaths: @@ -20,11 +20,11 @@ build: # Suggests: knitr, rmarkdown, testthat, igraph requirements: host: - - 'bioconductor-limma >=3.38.0,<3.39.0' + - 'bioconductor-limma >=3.40.0,<3.41.0' - r-base - 'r-corpcor >=1.6.9' run: - - 'bioconductor-limma >=3.38.0,<3.39.0' + - 'bioconductor-limma >=3.40.0,<3.41.0' - r-base - 'r-corpcor >=1.6.9' test: diff --git a/recipes/bioconductor-seq2pathway.data/meta.yaml b/recipes/bioconductor-seq2pathway.data/meta.yaml index 018f005c1f63e..751bcd7e55da4 100644 --- a/recipes/bioconductor-seq2pathway.data/meta.yaml +++ b/recipes/bioconductor-seq2pathway.data/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.14.0" %} +{% set version = "1.16.0" %} {% set name = "seq2pathway.data" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,9 +10,9 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: ca93e7796ded3a3f92e56f3539a39291 + md5: a41f1f988fee568e2437562bfca8703c build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ @@ -22,7 +22,7 @@ requirements: - r-base run: - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-seq2pathway.data/post-link.sh b/recipes/bioconductor-seq2pathway.data/post-link.sh index 66950da1c447b..d647ab9fa7543 100644 --- a/recipes/bioconductor-seq2pathway.data/post-link.sh +++ b/recipes/bioconductor-seq2pathway.data/post-link.sh @@ -1,11 +1,11 @@ #!/bin/bash -FN="seq2pathway.data_1.14.0.tar.gz" +FN="seq2pathway.data_1.16.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/experiment/src/contrib/seq2pathway.data_1.14.0.tar.gz" - "https://bioarchive.galaxyproject.org/seq2pathway.data_1.14.0.tar.gz" - "https://depot.galaxyproject.org/software/bioconductor-seq2pathway.data/bioconductor-seq2pathway.data_1.14.0_src_all.tar.gz" + "https://bioconductor.org/packages/3.9/data/experiment/src/contrib/seq2pathway.data_1.16.0.tar.gz" + "https://bioarchive.galaxyproject.org/seq2pathway.data_1.16.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-seq2pathway.data/bioconductor-seq2pathway.data_1.16.0_src_all.tar.gz" ) -MD5="ca93e7796ded3a3f92e56f3539a39291" +MD5="a41f1f988fee568e2437562bfca8703c" # Use a staging area in the conda dir rather than temp dirs, both to avoid # permission issues as well as to have things downloaded in a predictable @@ -16,7 +16,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-seq2pathway/meta.yaml b/recipes/bioconductor-seq2pathway/meta.yaml index f0c0d2ea73183..a1dad3f206ecb 100644 --- a/recipes/bioconductor-seq2pathway/meta.yaml +++ b/recipes/bioconductor-seq2pathway/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.14.0" %} +{% set version = "1.16.0" %} {% set name = "seq2pathway" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,26 +10,26 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 3902ddfb016b893e874cd6eadc13c1d2 + md5: 37e014a88787011d7643a594a538b159 build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ noarch: generic requirements: host: - - 'bioconductor-biomart >=2.38.0,<2.39.0' - - 'bioconductor-genomicranges >=1.34.0,<1.35.0' - - 'bioconductor-seq2pathway.data >=1.14.0,<1.15.0' + - 'bioconductor-biomart >=2.40.0,<2.41.0' + - 'bioconductor-genomicranges >=1.36.0,<1.37.0' + - 'bioconductor-seq2pathway.data >=1.16.0,<1.17.0' - r-base - r-gsa - r-nnet - r-wgcna run: - - 'bioconductor-biomart >=2.38.0,<2.39.0' - - 'bioconductor-genomicranges >=1.34.0,<1.35.0' - - 'bioconductor-seq2pathway.data >=1.14.0,<1.15.0' + - 'bioconductor-biomart >=2.40.0,<2.41.0' + - 'bioconductor-genomicranges >=1.36.0,<1.37.0' + - 'bioconductor-seq2pathway.data >=1.16.0,<1.17.0' - r-base - r-gsa - r-nnet diff --git a/recipes/bioconductor-seqarray/meta.yaml b/recipes/bioconductor-seqarray/meta.yaml index 3d5e946905fcd..c354dc11d3631 100644 --- a/recipes/bioconductor-seqarray/meta.yaml +++ b/recipes/bioconductor-seqarray/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.22.2" %} +{% set version = "1.24.0" %} {% set name = "SeqArray" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 8466db82f29db889abcaa8d5e2ac89c2 + md5: 3ea2191e494c1722c1e0ae62d521478f build: number: 0 rpaths: @@ -19,20 +19,20 @@ build: # Suggests: Biobase, BiocGenerics, BiocParallel, RUnit, Rcpp, SNPRelate, digest, crayon, knitr, Rsamtools, VariantAnnotation requirements: host: - - 'bioconductor-biostrings >=2.50.0,<2.51.0' - - 'bioconductor-gdsfmt >=1.18.0,<1.19.0' - - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' - - 'bioconductor-genomicranges >=1.34.0,<1.35.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-biostrings >=2.52.0,<2.53.0' + - 'bioconductor-gdsfmt >=1.20.0,<1.21.0' + - 'bioconductor-genomeinfodb >=1.20.0,<1.21.0' + - 'bioconductor-genomicranges >=1.36.0,<1.37.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' - r-base run: - - 'bioconductor-biostrings >=2.50.0,<2.51.0' - - 'bioconductor-gdsfmt >=1.18.0,<1.19.0' - - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' - - 'bioconductor-genomicranges >=1.34.0,<1.35.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-biostrings >=2.52.0,<2.53.0' + - 'bioconductor-gdsfmt >=1.20.0,<1.21.0' + - 'bioconductor-genomeinfodb >=1.20.0,<1.21.0' + - 'bioconductor-genomicranges >=1.36.0,<1.37.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' - r-base build: - {{ compiler('c') }} @@ -44,5 +44,5 @@ test: about: home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: GPL-3 - summary: 'Big data management of whole-genome sequencing variant calls with thousands of individuals: genotypic data (e.g., SNVs, indels and structural variation calls) and annotations in SeqArray files are stored in an array-oriented and compressed manner, with efficient data access using the R programming language.' + summary: 'Data management of large-scale whole-genome sequencing variant calls with thousands of individuals: genotypic data (e.g., SNVs, indels and structural variation calls) and annotations in SeqArray files are stored in an array-oriented and compressed manner, with efficient data access using the R programming language.' diff --git a/recipes/bioconductor-seqbias/meta.yaml b/recipes/bioconductor-seqbias/meta.yaml index fad23e53893f3..903030aa833a9 100644 --- a/recipes/bioconductor-seqbias/meta.yaml +++ b/recipes/bioconductor-seqbias/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.30.0" %} +{% set version = "1.32.0" %} {% set name = "seqbias" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: a7246cbe2d95208f29cf3651e25b9688 + md5: c4c6f16f1dffca33016753a4ed70d8b3 build: number: 0 rpaths: @@ -19,16 +19,14 @@ build: # Suggests: Rsamtools, ggplot2 requirements: host: - - 'bioconductor-biostrings >=2.50.0,<2.51.0' - - 'bioconductor-genomicranges >=1.34.0,<1.35.0' - - 'bioconductor-rsamtools >=1.34.0,<1.35.0' - - 'bioconductor-zlibbioc >=1.28.0,<1.29.0' + - 'bioconductor-biostrings >=2.52.0,<2.53.0' + - 'bioconductor-genomicranges >=1.36.0,<1.37.0' + - 'bioconductor-rhtslib >=1.16.0,<1.17.0' - r-base run: - - 'bioconductor-biostrings >=2.50.0,<2.51.0' - - 'bioconductor-genomicranges >=1.34.0,<1.35.0' - - 'bioconductor-rsamtools >=1.34.0,<1.35.0' - - 'bioconductor-zlibbioc >=1.28.0,<1.29.0' + - 'bioconductor-biostrings >=2.52.0,<2.53.0' + - 'bioconductor-genomicranges >=1.36.0,<1.37.0' + - 'bioconductor-rhtslib >=1.16.0,<1.17.0' - r-base build: - {{ compiler('c') }} diff --git a/recipes/bioconductor-seqc/meta.yaml b/recipes/bioconductor-seqc/meta.yaml index 6f1ab46abeb57..b88ce8cc50b87 100644 --- a/recipes/bioconductor-seqc/meta.yaml +++ b/recipes/bioconductor-seqc/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.16.0" %} +{% set version = "1.18.0" %} {% set name = "seqc" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 376dcb3255c528683e1c4be13ee3c5c5 + md5: 8ed0537e3d25d12ed357d0e570e30049 build: number: 0 rpaths: @@ -19,12 +19,12 @@ build: noarch: generic requirements: host: - - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' - r-base run: - - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-seqc/post-link.sh b/recipes/bioconductor-seqc/post-link.sh index eda8c5cce93b2..08a61c008fc86 100644 --- a/recipes/bioconductor-seqc/post-link.sh +++ b/recipes/bioconductor-seqc/post-link.sh @@ -1,11 +1,11 @@ #!/bin/bash -FN="seqc_1.16.0.tar.gz" +FN="seqc_1.18.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/experiment/src/contrib/seqc_1.16.0.tar.gz" - "https://bioarchive.galaxyproject.org/seqc_1.16.0.tar.gz" - "https://depot.galaxyproject.org/software/bioconductor-seqc/bioconductor-seqc_1.16.0_src_all.tar.gz" + "https://bioconductor.org/packages/3.9/data/experiment/src/contrib/seqc_1.18.0.tar.gz" + "https://bioarchive.galaxyproject.org/seqc_1.18.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-seqc/bioconductor-seqc_1.18.0_src_all.tar.gz" ) -MD5="376dcb3255c528683e1c4be13ee3c5c5" +MD5="8ed0537e3d25d12ed357d0e570e30049" # Use a staging area in the conda dir rather than temp dirs, both to avoid # permission issues as well as to have things downloaded in a predictable @@ -16,7 +16,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-seqcat/meta.yaml b/recipes/bioconductor-seqcat/meta.yaml index 5f00e11fa8439..0267d88edb2c1 100644 --- a/recipes/bioconductor-seqcat/meta.yaml +++ b/recipes/bioconductor-seqcat/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.4.1" %} +{% set version = "1.6.0" %} {% set name = "seqCAT" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: e2742e15dd741cb9369fbafc2da0b3e4 + md5: 95bbbd1158c0c8429095eeba482f6a76 build: number: 0 rpaths: @@ -20,26 +20,26 @@ build: # Suggests: knitr, BiocStyle, rmarkdown, testthat, BiocManager requirements: host: - - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' - - 'bioconductor-genomicranges >=1.34.0,<1.35.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' - - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' - - 'bioconductor-variantannotation >=1.28.0,<1.29.0' - - 'r-base' + - 'bioconductor-genomeinfodb >=1.20.0,<1.21.0' + - 'bioconductor-genomicranges >=1.36.0,<1.37.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' + - 'bioconductor-summarizedexperiment >=1.14.0,<1.15.0' + - 'bioconductor-variantannotation >=1.30.0,<1.31.0' + - r-base - 'r-dplyr >=0.5.0' - 'r-ggplot2 >=2.2.1' - 'r-lazyeval >=0.2.0' - 'r-scales >=0.4.1' - 'r-tidyr >=0.6.1' run: - - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' - - 'bioconductor-genomicranges >=1.34.0,<1.35.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' - - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' - - 'bioconductor-variantannotation >=1.28.0,<1.29.0' - - 'r-base' + - 'bioconductor-genomeinfodb >=1.20.0,<1.21.0' + - 'bioconductor-genomicranges >=1.36.0,<1.37.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' + - 'bioconductor-summarizedexperiment >=1.14.0,<1.15.0' + - 'bioconductor-variantannotation >=1.30.0,<1.31.0' + - r-base - 'r-dplyr >=0.5.0' - 'r-ggplot2 >=2.2.1' - 'r-lazyeval >=0.2.0' diff --git a/recipes/bioconductor-seqcna.annot/meta.yaml b/recipes/bioconductor-seqcna.annot/meta.yaml index 80d2785840518..7d6b57ce5eb49 100644 --- a/recipes/bioconductor-seqcna.annot/meta.yaml +++ b/recipes/bioconductor-seqcna.annot/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.18.0" %} +{% set version = "1.20.0" %} {% set name = "seqCNA.annot" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,9 +10,9 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: a83620fb92adae77c4f61769854844a6 + md5: 4a10eacbb147f709e82af786f2566def build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ @@ -22,7 +22,7 @@ requirements: - r-base run: - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-seqcna.annot/post-link.sh b/recipes/bioconductor-seqcna.annot/post-link.sh index 5d8fffa78ba89..82190348650f3 100644 --- a/recipes/bioconductor-seqcna.annot/post-link.sh +++ b/recipes/bioconductor-seqcna.annot/post-link.sh @@ -1,11 +1,11 @@ #!/bin/bash -FN="seqCNA.annot_1.18.0.tar.gz" +FN="seqCNA.annot_1.20.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/experiment/src/contrib/seqCNA.annot_1.18.0.tar.gz" - "https://bioarchive.galaxyproject.org/seqCNA.annot_1.18.0.tar.gz" - "https://depot.galaxyproject.org/software/bioconductor-seqcna.annot/bioconductor-seqcna.annot_1.18.0_src_all.tar.gz" + "https://bioconductor.org/packages/3.9/data/experiment/src/contrib/seqCNA.annot_1.20.0.tar.gz" + "https://bioarchive.galaxyproject.org/seqCNA.annot_1.20.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-seqcna.annot/bioconductor-seqcna.annot_1.20.0_src_all.tar.gz" ) -MD5="a83620fb92adae77c4f61769854844a6" +MD5="4a10eacbb147f709e82af786f2566def" # Use a staging area in the conda dir rather than temp dirs, both to avoid # permission issues as well as to have things downloaded in a predictable @@ -16,7 +16,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-seqcna/meta.yaml b/recipes/bioconductor-seqcna/meta.yaml index a75654e303535..6608e0c0ceeb9 100644 --- a/recipes/bioconductor-seqcna/meta.yaml +++ b/recipes/bioconductor-seqcna/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.28.0" %} +{% set version = "1.30.0" %} {% set name = "seqCNA" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 0942b2ccaa95004fcf5b5155bede0e76 + md5: 4940c184d6dea7e54e8f31a025d39034 build: number: 0 rpaths: @@ -19,17 +19,19 @@ build: # SystemRequirements: samtools requirements: host: - - 'bioconductor-glad >=2.46.0,<2.47.0' - - 'bioconductor-seqcna.annot >=1.18.0,<1.19.0' + - 'bioconductor-glad >=2.48.0,<2.49.0' + - 'bioconductor-seqcna.annot >=1.20.0,<1.21.0' - 'r-adehabitatlt >=0.3.4' - r-base - 'r-dosnow >=1.0.5' + - samtools run: - - 'bioconductor-glad >=2.46.0,<2.47.0' - - 'bioconductor-seqcna.annot >=1.18.0,<1.19.0' + - 'bioconductor-glad >=2.48.0,<2.49.0' + - 'bioconductor-seqcna.annot >=1.20.0,<1.21.0' - 'r-adehabitatlt >=0.3.4' - r-base - 'r-dosnow >=1.0.5' + - samtools build: - {{ compiler('c') }} - {{ compiler('cxx') }} diff --git a/recipes/bioconductor-seqcombo/meta.yaml b/recipes/bioconductor-seqcombo/meta.yaml index 199b7be42a3c5..b9b2680c4db2e 100644 --- a/recipes/bioconductor-seqcombo/meta.yaml +++ b/recipes/bioconductor-seqcombo/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.4.0" %} +{% set version = "1.6.0" %} {% set name = "seqcombo" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 11fc14a9982f27f6dee303f81a268f6b + md5: ebf450a509b8bbd98589d6103a2b038b build: number: 0 rpaths: @@ -20,7 +20,7 @@ build: # Suggests: emojifont, knitr, prettydoc, tibble requirements: host: - - 'bioconductor-biostrings >=2.50.0,<2.51.0' + - 'bioconductor-biostrings >=2.52.0,<2.53.0' - r-base - r-cowplot - r-dplyr @@ -29,7 +29,7 @@ requirements: - r-magrittr - r-rvcheck run: - - 'bioconductor-biostrings >=2.50.0,<2.51.0' + - 'bioconductor-biostrings >=2.52.0,<2.53.0' - r-base - r-cowplot - r-dplyr diff --git a/recipes/bioconductor-seqgsea/meta.yaml b/recipes/bioconductor-seqgsea/meta.yaml index f12adefff49a1..dde4e832fe025 100644 --- a/recipes/bioconductor-seqgsea/meta.yaml +++ b/recipes/bioconductor-seqgsea/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.22.0" %} +{% set version = "1.24.0" %} {% set name = "SeqGSEA" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: d9b007488cfb754cb9f146925d1e4bf8 + md5: 99baf889467af15810cf88111873c40f build: number: 0 rpaths: @@ -20,15 +20,15 @@ build: # Suggests: easyRNASeq, GenomicRanges requirements: host: - - 'bioconductor-biobase >=2.42.0,<2.43.0' - - 'bioconductor-biomart >=2.38.0,<2.39.0' - - 'bioconductor-deseq >=1.34.0,<1.35.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' + - 'bioconductor-biomart >=2.40.0,<2.41.0' + - 'bioconductor-deseq >=1.36.0,<1.37.0' - r-base - r-doparallel run: - - 'bioconductor-biobase >=2.42.0,<2.43.0' - - 'bioconductor-biomart >=2.38.0,<2.39.0' - - 'bioconductor-deseq >=1.34.0,<1.35.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' + - 'bioconductor-biomart >=2.40.0,<2.41.0' + - 'bioconductor-deseq >=1.36.0,<1.37.0' - r-base - r-doparallel test: diff --git a/recipes/bioconductor-seqlogo/meta.yaml b/recipes/bioconductor-seqlogo/meta.yaml index ad923c3d42dcf..2b89916c93d2f 100644 --- a/recipes/bioconductor-seqlogo/meta.yaml +++ b/recipes/bioconductor-seqlogo/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.48.0" %} +{% set version = "1.50.0" %} {% set name = "seqLogo" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 435a5d989d6fcb86466ab7bbd546bf70 + md5: 7d245f94e0c48b23022ad3b692187cb7 build: number: 0 rpaths: diff --git a/recipes/bioconductor-seqpattern/meta.yaml b/recipes/bioconductor-seqpattern/meta.yaml index 957643481125c..cc90f243dadb8 100644 --- a/recipes/bioconductor-seqpattern/meta.yaml +++ b/recipes/bioconductor-seqpattern/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.14.0" %} +{% set version = "1.16.0" %} {% set name = "seqPattern" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: eaa324090a3e3aea517439104aff6721 + md5: 44e22955071d0a0964000501a064f5ee build: number: 0 rpaths: @@ -20,16 +20,16 @@ build: # Suggests: BSgenome.Drerio.UCSC.danRer7, CAGEr, RUnit, BiocGenerics, BiocStyle requirements: host: - - 'bioconductor-biostrings >=2.50.0,<2.51.0' - - 'bioconductor-genomicranges >=1.34.0,<1.35.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-biostrings >=2.52.0,<2.53.0' + - 'bioconductor-genomicranges >=1.36.0,<1.37.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' - r-base - r-kernsmooth - r-plotrix run: - - 'bioconductor-biostrings >=2.50.0,<2.51.0' - - 'bioconductor-genomicranges >=1.34.0,<1.35.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-biostrings >=2.52.0,<2.53.0' + - 'bioconductor-genomicranges >=1.36.0,<1.37.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' - r-base - r-kernsmooth - r-plotrix diff --git a/recipes/bioconductor-seqplots/meta.yaml b/recipes/bioconductor-seqplots/meta.yaml index 8871035b4c27c..564f0bb54f3f6 100644 --- a/recipes/bioconductor-seqplots/meta.yaml +++ b/recipes/bioconductor-seqplots/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.20.0" %} +{% set version = "1.21.1" %} {% set name = "seqplots" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: c4103c7256e3428c1877dd6536fc8795 + md5: d299aca2f3a5ef7673379d9f74195459 build: number: 0 rpaths: @@ -20,15 +20,15 @@ build: # Suggests: testthat, BiocStyle, knitr, rmarkdown, covr requirements: host: - - 'bioconductor-biostrings >=2.50.0,<2.51.0' - - 'bioconductor-bsgenome >=1.50.0,<1.51.0' - - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' - - 'bioconductor-genomicalignments >=1.18.0,<1.19.0' - - 'bioconductor-genomicranges >=1.34.0,<1.35.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-rsamtools >=1.34.0,<1.35.0' - - 'bioconductor-rtracklayer >=1.42.0,<1.43.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-biostrings >=2.52.0,<2.53.0' + - 'bioconductor-bsgenome >=1.52.0,<1.53.0' + - 'bioconductor-genomeinfodb >=1.20.0,<1.21.0' + - 'bioconductor-genomicalignments >=1.20.0,<1.21.0' + - 'bioconductor-genomicranges >=1.36.0,<1.37.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-rsamtools >=2.0.0,<2.1.0' + - 'bioconductor-rtracklayer >=1.44.0,<1.45.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' - r-base - r-biocmanager - r-class @@ -46,15 +46,15 @@ requirements: - r-rsqlite - 'r-shiny >=0.13.0' run: - - 'bioconductor-biostrings >=2.50.0,<2.51.0' - - 'bioconductor-bsgenome >=1.50.0,<1.51.0' - - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' - - 'bioconductor-genomicalignments >=1.18.0,<1.19.0' - - 'bioconductor-genomicranges >=1.34.0,<1.35.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-rsamtools >=1.34.0,<1.35.0' - - 'bioconductor-rtracklayer >=1.42.0,<1.43.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-biostrings >=2.52.0,<2.53.0' + - 'bioconductor-bsgenome >=1.52.0,<1.53.0' + - 'bioconductor-genomeinfodb >=1.20.0,<1.21.0' + - 'bioconductor-genomicalignments >=1.20.0,<1.21.0' + - 'bioconductor-genomicranges >=1.36.0,<1.37.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-rsamtools >=2.0.0,<2.1.0' + - 'bioconductor-rtracklayer >=1.44.0,<1.45.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' - r-base - r-biocmanager - r-class diff --git a/recipes/bioconductor-seqsetvis/meta.yaml b/recipes/bioconductor-seqsetvis/meta.yaml index 1bd5578331264..ff3ec54e96f05 100644 --- a/recipes/bioconductor-seqsetvis/meta.yaml +++ b/recipes/bioconductor-seqsetvis/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.2.0" %} +{% set version = "1.4.0" %} {% set name = "seqsetvis" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: be248a791399d770509db66a23438452 + md5: 6fbe4689032ce83b38ffb48b78bb60bf build: number: 0 rpaths: @@ -20,29 +20,35 @@ build: # Suggests: BiocFileCache, BiocManager, BiocStyle, ChIPpeakAnno, covr, cowplot, knitr, rmarkdown, testthat requirements: host: - - 'bioconductor-genomicranges >=1.34.0,<1.35.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-limma >=3.38.0,<3.39.0' - - 'bioconductor-rsamtools >=1.34.0,<1.35.0' - - 'bioconductor-rtracklayer >=1.42.0,<1.43.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-genomeinfodb >=1.20.0,<1.21.0' + - 'bioconductor-genomicalignments >=1.20.0,<1.21.0' + - 'bioconductor-genomicranges >=1.36.0,<1.37.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-limma >=3.40.0,<3.41.0' + - 'bioconductor-rsamtools >=2.0.0,<2.1.0' + - 'bioconductor-rtracklayer >=1.44.0,<1.45.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' - r-base - r-data.table - r-eulerr - r-ggplot2 + - r-pbapply - r-png - r-rcolorbrewer run: - - 'bioconductor-genomicranges >=1.34.0,<1.35.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-limma >=3.38.0,<3.39.0' - - 'bioconductor-rsamtools >=1.34.0,<1.35.0' - - 'bioconductor-rtracklayer >=1.42.0,<1.43.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-genomeinfodb >=1.20.0,<1.21.0' + - 'bioconductor-genomicalignments >=1.20.0,<1.21.0' + - 'bioconductor-genomicranges >=1.36.0,<1.37.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-limma >=3.40.0,<3.41.0' + - 'bioconductor-rsamtools >=2.0.0,<2.1.0' + - 'bioconductor-rtracklayer >=1.44.0,<1.45.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' - r-base - r-data.table - r-eulerr - r-ggplot2 + - r-pbapply - r-png - r-rcolorbrewer test: @@ -51,5 +57,5 @@ test: about: home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: 'MIT + file LICENSE' - summary: 'seqsetvis enables the visualization and analysis of multiple genomic datasets. Although seqsetvis was designed for the comparison of mulitple ChIP-seq datasets, this package is domain-agnostic and allows the processing of multiple genomic coordinate files (bed-like files) and signal files (bigwig files or bam pileups).' + summary: 'seqsetvis enables the visualization and analysis of multiple genomic samples. Although seqsetvis was designed for the comparison of mulitple ChIP-seq samples, this package is domain-agnostic and allows the processing of multiple genomic coordinate files (bed-like files) and signal files (bigwig files or bam pileups).' diff --git a/recipes/bioconductor-seqsqc/meta.yaml b/recipes/bioconductor-seqsqc/meta.yaml index af0e4b912482a..07e49e52ea18b 100644 --- a/recipes/bioconductor-seqsqc/meta.yaml +++ b/recipes/bioconductor-seqsqc/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.4.0" %} +{% set version = "1.6.0" %} {% set name = "SeqSQC" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 567ec0880b33d8207b237e337e17fb98 + md5: 612ddfb4d761b1e6cd4cce005f087c1a build: number: 0 rpaths: @@ -20,12 +20,12 @@ build: # Suggests: BiocStyle, knitr, testthat requirements: host: - - 'bioconductor-experimenthub >=1.8.0,<1.9.0' - - 'bioconductor-gdsfmt >=1.18.0,<1.19.0' - - 'bioconductor-genomicranges >=1.34.0,<1.35.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' - - 'bioconductor-snprelate >=1.16.0,<1.17.0' + - 'bioconductor-experimenthub >=1.10.0,<1.11.0' + - 'bioconductor-gdsfmt >=1.20.0,<1.21.0' + - 'bioconductor-genomicranges >=1.36.0,<1.37.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' + - 'bioconductor-snprelate >=1.18.0,<1.19.0' - r-base - r-e1071 - r-ggally @@ -35,12 +35,12 @@ requirements: - r-reshape2 - r-rmarkdown run: - - 'bioconductor-experimenthub >=1.8.0,<1.9.0' - - 'bioconductor-gdsfmt >=1.18.0,<1.19.0' - - 'bioconductor-genomicranges >=1.34.0,<1.35.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' - - 'bioconductor-snprelate >=1.16.0,<1.17.0' + - 'bioconductor-experimenthub >=1.10.0,<1.11.0' + - 'bioconductor-gdsfmt >=1.20.0,<1.21.0' + - 'bioconductor-genomicranges >=1.36.0,<1.37.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' + - 'bioconductor-snprelate >=1.18.0,<1.19.0' - r-base - r-e1071 - r-ggally diff --git a/recipes/bioconductor-seqtools/meta.yaml b/recipes/bioconductor-seqtools/meta.yaml index 6daed11dbc373..c2d6276f723d9 100644 --- a/recipes/bioconductor-seqtools/meta.yaml +++ b/recipes/bioconductor-seqtools/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.16.0" %} +{% set version = "1.18.0" %} {% set name = "seqTools" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: fb3f61a5e3916be5eb4ab19e44b857d5 + md5: 904b4952c0d23d19c87d8602bceeb870 build: number: 0 rpaths: @@ -19,10 +19,10 @@ build: # Suggests: RUnit, BiocGenerics requirements: host: - - 'bioconductor-zlibbioc >=1.28.0,<1.29.0' + - 'bioconductor-zlibbioc >=1.30.0,<1.31.0' - r-base run: - - 'bioconductor-zlibbioc >=1.28.0,<1.29.0' + - 'bioconductor-zlibbioc >=1.30.0,<1.31.0' - r-base build: - {{ compiler('c') }} diff --git a/recipes/bioconductor-seqvartools/meta.yaml b/recipes/bioconductor-seqvartools/meta.yaml index fa1814f7ea22e..0baf672f583fb 100644 --- a/recipes/bioconductor-seqvartools/meta.yaml +++ b/recipes/bioconductor-seqvartools/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.20.0" %} +{% set version = "1.22.0" %} {% set name = "SeqVarTools" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 7543f794ecea97ebbb71eaf8171f0af1 + md5: 59346cf539f2ccb4f4a793895400071c build: number: 0 rpaths: @@ -20,30 +20,32 @@ build: # Suggests: BiocGenerics, BiocStyle, RUnit, stringr requirements: host: - - 'bioconductor-biobase >=2.42.0,<2.43.0' - - 'bioconductor-gdsfmt >=1.18.0,<1.19.0' - - 'bioconductor-genomicranges >=1.34.0,<1.35.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' - - 'bioconductor-seqarray >=1.22.0,<1.23.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' + - 'bioconductor-gdsfmt >=1.20.0,<1.21.0' + - 'bioconductor-genomicranges >=1.36.0,<1.37.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' + - 'bioconductor-seqarray >=1.24.0,<1.25.0' - r-base - r-dplyr - r-gwasexacthw - r-logistf - r-matrix + - r-rlang - r-tidyr run: - - 'bioconductor-biobase >=2.42.0,<2.43.0' - - 'bioconductor-gdsfmt >=1.18.0,<1.19.0' - - 'bioconductor-genomicranges >=1.34.0,<1.35.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' - - 'bioconductor-seqarray >=1.22.0,<1.23.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' + - 'bioconductor-gdsfmt >=1.20.0,<1.21.0' + - 'bioconductor-genomicranges >=1.36.0,<1.37.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' + - 'bioconductor-seqarray >=1.24.0,<1.25.0' - r-base - r-dplyr - r-gwasexacthw - r-logistf - r-matrix + - r-rlang - r-tidyr test: commands: diff --git a/recipes/bioconductor-serumstimulation/meta.yaml b/recipes/bioconductor-serumstimulation/meta.yaml index 0553b876fd924..203b2f2f31db9 100644 --- a/recipes/bioconductor-serumstimulation/meta.yaml +++ b/recipes/bioconductor-serumstimulation/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.18.0" %} +{% set version = "1.20.0" %} {% set name = "serumStimulation" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 702b8e053465a52491f19961654f3dc0 + md5: 7fabd88ad4038ffd70bb9b8b27738947 build: number: 0 rpaths: @@ -22,7 +22,7 @@ requirements: - r-base run: - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-serumstimulation/post-link.sh b/recipes/bioconductor-serumstimulation/post-link.sh index f837c5eab6f11..2ee855fdea84a 100644 --- a/recipes/bioconductor-serumstimulation/post-link.sh +++ b/recipes/bioconductor-serumstimulation/post-link.sh @@ -1,11 +1,11 @@ #!/bin/bash -FN="serumStimulation_1.18.0.tar.gz" +FN="serumStimulation_1.20.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/experiment/src/contrib/serumStimulation_1.18.0.tar.gz" - "https://bioarchive.galaxyproject.org/serumStimulation_1.18.0.tar.gz" - "https://depot.galaxyproject.org/software/bioconductor-serumstimulation/bioconductor-serumstimulation_1.18.0_src_all.tar.gz" + "https://bioconductor.org/packages/3.9/data/experiment/src/contrib/serumStimulation_1.20.0.tar.gz" + "https://bioarchive.galaxyproject.org/serumStimulation_1.20.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-serumstimulation/bioconductor-serumstimulation_1.20.0_src_all.tar.gz" ) -MD5="702b8e053465a52491f19961654f3dc0" +MD5="7fabd88ad4038ffd70bb9b8b27738947" # Use a staging area in the conda dir rather than temp dirs, both to avoid # permission issues as well as to have things downloaded in a predictable @@ -16,7 +16,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-sesame/meta.yaml b/recipes/bioconductor-sesame/meta.yaml index a2b861c258264..b5e479095ac38 100644 --- a/recipes/bioconductor-sesame/meta.yaml +++ b/recipes/bioconductor-sesame/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.0.0" %} +{% set version = "1.2.0" %} {% set name = "sesame" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,40 +10,44 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 39b48bfe5a5aca7b74685fd0a922aed4 + md5: c9e4ba0dc614dc3c0f55849a40b2535d build: number: 0 rpaths: - lib/R/lib/ - lib/ noarch: generic -# Suggests: scales, knitr, rmarkdown, testthat, minfi, SummarizedExperiment, FlowSorted.CordBloodNorway.450k +# Suggests: scales, knitr, rmarkdown, testthat, minfi, SummarizedExperiment, FlowSorted.CordBloodNorway.450k, FlowSorted.Blood.450k, dplyr, tidyr, BiocStyle requirements: host: - - 'bioconductor-dnacopy >=1.56.0,<1.57.0' - - 'bioconductor-genomicranges >=1.34.0,<1.35.0' - - 'bioconductor-illuminaio >=0.24.0,<0.25.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-preprocesscore >=1.44.0,<1.45.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' - - 'bioconductor-sesamedata >=1.0.0,<1.1.0' + - 'bioconductor-biocparallel >=1.18.0,<1.19.0' + - 'bioconductor-dnacopy >=1.58.0,<1.59.0' + - 'bioconductor-genomicranges >=1.36.0,<1.37.0' + - 'bioconductor-illuminaio >=0.26.0,<0.27.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-preprocesscore >=1.46.0,<1.47.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' + - 'bioconductor-sesamedata >=1.2.0,<1.3.0' - r-base - r-ggplot2 - r-mass + - r-matrixstats - r-r6 - r-randomforest - r-wheatmap run: - - 'bioconductor-dnacopy >=1.56.0,<1.57.0' - - 'bioconductor-genomicranges >=1.34.0,<1.35.0' - - 'bioconductor-illuminaio >=0.24.0,<0.25.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-preprocesscore >=1.44.0,<1.45.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' - - 'bioconductor-sesamedata >=1.0.0,<1.1.0' + - 'bioconductor-biocparallel >=1.18.0,<1.19.0' + - 'bioconductor-dnacopy >=1.58.0,<1.59.0' + - 'bioconductor-genomicranges >=1.36.0,<1.37.0' + - 'bioconductor-illuminaio >=0.26.0,<0.27.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-preprocesscore >=1.46.0,<1.47.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' + - 'bioconductor-sesamedata >=1.2.0,<1.3.0' - r-base - r-ggplot2 - r-mass + - r-matrixstats - r-r6 - r-randomforest - r-wheatmap diff --git a/recipes/bioconductor-sesamedata/meta.yaml b/recipes/bioconductor-sesamedata/meta.yaml index a0b341069205e..059ff9ca9ca18 100644 --- a/recipes/bioconductor-sesamedata/meta.yaml +++ b/recipes/bioconductor-sesamedata/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.0.0" %} +{% set version = "1.2.0" %} {% set name = "sesameData" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,9 +10,9 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: dc24068fe6bdc6ef7e62c89c38b8d949 + md5: 1be0375bcd00351ee53e3ea7b812bfab build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ @@ -20,16 +20,16 @@ build: # Suggests: GenomicRanges, BiocGenerics, sesame, testthat, knitr requirements: host: - - 'bioconductor-annotationhub >=2.14.0,<2.15.0' - - 'bioconductor-experimenthub >=1.8.0,<1.9.0' + - 'bioconductor-annotationhub >=2.16.0,<2.17.0' + - 'bioconductor-experimenthub >=1.10.0,<1.11.0' - r-base - r-curl run: - - 'bioconductor-annotationhub >=2.14.0,<2.15.0' - - 'bioconductor-experimenthub >=1.8.0,<1.9.0' + - 'bioconductor-annotationhub >=2.16.0,<2.17.0' + - 'bioconductor-experimenthub >=1.10.0,<1.11.0' - r-base - r-curl - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-sesamedata/post-link.sh b/recipes/bioconductor-sesamedata/post-link.sh index 8aa3e506eb1b4..f811aa678ad8d 100644 --- a/recipes/bioconductor-sesamedata/post-link.sh +++ b/recipes/bioconductor-sesamedata/post-link.sh @@ -1,11 +1,11 @@ #!/bin/bash -FN="sesameData_1.0.0.tar.gz" +FN="sesameData_1.2.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/experiment/src/contrib/sesameData_1.0.0.tar.gz" - "https://bioarchive.galaxyproject.org/sesameData_1.0.0.tar.gz" - "https://depot.galaxyproject.org/software/bioconductor-sesamedata/bioconductor-sesamedata_1.0.0_src_all.tar.gz" + "https://bioconductor.org/packages/3.9/data/experiment/src/contrib/sesameData_1.2.0.tar.gz" + "https://bioarchive.galaxyproject.org/sesameData_1.2.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-sesamedata/bioconductor-sesamedata_1.2.0_src_all.tar.gz" ) -MD5="dc24068fe6bdc6ef7e62c89c38b8d949" +MD5="1be0375bcd00351ee53e3ea7b812bfab" # Use a staging area in the conda dir rather than temp dirs, both to avoid # permission issues as well as to have things downloaded in a predictable @@ -16,7 +16,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-sevenbridges/meta.yaml b/recipes/bioconductor-sevenbridges/meta.yaml index fb031469f80a7..0b7364df05681 100644 --- a/recipes/bioconductor-sevenbridges/meta.yaml +++ b/recipes/bioconductor-sevenbridges/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.12.5" %} +{% set version = "1.14.0" %} {% set name = "sevenbridges" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - sha256: 4a1dda633ac2a261262e64fad80d608c311323f11eeea50d60912d7536953b97 + md5: 1b618e2203f2178101f52ccce203e42c build: number: 0 rpaths: @@ -20,7 +20,7 @@ build: # Suggests: knitr, rmarkdown, testthat, readr requirements: host: - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' - r-base - r-curl - r-docopt @@ -32,7 +32,7 @@ requirements: - r-uuid - r-yaml run: - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' - r-base - r-curl - r-docopt diff --git a/recipes/bioconductor-sevenc/meta.yaml b/recipes/bioconductor-sevenc/meta.yaml index 0d6af838112e1..2bbe67533bf66 100644 --- a/recipes/bioconductor-sevenc/meta.yaml +++ b/recipes/bioconductor-sevenc/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.2.0" %} +{% set version = "1.4.0" %} {% set name = "sevenC" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 276812bfe5e2ed5a8d6e7cd28c4effb9 + md5: 81ac097106bad8243943bcca8cc969c7 build: number: 0 rpaths: @@ -20,26 +20,26 @@ build: # Suggests: testthat, BiocStyle, knitr, rmarkdown, GenomicInteractions, covr requirements: host: - - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' - - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' - - 'bioconductor-genomicranges >=1.34.0,<1.35.0' - - 'bioconductor-interactionset >=1.10.0,<1.11.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-rtracklayer >=1.42.0,<1.43.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-biocgenerics >=0.30.0,<0.31.0' + - 'bioconductor-genomeinfodb >=1.20.0,<1.21.0' + - 'bioconductor-genomicranges >=1.36.0,<1.37.0' + - 'bioconductor-interactionset >=1.12.0,<1.13.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-rtracklayer >=1.44.0,<1.45.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' - r-base - 'r-boot >=1.3-20' - 'r-data.table >=1.10.4' - 'r-purrr >=0.2.2' - 'r-readr >=1.1.0' run: - - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' - - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' - - 'bioconductor-genomicranges >=1.34.0,<1.35.0' - - 'bioconductor-interactionset >=1.10.0,<1.11.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-rtracklayer >=1.42.0,<1.43.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-biocgenerics >=0.30.0,<0.31.0' + - 'bioconductor-genomeinfodb >=1.20.0,<1.21.0' + - 'bioconductor-genomicranges >=1.36.0,<1.37.0' + - 'bioconductor-interactionset >=1.12.0,<1.13.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-rtracklayer >=1.44.0,<1.45.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' - r-base - 'r-boot >=1.3-20' - 'r-data.table >=1.10.4' diff --git a/recipes/bioconductor-seventygenedata/meta.yaml b/recipes/bioconductor-seventygenedata/meta.yaml index fc80f425fa5c7..2e7d14c8db406 100644 --- a/recipes/bioconductor-seventygenedata/meta.yaml +++ b/recipes/bioconductor-seventygenedata/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.18.0" %} +{% set version = "1.20.0" %} {% set name = "seventyGeneData" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: f5232714137c1bb3d94e058b651ab041 + md5: 8a2c6bc5c05bb81a31f58667cde3018d build: number: 0 rpaths: @@ -23,7 +23,7 @@ requirements: - r-base run: - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-seventygenedata/post-link.sh b/recipes/bioconductor-seventygenedata/post-link.sh index 4287fdf2c564b..88bd216ea71b7 100644 --- a/recipes/bioconductor-seventygenedata/post-link.sh +++ b/recipes/bioconductor-seventygenedata/post-link.sh @@ -1,11 +1,11 @@ #!/bin/bash -FN="seventyGeneData_1.18.0.tar.gz" +FN="seventyGeneData_1.20.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/experiment/src/contrib/seventyGeneData_1.18.0.tar.gz" - "https://bioarchive.galaxyproject.org/seventyGeneData_1.18.0.tar.gz" - "https://depot.galaxyproject.org/software/bioconductor-seventygenedata/bioconductor-seventygenedata_1.18.0_src_all.tar.gz" + "https://bioconductor.org/packages/3.9/data/experiment/src/contrib/seventyGeneData_1.20.0.tar.gz" + "https://bioarchive.galaxyproject.org/seventyGeneData_1.20.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-seventygenedata/bioconductor-seventygenedata_1.20.0_src_all.tar.gz" ) -MD5="f5232714137c1bb3d94e058b651ab041" +MD5="8a2c6bc5c05bb81a31f58667cde3018d" # Use a staging area in the conda dir rather than temp dirs, both to avoid # permission issues as well as to have things downloaded in a predictable @@ -16,7 +16,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-sgseq/meta.yaml b/recipes/bioconductor-sgseq/meta.yaml index 441ec1ee4a005..dd155352152dc 100644 --- a/recipes/bioconductor-sgseq/meta.yaml +++ b/recipes/bioconductor-sgseq/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.16.2" %} +{% set version = "1.18.0" %} {% set name = "SGSeq" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 031623023d4aae8f1ea43b159ffe13ab + md5: d9a682543d590316afbaacd1391433cf build: number: 0 rpaths: @@ -20,34 +20,34 @@ build: # Suggests: BiocStyle, BSgenome.Hsapiens.UCSC.hg19, TxDb.Hsapiens.UCSC.hg19.knownGene, knitr, rmarkdown requirements: host: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' - - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' - - 'bioconductor-biostrings >=2.50.0,<2.51.0' - - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' - - 'bioconductor-genomicalignments >=1.18.0,<1.19.0' - - 'bioconductor-genomicfeatures >=1.34.0,<1.35.0' - - 'bioconductor-genomicranges >=1.34.0,<1.35.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-rsamtools >=1.34.0,<1.35.0' - - 'bioconductor-rtracklayer >=1.42.0,<1.43.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' - - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' + - 'bioconductor-biocgenerics >=0.30.0,<0.31.0' + - 'bioconductor-biostrings >=2.52.0,<2.53.0' + - 'bioconductor-genomeinfodb >=1.20.0,<1.21.0' + - 'bioconductor-genomicalignments >=1.20.0,<1.21.0' + - 'bioconductor-genomicfeatures >=1.36.0,<1.37.0' + - 'bioconductor-genomicranges >=1.36.0,<1.37.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-rsamtools >=2.0.0,<2.1.0' + - 'bioconductor-rtracklayer >=1.44.0,<1.45.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' + - 'bioconductor-summarizedexperiment >=1.14.0,<1.15.0' - r-base - r-igraph - r-runit run: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' - - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' - - 'bioconductor-biostrings >=2.50.0,<2.51.0' - - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' - - 'bioconductor-genomicalignments >=1.18.0,<1.19.0' - - 'bioconductor-genomicfeatures >=1.34.0,<1.35.0' - - 'bioconductor-genomicranges >=1.34.0,<1.35.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-rsamtools >=1.34.0,<1.35.0' - - 'bioconductor-rtracklayer >=1.42.0,<1.43.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' - - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' + - 'bioconductor-biocgenerics >=0.30.0,<0.31.0' + - 'bioconductor-biostrings >=2.52.0,<2.53.0' + - 'bioconductor-genomeinfodb >=1.20.0,<1.21.0' + - 'bioconductor-genomicalignments >=1.20.0,<1.21.0' + - 'bioconductor-genomicfeatures >=1.36.0,<1.37.0' + - 'bioconductor-genomicranges >=1.36.0,<1.37.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-rsamtools >=2.0.0,<2.1.0' + - 'bioconductor-rtracklayer >=1.44.0,<1.45.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' + - 'bioconductor-summarizedexperiment >=1.14.0,<1.15.0' - r-base - r-igraph - r-runit diff --git a/recipes/bioconductor-shdz.db/meta.yaml b/recipes/bioconductor-shdz.db/meta.yaml index 23642c3e2f5b1..fa5dd41646d39 100644 --- a/recipes/bioconductor-shdz.db/meta.yaml +++ b/recipes/bioconductor-shdz.db/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.2.3" %} {% set name = "SHDZ.db" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -12,7 +12,7 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' md5: 63c4439a272a5cd0c4746e9e53a7bdc7 build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ @@ -20,14 +20,14 @@ build: # Suggests: DBI, annotate, RUnit requirements: host: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' - - 'bioconductor-org.hs.eg.db >=3.7.0,<3.8.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' + - 'bioconductor-org.hs.eg.db >=3.8.0,<3.9.0' - r-base run: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' - - 'bioconductor-org.hs.eg.db >=3.7.0,<3.8.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' + - 'bioconductor-org.hs.eg.db >=3.8.0,<3.9.0' - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-shdz.db/post-link.sh b/recipes/bioconductor-shdz.db/post-link.sh index 574476e938bf5..5b209fc737272 100644 --- a/recipes/bioconductor-shdz.db/post-link.sh +++ b/recipes/bioconductor-shdz.db/post-link.sh @@ -1,9 +1,10 @@ #!/bin/bash FN="SHDZ.db_3.2.3.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/SHDZ.db_3.2.3.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/SHDZ.db_3.2.3.tar.gz" "https://bioarchive.galaxyproject.org/SHDZ.db_3.2.3.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-shdz.db/bioconductor-shdz.db_3.2.3_src_all.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-shdz.db/bioconductor-shdz.db_3.2.3_src_all.tar.gz" ) MD5="63c4439a272a5cd0c4746e9e53a7bdc7" @@ -16,7 +17,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-shinymethyl/meta.yaml b/recipes/bioconductor-shinymethyl/meta.yaml index d51c5c762b657..aab70afb7dc1e 100644 --- a/recipes/bioconductor-shinymethyl/meta.yaml +++ b/recipes/bioconductor-shinymethyl/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.18.0" %} +{% set version = "1.20.0" %} {% set name = "shinyMethyl" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: fb818769476e39badee29c91a49736dc + md5: 4ce2a8ab4a4cd25c1d9d222ff8aa4147 build: number: 0 rpaths: @@ -20,17 +20,17 @@ build: # Suggests: shinyMethylData, minfiData, BiocStyle, RUnit, digest, knitr requirements: host: - - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' + - 'bioconductor-biocgenerics >=0.30.0,<0.31.0' - 'bioconductor-illuminahumanmethylation450kmanifest >=0.4.0,<0.5.0' - - 'bioconductor-minfi >=1.28.0,<1.29.0' + - 'bioconductor-minfi >=1.30.0,<1.31.0' - r-base - r-matrixstats - r-rcolorbrewer - 'r-shiny >=0.13.2' run: - - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' + - 'bioconductor-biocgenerics >=0.30.0,<0.31.0' - 'bioconductor-illuminahumanmethylation450kmanifest >=0.4.0,<0.5.0' - - 'bioconductor-minfi >=1.28.0,<1.29.0' + - 'bioconductor-minfi >=1.30.0,<1.31.0' - r-base - r-matrixstats - r-rcolorbrewer diff --git a/recipes/bioconductor-shinymethyldata/meta.yaml b/recipes/bioconductor-shinymethyldata/meta.yaml index aefef7b0266ff..d58f86f6c2ff8 100644 --- a/recipes/bioconductor-shinymethyldata/meta.yaml +++ b/recipes/bioconductor-shinymethyldata/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.2.0" %} +{% set version = "1.4.0" %} {% set name = "shinyMethylData" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: c7cfcef8e0c7dff18eb34609812ea3b4 + md5: f646ba21155e7392c9b00814e56e6967 build: number: 0 rpaths: @@ -22,7 +22,7 @@ requirements: - r-base run: - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-shinymethyldata/post-link.sh b/recipes/bioconductor-shinymethyldata/post-link.sh index 15f332904320b..b82be8a7c4c4b 100644 --- a/recipes/bioconductor-shinymethyldata/post-link.sh +++ b/recipes/bioconductor-shinymethyldata/post-link.sh @@ -1,11 +1,11 @@ #!/bin/bash -FN="shinyMethylData_1.2.0.tar.gz" +FN="shinyMethylData_1.4.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/experiment/src/contrib/shinyMethylData_1.2.0.tar.gz" - "https://bioarchive.galaxyproject.org/shinyMethylData_1.2.0.tar.gz" - "https://depot.galaxyproject.org/software/bioconductor-shinymethyldata/bioconductor-shinymethyldata_1.2.0_src_all.tar.gz" + "https://bioconductor.org/packages/3.9/data/experiment/src/contrib/shinyMethylData_1.4.0.tar.gz" + "https://bioarchive.galaxyproject.org/shinyMethylData_1.4.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-shinymethyldata/bioconductor-shinymethyldata_1.4.0_src_all.tar.gz" ) -MD5="c7cfcef8e0c7dff18eb34609812ea3b4" +MD5="f646ba21155e7392c9b00814e56e6967" # Use a staging area in the conda dir rather than temp dirs, both to avoid # permission issues as well as to have things downloaded in a predictable @@ -16,7 +16,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-shinytandem/meta.yaml b/recipes/bioconductor-shinytandem/meta.yaml index bc2dd28b9bbb7..e3c04d2a21ed7 100644 --- a/recipes/bioconductor-shinytandem/meta.yaml +++ b/recipes/bioconductor-shinytandem/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.20.1" %} +{% set version = "1.22.0" %} {% set name = "shinyTANDEM" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,22 +10,22 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 214390e95f00e0aa251e71caae2f37c9 + md5: 9d5e6eaa09ab0512d77bcb5c0821d759 build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ noarch: generic requirements: host: - - 'bioconductor-rtandem >=1.22.0,<1.23.0' + - 'bioconductor-rtandem >=1.24.0,<1.25.0' - r-base - r-mixtools - r-shiny - r-xtable run: - - 'bioconductor-rtandem >=1.22.0,<1.23.0' + - 'bioconductor-rtandem >=1.24.0,<1.25.0' - r-base - r-mixtools - r-shiny diff --git a/recipes/bioconductor-shortread/meta.yaml b/recipes/bioconductor-shortread/meta.yaml index b1471dc0521ad..41a7f8fdf7a09 100644 --- a/recipes/bioconductor-shortread/meta.yaml +++ b/recipes/bioconductor-shortread/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.40.0" %} +{% set version = "1.42.0" %} {% set name = "ShortRead" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 455d4397ae013d40ad8f5eb6e215d6b7 + md5: 2acf79d7db1b63a807cc4a3e597b80bc build: number: 0 rpaths: @@ -19,35 +19,35 @@ build: # Suggests: BiocStyle, RUnit, biomaRt, GenomicFeatures, yeastNagalakshmi requirements: host: - - 'bioconductor-biobase >=2.42.0,<2.43.0' - - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' - - 'bioconductor-biocparallel >=1.16.0,<1.17.0' - - 'bioconductor-biostrings >=2.50.0,<2.51.0' - - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' - - 'bioconductor-genomicalignments >=1.18.0,<1.19.0' - - 'bioconductor-genomicranges >=1.34.0,<1.35.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-rsamtools >=1.34.0,<1.35.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' - - 'bioconductor-xvector >=0.22.0,<0.23.0' - - 'bioconductor-zlibbioc >=1.28.0,<1.29.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' + - 'bioconductor-biocgenerics >=0.30.0,<0.31.0' + - 'bioconductor-biocparallel >=1.18.0,<1.19.0' + - 'bioconductor-biostrings >=2.52.0,<2.53.0' + - 'bioconductor-genomeinfodb >=1.20.0,<1.21.0' + - 'bioconductor-genomicalignments >=1.20.0,<1.21.0' + - 'bioconductor-genomicranges >=1.36.0,<1.37.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-rsamtools >=2.0.0,<2.1.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' + - 'bioconductor-xvector >=0.24.0,<0.25.0' + - 'bioconductor-zlibbioc >=1.30.0,<1.31.0' - r-base - r-hwriter - r-lattice - r-latticeextra run: - - 'bioconductor-biobase >=2.42.0,<2.43.0' - - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' - - 'bioconductor-biocparallel >=1.16.0,<1.17.0' - - 'bioconductor-biostrings >=2.50.0,<2.51.0' - - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' - - 'bioconductor-genomicalignments >=1.18.0,<1.19.0' - - 'bioconductor-genomicranges >=1.34.0,<1.35.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-rsamtools >=1.34.0,<1.35.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' - - 'bioconductor-xvector >=0.22.0,<0.23.0' - - 'bioconductor-zlibbioc >=1.28.0,<1.29.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' + - 'bioconductor-biocgenerics >=0.30.0,<0.31.0' + - 'bioconductor-biocparallel >=1.18.0,<1.19.0' + - 'bioconductor-biostrings >=2.52.0,<2.53.0' + - 'bioconductor-genomeinfodb >=1.20.0,<1.21.0' + - 'bioconductor-genomicalignments >=1.20.0,<1.21.0' + - 'bioconductor-genomicranges >=1.36.0,<1.37.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-rsamtools >=2.0.0,<2.1.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' + - 'bioconductor-xvector >=0.24.0,<0.25.0' + - 'bioconductor-zlibbioc >=1.30.0,<1.31.0' - r-base - r-hwriter - r-lattice diff --git a/recipes/bioconductor-siamcat/meta.yaml b/recipes/bioconductor-siamcat/meta.yaml index 4949dc5008e11..a2530695ddfa0 100644 --- a/recipes/bioconductor-siamcat/meta.yaml +++ b/recipes/bioconductor-siamcat/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.2.0" %} +{% set version = "1.4.0" %} {% set name = "SIAMCAT" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 06b5bd798aee4515ec2b3a0d79104cd7 + md5: 2966081b0a9da9d2182c528d48b5f065 build: number: 0 rpaths: @@ -20,7 +20,7 @@ build: # Suggests: BiocStyle, optparse, testthat, knitr, rmarkdown requirements: host: - - 'bioconductor-phyloseq >=1.26.0,<1.27.0' + - 'bioconductor-phyloseq >=1.28.0,<1.29.0' - r-base - r-beanplot - r-corrplot @@ -33,12 +33,13 @@ requirements: - r-mlr - r-paramhelpers - r-proc + - r-progress - r-prroc - r-rcolorbrewer - r-scales - r-stringr run: - - 'bioconductor-phyloseq >=1.26.0,<1.27.0' + - 'bioconductor-phyloseq >=1.28.0,<1.29.0' - r-base - r-beanplot - r-corrplot @@ -51,6 +52,7 @@ requirements: - r-mlr - r-paramhelpers - r-proc + - r-progress - r-prroc - r-rcolorbrewer - r-scales diff --git a/recipes/bioconductor-sictools/build.sh b/recipes/bioconductor-sictools/build.sh index 718841ba0eefb..c1d13421f5f1e 100644 --- a/recipes/bioconductor-sictools/build.sh +++ b/recipes/bioconductor-sictools/build.sh @@ -8,13 +8,4 @@ CXX=$CXX CXX98=$CXX CXX11=$CXX CXX14=$CXX" > ~/.R/Makevars -export C_INCLUDE_PATH=${PATH}/include -export LIBRARY_PATH=${PATH}/lib - -export LDFLAGS="-L$PREFIX/lib" -# https://github.com/samtools/samtools/issues/577 -if [[ "$(uname)" == "Linux" ]] ; then - export LDFLAGS="$LDFLAGS -Wl,--add-needed" -fi -cd src && make CC=$CC CFLAGS="$CFLAGS" && cd .. -$R CMD INSTALL --build . +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-sictools/meta.yaml b/recipes/bioconductor-sictools/meta.yaml index 5406989c711d8..36af15e5b3775 100644 --- a/recipes/bioconductor-sictools/meta.yaml +++ b/recipes/bioconductor-sictools/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.12.0" %} +{% set version = "1.14.0" %} {% set name = "SICtools" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 4e9730f2194cfb50c7808bfe43f0c3af + md5: a83288a7b568a23fb4e341d02898c93f build: number: 0 rpaths: @@ -19,27 +19,25 @@ build: # Suggests: knitr, RUnit, BiocGenerics requirements: host: - - 'bioconductor-biostrings >=2.50.0,<2.51.0' - - 'bioconductor-genomicranges >=1.34.0,<1.35.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-rsamtools >=1.34.0,<1.35.0' + - 'bioconductor-biostrings >=2.52.0,<2.53.0' + - 'bioconductor-genomicranges >=1.36.0,<1.37.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-rsamtools >=2.0.0,<2.1.0' - r-base - 'r-doparallel >=1.0.8' - 'r-matrixstats >=0.10.0' - 'r-plyr >=1.8.3' - 'r-stringr >=0.6.2' - - zlib run: - - 'bioconductor-biostrings >=2.50.0,<2.51.0' - - 'bioconductor-genomicranges >=1.34.0,<1.35.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-rsamtools >=1.34.0,<1.35.0' + - 'bioconductor-biostrings >=2.52.0,<2.53.0' + - 'bioconductor-genomicranges >=1.36.0,<1.37.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-rsamtools >=2.0.0,<2.1.0' - r-base - 'r-doparallel >=1.0.8' - 'r-matrixstats >=0.10.0' - 'r-plyr >=1.8.3' - 'r-stringr >=0.6.2' - - zlib build: - {{ compiler('c') }} - make diff --git a/recipes/bioconductor-sift.hsapiens.dbsnp132/meta.yaml b/recipes/bioconductor-sift.hsapiens.dbsnp132/meta.yaml index 44fcf8a40a1af..2d35208887d32 100644 --- a/recipes/bioconductor-sift.hsapiens.dbsnp132/meta.yaml +++ b/recipes/bioconductor-sift.hsapiens.dbsnp132/meta.yaml @@ -1,6 +1,6 @@ {% set version = "1.0.2" %} {% set name = "SIFT.Hsapiens.dbSNP132" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -12,23 +12,23 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' md5: c374f0bf4c99357cfe99e0b192c00d75 build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' - - 'bioconductor-variantannotation >=1.28.0,<1.29.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' + - 'bioconductor-variantannotation >=1.30.0,<1.31.0' - r-base - 'r-rsqlite >=0.11.0' run: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' - - 'bioconductor-variantannotation >=1.28.0,<1.29.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' + - 'bioconductor-variantannotation >=1.30.0,<1.31.0' - r-base - 'r-rsqlite >=0.11.0' - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-sift.hsapiens.dbsnp132/post-link.sh b/recipes/bioconductor-sift.hsapiens.dbsnp132/post-link.sh index 14dcbf4ad9771..d79cb96663245 100644 --- a/recipes/bioconductor-sift.hsapiens.dbsnp132/post-link.sh +++ b/recipes/bioconductor-sift.hsapiens.dbsnp132/post-link.sh @@ -1,9 +1,10 @@ #!/bin/bash FN="SIFT.Hsapiens.dbSNP132_1.0.2.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/SIFT.Hsapiens.dbSNP132_1.0.2.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/SIFT.Hsapiens.dbSNP132_1.0.2.tar.gz" "https://bioarchive.galaxyproject.org/SIFT.Hsapiens.dbSNP132_1.0.2.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-sift.hsapiens.dbsnp132/bioconductor-sift.hsapiens.dbsnp132_1.0.2_src_all.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-sift.hsapiens.dbsnp132/bioconductor-sift.hsapiens.dbsnp132_1.0.2_src_all.tar.gz" ) MD5="c374f0bf4c99357cfe99e0b192c00d75" @@ -16,7 +17,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-sift.hsapiens.dbsnp137/meta.yaml b/recipes/bioconductor-sift.hsapiens.dbsnp137/meta.yaml index 4289cca0a5ce5..1ce5e64678494 100644 --- a/recipes/bioconductor-sift.hsapiens.dbsnp137/meta.yaml +++ b/recipes/bioconductor-sift.hsapiens.dbsnp137/meta.yaml @@ -1,6 +1,6 @@ {% set version = "1.0.0" %} {% set name = "SIFT.Hsapiens.dbSNP137" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -12,23 +12,23 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' md5: 3c3e73f826399af5ff368d1aab12cfd1 build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' - - 'bioconductor-variantannotation >=1.28.0,<1.29.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' + - 'bioconductor-variantannotation >=1.30.0,<1.31.0' - r-base - 'r-rsqlite >=0.11.0' run: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' - - 'bioconductor-variantannotation >=1.28.0,<1.29.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' + - 'bioconductor-variantannotation >=1.30.0,<1.31.0' - r-base - 'r-rsqlite >=0.11.0' - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-sift.hsapiens.dbsnp137/post-link.sh b/recipes/bioconductor-sift.hsapiens.dbsnp137/post-link.sh index fba7b3de0e899..3852f867e5912 100644 --- a/recipes/bioconductor-sift.hsapiens.dbsnp137/post-link.sh +++ b/recipes/bioconductor-sift.hsapiens.dbsnp137/post-link.sh @@ -1,9 +1,10 @@ #!/bin/bash FN="SIFT.Hsapiens.dbSNP137_1.0.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/SIFT.Hsapiens.dbSNP137_1.0.0.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/SIFT.Hsapiens.dbSNP137_1.0.0.tar.gz" "https://bioarchive.galaxyproject.org/SIFT.Hsapiens.dbSNP137_1.0.0.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-sift.hsapiens.dbsnp137/bioconductor-sift.hsapiens.dbsnp137_1.0.0_src_all.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-sift.hsapiens.dbsnp137/bioconductor-sift.hsapiens.dbsnp137_1.0.0_src_all.tar.gz" ) MD5="3c3e73f826399af5ff368d1aab12cfd1" @@ -16,7 +17,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-sigar/meta.yaml b/recipes/bioconductor-sigar/meta.yaml index b3a895c435633..eaf3811e5bcdd 100644 --- a/recipes/bioconductor-sigar/meta.yaml +++ b/recipes/bioconductor-sigar/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.30.0" %} +{% set version = "1.32.0" %} {% set name = "sigaR" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: f27d79fb98bc4327fbc638f140a3f0d7 + md5: 593f28de781124788a38acc25e3e95ea build: number: 0 rpaths: @@ -20,10 +20,10 @@ build: # Suggests: CGHcall requirements: host: - - 'bioconductor-biobase >=2.42.0,<2.43.0' - - 'bioconductor-cghbase >=1.42.0,<1.43.0' - - 'bioconductor-limma >=3.38.0,<3.39.0' - - 'bioconductor-marray >=1.60.0,<1.61.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' + - 'bioconductor-cghbase >=1.44.0,<1.45.0' + - 'bioconductor-limma >=3.40.0,<3.41.0' + - 'bioconductor-marray >=1.62.0,<1.63.0' - r-base - 'r-corpcor >=1.6.2' - r-igraph @@ -33,10 +33,10 @@ requirements: - r-quadprog - r-snowfall run: - - 'bioconductor-biobase >=2.42.0,<2.43.0' - - 'bioconductor-cghbase >=1.42.0,<1.43.0' - - 'bioconductor-limma >=3.38.0,<3.39.0' - - 'bioconductor-marray >=1.60.0,<1.61.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' + - 'bioconductor-cghbase >=1.44.0,<1.45.0' + - 'bioconductor-limma >=3.40.0,<3.41.0' + - 'bioconductor-marray >=1.62.0,<1.63.0' - r-base - 'r-corpcor >=1.6.2' - r-igraph diff --git a/recipes/bioconductor-sigcheck/meta.yaml b/recipes/bioconductor-sigcheck/meta.yaml index c268948558dd4..707674f8884e8 100644 --- a/recipes/bioconductor-sigcheck/meta.yaml +++ b/recipes/bioconductor-sigcheck/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "2.14.0" %} +{% set version = "2.16.0" %} {% set name = "SigCheck" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: f63b63b11545697c94145639594dd0bb + md5: c976fbe0fc31ae7bfdbee833ba2a1af8 build: number: 0 rpaths: @@ -20,16 +20,16 @@ build: # Suggests: BiocStyle, breastCancerNKI, qusage requirements: host: - - 'bioconductor-biobase >=2.42.0,<2.43.0' - - 'bioconductor-biocparallel >=1.16.0,<1.17.0' - - 'bioconductor-mlinterfaces >=1.62.0,<1.63.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' + - 'bioconductor-biocparallel >=1.18.0,<1.19.0' + - 'bioconductor-mlinterfaces >=1.64.0,<1.65.0' - r-base - r-e1071 - r-survival run: - - 'bioconductor-biobase >=2.42.0,<2.43.0' - - 'bioconductor-biocparallel >=1.16.0,<1.17.0' - - 'bioconductor-mlinterfaces >=1.62.0,<1.63.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' + - 'bioconductor-biocparallel >=1.18.0,<1.19.0' + - 'bioconductor-mlinterfaces >=1.64.0,<1.65.0' - r-base - r-e1071 - r-survival diff --git a/recipes/bioconductor-sigfeature/meta.yaml b/recipes/bioconductor-sigfeature/meta.yaml index 825b662899333..bdb1fd5130901 100644 --- a/recipes/bioconductor-sigfeature/meta.yaml +++ b/recipes/bioconductor-sigfeature/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.0.0" %} +{% set version = "1.2.0" %} {% set name = "sigFeature" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 5e75e6f3818225a0b8135d9cd4acaaa6 + md5: 8fdee0fdd11816dea036a8bcc43f714b build: number: 0 rpaths: @@ -20,9 +20,9 @@ build: # Suggests: RUnit, BiocGenerics, knitr requirements: host: - - 'bioconductor-biocparallel >=1.16.0,<1.17.0' - - 'bioconductor-biocviews >=1.50.0,<1.51.0' - - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' + - 'bioconductor-biocparallel >=1.18.0,<1.19.0' + - 'bioconductor-biocviews >=1.52.0,<1.53.0' + - 'bioconductor-summarizedexperiment >=1.14.0,<1.15.0' - r-base - r-e1071 - r-matrix @@ -32,9 +32,9 @@ requirements: - r-rcolorbrewer - r-sparsem run: - - 'bioconductor-biocparallel >=1.16.0,<1.17.0' - - 'bioconductor-biocviews >=1.50.0,<1.51.0' - - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' + - 'bioconductor-biocparallel >=1.18.0,<1.19.0' + - 'bioconductor-biocviews >=1.52.0,<1.53.0' + - 'bioconductor-summarizedexperiment >=1.14.0,<1.15.0' - r-base - r-e1071 - r-matrix diff --git a/recipes/bioconductor-sigfuge/meta.yaml b/recipes/bioconductor-sigfuge/meta.yaml index d2e4dede1540f..35abcd2189ef8 100644 --- a/recipes/bioconductor-sigfuge/meta.yaml +++ b/recipes/bioconductor-sigfuge/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.20.0" %} +{% set version = "1.22.0" %} {% set name = "SigFuge" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 617321ada3ea3a85d48d9643d6d64ecc + md5: 630ba0ad1edb05c6c3f19b8d612e8163 build: number: 0 rpaths: @@ -20,14 +20,14 @@ build: # Suggests: org.Hs.eg.db, prebsdata, Rsamtools (>= 1.17.0), TxDb.Hsapiens.UCSC.hg19.knownGene, BiocStyle requirements: host: - - 'bioconductor-genomicranges >=1.34.0,<1.35.0' + - 'bioconductor-genomicranges >=1.36.0,<1.37.0' - r-base - r-ggplot2 - r-matlab - r-reshape - r-sigclust run: - - 'bioconductor-genomicranges >=1.34.0,<1.35.0' + - 'bioconductor-genomicranges >=1.36.0,<1.37.0' - r-base - r-ggplot2 - r-matlab diff --git a/recipes/bioconductor-siggenes/meta.yaml b/recipes/bioconductor-siggenes/meta.yaml index 66ebd60bd2322..cc4eb8095d905 100644 --- a/recipes/bioconductor-siggenes/meta.yaml +++ b/recipes/bioconductor-siggenes/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.56.0" %} +{% set version = "1.58.0" %} {% set name = "siggenes" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,23 +10,25 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 28a8f05b99d9576b8ace9ea342efe70c + md5: c94454bf57390fbc699c3b02144177d6 build: number: 0 rpaths: - lib/R/lib/ - lib/ noarch: generic -# Suggests: affy, annotate, genefilter, KernSmooth, scrime (>= 1.2.5) +# Suggests: affy, annotate, genefilter, KernSmooth requirements: host: - - 'bioconductor-biobase >=2.42.0,<2.43.0' - - 'bioconductor-multtest >=2.38.0,<2.39.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' + - 'bioconductor-multtest >=2.40.0,<2.41.0' - r-base + - 'r-scrime >=1.2.5' run: - - 'bioconductor-biobase >=2.42.0,<2.43.0' - - 'bioconductor-multtest >=2.38.0,<2.39.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' + - 'bioconductor-multtest >=2.40.0,<2.41.0' - r-base + - 'r-scrime >=1.2.5' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-sights/meta.yaml b/recipes/bioconductor-sights/meta.yaml index e77c3298cf947..bb1057304eba6 100644 --- a/recipes/bioconductor-sights/meta.yaml +++ b/recipes/bioconductor-sights/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.8.1" %} +{% set version = "1.10.0" %} {% set name = "sights" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - sha256: b61eb75ea849739c324e0fbbe02b28810d18453621697f1f679c68ac7080ac93 + md5: 114674c0f24aeacc971a581bb3f50cd3 build: number: 0 rpaths: @@ -20,14 +20,14 @@ build: # Suggests: testthat, knitr, rmarkdown, ggthemes, gridExtra, xlsx requirements: host: - - 'bioconductor-qvalue >=2.14.0,<2.15.0' + - 'bioconductor-qvalue >=2.16.0,<2.17.0' - r-base - 'r-ggplot2 >=2.0' - 'r-lattice >=0.2' - 'r-mass >=7.3' - 'r-reshape2 >=1.4' run: - - 'bioconductor-qvalue >=2.14.0,<2.15.0' + - 'bioconductor-qvalue >=2.16.0,<2.17.0' - r-base - 'r-ggplot2 >=2.0' - 'r-lattice >=0.2' diff --git a/recipes/bioconductor-signer/meta.yaml b/recipes/bioconductor-signer/meta.yaml index 8d757a8cf4327..2a98235ba68bc 100644 --- a/recipes/bioconductor-signer/meta.yaml +++ b/recipes/bioconductor-signer/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.8.0" %} +{% set version = "1.10.0" %} {% set name = "signeR" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 79074171d5f1f9af6f93abcfcc96cbe1 + md5: eb18254515946efe1641254d1e3bd639 build: number: 0 rpaths: @@ -20,10 +20,10 @@ build: # SystemRequirements: C++11 requirements: host: - - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' - - 'bioconductor-biostrings >=2.50.0,<2.51.0' - - 'bioconductor-genomicranges >=1.34.0,<1.35.0' - - 'bioconductor-variantannotation >=1.28.0,<1.29.0' + - 'bioconductor-biocgenerics >=0.30.0,<0.31.0' + - 'bioconductor-biostrings >=2.52.0,<2.53.0' + - 'bioconductor-genomicranges >=1.36.0,<1.37.0' + - 'bioconductor-variantannotation >=1.30.0,<1.31.0' - r-base - r-class - r-nloptr @@ -32,10 +32,10 @@ requirements: - r-rcpp - 'r-rcpparmadillo >=0.7.100' run: - - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' - - 'bioconductor-biostrings >=2.50.0,<2.51.0' - - 'bioconductor-genomicranges >=1.34.0,<1.35.0' - - 'bioconductor-variantannotation >=1.28.0,<1.29.0' + - 'bioconductor-biocgenerics >=0.30.0,<0.31.0' + - 'bioconductor-biostrings >=2.52.0,<2.53.0' + - 'bioconductor-genomicranges >=1.36.0,<1.37.0' + - 'bioconductor-variantannotation >=1.30.0,<1.31.0' - r-base - r-class - r-nloptr diff --git a/recipes/bioconductor-signet/meta.yaml b/recipes/bioconductor-signet/meta.yaml index 0855f077d79c9..12f08f87742d5 100644 --- a/recipes/bioconductor-signet/meta.yaml +++ b/recipes/bioconductor-signet/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.2.2" %} +{% set version = "1.4.0" %} {% set name = "signet" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: e4c4ef194cd4a7f22e5a45da76dd3f5b + md5: e1799bca498f155881e1eadfc9934cd5 build: number: 0 rpaths: @@ -20,13 +20,13 @@ build: # Suggests: graphite, BiocStyle, knitr, rmarkdown requirements: host: - - 'bioconductor-graph >=1.60.0,<1.61.0' - - 'bioconductor-rbgl >=1.58.0,<1.59.0' + - 'bioconductor-graph >=1.62.0,<1.63.0' + - 'bioconductor-rbgl >=1.60.0,<1.61.0' - r-base - r-igraph run: - - 'bioconductor-graph >=1.60.0,<1.61.0' - - 'bioconductor-rbgl >=1.58.0,<1.59.0' + - 'bioconductor-graph >=1.62.0,<1.63.0' + - 'bioconductor-rbgl >=1.60.0,<1.61.0' - r-base - r-igraph test: diff --git a/recipes/bioconductor-sigpathway/meta.yaml b/recipes/bioconductor-sigpathway/meta.yaml index fdb3aa1b0f153..2d6a5379e13c4 100644 --- a/recipes/bioconductor-sigpathway/meta.yaml +++ b/recipes/bioconductor-sigpathway/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.50.0" %} +{% set version = "1.52.0" %} {% set name = "sigPathway" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: b825fbbd08a65e76c61fef39eab3492b + md5: e6b44d4bb6be64e4b25ac5a1682aa9f2 build: number: 0 rpaths: diff --git a/recipes/bioconductor-sigsquared/meta.yaml b/recipes/bioconductor-sigsquared/meta.yaml index f9aa26e6d34e5..4cfd532699543 100644 --- a/recipes/bioconductor-sigsquared/meta.yaml +++ b/recipes/bioconductor-sigsquared/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.14.0" %} +{% set version = "1.16.0" %} {% set name = "sigsquared" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 3cc54becc997d3072a3c626a4267462b + md5: c2a6ab23b6c6df437e2164bd22741a06 build: number: 0 rpaths: @@ -20,11 +20,11 @@ build: # Suggests: RUnit, BiocGenerics requirements: host: - - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' - r-base - r-survival run: - - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' - r-base - r-survival test: diff --git a/recipes/bioconductor-silva128.1mgdb/meta.yaml b/recipes/bioconductor-silva128.1mgdb/meta.yaml index 04dff277e7e1e..854acda9df15b 100644 --- a/recipes/bioconductor-silva128.1mgdb/meta.yaml +++ b/recipes/bioconductor-silva128.1mgdb/meta.yaml @@ -1,6 +1,6 @@ {% set version = "1.00.0" %} {% set name = "silva128.1MgDb" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -12,19 +12,19 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' md5: f73cc038441a0a166c07582eec9a77b4 build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ noarch: generic requirements: host: - - 'bioconductor-metagenomefeatures >=2.2.0,<2.3.0' + - 'bioconductor-metagenomefeatures >=2.4.0,<2.5.0' - r-base run: - - 'bioconductor-metagenomefeatures >=2.2.0,<2.3.0' + - 'bioconductor-metagenomefeatures >=2.4.0,<2.5.0' - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-silva128.1mgdb/post-link.sh b/recipes/bioconductor-silva128.1mgdb/post-link.sh index 29dd5a637bd78..aa2eefdc01b60 100644 --- a/recipes/bioconductor-silva128.1mgdb/post-link.sh +++ b/recipes/bioconductor-silva128.1mgdb/post-link.sh @@ -1,9 +1,10 @@ #!/bin/bash FN="silva128.1MgDb_1.00.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/silva128.1MgDb_1.00.0.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/silva128.1MgDb_1.00.0.tar.gz" "https://bioarchive.galaxyproject.org/silva128.1MgDb_1.00.0.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-silva128.1mgdb/bioconductor-silva128.1mgdb_1.00.0_src_all.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-silva128.1mgdb/bioconductor-silva128.1mgdb_1.00.0_src_all.tar.gz" ) MD5="f73cc038441a0a166c07582eec9a77b4" @@ -16,7 +17,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-sim/meta.yaml b/recipes/bioconductor-sim/meta.yaml index 9cda5dc1e8a53..3666c0789d963 100644 --- a/recipes/bioconductor-sim/meta.yaml +++ b/recipes/bioconductor-sim/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.52.0" %} +{% set version = "1.54.0" %} {% set name = "SIM" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,22 +10,22 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 1c7164bbcfbc8d3dfb2495875c3aa478 + md5: 889785353c57a16d34e19c3c62652cea build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ # Suggests: biomaRt, RColorBrewer requirements: host: - - 'bioconductor-globaltest >=5.36.0,<5.37.0' - - 'bioconductor-quantsmooth >=1.48.0,<1.49.0' + - 'bioconductor-globaltest >=5.38.0,<5.39.0' + - 'bioconductor-quantsmooth >=1.50.0,<1.51.0' - r-base - r-quantreg run: - - 'bioconductor-globaltest >=5.36.0,<5.37.0' - - 'bioconductor-quantsmooth >=1.48.0,<1.49.0' + - 'bioconductor-globaltest >=5.38.0,<5.39.0' + - 'bioconductor-quantsmooth >=1.50.0,<1.51.0' - r-base - r-quantreg build: diff --git a/recipes/bioconductor-simat/meta.yaml b/recipes/bioconductor-simat/meta.yaml index 48dbe8c81eba6..1f6396320cf91 100644 --- a/recipes/bioconductor-simat/meta.yaml +++ b/recipes/bioconductor-simat/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.14.0" %} +{% set version = "1.16.0" %} {% set name = "SIMAT" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: a72965e304ff7a6e7b8a499e648aa2d7 + md5: 205568831e77d3ad2c948c59897a98ac build: number: 0 rpaths: @@ -19,13 +19,13 @@ build: # Suggests: RUnit, BiocGenerics requirements: host: - - 'bioconductor-mzr >=2.16.0,<2.17.0' + - 'bioconductor-mzr >=2.18.0,<2.19.0' - r-base - r-ggplot2 - 'r-rcpp >=0.11.3' - r-reshape2 run: - - 'bioconductor-mzr >=2.16.0,<2.17.0' + - 'bioconductor-mzr >=2.18.0,<2.19.0' - r-base - r-ggplot2 - 'r-rcpp >=0.11.3' diff --git a/recipes/bioconductor-simbindprofiles/meta.yaml b/recipes/bioconductor-simbindprofiles/meta.yaml index e36298d7af151..159f26482608e 100644 --- a/recipes/bioconductor-simbindprofiles/meta.yaml +++ b/recipes/bioconductor-simbindprofiles/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.20.0" %} +{% set version = "1.22.0" %} {% set name = "SimBindProfiles" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,24 +10,24 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 1bebc53f15f0afdd77b7512beaf06c28 + md5: a8a894ca754170d902be58c782e9644b build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ noarch: generic requirements: host: - - 'bioconductor-biobase >=2.42.0,<2.43.0' - - 'bioconductor-limma >=3.38.0,<3.39.0' - - 'bioconductor-ringo >=1.46.0,<1.47.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' + - 'bioconductor-limma >=3.40.0,<3.41.0' + - 'bioconductor-ringo >=1.48.0,<1.49.0' - r-base - r-mclust run: - - 'bioconductor-biobase >=2.42.0,<2.43.0' - - 'bioconductor-limma >=3.38.0,<3.39.0' - - 'bioconductor-ringo >=1.46.0,<1.47.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' + - 'bioconductor-limma >=3.40.0,<3.41.0' + - 'bioconductor-ringo >=1.48.0,<1.49.0' - r-base - r-mclust test: diff --git a/recipes/bioconductor-simd/meta.yaml b/recipes/bioconductor-simd/meta.yaml index 75a79cbe642a2..b11e234382077 100644 --- a/recipes/bioconductor-simd/meta.yaml +++ b/recipes/bioconductor-simd/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.0.0" %} +{% set version = "1.2.0" %} {% set name = "SIMD" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 385e8cbf0131d3ef3707b6ba582948e8 + md5: f16d1032aca332c206c4f96d1eb967cf build: number: 0 rpaths: @@ -19,13 +19,13 @@ build: # Suggests: BiocStyle, knitr,rmarkdown requirements: host: - - 'bioconductor-edger >=3.24.0,<3.25.0' - - 'bioconductor-methylmnm >=1.20.0,<1.21.0' + - 'bioconductor-edger >=3.26.0,<3.27.0' + - 'bioconductor-methylmnm >=1.22.0,<1.23.0' - r-base - r-statmod run: - - 'bioconductor-edger >=3.24.0,<3.25.0' - - 'bioconductor-methylmnm >=1.20.0,<1.21.0' + - 'bioconductor-edger >=3.26.0,<3.27.0' + - 'bioconductor-methylmnm >=1.22.0,<1.23.0' - r-base - r-statmod build: diff --git a/recipes/bioconductor-similarpeak/meta.yaml b/recipes/bioconductor-similarpeak/meta.yaml index ad627b701ce47..24c648a4f9f3e 100644 --- a/recipes/bioconductor-similarpeak/meta.yaml +++ b/recipes/bioconductor-similarpeak/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.14.0" %} +{% set version = "1.16.0" %} {% set name = "similaRpeak" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 5131bceb89b919a1df752c9047a55671 + md5: cbe863e05270e59cb80abd239fbd1182 build: number: 0 rpaths: diff --git a/recipes/bioconductor-simlr/meta.yaml b/recipes/bioconductor-simlr/meta.yaml index 464b635b28aea..3b068c318d991 100644 --- a/recipes/bioconductor-simlr/meta.yaml +++ b/recipes/bioconductor-simlr/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.8.1" %} +{% set version = "1.10.0" %} {% set name = "SIMLR" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: e3b90e0d215caef03ff0522962420118 + md5: e4b3f7ebe8ef92491f009efc463ccd2c build: number: 0 rpaths: diff --git a/recipes/bioconductor-simpintlists/meta.yaml b/recipes/bioconductor-simpintlists/meta.yaml index e62148f594c5b..efba566824c23 100644 --- a/recipes/bioconductor-simpintlists/meta.yaml +++ b/recipes/bioconductor-simpintlists/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.18.0" %} +{% set version = "1.20.0" %} {% set name = "simpIntLists" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 9276ea6e949af976d59fe3317bb0e208 + md5: 27879fea1d9ddd0404829b7de8eaae77 build: number: 0 rpaths: @@ -22,7 +22,7 @@ requirements: - r-base run: - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-simpintlists/post-link.sh b/recipes/bioconductor-simpintlists/post-link.sh index 62006cae2152e..fcc0f07d1d99d 100644 --- a/recipes/bioconductor-simpintlists/post-link.sh +++ b/recipes/bioconductor-simpintlists/post-link.sh @@ -1,11 +1,11 @@ #!/bin/bash -FN="simpIntLists_1.18.0.tar.gz" +FN="simpIntLists_1.20.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/experiment/src/contrib/simpIntLists_1.18.0.tar.gz" - "https://bioarchive.galaxyproject.org/simpIntLists_1.18.0.tar.gz" - "https://depot.galaxyproject.org/software/bioconductor-simpintlists/bioconductor-simpintlists_1.18.0_src_all.tar.gz" + "https://bioconductor.org/packages/3.9/data/experiment/src/contrib/simpIntLists_1.20.0.tar.gz" + "https://bioarchive.galaxyproject.org/simpIntLists_1.20.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-simpintlists/bioconductor-simpintlists_1.20.0_src_all.tar.gz" ) -MD5="9276ea6e949af976d59fe3317bb0e208" +MD5="27879fea1d9ddd0404829b7de8eaae77" # Use a staging area in the conda dir rather than temp dirs, both to avoid # permission issues as well as to have things downloaded in a predictable @@ -16,7 +16,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-simpleaffy/meta.yaml b/recipes/bioconductor-simpleaffy/meta.yaml index 3e16de8309b36..213d051ae998f 100644 --- a/recipes/bioconductor-simpleaffy/meta.yaml +++ b/recipes/bioconductor-simpleaffy/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "2.58.0" %} +{% set version = "2.60.0" %} {% set name = "simpleaffy" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: f6d7cbd0c17d30f74cf54782be74fbba + md5: cdc3ec6c91a8a9495b4bf5af62a5b1c8 build: number: 0 rpaths: @@ -18,18 +18,18 @@ build: - lib/ requirements: host: - - 'bioconductor-affy >=1.60.0,<1.61.0' - - 'bioconductor-biobase >=2.42.0,<2.43.0' - - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' - - 'bioconductor-gcrma >=2.54.0,<2.55.0' - - 'bioconductor-genefilter >=1.64.0,<1.65.0' + - 'bioconductor-affy >=1.62.0,<1.63.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' + - 'bioconductor-biocgenerics >=0.30.0,<0.31.0' + - 'bioconductor-gcrma >=2.56.0,<2.57.0' + - 'bioconductor-genefilter >=1.66.0,<1.67.0' - r-base run: - - 'bioconductor-affy >=1.60.0,<1.61.0' - - 'bioconductor-biobase >=2.42.0,<2.43.0' - - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' - - 'bioconductor-gcrma >=2.54.0,<2.55.0' - - 'bioconductor-genefilter >=1.64.0,<1.65.0' + - 'bioconductor-affy >=1.62.0,<1.63.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' + - 'bioconductor-biocgenerics >=0.30.0,<0.31.0' + - 'bioconductor-gcrma >=2.56.0,<2.57.0' + - 'bioconductor-genefilter >=1.66.0,<1.67.0' - r-base build: - {{ compiler('c') }} diff --git a/recipes/bioconductor-simulatorz/meta.yaml b/recipes/bioconductor-simulatorz/meta.yaml index 78e2fdbc3a63f..52e7da0e8c095 100644 --- a/recipes/bioconductor-simulatorz/meta.yaml +++ b/recipes/bioconductor-simulatorz/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.16.0" %} +{% set version = "1.18.0" %} {% set name = "simulatorZ" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 23b14912a86f22445fa0b20ccb9a8769 + md5: c4e86e7faa46af6795bc943eb311384e build: number: 0 rpaths: @@ -19,20 +19,20 @@ build: # Suggests: RUnit, BiocStyle, curatedOvarianData, parathyroidSE, superpc requirements: host: - - 'bioconductor-biobase >=2.42.0,<2.43.0' - - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' - - 'bioconductor-genomicranges >=1.34.0,<1.35.0' - - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' + - 'bioconductor-biocgenerics >=0.30.0,<0.31.0' + - 'bioconductor-genomicranges >=1.36.0,<1.37.0' + - 'bioconductor-summarizedexperiment >=1.14.0,<1.15.0' - r-base - r-coxboost - r-gbm - r-hmisc - r-survival run: - - 'bioconductor-biobase >=2.42.0,<2.43.0' - - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' - - 'bioconductor-genomicranges >=1.34.0,<1.35.0' - - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' + - 'bioconductor-biocgenerics >=0.30.0,<0.31.0' + - 'bioconductor-genomicranges >=1.36.0,<1.37.0' + - 'bioconductor-summarizedexperiment >=1.14.0,<1.15.0' - r-base - r-coxboost - r-gbm diff --git a/recipes/bioconductor-sincell/meta.yaml b/recipes/bioconductor-sincell/meta.yaml index 8933f237c2c4f..05b65b3bb27c6 100644 --- a/recipes/bioconductor-sincell/meta.yaml +++ b/recipes/bioconductor-sincell/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.14.1" %} +{% set version = "1.16.0" %} {% set name = "sincell" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 8a94aea3ba1a97114386f0d05daaab01 + md5: e5fe14dc73fdf0a8acc9e2cd85558d33 build: number: 0 rpaths: diff --git a/recipes/bioconductor-single.mtec.transcriptomes/meta.yaml b/recipes/bioconductor-single.mtec.transcriptomes/meta.yaml index 9e95e63e05d1b..daafd3efa2df9 100644 --- a/recipes/bioconductor-single.mtec.transcriptomes/meta.yaml +++ b/recipes/bioconductor-single.mtec.transcriptomes/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.10.0" %} +{% set version = "1.12.0" %} {% set name = "Single.mTEC.Transcriptomes" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: b56327144804cf3af178a5750b028707 + md5: 8d1e883b5ca8e20ba358a4988827fb6c build: number: 0 rpaths: @@ -23,7 +23,7 @@ requirements: - r-base run: - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-single.mtec.transcriptomes/post-link.sh b/recipes/bioconductor-single.mtec.transcriptomes/post-link.sh index 52f6dbc21654d..5ee1b29efa6de 100644 --- a/recipes/bioconductor-single.mtec.transcriptomes/post-link.sh +++ b/recipes/bioconductor-single.mtec.transcriptomes/post-link.sh @@ -1,11 +1,11 @@ #!/bin/bash -FN="Single.mTEC.Transcriptomes_1.10.0.tar.gz" +FN="Single.mTEC.Transcriptomes_1.12.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/experiment/src/contrib/Single.mTEC.Transcriptomes_1.10.0.tar.gz" - "https://bioarchive.galaxyproject.org/Single.mTEC.Transcriptomes_1.10.0.tar.gz" - "https://depot.galaxyproject.org/software/bioconductor-single.mtec.transcriptomes/bioconductor-single.mtec.transcriptomes_1.10.0_src_all.tar.gz" + "https://bioconductor.org/packages/3.9/data/experiment/src/contrib/Single.mTEC.Transcriptomes_1.12.0.tar.gz" + "https://bioarchive.galaxyproject.org/Single.mTEC.Transcriptomes_1.12.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-single.mtec.transcriptomes/bioconductor-single.mtec.transcriptomes_1.12.0_src_all.tar.gz" ) -MD5="b56327144804cf3af178a5750b028707" +MD5="8d1e883b5ca8e20ba358a4988827fb6c" # Use a staging area in the conda dir rather than temp dirs, both to avoid # permission issues as well as to have things downloaded in a predictable @@ -16,7 +16,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-singlecellexperiment/meta.yaml b/recipes/bioconductor-singlecellexperiment/meta.yaml index 15cf632871b26..6ab39aae522e1 100644 --- a/recipes/bioconductor-singlecellexperiment/meta.yaml +++ b/recipes/bioconductor-singlecellexperiment/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.4.0" %} +{% set version = "1.6.0" %} {% set name = "SingleCellExperiment" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,24 +10,24 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 42e03af7c4955e1c6fe7afa9d45c7f34 + md5: e100bdfc9835d03ae02111994ec5e4d4 build: number: 0 rpaths: - lib/R/lib/ - lib/ noarch: generic -# Suggests: testthat, BiocStyle, knitr, rmarkdown, scRNAseq, magrittr, Rtsne +# Suggests: testthat, BiocStyle, knitr, rmarkdown, scRNAseq, magrittr, Rtsne, Matrix requirements: host: - - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' - - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' + - 'bioconductor-biocgenerics >=0.30.0,<0.31.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' + - 'bioconductor-summarizedexperiment >=1.14.0,<1.15.0' - r-base run: - - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' - - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' + - 'bioconductor-biocgenerics >=0.30.0,<0.31.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' + - 'bioconductor-summarizedexperiment >=1.14.0,<1.15.0' - r-base test: commands: diff --git a/recipes/bioconductor-singlecelltk/meta.yaml b/recipes/bioconductor-singlecelltk/meta.yaml index 0b4d63e5392c2..81fb92506f815 100644 --- a/recipes/bioconductor-singlecelltk/meta.yaml +++ b/recipes/bioconductor-singlecelltk/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.2.3" %} +{% set version = "1.4.0" %} {% set name = "singleCellTK" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,31 +10,31 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 52c4647995b617eba6f157ee2678c058 + md5: 27a03a7ff4f1da68d92660342e6f74d7 build: number: 0 rpaths: - lib/R/lib/ - lib/ noarch: generic -# Suggests: testthat, Rsubread, BiocStyle, knitr, bladderbatch, rmarkdown, org.Mm.eg.db, org.Hs.eg.db, scRNAseq, xtable, spelling +# Suggests: testthat, Rsubread, BiocStyle, knitr, bladderbatch, rmarkdown, org.Mm.eg.db, org.Hs.eg.db, scRNAseq, xtable, spelling, GSEABase requirements: host: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' - - 'bioconductor-biobase >=2.42.0,<2.43.0' - - 'bioconductor-complexheatmap >=1.20.0,<1.21.0' - - 'bioconductor-delayedarray >=0.8.0,<0.9.0' - - 'bioconductor-deseq2 >=1.22.0,<1.23.0' - - 'bioconductor-ggtree >=1.14.0,<1.15.0' - - 'bioconductor-gsva >=1.30.0,<1.31.0' - - 'bioconductor-gsvadata >=1.18.0,<1.19.0' - - 'bioconductor-limma >=3.38.0,<3.39.0' - - 'bioconductor-mast >=1.8.0,<1.9.0' - - 'bioconductor-multtest >=2.38.0,<2.39.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' - - 'bioconductor-singlecellexperiment >=1.4.0,<1.5.0' - - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' - - 'bioconductor-sva >=3.30.0,<3.31.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' + - 'bioconductor-complexheatmap >=2.0.0,<2.1.0' + - 'bioconductor-delayedarray >=0.10.0,<0.11.0' + - 'bioconductor-deseq2 >=1.24.0,<1.25.0' + - 'bioconductor-ggtree >=1.16.0,<1.17.0' + - 'bioconductor-gsva >=1.32.0,<1.33.0' + - 'bioconductor-gsvadata >=1.20.0,<1.21.0' + - 'bioconductor-limma >=3.40.0,<3.41.0' + - 'bioconductor-mast >=1.10.0,<1.11.0' + - 'bioconductor-multtest >=2.40.0,<2.41.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' + - 'bioconductor-singlecellexperiment >=1.6.0,<1.7.0' + - 'bioconductor-summarizedexperiment >=1.14.0,<1.15.0' + - 'bioconductor-sva >=3.32.0,<3.33.0' - r-ape - r-base - r-circlize @@ -54,22 +54,24 @@ requirements: - r-shinyalert - r-shinycssloaders - r-shinyjs + - r-shinythemes + - r-umap run: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' - - 'bioconductor-biobase >=2.42.0,<2.43.0' - - 'bioconductor-complexheatmap >=1.20.0,<1.21.0' - - 'bioconductor-delayedarray >=0.8.0,<0.9.0' - - 'bioconductor-deseq2 >=1.22.0,<1.23.0' - - 'bioconductor-ggtree >=1.14.0,<1.15.0' - - 'bioconductor-gsva >=1.30.0,<1.31.0' - - 'bioconductor-gsvadata >=1.18.0,<1.19.0' - - 'bioconductor-limma >=3.38.0,<3.39.0' - - 'bioconductor-mast >=1.8.0,<1.9.0' - - 'bioconductor-multtest >=2.38.0,<2.39.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' - - 'bioconductor-singlecellexperiment >=1.4.0,<1.5.0' - - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' - - 'bioconductor-sva >=3.30.0,<3.31.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' + - 'bioconductor-complexheatmap >=2.0.0,<2.1.0' + - 'bioconductor-delayedarray >=0.10.0,<0.11.0' + - 'bioconductor-deseq2 >=1.24.0,<1.25.0' + - 'bioconductor-ggtree >=1.16.0,<1.17.0' + - 'bioconductor-gsva >=1.32.0,<1.33.0' + - 'bioconductor-gsvadata >=1.20.0,<1.21.0' + - 'bioconductor-limma >=3.40.0,<3.41.0' + - 'bioconductor-mast >=1.10.0,<1.11.0' + - 'bioconductor-multtest >=2.40.0,<2.41.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' + - 'bioconductor-singlecellexperiment >=1.6.0,<1.7.0' + - 'bioconductor-summarizedexperiment >=1.14.0,<1.15.0' + - 'bioconductor-sva >=3.32.0,<3.33.0' - r-ape - r-base - r-circlize @@ -89,6 +91,8 @@ requirements: - r-shinyalert - r-shinycssloaders - r-shinyjs + - r-shinythemes + - r-umap test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-singscore/meta.yaml b/recipes/bioconductor-singscore/meta.yaml index c15565060c5a1..ef7a178d7ef3b 100644 --- a/recipes/bioconductor-singscore/meta.yaml +++ b/recipes/bioconductor-singscore/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.2.2" %} +{% set version = "1.4.0" %} {% set name = "singscore" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 8e278c32b376aafa623be1dd5e33d78b + md5: 22d04aef20157eb31727850d14d61ef8 build: number: 0 rpaths: @@ -20,38 +20,40 @@ build: # Suggests: knitr, rmarkdown, testthat requirements: host: - - 'bioconductor-biobase >=2.42.0,<2.43.0' - - 'bioconductor-biocparallel >=1.16.0,<1.17.0' - - 'bioconductor-edger >=3.24.0,<3.25.0' - - 'bioconductor-gseabase >=1.44.0,<1.45.0' - - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' + - 'bioconductor-biocparallel >=1.18.0,<1.19.0' + - 'bioconductor-edger >=3.26.0,<3.27.0' + - 'bioconductor-gseabase >=1.46.0,<1.47.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' + - 'bioconductor-summarizedexperiment >=1.14.0,<1.15.0' - r-base - r-ggplot2 - r-ggrepel - - r-ggsci - r-magrittr - r-matrixstats - r-plotly - r-plyr - r-rcolorbrewer - r-reshape + - r-reshape2 - r-tidyr run: - - 'bioconductor-biobase >=2.42.0,<2.43.0' - - 'bioconductor-biocparallel >=1.16.0,<1.17.0' - - 'bioconductor-edger >=3.24.0,<3.25.0' - - 'bioconductor-gseabase >=1.44.0,<1.45.0' - - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' + - 'bioconductor-biocparallel >=1.18.0,<1.19.0' + - 'bioconductor-edger >=3.26.0,<3.27.0' + - 'bioconductor-gseabase >=1.46.0,<1.47.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' + - 'bioconductor-summarizedexperiment >=1.14.0,<1.15.0' - r-base - r-ggplot2 - r-ggrepel - - r-ggsci - r-magrittr - r-matrixstats - r-plotly - r-plyr - r-rcolorbrewer - r-reshape + - r-reshape2 - r-tidyr test: commands: diff --git a/recipes/bioconductor-sispa/meta.yaml b/recipes/bioconductor-sispa/meta.yaml index 935f14141a6c1..4007cdd8f3248 100644 --- a/recipes/bioconductor-sispa/meta.yaml +++ b/recipes/bioconductor-sispa/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.12.0" %} +{% set version = "1.14.0" %} {% set name = "SISPA" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 31a2981180fb569f9bceaedf950c2ac0 + md5: 9055444742c1fce2978063c887f3b2d1 build: number: 0 rpaths: @@ -20,16 +20,16 @@ build: # Suggests: knitr requirements: host: - - 'bioconductor-genefilter >=1.64.0,<1.65.0' - - 'bioconductor-gsva >=1.30.0,<1.31.0' + - 'bioconductor-genefilter >=1.66.0,<1.67.0' + - 'bioconductor-gsva >=1.32.0,<1.33.0' - r-base - r-changepoint - r-data.table - r-ggplot2 - r-plyr run: - - 'bioconductor-genefilter >=1.64.0,<1.65.0' - - 'bioconductor-gsva >=1.30.0,<1.31.0' + - 'bioconductor-genefilter >=1.66.0,<1.67.0' + - 'bioconductor-gsva >=1.32.0,<1.33.0' - r-base - r-changepoint - r-data.table diff --git a/recipes/bioconductor-sitepath/build.sh b/recipes/bioconductor-sitepath/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-sitepath/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-sitepath/meta.yaml b/recipes/bioconductor-sitepath/meta.yaml new file mode 100644 index 0000000000000..500fc46a2a634 --- /dev/null +++ b/recipes/bioconductor-sitepath/meta.yaml @@ -0,0 +1,42 @@ +{% set version = "1.0.1" %} +{% set name = "sitePath" %} +{% set bioc = "3.9" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: db52a84101a3b28cfea53c10edb2301b +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ +# Suggests: testthat, knitr, rmarkdown, BiocStyle +requirements: + host: + - r-ape + - r-base + - r-rcpp + - r-seqinr + run: + - r-ape + - r-base + - r-rcpp + - r-seqinr + build: + - {{ compiler('c') }} + - {{ compiler('cxx') }} + - make +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: 'MIT + file LICENSE' + summary: 'The package does hierarchical search for fixation events given multiple sequence alignment and phylogenetic tree. These fixation events can be specific to a phylogenetic lineages or shared by multiple lineages.' + diff --git a/recipes/bioconductor-sizepower/meta.yaml b/recipes/bioconductor-sizepower/meta.yaml index 4e0ca181e4303..eba354f2e247e 100644 --- a/recipes/bioconductor-sizepower/meta.yaml +++ b/recipes/bioconductor-sizepower/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.52.0" %} +{% set version = "1.54.0" %} {% set name = "sizepower" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: bdccb70dcc32782ba50646a7f9e521fe + md5: aa63d5cfb52739ea3c771254418d12a9 build: number: 0 rpaths: diff --git a/recipes/bioconductor-skewr/meta.yaml b/recipes/bioconductor-skewr/meta.yaml index d8834233feaa5..00b64fc3287c4 100644 --- a/recipes/bioconductor-skewr/meta.yaml +++ b/recipes/bioconductor-skewr/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.14.0" %} +{% set version = "1.16.0" %} {% set name = "skewr" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 96a073b45b0870dedd69129cc678075a + md5: 0e217f39aa6dbe285584453fa6e5e710 build: number: 0 rpaths: @@ -21,19 +21,19 @@ build: requirements: host: - 'bioconductor-illuminahumanmethylation450kmanifest >=0.4.0,<0.5.0' - - 'bioconductor-methylumi >=2.28.0,<2.29.0' - - 'bioconductor-minfi >=1.28.0,<1.29.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' - - 'bioconductor-watermelon >=1.26.0,<1.27.0' + - 'bioconductor-methylumi >=2.30.0,<2.31.0' + - 'bioconductor-minfi >=1.30.0,<1.31.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' + - 'bioconductor-watermelon >=1.28.0,<1.29.0' - r-base - r-mixsmsn - r-rcolorbrewer run: - 'bioconductor-illuminahumanmethylation450kmanifest >=0.4.0,<0.5.0' - - 'bioconductor-methylumi >=2.28.0,<2.29.0' - - 'bioconductor-minfi >=1.28.0,<1.29.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' - - 'bioconductor-watermelon >=1.26.0,<1.27.0' + - 'bioconductor-methylumi >=2.30.0,<2.31.0' + - 'bioconductor-minfi >=1.30.0,<1.31.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' + - 'bioconductor-watermelon >=1.28.0,<1.29.0' - r-base - r-mixsmsn - r-rcolorbrewer diff --git a/recipes/bioconductor-slalom/meta.yaml b/recipes/bioconductor-slalom/meta.yaml index 99565dace70b6..b1a37df2c5450 100644 --- a/recipes/bioconductor-slalom/meta.yaml +++ b/recipes/bioconductor-slalom/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.4.1" %} +{% set version = "1.6.0" %} {% set name = "slalom" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 920a089b8e6c917ad80a825bfaec1775 + md5: 76c07e6bd25335b1c7ddd97569ee927b build: number: 0 rpaths: @@ -19,9 +19,9 @@ build: # Suggests: knitr, rhdf5, scater, testthat requirements: host: - - 'bioconductor-gseabase >=1.44.0,<1.45.0' - - 'bioconductor-singlecellexperiment >=1.4.0,<1.5.0' - - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' + - 'bioconductor-gseabase >=1.46.0,<1.47.0' + - 'bioconductor-singlecellexperiment >=1.6.0,<1.7.0' + - 'bioconductor-summarizedexperiment >=1.14.0,<1.15.0' - r-base - r-bh - r-ggplot2 @@ -29,9 +29,9 @@ requirements: - r-rcpparmadillo - r-rsvd run: - - 'bioconductor-gseabase >=1.44.0,<1.45.0' - - 'bioconductor-singlecellexperiment >=1.4.0,<1.5.0' - - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' + - 'bioconductor-gseabase >=1.46.0,<1.47.0' + - 'bioconductor-singlecellexperiment >=1.6.0,<1.7.0' + - 'bioconductor-summarizedexperiment >=1.14.0,<1.15.0' - r-base - r-bh - r-ggplot2 diff --git a/recipes/bioconductor-slgi/meta.yaml b/recipes/bioconductor-slgi/meta.yaml index a714b894b500c..86125e96dc062 100644 --- a/recipes/bioconductor-slgi/meta.yaml +++ b/recipes/bioconductor-slgi/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.42.0" %} +{% set version = "1.44.0" %} {% set name = "SLGI" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: ea0839feb33db33273540c5495db717a + md5: dfff03ee3b9f7397bd81b0fa38743465 build: number: 0 rpaths: @@ -20,19 +20,19 @@ build: # Suggests: GO.db, org.Sc.sgd.db requirements: host: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' - - 'bioconductor-biobase >=2.42.0,<2.43.0' - - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' - - 'bioconductor-go.db >=3.7.0,<3.8.0' - - 'bioconductor-scisi >=1.54.0,<1.55.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' + - 'bioconductor-biocgenerics >=0.30.0,<0.31.0' + - 'bioconductor-go.db >=3.8.0,<3.9.0' + - 'bioconductor-scisi >=1.56.0,<1.57.0' - r-base - r-lattice run: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' - - 'bioconductor-biobase >=2.42.0,<2.43.0' - - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' - - 'bioconductor-go.db >=3.7.0,<3.8.0' - - 'bioconductor-scisi >=1.54.0,<1.55.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' + - 'bioconductor-biocgenerics >=0.30.0,<0.31.0' + - 'bioconductor-go.db >=3.8.0,<3.9.0' + - 'bioconductor-scisi >=1.56.0,<1.57.0' - r-base - r-lattice test: diff --git a/recipes/bioconductor-slingshot/meta.yaml b/recipes/bioconductor-slingshot/meta.yaml index 7904bfc70ccee..052ed518bc760 100644 --- a/recipes/bioconductor-slingshot/meta.yaml +++ b/recipes/bioconductor-slingshot/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.0.0" %} +{% set version = "1.2.0" %} {% set name = "slingshot" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,19 +10,19 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 429308c9bbe073d329feedfe57ae773e + md5: f7080eedc58ac571193933bc5808dbcf build: number: 0 rpaths: - lib/R/lib/ - lib/ noarch: generic -# Suggests: BiocGenerics, destiny, gam, knitr, mclust, RColorBrewer, rmarkdown, splatter, testthat, covr +# Suggests: BiocGenerics, BiocStyle, destiny, gam, knitr, mclust, RColorBrewer, rmarkdown, testthat, covr requirements: host: - - 'bioconductor-clusterexperiment >=2.2.0,<2.3.0' - - 'bioconductor-singlecellexperiment >=1.4.0,<1.5.0' - - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' + - 'bioconductor-clusterexperiment >=2.4.0,<2.5.0' + - 'bioconductor-singlecellexperiment >=1.6.0,<1.7.0' + - 'bioconductor-summarizedexperiment >=1.14.0,<1.15.0' - r-ape - r-base - r-igraph @@ -30,9 +30,9 @@ requirements: - 'r-princurve >=2.0.4' - r-rgl run: - - 'bioconductor-clusterexperiment >=2.2.0,<2.3.0' - - 'bioconductor-singlecellexperiment >=1.4.0,<1.5.0' - - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' + - 'bioconductor-clusterexperiment >=2.4.0,<2.5.0' + - 'bioconductor-singlecellexperiment >=1.6.0,<1.7.0' + - 'bioconductor-summarizedexperiment >=1.14.0,<1.15.0' - r-ape - r-base - r-igraph @@ -46,8 +46,7 @@ about: home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: Artistic-2.0 summary: 'Provides functions for inferring continuous, branching lineage structures in low-dimensional data. Slingshot was designed to model developmental trajectories in single-cell RNA sequencing data and serve as a component in an analysis pipeline after dimensionality reduction and clustering. It is flexible enough to handle arbitrarily many branching events and allows for the incorporation of prior knowledge through supervised graph construction.' - extra: container: - # needed for libGL.so.1 extended-base: true + diff --git a/recipes/bioconductor-slinky/meta.yaml b/recipes/bioconductor-slinky/meta.yaml index b9119fae93152..dacae076c149b 100644 --- a/recipes/bioconductor-slinky/meta.yaml +++ b/recipes/bioconductor-slinky/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.0.0" %} +{% set version = "1.2.0" %} {% set name = "slinky" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 625f2eaba2348facd2f298f822fe12c8 + md5: 5bbd1b1b668790473b668873db8c57c0 build: number: 0 rpaths: @@ -20,8 +20,8 @@ build: # Suggests: GeoDE, doParallel, testthat, knitr, rmarkdown, ggplot2, Rtsne, Biobase, BiocStyle requirements: host: - - 'bioconductor-rhdf5 >=2.26.0,<2.27.0' - - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' + - 'bioconductor-rhdf5 >=2.28.0,<2.29.0' + - 'bioconductor-summarizedexperiment >=1.14.0,<1.15.0' - r-base - r-curl - r-dplyr @@ -31,8 +31,8 @@ requirements: - r-readr - r-tidyr run: - - 'bioconductor-rhdf5 >=2.26.0,<2.27.0' - - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' + - 'bioconductor-rhdf5 >=2.28.0,<2.29.0' + - 'bioconductor-summarizedexperiment >=1.14.0,<1.15.0' - r-base - r-curl - r-dplyr diff --git a/recipes/bioconductor-slqpcr/meta.yaml b/recipes/bioconductor-slqpcr/meta.yaml index 1d0878164f3c3..0a21da9804f16 100644 --- a/recipes/bioconductor-slqpcr/meta.yaml +++ b/recipes/bioconductor-slqpcr/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.48.0" %} +{% set version = "1.50.0" %} {% set name = "SLqPCR" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: e1902128c0521f0f1c815fa130cccf05 + md5: 9bc228a165da0ae0713484af9968369f build: number: 0 rpaths: diff --git a/recipes/bioconductor-smad/build.sh b/recipes/bioconductor-smad/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-smad/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-smad/meta.yaml b/recipes/bioconductor-smad/meta.yaml new file mode 100644 index 0000000000000..b7d2676e5c2e7 --- /dev/null +++ b/recipes/bioconductor-smad/meta.yaml @@ -0,0 +1,46 @@ +{% set version = "1.0.0" %} +{% set name = "SMAD" %} +{% set bioc = "3.9" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: 9178636a8c2ce9b6541b26e16744b2e6 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ +# Suggests: knitr, rmarkdown, testthat, BiocStyle +requirements: + host: + - r-base + - r-dplyr + - 'r-magrittr >=1.5' + - r-matrixstats + - 'r-rcpp >=1.0.0' + - r-tidyr + run: + - r-base + - r-dplyr + - 'r-magrittr >=1.5' + - r-matrixstats + - 'r-rcpp >=1.0.0' + - r-tidyr + build: + - {{ compiler('c') }} + - {{ compiler('cxx') }} + - make +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: 'MIT + file LICENSE' + summary: 'Assigning probability scores to prey proteins captured in affinity purification mass spectrometry (AP-MS) expriments to infer protein- protein interactions. The output would facilitate non-specific background removal as contaminants are commonly found in AP-MS data.' + diff --git a/recipes/bioconductor-smap/meta.yaml b/recipes/bioconductor-smap/meta.yaml index 2cf845a4ec43f..c7e884f716b6c 100644 --- a/recipes/bioconductor-smap/meta.yaml +++ b/recipes/bioconductor-smap/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.46.0" %} +{% set version = "1.48.0" %} {% set name = "SMAP" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: abf9f359b95a13d9b914fb977ad1b6b7 + md5: e7f7c7e177651e2116ee07d18352404e build: number: 0 rpaths: diff --git a/recipes/bioconductor-smite/meta.yaml b/recipes/bioconductor-smite/meta.yaml index 9ef46f3494d7d..5d3ee1c11e3d1 100644 --- a/recipes/bioconductor-smite/meta.yaml +++ b/recipes/bioconductor-smite/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.10.0" %} +{% set version = "1.12.0" %} {% set name = "SMITE" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 728be7e8265d62f2288db5acbabc2961 + md5: 958783774ed22e06691609c65a2bf1fb build: number: 0 rpaths: @@ -20,17 +20,17 @@ build: # Suggests: knitr requirements: host: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' - - 'bioconductor-biobase >=2.42.0,<2.43.0' - - 'bioconductor-bionet >=1.42.0,<1.43.0' - - 'bioconductor-genelendatabase >=1.18.0,<1.19.0' - - 'bioconductor-genomicranges >=1.34.0,<1.35.0' - - 'bioconductor-goseq >=1.34.0,<1.35.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' + - 'bioconductor-bionet >=1.44.0,<1.45.0' + - 'bioconductor-genelendatabase >=1.20.0,<1.21.0' + - 'bioconductor-genomicranges >=1.36.0,<1.37.0' + - 'bioconductor-goseq >=1.36.0,<1.37.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' - 'bioconductor-kegg.db >=3.2.0,<3.3.0' - - 'bioconductor-org.hs.eg.db >=3.7.0,<3.8.0' - - 'bioconductor-reactome.db >=1.66.0,<1.67.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-org.hs.eg.db >=3.8.0,<3.9.0' + - 'bioconductor-reactome.db >=1.68.0,<1.69.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' - r-base - r-ggplot2 - r-hmisc @@ -38,17 +38,17 @@ requirements: - r-plyr - r-scales run: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' - - 'bioconductor-biobase >=2.42.0,<2.43.0' - - 'bioconductor-bionet >=1.42.0,<1.43.0' - - 'bioconductor-genelendatabase >=1.18.0,<1.19.0' - - 'bioconductor-genomicranges >=1.34.0,<1.35.0' - - 'bioconductor-goseq >=1.34.0,<1.35.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' + - 'bioconductor-bionet >=1.44.0,<1.45.0' + - 'bioconductor-genelendatabase >=1.20.0,<1.21.0' + - 'bioconductor-genomicranges >=1.36.0,<1.37.0' + - 'bioconductor-goseq >=1.36.0,<1.37.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' - 'bioconductor-kegg.db >=3.2.0,<3.3.0' - - 'bioconductor-org.hs.eg.db >=3.7.0,<3.8.0' - - 'bioconductor-reactome.db >=1.66.0,<1.67.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-org.hs.eg.db >=3.8.0,<3.9.0' + - 'bioconductor-reactome.db >=1.68.0,<1.69.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' - r-base - r-ggplot2 - r-hmisc diff --git a/recipes/bioconductor-snadata/meta.yaml b/recipes/bioconductor-snadata/meta.yaml index 60d45164b2785..286852b06918b 100644 --- a/recipes/bioconductor-snadata/meta.yaml +++ b/recipes/bioconductor-snadata/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.28.0" %} +{% set version = "1.30.0" %} {% set name = "SNAData" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: f7bb6899038f7adb395147bf50e203c2 + md5: aebebfd31a60cb7878138c1aadea000d build: number: 0 rpaths: @@ -20,12 +20,12 @@ build: # Suggests: Rgraphviz requirements: host: - - 'bioconductor-graph >=1.60.0,<1.61.0' + - 'bioconductor-graph >=1.62.0,<1.63.0' - r-base run: - - 'bioconductor-graph >=1.60.0,<1.61.0' + - 'bioconductor-graph >=1.62.0,<1.63.0' - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-snadata/post-link.sh b/recipes/bioconductor-snadata/post-link.sh index 3e3a03a4a6ccf..1c2da43e5e77b 100644 --- a/recipes/bioconductor-snadata/post-link.sh +++ b/recipes/bioconductor-snadata/post-link.sh @@ -1,11 +1,11 @@ #!/bin/bash -FN="SNAData_1.28.0.tar.gz" +FN="SNAData_1.30.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/experiment/src/contrib/SNAData_1.28.0.tar.gz" - "https://bioarchive.galaxyproject.org/SNAData_1.28.0.tar.gz" - "https://depot.galaxyproject.org/software/bioconductor-snadata/bioconductor-snadata_1.28.0_src_all.tar.gz" + "https://bioconductor.org/packages/3.9/data/experiment/src/contrib/SNAData_1.30.0.tar.gz" + "https://bioarchive.galaxyproject.org/SNAData_1.30.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-snadata/bioconductor-snadata_1.30.0_src_all.tar.gz" ) -MD5="f7bb6899038f7adb395147bf50e203c2" +MD5="aebebfd31a60cb7878138c1aadea000d" # Use a staging area in the conda dir rather than temp dirs, both to avoid # permission issues as well as to have things downloaded in a predictable @@ -16,7 +16,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-snagee/meta.yaml b/recipes/bioconductor-snagee/meta.yaml index 93ff26c0f0b91..b8fb45b172b67 100644 --- a/recipes/bioconductor-snagee/meta.yaml +++ b/recipes/bioconductor-snagee/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.22.0" %} +{% set version = "1.24.0" %} {% set name = "SNAGEE" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: d1587c20f9e38e9a8d85219ff149ce1d + md5: fea3ccc1b2941228ac53614c78d42f5e build: number: 0 rpaths: @@ -20,10 +20,10 @@ build: # Suggests: ALL, hgu95av2.db requirements: host: - - 'bioconductor-snageedata >=1.18.0,<1.19.0' + - 'bioconductor-snageedata >=1.20.0,<1.21.0' - r-base run: - - 'bioconductor-snageedata >=1.18.0,<1.19.0' + - 'bioconductor-snageedata >=1.20.0,<1.21.0' - r-base test: commands: diff --git a/recipes/bioconductor-snageedata/meta.yaml b/recipes/bioconductor-snageedata/meta.yaml index 07df1cfa473af..f980f1791d628 100644 --- a/recipes/bioconductor-snageedata/meta.yaml +++ b/recipes/bioconductor-snageedata/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.18.0" %} +{% set version = "1.20.0" %} {% set name = "SNAGEEdata" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 4b880530c37c0d088386211817f6f07b + md5: 6f95756e911a82831c37171ed8192d7a build: number: 0 rpaths: @@ -23,7 +23,7 @@ requirements: - r-base run: - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-snageedata/post-link.sh b/recipes/bioconductor-snageedata/post-link.sh index 8a6536754726b..5fba28e15a7e7 100644 --- a/recipes/bioconductor-snageedata/post-link.sh +++ b/recipes/bioconductor-snageedata/post-link.sh @@ -1,11 +1,11 @@ #!/bin/bash -FN="SNAGEEdata_1.18.0.tar.gz" +FN="SNAGEEdata_1.20.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/experiment/src/contrib/SNAGEEdata_1.18.0.tar.gz" - "https://bioarchive.galaxyproject.org/SNAGEEdata_1.18.0.tar.gz" - "https://depot.galaxyproject.org/software/bioconductor-snageedata/bioconductor-snageedata_1.18.0_src_all.tar.gz" + "https://bioconductor.org/packages/3.9/data/experiment/src/contrib/SNAGEEdata_1.20.0.tar.gz" + "https://bioarchive.galaxyproject.org/SNAGEEdata_1.20.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-snageedata/bioconductor-snageedata_1.20.0_src_all.tar.gz" ) -MD5="4b880530c37c0d088386211817f6f07b" +MD5="6f95756e911a82831c37171ed8192d7a" # Use a staging area in the conda dir rather than temp dirs, both to avoid # permission issues as well as to have things downloaded in a predictable @@ -16,7 +16,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-snapcgh/meta.yaml b/recipes/bioconductor-snapcgh/meta.yaml index bf834da188b57..78be7d68881fd 100644 --- a/recipes/bioconductor-snapcgh/meta.yaml +++ b/recipes/bioconductor-snapcgh/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.52.0" %} +{% set version = "1.54.0" %} {% set name = "snapCGH" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 6aefaf2fe3f35acb952a03488c44ffb9 + md5: 421d82a4d75f4c064f215b77e2bf7d23 build: number: 0 rpaths: @@ -18,19 +18,19 @@ build: - lib/ requirements: host: - - 'bioconductor-acgh >=1.60.0,<1.61.0' - - 'bioconductor-dnacopy >=1.56.0,<1.57.0' - - 'bioconductor-glad >=2.46.0,<2.47.0' - - 'bioconductor-limma >=3.38.0,<3.39.0' - - 'bioconductor-tilingarray >=1.60.0,<1.61.0' + - 'bioconductor-acgh >=1.62.0,<1.63.0' + - 'bioconductor-dnacopy >=1.58.0,<1.59.0' + - 'bioconductor-glad >=2.48.0,<2.49.0' + - 'bioconductor-limma >=3.40.0,<3.41.0' + - 'bioconductor-tilingarray >=1.62.0,<1.63.0' - r-base - r-cluster run: - - 'bioconductor-acgh >=1.60.0,<1.61.0' - - 'bioconductor-dnacopy >=1.56.0,<1.57.0' - - 'bioconductor-glad >=2.46.0,<2.47.0' - - 'bioconductor-limma >=3.38.0,<3.39.0' - - 'bioconductor-tilingarray >=1.60.0,<1.61.0' + - 'bioconductor-acgh >=1.62.0,<1.63.0' + - 'bioconductor-dnacopy >=1.58.0,<1.59.0' + - 'bioconductor-glad >=2.48.0,<2.49.0' + - 'bioconductor-limma >=3.40.0,<3.41.0' + - 'bioconductor-tilingarray >=1.62.0,<1.63.0' - r-base - r-cluster build: diff --git a/recipes/bioconductor-snm/meta.yaml b/recipes/bioconductor-snm/meta.yaml index bdbae809c0804..1e5ce73283106 100644 --- a/recipes/bioconductor-snm/meta.yaml +++ b/recipes/bioconductor-snm/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.30.0" %} +{% set version = "1.32.0" %} {% set name = "snm" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: c3d4d6770565f32fb9b1b3e1bbaf30ee + md5: 582f0ede18333be9c56f09fb59898af6 build: number: 0 rpaths: diff --git a/recipes/bioconductor-snpchip/meta.yaml b/recipes/bioconductor-snpchip/meta.yaml index 2de4085c8f431..eb1c1b723254f 100644 --- a/recipes/bioconductor-snpchip/meta.yaml +++ b/recipes/bioconductor-snpchip/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "2.28.0" %} +{% set version = "2.30.0" %} {% set name = "SNPchip" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 6aa3050529ceb3c1500f56d0eb663982 + md5: 7f754e0adc04950c72bdf08c4944374b build: number: 0 rpaths: @@ -20,24 +20,24 @@ build: # Suggests: crlmm (>= 1.17.14), RUnit requirements: host: - - 'bioconductor-biobase >=2.42.0,<2.43.0' - - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' - - 'bioconductor-genomicranges >=1.34.0,<1.35.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-oligoclasses >=1.44.0,<1.45.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' - - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' + - 'bioconductor-genomeinfodb >=1.20.0,<1.21.0' + - 'bioconductor-genomicranges >=1.36.0,<1.37.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-oligoclasses >=1.46.0,<1.47.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' + - 'bioconductor-summarizedexperiment >=1.14.0,<1.15.0' - r-base - r-foreach - r-lattice run: - - 'bioconductor-biobase >=2.42.0,<2.43.0' - - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' - - 'bioconductor-genomicranges >=1.34.0,<1.35.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-oligoclasses >=1.44.0,<1.45.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' - - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' + - 'bioconductor-genomeinfodb >=1.20.0,<1.21.0' + - 'bioconductor-genomicranges >=1.36.0,<1.37.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-oligoclasses >=1.46.0,<1.47.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' + - 'bioconductor-summarizedexperiment >=1.14.0,<1.15.0' - r-base - r-foreach - r-lattice diff --git a/recipes/bioconductor-snpediar/meta.yaml b/recipes/bioconductor-snpediar/meta.yaml index a280f94137447..ef2a28b978dac 100644 --- a/recipes/bioconductor-snpediar/meta.yaml +++ b/recipes/bioconductor-snpediar/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.8.0" %} +{% set version = "1.10.0" %} {% set name = "SNPediaR" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: a1ee826e42e3caa1231e1616d5a0944f + md5: 9b5250e8021dc88cd29b37c1c1a5db03 build: number: 0 rpaths: diff --git a/recipes/bioconductor-snphood/meta.yaml b/recipes/bioconductor-snphood/meta.yaml index c4c313226d84e..72456edbb5ef5 100644 --- a/recipes/bioconductor-snphood/meta.yaml +++ b/recipes/bioconductor-snphood/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.12.0" %} +{% set version = "1.14.0" %} {% set name = "SNPhood" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 7f665ce6a2a88a8df7aee41bd46d4930 + md5: 3dcba58f2b36e47a0624d150b80e2bd7 build: number: 0 rpaths: @@ -20,17 +20,17 @@ build: # Suggests: BiocStyle, knitr, pryr, rmarkdown, SNPhoodData, corrplot requirements: host: - - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' - - 'bioconductor-biocparallel >=1.16.0,<1.17.0' - - 'bioconductor-biostrings >=2.50.0,<2.51.0' - - 'bioconductor-deseq2 >=1.22.0,<1.23.0' - - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' - - 'bioconductor-genomicranges >=1.34.0,<1.35.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-rsamtools >=1.34.0,<1.35.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' - - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' - - 'bioconductor-variantannotation >=1.28.0,<1.29.0' + - 'bioconductor-biocgenerics >=0.30.0,<0.31.0' + - 'bioconductor-biocparallel >=1.18.0,<1.19.0' + - 'bioconductor-biostrings >=2.52.0,<2.53.0' + - 'bioconductor-deseq2 >=1.24.0,<1.25.0' + - 'bioconductor-genomeinfodb >=1.20.0,<1.21.0' + - 'bioconductor-genomicranges >=1.36.0,<1.37.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-rsamtools >=2.0.0,<2.1.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' + - 'bioconductor-summarizedexperiment >=1.14.0,<1.15.0' + - 'bioconductor-variantannotation >=1.30.0,<1.31.0' - r-base - r-checkmate - r-cluster @@ -42,17 +42,17 @@ requirements: - r-reshape2 - r-scales run: - - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' - - 'bioconductor-biocparallel >=1.16.0,<1.17.0' - - 'bioconductor-biostrings >=2.50.0,<2.51.0' - - 'bioconductor-deseq2 >=1.22.0,<1.23.0' - - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' - - 'bioconductor-genomicranges >=1.34.0,<1.35.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-rsamtools >=1.34.0,<1.35.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' - - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' - - 'bioconductor-variantannotation >=1.28.0,<1.29.0' + - 'bioconductor-biocgenerics >=0.30.0,<0.31.0' + - 'bioconductor-biocparallel >=1.18.0,<1.19.0' + - 'bioconductor-biostrings >=2.52.0,<2.53.0' + - 'bioconductor-deseq2 >=1.24.0,<1.25.0' + - 'bioconductor-genomeinfodb >=1.20.0,<1.21.0' + - 'bioconductor-genomicranges >=1.36.0,<1.37.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-rsamtools >=2.0.0,<2.1.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' + - 'bioconductor-summarizedexperiment >=1.14.0,<1.15.0' + - 'bioconductor-variantannotation >=1.30.0,<1.31.0' - r-base - r-checkmate - r-cluster diff --git a/recipes/bioconductor-snphooddata/meta.yaml b/recipes/bioconductor-snphooddata/meta.yaml index 86cb3c80fb78e..05f119f385cde 100644 --- a/recipes/bioconductor-snphooddata/meta.yaml +++ b/recipes/bioconductor-snphooddata/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.12.0" %} +{% set version = "1.14.0" %} {% set name = "SNPhoodData" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 5036868e32ed51fd9ffa32bfeb992051 + md5: 932f101b78576f7a6407704d3031fdbf build: number: 0 rpaths: @@ -23,7 +23,7 @@ requirements: - r-base run: - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-snphooddata/post-link.sh b/recipes/bioconductor-snphooddata/post-link.sh index dd3e2a505e2e7..6d7168385166e 100644 --- a/recipes/bioconductor-snphooddata/post-link.sh +++ b/recipes/bioconductor-snphooddata/post-link.sh @@ -1,11 +1,11 @@ #!/bin/bash -FN="SNPhoodData_1.12.0.tar.gz" +FN="SNPhoodData_1.14.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/experiment/src/contrib/SNPhoodData_1.12.0.tar.gz" - "https://bioarchive.galaxyproject.org/SNPhoodData_1.12.0.tar.gz" - "https://depot.galaxyproject.org/software/bioconductor-snphooddata/bioconductor-snphooddata_1.12.0_src_all.tar.gz" + "https://bioconductor.org/packages/3.9/data/experiment/src/contrib/SNPhoodData_1.14.0.tar.gz" + "https://bioarchive.galaxyproject.org/SNPhoodData_1.14.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-snphooddata/bioconductor-snphooddata_1.14.0_src_all.tar.gz" ) -MD5="5036868e32ed51fd9ffa32bfeb992051" +MD5="932f101b78576f7a6407704d3031fdbf" # Use a staging area in the conda dir rather than temp dirs, both to avoid # permission issues as well as to have things downloaded in a predictable @@ -16,7 +16,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-snplocs.hsapiens.dbsnp.20101109/meta.yaml b/recipes/bioconductor-snplocs.hsapiens.dbsnp.20101109/meta.yaml index 8293358f1a3d4..c184535ee776e 100644 --- a/recipes/bioconductor-snplocs.hsapiens.dbsnp.20101109/meta.yaml +++ b/recipes/bioconductor-snplocs.hsapiens.dbsnp.20101109/meta.yaml @@ -1,6 +1,6 @@ {% set version = "0.99.7" %} {% set name = "SNPlocs.Hsapiens.dbSNP.20101109" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -12,7 +12,7 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' md5: d18cef7792978f5827025671b1866230 build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ @@ -20,16 +20,16 @@ build: # Suggests: Biostrings, BSgenome (>= 1.16.1), BSgenome.Hsapiens.UCSC.hg19 requirements: host: - - 'bioconductor-genomicranges >=1.34.0,<1.35.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-genomicranges >=1.36.0,<1.37.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' - r-base run: - - 'bioconductor-genomicranges >=1.34.0,<1.35.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-genomicranges >=1.36.0,<1.37.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-snplocs.hsapiens.dbsnp.20101109/post-link.sh b/recipes/bioconductor-snplocs.hsapiens.dbsnp.20101109/post-link.sh index 60602e3bcf6a2..dd10731990cca 100644 --- a/recipes/bioconductor-snplocs.hsapiens.dbsnp.20101109/post-link.sh +++ b/recipes/bioconductor-snplocs.hsapiens.dbsnp.20101109/post-link.sh @@ -1,9 +1,10 @@ #!/bin/bash FN="SNPlocs.Hsapiens.dbSNP.20101109_0.99.7.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/SNPlocs.Hsapiens.dbSNP.20101109_0.99.7.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/SNPlocs.Hsapiens.dbSNP.20101109_0.99.7.tar.gz" "https://bioarchive.galaxyproject.org/SNPlocs.Hsapiens.dbSNP.20101109_0.99.7.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-snplocs.hsapiens.dbsnp.20101109/bioconductor-snplocs.hsapiens.dbsnp.20101109_0.99.7_src_all.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-snplocs.hsapiens.dbsnp.20101109/bioconductor-snplocs.hsapiens.dbsnp.20101109_0.99.7_src_all.tar.gz" ) MD5="d18cef7792978f5827025671b1866230" @@ -16,7 +17,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-snplocs.hsapiens.dbsnp.20120608/meta.yaml b/recipes/bioconductor-snplocs.hsapiens.dbsnp.20120608/meta.yaml index eab7d5f6f79a7..3aea380c3a629 100644 --- a/recipes/bioconductor-snplocs.hsapiens.dbsnp.20120608/meta.yaml +++ b/recipes/bioconductor-snplocs.hsapiens.dbsnp.20120608/meta.yaml @@ -1,6 +1,6 @@ {% set version = "0.99.11" %} {% set name = "SNPlocs.Hsapiens.dbSNP.20120608" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -12,7 +12,7 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' md5: 6f06b9f619994b2a9b0fd780ead2f0cc build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ @@ -20,16 +20,16 @@ build: # Suggests: Biostrings, BSgenome.Hsapiens.UCSC.hg19 (>= 1.3.19) requirements: host: - - 'bioconductor-bsgenome >=1.50.0,<1.51.0' - - 'bioconductor-genomicranges >=1.34.0,<1.35.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-bsgenome >=1.52.0,<1.53.0' + - 'bioconductor-genomicranges >=1.36.0,<1.37.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' - r-base run: - - 'bioconductor-bsgenome >=1.50.0,<1.51.0' - - 'bioconductor-genomicranges >=1.34.0,<1.35.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-bsgenome >=1.52.0,<1.53.0' + - 'bioconductor-genomicranges >=1.36.0,<1.37.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-snplocs.hsapiens.dbsnp.20120608/post-link.sh b/recipes/bioconductor-snplocs.hsapiens.dbsnp.20120608/post-link.sh index 62604bab32d7e..e505fbdc23e27 100644 --- a/recipes/bioconductor-snplocs.hsapiens.dbsnp.20120608/post-link.sh +++ b/recipes/bioconductor-snplocs.hsapiens.dbsnp.20120608/post-link.sh @@ -1,9 +1,10 @@ #!/bin/bash FN="SNPlocs.Hsapiens.dbSNP.20120608_0.99.11.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/SNPlocs.Hsapiens.dbSNP.20120608_0.99.11.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/SNPlocs.Hsapiens.dbSNP.20120608_0.99.11.tar.gz" "https://bioarchive.galaxyproject.org/SNPlocs.Hsapiens.dbSNP.20120608_0.99.11.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-snplocs.hsapiens.dbsnp.20120608/bioconductor-snplocs.hsapiens.dbsnp.20120608_0.99.11_src_all.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-snplocs.hsapiens.dbsnp.20120608/bioconductor-snplocs.hsapiens.dbsnp.20120608_0.99.11_src_all.tar.gz" ) MD5="6f06b9f619994b2a9b0fd780ead2f0cc" @@ -16,7 +17,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-snplocs.hsapiens.dbsnp141.grch38/meta.yaml b/recipes/bioconductor-snplocs.hsapiens.dbsnp141.grch38/meta.yaml index 33e135c3d6f72..951423aa2659a 100644 --- a/recipes/bioconductor-snplocs.hsapiens.dbsnp141.grch38/meta.yaml +++ b/recipes/bioconductor-snplocs.hsapiens.dbsnp141.grch38/meta.yaml @@ -1,6 +1,6 @@ {% set version = "0.99.11" %} {% set name = "SNPlocs.Hsapiens.dbSNP141.GRCh38" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -12,7 +12,7 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' md5: 40b55447c33e9d72c2ae8e8fe7f484be build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ @@ -20,20 +20,20 @@ build: # Suggests: Biostrings, BSgenome.Hsapiens.NCBI.GRCh38 (>= 1.3.19) requirements: host: - - 'bioconductor-bsgenome >=1.50.0,<1.51.0' - - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' - - 'bioconductor-genomicranges >=1.34.0,<1.35.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-bsgenome >=1.52.0,<1.53.0' + - 'bioconductor-genomeinfodb >=1.20.0,<1.21.0' + - 'bioconductor-genomicranges >=1.36.0,<1.37.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' - r-base run: - - 'bioconductor-bsgenome >=1.50.0,<1.51.0' - - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' - - 'bioconductor-genomicranges >=1.34.0,<1.35.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-bsgenome >=1.52.0,<1.53.0' + - 'bioconductor-genomeinfodb >=1.20.0,<1.21.0' + - 'bioconductor-genomicranges >=1.36.0,<1.37.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-snplocs.hsapiens.dbsnp141.grch38/post-link.sh b/recipes/bioconductor-snplocs.hsapiens.dbsnp141.grch38/post-link.sh index d321ba423eecd..d120ac2b23fee 100644 --- a/recipes/bioconductor-snplocs.hsapiens.dbsnp141.grch38/post-link.sh +++ b/recipes/bioconductor-snplocs.hsapiens.dbsnp141.grch38/post-link.sh @@ -1,9 +1,10 @@ #!/bin/bash FN="SNPlocs.Hsapiens.dbSNP141.GRCh38_0.99.11.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/SNPlocs.Hsapiens.dbSNP141.GRCh38_0.99.11.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/SNPlocs.Hsapiens.dbSNP141.GRCh38_0.99.11.tar.gz" "https://bioarchive.galaxyproject.org/SNPlocs.Hsapiens.dbSNP141.GRCh38_0.99.11.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-snplocs.hsapiens.dbsnp141.grch38/bioconductor-snplocs.hsapiens.dbsnp141.grch38_0.99.11_src_all.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-snplocs.hsapiens.dbsnp141.grch38/bioconductor-snplocs.hsapiens.dbsnp141.grch38_0.99.11_src_all.tar.gz" ) MD5="40b55447c33e9d72c2ae8e8fe7f484be" @@ -16,7 +17,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-snplocs.hsapiens.dbsnp142.grch37/meta.yaml b/recipes/bioconductor-snplocs.hsapiens.dbsnp142.grch37/meta.yaml index 52075d232b155..5cdbbedfbd748 100644 --- a/recipes/bioconductor-snplocs.hsapiens.dbsnp142.grch37/meta.yaml +++ b/recipes/bioconductor-snplocs.hsapiens.dbsnp142.grch37/meta.yaml @@ -1,6 +1,6 @@ {% set version = "0.99.5" %} {% set name = "SNPlocs.Hsapiens.dbSNP142.GRCh37" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -12,7 +12,7 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' md5: 3038e4f766d3e24f5b7286961a03ba35 build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ @@ -20,18 +20,18 @@ build: # Suggests: Biostrings, BSgenome.Hsapiens.UCSC.hg19, BSgenome.Hsapiens.UCSC.hg19.masked (>= 1.3.19) requirements: host: - - 'bioconductor-bsgenome >=1.50.0,<1.51.0' - - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' - - 'bioconductor-genomicranges >=1.34.0,<1.35.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-bsgenome >=1.52.0,<1.53.0' + - 'bioconductor-genomeinfodb >=1.20.0,<1.21.0' + - 'bioconductor-genomicranges >=1.36.0,<1.37.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' - r-base run: - - 'bioconductor-bsgenome >=1.50.0,<1.51.0' - - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' - - 'bioconductor-genomicranges >=1.34.0,<1.35.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-bsgenome >=1.52.0,<1.53.0' + - 'bioconductor-genomeinfodb >=1.20.0,<1.21.0' + - 'bioconductor-genomicranges >=1.36.0,<1.37.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-snplocs.hsapiens.dbsnp142.grch37/post-link.sh b/recipes/bioconductor-snplocs.hsapiens.dbsnp142.grch37/post-link.sh index ecd54c67f299c..33540e8b8f680 100644 --- a/recipes/bioconductor-snplocs.hsapiens.dbsnp142.grch37/post-link.sh +++ b/recipes/bioconductor-snplocs.hsapiens.dbsnp142.grch37/post-link.sh @@ -1,9 +1,10 @@ #!/bin/bash FN="SNPlocs.Hsapiens.dbSNP142.GRCh37_0.99.5.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/SNPlocs.Hsapiens.dbSNP142.GRCh37_0.99.5.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/SNPlocs.Hsapiens.dbSNP142.GRCh37_0.99.5.tar.gz" "https://bioarchive.galaxyproject.org/SNPlocs.Hsapiens.dbSNP142.GRCh37_0.99.5.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-snplocs.hsapiens.dbsnp142.grch37/bioconductor-snplocs.hsapiens.dbsnp142.grch37_0.99.5_src_all.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-snplocs.hsapiens.dbsnp142.grch37/bioconductor-snplocs.hsapiens.dbsnp142.grch37_0.99.5_src_all.tar.gz" ) MD5="3038e4f766d3e24f5b7286961a03ba35" @@ -16,7 +17,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-snplocs.hsapiens.dbsnp144.grch37/meta.yaml b/recipes/bioconductor-snplocs.hsapiens.dbsnp144.grch37/meta.yaml index cbf0e264941c3..686465503a808 100644 --- a/recipes/bioconductor-snplocs.hsapiens.dbsnp144.grch37/meta.yaml +++ b/recipes/bioconductor-snplocs.hsapiens.dbsnp144.grch37/meta.yaml @@ -1,6 +1,6 @@ {% set version = "0.99.20" %} {% set name = "SNPlocs.Hsapiens.dbSNP144.GRCh37" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -12,7 +12,7 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' md5: bd338bb583cacc18f210e871dac79ebf build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ @@ -20,22 +20,22 @@ build: # Suggests: Biostrings, BSgenome.Hsapiens.UCSC.hg19 requirements: host: - - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' - - 'bioconductor-bsgenome >=1.50.0,<1.51.0' - - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' - - 'bioconductor-genomicranges >=1.34.0,<1.35.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-biocgenerics >=0.30.0,<0.31.0' + - 'bioconductor-bsgenome >=1.52.0,<1.53.0' + - 'bioconductor-genomeinfodb >=1.20.0,<1.21.0' + - 'bioconductor-genomicranges >=1.36.0,<1.37.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' - r-base run: - - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' - - 'bioconductor-bsgenome >=1.50.0,<1.51.0' - - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' - - 'bioconductor-genomicranges >=1.34.0,<1.35.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-biocgenerics >=0.30.0,<0.31.0' + - 'bioconductor-bsgenome >=1.52.0,<1.53.0' + - 'bioconductor-genomeinfodb >=1.20.0,<1.21.0' + - 'bioconductor-genomicranges >=1.36.0,<1.37.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-snplocs.hsapiens.dbsnp144.grch37/post-link.sh b/recipes/bioconductor-snplocs.hsapiens.dbsnp144.grch37/post-link.sh index adba749e3d77f..e8035a4575d66 100644 --- a/recipes/bioconductor-snplocs.hsapiens.dbsnp144.grch37/post-link.sh +++ b/recipes/bioconductor-snplocs.hsapiens.dbsnp144.grch37/post-link.sh @@ -1,9 +1,10 @@ #!/bin/bash FN="SNPlocs.Hsapiens.dbSNP144.GRCh37_0.99.20.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/SNPlocs.Hsapiens.dbSNP144.GRCh37_0.99.20.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/SNPlocs.Hsapiens.dbSNP144.GRCh37_0.99.20.tar.gz" "https://bioarchive.galaxyproject.org/SNPlocs.Hsapiens.dbSNP144.GRCh37_0.99.20.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-snplocs.hsapiens.dbsnp144.grch37/bioconductor-snplocs.hsapiens.dbsnp144.grch37_0.99.20_src_all.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-snplocs.hsapiens.dbsnp144.grch37/bioconductor-snplocs.hsapiens.dbsnp144.grch37_0.99.20_src_all.tar.gz" ) MD5="bd338bb583cacc18f210e871dac79ebf" @@ -16,7 +17,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-snplocs.hsapiens.dbsnp144.grch38/meta.yaml b/recipes/bioconductor-snplocs.hsapiens.dbsnp144.grch38/meta.yaml index 26b65ce732285..c4373c4b856dd 100644 --- a/recipes/bioconductor-snplocs.hsapiens.dbsnp144.grch38/meta.yaml +++ b/recipes/bioconductor-snplocs.hsapiens.dbsnp144.grch38/meta.yaml @@ -1,6 +1,6 @@ {% set version = "0.99.20" %} {% set name = "SNPlocs.Hsapiens.dbSNP144.GRCh38" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -12,7 +12,7 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' md5: 128c95e327adf72ae137fb5ae58270fc build: - number: 4 + number: 5 rpaths: - lib/R/lib/ - lib/ @@ -20,22 +20,22 @@ build: # Suggests: Biostrings, BSgenome.Hsapiens.UCSC.hg38 requirements: host: - - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' - - 'bioconductor-bsgenome >=1.50.0,<1.51.0' - - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' - - 'bioconductor-genomicranges >=1.34.0,<1.35.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-biocgenerics >=0.30.0,<0.31.0' + - 'bioconductor-bsgenome >=1.52.0,<1.53.0' + - 'bioconductor-genomeinfodb >=1.20.0,<1.21.0' + - 'bioconductor-genomicranges >=1.36.0,<1.37.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' - r-base run: - - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' - - 'bioconductor-bsgenome >=1.50.0,<1.51.0' - - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' - - 'bioconductor-genomicranges >=1.34.0,<1.35.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-biocgenerics >=0.30.0,<0.31.0' + - 'bioconductor-bsgenome >=1.52.0,<1.53.0' + - 'bioconductor-genomeinfodb >=1.20.0,<1.21.0' + - 'bioconductor-genomicranges >=1.36.0,<1.37.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-snplocs.hsapiens.dbsnp144.grch38/post-link.sh b/recipes/bioconductor-snplocs.hsapiens.dbsnp144.grch38/post-link.sh index d376e09e0cb41..f36e9df376a17 100644 --- a/recipes/bioconductor-snplocs.hsapiens.dbsnp144.grch38/post-link.sh +++ b/recipes/bioconductor-snplocs.hsapiens.dbsnp144.grch38/post-link.sh @@ -1,7 +1,7 @@ #!/bin/bash FN="SNPlocs.Hsapiens.dbSNP144.GRCh38_0.99.20.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/SNPlocs.Hsapiens.dbSNP144.GRCh38_0.99.20.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/SNPlocs.Hsapiens.dbSNP144.GRCh38_0.99.20.tar.gz" "https://bioarchive.galaxyproject.org/SNPlocs.Hsapiens.dbSNP144.GRCh38_0.99.20.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-snplocs.hsapiens.dbsnp144.grch38/bioconductor-snplocs.hsapiens.dbsnp144.grch38_0.99.20_src_all.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-snplocs.hsapiens.dbsnp144.grch38/bioconductor-snplocs.hsapiens.dbsnp144.grch38_0.99.20_src_all.tar.gz" @@ -17,7 +17,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-snplocs.hsapiens.dbsnp149.grch38/meta.yaml b/recipes/bioconductor-snplocs.hsapiens.dbsnp149.grch38/meta.yaml index faeac51916ae9..deabef06c2794 100644 --- a/recipes/bioconductor-snplocs.hsapiens.dbsnp149.grch38/meta.yaml +++ b/recipes/bioconductor-snplocs.hsapiens.dbsnp149.grch38/meta.yaml @@ -1,6 +1,6 @@ {% set version = "0.99.20" %} {% set name = "SNPlocs.Hsapiens.dbSNP149.GRCh38" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -12,7 +12,7 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' md5: 8cf749a8649a53449066b54160a3745c build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ @@ -20,22 +20,22 @@ build: # Suggests: Biostrings, BSgenome.Hsapiens.UCSC.hg38 requirements: host: - - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' - - 'bioconductor-bsgenome >=1.50.0,<1.51.0' - - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' - - 'bioconductor-genomicranges >=1.34.0,<1.35.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-biocgenerics >=0.30.0,<0.31.0' + - 'bioconductor-bsgenome >=1.52.0,<1.53.0' + - 'bioconductor-genomeinfodb >=1.20.0,<1.21.0' + - 'bioconductor-genomicranges >=1.36.0,<1.37.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' - r-base run: - - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' - - 'bioconductor-bsgenome >=1.50.0,<1.51.0' - - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' - - 'bioconductor-genomicranges >=1.34.0,<1.35.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-biocgenerics >=0.30.0,<0.31.0' + - 'bioconductor-bsgenome >=1.52.0,<1.53.0' + - 'bioconductor-genomeinfodb >=1.20.0,<1.21.0' + - 'bioconductor-genomicranges >=1.36.0,<1.37.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-snplocs.hsapiens.dbsnp149.grch38/post-link.sh b/recipes/bioconductor-snplocs.hsapiens.dbsnp149.grch38/post-link.sh index e9c5331abe8b3..84306d53733a1 100644 --- a/recipes/bioconductor-snplocs.hsapiens.dbsnp149.grch38/post-link.sh +++ b/recipes/bioconductor-snplocs.hsapiens.dbsnp149.grch38/post-link.sh @@ -1,9 +1,10 @@ #!/bin/bash FN="SNPlocs.Hsapiens.dbSNP149.GRCh38_0.99.20.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/SNPlocs.Hsapiens.dbSNP149.GRCh38_0.99.20.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/SNPlocs.Hsapiens.dbSNP149.GRCh38_0.99.20.tar.gz" "https://bioarchive.galaxyproject.org/SNPlocs.Hsapiens.dbSNP149.GRCh38_0.99.20.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-snplocs.hsapiens.dbsnp149.grch38/bioconductor-snplocs.hsapiens.dbsnp149.grch38_0.99.20_src_all.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-snplocs.hsapiens.dbsnp149.grch38/bioconductor-snplocs.hsapiens.dbsnp149.grch38_0.99.20_src_all.tar.gz" ) MD5="8cf749a8649a53449066b54160a3745c" @@ -16,7 +17,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-snplocs.hsapiens.dbsnp150.grch38/meta.yaml b/recipes/bioconductor-snplocs.hsapiens.dbsnp150.grch38/meta.yaml index dd2a1209ff321..e41ce30beb132 100644 --- a/recipes/bioconductor-snplocs.hsapiens.dbsnp150.grch38/meta.yaml +++ b/recipes/bioconductor-snplocs.hsapiens.dbsnp150.grch38/meta.yaml @@ -1,6 +1,6 @@ {% set version = "0.99.20" %} {% set name = "SNPlocs.Hsapiens.dbSNP150.GRCh38" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -12,7 +12,7 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' md5: 575a7aaa9125d52ca0634b3ac586c9a7 build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ @@ -20,22 +20,22 @@ build: # Suggests: Biostrings, BSgenome.Hsapiens.UCSC.hg38 requirements: host: - - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' - - 'bioconductor-bsgenome >=1.50.0,<1.51.0' - - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' - - 'bioconductor-genomicranges >=1.34.0,<1.35.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-biocgenerics >=0.30.0,<0.31.0' + - 'bioconductor-bsgenome >=1.52.0,<1.53.0' + - 'bioconductor-genomeinfodb >=1.20.0,<1.21.0' + - 'bioconductor-genomicranges >=1.36.0,<1.37.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' - r-base run: - - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' - - 'bioconductor-bsgenome >=1.50.0,<1.51.0' - - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' - - 'bioconductor-genomicranges >=1.34.0,<1.35.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-biocgenerics >=0.30.0,<0.31.0' + - 'bioconductor-bsgenome >=1.52.0,<1.53.0' + - 'bioconductor-genomeinfodb >=1.20.0,<1.21.0' + - 'bioconductor-genomicranges >=1.36.0,<1.37.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-snplocs.hsapiens.dbsnp150.grch38/post-link.sh b/recipes/bioconductor-snplocs.hsapiens.dbsnp150.grch38/post-link.sh index 99f56d0227806..185aacb6298e9 100644 --- a/recipes/bioconductor-snplocs.hsapiens.dbsnp150.grch38/post-link.sh +++ b/recipes/bioconductor-snplocs.hsapiens.dbsnp150.grch38/post-link.sh @@ -1,9 +1,10 @@ #!/bin/bash FN="SNPlocs.Hsapiens.dbSNP150.GRCh38_0.99.20.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/SNPlocs.Hsapiens.dbSNP150.GRCh38_0.99.20.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/SNPlocs.Hsapiens.dbSNP150.GRCh38_0.99.20.tar.gz" "https://bioarchive.galaxyproject.org/SNPlocs.Hsapiens.dbSNP150.GRCh38_0.99.20.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-snplocs.hsapiens.dbsnp150.grch38/bioconductor-snplocs.hsapiens.dbsnp150.grch38_0.99.20_src_all.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-snplocs.hsapiens.dbsnp150.grch38/bioconductor-snplocs.hsapiens.dbsnp150.grch38_0.99.20_src_all.tar.gz" ) MD5="575a7aaa9125d52ca0634b3ac586c9a7" @@ -16,7 +17,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-snplocs.hsapiens.dbsnp151.grch38/meta.yaml b/recipes/bioconductor-snplocs.hsapiens.dbsnp151.grch38/meta.yaml index 7e06571207eed..80c25d654628a 100644 --- a/recipes/bioconductor-snplocs.hsapiens.dbsnp151.grch38/meta.yaml +++ b/recipes/bioconductor-snplocs.hsapiens.dbsnp151.grch38/meta.yaml @@ -1,6 +1,6 @@ {% set version = "0.99.20" %} {% set name = "SNPlocs.Hsapiens.dbSNP151.GRCh38" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -12,7 +12,7 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' md5: 0c1637530d42b10d3e6b8dead09454e7 build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ @@ -20,22 +20,22 @@ build: # Suggests: Biostrings, BSgenome.Hsapiens.UCSC.hg38 requirements: host: - - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' - - 'bioconductor-bsgenome >=1.50.0,<1.51.0' - - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' - - 'bioconductor-genomicranges >=1.34.0,<1.35.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-biocgenerics >=0.30.0,<0.31.0' + - 'bioconductor-bsgenome >=1.52.0,<1.53.0' + - 'bioconductor-genomeinfodb >=1.20.0,<1.21.0' + - 'bioconductor-genomicranges >=1.36.0,<1.37.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' - r-base run: - - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' - - 'bioconductor-bsgenome >=1.50.0,<1.51.0' - - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' - - 'bioconductor-genomicranges >=1.34.0,<1.35.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-biocgenerics >=0.30.0,<0.31.0' + - 'bioconductor-bsgenome >=1.52.0,<1.53.0' + - 'bioconductor-genomeinfodb >=1.20.0,<1.21.0' + - 'bioconductor-genomicranges >=1.36.0,<1.37.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-snplocs.hsapiens.dbsnp151.grch38/post-link.sh b/recipes/bioconductor-snplocs.hsapiens.dbsnp151.grch38/post-link.sh index d0046aad25ddc..255096770bc6f 100644 --- a/recipes/bioconductor-snplocs.hsapiens.dbsnp151.grch38/post-link.sh +++ b/recipes/bioconductor-snplocs.hsapiens.dbsnp151.grch38/post-link.sh @@ -1,9 +1,10 @@ #!/bin/bash FN="SNPlocs.Hsapiens.dbSNP151.GRCh38_0.99.20.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/SNPlocs.Hsapiens.dbSNP151.GRCh38_0.99.20.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/SNPlocs.Hsapiens.dbSNP151.GRCh38_0.99.20.tar.gz" "https://bioarchive.galaxyproject.org/SNPlocs.Hsapiens.dbSNP151.GRCh38_0.99.20.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-snplocs.hsapiens.dbsnp151.grch38/bioconductor-snplocs.hsapiens.dbsnp151.grch38_0.99.20_src_all.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-snplocs.hsapiens.dbsnp151.grch38/bioconductor-snplocs.hsapiens.dbsnp151.grch38_0.99.20_src_all.tar.gz" ) MD5="0c1637530d42b10d3e6b8dead09454e7" @@ -16,7 +17,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-snprelate/meta.yaml b/recipes/bioconductor-snprelate/meta.yaml index 0414e5d38c323..325eabf773512 100644 --- a/recipes/bioconductor-snprelate/meta.yaml +++ b/recipes/bioconductor-snprelate/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.16.0" %} +{% set version = "1.18.0" %} {% set name = "SNPRelate" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 9c7ebe9e6249405c2982d1cb812bec74 + md5: c6c8469a3a7672844c59d5069400d09b build: number: 0 rpaths: @@ -19,10 +19,10 @@ build: # Suggests: parallel, Matrix, RUnit, knitr, MASS, BiocGenerics requirements: host: - - 'bioconductor-gdsfmt >=1.18.0,<1.19.0' + - 'bioconductor-gdsfmt >=1.20.0,<1.21.0' - r-base run: - - 'bioconductor-gdsfmt >=1.18.0,<1.19.0' + - 'bioconductor-gdsfmt >=1.20.0,<1.21.0' - r-base build: - {{ compiler('c') }} diff --git a/recipes/bioconductor-snpstats/meta.yaml b/recipes/bioconductor-snpstats/meta.yaml index 18c27e96ae303..64a22119cd13e 100644 --- a/recipes/bioconductor-snpstats/meta.yaml +++ b/recipes/bioconductor-snpstats/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.32.0" %} +{% set version = "1.34.0" %} {% set name = "snpStats" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 1c1a4fecfb47e7fd1e567eed1dbf2e26 + md5: b4a3c967936226141b748b94b9d8e008 build: number: 0 rpaths: @@ -19,14 +19,14 @@ build: # Suggests: hexbin requirements: host: - - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' - - 'bioconductor-zlibbioc >=1.28.0,<1.29.0' + - 'bioconductor-biocgenerics >=0.30.0,<0.31.0' + - 'bioconductor-zlibbioc >=1.30.0,<1.31.0' - r-base - r-matrix - r-survival run: - - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' - - 'bioconductor-zlibbioc >=1.28.0,<1.29.0' + - 'bioconductor-biocgenerics >=0.30.0,<0.31.0' + - 'bioconductor-zlibbioc >=1.30.0,<1.31.0' - r-base - r-matrix - r-survival diff --git a/recipes/bioconductor-soggi/meta.yaml b/recipes/bioconductor-soggi/meta.yaml index 4106026d13d10..80f8dbd97a71f 100644 --- a/recipes/bioconductor-soggi/meta.yaml +++ b/recipes/bioconductor-soggi/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.14.0" %} +{% set version = "1.16.0" %} {% set name = "soGGi" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: e5d0416ddfb35676209c266b0899cbf2 + md5: 099cf8703b747d9c23f391267c3d035c build: number: 0 rpaths: @@ -20,36 +20,36 @@ build: # Suggests: testthat, BiocStyle, knitr requirements: host: - - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' - - 'bioconductor-biocparallel >=1.16.0,<1.17.0' - - 'bioconductor-biostrings >=2.50.0,<2.51.0' - - 'bioconductor-chipseq >=1.32.0,<1.33.0' - - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' - - 'bioconductor-genomicalignments >=1.18.0,<1.19.0' - - 'bioconductor-genomicranges >=1.34.0,<1.35.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-preprocesscore >=1.44.0,<1.45.0' - - 'bioconductor-rsamtools >=1.34.0,<1.35.0' - - 'bioconductor-rtracklayer >=1.42.0,<1.43.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' - - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' + - 'bioconductor-biocgenerics >=0.30.0,<0.31.0' + - 'bioconductor-biocparallel >=1.18.0,<1.19.0' + - 'bioconductor-biostrings >=2.52.0,<2.53.0' + - 'bioconductor-chipseq >=1.34.0,<1.35.0' + - 'bioconductor-genomeinfodb >=1.20.0,<1.21.0' + - 'bioconductor-genomicalignments >=1.20.0,<1.21.0' + - 'bioconductor-genomicranges >=1.36.0,<1.37.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-preprocesscore >=1.46.0,<1.47.0' + - 'bioconductor-rsamtools >=2.0.0,<2.1.0' + - 'bioconductor-rtracklayer >=1.44.0,<1.45.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' + - 'bioconductor-summarizedexperiment >=1.14.0,<1.15.0' - r-base - r-ggplot2 - r-reshape2 run: - - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' - - 'bioconductor-biocparallel >=1.16.0,<1.17.0' - - 'bioconductor-biostrings >=2.50.0,<2.51.0' - - 'bioconductor-chipseq >=1.32.0,<1.33.0' - - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' - - 'bioconductor-genomicalignments >=1.18.0,<1.19.0' - - 'bioconductor-genomicranges >=1.34.0,<1.35.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-preprocesscore >=1.44.0,<1.45.0' - - 'bioconductor-rsamtools >=1.34.0,<1.35.0' - - 'bioconductor-rtracklayer >=1.42.0,<1.43.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' - - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' + - 'bioconductor-biocgenerics >=0.30.0,<0.31.0' + - 'bioconductor-biocparallel >=1.18.0,<1.19.0' + - 'bioconductor-biostrings >=2.52.0,<2.53.0' + - 'bioconductor-chipseq >=1.34.0,<1.35.0' + - 'bioconductor-genomeinfodb >=1.20.0,<1.21.0' + - 'bioconductor-genomicalignments >=1.20.0,<1.21.0' + - 'bioconductor-genomicranges >=1.36.0,<1.37.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-preprocesscore >=1.46.0,<1.47.0' + - 'bioconductor-rsamtools >=2.0.0,<2.1.0' + - 'bioconductor-rtracklayer >=1.44.0,<1.45.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' + - 'bioconductor-summarizedexperiment >=1.14.0,<1.15.0' - r-base - r-ggplot2 - r-reshape2 diff --git a/recipes/bioconductor-somaticadata/meta.yaml b/recipes/bioconductor-somaticadata/meta.yaml index ce661aa7ccb94..26af8df15b155 100644 --- a/recipes/bioconductor-somaticadata/meta.yaml +++ b/recipes/bioconductor-somaticadata/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.20.0" %} +{% set version = "1.22.0" %} {% set name = "SomatiCAData" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 1b0e5b1b155926d58365e3c7daf478a1 + md5: 59d6519327a11557942dceb5765787bb build: number: 0 rpaths: @@ -22,7 +22,7 @@ requirements: - r-base run: - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-somaticadata/post-link.sh b/recipes/bioconductor-somaticadata/post-link.sh index e83e2a95d43aa..ffa62651608aa 100644 --- a/recipes/bioconductor-somaticadata/post-link.sh +++ b/recipes/bioconductor-somaticadata/post-link.sh @@ -1,11 +1,11 @@ #!/bin/bash -FN="SomatiCAData_1.20.0.tar.gz" +FN="SomatiCAData_1.22.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/experiment/src/contrib/SomatiCAData_1.20.0.tar.gz" - "https://bioarchive.galaxyproject.org/SomatiCAData_1.20.0.tar.gz" - "https://depot.galaxyproject.org/software/bioconductor-somaticadata/bioconductor-somaticadata_1.20.0_src_all.tar.gz" + "https://bioconductor.org/packages/3.9/data/experiment/src/contrib/SomatiCAData_1.22.0.tar.gz" + "https://bioarchive.galaxyproject.org/SomatiCAData_1.22.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-somaticadata/bioconductor-somaticadata_1.22.0_src_all.tar.gz" ) -MD5="1b0e5b1b155926d58365e3c7daf478a1" +MD5="59d6519327a11557942dceb5765787bb" # Use a staging area in the conda dir rather than temp dirs, both to avoid # permission issues as well as to have things downloaded in a predictable @@ -16,7 +16,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-somaticcanceralterations/meta.yaml b/recipes/bioconductor-somaticcanceralterations/meta.yaml index 9cf9852f94b5f..321712ff06515 100644 --- a/recipes/bioconductor-somaticcanceralterations/meta.yaml +++ b/recipes/bioconductor-somaticcanceralterations/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.18.0" %} +{% set version = "1.20.0" %} {% set name = "SomaticCancerAlterations" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 75e6cde71f730fa57516677022042573 + md5: aaf2b8c5ef006b545d1c383fefa35dca build: number: 0 rpaths: @@ -20,20 +20,20 @@ build: # Suggests: testthat, ggbio, ggplot2, knitr requirements: host: - - 'bioconductor-exomecopy >=1.28.0,<1.29.0' - - 'bioconductor-genomicranges >=1.34.0,<1.35.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-exomecopy >=1.30.0,<1.31.0' + - 'bioconductor-genomicranges >=1.36.0,<1.37.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' - r-base - r-stringr run: - - 'bioconductor-exomecopy >=1.28.0,<1.29.0' - - 'bioconductor-genomicranges >=1.34.0,<1.35.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-exomecopy >=1.30.0,<1.31.0' + - 'bioconductor-genomicranges >=1.36.0,<1.37.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' - r-base - r-stringr - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-somaticcanceralterations/post-link.sh b/recipes/bioconductor-somaticcanceralterations/post-link.sh index a988530f2b9fc..6ac21f0a46920 100644 --- a/recipes/bioconductor-somaticcanceralterations/post-link.sh +++ b/recipes/bioconductor-somaticcanceralterations/post-link.sh @@ -1,11 +1,11 @@ #!/bin/bash -FN="SomaticCancerAlterations_1.18.0.tar.gz" +FN="SomaticCancerAlterations_1.20.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/experiment/src/contrib/SomaticCancerAlterations_1.18.0.tar.gz" - "https://bioarchive.galaxyproject.org/SomaticCancerAlterations_1.18.0.tar.gz" - "https://depot.galaxyproject.org/software/bioconductor-somaticcanceralterations/bioconductor-somaticcanceralterations_1.18.0_src_all.tar.gz" + "https://bioconductor.org/packages/3.9/data/experiment/src/contrib/SomaticCancerAlterations_1.20.0.tar.gz" + "https://bioarchive.galaxyproject.org/SomaticCancerAlterations_1.20.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-somaticcanceralterations/bioconductor-somaticcanceralterations_1.20.0_src_all.tar.gz" ) -MD5="75e6cde71f730fa57516677022042573" +MD5="aaf2b8c5ef006b545d1c383fefa35dca" # Use a staging area in the conda dir rather than temp dirs, both to avoid # permission issues as well as to have things downloaded in a predictable @@ -16,7 +16,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-somaticsignatures/meta.yaml b/recipes/bioconductor-somaticsignatures/meta.yaml index e51714edf2095..0c0a4a9995d13 100644 --- a/recipes/bioconductor-somaticsignatures/meta.yaml +++ b/recipes/bioconductor-somaticsignatures/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "2.18.0" %} +{% set version = "2.20.0" %} {% set name = "SomaticSignatures" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: aecea0dbbe1b16434e7e47466cfea941 + md5: e58cba6da7933d68912454b2b628bcad build: number: 0 rpaths: @@ -20,30 +20,30 @@ build: # Suggests: testthat, knitr, parallel, BSgenome.Hsapiens.1000genomes.hs37d5, SomaticCancerAlterations, ggdendro, fastICA, sva requirements: host: - - 'bioconductor-biobase >=2.42.0,<2.43.0' - - 'bioconductor-biostrings >=2.50.0,<2.51.0' - - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' - - 'bioconductor-genomicranges >=1.34.0,<1.35.0' - - 'bioconductor-ggbio >=1.30.0,<1.31.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-pcamethods >=1.74.0,<1.75.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' - - 'bioconductor-variantannotation >=1.28.0,<1.29.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' + - 'bioconductor-biostrings >=2.52.0,<2.53.0' + - 'bioconductor-genomeinfodb >=1.20.0,<1.21.0' + - 'bioconductor-genomicranges >=1.36.0,<1.37.0' + - 'bioconductor-ggbio >=1.32.0,<1.33.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-pcamethods >=1.76.0,<1.77.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' + - 'bioconductor-variantannotation >=1.30.0,<1.31.0' - r-base - r-ggplot2 - r-nmf - r-proxy - r-reshape2 run: - - 'bioconductor-biobase >=2.42.0,<2.43.0' - - 'bioconductor-biostrings >=2.50.0,<2.51.0' - - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' - - 'bioconductor-genomicranges >=1.34.0,<1.35.0' - - 'bioconductor-ggbio >=1.30.0,<1.31.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-pcamethods >=1.74.0,<1.75.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' - - 'bioconductor-variantannotation >=1.28.0,<1.29.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' + - 'bioconductor-biostrings >=2.52.0,<2.53.0' + - 'bioconductor-genomeinfodb >=1.20.0,<1.21.0' + - 'bioconductor-genomicranges >=1.36.0,<1.37.0' + - 'bioconductor-ggbio >=1.32.0,<1.33.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-pcamethods >=1.76.0,<1.77.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' + - 'bioconductor-variantannotation >=1.30.0,<1.31.0' - r-base - r-ggplot2 - r-nmf diff --git a/recipes/bioconductor-soybeancdf/meta.yaml b/recipes/bioconductor-soybeancdf/meta.yaml index 90dee026bbdac..72f4329aa3591 100644 --- a/recipes/bioconductor-soybeancdf/meta.yaml +++ b/recipes/bioconductor-soybeancdf/meta.yaml @@ -1,6 +1,6 @@ {% set version = "2.18.0" %} {% set name = "soybeancdf" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -12,19 +12,19 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: a18e0ba5dbcf2291bdec91091dc528e6 build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' - r-base run: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-soybeancdf/post-link.sh b/recipes/bioconductor-soybeancdf/post-link.sh index 5d3d74add336b..55ba2e930cf96 100644 --- a/recipes/bioconductor-soybeancdf/post-link.sh +++ b/recipes/bioconductor-soybeancdf/post-link.sh @@ -1,9 +1,10 @@ #!/bin/bash FN="soybeancdf_2.18.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/soybeancdf_2.18.0.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/soybeancdf_2.18.0.tar.gz" "https://bioarchive.galaxyproject.org/soybeancdf_2.18.0.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-soybeancdf/bioconductor-soybeancdf_2.18.0_src_all.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-soybeancdf/bioconductor-soybeancdf_2.18.0_src_all.tar.gz" ) MD5="a18e0ba5dbcf2291bdec91091dc528e6" @@ -16,7 +17,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-soybeanprobe/meta.yaml b/recipes/bioconductor-soybeanprobe/meta.yaml index 3c9345d280830..5b276f3f7c6c9 100644 --- a/recipes/bioconductor-soybeanprobe/meta.yaml +++ b/recipes/bioconductor-soybeanprobe/meta.yaml @@ -1,6 +1,6 @@ {% set version = "2.18.0" %} {% set name = "soybeanprobe" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -12,19 +12,19 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 3057a5c387ff35b6c647c4db27041a13 build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' - r-base run: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-soybeanprobe/post-link.sh b/recipes/bioconductor-soybeanprobe/post-link.sh index 33023018b68b2..afd201c12390d 100644 --- a/recipes/bioconductor-soybeanprobe/post-link.sh +++ b/recipes/bioconductor-soybeanprobe/post-link.sh @@ -1,9 +1,10 @@ #!/bin/bash FN="soybeanprobe_2.18.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/soybeanprobe_2.18.0.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/soybeanprobe_2.18.0.tar.gz" "https://bioarchive.galaxyproject.org/soybeanprobe_2.18.0.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-soybeanprobe/bioconductor-soybeanprobe_2.18.0_src_all.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-soybeanprobe/bioconductor-soybeanprobe_2.18.0_src_all.tar.gz" ) MD5="3057a5c387ff35b6c647c4db27041a13" @@ -16,7 +17,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-spacepac/meta.yaml b/recipes/bioconductor-spacepac/meta.yaml index ffcd875dd1616..26950243624d2 100644 --- a/recipes/bioconductor-spacepac/meta.yaml +++ b/recipes/bioconductor-spacepac/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.20.0" %} +{% set version = "1.22.0" %} {% set name = "SpacePAC" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: f5a76a8b5ee150030fcaec81b61c6119 + md5: 95329db0a49f8763beb15579fd6c86cc build: number: 0 rpaths: @@ -20,10 +20,10 @@ build: # Suggests: RUnit, BiocGenerics, rgl requirements: host: - - 'bioconductor-ipac >=1.26.0,<1.27.0' + - 'bioconductor-ipac >=1.28.0,<1.29.0' - r-base run: - - 'bioconductor-ipac >=1.26.0,<1.27.0' + - 'bioconductor-ipac >=1.28.0,<1.29.0' - r-base test: commands: diff --git a/recipes/bioconductor-sparsedossa/meta.yaml b/recipes/bioconductor-sparsedossa/meta.yaml index b4a8ac34f62ba..ab95156ab4e99 100644 --- a/recipes/bioconductor-sparsedossa/meta.yaml +++ b/recipes/bioconductor-sparsedossa/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.6.1" %} +{% set version = "1.8.0" %} {% set name = "sparseDOSSA" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 9e7046fa4bc0bd007589073a9784f89b + md5: 1ba9d3c5f2a18a6e5885a628f8e805ef build: number: 0 rpaths: diff --git a/recipes/bioconductor-sparsenetgls/meta.yaml b/recipes/bioconductor-sparsenetgls/meta.yaml index d550a3507bcf6..c5234f4608fe4 100644 --- a/recipes/bioconductor-sparsenetgls/meta.yaml +++ b/recipes/bioconductor-sparsenetgls/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.0.1" %} +{% set version = "1.2.0" %} {% set name = "sparsenetgls" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 7ef7d3b5a974cbdcaca5c4db001fab0a + md5: eb62a6fdb54d805ca4e657806b5e1d2f build: number: 0 rpaths: diff --git a/recipes/bioconductor-sparsesignatures/meta.yaml b/recipes/bioconductor-sparsesignatures/meta.yaml index 553cefbaff624..26734bd5dd472 100644 --- a/recipes/bioconductor-sparsesignatures/meta.yaml +++ b/recipes/bioconductor-sparsesignatures/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.2.0" %} +{% set version = "1.4.0" %} {% set name = "SparseSignatures" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: dcbc3c8a105ae46137b771ba2ec0735f + md5: ef3f68da832a955cea902fe55e383334 build: number: 0 rpaths: @@ -20,12 +20,12 @@ build: # Suggests: BiocGenerics, BiocStyle, testthat, knitr, requirements: host: - - 'bioconductor-biostrings >=2.50.0,<2.51.0' - - 'bioconductor-bsgenome >=1.50.0,<1.51.0' - - 'bioconductor-bsgenome.hsapiens.1000genomes.hs37d5 >=0.99.0,<0.100.0' - - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' - - 'bioconductor-genomicranges >=1.34.0,<1.35.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-biostrings >=2.52.0,<2.53.0' + - 'bioconductor-bsgenome >=1.52.0,<1.53.0' + - 'bioconductor-bsgenome.hsapiens.1000genomes.hs37d5 >=1.0.0,<1.1.0' + - 'bioconductor-genomeinfodb >=1.20.0,<1.21.0' + - 'bioconductor-genomicranges >=1.36.0,<1.37.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' - r-base - r-data.table - r-ggplot2 @@ -34,12 +34,12 @@ requirements: - r-nnlasso - r-nnls run: - - 'bioconductor-biostrings >=2.50.0,<2.51.0' - - 'bioconductor-bsgenome >=1.50.0,<1.51.0' - - 'bioconductor-bsgenome.hsapiens.1000genomes.hs37d5 >=0.99.0,<0.100.0' - - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' - - 'bioconductor-genomicranges >=1.34.0,<1.35.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-biostrings >=2.52.0,<2.53.0' + - 'bioconductor-bsgenome >=1.52.0,<1.53.0' + - 'bioconductor-bsgenome.hsapiens.1000genomes.hs37d5 >=1.0.0,<1.1.0' + - 'bioconductor-genomeinfodb >=1.20.0,<1.21.0' + - 'bioconductor-genomicranges >=1.36.0,<1.37.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' - r-base - r-data.table - r-ggplot2 diff --git a/recipes/bioconductor-spatialcpie/build.sh b/recipes/bioconductor-spatialcpie/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-spatialcpie/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-spatialcpie/meta.yaml b/recipes/bioconductor-spatialcpie/meta.yaml new file mode 100644 index 0000000000000..5552cd088ca78 --- /dev/null +++ b/recipes/bioconductor-spatialcpie/meta.yaml @@ -0,0 +1,69 @@ +{% set version = "1.0.0" %} +{% set name = "SpatialCPie" %} +{% set bioc = "3.9" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: 4f03a2bb6e955655a7d760f494379e9d +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: BiocStyle (>= 2.8.2), jpeg (>= 0.1-8), knitr (>= 1.20), rmarkdown (>= 1.10), testthat (>= 2.0.0) +requirements: + host: + - 'bioconductor-summarizedexperiment >=1.14.0,<1.15.0' + - r-base + - 'r-colorspace >=1.3-2' + - 'r-dplyr >=0.7.6' + - 'r-ggiraph >=0.5.0' + - 'r-ggplot2 >=3.0.0' + - 'r-ggrepel >=0.8.0' + - 'r-igraph >=1.2.2' + - 'r-lpsolve >=5.6.13' + - 'r-miniui >=0.1.1.1' + - 'r-purrr >=0.2.5' + - 'r-readr >=1.1.1' + - 'r-rlang >=0.2.2' + - 'r-scatterpie >=0.1.2' + - 'r-shiny >=1.1.0' + - 'r-tibble >=1.4.2' + - 'r-tidyr >=0.8.1' + - 'r-tidyselect >=0.2.4' + - 'r-zeallot >=0.1.0' + run: + - 'bioconductor-summarizedexperiment >=1.14.0,<1.15.0' + - r-base + - 'r-colorspace >=1.3-2' + - 'r-dplyr >=0.7.6' + - 'r-ggiraph >=0.5.0' + - 'r-ggplot2 >=3.0.0' + - 'r-ggrepel >=0.8.0' + - 'r-igraph >=1.2.2' + - 'r-lpsolve >=5.6.13' + - 'r-miniui >=0.1.1.1' + - 'r-purrr >=0.2.5' + - 'r-readr >=1.1.1' + - 'r-rlang >=0.2.2' + - 'r-scatterpie >=0.1.2' + - 'r-shiny >=1.1.0' + - 'r-tibble >=1.4.2' + - 'r-tidyr >=0.8.1' + - 'r-tidyselect >=0.2.4' + - 'r-zeallot >=0.1.0' +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: 'MIT + file LICENSE' + summary: 'SpatialCPie is an R package designed to facilitate cluster evaluation for spatial transcriptomics data by providing intuitive visualizations that display the relationships between clusters in order to guide the user during cluster identification and other downstream applications. The package is built around a shiny "gadget" to allow the exploration of the data with multiple plots in parallel and an interactive UI. The user can easily toggle between different cluster resolutions in order to choose the most appropriate visual cues.' + diff --git a/recipes/bioconductor-specl/meta.yaml b/recipes/bioconductor-specl/meta.yaml index 2cb2a9f77e152..378f36f136d6b 100644 --- a/recipes/bioconductor-specl/meta.yaml +++ b/recipes/bioconductor-specl/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.16.1" %} +{% set version = "1.18.0" %} {% set name = "specL" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,25 +10,25 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 774f0ddb159c33a064c365095404f807 + md5: 4a1307fb9987edd64375397ee5c88b40 build: number: 0 rpaths: - lib/R/lib/ - lib/ noarch: generic -# Suggests: BiocGenerics, BiocStyle (>= 2.2.1), knitr (>= 1.15.1), msqc1 (>= 1.0.0), plotrix (>= 3.6.4), prozor (>= 0.2.2), RUnit (>= 0.4.31) +# Suggests: BiocGenerics, BiocStyle (>= 2.2.1), knitr (>= 1.15.1), msqc1 (>= 1.0.0), rmarkdown, RUnit (>= 0.4.31) requirements: host: - r-base - 'r-dbi >=0.5.1' - - 'r-protviz >=0.2.45' + - 'r-protviz >=0.4.0' - 'r-rsqlite >=1.1.2' - 'r-seqinr >=3.3.3' run: - r-base - 'r-dbi >=0.5.1' - - 'r-protviz >=0.2.45' + - 'r-protviz >=0.4.0' - 'r-rsqlite >=1.1.2' - 'r-seqinr >=3.3.3' test: diff --git a/recipes/bioconductor-specond/meta.yaml b/recipes/bioconductor-specond/meta.yaml index 7e1447a21a26e..d1b8e2233b2f3 100644 --- a/recipes/bioconductor-specond/meta.yaml +++ b/recipes/bioconductor-specond/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.36.0" %} +{% set version = "1.38.0" %} {% set name = "SpeCond" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 917e0149bfc0891249d1008f26e5ffb4 + md5: 249bc80969357bdfbc83be3ab304ce47 build: number: 0 rpaths: @@ -19,14 +19,14 @@ build: noarch: generic requirements: host: - - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' - r-base - r-fields - 'r-hwriter >=1.1' - 'r-mclust >=3.3.1' - r-rcolorbrewer run: - - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' - r-base - r-fields - 'r-hwriter >=1.1' diff --git a/recipes/bioconductor-spectraltad/build.sh b/recipes/bioconductor-spectraltad/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-spectraltad/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-spectraltad/meta.yaml b/recipes/bioconductor-spectraltad/meta.yaml new file mode 100644 index 0000000000000..a9e6336fb646e --- /dev/null +++ b/recipes/bioconductor-spectraltad/meta.yaml @@ -0,0 +1,49 @@ +{% set version = "1.0.0" %} +{% set name = "SpectralTAD" %} +{% set bioc = "3.9" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: 1323e09936b7b05ce36f348196042062 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: BiocCheck, BiocManager, BiocStyle, knitr, rmarkdown, microbenchmark, testthat +requirements: + host: + - 'bioconductor-biocparallel >=1.18.0,<1.19.0' + - 'bioconductor-genomicranges >=1.36.0,<1.37.0' + - 'bioconductor-hiccompare >=1.6.0,<1.7.0' + - r-base + - r-cluster + - r-dplyr + - r-magrittr + - r-matrix + - r-primme + run: + - 'bioconductor-biocparallel >=1.18.0,<1.19.0' + - 'bioconductor-genomicranges >=1.36.0,<1.37.0' + - 'bioconductor-hiccompare >=1.6.0,<1.7.0' + - r-base + - r-cluster + - r-dplyr + - r-magrittr + - r-matrix + - r-primme +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: 'MIT + file LICENSE' + summary: 'SpectralTAD is an R package designed to identify Topologically Associated Domains (TADs) from Hi-C contact matrices. It uses a modified version of spectral clustering that uses a sliding window to quickly detect TADs. The function works on a range of different formats of contact matrices and returns a bed file of TAD coordinates. The method does not require users to adjust any parameters to work and gives them control over the number of hierarchical levels to be returned.' + diff --git a/recipes/bioconductor-spem/meta.yaml b/recipes/bioconductor-spem/meta.yaml index 5ad0660629491..8b6f048a70f35 100644 --- a/recipes/bioconductor-spem/meta.yaml +++ b/recipes/bioconductor-spem/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.22.0" %} +{% set version = "1.24.0" %} {% set name = "SPEM" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: ef4d7302fe48373c81e008ad7e21a1f6 + md5: c13851d7ae3e607c65b7c5803953bd4e build: number: 0 rpaths: @@ -19,11 +19,11 @@ build: noarch: generic requirements: host: - - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' - r-base - r-rsolnp run: - - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' - r-base - r-rsolnp test: diff --git a/recipes/bioconductor-spia/meta.yaml b/recipes/bioconductor-spia/meta.yaml index 22ea536c2f046..af03c3e8182c6 100644 --- a/recipes/bioconductor-spia/meta.yaml +++ b/recipes/bioconductor-spia/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "2.34.0" %} +{% set version = "2.36.0" %} {% set name = "SPIA" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: b78883062aeacd45a6739f7f23e551b9 + md5: 05858d5358afe0cb844469f5241fb2d8 build: number: 0 rpaths: @@ -20,10 +20,10 @@ build: # Suggests: graph, Rgraphviz, hgu133plus2.db requirements: host: - - 'bioconductor-kegggraph >=1.42.0,<1.43.0' + - 'bioconductor-kegggraph >=1.44.0,<1.45.0' - r-base run: - - 'bioconductor-kegggraph >=1.42.0,<1.43.0' + - 'bioconductor-kegggraph >=1.44.0,<1.45.0' - r-base test: commands: diff --git a/recipes/bioconductor-spidermir/meta.yaml b/recipes/bioconductor-spidermir/meta.yaml index c06e6db931414..7bcb454a18634 100644 --- a/recipes/bioconductor-spidermir/meta.yaml +++ b/recipes/bioconductor-spidermir/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.12.0" %} +{% set version = "1.14.0" %} {% set name = "SpidermiR" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: d890b86719a3392cd8daf279d69e0e78 + md5: 6103a9e30ea7b6bcad2351ebb4ed754f build: number: 0 rpaths: @@ -20,11 +20,11 @@ build: # Suggests: BiocStyle, knitr, rmarkdown, testthat, devtools, roxygen2 requirements: host: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' - - 'bioconductor-mirnatap >=1.16.0,<1.17.0' - - 'bioconductor-mirnatap.db >=0.99.0,<0.100.0' - - 'bioconductor-org.hs.eg.db >=3.7.0,<3.8.0' - - 'bioconductor-tcgabiolinks >=2.10.0,<2.11.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' + - 'bioconductor-mirnatap >=1.18.0,<1.19.0' + - 'bioconductor-mirnatap.db >=1.0.0,<1.1.0' + - 'bioconductor-org.hs.eg.db >=3.8.0,<3.9.0' + - 'bioconductor-tcgabiolinks >=2.12.0,<2.13.0' - r-base - r-gdata - r-ggplot2 @@ -37,11 +37,11 @@ requirements: - r-networkd3 - r-visnetwork run: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' - - 'bioconductor-mirnatap >=1.16.0,<1.17.0' - - 'bioconductor-mirnatap.db >=0.99.0,<0.100.0' - - 'bioconductor-org.hs.eg.db >=3.7.0,<3.8.0' - - 'bioconductor-tcgabiolinks >=2.10.0,<2.11.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' + - 'bioconductor-mirnatap >=1.18.0,<1.19.0' + - 'bioconductor-mirnatap.db >=1.0.0,<1.1.0' + - 'bioconductor-org.hs.eg.db >=3.8.0,<3.9.0' + - 'bioconductor-tcgabiolinks >=2.12.0,<2.13.0' - r-base - r-gdata - r-ggplot2 @@ -59,7 +59,7 @@ test: about: home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: 'GPL (>= 3)' - summary: 'The aims of SpidermiR are : i) facilitate the network open-access data retrieval from GeneMania data, ii) prepare the data using the appropriate gene nomenclature, iii) integration of miRNA data in a specific network, iv) provide different standard analyses and v) allow the user to visualize the results. In more detail, the package provides multiple methods for query, prepare and download network data (GeneMania), and the integration with validated and predicted miRNA data (mirWalk, miR2Disease,miRTar, miRTarBase, miRandola,Pharmaco-miR,DIANA, Miranda, PicTar and TargetScan) and the use of standard analysis (igraph) and visualization methods (networkD3).' + summary: 'The aims of SpidermiR are : i) facilitate the network open-access data retrieval from GeneMania data, ii) prepare the data using the appropriate gene nomenclature, iii) integration of miRNA data in a specific network, iv) provide different standard analyses and v) allow the user to visualize the results. In more detail, the package provides multiple methods for query, prepare and download network data (GeneMania), and the integration with validated and predicted miRNA data (mirWalk, miRTarBase, miRandola,Pharmaco-miR,DIANA, Miranda, PicTar and TargetScan) and the use of standard analysis (igraph) and visualization methods (networkD3).' extra: identifiers: - biotools:spidermir diff --git a/recipes/bioconductor-spikein/meta.yaml b/recipes/bioconductor-spikein/meta.yaml index 1d8d3ab740701..91be218f2d032 100644 --- a/recipes/bioconductor-spikein/meta.yaml +++ b/recipes/bioconductor-spikein/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.24.0" %} +{% set version = "1.26.0" %} {% set name = "SpikeIn" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: c9e1bcb003e2a9789fd4f48e5c98430a + md5: 3c7f3d87c555ee68feafd95a518caf1d build: number: 0 rpaths: @@ -19,12 +19,12 @@ build: noarch: generic requirements: host: - - 'bioconductor-affy >=1.60.0,<1.61.0' + - 'bioconductor-affy >=1.62.0,<1.63.0' - r-base run: - - 'bioconductor-affy >=1.60.0,<1.61.0' + - 'bioconductor-affy >=1.62.0,<1.63.0' - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-spikein/post-link.sh b/recipes/bioconductor-spikein/post-link.sh index 3edeaf1046b5b..95d6042c4cf06 100644 --- a/recipes/bioconductor-spikein/post-link.sh +++ b/recipes/bioconductor-spikein/post-link.sh @@ -1,11 +1,11 @@ #!/bin/bash -FN="SpikeIn_1.24.0.tar.gz" +FN="SpikeIn_1.26.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/experiment/src/contrib/SpikeIn_1.24.0.tar.gz" - "https://bioarchive.galaxyproject.org/SpikeIn_1.24.0.tar.gz" - "https://depot.galaxyproject.org/software/bioconductor-spikein/bioconductor-spikein_1.24.0_src_all.tar.gz" + "https://bioconductor.org/packages/3.9/data/experiment/src/contrib/SpikeIn_1.26.0.tar.gz" + "https://bioarchive.galaxyproject.org/SpikeIn_1.26.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-spikein/bioconductor-spikein_1.26.0_src_all.tar.gz" ) -MD5="c9e1bcb003e2a9789fd4f48e5c98430a" +MD5="3c7f3d87c555ee68feafd95a518caf1d" # Use a staging area in the conda dir rather than temp dirs, both to avoid # permission issues as well as to have things downloaded in a predictable @@ -16,7 +16,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-spikeinsubset/meta.yaml b/recipes/bioconductor-spikeinsubset/meta.yaml index af8726aef9550..0851272f9cdad 100644 --- a/recipes/bioconductor-spikeinsubset/meta.yaml +++ b/recipes/bioconductor-spikeinsubset/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.22.0" %} +{% set version = "1.24.0" %} {% set name = "SpikeInSubset" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: adc9c4e0f5abe8c9b0c789a3698e5f5a + md5: 5b7cc17fe60a8c139f555c9ddd25eada build: number: 0 rpaths: @@ -19,14 +19,14 @@ build: noarch: generic requirements: host: - - 'bioconductor-affy >=1.60.0,<1.61.0' - - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-affy >=1.62.0,<1.63.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' - r-base run: - - 'bioconductor-affy >=1.60.0,<1.61.0' - - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-affy >=1.62.0,<1.63.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-spikeinsubset/post-link.sh b/recipes/bioconductor-spikeinsubset/post-link.sh index 6bc12e1443bf1..0c18c863499ea 100644 --- a/recipes/bioconductor-spikeinsubset/post-link.sh +++ b/recipes/bioconductor-spikeinsubset/post-link.sh @@ -1,11 +1,11 @@ #!/bin/bash -FN="SpikeInSubset_1.22.0.tar.gz" +FN="SpikeInSubset_1.24.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/experiment/src/contrib/SpikeInSubset_1.22.0.tar.gz" - "https://bioarchive.galaxyproject.org/SpikeInSubset_1.22.0.tar.gz" - "https://depot.galaxyproject.org/software/bioconductor-spikeinsubset/bioconductor-spikeinsubset_1.22.0_src_all.tar.gz" + "https://bioconductor.org/packages/3.9/data/experiment/src/contrib/SpikeInSubset_1.24.0.tar.gz" + "https://bioarchive.galaxyproject.org/SpikeInSubset_1.24.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-spikeinsubset/bioconductor-spikeinsubset_1.24.0_src_all.tar.gz" ) -MD5="adc9c4e0f5abe8c9b0c789a3698e5f5a" +MD5="5b7cc17fe60a8c139f555c9ddd25eada" # Use a staging area in the conda dir rather than temp dirs, both to avoid # permission issues as well as to have things downloaded in a predictable @@ -16,7 +16,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-spikeli/meta.yaml b/recipes/bioconductor-spikeli/meta.yaml index 24bde2352f7de..469a7b5cd3cb1 100644 --- a/recipes/bioconductor-spikeli/meta.yaml +++ b/recipes/bioconductor-spikeli/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "2.42.0" %} +{% set version = "2.44.0" %} {% set name = "spikeLI" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: fede6083947ebb7ce4bacafce63b56c6 + md5: e798132e48ea94e6d4b72adf02168053 build: number: 0 rpaths: diff --git a/recipes/bioconductor-spktools/meta.yaml b/recipes/bioconductor-spktools/meta.yaml index d2b2033138021..faccc8963c223 100644 --- a/recipes/bioconductor-spktools/meta.yaml +++ b/recipes/bioconductor-spktools/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.38.0" %} +{% set version = "1.40.0" %} {% set name = "spkTools" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 5a5c7b1b12e15ddcead01e006f4d8294 + md5: e32f80e2fed6f1f564a83289c806d9dd build: number: 0 rpaths: @@ -20,12 +20,12 @@ build: # Suggests: xtable requirements: host: - - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' - r-base - r-gtools - r-rcolorbrewer run: - - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' - r-base - r-gtools - r-rcolorbrewer diff --git a/recipes/bioconductor-splatter/meta.yaml b/recipes/bioconductor-splatter/meta.yaml index f6e82d210cdac..9058d01d57545 100644 --- a/recipes/bioconductor-splatter/meta.yaml +++ b/recipes/bioconductor-splatter/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.6.1" %} +{% set version = "1.8.0" %} {% set name = "splatter" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,22 +10,22 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: d191f036bf700775249fceb024f61dc1 + md5: 2b0f09cff1c1378eb497050c8bf87fd6 build: number: 0 rpaths: - lib/R/lib/ - lib/ noarch: generic -# Suggests: BiocStyle, covr, cowplot, knitr, limSolve, lme4, progress, pscl, testthat, rmarkdown, S4Vectors, scDD, scran, mfa, phenopath, BASiCS, zinbwave, SparseDC, BiocManager +# Suggests: BiocStyle, covr, cowplot, knitr, limSolve, lme4, progress, pscl, testthat, rmarkdown, S4Vectors, scDD, scran, mfa, phenopath, BASiCS, zinbwave, SparseDC, BiocManager, spelling requirements: host: - - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' - - 'bioconductor-biocparallel >=1.16.0,<1.17.0' - - 'bioconductor-edger >=3.24.0,<3.25.0' - - 'bioconductor-scater >=1.10.0,<1.11.0' - - 'bioconductor-singlecellexperiment >=1.4.0,<1.5.0' - - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' + - 'bioconductor-biocgenerics >=0.30.0,<0.31.0' + - 'bioconductor-biocparallel >=1.18.0,<1.19.0' + - 'bioconductor-edger >=3.26.0,<3.27.0' + - 'bioconductor-scater >=1.12.0,<1.13.0' + - 'bioconductor-singlecellexperiment >=1.6.0,<1.7.0' + - 'bioconductor-summarizedexperiment >=1.14.0,<1.15.0' - r-akima - r-base - r-checkmate @@ -36,12 +36,12 @@ requirements: - r-matrixstats - r-scales run: - - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' - - 'bioconductor-biocparallel >=1.16.0,<1.17.0' - - 'bioconductor-edger >=3.24.0,<3.25.0' - - 'bioconductor-scater >=1.10.0,<1.11.0' - - 'bioconductor-singlecellexperiment >=1.4.0,<1.5.0' - - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' + - 'bioconductor-biocgenerics >=0.30.0,<0.31.0' + - 'bioconductor-biocparallel >=1.18.0,<1.19.0' + - 'bioconductor-edger >=3.26.0,<3.27.0' + - 'bioconductor-scater >=1.12.0,<1.13.0' + - 'bioconductor-singlecellexperiment >=1.6.0,<1.7.0' + - 'bioconductor-summarizedexperiment >=1.14.0,<1.15.0' - r-akima - r-base - r-checkmate diff --git a/recipes/bioconductor-splicegear/meta.yaml b/recipes/bioconductor-splicegear/meta.yaml index 6f9caefb3356a..7d14c22b8154e 100644 --- a/recipes/bioconductor-splicegear/meta.yaml +++ b/recipes/bioconductor-splicegear/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.54.0" %} +{% set version = "1.56.0" %} {% set name = "splicegear" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 16c969a97b03236c8d94b1edf5ba43fd + md5: da2235139f269f64a9d7ffbc7ef13888 build: number: 0 rpaths: @@ -19,13 +19,13 @@ build: noarch: generic requirements: host: - - 'bioconductor-annotate >=1.60.0,<1.61.0' - - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-annotate >=1.62.0,<1.63.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' - r-base - r-xml run: - - 'bioconductor-annotate >=1.60.0,<1.61.0' - - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-annotate >=1.62.0,<1.63.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' - r-base - r-xml test: diff --git a/recipes/bioconductor-splicesites/meta.yaml b/recipes/bioconductor-splicesites/meta.yaml index fd090b8077c67..d41554ac01d74 100644 --- a/recipes/bioconductor-splicesites/meta.yaml +++ b/recipes/bioconductor-splicesites/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.30.0" %} +{% set version = "1.31.0" %} {% set name = "spliceSites" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: cfcde22a0fadd95d33faf18e95e1182f + md5: 78ba99a8c7758e468e27e4d8657b5ec8 build: number: 0 rpaths: @@ -18,21 +18,21 @@ build: - lib/ requirements: host: - - 'bioconductor-biobase >=2.42.0,<2.43.0' - - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' - - 'bioconductor-biostrings >=2.50.0,<2.51.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-seqlogo >=1.48.0,<1.49.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' + - 'bioconductor-biocgenerics >=0.30.0,<0.31.0' + - 'bioconductor-biostrings >=2.52.0,<2.53.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-seqlogo >=1.50.0,<1.51.0' - r-base - r-doby - 'r-rbamtools >=2.14.3' - 'r-refgenome >=1.6.0' run: - - 'bioconductor-biobase >=2.42.0,<2.43.0' - - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' - - 'bioconductor-biostrings >=2.50.0,<2.51.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-seqlogo >=1.48.0,<1.49.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' + - 'bioconductor-biocgenerics >=0.30.0,<0.31.0' + - 'bioconductor-biostrings >=2.52.0,<2.53.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-seqlogo >=1.50.0,<1.51.0' - r-base - r-doby - 'r-rbamtools >=2.14.3' diff --git a/recipes/bioconductor-splicinggraphs/meta.yaml b/recipes/bioconductor-splicinggraphs/meta.yaml index d6a84b321eb14..bfa68f0c5f7d0 100644 --- a/recipes/bioconductor-splicinggraphs/meta.yaml +++ b/recipes/bioconductor-splicinggraphs/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.22.1" %} +{% set version = "1.24.0" %} {% set name = "SplicingGraphs" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: b0a095f5bd1f2ad7309a3ca8bcef3d7c + md5: e5aa51b3ab50aa58556e05559f6fee1e build: number: 0 rpaths: @@ -20,29 +20,31 @@ build: # Suggests: igraph, Gviz, TxDb.Hsapiens.UCSC.hg19.knownGene, RNAseqData.HNRNPC.bam.chr14, RUnit requirements: host: - - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' - - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' - - 'bioconductor-genomicalignments >=1.18.0,<1.19.0' - - 'bioconductor-genomicfeatures >=1.34.0,<1.35.0' - - 'bioconductor-genomicranges >=1.34.0,<1.35.0' - - 'bioconductor-graph >=1.60.0,<1.61.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-rgraphviz >=2.26.0,<2.27.0' - - 'bioconductor-rsamtools >=1.34.0,<1.35.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-biocgenerics >=0.30.0,<0.31.0' + - 'bioconductor-biocparallel >=1.18.0,<1.19.0' + - 'bioconductor-genomeinfodb >=1.20.0,<1.21.0' + - 'bioconductor-genomicalignments >=1.20.0,<1.21.0' + - 'bioconductor-genomicfeatures >=1.36.0,<1.37.0' + - 'bioconductor-genomicranges >=1.36.0,<1.37.0' + - 'bioconductor-graph >=1.62.0,<1.63.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-rgraphviz >=2.28.0,<2.29.0' + - 'bioconductor-rsamtools >=2.0.0,<2.1.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' - r-base - r-igraph run: - - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' - - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' - - 'bioconductor-genomicalignments >=1.18.0,<1.19.0' - - 'bioconductor-genomicfeatures >=1.34.0,<1.35.0' - - 'bioconductor-genomicranges >=1.34.0,<1.35.0' - - 'bioconductor-graph >=1.60.0,<1.61.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-rgraphviz >=2.26.0,<2.27.0' - - 'bioconductor-rsamtools >=1.34.0,<1.35.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-biocgenerics >=0.30.0,<0.31.0' + - 'bioconductor-biocparallel >=1.18.0,<1.19.0' + - 'bioconductor-genomeinfodb >=1.20.0,<1.21.0' + - 'bioconductor-genomicalignments >=1.20.0,<1.21.0' + - 'bioconductor-genomicfeatures >=1.36.0,<1.37.0' + - 'bioconductor-genomicranges >=1.36.0,<1.37.0' + - 'bioconductor-graph >=1.62.0,<1.63.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-rgraphviz >=2.28.0,<2.29.0' + - 'bioconductor-rsamtools >=2.0.0,<2.1.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' - r-base - r-igraph test: diff --git a/recipes/bioconductor-splinetimer/meta.yaml b/recipes/bioconductor-splinetimer/meta.yaml index f94599e8a617e..1ade160751271 100644 --- a/recipes/bioconductor-splinetimer/meta.yaml +++ b/recipes/bioconductor-splinetimer/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.10.0" %} +{% set version = "1.12.0" %} {% set name = "splineTimeR" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 62d088b9c08349611d18aee11eb7612e + md5: 087bdcfe5bd324e43166561b5cccae72 build: number: 0 rpaths: @@ -20,20 +20,20 @@ build: # Suggests: knitr requirements: host: - - 'bioconductor-biobase >=2.42.0,<2.43.0' - - 'bioconductor-fis >=1.10.0,<1.11.0' - - 'bioconductor-gseabase >=1.44.0,<1.45.0' - - 'bioconductor-limma >=3.38.0,<3.39.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' + - 'bioconductor-fis >=1.12.0,<1.13.0' + - 'bioconductor-gseabase >=1.46.0,<1.47.0' + - 'bioconductor-limma >=3.40.0,<3.41.0' - r-base - 'r-genenet >=1.2.13' - r-gtools - r-igraph - 'r-longitudinal >=1.1.12' run: - - 'bioconductor-biobase >=2.42.0,<2.43.0' - - 'bioconductor-fis >=1.10.0,<1.11.0' - - 'bioconductor-gseabase >=1.44.0,<1.45.0' - - 'bioconductor-limma >=3.38.0,<3.39.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' + - 'bioconductor-fis >=1.12.0,<1.13.0' + - 'bioconductor-gseabase >=1.46.0,<1.47.0' + - 'bioconductor-limma >=3.40.0,<3.41.0' - r-base - 'r-genenet >=1.2.13' - r-gtools diff --git a/recipes/bioconductor-splinter/meta.yaml b/recipes/bioconductor-splinter/meta.yaml index 7b8864b06d79f..dcda8c7552769 100644 --- a/recipes/bioconductor-splinter/meta.yaml +++ b/recipes/bioconductor-splinter/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.8.0" %} +{% set version = "1.10.0" %} {% set name = "SPLINTER" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: afe89b12425d88857eb0177f679efad5 + md5: 5c17e4a4d35dbb15fd8210289957752d build: number: 0 rpaths: @@ -20,34 +20,34 @@ build: # Suggests: BiocStyle, knitr, rmarkdown requirements: host: - - 'bioconductor-biomart >=2.38.0,<2.39.0' - - 'bioconductor-biostrings >=2.50.0,<2.51.0' + - 'bioconductor-biomart >=2.40.0,<2.41.0' + - 'bioconductor-biostrings >=2.52.0,<2.53.0' - 'bioconductor-bsgenome.mmusculus.ucsc.mm9 >=1.4.0,<1.5.0' - - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' - - 'bioconductor-genomicalignments >=1.18.0,<1.19.0' - - 'bioconductor-genomicfeatures >=1.34.0,<1.35.0' - - 'bioconductor-genomicranges >=1.34.0,<1.35.0' - - 'bioconductor-gviz >=1.26.0,<1.27.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' - - 'bioconductor-seqlogo >=1.48.0,<1.49.0' + - 'bioconductor-genomeinfodb >=1.20.0,<1.21.0' + - 'bioconductor-genomicalignments >=1.20.0,<1.21.0' + - 'bioconductor-genomicfeatures >=1.36.0,<1.37.0' + - 'bioconductor-genomicranges >=1.36.0,<1.37.0' + - 'bioconductor-gviz >=1.28.0,<1.29.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' + - 'bioconductor-seqlogo >=1.50.0,<1.51.0' - r-base - r-ggplot2 - r-googlevis - r-plyr - r-stringr run: - - 'bioconductor-biomart >=2.38.0,<2.39.0' - - 'bioconductor-biostrings >=2.50.0,<2.51.0' + - 'bioconductor-biomart >=2.40.0,<2.41.0' + - 'bioconductor-biostrings >=2.52.0,<2.53.0' - 'bioconductor-bsgenome.mmusculus.ucsc.mm9 >=1.4.0,<1.5.0' - - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' - - 'bioconductor-genomicalignments >=1.18.0,<1.19.0' - - 'bioconductor-genomicfeatures >=1.34.0,<1.35.0' - - 'bioconductor-genomicranges >=1.34.0,<1.35.0' - - 'bioconductor-gviz >=1.26.0,<1.27.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' - - 'bioconductor-seqlogo >=1.48.0,<1.49.0' + - 'bioconductor-genomeinfodb >=1.20.0,<1.21.0' + - 'bioconductor-genomicalignments >=1.20.0,<1.21.0' + - 'bioconductor-genomicfeatures >=1.36.0,<1.37.0' + - 'bioconductor-genomicranges >=1.36.0,<1.37.0' + - 'bioconductor-gviz >=1.28.0,<1.29.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' + - 'bioconductor-seqlogo >=1.50.0,<1.51.0' - r-base - r-ggplot2 - r-googlevis diff --git a/recipes/bioconductor-splots/meta.yaml b/recipes/bioconductor-splots/meta.yaml index c85ea103d779f..d811d908b173d 100644 --- a/recipes/bioconductor-splots/meta.yaml +++ b/recipes/bioconductor-splots/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.48.0" %} +{% set version = "1.50.0" %} {% set name = "splots" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 58d6a7e42306390dffe15484f0540ffb + md5: 2c8f3ef1599114a9a9dfc9827b5d72fe build: number: 0 rpaths: diff --git a/recipes/bioconductor-sponge/meta.yaml b/recipes/bioconductor-sponge/meta.yaml index c5a9579183ecb..e9b922167e6cf 100644 --- a/recipes/bioconductor-sponge/meta.yaml +++ b/recipes/bioconductor-sponge/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.4.0" %} +{% set version = "1.6.0" %} {% set name = "SPONGE" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 6761d96ab04189f01b7bd9260428e22c + md5: 39b24c15dcd3585f26cb43bb873f2cf5 build: number: 0 rpaths: @@ -20,7 +20,7 @@ build: # Suggests: testthat, knitr, rmarkdown, visNetwork, ggplot2, ggrepel, gridExtra, digest, doParallel, bigmemory requirements: host: - - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' - r-base - r-data.table - r-dorng @@ -34,7 +34,7 @@ requirements: - r-mass - r-ppcor run: - - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' - r-base - r-data.table - r-dorng diff --git a/recipes/bioconductor-spotsegmentation/meta.yaml b/recipes/bioconductor-spotsegmentation/meta.yaml index 389598b4a4c5b..735d550e87b1d 100644 --- a/recipes/bioconductor-spotsegmentation/meta.yaml +++ b/recipes/bioconductor-spotsegmentation/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.56.0" %} +{% set version = "1.58.0" %} {% set name = "spotSegmentation" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 1ea2481528bffefd86889ec081f29124 + md5: 893e935858ac11b3273ec21bd6906553 build: number: 0 rpaths: diff --git a/recipes/bioconductor-squadd/meta.yaml b/recipes/bioconductor-squadd/meta.yaml index 12a125820042b..2570c80b177bc 100644 --- a/recipes/bioconductor-squadd/meta.yaml +++ b/recipes/bioconductor-squadd/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.32.0" %} +{% set version = "1.34.0" %} {% set name = "SQUADD" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 6ec1ec80c00a53aa607426cfa2c15f8b + md5: e285eaeca7faf352ae6240b30dff480b build: number: 0 rpaths: diff --git a/recipes/bioconductor-sracipe/build.sh b/recipes/bioconductor-sracipe/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-sracipe/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-sracipe/meta.yaml b/recipes/bioconductor-sracipe/meta.yaml new file mode 100644 index 0000000000000..9ee7cde00f2e2 --- /dev/null +++ b/recipes/bioconductor-sracipe/meta.yaml @@ -0,0 +1,62 @@ +{% set version = "1.0.0" %} +{% set name = "sRACIPE" %} +{% set bioc = "3.9" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: 4fff473e90b2561fc312ee61a5ea4423 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ +# Suggests: knitr, BiocStyle, rmarkdown +requirements: + host: + - 'bioconductor-biocgenerics >=0.30.0,<0.31.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' + - 'bioconductor-summarizedexperiment >=1.14.0,<1.15.0' + - r-base + - r-ggplot2 + - r-gplots + - r-gridextra + - r-htmlwidgets + - r-mass + - r-rcolorbrewer + - r-rcpp + - r-reshape2 + - r-umap + - r-visnetwork + run: + - 'bioconductor-biocgenerics >=0.30.0,<0.31.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' + - 'bioconductor-summarizedexperiment >=1.14.0,<1.15.0' + - r-base + - r-ggplot2 + - r-gplots + - r-gridextra + - r-htmlwidgets + - r-mass + - r-rcolorbrewer + - r-rcpp + - r-reshape2 + - r-umap + - r-visnetwork + build: + - {{ compiler('c') }} + - {{ compiler('cxx') }} + - make +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: 'MIT + file LICENSE' + summary: 'sRACIPE implements a randomization-based method for gene circuit modeling. It allows us to study the effect of both the gene expression noise and the parametric variation on any gene regulatory circuit (GRC) using only its topology, and simulates an ensemble of models with random kinetic parameters at multiple noise levels. Statistical analysis of the generated gene expressions reveals the basin of attraction and stability of various phenotypic states and their changes associated with intrinsic and extrinsic noises. sRACIPE provides a holistic picture to evaluate the effects of both the stochastic nature of cellular processes and the parametric variation.' + diff --git a/recipes/bioconductor-sradb/meta.yaml b/recipes/bioconductor-sradb/meta.yaml index 1e5fbdf351824..4a5d632c40644 100644 --- a/recipes/bioconductor-sradb/meta.yaml +++ b/recipes/bioconductor-sradb/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.44.0" %} +{% set version = "1.46.0" %} {% set name = "SRAdb" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,9 +10,9 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: a37d04633f80e87dd7e9a5398712445f + md5: 227f399b7b8f1c93a2bd8e374da80c89 build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ @@ -20,14 +20,14 @@ build: # Suggests: Rgraphviz requirements: host: - - 'bioconductor-geoquery >=2.50.0,<2.51.0' - - 'bioconductor-graph >=1.60.0,<1.61.0' + - 'bioconductor-geoquery >=2.52.0,<2.53.0' + - 'bioconductor-graph >=1.62.0,<1.63.0' - r-base - r-rcurl - r-rsqlite run: - - 'bioconductor-geoquery >=2.50.0,<2.51.0' - - 'bioconductor-graph >=1.60.0,<1.61.0' + - 'bioconductor-geoquery >=2.52.0,<2.53.0' + - 'bioconductor-graph >=1.62.0,<1.63.0' - r-base - r-rcurl - r-rsqlite diff --git a/recipes/bioconductor-srap/meta.yaml b/recipes/bioconductor-srap/meta.yaml index 4224ec04327db..70cb4bb23e2fc 100644 --- a/recipes/bioconductor-srap/meta.yaml +++ b/recipes/bioconductor-srap/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.22.0" %} +{% set version = "1.24.0" %} {% set name = "sRAP" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 5ae1daf3d036da49f0c51a31658604a3 + md5: 32f1b0383bfa5e1961a3cd7550c9d7de build: number: 0 rpaths: @@ -19,14 +19,14 @@ build: noarch: generic requirements: host: - - 'bioconductor-qvalue >=2.14.0,<2.15.0' + - 'bioconductor-qvalue >=2.16.0,<2.17.0' - r-base - r-gplots - r-pls - r-rocr - r-writexls run: - - 'bioconductor-qvalue >=2.14.0,<2.15.0' + - 'bioconductor-qvalue >=2.16.0,<2.17.0' - r-base - r-gplots - r-pls diff --git a/recipes/bioconductor-srgnet/meta.yaml b/recipes/bioconductor-srgnet/meta.yaml index 285afe914c189..5c9d9ccfacb15 100644 --- a/recipes/bioconductor-srgnet/meta.yaml +++ b/recipes/bioconductor-srgnet/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.8.0" %} +{% set version = "1.10.0" %} {% set name = "SRGnet" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: ee9c754e6be1b8a5fb9653285327c1fc + md5: 5f5d012b47227cdcce9fb96c2afe7516 build: number: 0 rpaths: @@ -20,8 +20,8 @@ build: # Suggests: knitr, rmarkdown requirements: host: - - 'bioconductor-ebcoexpress >=1.26.0,<1.27.0' - - 'bioconductor-limma >=3.38.0,<3.39.0' + - 'bioconductor-ebcoexpress >=1.28.0,<1.29.0' + - 'bioconductor-limma >=3.40.0,<3.41.0' - r-base - 'r-dmwr >=0.4.1' - 'r-gbm >=2.1.1' @@ -31,8 +31,8 @@ requirements: - r-matrixstats - 'r-pvclust >=2.0-0' run: - - 'bioconductor-ebcoexpress >=1.26.0,<1.27.0' - - 'bioconductor-limma >=3.38.0,<3.39.0' + - 'bioconductor-ebcoexpress >=1.28.0,<1.29.0' + - 'bioconductor-limma >=3.40.0,<3.41.0' - r-base - 'r-dmwr >=0.4.1' - 'r-gbm >=2.1.1' diff --git a/recipes/bioconductor-srnadiff/meta.yaml b/recipes/bioconductor-srnadiff/meta.yaml index 481a797bd927e..5452f1b2c17ff 100644 --- a/recipes/bioconductor-srnadiff/meta.yaml +++ b/recipes/bioconductor-srnadiff/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.2.0" %} +{% set version = "1.4.0" %} {% set name = "srnadiff" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: edddb2ffd09fabfb744f6a1c42267ca5 + md5: 1930356d9b2cdcb4f1ec5d7903dac725 build: number: 0 rpaths: @@ -20,35 +20,35 @@ build: # SystemRequirements: C++11 requirements: host: - - 'bioconductor-biocparallel >=1.16.0,<1.17.0' - - 'bioconductor-biocstyle >=2.10.0,<2.11.0' - - 'bioconductor-deseq2 >=1.22.0,<1.23.0' - - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' - - 'bioconductor-genomicalignments >=1.18.0,<1.19.0' - - 'bioconductor-genomicfeatures >=1.34.0,<1.35.0' - - 'bioconductor-genomicranges >=1.34.0,<1.35.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-rsamtools >=1.34.0,<1.35.0' - - 'bioconductor-rtracklayer >=1.42.0,<1.43.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' - - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' + - 'bioconductor-biocparallel >=1.18.0,<1.19.0' + - 'bioconductor-biocstyle >=2.12.0,<2.13.0' + - 'bioconductor-deseq2 >=1.24.0,<1.25.0' + - 'bioconductor-genomeinfodb >=1.20.0,<1.21.0' + - 'bioconductor-genomicalignments >=1.20.0,<1.21.0' + - 'bioconductor-genomicfeatures >=1.36.0,<1.37.0' + - 'bioconductor-genomicranges >=1.36.0,<1.37.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-rsamtools >=2.0.0,<2.1.0' + - 'bioconductor-rtracklayer >=1.44.0,<1.45.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' + - 'bioconductor-summarizedexperiment >=1.14.0,<1.15.0' - r-base - r-devtools - r-ggplot2 - 'r-rcpp >=0.12.8' run: - - 'bioconductor-biocparallel >=1.16.0,<1.17.0' - - 'bioconductor-biocstyle >=2.10.0,<2.11.0' - - 'bioconductor-deseq2 >=1.22.0,<1.23.0' - - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' - - 'bioconductor-genomicalignments >=1.18.0,<1.19.0' - - 'bioconductor-genomicfeatures >=1.34.0,<1.35.0' - - 'bioconductor-genomicranges >=1.34.0,<1.35.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-rsamtools >=1.34.0,<1.35.0' - - 'bioconductor-rtracklayer >=1.42.0,<1.43.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' - - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' + - 'bioconductor-biocparallel >=1.18.0,<1.19.0' + - 'bioconductor-biocstyle >=2.12.0,<2.13.0' + - 'bioconductor-deseq2 >=1.24.0,<1.25.0' + - 'bioconductor-genomeinfodb >=1.20.0,<1.21.0' + - 'bioconductor-genomicalignments >=1.20.0,<1.21.0' + - 'bioconductor-genomicfeatures >=1.36.0,<1.37.0' + - 'bioconductor-genomicranges >=1.36.0,<1.37.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-rsamtools >=2.0.0,<2.1.0' + - 'bioconductor-rtracklayer >=1.44.0,<1.45.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' + - 'bioconductor-summarizedexperiment >=1.14.0,<1.15.0' - r-base - r-devtools - r-ggplot2 diff --git a/recipes/bioconductor-sscore/meta.yaml b/recipes/bioconductor-sscore/meta.yaml index 5f1c4de66daf6..137c72dfdea56 100644 --- a/recipes/bioconductor-sscore/meta.yaml +++ b/recipes/bioconductor-sscore/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.54.0" %} +{% set version = "1.56.0" %} {% set name = "sscore" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 8d7cc52c819e22d0264a1ca6fff19327 + md5: 254afef6aa7ebccfbfa5e8eee9bb51ed build: number: 0 rpaths: @@ -20,12 +20,12 @@ build: # Suggests: affydata requirements: host: - - 'bioconductor-affy >=1.60.0,<1.61.0' - - 'bioconductor-affyio >=1.52.0,<1.53.0' + - 'bioconductor-affy >=1.62.0,<1.63.0' + - 'bioconductor-affyio >=1.54.0,<1.55.0' - r-base run: - - 'bioconductor-affy >=1.60.0,<1.61.0' - - 'bioconductor-affyio >=1.52.0,<1.53.0' + - 'bioconductor-affy >=1.62.0,<1.63.0' + - 'bioconductor-affyio >=1.54.0,<1.55.0' - r-base test: commands: diff --git a/recipes/bioconductor-sscu/meta.yaml b/recipes/bioconductor-sscu/meta.yaml index 5384bd113228d..f94780ce7ecf7 100644 --- a/recipes/bioconductor-sscu/meta.yaml +++ b/recipes/bioconductor-sscu/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "2.12.0" %} +{% set version = "2.14.0" %} {% set name = "sscu" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: ddbb17a9eb6ef4599fd888772c389faa + md5: 8364ac315f1ff2d0a9ef8ae5d34e6660 build: number: 0 rpaths: @@ -20,13 +20,13 @@ build: # Suggests: knitr, rmarkdown requirements: host: - - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' - - 'bioconductor-biostrings >=2.50.0,<2.51.0' + - 'bioconductor-biocgenerics >=0.30.0,<0.31.0' + - 'bioconductor-biostrings >=2.52.0,<2.53.0' - r-base - 'r-seqinr >=3.1-3' run: - - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' - - 'bioconductor-biostrings >=2.50.0,<2.51.0' + - 'bioconductor-biocgenerics >=0.30.0,<0.31.0' + - 'bioconductor-biostrings >=2.52.0,<2.53.0' - r-base - 'r-seqinr >=3.1-3' test: diff --git a/recipes/bioconductor-sseq/meta.yaml b/recipes/bioconductor-sseq/meta.yaml index 74a969a3e9f19..992c595c2f248 100644 --- a/recipes/bioconductor-sseq/meta.yaml +++ b/recipes/bioconductor-sseq/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.20.1" %} +{% set version = "1.22.0" %} {% set name = "sSeq" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: c22354e791a94efc8d6f4c06394b670f8058128963fa36696e7662931e4ec521 + md5: a0cf6cbf0c4553d99b106c4024fec9cf build: number: 0 rpaths: diff --git a/recipes/bioconductor-ssize/meta.yaml b/recipes/bioconductor-ssize/meta.yaml index a3425b130145a..748b5ed912a1d 100644 --- a/recipes/bioconductor-ssize/meta.yaml +++ b/recipes/bioconductor-ssize/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.56.0" %} +{% set version = "1.58.0" %} {% set name = "ssize" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 0f17e8554718d39959b9edaa732f3c5e + md5: 7d17f1fdee61e0f0c017a2a2d8533404 build: number: 0 rpaths: diff --git a/recipes/bioconductor-sspa/meta.yaml b/recipes/bioconductor-sspa/meta.yaml index 3d5c16b01f28d..c16afd873391a 100644 --- a/recipes/bioconductor-sspa/meta.yaml +++ b/recipes/bioconductor-sspa/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "2.22.1" %} +{% set version = "2.24.0" %} {% set name = "SSPA" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 76570fc7a92c3d5619cd407574f1b597 + md5: ec400994bc750810cb5652358de4d38d build: number: 0 rpaths: @@ -19,13 +19,13 @@ build: # Suggests: BiocStyle, genefilter, edgeR, DESeq requirements: host: - - 'bioconductor-limma >=3.38.0,<3.39.0' - - 'bioconductor-qvalue >=2.14.0,<2.15.0' + - 'bioconductor-limma >=3.40.0,<3.41.0' + - 'bioconductor-qvalue >=2.16.0,<2.17.0' - r-base - r-lattice run: - - 'bioconductor-limma >=3.38.0,<3.39.0' - - 'bioconductor-qvalue >=2.14.0,<2.15.0' + - 'bioconductor-limma >=3.40.0,<3.41.0' + - 'bioconductor-qvalue >=2.16.0,<2.17.0' - r-base - r-lattice build: diff --git a/recipes/bioconductor-ssrch/build.sh b/recipes/bioconductor-ssrch/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-ssrch/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-ssrch/meta.yaml b/recipes/bioconductor-ssrch/meta.yaml new file mode 100644 index 0000000000000..e70eb76423d93 --- /dev/null +++ b/recipes/bioconductor-ssrch/meta.yaml @@ -0,0 +1,37 @@ +{% set version = "1.0.0" %} +{% set name = "ssrch" %} +{% set bioc = "3.9" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + md5: 078f631b72a285cc9900365f94c53e88 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: knitr, testthat +requirements: + host: + - r-base + - r-dt + - r-shiny + run: + - r-base + - r-dt + - r-shiny +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'Demonstrate tokenization and a search gadget for collections of CSV files.' + diff --git a/recipes/bioconductor-ssviz/meta.yaml b/recipes/bioconductor-ssviz/meta.yaml index ab3329ff95dd4..db7239cf20e44 100644 --- a/recipes/bioconductor-ssviz/meta.yaml +++ b/recipes/bioconductor-ssviz/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.16.0" %} +{% set version = "1.18.0" %} {% set name = "ssviz" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 325ecbdd8831f8b52db0205cb4d058b0 + md5: 0291740010847bf4370419650591367d build: number: 0 rpaths: @@ -20,15 +20,15 @@ build: # Suggests: knitr requirements: host: - - 'bioconductor-biostrings >=2.50.0,<2.51.0' - - 'bioconductor-rsamtools >=1.34.0,<1.35.0' + - 'bioconductor-biostrings >=2.52.0,<2.53.0' + - 'bioconductor-rsamtools >=2.0.0,<2.1.0' - r-base - r-ggplot2 - r-rcolorbrewer - r-reshape run: - - 'bioconductor-biostrings >=2.50.0,<2.51.0' - - 'bioconductor-rsamtools >=1.34.0,<1.35.0' + - 'bioconductor-biostrings >=2.52.0,<2.53.0' + - 'bioconductor-rsamtools >=2.0.0,<2.1.0' - r-base - r-ggplot2 - r-rcolorbrewer diff --git a/recipes/bioconductor-stager/meta.yaml b/recipes/bioconductor-stager/meta.yaml index 510c4a4dd6664..ca8e0d2b7f61f 100644 --- a/recipes/bioconductor-stager/meta.yaml +++ b/recipes/bioconductor-stager/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.4.0" %} +{% set version = "1.6.0" %} {% set name = "stageR" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 3940cc6f065042cc8dd0c135109ec057 + md5: 1b9cf571fb3a6b3853fa6ede1dcbe631 build: number: 0 rpaths: @@ -20,10 +20,10 @@ build: # Suggests: knitr, rmarkdown, BiocStyle, methods, Biobase, edgeR, limma, DEXSeq, testthat requirements: host: - - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' + - 'bioconductor-summarizedexperiment >=1.14.0,<1.15.0' - r-base run: - - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' + - 'bioconductor-summarizedexperiment >=1.14.0,<1.15.0' - r-base test: commands: diff --git a/recipes/bioconductor-stan/meta.yaml b/recipes/bioconductor-stan/meta.yaml index 4cde1e2020b83..f4a807d26bbfc 100644 --- a/recipes/bioconductor-stan/meta.yaml +++ b/recipes/bioconductor-stan/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "2.10.0" %} +{% set version = "2.12.0" %} {% set name = "STAN" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 02085333ba8cd5929612477801e2683f + md5: 09bb714458ce2996b7cebdd743bb78d6 build: number: 0 rpaths: @@ -19,22 +19,22 @@ build: # Suggests: BiocStyle, gplots, knitr requirements: host: - - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' - - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' - - 'bioconductor-genomicranges >=1.34.0,<1.35.0' - - 'bioconductor-gviz >=1.26.0,<1.27.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-biocgenerics >=0.30.0,<0.31.0' + - 'bioconductor-genomeinfodb >=1.20.0,<1.21.0' + - 'bioconductor-genomicranges >=1.36.0,<1.37.0' + - 'bioconductor-gviz >=1.28.0,<1.29.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' - r-base - r-poilog - r-rsolnp run: - - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' - - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' - - 'bioconductor-genomicranges >=1.34.0,<1.35.0' - - 'bioconductor-gviz >=1.26.0,<1.27.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-biocgenerics >=0.30.0,<0.31.0' + - 'bioconductor-genomeinfodb >=1.20.0,<1.21.0' + - 'bioconductor-genomicranges >=1.36.0,<1.37.0' + - 'bioconductor-gviz >=1.28.0,<1.29.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' - r-base - r-poilog - r-rsolnp diff --git a/recipes/bioconductor-starank/meta.yaml b/recipes/bioconductor-starank/meta.yaml index 5e4d4dddfe197..26abefcf30dda 100644 --- a/recipes/bioconductor-starank/meta.yaml +++ b/recipes/bioconductor-starank/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.24.1" %} +{% set version = "1.26.0" %} {% set name = "staRank" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: f120f8fea27077644d6f929a995fef73 + md5: 9cf9bea816f7bf9b14eb6633e685c42a build: number: 0 rpaths: @@ -19,10 +19,10 @@ build: noarch: generic requirements: host: - - 'bioconductor-cellhts2 >=2.46.0,<2.47.0' + - 'bioconductor-cellhts2 >=2.48.0,<2.49.0' - r-base run: - - 'bioconductor-cellhts2 >=2.46.0,<2.47.0' + - 'bioconductor-cellhts2 >=2.48.0,<2.49.0' - r-base test: commands: diff --git a/recipes/bioconductor-starbiotrek/meta.yaml b/recipes/bioconductor-starbiotrek/meta.yaml index 1b56ed957a57b..d43fbd8aa42ba 100644 --- a/recipes/bioconductor-starbiotrek/meta.yaml +++ b/recipes/bioconductor-starbiotrek/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.8.1" %} +{% set version = "1.10.0" %} {% set name = "StarBioTrek" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,9 +10,9 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 134c8a0dccdc922526b49890f76fecd4 + md5: aad2f6de9be8593284c27883bbb0f54d build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ @@ -20,22 +20,26 @@ build: # Suggests: BiocStyle, knitr, rmarkdown, testthat, devtools, roxygen2, qgraph, png, grid requirements: host: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' - - 'bioconductor-keggrest >=1.22.0,<1.23.0' - - 'bioconductor-org.hs.eg.db >=3.7.0,<3.8.0' - - 'bioconductor-spidermir >=1.12.0,<1.13.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' + - 'bioconductor-graphite >=1.30.0,<1.31.0' + - 'bioconductor-spidermir >=1.14.0,<1.15.0' - r-base - r-e1071 + - r-ggplot2 - r-igraph + - r-mlmetrics + - r-reshape2 - r-rocr run: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' - - 'bioconductor-keggrest >=1.22.0,<1.23.0' - - 'bioconductor-org.hs.eg.db >=3.7.0,<3.8.0' - - 'bioconductor-spidermir >=1.12.0,<1.13.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' + - 'bioconductor-graphite >=1.30.0,<1.31.0' + - 'bioconductor-spidermir >=1.14.0,<1.15.0' - r-base - r-e1071 + - r-ggplot2 - r-igraph + - r-mlmetrics + - r-reshape2 - r-rocr test: commands: diff --git a/recipes/bioconductor-starr/meta.yaml b/recipes/bioconductor-starr/meta.yaml index ee395e002bd74..e28e49e24ce37 100644 --- a/recipes/bioconductor-starr/meta.yaml +++ b/recipes/bioconductor-starr/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.38.0" %} +{% set version = "1.40.0" %} {% set name = "Starr" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: eec8e43bb3dc5d143b06de2f7cda0982 + md5: 4ebd6e35c4fbd774b229d172c6aec891 build: number: 0 rpaths: @@ -18,18 +18,18 @@ build: - lib/ requirements: host: - - 'bioconductor-affxparser >=1.54.0,<1.55.0' - - 'bioconductor-affy >=1.60.0,<1.61.0' - - 'bioconductor-ringo >=1.46.0,<1.47.0' - - 'bioconductor-zlibbioc >=1.28.0,<1.29.0' + - 'bioconductor-affxparser >=1.56.0,<1.57.0' + - 'bioconductor-affy >=1.62.0,<1.63.0' + - 'bioconductor-ringo >=1.48.0,<1.49.0' + - 'bioconductor-zlibbioc >=1.30.0,<1.31.0' - r-base - r-mass - r-pspline run: - - 'bioconductor-affxparser >=1.54.0,<1.55.0' - - 'bioconductor-affy >=1.60.0,<1.61.0' - - 'bioconductor-ringo >=1.46.0,<1.47.0' - - 'bioconductor-zlibbioc >=1.28.0,<1.29.0' + - 'bioconductor-affxparser >=1.56.0,<1.57.0' + - 'bioconductor-affy >=1.62.0,<1.63.0' + - 'bioconductor-ringo >=1.48.0,<1.49.0' + - 'bioconductor-zlibbioc >=1.30.0,<1.31.0' - r-base - r-mass - r-pspline diff --git a/recipes/bioconductor-stategra/meta.yaml b/recipes/bioconductor-stategra/meta.yaml index 5f1dff73540a4..e4112ed2058cd 100644 --- a/recipes/bioconductor-stategra/meta.yaml +++ b/recipes/bioconductor-stategra/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.18.0" %} +{% set version = "1.20.0" %} {% set name = "STATegRa" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 12ca7c3e81a4757ca68d7eb69a95e65a + md5: 791f82ccec2a724a053db16fdf0de4ee build: number: 0 rpaths: @@ -20,10 +20,10 @@ build: # Suggests: RUnit, BiocGenerics, knitr (>= 1.6), rmarkdown, BiocStyle (>= 1.3), roxygen2, doSNOW requirements: host: - - 'bioconductor-affy >=1.60.0,<1.61.0' - - 'bioconductor-biobase >=2.42.0,<2.43.0' - - 'bioconductor-edger >=3.24.0,<3.25.0' - - 'bioconductor-limma >=3.38.0,<3.39.0' + - 'bioconductor-affy >=1.62.0,<1.63.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' + - 'bioconductor-edger >=3.26.0,<3.27.0' + - 'bioconductor-limma >=3.40.0,<3.41.0' - r-base - r-calibrate - r-foreach @@ -32,10 +32,10 @@ requirements: - r-gridextra - r-mass run: - - 'bioconductor-affy >=1.60.0,<1.61.0' - - 'bioconductor-biobase >=2.42.0,<2.43.0' - - 'bioconductor-edger >=3.24.0,<3.25.0' - - 'bioconductor-limma >=3.38.0,<3.39.0' + - 'bioconductor-affy >=1.62.0,<1.63.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' + - 'bioconductor-edger >=3.26.0,<3.27.0' + - 'bioconductor-limma >=3.40.0,<3.41.0' - r-base - r-calibrate - r-foreach diff --git a/recipes/bioconductor-stattarget/meta.yaml b/recipes/bioconductor-stattarget/meta.yaml index a55efe1e0ff26..accb1bd413928 100644 --- a/recipes/bioconductor-stattarget/meta.yaml +++ b/recipes/bioconductor-stattarget/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.12.1" %} +{% set version = "1.14.0" %} {% set name = "statTarget" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: 20e386a8c88d1eb9504534aed38a37df01f491537258f2ce4ad73436015868a5 + md5: a1cd757f8125fb68893927e63977b32f build: number: 0 rpaths: @@ -20,8 +20,8 @@ build: # Suggests: testthat, BiocStyle, knitr, rmarkdown, gWidgets2,gWidgets2RGtk2,RGtk2 requirements: host: - - 'bioconductor-impute >=1.56.0,<1.57.0' - - 'bioconductor-roc >=1.58.0,<1.59.0' + - 'bioconductor-impute >=1.58.0,<1.59.0' + - 'bioconductor-roc >=1.60.0,<1.61.0' - r-base - r-pdist - r-pls @@ -29,8 +29,8 @@ requirements: - r-randomforest - r-rrcov run: - - 'bioconductor-impute >=1.56.0,<1.57.0' - - 'bioconductor-roc >=1.58.0,<1.59.0' + - 'bioconductor-impute >=1.58.0,<1.59.0' + - 'bioconductor-roc >=1.60.0,<1.61.0' - r-base - r-pdist - r-pls diff --git a/recipes/bioconductor-stemhypoxia/meta.yaml b/recipes/bioconductor-stemhypoxia/meta.yaml index 0af0d7f68d74d..0bee4c0b5e6ab 100644 --- a/recipes/bioconductor-stemhypoxia/meta.yaml +++ b/recipes/bioconductor-stemhypoxia/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.18.0" %} +{% set version = "1.20.0" %} {% set name = "stemHypoxia" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 1fb8f0225f86414a4c7870ce3c2969bd + md5: a70572433e20a5cc9cdbac997ab05728 build: number: 0 rpaths: @@ -22,7 +22,7 @@ requirements: - r-base run: - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-stemhypoxia/post-link.sh b/recipes/bioconductor-stemhypoxia/post-link.sh index 8e248bcaa3597..ffb6f7c0a96eb 100644 --- a/recipes/bioconductor-stemhypoxia/post-link.sh +++ b/recipes/bioconductor-stemhypoxia/post-link.sh @@ -1,11 +1,11 @@ #!/bin/bash -FN="stemHypoxia_1.18.0.tar.gz" +FN="stemHypoxia_1.20.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/experiment/src/contrib/stemHypoxia_1.18.0.tar.gz" - "https://bioarchive.galaxyproject.org/stemHypoxia_1.18.0.tar.gz" - "https://depot.galaxyproject.org/software/bioconductor-stemhypoxia/bioconductor-stemhypoxia_1.18.0_src_all.tar.gz" + "https://bioconductor.org/packages/3.9/data/experiment/src/contrib/stemHypoxia_1.20.0.tar.gz" + "https://bioarchive.galaxyproject.org/stemHypoxia_1.20.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-stemhypoxia/bioconductor-stemhypoxia_1.20.0_src_all.tar.gz" ) -MD5="1fb8f0225f86414a4c7870ce3c2969bd" +MD5="a70572433e20a5cc9cdbac997ab05728" # Use a staging area in the conda dir rather than temp dirs, both to avoid # permission issues as well as to have things downloaded in a predictable @@ -16,7 +16,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-stepnorm/meta.yaml b/recipes/bioconductor-stepnorm/meta.yaml index 8588be06a15e6..796159262c615 100644 --- a/recipes/bioconductor-stepnorm/meta.yaml +++ b/recipes/bioconductor-stepnorm/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.54.0" %} +{% set version = "1.56.0" %} {% set name = "stepNorm" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 76233358af8236df8f33b593e9699f05 + md5: 43370d0d5c7c251b3443035533114e4c build: number: 0 rpaths: @@ -19,11 +19,11 @@ build: noarch: generic requirements: host: - - 'bioconductor-marray >=1.60.0,<1.61.0' + - 'bioconductor-marray >=1.62.0,<1.63.0' - r-base - r-mass run: - - 'bioconductor-marray >=1.60.0,<1.61.0' + - 'bioconductor-marray >=1.62.0,<1.63.0' - r-base - r-mass test: diff --git a/recipes/bioconductor-stjudem/meta.yaml b/recipes/bioconductor-stjudem/meta.yaml index 5b49299c7e85f..b13d70861847d 100644 --- a/recipes/bioconductor-stjudem/meta.yaml +++ b/recipes/bioconductor-stjudem/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.22.0" %} +{% set version = "1.24.0" %} {% set name = "stjudem" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 73c7d2523afdebc972054b62080d37c7 + md5: 35358ac2317e7d083d373b6db1d0cbd9 build: number: 0 rpaths: @@ -22,7 +22,7 @@ requirements: - r-base run: - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-stjudem/post-link.sh b/recipes/bioconductor-stjudem/post-link.sh index 72a4fba8f2662..b80d90b9cd207 100644 --- a/recipes/bioconductor-stjudem/post-link.sh +++ b/recipes/bioconductor-stjudem/post-link.sh @@ -1,11 +1,11 @@ #!/bin/bash -FN="stjudem_1.22.0.tar.gz" +FN="stjudem_1.24.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/experiment/src/contrib/stjudem_1.22.0.tar.gz" - "https://bioarchive.galaxyproject.org/stjudem_1.22.0.tar.gz" - "https://depot.galaxyproject.org/software/bioconductor-stjudem/bioconductor-stjudem_1.22.0_src_all.tar.gz" + "https://bioconductor.org/packages/3.9/data/experiment/src/contrib/stjudem_1.24.0.tar.gz" + "https://bioarchive.galaxyproject.org/stjudem_1.24.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-stjudem/bioconductor-stjudem_1.24.0_src_all.tar.gz" ) -MD5="73c7d2523afdebc972054b62080d37c7" +MD5="35358ac2317e7d083d373b6db1d0cbd9" # Use a staging area in the conda dir rather than temp dirs, both to avoid # permission issues as well as to have things downloaded in a predictable @@ -16,7 +16,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-strandcheckr/meta.yaml b/recipes/bioconductor-strandcheckr/meta.yaml index 13a98598a7f9c..359ed102e5cc4 100644 --- a/recipes/bioconductor-strandcheckr/meta.yaml +++ b/recipes/bioconductor-strandcheckr/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.0.0" %} +{% set version = "1.2.0" %} {% set name = "strandCheckR" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 3db4172a54f75b10ab4bde8805a76d43 + md5: e91277aa868d4dcadcab553ba630f229 build: number: 0 rpaths: @@ -20,13 +20,13 @@ build: # Suggests: BiocStyle, knitr, testthat requirements: host: - - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' - - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' - - 'bioconductor-genomicalignments >=1.18.0,<1.19.0' - - 'bioconductor-genomicranges >=1.34.0,<1.35.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-rsamtools >=1.34.0,<1.35.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-biocgenerics >=0.30.0,<0.31.0' + - 'bioconductor-genomeinfodb >=1.20.0,<1.21.0' + - 'bioconductor-genomicalignments >=1.20.0,<1.21.0' + - 'bioconductor-genomicranges >=1.36.0,<1.37.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-rsamtools >=2.0.0,<2.1.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' - 'bioconductor-txdb.hsapiens.ucsc.hg38.knowngene >=3.4.0,<3.5.0' - r-base - r-dplyr @@ -36,13 +36,13 @@ requirements: - r-reshape2 - r-stringr run: - - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' - - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' - - 'bioconductor-genomicalignments >=1.18.0,<1.19.0' - - 'bioconductor-genomicranges >=1.34.0,<1.35.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-rsamtools >=1.34.0,<1.35.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-biocgenerics >=0.30.0,<0.31.0' + - 'bioconductor-genomeinfodb >=1.20.0,<1.21.0' + - 'bioconductor-genomicalignments >=1.20.0,<1.21.0' + - 'bioconductor-genomicranges >=1.36.0,<1.37.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-rsamtools >=2.0.0,<2.1.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' - 'bioconductor-txdb.hsapiens.ucsc.hg38.knowngene >=3.4.0,<3.5.0' - r-base - r-dplyr diff --git a/recipes/bioconductor-streamer/meta.yaml b/recipes/bioconductor-streamer/meta.yaml index 2c16cad79ea11..88d0786602c36 100644 --- a/recipes/bioconductor-streamer/meta.yaml +++ b/recipes/bioconductor-streamer/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.28.0" %} +{% set version = "1.30.0" %} {% set name = "Streamer" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: a9e80579a4fbeb9963df11b2a97b4e70 + md5: 07e0a31b38c7d1bac26b07d7715800d8 build: number: 0 rpaths: @@ -19,14 +19,14 @@ build: # Suggests: RUnit, Rsamtools (>= 1.5.53), GenomicAlignments, Rgraphviz requirements: host: - - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' - - 'bioconductor-graph >=1.60.0,<1.61.0' - - 'bioconductor-rbgl >=1.58.0,<1.59.0' + - 'bioconductor-biocgenerics >=0.30.0,<0.31.0' + - 'bioconductor-graph >=1.62.0,<1.63.0' + - 'bioconductor-rbgl >=1.60.0,<1.61.0' - r-base run: - - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' - - 'bioconductor-graph >=1.60.0,<1.61.0' - - 'bioconductor-rbgl >=1.58.0,<1.59.0' + - 'bioconductor-biocgenerics >=0.30.0,<0.31.0' + - 'bioconductor-graph >=1.62.0,<1.63.0' + - 'bioconductor-rbgl >=1.60.0,<1.61.0' - r-base build: - {{ compiler('c') }} diff --git a/recipes/bioconductor-stringdb/meta.yaml b/recipes/bioconductor-stringdb/meta.yaml index 2da19d15223f6..81853791b5a24 100644 --- a/recipes/bioconductor-stringdb/meta.yaml +++ b/recipes/bioconductor-stringdb/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.22.0" %} +{% set version = "1.24.0" %} {% set name = "STRINGdb" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: bf498d4d580ffc25bca94edcc21934b5 + md5: 852af459f0bf6827166b50f9e4c78387 build: number: 0 rpaths: diff --git a/recipes/bioconductor-stroma4/meta.yaml b/recipes/bioconductor-stroma4/meta.yaml index 6eb1102d5e219..cbbfc2b40ded0 100644 --- a/recipes/bioconductor-stroma4/meta.yaml +++ b/recipes/bioconductor-stroma4/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.6.1" %} +{% set version = "1.8.0" %} {% set name = "STROMA4" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: c30d6d00eb22cdbd69ed622d4a653ee367fb42f0e5b6976feaf239f42bc285c7 + md5: d867e3054739383929d535c47366114b build: number: 0 rpaths: @@ -20,14 +20,14 @@ build: # Suggests: breastCancerMAINZ requirements: host: - - 'bioconductor-biobase >=2.42.0,<2.43.0' - - 'bioconductor-biocparallel >=1.16.0,<1.17.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' + - 'bioconductor-biocparallel >=1.18.0,<1.19.0' - r-base - r-cluster - r-matrixstats run: - - 'bioconductor-biobase >=2.42.0,<2.43.0' - - 'bioconductor-biocparallel >=1.16.0,<1.17.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' + - 'bioconductor-biocparallel >=1.18.0,<1.19.0' - r-base - r-cluster - r-matrixstats diff --git a/recipes/bioconductor-structstrings/build.sh b/recipes/bioconductor-structstrings/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-structstrings/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-structstrings/meta.yaml b/recipes/bioconductor-structstrings/meta.yaml new file mode 100644 index 0000000000000..b745f962cd9ae --- /dev/null +++ b/recipes/bioconductor-structstrings/meta.yaml @@ -0,0 +1,51 @@ +{% set version = "1.0.0" %} +{% set name = "Structstrings" %} +{% set bioc = "3.9" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: aa07cf516ac94026a516e03dbbe6b9b9 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ +# Suggests: testthat, knitr, rmarkdown, tRNAscanImport, BiocStyle +requirements: + host: + - 'bioconductor-biocgenerics >=0.30.0,<0.31.0' + - 'bioconductor-biostrings >=2.52.0,<2.53.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' + - 'bioconductor-xvector >=0.24.0,<0.25.0' + - r-assertive + - r-base + - r-stringi + - r-stringr + run: + - 'bioconductor-biocgenerics >=0.30.0,<0.31.0' + - 'bioconductor-biostrings >=2.52.0,<2.53.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' + - 'bioconductor-xvector >=0.24.0,<0.25.0' + - r-assertive + - r-base + - r-stringi + - r-stringr + build: + - {{ compiler('c') }} + - make +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'The Structstrings package implements the widely used dot bracket annotation for storing base pairing information in structured RNA. Structstrings uses the infrastructure provided by the Biostrings package and derives the DotBracketString and related classes from the BString class. From these, base pair tables can be produced for in depth analysis. In addition, the loop indices of the base pairs can be retrieved as well. For better efficiency, information conversion is implemented in C, inspired to a large extend by the ViennaRNA package.' + diff --git a/recipes/bioconductor-structuralvariantannotation/build.sh b/recipes/bioconductor-structuralvariantannotation/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-structuralvariantannotation/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-structuralvariantannotation/meta.yaml b/recipes/bioconductor-structuralvariantannotation/meta.yaml new file mode 100644 index 0000000000000..c4f0ed56ce6d4 --- /dev/null +++ b/recipes/bioconductor-structuralvariantannotation/meta.yaml @@ -0,0 +1,51 @@ +{% set version = "1.0.0" %} +{% set name = "StructuralVariantAnnotation" %} +{% set bioc = "3.9" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: c6694f42d008a2308d1cc670a12df37d +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: BSgenome.Hsapiens.UCSC.hg19, ggplot2, devtools, testthat, roxygen2, covr, knitr, plyranges, ggbio, biovizBase, circlize, tictoc, GenomeInfoDb, IRanges, S4Vectors, SummarizedExperiment +requirements: + host: + - 'bioconductor-biocgenerics >=0.30.0,<0.31.0' + - 'bioconductor-biostrings >=2.52.0,<2.53.0' + - 'bioconductor-genomicranges >=1.36.0,<1.37.0' + - 'bioconductor-rtracklayer >=1.44.0,<1.45.0' + - 'bioconductor-variantannotation >=1.30.0,<1.31.0' + - r-assertthat + - r-base + - r-dplyr + - r-rlang + - r-stringr + run: + - 'bioconductor-biocgenerics >=0.30.0,<0.31.0' + - 'bioconductor-biostrings >=2.52.0,<2.53.0' + - 'bioconductor-genomicranges >=1.36.0,<1.37.0' + - 'bioconductor-rtracklayer >=1.44.0,<1.45.0' + - 'bioconductor-variantannotation >=1.30.0,<1.31.0' + - r-assertthat + - r-base + - r-dplyr + - r-rlang + - r-stringr +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: GPL-3 + summary: 'StructuralVariantAnnotation contains useful helper functions for dealing with structural variants in VCF format. The packages contains functions for parsing VCFs from a number of popular callers as well as functions for dealing with breakpoints involving two separate genomic loci encoded as GRanges objects.' + diff --git a/recipes/bioconductor-subcellbarcode/build.sh b/recipes/bioconductor-subcellbarcode/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-subcellbarcode/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-subcellbarcode/meta.yaml b/recipes/bioconductor-subcellbarcode/meta.yaml new file mode 100644 index 0000000000000..eece5eec2c853 --- /dev/null +++ b/recipes/bioconductor-subcellbarcode/meta.yaml @@ -0,0 +1,49 @@ +{% set version = "1.0.0" %} +{% set name = "SubCellBarCode" %} +{% set bioc = "3.9" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: fbc0ec18e594e7bbaaeded98aa0a8794 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: knitr, rmarkdown, BiocStyle +requirements: + host: + - r-base + - r-caret + - r-e1071 + - r-ggplot2 + - r-ggrepel + - r-gridextra + - r-networkd3 + - r-rtsne + - r-scatterplot3d + run: + - r-base + - r-caret + - r-e1071 + - r-ggplot2 + - r-ggrepel + - r-gridextra + - r-networkd3 + - r-rtsne + - r-scatterplot3d +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: GPL-2 + summary: 'Mass-Spectrometry based spatial proteomics have enabled the proteome-wide mapping of protein subcellular localization (Orre et al. 2019, Molecular Cell). SubCellBarCode R package robustly classifies proteins into corresponding subcellular localization.' + diff --git a/recipes/bioconductor-subseq/meta.yaml b/recipes/bioconductor-subseq/meta.yaml index be8fda21f0b2d..1375878e66f77 100644 --- a/recipes/bioconductor-subseq/meta.yaml +++ b/recipes/bioconductor-subseq/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.12.1" %} +{% set version = "1.14.0" %} {% set name = "subSeq" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: 89e234cab535c4adc8289d51a4409d4803089770c2310cf3aa87073bc8502e94 + md5: 7c8e235019360f80bfb607b98a7d95ca build: number: 0 rpaths: @@ -20,8 +20,8 @@ build: # Suggests: limma, edgeR, DESeq2, DEXSeq (>= 1.9.7), testthat, knitr requirements: host: - - 'bioconductor-biobase >=2.42.0,<2.43.0' - - 'bioconductor-qvalue >=2.14.0,<2.15.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' + - 'bioconductor-qvalue >=2.16.0,<2.17.0' - r-base - r-data.table - r-digest @@ -30,8 +30,8 @@ requirements: - r-magrittr - r-tidyr run: - - 'bioconductor-biobase >=2.42.0,<2.43.0' - - 'bioconductor-qvalue >=2.14.0,<2.15.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' + - 'bioconductor-qvalue >=2.16.0,<2.17.0' - r-base - r-data.table - r-digest diff --git a/recipes/bioconductor-sugarcanecdf/meta.yaml b/recipes/bioconductor-sugarcanecdf/meta.yaml index ec5aac9c23ce5..bad33d6440856 100644 --- a/recipes/bioconductor-sugarcanecdf/meta.yaml +++ b/recipes/bioconductor-sugarcanecdf/meta.yaml @@ -1,6 +1,6 @@ {% set version = "2.18.0" %} {% set name = "sugarcanecdf" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -12,19 +12,19 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: f66d51868068f83d3693d3cb05be418a build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' - r-base run: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-sugarcanecdf/post-link.sh b/recipes/bioconductor-sugarcanecdf/post-link.sh index d5843f2a22de7..13b3ae1a66bc7 100644 --- a/recipes/bioconductor-sugarcanecdf/post-link.sh +++ b/recipes/bioconductor-sugarcanecdf/post-link.sh @@ -1,9 +1,10 @@ #!/bin/bash FN="sugarcanecdf_2.18.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/sugarcanecdf_2.18.0.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/sugarcanecdf_2.18.0.tar.gz" "https://bioarchive.galaxyproject.org/sugarcanecdf_2.18.0.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-sugarcanecdf/bioconductor-sugarcanecdf_2.18.0_src_all.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-sugarcanecdf/bioconductor-sugarcanecdf_2.18.0_src_all.tar.gz" ) MD5="f66d51868068f83d3693d3cb05be418a" @@ -16,7 +17,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-sugarcaneprobe/meta.yaml b/recipes/bioconductor-sugarcaneprobe/meta.yaml index 77e010169b381..29b4757bcae04 100644 --- a/recipes/bioconductor-sugarcaneprobe/meta.yaml +++ b/recipes/bioconductor-sugarcaneprobe/meta.yaml @@ -1,6 +1,6 @@ {% set version = "2.18.0" %} {% set name = "sugarcaneprobe" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -12,19 +12,19 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 66c101ac73e9235d258b9f996c42778e build: - number: 1 + number: 2 rpaths: - lib/R/lib/ - lib/ noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' - r-base run: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-sugarcaneprobe/post-link.sh b/recipes/bioconductor-sugarcaneprobe/post-link.sh index 5b1924c29523c..1a256748718ab 100644 --- a/recipes/bioconductor-sugarcaneprobe/post-link.sh +++ b/recipes/bioconductor-sugarcaneprobe/post-link.sh @@ -1,9 +1,10 @@ #!/bin/bash FN="sugarcaneprobe_2.18.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/sugarcaneprobe_2.18.0.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/sugarcaneprobe_2.18.0.tar.gz" "https://bioarchive.galaxyproject.org/sugarcaneprobe_2.18.0.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-sugarcaneprobe/bioconductor-sugarcaneprobe_2.18.0_src_all.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-sugarcaneprobe/bioconductor-sugarcaneprobe_2.18.0_src_all.tar.gz" ) MD5="66c101ac73e9235d258b9f996c42778e" @@ -16,7 +17,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-summarizedbenchmark/meta.yaml b/recipes/bioconductor-summarizedbenchmark/meta.yaml index 2db901e41ef8c..85c44833dc147 100644 --- a/recipes/bioconductor-summarizedbenchmark/meta.yaml +++ b/recipes/bioconductor-summarizedbenchmark/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "2.0.0" %} +{% set version = "2.2.0" %} {% set name = "SummarizedBenchmark" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 292d21d10c1ede88ed9c6be5f2d704fb + md5: 1f582086c51cb47983e411ab5b16c139 build: number: 0 rpaths: @@ -20,10 +20,10 @@ build: # Suggests: iCOBRA, BiocStyle, knitr, magrittr, IHW, qvalue, testthat, DESeq2, edgeR, limma, tximport, readr, scRNAseq, splatter, scater, rnaseqcomp, biomaRt requirements: host: - - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' - - 'bioconductor-biocparallel >=1.16.0,<1.17.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' - - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' + - 'bioconductor-biocgenerics >=0.30.0,<0.31.0' + - 'bioconductor-biocparallel >=1.18.0,<1.19.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' + - 'bioconductor-summarizedexperiment >=1.14.0,<1.15.0' - r-base - r-crayon - r-digest @@ -37,10 +37,10 @@ requirements: - r-tidyr - r-upsetr run: - - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' - - 'bioconductor-biocparallel >=1.16.0,<1.17.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' - - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' + - 'bioconductor-biocgenerics >=0.30.0,<0.31.0' + - 'bioconductor-biocparallel >=1.18.0,<1.19.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' + - 'bioconductor-summarizedexperiment >=1.14.0,<1.15.0' - r-base - r-crayon - r-digest diff --git a/recipes/bioconductor-summarizedexperiment/meta.yaml b/recipes/bioconductor-summarizedexperiment/meta.yaml index 2e3ea4c154ba3..29b6919489f1c 100644 --- a/recipes/bioconductor-summarizedexperiment/meta.yaml +++ b/recipes/bioconductor-summarizedexperiment/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.12.0" %} +{% set version = "1.14.0" %} {% set name = "SummarizedExperiment" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 5738caa020eb8f8c7f399d9e799500ad + md5: 8bf661a8b12b424da64db8dd6e487beb build: number: 0 rpaths: @@ -20,23 +20,23 @@ build: # Suggests: annotate, AnnotationDbi, hgu95av2.db, GenomicFeatures, TxDb.Hsapiens.UCSC.hg19.knownGene, BiocStyle, knitr, rmarkdown, digest, jsonlite, rhdf5, HDF5Array (>= 1.7.5), airway, RUnit, testthat requirements: host: - - 'bioconductor-biobase >=2.42.0,<2.43.0' - - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' - - 'bioconductor-delayedarray >=0.8.0,<0.9.0' - - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' - - 'bioconductor-genomicranges >=1.34.0,<1.35.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' + - 'bioconductor-biocgenerics >=0.30.0,<0.31.0' + - 'bioconductor-delayedarray >=0.10.0,<0.11.0' + - 'bioconductor-genomeinfodb >=1.20.0,<1.21.0' + - 'bioconductor-genomicranges >=1.36.0,<1.37.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' - r-base - r-matrix run: - - 'bioconductor-biobase >=2.42.0,<2.43.0' - - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' - - 'bioconductor-delayedarray >=0.8.0,<0.9.0' - - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' - - 'bioconductor-genomicranges >=1.34.0,<1.35.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' + - 'bioconductor-biocgenerics >=0.30.0,<0.31.0' + - 'bioconductor-delayedarray >=0.10.0,<0.11.0' + - 'bioconductor-genomeinfodb >=1.20.0,<1.21.0' + - 'bioconductor-genomicranges >=1.36.0,<1.37.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' - r-base - r-matrix test: diff --git a/recipes/bioconductor-suprahex/meta.yaml b/recipes/bioconductor-suprahex/meta.yaml index 6671a4baf46ea..c6c4d4ed702f7 100644 --- a/recipes/bioconductor-suprahex/meta.yaml +++ b/recipes/bioconductor-suprahex/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.20.0" %} +{% set version = "1.22.0" %} {% set name = "supraHex" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 6a9ce3e5a00dca2709dfbb1569546767 + md5: 3240782128afb1c78fdc29275638d33c build: number: 0 rpaths: diff --git a/recipes/bioconductor-survcomp/meta.yaml b/recipes/bioconductor-survcomp/meta.yaml index 1fd32e4594eb0..aefb7875a6065 100644 --- a/recipes/bioconductor-survcomp/meta.yaml +++ b/recipes/bioconductor-survcomp/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.32.0" %} +{% set version = "1.34.0" %} {% set name = "survcomp" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 9deb430d0aa94bc4738bbed9828cbf08 + md5: 691520534d33eba80a1a36a6099d3354 build: number: 0 rpaths: diff --git a/recipes/bioconductor-survtype/build.sh b/recipes/bioconductor-survtype/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-survtype/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-survtype/meta.yaml b/recipes/bioconductor-survtype/meta.yaml new file mode 100644 index 0000000000000..e12bbed1efad6 --- /dev/null +++ b/recipes/bioconductor-survtype/meta.yaml @@ -0,0 +1,43 @@ +{% set version = "1.0.0" %} +{% set name = "survtype" %} +{% set bioc = "3.9" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + md5: 71412d425518d026431e1e2815910a68 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: maftools, scales, knitr +requirements: + host: + - 'bioconductor-summarizedexperiment >=1.14.0,<1.15.0' + - r-base + - r-clustvarsel + - r-pheatmap + - r-survival + - r-survminer + run: + - 'bioconductor-summarizedexperiment >=1.14.0,<1.15.0' + - r-base + - r-clustvarsel + - r-pheatmap + - r-survival + - r-survminer +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'Subtypes are defined as groups of samples that have distinct molecular and clinical features. Genomic data can be analyzed for discovering patient subtypes, associated with clinical data, especially for survival information. This package is aimed to identify subtypes that are both clinically relevant and biologically meaningful.' + diff --git a/recipes/bioconductor-sushi/meta.yaml b/recipes/bioconductor-sushi/meta.yaml index 406d8193bb07f..54c536aa8d58c 100644 --- a/recipes/bioconductor-sushi/meta.yaml +++ b/recipes/bioconductor-sushi/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.20.0" %} +{% set version = "1.22.0" %} {% set name = "Sushi" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 1dd42cecf0f9fcc2ce3e5da994e42c4a + md5: 5e1d6b719a627e5376aeb07b0e59074d build: number: 0 rpaths: @@ -19,11 +19,11 @@ build: noarch: generic requirements: host: - - 'bioconductor-biomart >=2.38.0,<2.39.0' + - 'bioconductor-biomart >=2.40.0,<2.41.0' - r-base - r-zoo run: - - 'bioconductor-biomart >=2.38.0,<2.39.0' + - 'bioconductor-biomart >=2.40.0,<2.41.0' - r-base - r-zoo test: diff --git a/recipes/bioconductor-sva/meta.yaml b/recipes/bioconductor-sva/meta.yaml index 52537d55ca050..bd0a270ff316e 100644 --- a/recipes/bioconductor-sva/meta.yaml +++ b/recipes/bioconductor-sva/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "3.30.1" %} +{% set version = "3.32.0" %} {% set name = "sva" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - sha256: 1872da8a1b041a13b9d8d3135f93587f572c95b720c5abdd784075591851f233 + md5: 63a2a6b9e63399130daf914f7be63edf build: number: 0 rpaths: @@ -19,16 +19,16 @@ build: # Suggests: pamr, bladderbatch, BiocStyle, zebrafishRNASeq, testthat requirements: host: - - 'bioconductor-biocparallel >=1.16.0,<1.17.0' - - 'bioconductor-genefilter >=1.64.0,<1.65.0' - - 'bioconductor-limma >=3.38.0,<3.39.0' + - 'bioconductor-biocparallel >=1.18.0,<1.19.0' + - 'bioconductor-genefilter >=1.66.0,<1.67.0' + - 'bioconductor-limma >=3.40.0,<3.41.0' - r-base - r-matrixstats - r-mgcv run: - - 'bioconductor-biocparallel >=1.16.0,<1.17.0' - - 'bioconductor-genefilter >=1.64.0,<1.65.0' - - 'bioconductor-limma >=3.38.0,<3.39.0' + - 'bioconductor-biocparallel >=1.18.0,<1.19.0' + - 'bioconductor-genefilter >=1.66.0,<1.67.0' + - 'bioconductor-limma >=3.40.0,<3.41.0' - r-base - r-matrixstats - r-mgcv diff --git a/recipes/bioconductor-svaplsseq/meta.yaml b/recipes/bioconductor-svaplsseq/meta.yaml index 67f4e6c011e20..2f97ab1ed0520 100644 --- a/recipes/bioconductor-svaplsseq/meta.yaml +++ b/recipes/bioconductor-svaplsseq/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.8.1" %} +{% set version = "1.10.0" %} {% set name = "SVAPLSseq" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: f5c96fa7eb7d472cd2ddedaee359fdce + md5: 081e1b03e8e5e7cfbab31ed3e4e5e408 build: number: 0 rpaths: @@ -20,17 +20,17 @@ build: # Suggests: BiocStyle requirements: host: - - 'bioconductor-edger >=3.24.0,<3.25.0' - - 'bioconductor-limma >=3.38.0,<3.39.0' - - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' + - 'bioconductor-edger >=3.26.0,<3.27.0' + - 'bioconductor-limma >=3.40.0,<3.41.0' + - 'bioconductor-summarizedexperiment >=1.14.0,<1.15.0' - r-base - r-ggplot2 - r-lmtest - r-pls run: - - 'bioconductor-edger >=3.24.0,<3.25.0' - - 'bioconductor-limma >=3.38.0,<3.39.0' - - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' + - 'bioconductor-edger >=3.26.0,<3.27.0' + - 'bioconductor-limma >=3.40.0,<3.41.0' + - 'bioconductor-summarizedexperiment >=1.14.0,<1.15.0' - r-base - r-ggplot2 - r-lmtest diff --git a/recipes/bioconductor-svm2crm/meta.yaml b/recipes/bioconductor-svm2crm/meta.yaml index 9cc6156d51ea9..7afb861c5d0fa 100644 --- a/recipes/bioconductor-svm2crm/meta.yaml +++ b/recipes/bioconductor-svm2crm/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.14.0" %} +{% set version = "1.15.1" %} {% set name = "SVM2CRM" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 406904f28e8238f547ecc79b2d562ffd + md5: 3de82245555cc7713269fbcc6a1b4de8 build: number: 0 rpaths: @@ -19,11 +19,11 @@ build: noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' - - 'bioconductor-genomicranges >=1.34.0,<1.35.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-rtracklayer >=1.42.0,<1.43.0' - - 'bioconductor-svm2crmdata >=1.14.0,<1.15.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' + - 'bioconductor-genomicranges >=1.36.0,<1.37.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-rtracklayer >=1.44.0,<1.45.0' + - 'bioconductor-svm2crmdata >=1.16.0,<1.17.0' - r-base - r-liblinear - r-mclust @@ -33,11 +33,11 @@ requirements: - r-verification - r-zoo run: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' - - 'bioconductor-genomicranges >=1.34.0,<1.35.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-rtracklayer >=1.42.0,<1.43.0' - - 'bioconductor-svm2crmdata >=1.14.0,<1.15.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' + - 'bioconductor-genomicranges >=1.36.0,<1.37.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-rtracklayer >=1.44.0,<1.45.0' + - 'bioconductor-svm2crmdata >=1.16.0,<1.17.0' - r-base - r-liblinear - r-mclust diff --git a/recipes/bioconductor-svm2crmdata/meta.yaml b/recipes/bioconductor-svm2crmdata/meta.yaml index 94c82d909df79..2d2998662fe03 100644 --- a/recipes/bioconductor-svm2crmdata/meta.yaml +++ b/recipes/bioconductor-svm2crmdata/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.14.0" %} +{% set version = "1.16.0" %} {% set name = "SVM2CRMdata" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 67239ac74ee3b881f2070be62472e43b + md5: 205df5b059ee9465b8d95c0ed1f6d4dc build: number: 0 rpaths: @@ -22,7 +22,7 @@ requirements: - r-base run: - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-svm2crmdata/post-link.sh b/recipes/bioconductor-svm2crmdata/post-link.sh index 9dd18cc9985ff..e3c45b1ca8abe 100644 --- a/recipes/bioconductor-svm2crmdata/post-link.sh +++ b/recipes/bioconductor-svm2crmdata/post-link.sh @@ -1,11 +1,11 @@ #!/bin/bash -FN="SVM2CRMdata_1.14.0.tar.gz" +FN="SVM2CRMdata_1.16.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/experiment/src/contrib/SVM2CRMdata_1.14.0.tar.gz" - "https://bioarchive.galaxyproject.org/SVM2CRMdata_1.14.0.tar.gz" - "https://depot.galaxyproject.org/software/bioconductor-svm2crmdata/bioconductor-svm2crmdata_1.14.0_src_all.tar.gz" + "https://bioconductor.org/packages/3.9/data/experiment/src/contrib/SVM2CRMdata_1.16.0.tar.gz" + "https://bioarchive.galaxyproject.org/SVM2CRMdata_1.16.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-svm2crmdata/bioconductor-svm2crmdata_1.16.0_src_all.tar.gz" ) -MD5="67239ac74ee3b881f2070be62472e43b" +MD5="205df5b059ee9465b8d95c0ed1f6d4dc" # Use a staging area in the conda dir rather than temp dirs, both to avoid # permission issues as well as to have things downloaded in a predictable @@ -16,7 +16,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-swath2stats/meta.yaml b/recipes/bioconductor-swath2stats/meta.yaml index 7fa06bdd6b865..7b722ade91e2a 100644 --- a/recipes/bioconductor-swath2stats/meta.yaml +++ b/recipes/bioconductor-swath2stats/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.12.1" %} +{% set version = "1.14.0" %} {% set name = "SWATH2stats" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,23 +10,23 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: b9a0757b467c76b415777e94fd0e2da9 + md5: 33a9b321934d71a2ea7911d029b02c38 build: number: 0 rpaths: - lib/R/lib/ - lib/ noarch: generic -# Suggests: testthat, aLFQ, knitr, PECA +# Suggests: testthat, knitr requirements: host: - - 'bioconductor-biomart >=2.38.0,<2.39.0' + - 'bioconductor-biomart >=2.40.0,<2.41.0' - r-base - r-data.table - r-ggplot2 - r-reshape2 run: - - 'bioconductor-biomart >=2.38.0,<2.39.0' + - 'bioconductor-biomart >=2.40.0,<2.41.0' - r-base - r-data.table - r-ggplot2 diff --git a/recipes/bioconductor-swathxtend/meta.yaml b/recipes/bioconductor-swathxtend/meta.yaml index 8e36a6de36ba5..9994fb598f731 100644 --- a/recipes/bioconductor-swathxtend/meta.yaml +++ b/recipes/bioconductor-swathxtend/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "2.4.0" %} +{% set version = "2.6.0" %} {% set name = "SwathXtend" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 4be2d18fb48add8b1212d8c1e906ecec + md5: 4064834ca97a9aaab22e43c7c107b19a build: number: 0 rpaths: diff --git a/recipes/bioconductor-swfdr/meta.yaml b/recipes/bioconductor-swfdr/meta.yaml index 7b53c64209038..420f8e7459256 100644 --- a/recipes/bioconductor-swfdr/meta.yaml +++ b/recipes/bioconductor-swfdr/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.8.0" %} +{% set version = "1.10.0" %} {% set name = "swfdr" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: edaa6e7aa6de877fd3b61d4c03daa5fe + md5: 4e27c02e3839b79035a2c963b69e2cc3 build: number: 0 rpaths: diff --git a/recipes/bioconductor-swimr/meta.yaml b/recipes/bioconductor-swimr/meta.yaml index c833ef2acee94..c260017a1829e 100644 --- a/recipes/bioconductor-swimr/meta.yaml +++ b/recipes/bioconductor-swimr/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.20.0" %} +{% set version = "1.22.0" %} {% set name = "SwimR" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 98716966952df5504255e41de4e57055 + md5: f6e8d33f09e824b7dd8cfbac70d70245 build: number: 0 rpaths: diff --git a/recipes/bioconductor-switchbox/meta.yaml b/recipes/bioconductor-switchbox/meta.yaml index caa9acdf86753..69ef504566303 100644 --- a/recipes/bioconductor-switchbox/meta.yaml +++ b/recipes/bioconductor-switchbox/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.18.0" %} +{% set version = "1.20.0" %} {% set name = "switchBox" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 383194e52f750c3c3ef7764ca66bcdb3 + md5: 9485b5713f5dd142fb2fa58cb698cdae build: number: 0 rpaths: diff --git a/recipes/bioconductor-switchde/meta.yaml b/recipes/bioconductor-switchde/meta.yaml index 4305a241b4b33..a4146d84601b5 100644 --- a/recipes/bioconductor-switchde/meta.yaml +++ b/recipes/bioconductor-switchde/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.8.0" %} +{% set version = "1.10.0" %} {% set name = "switchde" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 14868aa05edbb0a7fdf44d890bef9144 + md5: 352c860f4f9d8494214110aedf58b29e build: number: 0 rpaths: @@ -20,14 +20,14 @@ build: # Suggests: knitr, rmarkdown, BiocStyle, testthat, numDeriv, tidyr requirements: host: - - 'bioconductor-singlecellexperiment >=1.4.0,<1.5.0' - - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' + - 'bioconductor-singlecellexperiment >=1.6.0,<1.7.0' + - 'bioconductor-summarizedexperiment >=1.14.0,<1.15.0' - r-base - r-dplyr - r-ggplot2 run: - - 'bioconductor-singlecellexperiment >=1.4.0,<1.5.0' - - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' + - 'bioconductor-singlecellexperiment >=1.6.0,<1.7.0' + - 'bioconductor-summarizedexperiment >=1.14.0,<1.15.0' - r-base - r-dplyr - r-ggplot2 diff --git a/recipes/bioconductor-synapter/meta.yaml b/recipes/bioconductor-synapter/meta.yaml index e38c1ad140d9e..6d18882c32f61 100644 --- a/recipes/bioconductor-synapter/meta.yaml +++ b/recipes/bioconductor-synapter/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "2.6.1" %} +{% set version = "2.8.0" %} {% set name = "synapter" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 9a66a45988875d007038bae143ce4ea7 + md5: 2b64d567dd67bdcf3bdf64bac0a0e2ef build: number: 0 rpaths: @@ -20,12 +20,12 @@ build: # Suggests: synapterdata (>= 1.13.2), xtable, testthat (>= 0.8), BRAIN, BiocStyle requirements: host: - - 'bioconductor-biobase >=2.42.0,<2.43.0' - - 'bioconductor-biostrings >=2.50.0,<2.51.0' - - 'bioconductor-cleaver >=1.20.0,<1.21.0' - - 'bioconductor-msnbase >=2.8.0,<2.9.0' - - 'bioconductor-multtest >=2.38.0,<2.39.0' - - 'bioconductor-qvalue >=2.14.0,<2.15.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' + - 'bioconductor-biostrings >=2.52.0,<2.53.0' + - 'bioconductor-cleaver >=1.22.0,<1.23.0' + - 'bioconductor-msnbase >=2.10.0,<2.11.0' + - 'bioconductor-multtest >=2.40.0,<2.41.0' + - 'bioconductor-qvalue >=2.16.0,<2.17.0' - r-base - r-knitr - r-lattice @@ -33,12 +33,12 @@ requirements: - 'r-readr >=0.2' - 'r-rmarkdown >=1.0' run: - - 'bioconductor-biobase >=2.42.0,<2.43.0' - - 'bioconductor-biostrings >=2.50.0,<2.51.0' - - 'bioconductor-cleaver >=1.20.0,<1.21.0' - - 'bioconductor-msnbase >=2.8.0,<2.9.0' - - 'bioconductor-multtest >=2.38.0,<2.39.0' - - 'bioconductor-qvalue >=2.14.0,<2.15.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' + - 'bioconductor-biostrings >=2.52.0,<2.53.0' + - 'bioconductor-cleaver >=1.22.0,<1.23.0' + - 'bioconductor-msnbase >=2.10.0,<2.11.0' + - 'bioconductor-multtest >=2.40.0,<2.41.0' + - 'bioconductor-qvalue >=2.16.0,<2.17.0' - r-base - r-knitr - r-lattice diff --git a/recipes/bioconductor-synapterdata/meta.yaml b/recipes/bioconductor-synapterdata/meta.yaml index 6ac073476601d..3614195823978 100644 --- a/recipes/bioconductor-synapterdata/meta.yaml +++ b/recipes/bioconductor-synapterdata/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.20.0" %} +{% set version = "1.22.0" %} {% set name = "synapterdata" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: a13fa15f1bcbfa6495cce58c3d439a0e + md5: 65584fbc942c508d5dd722f1eebc73d7 build: number: 0 rpaths: @@ -19,12 +19,12 @@ build: noarch: generic requirements: host: - - 'bioconductor-synapter >=2.6.0,<2.7.0' + - 'bioconductor-synapter >=2.8.0,<2.9.0' - r-base run: - - 'bioconductor-synapter >=2.6.0,<2.7.0' + - 'bioconductor-synapter >=2.8.0,<2.9.0' - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-synapterdata/post-link.sh b/recipes/bioconductor-synapterdata/post-link.sh index b8388e8adf2e0..a319f6c51ba11 100644 --- a/recipes/bioconductor-synapterdata/post-link.sh +++ b/recipes/bioconductor-synapterdata/post-link.sh @@ -1,11 +1,11 @@ #!/bin/bash -FN="synapterdata_1.20.0.tar.gz" +FN="synapterdata_1.22.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/experiment/src/contrib/synapterdata_1.20.0.tar.gz" - "https://bioarchive.galaxyproject.org/synapterdata_1.20.0.tar.gz" - "https://depot.galaxyproject.org/software/bioconductor-synapterdata/bioconductor-synapterdata_1.20.0_src_all.tar.gz" + "https://bioconductor.org/packages/3.9/data/experiment/src/contrib/synapterdata_1.22.0.tar.gz" + "https://bioarchive.galaxyproject.org/synapterdata_1.22.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-synapterdata/bioconductor-synapterdata_1.22.0_src_all.tar.gz" ) -MD5="a13fa15f1bcbfa6495cce58c3d439a0e" +MD5="65584fbc942c508d5dd722f1eebc73d7" # Use a staging area in the conda dir rather than temp dirs, both to avoid # permission issues as well as to have things downloaded in a predictable @@ -16,7 +16,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-synergyfinder/meta.yaml b/recipes/bioconductor-synergyfinder/meta.yaml index 144c32db44b37..b135827e54700 100644 --- a/recipes/bioconductor-synergyfinder/meta.yaml +++ b/recipes/bioconductor-synergyfinder/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.8.0" %} +{% set version = "1.10.0" %} {% set name = "synergyfinder" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: e3f9aa7ba027416ec0644f9bf85f5376 + md5: 60dd49ac4eac7837fe54a7ec859a80ec build: number: 0 rpaths: diff --git a/recipes/bioconductor-synlet/meta.yaml b/recipes/bioconductor-synlet/meta.yaml index ce13cd1b3405d..cefed6fe7a265 100644 --- a/recipes/bioconductor-synlet/meta.yaml +++ b/recipes/bioconductor-synlet/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.12.1" %} +{% set version = "1.14.0" %} {% set name = "synlet" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - sha256: cfeb61b9f0bd9e5f52a46c2d3deafae5096999715403dd8208d1f6b930862f8f + md5: 048ac0523519b6ae3d9ab94f22c50371 build: number: 0 rpaths: @@ -20,7 +20,7 @@ build: # Suggests: knitr, testthat requirements: host: - - 'bioconductor-rankprod >=3.8.0,<3.9.0' + - 'bioconductor-rankprod >=3.10.0,<3.11.0' - r-base - r-doby - r-dplyr @@ -29,7 +29,7 @@ requirements: - r-rcolorbrewer - r-reshape2 run: - - 'bioconductor-rankprod >=3.8.0,<3.9.0' + - 'bioconductor-rankprod >=3.10.0,<3.11.0' - r-base - r-doby - r-dplyr diff --git a/recipes/bioconductor-synmut/build.sh b/recipes/bioconductor-synmut/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-synmut/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-synmut/meta.yaml b/recipes/bioconductor-synmut/meta.yaml new file mode 100644 index 0000000000000..6641e9bd052e2 --- /dev/null +++ b/recipes/bioconductor-synmut/meta.yaml @@ -0,0 +1,41 @@ +{% set version = "1.0.0" %} +{% set name = "SynMut" %} +{% set bioc = "3.9" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: 3e8d1d7acf16f8f17ee1b58df9b52e01 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: BiocManager, knitr, rmarkdown, testthat, devtools, prettydoc, glue +requirements: + host: + - 'bioconductor-biocgenerics >=0.30.0,<0.31.0' + - 'bioconductor-biostrings >=2.52.0,<2.53.0' + - r-base + - r-seqinr + - r-stringr + run: + - 'bioconductor-biocgenerics >=0.30.0,<0.31.0' + - 'bioconductor-biostrings >=2.52.0,<2.53.0' + - r-base + - r-seqinr + - r-stringr +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: GPL-2 + summary: 'There are increasing demands on designing virus mutants with specific dinucleotide or codon composition. This tool can take both dinucleotide preference and/or codon usage bias into account while designing mutants. It is a powerful tool for in silico designs of DNA sequence mutants.' + diff --git a/recipes/bioconductor-systempiper/meta.yaml b/recipes/bioconductor-systempiper/meta.yaml index 905d43595aecc..c399020da500e 100644 --- a/recipes/bioconductor-systempiper/meta.yaml +++ b/recipes/bioconductor-systempiper/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.16.0" %} +{% set version = "1.18.0" %} {% set name = "systemPipeR" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: a11f46fe7541f5ab67ddba04144771b7 + md5: 05db55dab25ac53beef5ed2b81c55932 build: number: 0 rpaths: @@ -21,45 +21,47 @@ build: # SystemRequirements: systemPipeR can be used to run external command-line software (e.g. short read aligners), but the corresponding tool needs to be installed on a system. requirements: host: - - 'bioconductor-annotate >=1.60.0,<1.61.0' - - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' - - 'bioconductor-biostrings >=2.50.0,<2.51.0' - - 'bioconductor-deseq2 >=1.22.0,<1.23.0' - - 'bioconductor-edger >=3.24.0,<3.25.0' - - 'bioconductor-genomicfeatures >=1.34.0,<1.35.0' - - 'bioconductor-genomicranges >=1.34.0,<1.35.0' - - 'bioconductor-go.db >=3.7.0,<3.8.0' - - 'bioconductor-gostats >=2.48.0,<2.49.0' - - 'bioconductor-limma >=3.38.0,<3.39.0' - - 'bioconductor-rsamtools >=1.34.0,<1.35.0' - - 'bioconductor-shortread >=1.40.0,<1.41.0' - - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' - - 'bioconductor-variantannotation >=1.28.0,<1.29.0' + - 'bioconductor-annotate >=1.62.0,<1.63.0' + - 'bioconductor-biocgenerics >=0.30.0,<0.31.0' + - 'bioconductor-biostrings >=2.52.0,<2.53.0' + - 'bioconductor-deseq2 >=1.24.0,<1.25.0' + - 'bioconductor-edger >=3.26.0,<3.27.0' + - 'bioconductor-genomicfeatures >=1.36.0,<1.37.0' + - 'bioconductor-genomicranges >=1.36.0,<1.37.0' + - 'bioconductor-go.db >=3.8.0,<3.9.0' + - 'bioconductor-gostats >=2.50.0,<2.51.0' + - 'bioconductor-limma >=3.40.0,<3.41.0' + - 'bioconductor-rsamtools >=2.0.0,<2.1.0' + - 'bioconductor-shortread >=1.42.0,<1.43.0' + - 'bioconductor-summarizedexperiment >=1.14.0,<1.15.0' + - 'bioconductor-variantannotation >=1.30.0,<1.31.0' - r-base - - r-batchjobs + - r-batchtools - r-ggplot2 - r-pheatmap - r-rjson + - r-yaml run: - - 'bioconductor-annotate >=1.60.0,<1.61.0' - - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' - - 'bioconductor-biostrings >=2.50.0,<2.51.0' - - 'bioconductor-deseq2 >=1.22.0,<1.23.0' - - 'bioconductor-edger >=3.24.0,<3.25.0' - - 'bioconductor-genomicfeatures >=1.34.0,<1.35.0' - - 'bioconductor-genomicranges >=1.34.0,<1.35.0' - - 'bioconductor-go.db >=3.7.0,<3.8.0' - - 'bioconductor-gostats >=2.48.0,<2.49.0' - - 'bioconductor-limma >=3.38.0,<3.39.0' - - 'bioconductor-rsamtools >=1.34.0,<1.35.0' - - 'bioconductor-shortread >=1.40.0,<1.41.0' - - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' - - 'bioconductor-variantannotation >=1.28.0,<1.29.0' + - 'bioconductor-annotate >=1.62.0,<1.63.0' + - 'bioconductor-biocgenerics >=0.30.0,<0.31.0' + - 'bioconductor-biostrings >=2.52.0,<2.53.0' + - 'bioconductor-deseq2 >=1.24.0,<1.25.0' + - 'bioconductor-edger >=3.26.0,<3.27.0' + - 'bioconductor-genomicfeatures >=1.36.0,<1.37.0' + - 'bioconductor-genomicranges >=1.36.0,<1.37.0' + - 'bioconductor-go.db >=3.8.0,<3.9.0' + - 'bioconductor-gostats >=2.50.0,<2.51.0' + - 'bioconductor-limma >=3.40.0,<3.41.0' + - 'bioconductor-rsamtools >=2.0.0,<2.1.0' + - 'bioconductor-shortread >=1.42.0,<1.43.0' + - 'bioconductor-summarizedexperiment >=1.14.0,<1.15.0' + - 'bioconductor-variantannotation >=1.30.0,<1.31.0' - r-base - - r-batchjobs + - r-batchtools - r-ggplot2 - r-pheatmap - r-rjson + - r-yaml test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-systempiperdata/meta.yaml b/recipes/bioconductor-systempiperdata/meta.yaml index e7696b2150ab6..866a2f04a74e9 100644 --- a/recipes/bioconductor-systempiperdata/meta.yaml +++ b/recipes/bioconductor-systempiperdata/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.10.0" %} +{% set version = "1.12.0" %} {% set name = "systemPipeRdata" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: ba76fafb811f95cbaba27ef3953e55b3 + md5: c8d11c0e23f871eea5f073d749b26be0 build: number: 0 rpaths: @@ -20,12 +20,12 @@ build: # Suggests: RUnit, BiocStyle, knitr, rmarkdown, systemPipeR requirements: host: - - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' + - 'bioconductor-biocgenerics >=0.30.0,<0.31.0' - r-base run: - - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' + - 'bioconductor-biocgenerics >=0.30.0,<0.31.0' - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-systempiperdata/post-link.sh b/recipes/bioconductor-systempiperdata/post-link.sh index 9227607e5f871..7872d13ebef88 100644 --- a/recipes/bioconductor-systempiperdata/post-link.sh +++ b/recipes/bioconductor-systempiperdata/post-link.sh @@ -1,11 +1,11 @@ #!/bin/bash -FN="systemPipeRdata_1.10.0.tar.gz" +FN="systemPipeRdata_1.12.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/experiment/src/contrib/systemPipeRdata_1.10.0.tar.gz" - "https://bioarchive.galaxyproject.org/systemPipeRdata_1.10.0.tar.gz" - "https://depot.galaxyproject.org/software/bioconductor-systempiperdata/bioconductor-systempiperdata_1.10.0_src_all.tar.gz" + "https://bioconductor.org/packages/3.9/data/experiment/src/contrib/systemPipeRdata_1.12.0.tar.gz" + "https://bioarchive.galaxyproject.org/systemPipeRdata_1.12.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-systempiperdata/bioconductor-systempiperdata_1.12.0_src_all.tar.gz" ) -MD5="ba76fafb811f95cbaba27ef3953e55b3" +MD5="c8d11c0e23f871eea5f073d749b26be0" # Use a staging area in the conda dir rather than temp dirs, both to avoid # permission issues as well as to have things downloaded in a predictable @@ -16,7 +16,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-tabulamurisdata/meta.yaml b/recipes/bioconductor-tabulamurisdata/meta.yaml index 6d8c8c380d46d..7bf514210c2d6 100644 --- a/recipes/bioconductor-tabulamurisdata/meta.yaml +++ b/recipes/bioconductor-tabulamurisdata/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.0.0" %} +{% set version = "1.2.0" %} {% set name = "TabulaMurisData" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 1b4f8f16754586ce5866ac90de5ac0a4 + md5: ba5ccbb99aed729f12a3805313f53cd3 build: number: 0 rpaths: @@ -20,12 +20,12 @@ build: # Suggests: knitr, rmarkdown, BiocStyle, SingleCellExperiment, scran, scater, iSEE, testthat requirements: host: - - 'bioconductor-experimenthub >=1.8.0,<1.9.0' + - 'bioconductor-experimenthub >=1.10.0,<1.11.0' - r-base run: - - 'bioconductor-experimenthub >=1.8.0,<1.9.0' + - 'bioconductor-experimenthub >=1.10.0,<1.11.0' - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-tabulamurisdata/post-link.sh b/recipes/bioconductor-tabulamurisdata/post-link.sh index ce1904f6ae2c1..00d6ddac4498a 100644 --- a/recipes/bioconductor-tabulamurisdata/post-link.sh +++ b/recipes/bioconductor-tabulamurisdata/post-link.sh @@ -1,11 +1,11 @@ #!/bin/bash -FN="TabulaMurisData_1.0.0.tar.gz" +FN="TabulaMurisData_1.2.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/experiment/src/contrib/TabulaMurisData_1.0.0.tar.gz" - "https://bioarchive.galaxyproject.org/TabulaMurisData_1.0.0.tar.gz" - "https://depot.galaxyproject.org/software/bioconductor-tabulamurisdata/bioconductor-tabulamurisdata_1.0.0_src_all.tar.gz" + "https://bioconductor.org/packages/3.9/data/experiment/src/contrib/TabulaMurisData_1.2.0.tar.gz" + "https://bioarchive.galaxyproject.org/TabulaMurisData_1.2.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-tabulamurisdata/bioconductor-tabulamurisdata_1.2.0_src_all.tar.gz" ) -MD5="1b4f8f16754586ce5866ac90de5ac0a4" +MD5="ba5ccbb99aed729f12a3805313f53cd3" # Use a staging area in the conda dir rather than temp dirs, both to avoid # permission issues as well as to have things downloaded in a predictable @@ -16,7 +16,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-targetscan.hs.eg.db/meta.yaml b/recipes/bioconductor-targetscan.hs.eg.db/meta.yaml index a95325a2a1951..3675d37c2aab1 100644 --- a/recipes/bioconductor-targetscan.hs.eg.db/meta.yaml +++ b/recipes/bioconductor-targetscan.hs.eg.db/meta.yaml @@ -1,6 +1,6 @@ {% set version = "0.6.1" %} {% set name = "targetscan.Hs.eg.db" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -12,19 +12,19 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' md5: d10569315400f6c1b95ad2688632b6de build: - number: 1 + number: 2 rpaths: - lib/R/lib/ - lib/ noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' - r-base run: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-targetscan.hs.eg.db/post-link.sh b/recipes/bioconductor-targetscan.hs.eg.db/post-link.sh index b3ddb56af4488..061327cb6d0ed 100644 --- a/recipes/bioconductor-targetscan.hs.eg.db/post-link.sh +++ b/recipes/bioconductor-targetscan.hs.eg.db/post-link.sh @@ -1,7 +1,7 @@ #!/bin/bash FN="targetscan.Hs.eg.db_0.6.1.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/targetscan.Hs.eg.db_0.6.1.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/targetscan.Hs.eg.db_0.6.1.tar.gz" "https://bioarchive.galaxyproject.org/targetscan.Hs.eg.db_0.6.1.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-targetscan.hs.eg.db/bioconductor-targetscan.hs.eg.db_0.6.1_src_all.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-targetscan.hs.eg.db/bioconductor-targetscan.hs.eg.db_0.6.1_src_all.tar.gz" @@ -17,7 +17,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-targetscan.mm.eg.db/meta.yaml b/recipes/bioconductor-targetscan.mm.eg.db/meta.yaml index c38332d64a0a1..bb2723c67a94f 100644 --- a/recipes/bioconductor-targetscan.mm.eg.db/meta.yaml +++ b/recipes/bioconductor-targetscan.mm.eg.db/meta.yaml @@ -1,6 +1,6 @@ {% set version = "0.6.1" %} {% set name = "targetscan.Mm.eg.db" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -12,19 +12,19 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' md5: 1830815c9d1383739f1ff152da0508c5 build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' - r-base run: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-targetscan.mm.eg.db/post-link.sh b/recipes/bioconductor-targetscan.mm.eg.db/post-link.sh index f4772f6e6e648..ade859bad3491 100644 --- a/recipes/bioconductor-targetscan.mm.eg.db/post-link.sh +++ b/recipes/bioconductor-targetscan.mm.eg.db/post-link.sh @@ -1,9 +1,10 @@ #!/bin/bash FN="targetscan.Mm.eg.db_0.6.1.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/targetscan.Mm.eg.db_0.6.1.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/targetscan.Mm.eg.db_0.6.1.tar.gz" "https://bioarchive.galaxyproject.org/targetscan.Mm.eg.db_0.6.1.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-targetscan.mm.eg.db/bioconductor-targetscan.mm.eg.db_0.6.1_src_all.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-targetscan.mm.eg.db/bioconductor-targetscan.mm.eg.db_0.6.1_src_all.tar.gz" ) MD5="1830815c9d1383739f1ff152da0508c5" @@ -16,7 +17,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-targetscore/meta.yaml b/recipes/bioconductor-targetscore/meta.yaml index 833d0030e5409..20d844266301a 100644 --- a/recipes/bioconductor-targetscore/meta.yaml +++ b/recipes/bioconductor-targetscore/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.20.0" %} +{% set version = "1.22.0" %} {% set name = "TargetScore" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 4334b96fdaf7f911bc922ba9d7d1c1a4 + md5: 713b143fd0c2cfeecf59d93d412ab509 build: number: 0 rpaths: diff --git a/recipes/bioconductor-targetscoredata/meta.yaml b/recipes/bioconductor-targetscoredata/meta.yaml index 2d6df33fa8796..bc0b35020e015 100644 --- a/recipes/bioconductor-targetscoredata/meta.yaml +++ b/recipes/bioconductor-targetscoredata/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.18.0" %} +{% set version = "1.20.0" %} {% set name = "TargetScoreData" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: fd759e7712396b9f33e3ad26502a7762 + md5: efd1b3db6b4f1ed8c3ac1ddb159a811e build: number: 0 rpaths: @@ -23,7 +23,7 @@ requirements: - r-base run: - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-targetscoredata/post-link.sh b/recipes/bioconductor-targetscoredata/post-link.sh index 3a019bc3a630a..efb0a22090818 100644 --- a/recipes/bioconductor-targetscoredata/post-link.sh +++ b/recipes/bioconductor-targetscoredata/post-link.sh @@ -1,11 +1,11 @@ #!/bin/bash -FN="TargetScoreData_1.18.0.tar.gz" +FN="TargetScoreData_1.20.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/experiment/src/contrib/TargetScoreData_1.18.0.tar.gz" - "https://bioarchive.galaxyproject.org/TargetScoreData_1.18.0.tar.gz" - "https://depot.galaxyproject.org/software/bioconductor-targetscoredata/bioconductor-targetscoredata_1.18.0_src_all.tar.gz" + "https://bioconductor.org/packages/3.9/data/experiment/src/contrib/TargetScoreData_1.20.0.tar.gz" + "https://bioarchive.galaxyproject.org/TargetScoreData_1.20.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-targetscoredata/bioconductor-targetscoredata_1.20.0_src_all.tar.gz" ) -MD5="fd759e7712396b9f33e3ad26502a7762" +MD5="efd1b3db6b4f1ed8c3ac1ddb159a811e" # Use a staging area in the conda dir rather than temp dirs, both to avoid # permission issues as well as to have things downloaded in a predictable @@ -16,7 +16,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-targetsearch/meta.yaml b/recipes/bioconductor-targetsearch/meta.yaml index 7af08e96471e3..442552a896286 100644 --- a/recipes/bioconductor-targetsearch/meta.yaml +++ b/recipes/bioconductor-targetsearch/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.38.1" %} +{% set version = "1.40.0" %} {% set name = "TargetSearch" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 037931da176f5fd0a40ae3a80209e3d7 + md5: c6a1de576712f6fac0b7aa82d5a85194 build: number: 0 rpaths: diff --git a/recipes/bioconductor-targetsearchdata/meta.yaml b/recipes/bioconductor-targetsearchdata/meta.yaml index 02ab3c3be28b2..d5e8fbe1fcfd4 100644 --- a/recipes/bioconductor-targetsearchdata/meta.yaml +++ b/recipes/bioconductor-targetsearchdata/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.20.0" %} +{% set version = "1.22.0" %} {% set name = "TargetSearchData" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: f22282a97204579a09ebe055434811b6 + md5: 5930865598f2ac84a58a11111f3ba7ac build: number: 0 rpaths: @@ -22,7 +22,7 @@ requirements: - r-base run: - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-targetsearchdata/post-link.sh b/recipes/bioconductor-targetsearchdata/post-link.sh index e235183dc8f56..8c2e1a951e2af 100644 --- a/recipes/bioconductor-targetsearchdata/post-link.sh +++ b/recipes/bioconductor-targetsearchdata/post-link.sh @@ -1,11 +1,11 @@ #!/bin/bash -FN="TargetSearchData_1.20.0.tar.gz" +FN="TargetSearchData_1.22.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/experiment/src/contrib/TargetSearchData_1.20.0.tar.gz" - "https://bioarchive.galaxyproject.org/TargetSearchData_1.20.0.tar.gz" - "https://depot.galaxyproject.org/software/bioconductor-targetsearchdata/bioconductor-targetsearchdata_1.20.0_src_all.tar.gz" + "https://bioconductor.org/packages/3.9/data/experiment/src/contrib/TargetSearchData_1.22.0.tar.gz" + "https://bioarchive.galaxyproject.org/TargetSearchData_1.22.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-targetsearchdata/bioconductor-targetsearchdata_1.22.0_src_all.tar.gz" ) -MD5="f22282a97204579a09ebe055434811b6" +MD5="5930865598f2ac84a58a11111f3ba7ac" # Use a staging area in the conda dir rather than temp dirs, both to avoid # permission issues as well as to have things downloaded in a predictable @@ -16,7 +16,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-tarseqqc/meta.yaml b/recipes/bioconductor-tarseqqc/meta.yaml index 8caae23b4d2a6..d488e5eb027fe 100644 --- a/recipes/bioconductor-tarseqqc/meta.yaml +++ b/recipes/bioconductor-tarseqqc/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.12.0" %} +{% set version = "1.14.0" %} {% set name = "TarSeqQC" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: d63b65c61556d88e875ac624b4142756 + md5: 64224f22c12b68e8a610213a6983f260 build: number: 0 rpaths: @@ -20,15 +20,15 @@ build: # Suggests: BiocManager, RUnit requirements: host: - - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' - - 'bioconductor-biocparallel >=1.16.0,<1.17.0' - - 'bioconductor-biostrings >=2.50.0,<2.51.0' - - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' - - 'bioconductor-genomicalignments >=1.18.0,<1.19.0' - - 'bioconductor-genomicranges >=1.34.0,<1.35.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-rsamtools >=1.34.0,<1.35.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-biocgenerics >=0.30.0,<0.31.0' + - 'bioconductor-biocparallel >=1.18.0,<1.19.0' + - 'bioconductor-biostrings >=2.52.0,<2.53.0' + - 'bioconductor-genomeinfodb >=1.20.0,<1.21.0' + - 'bioconductor-genomicalignments >=1.20.0,<1.21.0' + - 'bioconductor-genomicranges >=1.36.0,<1.37.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-rsamtools >=2.0.0,<2.1.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' - r-base - r-cowplot - r-ggplot2 @@ -37,15 +37,15 @@ requirements: - r-plyr - r-reshape2 run: - - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' - - 'bioconductor-biocparallel >=1.16.0,<1.17.0' - - 'bioconductor-biostrings >=2.50.0,<2.51.0' - - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' - - 'bioconductor-genomicalignments >=1.18.0,<1.19.0' - - 'bioconductor-genomicranges >=1.34.0,<1.35.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-rsamtools >=1.34.0,<1.35.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-biocgenerics >=0.30.0,<0.31.0' + - 'bioconductor-biocparallel >=1.18.0,<1.19.0' + - 'bioconductor-biostrings >=2.52.0,<2.53.0' + - 'bioconductor-genomeinfodb >=1.20.0,<1.21.0' + - 'bioconductor-genomicalignments >=1.20.0,<1.21.0' + - 'bioconductor-genomicranges >=1.36.0,<1.37.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-rsamtools >=2.0.0,<2.1.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' - r-base - r-cowplot - r-ggplot2 diff --git a/recipes/bioconductor-tbx20bamsubset/meta.yaml b/recipes/bioconductor-tbx20bamsubset/meta.yaml index b572a6ee964cb..d9d0b2ace403b 100644 --- a/recipes/bioconductor-tbx20bamsubset/meta.yaml +++ b/recipes/bioconductor-tbx20bamsubset/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.18.0" %} +{% set version = "1.20.0" %} {% set name = "TBX20BamSubset" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 6b04fa46c1d81b4965a59ac7a3cbde37 + md5: bb066042b00d5950e90ce73215301c43 build: number: 0 rpaths: @@ -19,14 +19,14 @@ build: noarch: generic requirements: host: - - 'bioconductor-rsamtools >=1.34.0,<1.35.0' + - 'bioconductor-rsamtools >=2.0.0,<2.1.0' - r-base - r-xtable run: - - 'bioconductor-rsamtools >=1.34.0,<1.35.0' + - 'bioconductor-rsamtools >=2.0.0,<2.1.0' - r-base - r-xtable - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-tbx20bamsubset/post-link.sh b/recipes/bioconductor-tbx20bamsubset/post-link.sh index b610888040e66..4f6b45092c4ce 100644 --- a/recipes/bioconductor-tbx20bamsubset/post-link.sh +++ b/recipes/bioconductor-tbx20bamsubset/post-link.sh @@ -1,11 +1,11 @@ #!/bin/bash -FN="TBX20BamSubset_1.18.0.tar.gz" +FN="TBX20BamSubset_1.20.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/experiment/src/contrib/TBX20BamSubset_1.18.0.tar.gz" - "https://bioarchive.galaxyproject.org/TBX20BamSubset_1.18.0.tar.gz" - "https://depot.galaxyproject.org/software/bioconductor-tbx20bamsubset/bioconductor-tbx20bamsubset_1.18.0_src_all.tar.gz" + "https://bioconductor.org/packages/3.9/data/experiment/src/contrib/TBX20BamSubset_1.20.0.tar.gz" + "https://bioarchive.galaxyproject.org/TBX20BamSubset_1.20.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-tbx20bamsubset/bioconductor-tbx20bamsubset_1.20.0_src_all.tar.gz" ) -MD5="6b04fa46c1d81b4965a59ac7a3cbde37" +MD5="bb066042b00d5950e90ce73215301c43" # Use a staging area in the conda dir rather than temp dirs, both to avoid # permission issues as well as to have things downloaded in a predictable @@ -16,7 +16,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-tcc/meta.yaml b/recipes/bioconductor-tcc/meta.yaml index 241fd04f9dfd4..db3597e1806bc 100644 --- a/recipes/bioconductor-tcc/meta.yaml +++ b/recipes/bioconductor-tcc/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.22.0" %} +{% set version = "1.24.0" %} {% set name = "TCC" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 029f04706733a7472728b005b8591b43 + md5: fca8112eea20197cfefa1b0c2e35eb7c build: number: 0 rpaths: @@ -20,18 +20,18 @@ build: # Suggests: RUnit, BiocGenerics requirements: host: - - 'bioconductor-bayseq >=2.16.0,<2.17.0' - - 'bioconductor-deseq >=1.34.0,<1.35.0' - - 'bioconductor-deseq2 >=1.22.0,<1.23.0' - - 'bioconductor-edger >=3.24.0,<3.25.0' - - 'bioconductor-roc >=1.58.0,<1.59.0' + - 'bioconductor-bayseq >=2.18.0,<2.19.0' + - 'bioconductor-deseq >=1.36.0,<1.37.0' + - 'bioconductor-deseq2 >=1.24.0,<1.25.0' + - 'bioconductor-edger >=3.26.0,<3.27.0' + - 'bioconductor-roc >=1.60.0,<1.61.0' - r-base run: - - 'bioconductor-bayseq >=2.16.0,<2.17.0' - - 'bioconductor-deseq >=1.34.0,<1.35.0' - - 'bioconductor-deseq2 >=1.22.0,<1.23.0' - - 'bioconductor-edger >=3.24.0,<3.25.0' - - 'bioconductor-roc >=1.58.0,<1.59.0' + - 'bioconductor-bayseq >=2.18.0,<2.19.0' + - 'bioconductor-deseq >=1.36.0,<1.37.0' + - 'bioconductor-deseq2 >=1.24.0,<1.25.0' + - 'bioconductor-edger >=3.26.0,<3.27.0' + - 'bioconductor-roc >=1.60.0,<1.61.0' - r-base test: commands: diff --git a/recipes/bioconductor-tcgabiolinks/meta.yaml b/recipes/bioconductor-tcgabiolinks/meta.yaml index 632d0e553e2e5..3b6ad4e8df706 100644 --- a/recipes/bioconductor-tcgabiolinks/meta.yaml +++ b/recipes/bioconductor-tcgabiolinks/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "2.10.0" %} +{% set version = "2.12.0" %} {% set name = "TCGAbiolinks" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 226a9f591c6778490b31ccc92c207ee1 + md5: 75a4a5577c4bf184f71631f42eded653 build: number: 0 rpaths: @@ -20,20 +20,21 @@ build: # Suggests: png, BiocStyle, rmarkdown, devtools, maftools, parmigene, c3net, minet, dnet, Biobase, affy, testthat, pathview, clusterProfiler, igraph, supraHex requirements: host: - - 'bioconductor-biomart >=2.38.0,<2.39.0' - - 'bioconductor-complexheatmap >=1.20.0,<1.21.0' - - 'bioconductor-consensusclusterplus >=1.46.0,<1.47.0' - - 'bioconductor-edaseq >=2.16.0,<2.17.0' - - 'bioconductor-edger >=3.24.0,<3.25.0' - - 'bioconductor-genefilter >=1.64.0,<1.65.0' - - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' - - 'bioconductor-genomicfeatures >=1.34.0,<1.35.0' - - 'bioconductor-genomicranges >=1.34.0,<1.35.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-limma >=3.38.0,<3.39.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' - - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' - - 'bioconductor-sva >=3.30.0,<3.31.0' + - 'bioconductor-biomart >=2.40.0,<2.41.0' + - 'bioconductor-complexheatmap >=2.0.0,<2.1.0' + - 'bioconductor-consensusclusterplus >=1.48.0,<1.49.0' + - 'bioconductor-edaseq >=2.18.0,<2.19.0' + - 'bioconductor-edger >=3.26.0,<3.27.0' + - 'bioconductor-genefilter >=1.66.0,<1.67.0' + - 'bioconductor-genomeinfodb >=1.20.0,<1.21.0' + - 'bioconductor-genomicfeatures >=1.36.0,<1.37.0' + - 'bioconductor-genomicranges >=1.36.0,<1.37.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-limma >=3.40.0,<3.41.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' + - 'bioconductor-sesame >=1.2.0,<1.3.0' + - 'bioconductor-summarizedexperiment >=1.14.0,<1.15.0' + - 'bioconductor-sva >=3.32.0,<3.33.0' - r-base - r-circlize - r-data.table @@ -49,6 +50,7 @@ requirements: - r-knitr - r-matlab - r-plyr + - r-purrr - r-r.utils - r-rcolorbrewer - r-readr @@ -59,23 +61,25 @@ requirements: - r-survival - r-survminer - r-tibble + - r-tidyr - 'r-xml >=3.98.0' - r-xml2 run: - - 'bioconductor-biomart >=2.38.0,<2.39.0' - - 'bioconductor-complexheatmap >=1.20.0,<1.21.0' - - 'bioconductor-consensusclusterplus >=1.46.0,<1.47.0' - - 'bioconductor-edaseq >=2.16.0,<2.17.0' - - 'bioconductor-edger >=3.24.0,<3.25.0' - - 'bioconductor-genefilter >=1.64.0,<1.65.0' - - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' - - 'bioconductor-genomicfeatures >=1.34.0,<1.35.0' - - 'bioconductor-genomicranges >=1.34.0,<1.35.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-limma >=3.38.0,<3.39.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' - - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' - - 'bioconductor-sva >=3.30.0,<3.31.0' + - 'bioconductor-biomart >=2.40.0,<2.41.0' + - 'bioconductor-complexheatmap >=2.0.0,<2.1.0' + - 'bioconductor-consensusclusterplus >=1.48.0,<1.49.0' + - 'bioconductor-edaseq >=2.18.0,<2.19.0' + - 'bioconductor-edger >=3.26.0,<3.27.0' + - 'bioconductor-genefilter >=1.66.0,<1.67.0' + - 'bioconductor-genomeinfodb >=1.20.0,<1.21.0' + - 'bioconductor-genomicfeatures >=1.36.0,<1.37.0' + - 'bioconductor-genomicranges >=1.36.0,<1.37.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-limma >=3.40.0,<3.41.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' + - 'bioconductor-sesame >=1.2.0,<1.3.0' + - 'bioconductor-summarizedexperiment >=1.14.0,<1.15.0' + - 'bioconductor-sva >=3.32.0,<3.33.0' - r-base - r-circlize - r-data.table @@ -91,6 +95,7 @@ requirements: - r-knitr - r-matlab - r-plyr + - r-purrr - r-r.utils - r-rcolorbrewer - r-readr @@ -101,6 +106,7 @@ requirements: - r-survival - r-survminer - r-tibble + - r-tidyr - 'r-xml >=3.98.0' - r-xml2 test: diff --git a/recipes/bioconductor-tcgabiolinksgui.data/meta.yaml b/recipes/bioconductor-tcgabiolinksgui.data/meta.yaml index cc8a6de07d61f..d78476b79667d 100644 --- a/recipes/bioconductor-tcgabiolinksgui.data/meta.yaml +++ b/recipes/bioconductor-tcgabiolinksgui.data/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.2.0" %} +{% set version = "1.4.0" %} {% set name = "TCGAbiolinksGUI.data" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: b3eeb50a569df22c6434bd7ff06fa460 + md5: 919f2748bfd2dab5e1b95969a4a212ae build: number: 0 rpaths: @@ -23,7 +23,7 @@ requirements: - r-base run: - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-tcgabiolinksgui.data/post-link.sh b/recipes/bioconductor-tcgabiolinksgui.data/post-link.sh index 7c1525baf9af5..761dd81c6565d 100644 --- a/recipes/bioconductor-tcgabiolinksgui.data/post-link.sh +++ b/recipes/bioconductor-tcgabiolinksgui.data/post-link.sh @@ -1,11 +1,11 @@ #!/bin/bash -FN="TCGAbiolinksGUI.data_1.2.0.tar.gz" +FN="TCGAbiolinksGUI.data_1.4.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/experiment/src/contrib/TCGAbiolinksGUI.data_1.2.0.tar.gz" - "https://bioarchive.galaxyproject.org/TCGAbiolinksGUI.data_1.2.0.tar.gz" - "https://depot.galaxyproject.org/software/bioconductor-tcgabiolinksgui.data/bioconductor-tcgabiolinksgui.data_1.2.0_src_all.tar.gz" + "https://bioconductor.org/packages/3.9/data/experiment/src/contrib/TCGAbiolinksGUI.data_1.4.0.tar.gz" + "https://bioarchive.galaxyproject.org/TCGAbiolinksGUI.data_1.4.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-tcgabiolinksgui.data/bioconductor-tcgabiolinksgui.data_1.4.0_src_all.tar.gz" ) -MD5="b3eeb50a569df22c6434bd7ff06fa460" +MD5="919f2748bfd2dab5e1b95969a4a212ae" # Use a staging area in the conda dir rather than temp dirs, both to avoid # permission issues as well as to have things downloaded in a predictable @@ -16,7 +16,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-tcgabiolinksgui/meta.yaml b/recipes/bioconductor-tcgabiolinksgui/meta.yaml index becb4f78b11bf..556f8cac9aace 100644 --- a/recipes/bioconductor-tcgabiolinksgui/meta.yaml +++ b/recipes/bioconductor-tcgabiolinksgui/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.8.0" %} +{% set version = "1.10.0" %} {% set name = "TCGAbiolinksGUI" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 2304d156949603d34060268a2b5fa0b4 + md5: 5659ea97fe997bdd4013460c59513a39 build: number: 0 rpaths: @@ -20,20 +20,14 @@ build: # Suggests: testthat, dplyr, knitr, roxygen2, devtools, rvest, xml2, BiocStyle, animation, pander requirements: host: - - 'bioconductor-clusterprofiler >=3.10.0,<3.11.0' - - 'bioconductor-elmer >=2.6.0,<2.7.0' - - 'bioconductor-illuminahumanmethylation27kanno.ilmn12.hg19 >=0.6.0,<0.7.0' - - 'bioconductor-illuminahumanmethylation27kmanifest >=0.4.0,<0.5.0' - - 'bioconductor-illuminahumanmethylation450kanno.ilmn12.hg19 >=0.6.0,<0.7.0' - - 'bioconductor-illuminahumanmethylation450kmanifest >=0.4.0,<0.5.0' - - 'bioconductor-illuminahumanmethylationepicanno.ilm10b2.hg19 >=0.6.0,<0.7.0' - - 'bioconductor-illuminahumanmethylationepicmanifest >=0.3.0,<0.4.0' - - 'bioconductor-maftools >=1.8.0,<1.9.0' - - 'bioconductor-minfi >=1.28.0,<1.29.0' - - 'bioconductor-pathview >=1.22.0,<1.23.0' - - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' - - 'bioconductor-tcgabiolinks >=2.10.0,<2.11.0' - - 'bioconductor-tcgabiolinksgui.data >=1.2.0,<1.3.0' + - 'bioconductor-clusterprofiler >=3.12.0,<3.13.0' + - 'bioconductor-elmer >=2.8.0,<2.9.0' + - 'bioconductor-maftools >=2.0.0,<2.1.0' + - 'bioconductor-pathview >=1.24.0,<1.25.0' + - 'bioconductor-sesame >=1.2.0,<1.3.0' + - 'bioconductor-summarizedexperiment >=1.14.0,<1.15.0' + - 'bioconductor-tcgabiolinks >=2.12.0,<2.13.0' + - 'bioconductor-tcgabiolinksgui.data >=1.4.0,<1.5.0' - r-base - r-caret - r-colourpicker @@ -51,20 +45,14 @@ requirements: - 'r-shinyjs >=0.7' - 'r-stringr >=1.1.0' run: - - 'bioconductor-clusterprofiler >=3.10.0,<3.11.0' - - 'bioconductor-elmer >=2.6.0,<2.7.0' - - 'bioconductor-illuminahumanmethylation27kanno.ilmn12.hg19 >=0.6.0,<0.7.0' - - 'bioconductor-illuminahumanmethylation27kmanifest >=0.4.0,<0.5.0' - - 'bioconductor-illuminahumanmethylation450kanno.ilmn12.hg19 >=0.6.0,<0.7.0' - - 'bioconductor-illuminahumanmethylation450kmanifest >=0.4.0,<0.5.0' - - 'bioconductor-illuminahumanmethylationepicanno.ilm10b2.hg19 >=0.6.0,<0.7.0' - - 'bioconductor-illuminahumanmethylationepicmanifest >=0.3.0,<0.4.0' - - 'bioconductor-maftools >=1.8.0,<1.9.0' - - 'bioconductor-minfi >=1.28.0,<1.29.0' - - 'bioconductor-pathview >=1.22.0,<1.23.0' - - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' - - 'bioconductor-tcgabiolinks >=2.10.0,<2.11.0' - - 'bioconductor-tcgabiolinksgui.data >=1.2.0,<1.3.0' + - 'bioconductor-clusterprofiler >=3.12.0,<3.13.0' + - 'bioconductor-elmer >=2.8.0,<2.9.0' + - 'bioconductor-maftools >=2.0.0,<2.1.0' + - 'bioconductor-pathview >=1.24.0,<1.25.0' + - 'bioconductor-sesame >=1.2.0,<1.3.0' + - 'bioconductor-summarizedexperiment >=1.14.0,<1.15.0' + - 'bioconductor-tcgabiolinks >=2.12.0,<2.13.0' + - 'bioconductor-tcgabiolinksgui.data >=1.4.0,<1.5.0' - r-base - r-caret - r-colourpicker diff --git a/recipes/bioconductor-tcgacrcmirna/meta.yaml b/recipes/bioconductor-tcgacrcmirna/meta.yaml index d7f850593cf53..ef7d2aa12fbe4 100644 --- a/recipes/bioconductor-tcgacrcmirna/meta.yaml +++ b/recipes/bioconductor-tcgacrcmirna/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.2.0" %} +{% set version = "1.4.0" %} {% set name = "TCGAcrcmiRNA" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 75d707e6d1c7feb9d4dfd5d6e62f9c3a + md5: 9fb98232249dc4c36f0b455b4bcbfb36 build: number: 0 rpaths: @@ -19,12 +19,12 @@ build: noarch: generic requirements: host: - - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' - r-base run: - - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-tcgacrcmirna/post-link.sh b/recipes/bioconductor-tcgacrcmirna/post-link.sh index fb226e8abee35..8f3e5ef4ee95a 100644 --- a/recipes/bioconductor-tcgacrcmirna/post-link.sh +++ b/recipes/bioconductor-tcgacrcmirna/post-link.sh @@ -1,11 +1,11 @@ #!/bin/bash -FN="TCGAcrcmiRNA_1.2.0.tar.gz" +FN="TCGAcrcmiRNA_1.4.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/experiment/src/contrib/TCGAcrcmiRNA_1.2.0.tar.gz" - "https://bioarchive.galaxyproject.org/TCGAcrcmiRNA_1.2.0.tar.gz" - "https://depot.galaxyproject.org/software/bioconductor-tcgacrcmirna/bioconductor-tcgacrcmirna_1.2.0_src_all.tar.gz" + "https://bioconductor.org/packages/3.9/data/experiment/src/contrib/TCGAcrcmiRNA_1.4.0.tar.gz" + "https://bioarchive.galaxyproject.org/TCGAcrcmiRNA_1.4.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-tcgacrcmirna/bioconductor-tcgacrcmirna_1.4.0_src_all.tar.gz" ) -MD5="75d707e6d1c7feb9d4dfd5d6e62f9c3a" +MD5="9fb98232249dc4c36f0b455b4bcbfb36" # Use a staging area in the conda dir rather than temp dirs, both to avoid # permission issues as well as to have things downloaded in a predictable @@ -16,7 +16,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-tcgacrcmrna/meta.yaml b/recipes/bioconductor-tcgacrcmrna/meta.yaml index f57bc8041eb76..35d0b3449e5c5 100644 --- a/recipes/bioconductor-tcgacrcmrna/meta.yaml +++ b/recipes/bioconductor-tcgacrcmrna/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.2.0" %} +{% set version = "1.4.0" %} {% set name = "TCGAcrcmRNA" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,21 +10,21 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 4d499e122eee3f40019b944889a63fe4 + md5: 210ae0298467a9daaf342873ee1a9504 build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ noarch: generic requirements: host: - - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' - r-base run: - - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-tcgacrcmrna/post-link.sh b/recipes/bioconductor-tcgacrcmrna/post-link.sh index b5abe21c42c1a..f7692709c430a 100644 --- a/recipes/bioconductor-tcgacrcmrna/post-link.sh +++ b/recipes/bioconductor-tcgacrcmrna/post-link.sh @@ -1,11 +1,11 @@ #!/bin/bash -FN="TCGAcrcmRNA_1.2.0.tar.gz" +FN="TCGAcrcmRNA_1.4.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/experiment/src/contrib/TCGAcrcmRNA_1.2.0.tar.gz" - "https://bioarchive.galaxyproject.org/TCGAcrcmRNA_1.2.0.tar.gz" - "https://depot.galaxyproject.org/software/bioconductor-tcgacrcmrna/bioconductor-tcgacrcmrna_1.2.0_src_all.tar.gz" + "https://bioconductor.org/packages/3.9/data/experiment/src/contrib/TCGAcrcmRNA_1.4.0.tar.gz" + "https://bioarchive.galaxyproject.org/TCGAcrcmRNA_1.4.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-tcgacrcmrna/bioconductor-tcgacrcmrna_1.4.0_src_all.tar.gz" ) -MD5="4d499e122eee3f40019b944889a63fe4" +MD5="210ae0298467a9daaf342873ee1a9504" # Use a staging area in the conda dir rather than temp dirs, both to avoid # permission issues as well as to have things downloaded in a predictable @@ -16,7 +16,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-tcgamethylation450k/meta.yaml b/recipes/bioconductor-tcgamethylation450k/meta.yaml index ed92676c33c70..29523916210d7 100644 --- a/recipes/bioconductor-tcgamethylation450k/meta.yaml +++ b/recipes/bioconductor-tcgamethylation450k/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.18.0" %} +{% set version = "1.20.0" %} {% set name = "TCGAMethylation450k" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 71ce8ebbc5ddcf78fe3c6995ee2c64f5 + md5: 84b02ffc29f555bdb04e40476fd86fff build: number: 0 rpaths: @@ -22,7 +22,7 @@ requirements: - r-base run: - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-tcgamethylation450k/post-link.sh b/recipes/bioconductor-tcgamethylation450k/post-link.sh index 7d5d3dcd1158f..6f920df35db92 100644 --- a/recipes/bioconductor-tcgamethylation450k/post-link.sh +++ b/recipes/bioconductor-tcgamethylation450k/post-link.sh @@ -1,11 +1,11 @@ #!/bin/bash -FN="TCGAMethylation450k_1.18.0.tar.gz" +FN="TCGAMethylation450k_1.20.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/experiment/src/contrib/TCGAMethylation450k_1.18.0.tar.gz" - "https://bioarchive.galaxyproject.org/TCGAMethylation450k_1.18.0.tar.gz" - "https://depot.galaxyproject.org/software/bioconductor-tcgamethylation450k/bioconductor-tcgamethylation450k_1.18.0_src_all.tar.gz" + "https://bioconductor.org/packages/3.9/data/experiment/src/contrib/TCGAMethylation450k_1.20.0.tar.gz" + "https://bioarchive.galaxyproject.org/TCGAMethylation450k_1.20.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-tcgamethylation450k/bioconductor-tcgamethylation450k_1.20.0_src_all.tar.gz" ) -MD5="71ce8ebbc5ddcf78fe3c6995ee2c64f5" +MD5="84b02ffc29f555bdb04e40476fd86fff" # Use a staging area in the conda dir rather than temp dirs, both to avoid # permission issues as well as to have things downloaded in a predictable @@ -16,7 +16,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-tcgautils/meta.yaml b/recipes/bioconductor-tcgautils/meta.yaml index 0afd213ad4f68..4b9964a726926 100644 --- a/recipes/bioconductor-tcgautils/meta.yaml +++ b/recipes/bioconductor-tcgautils/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.2.1" %} +{% set version = "1.4.0" %} {% set name = "TCGAutils" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,43 +10,43 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: ded15c4190f16c090858878e53fab751 + md5: 259096a77cd358b89971bd9806f25413 build: number: 0 rpaths: - lib/R/lib/ - lib/ noarch: generic -# Suggests: BiocStyle, curatedTCGAData, devtools, impute, knitr, magrittr, mirbase.db, org.Hs.eg.db, readr, RTCGAToolbox (>= 2.7.5), testthat, TxDb.Hsapiens.UCSC.hg19.knownGene, +# Suggests: BiocFileCache, BiocStyle, curatedTCGAData, devtools, dplyr, IlluminaHumanMethylation450kanno.ilmn12.hg19, impute, knitr, magrittr, minfi, mirbase.db, org.Hs.eg.db, readr, RTCGAToolbox (>= 2.7.5), rtracklayer, R.utils, testthat, TxDb.Hsapiens.UCSC.hg19.knownGene, requirements: host: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' - - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' - - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' - - 'bioconductor-genomicdatacommons >=1.6.0,<1.7.0' - - 'bioconductor-genomicfeatures >=1.34.0,<1.35.0' - - 'bioconductor-genomicranges >=1.34.0,<1.35.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-multiassayexperiment >=1.8.0,<1.9.0' - - 'bioconductor-raggedexperiment >=1.6.0,<1.7.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' - - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' + - 'bioconductor-biocgenerics >=0.30.0,<0.31.0' + - 'bioconductor-genomeinfodb >=1.20.0,<1.21.0' + - 'bioconductor-genomicdatacommons >=1.8.0,<1.9.0' + - 'bioconductor-genomicfeatures >=1.36.0,<1.37.0' + - 'bioconductor-genomicranges >=1.36.0,<1.37.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-multiassayexperiment >=1.10.0,<1.11.0' + - 'bioconductor-raggedexperiment >=1.8.0,<1.9.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' + - 'bioconductor-summarizedexperiment >=1.14.0,<1.15.0' - r-base - r-rvest - r-stringr - r-xml2 run: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' - - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' - - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' - - 'bioconductor-genomicdatacommons >=1.6.0,<1.7.0' - - 'bioconductor-genomicfeatures >=1.34.0,<1.35.0' - - 'bioconductor-genomicranges >=1.34.0,<1.35.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-multiassayexperiment >=1.8.0,<1.9.0' - - 'bioconductor-raggedexperiment >=1.6.0,<1.7.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' - - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' + - 'bioconductor-biocgenerics >=0.30.0,<0.31.0' + - 'bioconductor-genomeinfodb >=1.20.0,<1.21.0' + - 'bioconductor-genomicdatacommons >=1.8.0,<1.9.0' + - 'bioconductor-genomicfeatures >=1.36.0,<1.37.0' + - 'bioconductor-genomicranges >=1.36.0,<1.37.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-multiassayexperiment >=1.10.0,<1.11.0' + - 'bioconductor-raggedexperiment >=1.8.0,<1.9.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' + - 'bioconductor-summarizedexperiment >=1.14.0,<1.15.0' - r-base - r-rvest - r-stringr diff --git a/recipes/bioconductor-tcgawgbsdata.hg19/meta.yaml b/recipes/bioconductor-tcgawgbsdata.hg19/meta.yaml index 6074ea92ee910..e44136a9891ef 100644 --- a/recipes/bioconductor-tcgawgbsdata.hg19/meta.yaml +++ b/recipes/bioconductor-tcgawgbsdata.hg19/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.0.0" %} +{% set version = "1.2.0" %} {% set name = "tcgaWGBSData.hg19" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,25 +10,25 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: e614d37504300366b89e08aae9d82902 + md5: 0016ac6074b918439dac0a52151c4ffa build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ noarch: generic requirements: host: - - 'bioconductor-bsseq >=1.18.0,<1.19.0' - - 'bioconductor-experimenthub >=1.8.0,<1.9.0' + - 'bioconductor-bsseq >=1.20.0,<1.21.0' + - 'bioconductor-experimenthub >=1.10.0,<1.11.0' - r-base - r-knitr run: - - 'bioconductor-bsseq >=1.18.0,<1.19.0' - - 'bioconductor-experimenthub >=1.8.0,<1.9.0' + - 'bioconductor-bsseq >=1.20.0,<1.21.0' + - 'bioconductor-experimenthub >=1.10.0,<1.11.0' - r-base - r-knitr - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-tcgawgbsdata.hg19/post-link.sh b/recipes/bioconductor-tcgawgbsdata.hg19/post-link.sh index 1afad2749d6b5..400a7f24fa889 100644 --- a/recipes/bioconductor-tcgawgbsdata.hg19/post-link.sh +++ b/recipes/bioconductor-tcgawgbsdata.hg19/post-link.sh @@ -1,11 +1,11 @@ #!/bin/bash -FN="tcgaWGBSData.hg19_1.0.0.tar.gz" +FN="tcgaWGBSData.hg19_1.2.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/experiment/src/contrib/tcgaWGBSData.hg19_1.0.0.tar.gz" - "https://bioarchive.galaxyproject.org/tcgaWGBSData.hg19_1.0.0.tar.gz" - "https://depot.galaxyproject.org/software/bioconductor-tcgawgbsdata.hg19/bioconductor-tcgawgbsdata.hg19_1.0.0_src_all.tar.gz" + "https://bioconductor.org/packages/3.9/data/experiment/src/contrib/tcgaWGBSData.hg19_1.2.0.tar.gz" + "https://bioarchive.galaxyproject.org/tcgaWGBSData.hg19_1.2.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-tcgawgbsdata.hg19/bioconductor-tcgawgbsdata.hg19_1.2.0_src_all.tar.gz" ) -MD5="e614d37504300366b89e08aae9d82902" +MD5="0016ac6074b918439dac0a52151c4ffa" # Use a staging area in the conda dir rather than temp dirs, both to avoid # permission issues as well as to have things downloaded in a predictable @@ -16,7 +16,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-tcgaworkflowdata/meta.yaml b/recipes/bioconductor-tcgaworkflowdata/meta.yaml index bb1552eb7abd4..73f6309951b3c 100644 --- a/recipes/bioconductor-tcgaworkflowdata/meta.yaml +++ b/recipes/bioconductor-tcgaworkflowdata/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.6.0" %} +{% set version = "1.8.0" %} {% set name = "TCGAWorkflowData" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 3c147bc7cf5ba811e359f12db8e7b42a + md5: 90d52109bd55f983c51da4ae7bc8a63c build: number: 0 rpaths: @@ -20,12 +20,12 @@ build: # Suggests: knitr, rmarkdown, pander, testthat requirements: host: - - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' + - 'bioconductor-summarizedexperiment >=1.14.0,<1.15.0' - r-base run: - - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' + - 'bioconductor-summarizedexperiment >=1.14.0,<1.15.0' - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-tcgaworkflowdata/post-link.sh b/recipes/bioconductor-tcgaworkflowdata/post-link.sh index cf88a138539df..48c0b82db795b 100644 --- a/recipes/bioconductor-tcgaworkflowdata/post-link.sh +++ b/recipes/bioconductor-tcgaworkflowdata/post-link.sh @@ -1,11 +1,11 @@ #!/bin/bash -FN="TCGAWorkflowData_1.6.0.tar.gz" +FN="TCGAWorkflowData_1.8.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/experiment/src/contrib/TCGAWorkflowData_1.6.0.tar.gz" - "https://bioarchive.galaxyproject.org/TCGAWorkflowData_1.6.0.tar.gz" - "https://depot.galaxyproject.org/software/bioconductor-tcgaworkflowdata/bioconductor-tcgaworkflowdata_1.6.0_src_all.tar.gz" + "https://bioconductor.org/packages/3.9/data/experiment/src/contrib/TCGAWorkflowData_1.8.0.tar.gz" + "https://bioarchive.galaxyproject.org/TCGAWorkflowData_1.8.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-tcgaworkflowdata/bioconductor-tcgaworkflowdata_1.8.0_src_all.tar.gz" ) -MD5="3c147bc7cf5ba811e359f12db8e7b42a" +MD5="90d52109bd55f983c51da4ae7bc8a63c" # Use a staging area in the conda dir rather than temp dirs, both to avoid # permission issues as well as to have things downloaded in a predictable @@ -16,7 +16,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-tcseq/meta.yaml b/recipes/bioconductor-tcseq/meta.yaml index abb0e960b3e88..88b1b1c96d873 100644 --- a/recipes/bioconductor-tcseq/meta.yaml +++ b/recipes/bioconductor-tcseq/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.6.0" %} +{% set version = "1.8.0" %} {% set name = "TCseq" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 5300ccb82f5f6de70b89fa1b1a8cd01d + md5: 238ceb170a9261e3a3e8c0dcca57f072 build: number: 0 rpaths: @@ -20,13 +20,13 @@ build: # Suggests: testthat requirements: host: - - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' - - 'bioconductor-edger >=3.24.0,<3.25.0' - - 'bioconductor-genomicalignments >=1.18.0,<1.19.0' - - 'bioconductor-genomicranges >=1.34.0,<1.35.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-rsamtools >=1.34.0,<1.35.0' - - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' + - 'bioconductor-biocgenerics >=0.30.0,<0.31.0' + - 'bioconductor-edger >=3.26.0,<3.27.0' + - 'bioconductor-genomicalignments >=1.20.0,<1.21.0' + - 'bioconductor-genomicranges >=1.36.0,<1.37.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-rsamtools >=2.0.0,<2.1.0' + - 'bioconductor-summarizedexperiment >=1.14.0,<1.15.0' - r-base - r-cluster - r-e1071 @@ -34,13 +34,13 @@ requirements: - r-locfit - r-reshape2 run: - - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' - - 'bioconductor-edger >=3.24.0,<3.25.0' - - 'bioconductor-genomicalignments >=1.18.0,<1.19.0' - - 'bioconductor-genomicranges >=1.34.0,<1.35.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-rsamtools >=1.34.0,<1.35.0' - - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' + - 'bioconductor-biocgenerics >=0.30.0,<0.31.0' + - 'bioconductor-edger >=3.26.0,<3.27.0' + - 'bioconductor-genomicalignments >=1.20.0,<1.21.0' + - 'bioconductor-genomicranges >=1.36.0,<1.37.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-rsamtools >=2.0.0,<2.1.0' + - 'bioconductor-summarizedexperiment >=1.14.0,<1.15.0' - r-base - r-cluster - r-e1071 diff --git a/recipes/bioconductor-tdaracne/meta.yaml b/recipes/bioconductor-tdaracne/meta.yaml index 07892dd058921..dd041c2540ef5 100644 --- a/recipes/bioconductor-tdaracne/meta.yaml +++ b/recipes/bioconductor-tdaracne/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.32.0" %} +{% set version = "1.34.0" %} {% set name = "TDARACNE" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 5d2edadc66ee9cc1e3984fb1845314fb + md5: 45e12f3cf2d2301ac0e5ad0eaacb41db build: number: 0 rpaths: @@ -19,13 +19,13 @@ build: noarch: generic requirements: host: - - 'bioconductor-biobase >=2.42.0,<2.43.0' - - 'bioconductor-rgraphviz >=2.26.0,<2.27.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' + - 'bioconductor-rgraphviz >=2.28.0,<2.29.0' - r-base - r-genkern run: - - 'bioconductor-biobase >=2.42.0,<2.43.0' - - 'bioconductor-rgraphviz >=2.26.0,<2.27.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' + - 'bioconductor-rgraphviz >=2.28.0,<2.29.0' - r-base - r-genkern test: diff --git a/recipes/bioconductor-tenxbraindata/meta.yaml b/recipes/bioconductor-tenxbraindata/meta.yaml index 1c587c5998fbb..fb0b736d027b6 100644 --- a/recipes/bioconductor-tenxbraindata/meta.yaml +++ b/recipes/bioconductor-tenxbraindata/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.2.0" %} +{% set version = "1.4.0" %} {% set name = "TENxBrainData" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 8f4e0317f3db09ed897fc30484e48115 + md5: 7e6d88a566de22896659fada4fd8192b build: number: 0 rpaths: @@ -20,18 +20,18 @@ build: # Suggests: knitr, BiocStyle, snow, BiocFileCache, BiocParallel, data.table requirements: host: - - 'bioconductor-annotationhub >=2.14.0,<2.15.0' - - 'bioconductor-experimenthub >=1.8.0,<1.9.0' - - 'bioconductor-hdf5array >=1.10.0,<1.11.0' - - 'bioconductor-singlecellexperiment >=1.4.0,<1.5.0' + - 'bioconductor-annotationhub >=2.16.0,<2.17.0' + - 'bioconductor-experimenthub >=1.10.0,<1.11.0' + - 'bioconductor-hdf5array >=1.12.0,<1.13.0' + - 'bioconductor-singlecellexperiment >=1.6.0,<1.7.0' - r-base run: - - 'bioconductor-annotationhub >=2.14.0,<2.15.0' - - 'bioconductor-experimenthub >=1.8.0,<1.9.0' - - 'bioconductor-hdf5array >=1.10.0,<1.11.0' - - 'bioconductor-singlecellexperiment >=1.4.0,<1.5.0' + - 'bioconductor-annotationhub >=2.16.0,<2.17.0' + - 'bioconductor-experimenthub >=1.10.0,<1.11.0' + - 'bioconductor-hdf5array >=1.12.0,<1.13.0' + - 'bioconductor-singlecellexperiment >=1.6.0,<1.7.0' - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-tenxbraindata/post-link.sh b/recipes/bioconductor-tenxbraindata/post-link.sh index d64f3f7b7b21d..f568ac500c7f3 100644 --- a/recipes/bioconductor-tenxbraindata/post-link.sh +++ b/recipes/bioconductor-tenxbraindata/post-link.sh @@ -1,11 +1,11 @@ #!/bin/bash -FN="TENxBrainData_1.2.0.tar.gz" +FN="TENxBrainData_1.4.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/experiment/src/contrib/TENxBrainData_1.2.0.tar.gz" - "https://bioarchive.galaxyproject.org/TENxBrainData_1.2.0.tar.gz" - "https://depot.galaxyproject.org/software/bioconductor-tenxbraindata/bioconductor-tenxbraindata_1.2.0_src_all.tar.gz" + "https://bioconductor.org/packages/3.9/data/experiment/src/contrib/TENxBrainData_1.4.0.tar.gz" + "https://bioarchive.galaxyproject.org/TENxBrainData_1.4.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-tenxbraindata/bioconductor-tenxbraindata_1.4.0_src_all.tar.gz" ) -MD5="8f4e0317f3db09ed897fc30484e48115" +MD5="7e6d88a566de22896659fada4fd8192b" # Use a staging area in the conda dir rather than temp dirs, both to avoid # permission issues as well as to have things downloaded in a predictable @@ -16,7 +16,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-tenxpbmcdata/meta.yaml b/recipes/bioconductor-tenxpbmcdata/meta.yaml index 757de2704bde7..619c600ce9444 100644 --- a/recipes/bioconductor-tenxpbmcdata/meta.yaml +++ b/recipes/bioconductor-tenxpbmcdata/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.0.0" %} +{% set version = "1.2.0" %} {% set name = "TENxPBMCData" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 51a0e7d6a73413d7275fe368de4471bf + md5: ffe941067700fd429028dda58bf5fc3e build: number: 0 rpaths: @@ -20,18 +20,18 @@ build: # Suggests: knitr, BiocStyle, snow, BiocFileCache, BiocParallel requirements: host: - - 'bioconductor-annotationhub >=2.14.0,<2.15.0' - - 'bioconductor-experimenthub >=1.8.0,<1.9.0' - - 'bioconductor-hdf5array >=1.10.0,<1.11.0' - - 'bioconductor-singlecellexperiment >=1.4.0,<1.5.0' + - 'bioconductor-annotationhub >=2.16.0,<2.17.0' + - 'bioconductor-experimenthub >=1.10.0,<1.11.0' + - 'bioconductor-hdf5array >=1.12.0,<1.13.0' + - 'bioconductor-singlecellexperiment >=1.6.0,<1.7.0' - r-base run: - - 'bioconductor-annotationhub >=2.14.0,<2.15.0' - - 'bioconductor-experimenthub >=1.8.0,<1.9.0' - - 'bioconductor-hdf5array >=1.10.0,<1.11.0' - - 'bioconductor-singlecellexperiment >=1.4.0,<1.5.0' + - 'bioconductor-annotationhub >=2.16.0,<2.17.0' + - 'bioconductor-experimenthub >=1.10.0,<1.11.0' + - 'bioconductor-hdf5array >=1.12.0,<1.13.0' + - 'bioconductor-singlecellexperiment >=1.6.0,<1.7.0' - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-tenxpbmcdata/post-link.sh b/recipes/bioconductor-tenxpbmcdata/post-link.sh index 57618d3705910..701756a4dafad 100644 --- a/recipes/bioconductor-tenxpbmcdata/post-link.sh +++ b/recipes/bioconductor-tenxpbmcdata/post-link.sh @@ -1,11 +1,11 @@ #!/bin/bash -FN="TENxPBMCData_1.0.0.tar.gz" +FN="TENxPBMCData_1.2.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/experiment/src/contrib/TENxPBMCData_1.0.0.tar.gz" - "https://bioarchive.galaxyproject.org/TENxPBMCData_1.0.0.tar.gz" - "https://depot.galaxyproject.org/software/bioconductor-tenxpbmcdata/bioconductor-tenxpbmcdata_1.0.0_src_all.tar.gz" + "https://bioconductor.org/packages/3.9/data/experiment/src/contrib/TENxPBMCData_1.2.0.tar.gz" + "https://bioarchive.galaxyproject.org/TENxPBMCData_1.2.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-tenxpbmcdata/bioconductor-tenxpbmcdata_1.2.0_src_all.tar.gz" ) -MD5="51a0e7d6a73413d7275fe368de4471bf" +MD5="ffe941067700fd429028dda58bf5fc3e" # Use a staging area in the conda dir rather than temp dirs, both to avoid # permission issues as well as to have things downloaded in a predictable @@ -16,7 +16,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-tenxplore/meta.yaml b/recipes/bioconductor-tenxplore/meta.yaml index f43d8d8cdf4be..a867ce79953af 100644 --- a/recipes/bioconductor-tenxplore/meta.yaml +++ b/recipes/bioconductor-tenxplore/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.4.0" %} +{% set version = "1.6.0" %} {% set name = "tenXplore" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 5976e4b5b299bcaebe96b3d2e9d3bd21 + md5: 7f5c9cc74049ba207a634e77e69a785a build: number: 0 rpaths: @@ -20,20 +20,20 @@ build: # Suggests: org.Hs.eg.db, testthat, knitr requirements: host: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' - - 'bioconductor-ontoproc >=1.4.0,<1.5.0' - - 'bioconductor-org.mm.eg.db >=3.7.0,<3.8.0' - - 'bioconductor-restfulse >=1.4.0,<1.5.0' - - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' + - 'bioconductor-ontoproc >=1.6.0,<1.7.0' + - 'bioconductor-org.mm.eg.db >=3.8.0,<3.9.0' + - 'bioconductor-restfulse >=1.6.0,<1.7.0' + - 'bioconductor-summarizedexperiment >=1.14.0,<1.15.0' - r-base - r-matrixstats - r-shiny run: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' - - 'bioconductor-ontoproc >=1.4.0,<1.5.0' - - 'bioconductor-org.mm.eg.db >=3.7.0,<3.8.0' - - 'bioconductor-restfulse >=1.4.0,<1.5.0' - - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' + - 'bioconductor-ontoproc >=1.6.0,<1.7.0' + - 'bioconductor-org.mm.eg.db >=3.8.0,<3.9.0' + - 'bioconductor-restfulse >=1.6.0,<1.7.0' + - 'bioconductor-summarizedexperiment >=1.14.0,<1.15.0' - r-base - r-matrixstats - r-shiny diff --git a/recipes/bioconductor-teqc/meta.yaml b/recipes/bioconductor-teqc/meta.yaml index badfe451541e4..ee68b775b58ec 100644 --- a/recipes/bioconductor-teqc/meta.yaml +++ b/recipes/bioconductor-teqc/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "4.4.0" %} +{% set version = "4.6.0" %} {% set name = "TEQC" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 85ceae4d51ead9716d90df8bc38e60a8 + md5: fe0e50b70cff7c55f8f0efb0f878d168 build: number: 0 rpaths: @@ -19,17 +19,17 @@ build: noarch: generic requirements: host: - - 'bioconductor-biobase >=2.42.0,<2.43.0' - - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-rsamtools >=1.34.0,<1.35.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' + - 'bioconductor-biocgenerics >=0.30.0,<0.31.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-rsamtools >=2.0.0,<2.1.0' - r-base - r-hwriter run: - - 'bioconductor-biobase >=2.42.0,<2.43.0' - - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-rsamtools >=1.34.0,<1.35.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' + - 'bioconductor-biocgenerics >=0.30.0,<0.31.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-rsamtools >=2.0.0,<2.1.0' - r-base - r-hwriter test: diff --git a/recipes/bioconductor-ternarynet/meta.yaml b/recipes/bioconductor-ternarynet/meta.yaml index 3ef2b456ffa54..ef0cba25a5339 100644 --- a/recipes/bioconductor-ternarynet/meta.yaml +++ b/recipes/bioconductor-ternarynet/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.26.0" %} +{% set version = "1.28.0" %} {% set name = "ternarynet" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: fcc0042c1e0dbfc502572cd0f4b0a3cf + md5: ca477fd797c3c2e465d68beea471b776 build: number: 0 rpaths: diff --git a/recipes/bioconductor-test1cdf/meta.yaml b/recipes/bioconductor-test1cdf/meta.yaml index 5ee70a1d59358..dee4ce899d569 100644 --- a/recipes/bioconductor-test1cdf/meta.yaml +++ b/recipes/bioconductor-test1cdf/meta.yaml @@ -1,6 +1,6 @@ {% set version = "2.18.0" %} {% set name = "test1cdf" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -12,19 +12,19 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 8c94708b49ccc7bbf127485155970b9b build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' - r-base run: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-test1cdf/post-link.sh b/recipes/bioconductor-test1cdf/post-link.sh index 3df39556854dc..a1d4cca199f72 100644 --- a/recipes/bioconductor-test1cdf/post-link.sh +++ b/recipes/bioconductor-test1cdf/post-link.sh @@ -1,9 +1,10 @@ #!/bin/bash FN="test1cdf_2.18.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/test1cdf_2.18.0.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/test1cdf_2.18.0.tar.gz" "https://bioarchive.galaxyproject.org/test1cdf_2.18.0.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-test1cdf/bioconductor-test1cdf_2.18.0_src_all.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-test1cdf/bioconductor-test1cdf_2.18.0_src_all.tar.gz" ) MD5="8c94708b49ccc7bbf127485155970b9b" @@ -16,7 +17,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-test2cdf/meta.yaml b/recipes/bioconductor-test2cdf/meta.yaml index 4c0ec817e77ed..14b9d03de6c65 100644 --- a/recipes/bioconductor-test2cdf/meta.yaml +++ b/recipes/bioconductor-test2cdf/meta.yaml @@ -1,6 +1,6 @@ {% set version = "2.18.0" %} {% set name = "test2cdf" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -12,19 +12,19 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 0d1c20d6450dfc83d62214be9dc46b5f build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' - r-base run: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-test2cdf/post-link.sh b/recipes/bioconductor-test2cdf/post-link.sh index 91cb0cde4abf5..e55b5c5e699d1 100644 --- a/recipes/bioconductor-test2cdf/post-link.sh +++ b/recipes/bioconductor-test2cdf/post-link.sh @@ -1,9 +1,10 @@ #!/bin/bash FN="test2cdf_2.18.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/test2cdf_2.18.0.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/test2cdf_2.18.0.tar.gz" "https://bioarchive.galaxyproject.org/test2cdf_2.18.0.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-test2cdf/bioconductor-test2cdf_2.18.0_src_all.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-test2cdf/bioconductor-test2cdf_2.18.0_src_all.tar.gz" ) MD5="0d1c20d6450dfc83d62214be9dc46b5f" @@ -16,7 +17,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-test3cdf/meta.yaml b/recipes/bioconductor-test3cdf/meta.yaml index 772f1fe5d93fc..723e28aec26ae 100644 --- a/recipes/bioconductor-test3cdf/meta.yaml +++ b/recipes/bioconductor-test3cdf/meta.yaml @@ -1,6 +1,6 @@ {% set version = "2.18.0" %} {% set name = "test3cdf" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -12,19 +12,19 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 9904e7fa6599f68400a9b77d0caa159a build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' - r-base run: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-test3cdf/post-link.sh b/recipes/bioconductor-test3cdf/post-link.sh index 512f346fe8dd7..413637f27554b 100644 --- a/recipes/bioconductor-test3cdf/post-link.sh +++ b/recipes/bioconductor-test3cdf/post-link.sh @@ -1,9 +1,10 @@ #!/bin/bash FN="test3cdf_2.18.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/test3cdf_2.18.0.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/test3cdf_2.18.0.tar.gz" "https://bioarchive.galaxyproject.org/test3cdf_2.18.0.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-test3cdf/bioconductor-test3cdf_2.18.0_src_all.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-test3cdf/bioconductor-test3cdf_2.18.0_src_all.tar.gz" ) MD5="9904e7fa6599f68400a9b77d0caa159a" @@ -16,7 +17,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-test3probe/meta.yaml b/recipes/bioconductor-test3probe/meta.yaml index 692d25074314a..fc91f0f0b090c 100644 --- a/recipes/bioconductor-test3probe/meta.yaml +++ b/recipes/bioconductor-test3probe/meta.yaml @@ -1,6 +1,6 @@ {% set version = "2.18.0" %} {% set name = "test3probe" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -12,19 +12,19 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: ffcbfee4e5c486fd03b2b9b64820340c build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' - r-base run: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-test3probe/post-link.sh b/recipes/bioconductor-test3probe/post-link.sh index 7a23e0098c7a7..fcc71172d3e27 100644 --- a/recipes/bioconductor-test3probe/post-link.sh +++ b/recipes/bioconductor-test3probe/post-link.sh @@ -1,9 +1,10 @@ #!/bin/bash FN="test3probe_2.18.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/test3probe_2.18.0.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/test3probe_2.18.0.tar.gz" "https://bioarchive.galaxyproject.org/test3probe_2.18.0.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-test3probe/bioconductor-test3probe_2.18.0_src_all.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-test3probe/bioconductor-test3probe_2.18.0_src_all.tar.gz" ) MD5="ffcbfee4e5c486fd03b2b9b64820340c" @@ -16,7 +17,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-tfarm/meta.yaml b/recipes/bioconductor-tfarm/meta.yaml index 58988e1ce47ac..b0421afa31968 100644 --- a/recipes/bioconductor-tfarm/meta.yaml +++ b/recipes/bioconductor-tfarm/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.4.0" %} +{% set version = "1.6.0" %} {% set name = "TFARM" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: de70bbb6c08b094687d9a0c8c1b80307 + md5: 6f91d5a29a0274ee1344694c44f9ce21 build: number: 0 rpaths: @@ -20,13 +20,13 @@ build: # Suggests: BiocStyle, knitr, plyr requirements: host: - - 'bioconductor-genomicranges >=1.34.0,<1.35.0' + - 'bioconductor-genomicranges >=1.36.0,<1.37.0' - r-arules - r-base - r-fields - r-stringr run: - - 'bioconductor-genomicranges >=1.34.0,<1.35.0' + - 'bioconductor-genomicranges >=1.36.0,<1.37.0' - r-arules - r-base - r-fields diff --git a/recipes/bioconductor-tfbstools/meta.yaml b/recipes/bioconductor-tfbstools/meta.yaml index 656b98b2051e0..eadf2ce33024d 100644 --- a/recipes/bioconductor-tfbstools/meta.yaml +++ b/recipes/bioconductor-tfbstools/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.20.0" %} +{% set version = "1.22.0" %} {% set name = "TFBSTools" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,29 +10,29 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: e3c9e0fb66c9e32d883aaa5f22d86201 + md5: 86c488ad257f26c6dfbe116bb981100f build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ # Suggests: BiocStyle(>= 1.7.7), JASPAR2014(>= 1.4.0), knitr(>= 1.11), testthat, JASPAR2016(>= 1.0.0) requirements: host: - - 'bioconductor-biobase >=2.42.0,<2.43.0' - - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' - - 'bioconductor-biocparallel >=1.16.0,<1.17.0' - - 'bioconductor-biostrings >=2.50.0,<2.51.0' - - 'bioconductor-bsgenome >=1.50.0,<1.51.0' - - 'bioconductor-cner >=1.18.0,<1.19.0' - - 'bioconductor-dirichletmultinomial >=1.24.0,<1.25.0' - - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' - - 'bioconductor-genomicranges >=1.34.0,<1.35.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-rtracklayer >=1.42.0,<1.43.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' - - 'bioconductor-seqlogo >=1.48.0,<1.49.0' - - 'bioconductor-xvector >=0.22.0,<0.23.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' + - 'bioconductor-biocgenerics >=0.30.0,<0.31.0' + - 'bioconductor-biocparallel >=1.18.0,<1.19.0' + - 'bioconductor-biostrings >=2.52.0,<2.53.0' + - 'bioconductor-bsgenome >=1.52.0,<1.53.0' + - 'bioconductor-cner >=1.20.0,<1.21.0' + - 'bioconductor-dirichletmultinomial >=1.26.0,<1.27.0' + - 'bioconductor-genomeinfodb >=1.20.0,<1.21.0' + - 'bioconductor-genomicranges >=1.36.0,<1.37.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-rtracklayer >=1.44.0,<1.45.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' + - 'bioconductor-seqlogo >=1.50.0,<1.51.0' + - 'bioconductor-xvector >=0.24.0,<0.25.0' - r-base - 'r-catools >=1.17.1' - 'r-dbi >=0.6' @@ -41,20 +41,20 @@ requirements: - 'r-tfmpvalue >=0.0.5' - 'r-xml >=3.98-1.3' run: - - 'bioconductor-biobase >=2.42.0,<2.43.0' - - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' - - 'bioconductor-biocparallel >=1.16.0,<1.17.0' - - 'bioconductor-biostrings >=2.50.0,<2.51.0' - - 'bioconductor-bsgenome >=1.50.0,<1.51.0' - - 'bioconductor-cner >=1.18.0,<1.19.0' - - 'bioconductor-dirichletmultinomial >=1.24.0,<1.25.0' - - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' - - 'bioconductor-genomicranges >=1.34.0,<1.35.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-rtracklayer >=1.42.0,<1.43.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' - - 'bioconductor-seqlogo >=1.48.0,<1.49.0' - - 'bioconductor-xvector >=0.22.0,<0.23.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' + - 'bioconductor-biocgenerics >=0.30.0,<0.31.0' + - 'bioconductor-biocparallel >=1.18.0,<1.19.0' + - 'bioconductor-biostrings >=2.52.0,<2.53.0' + - 'bioconductor-bsgenome >=1.52.0,<1.53.0' + - 'bioconductor-cner >=1.20.0,<1.21.0' + - 'bioconductor-dirichletmultinomial >=1.26.0,<1.27.0' + - 'bioconductor-genomeinfodb >=1.20.0,<1.21.0' + - 'bioconductor-genomicranges >=1.36.0,<1.37.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-rtracklayer >=1.44.0,<1.45.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' + - 'bioconductor-seqlogo >=1.50.0,<1.51.0' + - 'bioconductor-xvector >=0.24.0,<0.25.0' - r-base - 'r-catools >=1.17.1' - 'r-dbi >=0.6' diff --git a/recipes/bioconductor-tfea.chip/meta.yaml b/recipes/bioconductor-tfea.chip/meta.yaml index 2c7660edbceff..bb705469c2b94 100644 --- a/recipes/bioconductor-tfea.chip/meta.yaml +++ b/recipes/bioconductor-tfea.chip/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.2.1" %} +{% set version = "1.4.0" %} {% set name = "TFEA.ChIP" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,32 +10,30 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 55ca97012018846d2c744bdf33991429 + md5: f7ece8887d78ab79c064ffeb560ad2fa build: number: 0 rpaths: - lib/R/lib/ - lib/ noarch: generic -# Suggests: knitr, rmarkdown, S4Vectors, plotly, scales, tidyr, ggplot2, GSEABase, DESeq2, BiocGenerics +# Suggests: knitr, rmarkdown, S4Vectors, plotly, scales, tidyr, ggplot2, GSEABase, DESeq2, BiocGenerics, ggrepel, rcompanion, TxDb.Hsapiens.UCSC.hg19.knownGene requirements: host: - - 'bioconductor-biomart >=2.38.0,<2.39.0' - - 'bioconductor-genomicfeatures >=1.34.0,<1.35.0' - - 'bioconductor-genomicranges >=1.34.0,<1.35.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-org.hs.eg.db >=3.7.0,<3.8.0' - - 'bioconductor-txdb.hsapiens.ucsc.hg19.knowngene >=3.2.0,<3.3.0' + - 'bioconductor-biomart >=2.40.0,<2.41.0' + - 'bioconductor-genomicfeatures >=1.36.0,<1.37.0' + - 'bioconductor-genomicranges >=1.36.0,<1.37.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-org.hs.eg.db >=3.8.0,<3.9.0' - r-base - r-dplyr - r-r.utils run: - - 'bioconductor-biomart >=2.38.0,<2.39.0' - - 'bioconductor-genomicfeatures >=1.34.0,<1.35.0' - - 'bioconductor-genomicranges >=1.34.0,<1.35.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-org.hs.eg.db >=3.7.0,<3.8.0' - - 'bioconductor-txdb.hsapiens.ucsc.hg19.knowngene >=3.2.0,<3.3.0' + - 'bioconductor-biomart >=2.40.0,<2.41.0' + - 'bioconductor-genomicfeatures >=1.36.0,<1.37.0' + - 'bioconductor-genomicranges >=1.36.0,<1.37.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-org.hs.eg.db >=3.8.0,<3.9.0' - r-base - r-dplyr - r-r.utils diff --git a/recipes/bioconductor-tfhaz/meta.yaml b/recipes/bioconductor-tfhaz/meta.yaml index 5c47b8284f660..0adfb4f787caa 100644 --- a/recipes/bioconductor-tfhaz/meta.yaml +++ b/recipes/bioconductor-tfhaz/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.4.0" %} +{% set version = "1.6.0" %} {% set name = "TFHAZ" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: b2e9eef46b67621c17b58309ff630b22 + md5: 1d737554beb95e3dcbcf1d78a2ee6f19 build: number: 0 rpaths: @@ -20,14 +20,14 @@ build: # Suggests: BiocStyle, knitr, rmarkdown requirements: host: - - 'bioconductor-genomicranges >=1.34.0,<1.35.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-genomicranges >=1.36.0,<1.37.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' - r-base run: - - 'bioconductor-genomicranges >=1.34.0,<1.35.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-genomicranges >=1.36.0,<1.37.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' - r-base test: commands: diff --git a/recipes/bioconductor-tfutils/meta.yaml b/recipes/bioconductor-tfutils/meta.yaml index 04fa46c734466..291839ae79fda 100644 --- a/recipes/bioconductor-tfutils/meta.yaml +++ b/recipes/bioconductor-tfutils/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.2.0" %} +{% set version = "1.4.0" %} {% set name = "TFutils" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: f8cdec899590e3cd9198bd3e63c27d01 + md5: cdde742d1336acd93fb1a2f0ed74a1d4 build: number: 0 rpaths: diff --git a/recipes/bioconductor-tigre/meta.yaml b/recipes/bioconductor-tigre/meta.yaml index fb15aeeb75904..305c7bbdd43d3 100644 --- a/recipes/bioconductor-tigre/meta.yaml +++ b/recipes/bioconductor-tigre/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.36.0" %} +{% set version = "1.38.0" %} {% set name = "tigre" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 96d6f5cdec071763b3695fab44ae87cb + md5: af4ce4d96d3000ecaa64b6f65c77c023 build: number: 0 rpaths: @@ -19,19 +19,19 @@ build: # Suggests: drosgenome1.db, puma, lumi, BiocStyle, BiocManager requirements: host: - - 'bioconductor-annotate >=1.60.0,<1.61.0' - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' - - 'bioconductor-biobase >=2.42.0,<2.43.0' - - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' + - 'bioconductor-annotate >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' + - 'bioconductor-biocgenerics >=0.30.0,<0.31.0' - r-base - r-dbi - r-gplots - r-rsqlite run: - - 'bioconductor-annotate >=1.60.0,<1.61.0' - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' - - 'bioconductor-biobase >=2.42.0,<2.43.0' - - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' + - 'bioconductor-annotate >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' + - 'bioconductor-biocgenerics >=0.30.0,<0.31.0' - r-base - r-dbi - r-gplots diff --git a/recipes/bioconductor-tilingarray/meta.yaml b/recipes/bioconductor-tilingarray/meta.yaml index 99bfcc26b88c1..f9729ca76c5a7 100644 --- a/recipes/bioconductor-tilingarray/meta.yaml +++ b/recipes/bioconductor-tilingarray/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.60.0" %} +{% set version = "1.62.0" %} {% set name = "tilingArray" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: eae54973c3f6bd1f99ddb4df77d0377a + md5: 963b2f24edfea1b4c6351745fdb4c697 build: number: 0 rpaths: @@ -18,19 +18,19 @@ build: - lib/ requirements: host: - - 'bioconductor-affy >=1.60.0,<1.61.0' - - 'bioconductor-biobase >=2.42.0,<2.43.0' - - 'bioconductor-genefilter >=1.64.0,<1.65.0' - - 'bioconductor-vsn >=3.50.0,<3.51.0' + - 'bioconductor-affy >=1.62.0,<1.63.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' + - 'bioconductor-genefilter >=1.66.0,<1.67.0' + - 'bioconductor-vsn >=3.52.0,<3.53.0' - r-base - r-pixmap - r-rcolorbrewer - r-strucchange run: - - 'bioconductor-affy >=1.60.0,<1.61.0' - - 'bioconductor-biobase >=2.42.0,<2.43.0' - - 'bioconductor-genefilter >=1.64.0,<1.65.0' - - 'bioconductor-vsn >=3.50.0,<3.51.0' + - 'bioconductor-affy >=1.62.0,<1.63.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' + - 'bioconductor-genefilter >=1.66.0,<1.67.0' + - 'bioconductor-vsn >=3.52.0,<3.53.0' - r-base - r-pixmap - r-rcolorbrewer diff --git a/recipes/bioconductor-timecourse/meta.yaml b/recipes/bioconductor-timecourse/meta.yaml index 1d0211b82203c..152379ae6790a 100644 --- a/recipes/bioconductor-timecourse/meta.yaml +++ b/recipes/bioconductor-timecourse/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.54.0" %} +{% set version = "1.56.0" %} {% set name = "timecourse" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: f951b9aa3b8398f16a99b0534c58c94f + md5: 3e05749c495fb39c49af5be361e4e16f build: number: 0 rpaths: @@ -19,15 +19,15 @@ build: noarch: generic requirements: host: - - 'bioconductor-biobase >=2.42.0,<2.43.0' - - 'bioconductor-limma >=3.38.0,<3.39.0' - - 'bioconductor-marray >=1.60.0,<1.61.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' + - 'bioconductor-limma >=3.40.0,<3.41.0' + - 'bioconductor-marray >=1.62.0,<1.63.0' - r-base - r-mass run: - - 'bioconductor-biobase >=2.42.0,<2.43.0' - - 'bioconductor-limma >=3.38.0,<3.39.0' - - 'bioconductor-marray >=1.60.0,<1.61.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' + - 'bioconductor-limma >=3.40.0,<3.41.0' + - 'bioconductor-marray >=1.62.0,<1.63.0' - r-base - r-mass test: diff --git a/recipes/bioconductor-timerquant/meta.yaml b/recipes/bioconductor-timerquant/meta.yaml index 1a5d03201edea..9ce8ec175effa 100644 --- a/recipes/bioconductor-timerquant/meta.yaml +++ b/recipes/bioconductor-timerquant/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.12.0" %} +{% set version = "1.14.0" %} {% set name = "TimerQuant" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 6b6d3bd75b7a51740ede49802179a8e3 + md5: 3e09837187e65aa1b4f59165a35c7df4 build: number: 0 rpaths: @@ -35,7 +35,7 @@ requirements: - r-gridextra - r-locfit - r-shiny - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-timerquant/post-link.sh b/recipes/bioconductor-timerquant/post-link.sh index d69dd6b8405c4..6d3ea37127b10 100644 --- a/recipes/bioconductor-timerquant/post-link.sh +++ b/recipes/bioconductor-timerquant/post-link.sh @@ -1,11 +1,11 @@ #!/bin/bash -FN="TimerQuant_1.12.0.tar.gz" +FN="TimerQuant_1.14.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/experiment/src/contrib/TimerQuant_1.12.0.tar.gz" - "https://bioarchive.galaxyproject.org/TimerQuant_1.12.0.tar.gz" - "https://depot.galaxyproject.org/software/bioconductor-timerquant/bioconductor-timerquant_1.12.0_src_all.tar.gz" + "https://bioconductor.org/packages/3.9/data/experiment/src/contrib/TimerQuant_1.14.0.tar.gz" + "https://bioarchive.galaxyproject.org/TimerQuant_1.14.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-timerquant/bioconductor-timerquant_1.14.0_src_all.tar.gz" ) -MD5="6b6d3bd75b7a51740ede49802179a8e3" +MD5="3e09837187e65aa1b4f59165a35c7df4" # Use a staging area in the conda dir rather than temp dirs, both to avoid # permission issues as well as to have things downloaded in a predictable @@ -16,7 +16,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-timescape/meta.yaml b/recipes/bioconductor-timescape/meta.yaml index ad57326f06681..1c72c57f6d683 100644 --- a/recipes/bioconductor-timescape/meta.yaml +++ b/recipes/bioconductor-timescape/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.6.0" %} +{% set version = "1.8.0" %} {% set name = "timescape" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 4559bf51a0edf576108683f5b8e96652 + md5: 5ef9863c6b75dc7cab6e337e3dd8f611 build: number: 0 rpaths: diff --git a/recipes/bioconductor-timeseriesexperiment/meta.yaml b/recipes/bioconductor-timeseriesexperiment/meta.yaml index 91ff2354b54a0..9d7a94c602ecb 100644 --- a/recipes/bioconductor-timeseriesexperiment/meta.yaml +++ b/recipes/bioconductor-timeseriesexperiment/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.0.2" %} +{% set version = "1.2.0" %} {% set name = "TimeSeriesExperiment" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 4d18d484844eb407dd220a972c1d975a + md5: ff6f8001e8dbed206a226c83489b948e build: number: 0 rpaths: @@ -20,11 +20,11 @@ build: # Suggests: Biobase, BiocFileCache (>= 1.5.8), circlize, ComplexHeatmap, GO.db, grDevices, grid, knitr, org.Mm.eg.db, org.Hs.eg.db, MASS, RColorBrewer, rmarkdown, UpSetR, requirements: host: - - 'bioconductor-deseq2 >=1.22.0,<1.23.0' - - 'bioconductor-edger >=3.24.0,<3.25.0' - - 'bioconductor-limma >=3.38.0,<3.39.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' - - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' + - 'bioconductor-deseq2 >=1.24.0,<1.25.0' + - 'bioconductor-edger >=3.26.0,<3.27.0' + - 'bioconductor-limma >=3.40.0,<3.41.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' + - 'bioconductor-summarizedexperiment >=1.14.0,<1.15.0' - r-base - r-dplyr - r-dynamictreecut @@ -37,11 +37,11 @@ requirements: - r-vegan - r-viridis run: - - 'bioconductor-deseq2 >=1.22.0,<1.23.0' - - 'bioconductor-edger >=3.24.0,<3.25.0' - - 'bioconductor-limma >=3.38.0,<3.39.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' - - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' + - 'bioconductor-deseq2 >=1.24.0,<1.25.0' + - 'bioconductor-edger >=3.26.0,<3.27.0' + - 'bioconductor-limma >=3.40.0,<3.41.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' + - 'bioconductor-summarizedexperiment >=1.14.0,<1.15.0' - r-base - r-dplyr - r-dynamictreecut diff --git a/recipes/bioconductor-tin/meta.yaml b/recipes/bioconductor-tin/meta.yaml index a4f8840b38f6e..29d45a6ad9ba6 100644 --- a/recipes/bioconductor-tin/meta.yaml +++ b/recipes/bioconductor-tin/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.14.0" %} +{% set version = "1.16.0" %} {% set name = "TIN" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 924d7dc26022c2ca5d9923d05de34c83 + md5: 7e16046e63dfdf805d974e4d65aa2c88 build: number: 0 rpaths: @@ -20,7 +20,7 @@ build: # Suggests: knitr, aroma.light, affxparser, RUnit, BiocGenerics requirements: host: - - 'bioconductor-impute >=1.56.0,<1.57.0' + - 'bioconductor-impute >=1.58.0,<1.59.0' - r-aroma.affymetrix - r-base - r-data.table @@ -28,7 +28,7 @@ requirements: - r-stringr - r-wgcna run: - - 'bioconductor-impute >=1.56.0,<1.57.0' + - 'bioconductor-impute >=1.58.0,<1.59.0' - r-aroma.affymetrix - r-base - r-data.table diff --git a/recipes/bioconductor-tinesath1cdf/meta.yaml b/recipes/bioconductor-tinesath1cdf/meta.yaml index 38830397a9fe7..96ce1227dc458 100644 --- a/recipes/bioconductor-tinesath1cdf/meta.yaml +++ b/recipes/bioconductor-tinesath1cdf/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.20.0" %} +{% set version = "1.22.0" %} {% set name = "tinesath1cdf" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 95e256c032576c0eb2eb21d479ae5e68 + md5: c75413e9dc533ceb727d576dfbbdac49 build: number: 0 rpaths: @@ -22,7 +22,7 @@ requirements: - r-base run: - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-tinesath1cdf/post-link.sh b/recipes/bioconductor-tinesath1cdf/post-link.sh index 11c278b350fd9..e6094fb752ba1 100644 --- a/recipes/bioconductor-tinesath1cdf/post-link.sh +++ b/recipes/bioconductor-tinesath1cdf/post-link.sh @@ -1,11 +1,11 @@ #!/bin/bash -FN="tinesath1cdf_1.20.0.tar.gz" +FN="tinesath1cdf_1.22.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/experiment/src/contrib/tinesath1cdf_1.20.0.tar.gz" - "https://bioarchive.galaxyproject.org/tinesath1cdf_1.20.0.tar.gz" - "https://depot.galaxyproject.org/software/bioconductor-tinesath1cdf/bioconductor-tinesath1cdf_1.20.0_src_all.tar.gz" + "https://bioconductor.org/packages/3.9/data/experiment/src/contrib/tinesath1cdf_1.22.0.tar.gz" + "https://bioarchive.galaxyproject.org/tinesath1cdf_1.22.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-tinesath1cdf/bioconductor-tinesath1cdf_1.22.0_src_all.tar.gz" ) -MD5="95e256c032576c0eb2eb21d479ae5e68" +MD5="c75413e9dc533ceb727d576dfbbdac49" # Use a staging area in the conda dir rather than temp dirs, both to avoid # permission issues as well as to have things downloaded in a predictable @@ -16,7 +16,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-tinesath1probe/meta.yaml b/recipes/bioconductor-tinesath1probe/meta.yaml index 702c850aa16b8..02a3d1d29a89e 100644 --- a/recipes/bioconductor-tinesath1probe/meta.yaml +++ b/recipes/bioconductor-tinesath1probe/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.20.0" %} +{% set version = "1.22.0" %} {% set name = "tinesath1probe" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 8c43dc2ede1e42e22779059c5a6925f0 + md5: 6fe2994d1ed55ca9ef93b47721ea464c build: number: 0 rpaths: @@ -19,12 +19,12 @@ build: noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' - r-base run: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-tinesath1probe/post-link.sh b/recipes/bioconductor-tinesath1probe/post-link.sh index 31a46c0611e14..fcacaab3c785c 100644 --- a/recipes/bioconductor-tinesath1probe/post-link.sh +++ b/recipes/bioconductor-tinesath1probe/post-link.sh @@ -1,11 +1,11 @@ #!/bin/bash -FN="tinesath1probe_1.20.0.tar.gz" +FN="tinesath1probe_1.22.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/experiment/src/contrib/tinesath1probe_1.20.0.tar.gz" - "https://bioarchive.galaxyproject.org/tinesath1probe_1.20.0.tar.gz" - "https://depot.galaxyproject.org/software/bioconductor-tinesath1probe/bioconductor-tinesath1probe_1.20.0_src_all.tar.gz" + "https://bioconductor.org/packages/3.9/data/experiment/src/contrib/tinesath1probe_1.22.0.tar.gz" + "https://bioarchive.galaxyproject.org/tinesath1probe_1.22.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-tinesath1probe/bioconductor-tinesath1probe_1.22.0_src_all.tar.gz" ) -MD5="8c43dc2ede1e42e22779059c5a6925f0" +MD5="6fe2994d1ed55ca9ef93b47721ea464c" # Use a staging area in the conda dir rather than temp dirs, both to avoid # permission issues as well as to have things downloaded in a predictable @@ -16,7 +16,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-tissueenrich/meta.yaml b/recipes/bioconductor-tissueenrich/meta.yaml index 3ed29428f60d9..f7c138d6cdd59 100644 --- a/recipes/bioconductor-tissueenrich/meta.yaml +++ b/recipes/bioconductor-tissueenrich/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.2.1" %} +{% set version = "1.4.0" %} {% set name = "TissueEnrich" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: e35456c0b1b802568e099654a8d933e6 + md5: abe2e3bea8d122818d70045a90d00ad2 build: number: 0 rpaths: @@ -20,16 +20,16 @@ build: # Suggests: knitr, rmarkdown, testthat requirements: host: - - 'bioconductor-gseabase >=1.44.0,<1.45.0' - - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' + - 'bioconductor-gseabase >=1.46.0,<1.47.0' + - 'bioconductor-summarizedexperiment >=1.14.0,<1.15.0' - r-base - 'r-dplyr >=0.7.3' - 'r-ensurer >=1.1.0' - 'r-ggplot2 >=2.2.1' - 'r-tidyr >=0.8.0' run: - - 'bioconductor-gseabase >=1.44.0,<1.45.0' - - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' + - 'bioconductor-gseabase >=1.46.0,<1.47.0' + - 'bioconductor-summarizedexperiment >=1.14.0,<1.15.0' - r-base - 'r-dplyr >=0.7.3' - 'r-ensurer >=1.1.0' diff --git a/recipes/bioconductor-tissuetreg/meta.yaml b/recipes/bioconductor-tissuetreg/meta.yaml index f642ded770d16..d3e97185d0316 100644 --- a/recipes/bioconductor-tissuetreg/meta.yaml +++ b/recipes/bioconductor-tissuetreg/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.2.0" %} +{% set version = "1.4.0" %} {% set name = "tissueTreg" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 36f57ef9bb4affda62e679798e2fca58 + md5: 3aecd23a2936c42a2abc0f292bfc4615 build: number: 0 rpaths: @@ -23,7 +23,7 @@ requirements: - r-base run: - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-tissuetreg/post-link.sh b/recipes/bioconductor-tissuetreg/post-link.sh index 87f6e6d8d6ea5..b6934b77a10c3 100644 --- a/recipes/bioconductor-tissuetreg/post-link.sh +++ b/recipes/bioconductor-tissuetreg/post-link.sh @@ -1,11 +1,11 @@ #!/bin/bash -FN="tissueTreg_1.2.0.tar.gz" +FN="tissueTreg_1.4.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/experiment/src/contrib/tissueTreg_1.2.0.tar.gz" - "https://bioarchive.galaxyproject.org/tissueTreg_1.2.0.tar.gz" - "https://depot.galaxyproject.org/software/bioconductor-tissuetreg/bioconductor-tissuetreg_1.2.0_src_all.tar.gz" + "https://bioconductor.org/packages/3.9/data/experiment/src/contrib/tissueTreg_1.4.0.tar.gz" + "https://bioarchive.galaxyproject.org/tissueTreg_1.4.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-tissuetreg/bioconductor-tissuetreg_1.4.0_src_all.tar.gz" ) -MD5="36f57ef9bb4affda62e679798e2fca58" +MD5="3aecd23a2936c42a2abc0f292bfc4615" # Use a staging area in the conda dir rather than temp dirs, both to avoid # permission issues as well as to have things downloaded in a predictable @@ -16,7 +16,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-titancna/build.sh b/recipes/bioconductor-titancna/build.sh index 0dca07351f4ed..c1d13421f5f1e 100644 --- a/recipes/bioconductor-titancna/build.sh +++ b/recipes/bioconductor-titancna/build.sh @@ -8,23 +8,4 @@ CXX=$CXX CXX98=$CXX CXX11=$CXX CXX14=$CXX" > ~/.R/Makevars -$R CMD INSTALL --build . - -# TitanCNA wrapper scripts and data -outdir=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM -mkdir -p $outdir/scripts/R_scripts -mkdir -p $outdir/data -mkdir -p $PREFIX/bin - -perl -pi -e 'print "#!/opt/anaconda1anaconda2anaconda3/bin/Rscript\n" if $. == 1' scripts/R_scripts/selectSolution.R -sed -i.bak 's:/usr/bin/env Rscript:/opt/anaconda1anaconda2anaconda3/bin/Rscript:' scripts/R_scripts/titanCNA.R - -mv scripts/R_scripts/selectSolution.R $outdir/scripts/R_scripts/titanCNA_selectSolution.R -mv scripts/R_scripts/titanCNA.R $outdir/scripts/R_scripts/titanCNA.R - -chmod a+x $outdir/scripts/R_scripts/*.R -ln -s $outdir/scripts/R_scripts/titanCNA.R $PREFIX/bin -ln -s $outdir/scripts/R_scripts/titanCNA_selectSolution.R $PREFIX/bin - -# Retrieve external data we want to link into the run -wget --no-check-certificate -O $outdir/data/cytoBand_hg38.txt https://raw.githubusercontent.com/broadinstitute/ichorCNA/master/inst/extdata/cytoBand_hg38.txt +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-titancna/meta.yaml b/recipes/bioconductor-titancna/meta.yaml index 3efaf7b8e0c0d..33eaad77a7eb8 100644 --- a/recipes/bioconductor-titancna/meta.yaml +++ b/recipes/bioconductor-titancna/meta.yaml @@ -1,16 +1,16 @@ -{% set version = "1.20.1" %} +{% set version = "1.22.0" %} {% set name = "TitanCNA" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: - url: https://github.com/gavinha/TitanCNA/archive/60408ca.tar.gz - # - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - # - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - # - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 3f8a6a66e55c6d251a79a82bde504977 + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: cd6bd09f869c39c044d50b873d8f5dd9 build: number: 0 rpaths: @@ -18,21 +18,19 @@ build: - lib/ requirements: host: - - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' - - 'bioconductor-genomicranges >=1.34.0,<1.35.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-rsamtools >=1.34.0,<1.35.0' - - 'bioconductor-variantannotation >=1.28.0,<1.29.0' + - 'bioconductor-genomeinfodb >=1.20.0,<1.21.0' + - 'bioconductor-genomicranges >=1.36.0,<1.37.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-variantannotation >=1.30.0,<1.31.0' - r-base - 'r-data.table >=1.10.4' - 'r-dplyr >=0.5.0' - 'r-foreach >=1.4.3' run: - - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' - - 'bioconductor-genomicranges >=1.34.0,<1.35.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-rsamtools >=1.34.0,<1.35.0' - - 'bioconductor-variantannotation >=1.28.0,<1.29.0' + - 'bioconductor-genomeinfodb >=1.20.0,<1.21.0' + - 'bioconductor-genomicranges >=1.36.0,<1.37.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-variantannotation >=1.30.0,<1.31.0' - r-base - 'r-data.table >=1.10.4' - 'r-dplyr >=0.5.0' @@ -46,7 +44,7 @@ test: about: home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: GPL-3 - summary: 'Hidden Markov model to segment and predict regions of subclonal copy number alterations (CNA) and loss of heterozygosity (LOH), and estimate cellular prevalenece of clonal clusters in tumour whole genome sequencing data.' + summary: 'Hidden Markov model to segment and predict regions of subclonal copy number alterations (CNA) and loss of heterozygosity (LOH), and estimate cellular prevalence of clonal clusters in tumour whole genome sequencing data.' extra: identifiers: - biotools:titancna diff --git a/recipes/bioconductor-tkwidgets/meta.yaml b/recipes/bioconductor-tkwidgets/meta.yaml index 0335f3eaa14dd..f6ba119806095 100644 --- a/recipes/bioconductor-tkwidgets/meta.yaml +++ b/recipes/bioconductor-tkwidgets/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.60.0" %} +{% set version = "1.62.0" %} {% set name = "tkWidgets" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 0e005bd310c9b2eceacac768781a3a61 + md5: 63a82dadcb462d25e62fc608eb1f9a44 build: number: 0 rpaths: @@ -20,12 +20,12 @@ build: # Suggests: Biobase, hgu95av2 requirements: host: - - 'bioconductor-dyndoc >=1.60.0,<1.61.0' - - 'bioconductor-widgettools >=1.60.0,<1.61.0' + - 'bioconductor-dyndoc >=1.62.0,<1.63.0' + - 'bioconductor-widgettools >=1.62.0,<1.63.0' - r-base run: - - 'bioconductor-dyndoc >=1.60.0,<1.61.0' - - 'bioconductor-widgettools >=1.60.0,<1.61.0' + - 'bioconductor-dyndoc >=1.62.0,<1.63.0' + - 'bioconductor-widgettools >=1.62.0,<1.63.0' - r-base test: commands: diff --git a/recipes/bioconductor-tmixclust/meta.yaml b/recipes/bioconductor-tmixclust/meta.yaml index 1e89ce63f6e66..81ae3ec30570d 100644 --- a/recipes/bioconductor-tmixclust/meta.yaml +++ b/recipes/bioconductor-tmixclust/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.4.0" %} +{% set version = "1.6.0" %} {% set name = "TMixClust" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 60760731b1fdae8cf110d2407173bdb5 + md5: 7633db1f9553d931f0efd03a8cdeeea9 build: number: 0 rpaths: @@ -20,9 +20,9 @@ build: # Suggests: rmarkdown, knitr, BiocStyle, testthat requirements: host: - - 'bioconductor-biobase >=2.42.0,<2.43.0' - - 'bioconductor-biocparallel >=1.16.0,<1.17.0' - - 'bioconductor-spem >=1.22.0,<1.23.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' + - 'bioconductor-biocparallel >=1.18.0,<1.19.0' + - 'bioconductor-spem >=1.24.0,<1.25.0' - r-base - r-cluster - r-flexclust @@ -30,9 +30,9 @@ requirements: - r-mvtnorm - r-zoo run: - - 'bioconductor-biobase >=2.42.0,<2.43.0' - - 'bioconductor-biocparallel >=1.16.0,<1.17.0' - - 'bioconductor-spem >=1.22.0,<1.23.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' + - 'bioconductor-biocparallel >=1.18.0,<1.19.0' + - 'bioconductor-spem >=1.24.0,<1.25.0' - r-base - r-cluster - r-flexclust diff --git a/recipes/bioconductor-tnbc.cms/build.sh b/recipes/bioconductor-tnbc.cms/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-tnbc.cms/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-tnbc.cms/meta.yaml b/recipes/bioconductor-tnbc.cms/meta.yaml new file mode 100644 index 0000000000000..d61e36e3faebf --- /dev/null +++ b/recipes/bioconductor-tnbc.cms/meta.yaml @@ -0,0 +1,59 @@ +{% set version = "1.0.0" %} +{% set name = "TNBC.CMS" %} +{% set bioc = "3.9" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: 334ca8992244973ec79711cc248de7a6 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: knitr +requirements: + host: + - 'bioconductor-gsva >=1.32.0,<1.33.0' + - 'bioconductor-summarizedexperiment >=1.14.0,<1.15.0' + - r-base + - r-e1071 + - r-forestplot + - r-ggally + - r-ggplot2 + - r-ggpubr + - r-pheatmap + - r-pracma + - r-quadprog + - r-r.utils + - r-rcolorbrewer + - r-survival + run: + - 'bioconductor-gsva >=1.32.0,<1.33.0' + - 'bioconductor-summarizedexperiment >=1.14.0,<1.15.0' + - r-base + - r-e1071 + - r-forestplot + - r-ggally + - r-ggplot2 + - r-ggpubr + - r-pheatmap + - r-pracma + - r-quadprog + - r-r.utils + - r-rcolorbrewer + - r-survival +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: GPL-3 + summary: 'This package implements a machine learning-based classifier for the assignment of consensus molecular subtypes to TNBC samples. It also provides functions to summarize genomic and clinical characteristics.' + diff --git a/recipes/bioconductor-tnt/meta.yaml b/recipes/bioconductor-tnt/meta.yaml index 200b18bd17748..e6a62326dd6fe 100644 --- a/recipes/bioconductor-tnt/meta.yaml +++ b/recipes/bioconductor-tnt/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.4.0" %} +{% set version = "1.6.0" %} {% set name = "TnT" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: fe8a6e7598825b862f8fcba6bddebc71 + md5: 675d363f8421f4123ed82a93a774a6f7 build: number: 0 rpaths: @@ -20,22 +20,22 @@ build: # Suggests: GenomicFeatures, shiny, BiocManager, rmarkdown, testthat requirements: host: - - 'bioconductor-biobase >=2.42.0,<2.43.0' - - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' - - 'bioconductor-genomicranges >=1.34.0,<1.35.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' + - 'bioconductor-genomeinfodb >=1.20.0,<1.21.0' + - 'bioconductor-genomicranges >=1.36.0,<1.37.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' - r-base - r-data.table - r-htmlwidgets - r-jsonlite - r-knitr run: - - 'bioconductor-biobase >=2.42.0,<2.43.0' - - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' - - 'bioconductor-genomicranges >=1.34.0,<1.35.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' + - 'bioconductor-genomeinfodb >=1.20.0,<1.21.0' + - 'bioconductor-genomicranges >=1.36.0,<1.37.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' - r-base - r-data.table - r-htmlwidgets diff --git a/recipes/bioconductor-tofsims/meta.yaml b/recipes/bioconductor-tofsims/meta.yaml index 4a6846e9bd940..33a192295877f 100644 --- a/recipes/bioconductor-tofsims/meta.yaml +++ b/recipes/bioconductor-tofsims/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.10.1" %} +{% set version = "1.12.0" %} {% set name = "tofsims" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: c2dd08ba481e1d82632d1f7a33eda2c3 + md5: c755f0f4521b6d0d6ea6e8f113be7e14 build: number: 0 rpaths: @@ -19,7 +19,7 @@ build: # Suggests: EBImage, knitr, rmarkdown, testthat, tofsimsData, BiocParallel, RColorBrewer requirements: host: - - 'bioconductor-protgenerics >=1.14.0,<1.15.0' + - 'bioconductor-protgenerics >=1.16.0,<1.17.0' - r-als - r-base - r-chemometricswithr @@ -27,9 +27,8 @@ requirements: - 'r-rcpp >=0.11.2' - r-rcpparmadillo - r-signal - - openblas run: - - 'bioconductor-protgenerics >=1.14.0,<1.15.0' + - 'bioconductor-protgenerics >=1.16.0,<1.17.0' - r-als - r-base - r-chemometricswithr @@ -37,7 +36,6 @@ requirements: - 'r-rcpp >=0.11.2' - r-rcpparmadillo - r-signal - - openblas build: - {{ compiler('c') }} - {{ compiler('cxx') }} diff --git a/recipes/bioconductor-tofsimsdata/meta.yaml b/recipes/bioconductor-tofsimsdata/meta.yaml index 031f0fbcb6a9d..c60d60d7a9ce2 100644 --- a/recipes/bioconductor-tofsimsdata/meta.yaml +++ b/recipes/bioconductor-tofsimsdata/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.10.0" %} +{% set version = "1.12.0" %} {% set name = "tofsimsData" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 545622a01ba2067b1cf805f07367a83a + md5: 5d746a53346a01cbf016e711cc70bdd9 build: number: 0 rpaths: @@ -23,7 +23,7 @@ requirements: - r-base run: - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-tofsimsdata/post-link.sh b/recipes/bioconductor-tofsimsdata/post-link.sh index 4c5ae5383dd65..96523d3e21630 100644 --- a/recipes/bioconductor-tofsimsdata/post-link.sh +++ b/recipes/bioconductor-tofsimsdata/post-link.sh @@ -1,11 +1,11 @@ #!/bin/bash -FN="tofsimsData_1.10.0.tar.gz" +FN="tofsimsData_1.12.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/experiment/src/contrib/tofsimsData_1.10.0.tar.gz" - "https://bioarchive.galaxyproject.org/tofsimsData_1.10.0.tar.gz" - "https://depot.galaxyproject.org/software/bioconductor-tofsimsdata/bioconductor-tofsimsdata_1.10.0_src_all.tar.gz" + "https://bioconductor.org/packages/3.9/data/experiment/src/contrib/tofsimsData_1.12.0.tar.gz" + "https://bioarchive.galaxyproject.org/tofsimsData_1.12.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-tofsimsdata/bioconductor-tofsimsdata_1.12.0_src_all.tar.gz" ) -MD5="545622a01ba2067b1cf805f07367a83a" +MD5="5d746a53346a01cbf016e711cc70bdd9" # Use a staging area in the conda dir rather than temp dirs, both to avoid # permission issues as well as to have things downloaded in a predictable @@ -16,7 +16,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-tomatocdf/meta.yaml b/recipes/bioconductor-tomatocdf/meta.yaml index 6ba0bdc6e2879..8ff0fc5f157a8 100644 --- a/recipes/bioconductor-tomatocdf/meta.yaml +++ b/recipes/bioconductor-tomatocdf/meta.yaml @@ -1,6 +1,6 @@ {% set version = "2.18.0" %} {% set name = "tomatocdf" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -12,19 +12,19 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 200efc0637788d4bd3263fc9183c1aa6 build: - number: 1 + number: 2 rpaths: - lib/R/lib/ - lib/ noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' - r-base run: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-tomatocdf/post-link.sh b/recipes/bioconductor-tomatocdf/post-link.sh index 3fbf46a056613..57b5a541c7997 100644 --- a/recipes/bioconductor-tomatocdf/post-link.sh +++ b/recipes/bioconductor-tomatocdf/post-link.sh @@ -1,9 +1,10 @@ #!/bin/bash FN="tomatocdf_2.18.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/tomatocdf_2.18.0.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/tomatocdf_2.18.0.tar.gz" "https://bioarchive.galaxyproject.org/tomatocdf_2.18.0.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-tomatocdf/bioconductor-tomatocdf_2.18.0_src_all.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-tomatocdf/bioconductor-tomatocdf_2.18.0_src_all.tar.gz" ) MD5="200efc0637788d4bd3263fc9183c1aa6" @@ -16,7 +17,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-tomatoprobe/meta.yaml b/recipes/bioconductor-tomatoprobe/meta.yaml index bb918297ca172..6bab60ac466d6 100644 --- a/recipes/bioconductor-tomatoprobe/meta.yaml +++ b/recipes/bioconductor-tomatoprobe/meta.yaml @@ -1,6 +1,6 @@ {% set version = "2.18.0" %} {% set name = "tomatoprobe" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -12,19 +12,19 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 72020469f35c19399fd0be9eaffd8e77 build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' - r-base run: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-tomatoprobe/post-link.sh b/recipes/bioconductor-tomatoprobe/post-link.sh index 1755656e9498a..26e850320507d 100644 --- a/recipes/bioconductor-tomatoprobe/post-link.sh +++ b/recipes/bioconductor-tomatoprobe/post-link.sh @@ -1,9 +1,10 @@ #!/bin/bash FN="tomatoprobe_2.18.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/tomatoprobe_2.18.0.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/tomatoprobe_2.18.0.tar.gz" "https://bioarchive.galaxyproject.org/tomatoprobe_2.18.0.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-tomatoprobe/bioconductor-tomatoprobe_2.18.0_src_all.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-tomatoprobe/bioconductor-tomatoprobe_2.18.0_src_all.tar.gz" ) MD5="72020469f35c19399fd0be9eaffd8e77" @@ -16,7 +17,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-topaseq/meta.yaml b/recipes/bioconductor-topaseq/meta.yaml index e8dfc81a7a1a1..85052ce84015c 100644 --- a/recipes/bioconductor-topaseq/meta.yaml +++ b/recipes/bioconductor-topaseq/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.16.0" %} +{% set version = "1.17.1" %} {% set name = "ToPASeq" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 8282cfb442516b8e14e2b6a62c525a1d + md5: d415cab01425acafa7e6fa5a6d04544d build: number: 0 rpaths: @@ -19,13 +19,13 @@ build: # Suggests: BiocStyle, EnrichmentBrowser, airway, knitr, rmarkdown requirements: host: - - 'bioconductor-graph >=1.60.0,<1.61.0' - - 'bioconductor-graphite >=1.28.0,<1.29.0' + - 'bioconductor-graph >=1.62.0,<1.63.0' + - 'bioconductor-graphite >=1.30.0,<1.31.0' - r-base - r-rcpp run: - - 'bioconductor-graph >=1.60.0,<1.61.0' - - 'bioconductor-graphite >=1.28.0,<1.29.0' + - 'bioconductor-graph >=1.62.0,<1.63.0' + - 'bioconductor-graphite >=1.30.0,<1.31.0' - r-base - r-rcpp build: diff --git a/recipes/bioconductor-topconfects/build.sh b/recipes/bioconductor-topconfects/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-topconfects/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-topconfects/meta.yaml b/recipes/bioconductor-topconfects/meta.yaml new file mode 100644 index 0000000000000..abf687e732c3c --- /dev/null +++ b/recipes/bioconductor-topconfects/meta.yaml @@ -0,0 +1,37 @@ +{% set version = "1.0.0" %} +{% set name = "topconfects" %} +{% set bioc = "3.9" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + md5: ea5b0562970d893074b3f14aaf3d6275 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: limma, edgeR, DESeq2, NBPSeq, dplyr, testthat, knitr, rmarkdown, reshape2, tidyr, readr, org.At.tair.db, AnnotationDbi +requirements: + host: + - r-assertthat + - r-base + - r-ggplot2 + run: + - r-assertthat + - r-base + - r-ggplot2 +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: 'LGPL-2.1 | file LICENSE' + summary: 'Find the largest confident effect sizes from a large collection, while maintaining False Discovery Rate and False Coverage-statement Rate control. The main application is differential gene expression analysis, providing genes ranked in order of confident log2 fold change.' + diff --git a/recipes/bioconductor-topdownr/meta.yaml b/recipes/bioconductor-topdownr/meta.yaml index 2ed3e9d83f942..45fa7d1523a59 100644 --- a/recipes/bioconductor-topdownr/meta.yaml +++ b/recipes/bioconductor-topdownr/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.4.1" %} +{% set version = "1.6.0" %} {% set name = "topdownr" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,34 +10,34 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: adc072328cc05e4faf4523c59dd94ca7 + md5: 66c9aecc5aeda8dc3ba496326e1bf899 build: number: 0 rpaths: - lib/R/lib/ - lib/ noarch: generic -# Suggests: topdownrdata (>= 0.2), knitr, ranger, testthat, BiocStyle +# Suggests: topdownrdata (>= 0.2), knitr, ranger, testthat, BiocStyle, xml2 requirements: host: - - 'bioconductor-biobase >=2.42.0,<2.43.0' - - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' - - 'bioconductor-biostrings >=2.50.0,<2.51.0' - - 'bioconductor-msnbase >=2.8.0,<2.9.0' - - 'bioconductor-mzr >=2.16.0,<2.17.0' - - 'bioconductor-protgenerics >=1.14.0,<1.15.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' + - 'bioconductor-biocgenerics >=0.30.0,<0.31.0' + - 'bioconductor-biostrings >=2.52.0,<2.53.0' + - 'bioconductor-msnbase >=2.10.0,<2.11.0' + - 'bioconductor-mzr >=2.18.0,<2.19.0' + - 'bioconductor-protgenerics >=1.16.0,<1.17.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' - r-base - 'r-ggplot2 >=2.2.1' - 'r-matrix >=1.2.10' run: - - 'bioconductor-biobase >=2.42.0,<2.43.0' - - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' - - 'bioconductor-biostrings >=2.50.0,<2.51.0' - - 'bioconductor-msnbase >=2.8.0,<2.9.0' - - 'bioconductor-mzr >=2.16.0,<2.17.0' - - 'bioconductor-protgenerics >=1.14.0,<1.15.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' + - 'bioconductor-biocgenerics >=0.30.0,<0.31.0' + - 'bioconductor-biostrings >=2.52.0,<2.53.0' + - 'bioconductor-msnbase >=2.10.0,<2.11.0' + - 'bioconductor-mzr >=2.18.0,<2.19.0' + - 'bioconductor-protgenerics >=1.16.0,<1.17.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' - r-base - 'r-ggplot2 >=2.2.1' - 'r-matrix >=1.2.10' diff --git a/recipes/bioconductor-topdownrdata/meta.yaml b/recipes/bioconductor-topdownrdata/meta.yaml index 83730fe5c2441..51048c308e845 100644 --- a/recipes/bioconductor-topdownrdata/meta.yaml +++ b/recipes/bioconductor-topdownrdata/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.4.0" %} +{% set version = "1.6.0" %} {% set name = "topdownrdata" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 2e25621bd796b78859795b7f5158a289 + md5: 4d7e386274b91c3c71ab578ee607b393 build: number: 0 rpaths: @@ -19,12 +19,12 @@ build: noarch: generic requirements: host: - - 'bioconductor-topdownr >=1.4.0,<1.5.0' + - 'bioconductor-topdownr >=1.6.0,<1.7.0' - r-base run: - - 'bioconductor-topdownr >=1.4.0,<1.5.0' + - 'bioconductor-topdownr >=1.6.0,<1.7.0' - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-topdownrdata/post-link.sh b/recipes/bioconductor-topdownrdata/post-link.sh index 8a905529e3e13..3fe92c61c802a 100644 --- a/recipes/bioconductor-topdownrdata/post-link.sh +++ b/recipes/bioconductor-topdownrdata/post-link.sh @@ -1,11 +1,11 @@ #!/bin/bash -FN="topdownrdata_1.4.0.tar.gz" +FN="topdownrdata_1.6.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/experiment/src/contrib/topdownrdata_1.4.0.tar.gz" - "https://bioarchive.galaxyproject.org/topdownrdata_1.4.0.tar.gz" - "https://depot.galaxyproject.org/software/bioconductor-topdownrdata/bioconductor-topdownrdata_1.4.0_src_all.tar.gz" + "https://bioconductor.org/packages/3.9/data/experiment/src/contrib/topdownrdata_1.6.0.tar.gz" + "https://bioarchive.galaxyproject.org/topdownrdata_1.6.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-topdownrdata/bioconductor-topdownrdata_1.6.0_src_all.tar.gz" ) -MD5="2e25621bd796b78859795b7f5158a289" +MD5="4d7e386274b91c3c71ab578ee607b393" # Use a staging area in the conda dir rather than temp dirs, both to avoid # permission issues as well as to have things downloaded in a predictable @@ -16,7 +16,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-topgo/meta.yaml b/recipes/bioconductor-topgo/meta.yaml index 36e71c90000c4..4927e2e8bc3c9 100644 --- a/recipes/bioconductor-topgo/meta.yaml +++ b/recipes/bioconductor-topgo/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "2.34.0" %} +{% set version = "2.36.0" %} {% set name = "topGO" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: c46fdfda730504443c46c4b4bed95f00 + md5: 1f8b5fde4b87b14b275958ec40712a79 build: number: 0 rpaths: @@ -20,22 +20,22 @@ build: # Suggests: ALL, hgu95av2.db, hgu133a.db, genefilter, xtable, multtest, Rgraphviz, globaltest requirements: host: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' - - 'bioconductor-biobase >=2.42.0,<2.43.0' - - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' - - 'bioconductor-go.db >=3.7.0,<3.8.0' - - 'bioconductor-graph >=1.60.0,<1.61.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' + - 'bioconductor-biocgenerics >=0.30.0,<0.31.0' + - 'bioconductor-go.db >=3.8.0,<3.9.0' + - 'bioconductor-graph >=1.62.0,<1.63.0' - r-base - r-dbi - r-lattice - r-matrixstats - 'r-sparsem >=0.73' run: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' - - 'bioconductor-biobase >=2.42.0,<2.43.0' - - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' - - 'bioconductor-go.db >=3.7.0,<3.8.0' - - 'bioconductor-graph >=1.60.0,<1.61.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' + - 'bioconductor-biocgenerics >=0.30.0,<0.31.0' + - 'bioconductor-go.db >=3.8.0,<3.9.0' + - 'bioconductor-graph >=1.62.0,<1.63.0' - r-base - r-dbi - r-lattice diff --git a/recipes/bioconductor-tpp/meta.yaml b/recipes/bioconductor-tpp/meta.yaml index 127b54c5de790..0b442bfe2312a 100644 --- a/recipes/bioconductor-tpp/meta.yaml +++ b/recipes/bioconductor-tpp/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "3.10.1" %} +{% set version = "3.12.0" %} {% set name = "TPP" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: 371ca1635525c7045aa2990f90813b72252f519c3d0db115bc85fcaa3eec2e03 + md5: 79841b7f3c13fccd119c8d6d53961859 build: number: 0 rpaths: @@ -20,9 +20,9 @@ build: # Suggests: BiocStyle, testthat requirements: host: - - 'bioconductor-biobase >=2.42.0,<2.43.0' - - 'bioconductor-biobroom >=1.14.0,<1.15.0' - - 'bioconductor-limma >=3.38.0,<3.39.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' + - 'bioconductor-biobroom >=1.16.0,<1.17.0' + - 'bioconductor-limma >=3.40.0,<3.41.0' - r-base - r-broom - r-data.table @@ -50,9 +50,9 @@ requirements: - r-venndiagram - r-vgam run: - - 'bioconductor-biobase >=2.42.0,<2.43.0' - - 'bioconductor-biobroom >=1.14.0,<1.15.0' - - 'bioconductor-limma >=3.38.0,<3.39.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' + - 'bioconductor-biobroom >=1.16.0,<1.17.0' + - 'bioconductor-limma >=3.40.0,<3.41.0' - r-base - r-broom - r-data.table diff --git a/recipes/bioconductor-tpp2d/build.sh b/recipes/bioconductor-tpp2d/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-tpp2d/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-tpp2d/meta.yaml b/recipes/bioconductor-tpp2d/meta.yaml new file mode 100644 index 0000000000000..5c3824132bf58 --- /dev/null +++ b/recipes/bioconductor-tpp2d/meta.yaml @@ -0,0 +1,49 @@ +{% set version = "1.0.0" %} +{% set name = "TPP2D" %} +{% set bioc = "3.9" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: 247c693ff556cb10fdd97ec017becfd0 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: knitr, testthat +requirements: + host: + - r-base + - r-doparallel + - r-dplyr + - r-foreach + - r-ggplot2 + - r-openxlsx + - r-rcurl + - r-stringr + - r-tidyr + run: + - r-base + - r-doparallel + - r-dplyr + - r-foreach + - r-ggplot2 + - r-openxlsx + - r-rcurl + - r-stringr + - r-tidyr +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: GPL-3 + summary: 'FDR-controlled analysis of 2D-TPP experiments by functional analysis of dose-response curves across temperatures.' + diff --git a/recipes/bioconductor-tracktables/meta.yaml b/recipes/bioconductor-tracktables/meta.yaml index e2183d3479dde..21f7e41412422 100644 --- a/recipes/bioconductor-tracktables/meta.yaml +++ b/recipes/bioconductor-tracktables/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.16.0" %} +{% set version = "1.18.0" %} {% set name = "tracktables" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 838950811dd0ae1fc902181f7ecca4ab + md5: 27834eb1c38a78d2b4a18110bc8c89cc build: number: 0 rpaths: @@ -20,20 +20,20 @@ build: # Suggests: knitr, BiocStyle requirements: host: - - 'bioconductor-genomicranges >=1.34.0,<1.35.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-rsamtools >=1.34.0,<1.35.0' - - 'bioconductor-xvector >=0.22.0,<0.23.0' + - 'bioconductor-genomicranges >=1.36.0,<1.37.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-rsamtools >=2.0.0,<2.1.0' + - 'bioconductor-xvector >=0.24.0,<0.25.0' - r-base - r-rcolorbrewer - r-stringr - r-tractor.base - r-xml run: - - 'bioconductor-genomicranges >=1.34.0,<1.35.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-rsamtools >=1.34.0,<1.35.0' - - 'bioconductor-xvector >=0.22.0,<0.23.0' + - 'bioconductor-genomicranges >=1.36.0,<1.37.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-rsamtools >=2.0.0,<2.1.0' + - 'bioconductor-xvector >=0.24.0,<0.25.0' - r-base - r-rcolorbrewer - r-stringr diff --git a/recipes/bioconductor-trackviewer/meta.yaml b/recipes/bioconductor-trackviewer/meta.yaml index 2a18bc9a27485..6f162bb963fd6 100644 --- a/recipes/bioconductor-trackviewer/meta.yaml +++ b/recipes/bioconductor-trackviewer/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.18.0" %} +{% set version = "1.20.0" %} {% set name = "trackViewer" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,9 +10,9 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 35615fefb813c4b05703a35cc04a7ea2 + md5: 6d3b3a677e7eb18db075666246bad4b4 build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ @@ -20,40 +20,40 @@ build: # Suggests: biomaRt, TxDb.Hsapiens.UCSC.hg19.knownGene, RUnit, org.Hs.eg.db, BiocStyle, knitr, VariantAnnotation requirements: host: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' - - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' - - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' - - 'bioconductor-genomicalignments >=1.18.0,<1.19.0' - - 'bioconductor-genomicfeatures >=1.34.0,<1.35.0' - - 'bioconductor-genomicranges >=1.34.0,<1.35.0' - - 'bioconductor-graph >=1.60.0,<1.61.0' - - 'bioconductor-gviz >=1.26.0,<1.27.0' - - 'bioconductor-interactionset >=1.10.0,<1.11.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-rgraphviz >=2.26.0,<2.27.0' - - 'bioconductor-rsamtools >=1.34.0,<1.35.0' - - 'bioconductor-rtracklayer >=1.42.0,<1.43.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' + - 'bioconductor-biocgenerics >=0.30.0,<0.31.0' + - 'bioconductor-genomeinfodb >=1.20.0,<1.21.0' + - 'bioconductor-genomicalignments >=1.20.0,<1.21.0' + - 'bioconductor-genomicfeatures >=1.36.0,<1.37.0' + - 'bioconductor-genomicranges >=1.36.0,<1.37.0' + - 'bioconductor-graph >=1.62.0,<1.63.0' + - 'bioconductor-gviz >=1.28.0,<1.29.0' + - 'bioconductor-interactionset >=1.12.0,<1.13.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-rgraphviz >=2.28.0,<2.29.0' + - 'bioconductor-rsamtools >=2.0.0,<2.1.0' + - 'bioconductor-rtracklayer >=1.44.0,<1.45.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' - r-base - r-grimport - r-htmlwidgets - r-plotrix - r-scales run: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' - - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' - - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' - - 'bioconductor-genomicalignments >=1.18.0,<1.19.0' - - 'bioconductor-genomicfeatures >=1.34.0,<1.35.0' - - 'bioconductor-genomicranges >=1.34.0,<1.35.0' - - 'bioconductor-graph >=1.60.0,<1.61.0' - - 'bioconductor-gviz >=1.26.0,<1.27.0' - - 'bioconductor-interactionset >=1.10.0,<1.11.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-rgraphviz >=2.26.0,<2.27.0' - - 'bioconductor-rsamtools >=1.34.0,<1.35.0' - - 'bioconductor-rtracklayer >=1.42.0,<1.43.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' + - 'bioconductor-biocgenerics >=0.30.0,<0.31.0' + - 'bioconductor-genomeinfodb >=1.20.0,<1.21.0' + - 'bioconductor-genomicalignments >=1.20.0,<1.21.0' + - 'bioconductor-genomicfeatures >=1.36.0,<1.37.0' + - 'bioconductor-genomicranges >=1.36.0,<1.37.0' + - 'bioconductor-graph >=1.62.0,<1.63.0' + - 'bioconductor-gviz >=1.28.0,<1.29.0' + - 'bioconductor-interactionset >=1.12.0,<1.13.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-rgraphviz >=2.28.0,<2.29.0' + - 'bioconductor-rsamtools >=2.0.0,<2.1.0' + - 'bioconductor-rtracklayer >=1.44.0,<1.45.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' - r-base - r-grimport - r-htmlwidgets diff --git a/recipes/bioconductor-transcriptogramer/meta.yaml b/recipes/bioconductor-transcriptogramer/meta.yaml index 06fc840350fb5..6fb355a5d160b 100644 --- a/recipes/bioconductor-transcriptogramer/meta.yaml +++ b/recipes/bioconductor-transcriptogramer/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.4.1" %} +{% set version = "1.6.0" %} {% set name = "transcriptogramer" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: f47441df0de365c755ad232153eb8082 + md5: a41827768111c0fd7ef4e0345d7dbd11 build: number: 0 rpaths: @@ -21,10 +21,10 @@ build: # SystemRequirements: Java Runtime Environment (>= 6) requirements: host: - - 'bioconductor-biomart >=2.38.0,<2.39.0' - - 'bioconductor-limma >=3.38.0,<3.39.0' - - 'bioconductor-reder >=1.30.0,<1.31.0' - - 'bioconductor-topgo >=2.34.0,<2.35.0' + - 'bioconductor-biomart >=2.40.0,<2.41.0' + - 'bioconductor-limma >=3.40.0,<3.41.0' + - 'bioconductor-reder >=1.32.0,<1.33.0' + - 'bioconductor-topgo >=2.36.0,<2.37.0' - r-base - r-data.table - r-dosnow @@ -34,11 +34,12 @@ requirements: - r-progress - r-snow - r-tidyr + - openjdk 8.* run: - - 'bioconductor-biomart >=2.38.0,<2.39.0' - - 'bioconductor-limma >=3.38.0,<3.39.0' - - 'bioconductor-reder >=1.30.0,<1.31.0' - - 'bioconductor-topgo >=2.34.0,<2.35.0' + - 'bioconductor-biomart >=2.40.0,<2.41.0' + - 'bioconductor-limma >=3.40.0,<3.41.0' + - 'bioconductor-reder >=1.32.0,<1.33.0' + - 'bioconductor-topgo >=2.36.0,<2.37.0' - r-base - r-data.table - r-dosnow @@ -48,6 +49,7 @@ requirements: - r-progress - r-snow - r-tidyr + - openjdk 8.* test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-transcriptr/meta.yaml b/recipes/bioconductor-transcriptr/meta.yaml index 57d2d42950ce7..6bf3c5b9eb5a2 100644 --- a/recipes/bioconductor-transcriptr/meta.yaml +++ b/recipes/bioconductor-transcriptr/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.10.0" %} +{% set version = "1.12.0" %} {% set name = "transcriptR" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 5679fd797416d2b8b93daa5cf72acb27 + md5: 2e6fb8d3922b8fa74f382f35027e0ad5 build: number: 0 rpaths: @@ -20,16 +20,16 @@ build: # Suggests: BiocStyle, knitr, rmarkdown, TxDb.Hsapiens.UCSC.hg19.knownGene, testthat requirements: host: - - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' - - 'bioconductor-chipseq >=1.32.0,<1.33.0' - - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' - - 'bioconductor-genomicalignments >=1.18.0,<1.19.0' - - 'bioconductor-genomicfeatures >=1.34.0,<1.35.0' - - 'bioconductor-genomicranges >=1.34.0,<1.35.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-rsamtools >=1.34.0,<1.35.0' - - 'bioconductor-rtracklayer >=1.42.0,<1.43.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-biocgenerics >=0.30.0,<0.31.0' + - 'bioconductor-chipseq >=1.34.0,<1.35.0' + - 'bioconductor-genomeinfodb >=1.20.0,<1.21.0' + - 'bioconductor-genomicalignments >=1.20.0,<1.21.0' + - 'bioconductor-genomicfeatures >=1.36.0,<1.37.0' + - 'bioconductor-genomicranges >=1.36.0,<1.37.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-rsamtools >=2.0.0,<2.1.0' + - 'bioconductor-rtracklayer >=1.44.0,<1.45.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' - r-base - r-caret - r-e1071 @@ -37,16 +37,16 @@ requirements: - r-proc - r-reshape2 run: - - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' - - 'bioconductor-chipseq >=1.32.0,<1.33.0' - - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' - - 'bioconductor-genomicalignments >=1.18.0,<1.19.0' - - 'bioconductor-genomicfeatures >=1.34.0,<1.35.0' - - 'bioconductor-genomicranges >=1.34.0,<1.35.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-rsamtools >=1.34.0,<1.35.0' - - 'bioconductor-rtracklayer >=1.42.0,<1.43.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-biocgenerics >=0.30.0,<0.31.0' + - 'bioconductor-chipseq >=1.34.0,<1.35.0' + - 'bioconductor-genomeinfodb >=1.20.0,<1.21.0' + - 'bioconductor-genomicalignments >=1.20.0,<1.21.0' + - 'bioconductor-genomicfeatures >=1.36.0,<1.37.0' + - 'bioconductor-genomicranges >=1.36.0,<1.37.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-rsamtools >=2.0.0,<2.1.0' + - 'bioconductor-rtracklayer >=1.44.0,<1.45.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' - r-base - r-caret - r-e1071 diff --git a/recipes/bioconductor-transite/meta.yaml b/recipes/bioconductor-transite/meta.yaml index 4acb9da24c1cb..6a00111654221 100644 --- a/recipes/bioconductor-transite/meta.yaml +++ b/recipes/bioconductor-transite/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.0.1" %} +{% set version = "1.2.0" %} {% set name = "transite" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 3ea8de97f52ef44e0e45d27f81a95ee2 + md5: a639bc024ae0cbb702b2863c7825a948 build: number: 0 rpaths: @@ -20,9 +20,9 @@ build: # SystemRequirements: C++11 requirements: host: - - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' - - 'bioconductor-biostrings >=2.50.0,<2.51.0' - - 'bioconductor-genomicranges >=1.34.0,<1.35.0' + - 'bioconductor-biocgenerics >=0.30.0,<0.31.0' + - 'bioconductor-biostrings >=2.52.0,<2.53.0' + - 'bioconductor-genomicranges >=1.36.0,<1.37.0' - r-base - 'r-dplyr >=0.7.6' - 'r-ggplot2 >=3.0.0' @@ -32,9 +32,9 @@ requirements: - 'r-scales >=1.0.0' - 'r-tfmpvalue >=0.0.8' run: - - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' - - 'bioconductor-biostrings >=2.50.0,<2.51.0' - - 'bioconductor-genomicranges >=1.34.0,<1.35.0' + - 'bioconductor-biocgenerics >=0.30.0,<0.31.0' + - 'bioconductor-biostrings >=2.52.0,<2.53.0' + - 'bioconductor-genomicranges >=1.36.0,<1.37.0' - r-base - 'r-dplyr >=0.7.6' - 'r-ggplot2 >=3.0.0' diff --git a/recipes/bioconductor-translatome/meta.yaml b/recipes/bioconductor-translatome/meta.yaml index b6c5782caaefa..a1d2f5fed005d 100644 --- a/recipes/bioconductor-translatome/meta.yaml +++ b/recipes/bioconductor-translatome/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.20.0" %} +{% set version = "1.22.0" %} {% set name = "tRanslatome" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: b426345db745c8c6e163c2a6a15a533e + md5: a134a291903997bd6feeb71756a0164b build: number: 0 rpaths: @@ -19,32 +19,32 @@ build: noarch: generic requirements: host: - - 'bioconductor-anota >=1.30.0,<1.31.0' - - 'bioconductor-biobase >=2.42.0,<2.43.0' - - 'bioconductor-deseq >=1.34.0,<1.35.0' - - 'bioconductor-edger >=3.24.0,<3.25.0' - - 'bioconductor-gosemsim >=2.8.0,<2.9.0' - - 'bioconductor-heatplus >=2.28.0,<2.29.0' - - 'bioconductor-limma >=3.38.0,<3.39.0' - - 'bioconductor-org.hs.eg.db >=3.7.0,<3.8.0' - - 'bioconductor-rankprod >=3.8.0,<3.9.0' - - 'bioconductor-sigpathway >=1.50.0,<1.51.0' - - 'bioconductor-topgo >=2.34.0,<2.35.0' + - 'bioconductor-anota >=1.32.0,<1.33.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' + - 'bioconductor-deseq >=1.36.0,<1.37.0' + - 'bioconductor-edger >=3.26.0,<3.27.0' + - 'bioconductor-gosemsim >=2.10.0,<2.11.0' + - 'bioconductor-heatplus >=2.30.0,<2.31.0' + - 'bioconductor-limma >=3.40.0,<3.41.0' + - 'bioconductor-org.hs.eg.db >=3.8.0,<3.9.0' + - 'bioconductor-rankprod >=3.10.0,<3.11.0' + - 'bioconductor-sigpathway >=1.52.0,<1.53.0' + - 'bioconductor-topgo >=2.36.0,<2.37.0' - r-base - r-gplots - r-plotrix run: - - 'bioconductor-anota >=1.30.0,<1.31.0' - - 'bioconductor-biobase >=2.42.0,<2.43.0' - - 'bioconductor-deseq >=1.34.0,<1.35.0' - - 'bioconductor-edger >=3.24.0,<3.25.0' - - 'bioconductor-gosemsim >=2.8.0,<2.9.0' - - 'bioconductor-heatplus >=2.28.0,<2.29.0' - - 'bioconductor-limma >=3.38.0,<3.39.0' - - 'bioconductor-org.hs.eg.db >=3.7.0,<3.8.0' - - 'bioconductor-rankprod >=3.8.0,<3.9.0' - - 'bioconductor-sigpathway >=1.50.0,<1.51.0' - - 'bioconductor-topgo >=2.34.0,<2.35.0' + - 'bioconductor-anota >=1.32.0,<1.33.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' + - 'bioconductor-deseq >=1.36.0,<1.37.0' + - 'bioconductor-edger >=3.26.0,<3.27.0' + - 'bioconductor-gosemsim >=2.10.0,<2.11.0' + - 'bioconductor-heatplus >=2.30.0,<2.31.0' + - 'bioconductor-limma >=3.40.0,<3.41.0' + - 'bioconductor-org.hs.eg.db >=3.8.0,<3.9.0' + - 'bioconductor-rankprod >=3.10.0,<3.11.0' + - 'bioconductor-sigpathway >=1.52.0,<1.53.0' + - 'bioconductor-topgo >=2.36.0,<2.37.0' - r-base - r-gplots - r-plotrix diff --git a/recipes/bioconductor-transview/meta.yaml b/recipes/bioconductor-transview/meta.yaml index 7a4305dbe0195..47a904f809754 100644 --- a/recipes/bioconductor-transview/meta.yaml +++ b/recipes/bioconductor-transview/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.26.0" %} +{% set version = "1.28.0" %} {% set name = "TransView" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 88fdd4448b4e7c5d8b6e434e1079134f + md5: c572af7e22e6181d79bf7d59c3a8fe56 build: number: 0 rpaths: @@ -19,21 +19,21 @@ build: # Suggests: RUnit, pasillaBamSubset, BiocManager requirements: host: - - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' - - 'bioconductor-genomicranges >=1.34.0,<1.35.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-rsamtools >=1.34.0,<1.35.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' - - 'bioconductor-zlibbioc >=1.28.0,<1.29.0' + - 'bioconductor-biocgenerics >=0.30.0,<0.31.0' + - 'bioconductor-genomicranges >=1.36.0,<1.37.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-rhtslib >=1.16.0,<1.17.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' + - 'bioconductor-zlibbioc >=1.30.0,<1.31.0' - r-base - r-gplots run: - - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' - - 'bioconductor-genomicranges >=1.34.0,<1.35.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-rsamtools >=1.34.0,<1.35.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' - - 'bioconductor-zlibbioc >=1.28.0,<1.29.0' + - 'bioconductor-biocgenerics >=0.30.0,<0.31.0' + - 'bioconductor-genomicranges >=1.36.0,<1.37.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-rhtslib >=1.16.0,<1.17.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' + - 'bioconductor-zlibbioc >=1.30.0,<1.31.0' - r-base - r-gplots build: diff --git a/recipes/bioconductor-traser/meta.yaml b/recipes/bioconductor-traser/meta.yaml index 675f32fd398a6..ebe688a991764 100644 --- a/recipes/bioconductor-traser/meta.yaml +++ b/recipes/bioconductor-traser/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.12.0" %} +{% set version = "1.14.0" %} {% set name = "traseR" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: bcd587ebb46cd8b95863d9e31fe95bbc + md5: 8e936f90626d084548bd4e448de29c8a build: number: 0 rpaths: @@ -21,13 +21,13 @@ build: requirements: host: - 'bioconductor-bsgenome.hsapiens.ucsc.hg19 >=1.4.0,<1.5.0' - - 'bioconductor-genomicranges >=1.34.0,<1.35.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-genomicranges >=1.36.0,<1.37.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' - r-base run: - 'bioconductor-bsgenome.hsapiens.ucsc.hg19 >=1.4.0,<1.5.0' - - 'bioconductor-genomicranges >=1.34.0,<1.35.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-genomicranges >=1.36.0,<1.37.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' - r-base test: commands: diff --git a/recipes/bioconductor-treeio/meta.yaml b/recipes/bioconductor-treeio/meta.yaml index f0ccbf306123e..dd64f21ec0cf9 100644 --- a/recipes/bioconductor-treeio/meta.yaml +++ b/recipes/bioconductor-treeio/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.6.2" %} +{% set version = "1.8.0" %} {% set name = "treeio" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,14 +10,14 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - sha256: 4c287e7376142745ccc1130bab3a63181fb7b1c1b5422b3423097f8fea907e3b + md5: 5e3a23b2ce89217a8ce5a1b1ff6a13b1 build: number: 0 rpaths: - lib/R/lib/ - lib/ noarch: generic -# Suggests: ggplot2, ggtree, knitr, prettydoc, testthat, tidyr +# Suggests: Biostrings, ggplot2, ggtree, knitr, phangorn, prettydoc, testthat, tidyr requirements: host: - r-ape @@ -26,9 +26,8 @@ requirements: - r-jsonlite - r-magrittr - r-rlang - - r-rvcheck - r-tibble - - 'r-tidytree >=0.1.7' + - 'r-tidytree >=0.2.3' run: - r-ape - r-base @@ -36,9 +35,8 @@ requirements: - r-jsonlite - r-magrittr - r-rlang - - r-rvcheck - r-tibble - - 'r-tidytree >=0.1.7' + - 'r-tidytree >=0.2.3' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-treesummarizedexperiment/build.sh b/recipes/bioconductor-treesummarizedexperiment/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-treesummarizedexperiment/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-treesummarizedexperiment/meta.yaml b/recipes/bioconductor-treesummarizedexperiment/meta.yaml new file mode 100644 index 0000000000000..8e2092071895b --- /dev/null +++ b/recipes/bioconductor-treesummarizedexperiment/meta.yaml @@ -0,0 +1,43 @@ +{% set version = "1.0.0" %} +{% set name = "TreeSummarizedExperiment" %} +{% set bioc = "3.9" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: 494e83b65a63c0d6e989ef41c36c87a6 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: ggtree, BiocStyle, knitr, rmarkdown, testthat +requirements: + host: + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' + - 'bioconductor-singlecellexperiment >=1.6.0,<1.7.0' + - 'bioconductor-summarizedexperiment >=1.14.0,<1.15.0' + - r-ape + - r-base + - r-dplyr + run: + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' + - 'bioconductor-singlecellexperiment >=1.6.0,<1.7.0' + - 'bioconductor-summarizedexperiment >=1.14.0,<1.15.0' + - r-ape + - r-base + - r-dplyr +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: 'GPL (>=2)' + summary: 'TreeSummarizedExperiment has extended SingleCellExperiment to include hierarchical information on the rows or columns of the rectangular data.' + diff --git a/recipes/bioconductor-trena/meta.yaml b/recipes/bioconductor-trena/meta.yaml index 32fd5eb3166fc..57b76af8db6f5 100644 --- a/recipes/bioconductor-trena/meta.yaml +++ b/recipes/bioconductor-trena/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.4.2" %} +{% set version = "1.6.0" %} {% set name = "trena" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 2860c7d847193071a608d566bcccf9ba + md5: 389c9ee53787c760bddf50a2ca5e75c4 build: number: 0 rpaths: @@ -20,48 +20,48 @@ build: # Suggests: RUnit, plyr, knitr, BiocGenerics, rmarkdown requirements: host: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' - - 'bioconductor-biocparallel >=1.16.0,<1.17.0' - - 'bioconductor-biomart >=2.38.0,<2.39.0' - - 'bioconductor-biostrings >=2.50.0,<2.51.0' - - 'bioconductor-bsgenome >=1.50.0,<1.51.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' + - 'bioconductor-biocparallel >=1.18.0,<1.19.0' + - 'bioconductor-biomart >=2.40.0,<2.41.0' + - 'bioconductor-biostrings >=2.52.0,<2.53.0' + - 'bioconductor-bsgenome >=1.52.0,<1.53.0' - 'bioconductor-bsgenome.hsapiens.ucsc.hg19 >=1.4.0,<1.5.0' - 'bioconductor-bsgenome.hsapiens.ucsc.hg38 >=1.4.0,<1.5.0' - 'bioconductor-bsgenome.mmusculus.ucsc.mm10 >=1.4.0,<1.5.0' - - 'bioconductor-genomicranges >=1.34.0,<1.35.0' - - 'bioconductor-motifdb >=1.24.0,<1.25.0' - - 'bioconductor-org.hs.eg.db >=3.7.0,<3.8.0' - - 'bioconductor-snplocs.hsapiens.dbsnp150.grch38 >=0.99.0,<0.100.0' + - 'bioconductor-genomicranges >=1.36.0,<1.37.0' + - 'bioconductor-motifdb >=1.26.0,<1.27.0' + - 'bioconductor-org.hs.eg.db >=3.8.0,<3.9.0' + - 'bioconductor-snplocs.hsapiens.dbsnp150.grch38 >=1.0.0,<1.1.0' - r-base - r-dbi - r-flare - 'r-glmnet >=2.0.3' - r-lassopv - r-randomforest - - r-rmariadb + - r-rmysql - r-rpostgresql - r-rsqlite - r-vbsr run: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' - - 'bioconductor-biocparallel >=1.16.0,<1.17.0' - - 'bioconductor-biomart >=2.38.0,<2.39.0' - - 'bioconductor-biostrings >=2.50.0,<2.51.0' - - 'bioconductor-bsgenome >=1.50.0,<1.51.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' + - 'bioconductor-biocparallel >=1.18.0,<1.19.0' + - 'bioconductor-biomart >=2.40.0,<2.41.0' + - 'bioconductor-biostrings >=2.52.0,<2.53.0' + - 'bioconductor-bsgenome >=1.52.0,<1.53.0' - 'bioconductor-bsgenome.hsapiens.ucsc.hg19 >=1.4.0,<1.5.0' - 'bioconductor-bsgenome.hsapiens.ucsc.hg38 >=1.4.0,<1.5.0' - 'bioconductor-bsgenome.mmusculus.ucsc.mm10 >=1.4.0,<1.5.0' - - 'bioconductor-genomicranges >=1.34.0,<1.35.0' - - 'bioconductor-motifdb >=1.24.0,<1.25.0' - - 'bioconductor-org.hs.eg.db >=3.7.0,<3.8.0' - - 'bioconductor-snplocs.hsapiens.dbsnp150.grch38 >=0.99.0,<0.100.0' + - 'bioconductor-genomicranges >=1.36.0,<1.37.0' + - 'bioconductor-motifdb >=1.26.0,<1.27.0' + - 'bioconductor-org.hs.eg.db >=3.8.0,<3.9.0' + - 'bioconductor-snplocs.hsapiens.dbsnp150.grch38 >=1.0.0,<1.1.0' - r-base - r-dbi - r-flare - 'r-glmnet >=2.0.3' - r-lassopv - r-randomforest - - r-rmariadb + - r-rmysql - r-rpostgresql - r-rsqlite - r-vbsr diff --git a/recipes/bioconductor-trendy/meta.yaml b/recipes/bioconductor-trendy/meta.yaml index ac8ba8cef7a53..509a7b670655f 100644 --- a/recipes/bioconductor-trendy/meta.yaml +++ b/recipes/bioconductor-trendy/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.4.4" %} +{% set version = "1.6.0" %} {% set name = "Trendy" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: b241eb53098d304f8aea824ded380e36 + md5: a19522e1b2b5bd88ab336d11d6c763ab build: number: 0 rpaths: @@ -20,9 +20,9 @@ build: # Suggests: BiocStyle, knitr, rmarkdown, devtools requirements: host: - - 'bioconductor-biocparallel >=1.16.0,<1.17.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' - - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' + - 'bioconductor-biocparallel >=1.18.0,<1.19.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' + - 'bioconductor-summarizedexperiment >=1.14.0,<1.15.0' - r-base - r-dt - r-gplots @@ -31,9 +31,9 @@ requirements: - r-shiny - r-shinyfiles run: - - 'bioconductor-biocparallel >=1.16.0,<1.17.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' - - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' + - 'bioconductor-biocparallel >=1.18.0,<1.19.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' + - 'bioconductor-summarizedexperiment >=1.14.0,<1.15.0' - r-base - r-dt - r-gplots diff --git a/recipes/bioconductor-triform/meta.yaml b/recipes/bioconductor-triform/meta.yaml index 3a3d8e75cee3e..63237e161a186 100644 --- a/recipes/bioconductor-triform/meta.yaml +++ b/recipes/bioconductor-triform/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.24.0" %} +{% set version = "1.26.0" %} {% set name = "triform" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 5d97100c4ecccc587a7c339338499e6a + md5: 61db5830197b876cd9d640bcd7a03f40 build: number: 0 rpaths: @@ -20,13 +20,13 @@ build: # Suggests: RUnit requirements: host: - - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-biocgenerics >=0.30.0,<0.31.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' - r-base - r-yaml run: - - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-biocgenerics >=0.30.0,<0.31.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' - r-base - r-yaml test: diff --git a/recipes/bioconductor-trigger/meta.yaml b/recipes/bioconductor-trigger/meta.yaml index 6f39bd91a7fb6..247441588e653 100644 --- a/recipes/bioconductor-trigger/meta.yaml +++ b/recipes/bioconductor-trigger/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.28.0" %} +{% set version = "1.30.0" %} {% set name = "trigger" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 26b0b707b709215845adcd78059c142f + md5: e9d1aef5130094557987635cbe0e2a63 build: number: 0 rpaths: @@ -18,14 +18,14 @@ build: - lib/ requirements: host: - - 'bioconductor-qvalue >=2.14.0,<2.15.0' - - 'bioconductor-sva >=3.30.0,<3.31.0' + - 'bioconductor-qvalue >=2.16.0,<2.17.0' + - 'bioconductor-sva >=3.32.0,<3.33.0' - r-base - r-corpcor - r-qtl run: - - 'bioconductor-qvalue >=2.14.0,<2.15.0' - - 'bioconductor-sva >=3.30.0,<3.31.0' + - 'bioconductor-qvalue >=2.16.0,<2.17.0' + - 'bioconductor-sva >=3.32.0,<3.33.0' - r-base - r-corpcor - r-qtl diff --git a/recipes/bioconductor-trio/meta.yaml b/recipes/bioconductor-trio/meta.yaml index 437f1cb79d8ed..366d1c53f224d 100644 --- a/recipes/bioconductor-trio/meta.yaml +++ b/recipes/bioconductor-trio/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "3.20.0" %} +{% set version = "3.22.0" %} {% set name = "trio" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,19 +10,25 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 742ef152b1d4cd230c557dba4bd308a8 + md5: 05513e6f64ed404eba923616608254ff build: number: 0 rpaths: - lib/R/lib/ - lib/ noarch: generic -# Suggests: survival, haplo.stats, mcbiopi, siggenes, splines, LogicReg (>= 1.5.3), logicFS (>= 1.28.1), KernSmooth, VariantAnnotation +# Suggests: haplo.stats, mcbiopi, splines, logicFS (>= 1.28.1), KernSmooth, VariantAnnotation requirements: host: + - 'bioconductor-siggenes >=1.58.0,<1.59.0' - r-base + - 'r-logicreg >=1.5.3' + - r-survival run: + - 'bioconductor-siggenes >=1.58.0,<1.59.0' - r-base + - 'r-logicreg >=1.5.3' + - r-survival test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-triplex/meta.yaml b/recipes/bioconductor-triplex/meta.yaml index e5225d61d9440..9b595aacdac0d 100644 --- a/recipes/bioconductor-triplex/meta.yaml +++ b/recipes/bioconductor-triplex/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.22.0" %} +{% set version = "1.24.0" %} {% set name = "triplex" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: a155c67050549f90fb2e1565b36e7f6f + md5: 28768817386594eb3fc15f0d055b8fb5 build: number: 0 rpaths: @@ -19,18 +19,18 @@ build: # Suggests: rgl (>= 0.93.932), BSgenome.Celegans.UCSC.ce10, rtracklayer, GenomeGraphs requirements: host: - - 'bioconductor-biostrings >=2.50.0,<2.51.0' - - 'bioconductor-genomicranges >=1.34.0,<1.35.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' - - 'bioconductor-xvector >=0.22.0,<0.23.0' + - 'bioconductor-biostrings >=2.52.0,<2.53.0' + - 'bioconductor-genomicranges >=1.36.0,<1.37.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' + - 'bioconductor-xvector >=0.24.0,<0.25.0' - r-base run: - - 'bioconductor-biostrings >=2.50.0,<2.51.0' - - 'bioconductor-genomicranges >=1.34.0,<1.35.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' - - 'bioconductor-xvector >=0.22.0,<0.23.0' + - 'bioconductor-biostrings >=2.52.0,<2.53.0' + - 'bioconductor-genomicranges >=1.36.0,<1.37.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' + - 'bioconductor-xvector >=0.24.0,<0.25.0' - r-base build: - {{ compiler('c') }} diff --git a/recipes/bioconductor-trna/meta.yaml b/recipes/bioconductor-trna/meta.yaml index 4ea286878ad00..f0753549967c2 100644 --- a/recipes/bioconductor-trna/meta.yaml +++ b/recipes/bioconductor-trna/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.0.0" %} +{% set version = "1.2.0" %} {% set name = "tRNA" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: f53b7c910a0519debc047e4df784a63a + md5: 83a45ddc9ece500570d3b741fa40bbe8 build: number: 0 rpaths: @@ -20,24 +20,28 @@ build: # Suggests: knitr, rmarkdown, testthat, BiocStyle, tRNAscanImport requirements: host: - - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' - - 'bioconductor-biostrings >=2.50.0,<2.51.0' - - 'bioconductor-genomicranges >=1.34.0,<1.35.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' - - 'bioconductor-xvector >=0.22.0,<0.23.0' + - 'bioconductor-biocgenerics >=0.30.0,<0.31.0' + - 'bioconductor-biostrings >=2.52.0,<2.53.0' + - 'bioconductor-genomicranges >=1.36.0,<1.37.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-modstrings >=1.0.0,<1.1.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' + - 'bioconductor-structstrings >=1.0.0,<1.1.0' + - 'bioconductor-xvector >=0.24.0,<0.25.0' - r-assertive - r-base - r-ggplot2 - r-scales - r-stringr run: - - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' - - 'bioconductor-biostrings >=2.50.0,<2.51.0' - - 'bioconductor-genomicranges >=1.34.0,<1.35.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' - - 'bioconductor-xvector >=0.22.0,<0.23.0' + - 'bioconductor-biocgenerics >=0.30.0,<0.31.0' + - 'bioconductor-biostrings >=2.52.0,<2.53.0' + - 'bioconductor-genomicranges >=1.36.0,<1.37.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-modstrings >=1.0.0,<1.1.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' + - 'bioconductor-structstrings >=1.0.0,<1.1.0' + - 'bioconductor-xvector >=0.24.0,<0.25.0' - r-assertive - r-base - r-ggplot2 diff --git a/recipes/bioconductor-trnadbimport/meta.yaml b/recipes/bioconductor-trnadbimport/meta.yaml index 5a79e0ab333da..493b264810a5c 100644 --- a/recipes/bioconductor-trnadbimport/meta.yaml +++ b/recipes/bioconductor-trnadbimport/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.0.0" %} +{% set version = "1.2.0" %} {% set name = "tRNAdbImport" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 97017b574dee15ec399bab8a5cf095c4 + md5: 09d4f816f77a431b6b2e55472715751b build: number: 0 rpaths: @@ -20,22 +20,26 @@ build: # Suggests: knitr, rmarkdown, testthat, httptest, BiocStyle, rtracklayer requirements: host: - - 'bioconductor-biostrings >=2.50.0,<2.51.0' - - 'bioconductor-genomicranges >=1.34.0,<1.35.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' - - 'bioconductor-trna >=1.0.0,<1.1.0' + - 'bioconductor-biostrings >=2.52.0,<2.53.0' + - 'bioconductor-genomicranges >=1.36.0,<1.37.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-modstrings >=1.0.0,<1.1.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' + - 'bioconductor-structstrings >=1.0.0,<1.1.0' + - 'bioconductor-trna >=1.2.0,<1.3.0' - r-assertive - r-base - r-httr - r-stringr - r-xml2 run: - - 'bioconductor-biostrings >=2.50.0,<2.51.0' - - 'bioconductor-genomicranges >=1.34.0,<1.35.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' - - 'bioconductor-trna >=1.0.0,<1.1.0' + - 'bioconductor-biostrings >=2.52.0,<2.53.0' + - 'bioconductor-genomicranges >=1.36.0,<1.37.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-modstrings >=1.0.0,<1.1.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' + - 'bioconductor-structstrings >=1.0.0,<1.1.0' + - 'bioconductor-trna >=1.2.0,<1.3.0' - r-assertive - r-base - r-httr diff --git a/recipes/bioconductor-trnascanimport/meta.yaml b/recipes/bioconductor-trnascanimport/meta.yaml index fe89f53d71cef..9f6f0432737ae 100644 --- a/recipes/bioconductor-trnascanimport/meta.yaml +++ b/recipes/bioconductor-trnascanimport/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.2.0" %} +{% set version = "1.4.0" %} {% set name = "tRNAscanImport" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 00c52e3ddec9433db1e2422ee3da4b4f + md5: edbd752cae1ef48fe8bc58978d0654c6 build: number: 0 rpaths: @@ -20,24 +20,26 @@ build: # Suggests: BiocStyle, knitr, rmarkdown, testthat, ggplot2 requirements: host: - - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' - - 'bioconductor-biostrings >=2.50.0,<2.51.0' - - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' - - 'bioconductor-genomicranges >=1.34.0,<1.35.0' - - 'bioconductor-rtracklayer >=1.42.0,<1.43.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' - - 'bioconductor-trna >=1.0.0,<1.1.0' + - 'bioconductor-biocgenerics >=0.30.0,<0.31.0' + - 'bioconductor-biostrings >=2.52.0,<2.53.0' + - 'bioconductor-genomeinfodb >=1.20.0,<1.21.0' + - 'bioconductor-genomicranges >=1.36.0,<1.37.0' + - 'bioconductor-rtracklayer >=1.44.0,<1.45.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' + - 'bioconductor-structstrings >=1.0.0,<1.1.0' + - 'bioconductor-trna >=1.2.0,<1.3.0' - r-assertive - r-base - r-stringr run: - - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' - - 'bioconductor-biostrings >=2.50.0,<2.51.0' - - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' - - 'bioconductor-genomicranges >=1.34.0,<1.35.0' - - 'bioconductor-rtracklayer >=1.42.0,<1.43.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' - - 'bioconductor-trna >=1.0.0,<1.1.0' + - 'bioconductor-biocgenerics >=0.30.0,<0.31.0' + - 'bioconductor-biostrings >=2.52.0,<2.53.0' + - 'bioconductor-genomeinfodb >=1.20.0,<1.21.0' + - 'bioconductor-genomicranges >=1.36.0,<1.37.0' + - 'bioconductor-rtracklayer >=1.44.0,<1.45.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' + - 'bioconductor-structstrings >=1.0.0,<1.1.0' + - 'bioconductor-trna >=1.2.0,<1.3.0' - r-assertive - r-base - r-stringr diff --git a/recipes/bioconductor-tronco/meta.yaml b/recipes/bioconductor-tronco/meta.yaml index 78cb2a9667091..0a8dbc02a8881 100644 --- a/recipes/bioconductor-tronco/meta.yaml +++ b/recipes/bioconductor-tronco/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "2.14.2" %} +{% set version = "2.16.0" %} {% set name = "TRONCO" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,17 +10,17 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: e93b2f90880b287243cee99769f1efc6 + md5: 9b19fee1d9d9ab3192f33f298381b57f build: number: 0 rpaths: - lib/R/lib/ - lib/ noarch: generic -# Suggests: BiocGenerics, BiocStyle, testthat, knitr, +# Suggests: BiocGenerics, BiocStyle, testthat, knitr, rWikiPathways requirements: host: - - 'bioconductor-rgraphviz >=2.26.0,<2.27.0' + - 'bioconductor-rgraphviz >=2.28.0,<2.29.0' - r-base - r-bnlearn - r-cgdsr @@ -37,7 +37,7 @@ requirements: - r-scales - r-xtable run: - - 'bioconductor-rgraphviz >=2.26.0,<2.27.0' + - 'bioconductor-rgraphviz >=2.28.0,<2.29.0' - r-base - r-bnlearn - r-cgdsr diff --git a/recipes/bioconductor-tscan/meta.yaml b/recipes/bioconductor-tscan/meta.yaml index cd08a4765b46a..e88e54cb07335 100644 --- a/recipes/bioconductor-tscan/meta.yaml +++ b/recipes/bioconductor-tscan/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.20.0" %} +{% set version = "1.22.0" %} {% set name = "TSCAN" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 88f8eead43b40eeacfd6546d0f7ad3e5 + md5: 491016115994ed83297b07684af897e2 build: number: 0 rpaths: diff --git a/recipes/bioconductor-tspair/meta.yaml b/recipes/bioconductor-tspair/meta.yaml index d68e891aca92b..5c0bdbee369fa 100644 --- a/recipes/bioconductor-tspair/meta.yaml +++ b/recipes/bioconductor-tspair/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.40.0" %} +{% set version = "1.42.0" %} {% set name = "tspair" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 8f240fd93f65564edf17897732940e17 + md5: 0fe6764ba9edb91989fc0d238b12dde5 build: number: 0 rpaths: @@ -18,10 +18,10 @@ build: - lib/ requirements: host: - - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' - r-base run: - - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' - r-base build: - {{ compiler('c') }} diff --git a/recipes/bioconductor-tsrchitect/meta.yaml b/recipes/bioconductor-tsrchitect/meta.yaml index a11d5730ec407..55e8eccb5f7b1 100644 --- a/recipes/bioconductor-tsrchitect/meta.yaml +++ b/recipes/bioconductor-tsrchitect/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.8.9" %} +{% set version = "1.10.0" %} {% set name = "TSRchitect" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: ffb55c47e0e9ba14edd48bcd48bb0330 + md5: f7000c0086b78c4af6366a820a25d261 build: number: 0 rpaths: @@ -20,31 +20,31 @@ build: # Suggests: ENCODExplorer, ggplot2, knitr, rmarkdown requirements: host: - - 'bioconductor-annotationhub >=2.14.0,<2.15.0' - - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' - - 'bioconductor-biocparallel >=1.16.0,<1.17.0' - - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' - - 'bioconductor-genomicalignments >=1.18.0,<1.19.0' - - 'bioconductor-genomicranges >=1.34.0,<1.35.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-rsamtools >=1.34.0,<1.35.0' - - 'bioconductor-rtracklayer >=1.42.0,<1.43.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' - - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' + - 'bioconductor-annotationhub >=2.16.0,<2.17.0' + - 'bioconductor-biocgenerics >=0.30.0,<0.31.0' + - 'bioconductor-biocparallel >=1.18.0,<1.19.0' + - 'bioconductor-genomeinfodb >=1.20.0,<1.21.0' + - 'bioconductor-genomicalignments >=1.20.0,<1.21.0' + - 'bioconductor-genomicranges >=1.36.0,<1.37.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-rsamtools >=2.0.0,<2.1.0' + - 'bioconductor-rtracklayer >=1.44.0,<1.45.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' + - 'bioconductor-summarizedexperiment >=1.14.0,<1.15.0' - r-base - r-gtools run: - - 'bioconductor-annotationhub >=2.14.0,<2.15.0' - - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' - - 'bioconductor-biocparallel >=1.16.0,<1.17.0' - - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' - - 'bioconductor-genomicalignments >=1.18.0,<1.19.0' - - 'bioconductor-genomicranges >=1.34.0,<1.35.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-rsamtools >=1.34.0,<1.35.0' - - 'bioconductor-rtracklayer >=1.42.0,<1.43.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' - - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' + - 'bioconductor-annotationhub >=2.16.0,<2.17.0' + - 'bioconductor-biocgenerics >=0.30.0,<0.31.0' + - 'bioconductor-biocparallel >=1.18.0,<1.19.0' + - 'bioconductor-genomeinfodb >=1.20.0,<1.21.0' + - 'bioconductor-genomicalignments >=1.20.0,<1.21.0' + - 'bioconductor-genomicranges >=1.36.0,<1.37.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-rsamtools >=2.0.0,<2.1.0' + - 'bioconductor-rtracklayer >=1.44.0,<1.45.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' + - 'bioconductor-summarizedexperiment >=1.14.0,<1.15.0' - r-base - r-gtools test: @@ -53,5 +53,5 @@ test: about: home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: GPL-3 - summary: 'In recent years, large-scale transcriptional sequence data has yielded considerable insights into the nature of gene expression and regulation in eukaryotes. Techniques that identify the 5'' end of mRNAs, most notably CAGE, have mapped the promoter landscape across a number of model organisms. Due to the variability of TSS distributions and the transcriptional noise present in datasets, precisely identifying the active promoter(s) for genes from these datasets is not straightforward. TSRchitect allows the user to efficiently identify the putative promoter (the transcription start region, or TSR) from a variety of TSS profiling data types, including both single-end (e.g. CAGE) as well as paired-end (RAMPAGE, PEAT, STRIPE-seq). In addition, (new with version 1.3.0) TSRchitect provides the ability to import aligned EST and cDNA data. Along with the coordiantes of identified TSRs, TSRchitect also calculates the width, abundance and two forms of the Shape Index, and handles biological replicates for expression profiling. Finally, TSRchitect imports annotation files, allowing the user to associate identified promoters with genes and other genomic features. Three detailed examples of TSRchitect''s utility are provided in the User''s Guide, included with this package.' + summary: 'In recent years, large-scale transcriptional sequence data has yielded considerable insights into the nature of gene expression and regulation in eukaryotes. Techniques that identify the 5'' end of mRNAs, most notably CAGE, have mapped the promoter landscape across a number of model organisms. Due to the variability of TSS distributions and the transcriptional noise present in datasets, precisely identifying the active promoter(s) for genes from these datasets is not straightforward. TSRchitect allows the user to efficiently identify the putative promoter (the transcription start region, or TSR) from a variety of TSS profiling data types, including both single-end (e.g. CAGE) as well as paired-end (RAMPAGE, PEAT). In addition, (new with version 1.2.0) TSRchitect provides the ability to import aligned EST and cDNA data. Along with the coordiantes of identified TSRs, TSRchitect also calculates the width, abundance and Shape Index, and handles biological replicates for expression profiling. Finally, TSRchitect imports annotation files, allowing the user to associate identified promoters with genes and other genomic features. Three detailed examples of TSRchitect''s utility are provided in the User''s Guide, included with this package.' diff --git a/recipes/bioconductor-tssi/meta.yaml b/recipes/bioconductor-tssi/meta.yaml index abc18cd0572c2..8cb112dc02d6d 100644 --- a/recipes/bioconductor-tssi/meta.yaml +++ b/recipes/bioconductor-tssi/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.28.0" %} +{% set version = "1.29.0" %} {% set name = "TSSi" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 71fb81d19b05b106eaf0a34f8975d6b1 + md5: e73802f58fd8a5199b7f11ec187658f4 build: number: 0 rpaths: @@ -19,19 +19,19 @@ build: # Suggests: rtracklayer requirements: host: - - 'bioconductor-biobase >=2.42.0,<2.43.0' - - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' + - 'bioconductor-biocgenerics >=0.30.0,<0.31.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' - r-base - r-hmisc - r-minqa - r-plyr run: - - 'bioconductor-biobase >=2.42.0,<2.43.0' - - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' + - 'bioconductor-biocgenerics >=0.30.0,<0.31.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' - r-base - r-hmisc - r-minqa diff --git a/recipes/bioconductor-ttmap/meta.yaml b/recipes/bioconductor-ttmap/meta.yaml index e684f939ddd77..d9efc1c0cc5c3 100644 --- a/recipes/bioconductor-ttmap/meta.yaml +++ b/recipes/bioconductor-ttmap/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.4.0" %} +{% set version = "1.6.0" %} {% set name = "TTMap" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: b9749313b878fae1dd4ed81a16b7271d + md5: 94912c9b54264cb232dba0980ffe4c10 build: number: 0 rpaths: @@ -20,14 +20,14 @@ build: # Suggests: BiocStyle, airway requirements: host: - - 'bioconductor-biobase >=2.42.0,<2.43.0' - - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' + - 'bioconductor-summarizedexperiment >=1.14.0,<1.15.0' - r-base - r-colorramps - r-rgl run: - - 'bioconductor-biobase >=2.42.0,<2.43.0' - - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' + - 'bioconductor-summarizedexperiment >=1.14.0,<1.15.0' - r-base - r-colorramps - r-rgl @@ -38,8 +38,7 @@ about: home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: GPL-2 summary: 'TTMap is a clustering method that groups together samples with the same deviation in comparison to a control group. It is specially useful when the data is small. It is parameter free.' - extra: container: - # needs libGL.so.1 extended-base: true + diff --git a/recipes/bioconductor-turbonorm/meta.yaml b/recipes/bioconductor-turbonorm/meta.yaml index a519edeb655ce..dbca347c50d16 100644 --- a/recipes/bioconductor-turbonorm/meta.yaml +++ b/recipes/bioconductor-turbonorm/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.30.0" %} +{% set version = "1.32.0" %} {% set name = "TurboNorm" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,26 +10,26 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: c258665eba34296ed6a5f6e4b7e8ddd5 + md5: d06683056c54c3b734e7877a3e11f49d build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ # Suggests: BiocStyle, affydata requirements: host: - - 'bioconductor-affy >=1.60.0,<1.61.0' - - 'bioconductor-convert >=1.58.0,<1.59.0' - - 'bioconductor-limma >=3.38.0,<3.39.0' - - 'bioconductor-marray >=1.60.0,<1.61.0' + - 'bioconductor-affy >=1.62.0,<1.63.0' + - 'bioconductor-convert >=1.60.0,<1.61.0' + - 'bioconductor-limma >=3.40.0,<3.41.0' + - 'bioconductor-marray >=1.62.0,<1.63.0' - r-base - r-lattice run: - - 'bioconductor-affy >=1.60.0,<1.61.0' - - 'bioconductor-convert >=1.58.0,<1.59.0' - - 'bioconductor-limma >=3.38.0,<3.39.0' - - 'bioconductor-marray >=1.60.0,<1.61.0' + - 'bioconductor-affy >=1.62.0,<1.63.0' + - 'bioconductor-convert >=1.60.0,<1.61.0' + - 'bioconductor-limma >=3.40.0,<3.41.0' + - 'bioconductor-marray >=1.62.0,<1.63.0' - r-base - r-lattice build: diff --git a/recipes/bioconductor-tvtb/meta.yaml b/recipes/bioconductor-tvtb/meta.yaml index 984fc50961aa5..17800b3b875ad 100644 --- a/recipes/bioconductor-tvtb/meta.yaml +++ b/recipes/bioconductor-tvtb/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.8.0" %} +{% set version = "1.10.0" %} {% set name = "TVTB" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: cba10d6dc0358c99d2ab92e861786a9b + md5: 0de5a74af139bcc9791d456a3952c739 build: number: 0 rpaths: @@ -20,41 +20,41 @@ build: # Suggests: EnsDb.Hsapiens.v75 (>= 0.99.7), shiny (>= 0.13.2.9005), DT (>= 0.1.67), rtracklayer, BiocStyle (>= 2.5.19), knitr (>= 1.12), rmarkdown, testthat, covr, pander requirements: host: - - 'bioconductor-annotationfilter >=1.6.0,<1.7.0' - - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' - - 'bioconductor-biocparallel >=1.16.0,<1.17.0' - - 'bioconductor-biostrings >=2.50.0,<2.51.0' - - 'bioconductor-ensembldb >=2.6.0,<2.7.0' - - 'bioconductor-ensemblvep >=1.24.0,<1.25.0' - - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' - - 'bioconductor-genomicranges >=1.34.0,<1.35.0' - - 'bioconductor-gviz >=1.26.0,<1.27.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-limma >=3.38.0,<3.39.0' - - 'bioconductor-rsamtools >=1.34.0,<1.35.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' - - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' - - 'bioconductor-variantannotation >=1.28.0,<1.29.0' + - 'bioconductor-annotationfilter >=1.8.0,<1.9.0' + - 'bioconductor-biocgenerics >=0.30.0,<0.31.0' + - 'bioconductor-biocparallel >=1.18.0,<1.19.0' + - 'bioconductor-biostrings >=2.52.0,<2.53.0' + - 'bioconductor-ensembldb >=2.8.0,<2.9.0' + - 'bioconductor-ensemblvep >=1.26.0,<1.27.0' + - 'bioconductor-genomeinfodb >=1.20.0,<1.21.0' + - 'bioconductor-genomicranges >=1.36.0,<1.37.0' + - 'bioconductor-gviz >=1.28.0,<1.29.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-limma >=3.40.0,<3.41.0' + - 'bioconductor-rsamtools >=2.0.0,<2.1.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' + - 'bioconductor-summarizedexperiment >=1.14.0,<1.15.0' + - 'bioconductor-variantannotation >=1.30.0,<1.31.0' - r-base - r-ggally - r-ggplot2 - r-reshape2 run: - - 'bioconductor-annotationfilter >=1.6.0,<1.7.0' - - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' - - 'bioconductor-biocparallel >=1.16.0,<1.17.0' - - 'bioconductor-biostrings >=2.50.0,<2.51.0' - - 'bioconductor-ensembldb >=2.6.0,<2.7.0' - - 'bioconductor-ensemblvep >=1.24.0,<1.25.0' - - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' - - 'bioconductor-genomicranges >=1.34.0,<1.35.0' - - 'bioconductor-gviz >=1.26.0,<1.27.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-limma >=3.38.0,<3.39.0' - - 'bioconductor-rsamtools >=1.34.0,<1.35.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' - - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' - - 'bioconductor-variantannotation >=1.28.0,<1.29.0' + - 'bioconductor-annotationfilter >=1.8.0,<1.9.0' + - 'bioconductor-biocgenerics >=0.30.0,<0.31.0' + - 'bioconductor-biocparallel >=1.18.0,<1.19.0' + - 'bioconductor-biostrings >=2.52.0,<2.53.0' + - 'bioconductor-ensembldb >=2.8.0,<2.9.0' + - 'bioconductor-ensemblvep >=1.26.0,<1.27.0' + - 'bioconductor-genomeinfodb >=1.20.0,<1.21.0' + - 'bioconductor-genomicranges >=1.36.0,<1.37.0' + - 'bioconductor-gviz >=1.28.0,<1.29.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-limma >=3.40.0,<3.41.0' + - 'bioconductor-rsamtools >=2.0.0,<2.1.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' + - 'bioconductor-summarizedexperiment >=1.14.0,<1.15.0' + - 'bioconductor-variantannotation >=1.30.0,<1.31.0' - r-base - r-ggally - r-ggplot2 diff --git a/recipes/bioconductor-tweedeseq/meta.yaml b/recipes/bioconductor-tweedeseq/meta.yaml index 5b8d9804aaf75..130eb887c5a53 100644 --- a/recipes/bioconductor-tweedeseq/meta.yaml +++ b/recipes/bioconductor-tweedeseq/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.28.1" %} +{% set version = "1.30.0" %} {% set name = "tweeDEseq" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 0b4fcd5b9cf52acb8bbf3292d4dd2aac + md5: 328bd849d5545d4448815eda8d57bc55 build: number: 0 rpaths: @@ -19,15 +19,15 @@ build: # Suggests: tweeDEseqCountData, xtable requirements: host: - - 'bioconductor-cqn >=1.28.0,<1.29.0' - - 'bioconductor-edger >=3.24.0,<3.25.0' - - 'bioconductor-limma >=3.38.0,<3.39.0' + - 'bioconductor-cqn >=1.30.0,<1.31.0' + - 'bioconductor-edger >=3.26.0,<3.27.0' + - 'bioconductor-limma >=3.40.0,<3.41.0' - r-base - r-mass run: - - 'bioconductor-cqn >=1.28.0,<1.29.0' - - 'bioconductor-edger >=3.24.0,<3.25.0' - - 'bioconductor-limma >=3.38.0,<3.39.0' + - 'bioconductor-cqn >=1.30.0,<1.31.0' + - 'bioconductor-edger >=3.26.0,<3.27.0' + - 'bioconductor-limma >=3.40.0,<3.41.0' - r-base - r-mass build: diff --git a/recipes/bioconductor-tweedeseqcountdata/meta.yaml b/recipes/bioconductor-tweedeseqcountdata/meta.yaml index 65255c5193550..c621e027067ae 100644 --- a/recipes/bioconductor-tweedeseqcountdata/meta.yaml +++ b/recipes/bioconductor-tweedeseqcountdata/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.20.0" %} +{% set version = "1.22.0" %} {% set name = "tweeDEseqCountData" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: aaea601e98d23f6e80db25f3eabe68c3 + md5: 7da122e4ba4097fa0742d460abc0b6b1 build: number: 0 rpaths: @@ -19,12 +19,12 @@ build: noarch: generic requirements: host: - - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' - r-base run: - - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-tweedeseqcountdata/post-link.sh b/recipes/bioconductor-tweedeseqcountdata/post-link.sh index 66f8ac45b7693..b546268bbc7e0 100644 --- a/recipes/bioconductor-tweedeseqcountdata/post-link.sh +++ b/recipes/bioconductor-tweedeseqcountdata/post-link.sh @@ -1,11 +1,11 @@ #!/bin/bash -FN="tweeDEseqCountData_1.20.0.tar.gz" +FN="tweeDEseqCountData_1.22.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/experiment/src/contrib/tweeDEseqCountData_1.20.0.tar.gz" - "https://bioarchive.galaxyproject.org/tweeDEseqCountData_1.20.0.tar.gz" - "https://depot.galaxyproject.org/software/bioconductor-tweedeseqcountdata/bioconductor-tweedeseqcountdata_1.20.0_src_all.tar.gz" + "https://bioconductor.org/packages/3.9/data/experiment/src/contrib/tweeDEseqCountData_1.22.0.tar.gz" + "https://bioarchive.galaxyproject.org/tweeDEseqCountData_1.22.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-tweedeseqcountdata/bioconductor-tweedeseqcountdata_1.22.0_src_all.tar.gz" ) -MD5="aaea601e98d23f6e80db25f3eabe68c3" +MD5="7da122e4ba4097fa0742d460abc0b6b1" # Use a staging area in the conda dir rather than temp dirs, both to avoid # permission issues as well as to have things downloaded in a predictable @@ -16,7 +16,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-twilight/meta.yaml b/recipes/bioconductor-twilight/meta.yaml index f151f83bacdc8..3052912b9d0a3 100644 --- a/recipes/bioconductor-twilight/meta.yaml +++ b/recipes/bioconductor-twilight/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.58.0" %} +{% set version = "1.60.0" %} {% set name = "twilight" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,19 +10,19 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: bdc31d1f7e094aa3d2e3eb436b9b6306 + md5: 6d152a6e78dbd5b054dcd1a492d585c9 build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ # Suggests: golubEsets (>= 1.4.2), vsn (>= 1.7.2) requirements: host: - - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' - r-base run: - - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' - r-base build: - {{ compiler('c') }} diff --git a/recipes/bioconductor-twoddpcr/meta.yaml b/recipes/bioconductor-twoddpcr/meta.yaml index 5b6fc8a34fed6..826af49051ace 100644 --- a/recipes/bioconductor-twoddpcr/meta.yaml +++ b/recipes/bioconductor-twoddpcr/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.6.0" %} +{% set version = "1.8.0" %} {% set name = "twoddpcr" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 42ab6dd8305e75b8029b4c69abeb5b7d + md5: 6d28c4a0a1965a0630e5a4382d97c0c8 build: number: 0 rpaths: @@ -20,7 +20,7 @@ build: # Suggests: devtools, knitr, reshape2, rmarkdown, testthat, BiocStyle requirements: host: - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' - r-base - r-class - r-ggplot2 @@ -29,7 +29,7 @@ requirements: - r-scales - r-shiny run: - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' - r-base - r-class - r-ggplot2 diff --git a/recipes/bioconductor-txdb.athaliana.biomart.plantsmart22/meta.yaml b/recipes/bioconductor-txdb.athaliana.biomart.plantsmart22/meta.yaml index 3af100f1da538..1a8ecba775e76 100644 --- a/recipes/bioconductor-txdb.athaliana.biomart.plantsmart22/meta.yaml +++ b/recipes/bioconductor-txdb.athaliana.biomart.plantsmart22/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.0.1" %} {% set name = "TxDb.Athaliana.BioMart.plantsmart22" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -12,21 +12,21 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' md5: 3bab54295e300fedba99eef521220e50 build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' - - 'bioconductor-genomicfeatures >=1.34.0,<1.35.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' + - 'bioconductor-genomicfeatures >=1.36.0,<1.37.0' - r-base run: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' - - 'bioconductor-genomicfeatures >=1.34.0,<1.35.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' + - 'bioconductor-genomicfeatures >=1.36.0,<1.37.0' - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-txdb.athaliana.biomart.plantsmart22/post-link.sh b/recipes/bioconductor-txdb.athaliana.biomart.plantsmart22/post-link.sh index 75f00aba1fe80..ab0b2adc63656 100644 --- a/recipes/bioconductor-txdb.athaliana.biomart.plantsmart22/post-link.sh +++ b/recipes/bioconductor-txdb.athaliana.biomart.plantsmart22/post-link.sh @@ -1,9 +1,10 @@ #!/bin/bash FN="TxDb.Athaliana.BioMart.plantsmart22_3.0.1.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/TxDb.Athaliana.BioMart.plantsmart22_3.0.1.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/TxDb.Athaliana.BioMart.plantsmart22_3.0.1.tar.gz" "https://bioarchive.galaxyproject.org/TxDb.Athaliana.BioMart.plantsmart22_3.0.1.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-txdb.athaliana.biomart.plantsmart22/bioconductor-txdb.athaliana.biomart.plantsmart22_3.0.1_src_all.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-txdb.athaliana.biomart.plantsmart22/bioconductor-txdb.athaliana.biomart.plantsmart22_3.0.1_src_all.tar.gz" ) MD5="3bab54295e300fedba99eef521220e50" @@ -16,7 +17,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-txdb.athaliana.biomart.plantsmart25/meta.yaml b/recipes/bioconductor-txdb.athaliana.biomart.plantsmart25/meta.yaml index 213070cbbc969..aa1a1c6e5725b 100644 --- a/recipes/bioconductor-txdb.athaliana.biomart.plantsmart25/meta.yaml +++ b/recipes/bioconductor-txdb.athaliana.biomart.plantsmart25/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.1.3" %} {% set name = "TxDb.Athaliana.BioMart.plantsmart25" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -12,21 +12,21 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' md5: eb007c07317b9717c76949e5ed999978 build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' - - 'bioconductor-genomicfeatures >=1.34.0,<1.35.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' + - 'bioconductor-genomicfeatures >=1.36.0,<1.37.0' - r-base run: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' - - 'bioconductor-genomicfeatures >=1.34.0,<1.35.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' + - 'bioconductor-genomicfeatures >=1.36.0,<1.37.0' - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-txdb.athaliana.biomart.plantsmart25/post-link.sh b/recipes/bioconductor-txdb.athaliana.biomart.plantsmart25/post-link.sh index 2453fb11731e2..f502c2bdff39c 100644 --- a/recipes/bioconductor-txdb.athaliana.biomart.plantsmart25/post-link.sh +++ b/recipes/bioconductor-txdb.athaliana.biomart.plantsmart25/post-link.sh @@ -1,9 +1,10 @@ #!/bin/bash FN="TxDb.Athaliana.BioMart.plantsmart25_3.1.3.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/TxDb.Athaliana.BioMart.plantsmart25_3.1.3.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/TxDb.Athaliana.BioMart.plantsmart25_3.1.3.tar.gz" "https://bioarchive.galaxyproject.org/TxDb.Athaliana.BioMart.plantsmart25_3.1.3.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-txdb.athaliana.biomart.plantsmart25/bioconductor-txdb.athaliana.biomart.plantsmart25_3.1.3_src_all.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-txdb.athaliana.biomart.plantsmart25/bioconductor-txdb.athaliana.biomart.plantsmart25_3.1.3_src_all.tar.gz" ) MD5="eb007c07317b9717c76949e5ed999978" @@ -16,7 +17,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-txdb.athaliana.biomart.plantsmart28/meta.yaml b/recipes/bioconductor-txdb.athaliana.biomart.plantsmart28/meta.yaml index 6fae92861abab..f7bf7e8bd564d 100644 --- a/recipes/bioconductor-txdb.athaliana.biomart.plantsmart28/meta.yaml +++ b/recipes/bioconductor-txdb.athaliana.biomart.plantsmart28/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.2.2" %} {% set name = "TxDb.Athaliana.BioMart.plantsmart28" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -12,21 +12,21 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' md5: 9ed52284f01e08fc382db179b544bb17 build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' - - 'bioconductor-genomicfeatures >=1.34.0,<1.35.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' + - 'bioconductor-genomicfeatures >=1.36.0,<1.37.0' - r-base run: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' - - 'bioconductor-genomicfeatures >=1.34.0,<1.35.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' + - 'bioconductor-genomicfeatures >=1.36.0,<1.37.0' - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-txdb.athaliana.biomart.plantsmart28/post-link.sh b/recipes/bioconductor-txdb.athaliana.biomart.plantsmart28/post-link.sh index c6d708042efbe..3a655c16aa6a4 100644 --- a/recipes/bioconductor-txdb.athaliana.biomart.plantsmart28/post-link.sh +++ b/recipes/bioconductor-txdb.athaliana.biomart.plantsmart28/post-link.sh @@ -1,9 +1,10 @@ #!/bin/bash FN="TxDb.Athaliana.BioMart.plantsmart28_3.2.2.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/TxDb.Athaliana.BioMart.plantsmart28_3.2.2.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/TxDb.Athaliana.BioMart.plantsmart28_3.2.2.tar.gz" "https://bioarchive.galaxyproject.org/TxDb.Athaliana.BioMart.plantsmart28_3.2.2.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-txdb.athaliana.biomart.plantsmart28/bioconductor-txdb.athaliana.biomart.plantsmart28_3.2.2_src_all.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-txdb.athaliana.biomart.plantsmart28/bioconductor-txdb.athaliana.biomart.plantsmart28_3.2.2_src_all.tar.gz" ) MD5="9ed52284f01e08fc382db179b544bb17" @@ -16,7 +17,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-txdb.btaurus.ucsc.bostau8.refgene/meta.yaml b/recipes/bioconductor-txdb.btaurus.ucsc.bostau8.refgene/meta.yaml index 991a1f35ea4b6..7b03fc40f3e19 100644 --- a/recipes/bioconductor-txdb.btaurus.ucsc.bostau8.refgene/meta.yaml +++ b/recipes/bioconductor-txdb.btaurus.ucsc.bostau8.refgene/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "3.4.4" %} +{% set version = "3.4.6" %} {% set name = "TxDb.Btaurus.UCSC.bosTau8.refGene" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 4c5973c4153ff02dd768324291631d1e + md5: 3ae01e38e8965b61a3e25ed9085718c4 build: number: 0 rpaths: @@ -19,14 +19,14 @@ build: noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' - - 'bioconductor-genomicfeatures >=1.34.0,<1.35.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' + - 'bioconductor-genomicfeatures >=1.36.0,<1.37.0' - r-base run: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' - - 'bioconductor-genomicfeatures >=1.34.0,<1.35.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' + - 'bioconductor-genomicfeatures >=1.36.0,<1.37.0' - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-txdb.btaurus.ucsc.bostau8.refgene/post-link.sh b/recipes/bioconductor-txdb.btaurus.ucsc.bostau8.refgene/post-link.sh index 0b7574d57c815..30c09fb867ca0 100644 --- a/recipes/bioconductor-txdb.btaurus.ucsc.bostau8.refgene/post-link.sh +++ b/recipes/bioconductor-txdb.btaurus.ucsc.bostau8.refgene/post-link.sh @@ -1,11 +1,11 @@ #!/bin/bash -FN="TxDb.Btaurus.UCSC.bosTau8.refGene_3.4.4.tar.gz" +FN="TxDb.Btaurus.UCSC.bosTau8.refGene_3.4.6.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/TxDb.Btaurus.UCSC.bosTau8.refGene_3.4.4.tar.gz" - "https://bioarchive.galaxyproject.org/TxDb.Btaurus.UCSC.bosTau8.refGene_3.4.4.tar.gz" - "https://depot.galaxyproject.org/software/bioconductor-txdb.btaurus.ucsc.bostau8.refgene/bioconductor-txdb.btaurus.ucsc.bostau8.refgene_3.4.4_src_all.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/TxDb.Btaurus.UCSC.bosTau8.refGene_3.4.6.tar.gz" + "https://bioarchive.galaxyproject.org/TxDb.Btaurus.UCSC.bosTau8.refGene_3.4.6.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-txdb.btaurus.ucsc.bostau8.refgene/bioconductor-txdb.btaurus.ucsc.bostau8.refgene_3.4.6_src_all.tar.gz" ) -MD5="4c5973c4153ff02dd768324291631d1e" +MD5="3ae01e38e8965b61a3e25ed9085718c4" # Use a staging area in the conda dir rather than temp dirs, both to avoid # permission issues as well as to have things downloaded in a predictable @@ -16,7 +16,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-txdb.celegans.ucsc.ce11.ensgene/meta.yaml b/recipes/bioconductor-txdb.celegans.ucsc.ce11.ensgene/meta.yaml new file mode 100644 index 0000000000000..43518e0bf5c91 --- /dev/null +++ b/recipes/bioconductor-txdb.celegans.ucsc.ce11.ensgene/meta.yaml @@ -0,0 +1,37 @@ +{% set version = "3.4.6" %} +{% set name = "TxDb.Celegans.UCSC.ce11.ensGene" %} +{% set bioc = "3.9" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: e33a9206a35200e71aac67252fd87e02 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +requirements: + host: + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' + - 'bioconductor-genomicfeatures >=1.36.0,<1.37.0' + - r-base + run: + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' + - 'bioconductor-genomicfeatures >=1.36.0,<1.37.0' + - r-base + - curl +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'Exposes an annotation databases generated from UCSC by exposing these as TxDb objects' + diff --git a/recipes/bioconductor-txdb.celegans.ucsc.ce11.ensgene/post-link.sh b/recipes/bioconductor-txdb.celegans.ucsc.ce11.ensgene/post-link.sh new file mode 100644 index 0000000000000..bcd4951fc882b --- /dev/null +++ b/recipes/bioconductor-txdb.celegans.ucsc.ce11.ensgene/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="TxDb.Celegans.UCSC.ce11.ensGene_3.4.6.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/TxDb.Celegans.UCSC.ce11.ensGene_3.4.6.tar.gz" + "https://bioarchive.galaxyproject.org/TxDb.Celegans.UCSC.ce11.ensGene_3.4.6.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-txdb.celegans.ucsc.ce11.ensgene/bioconductor-txdb.celegans.ucsc.ce11.ensgene_3.4.6_src_all.tar.gz" +) +MD5="e33a9206a35200e71aac67252fd87e02" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + curl $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-txdb.celegans.ucsc.ce11.ensgene/pre-unlink.sh b/recipes/bioconductor-txdb.celegans.ucsc.ce11.ensgene/pre-unlink.sh new file mode 100644 index 0000000000000..d9f9d2eb1cd78 --- /dev/null +++ b/recipes/bioconductor-txdb.celegans.ucsc.ce11.ensgene/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ TxDb.Celegans.UCSC.ce11.ensGene diff --git a/recipes/bioconductor-txdb.celegans.ucsc.ce11.refgene/meta.yaml b/recipes/bioconductor-txdb.celegans.ucsc.ce11.refgene/meta.yaml index a8b67190e557c..a6fc9e6b6c4d6 100644 --- a/recipes/bioconductor-txdb.celegans.ucsc.ce11.refgene/meta.yaml +++ b/recipes/bioconductor-txdb.celegans.ucsc.ce11.refgene/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "3.4.4" %} +{% set version = "3.4.6" %} {% set name = "TxDb.Celegans.UCSC.ce11.refGene" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 3952ad139ed6e3cc7d210cc994c53b3e + md5: 3765169432e745aff5e85afd239066ca build: number: 0 rpaths: @@ -19,14 +19,14 @@ build: noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' - - 'bioconductor-genomicfeatures >=1.34.0,<1.35.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' + - 'bioconductor-genomicfeatures >=1.36.0,<1.37.0' - r-base run: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' - - 'bioconductor-genomicfeatures >=1.34.0,<1.35.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' + - 'bioconductor-genomicfeatures >=1.36.0,<1.37.0' - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-txdb.celegans.ucsc.ce11.refgene/post-link.sh b/recipes/bioconductor-txdb.celegans.ucsc.ce11.refgene/post-link.sh index 1fc822ae2a775..322139e1533cf 100644 --- a/recipes/bioconductor-txdb.celegans.ucsc.ce11.refgene/post-link.sh +++ b/recipes/bioconductor-txdb.celegans.ucsc.ce11.refgene/post-link.sh @@ -1,11 +1,11 @@ #!/bin/bash -FN="TxDb.Celegans.UCSC.ce11.refGene_3.4.4.tar.gz" +FN="TxDb.Celegans.UCSC.ce11.refGene_3.4.6.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/TxDb.Celegans.UCSC.ce11.refGene_3.4.4.tar.gz" - "https://bioarchive.galaxyproject.org/TxDb.Celegans.UCSC.ce11.refGene_3.4.4.tar.gz" - "https://depot.galaxyproject.org/software/bioconductor-txdb.celegans.ucsc.ce11.refgene/bioconductor-txdb.celegans.ucsc.ce11.refgene_3.4.4_src_all.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/TxDb.Celegans.UCSC.ce11.refGene_3.4.6.tar.gz" + "https://bioarchive.galaxyproject.org/TxDb.Celegans.UCSC.ce11.refGene_3.4.6.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-txdb.celegans.ucsc.ce11.refgene/bioconductor-txdb.celegans.ucsc.ce11.refgene_3.4.6_src_all.tar.gz" ) -MD5="3952ad139ed6e3cc7d210cc994c53b3e" +MD5="3765169432e745aff5e85afd239066ca" # Use a staging area in the conda dir rather than temp dirs, both to avoid # permission issues as well as to have things downloaded in a predictable @@ -16,7 +16,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-txdb.celegans.ucsc.ce6.ensgene/meta.yaml b/recipes/bioconductor-txdb.celegans.ucsc.ce6.ensgene/meta.yaml index f001c182cc657..ba29cfe5ff725 100644 --- a/recipes/bioconductor-txdb.celegans.ucsc.ce6.ensgene/meta.yaml +++ b/recipes/bioconductor-txdb.celegans.ucsc.ce6.ensgene/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.2.2" %} {% set name = "TxDb.Celegans.UCSC.ce6.ensGene" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -12,21 +12,21 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' md5: 215c2edd440a3df8229fe6a75b431aa8 build: - number: 4 + number: 5 rpaths: - lib/R/lib/ - lib/ noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' - - 'bioconductor-genomicfeatures >=1.34.0,<1.35.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' + - 'bioconductor-genomicfeatures >=1.36.0,<1.37.0' - r-base run: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' - - 'bioconductor-genomicfeatures >=1.34.0,<1.35.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' + - 'bioconductor-genomicfeatures >=1.36.0,<1.37.0' - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-txdb.celegans.ucsc.ce6.ensgene/post-link.sh b/recipes/bioconductor-txdb.celegans.ucsc.ce6.ensgene/post-link.sh index ead01900cdb01..1807597c8b457 100644 --- a/recipes/bioconductor-txdb.celegans.ucsc.ce6.ensgene/post-link.sh +++ b/recipes/bioconductor-txdb.celegans.ucsc.ce6.ensgene/post-link.sh @@ -1,7 +1,7 @@ #!/bin/bash FN="TxDb.Celegans.UCSC.ce6.ensGene_3.2.2.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/TxDb.Celegans.UCSC.ce6.ensGene_3.2.2.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/TxDb.Celegans.UCSC.ce6.ensGene_3.2.2.tar.gz" "https://bioarchive.galaxyproject.org/TxDb.Celegans.UCSC.ce6.ensGene_3.2.2.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-txdb.celegans.ucsc.ce6.ensgene/bioconductor-txdb.celegans.ucsc.ce6.ensgene_3.2.2_src_all.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-txdb.celegans.ucsc.ce6.ensgene/bioconductor-txdb.celegans.ucsc.ce6.ensgene_3.2.2_src_all.tar.gz" @@ -17,7 +17,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-txdb.cfamiliaris.ucsc.canfam3.refgene/meta.yaml b/recipes/bioconductor-txdb.cfamiliaris.ucsc.canfam3.refgene/meta.yaml index 5acc9d8140230..901dade0477ef 100644 --- a/recipes/bioconductor-txdb.cfamiliaris.ucsc.canfam3.refgene/meta.yaml +++ b/recipes/bioconductor-txdb.cfamiliaris.ucsc.canfam3.refgene/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "3.4.4" %} +{% set version = "3.4.6" %} {% set name = "TxDb.Cfamiliaris.UCSC.canFam3.refGene" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 8bc49815d284a193ab9c1db2fa32cb64 + md5: 23c07a83a974b72a78871e41111def3e build: number: 0 rpaths: @@ -19,14 +19,14 @@ build: noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' - - 'bioconductor-genomicfeatures >=1.34.0,<1.35.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' + - 'bioconductor-genomicfeatures >=1.36.0,<1.37.0' - r-base run: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' - - 'bioconductor-genomicfeatures >=1.34.0,<1.35.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' + - 'bioconductor-genomicfeatures >=1.36.0,<1.37.0' - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-txdb.cfamiliaris.ucsc.canfam3.refgene/post-link.sh b/recipes/bioconductor-txdb.cfamiliaris.ucsc.canfam3.refgene/post-link.sh index 4e54219278311..2df5112a79fdd 100644 --- a/recipes/bioconductor-txdb.cfamiliaris.ucsc.canfam3.refgene/post-link.sh +++ b/recipes/bioconductor-txdb.cfamiliaris.ucsc.canfam3.refgene/post-link.sh @@ -1,11 +1,11 @@ #!/bin/bash -FN="TxDb.Cfamiliaris.UCSC.canFam3.refGene_3.4.4.tar.gz" +FN="TxDb.Cfamiliaris.UCSC.canFam3.refGene_3.4.6.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/TxDb.Cfamiliaris.UCSC.canFam3.refGene_3.4.4.tar.gz" - "https://bioarchive.galaxyproject.org/TxDb.Cfamiliaris.UCSC.canFam3.refGene_3.4.4.tar.gz" - "https://depot.galaxyproject.org/software/bioconductor-txdb.cfamiliaris.ucsc.canfam3.refgene/bioconductor-txdb.cfamiliaris.ucsc.canfam3.refgene_3.4.4_src_all.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/TxDb.Cfamiliaris.UCSC.canFam3.refGene_3.4.6.tar.gz" + "https://bioarchive.galaxyproject.org/TxDb.Cfamiliaris.UCSC.canFam3.refGene_3.4.6.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-txdb.cfamiliaris.ucsc.canfam3.refgene/bioconductor-txdb.cfamiliaris.ucsc.canfam3.refgene_3.4.6_src_all.tar.gz" ) -MD5="8bc49815d284a193ab9c1db2fa32cb64" +MD5="23c07a83a974b72a78871e41111def3e" # Use a staging area in the conda dir rather than temp dirs, both to avoid # permission issues as well as to have things downloaded in a predictable @@ -16,7 +16,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-txdb.dmelanogaster.ucsc.dm3.ensgene/meta.yaml b/recipes/bioconductor-txdb.dmelanogaster.ucsc.dm3.ensgene/meta.yaml index 34734014178b0..98c2b105c850c 100644 --- a/recipes/bioconductor-txdb.dmelanogaster.ucsc.dm3.ensgene/meta.yaml +++ b/recipes/bioconductor-txdb.dmelanogaster.ucsc.dm3.ensgene/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.2.2" %} {% set name = "TxDb.Dmelanogaster.UCSC.dm3.ensGene" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -12,21 +12,21 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' md5: 46b7ffe0c516edf8a2a3b5d78e0d8b67 build: - number: 5 + number: 6 rpaths: - lib/R/lib/ - lib/ noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' - - 'bioconductor-genomicfeatures >=1.34.0,<1.35.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' + - 'bioconductor-genomicfeatures >=1.36.0,<1.37.0' - r-base run: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' - - 'bioconductor-genomicfeatures >=1.34.0,<1.35.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' + - 'bioconductor-genomicfeatures >=1.36.0,<1.37.0' - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-txdb.dmelanogaster.ucsc.dm3.ensgene/post-link.sh b/recipes/bioconductor-txdb.dmelanogaster.ucsc.dm3.ensgene/post-link.sh index 6b14a5faa8769..8503c01bbf063 100644 --- a/recipes/bioconductor-txdb.dmelanogaster.ucsc.dm3.ensgene/post-link.sh +++ b/recipes/bioconductor-txdb.dmelanogaster.ucsc.dm3.ensgene/post-link.sh @@ -1,7 +1,7 @@ #!/bin/bash FN="TxDb.Dmelanogaster.UCSC.dm3.ensGene_3.2.2.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/TxDb.Dmelanogaster.UCSC.dm3.ensGene_3.2.2.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/TxDb.Dmelanogaster.UCSC.dm3.ensGene_3.2.2.tar.gz" "https://bioarchive.galaxyproject.org/TxDb.Dmelanogaster.UCSC.dm3.ensGene_3.2.2.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-txdb.dmelanogaster.ucsc.dm3.ensgene/bioconductor-txdb.dmelanogaster.ucsc.dm3.ensgene_3.2.2_src_all.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-txdb.dmelanogaster.ucsc.dm3.ensgene/bioconductor-txdb.dmelanogaster.ucsc.dm3.ensgene_3.2.2_src_all.tar.gz" @@ -17,7 +17,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-txdb.dmelanogaster.ucsc.dm6.ensgene/meta.yaml b/recipes/bioconductor-txdb.dmelanogaster.ucsc.dm6.ensgene/meta.yaml index c7cd4bb3fcfb5..276d5bff0381c 100644 --- a/recipes/bioconductor-txdb.dmelanogaster.ucsc.dm6.ensgene/meta.yaml +++ b/recipes/bioconductor-txdb.dmelanogaster.ucsc.dm6.ensgene/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "3.4.4" %} +{% set version = "3.4.6" %} {% set name = "TxDb.Dmelanogaster.UCSC.dm6.ensGene" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 7cad715c42d1f960c0e54905ec6612d7 + md5: 3f44aee6ed70de5594d80262674c0e15 build: number: 0 rpaths: @@ -19,14 +19,14 @@ build: noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' - - 'bioconductor-genomicfeatures >=1.34.0,<1.35.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' + - 'bioconductor-genomicfeatures >=1.36.0,<1.37.0' - r-base run: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' - - 'bioconductor-genomicfeatures >=1.34.0,<1.35.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' + - 'bioconductor-genomicfeatures >=1.36.0,<1.37.0' - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-txdb.dmelanogaster.ucsc.dm6.ensgene/post-link.sh b/recipes/bioconductor-txdb.dmelanogaster.ucsc.dm6.ensgene/post-link.sh index c52879c46ddf5..70ac51af4666c 100644 --- a/recipes/bioconductor-txdb.dmelanogaster.ucsc.dm6.ensgene/post-link.sh +++ b/recipes/bioconductor-txdb.dmelanogaster.ucsc.dm6.ensgene/post-link.sh @@ -1,11 +1,11 @@ #!/bin/bash -FN="TxDb.Dmelanogaster.UCSC.dm6.ensGene_3.4.4.tar.gz" +FN="TxDb.Dmelanogaster.UCSC.dm6.ensGene_3.4.6.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/TxDb.Dmelanogaster.UCSC.dm6.ensGene_3.4.4.tar.gz" - "https://bioarchive.galaxyproject.org/TxDb.Dmelanogaster.UCSC.dm6.ensGene_3.4.4.tar.gz" - "https://depot.galaxyproject.org/software/bioconductor-txdb.dmelanogaster.ucsc.dm6.ensgene/bioconductor-txdb.dmelanogaster.ucsc.dm6.ensgene_3.4.4_src_all.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/TxDb.Dmelanogaster.UCSC.dm6.ensGene_3.4.6.tar.gz" + "https://bioarchive.galaxyproject.org/TxDb.Dmelanogaster.UCSC.dm6.ensGene_3.4.6.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-txdb.dmelanogaster.ucsc.dm6.ensgene/bioconductor-txdb.dmelanogaster.ucsc.dm6.ensgene_3.4.6_src_all.tar.gz" ) -MD5="7cad715c42d1f960c0e54905ec6612d7" +MD5="3f44aee6ed70de5594d80262674c0e15" # Use a staging area in the conda dir rather than temp dirs, both to avoid # permission issues as well as to have things downloaded in a predictable @@ -16,7 +16,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-txdb.drerio.ucsc.danrer10.refgene/meta.yaml b/recipes/bioconductor-txdb.drerio.ucsc.danrer10.refgene/meta.yaml index 8c1d181205c0f..b8ec2cee53e11 100644 --- a/recipes/bioconductor-txdb.drerio.ucsc.danrer10.refgene/meta.yaml +++ b/recipes/bioconductor-txdb.drerio.ucsc.danrer10.refgene/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "3.4.4" %} +{% set version = "3.4.6" %} {% set name = "TxDb.Drerio.UCSC.danRer10.refGene" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: aba2cc25f7893d09c3f64e32f0771691 + md5: fef9bbec3809e1b69991516988f146fb build: number: 0 rpaths: @@ -19,14 +19,14 @@ build: noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' - - 'bioconductor-genomicfeatures >=1.34.0,<1.35.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' + - 'bioconductor-genomicfeatures >=1.36.0,<1.37.0' - r-base run: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' - - 'bioconductor-genomicfeatures >=1.34.0,<1.35.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' + - 'bioconductor-genomicfeatures >=1.36.0,<1.37.0' - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-txdb.drerio.ucsc.danrer10.refgene/post-link.sh b/recipes/bioconductor-txdb.drerio.ucsc.danrer10.refgene/post-link.sh index 018fae9b6ad3d..a581a96d2b7e9 100644 --- a/recipes/bioconductor-txdb.drerio.ucsc.danrer10.refgene/post-link.sh +++ b/recipes/bioconductor-txdb.drerio.ucsc.danrer10.refgene/post-link.sh @@ -1,11 +1,11 @@ #!/bin/bash -FN="TxDb.Drerio.UCSC.danRer10.refGene_3.4.4.tar.gz" +FN="TxDb.Drerio.UCSC.danRer10.refGene_3.4.6.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/TxDb.Drerio.UCSC.danRer10.refGene_3.4.4.tar.gz" - "https://bioarchive.galaxyproject.org/TxDb.Drerio.UCSC.danRer10.refGene_3.4.4.tar.gz" - "https://depot.galaxyproject.org/software/bioconductor-txdb.drerio.ucsc.danrer10.refgene/bioconductor-txdb.drerio.ucsc.danrer10.refgene_3.4.4_src_all.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/TxDb.Drerio.UCSC.danRer10.refGene_3.4.6.tar.gz" + "https://bioarchive.galaxyproject.org/TxDb.Drerio.UCSC.danRer10.refGene_3.4.6.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-txdb.drerio.ucsc.danrer10.refgene/bioconductor-txdb.drerio.ucsc.danrer10.refgene_3.4.6_src_all.tar.gz" ) -MD5="aba2cc25f7893d09c3f64e32f0771691" +MD5="fef9bbec3809e1b69991516988f146fb" # Use a staging area in the conda dir rather than temp dirs, both to avoid # permission issues as well as to have things downloaded in a predictable @@ -16,7 +16,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-txdb.drerio.ucsc.danrer11.refgene/meta.yaml b/recipes/bioconductor-txdb.drerio.ucsc.danrer11.refgene/meta.yaml new file mode 100644 index 0000000000000..bbbc789af1f49 --- /dev/null +++ b/recipes/bioconductor-txdb.drerio.ucsc.danrer11.refgene/meta.yaml @@ -0,0 +1,37 @@ +{% set version = "3.4.6" %} +{% set name = "TxDb.Drerio.UCSC.danRer11.refGene" %} +{% set bioc = "3.9" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: 3d4ded4cec068a807b8b86b31389b677 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +requirements: + host: + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' + - 'bioconductor-genomicfeatures >=1.36.0,<1.37.0' + - r-base + run: + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' + - 'bioconductor-genomicfeatures >=1.36.0,<1.37.0' + - r-base + - curl +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'Exposes an annotation databases generated from UCSC by exposing these as TxDb objects' + diff --git a/recipes/bioconductor-txdb.drerio.ucsc.danrer11.refgene/post-link.sh b/recipes/bioconductor-txdb.drerio.ucsc.danrer11.refgene/post-link.sh new file mode 100644 index 0000000000000..34e3033e66ee3 --- /dev/null +++ b/recipes/bioconductor-txdb.drerio.ucsc.danrer11.refgene/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="TxDb.Drerio.UCSC.danRer11.refGene_3.4.6.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/TxDb.Drerio.UCSC.danRer11.refGene_3.4.6.tar.gz" + "https://bioarchive.galaxyproject.org/TxDb.Drerio.UCSC.danRer11.refGene_3.4.6.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-txdb.drerio.ucsc.danrer11.refgene/bioconductor-txdb.drerio.ucsc.danrer11.refgene_3.4.6_src_all.tar.gz" +) +MD5="3d4ded4cec068a807b8b86b31389b677" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + curl $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-txdb.drerio.ucsc.danrer11.refgene/pre-unlink.sh b/recipes/bioconductor-txdb.drerio.ucsc.danrer11.refgene/pre-unlink.sh new file mode 100644 index 0000000000000..34050961aaab9 --- /dev/null +++ b/recipes/bioconductor-txdb.drerio.ucsc.danrer11.refgene/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ TxDb.Drerio.UCSC.danRer11.refGene diff --git a/recipes/bioconductor-txdb.ggallus.ucsc.galgal4.refgene/meta.yaml b/recipes/bioconductor-txdb.ggallus.ucsc.galgal4.refgene/meta.yaml index 8855443d7d2a5..0062802040f7b 100644 --- a/recipes/bioconductor-txdb.ggallus.ucsc.galgal4.refgene/meta.yaml +++ b/recipes/bioconductor-txdb.ggallus.ucsc.galgal4.refgene/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "3.4.4" %} +{% set version = "3.4.6" %} {% set name = "TxDb.Ggallus.UCSC.galGal4.refGene" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: ed0a1620fa3031845720d5373a1a7716 + md5: fa3014553b93c5d97f97b5a7e2969a05 build: number: 0 rpaths: @@ -19,14 +19,14 @@ build: noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' - - 'bioconductor-genomicfeatures >=1.34.0,<1.35.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' + - 'bioconductor-genomicfeatures >=1.36.0,<1.37.0' - r-base run: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' - - 'bioconductor-genomicfeatures >=1.34.0,<1.35.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' + - 'bioconductor-genomicfeatures >=1.36.0,<1.37.0' - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-txdb.ggallus.ucsc.galgal4.refgene/post-link.sh b/recipes/bioconductor-txdb.ggallus.ucsc.galgal4.refgene/post-link.sh index 42e51aed34abb..9b082b8cadd8a 100644 --- a/recipes/bioconductor-txdb.ggallus.ucsc.galgal4.refgene/post-link.sh +++ b/recipes/bioconductor-txdb.ggallus.ucsc.galgal4.refgene/post-link.sh @@ -1,11 +1,11 @@ #!/bin/bash -FN="TxDb.Ggallus.UCSC.galGal4.refGene_3.4.4.tar.gz" +FN="TxDb.Ggallus.UCSC.galGal4.refGene_3.4.6.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/TxDb.Ggallus.UCSC.galGal4.refGene_3.4.4.tar.gz" - "https://bioarchive.galaxyproject.org/TxDb.Ggallus.UCSC.galGal4.refGene_3.4.4.tar.gz" - "https://depot.galaxyproject.org/software/bioconductor-txdb.ggallus.ucsc.galgal4.refgene/bioconductor-txdb.ggallus.ucsc.galgal4.refgene_3.4.4_src_all.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/TxDb.Ggallus.UCSC.galGal4.refGene_3.4.6.tar.gz" + "https://bioarchive.galaxyproject.org/TxDb.Ggallus.UCSC.galGal4.refGene_3.4.6.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-txdb.ggallus.ucsc.galgal4.refgene/bioconductor-txdb.ggallus.ucsc.galgal4.refgene_3.4.6_src_all.tar.gz" ) -MD5="ed0a1620fa3031845720d5373a1a7716" +MD5="fa3014553b93c5d97f97b5a7e2969a05" # Use a staging area in the conda dir rather than temp dirs, both to avoid # permission issues as well as to have things downloaded in a predictable @@ -16,7 +16,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-txdb.ggallus.ucsc.galgal5.refgene/meta.yaml b/recipes/bioconductor-txdb.ggallus.ucsc.galgal5.refgene/meta.yaml index 49a68faa60acd..2087135a8914f 100644 --- a/recipes/bioconductor-txdb.ggallus.ucsc.galgal5.refgene/meta.yaml +++ b/recipes/bioconductor-txdb.ggallus.ucsc.galgal5.refgene/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "3.4.4" %} +{% set version = "3.4.6" %} {% set name = "TxDb.Ggallus.UCSC.galGal5.refGene" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: bab2647bf88285a3e417524b9801cb29 + md5: 7a232a5afd00f6dd1313f36878a1f773 build: number: 0 rpaths: @@ -19,14 +19,14 @@ build: noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' - - 'bioconductor-genomicfeatures >=1.34.0,<1.35.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' + - 'bioconductor-genomicfeatures >=1.36.0,<1.37.0' - r-base run: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' - - 'bioconductor-genomicfeatures >=1.34.0,<1.35.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' + - 'bioconductor-genomicfeatures >=1.36.0,<1.37.0' - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-txdb.ggallus.ucsc.galgal5.refgene/post-link.sh b/recipes/bioconductor-txdb.ggallus.ucsc.galgal5.refgene/post-link.sh index 944ff30d1f5e5..53abb3e437818 100644 --- a/recipes/bioconductor-txdb.ggallus.ucsc.galgal5.refgene/post-link.sh +++ b/recipes/bioconductor-txdb.ggallus.ucsc.galgal5.refgene/post-link.sh @@ -1,11 +1,11 @@ #!/bin/bash -FN="TxDb.Ggallus.UCSC.galGal5.refGene_3.4.4.tar.gz" +FN="TxDb.Ggallus.UCSC.galGal5.refGene_3.4.6.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/TxDb.Ggallus.UCSC.galGal5.refGene_3.4.4.tar.gz" - "https://bioarchive.galaxyproject.org/TxDb.Ggallus.UCSC.galGal5.refGene_3.4.4.tar.gz" - "https://depot.galaxyproject.org/software/bioconductor-txdb.ggallus.ucsc.galgal5.refgene/bioconductor-txdb.ggallus.ucsc.galgal5.refgene_3.4.4_src_all.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/TxDb.Ggallus.UCSC.galGal5.refGene_3.4.6.tar.gz" + "https://bioarchive.galaxyproject.org/TxDb.Ggallus.UCSC.galGal5.refGene_3.4.6.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-txdb.ggallus.ucsc.galgal5.refgene/bioconductor-txdb.ggallus.ucsc.galgal5.refgene_3.4.6_src_all.tar.gz" ) -MD5="bab2647bf88285a3e417524b9801cb29" +MD5="7a232a5afd00f6dd1313f36878a1f773" # Use a staging area in the conda dir rather than temp dirs, both to avoid # permission issues as well as to have things downloaded in a predictable @@ -16,7 +16,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-txdb.hsapiens.biomart.igis/meta.yaml b/recipes/bioconductor-txdb.hsapiens.biomart.igis/meta.yaml index e83d0aec93abb..403f0f5bbe7e3 100644 --- a/recipes/bioconductor-txdb.hsapiens.biomart.igis/meta.yaml +++ b/recipes/bioconductor-txdb.hsapiens.biomart.igis/meta.yaml @@ -1,6 +1,6 @@ {% set version = "2.3.2" %} {% set name = "TxDb.Hsapiens.BioMart.igis" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -12,21 +12,21 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' md5: 75b793928d29bcd3f069b5986bc2cfae build: - number: 1 + number: 2 rpaths: - lib/R/lib/ - lib/ noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' - - 'bioconductor-genomicfeatures >=1.34.0,<1.35.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' + - 'bioconductor-genomicfeatures >=1.36.0,<1.37.0' - r-base run: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' - - 'bioconductor-genomicfeatures >=1.34.0,<1.35.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' + - 'bioconductor-genomicfeatures >=1.36.0,<1.37.0' - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-txdb.hsapiens.biomart.igis/post-link.sh b/recipes/bioconductor-txdb.hsapiens.biomart.igis/post-link.sh index e9d62d98e57f3..16a3570943cfe 100644 --- a/recipes/bioconductor-txdb.hsapiens.biomart.igis/post-link.sh +++ b/recipes/bioconductor-txdb.hsapiens.biomart.igis/post-link.sh @@ -1,9 +1,10 @@ #!/bin/bash FN="TxDb.Hsapiens.BioMart.igis_2.3.2.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/TxDb.Hsapiens.BioMart.igis_2.3.2.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/TxDb.Hsapiens.BioMart.igis_2.3.2.tar.gz" "https://bioarchive.galaxyproject.org/TxDb.Hsapiens.BioMart.igis_2.3.2.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-txdb.hsapiens.biomart.igis/bioconductor-txdb.hsapiens.biomart.igis_2.3.2_src_all.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-txdb.hsapiens.biomart.igis/bioconductor-txdb.hsapiens.biomart.igis_2.3.2_src_all.tar.gz" ) MD5="75b793928d29bcd3f069b5986bc2cfae" @@ -16,7 +17,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-txdb.hsapiens.ucsc.hg18.knowngene/meta.yaml b/recipes/bioconductor-txdb.hsapiens.ucsc.hg18.knowngene/meta.yaml index 5bbb9221149b4..214ae585211e5 100644 --- a/recipes/bioconductor-txdb.hsapiens.ucsc.hg18.knowngene/meta.yaml +++ b/recipes/bioconductor-txdb.hsapiens.ucsc.hg18.knowngene/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.2.2" %} {% set name = "TxDb.Hsapiens.UCSC.hg18.knownGene" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -12,21 +12,21 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' md5: e8b32a672e87345c72bb30be73d1e2d6 build: - number: 4 + number: 5 rpaths: - lib/R/lib/ - lib/ noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' - - 'bioconductor-genomicfeatures >=1.34.0,<1.35.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' + - 'bioconductor-genomicfeatures >=1.36.0,<1.37.0' - r-base run: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' - - 'bioconductor-genomicfeatures >=1.34.0,<1.35.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' + - 'bioconductor-genomicfeatures >=1.36.0,<1.37.0' - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-txdb.hsapiens.ucsc.hg18.knowngene/post-link.sh b/recipes/bioconductor-txdb.hsapiens.ucsc.hg18.knowngene/post-link.sh index be11859325656..1a9c04dff3ba6 100644 --- a/recipes/bioconductor-txdb.hsapiens.ucsc.hg18.knowngene/post-link.sh +++ b/recipes/bioconductor-txdb.hsapiens.ucsc.hg18.knowngene/post-link.sh @@ -1,7 +1,7 @@ #!/bin/bash FN="TxDb.Hsapiens.UCSC.hg18.knownGene_3.2.2.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/TxDb.Hsapiens.UCSC.hg18.knownGene_3.2.2.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/TxDb.Hsapiens.UCSC.hg18.knownGene_3.2.2.tar.gz" "https://bioarchive.galaxyproject.org/TxDb.Hsapiens.UCSC.hg18.knownGene_3.2.2.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-txdb.hsapiens.ucsc.hg18.knowngene/bioconductor-txdb.hsapiens.ucsc.hg18.knowngene_3.2.2_src_all.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-txdb.hsapiens.ucsc.hg18.knowngene/bioconductor-txdb.hsapiens.ucsc.hg18.knowngene_3.2.2_src_all.tar.gz" @@ -17,7 +17,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-txdb.hsapiens.ucsc.hg19.knowngene/meta.yaml b/recipes/bioconductor-txdb.hsapiens.ucsc.hg19.knowngene/meta.yaml index a1111cc3df693..b0f3641ca8a45 100644 --- a/recipes/bioconductor-txdb.hsapiens.ucsc.hg19.knowngene/meta.yaml +++ b/recipes/bioconductor-txdb.hsapiens.ucsc.hg19.knowngene/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.2.2" %} {% set name = "TxDb.Hsapiens.UCSC.hg19.knownGene" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -12,21 +12,21 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' md5: 61be88a81433958571b57d0952be48a0 build: - number: 4 + number: 5 rpaths: - lib/R/lib/ - lib/ noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' - - 'bioconductor-genomicfeatures >=1.34.0,<1.35.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' + - 'bioconductor-genomicfeatures >=1.36.0,<1.37.0' - r-base run: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' - - 'bioconductor-genomicfeatures >=1.34.0,<1.35.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' + - 'bioconductor-genomicfeatures >=1.36.0,<1.37.0' - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-txdb.hsapiens.ucsc.hg19.knowngene/post-link.sh b/recipes/bioconductor-txdb.hsapiens.ucsc.hg19.knowngene/post-link.sh index 0a43adeff4d3f..b8cf799e0274e 100644 --- a/recipes/bioconductor-txdb.hsapiens.ucsc.hg19.knowngene/post-link.sh +++ b/recipes/bioconductor-txdb.hsapiens.ucsc.hg19.knowngene/post-link.sh @@ -1,7 +1,7 @@ #!/bin/bash FN="TxDb.Hsapiens.UCSC.hg19.knownGene_3.2.2.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/TxDb.Hsapiens.UCSC.hg19.knownGene_3.2.2.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/TxDb.Hsapiens.UCSC.hg19.knownGene_3.2.2.tar.gz" "https://bioarchive.galaxyproject.org/TxDb.Hsapiens.UCSC.hg19.knownGene_3.2.2.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-txdb.hsapiens.ucsc.hg19.knowngene/bioconductor-txdb.hsapiens.ucsc.hg19.knowngene_3.2.2_src_all.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-txdb.hsapiens.ucsc.hg19.knowngene/bioconductor-txdb.hsapiens.ucsc.hg19.knowngene_3.2.2_src_all.tar.gz" @@ -17,7 +17,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-txdb.hsapiens.ucsc.hg19.lincrnastranscripts/meta.yaml b/recipes/bioconductor-txdb.hsapiens.ucsc.hg19.lincrnastranscripts/meta.yaml index 0341ee6495102..cb0b498160b4d 100644 --- a/recipes/bioconductor-txdb.hsapiens.ucsc.hg19.lincrnastranscripts/meta.yaml +++ b/recipes/bioconductor-txdb.hsapiens.ucsc.hg19.lincrnastranscripts/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.2.2" %} {% set name = "TxDb.Hsapiens.UCSC.hg19.lincRNAsTranscripts" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -12,21 +12,21 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' md5: a0d61cd90639c40b3d0bb6bdb043cf12 build: - number: 6 + number: 7 rpaths: - lib/R/lib/ - lib/ noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' - - 'bioconductor-genomicfeatures >=1.34.0,<1.35.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' + - 'bioconductor-genomicfeatures >=1.36.0,<1.37.0' - r-base run: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' - - 'bioconductor-genomicfeatures >=1.34.0,<1.35.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' + - 'bioconductor-genomicfeatures >=1.36.0,<1.37.0' - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-txdb.hsapiens.ucsc.hg19.lincrnastranscripts/post-link.sh b/recipes/bioconductor-txdb.hsapiens.ucsc.hg19.lincrnastranscripts/post-link.sh index 6c08f9edf1b4e..469322cb0d0e7 100644 --- a/recipes/bioconductor-txdb.hsapiens.ucsc.hg19.lincrnastranscripts/post-link.sh +++ b/recipes/bioconductor-txdb.hsapiens.ucsc.hg19.lincrnastranscripts/post-link.sh @@ -1,7 +1,7 @@ #!/bin/bash FN="TxDb.Hsapiens.UCSC.hg19.lincRNAsTranscripts_3.2.2.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/TxDb.Hsapiens.UCSC.hg19.lincRNAsTranscripts_3.2.2.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/TxDb.Hsapiens.UCSC.hg19.lincRNAsTranscripts_3.2.2.tar.gz" "https://bioarchive.galaxyproject.org/TxDb.Hsapiens.UCSC.hg19.lincRNAsTranscripts_3.2.2.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-txdb.hsapiens.ucsc.hg19.lincrnastranscripts/bioconductor-txdb.hsapiens.ucsc.hg19.lincrnastranscripts_3.2.2_src_all.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-txdb.hsapiens.ucsc.hg19.lincrnastranscripts/bioconductor-txdb.hsapiens.ucsc.hg19.lincrnastranscripts_3.2.2_src_all.tar.gz" @@ -17,7 +17,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-txdb.hsapiens.ucsc.hg38.knowngene/meta.yaml b/recipes/bioconductor-txdb.hsapiens.ucsc.hg38.knowngene/meta.yaml index e207abf3b0650..1de518ea0fe4a 100644 --- a/recipes/bioconductor-txdb.hsapiens.ucsc.hg38.knowngene/meta.yaml +++ b/recipes/bioconductor-txdb.hsapiens.ucsc.hg38.knowngene/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "3.4.0" %} +{% set version = "3.4.6" %} {% set name = "TxDb.Hsapiens.UCSC.hg38.knownGene" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,23 +10,23 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 1d5e07631ea58e96b11905d39e76ca6e + md5: 322952c40c9ef5d9a440c8e88e8fd5bf build: - number: 4 + number: 0 rpaths: - lib/R/lib/ - lib/ noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' - - 'bioconductor-genomicfeatures >=1.34.0,<1.35.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' + - 'bioconductor-genomicfeatures >=1.36.0,<1.37.0' - r-base run: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' - - 'bioconductor-genomicfeatures >=1.34.0,<1.35.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' + - 'bioconductor-genomicfeatures >=1.36.0,<1.37.0' - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-txdb.hsapiens.ucsc.hg38.knowngene/post-link.sh b/recipes/bioconductor-txdb.hsapiens.ucsc.hg38.knowngene/post-link.sh index ca419c728fb28..0f66a1671e046 100644 --- a/recipes/bioconductor-txdb.hsapiens.ucsc.hg38.knowngene/post-link.sh +++ b/recipes/bioconductor-txdb.hsapiens.ucsc.hg38.knowngene/post-link.sh @@ -1,12 +1,11 @@ #!/bin/bash -FN="TxDb.Hsapiens.UCSC.hg38.knownGene_3.4.0.tar.gz" +FN="TxDb.Hsapiens.UCSC.hg38.knownGene_3.4.6.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/TxDb.Hsapiens.UCSC.hg38.knownGene_3.4.0.tar.gz" - "https://bioarchive.galaxyproject.org/TxDb.Hsapiens.UCSC.hg38.knownGene_3.4.0.tar.gz" - "https://depot.galaxyproject.org/software/bioconductor-txdb.hsapiens.ucsc.hg38.knowngene/bioconductor-txdb.hsapiens.ucsc.hg38.knowngene_3.4.0_src_all.tar.gz" - "https://depot.galaxyproject.org/software/bioconductor-txdb.hsapiens.ucsc.hg38.knowngene/bioconductor-txdb.hsapiens.ucsc.hg38.knowngene_3.4.0_src_all.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/TxDb.Hsapiens.UCSC.hg38.knownGene_3.4.6.tar.gz" + "https://bioarchive.galaxyproject.org/TxDb.Hsapiens.UCSC.hg38.knownGene_3.4.6.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-txdb.hsapiens.ucsc.hg38.knowngene/bioconductor-txdb.hsapiens.ucsc.hg38.knowngene_3.4.6_src_all.tar.gz" ) -MD5="1d5e07631ea58e96b11905d39e76ca6e" +MD5="322952c40c9ef5d9a440c8e88e8fd5bf" # Use a staging area in the conda dir rather than temp dirs, both to avoid # permission issues as well as to have things downloaded in a predictable @@ -17,7 +16,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-txdb.mmulatta.ucsc.rhemac3.refgene/meta.yaml b/recipes/bioconductor-txdb.mmulatta.ucsc.rhemac3.refgene/meta.yaml index f36a0a803c163..6dd31348ca8ab 100644 --- a/recipes/bioconductor-txdb.mmulatta.ucsc.rhemac3.refgene/meta.yaml +++ b/recipes/bioconductor-txdb.mmulatta.ucsc.rhemac3.refgene/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "3.4.4" %} +{% set version = "3.4.6" %} {% set name = "TxDb.Mmulatta.UCSC.rheMac3.refGene" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: f395dba94db765148ac814a1330f7ade + md5: 2983fa866d080962334f200709809bce build: number: 0 rpaths: @@ -19,14 +19,14 @@ build: noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' - - 'bioconductor-genomicfeatures >=1.34.0,<1.35.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' + - 'bioconductor-genomicfeatures >=1.36.0,<1.37.0' - r-base run: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' - - 'bioconductor-genomicfeatures >=1.34.0,<1.35.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' + - 'bioconductor-genomicfeatures >=1.36.0,<1.37.0' - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-txdb.mmulatta.ucsc.rhemac3.refgene/post-link.sh b/recipes/bioconductor-txdb.mmulatta.ucsc.rhemac3.refgene/post-link.sh index 407e8d791d1e7..06459e0bc5ca4 100644 --- a/recipes/bioconductor-txdb.mmulatta.ucsc.rhemac3.refgene/post-link.sh +++ b/recipes/bioconductor-txdb.mmulatta.ucsc.rhemac3.refgene/post-link.sh @@ -1,11 +1,11 @@ #!/bin/bash -FN="TxDb.Mmulatta.UCSC.rheMac3.refGene_3.4.4.tar.gz" +FN="TxDb.Mmulatta.UCSC.rheMac3.refGene_3.4.6.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/TxDb.Mmulatta.UCSC.rheMac3.refGene_3.4.4.tar.gz" - "https://bioarchive.galaxyproject.org/TxDb.Mmulatta.UCSC.rheMac3.refGene_3.4.4.tar.gz" - "https://depot.galaxyproject.org/software/bioconductor-txdb.mmulatta.ucsc.rhemac3.refgene/bioconductor-txdb.mmulatta.ucsc.rhemac3.refgene_3.4.4_src_all.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/TxDb.Mmulatta.UCSC.rheMac3.refGene_3.4.6.tar.gz" + "https://bioarchive.galaxyproject.org/TxDb.Mmulatta.UCSC.rheMac3.refGene_3.4.6.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-txdb.mmulatta.ucsc.rhemac3.refgene/bioconductor-txdb.mmulatta.ucsc.rhemac3.refgene_3.4.6_src_all.tar.gz" ) -MD5="f395dba94db765148ac814a1330f7ade" +MD5="2983fa866d080962334f200709809bce" # Use a staging area in the conda dir rather than temp dirs, both to avoid # permission issues as well as to have things downloaded in a predictable @@ -16,7 +16,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-txdb.mmulatta.ucsc.rhemac8.refgene/meta.yaml b/recipes/bioconductor-txdb.mmulatta.ucsc.rhemac8.refgene/meta.yaml index 1d2c548b05f1c..3d38101a795c2 100644 --- a/recipes/bioconductor-txdb.mmulatta.ucsc.rhemac8.refgene/meta.yaml +++ b/recipes/bioconductor-txdb.mmulatta.ucsc.rhemac8.refgene/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "3.4.4" %} +{% set version = "3.4.6" %} {% set name = "TxDb.Mmulatta.UCSC.rheMac8.refGene" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: b4a10fc4c1a277f8eba66da3ab697ff5 + md5: 01904f7252aab56c92e86a364a9a3fc2 build: number: 0 rpaths: @@ -19,14 +19,14 @@ build: noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' - - 'bioconductor-genomicfeatures >=1.34.0,<1.35.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' + - 'bioconductor-genomicfeatures >=1.36.0,<1.37.0' - r-base run: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' - - 'bioconductor-genomicfeatures >=1.34.0,<1.35.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' + - 'bioconductor-genomicfeatures >=1.36.0,<1.37.0' - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-txdb.mmulatta.ucsc.rhemac8.refgene/post-link.sh b/recipes/bioconductor-txdb.mmulatta.ucsc.rhemac8.refgene/post-link.sh index 2e310cd7520f5..ffe5762e7ac18 100644 --- a/recipes/bioconductor-txdb.mmulatta.ucsc.rhemac8.refgene/post-link.sh +++ b/recipes/bioconductor-txdb.mmulatta.ucsc.rhemac8.refgene/post-link.sh @@ -1,11 +1,11 @@ #!/bin/bash -FN="TxDb.Mmulatta.UCSC.rheMac8.refGene_3.4.4.tar.gz" +FN="TxDb.Mmulatta.UCSC.rheMac8.refGene_3.4.6.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/TxDb.Mmulatta.UCSC.rheMac8.refGene_3.4.4.tar.gz" - "https://bioarchive.galaxyproject.org/TxDb.Mmulatta.UCSC.rheMac8.refGene_3.4.4.tar.gz" - "https://depot.galaxyproject.org/software/bioconductor-txdb.mmulatta.ucsc.rhemac8.refgene/bioconductor-txdb.mmulatta.ucsc.rhemac8.refgene_3.4.4_src_all.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/TxDb.Mmulatta.UCSC.rheMac8.refGene_3.4.6.tar.gz" + "https://bioarchive.galaxyproject.org/TxDb.Mmulatta.UCSC.rheMac8.refGene_3.4.6.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-txdb.mmulatta.ucsc.rhemac8.refgene/bioconductor-txdb.mmulatta.ucsc.rhemac8.refgene_3.4.6_src_all.tar.gz" ) -MD5="b4a10fc4c1a277f8eba66da3ab697ff5" +MD5="01904f7252aab56c92e86a364a9a3fc2" # Use a staging area in the conda dir rather than temp dirs, both to avoid # permission issues as well as to have things downloaded in a predictable @@ -16,7 +16,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-txdb.mmusculus.ucsc.mm10.ensgene/meta.yaml b/recipes/bioconductor-txdb.mmusculus.ucsc.mm10.ensgene/meta.yaml index d8a9c40927bca..879c78b3a5f83 100644 --- a/recipes/bioconductor-txdb.mmusculus.ucsc.mm10.ensgene/meta.yaml +++ b/recipes/bioconductor-txdb.mmusculus.ucsc.mm10.ensgene/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.4.0" %} {% set name = "TxDb.Mmusculus.UCSC.mm10.ensGene" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -12,21 +12,21 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' md5: 88d65b714d1f86b456aee2b8524e9d84 build: - number: 5 + number: 6 rpaths: - lib/R/lib/ - lib/ noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' - - 'bioconductor-genomicfeatures >=1.34.0,<1.35.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' + - 'bioconductor-genomicfeatures >=1.36.0,<1.37.0' - r-base run: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' - - 'bioconductor-genomicfeatures >=1.34.0,<1.35.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' + - 'bioconductor-genomicfeatures >=1.36.0,<1.37.0' - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-txdb.mmusculus.ucsc.mm10.ensgene/post-link.sh b/recipes/bioconductor-txdb.mmusculus.ucsc.mm10.ensgene/post-link.sh index dc07e46ba4753..650dad84f57ea 100644 --- a/recipes/bioconductor-txdb.mmusculus.ucsc.mm10.ensgene/post-link.sh +++ b/recipes/bioconductor-txdb.mmusculus.ucsc.mm10.ensgene/post-link.sh @@ -1,7 +1,7 @@ #!/bin/bash FN="TxDb.Mmusculus.UCSC.mm10.ensGene_3.4.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/TxDb.Mmusculus.UCSC.mm10.ensGene_3.4.0.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/TxDb.Mmusculus.UCSC.mm10.ensGene_3.4.0.tar.gz" "https://bioarchive.galaxyproject.org/TxDb.Mmusculus.UCSC.mm10.ensGene_3.4.0.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-txdb.mmusculus.ucsc.mm10.ensgene/bioconductor-txdb.mmusculus.ucsc.mm10.ensgene_3.4.0_src_all.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-txdb.mmusculus.ucsc.mm10.ensgene/bioconductor-txdb.mmusculus.ucsc.mm10.ensgene_3.4.0_src_all.tar.gz" @@ -17,7 +17,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-txdb.mmusculus.ucsc.mm10.knowngene/meta.yaml b/recipes/bioconductor-txdb.mmusculus.ucsc.mm10.knowngene/meta.yaml index 21fd3bbade05f..eac8c168fb7b9 100644 --- a/recipes/bioconductor-txdb.mmusculus.ucsc.mm10.knowngene/meta.yaml +++ b/recipes/bioconductor-txdb.mmusculus.ucsc.mm10.knowngene/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "3.4.4" %} +{% set version = "3.4.7" %} {% set name = "TxDb.Mmusculus.UCSC.mm10.knownGene" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 48c7efbd3a3004a0760b56b4858cc6c7 + md5: 48ca12361578a95864fc4c59524b61e9 build: number: 0 rpaths: @@ -19,14 +19,14 @@ build: noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' - - 'bioconductor-genomicfeatures >=1.34.0,<1.35.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' + - 'bioconductor-genomicfeatures >=1.36.0,<1.37.0' - r-base run: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' - - 'bioconductor-genomicfeatures >=1.34.0,<1.35.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' + - 'bioconductor-genomicfeatures >=1.36.0,<1.37.0' - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-txdb.mmusculus.ucsc.mm10.knowngene/post-link.sh b/recipes/bioconductor-txdb.mmusculus.ucsc.mm10.knowngene/post-link.sh index 6cf573cd948bf..3dfd40e8c0949 100644 --- a/recipes/bioconductor-txdb.mmusculus.ucsc.mm10.knowngene/post-link.sh +++ b/recipes/bioconductor-txdb.mmusculus.ucsc.mm10.knowngene/post-link.sh @@ -1,11 +1,11 @@ #!/bin/bash -FN="TxDb.Mmusculus.UCSC.mm10.knownGene_3.4.4.tar.gz" +FN="TxDb.Mmusculus.UCSC.mm10.knownGene_3.4.7.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/TxDb.Mmusculus.UCSC.mm10.knownGene_3.4.4.tar.gz" - "https://bioarchive.galaxyproject.org/TxDb.Mmusculus.UCSC.mm10.knownGene_3.4.4.tar.gz" - "https://depot.galaxyproject.org/software/bioconductor-txdb.mmusculus.ucsc.mm10.knowngene/bioconductor-txdb.mmusculus.ucsc.mm10.knowngene_3.4.4_src_all.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/TxDb.Mmusculus.UCSC.mm10.knownGene_3.4.7.tar.gz" + "https://bioarchive.galaxyproject.org/TxDb.Mmusculus.UCSC.mm10.knownGene_3.4.7.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-txdb.mmusculus.ucsc.mm10.knowngene/bioconductor-txdb.mmusculus.ucsc.mm10.knowngene_3.4.7_src_all.tar.gz" ) -MD5="48c7efbd3a3004a0760b56b4858cc6c7" +MD5="48ca12361578a95864fc4c59524b61e9" # Use a staging area in the conda dir rather than temp dirs, both to avoid # permission issues as well as to have things downloaded in a predictable @@ -16,7 +16,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-txdb.mmusculus.ucsc.mm9.knowngene/meta.yaml b/recipes/bioconductor-txdb.mmusculus.ucsc.mm9.knowngene/meta.yaml index 079710f54bec6..843eabcb9dc40 100644 --- a/recipes/bioconductor-txdb.mmusculus.ucsc.mm9.knowngene/meta.yaml +++ b/recipes/bioconductor-txdb.mmusculus.ucsc.mm9.knowngene/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.2.2" %} {% set name = "TxDb.Mmusculus.UCSC.mm9.knownGene" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -12,21 +12,21 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' md5: cb72af039b011033477363bda8ed9104 build: - number: 4 + number: 5 rpaths: - lib/R/lib/ - lib/ noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' - - 'bioconductor-genomicfeatures >=1.34.0,<1.35.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' + - 'bioconductor-genomicfeatures >=1.36.0,<1.37.0' - r-base run: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' - - 'bioconductor-genomicfeatures >=1.34.0,<1.35.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' + - 'bioconductor-genomicfeatures >=1.36.0,<1.37.0' - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-txdb.mmusculus.ucsc.mm9.knowngene/post-link.sh b/recipes/bioconductor-txdb.mmusculus.ucsc.mm9.knowngene/post-link.sh index 47194c9c45f5c..589228022d746 100644 --- a/recipes/bioconductor-txdb.mmusculus.ucsc.mm9.knowngene/post-link.sh +++ b/recipes/bioconductor-txdb.mmusculus.ucsc.mm9.knowngene/post-link.sh @@ -1,7 +1,7 @@ #!/bin/bash FN="TxDb.Mmusculus.UCSC.mm9.knownGene_3.2.2.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/TxDb.Mmusculus.UCSC.mm9.knownGene_3.2.2.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/TxDb.Mmusculus.UCSC.mm9.knownGene_3.2.2.tar.gz" "https://bioarchive.galaxyproject.org/TxDb.Mmusculus.UCSC.mm9.knownGene_3.2.2.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-txdb.mmusculus.ucsc.mm9.knowngene/bioconductor-txdb.mmusculus.ucsc.mm9.knowngene_3.2.2_src_all.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-txdb.mmusculus.ucsc.mm9.knowngene/bioconductor-txdb.mmusculus.ucsc.mm9.knowngene_3.2.2_src_all.tar.gz" @@ -17,7 +17,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-txdb.ptroglodytes.ucsc.pantro4.refgene/meta.yaml b/recipes/bioconductor-txdb.ptroglodytes.ucsc.pantro4.refgene/meta.yaml index 0a1bb081ff008..fd6b4f08ff697 100644 --- a/recipes/bioconductor-txdb.ptroglodytes.ucsc.pantro4.refgene/meta.yaml +++ b/recipes/bioconductor-txdb.ptroglodytes.ucsc.pantro4.refgene/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "3.4.4" %} +{% set version = "3.4.6" %} {% set name = "TxDb.Ptroglodytes.UCSC.panTro4.refGene" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,23 +10,23 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 85e52cd67bc1433b4cc4553022778fec + md5: 4cc70fea8cd33576909f8729af2e9a51 build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' - - 'bioconductor-genomicfeatures >=1.34.0,<1.35.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' + - 'bioconductor-genomicfeatures >=1.36.0,<1.37.0' - r-base run: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' - - 'bioconductor-genomicfeatures >=1.34.0,<1.35.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' + - 'bioconductor-genomicfeatures >=1.36.0,<1.37.0' - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-txdb.ptroglodytes.ucsc.pantro4.refgene/post-link.sh b/recipes/bioconductor-txdb.ptroglodytes.ucsc.pantro4.refgene/post-link.sh index a1203dfa2bd68..3d5c29db0f211 100644 --- a/recipes/bioconductor-txdb.ptroglodytes.ucsc.pantro4.refgene/post-link.sh +++ b/recipes/bioconductor-txdb.ptroglodytes.ucsc.pantro4.refgene/post-link.sh @@ -1,11 +1,11 @@ #!/bin/bash -FN="TxDb.Ptroglodytes.UCSC.panTro4.refGene_3.4.4.tar.gz" +FN="TxDb.Ptroglodytes.UCSC.panTro4.refGene_3.4.6.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/TxDb.Ptroglodytes.UCSC.panTro4.refGene_3.4.4.tar.gz" - "https://bioarchive.galaxyproject.org/TxDb.Ptroglodytes.UCSC.panTro4.refGene_3.4.4.tar.gz" - "https://depot.galaxyproject.org/software/bioconductor-txdb.ptroglodytes.ucsc.pantro4.refgene/bioconductor-txdb.ptroglodytes.ucsc.pantro4.refgene_3.4.4_src_all.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/TxDb.Ptroglodytes.UCSC.panTro4.refGene_3.4.6.tar.gz" + "https://bioarchive.galaxyproject.org/TxDb.Ptroglodytes.UCSC.panTro4.refGene_3.4.6.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-txdb.ptroglodytes.ucsc.pantro4.refgene/bioconductor-txdb.ptroglodytes.ucsc.pantro4.refgene_3.4.6_src_all.tar.gz" ) -MD5="85e52cd67bc1433b4cc4553022778fec" +MD5="4cc70fea8cd33576909f8729af2e9a51" # Use a staging area in the conda dir rather than temp dirs, both to avoid # permission issues as well as to have things downloaded in a predictable @@ -16,7 +16,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-txdb.ptroglodytes.ucsc.pantro5.refgene/meta.yaml b/recipes/bioconductor-txdb.ptroglodytes.ucsc.pantro5.refgene/meta.yaml index 71cd837ec2737..b9b3e164647cd 100644 --- a/recipes/bioconductor-txdb.ptroglodytes.ucsc.pantro5.refgene/meta.yaml +++ b/recipes/bioconductor-txdb.ptroglodytes.ucsc.pantro5.refgene/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "3.4.4" %} +{% set version = "3.4.6" %} {% set name = "TxDb.Ptroglodytes.UCSC.panTro5.refGene" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 778842f0216030a8d60674c7e04fbc47 + md5: 7a56692007154b6a83b70a4c6e5a9ebb build: number: 0 rpaths: @@ -19,14 +19,14 @@ build: noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' - - 'bioconductor-genomicfeatures >=1.34.0,<1.35.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' + - 'bioconductor-genomicfeatures >=1.36.0,<1.37.0' - r-base run: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' - - 'bioconductor-genomicfeatures >=1.34.0,<1.35.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' + - 'bioconductor-genomicfeatures >=1.36.0,<1.37.0' - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-txdb.ptroglodytes.ucsc.pantro5.refgene/post-link.sh b/recipes/bioconductor-txdb.ptroglodytes.ucsc.pantro5.refgene/post-link.sh index 1c210dd028388..540d99cab4891 100644 --- a/recipes/bioconductor-txdb.ptroglodytes.ucsc.pantro5.refgene/post-link.sh +++ b/recipes/bioconductor-txdb.ptroglodytes.ucsc.pantro5.refgene/post-link.sh @@ -1,11 +1,11 @@ #!/bin/bash -FN="TxDb.Ptroglodytes.UCSC.panTro5.refGene_3.4.4.tar.gz" +FN="TxDb.Ptroglodytes.UCSC.panTro5.refGene_3.4.6.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/TxDb.Ptroglodytes.UCSC.panTro5.refGene_3.4.4.tar.gz" - "https://bioarchive.galaxyproject.org/TxDb.Ptroglodytes.UCSC.panTro5.refGene_3.4.4.tar.gz" - "https://depot.galaxyproject.org/software/bioconductor-txdb.ptroglodytes.ucsc.pantro5.refgene/bioconductor-txdb.ptroglodytes.ucsc.pantro5.refgene_3.4.4_src_all.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/TxDb.Ptroglodytes.UCSC.panTro5.refGene_3.4.6.tar.gz" + "https://bioarchive.galaxyproject.org/TxDb.Ptroglodytes.UCSC.panTro5.refGene_3.4.6.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-txdb.ptroglodytes.ucsc.pantro5.refgene/bioconductor-txdb.ptroglodytes.ucsc.pantro5.refgene_3.4.6_src_all.tar.gz" ) -MD5="778842f0216030a8d60674c7e04fbc47" +MD5="7a56692007154b6a83b70a4c6e5a9ebb" # Use a staging area in the conda dir rather than temp dirs, both to avoid # permission issues as well as to have things downloaded in a predictable @@ -16,7 +16,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-txdb.rnorvegicus.biomart.igis/meta.yaml b/recipes/bioconductor-txdb.rnorvegicus.biomart.igis/meta.yaml index c53a22c366db2..fdeb3b0f869d3 100644 --- a/recipes/bioconductor-txdb.rnorvegicus.biomart.igis/meta.yaml +++ b/recipes/bioconductor-txdb.rnorvegicus.biomart.igis/meta.yaml @@ -1,6 +1,6 @@ {% set version = "2.3.2" %} {% set name = "TxDb.Rnorvegicus.BioMart.igis" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -12,21 +12,21 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' md5: eaf695f63cd021074d68c76d148cdfb7 build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' - - 'bioconductor-genomicfeatures >=1.34.0,<1.35.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' + - 'bioconductor-genomicfeatures >=1.36.0,<1.37.0' - r-base run: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' - - 'bioconductor-genomicfeatures >=1.34.0,<1.35.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' + - 'bioconductor-genomicfeatures >=1.36.0,<1.37.0' - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-txdb.rnorvegicus.biomart.igis/post-link.sh b/recipes/bioconductor-txdb.rnorvegicus.biomart.igis/post-link.sh index 6f862f7744371..67f24c0701b5b 100644 --- a/recipes/bioconductor-txdb.rnorvegicus.biomart.igis/post-link.sh +++ b/recipes/bioconductor-txdb.rnorvegicus.biomart.igis/post-link.sh @@ -1,9 +1,10 @@ #!/bin/bash FN="TxDb.Rnorvegicus.BioMart.igis_2.3.2.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/TxDb.Rnorvegicus.BioMart.igis_2.3.2.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/TxDb.Rnorvegicus.BioMart.igis_2.3.2.tar.gz" "https://bioarchive.galaxyproject.org/TxDb.Rnorvegicus.BioMart.igis_2.3.2.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-txdb.rnorvegicus.biomart.igis/bioconductor-txdb.rnorvegicus.biomart.igis_2.3.2_src_all.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-txdb.rnorvegicus.biomart.igis/bioconductor-txdb.rnorvegicus.biomart.igis_2.3.2_src_all.tar.gz" ) MD5="eaf695f63cd021074d68c76d148cdfb7" @@ -16,7 +17,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-txdb.rnorvegicus.ucsc.rn4.ensgene/meta.yaml b/recipes/bioconductor-txdb.rnorvegicus.ucsc.rn4.ensgene/meta.yaml index 9eb62dbc3b7ee..e39b74e785ea7 100644 --- a/recipes/bioconductor-txdb.rnorvegicus.ucsc.rn4.ensgene/meta.yaml +++ b/recipes/bioconductor-txdb.rnorvegicus.ucsc.rn4.ensgene/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.2.2" %} {% set name = "TxDb.Rnorvegicus.UCSC.rn4.ensGene" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -12,21 +12,21 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' md5: 6bf2ebc522c2828c036e52b2028792c1 build: - number: 4 + number: 5 rpaths: - lib/R/lib/ - lib/ noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' - - 'bioconductor-genomicfeatures >=1.34.0,<1.35.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' + - 'bioconductor-genomicfeatures >=1.36.0,<1.37.0' - r-base run: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' - - 'bioconductor-genomicfeatures >=1.34.0,<1.35.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' + - 'bioconductor-genomicfeatures >=1.36.0,<1.37.0' - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-txdb.rnorvegicus.ucsc.rn4.ensgene/post-link.sh b/recipes/bioconductor-txdb.rnorvegicus.ucsc.rn4.ensgene/post-link.sh index 4ae5817baed38..681356e30b3d9 100644 --- a/recipes/bioconductor-txdb.rnorvegicus.ucsc.rn4.ensgene/post-link.sh +++ b/recipes/bioconductor-txdb.rnorvegicus.ucsc.rn4.ensgene/post-link.sh @@ -1,7 +1,7 @@ #!/bin/bash FN="TxDb.Rnorvegicus.UCSC.rn4.ensGene_3.2.2.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/TxDb.Rnorvegicus.UCSC.rn4.ensGene_3.2.2.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/TxDb.Rnorvegicus.UCSC.rn4.ensGene_3.2.2.tar.gz" "https://bioarchive.galaxyproject.org/TxDb.Rnorvegicus.UCSC.rn4.ensGene_3.2.2.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-txdb.rnorvegicus.ucsc.rn4.ensgene/bioconductor-txdb.rnorvegicus.ucsc.rn4.ensgene_3.2.2_src_all.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-txdb.rnorvegicus.ucsc.rn4.ensgene/bioconductor-txdb.rnorvegicus.ucsc.rn4.ensgene_3.2.2_src_all.tar.gz" @@ -17,7 +17,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-txdb.rnorvegicus.ucsc.rn5.refgene/meta.yaml b/recipes/bioconductor-txdb.rnorvegicus.ucsc.rn5.refgene/meta.yaml index a5b597e00b2cd..20ddcfa3e7494 100644 --- a/recipes/bioconductor-txdb.rnorvegicus.ucsc.rn5.refgene/meta.yaml +++ b/recipes/bioconductor-txdb.rnorvegicus.ucsc.rn5.refgene/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "3.4.4" %} +{% set version = "3.4.6" %} {% set name = "TxDb.Rnorvegicus.UCSC.rn5.refGene" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: edb5a69c1aab095e285d902b8edddddc + md5: e525b207eab3a82450104e7349ccf5cc build: number: 0 rpaths: @@ -19,14 +19,14 @@ build: noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' - - 'bioconductor-genomicfeatures >=1.34.0,<1.35.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' + - 'bioconductor-genomicfeatures >=1.36.0,<1.37.0' - r-base run: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' - - 'bioconductor-genomicfeatures >=1.34.0,<1.35.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' + - 'bioconductor-genomicfeatures >=1.36.0,<1.37.0' - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-txdb.rnorvegicus.ucsc.rn5.refgene/post-link.sh b/recipes/bioconductor-txdb.rnorvegicus.ucsc.rn5.refgene/post-link.sh index 8df704c5ee456..0213ae9491fc3 100644 --- a/recipes/bioconductor-txdb.rnorvegicus.ucsc.rn5.refgene/post-link.sh +++ b/recipes/bioconductor-txdb.rnorvegicus.ucsc.rn5.refgene/post-link.sh @@ -1,11 +1,11 @@ #!/bin/bash -FN="TxDb.Rnorvegicus.UCSC.rn5.refGene_3.4.4.tar.gz" +FN="TxDb.Rnorvegicus.UCSC.rn5.refGene_3.4.6.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/TxDb.Rnorvegicus.UCSC.rn5.refGene_3.4.4.tar.gz" - "https://bioarchive.galaxyproject.org/TxDb.Rnorvegicus.UCSC.rn5.refGene_3.4.4.tar.gz" - "https://depot.galaxyproject.org/software/bioconductor-txdb.rnorvegicus.ucsc.rn5.refgene/bioconductor-txdb.rnorvegicus.ucsc.rn5.refgene_3.4.4_src_all.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/TxDb.Rnorvegicus.UCSC.rn5.refGene_3.4.6.tar.gz" + "https://bioarchive.galaxyproject.org/TxDb.Rnorvegicus.UCSC.rn5.refGene_3.4.6.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-txdb.rnorvegicus.ucsc.rn5.refgene/bioconductor-txdb.rnorvegicus.ucsc.rn5.refgene_3.4.6_src_all.tar.gz" ) -MD5="edb5a69c1aab095e285d902b8edddddc" +MD5="e525b207eab3a82450104e7349ccf5cc" # Use a staging area in the conda dir rather than temp dirs, both to avoid # permission issues as well as to have things downloaded in a predictable @@ -16,7 +16,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-txdb.rnorvegicus.ucsc.rn6.refgene/meta.yaml b/recipes/bioconductor-txdb.rnorvegicus.ucsc.rn6.refgene/meta.yaml index 336a2e70125ac..546bd97185a59 100644 --- a/recipes/bioconductor-txdb.rnorvegicus.ucsc.rn6.refgene/meta.yaml +++ b/recipes/bioconductor-txdb.rnorvegicus.ucsc.rn6.refgene/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "3.4.4" %} +{% set version = "3.4.6" %} {% set name = "TxDb.Rnorvegicus.UCSC.rn6.refGene" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 517b65f7a796f7c7c4f4cce2673bbb0c + md5: ea525daa75bcf165eb24f6e93f4dbf6c build: number: 0 rpaths: @@ -19,14 +19,14 @@ build: noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' - - 'bioconductor-genomicfeatures >=1.34.0,<1.35.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' + - 'bioconductor-genomicfeatures >=1.36.0,<1.37.0' - r-base run: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' - - 'bioconductor-genomicfeatures >=1.34.0,<1.35.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' + - 'bioconductor-genomicfeatures >=1.36.0,<1.37.0' - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-txdb.rnorvegicus.ucsc.rn6.refgene/post-link.sh b/recipes/bioconductor-txdb.rnorvegicus.ucsc.rn6.refgene/post-link.sh index 94338ff73ac9e..2f4dc5ad764f9 100644 --- a/recipes/bioconductor-txdb.rnorvegicus.ucsc.rn6.refgene/post-link.sh +++ b/recipes/bioconductor-txdb.rnorvegicus.ucsc.rn6.refgene/post-link.sh @@ -1,11 +1,11 @@ #!/bin/bash -FN="TxDb.Rnorvegicus.UCSC.rn6.refGene_3.4.4.tar.gz" +FN="TxDb.Rnorvegicus.UCSC.rn6.refGene_3.4.6.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/TxDb.Rnorvegicus.UCSC.rn6.refGene_3.4.4.tar.gz" - "https://bioarchive.galaxyproject.org/TxDb.Rnorvegicus.UCSC.rn6.refGene_3.4.4.tar.gz" - "https://depot.galaxyproject.org/software/bioconductor-txdb.rnorvegicus.ucsc.rn6.refgene/bioconductor-txdb.rnorvegicus.ucsc.rn6.refgene_3.4.4_src_all.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/TxDb.Rnorvegicus.UCSC.rn6.refGene_3.4.6.tar.gz" + "https://bioarchive.galaxyproject.org/TxDb.Rnorvegicus.UCSC.rn6.refGene_3.4.6.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-txdb.rnorvegicus.ucsc.rn6.refgene/bioconductor-txdb.rnorvegicus.ucsc.rn6.refgene_3.4.6_src_all.tar.gz" ) -MD5="517b65f7a796f7c7c4f4cce2673bbb0c" +MD5="ea525daa75bcf165eb24f6e93f4dbf6c" # Use a staging area in the conda dir rather than temp dirs, both to avoid # permission issues as well as to have things downloaded in a predictable @@ -16,7 +16,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-txdb.scerevisiae.ucsc.saccer2.sgdgene/meta.yaml b/recipes/bioconductor-txdb.scerevisiae.ucsc.saccer2.sgdgene/meta.yaml index e984d0b7a9346..482690b692dac 100644 --- a/recipes/bioconductor-txdb.scerevisiae.ucsc.saccer2.sgdgene/meta.yaml +++ b/recipes/bioconductor-txdb.scerevisiae.ucsc.saccer2.sgdgene/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.2.2" %} {% set name = "TxDb.Scerevisiae.UCSC.sacCer2.sgdGene" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -12,21 +12,21 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' md5: 8ce83ef2ba6cfc69f9b4435a0a047819 build: - number: 7 + number: 8 rpaths: - lib/R/lib/ - lib/ noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' - - 'bioconductor-genomicfeatures >=1.34.0,<1.35.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' + - 'bioconductor-genomicfeatures >=1.36.0,<1.37.0' - r-base run: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' - - 'bioconductor-genomicfeatures >=1.34.0,<1.35.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' + - 'bioconductor-genomicfeatures >=1.36.0,<1.37.0' - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-txdb.scerevisiae.ucsc.saccer2.sgdgene/post-link.sh b/recipes/bioconductor-txdb.scerevisiae.ucsc.saccer2.sgdgene/post-link.sh index 40fb88d833a30..01ee0807a4a01 100644 --- a/recipes/bioconductor-txdb.scerevisiae.ucsc.saccer2.sgdgene/post-link.sh +++ b/recipes/bioconductor-txdb.scerevisiae.ucsc.saccer2.sgdgene/post-link.sh @@ -1,7 +1,7 @@ #!/bin/bash FN="TxDb.Scerevisiae.UCSC.sacCer2.sgdGene_3.2.2.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/TxDb.Scerevisiae.UCSC.sacCer2.sgdGene_3.2.2.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/TxDb.Scerevisiae.UCSC.sacCer2.sgdGene_3.2.2.tar.gz" "https://bioarchive.galaxyproject.org/TxDb.Scerevisiae.UCSC.sacCer2.sgdGene_3.2.2.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-txdb.scerevisiae.ucsc.saccer2.sgdgene/bioconductor-txdb.scerevisiae.ucsc.saccer2.sgdgene_3.2.2_src_all.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-txdb.scerevisiae.ucsc.saccer2.sgdgene/bioconductor-txdb.scerevisiae.ucsc.saccer2.sgdgene_3.2.2_src_all.tar.gz" @@ -17,7 +17,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-txdb.scerevisiae.ucsc.saccer3.sgdgene/meta.yaml b/recipes/bioconductor-txdb.scerevisiae.ucsc.saccer3.sgdgene/meta.yaml index 3896cc46db8ee..fcac44a69f560 100644 --- a/recipes/bioconductor-txdb.scerevisiae.ucsc.saccer3.sgdgene/meta.yaml +++ b/recipes/bioconductor-txdb.scerevisiae.ucsc.saccer3.sgdgene/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.2.2" %} {% set name = "TxDb.Scerevisiae.UCSC.sacCer3.sgdGene" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -12,21 +12,21 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' md5: afb23b3265730b9e59c2f07ab37cc3a0 build: - number: 10 + number: 11 rpaths: - lib/R/lib/ - lib/ noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' - - 'bioconductor-genomicfeatures >=1.34.0,<1.35.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' + - 'bioconductor-genomicfeatures >=1.36.0,<1.37.0' - r-base run: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' - - 'bioconductor-genomicfeatures >=1.34.0,<1.35.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' + - 'bioconductor-genomicfeatures >=1.36.0,<1.37.0' - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-txdb.scerevisiae.ucsc.saccer3.sgdgene/post-link.sh b/recipes/bioconductor-txdb.scerevisiae.ucsc.saccer3.sgdgene/post-link.sh index 32d7dfa5fc6ca..6d445267e122f 100644 --- a/recipes/bioconductor-txdb.scerevisiae.ucsc.saccer3.sgdgene/post-link.sh +++ b/recipes/bioconductor-txdb.scerevisiae.ucsc.saccer3.sgdgene/post-link.sh @@ -1,7 +1,7 @@ #!/bin/bash FN="TxDb.Scerevisiae.UCSC.sacCer3.sgdGene_3.2.2.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/TxDb.Scerevisiae.UCSC.sacCer3.sgdGene_3.2.2.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/TxDb.Scerevisiae.UCSC.sacCer3.sgdGene_3.2.2.tar.gz" "https://bioarchive.galaxyproject.org/TxDb.Scerevisiae.UCSC.sacCer3.sgdGene_3.2.2.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-txdb.scerevisiae.ucsc.saccer3.sgdgene/bioconductor-txdb.scerevisiae.ucsc.saccer3.sgdgene_3.2.2_src_all.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-txdb.scerevisiae.ucsc.saccer3.sgdgene/bioconductor-txdb.scerevisiae.ucsc.saccer3.sgdgene_3.2.2_src_all.tar.gz" @@ -17,7 +17,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-txdb.sscrofa.ucsc.susscr11.refgene/meta.yaml b/recipes/bioconductor-txdb.sscrofa.ucsc.susscr11.refgene/meta.yaml index 927d6d8177410..c93debdc76fd8 100644 --- a/recipes/bioconductor-txdb.sscrofa.ucsc.susscr11.refgene/meta.yaml +++ b/recipes/bioconductor-txdb.sscrofa.ucsc.susscr11.refgene/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "3.4.4" %} +{% set version = "3.4.6" %} {% set name = "TxDb.Sscrofa.UCSC.susScr11.refGene" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 7db4a04d14f707e53e5a921f125f8ea1 + md5: 21086add466ed6fff7ee756927614bb3 build: number: 0 rpaths: @@ -19,14 +19,14 @@ build: noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' - - 'bioconductor-genomicfeatures >=1.34.0,<1.35.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' + - 'bioconductor-genomicfeatures >=1.36.0,<1.37.0' - r-base run: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' - - 'bioconductor-genomicfeatures >=1.34.0,<1.35.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' + - 'bioconductor-genomicfeatures >=1.36.0,<1.37.0' - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-txdb.sscrofa.ucsc.susscr11.refgene/post-link.sh b/recipes/bioconductor-txdb.sscrofa.ucsc.susscr11.refgene/post-link.sh index 651c4a9c44181..42a041ed89e28 100644 --- a/recipes/bioconductor-txdb.sscrofa.ucsc.susscr11.refgene/post-link.sh +++ b/recipes/bioconductor-txdb.sscrofa.ucsc.susscr11.refgene/post-link.sh @@ -1,11 +1,11 @@ #!/bin/bash -FN="TxDb.Sscrofa.UCSC.susScr11.refGene_3.4.4.tar.gz" +FN="TxDb.Sscrofa.UCSC.susScr11.refGene_3.4.6.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/TxDb.Sscrofa.UCSC.susScr11.refGene_3.4.4.tar.gz" - "https://bioarchive.galaxyproject.org/TxDb.Sscrofa.UCSC.susScr11.refGene_3.4.4.tar.gz" - "https://depot.galaxyproject.org/software/bioconductor-txdb.sscrofa.ucsc.susscr11.refgene/bioconductor-txdb.sscrofa.ucsc.susscr11.refgene_3.4.4_src_all.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/TxDb.Sscrofa.UCSC.susScr11.refGene_3.4.6.tar.gz" + "https://bioarchive.galaxyproject.org/TxDb.Sscrofa.UCSC.susScr11.refGene_3.4.6.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-txdb.sscrofa.ucsc.susscr11.refgene/bioconductor-txdb.sscrofa.ucsc.susscr11.refgene_3.4.6_src_all.tar.gz" ) -MD5="7db4a04d14f707e53e5a921f125f8ea1" +MD5="21086add466ed6fff7ee756927614bb3" # Use a staging area in the conda dir rather than temp dirs, both to avoid # permission issues as well as to have things downloaded in a predictable @@ -16,7 +16,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-txdb.sscrofa.ucsc.susscr3.refgene/meta.yaml b/recipes/bioconductor-txdb.sscrofa.ucsc.susscr3.refgene/meta.yaml index e333266050793..aa910773509b9 100644 --- a/recipes/bioconductor-txdb.sscrofa.ucsc.susscr3.refgene/meta.yaml +++ b/recipes/bioconductor-txdb.sscrofa.ucsc.susscr3.refgene/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "3.4.4" %} +{% set version = "3.4.6" %} {% set name = "TxDb.Sscrofa.UCSC.susScr3.refGene" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: a98f0f01b07cfac30de6c028cb79f747 + md5: 17a9e1a37e5f3fd23f6cfb753d1ad8f2 build: number: 0 rpaths: @@ -19,14 +19,14 @@ build: noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' - - 'bioconductor-genomicfeatures >=1.34.0,<1.35.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' + - 'bioconductor-genomicfeatures >=1.36.0,<1.37.0' - r-base run: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' - - 'bioconductor-genomicfeatures >=1.34.0,<1.35.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' + - 'bioconductor-genomicfeatures >=1.36.0,<1.37.0' - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-txdb.sscrofa.ucsc.susscr3.refgene/post-link.sh b/recipes/bioconductor-txdb.sscrofa.ucsc.susscr3.refgene/post-link.sh index b918b0d37500b..ee309188b2123 100644 --- a/recipes/bioconductor-txdb.sscrofa.ucsc.susscr3.refgene/post-link.sh +++ b/recipes/bioconductor-txdb.sscrofa.ucsc.susscr3.refgene/post-link.sh @@ -1,11 +1,11 @@ #!/bin/bash -FN="TxDb.Sscrofa.UCSC.susScr3.refGene_3.4.4.tar.gz" +FN="TxDb.Sscrofa.UCSC.susScr3.refGene_3.4.6.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/TxDb.Sscrofa.UCSC.susScr3.refGene_3.4.4.tar.gz" - "https://bioarchive.galaxyproject.org/TxDb.Sscrofa.UCSC.susScr3.refGene_3.4.4.tar.gz" - "https://depot.galaxyproject.org/software/bioconductor-txdb.sscrofa.ucsc.susscr3.refgene/bioconductor-txdb.sscrofa.ucsc.susscr3.refgene_3.4.4_src_all.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/TxDb.Sscrofa.UCSC.susScr3.refGene_3.4.6.tar.gz" + "https://bioarchive.galaxyproject.org/TxDb.Sscrofa.UCSC.susScr3.refGene_3.4.6.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-txdb.sscrofa.ucsc.susscr3.refgene/bioconductor-txdb.sscrofa.ucsc.susscr3.refgene_3.4.6_src_all.tar.gz" ) -MD5="a98f0f01b07cfac30de6c028cb79f747" +MD5="17a9e1a37e5f3fd23f6cfb753d1ad8f2" # Use a staging area in the conda dir rather than temp dirs, both to avoid # permission issues as well as to have things downloaded in a predictable @@ -16,7 +16,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-tximeta/meta.yaml b/recipes/bioconductor-tximeta/meta.yaml index 2fc712a8c444c..5ea2d5958d0a2 100644 --- a/recipes/bioconductor-tximeta/meta.yaml +++ b/recipes/bioconductor-tximeta/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.0.3" %} +{% set version = "1.2.0" %} {% set name = "tximeta" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,37 +10,41 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: ee9fda484e8a56ee554d4f6bf85773d0 + md5: 446e0910bcaf29af9958373787337982 build: number: 0 rpaths: - lib/R/lib/ - lib/ noarch: generic -# Suggests: knitr, rmarkdown, testthat, tximportData, org.Dm.eg.db, DESeq2, devtools +# Suggests: knitr, rmarkdown, testthat, tximportData, org.Dm.eg.db, DESeq2, edgeR, devtools requirements: host: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' - - 'bioconductor-biocfilecache >=1.6.0,<1.7.0' - - 'bioconductor-ensembldb >=2.6.0,<2.7.0' - - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' - - 'bioconductor-genomicfeatures >=1.34.0,<1.35.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' - - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' - - 'bioconductor-tximport >=1.10.0,<1.11.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' + - 'bioconductor-biocfilecache >=1.8.0,<1.9.0' + - 'bioconductor-biostrings >=2.52.0,<2.53.0' + - 'bioconductor-ensembldb >=2.8.0,<2.9.0' + - 'bioconductor-genomeinfodb >=1.20.0,<1.21.0' + - 'bioconductor-genomicfeatures >=1.36.0,<1.37.0' + - 'bioconductor-genomicranges >=1.36.0,<1.37.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' + - 'bioconductor-summarizedexperiment >=1.14.0,<1.15.0' + - 'bioconductor-tximport >=1.12.0,<1.13.0' - r-base - r-jsonlite - r-rappdirs - r-tibble run: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' - - 'bioconductor-biocfilecache >=1.6.0,<1.7.0' - - 'bioconductor-ensembldb >=2.6.0,<2.7.0' - - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' - - 'bioconductor-genomicfeatures >=1.34.0,<1.35.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' - - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' - - 'bioconductor-tximport >=1.10.0,<1.11.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' + - 'bioconductor-biocfilecache >=1.8.0,<1.9.0' + - 'bioconductor-biostrings >=2.52.0,<2.53.0' + - 'bioconductor-ensembldb >=2.8.0,<2.9.0' + - 'bioconductor-genomeinfodb >=1.20.0,<1.21.0' + - 'bioconductor-genomicfeatures >=1.36.0,<1.37.0' + - 'bioconductor-genomicranges >=1.36.0,<1.37.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' + - 'bioconductor-summarizedexperiment >=1.14.0,<1.15.0' + - 'bioconductor-tximport >=1.12.0,<1.13.0' - r-base - r-jsonlite - r-rappdirs diff --git a/recipes/bioconductor-tximport/meta.yaml b/recipes/bioconductor-tximport/meta.yaml index 5090e9e4a4ed8..7d4da850d1424 100644 --- a/recipes/bioconductor-tximport/meta.yaml +++ b/recipes/bioconductor-tximport/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.10.1" %} +{% set version = "1.12.0" %} {% set name = "tximport" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,14 +10,14 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - sha256: 9490d6dc5d4ff9ffa4427597a2c8c247b18896a3af5a005825eb32505b02979b + md5: f513eb1d69d6f69f4fef693fe3cddc7c build: number: 0 rpaths: - lib/R/lib/ - lib/ noarch: generic -# Suggests: knitr, rmarkdown, testthat, tximportData, TxDb.Hsapiens.UCSC.hg19.knownGene, readr (>= 0.2.2), limma, edgeR, DESeq2 (>= 1.11.6), rhdf5, jsonlite, matrixStats +# Suggests: knitr, rmarkdown, testthat, tximportData, TxDb.Hsapiens.UCSC.hg19.knownGene, readr (>= 0.2.2), limma, edgeR, DESeq2 (>= 1.11.6), rhdf5, jsonlite, matrixStats, Matrix requirements: host: - r-base diff --git a/recipes/bioconductor-tximportdata/meta.yaml b/recipes/bioconductor-tximportdata/meta.yaml index eaffa39e5fd40..b2fec498df164 100644 --- a/recipes/bioconductor-tximportdata/meta.yaml +++ b/recipes/bioconductor-tximportdata/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.10.0" %} +{% set version = "1.12.0" %} {% set name = "tximportData" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 54178cc67ba022548272a2474fcecaac + md5: 8ac5ace87e64a47a3b4c68acfd5ae976 build: number: 0 rpaths: @@ -23,7 +23,7 @@ requirements: - r-base run: - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-tximportdata/post-link.sh b/recipes/bioconductor-tximportdata/post-link.sh index 048a7fc28f072..8b553778615ce 100644 --- a/recipes/bioconductor-tximportdata/post-link.sh +++ b/recipes/bioconductor-tximportdata/post-link.sh @@ -1,11 +1,11 @@ #!/bin/bash -FN="tximportData_1.10.0.tar.gz" +FN="tximportData_1.12.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/experiment/src/contrib/tximportData_1.10.0.tar.gz" - "https://bioarchive.galaxyproject.org/tximportData_1.10.0.tar.gz" - "https://depot.galaxyproject.org/software/bioconductor-tximportdata/bioconductor-tximportdata_1.10.0_src_all.tar.gz" + "https://bioconductor.org/packages/3.9/data/experiment/src/contrib/tximportData_1.12.0.tar.gz" + "https://bioarchive.galaxyproject.org/tximportData_1.12.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-tximportdata/bioconductor-tximportdata_1.12.0_src_all.tar.gz" ) -MD5="54178cc67ba022548272a2474fcecaac" +MD5="8ac5ace87e64a47a3b4c68acfd5ae976" # Use a staging area in the conda dir rather than temp dirs, both to avoid # permission issues as well as to have things downloaded in a predictable @@ -16,7 +16,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-txreginfra/meta.yaml b/recipes/bioconductor-txreginfra/meta.yaml index f9f282c0a6fdd..d169337ce8366 100644 --- a/recipes/bioconductor-txreginfra/meta.yaml +++ b/recipes/bioconductor-txreginfra/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.2.0" %} +{% set version = "1.4.0" %} {% set name = "TxRegInfra" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,34 +10,34 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: c09e95c44aca076760777fa3c89538eb + md5: 0a98c2779acd1d29ecd084e85045555e build: number: 0 rpaths: - lib/R/lib/ - lib/ noarch: generic -# Suggests: knitr, GenomicFiles, EnsDb.Hsapiens.v75, testthat, biovizBase (>= 1.27.2), Gviz, AnnotationFilter, ensembldb +# Suggests: knitr, GenomicFiles, EnsDb.Hsapiens.v75, testthat, shiny, biovizBase (>= 1.27.2), Gviz, AnnotationFilter, ensembldb, ontoProc requirements: host: - - 'bioconductor-biocparallel >=1.16.0,<1.17.0' - - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' - - 'bioconductor-genomicranges >=1.34.0,<1.35.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-raggedexperiment >=1.6.0,<1.7.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' - - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' + - 'bioconductor-biocparallel >=1.18.0,<1.19.0' + - 'bioconductor-genomeinfodb >=1.20.0,<1.21.0' + - 'bioconductor-genomicranges >=1.36.0,<1.37.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-raggedexperiment >=1.8.0,<1.9.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' + - 'bioconductor-summarizedexperiment >=1.14.0,<1.15.0' - r-base - r-mongolite - r-rjson run: - - 'bioconductor-biocparallel >=1.16.0,<1.17.0' - - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' - - 'bioconductor-genomicranges >=1.34.0,<1.35.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-raggedexperiment >=1.6.0,<1.7.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' - - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' + - 'bioconductor-biocparallel >=1.18.0,<1.19.0' + - 'bioconductor-genomeinfodb >=1.20.0,<1.21.0' + - 'bioconductor-genomicranges >=1.36.0,<1.37.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-raggedexperiment >=1.8.0,<1.9.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' + - 'bioconductor-summarizedexperiment >=1.14.0,<1.15.0' - r-base - r-mongolite - r-rjson diff --git a/recipes/bioconductor-typeinfo/meta.yaml b/recipes/bioconductor-typeinfo/meta.yaml index a607feed620f3..b2fb4029a42b2 100644 --- a/recipes/bioconductor-typeinfo/meta.yaml +++ b/recipes/bioconductor-typeinfo/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.48.0" %} +{% set version = "1.50.0" %} {% set name = "TypeInfo" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 1923e893a75108abebee8fc64984144e + md5: 5bf254f161ba0b8610042a08c62c9abf build: number: 0 rpaths: diff --git a/recipes/bioconductor-u133aaofav2cdf/meta.yaml b/recipes/bioconductor-u133aaofav2cdf/meta.yaml index cb166ddff5ae9..35af78527498b 100644 --- a/recipes/bioconductor-u133aaofav2cdf/meta.yaml +++ b/recipes/bioconductor-u133aaofav2cdf/meta.yaml @@ -1,6 +1,6 @@ {% set version = "2.18.0" %} {% set name = "u133aaofav2cdf" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -12,19 +12,19 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 716483ddb6664b8b7f0c58cd21136e8b build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' - r-base run: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-u133aaofav2cdf/post-link.sh b/recipes/bioconductor-u133aaofav2cdf/post-link.sh index fd172e0d773b4..f8ab93f0b4554 100644 --- a/recipes/bioconductor-u133aaofav2cdf/post-link.sh +++ b/recipes/bioconductor-u133aaofav2cdf/post-link.sh @@ -1,9 +1,10 @@ #!/bin/bash FN="u133aaofav2cdf_2.18.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/u133aaofav2cdf_2.18.0.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/u133aaofav2cdf_2.18.0.tar.gz" "https://bioarchive.galaxyproject.org/u133aaofav2cdf_2.18.0.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-u133aaofav2cdf/bioconductor-u133aaofav2cdf_2.18.0_src_all.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-u133aaofav2cdf/bioconductor-u133aaofav2cdf_2.18.0_src_all.tar.gz" ) MD5="716483ddb6664b8b7f0c58cd21136e8b" @@ -16,7 +17,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-u133x3p.db/meta.yaml b/recipes/bioconductor-u133x3p.db/meta.yaml index 9787bea5308f2..0fd78c18f75cc 100644 --- a/recipes/bioconductor-u133x3p.db/meta.yaml +++ b/recipes/bioconductor-u133x3p.db/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.2.3" %} {% set name = "u133x3p.db" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -12,7 +12,7 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 1a36a09dc64b94728bf6ac75600b40c6 build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ @@ -20,14 +20,14 @@ build: # Suggests: DBI, annotate, RUnit requirements: host: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' - - 'bioconductor-org.hs.eg.db >=3.7.0,<3.8.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' + - 'bioconductor-org.hs.eg.db >=3.8.0,<3.9.0' - r-base run: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' - - 'bioconductor-org.hs.eg.db >=3.7.0,<3.8.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' + - 'bioconductor-org.hs.eg.db >=3.8.0,<3.9.0' - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-u133x3p.db/post-link.sh b/recipes/bioconductor-u133x3p.db/post-link.sh index 8b5f650a67943..902b0673bb6e7 100644 --- a/recipes/bioconductor-u133x3p.db/post-link.sh +++ b/recipes/bioconductor-u133x3p.db/post-link.sh @@ -1,9 +1,10 @@ #!/bin/bash FN="u133x3p.db_3.2.3.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/u133x3p.db_3.2.3.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/u133x3p.db_3.2.3.tar.gz" "https://bioarchive.galaxyproject.org/u133x3p.db_3.2.3.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-u133x3p.db/bioconductor-u133x3p.db_3.2.3_src_all.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-u133x3p.db/bioconductor-u133x3p.db_3.2.3_src_all.tar.gz" ) MD5="1a36a09dc64b94728bf6ac75600b40c6" @@ -16,7 +17,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-u133x3pcdf/meta.yaml b/recipes/bioconductor-u133x3pcdf/meta.yaml index dc9cb442ead45..d62f9b5729642 100644 --- a/recipes/bioconductor-u133x3pcdf/meta.yaml +++ b/recipes/bioconductor-u133x3pcdf/meta.yaml @@ -1,6 +1,6 @@ {% set version = "2.18.0" %} {% set name = "u133x3pcdf" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -12,19 +12,19 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: ee4e62041bc8c63813e8cf8400ece2f3 build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' - r-base run: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-u133x3pcdf/post-link.sh b/recipes/bioconductor-u133x3pcdf/post-link.sh index 32627ff8d312f..b6264bb09b909 100644 --- a/recipes/bioconductor-u133x3pcdf/post-link.sh +++ b/recipes/bioconductor-u133x3pcdf/post-link.sh @@ -1,9 +1,10 @@ #!/bin/bash FN="u133x3pcdf_2.18.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/u133x3pcdf_2.18.0.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/u133x3pcdf_2.18.0.tar.gz" "https://bioarchive.galaxyproject.org/u133x3pcdf_2.18.0.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-u133x3pcdf/bioconductor-u133x3pcdf_2.18.0_src_all.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-u133x3pcdf/bioconductor-u133x3pcdf_2.18.0_src_all.tar.gz" ) MD5="ee4e62041bc8c63813e8cf8400ece2f3" @@ -16,7 +17,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-u133x3pprobe/meta.yaml b/recipes/bioconductor-u133x3pprobe/meta.yaml index d981fe282b9e2..0a6add33b920f 100644 --- a/recipes/bioconductor-u133x3pprobe/meta.yaml +++ b/recipes/bioconductor-u133x3pprobe/meta.yaml @@ -1,6 +1,6 @@ {% set version = "2.18.0" %} {% set name = "u133x3pprobe" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -12,19 +12,19 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 81e2b00985688160805147bef0c638be build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' - r-base run: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-u133x3pprobe/post-link.sh b/recipes/bioconductor-u133x3pprobe/post-link.sh index 25a8fe1f784ec..432ad5beb6d87 100644 --- a/recipes/bioconductor-u133x3pprobe/post-link.sh +++ b/recipes/bioconductor-u133x3pprobe/post-link.sh @@ -1,9 +1,10 @@ #!/bin/bash FN="u133x3pprobe_2.18.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/u133x3pprobe_2.18.0.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/u133x3pprobe_2.18.0.tar.gz" "https://bioarchive.galaxyproject.org/u133x3pprobe_2.18.0.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-u133x3pprobe/bioconductor-u133x3pprobe_2.18.0_src_all.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-u133x3pprobe/bioconductor-u133x3pprobe_2.18.0_src_all.tar.gz" ) MD5="81e2b00985688160805147bef0c638be" @@ -16,7 +17,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-ularcirc/meta.yaml b/recipes/bioconductor-ularcirc/meta.yaml index 76af3ce0453a1..6623c7949afc7 100644 --- a/recipes/bioconductor-ularcirc/meta.yaml +++ b/recipes/bioconductor-ularcirc/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.0.0" %} +{% set version = "1.2.0" %} {% set name = "Ularcirc" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: e8b3ed9cba2d1b3f52f2a1252107ec0f + md5: cac7eed2dd251ed7ed2ae5a9eefe40e7 build: number: 0 rpaths: @@ -20,17 +20,19 @@ build: # Suggests: knitr, rmarkdown requirements: host: - - 'bioconductor-annotationhub >=2.14.0,<2.15.0' - - 'bioconductor-biostrings >=2.50.0,<2.51.0' - - 'bioconductor-bsgenome >=1.50.0,<1.51.0' - - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' + - 'bioconductor-annotationhub >=2.16.0,<2.17.0' + - 'bioconductor-biostrings >=2.52.0,<2.53.0' + - 'bioconductor-bsgenome >=1.52.0,<1.53.0' + - 'bioconductor-genomeinfodb >=1.20.0,<1.21.0' - 'bioconductor-genomeinfodbdata >=1.2.0,<1.3.0' - - 'bioconductor-genomicfeatures >=1.34.0,<1.35.0' + - 'bioconductor-genomicfeatures >=1.36.0,<1.37.0' - 'bioconductor-mirbase.db >=1.2.0,<1.3.0' - - 'bioconductor-sushi >=1.20.0,<1.21.0' + - 'bioconductor-sushi >=1.22.0,<1.23.0' - r-base - 'r-data.table >=1.9.4' - r-dt + - r-ggplot2 + - r-ggrepel - r-gsubfn - r-httpuv - r-moments @@ -38,17 +40,19 @@ requirements: - r-shinyfiles - r-yaml run: - - 'bioconductor-annotationhub >=2.14.0,<2.15.0' - - 'bioconductor-biostrings >=2.50.0,<2.51.0' - - 'bioconductor-bsgenome >=1.50.0,<1.51.0' - - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' + - 'bioconductor-annotationhub >=2.16.0,<2.17.0' + - 'bioconductor-biostrings >=2.52.0,<2.53.0' + - 'bioconductor-bsgenome >=1.52.0,<1.53.0' + - 'bioconductor-genomeinfodb >=1.20.0,<1.21.0' - 'bioconductor-genomeinfodbdata >=1.2.0,<1.3.0' - - 'bioconductor-genomicfeatures >=1.34.0,<1.35.0' + - 'bioconductor-genomicfeatures >=1.36.0,<1.37.0' - 'bioconductor-mirbase.db >=1.2.0,<1.3.0' - - 'bioconductor-sushi >=1.20.0,<1.21.0' + - 'bioconductor-sushi >=1.22.0,<1.23.0' - r-base - 'r-data.table >=1.9.4' - r-dt + - r-ggplot2 + - r-ggrepel - r-gsubfn - r-httpuv - r-moments diff --git a/recipes/bioconductor-undo/meta.yaml b/recipes/bioconductor-undo/meta.yaml index 7dd6b0b917a6c..ccdae2e6cbfc6 100644 --- a/recipes/bioconductor-undo/meta.yaml +++ b/recipes/bioconductor-undo/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.24.0" %} +{% set version = "1.26.0" %} {% set name = "UNDO" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: f1e2a4e8cc746b0f2e99793229b09d79 + md5: 67d97af911e0fbcf1966e80baf739023 build: number: 0 rpaths: @@ -19,15 +19,15 @@ build: noarch: generic requirements: host: - - 'bioconductor-biobase >=2.42.0,<2.43.0' - - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' + - 'bioconductor-biocgenerics >=0.30.0,<0.31.0' - r-base - r-boot - r-mass - r-nnls run: - - 'bioconductor-biobase >=2.42.0,<2.43.0' - - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' + - 'bioconductor-biocgenerics >=0.30.0,<0.31.0' - r-base - r-boot - r-mass diff --git a/recipes/bioconductor-unifiedwmwqpcr/meta.yaml b/recipes/bioconductor-unifiedwmwqpcr/meta.yaml index 4aa69fdf1d468..7b81299ecb129 100644 --- a/recipes/bioconductor-unifiedwmwqpcr/meta.yaml +++ b/recipes/bioconductor-unifiedwmwqpcr/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.18.0" %} +{% set version = "1.20.0" %} {% set name = "unifiedWMWqPCR" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: d0bc72990976a0e11766f9f46402a588 + md5: a875b0d414ebd3efb3a98188424b72ad build: number: 0 rpaths: @@ -19,12 +19,12 @@ build: noarch: generic requirements: host: - - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' - - 'bioconductor-htqpcr >=1.36.0,<1.37.0' + - 'bioconductor-biocgenerics >=0.30.0,<0.31.0' + - 'bioconductor-htqpcr >=1.38.0,<1.39.0' - r-base run: - - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' - - 'bioconductor-htqpcr >=1.36.0,<1.37.0' + - 'bioconductor-biocgenerics >=0.30.0,<0.31.0' + - 'bioconductor-htqpcr >=1.38.0,<1.39.0' - r-base test: commands: diff --git a/recipes/bioconductor-uniprot.ws/meta.yaml b/recipes/bioconductor-uniprot.ws/meta.yaml index 963fc3b9feb03..108667800a0b2 100644 --- a/recipes/bioconductor-uniprot.ws/meta.yaml +++ b/recipes/bioconductor-uniprot.ws/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "2.22.0" %} +{% set version = "2.24.0" %} {% set name = "UniProt.ws" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 54f202f10a75478ae02ca20a309c231b + md5: 665f3c1634b3d2c19375fe869d309ef2 build: number: 0 rpaths: @@ -20,17 +20,17 @@ build: # Suggests: RUnit requirements: host: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' - - 'bioconductor-biocfilecache >=1.6.0,<1.7.0' - - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' + - 'bioconductor-biocfilecache >=1.8.0,<1.9.0' + - 'bioconductor-biocgenerics >=0.30.0,<0.31.0' - r-base - r-rappdirs - r-rcurl - r-rsqlite run: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' - - 'bioconductor-biocfilecache >=1.6.0,<1.7.0' - - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' + - 'bioconductor-biocfilecache >=1.8.0,<1.9.0' + - 'bioconductor-biocgenerics >=0.30.0,<0.31.0' - r-base - r-rappdirs - r-rcurl diff --git a/recipes/bioconductor-uniquorn/meta.yaml b/recipes/bioconductor-uniquorn/meta.yaml index ee0bae0160544..ec9d1686d5ac4 100644 --- a/recipes/bioconductor-uniquorn/meta.yaml +++ b/recipes/bioconductor-uniquorn/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "2.2.0" %} +{% set version = "2.4.0" %} {% set name = "Uniquorn" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 2306a39e0dba09bf225b18f83cb40153 + md5: 5aa74d4ee015b2618a9caef436b09852 build: number: 0 rpaths: @@ -20,22 +20,20 @@ build: # Suggests: testthat, knitr, rmarkdown, BiocGenerics, RUnit requirements: host: - - 'bioconductor-genomicranges >=1.34.0,<1.35.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-variantannotation >=1.28.0,<1.29.0' + - 'bioconductor-genomicranges >=1.36.0,<1.37.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-variantannotation >=1.30.0,<1.31.0' - r-base - - r-data.table - r-doparallel - r-foreach - r-r.utils - r-stringr - r-writexls run: - - 'bioconductor-genomicranges >=1.34.0,<1.35.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-variantannotation >=1.28.0,<1.29.0' + - 'bioconductor-genomicranges >=1.36.0,<1.37.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-variantannotation >=1.30.0,<1.31.0' - r-base - - r-data.table - r-doparallel - r-foreach - r-r.utils diff --git a/recipes/bioconductor-universalmotif/meta.yaml b/recipes/bioconductor-universalmotif/meta.yaml index f375db1c5ca7f..bd58c97613538 100644 --- a/recipes/bioconductor-universalmotif/meta.yaml +++ b/recipes/bioconductor-universalmotif/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.0.12" %} +{% set version = "1.2.0" %} {% set name = "universalmotif" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,18 +10,19 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 8d36f424357b4375e4cd623bd7c6cf4e + md5: 62377460cf3837d20a9b12e745820cb8 build: number: 0 rpaths: - lib/R/lib/ - lib/ -# Suggests: knitr, BiocStyle, TFBSTools, MotIV, PWMEnrich, motifStack, seqLogo, rmarkdown, MotifDb, testthat, rGADEM, motifRG, motifbreakR, RcisTarget, motifcounter, Logolas, BiocParallel, BCRANK +# Suggests: spelling, knitr, BiocStyle, TFBSTools, rmarkdown, MotifDb, testthat, Logolas, BiocParallel, seqLogo, motifStack requirements: host: - - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' - - 'bioconductor-biostrings >=2.50.0,<2.51.0' - - 'bioconductor-ggtree >=1.14.0,<1.15.0' + - 'bioconductor-biocgenerics >=0.30.0,<0.31.0' + - 'bioconductor-biostrings >=2.52.0,<2.53.0' + - 'bioconductor-ggtree >=1.16.0,<1.17.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' - r-ape - r-base - r-ggplot2 @@ -30,10 +31,12 @@ requirements: - r-processx - r-rcpp - 'r-rdpack >=0.7' + - r-yaml run: - - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' - - 'bioconductor-biostrings >=2.50.0,<2.51.0' - - 'bioconductor-ggtree >=1.14.0,<1.15.0' + - 'bioconductor-biocgenerics >=0.30.0,<0.31.0' + - 'bioconductor-biostrings >=2.52.0,<2.53.0' + - 'bioconductor-ggtree >=1.16.0,<1.17.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' - r-ape - r-base - r-ggplot2 @@ -42,6 +45,7 @@ requirements: - r-processx - r-rcpp - 'r-rdpack >=0.7' + - r-yaml build: - {{ compiler('c') }} - {{ compiler('cxx') }} diff --git a/recipes/bioconductor-usort/meta.yaml b/recipes/bioconductor-usort/meta.yaml index 79a2c6fafeabe..86b248e19c32b 100644 --- a/recipes/bioconductor-usort/meta.yaml +++ b/recipes/bioconductor-usort/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.8.0" %} +{% set version = "1.10.0" %} {% set name = "uSORT" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: e92645ff56f39c741d9c721c91648168 + md5: ef09d8818585ffdd4003c1914c68e7a6 build: number: 0 rpaths: @@ -20,9 +20,9 @@ build: # Suggests: knitr, RUnit, testthat, ggplot2 requirements: host: - - 'bioconductor-biobase >=2.42.0,<2.43.0' - - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' - - 'bioconductor-monocle >=2.10.0,<2.11.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' + - 'bioconductor-biocgenerics >=0.30.0,<0.31.0' + - 'bioconductor-monocle >=2.12.0,<2.13.0' - r-base - r-cluster - r-fpc @@ -34,9 +34,9 @@ requirements: - r-rspectra - r-vgam run: - - 'bioconductor-biobase >=2.42.0,<2.43.0' - - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' - - 'bioconductor-monocle >=2.10.0,<2.11.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' + - 'bioconductor-biocgenerics >=0.30.0,<0.31.0' + - 'bioconductor-monocle >=2.12.0,<2.13.0' - r-base - r-cluster - r-fpc diff --git a/recipes/bioconductor-vanillaice/meta.yaml b/recipes/bioconductor-vanillaice/meta.yaml index 4c07ef39297c2..25a4263613daa 100644 --- a/recipes/bioconductor-vanillaice/meta.yaml +++ b/recipes/bioconductor-vanillaice/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.44.0" %} +{% set version = "1.46.0" %} {% set name = "VanillaICE" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: ea6bd436eab15fa26a9809990494a9a2 + md5: 696d4f2c8aae09dc6a28456bab72f843 build: number: 0 rpaths: @@ -19,32 +19,32 @@ build: # Suggests: RUnit, SNPchip, human610quadv1bCrlmm, ArrayTV requirements: host: - - 'bioconductor-biobase >=2.42.0,<2.43.0' - - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' - - 'bioconductor-bsgenome.hsapiens.ucsc.hg18 >=1.3.0,<1.4.0' - - 'bioconductor-crlmm >=1.40.0,<1.41.0' - - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' - - 'bioconductor-genomicranges >=1.34.0,<1.35.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-oligoclasses >=1.44.0,<1.45.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' - - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' + - 'bioconductor-biocgenerics >=0.30.0,<0.31.0' + - 'bioconductor-bsgenome.hsapiens.ucsc.hg18 >=1.4.0,<1.5.0' + - 'bioconductor-crlmm >=1.42.0,<1.43.0' + - 'bioconductor-genomeinfodb >=1.20.0,<1.21.0' + - 'bioconductor-genomicranges >=1.36.0,<1.37.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-oligoclasses >=1.46.0,<1.47.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' + - 'bioconductor-summarizedexperiment >=1.14.0,<1.15.0' - r-base - r-data.table - r-foreach - r-lattice - r-matrixstats run: - - 'bioconductor-biobase >=2.42.0,<2.43.0' - - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' - - 'bioconductor-bsgenome.hsapiens.ucsc.hg18 >=1.3.0,<1.4.0' - - 'bioconductor-crlmm >=1.40.0,<1.41.0' - - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' - - 'bioconductor-genomicranges >=1.34.0,<1.35.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-oligoclasses >=1.44.0,<1.45.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' - - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' + - 'bioconductor-biocgenerics >=0.30.0,<0.31.0' + - 'bioconductor-bsgenome.hsapiens.ucsc.hg18 >=1.4.0,<1.5.0' + - 'bioconductor-crlmm >=1.42.0,<1.43.0' + - 'bioconductor-genomeinfodb >=1.20.0,<1.21.0' + - 'bioconductor-genomicranges >=1.36.0,<1.37.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-oligoclasses >=1.46.0,<1.47.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' + - 'bioconductor-summarizedexperiment >=1.14.0,<1.15.0' - r-base - r-data.table - r-foreach diff --git a/recipes/bioconductor-variancepartition/meta.yaml b/recipes/bioconductor-variancepartition/meta.yaml index 09a9aa9d63950..164c043c3c0d1 100644 --- a/recipes/bioconductor-variancepartition/meta.yaml +++ b/recipes/bioconductor-variancepartition/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.12.3" %} +{% set version = "1.14.0" %} {% set name = "variancePartition" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: d1f7d173b89cf1f2e4d5a82c726e1d744aaebe7b6fb00236eb8010215e204beb + md5: a17c9b8546466091a009e16ab7f365e4 build: number: 0 rpaths: @@ -20,8 +20,8 @@ build: # Suggests: BiocStyle, knitr, pander, rmarkdown, edgeR, dendextend, tximport, tximportData, ballgown, DESeq2, RUnit, BiocGenerics, r2glmm, readr requirements: host: - - 'bioconductor-biobase >=2.42.0,<2.43.0' - - 'bioconductor-limma >=3.38.0,<3.39.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' + - 'bioconductor-limma >=3.40.0,<3.41.0' - r-base - r-colorramps - r-doparallel @@ -33,12 +33,12 @@ requirements: - r-lmertest - r-mass - 'r-pbkrtest >=0.4-4' + - r-progress - r-reshape2 - r-scales - - r-progress run: - - 'bioconductor-biobase >=2.42.0,<2.43.0' - - 'bioconductor-limma >=3.38.0,<3.39.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' + - 'bioconductor-limma >=3.40.0,<3.41.0' - r-base - r-colorramps - r-doparallel @@ -50,9 +50,9 @@ requirements: - r-lmertest - r-mass - 'r-pbkrtest >=0.4-4' + - r-progress - r-reshape2 - r-scales - - r-progress test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-variantannotation/meta.yaml b/recipes/bioconductor-variantannotation/meta.yaml index 74d5342454a7f..9599f367ee80d 100644 --- a/recipes/bioconductor-variantannotation/meta.yaml +++ b/recipes/bioconductor-variantannotation/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.28.3" %} +{% set version = "1.30.0" %} {% set name = "VariantAnnotation" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 794af6309fedd19426ef39df2a0907e2 + md5: 1914705cedb8080c17960935bdb696fe build: number: 0 rpaths: @@ -19,39 +19,41 @@ build: # Suggests: RUnit, AnnotationHub, BSgenome.Hsapiens.UCSC.hg19, TxDb.Hsapiens.UCSC.hg19.knownGene, SNPlocs.Hsapiens.dbSNP.20101109, SIFT.Hsapiens.dbSNP132, SIFT.Hsapiens.dbSNP137, PolyPhen.Hsapiens.dbSNP131, snpStats, ggplot2, BiocStyle requirements: host: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' - - 'bioconductor-biobase >=2.42.0,<2.43.0' - - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' - - 'bioconductor-biostrings >=2.50.0,<2.51.0' - - 'bioconductor-bsgenome >=1.50.0,<1.51.0' - - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' - - 'bioconductor-genomicfeatures >=1.34.0,<1.35.0' - - 'bioconductor-genomicranges >=1.34.0,<1.35.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-rsamtools >=1.34.0,<1.35.0' - - 'bioconductor-rtracklayer >=1.42.0,<1.43.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' - - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' - - 'bioconductor-xvector >=0.22.0,<0.23.0' - - 'bioconductor-zlibbioc >=1.28.0,<1.29.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' + - 'bioconductor-biocgenerics >=0.30.0,<0.31.0' + - 'bioconductor-biostrings >=2.52.0,<2.53.0' + - 'bioconductor-bsgenome >=1.52.0,<1.53.0' + - 'bioconductor-genomeinfodb >=1.20.0,<1.21.0' + - 'bioconductor-genomicfeatures >=1.36.0,<1.37.0' + - 'bioconductor-genomicranges >=1.36.0,<1.37.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-rhtslib >=1.16.0,<1.17.0' + - 'bioconductor-rsamtools >=2.0.0,<2.1.0' + - 'bioconductor-rtracklayer >=1.44.0,<1.45.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' + - 'bioconductor-summarizedexperiment >=1.14.0,<1.15.0' + - 'bioconductor-xvector >=0.24.0,<0.25.0' + - 'bioconductor-zlibbioc >=1.30.0,<1.31.0' - r-base - r-dbi run: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' - - 'bioconductor-biobase >=2.42.0,<2.43.0' - - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' - - 'bioconductor-biostrings >=2.50.0,<2.51.0' - - 'bioconductor-bsgenome >=1.50.0,<1.51.0' - - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' - - 'bioconductor-genomicfeatures >=1.34.0,<1.35.0' - - 'bioconductor-genomicranges >=1.34.0,<1.35.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-rsamtools >=1.34.0,<1.35.0' - - 'bioconductor-rtracklayer >=1.42.0,<1.43.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' - - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' - - 'bioconductor-xvector >=0.22.0,<0.23.0' - - 'bioconductor-zlibbioc >=1.28.0,<1.29.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' + - 'bioconductor-biocgenerics >=0.30.0,<0.31.0' + - 'bioconductor-biostrings >=2.52.0,<2.53.0' + - 'bioconductor-bsgenome >=1.52.0,<1.53.0' + - 'bioconductor-genomeinfodb >=1.20.0,<1.21.0' + - 'bioconductor-genomicfeatures >=1.36.0,<1.37.0' + - 'bioconductor-genomicranges >=1.36.0,<1.37.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-rhtslib >=1.16.0,<1.17.0' + - 'bioconductor-rsamtools >=2.0.0,<2.1.0' + - 'bioconductor-rtracklayer >=1.44.0,<1.45.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' + - 'bioconductor-summarizedexperiment >=1.14.0,<1.15.0' + - 'bioconductor-xvector >=0.24.0,<0.25.0' + - 'bioconductor-zlibbioc >=1.30.0,<1.31.0' - r-base - r-dbi build: diff --git a/recipes/bioconductor-variantfiltering/meta.yaml b/recipes/bioconductor-variantfiltering/meta.yaml index c6d42d6ccd67d..68680da32eb04 100644 --- a/recipes/bioconductor-variantfiltering/meta.yaml +++ b/recipes/bioconductor-variantfiltering/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.18.0" %} +{% set version = "1.20.0" %} {% set name = "VariantFiltering" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 1ce3cd46b70fd5e9ca215f125d36317f + md5: 4efa6821bd6877fc2320cbf3a6d22226 build: number: 0 rpaths: @@ -19,25 +19,25 @@ build: # Suggests: RUnit, BiocStyle, org.Hs.eg.db, BSgenome.Hsapiens.1000genomes.hs37d5, TxDb.Hsapiens.UCSC.hg19.knownGene, SNPlocs.Hsapiens.dbSNP144.GRCh37, MafDb.1Kgenomes.phase1.hs37d5, phastCons100way.UCSC.hg19, PolyPhen.Hsapiens.dbSNP131, SIFT.Hsapiens.dbSNP137 requirements: host: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' - - 'bioconductor-biobase >=2.42.0,<2.43.0' - - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' - - 'bioconductor-biocparallel >=1.16.0,<1.17.0' - - 'bioconductor-biostrings >=2.50.0,<2.51.0' - - 'bioconductor-bsgenome >=1.50.0,<1.51.0' - - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' - - 'bioconductor-genomicfeatures >=1.34.0,<1.35.0' - - 'bioconductor-genomicranges >=1.34.0,<1.35.0' - - 'bioconductor-genomicscores >=1.6.0,<1.7.0' - - 'bioconductor-graph >=1.60.0,<1.61.0' - - 'bioconductor-gviz >=1.26.0,<1.27.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-rbgl >=1.58.0,<1.59.0' - - 'bioconductor-rsamtools >=1.34.0,<1.35.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' - - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' - - 'bioconductor-variantannotation >=1.28.0,<1.29.0' - - 'bioconductor-xvector >=0.22.0,<0.23.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' + - 'bioconductor-biocgenerics >=0.30.0,<0.31.0' + - 'bioconductor-biocparallel >=1.18.0,<1.19.0' + - 'bioconductor-biostrings >=2.52.0,<2.53.0' + - 'bioconductor-bsgenome >=1.52.0,<1.53.0' + - 'bioconductor-genomeinfodb >=1.20.0,<1.21.0' + - 'bioconductor-genomicfeatures >=1.36.0,<1.37.0' + - 'bioconductor-genomicranges >=1.36.0,<1.37.0' + - 'bioconductor-genomicscores >=1.8.0,<1.9.0' + - 'bioconductor-graph >=1.62.0,<1.63.0' + - 'bioconductor-gviz >=1.28.0,<1.29.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-rbgl >=1.60.0,<1.61.0' + - 'bioconductor-rsamtools >=2.0.0,<2.1.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' + - 'bioconductor-summarizedexperiment >=1.14.0,<1.15.0' + - 'bioconductor-variantannotation >=1.30.0,<1.31.0' + - 'bioconductor-xvector >=0.24.0,<0.25.0' - r-base - r-dt - r-shiny @@ -45,25 +45,25 @@ requirements: - r-shinythemes - r-shinytree run: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' - - 'bioconductor-biobase >=2.42.0,<2.43.0' - - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' - - 'bioconductor-biocparallel >=1.16.0,<1.17.0' - - 'bioconductor-biostrings >=2.50.0,<2.51.0' - - 'bioconductor-bsgenome >=1.50.0,<1.51.0' - - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' - - 'bioconductor-genomicfeatures >=1.34.0,<1.35.0' - - 'bioconductor-genomicranges >=1.34.0,<1.35.0' - - 'bioconductor-genomicscores >=1.6.0,<1.7.0' - - 'bioconductor-graph >=1.60.0,<1.61.0' - - 'bioconductor-gviz >=1.26.0,<1.27.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-rbgl >=1.58.0,<1.59.0' - - 'bioconductor-rsamtools >=1.34.0,<1.35.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' - - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' - - 'bioconductor-variantannotation >=1.28.0,<1.29.0' - - 'bioconductor-xvector >=0.22.0,<0.23.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' + - 'bioconductor-biocgenerics >=0.30.0,<0.31.0' + - 'bioconductor-biocparallel >=1.18.0,<1.19.0' + - 'bioconductor-biostrings >=2.52.0,<2.53.0' + - 'bioconductor-bsgenome >=1.52.0,<1.53.0' + - 'bioconductor-genomeinfodb >=1.20.0,<1.21.0' + - 'bioconductor-genomicfeatures >=1.36.0,<1.37.0' + - 'bioconductor-genomicranges >=1.36.0,<1.37.0' + - 'bioconductor-genomicscores >=1.8.0,<1.9.0' + - 'bioconductor-graph >=1.62.0,<1.63.0' + - 'bioconductor-gviz >=1.28.0,<1.29.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-rbgl >=1.60.0,<1.61.0' + - 'bioconductor-rsamtools >=2.0.0,<2.1.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' + - 'bioconductor-summarizedexperiment >=1.14.0,<1.15.0' + - 'bioconductor-variantannotation >=1.30.0,<1.31.0' + - 'bioconductor-xvector >=0.24.0,<0.25.0' - r-base - r-dt - r-shiny diff --git a/recipes/bioconductor-varianttools/meta.yaml b/recipes/bioconductor-varianttools/meta.yaml index 649a5523b0c5e..62f7092fc66a3 100644 --- a/recipes/bioconductor-varianttools/meta.yaml +++ b/recipes/bioconductor-varianttools/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.24.0" %} +{% set version = "1.26.0" %} {% set name = "VariantTools" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 58f5a5c644464fcac6ee6eb7ef3b1aa9 + md5: 85a1a309d99c466cbdc3c60748994bcc build: number: 0 rpaths: @@ -20,35 +20,35 @@ build: # Suggests: RUnit, LungCancerLines (>= 0.0.6), RBGL, graph, gmapR (>= 1.21.3) requirements: host: - - 'bioconductor-biobase >=2.42.0,<2.43.0' - - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' - - 'bioconductor-biocparallel >=1.16.0,<1.17.0' - - 'bioconductor-biostrings >=2.50.0,<2.51.0' - - 'bioconductor-bsgenome >=1.50.0,<1.51.0' - - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' - - 'bioconductor-genomicfeatures >=1.34.0,<1.35.0' - - 'bioconductor-genomicranges >=1.34.0,<1.35.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-rsamtools >=1.34.0,<1.35.0' - - 'bioconductor-rtracklayer >=1.42.0,<1.43.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' - - 'bioconductor-variantannotation >=1.28.0,<1.29.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' + - 'bioconductor-biocgenerics >=0.30.0,<0.31.0' + - 'bioconductor-biocparallel >=1.18.0,<1.19.0' + - 'bioconductor-biostrings >=2.52.0,<2.53.0' + - 'bioconductor-bsgenome >=1.52.0,<1.53.0' + - 'bioconductor-genomeinfodb >=1.20.0,<1.21.0' + - 'bioconductor-genomicfeatures >=1.36.0,<1.37.0' + - 'bioconductor-genomicranges >=1.36.0,<1.37.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-rsamtools >=2.0.0,<2.1.0' + - 'bioconductor-rtracklayer >=1.44.0,<1.45.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' + - 'bioconductor-variantannotation >=1.30.0,<1.31.0' - r-base - r-matrix run: - - 'bioconductor-biobase >=2.42.0,<2.43.0' - - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' - - 'bioconductor-biocparallel >=1.16.0,<1.17.0' - - 'bioconductor-biostrings >=2.50.0,<2.51.0' - - 'bioconductor-bsgenome >=1.50.0,<1.51.0' - - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' - - 'bioconductor-genomicfeatures >=1.34.0,<1.35.0' - - 'bioconductor-genomicranges >=1.34.0,<1.35.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-rsamtools >=1.34.0,<1.35.0' - - 'bioconductor-rtracklayer >=1.42.0,<1.43.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' - - 'bioconductor-variantannotation >=1.28.0,<1.29.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' + - 'bioconductor-biocgenerics >=0.30.0,<0.31.0' + - 'bioconductor-biocparallel >=1.18.0,<1.19.0' + - 'bioconductor-biostrings >=2.52.0,<2.53.0' + - 'bioconductor-bsgenome >=1.52.0,<1.53.0' + - 'bioconductor-genomeinfodb >=1.20.0,<1.21.0' + - 'bioconductor-genomicfeatures >=1.36.0,<1.37.0' + - 'bioconductor-genomicranges >=1.36.0,<1.37.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-rsamtools >=2.0.0,<2.1.0' + - 'bioconductor-rtracklayer >=1.44.0,<1.45.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' + - 'bioconductor-variantannotation >=1.30.0,<1.31.0' - r-base - r-matrix test: diff --git a/recipes/bioconductor-varianttoolsdata/meta.yaml b/recipes/bioconductor-varianttoolsdata/meta.yaml index 417fc548956f5..eee43972737ee 100644 --- a/recipes/bioconductor-varianttoolsdata/meta.yaml +++ b/recipes/bioconductor-varianttoolsdata/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.6.0" %} +{% set version = "1.8.0" %} {% set name = "VariantToolsData" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 6d1a1707b091b0d4beeb7f2cf0f9fb7f + md5: dd2739d2dc782b7ff7778010799037f9 build: number: 0 rpaths: @@ -20,16 +20,16 @@ build: # Suggests: VariantTools (>= 1.3.4), gmapR (>= 1.3.3), BiocStyle requirements: host: - - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' - - 'bioconductor-genomicranges >=1.34.0,<1.35.0' - - 'bioconductor-variantannotation >=1.28.0,<1.29.0' + - 'bioconductor-biocgenerics >=0.30.0,<0.31.0' + - 'bioconductor-genomicranges >=1.36.0,<1.37.0' + - 'bioconductor-variantannotation >=1.30.0,<1.31.0' - r-base run: - - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' - - 'bioconductor-genomicranges >=1.34.0,<1.35.0' - - 'bioconductor-variantannotation >=1.28.0,<1.29.0' + - 'bioconductor-biocgenerics >=0.30.0,<0.31.0' + - 'bioconductor-genomicranges >=1.36.0,<1.37.0' + - 'bioconductor-variantannotation >=1.30.0,<1.31.0' - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-varianttoolsdata/post-link.sh b/recipes/bioconductor-varianttoolsdata/post-link.sh index 35c1c81836b4f..bf84675d1b9e7 100644 --- a/recipes/bioconductor-varianttoolsdata/post-link.sh +++ b/recipes/bioconductor-varianttoolsdata/post-link.sh @@ -1,11 +1,11 @@ #!/bin/bash -FN="VariantToolsData_1.6.0.tar.gz" +FN="VariantToolsData_1.8.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/experiment/src/contrib/VariantToolsData_1.6.0.tar.gz" - "https://bioarchive.galaxyproject.org/VariantToolsData_1.6.0.tar.gz" - "https://depot.galaxyproject.org/software/bioconductor-varianttoolsdata/bioconductor-varianttoolsdata_1.6.0_src_all.tar.gz" + "https://bioconductor.org/packages/3.9/data/experiment/src/contrib/VariantToolsData_1.8.0.tar.gz" + "https://bioarchive.galaxyproject.org/VariantToolsData_1.8.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-varianttoolsdata/bioconductor-varianttoolsdata_1.8.0_src_all.tar.gz" ) -MD5="6d1a1707b091b0d4beeb7f2cf0f9fb7f" +MD5="dd2739d2dc782b7ff7778010799037f9" # Use a staging area in the conda dir rather than temp dirs, both to avoid # permission issues as well as to have things downloaded in a predictable @@ -16,7 +16,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-vbmp/meta.yaml b/recipes/bioconductor-vbmp/meta.yaml index cde6a125b98f2..0c9f0f86537ed 100644 --- a/recipes/bioconductor-vbmp/meta.yaml +++ b/recipes/bioconductor-vbmp/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.50.0" %} +{% set version = "1.52.0" %} {% set name = "vbmp" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 775146794e65565df652e53d0330aff5 + md5: 21ab3d751b86edfdda86f27a23cd01d6 build: number: 0 rpaths: diff --git a/recipes/bioconductor-vcfarray/build.sh b/recipes/bioconductor-vcfarray/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-vcfarray/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-vcfarray/meta.yaml b/recipes/bioconductor-vcfarray/meta.yaml new file mode 100644 index 0000000000000..2af7483020c03 --- /dev/null +++ b/recipes/bioconductor-vcfarray/meta.yaml @@ -0,0 +1,47 @@ +{% set version = "1.0.0" %} +{% set name = "VCFArray" %} +{% set bioc = "3.9" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: 3ad451f6746ffa7b7805da7bbbfffb7b +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: BiocStyle, BiocManager, testthat, knitr, rmarkdown +requirements: + host: + - 'bioconductor-biocgenerics >=0.30.0,<0.31.0' + - 'bioconductor-delayedarray >=0.10.0,<0.11.0' + - 'bioconductor-genomicfiles >=1.20.0,<1.21.0' + - 'bioconductor-genomicranges >=1.36.0,<1.37.0' + - 'bioconductor-rsamtools >=2.0.0,<2.1.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' + - 'bioconductor-variantannotation >=1.30.0,<1.31.0' + - r-base + run: + - 'bioconductor-biocgenerics >=0.30.0,<0.31.0' + - 'bioconductor-delayedarray >=0.10.0,<0.11.0' + - 'bioconductor-genomicfiles >=1.20.0,<1.21.0' + - 'bioconductor-genomicranges >=1.36.0,<1.37.0' + - 'bioconductor-rsamtools >=2.0.0,<2.1.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' + - 'bioconductor-variantannotation >=1.30.0,<1.31.0' + - r-base +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: GPL-3 + summary: 'VCFArray extends the DelayedArray to represent VCF data entries as array-like objects with on-disk / remote VCF file as backend. Data entries from VCF files, including info fields, FORMAT fields, and the fixed columns (REF, ALT, QUAL, FILTER) could be converted into VCFArray instances with different dimensions.' + diff --git a/recipes/bioconductor-vega/meta.yaml b/recipes/bioconductor-vega/meta.yaml index f8b577d3139ff..1dbd4d0cad860 100644 --- a/recipes/bioconductor-vega/meta.yaml +++ b/recipes/bioconductor-vega/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.30.0" %} +{% set version = "1.32.0" %} {% set name = "Vega" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 909008499be8b351162b36976db05a5b + md5: d17f38e24edcd024c6650bf651fb2c13 build: number: 0 rpaths: diff --git a/recipes/bioconductor-vegamc/meta.yaml b/recipes/bioconductor-vegamc/meta.yaml index 5e47bd6025c9d..f5b1158cd92e0 100644 --- a/recipes/bioconductor-vegamc/meta.yaml +++ b/recipes/bioconductor-vegamc/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "3.20.0" %} +{% set version = "3.22.0" %} {% set name = "VegaMC" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: c3e60f589acb272536f80e01eb14e83f + md5: 38314360580b97f46f7cb17fc46e15a8 build: number: 0 rpaths: @@ -18,14 +18,14 @@ build: - lib/ requirements: host: - - 'bioconductor-biobase >=2.42.0,<2.43.0' - - 'bioconductor-biomart >=2.38.0,<2.39.0' - - 'bioconductor-genoset >=1.38.0,<1.39.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' + - 'bioconductor-biomart >=2.40.0,<2.41.0' + - 'bioconductor-genoset >=1.40.0,<1.41.0' - r-base run: - - 'bioconductor-biobase >=2.42.0,<2.43.0' - - 'bioconductor-biomart >=2.38.0,<2.39.0' - - 'bioconductor-genoset >=1.38.0,<1.39.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' + - 'bioconductor-biomart >=2.40.0,<2.41.0' + - 'bioconductor-genoset >=1.40.0,<1.41.0' - r-base build: - {{ compiler('c') }} diff --git a/recipes/bioconductor-venndetail/build.sh b/recipes/bioconductor-venndetail/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-venndetail/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-venndetail/meta.yaml b/recipes/bioconductor-venndetail/meta.yaml new file mode 100644 index 0000000000000..7b1d4b8cb4dbe --- /dev/null +++ b/recipes/bioconductor-venndetail/meta.yaml @@ -0,0 +1,47 @@ +{% set version = "1.0.0" %} +{% set name = "VennDetail" %} +{% set bioc = "3.9" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: d24d8074ee336afe8681eb2de65b485c +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: knitr, rmarkdown, testthat +requirements: + host: + - r-base + - r-dplyr + - r-ggplot2 + - r-magrittr + - r-purrr + - r-tibble + - r-upsetr + - r-venndiagram + run: + - r-base + - r-dplyr + - r-ggplot2 + - r-magrittr + - r-purrr + - r-tibble + - r-upsetr + - r-venndiagram +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: GPL-2 + summary: 'A set of functions to generate high-resolution Venn,Vennpie plot,extract and combine details of these subsets with user datasets in data frame is available.' + diff --git a/recipes/bioconductor-vidger/meta.yaml b/recipes/bioconductor-vidger/meta.yaml index 51e9f28d3f5b2..4a955e921015d 100644 --- a/recipes/bioconductor-vidger/meta.yaml +++ b/recipes/bioconductor-vidger/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.2.0" %} +{% set version = "1.4.0" %} {% set name = "vidger" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: d4f2fe186eca458410c0b57f166f8500 + md5: dfcf52a1cd622ac1622d2eb2c2d34305 build: number: 0 rpaths: @@ -20,10 +20,10 @@ build: # Suggests: BiocStyle, testthat requirements: host: - - 'bioconductor-biobase >=2.42.0,<2.43.0' - - 'bioconductor-deseq2 >=1.22.0,<1.23.0' - - 'bioconductor-edger >=3.24.0,<3.25.0' - - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' + - 'bioconductor-deseq2 >=1.24.0,<1.25.0' + - 'bioconductor-edger >=3.26.0,<3.27.0' + - 'bioconductor-summarizedexperiment >=1.14.0,<1.15.0' - r-base - r-ggally - r-ggplot2 @@ -34,10 +34,10 @@ requirements: - r-scales - r-tidyr run: - - 'bioconductor-biobase >=2.42.0,<2.43.0' - - 'bioconductor-deseq2 >=1.22.0,<1.23.0' - - 'bioconductor-edger >=3.24.0,<3.25.0' - - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' + - 'bioconductor-deseq2 >=1.24.0,<1.25.0' + - 'bioconductor-edger >=3.26.0,<3.27.0' + - 'bioconductor-summarizedexperiment >=1.14.0,<1.15.0' - r-base - r-ggally - r-ggplot2 diff --git a/recipes/bioconductor-viper/meta.yaml b/recipes/bioconductor-viper/meta.yaml index 68d4287efedf9..f9c0007fa39dc 100644 --- a/recipes/bioconductor-viper/meta.yaml +++ b/recipes/bioconductor-viper/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.16.0" %} +{% set version = "1.17.0" %} {% set name = "viper" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 88466e58bd88dc075343d450c2688b68 + md5: a419781099c2560cfe24b5c702e5cf0a build: number: 0 rpaths: @@ -20,13 +20,13 @@ build: # Suggests: bcellViper requirements: host: - - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' - r-base - r-e1071 - r-kernsmooth - r-mixtools run: - - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' - r-base - r-e1071 - r-kernsmooth diff --git a/recipes/bioconductor-vitisviniferacdf/meta.yaml b/recipes/bioconductor-vitisviniferacdf/meta.yaml index bde4c9338152b..0c6447f344b34 100644 --- a/recipes/bioconductor-vitisviniferacdf/meta.yaml +++ b/recipes/bioconductor-vitisviniferacdf/meta.yaml @@ -1,6 +1,6 @@ {% set version = "2.18.0" %} {% set name = "vitisviniferacdf" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -12,19 +12,19 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 8eb491f3ffa3ff0814f5c155787ae160 build: - number: 1 + number: 2 rpaths: - lib/R/lib/ - lib/ noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' - r-base run: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-vitisviniferacdf/post-link.sh b/recipes/bioconductor-vitisviniferacdf/post-link.sh index 30da75c70b202..5804fe20ab150 100644 --- a/recipes/bioconductor-vitisviniferacdf/post-link.sh +++ b/recipes/bioconductor-vitisviniferacdf/post-link.sh @@ -1,9 +1,10 @@ #!/bin/bash FN="vitisviniferacdf_2.18.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/vitisviniferacdf_2.18.0.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/vitisviniferacdf_2.18.0.tar.gz" "https://bioarchive.galaxyproject.org/vitisviniferacdf_2.18.0.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-vitisviniferacdf/bioconductor-vitisviniferacdf_2.18.0_src_all.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-vitisviniferacdf/bioconductor-vitisviniferacdf_2.18.0_src_all.tar.gz" ) MD5="8eb491f3ffa3ff0814f5c155787ae160" @@ -16,7 +17,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-vitisviniferaprobe/meta.yaml b/recipes/bioconductor-vitisviniferaprobe/meta.yaml index 5e201142ef935..4c817ee702f81 100644 --- a/recipes/bioconductor-vitisviniferaprobe/meta.yaml +++ b/recipes/bioconductor-vitisviniferaprobe/meta.yaml @@ -1,6 +1,6 @@ {% set version = "2.18.0" %} {% set name = "vitisviniferaprobe" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -12,19 +12,19 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 386c0d5e37896d073ac20970e88b3160 build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' - r-base run: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-vitisviniferaprobe/post-link.sh b/recipes/bioconductor-vitisviniferaprobe/post-link.sh index 4fabb354f6bdf..5f81c5f06192e 100644 --- a/recipes/bioconductor-vitisviniferaprobe/post-link.sh +++ b/recipes/bioconductor-vitisviniferaprobe/post-link.sh @@ -1,9 +1,10 @@ #!/bin/bash FN="vitisviniferaprobe_2.18.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/vitisviniferaprobe_2.18.0.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/vitisviniferaprobe_2.18.0.tar.gz" "https://bioarchive.galaxyproject.org/vitisviniferaprobe_2.18.0.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-vitisviniferaprobe/bioconductor-vitisviniferaprobe_2.18.0_src_all.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-vitisviniferaprobe/bioconductor-vitisviniferaprobe_2.18.0_src_all.tar.gz" ) MD5="386c0d5e37896d073ac20970e88b3160" @@ -16,7 +17,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-vsn/meta.yaml b/recipes/bioconductor-vsn/meta.yaml index e2851a42f7d6b..1d00eb0c691b3 100644 --- a/recipes/bioconductor-vsn/meta.yaml +++ b/recipes/bioconductor-vsn/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "3.50.0" %} +{% set version = "3.52.0" %} {% set name = "vsn" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: bf53a681b9b9bdfce2b27cb556e2b9d0 + md5: b6164fe0b1b5f91991abd9e948e2bb69 build: number: 0 rpaths: @@ -19,16 +19,16 @@ build: # Suggests: affydata, hgu95av2cdf, BiocStyle, knitr, dplyr, testthat requirements: host: - - 'bioconductor-affy >=1.60.0,<1.61.0' - - 'bioconductor-biobase >=2.42.0,<2.43.0' - - 'bioconductor-limma >=3.38.0,<3.39.0' + - 'bioconductor-affy >=1.62.0,<1.63.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' + - 'bioconductor-limma >=3.40.0,<3.41.0' - r-base - r-ggplot2 - r-lattice run: - - 'bioconductor-affy >=1.60.0,<1.61.0' - - 'bioconductor-biobase >=2.42.0,<2.43.0' - - 'bioconductor-limma >=3.38.0,<3.39.0' + - 'bioconductor-affy >=1.62.0,<1.63.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' + - 'bioconductor-limma >=3.40.0,<3.41.0' - r-base - r-ggplot2 - r-lattice diff --git a/recipes/bioconductor-vtpnet/meta.yaml b/recipes/bioconductor-vtpnet/meta.yaml index d51d1a3fd1991..441bfc95c7d97 100644 --- a/recipes/bioconductor-vtpnet/meta.yaml +++ b/recipes/bioconductor-vtpnet/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "0.22.0" %} +{% set version = "0.24.0" %} {% set name = "vtpnet" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: c72d10bf3d20932c1847fa2aad5f914e + md5: 51681bfcca401ee6ebb659675afd5773 build: number: 0 rpaths: @@ -20,16 +20,16 @@ build: # Suggests: MotifDb, VariantAnnotation, Rgraphviz requirements: host: - - 'bioconductor-genomicranges >=1.34.0,<1.35.0' - - 'bioconductor-graph >=1.60.0,<1.61.0' - - 'bioconductor-gwascat >=2.14.0,<2.15.0' + - 'bioconductor-genomicranges >=1.36.0,<1.37.0' + - 'bioconductor-graph >=1.62.0,<1.63.0' + - 'bioconductor-gwascat >=2.16.0,<2.17.0' - r-base - r-doparallel - r-foreach run: - - 'bioconductor-genomicranges >=1.34.0,<1.35.0' - - 'bioconductor-graph >=1.60.0,<1.61.0' - - 'bioconductor-gwascat >=2.14.0,<2.15.0' + - 'bioconductor-genomicranges >=1.36.0,<1.37.0' + - 'bioconductor-graph >=1.62.0,<1.63.0' + - 'bioconductor-gwascat >=2.16.0,<2.17.0' - r-base - r-doparallel - r-foreach diff --git a/recipes/bioconductor-vulcan/meta.yaml b/recipes/bioconductor-vulcan/meta.yaml index cfbfaa539b091..f4f6c9e1438b5 100644 --- a/recipes/bioconductor-vulcan/meta.yaml +++ b/recipes/bioconductor-vulcan/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.4.0" %} +{% set version = "1.6.0" %} {% set name = "vulcan" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: bdec6ffd2a60d2f83183dd2c76bcb637 + md5: 291cee1c7a3f49263fa5d52a788e5ddf build: number: 0 rpaths: @@ -20,15 +20,15 @@ build: # Suggests: vulcandata requirements: host: - - 'bioconductor-biobase >=2.42.0,<2.43.0' - - 'bioconductor-chippeakanno >=3.16.0,<3.17.0' - - 'bioconductor-csaw >=1.16.0,<1.17.0' - - 'bioconductor-deseq >=1.34.0,<1.35.0' - - 'bioconductor-diffbind >=2.10.0,<2.11.0' - - 'bioconductor-genomicranges >=1.34.0,<1.35.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' + - 'bioconductor-chippeakanno >=3.18.0,<3.19.0' + - 'bioconductor-csaw >=1.18.0,<1.19.0' + - 'bioconductor-deseq >=1.36.0,<1.37.0' + - 'bioconductor-diffbind >=2.12.0,<2.13.0' + - 'bioconductor-genomicranges >=1.36.0,<1.37.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' - 'bioconductor-txdb.hsapiens.ucsc.hg19.knowngene >=3.2.0,<3.3.0' - - 'bioconductor-viper >=1.16.0,<1.17.0' + - 'bioconductor-viper >=1.18.0,<1.19.0' - r-base - r-catools - r-gplots @@ -36,15 +36,15 @@ requirements: - r-wordcloud - r-zoo run: - - 'bioconductor-biobase >=2.42.0,<2.43.0' - - 'bioconductor-chippeakanno >=3.16.0,<3.17.0' - - 'bioconductor-csaw >=1.16.0,<1.17.0' - - 'bioconductor-deseq >=1.34.0,<1.35.0' - - 'bioconductor-diffbind >=2.10.0,<2.11.0' - - 'bioconductor-genomicranges >=1.34.0,<1.35.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' + - 'bioconductor-chippeakanno >=3.18.0,<3.19.0' + - 'bioconductor-csaw >=1.18.0,<1.19.0' + - 'bioconductor-deseq >=1.36.0,<1.37.0' + - 'bioconductor-diffbind >=2.12.0,<2.13.0' + - 'bioconductor-genomicranges >=1.36.0,<1.37.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' - 'bioconductor-txdb.hsapiens.ucsc.hg19.knowngene >=3.2.0,<3.3.0' - - 'bioconductor-viper >=1.16.0,<1.17.0' + - 'bioconductor-viper >=1.18.0,<1.19.0' - r-base - r-catools - r-gplots diff --git a/recipes/bioconductor-vulcandata/meta.yaml b/recipes/bioconductor-vulcandata/meta.yaml index 7c0efa4ece950..f9867dc8d8bc2 100644 --- a/recipes/bioconductor-vulcandata/meta.yaml +++ b/recipes/bioconductor-vulcandata/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.4.0" %} +{% set version = "1.6.0" %} {% set name = "vulcandata" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 65a1dc1a4c75edacf512fe57434790e2 + md5: f4b88fcd71e15eaa28291dfa423b90b5 build: number: 0 rpaths: @@ -22,7 +22,7 @@ requirements: - r-base run: - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-vulcandata/post-link.sh b/recipes/bioconductor-vulcandata/post-link.sh index 90d30a95d00cc..5724ba77b6095 100644 --- a/recipes/bioconductor-vulcandata/post-link.sh +++ b/recipes/bioconductor-vulcandata/post-link.sh @@ -1,11 +1,11 @@ #!/bin/bash -FN="vulcandata_1.4.0.tar.gz" +FN="vulcandata_1.6.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/experiment/src/contrib/vulcandata_1.4.0.tar.gz" - "https://bioarchive.galaxyproject.org/vulcandata_1.4.0.tar.gz" - "https://depot.galaxyproject.org/software/bioconductor-vulcandata/bioconductor-vulcandata_1.4.0_src_all.tar.gz" + "https://bioconductor.org/packages/3.9/data/experiment/src/contrib/vulcandata_1.6.0.tar.gz" + "https://bioarchive.galaxyproject.org/vulcandata_1.6.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-vulcandata/bioconductor-vulcandata_1.6.0_src_all.tar.gz" ) -MD5="65a1dc1a4c75edacf512fe57434790e2" +MD5="f4b88fcd71e15eaa28291dfa423b90b5" # Use a staging area in the conda dir rather than temp dirs, both to avoid # permission issues as well as to have things downloaded in a predictable @@ -16,7 +16,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-watermelon/meta.yaml b/recipes/bioconductor-watermelon/meta.yaml index d3ebfb2c86c8d..0d8b5a9bf99c4 100644 --- a/recipes/bioconductor-watermelon/meta.yaml +++ b/recipes/bioconductor-watermelon/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.26.0" %} +{% set version = "1.28.0" %} {% set name = "wateRmelon" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 850367d09d233968ac5b418f29de23a4 + md5: 23f2dd01b0492239c6050e8483f3f007 build: number: 0 rpaths: @@ -20,23 +20,23 @@ build: # Suggests: RPMM, IlluminaHumanMethylationEPICanno.ilm10b2.hg19, IlluminaHumanMethylationEPICmanifest, irlba requirements: host: - - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' - 'bioconductor-illuminahumanmethylation450kanno.ilmn12.hg19 >=0.6.0,<0.7.0' - - 'bioconductor-illuminaio >=0.24.0,<0.25.0' - - 'bioconductor-limma >=3.38.0,<3.39.0' - - 'bioconductor-lumi >=2.34.0,<2.35.0' - - 'bioconductor-methylumi >=2.28.0,<2.29.0' - - 'bioconductor-roc >=1.58.0,<1.59.0' + - 'bioconductor-illuminaio >=0.26.0,<0.27.0' + - 'bioconductor-limma >=3.40.0,<3.41.0' + - 'bioconductor-lumi >=2.36.0,<2.37.0' + - 'bioconductor-methylumi >=2.30.0,<2.31.0' + - 'bioconductor-roc >=1.60.0,<1.61.0' - r-base - r-matrixstats run: - - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' - 'bioconductor-illuminahumanmethylation450kanno.ilmn12.hg19 >=0.6.0,<0.7.0' - - 'bioconductor-illuminaio >=0.24.0,<0.25.0' - - 'bioconductor-limma >=3.38.0,<3.39.0' - - 'bioconductor-lumi >=2.34.0,<2.35.0' - - 'bioconductor-methylumi >=2.28.0,<2.29.0' - - 'bioconductor-roc >=1.58.0,<1.59.0' + - 'bioconductor-illuminaio >=0.26.0,<0.27.0' + - 'bioconductor-limma >=3.40.0,<3.41.0' + - 'bioconductor-lumi >=2.36.0,<2.37.0' + - 'bioconductor-methylumi >=2.30.0,<2.31.0' + - 'bioconductor-roc >=1.60.0,<1.61.0' - r-base - r-matrixstats test: diff --git a/recipes/bioconductor-wavcluster/meta.yaml b/recipes/bioconductor-wavcluster/meta.yaml index 9dae9a0067d92..16b10a3c5a482 100644 --- a/recipes/bioconductor-wavcluster/meta.yaml +++ b/recipes/bioconductor-wavcluster/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "2.16.0" %} +{% set version = "2.18.0" %} {% set name = "wavClusteR" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: c27ac709b57b39907a298c5d8233757a + md5: b592350ba78ab24461ef82372e07f26d build: number: 0 rpaths: @@ -20,14 +20,14 @@ build: # Suggests: BiocStyle, knitr, rmarkdown, BSgenome.Hsapiens.UCSC.hg19 requirements: host: - - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' - - 'bioconductor-biostrings >=2.50.0,<2.51.0' - - 'bioconductor-genomicfeatures >=1.34.0,<1.35.0' - - 'bioconductor-genomicranges >=1.34.0,<1.35.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-rsamtools >=1.34.0,<1.35.0' - - 'bioconductor-rtracklayer >=1.42.0,<1.43.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-biocgenerics >=0.30.0,<0.31.0' + - 'bioconductor-biostrings >=2.52.0,<2.53.0' + - 'bioconductor-genomicfeatures >=1.36.0,<1.37.0' + - 'bioconductor-genomicranges >=1.36.0,<1.37.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-rsamtools >=2.0.0,<2.1.0' + - 'bioconductor-rtracklayer >=1.44.0,<1.45.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' - r-base - r-foreach - r-ggplot2 @@ -37,14 +37,14 @@ requirements: - r-stringr - r-wmtsa run: - - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' - - 'bioconductor-biostrings >=2.50.0,<2.51.0' - - 'bioconductor-genomicfeatures >=1.34.0,<1.35.0' - - 'bioconductor-genomicranges >=1.34.0,<1.35.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-rsamtools >=1.34.0,<1.35.0' - - 'bioconductor-rtracklayer >=1.42.0,<1.43.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-biocgenerics >=0.30.0,<0.31.0' + - 'bioconductor-biostrings >=2.52.0,<2.53.0' + - 'bioconductor-genomicfeatures >=1.36.0,<1.37.0' + - 'bioconductor-genomicranges >=1.36.0,<1.37.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-rsamtools >=2.0.0,<2.1.0' + - 'bioconductor-rtracklayer >=1.44.0,<1.45.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' - r-base - r-foreach - r-ggplot2 diff --git a/recipes/bioconductor-wavetiling/meta.yaml b/recipes/bioconductor-wavetiling/meta.yaml index 4c1ec00237381..d174e59e8d335 100644 --- a/recipes/bioconductor-wavetiling/meta.yaml +++ b/recipes/bioconductor-wavetiling/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.24.0" %} +{% set version = "1.26.0" %} {% set name = "waveTiling" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 80d2a5104b88c2621ded2314d7a986ba + md5: 414c7fe83b3ad0b3aca89070936e1d4c build: number: 0 rpaths: @@ -19,27 +19,27 @@ build: # Suggests: BSgenome, BSgenome.Athaliana.TAIR.TAIR9, waveTilingData, pd.atdschip.tiling, TxDb.Athaliana.BioMart.plantsmart22 requirements: host: - - 'bioconductor-affy >=1.60.0,<1.61.0' - - 'bioconductor-biobase >=2.42.0,<2.43.0' - - 'bioconductor-biostrings >=2.50.0,<2.51.0' - - 'bioconductor-genomegraphs >=1.42.0,<1.43.0' - - 'bioconductor-genomicranges >=1.34.0,<1.35.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-oligo >=1.46.0,<1.47.0' - - 'bioconductor-oligoclasses >=1.44.0,<1.45.0' - - 'bioconductor-preprocesscore >=1.44.0,<1.45.0' + - 'bioconductor-affy >=1.62.0,<1.63.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' + - 'bioconductor-biostrings >=2.52.0,<2.53.0' + - 'bioconductor-genomegraphs >=1.44.0,<1.45.0' + - 'bioconductor-genomicranges >=1.36.0,<1.37.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-oligo >=1.48.0,<1.49.0' + - 'bioconductor-oligoclasses >=1.46.0,<1.47.0' + - 'bioconductor-preprocesscore >=1.46.0,<1.47.0' - r-base - r-waveslim run: - - 'bioconductor-affy >=1.60.0,<1.61.0' - - 'bioconductor-biobase >=2.42.0,<2.43.0' - - 'bioconductor-biostrings >=2.50.0,<2.51.0' - - 'bioconductor-genomegraphs >=1.42.0,<1.43.0' - - 'bioconductor-genomicranges >=1.34.0,<1.35.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-oligo >=1.46.0,<1.47.0' - - 'bioconductor-oligoclasses >=1.44.0,<1.45.0' - - 'bioconductor-preprocesscore >=1.44.0,<1.45.0' + - 'bioconductor-affy >=1.62.0,<1.63.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' + - 'bioconductor-biostrings >=2.52.0,<2.53.0' + - 'bioconductor-genomegraphs >=1.44.0,<1.45.0' + - 'bioconductor-genomicranges >=1.36.0,<1.37.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-oligo >=1.48.0,<1.49.0' + - 'bioconductor-oligoclasses >=1.46.0,<1.47.0' + - 'bioconductor-preprocesscore >=1.46.0,<1.47.0' - r-base - r-waveslim build: diff --git a/recipes/bioconductor-wavetilingdata/meta.yaml b/recipes/bioconductor-wavetilingdata/meta.yaml index 3f7383a954a10..0823919d3a7a7 100644 --- a/recipes/bioconductor-wavetilingdata/meta.yaml +++ b/recipes/bioconductor-wavetilingdata/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.18.0" %} +{% set version = "1.20.0" %} {% set name = "waveTilingData" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 4fe1e828f7c998a4d3c9621886e5c5f1 + md5: b6a9a41570c55fa3057b879f72817f6d build: number: 0 rpaths: @@ -22,7 +22,7 @@ requirements: - r-base run: - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-wavetilingdata/post-link.sh b/recipes/bioconductor-wavetilingdata/post-link.sh index 223c3ba3a8318..c628435f6fa4d 100644 --- a/recipes/bioconductor-wavetilingdata/post-link.sh +++ b/recipes/bioconductor-wavetilingdata/post-link.sh @@ -1,11 +1,11 @@ #!/bin/bash -FN="waveTilingData_1.18.0.tar.gz" +FN="waveTilingData_1.20.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/experiment/src/contrib/waveTilingData_1.18.0.tar.gz" - "https://bioarchive.galaxyproject.org/waveTilingData_1.18.0.tar.gz" - "https://depot.galaxyproject.org/software/bioconductor-wavetilingdata/bioconductor-wavetilingdata_1.18.0_src_all.tar.gz" + "https://bioconductor.org/packages/3.9/data/experiment/src/contrib/waveTilingData_1.20.0.tar.gz" + "https://bioarchive.galaxyproject.org/waveTilingData_1.20.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-wavetilingdata/bioconductor-wavetilingdata_1.20.0_src_all.tar.gz" ) -MD5="4fe1e828f7c998a4d3c9621886e5c5f1" +MD5="b6a9a41570c55fa3057b879f72817f6d" # Use a staging area in the conda dir rather than temp dirs, both to avoid # permission issues as well as to have things downloaded in a predictable @@ -16,7 +16,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-weaver/meta.yaml b/recipes/bioconductor-weaver/meta.yaml index f9d779dba3583..abf20502693a1 100644 --- a/recipes/bioconductor-weaver/meta.yaml +++ b/recipes/bioconductor-weaver/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.48.0" %} +{% set version = "1.50.0" %} {% set name = "weaver" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 9b2abdd081e7f54dff55bfd0fe27512c + md5: 50bde89ae215d49e504f77727c84af60 build: number: 0 rpaths: diff --git a/recipes/bioconductor-webbioc/meta.yaml b/recipes/bioconductor-webbioc/meta.yaml index fa011d9b174f3..b630553c953d9 100644 --- a/recipes/bioconductor-webbioc/meta.yaml +++ b/recipes/bioconductor-webbioc/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.54.0" %} +{% set version = "1.56.0" %} {% set name = "webbioc" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: d08d8ccc53dc8c06d1472dc5e6e528d4 + md5: c0e717b515a7a27f4371fbabd72f5147 build: number: 0 rpaths: @@ -20,25 +20,29 @@ build: # SystemRequirements: Unix, Perl (>= 5.6.0), Netpbm requirements: host: - - 'bioconductor-affy >=1.60.0,<1.61.0' - - 'bioconductor-annaffy >=1.54.0,<1.55.0' - - 'bioconductor-biobase >=2.42.0,<2.43.0' - - 'bioconductor-gcrma >=2.54.0,<2.55.0' - - 'bioconductor-multtest >=2.38.0,<2.39.0' - - 'bioconductor-qvalue >=2.14.0,<2.15.0' - - 'bioconductor-vsn >=3.50.0,<3.51.0' + - 'bioconductor-affy >=1.62.0,<1.63.0' + - 'bioconductor-annaffy >=1.56.0,<1.57.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' + - 'bioconductor-gcrma >=2.56.0,<2.57.0' + - 'bioconductor-multtest >=2.40.0,<2.41.0' + - 'bioconductor-qvalue >=2.16.0,<2.17.0' + - 'bioconductor-vsn >=3.52.0,<3.53.0' - r-base - r-biocmanager + - perl + - netpbm run: - - 'bioconductor-affy >=1.60.0,<1.61.0' - - 'bioconductor-annaffy >=1.54.0,<1.55.0' - - 'bioconductor-biobase >=2.42.0,<2.43.0' - - 'bioconductor-gcrma >=2.54.0,<2.55.0' - - 'bioconductor-multtest >=2.38.0,<2.39.0' - - 'bioconductor-qvalue >=2.14.0,<2.15.0' - - 'bioconductor-vsn >=3.50.0,<3.51.0' + - 'bioconductor-affy >=1.62.0,<1.63.0' + - 'bioconductor-annaffy >=1.56.0,<1.57.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' + - 'bioconductor-gcrma >=2.56.0,<2.57.0' + - 'bioconductor-multtest >=2.40.0,<2.41.0' + - 'bioconductor-qvalue >=2.16.0,<2.17.0' + - 'bioconductor-vsn >=3.52.0,<3.53.0' - r-base - r-biocmanager + - perl + - netpbm test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-wes.1kg.wugsc/meta.yaml b/recipes/bioconductor-wes.1kg.wugsc/meta.yaml index 454eca7497d3a..56e7a748e1bd6 100644 --- a/recipes/bioconductor-wes.1kg.wugsc/meta.yaml +++ b/recipes/bioconductor-wes.1kg.wugsc/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.14.0" %} +{% set version = "1.16.0" %} {% set name = "WES.1KG.WUGSC" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: d1013abff0fe02136aab55a3354529ee + md5: 6d660e6f8bddd1aa81e578e887a8712b build: number: 0 rpaths: @@ -22,7 +22,7 @@ requirements: - r-base run: - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-wes.1kg.wugsc/post-link.sh b/recipes/bioconductor-wes.1kg.wugsc/post-link.sh index bb8e8e3a080f9..42fbf6c6f4441 100644 --- a/recipes/bioconductor-wes.1kg.wugsc/post-link.sh +++ b/recipes/bioconductor-wes.1kg.wugsc/post-link.sh @@ -1,11 +1,11 @@ #!/bin/bash -FN="WES.1KG.WUGSC_1.14.0.tar.gz" +FN="WES.1KG.WUGSC_1.16.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/experiment/src/contrib/WES.1KG.WUGSC_1.14.0.tar.gz" - "https://bioarchive.galaxyproject.org/WES.1KG.WUGSC_1.14.0.tar.gz" - "https://depot.galaxyproject.org/software/bioconductor-wes.1kg.wugsc/bioconductor-wes.1kg.wugsc_1.14.0_src_all.tar.gz" + "https://bioconductor.org/packages/3.9/data/experiment/src/contrib/WES.1KG.WUGSC_1.16.0.tar.gz" + "https://bioarchive.galaxyproject.org/WES.1KG.WUGSC_1.16.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-wes.1kg.wugsc/bioconductor-wes.1kg.wugsc_1.16.0_src_all.tar.gz" ) -MD5="d1013abff0fe02136aab55a3354529ee" +MD5="6d660e6f8bddd1aa81e578e887a8712b" # Use a staging area in the conda dir rather than temp dirs, both to avoid # permission issues as well as to have things downloaded in a predictable @@ -16,7 +16,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-wheatcdf/meta.yaml b/recipes/bioconductor-wheatcdf/meta.yaml index a85e44f45821a..fe38322cade42 100644 --- a/recipes/bioconductor-wheatcdf/meta.yaml +++ b/recipes/bioconductor-wheatcdf/meta.yaml @@ -1,6 +1,6 @@ {% set version = "2.18.0" %} {% set name = "wheatcdf" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -12,19 +12,19 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 0abeeeb9700b8d93a1a83769bdd8480f build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' - r-base run: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-wheatcdf/post-link.sh b/recipes/bioconductor-wheatcdf/post-link.sh index 5658a300de096..6eb24e0c62a06 100644 --- a/recipes/bioconductor-wheatcdf/post-link.sh +++ b/recipes/bioconductor-wheatcdf/post-link.sh @@ -1,9 +1,10 @@ #!/bin/bash FN="wheatcdf_2.18.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/wheatcdf_2.18.0.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/wheatcdf_2.18.0.tar.gz" "https://bioarchive.galaxyproject.org/wheatcdf_2.18.0.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-wheatcdf/bioconductor-wheatcdf_2.18.0_src_all.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-wheatcdf/bioconductor-wheatcdf_2.18.0_src_all.tar.gz" ) MD5="0abeeeb9700b8d93a1a83769bdd8480f" @@ -16,7 +17,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-wheatprobe/meta.yaml b/recipes/bioconductor-wheatprobe/meta.yaml index fb2fc74710227..5f302ad851c56 100644 --- a/recipes/bioconductor-wheatprobe/meta.yaml +++ b/recipes/bioconductor-wheatprobe/meta.yaml @@ -1,6 +1,6 @@ {% set version = "2.18.0" %} {% set name = "wheatprobe" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -12,19 +12,19 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: b602d5050239850515be9dce12286360 build: - number: 1 + number: 2 rpaths: - lib/R/lib/ - lib/ noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' - r-base run: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-wheatprobe/post-link.sh b/recipes/bioconductor-wheatprobe/post-link.sh index fcf9571ef0b4f..1c7b145e2b168 100644 --- a/recipes/bioconductor-wheatprobe/post-link.sh +++ b/recipes/bioconductor-wheatprobe/post-link.sh @@ -1,9 +1,10 @@ #!/bin/bash FN="wheatprobe_2.18.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/wheatprobe_2.18.0.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/wheatprobe_2.18.0.tar.gz" "https://bioarchive.galaxyproject.org/wheatprobe_2.18.0.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-wheatprobe/bioconductor-wheatprobe_2.18.0_src_all.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-wheatprobe/bioconductor-wheatprobe_2.18.0_src_all.tar.gz" ) MD5="b602d5050239850515be9dce12286360" @@ -16,7 +17,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-widgettools/meta.yaml b/recipes/bioconductor-widgettools/meta.yaml index 5d3ccaf1c957d..211194bf1ea7b 100644 --- a/recipes/bioconductor-widgettools/meta.yaml +++ b/recipes/bioconductor-widgettools/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.60.0" %} +{% set version = "1.62.0" %} {% set name = "widgetTools" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: c317790521ce4176632769af78d89b4f + md5: bd26f959ba3f6851cb0d1ea2346bf0dd build: number: 0 rpaths: diff --git a/recipes/bioconductor-wiggleplotr/meta.yaml b/recipes/bioconductor-wiggleplotr/meta.yaml index 6c8a0a54a703a..79599929bf3a8 100644 --- a/recipes/bioconductor-wiggleplotr/meta.yaml +++ b/recipes/bioconductor-wiggleplotr/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.6.0" %} +{% set version = "1.8.0" %} {% set name = "wiggleplotr" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 4385b0b448bb77ee6948c0a42a08962e + md5: e8a1ac4ab6c1eed1878c34273ae48c02 build: number: 0 rpaths: @@ -20,11 +20,11 @@ build: # Suggests: knitr, rmarkdown, biomaRt, GenomicFeatures, testthat, ensembldb, EnsDb.Hsapiens.v86, org.Hs.eg.db, TxDb.Hsapiens.UCSC.hg38.knownGene, AnnotationDbi, AnnotationFilter requirements: host: - - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' - - 'bioconductor-genomicranges >=1.34.0,<1.35.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-rtracklayer >=1.42.0,<1.43.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-genomeinfodb >=1.20.0,<1.21.0' + - 'bioconductor-genomicranges >=1.36.0,<1.37.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-rtracklayer >=1.44.0,<1.45.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' - r-assertthat - r-base - r-cowplot @@ -32,11 +32,11 @@ requirements: - 'r-ggplot2 >=2.2.0' - r-purrr run: - - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' - - 'bioconductor-genomicranges >=1.34.0,<1.35.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-rtracklayer >=1.42.0,<1.43.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-genomeinfodb >=1.20.0,<1.21.0' + - 'bioconductor-genomicranges >=1.36.0,<1.37.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-rtracklayer >=1.44.0,<1.45.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' - r-assertthat - r-base - r-cowplot diff --git a/recipes/bioconductor-worm.db0/meta.yaml b/recipes/bioconductor-worm.db0/meta.yaml index 68bc101fb78da..b5781827985c7 100644 --- a/recipes/bioconductor-worm.db0/meta.yaml +++ b/recipes/bioconductor-worm.db0/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "3.7.1" %} +{% set version = "3.8.2" %} {% set name = "worm.db0" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 65473df3ea58399054f7c71a53d33362 + md5: 5975ea35d6c925bf2bfd0cdeb9b16667 build: number: 0 rpaths: @@ -19,12 +19,12 @@ build: noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' - r-base run: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-worm.db0/post-link.sh b/recipes/bioconductor-worm.db0/post-link.sh index a529de249585a..fd4def158606a 100644 --- a/recipes/bioconductor-worm.db0/post-link.sh +++ b/recipes/bioconductor-worm.db0/post-link.sh @@ -1,11 +1,11 @@ #!/bin/bash -FN="worm.db0_3.7.1.tar.gz" +FN="worm.db0_3.8.2.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/worm.db0_3.7.1.tar.gz" - "https://bioarchive.galaxyproject.org/worm.db0_3.7.1.tar.gz" - "https://depot.galaxyproject.org/software/bioconductor-worm.db0/bioconductor-worm.db0_3.7.1_src_all.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/worm.db0_3.8.2.tar.gz" + "https://bioarchive.galaxyproject.org/worm.db0_3.8.2.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-worm.db0/bioconductor-worm.db0_3.8.2_src_all.tar.gz" ) -MD5="65473df3ea58399054f7c71a53d33362" +MD5="5975ea35d6c925bf2bfd0cdeb9b16667" # Use a staging area in the conda dir rather than temp dirs, both to avoid # permission issues as well as to have things downloaded in a predictable @@ -16,7 +16,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-wrench/meta.yaml b/recipes/bioconductor-wrench/meta.yaml index 0b9112230adef..cee6448ac4c0c 100644 --- a/recipes/bioconductor-wrench/meta.yaml +++ b/recipes/bioconductor-wrench/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.0.0" %} +{% set version = "1.2.0" %} {% set name = "Wrench" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: a13adf697da0006944f1f36b3c5748e5 + md5: 088707f696c3854c4c4631811ab83130 build: number: 0 rpaths: @@ -20,12 +20,12 @@ build: # Suggests: knitr, rmarkdown, metagenomeSeq, DESeq2, edgeR requirements: host: - - 'bioconductor-limma >=3.38.0,<3.39.0' + - 'bioconductor-limma >=3.40.0,<3.41.0' - r-base - r-locfit - r-matrixstats run: - - 'bioconductor-limma >=3.38.0,<3.39.0' + - 'bioconductor-limma >=3.40.0,<3.41.0' - r-base - r-locfit - r-matrixstats diff --git a/recipes/bioconductor-xbseq/meta.yaml b/recipes/bioconductor-xbseq/meta.yaml index 3a7552ef45c76..0770b46fb2519 100644 --- a/recipes/bioconductor-xbseq/meta.yaml +++ b/recipes/bioconductor-xbseq/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.14.0" %} +{% set version = "1.16.0" %} {% set name = "XBSeq" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: fdc86bd68c94758b19a8a3fdefe2294a + md5: 48b45d27904653568eb5f44f98fed19a build: number: 0 rpaths: @@ -20,9 +20,9 @@ build: # Suggests: knitr, DESeq, rmarkdown, BiocStyle, testthat requirements: host: - - 'bioconductor-biobase >=2.42.0,<2.43.0' - - 'bioconductor-deseq2 >=1.22.0,<1.23.0' - - 'bioconductor-roar >=1.18.0,<1.19.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' + - 'bioconductor-deseq2 >=1.24.0,<1.25.0' + - 'bioconductor-roar >=1.20.0,<1.21.0' - r-base - r-dplyr - r-ggplot2 @@ -31,9 +31,9 @@ requirements: - r-matrixstats - r-pracma run: - - 'bioconductor-biobase >=2.42.0,<2.43.0' - - 'bioconductor-deseq2 >=1.22.0,<1.23.0' - - 'bioconductor-roar >=1.18.0,<1.19.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' + - 'bioconductor-deseq2 >=1.24.0,<1.25.0' + - 'bioconductor-roar >=1.20.0,<1.21.0' - r-base - r-dplyr - r-ggplot2 diff --git a/recipes/bioconductor-xcms/meta.yaml b/recipes/bioconductor-xcms/meta.yaml index a4e97cc10d6c3..2457244d08ea6 100644 --- a/recipes/bioconductor-xcms/meta.yaml +++ b/recipes/bioconductor-xcms/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "3.4.4" %} +{% set version = "3.6.0" %} {% set name = "xcms" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,24 +10,24 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 5bcf252ec53c7720a67f1785e4693005 + md5: 38083e74761278cc928f8519d1f53f80 build: number: 0 rpaths: - lib/R/lib/ - lib/ -# Suggests: BiocStyle, caTools, knitr (>= 1.1.0), faahKO, msdata, ncdf4, rgl, microbenchmark, testthat, pander, magrittr, MALDIquant +# Suggests: BiocStyle, caTools, knitr (>= 1.1.0), faahKO, msdata, ncdf4, rgl, microbenchmark, testthat, pander, magrittr, MALDIquant, pheatmap requirements: host: - - 'bioconductor-biobase >=2.42.0,<2.43.0' - - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' - - 'bioconductor-biocparallel >=1.16.0,<1.17.0' - - 'bioconductor-massspecwavelet >=1.48.0,<1.49.0' - - 'bioconductor-msnbase >=2.8.0,<2.9.0' - - 'bioconductor-multtest >=2.38.0,<2.39.0' - - 'bioconductor-mzr >=2.16.0,<2.17.0' - - 'bioconductor-protgenerics >=1.14.0,<1.15.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' + - 'bioconductor-biocgenerics >=0.30.0,<0.31.0' + - 'bioconductor-biocparallel >=1.18.0,<1.19.0' + - 'bioconductor-massspecwavelet >=1.50.0,<1.51.0' + - 'bioconductor-msnbase >=2.10.0,<2.11.0' + - 'bioconductor-multtest >=2.40.0,<2.41.0' + - 'bioconductor-mzr >=2.18.0,<2.19.0' + - 'bioconductor-protgenerics >=1.16.0,<1.17.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' - r-base - r-lattice - r-plyr @@ -35,15 +35,15 @@ requirements: - r-rcolorbrewer - r-robustbase run: - - 'bioconductor-biobase >=2.42.0,<2.43.0' - - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' - - 'bioconductor-biocparallel >=1.16.0,<1.17.0' - - 'bioconductor-massspecwavelet >=1.48.0,<1.49.0' - - 'bioconductor-msnbase >=2.8.0,<2.9.0' - - 'bioconductor-multtest >=2.38.0,<2.39.0' - - 'bioconductor-mzr >=2.16.0,<2.17.0' - - 'bioconductor-protgenerics >=1.14.0,<1.15.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' + - 'bioconductor-biocgenerics >=0.30.0,<0.31.0' + - 'bioconductor-biocparallel >=1.18.0,<1.19.0' + - 'bioconductor-massspecwavelet >=1.50.0,<1.51.0' + - 'bioconductor-msnbase >=2.10.0,<2.11.0' + - 'bioconductor-multtest >=2.40.0,<2.41.0' + - 'bioconductor-mzr >=2.18.0,<2.19.0' + - 'bioconductor-protgenerics >=1.16.0,<1.17.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' - r-base - r-lattice - r-plyr diff --git a/recipes/bioconductor-xde/meta.yaml b/recipes/bioconductor-xde/meta.yaml index 751c72ab8ce2a..c99d102c658ed 100644 --- a/recipes/bioconductor-xde/meta.yaml +++ b/recipes/bioconductor-xde/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "2.28.0" %} +{% set version = "2.30.0" %} {% set name = "XDE" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: be18c127b068e92c2811ceaf408326e0 + md5: 1edf40b637ab430bbb22f79a1d35d1d8 build: number: 0 rpaths: @@ -19,23 +19,23 @@ build: # Suggests: MASS, RUnit requirements: host: - - 'bioconductor-biobase >=2.42.0,<2.43.0' - - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' - - 'bioconductor-genefilter >=1.64.0,<1.65.0' - - 'bioconductor-genemeta >=1.54.0,<1.55.0' - - 'bioconductor-mergemaid >=2.54.0,<2.55.0' - - 'bioconductor-siggenes >=1.56.0,<1.57.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' + - 'bioconductor-biocgenerics >=0.30.0,<0.31.0' + - 'bioconductor-genefilter >=1.66.0,<1.67.0' + - 'bioconductor-genemeta >=1.56.0,<1.57.0' + - 'bioconductor-mergemaid >=2.56.0,<2.57.0' + - 'bioconductor-siggenes >=1.58.0,<1.59.0' - r-base - r-gtools - r-mvtnorm - r-rcolorbrewer run: - - 'bioconductor-biobase >=2.42.0,<2.43.0' - - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' - - 'bioconductor-genefilter >=1.64.0,<1.65.0' - - 'bioconductor-genemeta >=1.54.0,<1.55.0' - - 'bioconductor-mergemaid >=2.54.0,<2.55.0' - - 'bioconductor-siggenes >=1.56.0,<1.57.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' + - 'bioconductor-biocgenerics >=0.30.0,<0.31.0' + - 'bioconductor-genefilter >=1.66.0,<1.67.0' + - 'bioconductor-genemeta >=1.56.0,<1.57.0' + - 'bioconductor-mergemaid >=2.56.0,<2.57.0' + - 'bioconductor-siggenes >=1.58.0,<1.59.0' - r-base - r-gtools - r-mvtnorm diff --git a/recipes/bioconductor-xenopus.db0/meta.yaml b/recipes/bioconductor-xenopus.db0/meta.yaml index 5e7f0076609dc..1b1fbfdd8e2d8 100644 --- a/recipes/bioconductor-xenopus.db0/meta.yaml +++ b/recipes/bioconductor-xenopus.db0/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "3.7.1" %} +{% set version = "3.8.2" %} {% set name = "xenopus.db0" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 6a34dd176e70d66d4acda7a141e09ef5 + md5: 199efa5f20b5dd8fc16aaeac9f0d9eeb build: number: 0 rpaths: @@ -19,12 +19,12 @@ build: noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' - r-base run: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-xenopus.db0/post-link.sh b/recipes/bioconductor-xenopus.db0/post-link.sh index c4321ffd699de..cc52ce3858b73 100644 --- a/recipes/bioconductor-xenopus.db0/post-link.sh +++ b/recipes/bioconductor-xenopus.db0/post-link.sh @@ -1,11 +1,11 @@ #!/bin/bash -FN="xenopus.db0_3.7.1.tar.gz" +FN="xenopus.db0_3.8.2.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/xenopus.db0_3.7.1.tar.gz" - "https://bioarchive.galaxyproject.org/xenopus.db0_3.7.1.tar.gz" - "https://depot.galaxyproject.org/software/bioconductor-xenopus.db0/bioconductor-xenopus.db0_3.7.1_src_all.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/xenopus.db0_3.8.2.tar.gz" + "https://bioarchive.galaxyproject.org/xenopus.db0_3.8.2.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-xenopus.db0/bioconductor-xenopus.db0_3.8.2_src_all.tar.gz" ) -MD5="6a34dd176e70d66d4acda7a141e09ef5" +MD5="199efa5f20b5dd8fc16aaeac9f0d9eeb" # Use a staging area in the conda dir rather than temp dirs, both to avoid # permission issues as well as to have things downloaded in a predictable @@ -16,7 +16,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-xenopuslaeviscdf/meta.yaml b/recipes/bioconductor-xenopuslaeviscdf/meta.yaml index 69bf07308b8f9..59bdcac073273 100644 --- a/recipes/bioconductor-xenopuslaeviscdf/meta.yaml +++ b/recipes/bioconductor-xenopuslaeviscdf/meta.yaml @@ -1,6 +1,6 @@ {% set version = "2.18.0" %} {% set name = "xenopuslaeviscdf" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -12,19 +12,19 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 9d09ff76471ae60faf71090e0638f240 build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' - r-base run: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-xenopuslaeviscdf/post-link.sh b/recipes/bioconductor-xenopuslaeviscdf/post-link.sh index cbdd908f7ad6f..26a7378b46b7e 100644 --- a/recipes/bioconductor-xenopuslaeviscdf/post-link.sh +++ b/recipes/bioconductor-xenopuslaeviscdf/post-link.sh @@ -1,9 +1,10 @@ #!/bin/bash FN="xenopuslaeviscdf_2.18.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/xenopuslaeviscdf_2.18.0.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/xenopuslaeviscdf_2.18.0.tar.gz" "https://bioarchive.galaxyproject.org/xenopuslaeviscdf_2.18.0.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-xenopuslaeviscdf/bioconductor-xenopuslaeviscdf_2.18.0_src_all.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-xenopuslaeviscdf/bioconductor-xenopuslaeviscdf_2.18.0_src_all.tar.gz" ) MD5="9d09ff76471ae60faf71090e0638f240" @@ -16,7 +17,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-xenopuslaevisprobe/meta.yaml b/recipes/bioconductor-xenopuslaevisprobe/meta.yaml index cdf4f6aac5897..92f7b480cbad5 100644 --- a/recipes/bioconductor-xenopuslaevisprobe/meta.yaml +++ b/recipes/bioconductor-xenopuslaevisprobe/meta.yaml @@ -1,6 +1,6 @@ {% set version = "2.18.0" %} {% set name = "xenopuslaevisprobe" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -12,19 +12,19 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 06a25268a5ab57bddf28bbb364ea977b build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' - r-base run: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-xenopuslaevisprobe/post-link.sh b/recipes/bioconductor-xenopuslaevisprobe/post-link.sh index 3f8831f84392d..52143bda78324 100644 --- a/recipes/bioconductor-xenopuslaevisprobe/post-link.sh +++ b/recipes/bioconductor-xenopuslaevisprobe/post-link.sh @@ -1,9 +1,10 @@ #!/bin/bash FN="xenopuslaevisprobe_2.18.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/xenopuslaevisprobe_2.18.0.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/xenopuslaevisprobe_2.18.0.tar.gz" "https://bioarchive.galaxyproject.org/xenopuslaevisprobe_2.18.0.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-xenopuslaevisprobe/bioconductor-xenopuslaevisprobe_2.18.0_src_all.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-xenopuslaevisprobe/bioconductor-xenopuslaevisprobe_2.18.0_src_all.tar.gz" ) MD5="06a25268a5ab57bddf28bbb364ea977b" @@ -16,7 +17,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-xeva/build.sh b/recipes/bioconductor-xeva/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-xeva/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-xeva/meta.yaml b/recipes/bioconductor-xeva/meta.yaml new file mode 100644 index 0000000000000..ea45bb985225d --- /dev/null +++ b/recipes/bioconductor-xeva/meta.yaml @@ -0,0 +1,53 @@ +{% set version = "1.0.0" %} +{% set name = "Xeva" %} +{% set bioc = "3.9" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: 709b12e8a7638bd2fc04e4efe5a49da7 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: BiocStyle, knitr, rmarkdown +requirements: + host: + - 'bioconductor-biobase >=2.44.0,<2.45.0' + - 'bioconductor-complexheatmap >=2.0.0,<2.1.0' + - 'bioconductor-pharmacogx >=1.14.0,<1.15.0' + - r-base + - r-bbmisc + - r-doparallel + - r-downloader + - r-ggplot2 + - r-nlme + - r-rmisc + - r-scales + run: + - 'bioconductor-biobase >=2.44.0,<2.45.0' + - 'bioconductor-complexheatmap >=2.0.0,<2.1.0' + - 'bioconductor-pharmacogx >=1.14.0,<1.15.0' + - r-base + - r-bbmisc + - r-doparallel + - r-downloader + - r-ggplot2 + - r-nlme + - r-rmisc + - r-scales +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: GPL-3 + summary: 'Contains set of functions to perform analysis of patient-derived xenograft (PDX) data.' + diff --git a/recipes/bioconductor-xhybcasneuf/meta.yaml b/recipes/bioconductor-xhybcasneuf/meta.yaml index c6aaebd59fc6c..022f39bb5692c 100644 --- a/recipes/bioconductor-xhybcasneuf/meta.yaml +++ b/recipes/bioconductor-xhybcasneuf/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.20.0" %} +{% set version = "1.22.0" %} {% set name = "XhybCasneuf" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: e31cf97fb07e30678b32d6db51a6cea5 + md5: 0d53ee29e521d6b33cb3dc9073970b58 build: number: 0 rpaths: @@ -19,18 +19,18 @@ build: noarch: generic requirements: host: - - 'bioconductor-affy >=1.60.0,<1.61.0' + - 'bioconductor-affy >=1.62.0,<1.63.0' - 'bioconductor-ath1121501cdf >=2.18.0,<2.19.0' - - 'bioconductor-tinesath1cdf >=1.20.0,<1.21.0' + - 'bioconductor-tinesath1cdf >=1.22.0,<1.23.0' - r-base - r-rcolorbrewer run: - - 'bioconductor-affy >=1.60.0,<1.61.0' + - 'bioconductor-affy >=1.62.0,<1.63.0' - 'bioconductor-ath1121501cdf >=2.18.0,<2.19.0' - - 'bioconductor-tinesath1cdf >=1.20.0,<1.21.0' + - 'bioconductor-tinesath1cdf >=1.22.0,<1.23.0' - r-base - r-rcolorbrewer - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-xhybcasneuf/post-link.sh b/recipes/bioconductor-xhybcasneuf/post-link.sh index 94cb795e2cc1c..d46efb248fde7 100644 --- a/recipes/bioconductor-xhybcasneuf/post-link.sh +++ b/recipes/bioconductor-xhybcasneuf/post-link.sh @@ -1,11 +1,11 @@ #!/bin/bash -FN="XhybCasneuf_1.20.0.tar.gz" +FN="XhybCasneuf_1.22.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/experiment/src/contrib/XhybCasneuf_1.20.0.tar.gz" - "https://bioarchive.galaxyproject.org/XhybCasneuf_1.20.0.tar.gz" - "https://depot.galaxyproject.org/software/bioconductor-xhybcasneuf/bioconductor-xhybcasneuf_1.20.0_src_all.tar.gz" + "https://bioconductor.org/packages/3.9/data/experiment/src/contrib/XhybCasneuf_1.22.0.tar.gz" + "https://bioarchive.galaxyproject.org/XhybCasneuf_1.22.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-xhybcasneuf/bioconductor-xhybcasneuf_1.22.0_src_all.tar.gz" ) -MD5="e31cf97fb07e30678b32d6db51a6cea5" +MD5="0d53ee29e521d6b33cb3dc9073970b58" # Use a staging area in the conda dir rather than temp dirs, both to avoid # permission issues as well as to have things downloaded in a predictable @@ -16,7 +16,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-xina/meta.yaml b/recipes/bioconductor-xina/meta.yaml index 04de52201534f..2c499653db545 100644 --- a/recipes/bioconductor-xina/meta.yaml +++ b/recipes/bioconductor-xina/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.0.1" %} +{% set version = "1.2.0" %} {% set name = "XINA" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: 77d507034c8d293b7473adaa0db0dfd38dabde707304dd4ce224807ce3668f3f + md5: 11a837fef20ddc8e6355771f1a8b00af build: number: 0 rpaths: @@ -20,8 +20,8 @@ build: # Suggests: knitr, rmarkdown requirements: host: - - 'bioconductor-biobase >=2.42.0,<2.43.0' - - 'bioconductor-stringdb >=1.22.0,<1.23.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' + - 'bioconductor-stringdb >=1.24.0,<1.25.0' - r-alluvial - r-base - r-ggplot2 @@ -30,8 +30,8 @@ requirements: - r-mclust - r-plyr run: - - 'bioconductor-biobase >=2.42.0,<2.43.0' - - 'bioconductor-stringdb >=1.22.0,<1.23.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' + - 'bioconductor-stringdb >=1.24.0,<1.25.0' - r-alluvial - r-base - r-ggplot2 diff --git a/recipes/bioconductor-xlaevis.db/meta.yaml b/recipes/bioconductor-xlaevis.db/meta.yaml index 8ae2c0b49841a..c42d3a6b22527 100644 --- a/recipes/bioconductor-xlaevis.db/meta.yaml +++ b/recipes/bioconductor-xlaevis.db/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.2.3" %} {% set name = "xlaevis.db" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -12,7 +12,7 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: deaffe47b4ee48a7edb159d8104dc241 build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ @@ -20,14 +20,14 @@ build: # Suggests: DBI, annotate, RUnit requirements: host: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' - - 'bioconductor-org.xl.eg.db >=3.7.0,<3.8.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' + - 'bioconductor-org.xl.eg.db >=3.8.0,<3.9.0' - r-base run: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' - - 'bioconductor-org.xl.eg.db >=3.7.0,<3.8.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' + - 'bioconductor-org.xl.eg.db >=3.8.0,<3.9.0' - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-xlaevis.db/post-link.sh b/recipes/bioconductor-xlaevis.db/post-link.sh index a04b02ff38346..b6e365f60abc4 100644 --- a/recipes/bioconductor-xlaevis.db/post-link.sh +++ b/recipes/bioconductor-xlaevis.db/post-link.sh @@ -1,9 +1,10 @@ #!/bin/bash FN="xlaevis.db_3.2.3.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/xlaevis.db_3.2.3.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/xlaevis.db_3.2.3.tar.gz" "https://bioarchive.galaxyproject.org/xlaevis.db_3.2.3.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-xlaevis.db/bioconductor-xlaevis.db_3.2.3_src_all.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-xlaevis.db/bioconductor-xlaevis.db_3.2.3_src_all.tar.gz" ) MD5="deaffe47b4ee48a7edb159d8104dc241" @@ -16,7 +17,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-xlaevis2cdf/meta.yaml b/recipes/bioconductor-xlaevis2cdf/meta.yaml index 28a8484285f0e..5f3336ebae204 100644 --- a/recipes/bioconductor-xlaevis2cdf/meta.yaml +++ b/recipes/bioconductor-xlaevis2cdf/meta.yaml @@ -1,6 +1,6 @@ {% set version = "2.18.0" %} {% set name = "xlaevis2cdf" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -12,19 +12,19 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 9e4a80d66397299b4e66a8d6715ca4aa build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' - r-base run: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-xlaevis2cdf/post-link.sh b/recipes/bioconductor-xlaevis2cdf/post-link.sh index bf1672f70f2f7..98d1e7301797e 100644 --- a/recipes/bioconductor-xlaevis2cdf/post-link.sh +++ b/recipes/bioconductor-xlaevis2cdf/post-link.sh @@ -1,9 +1,10 @@ #!/bin/bash FN="xlaevis2cdf_2.18.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/xlaevis2cdf_2.18.0.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/xlaevis2cdf_2.18.0.tar.gz" "https://bioarchive.galaxyproject.org/xlaevis2cdf_2.18.0.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-xlaevis2cdf/bioconductor-xlaevis2cdf_2.18.0_src_all.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-xlaevis2cdf/bioconductor-xlaevis2cdf_2.18.0_src_all.tar.gz" ) MD5="9e4a80d66397299b4e66a8d6715ca4aa" @@ -16,7 +17,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-xlaevis2probe/meta.yaml b/recipes/bioconductor-xlaevis2probe/meta.yaml index 0d0faa1a6c2d0..c021fba5f82c6 100644 --- a/recipes/bioconductor-xlaevis2probe/meta.yaml +++ b/recipes/bioconductor-xlaevis2probe/meta.yaml @@ -1,6 +1,6 @@ {% set version = "2.18.0" %} {% set name = "xlaevis2probe" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -12,19 +12,19 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: d86f8a05e106eb3123435da233ff851d build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' - r-base run: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-xlaevis2probe/post-link.sh b/recipes/bioconductor-xlaevis2probe/post-link.sh index ac5de06d54476..1657249279107 100644 --- a/recipes/bioconductor-xlaevis2probe/post-link.sh +++ b/recipes/bioconductor-xlaevis2probe/post-link.sh @@ -1,9 +1,10 @@ #!/bin/bash FN="xlaevis2probe_2.18.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/xlaevis2probe_2.18.0.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/xlaevis2probe_2.18.0.tar.gz" "https://bioarchive.galaxyproject.org/xlaevis2probe_2.18.0.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-xlaevis2probe/bioconductor-xlaevis2probe_2.18.0_src_all.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-xlaevis2probe/bioconductor-xlaevis2probe_2.18.0_src_all.tar.gz" ) MD5="d86f8a05e106eb3123435da233ff851d" @@ -16,7 +17,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-xmapbridge/meta.yaml b/recipes/bioconductor-xmapbridge/meta.yaml index 4964240880db1..901c6f254020b 100644 --- a/recipes/bioconductor-xmapbridge/meta.yaml +++ b/recipes/bioconductor-xmapbridge/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.40.0" %} +{% set version = "1.42.0" %} {% set name = "xmapbridge" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: aad45dacbe7c31b2569b42e38cea5131 + md5: 2189c4291651059f7c79c3f563427579 build: number: 0 rpaths: diff --git a/recipes/bioconductor-xps/meta.yaml b/recipes/bioconductor-xps/meta.yaml index 22968a6433a9c..98073214ec76d 100644 --- a/recipes/bioconductor-xps/meta.yaml +++ b/recipes/bioconductor-xps/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.42.0" %} +{% set version = "1.44.0" %} {% set name = "xps" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 7778907ce1572ac8dddb9cf753dd1b68 + md5: 878e84b32b583d4957a8585a22adb0eb build: number: 0 rpaths: @@ -21,8 +21,10 @@ build: requirements: host: - r-base + - root5 5.34.36 run: - r-base + - root5 5.34.36 build: - {{ compiler('c') }} - {{ compiler('cxx') }} diff --git a/recipes/bioconductor-xtrasnplocs.hsapiens.dbsnp141.grch38/meta.yaml b/recipes/bioconductor-xtrasnplocs.hsapiens.dbsnp141.grch38/meta.yaml index bc86a8b4443b2..562fed1fb6a46 100644 --- a/recipes/bioconductor-xtrasnplocs.hsapiens.dbsnp141.grch38/meta.yaml +++ b/recipes/bioconductor-xtrasnplocs.hsapiens.dbsnp141.grch38/meta.yaml @@ -1,6 +1,6 @@ {% set version = "0.99.12" %} {% set name = "XtraSNPlocs.Hsapiens.dbSNP141.GRCh38" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -12,7 +12,7 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' md5: 2b9d4036b9baff400a811fd69c910cff build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ @@ -20,20 +20,20 @@ build: # Suggests: SNPlocs.Hsapiens.dbSNP141.GRCh38, BSgenome.Hsapiens.NCBI.GRCh38 (>= 1.3.19) requirements: host: - - 'bioconductor-bsgenome >=1.50.0,<1.51.0' - - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' - - 'bioconductor-genomicranges >=1.34.0,<1.35.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-bsgenome >=1.52.0,<1.53.0' + - 'bioconductor-genomeinfodb >=1.20.0,<1.21.0' + - 'bioconductor-genomicranges >=1.36.0,<1.37.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' - r-base run: - - 'bioconductor-bsgenome >=1.50.0,<1.51.0' - - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' - - 'bioconductor-genomicranges >=1.34.0,<1.35.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-bsgenome >=1.52.0,<1.53.0' + - 'bioconductor-genomeinfodb >=1.20.0,<1.21.0' + - 'bioconductor-genomicranges >=1.36.0,<1.37.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-xtrasnplocs.hsapiens.dbsnp141.grch38/post-link.sh b/recipes/bioconductor-xtrasnplocs.hsapiens.dbsnp141.grch38/post-link.sh index de42b0f4e3d9a..492c841580c19 100644 --- a/recipes/bioconductor-xtrasnplocs.hsapiens.dbsnp141.grch38/post-link.sh +++ b/recipes/bioconductor-xtrasnplocs.hsapiens.dbsnp141.grch38/post-link.sh @@ -1,9 +1,10 @@ #!/bin/bash FN="XtraSNPlocs.Hsapiens.dbSNP141.GRCh38_0.99.12.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/XtraSNPlocs.Hsapiens.dbSNP141.GRCh38_0.99.12.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/XtraSNPlocs.Hsapiens.dbSNP141.GRCh38_0.99.12.tar.gz" "https://bioarchive.galaxyproject.org/XtraSNPlocs.Hsapiens.dbSNP141.GRCh38_0.99.12.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-xtrasnplocs.hsapiens.dbsnp141.grch38/bioconductor-xtrasnplocs.hsapiens.dbsnp141.grch38_0.99.12_src_all.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-xtrasnplocs.hsapiens.dbsnp141.grch38/bioconductor-xtrasnplocs.hsapiens.dbsnp141.grch38_0.99.12_src_all.tar.gz" ) MD5="2b9d4036b9baff400a811fd69c910cff" @@ -16,7 +17,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-xtrasnplocs.hsapiens.dbsnp144.grch37/meta.yaml b/recipes/bioconductor-xtrasnplocs.hsapiens.dbsnp144.grch37/meta.yaml index a6690b4736687..f51801d4d2bcf 100644 --- a/recipes/bioconductor-xtrasnplocs.hsapiens.dbsnp144.grch37/meta.yaml +++ b/recipes/bioconductor-xtrasnplocs.hsapiens.dbsnp144.grch37/meta.yaml @@ -1,6 +1,6 @@ {% set version = "0.99.12" %} {% set name = "XtraSNPlocs.Hsapiens.dbSNP144.GRCh37" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -12,7 +12,7 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' md5: 758d024c50d2349036dc27cc689b4e5a build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ @@ -20,22 +20,22 @@ build: # Suggests: Biostrings, BSgenome.Hsapiens.UCSC.hg19, SNPlocs.Hsapiens.dbSNP144.GRCh37 requirements: host: - - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' - - 'bioconductor-bsgenome >=1.50.0,<1.51.0' - - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' - - 'bioconductor-genomicranges >=1.34.0,<1.35.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-biocgenerics >=0.30.0,<0.31.0' + - 'bioconductor-bsgenome >=1.52.0,<1.53.0' + - 'bioconductor-genomeinfodb >=1.20.0,<1.21.0' + - 'bioconductor-genomicranges >=1.36.0,<1.37.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' - r-base run: - - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' - - 'bioconductor-bsgenome >=1.50.0,<1.51.0' - - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' - - 'bioconductor-genomicranges >=1.34.0,<1.35.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-biocgenerics >=0.30.0,<0.31.0' + - 'bioconductor-bsgenome >=1.52.0,<1.53.0' + - 'bioconductor-genomeinfodb >=1.20.0,<1.21.0' + - 'bioconductor-genomicranges >=1.36.0,<1.37.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-xtrasnplocs.hsapiens.dbsnp144.grch37/post-link.sh b/recipes/bioconductor-xtrasnplocs.hsapiens.dbsnp144.grch37/post-link.sh index 92864657f21b7..16583f83b3f49 100644 --- a/recipes/bioconductor-xtrasnplocs.hsapiens.dbsnp144.grch37/post-link.sh +++ b/recipes/bioconductor-xtrasnplocs.hsapiens.dbsnp144.grch37/post-link.sh @@ -1,9 +1,10 @@ #!/bin/bash FN="XtraSNPlocs.Hsapiens.dbSNP144.GRCh37_0.99.12.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/XtraSNPlocs.Hsapiens.dbSNP144.GRCh37_0.99.12.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/XtraSNPlocs.Hsapiens.dbSNP144.GRCh37_0.99.12.tar.gz" "https://bioarchive.galaxyproject.org/XtraSNPlocs.Hsapiens.dbSNP144.GRCh37_0.99.12.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-xtrasnplocs.hsapiens.dbsnp144.grch37/bioconductor-xtrasnplocs.hsapiens.dbsnp144.grch37_0.99.12_src_all.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-xtrasnplocs.hsapiens.dbsnp144.grch37/bioconductor-xtrasnplocs.hsapiens.dbsnp144.grch37_0.99.12_src_all.tar.gz" ) MD5="758d024c50d2349036dc27cc689b4e5a" @@ -16,7 +17,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-xtrasnplocs.hsapiens.dbsnp144.grch38/meta.yaml b/recipes/bioconductor-xtrasnplocs.hsapiens.dbsnp144.grch38/meta.yaml index aa003a30e558f..83302f4ad1cf1 100644 --- a/recipes/bioconductor-xtrasnplocs.hsapiens.dbsnp144.grch38/meta.yaml +++ b/recipes/bioconductor-xtrasnplocs.hsapiens.dbsnp144.grch38/meta.yaml @@ -1,6 +1,6 @@ {% set version = "0.99.12" %} {% set name = "XtraSNPlocs.Hsapiens.dbSNP144.GRCh38" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -12,7 +12,7 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' md5: c617aa805c7ecf60ee9283eb3c51b1c7 build: - number: 1 + number: 2 rpaths: - lib/R/lib/ - lib/ @@ -20,22 +20,22 @@ build: # Suggests: Biostrings, BSgenome.Hsapiens.UCSC.hg38, SNPlocs.Hsapiens.dbSNP144.GRCh38 requirements: host: - - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' - - 'bioconductor-bsgenome >=1.50.0,<1.51.0' - - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' - - 'bioconductor-genomicranges >=1.34.0,<1.35.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-biocgenerics >=0.30.0,<0.31.0' + - 'bioconductor-bsgenome >=1.52.0,<1.53.0' + - 'bioconductor-genomeinfodb >=1.20.0,<1.21.0' + - 'bioconductor-genomicranges >=1.36.0,<1.37.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' - r-base run: - - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' - - 'bioconductor-bsgenome >=1.50.0,<1.51.0' - - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' - - 'bioconductor-genomicranges >=1.34.0,<1.35.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-biocgenerics >=0.30.0,<0.31.0' + - 'bioconductor-bsgenome >=1.52.0,<1.53.0' + - 'bioconductor-genomeinfodb >=1.20.0,<1.21.0' + - 'bioconductor-genomicranges >=1.36.0,<1.37.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-xtrasnplocs.hsapiens.dbsnp144.grch38/post-link.sh b/recipes/bioconductor-xtrasnplocs.hsapiens.dbsnp144.grch38/post-link.sh index a8a9c5f4167cf..411b136218f8f 100644 --- a/recipes/bioconductor-xtrasnplocs.hsapiens.dbsnp144.grch38/post-link.sh +++ b/recipes/bioconductor-xtrasnplocs.hsapiens.dbsnp144.grch38/post-link.sh @@ -1,9 +1,10 @@ #!/bin/bash FN="XtraSNPlocs.Hsapiens.dbSNP144.GRCh38_0.99.12.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/XtraSNPlocs.Hsapiens.dbSNP144.GRCh38_0.99.12.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/XtraSNPlocs.Hsapiens.dbSNP144.GRCh38_0.99.12.tar.gz" "https://bioarchive.galaxyproject.org/XtraSNPlocs.Hsapiens.dbSNP144.GRCh38_0.99.12.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-xtrasnplocs.hsapiens.dbsnp144.grch38/bioconductor-xtrasnplocs.hsapiens.dbsnp144.grch38_0.99.12_src_all.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-xtrasnplocs.hsapiens.dbsnp144.grch38/bioconductor-xtrasnplocs.hsapiens.dbsnp144.grch38_0.99.12_src_all.tar.gz" ) MD5="c617aa805c7ecf60ee9283eb3c51b1c7" @@ -16,7 +17,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-xtropicaliscdf/meta.yaml b/recipes/bioconductor-xtropicaliscdf/meta.yaml index 07b3e0407711b..534f6e0d88e35 100644 --- a/recipes/bioconductor-xtropicaliscdf/meta.yaml +++ b/recipes/bioconductor-xtropicaliscdf/meta.yaml @@ -1,6 +1,6 @@ {% set version = "2.18.0" %} {% set name = "xtropicaliscdf" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -12,19 +12,19 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 253e3cde76a393789e124f395820e947 build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' - r-base run: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-xtropicaliscdf/post-link.sh b/recipes/bioconductor-xtropicaliscdf/post-link.sh index fecf7eda931b4..024451cf0d1b5 100644 --- a/recipes/bioconductor-xtropicaliscdf/post-link.sh +++ b/recipes/bioconductor-xtropicaliscdf/post-link.sh @@ -1,9 +1,10 @@ #!/bin/bash FN="xtropicaliscdf_2.18.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/xtropicaliscdf_2.18.0.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/xtropicaliscdf_2.18.0.tar.gz" "https://bioarchive.galaxyproject.org/xtropicaliscdf_2.18.0.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-xtropicaliscdf/bioconductor-xtropicaliscdf_2.18.0_src_all.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-xtropicaliscdf/bioconductor-xtropicaliscdf_2.18.0_src_all.tar.gz" ) MD5="253e3cde76a393789e124f395820e947" @@ -16,7 +17,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-xtropicalisprobe/meta.yaml b/recipes/bioconductor-xtropicalisprobe/meta.yaml index e712ce373fc29..e817b02612156 100644 --- a/recipes/bioconductor-xtropicalisprobe/meta.yaml +++ b/recipes/bioconductor-xtropicalisprobe/meta.yaml @@ -1,6 +1,6 @@ {% set version = "2.18.0" %} {% set name = "xtropicalisprobe" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -12,19 +12,19 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 43d15a7e12edaec1bb5f24b87498b599 build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' - r-base run: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-xtropicalisprobe/post-link.sh b/recipes/bioconductor-xtropicalisprobe/post-link.sh index 55085965cfc1c..e10494fe82a2c 100644 --- a/recipes/bioconductor-xtropicalisprobe/post-link.sh +++ b/recipes/bioconductor-xtropicalisprobe/post-link.sh @@ -1,9 +1,10 @@ #!/bin/bash FN="xtropicalisprobe_2.18.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/xtropicalisprobe_2.18.0.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/xtropicalisprobe_2.18.0.tar.gz" "https://bioarchive.galaxyproject.org/xtropicalisprobe_2.18.0.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-xtropicalisprobe/bioconductor-xtropicalisprobe_2.18.0_src_all.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-xtropicalisprobe/bioconductor-xtropicalisprobe_2.18.0_src_all.tar.gz" ) MD5="43d15a7e12edaec1bb5f24b87498b599" @@ -16,7 +17,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-xvector/meta.yaml b/recipes/bioconductor-xvector/meta.yaml index 419fce739b6e7..dfd17df38af6e 100644 --- a/recipes/bioconductor-xvector/meta.yaml +++ b/recipes/bioconductor-xvector/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "0.22.0" %} +{% set version = "0.24.0" %} {% set name = "XVector" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 464c4abd6b6134b894a885f7f42e2ff8 + md5: 044b4a98817641e21cf73a754f3220dc build: number: 0 rpaths: @@ -19,16 +19,16 @@ build: # Suggests: Biostrings, drosophila2probe, RUnit requirements: host: - - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' - - 'bioconductor-zlibbioc >=1.28.0,<1.29.0' + - 'bioconductor-biocgenerics >=0.30.0,<0.31.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' + - 'bioconductor-zlibbioc >=1.30.0,<1.31.0' - r-base run: - - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' - - 'bioconductor-zlibbioc >=1.28.0,<1.29.0' + - 'bioconductor-biocgenerics >=0.30.0,<0.31.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' + - 'bioconductor-zlibbioc >=1.30.0,<1.31.0' - r-base build: - {{ compiler('c') }} @@ -39,7 +39,7 @@ test: about: home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: Artistic-2.0 - summary: 'Memory efficient S4 classes for storing sequences "externally" (behind an R external pointer, or on disk).' + summary: 'Provides memory efficient S4 classes for storing sequences "externally" (e.g. behind an R external pointer, or on disk).' extra: identifiers: - biotools:xvector diff --git a/recipes/bioconductor-yamss/meta.yaml b/recipes/bioconductor-yamss/meta.yaml index 2896211255177..4ef2de9a01fee 100644 --- a/recipes/bioconductor-yamss/meta.yaml +++ b/recipes/bioconductor-yamss/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.8.1" %} +{% set version = "1.10.0" %} {% set name = "yamss" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 2eae19bf5906a912a04d9fb0c2a31445 + md5: 35ad2405c4a91122902b1e7678c11b99 build: number: 0 rpaths: @@ -20,24 +20,24 @@ build: # Suggests: BiocStyle, knitr, rmarkdown, digest, mtbls2, testthat requirements: host: - - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' - - 'bioconductor-ebimage >=4.24.0,<4.25.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-limma >=3.38.0,<3.39.0' - - 'bioconductor-mzr >=2.16.0,<2.17.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' - - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' + - 'bioconductor-biocgenerics >=0.30.0,<0.31.0' + - 'bioconductor-ebimage >=4.26.0,<4.27.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-limma >=3.40.0,<3.41.0' + - 'bioconductor-mzr >=2.18.0,<2.19.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' + - 'bioconductor-summarizedexperiment >=1.14.0,<1.15.0' - r-base - r-data.table - r-matrix run: - - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' - - 'bioconductor-ebimage >=4.24.0,<4.25.0' - - 'bioconductor-iranges >=2.16.0,<2.17.0' - - 'bioconductor-limma >=3.38.0,<3.39.0' - - 'bioconductor-mzr >=2.16.0,<2.17.0' - - 'bioconductor-s4vectors >=0.20.0,<0.21.0' - - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' + - 'bioconductor-biocgenerics >=0.30.0,<0.31.0' + - 'bioconductor-ebimage >=4.26.0,<4.27.0' + - 'bioconductor-iranges >=2.18.0,<2.19.0' + - 'bioconductor-limma >=3.40.0,<3.41.0' + - 'bioconductor-mzr >=2.18.0,<2.19.0' + - 'bioconductor-s4vectors >=0.22.0,<0.23.0' + - 'bioconductor-summarizedexperiment >=1.14.0,<1.15.0' - r-base - r-data.table - r-matrix diff --git a/recipes/bioconductor-yapsa/meta.yaml b/recipes/bioconductor-yapsa/meta.yaml index f6efdc3694201..8e6a88302ed99 100644 --- a/recipes/bioconductor-yapsa/meta.yaml +++ b/recipes/bioconductor-yapsa/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.8.0" %} +{% set version = "1.10.0" %} {% set name = "YAPSA" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 09ee5f1de2127297df5914ec0082103b + md5: d87bbdd5a4d435c4ba8892bfb3d731bf build: number: 0 rpaths: @@ -20,13 +20,13 @@ build: # Suggests: BSgenome.Hsapiens.UCSC.hg19, testthat, BiocStyle, knitr, rmarkdown requirements: host: - - 'bioconductor-complexheatmap >=1.20.0,<1.21.0' - - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' - - 'bioconductor-genomicranges >=1.34.0,<1.35.0' - - 'bioconductor-gtrellis >=1.14.0,<1.15.0' - - 'bioconductor-keggrest >=1.22.0,<1.23.0' - - 'bioconductor-somaticsignatures >=2.18.0,<2.19.0' - - 'bioconductor-variantannotation >=1.28.0,<1.29.0' + - 'bioconductor-complexheatmap >=2.0.0,<2.1.0' + - 'bioconductor-genomeinfodb >=1.20.0,<1.21.0' + - 'bioconductor-genomicranges >=1.36.0,<1.37.0' + - 'bioconductor-gtrellis >=1.16.0,<1.17.0' + - 'bioconductor-keggrest >=1.24.0,<1.25.0' + - 'bioconductor-somaticsignatures >=2.20.0,<2.21.0' + - 'bioconductor-variantannotation >=1.30.0,<1.31.0' - r-base - r-circlize - r-corrplot @@ -38,13 +38,13 @@ requirements: - r-pmcmr - r-reshape2 run: - - 'bioconductor-complexheatmap >=1.20.0,<1.21.0' - - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' - - 'bioconductor-genomicranges >=1.34.0,<1.35.0' - - 'bioconductor-gtrellis >=1.14.0,<1.15.0' - - 'bioconductor-keggrest >=1.22.0,<1.23.0' - - 'bioconductor-somaticsignatures >=2.18.0,<2.19.0' - - 'bioconductor-variantannotation >=1.28.0,<1.29.0' + - 'bioconductor-complexheatmap >=2.0.0,<2.1.0' + - 'bioconductor-genomeinfodb >=1.20.0,<1.21.0' + - 'bioconductor-genomicranges >=1.36.0,<1.37.0' + - 'bioconductor-gtrellis >=1.16.0,<1.17.0' + - 'bioconductor-keggrest >=1.24.0,<1.25.0' + - 'bioconductor-somaticsignatures >=2.20.0,<2.21.0' + - 'bioconductor-variantannotation >=1.30.0,<1.31.0' - r-base - r-circlize - r-corrplot diff --git a/recipes/bioconductor-yaqcaffy/meta.yaml b/recipes/bioconductor-yaqcaffy/meta.yaml index b2ed4ce81dc39..1d51b5d5828a8 100644 --- a/recipes/bioconductor-yaqcaffy/meta.yaml +++ b/recipes/bioconductor-yaqcaffy/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.42.0" %} +{% set version = "1.44.0" %} {% set name = "yaqcaffy" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 0ac961004e53ff216bcfa89616c92b56 + md5: 13ea77a9822e21b130a92bc5ecab266b build: number: 0 rpaths: @@ -20,10 +20,10 @@ build: # Suggests: MAQCsubsetAFX, affydata, xtable, tcltk2, tcltk requirements: host: - - 'bioconductor-simpleaffy >=2.58.0,<2.59.0' + - 'bioconductor-simpleaffy >=2.60.0,<2.61.0' - r-base run: - - 'bioconductor-simpleaffy >=2.58.0,<2.59.0' + - 'bioconductor-simpleaffy >=2.60.0,<2.61.0' - r-base test: commands: diff --git a/recipes/bioconductor-yarn/meta.yaml b/recipes/bioconductor-yarn/meta.yaml index 7f2548e2397e5..48db3ba9e1ad8 100644 --- a/recipes/bioconductor-yarn/meta.yaml +++ b/recipes/bioconductor-yarn/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.8.0" %} +{% set version = "1.10.0" %} {% set name = "yarn" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 9c0b6f644acc014874a723bd1e69115b + md5: d4cd04eecea5405c57a9c7d79763de11 build: number: 0 rpaths: @@ -20,12 +20,12 @@ build: # Suggests: knitr, rmarkdown, testthat (>= 0.8) requirements: host: - - 'bioconductor-biobase >=2.42.0,<2.43.0' - - 'bioconductor-biomart >=2.38.0,<2.39.0' - - 'bioconductor-edger >=3.24.0,<3.25.0' - - 'bioconductor-limma >=3.38.0,<3.39.0' - - 'bioconductor-preprocesscore >=1.44.0,<1.45.0' - - 'bioconductor-quantro >=1.16.0,<1.17.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' + - 'bioconductor-biomart >=2.40.0,<2.41.0' + - 'bioconductor-edger >=3.26.0,<3.27.0' + - 'bioconductor-limma >=3.40.0,<3.41.0' + - 'bioconductor-preprocesscore >=1.46.0,<1.47.0' + - 'bioconductor-quantro >=1.18.0,<1.19.0' - r-base - r-downloader - r-gplots @@ -33,12 +33,12 @@ requirements: - r-rcolorbrewer - r-readr run: - - 'bioconductor-biobase >=2.42.0,<2.43.0' - - 'bioconductor-biomart >=2.38.0,<2.39.0' - - 'bioconductor-edger >=3.24.0,<3.25.0' - - 'bioconductor-limma >=3.38.0,<3.39.0' - - 'bioconductor-preprocesscore >=1.44.0,<1.45.0' - - 'bioconductor-quantro >=1.16.0,<1.17.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' + - 'bioconductor-biomart >=2.40.0,<2.41.0' + - 'bioconductor-edger >=3.26.0,<3.27.0' + - 'bioconductor-limma >=3.40.0,<3.41.0' + - 'bioconductor-preprocesscore >=1.46.0,<1.47.0' + - 'bioconductor-quantro >=1.18.0,<1.19.0' - r-base - r-downloader - r-gplots diff --git a/recipes/bioconductor-ye6100subacdf/meta.yaml b/recipes/bioconductor-ye6100subacdf/meta.yaml index 65cdc89eb304a..3fbbda573641b 100644 --- a/recipes/bioconductor-ye6100subacdf/meta.yaml +++ b/recipes/bioconductor-ye6100subacdf/meta.yaml @@ -1,6 +1,6 @@ {% set version = "2.18.0" %} {% set name = "ye6100subacdf" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -12,19 +12,19 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 27bd71410956bfe8bffc8de14b85bdb0 build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' - r-base run: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-ye6100subacdf/post-link.sh b/recipes/bioconductor-ye6100subacdf/post-link.sh index 2618040a506ee..2c9aac48b73ab 100644 --- a/recipes/bioconductor-ye6100subacdf/post-link.sh +++ b/recipes/bioconductor-ye6100subacdf/post-link.sh @@ -1,9 +1,10 @@ #!/bin/bash FN="ye6100subacdf_2.18.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/ye6100subacdf_2.18.0.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/ye6100subacdf_2.18.0.tar.gz" "https://bioarchive.galaxyproject.org/ye6100subacdf_2.18.0.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-ye6100subacdf/bioconductor-ye6100subacdf_2.18.0_src_all.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-ye6100subacdf/bioconductor-ye6100subacdf_2.18.0_src_all.tar.gz" ) MD5="27bd71410956bfe8bffc8de14b85bdb0" @@ -16,7 +17,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-ye6100subbcdf/meta.yaml b/recipes/bioconductor-ye6100subbcdf/meta.yaml index 6e21f36d705c2..1696f9abbf49f 100644 --- a/recipes/bioconductor-ye6100subbcdf/meta.yaml +++ b/recipes/bioconductor-ye6100subbcdf/meta.yaml @@ -1,6 +1,6 @@ {% set version = "2.18.0" %} {% set name = "ye6100subbcdf" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -12,19 +12,19 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: ee9ec4bd941940745bad538d79bfeab4 build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' - r-base run: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-ye6100subbcdf/post-link.sh b/recipes/bioconductor-ye6100subbcdf/post-link.sh index 5cdf064d86bfb..db8a3dcd07637 100644 --- a/recipes/bioconductor-ye6100subbcdf/post-link.sh +++ b/recipes/bioconductor-ye6100subbcdf/post-link.sh @@ -1,9 +1,10 @@ #!/bin/bash FN="ye6100subbcdf_2.18.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/ye6100subbcdf_2.18.0.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/ye6100subbcdf_2.18.0.tar.gz" "https://bioarchive.galaxyproject.org/ye6100subbcdf_2.18.0.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-ye6100subbcdf/bioconductor-ye6100subbcdf_2.18.0_src_all.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-ye6100subbcdf/bioconductor-ye6100subbcdf_2.18.0_src_all.tar.gz" ) MD5="ee9ec4bd941940745bad538d79bfeab4" @@ -16,7 +17,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-ye6100subccdf/meta.yaml b/recipes/bioconductor-ye6100subccdf/meta.yaml index 62399d9de555d..488356b67c9fb 100644 --- a/recipes/bioconductor-ye6100subccdf/meta.yaml +++ b/recipes/bioconductor-ye6100subccdf/meta.yaml @@ -1,6 +1,6 @@ {% set version = "2.18.0" %} {% set name = "ye6100subccdf" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -12,19 +12,19 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: fcdfed29a695fe53b62bacfe13dfe0c1 build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' - r-base run: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-ye6100subccdf/post-link.sh b/recipes/bioconductor-ye6100subccdf/post-link.sh index c7287c2554bd0..ac62a70906b54 100644 --- a/recipes/bioconductor-ye6100subccdf/post-link.sh +++ b/recipes/bioconductor-ye6100subccdf/post-link.sh @@ -1,9 +1,10 @@ #!/bin/bash FN="ye6100subccdf_2.18.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/ye6100subccdf_2.18.0.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/ye6100subccdf_2.18.0.tar.gz" "https://bioarchive.galaxyproject.org/ye6100subccdf_2.18.0.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-ye6100subccdf/bioconductor-ye6100subccdf_2.18.0_src_all.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-ye6100subccdf/bioconductor-ye6100subccdf_2.18.0_src_all.tar.gz" ) MD5="fcdfed29a695fe53b62bacfe13dfe0c1" @@ -16,7 +17,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-ye6100subdcdf/meta.yaml b/recipes/bioconductor-ye6100subdcdf/meta.yaml index 3a9dd0b43eb16..7ccad6e8382e2 100644 --- a/recipes/bioconductor-ye6100subdcdf/meta.yaml +++ b/recipes/bioconductor-ye6100subdcdf/meta.yaml @@ -1,6 +1,6 @@ {% set version = "2.18.0" %} {% set name = "ye6100subdcdf" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -12,19 +12,19 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 521b501ddbcdc680c3d27b5b201029b1 build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' - r-base run: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-ye6100subdcdf/post-link.sh b/recipes/bioconductor-ye6100subdcdf/post-link.sh index 239e87d187afe..1105a29f6379e 100644 --- a/recipes/bioconductor-ye6100subdcdf/post-link.sh +++ b/recipes/bioconductor-ye6100subdcdf/post-link.sh @@ -1,9 +1,10 @@ #!/bin/bash FN="ye6100subdcdf_2.18.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/ye6100subdcdf_2.18.0.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/ye6100subdcdf_2.18.0.tar.gz" "https://bioarchive.galaxyproject.org/ye6100subdcdf_2.18.0.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-ye6100subdcdf/bioconductor-ye6100subdcdf_2.18.0_src_all.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-ye6100subdcdf/bioconductor-ye6100subdcdf_2.18.0_src_all.tar.gz" ) MD5="521b501ddbcdc680c3d27b5b201029b1" @@ -16,7 +17,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-yeast.db0/meta.yaml b/recipes/bioconductor-yeast.db0/meta.yaml index d9a923c206e21..fc002f6000cfc 100644 --- a/recipes/bioconductor-yeast.db0/meta.yaml +++ b/recipes/bioconductor-yeast.db0/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "3.7.1" %} +{% set version = "3.8.2" %} {% set name = "yeast.db0" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: d46ddb0d3ab987389ada054068806531 + md5: 550cd8cf56dd2a399588a06e8dfe6677 build: number: 0 rpaths: @@ -19,12 +19,12 @@ build: noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' - r-base run: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-yeast.db0/post-link.sh b/recipes/bioconductor-yeast.db0/post-link.sh index 9e448c9dabaf2..ac839cbbe4d0e 100644 --- a/recipes/bioconductor-yeast.db0/post-link.sh +++ b/recipes/bioconductor-yeast.db0/post-link.sh @@ -1,11 +1,11 @@ #!/bin/bash -FN="yeast.db0_3.7.1.tar.gz" +FN="yeast.db0_3.8.2.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/yeast.db0_3.7.1.tar.gz" - "https://bioarchive.galaxyproject.org/yeast.db0_3.7.1.tar.gz" - "https://depot.galaxyproject.org/software/bioconductor-yeast.db0/bioconductor-yeast.db0_3.7.1_src_all.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/yeast.db0_3.8.2.tar.gz" + "https://bioarchive.galaxyproject.org/yeast.db0_3.8.2.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-yeast.db0/bioconductor-yeast.db0_3.8.2_src_all.tar.gz" ) -MD5="d46ddb0d3ab987389ada054068806531" +MD5="550cd8cf56dd2a399588a06e8dfe6677" # Use a staging area in the conda dir rather than temp dirs, both to avoid # permission issues as well as to have things downloaded in a predictable @@ -16,7 +16,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-yeast2.db/meta.yaml b/recipes/bioconductor-yeast2.db/meta.yaml index f3f140ed4ef7b..56201dc3b92ec 100644 --- a/recipes/bioconductor-yeast2.db/meta.yaml +++ b/recipes/bioconductor-yeast2.db/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.2.3" %} {% set name = "yeast2.db" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -12,7 +12,7 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 818981b9562630e8a219dbe23a316e08 build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ @@ -20,14 +20,14 @@ build: # Suggests: DBI, annotate, RUnit requirements: host: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' - - 'bioconductor-org.sc.sgd.db >=3.7.0,<3.8.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' + - 'bioconductor-org.sc.sgd.db >=3.8.0,<3.9.0' - r-base run: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' - - 'bioconductor-org.sc.sgd.db >=3.7.0,<3.8.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' + - 'bioconductor-org.sc.sgd.db >=3.8.0,<3.9.0' - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-yeast2.db/post-link.sh b/recipes/bioconductor-yeast2.db/post-link.sh index 2c41d332811a0..c1a27e56faaa8 100644 --- a/recipes/bioconductor-yeast2.db/post-link.sh +++ b/recipes/bioconductor-yeast2.db/post-link.sh @@ -1,9 +1,10 @@ #!/bin/bash FN="yeast2.db_3.2.3.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/yeast2.db_3.2.3.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/yeast2.db_3.2.3.tar.gz" "https://bioarchive.galaxyproject.org/yeast2.db_3.2.3.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-yeast2.db/bioconductor-yeast2.db_3.2.3_src_all.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-yeast2.db/bioconductor-yeast2.db_3.2.3_src_all.tar.gz" ) MD5="818981b9562630e8a219dbe23a316e08" @@ -16,7 +17,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-yeast2cdf/meta.yaml b/recipes/bioconductor-yeast2cdf/meta.yaml index bed0e8e0b079d..6b6c77f895710 100644 --- a/recipes/bioconductor-yeast2cdf/meta.yaml +++ b/recipes/bioconductor-yeast2cdf/meta.yaml @@ -1,6 +1,6 @@ {% set version = "2.18.0" %} {% set name = "yeast2cdf" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -12,19 +12,19 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 0a718d78ae56bef9bad8168123038ac8 build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' - r-base run: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-yeast2cdf/post-link.sh b/recipes/bioconductor-yeast2cdf/post-link.sh index 01617c9253c56..476c42a41ffe5 100644 --- a/recipes/bioconductor-yeast2cdf/post-link.sh +++ b/recipes/bioconductor-yeast2cdf/post-link.sh @@ -1,9 +1,10 @@ #!/bin/bash FN="yeast2cdf_2.18.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/yeast2cdf_2.18.0.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/yeast2cdf_2.18.0.tar.gz" "https://bioarchive.galaxyproject.org/yeast2cdf_2.18.0.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-yeast2cdf/bioconductor-yeast2cdf_2.18.0_src_all.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-yeast2cdf/bioconductor-yeast2cdf_2.18.0_src_all.tar.gz" ) MD5="0a718d78ae56bef9bad8168123038ac8" @@ -16,7 +17,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-yeast2probe/meta.yaml b/recipes/bioconductor-yeast2probe/meta.yaml index 75b46f74ca1a1..fed961d0cd38a 100644 --- a/recipes/bioconductor-yeast2probe/meta.yaml +++ b/recipes/bioconductor-yeast2probe/meta.yaml @@ -1,6 +1,6 @@ {% set version = "2.18.0" %} {% set name = "yeast2probe" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -12,19 +12,19 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 3f52a2b7bd379624bc2966ca28c9ddf9 build: - number: 1 + number: 2 rpaths: - lib/R/lib/ - lib/ noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' - r-base run: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-yeast2probe/post-link.sh b/recipes/bioconductor-yeast2probe/post-link.sh index 8dc1b937783f7..0f9426d6e350b 100644 --- a/recipes/bioconductor-yeast2probe/post-link.sh +++ b/recipes/bioconductor-yeast2probe/post-link.sh @@ -1,9 +1,10 @@ #!/bin/bash FN="yeast2probe_2.18.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/yeast2probe_2.18.0.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/yeast2probe_2.18.0.tar.gz" "https://bioarchive.galaxyproject.org/yeast2probe_2.18.0.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-yeast2probe/bioconductor-yeast2probe_2.18.0_src_all.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-yeast2probe/bioconductor-yeast2probe_2.18.0_src_all.tar.gz" ) MD5="3f52a2b7bd379624bc2966ca28c9ddf9" @@ -16,7 +17,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-yeastcc/meta.yaml b/recipes/bioconductor-yeastcc/meta.yaml index f388925709d50..0877c5699f589 100644 --- a/recipes/bioconductor-yeastcc/meta.yaml +++ b/recipes/bioconductor-yeastcc/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.22.0" %} +{% set version = "1.24.0" %} {% set name = "yeastCC" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 5b31b8fadb3318846770cdd2f6b620a1 + md5: 55504ef44f97f3cf418c6817f9884538 build: number: 0 rpaths: @@ -19,12 +19,12 @@ build: noarch: generic requirements: host: - - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' - r-base run: - - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-yeastcc/post-link.sh b/recipes/bioconductor-yeastcc/post-link.sh index b27cb838f300a..86e54185cb9c5 100644 --- a/recipes/bioconductor-yeastcc/post-link.sh +++ b/recipes/bioconductor-yeastcc/post-link.sh @@ -1,11 +1,11 @@ #!/bin/bash -FN="yeastCC_1.22.0.tar.gz" +FN="yeastCC_1.24.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/experiment/src/contrib/yeastCC_1.22.0.tar.gz" - "https://bioarchive.galaxyproject.org/yeastCC_1.22.0.tar.gz" - "https://depot.galaxyproject.org/software/bioconductor-yeastcc/bioconductor-yeastcc_1.22.0_src_all.tar.gz" + "https://bioconductor.org/packages/3.9/data/experiment/src/contrib/yeastCC_1.24.0.tar.gz" + "https://bioarchive.galaxyproject.org/yeastCC_1.24.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-yeastcc/bioconductor-yeastcc_1.24.0_src_all.tar.gz" ) -MD5="5b31b8fadb3318846770cdd2f6b620a1" +MD5="55504ef44f97f3cf418c6817f9884538" # Use a staging area in the conda dir rather than temp dirs, both to avoid # permission issues as well as to have things downloaded in a predictable @@ -16,7 +16,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-yeastexpdata/meta.yaml b/recipes/bioconductor-yeastexpdata/meta.yaml index 11ed05948917e..36fc8525b9435 100644 --- a/recipes/bioconductor-yeastexpdata/meta.yaml +++ b/recipes/bioconductor-yeastexpdata/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "0.28.0" %} +{% set version = "0.30.0" %} {% set name = "yeastExpData" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,9 +10,9 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: ab56e8741e012db8ce829bb43673cb35 + md5: 92da053cb8de00d3e1bbf897491b8177 build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ @@ -20,12 +20,12 @@ build: # Suggests: Biobase, GO.db, RBGL, org.Sc.sgd.db requirements: host: - - 'bioconductor-graph >=1.60.0,<1.61.0' + - 'bioconductor-graph >=1.62.0,<1.63.0' - r-base run: - - 'bioconductor-graph >=1.60.0,<1.61.0' + - 'bioconductor-graph >=1.62.0,<1.63.0' - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-yeastexpdata/post-link.sh b/recipes/bioconductor-yeastexpdata/post-link.sh index 3cda6d63cb218..a4008dfac8468 100644 --- a/recipes/bioconductor-yeastexpdata/post-link.sh +++ b/recipes/bioconductor-yeastexpdata/post-link.sh @@ -1,11 +1,11 @@ #!/bin/bash -FN="yeastExpData_0.28.0.tar.gz" +FN="yeastExpData_0.30.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/experiment/src/contrib/yeastExpData_0.28.0.tar.gz" - "https://bioarchive.galaxyproject.org/yeastExpData_0.28.0.tar.gz" - "https://depot.galaxyproject.org/software/bioconductor-yeastexpdata/bioconductor-yeastexpdata_0.28.0_src_all.tar.gz" + "https://bioconductor.org/packages/3.9/data/experiment/src/contrib/yeastExpData_0.30.0.tar.gz" + "https://bioarchive.galaxyproject.org/yeastExpData_0.30.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-yeastexpdata/bioconductor-yeastexpdata_0.30.0_src_all.tar.gz" ) -MD5="ab56e8741e012db8ce829bb43673cb35" +MD5="92da053cb8de00d3e1bbf897491b8177" # Use a staging area in the conda dir rather than temp dirs, both to avoid # permission issues as well as to have things downloaded in a predictable @@ -16,7 +16,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-yeastgsdata/meta.yaml b/recipes/bioconductor-yeastgsdata/meta.yaml index cbe32f8bb6c07..e06707a1a0a61 100644 --- a/recipes/bioconductor-yeastgsdata/meta.yaml +++ b/recipes/bioconductor-yeastgsdata/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "0.20.0" %} +{% set version = "0.22.0" %} {% set name = "yeastGSData" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 16b3bf8e7fbdcabb099a801c9076f5e8 + md5: 76b11f991c186a0141182b94668dfb70 build: number: 0 rpaths: @@ -22,7 +22,7 @@ requirements: - r-base run: - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-yeastgsdata/post-link.sh b/recipes/bioconductor-yeastgsdata/post-link.sh index ec8ec8c753cd6..608323e8e4c66 100644 --- a/recipes/bioconductor-yeastgsdata/post-link.sh +++ b/recipes/bioconductor-yeastgsdata/post-link.sh @@ -1,11 +1,11 @@ #!/bin/bash -FN="yeastGSData_0.20.0.tar.gz" +FN="yeastGSData_0.22.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/experiment/src/contrib/yeastGSData_0.20.0.tar.gz" - "https://bioarchive.galaxyproject.org/yeastGSData_0.20.0.tar.gz" - "https://depot.galaxyproject.org/software/bioconductor-yeastgsdata/bioconductor-yeastgsdata_0.20.0_src_all.tar.gz" + "https://bioconductor.org/packages/3.9/data/experiment/src/contrib/yeastGSData_0.22.0.tar.gz" + "https://bioarchive.galaxyproject.org/yeastGSData_0.22.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-yeastgsdata/bioconductor-yeastgsdata_0.22.0_src_all.tar.gz" ) -MD5="16b3bf8e7fbdcabb099a801c9076f5e8" +MD5="76b11f991c186a0141182b94668dfb70" # Use a staging area in the conda dir rather than temp dirs, both to avoid # permission issues as well as to have things downloaded in a predictable @@ -16,7 +16,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-yeastnagalakshmi/meta.yaml b/recipes/bioconductor-yeastnagalakshmi/meta.yaml index b25b3c9ad9866..eba9d192f9af6 100644 --- a/recipes/bioconductor-yeastnagalakshmi/meta.yaml +++ b/recipes/bioconductor-yeastnagalakshmi/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.18.0" %} +{% set version = "1.20.0" %} {% set name = "yeastNagalakshmi" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: c3f3493454c6d90bb79f06fa54021ee1 + md5: 756b38f28259e1a99dec46e80bd64646 build: number: 0 rpaths: @@ -22,7 +22,7 @@ requirements: - r-base run: - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-yeastnagalakshmi/post-link.sh b/recipes/bioconductor-yeastnagalakshmi/post-link.sh index 661216218f98b..4269f1355651c 100644 --- a/recipes/bioconductor-yeastnagalakshmi/post-link.sh +++ b/recipes/bioconductor-yeastnagalakshmi/post-link.sh @@ -1,11 +1,11 @@ #!/bin/bash -FN="yeastNagalakshmi_1.18.0.tar.gz" +FN="yeastNagalakshmi_1.20.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/experiment/src/contrib/yeastNagalakshmi_1.18.0.tar.gz" - "https://bioarchive.galaxyproject.org/yeastNagalakshmi_1.18.0.tar.gz" - "https://depot.galaxyproject.org/software/bioconductor-yeastnagalakshmi/bioconductor-yeastnagalakshmi_1.18.0_src_all.tar.gz" + "https://bioconductor.org/packages/3.9/data/experiment/src/contrib/yeastNagalakshmi_1.20.0.tar.gz" + "https://bioarchive.galaxyproject.org/yeastNagalakshmi_1.20.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-yeastnagalakshmi/bioconductor-yeastnagalakshmi_1.20.0_src_all.tar.gz" ) -MD5="c3f3493454c6d90bb79f06fa54021ee1" +MD5="756b38f28259e1a99dec46e80bd64646" # Use a staging area in the conda dir rather than temp dirs, both to avoid # permission issues as well as to have things downloaded in a predictable @@ -16,7 +16,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-yeastrnaseq/meta.yaml b/recipes/bioconductor-yeastrnaseq/meta.yaml index 7ceaa51265d2a..5f461c76ffc67 100644 --- a/recipes/bioconductor-yeastrnaseq/meta.yaml +++ b/recipes/bioconductor-yeastrnaseq/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "0.20.0" %} +{% set version = "0.22.0" %} {% set name = "yeastRNASeq" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: a642a1c83917e78e156bc3841e609f7b + md5: d49325eb63e76bea71a4e26d08e877ac build: number: 0 rpaths: @@ -23,7 +23,7 @@ requirements: - r-base run: - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-yeastrnaseq/post-link.sh b/recipes/bioconductor-yeastrnaseq/post-link.sh index 4dcd6dc9e6b4b..20a662cad151d 100644 --- a/recipes/bioconductor-yeastrnaseq/post-link.sh +++ b/recipes/bioconductor-yeastrnaseq/post-link.sh @@ -1,11 +1,11 @@ #!/bin/bash -FN="yeastRNASeq_0.20.0.tar.gz" +FN="yeastRNASeq_0.22.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/experiment/src/contrib/yeastRNASeq_0.20.0.tar.gz" - "https://bioarchive.galaxyproject.org/yeastRNASeq_0.20.0.tar.gz" - "https://depot.galaxyproject.org/software/bioconductor-yeastrnaseq/bioconductor-yeastrnaseq_0.20.0_src_all.tar.gz" + "https://bioconductor.org/packages/3.9/data/experiment/src/contrib/yeastRNASeq_0.22.0.tar.gz" + "https://bioarchive.galaxyproject.org/yeastRNASeq_0.22.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-yeastrnaseq/bioconductor-yeastrnaseq_0.22.0_src_all.tar.gz" ) -MD5="a642a1c83917e78e156bc3841e609f7b" +MD5="d49325eb63e76bea71a4e26d08e877ac" # Use a staging area in the conda dir rather than temp dirs, both to avoid # permission issues as well as to have things downloaded in a predictable @@ -16,7 +16,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-ygs98.db/meta.yaml b/recipes/bioconductor-ygs98.db/meta.yaml index b6ddb4d4fad59..52239101829be 100644 --- a/recipes/bioconductor-ygs98.db/meta.yaml +++ b/recipes/bioconductor-ygs98.db/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.2.3" %} {% set name = "ygs98.db" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -12,7 +12,7 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: ddbf44a3db85a114be4477f917f3a724 build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ @@ -20,14 +20,14 @@ build: # Suggests: DBI, annotate, RUnit requirements: host: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' - - 'bioconductor-org.sc.sgd.db >=3.7.0,<3.8.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' + - 'bioconductor-org.sc.sgd.db >=3.8.0,<3.9.0' - r-base run: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' - - 'bioconductor-org.sc.sgd.db >=3.7.0,<3.8.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' + - 'bioconductor-org.sc.sgd.db >=3.8.0,<3.9.0' - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-ygs98.db/post-link.sh b/recipes/bioconductor-ygs98.db/post-link.sh index 376c52aee9af4..4e0c0f37a7c7a 100644 --- a/recipes/bioconductor-ygs98.db/post-link.sh +++ b/recipes/bioconductor-ygs98.db/post-link.sh @@ -1,9 +1,10 @@ #!/bin/bash FN="ygs98.db_3.2.3.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/ygs98.db_3.2.3.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/ygs98.db_3.2.3.tar.gz" "https://bioarchive.galaxyproject.org/ygs98.db_3.2.3.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-ygs98.db/bioconductor-ygs98.db_3.2.3_src_all.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-ygs98.db/bioconductor-ygs98.db_3.2.3_src_all.tar.gz" ) MD5="ddbf44a3db85a114be4477f917f3a724" @@ -16,7 +17,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-ygs98cdf/meta.yaml b/recipes/bioconductor-ygs98cdf/meta.yaml index 2416c8ea0c6c5..26a4997f55420 100644 --- a/recipes/bioconductor-ygs98cdf/meta.yaml +++ b/recipes/bioconductor-ygs98cdf/meta.yaml @@ -1,6 +1,6 @@ {% set version = "2.18.0" %} {% set name = "ygs98cdf" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -12,19 +12,19 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: ec7df7564cf28e093646325ec55baf1e build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' - r-base run: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-ygs98cdf/post-link.sh b/recipes/bioconductor-ygs98cdf/post-link.sh index 2a69683f8e061..5b09fd4a8c4fe 100644 --- a/recipes/bioconductor-ygs98cdf/post-link.sh +++ b/recipes/bioconductor-ygs98cdf/post-link.sh @@ -1,9 +1,10 @@ #!/bin/bash FN="ygs98cdf_2.18.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/ygs98cdf_2.18.0.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/ygs98cdf_2.18.0.tar.gz" "https://bioarchive.galaxyproject.org/ygs98cdf_2.18.0.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-ygs98cdf/bioconductor-ygs98cdf_2.18.0_src_all.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-ygs98cdf/bioconductor-ygs98cdf_2.18.0_src_all.tar.gz" ) MD5="ec7df7564cf28e093646325ec55baf1e" @@ -16,7 +17,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-ygs98frmavecs/meta.yaml b/recipes/bioconductor-ygs98frmavecs/meta.yaml index ae3b79580552b..0b3f9f4327dbe 100644 --- a/recipes/bioconductor-ygs98frmavecs/meta.yaml +++ b/recipes/bioconductor-ygs98frmavecs/meta.yaml @@ -1,6 +1,6 @@ {% set version = "1.3.0" %} {% set name = "ygs98frmavecs" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -12,7 +12,7 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: e78c8447eb381b91dafb2f9688da39dc build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ @@ -22,7 +22,7 @@ requirements: - r-base run: - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-ygs98frmavecs/post-link.sh b/recipes/bioconductor-ygs98frmavecs/post-link.sh index 4adc28aa1f698..5bcf9b00fe683 100644 --- a/recipes/bioconductor-ygs98frmavecs/post-link.sh +++ b/recipes/bioconductor-ygs98frmavecs/post-link.sh @@ -1,9 +1,10 @@ #!/bin/bash FN="ygs98frmavecs_1.3.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/ygs98frmavecs_1.3.0.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/ygs98frmavecs_1.3.0.tar.gz" "https://bioarchive.galaxyproject.org/ygs98frmavecs_1.3.0.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-ygs98frmavecs/bioconductor-ygs98frmavecs_1.3.0_src_all.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-ygs98frmavecs/bioconductor-ygs98frmavecs_1.3.0_src_all.tar.gz" ) MD5="e78c8447eb381b91dafb2f9688da39dc" @@ -16,7 +17,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-ygs98probe/meta.yaml b/recipes/bioconductor-ygs98probe/meta.yaml index 3953d966a2ce2..70b2ccac22041 100644 --- a/recipes/bioconductor-ygs98probe/meta.yaml +++ b/recipes/bioconductor-ygs98probe/meta.yaml @@ -1,6 +1,6 @@ {% set version = "2.18.0" %} {% set name = "ygs98probe" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -12,19 +12,19 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: f40f21d7074818a4ee74a45b5533e89d build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' - r-base run: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-ygs98probe/post-link.sh b/recipes/bioconductor-ygs98probe/post-link.sh index 1b11221cbd2ed..8a55bd647d718 100644 --- a/recipes/bioconductor-ygs98probe/post-link.sh +++ b/recipes/bioconductor-ygs98probe/post-link.sh @@ -1,9 +1,10 @@ #!/bin/bash FN="ygs98probe_2.18.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/ygs98probe_2.18.0.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/ygs98probe_2.18.0.tar.gz" "https://bioarchive.galaxyproject.org/ygs98probe_2.18.0.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-ygs98probe/bioconductor-ygs98probe_2.18.0_src_all.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-ygs98probe/bioconductor-ygs98probe_2.18.0_src_all.tar.gz" ) MD5="f40f21d7074818a4ee74a45b5533e89d" @@ -16,7 +17,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-yri1kgv/meta.yaml b/recipes/bioconductor-yri1kgv/meta.yaml index 5f7978263a80e..8c4885f5a7686 100644 --- a/recipes/bioconductor-yri1kgv/meta.yaml +++ b/recipes/bioconductor-yri1kgv/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "0.24.0" %} +{% set version = "0.26.0" %} {% set name = "yri1kgv" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 6b8aff46adfa18440787125c32b2eac5 + md5: 323d8f0ad9c359b2acf16f7802c5efdd build: number: 0 rpaths: @@ -19,14 +19,14 @@ build: noarch: generic requirements: host: - - 'bioconductor-biobase >=2.42.0,<2.43.0' - - 'bioconductor-ggbase >=3.44.0,<3.45.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' + - 'bioconductor-ggbase >=3.46.0,<3.47.0' - r-base run: - - 'bioconductor-biobase >=2.42.0,<2.43.0' - - 'bioconductor-ggbase >=3.44.0,<3.45.0' + - 'bioconductor-biobase >=2.44.0,<2.45.0' + - 'bioconductor-ggbase >=3.46.0,<3.47.0' - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-yri1kgv/post-link.sh b/recipes/bioconductor-yri1kgv/post-link.sh index 66e82306e37cb..d7ab3eb0e8f61 100644 --- a/recipes/bioconductor-yri1kgv/post-link.sh +++ b/recipes/bioconductor-yri1kgv/post-link.sh @@ -1,11 +1,11 @@ #!/bin/bash -FN="yri1kgv_0.24.0.tar.gz" +FN="yri1kgv_0.26.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/experiment/src/contrib/yri1kgv_0.24.0.tar.gz" - "https://bioarchive.galaxyproject.org/yri1kgv_0.24.0.tar.gz" - "https://depot.galaxyproject.org/software/bioconductor-yri1kgv/bioconductor-yri1kgv_0.24.0_src_all.tar.gz" + "https://bioconductor.org/packages/3.9/data/experiment/src/contrib/yri1kgv_0.26.0.tar.gz" + "https://bioarchive.galaxyproject.org/yri1kgv_0.26.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-yri1kgv/bioconductor-yri1kgv_0.26.0_src_all.tar.gz" ) -MD5="6b8aff46adfa18440787125c32b2eac5" +MD5="323d8f0ad9c359b2acf16f7802c5efdd" # Use a staging area in the conda dir rather than temp dirs, both to avoid # permission issues as well as to have things downloaded in a predictable @@ -16,7 +16,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-yrimulti/meta.yaml b/recipes/bioconductor-yrimulti/meta.yaml index f2172519b1f22..6e8c92b518b60 100644 --- a/recipes/bioconductor-yrimulti/meta.yaml +++ b/recipes/bioconductor-yrimulti/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "0.12.0" %} +{% set version = "0.14.0" %} {% set name = "yriMulti" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: a5ac85ebbea7b116ab9a5200658fbab6 + md5: 7701a6d945562afbfed3d9c4f620ef89 build: number: 0 rpaths: @@ -20,30 +20,30 @@ build: # Suggests: erma, BiocStyle, knitr, rmarkdown, gQTLstats (>= 1.9.2), doParallel, geuvPack, knitcitations, bibtex requirements: host: - - 'bioconductor-dsqtl >=0.20.0,<0.21.0' - - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' - - 'bioconductor-genomicfiles >=1.18.0,<1.19.0' - - 'bioconductor-genomicranges >=1.34.0,<1.35.0' - - 'bioconductor-geuvpack >=1.14.0,<1.15.0' - - 'bioconductor-gqtlbase >=1.14.0,<1.15.0' - - 'bioconductor-homo.sapiens >=1.3.0,<1.4.0' - - 'bioconductor-multiassayexperiment >=1.8.0,<1.9.0' - - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' - - 'bioconductor-variantannotation >=1.28.0,<1.29.0' + - 'bioconductor-dsqtl >=0.22.0,<0.23.0' + - 'bioconductor-genomeinfodb >=1.20.0,<1.21.0' + - 'bioconductor-genomicfiles >=1.20.0,<1.21.0' + - 'bioconductor-genomicranges >=1.36.0,<1.37.0' + - 'bioconductor-geuvpack >=1.16.0,<1.17.0' + - 'bioconductor-gqtlbase >=1.16.0,<1.17.0' + - 'bioconductor-homo.sapiens >=1.4.0,<1.5.0' + - 'bioconductor-multiassayexperiment >=1.10.0,<1.11.0' + - 'bioconductor-summarizedexperiment >=1.14.0,<1.15.0' + - 'bioconductor-variantannotation >=1.30.0,<1.31.0' - r-base run: - - 'bioconductor-dsqtl >=0.20.0,<0.21.0' - - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' - - 'bioconductor-genomicfiles >=1.18.0,<1.19.0' - - 'bioconductor-genomicranges >=1.34.0,<1.35.0' - - 'bioconductor-geuvpack >=1.14.0,<1.15.0' - - 'bioconductor-gqtlbase >=1.14.0,<1.15.0' - - 'bioconductor-homo.sapiens >=1.3.0,<1.4.0' - - 'bioconductor-multiassayexperiment >=1.8.0,<1.9.0' - - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' - - 'bioconductor-variantannotation >=1.28.0,<1.29.0' + - 'bioconductor-dsqtl >=0.22.0,<0.23.0' + - 'bioconductor-genomeinfodb >=1.20.0,<1.21.0' + - 'bioconductor-genomicfiles >=1.20.0,<1.21.0' + - 'bioconductor-genomicranges >=1.36.0,<1.37.0' + - 'bioconductor-geuvpack >=1.16.0,<1.17.0' + - 'bioconductor-gqtlbase >=1.16.0,<1.17.0' + - 'bioconductor-homo.sapiens >=1.4.0,<1.5.0' + - 'bioconductor-multiassayexperiment >=1.10.0,<1.11.0' + - 'bioconductor-summarizedexperiment >=1.14.0,<1.15.0' + - 'bioconductor-variantannotation >=1.30.0,<1.31.0' - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-yrimulti/post-link.sh b/recipes/bioconductor-yrimulti/post-link.sh index 8e656e8758c42..1624a755a6c03 100644 --- a/recipes/bioconductor-yrimulti/post-link.sh +++ b/recipes/bioconductor-yrimulti/post-link.sh @@ -1,11 +1,11 @@ #!/bin/bash -FN="yriMulti_0.12.0.tar.gz" +FN="yriMulti_0.14.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/experiment/src/contrib/yriMulti_0.12.0.tar.gz" - "https://bioarchive.galaxyproject.org/yriMulti_0.12.0.tar.gz" - "https://depot.galaxyproject.org/software/bioconductor-yrimulti/bioconductor-yrimulti_0.12.0_src_all.tar.gz" + "https://bioconductor.org/packages/3.9/data/experiment/src/contrib/yriMulti_0.14.0.tar.gz" + "https://bioarchive.galaxyproject.org/yriMulti_0.14.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-yrimulti/bioconductor-yrimulti_0.14.0_src_all.tar.gz" ) -MD5="a5ac85ebbea7b116ab9a5200658fbab6" +MD5="7701a6d945562afbfed3d9c4f620ef89" # Use a staging area in the conda dir rather than temp dirs, both to avoid # permission issues as well as to have things downloaded in a predictable @@ -16,7 +16,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-zebrafish.db/meta.yaml b/recipes/bioconductor-zebrafish.db/meta.yaml index e692f4e0e659d..343f1a10ecac0 100644 --- a/recipes/bioconductor-zebrafish.db/meta.yaml +++ b/recipes/bioconductor-zebrafish.db/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.2.3" %} {% set name = "zebrafish.db" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -12,7 +12,7 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: bd3924751e782a01b08d82b0aae07579 build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ @@ -20,14 +20,14 @@ build: # Suggests: DBI, annotate, RUnit requirements: host: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' - - 'bioconductor-org.dr.eg.db >=3.7.0,<3.8.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' + - 'bioconductor-org.dr.eg.db >=3.8.0,<3.9.0' - r-base run: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' - - 'bioconductor-org.dr.eg.db >=3.7.0,<3.8.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' + - 'bioconductor-org.dr.eg.db >=3.8.0,<3.9.0' - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-zebrafish.db/post-link.sh b/recipes/bioconductor-zebrafish.db/post-link.sh index 316ee83efeb54..b6ecee08f668f 100644 --- a/recipes/bioconductor-zebrafish.db/post-link.sh +++ b/recipes/bioconductor-zebrafish.db/post-link.sh @@ -1,9 +1,10 @@ #!/bin/bash FN="zebrafish.db_3.2.3.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/zebrafish.db_3.2.3.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/zebrafish.db_3.2.3.tar.gz" "https://bioarchive.galaxyproject.org/zebrafish.db_3.2.3.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-zebrafish.db/bioconductor-zebrafish.db_3.2.3_src_all.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-zebrafish.db/bioconductor-zebrafish.db_3.2.3_src_all.tar.gz" ) MD5="bd3924751e782a01b08d82b0aae07579" @@ -16,7 +17,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-zebrafish.db0/meta.yaml b/recipes/bioconductor-zebrafish.db0/meta.yaml index 7058fe55e0482..403499b9e000f 100644 --- a/recipes/bioconductor-zebrafish.db0/meta.yaml +++ b/recipes/bioconductor-zebrafish.db0/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "3.7.1" %} +{% set version = "3.8.2" %} {% set name = "zebrafish.db0" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: a8cb94655507b3640f4c2cd59816597a + md5: 0fcbb88a589acd7b0ed8b07f6d455477 build: number: 0 rpaths: @@ -19,12 +19,12 @@ build: noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' - r-base run: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-zebrafish.db0/post-link.sh b/recipes/bioconductor-zebrafish.db0/post-link.sh index 94cc8207d9082..05bd7700943d8 100644 --- a/recipes/bioconductor-zebrafish.db0/post-link.sh +++ b/recipes/bioconductor-zebrafish.db0/post-link.sh @@ -1,11 +1,11 @@ #!/bin/bash -FN="zebrafish.db0_3.7.1.tar.gz" +FN="zebrafish.db0_3.8.2.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/zebrafish.db0_3.7.1.tar.gz" - "https://bioarchive.galaxyproject.org/zebrafish.db0_3.7.1.tar.gz" - "https://depot.galaxyproject.org/software/bioconductor-zebrafish.db0/bioconductor-zebrafish.db0_3.7.1_src_all.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/zebrafish.db0_3.8.2.tar.gz" + "https://bioarchive.galaxyproject.org/zebrafish.db0_3.8.2.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-zebrafish.db0/bioconductor-zebrafish.db0_3.8.2_src_all.tar.gz" ) -MD5="a8cb94655507b3640f4c2cd59816597a" +MD5="0fcbb88a589acd7b0ed8b07f6d455477" # Use a staging area in the conda dir rather than temp dirs, both to avoid # permission issues as well as to have things downloaded in a predictable @@ -16,7 +16,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-zebrafishcdf/meta.yaml b/recipes/bioconductor-zebrafishcdf/meta.yaml index 952e178d258b8..321c1eae1eb65 100644 --- a/recipes/bioconductor-zebrafishcdf/meta.yaml +++ b/recipes/bioconductor-zebrafishcdf/meta.yaml @@ -1,6 +1,6 @@ {% set version = "2.18.0" %} {% set name = "zebrafishcdf" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -12,19 +12,19 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 04edbb632600c97610b86423c2d850e7 build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' - r-base run: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-zebrafishcdf/post-link.sh b/recipes/bioconductor-zebrafishcdf/post-link.sh index 5040b0d7752d0..55c2d5811650e 100644 --- a/recipes/bioconductor-zebrafishcdf/post-link.sh +++ b/recipes/bioconductor-zebrafishcdf/post-link.sh @@ -1,9 +1,10 @@ #!/bin/bash FN="zebrafishcdf_2.18.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/zebrafishcdf_2.18.0.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/zebrafishcdf_2.18.0.tar.gz" "https://bioarchive.galaxyproject.org/zebrafishcdf_2.18.0.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-zebrafishcdf/bioconductor-zebrafishcdf_2.18.0_src_all.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-zebrafishcdf/bioconductor-zebrafishcdf_2.18.0_src_all.tar.gz" ) MD5="04edbb632600c97610b86423c2d850e7" @@ -16,7 +17,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-zebrafishprobe/meta.yaml b/recipes/bioconductor-zebrafishprobe/meta.yaml index 130a70a554fd7..20a0f305ac8d3 100644 --- a/recipes/bioconductor-zebrafishprobe/meta.yaml +++ b/recipes/bioconductor-zebrafishprobe/meta.yaml @@ -1,6 +1,6 @@ {% set version = "2.18.0" %} {% set name = "zebrafishprobe" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -12,19 +12,19 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: eea2747859afa763addc7313ab0a2452 build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' - r-base run: - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-annotationdbi >=1.46.0,<1.47.0' - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-zebrafishprobe/post-link.sh b/recipes/bioconductor-zebrafishprobe/post-link.sh index 8a5ba85263e7b..f4ede1b5bec64 100644 --- a/recipes/bioconductor-zebrafishprobe/post-link.sh +++ b/recipes/bioconductor-zebrafishprobe/post-link.sh @@ -1,9 +1,10 @@ #!/bin/bash FN="zebrafishprobe_2.18.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/zebrafishprobe_2.18.0.tar.gz" + "https://bioconductor.org/packages/3.9/data/annotation/src/contrib/zebrafishprobe_2.18.0.tar.gz" "https://bioarchive.galaxyproject.org/zebrafishprobe_2.18.0.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-zebrafishprobe/bioconductor-zebrafishprobe_2.18.0_src_all.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-zebrafishprobe/bioconductor-zebrafishprobe_2.18.0_src_all.tar.gz" ) MD5="eea2747859afa763addc7313ab0a2452" @@ -16,7 +17,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-zebrafishrnaseq/meta.yaml b/recipes/bioconductor-zebrafishrnaseq/meta.yaml index b6f0a7bdee44c..40e9f9ffa686f 100644 --- a/recipes/bioconductor-zebrafishrnaseq/meta.yaml +++ b/recipes/bioconductor-zebrafishrnaseq/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.2.0" %} +{% set version = "1.4.0" %} {% set name = "zebrafishRNASeq" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: f29dab65186b6775efb0a5e5eaeae5e0 + md5: de296bfd0e03bcb980519bb70371b65b build: number: 0 rpaths: @@ -23,7 +23,7 @@ requirements: - r-base run: - r-base - - wget + - curl test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-zebrafishrnaseq/post-link.sh b/recipes/bioconductor-zebrafishrnaseq/post-link.sh index 3ea10eaab419a..5c9269ba7c415 100644 --- a/recipes/bioconductor-zebrafishrnaseq/post-link.sh +++ b/recipes/bioconductor-zebrafishrnaseq/post-link.sh @@ -1,11 +1,11 @@ #!/bin/bash -FN="zebrafishRNASeq_1.2.0.tar.gz" +FN="zebrafishRNASeq_1.4.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.8/data/experiment/src/contrib/zebrafishRNASeq_1.2.0.tar.gz" - "https://bioarchive.galaxyproject.org/zebrafishRNASeq_1.2.0.tar.gz" - "https://depot.galaxyproject.org/software/bioconductor-zebrafishrnaseq/bioconductor-zebrafishrnaseq_1.2.0_src_all.tar.gz" + "https://bioconductor.org/packages/3.9/data/experiment/src/contrib/zebrafishRNASeq_1.4.0.tar.gz" + "https://bioarchive.galaxyproject.org/zebrafishRNASeq_1.4.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-zebrafishrnaseq/bioconductor-zebrafishrnaseq_1.4.0_src_all.tar.gz" ) -MD5="f29dab65186b6775efb0a5e5eaeae5e0" +MD5="de296bfd0e03bcb980519bb70371b65b" # Use a staging area in the conda dir rather than temp dirs, both to avoid # permission issues as well as to have things downloaded in a predictable @@ -16,7 +16,7 @@ TARBALL=$STAGING/$FN SUCCESS=0 for URL in ${URLS[@]}; do - wget -O- -q $URL > $TARBALL + curl $URL > $TARBALL [[ $? == 0 ]] || continue # Platform-specific md5sum checks. diff --git a/recipes/bioconductor-zfpkm/meta.yaml b/recipes/bioconductor-zfpkm/meta.yaml index 311eafd497285..4724aaccb7408 100644 --- a/recipes/bioconductor-zfpkm/meta.yaml +++ b/recipes/bioconductor-zfpkm/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.4.0" %} +{% set version = "1.6.0" %} {% set name = "zFPKM" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 563d34bd16b73596c886bf427f11fab4 + md5: 1c309bf1b7bf6f1a32df581d3543b068 build: number: 0 rpaths: @@ -20,14 +20,14 @@ build: # Suggests: knitr, limma, edgeR, GEOquery, stringr, printr requirements: host: - - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' + - 'bioconductor-summarizedexperiment >=1.14.0,<1.15.0' - r-base - r-checkmate - r-dplyr - r-ggplot2 - r-tidyr run: - - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' + - 'bioconductor-summarizedexperiment >=1.14.0,<1.15.0' - r-base - r-checkmate - r-dplyr diff --git a/recipes/bioconductor-zinbwave/meta.yaml b/recipes/bioconductor-zinbwave/meta.yaml index d0984a31a87a7..a06caca0d9c65 100644 --- a/recipes/bioconductor-zinbwave/meta.yaml +++ b/recipes/bioconductor-zinbwave/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.4.0" %} +{% set version = "1.6.0" %} {% set name = "zinbwave" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 06892200948d0ebe42ae058931695366 + md5: 7031ddba832cffbed304c94c692c2d9d build: number: 0 rpaths: @@ -20,22 +20,22 @@ build: # Suggests: knitr, rmarkdown, testthat, matrixStats, magrittr, scRNAseq, ggplot2, biomaRt, BiocStyle, Rtsne, DESeq2, Seurat requirements: host: - - 'bioconductor-biocparallel >=1.16.0,<1.17.0' - - 'bioconductor-edger >=3.24.0,<3.25.0' - - 'bioconductor-genefilter >=1.64.0,<1.65.0' - - 'bioconductor-singlecellexperiment >=1.4.0,<1.5.0' - - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' + - 'bioconductor-biocparallel >=1.18.0,<1.19.0' + - 'bioconductor-edger >=3.26.0,<3.27.0' + - 'bioconductor-genefilter >=1.66.0,<1.67.0' + - 'bioconductor-singlecellexperiment >=1.6.0,<1.7.0' + - 'bioconductor-summarizedexperiment >=1.14.0,<1.15.0' - r-base - r-copula - r-glmnet - r-matrix - r-softimpute run: - - 'bioconductor-biocparallel >=1.16.0,<1.17.0' - - 'bioconductor-edger >=3.24.0,<3.25.0' - - 'bioconductor-genefilter >=1.64.0,<1.65.0' - - 'bioconductor-singlecellexperiment >=1.4.0,<1.5.0' - - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' + - 'bioconductor-biocparallel >=1.18.0,<1.19.0' + - 'bioconductor-edger >=3.26.0,<3.27.0' + - 'bioconductor-genefilter >=1.66.0,<1.67.0' + - 'bioconductor-singlecellexperiment >=1.6.0,<1.7.0' + - 'bioconductor-summarizedexperiment >=1.14.0,<1.15.0' - r-base - r-copula - r-glmnet diff --git a/recipes/bioconductor-zlibbioc/meta.yaml b/recipes/bioconductor-zlibbioc/meta.yaml index 60e46f4f69f4c..64ff4c399021c 100644 --- a/recipes/bioconductor-zlibbioc/meta.yaml +++ b/recipes/bioconductor-zlibbioc/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.28.0" %} +{% set version = "1.30.0" %} {% set name = "zlibbioc" %} -{% set bioc = "3.8" %} +{% set bioc = "3.9" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: a92d411b500d3f88434653351a8e9aea + md5: 8e2b5b596ee4d13aca3e195724d28209 build: number: 0 rpaths: diff --git a/recipes/das_tool/meta.yaml b/recipes/das_tool/meta.yaml index 05eff880b4e56..6c384b9ff694b 100644 --- a/recipes/das_tool/meta.yaml +++ b/recipes/das_tool/meta.yaml @@ -11,7 +11,7 @@ source: sha256: {{ sha256 }} build: - number: + number: 0 skip: True # [not linux] rpaths: - lib/R/lib/ diff --git a/recipes/hyphy/2.3.11/conda_build_config.yaml b/recipes/hyphy/2.3.11/conda_build_config.yaml deleted file mode 100644 index a864705eed8d4..0000000000000 --- a/recipes/hyphy/2.3.11/conda_build_config.yaml +++ /dev/null @@ -1,6 +0,0 @@ -c_compiler: - - gcc # [linux] - - clang # [osx] -cxx_compiler: - - gxx # [linux] - - clangxx # [osx] diff --git a/recipes/perl-bio-db-hts/meta.yaml b/recipes/perl-bio-db-hts/meta.yaml index f10d363736937..0ddc51d3f34ac 100644 --- a/recipes/perl-bio-db-hts/meta.yaml +++ b/recipes/perl-bio-db-hts/meta.yaml @@ -13,6 +13,8 @@ build: skip: true # [osx] requirements: + build: + - {{ compiler('c') }} host: - zlib - perl diff --git a/recipes/pygtftk/conda_build_config.yaml b/recipes/pygtftk/conda_build_config.yaml deleted file mode 100644 index a864705eed8d4..0000000000000 --- a/recipes/pygtftk/conda_build_config.yaml +++ /dev/null @@ -1,6 +0,0 @@ -c_compiler: - - gcc # [linux] - - clang # [osx] -cxx_compiler: - - gxx # [linux] - - clangxx # [osx] diff --git a/recipes/seqhax/meta.yaml b/recipes/seqhax/meta.yaml index bc017c9220db0..479c7ceb17993 100644 --- a/recipes/seqhax/meta.yaml +++ b/recipes/seqhax/meta.yaml @@ -10,6 +10,7 @@ source: sha256: {{ sha256 }} build: + number: 0 skip: true # [not linux] requirements: