R lncpipereporter #12102
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R lncpipereporter #12102
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likelet
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Nov 16, 2018
likelet
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- I have read the guidelines for bioconda recipes.
- This PR adds a new recipe.
- AFAIK, this recipe is directly relevant to the biological sciences (otherwise, please submit to the more general purpose conda-forge channel).
- This PR updates an existing recipe.
- This PR does something else (explain below).
bgruening
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Dec 9, 2018
* r-classdiscovery (#12105) * r-oompabase * r-classdiscovery * Remove oompabase * Fixed Dependency Biobase * R lncpipereporter (#12102) * ADD lncPipeReporter * update * update * seqkit 0.9.2 (#12110) * Update fastq-scan to v0.3 (#12109) * Add perl-clone-choose (#12108) * Update perl-hash-merge to 0.300 (#11941) * Update perl-hash-merge to 0.300 * Update perl-hash-merge to 0.300 * Update meta.yaml * Update perl-file-slurper to 0.012 (#11910) * Update perl-file-slurper to 0.012 * Adding dependencies * Update perl-moo to 2.003004 (#11897) * Update perl-moo to 2.003004 * Update meta.yaml * Add deeptoolsintervals (#12114) * Add deeptoolsintervals * blah * No nose in the mulled container * Fix octopus binary "invalid instruction" (-march too new) (#11822) * This attempts to make the binary more portable by only requiring Sandybridge. * Fix march set to native * Update perl-bio-asn1-entrezgene to 1.73 (#11914) * Update perl-bio-asn1-entrezgene to 1.73 * Update perl-bio-asn1-entrezgene to 1.73 * Update meta.yaml * Update perl-file-slurp to 9999.25 (#12127) * Update manta to 1.5.0 (#12126) * Update nanocomp to 1.0.0 (#12124) * Update masurca to 3.2.9 (#12121) * Update beagle-lib to 3.1.1 (#12119) * Update r-spocc to 0.9.0 (#12118) * Update kallisto to 0.45.0 (#12117) * Update validators to 0.12.3 (#12116) * Update illumina-interop to 1.1.7 (#12115) * Update umi_tools to 0.5.5 (#12123) * Update tiptoft to 1.0.0 (#12122) * Update: TitanCNA with fix for hg38 plotting (#12130) * blockclust (#12111) * added eden 1.1 version used in blockclust * Update meta.yaml * eden checksum and test * added zlib requirement * add include and lib paths to build.sh * add include and lib paths to build.sh * modify makefile flags using sed * modify makefile flags using sed * use c++ * Update build.sh * Update build.sh * LDFLAGS not used in makefile * remove v1.1 * add blockclust 1.1.0 recipe * skip osx build * added tarball url and checksum; removed conda_build_config.yaml * Update meta.yaml * Update meta.yaml * Update meta.yaml * Update meta.yaml * Update chewbbaca to 2.0.16 (#12132) * Update abeona to 0.40.0 (#12131) * ping to eden 1.1 (#12134) * clean swap file (#12137) * Update corset to 1.07 (#12143) * Update peddy to 0.4.3 (#12144) * blockclust latest source and added cloudpickle as requirement (#12142) * Update nanomath to 0.22.0 (#12149) * Update pymvpa to 2.6.5 (#12152) * Updated to version 1.4.0 (#12138) * Updated to version 1.4.0 * Resetting build number to 0 and build->host * Update transdecoder to 5.5.0 (#12172) * Update gridss to 2.0.1 (#12190) * Update tracer to 1.7.1 (#12189) * Update flowcraft to 1.4.0 (#12179) * Update seqbuster to 3.2 (#12182) * Update perl-io-compress to 2.081 (#12201) * Update twobitreader to 3.1.6 (#12205) * Update twobitreader to 3.1.6 * Update meta.yaml * Update gtfparse to 1.2.0 (#12186) * Update gtfparse to 1.2.0 * remove compiler * Update htseq to 0.11.0 (#12177) * Update htseq to 0.11.0 * add compiler * Update htseq to 0.11.0 (#12239) [testing co-author] * Update htseq to 0.11.0 * add compiler Co-authored-by: Bjoern Gruening <bjoern.gruening@gmail.com> * alfred v0.1.16 (#12240) * alfred v0.1.16 * makefile patch * makefile patch * Update scrm to 1.7.3 (#12150) * Update scrm to 1.7.3 * Update scrm to 1.7.3 * Mob suite update 1.4.8 --> 1.4.9 (#12244) We fixed a small bug related to repetitive elements database reconstruction on each run. Should only run once during the first mob_typer run. Should be good now for parallel runs. * PeptideShaker updated to v1.16.35 & SearchGUI updated to 3.3.9 (#12241) * PeptideShaker updated to v1.16.32 SearchGUI updated to v3.3.6 * PeptideShaker updated to v1.16.35 * SearchGUI updated to v3.3.9 * First attempt at a recipe for ncrf (#12101) * First attempt at a recipe for ncrf * changed from copies to symlinks * including absolute path in symlinks * PacBio: Update `pbmm2` to version 0.11.0 (#12246) * Gimmemotifs version 0.13.0 (#12245) * new release to fix numpy incompatibility * GimmeMotifs 0.13.0 release test * numpy 1.15 * version 0.13.0 * Fix about:home and extra: * PacBio: Update `isoseq3` to version 3.1.0 (#12263) * add python to host section (#12264) * Update confindr to 0.4.7 (#12266) * new build of GRiD (#12269) * update grid * update build num * edit grid to use mosdepth for depth coverage * edit grid to use mosdepth for depth coverage * Update meta.yaml * new build for grid * Update meta.yaml * peptideshaker, searchgui: version bump (#12136) * peptideshaker, searchgui: version bump solving compomics/searchgui#192 * Update peptide-shaker.py * searchgui: added c compiler for building test if linking errors go away this way * searchgui: removed noarch * Update: bcbio, bcbio-vm with CWL non-human fixes (bcbio/bcbio-nextgen#2473) (#12273) * Make snakemake a noarch package. (#12274) * noarch: python in combination with version constraint * Cleanup deps and simplify version definition. * Genenotebook v0.1.9 (#12277) * genenotebook recipe * About * Package name * License * sha256sum * Update build.sh * Make bin dir * Change ln to cp * New symlink strategy * Build from prebundled tarball * genenotebook v0.1.2 * version fix * retry * fix * build number * genenotebook v0.1.3 * genenotebook v0.1.3 * new build procedure * change run dependencies * build * restore build procedure * Fix summary * dependency versions * v0.1.5 * version fix * v0.1.6 * reset build number * build number * genenotebook v0.1.7 * v0.1.8 * v0.1.9 * Create r-airr recipe (#12284) * Create r-airr recipe using bgruening/conda_r_skeleton_helper * Update meta.yaml * Findbin::Real added (#12291) * Added version bump to 1.3 (#12292) * ngs-bits 2018_11 (#12262) * Updated ngs-bits to version 2018_10 * Updated ngs-bits to version 2018_11 * minor edit in grid (#12287) * update grid * update build num * edit grid to use mosdepth for depth coverage * edit grid to use mosdepth for depth coverage * Update meta.yaml * new build for grid * Update meta.yaml * minor edit to grid * Fred2 update (#12259) * Update FRED2 Recipe * msstitch version 2.9 (#12296) * r-mvr (#12300) This is a non-parametric method for joint adaptive mean-variance regularization and variance sta- bilization of high-dimensional data. * Bump to Gromacs 2018.3 + re-enable OSX build (#12299) * Gromacs 2018.3 + re-enable osx build See also #7825 on OSX build Include RRID for Gromacs (see bioconda/bioconda-utils#252) * disabled ocl-icd on osx; not available (or needed?) https://anaconda.org/conda-forge/ocl-icd * pyGenomeTracks update of dependencies (#12279) * Update pyGenomeTracks recipe to enable py3 support and updating outdated dependecy list * Increase build number * Update meta.yaml * Exclude Python 3.5 * Gromacs 2018.4 (#12302) * quast 5.0.2 (#12303) * Update meta.yaml (#12275) * Update meta.yaml r-rsqlite version dependency added * Update meta.yaml Updated build number to 1 * Use the extended-base container because of wget issues when downloading databases (#12297) * Update duphold to 0.1.0 (#12257) * Update flashlfq to 0.1.109 (#12256) * Update planemo to 0.57.0 (#12251) * Update meta.yaml (#12258) * Update scalpel to 0.5.4 (#12249) * Update scalpel to 0.5.4 * Fix url * edit grid (#12298) * update grid * update build num * edit grid to use mosdepth for depth coverage * edit grid to use mosdepth for depth coverage * Update meta.yaml * new build for grid * Update meta.yaml * minor edit to grid * minor edit to recipe grid * added feather to deps (#12293) * R tigger (#12286) * Create recipe for r-tigger (#12271) * Create recipe for r-tigger using bgruening/conda_r_skeleton_helper. * Delete bld.bat * Remove windows support * update scprep to v0.8.1 (#12306) * Update nanoget to 1.7.5 (#12252) * Update nanoget to 1.7.5 * Bump to version 1.7.6 should fix the README.md problem * gffcompare: version bump (#12308) * Update: cromwell (36), bcbio (Cromwell Docker runs) (#12307) * Update: cromwell (36), bcbio (Cromwell Docker runs) * Pin java to 8 to avoid compile errors on 11 * HiCExplorer update to version 2.2-beta (#12309) * HiCExplorer update to version 2.2-beta * Remove of '-' from version number * Numpy set to 1.15 * Update meta.yaml * upgrade to version 2.8.1 (#12316) * Create Airr recipe (#12318) * Create AIRR recipe using conda skeleton pypi. * Add noarch python * Clean host requirements * Added nimnexus [v0.1] (#12133) * added nimnexus * Fix sha * Update build.sh * Update meta.yaml * Update meta.yaml * Update meta.yaml * [WIP] Add R-loom (#12320) * initial WIP skeleton * Update meta.yaml * Update meta.yaml * Update meta.yaml * try osx * Create Changeo recipe (#12321) * Create changeo recipe using conda skeleton pypi. * EDIT about section * ADD noarch generic * Update noarch to python * Clean host requirements * Add test for scripts * Change requirement to python>=3.4 * Add noarch pyton * r-corbi (#12325) * r-nam (#12327) * Update pybedtools to 0.8.0 (#12324) * Update pybedtools to 0.8.0 * rm cython requirement * MSGFplus does not work with newer Java (#12330) * Trying to not use a very new java version since the latest versions have dropped some classes * Increment build * Update atropos to 1.1.21 (#12322) * Update CONCOCT to 0.4.2 (#12317) * Update CONCOCT to 0.4.2 * Wrong shasum given * Reset build number for new version * New: gvcfgenotyper for joint calling with Illumina strelka2 (#12331) * Apparently we need openJDK to be below 9, not below 11 as in the previous PR (#12332) * Update Picard to 2.18.17. (#12333) * Unblacklist IgDiscover (#12335) * PacBio: Add missing licenses and post-link message (#12334) * Bioconductor DEqMS package (#12336) * Bioconductor DEqMS package * Limma version could be set lower (checked with the bioconductor recipe page) to include limma in bioconda * Genenotebook v0.1.10 (#12337) * genenotebook recipe * About * Package name * License * sha256sum * Update build.sh * Make bin dir * Change ln to cp * New symlink strategy * Build from prebundled tarball * genenotebook v0.1.2 * version fix * retry * fix * build number * genenotebook v0.1.3 * genenotebook v0.1.3 * new build procedure * change run dependencies * build * restore build procedure * Fix summary * dependency versions * v0.1.5 * version fix * v0.1.6 * reset build number * build number * genenotebook v0.1.7 * v0.1.8 * v0.1.9 * v0.1.10 * removed cloudpickle requirement for blockclust (#12242) * blockclust latest source and added cloudpickle as requirement * removed cloudpickle requirement for blockclust * added a tagged release to the source * back to source url but with release tarball and checksum * R guilds (#12341) * Strict rec (#12113) * added metawrap * fixed perl and jdk * added more strict req * fixed java and perl * removed extra boost * Update qcat to v1.0.1 (#12343) * Add better error checking (#12345) * Add mhcnames python package (#12349) * Add MHCflurry pMHC class I binding affinity prediction tool (#12346) * Bump pilon (#12354) * Update pronto to 0.11.1 (#12377) * Update perl-json-xs to 4.0 (#12373) * Update planemo to 0.57.1 (#12370) * Update snippy to 4.3.6 (#12372) * Update intarna to 2.3.1 (#12367) * Update agfusion to 1.231 (#12366) * Update bioconda-utils to 0.15.0 (#12359) * Update mapdamage2 to 2.0.9 (#12358) * Update scanpy to 1.3.4 (#12357) * Update goatools to 0.8.11 (#12361) * Update perl-math-random-mt-auto to 6.23 (#12362) * Update kipoi to 0.6.3 (#12374) * Update kipoi_veff to 0.2.1 (#12364) * Update perl-object-insideout to 4.05 (#12380) * Update sevenbridges-python to 0.17.1 (#12379) * Update nanosv to 1.2.3 (#12378) * Update starfish to 0.0.30 (#12368) * Update clust to 1.8.10 (#12356) * Update pypairs to 2.0.6 (#12381) * Update khmer to 3.0.0a2 (#12360) * Update flashlfq to 0.1.110 (#12385) * Update perl-algorithm-cluster to 1.57 (#12384) * Update arvados-python-client to 1.2.0.20181121194423 (#12382) * Update avro-cwl to 1.8.9 (#12355) * Update avro-cwl to 1.8.9 * Set noarch: python * r-breakaway (#12386) * R sads (#12388) * Update python-sortedcontainers to 2.1.0 (#12383) * r-ebimetagenomics (#12339) * pin armadilo on major version (#12389) * IgDiscover version 0.11 (#12351) * IgDiscover version 0.11 * IgDiscover requires Python 3.6 * Fix build on macOS with a small patch * Remove unneeded host dependencies * Update goatools to 0.8.12 (#12391) * Update bioconda-utils to 0.15.1 (#12390) * R ebimetagenomics (#12393) * Add dimspy recipes for reference purposes (#12387) * Add dimspy recipes for reference purposes * Remove filename * remove from blacklist * Update build-fail-blacklist * Added BioExcel_SeqQC to bioconda-recipes (#12276) * PacBio: Update pbalign to 0.3.2 (#12396) * PacBio: Update pbalign to 0.3.2 Closes: PacificBiosciences/pbbioconda#39 * add bgreat to bioconda (#12350) * bgreat addition * zlib in build should not be needed * btrim integration to conda (#12395) * Format sleuth recipe. Trigger rebuild because latest version was never uploaded for some reason. (#12399) * PacBio: Update `pbsv2` to version 2.1.0 (#12400) * Genenotebook v0.1.11 (#12398) * genenotebook recipe * About * Package name * License * sha256sum * Update build.sh * Make bin dir * Change ln to cp * New symlink strategy * Build from prebundled tarball * genenotebook v0.1.2 * version fix * retry * fix * build number * genenotebook v0.1.3 * genenotebook v0.1.3 * new build procedure * change run dependencies * build * restore build procedure * Fix summary * dependency versions * v0.1.5 * version fix * v0.1.6 * reset build number * build number * genenotebook v0.1.7 * v0.1.8 * v0.1.9 * v0.1.10 * v0.1.11 * prosolo: new package version 0.6.0 (#12397) * Update sevenbridges-python to 0.17.2 (#12404) * Add recipe for ICED (#12406) * Downgrade version for iced (#12409) * Update recipe for libstatgen 1.0.5 (#12348) * Add recipe for libstatgen-1.0.5 * Update iced to 0.5.0 (#12411) * Update perl-test2-suite to 0.000116 (#12412) * fix compatibility with other tools (#12415) * Restore dexseq python helper scripts (#12352) * Restore dexseq python helper scripts * Add python requirement for helper scripts * Add python noarch to build section * pin it to python2k * Add htseq requirement, support only python <3 for now * Genenotebook v0.1.12 (#12418) * genenotebook recipe * About * Package name * License * sha256sum * Update build.sh * Make bin dir * Change ln to cp * New symlink strategy * Build from prebundled tarball * genenotebook v0.1.2 * version fix * retry * fix * build number * genenotebook v0.1.3 * genenotebook v0.1.3 * new build procedure * change run dependencies * build * restore build procedure * Fix summary * dependency versions * v0.1.5 * version fix * v0.1.6 * reset build number * build number * genenotebook v0.1.7 * v0.1.8 * v0.1.9 * v0.1.10 * v0.1.11 * v0.1.12 * updated source * added medpy recipe (#12417) * added medpy recipe * removed osx from build * Update meta.yaml * Update meta.yaml * add boost and a compiler * Update meta.yaml * Update meta.yaml * add itk * Updated ddrage to version 1.6.1. (#12421) * Add r-mcpcounter recipe. (#12261) * Add MCPcounter recipe. * fix lint: remove 'fn' * fix license_file, version number and doi * Update DEXSeq requirements to force compatible HTSeq version (#12423) * ARB: Pin glib (#11782) * Pin glib * Update meta.yaml * Update meta.yaml * Work around CB3 issues * Work around bioconda-utils lint false positive * Disable lint check should_not_be_noarch * Can't reference other packages built in recipe from anything but run * Move perl to host section. Maybe that helps. * constraining interpreter version breaks with CB3? * disable perl version constraint :( * Update meta.yaml (#12426) * stacks: fix for fix 'fixing' @ in exe_path (#12420) * stacks: fix for fix 'fixing' @ in exe_path the previous fix #11580 tried to solve the problem with the @ in the exe_path by setting this variable empty. But the perl scripts - append a / to the empty string and (i.e. the bin path gets /binary) - check for file presence (problem: neither binary nor /binary are present) Now I quote the @ in the exe_path. * stacks: add refmap bugfix * Genenotebook v0.1.13 (#12424) * genenotebook recipe * About * Package name * License * sha256sum * Update build.sh * Make bin dir * Change ln to cp * New symlink strategy * Build from prebundled tarball * genenotebook v0.1.2 * version fix * retry * fix * build number * genenotebook v0.1.3 * genenotebook v0.1.3 * new build procedure * change run dependencies * build * restore build procedure * Fix summary * dependency versions * v0.1.5 * version fix * v0.1.6 * reset build number * build number * genenotebook v0.1.7 * v0.1.8 * v0.1.9 * v0.1.10 * v0.1.11 * v0.1.12 * updated source * v0.1.13 * metaQuantome (#12413) replaces metaquant, which is now deprecated. * New MMseqs2 release 7-4e23d (#12432) New mmseqs2 release 7-4e23d * update spades to 3.13.0 (#12408) * update spades to 3.13.0 * spades: removed dipspades; added 3.12.0 recipe in subdir * bumped build number for 3.11.1 due to CI failure * Update Crossmap to 0.3.1 (#12439) * Update Crossmap to 0.3.1 * Make metaquantome dependencies more specific (#12442) * less stringent deps * bump build * pin goatools * test extra pins * integration of bcool to bioconda (#12422) * Update hifive to 1.5.7 (#12433) * Update scvi to 0.2.3 (#12434) * Update Subread from 1.6.2 to 1.6.3. (#12425) * Update Subread from 1.6.2 to 1.6.3. * Subread executable coverageCount has been removed. https://groups.google.com/d/msg/subread/Au1CpKGAXaA/KndhDbrfAwAJ * UCSC Cell Browser 0.4.23 (#12347) * Starting files for ucsc-cell-browser * Customised recipe for ucsc-cell-browser * meta update for ucsc-cell-browser * Changes cbTrackHub to cbHub * Point to static release * Moves to 0.25 * Updates sha hash for ucsc-browser * Reverts to 0.1.9 * At ebi * Update meta.yaml * pins numpy to last know working version * Back to 0.25, no numpy pinning. * Remove git, pin python and numpy. Add build section. * Update meta.yaml * Update meta.yaml * Move to 0.4.20 without skeleton on provisional commit * Typo on executable name * Moves to release version and adds dependencies for converters * Update libstatgen to 1.0.14 (#12437) * Update arvados-python-client to 1.2.1 (#12438) * Update tirmite to 1.1.3 (#12435) * Bump metaquantome (#12449) * less stringent deps * bump build * pin goatools * test extra pins * bump metaquantome to 0.99.3 * Update ADAM to 0.25.0 (#12445) * Update: bcbio, bcbio-vm with viral QC, Docker fixes (#12453) * update rgi4.2.2 recipe (#12282) * update to enforce python3.6 and load card.json * remove lines from build.sh * update build number * make PR comment changes * add test to verify db is loaded * update build script * update build script * fix lint errors * fix linting errors * fix liniting errors * fix linting errors * fix linting errors * fix linting errors * fix linting errors * fix linting errors * fix linting errors * fix linting errors * fix linting errors * revert test change * Add CRAN R package leapp. (#12428) * Bump DECIPHER to Bioconductor 3.7 (#12463) * Bump DECIPHER to Bioconductor 3.7 * Change r-rsqlite version dependency * Update meta.yaml * updated scVI to 0.2.3 (#12429) * Add recipe for PyAAVF 0.1.0 (#12451) * Add recipe for PyAAVF 0.1.0 * Fix linting error * seqkit 0.9.3 (#12455) * HTSeq - Pin numpy version (#12467) * update eigensoft to 7.2.1 (#12469) * Update scnic to 0.6.0 (#12436) * Update scnic to 0.6.0 * Work around fastspar insufficient armadillo pin * fix pin * GimmeMotifs 0.13.1 (#12471) * Bumped version to newest, with introspective text (#12461) * Update Segway 2.0.2 recipe to use older depedencies (#11803) * Update Segway 2.0.2 recipe to use older depedencies * Update maximum genomedata version supported * Update build number * Fix missing older dependency information * Update meta.yaml * updating dependencies for reparation_blast (#12443) * updating dependencies for reparation_blast * changed dependency of pysam * Added DropletUtils package (#12448) * Create recipe for SVIM (#12272) * add svim recipe * fix bugs in svim recipe * replace source file * remove license file * Lowercase biopython * upgrade to svim 0.4.1 * add GPL LICENSE file, allow python 3.6.* patch releases, add minimap2 dependency * fix python version * try to fix lint error * replace "skip: True" with "noarch: python" * Update bioconductor-biocgenerics (#12477) * [X] I have read the [guidelines for bioconda recipes](https://bioconda.github.io/guidelines.html). * [ ] This PR adds a new recipe. * [ ] AFAIK, this recipe **is directly relevant to the biological sciences** (otherwise, please submit to the more general purpose [conda-forge channel](https://conda-forge.org/docs/)). * [X] This PR updates an existing recipe. * [ ] This PR does something else (explain below). * Irida sistr results 0.6.0 (#12478) * Update irida-sistr-results to 0.6.0 * Fixed dependency string * Adding recipe for clinvar-tsv v0.1.0. (#12481) * no fixed boost version (#12483) * New recipe: pysradb (#12470) * Pyseer 1.2.0 (#12444) * Update pyseer to 1.1.2 * Update pyseer to 1.2.0 * Update pyseer to 1.2.0 Update pyseer to 1.2.0 Update pyseer to 1.2.0 (fixed) * Final touches to pyseer 1.2.0 * Additional update to pyseer recipe * sentieon: minor version bump to 201808.01 (#12480) * adding java to mutations recipe (#12485) * Update ncrf to 1.00.06 (#12369) * Update ncrf to 1.00.06 * Update test string * Bump umitools (#12486) * Mob suite version 1.4.9 no arch build number 2 (#12479) * Updated to version 1.4.9 * Downgraded to python >= 3.4 to accomodate lowandrew request * new build * no arch commit for python 3.4 * no arch conda package version * Set build number to 1 * Update r-goeveg to 0.4.2 (#12375) * Update r-goeveg to 0.4.2 * Add r-hmisc as dependency * Removes r-seurat-scripts from blacklisting (#12489) * Removes r-seurat-scripts from blacklisting * Unblacklist some non bioconductor packages * For VarDict-Java, install utility scripts. (#12488) * For VarDict-Java, install utility scripts. Utility script that were previously only shipped with VarDict are not part of VarDict-Java as well, making installation of both packages unnecessary. * Bump build. * Improve variable name. * Make vardict depend on vardict-java for utility scripts. * Pin compatible numpy for older HTSEQ versions (#12490) * Pin compatible numpy for older HTSEQ versions This is required to keep older versions of HTSEQ functional * HTSeq - update old versions to build properly with new build system * HTSeq 0.6.1 - Increment build number * add recipe for r-epic (#12473) * Add new recipe - RVTESTS (#12465) * Add rvtests * Update pre-req * Update meta.yaml * Update build.sh * Update build.sh * Update meta.yaml * Update build.sh * Update build.sh * Update build.sh * Update build.sh * Update build.sh * Update build.sh * Update build.sh * Update build.sh * Update meta.yaml * Update meta.yaml * Update build.sh * Update build.sh * Update build.sh * Update meta.yaml * Update meta.yaml * Update meta.yaml * Create LICENSE * Update meta.yaml * Update meta.yaml * Update build.sh * Update build.sh * Update build.sh * Update meta.yaml * Update meta.yaml * Update meta.yaml * Update build.sh * Create run_test.sh * Update meta.yaml * Delete run_test.sh * Update build.sh * Update meta.yaml * Update build.sh * Update meta.yaml * Update meta.yaml * Update meta.yaml * Update meta.yaml * Update build.sh * Update meta.yaml * Update build.sh * Update build.sh * Update build.sh * Update build.sh * Update build.sh * Update meta.yaml * Update meta.yaml * Update build.sh * Update meta.yaml * Update meta.yaml * Update meta.yaml * Adding recipe for var-agg v0.1.0 (#12482) * Adding recipe for var-agg v0.1.0 * runtime deps do have run-exports defined * move rust into the host section * Adding dependency to clangdev * Adding var-agg v0.1.1. (#12495) * [WIP] Salmon v0.12.0 --- try to fix OSX build for real (#12441) Salmon v0.12.0 --- version bump and fix OSX build * Considerable updates in terms of features and fixes (check release notes). * Fix OSX build that would compile, but segfault in quant (but only when built on "old" OSX). * Performancean alytics (#12498) * Add bioconductor package RNASeqR * Add performanceanalytics * Performancean alytics (#12499) * Add bioconductor package RNASeqR * Add performanceanalytics * Move recipes/r-performanceanalytics and add r-rafalib * Move r-performanceanalytics/ to recipes * Update recipes/r-performanceanalytics * Update r-rafalib * Remove recipes/r-performanceanalytics/bld.bat * Remove recipes/r-performanceanalytics * Update r-performanceanalytics/ * Update r-performanceanalytics/ * Add r-performanceanalytics/ * remove r-performanceanalytics * Add performanceanalytics * Remove r-performanceanalytics * Update Picard to 2.18.20. (#12501) * Update vsearch to 2.10.0. (#12504) * Update Purge Haplotigs to v1.0.4 (#12497) * Update duphold to 0.1.1 (#12516) * Update starfish to 0.0.31 (#12515) * Update perl-term-app-roles to 0.02 (#12512) * Update perl-dbd-sqlite to 1.60 (#12511) * Update perl-json to 4.00 (#12509) * Update kipoi to 0.6.5 (#12508) * Update illumina-interop to 1.1.8 (#12507) * Update beagle-lib to 3.1.2 (#12523) * Update pysradb to 0.3.0 (#12522) * Update bioconda-utils to 0.15.2 (#12525) * Update perl-json-pp to 4.0 (#12524) * Update perl-term-table to 0.013 (#12529) * Update abyss to 2.1.5 (#12528) * Update perl-test2-suite to 0.000117 (#12527) * Update wtforms-alchemy to 0.16.8 (#12505) * Update perl-carp-clan to 6.07 (#12518) * Update perl-date-manip to 6.75 (#12519) * Update to bioconductor 3.8, use gcc7 in bulk * Should have double checked the circleci yaml * fix a few shell files * copy over bulk change
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