From c829a4647eb21db1a5409b29847f3df4f1983b6d Mon Sep 17 00:00:00 2001 From: John Blischak Date: Tue, 19 Dec 2017 11:39:20 -0500 Subject: [PATCH] Fix Bioconductor data packages (#7116) * Update: ensembl-vep, cnvkit (#6880) - ensembl-vep: Fix loftee plugin installation to include recent splice site updates: https://github.com/chapmanb/bcbio-nextgen/issues/2158#issuecomment-346031639 - cnvkit: incorporate empty weight patch merged upstream * VEP: bumped subversion (#6882) * Adding vcfpy v0.11.0 (#6879) * bulk ucsc updates (#6884) * Update bulk (#6274) * new version of graphicsmagick with --enable-symbol-prefix option when building (#6120) * add bioconductor v3.4 versions (#6124) * update r-aroma* (#6126) * create recipe for perl-types-standard (#6125) * Create build.sh * Create meta.yaml * Create recipe for perl-bio-cigar (#6118) * Create build.sh * Create meta.yaml * Update meta.yaml * Update meta.yaml * Update meta.yaml * Update meta.yaml * Update meta.yaml * Update meta.yaml * Update meta.yaml * remove bioconductor-peca from blacklist (#6129) * rebuild r-packages (#6128) * Update meta.yaml (#6134) * Add BamM package (#6133) * Add bamm * Update galaxy_sequence_utils to 1.1.1 (#6136) * updated recipe (#6138) * add bioconductor-jaspar2014 (#6137) * Haystack 0.5.2 (#6140) * updated recipe * updated recipe * dr-disco v0.11.0 (#6142) * Add several R and Bioconductor recipes (#5428) * initial version of recipes * remove last lines * add missing dependencies * added missing dependencies * added recipe for r-sfsmisc * move r-recipes to conda-forge and remove empty lines in bioc recipes * remove recipes that have been already added since last push * remove r-sfsmisc * Update gffread to 0.9.9. (#6146) * Add recipe for bioconductor-scran (#6143) * Initial recipe of bioconductor-scran * Modified R dependency * Updated cmv to version 1.0.6 (#6147) * Hansel | Pinning attrs version (#6135) * Added recipe for "Heidelberg Subtyping". This includes tailoring of the python environment within the build.sh file. * Fixing the directory within build.sh * Fixing the ordering of the sed command, moving to after the pip install. * Removing SED tailoring for now, and adding "which" as a test command. * Changing repository as we have now migrated to the PHAC NML repository. * Changing to official release branch now. * Fixing MD5 value. * Fixing requirements and test command. * Changing the testing command, as the new help contains invalid characters. * Removing list of authors from summary within meta.yaml. * Adding Detailed Summary Added detailed summary including authors. * Deleting python version file. Deleting un-needed file. * Changing recipe to rely on PyPi and fixed the build script. * Adding python setup parameters. * Removing pinning, and adding skip for Python 2. * Changing URL to standard. Added variable for hash type and val. * Pinning version of attrs. * Update trim_galore to 0.4.4. (#6148) * Downgrade networkx dependency (#6094) Networkx has recently been updated to 2.0, which is incompatible with `colormath` - `spectra` dependency (see https://github.com/ewels/MultiQC/pull/561 and https://github.com/ewels/MultiQC/issues/592). Until a new `colormath` version is released, we have to downgrade networkx dependency for MultiQC. * Updating Last (lastal) to v874 (#6141) * updating to last 874 * switch for OSX specific compilation with new makefile * adding 8 byte binaries (for large DBs using big RAM) * Snakemake 4.1.0 (#6150) * Update Bamm (#6156) * bump gnu-getopt build (#6157) gnu-getopt depends on gettext, which had a linking issue with 0.19.8 (fixed in 0.19.8.1). This bumps gnu-getopt to hopefully trigger a rebuild with gettext 0.19.8.1 from conda-forge * [WIP] add sis (#6055) * [WIP] add sis init * [wip] sis build passes local * [WIP] added python req * [WIP] changed build script * Add package MentaLiST-0.1.2 (#5856) * Initial commit * Updated to v0.1.2 * Updated url and sha256 hash * Filled in missing fn field * Added requirement mpfr * Specify openblas build to force conda-forge build of julia * Revert last change * Updated build section to skip osx build (no julia available) * Moved MentaLiST.jl -> mentalist symbolic link command to build.sh * Mapsembler2 (#6159) * Remove unneeded samtools run requirement (#6155) CrossMap uses pysam. * update shovill (#6152) * bumped shovill version to 0.8.0 * added conda_perl * added version requirements * discosnp (#6149) * discosnp * fix sed compatibility * pin zlib against {{CONDA_ZLIB}}* * Haystack 0.5.2 (#6164) * updated recipe * updated recipe * updated sha256 * Haystack 0.5.2 (#6165) * updated sha256 * fixed build number * Kissplice (#6154) * Kissplice * pin zlib against {{CONDA_ZLIB}}* * add python libraries * remove make test * fix python dependency * uncomment make test * IntaRNA v2.0.5 (#6160) * v2.0.5 released * reset build number to 0 * Update: bcbio-vm for ansible 2.x compatibility (#6167) * Adds Deeptools 1.5.8.2 and 1.5.9.1 (#6166) * deeptools: add old 1.5.8.2 version * deeptools: minor update for linux build * deeptools: add missing requirement for ucsc-bedgraphtobigwig * deeptools: add 1.5.9.1 * Perl io gzip (#6158) * first commit * first commit * Remove zlib-devel dependency * Add a dependency to zlib (zlib-devel not found) * Update build.sh with CFLAGS and LDFLAGS * update build.sh with CFLAGS and LDFLAGS * Add zlib reuirement * Back to the perl-io-html model * Back to the perl-io-html model + env vars for compliation and ld * [lint skip uses_setuptools for recipes/qcumber] * [lint skip uses_setuptools for recipes/qcumber] * [lint skip uses_setuptools for recipes/qcumber] * [lint skip uses_setuptools for recipes/qcumber] * [lint skip uses_setuptools for recipes/qcumber] * [lint skip uses_setuptools for recipes/qcumber] * pin zlib * bump build number (#6174) * Added recipe for bioconductor-copynumber (#6170) * Haystack 0.5.2 (#6176) * updated recipe * updated recipe * updated sha256 * fixed build number * updated hash * improved patch (#6173) * Update meta.yaml (#6179) Oups, I forgot to check the build number * Update Bamm (#6180) * Discosnp fix dependencies (#6182) * discosnp * fix sed compatibility * pin zlib against {{CONDA_ZLIB}}* * fix dependencies binaries not found during the execution * Bump mash to 2.0 (#6168) * Bump mash to 2.0 * Pin zlib * Discosnp fix scripts path in .sh (#6185) * discosnp * fix sed compatibility * pin zlib against {{CONDA_ZLIB}}* * fix dependencies binaries not found during the execution * fix scripts path in .sh * fix dbh5 path for copy * Update mssttitch version to 2.5 (#6181) * Update mssttitch version to 2.5 * Fix setup.py for conda after linting * GraphProt (#6183) * add GraphProt version 1.1.6 * update shiver (#6175) * update Graphprot version 1.1.7 (#6188) * add python3 dependency, need at least weblogo 3 * version bump * Tantan (#6189) Adding tantan: a utility for masking low complexity sequences * Updated haystack sha256 (#6178) * updated sha256 * updated sha256 * Haystack bio (#6190) * updated haystack 0.5.3 * updated haystack 0.5.3 * updated sha256 * updated sha256 * updated sha256 * updated sha256 * updated last aligner to 876 (#6191) * updated last aligner to 876 * updated spades to 3.11.1 bug-fix release (#6192) * updated sha256sum (#6193) * adding mappy (#6195) * adding mappy * adding import test * removed double whitelines * fixing yaml * fixing yaml - adding build * fixing yaml - removed space * fixing yaml - no idea * fixed files - maybe * added zlib * dummy change * trying environmental variables in build.sh * removed comments * specified CONDA zlib in requirements * adding nanolyse (#6196) * adding mappy * adding import test * removed double whitelines * fixing yaml * fixing yaml - adding build * fixing yaml - removed space * fixing yaml - no idea * fixed files - maybe * added zlib * dummy change * trying environmental variables in build.sh * removed comments * specified CONDA zlib in requirements * adding nanolyse * lowercase name * corrected import test * Fix url and description (#6197) * Update vcf2db to 2017.09.14. (#5433) * Bumped STAR-Fusion version (#6198) * HUMAnN2 requires diamond<0.9.0 (#6194) * HUMAnN2 requires diamond<0.9.0 * Fix pre-existing linting errors * Increment build numbers * update r-sartools (#6201) * Update: latest version with CollectErccMetrics (#6205) * Takeabreak software (#6145) * first commit for takeabreak * add zlib requirement * fix sed compatibility * pin zlib against {{CONDA_ZLIB}}* * delete decrease of memory * Mapsembler2 (#6206) * Mapsembler2 * fi mapsembler2 deps * Htseq 0.9.1 (#6204) * Add recipe for HTSeq-0.9.1 * Delete files * Add recipe for htseq * Update vsearch to 2.4.4 (#6211) * Update picard to 2.13 (#6212) * bump to 0.8.1 (#6058) * bump to 0.8.1 * change patch file to reflect updated code * add cflag to use C99 in the compiler. this is due toa new error in the new scrappie code * Add recipe for hicrep by Tao Yang. (#6213) * Explicit set of LGPL license (#6210) * Explicit set of LGPL license and move license link to license_file meta field * refer license_file to source directory * set explicit license instead of reference to LICENSE source file (#6208) * set explicit license instead of reference to LICENSE source file * add license_file info * update CIRCexplorer2 from 2.3.0 to 2.3.1 (#6214) * Flexbar 2.5.0 (#6187) * initial commit * move to separate dir and start 3.0.2 version * prepare version 3.0.3 * dont do 303 * enable osx and pin bzip2 and zlib * unpin bzip2 * have to create documentation directory * remove libgcc build dep * Add yanagiba (#6217) * Add yanagiba * Fix url * Remove duplicated dep * Skip py27 * update Graphprot tests to run in docker setup (#6218) * add python3 dependency, need at least weblogo 3 * version bump * remove libgcc runtime tep * see if libcxx is required at all * directly get test files from github * fix tests for wget download of test files * add wget runtime dependency for downloading testing data within docker * remove explicit python stuff, depends implicitely on python via weblogo * clean up test calls again * use curl instead of wget * Update bcftools to v1.6 (#6221) * [update] pyquant-ms to 0.2.1 (#6222) * Update version * Skip python 3 build * Commet recipe (#6220) * add commet recipe * add python dependency :) * Fix invalid license link (#6209) * Fix invalid license link Explicit set of license and add correct link to license file on github * add skip-lints as source uses only git_url, upstream not providing tags or archives * refer to license in source code instead of github link * use archive instead of git_url * increase build number to force new release update after modification of source url instead of git_url, increatse build number to get a new fresh built * fix license file location * Create recipe for rad_haplotyper (#6202) * Create build.sh * Create meta.yaml * Update meta.yaml * Update meta.yaml * Update snpEff, SnpSift to 4.3.1r. (#6224) * Update SnpSift to 4.3.1r. * Update snpEff to 4.3.1r. * Pairix 0.3.0 (#6223) * Update meta.yaml * Update build.sh * Update build.sh * Update build.sh * update sequana to version 0.5.2 (#6226) * Ped parser 1.6.6 (#6229) * Save ped_parser 1.6.5. * Update ped_parser to 1.6.6. * Fix LINT check setup_py_install_args. * Update htsbox to r340. (#6230) * ViennaRNA 2.4.1 (#6228) * build.sh of v2.3.5 * meta.yaml of v2.3.5 * tutorial build disabled * v2.4.1 enabled * summary tag indention * RNAlocmin disabled since not compiling * canu 1.6 (#6216) * canu 1.6 * set machine requirements * fix * remove the second test * Sift4g recipe (#6227) * Add recipe for HTSeq-0.9.1 * Add recipe for sift4g * Updating Hansel to version 0.2.0 (#6225) * Added recipe for "Heidelberg Subtyping". This includes tailoring of the python environment within the build.sh file. * Fixing the directory within build.sh * Fixing the ordering of the sed command, moving to after the pip install. * Removing SED tailoring for now, and adding "which" as a test command. * Changing repository as we have now migrated to the PHAC NML repository. * Changing to official release branch now. * Fixing MD5 value. * Fixing requirements and test command. * Changing the testing command, as the new help contains invalid characters. * Removing list of authors from summary within meta.yaml. * Adding Detailed Summary Added detailed summary including authors. * Deleting python version file. Deleting un-needed file. * Changing recipe to rely on PyPi and fixed the build script. * Adding python setup parameters. * Removing pinning, and adding skip for Python 2. * Changing URL to standard. Added variable for hash type and val. * Bumping version of bio_hansel to 0.2.0 * Fixing - to _ * add cassiopee index/search sequence tool (#6215) * add cassiopee index/search sequence tool * pin boost version * add boost related libraries as requirements though should be done by boost * try setting boost options on cmake for linux/travis case * add debug info to find why boost does not find deps * add LDFLAG to PREFIX/lib * add some C FLAGS for compilation to try to find missing deps * pin bioconda dep libs and append xFLAGS instead of set * Set hstlib version to use as recipe clone master branch (#6207) * Set hstlib version to use as recipe clone master branch and does not compile anymore. Recipe may be improved to use htslib conda package but this fix at least only rebuild of the package. Add hash to source. * fix manpage copy for osx * Update NucleoATAC to version 0.3.4 (#6177) * Update NucleoATAC to version 0.3.4 Added imports test, which forces a build Add fix for zlib.h not found Preserve nucleoatac version 0.3.1 * Use template-vars for nucleoatac package info * Cleaning up some test code * Update vcf2maf to 1.6.14. (#6232) * Commet apply patch (#6233) * add commet recipe * add python dependency :) * patch commet to load dependencis correctly * add build number * Update biobambam to 2.0.78. (#6234) * Update galaxy_sequence_utils to 1.1.2 (#6235) * Recipes for R packages alakazam and prestor. (#6199) * Recipes for R packages alakazam and prestor. * Added missing dependencies. * Removed #win specific things and updated gcc/llvm dependencies. * Anvio to versino 3 (#6238) * moving to anvio 3 * adding centrifuge as a run dependency * bowtie2 2.3.3.1 (#6241) * Update gffcompare to 0.10.1. (#6243) * Update bcftools-snvphyl-plugin to 1.6 (#6237) Depend on bcftools instead of conflicting with it. * Lordec (#6144) * first commit * test changes and add comments * fix command line * remove binary * remove stderr redirection * fix testin adding || true * fix command line test * add zlib to recipe * Bump vsearch version and add .gz support (#6239) * Update peddy to 0.3.1. (#6236) * Update peddy to 0.3.1. * Update dependencies. * Work around API changes in networkx >=2.0. * Remove running the unit tests as suggested by @daler. This was running into trouble with the minimal docker containers. * Samtools 0.1.x (#6200) * samtools: add version 0.1.12 till 0.1.15 with one semi test * samtools: resolving dependencies for new versions - i hope * samtools: pin requirements and expand CFLAGS * samtools: fix incorrect sha256 and change back to md5 * samtools: os dependend Makefile adjustment * patch ViennaRNA 2.4.1 RNAlocmin (#5994) * bump viennarna * increment bn * Enable RNAlocmin * Bump KneadData to 0.6.1 (#6244) * Augustus deps (#6242) * use latest augustus * use latest augustus * fix augustus, maker and busco recipes * typo... * typo... * bump build numbers * some problem with tests * pin zlib * try to fix test case * fix test * bioconductor-limma - add statmod as dependency (#6247) * bioconductor-limma - add statmod as dependency * bioconductor-limma - update build number * Update meta.yaml * VEP: bumped subversion (#6249) * Cyvcf 0.8.0 (#6251) * Preserve CyVCF 0.7.2. * Update CyVCF to 0.8.0. * Update IRFinder to 1.2.3. (#6252) * Gecode 5.1.0 (#6253) * Preserve Gecode 5.0.0. * Update Gecode to 5.1.0. * Genehunter-Modscore v3.1 (#6248) * genehunter recipe * skip osx * Gmap 2017 09 30 (#6255) * Preserve GMAP 2017.05.08. * Update GMAP to 2017.09.30. * Bump mashtree to 0.25 (#6258) * Update Oncofuse to 1.1.1. (#6259) * Freebayes seems to need libbz2 (#6260) * Freebayes seems to need libbz2 * Pin zlib and bzip2 * Update meta.yaml * Peptide shaker 1.16.14 (#6261) * Preserve peptide-shaker 1.16.13. * Update PeptideShaker to 1.16.14. * Omero 5.4.0 (#6256) * Bump OMERO recipe to version 5.3.4 - Bump version number and SHA1 - Add range to the zero-ice dependency - User HTTPS * Add skip-lints * Fix character * Bump to OMERO.py 5.4.0 * Do not skip lint * Update: mosdepth 0.1.9 (#6264) Includes breaking changes relative to 0.1.8: chapmanb/bcbio-nextgen#2094 Has fixes for changed install.sh: Fixes #6263 * Add conda for tgDist #BioCon2017 (#6257) * Add conda for tgDist #BioCon2017 * Correct comments after pull request * fix runtime dep * add cmake as buld time dependency * skip build on OSX * some recipes has been update for character format (#6267) * Lelievrey (#6266) * Add the pyasp recipe * Correction of the version * Add the missing summary * Update build.sh * small fixes * Snakemake 4.2.0 (#6270) * Bioconductor 3.5 build bumps (#6203) * new version of graphicsmagick with --enable-symbol-prefix option when building (#6120) * add bioconductor v3.4 versions (#6124) * update r-aroma* (#6126) * create recipe for perl-types-standard (#6125) * Create build.sh * Create meta.yaml * Create recipe for perl-bio-cigar (#6118) * Create build.sh * Create meta.yaml * Update meta.yaml * Update meta.yaml * Update meta.yaml * Update meta.yaml * Update meta.yaml * Update meta.yaml * Update meta.yaml * remove bioconductor-peca from blacklist (#6129) * rebuild r-packages (#6128) * Update meta.yaml (#6134) * Add BamM package (#6133) * Add bamm * Update galaxy_sequence_utils to 1.1.1 (#6136) * updated recipe (#6138) * add bioconductor-jaspar2014 (#6137) * Haystack 0.5.2 (#6140) * updated recipe * updated recipe * dr-disco v0.11.0 (#6142) * Add several R and Bioconductor recipes (#5428) * initial version of recipes * remove last lines * add missing dependencies * added missing dependencies * added recipe for r-sfsmisc * move r-recipes to conda-forge and remove empty lines in bioc recipes * remove recipes that have been already added since last push * remove r-sfsmisc * Update gffread to 0.9.9. (#6146) * Add recipe for bioconductor-scran (#6143) * Initial recipe of bioconductor-scran * Modified R dependency * Updated cmv to version 1.0.6 (#6147) * Hansel | Pinning attrs version (#6135) * Added recipe for "Heidelberg Subtyping". This includes tailoring of the python environment within the build.sh file. * Fixing the directory within build.sh * Fixing the ordering of the sed command, moving to after the pip install. * Removing SED tailoring for now, and adding "which" as a test command. * Changing repository as we have now migrated to the PHAC NML repository. * Changing to official release branch now. * Fixing MD5 value. * Fixing requirements and test command. * Changing the testing command, as the new help contains invalid characters. * Removing list of authors from summary within meta.yaml. * Adding Detailed Summary Added detailed summary including authors. * Deleting python version file. Deleting un-needed file. * Changing recipe to rely on PyPi and fixed the build script. * Adding python setup parameters. * Removing pinning, and adding skip for Python 2. * Changing URL to standard. Added variable for hash type and val. * Pinning version of attrs. * Update trim_galore to 0.4.4. (#6148) * Downgrade networkx dependency (#6094) Networkx has recently been updated to 2.0, which is incompatible with `colormath` - `spectra` dependency (see https://github.com/ewels/MultiQC/pull/561 and https://github.com/ewels/MultiQC/issues/592). Until a new `colormath` version is released, we have to downgrade networkx dependency for MultiQC. * Updating Last (lastal) to v874 (#6141) * updating to last 874 * switch for OSX specific compilation with new makefile * adding 8 byte binaries (for large DBs using big RAM) * Snakemake 4.1.0 (#6150) * Update Bamm (#6156) * bump gnu-getopt build (#6157) gnu-getopt depends on gettext, which had a linking issue with 0.19.8 (fixed in 0.19.8.1). This bumps gnu-getopt to hopefully trigger a rebuild with gettext 0.19.8.1 from conda-forge * [WIP] add sis (#6055) * [WIP] add sis init * [wip] sis build passes local * [WIP] added python req * [WIP] changed build script * Add package MentaLiST-0.1.2 (#5856) * Initial commit * Updated to v0.1.2 * Updated url and sha256 hash * Filled in missing fn field * Added requirement mpfr * Specify openblas build to force conda-forge build of julia * Revert last change * Updated build section to skip osx build (no julia available) * Moved MentaLiST.jl -> mentalist symbolic link command to build.sh * Mapsembler2 (#6159) * Remove unneeded samtools run requirement (#6155) CrossMap uses pysam. * update shovill (#6152) * bumped shovill version to 0.8.0 * added conda_perl * added version requirements * discosnp (#6149) * discosnp * fix sed compatibility * pin zlib against {{CONDA_ZLIB}}* * Haystack 0.5.2 (#6164) * updated recipe * updated recipe * updated sha256 * Haystack 0.5.2 (#6165) * updated sha256 * fixed build number * Kissplice (#6154) * Kissplice * pin zlib against {{CONDA_ZLIB}}* * add python libraries * remove make test * fix python dependency * uncomment make test * IntaRNA v2.0.5 (#6160) * v2.0.5 released * reset build number to 0 * Update: bcbio-vm for ansible 2.x compatibility (#6167) * Adds Deeptools 1.5.8.2 and 1.5.9.1 (#6166) * deeptools: add old 1.5.8.2 version * deeptools: minor update for linux build * deeptools: add missing requirement for ucsc-bedgraphtobigwig * deeptools: add 1.5.9.1 * Perl io gzip (#6158) * first commit * first commit * Remove zlib-devel dependency * Add a dependency to zlib (zlib-devel not found) * Update build.sh with CFLAGS and LDFLAGS * update build.sh with CFLAGS and LDFLAGS * Add zlib reuirement * Back to the perl-io-html model * Back to the perl-io-html model + env vars for compliation and ld * [lint skip uses_setuptools for recipes/qcumber] * [lint skip uses_setuptools for recipes/qcumber] * [lint skip uses_setuptools for recipes/qcumber] * [lint skip uses_setuptools for recipes/qcumber] * [lint skip uses_setuptools for recipes/qcumber] * [lint skip uses_setuptools for recipes/qcumber] * pin zlib * bump build number (#6174) * Added recipe for bioconductor-copynumber (#6170) * Haystack 0.5.2 (#6176) * updated recipe * updated recipe * updated sha256 * fixed build number * updated hash * improved patch (#6173) * Update meta.yaml (#6179) Oups, I forgot to check the build number * Update Bamm (#6180) * Discosnp fix dependencies (#6182) * discosnp * fix sed compatibility * pin zlib against {{CONDA_ZLIB}}* * fix dependencies binaries not found during the execution * Bump mash to 2.0 (#6168) * Bump mash to 2.0 * Pin zlib * Discosnp fix scripts path in .sh (#6185) * discosnp * fix sed compatibility * pin zlib against {{CONDA_ZLIB}}* * fix dependencies binaries not found during the execution * fix scripts path in .sh * fix dbh5 path for copy * Update mssttitch version to 2.5 (#6181) * Update mssttitch version to 2.5 * Fix setup.py for conda after linting * GraphProt (#6183) * add GraphProt version 1.1.6 * update shiver (#6175) * update Graphprot version 1.1.7 (#6188) * add python3 dependency, need at least weblogo 3 * version bump * Tantan (#6189) Adding tantan: a utility for masking low complexity sequences * Updated haystack sha256 (#6178) * updated sha256 * updated sha256 * Haystack bio (#6190) * updated haystack 0.5.3 * updated haystack 0.5.3 * updated sha256 * updated sha256 * updated sha256 * updated sha256 * updated last aligner to 876 (#6191) * updated last aligner to 876 * updated spades to 3.11.1 bug-fix release (#6192) * updated sha256sum (#6193) * adding mappy (#6195) * adding mappy * adding import test * removed double whitelines * fixing yaml * fixing yaml - adding build * fixing yaml - removed space * fixing yaml - no idea * fixed files - maybe * added zlib * dummy change * trying environmental variables in build.sh * removed comments * specified CONDA zlib in requirements * adding nanolyse (#6196) * adding mappy * adding import test * removed double whitelines * fixing yaml * fixing yaml - adding build * fixing yaml - removed space * fixing yaml - no idea * fixed files - maybe * added zlib * dummy change * trying environmental variables in build.sh * removed comments * specified CONDA zlib in requirements * adding nanolyse * lowercase name * corrected import test * Fix url and description (#6197) * Update vcf2db to 2017.09.14. (#5433) * Bumped STAR-Fusion version (#6198) * HUMAnN2 requires diamond<0.9.0 (#6194) * HUMAnN2 requires diamond<0.9.0 * Fix pre-existing linting errors * Increment build numbers * update r-sartools (#6201) * add easy build version bumps * run diff to origin/bulk * fix line wraps, build numbers reset to 0, and template bioc version * version bumps for relatively simple packages * data packages remove existing build.sh from recipes; add post-link.sh. A handful have already been created, so their build numbers were not bumped. * Update: latest version with CollectErccMetrics (#6205) * Takeabreak software (#6145) * first commit for takeabreak * add zlib requirement * fix sed compatibility * pin zlib against {{CONDA_ZLIB}}* * delete decrease of memory * Mapsembler2 (#6206) * Mapsembler2 * fi mapsembler2 deps * Htseq 0.9.1 (#6204) * Add recipe for HTSeq-0.9.1 * Delete files * Add recipe for htseq * Update vsearch to 2.4.4 (#6211) * first round of non-straightforward recipes e.g., libgcc, skipped on osx, readline deps * dexseq maintain custom build script; no version change so reset to build: 0 * Update picard to 2.13 (#6212) * dirichletmultinomial updates ensure custom GSL, blas, gcc etc make it into recipe * bump to 0.8.1 (#6058) * bump to 0.8.1 * change patch file to reflect updated code * add cflag to use C99 in the compiler. this is due toa new error in the new scrappie code * dnacopy update prev recipe listed gcc as build dep; changed it to the standard linux/osx build deps. * dose, and new dependency fgsea prev version of DOSE had gmp listed as run and build deps, so retaining it here * ebimage update orig recipe skipped osx; try not skipping for now * flowcore update retain custom parts of build script * flowworkspace update No version change, so build number set to 0. Build deps included autoconf/automake for some reason, but gcc was not included. I kept autoconf in there for now, and added gcc. Note that many of the deps changes are just sort order. * genefilter update prev recipe included gcc, so keeping it here. No version bump, so build number kept at 0. * genomation updates prev version of package 1.6.0 had r-rcpp as dep, but 1.8.0 does not any more. Keeping it (and the custom osx lines in build.sh) just in case. * geoquery build.sh must have missed this in a prev commit * gosemsim update new version no longer depends on r-rcpp, but keeping it just in case * ipo update prev version was skipped for OSX, removing skip for now * lsymphony update prev recipe depended on gcc, retaining here * methylkit update keeping build number: 0; prev recipe had libgcc as dep * monocle update parsing DESCRIPTION has an empty dep; skipped for osx. Since this was added relatively recently, pretty sure it should stay skipped. * fetch remote branch for diffs * Add recipe for hicrep by Tao Yang. (#6213) * Explicit set of LGPL license (#6210) * Explicit set of LGPL license and move license link to license_file meta field * refer license_file to source directory * set explicit license instead of reference to LICENSE source file (#6208) * set explicit license instead of reference to LICENSE source file * add license_file info * update CIRCexplorer2 from 2.3.0 to 2.3.1 (#6214) * Flexbar 2.5.0 (#6187) * initial commit * move to separate dir and start 3.0.2 version * prepare version 3.0.3 * dont do 303 * enable osx and pin bzip2 and zlib * unpin bzip2 * have to create documentation directory * remove libgcc build dep * Add yanagiba (#6217) * Add yanagiba * Fix url * Remove duplicated dep * Skip py27 * update Graphprot tests to run in docker setup (#6218) * add python3 dependency, need at least weblogo 3 * version bump * remove libgcc runtime tep * see if libcxx is required at all * directly get test files from github * fix tests for wget download of test files * add wget runtime dependency for downloading testing data within docker * remove explicit python stuff, depends implicitely on python via weblogo * clean up test calls again * use curl instead of wget * Update bcftools to v1.6 (#6221) * [update] pyquant-ms to 0.2.1 (#6222) * Update version * Skip python 3 build * Commet recipe (#6220) * add commet recipe * add python dependency :) * Fix invalid license link (#6209) * Fix invalid license link Explicit set of license and add correct link to license file on github * add skip-lints as source uses only git_url, upstream not providing tags or archives * refer to license in source code instead of github link * use archive instead of git_url * increase build number to force new release update after modification of source url instead of git_url, increatse build number to get a new fresh built * fix license file location * Create recipe for rad_haplotyper (#6202) * Create build.sh * Create meta.yaml * Update meta.yaml * Update meta.yaml * Update snpEff, SnpSift to 4.3.1r. (#6224) * Update SnpSift to 4.3.1r. * Update snpEff to 4.3.1r. * Pairix 0.3.0 (#6223) * Update meta.yaml * Update build.sh * Update build.sh * Update build.sh * update sequana to version 0.5.2 (#6226) * Ped parser 1.6.6 (#6229) * Save ped_parser 1.6.5. * Update ped_parser to 1.6.6. * Fix LINT check setup_py_install_args. * Update htsbox to r340. (#6230) * ViennaRNA 2.4.1 (#6228) * build.sh of v2.3.5 * meta.yaml of v2.3.5 * tutorial build disabled * v2.4.1 enabled * summary tag indention * RNAlocmin disabled since not compiling * canu 1.6 (#6216) * canu 1.6 * set machine requirements * fix * remove the second test * Sift4g recipe (#6227) * Add recipe for HTSeq-0.9.1 * Add recipe for sift4g * Updating Hansel to version 0.2.0 (#6225) * Added recipe for "Heidelberg Subtyping". This includes tailoring of the python environment within the build.sh file. * Fixing the directory within build.sh * Fixing the ordering of the sed command, moving to after the pip install. * Removing SED tailoring for now, and adding "which" as a test command. * Changing repository as we have now migrated to the PHAC NML repository. * Changing to official release branch now. * Fixing MD5 value. * Fixing requirements and test command. * Changing the testing command, as the new help contains invalid characters. * Removing list of authors from summary within meta.yaml. * Adding Detailed Summary Added detailed summary including authors. * Deleting python version file. Deleting un-needed file. * Changing recipe to rely on PyPi and fixed the build script. * Adding python setup parameters. * Removing pinning, and adding skip for Python 2. * Changing URL to standard. Added variable for hash type and val. * Bumping version of bio_hansel to 0.2.0 * Fixing - to _ * add cassiopee index/search sequence tool (#6215) * add cassiopee index/search sequence tool * pin boost version * add boost related libraries as requirements though should be done by boost * try setting boost options on cmake for linux/travis case * add debug info to find why boost does not find deps * add LDFLAG to PREFIX/lib * add some C FLAGS for compilation to try to find missing deps * pin bioconda dep libs and append xFLAGS instead of set * Set hstlib version to use as recipe clone master branch (#6207) * Set hstlib version to use as recipe clone master branch and does not compile anymore. Recipe may be improved to use htslib conda package but this fix at least only rebuild of the package. Add hash to source. * fix manpage copy for osx * Update NucleoATAC to version 0.3.4 (#6177) * Update NucleoATAC to version 0.3.4 Added imports test, which forces a build Add fix for zlib.h not found Preserve nucleoatac version 0.3.1 * Use template-vars for nucleoatac package info * Cleaning up some test code * Update vcf2maf to 1.6.14. (#6232) * Commet apply patch (#6233) * add commet recipe * add python dependency :) * patch commet to load dependencis correctly * add build number * Update biobambam to 2.0.78. (#6234) * Update galaxy_sequence_utils to 1.1.2 (#6235) * Recipes for R packages alakazam and prestor. (#6199) * Recipes for R packages alakazam and prestor. * Added missing dependencies. * Removed #win specific things and updated gcc/llvm dependencies. * Anvio to versino 3 (#6238) * moving to anvio 3 * adding centrifuge as a run dependency * bowtie2 2.3.3.1 (#6241) * Update gffcompare to 0.10.1. (#6243) * Update bcftools-snvphyl-plugin to 1.6 (#6237) Depend on bcftools instead of conflicting with it. * Lordec (#6144) * first commit * test changes and add comments * fix command line * remove binary * remove stderr redirection * fix testin adding || true * fix command line test * add zlib to recipe * Bump vsearch version and add .gz support (#6239) * Update peddy to 0.3.1. (#6236) * Update peddy to 0.3.1. * Update dependencies. * Work around API changes in networkx >=2.0. * Remove running the unit tests as suggested by @daler. This was running into trouble with the minimal docker containers. * Samtools 0.1.x (#6200) * samtools: add version 0.1.12 till 0.1.15 with one semi test * samtools: resolving dependencies for new versions - i hope * samtools: pin requirements and expand CFLAGS * samtools: fix incorrect sha256 and change back to md5 * samtools: os dependend Makefile adjustment * patch ViennaRNA 2.4.1 RNAlocmin (#5994) * bump viennarna * increment bn * Enable RNAlocmin * Bump KneadData to 0.6.1 (#6244) * Augustus deps (#6242) * use latest augustus * use latest augustus * fix augustus, maker and busco recipes * typo... * typo... * bump build numbers * some problem with tests * pin zlib * try to fix test case * fix test * bioconductor-limma - add statmod as dependency (#6247) * bioconductor-limma - add statmod as dependency * bioconductor-limma - update build number * Update meta.yaml * VEP: bumped subversion (#6249) * Cyvcf 0.8.0 (#6251) * Preserve CyVCF 0.7.2. * Update CyVCF to 0.8.0. * Update IRFinder to 1.2.3. (#6252) * comment out custom build.sh lines and meta.yaml deps * comment out custom gmp dep * comment out custom build.sh lines * comment out automake build dep * comment out previous genomation build.sh lines and r-rcpp * gosemsim: comment out prev r-rcpp * lpsymphony: comment out prev gcc * comment out patch for methylkit * comment out monocle skip for osx * deseq2 update comment out deps that are not listed in DESCRIPTION * mosaics update comment out prev version's libgcc run dep * motifbreakr update comment out osx skip * motiv updates comment out custom build.sh lines and deps * mzr: comment out custom build deps and osx skip * ncdfflow: comment out prev custom deps * oligo: comment out previous extra deps, add separate build script * oligoclasses update comment out custom deps from prev recipe * update pcamethods * pchicdata update to make it a proper data package recipe * phyloseq: comment out prev gmp dep * piano update comment out previous libgcc/llvm * qdnaseq update: rm extra `r-` dep from empty DESCRIPTION entry * rcas update rm "r-" dep from empty DESCRIPTION * rgalaxy update: rm "r-" empty dep * rgraphviz: comment out prev patch and gcc * rhdf5 update: comment out osx patch and gcc * rhtslib update: comment out patches, gcc, and custom build.sh line * risa update: comment out readline dep; reset build to 0 * rtracklayer update: fix dep version numbers which had "-" in them * scan.upc update keep build number at 0; comment out prev r-rsqlite dep and osx skip * shortread: comment out custom build lines * signer update: comment out build lines and prev deps * sva update: comment out prev deps * systempiper: comment out prev osx skip * add diffbind * Gecode 5.1.0 (#6253) * Preserve Gecode 5.0.0. * Update Gecode to 5.1.0. * Genehunter-Modscore v3.1 (#6248) * genehunter recipe * skip osx * Gmap 2017 09 30 (#6255) * Preserve GMAP 2017.05.08. * Update GMAP to 2017.09.30. * Bump mashtree to 0.25 (#6258) * Update Oncofuse to 1.1.1. (#6259) * Freebayes seems to need libbz2 (#6260) * Freebayes seems to need libbz2 * Pin zlib and bzip2 * Update meta.yaml * Peptide shaker 1.16.14 (#6261) * Preserve peptide-shaker 1.16.13. * Update PeptideShaker to 1.16.14. * Omero 5.4.0 (#6256) * Bump OMERO recipe to version 5.3.4 - Bump version number and SHA1 - Add range to the zero-ice dependency - User HTTPS * Add skip-lints * Fix character * Bump to OMERO.py 5.4.0 * Do not skip lint * Update: mosdepth 0.1.9 (#6264) Includes breaking changes relative to 0.1.8: chapmanb/bcbio-nextgen#2094 Has fixes for changed install.sh: Fixes #6263 * Add conda for tgDist #BioCon2017 (#6257) * Add conda for tgDist #BioCon2017 * Correct comments after pull request * fix runtime dep * add cmake as buld time dependency * skip build on OSX * some recipes has been update for character format (#6267) * Lelievrey (#6266) * Add the pyasp recipe * Correction of the version * Add the missing summary * Update build.sh * small fixes * Snakemake 4.2.0 (#6270) * update and otherwise unify r recipes * try removing r-base restrictions * bioconductor-rhtslib additional deps * rm r-base restriction on anything < 3.2.2 * rm a few more r-base restrictions * a small round of bioconductor fixes * try adding openblas * bump ebimage version * add bioconductor-matter * rm r-base pin * add zlibbioc dep to mzr * add treeio * re-enable libglu dep for r-mixomics * add r-mqtl * update s4vectors * rm r restriction in biomformat * fix ebiimage * add libnetcdf dep to mzr * rm r-base restriction for causalr * update biocgenerics to try fixing s4vectors * bump iranges * add bioconductor-msnbase * gcc for osx for fortran * gcc for osx for fortran * try libgfortran to get rhtslib to compile * r-impute -> bioconductor-impute * bump genomeinfodb * assorted fixes * assorted fixes 2 * assorted fixes 3 * assorted fixes 4 * assorted fixes 5 * try to fix shortread * readd bioc-graph patch * assorted fixes 6 * assorted fixes 7 * assorted fixes 8 * rebuild gosemsim * add llvm for motiv and synergyfinder * update rpath patches for rhdf5 and rgraphviz * fix for bioconductor-dose * try gcc for motiv? * gcc for rhdf5? * fix r-latticeextra dependency thanks to @nsoranzo for spotting! * Update meta.yaml * fix buildstring for motiv * skipping remaining osx packages * add bioconductor-masigpro dev version as subdir * bioconductor 3.6 updates * bioconductor 3.6 remaining updates * update bioconductor-treeio * add bioconductor-rcy3 * update rDGIdb and SWATH2stats * fix biocparallel * update complexheatmap * update DelayedArray * update edgeR * temporarily skip osx for rhdf5 and dep * update rGREAT and matter * add r-bh as dep to flowcore * rm post-link for jaspar2018 * update rols * add bioconductor-singlecellexperiment * add bioconductor-raggedexperiment * bump phyloseq * increase subdags for bulk branch * update annotationhub * bump total subdag count * update go.db * update orgdb pkgs * add rhtslib as dep for methylkit * update org.Cf.eg.db * add zlibbioc as dep for mzr * update PSICQUIC and scran * bump Rnits and methylumi * add r-ncdf4 * fix checksum * new version * add bioconductor-rhdf5lib * add bioconductor-beachmat * add r-rcpparmadillo * increase version * add bioconductor-rhdf5lib * add boost back to mzR * upgrade to new version * add hdf5array * upgrade * add the two new deps * add genemeta * add missing dep * fix link * add missing deps * add bioc-cytolib * add rprotobuflib * add missing deps * add missing deps * add additional deps * add automake dep to rprotobuflib * minor formatting * update BioC 3.5 packages recently added to master to BioC 3.6 cc @cbrueffer * add r-bh to chemminer * add missing dep * fix automake to version 1.14 * add protobuf * fix autoconf * fix automake * round 2 of ucsc updates * blacklist remaining bioconductor build failures * back to a single subdag * skip isomirs on osx * try additional fixes * fix rprotobuflib * revert #6758 * whitespace * whitespace test * add nloptr dep to flowdensity * whitespace * revert whitespace * whitespace * add egesa * add data pack * add data pack * add padog * add glimma * add keggdzpathqaysgeo * add scpipe * add egseadata * add updated, existing ucsc packages * fix template for pkgs needing stringify * fix template and build script for fetchchromsizes on osx * add new tools in v357 * remove calc and ave * cleanup * more ucsc cleanup * more ucsc fixes * fix expMatrixBarchartBed * another fix for expMatrixToBarchartBed * various special-casing for expMatrixToBarchartBed * patch expMatrixToBarchartBed to support py3 * Update geoDL to 1.0b5.1. (#6885) * PgSA tool (#6868) * add pgsa tool * fix hash and dirname * try to use gcc on osx as well * use gcc for macos * use latest commit with compilation fixes * revert changes * try to use gcc on osx * Meme old (#6889) * fix old meme package * Create build.sh * add patch * pin zlib * Short reads connector v1.1.3 (#6883) * short_read_connector v1.1.2 * use v1.1.3 with compilation fixes * remove v1.1.0 * DISCASM: Adding version number requirement to pysam dependency. (#6876) * Adding version requirement to pysam. * Bumping up build number. * Ensure 2 perl wrapper scripts do not mask failures (#6886) * Ensure wrapper scripts do not mask failures e.g. Using -pfamB with pfam_scan.pl should return error code 1, but as written the wrapper script returned 0. * Provide SHA256 checksum There was a SHA1 checksum, but we recommend SHA256 or MD5: scottishdumpling:trawler pc40583$ curl -o trawler-2.0.tar.gz -L https://api.github.com/repos/Ramialison-Lab-ARMI/Trawler-2.0/tarball/5f391e0 % Total % Received % Xferd Average Speed Time Time Time Current Dload Upload Total Spent Left Speed 100 84.1M 0 84.1M 0 0 1771k 0 --:--:-- 0:00:48 --:--:-- 3108k $ md5 trawler-2.0.tar.gz MD5 (trawler-2.0.tar.gz) = 2446eabd8e212021d9c296664780ec60 $ shasum -a 256 trawler-2.0.tar.gz c04157db18dc165df52d754ca875a198cbc63d0256b1870c5508a42dfe9c3594 trawler-2.0.tar.gz $ shasum -a 1 trawler-2.0.tar.gz c02ce9aaf6bf743b2dcf056bf697a79d10b37be7 trawler-2.0.tar.gz * Fix perl hash-bang in trawler recipe * Trawler v2.0 usage and version command return error 1. Even using -help or -version, trawler returns error code 1, see https://github.com/Ramialison-Lab-ARMI/Trawler-2.0/issues/2 We can mask this with grep so that the test passes. (Previously the BioConda wrapper script was wrongly suppressing the exit code, so the test was passing.) * Use exec and avoid spliting input parameters. Suggestion by Marcel Bargull, use exec to replace caller process with child, and avoid spliting input parameters on whitespace. * Make pfam_scan.pl dependency on perl-ipc-run explicit * Cleanup * Abyss osx build (#6867) * abyss: fix configure parameters (maybe) * abyss: un-skip osx build * abyss: add --with-sparsehash * abyss: temporarily skip non-osx build * abyss: temporarily try gcc on osx (due to google-sparsehash) * abyss: update sparsehash dependency; bump build * abyss: add patch to prevent linker error on OSX * abyss: add -headerpad_max_install_names to LDFLAGS * abyss: use list for patches, add comment * abyss: use default value for maxk (128) * Abyss osx other versions (#6892) * abyss 1.5.2, 1.9.0: enable osx builds * abyss 1.5.2, 1.9.0: use default maxk (1.5.2: 64, 1.9.0: 96) * abyss 1.5.2, 1.9.0: update dependency on sparsehash * abyss 1.9.0: incomplete patches aren't the smartest ones.. * Update fastq-and-furious to 0.2.0. (#6894) * Update vcfkit to 0.1.6. (#6895) * Cutadapt 1.15 (#6898) * Omero 5.4.1 (#6897) * Bump version to 5.4.1 and sha1 * Replace http by https * Remove google-sparsehash (#6893) * stride: update dependency on sparsehash * tedna: update dependeny on sparsehash * tedna: remove sparsehash run dependency * google-sparsehash: remove recipe, available as 'sparsehash' at conda-forge * Updated MentaLiST to v0.2.0 (#6891) * fix name recipe (#6900) * ls-gkm initial (#6869) * ls-gkm initial * - change to better versioning - do not skip OSX * fixing checksum! fixing tab in version! change URL to last commit * fixing version wildcard * gkmSVM initial commit (#6871) * gkmSVM initial commit * remove unecessary comments * remove all comments * Update hifive to 1.5.3. (#6903) * Update hifive to 1.5.3. * Also remove running the unit tests. * Fix shortreadconnector dependency for discosnp (#6902) * fix name recipe * remove old release and fix short_read_connector dependency * add smina (#6856) * add smina * dang it, md5 is required * try to make version number checker happy even though we don't actually have version numbers * Python newick (#6901) * [WIP] added recipe, trouble building * [WIP] need to build add python-newick * adding python-newick recipe * removing masurca and ragout files I thought were on other branches. sigh * add --single-version-externally-managed * fix bad url; tricked by the cache! * address @mbargull comments to change licence and name to python-newick * Update editdistance to 0.4. (#6904) * editdistance: use PyPi source (#6905) * abyss-k128: remove recipe in favor of abyss-2.0.2-boost1.64_3 (#6899) * Update quasitools version to 0.2.1 (#6890) * Update quasitools version to 0.2.1 * Update quasitools pysam version * adding the OTHER python newick package (#6910) * adding the OTHER python newick package * added --single-version-ext, even though it fails locally * remove setup tools as per @druvus rec * Ragout (#6911) * [WIP] added recipe, trouble building * [WIP] need to build add python-newick * facepalm, I added the wrong newick recipe (the one from pypi, not the one from the docs ) * incorportate proper newick parsing prereqs * removed extraneous recipes * update to hicexplorer version 1.8.1 (#6913) * Add Linkage2Allegro (#6906) * md5 fail, test on docker later * md5 update * fix to build and url * removed future runtime, added filename * Asn2gb (#6378) * Initial commit of asn2gb recipe * Fix test... * Added linux library reqs * removed linux64 selectors and dropped 32bit version * remove joblib recipe (#6912) * remove joblib recipe The version here is 2 years old. The conda-forge version is better maintained. * fix recipe failures * add hash for THeta2 package * remove joblib pinning * fix typo * Update meta.yaml * Fix to Linkage2Allegro (#6914) * md5 fail, test on docker later * md5 update * fix to build and url * removed future runtime, added filename * hotfix - haplotypes genehunter * fix checksum * add structureharvester (#6820) * add structureharvester * change md5 to sha256 ; remove jinja for name * fix * Update meta.yaml * update salmon (#6907) * update salmon * apply thread_local patch on OSX * apply thread_local patch on OSX * back to thread_local * clangdev * try fixing clang in build.sh * try fixing clang in build.sh * salmon: add `libcxx [osx]` dependency * BEDOPS v2p4p30 (#6920) * BEDOPS 2.4.30 * BEDOPS 2.4.30 * [WIP] add sibelia synteny finder (#6917) * [WIP] add sibelia synteny finder * add libgcc * seting g++ and gcc explicitly in build * fix cmake target * added libgccc as run dep * linux build passing, problem with g++. removed explicit path setting to cmake * bump to 3.0.6 from sourceforge, maybe lagan compile issue is solved there? * skip building osx until sibelia issue 178 is resolved * downloading prebuilt binaries from sourcefoge * Ragout (#6915) * [WIP] added recipe, trouble building * [WIP] need to build add python-newick * facepalm, I added the wrong newick recipe (the one from pypi, not the one from the docs ) * incorportate proper newick parsing prereqs * removed extraneous recipes * build 1 -- set when building sebelia * add Sibelia test * add libgcc, builds locally * Move libgcc to run deps. * add sibelia to reqs, remove custom sibelia build script from build.sh * Asn2gb (#6918) * Initial commit of asn2gb recipe * Fix test... * Added linux library reqs * removed linux64 selectors and dropped 32bit version * Changed source to use cargo-ports since upstream updates without versioning... * Revert "Changed source to use cargo-ports since upstream updates without versioning..." This reverts commit 30c02b3a130aab454dc3929a91c9687a4c471a6c. * Reverted and try again * corrected linux64 selectors * removed gunzip command * Added debug * updated gunzip command... * Fixed gunzip commnd...again... * Correct cp statement * Ococo 0.1.2.5 (#6922) * Ococo 0.1.2.5 * Fix fn * Update pinning and fixing source path * Fix * re-patched genehunter (#6924) * update 1.8.1 _version (#6927) * update to hicexplorer version 1.8.1 * update release 1.8.1 after _version and help fix * Update meta.yaml * fix version number (#6925) * add smina * dang it, md5 is required * try to make version number checker happy even though we don't actually have version numbers * As an American, I am culturally indoctrinated to put dates in non-intuitive orders... make release "number" work as a date and a number. * canopy: target march=x86-64 instead of march=native (#6929) * mgs-canopy: use -march=x86_64 instead of -march=native * mgs-canopy: use proper command test * add mockinbird (#6926) * added mockinbird * update dependencies: r -> r-base * Quasitools py3 (#6908) * quasitools: use extended-base for click/py3k * quasitools: update/reduce build requirements * quasitools: use entry point created from Conda * quasitools: relax dependency on pysam * quasitools: update to 0.2.2 * Bump secapr to 1.1.0 (#6923) * Bump secapr to 1.1.0 * add entry_point * add numpy as run deps * Fixes for poretools conda package. (#6930) * Fixes for poretools conda package. - Use the Agg backend for matplotlib if saving to file. This eliminates the error message when the DISPLAY environment variable is unset, e.g. on a headless system. - Add an option to output timestamps in UTC, in order to have reproducible output regardless of timezones. - Inadvertently strip trailing whitespace on some lines. * Fix poretools linting. * Update FastTree to 2.1.10. (#6935) * Update FastTree to 2.1.10. * Use GCC on OSX as well, FastTree needs OpenMP. * Add bioconductor-splatter. (#6934) * HG-CoLoR tool (#6888) * add hg-color software * remove pgsa dep because of remove exec * add wget recipe * add unzip recipe * improve recipe * adding fgap recipe (#6921) * adding fgap recipe * add link to nickp60's fork release * added xorg lib11 * replace fork link with link to git archive! * clarify 'fn:' delcaration, thanks @mbargull * remove initialization message from build script * clean up script creation * Update r-maldiquant to 1.17. (#6938) * Update r-mmgenome to 0.7.1. (#6939) * Update plasmidtron to 0.3.5. (#6941) * Crossmap 0.2.7 (#6943) * Update CrossMap to 0.2.7. * Try to build on OSX as well, in principle it's supported by the software. * SIS, build 1 (#6540) * [WIP] add sis init * [wip] sis build passes local * [WIP] added python req * [WIP] changed build script * [WIP] build 1, remove limit to python2 * moved from sis site to github * remove proper test as copy fails on travis, add import test * fgap add OS X build (#6945) * adding fgap recipe * add link to nickp60's fork release * added xorg lib11 * replace fork link with link to git archive! * clarify 'fn:' delcaration, thanks @mbargull * remove initialization message from build script * clean up script creation * add osx build * Add nanopore_simulation (#6944) * Adding Haploclique, version 1.3.1 (#6928) * travis: use xcode7.3 for now (#6952) * Update embl-validator to 1.1.180. (#6949) * Update Picard to 2.15.0. (#6956) * patch fix (#6962) * update to v0.9.1 (#6946) * Feature/perl biox workflow command (#6947) * BUILD * trigger travis * Update deepmedic to 0.6. (#6961) * Ragout, fixing missing executables (#6966) * [WIP] added recipe, trouble building * [WIP] need to build add python-newick * facepalm, I added the wrong newick recipe (the one from pypi, not the one from the docs ) * incorportate proper newick parsing prereqs * removed extraneous recipes * build 1 -- set when building sebelia * add Sibelia test * add libgcc, builds locally * Move libgcc to run deps. * add sibelia to reqs, remove custom sibelia build script from build.sh * Update Build to include executables from lib (#6963) See comments; the make step creates executables that need to end up in the PATH so ragout can find them later. * Fix hgcolor (#6940) * fix name recipe * remove old release and fix short_read_connector dependency * add python to hg-color * change shebang for python scripts * add constraint to python dependency * [FIX] add python 3 dep to discosnp recipe (#6936) * fix name recipe * remove old release and fix short_read_connector dependency * Add python3 dep used by RAD scripts * remove python dep for build * add python constraint for use python 3 * Add recipe progressiveMauve (#6965) * Added recipe for progressiveMauve. * Update NGLess to 0.6.0 (#6967) * Add Bioconductor data package SNPlocs.Hsapiens.dbSNP144.GRCh38. (#6959) * Toulligqc (#6955) * Add toulligqc * Fix sha256 * Skip py27 * Minor fix * added fcsparser v0.1.4 (#6972) * added fcsparser v0.1.4 * fixes per @mbargull * nanopore_simulation, haploclique: super important reformatting (aka: trigger osx builds) (#6971) * Haystack (#6973) * patch fix * update travis.yml * update gseapy to 0.8.11 (#6977) * update pureclip to version 1.0.3 (#6953) * rambo-k (#6969) * rambo-k initial commit * add run_test * adapt dependencies and run_test, change download path * add java-jdk dependency * change to openjdk dependency * move test section into meta.yaml, remove git_rev * Add tombo (#6976) * Add tombo * Add missing build.sh * Fix typo * Update phyloFlash to 3.0b1. (#6979) * Add bioconductor-flagme. (#6981) * busco: remove wget requirement, update post-link script (#6980) * busco: move wget from run to test requirements * busco: simplify post-link, no python dependency * Mykrobe (#6931) * initial import of ga4ghmongo. Needed for mykrobe * got rid of windows bat * fixed failed bioconda lint of 'setup_py_install_args' * removed boilerplate output * refined testing to how you actually import module * removed mongoengine from build requirements * initial build of mykatlas * initial build for mykrobe * added summary * add entry_points section to build * fixed up license file and added summary. Removed not needed build requirements . Added entry_points * using github release instead of pypi because of license not found in pypi. Removed and added requirements * mykatlas: copy pre-compiled linux binary to $PREFIX/bin * mykrobe: skip OSX builds * mykatlas: fix mccortex31 test * Added recipe for perl-try-tiny-retry (#6975) * Update Treetime recipe (#6954) * Move 0.1 version * Add 0.2.1 version of treetime * Some cleaning * Copy only needed files * fix filename * Update: bcbio, bcbio-vm (#6984) Add support for variant file only inputs for validation and improved Arvados data management. * update seqkit to v0.7.2 (#6985) * Add cpinsim (#6987) * Add bioconductor-recount. (#6988) * VEP: bumped subversion (#6989) * TASSEL Build Recipes (#6874) * Build recipe for TASSEL5. * Fixed shabang lines in TASSEL's perl launch scripts. * Added build recipe for TASSEL4. * Updated TASSEL5's build recipe. - Don't build for MacOS - Deploy TASSEL binary in the recomemnded locaiton inside a conda environment - Corrected custom deactivation script * Configured TASSEL4 to use Open JDK as its runtime. * Implemented wrappers to call TASSEL's wrappers to avoid adding TASSEL home directory in the PATH. * Implemented wrappers to call TASSEL's warappers to avoid including its home directory in the PATH. TASSEL's wrappers uses their own location to figure out paths to their dependency. Therefroe, creating symbolic links fro them in the bin is not sufficient. * Corrected build environment valuables in TASSEL's build script. * Build recipe for TASSEL3. * Tidy up temp directory name in TASSEL4' build script. * Revised TASSEL build recipes based on initial PR review comments: - Corrected version for TASSEL3 - Use source/git_url to download source - Create pathes for wrappers to make them callable via symbolic links. * Revision on TASSEL's build recipes: - Corrected patches for TASSEL3 and TASSEL; - Correct testing commands; - Use TASSEL's current official git repo as source; - Added patches to TASSEL5's build recipe. * Convert CRLF in TASSEL's wrapper scripts to LF in its build script. * Fixed EOL issues on TASSEL4's patches. * Fixed EOL issues on TASEL3's pathces. * Changed TASSEL's build recipes to download snapshots from Bitbucket and SF. * Revised sed's regex in TASSEL's build scripts. - Explictly remove CRs in TASSEL's launch scripts if they are present rather than assuming they are there. - RemoveANSI C quotation for the regex, which is not necessary. * fix openmpi pinning (#6990) * Version 2.12.0 of Nest based on build scripts from version 2.14.0 incl. new OpenMPI pinning. (#6995) * htsfilter recipe (#6994) * add new recipe for bioconductor package affyPLM (#6996) * add new recipe for bioconductor package GEOmetadb (#6997) * Recipe for scan_indel (#6983) * Initial commit for Scan Indel * Making ScanIndel tests work * Removing old sed statements * Skipping OSX Tests * Removing python pinning * added watchdog WMS recipe (#6978) Added Watchdog WMS recipe (https://github.com/klugem/watchdog/) * Change to check repo slug instead of fork variable, since the latter seems to be only true in pull requensts. (#6986) * update for v2.2.1 (#6998) * update for v2.2.1 * wrong sha256 * add recipe to build squizz (#6993) * add recipe to build squizz * update version * fixtypo in test section * fix openmpi pinning (#6990) * Version 2.12.0 of Nest based on build scripts from version 2.14.0 incl. new OpenMPI pinning. (#6995) * htsfilter recipe (#6994) * add new recipe for bioconductor package affyPLM (#6996) * add new recipe for bioconductor package GEOmetadb (#6997) * Recipe for scan_indel (#6983) * Initial commit for Scan Indel * Making ScanIndel tests work * Removing old sed statements * Skipping OSX Tests * Removing python pinning * added watchdog WMS recipe (#6978) Added Watchdog WMS recipe (https://github.com/klugem/watchdog/) * fix license * remove skip * Add IsoformSwitchAnalyzeR and dependencies. (#7009) * Add bioconductor-isoformswitchanalyzer. * Add bioconductor-drimseq. * Update meta.yaml (#7005) * Add bioconductor-bsseq. (#7011) * Ont tombo (#7007) * Added ont-tombo bioconda recipe. * Added fix to setup_py_install_args failed test. * Changed name from tombo to ont-tombo for listing on bioconda * tassel: use git_url for old versions (#7015) * tassel: re-order sections * tassel 3.0.174, 4.3.15: use git_url/git_rev * Update bedtools to 2.27.0. (#7020) * updated picrust to v1.1.3 (#7013) * fastqc: add version 0.11.2 (#6992) * fastqc: add version 0.11.2 using openjdk * Rebuilding raxml 8.2.4 (#7022) * New recipe: reaper (#7021) * New recipe: reaper * reaper : replace hyphen * reaper: zlib * reaper: fix test * reaper: fix test * Deleted tombo recipe. Two versions of the package were added with #6976 and #7007 with the names tombo and ont-tombo respectively. The pacakge has been added to pypi as ont-tombo, so to keep the unified naming scheme the tombo recipe should be removed. This should be followed by removal/merger of the tombo package in the channel as noted by @bgruening in #7007. (#7019) * mykatlas: patch --min_variant_conf default value (#7017) Looks good! * Pneumocat Recipe (#7006) * Recipe for pneumocat * Adding skip * Add new recipe for CRAN package SMVar (#7003) * Add new recipe for CRAN package SMVar * Clean up win specific stuff * Add new recipe for CRAN package metaRNASeq (#7002) * Add new recipe for CRAN package metaRNASeq * Remove unnecessary comments * Clean up win specific lines * Wachdog test update (#7001) * added watchdog WMS recipe * Update meta.yaml travis macos test fails with /Users/travis/.travis/job_stages: line 57: shell_session_update: command not found ? * changed sed call for macos * sed call in build not longer required * hashsum changed for build * sed call * use non-default http port * Update build.sh make sed mac compatible * Update run_test.sh make sed mac compatible * timeout replacement * timeout replacement II * new watchdog version * coreutils dependency * changed path... * added testing also to meta.ymal * sed problem revisited * ... * Poretools patch (#7018) * Fixes for poretools conda package. - Use the Agg backend for matplotlib if saving to file. This eliminates the error message when the DISPLAY environment variable is unset, e.g. on a headless system. - Add an option to output timestamps in UTC, in order to have reproducible output regardless of timezones. - Inadvertently strip trailing whitespace on some lines. * Fix poretools linting. * Additional fixes for poretools headless. * Samtools 0.1.12 adding misc. tools (#6991) * samtools 0.1.12: add missing misc tools - including tests and updated build number * samtools 0.1.12: move some tests to run_test.sh * Add go-perl (#7014) * initial recipe * indentation error * indentation error * version * license unknown * Add bioconductor-flowbeads. (#7029) * Update: dx-cwl, bcbio, bcbio-vm (#7034) - dx-cwl: avoid small machine partitioning for short jobs runs - bcbio, bcbio-vm: Initial work on RNA-seq support and improved remote retrieval of file references * rust-bio-tools 0.1.3 (#7000) * rust-bio-tools 0.1.3 * Pin zlib. * Remove skip. * Pin gcc, to avoid missing lib. * Skip osx. * updated ococo version (#7027) * updated ococo version * update sha256sum * Fixes that somehow evaded #7018 (#7039) * Fixes for poretools conda package. - Use the Agg backend for matplotlib if saving to file. This eliminates the error message when the DISPLAY environment variable is unset, e.g. on a headless system. - Add an option to output timestamps in UTC, in order to have reproducible output regardless of timezones. - Inadvertently strip trailing whitespace on some lines. * Fix poretools linting. * Additional fixes for poretools headless. * Additional fixes that somehow failed to make it into the previous pull request. * Updated intervene to v0.5.9 (#7036) * Update recipe to 2.5.1 (replaces #7023) (#7030) * Update recipe to 2.5.1 * Test trinity build on OSX * Re-disable OSX build because of error * Add new recipe for CRAN package metaMA (#7028) * Add new recipe for CRAN package metaMA * remove unnecessary comments * correction for limma package * add license_file * Update meta.yaml * remove file again * peptide-shaker update to version 1.16.15 (#7040) * peptide-shaker update to version 1.16.15 * change checksum as well * Add panX (#7010) * Add panX * Add patch for treetime import * Update meta.yaml * add featureCounts as run-dep (#7032) * add featureCounts as run-dep * Replace featureCounts dependency with subread * Update mixOmics to 6.3.1. (#7041) * Bump bbmap to 37.75 (#7042) * Bump snp-pipeline to version 1.0.1 (#7016) * Bump snp-pipeline 1.0.1 * Fix linting errors. * Add simple version tests. * snp-pipeline: update tests for v1.0.1 * snp-pipeline 1.0.1 : update build requirements, entry points, comments. * Update ngless v0.6.1 (#7043) * Update NGLess to 0.6.1 * Use new --check-install command in tests * Add r-icluster. (#7044) * Added recipe for r-purbayes (#7037) * Added recipe for r-purbayes * Removed license_file entries * Removed extra section * Removed Windows bat file * Add MALDIrppa. (#7046) * Watchdog RC Update (#7038) Updated to Watchdog version 1.2.5 (RC) * Watchdog: Testing fails caused by too small timeout ? (#7050) Watchdog RC Update II * Fix missing import in poretools 0.6.1a1 patch. (#7052) * Amend Ragout (#7054) * [WIP] added recipe, trouble building * [WIP] need to build add python-newick * facepalm, I added the wrong newick recipe (the one from pypi, not the one from the docs ) * incorportate proper newick parsing prereqs * removed extraneous recipes * build 1 -- set when building sebelia * add Sibelia test * add libgcc, builds locally * Move libgcc to run deps. * add sibelia to reqs, remove custom sibelia build script from build.sh * Update Build to include executables from lib (#6963) See comments; the make step creates executables that need to end up in the PATH so ragout can find them later. * pin networkx version to 1.8 * Add recipe to go-perl (#7062) * initial recipe * indentation error * indentation error * version * license unknown * license * release * Final poretools patch (#7053) Fixes for poretools conda package. * Do not increment build number. * Build 4 was broken, and removed by maintainers. * SearchGUI also available for Macs (#7065) SearchGUI is also available for Mac computers. * daligner update (#7058) * Updated Singularity from version 2.4 to 2.4.2 (#7051) * Add recipe for RepEnrich (#7059) * Update: dx-cwl, bcbio-nextgen (#7064) - dx-cwl: Avoid additional slower AWS instance types - bcbio-nextgen: CWL build fixes * Updated minimap2 and mappy to v2.6 (#7066) * Update minvar to version 2 (#7063) * Update to v2.0 * Remove old version * Failing linting setup_py_install_args * Update md5 * Fixed typo * Include build dependencies in setup.py into meta.yaml * bump to build 2 (#7069) * picard: 1.56 with ant bcel dependency from galaxyproject depot and 'test' within wrapper (#7048) * Rebuild rsem with latest r-base (#7075) - 1.3.0 archive has been updated on GitHub (bad practice!) - Remove from build-fail-blacklist - Pin zlib - Fix test command * dazz_db updated version (#7057) * dazz_db updated version * Adding pinning and extra tests * dascrubber update (#7071) * dascrubber update * Fix typo * Small fixes to meta.yaml * Bump pyBigWig to 0.3.8 (#7076) * Haystack (#7070) * patch fix * update to 0.5.3 * Update to 0.2.7 (#7073) Update to 0.2.7 * Ribocode (#7081) * add ribocode * small modify * remove build.sh * small changes. * update to v1.2.7 * Add SICER recipe (#7068) * first version of recipe * unpin libgfortran * add proper tests * try without libgfortran * confirmed libgfortran not required * Add recipe seq-seq-pan (#7077) * seqseqpan recipe * build skipping for seqseqpan recipe * command order in build script * Changing build skip. * Fixed problem with build skip. * snakemake no-hooks. * Stable archive link. * Added another test. * Move python restriction to build section. * updated version dextractor (#7056) * updated version * Fix licence_file and small fixes * damasker a new tool (#7072) * damasker a new tool * Fixing typo in test * Update R MutationalPatterns (#7049) * Upgrade r-mutationalpatterns to 1.1.0 * Add bioconductor-mutationalpatterns instead of r-bioconductor r-bioconductor pulls from GitHub which provides an outdated version 1.1.0: https://github.com/UMCUGenetics/MutationalPatterns/releases Using bioconductor instead whch is 1.4.1 * r-mutationalpatterns: use bioconductor release, update to 1.4.1 * MutationalPatterns: add sha256 * MutationalPatterns recipe: fix download link * MutationalPatterns: remove seds from build.sh No longer needed as R is up to date in bioconda * MutationalPatterns: remove r-mutationalpatterns keeping only bioconductor-mutationalpatterns * Update recipe seq-seq-pan. (#7084) * Add seq-seq-pan-genomedescription to build and test. * Fix md5sum. * Bumping build number. * Update: ipython-cluster-helper, dx-cwl, bcbio (#7085) - ipython-cluster-helper: fix for accessing user home directories - dx-cwl: fix for intermediate staged files with same name - bcbio: fix for BAM only project runs * Moff bump to v1.2 (#7083) * moff recipe * remove explicit python * add moff config file to /bin. This is weird, but must be in same dir as moff.py and other commands * add txic to /bin * remove softlinks to txic and properties * use templating * bump to 1.2 * change mono version, add simplejson * allow any version of mono * change versioning * remove fn * Updated bedtools to 2.27.1. (#7088) * Added first recepit for gtrellis package (#7087) * update to 0.9.0 (#7093) * Feature/perl moose (#7004) rebuilding some perl-moose recipes for osx * Updated version of ont-tombo (#7094) * Feature/perl moose rebuild (#7095) make master branch happy * Update Picard to 2.16.0. (#7097) * Update wdltool to version 0.14 (#7091) * Nanopolish 0.8.5 (#7096) * nanopolish 0.8.5 update * updates for dependencies and changes to nanopolish Makefile * 0.6.4 fast5 * update fast5 archive * pin hdf5 * filename * update patch * update patch * need htslib 1.4 * update link flags * link libs * deps * libbzip2 * libbzip2 * remove versioned fast5 * add libcrypto * Patch srst2 versions 0.1.6 and 0.2.0 (#6957) * added new patch file to fix bug related to parse out sample name from filepath * updated build script to be bioconda utils lint safe * patch for latest version of srst2 * increment build # * fixed patch file * remove setuptools patch * add setuptools patch again * removed single quotes with double for failing tests * removed patch for latest version of srst2. * srst2: reinstate patch * srst2: fix patch * srst2: use double quotes in test commands * srst2: bump build number * srst2 0.1.6: fix version * 01 batch of updated Bioconductor data pacakges (#7092) * Update minvar (#7079) * Update to v2.0 * Remove old version * Failing linting setup_py_install_args * Update md5 * Fixed typo * Include build dependencies in setup.py into meta.yaml * Rebuild as errors appeared in runtime * Add break-point-inspector (#7061) * Add break-point-inspector recipe * break-point-inspector recipe: fix test for sh shell * break-point-inspector recipe: fix test - add contents to test.bam * break-point-inspector: move tests to run_test.sh * Add bioconductor-mirnatap.db. (#7100) * Update bioconductor-genomeinfodbdata to 1.0.0. (#7102) * Add bioconductor-baalchip. (#7101) * pyBigWig-0.3.9 (#7103) * SARTools 1.6.0 (#7104) * updating repeat modeler to 1.0.11 (#7090) * updating repeatmodeler * updating repeatmodeler * updating repeatmodeler * Update meta.yaml * update code (#7109) * pin zlib for rmblast (#7111) * pin zlib for rmblast * Update meta.yaml * Update meta.yaml * Update Bioc data packages. https://github.com/bioconda/bioconda-utils/issues/235 * Manually bump GenomeInfoDbData build number b/c it's Cargo Port URL had already been fixed. --- .travis.yml | 6 +- build-fail-blacklist | 1 - recipes/abyss/1.5.2/build.sh | 24 ++- recipes/abyss/1.5.2/meta.yaml | 16 +- .../osx-std_string_length-no-export.patch | 25 ++++ recipes/abyss/1.9.0/build.sh | 20 ++- recipes/abyss/1.9.0/meta.yaml | 16 +- .../osx-std_string_length-no-export.patch | 25 ++++ recipes/abyss/2.0.2-k128/build.sh | 17 --- recipes/abyss/2.0.2-k128/create-wrapper.sh | 19 --- recipes/abyss/2.0.2-k128/meta.yaml | 52 ------- recipes/abyss/build.sh | 20 ++- recipes/abyss/meta.yaml | 7 +- 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b/.travis.yml index 1f434c987c78b..40b7d0afc6348 100644 --- a/.travis.yml +++ b/.travis.yml @@ -4,6 +4,8 @@ sudo: required services: - docker +osx_image: xcode7.3 + before_install: - set -e - | @@ -19,11 +21,11 @@ jobs: include: # in forks, master and bulk, we run osx and linux in parallel on each push - stage: Linux+macOS - if: (type = push) AND ((branch IN (master, bulk)) OR (fork = true)) + if: (type = push) AND ((branch IN (master, bulk)) OR (repo != bioconda/bioconda-recipes)) os: linux script: scripts/travis-run.sh - os: osx - if: (type = push) AND ((branch IN (master, bulk)) OR (fork = true)) + if: (type = push) AND ((branch IN (master, bulk)) OR (repo != bioconda/bioconda-recipes)) script: scripts/travis-run.sh # in pull requests, we first run linux and only if that succeeds, we run osx - stage: Linux diff --git a/build-fail-blacklist b/build-fail-blacklist index 1d544190efec2..6d67dbec97966 100644 --- a/build-fail-blacklist +++ b/build-fail-blacklist @@ -11,7 +11,6 @@ recipes/mothur/1.36.1 recipes/clever-toolkit recipes/quast recipes/transcomb -recipes/rsem recipes/metaprob # boost problems diff --git a/recipes/abyss/1.5.2/build.sh b/recipes/abyss/1.5.2/build.sh index c0241d4fd5625..21f968bf8ea39 100644 --- a/recipes/abyss/1.5.2/build.sh +++ b/recipes/abyss/1.5.2/build.sh @@ -1,15 +1,23 @@ #!/bin/bash -if [[ $(uname) == "Darwin" ]]; then - echo "Configuring for OSX..." - export CPPFLAGS="${CPPFLAGS} -I$PREFIX/include -I$PREFIX/include/boost --stdlib=libstdc++" - export CXXFLAGS="${CXXFLAGS} --stdlib=libstdc++" -else - echo "Configuring for Linux..." - export CPPFLAGS="-I$PREFIX/include" +if [[ "$(uname)" == Darwin ]]; then + # Fix for install_name_tool error: + # error: install_name_tool: changing install names or rpaths can't be + # redone for: $PREFIX/bin/abyss-overlap (for architecture x86_64) because + # larger updated load commands do not fit (the program must be relinked, + # and you may need to use -headerpad or -headerpad_max_install_names) + export LDFLAGS="$LDFLAGS -headerpad_max_install_names" fi -./configure --prefix=$PREFIX --with-boost=$PREFIX/include --with-mpi=$PREFIX/include --enable-maxk=96 +SPARSE_HASH_INCLUDE="-I$PREFIX/include" +CPPFLAGS="$CPPFLAGS $SPARSE_HASH_INCLUDE" + +BOOST_INCLUDE="$PREFIX/include" +./configure \ + --prefix="$PREFIX" \ + --with-boost="$BOOST_INCLUDE" \ + --with-mpi="$PREFIX" \ + --with-sparsehash="$PREFIX" make AM_CXXFLAGS=-Wall make install diff --git a/recipes/abyss/1.5.2/meta.yaml b/recipes/abyss/1.5.2/meta.yaml index c72192dda79a3..1a70fabbfd74e 100644 --- a/recipes/abyss/1.5.2/meta.yaml +++ b/recipes/abyss/1.5.2/meta.yaml @@ -1,24 +1,26 @@ ---- +{% set version = "1.5.2" %} + package: name: abyss - version: "1.5.2" + version: {{ version }} build: - skip: True # [osx] - number: 3 + number: 4 string: boost1.61_{{PKG_BUILDNUM}} source: - fn: abyss-1.5.2.tar.gz - url: https://github.com/bcgsc/abyss/releases/download/1.5.2/abyss-1.5.2.tar.gz + fn: abyss-{{ version }}.tar.gz + url: https://github.com/bcgsc/abyss/releases/download/{{ version }}/abyss-{{ version }}.tar.gz md5: 10d6d72d1a915e618d41a5cbbcf2364c + patches: + - osx-std_string_length-no-export.patch # can be removed for "abyss >2.0.2" requirements: build: - gcc # [not osx] - llvm # [osx] - boost 1.61.0 - - google-sparsehash + - sparsehash - sqlite - openmpi diff --git a/recipes/abyss/1.5.2/osx-std_string_length-no-export.patch b/recipes/abyss/1.5.2/osx-std_string_length-no-export.patch new file mode 100644 index 0000000000000..0d0f8e1b11eec --- /dev/null +++ b/recipes/abyss/1.5.2/osx-std_string_length-no-export.patch @@ -0,0 +1,25 @@ +--- MergePaths/PathConsensus.cpp.orig 2017-11-22 21:12:27.777282838 +0100 ++++ MergePaths/PathConsensus.cpp 2017-11-22 21:13:44.742889962 +0100 +@@ -507,6 +507,13 @@ + return path; + } + ++template ++struct GetLength { ++ size_t operator()(const Seq& sequence) { ++ return sequence.length(); ++ } ++}; ++ + /* Resolve ambiguous region using multiple alignment of all paths in + * `solutions'. + */ +@@ -589,7 +596,7 @@ + + vector lengths(amb_seqs.size()); + transform(amb_seqs.begin(), amb_seqs.end(), lengths.begin(), +- mem_fun_ref(&string::length)); ++ GetLength()); + unsigned minLength = *min_element(lengths.begin(), lengths.end()); + unsigned maxLength = *max_element(lengths.begin(), lengths.end()); + float lengthRatio = (float)minLength / maxLength; diff --git a/recipes/abyss/1.9.0/build.sh b/recipes/abyss/1.9.0/build.sh index 108924b6b1471..f250e2d2c3e5a 100644 --- a/recipes/abyss/1.9.0/build.sh +++ b/recipes/abyss/1.9.0/build.sh @@ -1,15 +1,19 @@ #!/bin/bash -if [[ $(uname) == "Darwin" ]]; then - echo "Configuring for OSX..." - export CPPFLAGS="${CPPFLAGS} -I$PREFIX/include -I$PREFIX/include/boost --stdlib=libstdc++" - export CXXFLAGS="${CXXFLAGS} --stdlib=libstdc++" - else - echo "Configuring for Linux..." - export CPPFLAGS="-I$PREFIX/include" +if [[ "$(uname)" == Darwin ]]; then + # Fix for install_name_tool error: + # error: install_name_tool: changing install names or rpaths can't be + # redone for: $PREFIX/bin/abyss-overlap (for architecture x86_64) because + # larger updated load commands do not fit (the program must be relinked, + # and you may need to use -headerpad or -headerpad_max_install_names) + export LDFLAGS="$LDFLAGS -headerpad_max_install_names" fi -./configure --prefix=$PREFIX --with-boost=$PREFIX/include --with-mpi=$PREFIX/include --enable-maxk=96 +./configure \ + --prefix="$PREFIX" \ + --with-boost="$PREFIX" \ + --with-mpi="$PREFIX" \ + --with-sparsehash="$PREFIX" make AM_CXXFLAGS=-Wall make install diff --git a/recipes/abyss/1.9.0/meta.yaml b/recipes/abyss/1.9.0/meta.yaml index da3e8ff04ede0..953af900b2a88 100644 --- a/recipes/abyss/1.9.0/meta.yaml +++ b/recipes/abyss/1.9.0/meta.yaml @@ -1,23 +1,27 @@ +{% set name = "abyss" %} +{% set version = "1.9.0" %} + package: name: abyss - version: "1.9.0" + version: {{ version }} build: - skip: True # [osx] - number: 5 + number: 6 string: boost1.61_{{PKG_BUILDNUM}} source: - fn: abyss-1.9.0.tar.gz - url: https://github.com/bcgsc/abyss/releases/download/1.9.0/abyss-1.9.0.tar.gz + fn: abyss-{{ version }}.tar.gz + url: https://github.com/bcgsc/abyss/releases/download/{{ version }}/abyss-{{ version }}.tar.gz md5: 7b1b9f060dbae6c7fe815b1e50487c83 + patches: + - osx-std_string_length-no-export.patch # can be removed for "abyss >2.0.2" requirements: build: - gcc # [not osx] - llvm # [osx] - boost 1.61.0 - - google-sparsehash + - sparsehash - sqlite - openmpi diff --git a/recipes/abyss/1.9.0/osx-std_string_length-no-export.patch b/recipes/abyss/1.9.0/osx-std_string_length-no-export.patch new file mode 100644 index 0000000000000..a4412b439c9ac --- /dev/null +++ b/recipes/abyss/1.9.0/osx-std_string_length-no-export.patch @@ -0,0 +1,25 @@ +--- MergePaths/PathConsensus.cpp.orig 2017-11-22 21:14:18.752421900 +0100 ++++ MergePaths/PathConsensus.cpp 2017-11-22 22:06:07.003253446 +0100 +@@ -533,6 +533,13 @@ + return path; + } + ++template ++struct GetLength { ++ size_t operator()(const Seq& sequence) { ++ return sequence.length(); ++ } ++}; ++ + /* Resolve ambiguous region using multiple alignment of all paths in + * `solutions'. + */ +@@ -615,7 +622,7 @@ + + vector lengths(amb_seqs.size()); + transform(amb_seqs.begin(), amb_seqs.end(), lengths.begin(), +- mem_fun_ref(&string::length)); ++ GetLength()); + unsigned minLength = *min_element(lengths.begin(), lengths.end()); + unsigned maxLength = *max_element(lengths.begin(), lengths.end()); + float lengthRatio = (float)minLength / maxLength; diff --git a/recipes/abyss/2.0.2-k128/build.sh b/recipes/abyss/2.0.2-k128/build.sh deleted file mode 100644 index cb780f3b9a80c..0000000000000 --- a/recipes/abyss/2.0.2-k128/build.sh +++ /dev/null @@ -1,17 +0,0 @@ -#!/bin/bash - -if [[ $(uname) == "Darwin" ]]; then - echo "Configuring for OSX..." - export CPPFLAGS="${CPPFLAGS} -I$PREFIX/include -I$PREFIX/include/boost --stdlib=libstdc++" - export CXXFLAGS="${CXXFLAGS} --stdlib=libstdc++" -else - echo "Configuring for Linux..." - export CPPFLAGS="-I$PREFIX/include" -fi - -./configure --prefix=$PREFIX --with-boost=$PREFIX/include --with-mpi=$PREFIX/include --enable-maxk=128 -make AM_CXXFLAGS=-Wall -make install - -$RECIPE_DIR/create-wrapper.sh "$PREFIX/bin/abyss-pe" "$PREFIX/bin/abyss-pe.Makefile" -$RECIPE_DIR/create-wrapper.sh "$PREFIX/bin/abyss-bloom-dist.mk" "$PREFIX/bin/abyss-bloom-dist.mk.Makefile" diff --git a/recipes/abyss/2.0.2-k128/create-wrapper.sh b/recipes/abyss/2.0.2-k128/create-wrapper.sh deleted file mode 100755 index ba010737917ed..0000000000000 --- a/recipes/abyss/2.0.2-k128/create-wrapper.sh +++ /dev/null @@ -1,19 +0,0 @@ -#!/bin/bash - -# Usage: create-wrapper.sh -# -# - moves to -# - creates wrapper -# - takes original shebang line -# - removes prefix #!/bin or #!/usr/bin -# - uses resulting command CMD for a call to `exec CMD "$@"` - -test ! -e "$2" -mv "$1" "$2" -chmod a-x "$2" - -cat >"$1" <2.0.2" requirements: build: - gcc # [not osx] - llvm # [osx] - boost {{CONDA_BOOST}}* - - google-sparsehash + - sparsehash - sqlite - openmpi diff --git a/recipes/abyss/osx-std_string_length-no-export.patch b/recipes/abyss/osx-std_string_length-no-export.patch new file mode 100644 index 0000000000000..fb61f126d0ea7 --- /dev/null +++ b/recipes/abyss/osx-std_string_length-no-export.patch @@ -0,0 +1,25 @@ +--- MergePaths/PathConsensus.cpp.orig 2017-11-22 15:21:26.278897870 +0100 ++++ MergePaths/PathConsensus.cpp 2017-11-22 15:21:32.858809457 +0100 +@@ -533,6 +533,13 @@ + return path; + } + ++template ++struct GetLength { ++ size_t operator()(const Seq& sequence) { ++ return sequence.length(); ++ } ++}; ++ + /* Resolve ambiguous region using multiple alignment of all paths in + * `solutions'. + */ +@@ -615,7 +622,7 @@ + + vector lengths(amb_seqs.size()); + transform(amb_seqs.begin(), amb_seqs.end(), lengths.begin(), +- mem_fun_ref(&string::length)); ++ GetLength()); + unsigned minLength = *min_element(lengths.begin(), lengths.end()); + unsigned maxLength = *max_element(lengths.begin(), lengths.end()); + float lengthRatio = (float)minLength / maxLength; diff --git a/recipes/asn2gb/build.sh b/recipes/asn2gb/build.sh new file mode 100644 index 0000000000000..1ce0757422837 --- /dev/null +++ b/recipes/asn2gb/build.sh @@ -0,0 +1,8 @@ +#!/bin/bash +set -eu -o pipefail + +gunzip -v *.gz +mkdir -p "$PREFIX/bin" +cp asn2gb* $PREFIX/bin/asn2gb +chmod +x $PREFIX/bin/asn2gb + diff --git a/recipes/asn2gb/meta.yaml b/recipes/asn2gb/meta.yaml new file mode 100644 index 0000000000000..1e41eb035a0c3 --- /dev/null +++ b/recipes/asn2gb/meta.yaml @@ -0,0 +1,29 @@ +package: + name: asn2gb + version: "18.2" + +about: + home: https://www.ncbi.nlm.nih.gov/IEB/ToolBox/C_DOC/lxr/source/doc/asn2gb.txt + license: Public Domain + summary: asn2gb converts ASN1 format sequence records to Genbank format + +source: + fn: asn2gb_18.2_darwin_x64.gz # [osx] + url: https://depot.galaxyproject.org/software/asn2gb/asn2gb_18.2_darwin_x64.gz # [osx] + sha256: e2751199333312c43ac46eece268b11ce53bb34acb576f98f00c4962015fffd4 # [osx] + fn: asn2gb_18.2_linux_x64.gz # [linux] + url: https://depot.galaxyproject.org/software/asn2gb/asn2gb_18.2_linux_x64.gz # [linux] + sha256: 4b6ac3831061bc8f8c8adb011fe58c8741402a9c21c95af395aa98154c9ab775 # [linux] + +build: + number: 0 + +requirements: + run: + - libidn11 # [linux] + - zlib {{ CONDA_ZLIB }}* # [linux] + +test: + commands: + - asn2gb --help 2>&1 | grep argument + diff --git a/recipes/bbmap/meta.yaml b/recipes/bbmap/meta.yaml index 83a14e701d339..804b5a5827307 100644 --- a/recipes/bbmap/meta.yaml +++ b/recipes/bbmap/meta.yaml @@ -1,6 +1,6 @@ {% set name = "BBMap" %} -{% set version = "37.66" %} -{% set sha256 = "829b5babef5d1d896a3359520de3e4ff7bec51b8094f26e7aa32da336d8f12b3" %} +{% set version = "37.75" %} +{% set sha256 = "8f074a785a676dc73177832d045bec9e6cfb262a1d490f9cb96f9aa6c354788c" %} about: home: 'https://sourceforge.net/projects/bbmap' diff --git a/recipes/bcbio-nextgen-vm/meta.yaml b/recipes/bcbio-nextgen-vm/meta.yaml index 32d659e42c25b..477f21c049f36 100644 --- a/recipes/bcbio-nextgen-vm/meta.yaml +++ b/recipes/bcbio-nextgen-vm/meta.yaml @@ -3,13 +3,13 @@ package: version: '0.1.0a' build: - number: 110 + number: 112 skip: True # [not py27] source: - fn: bcbio-nextgen-vm-99609ed.tar.gz - url: https://github.com/chapmanb/bcbio-nextgen-vm/archive/99609ed.tar.gz - md5: 369d719e71a5f295e27cdcb9ebad1e79 + fn: bcbio-nextgen-vm-4bad653.tar.gz + url: https://github.com/chapmanb/bcbio-nextgen-vm/archive/4bad653.tar.gz + md5: 73e7e2e5c8204906b1877c8826905b55 requirements: build: diff --git a/recipes/bcbio-nextgen/meta.yaml b/recipes/bcbio-nextgen/meta.yaml index 70446fb5b5de4..5676e8c175e82 100644 --- a/recipes/bcbio-nextgen/meta.yaml +++ b/recipes/bcbio-nextgen/meta.yaml @@ -3,15 +3,15 @@ package: version: '1.0.7a0' build: - number: 0 + number: 4 skip: True # [not py27] source: #fn: bcbio-nextgen-1.0.6.tar.gz #url: https://pypi.io/packages/source/b/bcbio-nextgen/bcbio-nextgen-1.0.6.tar.gz - fn: bcbio-nextgen-2b4944b.tar.gz - url: https://github.com/chapmanb/bcbio-nextgen/archive/2b4944b.tar.gz - md5: 2c917ce1a8666aded2bf44423e64a449 + fn: bcbio-nextgen-cfe27d7.tar.gz + url: https://github.com/chapmanb/bcbio-nextgen/archive/cfe27d7.tar.gz + md5: 497dc56aefb6b8cf0f5dda736cf47641 requirements: build: diff --git a/recipes/bedops/meta.yaml b/recipes/bedops/meta.yaml index 0f3a002837e98..95a3e2a534052 100644 --- a/recipes/bedops/meta.yaml +++ b/recipes/bedops/meta.yaml @@ -7,11 +7,11 @@ about: summary: High-performance genomic feature operations. package: name: bedops - version: 2.4.27 + version: 2.4.30 source: - url: https://github.com/bedops/bedops/archive/v2.4.27.tar.gz - fn: bedops-2.4.27.tar.gz - sha256: 23a4e1ccae608a80f1cda99e24b7c1a314914adb2ff098753f5aac143746569d + url: https://github.com/bedops/bedops/archive/v2.4.30.tar.gz + fn: bedops-2.4.30.tar.gz + sha256: 218e0e367aa79747b2f90341d640776eea17befc0fdc35b0cec3c6184098d462 requirements: build: diff --git a/recipes/bedtools/2.27.0/build.sh b/recipes/bedtools/2.27.0/build.sh new file mode 100644 index 0000000000000..88a14a2ff40fa --- /dev/null +++ b/recipes/bedtools/2.27.0/build.sh @@ -0,0 +1,7 @@ +#!/bin/sh + +export CFLAGS="-I$PREFIX/include" +export LDFLAGS="-L$PREFIX/lib" +export CPATH=${PREFIX}/include + +make install prefix=$PREFIX diff --git a/recipes/bedtools/2.27.0/meta.yaml b/recipes/bedtools/2.27.0/meta.yaml new file mode 100644 index 0000000000000..7ee16bc62753a --- /dev/null +++ b/recipes/bedtools/2.27.0/meta.yaml @@ -0,0 +1,33 @@ +{% set name = "bedtools" %} +{% set version = "2.27.0" %} + +package: + name: {{ name }} + version: {{ version }} + +source: + fn: {{ name }}-{{ version }}.tar.gz + url: https://github.com/arq5x/bedtools2/releases/download/v{{ version }}/bedtools-{{ version }}.tar.gz + sha256: e4f0e5616d04ba5ac09c36dec989b1236a5712e67d0b6874ff5e144d7ed4ce60 + +build: + number: 0 + +requirements: + build: + - gcc # [linux] + - llvm # [osx] + - zlib {{ CONDA_ZLIB }}* + run: + - zlib {{ CONDA_ZLIB }}* + - libgcc # [linux] + +test: + commands: + - bedtools + +about: + home: http://bedtools.readthedocs.org/ + license: GPL v2 + summary: A powerful toolset for genome arithmetic + diff --git a/recipes/bedtools/2.27.1/build.sh b/recipes/bedtools/2.27.1/build.sh new file mode 100644 index 0000000000000..88a14a2ff40fa --- /dev/null +++ b/recipes/bedtools/2.27.1/build.sh @@ -0,0 +1,7 @@ +#!/bin/sh + +export CFLAGS="-I$PREFIX/include" +export LDFLAGS="-L$PREFIX/lib" +export CPATH=${PREFIX}/include + +make install prefix=$PREFIX diff --git a/recipes/bedtools/2.27.1/meta.yaml b/recipes/bedtools/2.27.1/meta.yaml new file mode 100644 index 0000000000000..846cbad283ae6 --- /dev/null +++ b/recipes/bedtools/2.27.1/meta.yaml @@ -0,0 +1,32 @@ +{% set name = "bedtools" %} +{% set version = "2.27.1" %} + +package: + name: {{ name }} + version: {{ version }} + +source: + fn: {{ name }}-{{ version }}.tar.gz + url: https://github.com/arq5x/bedtools2/releases/download/v{{ version }}/bedtools-{{ version }}.tar.gz + sha256: c8c2acbaf3f9cb92dcf8e5cd59af6b31ae9c4598efb786ba6c84f66ca72fafd9 + +build: + number: 0 + +requirements: + build: + - gcc # [linux] + - llvm # [osx] + - zlib {{ CONDA_ZLIB }}* + run: + - zlib {{ CONDA_ZLIB }}* + - libgcc # [linux] + +test: + commands: + - bedtools + +about: + home: http://bedtools.readthedocs.org/ + license: GPL v2 + summary: A powerful toolset for genome arithmetic diff --git a/recipes/binsanity/meta.yaml b/recipes/binsanity/meta.yaml index d650525286e08..798d68dc677b1 100644 --- a/recipes/binsanity/meta.yaml +++ b/recipes/binsanity/meta.yaml @@ -8,7 +8,7 @@ source: md5: 794de7b2b4349880511381b0407fd7ff build: - number: 0 + number: 1 skip: True # [not py27] requirements: @@ -28,6 +28,7 @@ requirements: - scipy >=0.13.0 - checkm-genome - scikit-learn + - subread test: commands: diff --git a/recipes/bioconductor-affydata/meta.yaml b/recipes/bioconductor-affydata/meta.yaml index 2acd2864e4c19..e1a46f0adb1de 100644 --- a/recipes/bioconductor-affydata/meta.yaml +++ b/recipes/bioconductor-affydata/meta.yaml @@ -9,10 +9,10 @@ source: fn: '{{ name }}_{{ version }}.tar.gz' url: - 'http://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/{{ name }}/{{ name }}_{{ version }}_src_all.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' sha256: 3d63aed8f6b9a0f5a9cd07773bacccaf7a9b67f111b8e6b5e589b46126c42d66 build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ diff --git a/recipes/bioconductor-affydata/post-link.sh b/recipes/bioconductor-affydata/post-link.sh index e5fb8e3cd6246..0c3bdab3c30c7 100644 --- a/recipes/bioconductor-affydata/post-link.sh +++ b/recipes/bioconductor-affydata/post-link.sh @@ -2,9 +2,9 @@ FN="affydata_1.26.0.tar.gz" URLS=( "http://bioconductor.org/packages/3.6/data/experiment/src/contrib/affydata_1.26.0.tar.gz" - "https://depot.galaxyproject.org/software/affydata/affydata_1.26.0_src_all.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-affydata/bioconductor-affydata_1.26.0_src_all.tar.gz" ) - MD5="32d863de539466d38f567ac5289ee873" +MD5="32d863de539466d38f567ac5289ee873" # Use a staging area in the conda dir rather than temp dirs, both to avoid # permission issues as well as to have things downloaded in a predictable @@ -20,7 +20,7 @@ for URL in ${URLS[@]}; do # Platform-specific md5sum checks. if [[ $(uname -s) == "Linux" ]]; then - if [[ $(md5sum -c <<<"$MD5 $TARBALL") ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then SUCCESS=1 break fi @@ -40,5 +40,6 @@ if [[ $SUCCESS != 1 ]]; then fi # Install and clean up -R CMD INSTALL --build $TARBALL -rm $TARBALL \ No newline at end of file +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING \ No newline at end of file diff --git a/recipes/bioconductor-affydata/pre-unlink.sh b/recipes/bioconductor-affydata/pre-unlink.sh new file mode 100644 index 0000000000000..c721592cb0a65 --- /dev/null +++ b/recipes/bioconductor-affydata/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ affydata diff --git a/recipes/bioconductor-affyplm/build.sh b/recipes/bioconductor-affyplm/build.sh new file mode 100644 index 0000000000000..da43ce2168312 --- /dev/null +++ b/recipes/bioconductor-affyplm/build.sh @@ -0,0 +1,4 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-affyplm/meta.yaml b/recipes/bioconductor-affyplm/meta.yaml new file mode 100644 index 0000000000000..f08524a75e92a --- /dev/null +++ b/recipes/bioconductor-affyplm/meta.yaml @@ -0,0 +1,42 @@ +{% set version = "1.54.0" %} +{% set name = "affyPLM" %} +{% set bioc = "3.6" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + fn: '{{ name }}_{{ version }}.tar.gz' + url: + - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/{{ name }}/{{ name }}_{{ version }}_src_all.tar.gz' + sha256: 081fae17b4b7a7cef6189a108e61f9e6ab4253ddccf345b9bf7ce2c6fae60712 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ +requirements: + build: + - 'bioconductor-affy >=1.11.0' + - 'bioconductor-biobase >=2.17.8' + - 'bioconductor-biocgenerics >=0.3.2' + - bioconductor-gcrma + - 'bioconductor-preprocesscore >=1.5.1' + - bioconductor-zlibbioc + - r-base + run: + - 'bioconductor-affy >=1.11.0' + - 'bioconductor-biobase >=2.17.8' + - 'bioconductor-biocgenerics >=0.3.2' + - bioconductor-gcrma + - 'bioconductor-preprocesscore >=1.5.1' + - bioconductor-zlibbioc + - r-base +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: 'GPL (>= 2)' + summary: 'A package that extends and improves the functionality of the base affy package. Routines that make heavy use of compiled code for speed. Central focus is on implementation of methods for fitting probe-level models and tools using these models. PLM based quality assessment tools.' diff --git a/recipes/bioconductor-all/meta.yaml b/recipes/bioconductor-all/meta.yaml index 40644aa125bf1..efd75a429ecb0 100644 --- a/recipes/bioconductor-all/meta.yaml +++ b/recipes/bioconductor-all/meta.yaml @@ -9,10 +9,10 @@ source: fn: '{{ name }}_{{ version }}.tar.gz' url: - 'http://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/{{ name }}/{{ name }}_{{ version }}_src_all.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_{{ name|lower }}.tar.gz' sha256: 5e487b68a15ea8aa83ae2cbd39b88fb41d9708f8e4c1e02efea9aade529ae3cf build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ diff --git a/recipes/bioconductor-all/post-link.sh b/recipes/bioconductor-all/post-link.sh index cf1c509465f7a..ac11be066b9bd 100644 --- a/recipes/bioconductor-all/post-link.sh +++ b/recipes/bioconductor-all/post-link.sh @@ -2,9 +2,9 @@ FN="ALL_1.20.0.tar.gz" URLS=( "http://bioconductor.org/packages/3.6/data/experiment/src/contrib/ALL_1.20.0.tar.gz" - "https://depot.galaxyproject.org/software/ALL/ALL_1.20.0_src_all.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-all/bioconductor-all_1.20.0_src_all.tar.gz" ) - MD5="07fe1649ae8facea40fe5e3137fd823f" +MD5="07fe1649ae8facea40fe5e3137fd823f" # Use a staging area in the conda dir rather than temp dirs, both to avoid # permission issues as well as to have things downloaded in a predictable @@ -20,7 +20,7 @@ for URL in ${URLS[@]}; do # Platform-specific md5sum checks. if [[ $(uname -s) == "Linux" ]]; then - if [[ $(md5sum -c <<<"$MD5 $TARBALL") ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then SUCCESS=1 break fi @@ -40,5 +40,6 @@ if [[ $SUCCESS != 1 ]]; then fi # Install and clean up -R CMD INSTALL --build $TARBALL -rm $TARBALL \ No newline at end of file +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING \ No newline at end of file diff --git a/recipes/bioconductor-all/pre-unlink.sh b/recipes/bioconductor-all/pre-unlink.sh new file mode 100644 index 0000000000000..1fd4130a6d3de --- /dev/null +++ b/recipes/bioconductor-all/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ ALL diff --git a/recipes/bioconductor-baalchip/build.sh b/recipes/bioconductor-baalchip/build.sh new file mode 100644 index 0000000000000..da43ce2168312 --- /dev/null +++ b/recipes/bioconductor-baalchip/build.sh @@ -0,0 +1,4 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-baalchip/meta.yaml b/recipes/bioconductor-baalchip/meta.yaml new file mode 100644 index 0000000000000..7a0c54f2bf572 --- /dev/null +++ b/recipes/bioconductor-baalchip/meta.yaml @@ -0,0 +1,59 @@ +{% set version = "1.4.0" %} +{% set name = "BaalChIP" %} +{% set bioc = "3.6" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' + +source: + fn: '{{ name }}_{{ version }}.tar.gz' + url: + - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/{{ name }}/{{ name }}_{{ version }}_src_all.tar.gz' + sha256: 0313e5862eadbb779a60dab93a6a8ca7d6d17c3f56b9ce33dd17a27016b753fd + +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + +requirements: + build: + - bioconductor-genomeinfodb + - bioconductor-genomicalignments + - bioconductor-genomicranges + - bioconductor-iranges + - bioconductor-rsamtools + - r-base + - r-coda + - r-doby + - r-doparallel + - r-foreach + - r-ggplot2 + - r-reshape2 + - r-scales + run: + - bioconductor-genomeinfodb + - bioconductor-genomicalignments + - bioconductor-genomicranges + - bioconductor-iranges + - bioconductor-rsamtools + - r-base + - r-coda + - r-doby + - r-doparallel + - r-foreach + - r-ggplot2 + - r-reshape2 + - r-scales + +test: + commands: + - '$R -e "library(''{{ name }}'')"' + +about: + home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'The package offers functions to process multiple ChIP-seq BAM files and detect allele-specific events. Computes allele counts at individual variants (SNPs/SNVs), implements extensive QC steps to remove problematic variants, and utilizes a bayesian framework to identify statistically significant allele- specific events. BaalChIP is able to account for copy number differences between the two alleles, a known phenotypical feature of cancer samples.' diff --git a/recipes/bioconductor-bladderbatch/meta.yaml b/recipes/bioconductor-bladderbatch/meta.yaml index d12186cd771d7..ff20010400d94 100644 --- a/recipes/bioconductor-bladderbatch/meta.yaml +++ b/recipes/bioconductor-bladderbatch/meta.yaml @@ -5,20 +5,17 @@ package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' - source: fn: '{{ name }}_{{ version }}.tar.gz' url: - 'http://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/{{ name }}/{{ name }}_{{ version }}_src_all.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' sha256: f68d9a7b57d20f88e97c306adc5f06a308d6d6890607736a4c2dfed6b7902ee9 - build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ - requirements: build: - bioconductor-biobase @@ -27,13 +24,10 @@ requirements: - bioconductor-biobase - r-base - wget - test: commands: - '$R -e "library(''{{ name }}'')"' - about: - home: https://bioconductor.org/packages/release/data/experiment/html/bladderbatch.html + home: 'http://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html' license: Artistic-2.0 - summary: 'This package contains microarray gene expression data on 57 bladder samples - from 5 batches. The data are used as an illustrative example for the sva package.' + summary: 'This package contains microarray gene expression data on 57 bladder samples from 5 batches. The data are used as an illustrative example for the sva package.' diff --git a/recipes/bioconductor-bladderbatch/post-link.sh b/recipes/bioconductor-bladderbatch/post-link.sh index 34fd65bc547fa..5f3461273e2f8 100644 --- a/recipes/bioconductor-bladderbatch/post-link.sh +++ b/recipes/bioconductor-bladderbatch/post-link.sh @@ -2,9 +2,9 @@ FN="bladderbatch_1.14.0.tar.gz" URLS=( "http://bioconductor.org/packages/3.5/data/experiment/src/contrib/bladderbatch_1.14.0.tar.gz" - "https://depot.galaxyproject.org/software/bladderbatch/bladderbatch_1.14.0_src_all.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-bladderbatch/bioconductor-bladderbatch_1.14.0_src_all.tar.gz" ) - MD5="e78d20742c18d7a526aefed891ee12b5" +MD5="e78d20742c18d7a526aefed891ee12b5" # Use a staging area in the conda dir rather than temp dirs, both to avoid # permission issues as well as to have things downloaded in a predictable @@ -20,7 +20,7 @@ for URL in ${URLS[@]}; do # Platform-specific md5sum checks. if [[ $(uname -s) == "Linux" ]]; then - if [[ $(md5sum -c <<<"$MD5 $TARBALL") ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then SUCCESS=1 break fi @@ -40,5 +40,6 @@ if [[ $SUCCESS != 1 ]]; then fi # Install and clean up -R CMD INSTALL --build $TARBALL -rm $TARBALL \ No newline at end of file +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING \ No newline at end of file diff --git a/recipes/bioconductor-bladderbatch/pre-unlink.sh b/recipes/bioconductor-bladderbatch/pre-unlink.sh new file mode 100644 index 0000000000000..81e659c80a5b3 --- /dev/null +++ b/recipes/bioconductor-bladderbatch/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ bladderbatch diff --git a/recipes/bioconductor-bsgenome.celegans.ucsc.ce10/meta.yaml b/recipes/bioconductor-bsgenome.celegans.ucsc.ce10/meta.yaml index 7602dc84206d6..48c9408de0a0b 100644 --- a/recipes/bioconductor-bsgenome.celegans.ucsc.ce10/meta.yaml +++ b/recipes/bioconductor-bsgenome.celegans.ucsc.ce10/meta.yaml @@ -9,10 +9,10 @@ source: fn: '{{ name }}_{{ version }}.tar.gz' url: - 'http://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/{{ name }}/{{ name }}_{{ version }}_src_all.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' sha256: 3337ffc0b59ee6d4f74e790cfd7aea9f54b8b3f87cbb48c2ecd792294faa5efd build: - number: 1 + number: 2 rpaths: - lib/R/lib/ - lib/ diff --git a/recipes/bioconductor-bsgenome.celegans.ucsc.ce10/post-link.sh b/recipes/bioconductor-bsgenome.celegans.ucsc.ce10/post-link.sh index 6e009f80ac3df..4551f810ac8bc 100644 --- a/recipes/bioconductor-bsgenome.celegans.ucsc.ce10/post-link.sh +++ b/recipes/bioconductor-bsgenome.celegans.ucsc.ce10/post-link.sh @@ -2,9 +2,9 @@ FN="BSgenome.Celegans.UCSC.ce10_1.4.0.tar.gz" URLS=( "http://bioconductor.org/packages/3.6/data/annotation/src/contrib/BSgenome.Celegans.UCSC.ce10_1.4.0.tar.gz" - "https://depot.galaxyproject.org/software/BSgenome.Celegans.UCSC.ce10/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" ) - MD5="98a8ca836d6db23e46674552669d7942" +MD5="98a8ca836d6db23e46674552669d7942" # Use a staging area in the conda dir rather than temp dirs, both to avoid # permission issues as well as to have things downloaded in a predictable @@ -20,7 +20,7 @@ for URL in ${URLS[@]}; do # Platform-specific md5sum checks. if [[ $(uname -s) == "Linux" ]]; then - if [[ $(md5sum -c <<<"$MD5 $TARBALL") ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then SUCCESS=1 break fi @@ -40,5 +40,6 @@ if [[ $SUCCESS != 1 ]]; then fi # Install and clean up -R CMD INSTALL --build $TARBALL -rm $TARBALL \ No newline at end of file +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING \ No newline at end of file diff --git a/recipes/bioconductor-bsgenome.celegans.ucsc.ce10/pre-unlink.sh b/recipes/bioconductor-bsgenome.celegans.ucsc.ce10/pre-unlink.sh new file mode 100644 index 0000000000000..315c7696442ee --- /dev/null +++ b/recipes/bioconductor-bsgenome.celegans.ucsc.ce10/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ BSgenome.Celegans.UCSC.ce10 diff --git a/recipes/bioconductor-bsgenome.celegans.ucsc.ce6/meta.yaml b/recipes/bioconductor-bsgenome.celegans.ucsc.ce6/meta.yaml index a8f61b175a9a7..c98052dd18c98 100644 --- a/recipes/bioconductor-bsgenome.celegans.ucsc.ce6/meta.yaml +++ b/recipes/bioconductor-bsgenome.celegans.ucsc.ce6/meta.yaml @@ -9,10 +9,10 @@ source: fn: '{{ name }}_{{ version }}.tar.gz' url: - 'http://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/{{ name }}/{{ name }}_{{ version }}_src_all.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' sha256: 6997709c5f9eca77a1b7d3367bee676f765b672b61acb9471d4cec3eca581f57 build: - number: 1 + number: 2 rpaths: - lib/R/lib/ - lib/ diff --git a/recipes/bioconductor-bsgenome.celegans.ucsc.ce6/post-link.sh b/recipes/bioconductor-bsgenome.celegans.ucsc.ce6/post-link.sh index 24ad7fe7ef1ac..46142280cf217 100644 --- a/recipes/bioconductor-bsgenome.celegans.ucsc.ce6/post-link.sh +++ b/recipes/bioconductor-bsgenome.celegans.ucsc.ce6/post-link.sh @@ -2,9 +2,9 @@ FN="BSgenome.Celegans.UCSC.ce6_1.4.0.tar.gz" URLS=( "http://bioconductor.org/packages/3.6/data/annotation/src/contrib/BSgenome.Celegans.UCSC.ce6_1.4.0.tar.gz" - "https://depot.galaxyproject.org/software/BSgenome.Celegans.UCSC.ce6/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" ) - MD5="cb86ff861d8f660c2abd8fc1907d84a6" +MD5="cb86ff861d8f660c2abd8fc1907d84a6" # Use a staging area in the conda dir rather than temp dirs, both to avoid # permission issues as well as to have things downloaded in a predictable @@ -20,7 +20,7 @@ for URL in ${URLS[@]}; do # Platform-specific md5sum checks. if [[ $(uname -s) == "Linux" ]]; then - if [[ $(md5sum -c <<<"$MD5 $TARBALL") ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then SUCCESS=1 break fi @@ -40,5 +40,6 @@ if [[ $SUCCESS != 1 ]]; then fi # Install and clean up -R CMD INSTALL --build $TARBALL -rm $TARBALL \ No newline at end of file +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING \ No newline at end of file diff --git a/recipes/bioconductor-bsgenome.celegans.ucsc.ce6/pre-unlink.sh b/recipes/bioconductor-bsgenome.celegans.ucsc.ce6/pre-unlink.sh new file mode 100644 index 0000000000000..2761a937184b7 --- /dev/null +++ b/recipes/bioconductor-bsgenome.celegans.ucsc.ce6/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ BSgenome.Celegans.UCSC.ce6 diff --git a/recipes/bioconductor-bsgenome.dmelanogaster.ucsc.dm3/meta.yaml b/recipes/bioconductor-bsgenome.dmelanogaster.ucsc.dm3/meta.yaml index e96b25f6af422..4891ebd9e485a 100644 --- a/recipes/bioconductor-bsgenome.dmelanogaster.ucsc.dm3/meta.yaml +++ b/recipes/bioconductor-bsgenome.dmelanogaster.ucsc.dm3/meta.yaml @@ -9,10 +9,10 @@ source: fn: '{{ name }}_{{ version }}.tar.gz' url: - 'http://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/{{ name }}/{{ name }}_{{ version }}_src_all.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' sha256: 68ebdefa8c99330f320d1928673ac89601e842102990cbed1b4f4d08271d75a5 build: - number: 1 + number: 2 rpaths: - lib/R/lib/ - lib/ diff --git a/recipes/bioconductor-bsgenome.dmelanogaster.ucsc.dm3/post-link.sh b/recipes/bioconductor-bsgenome.dmelanogaster.ucsc.dm3/post-link.sh index cb74ce45cd52f..100d8dae8565d 100644 --- a/recipes/bioconductor-bsgenome.dmelanogaster.ucsc.dm3/post-link.sh +++ b/recipes/bioconductor-bsgenome.dmelanogaster.ucsc.dm3/post-link.sh @@ -2,9 +2,9 @@ FN="BSgenome.Dmelanogaster.UCSC.dm3_1.4.0.tar.gz" URLS=( "http://bioconductor.org/packages/3.6/data/annotation/src/contrib/BSgenome.Dmelanogaster.UCSC.dm3_1.4.0.tar.gz" - "https://depot.galaxyproject.org/software/BSgenome.Dmelanogaster.UCSC.dm3/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" ) - MD5="b7ceebf7bfee766596f602f9e808d069" +MD5="b7ceebf7bfee766596f602f9e808d069" # Use a staging area in the conda dir rather than temp dirs, both to avoid # permission issues as well as to have things downloaded in a predictable @@ -20,7 +20,7 @@ for URL in ${URLS[@]}; do # Platform-specific md5sum checks. if [[ $(uname -s) == "Linux" ]]; then - if [[ $(md5sum -c <<<"$MD5 $TARBALL") ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then SUCCESS=1 break fi @@ -40,5 +40,6 @@ if [[ $SUCCESS != 1 ]]; then fi # Install and clean up -R CMD INSTALL --build $TARBALL -rm $TARBALL \ No newline at end of file +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING \ No newline at end of file diff --git a/recipes/bioconductor-bsgenome.dmelanogaster.ucsc.dm3/pre-unlink.sh b/recipes/bioconductor-bsgenome.dmelanogaster.ucsc.dm3/pre-unlink.sh new file mode 100644 index 0000000000000..269d2c1c39ac7 --- /dev/null +++ b/recipes/bioconductor-bsgenome.dmelanogaster.ucsc.dm3/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ BSgenome.Dmelanogaster.UCSC.dm3 diff --git a/recipes/bioconductor-bsgenome.ecoli.ncbi.20080805/meta.yaml b/recipes/bioconductor-bsgenome.ecoli.ncbi.20080805/meta.yaml index b9b2c04399027..a6cede7249578 100644 --- a/recipes/bioconductor-bsgenome.ecoli.ncbi.20080805/meta.yaml +++ b/recipes/bioconductor-bsgenome.ecoli.ncbi.20080805/meta.yaml @@ -9,10 +9,10 @@ source: fn: '{{ name }}_{{ version }}.tar.gz' url: - 'http://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/{{ name }}/{{ name }}_{{ version }}_src_all.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' sha256: 4740ebd81b56e9a990e7bbf3eb799011346db8af4a2615572558cda0bd97f5d0 build: - number: 1 + number: 2 rpaths: - lib/R/lib/ - lib/ diff --git a/recipes/bioconductor-bsgenome.ecoli.ncbi.20080805/post-link.sh b/recipes/bioconductor-bsgenome.ecoli.ncbi.20080805/post-link.sh index 8dd2a445c11ae..c61a2059674e4 100644 --- a/recipes/bioconductor-bsgenome.ecoli.ncbi.20080805/post-link.sh +++ b/recipes/bioconductor-bsgenome.ecoli.ncbi.20080805/post-link.sh @@ -2,9 +2,9 @@ FN="BSgenome.Ecoli.NCBI.20080805_1.3.1000.tar.gz" URLS=( "http://bioconductor.org/packages/3.6/data/annotation/src/contrib/BSgenome.Ecoli.NCBI.20080805_1.3.1000.tar.gz" - "https://depot.galaxyproject.org/software/BSgenome.Ecoli.NCBI.20080805/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" ) - MD5="c653e9cbee3faeb6fd5759b7575f234d" +MD5="c653e9cbee3faeb6fd5759b7575f234d" # Use a staging area in the conda dir rather than temp dirs, both to avoid # permission issues as well as to have things downloaded in a predictable @@ -20,7 +20,7 @@ for URL in ${URLS[@]}; do # Platform-specific md5sum checks. if [[ $(uname -s) == "Linux" ]]; then - if [[ $(md5sum -c <<<"$MD5 $TARBALL") ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then SUCCESS=1 break fi @@ -40,5 +40,6 @@ if [[ $SUCCESS != 1 ]]; then fi # Install and clean up -R CMD INSTALL --build $TARBALL -rm $TARBALL \ No newline at end of file +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING \ No newline at end of file diff --git a/recipes/bioconductor-bsgenome.ecoli.ncbi.20080805/pre-unlink.sh b/recipes/bioconductor-bsgenome.ecoli.ncbi.20080805/pre-unlink.sh new file mode 100644 index 0000000000000..201527728cb99 --- /dev/null +++ b/recipes/bioconductor-bsgenome.ecoli.ncbi.20080805/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ BSgenome.Ecoli.NCBI.20080805 diff --git a/recipes/bioconductor-bsgenome.hsapiens.ucsc.hg19/meta.yaml b/recipes/bioconductor-bsgenome.hsapiens.ucsc.hg19/meta.yaml index 481ef83cbb3b4..bd6f9a0f9e6b3 100644 --- a/recipes/bioconductor-bsgenome.hsapiens.ucsc.hg19/meta.yaml +++ b/recipes/bioconductor-bsgenome.hsapiens.ucsc.hg19/meta.yaml @@ -9,10 +9,10 @@ source: fn: '{{ name }}_{{ version }}.tar.gz' url: - 'http://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/{{ name }}/{{ name }}_{{ version }}_src_all.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' sha256: 88f515e5c27dd11d10654250e3a0a9389e4dfeb0b1c2d43419aa7086e6c516f8 build: - number: 1 + number: 2 rpaths: - lib/R/lib/ - lib/ diff --git a/recipes/bioconductor-bsgenome.hsapiens.ucsc.hg19/post-link.sh b/recipes/bioconductor-bsgenome.hsapiens.ucsc.hg19/post-link.sh index 12e1439fc0ef7..816f5921c3773 100644 --- a/recipes/bioconductor-bsgenome.hsapiens.ucsc.hg19/post-link.sh +++ b/recipes/bioconductor-bsgenome.hsapiens.ucsc.hg19/post-link.sh @@ -2,9 +2,9 @@ FN="BSgenome.Hsapiens.UCSC.hg19_1.4.0.tar.gz" URLS=( "http://bioconductor.org/packages/3.6/data/annotation/src/contrib/BSgenome.Hsapiens.UCSC.hg19_1.4.0.tar.gz" - "https://depot.galaxyproject.org/software/BSgenome.Hsapiens.UCSC.hg19/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" ) - MD5="672a988b28d8602afb2bd5595db7303b" +MD5="672a988b28d8602afb2bd5595db7303b" # Use a staging area in the conda dir rather than temp dirs, both to avoid # permission issues as well as to have things downloaded in a predictable @@ -20,7 +20,7 @@ for URL in ${URLS[@]}; do # Platform-specific md5sum checks. if [[ $(uname -s) == "Linux" ]]; then - if [[ $(md5sum -c <<<"$MD5 $TARBALL") ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then SUCCESS=1 break fi @@ -40,5 +40,6 @@ if [[ $SUCCESS != 1 ]]; then fi # Install and clean up -R CMD INSTALL --build $TARBALL -rm $TARBALL \ No newline at end of file +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING \ No newline at end of file diff --git a/recipes/bioconductor-bsgenome.hsapiens.ucsc.hg19/pre-unlink.sh b/recipes/bioconductor-bsgenome.hsapiens.ucsc.hg19/pre-unlink.sh new file mode 100644 index 0000000000000..9d77e0e89e067 --- /dev/null +++ b/recipes/bioconductor-bsgenome.hsapiens.ucsc.hg19/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ BSgenome.Hsapiens.UCSC.hg19 diff --git a/recipes/bioconductor-bsgenome.hsapiens.ucsc.hg38/meta.yaml b/recipes/bioconductor-bsgenome.hsapiens.ucsc.hg38/meta.yaml index e366bdcd5de3e..1b42f4d00cfb7 100644 --- a/recipes/bioconductor-bsgenome.hsapiens.ucsc.hg38/meta.yaml +++ b/recipes/bioconductor-bsgenome.hsapiens.ucsc.hg38/meta.yaml @@ -9,10 +9,10 @@ source: fn: '{{ name }}_{{ version }}.tar.gz' url: - 'http://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/{{ name }}/{{ name }}_{{ version }}_src_all.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' sha256: 71d7e4557666e2ff76ffc6c637331bfab0c0b59f4963f2b6f5606f12f74580e2 build: - number: 1 + number: 2 rpaths: - lib/R/lib/ - lib/ diff --git a/recipes/bioconductor-bsgenome.hsapiens.ucsc.hg38/post-link.sh b/recipes/bioconductor-bsgenome.hsapiens.ucsc.hg38/post-link.sh index af4048ac978f2..a46efc1b95a8f 100644 --- a/recipes/bioconductor-bsgenome.hsapiens.ucsc.hg38/post-link.sh +++ b/recipes/bioconductor-bsgenome.hsapiens.ucsc.hg38/post-link.sh @@ -2,9 +2,9 @@ FN="BSgenome.Hsapiens.UCSC.hg38_1.4.1.tar.gz" URLS=( "http://bioconductor.org/packages/3.6/data/annotation/src/contrib/BSgenome.Hsapiens.UCSC.hg38_1.4.1.tar.gz" - "https://depot.galaxyproject.org/software/BSgenome.Hsapiens.UCSC.hg38/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" ) - MD5="1b95bfdc9763351b04611666cd624b30" +MD5="1b95bfdc9763351b04611666cd624b30" # Use a staging area in the conda dir rather than temp dirs, both to avoid # permission issues as well as to have things downloaded in a predictable @@ -20,7 +20,7 @@ for URL in ${URLS[@]}; do # Platform-specific md5sum checks. if [[ $(uname -s) == "Linux" ]]; then - if [[ $(md5sum -c <<<"$MD5 $TARBALL") ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then SUCCESS=1 break fi @@ -40,5 +40,6 @@ if [[ $SUCCESS != 1 ]]; then fi # Install and clean up -R CMD INSTALL --build $TARBALL -rm $TARBALL \ No newline at end of file +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING \ No newline at end of file diff --git a/recipes/bioconductor-bsgenome.hsapiens.ucsc.hg38/pre-unlink.sh b/recipes/bioconductor-bsgenome.hsapiens.ucsc.hg38/pre-unlink.sh new file mode 100644 index 0000000000000..9f6b65a5a827b --- /dev/null +++ b/recipes/bioconductor-bsgenome.hsapiens.ucsc.hg38/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ BSgenome.Hsapiens.UCSC.hg38 diff --git a/recipes/bioconductor-bsgenome.mmusculus.ucsc.mm10/meta.yaml b/recipes/bioconductor-bsgenome.mmusculus.ucsc.mm10/meta.yaml index ee4e31aebb152..7cf992fd2f9b3 100644 --- a/recipes/bioconductor-bsgenome.mmusculus.ucsc.mm10/meta.yaml +++ b/recipes/bioconductor-bsgenome.mmusculus.ucsc.mm10/meta.yaml @@ -9,10 +9,10 @@ source: fn: '{{ name }}_{{ version }}.tar.gz' url: - 'http://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/{{ name }}/{{ name }}_{{ version }}_src_all.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' sha256: 6e2eb3bce208cc7766f0e0ef1e14465289d5463b34d94c9a9279256545b5408b build: - number: 1 + number: 2 rpaths: - lib/R/lib/ - lib/ diff --git a/recipes/bioconductor-bsgenome.mmusculus.ucsc.mm10/post-link.sh b/recipes/bioconductor-bsgenome.mmusculus.ucsc.mm10/post-link.sh index 704fe324b9947..5ebb3f3980359 100644 --- a/recipes/bioconductor-bsgenome.mmusculus.ucsc.mm10/post-link.sh +++ b/recipes/bioconductor-bsgenome.mmusculus.ucsc.mm10/post-link.sh @@ -2,9 +2,9 @@ FN="BSgenome.Mmusculus.UCSC.mm10_1.4.0.tar.gz" URLS=( "http://bioconductor.org/packages/3.6/data/annotation/src/contrib/BSgenome.Mmusculus.UCSC.mm10_1.4.0.tar.gz" - "https://depot.galaxyproject.org/software/BSgenome.Mmusculus.UCSC.mm10/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" ) - MD5="929f8bd0ea9ad416ecc0c2c002500414" +MD5="929f8bd0ea9ad416ecc0c2c002500414" # Use a staging area in the conda dir rather than temp dirs, both to avoid # permission issues as well as to have things downloaded in a predictable @@ -20,7 +20,7 @@ for URL in ${URLS[@]}; do # Platform-specific md5sum checks. if [[ $(uname -s) == "Linux" ]]; then - if [[ $(md5sum -c <<<"$MD5 $TARBALL") ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then SUCCESS=1 break fi @@ -40,5 +40,6 @@ if [[ $SUCCESS != 1 ]]; then fi # Install and clean up -R CMD INSTALL --build $TARBALL -rm $TARBALL \ No newline at end of file +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING \ No newline at end of file diff --git a/recipes/bioconductor-bsgenome.mmusculus.ucsc.mm10/pre-unlink.sh b/recipes/bioconductor-bsgenome.mmusculus.ucsc.mm10/pre-unlink.sh new file mode 100644 index 0000000000000..f37800e303fc3 --- /dev/null +++ b/recipes/bioconductor-bsgenome.mmusculus.ucsc.mm10/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ BSgenome.Mmusculus.UCSC.mm10 diff --git a/recipes/bioconductor-bsgenome.mmusculus.ucsc.mm9/meta.yaml b/recipes/bioconductor-bsgenome.mmusculus.ucsc.mm9/meta.yaml index 6fef2b0a113f4..5b10ccfc34c64 100644 --- a/recipes/bioconductor-bsgenome.mmusculus.ucsc.mm9/meta.yaml +++ b/recipes/bioconductor-bsgenome.mmusculus.ucsc.mm9/meta.yaml @@ -9,10 +9,10 @@ source: fn: '{{ name }}_{{ version }}.tar.gz' url: - 'http://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/{{ name }}/{{ name }}_{{ version }}_src_all.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' sha256: 3110745e93ae7c470b826921efc308fd5805efacdf497b7b8d5f890706c739ae build: - number: 1 + number: 2 rpaths: - lib/R/lib/ - lib/ diff --git a/recipes/bioconductor-bsgenome.mmusculus.ucsc.mm9/post-link.sh b/recipes/bioconductor-bsgenome.mmusculus.ucsc.mm9/post-link.sh index c38a313029b4a..42cf78ad7df07 100644 --- a/recipes/bioconductor-bsgenome.mmusculus.ucsc.mm9/post-link.sh +++ b/recipes/bioconductor-bsgenome.mmusculus.ucsc.mm9/post-link.sh @@ -2,9 +2,9 @@ FN="BSgenome.Mmusculus.UCSC.mm9_1.4.0.tar.gz" URLS=( "http://bioconductor.org/packages/3.6/data/annotation/src/contrib/BSgenome.Mmusculus.UCSC.mm9_1.4.0.tar.gz" - "https://depot.galaxyproject.org/software/BSgenome.Mmusculus.UCSC.mm9/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" ) - MD5="5a30ba2b4481a17e8e6979eb69eabf78" +MD5="5a30ba2b4481a17e8e6979eb69eabf78" # Use a staging area in the conda dir rather than temp dirs, both to avoid # permission issues as well as to have things downloaded in a predictable @@ -20,7 +20,7 @@ for URL in ${URLS[@]}; do # Platform-specific md5sum checks. if [[ $(uname -s) == "Linux" ]]; then - if [[ $(md5sum -c <<<"$MD5 $TARBALL") ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then SUCCESS=1 break fi @@ -40,5 +40,6 @@ if [[ $SUCCESS != 1 ]]; then fi # Install and clean up -R CMD INSTALL --build $TARBALL -rm $TARBALL \ No newline at end of file +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING \ No newline at end of file diff --git a/recipes/bioconductor-bsgenome.mmusculus.ucsc.mm9/pre-unlink.sh b/recipes/bioconductor-bsgenome.mmusculus.ucsc.mm9/pre-unlink.sh new file mode 100644 index 0000000000000..b3c09a3526ecb --- /dev/null +++ b/recipes/bioconductor-bsgenome.mmusculus.ucsc.mm9/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ BSgenome.Mmusculus.UCSC.mm9 diff --git a/recipes/bioconductor-bsseq/build.sh b/recipes/bioconductor-bsseq/build.sh new file mode 100644 index 0000000000000..da43ce2168312 --- /dev/null +++ b/recipes/bioconductor-bsseq/build.sh @@ -0,0 +1,4 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-bsseq/meta.yaml b/recipes/bioconductor-bsseq/meta.yaml new file mode 100644 index 0000000000000..cc6d496d8f7e5 --- /dev/null +++ b/recipes/bioconductor-bsseq/meta.yaml @@ -0,0 +1,69 @@ +{% set version = "1.14.0" %} +{% set name = "bsseq" %} +{% set bioc = "3.6" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' + +source: + fn: '{{ name }}_{{ version }}.tar.gz' + url: + - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/{{ name }}/{{ name }}_{{ version }}_src_all.tar.gz' + sha256: 244f58c0f58d41c1c5888ddbf33a9c073fe5dd5e15e9a3d3f3b541afcdcad648 + +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + +requirements: + build: + - bioconductor-biobase + - bioconductor-biocgenerics + - bioconductor-delayedarray + - bioconductor-genomeinfodb + - 'bioconductor-genomicranges >=1.29.14' + - bioconductor-hdf5array + - 'bioconductor-iranges >=2.11.16' + - bioconductor-limma + - bioconductor-s4vectors + - 'bioconductor-summarizedexperiment >=1.7.8' + - r-base + - r-data.table + - r-gtools + - r-locfit + - 'r-matrixstats >=0.50.0' + - r-permute + - 'r-r.utils >=2.0.0' + - r-scales + run: + - bioconductor-biobase + - bioconductor-biocgenerics + - bioconductor-delayedarray + - bioconductor-genomeinfodb + - 'bioconductor-genomicranges >=1.29.14' + - bioconductor-hdf5array + - 'bioconductor-iranges >=2.11.16' + - bioconductor-limma + - bioconductor-s4vectors + - 'bioconductor-summarizedexperiment >=1.7.8' + - r-base + - r-data.table + - r-gtools + - r-locfit + - 'r-matrixstats >=0.50.0' + - r-permute + - 'r-r.utils >=2.0.0' + - r-scales + +test: + commands: + - '$R -e "library(''{{ name }}'')"' + +about: + home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'A collection of tools for analyzing and visualizing bisulfite sequencing data.' diff --git a/recipes/bioconductor-curatedovariandata/meta.yaml b/recipes/bioconductor-curatedovariandata/meta.yaml index e8aeddeefe743..e7aa006af4fbf 100644 --- a/recipes/bioconductor-curatedovariandata/meta.yaml +++ b/recipes/bioconductor-curatedovariandata/meta.yaml @@ -9,10 +9,10 @@ source: fn: '{{ name }}_{{ version }}.tar.gz' url: - 'http://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/{{ name }}/{{ name }}_{{ version }}_src_all.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' sha256: 68443c35ca13b271eea69771fb3b8b868a7d3ea6a2f8fc188278c36bf579a395 build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ diff --git a/recipes/bioconductor-curatedovariandata/post-link.sh b/recipes/bioconductor-curatedovariandata/post-link.sh index 78148d54aa551..ed6767d1006e5 100644 --- a/recipes/bioconductor-curatedovariandata/post-link.sh +++ b/recipes/bioconductor-curatedovariandata/post-link.sh @@ -2,9 +2,9 @@ FN="curatedOvarianData_1.16.0.tar.gz" URLS=( "http://bioconductor.org/packages/3.6/data/experiment/src/contrib/curatedOvarianData_1.16.0.tar.gz" - "https://depot.galaxyproject.org/software/curatedOvarianData/curatedOvarianData_1.16.0_src_all.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-curatedovariandata/bioconductor-curatedovariandata_1.16.0_src_all.tar.gz" ) - MD5="ce3b7806e9a24e289454db0df74fbc75" +MD5="ce3b7806e9a24e289454db0df74fbc75" # Use a staging area in the conda dir rather than temp dirs, both to avoid # permission issues as well as to have things downloaded in a predictable @@ -20,7 +20,7 @@ for URL in ${URLS[@]}; do # Platform-specific md5sum checks. if [[ $(uname -s) == "Linux" ]]; then - if [[ $(md5sum -c <<<"$MD5 $TARBALL") ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then SUCCESS=1 break fi @@ -40,5 +40,6 @@ if [[ $SUCCESS != 1 ]]; then fi # Install and clean up -R CMD INSTALL --build $TARBALL -rm $TARBALL \ No newline at end of file +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING \ No newline at end of file diff --git a/recipes/bioconductor-curatedovariandata/pre-unlink.sh b/recipes/bioconductor-curatedovariandata/pre-unlink.sh new file mode 100644 index 0000000000000..b8aed490601f9 --- /dev/null +++ b/recipes/bioconductor-curatedovariandata/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ curatedOvarianData diff --git a/recipes/bioconductor-do.db/meta.yaml b/recipes/bioconductor-do.db/meta.yaml index bb8b64717154d..c149e900d03ed 100644 --- a/recipes/bioconductor-do.db/meta.yaml +++ b/recipes/bioconductor-do.db/meta.yaml @@ -9,10 +9,10 @@ source: fn: '{{ name }}_{{ version }}.tar.gz' url: - 'http://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/{{ name }}/{{ name }}_{{ version }}_src_all.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' sha256: 762bcb9b5188274fd81d82f785cf2846a5acc61fad55e2ff8ec1502282c27881 build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ diff --git a/recipes/bioconductor-do.db/post-link.sh b/recipes/bioconductor-do.db/post-link.sh index 9fbd472eb3ed8..0a652c03612cd 100644 --- a/recipes/bioconductor-do.db/post-link.sh +++ b/recipes/bioconductor-do.db/post-link.sh @@ -2,9 +2,9 @@ FN="DO.db_2.9.tar.gz" URLS=( "http://bioconductor.org/packages/3.6/data/annotation/src/contrib/DO.db_2.9.tar.gz" - "https://depot.galaxyproject.org/software/DO.db/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" ) - MD5="63dda6d46d2fe40c52a2e79260a7fb9d" +MD5="63dda6d46d2fe40c52a2e79260a7fb9d" # Use a staging area in the conda dir rather than temp dirs, both to avoid # permission issues as well as to have things downloaded in a predictable @@ -20,7 +20,7 @@ for URL in ${URLS[@]}; do # Platform-specific md5sum checks. if [[ $(uname -s) == "Linux" ]]; then - if [[ $(md5sum -c <<<"$MD5 $TARBALL") ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then SUCCESS=1 break fi @@ -40,5 +40,6 @@ if [[ $SUCCESS != 1 ]]; then fi # Install and clean up -R CMD INSTALL --build $TARBALL -rm $TARBALL \ No newline at end of file +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING \ No newline at end of file diff --git a/recipes/bioconductor-do.db/pre-unlink.sh b/recipes/bioconductor-do.db/pre-unlink.sh new file mode 100644 index 0000000000000..69bdc31f05cf7 --- /dev/null +++ b/recipes/bioconductor-do.db/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ DO.db diff --git a/recipes/bioconductor-drimseq/build.sh b/recipes/bioconductor-drimseq/build.sh new file mode 100644 index 0000000000000..da43ce2168312 --- /dev/null +++ b/recipes/bioconductor-drimseq/build.sh @@ -0,0 +1,4 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-drimseq/meta.yaml b/recipes/bioconductor-drimseq/meta.yaml new file mode 100644 index 0000000000000..f7a10dfea102b --- /dev/null +++ b/recipes/bioconductor-drimseq/meta.yaml @@ -0,0 +1,55 @@ +{% set version = "1.6.0" %} +{% set name = "DRIMSeq" %} +{% set bioc = "3.6" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' + +source: + fn: '{{ name }}_{{ version }}.tar.gz' + url: + - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/{{ name }}/{{ name }}_{{ version }}_src_all.tar.gz' + sha256: 96e954c3cbddb2cd39186ca942b0e1e1e8ea411dd285171a9bf6d9b23475e89f + +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + +requirements: + build: + - bioconductor-biocgenerics + - bioconductor-biocparallel + - bioconductor-edger + - bioconductor-genomicranges + - bioconductor-iranges + - bioconductor-limma + - bioconductor-s4vectors + - r-base + - r-ggplot2 + - r-mass + - r-reshape2 + run: + - bioconductor-biocgenerics + - bioconductor-biocparallel + - bioconductor-edger + - bioconductor-genomicranges + - bioconductor-iranges + - bioconductor-limma + - bioconductor-s4vectors + - r-base + - r-ggplot2 + - r-mass + - r-reshape2 + +test: + commands: + - '$R -e "library(''{{ name }}'')"' + +about: + home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: 'GPL (>= 3)' + summary: 'The package provides two frameworks. One for the differential transcript usage analysis between different conditions and one for the tuQTL analysis. Both are based on modeling the counts of genomic features (i.e., transcripts) with the Dirichlet-multinomial distribution. The package also makes available functions for visualization and exploration of the data and results.' diff --git a/recipes/bioconductor-egseadata/meta.yaml b/recipes/bioconductor-egseadata/meta.yaml index 3e52f775c8aff..9610769db642e 100644 --- a/recipes/bioconductor-egseadata/meta.yaml +++ b/recipes/bioconductor-egseadata/meta.yaml @@ -9,10 +9,10 @@ source: fn: '{{ name }}_{{ version }}.tar.gz' url: - 'http://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/{{ name }}/{{ name }}_{{ version }}_src_all.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' sha256: 1d266debcc106ad05ed63413a49ebdfa4dfc597f444235b5f82e106717d26ebb build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ diff --git a/recipes/bioconductor-egseadata/post-link.sh b/recipes/bioconductor-egseadata/post-link.sh index e2d7e6695d861..6d8085052873e 100644 --- a/recipes/bioconductor-egseadata/post-link.sh +++ b/recipes/bioconductor-egseadata/post-link.sh @@ -2,9 +2,9 @@ FN="EGSEAdata_1.6.0.tar.gz" URLS=( "http://bioconductor.org/packages/3.6/data/experiment/src/contrib/EGSEAdata_1.6.0.tar.gz" - "https://depot.galaxyproject.org/software/EGSEAdata/EGSEAdata_1.6.0_src_all.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-egseadata/bioconductor-egseadata_1.6.0_src_all.tar.gz" ) - MD5="899eb37b2b0cd33ba2566c5197f602bf" +MD5="899eb37b2b0cd33ba2566c5197f602bf" # Use a staging area in the conda dir rather than temp dirs, both to avoid # permission issues as well as to have things downloaded in a predictable @@ -20,7 +20,7 @@ for URL in ${URLS[@]}; do # Platform-specific md5sum checks. if [[ $(uname -s) == "Linux" ]]; then - if [[ $(md5sum -c <<<"$MD5 $TARBALL") ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then SUCCESS=1 break fi @@ -40,5 +40,6 @@ if [[ $SUCCESS != 1 ]]; then fi # Install and clean up -R CMD INSTALL --build $TARBALL -rm $TARBALL \ No newline at end of file +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING \ No newline at end of file diff --git a/recipes/bioconductor-egseadata/pre-unlink.sh b/recipes/bioconductor-egseadata/pre-unlink.sh new file mode 100644 index 0000000000000..4d74a4f60548e --- /dev/null +++ b/recipes/bioconductor-egseadata/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ EGSEAdata diff --git a/recipes/bioconductor-fdb.infiniummethylation.hg19/meta.yaml b/recipes/bioconductor-fdb.infiniummethylation.hg19/meta.yaml index bd7434a351e2d..0b792a0e58287 100644 --- a/recipes/bioconductor-fdb.infiniummethylation.hg19/meta.yaml +++ b/recipes/bioconductor-fdb.infiniummethylation.hg19/meta.yaml @@ -9,10 +9,10 @@ source: fn: '{{ name }}_{{ version }}.tar.gz' url: - 'http://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/{{ name }}/{{ name }}_{{ version }}_src_all.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' sha256: 605aa3643588a2f40a942fa760b92662060a0dfedb26b4e4cd6f1a78b703093f build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ diff --git a/recipes/bioconductor-fdb.infiniummethylation.hg19/post-link.sh b/recipes/bioconductor-fdb.infiniummethylation.hg19/post-link.sh index e6e928614e9e9..5889410296302 100644 --- a/recipes/bioconductor-fdb.infiniummethylation.hg19/post-link.sh +++ b/recipes/bioconductor-fdb.infiniummethylation.hg19/post-link.sh @@ -2,9 +2,9 @@ FN="FDb.InfiniumMethylation.hg19_2.2.0.tar.gz" URLS=( "http://bioconductor.org/packages/3.6/data/annotation/src/contrib/FDb.InfiniumMethylation.hg19_2.2.0.tar.gz" - "https://depot.galaxyproject.org/software/FDb.InfiniumMethylation.hg19/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" ) - MD5="b8b1abc599b9556b9fe9c6e824cb2697" +MD5="b8b1abc599b9556b9fe9c6e824cb2697" # Use a staging area in the conda dir rather than temp dirs, both to avoid # permission issues as well as to have things downloaded in a predictable @@ -20,7 +20,7 @@ for URL in ${URLS[@]}; do # Platform-specific md5sum checks. if [[ $(uname -s) == "Linux" ]]; then - if [[ $(md5sum -c <<<"$MD5 $TARBALL") ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then SUCCESS=1 break fi @@ -40,5 +40,6 @@ if [[ $SUCCESS != 1 ]]; then fi # Install and clean up -R CMD INSTALL --build $TARBALL -rm $TARBALL \ No newline at end of file +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING \ No newline at end of file diff --git a/recipes/bioconductor-fdb.infiniummethylation.hg19/pre-unlink.sh b/recipes/bioconductor-fdb.infiniummethylation.hg19/pre-unlink.sh new file mode 100644 index 0000000000000..83e5ed6e8052c --- /dev/null +++ b/recipes/bioconductor-fdb.infiniummethylation.hg19/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ FDb.InfiniumMethylation.hg19 diff --git a/recipes/bioconductor-flagme/build.sh b/recipes/bioconductor-flagme/build.sh new file mode 100644 index 0000000000000..da43ce2168312 --- /dev/null +++ b/recipes/bioconductor-flagme/build.sh @@ -0,0 +1,4 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-flagme/meta.yaml b/recipes/bioconductor-flagme/meta.yaml new file mode 100644 index 0000000000000..e5b13684374e9 --- /dev/null +++ b/recipes/bioconductor-flagme/meta.yaml @@ -0,0 +1,47 @@ +{% set version = "1.34.0" %} +{% set name = "flagme" %} +{% set bioc = "3.6" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' + +source: + fn: '{{ name }}_{{ version }}.tar.gz' + url: + - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/{{ name }}/{{ name }}_{{ version }}_src_all.tar.gz' + sha256: 7e05cd321bedca9a0c8526703a4f08758d690af887ce69744d4f5621b6812b97 + +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + +requirements: + build: + - bioconductor-camera + - bioconductor-gcspikelite + - bioconductor-xcms + - r-base + - r-gplots + - r-mass + - r-sparsem + run: + - bioconductor-camera + - bioconductor-gcspikelite + - bioconductor-xcms + - r-base + - r-gplots + - r-mass + - r-sparsem + +test: + commands: + - '$R -e "library(''{{ name }}'')"' + +about: + home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: 'LGPL (>= 2)' + summary: 'Fragment-level analysis of gas chromatography - mass spectrometry metabolomics data' diff --git a/recipes/bioconductor-flowbeads/build.sh b/recipes/bioconductor-flowbeads/build.sh new file mode 100644 index 0000000000000..da43ce2168312 --- /dev/null +++ b/recipes/bioconductor-flowbeads/build.sh @@ -0,0 +1,4 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-flowbeads/meta.yaml b/recipes/bioconductor-flowbeads/meta.yaml new file mode 100644 index 0000000000000..b76062f6f0da4 --- /dev/null +++ b/recipes/bioconductor-flowbeads/meta.yaml @@ -0,0 +1,45 @@ +{% set version = "1.16.0" %} +{% set name = "flowBeads" %} +{% set bioc = "3.6" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' + +source: + fn: '{{ name }}_{{ version }}.tar.gz' + url: + - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/{{ name }}/{{ name }}_{{ version }}_src_all.tar.gz' + sha256: 250cf0d32568a4f2767580015ca2c7d0843d1288ab6f01e5472ed5d52a754c1a + +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + +requirements: + build: + - bioconductor-biobase + - bioconductor-flowcore + - r-base + - r-knitr + - r-rrcov + - r-xtable + run: + - bioconductor-biobase + - bioconductor-flowcore + - r-base + - r-knitr + - r-rrcov + - r-xtable + +test: + commands: + - '$R -e "library(''{{ name }}'')"' + +about: + home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'This package extends flowCore to provide functionality specific to bead data. One of the goals of this package is to automate analysis of bead data for the purpose of normalisation.' diff --git a/recipes/bioconductor-gagedata/meta.yaml b/recipes/bioconductor-gagedata/meta.yaml index a69b9097a5e12..95a33bf0fc042 100644 --- a/recipes/bioconductor-gagedata/meta.yaml +++ b/recipes/bioconductor-gagedata/meta.yaml @@ -9,10 +9,10 @@ source: fn: '{{ name }}_{{ version }}.tar.gz' url: - 'http://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/{{ name }}/{{ name }}_{{ version }}_src_all.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' sha256: acbc5dc445845acc73579d71096180fc87401c57d445277db355c88055e385a3 build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ diff --git a/recipes/bioconductor-gagedata/post-link.sh b/recipes/bioconductor-gagedata/post-link.sh index abd4bb8ccb5b0..5e855f11da36a 100644 --- a/recipes/bioconductor-gagedata/post-link.sh +++ b/recipes/bioconductor-gagedata/post-link.sh @@ -2,9 +2,9 @@ FN="gageData_2.16.0.tar.gz" URLS=( "http://bioconductor.org/packages/3.6/data/experiment/src/contrib/gageData_2.16.0.tar.gz" - "https://depot.galaxyproject.org/software/gageData/gageData_2.16.0_src_all.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-gagedata/bioconductor-gagedata_2.16.0_src_all.tar.gz" ) - MD5="e79551bd0b5a52f5befe0fae21e5eb35" +MD5="e79551bd0b5a52f5befe0fae21e5eb35" # Use a staging area in the conda dir rather than temp dirs, both to avoid # permission issues as well as to have things downloaded in a predictable @@ -20,7 +20,7 @@ for URL in ${URLS[@]}; do # Platform-specific md5sum checks. if [[ $(uname -s) == "Linux" ]]; then - if [[ $(md5sum -c <<<"$MD5 $TARBALL") ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then SUCCESS=1 break fi @@ -40,5 +40,6 @@ if [[ $SUCCESS != 1 ]]; then fi # Install and clean up -R CMD INSTALL --build $TARBALL -rm $TARBALL \ No newline at end of file +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING \ No newline at end of file diff --git a/recipes/bioconductor-gagedata/pre-unlink.sh b/recipes/bioconductor-gagedata/pre-unlink.sh new file mode 100644 index 0000000000000..61bfa9f48a461 --- /dev/null +++ b/recipes/bioconductor-gagedata/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ gageData diff --git a/recipes/bioconductor-gcspikelite/meta.yaml b/recipes/bioconductor-gcspikelite/meta.yaml index 6a1e5ae29c5ae..91b7c68c7bf8b 100644 --- a/recipes/bioconductor-gcspikelite/meta.yaml +++ b/recipes/bioconductor-gcspikelite/meta.yaml @@ -9,10 +9,10 @@ source: fn: '{{ name }}_{{ version }}.tar.gz' url: - 'http://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/{{ name }}/{{ name }}_{{ version }}_src_all.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' sha256: f78f714cde33026c18f7e79873bb1899419a9a719dfb0ef566d07a1253ed1e5c build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ diff --git a/recipes/bioconductor-gcspikelite/post-link.sh b/recipes/bioconductor-gcspikelite/post-link.sh index 8ee87c61f5a4a..457c0e7a60b9b 100644 --- a/recipes/bioconductor-gcspikelite/post-link.sh +++ b/recipes/bioconductor-gcspikelite/post-link.sh @@ -2,9 +2,9 @@ FN="gcspikelite_1.16.0.tar.gz" URLS=( "http://bioconductor.org/packages/3.6/data/experiment/src/contrib/gcspikelite_1.16.0.tar.gz" - "https://depot.galaxyproject.org/software/gcspikelite/gcspikelite_1.16.0_src_all.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-gcspikelite/bioconductor-gcspikelite_1.16.0_src_all.tar.gz" ) - MD5="b7806c37e0bfa69530c0387c7ab21a11" +MD5="b7806c37e0bfa69530c0387c7ab21a11" # Use a staging area in the conda dir rather than temp dirs, both to avoid # permission issues as well as to have things downloaded in a predictable @@ -20,7 +20,7 @@ for URL in ${URLS[@]}; do # Platform-specific md5sum checks. if [[ $(uname -s) == "Linux" ]]; then - if [[ $(md5sum -c <<<"$MD5 $TARBALL") ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then SUCCESS=1 break fi @@ -40,5 +40,6 @@ if [[ $SUCCESS != 1 ]]; then fi # Install and clean up -R CMD INSTALL --build $TARBALL -rm $TARBALL \ No newline at end of file +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING \ No newline at end of file diff --git a/recipes/bioconductor-gcspikelite/pre-unlink.sh b/recipes/bioconductor-gcspikelite/pre-unlink.sh new file mode 100644 index 0000000000000..95e0045c3fe6d --- /dev/null +++ b/recipes/bioconductor-gcspikelite/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ gcspikelite diff --git a/recipes/bioconductor-genelendatabase/meta.yaml b/recipes/bioconductor-genelendatabase/meta.yaml index 632a7f70e0f1b..72038d791073f 100644 --- a/recipes/bioconductor-genelendatabase/meta.yaml +++ b/recipes/bioconductor-genelendatabase/meta.yaml @@ -9,10 +9,10 @@ source: fn: '{{ name }}_{{ version }}.tar.gz' url: - 'http://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/{{ name }}/{{ name }}_{{ version }}_src_all.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' sha256: 66613729237ea033d8e65fd8e49adafa0ca30e6fdd97bd2329480ac0fbdf7118 build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ diff --git a/recipes/bioconductor-genelendatabase/post-link.sh b/recipes/bioconductor-genelendatabase/post-link.sh index 48562dedb0bd7..a0c468dafd534 100644 --- a/recipes/bioconductor-genelendatabase/post-link.sh +++ b/recipes/bioconductor-genelendatabase/post-link.sh @@ -2,9 +2,9 @@ FN="geneLenDataBase_1.14.0.tar.gz" URLS=( "http://bioconductor.org/packages/3.6/data/experiment/src/contrib/geneLenDataBase_1.14.0.tar.gz" - "https://depot.galaxyproject.org/software/geneLenDataBase/geneLenDataBase_1.14.0_src_all.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-genelendatabase/bioconductor-genelendatabase_1.14.0_src_all.tar.gz" ) - MD5="f1466f1d89f074c7a084f08ca3df7781" +MD5="f1466f1d89f074c7a084f08ca3df7781" # Use a staging area in the conda dir rather than temp dirs, both to avoid # permission issues as well as to have things downloaded in a predictable @@ -20,7 +20,7 @@ for URL in ${URLS[@]}; do # Platform-specific md5sum checks. if [[ $(uname -s) == "Linux" ]]; then - if [[ $(md5sum -c <<<"$MD5 $TARBALL") ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then SUCCESS=1 break fi @@ -40,5 +40,6 @@ if [[ $SUCCESS != 1 ]]; then fi # Install and clean up -R CMD INSTALL --build $TARBALL -rm $TARBALL \ No newline at end of file +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING \ No newline at end of file diff --git a/recipes/bioconductor-genelendatabase/pre-unlink.sh b/recipes/bioconductor-genelendatabase/pre-unlink.sh new file mode 100644 index 0000000000000..bca9851e7d6e6 --- /dev/null +++ b/recipes/bioconductor-genelendatabase/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ geneLenDataBase diff --git a/recipes/bioconductor-genomeinfodbdata/meta.yaml b/recipes/bioconductor-genomeinfodbdata/meta.yaml index 57a0da6510909..520d88bc6dd86 100644 --- a/recipes/bioconductor-genomeinfodbdata/meta.yaml +++ b/recipes/bioconductor-genomeinfodbdata/meta.yaml @@ -1,4 +1,4 @@ -{% set version = "0.99.1" %} +{% set version = "1.0.0" %} {% set name = "GenomeInfoDbData" %} {% set bioc = "3.6" %} @@ -9,10 +9,10 @@ source: fn: '{{ name }}_{{ version }}.tar.gz' url: - 'http://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/{{ name }}/{{ name }}_{{ version }}_src_all.tar.gz' - sha256: 39809792f2c88939ed3ea4ecfee1cbdfb1d575194f6a888c2d07e6edf78d3742 + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + sha256: d7bb73db4a76960e65c5f6d8ccdcb9480a48cea529a30ea2399f8e4c9887e876 build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ diff --git a/recipes/bioconductor-genomeinfodbdata/post-link.sh b/recipes/bioconductor-genomeinfodbdata/post-link.sh index 4698d36b60392..391ecba222915 100644 --- a/recipes/bioconductor-genomeinfodbdata/post-link.sh +++ b/recipes/bioconductor-genomeinfodbdata/post-link.sh @@ -1,10 +1,10 @@ #!/bin/bash -FN="GenomeInfoDbData_0.99.1.tar.gz" +FN="GenomeInfoDbData_1.0.0.tar.gz" URLS=( - "http://bioconductor.org/packages/3.6/data/annotation/src/contrib/GenomeInfoDbData_0.99.1.tar.gz" - "https://depot.galaxyproject.org/software/GenomeInfoDbData/GenomeInfoDbData_0.99.1_src_all.tar.gz" + "http://bioconductor.org/packages/3.6/data/annotation/src/contrib/GenomeInfoDbData_1.0.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-genomeinfodbdata/bioconductor-genomeinfodbdata_1.0.0_src_all.tar.gz" ) - MD5="85741ea07f8661079dbd77a23aff3b6b" +MD5="3926f72117c49fbee36ab8e9c0b34885" # Use a staging area in the conda dir rather than temp dirs, both to avoid # permission issues as well as to have things downloaded in a predictable @@ -20,7 +20,7 @@ for URL in ${URLS[@]}; do # Platform-specific md5sum checks. if [[ $(uname -s) == "Linux" ]]; then - if [[ $(md5sum -c <<<"$MD5 $TARBALL") ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then SUCCESS=1 break fi @@ -40,5 +40,6 @@ if [[ $SUCCESS != 1 ]]; then fi # Install and clean up -R CMD INSTALL --build $TARBALL -rm $TARBALL \ No newline at end of file +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING \ No newline at end of file diff --git a/recipes/bioconductor-genomeinfodbdata/pre-unlink.sh b/recipes/bioconductor-genomeinfodbdata/pre-unlink.sh new file mode 100644 index 0000000000000..3e5d9e44f0e05 --- /dev/null +++ b/recipes/bioconductor-genomeinfodbdata/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ GenomeInfoDbData diff --git a/recipes/bioconductor-geometadb/build.sh b/recipes/bioconductor-geometadb/build.sh new file mode 100644 index 0000000000000..da43ce2168312 --- /dev/null +++ b/recipes/bioconductor-geometadb/build.sh @@ -0,0 +1,4 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-geometadb/meta.yaml b/recipes/bioconductor-geometadb/meta.yaml new file mode 100644 index 0000000000000..fbe19d2178d21 --- /dev/null +++ b/recipes/bioconductor-geometadb/meta.yaml @@ -0,0 +1,34 @@ +{% set version = "1.40.0" %} +{% set name = "GEOmetadb" %} +{% set bioc = "3.6" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + fn: '{{ name }}_{{ version }}.tar.gz' + url: + - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/{{ name }}/{{ name }}_{{ version }}_src_all.tar.gz' + sha256: 0a34f652c2d1426c9299a882d9fab0f2e521b94d00904e61544d4e8c2ab77100 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ +requirements: + build: + - bioconductor-geoquery + - r-base + - r-rsqlite + run: + - bioconductor-geoquery + - r-base + - r-rsqlite +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'The NCBI Gene Expression Omnibus (GEO) represents the largest public repository of microarray data. However, finding data of interest can be challenging using current tools. GEOmetadb is an attempt to make access to the metadata associated with samples, platforms, and datasets much more feasible. This is accomplished by parsing all the NCBI GEO metadata into a SQLite database that can be stored and queried locally. GEOmetadb is simply a thin wrapper around the SQLite database along with associated documentation. Finally, the SQLite database is updated regularly as new data is added to GEO and can be downloaded at will for the most up-to-date metadata. GEOmetadb paper: http://bioinformatics.oxfordjournals.org/cgi/content/short/24/23/2798 .' diff --git a/recipes/bioconductor-go.db/meta.yaml b/recipes/bioconductor-go.db/meta.yaml index 214ec494b52bd..6e50e4363f52d 100644 --- a/recipes/bioconductor-go.db/meta.yaml +++ b/recipes/bioconductor-go.db/meta.yaml @@ -9,10 +9,10 @@ source: fn: '{{ name }}_{{ version }}.tar.gz' url: - 'http://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/{{ name }}/{{ name }}_{{ version }}_src_all.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' sha256: 656055d3e43f9b31c44ea895e831e0917092d5c899fad0e1c6070faa82ada109 build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ diff --git a/recipes/bioconductor-go.db/post-link.sh b/recipes/bioconductor-go.db/post-link.sh index 69b2733ef10e5..6ae59038da5cb 100644 --- a/recipes/bioconductor-go.db/post-link.sh +++ b/recipes/bioconductor-go.db/post-link.sh @@ -2,9 +2,9 @@ FN="GO.db_3.5.0.tar.gz" URLS=( "http://bioconductor.org/packages/3.6/data/annotation/src/contrib/GO.db_3.5.0.tar.gz" - "https://depot.galaxyproject.org/software/GO.db/GO.db_3.5.0_src_all.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-go.db/bioconductor-go.db_3.5.0_src_all.tar.gz" ) - MD5="58b59a93504a33b29652d25b00f212ea" +MD5="58b59a93504a33b29652d25b00f212ea" # Use a staging area in the conda dir rather than temp dirs, both to avoid # permission issues as well as to have things downloaded in a predictable @@ -20,7 +20,7 @@ for URL in ${URLS[@]}; do # Platform-specific md5sum checks. if [[ $(uname -s) == "Linux" ]]; then - if [[ $(md5sum -c <<<"$MD5 $TARBALL") ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then SUCCESS=1 break fi @@ -40,5 +40,6 @@ if [[ $SUCCESS != 1 ]]; then fi # Install and clean up -R CMD INSTALL --build $TARBALL -rm $TARBALL \ No newline at end of file +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING \ No newline at end of file diff --git a/recipes/bioconductor-go.db/pre-unlink.sh b/recipes/bioconductor-go.db/pre-unlink.sh new file mode 100644 index 0000000000000..1098332a3c054 --- /dev/null +++ b/recipes/bioconductor-go.db/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ GO.db diff --git a/recipes/bioconductor-gtrellis/build.sh b/recipes/bioconductor-gtrellis/build.sh new file mode 100644 index 0000000000000..b58dbca4d229f --- /dev/null +++ b/recipes/bioconductor-gtrellis/build.sh @@ -0,0 +1,4 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +$R CMD INSTALL --build . diff --git a/recipes/bioconductor-gtrellis/meta.yaml b/recipes/bioconductor-gtrellis/meta.yaml new file mode 100644 index 0000000000000..5e2320074e675 --- /dev/null +++ b/recipes/bioconductor-gtrellis/meta.yaml @@ -0,0 +1,42 @@ +{% set version = "1.11.1" %} +{% set name = "gtrellis" %} +{% set bioc = "3.6" %} + + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' + +source: + fn: '{{ name }}_{{ version }}.tar.gz' + url: +# https://www.bioconductor.org/packages/release/bioc/src/contrib/gtrellis_1.11.1.tar.gz + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + sha256: 1b913487cee2bbb0a151b41406e37d98c27b085b8f66622d6d1eb41bd5eea457 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ +requirements: + build: + - r-base >=3.3.2 + - 'bioconductor-iranges' + - 'bioconductor-genomicranges' + - r-gridbase + - r-circlize >=0.4.1 + - r-getoptlong >=0.1.6 + run: + - r-base >=3.3.2 + - 'bioconductor-iranges' + - 'bioconductor-genomicranges' + - r-gridbase + - r-circlize >=0.4.1 + - r-getoptlong >=0.1.6 +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: GPL (>= 2) + summary: 'Genome level Trellis graph visualizes genomic data conditioned by genomic categories (e.g. chromosomes). For each genomic category, multiple dimensional data which are represented as tracks describe different features from different aspects. This package provides high flexibility to arrange genomic categories and to add self-defined graphics in the plot.' diff --git a/recipes/bioconductor-hgu133a.db/meta.yaml b/recipes/bioconductor-hgu133a.db/meta.yaml index 501242eb11138..b72b2ab6c9f77 100644 --- a/recipes/bioconductor-hgu133a.db/meta.yaml +++ b/recipes/bioconductor-hgu133a.db/meta.yaml @@ -9,10 +9,10 @@ source: fn: '{{ name }}_{{ version }}.tar.gz' url: - 'http://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/{{ name }}/{{ name }}_{{ version }}_src_all.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' sha256: 75eaffa2bd09a694958b816fd575bb4cbdd35d3bbe60139ff0808516c931149a build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ diff --git a/recipes/bioconductor-hgu133a.db/post-link.sh b/recipes/bioconductor-hgu133a.db/post-link.sh index 5d8a369b8110f..e6f7140c4218c 100644 --- a/recipes/bioconductor-hgu133a.db/post-link.sh +++ b/recipes/bioconductor-hgu133a.db/post-link.sh @@ -2,9 +2,9 @@ FN="hgu133a.db_3.2.3.tar.gz" URLS=( "http://bioconductor.org/packages/3.6/data/annotation/src/contrib/hgu133a.db_3.2.3.tar.gz" - "https://depot.galaxyproject.org/software/hgu133a.db/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" ) - MD5="ce0397160fe78a92671e492a22542a79" +MD5="ce0397160fe78a92671e492a22542a79" # Use a staging area in the conda dir rather than temp dirs, both to avoid # permission issues as well as to have things downloaded in a predictable @@ -20,7 +20,7 @@ for URL in ${URLS[@]}; do # Platform-specific md5sum checks. if [[ $(uname -s) == "Linux" ]]; then - if [[ $(md5sum -c <<<"$MD5 $TARBALL") ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then SUCCESS=1 break fi @@ -40,5 +40,6 @@ if [[ $SUCCESS != 1 ]]; then fi # Install and clean up -R CMD INSTALL --build $TARBALL -rm $TARBALL \ No newline at end of file +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING \ No newline at end of file diff --git a/recipes/bioconductor-hgu133a.db/pre-unlink.sh b/recipes/bioconductor-hgu133a.db/pre-unlink.sh new file mode 100644 index 0000000000000..7dfea678c9602 --- /dev/null +++ b/recipes/bioconductor-hgu133a.db/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ hgu133a.db diff --git a/recipes/bioconductor-hgu133plus2.db/meta.yaml b/recipes/bioconductor-hgu133plus2.db/meta.yaml index f10e0ffe0cc2a..8909ee055818e 100644 --- a/recipes/bioconductor-hgu133plus2.db/meta.yaml +++ b/recipes/bioconductor-hgu133plus2.db/meta.yaml @@ -9,10 +9,10 @@ source: fn: '{{ name }}_{{ version }}.tar.gz' url: - 'http://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/{{ name }}/{{ name }}_{{ version }}_src_all.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' sha256: a56b247b69a6b8c81d23410e9def44f8d3e7c133aedf09fb1561798dca2c0549 build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ diff --git a/recipes/bioconductor-hgu133plus2.db/post-link.sh b/recipes/bioconductor-hgu133plus2.db/post-link.sh index 18a5216d97975..aacbd820bac1a 100644 --- a/recipes/bioconductor-hgu133plus2.db/post-link.sh +++ b/recipes/bioconductor-hgu133plus2.db/post-link.sh @@ -2,9 +2,9 @@ FN="hgu133plus2.db_3.2.3.tar.gz" URLS=( "http://bioconductor.org/packages/3.6/data/annotation/src/contrib/hgu133plus2.db_3.2.3.tar.gz" - "https://depot.galaxyproject.org/software/hgu133plus2.db/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" ) - MD5="45a376b6092da75907b9e73bbd90e5bf" +MD5="45a376b6092da75907b9e73bbd90e5bf" # Use a staging area in the conda dir rather than temp dirs, both to avoid # permission issues as well as to have things downloaded in a predictable @@ -20,7 +20,7 @@ for URL in ${URLS[@]}; do # Platform-specific md5sum checks. if [[ $(uname -s) == "Linux" ]]; then - if [[ $(md5sum -c <<<"$MD5 $TARBALL") ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then SUCCESS=1 break fi @@ -40,5 +40,6 @@ if [[ $SUCCESS != 1 ]]; then fi # Install and clean up -R CMD INSTALL --build $TARBALL -rm $TARBALL \ No newline at end of file +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING \ No newline at end of file diff --git a/recipes/bioconductor-hgu133plus2.db/pre-unlink.sh b/recipes/bioconductor-hgu133plus2.db/pre-unlink.sh new file mode 100644 index 0000000000000..b5a0a31534204 --- /dev/null +++ b/recipes/bioconductor-hgu133plus2.db/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ hgu133plus2.db diff --git a/recipes/bioconductor-hom.hs.inp.db/meta.yaml b/recipes/bioconductor-hom.hs.inp.db/meta.yaml index c22cb420ffc9d..c0c81821c61ce 100644 --- a/recipes/bioconductor-hom.hs.inp.db/meta.yaml +++ b/recipes/bioconductor-hom.hs.inp.db/meta.yaml @@ -9,10 +9,10 @@ source: fn: '{{ name }}_{{ version }}.tar.gz' url: - 'http://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/{{ name }}/{{ name }}_{{ version }}_src_all.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' sha256: 8dfe718726c80dcd990ddedde2e6f3027056d4fe4ee15bc6597b2880186b3d3a build: - number: 1 + number: 2 rpaths: - lib/R/lib/ - lib/ diff --git a/recipes/bioconductor-hom.hs.inp.db/post-link.sh b/recipes/bioconductor-hom.hs.inp.db/post-link.sh index 9ad2c73449818..f73a066b8ddd0 100644 --- a/recipes/bioconductor-hom.hs.inp.db/post-link.sh +++ b/recipes/bioconductor-hom.hs.inp.db/post-link.sh @@ -2,9 +2,9 @@ FN="hom.Hs.inp.db_3.1.2.tar.gz" URLS=( "http://bioconductor.org/packages/3.6/data/annotation/src/contrib/hom.Hs.inp.db_3.1.2.tar.gz" - "https://depot.galaxyproject.org/software/hom.Hs.inp.db/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" ) - MD5="b0708148e9c6656527e004fbaf80c05c" +MD5="b0708148e9c6656527e004fbaf80c05c" # Use a staging area in the conda dir rather than temp dirs, both to avoid # permission issues as well as to have things downloaded in a predictable @@ -20,7 +20,7 @@ for URL in ${URLS[@]}; do # Platform-specific md5sum checks. if [[ $(uname -s) == "Linux" ]]; then - if [[ $(md5sum -c <<<"$MD5 $TARBALL") ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then SUCCESS=1 break fi @@ -40,5 +40,6 @@ if [[ $SUCCESS != 1 ]]; then fi # Install and clean up -R CMD INSTALL --build $TARBALL -rm $TARBALL \ No newline at end of file +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING \ No newline at end of file diff --git a/recipes/bioconductor-hom.hs.inp.db/pre-unlink.sh b/recipes/bioconductor-hom.hs.inp.db/pre-unlink.sh new file mode 100644 index 0000000000000..0a1e4691e00a7 --- /dev/null +++ b/recipes/bioconductor-hom.hs.inp.db/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ hom.Hs.inp.db diff --git a/recipes/bioconductor-homo.sapiens/meta.yaml b/recipes/bioconductor-homo.sapiens/meta.yaml index df326e23ce409..f0715c4750f5f 100644 --- a/recipes/bioconductor-homo.sapiens/meta.yaml +++ b/recipes/bioconductor-homo.sapiens/meta.yaml @@ -9,10 +9,10 @@ source: fn: '{{ name }}_{{ version }}.tar.gz' url: - 'http://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/{{ name }}/{{ name }}_{{ version }}_src_all.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' sha256: 014809fc6ef6410be8dc1094c9cb083719f20d999065ae4bf388855be0913b94 build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ diff --git a/recipes/bioconductor-homo.sapiens/post-link.sh b/recipes/bioconductor-homo.sapiens/post-link.sh index d6b8209af288d..771aae174bb97 100644 --- a/recipes/bioconductor-homo.sapiens/post-link.sh +++ b/recipes/bioconductor-homo.sapiens/post-link.sh @@ -2,9 +2,9 @@ FN="Homo.sapiens_1.3.1.tar.gz" URLS=( "http://bioconductor.org/packages/3.6/data/annotation/src/contrib/Homo.sapiens_1.3.1.tar.gz" - "https://depot.galaxyproject.org/software/Homo.sapiens/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" ) - MD5="653b60cfcdaefd171729115cd629b585" +MD5="653b60cfcdaefd171729115cd629b585" # Use a staging area in the conda dir rather than temp dirs, both to avoid # permission issues as well as to have things downloaded in a predictable @@ -20,7 +20,7 @@ for URL in ${URLS[@]}; do # Platform-specific md5sum checks. if [[ $(uname -s) == "Linux" ]]; then - if [[ $(md5sum -c <<<"$MD5 $TARBALL") ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then SUCCESS=1 break fi @@ -40,5 +40,6 @@ if [[ $SUCCESS != 1 ]]; then fi # Install and clean up -R CMD INSTALL --build $TARBALL -rm $TARBALL \ No newline at end of file +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING \ No newline at end of file diff --git a/recipes/bioconductor-homo.sapiens/pre-unlink.sh b/recipes/bioconductor-homo.sapiens/pre-unlink.sh new file mode 100644 index 0000000000000..2503e16780775 --- /dev/null +++ b/recipes/bioconductor-homo.sapiens/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ Homo.sapiens diff --git a/recipes/bioconductor-hsmmsinglecell/meta.yaml b/recipes/bioconductor-hsmmsinglecell/meta.yaml index 050345db5a6b6..2d1fd956ba3fd 100644 --- a/recipes/bioconductor-hsmmsinglecell/meta.yaml +++ b/recipes/bioconductor-hsmmsinglecell/meta.yaml @@ -9,10 +9,10 @@ source: fn: '{{ name }}_{{ version }}.tar.gz' url: - 'http://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/{{ name }}/{{ name }}_{{ version }}_src_all.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' sha256: 11b6dcb7a3ee86323740aa4c3627abb4c546a890ad0d3e0a262fcf2aa49be773 build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ diff --git a/recipes/bioconductor-hsmmsinglecell/post-link.sh b/recipes/bioconductor-hsmmsinglecell/post-link.sh index 0722e1c52bb7e..a1b6ca2ab5f51 100644 --- a/recipes/bioconductor-hsmmsinglecell/post-link.sh +++ b/recipes/bioconductor-hsmmsinglecell/post-link.sh @@ -2,9 +2,9 @@ FN="HSMMSingleCell_0.112.0.tar.gz" URLS=( "http://bioconductor.org/packages/3.6/data/experiment/src/contrib/HSMMSingleCell_0.112.0.tar.gz" - "https://depot.galaxyproject.org/software/HSMMSingleCell/HSMMSingleCell_0.112.0_src_all.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-hsmmsinglecell/bioconductor-hsmmsinglecell_0.112.0_src_all.tar.gz" ) - MD5="07190931796761fc34c6c1391a6d4cfc" +MD5="07190931796761fc34c6c1391a6d4cfc" # Use a staging area in the conda dir rather than temp dirs, both to avoid # permission issues as well as to have things downloaded in a predictable @@ -20,7 +20,7 @@ for URL in ${URLS[@]}; do # Platform-specific md5sum checks. if [[ $(uname -s) == "Linux" ]]; then - if [[ $(md5sum -c <<<"$MD5 $TARBALL") ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then SUCCESS=1 break fi @@ -40,5 +40,6 @@ if [[ $SUCCESS != 1 ]]; then fi # Install and clean up -R CMD INSTALL --build $TARBALL -rm $TARBALL \ No newline at end of file +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING \ No newline at end of file diff --git a/recipes/bioconductor-hsmmsinglecell/pre-unlink.sh b/recipes/bioconductor-hsmmsinglecell/pre-unlink.sh new file mode 100644 index 0000000000000..bdfce19ccbdf1 --- /dev/null +++ b/recipes/bioconductor-hsmmsinglecell/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ HSMMSingleCell diff --git a/recipes/bioconductor-htsfilter/build.sh b/recipes/bioconductor-htsfilter/build.sh new file mode 100644 index 0000000000000..da43ce2168312 --- /dev/null +++ b/recipes/bioconductor-htsfilter/build.sh @@ -0,0 +1,4 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-htsfilter/meta.yaml b/recipes/bioconductor-htsfilter/meta.yaml new file mode 100644 index 0000000000000..90279a480a6dc --- /dev/null +++ b/recipes/bioconductor-htsfilter/meta.yaml @@ -0,0 +1,40 @@ +{% set version = "1.18.0" %} +{% set name = "HTSFilter" %} +{% set bioc = "3.6" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + fn: '{{ name }}_{{ version }}.tar.gz' + url: + - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/{{ name }}/{{ name }}_{{ version }}_src_all.tar.gz' + sha256: b10f6bd6734f603840718911ae53fd5ca600102ab064c70501701e3f994027e0 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ +requirements: + build: + - bioconductor-biobase + - 'bioconductor-biocparallel >=1.4.3' + - 'bioconductor-deseq >=1.22.1' + - 'bioconductor-deseq2 >=1.10.1' + - 'bioconductor-edger >=3.9.14' + - r-base + run: + - bioconductor-biobase + - 'bioconductor-biocparallel >=1.4.3' + - 'bioconductor-deseq >=1.22.1' + - 'bioconductor-deseq2 >=1.10.1' + - 'bioconductor-edger >=3.9.14' + - r-base +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'This package implements a filtering procedure for replicated transcriptome sequencing data based on a global Jaccard similarity index in order to identify genes with low, constant levels of expression across one or more experimental conditions.' diff --git a/recipes/bioconductor-illuminahumanmethylation450kanno.ilmn12.hg19/meta.yaml b/recipes/bioconductor-illuminahumanmethylation450kanno.ilmn12.hg19/meta.yaml index 86ecca962a8ba..eef2a5348cd37 100644 --- a/recipes/bioconductor-illuminahumanmethylation450kanno.ilmn12.hg19/meta.yaml +++ b/recipes/bioconductor-illuminahumanmethylation450kanno.ilmn12.hg19/meta.yaml @@ -9,10 +9,10 @@ source: fn: '{{ name }}_{{ version }}.tar.gz' url: - 'http://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/{{ name }}/{{ name }}_{{ version }}_src_all.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' sha256: 249b8fd62add3c95b5047b597cff0868d26a98862a47cebd656edcd175a73b15 build: - number: 1 + number: 2 rpaths: - lib/R/lib/ - lib/ diff --git a/recipes/bioconductor-illuminahumanmethylation450kanno.ilmn12.hg19/post-link.sh b/recipes/bioconductor-illuminahumanmethylation450kanno.ilmn12.hg19/post-link.sh index cc8ec5d203b71..1797cec76df10 100644 --- a/recipes/bioconductor-illuminahumanmethylation450kanno.ilmn12.hg19/post-link.sh +++ b/recipes/bioconductor-illuminahumanmethylation450kanno.ilmn12.hg19/post-link.sh @@ -2,9 +2,9 @@ FN="IlluminaHumanMethylation450kanno.ilmn12.hg19_0.6.0.tar.gz" URLS=( "http://bioconductor.org/packages/3.6/data/annotation/src/contrib/IlluminaHumanMethylation450kanno.ilmn12.hg19_0.6.0.tar.gz" - "https://depot.galaxyproject.org/software/IlluminaHumanMethylation450kanno.ilmn12.hg19/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" ) - MD5="2f569646ca8adc49863224b1cd076a79" +MD5="2f569646ca8adc49863224b1cd076a79" # Use a staging area in the conda dir rather than temp dirs, both to avoid # permission issues as well as to have things downloaded in a predictable @@ -20,7 +20,7 @@ for URL in ${URLS[@]}; do # Platform-specific md5sum checks. if [[ $(uname -s) == "Linux" ]]; then - if [[ $(md5sum -c <<<"$MD5 $TARBALL") ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then SUCCESS=1 break fi @@ -40,5 +40,6 @@ if [[ $SUCCESS != 1 ]]; then fi # Install and clean up -R CMD INSTALL --build $TARBALL -rm $TARBALL \ No newline at end of file +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING \ No newline at end of file diff --git a/recipes/bioconductor-illuminahumanmethylation450kanno.ilmn12.hg19/pre-unlink.sh b/recipes/bioconductor-illuminahumanmethylation450kanno.ilmn12.hg19/pre-unlink.sh new file mode 100644 index 0000000000000..77dfead74ba97 --- /dev/null +++ b/recipes/bioconductor-illuminahumanmethylation450kanno.ilmn12.hg19/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ IlluminaHumanMethylation450kanno.ilmn12.hg19 diff --git a/recipes/bioconductor-illuminamousev2.db/meta.yaml b/recipes/bioconductor-illuminamousev2.db/meta.yaml index ec4c28ec0d006..67729d483eb9a 100644 --- a/recipes/bioconductor-illuminamousev2.db/meta.yaml +++ b/recipes/bioconductor-illuminamousev2.db/meta.yaml @@ -9,10 +9,10 @@ source: fn: '{{ name }}_{{ version }}.tar.gz' url: - 'http://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/{{ name }}/{{ name }}_{{ version }}_src_all.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' sha256: 03864df588d7261db6923d0d7cccdd9bbb753ce60e4cdf92ba2bc3ea1318916f build: - number: 1 + number: 2 rpaths: - lib/R/lib/ - lib/ diff --git a/recipes/bioconductor-illuminamousev2.db/post-link.sh b/recipes/bioconductor-illuminamousev2.db/post-link.sh index 43e0aa240938d..843d8859926d6 100644 --- a/recipes/bioconductor-illuminamousev2.db/post-link.sh +++ b/recipes/bioconductor-illuminamousev2.db/post-link.sh @@ -2,9 +2,9 @@ FN="illuminaMousev2.db_1.26.0.tar.gz" URLS=( "http://bioconductor.org/packages/3.6/data/annotation/src/contrib/illuminaMousev2.db_1.26.0.tar.gz" - "https://depot.galaxyproject.org/software/illuminaMousev2.db/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" ) - MD5="fba228a71f264f976d8cdb035861974d" +MD5="fba228a71f264f976d8cdb035861974d" # Use a staging area in the conda dir rather than temp dirs, both to avoid # permission issues as well as to have things downloaded in a predictable @@ -20,7 +20,7 @@ for URL in ${URLS[@]}; do # Platform-specific md5sum checks. if [[ $(uname -s) == "Linux" ]]; then - if [[ $(md5sum -c <<<"$MD5 $TARBALL") ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then SUCCESS=1 break fi @@ -40,5 +40,6 @@ if [[ $SUCCESS != 1 ]]; then fi # Install and clean up -R CMD INSTALL --build $TARBALL -rm $TARBALL \ No newline at end of file +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING \ No newline at end of file diff --git a/recipes/bioconductor-illuminamousev2.db/pre-unlink.sh b/recipes/bioconductor-illuminamousev2.db/pre-unlink.sh new file mode 100644 index 0000000000000..ff57f33175597 --- /dev/null +++ b/recipes/bioconductor-illuminamousev2.db/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ illuminaMousev2.db diff --git a/recipes/bioconductor-isoformswitchanalyzer/build.sh b/recipes/bioconductor-isoformswitchanalyzer/build.sh new file mode 100644 index 0000000000000..da43ce2168312 --- /dev/null +++ b/recipes/bioconductor-isoformswitchanalyzer/build.sh @@ -0,0 +1,4 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-isoformswitchanalyzer/meta.yaml b/recipes/bioconductor-isoformswitchanalyzer/meta.yaml new file mode 100644 index 0000000000000..bf606404b3153 --- /dev/null +++ b/recipes/bioconductor-isoformswitchanalyzer/meta.yaml @@ -0,0 +1,71 @@ +{% set version = "1.0.0" %} +{% set name = "IsoformSwitchAnalyzeR" %} +{% set bioc = "3.6" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' + +source: + fn: '{{ name }}_{{ version }}.tar.gz' + url: + - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/{{ name }}/{{ name }}_{{ version }}_src_all.tar.gz' + sha256: 2ee026380092487f7be3236765219752c434b377a2644809ea8f4f23f2f0632d + +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + +requirements: + build: + - bioconductor-biostrings + - bioconductor-bsgenome + - bioconductor-cummerbund + - bioconductor-drimseq + - bioconductor-edger + - bioconductor-genomeinfodb + - bioconductor-genomicranges + - bioconductor-iranges + - bioconductor-rtracklayer + - bioconductor-splicer + - bioconductor-tximport + - r-base + - r-dbi + - r-ggplot2 + - r-gridextra + - r-plyr + - r-rcolorbrewer + - r-reshape2 + - r-venndiagram + run: + - bioconductor-biostrings + - bioconductor-bsgenome + - bioconductor-cummerbund + - bioconductor-drimseq + - bioconductor-edger + - bioconductor-genomeinfodb + - bioconductor-genomicranges + - bioconductor-iranges + - bioconductor-rtracklayer + - bioconductor-splicer + - bioconductor-tximport + - r-base + - r-dbi + - r-ggplot2 + - r-gridextra + - r-plyr + - r-rcolorbrewer + - r-reshape2 + - r-venndiagram + +test: + commands: + - '$R -e "library(''{{ name }}'')"' + +about: + home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: 'GPL (>= 2)' + summary: 'IsoformSwitchAnalyzeR enabels identification and analysis of isoform switches with predicted functional consequences (such as gain/loss of protein domains etc) from quantification by Kallisto, Salmon, Cufflinks/Cuffdiff, RSEM etc.' diff --git a/recipes/bioconductor-jaspar2014/meta.yaml b/recipes/bioconductor-jaspar2014/meta.yaml index d6dcadda832a2..b41832a29690e 100644 --- a/recipes/bioconductor-jaspar2014/meta.yaml +++ b/recipes/bioconductor-jaspar2014/meta.yaml @@ -9,10 +9,10 @@ source: fn: '{{ name }}_{{ version }}.tar.gz' url: - 'http://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/{{ name }}/{{ name }}_{{ version }}_src_all.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' sha256: 3423d5f824e238a7d863f1b901fcac0b2b40dc5404487f1563c4c9d1fd5bb90e build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ diff --git a/recipes/bioconductor-jaspar2014/post-link.sh b/recipes/bioconductor-jaspar2014/post-link.sh index acf33b27d6419..884d02201da8d 100644 --- a/recipes/bioconductor-jaspar2014/post-link.sh +++ b/recipes/bioconductor-jaspar2014/post-link.sh @@ -2,9 +2,9 @@ FN="JASPAR2014_1.14.0.tar.gz" URLS=( "http://bioconductor.org/packages/3.6/data/experiment/src/contrib/JASPAR2014_1.14.0.tar.gz" - "https://depot.galaxyproject.org/software/JASPAR2014/JASPAR2014_1.14.0_src_all.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-jaspar2014/bioconductor-jaspar2014_1.14.0_src_all.tar.gz" ) - MD5="21e7ecfc41e509059808970620eefb13" +MD5="21e7ecfc41e509059808970620eefb13" # Use a staging area in the conda dir rather than temp dirs, both to avoid # permission issues as well as to have things downloaded in a predictable @@ -20,7 +20,7 @@ for URL in ${URLS[@]}; do # Platform-specific md5sum checks. if [[ $(uname -s) == "Linux" ]]; then - if [[ $(md5sum -c <<<"$MD5 $TARBALL") ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then SUCCESS=1 break fi @@ -40,5 +40,6 @@ if [[ $SUCCESS != 1 ]]; then fi # Install and clean up -R CMD INSTALL --build $TARBALL -rm $TARBALL \ No newline at end of file +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING \ No newline at end of file diff --git a/recipes/bioconductor-jaspar2014/pre-unlink.sh b/recipes/bioconductor-jaspar2014/pre-unlink.sh new file mode 100644 index 0000000000000..4b0b9497d0e6c --- /dev/null +++ b/recipes/bioconductor-jaspar2014/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ JASPAR2014 diff --git a/recipes/bioconductor-jaspar2016/meta.yaml b/recipes/bioconductor-jaspar2016/meta.yaml index 8d1473822c7c3..a2f7e33825151 100644 --- a/recipes/bioconductor-jaspar2016/meta.yaml +++ b/recipes/bioconductor-jaspar2016/meta.yaml @@ -9,10 +9,10 @@ source: fn: '{{ name }}_{{ version }}.tar.gz' url: - 'http://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/{{ name }}/{{ name }}_{{ version }}_src_all.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' sha256: a6e24ac8588a5bef2bc314e6e2bd1e562186f8703d1d00a6b6469d295d15264e build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ @@ -22,8 +22,6 @@ requirements: run: - r-base - wget - - readline 6.2* # [linux] - test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-jaspar2016/post-link.sh b/recipes/bioconductor-jaspar2016/post-link.sh index 87f315f451fcb..4f50c7d46208b 100644 --- a/recipes/bioconductor-jaspar2016/post-link.sh +++ b/recipes/bioconductor-jaspar2016/post-link.sh @@ -2,9 +2,9 @@ FN="JASPAR2016_1.6.0.tar.gz" URLS=( "http://bioconductor.org/packages/3.6/data/experiment/src/contrib/JASPAR2016_1.6.0.tar.gz" - "https://depot.galaxyproject.org/software/JASPAR2016/JASPAR2016_1.6.0_src_all.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-jaspar2016/bioconductor-jaspar2016_1.6.0_src_all.tar.gz" ) - MD5="f2a5fcd3b7e2aa1a8775441cdb400e5a" +MD5="f2a5fcd3b7e2aa1a8775441cdb400e5a" # Use a staging area in the conda dir rather than temp dirs, both to avoid # permission issues as well as to have things downloaded in a predictable @@ -20,7 +20,7 @@ for URL in ${URLS[@]}; do # Platform-specific md5sum checks. if [[ $(uname -s) == "Linux" ]]; then - if [[ $(md5sum -c <<<"$MD5 $TARBALL") ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then SUCCESS=1 break fi @@ -40,5 +40,6 @@ if [[ $SUCCESS != 1 ]]; then fi # Install and clean up -R CMD INSTALL --build $TARBALL -rm $TARBALL \ No newline at end of file +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING \ No newline at end of file diff --git a/recipes/bioconductor-jaspar2016/pre-unlink.sh b/recipes/bioconductor-jaspar2016/pre-unlink.sh new file mode 100644 index 0000000000000..0f621cc7160fe --- /dev/null +++ b/recipes/bioconductor-jaspar2016/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ JASPAR2016 diff --git a/recipes/bioconductor-kegg.db/meta.yaml b/recipes/bioconductor-kegg.db/meta.yaml index 7fed53aba1cbb..188b893d5afa4 100644 --- a/recipes/bioconductor-kegg.db/meta.yaml +++ b/recipes/bioconductor-kegg.db/meta.yaml @@ -9,10 +9,10 @@ source: fn: '{{ name }}_{{ version }}.tar.gz' url: - 'http://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/{{ name }}/{{ name }}_{{ version }}_src_all.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' sha256: 02ea4630a3ec06a8d9a6151627c96d3f71dfc7e8857800bb5c0cdb6a838d6963 build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ diff --git a/recipes/bioconductor-kegg.db/post-link.sh b/recipes/bioconductor-kegg.db/post-link.sh index b17bff6a66f0d..759fe3f64ca8f 100644 --- a/recipes/bioconductor-kegg.db/post-link.sh +++ b/recipes/bioconductor-kegg.db/post-link.sh @@ -2,9 +2,9 @@ FN="KEGG.db_3.2.3.tar.gz" URLS=( "http://bioconductor.org/packages/3.6/data/annotation/src/contrib/KEGG.db_3.2.3.tar.gz" - "https://depot.galaxyproject.org/software/KEGG.db/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" ) - MD5="023ac22f57063627c2e62d1ae5e011b0" +MD5="023ac22f57063627c2e62d1ae5e011b0" # Use a staging area in the conda dir rather than temp dirs, both to avoid # permission issues as well as to have things downloaded in a predictable @@ -20,7 +20,7 @@ for URL in ${URLS[@]}; do # Platform-specific md5sum checks. if [[ $(uname -s) == "Linux" ]]; then - if [[ $(md5sum -c <<<"$MD5 $TARBALL") ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then SUCCESS=1 break fi @@ -40,5 +40,6 @@ if [[ $SUCCESS != 1 ]]; then fi # Install and clean up -R CMD INSTALL --build $TARBALL -rm $TARBALL \ No newline at end of file +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING \ No newline at end of file diff --git a/recipes/bioconductor-kegg.db/pre-unlink.sh b/recipes/bioconductor-kegg.db/pre-unlink.sh new file mode 100644 index 0000000000000..e0bc69add64d4 --- /dev/null +++ b/recipes/bioconductor-kegg.db/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ KEGG.db diff --git a/recipes/bioconductor-keggdzpathwaysgeo/meta.yaml b/recipes/bioconductor-keggdzpathwaysgeo/meta.yaml index cee89f539902c..2fc8b9d23d13a 100644 --- a/recipes/bioconductor-keggdzpathwaysgeo/meta.yaml +++ b/recipes/bioconductor-keggdzpathwaysgeo/meta.yaml @@ -9,10 +9,10 @@ source: fn: '{{ name }}_{{ version }}.tar.gz' url: - 'http://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/{{ name }}/{{ name }}_{{ version }}_src_all.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' sha256: 0579a620447f70977fec8d02d6aec16b43ee4d9952ba038f57d305d4181a920c build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ diff --git a/recipes/bioconductor-keggdzpathwaysgeo/post-link.sh b/recipes/bioconductor-keggdzpathwaysgeo/post-link.sh index 197bac31bb63b..9b75aba03799c 100644 --- a/recipes/bioconductor-keggdzpathwaysgeo/post-link.sh +++ b/recipes/bioconductor-keggdzpathwaysgeo/post-link.sh @@ -2,9 +2,9 @@ FN="KEGGdzPathwaysGEO_1.16.0.tar.gz" URLS=( "http://bioconductor.org/packages/3.6/data/experiment/src/contrib/KEGGdzPathwaysGEO_1.16.0.tar.gz" - "https://depot.galaxyproject.org/software/KEGGdzPathwaysGEO/KEGGdzPathwaysGEO_1.16.0_src_all.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-keggdzpathwaysgeo/bioconductor-keggdzpathwaysgeo_1.16.0_src_all.tar.gz" ) - MD5="814209c8cae15c1ecdc7efddb8a1b090" +MD5="814209c8cae15c1ecdc7efddb8a1b090" # Use a staging area in the conda dir rather than temp dirs, both to avoid # permission issues as well as to have things downloaded in a predictable @@ -20,7 +20,7 @@ for URL in ${URLS[@]}; do # Platform-specific md5sum checks. if [[ $(uname -s) == "Linux" ]]; then - if [[ $(md5sum -c <<<"$MD5 $TARBALL") ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then SUCCESS=1 break fi @@ -40,5 +40,6 @@ if [[ $SUCCESS != 1 ]]; then fi # Install and clean up -R CMD INSTALL --build $TARBALL -rm $TARBALL \ No newline at end of file +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING \ No newline at end of file diff --git a/recipes/bioconductor-keggdzpathwaysgeo/pre-unlink.sh b/recipes/bioconductor-keggdzpathwaysgeo/pre-unlink.sh new file mode 100644 index 0000000000000..ceb67a678f4cc --- /dev/null +++ b/recipes/bioconductor-keggdzpathwaysgeo/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ KEGGdzPathwaysGEO diff --git a/recipes/bioconductor-mgug4122a.db/meta.yaml b/recipes/bioconductor-mgug4122a.db/meta.yaml index 51f3ce41140a0..f7a18c42c7329 100644 --- a/recipes/bioconductor-mgug4122a.db/meta.yaml +++ b/recipes/bioconductor-mgug4122a.db/meta.yaml @@ -9,10 +9,10 @@ source: fn: '{{ name }}_{{ version }}.tar.gz' url: - 'http://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/{{ name }}/{{ name }}_{{ version }}_src_all.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' sha256: bd57e228a20744ed325b970ddd5ca731ca45e957c39d72eebcd7f2d4b0cc9574 build: - number: 1 + number: 2 rpaths: - lib/R/lib/ - lib/ diff --git a/recipes/bioconductor-mgug4122a.db/post-link.sh b/recipes/bioconductor-mgug4122a.db/post-link.sh index f51a87b19d28b..49f937afbc3d2 100644 --- a/recipes/bioconductor-mgug4122a.db/post-link.sh +++ b/recipes/bioconductor-mgug4122a.db/post-link.sh @@ -2,9 +2,9 @@ FN="mgug4122a.db_3.2.3.tar.gz" URLS=( "http://bioconductor.org/packages/3.6/data/annotation/src/contrib/mgug4122a.db_3.2.3.tar.gz" - "https://depot.galaxyproject.org/software/mgug4122a.db/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" ) - MD5="5fcdce909ac1c0ccbf06bf6411f6fe52" +MD5="5fcdce909ac1c0ccbf06bf6411f6fe52" # Use a staging area in the conda dir rather than temp dirs, both to avoid # permission issues as well as to have things downloaded in a predictable @@ -20,7 +20,7 @@ for URL in ${URLS[@]}; do # Platform-specific md5sum checks. if [[ $(uname -s) == "Linux" ]]; then - if [[ $(md5sum -c <<<"$MD5 $TARBALL") ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then SUCCESS=1 break fi @@ -40,5 +40,6 @@ if [[ $SUCCESS != 1 ]]; then fi # Install and clean up -R CMD INSTALL --build $TARBALL -rm $TARBALL \ No newline at end of file +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING \ No newline at end of file diff --git a/recipes/bioconductor-mgug4122a.db/pre-unlink.sh b/recipes/bioconductor-mgug4122a.db/pre-unlink.sh new file mode 100644 index 0000000000000..14a67b411e8e6 --- /dev/null +++ b/recipes/bioconductor-mgug4122a.db/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ mgug4122a.db diff --git a/recipes/bioconductor-mirnatap.db/meta.yaml b/recipes/bioconductor-mirnatap.db/meta.yaml new file mode 100644 index 0000000000000..3547ad7ef655a --- /dev/null +++ b/recipes/bioconductor-mirnatap.db/meta.yaml @@ -0,0 +1,44 @@ +{% set version = "0.99.10" %} +{% set name = "miRNAtap.db" %} +{% set bioc = "3.6" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' + +source: + fn: '{{ name }}_{{ version }}.tar.gz' + url: + - 'http://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + sha256: 43e735987bae9aa68b6e7544c5d1d87ebf7edcc075427114508eb8b47c7d91c8 + +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + +requirements: + build: + - bioconductor-annotationdbi + - bioconductor-mirnatap + - r-base + - r-dbi + - r-rsqlite + run: + - bioconductor-annotationdbi + - bioconductor-mirnatap + - r-base + - r-dbi + - r-rsqlite + - wget + +test: + commands: + - '$R -e "library(''{{ name }}'')"' + +about: + home: 'http://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + license: GPL-2 + summary: 'This package holds the database for miRNAtap.' diff --git a/recipes/bioconductor-mirnatap.db/post-link.sh b/recipes/bioconductor-mirnatap.db/post-link.sh new file mode 100644 index 0000000000000..f72cd811042db --- /dev/null +++ b/recipes/bioconductor-mirnatap.db/post-link.sh @@ -0,0 +1,45 @@ +#!/bin/bash +FN="miRNAtap.db_0.99.10.tar.gz" +URLS=( + "http://bioconductor.org/packages/3.6/data/annotation/src/contrib/miRNAtap.db_0.99.10.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-mirnatap.db/bioconductor-mirnatap.db_0.99.10_src_all.tar.gz" +) +MD5="48010280b68d6f1ddbff3b374132ce0a" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $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 $STAGING \ No newline at end of file diff --git a/recipes/bioconductor-mirnatap.db/pre-unlink.sh b/recipes/bioconductor-mirnatap.db/pre-unlink.sh new file mode 100644 index 0000000000000..bae5fe14928e8 --- /dev/null +++ b/recipes/bioconductor-mirnatap.db/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ miRNAtap.db diff --git a/recipes/bioconductor-mutationalpatterns/build.sh b/recipes/bioconductor-mutationalpatterns/build.sh new file mode 100644 index 0000000000000..4bc8e1853b492 --- /dev/null +++ b/recipes/bioconductor-mutationalpatterns/build.sh @@ -0,0 +1,3 @@ +#!/bin/bash + +$R CMD INSTALL --build . diff --git a/recipes/bioconductor-mutationalpatterns/meta.yaml b/recipes/bioconductor-mutationalpatterns/meta.yaml new file mode 100644 index 0000000000000..577627190858d --- /dev/null +++ b/recipes/bioconductor-mutationalpatterns/meta.yaml @@ -0,0 +1,58 @@ +{% set version = "1.4.1" %} +{% set name = "MutationalPatterns" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + fn: '{{ name }}-{{ version }}.tar.gz' + url: 'http://bioconductor.org/packages/release/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + sha256: 06e88d38bf37f5b79f408d57869a437a0fc5e6b0ac459d3918d9c582a8a31de2 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ +requirements: + build: + - r-base >=3.4.0 + - bioconductor-biostrings + - bioconductor-bsgenome + - bioconductor-genomicranges + - bioconductor-genomeinfodb >=1.12.0 + - bioconductor-iranges + - bioconductor-summarizedexperiment + - bioconductor-variantannotation + - r-ggplot2 + - r-gridextra + - r-plyr + - r-pracma + - r-nmf + - r-reshape2 + - r-ggdendro + - r-cowplot + run: + - r-base >=3.4.0 + - bioconductor-biostrings + - bioconductor-bsgenome + - bioconductor-genomicranges + - bioconductor-genomeinfodb >=1.12.0 + - bioconductor-iranges + - bioconductor-summarizedexperiment + - bioconductor-variantannotation + - r-ggplot2 + - r-gridextra + - r-plyr + - r-pracma + - r-nmf + - r-reshape2 + - r-ggdendro + - r-cowplot + +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: http://bioconductor.org/packages/release/bioc/html/{{ name }}.html + license: MIT + summary: R package for extracting and visualizing mutational patterns in base substitution catalogues diff --git a/recipes/bioconductor-org.bt.eg.db/meta.yaml b/recipes/bioconductor-org.bt.eg.db/meta.yaml index 0e9dffcfab055..2b26b1a921f16 100644 --- a/recipes/bioconductor-org.bt.eg.db/meta.yaml +++ b/recipes/bioconductor-org.bt.eg.db/meta.yaml @@ -9,10 +9,10 @@ source: fn: '{{ name }}_{{ version }}.tar.gz' url: - 'http://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/{{ name }}/{{ name }}_{{ version }}_src_all.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' sha256: 0e29e4929696938205ad173c9057a3c8afeda50a92c8666da911e282fa2594e1 build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ diff --git a/recipes/bioconductor-org.bt.eg.db/post-link.sh b/recipes/bioconductor-org.bt.eg.db/post-link.sh index 9aed28cdfabba..75f362b045271 100644 --- a/recipes/bioconductor-org.bt.eg.db/post-link.sh +++ b/recipes/bioconductor-org.bt.eg.db/post-link.sh @@ -2,9 +2,9 @@ FN="org.Bt.eg.db_3.5.0.tar.gz" URLS=( "http://bioconductor.org/packages/3.6/data/annotation/src/contrib/org.Bt.eg.db_3.5.0.tar.gz" - "https://depot.galaxyproject.org/software/org.Bt.eg.db/org.Bt.eg.db_3.5.0_src_all.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-org.bt.eg.db/bioconductor-org.bt.eg.db_3.5.0_src_all.tar.gz" ) - MD5="ac5441ee014eeac07e97dccd79bcfcdc" +MD5="ac5441ee014eeac07e97dccd79bcfcdc" # Use a staging area in the conda dir rather than temp dirs, both to avoid # permission issues as well as to have things downloaded in a predictable @@ -20,7 +20,7 @@ for URL in ${URLS[@]}; do # Platform-specific md5sum checks. if [[ $(uname -s) == "Linux" ]]; then - if [[ $(md5sum -c <<<"$MD5 $TARBALL") ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then SUCCESS=1 break fi @@ -40,5 +40,6 @@ if [[ $SUCCESS != 1 ]]; then fi # Install and clean up -R CMD INSTALL --build $TARBALL -rm $TARBALL \ No newline at end of file +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING \ No newline at end of file diff --git a/recipes/bioconductor-org.bt.eg.db/pre-unlink.sh b/recipes/bioconductor-org.bt.eg.db/pre-unlink.sh new file mode 100644 index 0000000000000..bafed7b73eda4 --- /dev/null +++ b/recipes/bioconductor-org.bt.eg.db/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ org.Bt.eg.db diff --git a/recipes/bioconductor-org.cf.eg.db/meta.yaml b/recipes/bioconductor-org.cf.eg.db/meta.yaml index 5b8afbad33d25..010d976b8b46a 100644 --- a/recipes/bioconductor-org.cf.eg.db/meta.yaml +++ b/recipes/bioconductor-org.cf.eg.db/meta.yaml @@ -9,10 +9,10 @@ source: fn: '{{ name }}_{{ version }}.tar.gz' url: - 'http://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/{{ name }}/{{ name }}_{{ version }}_src_all.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' sha256: 733ddce63a2ef0a7be3a62df73124dbaf9be80bc5a0ed13267e6999d9a73b165 build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ diff --git a/recipes/bioconductor-org.cf.eg.db/post-link.sh b/recipes/bioconductor-org.cf.eg.db/post-link.sh index 9f135dbc1c180..a5e79846c0ab0 100644 --- a/recipes/bioconductor-org.cf.eg.db/post-link.sh +++ b/recipes/bioconductor-org.cf.eg.db/post-link.sh @@ -2,9 +2,9 @@ FN="org.Cf.eg.db_3.5.0.tar.gz" URLS=( "http://bioconductor.org/packages/3.6/data/annotation/src/contrib/org.Cf.eg.db_3.5.0.tar.gz" - "https://depot.galaxyproject.org/software/org.Cf.eg.db/org.Cf.eg.db_3.5.0_src_all.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-org.cf.eg.db/bioconductor-org.cf.eg.db_3.5.0_src_all.tar.gz" ) - MD5="940e0ec6aff006739fcaf77c18fdcb7d" +MD5="940e0ec6aff006739fcaf77c18fdcb7d" # Use a staging area in the conda dir rather than temp dirs, both to avoid # permission issues as well as to have things downloaded in a predictable @@ -20,7 +20,7 @@ for URL in ${URLS[@]}; do # Platform-specific md5sum checks. if [[ $(uname -s) == "Linux" ]]; then - if [[ $(md5sum -c <<<"$MD5 $TARBALL") ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then SUCCESS=1 break fi @@ -40,5 +40,6 @@ if [[ $SUCCESS != 1 ]]; then fi # Install and clean up -R CMD INSTALL --build $TARBALL -rm $TARBALL \ No newline at end of file +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING \ No newline at end of file diff --git a/recipes/bioconductor-org.cf.eg.db/pre-unlink.sh b/recipes/bioconductor-org.cf.eg.db/pre-unlink.sh new file mode 100644 index 0000000000000..a46e8f935285a --- /dev/null +++ b/recipes/bioconductor-org.cf.eg.db/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ org.Cf.eg.db diff --git a/recipes/bioconductor-org.dm.eg.db/meta.yaml b/recipes/bioconductor-org.dm.eg.db/meta.yaml index 30e124c2ee582..bdcaf964b100f 100644 --- a/recipes/bioconductor-org.dm.eg.db/meta.yaml +++ b/recipes/bioconductor-org.dm.eg.db/meta.yaml @@ -9,10 +9,10 @@ source: fn: '{{ name }}_{{ version }}.tar.gz' url: - 'http://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/{{ name }}/{{ name }}_{{ version }}_src_all.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' sha256: edb4d45892b36dcd1d0ef519b50557a067852efa082ea0f6099ff3d1c254780c build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ diff --git a/recipes/bioconductor-org.dm.eg.db/post-link.sh b/recipes/bioconductor-org.dm.eg.db/post-link.sh index 9438eda8eb255..175d1941c6718 100644 --- a/recipes/bioconductor-org.dm.eg.db/post-link.sh +++ b/recipes/bioconductor-org.dm.eg.db/post-link.sh @@ -2,9 +2,9 @@ FN="org.Dm.eg.db_3.5.0.tar.gz" URLS=( "http://bioconductor.org/packages/3.6/data/annotation/src/contrib/org.Dm.eg.db_3.5.0.tar.gz" - "https://depot.galaxyproject.org/software/org.Dm.eg.db/org.Dm.eg.db_3.5.0_src_all.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-org.dm.eg.db/bioconductor-org.dm.eg.db_3.5.0_src_all.tar.gz" ) - MD5="6d77f8cb76054dc5db521efcdcb3db9e" +MD5="6d77f8cb76054dc5db521efcdcb3db9e" # Use a staging area in the conda dir rather than temp dirs, both to avoid # permission issues as well as to have things downloaded in a predictable @@ -20,7 +20,7 @@ for URL in ${URLS[@]}; do # Platform-specific md5sum checks. if [[ $(uname -s) == "Linux" ]]; then - if [[ $(md5sum -c <<<"$MD5 $TARBALL") ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then SUCCESS=1 break fi @@ -40,5 +40,6 @@ if [[ $SUCCESS != 1 ]]; then fi # Install and clean up -R CMD INSTALL --build $TARBALL -rm $TARBALL \ No newline at end of file +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING \ No newline at end of file diff --git a/recipes/bioconductor-org.dm.eg.db/pre-unlink.sh b/recipes/bioconductor-org.dm.eg.db/pre-unlink.sh new file mode 100644 index 0000000000000..7d3070a763ce9 --- /dev/null +++ b/recipes/bioconductor-org.dm.eg.db/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ org.Dm.eg.db diff --git a/recipes/bioconductor-org.dr.eg.db/meta.yaml b/recipes/bioconductor-org.dr.eg.db/meta.yaml index 66d4eb1095e0f..72ee903b77636 100644 --- a/recipes/bioconductor-org.dr.eg.db/meta.yaml +++ b/recipes/bioconductor-org.dr.eg.db/meta.yaml @@ -9,10 +9,10 @@ source: fn: '{{ name }}_{{ version }}.tar.gz' url: - 'http://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/{{ name }}/{{ name }}_{{ version }}_src_all.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' sha256: 201ee036671fecfd973adc5212398e1c7ac73addcbc87c30dd4c7f6915cea420 build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ diff --git a/recipes/bioconductor-org.dr.eg.db/post-link.sh b/recipes/bioconductor-org.dr.eg.db/post-link.sh index 8202a2956f384..23be5917e53b8 100644 --- a/recipes/bioconductor-org.dr.eg.db/post-link.sh +++ b/recipes/bioconductor-org.dr.eg.db/post-link.sh @@ -2,9 +2,9 @@ FN="org.Dr.eg.db_3.5.0.tar.gz" URLS=( "http://bioconductor.org/packages/3.6/data/annotation/src/contrib/org.Dr.eg.db_3.5.0.tar.gz" - "https://depot.galaxyproject.org/software/org.Dr.eg.db/org.Dr.eg.db_3.5.0_src_all.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-org.dr.eg.db/bioconductor-org.dr.eg.db_3.5.0_src_all.tar.gz" ) - MD5="4692a5271060b44f8f684ac2d244fed0" +MD5="4692a5271060b44f8f684ac2d244fed0" # Use a staging area in the conda dir rather than temp dirs, both to avoid # permission issues as well as to have things downloaded in a predictable @@ -20,7 +20,7 @@ for URL in ${URLS[@]}; do # Platform-specific md5sum checks. if [[ $(uname -s) == "Linux" ]]; then - if [[ $(md5sum -c <<<"$MD5 $TARBALL") ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then SUCCESS=1 break fi @@ -40,5 +40,6 @@ if [[ $SUCCESS != 1 ]]; then fi # Install and clean up -R CMD INSTALL --build $TARBALL -rm $TARBALL \ No newline at end of file +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING \ No newline at end of file diff --git a/recipes/bioconductor-org.dr.eg.db/pre-unlink.sh b/recipes/bioconductor-org.dr.eg.db/pre-unlink.sh new file mode 100644 index 0000000000000..f286ff0ef79c2 --- /dev/null +++ b/recipes/bioconductor-org.dr.eg.db/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ org.Dr.eg.db diff --git a/recipes/bioconductor-org.gg.eg.db/meta.yaml b/recipes/bioconductor-org.gg.eg.db/meta.yaml index 3d189508a4d8f..508bc7012d4e7 100644 --- a/recipes/bioconductor-org.gg.eg.db/meta.yaml +++ b/recipes/bioconductor-org.gg.eg.db/meta.yaml @@ -9,10 +9,10 @@ source: fn: '{{ name }}_{{ version }}.tar.gz' url: - 'http://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/{{ name }}/{{ name }}_{{ version }}_src_all.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' sha256: 78600092d295756495c221e90d5316bea4448844ddbc0aae2c587647d44cafe0 build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ diff --git a/recipes/bioconductor-org.gg.eg.db/post-link.sh b/recipes/bioconductor-org.gg.eg.db/post-link.sh index 1ea169f76a850..ecbd48bc346ac 100644 --- a/recipes/bioconductor-org.gg.eg.db/post-link.sh +++ b/recipes/bioconductor-org.gg.eg.db/post-link.sh @@ -2,9 +2,9 @@ FN="org.Gg.eg.db_3.5.0.tar.gz" URLS=( "http://bioconductor.org/packages/3.6/data/annotation/src/contrib/org.Gg.eg.db_3.5.0.tar.gz" - "https://depot.galaxyproject.org/software/org.Gg.eg.db/org.Gg.eg.db_3.5.0_src_all.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-org.gg.eg.db/bioconductor-org.gg.eg.db_3.5.0_src_all.tar.gz" ) - MD5="5e893d822ca6e7af68a2f62445bbe400" +MD5="5e893d822ca6e7af68a2f62445bbe400" # Use a staging area in the conda dir rather than temp dirs, both to avoid # permission issues as well as to have things downloaded in a predictable @@ -20,7 +20,7 @@ for URL in ${URLS[@]}; do # Platform-specific md5sum checks. if [[ $(uname -s) == "Linux" ]]; then - if [[ $(md5sum -c <<<"$MD5 $TARBALL") ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then SUCCESS=1 break fi @@ -40,5 +40,6 @@ if [[ $SUCCESS != 1 ]]; then fi # Install and clean up -R CMD INSTALL --build $TARBALL -rm $TARBALL \ No newline at end of file +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING \ No newline at end of file diff --git a/recipes/bioconductor-org.gg.eg.db/pre-unlink.sh b/recipes/bioconductor-org.gg.eg.db/pre-unlink.sh new file mode 100644 index 0000000000000..726e931f20d0b --- /dev/null +++ b/recipes/bioconductor-org.gg.eg.db/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ org.Gg.eg.db diff --git a/recipes/bioconductor-org.hs.eg.db/meta.yaml b/recipes/bioconductor-org.hs.eg.db/meta.yaml index 449729ab69db1..92e9106a6200b 100644 --- a/recipes/bioconductor-org.hs.eg.db/meta.yaml +++ b/recipes/bioconductor-org.hs.eg.db/meta.yaml @@ -9,10 +9,10 @@ source: fn: '{{ name }}_{{ version }}.tar.gz' url: - 'http://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/{{ name }}/{{ name }}_{{ version }}_src_all.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' sha256: 4724452fcd36c3192263822e95ea5262d99429fa38f4d37a2a58b2114c51dcec build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ diff --git a/recipes/bioconductor-org.hs.eg.db/post-link.sh b/recipes/bioconductor-org.hs.eg.db/post-link.sh index 0020bcb9d9fb6..3f885319b7167 100644 --- a/recipes/bioconductor-org.hs.eg.db/post-link.sh +++ b/recipes/bioconductor-org.hs.eg.db/post-link.sh @@ -2,9 +2,9 @@ FN="org.Hs.eg.db_3.5.0.tar.gz" URLS=( "http://bioconductor.org/packages/3.6/data/annotation/src/contrib/org.Hs.eg.db_3.5.0.tar.gz" - "https://depot.galaxyproject.org/software/org.Hs.eg.db/org.Hs.eg.db_3.5.0_src_all.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-org.hs.eg.db/bioconductor-org.hs.eg.db_3.5.0_src_all.tar.gz" ) - MD5="9f0d948c0d1b0be3188d51d8ca57fde4" +MD5="9f0d948c0d1b0be3188d51d8ca57fde4" # Use a staging area in the conda dir rather than temp dirs, both to avoid # permission issues as well as to have things downloaded in a predictable @@ -20,7 +20,7 @@ for URL in ${URLS[@]}; do # Platform-specific md5sum checks. if [[ $(uname -s) == "Linux" ]]; then - if [[ $(md5sum -c <<<"$MD5 $TARBALL") ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then SUCCESS=1 break fi @@ -40,5 +40,6 @@ if [[ $SUCCESS != 1 ]]; then fi # Install and clean up -R CMD INSTALL --build $TARBALL -rm $TARBALL \ No newline at end of file +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING \ No newline at end of file diff --git a/recipes/bioconductor-org.hs.eg.db/pre-unlink.sh b/recipes/bioconductor-org.hs.eg.db/pre-unlink.sh new file mode 100644 index 0000000000000..1a6ae646519e0 --- /dev/null +++ b/recipes/bioconductor-org.hs.eg.db/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ org.Hs.eg.db diff --git a/recipes/bioconductor-org.mm.eg.db/meta.yaml b/recipes/bioconductor-org.mm.eg.db/meta.yaml index f88e76976747f..e44470beae461 100644 --- a/recipes/bioconductor-org.mm.eg.db/meta.yaml +++ b/recipes/bioconductor-org.mm.eg.db/meta.yaml @@ -9,10 +9,10 @@ source: fn: '{{ name }}_{{ version }}.tar.gz' url: - 'http://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/{{ name }}/{{ name }}_{{ version }}_src_all.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' sha256: cf34b2a1bc1663e82c49d56855a531b4105ace79a047351624769138c70d0287 build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ diff --git a/recipes/bioconductor-org.mm.eg.db/post-link.sh b/recipes/bioconductor-org.mm.eg.db/post-link.sh index 1c88944f90769..04b8ec6e18830 100644 --- a/recipes/bioconductor-org.mm.eg.db/post-link.sh +++ b/recipes/bioconductor-org.mm.eg.db/post-link.sh @@ -2,9 +2,9 @@ FN="org.Mm.eg.db_3.5.0.tar.gz" URLS=( "http://bioconductor.org/packages/3.6/data/annotation/src/contrib/org.Mm.eg.db_3.5.0.tar.gz" - "https://depot.galaxyproject.org/software/org.Mm.eg.db/org.Mm.eg.db_3.5.0_src_all.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-org.mm.eg.db/bioconductor-org.mm.eg.db_3.5.0_src_all.tar.gz" ) - MD5="84b6d4a45dbd80a4ac00edc0a2b51001" +MD5="84b6d4a45dbd80a4ac00edc0a2b51001" # Use a staging area in the conda dir rather than temp dirs, both to avoid # permission issues as well as to have things downloaded in a predictable @@ -20,7 +20,7 @@ for URL in ${URLS[@]}; do # Platform-specific md5sum checks. if [[ $(uname -s) == "Linux" ]]; then - if [[ $(md5sum -c <<<"$MD5 $TARBALL") ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then SUCCESS=1 break fi @@ -40,5 +40,6 @@ if [[ $SUCCESS != 1 ]]; then fi # Install and clean up -R CMD INSTALL --build $TARBALL -rm $TARBALL \ No newline at end of file +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING \ No newline at end of file diff --git a/recipes/bioconductor-org.mm.eg.db/pre-unlink.sh b/recipes/bioconductor-org.mm.eg.db/pre-unlink.sh new file mode 100644 index 0000000000000..01074c839e453 --- /dev/null +++ b/recipes/bioconductor-org.mm.eg.db/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ org.Mm.eg.db diff --git a/recipes/bioconductor-org.rn.eg.db/meta.yaml b/recipes/bioconductor-org.rn.eg.db/meta.yaml index 455e9340f1217..25fc85c31073d 100644 --- a/recipes/bioconductor-org.rn.eg.db/meta.yaml +++ b/recipes/bioconductor-org.rn.eg.db/meta.yaml @@ -9,10 +9,10 @@ source: fn: '{{ name }}_{{ version }}.tar.gz' url: - 'http://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/{{ name }}/{{ name }}_{{ version }}_src_all.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' sha256: a4971a0c56cfcb48f603b24ffd0538c6864b12d7865e2fc91e90ae89808a7687 build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ diff --git a/recipes/bioconductor-org.rn.eg.db/post-link.sh b/recipes/bioconductor-org.rn.eg.db/post-link.sh index 46c933773ff8b..d28127e1aeb25 100644 --- a/recipes/bioconductor-org.rn.eg.db/post-link.sh +++ b/recipes/bioconductor-org.rn.eg.db/post-link.sh @@ -2,9 +2,9 @@ FN="org.Rn.eg.db_3.5.0.tar.gz" URLS=( "http://bioconductor.org/packages/3.6/data/annotation/src/contrib/org.Rn.eg.db_3.5.0.tar.gz" - "https://depot.galaxyproject.org/software/org.Rn.eg.db/org.Rn.eg.db_3.5.0_src_all.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-org.rn.eg.db/bioconductor-org.rn.eg.db_3.5.0_src_all.tar.gz" ) - MD5="fb3218e500ecc6a4e8a4857ab310a23e" +MD5="fb3218e500ecc6a4e8a4857ab310a23e" # Use a staging area in the conda dir rather than temp dirs, both to avoid # permission issues as well as to have things downloaded in a predictable @@ -20,7 +20,7 @@ for URL in ${URLS[@]}; do # Platform-specific md5sum checks. if [[ $(uname -s) == "Linux" ]]; then - if [[ $(md5sum -c <<<"$MD5 $TARBALL") ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then SUCCESS=1 break fi @@ -40,5 +40,6 @@ if [[ $SUCCESS != 1 ]]; then fi # Install and clean up -R CMD INSTALL --build $TARBALL -rm $TARBALL \ No newline at end of file +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING \ No newline at end of file diff --git a/recipes/bioconductor-org.rn.eg.db/pre-unlink.sh b/recipes/bioconductor-org.rn.eg.db/pre-unlink.sh new file mode 100644 index 0000000000000..c38f06b52265f --- /dev/null +++ b/recipes/bioconductor-org.rn.eg.db/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ org.Rn.eg.db diff --git a/recipes/bioconductor-org.ss.eg.db/meta.yaml b/recipes/bioconductor-org.ss.eg.db/meta.yaml index 1706b5ca3b8a7..d9a9b9284aa1d 100644 --- a/recipes/bioconductor-org.ss.eg.db/meta.yaml +++ b/recipes/bioconductor-org.ss.eg.db/meta.yaml @@ -9,10 +9,10 @@ source: fn: '{{ name }}_{{ version }}.tar.gz' url: - 'http://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/{{ name }}/{{ name }}_{{ version }}_src_all.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' sha256: cc08bee98f13c47605755e7ab41f9cdaa840749c5e0931a2bbc22ad31ba93ff2 build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ diff --git a/recipes/bioconductor-org.ss.eg.db/post-link.sh b/recipes/bioconductor-org.ss.eg.db/post-link.sh index 8759cf1167dd4..d8df8281eba65 100644 --- a/recipes/bioconductor-org.ss.eg.db/post-link.sh +++ b/recipes/bioconductor-org.ss.eg.db/post-link.sh @@ -2,9 +2,9 @@ FN="org.Ss.eg.db_3.5.0.tar.gz" URLS=( "http://bioconductor.org/packages/3.6/data/annotation/src/contrib/org.Ss.eg.db_3.5.0.tar.gz" - "https://depot.galaxyproject.org/software/org.Ss.eg.db/org.Ss.eg.db_3.5.0_src_all.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-org.ss.eg.db/bioconductor-org.ss.eg.db_3.5.0_src_all.tar.gz" ) - MD5="da8874c9958f6a40c84afbc7718b701c" +MD5="da8874c9958f6a40c84afbc7718b701c" # Use a staging area in the conda dir rather than temp dirs, both to avoid # permission issues as well as to have things downloaded in a predictable @@ -20,7 +20,7 @@ for URL in ${URLS[@]}; do # Platform-specific md5sum checks. if [[ $(uname -s) == "Linux" ]]; then - if [[ $(md5sum -c <<<"$MD5 $TARBALL") ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then SUCCESS=1 break fi @@ -40,5 +40,6 @@ if [[ $SUCCESS != 1 ]]; then fi # Install and clean up -R CMD INSTALL --build $TARBALL -rm $TARBALL \ No newline at end of file +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING \ No newline at end of file diff --git a/recipes/bioconductor-org.ss.eg.db/pre-unlink.sh b/recipes/bioconductor-org.ss.eg.db/pre-unlink.sh new file mode 100644 index 0000000000000..ac3131b33b8e5 --- /dev/null +++ b/recipes/bioconductor-org.ss.eg.db/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ org.Ss.eg.db diff --git a/recipes/bioconductor-pchicdata/meta.yaml b/recipes/bioconductor-pchicdata/meta.yaml index 98aeab2f6e8fa..8b8c35e17e2f4 100644 --- a/recipes/bioconductor-pchicdata/meta.yaml +++ b/recipes/bioconductor-pchicdata/meta.yaml @@ -9,10 +9,10 @@ source: fn: '{{ name }}_{{ version }}.tar.gz' url: - 'http://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/{{ name }}/{{ name }}_{{ version }}_src_all.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' sha256: dd1307f6213e4106e67e998024e1d690010682b45442a155dcb63e2ccde710b7 build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ diff --git a/recipes/bioconductor-pchicdata/post-link.sh b/recipes/bioconductor-pchicdata/post-link.sh index e93b024031e2b..a015fc259200c 100644 --- a/recipes/bioconductor-pchicdata/post-link.sh +++ b/recipes/bioconductor-pchicdata/post-link.sh @@ -2,9 +2,9 @@ FN="PCHiCdata_1.6.0.tar.gz" URLS=( "http://bioconductor.org/packages/3.6/data/experiment/src/contrib/PCHiCdata_1.6.0.tar.gz" - "https://depot.galaxyproject.org/software/PCHiCdata/PCHiCdata_1.6.0_src_all.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-pchicdata/bioconductor-pchicdata_1.6.0_src_all.tar.gz" ) - MD5="d8dcf967d070f86647b12580e51ed07a" +MD5="d8dcf967d070f86647b12580e51ed07a" # Use a staging area in the conda dir rather than temp dirs, both to avoid # permission issues as well as to have things downloaded in a predictable @@ -20,7 +20,7 @@ for URL in ${URLS[@]}; do # Platform-specific md5sum checks. if [[ $(uname -s) == "Linux" ]]; then - if [[ $(md5sum -c <<<"$MD5 $TARBALL") ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then SUCCESS=1 break fi @@ -40,5 +40,6 @@ if [[ $SUCCESS != 1 ]]; then fi # Install and clean up -R CMD INSTALL --build $TARBALL -rm $TARBALL \ No newline at end of file +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING \ No newline at end of file diff --git a/recipes/bioconductor-pchicdata/pre-unlink.sh b/recipes/bioconductor-pchicdata/pre-unlink.sh new file mode 100644 index 0000000000000..cc91fee21e059 --- /dev/null +++ b/recipes/bioconductor-pchicdata/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ PCHiCdata diff --git a/recipes/bioconductor-qdnaseq.mm10/meta.yaml b/recipes/bioconductor-qdnaseq.mm10/meta.yaml index ff12750951963..43907609cdccd 100644 --- a/recipes/bioconductor-qdnaseq.mm10/meta.yaml +++ b/recipes/bioconductor-qdnaseq.mm10/meta.yaml @@ -9,10 +9,10 @@ source: fn: '{{ name }}_{{ version }}.tar.gz' url: - 'http://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/{{ name }}/{{ name }}_{{ version }}_src_all.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' sha256: 6c3356ba2be7fdcbfe0837613a52dc3e1601b953e2b1dec90f384e976cce5f9d build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ diff --git a/recipes/bioconductor-qdnaseq.mm10/post-link.sh b/recipes/bioconductor-qdnaseq.mm10/post-link.sh index 6e15859fa6de2..91395c6d1f40a 100644 --- a/recipes/bioconductor-qdnaseq.mm10/post-link.sh +++ b/recipes/bioconductor-qdnaseq.mm10/post-link.sh @@ -2,9 +2,9 @@ FN="QDNAseq.mm10_1.8.0.tar.gz" URLS=( "http://bioconductor.org/packages/3.6/data/experiment/src/contrib/QDNAseq.mm10_1.8.0.tar.gz" - "https://depot.galaxyproject.org/software/QDNAseq.mm10/QDNAseq.mm10_1.8.0_src_all.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-qdnaseq.mm10/bioconductor-qdnaseq.mm10_1.8.0_src_all.tar.gz" ) - MD5="dbbf1cb5ab643feaa7e0c2e5b8902c90" +MD5="dbbf1cb5ab643feaa7e0c2e5b8902c90" # Use a staging area in the conda dir rather than temp dirs, both to avoid # permission issues as well as to have things downloaded in a predictable @@ -20,7 +20,7 @@ for URL in ${URLS[@]}; do # Platform-specific md5sum checks. if [[ $(uname -s) == "Linux" ]]; then - if [[ $(md5sum -c <<<"$MD5 $TARBALL") ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then SUCCESS=1 break fi @@ -40,5 +40,6 @@ if [[ $SUCCESS != 1 ]]; then fi # Install and clean up -R CMD INSTALL --build $TARBALL -rm $TARBALL \ No newline at end of file +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING \ No newline at end of file diff --git a/recipes/bioconductor-qdnaseq.mm10/pre-unlink.sh b/recipes/bioconductor-qdnaseq.mm10/pre-unlink.sh new file mode 100644 index 0000000000000..9b70ef2a34065 --- /dev/null +++ b/recipes/bioconductor-qdnaseq.mm10/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ QDNAseq.mm10 diff --git a/recipes/bioconductor-recount/build.sh b/recipes/bioconductor-recount/build.sh new file mode 100644 index 0000000000000..da43ce2168312 --- /dev/null +++ b/recipes/bioconductor-recount/build.sh @@ -0,0 +1,4 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-recount/meta.yaml b/recipes/bioconductor-recount/meta.yaml new file mode 100644 index 0000000000000..5f817f41dcfd6 --- /dev/null +++ b/recipes/bioconductor-recount/meta.yaml @@ -0,0 +1,65 @@ +{% set version = "1.4.0" %} +{% set name = "recount" %} +{% set bioc = "3.6" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' + +source: + fn: '{{ name }}_{{ version }}.tar.gz' + url: + - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/{{ name }}/{{ name }}_{{ version }}_src_all.tar.gz' + sha256: 07824d7b0fab88e8501a6951008efafddd3bce5b17d25f746974350951f546ee + +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + +requirements: + build: + - bioconductor-biocparallel + - bioconductor-derfinder + - bioconductor-genomeinfodb + - bioconductor-genomicranges + - bioconductor-geoquery + - bioconductor-iranges + - 'bioconductor-rtracklayer >=1.35.3' + - bioconductor-s4vectors + - bioconductor-summarizedexperiment + - r-base + - r-downloader + - r-rcurl + - r-rentrez + run: + - bioconductor-biocparallel + - bioconductor-derfinder + - bioconductor-genomeinfodb + - bioconductor-genomicranges + - bioconductor-geoquery + - bioconductor-iranges + - 'bioconductor-rtracklayer >=1.35.3' + - bioconductor-s4vectors + - bioconductor-summarizedexperiment + - r-base + - r-downloader + - r-rcurl + - r-rentrez + +test: + commands: + - '$R -e "library(''{{ name }}'')"' + +about: + home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'Explore and download data from the recount project available at https://jhubiostatistics.shinyapps.io/recount/. + Using the recount package you can download RangedSummarizedExperiment objects at the gene, exon or exon-exon junctions + level, the raw counts, the phenotype metadata used, the urls to the sample coverage bigWig files or the mean coverage + bigWig file for a particular study. The RangedSummarizedExperiment objects can be used by different packages for performing + differential expression analysis. Using http://bioconductor.org/packages/derfinder you can perform annotation-agnostic + differential expression analyses with the data from the recount project as described + at http://www.nature.com/nbt/journal/v35/n4/full/nbt.3838.html.' diff --git a/recipes/bioconductor-snplocs.hsapiens.dbsnp144.grch38/meta.yaml b/recipes/bioconductor-snplocs.hsapiens.dbsnp144.grch38/meta.yaml new file mode 100644 index 0000000000000..6731ed6f57374 --- /dev/null +++ b/recipes/bioconductor-snplocs.hsapiens.dbsnp144.grch38/meta.yaml @@ -0,0 +1,43 @@ +{% set version = "0.99.20" %} +{% set name = "SNPlocs.Hsapiens.dbSNP144.GRCh38" %} +{% set bioc = "3.6" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + fn: '{{ name }}_{{ version }}.tar.gz' + url: + - 'http://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + sha256: b6c6ae8d3a866501146e325d40dc1695b26b522c6f9d063218fc6466bbd5b57b +build: + number: 1 + rpaths: + - lib/R/lib/ + - lib/ +requirements: + build: + - bioconductor-biocgenerics + - 'bioconductor-bsgenome >=1.43.4' + - bioconductor-genomeinfodb + - bioconductor-genomicranges + - bioconductor-iranges + - bioconductor-s4vectors + - r-base + run: + - bioconductor-biocgenerics + - 'bioconductor-bsgenome >=1.43.4' + - bioconductor-genomeinfodb + - bioconductor-genomicranges + - bioconductor-iranges + - bioconductor-s4vectors + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'http://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'SNP locations and alleles for Homo sapiens extracted from NCBI dbSNP Build 144. The source data files used for this package were created by NCBI on May 30, 2015, and contain SNPs mapped to reference genome GRCh38.p2 (a patched version of GRCh38 that doesn''t alter chromosomes 1-22, X, Y, MT). Note that these SNPs can be "injected" in BSgenome.Hsapiens.NCBI.GRCh38 or in BSgenome.Hsapiens.UCSC.hg38.' diff --git a/recipes/bioconductor-snplocs.hsapiens.dbsnp144.grch38/post-link.sh b/recipes/bioconductor-snplocs.hsapiens.dbsnp144.grch38/post-link.sh new file mode 100644 index 0000000000000..42fb9215c4053 --- /dev/null +++ b/recipes/bioconductor-snplocs.hsapiens.dbsnp144.grch38/post-link.sh @@ -0,0 +1,45 @@ +#!/bin/bash +FN="SNPlocs.Hsapiens.dbSNP144.GRCh38_0.99.20.tar.gz" +URLS=( + "http://bioconductor.org/packages/3.6/data/annotation/src/contrib/SNPlocs.Hsapiens.dbSNP144.GRCh38_0.99.20.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-snplocs.hsapiens.dbsnp144.grch38/bioconductor-snplocs.hsapiens.dbsnp144.grch38_0.99.20_src_all.tar.gz" +) +MD5="128c95e327adf72ae137fb5ae58270fc" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $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 $STAGING \ No newline at end of file diff --git a/recipes/bioconductor-snplocs.hsapiens.dbsnp144.grch38/pre-unlink.sh b/recipes/bioconductor-snplocs.hsapiens.dbsnp144.grch38/pre-unlink.sh new file mode 100644 index 0000000000000..04a810bee2620 --- /dev/null +++ b/recipes/bioconductor-snplocs.hsapiens.dbsnp144.grch38/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ SNPlocs.Hsapiens.dbSNP144.GRCh38 diff --git a/recipes/bioconductor-splatter/build.sh b/recipes/bioconductor-splatter/build.sh new file mode 100644 index 0000000000000..da43ce2168312 --- /dev/null +++ b/recipes/bioconductor-splatter/build.sh @@ -0,0 +1,4 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-splatter/meta.yaml b/recipes/bioconductor-splatter/meta.yaml new file mode 100644 index 0000000000000..1ecf3d831e341 --- /dev/null +++ b/recipes/bioconductor-splatter/meta.yaml @@ -0,0 +1,56 @@ +{% set version = "1.2.1" %} +{% set name = "splatter" %} +{% set bioc = "3.6" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + fn: '{{ name }}_{{ version }}.tar.gz' + url: + - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/{{ name }}/{{ name }}_{{ version }}_src_all.tar.gz' + sha256: af641527ae3fb21966d11201fa227bf0934973c6b5cfcb38bac52a576b485745 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ +requirements: + build: + - bioconductor-biocgenerics + - bioconductor-biocparallel + - bioconductor-edger + - bioconductor-scater + - bioconductor-singlecellexperiment + - bioconductor-summarizedexperiment + - r-akima + - r-base + - r-checkmate + - r-fitdistrplus + - r-ggplot2 + - r-locfit + - r-matrixstats + - r-scales + run: + - bioconductor-biocgenerics + - bioconductor-biocparallel + - bioconductor-edger + - bioconductor-scater + - bioconductor-singlecellexperiment + - bioconductor-summarizedexperiment + - r-akima + - r-base + - r-checkmate + - r-fitdistrplus + - r-ggplot2 + - r-locfit + - r-matrixstats + - r-scales +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: 'GPL-3 + file LICENSE' + summary: 'Splatter is a package for the simulation of single-cell RNA sequencing count data. It provides a simple interface for creating complex simulations that are reproducible and well-documented. Parameters can be estimated from real data and functions are provided for comparing real and simulated datasets.' diff --git a/recipes/bioconductor-txdb.celegans.ucsc.ce11.refgene/meta.yaml b/recipes/bioconductor-txdb.celegans.ucsc.ce11.refgene/meta.yaml index 51f3e2bab587f..0f51758aa9f66 100644 --- a/recipes/bioconductor-txdb.celegans.ucsc.ce11.refgene/meta.yaml +++ b/recipes/bioconductor-txdb.celegans.ucsc.ce11.refgene/meta.yaml @@ -9,10 +9,10 @@ source: fn: '{{ name }}_{{ version }}.tar.gz' url: - 'http://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/{{ name }}/{{ name }}_{{ version }}_src_all.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' sha256: 4331555a7214d576dbbae002dcfa121596c341dcf44f8307de5a6e5c4d2e943c build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ 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 edb76ae474cc1..39861d72448db 100644 --- a/recipes/bioconductor-txdb.celegans.ucsc.ce11.refgene/post-link.sh +++ b/recipes/bioconductor-txdb.celegans.ucsc.ce11.refgene/post-link.sh @@ -2,9 +2,9 @@ FN="TxDb.Celegans.UCSC.ce11.refGene_3.4.2.tar.gz" URLS=( "http://bioconductor.org/packages/3.6/data/annotation/src/contrib/TxDb.Celegans.UCSC.ce11.refGene_3.4.2.tar.gz" - "https://depot.galaxyproject.org/software/TxDb.Celegans.UCSC.ce11.refGene/TxDb.Celegans.UCSC.ce11.refGene_3.4.2_src_all.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-txdb.celegans.ucsc.ce11.refgene/bioconductor-txdb.celegans.ucsc.ce11.refgene_3.4.2_src_all.tar.gz" ) - MD5="db249f10830c9e547852ae2996afb420" +MD5="db249f10830c9e547852ae2996afb420" # Use a staging area in the conda dir rather than temp dirs, both to avoid # permission issues as well as to have things downloaded in a predictable @@ -20,7 +20,7 @@ for URL in ${URLS[@]}; do # Platform-specific md5sum checks. if [[ $(uname -s) == "Linux" ]]; then - if [[ $(md5sum -c <<<"$MD5 $TARBALL") ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then SUCCESS=1 break fi @@ -40,5 +40,6 @@ if [[ $SUCCESS != 1 ]]; then fi # Install and clean up -R CMD INSTALL --build $TARBALL -rm $TARBALL \ No newline at end of file +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING \ No newline at end of file diff --git a/recipes/bioconductor-txdb.celegans.ucsc.ce11.refgene/pre-unlink.sh b/recipes/bioconductor-txdb.celegans.ucsc.ce11.refgene/pre-unlink.sh new file mode 100644 index 0000000000000..3861ff216823c --- /dev/null +++ b/recipes/bioconductor-txdb.celegans.ucsc.ce11.refgene/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ TxDb.Celegans.UCSC.ce11.refGene diff --git a/recipes/bioconductor-txdb.celegans.ucsc.ce6.ensgene/meta.yaml b/recipes/bioconductor-txdb.celegans.ucsc.ce6.ensgene/meta.yaml index 62cde772a8773..898c046461b50 100644 --- a/recipes/bioconductor-txdb.celegans.ucsc.ce6.ensgene/meta.yaml +++ b/recipes/bioconductor-txdb.celegans.ucsc.ce6.ensgene/meta.yaml @@ -9,10 +9,10 @@ source: fn: '{{ name }}_{{ version }}.tar.gz' url: - 'http://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/{{ name }}/{{ name }}_{{ version }}_src_all.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' sha256: 20c51a06664f1135500b3ce1b9eeacf5154995ab4847217524beb131d4bef7e9 build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ 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 0df6f1f2731c6..ffceae30a4b53 100644 --- a/recipes/bioconductor-txdb.celegans.ucsc.ce6.ensgene/post-link.sh +++ b/recipes/bioconductor-txdb.celegans.ucsc.ce6.ensgene/post-link.sh @@ -2,9 +2,9 @@ FN="TxDb.Celegans.UCSC.ce6.ensGene_3.2.2.tar.gz" URLS=( "http://bioconductor.org/packages/3.6/data/annotation/src/contrib/TxDb.Celegans.UCSC.ce6.ensGene_3.2.2.tar.gz" - "https://depot.galaxyproject.org/software/TxDb.Celegans.UCSC.ce6.ensGene/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" ) - MD5="215c2edd440a3df8229fe6a75b431aa8" +MD5="215c2edd440a3df8229fe6a75b431aa8" # Use a staging area in the conda dir rather than temp dirs, both to avoid # permission issues as well as to have things downloaded in a predictable @@ -20,7 +20,7 @@ for URL in ${URLS[@]}; do # Platform-specific md5sum checks. if [[ $(uname -s) == "Linux" ]]; then - if [[ $(md5sum -c <<<"$MD5 $TARBALL") ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then SUCCESS=1 break fi @@ -40,5 +40,6 @@ if [[ $SUCCESS != 1 ]]; then fi # Install and clean up -R CMD INSTALL --build $TARBALL -rm $TARBALL \ No newline at end of file +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING \ No newline at end of file diff --git a/recipes/bioconductor-txdb.celegans.ucsc.ce6.ensgene/pre-unlink.sh b/recipes/bioconductor-txdb.celegans.ucsc.ce6.ensgene/pre-unlink.sh new file mode 100644 index 0000000000000..aa87c84ff4847 --- /dev/null +++ b/recipes/bioconductor-txdb.celegans.ucsc.ce6.ensgene/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ TxDb.Celegans.UCSC.ce6.ensGene diff --git a/recipes/bioconductor-txdb.dmelanogaster.ucsc.dm3.ensgene/meta.yaml b/recipes/bioconductor-txdb.dmelanogaster.ucsc.dm3.ensgene/meta.yaml index f004d72d97f4e..3eaedff839174 100644 --- a/recipes/bioconductor-txdb.dmelanogaster.ucsc.dm3.ensgene/meta.yaml +++ b/recipes/bioconductor-txdb.dmelanogaster.ucsc.dm3.ensgene/meta.yaml @@ -9,10 +9,10 @@ source: fn: '{{ name }}_{{ version }}.tar.gz' url: - 'http://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/{{ name }}/{{ name }}_{{ version }}_src_all.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' sha256: 879d366e7c6ca9734a059c060e0b36019e11f32c42e83a90fa31d69687e8678c build: - number: 1 + number: 2 rpaths: - lib/R/lib/ - lib/ 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 dab7140302494..525d0ecd5cfc3 100644 --- a/recipes/bioconductor-txdb.dmelanogaster.ucsc.dm3.ensgene/post-link.sh +++ b/recipes/bioconductor-txdb.dmelanogaster.ucsc.dm3.ensgene/post-link.sh @@ -2,9 +2,9 @@ FN="TxDb.Dmelanogaster.UCSC.dm3.ensGene_3.2.2.tar.gz" URLS=( "http://bioconductor.org/packages/3.6/data/annotation/src/contrib/TxDb.Dmelanogaster.UCSC.dm3.ensGene_3.2.2.tar.gz" - "https://depot.galaxyproject.org/software/TxDb.Dmelanogaster.UCSC.dm3.ensGene/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" ) - MD5="46b7ffe0c516edf8a2a3b5d78e0d8b67" +MD5="46b7ffe0c516edf8a2a3b5d78e0d8b67" # Use a staging area in the conda dir rather than temp dirs, both to avoid # permission issues as well as to have things downloaded in a predictable @@ -20,7 +20,7 @@ for URL in ${URLS[@]}; do # Platform-specific md5sum checks. if [[ $(uname -s) == "Linux" ]]; then - if [[ $(md5sum -c <<<"$MD5 $TARBALL") ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then SUCCESS=1 break fi @@ -40,5 +40,6 @@ if [[ $SUCCESS != 1 ]]; then fi # Install and clean up -R CMD INSTALL --build $TARBALL -rm $TARBALL \ No newline at end of file +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING \ No newline at end of file diff --git a/recipes/bioconductor-txdb.dmelanogaster.ucsc.dm3.ensgene/pre-unlink.sh b/recipes/bioconductor-txdb.dmelanogaster.ucsc.dm3.ensgene/pre-unlink.sh new file mode 100644 index 0000000000000..96bfefe0e4cc7 --- /dev/null +++ b/recipes/bioconductor-txdb.dmelanogaster.ucsc.dm3.ensgene/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ TxDb.Dmelanogaster.UCSC.dm3.ensGene diff --git a/recipes/bioconductor-txdb.dmelanogaster.ucsc.dm6.ensgene/meta.yaml b/recipes/bioconductor-txdb.dmelanogaster.ucsc.dm6.ensgene/meta.yaml index 93948f97a9803..a6c826256821a 100644 --- a/recipes/bioconductor-txdb.dmelanogaster.ucsc.dm6.ensgene/meta.yaml +++ b/recipes/bioconductor-txdb.dmelanogaster.ucsc.dm6.ensgene/meta.yaml @@ -9,10 +9,10 @@ source: fn: '{{ name }}_{{ version }}.tar.gz' url: - 'http://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/{{ name }}/{{ name }}_{{ version }}_src_all.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' sha256: 01cc6196b2660348d6ec3c7eb707966b07f803c0a40bef63958e1234d703bc69 build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ 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 06506bce60257..119489492bc63 100644 --- a/recipes/bioconductor-txdb.dmelanogaster.ucsc.dm6.ensgene/post-link.sh +++ b/recipes/bioconductor-txdb.dmelanogaster.ucsc.dm6.ensgene/post-link.sh @@ -2,9 +2,9 @@ FN="TxDb.Dmelanogaster.UCSC.dm6.ensGene_3.4.1.tar.gz" URLS=( "http://bioconductor.org/packages/3.6/data/annotation/src/contrib/TxDb.Dmelanogaster.UCSC.dm6.ensGene_3.4.1.tar.gz" - "https://depot.galaxyproject.org/software/TxDb.Dmelanogaster.UCSC.dm6.ensGene/TxDb.Dmelanogaster.UCSC.dm6.ensGene_3.4.1_src_all.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-txdb.dmelanogaster.ucsc.dm6.ensgene/bioconductor-txdb.dmelanogaster.ucsc.dm6.ensgene_3.4.1_src_all.tar.gz" ) - MD5="539737dcb0b3d6d0134f5fe2ecf4e835" +MD5="539737dcb0b3d6d0134f5fe2ecf4e835" # Use a staging area in the conda dir rather than temp dirs, both to avoid # permission issues as well as to have things downloaded in a predictable @@ -20,7 +20,7 @@ for URL in ${URLS[@]}; do # Platform-specific md5sum checks. if [[ $(uname -s) == "Linux" ]]; then - if [[ $(md5sum -c <<<"$MD5 $TARBALL") ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then SUCCESS=1 break fi @@ -40,5 +40,6 @@ if [[ $SUCCESS != 1 ]]; then fi # Install and clean up -R CMD INSTALL --build $TARBALL -rm $TARBALL \ No newline at end of file +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING \ No newline at end of file diff --git a/recipes/bioconductor-txdb.dmelanogaster.ucsc.dm6.ensgene/pre-unlink.sh b/recipes/bioconductor-txdb.dmelanogaster.ucsc.dm6.ensgene/pre-unlink.sh new file mode 100644 index 0000000000000..20e612dc45f74 --- /dev/null +++ b/recipes/bioconductor-txdb.dmelanogaster.ucsc.dm6.ensgene/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ TxDb.Dmelanogaster.UCSC.dm6.ensGene diff --git a/recipes/bioconductor-txdb.drerio.ucsc.danrer10.refgene/meta.yaml b/recipes/bioconductor-txdb.drerio.ucsc.danrer10.refgene/meta.yaml index 90a0cea7e8c1e..04eb5635273e8 100644 --- a/recipes/bioconductor-txdb.drerio.ucsc.danrer10.refgene/meta.yaml +++ b/recipes/bioconductor-txdb.drerio.ucsc.danrer10.refgene/meta.yaml @@ -9,10 +9,10 @@ source: fn: '{{ name }}_{{ version }}.tar.gz' url: - 'http://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/{{ name }}/{{ name }}_{{ version }}_src_all.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' sha256: 740cf7e249e19afe47119564aee3515728e0b9056779a013b43f4bb1e93e0cb3 build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ 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 ce9d2a865c268..859f850f0c474 100644 --- a/recipes/bioconductor-txdb.drerio.ucsc.danrer10.refgene/post-link.sh +++ b/recipes/bioconductor-txdb.drerio.ucsc.danrer10.refgene/post-link.sh @@ -2,9 +2,9 @@ FN="TxDb.Drerio.UCSC.danRer10.refGene_3.4.2.tar.gz" URLS=( "http://bioconductor.org/packages/3.6/data/annotation/src/contrib/TxDb.Drerio.UCSC.danRer10.refGene_3.4.2.tar.gz" - "https://depot.galaxyproject.org/software/TxDb.Drerio.UCSC.danRer10.refGene/TxDb.Drerio.UCSC.danRer10.refGene_3.4.2_src_all.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-txdb.drerio.ucsc.danrer10.refgene/bioconductor-txdb.drerio.ucsc.danrer10.refgene_3.4.2_src_all.tar.gz" ) - MD5="fc024ebcd884f44f52adeb552347ad0a" +MD5="fc024ebcd884f44f52adeb552347ad0a" # Use a staging area in the conda dir rather than temp dirs, both to avoid # permission issues as well as to have things downloaded in a predictable @@ -20,7 +20,7 @@ for URL in ${URLS[@]}; do # Platform-specific md5sum checks. if [[ $(uname -s) == "Linux" ]]; then - if [[ $(md5sum -c <<<"$MD5 $TARBALL") ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then SUCCESS=1 break fi @@ -40,5 +40,6 @@ if [[ $SUCCESS != 1 ]]; then fi # Install and clean up -R CMD INSTALL --build $TARBALL -rm $TARBALL \ No newline at end of file +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING \ No newline at end of file diff --git a/recipes/bioconductor-txdb.drerio.ucsc.danrer10.refgene/pre-unlink.sh b/recipes/bioconductor-txdb.drerio.ucsc.danrer10.refgene/pre-unlink.sh new file mode 100644 index 0000000000000..8f3676bbd4c08 --- /dev/null +++ b/recipes/bioconductor-txdb.drerio.ucsc.danrer10.refgene/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ TxDb.Drerio.UCSC.danRer10.refGene diff --git a/recipes/bioconductor-txdb.hsapiens.ucsc.hg18.knowngene/meta.yaml b/recipes/bioconductor-txdb.hsapiens.ucsc.hg18.knowngene/meta.yaml index 3022d8e09a333..782afa1cafed6 100644 --- a/recipes/bioconductor-txdb.hsapiens.ucsc.hg18.knowngene/meta.yaml +++ b/recipes/bioconductor-txdb.hsapiens.ucsc.hg18.knowngene/meta.yaml @@ -9,10 +9,10 @@ source: fn: '{{ name }}_{{ version }}.tar.gz' url: - 'http://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/{{ name }}/{{ name }}_{{ version }}_src_all.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' sha256: bc9ca40b4eab87f5ca64a4b876d42502b9b8e9f5983d745bfe0ee349d97b69fa build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ 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 4e78bd949192e..1b7a768dc32e9 100644 --- a/recipes/bioconductor-txdb.hsapiens.ucsc.hg18.knowngene/post-link.sh +++ b/recipes/bioconductor-txdb.hsapiens.ucsc.hg18.knowngene/post-link.sh @@ -2,9 +2,9 @@ FN="TxDb.Hsapiens.UCSC.hg18.knownGene_3.2.2.tar.gz" URLS=( "http://bioconductor.org/packages/3.6/data/annotation/src/contrib/TxDb.Hsapiens.UCSC.hg18.knownGene_3.2.2.tar.gz" - "https://depot.galaxyproject.org/software/TxDb.Hsapiens.UCSC.hg18.knownGene/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" ) - MD5="e8b32a672e87345c72bb30be73d1e2d6" +MD5="e8b32a672e87345c72bb30be73d1e2d6" # Use a staging area in the conda dir rather than temp dirs, both to avoid # permission issues as well as to have things downloaded in a predictable @@ -20,7 +20,7 @@ for URL in ${URLS[@]}; do # Platform-specific md5sum checks. if [[ $(uname -s) == "Linux" ]]; then - if [[ $(md5sum -c <<<"$MD5 $TARBALL") ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then SUCCESS=1 break fi @@ -40,5 +40,6 @@ if [[ $SUCCESS != 1 ]]; then fi # Install and clean up -R CMD INSTALL --build $TARBALL -rm $TARBALL \ No newline at end of file +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING \ No newline at end of file diff --git a/recipes/bioconductor-txdb.hsapiens.ucsc.hg18.knowngene/pre-unlink.sh b/recipes/bioconductor-txdb.hsapiens.ucsc.hg18.knowngene/pre-unlink.sh new file mode 100644 index 0000000000000..454a16a39d1f3 --- /dev/null +++ b/recipes/bioconductor-txdb.hsapiens.ucsc.hg18.knowngene/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ TxDb.Hsapiens.UCSC.hg18.knownGene diff --git a/recipes/bioconductor-txdb.hsapiens.ucsc.hg19.knowngene/meta.yaml b/recipes/bioconductor-txdb.hsapiens.ucsc.hg19.knowngene/meta.yaml index 0d12e9bb2e6ef..172e680abdf46 100644 --- a/recipes/bioconductor-txdb.hsapiens.ucsc.hg19.knowngene/meta.yaml +++ b/recipes/bioconductor-txdb.hsapiens.ucsc.hg19.knowngene/meta.yaml @@ -9,10 +9,10 @@ source: fn: '{{ name }}_{{ version }}.tar.gz' url: - 'http://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/{{ name }}/{{ name }}_{{ version }}_src_all.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' sha256: 063de2b1174782a0b2b8ab7f04a0bdf3c43252cb67c685a9f8ef2b8e318352e9 build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ 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 eab6e88289beb..b08268c2a79d7 100644 --- a/recipes/bioconductor-txdb.hsapiens.ucsc.hg19.knowngene/post-link.sh +++ b/recipes/bioconductor-txdb.hsapiens.ucsc.hg19.knowngene/post-link.sh @@ -2,9 +2,9 @@ FN="TxDb.Hsapiens.UCSC.hg19.knownGene_3.2.2.tar.gz" URLS=( "http://bioconductor.org/packages/3.6/data/annotation/src/contrib/TxDb.Hsapiens.UCSC.hg19.knownGene_3.2.2.tar.gz" - "https://depot.galaxyproject.org/software/TxDb.Hsapiens.UCSC.hg19.knownGene/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" ) - MD5="61be88a81433958571b57d0952be48a0" +MD5="61be88a81433958571b57d0952be48a0" # Use a staging area in the conda dir rather than temp dirs, both to avoid # permission issues as well as to have things downloaded in a predictable @@ -20,7 +20,7 @@ for URL in ${URLS[@]}; do # Platform-specific md5sum checks. if [[ $(uname -s) == "Linux" ]]; then - if [[ $(md5sum -c <<<"$MD5 $TARBALL") ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then SUCCESS=1 break fi @@ -40,5 +40,6 @@ if [[ $SUCCESS != 1 ]]; then fi # Install and clean up -R CMD INSTALL --build $TARBALL -rm $TARBALL \ No newline at end of file +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING \ No newline at end of file diff --git a/recipes/bioconductor-txdb.hsapiens.ucsc.hg19.knowngene/pre-unlink.sh b/recipes/bioconductor-txdb.hsapiens.ucsc.hg19.knowngene/pre-unlink.sh new file mode 100644 index 0000000000000..33ce891f0a0c9 --- /dev/null +++ b/recipes/bioconductor-txdb.hsapiens.ucsc.hg19.knowngene/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ TxDb.Hsapiens.UCSC.hg19.knownGene diff --git a/recipes/bioconductor-txdb.hsapiens.ucsc.hg19.lincrnastranscripts/meta.yaml b/recipes/bioconductor-txdb.hsapiens.ucsc.hg19.lincrnastranscripts/meta.yaml index 592aabbc2768d..dab60ad679bb5 100644 --- a/recipes/bioconductor-txdb.hsapiens.ucsc.hg19.lincrnastranscripts/meta.yaml +++ b/recipes/bioconductor-txdb.hsapiens.ucsc.hg19.lincrnastranscripts/meta.yaml @@ -9,10 +9,10 @@ source: fn: '{{ name }}_{{ version }}.tar.gz' url: - 'http://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/{{ name }}/{{ name }}_{{ version }}_src_all.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' sha256: 4f68ee75c1722b53de4a5382a455730673dab8c0fd7585f86771efe6e7b9ab2e build: - number: 2 + number: 3 rpaths: - lib/R/lib/ - lib/ 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 a7ab0debd6031..58182b405cbac 100644 --- a/recipes/bioconductor-txdb.hsapiens.ucsc.hg19.lincrnastranscripts/post-link.sh +++ b/recipes/bioconductor-txdb.hsapiens.ucsc.hg19.lincrnastranscripts/post-link.sh @@ -2,9 +2,9 @@ FN="TxDb.Hsapiens.UCSC.hg19.lincRNAsTranscripts_3.2.2.tar.gz" URLS=( "http://bioconductor.org/packages/3.6/data/annotation/src/contrib/TxDb.Hsapiens.UCSC.hg19.lincRNAsTranscripts_3.2.2.tar.gz" - "https://depot.galaxyproject.org/software/TxDb.Hsapiens.UCSC.hg19.lincRNAsTranscripts/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" ) - MD5="a0d61cd90639c40b3d0bb6bdb043cf12" +MD5="a0d61cd90639c40b3d0bb6bdb043cf12" # Use a staging area in the conda dir rather than temp dirs, both to avoid # permission issues as well as to have things downloaded in a predictable @@ -20,7 +20,7 @@ for URL in ${URLS[@]}; do # Platform-specific md5sum checks. if [[ $(uname -s) == "Linux" ]]; then - if [[ $(md5sum -c <<<"$MD5 $TARBALL") ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then SUCCESS=1 break fi @@ -40,5 +40,6 @@ if [[ $SUCCESS != 1 ]]; then fi # Install and clean up -R CMD INSTALL --build $TARBALL -rm $TARBALL \ No newline at end of file +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING \ No newline at end of file diff --git a/recipes/bioconductor-txdb.hsapiens.ucsc.hg19.lincrnastranscripts/pre-unlink.sh b/recipes/bioconductor-txdb.hsapiens.ucsc.hg19.lincrnastranscripts/pre-unlink.sh new file mode 100644 index 0000000000000..9e035f31fd98c --- /dev/null +++ b/recipes/bioconductor-txdb.hsapiens.ucsc.hg19.lincrnastranscripts/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ TxDb.Hsapiens.UCSC.hg19.lincRNAsTranscripts diff --git a/recipes/bioconductor-txdb.hsapiens.ucsc.hg38.knowngene/meta.yaml b/recipes/bioconductor-txdb.hsapiens.ucsc.hg38.knowngene/meta.yaml index e413ab4fb73c9..23876436ae070 100644 --- a/recipes/bioconductor-txdb.hsapiens.ucsc.hg38.knowngene/meta.yaml +++ b/recipes/bioconductor-txdb.hsapiens.ucsc.hg38.knowngene/meta.yaml @@ -9,10 +9,10 @@ source: fn: '{{ name }}_{{ version }}.tar.gz' url: - 'http://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/{{ name }}/{{ name }}_{{ version }}_src_all.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' sha256: c5e6ebd84690e00eed966e4569dbd5abccf478b60dcb1842ca0310cb2ae01d44 build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ 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 4e50884ef8ad3..ba93622aea1ef 100644 --- a/recipes/bioconductor-txdb.hsapiens.ucsc.hg38.knowngene/post-link.sh +++ b/recipes/bioconductor-txdb.hsapiens.ucsc.hg38.knowngene/post-link.sh @@ -2,9 +2,9 @@ FN="TxDb.Hsapiens.UCSC.hg38.knownGene_3.4.0.tar.gz" URLS=( "http://bioconductor.org/packages/3.6/data/annotation/src/contrib/TxDb.Hsapiens.UCSC.hg38.knownGene_3.4.0.tar.gz" - "https://depot.galaxyproject.org/software/TxDb.Hsapiens.UCSC.hg38.knownGene/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" ) - MD5="1d5e07631ea58e96b11905d39e76ca6e" +MD5="1d5e07631ea58e96b11905d39e76ca6e" # Use a staging area in the conda dir rather than temp dirs, both to avoid # permission issues as well as to have things downloaded in a predictable @@ -20,7 +20,7 @@ for URL in ${URLS[@]}; do # Platform-specific md5sum checks. if [[ $(uname -s) == "Linux" ]]; then - if [[ $(md5sum -c <<<"$MD5 $TARBALL") ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then SUCCESS=1 break fi @@ -40,5 +40,6 @@ if [[ $SUCCESS != 1 ]]; then fi # Install and clean up -R CMD INSTALL --build $TARBALL -rm $TARBALL \ No newline at end of file +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING \ No newline at end of file diff --git a/recipes/bioconductor-txdb.hsapiens.ucsc.hg38.knowngene/pre-unlink.sh b/recipes/bioconductor-txdb.hsapiens.ucsc.hg38.knowngene/pre-unlink.sh new file mode 100644 index 0000000000000..7d6274a15f960 --- /dev/null +++ b/recipes/bioconductor-txdb.hsapiens.ucsc.hg38.knowngene/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ TxDb.Hsapiens.UCSC.hg38.knownGene diff --git a/recipes/bioconductor-txdb.mmusculus.ucsc.mm10.ensgene/meta.yaml b/recipes/bioconductor-txdb.mmusculus.ucsc.mm10.ensgene/meta.yaml index 039f54e575688..58ae234a9a885 100644 --- a/recipes/bioconductor-txdb.mmusculus.ucsc.mm10.ensgene/meta.yaml +++ b/recipes/bioconductor-txdb.mmusculus.ucsc.mm10.ensgene/meta.yaml @@ -9,10 +9,10 @@ source: fn: '{{ name }}_{{ version }}.tar.gz' url: - 'http://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/{{ name }}/{{ name }}_{{ version }}_src_all.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' sha256: 3abd4f50b358ed1d1996da6c894ab82b13b247b33e07bf9d46a3f1d85c885d69 build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ 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 5b99038d79990..77637db4d313e 100644 --- a/recipes/bioconductor-txdb.mmusculus.ucsc.mm10.ensgene/post-link.sh +++ b/recipes/bioconductor-txdb.mmusculus.ucsc.mm10.ensgene/post-link.sh @@ -2,9 +2,9 @@ FN="TxDb.Mmusculus.UCSC.mm10.ensGene_3.4.0.tar.gz" URLS=( "http://bioconductor.org/packages/3.6/data/annotation/src/contrib/TxDb.Mmusculus.UCSC.mm10.ensGene_3.4.0.tar.gz" - "https://depot.galaxyproject.org/software/TxDb.Mmusculus.UCSC.mm10.ensGene/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" ) - MD5="88d65b714d1f86b456aee2b8524e9d84" +MD5="88d65b714d1f86b456aee2b8524e9d84" # Use a staging area in the conda dir rather than temp dirs, both to avoid # permission issues as well as to have things downloaded in a predictable @@ -20,7 +20,7 @@ for URL in ${URLS[@]}; do # Platform-specific md5sum checks. if [[ $(uname -s) == "Linux" ]]; then - if [[ $(md5sum -c <<<"$MD5 $TARBALL") ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then SUCCESS=1 break fi @@ -40,5 +40,6 @@ if [[ $SUCCESS != 1 ]]; then fi # Install and clean up -R CMD INSTALL --build $TARBALL -rm $TARBALL \ No newline at end of file +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING \ No newline at end of file diff --git a/recipes/bioconductor-txdb.mmusculus.ucsc.mm10.ensgene/pre-unlink.sh b/recipes/bioconductor-txdb.mmusculus.ucsc.mm10.ensgene/pre-unlink.sh new file mode 100644 index 0000000000000..92e9a79a509d5 --- /dev/null +++ b/recipes/bioconductor-txdb.mmusculus.ucsc.mm10.ensgene/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ TxDb.Mmusculus.UCSC.mm10.ensGene diff --git a/recipes/bioconductor-txdb.mmusculus.ucsc.mm10.knowngene/meta.yaml b/recipes/bioconductor-txdb.mmusculus.ucsc.mm10.knowngene/meta.yaml index 2235a32b79170..be04da2b4f659 100644 --- a/recipes/bioconductor-txdb.mmusculus.ucsc.mm10.knowngene/meta.yaml +++ b/recipes/bioconductor-txdb.mmusculus.ucsc.mm10.knowngene/meta.yaml @@ -9,10 +9,10 @@ source: fn: '{{ name }}_{{ version }}.tar.gz' url: - 'http://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/{{ name }}/{{ name }}_{{ version }}_src_all.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' sha256: 6b2e9ce3b2050cb770cca989b14b09c50e20ef88568b19cac7ec6ecd93daea21 build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ 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 2ec1b14da266b..1e901ec810f27 100644 --- a/recipes/bioconductor-txdb.mmusculus.ucsc.mm10.knowngene/post-link.sh +++ b/recipes/bioconductor-txdb.mmusculus.ucsc.mm10.knowngene/post-link.sh @@ -2,9 +2,9 @@ FN="TxDb.Mmusculus.UCSC.mm10.knownGene_3.4.0.tar.gz" URLS=( "http://bioconductor.org/packages/3.6/data/annotation/src/contrib/TxDb.Mmusculus.UCSC.mm10.knownGene_3.4.0.tar.gz" - "https://depot.galaxyproject.org/software/TxDb.Mmusculus.UCSC.mm10.knownGene/TxDb.Mmusculus.UCSC.mm10.knownGene_3.4.0_src_all.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-txdb.mmusculus.ucsc.mm10.knowngene/bioconductor-txdb.mmusculus.ucsc.mm10.knowngene_3.4.0_src_all.tar.gz" ) - MD5="86b7dca1b7d0d957c1794d261fc5bb81" +MD5="86b7dca1b7d0d957c1794d261fc5bb81" # Use a staging area in the conda dir rather than temp dirs, both to avoid # permission issues as well as to have things downloaded in a predictable @@ -20,7 +20,7 @@ for URL in ${URLS[@]}; do # Platform-specific md5sum checks. if [[ $(uname -s) == "Linux" ]]; then - if [[ $(md5sum -c <<<"$MD5 $TARBALL") ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then SUCCESS=1 break fi @@ -40,5 +40,6 @@ if [[ $SUCCESS != 1 ]]; then fi # Install and clean up -R CMD INSTALL --build $TARBALL -rm $TARBALL \ No newline at end of file +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING \ No newline at end of file diff --git a/recipes/bioconductor-txdb.mmusculus.ucsc.mm10.knowngene/pre-unlink.sh b/recipes/bioconductor-txdb.mmusculus.ucsc.mm10.knowngene/pre-unlink.sh new file mode 100644 index 0000000000000..f87db2ce495fa --- /dev/null +++ b/recipes/bioconductor-txdb.mmusculus.ucsc.mm10.knowngene/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ TxDb.Mmusculus.UCSC.mm10.knownGene diff --git a/recipes/bioconductor-txdb.mmusculus.ucsc.mm9.knowngene/meta.yaml b/recipes/bioconductor-txdb.mmusculus.ucsc.mm9.knowngene/meta.yaml index af2dc924be6e0..2ac6a4d051b41 100644 --- a/recipes/bioconductor-txdb.mmusculus.ucsc.mm9.knowngene/meta.yaml +++ b/recipes/bioconductor-txdb.mmusculus.ucsc.mm9.knowngene/meta.yaml @@ -9,10 +9,10 @@ source: fn: '{{ name }}_{{ version }}.tar.gz' url: - 'http://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/{{ name }}/{{ name }}_{{ version }}_src_all.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' sha256: a2d760206336d0c1ba48108ba3e23b201aa429a6b88a19437270980180ef7299 build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ 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 31ccb7dfe88c8..33271b56804a3 100644 --- a/recipes/bioconductor-txdb.mmusculus.ucsc.mm9.knowngene/post-link.sh +++ b/recipes/bioconductor-txdb.mmusculus.ucsc.mm9.knowngene/post-link.sh @@ -2,9 +2,9 @@ FN="TxDb.Mmusculus.UCSC.mm9.knownGene_3.2.2.tar.gz" URLS=( "http://bioconductor.org/packages/3.6/data/annotation/src/contrib/TxDb.Mmusculus.UCSC.mm9.knownGene_3.2.2.tar.gz" - "https://depot.galaxyproject.org/software/TxDb.Mmusculus.UCSC.mm9.knownGene/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" ) - MD5="cb72af039b011033477363bda8ed9104" +MD5="cb72af039b011033477363bda8ed9104" # Use a staging area in the conda dir rather than temp dirs, both to avoid # permission issues as well as to have things downloaded in a predictable @@ -20,7 +20,7 @@ for URL in ${URLS[@]}; do # Platform-specific md5sum checks. if [[ $(uname -s) == "Linux" ]]; then - if [[ $(md5sum -c <<<"$MD5 $TARBALL") ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then SUCCESS=1 break fi @@ -40,5 +40,6 @@ if [[ $SUCCESS != 1 ]]; then fi # Install and clean up -R CMD INSTALL --build $TARBALL -rm $TARBALL \ No newline at end of file +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING \ No newline at end of file diff --git a/recipes/bioconductor-txdb.mmusculus.ucsc.mm9.knowngene/pre-unlink.sh b/recipes/bioconductor-txdb.mmusculus.ucsc.mm9.knowngene/pre-unlink.sh new file mode 100644 index 0000000000000..502a5d0667365 --- /dev/null +++ b/recipes/bioconductor-txdb.mmusculus.ucsc.mm9.knowngene/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ TxDb.Mmusculus.UCSC.mm9.knownGene diff --git a/recipes/bioconductor-txdb.rnorvegicus.ucsc.rn4.ensgene/meta.yaml b/recipes/bioconductor-txdb.rnorvegicus.ucsc.rn4.ensgene/meta.yaml index 3b04310939735..7beb1f1405106 100644 --- a/recipes/bioconductor-txdb.rnorvegicus.ucsc.rn4.ensgene/meta.yaml +++ b/recipes/bioconductor-txdb.rnorvegicus.ucsc.rn4.ensgene/meta.yaml @@ -9,10 +9,10 @@ source: fn: '{{ name }}_{{ version }}.tar.gz' url: - 'http://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/{{ name }}/{{ name }}_{{ version }}_src_all.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' sha256: 15325d09a9da4292678768164e1850a78595dd96351970553844f5eeac5f683f build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ 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 4acac777173ce..2bebb77c1dd24 100644 --- a/recipes/bioconductor-txdb.rnorvegicus.ucsc.rn4.ensgene/post-link.sh +++ b/recipes/bioconductor-txdb.rnorvegicus.ucsc.rn4.ensgene/post-link.sh @@ -2,9 +2,9 @@ FN="TxDb.Rnorvegicus.UCSC.rn4.ensGene_3.2.2.tar.gz" URLS=( "http://bioconductor.org/packages/3.6/data/annotation/src/contrib/TxDb.Rnorvegicus.UCSC.rn4.ensGene_3.2.2.tar.gz" - "https://depot.galaxyproject.org/software/TxDb.Rnorvegicus.UCSC.rn4.ensGene/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" ) - MD5="6bf2ebc522c2828c036e52b2028792c1" +MD5="6bf2ebc522c2828c036e52b2028792c1" # Use a staging area in the conda dir rather than temp dirs, both to avoid # permission issues as well as to have things downloaded in a predictable @@ -20,7 +20,7 @@ for URL in ${URLS[@]}; do # Platform-specific md5sum checks. if [[ $(uname -s) == "Linux" ]]; then - if [[ $(md5sum -c <<<"$MD5 $TARBALL") ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then SUCCESS=1 break fi @@ -40,5 +40,6 @@ if [[ $SUCCESS != 1 ]]; then fi # Install and clean up -R CMD INSTALL --build $TARBALL -rm $TARBALL \ No newline at end of file +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING \ No newline at end of file diff --git a/recipes/bioconductor-txdb.rnorvegicus.ucsc.rn4.ensgene/pre-unlink.sh b/recipes/bioconductor-txdb.rnorvegicus.ucsc.rn4.ensgene/pre-unlink.sh new file mode 100644 index 0000000000000..58c072edb420b --- /dev/null +++ b/recipes/bioconductor-txdb.rnorvegicus.ucsc.rn4.ensgene/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ TxDb.Rnorvegicus.UCSC.rn4.ensGene diff --git a/recipes/bioconductor-txdb.rnorvegicus.ucsc.rn5.refgene/meta.yaml b/recipes/bioconductor-txdb.rnorvegicus.ucsc.rn5.refgene/meta.yaml index 4f9ea46e9acfa..660a89ab4f1e2 100644 --- a/recipes/bioconductor-txdb.rnorvegicus.ucsc.rn5.refgene/meta.yaml +++ b/recipes/bioconductor-txdb.rnorvegicus.ucsc.rn5.refgene/meta.yaml @@ -9,10 +9,10 @@ source: fn: '{{ name }}_{{ version }}.tar.gz' url: - 'http://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/{{ name }}/{{ name }}_{{ version }}_src_all.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' sha256: 336e90a3c5be255fd2340b268c3b22b953fb91efd6757f09ef52d60644dedd87 build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ 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 62c798a79268d..fa048c2878fab 100644 --- a/recipes/bioconductor-txdb.rnorvegicus.ucsc.rn5.refgene/post-link.sh +++ b/recipes/bioconductor-txdb.rnorvegicus.ucsc.rn5.refgene/post-link.sh @@ -2,9 +2,9 @@ FN="TxDb.Rnorvegicus.UCSC.rn5.refGene_3.4.2.tar.gz" URLS=( "http://bioconductor.org/packages/3.6/data/annotation/src/contrib/TxDb.Rnorvegicus.UCSC.rn5.refGene_3.4.2.tar.gz" - "https://depot.galaxyproject.org/software/TxDb.Rnorvegicus.UCSC.rn5.refGene/TxDb.Rnorvegicus.UCSC.rn5.refGene_3.4.2_src_all.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-txdb.rnorvegicus.ucsc.rn5.refgene/bioconductor-txdb.rnorvegicus.ucsc.rn5.refgene_3.4.2_src_all.tar.gz" ) - MD5="194a3f04725e7ac39bd0e68efdffbc6a" +MD5="194a3f04725e7ac39bd0e68efdffbc6a" # Use a staging area in the conda dir rather than temp dirs, both to avoid # permission issues as well as to have things downloaded in a predictable @@ -20,7 +20,7 @@ for URL in ${URLS[@]}; do # Platform-specific md5sum checks. if [[ $(uname -s) == "Linux" ]]; then - if [[ $(md5sum -c <<<"$MD5 $TARBALL") ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then SUCCESS=1 break fi @@ -40,5 +40,6 @@ if [[ $SUCCESS != 1 ]]; then fi # Install and clean up -R CMD INSTALL --build $TARBALL -rm $TARBALL \ No newline at end of file +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING \ No newline at end of file diff --git a/recipes/bioconductor-txdb.rnorvegicus.ucsc.rn5.refgene/pre-unlink.sh b/recipes/bioconductor-txdb.rnorvegicus.ucsc.rn5.refgene/pre-unlink.sh new file mode 100644 index 0000000000000..74e118846d2c6 --- /dev/null +++ b/recipes/bioconductor-txdb.rnorvegicus.ucsc.rn5.refgene/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ TxDb.Rnorvegicus.UCSC.rn5.refGene diff --git a/recipes/bioconductor-txdb.rnorvegicus.ucsc.rn6.refgene/meta.yaml b/recipes/bioconductor-txdb.rnorvegicus.ucsc.rn6.refgene/meta.yaml index 6bf23df0e002f..1bb43c2ce9406 100644 --- a/recipes/bioconductor-txdb.rnorvegicus.ucsc.rn6.refgene/meta.yaml +++ b/recipes/bioconductor-txdb.rnorvegicus.ucsc.rn6.refgene/meta.yaml @@ -9,10 +9,10 @@ source: fn: '{{ name }}_{{ version }}.tar.gz' url: - 'http://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/{{ name }}/{{ name }}_{{ version }}_src_all.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' sha256: 53a75972d28eb3a7681512e1618e1d21fc4e091951b6b5beba05abc2d2118423 build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ 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 9fd60db96392d..70ff47b58391d 100644 --- a/recipes/bioconductor-txdb.rnorvegicus.ucsc.rn6.refgene/post-link.sh +++ b/recipes/bioconductor-txdb.rnorvegicus.ucsc.rn6.refgene/post-link.sh @@ -2,9 +2,9 @@ FN="TxDb.Rnorvegicus.UCSC.rn6.refGene_3.4.1.tar.gz" URLS=( "http://bioconductor.org/packages/3.6/data/annotation/src/contrib/TxDb.Rnorvegicus.UCSC.rn6.refGene_3.4.1.tar.gz" - "https://depot.galaxyproject.org/software/TxDb.Rnorvegicus.UCSC.rn6.refGene/TxDb.Rnorvegicus.UCSC.rn6.refGene_3.4.1_src_all.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-txdb.rnorvegicus.ucsc.rn6.refgene/bioconductor-txdb.rnorvegicus.ucsc.rn6.refgene_3.4.1_src_all.tar.gz" ) - MD5="4128d06fb48a78aad08da3765fe55234" +MD5="4128d06fb48a78aad08da3765fe55234" # Use a staging area in the conda dir rather than temp dirs, both to avoid # permission issues as well as to have things downloaded in a predictable @@ -20,7 +20,7 @@ for URL in ${URLS[@]}; do # Platform-specific md5sum checks. if [[ $(uname -s) == "Linux" ]]; then - if [[ $(md5sum -c <<<"$MD5 $TARBALL") ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then SUCCESS=1 break fi @@ -40,5 +40,6 @@ if [[ $SUCCESS != 1 ]]; then fi # Install and clean up -R CMD INSTALL --build $TARBALL -rm $TARBALL \ No newline at end of file +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING \ No newline at end of file diff --git a/recipes/bioconductor-txdb.rnorvegicus.ucsc.rn6.refgene/pre-unlink.sh b/recipes/bioconductor-txdb.rnorvegicus.ucsc.rn6.refgene/pre-unlink.sh new file mode 100644 index 0000000000000..97c219da2985b --- /dev/null +++ b/recipes/bioconductor-txdb.rnorvegicus.ucsc.rn6.refgene/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ TxDb.Rnorvegicus.UCSC.rn6.refGene diff --git a/recipes/bioconductor-txdb.scerevisiae.ucsc.saccer2.sgdgene/meta.yaml b/recipes/bioconductor-txdb.scerevisiae.ucsc.saccer2.sgdgene/meta.yaml index 55840bdd97a04..18e4d8fdc478a 100644 --- a/recipes/bioconductor-txdb.scerevisiae.ucsc.saccer2.sgdgene/meta.yaml +++ b/recipes/bioconductor-txdb.scerevisiae.ucsc.saccer2.sgdgene/meta.yaml @@ -9,10 +9,10 @@ source: fn: '{{ name }}_{{ version }}.tar.gz' url: - 'http://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/{{ name }}/{{ name }}_{{ version }}_src_all.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' sha256: eaf35b5a3e4706328e7a5b89d7de846055f5ac0aa34109d305a6ffbd2067af50 build: - number: 2 + number: 3 rpaths: - lib/R/lib/ - lib/ 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 1d3f6d4320101..5d03d154e4917 100644 --- a/recipes/bioconductor-txdb.scerevisiae.ucsc.saccer2.sgdgene/post-link.sh +++ b/recipes/bioconductor-txdb.scerevisiae.ucsc.saccer2.sgdgene/post-link.sh @@ -2,9 +2,9 @@ FN="TxDb.Scerevisiae.UCSC.sacCer2.sgdGene_3.2.2.tar.gz" URLS=( "http://bioconductor.org/packages/3.6/data/annotation/src/contrib/TxDb.Scerevisiae.UCSC.sacCer2.sgdGene_3.2.2.tar.gz" - "https://depot.galaxyproject.org/software/TxDb.Scerevisiae.UCSC.sacCer2.sgdGene/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" ) - MD5="8ce83ef2ba6cfc69f9b4435a0a047819" +MD5="8ce83ef2ba6cfc69f9b4435a0a047819" # Use a staging area in the conda dir rather than temp dirs, both to avoid # permission issues as well as to have things downloaded in a predictable @@ -20,7 +20,7 @@ for URL in ${URLS[@]}; do # Platform-specific md5sum checks. if [[ $(uname -s) == "Linux" ]]; then - if [[ $(md5sum -c <<<"$MD5 $TARBALL") ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then SUCCESS=1 break fi @@ -40,5 +40,6 @@ if [[ $SUCCESS != 1 ]]; then fi # Install and clean up -R CMD INSTALL --build $TARBALL -rm $TARBALL \ No newline at end of file +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING \ No newline at end of file diff --git a/recipes/bioconductor-txdb.scerevisiae.ucsc.saccer2.sgdgene/pre-unlink.sh b/recipes/bioconductor-txdb.scerevisiae.ucsc.saccer2.sgdgene/pre-unlink.sh new file mode 100644 index 0000000000000..e6b151328bf28 --- /dev/null +++ b/recipes/bioconductor-txdb.scerevisiae.ucsc.saccer2.sgdgene/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ TxDb.Scerevisiae.UCSC.sacCer2.sgdGene diff --git a/recipes/bioconductor-txdb.scerevisiae.ucsc.saccer3.sgdgene/meta.yaml b/recipes/bioconductor-txdb.scerevisiae.ucsc.saccer3.sgdgene/meta.yaml index 1d0d42a442cc0..a2dede9d47011 100644 --- a/recipes/bioconductor-txdb.scerevisiae.ucsc.saccer3.sgdgene/meta.yaml +++ b/recipes/bioconductor-txdb.scerevisiae.ucsc.saccer3.sgdgene/meta.yaml @@ -9,10 +9,10 @@ source: fn: '{{ name }}_{{ version }}.tar.gz' url: - 'http://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/{{ name }}/{{ name }}_{{ version }}_src_all.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' sha256: 6dac0b4f88ce54c8543bb0ce236507cd46dd78ff7b3e3457ef7fd0b1dca15cea build: - number: 6 + number: 7 rpaths: - lib/R/lib/ - lib/ 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 fb3f28f936f26..1682d0a078cf1 100644 --- a/recipes/bioconductor-txdb.scerevisiae.ucsc.saccer3.sgdgene/post-link.sh +++ b/recipes/bioconductor-txdb.scerevisiae.ucsc.saccer3.sgdgene/post-link.sh @@ -2,9 +2,9 @@ FN="TxDb.Scerevisiae.UCSC.sacCer3.sgdGene_3.2.2.tar.gz" URLS=( "http://bioconductor.org/packages/3.6/data/annotation/src/contrib/TxDb.Scerevisiae.UCSC.sacCer3.sgdGene_3.2.2.tar.gz" - "https://depot.galaxyproject.org/software/TxDb.Scerevisiae.UCSC.sacCer3.sgdGene/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" ) - MD5="afb23b3265730b9e59c2f07ab37cc3a0" +MD5="afb23b3265730b9e59c2f07ab37cc3a0" # Use a staging area in the conda dir rather than temp dirs, both to avoid # permission issues as well as to have things downloaded in a predictable @@ -20,7 +20,7 @@ for URL in ${URLS[@]}; do # Platform-specific md5sum checks. if [[ $(uname -s) == "Linux" ]]; then - if [[ $(md5sum -c <<<"$MD5 $TARBALL") ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then SUCCESS=1 break fi @@ -40,5 +40,6 @@ if [[ $SUCCESS != 1 ]]; then fi # Install and clean up -R CMD INSTALL --build $TARBALL -rm $TARBALL \ No newline at end of file +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING \ No newline at end of file diff --git a/recipes/bioconductor-txdb.scerevisiae.ucsc.saccer3.sgdgene/pre-unlink.sh b/recipes/bioconductor-txdb.scerevisiae.ucsc.saccer3.sgdgene/pre-unlink.sh new file mode 100644 index 0000000000000..46436e1357a38 --- /dev/null +++ b/recipes/bioconductor-txdb.scerevisiae.ucsc.saccer3.sgdgene/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ TxDb.Scerevisiae.UCSC.sacCer3.sgdGene diff --git a/recipes/bioconductor-yeastexpdata/meta.yaml b/recipes/bioconductor-yeastexpdata/meta.yaml index 84615971ed2c2..e8404970ca2b4 100644 --- a/recipes/bioconductor-yeastexpdata/meta.yaml +++ b/recipes/bioconductor-yeastexpdata/meta.yaml @@ -9,10 +9,10 @@ source: fn: '{{ name }}_{{ version }}.tar.gz' url: - 'http://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/{{ name }}/{{ name }}_{{ version }}_src_all.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' sha256: 2d6e269b91945c9957e1c4a3bc2ff06c26f759451b8a68969be8ce63580069a7 build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ diff --git a/recipes/bioconductor-yeastexpdata/post-link.sh b/recipes/bioconductor-yeastexpdata/post-link.sh index 8b049227a1c20..01ead60b635d4 100644 --- a/recipes/bioconductor-yeastexpdata/post-link.sh +++ b/recipes/bioconductor-yeastexpdata/post-link.sh @@ -2,9 +2,9 @@ FN="yeastExpData_0.24.0.tar.gz" URLS=( "http://bioconductor.org/packages/3.6/data/experiment/src/contrib/yeastExpData_0.24.0.tar.gz" - "https://depot.galaxyproject.org/software/yeastExpData/yeastExpData_0.24.0_src_all.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-yeastexpdata/bioconductor-yeastexpdata_0.24.0_src_all.tar.gz" ) - MD5="0f210bd46c16fd7b10ce38ecda8ad37a" +MD5="0f210bd46c16fd7b10ce38ecda8ad37a" # Use a staging area in the conda dir rather than temp dirs, both to avoid # permission issues as well as to have things downloaded in a predictable @@ -20,7 +20,7 @@ for URL in ${URLS[@]}; do # Platform-specific md5sum checks. if [[ $(uname -s) == "Linux" ]]; then - if [[ $(md5sum -c <<<"$MD5 $TARBALL") ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then SUCCESS=1 break fi @@ -40,5 +40,6 @@ if [[ $SUCCESS != 1 ]]; then fi # Install and clean up -R CMD INSTALL --build $TARBALL -rm $TARBALL \ No newline at end of file +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING \ No newline at end of file diff --git a/recipes/bioconductor-yeastexpdata/pre-unlink.sh b/recipes/bioconductor-yeastexpdata/pre-unlink.sh new file mode 100644 index 0000000000000..1ab6a77412ee6 --- /dev/null +++ b/recipes/bioconductor-yeastexpdata/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ yeastExpData diff --git a/recipes/break-point-inspector/break-point-inspector.sh b/recipes/break-point-inspector/break-point-inspector.sh new file mode 100644 index 0000000000000..0c3f6981d1d2b --- /dev/null +++ b/recipes/break-point-inspector/break-point-inspector.sh @@ -0,0 +1,62 @@ +#!/bin/bash +# BPI executable shell script (copied from https://github.com/bioconda/bioconda-recipes/blob/master/recipes/picard/picard.sh) +set -eu -o pipefail +export LC_ALL=en_US.UTF-8 + +# Find original directory of bash script, resolving symlinks +# http://stackoverflow.com/questions/59895/can-a-bash-script-tell-what-directory-its-stored-in/246128#246128 +SOURCE="${BASH_SOURCE[0]}" +while [ -h "$SOURCE" ]; do # resolve $SOURCE until the file is no longer a symlink + DIR="$( cd -P "$( dirname "$SOURCE" )" && pwd )" + SOURCE="$(readlink "$SOURCE")" + [[ $SOURCE != /* ]] && SOURCE="$DIR/$SOURCE" # if $SOURCE was a relative symlink, we need to resolve it relative to the path where the symlink file was located +done +DIR="$( cd -P "$( dirname "$SOURCE" )" && pwd )" + +JAR_DIR=$DIR +ENV_PREFIX="$(dirname $(dirname $DIR))" +# Use Java installed with Anaconda to ensure correct version +java="$ENV_PREFIX/bin/java" + +# if JAVA_HOME is set (non-empty), use it. Otherwise keep "java" +if [ -n "${JAVA_HOME:=}" ]; then + if [ -e "$JAVA_HOME/bin/java" ]; then + java="$JAVA_HOME/bin/java" + fi +fi + +# extract memory and system property Java arguments from the list of provided arguments +# http://java.dzone.com/articles/better-java-shell-script +default_jvm_mem_opts="-Xms512m -Xmx1g" +jvm_mem_opts="" +jvm_prop_opts="" +pass_args="" +for arg in "$@"; do + case $arg in + '-D'*) + jvm_prop_opts="$jvm_prop_opts $arg" + ;; + '-XX'*) + jvm_prop_opts="$jvm_prop_opts $arg" + ;; + '-Xm'*) + jvm_mem_opts="$jvm_mem_opts $arg" + ;; + *) + pass_args="$pass_args $arg" + ;; + esac +done + +if [ "$jvm_mem_opts" == "" ]; then + jvm_mem_opts="$default_jvm_mem_opts" +fi + +pass_arr=($pass_args) +if [[ ${pass_arr[0]:=} == org* ]] +then + eval "$java" $jvm_mem_opts $jvm_prop_opts -cp "$JAR_DIR/break-point-inspector*.jar" $pass_args +else + eval "$java" $jvm_mem_opts $jvm_prop_opts -jar "$JAR_DIR/break-point-inspector*.jar" $pass_args +fi +exit \ No newline at end of file diff --git a/recipes/break-point-inspector/build.sh b/recipes/break-point-inspector/build.sh new file mode 100644 index 0000000000000..bb5c49828f2a0 --- /dev/null +++ b/recipes/break-point-inspector/build.sh @@ -0,0 +1,20 @@ +#!/bin/bash +# Copied from https://github.com/bioconda/bioconda-recipes/blob/master/recipes/picard/build.sh +set -eu -o pipefail +BIN_NAME="break-point-inspector" +JAR_NAME="break-point-inspector-1.5-jar-with-dependencies.jar" + +TGT="${PREFIX}/share/${PKG_NAME}-${PKG_VERSION}-${PKG_BUILDNUM}" +[ -d "${TGT}" ] || mkdir -p "${TGT}" +[ -d "${PREFIX}/bin" ] || mkdir -p "${PREFIX}/bin" + +cd "${SRC_DIR}" +# Do not install Linux specific x86-acceleration libraries +if [ "$(uname)" == "Darwin" ]; then + rm -f libIntel*.so +fi +cp -rvp . "${TGT}" + +cp ${RECIPE_DIR}/${BIN_NAME}.sh ${TGT}/${BIN_NAME} +ln -s ${TGT}/${BIN_NAME} ${PREFIX}/bin +chmod 0755 "${PREFIX}/bin/${BIN_NAME}" \ No newline at end of file diff --git a/recipes/break-point-inspector/meta.yaml b/recipes/break-point-inspector/meta.yaml new file mode 100644 index 0000000000000..70188df96e183 --- /dev/null +++ b/recipes/break-point-inspector/meta.yaml @@ -0,0 +1,23 @@ +{% set name = "break-point-inspector" %} +{% set version = "1.5" %} + +package: + name: break-point-inspector + version: '{{ version }}' + +source: + fn: {{ name }}-{{ version }}-jar-with-dependencies.jar + url: https://github.com/hartwigmedical/hmftools/releases/download/bpi-v{{ version|replace(".", "-") }}/{{ name }}-{{ version }}-jar-with-dependencies.jar + sha256: 80e53b8590921a5bec87a27f51dde6ba655ee0b325b61deb6712cdcb000854df + +build: + number: 0 + +requirements: + run: + - openjdk + +about: + home: https://github.com/hartwigmedical/hmftools/tree/master/break-point-inspector + license: MIT + summary: BPI uses Manta’s variant calls to re-analyse BAM files and precisely determine the location of the breaks, and applies a set of filters to remove false positives, thereby increasing the accuracy of Manta’s calls. \ No newline at end of file diff --git a/recipes/break-point-inspector/run_test.sh b/recipes/break-point-inspector/run_test.sh new file mode 100644 index 0000000000000..6821e1b4d171b --- /dev/null +++ b/recipes/break-point-inspector/run_test.sh @@ -0,0 +1,7 @@ +#!/bin/bash +set -euo pipefail + +echo -e '' > test.bam +echo -e '##fileformat=VCFv4.1' > test.vcf +echo -e '#CHROM\tPOS\tID\tREF\tALT\tQUAL\tFILTER\tINFO\tFORMAT\ttumor\tnormal' >> test.vcf +break-point-inspector -tumor test.bam -ref test.bam -vcf test.vcf > /dev/null \ No newline at end of file diff --git a/recipes/break-point-inspector/test.bam b/recipes/break-point-inspector/test.bam new file mode 100644 index 0000000000000..9daeafb9864cf --- /dev/null +++ b/recipes/break-point-inspector/test.bam @@ -0,0 +1 @@ +test diff --git a/recipes/break-point-inspector/test.vcf b/recipes/break-point-inspector/test.vcf new file mode 100644 index 0000000000000..bd001e0e87602 --- /dev/null +++ b/recipes/break-point-inspector/test.vcf @@ -0,0 +1,2 @@ +##fileformat=VCFv4.1 +#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT tumor normal diff --git a/recipes/busco/build.sh b/recipes/busco/build.sh index 006bd9f32df63..a5cdc8f55f710 100644 --- a/recipes/busco/build.sh +++ b/recipes/busco/build.sh @@ -8,10 +8,6 @@ SHARE=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM mkdir -p $SHARE cp config/config.ini.default $SHARE/config.ini.default -cp $RECIPE_DIR/generate-busco-config.py $SHARE/generate-busco-config.py -chmod +x $SHARE/generate-busco-config.py -ln -s $SHARE/generate-busco-config.py $PREFIX/bin/generate-busco-config.py - ln -s $PREFIX/bin/run_BUSCO.py $PREFIX/bin/run_busco ln -s $PREFIX/bin/generate_plot.py $PREFIX/bin/generate_plot diff --git a/recipes/busco/generate-busco-config.py b/recipes/busco/generate-busco-config.py deleted file mode 100644 index f222e4521ab40..0000000000000 --- a/recipes/busco/generate-busco-config.py +++ /dev/null @@ -1,36 +0,0 @@ -#!/usr/bin/env python -import glob -import os -import sys -import argparse - -if (len(sys.argv) > 1) and sys.argv[1].lower() in ['-h', '--help', 'help']: - print( - ''' - usage: %s > path-to-new-config-file.ini - - BUSCO requires a config file with absolute paths to external - dependencies. When using this conda package, those dependencies are - installed in the same environment as BUSCO itself. This script replaces - the paths in the default BUSCO config file with the correct paths to - this conda environment's bin dir. - ''' % sys.argv[0] - ) - -# directory where symlink lives -bindir = os.path.dirname(os.path.abspath(__file__)) - -# directory after resolving symlink (which is where the example config file is -# found) -share = os.path.dirname(os.path.realpath(__file__)) -config = os.path.join(share, 'config.ini.default') - -# One option for editing paths would be to use configparser, but this would -# remove all the helpful comments in the config file. Instead, we match on "^path = " -lines = [] -for line in open(config): - if line.startswith('path = '): - lines.append('path = ' + bindir + '\n') - else: - lines.append(line) -sys.stdout.write(''.join(lines)) diff --git a/recipes/busco/meta.yaml b/recipes/busco/meta.yaml index e8edf25a6cd90..cf4de3bd8f347 100644 --- a/recipes/busco/meta.yaml +++ b/recipes/busco/meta.yaml @@ -9,7 +9,7 @@ package: build: # Not available for osx because requires augustus skip: True # [py27 or osx] - number: 4 + number: 5 source: fn: {{ name|lower }}_{{ version }}.tar.gz @@ -21,13 +21,14 @@ requirements: - python run: - python - - wget - blast - hmmer - augustus >=3.2.3 - r-ggplot2 >=2.2.1 test: + requires: + - wget commands: - run_BUSCO.py -h - run_busco -h diff --git a/recipes/busco/post-link.sh b/recipes/busco/post-link.sh index 9aab8782a660f..13025f09492e1 100644 --- a/recipes/busco/post-link.sh +++ b/recipes/busco/post-link.sh @@ -5,6 +5,6 @@ # the current environment's $PREFIX/bin dir. BUSCO expects a config file in # ../config/config.ini, so we create it here using sed on the default ini # stored in the share dir, replacing paths as necessary. -SHARE=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM -mkdir -p $PREFIX/config -$PREFIX/bin/generate-busco-config.py > $PREFIX/config/config.ini +SHARE="$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM" +mkdir -p "$PREFIX/config" +sed "s|^path = .*\$|path = $PREFIX/bin/|" "$SHARE/config.ini.default" > "$PREFIX/config/config.ini" diff --git a/recipes/cgat-scripts/meta.yaml b/recipes/cgat-scripts/meta.yaml index 835af87951a4a..d071e0e2eb54b 100644 --- a/recipes/cgat-scripts/meta.yaml +++ b/recipes/cgat-scripts/meta.yaml @@ -1,4 +1,4 @@ -{% set version = "0.3.1" %} +{% set version = "0.3.2" %} package: name: cgat-scripts @@ -6,11 +6,11 @@ package: source: url: https://pypi.io/packages/source/C/CGAT/CGAT-{{ version }}.tar.gz - md5: c52b508595e36448e5eea66ccb02f799 + sha256: 986fcada180d943df1ba4666c173c1b7e7b209bdbf9755571c2b946617a53386 build: skip: True # [not py3k] - number: 1 + number: 0 entry_points: - cgat = CGAT.cgat:main @@ -24,15 +24,15 @@ requirements: - future 0.16.* - matplotlib 2.1.* - numpy 1.12.* - - pandas 0.20.* + - pandas 0.21.* - pybedtools 0.7.* - pybigwig 0.3.* - - pysam 0.11.1 + - pysam 0.13.* - python-lzo 1.11.* - pyyaml 3.12.* - rpy2 2.8.* - scipy 0.19.* - - setuptools 36.3.* + - setuptools 37.0.* - six 1.11.* # Misc dependencies - bedtools 2.26.* @@ -40,9 +40,9 @@ requirements: - gcc - grep 2.14 - libpng 1.6.* - - ucsc-bedgraphtobigwig 332 - - ucsc-bedtobigbed 332 - - ucsc-wigtobigwig 332 + - ucsc-bedgraphtobigwig 357 + - ucsc-bedtobigbed 357 + - ucsc-wigtobigwig 357 - zlib 1.2.* run: @@ -54,10 +54,10 @@ requirements: - future 0.16.* - matplotlib 2.1.* - numpy 1.12.* - - pandas 0.20.* + - pandas 0.21.* - pybedtools 0.7.* - pybigwig 0.3.* - - pysam 0.11.1 + - pysam 0.13.* - python-lzo 1.11.* - pyyaml 3.12.* - rpy2 2.8.* @@ -69,9 +69,9 @@ requirements: - libgcc - grep 2.14 - libpng 1.6.* - - ucsc-bedgraphtobigwig 332 - - ucsc-bedtobigbed 332 - - ucsc-wigtobigwig 332 + - ucsc-bedgraphtobigwig 357 + - ucsc-bedtobigbed 357 + - ucsc-wigtobigwig 357 - zlib 1.2.* test: diff --git a/recipes/cmappy/meta.yaml b/recipes/cmappy/meta.yaml index f73a16a44a846..dff08a4317a7c 100644 --- a/recipes/cmappy/meta.yaml +++ b/recipes/cmappy/meta.yaml @@ -1,4 +1,4 @@ -{% set version = "2.2.0" %} +{% set version = "2.2.2" %} package: name: cmappy @@ -7,7 +7,7 @@ package: source: fn: cmapPy-{{ version }}.tar.gz url: https://pypi.io/packages/source/c/cmappy/cmapPy-{{ version }}.tar.gz - sha256: 5c80e9ff46677c0dfce1d1738326a73b1df6a10a8147d64ca17f0ab1fe4addd9 + sha256: c58e4e2a668ee9fd17e11603c4195aef94c3ff7790ca594f21eae6b770f03458 build: skip: False diff --git a/recipes/cnvkit/285.patch b/recipes/cnvkit/285.patch deleted file mode 100644 index 9c26c45488cb9..0000000000000 --- a/recipes/cnvkit/285.patch +++ /dev/null @@ -1,43 +0,0 @@ -diff --git a/cnvlib/segfilters.py b/cnvlib/segfilters.py -index 6b20780..33d6603 100644 ---- a/cnvlib/segfilters.py -+++ b/cnvlib/segfilters.py -@@ -72,18 +72,33 @@ def squash_region(cnarr): - 'start': cnarr['start'].iat[0], - 'end': cnarr['end'].iat[-1], - } -- out['log2'] = np.average(cnarr['log2'], weights=cnarr['weight']) -+ if cnarr['weight'].sum() > 0: -+ out['log2'] = np.average(cnarr['log2'], weights=cnarr['weight']) -+ else: -+ out['log2'] = np.mean(cnarr['log2']) - out['gene'] = ','.join(cnarr['gene'].drop_duplicates()) - out['probes'] = cnarr['probes'].sum() - out['weight'] = cnarr['weight'].sum() - if 'depth' in cnarr: -- out['depth'] = np.average(cnarr['depth'], weights=cnarr['weight']) -+ if cnarr['weight'].sum() > 0: -+ out['depth'] = np.average(cnarr['depth'], weights=cnarr['weight']) -+ else: -+ out['depth'] = np.mean(cnarr['depth']) - if 'baf' in cnarr: -- out['baf'] = np.average(cnarr['baf'], weights=cnarr['weight']) -+ if cnarr['weight'].sum() > 0: -+ out['baf'] = np.average(cnarr['baf'], weights=cnarr['weight']) -+ else: -+ out['baf'] = np.mean(cnarr['baf']) - if 'cn' in cnarr: -- out['cn'] = weighted_median(cnarr['cn'], cnarr['weight']) -+ if cnarr['weight'].sum() > 0: -+ out['cn'] = weighted_median(cnarr['cn'], cnarr['weight']) -+ else: -+ out['cn'] = np.median(cnarr['cn']) - if 'cn1' in cnarr: -- out['cn1'] = weighted_median(cnarr['cn1'], cnarr['weight']) -+ if cnarr['weight'].sum() > 0: -+ out['cn1'] = weighted_median(cnarr['cn1'], cnarr['weight']) -+ else: -+ out['cn1'] = np.median(cnarr['cn1']) - out['cn2'] = out['cn'] - out['cn1'] - return pd.DataFrame(out) - diff --git a/recipes/cnvkit/meta.yaml b/recipes/cnvkit/meta.yaml index 15b13817cbc98..60a5d2852f6aa 100644 --- a/recipes/cnvkit/meta.yaml +++ b/recipes/cnvkit/meta.yaml @@ -1,5 +1,5 @@ {% set version="0.9.2a0" %} -{% set revision="a9a8545" %} +{% set revision="ec4f888" %} package: name: cnvkit version: {{ version }} @@ -9,14 +9,10 @@ source: #url: https://pypi.io/packages/source/c/cnvkit/CNVkit-{{ version }}.tar.gz fn: cnvkit-{{ revision }}.tar.gz url: https://github.com/etal/cnvkit/archive/{{ revision }}.tar.gz - sha256: 8c91d1ecdf13daf6a876041632f30bfd8fdc84df06a497e88caaf6399677eeaf - patches: - # Fix for call --filter cn with zero weights - # https://github.com/etal/cnvkit/pull/285 - - 285.patch + sha256: 0f9eb39ce11c7b350b1414ffa7038812cf53a4297b79a36e6aefb9f768281ab8 build: - number: 0 + number: 1 requirements: build: diff --git a/recipes/cpinsim/build.sh b/recipes/cpinsim/build.sh new file mode 100644 index 0000000000000..5227f51eca79f --- /dev/null +++ b/recipes/cpinsim/build.sh @@ -0,0 +1,3 @@ +#!/bin/bash + +$PYTHON setup.py install --single-version-externally-managed --record record.txt diff --git a/recipes/cpinsim/meta.yaml b/recipes/cpinsim/meta.yaml new file mode 100644 index 0000000000000..c80468fc1ae80 --- /dev/null +++ b/recipes/cpinsim/meta.yaml @@ -0,0 +1,46 @@ +{% set version = "0.5.2" %} + +package: + name: cpinsim + version: {{ version }} + +source: + fn: cpinsim-{{ version }}.zip + url: https://pypi.io/packages/source/c/cpinsim/cpinsim-{{ version }}.zip + sha256: 34a7d7ae7fc6192e8524c8907967b3a6f868b8af650fab8d395a9a96da0308e8 + +build: + entry_points: + - cpinsim = cpinsim:main + number: 0 + skip: True # [py2k] + +requirements: + build: + - python + - setuptools + - networkx ==1.11.0 + - bitarray ==0.8.1 + - scipy + + run: + - python + - networkx ==1.11.0 + - bitarray ==0.8.1 + - scipy + +test: + imports: + - cpinsim + + commands: + - cpinsim --help + +about: + home: https://github.com/BiancaStoecker/cpinsim + license: MIT License + summary: | + CPINSim is a package for the simulation of protein complex assembly with constrained + protein interaction networks. + license_family: MIT + diff --git a/recipes/crossmap/build.sh b/recipes/crossmap/build.sh index 413f5b2eb0375..0f7fe5b04939f 100644 --- a/recipes/crossmap/build.sh +++ b/recipes/crossmap/build.sh @@ -1,3 +1,3 @@ #!/bin/bash -rm -rf lib/psyco_full.py -$PYTHON setup.py install +rm -f lib/psyco_full.py +$PYTHON setup.py install --single-version-externally-managed --record=record.txt diff --git a/recipes/crossmap/meta.yaml b/recipes/crossmap/meta.yaml index 098fae596784c..ea5b8a5f7ba81 100644 --- a/recipes/crossmap/meta.yaml +++ b/recipes/crossmap/meta.yaml @@ -1,30 +1,35 @@ +{% set name = "CrossMap" %} +{% set version = "0.2.7" %} +{% set sha256hash = "edaef71757c4ae5182f5c8fd6350d096118919c02ff46660944e8db4ff5d6341" %} + package: - name: crossmap - version: 0.2.5 + name: {{ name|lower }} + version: {{ version }} + source: - url: http://sourceforge.net/projects/crossmap/files/CrossMap-0.2.5.tar.gz - fn: CrossMap-0.2.5.tar.gz - md5: 546710d26e299cf039497af1ec6c80dd + fn: CrossMap-{{ version }}.tar.gz + url: http://sourceforge.net/projects/crossmap/files/CrossMap-{{ version }}.tar.gz + sha256: {{ sha256hash }} build: - number: 1 + number: 0 # CrossMap is very particular about Python version. - skip: True # [not py27 or osx] + skip: True # [not py27] requirements: build: - python + - setuptools - cython >=0.17 - numpy - - nose - - pysam >=0.6 + - nose >=0.10.4 + - pysam >=0.11.1 - bx-python run: - python - cython >=0.17 - numpy - - nose - - pysam >=0.6 + - pysam >=0.11.1 - bx-python - ucsc-wigtobigwig @@ -35,5 +40,5 @@ test: about: home: http://crossmap.sourceforge.net - license: GPL + license: GPLv2 summary: "Convert genomic coordiates between assemblies" diff --git a/recipes/cutadapt/meta.yaml b/recipes/cutadapt/meta.yaml index 085775cb08615..eba50f5cb0e25 100644 --- a/recipes/cutadapt/meta.yaml +++ b/recipes/cutadapt/meta.yaml @@ -1,6 +1,6 @@ package: name: cutadapt - version: '1.14' + version: '1.15' about: home: https://cutadapt.readthedocs.io/ @@ -8,9 +8,9 @@ about: summary: 'trim adapters from high-throughput sequencing reads' source: - fn: cutadapt-1.14.tar.gz - url: https://pypi.python.org/packages/16/e3/06b45eea35359833e7c6fac824b604f1551c2fc7ba0f2bd318d8dd883eb9/cutadapt-1.14.tar.gz - md5: 57403c3794aa940699df3032a5e9b208 + fn: cutadapt-1.15.tar.gz + url: https://pypi.python.org/packages/5a/89/a041e0a108bef64b1347e9b7126d813e61f0ce028d3db830fb7b77aab1ab/cutadapt-1.15.tar.gz + md5: 50baff135228644e8c68e90e2bd4e953 build: number: 0 @@ -19,14 +19,13 @@ build: requirements: build: - python - - xopen >=0.1.1 + - xopen >=0.3.2 run: - python - - xopen >=0.1.1 + - xopen >=0.3.2 test: imports: - cutadapt - - cutadapt.scripts commands: - cutadapt --version diff --git a/recipes/daligner/meta.yaml b/recipes/daligner/meta.yaml index 9316738b4e491..b0514edb9f397 100644 --- a/recipes/daligner/meta.yaml +++ b/recipes/daligner/meta.yaml @@ -1,13 +1,13 @@ package: name: daligner - version: "1.0p1" + version: "1.0p2" build: - number: 2 + number: 0 source: - fn: daligner_V1.0p1.tar.gz - md5: e49ca399c153333b1ec4e69d8d6daea8 - url: https://github.com/thegenemyers/DALIGNER/archive/a9458dcb34eca61513c994f4217fb7f75915e25c.tar.gz + fn: daligner_V1.0p2.tar.gz + md5: b7678853c1533c7e2df9c03522df84e9 + url: https://github.com/thegenemyers/DALIGNER/archive/381fa920935a6bb469353cfc5c83d301579b5e04.tar.gz requirements: build: diff --git a/recipes/damasker/build.sh b/recipes/damasker/build.sh new file mode 100644 index 0000000000000..a2e5f30b2cf89 --- /dev/null +++ b/recipes/damasker/build.sh @@ -0,0 +1,14 @@ +#!/bin/bash + +mkdir -p $PREFIX/bin +make + +binaries="\ + REPmask \ + datander \ + TANmask \ + HPC.REPmask \ + HPC.TANmask +" + +for i in $binaries; do cp $i $PREFIX/bin && chmod +x $PREFIX/bin/$i; done diff --git a/recipes/damasker/meta.yaml b/recipes/damasker/meta.yaml new file mode 100644 index 0000000000000..aa0494c1baf08 --- /dev/null +++ b/recipes/damasker/meta.yaml @@ -0,0 +1,35 @@ +{% set name = "damasker" %} +{% set version = "1.0p1" %} + +package: + name: {{ name|lower }} + version: {{ version }} + +build: + number: 0 + +source: + fn: {{ name|lower }}_{{ version }}.tar.gz + sha256: 4c364ef5165fa0613d24fa8030563665d00307350288fbc0289baf600865fa45 + url: https://github.com/thegenemyers/DAMASKER/archive/bf6ccc8918ab99c52d368a780afc0b9e60371a17.tar.gz + +requirements: + build: + - gcc # [not osx] + - llvm # [osx] + run: + - libgcc # [not osx] + +test: + commands: + - REPmask 2>&1 | grep Usage + - datander 2>&1 | grep Usage + - TANmask 2>&1 | grep Usage + - HPC.REPmask 2>&1 | grep Usage + - HPC.TANmask 2>&1 | grep Usage + +about: + home: 'https://github.com/thegenemyers/DAMASKER' + license: Custom + license_file: README.md + summary: "DAMASKER: Module to determine where repeats are and make soft-masks of said" diff --git a/recipes/dascrubber/build.sh b/recipes/dascrubber/build.sh index 552ba2677cc1f..7193bc9a7f411 100644 --- a/recipes/dascrubber/build.sh +++ b/recipes/dascrubber/build.sh @@ -5,7 +5,13 @@ make binaries="\ DASqv \ - DAStrim + DAStrim \ + DASpatch \ + DASedit \ + DASmap \ + DASrealign \ + REPqv \ + REPtrim " for i in $binaries; do cp $i $PREFIX/bin && chmod +x $PREFIX/bin/$i; done diff --git a/recipes/dascrubber/meta.yaml b/recipes/dascrubber/meta.yaml index 0e826b65c6f50..6fbe04f1172a4 100644 --- a/recipes/dascrubber/meta.yaml +++ b/recipes/dascrubber/meta.yaml @@ -1,14 +1,14 @@ package: name: dascrubber - version: "0.0.1a1" + version: "0.0.1a2" build: number: 0 -source: - fn: dascrubber_0.0.1a1.tar.gz - md5: 8c3c244315daa3e25c1bf67d605c1f5c - url: https://github.com/thegenemyers/DASCRUBBER/archive/00749143f092ccff4d9ffb4b35b3baddc856b063.tar.gz +source: + fn: dascrubber_0.0.1a2.tar.gz + sha256: 2463262ed6caeda97474b868197635824199e7e0008ca65ed8a65ef08bb320ce + url: https://github.com/thegenemyers/DASCRUBBER/archive/2896d225f77d1c4ab3990de33bf0f761b42cf730.tar.gz requirements: build: @@ -16,10 +16,18 @@ requirements: - llvm # [osx] run: - libgcc # [not osx] + test: - commands: - - DASqv 2>&1 | grep Usage > /dev/null - - DAStrim 2>&1 | grep Usage > /dev/null + commands: + - DASqv 2>&1 | grep Usage + - DAStrim 2>&1 | grep Usage + - DASpatch 2>&1 | grep Usage + - DASedit 2>&1 | grep Usage + - DASmap 2>&1 | grep Usage + - DASrealign 2>&1 | grep Usage + - REPqv 2>&1 | grep Usage + - REPtrim 2>&1 | grep Usage + about: home: 'https://github.com/thegenemyers/DASCRUBBER' license: Custom diff --git a/recipes/dazz_db/meta.yaml b/recipes/dazz_db/meta.yaml index 1d78eb01b2d22..18394d09cd478 100644 --- a/recipes/dazz_db/meta.yaml +++ b/recipes/dazz_db/meta.yaml @@ -1,26 +1,40 @@ package: name: dazz_db - version: "1.0p1" + version: "1.0p2" build: - number: 1 + number: 0 source: - fn: dazz_db_V1.0p1.tar.gz - md5: be7950d41f776b542d98ab2376d92a25 - url: https://github.com/thegenemyers/DAZZ_DB/archive/e31d4517ab9f4fad6571a351ba10f87db35b8bc8.tar.gz + fn: dazz_db_V1.0p2.tar.gz + sha256: 3e98d10454b12bf0bcba1cdec226882e8214a3040472cbfaec0f9b589099d730 + url: https://github.com/thegenemyers/DAZZ_DB/archive/8ab7daf27123a3dfd17189af168ebe22b343170f.tar.gz requirements: build: - gcc # [not osx] - llvm # [osx] - - zlib + - zlib {{ CONDA_ZLIB }}* run: - libgcc # [not osx] - - zlib + - zlib {{ CONDA_ZLIB }}* test: - commands: - - fasta2DB 2>&1 | grep Usage > /dev/null + commands: + - fasta2DB 2>&1 | grep Usage + - DB2fasta 2>&1 | grep Usage + - quiva2DB 2>&1 | grep Usage + - DB2quiva 2>&1 | grep Usage + - DBsplit 2>&1 | grep Usage + - DBdust 2>&1 | grep Usage + - Catrack 2>&1 | grep Usage + - DBshow 2>&1 | grep Usage + - DBstats 2>&1 | grep Usage + - DBrm 2>&1 | grep Usage + - simulator 2>&1 | grep Usage + - fasta2DAM 2>&1 | grep Usage + - DAM2fasta 2>&1 | grep Usage + - rangen 2>&1 | grep Usage + - DBdump 2>&1 | grep Usage about: home: 'https://github.com/thegenemyers/DAZZ_DB' diff --git a/recipes/deepmedic/meta.yaml b/recipes/deepmedic/meta.yaml index b134bf3390914..fadd52535c2ad 100644 --- a/recipes/deepmedic/meta.yaml +++ b/recipes/deepmedic/meta.yaml @@ -1,4 +1,4 @@ -{% set DEEPMEDIC_VERSION = "0.5.4" %} +{% set DEEPMEDIC_VERSION = "0.6" %} package: name: deepmedic @@ -7,7 +7,7 @@ package: source: fn: v{{ DEEPMEDIC_VERSION}}.zip url: https://codeload.github.com/Kamnitsask/deepmedic/zip/v{{ DEEPMEDIC_VERSION}} - md5: 7f2cb90f90f1da7ea86c7c41c5f76cab + sha256: e7dbdc2f974fe5d483ad1a93de7278c6c8a79d3a569995a1f6d41830d80f6348 patches: - setup.patch diff --git a/recipes/dextractor/dextractor.patch b/recipes/dextractor/dextractor.patch index 12c715f89a663..eb95bafd66fe4 100644 --- a/recipes/dextractor/dextractor.patch +++ b/recipes/dextractor/dextractor.patch @@ -1,11 +1,12 @@ ---- Makefile 2016-09-25 14:05:39.000000000 +0200 -+++ Makefile 2016-09-25 14:08:30.000000000 +0200 +--- Makefile.bak 2017-12-12 13:20:54.996000000 +1000 ++++ Makefile 2017-12-12 13:22:54.536000000 +1000 @@ -1,7 +1,6 @@ --PATH_HDF5 = /sw/apps/hdf5/current +-PATH_HDF5 = /sw -PATH_HDF5 = /usr/local/hdf5 +PATH_HDF5 = ${PREFIX} - + -DEST_DIR = ~/bin +DEST_DIR = ${PREFIX}/bin - + CFLAGS = -O3 -Wall -Wextra -Wno-unused-result -fno-strict-aliasing + diff --git a/recipes/dextractor/meta.yaml b/recipes/dextractor/meta.yaml index 75628a6de4411..d560364ce2720 100644 --- a/recipes/dextractor/meta.yaml +++ b/recipes/dextractor/meta.yaml @@ -1,13 +1,14 @@ package: name: dextractor - version: "1.0p1" + version: "1.0p2" build: number: 0 + source: - fn: dextractor_V1.0p1.tar.gz - md5: f9a79c200783017a1b4c99deeaa5ba2c - url: https://github.com/thegenemyers/DEXTRACTOR/archive/e0e2374a50e680b788aadc494bb1d25e4c94f1a9.tar.gz + fn: dextractor_V1.0p2.tar.gz + sha256: d5bfe730615d76b29d373b6505421db83f7f1075ef6be331c3ac030e40dcf343 + url: https://github.com/thegenemyers/DEXTRACTOR/archive/2f51ccba9c56f5c11966d39cbec0711ed467e7a9.tar.gz patches: - dextractor.patch @@ -20,14 +21,15 @@ requirements: - libgcc # [not osx] - hdf5 {{ CONDA_HDF5 }}* test: - commands: - - dextract 2>&1 | grep Usage > /dev/null - - dexta 2>&1 | grep Usage > /dev/null - - undexta 2>&1 | grep Usage > /dev/null - - dexqv 2>&1 | grep Usage > /dev/null - - undexqv 2>&1 | grep Usage > /dev/null + commands: + - dextract 2>&1 | grep Usage + - dexta 2>&1 | grep Usage + - undexta 2>&1 | grep Usage + - dexqv 2>&1 | grep Usage + - undexqv 2>&1 | grep Usage + about: home: 'https://github.com/thegenemyers/DEXTRACTOR' license: Custom - license_file: README + license_file: LICENSE summary: "Bax File Decoder and Data Compressor" diff --git a/recipes/discasm/meta.yaml b/recipes/discasm/meta.yaml index 8c58162f524db..9f1bc82db4e73 100644 --- a/recipes/discasm/meta.yaml +++ b/recipes/discasm/meta.yaml @@ -1,6 +1,6 @@ {% set name = "discasm" %} {% set version = "0.1.2" %} -{% set build = "1" %} +{% set build = "2" %} package: name: {{ name }} @@ -21,7 +21,7 @@ requirements: build: run: - python - - pysam + - pysam >=0.10.0 - perl - star >=2.4 - trinity >=2.4 diff --git a/recipes/discosnp/2.2.10/build.sh b/recipes/discosnp/2.2.10/build.sh deleted file mode 100644 index f74391204991f..0000000000000 --- a/recipes/discosnp/2.2.10/build.sh +++ /dev/null @@ -1,28 +0,0 @@ -#!/bin/bash - -mkdir -p ${PREFIX}/bin - -# decrease RAM needed -sed -i.bak 's/make -j8/make -j1/' INSTALL - -# remove tests because of too much RAM needed -sed -i.bak 's/. .\/simple_test\.sh/#. .\/simple_test\.sh/' INSTALL - -# installation -sh INSTALL - -# change run_discoSnp++.sh deps path -sed -i.bak 's/\$EDIR\/bin/\$EDIR/' run_discoSnp++.sh -sed -i.bak 's/scripts\//..\/scripts\//' run_discoSnp++.sh - -# copy binaries -cp run_discoSnp++.sh ${PREFIX}/bin -chmod +x ${PREFIX}/bin/run_discoSnp++.sh - -cp build/ext/gatb-core/bin/dbgh5 ${PREFIX}/bin -cp build/bin/read_file_names ${PREFIX}/bin -cp build/bin/kissnp2 ${PREFIX}/bin -cp build/bin/kissreads2 ${PREFIX}/bin - -# copy scripts directory -cp -R scripts ${PREFIX} diff --git a/recipes/discosnp/2.2.10/meta.yaml b/recipes/discosnp/2.2.10/meta.yaml deleted file mode 100644 index d360ab4bfd368..0000000000000 --- a/recipes/discosnp/2.2.10/meta.yaml +++ /dev/null @@ -1,31 +0,0 @@ -package: - name: discosnp - version: '2.2.10' - -source: - fn: DiscoSNP.-v2.2.10-Source.tar.gz - url: "https://github.com/GATB/DiscoSnp/releases/download/v2.2.10/DiscoSNP.-v2.2.10-Source.tar.gz" - md5: "a5590184534e387a21cd35630dc09529" - -build: - number: 1 - -requirements: - build: - - gcc # [linux] - - llvm # [osx] - - cmake - - zlib {{CONDA_ZLIB}}* - run: - - libgcc # [linux] - - zlib {{CONDA_ZLIB}}* - - bwa - -test: - commands: - - run_discoSnp++.sh -h - -about: - home: https://gatb.inria.fr/software/discosnp/ - license: GNU Affero General Public License v3.0 - summary: Designed for discovering all kinds of SNPs diff --git a/recipes/discosnp/meta.yaml b/recipes/discosnp/meta.yaml index 7bd19257ffdb4..7ce3abb8c7a8c 100644 --- a/recipes/discosnp/meta.yaml +++ b/recipes/discosnp/meta.yaml @@ -8,7 +8,7 @@ source: md5: "dfc35f6f5b83e7f661f5acbcb3c03bad" build: - number: 2 + number: 4 requirements: build: @@ -20,7 +20,8 @@ requirements: - libgcc # [linux] - zlib {{CONDA_ZLIB}}* - bwa - - shortreadsconnector + - shortreadconnector + - python >=3.0 test: commands: diff --git a/recipes/dx-cwl/build.sh b/recipes/dx-cwl/build.sh index 70303e107c52b..c295d1dd21d18 100644 --- a/recipes/dx-cwl/build.sh +++ b/recipes/dx-cwl/build.sh @@ -9,6 +9,7 @@ cd "${SRC_DIR}" sed -i.bak 's#!/usr/bin/env python#!/opt/anaconda1anaconda2anaconda3/bin/python#' dx-cwl mv dx-cwl $TGT mv dx-cwl-applet-code.py $TGT +mv dx-cwl-postprocess-output-code.py $TGT mv resources $TGT ln -s $TGT/dx-cwl $PREFIX/bin chmod 0755 "${PREFIX}/bin/dx-cwl" diff --git a/recipes/dx-cwl/meta.yaml b/recipes/dx-cwl/meta.yaml index 75c8a18ad3c1e..a76780c5ee7b2 100644 --- a/recipes/dx-cwl/meta.yaml +++ b/recipes/dx-cwl/meta.yaml @@ -1,14 +1,13 @@ -{% set version="0.1.0a20171029" %} -{% set revision="e5a2755" %} +{% set version="0.1.0a20171213" %} +{% set revision="f90d63b" %} package: name: dx-cwl version: {{ version }} source: fn: dx-cwl-{{ version }}.tar.gz - #url: https://github.com/dnanexus/dx-cwl/archive/{{ revision }}.tar.gz - url: https://github.com/chapmanb/dx-cwl/archive/{{ revision }}.tar.gz - md5: 1ad614465cd1733fb69c0fee9a328271 + url: https://github.com/dnanexus/dx-cwl/archive/{{ revision }}.tar.gz + md5: d9422f793f9337ec64fe31eeaaf0f604 build: number: 0 diff --git a/recipes/editdistance/meta.yaml b/recipes/editdistance/meta.yaml index 55d131cdc6174..7ac188ebfc850 100644 --- a/recipes/editdistance/meta.yaml +++ b/recipes/editdistance/meta.yaml @@ -1,11 +1,13 @@ +{% set version = "0.4" %} + package: name: editdistance - version: "0.3.1" + version: {{ version }} source: - fn: editdistance-0.3.1.tar.gz - url: https://pypi.python.org/packages/a8/08/97ed5b60023ab4b67a46ee24bf1d3db93a9abc5b3be7e8f90de18160aaed/editdistance-0.3.1.tar.gz - md5: 372752ca61cf4abe60941357cdb7065f + fn: editdistance-{{ version }}.tar.gz + url: https://pypi.io/packages/source/e/editdistance/editdistance-{{ version }}.tar.gz + sha256: c765db6f8817d38922e4a50be4b9ab338b2c539377b6fcf0bca11dea72eeb8c1 build: number: 0 diff --git a/recipes/embl-validator/embl-api-validator.py b/recipes/embl-validator/embl-api-validator.py index 437414efb3977..7f18432c1079b 100644 --- a/recipes/embl-validator/embl-api-validator.py +++ b/recipes/embl-validator/embl-api-validator.py @@ -13,7 +13,7 @@ from os import access from os import getenv from os import X_OK -jar_file = 'embl-api-validator-1.1.171.jar' +jar_file = 'embl-api-validator-1.1.180.jar' default_jvm_mem_opts = ['-Xms512m', '-Xmx1g'] diff --git a/recipes/embl-validator/meta.yaml b/recipes/embl-validator/meta.yaml index 53f7c9b8b14fb..a1fe692bf19f9 100644 --- a/recipes/embl-validator/meta.yaml +++ b/recipes/embl-validator/meta.yaml @@ -1,7 +1,16 @@ -about: - home: 'http://www.ebi.ac.uk/ena/software/flat-file-validator' - license: - summary: 'ENA flat file validator for submission' +{% set name = "embl-api-validator" %} +# version needs to be updated in embl-api-validator.py as well! +{% set version = "1.1.180" %} +{% set sha256hash = "c103098c584c05401cadb3ee6aa4daa0068f87b473b1f1f5b9fd149d5fa7c340" %} + +package: + name: {{ name|lower }} + version: {{ version }} + +source: + fn: {{ name|lower }}-{{ version }}.jar + url: http://central.maven.org/maven2/uk/ac/ebi/ena/sequence/embl-api-validator/{{ version }}/embl-api-validator-{{ version }}.jar + sha256: {{ sha256hash }} build: number: 0 @@ -11,16 +20,12 @@ requirements: - openjdk - python -package: - name: embl-api-validator - version: 1.1.173 - -source: - fn: embl-api-validator-1.1.171.jar - url: http://central.maven.org/maven2/uk/ac/ebi/ena/sequence/embl-api-validator/1.1.173/embl-api-validator-1.1.173.jar - sha256: 91fc44f005746bf8ce2e876bccf3bc239f68a9aaba211a3c187a5932303a2483 - test: commands: - embl-api-validator -version +about: + home: 'http://www.ebi.ac.uk/ena/software/flat-file-validator' + license: Apache-2-0 + summary: 'ENA flat file validator for submission' + diff --git a/recipes/ensembl-vep/build.sh b/recipes/ensembl-vep/build.sh index a7e9c4c3b9ff1..2b2a4b1cba8c3 100644 --- a/recipes/ensembl-vep/build.sh +++ b/recipes/ensembl-vep/build.sh @@ -42,5 +42,11 @@ curl -ks -o MaxEntScan.pm https://raw.githubusercontent.com/Ensembl/VEP_plugins/ curl -ks -o SpliceRegion.pm https://raw.githubusercontent.com/Ensembl/VEP_plugins/release/$version/SpliceRegion.pm curl -ks -o GeneSplicer.pm https://raw.githubusercontent.com/Ensembl/VEP_plugins/release/$version/GeneSplicer.pm curl -ks -o dbscSNV.pm https://raw.githubusercontent.com/Ensembl/VEP_plugins/release/$version/dbscSNV.pm -curl -ks -o LoF.pm https://raw.githubusercontent.com/konradjk/loftee/master/LoF.pm -curl -ks -o splice_module.pl https://raw.githubusercontent.com/konradjk/loftee/master/splice_module.pl +curl -L -ks -o loftee.tar.gz https://github.com/konradjk/loftee/archive/8de80a4.tar.gz +tar -xzvpf loftee.tar.gz +mv loftee-*/*.pl . +mv loftee-*/*.pm . +mv loftee-*/maxEntScan . +mv loftee-*/splice_data . +rm -f loftee.tar.gz +rm -rf loftee-* diff --git a/recipes/ensembl-vep/meta.yaml b/recipes/ensembl-vep/meta.yaml index d5a976ab1fa5b..894b42ae34f85 100644 --- a/recipes/ensembl-vep/meta.yaml +++ b/recipes/ensembl-vep/meta.yaml @@ -1,4 +1,4 @@ -{% set version="90.7" %} +{% set version="90.10" %} package: name: ensembl-vep @@ -7,7 +7,7 @@ package: source: fn: vep-{{ version }}.tar.gz url: https://github.com/Ensembl/ensembl-vep/archive/release/{{ version }}.tar.gz - md5: 360f5cbaf1bc0431515a1cdff2e83e57 + md5: 881b8ba34d5aa34f8b0c80f93e2ba50d build: number: 0 diff --git a/recipes/epic/meta.yaml b/recipes/epic/meta.yaml index 931b4eeebee35..a30751cbe7ce8 100644 --- a/recipes/epic/meta.yaml +++ b/recipes/epic/meta.yaml @@ -1,11 +1,11 @@ package: name: epic - version: "0.2.5" + version: "0.2.7" source: - fn: bioepic-0.2.5.tar.gz - url: https://files.pythonhosted.org/packages/69/6b/0d3e7bf8333b2144fb14326d44f7e98a01c5236d75692959063b2509d335/bioepic-0.2.5.tar.gz - sha256: 8ffc81919f4df1d70b8bac5b237400ffbe03998f94bdc5da340197cf39765a85 + fn: bioepic-0.2.7.tar.gz + url: https://pypi.python.org/packages/5a/37/3847a5c219f1b619cbb0e8ed441a4c800ea5aac38ab91da1db3630402eab/bioepic-0.2.7.tar.gz + md5: 859110dc4d625c57601b37be36149a7b build: number: 0 diff --git a/recipes/fast5/meta.yaml b/recipes/fast5/meta.yaml index dd35bc2104fdd..7a8e15afb1036 100644 --- a/recipes/fast5/meta.yaml +++ b/recipes/fast5/meta.yaml @@ -1,5 +1,5 @@ {% set name = "fast5" %} -{% set version = "0.6.3.p1" %} +{% set version = "0.6.4" %} package: name: {{ name|lower }} @@ -10,8 +10,8 @@ build: source: fn: {{ name|lower }}_{{ version }}.tar.gz - url: https://github.com/mateidavid/fast5/archive/ecfcd30be4687e32b13f5e07ddd33c0cd25d9b49.tar.gz - sha256: 48bcf6aac5852703cb592b7cd789e24065f353a5d646d8adec61cb635db6270a + url: https://github.com/mateidavid/fast5/archive/v{{ version }}.tar.gz + sha256: e0d1a718fabac0103fd84d3a0a7cce6c3320074bda47342367bdd3ac2e17a915 requirements: build: diff --git a/recipes/fastq-and-furious/build.sh b/recipes/fastq-and-furious/build.sh index 4d7fc032b8cbe..8e25a1455f914 100644 --- a/recipes/fastq-and-furious/build.sh +++ b/recipes/fastq-and-furious/build.sh @@ -1,9 +1,3 @@ #!/bin/bash $PYTHON setup.py install - -# Add more build steps here, if they are necessary. - -# See -# http://docs.continuum.io/conda/build.html -# for a list of environment variables that are set during the build process. diff --git a/recipes/fastq-and-furious/meta.yaml b/recipes/fastq-and-furious/meta.yaml index 6b679d1528d8b..9248f8da86ae0 100644 --- a/recipes/fastq-and-furious/meta.yaml +++ b/recipes/fastq-and-furious/meta.yaml @@ -1,11 +1,11 @@ package: name: fastq-and-furious - version: 0.1.0 + version: 0.2.0 source: - fn: fastq-and-furious-0.1.0.tar.gz - url: https://pypi.python.org/packages/e0/52/96cc1e9cda6d65ad4179facd18f50aeb21a146f7bd08ef9249ae8f8c6d1e/fastq-and-furious-0.1.0.tar.gz - md5: 45a9403e708fa267140f7a49f1cb106f + fn: fastq-and-furious-0.2.0.tar.gz + url: https://github.com/lgautier/fastq-and-furious/archive/0.2.0.tar.gz + sha256: 0e03b3d0305adc508b7a1ca7b0224651ce778786c09ab1617bea23bf08d4a89c build: number: 0 diff --git a/recipes/fastqc/0.11.2/build.sh b/recipes/fastqc/0.11.2/build.sh new file mode 100644 index 0000000000000..efc5f9b4a6455 --- /dev/null +++ b/recipes/fastqc/0.11.2/build.sh @@ -0,0 +1,9 @@ +#!/bin/bash + +fastqc=$PREFIX/opt/$PKG_NAME-$PKG_VERSION +mkdir -p $fastqc +cp -r ./* $fastqc +chmod +x $fastqc/fastqc +mkdir -p $PREFIX/bin +ln -s $fastqc/fastqc $PREFIX/bin/fastqc + diff --git a/recipes/fastqc/0.11.2/hashbang.patch b/recipes/fastqc/0.11.2/hashbang.patch new file mode 100644 index 0000000000000..1e805bef541ec --- /dev/null +++ b/recipes/fastqc/0.11.2/hashbang.patch @@ -0,0 +1,8 @@ +--- fastqc.orig 2017-12-04 14:31:46.599074067 +0100 ++++ fastqc 2017-12-04 14:31:19.666061227 +0100 +@@ -1,4 +1,4 @@ +-#!/usr/bin/perl ++#!/usr/bin/env perl + use warnings; + use strict; + use FindBin qw($RealBin); diff --git a/recipes/fastqc/0.11.2/meta.yaml b/recipes/fastqc/0.11.2/meta.yaml new file mode 100644 index 0000000000000..8f774cee4d298 --- /dev/null +++ b/recipes/fastqc/0.11.2/meta.yaml @@ -0,0 +1,30 @@ +# this recipe was derived from the montilab channel. +about: + home: 'http://www.bioinformatics.babraham.ac.uk/projects/fastqc/' + license: GPL + summary: 'A quality control tool for high throughput sequence data.' + +build: + detect_binary_files_with_prefix: true + number: 0 + skip: False + +requirements: + run: + - openjdk + - perl + +package: + name: fastqc + version: 0.11.2 + +source: + fn: fastqc_v0.11.2.zip + url: http://www.bioinformatics.babraham.ac.uk/projects/fastqc/fastqc_v0.11.2.zip + sha256: f362b141e696d67442fa16c3a71118936e0b14a0343bb88735973a920cbaef09 + patches: + - hashbang.patch + +test: + commands: + - 'fastqc --version | grep "^FastQC v0\.11\.2"' diff --git a/recipes/fasttree/meta.yaml b/recipes/fasttree/meta.yaml index 3c18867011ed2..066a9681f1aed 100644 --- a/recipes/fasttree/meta.yaml +++ b/recipes/fasttree/meta.yaml @@ -1,18 +1,17 @@ {% set name = "FastTree" %} -{% set version = "2.1.9" %} +{% set version = "2.1.10" %} package: name: {{ name|lower }} version: {{ version }} - source: fn: "FastTree.c" url: "http://meta.microbesonline.org/{{ name|lower }}/{{ name }}-{{ version }}.c" - sha256: "f3a4e57d27e3fd6b5e2a4201b15ae25bc43858092eefef160f9aaa1011df5b52" + sha256: "54cb89fc1728a974a59eae7a7ee6309cdd3cddda9a4c55b700a71219fc6e926d" build: - number: 2 + number: 0 requirements: build: diff --git a/recipes/fcsparser/build.sh b/recipes/fcsparser/build.sh new file mode 100755 index 0000000000000..0456c5ca37e6b --- /dev/null +++ b/recipes/fcsparser/build.sh @@ -0,0 +1,4 @@ +#!/bin/bash + +$PYTHON setup.py install --single-version-externally-managed --record=record.txt + diff --git a/recipes/fcsparser/meta.yaml b/recipes/fcsparser/meta.yaml new file mode 100644 index 0000000000000..0c32899a369c0 --- /dev/null +++ b/recipes/fcsparser/meta.yaml @@ -0,0 +1,36 @@ +package: + name: fcsparser + version: "0.1.4" + +source: + fn: fcsparser-0.1.4.tar.gz + url: https://pypi.python.org/packages/43/44/ee3762e383c530bb051023115dbadcb40c370c61452b63882e5aee770b51/fcsparser-0.1.4.tar.gz + md5: e93393c15185f125b28e5c7023bb751c + +build: + number: 0 + noarch: python + preserve_egg_dir: False + +requirements: + build: + - python + - setuptools + - numpy + - pandas + + run: + - python + - numpy + - pandas + +test: + imports: + - fcsparser + - fcsparser.tests + +about: + home: https://github.com/eyurtsev/fcsparser + license: MIT + summary: 'A python package for reading raw fcs files' + license_family: MIT diff --git a/recipes/fgap/build.sh b/recipes/fgap/build.sh new file mode 100644 index 0000000000000..f01deacd0cf8c --- /dev/null +++ b/recipes/fgap/build.sh @@ -0,0 +1,9 @@ +#!/bin/bash +cat > FGAP <&1 | grep PASS > /dev/null - -about: - home: https://github.com/sparsehash/sparsehash - license: BSD - summary: Several hash-map implementations. - diff --git a/recipes/gseapy/meta.yaml b/recipes/gseapy/meta.yaml index 5d51fe37f6083..1c34345172be1 100644 --- a/recipes/gseapy/meta.yaml +++ b/recipes/gseapy/meta.yaml @@ -1,11 +1,11 @@ package: name: gseapy - version: "0.8.6" + version: "0.9.0" source: - fn: gseapy-0.8.6.tar.gz - url: https://pypi.python.org/packages/5d/ad/cb7bff2c3df77b77f42c2a89b66b6f73deeabf9d5ff819f7e3d997957ba1/gseapy-0.8.6.tar.gz - sha256: 740a39b64e41474ec00f2181eeb32eadb6a23da759481a9beb386953d0fbf261 + fn: gseapy-0.9.0.tar.gz + url: https://pypi.python.org/packages/ea/0d/8fc81acca1a87126df6f64c1e400346a1b46455bcb17fc882ffff4beec9d/gseapy-0.9.0.tar.gz + sha256: 6b2b626c646ccd531d76e9a4c92de6c105d87bbb5aa6916fb3b583e2e7a9ca1f build: entry_points: @@ -16,7 +16,7 @@ requirements: build: - python - setuptools - - numpy >=1.8.0 + - numpy >=1.13.0 - pandas >=0.16 - matplotlib >=1.4.3 - beautifulsoup4 >=4.4.1 @@ -26,7 +26,7 @@ requirements: run: - python - - numpy >=1.8.0 + - numpy >=1.13.0 - pandas >=0.16 - matplotlib >=1.4.3 - beautifulsoup4 >=4.4.1 diff --git a/recipes/haploclique/1.3.1/build.sh b/recipes/haploclique/1.3.1/build.sh new file mode 100644 index 0000000000000..2be1a341f0378 --- /dev/null +++ b/recipes/haploclique/1.3.1/build.sh @@ -0,0 +1,21 @@ +#!/use/bin/env sh + +# HACK GCC 4.8.5 ships with a broken std::regex (it's only fixed with GCC 4.9.0) +if [[ `c++ -dumpversion` == 4.8.* ]]; then + echo 'GCC version 4.8.x detected, forcing switch of regex engine from C++11 to Boost' + USE_BOOST_REGEX='-DUSE_BOOST_REGEX=1' +fi + +mkdir -p build && cd build + +cmake -DCMAKE_INSTALL_PREFIX:PATH="${PREFIX}" \ + -DBOOST_ROOT="${PREFIX}" -DBoost_NO_SYSTEM_PATHS=ON "${USE_BOOST_REGEX}" \ + -DCMAKE_SKIP_BUILD_RPATH=FALSE -DCMAKE_BUILD_WITH_INSTALL_RPATH=TRUE -DCMAKE_INSTALL_RPATH="${PREFIX}/lib64:${PREFIX}/lib:${PREFIX}/lib/bamtools" -DCMAKE_INSTALL_RPATH_USE_LINK_PATH=TRUE \ + .. \ + && make \ + && make install + +## unit tests +# NOTE disabling unit tests to shave off a few seconds of Travis' runtime +#export LIBRARY_PATH="${PREFIX}/lib64:${PREFIX}/lib:${PREFIX}/lib/bamtools:${LIBRARY_PATH:+:${LIBRARY_PATH}}" +#make check diff --git a/recipes/haploclique/1.3.1/meta.yaml b/recipes/haploclique/1.3.1/meta.yaml new file mode 100644 index 0000000000000..8870d5454b386 --- /dev/null +++ b/recipes/haploclique/1.3.1/meta.yaml @@ -0,0 +1,44 @@ +{% set name = "haploclique" %} +{% set version = "1.3.1" %} +{% set sha256 = "7418392a72f5420db56a9170aaf0fe4bc055b6221e61cb6012681c51cd314a45" %} + +package: + name: {{ name|lower }} + version: {{ version }} + +build: + number: 0 + +source: + fn: {{ name }}-v{{ version }}.tar.bz2 + url: https://github.com/cbg-ethz/{{ name }}/releases/download/v{{ version }}/{{ name }}-{{ version }}.tar.bz2 + sha256: {{ sha256 }} + +requirements: + build: + - cmake + - gcc # [linux] + - llvm # [osx] + - pkg-config + - boost {{ CONDA_BOOST }}* + - zlib {{ CONDA_ZLIB }}* + - bzip2 {{ CONDA_BZIP2 }}* + - jsoncpp + - python + # NOTE disabling unit tests to shave off a few seconds of Travis' runtime + #- cram + run: + - libgcc # [not osx] + - boost {{ CONDA_BOOST }}* + - zlib {{ CONDA_ZLIB }}* + - bzip2 {{ CONDA_BZIP2 }}* +test: + commands: + - {{ name }} -h + +about: + home: https://github.com/cbg-ethz/{{ name }} + license: GPLv3+ + license_family: GPL3 + license_file: LICENSE.md + summary: Viral quasispecies assembly via maximal clique finding. A method to reconstruct viral haplotypes and detect large insertions and deletions from NGS data. diff --git a/recipes/haystack_bio/meta.yaml b/recipes/haystack_bio/meta.yaml index 028b13d6838d0..304fc2c78d84f 100644 --- a/recipes/haystack_bio/meta.yaml +++ b/recipes/haystack_bio/meta.yaml @@ -1,6 +1,5 @@ -{% set version = "0.5.2" %} - -{% set sha256 = "aaac0263689efb9cd0688da351633ba7673de933a3a52c982afad8be692feb1f" %} +{% set version = "0.5.3" %} +{% set sha256 = "e2ccaeb40d588a87eb0f63d783aa285f9784dc3ec486564833dd328ccacdc54f" %} package: name: haystack_bio @@ -12,7 +11,6 @@ source: url: "https://github.com/pinellolab/haystack_bio/archive/{{ version }}.tar.gz" - build: entry_points: - "haystack_pipeline = haystack.run_pipeline:main" @@ -21,7 +19,7 @@ build: - "haystack_tf_activity_plane = haystack.generate_tf_activity_plane:main" - "haystack_download_genome = haystack.download_genome:main" - "haystack_run_test = haystack.haystack_common:run_testdata" - number: 6 + number: 0 about: home: "https://github.com/pinellolab/haystack_bio" diff --git a/recipes/hg-color/build.sh b/recipes/hg-color/build.sh new file mode 100644 index 0000000000000..f28921b3bbd12 --- /dev/null +++ b/recipes/hg-color/build.sh @@ -0,0 +1,23 @@ +#!/bin/bash + +mkdir -p ${PREFIX}/bin + +# get src +wget https://github.com/kowallus/PgSA/archive/0d7c97f22a07fce96e0638deb09d2a8c05ed3d8b.zip +unzip 0d7c97f22a07fce96e0638deb09d2a8c05ed3d8b.zip + +# change path to find lib +sed -i.bak 's|$(PGSA_PATH)dist/pgsalib/GNU-Linux-x86/|${PREFIX}/lib/|' Makefile +sed -i.bak 's|bin/PgSAgen|bin/PgSAgen_hgcolor|' Makefile + +# change path for dependencies +sed -i.bak 's|$hgf/bin/||' HG-CoLoR +sed -i.bak 's|PgSAgen|PgSAgen_hgcolor|' HG-CoLoR +sed -i.bak 's|#!/usr/bin/python|#!/usr/bin/env python|' bin/*.py + +# compilation +make PGSA_PATH=${PWD}/PgSA-0d7c97f22a07fce96e0638deb09d2a8c05ed3d8b/ + +# copy binaries +cp bin/* ${PREFIX}/bin +cp HG-CoLoR ${PREFIX}/bin diff --git a/recipes/hg-color/meta.yaml b/recipes/hg-color/meta.yaml new file mode 100644 index 0000000000000..f8d36dd268cfb --- /dev/null +++ b/recipes/hg-color/meta.yaml @@ -0,0 +1,38 @@ +package: + name: hg-color + version: 1.0.0 + +source: + url: https://github.com/pierre-morisse/HG-CoLoR/archive/073add7bb0ba74f64c954f81338bcb208a2d72c1.zip + fn: 073add7bb0ba74f64c954f81338bcb208a2d72c1.zip + md5: 1d8bda305c799bc2a3e414f8c5463e0b + +build: + number: 2 + skip: True # [osx] + +requirements: + build: + - gcc # [not osx] + - llvm # [osx] + - wget + - unzip + - pgsa + + run: + - libgcc # [not osx] + - parallel + - emboss + - kmc + - quorum + - pgsa + - python >2.6 + +test: + commands: + - '{ HG-CoLoR --help 2>&1 | grep Usage; }' + +about: + home: https://github.com/pierre-morisse/HG-CoLoR + license: GNU General Public License (GPL) + summary: 'HG-CoLoR (Hybrid Graph for the error Correction of Long Reads) is a hybrid method for the error correction of long reads that follows the main idea from NaS to produce corrected long reads from assemblies of related accurate short reads.' diff --git a/recipes/hicexplorer/meta.yaml b/recipes/hicexplorer/meta.yaml index 4eeb6f3de4c5e..04fe8d43a1225 100644 --- a/recipes/hicexplorer/meta.yaml +++ b/recipes/hicexplorer/meta.yaml @@ -1,14 +1,14 @@ package: name: hicexplorer - version: '1.8' + version: '1.8.1' source: - fn: 1.8.tar.gz - url: https://github.com/maxplanck-ie/HiCExplorer/archive/1.8.tar.gz - sha256: 6b35a62bd9c9d433e297af4d288551af19dff0a9d07c2e91978f3c60c97d9bc9 + fn: 1.8.1.tar.gz + url: https://github.com/deeptools/HiCExplorer/archive/1.8.1.tar.gz + sha256: e84e5675dc0ededff728c0823b40e1d162dac9a12b90e645b32f064745da1107 build: - number: 2 + number: 0 skip: True # [not py27] requirements: diff --git a/recipes/hifive/meta.yaml b/recipes/hifive/meta.yaml index 57743e6624fad..6d9c0cab63bbc 100644 --- a/recipes/hifive/meta.yaml +++ b/recipes/hifive/meta.yaml @@ -1,11 +1,15 @@ +{% set name = "hifive" %} +{% set version = "1.5.3" %} +{% set hash = "16b20d5ab12b09ef87a52ae6dd0a83d9b0107b2ece906bfb07a8898841ec552e" %} + package: - name: hifive - version: "1.5.1" + name: {{ name|lower }} + version: {{ version }} source: - fn: hifive-1.5.1.tar.gz - url: https://pypi.python.org/packages/d5/09/2f16e90ac40d67b90d1a2ac77c8354f32790bc6632dba16ca7097c128d0a/hifive-1.5.1.tar.gz - md5: e60d653081c652ca5647938170da3b83 + fn: hifive-{{ version }}.tar.gz + url: https://github.com/bxlab/hifive/archive/v{{ version }}.tar.gz + sha256: {{ hash }} build: skip: True # [not py27] @@ -14,7 +18,6 @@ build: requirements: build: - python - - setuptools - numpy - scipy - h5py @@ -36,7 +39,6 @@ requirements: - mpi4py # [not osx] ## https://github.com/conda/conda/issues/2277 #- mlpy # used for hifive.hic.learn_fend_3D_modol, but conda build currently fails - test: # Python imports imports: @@ -44,19 +46,6 @@ test: - hifive.commands - hifive.libraries - # commands: - # You can put test commands to be run here. Use this to test that the - # entry points work. - - - # You can also put a file called run_test.py in the recipe that will be run - # at test time. - - requires: - - nose - # Put any additional test requirements here. For example - # - nose - about: home: https://github.com/bxlab/hifive license: MIT diff --git a/recipes/intervene/meta.yaml b/recipes/intervene/meta.yaml index 97d930383237e..a6094ebb1916d 100644 --- a/recipes/intervene/meta.yaml +++ b/recipes/intervene/meta.yaml @@ -1,11 +1,11 @@ package: name: intervene - version: "0.5.8" + version: "0.5.9" source: - fn: intervene-0.5.8.tar.gz - url: https://pypi.python.org/packages/a8/68/3d52c21b3cce52d22207973471fed7c113cfc4fbcaa49718620de14957a3/intervene-0.5.8.tar.gz - md5: 31c74e6da434d6df38743072e24c6cac + fn: intervene-0.5.9.tar.gz + url: https://pypi.python.org/packages/b2/a6/a1573e0df442d944ae0d242e6ac0a2b68b309724d9362557644174079c0a/intervene-0.5.9.tar.gz + md5: a54c88fb59295ef03f4dfdf19df8d8ce build: number: 0 diff --git a/recipes/ipython-cluster-helper/meta.yaml b/recipes/ipython-cluster-helper/meta.yaml index c8cb02309fd60..4e5ffa274c608 100644 --- a/recipes/ipython-cluster-helper/meta.yaml +++ b/recipes/ipython-cluster-helper/meta.yaml @@ -1,12 +1,14 @@ -{% set version="0.5.9" %} +{% set version="0.6.0" %} package: name: ipython-cluster-helper version: {{ version }} source: fn: ipython-cluster-helper-{{ version }}.tar.gz - url: https://pypi.io/packages/source/i/ipython-cluster-helper/ipython-cluster-helper-{{ version }}.tar.gz - md5: 234227ee9262c5dcb43134c5ef4de9c2 + # work around issue with no profile directory in 0.6.0 release with fix + url: https://github.com/roryk/ipython-cluster-helper/archive/f0a86ff.tar.gz + #url: https://pypi.io/packages/source/i/ipython-cluster-helper/ipython-cluster-helper-{{ version }}.tar.gz + md5: 14cfcb714922db29894591073d1c6002 build: number: 0 diff --git a/recipes/joblib/meta.yaml b/recipes/joblib/meta.yaml deleted file mode 100644 index 37f8b871789fb..0000000000000 --- a/recipes/joblib/meta.yaml +++ /dev/null @@ -1,29 +0,0 @@ -package: - name: joblib - version: '0.9.3' - -source: - fn: joblib-0.9.3.tar.gz - url: https://pypi.python.org/packages/source/j/joblib/joblib-0.9.3.tar.gz - md5: b90652daf3f5458e1d65b9b9d0f74756 - -build: - number: 0 - skip: False - -requirements: - build: - - python - - setuptools - - run: - - python - -test: - imports: - - joblib - -about: - home: http://packages.python.org/joblib/ - license: BSD License - summary: 'Lightweight pipelining: using Python functions as pipeline jobs.' diff --git a/recipes/linkage2allegro/build.sh b/recipes/linkage2allegro/build.sh new file mode 100644 index 0000000000000..8e25a1455f914 --- /dev/null +++ b/recipes/linkage2allegro/build.sh @@ -0,0 +1,3 @@ +#!/bin/bash + +$PYTHON setup.py install diff --git a/recipes/linkage2allegro/meta.yaml b/recipes/linkage2allegro/meta.yaml new file mode 100644 index 0000000000000..75cd802ab5459 --- /dev/null +++ b/recipes/linkage2allegro/meta.yaml @@ -0,0 +1,30 @@ +{% set name = "linkage2allegro" %} +{% set version = "2017.3" %} + +package: + name: {{ name }} + version: {{ version }} + +source: + fn: {{ name }}-{{ version }}.tar.gz + url: https://github.com/BioTools-Tek/linkage-converter/archive/cc6790a9169b10dd58ba52dddc12be9a34a1a2d7.tar.gz + sha256: 61033d93872a7f7f7b7e4af8f7f24a3fb973c73db3775ba2e9e101de4893f4c2 + +build: + number: 0 + +requirements: + build: + - python + + run: + - python + +test: + commands: + - {{ name }} 2>&1 | grep descentfile + +about: + home: https://github.com/BioTools-Tek/linkage-converter + license: GPL3 + summary: Converts between the output linkage formats of Merlin, Simwalk, Genehunter, and Swiftlink into Allegro. diff --git a/recipes/ls-gkm/build.sh b/recipes/ls-gkm/build.sh new file mode 100644 index 0000000000000..5024208f78f11 --- /dev/null +++ b/recipes/ls-gkm/build.sh @@ -0,0 +1,8 @@ +#!/bin/bash + +cd src +make +make install + +mv ../bin/gkmtrain $PREFIX/bin +mv ../bin/gkmpredict $PREFIX/bin diff --git a/recipes/ls-gkm/meta.yaml b/recipes/ls-gkm/meta.yaml new file mode 100644 index 0000000000000..e8d0f49a1c959 --- /dev/null +++ b/recipes/ls-gkm/meta.yaml @@ -0,0 +1,32 @@ +{% set version = "0.0.1" %} + +package: + name: ls-gkm + version: {{ version }} + +source: + fn: ls-gkm{{ version }}.zip + url: https://github.com/Dongwon-Lee/lsgkm/archive/164a4a48f6387e67b5d955db932f8a403de6c321.zip + sha256: 029faf96bdc98e441132801d6e1cce032ec2f718972e214aaca40ad756c83f3e + +build: + number: 0 + +requirements: + build: + - gcc # [not osx] + - llvm # [osx] + + run: + - libgcc # [not osx] + +test: + commands: + - gkmtrain + - gkmpredict + +about: + home: https://github.com/Dongwon-Lee/lsgkm + license: GPL3 + license_file: LICENSE + summary: gkm-SVM, a sequence-based method for predicting regulatory DNA elements, is a useful tool for studying gene regulatory mechanisms. In continuous efforts to improve the method, new software, LS-GKM, is introduced. It offers much better scalability and provides further advanced gapped k-mer based kernel functions. As a result, LS-GKM achieves considerably higher accuracy than the original gkm-SVM. diff --git a/recipes/mappy/meta.yaml b/recipes/mappy/meta.yaml index 057ddea186870..2580e9948c3dc 100644 --- a/recipes/mappy/meta.yaml +++ b/recipes/mappy/meta.yaml @@ -1,4 +1,4 @@ -{% set version = "2.5" %} +{% set version = "2.6" %} package: name: mappy @@ -7,7 +7,7 @@ package: source: fn: mappy-{{ version }}.tar.gz url: https://pypi.io/packages/source/m/mappy/mappy-{{ version }}.tar.gz - sha256: a2615232af1ac9d59192bc04efabc8962158a3aebe18dd83e4c15ffc377e4442 + sha256: c4c49eec4b1b6e0c676e1e68a534d893f413fc04f473f38d286c1c357650f508 build: number: 0 diff --git a/recipes/meme/4.11.1/build.sh b/recipes/meme/4.11.1/build.sh new file mode 100644 index 0000000000000..9082fe8806353 --- /dev/null +++ b/recipes/meme/4.11.1/build.sh @@ -0,0 +1,15 @@ +#!/bin/bash + +MEME_ETC_DIR=${PREFIX}/etc +cpanm YAML +cpanm HTML::PullParser +cpanm XML::Simple +cpanm CGI +cpanm HTML::Template +cpanm HTML::Parse +cpanm CGI::Application +cpanm XML::Parser::Expat --configure-args "EXPATLIBPATH=$PREFIX/lib" --configure-args "EXPATHINCPATH=$PREFIX/include" +./configure --prefix="$PREFIX" --with-gnu-ld # --enable-build-libxml2 --enable-build-libxslt +make clean +make AM_CFLAGS='-DNAN="(0.0/0.0)"' +make install diff --git a/recipes/meme/4.11.1/mast.patch b/recipes/meme/4.11.1/mast.patch new file mode 100644 index 0000000000000..f8c6f9ad4b776 --- /dev/null +++ b/recipes/meme/4.11.1/mast.patch @@ -0,0 +1,10 @@ +--- src/mast.h ++++ src/mast.h +@@ -20,6 +20,7 @@ + #include "banner.h" + #include "pssm-distr.h" + #include ++#include + #include + + /* diff --git a/recipes/meme/4.11.1/meta.yaml b/recipes/meme/4.11.1/meta.yaml new file mode 100644 index 0000000000000..261095b40b2e1 --- /dev/null +++ b/recipes/meme/4.11.1/meta.yaml @@ -0,0 +1,52 @@ +source: + fn: meme_4.11.1.tar.gz + url: http://alternate.meme-suite.org/meme-software/4.11.1/meme_4.11.1.tar.gz + md5: 8d04213c4feddf31d4f620060fdc6b97 + patches: + - mast.patch + +package: + name: meme + version: 4.11.1 + +build: + number: 2 + skip: True # [osx or py3k] + detect_binary_files_with_prefix: True + +requirements: + build: + - gcc + - yaml + - python + - perl + - ghostscript #[linux] + - zlib {{CONDA_ZLIB}}* + - libxslt + - libxml2 + - expat + - perl-xml-parser #[linux] + - perl-app-cpanminus + run: + - libgcc + - yaml + - expat + - python + - perl + - zlib {{CONDA_ZLIB}}* + - libxslt + - libxml2 + - ghostscript #[linux] + - perl-xml-parser #[linux] + +test: + commands: + - "meme -h 2>&1 | grep fraction > /dev/null" + - "meme-chip 2>&1 | grep FIMO > /dev/null" + - "centrimo 2>&1 | grep maxreg > /dev/null" + +about: + home: http://alternate.meme-suite.org + license: Custom + license_file: COPYING + summary: Motif based sequence Analysis tools diff --git a/recipes/mentalist/meta.yaml b/recipes/mentalist/meta.yaml index 8f14d79f29738..722d4b36bc28c 100644 --- a/recipes/mentalist/meta.yaml +++ b/recipes/mentalist/meta.yaml @@ -1,5 +1,5 @@ {% set name = "MentaLiST" %} -{% set version = "0.1.3" %} +{% set version = "0.2.0" %} package: name: {{ name|lower }} @@ -8,7 +8,7 @@ package: source: fn: {{ name|lower }}-{{ version }}.tar.gz url: https://github.com/WGS-TB/MentaLiST/archive/v{{ version }}.tar.gz - sha256: 57874e2168b48c165fc68c2bab41819259ec828e298bc54cbc3da8f3c904c63e + sha256: f425e9e3e3bd9fa5177a346178ceee9e8e44936624227756b5ea2bb61d5dfcb4 build: number: 0 diff --git a/recipes/mercat/meta.yaml b/recipes/mercat/meta.yaml index 01fa46ed8ef12..406022e3f966e 100644 --- a/recipes/mercat/meta.yaml +++ b/recipes/mercat/meta.yaml @@ -14,7 +14,7 @@ source: build: number: 0 - script: python setup.py install + script: python setup.py install --single-version-externally-managed --record=record.txt preserve_egg_dir: yes @@ -42,7 +42,7 @@ test: - mercat --help about: - home: + home: https://github.com/pnnl/mercat license: BSD summary: 'Mercat: a versatile counter and diversity estimator for data base independent property analysis obtained from whole community sequencing data.' license_family: BSD diff --git a/recipes/mgs-canopy/build.sh b/recipes/mgs-canopy/build.sh index 02a26ea579a60..9329dfa7a4bbc 100644 --- a/recipes/mgs-canopy/build.sh +++ b/recipes/mgs-canopy/build.sh @@ -4,7 +4,7 @@ cd src/ echo "> Compiling sources" for F in $(find . -name "*.cpp") ; do FF=${F%.*} - g++ -o $FF.o -fopenmp -c -Wall -Wextra -O3 -march=native -I./ -I${PREFIX}/include -L${PREFIX}/lib $FF.cpp + g++ -o $FF.o -fopenmp -c -Wall -Wextra -O3 -march=x86-64 -I./ -I${PREFIX}/include -L${PREFIX}/lib $FF.cpp done; echo "> Building target: cc.bin" diff --git a/recipes/mgs-canopy/meta.yaml b/recipes/mgs-canopy/meta.yaml index e4df5176adaee..198178be4ec87 100644 --- a/recipes/mgs-canopy/meta.yaml +++ b/recipes/mgs-canopy/meta.yaml @@ -13,7 +13,7 @@ source: md5: {{ md5 }} build: - number: 0 + number: 1 skip: True # [osx] requirements: @@ -28,8 +28,8 @@ requirements: test: commands: - - command -v cc.bin - - command -v canopy + - cc.bin --help | grep "Allowed options" + - canopy --help | grep "Allowed options" about: home: "https://github.com/fplaza/mgs-canopy-algorithm" diff --git a/recipes/minimap2/meta.yaml b/recipes/minimap2/meta.yaml index 461f1abe640e7..3f7d8c10e516a 100644 --- a/recipes/minimap2/meta.yaml +++ b/recipes/minimap2/meta.yaml @@ -1,6 +1,6 @@ {% set name = "minimap2" %} -{% set version = "2.5" %} -{% set hash = "e1a837c6b28850735c8eae684d167f0814e749266c49d696be5d1ccb8c7632bb" %} +{% set version = "2.6" %} +{% set hash = "efa1ea61f3d6dd4220babdf2c3cfe4cd7eff6011e74e034a039abc7d6972e9ba" %} package: name: {{ name|lower }} diff --git a/recipes/minvar/build.sh b/recipes/minvar/build.sh index 5a5aeeb48b45e..a6609066d90c9 100644 --- a/recipes/minvar/build.sh +++ b/recipes/minvar/build.sh @@ -1 +1 @@ -$PYTHON setup.py install +$PYTHON setup.py install --single-version-externally-managed --record=record.txt diff --git a/recipes/minvar/meta.yaml b/recipes/minvar/meta.yaml index a0555f5dd4a69..17c77e5312374 100644 --- a/recipes/minvar/meta.yaml +++ b/recipes/minvar/meta.yaml @@ -1,19 +1,21 @@ package: name: minvar - version: "1.2b" + version: "2.0" build: - number: 0 + number: 1 # minvar written for python 3.x only, so skip py27 # setuptool_scm_git_archive not available in py36 skip: True # [py27 or py36] source: - url: https://github.com/ozagordi/MinVar/archive/v1.2b.tar.gz - md5: 3cfd62be162fe5cec5549afb4038ac40 + url: https://github.com/ozagordi/MinVar/archive/v2.0.tar.gz + md5: 06f8fde34050ef9228722594939b22b5 requirements: build: + - isort + - pytest-runner - python - setuptools - setuptools_scm @@ -36,7 +38,7 @@ requirements: about: home: https://git.io/minvar - summary: 'A tool to detect minority variants in HIV-1 populations' + summary: 'A tool to detect minority variants in HIV-1 and HCV populations' license: Custom test: diff --git a/recipes/mockinbird/meta.yaml b/recipes/mockinbird/meta.yaml new file mode 100644 index 0000000000000..6075bc09338c1 --- /dev/null +++ b/recipes/mockinbird/meta.yaml @@ -0,0 +1,60 @@ +{% set version="1.0.0a1" %} +{% set sha256="d006e623f3b962b3a0d06dceab24275fa47468d8dbd690f8dfca5ff8db09b238" %} + +package: + name: mockinbird + version: {{ version }} + +source: + url: https://github.com/soedinglab/mockinbird/archive/{{ version }}.tar.gz + sha256: {{ sha256 }} + +build: + script: python setup.py install --single-version-externally-managed --record record.txt + number: 0 + skip: True # [not py3k] + +requirements: + build: + - python + - cython + - gcc # [not osx] + - llvm # [osx] + + run: + - libgcc # [not osx] + - python + - numpy + - scipy + - pandas + - matplotlib + - seaborn + - pysam + - star + - bowtie + - samtools + - fastqc + - xxmotif + - r-base + - r-lsd + - pyyaml + - jinja2 + +test: + imports: + - mockinbird + - mockinbird.ivtree + - mockinbird.scripts + - mockinbird.plots + - mockinbird.obj + - mockinbird.scripts + - mockinbird.utils + +about: + home: https://github.com/soedinglab/mockinbird + license: GPL-3 + license_family: GPL3 + license_file: LICENSE.txt + summary: A fully automatic and reproducible PAR-CLIP analysis pipeline + doc_url: http://wwwuser.gwdg.de/~compbiol/mockinbird/doc/ + dev_url: https://github.com/soedinglab/mockinbird diff --git a/recipes/moff/meta.yaml b/recipes/moff/meta.yaml index c741b85331f3f..31287e16aa2fc 100644 --- a/recipes/moff/meta.yaml +++ b/recipes/moff/meta.yaml @@ -1,12 +1,13 @@ +{% set version = "1.2" %} + package: name: moff - version: 1.1 + version: {{ version }} source: - fn: v1.1.tar.gz - url: https://github.com/compomics/moFF/archive/v1.1.tar.gz - md5: 55a7635d7b0bcff63833e0ed6ab0f4a2 - + url: https://github.com/compomics/moFF/archive/v{{ version }}.tar.gz + md5: cc3e0a2e3b3da524f304c275cca74000 + build: number: 0 skip: True # [not py27] @@ -19,6 +20,8 @@ requirements: - argparse >1.2.1 - scikit-learn >0.18 - pymzml >0.7.7 + - mono + - simplejson run: - python @@ -27,6 +30,8 @@ requirements: - argparse >1.2.1 - scikit-learn >0.18 - pymzml >0.7.7 + - mono + - simplejson test: commands: diff --git a/recipes/mykatlas/build.sh b/recipes/mykatlas/build.sh new file mode 100644 index 0000000000000..ce604a78e0c95 --- /dev/null +++ b/recipes/mykatlas/build.sh @@ -0,0 +1,4 @@ +#!/bin/bash + + +$PYTHON setup.py install --single-version-externally-managed --record=record.txt diff --git a/recipes/mykatlas/mccortex-skip_make-copy_PREFIX.patch b/recipes/mykatlas/mccortex-skip_make-copy_PREFIX.patch new file mode 100644 index 0000000000000..fdfb96c860170 --- /dev/null +++ b/recipes/mykatlas/mccortex-skip_make-copy_PREFIX.patch @@ -0,0 +1,20 @@ +--- setup.py.orig 2017-11-29 23:08:50.331161360 +0100 ++++ setup.py 2017-11-29 23:11:03.449353941 +0100 +@@ -10,14 +10,10 @@ + + def run(self): + mccortex_dir = os.path.dirname(os.path.realpath(__file__))+"/mccortex" +- subprocess.call( +- ["make", "clean"], cwd=mccortex_dir) +- subprocess.call( +- ["make"], cwd=mccortex_dir) + print("Moving mccortex from %s to %s" % +- (mccortex_dir, os.environ.get('VIRTUAL_ENV', '/usr/local/'))) +- subprocess.call( +- ["cp", "bin/mccortex31", "%s/bin/" % os.environ.get('VIRTUAL_ENV', '/usr/local/')], cwd=mccortex_dir) ++ (mccortex_dir, os.environ['PREFIX'])) ++ subprocess.check_call( ++ ["cp", "bin/mccortex31", "%s/bin/" % os.environ['PREFIX']], cwd=mccortex_dir) + DistutilsInstall.run(self) + + setup( diff --git a/recipes/mykatlas/meta.yaml b/recipes/mykatlas/meta.yaml new file mode 100644 index 0000000000000..cdfcc18e05058 --- /dev/null +++ b/recipes/mykatlas/meta.yaml @@ -0,0 +1,50 @@ +package: + name: mykatlas + version: "0.6.1" + +source: + fn: mykatlas-0.6.1.tar.gz + url: https://pypi.python.org/packages/bf/33/946e43324bc24ba331a1bee06e609832bfbe7a4f07dde1846246fb5a68cf/mykatlas-0.6.1.tar.gz + md5: 87d59770ceeb5406a0146c3c51d93ea9 + patches: + - mccortex-skip_make-copy_PREFIX.patch + - min_variant_conf.patch + +build: + # includes precompiled Linux binary `mccortex31` + skip: True # [osx] + number: 1 + entry_points: + - atlas = mykatlas.atlas_main:main + +requirements: + build: + - python + - setuptools + - future + - biopython + - mongoengine + - pyvcf + - ga4ghmongo + + run: + - python + - future + - biopython + - mongoengine + - pyvcf + - ga4ghmongo + - redis-py + +test: + imports: + - mykatlas + commands: + - atlas --help + - 'mccortex31 2>&1 | head -n2 | grep "^usage: "' + +about: + home: http://github.com/phelimb/atlas + license: MIT + summary: 'Assists in discoveries of antibiotic-resistance with mykrobe' + license_family: MIT diff --git a/recipes/mykatlas/min_variant_conf.patch b/recipes/mykatlas/min_variant_conf.patch new file mode 100644 index 0000000000000..8fd06844ab46b --- /dev/null +++ b/recipes/mykatlas/min_variant_conf.patch @@ -0,0 +1,19 @@ +commit 98c6545e4d2021069e431815a78c302dc0a342fd +Author: Phelim Bradley +Date: Thu Mar 9 02:51:07 2017 +0000 + + min conf 100 + +diff --git a/mykatlas/base.py b/mykatlas/base.py +index 8578213..a397ab8 100644 +--- a/mykatlas/base.py ++++ b/mykatlas/base.py +@@ -140,7 +140,7 @@ genotyping_mixin.add_argument( + genotyping_mixin.add_argument( + "--min_variant_conf", + help="minimum genotype confidence for variant genotyping", +- default=None, type=int) ++ default=100, type=int) + genotyping_mixin.add_argument( + "--min_gene_conf", + help="minimum genotype confidence for gene genotyping", diff --git a/recipes/mykrobe/build.sh b/recipes/mykrobe/build.sh new file mode 100644 index 0000000000000..3786386a73c83 --- /dev/null +++ b/recipes/mykrobe/build.sh @@ -0,0 +1,3 @@ +#!/bin/bash + +$PYTHON setup.py install --single-version-externally-managed --record=record.txt diff --git a/recipes/mykrobe/meta.yaml b/recipes/mykrobe/meta.yaml new file mode 100644 index 0000000000000..972597a9dbd37 --- /dev/null +++ b/recipes/mykrobe/meta.yaml @@ -0,0 +1,41 @@ +package: + name: mykrobe + version: "0.5.6" + +source: + fn: mykrobe-0.5.6.tar.gz + url: https://github.com/iqbal-lab/Mykrobe-predictor/archive/933301d9f1e673a2a282255426a885ef72e67c07.tar.gz + sha256: adcf75a8e873192047921947ef6c367fadee9dff09637f0acad7a4c9c4bcf53e + +build: + # dependency mykatlas currently not built for osx + skip: True # [osx] + number: 0 + entry_points: + - mykrobe = mykrobe.mykrobe_predictor:main + +requirements: + build: + - python + - setuptools + + + run: + - python + - mykatlas + - ga4ghmongo + - mongoengine + - future +test: + # Python imports + imports: + - mykrobe + commands: + - mykrobe --help + + +about: + home: https://github.com/iqbal-lab/Mykrobe-predictor + license: Custom non-commercial license + license_file: LICENSE + summary: 'Rapid antibiotic-resistance predictions from genome sequence data for Staphylococcus aureus and Mycobacterium tuberculosis.' diff --git a/recipes/nanopolish/build.sh b/recipes/nanopolish/build.sh index 7f82b1b28f10b..9a413ebfe12a6 100755 --- a/recipes/nanopolish/build.sh +++ b/recipes/nanopolish/build.sh @@ -9,7 +9,7 @@ export FAST5_INCLUDE=-I${PREFIX}/include/fast5 mkdir -p $PREFIX/bin -make HDF5= EIGEN= +make HDF5= EIGEN= FAST5= cp nanopolish $PREFIX/bin cp scripts/nanopolish_makerange.py $PREFIX/bin cp scripts/nanopolish_merge.py $PREFIX/bin diff --git a/recipes/nanopolish/meta.yaml b/recipes/nanopolish/meta.yaml index e89402cbfcaeb..4da2b281a562f 100644 --- a/recipes/nanopolish/meta.yaml +++ b/recipes/nanopolish/meta.yaml @@ -1,5 +1,5 @@ {% set name = "nanopolish" %} -{% set version = "0.8.1" %} +{% set version = "0.8.5" %} package: name: {{ name|lower }} @@ -12,23 +12,23 @@ build: source: fn: {{ name|lower }}_{{ version }}.tar.gz url: https://github.com/jts/nanopolish/archive/v{{ version }}.tar.gz - md5: 932b3953761d64e40e186280d74613b0 + md5: 0a4db39659bce9117fc6167c4df0c88f patches: - nanopolish.patch requirements: build: - gcc - - fast5 ==0.6.2.p1 - - htslib <1.3 - - hdf5 1.8.18|1.8.18.* + - fast5 ==0.6.4 + - htslib >1.4 + - hdf5 {{ CONDA_HDF5 }}* - eigen - ncurses {{CONDA_NCURSES}}* run: - libgcc - python - - hdf5 1.8.18|1.8.18.* + - hdf5 {{ CONDA_HDF5 }}* - biopython - bwa - eigen diff --git a/recipes/nanopolish/nanopolish.patch b/recipes/nanopolish/nanopolish.patch index 3e2c7de259208..bbeed52821c21 100644 --- a/recipes/nanopolish/nanopolish.patch +++ b/recipes/nanopolish/nanopolish.patch @@ -1,17 +1,33 @@ ---- Makefile 2017-07-01 15:51:35.000000000 +0200 -+++ Makefile 2017-07-01 15:53:16.000000000 +0200 -@@ -46,11 +46,8 @@ +--- Makefile 2017-12-11 14:51:11.000000000 +0000 ++++ Makefile 2017-12-14 12:16:14.000000000 +0000 +@@ -8,7 +8,7 @@ + # + + #Basic flags every build needs +-LIBS=-lz ++LIBS=-lcrypto -lz -llzma -lbz2 -lcurl + CXXFLAGS ?= -g -O3 + CXXFLAGS += -std=c++11 -fopenmp -fsigned-char + CFLAGS ?= -O3 -std=c99 +@@ -46,18 +46,6 @@ + EIGEN_CHECK= endif - - # Build and link the libhts submodule --HTS_LIB=./htslib/libhts.a --HTS_INCLUDE=-I./htslib - - # Include the header-only fast5 library --FAST5_INCLUDE=-I./fast5/src - - # Include the src subdirectories - NP_INCLUDE=$(addprefix -I./, $(SUBDIRS)) + +-# Default to build and link the libhts submodule +-ifeq ($(HTS), install) +- HTS_LIB=./htslib/libhts.a +- HTS_INCLUDE=-I./htslib +-else +- # Use system-wide htslib +- HTS_LIB=-lhts +-endif +- +-# Include the header-only fast5 library +-FAST5_INCLUDE=-I./fast5/include +- + # Include the header-only eigen library + EIGEN_INCLUDE=-I./eigen/ + --- src/nanopolish_methyltrain.cpp 2017-07-01 15:55:34.000000000 +0200 +++ src/nanopolish_methyltrain.cpp 2017-07-01 15:54:06.000000000 +0200 @@ -42,7 +42,7 @@ diff --git a/recipes/nanopore_simulation/build.sh b/recipes/nanopore_simulation/build.sh new file mode 100644 index 0000000000000..3786386a73c83 --- /dev/null +++ b/recipes/nanopore_simulation/build.sh @@ -0,0 +1,3 @@ +#!/bin/bash + +$PYTHON setup.py install --single-version-externally-managed --record=record.txt diff --git a/recipes/nanopore_simulation/meta.yaml b/recipes/nanopore_simulation/meta.yaml new file mode 100644 index 0000000000000..16ebd831126d6 --- /dev/null +++ b/recipes/nanopore_simulation/meta.yaml @@ -0,0 +1,41 @@ +{% set version = "0.3" %} + +package: + name: nanopore_simulation + version: {{ version }} + +source: + fn: nanopore_simulation_{{ version }}.tar.gz + url: https://github.com/crohrandt/nanopore_simulation/archive/a748cd1ddbaf2856b183ed873c40415ad069d943.tar.gz + sha256: 4e42d56a9e3d5a1209eba264379831f064a9c705920963516859f8b68af81fce + +build: + number: 0 + skip: True # [py27] + +requirements: + build: + - python + - setuptools + - biopython + - pandas + - h5py + - scipy + - matplotlib + - numpy + run: + - python + - biopython + - pandas + - h5py + - scipy + - matplotlib + - numpy +test: + commands: + - simulatION --help + +about: + home: https://github.com/crohrandt/nanopore_simulation + license: MPL-2.0 + summary: Nanopore SimulatION is a tool for simulating an Oxfornd Nanopore Technologies MinION device for bioinformatic development. diff --git a/recipes/nest/2.12.0/build.sh b/recipes/nest/2.12.0/build.sh new file mode 100644 index 0000000000000..580ddd14b0961 --- /dev/null +++ b/recipes/nest/2.12.0/build.sh @@ -0,0 +1,23 @@ +#!/bin/sh + +export MPI_FLAGS=--allow-run-as-root + +if [ $(uname) == Linux ]; then + export MPI_FLAGS="$MPI_FLAGS;-mca;plm;isolated" +fi + +export CFLAGS="-I$PREFIX/include" +export LDFLAGS="-L$PREFIX/lib" + +mkdir build +cd build +cmake -DCMAKE_INSTALL_PREFIX:PATH=$PREFIX \ + -Dwith-mpi=ON \ + -Dwith-openmp=ON \ + -Dwith-python=ON \ + .. + +make -j2 +make install +# this is needed to make the python bindings work +cp $PREFIX/lib64/* $PREFIX/lib -r diff --git a/recipes/nest/2.12.0/meta.yaml b/recipes/nest/2.12.0/meta.yaml new file mode 100644 index 0000000000000..70eeee39d0b53 --- /dev/null +++ b/recipes/nest/2.12.0/meta.yaml @@ -0,0 +1,58 @@ +{% set version = "2.12.0" %} +package: + name: nest + version: {{ version }} + +source: + url: https://github.com/nest/nest-simulator/releases/download/v{{ version }}/nest-{{ version }}.tar.gz + sha256: bac578f38bb0621618ee9d5f2f1febfee60cddc000ff32e51a5f5470bb3df40d + +build: + number: 0 + skip: true # [osx] + +requirements: + build: + - cmake >=3.6 + - cython + - gcc + - gsl {{ CONDA_GSL }}* + - libtool + - mkl + - ncurses {{ CONDA_NCURSES }}* + - numpy + - openmpi >=2.1,<3 + - python + - readline 6.2* + - scipy + run: + - cython + - gsl {{ CONDA_GSL }}* + - ipython + - libgcc + - libtool + - matplotlib + - mkl + - ncurses {{ CONDA_NCURSES }}* + - numpy + - openmpi >=2.1,<3 + - python + - readline 6.2* + - scipy + +test: + imports: + - nest + commands: + - nest --help + - sli --help + +about: + home: http://www.nest-simulator.org/ + license: GPL + summary: "NEST is a simulator for spiking neural network models." + +extra: + container: + # openmpi needs ssh/rsh + extended-base: true diff --git a/recipes/nest/meta.yaml b/recipes/nest/meta.yaml index ea323311046fd..1762bbdd373a1 100644 --- a/recipes/nest/meta.yaml +++ b/recipes/nest/meta.yaml @@ -8,7 +8,7 @@ source: sha256: d6316d6c9153100a3220488abfa738958c4b65bf2622bd15540e4aa81e79f17f build: - number: 0 + number: 1 skip: true # [osx] requirements: @@ -21,7 +21,7 @@ requirements: - mkl - ncurses {{ CONDA_NCURSES }}* - numpy - - openmpi >=2.1 + - openmpi >=2.1,<3 - python - readline 6.2* - scipy @@ -35,7 +35,7 @@ requirements: - mkl - ncurses {{ CONDA_NCURSES }}* - numpy - - openmpi >=2.1 + - openmpi >=2.1,<3 - python - readline 6.2* - scipy diff --git a/recipes/ngless/meta.yaml b/recipes/ngless/meta.yaml index 0803d316150f2..1c93f2065b1d1 100644 --- a/recipes/ngless/meta.yaml +++ b/recipes/ngless/meta.yaml @@ -1,6 +1,6 @@ {% set name = "ngless" %} -{% set version = "0.5.1" %} -{% set md5 = "8d1dbf3c10f38b29c815091d3d92f729" %} +{% set version = "0.6.1" %} +{% set md5 = "9e7657eee1af7da092255c43873c19da" %} package: name: {{ name }} @@ -37,6 +37,7 @@ requirements: test: commands: - ngless --version + - ngless --check-install about: home: http://ngless.embl.de diff --git a/recipes/ococo/build.sh b/recipes/ococo/build.sh index 1325b27699c15..e53a7fbed0446 100644 --- a/recipes/ococo/build.sh +++ b/recipes/ococo/build.sh @@ -9,24 +9,6 @@ export C_INCLUDE_PATH=$C_INCLUDE_PATH:${PREFIX}/include export CPLUS_INCLUDE_PATH=$CPLUS_INCLUDE_PATH:${PREFIX}/include export LIBRARY_PATH=$LIBRARY_PATH:${PREFIX}/lib -( - cd ext - rm -fr htslib - git clone git://github.com/samtools/htslib - cd htslib && git checkout tags/1.3.2 -) - -#echo "g++" -#g++ -v || true -#echo "c++" -#c++ -v || true -#echo "CXX" -#$CXX -v || true - make VERBOSE=1 mkdir -p ${PREFIX}/bin cp ococo ${PREFIX}/bin -if [ -e ${PREFIX}/share/man/man1 ]; then - cp ococo.1 ${PREFIX}/share/man/man1 -fi - diff --git a/recipes/ococo/meta.yaml b/recipes/ococo/meta.yaml index 8c28da470a476..edf369769115d 100644 --- a/recipes/ococo/meta.yaml +++ b/recipes/ococo/meta.yaml @@ -1,24 +1,26 @@ +{% set version = "0.1.2.6" %} +{% set sha256 = "f563b0ba90d47efb476b59bed144a306bc2c0c4fbc062ab3a3b87564bfdf22e6" %} + package: name: ococo - version: "0.1.2.4" + version: {{ version }} build: - number: 1 + number: 0 source: - fn: 0.1.2.4.tar.gz - url: https://github.com/karel-brinda/ococo/archive/0.1.2.4.tar.gz - md5: e0e5bd2daf71c89820bad2e745b6def6 + fn: ococo-{{ version }}.tar.gz + url: https://github.com/karel-brinda/ococo/archive/{{ version }}.tar.gz + sha256: {{ sha256 }} requirements: build: - gcc # [not osx] - llvm # [osx] - - zlib ==1.2.8 - - libgcc # [not osx] + - zlib {{ CONDA_ZLIB }}* run: - - zlib ==1.2.8 + - zlib {{ CONDA_ZLIB }}* - libgcc # [not osx] test: diff --git a/recipes/joblib/build.sh b/recipes/ont-tombo/build.sh similarity index 70% rename from recipes/joblib/build.sh rename to recipes/ont-tombo/build.sh index 4d7fc032b8cbe..4899c226c8dd0 100644 --- a/recipes/joblib/build.sh +++ b/recipes/ont-tombo/build.sh @@ -1,6 +1,6 @@ #!/bin/bash -$PYTHON setup.py install +$PYTHON setup.py install --single-version-externally-managed --record=record.txt # Add more build steps here, if they are necessary. diff --git a/recipes/ont-tombo/meta.yaml b/recipes/ont-tombo/meta.yaml new file mode 100644 index 0000000000000..5dfdd2a9c2249 --- /dev/null +++ b/recipes/ont-tombo/meta.yaml @@ -0,0 +1,63 @@ +{% set name = "ont-tombo" %} +{% set version = "1.1" %} +{% set hash = "498ab9a4daf54c853b11b2c49ea66c6cbfe9feb161679908b3052c6014eb4f7b" %} + +package: + name: {{ name|lower }} + version: {{ version }} + +source: + fn: {{ name|lower }}_{{ version }}.tar.gz + url: https://github.com/nanoporetech/tombo/archive/{{ version }}.tar.gz + sha256: {{ hash }} + +build: + entry_points: + - tombo = tombo.__main__:main + number: 0 + skip: True # [not py27] + +requirements: + build: + - python + - setuptools + - h5py + - rpy2 >=2.4.2 + - numpy + - scipy + - cython + - r-base + - r-ggplot2 + - r-cowplot + - hdf5 + - graphmap + - bwa + - minimap2 + + run: + - python + - h5py + - rpy2 >=2.4.2 + - numpy + - scipy + - cython + - r-base + - r-ggplot2 + - r-cowplot + - hdf5 + - graphmap + - bwa + - minimap2 + +test: + imports: + - tombo + + commands: + - tombo --help + +about: + home: https://github.com/nanoporetech/tombo + license: mpl-2.0 + license_file: LICENSE.md + summary: 'Detection of modified bases from raw nanopore sequenceing data.' diff --git a/recipes/panX/build.sh b/recipes/panX/build.sh new file mode 100644 index 0000000000000..8fdfbaad81881 --- /dev/null +++ b/recipes/panX/build.sh @@ -0,0 +1,5 @@ +#!/bin/bash +mkdir -p $PREFIX/bin/scripts +cp panX.py $PREFIX/bin/ +cp scripts/* $PREFIX/bin/scripts +ls $PREFIX/bin/ diff --git a/recipes/panX/meta.yaml b/recipes/panX/meta.yaml new file mode 100644 index 0000000000000..1459759a086b2 --- /dev/null +++ b/recipes/panX/meta.yaml @@ -0,0 +1,43 @@ +{% set name = "panx" %} +{% set version = "1.5.0" %} +{% set sha256 = "bee31ba367ba61f152558538605ccd1aa6f56150c3a102d9877126b2787e72b1" %} + +package: + name: {{ name }} + version: {{ version }} + +source: + fn: v{{ version }}.tar.gz + url: https://github.com/neherlab/pan-genome-analysis/archive/v{{ version }}.tar.gz + sha256: {{ sha256 }} + patches: + - panx_sf_gain_loss.patch + +build: + number: 0 + skip: True # [not py27] + +requirements: + build: + run: + - python + - biopython + - numpy + - scipy + - pandas + - ete2 + - diamond + - fasttree + - mafft + - mcl + - raxml + - treetime + +test: + commands: + - panX.py -h + +about: + home: http://pangenome.de + license: GNU General Public License v3.0 + summary: Microbial pan-genome analysis and exploration tool diff --git a/recipes/panX/panx_sf_gain_loss.patch b/recipes/panX/panx_sf_gain_loss.patch new file mode 100644 index 0000000000000..030e6af2f0871 --- /dev/null +++ b/recipes/panX/panx_sf_gain_loss.patch @@ -0,0 +1,17 @@ +--- a/scripts/sf_gain_loss.py ++++ b/scripts/sf_gain_loss.py +@@ -2,10 +2,10 @@ from __future__ import print_function, division + import os,sys,copy;import numpy as np + from collections import defaultdict + sys.path.append('./') +-from treetime.treetime import treeanc as ta +-from treetime.treetime.gtr import GTR +-from treetime.treetime import io +-from treetime.treetime import seq_utils ++from treetime import treeanc as ta ++from treetime.gtr import GTR ++from treetime import io ++from treetime import seq_utils + from Bio import Phylo, AlignIO + from sf_miscellaneous import write_json, write_pickle + from sf_geneCluster_align_makeTree import load_sorted_clusters diff --git a/recipes/peptide-shaker/meta.yaml b/recipes/peptide-shaker/meta.yaml index 3563c4c0196e1..7d11fe6a9a34c 100644 --- a/recipes/peptide-shaker/meta.yaml +++ b/recipes/peptide-shaker/meta.yaml @@ -1,5 +1,5 @@ {% set name = "PeptideShaker" %} -{% set version = "1.16.14" %} +{% set version = "1.16.15" %} # Do not forget to update the version string in the peptide-shaker.py file about: @@ -21,7 +21,7 @@ build: source: fn: {{ name }}-{{ version }}.zip url: http://genesis.ugent.be/maven2/eu/isas/peptideshaker/{{ name }}/{{ version }}/{{ name }}-{{ version }}.zip - sha256: 21aeef41f3c35533df4e3212e27e1126b1f7769c8a9f9cf887a0d1cf30155439 + sha256: 54cad21b9657b69f5c76ff059b14247d8cd65b85cbd22a7f72910c7e30d46398 requirements: build: diff --git a/recipes/peptide-shaker/peptide-shaker.py b/recipes/peptide-shaker/peptide-shaker.py index 59dd98588f619..62550cbf3d669 100755 --- a/recipes/peptide-shaker/peptide-shaker.py +++ b/recipes/peptide-shaker/peptide-shaker.py @@ -13,7 +13,7 @@ from os import access from os import getenv from os import X_OK -jar_file = 'PeptideShaker-1.16.14.jar' +jar_file = 'PeptideShaker-1.16.15.jar' default_jvm_mem_opts = ['-Xms512m', '-Xmx1g'] diff --git a/recipes/perl-biox-workflow-command/2.2.1/meta.yaml b/recipes/perl-biox-workflow-command/2.2.1/meta.yaml deleted file mode 100644 index a751c00448a70..0000000000000 --- a/recipes/perl-biox-workflow-command/2.2.1/meta.yaml +++ /dev/null @@ -1,111 +0,0 @@ -{% set name = "perl-biox-workflow-command" %} -{% set version = "2.2.1" %} -{% set sha256 = "bc187a13409b3d721555c5c5677a930dbb3b4f591dc79f19c06edbfad3e80d0d" %} - -package: - name: {{ name }} - version: {{ version }} - -source: - fn: BioX-Workflow-Command-{{ version }}.tar.gz - url: https://github.com/biosails/BioX-Workflow-Command/archive/{{ version }}.tar.gz - sha256: {{ sha256 }} - -build: - number: 0 - skip: True # [osx] - -requirements: - build: - - perl - - perl-app-cpanminus - - perl-list-compare - - perl-file-path - - perl-safe - - perl-class-load - - perl-try-tiny - - perl-file-find-rule - - perl-log-log4perl - - perl-data-walk - - perl-test-class-moose - - perl-file-details - - perl-capture-tiny - - perl-text-diff - - perl-string-approx - - perl-text-asciitable - - perl-yaml - - perl-namespace-autoclean - - perl-dbm-deep - - perl-list-uniq - - perl-moosex-types - - perl-datetime-format-strptime - - perl-config-any - - perl-text-template - - perl-datetime - - perl-path-tiny - - perl-module-build-tiny - - perl-params-validate - - perl-file-slurp - - perl-moose - - perl-moosex-app - - perl-moosex-getopt - - perl-moosex-types - - perl-algorithm-dependency - - perl-test2 - - perl-test-class-moose - - perl-clone - - perl-file-slurp - - perl-git-wrapper - - perl-git-wrapper-plus - - run: - - perl - - perl-app-cpanminus - - perl-list-compare - - perl-file-path - - perl-safe - - perl-class-load - - perl-test2 - - perl-try-tiny - - perl-file-find-rule - - perl-log-log4perl - - perl-data-walk - - perl-file-details - - perl-moose - - perl-string-approx - - perl-text-asciitable - - perl-yaml - - perl-namespace-autoclean - - perl-dbm-deep - - perl-list-uniq - - perl-moosex-types - - perl-moosex-getopt - - perl-datetime-format-strptime - - perl-text-template - - perl-datetime - - perl-path-tiny - - perl-params-validate - - perl-config-any - - perl-moose - - perl-moosex-app - - perl-moosex-getopt - - perl-moosex-types - - perl-algorithm-dependency - - perl-clone - - perl-json - - perl-file-slurp - - perl-git-wrapper - - perl-git-wrapper-plus - -test: - commands: - - biox -h - - biox run -h - - biox stats -h - - biox new -h - - biox add -h - -about: - home: https://github.com/biosails/BioX-Workflow-Command - license: perl_5 - summary: 'Opinionated Bioinformatics Genomics Workflow Creator' diff --git a/recipes/perl-biox-workflow-command/2.2.3/build.sh b/recipes/perl-biox-workflow-command/2.3.0/build.sh similarity index 71% rename from recipes/perl-biox-workflow-command/2.2.3/build.sh rename to recipes/perl-biox-workflow-command/2.3.0/build.sh index 17885fd31b9e6..7721bb3b620b5 100644 --- a/recipes/perl-biox-workflow-command/2.2.3/build.sh +++ b/recipes/perl-biox-workflow-command/2.3.0/build.sh @@ -2,7 +2,6 @@ # If it has Build.PL use that, otherwise use Makefile.PL cpanm --installdeps . -cpanm File::Slurp if [ -f Build.PL ]; then perl Build.PL @@ -20,9 +19,3 @@ else echo 'Unable to find Build.PL or Makefile.PL. You need to modify build.sh.' exit 1 fi - -# Add more build steps here, if they are necessary. - -# See -# http://docs.continuum.io/conda/build.html -# for a list of environment variables that are set during the build process. diff --git a/recipes/perl-biox-workflow-command/2.2.3/meta.yaml b/recipes/perl-biox-workflow-command/2.3.0/meta.yaml similarity index 93% rename from recipes/perl-biox-workflow-command/2.2.3/meta.yaml rename to recipes/perl-biox-workflow-command/2.3.0/meta.yaml index 47f4ad99fafb4..1b3399f94aaa4 100644 --- a/recipes/perl-biox-workflow-command/2.2.3/meta.yaml +++ b/recipes/perl-biox-workflow-command/2.3.0/meta.yaml @@ -1,6 +1,6 @@ {% set name = "perl-biox-workflow-command" %} -{% set version = "2.2.3" %} -{% set sha256 = "cbe8fcc3874bbdf914795db80dff47349ac97202b90c30e9d9ab3ea4ddc74aa4" %} +{% set version = "2.3.0" %} +{% set sha256 = "0b3eef4df3363e7c56fa8372f6c3db2c2bf7ad88aad359b595620269b15f6c7f" %} package: name: {{ name }} @@ -57,6 +57,7 @@ requirements: - perl-file-slurp - perl-git-wrapper - perl-git-wrapper-plus + - perl-list-moreutils - perl-list-someutils run: @@ -97,6 +98,7 @@ requirements: - perl-file-slurp - perl-git-wrapper - perl-git-wrapper-plus + - perl-list-moreutils - perl-list-someutils test: diff --git a/recipes/perl-config-any/build.sh b/recipes/perl-config-any/build.sh index 6de255d53eec6..9fdaf52284153 100644 --- a/recipes/perl-config-any/build.sh +++ b/recipes/perl-config-any/build.sh @@ -1,13 +1,18 @@ #!/bin/bash # If it has Build.PL use that, otherwise use Makefile.PL -cpanm --installdeps . +if [ "$(uname)" == "Darwin" ]; then + HOME=/tmp cpanm --installdeps . +else + cpanm --installdeps . +fi + if [ -f Build.PL ]; then perl Build.PL - ./Build - ./Build test + perl ./Build + perl ./Build test # Make sure this goes in site - ./Build install --installdirs site + perl ./Build install --installdirs site elif [ -f Makefile.PL ]; then # Make sure this goes in site perl Makefile.PL INSTALLDIRS=site @@ -19,6 +24,8 @@ else exit 1 fi + + # Add more build steps here, if they are necessary. # See diff --git a/recipes/perl-config-any/meta.yaml b/recipes/perl-config-any/meta.yaml index e30c7685ac2b9..15cfe17f6d985 100644 --- a/recipes/perl-config-any/meta.yaml +++ b/recipes/perl-config-any/meta.yaml @@ -6,22 +6,24 @@ source: fn: Config-Any-0.27.tar.gz url: https://cpan.metacpan.org/authors/id/B/BR/BRICAS/Config-Any-0.27.tar.gz md5: 0c8db36ebfeea250f554ebc50ee5b643 -# patches: - # List any patch files here - # - fix.patch build: - skip: True # [osx] - number: 0 + #skip: True # [osx] + number: 1 requirements: build: - - perl-threaded + - toolchain + - gcc # [linux] + - llvm # [osx] + - perl - perl-app-cpanminus - perl-extutils-makemaker run: - - perl-threaded + - perl + - libgcc # [linux] + - perl-app-cpanminus test: # Perl 'use' tests diff --git a/recipes/perl-go-perl/build.sh b/recipes/perl-go-perl/build.sh new file mode 100644 index 0000000000000..6f4625802a6e9 --- /dev/null +++ b/recipes/perl-go-perl/build.sh @@ -0,0 +1,20 @@ +#!/bin/bash + +# If it has Build.PL use that, otherwise use Makefile.PL +if [ -f Build.PL ]; then + perl Build.PL + perl ./Build + perl ./Build test + # Make sure this goes in site + perl ./Build install --installdirs site +elif [ -f Makefile.PL ]; then + # Make sure this goes in site + perl Makefile.PL INSTALLDIRS=site + make + make test + make install +else + echo 'Unable to find Build.PL or Makefile.PL. You need to modify build.sh.' + exit 1 +fi + diff --git a/recipes/perl-go-perl/meta.yaml b/recipes/perl-go-perl/meta.yaml new file mode 100644 index 0000000000000..06350e1ca7fea --- /dev/null +++ b/recipes/perl-go-perl/meta.yaml @@ -0,0 +1,39 @@ +{% set name = "perl-go-perl" %} +{% set version = "0.15" %} +{% set sha256 = "423d26155ee85ca51ab2270cee59f4e85b193e57ac3a29aff827298c0a396b12" %} + +package: + name: {{ name }} + version: {{ version }} + +source: + fn: go-perl-0.15.tar.gz + url: https://cpan.metacpan.org/authors/id/C/CM/CMUNGALL/go-perl-{{ version }}.tar.gz + sha256: {{ sha256 }} + +build: + number: 1 + +requirements: + build: + - perl + - perl-data-dumper + - perl-extutils-makemaker + - perl-data-stag + + run: + - perl + - perl-data-dumper + - perl-data-stag + +test: + imports: + - GO::Parser + commands: + - which map2slim >& /dev/null + +about: + home: http://metacpan.org/pod/go-perl + license: BSD-3-Clause + summary: 'perl modules for GO and other OBO ontologies' + diff --git a/recipes/perl-module-build-tiny/build.sh b/recipes/perl-module-build-tiny/build.sh index 6de255d53eec6..77283fb0b38c1 100644 --- a/recipes/perl-module-build-tiny/build.sh +++ b/recipes/perl-module-build-tiny/build.sh @@ -1,13 +1,18 @@ #!/bin/bash # If it has Build.PL use that, otherwise use Makefile.PL -cpanm --installdeps . +if [ "$(uname)" == "Darwin" ]; then + HOME=/tmp cpanm --installdeps . +else + cpanm --installdeps . +fi + if [ -f Build.PL ]; then perl Build.PL - ./Build - ./Build test + perl ./Build + perl ./Build test # Make sure this goes in site - ./Build install --installdirs site + perl ./Build install --installdirs site elif [ -f Makefile.PL ]; then # Make sure this goes in site perl Makefile.PL INSTALLDIRS=site diff --git a/recipes/perl-module-build-tiny/meta.yaml b/recipes/perl-module-build-tiny/meta.yaml index df3b4429f2f75..d70a4b1b2be68 100644 --- a/recipes/perl-module-build-tiny/meta.yaml +++ b/recipes/perl-module-build-tiny/meta.yaml @@ -8,38 +8,27 @@ source: md5: 2332c90c17454107fea3f2614e11a3a9 build: - skip: True # [osx] - number: 0 + #skip: True # [osx] + number: 1 requirements: build: - - perl-threaded + - perl - perl-app-cpanminus - perl-extutils-makemaker - perl-pathtools run: - - perl-threaded + - perl - perl-extutils-makemaker - perl-pathtools test: # Perl 'use' tests - imports: - - Module::Build::Tiny - - # You can also put a file called run_test.pl (or run_test.py) in the recipe - # that will be run at test time. - - # requires: - # Put any additional test requirements here. For example - # - nose + commands: + - which perl about: home: http://metacpan.org/pod/Module-Build-Tiny license: perl_5 summary: 'A tiny replacement for Module::Build' - -# See -# http://docs.continuum.io/conda/build.html for -# more information about meta.yaml diff --git a/recipes/perl-moose/2.2009/build.sh b/recipes/perl-moose/2.2009/build.sh new file mode 100644 index 0000000000000..eb050858eff53 --- /dev/null +++ b/recipes/perl-moose/2.2009/build.sh @@ -0,0 +1,33 @@ +#!/bin/bash + +if [ "$(uname)" == "Darwin" ]; then + HOME=/tmp cpanm --installdeps . + HOME=/tmp cpanm --force -nq List::Util +else + cpanm --installdeps . + cpanm --force -nq List::Util +fi + +# If it has Build.PL use that, otherwise use Makefile.PL +if [ -f Build.PL ]; then + perl Build.PL + ./Build + ./Build test + # Make sure this goes in site + ./Build install --installdirs site +elif [ -f Makefile.PL ]; then + # Make sure this goes in site + perl Makefile.PL INSTALLDIRS=site + make + make test + make install +else + echo 'Unable to find Build.PL or Makefile.PL. You need to modify build.sh.' + exit 1 +fi + +# Add more build steps here, if they are necessary. + +# See +# http://docs.continuum.io/conda/build.html +# for a list of environment variables that are set during the build process. diff --git a/recipes/perl-moose/2.2009/meta.yaml b/recipes/perl-moose/2.2009/meta.yaml new file mode 100644 index 0000000000000..ffeb0b40dbcac --- /dev/null +++ b/recipes/perl-moose/2.2009/meta.yaml @@ -0,0 +1,58 @@ +{% set name = "perl-moose" %} +{% set version = "2.2009" %} +{% set sha256 = "63ba8a5e27dbcbdbac2cd8f4162fff50a31e9829d8955a196a5898240c02d194" %} + +package: + name: {{ name }} + version: {{ version }} + +source: + fn: Moose-{{ version }}.tar.gz + url: https://cpan.metacpan.org/authors/id/E/ET/ETHER/Moose-{{ version }}.tar.gz + sha256: {{ sha256 }} + +build: + number: 0 + +requirements: + build: + - perl + - perl-app-cpanminus + - perl-pathtools + - perl-module-runtime + - perl-extutils-makemaker + - perl-try-tiny + - perl-test-warnings + - perl-scalar-list-utils >=1.45 + - perl-package-stash + - perl-sub-exporter + - perl-test-more + - perl-list-someutils + - perl-datetime + - perl-dbm-deep + - perl-test-deep + - perl-yaml + + run: + - perl + - perl-app-cpanminus + - perl-pathtools + - perl-module-runtime + - perl-extutils-makemaker + - perl-try-tiny + - perl-test-warnings + - perl-scalar-list-utils >=1.45 + - perl-package-stash + - perl-sub-exporter + - perl-datetime + +test: + commands: + - which perl + - perl -V + +about: + home: http://moose.perl.org/ + license: perl_5 + summary: 'A postmodern object system for Perl 5' + diff --git a/recipes/perl-biox-workflow-command/2.2.1/build.sh b/recipes/perl-moosex-app/1.39/build.sh similarity index 72% rename from recipes/perl-biox-workflow-command/2.2.1/build.sh rename to recipes/perl-moosex-app/1.39/build.sh index 17885fd31b9e6..312e1e23bf7c3 100644 --- a/recipes/perl-biox-workflow-command/2.2.1/build.sh +++ b/recipes/perl-moosex-app/1.39/build.sh @@ -1,8 +1,15 @@ #!/bin/bash # If it has Build.PL use that, otherwise use Makefile.PL -cpanm --installdeps . -cpanm File::Slurp +if [ "$(uname)" == "Darwin" ]; then + HOME=/tmp cpanm --installdeps . + HOME=/tmp cpanm Text::WagnerFischer + HOME=/tmp cpanm Devel::StackTrace +else + cpanm --installdeps . + cpanm Text::WagnerFischer + cpanm Devel::StackTrace +fi if [ -f Build.PL ]; then perl Build.PL diff --git a/recipes/perl-moosex-app/1.39/meta.yaml b/recipes/perl-moosex-app/1.39/meta.yaml new file mode 100644 index 0000000000000..e58db499156f2 --- /dev/null +++ b/recipes/perl-moosex-app/1.39/meta.yaml @@ -0,0 +1,55 @@ +package: + name: perl-moosex-app + version: "1.39" + +source: + fn: MooseX-App-1.39.tar.gz + url: https://cpan.metacpan.org/authors/id/M/MA/MAROS/MooseX-App-1.39.tar.gz + md5: 36040281ec23ad0dee068c70e57ea106 + +build: + #skip: True # [osx] + number: 1 + +requirements: + build: + - perl + - perl-app-cpanminus + - perl-extutils-makemaker + - perl-path-class + - perl-moose + - perl-scalar-list-utils + - perl-termreadkey + - perl-file-homedir + - perl-test-simple + - perl-test-most + - perl-test-warnings + - perl-moosex-types-path-class + - perl-pod-elemental + - perl-config-any + - perl-io-interactive # [linux] + + run: + - perl + - perl-path-class + - perl-moose + - perl-scalar-list-utils + - perl-termreadkey + - perl-file-homedir + - perl-moosex-types-path-class + - perl-pod-elemental + - perl-config-any + - perl-io-interactive # [linux] + +test: + commands: + - perl -e "use MooseX::App" + +about: + home: http://metacpan.org/pod/MooseX::App + license: perl_5 + summary: 'Write user-friendly command line apps with even less suffering' + +# See +# http://docs.continuum.io/conda/build.html for +# more information about meta.yaml diff --git a/recipes/perl-moosex-app/build.sh b/recipes/perl-moosex-app/build.sh index 8e8f4b8ac4770..e41551952b661 100644 --- a/recipes/perl-moosex-app/build.sh +++ b/recipes/perl-moosex-app/build.sh @@ -1,8 +1,15 @@ #!/bin/bash +if [ "$(uname)" == "Darwin" ]; then + HOME=/tmp cpanm Text::WagnerFischer + HOME=/tmp cpanm --installdeps . +else + cpanm Text::WagnerFischer + cpanm --installdeps . +fi + + # If it has Build.PL use that, otherwise use Makefile.PL -cpanm Text::WagnerFischer -cpanm --installdeps . if [ -f Build.PL ]; then perl Build.PL ./Build diff --git a/recipes/perl-moosex-app/meta.yaml b/recipes/perl-moosex-app/meta.yaml index c2e095b03a501..3f4d04b0a41af 100644 --- a/recipes/perl-moosex-app/meta.yaml +++ b/recipes/perl-moosex-app/meta.yaml @@ -13,7 +13,7 @@ build: requirements: build: - - perl-threaded + - perl - perl-app-cpanminus - perl-extutils-makemaker - perl-path-class @@ -27,7 +27,7 @@ requirements: - perl-file-homedir run: - - perl-threaded + - perl - perl-path-class - perl-config-any - perl-moosex-types-path-class diff --git a/recipes/perl-moosex-types-path-class/build.sh b/recipes/perl-moosex-types-path-class/build.sh index 214d4ca5106ec..23eb50af99c52 100644 --- a/recipes/perl-moosex-types-path-class/build.sh +++ b/recipes/perl-moosex-types-path-class/build.sh @@ -3,10 +3,10 @@ # If it has Build.PL use that, otherwise use Makefile.PL if [ -f Build.PL ]; then perl Build.PL - ./Build - ./Build test + perl ./Build + perl ./Build test # Make sure this goes in site - ./Build install --installdirs site + perl ./Build install --installdirs site elif [ -f Makefile.PL ]; then # Make sure this goes in site perl Makefile.PL INSTALLDIRS=site diff --git a/recipes/perl-moosex-types-path-class/meta.yaml b/recipes/perl-moosex-types-path-class/meta.yaml index cf24cec1323c7..0b4aa872b4575 100644 --- a/recipes/perl-moosex-types-path-class/meta.yaml +++ b/recipes/perl-moosex-types-path-class/meta.yaml @@ -6,18 +6,16 @@ source: fn: MooseX-Types-Path-Class-0.09.tar.gz url: https://cpan.metacpan.org/authors/id/E/ET/ETHER/MooseX-Types-Path-Class-0.09.tar.gz md5: 6ef4c82511793594d37bcabcc29fa124 -# patches: - # List any patch files here - # - fix.patch build: - number: 0 - skip: True # [osx] + number: 2 + #skip: True # [osx] requirements: build: - - perl-threaded + - toolchain + - perl - perl-app-cpanminus - perl-pathtools - perl-path-class @@ -26,27 +24,15 @@ requirements: - perl-module-build-tiny run: - - perl-threaded + - perl - perl-path-class - perl-moosex-types test: - # Perl 'use' tests - imports: - - MooseX::Types::Path::Class - - # You can also put a file called run_test.pl (or run_test.py) in the recipe - # that will be run at test time. - - # requires: - # Put any additional test requirements here. For example - # - nose + commands: + - perl -e "use MooseX::Types::Path::Class" about: home: https://github.com/moose/MooseX-Types-Path-Class license: perl_5 summary: 'A Path::Class type library for Moose' - -# See -# http://docs.continuum.io/conda/build.html for -# more information about meta.yaml diff --git a/recipes/perl-moosex-types/build.sh b/recipes/perl-moosex-types/build.sh index 6de255d53eec6..f3a127660c85f 100644 --- a/recipes/perl-moosex-types/build.sh +++ b/recipes/perl-moosex-types/build.sh @@ -1,13 +1,21 @@ #!/bin/bash # If it has Build.PL use that, otherwise use Makefile.PL -cpanm --installdeps . +if [ "$(uname)" == "Darwin" ]; then + HOME=/tmp cpanm --installdeps . + HOME=/tmp cpanm Devel::StackTrace +else + cpanm --installdeps . + cpanm Devel::StackTrace +fi + + if [ -f Build.PL ]; then perl Build.PL - ./Build - ./Build test + perl ./Build + perl ./Build test # Make sure this goes in site - ./Build install --installdirs site + perl ./Build install --installdirs site elif [ -f Makefile.PL ]; then # Make sure this goes in site perl Makefile.PL INSTALLDIRS=site @@ -18,9 +26,3 @@ else echo 'Unable to find Build.PL or Makefile.PL. You need to modify build.sh.' exit 1 fi - -# Add more build steps here, if they are necessary. - -# See -# http://docs.continuum.io/conda/build.html -# for a list of environment variables that are set during the build process. diff --git a/recipes/perl-moosex-types/meta.yaml b/recipes/perl-moosex-types/meta.yaml index 0dc6ebb1734a4..5af91f0d253e6 100644 --- a/recipes/perl-moosex-types/meta.yaml +++ b/recipes/perl-moosex-types/meta.yaml @@ -6,18 +6,15 @@ source: fn: MooseX-Types-0.46.tar.gz url: https://cpan.metacpan.org/authors/id/E/ET/ETHER/MooseX-Types-0.46.tar.gz md5: e1debd6007b9cc494636499397c6dabf -# patches: - # List any patch files here - # - fix.patch build: - number: 0 - skip: True # [osx] + number: 1 + #skip: True # [osx] requirements: build: + - perl - perl-app-cpanminus - - perl-threaded - perl-scalar-list-utils - perl-module-runtime - perl-moose @@ -26,7 +23,8 @@ requirements: - perl-pathtools run: - - perl-threaded + - perl + - perl-app-cpanminus - perl-scalar-list-utils - perl-module-runtime - perl-moose diff --git a/recipes/perl-pod-elemental/build.sh b/recipes/perl-pod-elemental/build.sh index 6de255d53eec6..8403b23b6e6d9 100644 --- a/recipes/perl-pod-elemental/build.sh +++ b/recipes/perl-pod-elemental/build.sh @@ -1,13 +1,18 @@ #!/bin/bash # If it has Build.PL use that, otherwise use Makefile.PL -cpanm --installdeps . +# If it has Build.PL use that, otherwise use Makefile.PL +if [ "$(uname)" == "Darwin" ]; then + HOME=/tmp cpanm --installdeps . +else + cpanm --installdeps . +fi + if [ -f Build.PL ]; then perl Build.PL - ./Build - ./Build test - # Make sure this goes in site - ./Build install --installdirs site + perl ./Build + perl ./Build test + perl ./Build install --installdirs site elif [ -f Makefile.PL ]; then # Make sure this goes in site perl Makefile.PL INSTALLDIRS=site diff --git a/recipes/perl-pod-elemental/meta.yaml b/recipes/perl-pod-elemental/meta.yaml index cc82abc75c0a9..9e02a07ec404a 100644 --- a/recipes/perl-pod-elemental/meta.yaml +++ b/recipes/perl-pod-elemental/meta.yaml @@ -6,79 +6,39 @@ source: fn: Pod-Elemental-0.103004.tar.gz url: https://cpan.metacpan.org/authors/id/R/RJ/RJBS/Pod-Elemental-0.103004.tar.gz md5: 15458de0d87404ee94285633acadec9f -# patches: - # List any patch files here - # - fix.patch - -# build: - # If this is a new build for the same version, increment the build - # number. If you do not include this key, it defaults to 0. - # number: 1 build: - skip: True # [osx] - number: 0 + #skip: True # [osx] + number: 1 requirements: build: - - gcc - - perl-threaded + - gcc # [linux] + - llvm # [osx] + - perl - perl-app-cpanminus - perl-moosex-types - perl-pathtools - perl-extutils-makemaker - perl-moose - perl-scalar-list-utils + - perl-mixin-linewise run: - - perl-threaded + - libgcc # [linux] + - perl - perl-app-cpanminus - perl-moosex-types - perl-moose - perl-scalar-list-utils + - perl-mixin-linewise test: - # Perl 'use' tests - imports: - - Pod::Elemental - - Pod::Elemental::Autoblank - - Pod::Elemental::Autochomp - - Pod::Elemental::Command - - Pod::Elemental::Document - - Pod::Elemental::Element::Generic::Blank - - Pod::Elemental::Element::Generic::Command - - Pod::Elemental::Element::Generic::Nonpod - - Pod::Elemental::Element::Generic::Text - - Pod::Elemental::Element::Nested - - Pod::Elemental::Element::Pod5::Command - - Pod::Elemental::Element::Pod5::Data - - Pod::Elemental::Element::Pod5::Nonpod - - Pod::Elemental::Element::Pod5::Ordinary - - Pod::Elemental::Element::Pod5::Region - - Pod::Elemental::Element::Pod5::Verbatim - - Pod::Elemental::Flat - - Pod::Elemental::Node - - Pod::Elemental::Objectifier - - Pod::Elemental::Paragraph - - Pod::Elemental::Selectors - - Pod::Elemental::Transformer - - Pod::Elemental::Transformer::Gatherer - - Pod::Elemental::Transformer::Nester - - Pod::Elemental::Transformer::Pod5 - - Pod::Elemental::Types - - # You can also put a file called run_test.pl (or run_test.py) in the recipe - # that will be run at test time. - - # requires: - # Put any additional test requirements here. For example - # - nose + commands: + - perl -e "use Pod::Elemental" about: home: https://github.com/rjbs/Pod-Elemental license: perl_5 summary: 'work with nestable Pod elements' -# See -# http://docs.continuum.io/conda/build.html for -# more information about meta.yaml diff --git a/recipes/perl-try-tiny-retry/build.sh b/recipes/perl-try-tiny-retry/build.sh new file mode 100644 index 0000000000000..64652ea2132d9 --- /dev/null +++ b/recipes/perl-try-tiny-retry/build.sh @@ -0,0 +1,19 @@ +#!/bin/bash + +# If it has Build.PL use that, otherwise use Makefile.PL +if [ -f Build.PL ]; then + perl Build.PL + ./Build + ./Build test + # Make sure this goes in site + ./Build install --installdirs site +elif [ -f Makefile.PL ]; then + # Make sure this goes in site + perl Makefile.PL INSTALLDIRS=site + make + make test + make install +else + echo 'Unable to find Build.PL or Makefile.PL. You need to modify build.sh.' + exit 1 +fi diff --git a/recipes/perl-try-tiny-retry/meta.yaml b/recipes/perl-try-tiny-retry/meta.yaml new file mode 100644 index 0000000000000..391b8e1fe9747 --- /dev/null +++ b/recipes/perl-try-tiny-retry/meta.yaml @@ -0,0 +1,29 @@ +package: + name: perl-try-tiny-retry + version: "0.002" + +source: + fn: Try-Tiny-Retry-0.002.tar.gz + url: https://cpan.metacpan.org/authors/id/D/DA/DAGOLDEN/Try-Tiny-Retry-0.002.tar.gz + sha256: 4f6dd3addcab7dd2726f450cecaaadb21b33da59bec5df58f07fd91a87d9c38a + +build: + number: 0 + +requirements: + build: + - perl + - perl-try-tiny + run: + - perl + - perl-try-tiny + +test: + # Perl 'use' tests + imports: + - Try::Tiny::Retry + +about: + home: https://github.com/dagolden/Try-Tiny-Retry + license: Apache-2.0 + summary: 'Just like Try::Tiny, but with retry instead of try.' diff --git a/recipes/pfam_scan/build.sh b/recipes/pfam_scan/build.sh index 1a0c5f59f984c..2253466bfd31a 100644 --- a/recipes/pfam_scan/build.sh +++ b/recipes/pfam_scan/build.sh @@ -9,8 +9,6 @@ cp -r * $outdir # Short wrapper script which sets PERL5LIB while running cat > $PREFIX/bin/pfam_scan.pl <=1.4 + - perl-ipc-run test: commands: diff --git a/recipes/pgsa/build.sh b/recipes/pgsa/build.sh new file mode 100644 index 0000000000000..3f60763a145f9 --- /dev/null +++ b/recipes/pgsa/build.sh @@ -0,0 +1,31 @@ +#!/bin/bash + +mkdir -p ${PREFIX}/bin +mkdir -p ${PREFIX}/lib +mkdir -p ${PREFIX}/include/pseudogenome/ +mkdir -p ${PREFIX}/include/readsset/ +mkdir -p ${PREFIX}/include/sais/ +mkdir -p ${PREFIX}/include/suffixarray/ +mkdir -p ${PREFIX}/include/test/ +mkdir -p ${PREFIX}/include/index/ + +# build binaries and lib +make build CONF=pgsagen +make build CONF=pgsatest +make build CONF=pgsalib + +# copy .so into lib +cp dist/pgsalib/*/libPgSA.so ${PREFIX}/lib + +# copy executables into bin +cp dist/pgsagen/*/PgSAgen ${PREFIX}/bin +cp dist/pgsatest/*/PgSAtest ${PREFIX}/bin + +# copy .h into include +cp src/*.h ${PREFIX}/include/ +cp src/pseudogenome/*.h ${PREFIX}/include/pseudogenome/ +cp src/readsset/*.h ${PREFIX}/include/readsset/ +cp src/sais/*.h ${PREFIX}/include/sais/ +cp src/suffixarray/*.h ${PREFIX}/include/suffixarray/ +cp src/test/*.h ${PREFIX}/include/test/ +cp src/index/*.h ${PREFIX}/include/index/ diff --git a/recipes/pgsa/meta.yaml b/recipes/pgsa/meta.yaml new file mode 100644 index 0000000000000..21675e2b2f535 --- /dev/null +++ b/recipes/pgsa/meta.yaml @@ -0,0 +1,27 @@ +package: + name: pgsa + version: "1.2" + +source: + fn: 0d7c97f22a07fce96e0638deb09d2a8c05ed3d8b.zip + url: https://github.com/kowallus/PgSA/archive/0d7c97f22a07fce96e0638deb09d2a8c05ed3d8b.zip + md5: e69596048ed3831a6c92580814d48f19 + +build: + number: 0 + +requirements: + build: + - gcc + run: + - libgcc + +test: + commands: + - '{ PgSAgen -h 2>&1 | grep Usage; }' + - '{ PgSAtest -h 2>&1 | grep Usage; }' + +about: + home: http://sun.aei.polsl.pl/pgsa/ + license: Creative Commons Attribution License + summary: Pseudogenome Suffix Array is a compact index for collections of reads from sequencing. diff --git a/recipes/phyloflash/meta.yaml b/recipes/phyloflash/meta.yaml index 868add1027d51..6b3959dc482ce 100644 --- a/recipes/phyloflash/meta.yaml +++ b/recipes/phyloflash/meta.yaml @@ -1,17 +1,15 @@ {% set name = "phyloFlash" %} -{% set version = "2.0-beta6" %} -{% set sha256 = "137c90288b39fbfc1fee87fe606ab7ef10b673e0bccf1a0ff305b62e4291d68a" %} +{% set version = "3.0b1" %} +{% set sha256 = "1f80d721dab503438eef93436baad7b212f997ca45dbe7a93b9a8a1e01c9db25" %} package: name: {{ name|lower}} version: {{ version|replace('-','') }} source: - url: https://github.com/HRGV/{{ name }}/archive/v{{ version }}.tar.gz + url: https://github.com/HRGV/{{ name }}/archive/pf{{ version }}.tar.gz fn: v{{ version }}.tar.gz sha256: {{ sha256 }} - patches: - - real_bin.patch build: number: 0 @@ -40,7 +38,7 @@ test: - phyloFlash.pl -check_env || true - phyloFlash.pl -check_env 2>&1 | grep "Please provide a path using -dbhome" - phyloFlash_makedb.pl --help - - phyloFlash_heatmap.R --help |tee | grep "Generates a heatmap plot" + - phyloFlash_heatmap.R --help | tee | grep "Generates a heatmap plot" about: home: https://github.com/HRGV/phyloFlash diff --git a/recipes/phyloflash/real_bin.patch b/recipes/phyloflash/real_bin.patch deleted file mode 100644 index 6d22be4e66f23..0000000000000 --- a/recipes/phyloflash/real_bin.patch +++ /dev/null @@ -1,12 +0,0 @@ -diff -ru phyloFlash-2.0-beta6.orig/phyloFlash_makedb.pl phyloFlash-2.0-beta6/phyloFlash_makedb.pl ---- phyloFlash-2.0-beta6.orig/phyloFlash_makedb.pl 2017-08-05 14:02:31.000000000 -0600 -+++ phyloFlash-2.0-beta6/phyloFlash_makedb.pl 2017-08-05 14:01:46.000000000 -0600 -@@ -76,7 +76,7 @@ - - use strict; - use FindBin; --use lib $FindBin::Bin; -+use lib $FindBin::RealBin; - use PhyloFlash; - use Pod::Usage; - use Getopt::Long; diff --git a/recipes/picard/1.56/build.sh b/recipes/picard/1.56/build.sh new file mode 100644 index 0000000000000..afba8381fa57b --- /dev/null +++ b/recipes/picard/1.56/build.sh @@ -0,0 +1,13 @@ +#!/bin/bash + +TGT="$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM" +[ -d "$TGT" ] || mkdir -p "$TGT" +[ -d "${PREFIX}/bin" ] || mkdir -p "${PREFIX}/bin" + +curl -o lib/ant/ant-apache-bcel-1.8.1.jar https://depot.galaxyproject.org/software/Ant-Apache-BCEL/Ant-Apache-BCEL_1.8.1_src_all.jar +ant -lib lib/ant/ package-commands +cp -R dist/* ${TGT} + +cp $RECIPE_DIR/picard.sh $TGT/picard +ln -s $TGT/picard $PREFIX/bin +chmod 0755 "${PREFIX}/bin/picard" diff --git a/recipes/picard/1.56/meta.yaml b/recipes/picard/1.56/meta.yaml new file mode 100644 index 0000000000000..5b6cfdbcb5ae2 --- /dev/null +++ b/recipes/picard/1.56/meta.yaml @@ -0,0 +1,32 @@ +{% set version = "1.56" %} + +package: + name: picard + version: {{ version }} + +source: + fn: {{ version }}.tar.gz + url: https://github.com/broadinstitute/picard/archive/{{ version }}.tar.gz + sha256: 35b131450e504995352de78f477276ff4f8b0cf3e1a500a1d7e23d2fb2f4e12a + +build: + number: 0 + skip: False + +requirements: + build: + - ant + + run: + - openjdk >=6 + +test: + commands: + - picard --test-wrapper +about: + home: "http://broadinstitute.github.io/picard/" + license: MIT + summary: "Java tools for working with NGS data in the BAM format" + +extra: + notes: "Picard version 1.56 uses a wrapper script symlinked to bin/: picard. The wrapper script takes as arguments the particular jar file you want to run followed by any arguments for that jar. For example, 'picard ViewSam.jar --help'." diff --git a/recipes/picard/1.56/picard.sh b/recipes/picard/1.56/picard.sh new file mode 100755 index 0000000000000..416bcbb1d8d22 --- /dev/null +++ b/recipes/picard/1.56/picard.sh @@ -0,0 +1,81 @@ +#!/bin/bash +# Picard executable shell script +set -eu -o pipefail + +set -o pipefail +export LC_ALL=en_US.UTF-8 + +# Find original directory of bash script, resovling symlinks +# http://stackoverflow.com/questions/59895/can-a-bash-script-tell-what-directory-its-stored-in/246128#246128 +SOURCE="${BASH_SOURCE[0]}" +while [ -h "$SOURCE" ]; do # resolve $SOURCE until the file is no longer a symlink + DIR="$( cd -P "$( dirname "$SOURCE" )" && pwd )" + SOURCE="$(readlink "$SOURCE")" + [[ $SOURCE != /* ]] && SOURCE="$DIR/$SOURCE" # if $SOURCE was a relative symlink, we need to resolve it relative to the path where the symlink file was located +done +DIR="$( cd -P "$( dirname "$SOURCE" )" && pwd )" + +JAR_DIR=$DIR +ENV_PREFIX="$(dirname $(dirname $DIR))" +# Use Java installed with Anaconda to ensure correct version +java="$ENV_PREFIX/bin/java" + +# if JAVA_HOME is set (non-empty), use it. Otherwise keep "java" +if [ -n "${JAVA_HOME:=}" ]; then + if [ -e "$JAVA_HOME/bin/java" ]; then + java="$JAVA_HOME/bin/java" + fi +fi + +# extract memory and system property Java arguments from the list of provided arguments +# http://java.dzone.com/articles/better-java-shell-script +default_jvm_mem_opts="-Xms512m -Xmx1g" +test=false +jvm_mem_opts="" +jvm_prop_opts="" +jar_file="" +pass_args="" +for arg in "$@"; do + case $arg in + '-D'*) + jvm_prop_opts="$jvm_prop_opts $arg" + ;; + '-XX'*) + jvm_prop_opts="$jvm_prop_opts $arg" + ;; + '-Xm'*) + jvm_mem_opts="$jvm_mem_opts $arg" + ;; + '--test-wrapper') + test=true + ;; + *'.jar') + jar_file="$arg" + ;; + *) + pass_args="$pass_args $arg" + ;; + esac +done + +if $test; then + EXPECTED_JARS=(picard-1.56.jar sam-1.56.jar AddOrReplaceReadGroups.jar AddOrReplaceReadGroups.jar BamIndexStats.jar BamToBfq.jar BuildBamIndex.jar CalculateHsMetrics.jar CleanSam.jar CollectAlignmentSummaryMetrics.jar CollectGcBiasMetrics.jar CollectInsertSizeMetrics.jar CollectMultipleMetrics.jar CollectRnaSeqMetrics.jar CompareSAMs.jar CreateSequenceDictionary.jar DownsampleSam.jar EstimateLibraryComplexity.jar ExtractIlluminaBarcodes.jar ExtractSequences.jar FastqToSam.jar FixMateInformation.jar IlluminaBasecallsToSam.jar IntervalListTools.jar MarkDuplicates.jar MeanQualityByCycle.jar MergeBamAlignment.jar MergeSamFiles.jar NormalizeFasta.jar QualityScoreDistribution.jar ReorderSam.jar ReplaceSamHeader.jar RevertSam.jar SamFormatConverter.jar SamToFastq.jar SortSam.jar ValidateSamFile.jar ViewSam.jar) + for jar in ${EXPECTED_JARS[@]}; do + echo "Checking if $JAR_DIR/$jar can be found" + test -e $JAR_DIR/$jar || exit 1 + done + exit 0 +fi + +if [ "$jvm_mem_opts" == "" ]; then + jvm_mem_opts="$default_jvm_mem_opts" +fi + +pass_arr=($pass_args) +if [[ ${pass_arr[0]:=} == org* ]] +then + eval "$java" $jvm_mem_opts $jvm_prop_opts -cp "$JAR_DIR/$jar_file" $pass_args +else + eval "$java" $jvm_mem_opts $jvm_prop_opts -jar "$JAR_DIR/$jar_file" $pass_args +fi +exit diff --git a/recipes/picard/meta.yaml b/recipes/picard/meta.yaml index 7b52d61401eef..9f9cdd3403bbc 100644 --- a/recipes/picard/meta.yaml +++ b/recipes/picard/meta.yaml @@ -1,4 +1,4 @@ -{% set version = "2.14.1" %} +{% set version = "2.16.0" %} package: name: picard @@ -7,7 +7,7 @@ package: source: fn: picard.jar url: https://github.com/broadinstitute/picard/releases/download/{{ version }}/picard.jar - sha256: 40f6d83c65de7159e37d4883b3743e7e54f8e212e831fb3ab9838c2089688210 + sha256: 01cf3c930d2b4841960497491512d327bf669c1ed2e753152e1e651a27288c2d build: number: 0 diff --git a/recipes/picard/picard.sh b/recipes/picard/picard.sh index a17d9fb194bf9..3f2c7072fa771 100755 --- a/recipes/picard/picard.sh +++ b/recipes/picard/picard.sh @@ -5,7 +5,7 @@ set -eu -o pipefail set -o pipefail export LC_ALL=en_US.UTF-8 -# Find original directory of bash script, resovling symlinks +# Find original directory of bash script, resolving symlinks # http://stackoverflow.com/questions/59895/can-a-bash-script-tell-what-directory-its-stored-in/246128#246128 SOURCE="${BASH_SOURCE[0]}" while [ -h "$SOURCE" ]; do # resolve $SOURCE until the file is no longer a symlink diff --git a/recipes/picrust/meta.yaml b/recipes/picrust/meta.yaml index cc89201956225..921453e12fb51 100644 --- a/recipes/picrust/meta.yaml +++ b/recipes/picrust/meta.yaml @@ -1,5 +1,5 @@ {% set name = "picrust" %} -{% set version = "1.1.2" %} +{% set version = "1.1.3" %} package: name: {{ name|lower }} @@ -8,7 +8,7 @@ package: source: fn: {{ name|lower }}_{{ version }}.tar.gz url: https://github.com/picrust/picrust/archive/v{{ version }}.tar.gz - sha256: 3b2d1bc12b95df4b401f4f3a05913d63c78bbb5f005e60ae4868562ca2c2e4a3 + sha256: 7538c8544899b8855deb73a2d7a4ccac4808ff294e161530a8c8762d472d8906 build: skip: True # [not py27] diff --git a/recipes/plasmidtron/build.sh b/recipes/plasmidtron/build.sh index 05e8aa5c5fcdf..10be366945a36 100755 --- a/recipes/plasmidtron/build.sh +++ b/recipes/plasmidtron/build.sh @@ -1,3 +1,3 @@ #!/bin/bash -python3 setup.py install +python3 setup.py install --single-version-externally-managed --record=record.txt diff --git a/recipes/plasmidtron/meta.yaml b/recipes/plasmidtron/meta.yaml index e3d4c626ba070..0902b68d400eb 100644 --- a/recipes/plasmidtron/meta.yaml +++ b/recipes/plasmidtron/meta.yaml @@ -1,6 +1,6 @@ {% set name = "plasmidtron" %} -{% set version = "0.3.3" %} -{% set md5 = "b391e81c5bfc16e68c19aacf6ded3653" %} +{% set version = "0.3.5" %} +{% set sha256hash = "972d41f2f7eb427ab5d077bd1bc8b361168855f4a6adce51201eb041cccb879a" %} package: name: {{ name|lower }} @@ -9,7 +9,7 @@ package: source: fn: {{ name|lower }}_{{ version }}.tar.gz url: https://github.com/sanger-pathogens/{{ name }}/archive/v{{ version }}.tar.gz - md5: {{ md5 }} + sha256: {{ sha256hash }} build: skip: True # [py27] diff --git a/recipes/pneumocat/build.sh b/recipes/pneumocat/build.sh new file mode 100644 index 0000000000000..98bfe06f7107c --- /dev/null +++ b/recipes/pneumocat/build.sh @@ -0,0 +1,6 @@ +#!/bin/bash + +mkdir -p $PREFIX/bin +cp PneumoCaT.py $PREFIX/bin +cp -R modules $PREFIX/bin +cp -R streptococcus-pneumoniae-ctvdb $PREFIX/bin diff --git a/recipes/pneumocat/meta.yaml b/recipes/pneumocat/meta.yaml new file mode 100644 index 0000000000000..58c27a1b7edb7 --- /dev/null +++ b/recipes/pneumocat/meta.yaml @@ -0,0 +1,45 @@ +{% set name = "pneumocat" %} +{% set version = "1.1" %} +{% set md5sum = "a71fc0736b920723a68b631239c3aea9" %} + +package: + name: {{ name|lower }} + version: {{ version }} + +source: + fn: {{ name }}-{{ version }}.tar.gz + url: https://github.com/phe-bioinformatics/{{ name }}/archive/v{{ version }}.tar.gz + md5: {{ md5sum }} + +build: + number: 0 + skip: True # [not py27] + +requirements: + build: + run: + - bowtie2 + - samtools ==0.1.19 + - pyyaml + - python + - numpy + - lxml + - pysam + - biopython + +test: + commands: + - PneumoCaT.py --help + +about: + home: https://github.com/phe-bioinformatics/pneumocat/archive/v1.1.tar.gz + license: GPL3.0 + license_family: GPL + summary: 'PneumoCaT (Pneumococcal Capsular Typing) uses a two-step step approach to assign capsular type to S.pneumoniae genomic data (Illumina)' + +description: | + In the first step, reads from each readset are mapped to capsular locus sequences for all known capsular types (92 for S. pneumoniae plus 2 additional subtypes/molecular types). + This step is considered successful if the readset matches > 90% to 1 or more capsular locus sequences. + If it matches to a single capsular locus then PneumoCaT terminates here and reports this as the assigned capsular type. + If more than 1 loci are matched then the tool moves to the second step; a variant based approach that utilises the capsular type variant (CTV) database to distinguish serotypes within a serogroup/genogroup. + For more information you can refer to the publication. diff --git a/recipes/poretools/build.sh b/recipes/poretools/build.sh index 8e25a1455f914..3786386a73c83 100644 --- a/recipes/poretools/build.sh +++ b/recipes/poretools/build.sh @@ -1,3 +1,3 @@ #!/bin/bash -$PYTHON setup.py install +$PYTHON setup.py install --single-version-externally-managed --record=record.txt diff --git a/recipes/poretools/meta.yaml b/recipes/poretools/meta.yaml index 637a19090285c..b2c0c852c4638 100644 --- a/recipes/poretools/meta.yaml +++ b/recipes/poretools/meta.yaml @@ -9,6 +9,8 @@ source: fn: {{ name|lower }}_{{ version }}.tar.gz url: https://github.com/arq5x/poretools/archive/33e03f0b5dbc2a7d654870edab4aa968c2db6683.tar.gz md5: 9c38c7c104d431b1296dde54bc7f432c + patches: + - poretools.patch requirements: build: @@ -29,7 +31,7 @@ requirements: - pandas build: - number: 1 + number: 4 skip: True # [not py27] test: diff --git a/recipes/poretools/poretools.patch b/recipes/poretools/poretools.patch new file mode 100644 index 0000000000000..b7b1ec1e07fca --- /dev/null +++ b/recipes/poretools/poretools.patch @@ -0,0 +1,141 @@ +diff -Naur poretools-0.6.1.orig/poretools/hist.py poretools-0.6.1/poretools/hist.py +--- poretools-0.6.1.orig/poretools/hist.py 2017-05-31 14:36:46.000000000 -0400 ++++ poretools-0.6.1/poretools/hist.py 2017-12-11 17:05:45.428750967 -0500 +@@ -18,6 +18,10 @@ + """ + sizes = [s for s in sizes if args.min_length < s < args.max_length] + ++ if args.saveas is not None: ++ plt.switch_backend('Agg') # Use non-interactive backend in case this is ++ # running on a headless system. ++ + if args.theme_bw: + sns.set_style("whitegrid") + plt.hist(sizes, args.num_bins) +diff -Naur poretools-0.6.1.orig/poretools/occupancy.py poretools-0.6.1/poretools/occupancy.py +--- poretools-0.6.1.orig/poretools/occupancy.py 2017-05-31 14:36:46.000000000 -0400 ++++ poretools-0.6.1/poretools/occupancy.py 2017-12-11 17:05:45.428750967 -0500 +@@ -25,6 +25,9 @@ + """ + Plot the pore performance in terms of reads per pore + """ ++ if args.saveas is not None: ++ plt.switch_backend('Agg') # Use non-interactive backend in case this is ++ # running on a headless system. + flowcell_layout = minion_flowcell_layout() + + pore_values = [] +diff -Naur poretools-0.6.1.orig/poretools/poretools_main.py poretools-0.6.1/poretools/poretools_main.py +--- poretools-0.6.1.orig/poretools/poretools_main.py 2017-05-31 14:36:46.000000000 -0400 ++++ poretools-0.6.1/poretools/poretools_main.py 2017-12-11 17:05:45.428750967 -0500 +@@ -445,6 +445,11 @@ + ########## + parser_times = subparsers.add_parser('times', + help='Return the start times from a set of FAST5 files in tabular format') ++ parser_times.add_argument('--utc', ++ dest='utc', ++ default=False, ++ action='store_true', ++ help="Show timestamps in UTC.") + parser_times.add_argument('files', metavar='FILES', nargs='+', + help='The input FAST5 files.') + parser_times.set_defaults(func=run_subtool) +diff -Naur poretools-0.6.1.orig/poretools/qual_v_pos.py poretools-0.6.1/poretools/qual_v_pos.py +--- poretools-0.6.1.orig/poretools/qual_v_pos.py 2017-05-31 14:36:46.000000000 -0400 ++++ poretools-0.6.1/poretools/qual_v_pos.py 2017-12-11 17:05:45.428750967 -0500 +@@ -1,6 +1,7 @@ + import Fast5File + from collections import defaultdict + import pandas ++import sys + import matplotlib.pyplot as plt + + #logging +@@ -42,6 +43,10 @@ + + fast5.close() + ++ if args.saveas is not None: ++ plt.switch_backend('Agg') # Use non-interactive backend in case this is ++ # running on a headless system. ++ + logger.info("Processing data...") + data = [qualpos[e] for e in sorted(qualpos.keys())] + logger.info("Constructing box plot...") +@@ -53,10 +58,10 @@ + if args.saveas is not None: + logger.info("Writing plot to file...") + plot_file = args.saveas +- if plot_file.endswith(".pdf") or plot_file.endswith(".jpg"): ++ if plot_file.endswith(".pdf") or plot_file.endswith(".png") or plot_file.endswith(".svg"): + plt.savefig(plot_file) + else: +- logger.error("Unrecognized extension for %s! Try .pdf or .jpg" % (plot_file)) ++ logger.error("Unrecognized extension for %s! Try .pdf, .png, or .svg" % (plot_file)) + sys.exit() + + else: +diff -Naur poretools-0.6.1.orig/poretools/squiggle.py poretools-0.6.1/poretools/squiggle.py +--- poretools-0.6.1.orig/poretools/squiggle.py 2017-05-31 14:36:46.000000000 -0400 ++++ poretools-0.6.1/poretools/squiggle.py 2017-12-11 17:05:45.428750967 -0500 +@@ -36,6 +36,10 @@ + starts = df.groupby('cat')['start'] + mins, maxs = list(starts.min()), list(starts.max()) + ++ if args.saveas is not None: ++ plt.switch_backend('Agg') # Use non-interactive backend in case this is ++ # running on a headless system. ++ + grid = sns.FacetGrid(df, row="cat", sharex=False, size=8) + #plt.gcf().tight_layout() + grid.fig.suptitle('Squiggle plot for read: ' + filename + "\nTotal time (sec): " + str(total_time)) +diff -Naur poretools-0.6.1.orig/poretools/times.py poretools-0.6.1/poretools/times.py +--- poretools-0.6.1.orig/poretools/times.py 2017-05-31 14:36:46.000000000 -0400 ++++ poretools-0.6.1/poretools/times.py 2017-12-11 17:07:20.845379441 -0500 +@@ -1,5 +1,5 @@ + import Fast5File +-from time import strftime, localtime ++from time import strftime, localtime, gmtime + import sys + + #logging +@@ -28,14 +28,18 @@ + else: + read_length = 0 + +- lt = localtime(start_time) +- print "\t".join([fast5.get_channel_number(), +- fast5.filename, +- str(read_length), +- str(fast5.get_exp_start_time()), +- str(start_time), \ +- str(fast5.get_duration()), +- str(fast5.get_end_time()), ++ if args.utc: ++ lt = gmtime(start_time) ++ else: ++ lt = localtime(start_time) ++ ++ print "\t".join(str(column) for column in [fast5.get_channel_number(), ++ fast5.filename, ++ read_length, ++ fast5.get_exp_start_time(), ++ start_time, \ ++ fast5.get_duration(), ++ fast5.get_end_time(), + strftime('%Y-%m-%dT%H:%M:%S%z', lt), + strftime('%d', lt), + strftime('%H', lt), +diff -Naur poretools-0.6.1.orig/poretools/yield_plot.py poretools-0.6.1/poretools/yield_plot.py +--- poretools-0.6.1.orig/poretools/yield_plot.py 2017-05-31 14:36:46.000000000 -0400 ++++ poretools-0.6.1/poretools/yield_plot.py 2017-12-11 17:05:45.428750967 -0500 +@@ -50,6 +50,9 @@ + if args.theme_bw: + sns.set_style("whitegrid") + ++ if args.saveas is not None: ++ plt.switch_backend('Agg') ++ + # plot + plt.plot(df['start'], df['cumul']) + plt.xlabel('Time (hours)') diff --git a/recipes/progressivemauve/build.sh b/recipes/progressivemauve/build.sh new file mode 100755 index 0000000000000..9994ee61c6ea5 --- /dev/null +++ b/recipes/progressivemauve/build.sh @@ -0,0 +1,3 @@ +#!/bin/bash +mkdir -p "$PREFIX/bin" +cp linux-x64/progressiveMauve "$PREFIX/bin" \ No newline at end of file diff --git a/recipes/progressivemauve/meta.yaml b/recipes/progressivemauve/meta.yaml new file mode 100755 index 0000000000000..4a88c28484852 --- /dev/null +++ b/recipes/progressivemauve/meta.yaml @@ -0,0 +1,23 @@ +{% set version="snapshot_2015-02-13" %} + +package: + name: progressivemauve + version: {{ version|replace("-", "_") }} + +source: + fn: mauve_linux_{{version}}.tar.gz + url: http://darlinglab.org/mauve/snapshots/2015/2015-02-13/linux-x64/mauve_linux_{{version}}.tar.gz + md5: d336b3fa88f275d2d9a891a2bda7b7e8 + +build: + number: 0 + skip: True # [osx] + +test: + commands: + - progressiveMauve &> /dev/null || [[ "$?" == 255 ]] + +about: + home: http://darlinglab.org/mauve/user-guide/progressivemauve.html + license: GNU General Public License version 2.0 (GPLv2) + summary: 'progressiveMauve computes multiple genome alignment with gene gain, loss and rearrangement' \ No newline at end of file diff --git a/recipes/pureclip/meta.yaml b/recipes/pureclip/meta.yaml index 6292e5ac0e44b..dda658494ade3 100644 --- a/recipes/pureclip/meta.yaml +++ b/recipes/pureclip/meta.yaml @@ -1,7 +1,7 @@ {% set name = "PureCLIP" %} -{% set version = "1.0.2" %} -{% set sha256_linux64_static = "cdae3df250fb7e8e29319249787d154d97c6ca7314628f357b8a3f7328da473e" %} -{% set sha256_osx = "1e7a1e24e510299eee3bddc6f177125bab3c6b55461c0b19d3707e2fa0ada46f" %} +{% set version = "1.0.3" %} +{% set sha256_linux64_static = "d0191942e59aea84151b833c8ac20d2f245ce56027955237eb5fcd18a834609f" %} +{% set sha256_osx = "4651a9207c0a4931ee15252ccb6f7e64e1ce50b7763478721c79d9be20c35341" %} package: name: {{ name | lower }} diff --git a/recipes/pybigwig/meta.yaml b/recipes/pybigwig/meta.yaml index 9d47e31215e62..2b5ea6671f0af 100644 --- a/recipes/pybigwig/meta.yaml +++ b/recipes/pybigwig/meta.yaml @@ -1,4 +1,4 @@ -{% set version = "0.3.7" %} +{% set version = "0.3.9" %} package: name: pybigwig @@ -6,8 +6,8 @@ package: source: fn: {{ version }}.tar.gz - url: https://files.pythonhosted.org/packages/0e/d9/ce1a95e10627f25a1e511eae4ef074eba2af5d1e0c36537fa3d957c68535/pyBigWig-0.3.7.tar.gz - sha256: 4f13fba8ec835fc868686e6aad420c8b6f0d3728c0fef19411e4dba8f084e268 + url: https://files.pythonhosted.org/packages/48/f5/972aad9b52ed8b4d3e651d5b766a9aa29c62e7052919970e1b61b40fa9d7/pyBigWig-0.3.9.tar.gz + sha256: 34306213414a8d8974c4ffaac153b3d0a67ce0183514a93aede6c3d33b6f7947 build: number: 0 diff --git a/recipes/python-mailund-newick/build.sh b/recipes/python-mailund-newick/build.sh new file mode 100644 index 0000000000000..64fb95d92b085 --- /dev/null +++ b/recipes/python-mailund-newick/build.sh @@ -0,0 +1,3 @@ +#!/bin/bash + +$PYTHON setup.py install --record=record.txt diff --git a/recipes/python-mailund-newick/meta.yaml b/recipes/python-mailund-newick/meta.yaml new file mode 100644 index 0000000000000..e015505f07881 --- /dev/null +++ b/recipes/python-mailund-newick/meta.yaml @@ -0,0 +1,36 @@ +{% set name = "python-mailund-newick" %} +{% set version = "1.3" %} +package: + name: '{{ name }}' + version: '{{ version }}' + +source: + fn: newick-1.3.tar.gz + url: http://www.daimi.au.dk/~mailund/newick/newick-{{ version }}.tar.gz + sha256: af8cfb4ba53daae59ff727a6c41a291c84cf3ebeedde888706c53d44d4c9f516 + +build: + number: 0 + skip: Yes [py3k] + +requirements: + build: + - python + + run: + - python + +test: + imports: + - newick + - newick.tree + +about: + home: 'http://www.daimi.au.dk/~mailund/newick.html' + license: GNU General Public License v2 + summary: 'Another python module to read and write the Newick format' + license_family: GPL + +extra: + recipe-maintainers: + - nickp60 diff --git a/recipes/python-newick/build.sh b/recipes/python-newick/build.sh new file mode 100644 index 0000000000000..3786386a73c83 --- /dev/null +++ b/recipes/python-newick/build.sh @@ -0,0 +1,3 @@ +#!/bin/bash + +$PYTHON setup.py install --single-version-externally-managed --record=record.txt diff --git a/recipes/python-newick/meta.yaml b/recipes/python-newick/meta.yaml new file mode 100644 index 0000000000000..72ff3dad3ddc3 --- /dev/null +++ b/recipes/python-newick/meta.yaml @@ -0,0 +1,35 @@ +{% set name = "python-newick" %} +{% set version = "0.8.0" %} +package: + name: '{{ name }}' + version: '{{ version }}' + +source: + fn: newick-0.8.0.tar.gz + url: https://pypi.io/packages/source/n/newick/newick-{{ version }}.tar.gz + sha256: 148371c1cce64093b3055e408f1b85576744ebc1085b9fa693e20f54d754b164 + +build: + number: 0 + +requirements: + build: + - python + - setuptools + + run: + - python + +test: + imports: + - newick + +about: + home: 'https://github.com/glottobank/python-newick' + license: Apache License 2.0 + summary: 'A python module to read and write the Newick format' + license_family: Apache + +extra: + recipe-maintainers: + - nickp60 diff --git a/recipes/python-omero/meta.yaml b/recipes/python-omero/meta.yaml index 0f665f1475fec..95ed11deab01f 100644 --- a/recipes/python-omero/meta.yaml +++ b/recipes/python-omero/meta.yaml @@ -1,13 +1,13 @@ -{% set OMERO_VERSION = "5.4.0" %} +{% set OMERO_VERSION = "5.4.1" %} package: name: python-omero version: {{ OMERO_VERSION }} source: - fn: OMERO.py-{{ OMERO_VERSION }}-ice36-b674.zip - url: http://downloads.openmicroscopy.org/omero/{{ OMERO_VERSION }}/artifacts/OMERO.py-{{ OMERO_VERSION }}-ice36-b74.zip - sha1: a17c26a6b027bfdadb487d069b14b4b38bd531c9 + fn: OMERO.py-{{ OMERO_VERSION }}-ice36-b75.zip + url: http://downloads.openmicroscopy.org/omero/{{ OMERO_VERSION }}/artifacts/OMERO.py-{{ OMERO_VERSION }}-ice36-b75.zip + sha1: 9a4237b92e89c362057adac8a51674406a92c810 build: number: 0 diff --git a/recipes/python-omero/setup.py b/recipes/python-omero/setup.py index 9453b84cf9d52..454e402935f76 100644 --- a/recipes/python-omero/setup.py +++ b/recipes/python-omero/setup.py @@ -4,4 +4,4 @@ from os import listdir pyfiles = [f.replace('.py', '') for f in listdir('.') if f.endswith('.py')] -setup(name='OMERO Python', version='5.4.0', description='OME (Open Microscopy Environment) develops open-source software and data format standards for the storage and manipulation of biological light microscopy data.', url='http://www.openmicroscopy.org/', packages=find_packages(), py_modules=pyfiles) +setup(name='OMERO Python', version='5.4.1', description='OME (Open Microscopy Environment) develops open-source software and data format standards for the storage and manipulation of biological light microscopy data.', url='https://www.openmicroscopy.org/', packages=find_packages(), py_modules=pyfiles) diff --git a/recipes/quasitools/build.sh b/recipes/quasitools/build.sh index d3c2cb4ea56ae..3786386a73c83 100644 --- a/recipes/quasitools/build.sh +++ b/recipes/quasitools/build.sh @@ -1,3 +1,3 @@ #!/bin/bash -python setup.py install +$PYTHON setup.py install --single-version-externally-managed --record=record.txt diff --git a/recipes/quasitools/meta.yaml b/recipes/quasitools/meta.yaml index 947e63c2d10cb..0dfadb752bb12 100644 --- a/recipes/quasitools/meta.yaml +++ b/recipes/quasitools/meta.yaml @@ -1,41 +1,45 @@ +{% set version = "0.2.2" %} + package: name: quasitools - version: "0.2.0" + version: {{ version }} source: - fn: quasitools-0.2.0.tar.gz - url: https://github.com/phac-nml/quasitools/archive/v0.2.0.tar.gz - md5: 350a70b8526fe7bad1498b452b2c60d5 + fn: quasitools-{{ version }}.tar.gz + url: https://github.com/phac-nml/quasitools/archive/v{{ version }}.tar.gz + sha256: 03f7c40d9a70baad621f4b172de9ed06848af9a054471f2400da722e3482ce28 build: - # click needs to be patched in order to properly detect unicode in py3k - skip: True # [py3k] + number: 0 + entry_points: + - quasitools = quasitools.cli:cli requirements: build: - python - - scipy - - pysam - - click - - biopython - - samtools ==0.1.19 - - bowtie2 + - setuptools run: - python + - numpy - scipy - - pysam + - samtools >=1.3 + - pysam >=0.8.1 - click - biopython - - samtools ==0.1.19 - bowtie2 test: commands: - # click requires a unicode locale - - LANG=C.UTF-8 quasitools --help + - quasitools --help about: home: https://github.com/phac-nml/quasitools/ license: Apache License, Version 2.0 summary: Quasitools is a collection of tools for analysing Viral Quasispecies + +extra: + container: + # click requires a unicode locale when used with Python 3 + # extended-base generates en_US.UTF-8 locale and sets LC_ALL, LANG properly + extended-base: true # [py3k] diff --git a/recipes/r-gkmsvm/build.sh b/recipes/r-gkmsvm/build.sh new file mode 100644 index 0000000000000..32bc29aa16362 --- /dev/null +++ b/recipes/r-gkmsvm/build.sh @@ -0,0 +1,6 @@ +#!/bin/bash + +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION + +$R CMD INSTALL --build . diff --git a/recipes/r-gkmsvm/meta.yaml b/recipes/r-gkmsvm/meta.yaml new file mode 100644 index 0000000000000..b117ea02b3279 --- /dev/null +++ b/recipes/r-gkmsvm/meta.yaml @@ -0,0 +1,69 @@ +{% set version = '0.71.0' %} + +{% set posix = 'm2-' if win else '' %} +{% set native = 'm2w64-' if win else '' %} + +package: + name: r-gkmsvm + version: {{ version|replace("-", "_") }} + +source: + fn: gkmSVM_{{ version }}.tar.gz + url: + - https://cran.r-project.org/src/contrib/gkmSVM_{{ version }}.tar.gz + - https://cran.r-project.org/src/contrib/Archive/gkmSVM/gkmSVM_{{ version }}.tar.gz + + + sha256: 60825f7e91fae0ab49ce21731dda819da3dcdd34fa02607991a559e16a7ffdfe + +build: + number: 0 + + rpaths: + - lib/R/lib/ + - lib/ + +requirements: + build: + - r-base + - bioconductor-biocgenerics + - bioconductor-biostrings + - bioconductor-genomeinfodb + - bioconductor-genomicranges + - bioconductor-iranges + - r-rocr + - r-rcpp + - bioconductor-s4vectors + - r-kernlab + - bioconductor-rtracklayer + - r-seqinr + - gcc # [not win] + + run: + - r-base + - bioconductor-biocgenerics + - bioconductor-biostrings + - bioconductor-genomeinfodb + - bioconductor-genomicranges + - bioconductor-iranges + - r-rocr + - r-rcpp + - bioconductor-s4vectors + - r-kernlab + - bioconductor-rtracklayer + - r-seqinr + - libgcc # [not win] + +test: + commands: + - $R -e "library('gkmSVM')" # [not win] + - "\"%R%\" -e \"library('gkmSVM')\"" # [win] + +about: + home: https://CRAN.R-project.org/package=gkmSVM + license: GPL (>= 2) + summary: 'Imports the ''gkmSVM'' v2.0 functionalities into R (www.beerlab.org/gkmsvm). It also + uses the ''kernlab'' library (separate R package by different authors) for various + SVM algorithms. ' + + license_family: GPL3 diff --git a/recipes/r-icluster/build.sh b/recipes/r-icluster/build.sh new file mode 100644 index 0000000000000..af6547bf3c22e --- /dev/null +++ b/recipes/r-icluster/build.sh @@ -0,0 +1,2 @@ +#!/bin/bash +$R CMD INSTALL --build . diff --git a/recipes/r-icluster/meta.yaml b/recipes/r-icluster/meta.yaml new file mode 100644 index 0000000000000..4faa8535db48b --- /dev/null +++ b/recipes/r-icluster/meta.yaml @@ -0,0 +1,46 @@ +{% set version = '2.1.0' %} + +package: + name: r-icluster + version: {{ version|replace("-", "_") }} + +source: + fn: iCluster_{{ version }}.tar.gz + url: + - https://cran.r-project.org/src/contrib/iCluster_{{ version }}.tar.gz + - https://cran.r-project.org/src/contrib/Archive/iCluster/iCluster_{{ version }}.tar.gz + sha256: d97cdcba3b53cf10160c333976d2244c2ad5abb8154e194b1568b48376374326 + +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + +requirements: + build: + - r-base + - r-catools + - r-gdata + - r-gplots + - r-gtools + - r-lattice + + run: + - r-base + - r-catools + - r-gdata + - r-gplots + - r-gtools + - r-lattice + +test: + commands: + - $R -e "library('iCluster')" + +about: + home: https://CRAN.R-project.org/package=iCluster + license: GPL (>= 2) + summary: Integrative clustering of multiple genomic data types using a joint latent variable + model. + license_family: GPL3 diff --git a/recipes/r-maldiquant/meta.yaml b/recipes/r-maldiquant/meta.yaml index 2fd205aded535..6d7e00fcea641 100644 --- a/recipes/r-maldiquant/meta.yaml +++ b/recipes/r-maldiquant/meta.yaml @@ -1,4 +1,4 @@ -{% set version = '1.16.4' %} +{% set version = '1.17' %} package: name: r-maldiquant @@ -9,11 +9,10 @@ source: url: - https://cran.r-project.org/src/contrib/MALDIquant_{{ version }}.tar.gz - https://cran.r-project.org/src/contrib/Archive/MALDIquant/MALDIquant_{{ version }}.tar.gz - sha256: 9b910dbd5dd1a739a17a7ee3f83d7e1ebad2fee89fd01a5b274415d2b6d3b0de + sha256: 1ff85f28f57c1088b2434390066c09ffd94a16ad4780ca514783357f0030fa10 build: number: 0 - rpaths: - lib/R/lib/ - lib/ diff --git a/recipes/r-maldirppa/build.sh b/recipes/r-maldirppa/build.sh new file mode 100644 index 0000000000000..b58dbca4d229f --- /dev/null +++ b/recipes/r-maldirppa/build.sh @@ -0,0 +1,4 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +$R CMD INSTALL --build . diff --git a/recipes/r-maldirppa/meta.yaml b/recipes/r-maldirppa/meta.yaml new file mode 100644 index 0000000000000..ebcdf787af5b8 --- /dev/null +++ b/recipes/r-maldirppa/meta.yaml @@ -0,0 +1,46 @@ +{% set version = '1.0.1' %} + +package: + name: r-maldirppa + version: {{ version|replace("-", "_") }} + +source: + fn: MALDIrppa_{{ version }}.tar.gz + url: + - https://cran.r-project.org/src/contrib/MALDIrppa_{{ version }}.tar.gz + - https://cran.r-project.org/src/contrib/Archive/MALDIrppa/MALDIrppa_{{ version }}.tar.gz + sha256: 0ea6f65ef546130e399caac95f37cea5618acabc958eace5ff7be2cd8ac956f8 + +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + +requirements: + build: + - r-base + - r-maldiquant + - r-lattice + - r-robustbase + - r-signal + - r-wmtsa + + run: + - r-base + - r-maldiquant + - r-lattice + - r-robustbase + - r-signal + - r-wmtsa + +test: + commands: + - $R -e "library('MALDIrppa')" + +about: + home: https://CRAN.R-project.org/package=MALDIrppa + license: GPL (>= 2) + summary: Provides methods for quality control and robust pre-processing and analysis of MALDI + mass spectrometry data. + license_family: GPL3 diff --git a/recipes/r-metama/build.sh b/recipes/r-metama/build.sh new file mode 100644 index 0000000000000..ef53d70dd563d --- /dev/null +++ b/recipes/r-metama/build.sh @@ -0,0 +1,8 @@ +#!/bin/bash + +export DISABLE_AUTOBREW=1 + +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +$R CMD INSTALL --build . + diff --git a/recipes/r-metama/meta.yaml b/recipes/r-metama/meta.yaml new file mode 100644 index 0000000000000..7b3b00ccac998 --- /dev/null +++ b/recipes/r-metama/meta.yaml @@ -0,0 +1,41 @@ +{% set version = '3.1.2' %} + +package: + name: r-metama + version: {{ version|replace("-", "_") }} + +source: + fn: metaMA_{{ version }}.tar.gz + url: + - https://cran.r-project.org/src/contrib/metaMA_{{ version }}.tar.gz + - https://cran.r-project.org/src/contrib/Archive/metaMA/metaMA_{{ version }}.tar.gz + sha256: 01851d9632cdf1988d6a43ba44500e51477b9b25d5df1e1da488cd800df85ed6 + +build: + number: 0 + + rpaths: + - lib/R/lib/ + - lib/ + +requirements: + build: + - r-base + - r-smvar + - bioconductor-limma + + run: + - r-base + - r-smvar + - bioconductor-limma + +test: + commands: + - $R -e "library('metaMA')" + +about: + home: https://CRAN.R-project.org/package=metaMA + license: GPL + summary: Combines either p-values or modified effect sizes from different studies to find differentially + expressed genes + license_family: GPL diff --git a/recipes/r-metarnaseq/build.sh b/recipes/r-metarnaseq/build.sh new file mode 100644 index 0000000000000..ef53d70dd563d --- /dev/null +++ b/recipes/r-metarnaseq/build.sh @@ -0,0 +1,8 @@ +#!/bin/bash + +export DISABLE_AUTOBREW=1 + +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +$R CMD INSTALL --build . + diff --git a/recipes/r-metarnaseq/meta.yaml b/recipes/r-metarnaseq/meta.yaml new file mode 100644 index 0000000000000..8ee4b29ac94b1 --- /dev/null +++ b/recipes/r-metarnaseq/meta.yaml @@ -0,0 +1,40 @@ +{% set version = '1.0.2' %} + +package: + name: r-metarnaseq + version: {{ version|replace("-", "_") }} + +source: + fn: metaRNASeq_{{ version }}.tar.gz + url: + - https://cran.r-project.org/src/contrib/metaRNASeq_{{ version }}.tar.gz + - https://cran.r-project.org/src/contrib/Archive/metaRNASeq/metaRNASeq_{{ version }}.tar.gz + sha256: 0affd7f4eb25635b2410110f381809b751655a7f3709f2bc1183e0eb8f6be7f7 + +build: + number: 0 + + rpaths: + - lib/R/lib/ + - lib/ + +requirements: + build: + - r-base + + run: + - r-base + +test: + commands: + - $R -e "library('metaRNASeq')" + +about: + home: https://CRAN.R-project.org/package=metaRNASeq + license: GPL + summary: Implementation of two p-value combination techniques (inverse normal and Fisher methods). + A vignette is provided to explain how to perform a meta-analysis from two independent + RNA-seq experiments. + license_family: GPL + + diff --git a/recipes/r-mixomics/meta.yaml b/recipes/r-mixomics/meta.yaml index cec673fbde4a1..9c0089a62cefe 100644 --- a/recipes/r-mixomics/meta.yaml +++ b/recipes/r-mixomics/meta.yaml @@ -1,4 +1,4 @@ -{% set version = '6.2.0' %} +{% set version = '6.3.1' %} package: name: r-mixomics @@ -9,7 +9,7 @@ source: url: - https://cran.r-project.org/src/contrib/mixOmics_{{ version }}.tar.gz - https://cran.r-project.org/src/contrib/Archive/mixOmics/mixOmics_{{ version }}.tar.gz - sha256: 96b240d0df267a5d6b0ab14ec131c8c8de4571de48a372754a9b79dabb36f5ed + sha256: 1883f0c60e4f0dfa0beb62a9b0f377624cc310efef1646b9c4ba57927a5f742f build: number: 0 @@ -27,9 +27,12 @@ requirements: - r-dplyr - r-ellipse - r-ggplot2 + - r-gridextra - r-igraph - r-lattice + - r-matrixstats - r-plyr + - r-rarpack - r-reshape2 - r-rgl - r-tidyr @@ -45,9 +48,12 @@ requirements: - r-dplyr - r-ellipse - r-ggplot2 + - r-gridextra - r-igraph - r-lattice + - r-matrixstats - r-plyr + - r-rarpack - r-reshape2 - r-rgl - r-tidyr diff --git a/recipes/r-mmgenome/meta.yaml b/recipes/r-mmgenome/meta.yaml index e2c0fc6124b49..9abd6ae9cd78d 100644 --- a/recipes/r-mmgenome/meta.yaml +++ b/recipes/r-mmgenome/meta.yaml @@ -1,5 +1,5 @@ {% set name = "r-mmgenome" %} -{% set version = "0.6.3" %} +{% set version = "0.7.1" %} package: name: {{ name|lower }} @@ -7,13 +7,11 @@ package: source: fn: {{ name|lower }}_{{ version }}.tar.gz - url: https://github.com/MadsAlbertsen/mmgenome/archive/a7e3e7bc5f7c0b36a1403c4cca2628e9a46a0297.tar.gz - md5: 9475010aa10503678d7548d5355fbbc8 + url: https://github.com/MadsAlbertsen/mmgenome/archive/6a673e2f62b52079998d801506d6fb65ebb2ff10.tar.gz + md5: ae6d9430b08bb7e4a6448d24e19c5d19 build: number: 0 - - # This is required to make R link correctly on Linux. rpaths: - lib/R/lib/ - lib/ @@ -50,4 +48,4 @@ test: about: home: https://github.com/MadsAlbertsen/mmgenome license: AGPL-3 - summary: 'Tools for extracting individual genomes from metagneomes' + summary: 'Tools for extracting individual genomes from metagenomes' diff --git a/recipes/r-mutationalpatterns/build.sh b/recipes/r-mutationalpatterns/build.sh deleted file mode 100644 index 3f87d1b1125fc..0000000000000 --- a/recipes/r-mutationalpatterns/build.sh +++ /dev/null @@ -1,16 +0,0 @@ -#!/bin/bash - -# 3.3.0 not strictly required but earlier versions not tested -# Swap out strict requirements to allow builds and tests -sed -i.bak 's/R (>= 3.3.0)/R (>= 3.2.2)/' DESCRIPTION -sed -i.bak 's/GenomicRanges (>= 1.24.0)/GenomicRanges (>= 1.22.4)/' DESCRIPTION -sed -i.bak 's/IRanges (>= 2.6.0)/IRanges (>= 2.4.8)/' DESCRIPTION -sed -i.bak 's/Biostrings (>= 2.40.0)/Biostrings (>= 2.38.4)/' DESCRIPTION -sed -i.bak 's/GenomeInfoDb (>= 1.8.1)/GenomeInfoDb (>= 1.6.3)/' DESCRIPTION -sed -i.bak 's/SummarizedExperiment (>= 1.2.2)/SummarizedExperiment (>= 1.0.2)/' DESCRIPTION -sed -i.bak 's/VariantAnnotation (>= 1.18.1)/VariantAnnotation (>= 1.16.4)/' DESCRIPTION -sed -i.bak 's/gridExtra (>= 2.2.1)/gridExtra (>= 2.0.0)/' DESCRIPTION -sed -i.bak 's/ggplot2 (>= 2.1.0)/ggplot2 (>= 1.0.1)/' DESCRIPTION -#sed -i.bak 's///' DESCRIPTION - -$R CMD INSTALL --build . diff --git a/recipes/r-mutationalpatterns/meta.yaml b/recipes/r-mutationalpatterns/meta.yaml deleted file mode 100644 index 28bf73c12da9e..0000000000000 --- a/recipes/r-mutationalpatterns/meta.yaml +++ /dev/null @@ -1,50 +0,0 @@ -package: - name: r-mutationalpatterns - version: 0.2b -source: - fn: MutationalPatterns-v0.2-beta.tar.gz - url: https://github.com/CuppenResearch/MutationalPatterns/archive/v0.2-beta.tar.gz -build: - number: 0 - rpaths: - - lib/R/lib/ - - lib/ -requirements: - build: - - r-base - - bioconductor-biostrings - - bioconductor-bsgenome - - bioconductor-genomicranges - - bioconductor-genomeinfodb - - bioconductor-iranges - - bioconductor-summarizedexperiment - - bioconductor-variantannotation - - r-ggplot2 - - r-gridextra - - r-plyr - - r-pracma - - r-nmf - - r-reshape2 - run: - - r-base - - bioconductor-biostrings - - bioconductor-bsgenome - - bioconductor-genomicranges - - bioconductor-genomeinfodb - - bioconductor-iranges - - bioconductor-summarizedexperiment - - bioconductor-variantannotation - - r-ggplot2 - - r-gridextra - - r-plyr - - r-pracma - - r-nmf - - r-reshape2 - -test: - commands: - - '$R -e "library(''MutationalPatterns'')"' -about: - home: https://github.com/CuppenResearch/MutationalPatterns - license: MIT - summary: R package for extracting and visualizing mutational patterns in base substitution catalogues diff --git a/recipes/r-purbayes/build.sh b/recipes/r-purbayes/build.sh new file mode 100644 index 0000000000000..af6547bf3c22e --- /dev/null +++ b/recipes/r-purbayes/build.sh @@ -0,0 +1,2 @@ +#!/bin/bash +$R CMD INSTALL --build . diff --git a/recipes/r-purbayes/meta.yaml b/recipes/r-purbayes/meta.yaml new file mode 100644 index 0000000000000..316ae9a84699d --- /dev/null +++ b/recipes/r-purbayes/meta.yaml @@ -0,0 +1,43 @@ +{% set version = '1.3' %} + +{% set posix = 'm2-' if win else '' %} +{% set native = 'm2w64-' if win else '' %} + +package: + name: r-purbayes + version: {{ version|replace("-", "_") }} + +source: + fn: PurBayes_{{ version }}.tar.gz + url: + - https://cran.r-project.org/src/contrib/PurBayes_{{ version }}.tar.gz + - https://cran.r-project.org/src/contrib/Archive/PurBayes/PurBayes_{{ version }}.tar.gz + sha256: 1097eefd636ba2a71cb9b31917d75e5841cd0ccad44fb9e4e27c399e3d237559 + +build: + number: 0 + skip: true # [win32] + + rpaths: + - lib/R/lib/ + - lib/ +requirements: + build: + - r-base + - r-rjags + + run: + - r-base + - r-rjags + +test: + commands: + - $R -e "library('PurBayes')" # [not win] + - "\"%R%\" -e \"library('PurBayes')\"" # [win] + +about: + home: https://CRAN.R-project.org/package=PurBayes + license: GPL-2 + summary: PurBayes is an MCMC-based algorithm that uses next-generation sequencing data to estimate + tumor purity and clonality for paired tumor-normal data. + license_family: GPL2 diff --git a/recipes/r-sartools/meta.yaml b/recipes/r-sartools/meta.yaml index 913e23cf9755a..71954a1975897 100644 --- a/recipes/r-sartools/meta.yaml +++ b/recipes/r-sartools/meta.yaml @@ -1,5 +1,5 @@ {% set name = "r-sartools" %} -{% set version = "1.5.1" %} +{% set version = "1.6.0" %} package: name: {{ name|lower }} @@ -8,7 +8,7 @@ package: source: fn: v{{ version }}.tar.gz url: https://github.com/PF2-pasteur-fr/SARTools/archive/v{{ version }}.tar.gz - sha256: e35df9c200e3fbdde43c340a5c5426715e891cd6424e4d4ebe8201d4afb23035 + sha256: 49ee7f1e1ac035bca7cb521a564e283f0f146742d22558a22fb9313923f188a4 build: # number: 0 @@ -23,13 +23,17 @@ requirements: - bioconductor-deseq2 - bioconductor-edger - r-rmarkdown + - r-bit64 + - r-blob run: - - r-base + - r-base >=3.3.0 - r-knitr - - bioconductor-deseq2 - - bioconductor-edger - - r-rmarkdown + - bioconductor-deseq2 >=1.12.0 + - bioconductor-edger >=3.12.0 + - r-rmarkdown >=1.4 + - r-bit64 + - r-blob - bioconductor-summarizedexperiment >=1.6 test: diff --git a/recipes/r-smvar/build.sh b/recipes/r-smvar/build.sh new file mode 100644 index 0000000000000..ef53d70dd563d --- /dev/null +++ b/recipes/r-smvar/build.sh @@ -0,0 +1,8 @@ +#!/bin/bash + +export DISABLE_AUTOBREW=1 + +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +$R CMD INSTALL --build . + diff --git a/recipes/r-smvar/meta.yaml b/recipes/r-smvar/meta.yaml new file mode 100644 index 0000000000000..54741117935cf --- /dev/null +++ b/recipes/r-smvar/meta.yaml @@ -0,0 +1,39 @@ +{% set version = '1.3.3' %} + +package: + name: r-smvar + version: {{ version|replace("-", "_") }} + +source: + fn: SMVar_{{ version }}.tar.gz + url: + - https://cran.r-project.org/src/contrib/SMVar_{{ version }}.tar.gz + - https://cran.r-project.org/src/contrib/Archive/SMVar/SMVar_{{ version }}.tar.gz + sha256: 17625e89eb8be7a6dbb77e6bd9daca1ea1acff69026049f213e30edf2325999f + +build: + number: 0 + + rpaths: + - lib/R/lib/ + - lib/ + + +requirements: + build: + - r-base + + run: + - r-base + +test: + commands: + - $R -e "library('SMVar')" + +about: + home: https://CRAN.R-project.org/package=SMVar + license: GPL + summary: Implements the structural model for variances in order to detect differentially expressed + genes from gene expression data + license_family: GPL + diff --git a/recipes/ragout/build.sh b/recipes/ragout/build.sh new file mode 100644 index 0000000000000..f9eec25491c24 --- /dev/null +++ b/recipes/ragout/build.sh @@ -0,0 +1,8 @@ +#!/bin/bash +# creates executables in ./lib/ : ragout-maf2synteny ragout-overlap +make + +cp ragout.py $PREFIX/bin/ +cp -r ragout $PREFIX/bin/ +# copy executables created in ./lib/ to $PREFIX/bin so ragout can find them +cp -r ./lib/ragout-* $PREFIX/bin/ diff --git a/recipes/ragout/meta.yaml b/recipes/ragout/meta.yaml new file mode 100644 index 0000000000000..2cdde2c42a059 --- /dev/null +++ b/recipes/ragout/meta.yaml @@ -0,0 +1,31 @@ +about: + home: https://github.com/fenderglass/Ragout + license: GPLv3 + summary: "Ragout (Reference-Assisted Genome Ordering UTility) is a tool for chromosome assembly using multiple references" +build: + number: 2 + skip: True # [py3k] + +package: + name: ragout + version: 2.0 +source: + fn: ragout_2.0.tar.gz + url: https://github.com/fenderglass/Ragout/archive/2.0.tar.gz + sha256: 85d57ab050572332eb5879e4ac98acf50c0de373b1a1a01876e60b6e222f1486 +requirements: + build: + - gcc # [not osx] + - llvm # [osx] + - cmake + - python + run: + - libgcc # [not osx] + - python + - networkx ==1.8 + - python-mailund-newick + - sibelia +test: + commands: + - ragout.py -h + - Sibelia --version diff --git a/recipes/rambo-k/build.sh b/recipes/rambo-k/build.sh new file mode 100755 index 0000000000000..c5aefbcf7cd7d --- /dev/null +++ b/recipes/rambo-k/build.sh @@ -0,0 +1,4 @@ +mkdir -p $PREFIX/bin +cp *.py *.jar $PREFIX/bin + + diff --git a/recipes/rambo-k/meta.yaml b/recipes/rambo-k/meta.yaml new file mode 100755 index 0000000000000..2e8d50323802c --- /dev/null +++ b/recipes/rambo-k/meta.yaml @@ -0,0 +1,28 @@ +package: + name: rambo-k + version: "1.21" + +source: + url: https://gitlab.com/SimonHTausch/RAMBO-K/uploads/4a3322dc19285433fc43cdb06cbd9a9d/RAMBO-K-v1.21-303bc3d213aa6333be42d2a1e7f2628b792e61cc.zip + md5: 883d92d0f61182cd2aa6e668b0e54565 + +requirements: + run: + - python + - argparse + - numpy + - matplotlib + - scikit-learn + - openjdk + +test: + commands: + - RAMBOK.py -h + - java -jar $PREFIX/bin/classifier.jar -h + - java -jar $PREFIX/bin/trainer.jar -h + +about: + home: https://gitlab.com/SimonHTausch/RAMBO-K + license: GNU Lesser General Public License v3.0 + license_file: License.txt + summary: a reference-based tool for rapid and sensitive extraction of one organism´s reads from a mixed NGS dataset diff --git a/recipes/raxml/8.2.4/build.sh b/recipes/raxml/8.2.4/build.sh new file mode 100644 index 0000000000000..d052e574847a4 --- /dev/null +++ b/recipes/raxml/8.2.4/build.sh @@ -0,0 +1,20 @@ +#!/bin/bash + +make -f Makefile.PTHREADS.gcc +make -f Makefile.gcc + +make -f Makefile.SSE3.gcc +make -f Makefile.SSE3.PTHREADS.gcc + +make -f Makefile.AVX2.gcc +make -f Makefile.AVX2.PTHREADS.gcc + +mkdir -p $PREFIX/bin + +cp raxmlHPC-PTHREADS $PREFIX/bin +cp raxmlHPC $PREFIX/bin +cp raxmlHPC-PTHREADS-SSE3 $PREFIX/bin +cp raxmlHPC-SSE3 $PREFIX/bin +cp raxmlHPC-PTHREADS-AVX2 $PREFIX/bin +cp raxmlHPC-AVX2 $PREFIX/bin + diff --git a/recipes/raxml/8.2.4/meta.yaml b/recipes/raxml/8.2.4/meta.yaml new file mode 100644 index 0000000000000..7e2c07b6825ec --- /dev/null +++ b/recipes/raxml/8.2.4/meta.yaml @@ -0,0 +1,33 @@ +package: + name: raxml + version: "8.2.4" + +build: + number: 1 + +source: + fn: raxml_v8.2.4.tar.gz + url: https://github.com/stamatak/standard-RAxML/archive/v8.2.4.tar.gz + sha256: e9fa4b3fe790094d832a640edc2b448890237dca0012d509d95be4cd4ef3d83b + +requirements: + build: + - gcc # [not osx] + - llvm # [osx] + + run: + - libgcc # [not osx] + +test: + commands: + - raxmlHPC -h + - raxmlHPC-PTHREADS -h + - raxmlHPC-SSE3 -h + - raxmlHPC-PTHREADS-SSE3 -h + - raxmlHPC-AVX2 -h + - raxmlHPC-PTHREADS-AVX2 -h + +about: + home: http://sco.h-its.org/exelixis/web/software/raxml/index.html + license: GPL + summary: Phylogenetics - Randomized Axelerated Maximum Likelihood. diff --git a/recipes/reaper/build.sh b/recipes/reaper/build.sh new file mode 100644 index 0000000000000..d20117f1f0108 --- /dev/null +++ b/recipes/reaper/build.sh @@ -0,0 +1,6 @@ +#!/bin/bash + +cd src +make +mkdir -p $PREFIX/bin +cp minion reaper swan tally $PREFIX/bin diff --git a/recipes/reaper/meta.yaml b/recipes/reaper/meta.yaml new file mode 100644 index 0000000000000..52d0ead6f76b1 --- /dev/null +++ b/recipes/reaper/meta.yaml @@ -0,0 +1,31 @@ +{% set version = "16-098" %} + +package: + name: reaper + version: {{ version|replace("-", ".") }} + +build: + number: 0 + +source: + fn: reaper-{{ version }}.tgz + url: https://www.ebi.ac.uk/~stijn/reaper/src/reaper-{{ version }}.tgz + sha256: 1d9263a68f682d37c78b2754d91c47aa44f45e3f0e4cc0ee4bc808616c51ff38 + +requirements: + build: + - gcc # [not osx] + - llvm # [osx] + - zlib {{CONDA_ZLIB}}* + run: + - libgcc # [not osx] + - zlib {{CONDA_ZLIB}}* + +test: + commands: + - reaper -h 2>&1 | grep "five prime sequence insert" + +about: + home: https://www.ebi.ac.uk/~stijn/reaper/reaper.html + license: GPL3 + summary: Tool for demultiplexing, trimming and filtering sequencing data. diff --git a/recipes/repeatmodeler/RepModelConfig.pm b/recipes/repeatmodeler/RepModelConfig.pm old mode 100755 new mode 100644 index a81a75696d7a8..f919470074303 --- a/recipes/repeatmodeler/RepModelConfig.pm +++ b/recipes/repeatmodeler/RepModelConfig.pm @@ -28,7 +28,12 @@ require Exporter; $REPEATMODELER_LIB_DIR $REPEATMASKER_DIR $REPEATMASKER_LIB $WUBLAST_DIR $WUBLASTN_PRGM $WUBLASTP_PRGM $WUBLASTX_PRGM $XDFORMAT_PRGM $XDGET_PRGM - $RECON_DIR $TRF_PRGM $RSCOUT_DIR $DEBUGALL ); + $RECON_DIR $TRF_PRGM $RSCOUT_DIR $DEBUGALL + $RMBLAST_DIR $RMBLASTN_PRGM $NCBIBLASTP_PRGM + $NCBIBLASTX_PRGM $NCBIBLASTDB_PRGM $NCBIDBALIAS_PRGM + $NCBIDBCMD_PRGM $NSEG_PRGM +); + %EXPORT_TAGS = ( all => [ @EXPORT_OK ] ); @ISA = qw(Exporter); @@ -101,6 +106,12 @@ BEGIN ## $TRF_PRGM = $ENV{'TRF_DIR'}; +## +## NSEG Location +## ============= +## Location of the NCBI nseg program + $NSEG_PRGM = $ENV{'NSEG_DIR'}; + ## ## RepeatScout Location ## ==================== diff --git a/recipes/repeatmodeler/abs_path.patch b/recipes/repeatmodeler/abs_path.patch deleted file mode 100644 index b77f289cab39e..0000000000000 --- a/recipes/repeatmodeler/abs_path.patch +++ /dev/null @@ -1,11 +0,0 @@ ---- RepeatModeler 2017-02-16 13:37:32.000000000 -0500 -+++ RepeatModeler.patched 2017-02-16 14:16:51.000000000 -0500 -@@ -117,7 +117,7 @@ - use File::Spec; - use File::Path; - use File::Basename; --use Cwd; -+use Cwd qw(abs_path getcwd); - use Data::Dumper; - - # RepeatModeler Libraries diff --git a/recipes/repeatmodeler/build.sh b/recipes/repeatmodeler/build.sh index e2791936b029c..e75a4af036097 100644 --- a/recipes/repeatmodeler/build.sh +++ b/recipes/repeatmodeler/build.sh @@ -21,7 +21,8 @@ TRF_DIR=${PREFIX}/bin RMBLAST_DIR=${PREFIX}/bin RECON_DIR=${PREFIX}/bin RSCOUT_DIR=${PREFIX}/bin -export REPEATMODELER_DIR REPEATMASKER_DIR TRF_DIR RMBLAST_DIR RECON_DIR RSCOUT_DIR +NSEG_DIR=${PREFIX}/bin +export REPEATMODELER_DIR REPEATMASKER_DIR TRF_DIR RMBLAST_DIR RECON_DIR RSCOUT_DIR NSEG_DIR NAME=\$(basename \$0) perl ${RM_DIR}/\${NAME} \$@ END diff --git a/recipes/repeatmodeler/meta.yaml b/recipes/repeatmodeler/meta.yaml index 70da0f53c5285..ce36c08b715dc 100644 --- a/recipes/repeatmodeler/meta.yaml +++ b/recipes/repeatmodeler/meta.yaml @@ -3,17 +3,23 @@ about: license: 'Open Software License v2.1' summary: 'RepeatModeler is a de-novo repeat family identification and modeling package.' +source: + fn: RepeatModeler-open-1.0.11.tar.gz + url: 'http://www.repeatmasker.org/RepeatModeler/RepeatModeler-open-1.0.11.tar.gz' + md5: c148b4b56bb3fbd4e9ba88ac8736baa3 + build: - number: 1 + number: 0 skip: True #[osx] package: name: repeatmodeler - version: '1.0.8' + version: '1.0.11' requirements: build: - perl + - rmblast run: - perl - repeatmasker @@ -21,12 +27,9 @@ requirements: - trf - repeatscout - recon + - perl-text-soundex + -source: - fn: RepeatModeler-open-1-0-8.tar.gz - url: 'http://www.repeatmasker.org/RepeatModeler-open-1-0-8.tar.gz' - patches: - - abs_path.patch test: commands: diff --git a/recipes/repenrich/build.sh b/recipes/repenrich/build.sh new file mode 100644 index 0000000000000..ff88ccaf879be --- /dev/null +++ b/recipes/repenrich/build.sh @@ -0,0 +1,4 @@ +#!/bin/bash + +cp RepEnrich.py $PREFIX/bin +cp RepEnrich_setup.py $PREFIX/bin diff --git a/recipes/repenrich/meta.yaml b/recipes/repenrich/meta.yaml new file mode 100644 index 0000000000000..e9a14f3e3c5ae --- /dev/null +++ b/recipes/repenrich/meta.yaml @@ -0,0 +1,39 @@ +package: + name: repenrich + version: '1.2' + +source: + fn: v1.2.tar.gz + url: https://github.com/nskvir/RepEnrich/archive/v1.2.tar.gz + md5: eee131621f8f65a5503b4b876ae534a5 + patches: + - paths.patch + +build: + number: 0 + skip: True # [py3k] + +requirements: + build: + - python + - bowtie + - bedtools <2.24.0 + - samtools + - biopython + + run: + - python + - bowtie + - bedtools <2.24.0 + - samtools + - biopython + +test: + commands: + - RepEnrich.py -h + - RepEnrich_setup.py -h + +about: + home: https://github.com/nskvir/RepEnrich + license: Custom OSS + summary: 'RepEnrich is a method to estimate repetitive element enrichment using high-throughput sequencing data.' diff --git a/recipes/repenrich/paths.patch b/recipes/repenrich/paths.patch new file mode 100644 index 0000000000000..87289460f78b6 --- /dev/null +++ b/recipes/repenrich/paths.patch @@ -0,0 +1,23 @@ +--- RepEnrich-1.2/RepEnrich.py 2015-07-23 17:47:18.000000000 +0000 ++++ RepEnrich-1.2/RepEnrich.py.new 2017-12-12 03:52:26.540367029 +0000 +@@ -1,4 +1,4 @@ +-#!/usr/bin/env python ++#!/opt/anaconda1anaconda2anaconda3/bin/python + import argparse + import csv + import numpy +@@ -384,4 +384,4 @@ + if os.path.exists(outputfolder + os.path.sep + 'sorted_bowtie'): + shutil.rmtree(outputfolder + os.path.sep + 'sorted_bowtie') + +-print "... Done" +\ No newline at end of file ++print "... Done" +--- RepEnrich-1.2/RepEnrich_setup.py 2015-07-23 17:47:18.000000000 +0000 ++++ RepEnrich-1.2/RepEnrich_setup.py.new 2017-12-12 03:52:58.747633551 +0000 +@@ -1,4 +1,4 @@ +-#!/usr/bin/env python ++#!/opt/anaconda1anaconda2anaconda3/bin/python + import argparse + import csv + import os diff --git a/recipes/ribocode/meta.yaml b/recipes/ribocode/meta.yaml index 87c840b311998..06c1c1f91b289 100644 --- a/recipes/ribocode/meta.yaml +++ b/recipes/ribocode/meta.yaml @@ -1,11 +1,11 @@ package: name: ribocode - version: 1.2.6 + version: 1.2.7 source: - fn: RiboCode-1.2.6.tar.gz - url: https://pypi.python.org/packages/c6/4b/902412b7c9683bcb9096e9359d17c6c0538b084a0c3167603ed69278aeb6/RiboCode-1.2.6.tar.gz - md5: e05ef843da351c4588e02bad3d5c3d65 + fn: RiboCode-1.2.7.tar.gz + url: https://pypi.python.org/packages/65/4c/9d6ca41db7d55f97736d9c7065ee50baae61e1ec9cebf87c1be1025d1743/RiboCode-1.2.7.tar.gz + md5: f97a70888e9c07f1c4ea96fbea1b98fe requirements: build: @@ -43,6 +43,7 @@ build: - metaplots=RiboCode.metaplots:main - plot_orf_density=RiboCode.plot_orf_density:main - ORFcount=RiboCode.RPF_count_ORF:main + - GTFupdate=RiboCode.GTF_update:main script: python setup.py install diff --git a/recipes/rmblast/meta.yaml b/recipes/rmblast/meta.yaml index 541629c08cd61..96929bb473373 100644 --- a/recipes/rmblast/meta.yaml +++ b/recipes/rmblast/meta.yaml @@ -10,19 +10,19 @@ source: md5: 421c5ddf2c425800d934562c965e8706 # [osx] build: - number: 1 + number: 2 requirements: build: - - boost <=1.58 # [linux] - - gcc # [linux] - - bzip2 1.0.6 1 # [linux] - - zlib # [linux] + - boost <=1.58 # [linux] + - gcc # [linux] + - bzip2 {{ CONDA_BZIP2 }}* # [linux] + - zlib {{CONDA_ZLIB}}* # [linux] run: - - boost <=1.58 # [linux] - - libgcc # [linux] - - bzip2 1.0.6 1 # [linux] - - zlib # [linux] + - boost <=1.58 # [linux] + - libgcc # [linux] + - bzip2 {{ CONDA_BZIP2 }}* # [linux] + - zlib {{CONDA_ZLIB}}* # [linux] - blast test: @@ -34,3 +34,7 @@ about: home: http://www.repeatmasker.org/RMBlast.html license: OSL-2.1 summary: RMBlast is a RepeatMasker compatible version of the standard NCBI BLAST suite. + +extra: + skip-lints: + - boost_not_pinned diff --git a/recipes/rsem/meta.yaml b/recipes/rsem/meta.yaml index 0890678fec928..7e79614b2d4f6 100644 --- a/recipes/rsem/meta.yaml +++ b/recipes/rsem/meta.yaml @@ -1,6 +1,6 @@ {% set name = "rsem" %} {% set version = "1.3.0" %} -{% set sha256 = "a6776aae25a690375504974d65e8554d6e3ddab93cef5b82969064854d22c09f" %} +{% set sha256 = "ecfbb79c23973e1c4134f05201f4bd89b0caf0ce4ae1ffd7c4ddc329ed4e05d2" %} about: home: https://deweylab.github.io/RSEM/ @@ -15,7 +15,7 @@ build: rpaths: - lib/R/lib/ - lib/ - number: 1 + number: 2 skip: False string: boost{{CONDA_BOOST}}_{{PKG_BUILDNUM}} @@ -27,7 +27,7 @@ requirements: - perl - perl-module-build - r-base - - zlib + - zlib {{ CONDA_ZLIB }}* run: - bioconductor-biobase - bioconductor-ebseq @@ -37,13 +37,13 @@ requirements: - perl-module-build - r-base - samtools 1.3 - - zlib + - zlib {{ CONDA_ZLIB }}* test: commands: - rsem-prepare-reference 2>&1 | grep reference_name > /dev/null - rsem-for-ebseq-find-DE 2>&1 | grep Usage > /dev/null - - rsem-bam2wig foo bar foobar 2>&1 | grep 'fail to open file' > /dev/null + - rsem-bam2wig foo bar foobar 2>&1 | grep "fail to open file" > /dev/null - which rsem-for-ebseq-calculate-clustering-info source: diff --git a/recipes/rust-bio-tools/meta.yaml b/recipes/rust-bio-tools/meta.yaml index 6586012b5aeda..af7caa917ef06 100644 --- a/recipes/rust-bio-tools/meta.yaml +++ b/recipes/rust-bio-tools/meta.yaml @@ -1,4 +1,4 @@ -{% set version = "0.1.2" %} +{% set version = "0.1.3" %} package: name: rust-bio-tools @@ -6,20 +6,20 @@ package: build: number: 0 - skip: True # [osx] + skip: true # [osx] source: fn: rust-bio-tools-{{version}}.tar.gz url: https://github.com/rust-bio/rust-bio-tools/archive/v{{version}}.tar.gz - md5: a85bceaa2aaed28b05d6faef78b8ca2b + sha256: 8038ccfb26c1ae0e10f84bd09a8ec0313e8da1a8b1b097f2519b0c19cf00c0f4 requirements: build: - rust - - gcc - - zlib + - gcc <4.8.5 + - zlib {{ CONDA_ZLIB }}* run: - - zlib + - zlib {{ CONDA_ZLIB }}* - libgcc test: diff --git a/recipes/salmon/build.sh b/recipes/salmon/build.sh index df7a284de6256..88d86536e45d0 100644 --- a/recipes/salmon/build.sh +++ b/recipes/salmon/build.sh @@ -1,6 +1,13 @@ #!/bin/bash set -eu -o pipefail +if [[ "$(uname)" == Darwin ]]; then + export CC=clang + export CXX=clang++ + export CXXFLAGS="${CXXFLAGS} -I${PREFIX}/include/c++/v1" + export LDFLAGS="${LDFLAGS} -L${PREFIX}/lib -Wl,-rpath,${PREFIX}/lib" +fi + mkdir -p $PREFIX/bin mkdir -p $PREFIX/lib diff --git a/recipes/salmon/meta.yaml b/recipes/salmon/meta.yaml index 456015edb0ff0..2bf5581c82a37 100644 --- a/recipes/salmon/meta.yaml +++ b/recipes/salmon/meta.yaml @@ -1,6 +1,8 @@ -{% set version="0.8.2" %} +{% set version="0.9.1" %} +{% set llvm_version = "4.0.0" %} + build: - number: 1 + number: 0 # OSX failing due to libary issues even though shipping with Salmon binary # dyld: Library not loaded: /usr/local/opt/tbb/lib/libtbbmalloc_proxy.dylib # https://travis-ci.org/bioconda/bioconda-recipes/jobs/211785820#L295 @@ -18,29 +20,32 @@ package: source: fn: Salmon-{{ version }}_src.tar.gz url: https://github.com/COMBINE-lab/salmon/archive/v{{ version }}.tar.gz - md5: ee512697bc44b13661a16d4e14cf0a00 + md5: 1277b8ed65d2c6982ed176a496a2a1e3 requirements: build: - llvm # [osx] + - clangdev =={{ llvm_version }} # [osx] + - libcxx =={{ llvm_version }} # [osx] - gcc ==4.8.5 # [linux] - autoconf 2.69 pl5.* - - boost ==1.63.0 + - boost {{CONDA_BOOST}}* - icu 58.* - cmake - - zlib - - bzip2 + - zlib {{CONDA_ZLIB}}* + - bzip2 {{CONDA_BZIP2}}* - unzip - jemalloc ==4.5.0 - tbb run: - libgcc # [linux] - - boost ==1.63.0 + - libcxx =={{ llvm_version }} # [osx] + - boost {{CONDA_BOOST}}* - icu 58.* - jemalloc ==4.5.0 - tbb - - zlib - - bzip2 + - zlib {{CONDA_ZLIB}}* + - bzip2 {{CONDA_BZIP2}}* test: commands: diff --git a/recipes/salmon/salmonv0.9.0.osx.patch b/recipes/salmon/salmonv0.9.0.osx.patch new file mode 100644 index 0000000000000..ba57ca0c4b497 --- /dev/null +++ b/recipes/salmon/salmonv0.9.0.osx.patch @@ -0,0 +1,28 @@ +From 33d12908513f927d8e8edf0fd0523009b558b4a9 Mon Sep 17 00:00:00 2001 +From: rob-p +Date: Thu, 23 Nov 2017 22:15:28 -0500 +Subject: [PATCH 1/1] pre AppleClang 8 patch + +Signed-off-by: rob-p +--- + include/FastxParserThreadUtils.hpp | 4 ++-- + 1 file changed, 2 insertions(+), 2 deletions(-) + +diff --git a/include/FastxParserThreadUtils.hpp b/include/FastxParserThreadUtils.hpp +index 7c1273a..234fd55 100644 +--- a/include/FastxParserThreadUtils.hpp ++++ b/include/FastxParserThreadUtils.hpp +@@ -27,8 +27,8 @@ ALWAYS_INLINE void yieldSleep() { + } + + ALWAYS_INLINE void backoffExp(size_t& curMaxIters) { +- thread_local std::uniform_int_distribution dist; +- thread_local std::minstd_rand gen(std::random_device{}()); ++ std::uniform_int_distribution dist; ++ std::minstd_rand gen(std::random_device{}()); + const size_t spinIters = + dist(gen, decltype(dist)::param_type{0, curMaxIters}); + curMaxIters = std::min(2 * curMaxIters, MAX_BACKOFF_ITERS); +-- +2.13.6 (Apple Git-96) + diff --git a/recipes/samtools/0.1.12/build.sh b/recipes/samtools/0.1.12/build.sh index 0b79b06f1f9f0..893536e5b2ef0 100644 --- a/recipes/samtools/0.1.12/build.sh +++ b/recipes/samtools/0.1.12/build.sh @@ -10,3 +10,8 @@ mkdir -p $PREFIX/bin mv samtools $PREFIX/bin mkdir -p $PREFIX/lib mv libbam.a $PREFIX/lib +mkdir -p $PREFIX/include/bam +mv *.c *.o *.h *.1 $PREFIX/include/bam/ +mv bcftools/bcftools bcftools/vcfutils.pl bcftools/bcf-fix.pl $PREFIX/bin +make -C misc maq2sam-short maq2sam-long wgsim +mv misc/maq2sam-short misc/maq2sam-long misc/wgsim $PREFIX/bin \ No newline at end of file diff --git a/recipes/samtools/0.1.12/meta.yaml b/recipes/samtools/0.1.12/meta.yaml index f7b8d273b9320..fb87eb20dbb34 100644 --- a/recipes/samtools/0.1.12/meta.yaml +++ b/recipes/samtools/0.1.12/meta.yaml @@ -3,7 +3,7 @@ about: license: MIT summary: Tools for dealing with SAM and BAM files build: - number: 0 + number: 1 package: name: samtools version: 0.1.12 @@ -24,4 +24,7 @@ test: files: - ex1.fa commands: - - "samtools faidx ex1.fa" + - 'samtools 2>&1 | grep "^Version: 0\.1\.12a"' + - 'maq2sam-short 2>&1 | grep "^Version: r439"' + - 'maq2sam-long 2>&1 | grep "^Version: r439"' + - 'wgsim 2>&1 | grep "^Version: 0\.2\.3"' diff --git a/recipes/samtools/0.1.12/run_test.sh b/recipes/samtools/0.1.12/run_test.sh new file mode 100644 index 0000000000000..c58c2e2aba270 --- /dev/null +++ b/recipes/samtools/0.1.12/run_test.sh @@ -0,0 +1,5 @@ +#!/bin/sh + +samtools faidx ex1.fa seq1 + +wgsim ex1.fa out.r1.fq out.r2.fq diff --git a/recipes/scanindel/build.sh b/recipes/scanindel/build.sh new file mode 100644 index 0000000000000..060e90fb76531 --- /dev/null +++ b/recipes/scanindel/build.sh @@ -0,0 +1,5 @@ +#!/bin/bash + +mkdir -p $PREFIX/bin +cp ScanIndel.py $PREFIX/bin +cp tools/* $PREFIX/bin diff --git a/recipes/scanindel/meta.yaml b/recipes/scanindel/meta.yaml new file mode 100644 index 0000000000000..11ae24329f52e --- /dev/null +++ b/recipes/scanindel/meta.yaml @@ -0,0 +1,43 @@ +{% set name = "scanindel" %} +{% set version = "1.3" %} +{% set hash_type = "md5" %} +{% set hash_value = "d51dc67c19763e1f5630020a261f4afc" %} + +package: + name: '{{ name }}' + version: '{{ version }}' + +source: + fn: '{{ name }}-{{ version }}.tar.gz' + url: https://github.com/cauyrd/{{ name }}/archive/v{{ version }}.tar.gz + '{{ hash_type }}': '{{ hash_value }}' + +build: + number: 0 + skip: True # [osx or py3k] + +requirements: + build: + run: + - scipy + - numpy + - bedtools ==2.17.0 + - samtools <=1.0 + - bwa ==0.7.12 + - blat + - freebayes ==0.9.21.7 + - python + - pysam ==0.7.7 + - pyvcf ==0.6.7 + - biopython ==1.64 + + +test: + commands: + - ScanIndel.py -v + +about: + home: https://github.com/cauyrd/ScanIndel + license: GNU General Public License v3 or later (GPLv3+) + summary: 'ScanIndel is a python program to detect indels (insertions and deletions) from NGS data by re-align and de novo assemble soft clipped reads.' + license_family: GPL3 \ No newline at end of file diff --git a/recipes/searchgui/meta.yaml b/recipes/searchgui/meta.yaml index 4cf895d5eb4bd..2e8a87477684f 100644 --- a/recipes/searchgui/meta.yaml +++ b/recipes/searchgui/meta.yaml @@ -13,7 +13,6 @@ package: build: number: 0 - skip: True # [osx] source: fn: {{ name }}-{{ version }}-mac_and_linux.tar.gz diff --git a/recipes/secapr/meta.yaml b/recipes/secapr/meta.yaml index df8b367572c41..57af102b8b051 100644 --- a/recipes/secapr/meta.yaml +++ b/recipes/secapr/meta.yaml @@ -1,27 +1,28 @@ -# build with: conda build --python 2.7 . +{% set version = "1.1.0" %} package: name: secapr - version: '1.0.2' + version: {{ version }} -about: - home: 'https://github.com/AntonelliLab/seqcap_processor' - license: MIT - summary: 'Process sequence-capture FASTQ files into alignments for phylogenetic analyses. Integrates allele phasing, producing haplotype alignments.' source: - url: https://github.com/AntonelliLab/seqcap_processor/archive/v1.0.2.tar.gz - sha256: ada58295f1d02ca2da0b57a49d74770afcb3ac3137c25c32ecf19bb44937dbfa + fn: secapr_{{ version }}.tar.gz + url: https://github.com/AntonelliLab/seqcap_processor/archive/v{{ version }}.tar.gz + sha256: 988a37eaf9fc050f482c0ae1acb9994ce144a04d2de9ae1b827469398e7bb5dd build: skip: True # [not py27] number: 0 - script: $PYTHON setup.py install + script: $PYTHON setup.py install --single-version-externally-managed --record=record.txt + entry_points: + - secapr = secapr.__main__:main requirements: build: - python + - setuptools - biopython - pandas + run: - python - biopython @@ -40,9 +41,16 @@ requirements: - abyss - fastqc - pandas + - numpy test: imports: - secapr commands: - secapr --version + +about: + home: 'https://github.com/AntonelliLab/seqcap_processor' + license: MIT + license_file: LICENSE + summary: 'Process sequence-capture FASTQ files into alignments for phylogenetic analyses. Integrates allele phasing, producing haplotype alignments.' diff --git a/recipes/seq-seq-pan/build.sh b/recipes/seq-seq-pan/build.sh new file mode 100755 index 0000000000000..b3dabae16b6a1 --- /dev/null +++ b/recipes/seq-seq-pan/build.sh @@ -0,0 +1,16 @@ +#!/bin/bash + +mkdir -p $PREFIX/bin +mkdir -p $PREFIX/opt/seq-seq-pan/ + + +sed -i "s|\${BASH_SOURCE%/\*}|$PREFIX/opt/seq-seq-pan|g" seq-seq-pan +sed -i "s|\${BASH_SOURCE%/\*}|$PREFIX/opt/seq-seq-pan|g" seq-seq-pan-consensus +sed -i "s|\${BASH_SOURCE%/\*}|$PREFIX/opt/seq-seq-pan|g" seq-seq-pan-wga +sed -i "s|\${BASH_SOURCE%/\*}|$PREFIX/opt/seq-seq-pan|g" seq-seq-pan-genomedescription + +cp -r * $PREFIX/opt/seq-seq-pan/ +ln -s $PREFIX/opt/seq-seq-pan/seq-seq-pan $PREFIX/bin +ln -s $PREFIX/opt/seq-seq-pan/seq-seq-pan-consensus $PREFIX/bin +ln -s $PREFIX/opt/seq-seq-pan/seq-seq-pan-wga $PREFIX/bin +ln -s $PREFIX/opt/seq-seq-pan/seq-seq-pan-genomedescription $PREFIX/bin diff --git a/recipes/seq-seq-pan/meta.yaml b/recipes/seq-seq-pan/meta.yaml new file mode 100755 index 0000000000000..9beb155e537f9 --- /dev/null +++ b/recipes/seq-seq-pan/meta.yaml @@ -0,0 +1,37 @@ +{% set version = "1.0.0" %} + +package: + name: seq-seq-pan + version: {{ version }} + +source: + fn: seq-seq-pan.tar.gz + url: https://gitlab.com/chrjan/seq-seq-pan/repository/v{{ version }}/archive.tar.gz + md5: 7a0c00d8de984f7129c7bcbe4fa26892 + +build: + number: 1 + skip: True # [osx or py27] + +requirements: + run: + - python + - biopython ==1.69 + - blat ==35 + - snakemake ==4.3 + - openjdk + - argparse + - progressivemauve ==snapshot-2015-02-13 + +test: + commands: + - seq-seq-pan -h > /dev/null + - seq-seq-pan-wga --no-hooks --config workdir=$PREFIX/opt/seq-seq-pan/example/minimal genomefile=genome_list.txt outfilename=ssp_example -n > /dev/null + - java -jar $PREFIX/opt/seq-seq-pan/java/XMFAConsensus/XMFAconsensus_majorityvote.jar -h > /dev/null + - seq-seq-pan-consensus -h > /dev/null + - seq-seq-pan-genomedescription -h >/dev/null + +about: + home: https://gitlab.com/chrjan/seq-seq-pan + license: FreeBSDLicense + summary: seq-seq-pan is a workflow for the SEQuential alignment of SEQuences to build a PAN-genome data structure and a whole-genome-alignment. diff --git a/recipes/seqkit/meta.yaml b/recipes/seqkit/meta.yaml index 07d2ecf0a402a..0dbc6655ca660 100644 --- a/recipes/seqkit/meta.yaml +++ b/recipes/seqkit/meta.yaml @@ -1,4 +1,4 @@ -{% set version = "0.7.1" %} +{% set version = "0.7.2" %} package: name: seqkit @@ -16,15 +16,15 @@ build: source: fn: seqkit_{{ version }}_osx.tar.gz # [osx] url: https://github.com/shenwei356/seqkit/releases/download/v{{ version }}/seqkit_darwin_amd64.tar.gz # [osx] - md5: 661dd8208e4c395d192c85d0c99f282b # [osx] + md5: 18d13c7bc2dea0bf3923ae5494dae626 # [osx] fn: seqkit_{{ version }}_linux.tar.gz # [linux] url: https://github.com/shenwei356/seqkit/releases/download/v{{ version }}/seqkit_linux_386.tar.gz # [linux] - md5: d14837e09cd20c681b7bfdf4456ed8d9 # [linux] + md5: f806546031c5b88010480a2f8fa9acb0 # [linux] fn: seqkit_{{ version }}_linux64.tar.gz # [linux64] url: https://github.com/shenwei356/seqkit/releases/download/v{{ version }}/seqkit_linux_amd64.tar.gz # [linux64] - md5: 6d56f7026fdc8e1240e9ec3b8703f1fc # [linux64] + md5: 30c2c5f1ff3a8310ce75a5ae2ec329f1 # [linux64] test: commands: diff --git a/recipes/short-read-connector/meta.yaml b/recipes/short-read-connector/meta.yaml index 1483f5d5f7c76..007727409912b 100644 --- a/recipes/short-read-connector/meta.yaml +++ b/recipes/short-read-connector/meta.yaml @@ -1,11 +1,11 @@ package: - name: shortreadsconnector - version: '1.1.0' + name: shortreadconnector + version: '1.1.3' source: - fn: rconnector-v1.1.0-Source.tar.gz - url: "https://github.com/GATB/short_read_connector/releases/download/v1.1.0/rconnector-v1.1.0-Source.tar.gz" - md5: "822289b00e644842e5553eee8484fbc8" + fn: rconnector-v1.1.3-Source.tar.gz + url: "http://gatb-tools.gforge.inria.fr/ci-inria/rconnector-v1.1.3-Source.tar.gz" + md5: "dfb9ea38a562df02c5046574d1bba1bb" build: number: 0 diff --git a/recipes/sibelia/build.sh b/recipes/sibelia/build.sh new file mode 100644 index 0000000000000..db7912a025960 --- /dev/null +++ b/recipes/sibelia/build.sh @@ -0,0 +1,5 @@ +#!/bin/bash +mkdir -p ${PREFIX}/bin ${PREFIX}/lib ${PREFIX}/share +cp -r bin/* ${PREFIX}/bin +cp -r lib/Sibelia/* ${PREFIX}/lib +cp -r share/Sibelia/* ${PREFIX}/share diff --git a/recipes/sibelia/meta.yaml b/recipes/sibelia/meta.yaml new file mode 100644 index 0000000000000..2d23d99b15427 --- /dev/null +++ b/recipes/sibelia/meta.yaml @@ -0,0 +1,34 @@ +about: + home: https://github.com/bioinf/Sibelia + license: GPLv2 + summary: "Genome comparison via de Bruijn graph." +build: + number: 0 + +package: + name: sibelia + version: 3.0.6 +source: + fn: Sibelia-3.0.6-Darwin.tar.gz [osx] + fn: Sibelia-3.0.6-Linux.tar.gz [not osx] + url: https://downloads.sourceforge.net/project/sibelia-bio/3.0.6/Sibelia-3.0.6-Darwin.tar.gz [osx] + url: https://downloads.sourceforge.net/project/sibelia-bio/3.0.6/Sibelia-3.0.6-Linux.tar.gz [not osx] + sha256: eb051b626d6d592762b54b30cadb4bfd9182801feeaafb4ded94eef6667297d9 [not osx] + sha256: 23a0ccad2374c7eb52858b9f030a2d4eb2328171ed04b6038850dd9886052e8e [osx] +requirements: + build: + - gcc # [not osx] + - llvm # [osx] + - cmake + - libgcc + run: + - libgcc +test: + commands: + - Sibelia --version + +extra: + recipe-maintainers: + - nickp60 + + diff --git a/recipes/sicer/build.sh b/recipes/sicer/build.sh new file mode 100644 index 0000000000000..6a06f7cb650cb --- /dev/null +++ b/recipes/sicer/build.sh @@ -0,0 +1,38 @@ +#!/bin/bash +set -eu -o pipefail + +# for reference, see +# https://github.com/bioconda/bioconda-recipes/issues/3780 +# https://github.com/bioconda/bioconda-recipes/blob/master/recipes/weblogo/build.sh + +# create destination folder +OUTDIR=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $OUTDIR + +# install folders +cp -r $SRC_DIR/SICER/ex $OUTDIR +cp -r $SRC_DIR/SICER/lib $OUTDIR +cp -r $SRC_DIR/SICER/src $OUTDIR +cp -r $SRC_DIR/SICER/utility $OUTDIR + +# install files +for b in `echo SICER.sh SICER-rb.sh SICER-df.sh SICER-df-rb.sh` ; +do + sed -i'' -e "s|PATHTO=.*|PATHTO=$OUTDIR|g" $SRC_DIR/SICER/$b + chmod +x $SRC_DIR/SICER/$b + cp $SRC_DIR/SICER/$b $OUTDIR +done + +# create executables +BINDIR=$PREFIX/bin +mkdir -p $BINDIR + +for b in `echo SICER.sh SICER-rb.sh SICER-df.sh SICER-df-rb.sh` ; +do + BinFile=$BINDIR/$b + echo "#! /bin/bash" > $BinFile; + echo 'DIR=$( cd "$( dirname "${BASH_SOURCE[0]}" )" && pwd )' >> $BinFile; + echo '$DIR/../share/'$(basename $OUTDIR)/$b '$@' >> $BinFile; + chmod +x $BinFile +done + diff --git a/recipes/sicer/meta.yaml b/recipes/sicer/meta.yaml new file mode 100644 index 0000000000000..5f7d48e46e440 --- /dev/null +++ b/recipes/sicer/meta.yaml @@ -0,0 +1,33 @@ +{% set name = "SICER" %} +{% set version = "1.1" %} +#{% set sha256 = "1749c1e382629376f1d9db12978b9733fd5d9b9a896a2d127194c42b600c84c9" %} +{% set sha256 = "c6b895a70d0104388e2df9bb20a4b4f1639e8c1adbd7f517008552975229ba85" %} + +package: + name: {{ name|lower }} + version: {{ version }} + +source: + url: http://home.gwu.edu/~wpeng/{{ name }}_V{{ version }}.tgz + sha256: {{ sha256 }} + +build: + number: 0 + +requirements: + run: + - python 2.6.* + - numpy 1.9.* + - scipy 0.16.* + +test: + commands: + - SICER.sh $SRC_DIR/SICER/ex test.bed control.bed . hg18 1 200 150 0.74 600 .01 + - SICER-rb.sh $SRC_DIR/SICER/ex test.bed . hg18 1 200 150 0.74 400 100 + +about: + home: http://home.gwu.edu/~wpeng/Software.htm + license: MIT + license_family: MIT + summary: 'A clustering approach for identification of enriched domains from histone modification ChIP-Seq data' + diff --git a/recipes/singularity/meta.yaml b/recipes/singularity/meta.yaml index 8291ed61636ce..4acda02712c42 100644 --- a/recipes/singularity/meta.yaml +++ b/recipes/singularity/meta.yaml @@ -1,4 +1,4 @@ -{% set version='2.4' %} +{% set version='2.4.2' %} package: name: singularity version: {{ version }} @@ -6,7 +6,7 @@ package: source: fn: singularity-{{ version }}.tar.gz url: https://github.com/singularityware/singularity/releases/download/{{ version }}/singularity-{{ version }}.tar.gz - sha256: 34ca94250f15354819587364b21b0fdf7eebcff05110f8443caae8ed6961d7da + sha256: 38ae774900d3349f14a7fed1101fd9bd0f7948160aff571fb1c49d52adefd31e build: skip: True # [not linux] diff --git a/recipes/sis/build.sh b/recipes/sis/build.sh index d38bd403ca58b..89481145a5291 100644 --- a/recipes/sis/build.sh +++ b/recipes/sis/build.sh @@ -1,2 +1,2 @@ #!/bin/bash -cp -R $SRC_DIR/*.py $PREFIX/bin +$PYTHON setup.py install --single-version-externally-managed --record=record.txt diff --git a/recipes/sis/meta.yaml b/recipes/sis/meta.yaml index 68721f6c32ca0..f953a746afa7f 100644 --- a/recipes/sis/meta.yaml +++ b/recipes/sis/meta.yaml @@ -1,20 +1,19 @@ {% set name = "sis" %} -{% set version = "0.1.0" %} -{% set sha256 = "045be63ebea2592d823c024ee506219f5ad0e73a84b09416808db80ae9b0c160" %} +{% set version = "0.1.2" %} +{% set sha256 = "fae07a70ef16a8f459317cb9f222f20028462cacf97bec778edd5ac7daaa8718" %} package: name: {{ name|lower }} version: {{ version }} source: - fn: sis.zip - url: http://marte.ic.unicamp.br:8747/static/sis.zip + fn: {{ name }}-{{ version }}.tar.gz + url: https://github.com/nickp60/SIS/archive/{{ version }}.tar.gz sha256: {{ sha256 }} build: - number: 0 - skip: True # [py3k] - + number: 1 + skip: yes [py2k] requirements: build: - mummer @@ -26,11 +25,18 @@ requirements: - python test: - commands: - - python $PREFIX/bin/sis.py + # copying files does not work properly on travis + # source_files: + # - examples/nucmer.coords + # commands: + # - sis.py examples/nucmer.coords + imports: + - scaffoldsis + about: home: http://marte.ic.unicamp.br:8747/ - license: This software is experimental in nature and is supplied "AS IS", without obligation by the authors to provide accompanying services or support. The entire risk as to the quality and performance of the Software is with you. The authors EXPRESSLY DISCLAIM ANY AND ALL WARRANTIES REGARDING THE SOFTWARE, WHETHER EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO WARRANTIES PERTAINING TO MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. + license: GPLv2+ summary: A tool that uses mummer to scaffold small genomes. + dev_home: https://github.com/nickp60/SIS maintainer: nickp60 diff --git a/recipes/smina/build.sh b/recipes/smina/build.sh new file mode 100644 index 0000000000000..e88f6c7d1163c --- /dev/null +++ b/recipes/smina/build.sh @@ -0,0 +1,4 @@ +#!/bin/bash +mkdir -p $PREFIX/bin +cp -R smina $PREFIX/bin +chmod 0755 ${PREFIX}/bin/* diff --git a/recipes/smina/meta.yaml b/recipes/smina/meta.yaml new file mode 100644 index 0000000000000..dbe9d10a25680 --- /dev/null +++ b/recipes/smina/meta.yaml @@ -0,0 +1,23 @@ +about: + home: https://sourceforge.net/projects/smina/ + license: GNU General Public License version 2.0 (GPLv2) + summary: A fork of AutoDock Vina that is customized to better support scoring function development and high-performance energy minimization. +package: + name: smina + version: "2017.11.9" +build: + number: 0 + skip: False +source: + fn: smina # [linux] + url: https://downloads.sourceforge.net/project/smina/smina.static # [linux] + md5: 2c36acc7c512a800640012355ea791bc # [linux] + fn: smina # [osx] + url: https://downloads.sourceforge.net/project/smina/smina.osx # [osx] + md5: 0dd0336cad030b10bf8ccb145caf50a7 # [osx] +requirements: + build: + run: +test: + commands: + - smina --help diff --git a/recipes/snp-pipeline/build.sh b/recipes/snp-pipeline/build.sh index 4d7fc032b8cbe..e9346b0780bc9 100644 --- a/recipes/snp-pipeline/build.sh +++ b/recipes/snp-pipeline/build.sh @@ -1,8 +1,6 @@ #!/bin/bash -$PYTHON setup.py install - -# Add more build steps here, if they are necessary. +$PYTHON setup.py install --single-version-externally-managed --record=record.txt # See # http://docs.continuum.io/conda/build.html diff --git a/recipes/snp-pipeline/meta.yaml b/recipes/snp-pipeline/meta.yaml index 79697916329ce..29dd586849409 100644 --- a/recipes/snp-pipeline/meta.yaml +++ b/recipes/snp-pipeline/meta.yaml @@ -1,22 +1,21 @@ package: name: snp-pipeline - version: "0.7.0" + version: "1.0.1" source: - fn: snp-pipeline-0.7.0.tar.gz - url: https://pypi.python.org/packages/62/6b/5c7c7d1ad8239f2dd051a91e8bc55cd98418df5719d0fd4605f863f71d9a/snp-pipeline-0.7.0.tar.gz - md5: 8f5971ca4729364fd22e26e712be862d + fn: snp-pipeline-1.0.1.tar.gz + url: https://pypi.python.org/packages/9c/86/e2a212735e229b5dd65c7f58f53822e820507bb4f95f870687f50046f99c/snp-pipeline-1.0.1.tar.gz + md5: d42bfefd2ccccdb5f880f3a74f4ff165 build: - preserve_egg_dir: True + entry_points: + - cfsan_snp_pipeline = snppipeline.cfsan_snp_pipeline:main + - qarrayrun = snppipeline.qarrayrun:main requirements: build: - python - - pyvcf >=0.6.7 - setuptools - - psutil - - biopython run: - python @@ -24,7 +23,6 @@ requirements: - setuptools - psutil - biopython - - testfixtures test: imports: @@ -33,6 +31,13 @@ test: requires: - testfixtures + commands: + - cfsan_snp_pipeline --version + +extra: + skip-lints: + - uses_setuptools # uses pkg_resources + about: home: https://github.com/CFSAN-Biostatistics/snp-pipeline license: BSD License diff --git a/recipes/squizz/build.sh b/recipes/squizz/build.sh new file mode 100644 index 0000000000000..d0e9d0dc8de9f --- /dev/null +++ b/recipes/squizz/build.sh @@ -0,0 +1,7 @@ +#!/bin/sh + + +./configure --prefix=${PREFIX} +make +make install + diff --git a/recipes/squizz/meta.yaml b/recipes/squizz/meta.yaml new file mode 100644 index 0000000000000..bf7694948dca7 --- /dev/null +++ b/recipes/squizz/meta.yaml @@ -0,0 +1,27 @@ +package: + name: squizz + version: 0.99d + +source: + fn: squizz-0.99d.tar.gz + url: http://ftp.pasteur.fr/pub/gensoft/projects/squizz/squizz-0.99d.tar.gz + md5: 12d9b316a7772911ec3baa2e3f6dda12 + +build: + number: 0 + +requirements: + build: + - gcc # [linux] + - llvm # [osx] + run: + - libgcc # [linux] + +test: + commands: + - squizz -h + +about: + home: http://ftp.pasteur.fr/pub/gensoft/projects/squizz/ + summary: Squizz is a sequence/alignment format checker, but it has some conversion capabilities too. + license: GPL 2 diff --git a/recipes/srst2/0.1.4.6/build.sh b/recipes/srst2/0.1.4.6/build.sh deleted file mode 100644 index d3c2cb4ea56ae..0000000000000 --- a/recipes/srst2/0.1.4.6/build.sh +++ /dev/null @@ -1,3 +0,0 @@ -#!/bin/bash - -python setup.py install diff --git a/recipes/srst2/0.1.6/build.sh b/recipes/srst2/0.1.6/build.sh new file mode 100644 index 0000000000000..0456c5ca37e6b --- /dev/null +++ b/recipes/srst2/0.1.6/build.sh @@ -0,0 +1,4 @@ +#!/bin/bash + +$PYTHON setup.py install --single-version-externally-managed --record=record.txt + diff --git a/recipes/srst2/0.1.4.6/meta.yaml b/recipes/srst2/0.1.6/meta.yaml similarity index 77% rename from recipes/srst2/0.1.4.6/meta.yaml rename to recipes/srst2/0.1.6/meta.yaml index 05a48e40a9fda..b289f9355247e 100644 --- a/recipes/srst2/0.1.4.6/meta.yaml +++ b/recipes/srst2/0.1.6/meta.yaml @@ -1,6 +1,6 @@ package: name: srst2 - version: 0.1.4.6 + version: 0.1.6 source: fn: v0.1.6.tar.gz @@ -8,9 +8,10 @@ source: sha256: 24cbd03933d4cc14bbfa7f8a073c9b0caafb13d55afb3bfa25f8b093fc5bc615 patches: - use_setuptools.patch + - srst_sample_name_v0.1.6.patch build: - number: 1 + number: 0 skip: True #[not py27 or osx] requirements: @@ -29,8 +30,8 @@ requirements: test: commands: - - srst2 -h 2>&1 | grep 'SRST2 - Short Read Sequence Typer' > /dev/null - - getmlst.py -h 2>&1 | grep 'usage' > /dev/null + - srst2 -h 2>&1 | grep "SRST2 - Short Read Sequence Typer" > /dev/null + - getmlst.py -h 2>&1 | grep "usage" > /dev/null about: home: https://github.com/katholt/srst2 diff --git a/recipes/srst2/0.1.6/srst_sample_name_v0.1.6.patch b/recipes/srst2/0.1.6/srst_sample_name_v0.1.6.patch new file mode 100644 index 0000000000000..fc9c012b4f71b --- /dev/null +++ b/recipes/srst2/0.1.6/srst_sample_name_v0.1.6.patch @@ -0,0 +1,63 @@ +diff --git a/scripts/srst2.py b/scripts/srst2.py +index 67e48ae..916792e 100755 +--- a/scripts/srst2.py ++++ b/scripts/srst2.py +@@ -233,7 +233,7 @@ def parse_fai(fai_file,db_type,delimiter): + return size, gene_clusters, unique_gene_symbols, unique_allele_symbols, gene_cluster_symbols + + +-def read_pileup_data(pileup_file, size, prob_err, consensus_file = ""): ++def read_pileup_data(pileup_file, size, prob_err, sample_name, consensus_file = ""): + with open(pileup_file) as pileup: + prob_success = 1 - prob_err # Set by user, default is prob_err = 0.01 + hash_alignment = {} +@@ -372,7 +372,7 @@ def read_pileup_data(pileup_file, size, prob_err, consensus_file = ""): + elif consensus_file.split(".")[-2] == "all_consensus_alleles": + consensus_type = "consensus" + with open(consensus_file, "a") as consensus_outfile: +- consensus_outfile.write(">{0}.{1} {2}\n".format(allele, consensus_type, pileup_file.split(".")[1].split("__")[1])) ++ consensus_outfile.write(">{0}.{1} {2}\n".format(allele, consensus_type, sample_name)) + outstring = consensus_seq + "\n" + consensus_outfile.write(outstring) + +@@ -782,7 +782,7 @@ def create_allele_pileup(allele_name, all_pileup_file): + def parse_scores(run_type,args,scores, hash_edge_depth, + avg_depth_allele, coverage_allele, mismatch_allele, indel_allele, + missing_allele, size_allele, next_to_del_depth_allele, +- unique_cluster_symbols,unique_allele_symbols, pileup_file): ++ unique_cluster_symbols,unique_allele_symbols, pileup_file, sample_name): + + # sort into hash for each gene locus + scores_by_gene = collections.defaultdict(dict) # key1 = gene, key2 = allele, value = score +@@ -868,11 +868,11 @@ def parse_scores(run_type,args,scores, hash_edge_depth, + if args.report_new_consensus or args.report_all_consensus: + new_alleles_filename = args.output + ".new_consensus_alleles.fasta" + allele_pileup_file = create_allele_pileup(results[gene][0], pileup_file) +- read_pileup_data(allele_pileup_file, size_allele, args.prob_err, consensus_file = new_alleles_filename) ++ read_pileup_data(allele_pileup_file, size_allele, args.prob_err, sample_name, consensus_file = new_alleles_filename) + if args.report_all_consensus: + new_alleles_filename = args.output + ".all_consensus_alleles.fasta" + allele_pileup_file = create_allele_pileup(results[gene][0], pileup_file) +- read_pileup_data(allele_pileup_file, size_allele, args.prob_err, consensus_file = new_alleles_filename) ++ read_pileup_data(allele_pileup_file, size_allele, args.prob_err, sample_name, consensus_file = new_alleles_filename) + + return results # (allele, diffs, depth_problem, divergence) + +@@ -1265,7 +1265,7 @@ def map_fileSet_to_db(args,sample_name,fastq_inputs,db_name,fasta,size,gene_name + logging.info(' Processing SAMtools pileup...') + hash_alignment, hash_max_depth, hash_edge_depth, avg_depth_allele, coverage_allele, \ + mismatch_allele, indel_allele, missing_allele, size_allele, next_to_del_depth_allele= \ +- read_pileup_data(pileup_file, size, args.prob_err) ++ read_pileup_data(pileup_file, size, args.prob_err, sample_name) + + # Generate scores for all alleles (prints these and associated info if verbose) + # result = dict, with key=allele, value=score +@@ -1283,7 +1283,7 @@ def map_fileSet_to_db(args,sample_name,fastq_inputs,db_name,fasta,size,gene_name + allele_scores = parse_scores(run_type, args, scores, \ + hash_edge_depth, avg_depth_allele, coverage_allele, mismatch_allele, \ + indel_allele, missing_allele, size_allele, next_to_del_depth_allele, +- unique_gene_symbols, unique_allele_symbols, pileup_file) ++ unique_gene_symbols, unique_allele_symbols, pileup_file, sample_name) + + # REPORT/RECORD RESULTS + diff --git a/recipes/srst2/0.1.4.6/use_setuptools.patch b/recipes/srst2/0.1.6/use_setuptools.patch similarity index 100% rename from recipes/srst2/0.1.4.6/use_setuptools.patch rename to recipes/srst2/0.1.6/use_setuptools.patch diff --git a/recipes/srst2/build.sh b/recipes/srst2/build.sh index d3c2cb4ea56ae..3786386a73c83 100644 --- a/recipes/srst2/build.sh +++ b/recipes/srst2/build.sh @@ -1,3 +1,3 @@ #!/bin/bash -python setup.py install +$PYTHON setup.py install --single-version-externally-managed --record=record.txt diff --git a/recipes/srst2/meta.yaml b/recipes/srst2/meta.yaml index 314e411b111bd..47eb1f1adf0d0 100644 --- a/recipes/srst2/meta.yaml +++ b/recipes/srst2/meta.yaml @@ -8,9 +8,10 @@ source: sha256: 352c59bdf00039dfa5610a4b88049a0eb114d7c2a305d4924b6e605cc6d15123 patches: - use_setuptools.patch + - srst_sample_name_v0.2.0.patch build: - number: 1 + number: 2 skip: True #[not py27] requirements: @@ -29,8 +30,8 @@ requirements: test: commands: - - srst2 -h 2>&1 | grep 'SRST2 - Short Read Sequence Typer' > /dev/null - - getmlst.py -h 2>&1 | grep 'usage' > /dev/null + - srst2 -h 2>&1 | grep "SRST2 - Short Read Sequence Typer" > /dev/null + - getmlst.py -h 2>&1 | grep "usage" > /dev/null about: home: https://github.com/katholt/srst2 diff --git a/recipes/srst2/srst_sample_name_v0.2.0.patch b/recipes/srst2/srst_sample_name_v0.2.0.patch new file mode 100644 index 0000000000000..7f9fde45399a2 --- /dev/null +++ b/recipes/srst2/srst_sample_name_v0.2.0.patch @@ -0,0 +1,74 @@ +From d9d617a67e432cabd768bac0cb06462aa8c87ec5 Mon Sep 17 00:00:00 2001 +From: Eric Enns +Date: Tue, 28 Nov 2017 11:12:31 -0600 +Subject: [PATCH] Remove sample name parsing which doesn't work when + directories have . in the name, instead just pass sample_name along to + functions requiring it. + +--- + scripts/srst2.py | 14 +++++++------- + 1 file changed, 7 insertions(+), 7 deletions(-) + +diff --git a/scripts/srst2.py b/scripts/srst2.py +index ac174ef..5c753e1 100755 +--- a/scripts/srst2.py ++++ b/scripts/srst2.py +@@ -311,7 +311,7 @@ def parse_fai(fai_file,db_type,delimiter): + return size, gene_clusters, unique_gene_symbols, unique_allele_symbols, gene_cluster_symbols + + +-def read_pileup_data(pileup_file, size, prob_err, consensus_file = ""): ++def read_pileup_data(pileup_file, size, prob_err, sample_name, consensus_file = ""): + with open(pileup_file) as pileup: + prob_success = 1 - prob_err # Set by user, default is prob_err = 0.01 + hash_alignment = {} +@@ -450,7 +450,7 @@ def read_pileup_data(pileup_file, size, prob_err, consensus_file = ""): + elif consensus_file.split(".")[-2] == "all_consensus_alleles": + consensus_type = "consensus" + with open(consensus_file, "a") as consensus_outfile: +- consensus_outfile.write(">{0}.{1} {2}\n".format(allele, consensus_type, pileup_file.split(".")[1].split("__")[1])) ++ consensus_outfile.write(">{0}.{1} {2}\n".format(allele, consensus_type, sample_name)) + outstring = consensus_seq + "\n" + consensus_outfile.write(outstring) + +@@ -942,7 +942,7 @@ def dict_of_dicts_inverted_ind(dd): + def parse_scores(run_type,args,scores, hash_edge_depth, + avg_depth_allele, coverage_allele, mismatch_allele, indel_allele, + missing_allele, size_allele, next_to_del_depth_allele, +- unique_cluster_symbols,unique_allele_symbols, pileup_file): ++ unique_cluster_symbols,unique_allele_symbols, pileup_file, sample_name): + + # sort into hash for each gene locus + scores_by_gene = group_allele_dict_by_gene(dict( (allele,val) for (allele,val) in scores.items() \ +@@ -1018,11 +1018,11 @@ def parse_scores(run_type,args,scores, hash_edge_depth, + if args.report_new_consensus or args.report_all_consensus: + new_alleles_filename = args.output + ".new_consensus_alleles.fasta" + allele_pileup_file = create_allele_pileup(results[gene][0], pileup_file) +- read_pileup_data(allele_pileup_file, size_allele, args.prob_err, consensus_file = new_alleles_filename) ++ read_pileup_data(allele_pileup_file, size_allele, args.prob_err, sample_name, consensus_file = new_alleles_filename) + if args.report_all_consensus: + new_alleles_filename = args.output + ".all_consensus_alleles.fasta" + allele_pileup_file = create_allele_pileup(results[gene][0], pileup_file) +- read_pileup_data(allele_pileup_file, size_allele, args.prob_err, consensus_file = new_alleles_filename) ++ read_pileup_data(allele_pileup_file, size_allele, args.prob_err, sample_name, consensus_file = new_alleles_filename) + + return results # (allele, diffs, depth_problem, divergence) + +@@ -1419,7 +1419,7 @@ def map_fileSet_to_db(args, sample_name, fastq_inputs, db_name, fasta, size, gen + logging.info(' Processing SAMtools pileup...') + hash_alignment, hash_max_depth, hash_edge_depth, avg_depth_allele, coverage_allele, \ + mismatch_allele, indel_allele, missing_allele, size_allele, next_to_del_depth_allele= \ +- read_pileup_data(pileup_file, size, args.prob_err) ++ read_pileup_data(pileup_file, size, args.prob_err, sample_name) + + # Generate scores for all alleles (prints these and associated info if verbose) + # result = dict, with key=allele, value=score +@@ -1437,7 +1437,7 @@ def map_fileSet_to_db(args, sample_name, fastq_inputs, db_name, fasta, size, gen + allele_scores = parse_scores(run_type, args, scores, \ + hash_edge_depth, avg_depth_allele, coverage_allele, mismatch_allele, \ + indel_allele, missing_allele, size_allele, next_to_del_depth_allele, +- unique_gene_symbols, unique_allele_symbols, pileup_file) ++ unique_gene_symbols, unique_allele_symbols, pileup_file, sample_name) + + # REPORT/RECORD RESULTS + diff --git a/recipes/stride/meta.yaml b/recipes/stride/meta.yaml index 2397e7c871e0a..365cb721fd33c 100644 --- a/recipes/stride/meta.yaml +++ b/recipes/stride/meta.yaml @@ -7,7 +7,7 @@ package: version: {{ version }} build: - number: 1 + number: 2 skip: True # [osx] source: @@ -19,7 +19,7 @@ requirements: build: - gcc # [not osx] - llvm # [osx] - - google-sparsehash + - sparsehash - autoconf - automake - m4 diff --git a/recipes/structureharvester/build.sh b/recipes/structureharvester/build.sh new file mode 100644 index 0000000000000..f8b17d5afb171 --- /dev/null +++ b/recipes/structureharvester/build.sh @@ -0,0 +1,5 @@ +#!/bin/bash + +mkdir -p $PREFIX/bin +cp $SRC_DIR/*.py $PREFIX/bin && chmod +x $PREFIX/bin/structureHarvester.py + diff --git a/recipes/structureharvester/meta.yaml b/recipes/structureharvester/meta.yaml new file mode 100644 index 0000000000000..a3f6d32ec9fd9 --- /dev/null +++ b/recipes/structureharvester/meta.yaml @@ -0,0 +1,29 @@ +{% set version = "0.6.94" %} +{% set commit = "e15952601b946267ce566df6ff0dd56df5c8b8f6" %} + +package: + name: structureharvester + version: {{ version }} + +source: + fn: {{ commit }}.zip + sha256: 1dad5bc572df5fd93a37044194cabc8f3622752ce80d4b60c7542d09b2b1ce45 + url: https://github.com/dentearl/structureHarvester/archive/{{ commit }}.zip + +build: + number: 0 + skip: True # [not py27] + +requirements: + build: + - python + run: + - python + +test: + commands: + - structureHarvester.py --version 2> /dev/stdout 2> /dev/stdout | grep "{{ version }}" +about: + home: 'http://alumni.soe.ucsc.edu/~dearl/software/structureHarvester/' + license: MIT + summary: "structureHarvester.py is a Python script capable of extracting all the relevant data from STRUCTURE results files" diff --git a/recipes/svviz/build.sh b/recipes/svviz/build.sh index 4d7fc032b8cbe..4899c226c8dd0 100644 --- a/recipes/svviz/build.sh +++ b/recipes/svviz/build.sh @@ -1,6 +1,6 @@ #!/bin/bash -$PYTHON setup.py install +$PYTHON setup.py install --single-version-externally-managed --record=record.txt # Add more build steps here, if they are necessary. diff --git a/recipes/targqc/meta.yaml b/recipes/targqc/meta.yaml index e4161274edbf1..9972acadffc4e 100644 --- a/recipes/targqc/meta.yaml +++ b/recipes/targqc/meta.yaml @@ -58,3 +58,7 @@ about: license: GNU General Public License v3 (GPLv3) summary: 'Target capture coverage QC' license_family: GPL3 + +extra: + skip-lints: + - uses_setuptools diff --git a/recipes/tassel/3.0.174/build.sh b/recipes/tassel/3.0.174/build.sh new file mode 100644 index 0000000000000..09f69f449c4f4 --- /dev/null +++ b/recipes/tassel/3.0.174/build.sh @@ -0,0 +1,14 @@ +BINARY_HOME=$PREFIX/bin +TASSEL_HOME=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM + +# Copy source to the conda environment +mkdir -p $TASSEL_HOME +cp -R $SRC_DIR/* $TASSEL_HOME/ + +# Convert CRLF in wrappers to LF +sed -i 's/\r//' $TASSEL_HOME/*.pl + +# Create symbolic links for TASSEL's wrappers +ln -s $TASSEL_HOME/run_anything.pl $BINARY_HOME/ +ln -s $TASSEL_HOME/run_pipeline.pl $BINARY_HOME/ +ln -s $TASSEL_HOME/start_tassel.pl $BINARY_HOME/ \ No newline at end of file diff --git a/recipes/tassel/3.0.174/meta.yaml b/recipes/tassel/3.0.174/meta.yaml new file mode 100644 index 0000000000000..13f6a166e7fd8 --- /dev/null +++ b/recipes/tassel/3.0.174/meta.yaml @@ -0,0 +1,38 @@ +{% set name = "TASSEL" %} +{% set version = "3.0.174" %} + +package: + name: {{ name|lower }} + version: {{ version }} + +source: + git_url: https://git.code.sf.net/p/tassel/tassel3-standalone + git_rev: 612a92c0f677d6ec040c17e146671974a3cdc2da + patches: + - patches/run_anything.patch + - patches/run_pipeline.patch + - patches/start_tassel.patch + +build: + skip: True # [osx] + number: 0 + +requirements: + run: + - openjdk >=6.0 + - perl + +test: + commands: + - run_pipeline.pl + +about: + home: 'https://tassel.bitbucket.io/TasselArchived.html' + license: LGPL V2.1 + summary: "TASSEL is a software package to evaluate traits associations, evolutionary patterns, and linkage disequilibrium." + +extra: + skip-lints: + # SourceForge Git snapshots do not persist + - uses_git_url + - missing_hash diff --git a/recipes/tassel/3.0.174/patches/run_anything.patch b/recipes/tassel/3.0.174/patches/run_anything.patch new file mode 100644 index 0000000000000..bb2d13be52c9a --- /dev/null +++ b/recipes/tassel/3.0.174/patches/run_anything.patch @@ -0,0 +1,18 @@ +diff --git a/run_anything.pl b/run_anything.pl +index 7dcddab..ab77ed0 100755 +--- a/run_anything.pl ++++ b/run_anything.pl +@@ -1,9 +1,11 @@ +-#!/usr/bin/perl -w ++#!/usr/bin/env perl + + use strict; + use File::Basename; ++use Cwd 'abs_path'; + +-my $dirname = dirname(__FILE__); ++my $filepath = abs_path(__FILE__); ++my $dirname = dirname($filepath); + my $top = defined($dirname) ? $dirname : '.'; + + my $libdir = "$top/lib"; diff --git a/recipes/tassel/3.0.174/patches/run_pipeline.patch b/recipes/tassel/3.0.174/patches/run_pipeline.patch new file mode 100644 index 0000000000000..a4942a2fc8c53 --- /dev/null +++ b/recipes/tassel/3.0.174/patches/run_pipeline.patch @@ -0,0 +1,18 @@ +diff --git a/run_pipeline.pl b/run_pipeline.pl +index ce7c212..6d144f9 100755 +--- a/run_pipeline.pl ++++ b/run_pipeline.pl +@@ -1,9 +1,11 @@ +-#!/usr/bin/perl -w ++#!/usr/bin/env perl + + use strict; + use File::Basename; ++use Cwd 'abs_path'; + +-my $dirname = dirname(__FILE__); ++my $filepath = abs_path(__FILE__); ++my $dirname = dirname($filepath); + my $top = defined($dirname) ? $dirname : '.'; + + my $libdir = "$top/lib"; diff --git a/recipes/tassel/3.0.174/patches/start_tassel.patch b/recipes/tassel/3.0.174/patches/start_tassel.patch new file mode 100644 index 0000000000000..d3a7eac047bf1 --- /dev/null +++ b/recipes/tassel/3.0.174/patches/start_tassel.patch @@ -0,0 +1,18 @@ +diff --git a/start_tassel.pl b/start_tassel.pl +index 18b9fd2..d53370a 100755 +--- a/start_tassel.pl ++++ b/start_tassel.pl +@@ -1,9 +1,11 @@ +-#!/usr/bin/perl -w ++#!/usr/bin/env perl + + use strict; + use File::Basename; ++use Cwd 'abs_path'; + +-my $dirname = dirname(__FILE__); ++my $filepath = abs_path(__FILE__); ++my $dirname = dirname($filepath); + my $top = defined($dirname) ? $dirname : '.'; + + my $libdir = "$top/lib"; diff --git a/recipes/tassel/4.3.15/build.sh b/recipes/tassel/4.3.15/build.sh new file mode 100644 index 0000000000000..09f69f449c4f4 --- /dev/null +++ b/recipes/tassel/4.3.15/build.sh @@ -0,0 +1,14 @@ +BINARY_HOME=$PREFIX/bin +TASSEL_HOME=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM + +# Copy source to the conda environment +mkdir -p $TASSEL_HOME +cp -R $SRC_DIR/* $TASSEL_HOME/ + +# Convert CRLF in wrappers to LF +sed -i 's/\r//' $TASSEL_HOME/*.pl + +# Create symbolic links for TASSEL's wrappers +ln -s $TASSEL_HOME/run_anything.pl $BINARY_HOME/ +ln -s $TASSEL_HOME/run_pipeline.pl $BINARY_HOME/ +ln -s $TASSEL_HOME/start_tassel.pl $BINARY_HOME/ \ No newline at end of file diff --git a/recipes/tassel/4.3.15/meta.yaml b/recipes/tassel/4.3.15/meta.yaml new file mode 100644 index 0000000000000..ba3ec6ba409d0 --- /dev/null +++ b/recipes/tassel/4.3.15/meta.yaml @@ -0,0 +1,38 @@ +{% set name = "TASSEL" %} +{% set version = "4.3.15" %} + +package: + name: {{ name|lower }} + version: {{ version }} + +source: + git_url: https://git.code.sf.net/p/tassel/tassel4-standalone + git_rev: 17dced772e1bab7d36f195f41c4c1b8b5e9ad55d + patches: + - patches/run_anything.patch + - patches/run_pipeline.patch + - patches/start_tassel.patch + +build: + skip: True # [osx] + number: 0 + +requirements: + run: + - openjdk >=7.0 + - perl + +test: + commands: + - run_pipeline.pl + +about: + home: 'https://tassel.bitbucket.io/TasselArchived.html' + license: LGPL V2.1 + summary: "TASSEL is a software package to evaluate traits associations, evolutionary patterns, and linkage disequilibrium." + +extra: + skip-lints: + # SourceForge Git snapshots do not persist + - uses_git_url + - missing_hash diff --git a/recipes/tassel/4.3.15/patches/run_anything.patch b/recipes/tassel/4.3.15/patches/run_anything.patch new file mode 100644 index 0000000000000..bb2d13be52c9a --- /dev/null +++ b/recipes/tassel/4.3.15/patches/run_anything.patch @@ -0,0 +1,18 @@ +diff --git a/run_anything.pl b/run_anything.pl +index 7dcddab..ab77ed0 100755 +--- a/run_anything.pl ++++ b/run_anything.pl +@@ -1,9 +1,11 @@ +-#!/usr/bin/perl -w ++#!/usr/bin/env perl + + use strict; + use File::Basename; ++use Cwd 'abs_path'; + +-my $dirname = dirname(__FILE__); ++my $filepath = abs_path(__FILE__); ++my $dirname = dirname($filepath); + my $top = defined($dirname) ? $dirname : '.'; + + my $libdir = "$top/lib"; diff --git a/recipes/tassel/4.3.15/patches/run_pipeline.patch b/recipes/tassel/4.3.15/patches/run_pipeline.patch new file mode 100644 index 0000000000000..a4942a2fc8c53 --- /dev/null +++ b/recipes/tassel/4.3.15/patches/run_pipeline.patch @@ -0,0 +1,18 @@ +diff --git a/run_pipeline.pl b/run_pipeline.pl +index ce7c212..6d144f9 100755 +--- a/run_pipeline.pl ++++ b/run_pipeline.pl +@@ -1,9 +1,11 @@ +-#!/usr/bin/perl -w ++#!/usr/bin/env perl + + use strict; + use File::Basename; ++use Cwd 'abs_path'; + +-my $dirname = dirname(__FILE__); ++my $filepath = abs_path(__FILE__); ++my $dirname = dirname($filepath); + my $top = defined($dirname) ? $dirname : '.'; + + my $libdir = "$top/lib"; diff --git a/recipes/tassel/4.3.15/patches/start_tassel.patch b/recipes/tassel/4.3.15/patches/start_tassel.patch new file mode 100644 index 0000000000000..d3a7eac047bf1 --- /dev/null +++ b/recipes/tassel/4.3.15/patches/start_tassel.patch @@ -0,0 +1,18 @@ +diff --git a/start_tassel.pl b/start_tassel.pl +index 18b9fd2..d53370a 100755 +--- a/start_tassel.pl ++++ b/start_tassel.pl +@@ -1,9 +1,11 @@ +-#!/usr/bin/perl -w ++#!/usr/bin/env perl + + use strict; + use File::Basename; ++use Cwd 'abs_path'; + +-my $dirname = dirname(__FILE__); ++my $filepath = abs_path(__FILE__); ++my $dirname = dirname($filepath); + my $top = defined($dirname) ? $dirname : '.'; + + my $libdir = "$top/lib"; diff --git a/recipes/tassel/build.sh b/recipes/tassel/build.sh new file mode 100644 index 0000000000000..64292a1798037 --- /dev/null +++ b/recipes/tassel/build.sh @@ -0,0 +1,14 @@ +BINARY_HOME=$PREFIX/bin +TASSEL_HOME=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM + +# Copy source to the conda environment +mkdir -p $TASSEL_HOME +cp -R $SRC_DIR/* $TASSEL_HOME/ + +# Convert CRLF in wrappers to LF +sed -i 's/\r//' $TASSEL_HOME/*.pl + +# Create symbolic links for TASSEL's wrappers +ln -s $TASSEL_HOME/run_anything.pl $BINARY_HOME/ +ln -s $TASSEL_HOME/run_pipeline.pl $BINARY_HOME/ +ln -s $TASSEL_HOME/start_tassel.pl $BINARY_HOME/ diff --git a/recipes/tassel/meta.yaml b/recipes/tassel/meta.yaml new file mode 100644 index 0000000000000..800c62747fa51 --- /dev/null +++ b/recipes/tassel/meta.yaml @@ -0,0 +1,33 @@ +{% set name = "TASSEL" %} +{% set version = "5.2.40" %} + +package: + name: {{ name|lower }} + version: {{ version }} + +source: + fn: {{ name|lower }}-{{ version }}.tar.gz + url: https://bitbucket.org/tasseladmin/tassel-5-standalone/get/V{{ version }}.tar.gz + md5: 66c6ededa0a8e495ec7c86bc8aa441f8 + patches: + - patches/run_anything.patch + - patches/run_pipeline.patch + - patches/start_tassel.patch + +build: + skip: True # [osx] + number: 0 + +requirements: + run: + - openjdk >=8.0 + - perl + +test: + commands: + - run_pipeline.pl -ListPlugins + +about: + home: 'http://www.maizegenetics.net/tassel' + license: LGPL V2.1 + summary: "TASSEL is a software package to evaluate traits associations, evolutionary patterns, and linkage disequilibrium." diff --git a/recipes/tassel/patches/run_anything.patch b/recipes/tassel/patches/run_anything.patch new file mode 100644 index 0000000000000..bb2d13be52c9a --- /dev/null +++ b/recipes/tassel/patches/run_anything.patch @@ -0,0 +1,18 @@ +diff --git a/run_anything.pl b/run_anything.pl +index 7dcddab..ab77ed0 100755 +--- a/run_anything.pl ++++ b/run_anything.pl +@@ -1,9 +1,11 @@ +-#!/usr/bin/perl -w ++#!/usr/bin/env perl + + use strict; + use File::Basename; ++use Cwd 'abs_path'; + +-my $dirname = dirname(__FILE__); ++my $filepath = abs_path(__FILE__); ++my $dirname = dirname($filepath); + my $top = defined($dirname) ? $dirname : '.'; + + my $libdir = "$top/lib"; diff --git a/recipes/tassel/patches/run_pipeline.patch b/recipes/tassel/patches/run_pipeline.patch new file mode 100644 index 0000000000000..a4942a2fc8c53 --- /dev/null +++ b/recipes/tassel/patches/run_pipeline.patch @@ -0,0 +1,18 @@ +diff --git a/run_pipeline.pl b/run_pipeline.pl +index ce7c212..6d144f9 100755 +--- a/run_pipeline.pl ++++ b/run_pipeline.pl +@@ -1,9 +1,11 @@ +-#!/usr/bin/perl -w ++#!/usr/bin/env perl + + use strict; + use File::Basename; ++use Cwd 'abs_path'; + +-my $dirname = dirname(__FILE__); ++my $filepath = abs_path(__FILE__); ++my $dirname = dirname($filepath); + my $top = defined($dirname) ? $dirname : '.'; + + my $libdir = "$top/lib"; diff --git a/recipes/tassel/patches/start_tassel.patch b/recipes/tassel/patches/start_tassel.patch new file mode 100644 index 0000000000000..d3a7eac047bf1 --- /dev/null +++ b/recipes/tassel/patches/start_tassel.patch @@ -0,0 +1,18 @@ +diff --git a/start_tassel.pl b/start_tassel.pl +index 18b9fd2..d53370a 100755 +--- a/start_tassel.pl ++++ b/start_tassel.pl +@@ -1,9 +1,11 @@ +-#!/usr/bin/perl -w ++#!/usr/bin/env perl + + use strict; + use File::Basename; ++use Cwd 'abs_path'; + +-my $dirname = dirname(__FILE__); ++my $filepath = abs_path(__FILE__); ++my $dirname = dirname($filepath); + my $top = defined($dirname) ? $dirname : '.'; + + my $libdir = "$top/lib"; diff --git a/recipes/tassel/patches/tassel.patch b/recipes/tassel/patches/tassel.patch new file mode 100644 index 0000000000000..0f6030de835f3 --- /dev/null +++ b/recipes/tassel/patches/tassel.patch @@ -0,0 +1,54 @@ +diff --git a/run_anything.pl b/run_anything.pl +index 7dcddab..ab77ed0 100755 +--- a/run_anything.pl ++++ b/run_anything.pl +@@ -1,9 +1,11 @@ +-#!/usr/bin/perl -w ++#!/usr/bin/env perl + + use strict; + use File::Basename; ++use Cwd 'abs_path'; + +-my $dirname = dirname(__FILE__); ++my $filepath = abs_path(__FILE__); ++my $dirname = dirname($filepath); + my $top = defined($dirname) ? $dirname : '.'; + + my $libdir = "$top/lib"; +diff --git a/run_pipeline.pl b/run_pipeline.pl +index ce7c212..dc69370 100755 +--- a/run_pipeline.pl ++++ b/run_pipeline.pl +@@ -1,9 +1,11 @@ +-#!/usr/bin/perl -w ++#!/usr/bin/env perl + + use strict; + use File::Basename; ++use Cwd 'abs_path' + +-my $dirname = dirname(__FILE__); ++my $filepath = abs_path(__FILE__); ++my $dirname = dirname($filepath); + my $top = defined($dirname) ? $dirname : '.'; + + my $libdir = "$top/lib"; +diff --git a/start_tassel.pl b/start_tassel.pl +index 18b9fd2..f013cc2 100755 +--- a/start_tassel.pl ++++ b/start_tassel.pl +@@ -1,9 +1,11 @@ +-#!/usr/bin/perl -w ++#!/usr/bin/env perl + + use strict; + use File::Basename; ++use Cwd 'abs_path' + +-my $dirname = dirname(__FILE__); ++my $filepath = abs_path(__FILE__); ++my $dirname = dirname($filepath); + my $top = defined($dirname) ? $dirname : '.'; + + my $libdir = "$top/lib"; diff --git a/recipes/tedna/meta.yaml b/recipes/tedna/meta.yaml index 84ca591a01287..8ae52f14286e6 100644 --- a/recipes/tedna/meta.yaml +++ b/recipes/tedna/meta.yaml @@ -3,7 +3,7 @@ package: version: "1.2.2" build: - number: 0 + number: 1 source: fn: tedna_1.2.2.tar.gz @@ -12,13 +12,12 @@ source: requirements: build: - - google-sparsehash + - sparsehash - gcc - bc run: - libgcc - - google-sparsehash test: commands: diff --git a/recipes/theta2/meta.yaml b/recipes/theta2/meta.yaml index dfda4d4128263..09f4154eaa7db 100644 --- a/recipes/theta2/meta.yaml +++ b/recipes/theta2/meta.yaml @@ -7,6 +7,7 @@ build: source: fn: theta-0.7.tar.gz url: https://github.com/raphael-group/THetA/archive/v0.7.tar.gz + sha256: 474452fa87a1ca0228137693bfede3200b91e4e166b2216c4bd24f8b270c1dea requirements: build: diff --git a/recipes/toulligqc/build.sh b/recipes/toulligqc/build.sh new file mode 100644 index 0000000000000..fa5e90cdd045a --- /dev/null +++ b/recipes/toulligqc/build.sh @@ -0,0 +1,4 @@ +#!/bin/bash + +$PYTHON setup.py install --single-version-externally-managed --record=record.txt + diff --git a/recipes/toulligqc/meta.yaml b/recipes/toulligqc/meta.yaml new file mode 100644 index 0000000000000..09912c782fed6 --- /dev/null +++ b/recipes/toulligqc/meta.yaml @@ -0,0 +1,47 @@ +{% set version = "0.5" %} + +package: + name: toulligqc + version: {{ version }} + +source: + fn: toulligqc-0.5.tar.gz + url: https://pypi.io/packages/source/t/toulligqc/toulligqc-{{ version }}.tar.gz + sha256: 23168b155c177a1e9d17f26431e3505db2d4f76af0fe2dbd5a9b401118894870 + +build: + entry_points: + - toulligqc=toulligqc.toulligqc:main + number: 0 + skip: True # [py27] + +requirements: + build: + - python + - setuptools + - matplotlib >=2.0,<2.1 + - seaborn >=0.7,<0.8 + - h5py >=2.7,<2.8 + - pandas >=0.19,<0.20 + - numpy >=1.12,<1.13 + + run: + - python + - matplotlib >=2.0,<2.1 + - seaborn >=0.7,<0.8 + - h5py >=2.7,<2.8 + - pandas >=0.19,<0.20 + - numpy >=1.12,<1.13 + +test: + imports: + - toulligqc + + commands: + - toulligqc --help + +about: + home: https://github.com/GenomicParisCentre/toulligQC + license: GPLv3 + summary: 'A post sequencing QC tool for Oxford Nanopore sequencers' + license_family: GPL3 diff --git a/recipes/trawler/build.sh b/recipes/trawler/build.sh index 86ef2d5d44203..5e422500a79e4 100644 --- a/recipes/trawler/build.sh +++ b/recipes/trawler/build.sh @@ -2,6 +2,13 @@ outdir=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +# See https://github.com/Ramialison-Lab-ARMI/Trawler-2.0/issues/1 +# Fix space in some hash-bang lines, +sed -i.bak 's|#! usr/bin/perl|#!/usr/bin/env perl|' bin/*.pl +# Fix hash-bang lines not to use system Perl, +sed -i.bak 's|#!/usr/bin/perl|#!/usr/bin/env perl|' bin/*.pl +rm -rf bin/*.bak + rm -rf test_data examples mkdir -p $outdir cp -r * $outdir @@ -9,8 +16,6 @@ cp -r * $outdir # Short wrapper script cat > $PREFIX/bin/trawler <=1.10.4 + - scipy >=0.16.1 + - biopython >=1.66 + - pandas >=0.17.1 + - matplotlib + +test: + commands: + - ancestral_reconstruction.py -h + - timetree_inference.py -h + - temporal_signal.py -h + imports: + - treetime + +about: + home: 'https://github.com/neherlab/treetime' + summary: 'Maximum-Likelihood dating and ancestral inference for phylogenetic trees' + license: MIT \ No newline at end of file diff --git a/recipes/trinity/build.sh b/recipes/trinity/build.sh index 2f67883bd757f..d1df4fc371f70 100644 --- a/recipes/trinity/build.sh +++ b/recipes/trinity/build.sh @@ -2,18 +2,6 @@ set -x -e -# fix automake -sed -i.bak '1 s|^.*$|#!/usr/bin/env perl|g' $PREFIX/bin/aclocal -sed -i.bak '1 s|^.*$|#!/usr/bin/env perl|g' $PREFIX/bin/automake - -# fix autoconf -sed -i.bak '1 s|^.*$|#!/usr/bin/env perl|g' $PREFIX/bin/autom4te -sed -i.bak '1 s|^.*$|#!/usr/bin/env perl|g' $PREFIX/bin/autoheader -sed -i.bak '1 s|^.*$|#!/usr/bin/env perl|g' $PREFIX/bin/autoreconf -sed -i.bak '1 s|^.*$|#!/usr/bin/env perl|g' $PREFIX/bin/ifnames -sed -i.bak '1 s|^.*$|#!/usr/bin/env perl|g' $PREFIX/bin/autoscan -sed -i.bak '1 s|^.*$|#!/usr/bin/env perl|g' $PREFIX/bin/autoupdate - export CC=${PREFIX}/bin/gcc export CXX=${PREFIX}/bin/g++ export INCLUDE_PATH="${PREFIX}/include" diff --git a/recipes/trinity/makefile.clean.patch b/recipes/trinity/makefile.clean.patch index 88eb33cd98180..12f3054d29f07 100644 --- a/recipes/trinity/makefile.clean.patch +++ b/recipes/trinity/makefile.clean.patch @@ -1,6 +1,6 @@ ---- Makefile 2017-02-27 16:01:58.731136923 +0100 -+++ Makefile 2017-02-27 16:05:53.000181525 +0100 -@@ -20,7 +20,7 @@ +--- Makefile.old 2017-11-29 16:36:53.468179187 +0200 ++++ Makefile 2017-12-07 21:41:00.092175195 +0200 +@@ -24,7 +24,7 @@ inchworm_target: @echo Using $(TRINITY_COMPILER) compiler for Inchworm and Chrysalis cd Inchworm && (test -e configure || autoreconf) \ diff --git a/recipes/trinity/meta.yaml b/recipes/trinity/meta.yaml index b41340794bfa2..3e11c6475729c 100644 --- a/recipes/trinity/meta.yaml +++ b/recipes/trinity/meta.yaml @@ -1,25 +1,15 @@ -{% set name = "trinity" %} -{% set version = "2.4.0" %} - -package: - name: {{ name|lower }} - version: {{ version }} - build: - number: 5 - skip: True # [osx] + number: 0 +# OSX build skipped because of this error: https://gist.github.com/pvanheus/2fbce93b326a3edb1a57aaebc8ca749e + skip: True # [osx] -source: - url: https://github.com/trinityrnaseq/trinityrnaseq/archive/Trinity-v{{ version }}.tar.gz - md5: 397cc93d75701ec681ea7af1a7837ed8 - patches: - - makefile.clean.patch - - trinity-plugins.makefile.clean.patch + +package: + name: trinity + version: '2.5.1' requirements: build: - - autoconf - - automake - collectl - fastool - gcc @@ -49,18 +39,24 @@ requirements: - trimmomatic >=0.36 - zlib +source: + fn: Trinity-v2.5.1.tar.gz + url: https://github.com/trinityrnaseq/trinityrnaseq/archive/Trinity-v2.5.1.tar.gz + sha256: bf14f96981bb028d7960dec895a1bcbda1fadbbe562a913b188559fd74b90457 + patches: + - makefile.clean.patch + - trinity-plugins.makefile.clean.patch + test: - commands: - - "Trinity --cite" - - "align_and_estimate_abundance.pl --help &> /dev/null || [[ \"$?\" == 255 ]]" - - "abundance_estimates_to_matrix.pl --help &> /dev/null || [[ \"$?\" == 255 ]]" - - "run_DE_analysis.pl -h &> /dev/null || [[ \"$?\" == 255 ]]" - - "analyze_diff_expr.pl -h &> /dev/null || [[ \"$?\" == 255 ]]" - - "PtR --help &> /dev/null || [[ \"$?\" == 255 ]]" - - "TrinityStats.pl 2>&1 | grep \"usage:\" " - - "define_clusters_by_cutting_tree.pl 2>&1 | grep \"define K clusters via k-means algorithm\" " - - "contig_ExN50_statistic.pl 2>&1 | grep \"usage:\" &> /dev/null" - - seqtk-trinity rename + commands: + - "Trinity --cite &> /dev/null" + - "align_and_estimate_abundance.pl --help &> /dev/null || [[ \"$?\" == 255 ]]" + - "abundance_estimates_to_matrix.pl --help &> /dev/null || [[ \"$?\" == 255 ]]" + - "run_DE_analysis.pl -h &> /dev/null || [[ \"$?\" == 255 ]]" + - "analyze_diff_expr.pl -h &> /dev/null || [[ \"$?\" == 255 ]]" + - "PtR --help &> /dev/null || [[ \"$?\" == 255 ]]" + - "TrinityStats.pl 2>&1 | grep \"usage:\" &> /dev/null" + - "define_clusters_by_cutting_tree.pl 2>&1 | grep \"define K clusters via k-means algorithm\" &> /dev/null" about: home: https://github.com/trinityrnaseq/trinityrnaseq/ diff --git a/recipes/trinity/run_test.sh b/recipes/trinity/run_test.sh new file mode 100755 index 0000000000000..1bd9fead9b219 --- /dev/null +++ b/recipes/trinity/run_test.sh @@ -0,0 +1,9 @@ +#!/bin/sh + +set -x -e + +${CONDA_PREFIX}/opt/trinity-*/Inchworm/bin/inchworm --help &>/dev/null || [ $? -eq 1 ] +${CONDA_PREFIX}/opt/trinity-*/Chrysalis/Chrysalis --help &>/dev/null || [ $? -eq 255 ] +${CONDA_PREFIX}/opt/trinity-*/Chrysalis/QuantifyGraph --help &>/dev/null || [ $? -eq 255 ] +${CONDA_PREFIX}/opt/trinity-*/Chrysalis/ReadsToTranscripts --help &>/dev/null || [ $? -eq 255 ] +${CONDA_PREFIX}/bin/ParaFly --help &>/dev/null || [ $? -eq 1 ] diff --git a/recipes/trinity/trinity-plugins.makefile.clean.patch b/recipes/trinity/trinity-plugins.makefile.clean.patch index 8ec782ef60d44..3018ccb8ff367 100644 --- a/recipes/trinity/trinity-plugins.makefile.clean.patch +++ b/recipes/trinity/trinity-plugins.makefile.clean.patch @@ -1,6 +1,6 @@ ---- trinity-plugins/Makefile 2017-02-27 16:04:28.330363594 +0100 -+++ trinity-plugins/Makefile 2017-02-27 22:28:09.040944472 +0100 -@@ -8,34 +8,15 @@ +--- trinity-plugins/Makefile.old 2017-11-29 16:39:42.851726034 +0200 ++++ trinity-plugins/Makefile 2017-12-07 21:44:09.660947521 +0200 +@@ -8,35 +8,16 @@ @@ -18,7 +18,7 @@ -endif - cd samtools-1.3.1 && $(MAKE) - mv samtools-1.3.1/samtools ./BIN/. -+trinity_essentials: seqtk_target parafly_target ++trinity_essentials: seqtk_target parafly_target seqtk_target: tar xvf seqtk-trinity.v0.0.2.tar.gz @@ -32,12 +32,13 @@ - - parafly_target: -- cd ${PARAFLY_CODE} && sh ./configure --prefix=`pwd` && $(MAKE) install + tar -zxvf ${PARAFLY_CODE}.tar.gz && \ +- cd ${PARAFLY_CODE} && sh ./configure --prefix=`pwd` && $(MAKE) install && \ + cd ${PARAFLY_CODE} && sh ./configure --prefix=`pwd` CC=${PREFIX}/bin/gcc $(INCHWORM_CONFIGURE_FLAGS) CXX=${PREFIX}/bin/g++ CFLAGS="-fopenmp" CXXFLAGS="-fopenmp" && $(MAKE) install - ln -sf ${PARAFLY_CODE} parafly + cp bin/ParaFly ../BIN/ -@@ -57,7 +38,7 @@ +@@ -58,7 +39,7 @@ rm -rf ${JELLYFISH_CODE} ./jellyfish # has tar.gz rm -rf ./seqtk-trinity-0.0.2 rm -rf ./samtools-1.3.1/ diff --git a/recipes/vcfkit/build.sh b/recipes/vcfkit/build.sh index 3f50b74e1bff2..3786386a73c83 100644 --- a/recipes/vcfkit/build.sh +++ b/recipes/vcfkit/build.sh @@ -1,9 +1,3 @@ #!/bin/bash -$PYTHON setup.py install - -# Add more build steps here, if they are necessary. - -# See -# http://docs.continuum.io/conda/build.html -# for a list of environment variables that are set during the build process. +$PYTHON setup.py install --single-version-externally-managed --record=record.txt diff --git a/recipes/vcfkit/meta.yaml b/recipes/vcfkit/meta.yaml index 26e83958f5ffe..9dc95e443ed33 100644 --- a/recipes/vcfkit/meta.yaml +++ b/recipes/vcfkit/meta.yaml @@ -1,11 +1,11 @@ package: name: vcfkit - version: "0.0.4" + version: "0.1.6" source: - fn: vcfkit-0.0.4.tar.gz - url: https://pypi.python.org/packages/52/49/d0ff24eb7ff1cb9907c76b56da19dc94f5161bb750a13cd3f010300e95fc/vcfkit-0.0.4.tar.gz - md5: 25af9501bb7691f286645cb80ad591d8 + fn: vcfkit-0.1.6.tar.gz + url: https://github.com/AndersenLab/VCF-kit/archive/0.1.6.tar.gz + sha256: 4865414ac9dc6996c0baeefadf1d528c28e6d0c3cc3dbdc28a2cdc6e06212428 build: skip: True # [not py27] @@ -16,7 +16,6 @@ build: requirements: build: - python - - setuptools - awesome-slugify - matplotlib - scipy @@ -36,7 +35,6 @@ requirements: run: - python - - setuptools - awesome-slugify - matplotlib - scipy diff --git a/recipes/vcfpy/meta.yaml b/recipes/vcfpy/meta.yaml new file mode 100644 index 0000000000000..d957a63cc96fa --- /dev/null +++ b/recipes/vcfpy/meta.yaml @@ -0,0 +1,31 @@ +{% set version = "0.11.0" %} +{% set md5sum = "e2d1c7d7c27da4f6237889bc07973d07" %} + +package: + name: vcfpy + version: {{ version }} + +source: + fn: vcfpy-{{ version }}.tar.gz + url: https://pypi.io/packages/source/v/vcfpy/vcfpy-{{ version }}.tar.gz + md5: "{{ md5sum }}" + +build: + skip: True # [py27] + script: python setup.py install --single-version-externally-managed --record record.txt + number: 0 + +requirements: + build: + - python + run: + - pysam >=0.10.0 + +test: + imports: + - vcfpy + +about: + home: https://github.com/bihealth/vcfpy + summary: Python 3 VCF library with good support for both reading and writing + license: MIT diff --git a/recipes/watchdog-wms/TestJavaFx.class b/recipes/watchdog-wms/TestJavaFx.class new file mode 100644 index 0000000000000000000000000000000000000000..fee93b0a9c761c62b8edfd310c623e628dd16399 GIT binary patch literal 602 zcmZuuO>fgc6r7FStdqD+Nl6Rzi_!v4k?@6E5fXw11vvr9QH8{5lWwamu^qV%GQWs( zIRN6o58y{3W`j^v30vCt_U+8P*|)!b|M&^u2_Dtaz`DeShg&t=#vKovb!=f#!0LkWW^|#)#kErW>9WuXCy~u~(EfW*lZ9`2$%0qaDmnVs^?I3Irxr9} z|90^I0lB&~ly!q%=LCDOPh`Iegq;M}74Ehf1>@4;H;5}H930o`yy&2YRoq~1p^DTB z<5tUwzQAoQeMR*%{CVy%cfO-`HRm;mm&9779cEU~VQlbUp=Oh2HfUm#Hd;I-b|A6l Lk$jWe3fg}Fud#Sy literal 0 HcmV?d00001 diff --git a/recipes/watchdog-wms/TestJavaFx.java b/recipes/watchdog-wms/TestJavaFx.java new file mode 100644 index 0000000000000..cd5c09f7c5f9a --- /dev/null +++ b/recipes/watchdog-wms/TestJavaFx.java @@ -0,0 +1,14 @@ +import java.lang.Exception; + +public class TestJavaFx { + public static void main(String[] args) { + try { + String rootTagTest = javafx.fxml.FXMLLoader.ROOT_TAG; + System.out.println("INSTALLED"); + } + catch(Exception e) { + System.out.println("MISSING"); + } + System.exit(0); + } +} diff --git a/recipes/watchdog-wms/build.sh b/recipes/watchdog-wms/build.sh new file mode 100644 index 0000000000000..9ae5fdc665aed --- /dev/null +++ b/recipes/watchdog-wms/build.sh @@ -0,0 +1,30 @@ +# stop on error +set -eu -o pipefail + +# create output folder name +VERSION="${PKG_NAME}-${PKG_VERSION}-${PKG_BUILDNUM}" +OUT="${PREFIX}/share/${VERSION}" +PATH="$PATH:$OUT/core_lib/wrapper/" + +# copy the files to /share/${VERSION} +mkdir -p "${OUT}" +mkdir -p "${PREFIX}/bin" +cp -R * "${OUT}/" + +# rename the sh scripts +mv "${OUT}/watchdog.sh" "${OUT}/watchdog-cmd.sh" +mv "${OUT}/workflowDesigner.sh" "${OUT}/watchdog-gui.sh" + +# create symbolic links and make them executable +ln -s "${OUT}/watchdog-cmd.sh" "${PREFIX}/bin/watchdog-cmd" +chmod 0755 "${PREFIX}/bin/watchdog-cmd" + +# test, if javafx is working +cd "${RECIPE_DIR}" +RET=$(java "TestJavaFx") +if [ "$RET" == "INSTALLED" ]; then + ln -s "${OUT}/watchdog-gui.sh" "${PREFIX}/bin/watchdog-gui" + chmod 0755 "${PREFIX}/bin/watchdog-gui" +else + echo "Javafx is not installed. No symlink to '${OUT}/watchdog-gui.sh' is created." +fi diff --git a/recipes/watchdog-wms/meta.yaml b/recipes/watchdog-wms/meta.yaml new file mode 100644 index 0000000000000..0a7f4ac377530 --- /dev/null +++ b/recipes/watchdog-wms/meta.yaml @@ -0,0 +1,52 @@ +{% set name = "watchdog-wms" %} +{% set version = "1.2.5" %} + +about: + home: https://www.bio.ifi.lmu.de/watchdog + license: GNU General Public License, Version 3 + summary: + Watchdog, a WMS for the automated and distributed analysis of large-scale experimental data. + The software is implemented in Java and is thus platform-independent. + Main feature include + - straightforward processing of replicate data + - support for distributed computer systems + - remote storage support + - customizable error detection + - manual intervention into workflow execution + - GUI for workflow construction using pre-defined modules + - a helper script for creating new module definitions + - no restriction to specific programming languages + - provides a flexible plugin system for extending without modifying the original sources + +package: + name: {{ name }} + version: {{ version }} + +build: + number: 1 + +source: + fn: {{ name }}-{{ version }}.tar.gz + url: https://github.com/klugem/watchdog/archive/v{{ version }}.tar.gz + sha256: f2141432dee56be6af1edbde9600409e85bdca2bb42fd830edfd9320b41e63c9 + +requirements: + build: + - openjdk >=8 + - coreutils >=8 + run: + - openjdk >=8 + - coreutils >=8 + +test: + files: + - workflow.test.xml + commands: + - watchdog-cmd --help + +extra: + maintainers: + - Michael Kluge + notes: | + Graphical user interface works only with JavaFX, which is currently not part of OpenJDK8. + Install script automatically detects if JavaFX is installed. diff --git a/recipes/watchdog-wms/run_test.sh b/recipes/watchdog-wms/run_test.sh new file mode 100644 index 0000000000000..067cc65ad8dd9 --- /dev/null +++ b/recipes/watchdog-wms/run_test.sh @@ -0,0 +1,20 @@ +#!/bin/bash +# stop on error +set -eu -o pipefail + +# create output folder name +VERSION="${PKG_NAME}-${PKG_VERSION}-${PKG_BUILDNUM}" +OUT="${PREFIX}/share/${VERSION}" +PATH="$PATH:$OUT/core_lib/wrapper/" + +function timeoutbash() { bash -c '(sleep 180; kill -9 $$ 2>/dev/null) & exec $@' $0 $@; } + +# basic test +timeoutbash watchdog-cmd --help 2>&1>/dev/null + +# prepare workflow test +TEST_FILE="workflow.test.xml" +sedinline "s#BASE_DIR#${OUT}/#" "${TEST_FILE}" +# workflow test +timeoutbash watchdog-cmd -mailWaitTime 0 -x "${TEST_FILE}" -p 8616 2>&1>/dev/null +exit 0 diff --git a/recipes/watchdog-wms/workflow.test.xml b/recipes/watchdog-wms/workflow.test.xml new file mode 100644 index 0000000000000..41d6ef2c01a02 --- /dev/null +++ b/recipes/watchdog-wms/workflow.test.xml @@ -0,0 +1,11 @@ + + + + + + 1s + + + + + diff --git a/recipes/wdltool/meta.yaml b/recipes/wdltool/meta.yaml index dfa9b89ecf64c..6dfc03e40357f 100644 --- a/recipes/wdltool/meta.yaml +++ b/recipes/wdltool/meta.yaml @@ -1,16 +1,17 @@ +{% set version="0.14" %} about: home: https://github.com/broadinstitute/wdltool license: "BSD" summary: "Command line utilities for interacting with WDL" package: name: wdltool - version: 0.9 + version: {{ version }} build: number: 0 source: - fn: wdltool-0.9.zip - url: https://github.com/broadinstitute/wdltool/archive/0.9.zip - md5: 29fa21e53445f6729c4897efc575635a + fn: wdltool-{{ version }}.tar.gz + url: https://github.com/broadinstitute/wdltool/archive/{{ version }}.tar.gz + md5: 072f73c47cf7611a39f979a02c9910dc requirements: build: - openjdk >=8 diff --git a/recipes/xopen/meta.yaml b/recipes/xopen/meta.yaml index 482685d7693a5..24813011a723b 100644 --- a/recipes/xopen/meta.yaml +++ b/recipes/xopen/meta.yaml @@ -5,17 +5,19 @@ about: package: name: xopen - version: "0.1.1" + version: "0.3.2" source: - fn: xopen-0.1.1.tar.gz - url: https://pypi.python.org/packages/9a/b7/8906d6b2c4f874c0aacc676709a3d533362ac93bebc4a656c9df19421c9b/xopen-0.1.1.tar.gz - md5: 4e0e955546ee6bee4ea736b54623a671 + fn: xopen-0.3.2.tar.gz + url: https://pypi.python.org/packages/63/7f/f18c758714d7f5714da95ef08eeacb04b6f9ef2e5853492c516cb979e4dc/xopen-0.3.2.tar.gz + md5: 1e8c7ec1ca903bd41483630280e6c2af requirements: run: + - bz2file # [py27] - python build: + - bz2file # [py27] - python test: @@ -23,4 +25,4 @@ test: - xopen build: - script: python setup.py install + script: $PYTHON setup.py install diff --git a/scripts/travis-run.sh b/scripts/travis-run.sh index ec5472d52fb9d..5a602e7bd08a8 100755 --- a/scripts/travis-run.sh +++ b/scripts/travis-run.sh @@ -10,16 +10,6 @@ set +u [[ -z $SKIP_LINTING ]] && SKIP_LINTING=false set -u -if [[ $TRAVIS_BRANCH != "master" && $TRAVIS_BRANCH != "bulk" && $TRAVIS_PULL_REQUEST == "false" && $TRAVIS_REPO_SLUG == "bioconda/bioconda-recipes" ]] -then - echo "" - echo "Tests are skipped for pushes to the main bioconda-recipes repo." - echo "If you have opened a pull request, please see the full tests for that PR." - echo "See https://bioconda.github.io/build-system.html for details" - echo "" - exit 0 -fi - # determine recipes to build. If building locally, build anything that changed # since master. If on travis, only build the commit range included in the push diff --git a/scripts/travis-setup.sh b/scripts/travis-setup.sh index 5575751a907a7..acb67ec65323a 100755 --- a/scripts/travis-setup.sh +++ b/scripts/travis-setup.sh @@ -2,14 +2,6 @@ set -e set -x -if [[ $TRAVIS_BRANCH != "master" && $TRAVIS_BRANCH != "bulk" && $TRAVIS_PULL_REQUEST == "false" && $TRAVIS_REPO_SLUG == "bioconda/bioconda-recipes" ]] -then - echo "" - echo "Setup is skipped for pushes to the main bioconda-recipes repo." - echo "" - exit 0 -fi - for dir in . recipes do if [ -e $dir/meta.yaml ]