diff --git a/.github/CODE_OF_CONDUCT.md b/.github/CODE_OF_CONDUCT.md new file mode 100644 index 0000000000000..966793f16fe8a --- /dev/null +++ b/.github/CODE_OF_CONDUCT.md @@ -0,0 +1,53 @@ +Bioconda Code of Conduct +======================== + +- Be respectful +- Be welcoming +- Be considerate +- Focus on what's best for the community +- Gracefully accept constructive criticism +- Show courtesy and respect towards other community members +- Be respectful of different viewpoints and experiences +- Use welcoming and inclusive language + +Reporting an issue +------------------ +If you see a violation of the code of conduct, please report it to a Bioconda core +member. You can find core members at +https://github.com/orgs/bioconda/teams/core/members, and emails on each users' +GitHub profile page. + +Enforcement +----------- +Upon receiving a report, the Bioconda core team will meet privately to discuss +the matter and determine the best course of action. + +Possible responses may include: + +- taking no further action (if we determine no violation occurred) +- a private reprimand from the core members to the individual(s) involved. In + this case, a core member will deliver that reprimand via email, copying the + rest of the core. +- a public reprimand. In this case a core member will deliver the reprimand via + the same channel as the violation occurred (e.g., via comment on PR or issue) + +- an imposed vacation (e.g., asking the individual to refrain from participating + for a week). A core member will deliver a request for the individual to take + such a "vacation" voluntarily, but if they don't disagree then a temporary + ban may be imposed. + +- a permanent or temporary ban from Bioconda + +Once a resolution is agreed upon, but before it is enacted, the core will +contact the original reporter and discuss the resolution and will note any +feedback for the record, but is not obligated to act on such feedback. + +The core will never publicly discuss the issue; any public statements will be +made by core members. + +If the incident involves a core member, the core member must recuse themselves +from the response process. + +This policy was modified from +https://www.djangoproject.com/conduct/enforcement-manual, [CCBY +3.0](https://creativecommons.org/licenses/by/3.0/) diff --git a/.github/welcome_new_contributor.md b/.github/welcome_new_contributor.md index 80e0879cec554..f0a6e2322e607 100644 --- a/.github/welcome_new_contributor.md +++ b/.github/welcome_new_contributor.md @@ -1,4 +1,4 @@ -Thanks for opening your first pull request! As you're new to bioconda, please read through our [documentation about contributing recipes](https://bioconda.github.io/contributing.html). If you need help, please ping one of the following teams: +Welcome to Bioconda, @{{user}}! Thank you for opening your first pull request! As you're new to Bioconda, please read through our [documentation about contributing recipes](https://bioconda.github.io/contributing.html). If you need help, please ping one of the following teams: - `@bioconda/haskel` for Haskell packages - `@bioconda/lib` for C/C++ packages @@ -8,5 +8,9 @@ Thanks for opening your first pull request! As you're new to bioconda, please re - `@bioconda/r` for R packages - `@bioconda/rust` for Rust packages - `@bioconda/core` in other cases + +You can also join our [Gitter channel](https://gitter.im/bioconda/Lobby) to find help. -Please ping `@bioconda/core` when your pull request is passing tests and ready to be merged. If you would like to be added to the bioconda team (so you can merge your own pull requests once all tests have passed) please mention that to `@bioconda/core` and they'll happily add you to the bioconda group. +Please ping `@bioconda/core` when your pull request is passing tests and ready to be merged. + +If you would like to join Bioconda, please mention that to `@bioconda/core` and they will happily send out an invitation link to you! diff --git a/build-fail-blacklist b/build-fail-blacklist index 75b8f4edbe60a..3277cb73f49c2 100644 --- a/build-fail-blacklist +++ b/build-fail-blacklist @@ -1,3 +1,10 @@ +# ../../utils//fileType/FileRecordTypeChecker.h:120:21: error: 'constexpr' needed for in-class initialization of static data member 'const float FileRecordTypeChecker::PERCENTAGE_PRINTABLE' of non-integral type [-fpermissive] +recipes/bedtools/2.20.1 +recipes/bedtools/2.19.1 + +# last-pair-probs.cc:501:10: error: cannot convert 'std::istream {aka std::basic_istream}' to 'bool' in return +recipes/last/638 + # Timeout downloading from sourceforge recipes/transcomb @@ -8,7 +15,6 @@ recipes/perl-sub-identify/0.12 recipes/perl-scalar-list-utils/1.45 recipes/perl-extutils-constant/0.24 recipes/seq-seq-pan -recipes/moods recipes/pylibseq recipes/metasnv recipes/gqt @@ -159,6 +165,14 @@ recipes/soapaligner # missing tarball recipes/metagene_annotator recipes/sloika +recipes/genometools +recipes/nanonet +recipes/knot +recipes/moreutils +recipes/jali +recipes/intervalstats +recipes/mrbayes +recipes/igvtools # missing dep recipes/oligotyping @@ -200,6 +214,7 @@ recipes/libmuscle # compilation error recipes/osra/2.0.1 +recipes/lightning # unable to access jarfile recipes/effectivet3 @@ -213,9 +228,6 @@ recipes/discovar-denovo # seqan errors recipes/bowtie/1.0.0 -# tarball missing -recipes/mrbayes - # depends on perl-pcap recipes/brass @@ -234,10 +246,6 @@ recipes/qiime/1.9.1 # requires wgs-assembler, which has a build fail recipes/sprai -# missing tarballs -recipes/genometools -recipes/nanonet - # missing dependency recipes/genomebaser recipes/garnet @@ -320,9 +328,6 @@ recipes/primerprospector # missing URL recipes/intemap -# compilation error -recipes/lightning - # zlib missing recipes/polymutt recipes/prophyle/0.2.1 @@ -495,9 +500,6 @@ recipes/perl-bio-db-sam recipes/krona/2.6 recipes/krona/2.5 -# tarball missing -recipes/igvtools - # /opt/conda/conda-bld/pash_1531691261758/_test_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_place/lib/ruby/2.4.0/rubygems/core_ext/kernel_require.rb:55:in `require': cannot load such file -- brl/util/textFileUtil (LoadError) recipes/pash @@ -537,26 +539,15 @@ recipes/ghc/6.8.3 # missing python dep recipes/hurry.filesize -# missing tarball -recipes/knot -recipes/moreutils - # compilation error, missing boost header recipes/k-slam -# missing tarball -recipes/jali -recipes/intervalstats - # failing recipes/igblast/1.4.0 # missing fortran lib, will fix this upstream recipes/ig-checkfcs -# I got far with desmon but not it fails inside Docker with a missing perl module -recipes/desman - # fortran missing :( recipes/fastspar @@ -722,7 +713,6 @@ recipes/bioconductor-org.mm.eg.db/3.3.0 recipes/bioconductor-qdnaseq.mm10/1.4.0 recipes/bioconductor-rgraphviz/2.13.0 recipes/bioconductor-ropls/1.2.14 -recipes/r-seurat/1.4.0.16 recipes/r-speaq/1.2.1 recipes/bioconductor-cummerbund/2.8.2 recipes/bioconductor-cummerbund/2.12.1 @@ -775,23 +765,6 @@ recipes/bioconductor-gladiatox recipes/bioconductor-biocgenerics # Build and rendering failures that are breaking bulk and the nightly uploads -recipes/samtools/0.1.19 -recipes/samtools/1.1 -recipes/last/490 -recipes/last/638 -recipes/last/874 -recipes/kat/2.0.8 -recipes/gromacs -recipes/braker -recipes/bowtie2/2.2.1 -recipes/bowtie2/2.2.4 -recipes/bowtie2/2.2.5 -recipes/bedtools/2.19.1 -recipes/bedtools/2.20.1 -recipes/bedtools/2.22 -recipes/bedtools/2.23.0 -recipes/bcftools -recipes/bcftools/1.3.1 recipes/sqt recipes/tepid recipes/aragorn/1.2.38 @@ -903,10 +876,7 @@ recipes/gromacs/2018 recipes/hr2 recipes/indelfixer recipes/je-suite -recipes/mafft/7.305 -recipes/mafft/7.310 recipes/mdust -recipes/meme/4.11.2 recipes/metacherchant recipes/mgltools recipes/mira @@ -937,7 +907,6 @@ recipes/regtools recipes/repeatscout recipes/rnacode/0.3 recipes/rna-seqc -recipes/rnashapes/2.1.6 recipes/rnastructure recipes/rnastructure/5.7 recipes/rnastructure/6.0 @@ -953,15 +922,11 @@ recipes/socru recipes/ssake recipes/subread recipes/tantan -recipes/tophat2/2.0.13 recipes/tophat-recondition recipes/tracer -recipes/trimmomatic/0.32 -recipes/trimmomatic/0.33 recipes/vcfsamplecompare recipes/watchdog-wms recipes/wdltool -recipes/weblogo/2.8.2 recipes/womtool recipes/xtandem recipes/yaha diff --git a/recipes/bcftools/1.3.1/build.sh b/recipes/bcftools/1.3.1/build.sh index 58a27f3d9bcd5..d1bcbd736b94f 100644 --- a/recipes/bcftools/1.3.1/build.sh +++ b/recipes/bcftools/1.3.1/build.sh @@ -2,4 +2,5 @@ export CPPFLAGS="-I$PREFIX/include" export LDFLAGS="-L$PREFIX/lib" -make prefix=$PREFIX CPPFLAGS=$CPPFLAGS LDFLAGS=$LDFLAGS plugins install +make all prefix=${PREFIX} CC=${CC} LDFLAGS="$LDFLAGS" CFLAGS="$CFLAGS" +make install prefix=${PREFIX} CC=${CC} LDFLAGS="$LDFLAGS" CFLAGS="$CFLAGS" diff --git a/recipes/bcftools/1.3.1/meta.yaml b/recipes/bcftools/1.3.1/meta.yaml index fa4bbee170b8e..0279cb5701dbf 100644 --- a/recipes/bcftools/1.3.1/meta.yaml +++ b/recipes/bcftools/1.3.1/meta.yaml @@ -1,20 +1,14 @@ -about: - home: https://github.com/samtools/bcftools - license: MIT - summary: BCFtools is a set of utilities that manipulate variant calls in the Variant - Call Format (VCF) and its binary counterpart BCF. All commands work transparently - with both VCFs and BCFs, both uncompressed and BGZF-compressed. Most commands - accept VCF, bgzipped VCF and BCF with filetype detected automatically even when - streaming from a pipe. Indexed VCF and BCF will work in all situations. Un-indexed - VCF and BCF and streams will work in most, but not all situations. - -build: - number: 4 - package: name: bcftools version: '1.3.1' +source: + sha256: 12c37a4054cbf1980223e2b3a80a7fdb3fd850324a4ba6832e38fdba91f1b924 + url: https://github.com/samtools/bcftools/releases/download/1.3.1/bcftools-1.3.1.tar.bz2 + +build: + number: 5 + requirements: build: - {{ compiler('c') }} @@ -23,16 +17,23 @@ requirements: run: - zlib -source: - sha256: 12c37a4054cbf1980223e2b3a80a7fdb3fd850324a4ba6832e38fdba91f1b924 - url: https://github.com/samtools/bcftools/releases/download/1.3.1/bcftools-1.3.1.tar.bz2 - test: commands: - "bcftools -h > /dev/null" - bcftools --version - bcftools plugin -lv +about: + home: https://github.com/samtools/bcftools + license: MIT + license_file: "LICENSE" + summary: BCFtools is a set of utilities that manipulate variant calls in the Variant + Call Format (VCF) and its binary counterpart BCF. All commands work transparently + with both VCFs and BCFs, both uncompressed and BGZF-compressed. Most commands + accept VCF, bgzipped VCF and BCF with filetype detected automatically even when + streaming from a pipe. Indexed VCF and BCF will work in all situations. Un-indexed + VCF and BCF and streams will work in most, but not all situations. + extra: identifiers: - biotools:bcftools diff --git a/recipes/bcftools/meta.yaml b/recipes/bcftools/meta.yaml index 7d483559add71..d0de65be7fe4a 100644 --- a/recipes/bcftools/meta.yaml +++ b/recipes/bcftools/meta.yaml @@ -1,19 +1,16 @@ {% set version="1.9" %} -about: - home: https://github.com/samtools/bcftools - license: MIT - summary: BCFtools is a set of utilities that manipulate variant calls in the Variant - Call Format (VCF) and its binary counterpart BCF. All commands work transparently - with both VCFs and BCFs, both uncompressed and BGZF-compressed. Most commands - accept VCF, bgzipped VCF and BCF with filetype detected automatically even when - streaming from a pipe. Indexed VCF and BCF will work in all situations. Un-indexed - VCF and BCF and streams will work in most, but not all situations. -build: - number: 3 package: name: bcftools version: {{ version }} + +build: + number: 4 + +source: + url: https://github.com/samtools/bcftools/releases/download/{{ version }}/bcftools-{{ version }}.tar.bz2 + sha256: 6f36d0e6f16ec4acf88649fb1565d443acf0ba40f25a9afd87f14d14d13070c8 + requirements: build: - {{ compiler('c') }} @@ -33,10 +30,6 @@ requirements: - zlib - libdeflate -source: - url: https://github.com/samtools/bcftools/releases/download/{{ version }}/bcftools-{{ version }}.tar.bz2 - sha256: 6f36d0e6f16ec4acf88649fb1565d443acf0ba40f25a9afd87f14d14d13070c8 - test: commands: - bcftools -h @@ -44,6 +37,16 @@ test: - bcftools plugin -lv #- plot-vcfstats -h 2>&1 | grep -q "Plots output of " +about: + home: https://github.com/samtools/bcftools + license: MIT + summary: BCFtools is a set of utilities that manipulate variant calls in the Variant + Call Format (VCF) and its binary counterpart BCF. All commands work transparently + with both VCFs and BCFs, both uncompressed and BGZF-compressed. Most commands + accept VCF, bgzipped VCF and BCF with filetype detected automatically even when + streaming from a pipe. Indexed VCF and BCF will work in all situations. Un-indexed + VCF and BCF and streams will work in most, but not all situations. + extra: identifiers: - biotools:bcftools diff --git a/recipes/bedtools/2.19.1/build.sh b/recipes/bedtools/2.19.1/build.sh index e829f0c73c5f9..cb1f36a5aba74 100644 --- a/recipes/bedtools/2.19.1/build.sh +++ b/recipes/bedtools/2.19.1/build.sh @@ -4,6 +4,6 @@ export CFLAGS="-I$PREFIX/include" export LDFLAGS="-L$PREFIX/lib" export CPATH=${PREFIX}/include -make +make prefix=$PREFIX CXX=$CXX CC=$CC LDFLAGS="-L$PREFIX/lib" mkdir -p $PREFIX/bin mv bin/* $PREFIX/bin/ diff --git a/recipes/bedtools/2.19.1/meta.yaml b/recipes/bedtools/2.19.1/meta.yaml index 092d51584cd5c..0a8acf5db1abe 100644 --- a/recipes/bedtools/2.19.1/meta.yaml +++ b/recipes/bedtools/2.19.1/meta.yaml @@ -1,31 +1,32 @@ -about: - home: http://bedtools.readthedocs.org/ - license: GPL v2 - summary: 'A swiss army knife for genome arithmetic. https://github.com/arq5x/bedtools2 ' - -build: - number: 2 - package: name: bedtools version: 2.19.1 +source: + sha256: 17253439e8191cb51a8bffba640c580e09ba158d3a0c66649e53d23ee3e50f77 + url: https://github.com/arq5x/bedtools2/releases/download/v2.19.1/bedtools-2.19.1.tar.gz + +build: + number: 3 + requirements: build: - {{ compiler('cxx') }} + - {{ compiler('c') }} host: - zlib run: - zlib -source: - sha256: 17253439e8191cb51a8bffba640c580e09ba158d3a0c66649e53d23ee3e50f77 - url: https://github.com/arq5x/bedtools2/releases/download/v2.19.1/bedtools-2.19.1.tar.gz - test: commands: - bedtools +about: + home: http://bedtools.readthedocs.org/ + license: GPL v2 + summary: 'A swiss army knife for genome arithmetic. https://github.com/arq5x/bedtools2 ' + extra: identifiers: - biotools:bedtools diff --git a/recipes/bedtools/2.20.1/build.sh b/recipes/bedtools/2.20.1/build.sh index e829f0c73c5f9..28f488f4b3c86 100644 --- a/recipes/bedtools/2.20.1/build.sh +++ b/recipes/bedtools/2.20.1/build.sh @@ -4,6 +4,6 @@ export CFLAGS="-I$PREFIX/include" export LDFLAGS="-L$PREFIX/lib" export CPATH=${PREFIX}/include -make -mkdir -p $PREFIX/bin -mv bin/* $PREFIX/bin/ +make prefix=$PREFIX CXX=$CXX CC=$CC LDFLAGS="-L$PREFIX/lib" +mkdir -p ${PREFIX}/bin +mv bin/* ${PREFIX}/bin/ diff --git a/recipes/bedtools/2.20.1/meta.yaml b/recipes/bedtools/2.20.1/meta.yaml index 880c9ac171a56..3625c0ae97898 100644 --- a/recipes/bedtools/2.20.1/meta.yaml +++ b/recipes/bedtools/2.20.1/meta.yaml @@ -1,31 +1,32 @@ -about: - home: http://bedtools.readthedocs.org/ - license: GPL v2 - summary: 'A swiss army knife for genome arithmetic. https://github.com/arq5x/bedtools2 ' - -build: - number: 2 - package: name: bedtools version: 2.20.1 +source: + sha256: b5401810f8b12b683575f0119521dda64ff2f0a59faa308357405c4ae4e328d3 + url: https://github.com/arq5x/bedtools2/releases/download/v2.20.1/bedtools-2.20.1.tar.gz + +build: + number: 3 + requirements: build: - {{ compiler('cxx') }} + - {{ compiler('c') }} host: - zlib run: - zlib -source: - sha256: b5401810f8b12b683575f0119521dda64ff2f0a59faa308357405c4ae4e328d3 - url: https://github.com/arq5x/bedtools2/releases/download/v2.20.1/bedtools-2.20.1.tar.gz - test: commands: - bedtools +about: + home: http://bedtools.readthedocs.org/ + license: GPL v2 + summary: 'A swiss army knife for genome arithmetic. https://github.com/arq5x/bedtools2 ' + extra: identifiers: - biotools:bedtools diff --git a/recipes/bedtools/2.22/build.sh b/recipes/bedtools/2.22/build.sh index 88a14a2ff40fa..69dc51361596b 100644 --- a/recipes/bedtools/2.22/build.sh +++ b/recipes/bedtools/2.22/build.sh @@ -4,4 +4,4 @@ export CFLAGS="-I$PREFIX/include" export LDFLAGS="-L$PREFIX/lib" export CPATH=${PREFIX}/include -make install prefix=$PREFIX +make install prefix=$PREFIX CXX=$CXX CC=$CC LDFLAGS="-L$PREFIX/lib" diff --git a/recipes/bedtools/2.22/meta.yaml b/recipes/bedtools/2.22/meta.yaml index 89aa6cdb89b2e..66c0a05ec68a1 100644 --- a/recipes/bedtools/2.22/meta.yaml +++ b/recipes/bedtools/2.22/meta.yaml @@ -1,31 +1,33 @@ -about: - home: http://bedtools.readthedocs.org/ - license: GPL v2 - summary: 'A swiss army knife for genome arithmetic. https://github.com/arq5x/bedtools2 ' - -build: - number: 2 - package: name: bedtools version: '2.22' +source: + sha256: 43ab5da6b41350bbef78ea2ee5be0609fb02d76b920a3301b687a39af7017233 + url: https://github.com/arq5x/bedtools2/releases/download/v2.22.1/bedtools-2.22.1.tar.gz + +build: + number: 3 + skip: True # [osx] + requirements: build: - {{ compiler('cxx') }} + - {{ compiler('c') }} host: - zlib run: - zlib -source: - sha256: 43ab5da6b41350bbef78ea2ee5be0609fb02d76b920a3301b687a39af7017233 - url: https://github.com/arq5x/bedtools2/releases/download/v2.22.1/bedtools-2.22.1.tar.gz - test: commands: - bedtools +about: + home: http://bedtools.readthedocs.org/ + license: GPL v2 + summary: 'A swiss army knife for genome arithmetic. https://github.com/arq5x/bedtools2 ' + extra: identifiers: - biotools:bedtools diff --git a/recipes/bedtools/2.23.0/build.sh b/recipes/bedtools/2.23.0/build.sh index 88a14a2ff40fa..69dc51361596b 100644 --- a/recipes/bedtools/2.23.0/build.sh +++ b/recipes/bedtools/2.23.0/build.sh @@ -4,4 +4,4 @@ export CFLAGS="-I$PREFIX/include" export LDFLAGS="-L$PREFIX/lib" export CPATH=${PREFIX}/include -make install prefix=$PREFIX +make install prefix=$PREFIX CXX=$CXX CC=$CC LDFLAGS="-L$PREFIX/lib" diff --git a/recipes/bedtools/2.23.0/meta.yaml b/recipes/bedtools/2.23.0/meta.yaml index 12c60f31d4367..0e617034b90e4 100644 --- a/recipes/bedtools/2.23.0/meta.yaml +++ b/recipes/bedtools/2.23.0/meta.yaml @@ -1,27 +1,33 @@ -about: - home: 'http://bedtools.readthedocs.org/' - license: 'GPL v2' - summary: 'A swiss army knife for genome arithmetic. https://github.com/arq5x/bedtools2 ' -build: - number: 2 package: name: bedtools version: '2.23.0' + +source: + sha256: 9dacaa561d11ce9835d1d51e5aeb092bcbe117b7119663ec9a671abac6a36056 + url: https://github.com/arq5x/bedtools2/archive/v2.23.0.tar.gz + +build: + number: 3 + skip: True # [osx] + requirements: build: - {{ compiler('cxx') }} + - {{ compiler('c') }} host: - zlib run: - zlib -source: - sha256: 9dacaa561d11ce9835d1d51e5aeb092bcbe117b7119663ec9a671abac6a36056 - url: https://github.com/arq5x/bedtools2/archive/v2.23.0.tar.gz test: commands: - bedtools +about: + home: 'http://bedtools.readthedocs.org/' + license: 'GPL v2' + summary: 'A swiss army knife for genome arithmetic. https://github.com/arq5x/bedtools2 ' + extra: identifiers: - biotools:bedtools diff --git a/recipes/biobb_analysis/build.sh b/recipes/biobb_analysis/build.sh index 92bce6a968d8b..ffb5d16814f33 100644 --- a/recipes/biobb_analysis/build.sh +++ b/recipes/biobb_analysis/build.sh @@ -22,6 +22,9 @@ cp $SP_DIR/biobb_analysis/gromacs/gmx_image.py $PREFIX/bin/gmx_image chmod u+x $SP_DIR/biobb_analysis/gromacs/gmx_trjconv_str.py cp $SP_DIR/biobb_analysis/gromacs/gmx_trjconv_str.py $PREFIX/bin/gmx_trjconv_str +chmod u+x $SP_DIR/biobb_analysis/gromacs/gmx_trjconv_str_ens.py +cp $SP_DIR/biobb_analysis/gromacs/gmx_trjconv_str_ens.py $PREFIX/bin/gmx_trjconv_str_ens + chmod u+x $SP_DIR/biobb_analysis/gromacs/gmx_trjconv_trj.py cp $SP_DIR/biobb_analysis/gromacs/gmx_trjconv_trj.py $PREFIX/bin/gmx_trjconv_trj diff --git a/recipes/biobb_analysis/meta.yaml b/recipes/biobb_analysis/meta.yaml index c7f7fe909cdc9..b9bb220000689 100644 --- a/recipes/biobb_analysis/meta.yaml +++ b/recipes/biobb_analysis/meta.yaml @@ -1,8 +1,8 @@ {% set name = "biobb_analysis" %} -{% set version = "1.0.1" %} +{% set version = "1.0.2" %} {% set file_ext = "tar.gz" %} {% set hash_type = "sha256" %} -{% set hash_value = "1c0b39e7367e4dc6d02379670891264244e89cd6303466fb61105ed961c9ed6d" %} +{% set hash_value = "afcdbf89b07bad0a920bd19a74b5c44632faf2a5973038d72925ecc004bf5c5c" %} package: name: '{{ name|lower }}' @@ -20,11 +20,11 @@ requirements: host: - python ==3.6.* - setuptools - - biobb_common ==0.1.4 + - biobb_common ==1.1.6 - gromacs ==2018.4 run: - python ==3.6.* - - biobb_common ==0.1.4 + - biobb_common ==1.1.6 - gromacs ==2018.4 test: imports: @@ -38,7 +38,11 @@ about: license_family: APACHE license_file: '' summary: Biobb_analysis is the Biobb module collection to perform analysis of molecular dynamics simulations. - description: "[![Documentation Status](https://readthedocs.org/projects/biobb-analysis/badge/?version=latest)](https://biobb-analysis.readthedocs.io/en/latest/?badge=latest)\n\ + description: "[![](https://readthedocs.org/projects/biobb-analysis/badge/?version=latest)](https://biobb-analysis.readthedocs.io/en/latest/?badge=latest)\ + \ [![](https://img.shields.io/badge/install%20with-bioconda-brightgreen.svg?style=flat)](https://anaconda.org/bioconda/biobb_analysis)\ + \ [![](https://quay.io/repository/biocontainers/biobb_io/status)](https://hub.docker.com/r/mmbirb/biobb_analysis)\ + \ [![](https://www.singularity-hub.org/static/img/hosted-singularity--hub-%23e32929.svg)](https://singularity-hub.org/collections/2423)\ + \ [![](https://img.shields.io/badge/License-Apache%202.0-blue.svg)](https://opensource.org/licenses/Apache-2.0)\n\ \n# biobb_analysis\n\n### Introduction\nBiobb_analysis is the Biobb module collection to perform analysis of molecular dynamics simulations.\nBiobb (BioExcel building blocks) packages are Python building blocks that\ncreate\ \ new layer of compatibility and interoperability over popular\nbioinformatics tools.\nThe latest documentation of this package can be found in our readthedocs site:\n[latest API documentation](http://biobb_analysis.readthedocs.io/en/latest/).\n\ \n\n### Copyright & Licensing\nThis software has been developed in the MMB group (http://mmb.irbbarcelona.org) at the\nBSC (http://www.bsc.es/) & IRB\ diff --git a/recipes/biobb_common/meta.yaml b/recipes/biobb_common/meta.yaml index 6c1f383add579..20d0408aec1c1 100644 --- a/recipes/biobb_common/meta.yaml +++ b/recipes/biobb_common/meta.yaml @@ -1,8 +1,8 @@ {% set name = "biobb_common" %} -{% set version = "0.1.5" %} +{% set version = "1.1.6" %} {% set file_ext = "tar.gz" %} {% set hash_type = "sha256" %} -{% set hash_value = "a3eeba6c0f531b3c5db77f99cfc317b110e4d8aea525e6558f0481cae5269e40" %} +{% set hash_value = "6fa6597626c508698f3b79dad11907c8ce3602134a2cf222821648badfd04cff" %} package: name: '{{ name|lower }}' diff --git a/recipes/biobb_io/meta.yaml b/recipes/biobb_io/meta.yaml index aa31a823bd4d7..6f2cedb10dd58 100644 --- a/recipes/biobb_io/meta.yaml +++ b/recipes/biobb_io/meta.yaml @@ -1,8 +1,8 @@ {% set name = "biobb_io" %} -{% set version = "0.1.4" %} +{% set version = "1.1.6" %} {% set file_ext = "tar.gz" %} {% set hash_type = "sha256" %} -{% set hash_value = "f933cefc0b95c978ac15dc1f7a5b71ce7eb70cafbb921b627293ea3b22b6a065" %} +{% set hash_value = "abaa266e05839fb6ffc473ced64811a54338a632636bcb187b14b811c4852afa" %} package: name: '{{ name|lower }}' @@ -18,12 +18,12 @@ build: requirements: host: - - python >=3 + - python ==3.6.* - setuptools - - biobb_common >=0.1.2 + - biobb_common ==1.1.6 run: - - python >=3 - - biobb_common >=0.1.2 + - python ==3.6.* + - biobb_common ==1.1.6 test: imports: - biobb_io diff --git a/recipes/biobb_md/build.sh b/recipes/biobb_md/build.sh index e3475ba9a58a6..e5d28cdab1ca7 100644 --- a/recipes/biobb_md/build.sh +++ b/recipes/biobb_md/build.sh @@ -30,3 +30,6 @@ cp $SP_DIR/biobb_md/gromacs/solvate.py $PREFIX/bin/solvate chmod u+x $SP_DIR/biobb_md/gromacs_extra/ndx2resttop.py cp $SP_DIR/biobb_md/gromacs_extra/ndx2resttop.py $PREFIX/bin/ndx2resttop + +chmod u+x $SP_DIR/biobb_md/gromacs_extra/append_ligand.py +cp $SP_DIR/biobb_md/gromacs_extra/append_ligand.py $PREFIX/bin/append_ligand diff --git a/recipes/biobb_md/meta.yaml b/recipes/biobb_md/meta.yaml index 49f327372cf92..cb3d45d531e86 100644 --- a/recipes/biobb_md/meta.yaml +++ b/recipes/biobb_md/meta.yaml @@ -1,8 +1,8 @@ {% set name = "biobb_md" %} -{% set version = "0.1.5" %} +{% set version = "1.1.6" %} {% set file_ext = "tar.gz" %} {% set hash_type = "sha256" %} -{% set hash_value = "4ebd24911526bd86451c2f2568af80f9c87c88dc9268bb0881739978d8447dec" %} +{% set hash_value = "33597a67fe2eaecac2eb5e823b5340fb55296508f59730cb485cc4ba5a2201b6" %} package: name: '{{ name|lower }}' @@ -18,14 +18,14 @@ build: requirements: host: - - python >=3 + - python ==3.6.* - setuptools - - biobb_common >=0.1.2 - - gromacs >=2018.4 + - biobb_common ==1.1.6 + - gromacs ==2019.1 run: - - python >=3 - - biobb_common >=0.1.2 - - gromacs >=2018.4 + - python ==3.6.* + - biobb_common ==1.1.6 + - gromacs ==2019.1 test: imports: - biobb_md diff --git a/recipes/biobb_model/meta.yaml b/recipes/biobb_model/meta.yaml index 6d25daa6847bf..960008fded75b 100644 --- a/recipes/biobb_model/meta.yaml +++ b/recipes/biobb_model/meta.yaml @@ -1,8 +1,8 @@ {% set name = "biobb_model" %} -{% set version = "0.1.8" %} +{% set version = "1.1.9" %} {% set file_ext = "tar.gz" %} {% set hash_type = "sha256" %} -{% set hash_value = "5072cf83122b25e1b2cb2be02ff59ad00804c6819a8d60c64b03b47f07a2904a" %} +{% set hash_value = "db32940f00e57ac7ed34caaffba03705a20c9e14c7524cfb516a3f9180622ef6" %} package: name: '{{ name|lower }}' @@ -20,11 +20,11 @@ requirements: host: - python ==3.6.* - setuptools - - biobb_common ==0.1.4 + - biobb_common ==1.1.6 - biobb_structure_checking ==1.0.6 run: - python ==3.6.* - - biobb_common ==0.1.4 + - biobb_common ==1.1.6 - biobb_structure_checking ==1.0.6 test: imports: diff --git a/recipes/biobb_pmx/build.sh b/recipes/biobb_pmx/build.sh new file mode 100644 index 0000000000000..6ec7fb431001e --- /dev/null +++ b/recipes/biobb_pmx/build.sh @@ -0,0 +1,14 @@ +#!/usr/bin/env bash + +python3 setup.py install --single-version-externally-managed --record=record.txt + +mkdir -p $PREFIX/bin + +chmod u+x $SP_DIR/biobb_pmx/pmx/mutate.py +cp $SP_DIR/biobb_pmx/pmx/mutate.py $PREFIX/bin/mutate + +chmod u+x $SP_DIR/biobb_pmx/pmx/analyse.py +cp $SP_DIR/biobb_pmx/pmx/analyse.py $PREFIX/bin/analyse + +chmod u+x $SP_DIR/biobb_pmx/pmx/gentop.py +cp $SP_DIR/biobb_pmx/pmx/gentop.py $PREFIX/bin/gentop diff --git a/recipes/biobb_pmx/meta.yaml b/recipes/biobb_pmx/meta.yaml new file mode 100644 index 0000000000000..bf4bbe70e058c --- /dev/null +++ b/recipes/biobb_pmx/meta.yaml @@ -0,0 +1,52 @@ +{% set name = "biobb_pmx" %} +{% set version = "1.0.0" %} +{% set file_ext = "tar.gz" %} +{% set hash_type = "sha256" %} +{% set hash_value = "83d2f1b3a9ab4f95e5d627bc746ea8342ffc96c4f696467fcfddbaf10b2da437" %} + +package: + name: '{{ name|lower }}' + version: '{{ version }}' + +source: + url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/{{ name }}-{{ version }}.{{ file_ext }} + '{{ hash_type }}': '{{ hash_value }}' + +build: + number: 0 + noarch: python + +requirements: + host: + - python ==3.6.* + - setuptools + - biobb_common ==1.1.6 + run: + - python ==3.6.* + - biobb_common ==1.1.6 +test: + imports: + - biobb_pmx + - biobb_pmx.pmx + - biobb_pmx.test + +about: + home: https://github.com/bioexcel/biobb_pmx + license: Apache Software License + license_family: APACHE + license_file: '' + summary: Biobb_pmx is the Biobb module collection to perform PMX (http://pmx.mpibpc.mpg.de) executions. + description: "[![](https://readthedocs.org/projects/biobb-pmx/badge/?version=latest)](https://biobb-pmx.readthedocs.io/en/latest/?badge=latest)\n[![](https://img.shields.io/badge/install%20with-bioconda-brightgreen.svg?style=flat)](https://anaconda.org/bioconda/biobb_pmx)\n\ + [![](https://quay.io/repository/biocontainers/biobb_pmx/status)](https://quay.io/repository/biocontainers/biobb_pmx)\n[![](https://www.singularity-hub.org/static/img/hosted-singularity--hub-%23e32929.svg)](https://www.singularity-hub.org/collections/2735/usage)\n\ + [![](https://img.shields.io/badge/License-Apache%202.0-blue.svg)](https://opensource.org/licenses/Apache-2.0)\n\n# biobb_pmx\n\n### Introduction\nBiobb_pmx is the Biobb module collection to perform\ + \ PMX (http://pmx.mpibpc.mpg.de) executions.\nBiobb (BioExcel building blocks) packages are Python building blocks that\ncreate new layer of compatibility and interoperability over popular\nbioinformatics\ + \ tools.\nThe latest documentation of this package can be found in our readthedocs site:\n[latest API documentation](http://biobb_pmx.readthedocs.io/en/latest/).\n\n### Version\nv1.0.0 April 2019 Release\n\ + \n### Copyright & Licensing\nThis software has been developed in the MMB group (http://mmb.irbbarcelona.org) at the\nBSC (http://www.bsc.es/) & IRB (https://www.irbbarcelona.org/) for the European BioExcel\ + \ (http://bioexcel.eu/), funded by the European Commission\n(EU H2020 [675728](http://cordis.europa.eu/projects/675728)).\n\n* (c) 2015-2019 [Barcelona Supercomputing Center](https://www.bsc.es/)\n\ + * (c) 2015-2019 [Institute for Research in Biomedicine](https://www.irbbarcelona.org/)\n\nLicensed under the\n[Apache License 2.0](https://www.apache.org/licenses/LICENSE-2.0), see the file\n[LICENSE](LICENSE)\ + \ for details.\n\n![](https://bioexcel.eu/wp-content/uploads/2015/12/Bioexcell_logo_1080px_transp.png \"Bioexcel\")\n\n\n" + doc_url: '' + dev_url: '' + +extra: + recipe-maintainers: '' diff --git a/recipes/bowtie2/2.2.1/build.sh b/recipes/bowtie2/2.2.1/build.sh index 41792e491fa35..70faeb3eb6431 100644 --- a/recipes/bowtie2/2.2.1/build.sh +++ b/recipes/bowtie2/2.2.1/build.sh @@ -1,9 +1,7 @@ #!/bin/bash set -eu -o pipefail -if [ "$(expr substr $(uname -s) 1 5)" == "Linux" ]; then - make -fi +make CXX=$CXX CPP=$CXX CC=$CC LDLIBS="-L$PREFIX/lib -lz -ltbb -ltbbmalloc -lpthread" binaries="\ bowtie2 \ diff --git a/recipes/bowtie2/2.2.1/meta.yaml b/recipes/bowtie2/2.2.1/meta.yaml index 89df12580c6a0..33b8952b8772a 100644 --- a/recipes/bowtie2/2.2.1/meta.yaml +++ b/recipes/bowtie2/2.2.1/meta.yaml @@ -1,14 +1,3 @@ -about: - home: 'http://bowtie-bio.sourceforge.net/bowtie2/index.shtml' - license: GPLv3 - summary: 'Bowtie 2 is an ultrafast and memory-efficient tool for aligning sequencing - reads to long reference sequences. It is particularly good at aligning reads of - about 50 up to 100s or 1,000s of characters, and particularly good at aligning - to relatively long (e.g. mammalian) genomes. Bowtie 2 indexes the genome with - an FM Index to keep its memory footprint small: for the human genome, its memory - footprint is typically around 3.2 GB. Bowtie 2 supports gapped, local, and paired-end - alignment modes. http://bowtie-bio.sourceforge.net/bowtie2/index.shtml ' - package: name: bowtie2 version: 2.2.1 @@ -18,7 +7,7 @@ source: sha256: 32728b127abf0a8c3aa48e6fb8bf81a9133f54da7e065c2a7bd3410704195f9d build: - number: 1 + number: 2 skip: True # [osx] requirements: @@ -38,6 +27,17 @@ test: - bowtie2-align-s --help - bowtie2_wrapper.sh -h +about: + home: 'http://bowtie-bio.sourceforge.net/bowtie2/index.shtml' + license: GPLv3 + summary: 'Bowtie 2 is an ultrafast and memory-efficient tool for aligning sequencing + reads to long reference sequences. It is particularly good at aligning reads of + about 50 up to 100s or 1,000s of characters, and particularly good at aligning + to relatively long (e.g. mammalian) genomes. Bowtie 2 indexes the genome with + an FM Index to keep its memory footprint small: for the human genome, its memory + footprint is typically around 3.2 GB. Bowtie 2 supports gapped, local, and paired-end + alignment modes. http://bowtie-bio.sourceforge.net/bowtie2/index.shtml ' + extra: identifiers: - biotools:bowtie2 diff --git a/recipes/bowtie2/2.2.4/build.sh b/recipes/bowtie2/2.2.4/build.sh index 41792e491fa35..0a6064f83144e 100644 --- a/recipes/bowtie2/2.2.4/build.sh +++ b/recipes/bowtie2/2.2.4/build.sh @@ -2,7 +2,7 @@ set -eu -o pipefail if [ "$(expr substr $(uname -s) 1 5)" == "Linux" ]; then - make + make CXX=${CXX} fi binaries="\ diff --git a/recipes/bowtie2/2.2.4/meta.yaml b/recipes/bowtie2/2.2.4/meta.yaml index b11303e2a0d12..275006cb62033 100644 --- a/recipes/bowtie2/2.2.4/meta.yaml +++ b/recipes/bowtie2/2.2.4/meta.yaml @@ -1,14 +1,3 @@ -about: - home: 'http://bowtie-bio.sourceforge.net/bowtie2/index.shtml' - license: GPLv3 - summary: 'Bowtie 2 is an ultrafast and memory-efficient tool for aligning sequencing - reads to long reference sequences. It is particularly good at aligning reads of - about 50 up to 100s or 1,000s of characters, and particularly good at aligning - to relatively long (e.g. mammalian) genomes. Bowtie 2 indexes the genome with - an FM Index to keep its memory footprint small: for the human genome, its memory - footprint is typically around 3.2 GB. Bowtie 2 supports gapped, local, and paired-end - alignment modes. http://bowtie-bio.sourceforge.net/bowtie2/index.shtml ' - package: name: bowtie2 version: 2.2.4 @@ -18,7 +7,7 @@ source: md5: d31294875092e76ebb061eadc7998582 build: - number: 3 + number: 4 skip: True # [osx] requirements: @@ -38,6 +27,17 @@ test: - bowtie2-align-s --help - bowtie2_wrapper.sh -h +about: + home: 'http://bowtie-bio.sourceforge.net/bowtie2/index.shtml' + license: GPLv3 + summary: 'Bowtie 2 is an ultrafast and memory-efficient tool for aligning sequencing + reads to long reference sequences. It is particularly good at aligning reads of + about 50 up to 100s or 1,000s of characters, and particularly good at aligning + to relatively long (e.g. mammalian) genomes. Bowtie 2 indexes the genome with + an FM Index to keep its memory footprint small: for the human genome, its memory + footprint is typically around 3.2 GB. Bowtie 2 supports gapped, local, and paired-end + alignment modes. http://bowtie-bio.sourceforge.net/bowtie2/index.shtml ' + extra: identifiers: - biotools:bowtie2 diff --git a/recipes/bowtie2/2.2.5/build.sh b/recipes/bowtie2/2.2.5/build.sh index dd462b4414662..7f4e56c8aaa1f 100644 --- a/recipes/bowtie2/2.2.5/build.sh +++ b/recipes/bowtie2/2.2.5/build.sh @@ -1,9 +1,7 @@ #!/bin/bash set -eu -o pipefail -if [ "$(expr substr $(uname -s) 1 5)" == "Linux" ]; then - make -fi +make CXX=$CXX CPP=$CXX CC=$CC LDLIBS="-L$PREFIX/lib -lz -ltbb -ltbbmalloc -lpthread" binaries="\ bowtie2 \ diff --git a/recipes/bowtie2/2.2.5/meta.yaml b/recipes/bowtie2/2.2.5/meta.yaml index 3c62150955be9..6801333f67d84 100644 --- a/recipes/bowtie2/2.2.5/meta.yaml +++ b/recipes/bowtie2/2.2.5/meta.yaml @@ -1,26 +1,14 @@ -about: - home: 'http://bowtie-bio.sourceforge.net/bowtie2/index.shtml' - license: GPLv3 - summary: 'Bowtie 2 is an ultrafast and memory-efficient tool for aligning sequencing - reads to long reference sequences. It is particularly good at aligning reads of - about 50 up to 100s or 1,000s of characters, and particularly good at aligning - to relatively long (e.g. mammalian) genomes. Bowtie 2 indexes the genome with - an FM Index to keep its memory footprint small: for the human genome, its memory - footprint is typically around 3.2 GB. Bowtie 2 supports gapped, local, and paired-end - alignment modes. http://bowtie-bio.sourceforge.net/bowtie2/index.shtml ' - package: name: bowtie2 version: 2.2.5 source: - url: http://downloads.sourceforge.net/project/bowtie-bio/bowtie2/2.2.5/bowtie2-2.2.5-source.zip # [linux] - sha256: e22766dd9421c10e82a3e207ee1f0eb924c025b909ad5fffa36633cd7978d3b0 # [linux] - url: http://downloads.sourceforge.net/project/bowtie-bio/bowtie2/2.2.5/bowtie2-2.2.5-macos-x86_64.zip # [osx] - sha256: 0f142477738accc73276f3e47877d54a64b6f7ac7911d0609b662adcd15374a0 # [osx] + url: http://downloads.sourceforge.net/project/bowtie-bio/bowtie2/2.2.5/bowtie2-2.2.5-source.zip + sha256: e22766dd9421c10e82a3e207ee1f0eb924c025b909ad5fffa36633cd7978d3b0 build: - number: 4 + number: 5 + skip: True # [osx] requirements: build: @@ -38,6 +26,17 @@ test: - bowtie2-inspect-l --help - bowtie2-align-s --help +about: + home: 'http://bowtie-bio.sourceforge.net/bowtie2/index.shtml' + license: GPLv3 + summary: 'Bowtie 2 is an ultrafast and memory-efficient tool for aligning sequencing + reads to long reference sequences. It is particularly good at aligning reads of + about 50 up to 100s or 1,000s of characters, and particularly good at aligning + to relatively long (e.g. mammalian) genomes. Bowtie 2 indexes the genome with + an FM Index to keep its memory footprint small: for the human genome, its memory + footprint is typically around 3.2 GB. Bowtie 2 supports gapped, local, and paired-end + alignment modes. http://bowtie-bio.sourceforge.net/bowtie2/index.shtml ' + extra: identifiers: - biotools:bowtie2 diff --git a/recipes/braker/meta.yaml b/recipes/braker/meta.yaml index e263f8fde2c3d..4c60b9e0f6bd4 100644 --- a/recipes/braker/meta.yaml +++ b/recipes/braker/meta.yaml @@ -1,16 +1,15 @@ -about: - home: http://bioinf.uni-greifswald.de/augustus/ - license: ' ' - summary: 'BRAKER1: Unsupervised RNA-Seq-based genome annotation with GeneMark-ET and AUGUSTUS' - -build: - number: 2 - skip: True # [osx] - package: name: braker version: '1.9' +source: + url: http://exon.gatech.edu/genemark/Braker/BRAKER1.tar.gz + sha256: 9e959984f739208d2a0aab4cc978e7b11db11a86a25fcc5b8f71c9a31e9239f2 + +build: + number: 3 + skip: True # [osx] + requirements: build: - perl-module-build @@ -20,11 +19,13 @@ requirements: - perl-pathtools - perl-scalar-util-numeric -source: - url: http://exon.gatech.edu/genemark/Braker/BRAKER1.tar.gz - sha256: 9e959984f739208d2a0aab4cc978e7b11db11a86a25fcc5b8f71c9a31e9239f2 - test: commands: - filterGenemark.pl --help - filterIntronsFindStrand.pl --help + +about: + home: http://bioinf.uni-greifswald.de/augustus/ + license: 'Artistic license' + license_file: 'licence.txt' + summary: 'BRAKER1: Unsupervised RNA-Seq-based genome annotation with GeneMark-ET and AUGUSTUS' diff --git a/recipes/cpat/meta.yaml b/recipes/cpat/meta.yaml index 130e1db188757..e2e914014de32 100644 --- a/recipes/cpat/meta.yaml +++ b/recipes/cpat/meta.yaml @@ -1,5 +1,5 @@ {% set name = "cpat" %} -{% set version = "1.2.4" %} +{% set version = "2.0.0" %} package: name: "{{ name|lower }}" @@ -7,12 +7,12 @@ package: build: noarch: python - number: 1 + number: 0 script: "{{ PYTHON }} -m pip install . --no-deps --ignore-installed -vv " source: - url: https://files.pythonhosted.org/packages/53/dd/f6e7fda49f3e64b68c606c480847fd06fbc364b77561cdb68482b41e163c/CPAT-1.2.4.tar.gz - sha256: 6a552174f24531f7a391b6d330cf03990161941d31a535814139ea1ae3cd1444 + url: https://files.pythonhosted.org/packages/5c/ed/0cb7373f623f6e0d4a642f54cef717d4c78de339e0499ff57649a7c1f25f/CPAT-2.0.0.tar.gz + sha256: bcd1fd8543f51c45abeeccf4612f059b46ee56c5a75877db9c170bf221a5b8f4 requirements: host: @@ -20,15 +20,13 @@ requirements: - bx-python - pip - nose - # CPAT explicitly checks if python's version string starts with 2.7 - - python >=2.7,<2.8 + - python >=3.5 - pysam - numpy - cython - run: - bx-python - - python >=2.7,<2.8 + - python >=3.5 - numpy - pysam - r-base diff --git a/recipes/crispritz/build.sh b/recipes/crispritz/build.sh index bc3c81c51895a..f803be2d30dc2 100644 --- a/recipes/crispritz/build.sh +++ b/recipes/crispritz/build.sh @@ -1,11 +1,11 @@ #!/bin/bash -make +make -f Makefile_conda mkdir -p $PREFIX/bin mkdir -p $PREFIX/opt/crispritz -chmod 700 -R * +chmod -R 700 . cp crispritz.py $PREFIX/bin cp buildTST $PREFIX/opt/crispritz cp searchTST $PREFIX/opt/crispritz cp searchBruteForce $PREFIX/opt/crispritz -cp -R sourceCode/Python_Scripts/ $PREFIX/opt/crispritz +cp -R sourceCode/Python_Scripts $PREFIX/opt/crispritz diff --git a/recipes/crispritz/meta.yaml b/recipes/crispritz/meta.yaml index a0b9611c54efd..68e8cda863268 100644 --- a/recipes/crispritz/meta.yaml +++ b/recipes/crispritz/meta.yaml @@ -1,4 +1,4 @@ -{% set version = "1.0.5" %} +{% set version = "1.1.0" %} package: name: crispritz @@ -6,17 +6,18 @@ package: source: url: https://github.com/InfOmics/CRISPRitz/archive/v{{ version }}.tar.gz - sha256: ec616f6f20c498dc6b84232c52daac4462640fd0e3630b1e267140e95d3e2f63 + sha256: d22091c8f3907eef8d371109a56c535562b345eb3ffda2791bec9eb63e5d179e build: - number: 0 - skip: True # [osx] + number: 1 requirements: build: - - {{compiler('cxx')}} =5.4 + - {{compiler('cxx')}} =5.4 # [not osx] + - {{compiler('cxx')}} # [osx] - make - boost + - openmp host: - intervaltree @@ -29,6 +30,7 @@ requirements: - bcftools - boost - tk + - openmp run: - intervaltree @@ -41,6 +43,7 @@ requirements: - bcftools - boost - tk + - openmp test: commands: diff --git a/recipes/crumble/build.sh b/recipes/crumble/build.sh new file mode 100644 index 0000000000000..62863f6437e04 --- /dev/null +++ b/recipes/crumble/build.sh @@ -0,0 +1,5 @@ +#!/bin/sh + +./configure --prefix=${PREFIX} +make +make install diff --git a/recipes/crumble/meta.yaml b/recipes/crumble/meta.yaml new file mode 100644 index 0000000000000..78e63b35051bb --- /dev/null +++ b/recipes/crumble/meta.yaml @@ -0,0 +1,36 @@ +{% set version = "0.8.1" %} +{% set sha256 = "8f31aee3e5a2e22be1c0020373a4f689d3f82f4fbd3bea1b2c78352ad8372599" %} + +package: + name: crumble + version: '{{version}}' + +build: + number: 0 + +source: + url: https://github.com/jkbonfield/crumble/releases/download/v{{ version }}/crumble-{{ version }}.tar.gz + sha256: {{ sha256 }} + +requirements: + build: + - {{ compiler('c') }} + host: + - htslib + - zlib + run: + - htslib + +test: + commands: + - "crumble -h |grep 'Usage: crumble'" + +about: + home: https://github.com/jkbonfield/crumble + #licence in describing paper is'OpenSource'. Asked for a specific type of license upstream https://github.com/jkbonfield/crumble/issues/7 + license: open source + summary: Controllable lossy compression of BAM/CRAM files + +extra: + recipe-maintainers: + - maarten-k diff --git a/recipes/csvtk/meta.yaml b/recipes/csvtk/meta.yaml index 73417bb26f6f1..4367ba171a185 100644 --- a/recipes/csvtk/meta.yaml +++ b/recipes/csvtk/meta.yaml @@ -1,4 +1,4 @@ -{% set version = "0.17.0" %} +{% set version = "0.18.0" %} package: name: csvtk @@ -15,11 +15,11 @@ build: source: url: https://github.com/shenwei356/csvtk/releases/download/v{{ version }}/csvtk_darwin_amd64.tar.gz # [osx] - md5: 7cd4adf1eaf7ad82550545d425f0dd4c # [osx] + md5: 771d0f5825ed9ee34ebdbb377ada10ed # [osx] url: https://github.com/shenwei356/csvtk/releases/download/v{{ version }}/csvtk_linux_386.tar.gz # [linux] - md5: 2fb0547bf91935e93fa1ae023c325c0e # [linux] + md5: eeb18ddc864d1e1ec491cb755aea88fe # [linux] url: https://github.com/shenwei356/csvtk/releases/download/v{{ version }}/csvtk_linux_amd64.tar.gz # [linux64] - md5: ccd86274e49796beda65a1f403e48df4 # [linux64] + md5: 5d9c00daf0670f3ed6a958c77cf58fb8 # [linux64] test: commands: diff --git a/recipes/deepac/meta.yaml b/recipes/deepac/meta.yaml index e6b8d841ab4f0..ca7e6da5d9c45 100755 --- a/recipes/deepac/meta.yaml +++ b/recipes/deepac/meta.yaml @@ -1,5 +1,5 @@ {% set name = "deepac" %} -{% set version = "0.9.2" %} +{% set version = "0.9.3" %} package: name: "{{ name|lower }}" @@ -7,7 +7,7 @@ package: source: url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/{{ name }}-{{ version }}.tar.gz - sha256: eaf429fa5e94c2bd38e465752acd5bd4730df2772316ab08a020dbb500a985ae + sha256: c65a5135d58e90ee50d2843b8bc0bba66116e629482afe73eac437a8a1d9a3e9 build: noarch: python @@ -35,8 +35,10 @@ requirements: # imports: # - deepac # - deepac.eval +# - deepac.tests # commands: # - deepac --help +# - deepac test about: home: https://gitlab.com/rki_bioinformatics/DeePaC diff --git a/recipes/deeptoolsintervals/meta.yaml b/recipes/deeptoolsintervals/meta.yaml index bf0807b306f30..90a4c9d718fcc 100644 --- a/recipes/deeptoolsintervals/meta.yaml +++ b/recipes/deeptoolsintervals/meta.yaml @@ -1,5 +1,5 @@ {% set name = "deeptoolsintervals" %} -{% set version = "0.1.7" %} +{% set version = "0.1.8" %} package: name: "{{ name|lower }}" @@ -7,10 +7,10 @@ package: source: url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/{{ name }}-{{ version }}.tar.gz - sha256: 4682808360a5b50b69b28ec1f9231dfe9443638d0a262f8a4a1403c30f1592be + sha256: 161a9c8b358f240929761a78c0dcad83da1dce8a9440cca2f4b25731cca38018 build: - number: 2 + number: 0 requirements: build: diff --git a/recipes/desman/meta.yaml b/recipes/desman/meta.yaml index 8dda0d46e960c..a45cc7e7dab26 100644 --- a/recipes/desman/meta.yaml +++ b/recipes/desman/meta.yaml @@ -1,38 +1,39 @@ +{% set name = "DESMAN" %} {% set version = "2.1" %} +{% set sha256 = "3bca35dcabf1ce540ea053aaae459971b1ea9a1300d0b544002f50873d6347a2" %} package: - name: desman + name: {{ name|lower }} version: {{ version }} build: - number: 1 + number: 2 skip: True # [py<35] source: url: https://github.com/chrisquince/DESMAN/archive/v{{ version }}.tar.gz - sha256: 3bca35dcabf1ce540ea053aaae459971b1ea9a1300d0b544002f50873d6347a2 + sha256: {{ sha256 }} requirements: + build: + - {{ compiler('c') }} host: - python - setuptools - - cython - - openblas - - numpy + - cython >=0.19.1 + - numpy >=1.7.1 - gsl - - pandas - - scipy + - pandas >=0.11.0 + - scipy >=0.12.0 run: - python - - cython - - perl - - openblas - - bcbiogff + - cython >=0.19.1 + - bcbio-gff - biopython - pysam - - scipy - - numpy - - pandas + - scipy >=0.12.0 + - numpy >=1.7.1 + - pandas >=0.11.0 - scikit-learn - gsl - r-getopt @@ -41,9 +42,6 @@ requirements: - r-labeling test: - imports: - - desman - - sampletau commands: - desman -h - CalcDelta.py -h @@ -52,12 +50,16 @@ test: - ExtractGenes.py -h - CalcGeneCov.py -h - GeneAssign.py -h + # When testing imports, desman and sampletau are treated as Perl modules instead of Python, hence these two tests: + - python -c "import desman" + - python -c "import sampletau" about: home: https://github.com/chrisquince/DESMAN license: BSD + license_family: BSD license_file: LICENSE.txt - summary: 'De novo Extraction of Strains from MetAgeNomes' + summary: "De novo Extraction of Strains from MetAgeNomes" extra: identifiers: diff --git a/recipes/ephemeris/meta.yaml b/recipes/ephemeris/meta.yaml index 8d8e16caf3c5d..0b9e04fd023b8 100644 --- a/recipes/ephemeris/meta.yaml +++ b/recipes/ephemeris/meta.yaml @@ -1,13 +1,13 @@ package: name: ephemeris - version: "0.8.0" + version: "0.9.0" source: - url: https://pypi.python.org/packages/5a/5a/99d572f9117c69d25a668f9a8c40e7f35c0271c8aee6a1d0f6e7d821f516/ephemeris-0.8.0.tar.gz - md5: 962ee07257e976729452bde670d03442 + url: https://files.pythonhosted.org/packages/64/c7/4f129498ee63988ec4216c8973bd4ca6f6357b28c9601ba616d4db547b1e/ephemeris-0.9.0.tar.gz + sha256: b7d5fd64f61b3dab0d3b38293d5bec6b1c9e36f24c2fcbe7b43e45f9e4597f56 build: - number: 2 + number: 0 noarch: python preserve_egg_dir: True entry_points: @@ -24,13 +24,10 @@ requirements: host: - python - pip - - setuptools - - pyyaml - - bioblend - - jinja2 run: - python - pyyaml + - galaxy-lib - bioblend - jinja2 diff --git a/recipes/fineradstructure/build.sh b/recipes/fineradstructure/build.sh new file mode 100644 index 0000000000000..f221acbf5884d --- /dev/null +++ b/recipes/fineradstructure/build.sh @@ -0,0 +1,10 @@ +#!/bin/bash +# https://bioconda.github.io/troubleshooting.html#zlib-errors +export CFLAGS="-I$PREFIX/include" +export LDFLAGS="-L$PREFIX/lib" +export CPATH=${PREFIX}/include +export LD_LIBRARY_PATH=$PREFIX/lib:$LD_LIBRARY_PATH + +./configure --prefix=$PREFIX --with-gsl-prefix=$PREFIX #--disable-gsltest +make +make install diff --git a/recipes/fineradstructure/meta.yaml b/recipes/fineradstructure/meta.yaml new file mode 100644 index 0000000000000..8187f5c982f6f --- /dev/null +++ b/recipes/fineradstructure/meta.yaml @@ -0,0 +1,37 @@ +{% set version = "0.3.2r109" %} +{% set sha256 = "ff05ff14388e786615c7788669cf2b910d38fc35f4f7fbb83f58539a11896083" %} + +package: + name: fineradstructure + version: {{ version }} + +build: + number: 0 + skip: True # [osx] + +source: + url: https://github.com/millanek/fineRADstructure/archive/v.{{ version }}.tar.gz + sha256: {{ sha256 }} + +requirements: + build: + - {{ compiler('c') }} + - {{ compiler('cxx') }} + - autoconf + - automake + host: + - zlib + - gsl + run: + - zlib + - gsl + +about: + home: http://cichlid.gurdon.cam.ac.uk/fineRADstructure.html + license: Attribution-NonCommercial-NoDerivs 3.0 Creative Commons Licence + summary: Inference of population structure from RAD datasets + +test: + commands: + - RADpainter + - finestructure -V diff --git a/recipes/fishtaco/meta.yaml b/recipes/fishtaco/meta.yaml index f38ab2ee4d064..d35f1a358293e 100644 --- a/recipes/fishtaco/meta.yaml +++ b/recipes/fishtaco/meta.yaml @@ -48,6 +48,8 @@ about: summary: 'FishTaco: a metagenomic computational framework, aiming to identify the taxa that are driving functional shifts in microbiomes.' extra: + autobump: + enable: False notes: >- With FishTaco 1.1.0 the license has been changed such that 1.1.0 and 1.1.1 cannot be distributed in the Bioconda channel. 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Copyright (c) 2007-2019 Gordon Gremme <gordon@gremme.org>
Copyright (c) 2007-2008 Center for Bioinformatics, University of Hamburg
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+ + + + diff --git a/recipes/genomethreader/meta.yaml b/recipes/genomethreader/meta.yaml index fac6854eb3334..81339a1e08acf 100644 --- a/recipes/genomethreader/meta.yaml +++ b/recipes/genomethreader/meta.yaml @@ -11,7 +11,7 @@ source: build: skip: True # [not linux] - number: 0 + number: 1 requirements: build: @@ -26,4 +26,10 @@ about: home: http://genomethreader.org/ summary: 'GenomeThreader is a software tool to compute gene structure predictions. The gene structure predictions are calculated using a similarity-based approach where additional cDNA/EST and/or protein sequences are used to predict gene structures via spliced alignments.' license: ISC + license_file: LICENSE dev_url: https://github.com/genometools/genomethreader + + +extra: + recipe-maintainers: + - lucventurini diff --git a/recipes/goatools/meta.yaml b/recipes/goatools/meta.yaml index a0184334b0190..70c8fd8f699da 100644 --- a/recipes/goatools/meta.yaml +++ b/recipes/goatools/meta.yaml @@ -1,11 +1,14 @@ -{% set version = "0.8.12" %} +{% set name = "goatools" %} +{% set version = "0.9.5" %} +{% set sha256 = "30592dd2dfbfa1ee697658242502cb4d9453d081b8c16817ecacdfc725f4c1d9" %} + package: - name: goatools + name: {{ name|lower }} version: '{{version}}' source: url: https://pypi.io/packages/source/g/goatools/goatools-{{version}}.tar.gz - sha256: b58f77321fc1c3393b7973b1dad7b08897394ae1465c036f91977e65383e5c7c + sha256: {{ sha256 }} build: noarch: python @@ -27,6 +30,7 @@ requirements: # - xlrd - pygraphviz - pydot + - requests test: commands: @@ -40,8 +44,8 @@ test: - goatools.associations about: - home: 'https://github.com/tanghaibao/goatools' - summary: 'Python scripts to find enrichment of GO terms' + home: https://github.com/tanghaibao/goatools + summary: "Python scripts to find enrichment of GO terms" license: BSD-2-Clause license_family: BSD diff --git a/recipes/gromacs/2018/meta.yaml b/recipes/gromacs/2018/meta.yaml index 49a689c24a85c..e48e00cb279fb 100644 --- a/recipes/gromacs/2018/meta.yaml +++ b/recipes/gromacs/2018/meta.yaml @@ -1,23 +1,17 @@ -about: - home: http://www.gromacs.org/ - license: GNU Lesser General Public License (LGPL) - summary: GROMACS is a versatile package to perform molecular dynamics. - package: name: gromacs version: 2018.6 -build: - number: 0 - # See http://manual.gromacs.org/documentation/ # for latest release. Note that version scheme changed from # 5.1 to 2016.x and 2018.x source: url: http://ftp.gromacs.org/pub/gromacs/gromacs-2018.6.tar.gz - md5: 997f2b8108197780d61b23b5eb05644a sha256: 94b0dbafe7b29a0fe509099caa4fc075e616eb0d6ab4a785c7072fd1b2c5aba0 +build: + number: 1 + requirements: build: - {{ compiler('cxx') }} @@ -39,6 +33,10 @@ test: commands: - gmx -version +about: + home: http://www.gromacs.org/ + license: GNU Lesser General Public License (LGPL) + summary: GROMACS is a versatile package to perform molecular dynamics. extra: identifiers: diff --git a/recipes/gromacs/2019/meta.yaml b/recipes/gromacs/2019/meta.yaml index efafa104893fb..26c4513bab3f1 100644 --- a/recipes/gromacs/2019/meta.yaml +++ b/recipes/gromacs/2019/meta.yaml @@ -3,26 +3,18 @@ # http://manual.gromacs.org/documentation/ {% set name = "gromacs" %} {% set version = "2019.1" %} -{% set md5 = "dccfadda6a7d4ab80fcb4059606a4ef3" %} # Calculate manually {% set sha256 = "b2c37ed2fcd0e64c4efcabdc8ee581143986527192e6e647a197c76d9c4583ec" %} - -about: - home: http://www.gromacs.org/ - license: GNU Lesser General Public License (LGPL) - summary: GROMACS is a versatile package to perform molecular dynamics. - package: name: gromacs version: {{ version }} build: - number: 1 + number: 2 source: url: http://ftp.gromacs.org/pub/gromacs/gromacs-{{ version }}.tar.gz - md5: {{ md5 }} sha256: {{ sha256 }} requirements: @@ -49,6 +41,10 @@ test: commands: - gmx -version +about: + home: http://www.gromacs.org/ + license: GNU Lesser General Public License (LGPL) + summary: GROMACS is a versatile package to perform molecular dynamics. extra: identifiers: diff --git a/recipes/insilicoseq/meta.yaml b/recipes/insilicoseq/meta.yaml index 6d01d59949b5c..ef0b43add36bc 100644 --- a/recipes/insilicoseq/meta.yaml +++ b/recipes/insilicoseq/meta.yaml @@ -1,5 +1,5 @@ -{% set version = "1.3.5" %} -{% set sha256 = "a90227ce29d6060acdf17ff6a3960add7566af824652cbbc26b8d0334e618df2" %} +{% set version = "1.3.6" %} +{% set sha256 = "e0ee4e37f0adeda6372001f2eea1cac70f0ee97d3765987eb839fd4717985052" %} package: name: insilicoseq @@ -24,7 +24,7 @@ requirements: - biopython - future - joblib - - numpy =1.16.2 + - numpy - pysam >=0.15.1 - python - requests @@ -47,3 +47,4 @@ about: extra: recipe-maintainers: - standage + - HadrienG diff --git a/recipes/isocor/meta.yaml b/recipes/isocor/meta.yaml index a40dd17e3eb48..7721d6263178f 100644 --- a/recipes/isocor/meta.yaml +++ b/recipes/isocor/meta.yaml @@ -1,10 +1,10 @@ package: name: "isocor" - version: "2.1.2" + version: "2.1.3" source: - url: https://files.pythonhosted.org/packages/cd/f7/6f13a5ee9f1c6b536349953157158d3c164d55949f4afb0b272b217c0d77/IsoCor-2.1.2.tar.gz - sha256: 264af24f07b4c28148416f00fe5dc3ea7bec3cdb97619ab897d3577439a27786 + url: https://files.pythonhosted.org/packages/2a/b8/5508b23f53c6db55b09c27f79da057748fde3a8adc43ed036786bfd5a945/IsoCor-2.1.3.tar.gz + sha256: aed965788ca23927711391f0af1e3d22d5db62bcb745461829792c1a7f838f21 build: number: 0 diff --git a/recipes/kat/2.0.8/meta.yaml b/recipes/kat/2.0.8/meta.yaml index 7fbca087dac59..c2b25ef1cdc84 100644 --- a/recipes/kat/2.0.8/meta.yaml +++ b/recipes/kat/2.0.8/meta.yaml @@ -1,20 +1,19 @@ -about: - home: https://github.com/TGAC/KAT/ - license: 'GPL3' - license_file: 'COPYING' - summary: 'KAT is a suite of tools that analyse jellyfish hashes or sequence files (fasta or fastq) using kmer counts' - -build: - number: 3 - skip: True # [osx] - package: name: kat version: '2.0.8' +source: + url: https://github.com/TGAC/KAT/archive/Release-2.0.8.tar.gz + sha1: 76f8a5fba81837dd20d00eaefb3709da476c1ca6 + +build: + number: 4 + skip: True # [osx] + requirements: build: - {{ compiler('c') }} + - {{ compiler('cxx') }} - autoconf - automake - libtool @@ -28,14 +27,16 @@ requirements: - gnuplot - jellyfish -source: - url: https://github.com/TGAC/KAT/archive/Release-2.0.8.tar.gz - sha1: 76f8a5fba81837dd20d00eaefb3709da476c1ca6 - test: commands: - kat --version +about: + home: https://github.com/TGAC/KAT/ + license: 'GPL3' + license_file: 'COPYING' + summary: 'KAT is a suite of tools that analyse jellyfish hashes or sequence files (fasta or fastq) using kmer counts' + extra: identifiers: - biotools:KAT diff --git a/recipes/last/490/build.sh b/recipes/last/490/build.sh index aadb4ff6d94d6..0e1cbe553e0fa 100644 --- a/recipes/last/490/build.sh +++ b/recipes/last/490/build.sh @@ -22,7 +22,7 @@ last-dotplot \ for i in $scripts; do cp $SRC_DIR/scripts/$i $PREFIX/bin && chmod +x $PREFIX/bin/$i; done -make +make CXX=${CXX} CC=${CC} mkdir -p $PREFIX/bin for i in $binaries; do cp $SRC_DIR/src/$i $PREFIX/bin && chmod +x $PREFIX/bin/$i; done diff --git a/recipes/last/490/meta.yaml b/recipes/last/490/meta.yaml index e30832b4807ea..d5e3dd3ce4a90 100644 --- a/recipes/last/490/meta.yaml +++ b/recipes/last/490/meta.yaml @@ -1,8 +1,3 @@ -about: - home: 'http://last.cbrc.jp/' - license: GPLv3 - summary: "LAST finds similar regions between sequences, and aligns them. It is designed for comparing large datasets to each other (e.g. vertebrate genomes and/or large numbers of DNA reads)." - package: name: last version: '490' @@ -15,13 +10,12 @@ source: - last-pair-probs.23patch build: - number: 3 + number: 4 requirements: build: - {{ compiler('cxx') }} - host: - - python + - {{ compiler('c') }} run: - python @@ -34,6 +28,11 @@ test: - "last-merge-batches -V" - "maf-convert -h" +about: + home: 'http://last.cbrc.jp/' + license: GPLv3 + summary: "LAST finds similar regions between sequences, and aligns them. It is designed for comparing large datasets to each other (e.g. vertebrate genomes and/or large numbers of DNA reads)." + extra: identifiers: - biotools:last diff --git a/recipes/last/638/build.sh b/recipes/last/638/build.sh index 6da6bf2a591b6..cae8657f76fc8 100644 --- a/recipes/last/638/build.sh +++ b/recipes/last/638/build.sh @@ -23,7 +23,7 @@ last-dotplot \ for i in $scripts; do cp $SRC_DIR/scripts/$i $PREFIX/bin && chmod +x $PREFIX/bin/$i; done chmod +x $SRC_DIR/build/* -make +make CXX=${CXX} CC=${CC} mkdir -p $PREFIX/bin for i in $binaries; do cp $SRC_DIR/src/$i $PREFIX/bin && chmod +x $PREFIX/bin/$i; done diff --git a/recipes/last/638/meta.yaml b/recipes/last/638/meta.yaml index a0db56fe99e96..a2083277a56da 100644 --- a/recipes/last/638/meta.yaml +++ b/recipes/last/638/meta.yaml @@ -1,8 +1,3 @@ -about: - home: 'http://last.cbrc.jp/' - license: GPLv3 - summary: "LAST finds similar regions between sequences, and aligns them. It is designed for comparing large datasets to each other (e.g. vertebrate genomes and/or large numbers of DNA reads)." - package: name: last version: '638' @@ -14,11 +9,12 @@ source: - maf-convert.23patch build: - number: 6 + number: 7 requirements: build: - {{ compiler('cxx') }} + - {{ compiler('c') }} host: - python run: @@ -33,6 +29,11 @@ test: - "last-merge-batches -V" - "maf-convert -h" +about: + home: 'http://last.cbrc.jp/' + license: GPLv3 + summary: "LAST finds similar regions between sequences, and aligns them. It is designed for comparing large datasets to each other (e.g. vertebrate genomes and/or large numbers of DNA reads)." + extra: identifiers: - biotools:last diff --git a/recipes/last/874/build.sh b/recipes/last/874/build.sh index 995403d9d6a22..fd9dadd53acd8 100644 --- a/recipes/last/874/build.sh +++ b/recipes/last/874/build.sh @@ -23,15 +23,12 @@ last-map-probs \ last-dotplot \ " -if [[ $(uname) == "Darwin" ]]; then - export CMAKE_CXX_FLAGS="-stdlib=libc++" -fi - for i in $scripts; do cp $SRC_DIR/scripts/$i $PREFIX/bin && chmod +x $PREFIX/bin/$i; done chmod +x $SRC_DIR/build/* -export LIBRARY_PATH=${PREFIX}/lib -make CXX="g++ $CMAKE_CXX_FLAGS -L${PREFIX}/lib" +pushd src +make CXX="$CXX" CXXFLAGS="${CXXFLAGS}" CFLAGS="${CFLAGS}" LDFLAGS="-L${PREFIX}/lib -lz" +popd mkdir -p $PREFIX/bin for i in $binaries; do cp $SRC_DIR/src/$i $PREFIX/bin && chmod +x $PREFIX/bin/$i; done diff --git a/recipes/last/874/meta.yaml b/recipes/last/874/meta.yaml index fbc7bfb961fd7..2600ae40eb6d9 100644 --- a/recipes/last/874/meta.yaml +++ b/recipes/last/874/meta.yaml @@ -1,8 +1,3 @@ -about: - home: 'http://last.cbrc.jp/' - license: GPLv3 - summary: "LAST finds similar regions between sequences, and aligns them. It is designed for comparing large datasets to each other (e.g. vertebrate genomes and/or large numbers of DNA reads)." - package: name: last version: '874' @@ -14,18 +9,18 @@ source: - maf-convert.23patch build: - number: 1 - skip: False + number: 2 requirements: build: - {{ compiler('cxx') }} - {{ compiler('c') }} host: - - python + - zlib run: - python - future + - zlib test: commands: @@ -38,6 +33,11 @@ test: - "last-merge-batches -V" - "maf-convert -h" +about: + home: 'http://last.cbrc.jp/' + license: GPLv3 + summary: "LAST finds similar regions between sequences, and aligns them. It is designed for comparing large datasets to each other (e.g. vertebrate genomes and/or large numbers of DNA reads)." + extra: identifiers: - biotools:last diff --git a/recipes/last/build.sh b/recipes/last/build.sh index 64cddad981b08..a11acca9863db 100644 --- a/recipes/last/build.sh +++ b/recipes/last/build.sh @@ -11,5 +11,5 @@ then fi cp ${SRC_DIR}/scripts/* ${PREFIX}/bin/ -make install CXX="g++ $CMAKE_CXX_FLAGS -I$PREFIX/include -L$PREFIX/lib" prefix=${PREFIX} +make install CXX="${CXX} $CMAKE_CXX_FLAGS -I$PREFIX/include -L$PREFIX/lib" prefix=${PREFIX} chmod +x ${PREFIX}/bin/* diff --git a/recipes/last/meta.yaml b/recipes/last/meta.yaml index fd833bb102871..bb191d2fe9d3b 100644 --- a/recipes/last/meta.yaml +++ b/recipes/last/meta.yaml @@ -11,14 +11,14 @@ source: url: http://last.cbrc.jp/{{ name|lower }}-{{ version }}.zip build: - number: 0 + number: 1 requirements: build: - {{ compiler('c') }} - - zlib + - {{ compiler('cxx') }} host: - - python + - zlib run: - zlib - python diff --git a/recipes/libsbml/build.sh b/recipes/libsbml/build.sh index 4dad93a1c02ab..a75c153696738 100644 --- a/recipes/libsbml/build.sh +++ b/recipes/libsbml/build.sh @@ -1,2 +1,13 @@ #!/bin/bash -$PYTHON setup.py install +mkdir build +cd build +cmake -DCMAKE_INSTALL_PREFIX=${PREFIX} \ + -DCMAKE_INSTALL_LIBDIR=${PREFIX}/lib \ + -DCMAKE_CXX_COMPILER=${CXX} \ + -DCMAKE_C_COMPILER=${CC} \ + -DWITH_SWIG=OFF \ + -DLIBXML_LIBRARY=${PREFIX}/lib \ + -DLIBXML_INCLUDE_DIR=${PREFIX}/include/libxml2 \ + .. +make +make install diff --git a/recipes/libsbml/meta.yaml b/recipes/libsbml/meta.yaml index 6158d5e1d4789..5434b34665a1c 100644 --- a/recipes/libsbml/meta.yaml +++ b/recipes/libsbml/meta.yaml @@ -1,35 +1,36 @@ -package: - name: python-libsbml - version: "5.12.0" +{% set version = "5.18.0" %} +{% set sha256 = "900a8a41682c6fe69b162bce45e4221d7e23f30acb6c3d3516d1d931f353936a" %} -source: - url: https://pypi.python.org/packages/source/p/python-libsbml/python-libsbml_5.12.0.tar.gz - md5: f05ed071b48702295a5ea44e52723247 - patches: - - fix_path.patch +package: + name: libsbml + version: {{ version }} build: - number: 2 - skip: True # [osx] + number: 0 + skip: True # [osx] + +source: + url: https://sourceforge.net/projects/sbml/files/libsbml/{{ version }}/stable/libSBML-{{ version }}-core-src.tar.gz + sha256: {{ sha256 }} requirements: build: - {{ compiler('c') }} + - {{ compiler('cxx') }} + - cmake host: - - python - - libxml2 - - bzip2 - libxml2 + - zlib run: - - python - - bzip2 - libxml2 + - zlib test: - imports: - - libsbml + commands: + - test -f ${PREFIX}/lib/libsbml.so # [linux] about: - home: http://sbml.org + home: http://sbml.org/Software/libSBML license: LGPL - summary: 'LibSBML Python API. LibSBML is a library for reading, writing and manipulating the Systems Biology Markup Language (SBML).' + license_file: 'LICENSE.txt' + summary: LibSBML is a free, open-source programming library to help you read, write, manipulate, translate, and validate SBML files and data streams. diff --git a/recipes/mfqe/build.sh b/recipes/mfqe/build.sh new file mode 100644 index 0000000000000..a7b858f65a7fc --- /dev/null +++ b/recipes/mfqe/build.sh @@ -0,0 +1,9 @@ +#!/bin/bash -e + +# Build statically linked binary with Rust +C_INCLUDE_PATH=$PREFIX/include \ +LIBRARY_PATH=$PREFIX/lib \ +cargo build --release + +# Install the binary +cp target/release/mfqe $PREFIX/bin diff --git a/recipes/mfqe/meta.yaml b/recipes/mfqe/meta.yaml new file mode 100644 index 0000000000000..f2627924c409c --- /dev/null +++ b/recipes/mfqe/meta.yaml @@ -0,0 +1,29 @@ +{% set version = "0.3.0" %} +{% set name = "mfqe" %} +{% set sha256 = "30602a768df0bbc52bbf96e7ca8fdd0eb0e80ca54a33169a3e99a1d433b6a7d7" %} + +package: + name: {{ name }} + version: {{ version }} + +build: + number: 0 + skip: True # [osx] + +source: + url: https://github.com/wwood/{{ name }}/archive/v{{version}}.tar.gz + sha256: {{ sha256 }} + +requirements: + build: + - rust >=1.19 + - {{ compiler('c') }} + +test: + commands: + - mfqe --help + +about: + home: https://github.com/wwood/mfqe + license: GPL3 + summary: mfqe is a tool for quickly seperating fastq files diff --git a/recipes/microhapulator/meta.yaml b/recipes/microhapulator/meta.yaml new file mode 100644 index 0000000000000..3e73fee6309cc --- /dev/null +++ b/recipes/microhapulator/meta.yaml @@ -0,0 +1,45 @@ +{% set version = "0.1.3" %} +{% set sha256 = "d613d1c4ec977feab1f3ec7a53835b6b2bde9d48af2036c2b910a4d1d943641a" %} + +package: + name: microhapulator + version: '{{version}}' + +source: + url: https://github.com/bioforensics/microhapulator/archive/{{ version }}.tar.gz + sha256: '{{sha256}}' + +build: + noarch: python + entry_points: + - mhpl8r = microhapulator.__main__:main + script: python -m pip install --no-deps --ignore-installed . + number: 0 + +requirements: + host: + - python >=3 + - pip + run: + - happer >=0.1 + - insilicoseq >=1.3.6 + - microhapdb >=0.3 + - numpy >=1.15.4 + - python >=3 + - pyfaidx >=0.5.5.2 + - pysam >=0.15.2 + +test: + imports: + - microhapulator + requires: + - pytest >=3.10 + - pytest-cov >=2.6 + - wget + +about: + home: https://github.com/bioforensics/MicroHapulator/ + license: BSD License + license_family: BSD + summary: Software package for simulating and analyzing microhaplotype sequence data. + dev_url: https://github.com/bioforensics/MicroHapulator/ diff --git a/recipes/microhapulator/run_test.sh b/recipes/microhapulator/run_test.sh new file mode 100755 index 0000000000000..3d3b741cfcb82 --- /dev/null +++ b/recipes/microhapulator/run_test.sh @@ -0,0 +1,10 @@ +#!/usr/bin/env bash +set -eo pipefail + +wget -O hg38.fasta.gz http://hgdownload.soe.ucsc.edu/goldenPath/hg38/bigZips/hg38.fa.gz +gunzip hg38.fasta.gz +faidx hg38.fasta chr1:100-150 > /dev/null + +pytest -m 'not known_failing' --cov=microhapulator --pyargs microhapulator + +rm -f hg38.fasta diff --git a/recipes/moods/meta.yaml b/recipes/moods/meta.yaml index 4e3e9b85749b1..e3bcfa0137f9a 100644 --- a/recipes/moods/meta.yaml +++ b/recipes/moods/meta.yaml @@ -9,11 +9,12 @@ source: md5: 40113c829ec6c699bd59978f313add1f build: - number: 3 + number: 4 requirements: build: - {{ compiler('c') }} + - {{ compiler('cxx') }} host: - python - swig # [py3k] diff --git a/recipes/ncls/meta.yaml b/recipes/ncls/meta.yaml index 1750eac9c56d6..61d797c73b473 100644 --- a/recipes/ncls/meta.yaml +++ b/recipes/ncls/meta.yaml @@ -7,7 +7,7 @@ source: sha256: 4fe09e183314bcaa2cd2391811999d1e10878126b64e052e34f7d207fbebd096 build: - number: 2 + number: 3 script: python setup.py install --single-version-externally-managed --record=record.txt requirements: @@ -15,10 +15,10 @@ requirements: {{ compiler('c') }} host: - cython - - numpy>=1.16.3 + - numpy run: - - numpy>=1.16.3 + - numpy test: # Python imports diff --git a/recipes/perl-bignum/build.sh b/recipes/perl-bignum/build.sh new file mode 100644 index 0000000000000..23eb50af99c52 --- /dev/null +++ b/recipes/perl-bignum/build.sh @@ -0,0 +1,25 @@ +#!/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 + +# 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-bignum/meta.yaml b/recipes/perl-bignum/meta.yaml new file mode 100644 index 0000000000000..b6ca3b0f23af3 --- /dev/null +++ b/recipes/perl-bignum/meta.yaml @@ -0,0 +1,35 @@ +{% set name = "perl-bignum" %} +{% set version = "0.51" %} +{% set sha256 = "8ac0f6efe0b6f24804690e53908bdc5346613667f1c0590d8cf808ec090e9c47" %} + +package: + name: {{ name }} + version: {{ version }} + +source: + url: https://cpan.metacpan.org/authors/id/P/PJ/PJACKLAM/bignum-0.51.tar.gz + sha256: {{ sha256 }} + +build: + number: 0 + +requirements: + host: + - perl + - perl-extutils-makemaker + - perl-math-bigint + - perl-math-bigrat + + run: + - perl + - perl-math-bigint + - perl-math-bigrat + +test: + imports: + - bignum + +about: + home: http://metacpan.org/pod/bignum + license: perl_5 + summary: 'Transparent BigNumber support for Perl' diff --git a/recipes/perl-const-fast/build.sh b/recipes/perl-const-fast/build.sh new file mode 100644 index 0000000000000..23eb50af99c52 --- /dev/null +++ b/recipes/perl-const-fast/build.sh @@ -0,0 +1,25 @@ +#!/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 + +# 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-const-fast/meta.yaml b/recipes/perl-const-fast/meta.yaml new file mode 100644 index 0000000000000..8334739483391 --- /dev/null +++ b/recipes/perl-const-fast/meta.yaml @@ -0,0 +1,40 @@ +{% set name = "perl-const-fast" %} +{% set version = "0.014" %} +{% set sha256 = "f805953a08c57846a16a4d85d7b766398afaf7c36c1465fcb1dea09e5fa394db" %} + +package: + name: {{ name }} + version: {{ version }} + +source: + url: https://cpan.metacpan.org/authors/id/L/LE/LEONT/Const-Fast-0.014.tar.gz + sha256: {{ sha256 }} + +build: + number: 0 + +requirements: + host: + - perl + - perl-test-fatal + - perl-storable + - perl-module-build-tiny + - perl-data-dumper + - perl-carp + - perl-file-temp + - perl-sub-exporter-progressive + + run: + - perl + - perl-carp + - perl-storable + - perl-sub-exporter-progressive + +test: + imports: + - Const::Fast + +about: + home: http://metacpan.org/pod/Const-Fast + license: perl_5 + summary: 'Facility for creating read-only scalars, arrays, and hashes' diff --git a/recipes/perl-dbd-pg/meta.yaml b/recipes/perl-dbd-pg/meta.yaml index bcf0841d53539..179bdcb378ecb 100644 --- a/recipes/perl-dbd-pg/meta.yaml +++ b/recipes/perl-dbd-pg/meta.yaml @@ -1,15 +1,17 @@ package: name: perl-dbd-pg - version: 3.7.4 + version: 3.8.0 source: - url: http://search.cpan.org/CPAN/authors/id/T/TU/TURNSTEP/DBD-Pg-3.7.4.tar.gz - sha256: 9ffa9c4e9d1d6b1483ec3259114b95998fd7e4a4168931c903b5ad5fd7a6783e + url: https://cpan.metacpan.org/authors/id/T/TU/TURNSTEP/DBD-Pg-3.8.0.tar.gz + sha256: e91c12643702496e1513f32c89e12313982ebafe0cb4a352d3dbbf3d804dd9e3 build: number: 0 requirements: + build: + - {{ compiler('c') }} host: - perl - perl-dbi diff --git a/recipes/perl-devel-size/meta.yaml b/recipes/perl-devel-size/meta.yaml index 8659e65e75af3..56d01d112f26f 100644 --- a/recipes/perl-devel-size/meta.yaml +++ b/recipes/perl-devel-size/meta.yaml @@ -1,15 +1,17 @@ package: name: perl-devel-size - version: "0.82" + version: "0.83" source: - url: https://cpan.metacpan.org/authors/id/N/NW/NWCLARK/Devel-Size-0.82.tar.gz - sha256: 8f04fd67b538c7665ddf8a6cba4ed7b3427c35ea2740e9c6e977dc68c18c7489 + url: https://cpan.metacpan.org/authors/id/N/NW/NWCLARK/Devel-Size-0.83.tar.gz + sha256: 757a67e0aa59ae103ea5ca092cbecc025644ebdc326731688ffab6f8823ef4b3 build: number: 0 requirements: + build: + - {{ compiler('c') }} host: - perl - perl-extutils-makemaker diff --git a/recipes/perl-html-form/meta.yaml b/recipes/perl-html-form/meta.yaml index 53b7b89ca1e73..7b6795768ba93 100644 --- a/recipes/perl-html-form/meta.yaml +++ b/recipes/perl-html-form/meta.yaml @@ -1,17 +1,17 @@ {% set name = "perl-html-form" %} -{% set version = "6.03" %} -{% set sha256 = "68c01d94f005d5ca9c4d55ad2a1bf3a8d034a5fc6db187d91a4c42f3fdc9fc36" %} +{% set version = "6.04" %} +{% set sha256 = "9cd557a8b61b9a98deceff259c4fb1d82df729ff9d0388f655b364dd16480080" %} package: name: {{ name }} version: {{ version }} source: - url: https://cpan.metacpan.org/authors/id/G/GA/GAAS/HTML-Form-6.03.tar.gz + url: https://cpan.metacpan.org/authors/id/O/OA/OALDERS/HTML-Form-6.04.tar.gz sha256: {{ sha256 }} build: - number: 1 + number: 0 requirements: host: diff --git a/recipes/perl-math-bigrat/build.sh b/recipes/perl-math-bigrat/build.sh new file mode 100644 index 0000000000000..23eb50af99c52 --- /dev/null +++ b/recipes/perl-math-bigrat/build.sh @@ -0,0 +1,25 @@ +#!/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 + +# 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-math-bigrat/meta.yaml b/recipes/perl-math-bigrat/meta.yaml new file mode 100644 index 0000000000000..18949f6c17d95 --- /dev/null +++ b/recipes/perl-math-bigrat/meta.yaml @@ -0,0 +1,33 @@ +{% set name = "perl-math-bigrat" %} +{% set version = "0.2614" %} +{% set sha256 = "cea6c20afc6c10a3dc3b62a71df3f842dce13898443bd827242ff3f09f1f3d59" %} + +package: + name: {{ name }} + version: {{ version }} + +source: + url: https://cpan.metacpan.org/authors/id/P/PJ/PJACKLAM/Math-BigRat-0.2614.tar.gz + sha256: {{ sha256 }} + +build: + number: 0 + +requirements: + host: + - perl + - perl-math-bigint + - perl-extutils-makemaker + + run: + - perl + - perl-math-bigint + +test: + imports: + - Math::BigRat + +about: + home: http://metacpan.org/pod/Math::BigRat + license: perl_5 + summary: 'Arbitrary big rational numbers' diff --git a/recipes/perl-sereal-decoder/meta.yaml b/recipes/perl-sereal-decoder/meta.yaml index 34ae76d0311cb..ceeb2cc707d33 100644 --- a/recipes/perl-sereal-decoder/meta.yaml +++ b/recipes/perl-sereal-decoder/meta.yaml @@ -1,15 +1,18 @@ package: name: perl-sereal-decoder - version: "4.005" + version: "4.007" source: - url: https://cpan.metacpan.org/authors/id/Y/YV/YVES/Sereal-Decoder-4.005.tar.gz - sha256: 043adad093d1bfdea1e637e1a6fe598291da244d18213e9e5486e313f0c25e9f + url: https://cpan.metacpan.org/authors/id/Y/YV/YVES/Sereal-Decoder-4.007.tar.gz + sha256: 0508118344682c22e179e85e69bb0771fb0af2965cfa5d7a7d5d097b69ffcc4b build: number: 0 requirements: + build: + - {{ compiler('c') }} + host: - perl - perl-file-path diff --git a/recipes/picard/meta.yaml b/recipes/picard/meta.yaml index 8718dd7b22563..779bdc5f6da23 100644 --- a/recipes/picard/meta.yaml +++ b/recipes/picard/meta.yaml @@ -1,5 +1,5 @@ -{% set version = "2.20.0" %} -{% set sha256 = "82aefbccb8bb7b2e8a472aa4f9888b228249205874f575748febc262cd8168fc" %} +{% set version = "2.20.1" %} +{% set sha256 = "55e7be9b005d2f9ee0d1afa50662f94d5a9f4dbf7bb2af988ad2784096d41df5" %} package: name: picard diff --git a/recipes/poppunk/meta.yaml b/recipes/poppunk/meta.yaml index ec208db903342..d1fbbd0598a26 100644 --- a/recipes/poppunk/meta.yaml +++ b/recipes/poppunk/meta.yaml @@ -1,4 +1,4 @@ -{% set version = "1.1.5" %} +{% set version = "1.1.6" %} {% set name = "PopPUNK" %} package: @@ -7,7 +7,7 @@ package: source: url: https://pypi.io/packages/source/p/{{ name|lower }}/{{ name|lower }}-{{ version }}.tar.gz - sha256: 7bd0cb3970883abe6747b7be78f113e1bdc1bcd76698e6c7ec94729d6c6c6c6d + sha256: 2bf88d6fd6dd24885d746b617d42cc73d3bef502fc4718e85e47dc5e2697804a build: number: 0 @@ -29,7 +29,6 @@ requirements: - numpy - mkl - scipy - - statsmodels - scikit-learn - dendropy - sharedmem diff --git a/recipes/pybigwig/meta.yaml b/recipes/pybigwig/meta.yaml index d7f37e121f2af..1ac085901efb2 100644 --- a/recipes/pybigwig/meta.yaml +++ b/recipes/pybigwig/meta.yaml @@ -1,12 +1,12 @@ -{% set version = "0.3.15" %} +{% set version = "0.3.16" %} package: name: pybigwig version: {{ version }} source: - url: https://files.pythonhosted.org/packages/99/c0/c53056f4496b2bacfaa014f0f3fc74934827cd4ce933f94fe870eaf65181/pyBigWig-0.3.15.tar.gz - sha256: 7e2c85b9ca826007a6c56907343b31fb86058a3b8d0bc9138c9de0a759d02e82 + url: https://files.pythonhosted.org/packages/67/c8/741cca63e6a8688ef22a605bb06cc849fc57df419027013f2d1181f184f8/pyBigWig-0.3.16.tar.gz + sha256: 1ec93c67089147cc918c7dbd69ff3cfbe0648e5b7b2e809c51f70daf668215d1 build: number: 0 diff --git a/recipes/pyranges/meta.yaml b/recipes/pyranges/meta.yaml index 6776e1c37fed0..815afae0e9434 100644 --- a/recipes/pyranges/meta.yaml +++ b/recipes/pyranges/meta.yaml @@ -1,8 +1,8 @@ {% set name = "pyranges" %} -{% set version = "0.0.39" %} +{% set version = "0.0.41" %} {% set file_ext = "tar.gz" %} {% set hash_type = "sha256" %} -{% set hash_value = "0a0e788367b59dc01d14bc09f050b8c5edf4b89ded7afd80cf55caf2512d36e6" %} +{% set hash_value = "de065b4543b784fb018fc2dc6bd7208d09a980ecf043c154ffbd06b66563b8d7" %} package: name: '{{ name|lower }}' diff --git a/recipes/python-libsbml/build.sh b/recipes/python-libsbml/build.sh new file mode 100644 index 0000000000000..4dad93a1c02ab --- /dev/null +++ b/recipes/python-libsbml/build.sh @@ -0,0 +1,2 @@ +#!/bin/bash +$PYTHON setup.py install diff --git a/recipes/libsbml/fix_path.patch b/recipes/python-libsbml/fix_path.patch similarity index 100% rename from recipes/libsbml/fix_path.patch rename to recipes/python-libsbml/fix_path.patch diff --git a/recipes/python-libsbml/meta.yaml b/recipes/python-libsbml/meta.yaml new file mode 100644 index 0000000000000..54acf7c845725 --- /dev/null +++ b/recipes/python-libsbml/meta.yaml @@ -0,0 +1,39 @@ +package: + name: python-libsbml + version: "5.12.0" + +source: + url: https://pypi.python.org/packages/source/p/python-libsbml/python-libsbml_5.12.0.tar.gz + md5: f05ed071b48702295a5ea44e52723247 + patches: + - fix_path.patch + +build: + number: 2 + skip: True # [osx] + +requirements: + build: + - {{ compiler('c') }} + host: + - python + - libxml2 + - bzip2 + - libxml2 + run: + - python + - bzip2 + - libxml2 + +test: + imports: + - libsbml + +about: + home: http://sbml.org + license: LGPL + summary: 'LibSBML Python API. LibSBML is a library for reading, writing and manipulating the Systems Biology Markup Language (SBML).' + +extra: + skip-lints: + - already_in_bioconda diff --git a/recipes/r-dartr/build.sh b/recipes/r-dartr/build.sh index 5bf492ab9fc06..4ddc13eed50c0 100644 --- a/recipes/r-dartr/build.sh +++ b/recipes/r-dartr/build.sh @@ -1 +1,2 @@ +export LD_LIBRARY_PATH=${BUILD_PREFIX}/x86_64-conda_cos6-linux-gnu/sysroot/usr/lib64 $R CMD INSTALL --build . diff --git a/recipes/r-dartr/meta.yaml b/recipes/r-dartr/meta.yaml index ad7b9ca50c803..546decbd1138e 100644 --- a/recipes/r-dartr/meta.yaml +++ b/recipes/r-dartr/meta.yaml @@ -1,4 +1,4 @@ -{% set version = '1.0.5' %} +{% set version = '1.1.11' %} package: name: r-dartr @@ -8,20 +8,25 @@ source: url: - {{ cran_mirror }}/src/contrib/dartR_{{ version }}.tar.gz - {{ cran_mirror }}/src/contrib/Archive/dartR/dartR_{{ version }}.tar.gz - sha256: fc2b5643ef222ac20e62c5899f8f36b5ba92bf9146b7a5e25457d7ac789fb3f5 + sha256: 28968f0137be05dcb1b58c2c7775b8f8c74990090edd264e74844752ef45e64c build: - number: 1 + number: 0 noarch: generic rpaths: - lib/R/lib/ - lib/ requirements: + build: + - {{ cdt('mesa-libgl-devel') }} + - {{ cdt('mesa-dri-drivers') }} + - {{ cdt('libselinux') }} + - {{ cdt('libxdamage') }} + - {{ cdt('libxxf86vm') }} + - {{ cdt('libxfixes') }} host: - r-base - - r-dbi - - r-demerelate - r-mass - bioconductor-snprelate - r-snpassoc @@ -34,25 +39,26 @@ requirements: - r-doparallel - r-foreach - r-ggplot2 - - r-misc3d - r-pca3d - r-pegas - - r-plotly - r-plyr - - r-quadprog - bioconductor-qvalue - r-reshape2 - r-rgdal - - r-rgl - r-seqinr - r-sp - r-stringr - r-tidyr - r-vegan + - r-gdistance + - r-hierfstat + - r-igraph + - r-leaflet + - r-mmod + - r-popgenreport + - r-rrblup run: - r-base - - r-dbi - - r-demerelate - r-mass - bioconductor-snprelate - r-snpassoc @@ -65,25 +71,28 @@ requirements: - r-doparallel - r-foreach - r-ggplot2 - - r-misc3d - r-pca3d - r-pegas - - r-plotly - r-plyr - - r-quadprog - bioconductor-qvalue - r-reshape2 - r-rgdal - - r-rgl - r-seqinr - r-sp - r-stringr - r-tidyr - r-vegan + - r-gdistance + - r-hierfstat + - r-igraph + - r-leaflet + - r-mmod + - r-popgenreport + - r-rrblup test: commands: - - $R -e "library('dartR')" + - LD_LIBRARY_PATH="${BUILD_PREFIX}/x86_64-conda_cos6-linux-gnu/sysroot/usr/lib64:/usr/lib/x86_64-linux-gnu/" $R -e "library('dartR')" about: home: https://CRAN.R-project.org/package=dartR diff --git a/recipes/r-hierfstat/build.sh b/recipes/r-hierfstat/build.sh new file mode 100644 index 0000000000000..161a759163365 --- /dev/null +++ b/recipes/r-hierfstat/build.sh @@ -0,0 +1,38 @@ +#!/bin/bash + +if [[ $target_platform =~ linux.* ]] || [[ $target_platform == win-32 ]] || [[ $target_platform == win-64 ]] || [[ $target_platform == osx-64 ]]; then + export DISABLE_AUTOBREW=1 + mv DESCRIPTION DESCRIPTION.old + grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION + $R CMD INSTALL --build . +else + mkdir -p $PREFIX/lib/R/library/hierfstat + mv * $PREFIX/lib/R/library/hierfstat + + if [[ $target_platform == osx-64 ]]; then + pushd $PREFIX + for libdir in lib/R/lib lib/R/modules lib/R/library lib/R/bin/exec sysroot/usr/lib; do + pushd $libdir || exit 1 + for SHARED_LIB in $(find . -type f -iname "*.dylib" -or -iname "*.so" -or -iname "R"); do + echo "fixing SHARED_LIB $SHARED_LIB" + install_name_tool -change /Library/Frameworks/R.framework/Versions/3.5.0-MRO/Resources/lib/libR.dylib "$PREFIX"/lib/R/lib/libR.dylib $SHARED_LIB || true + install_name_tool -change /Library/Frameworks/R.framework/Versions/3.5/Resources/lib/libR.dylib "$PREFIX"/lib/R/lib/libR.dylib $SHARED_LIB || true + install_name_tool -change /usr/local/clang4/lib/libomp.dylib "$PREFIX"/lib/libomp.dylib $SHARED_LIB || true + install_name_tool -change /usr/local/gfortran/lib/libgfortran.3.dylib "$PREFIX"/lib/libgfortran.3.dylib $SHARED_LIB || true + install_name_tool -change /Library/Frameworks/R.framework/Versions/3.5/Resources/lib/libquadmath.0.dylib "$PREFIX"/lib/libquadmath.0.dylib $SHARED_LIB || true + install_name_tool -change /usr/local/gfortran/lib/libquadmath.0.dylib "$PREFIX"/lib/libquadmath.0.dylib $SHARED_LIB || true + install_name_tool -change /Library/Frameworks/R.framework/Versions/3.5/Resources/lib/libgfortran.3.dylib "$PREFIX"/lib/libgfortran.3.dylib $SHARED_LIB || true + install_name_tool -change /usr/lib/libgcc_s.1.dylib "$PREFIX"/lib/libgcc_s.1.dylib $SHARED_LIB || true + install_name_tool -change /usr/lib/libiconv.2.dylib "$PREFIX"/sysroot/usr/lib/libiconv.2.dylib $SHARED_LIB || true + install_name_tool -change /usr/lib/libncurses.5.4.dylib "$PREFIX"/sysroot/usr/lib/libncurses.5.4.dylib $SHARED_LIB || true + install_name_tool -change /usr/lib/libicucore.A.dylib "$PREFIX"/sysroot/usr/lib/libicucore.A.dylib $SHARED_LIB || true + install_name_tool -change /usr/lib/libexpat.1.dylib "$PREFIX"/lib/libexpat.1.dylib $SHARED_LIB || true + install_name_tool -change /usr/lib/libcurl.4.dylib "$PREFIX"/lib/libcurl.4.dylib $SHARED_LIB || true + install_name_tool -change /usr/lib/libc++.1.dylib "$PREFIX"/lib/libc++.1.dylib $SHARED_LIB || true + install_name_tool -change /Library/Frameworks/R.framework/Versions/3.5/Resources/lib/libc++.1.dylib "$PREFIX"/lib/libc++.1.dylib $SHARED_LIB || true + done + popd + done + popd + fi +fi diff --git a/recipes/r-hierfstat/meta.yaml b/recipes/r-hierfstat/meta.yaml new file mode 100644 index 0000000000000..03bd02e78c63d --- /dev/null +++ b/recipes/r-hierfstat/meta.yaml @@ -0,0 +1,50 @@ +{% set version = '0.04-22' %} + +{% set posix = 'm2-' if win else '' %} +{% set native = 'm2w64-' if win else '' %} + +package: + name: r-hierfstat + version: {{ version|replace("-", "_") }} + +source: + url: + - {{ cran_mirror }}/src/contrib/hierfstat_{{ version }}.tar.gz + - {{ cran_mirror }}/src/contrib/Archive/hierfstat/hierfstat_{{ version }}.tar.gz + sha256: ddf9151b7492c8d13619402bf3bad741a4ea3a2fdb28e7c29a659b94c4165bb9 + +build: + number: 0 + + rpaths: + - lib/R/lib/ + - lib/ + +requirements: + host: + - r-base + - r-ade4 + - r-adegenet + - r-gtools + + run: + - r-base + - r-ade4 + - r-adegenet + - r-gtools + +test: + commands: + - $R -e "library('hierfstat')" # [not win] + +about: + home: http://www.r-project.org, http://github.com/jgx65/hierfstat + license: GPL (>= 2) + summary: Allows the estimation of hierarchical F-statistics from haploid or diploid genetic + data with any numbers of levels in the hierarchy, following the algorithm of Yang + (Evolution, 1998, 52(4):950-956; . Functions are also given + to test via randomisations the significance of each F and variance components, using + the likelihood-ratio statistics G. + license_family: GPL3 + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-2' + diff --git a/recipes/r-loose.rock/meta.yaml b/recipes/r-loose.rock/meta.yaml index 8423f89159d0d..2fb1f2fd83e1f 100644 --- a/recipes/r-loose.rock/meta.yaml +++ b/recipes/r-loose.rock/meta.yaml @@ -1,4 +1,4 @@ -{% set version = '1.0.9' %} +{% set version = '1.0.12' %} {% set posix = 'm2-' if win else '' %} {% set native = 'm2w64-' if win else '' %} @@ -10,7 +10,7 @@ source: url: - {{ cran_mirror }}/src/contrib/loose.rock_{{ version }}.tar.gz - {{ cran_mirror }}/src/contrib/Archive/loose.rock/loose.rock_{{ version }}.tar.gz - sha256: 1563a447383ad264d5fa37d33116082e9afaab918674dba27c3c2b77981ae10c + sha256: b4adda5e3db21ef9097682b9441f0bca6db95b4d1ce9b82544975d17fb271d5d build: number: 0 @@ -25,25 +25,21 @@ requirements: host: - r-base - r-mass - - bioconductor-biomart - r-digest - r-dplyr - r-futile.options - r-ggfortify - r-ggplot2 - r-reshape2 - - r-rlang run: - r-base - r-mass - - bioconductor-biomart - r-digest - r-dplyr - r-futile.options - r-ggfortify - r-ggplot2 - r-reshape2 - - r-rlang test: commands: diff --git a/recipes/r-mmod/build.sh b/recipes/r-mmod/build.sh new file mode 100644 index 0000000000000..2c7b7396c12f9 --- /dev/null +++ b/recipes/r-mmod/build.sh @@ -0,0 +1,38 @@ +#!/bin/bash + +if [[ $target_platform =~ linux.* ]] || [[ $target_platform == win-32 ]] || [[ $target_platform == win-64 ]] || [[ $target_platform == osx-64 ]]; then + export DISABLE_AUTOBREW=1 + mv DESCRIPTION DESCRIPTION.old + grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION + $R CMD INSTALL --build . +else + mkdir -p $PREFIX/lib/R/library/mmod + mv * $PREFIX/lib/R/library/mmod + + if [[ $target_platform == osx-64 ]]; then + pushd $PREFIX + for libdir in lib/R/lib lib/R/modules lib/R/library lib/R/bin/exec sysroot/usr/lib; do + pushd $libdir || exit 1 + for SHARED_LIB in $(find . -type f -iname "*.dylib" -or -iname "*.so" -or -iname "R"); do + echo "fixing SHARED_LIB $SHARED_LIB" + install_name_tool -change /Library/Frameworks/R.framework/Versions/3.5.0-MRO/Resources/lib/libR.dylib "$PREFIX"/lib/R/lib/libR.dylib $SHARED_LIB || true + install_name_tool -change /Library/Frameworks/R.framework/Versions/3.5/Resources/lib/libR.dylib "$PREFIX"/lib/R/lib/libR.dylib $SHARED_LIB || true + install_name_tool -change /usr/local/clang4/lib/libomp.dylib "$PREFIX"/lib/libomp.dylib $SHARED_LIB || true + install_name_tool -change /usr/local/gfortran/lib/libgfortran.3.dylib "$PREFIX"/lib/libgfortran.3.dylib $SHARED_LIB || true + install_name_tool -change /Library/Frameworks/R.framework/Versions/3.5/Resources/lib/libquadmath.0.dylib "$PREFIX"/lib/libquadmath.0.dylib $SHARED_LIB || true + install_name_tool -change /usr/local/gfortran/lib/libquadmath.0.dylib "$PREFIX"/lib/libquadmath.0.dylib $SHARED_LIB || true + install_name_tool -change /Library/Frameworks/R.framework/Versions/3.5/Resources/lib/libgfortran.3.dylib "$PREFIX"/lib/libgfortran.3.dylib $SHARED_LIB || true + install_name_tool -change /usr/lib/libgcc_s.1.dylib "$PREFIX"/lib/libgcc_s.1.dylib $SHARED_LIB || true + install_name_tool -change /usr/lib/libiconv.2.dylib "$PREFIX"/sysroot/usr/lib/libiconv.2.dylib $SHARED_LIB || true + install_name_tool -change /usr/lib/libncurses.5.4.dylib "$PREFIX"/sysroot/usr/lib/libncurses.5.4.dylib $SHARED_LIB || true + install_name_tool -change /usr/lib/libicucore.A.dylib "$PREFIX"/sysroot/usr/lib/libicucore.A.dylib $SHARED_LIB || true + install_name_tool -change /usr/lib/libexpat.1.dylib "$PREFIX"/lib/libexpat.1.dylib $SHARED_LIB || true + install_name_tool -change /usr/lib/libcurl.4.dylib "$PREFIX"/lib/libcurl.4.dylib $SHARED_LIB || true + install_name_tool -change /usr/lib/libc++.1.dylib "$PREFIX"/lib/libc++.1.dylib $SHARED_LIB || true + install_name_tool -change /Library/Frameworks/R.framework/Versions/3.5/Resources/lib/libc++.1.dylib "$PREFIX"/lib/libc++.1.dylib $SHARED_LIB || true + done + popd + done + popd + fi +fi diff --git a/recipes/r-mmod/meta.yaml b/recipes/r-mmod/meta.yaml new file mode 100644 index 0000000000000..de4df04f7c630 --- /dev/null +++ b/recipes/r-mmod/meta.yaml @@ -0,0 +1,43 @@ +{% set version = '1.3.3' %} + +{% set posix = 'm2-' if win else '' %} +{% set native = 'm2w64-' if win else '' %} + +package: + name: r-mmod + version: {{ version|replace("-", "_") }} + +source: + url: + - {{ cran_mirror }}/src/contrib/mmod_{{ version }}.tar.gz + - {{ cran_mirror }}/src/contrib/Archive/mmod/mmod_{{ version }}.tar.gz + sha256: c40bc308d1104a3eb10bfe47fd2efa7ac3247b5d8a7194a47c6a615a0f42e6b7 + +build: + number: 0 + + rpaths: + - lib/R/lib/ + - lib/ + +requirements: + host: + - r-base + - r-adegenet >=2.0 + - r-pegas + + run: + - r-base + - r-adegenet >=2.0 + - r-pegas + +test: + commands: + - $R -e "library('mmod')" + + +about: + home: https://github.com/dwinter/mmod + license: MIT + file LICENSE + summary: Provides functions for measuring population divergence from genotypic data. + license_family: MIT diff --git a/recipes/r-popgenreport/build.sh b/recipes/r-popgenreport/build.sh new file mode 100644 index 0000000000000..f0601defa4abf --- /dev/null +++ b/recipes/r-popgenreport/build.sh @@ -0,0 +1,38 @@ +#!/bin/bash + +if [[ $target_platform =~ linux.* ]] || [[ $target_platform == win-32 ]] || [[ $target_platform == win-64 ]] || [[ $target_platform == osx-64 ]]; then + export DISABLE_AUTOBREW=1 + mv DESCRIPTION DESCRIPTION.old + grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION + $R CMD INSTALL --build . +else + mkdir -p $PREFIX/lib/R/library/PopGenReport + mv * $PREFIX/lib/R/library/PopGenReport + + if [[ $target_platform == osx-64 ]]; then + pushd $PREFIX + for libdir in lib/R/lib lib/R/modules lib/R/library lib/R/bin/exec sysroot/usr/lib; do + pushd $libdir || exit 1 + for SHARED_LIB in $(find . -type f -iname "*.dylib" -or -iname "*.so" -or -iname "R"); do + echo "fixing SHARED_LIB $SHARED_LIB" + install_name_tool -change /Library/Frameworks/R.framework/Versions/3.5.0-MRO/Resources/lib/libR.dylib "$PREFIX"/lib/R/lib/libR.dylib $SHARED_LIB || true + install_name_tool -change /Library/Frameworks/R.framework/Versions/3.5/Resources/lib/libR.dylib "$PREFIX"/lib/R/lib/libR.dylib $SHARED_LIB || true + install_name_tool -change /usr/local/clang4/lib/libomp.dylib "$PREFIX"/lib/libomp.dylib $SHARED_LIB || true + install_name_tool -change /usr/local/gfortran/lib/libgfortran.3.dylib "$PREFIX"/lib/libgfortran.3.dylib $SHARED_LIB || true + install_name_tool -change /Library/Frameworks/R.framework/Versions/3.5/Resources/lib/libquadmath.0.dylib "$PREFIX"/lib/libquadmath.0.dylib $SHARED_LIB || true + install_name_tool -change /usr/local/gfortran/lib/libquadmath.0.dylib "$PREFIX"/lib/libquadmath.0.dylib $SHARED_LIB || true + install_name_tool -change /Library/Frameworks/R.framework/Versions/3.5/Resources/lib/libgfortran.3.dylib "$PREFIX"/lib/libgfortran.3.dylib $SHARED_LIB || true + install_name_tool -change /usr/lib/libgcc_s.1.dylib "$PREFIX"/lib/libgcc_s.1.dylib $SHARED_LIB || true + install_name_tool -change /usr/lib/libiconv.2.dylib "$PREFIX"/sysroot/usr/lib/libiconv.2.dylib $SHARED_LIB || true + install_name_tool -change /usr/lib/libncurses.5.4.dylib "$PREFIX"/sysroot/usr/lib/libncurses.5.4.dylib $SHARED_LIB || true + install_name_tool -change /usr/lib/libicucore.A.dylib "$PREFIX"/sysroot/usr/lib/libicucore.A.dylib $SHARED_LIB || true + install_name_tool -change /usr/lib/libexpat.1.dylib "$PREFIX"/lib/libexpat.1.dylib $SHARED_LIB || true + install_name_tool -change /usr/lib/libcurl.4.dylib "$PREFIX"/lib/libcurl.4.dylib $SHARED_LIB || true + install_name_tool -change /usr/lib/libc++.1.dylib "$PREFIX"/lib/libc++.1.dylib $SHARED_LIB || true + install_name_tool -change /Library/Frameworks/R.framework/Versions/3.5/Resources/lib/libc++.1.dylib "$PREFIX"/lib/libc++.1.dylib $SHARED_LIB || true + done + popd + done + popd + fi +fi diff --git a/recipes/r-popgenreport/meta.yaml b/recipes/r-popgenreport/meta.yaml new file mode 100644 index 0000000000000..8b81436f12149 --- /dev/null +++ b/recipes/r-popgenreport/meta.yaml @@ -0,0 +1,89 @@ +{% set version = '3.0.4' %} + +{% set posix = 'm2-' if win else '' %} +{% set native = 'm2w64-' if win else '' %} + +package: + name: r-popgenreport + version: {{ version|replace("-", "_") }} + +source: + url: + - {{ cran_mirror }}/src/contrib/PopGenReport_{{ version }}.tar.gz + - {{ cran_mirror }}/src/contrib/Archive/PopGenReport/PopGenReport_{{ version }}.tar.gz + sha256: 12e86d9d6e4ee3da17df46531657804e5f204452b867df1dc92e1733934b3275 + +build: + number: 0 + + rpaths: + - lib/R/lib/ + - lib/ + +# Suggests: +requirements: + host: + - r-base + - r-ggally + - r-r.utils + - r-rgooglemaps + - r-ade4 + - r-adegenet >=2.0.0 + - r-calibrate + - r-data.table + - r-dismo + - r-gap + - r-gdistance + - r-genetics + - r-ggplot2 + - r-knitr + - r-lattice + - r-mmod + - r-pegas + - r-plyr + - r-raster + - r-reshape + - r-rgdal + - r-sp + - r-vegan + - r-xtable + + run: + - r-base + - r-ggally + - r-r.utils + - r-rgooglemaps + - r-ade4 + - r-adegenet >=2.0.0 + - r-calibrate + - r-data.table + - r-dismo + - r-gap + - r-gdistance + - r-genetics + - r-ggplot2 + - r-knitr + - r-lattice + - r-mmod + - r-pegas + - r-plyr + - r-raster + - r-reshape + - r-rgdal + - r-sp + - r-vegan + - r-xtable + +test: + commands: + - $R -e "library('PopGenReport')" + +about: + home: https://github.com/green-striped-gecko/PopGenReport + license: GPL + summary: Provides beginner friendly framework to analyse population genetic data. Based on + 'adegenet' objects it uses 'knitr' to create comprehensive reports on spatial genetic + data. For detailed information how to use the package refer to the comprehensive + tutorials or visit . + license_family: GPL + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' diff --git a/recipes/rsem/01_fix_cxx_11.patch b/recipes/rsem/01_fix_cxx_11.patch new file mode 100644 index 0000000000000..44b6dd147d585 --- /dev/null +++ b/recipes/rsem/01_fix_cxx_11.patch @@ -0,0 +1,49 @@ +Fixes C++11: casting iostream to bool must be explicit + +diff -rNu RSEM-1.3.2.orig/buildReadIndex.cpp RSEM-1.3.2/buildReadIndex.cpp +--- RSEM-1.3.2.orig/buildReadIndex.cpp 2019-04-06 15:04:25.000000000 -0600 ++++ RSEM-1.3.2/buildReadIndex.cpp 2019-05-11 18:57:20.451993213 -0600 +@@ -37,15 +37,15 @@ + streampos pos = fin.tellg(); + success = true; + +- success = (getline(fin, line)); ++ success = (bool)(getline(fin, line)); + if (!success) continue; +- success = (getline(fin, line)); ++ success = (bool)(getline(fin, line)); + if (!success) continue; + + if (hasQ) { +- success = (getline(fin, line)); ++ success = (bool)(getline(fin, line)); + if (!success) continue; +- success = (getline(fin, line)); ++ success = (bool)(getline(fin, line)); + if (!success) continue; + } + +diff -rNu RSEM-1.3.2.orig/PairedEndHit.h RSEM-1.3.2/PairedEndHit.h +--- RSEM-1.3.2.orig/PairedEndHit.h 2019-04-06 15:04:25.000000000 -0600 ++++ RSEM-1.3.2/PairedEndHit.h 2019-05-11 18:57:51.399980833 -0600 +@@ -26,7 +26,7 @@ + + bool PairedEndHit::read(std::istream& in) { + conprb = 0.0; +- return (in>>sid>>pos>>insertL); ++ return (bool)(in>>sid>>pos>>insertL); + } + + void PairedEndHit::write(std::ostream& out) { +diff -rNu RSEM-1.3.2.orig/SingleHit.h RSEM-1.3.2/SingleHit.h +--- RSEM-1.3.2.orig/SingleHit.h 2019-04-06 15:04:25.000000000 -0600 ++++ RSEM-1.3.2/SingleHit.h 2019-05-11 18:59:11.543948700 -0600 +@@ -43,7 +43,7 @@ + + bool SingleHit::read(std::istream& in) { + conprb = 0.0; +- return (in>>sid>>pos); ++ return (bool)(in>>sid>>pos); + } + + void SingleHit::write(std::ostream& out) { diff --git a/recipes/rsem/02_fix_makefile.patch b/recipes/rsem/02_fix_makefile.patch new file mode 100644 index 0000000000000..ada2c5ee5d703 --- /dev/null +++ b/recipes/rsem/02_fix_makefile.patch @@ -0,0 +1,58 @@ +Removes vendored samtools and allows overriding compile flags + +diff -ru RSEM-1.3.2.orig/Makefile RSEM-1.3.2/Makefile +--- RSEM-1.3.2.orig/Makefile 2019-04-06 15:04:25.000000000 -0600 ++++ RSEM-1.3.2/Makefile 2019-05-11 19:02:37.320313844 -0600 +@@ -11,12 +11,12 @@ + BOOST = . + + # Compilation variables +-CXX = g++ +-CXXFLAGS = -std=gnu++98 -Wall -I. -I$(BOOST) -I$(SAMTOOLS)/$(HTSLIB) +-CPPFLAGS = ++CXX ?= g++ ++CXXFLAGS ?= -std=gnu++98 -Wall -I. -I$(BOOST) -I$(SAMTOOLS)/$(HTSLIB) ++CPPFLAGS ?= + +-LDFLAGS = +-LDLIBS = ++LDFLAGS ?= ++LDLIBS ?= + + # Installation variables + INSTALL = install +@@ -54,13 +54,11 @@ + + .PHONY : all ebseq pRSEM clean + +-all : $(PROGRAMS) $(SAMTOOLS)/samtools ++all : $(PROGRAMS) + + $(SAMTOOLS)/samtools : + cd $(SAMTOOLS) && $(CONFIGURE) --without-curses && $(MAKE) -f $(SAMTOOLS_MAKEFILE) samtools + +-$(SAMLIBS) : $(SAMTOOLS)/samtools +- + + # Compile objects + $(OBJS1) : +@@ -163,17 +161,14 @@ + + + # Install RSEM +-install : $(PROGRAMS) $(SCRIPTS) $(SAMTOOLS)/samtools rsem_perl_utils.pm +- $(INSTALL_DIR) $(DESTDIR)$(bindir) $(DESTDIR)$(bindir)/$(SAMTOOLS) ++install : $(PROGRAMS) $(SCRIPTS) rsem_perl_utils.pm ++ $(INSTALL_DIR) $(DESTDIR)$(bindir) + $(foreach prog,$(PROGRAMS),$(INSTALL_PROGRAM) $(prog) $(DESTDIR)$(bindir)/$(prog) ; $(STRIP) $(DESTDIR)$(bindir)/$(prog) ;) +- $(INSTALL_PROGRAM) $(SAMTOOLS)/samtools $(DESTDIR)$(bindir)/$(SAMTOOLS)/samtools +- $(STRIP) $(DESTDIR)$(bindir)/$(SAMTOOLS)/samtools + $(foreach script,$(SCRIPTS),$(INSTALL_PROGRAM) $(script) $(DESTDIR)$(bindir)/$(script) ;) + $(INSTALL_DATA) rsem_perl_utils.pm $(DESTDIR)$(bindir)/rsem_perl_utils.pm + + # Clean + clean : + rm -f *.o *~ $(PROGRAMS) +- cd $(SAMTOOLS) && $(MAKE) clean-all + cd EBSeq && $(MAKE) clean + cd pRSEM && $(MAKE) clean diff --git a/recipes/rsem/build.sh b/recipes/rsem/build.sh index 1d9889d6e81e3..71d7cf717ef61 100644 --- a/recipes/rsem/build.sh +++ b/recipes/rsem/build.sh @@ -1,113 +1,48 @@ -#!/usr/bin/env bash - -set -x -e - -pushd $SRC_DIR - -binaries="\ -convert-sam-for-rsem \ -EBSeq/rsem-for-ebseq-calculate-clustering-info \ -EBSeq/rsem-for-ebseq-find-DE \ -EBSeq/rsem-for-ebseq-generate-ngvector-from-clustering-info \ -extract-transcript-to-gene-map-from-trinity \ -rsem-bam2readdepth \ -rsem-bam2wig \ -rsem-build-read-index \ -rsem-calculate-credibility-intervals \ -rsem-calculate-expression \ -rsem-control-fdr \ -rsem-extract-reference-transcripts \ -rsem-generate-data-matrix \ -rsem-generate-ngvector \ -rsem-gen-transcript-plots \ -rsem-get-unique \ -rsem-gff3-to-gtf \ -rsem-parse-alignments \ -rsem-plot-model \ -rsem-plot-transcript-wiggles \ -rsem-prepare-reference \ -rsem-preref \ -rsem-refseq-extract-primary-assembly \ -rsem-run-ebseq \ -rsem-run-em \ -rsem-run-gibbs \ -rsem-sam-validator \ -rsem-scan-for-paired-end-reads \ -rsem-simulate-reads \ -rsem-synthesis-reference-transcripts \ -rsem-tbam2gbam \ -" - -export INCLUDE_PATH="${PREFIX}/include" -export LIBRARY_PATH="${PREFIX}/lib" -export LD_LIBRARY_PATH="${PREFIX}/lib" - -export LDFLAGS="-L${PREFIX}/lib" -export CPPFLAGS="-I${PREFIX}/include" -export CFLAGS="-I${PREFIX}/include" - -######################################################## -### Prepare Samtools/Htslib -######################################################## - -sed -i.bak 's/^CPPFLAGS =$//g' samtools-1.3/Makefile -sed -i.bak 's/^LDFLAGS =$//g' samtools-1.3/Makefile - -sed -i.bak 's/^CPPFLAGS =$//g' samtools-1.3/htslib-1.3/Makefile -sed -i.bak 's/^LDFLAGS =$//g' samtools-1.3/htslib-1.3/Makefile - -# varfilter.py in install fails because we don't install Python -sed -i.bak 's#misc/varfilter.py##g' samtools-1.3/Makefile - -# Remove rdynamic which can cause build issues on OSX -# https://sourceforge.net/p/samtools/mailman/message/34699333/ -sed -i.bak 's/ -rdynamic//g' samtools-1.3/Makefile -sed -i.bak 's/ -rdynamic//g' samtools-1.3/htslib-1.3/configure - -######################################################## -### Build rsem -######################################################## - -INSTALLDIR=$PREFIX/lib/rsem -BINDIR=$PREFIX/bin -mkdir -p $BINDIR -mkdir -p $INSTALLDIR - -make -make ebseq - -for i in $binaries; do cp $i $INSTALLDIR && chmod +x $INSTALLDIR/$(basename $i); done -for i in $binaries; do - echo "#!/usr/bin/env bash" > $BINDIR/$(basename $i); - echo 'DIR=$( cd "$( dirname "${BASH_SOURCE[0]}" )" && pwd )' >> $BINDIR/$(basename $i); - echo '$DIR/../lib/rsem/'$(basename $i) '$@' >> $BINDIR/$(basename $i); - chmod +x $BINDIR/$(basename $i); -done - -######################################################## -### Do Perl Things -######################################################## - - +#!/usr/bin/bash +set -x + +case `uname` in + Linux) + DSOSUF="so" + ;; + Darwin) + DSOSUF="dylib" + ;; + *) + echo "Unknown uname '`uname`'" >&2 + exit 1 +esac + +# main binaries +make \ + CXX=$CXX \ + CXXFLAGS="$CXXFLAGS" \ + CPPFLAGS="$CPPFLAGS -I$PREFIX/include -I." \ + SAMLIBS=$PREFIX/lib/libhts.$DSOSUF \ + SAMHEADERS=$PREFIX/include/htslib/sam.h \ + LDFLAGS="$LDFLAGS -L$PREFIX/lib" \ + prefix="$PREFIX" \ + install + +# EBSeq R scripts and one binary +sed -i.bak 's|#!/usr/bin/env Rscript|#!'$(which Rscript)'|' EBSeq/rsem-* +rm EBSeq/rsem-*.bak +make -C EBSeq CXX="$CXX $CXXFLAGS $LDFLAGS" rsem-for-ebseq-calculate-clustering-info +cp EBSeq/rsem-* $PREFIX/bin + +# Fix perl scripts and module +# move all perl stuff into a separate dir mkdir -p perl-build/lib -#mv *pl perl-build -mv *.pm perl-build/lib -mv rsem-calculate-expression perl-build -mv rsem-control-fdr perl-build -mv rsem-generate-data-matrix perl-build -mv rsem-plot-transcript-wiggles perl-build -mv rsem-prepare-reference perl-build -mv rsem-run-ebseq perl-build +mv $PREFIX/bin/rsem*.pm perl-build/lib +for n in $PREFIX/bin/rsem-*; do + if head -n1 "$n" | grep -q "env perl"; then + mv -v "$n" perl-build + fi +done +mv rsem-control-fdr rsem-run-ebseq perl-build cp ${RECIPE_DIR}/Build.PL perl-build - cd perl-build - +# now run perl install perl ./Build.PL - -# patch shebang line to make it shorter -perl -i.bak -wpe 's[^#!.+][#!/usr/bin/env perl]' Build - -./Build manifest -./Build install --installdirs site - -chmod u+rwx $PREFIX/bin/* +perl ./Build manifest +perl ./Build install --installdirs site diff --git a/recipes/rsem/meta.yaml b/recipes/rsem/meta.yaml index 7904bc1e1ebed..ce1c9e2aa05c1 100644 --- a/recipes/rsem/meta.yaml +++ b/recipes/rsem/meta.yaml @@ -1,4 +1,4 @@ -{% set version = "1.3.1" %} +{% set version = "1.3.2" %} package: name: rsem @@ -6,39 +6,43 @@ package: source: url: https://github.com/deweylab/RSEM/archive/v{{ version }}.tar.gz - sha256: 93c749a03ac16e94b1aab94d032d4fd5687d3261316ce943ecb89d3ae3ec2e11 + sha256: 7cf5538226330960415f759045fd6940fe39ed26955ba833e09dbfdf3332ec6b + patches: + - 01_fix_cxx_11.patch # iostreams must be cast to bool explicitly + - 02_fix_makefile.patch # de-vendor samtools and allow overriding *FLAGS build: rpaths: - lib/R/lib/ - lib/ - number: 1 + number: 0 requirements: build: - {{ compiler('c') }} host: - bioconductor-biobase - - boost - perl - perl-module-build - r-base + - samtools + - htslib - zlib run: - bioconductor-biobase - bioconductor-ebseq - - boost + - ucsc-bigwigsummary - perl - perl-module-build - r-base - - samtools 1.3 + - samtools - 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 "Failed to open file" > /dev/null - which rsem-for-ebseq-calculate-clustering-info about: diff --git a/recipes/samtools/0.1.19/meta.yaml b/recipes/samtools/0.1.19/meta.yaml index 70cad3a395dd9..0fbd7a0a6deef 100644 --- a/recipes/samtools/0.1.19/meta.yaml +++ b/recipes/samtools/0.1.19/meta.yaml @@ -1,15 +1,14 @@ -about: - home: https://github.com/samtools/samtools - license: MIT - summary: Tools for dealing with SAM and BAM files - -build: - number: 5 - package: name: samtools version: 0.1.19 +source: + sha256: d080c9d356e5f0ad334007e4461cbcee3c4ca97b8a7a5a48c44883cf9dee63d4 + url: http://depot.galaxyproject.org/package/source/samtools/samtools-0.1.19.tar.bz2 + +build: + number: 6 + requirements: build: - {{ compiler('c') }} @@ -20,14 +19,15 @@ requirements: - ncurses - zlib -source: - sha256: d080c9d356e5f0ad334007e4461cbcee3c4ca97b8a7a5a48c44883cf9dee63d4 - url: http://depot.galaxyproject.org/package/source/samtools/samtools-0.1.19.tar.bz2 - test: commands: - "samtools view --help 2>&1 | grep Notes" +about: + home: https://github.com/samtools/samtools + license: MIT + summary: Tools for dealing with SAM and BAM files + extra: identifiers: - biotools:samtools diff --git a/recipes/samtools/1.1/build.sh b/recipes/samtools/1.1/build.sh index bdfd59a3924f0..e6225bcfe1ac5 100644 --- a/recipes/samtools/1.1/build.sh +++ b/recipes/samtools/1.1/build.sh @@ -1,6 +1,6 @@ #!/bin/sh sed -i.bak -e 's/-lcurses/-lncurses/' Makefile sed -i.bak -e "s|CFLAGS=\s*-g\s*-Wall\s*-O2\s*|CFLAGS= -g -Wall -O2 -I$NCURSES_INCLUDE_PATH/ncurses/ -I$NCURSES_INCLUDE_PATH -L$NCURSES_LIB_PATH|g" Makefile -make +make CC=${CC} CFLAGS="${CFLAGS}" LDFLAGS="-L${PREFIX}/lib" mkdir -p $PREFIX/bin mv samtools $PREFIX/bin diff --git a/recipes/samtools/1.1/meta.yaml b/recipes/samtools/1.1/meta.yaml index d5a3cf5f2e2d7..f66ee0382bba8 100644 --- a/recipes/samtools/1.1/meta.yaml +++ b/recipes/samtools/1.1/meta.yaml @@ -1,32 +1,33 @@ -about: - home: https://github.com/samtools/samtools - license: MIT - summary: Tools for dealing with SAM, BAM and CRAM files - -build: - number: 2 - package: name: samtools version: '1.1' +source: + sha256: c24d26c303153d72b5bf3cc11f72c6c375a4ca1140cc485648c8c5473414b7f8 + url: http://downloads.sourceforge.net/project/samtools/samtools/1.1/samtools-1.1.tar.bz2 + +build: + number: 3 + requirements: build: - - ncurses + - {{ compiler('c') }} host: - zlib + - ncurses run: - ncurses - zlib -source: - sha256: c24d26c303153d72b5bf3cc11f72c6c375a4ca1140cc485648c8c5473414b7f8 - url: http://downloads.sourceforge.net/project/samtools/samtools/1.1/samtools-1.1.tar.bz2 - test: commands: - "samtools view --help 2>&1 | grep Notes > /dev/null" +about: + home: https://github.com/samtools/samtools + license: MIT + summary: Tools for dealing with SAM, BAM and CRAM files + extra: identifiers: - biotools:samtools diff --git a/recipes/scelvis/meta.yaml b/recipes/scelvis/meta.yaml index 0a0c07f68fa3a..439d89d452f09 100644 --- a/recipes/scelvis/meta.yaml +++ b/recipes/scelvis/meta.yaml @@ -1,5 +1,5 @@ -{% set version = "0.1.0" %} -{% set sha256 = "20bce881d8808c95c6f26c9e0db52e085d05e561af2c9f93d6b388921e4891da" %} +{% set version = "0.2.0" %} +{% set sha256 = "e4f8d4676e56dff25c4d3e328f50dbeaf407eaf34f9d157cc0d829a353d87e34" %} package: name: scelvis @@ -36,6 +36,9 @@ requirements: - attrs - logzero - ruamel_yaml + - fs + - fs.sshfs + - python-irodsclient test: imports: diff --git a/recipes/segway/meta.yaml b/recipes/segway/meta.yaml index d2936e8f85686..4f0021f0193f9 100644 --- a/recipes/segway/meta.yaml +++ b/recipes/segway/meta.yaml @@ -12,7 +12,7 @@ source: build: noarch: python - number: 0 + number: 1 requirements: host: @@ -25,7 +25,7 @@ requirements: - python - six - genomedata - - gmtk + - gmtk >=1.4.4=hd5b5912_5 - autolog - textinput - optbuild @@ -49,6 +49,8 @@ about: summary: 'a tool for easy pattern discovery and identification in functional genomics data.' extra: + recipe-maintainers: + - ericr86 identifiers: - doi:10.1093/bioinformatics/btx603 - biotools:segway diff --git a/recipes/sorted_nearest/meta.yaml b/recipes/sorted_nearest/meta.yaml index 9723404eaca3d..e3c92494b13eb 100644 --- a/recipes/sorted_nearest/meta.yaml +++ b/recipes/sorted_nearest/meta.yaml @@ -1,8 +1,8 @@ {% set name = "sorted_nearest" %} -{% set version = "0.0.17" %} +{% set version = "0.0.19" %} {% set file_ext = "tar.gz" %} {% set hash_type = "sha256" %} -{% set hash_value = "dc8c765ee7c56738fa5be16ec453e18978f1ecc7675832ab4c0cdf3a50115727" %} +{% set hash_value = "b321d05280c350c0606b172a7ab92065a1757cb5e8bbb43b163c6a93cd994939" %} package: name: '{{ name|lower }}' @@ -23,11 +23,11 @@ requirements: - python - setuptools - cython - - numpy>=1.16.3 + - numpy run: - python - cython - - numpy>=1.16.3 + - numpy test: imports: diff --git a/recipes/squeakr/build.sh b/recipes/squeakr/build.sh index a8b6dbf4d1c50..fbd00840d6fd0 100644 --- a/recipes/squeakr/build.sh +++ b/recipes/squeakr/build.sh @@ -1,17 +1,10 @@ #!/bin/bash -set -x -e - -mkdir -p $PREFIX/bin - -BUILD_OS=$(uname -s) - -if [ ${BUILD_OS} == "Darwin" ]; then - LDFLAGS="-stdlib=libc++ -L ${PREFIX}/lib" CXXFLAGS="-stdlib=libc++ -I ${PREFIX}/include" make - else - LDFLAGS="-L ${PREFIX}/lib" CXXFLAGS="-L ${PREFIX}/lib -I ${PREFIX}/include" make -fi - -cp squeakr-count $PREFIX/bin -cp squeakr-inner-prod $PREFIX/bin -cp squeakr-query $PREFIX/bin +make CC="${CC}" LD="${CXX}" CXX="${CXX}" \ + LDFLAGS="${LDFLAGS} -L${PREFIX}/lib -lpthread -lboost_system -lboost_thread -lm -lbz2 -lz -lrt" \ + CXXFLAGS="${CXXFLAGS} -I${PREFIX}/include -I. -I${SRC_DIR}/include" \ + CFLAGS="${CFLAGS} -I${PREFIX}/include -I. -I${SRC_DIR}/include" \ + ARCH="${ARCH}" + +install -d $PREFIX/bin +install squeakr $PREFIX/bin diff --git a/recipes/squeakr/meta.yaml b/recipes/squeakr/meta.yaml index e3be3a9e03d32..d4bf0d7c21150 100644 --- a/recipes/squeakr/meta.yaml +++ b/recipes/squeakr/meta.yaml @@ -1,16 +1,17 @@ -{% set version = "0.5" %} -{% set sha256 = "9931d35e71bca0b4f0e9d3865a7c3563b2d4e7bfa03871d113777188f9b75bab" %} +{% set version = "0.6" %} +{% set name = "squeakr" %} package: - name: squeakr + name: {{ name|lower }} version: {{ version }} source: - url: https://github.com/splatlab/squeakr/archive/v{{ version }}.tar.gz - sha256: {{ sha256 }} + url: https://github.com/splatlab/{{ name|lower }}/archive/V{{ version }}.tar.gz + sha256: 6738efd60a32362d98be311b949012a57787d0ee77679ac1016809267b6f29b2 build: - number: 2 + number: 0 + skip: True # [osx] requirements: build: @@ -20,16 +21,20 @@ requirements: - bzip2 - zlib - boost + - boost-cpp - openssl + - pthread-stubs run: - bzip2 - zlib - boost + - boost-cpp - openssl + - pthread-stubs test: commands: - - squeakr-count -h + - squeakr help -v about: home: https://github.com/splatlab/squeakr diff --git a/recipes/sv2/0001-fix-classifiers.patch b/recipes/sv2/0001-fix-classifiers.patch new file mode 100644 index 0000000000000..abb12b73664fb --- /dev/null +++ b/recipes/sv2/0001-fix-classifiers.patch @@ -0,0 +1,20 @@ +--- sv2/sv2Config.py 2019-05-13 18:49:12.499563961 +0200 ++++ sv2/sv2Config.py 2019-05-13 18:49:05.071423000 +0200 +@@ -1,4 +1,5 @@ + #!/usr/bin/env python2 ++import os.path + from sv2_backend import dump_json,errFH,get_path,query_yes_no + try:from configparser import ConfigParser + except ImportError:from ConfigParser import ConfigParser +@@ -11,7 +12,10 @@ + self.fh = Config.ini + else: + self.fh=get_path()+'/config/sv2.ini' +- self.json=get_path()+'/config/sv2_clf.json' ++ if os.path.exists(os.path.join(os.path.dirname(self.fh), 'sv2_clf.json')): ++ self.json=os.path.join(os.path.dirname(self.fh), 'sv2_clf.json') ++ else: ++ self.json=get_path()+'/config/sv2_clf.json' + self.fasta_chr_flag=False + self.clfs=None + self.gtclf={} # classifiers for genotyping diff --git a/recipes/sv2/meta.yaml b/recipes/sv2/meta.yaml index 8269b3bc396e0..df106f29f77c2 100644 --- a/recipes/sv2/meta.yaml +++ b/recipes/sv2/meta.yaml @@ -3,12 +3,22 @@ package: version: "1.4.3.4" build: - number: 1 + number: 2 skip: true # [py3k or osx] source: url: https://github.com/dantaki/SV2/releases/download/sv2v1.4.4/sv2-1.4.3.4.tar.gz sha256: cf033a2db55ba930190783f7fe19dbb8e56606a8665cca8b768a687f450c4e00 + patches: + # Allow specification of custom classifier paths. This appears to be + # necessary in the latest version as it does not find the built-in ones + # any more. Further, there is no way to configure them in the INI file + # anyway. With this patch, a custom classifier JSON file can be + # placed next to the custom configuration INI file. + # + # PR for upstream: + # - https://github.com/dantaki/SV2/pull/27 + - 0001-fix-classifiers.patch requirements: build: diff --git a/recipes/tobias/meta.yaml b/recipes/tobias/meta.yaml index e4b95d19be687..04011cd24d26e 100644 --- a/recipes/tobias/meta.yaml +++ b/recipes/tobias/meta.yaml @@ -1,5 +1,5 @@ {% set name = "tobias" %} -{% set version = "0.3.0" %} +{% set version = "0.5.0" %} package: name: {{ name|lower }} @@ -7,21 +7,23 @@ package: source: url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/{{ name }}-{{ version }}.tar.gz - sha256: 7c7de1efc97352b6fb7bc21a692c901dc7a8ab270a850445577ae1aa4155d0fc + sha256: ae14018c6992c6e8f415e142ee8bbcb3b0932927203fe2061a6ac87169631fef build: number: 0 - skip: True # [py27] - skip: True # [osx] + skip: True # [py27 or osx] requirements: host: - - python >=3 + - {{ compiler('gcc') }} + - python - setuptools - cython - numpy + build: + - numpy run: - - python >=3 + - python - numpy - scipy - pysam @@ -33,6 +35,7 @@ requirements: - pyBigWig - moods - pybedtools + - adjusttext test: commands: diff --git a/recipes/ymp/meta.yaml b/recipes/ymp/meta.yaml new file mode 100644 index 0000000000000..70938daeffb7c --- /dev/null +++ b/recipes/ymp/meta.yaml @@ -0,0 +1,90 @@ +{% set name = "ymp" %} +{% set version = "0.1.0" %} + +package: + name: "{{ name|lower }}" + version: "{{ version }}" + +source: + url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/{{ name }}-{{ version }}.tar.gz + sha256: 5e658389d29c9418c368476c24986f15484fd82eedd323ad4517ebc71af51d6f + +build: + number: 0 + entry_points: + - ymp=ymp.cli:main + noarch: python + script: "{{ PYTHON }} -m pip install . --no-deps --ignore-installed -vv" + +requirements: + host: + - python >=3.6 + - setuptools_scm >=3.2 + - pytest-runner + - aiohttp + - click + - click-completion + - coloredlogs + - drmaa + - networkx >=2 + - pandas >=0.20 + - pip + - ruamel.yaml >0.15 + - snakemake =5.4.* + - tqdm >=4.21.0 + - xdg + - xlrd + + run: + - python >=3.6 + - aiohttp + - click + - click-completion + - coloredlogs + - drmaa + - networkx >=2 + - pandas >=0.20 + - ruamel.yaml >0.15 + - snakemake =5.4.* + - tqdm >=4.21.0 + - xdg + - xlrd + - conda + +test: + imports: + - ymp + - ymp.cli + commands: + - ymp --help + - ymp init demo + - ymp make -n toy.assemble_megahit.map_bbmap + +about: + home: https://ymp.readthedocs.io + dev_url: https://github.com/epruesse/ymp + doc_url: https://ymp.readthedocs.io + license: GNU General Public v3 or later (GPLv3+) + license_family: GPL3 + license_file: LICENSE + summary: Create entire NGS pipelines with one command + description: | + YMP allows composing complex NGS data analysis workflows from + conceptual building blocks ("stages") using a single command line + statement. Pre-tested conda environments are installed on-the fly, + reference databases downloaded as needed and requested workflows + executed using Snakemake. + + With YMP, developing new pipelines or testing alternative + approaches using differnt tools or optimizing parameters becomes + easy. Results from previous results are reused where possible. The + collection of stages included with YMP is can be extended with + project specific YMP stage definitions or simple Snakefiles. + +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 + recipe-maintainers: + - epruesse