diff --git a/build-fail-blacklist b/build-fail-blacklist index 3277cb73f49c2..d6e27fcbe9031 100644 --- a/build-fail-blacklist +++ b/build-fail-blacklist @@ -94,6 +94,26 @@ recipes/stringtie/1.2.2 recipes/stringtie/1.2.4 recipes/stringtie/1.3.0 recipes/stringtie/1.3.3 +recipes/art/3.11.14 +recipes/bcbiogff/0.6.2 +recipes/biopet/0.8.0 +recipes/metfrag/2.3.1 +recipes/metfrag/2.4.2 +recipes/varscan/2.4.2 +recipes/bbmap/37.10 +recipes/bbmap/37.17 +recipes/bbmap/37.52 +recipes/bbmap/37.99 +recipes/gatk4/4.0.3.0 +recipes/mira/3.4.1.1 +recipes/mira/4.9.5 +recipes/mira/4.9.6 +recipes/ngmlr/0.2.3 +recipes/ngmlr/0.2.4 +recipes/rnastructure/5.7 +recipes/rnastructure/6.0 +recipes/snpeff/4.1l +recipes/snpeff/4.2 # stl_algobase.h:548:18: error: cannot bind non-const lvalue reference of type 'HitSink::batch&' to an rvalue of type 'std::remove_reference::type {aka HitSink::batch}' recipes/bowtie @@ -116,6 +136,10 @@ recipes/smina recipes/cmv recipes/fwdpp recipes/parafly +recipes/rdflib-jsonld +recipes/smashbenchmarking +recipes/saffrontree +recipes/slclust # tracking master branch recipes/frc @@ -253,6 +277,15 @@ recipes/tablet # RuntimeError: Setuptools downloading is disabled in conda build. Be sure to add all dependencies in the meta.yaml url=https://pypi.org/simple/funcsigs/ recipes/pytest-marks +recipes/hivtrace +recipes/imfusion/0.3.0 +recipes/imfusion/0.3.2 +recipes/poretools/0.5.1 +recipes/hubward +recipes/pasta/1.7.8 +recipes/pasta/0.2 +recipes/nucleoatac/0.3.1 +recipes/phylotoast # git checkout problem recipes/pbdagcon @@ -265,9 +298,6 @@ recipes/ms # GL missing, needs the extended base image recipes/emperor -# RuntimeError: Setuptools downloading is disabled in conda build. Be sure to add all dependencies in the meta.yaml url=https://pypi.org/simple/HyPhy/ -recipes/hivtrace - # sed: can't read /opt/conda/conda-bld/idba_1530055808563/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehol/bin/aclocal: No such file or directory recipes/idba @@ -292,30 +322,12 @@ recipes/metavelvet-sl-pipeline # CMake Error: CMAKE_C_COMPILER not set, after EnableLanguage recipes/openbabel/2.3.2 -# RuntimeError: Setuptools downloading is disabled in conda build. Be sure to add all dependencies in the meta.yaml url=https://files.pythonhosted.org/packages/source/c/certifi/certifi-2016.9.26.tar.gz#md5=baa81e951a29958563689d868ef1064d -recipes/imfusion/0.3.0 -recipes/imfusion/0.3.2 -recipes/poretools/0.5.1 - -# RuntimeError: Setuptools downloading is disabled in conda build. Be sure to add all dependencies in the meta.yaml url=https://pypi.org/simple/pyaml/# -recipes/hubward - -# RuntimeError: Setuptools downloading is disabled in conda build. Be sure to add all dependencies in the meta.yaml url=https://files.pythonhosted.org/packages/source/c/certifi/certifi-2016.9.26.tar.gz#md5=baa81e951a29958563689d868ef1064d -recipes/pasta/1.7.8 -recipes/pasta/0.2 - # Conflicting numpy and qiime recipes/koeken -# RuntimeError: Setuptools downloading is disabled in conda build. Be sure to add all dependencies in the meta.yaml url=https://files.pythonhosted.org/packages/source/c/certifi/certifi-2016.9.26.tar.gz#md5=baa81e951a29958563689d868ef1064d -recipes/nucleoatac/0.3.1 - # no clue currently recipes/hap.py -# RuntimeError: Setuptools downloading is disabled in conda build. Be sure to add all dependencies in the meta.yaml url=https://pypi.org/simple/click/ -recipes/phylotoast - # takes hours to build recipes/plastid @@ -331,6 +343,10 @@ recipes/intemap # zlib missing recipes/polymutt recipes/prophyle/0.2.1 +recipes/trimmomatic/0.35 +recipes/megahit +recipes/dsk +recipes/lofreq # /opt/rh/devtoolset-2/root/usr/libexec/gcc/x86_64-redhat-linux/4.8.2/ld: cannot find -lc recipes/piler @@ -356,17 +372,9 @@ recipes/pizzly # compiles its own zlib recipes/plink2 -# Unknown problems -recipes/rdflib-jsonld -recipes/smashbenchmarking - # natsort conflicts with python recipes/qcumber -# Unknown issues -recipes/saffrontree -recipes/slclust - # ModuleNotFoundError: No module named 'fasta', note that the project is deprecated in favor of pyfaidx recipes/pyfasta @@ -376,9 +384,6 @@ recipes/spanki # perl issues recipes/vcftools/0.1.11 -# zlib -recipes/trimmomatic/0.35 - # broken pipe recipes/antarna @@ -397,9 +402,6 @@ recipes/ngseqbasic recipes/footprint recipes/mirdeep2/2.0.0.8 -# zlib -recipes/megahit - # missing bioc package recipes/customprodb @@ -450,9 +452,6 @@ recipes/bumbershoot # /opt/conda/conda-bld/phipack_1530829563675/work/conda_build.sh: line 139: cd: src/: No such file or directory recipes/phipack -# zlib -recipes/dsk - # perl recipes/vcftools/0.1.10 @@ -462,9 +461,6 @@ recipes/prinseq # checking whether the C compiler works... no recipes/fastme -# but ['zlib'] not in reqs/run, i.e. it is overlinked (likely) or a missing dependency (less likely) -recipes/lofreq - # perl script could not be found recipes/rnaclust @@ -764,30 +760,8 @@ recipes/bioconductor-subcellbarcode recipes/bioconductor-gladiatox recipes/bioconductor-biocgenerics -# Build and rendering failures that are breaking bulk and the nightly uploads -recipes/sqt -recipes/tepid -recipes/aragorn/1.2.38 -recipes/art/3.11.14 -recipes/autodock-vina -recipes/bcbiogff/0.6.2 -recipes/bcbiogff -recipes/biopet/0.8.0 -recipes/biopet -recipes/blockbuster -recipes/metfrag -recipes/metfrag/2.3.1 -recipes/metfrag/2.4.2 -recipes/varscan/2.4.2 +# Source seems to have moved recipes/discovar -recipes/ccat/3.0 -recipes/transabyss -recipes/soapdenovo2-prepare -recipes/damidseq_pipeline -recipes/repeatmodeler -recipes/detonate -recipes/pal_finder -recipes/dfam # ld: unknown option: -T recipes/bioconductor-lpsymphony @@ -846,90 +820,8 @@ recipes/bioconductor-nanotubes recipes/bioconductor-msqc1 recipes/bioconductor-clumsiddata -# Rendering errors that are breaking bulk and the nightly upload -recipes/adam -recipes/albatradis -recipes/anise_basil -recipes/bamclipper -recipes/bbmap/37.10 -recipes/bbmap/37.17 -recipes/bbmap/37.52 -recipes/bbmap/37.62 -recipes/bbmap/37.99 -recipes/bcftools-snvphyl-plugin -recipes/biotradis -recipes/bsmap -recipes/cannoli -recipes/cgview -recipes/crisper_recognition_tool -recipes/Drop-seq_tools -recipes/dsh-bio -recipes/dwgsim -recipes/dxua -recipes/fastindep -recipes/fgbio -recipes/gatk4/4.0.3.0 -recipes/gatk-framework -recipes/gb_taxonomy_tools -recipes/genblastg -recipes/gromacs/2018 -recipes/hr2 -recipes/indelfixer -recipes/je-suite -recipes/mdust -recipes/metacherchant -recipes/mgltools -recipes/mira -recipes/mira/3.4.1.1 -recipes/mira/4.9.5 -recipes/mira/4.9.6 -recipes/mobster -recipes/mummer4 -recipes/mvicuna -recipes/netreg -recipes/ngmlr/0.2.3 -recipes/ngmlr/0.2.4 -recipes/npinv -recipes/opsin/1.4.0 -recipes/opsin/2.1.0 -recipes/opsin/2.4.0 -recipes/pathwaymatcher -recipes/pauda -recipes/pepnovo -recipes/pyteomics -recipes/qorts -recipes/rabix-bunny -recipes/ragout -recipes/rawtools -recipes/rdp_classifier/2.2 +# Source no longer exists at the URL recipes/recon -recipes/regtools -recipes/repeatscout -recipes/rnacode/0.3 -recipes/rna-seqc -recipes/rnastructure -recipes/rnastructure/5.7 -recipes/rnastructure/6.0 -recipes/seqbuster -recipes/seqcluster -recipes/shorah/1.1.3 -recipes/snpeff/4.1l -recipes/snpeff/4.2 -recipes/snver -recipes/soapdenovo2-errorcorrection -recipes/soapec -recipes/socru -recipes/ssake -recipes/subread -recipes/tantan -recipes/tophat-recondition -recipes/tracer -recipes/vcfsamplecompare -recipes/watchdog-wms -recipes/wdltool -recipes/womtool -recipes/xtandem -recipes/yaha # Depends on bioconductor-biocgenerics, which can't be built until after R 3.6.1 is released and conda-forge moves its pinnings recipes/bioconductor-a4 diff --git a/recipes/Drop-seq_tools/meta.yaml b/recipes/Drop-seq_tools/meta.yaml index 1e5e9549ad8df..0fae3220513ab 100644 --- a/recipes/Drop-seq_tools/meta.yaml +++ b/recipes/Drop-seq_tools/meta.yaml @@ -2,23 +2,17 @@ {% set version = "2.0.0" %} {% set versiongrep = "2.0.0(1ef3a59_1539205128)" %} -about: - home: http://mccarrolllab.com/dropseq/ - license: MIT License - license_family: MIT - summary: | - Package for the analysis of Drop-seq data developed by Jim Nemesh in the McCarroll Lab package: name: dropseq_tools version: {{ version }} -build: - number: 0 - source: url: https://github.com/broadinstitute/Drop-seq/releases/download/v{{ version }}/{{ name }}-{{ version }}.zip md5: 3032444ec1c747181c6e9394d1e2a914 +build: + number: 0 + requirements: run: - openjdk >=8 @@ -55,6 +49,13 @@ test: - 'TrimStartingSequence -- --help 2>&1 | grep "{{ versiongrep }}"' - 'ValidateReference -- --help 2>&1 | grep "{{ versiongrep }}"' +about: + home: http://mccarrolllab.com/dropseq/ + license: MIT License + license_family: MIT + summary: | + Package for the analysis of Drop-seq data developed by Jim Nemesh in the McCarroll Lab + extra: notes: | Drop-seq_tools utilities are wrapper shell scripts. To get help on individual tool, use e.g. `PolyATrimmer -- --help` diff --git a/recipes/adam/meta.yaml b/recipes/adam/meta.yaml index 5387c9a158941..333d856b88c55 100644 --- a/recipes/adam/meta.yaml +++ b/recipes/adam/meta.yaml @@ -1,18 +1,9 @@ {% set version="0.26.0" %} -about: - home: https://github.com/bigdatagenomics/adam - license: Apache 2 - summary: Genomics analysis platform built on Apache Avro, Apache Spark and Parquet - package: name: adam version: {{ version }} -build: - number: 1 - noarch: generic - source: url: https://search.maven.org/remotecontent?filepath=org/bdgenomics/adam/adam-distribution-spark2_2.11/{{ version }}/adam-distribution-spark2_2.11-{{ version }}-bin.tar.gz sha256: 17a8a5021ef23db9beea9047d4dba8351bfe9d51f9b332708654fa647a60e64d @@ -20,6 +11,10 @@ source: - adam-shell.patch - adam-submit.patch +build: + number: 1 + noarch: generic + requirements: build: run: @@ -30,3 +25,8 @@ test: commands: - adam-submit --help - adam-submit transform --help + +about: + home: https://github.com/bigdatagenomics/adam + license: Apache 2 + summary: Genomics analysis platform built on Apache Avro, Apache Spark and Parquet diff --git a/recipes/albatradis/meta.yaml b/recipes/albatradis/meta.yaml index 4accdc911a2b8..7560cef75caa0 100644 --- a/recipes/albatradis/meta.yaml +++ b/recipes/albatradis/meta.yaml @@ -1,14 +1,5 @@ {% set version="1.0.0" %} {% set revision="ee860d8a0c7ed01d648e24671b0c406058879d79" %} -about: - home: https://github.com/quadram-institute-bioscience/albatradis - license: 'GPLv3' - summary: 'Comparative TraDIS analysis' - -build: - number: 2 - skip: True # [osx] - script: python -m pip install --ignore-installed . package: name: albatradis @@ -19,6 +10,11 @@ source: git_rev: {{ revision }} md5: unused +build: + number: 2 + skip: True # [osx] + script: python -m pip install --ignore-installed . + requirements: host: - python >3 @@ -65,6 +61,11 @@ test: - albatradis-presence_absence -h - albatradis-artemis_project -h +about: + home: https://github.com/quadram-institute-bioscience/albatradis + license: 'GPLv3' + summary: 'Comparative TraDIS analysis' + extra: skip-lints: - uses_git_url diff --git a/recipes/anise_basil/meta.yaml b/recipes/anise_basil/meta.yaml index f1cd53daf3d48..dc7e912b0556e 100644 --- a/recipes/anise_basil/meta.yaml +++ b/recipes/anise_basil/meta.yaml @@ -1,23 +1,10 @@ {% set name = "anise_basil" %} {% set version="1.2.0" %} -about: - home: https://github.com/seqan/{{ name }} - license_file: LICENSE - license: BSD - summary: BASIL is a method to detect breakpoints for structural variants - (including insertion breakpoints) from aligned paired HTS reads in BAM - format. ANISE is a method for the assembly of large insertions from paired - reads in BAM format and a list candidate insert breakpoints as generated by - BASIL. - package: name: {{ name }} version: {{ version }} -build: - number: 0 - source: - url: https://github.com/holtgrewe/lemon-mirror/archive/8785a8ccaca992fa9b3baf21e837e888d696a219.tar.gz folder: lemon @@ -29,6 +16,9 @@ source: - url: https://github.com/seqan/{{ name }}/archive/v{{ version }}.tar.gz sha256: 05e727da4b6b4716aa6505a527947738302b3334625de20e0cbd4b604b528a01 +build: + number: 0 + requirements: build: - {{ compiler('cxx') }} @@ -47,6 +37,16 @@ test: - anise --help - filter_basil.py --help +about: + home: https://github.com/seqan/{{ name }} + license_file: LICENSE + license: BSD + summary: BASIL is a method to detect breakpoints for structural variants + (including insertion breakpoints) from aligned paired HTS reads in BAM + format. ANISE is a method for the assembly of large insertions from paired + reads in BAM format and a list candidate insert breakpoints as generated by + BASIL. + extra: identifiers: - doi:10.1093/bioinformatics/btv051 diff --git a/recipes/aragorn/1.2.38/build.sh b/recipes/aragorn/build.sh similarity index 100% rename from recipes/aragorn/1.2.38/build.sh rename to recipes/aragorn/build.sh diff --git a/recipes/aragorn/1.2.38/meta.yaml b/recipes/aragorn/meta.yaml similarity index 100% rename from recipes/aragorn/1.2.38/meta.yaml rename to recipes/aragorn/meta.yaml index 42e9b35bcceec..76dbbac5718c3 100644 --- a/recipes/aragorn/1.2.38/meta.yaml +++ b/recipes/aragorn/meta.yaml @@ -1,23 +1,23 @@ -about: - home: http://mbio-serv2.mbioekol.lu.se/ARAGORN/ - license: GPLv3 - summary: 'ARAGORN, tRNA (and tmRNA) detection' - -build: - number: 2 - package: name: aragorn version: 1.2.38 -requirements: - build: - - {{ compiler('c') }} - source: md5: 1df0ed600069e6f520e5cd989de1eaf0 url: http://mbio-serv2.mbioekol.lu.se/ARAGORN/Downloads/aragorn1.2.38.tgz +build: + number: 2 + +requirements: + build: + - {{ compiler('c') }} + test: commands: - aragorn + +about: + home: http://mbio-serv2.mbioekol.lu.se/ARAGORN/ + license: GPLv3 + summary: 'ARAGORN, tRNA (and tmRNA) detection' diff --git a/recipes/autodock-vina/meta.yaml b/recipes/autodock-vina/meta.yaml index 96251a19b63bc..361d8c2ef8d15 100644 --- a/recipes/autodock-vina/meta.yaml +++ b/recipes/autodock-vina/meta.yaml @@ -1,21 +1,25 @@ -about: - home: http://vina.scripps.edu/ - license: Apache License 2.0 - summary: AutoDock Vina is an open-source program for doing molecular docking package: name: autodock-vina version: 1.1.2 + build: number: 1 - skip: False + source: url: http://vina.scripps.edu/download/autodock_vina_1_1_2_linux_x86.tgz # [linux] md5: 2605b04cae5071cbb9640fe112a5c01d # [linux] url: http://vina.scripps.edu/download/autodock_vina_1_1_2_mac.tgz # [osx] md5: b8165555fa13132e0658c36005e0edf3 # [osx] + requirements: build: run: + test: commands: - vina --help + +about: + home: http://vina.scripps.edu/ + license: Apache License 2.0 + summary: AutoDock Vina is an open-source program for doing molecular docking diff --git a/recipes/bamclipper/meta.yaml b/recipes/bamclipper/meta.yaml index ed6bb7a9926bc..adf3607deb95c 100644 --- a/recipes/bamclipper/meta.yaml +++ b/recipes/bamclipper/meta.yaml @@ -2,16 +2,6 @@ {% set version = "1.0.0" %} {% set sha256 = "aa43e4f9cf6b1fb58ac2c6329acc9870e9522e5ba20286b50312ccf89a18f2fc" %} -about: - home: https://github.com/tommyau/bamclipper - license: MIT - license_family: MIT - license_file: LICENSE - summary: Remove primer sequence from BAM alignments by soft-clipping. - -build: - number: 0 - package: name: {{ name|lower }} version: {{ version }} @@ -20,6 +10,9 @@ source: sha256: {{ sha256 }} url: https://github.com/tommyau/{{ name|lower }}/archive/v{{ version }}.tar.gz +build: + number: 0 + requirements: host: - perl @@ -32,5 +25,12 @@ test: commands: - bamclipper.sh 2>&1 | grep "bamclipper.sh" > /dev/null +about: + home: https://github.com/tommyau/bamclipper + license: MIT + license_family: MIT + license_file: LICENSE + summary: Remove primer sequence from BAM alignments by soft-clipping. + extra: doi: 10.1038/s41598-017-01703-6 diff --git a/recipes/bbmap/37.62/meta.yaml b/recipes/bbmap/37.62/meta.yaml index a7406812bf92b..e727001d47f92 100644 --- a/recipes/bbmap/37.62/meta.yaml +++ b/recipes/bbmap/37.62/meta.yaml @@ -2,15 +2,6 @@ {% set version = "37.62" %} {% set sha256 = "95cc01f44e9fb44aeb4f6b17f5857c60a796bce4f9d3cfd313a0501b38d7f124" %} -about: - home: 'https://sourceforge.net/projects/bbmap' - license: "UC-LBL license (see package)" - summary: "BBMap is a short read aligner, as well as various other bioinformatic tools." - -build: - number: 1 - noarch: generic - package: name: {{ name|lower }} version: {{ version }} @@ -19,6 +10,10 @@ source: sha256: {{ sha256 }} url: http://downloads.sourceforge.net/project/{{ name|lower }}/{{ name }}_{{ version }}.tar.gz +build: + number: 1 + noarch: generic + requirements: build: - openjdk >=7.0 @@ -29,6 +24,11 @@ test: commands: - bbmap.sh -V 2>&1 | grep "Executing" > /dev/null +about: + home: 'https://sourceforge.net/projects/bbmap' + license: "UC-LBL license (see package)" + summary: "BBMap is a short read aligner, as well as various other bioinformatic tools." + extra: notes: | BBMap is a series of Java programs, but they come with a number of custom diff --git a/recipes/bcbiogff/meta.yaml b/recipes/bcbiogff/meta.yaml index 24502e23af5b2..0184af9228495 100644 --- a/recipes/bcbiogff/meta.yaml +++ b/recipes/bcbiogff/meta.yaml @@ -1,16 +1,15 @@ -about: - home: https://github.com/chapmanb/bcbb/blob/master/gff - license: Biopython License Agreement - summary: Read and write Generic Feature Format (GFF) with Biopython integration. +package: + name: bcbiogff + version: 0.6.4 + +source: + url: https://pypi.python.org/packages/94/df/e2d75cc688ac6eb53f5fb4e2cffd240596bbcd5be28bab8d4f6404a6f86c/bcbio-gff-0.6.4.tar.gz + md5: 26910c9f6317b47a9e09742ecf74ae62 build: noarch: python number: 1 -package: - name: bcbiogff - version: 0.6.4 - requirements: host: - python @@ -20,10 +19,11 @@ requirements: - six - biopython -source: - url: https://pypi.python.org/packages/94/df/e2d75cc688ac6eb53f5fb4e2cffd240596bbcd5be28bab8d4f6404a6f86c/bcbio-gff-0.6.4.tar.gz - md5: 26910c9f6317b47a9e09742ecf74ae62 - test: imports: - BCBio.GFF + +about: + home: https://github.com/chapmanb/bcbb/blob/master/gff + license: Biopython License Agreement + summary: Read and write Generic Feature Format (GFF) with Biopython integration. diff --git a/recipes/bcftools-snvphyl-plugin/meta.yaml b/recipes/bcftools-snvphyl-plugin/meta.yaml index 0436f1d0d05f0..44950a962dd3c 100644 --- a/recipes/bcftools-snvphyl-plugin/meta.yaml +++ b/recipes/bcftools-snvphyl-plugin/meta.yaml @@ -1,21 +1,18 @@ {% set version = "1.9" %} {% set sha256 = "6f36d0e6f16ec4acf88649fb1565d443acf0ba40f25a9afd87f14d14d13070c8" %} -about: - home: https://github.com/phac-nml/snvphyl-tools - license: Apache-2.0 - license_family: Apache - summary: The SNVPhyl (Single Nucleotide Variant PHYLogenomics) pipeline is a pipeline - for identifying Single Nucleotide Variants (SNV) within a collection\ of microbial - genomes and constructing a phylogenetic tree. This package is the bcftools C plugin - -build: - number: 1 - skip: true # [osx] package: name: bcftools-snvphyl-plugin version: '{{version}}' +source: + url: https://github.com/samtools/bcftools/releases/download/{{version}}/bcftools-{{version}}.tar.bz2 + sha256: '{{sha256}}' + +build: + number: 1 + skip: true # [osx] + requirements: build: - {{ compiler('c') }} @@ -31,10 +28,14 @@ requirements: - xz - zlib -source: - url: https://github.com/samtools/bcftools/releases/download/{{version}}/bcftools-{{version}}.tar.bz2 - sha256: '{{sha256}}' - test: commands: - bcftools plugin -lv | grep filter_snv_density + +about: + home: https://github.com/phac-nml/snvphyl-tools + license: Apache-2.0 + license_family: Apache + summary: The SNVPhyl (Single Nucleotide Variant PHYLogenomics) pipeline is a pipeline + for identifying Single Nucleotide Variants (SNV) within a collection\ of microbial + genomes and constructing a phylogenetic tree. This package is the bcftools C plugin diff --git a/recipes/biopet/meta.yaml b/recipes/biopet/meta.yaml index befa7891c0823..0539f92f601a6 100644 --- a/recipes/biopet/meta.yaml +++ b/recipes/biopet/meta.yaml @@ -1,16 +1,15 @@ -about: - home: https://github.com/biopet/biopet - summary: Biopet (Bio Pipeline Execution Toolkit) is the main pipeline development framework of the LUMC Sequencing Analysis Support Core team. - license: https://github.com/biopet/biopet/blob/develop/biopet-core/src/main/resources/nl/lumc/sasc/biopet/License.txt package: name: biopet version: 0.9.0 + source: url: https://github.com/biopet/biopet/releases/download/v0.9.0/Biopet-0.9.0-be7838f2.jar sha256: 50fb9ffec164b85bebb6e8d127e0ebf70ad608855011fd4b55276bcbb1970259 + build: noarch: generic number: 1 + requirements: host: run: @@ -20,7 +19,13 @@ requirements: - r-ggplot2 - r-reshape - r-argparse + test: commands: - biopet version - biopet license + +about: + home: https://github.com/biopet/biopet + summary: Biopet (Bio Pipeline Execution Toolkit) is the main pipeline development framework of the LUMC Sequencing Analysis Support Core team. + license: https://github.com/biopet/biopet/blob/develop/biopet-core/src/main/resources/nl/lumc/sasc/biopet/License.txt diff --git a/recipes/biotradis/meta.yaml b/recipes/biotradis/meta.yaml index 682c35bf94d12..dc7a9f6c48ee1 100644 --- a/recipes/biotradis/meta.yaml +++ b/recipes/biotradis/meta.yaml @@ -1,23 +1,18 @@ {% set version="1.4.1.dev" %} {% set revision="426f43bee3ddd12dda6d5802fa8be17075ef5ae1" %} -about: - home: https://github.com/sanger-pathogens/Bio-Tradis - license: 'GPLv3' - summary: 'A set of tools to analyse the output from TraDIS analyses' - -build: - number: 1 - skip: True # [osx] +package: + name: biotradis + version: {{ version }} source: git_url: https://github.com/sanger-pathogens/Bio-Tradis.git git_rev: {{ revision }} md5: unused -package: - name: biotradis - version: {{ version }} +build: + number: 1 + skip: True # [osx] requirements: build: @@ -46,6 +41,12 @@ test: - which check_tradis_tags - which add_tradis_tags - which tradis_comparison.R + +about: + home: https://github.com/sanger-pathogens/Bio-Tradis + license: 'GPLv3' + summary: 'A set of tools to analyse the output from TraDIS analyses' + extra: skip-lints: - uses_git_url diff --git a/recipes/blockbuster/meta.yaml b/recipes/blockbuster/meta.yaml index ee35e022bce13..7692af014d5ef 100644 --- a/recipes/blockbuster/meta.yaml +++ b/recipes/blockbuster/meta.yaml @@ -1,11 +1,3 @@ -about: - home: 'http://hoffmann.bioinf.uni-leipzig.de/LIFE/blockbuster.html' - summary: 'Blockbuster detects blocks of overlapping reads using a gaussian-distribution approach.' - license: The 3-Clause BSD License - -build: - number: 2 - package: name: blockbuster version: '0.0.1.1' @@ -14,6 +6,9 @@ source: md5: 23f971cbedfa70caf461e22f96b245c8 url: https://github.com/bgruening/download_store/raw/master/blockbuster/blockbuster-0.0.1.1.tar.gz +build: + number: 2 + requirements: build: - {{ compiler('cxx') }} @@ -21,3 +16,8 @@ requirements: test: commands: - 'blockbuster.x 2>&1 | grep "^usage" > /dev/null' + +about: + home: 'http://hoffmann.bioinf.uni-leipzig.de/LIFE/blockbuster.html' + summary: 'Blockbuster detects blocks of overlapping reads using a gaussian-distribution approach.' + license: The 3-Clause BSD License diff --git a/recipes/bsmap/meta.yaml b/recipes/bsmap/meta.yaml index 227c986cae540..4d355d1bb8e06 100644 --- a/recipes/bsmap/meta.yaml +++ b/recipes/bsmap/meta.yaml @@ -2,17 +2,6 @@ {% set version = "2.90" %} {% set sha256 = "8b5ae4ba404e898adac14b0338c88455f882bee556a92d269de87c993f007ac2" %} -about: - home: https://code.google.com/archive/p/bsmap/ - license: GNU GPL v3 - license_family: GPL - license_file: GPL_3.0.txt - summary: BSMAP is a short reads mapping software for bisulfite sequencing reads. - -build: - number: 2 - skip: True # [py3k] - package: name: {{ name|lower }} version: {{ version }} @@ -24,6 +13,10 @@ source: - path.patch - osx_compile.patch # [osx] +build: + number: 2 + skip: True # [py3k] + requirements: build: - {{ compiler('cxx') }} @@ -43,6 +36,13 @@ test: - methratio.py -h - sam2bam.sh -h +about: + home: https://code.google.com/archive/p/bsmap/ + license: GNU GPL v3 + license_family: GPL + license_file: GPL_3.0.txt + summary: BSMAP is a short reads mapping software for bisulfite sequencing reads. + extra: identifiers: - biotools:bsmap diff --git a/recipes/cannoli/meta.yaml b/recipes/cannoli/meta.yaml index d9319e5361ada..7c338bd486231 100644 --- a/recipes/cannoli/meta.yaml +++ b/recipes/cannoli/meta.yaml @@ -1,22 +1,17 @@ {% set version="0.2.0" %} -about: - home: https://github.com/bigdatagenomics/cannoli - license: Apache 2 - summary: Big Data Genomics ADAM Pipe API wrappers for bioinformatics tools - package: name: cannoli version: {{ version }} -build: - number: 1 - noarch: generic - source: url: https://search.maven.org/remotecontent?filepath=org/bdgenomics/cannoli/cannoli-distribution-spark2_2.11/{{ version }}/cannoli-distribution-spark2_2.11-{{ version }}-bin.tar.gz sha256: 919f695ac91e7e7e9ccd5e008b3300c3eb28581cdf9bebaa713935059aeaa1ca +build: + number: 1 + noarch: generic + requirements: build: run: @@ -27,3 +22,8 @@ test: commands: - cannoli-submit --help - cannoli-submit bedtoolsIntersect --help + +about: + home: https://github.com/bigdatagenomics/cannoli + license: Apache 2 + summary: Big Data Genomics ADAM Pipe API wrappers for bioinformatics tools diff --git a/recipes/ccat/3.0/build.sh b/recipes/ccat/build.sh similarity index 100% rename from recipes/ccat/3.0/build.sh rename to recipes/ccat/build.sh diff --git a/recipes/ccat/3.0/meta.yaml b/recipes/ccat/meta.yaml similarity index 95% rename from recipes/ccat/3.0/meta.yaml rename to recipes/ccat/meta.yaml index 56582f285923d..452c84b95fcb3 100644 --- a/recipes/ccat/3.0/meta.yaml +++ b/recipes/ccat/meta.yaml @@ -1,20 +1,24 @@ -about: - home: http://cmb.gis.a-star.edu.sg/ChIPSeq/paperCCAT.htm - license: - summary: CCAT is a software package for the analysis of ChIP-seq data with negative control. -build: - number: 2 - skip: True # [osx] package: name: ccat version: 3.0 + source: sha256: d8944465c8327bec22eb41059ba73f780fcdcedf4470507bfdae5a54c59a9b07 url: http://cmb.gis.a-star.edu.sg/ChIPSeq/tools/CCAT3.0.tar.gz + +build: + number: 2 + skip: True # [osx] + test: commands: - CCAT --help +about: + home: http://cmb.gis.a-star.edu.sg/ChIPSeq/paperCCAT.htm + license: unknown + summary: CCAT is a software package for the analysis of ChIP-seq data with negative control. + extra: identifiers: - biotools:CCAT diff --git a/recipes/cgview/meta.yaml b/recipes/cgview/meta.yaml index 392a793cd777e..4c0eddc94a59d 100644 --- a/recipes/cgview/meta.yaml +++ b/recipes/cgview/meta.yaml @@ -1,25 +1,18 @@ {% set name = "cgview" %} {% set version = "1.0" %} -about: - home: http://wishart.biology.ualberta.ca/cgview/ - license: GNU General Public License, Version 2.0 - summary: | - CGView is a Java package for generating high quality, zoomable maps of circular genomes. - Its primary purpose is to serve as a component of sequence annotation pipelines, as a - means of generating visual output suitable for the web. package: name: {{ name }} version: {{ version }} -build: - noarch: generic - number: 2 - source: url: https://depot.galaxyproject.org/software/cgview/{{ name }}_{{ version }}_src_all.zip sha256: fc5a2a2fd75b2b419da18d2ff88d6f75053102fb8d8e0fbab1b7ce740ebcf4d6 +build: + noarch: generic + number: 2 + requirements: host: run: @@ -32,3 +25,10 @@ test: commands: - cgview 2>&1 | grep ^Please +about: + home: http://wishart.biology.ualberta.ca/cgview/ + license: GNU General Public License, Version 2.0 + summary: | + CGView is a Java package for generating high quality, zoomable maps of circular genomes. + Its primary purpose is to serve as a component of sequence annotation pipelines, as a + means of generating visual output suitable for the web. diff --git a/recipes/crisper_recognition_tool/meta.yaml b/recipes/crisper_recognition_tool/meta.yaml index 6ca32b5beb88d..71c1b91acc33a 100644 --- a/recipes/crisper_recognition_tool/meta.yaml +++ b/recipes/crisper_recognition_tool/meta.yaml @@ -1,23 +1,18 @@ {% set name = "crisper_recognition_tool" %} {% set version = "1.2" %} -about: - home: http://www.room220.com/crt/ - license: Public domain software - summary: A tool for automatic detection of clustered regularly interspaced palindromic repeats (CRISPR). - package: name: crisper_recognition_tool version: {{ version }} -build: - noarch: generic - number: 1 - source: url: http://www.room220.com/crt/CRT1.2-CLI.jar.zip md5: 1300514e388821b885c2d5fa6d19f137 +build: + noarch: generic + number: 1 + requirements: host: run: @@ -27,3 +22,8 @@ requirements: test: commands: - crt -help + +about: + home: http://www.room220.com/crt/ + license: Public domain software + summary: A tool for automatic detection of clustered regularly interspaced palindromic repeats (CRISPR). diff --git a/recipes/damidseq_pipeline/meta.yaml b/recipes/damidseq_pipeline/meta.yaml index 413ef7310c2a7..3cba6b80f5efa 100644 --- a/recipes/damidseq_pipeline/meta.yaml +++ b/recipes/damidseq_pipeline/meta.yaml @@ -1,11 +1,3 @@ -about: - home: https://github.com/owenjm/damidseq_pipeline - license: 'GPL-2.0' - summary: 'An automated pipeline for processing DamID sequencing datasets' - -build: - number: 2 - package: name: damidseq_pipeline version: '1.4' @@ -14,6 +6,9 @@ source: url: https://github.com/owenjm/damidseq_pipeline/archive/1.4.tar.gz sha256: cf3a9608a5f5453f2d491bde3759eaf154909387c9b4a1f882be45b542acbe73 +build: + number: 2 + requirements: host: - perl @@ -29,3 +24,8 @@ test: - 'damidseq_pipeline --help 2>&1 || true' - 'gatc.track.maker.pl --help 2>&1 || true' - 'gff2tdf.pl --help 2>&1 || true' + +about: + home: https://github.com/owenjm/damidseq_pipeline + license: 'GPL-2.0' + summary: 'An automated pipeline for processing DamID sequencing datasets' diff --git a/recipes/detonate/meta.yaml b/recipes/detonate/meta.yaml index c4b0ebbae18a7..f65f023c1466f 100644 --- a/recipes/detonate/meta.yaml +++ b/recipes/detonate/meta.yaml @@ -1,27 +1,14 @@ -about: - home: 'http://deweylab.biostat.wisc.edu/detonate/' - license: 'GPL' - summary: 'DETONATE (DE novo TranscriptOme rNa-seq Assembly with or without - the Truth Evaluation) consists of two component packages, RSEM-EVAL and - REF-EVAL.' +package: + name: detonate + version: '1.11' source: url: https://github.com/deweylab/detonate/archive/1.11.tar.gz sha256: 3aa83407c21e5558c71a146a972cc1fe0de251d6468a2cbef7538385ef8b53b2 -# patches: -# - ref-eval.sam.Makefile.patch -# - ref-eval.Makefile.patch -# - ref-eval.sam.misc.Makefile.patch -# - rsem-eval.sam.Makefile.patch -# - rsem-eval.Makefile.patch build: number: 3 -package: - name: detonate - version: '1.11' - requirements: build: - {{ compiler('cxx') }} @@ -41,3 +28,10 @@ requirements: test: commands: - ref-eval --help + +about: + home: 'http://deweylab.biostat.wisc.edu/detonate/' + license: 'GPL' + summary: 'DETONATE (DE novo TranscriptOme rNa-seq Assembly with or without + the Truth Evaluation) consists of two component packages, RSEM-EVAL and + REF-EVAL.' diff --git a/recipes/dfam/meta.yaml b/recipes/dfam/meta.yaml index 889b03638ac36..deff3edeb65a1 100644 --- a/recipes/dfam/meta.yaml +++ b/recipes/dfam/meta.yaml @@ -1,16 +1,14 @@ -about: - home: dfam.org - license: 'GPL' - summary: 'The Dfam database is a collection of Repetitive DNA element sequence alignments, hidden Markov models (HMMs) and matches lists for complete Eukaryote genomes' - -build: - number: 1 - skip: True # [osx] - package: name: dfam version: '2.0' +source: + url: http://dfam.org/web_download/Tools/dfamscan.pl + sha256: e308e6a32ca42db00862b5eae461f97abd8979050241333656a415a3cda7a9e6 + +build: + number: 1 + skip: True # [osx] requirements: run: @@ -21,10 +19,12 @@ requirements: - hmmer - repeatmasker -source: - url: http://dfam.org/web_download/Tools/dfamscan.pl - test: commands: - dfamscan.pl --help 2>&1 |grep dfam_infile - download-dfam.py --help + +about: + home: dfam.org + license: 'GPL' + summary: 'The Dfam database is a collection of Repetitive DNA element sequence alignments, hidden Markov models (HMMs) and matches lists for complete Eukaryote genomes' diff --git a/recipes/discovar/meta.yaml b/recipes/discovar/meta.yaml index 4aca62ee8bc9c..ce487975c9270 100644 --- a/recipes/discovar/meta.yaml +++ b/recipes/discovar/meta.yaml @@ -1,23 +1,23 @@ -about: - home: https://www.broadinstitute.org/software/discovar - license: 'MIT' - summary: 'Suitable for variant calling with reference and de novo assembly of small genomes.' +package: + name: discovar + version: '52488' + +source: + url: ftp://ftp.broadinstitute.org/pub/crd/Discovar/latest_source_code/discovar-52488.tar.gz build: number: 1 skip: True # [osx] -package: - name: discovar - version: '52488' - requirements: build: - {{ compiler('c') }} run: -source: - url: ftp://ftp.broadinstitute.org/pub/crd/Discovar/latest_source_code/discovar-52488.tar.gz +about: + home: https://www.broadinstitute.org/software/discovar + license: 'MIT' + summary: 'Suitable for variant calling with reference and de novo assembly of small genomes.' extra: identifiers: diff --git a/recipes/dsh-bio/meta.yaml b/recipes/dsh-bio/meta.yaml index 364813d36cc67..564606b9da80c 100644 --- a/recipes/dsh-bio/meta.yaml +++ b/recipes/dsh-bio/meta.yaml @@ -1,23 +1,17 @@ {% set version="1.1" %} -about: - home: https://github.com/heuermh/dishevelled-bio - license: LGPL version 3 or later - license_file: COPYING.LESSER - summary: Tools for BED, FASTA, FASTQ, GFA1/2, GFF3, SAM, and VCF files - package: name: dsh-bio version: {{ version }} -build: - number: 1 - noarch: generic - source: url: https://search.maven.org/remotecontent?filepath=org/dishevelled/dsh-bio-tools/{{ version }}/dsh-bio-tools-{{ version }}-bin.tar.gz sha256: ee83f4875e15d0444d9230a4971514eba436585f6782240106075c63492ce853 +build: + number: 1 + noarch: generic + requirements: build: run: @@ -28,3 +22,9 @@ test: commands: - dsh-bio --help - dsh-split-bed --help + +about: + home: https://github.com/heuermh/dishevelled-bio + license: LGPL version 3 or later + license_file: COPYING.LESSER + summary: Tools for BED, FASTA, FASTQ, GFA1/2, GFF3, SAM, and VCF files diff --git a/recipes/dwgsim/meta.yaml b/recipes/dwgsim/meta.yaml index dd31724abb5db..9e2f5a0e10576 100644 --- a/recipes/dwgsim/meta.yaml +++ b/recipes/dwgsim/meta.yaml @@ -1,16 +1,14 @@ -about: - home: https://github.com/nh13/DWGSIM - license: GNU General Public License v2 (GPLv2) - license_family: GPL - summary: 'Whole Genome Simulator for Next-Generation Sequencing' - -build: - number: 5 - package: name: dwgsim version: '1.1.11' +source: + url: https://github.com/nh13/DWGSIM/archive/dwgsim.0.1.11.tar.gz + sha256: 49e4b558e313f4cd5755961f7f24ba48ad580c0324772d7080b59cb69ce0148b + +build: + number: 5 + requirements: build: - {{ compiler('c') }} @@ -25,6 +23,8 @@ test: commands: - printf ">a\nAAAAA" > ref.fa; dwgsim ref.fa pref -source: - url: https://github.com/nh13/DWGSIM/archive/dwgsim.0.1.11.tar.gz - sha256: 49e4b558e313f4cd5755961f7f24ba48ad580c0324772d7080b59cb69ce0148b +about: + home: https://github.com/nh13/DWGSIM + license: GNU General Public License v2 (GPLv2) + license_family: GPL + summary: 'Whole Genome Simulator for Next-Generation Sequencing' diff --git a/recipes/dxua/meta.yaml b/recipes/dxua/meta.yaml index 95d5fef196606..f6c3e5cf07a53 100644 --- a/recipes/dxua/meta.yaml +++ b/recipes/dxua/meta.yaml @@ -1,17 +1,14 @@ {% set version="1.5.26" %} -about: - home: 'https://wiki.dnanexus.com/Downloads#Upload-Agent' - license: "Apache v2.0" - summary: command-line tool for uploading files to the DNAnexus Platform package: name: dxua version: {{ version }} -requirements: -test: - commands: - - "dxua --help &> /dev/null" +source: + url: https://wiki.dnanexus.com/images/files/dnanexus-upload-agent-{{ version }}-linux.tar.gz #[linux] + md5: 2c9119f8f9289bfb1ed751bd151c6079 #[linux] + url: https://wiki.dnanexus.com/images/files/dnanexus-upload-agent-{{ version }}-osx.zip #[osx] + md5: 83fd9bf4bbee46c887e66195048f8e87 #[osx] build: number: 1 @@ -19,9 +16,13 @@ build: # https://travis-ci.org/bioconda/bioconda-recipes/jobs/243209079#L725 skip: true # [osx] -source: - url: https://wiki.dnanexus.com/images/files/dnanexus-upload-agent-{{ version }}-linux.tar.gz #[linux64] - md5: 2c9119f8f9289bfb1ed751bd151c6079 #[linux64] +requirements: - url: https://wiki.dnanexus.com/images/files/dnanexus-upload-agent-{{ version }}-osx.zip #[osx] - md5: 83fd9bf4bbee46c887e66195048f8e87 #[osx] +test: + commands: + - "dxua --help &> /dev/null" + +about: + home: 'https://wiki.dnanexus.com/Downloads#Upload-Agent' + license: "Apache v2.0" + summary: command-line tool for uploading files to the DNAnexus Platform diff --git a/recipes/fastindep/meta.yaml b/recipes/fastindep/meta.yaml index d48c9aab5f1b7..4636d57e0521a 100644 --- a/recipes/fastindep/meta.yaml +++ b/recipes/fastindep/meta.yaml @@ -1,8 +1,3 @@ -about: - home: 'https://github.com/endrebak/fastindep' - license: MIT - summary: "A fast random heuristic algorithm for identifying large sets of unrelated individuals and unrelated markers" - package: name: fastindep version: '1.0.0' @@ -11,6 +6,8 @@ source: md5: 0f00ec1afb663f290ce7ce472961f6e2 url: https://github.com/endrebak/fastindep/archive/1.0.0.tar.gz +build: + number: 1 requirements: build: @@ -23,6 +20,7 @@ test: - fastindep - fastindep-symmetry -build: - number: 1 - skip: False +about: + home: 'https://github.com/endrebak/fastindep' + license: MIT + summary: "A fast random heuristic algorithm for identifying large sets of unrelated individuals and unrelated markers" diff --git a/recipes/fgbio/meta.yaml b/recipes/fgbio/meta.yaml index d666df5fe9843..8f516ce5e9e37 100644 --- a/recipes/fgbio/meta.yaml +++ b/recipes/fgbio/meta.yaml @@ -1,22 +1,17 @@ {% set version="0.8.1" %} -about: - home: https://github.com/fulcrumgenomics/fgbio - license: MIT - summary: A set of tools for working with genomic and high throughput sequencing data, including UMIs - package: name: fgbio version: {{ version }} -build: - noarch: python - number: 1 - source: url: https://github.com/fulcrumgenomics/fgbio/releases/download/{{ version }}/fgbio-{{ version }}.jar sha256: 7688dac7aa7af0504bc718edba2793ed84d8ee61164f656a60335fd4ee4f2c8c +build: + noarch: generic + number: 1 + requirements: host: - openjdk >=8 @@ -28,3 +23,8 @@ test: commands: - 'fgbio 2>&1 | grep "CallMolecularConsensusReads"' - 'fgbio --version 2>&1 | grep "Version"' + +about: + home: https://github.com/fulcrumgenomics/fgbio + license: MIT + summary: A set of tools for working with genomic and high throughput sequencing data, including UMIs diff --git a/recipes/gatk-framework/meta.yaml b/recipes/gatk-framework/meta.yaml index 63dbca8f83e3f..b538b306721b8 100644 --- a/recipes/gatk-framework/meta.yaml +++ b/recipes/gatk-framework/meta.yaml @@ -1,20 +1,15 @@ -about: - home: https://github.com/chapmanb/gatk - license: MIT - summary: The core MIT-licensed Genome Analysis Toolkit (GATK) framework, free for all uses - package: name: gatk-framework version: '3.6.24' -build: - number: 5 - noarch: generic - source: url: https://github.com/chapmanb/gatk/releases/download/v3.6-24-framework/gatk-framework-3.6-24.tar.gz md5: 91f783c78569384ba8eccc747220adb2 +build: + number: 5 + noarch: generic + requirements: run: - openjdk >=8,<9 @@ -22,3 +17,8 @@ requirements: test: commands: - gatk-framework --version + +about: + home: https://github.com/chapmanb/gatk + license: MIT + summary: The core MIT-licensed Genome Analysis Toolkit (GATK) framework, free for all uses diff --git a/recipes/gb_taxonomy_tools/meta.yaml b/recipes/gb_taxonomy_tools/meta.yaml index e654c6ea1f621..17cb65053caae 100644 --- a/recipes/gb_taxonomy_tools/meta.yaml +++ b/recipes/gb_taxonomy_tools/meta.yaml @@ -1,19 +1,24 @@ -about: - home: https://github.com/spond/gb_taxonomy_tools - summary: These are four simple utilities which perform certain manipulations and visualization tasks on GenBank taxonomic information. - license: GNU General Public License v2.0 package: name: gb_taxonomy_tools version: 1.0.1 + +source: + url: https://github.com/spond/gb_taxonomy_tools/archive/1.0.1.tar.gz + sha256: d9c0901a66db19fc0f77d02316f663200f739db998746037fcf23e36db9377f4 + build: number: 0 skip: True # [osx] + requirements: build: - cmake + test: commands: - which taxonomy-reader -source: - url: https://github.com/spond/gb_taxonomy_tools/archive/1.0.1.tar.gz - sha256: d9c0901a66db19fc0f77d02316f663200f739db998746037fcf23e36db9377f4 + +about: + home: https://github.com/spond/gb_taxonomy_tools + summary: These are four simple utilities which perform certain manipulations and visualization tasks on GenBank taxonomic information. + license: GNU General Public License v2.0 diff --git a/recipes/genblastg/meta.yaml b/recipes/genblastg/meta.yaml index 01654d072b29e..ef963fc4c7e4f 100644 --- a/recipes/genblastg/meta.yaml +++ b/recipes/genblastg/meta.yaml @@ -1,17 +1,14 @@ -about: - home: http://genome.sfu.ca/genblast/download.html - license: 'GNU' - summary: 'genBlast is a program suite, consisting of two programs: genBlastA and genBlastG. - genBlastA parses local alignments, or high-scoring segment pairs (HSPs) - produced by local sequence alignment programs such as BLAST and WU-BLAST and identify groups of HSPs.' - -build: - number: 2 - package: name: genblastg version: '1.38' +source: + url: http://genome.sfu.ca/genblast/latest/genblast_v139.zip + sha256: 7934ef446d9b2f8fa80a6b53a2f001e2531edf2a2749545390e739ffa878e8d4 + +build: + number: 2 + requirements: build: - {{ compiler('c') }} @@ -21,10 +18,13 @@ requirements: - zlib - blast -source: - url: http://genome.sfu.ca/genblast/latest/genblast_v139.zip - sha256: 7934ef446d9b2f8fa80a6b53a2f001e2531edf2a2749545390e739ffa878e8d4 - test: commands: - genblastG + +about: + home: http://genome.sfu.ca/genblast/download.html + license: 'GNU' + summary: 'genBlast is a program suite, consisting of two programs: genBlastA and genBlastG. + genBlastA parses local alignments, or high-scoring segment pairs (HSPs) + produced by local sequence alignment programs such as BLAST and WU-BLAST and identify groups of HSPs.' diff --git a/recipes/hr2/meta.yaml b/recipes/hr2/meta.yaml index 94e8760767f60..0c7076507292b 100644 --- a/recipes/hr2/meta.yaml +++ b/recipes/hr2/meta.yaml @@ -1,29 +1,27 @@ -about: - home: http://fiehnlab.ucdavis.edu - license: GPL - summary: 'HR2 is a program to calculate elemental compositions for a given mass. This program and its documentation are Copyright (c) 1992-2005 by Joerg Hau' - -build: - number: 0 - package: name: hr2 version: 1.04 +source: + sha256: 51271469363b9bf59cb4065c0cb8a5436fd3ffd737de184362b02b5b5b1aa974 + url: https://github.com/fgiacomoni/HR2/archive/master.zip + +build: + number: 0 + requirements: build: - {{ compiler('cxx') }} - host: - zlib - run: - zlib -source: - sha256: 51271469363b9bf59cb4065c0cb8a5436fd3ffd737de184362b02b5b5b1aa974 - url: https://github.com/fgiacomoni/HR2/archive/master.zip - test: commands: - HR2.exe -v + +about: + home: http://fiehnlab.ucdavis.edu + license: GPL + summary: 'HR2 is a program to calculate elemental compositions for a given mass. This program and its documentation are Copyright (c) 1992-2005 by Joerg Hau' diff --git a/recipes/indelfixer/meta.yaml b/recipes/indelfixer/meta.yaml index d5c1647e03df1..0f33fd2db9f65 100644 --- a/recipes/indelfixer/meta.yaml +++ b/recipes/indelfixer/meta.yaml @@ -1,20 +1,15 @@ -about: - home: https://github.com/cbg-ethz/InDelFixer - license: GNU General Public License v3.0 - summary: A sensitive aligner for 454, Illumina and PacBio data, employing a full Smith-Waterman alignment against a reference. - package: name: indelfixer version: "1.1" -build: - number: 1 - noarch: generic - source: url: https://github.com/cbg-ethz/InDelFixer/releases/download/v1.1/InDelFixer.jar sha256: 7e4a84d8dde4f7cd02fe1efd13793b466ee1198c69df231b03884c6fc84f88af +build: + number: 1 + noarch: generic + requirements: build: run: @@ -24,6 +19,11 @@ test: commands: - InDelFixer +about: + home: https://github.com/cbg-ethz/InDelFixer + license: GNU General Public License v3.0 + summary: A sensitive aligner for 454, Illumina and PacBio data, employing a full Smith-Waterman alignment against a reference. + extra: notes: | InDelFixer is Java program that comes with a custom wrapper shell script. diff --git a/recipes/je-suite/meta.yaml b/recipes/je-suite/meta.yaml index 16f0d19a443d9..ea380bb73d171 100644 --- a/recipes/je-suite/meta.yaml +++ b/recipes/je-suite/meta.yaml @@ -1,25 +1,18 @@ {% set name = "je" %} {% set version = "1.2" %} -about: - home: https://gbcs.embl.de/Je - license: MIT License - license_family: MIT - summary: | - Je is a suite to handle barcoded fastq files with (or without) Unique Molecule Identifiers (UMIs) and filter - read duplicates using these UMIs package: name: je-suite version: {{ version }} -build: - number: 1 - noarch: generic - source: url: https://git.embl.de/grp-gbcs/Je/raw/release_{{ version }}/dist/{{ name }}_{{ version }}.tar.gz md5: 83960fb59a4915fff7cbbfc05f2d9f16 +build: + number: 1 + noarch: generic + requirements: build: run: @@ -29,6 +22,14 @@ test: commands: - je version +about: + home: https://gbcs.embl.de/Je + license: MIT License + license_family: MIT + summary: | + Je is a suite to handle barcoded fastq files with (or without) Unique Molecule Identifiers (UMIs) and filter + read duplicates using these UMIs + extra: notes: | Je is Java program that comes with a wrapper shell script. diff --git a/recipes/mdust/meta.yaml b/recipes/mdust/meta.yaml index 2f7540bedcc2a..a229e4f319cb5 100644 --- a/recipes/mdust/meta.yaml +++ b/recipes/mdust/meta.yaml @@ -1,10 +1,11 @@ -about: - home: "http://compbio.dfci.harvard.edu/tgi/" - license: The Artistic License - summary: mdust from DFCI Gene Indices Software Tools package: name: mdust version: 2006.10.17 + +source: + url: ftp://occams.dfci.harvard.edu/pub/bio/tgi/software/seqclean/mdust.tar.gz + sha256: 9722806920fc6772dc92f99e7a59554c5f7c35b596dca0df9ed03ff2e5c6440d + build: number: 1 skip: True # [osx] @@ -13,9 +14,12 @@ requirements: build: - {{ compiler('c') }} run: + test: commands: - 'mdust -h 2>&1|grep "Usage: mdust"' -source: - url: ftp://occams.dfci.harvard.edu/pub/bio/tgi/software/seqclean/mdust.tar.gz - sha256: 9722806920fc6772dc92f99e7a59554c5f7c35b596dca0df9ed03ff2e5c6440d + +about: + home: "http://compbio.dfci.harvard.edu/tgi/" + license: The Artistic License + summary: mdust from DFCI Gene Indices Software Tools diff --git a/recipes/metacherchant/meta.yaml b/recipes/metacherchant/meta.yaml index 9bb8f3726d70a..0e0e56adf93ff 100644 --- a/recipes/metacherchant/meta.yaml +++ b/recipes/metacherchant/meta.yaml @@ -2,15 +2,6 @@ {% set version = "0.1.0" %} {% set sha256 = "a150120bc8abbbe1225caa43d1804dfb9ed6d2d0ef2e583fafae804b44e94916" %} -about: - home: https://github.com/ctlab/metacherchant - license: MIT - summary: genomic environment analysis tool - -build: - number: 1 - noarch: generic - package: name: {{ name| lower }} version: {{ version }} @@ -19,6 +10,10 @@ source: url: https://github.com/will-rowe/{{ name| lower }}/archive/{{ version }}.tar.gz sha256: {{ sha256 }} +build: + number: 1 + noarch: generic + requirements: build: - openjdk >=7.0 @@ -28,3 +23,8 @@ requirements: test: commands: - metacherchant.sh + +about: + home: https://github.com/ctlab/metacherchant + license: MIT + summary: genomic environment analysis tool diff --git a/recipes/metfrag/meta.yaml b/recipes/metfrag/meta.yaml index f46f51e030f1c..9d79d76893b5f 100644 --- a/recipes/metfrag/meta.yaml +++ b/recipes/metfrag/meta.yaml @@ -1,8 +1,3 @@ -about: - home: http://c-ruttkies.github.io/MetFrag/ - license: GNU Lesser General Public License version 2.1 or later. - summary: MetFrag is a freely available software for the annotation of high precision tandem mass spectra of metabolites which is a first and critical step for the identification of a molecular structure. Candidate molecules of different databases are fragmented in silico and matched against mass to charge values. A score calculated using the fragment peak matches gives hints to the quality of the candidate spectrum assignment. - package: name: metfrag version: '2.4.5' @@ -24,3 +19,8 @@ requirements: test: commands: - metfrag --help + +about: + home: http://c-ruttkies.github.io/MetFrag/ + license: GNU Lesser General Public License version 2.1 or later. + summary: MetFrag is a freely available software for the annotation of high precision tandem mass spectra of metabolites which is a first and critical step for the identification of a molecular structure. Candidate molecules of different databases are fragmented in silico and matched against mass to charge values. A score calculated using the fragment peak matches gives hints to the quality of the candidate spectrum assignment. diff --git a/recipes/mgltools/meta.yaml b/recipes/mgltools/meta.yaml index 2864a0c8b6530..57fa0d627b6ee 100644 --- a/recipes/mgltools/meta.yaml +++ b/recipes/mgltools/meta.yaml @@ -1,21 +1,16 @@ -about: - home: http://mgltools.scripps.edu/ - license_file: LICENSES - summary: MGLTools is an program for visualization and analisys of molecular structures. - package: name: mgltools version: 1.5.6 -build: - number: 1 - source: url: http://mgltools.scripps.edu/downloads/downloads/tars/releases/REL1.5.6/mgltools_x86_64Linux2_1.5.6.tar.gz # [linux] md5: e3f62852c4d442a292dedbe6c79540ca # [linux] url: http://mgltools.scripps.edu/downloads/downloads/tars/releases/REL1.5.6/mgltools_i86Darwin9_1.5.6.tar.gz # [osx] md5: c515b187cddeec72fe5a81ecb4a92d6b # [osx] +build: + number: 1 + requirements: build: run: @@ -25,3 +20,8 @@ test: - pmv --help - prepare_ligand4.py - prepare_receptor4.py + +about: + home: http://mgltools.scripps.edu/ + license_file: LICENSES + summary: MGLTools is an program for visualization and analisys of molecular structures. diff --git a/recipes/mira/meta.yaml b/recipes/mira/meta.yaml index 880a94a65f53d..604e9502e4432 100644 --- a/recipes/mira/meta.yaml +++ b/recipes/mira/meta.yaml @@ -1,34 +1,32 @@ -about: - home: https://sourceforge.net/p/mira-assembler/wiki/Home/ - license: 'GNU General Public License v2 or later (GPLv2+)' - license_file: LICENCE - summary: 'MIRA is a whole genome shotgun and EST sequence assembler for Sanger, 454, Solexa (Illumina), IonTorrent data and PacBio (the later at the moment only CCS and error-corrected CLR reads)' +package: + name: mira + version: '4.0.2' build: number: 3 # TODO - this ought to work on osx as well - skip: True # [not linux64] + skip: True # [not linux] -package: - name: mira - version: '4.0.2' +source: + url: https://downloads.sourceforge.net/project/mira-assembler/MIRA/stable/mira_4.0.2_linux-gnu_x86_64_static.tar.bz2 # [linux] + sha256: d3c74a6b402192e01d10adb8dbdc3450d4033fa0e7662ce5ce5de4f8c1967813 # [linux] + url: https://downloads.sourceforge.net/project/mira-assembler/MIRA/stable/mira_4.0.2_darwin13.1.0_x86_64_static.tar.bz2 # [osx] + sha256: 3cdfba4be7bde1a97b15259b9fd3216c4369d906ea20f5f360f30dc0d83e7b8e # [osx] # No build requirements as using the author's binaries. requirements: build: run: -source: - url: https://downloads.sourceforge.net/project/mira-assembler/MIRA/stable/mira_4.0.2_linux-gnu_x86_64_static.tar.bz2 # [linux64] - md5: 1defc8b9a398691d9aab640cba41e36e # [linux64] - sha256: d3c74a6b402192e01d10adb8dbdc3450d4033fa0e7662ce5ce5de4f8c1967813 # [linux64] - url: https://downloads.sourceforge.net/project/mira-assembler/MIRA/stable/mira_4.0.2_darwin13.1.0_x86_64_static.tar.bz2 # [osx] - md5: 4ced4dc1fd412b3f8a5a802c076d2724 # [osx] - sha256: 3cdfba4be7bde1a97b15259b9fd3216c4369d906ea20f5f360f30dc0d83e7b8e # [osx] - test: commands: - - mira --help + - mira --help + +about: + home: https://sourceforge.net/p/mira-assembler/wiki/Home/ + license: 'GNU General Public License v2 or later (GPLv2+)' + license_file: LICENCE + summary: 'MIRA is a whole genome shotgun and EST sequence assembler for Sanger, 454, Solexa (Illumina), IonTorrent data and PacBio (the later at the moment only CCS and error-corrected CLR reads)' extra: identifiers: diff --git a/recipes/mobster/meta.yaml b/recipes/mobster/meta.yaml index 83d4ae2c44cef..9025f7e4d468d 100644 --- a/recipes/mobster/meta.yaml +++ b/recipes/mobster/meta.yaml @@ -1,10 +1,5 @@ {% set version = "0.2.4.1" %} -about: - home: https://github.com/jyhehir/mobster - license: GPL3 - summary: NGS tool for detecting MEI and gene retrotransposition events in WGS and WES data, see Thung et al. Genome Biol. 2014 for more information. - package: name: mobster version: {{ version }} @@ -30,6 +25,10 @@ test: - mobster --help - mobster-to-vcf --help +about: + home: https://github.com/jyhehir/mobster + license: GPL3 + summary: NGS tool for detecting MEI and gene retrotransposition events in WGS and WES data, see Thung et al. Genome Biol. 2014 for more information. extra: notes: | diff --git a/recipes/mummer4/meta.yaml b/recipes/mummer4/meta.yaml index 740b5cb081457..8f3deb93fecbd 100644 --- a/recipes/mummer4/meta.yaml +++ b/recipes/mummer4/meta.yaml @@ -1,21 +1,20 @@ {% set name = "mummer4" %} {% set version = "4.0.0beta2" %} -about: - home: 'https://mummer4.github.io/' - license: "The Artistic License 2.0" - summary: "MUMmer is a system for rapidly aligning entire genomes" -build: - number: 4 package: name: {{ name|lower }} version: {{ version }} + source: sha256: cece76e418bf9c294f348972e5b23a0230beeba7fd7d042d5584ce075ccd1b93 url: https://github.com/mummer4/mummer/releases/download/v{{ version }}/mummer-{{ version }}.tar.gz patches: - Makefile.am.patch # replaces some double quotes with single quotes to accomodate filepaths with '@' (Galaxy) - Makefile.in.patch + +build: + number: 4 + requirements: build: - {{ compiler('c') }} @@ -24,6 +23,7 @@ requirements: - perl run: - perl + test: commands: - "mummer 2>&1 | grep mummer &> /dev/null" @@ -31,3 +31,8 @@ test: - "nucmer 2>&1 | grep nucmer &> /dev/null" - "promer 2>&1 | grep promer &> /dev/null" - "show-aligns -h &> /dev/null" + +about: + home: 'https://mummer4.github.io/' + license: "The Artistic License 2.0" + summary: "MUMmer is a system for rapidly aligning entire genomes" diff --git a/recipes/mvicuna/meta.yaml b/recipes/mvicuna/meta.yaml index 35c8105006530..44a23b23cd854 100644 --- a/recipes/mvicuna/meta.yaml +++ b/recipes/mvicuna/meta.yaml @@ -1,8 +1,3 @@ -about: - home: 'https://www.broadinstitute.org/scientific-community/science/projects/viral-genomics/vicuna' - license: 'https://www.broadinstitute.org/node/4238' - summary: 'M-Vicuna is a modularized version of VICUNA, a de novo assembly program targeting populations with high mutation rates' - package: name: mvicuna version: '1.0' @@ -22,3 +17,8 @@ requirements: test: commands: - 'mvicuna -h | grep "Parameters" &> /dev/null' + +about: + home: 'https://www.broadinstitute.org/scientific-community/science/projects/viral-genomics/vicuna' + license: 'https://www.broadinstitute.org/node/4238' + summary: 'M-Vicuna is a modularized version of VICUNA, a de novo assembly program targeting populations with high mutation rates' diff --git a/recipes/netreg/meta.yaml b/recipes/netreg/meta.yaml index a8572a211c7b2..20d9d957a7a17 100644 --- a/recipes/netreg/meta.yaml +++ b/recipes/netreg/meta.yaml @@ -2,20 +2,17 @@ {% set version = "1.6.0" %} {% set sha256 = "5f766693ba0a6be7a0cf6fc98de2977f7c1b862bc9671d283b6910617a7cc1ea" %} -about: - home: https://github.com/dirmeier/netReg - license: GPL3 - summary: "netReg fits linear regression models using network-penalization." - license_file: LICENSE - doc_url: https://dirmeier.github.io/netReg/ - -build: - number: 0 - package: name: {{ name }} version: {{ version }} +source: + sha256: {{ sha256 }} + url: https://github.com/dirmeier/netReg/archive/v{{ version }}.tar.gz + +build: + number: 0 + requirements: build: - {{ compiler('c') }} @@ -33,10 +30,13 @@ requirements: - zlib - hdf5 -source: - sha256: {{ sha256 }} - url: https://github.com/dirmeier/netReg/archive/v{{ version }}.tar.gz - test: commands: - netReg -h + +about: + home: https://github.com/dirmeier/netReg + license: GPL3 + summary: "netReg fits linear regression models using network-penalization." + license_file: LICENSE + doc_url: https://dirmeier.github.io/netReg/ diff --git a/recipes/npinv/meta.yaml b/recipes/npinv/meta.yaml index f8a5c72a07dcf..224244c03d418 100644 --- a/recipes/npinv/meta.yaml +++ b/recipes/npinv/meta.yaml @@ -1,24 +1,18 @@ {% set name = "npinv" %} {% set version = "1.24" %} # Also update the version string in the npinv.py file - -about: - home: https://github.com/haojingshao/npInv - license: MIT - summary: an accurate tool for detecting and genotyping inversion using multiple alignment long reads - package: name: {{ name }} version: {{ version }} -build: - noarch: generic - number: 1 - source: url: https://github.com/haojingshao/npInv/releases/download/npInv{{ version }}/npInv{{ version }}.jar sha256: d58c5e20a3d795307517ef78bb1efe654f2f3040c461c3385fa9a406870b8816 +build: + noarch: generic + number: 1 + requirements: host: - openjdk >=8,<9 @@ -31,6 +25,11 @@ test: commands: - npinv --help +about: + home: https://github.com/haojingshao/npInv + license: MIT + summary: an accurate tool for detecting and genotyping inversion using multiple alignment long reads + extra: notes: | npinv is Java program that comes with a custom wrapper python script which I took from peptide-shaker. diff --git a/recipes/pal_finder/meta.yaml b/recipes/pal_finder/meta.yaml index 7495b2afcc42b..f0fce3ea4eb8a 100644 --- a/recipes/pal_finder/meta.yaml +++ b/recipes/pal_finder/meta.yaml @@ -1,27 +1,14 @@ -about: - home: 'http://sourceforge.net/projects/palfinder/' - license: "GPLv3" - summary: "Find microsatellite repeat elements from sequencing reads and design PCR primers to amplify them" - description: | - Finds microsatellite repeat elements directly from raw 454 - or Illumina paired-end sequencing reads, and designs PCR primers - to amplify these repeat loci in an automated fashion. Exact - matches to repeats or 2-, 3-, 4-, 5-, and/or 6-mers are located - and primer3 is then used to generate primer pairs to amplify - regions containing microsatellite loci. - package: name: pal_finder version: '0.02.04' -build: - number: 2 - skip: False - source: sha256: b9c578a4e7b1f6f03b9d05cd47876d057c4f304c42ae34c7c19ca9207403ad3b url: http://sourceforge.net/projects/palfinder/files/pal_finder_v0.02.04.tar.gz +build: + number: 2 + requirements: run: - perl @@ -30,3 +17,16 @@ requirements: test: commands: - pal_finder 2>&1 | grep "No control file given" > /dev/null + +about: + home: 'http://sourceforge.net/projects/palfinder/' + license: "GPLv3" + summary: "Find microsatellite repeat elements from sequencing reads and design PCR primers to amplify them" + description: | + Finds microsatellite repeat elements directly from raw 454 + or Illumina paired-end sequencing reads, and designs PCR primers + to amplify these repeat loci in an automated fashion. Exact + matches to repeats or 2-, 3-, 4-, 5-, and/or 6-mers are located + and primer3 is then used to generate primer pairs to amplify + regions containing microsatellite loci. + diff --git a/recipes/pathwaymatcher/meta.yaml b/recipes/pathwaymatcher/meta.yaml index 73fcf10bcbd05..f61d87fa67085 100644 --- a/recipes/pathwaymatcher/meta.yaml +++ b/recipes/pathwaymatcher/meta.yaml @@ -1,24 +1,18 @@ {% set name = "PathwayMatcher" %} {% set version = "1.9.1" %} -about: - home: https://github.com/PathwayAnalysisPlatform/PathwayMatcher - license: Apache License, Version 2.0 - summary: | - PathwayMatcher is a software tool writen in Java to search for pathways related to a list of proteins in Reactome. package: name: pathwaymatcher version: {{ version }} +source: + url: https://github.com/PathwayAnalysisPlatform/PathwayMatcher/releases/download/{{ version }}/{{ name }}.jar + sha256: 446e7c9349f4d71fb3fd7a4334acc4e8bda763544a4acc62a69fa49994aa7c78 build: noarch: generic number: 1 -source: - url: https://github.com/PathwayAnalysisPlatform/PathwayMatcher/releases/download/{{ version }}/{{ name }}.jar - sha256: 446e7c9349f4d71fb3fd7a4334acc4e8bda763544a4acc62a69fa49994aa7c78 - requirements: build: run: @@ -31,6 +25,12 @@ test: - pathwaymatcher src.main.java.no.uib.pap.pathwaymatcher.PathwayMatcher -t GENE -i genes.txt - pathwaymatcher.py -t GENE -i genes.txt +about: + home: https://github.com/PathwayAnalysisPlatform/PathwayMatcher + license: Apache License, Version 2.0 + summary: | + PathwayMatcher is a software tool writen in Java to search for pathways related to a list of proteins in Reactome. + extra: notes: | PathwayMatcher is Java program that comes with a custom wrapper shell script. diff --git a/recipes/pauda/meta.yaml b/recipes/pauda/meta.yaml index 0d88800f9f275..f5c75c6eacbe3 100644 --- a/recipes/pauda/meta.yaml +++ b/recipes/pauda/meta.yaml @@ -1,26 +1,26 @@ -about: - home: 'https://ab.inf.uni-tuebingen.de/software/pauda' - license: 'GPL' - summary: 'PAUDA is a new approach toward the problem of comparing DNA reads against a database of protein reference sequences that is applicable to very large datasets consisting of hundreds of millions or billions of reads.' +package: + name: pauda + version: '1.0.1' + +source: + url: 'http://ab.inf.uni-tuebingen.de/data/software/pauda/download/pauda-1.0.1.zip' + sha256: 7c5feecc226c83f1da124cade547dbe497e939fb04f9927b131afcd66e1cfd81 build: number: 1 skip: True #[not linux] -package: - name: pauda - version: '1.0.1' - requirements: run: - java-jdk - bowtie2 -source: - url: 'http://ab.inf.uni-tuebingen.de/data/software/pauda/download/pauda-1.0.1.zip' - sha256: 7c5feecc226c83f1da124cade547dbe497e939fb04f9927b131afcd66e1cfd81 - test: commands: - pauda-run | grep Usage > /dev/null - pauda-build | grep Usage > /dev/null + +about: + home: 'https://ab.inf.uni-tuebingen.de/software/pauda' + license: 'GPL' + summary: 'PAUDA is a new approach toward the problem of comparing DNA reads against a database of protein reference sequences that is applicable to very large datasets consisting of hundreds of millions or billions of reads.' diff --git a/recipes/pepnovo/meta.yaml b/recipes/pepnovo/meta.yaml index 1b4ba035de7f7..3ba9d64a7e523 100644 --- a/recipes/pepnovo/meta.yaml +++ b/recipes/pepnovo/meta.yaml @@ -1,20 +1,14 @@ -about: - home: http://proteomics.ucsd.edu/Software/PepNovo/ - license_file: LICENSE - summary: PepNovo serves as a high throughput de novo peptide sequencing tool for tandem mass spectrometry data - package: name: pepnovo version: 20101117 -build: - number: 1 - skip: False - source: url: http://proteomics.ucsd.edu/Software/PepNovo/PepNovo.20120423.zip md5: af2a863487cb53bf0e92f00d395c4f0d +build: + number: 1 + requirements: build: - {{ compiler('cxx') }} @@ -24,6 +18,11 @@ test: commands: - pepnovo -h 2>&1 | grep "PepNovo+" +about: + home: http://proteomics.ucsd.edu/Software/PepNovo/ + license_file: LICENSE + summary: PepNovo serves as a high throughput de novo peptide sequencing tool for tandem mass spectrometry data + extra: identifiers: - biotools:pepnovo diff --git a/recipes/pyteomics/meta.yaml b/recipes/pyteomics/meta.yaml index 7b7b4800abf23..1aa4258db8868 100644 --- a/recipes/pyteomics/meta.yaml +++ b/recipes/pyteomics/meta.yaml @@ -1,18 +1,17 @@ {% set version = "4.1.1" %} -about: - home: "https://bitbucket.org/levitsky/pyteomics" - license: "Apache License, Version 2.0" - summary: "A framework for proteomics data analysis." +package: + name: pyteomics + version: {{ version }} + +source: + url: https://pypi.io/packages/source/p/pyteomics/pyteomics-{{ version }}.tar.gz + sha256: 384e4e5eabdbfec39d7c38369278e386a074c7066f33052d7c313af40f1aa45e build: noarch: python number: 0 -package: - name: pyteomics - version: {{ version }} - requirements: host: - python @@ -25,16 +24,17 @@ requirements: - pandas - sqlalchemy -source: - url: https://pypi.io/packages/source/p/pyteomics/pyteomics-{{ version }}.tar.gz - sha256: 384e4e5eabdbfec39d7c38369278e386a074c7066f33052d7c313af40f1aa45e - test: imports: - pyteomics - pyteomics.mass - pyteomics.openms +about: + home: "https://bitbucket.org/levitsky/pyteomics" + license: "Apache License, Version 2.0" + summary: "A framework for proteomics data analysis." + extra: identifiers: - biotools:pyteomics diff --git a/recipes/qorts/meta.yaml b/recipes/qorts/meta.yaml index 9969d631d2ed1..a9033f63d9c3c 100644 --- a/recipes/qorts/meta.yaml +++ b/recipes/qorts/meta.yaml @@ -1,18 +1,15 @@ -about: - home: http://hartleys.github.io/QoRTs/ - license: Public Domain - summary: The QoRTs software package is a fast, efficient, and portable multifunction toolkit designed to assist in the analysis, quality control, and data management of RNA-Seq datasets. package: name: qorts version: 1.3.0 +source: + url: https://github.com/hartleys/QoRTs/releases/download/1.3.0/QoRTs.jar + md5: 2a2448470f2ce066e4624d4cc82a358c + build: noarch: generic number: 1 -source: - url: https://github.com/hartleys/QoRTs/releases/download/1.3.0/QoRTs.jar - md5: 2a2448470f2ce066e4624d4cc82a358c requirements: host: - python @@ -25,6 +22,11 @@ test: commands: - qorts QC --man &> /dev/null +about: + home: http://hartleys.github.io/QoRTs/ + license: Public Domain + summary: The QoRTs software package is a fast, efficient, and portable multifunction toolkit designed to assist in the analysis, quality control, and data management of RNA-Seq datasets. + extra: notes: | QoRTs is Java program that comes with a custom wrapper shell script. diff --git a/recipes/rabix-bunny/meta.yaml b/recipes/rabix-bunny/meta.yaml index f0c8a39b378f6..66d1390fb0d38 100644 --- a/recipes/rabix-bunny/meta.yaml +++ b/recipes/rabix-bunny/meta.yaml @@ -1,24 +1,18 @@ {% set version = "1.0.4" %} {% set subversion = "5" %} -about: - home: https://github.com/rabix/bunny - license: Apache v2 - summary: Open-source development kit for the Common Workflow Language from Seven Bridges. The Rabix executor Bunny, which can be used to execute apps locally from the command line. - package: name: rabix-bunny version: {{ version }} -build: - number: 7 - skip: False - noarch: generic - source: url: https://github.com/rabix/bunny/releases/download/v{{ version }}-{{ subversion }}/rabix-{{ version }}-TES.tar.gz md5: 6533e187795e0cc69b1dd3119a724a48 +build: + number: 7 + noarch: generic + requirements: run: - openjdk >=8,<9 @@ -26,3 +20,8 @@ requirements: test: commands: - rabix --version + +about: + home: https://github.com/rabix/bunny + license: Apache v2 + summary: Open-source development kit for the Common Workflow Language from Seven Bridges. The Rabix executor Bunny, which can be used to execute apps locally from the command line. diff --git a/recipes/ragout/meta.yaml b/recipes/ragout/meta.yaml index a2c8cf1cc3682..49fc1a4e528fd 100644 --- a/recipes/ragout/meta.yaml +++ b/recipes/ragout/meta.yaml @@ -1,17 +1,15 @@ -about: - home: https://github.com/fenderglass/Ragout - license: GPLv3 - summary: "A tool for chromosome-level scaffolding using multiple references" -build: - number: 5 - skip: True # [py3k] - package: name: ragout version: 2.2 + source: url: https://github.com/fenderglass/Ragout/archive/2.2.tar.gz sha256: 45d1662863d590415be3cb23f446cb1214f0865b7e0e5559ce2a5e3a456d5049 + +build: + number: 5 + skip: True # [py3k] + requirements: build: - {{ compiler('c') }} @@ -23,7 +21,13 @@ requirements: - decorator ==4.3.0 - networkx ==2.2 - sibelia + test: commands: - ragout -h - Sibelia --version + +about: + home: https://github.com/fenderglass/Ragout + license: GPLv3 + summary: "A tool for chromosome-level scaffolding using multiple references" diff --git a/recipes/rawtools/meta.yaml b/recipes/rawtools/meta.yaml index 14ace9d2c41fc..1f6d6f3ae7782 100644 --- a/recipes/rawtools/meta.yaml +++ b/recipes/rawtools/meta.yaml @@ -2,23 +2,18 @@ {% set version = "1.4.2" %} {% set sha256 = "bd106e6263994c728c00c0ec1a948b6783df5d18bfb1b46be357a25a40075e2a" %} -about: - home: https://github.com/kevinkovalchik/RawTools - license: Apache License, Version 2.0 - summary: RawTools is an open-source and freely available package designed to perform scan data parsing and quantification, and quality control analysis of Thermo Orbitrap raw mass spectrometer files. - package: name: rawtools version: {{ version }} -build: - noarch: generic - number: 0 - source: url: https://github.com/kevinkovalchik/RawTools/releases/download/{{ version }}/{{ name }}-{{ version }}.zip sha256: '{{ sha256 }}' +build: + noarch: generic + number: 0 + requirements: build: run: @@ -28,6 +23,11 @@ test: commands: - bash rawtools.sh parse -f void -p +about: + home: https://github.com/kevinkovalchik/RawTools + license: Apache License, Version 2.0 + summary: RawTools is an open-source and freely available package designed to perform scan data parsing and quantification, and quality control analysis of Thermo Orbitrap raw mass spectrometer files. + extra: notes: | RawTools is an open-source and freely available package designed to perform scan data parsing and quantification, and quality control analysis of Thermo Orbitrap raw mass spectrometer files. diff --git a/recipes/rdp_classifier/2.2/build.sh b/recipes/rdp_classifier/build.sh similarity index 100% rename from recipes/rdp_classifier/2.2/build.sh rename to recipes/rdp_classifier/build.sh diff --git a/recipes/rdp_classifier/2.2/meta.yaml b/recipes/rdp_classifier/meta.yaml similarity index 78% rename from recipes/rdp_classifier/2.2/meta.yaml rename to recipes/rdp_classifier/meta.yaml index 2110ce57d86a8..b418654cf19af 100644 --- a/recipes/rdp_classifier/2.2/meta.yaml +++ b/recipes/rdp_classifier/meta.yaml @@ -1,26 +1,25 @@ -about: - home: 'http://rdp.cme.msu.edu/' - license: "GPLv2" - summary: "Naive Bayesian classifier that can rapidly and accurately provide taxonomic assignments from domain to genus" - package: name: rdp_classifier version: 2.2 -build: - number: 1 - skip: False - source: fn: rdp_classifier_2.2.zip md5: 745db57e1644ca4cca8330bb954d0b2c sha256: 330a56cc6199a872723a9fee48dd5ae03c5f021c3fa26053c79338f7446a4599 url: https://sourceforge.net/projects/rdp-classifier/files/rdp-classifier/rdp_classifier_2.2.zip +build: + number: 1 + requirements: run: - - openjdk + - openjdk test: - commands: - - rdp_classifier 2>&1 | grep "^Command Error" | grep "queryFile must be specified$" > /dev/null + commands: + - rdp_classifier 2>&1 | grep "^Command Error" | grep "queryFile must be specified$" > /dev/null + +about: + home: 'http://rdp.cme.msu.edu/' + license: "GPLv2" + summary: "Naive Bayesian classifier that can rapidly and accurately provide taxonomic assignments from domain to genus" diff --git a/recipes/rdp_classifier/2.2/rdp_classifier.sh b/recipes/rdp_classifier/rdp_classifier.sh similarity index 100% rename from recipes/rdp_classifier/2.2/rdp_classifier.sh rename to recipes/rdp_classifier/rdp_classifier.sh diff --git a/recipes/recon/meta.yaml b/recipes/recon/meta.yaml index 291d5adef351d..ff9a4d24d67bf 100644 --- a/recipes/recon/meta.yaml +++ b/recipes/recon/meta.yaml @@ -1,24 +1,24 @@ -about: - home: http://eddylab.org/software/recon/ - license: 'GNU General Public License' - summary: 'The RECON package performs de novo identification and classification of repeat sequence families from genomic sequences.' +package: + name: recon + version: '1.08' + +source: + url: http://www.repeatmasker.org/RECON-1.08.tar.gz build: number: 1 skip: True # [not linux] -package: - name: recon - version: '1.08' - requirements: build: - {{ compiler('c') }} run: -source: - url: http://www.repeatmasker.org/RECON-1.08.tar.gz - test: commands: - imagespread 2>&1 | grep usage + +about: + home: http://eddylab.org/software/recon/ + license: 'GNU General Public License' + summary: 'The RECON package performs de novo identification and classification of repeat sequence families from genomic sequences.' diff --git a/recipes/regtools/meta.yaml b/recipes/regtools/meta.yaml index 124a9833b0d5d..a07f6b69f77ce 100644 --- a/recipes/regtools/meta.yaml +++ b/recipes/regtools/meta.yaml @@ -2,16 +2,6 @@ {% set version = "0.5.0" %} {% set sha256 = "c9a5f05b23ffb219c35d12a0403b34db7f7cee2b0be7dc3b6f71154dc838917e" %} -about: - home: https://github.com/griffithlab/regtools/ - license: MIT - license_family: MIT - license_file: LICENSE - summary: Tools that integrate DNA-seq and RNA-seq data to help interpret mutations in a regulatory and splicing context. - -build: - number: 0 - package: name: {{ name|lower }} version: {{ version }} @@ -20,6 +10,9 @@ source: sha256: {{ sha256 }} url: https://github.com/griffithlab/{{ name }}/archive/{{ version }}.tar.gz +build: + number: 0 + requirements: build: - cmake @@ -32,3 +25,10 @@ requirements: test: commands: - regtools --help + +about: + home: https://github.com/griffithlab/regtools/ + license: MIT + license_family: MIT + license_file: LICENSE + summary: Tools that integrate DNA-seq and RNA-seq data to help interpret mutations in a regulatory and splicing context. diff --git a/recipes/repeatmodeler/meta.yaml b/recipes/repeatmodeler/meta.yaml index 28103a1004228..078a7716cedae 100644 --- a/recipes/repeatmodeler/meta.yaml +++ b/recipes/repeatmodeler/meta.yaml @@ -1,7 +1,6 @@ -about: - home: 'http://www.repeatmasker.org/RepeatModeler.html' - license: 'Open Software License v2.1' - summary: 'RepeatModeler is a de-novo repeat family identification and modeling package.' +package: + name: repeatmodeler + version: '1.0.11' source: url: 'http://www.repeatmasker.org/RepeatModeler/RepeatModeler-open-1.0.11.tar.gz' @@ -11,10 +10,6 @@ build: number: 1 skip: True #[osx] -package: - name: repeatmodeler - version: '1.0.11' - requirements: build: - perl @@ -28,12 +23,15 @@ requirements: - recon - perl-text-soundex - - test: commands: - RepeatModeler > /dev/null +about: + home: 'http://www.repeatmasker.org/RepeatModeler.html' + license: 'Open Software License v2.1' + summary: 'RepeatModeler is a de-novo repeat family identification and modeling package.' + extra: identifiers: - biotools:RepeatModeler diff --git a/recipes/repeatscout/meta.yaml b/recipes/repeatscout/meta.yaml index d9839f0434afc..b854f1919ae96 100644 --- a/recipes/repeatscout/meta.yaml +++ b/recipes/repeatscout/meta.yaml @@ -1,25 +1,25 @@ -about: - home: http://repeatscout.bioprojects.org - license: 'GNU General Public License' - summary: 'De novo identification of repeat families in large genomes.' +package: + name: repeatscout + version: '1.0.5' + +source: + url: http://www.repeatmasker.org/RepeatScout-1.0.5.tar.gz + sha256: bda6f782382f2b7dcb6a004b7da586d5046b3c12429b158e24787be62de6199c build: number: 1 skip: True # [not linux] -package: - name: repeatscout - version: '1.0.5' - requirements: build: - {{ compiler('c') }} run: -source: - url: http://www.repeatmasker.org/RepeatScout-1.0.5.tar.gz - sha256: bda6f782382f2b7dcb6a004b7da586d5046b3c12429b158e24787be62de6199c - test: commands: - RepeatScout 2>&1 | grep Version + +about: + home: http://repeatscout.bioprojects.org + license: 'GNU General Public License' + summary: 'De novo identification of repeat families in large genomes.' diff --git a/recipes/rna-seqc/meta.yaml b/recipes/rna-seqc/meta.yaml index b66c4be235c88..f8edd58040ae3 100644 --- a/recipes/rna-seqc/meta.yaml +++ b/recipes/rna-seqc/meta.yaml @@ -1,14 +1,13 @@ {% set version = "1.1.8" %} -about: - home: http://archive.broadinstitute.org/cancer/cga/rna-seqc - license: None - summary: RNA-SeQC is a java program which computes a series of quality control metrics for RNA-seq data. The input can be one or more BAM files - package: name: rna-seqc version: {{ version }} +source: + url: http://www.broadinstitute.org/cancer/cga/tools/rnaseqc/RNA-SeQC_v1.1.8.jar + md5: 71d7b5d3b3dcc1893cdc7f6819185d41 + build: number: 2 noarch: generic @@ -22,6 +21,7 @@ test: - "{ rna-seqc || true; } | grep RNA-SeQC" - "{ rna-seqc || true; } | grep {{ version }}" -source: - url: http://www.broadinstitute.org/cancer/cga/tools/rnaseqc/RNA-SeQC_v1.1.8.jar - md5: 71d7b5d3b3dcc1893cdc7f6819185d41 +about: + home: http://archive.broadinstitute.org/cancer/cga/rna-seqc + license: None + summary: RNA-SeQC is a java program which computes a series of quality control metrics for RNA-seq data. The input can be one or more BAM files diff --git a/recipes/rnacode/0.3/build.sh b/recipes/rnacode/build.sh similarity index 100% rename from recipes/rnacode/0.3/build.sh rename to recipes/rnacode/build.sh diff --git a/recipes/rnacode/0.3/meta.yaml b/recipes/rnacode/meta.yaml similarity index 99% rename from recipes/rnacode/0.3/meta.yaml rename to recipes/rnacode/meta.yaml index 8aec1ce5993a5..e3f22bb1fc77b 100644 --- a/recipes/rnacode/0.3/meta.yaml +++ b/recipes/rnacode/meta.yaml @@ -1,22 +1,27 @@ -about: - home: http://wash.github.io/rnacode/ - license: '' - summary: 'RNAcode - Analyze the protein coding potential in multiple sequence alignments - RNAcode relies on evolutionary signatures including synonymous/conservative mutations - and conservation of the reading frame. It does not use any species specific sequence - characteristics whatsoever and does not use any machine learning techniques.' -build: - number: 1 - skip: True # [osx] package: name: rnacode version: '0.3' -requirements: - build: [] - run: [] + source: sha256: 86c600a07ecd04d243fd6eb3c6cc5b20fd6159f34f69423e7391c0ce8f311048 url: http://github.com/downloads/wash/rnacode/RNAcode-0.3.tar.gz + +build: + number: 1 + skip: True # [osx] + +requirements: + build: [] + run: [] + test: commands: - RNAcode --help &> /dev/null + +about: + home: http://wash.github.io/rnacode/ + license: '' + summary: 'RNAcode - Analyze the protein coding potential in multiple sequence alignments + RNAcode relies on evolutionary signatures including synonymous/conservative mutations + and conservation of the reading frame. It does not use any species specific sequence + characteristics whatsoever and does not use any machine learning techniques.' diff --git a/recipes/rnastructure/meta.yaml b/recipes/rnastructure/meta.yaml index fcbb0db7bbdd7..95b9a080994ef 100644 --- a/recipes/rnastructure/meta.yaml +++ b/recipes/rnastructure/meta.yaml @@ -1,44 +1,43 @@ -about: - home: http://rna.urmc.rochester.edu/RNAstructure.html - license: GPLv2 - license_family: GPL - license_file: gpl.txt - summary: 'RNAstructure is a complete package for RNA and DNA secondary structure prediction - and analysis. It includes algorithms for secondary structure prediction, including - facility to predict base pairing probabilities. It also can be used to predict - bimolecular structures and can predict the equilibrium binding affinity of an - oligonucleotide to a structured RNA target. This is useful for siRNA design. - It can also predict secondary structures common to two, unaligned sequences, - which is much more accurate than single sequence secondary structure prediction. - Finally, RNAstructure can take a number of different types of experiment mapping - data to constrain or restrain structure prediction. These include chemical mapping, - enzymatic mapping, NMR, and SHAPE data.' +package: + name: rnastructure + version: '6.1' + +source: + sha256: b9a5468a53a6546bcc060d7befc9466a6688f1d1c2611707630d991c69193ed5 + url: http://rna.urmc.rochester.edu/Releases/6.1/RNAstructureSource.tgz build: number: 0 skip: True # [osx] -package: - name: rnastructure - version: '6.1' - requirements: build: - {{ compiler('c') }} - {{ compiler('cxx') }} run: -source: - sha256: b9a5468a53a6546bcc060d7befc9466a6688f1d1c2611707630d991c69193ed5 - url: http://rna.urmc.rochester.edu/Releases/6.1/RNAstructureSource.tgz - - # In version 6.0, several commands are returning exit code 1 when called with # the -h option. Therefore, changed the modules that are tested. test: commands: - bifold -h +about: + home: http://rna.urmc.rochester.edu/RNAstructure.html + license: GPLv2 + license_family: GPL + license_file: gpl.txt + summary: 'RNAstructure is a complete package for RNA and DNA secondary structure prediction + and analysis. It includes algorithms for secondary structure prediction, including + facility to predict base pairing probabilities. It also can be used to predict + bimolecular structures and can predict the equilibrium binding affinity of an + oligonucleotide to a structured RNA target. This is useful for siRNA design. + It can also predict secondary structures common to two, unaligned sequences, + which is much more accurate than single sequence secondary structure prediction. + Finally, RNAstructure can take a number of different types of experiment mapping + data to constrain or restrain structure prediction. These include chemical mapping, + enzymatic mapping, NMR, and SHAPE data.' + extra: identifiers: - biotools:rnastructure diff --git a/recipes/seqbuster/meta.yaml b/recipes/seqbuster/meta.yaml index 26ca9ef9c3130..1d76b5abe06a6 100644 --- a/recipes/seqbuster/meta.yaml +++ b/recipes/seqbuster/meta.yaml @@ -1,8 +1,3 @@ -about: - home: https://github.com/lpantano/seqbuster - license: MIT - summary: miRNA and isomiR annotation - package: name: seqbuster version: '3.2' @@ -24,6 +19,11 @@ test: commands: - miraligner +about: + home: https://github.com/lpantano/seqbuster + license: MIT + summary: miRNA and isomiR annotation + extra: identifiers: - biotools:seqbuster diff --git a/recipes/seqcluster/meta.yaml b/recipes/seqcluster/meta.yaml index 298f3c31f6846..86f00542200d8 100644 --- a/recipes/seqcluster/meta.yaml +++ b/recipes/seqcluster/meta.yaml @@ -1,10 +1,5 @@ {% set tag="v1.2.4" %} -about: - home: https://github.com/lpantano/seqclsuter - license: MIT - summary: small RNA analysis from NGS data - package: name: seqcluster version: '1.2.4' @@ -12,6 +7,7 @@ package: source: url: https://github.com/lpantano/seqcluster/archive/{{ tag }}.tar.gz sha256: 2aa5e0be928f668b652b24d9fffa48ad1a793df112728b0edf4f7780dabb2ffa + build: number: 0 @@ -38,6 +34,11 @@ test: imports: - seqcluster +about: + home: https://github.com/lpantano/seqclsuter + license: MIT + summary: small RNA analysis from NGS data + extra: identifiers: - biotools:seqcluster diff --git a/recipes/shorah/1.1.3/meta.yaml b/recipes/shorah/1.1.3/meta.yaml index 941a3d4f47231..c34bf36e02597 100644 --- a/recipes/shorah/1.1.3/meta.yaml +++ b/recipes/shorah/1.1.3/meta.yaml @@ -2,23 +2,17 @@ {% set version = "1.1.3" %} {% set sha256 = "3b89623fcbef71193503adce5ea05fb62f4c1d9cb46c599705942a06ccfb8e87" %} -about: - summary: The Short Reads Assembly into Haplotypes (ShoRAH) program for inferring viral haplotypes from NGS data - home: https://github.com/cbg-ethz/{{ name }} - license: GPLv3 - license_family: GPL3 - package: name: {{ name|lower }} version: {{ version }} -build: - number: 2 - source: url: https://github.com/cbg-ethz/shorah/releases/download/v{{ version }}/{{ name }}-{{ version }}.tar.bz2 sha256: {{ sha256 }} +build: + number: 2 + requirements: build: - {{ compiler('c') }} @@ -46,19 +40,16 @@ test: - snv.py -h - amplian.py -h - fas2read.pl -h - - contain -h - b2w -h - diri_sampler -h - freqEst -h -# # quick test skipped to shave off a few seconds of CircleCi's runtime -# - amplian.py -b examples/amplicon_test/ampli_sorted.bam -f examples/amplicon_test/reference.fasta -# -# source_files: -# - examples/amplicon_test/ampli_sorted.bam -# - examples/amplicon_test/reference.fasta - +about: + summary: The Short Reads Assembly into Haplotypes (ShoRAH) program for inferring viral haplotypes from NGS data + home: https://github.com/cbg-ethz/{{ name }} + license: GPLv3 + license_family: GPL3 extra: identifiers: diff --git a/recipes/snver/meta.yaml b/recipes/snver/meta.yaml index 48adc19845992..11fe3802a1526 100644 --- a/recipes/snver/meta.yaml +++ b/recipes/snver/meta.yaml @@ -1,28 +1,18 @@ {% set name = "snver" %} {% set version = "0.5.3" %} -about: - home: http://snver.sourceforge.net/ - license: GNU General Public License version 3.0 (GPLv3) - license-file: LICENSE - summary: | - SNVer is a statistical tool for calling common and rare variants in analysis of pool or individual next-generation sequencing data. - It reports one single overall p-value for evaluating the significance of a candidate locus being a variant, based on which multiplicity control can be obtained. - Loci with any (low) coverage can be tested and depth of coverage will be quantitatively factored into final significance calculation. - SNVer runs very fast, making it feasible for analysis of whole-exome sequencing data, or even whole-genome sequencing data. - package: name: snver version: {{ version }} -build: - noarch: generic - number: 0 - source: url: https://sourceforge.net/projects/snver/files/SNVer-{{ version }}.tar.gz sha256: ac387873370941ab1b379def51252f40e819b0529e06f8cd8f04b61fea1b6cf8 +build: + noarch: generic + number: 0 + requirements: host: run: @@ -34,6 +24,16 @@ test: - snver - snver-pool +about: + home: http://snver.sourceforge.net/ + license: GNU General Public License version 3.0 (GPLv3) + license-file: LICENSE + summary: | + SNVer is a statistical tool for calling common and rare variants in analysis of pool or individual next-generation sequencing data. + It reports one single overall p-value for evaluating the significance of a candidate locus being a variant, based on which multiplicity control can be obtained. + Loci with any (low) coverage can be tested and depth of coverage will be quantitatively factored into final significance calculation. + SNVer runs very fast, making it feasible for analysis of whole-exome sequencing data, or even whole-genome sequencing data. + extra: notes: | SNVer is Java program that comes with a custom wrapper shell script. diff --git a/recipes/soapdenovo2-errorcorrection/meta.yaml b/recipes/soapdenovo2-errorcorrection/meta.yaml index 3b1c5051d26c9..4ed31de1c67dc 100644 --- a/recipes/soapdenovo2-errorcorrection/meta.yaml +++ b/recipes/soapdenovo2-errorcorrection/meta.yaml @@ -1,16 +1,15 @@ -about: - home: http://soap.genomics.org.cn/soapdenovo.html - license: 'GNU' - summary: 'Error correction for soapdenovo2.' +package: + name: soapdenovo2-errorcorrection + version: '2.0' + +source: + url: http://sourceforge.net/projects/soapdenovo2/files/ErrorCorrection/ErrorCorrection.tgz + sha256: 9f4f38ec0629045d0f2da67c8221636f545f1bdd500b7e4c0ad7e95db1794a8d build: number: 2 skip: True # [osx] -package: - name: soapdenovo2-errorcorrection - version: '2.0' - requirements: build: - {{ compiler('cxx') }} @@ -20,11 +19,12 @@ requirements: run: - zlib -source: - url: http://sourceforge.net/projects/soapdenovo2/files/ErrorCorrection/ErrorCorrection.tgz - sha256: 9f4f38ec0629045d0f2da67c8221636f545f1bdd500b7e4c0ad7e95db1794a8d - test: commands: # This isn't the most useful test, but in order to use the program one has to set `ulimit -l` to unlimited - which ErrorCorrection + +about: + home: http://soap.genomics.org.cn/soapdenovo.html + license: 'GNU' + summary: 'Error correction for soapdenovo2.' diff --git a/recipes/soapdenovo2-prepare/meta.yaml b/recipes/soapdenovo2-prepare/meta.yaml index c447997ded09b..5dff3cfe5d5c8 100644 --- a/recipes/soapdenovo2-prepare/meta.yaml +++ b/recipes/soapdenovo2-prepare/meta.yaml @@ -1,17 +1,16 @@ -about: - home: https://github.com/aquaskyline/SOAPdenovo2 - license: GPL-3.0 - license_family: GPL - license_file: '{{ RECIPE_DIR }}/LICENSE' - summary: SoapDenovo2 data prepare module using assembled contig to do scaffold assembly. - -build: - number: 3 - package: name: soapdenovo2-prepare version: 2.0 +source: + url: https://sourceforge.net/projects/soapdenovo2/files/Prepare/Prepare-src-v2.0.tgz + sha256: 97bfccede6bd138365d466f2d71685abaccd366ea69ae0a9d90598e4547f291f + patches: + - Makefile.osx.patch # [osx] + +build: + number: 3 + requirements: build: - {{ compiler('c') }} @@ -20,12 +19,13 @@ requirements: run: - zlib -source: - url: https://sourceforge.net/projects/soapdenovo2/files/Prepare/Prepare-src-v2.0.tgz - sha256: 97bfccede6bd138365d466f2d71685abaccd366ea69ae0a9d90598e4547f291f - patches: - - Makefile.osx.patch # [osx] - test: commands: - finalFusion + +about: + home: https://github.com/aquaskyline/SOAPdenovo2 + license: GPL-3.0 + license_family: GPL + license_file: '{{ RECIPE_DIR }}/LICENSE' + summary: SoapDenovo2 data prepare module using assembled contig to do scaffold assembly. diff --git a/recipes/soapec/meta.yaml b/recipes/soapec/meta.yaml index 1cbd6985100b5..4b22b2cf6e8c2 100644 --- a/recipes/soapec/meta.yaml +++ b/recipes/soapec/meta.yaml @@ -1,16 +1,15 @@ -about: - home: http://soap.genomics.org.cn/soapdenovo.html - license: 'GNU' - summary: 'a correction tool for SOAPdenovo' +package: + name: soapec + version: '2.03' + +source: + url: https://sourceforge.net/projects/soapdenovo2/files/ErrorCorrection/SOAPec_src_v2.03.tgz + sha256: d95faa1ebffc785bca134a72d88b336dd1a4797c526f5d66095db3d4c3ec3d24 build: number: 3 skip: True # [osx] -package: - name: soapec - version: '2.03' - requirements: build: - {{ compiler('cxx') }} @@ -18,10 +17,12 @@ requirements: - zlib run: - zlib -source: - url: https://sourceforge.net/projects/soapdenovo2/files/ErrorCorrection/SOAPec_src_v2.03.tgz - sha256: d95faa1ebffc785bca134a72d88b336dd1a4797c526f5d66095db3d4c3ec3d24 test: commands: - Corrector_AR -h + +about: + home: http://soap.genomics.org.cn/soapdenovo.html + license: 'GNU' + summary: 'a correction tool for SOAPdenovo' diff --git a/recipes/socru/meta.yaml b/recipes/socru/meta.yaml index 00d5d3455f4b5..78f1e1d55a886 100644 --- a/recipes/socru/meta.yaml +++ b/recipes/socru/meta.yaml @@ -1,16 +1,6 @@ {% set version="1.0.1" %} {% set revision="bd5816d7c0406805fc14a0de56b54df15f4114d8" %} -about: - home: https://github.com/quadram-institute-bioscience/socru - license: 'GPLv3' - summary: 'Order and orientation of complete bacterial genomes' - -build: - number: 0 - skip: True # [py27] - script: python -m pip install --no-deps --ignore-installed . - package: name: socru version: {{ version }} @@ -20,6 +10,11 @@ source: git_rev: {{ revision }} md5: unused +build: + number: 0 + skip: True # [py27] + script: python -m pip install --no-deps --ignore-installed . + requirements: host: - python @@ -41,6 +36,11 @@ test: commands: - socru --version +about: + home: https://github.com/quadram-institute-bioscience/socru + license: 'GPLv3' + summary: 'Order and orientation of complete bacterial genomes' + extra: skip-lints: - uses_git_url diff --git a/recipes/sqt/meta.yaml b/recipes/sqt/meta.yaml index 7c04c2a27fd2b..0cd02f50f46fb 100644 --- a/recipes/sqt/meta.yaml +++ b/recipes/sqt/meta.yaml @@ -1,8 +1,3 @@ -about: - home: https://bitbucket.org/marcelm/sqt - license: MIT - summary: 'Command-line tools for the analysis of high-throughput sequencing data' - package: name: sqt version: "0.8.0" @@ -11,6 +6,11 @@ source: url: https://pypi.python.org/packages/09/85/ec30aba5d8bcc54fadcb65ab3387a5ba7921e1d22c2f71a498187ba096d7/sqt-0.8.0.tar.gz md5: 5a6400b6cb5a331589f831ba0b6020f0 +build: + skip: True # [py27] + script: python -m pip install --no-deps --ignore-installed . + number: 2 + requirements: build: - {{ compiler('c') }} @@ -36,7 +36,7 @@ test: commands: - sqt --version -build: - skip: True # [py27] - script: python -m pip install --no-deps --ignore-installed . - number: 2 +about: + home: https://bitbucket.org/marcelm/sqt + license: MIT + summary: 'Command-line tools for the analysis of high-throughput sequencing data' diff --git a/recipes/ssake/meta.yaml b/recipes/ssake/meta.yaml index 9d5db7809603c..9ed4cae8e7e2d 100644 --- a/recipes/ssake/meta.yaml +++ b/recipes/ssake/meta.yaml @@ -2,17 +2,6 @@ {% set version = "4.0" %} {% set sha256 = "873361ee4121e5667a2db5329ed739410e63eb1db39a76f13f6951b85b5a9a23" %} -about: - home: https://github.com/warrenlr/SSAKE - license: GPL-2.0 - license_family: GPL - license_file: LICENSE - summary: SSAKE is a genomics application for de novo assembly of millions of very short DNA sequences. - -build: - number: 2 - skip: True # [py3k] - package: name: {{ name|lower }} version: {{ version }} @@ -23,6 +12,10 @@ source: patches: - pl_py_paths.patch +build: + number: 2 + skip: True # [py3k] + requirements: host: - python @@ -50,6 +43,13 @@ test: - TQSfastq.py -h - TQS.py -h +about: + home: https://github.com/warrenlr/SSAKE + license: GPL-2.0 + license_family: GPL + license_file: LICENSE + summary: SSAKE is a genomics application for de novo assembly of millions of very short DNA sequences. + extra: identifiers: - biotools:ssake diff --git a/recipes/subread/meta.yaml b/recipes/subread/meta.yaml index 8aa21b6fd3213..564b0c3999847 100644 --- a/recipes/subread/meta.yaml +++ b/recipes/subread/meta.yaml @@ -1,18 +1,14 @@ -about: - home: http://subread.sourceforge.net/ - license: GPLv3 - summary: High-performance read alignment, quantification, and mutation discovery package: name: subread version: 1.6.4 -build: - number: 1 - source: url: https://downloads.sourceforge.net/project/subread/subread-1.6.4/subread-1.6.4-source.tar.gz sha256: b7bd0ee3b0942d791aecce6454d2f3271c95a010beeeff2daf1ff71162e43969 +build: + number: 1 + requirements: build: - {{ compiler('c') }} @@ -20,6 +16,7 @@ requirements: - zlib run: - zlib + test: commands: - featureCounts -v @@ -33,6 +30,11 @@ test: - qualityScores - subread-fullscan || [[ $? == 255 ]] +about: + home: http://subread.sourceforge.net/ + license: GPLv3 + summary: High-performance read alignment, quantification, and mutation discovery + extra: identifiers: - biotools:subread diff --git a/recipes/tantan/meta.yaml b/recipes/tantan/meta.yaml index a6d037bf1e343..4917bcf52ebc0 100644 --- a/recipes/tantan/meta.yaml +++ b/recipes/tantan/meta.yaml @@ -1,8 +1,3 @@ -about: - home: 'http://cbrc3.cbrc.jp/~martin/tantan/' - license: GPLv3 - summary: "tantan is a tool for masking simple regions (low complexity and short-period tandem repeats) in biological sequences." - package: name: tantan version: '13' @@ -13,7 +8,6 @@ source: build: number: 1 - skip: False requirements: build: @@ -24,3 +18,8 @@ requirements: test: commands: - "tantan -h" + +about: + home: 'http://cbrc3.cbrc.jp/~martin/tantan/' + license: GPLv3 + summary: "tantan is a tool for masking simple regions (low complexity and short-period tandem repeats) in biological sequences." diff --git a/recipes/tepid/meta.yaml b/recipes/tepid/meta.yaml index a59bd8196a8b6..59b24e0d7bf5a 100644 --- a/recipes/tepid/meta.yaml +++ b/recipes/tepid/meta.yaml @@ -1,16 +1,15 @@ -about: - home: 'https://github.com/ListerLab/TEPID' - license: 'GPL' - summary: 'TEPID uses paired-end illumina sequencing reads to identify novel TE variants.' +package: + name: tepid + version: '0.8' + +source: + url: 'https://github.com/ListerLab/TEPID/archive/0.8.tar.gz' + sha256: 2f9ff777705f74abe54f916bd33783085696a4687c47efe61146dd9827c4e241 build: number: 1 skip: True # [not py27 or not linux] -package: - name: tepid - version: '0.8' - # numpy 1.9.2 was built against libgfortran 1.9.2 requirements: build: @@ -40,16 +39,17 @@ requirements: - bedtools ==2.25.0 - yaha -source: - url: 'https://github.com/ListerLab/TEPID/archive/0.8.tar.gz' - sha256: 2f9ff777705f74abe54f916bd33783085696a4687c47efe61146dd9827c4e241 - test: commands: - tepid-map | grep data - tepid-discover --version - tepid-refine --version +about: + home: 'https://github.com/ListerLab/TEPID' + license: 'GPL' + summary: 'TEPID uses paired-end illumina sequencing reads to identify novel TE variants.' + extra: skip-lints: - should_use_compilers diff --git a/recipes/tophat-recondition/meta.yaml b/recipes/tophat-recondition/meta.yaml index 3dff441dbc214..3d59c15a29b9a 100644 --- a/recipes/tophat-recondition/meta.yaml +++ b/recipes/tophat-recondition/meta.yaml @@ -1,14 +1,13 @@ -about: - home: https://github.com/cbrueffer/tophat-recondition - license: BSD_2_clause - summary: Post-processor for TopHat unmapped reads +package: + name: tophat-recondition + version: 1.4 build: number: 1 -package: - name: tophat-recondition - version: 1.4 +source: + url: https://github.com/cbrueffer/tophat-recondition/archive/v1.4.tar.gz + md5: 4062d5fa0a6f22eb7abed759d278bb34 requirements: host: @@ -21,6 +20,7 @@ test: commands: - (tophat-recondition -v 2>&1) > /dev/null -source: - url: https://github.com/cbrueffer/tophat-recondition/archive/v1.4.tar.gz - md5: 4062d5fa0a6f22eb7abed759d278bb34 +about: + home: https://github.com/cbrueffer/tophat-recondition + license: BSD_2_clause + summary: Post-processor for TopHat unmapped reads diff --git a/recipes/tracer/meta.yaml b/recipes/tracer/meta.yaml index 76566150f25a4..7d5e340a80b3b 100644 --- a/recipes/tracer/meta.yaml +++ b/recipes/tracer/meta.yaml @@ -1,26 +1,19 @@ {% set name = "tracer" %} {% set version = "1.7.1" %} {% set build = 1 %} - -about: - home: http://beast.community/{{ name }} - license: "LGPLv2.1" - summary: "Tracer is a program for analysing the trace files generated by Bayesian MCMC runs - (that is, the continuous parameter values sampled from the chain). It can be used - to analyse runs of BEAST, MrBayes, LAMARC and possibly other MCMC programs." package: name: {{ name|lower }} version: {{ version }} -build: - number: {{ build }} - noarch: generic - source: url: https://github.com/beast-dev/tracer/releases/download/v1.7.1/Tracer_v1.7.1.tgz sha256: 200d7ffa1e48994b71245994e299847ac2be72d3d5c37d9048418557e1d8c12e +build: + number: {{ build }} + noarch: generic + requirements: run: - openjdk @@ -29,6 +22,13 @@ test: commands: - jar -tf $PREFIX/lib/tracer.jar &> /dev/null +about: + home: http://beast.community/{{ name }} + license: "LGPLv2.1" + summary: "Tracer is a program for analysing the trace files generated by Bayesian MCMC runs + (that is, the continuous parameter values sampled from the chain). It can be used + to analyse runs of BEAST, MrBayes, LAMARC and possibly other MCMC programs." + extra: identifiers: - biotools:tracer diff --git a/recipes/transabyss/meta.yaml b/recipes/transabyss/meta.yaml index d90c70a8f66bb..3a9f02d305970 100644 --- a/recipes/transabyss/meta.yaml +++ b/recipes/transabyss/meta.yaml @@ -1,16 +1,19 @@ -about: - home: http://www.bcgsc.ca/platform/bioinfo/software/trans-abyss - license: 'GPL' - summary: 'de novo assembly of RNA-Seq data using ABySS' +package: + name: transabyss + version: '2.0.1' + +source: + url: https://github.com/bcgsc/transabyss/releases/download/2.0.1/transabyss-2.0.1.zip + sha256: 542779af2d1232ca872a57b922cfd32e1c6e9e7e0b5fae56ef2e7682dfdf6040 + patches: + - transabyss.patch + - transabyss-merge.patch + - package_info.patch build: skip: True # [py3k] number: 4 -package: - name: transabyss - version: '2.0.1' - requirements: host: - python @@ -22,15 +25,12 @@ requirements: - blat - python -source: - url: https://github.com/bcgsc/transabyss/releases/download/2.0.1/transabyss-2.0.1.zip - sha256: 542779af2d1232ca872a57b922cfd32e1c6e9e7e0b5fae56ef2e7682dfdf6040 - patches: - - transabyss.patch - - transabyss-merge.patch - - package_info.patch - test: commands: - transabyss --help - transabyss-merge --help + +about: + home: http://www.bcgsc.ca/platform/bioinfo/software/trans-abyss + license: 'GPL' + summary: 'de novo assembly of RNA-Seq data using ABySS' diff --git a/recipes/vcfsamplecompare/meta.yaml b/recipes/vcfsamplecompare/meta.yaml index c10bd96baa655..f0f0970d0919e 100644 --- a/recipes/vcfsamplecompare/meta.yaml +++ b/recipes/vcfsamplecompare/meta.yaml @@ -1,6 +1,29 @@ {% set name = "vcfsamplecompare" %} {% set realname = "vcfSampleCompare" %} {% set version = "v2.008" %} +package: + name: {{ name }} + version: {{ version }} + +source: + url: https://github.com/hepcat72/{{ realname }}/archive/{{ version }}.tar.gz + sha256: 6360ccae123099bdbbe7cc60d28aad7c62663bc127af16508e397c7acd07d775 + +build: + number: 0 + +requirements: + build: + - make + host: + - perl + run: + - perl + +test: + commands: + - {{ realname }}.pl --version + about: home: https://github.com/hepcat72/{{ realname }} license: GNU @@ -18,27 +41,6 @@ about: greatest difference is greedily discovered and chosen to represent the variant/row. -build: - number: 0 -package: - name: {{ name }} - version: {{ version }} -requirements: - build: - - make - host: - - perl - run: - - perl - -source: - url: https://github.com/hepcat72/{{ realname }}/archive/{{ version }}.tar.gz - sha256: 6360ccae123099bdbbe7cc60d28aad7c62663bc127af16508e397c7acd07d775 - -test: - commands: - - {{ realname }}.pl --version - extra: identifiers: - doi:10.5281/zenodo.1463080 diff --git a/recipes/watchdog-wms/meta.yaml b/recipes/watchdog-wms/meta.yaml index 274fe549415e6..7b3c3acb47bfb 100644 --- a/recipes/watchdog-wms/meta.yaml +++ b/recipes/watchdog-wms/meta.yaml @@ -1,34 +1,17 @@ {% set name = "watchdog-wms" %} {% set version = "1.2.7" %} -about: - home: https://www.bio.ifi.lmu.de/watchdog - license: GNU General Public License, Version 3 - summary: - Watchdog, a WMS for the automated and distributed analysis of large-scale experimental data. - The software is implemented in Java and is thus platform-independent. - Main feature include - straightforward processing of replicate data - support for distributed computer systems - remote storage support - customizable error detection - manual intervention into workflow execution - GUI for workflow construction using pre-defined modules - a helper script for creating new module definitions - no restriction to specific programming languages - provides a flexible plugin system for extending without modifying the original sources - package: name: {{ name }} version: {{ version }} -build: - number: 1 - source: url: https://github.com/klugem/watchdog/archive/v{{ version }}.tar.gz sha256: b38d7f8696a769487d31c83940e04804c0cbe0234cdc4e28fb6584e87dd5a7b8 +build: + number: 1 + requirements: build: - openjdk >=8 @@ -43,6 +26,23 @@ test: commands: - watchdog-cmd --help +about: + home: https://www.bio.ifi.lmu.de/watchdog + license: GNU General Public License, Version 3 + summary: + Watchdog, a WMS for the automated and distributed analysis of large-scale experimental data. + The software is implemented in Java and is thus platform-independent. + Main feature include + straightforward processing of replicate data + support for distributed computer systems + remote storage support + customizable error detection + manual intervention into workflow execution + GUI for workflow construction using pre-defined modules + a helper script for creating new module definitions + no restriction to specific programming languages + provides a flexible plugin system for extending without modifying the original sources + extra: maintainers: - Michael Kluge diff --git a/recipes/wdltool/meta.yaml b/recipes/wdltool/meta.yaml index ee15914feb65e..56270bf9725d7 100644 --- a/recipes/wdltool/meta.yaml +++ b/recipes/wdltool/meta.yaml @@ -1,17 +1,16 @@ {% set version="0.14" %} -about: - home: https://github.com/broadinstitute/wdltool - license: "BSD" - summary: "Command line utilities for interacting with WDL" package: name: wdltool version: {{ version }} -build: - noarch: python - number: 1 + source: url: https://github.com/broadinstitute/wdltool/archive/{{ version }}.tar.gz md5: 072f73c47cf7611a39f979a02c9910dc + +build: + noarch: python + number: 1 + requirements: host: - openjdk >=8 @@ -24,3 +23,8 @@ requirements: test: commands: - wdltool --help 2>&1 | grep "Performs full validation" + +about: + home: https://github.com/broadinstitute/wdltool + license: "BSD" + summary: "Command line utilities for interacting with WDL" diff --git a/recipes/womtool/meta.yaml b/recipes/womtool/meta.yaml index 83d0ce0f2eebf..b1a2d4d066143 100644 --- a/recipes/womtool/meta.yaml +++ b/recipes/womtool/meta.yaml @@ -1,25 +1,18 @@ {% set name="womtool" %} {% set version="40" %} -about: - home: https://cromwell.readthedocs.io/en/develop/WOMtool/ - license: BSD-3-Clause - license_family: BSD - license_file: LICENSE.txt - summary: "Command line utilities for interacting with WDL" - package: name: {{ name|lower }} version: {{ version }} -build: - noarch: python - number: 0 - source: url: https://github.com/broadinstitute/cromwell/archive/{{ version }}.tar.gz sha256: 16e5de6a98915132ff93193dad6df3c113f2d2625dd977fab294f1322e0b039b +build: + noarch: python + number: 0 + requirements: host: - openjdk=8 @@ -33,6 +26,13 @@ test: commands: - womtool --help +about: + home: https://cromwell.readthedocs.io/en/develop/WOMtool/ + license: BSD-3-Clause + license_family: BSD + license_file: LICENSE.txt + summary: "Command line utilities for interacting with WDL" + extra: identifiers: - biotools:womtool diff --git a/recipes/xtandem/meta.yaml b/recipes/xtandem/meta.yaml index 46888536f7f0d..50ccf34221757 100644 --- a/recipes/xtandem/meta.yaml +++ b/recipes/xtandem/meta.yaml @@ -1,22 +1,15 @@ -about: - home: http://www.thegpm.org/TANDEM/index.html - license: Artistic License - summary: X! Tandem open source is software that can match tandem mass spectra with peptide sequences, in a process that has come to be known as protein identification - package: name: xtandem version: 15.12.15.2 -build: - number: 2 - skip: False - source: url: https://depot.galaxyproject.org/software/xtandem/xtandem_15.12.15.2_src_all.zip md5: 40058cd84fc3f56d671d32ff393f7aa3 patches: - patch -# - makefile.patch + +build: + number: 2 requirements: build: @@ -32,6 +25,11 @@ test: commands: - xtandem help 2>&1 | grep 'TANDEM' +about: + home: http://www.thegpm.org/TANDEM/index.html + license: Artistic License + summary: X! Tandem open source is software that can match tandem mass spectra with peptide sequences, in a process that has come to be known as protein identification + extra: identifiers: - biotools:xtandem diff --git a/recipes/yaha/meta.yaml b/recipes/yaha/meta.yaml index 4121a39e84d0f..e1ba3b46f665e 100644 --- a/recipes/yaha/meta.yaml +++ b/recipes/yaha/meta.yaml @@ -1,25 +1,25 @@ -about: - home: 'https://github.com/GregoryFaust/yaha' - license: 'GPL' - summary: 'yaha is an open source, flexible, sensitive and accurate DNA aligner designed for single-end reads' +package: + name: yaha + version: '0.1.83' + +source: + url: 'https://github.com/GregoryFaust/yaha/releases/download/v0.1.83/yaha-0.1.83.tar.gz' + sha256: 76e052cd92630c6e9871412e37e46f18bfbbf7fc5dd2f345b3b9a73eb74939ef build: number: 1 skip: true #[not linux] -package: - name: yaha - version: '0.1.83' - requirements: build: - {{ compiler('c') }} - {{ compiler('cxx') }} -source: - url: 'https://github.com/GregoryFaust/yaha/releases/download/v0.1.83/yaha-0.1.83.tar.gz' - sha256: 76e052cd92630c6e9871412e37e46f18bfbbf7fc5dd2f345b3b9a73eb74939ef - test: commands: - yaha 2>&1 | grep version > /dev/null + +about: + home: 'https://github.com/GregoryFaust/yaha' + license: 'GPL' + summary: 'yaha is an open source, flexible, sensitive and accurate DNA aligner designed for single-end reads'