Package: bioconda2biocontainer
bioconda2biocontainerbioconda2biocontainerincludes a series of python scripts and API to query
the Biocontainer registry.Scriptsbioconda2biocontainerThis script search the Biocontainer registry and return the image name
for a Bioconda package. The images can be sorted by date, size or number of downloads.Optioncontainer_typecan be: Docker, Singularity or CondaList all available images for bedtools version 2.27.0>bioconda2biocontainer--package_namebedtools--package_version2.27.0--all
imageupdatedsizedownloadscontainer_type
https://depot.galaxyproject.org/singularity/bedtools:2.27.0--he513fc3_42019-10-27T05:29:00Z171786240Singularity
quay.io/biocontainers/bedtools:2.27.0--he513fc3_42019-10-26T00:00:00Z173328060Docker
https://depot.galaxyproject.org/singularity/bedtools:2.27.0--02019-08-27T18:20:00Z138854400Singularity
https://depot.galaxyproject.org/singularity/bedtools:2.27.0--12019-08-01T21:40:00Z138895360Singularity
https://depot.galaxyproject.org/singularity/bedtools:2.27.0--he860b03_32019-08-01T21:40:00Z133898240Singularity
https://depot.galaxyproject.org/singularity/bedtools:2.27.0--he941832_22019-08-01T21:40:00Z135495680Singularity
quay.io/biocontainers/bedtools:2.27.0--he860b03_32019-02-03T00:00:00Z134826600Docker
quay.io/biocontainers/bedtools:2.27.0--he941832_22018-06-25T00:00:00Z136522620Dockerbedtools==2.27.0--he860b03_32018-06-24T00:00:00Z112940735562Condabedtools==2.27.0--02018-06-24T00:00:00Z112940735562Condabedtools==2.27.0--12018-06-24T00:00:00Z112940735562Condabedtools==2.27.0--he941832_22018-06-24T00:00:00Z112940735562Condabedtools==2.27.0--he513fc3_42018-06-24T00:00:00Z112940735562Conda
quay.io/biocontainers/bedtools:2.27.0--12018-02-14T00:00:00Z140944670Docker
quay.io/biocontainers/bedtools:2.27.0--02017-12-07T00:00:00Z140872050DockerGet latest docker image for bedtools version 2.27.0>bioconda2biocontainer--package_namebedtools--package_version2.27.0--container_typeDocker
quay.io/biocontainers/bedtools:2.27.0--he513fc3_4Get smaller singularity image for bedtools version 2.27.0>bioconda2biocontainer--package_namebedtools--package_version2.27.0--container_typeSingularity--sort_by_size
https://depot.galaxyproject.org/singularity/bedtools:2.27.0--he860b03_3Get the conda package with more downloads for bedtools version 2.27.0>bioconda2biocontainer--package_namebedtools--package_version2.27.0--container_typeConda--sort_by_downloadbedtools==2.27.0--he860b03_3List all available versions for bedtools>bioconda2biocontainer--package_namebedtools
idversionurl
bedtools-v2.28.0v2.28.0http://api.biocontainers.pro/ga4gh/trs/v2/tools/bedtools/versions/bedtools-v2.28.0
bedtools-v2.27.1dfsg-4-debv2.27.1dfsg-4-debhttp://api.biocontainers.pro/ga4gh/trs/v2/tools/bedtools/versions/bedtools-v2.27.1dfsg-4-deb
bedtools-v2.27.0v2.27.0http://api.biocontainers.pro/ga4gh/trs/v2/tools/bedtools/versions/bedtools-v2.27.0
bedtools-v2.26.0dfsg-3-debv2.26.0dfsg-3-debhttp://api.biocontainers.pro/ga4gh/trs/v2/tools/bedtools/versions/bedtools-v2.26.0dfsg-3-deb
bedtools-v2.25.0v2.25.0http://api.biocontainers.pro/ga4gh/trs/v2/tools/bedtools/versions/bedtools-v2.25.0
bedtools-2.29.22.29.2http://api.biocontainers.pro/ga4gh/trs/v2/tools/bedtools/versions/bedtools-2.29.2
bedtools-2.29.12.29.1http://api.biocontainers.pro/ga4gh/trs/v2/tools/bedtools/versions/bedtools-2.29.1
bedtools-2.29.02.29.0http://api.biocontainers.pro/ga4gh/trs/v2/tools/bedtools/versions/bedtools-2.29.0
bedtools-2.28.02.28.0http://api.biocontainers.pro/ga4gh/trs/v2/tools/bedtools/versions/bedtools-2.28.0
bedtools-2.27.12.27.1http://api.biocontainers.pro/ga4gh/trs/v2/tools/bedtools/versions/bedtools-2.27.1
bedtools-2.27.02.27.0http://api.biocontainers.pro/ga4gh/trs/v2/tools/bedtools/versions/bedtools-2.27.0
bedtools-2.26.0gx2.26.0gxhttp://api.biocontainers.pro/ga4gh/trs/v2/tools/bedtools/versions/bedtools-2.26.0gx
bedtools-2.25.02.25.0http://api.biocontainers.pro/ga4gh/trs/v2/tools/bedtools/versions/bedtools-2.25.0
bedtools-2.23.02.23.0http://api.biocontainers.pro/ga4gh/trs/v2/tools/bedtools/versions/bedtools-2.23.0
bedtools-2.222.22http://api.biocontainers.pro/ga4gh/trs/v2/tools/bedtools/versions/bedtools-2.22
bedtools-2.20.12.20.1http://api.biocontainers.pro/ga4gh/trs/v2/tools/bedtools/versions/bedtools-2.20.1
bedtools-2.19.12.19.1http://api.biocontainers.pro/ga4gh/trs/v2/tools/bedtools/versions/bedtools-2.19.1
bedtools-2.17.02.17.0http://api.biocontainers.pro/ga4gh/trs/v2/tools/bedtools/versions/bedtools-2.17.0biocontainers-searchSearch tools in Biocontainers registry and return a TAB separated table with Name, Versions (comma separated),
Description, License and number of pulls.Search proteomics tools>biocontainers-search--search_termproteomics
nameversionsdescriptionlicensepulls
augustusv3.3.2dfsg-2-deb,v3.2.3dfsg-1-deb,3.3.3,3.3.2,3.3,3.2.3,3.2.2,3.1Augustusisaeukaryoticgenepredictiontool.itcanintegrateevidence,e.g.fromrna-seq,ests,proteomics,butcanalsopredictgenesabinitio.theppxextensiontoaugustuscantakeaproteinsequencemultiplesequencealignmentasinputtofindnewmembersofthefamilyinagenome.itcanberunthroughawebinterface(seehttps://bio.tools/webaugustus),ordownloadedandrunlocally.Artistic-1.0448371bioconductor-assessorf1.6.0,1.4.0,1.2.0,1.0.2AssessGenePredictionsUsingProteomicsandEvolutionaryConservationGPL-3915bioconductor-customprodb1.28.0,1.26.0,1.24.0,1.22.0,1.14.0Generatecustomizedproteindatabasefromngsdata,withafocusonrna-seqdata,forproteomicssearchNotavailable10520Search proteomics tools and return JSON data>biocontainers-search--search_termproteomics--json[{"contains":[],"description":"Augustus is a eukaryotic gene prediction tool. it can integrate evidence, e.g. from rna-seq, ests, proteomics, but can also predict genes ab initio. the ppx extension to augustus can take a protein sequence multiple sequence alignment as input to find new members of the family in a genome. it can be run through a web interface (see https://bio.tools/webaugustus), or downloaded and run locally.","id":"augustus","identifiers":["biotools:augustus","PMID:15215400"],"license":"Artistic-1.0","name":"augustus","organization":"biocontainers","pulls":448371,"tool_tags":["biology","bioinformatics","c++","commandline","program","calculation","utility","ncurses","analysing","biological-sequence"],"tool_url":"https://github.com/Gaius-Augustus/Augustus","toolclass":{"description":"CommandLineTool","id":"0","name":"CommandLineTool"},"url":"http://api.biocontainers.pro/ga4gh/trs/v2/tools/augustus","versions":[{"id":"augustus-3.2.3","meta_version":"3.2.3","name":"augustus","url":"http://api.biocontainers.pro/ga4gh/trs/v2/tools/augustus/versions/augustus-3.2.3"},{"id":"augustus-3.2.2","meta_version":"3.2.2","name":"augustus","url":"http://api.biocontainers.pro/ga4gh/trs/v2/tools/augustus/versions/augustus-3.2.2"},...bioconda2cwldockerThis script reads a conda env yaml file and replace, for each package in the environment, the images defined
in the CWL or Yaml files inside the directory passed in the optioncwl_pathExampleWe would like to use the CWLs defined in the repohttps://github.com/ncbi/cwl-ngs-workflows-cbbwith the versions
defined in this conda env:Conda env filename:rnaseqchannels:-conda-forge-bioconda-defaultsdependencies:-bedtools=2.29.2-fastqc=0.11.9-sra-tools=2.10.8-star=2.7.5aCloning the repo$gitclonehttps://github.com/ncbi/cwl-ngs-workflows-cbb
Cloninginto'cwl-ngs-workflows-cbb'...
remote:Enumeratingobjects:94,done.
remote:Countingobjects:100%(94/94),done.
remote:Compressingobjects:100%(69/69),done.
remote:Total1924(delta47),reused50(delta25),pack-reused1830Receivingobjects:100%(1924/1924),319.82KiB|3.48MiB/s,done.
Resolvingdeltas:100%(1216/1216),done.Print defined images for the tools in the CWLs$catcwl-ngs-workflows-cbb/tools/bedtools/bedtools.ymlclass:DockerRequirementdockerPull:quay.io/biocontainers/bedtools:2.28.0--hdf88d34_0

$catcwl-ngs-workflows-cbb/tools/fastqc/fastqc.ymlclass:DockerRequirementdockerPull:quay.io/biocontainers/fastqc:0.11.8--1

$catcwl-ngs-workflows-cbb/tools/sra-toolkit/sra-toolkit.ymlclass:DockerRequirementdockerPull:quay.io/biocontainers/sra-tools:2.10.7--pl526haddd2b5_1

$catcwl-ngs-workflows-cbb/tools/star/star.ymlclass:DockerRequirementdockerPull:quay.io/biocontainers/star:2.7.5a--0Running bioconda2cwldocker$bioconda2cwldocker--conda_env_fileconda-env.yaml--cwl_pathcwl-ngs-workflows-cbb/
bedtoolswithversion2.29.2updateimageto:quay.io/biocontainers/bedtools:2.29.2--hc088bd4_0cwl-ngs-workflows-cbb/tools/bedtools/bedtools.ymlwitholdimagereplaced:quay.io/biocontainers/bedtools:2.28.0--hdf88d34_0
fastqcwithversion0.11.9updateimageto:quay.io/biocontainers/fastqc:0.11.9--0cwl-ngs-workflows-cbb/tools/fastqc/fastqc.ymlwitholdimagereplaced:quay.io/biocontainers/fastqc:0.11.8--1
sra-toolswithversion2.10.8updateimageto:quay.io/biocontainers/sra-tools:2.10.8--pl526haddd2b5_0cwl-ngs-workflows-cbb/tools/sra-toolkit/sra-toolkit.ymlwitholdimagereplaced:quay.io/biocontainers/sra-tools:2.10.7--pl526haddd2b5_1Print new defined images for the tools in the CWLs$catcwl-ngs-workflows-cbb/tools/bedtools/bedtools.ymlclass:DockerRequirementdockerPull:quay.io/biocontainers/bedtools:2.29.2--hc088bd4_0

$catcwl-ngs-workflows-cbb/tools/fastqc/fastqc.ymlclass:DockerRequirementdockerPull:quay.io/biocontainers/fastqc:0.11.9--0

$catcwl-ngs-workflows-cbb/tools/sra-toolkit/sra-toolkit.ymlclass:DockerRequirementdockerPull:quay.io/biocontainers/sra-tools:2.10.8--pl526haddd2b5_0

$catcwl-ngs-workflows-cbb/tools/star/star.ymlclass:DockerRequirementdockerPull:quay.io/biocontainers/star:2.7.5a--0Note that the STAR image name was not changed as the CWL was using the same versionInstallpipinstallbioconda2biocontainerFor development:gitclonehttps://github.com/BioContainers/bioconda2biocontainercdbioconda2biocontainer
pipinstall-rrequirements/test.txt-e.TestTest configuration is defined in thetox.inifile and includespy.testtests
andflake8source code checker.You can run all of the tests:python setup.py testTo run just thepy.testtests, notflake8, and to re-use the currentvirtualenv:py.testAPIDemo>>>importjson>>>frombioconda2biocontainer.biocontainerimportfind_package_by_name>>>tool=find_package_by_name('bedtools')>>>print(json.dumps(tool,indent=4)){"contains":[],"description":"Bedtools is an extensive suite of utilities for comparing genomic features in bed format.","id":"bedtools","identifiers":["biotools:bedtools","PMID:20110278"],"license":"GPL-2.0","name":"bedtools","organization":"biocontainers","pulls":6111180,"tool_tags":["genomics"],"tool_url":"https://github.com/arq5x/bedtools2","toolclass":{"description":"CommandLineTool","id":"0","name":"CommandLineTool"},"url":"http://api.biocontainers.pro/ga4gh/trs/v2/tools/bedtools","versions":[{"id":"bedtools-v2.28.0","meta_version":"v2.28.0","name":"bedtools","url":"http://api.biocontainers.pro/ga4gh/trs/v2/tools/bedtools/versions/bedtools-v2.28.0"},{"id":"bedtools-v2.27.1dfsg-4-deb","meta_version":"v2.27.1dfsg-4-deb","name":"bedtools","url":"http://api.biocontainers.pro/ga4gh/trs/v2/tools/bedtools/versions/bedtools-v2.27.1dfsg-4-deb"},{"id":"bedtools-v2.27.0","meta_version":"v2.27.0","name":"bedtools","url":"http://api.biocontainers.pro/ga4gh/trs/v2/tools/bedtools/versions/bedtools-v2.27.0"},{"id":"bedtools-v2.26.0dfsg-3-deb","meta_version":"v2.26.0dfsg-3-deb","name":"bedtools","url":"http://api.biocontainers.pro/ga4gh/trs/v2/tools/bedtools/versions/bedtools-v2.26.0dfsg-3-deb"},{"id":"bedtools-v2.25.0","meta_version":"v2.25.0","name":"bedtools","url":"http://api.biocontainers.pro/ga4gh/trs/v2/tools/bedtools/versions/bedtools-v2.25.0"},{"id":"bedtools-2.29.2","meta_version":"2.29.2","name":"bedtools","url":"http://api.biocontainers.pro/ga4gh/trs/v2/tools/bedtools/versions/bedtools-2.29.2"},{"id":"bedtools-2.29.1","meta_version":"2.29.1","name":"bedtools","url":"http://api.biocontainers.pro/ga4gh/trs/v2/tools/bedtools/versions/bedtools-2.29.1"},{"id":"bedtools-2.29.0","meta_version":"2.29.0","name":"bedtools","url":"http://api.biocontainers.pro/ga4gh/trs/v2/tools/bedtools/versions/bedtools-2.29.0"},{"id":"bedtools-2.28.0","meta_version":"2.28.0","name":"bedtools","url":"http://api.biocontainers.pro/ga4gh/trs/v2/tools/bedtools/versions/bedtools-2.28.0"},{"id":"bedtools-2.27.1","meta_version":"2.27.1","name":"bedtools","url":"http://api.biocontainers.pro/ga4gh/trs/v2/tools/bedtools/versions/bedtools-2.27.1"},{"id":"bedtools-2.27.0","meta_version":"2.27.0","name":"bedtools","url":"http://api.biocontainers.pro/ga4gh/trs/v2/tools/bedtools/versions/bedtools-2.27.0"},{"id":"bedtools-2.26.0gx","meta_version":"2.26.0gx","name":"bedtools","url":"http://api.biocontainers.pro/ga4gh/trs/v2/tools/bedtools/versions/bedtools-2.26.0gx"},{"id":"bedtools-2.25.0","meta_version":"2.25.0","name":"bedtools","url":"http://api.biocontainers.pro/ga4gh/trs/v2/tools/bedtools/versions/bedtools-2.25.0"},{"id":"bedtools-2.23.0","meta_version":"2.23.0","name":"bedtools","url":"http://api.biocontainers.pro/ga4gh/trs/v2/tools/bedtools/versions/bedtools-2.23.0"},{"id":"bedtools-2.22","meta_version":"2.22","name":"bedtools","url":"http://api.biocontainers.pro/ga4gh/trs/v2/tools/bedtools/versions/bedtools-2.22"},{"id":"bedtools-2.20.1","meta_version":"2.20.1","name":"bedtools","url":"http://api.biocontainers.pro/ga4gh/trs/v2/tools/bedtools/versions/bedtools-2.20.1"},{"id":"bedtools-2.19.1","meta_version":"2.19.1","name":"bedtools","url":"http://api.biocontainers.pro/ga4gh/trs/v2/tools/bedtools/versions/bedtools-2.19.1"},{"id":"bedtools-2.17.0","meta_version":"2.17.0","name":"bedtools","url":"http://api.biocontainers.pro/ga4gh/trs/v2/tools/bedtools/versions/bedtools-2.17.0"}]}>>>