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Update/recipes biocontainers marco august21 (#432)
* added a bunch of quay.io/biocontainers * updated quay.io/biocontainers/samtools with a few extra aliases * added quay.io/biocontainers/beast2 * updated version tags in some quay.io/biocontainers, to match quay.io strings
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docker: quay.io/biocontainers/bamtools
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url: https://quay.io/repository/biocontainers/bamtools
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maintainer: '@marcodelapierre'
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description: 'C++ API and command-line toolkit for working with BAM data.'
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latest:
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2.5.1--h9a82719_9: sha256:1df72d906a4db1f47d71516a8f026eecd614271f9c4c8e5e8ccde9210fcde227
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tags:
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2.5.1--h9a82719_9: sha256:1df72d906a4db1f47d71516a8f026eecd614271f9c4c8e5e8ccde9210fcde227
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aliases:
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bamtools: /usr/local/bin/bamtools
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docker: quay.io/biocontainers/bbmap
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url: https://quay.io/repository/biocontainers/bbmap
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maintainer: '@marcodelapierre'
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description: 'BBMap is a short read aligner, as well as various other bioinformatic tools.'
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latest:
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38.91--he522d1c_1: sha256:5679f2c146844662be023769146fa787ea101f3dd833ade36aaa0bb533c9939a
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tags:
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38.89--h1296035_0: sha256:acc26b0e54b1323c2db287fabb8bffecda94e766b6759dfdddc7472687b52f33
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38.90--he522d1c_3: sha256:e85733071f68bc84959aa97155f9d13b87fdfd17f41703fe861c057a56dec2b0
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38.91--he522d1c_1: sha256:5679f2c146844662be023769146fa787ea101f3dd833ade36aaa0bb533c9939a
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aliases:
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a_sample_mt.sh: /usr/local/bin/a_sample_mt.sh
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addadapters.sh: /usr/local/bin/addadapters.sh
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addssu.sh: /usr/local/bin/addssu.sh
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adjusthomopolymers.sh: /usr/local/bin/adjusthomopolymers.sh
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alltoall.sh: /usr/local/bin/alltoall.sh
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analyzeaccession.sh: /usr/local/bin/analyzeaccession.sh
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analyzegenes.sh: /usr/local/bin/analyzegenes.sh
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analyzesketchresults.sh: /usr/local/bin/analyzesketchresults.sh
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applyvariants.sh: /usr/local/bin/applyvariants.sh
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bbcms.sh: /usr/local/bin/bbcms.sh
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bbcountunique.sh: /usr/local/bin/bbcountunique.sh
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bbduk.sh: /usr/local/bin/bbduk.sh
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bbest.sh: /usr/local/bin/bbest.sh
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bbfakereads.sh: /usr/local/bin/bbfakereads.sh
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bbmap.sh: /usr/local/bin/bbmap.sh
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bbmapskimmer.sh: /usr/local/bin/bbmapskimmer.sh
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bbmask.sh: /usr/local/bin/bbmask.sh
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bbmerge-auto.sh: /usr/local/bin/bbmerge-auto.sh
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bbmerge.sh: /usr/local/bin/bbmerge.sh
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bbnorm.sh: /usr/local/bin/bbnorm.sh
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bbrealign.sh: /usr/local/bin/bbrealign.sh
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bbrename.sh: /usr/local/bin/bbrename.sh
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bbsketch.sh: /usr/local/bin/bbsketch.sh
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bbsplit.sh: /usr/local/bin/bbsplit.sh
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bbsplitpairs.sh: /usr/local/bin/bbsplitpairs.sh
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bbstats.sh: /usr/local/bin/bbstats.sh
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bbversion.sh: /usr/local/bin/bbversion.sh
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bbwrap.sh: /usr/local/bin/bbwrap.sh
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bloomfilter.sh: /usr/local/bin/bloomfilter.sh
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build_env_setup.sh: /usr/local/bin/build_env_setup.sh
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calcmem.sh: /usr/local/bin/calcmem.sh
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calctruequality.sh: /usr/local/bin/calctruequality.sh
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callgenes.sh: /usr/local/bin/callgenes.sh
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callpeaks.sh: /usr/local/bin/callpeaks.sh
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callvariants.sh: /usr/local/bin/callvariants.sh
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callvariants2.sh: /usr/local/bin/callvariants2.sh
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clumpify.sh: /usr/local/bin/clumpify.sh
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commonkmers.sh: /usr/local/bin/commonkmers.sh
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comparegff.sh: /usr/local/bin/comparegff.sh
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comparesketch.sh: /usr/local/bin/comparesketch.sh
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comparessu.sh: /usr/local/bin/comparessu.sh
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comparevcf.sh: /usr/local/bin/comparevcf.sh
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conda_build.sh: /usr/local/bin/conda_build.sh
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consect.sh: /usr/local/bin/consect.sh
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consensus.sh: /usr/local/bin/consensus.sh
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countbarcodes.sh: /usr/local/bin/countbarcodes.sh
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countgc.sh: /usr/local/bin/countgc.sh
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countsharedlines.sh: /usr/local/bin/countsharedlines.sh
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crossblock.sh: /usr/local/bin/crossblock.sh
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crosscontaminate.sh: /usr/local/bin/crosscontaminate.sh
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cutgff.sh: /usr/local/bin/cutgff.sh
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cutprimers.sh: /usr/local/bin/cutprimers.sh
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decontaminate.sh: /usr/local/bin/decontaminate.sh
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dedupe.sh: /usr/local/bin/dedupe.sh
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dedupe2.sh: /usr/local/bin/dedupe2.sh
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dedupebymapping.sh: /usr/local/bin/dedupebymapping.sh
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demuxbyname.sh: /usr/local/bin/demuxbyname.sh
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diskbench.sh: /usr/local/bin/diskbench.sh
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estherfilter.sh: /usr/local/bin/estherfilter.sh
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explodetree.sh: /usr/local/bin/explodetree.sh
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fetchproks.sh: /usr/local/bin/fetchproks.sh
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filterassemblysummary.sh: /usr/local/bin/filterassemblysummary.sh
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filterbarcodes.sh: /usr/local/bin/filterbarcodes.sh
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filterbycoverage.sh: /usr/local/bin/filterbycoverage.sh
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filterbyname.sh: /usr/local/bin/filterbyname.sh
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filterbysequence.sh: /usr/local/bin/filterbysequence.sh
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filterbytaxa.sh: /usr/local/bin/filterbytaxa.sh
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filterbytile.sh: /usr/local/bin/filterbytile.sh
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filterlines.sh: /usr/local/bin/filterlines.sh
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filterqc.sh: /usr/local/bin/filterqc.sh
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filtersam.sh: /usr/local/bin/filtersam.sh
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filtersilva.sh: /usr/local/bin/filtersilva.sh
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filtersubs.sh: /usr/local/bin/filtersubs.sh
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filtervcf.sh: /usr/local/bin/filtervcf.sh
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fixgaps.sh: /usr/local/bin/fixgaps.sh
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fungalrelease.sh: /usr/local/bin/fungalrelease.sh
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fuse.sh: /usr/local/bin/fuse.sh
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gbff2gff.sh: /usr/local/bin/gbff2gff.sh
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getreads.sh: /usr/local/bin/getreads.sh
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gi2ancestors.sh: /usr/local/bin/gi2ancestors.sh
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gi2taxid.sh: /usr/local/bin/gi2taxid.sh
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gitable.sh: /usr/local/bin/gitable.sh
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grademerge.sh: /usr/local/bin/grademerge.sh
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gradesam.sh: /usr/local/bin/gradesam.sh
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icecreamfinder.sh: /usr/local/bin/icecreamfinder.sh
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icecreamgrader.sh: /usr/local/bin/icecreamgrader.sh
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icecreammaker.sh: /usr/local/bin/icecreammaker.sh
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idmatrix.sh: /usr/local/bin/idmatrix.sh
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idtree.sh: /usr/local/bin/idtree.sh
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invertkey.sh: /usr/local/bin/invertkey.sh
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kapastats.sh: /usr/local/bin/kapastats.sh
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kcompress.sh: /usr/local/bin/kcompress.sh
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keepbestcopy.sh: /usr/local/bin/keepbestcopy.sh
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khist.sh: /usr/local/bin/khist.sh
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kmercountexact.sh: /usr/local/bin/kmercountexact.sh
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kmercountmulti.sh: /usr/local/bin/kmercountmulti.sh
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kmercoverage.sh: /usr/local/bin/kmercoverage.sh
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kmerfilterset.sh: /usr/local/bin/kmerfilterset.sh
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kmerlimit.sh: /usr/local/bin/kmerlimit.sh
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kmerlimit2.sh: /usr/local/bin/kmerlimit2.sh
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kmerposition.sh: /usr/local/bin/kmerposition.sh
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kmutate.sh: /usr/local/bin/kmutate.sh
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lilypad.sh: /usr/local/bin/lilypad.sh
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loadreads.sh: /usr/local/bin/loadreads.sh
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loglog.sh: /usr/local/bin/loglog.sh
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makechimeras.sh: /usr/local/bin/makechimeras.sh
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makecontaminatedgenomes.sh: /usr/local/bin/makecontaminatedgenomes.sh
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makepolymers.sh: /usr/local/bin/makepolymers.sh
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mapPacBio.sh: /usr/local/bin/mapPacBio.sh
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matrixtocolumns.sh: /usr/local/bin/matrixtocolumns.sh
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mergeOTUs.sh: /usr/local/bin/mergeOTUs.sh
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mergebarcodes.sh: /usr/local/bin/mergebarcodes.sh
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mergepgm.sh: /usr/local/bin/mergepgm.sh
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mergeribo.sh: /usr/local/bin/mergeribo.sh
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mergesam.sh: /usr/local/bin/mergesam.sh
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mergesketch.sh: /usr/local/bin/mergesketch.sh
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mergesorted.sh: /usr/local/bin/mergesorted.sh
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msa.sh: /usr/local/bin/msa.sh
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mutate.sh: /usr/local/bin/mutate.sh
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muxbyname.sh: /usr/local/bin/muxbyname.sh
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partition.sh: /usr/local/bin/partition.sh
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phylip2fasta.sh: /usr/local/bin/phylip2fasta.sh
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pileup.sh: /usr/local/bin/pileup.sh
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plotflowcell.sh: /usr/local/bin/plotflowcell.sh
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plotgc.sh: /usr/local/bin/plotgc.sh
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postfilter.sh: /usr/local/bin/postfilter.sh
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printtime.sh: /usr/local/bin/printtime.sh
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processfrag.sh: /usr/local/bin/processfrag.sh
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processhi-c.sh: /usr/local/bin/processhi-c.sh
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processspeed.sh: /usr/local/bin/processspeed.sh
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randomgenome.sh: /usr/local/bin/randomgenome.sh
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randomreads.sh: /usr/local/bin/randomreads.sh
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readlength.sh: /usr/local/bin/readlength.sh
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readqc.sh: /usr/local/bin/readqc.sh
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reducesilva.sh: /usr/local/bin/reducesilva.sh
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reformat.sh: /usr/local/bin/reformat.sh
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reformatpb.sh: /usr/local/bin/reformatpb.sh
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removebadbarcodes.sh: /usr/local/bin/removebadbarcodes.sh
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removecatdogmousehuman.sh: /usr/local/bin/removecatdogmousehuman.sh
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removehuman.sh: /usr/local/bin/removehuman.sh
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removehuman2.sh: /usr/local/bin/removehuman2.sh
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removemicrobes.sh: /usr/local/bin/removemicrobes.sh
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removesmartbell.sh: /usr/local/bin/removesmartbell.sh
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rename.sh: /usr/local/bin/rename.sh
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renameimg.sh: /usr/local/bin/renameimg.sh
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repair.sh: /usr/local/bin/repair.sh
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replaceheaders.sh: /usr/local/bin/replaceheaders.sh
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representative.sh: /usr/local/bin/representative.sh
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rqcfilter.sh: /usr/local/bin/rqcfilter.sh
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rqcfilter2.sh: /usr/local/bin/rqcfilter2.sh
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runhmm.sh: /usr/local/bin/runhmm.sh
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samtoroc.sh: /usr/local/bin/samtoroc.sh
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seal.sh: /usr/local/bin/seal.sh
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sendsketch.sh: /usr/local/bin/sendsketch.sh
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shred.sh: /usr/local/bin/shred.sh
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shrinkaccession.sh: /usr/local/bin/shrinkaccession.sh
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shuffle.sh: /usr/local/bin/shuffle.sh
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shuffle2.sh: /usr/local/bin/shuffle2.sh
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sketch.sh: /usr/local/bin/sketch.sh
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sketchblacklist.sh: /usr/local/bin/sketchblacklist.sh
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sketchblacklist2.sh: /usr/local/bin/sketchblacklist2.sh
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sortbyname.sh: /usr/local/bin/sortbyname.sh
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splitbytaxa.sh: /usr/local/bin/splitbytaxa.sh
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splitnextera.sh: /usr/local/bin/splitnextera.sh
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splitribo.sh: /usr/local/bin/splitribo.sh
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splitsam.sh: /usr/local/bin/splitsam.sh
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splitsam4way.sh: /usr/local/bin/splitsam4way.sh
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splitsam6way.sh: /usr/local/bin/splitsam6way.sh
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stats.sh: /usr/local/bin/stats.sh
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statswrapper.sh: /usr/local/bin/statswrapper.sh
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streamsam.sh: /usr/local/bin/streamsam.sh
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subsketch.sh: /usr/local/bin/subsketch.sh
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summarizecontam.sh: /usr/local/bin/summarizecontam.sh
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summarizecoverage.sh: /usr/local/bin/summarizecoverage.sh
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summarizecrossblock.sh: /usr/local/bin/summarizecrossblock.sh
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summarizemerge.sh: /usr/local/bin/summarizemerge.sh
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summarizequast.sh: /usr/local/bin/summarizequast.sh
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summarizescafstats.sh: /usr/local/bin/summarizescafstats.sh
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summarizeseal.sh: /usr/local/bin/summarizeseal.sh
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summarizesketch.sh: /usr/local/bin/summarizesketch.sh
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synthmda.sh: /usr/local/bin/synthmda.sh
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tadpipe.sh: /usr/local/bin/tadpipe.sh
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tadpole.sh: /usr/local/bin/tadpole.sh
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tadwrapper.sh: /usr/local/bin/tadwrapper.sh
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taxonomy.sh: /usr/local/bin/taxonomy.sh
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taxserver.sh: /usr/local/bin/taxserver.sh
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taxsize.sh: /usr/local/bin/taxsize.sh
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taxtree.sh: /usr/local/bin/taxtree.sh
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testfilesystem.sh: /usr/local/bin/testfilesystem.sh
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testformat.sh: /usr/local/bin/testformat.sh
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testformat2.sh: /usr/local/bin/testformat2.sh
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tetramerfreq.sh: /usr/local/bin/tetramerfreq.sh
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textfile.sh: /usr/local/bin/textfile.sh
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translate6frames.sh: /usr/local/bin/translate6frames.sh
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unicode2ascii.sh: /usr/local/bin/unicode2ascii.sh
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unzip.sh: /usr/local/bin/unzip.sh
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vcf2gff.sh: /usr/local/bin/vcf2gff.sh
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webcheck.sh: /usr/local/bin/webcheck.sh
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docker: quay.io/biocontainers/bcftools
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url: https://quay.io/repository/biocontainers/bcftools
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maintainer: '@marcodelapierre'
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description: 'BCFtools is a program for variant calling and manipulating files in the Variant Call Format (VCF) and its binary counterpart BCF.'
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latest:
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1.13--h3a49de5_0: sha256:4eba5e6d3083a3e5c858bedb98d2148b0b27b3182c2462e82905721065bf4962
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tags:
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1.12--h45bccc9_1: sha256:46e9e8527167c0394a99a5f0f964c8af771f8349140062a3a2d32b1e348a9bf0
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1.13--h3a49de5_0: sha256:4eba5e6d3083a3e5c858bedb98d2148b0b27b3182c2462e82905721065bf4962
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aliases:
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bcftools: /usr/local/bin/bcftools
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bgzip: /usr/local/bin/bgzip
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color-chrs.pl: /usr/local/bin/color-chrs.pl
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guess-ploidy.py: /usr/local/bin/guess-ploidy.py
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htsfile: /usr/local/bin/htsfile
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tabix: /usr/local/bin/tabix
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vcfutils.pl: /usr/local/bin/vcfutils.pl
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docker: quay.io/biocontainers/beast2
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url: https://quay.io/repository/biocontainers/beast2
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maintainer: '@marcodelapierre'
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description: 'BEAST 2 is a cross-platform program for Bayesian phylogenetic analysis of molecular sequences.'
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latest:
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2.6.3--hf1b8bbb_0: sha256:e1445642dc3d56960309cfe8a6d7720650606f5577485eb16038fb9abb015d1d
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tags:
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2.6.3--hf1b8bbb_0: sha256:e1445642dc3d56960309cfe8a6d7720650606f5577485eb16038fb9abb015d1d
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aliases:
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beast: /usr/local/bin/beast
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beauti: /usr/local/bin/beauti
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densitree: /usr/local/bin/densitree
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treeannotator: /usr/local/bin/treeannotator
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env:
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DISPLAY: ""
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docker: quay.io/biocontainers/bedtools
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url: https://quay.io/repository/biocontainers/bedtools
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maintainer: '@marcodelapierre'
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description: 'Bedtools is the swiss army knife for genome arithmetic.'
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latest:
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2.30.0--h7d7f7ad_1: sha256:a2e163619a608525ff784ee296c6925bb75fdc243573fe07edad8c91ee1ad83d
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tags:
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2.30.0--h7d7f7ad_1: sha256:a2e163619a608525ff784ee296c6925bb75fdc243573fe07edad8c91ee1ad83d
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aliases:
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bedtools: /usr/local/bin/bedtools
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docker: quay.io/biocontainers/blast
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url: https://quay.io/repository/biocontainers/blast
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maintainer: '@marcodelapierre'
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description: 'BLAST finds regions of similarity between biological sequences.'
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latest:
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2.12.0--pl5262h3289130_0: sha256:a7eb056f5ca6a32551bf9f87b6b15acc45598cfef39bffdd672f59da3847cd18
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tags:
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2.10.1--pl526he19e7b1_3: sha256:f12a5a35a0e6645134fcfe8650b0d1b5ff1f486430828a4ec3c4c9bfe35a5d78
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2.11.0--pl5262h3289130_1: sha256:52e8e0ed12a0fe8854681dadb600e1d5599e04b960b01034cb53812fad944c3d
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2.12.0--pl5262h3289130_0: sha256:a7eb056f5ca6a32551bf9f87b6b15acc45598cfef39bffdd672f59da3847cd18
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aliases:
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blast_formatter: /usr/local/bin/blast_formatter
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blastdb_aliastool: /usr/local/bin/blastdb_aliastool
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blastdbcheck: /usr/local/bin/blastdbcheck
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blastdbcmd: /usr/local/bin/blastdbcmd
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blastn: /usr/local/bin/blastn
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blastp: /usr/local/bin/blastp
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blastx: /usr/local/bin/blastx
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cleanup-blastdb-volumes.py: /usr/local/bin/cleanup-blastdb-volumes.py
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convert2blastmask: /usr/local/bin/convert2blastmask
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deltablast: /usr/local/bin/deltablast
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eblast: /usr/local/bin/eblast
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makeblastdb: /usr/local/bin/makeblastdb
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psiblast: /usr/local/bin/psiblast
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rpsblast: /usr/local/bin/rpsblast
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rpstblastn: /usr/local/bin/rpstblastn
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tblastn: /usr/local/bin/tblastn
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tblastx: /usr/local/bin/tblastx
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update_blastdb.pl: /usr/local/bin/update_blastdb.pl
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docker: quay.io/biocontainers/bowtie2
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url: https://quay.io/repository/biocontainers/bowtie2
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maintainer: '@marcodelapierre'
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description: 'Bowtie 2 is an ultrafast and memory-efficient tool for aligning sequencing reads to long reference sequences.'
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latest:
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2.4.4--py39hbb4e92a_0: sha256:8295d4e8d7e665e9309cb8311a6aac6d4cc721b30e7e13135c18cd4016baad36
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tags:
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2.3.5.1--py37he513fc3_0: sha256:361034b738118d023b5ed35b070458864f23bf63de09017ac30d08ff48a815b0
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2.4.4--py39hbb4e92a_0: sha256:8295d4e8d7e665e9309cb8311a6aac6d4cc721b30e7e13135c18cd4016baad36
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aliases:
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bowtie2: /usr/local/bin/bowtie2
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bowtie2-align-l: /usr/local/bin/bowtie2-align-l
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bowtie2-align-s: /usr/local/bin/bowtie2-align-s
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bowtie2-build: /usr/local/bin/bowtie2-build
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bowtie2-build-l: /usr/local/bin/bowtie2-build-l
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bowtie2-build-s: /usr/local/bin/bowtie2-build-s
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bowtie2-inspect: /usr/local/bin/bowtie2-inspect
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bowtie2-inspect-l: /usr/local/bin/bowtie2-inspect-l
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bowtie2-inspect-s: /usr/local/bin/bowtie2-inspect-s
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docker: quay.io/biocontainers/bwa-mem2
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url: https://quay.io/repository/biocontainers/bwa-mem2
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maintainer: '@marcodelapierre'
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description: 'Bwa-mem2 is the next version of the bwa-mem algorithm in BWA.'
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latest:
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2.2.1--h9a82719_1: sha256:df29c78f3e199b8f1639f6fc53c47c039e23fb33d107ce53c6645e6bcc3a6415
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tags:
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2.2.1--h9a82719_1: sha256:df29c78f3e199b8f1639f6fc53c47c039e23fb33d107ce53c6645e6bcc3a6415
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aliases:
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bwa-mem2: /usr/local/bin/bwa-mem2
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docker: quay.io/biocontainers/bwa
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url: https://quay.io/repository/biocontainers/bwa
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maintainer: '@marcodelapierre'
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description: 'BWA is a program for aligning sequencing reads against a large reference genome.'
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latest:
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0.7.17--h5bf99c6_8: sha256:f8494324de6da332792dc8e4acc2549152375e1966c96163087d6ff6d42ff48c
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tags:
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0.7.17--h5bf99c6_8: sha256:f8494324de6da332792dc8e4acc2549152375e1966c96163087d6ff6d42ff48c
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aliases:
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bwa: /usr/local/bin/bwa
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docker: quay.io/biocontainers/multiqc
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url: https://quay.io/repository/biocontainers/multiqc
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maintainer: '@marcodelapierre'
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description: 'Aggregate results from bioinformatics analyses across many samples into a single report.'
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latest:
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1.11--pyhdfd78af_0: sha256:88df23fac5b9eecda9943d922f81b68e30188eb4dd7cbfe9554e952ff5a3b0ee
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tags:
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1.9--py_1: sha256:67cc651cb350b1ee2fc0929bd6bcd5189ec8c17f09566a3cd54cde7479e48a09
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1.10.1--pyhdfd78af_1: sha256:c64ea8fcaf49dfc4b0594bc7349e6d1a662eb4484f5aac3252f4eea86cad164c
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1.11--pyhdfd78af_0: sha256:88df23fac5b9eecda9943d922f81b68e30188eb4dd7cbfe9554e952ff5a3b0ee
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aliases:
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multiqc: /usr/local/bin/multiqc

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