├── .github └── workflows │ ├── build.yml │ └── conda.yml ├── .gitignore ├── .gitmodules ├── LICENSE ├── MANIFEST.md ├── PULL_REQUEST_TEMPLATE.md ├── README.md ├── abacas ├── 1.3.1-3-deb │ └── Dockerfile └── 1.3.1-5-deb │ └── Dockerfile ├── abyss ├── 1.9.0 │ └── Dockerfile ├── 2.0.2-2-deb │ └── Dockerfile └── 2.1.5-7-deb │ └── Dockerfile ├── acedb-other-belvu ├── 4.9.39dfsg.02-1-deb │ └── Dockerfile └── 4.9.39dfsg.02-4-deb │ └── Dockerfile ├── acedb-other-dotter ├── 4.9.39dfsg.02-1-deb │ └── Dockerfile └── 4.9.39dfsg.02-4-deb │ └── Dockerfile ├── acedb-other ├── 4.9.39dfsg.02-1-deb │ └── Dockerfile └── 4.9.39dfsg.02-4-deb │ └── Dockerfile ├── adapterremoval ├── 2.2.0-1-deb │ └── Dockerfile └── 2.2.3-1-deb │ └── Dockerfile ├── adun-core ├── 0.81-13-deb │ └── Dockerfile └── 0.81-9b2-deb │ └── Dockerfile ├── adun.app ├── 0.81-13-deb │ └── Dockerfile └── 0.81-9b2-deb │ └── Dockerfile ├── aegean ├── 0.15.2dfsg-1-deb │ └── Dockerfile └── 0.16.0dfsg-1-deb │ └── Dockerfile ├── aeskulap ├── 0.2.2-beta2git20180219.8787e95-2-deb │ └── Dockerfile └── 0.2.2b1git20161206-1-deb │ └── Dockerfile ├── aevol ├── 4.4-1b4-deb │ └── Dockerfile └── 5.0-2b1-deb │ └── Dockerfile ├── aghermann ├── 1.1.2-1-deb │ └── Dockerfile └── 1.1.2-2-deb │ └── Dockerfile ├── alien-hunter ├── 1.7-5-deb │ └── Dockerfile └── 1.7-7-deb │ └── Dockerfile ├── aliscore └── 2.0 │ └── Dockerfile ├── allcatchr └── 1.0.0 │ └── Dockerfile ├── alter-sequence-alignment ├── 1.3.3dfsg-1-deb │ └── Dockerfile └── 1.3.4-2-deb │ └── Dockerfile ├── altree ├── 1.3.1-4b2-deb │ └── Dockerfile └── 1.3.1-7b1-deb │ └── Dockerfile ├── amap-align ├── 2.2-6-deb │ └── Dockerfile └── 2.2git20080214.600fc29dfsg-1-deb │ └── Dockerfile ├── amide ├── 1.0.5-12b1-deb │ └── Dockerfile └── 1.0.5-7-deb │ └── Dockerfile ├── ampliconnoise ├── 1.29-6-deb │ └── Dockerfile └── 1.29-8-deb │ └── Dockerfile ├── andi ├── 0.10-2-deb │ └── Dockerfile └── 0.12-4-deb │ └── Dockerfile ├── anfo ├── 0.98-5-deb │ └── Dockerfile └── 0.98-7-deb │ └── Dockerfile ├── aragorn ├── 1.2.38-1-deb │ └── Dockerfile └── 1.2.38-2-deb │ └── Dockerfile ├── arden ├── 1.0-3-deb │ └── Dockerfile └── 1.0-4-deb │ └── Dockerfile ├── ariba ├── 2.13.3ds-1-deb │ └── Dockerfile └── 2.6.1ds-1-deb │ └── Dockerfile ├── art-nextgen-simulation-tools-profiles ├── 20160605dfsg-2-deb │ └── Dockerfile └── 20160605dfsg-3-deb │ └── Dockerfile ├── art-nextgen-simulation-tools ├── 20160605dfsg-2-deb │ └── Dockerfile └── 20160605dfsg-3-deb │ └── Dockerfile ├── artemis ├── 16.0.17dfsg-1-deb │ └── Dockerfile └── 17.0.1dfsg-2-deb │ └── Dockerfile ├── artfastqgenerator ├── 0.0.20150519-2-deb │ └── Dockerfile └── 0.0.20150519-3-deb │ └── Dockerfile ├── assemblytics └── 1.0ds-1-deb │ └── Dockerfile ├── atac ├── 020150903r2013-3-deb │ └── Dockerfile └── 020150903r2013-6-deb │ └── Dockerfile ├── augustus-data ├── 3.2.3dfsg-1-deb │ └── Dockerfile └── 3.3.2dfsg-2-deb │ └── Dockerfile ├── augustus ├── 3.2.3dfsg-1-deb │ └── Dockerfile └── 3.3.2dfsg-2-deb │ └── Dockerfile ├── autoclassweb ├── 1.2.0 │ └── Dockerfile ├── 2.1.1 │ └── Dockerfile └── 2.2.1 │ └── Dockerfile ├── autodock-getdata ├── 4.2.6-3-deb │ └── Dockerfile └── 4.2.6-6-deb │ └── Dockerfile ├── autodock-test ├── 4.2.6-3-deb │ └── Dockerfile └── 4.2.6-6-deb │ └── Dockerfile ├── autodock-vina ├── 1.1.2-3b6-deb │ └── Dockerfile └── 1.1.2-5b1-deb │ └── Dockerfile ├── autodock ├── 4.2.6-3b1-deb │ └── Dockerfile └── 4.2.6-6-deb │ └── Dockerfile ├── autogrid-test ├── 4.2.6-3-deb │ └── Dockerfile └── 4.2.6-6-deb │ └── Dockerfile ├── autogrid ├── 4.2.6-3b1-deb │ └── Dockerfile └── 4.2.6-6-deb │ └── Dockerfile ├── avivator └── 0.12.3 │ └── Dockerfile ├── avro ├── 1.8.1dfsg-1-deb-py2 │ └── Dockerfile ├── 1.8.1dfsg-1-deb-py3 │ └── Dockerfile ├── 1.8.2dfsg-2-deb-py2 │ └── Dockerfile └── 1.8.2dfsg-2-deb-py3 │ └── Dockerfile ├── axe-demultiplexer ├── 0.3.2dfsg1-1-deb │ └── Dockerfile └── 0.3.3dfsg-1-deb │ └── Dockerfile ├── baitfisher └── 1.2.7git20180107.e92dbf2dfsg-1-deb │ └── Dockerfile ├── bali-phy └── 3.4dfsg-1-deb │ └── Dockerfile ├── ball ├── 1.4.3beta1-3-deb-py2 │ └── Dockerfile └── 1.5.0git20180813.37fc53c-3-deb-py2 │ └── Dockerfile ├── ballview ├── 1.4.3beta1-3-deb-py2 │ └── Dockerfile ├── 1.4.3beta1-3-deb │ └── Dockerfile └── 1.5.0git20180813.37fc53c-3-deb │ └── Dockerfile ├── bamdst └── 1.0.9 │ └── Dockerfile ├── bamtools ├── 2.4.0 │ └── Dockerfile ├── 2.4.1dfsg-1-deb │ └── Dockerfile └── 2.5.1dfsg-3-deb │ └── Dockerfile ├── bandage └── 0.8.1-1-deb │ └── Dockerfile ├── barrnap ├── 0.7dfsg-2-deb │ └── Dockerfile └── 0.9dfsg-1-deb │ └── Dockerfile ├── bart-view └── 0.1.00-2-deb │ └── Dockerfile ├── bart ├── 0.4.00-1-deb │ └── Dockerfile └── 0.4.04-2-deb │ └── Dockerfile ├── bcbio ├── 1.1.2-3-deb-py3 │ └── Dockerfile └── 1.1.2-3-deb │ └── Dockerfile ├── bcftools ├── 1.3.1-1b1-deb │ └── Dockerfile ├── 1.5 │ └── Dockerfile └── 1.9-1-deb │ └── Dockerfile ├── beads └── 1.1.18dfsg-3-deb │ └── Dockerfile ├── beagle ├── 4.1160727-86adfsg-1-deb │ └── Dockerfile └── 5.0-180928dfsg-1-deb │ └── Dockerfile ├── beast-mcmc ├── 1.10.4dfsg-1-deb │ └── Dockerfile └── 1.8.4dfsg.1-1-deb │ └── Dockerfile ├── beast2-mcmc ├── 2.4.4dfsg-1-deb │ └── Dockerfile └── 2.5.1dfsg-2-deb │ └── Dockerfile ├── bedops ├── 2.4.35dfsg-1-deb │ └── Dockerfile └── 2.4.35dfsg-1bpo91-deb │ └── Dockerfile ├── bedtools-test ├── 2.26.0dfsg-3-deb │ └── Dockerfile └── 2.27.1dfsg-4-deb │ └── Dockerfile ├── bedtools ├── 2.25.0 │ └── Dockerfile ├── 2.26.0dfsg-3-deb │ └── Dockerfile ├── 2.27.0 │ └── Dockerfile ├── 2.27.1dfsg-4-deb │ └── Dockerfile └── 2.28.0 │ └── Dockerfile ├── belvu └── 4.44.1dfsg-3-deb │ └── Dockerfile ├── berkeley-express ├── 1.5.1-3b1-deb │ └── Dockerfile └── 1.5.2dfsg-1b2-deb │ └── Dockerfile ├── bio-eagle ├── 2.3-3-deb │ └── Dockerfile └── 2.4.1-1-deb │ └── Dockerfile ├── bio-rainbow ├── 2.0.4-1b1-deb │ └── Dockerfile └── 2.0.4dfsg-1-deb │ └── Dockerfile ├── bio-tradis ├── 1.3.3dfsg-3bpo91-deb │ └── Dockerfile └── 1.4.1dfsg-1-deb │ └── Dockerfile ├── bioconda.txt ├── bioconductor-affy └── 1.52.0-1-deb │ └── Dockerfile ├── bioconductor-affyio └── 1.44.0-1-deb │ └── Dockerfile ├── bioconductor-altcdfenvs └── 1-2.36.0-1-deb │ └── Dockerfile ├── bioconductor-annotate └── 1.52.1dfsg-1-deb │ └── Dockerfile ├── bioconductor-annotationdbi └── 1.36.1-2-deb │ └── Dockerfile ├── bioconductor-annotationhub └── 2.6.4-1-deb │ └── Dockerfile ├── bioconductor-aroma.light └── 3.4.0-1-deb │ └── Dockerfile ├── bioconductor-biobase └── 2.34.0-1-deb │ └── Dockerfile ├── bioconductor-biocgenerics └── 0.20.0-1-deb │ └── Dockerfile ├── bioconductor-biocinstaller └── 1.24.0-1-deb │ └── Dockerfile ├── bioconductor-biocparallel └── 1.8.1-1-deb │ └── Dockerfile ├── bioconductor-biomart └── 2.30.0-1-deb │ └── Dockerfile ├── bioconductor-biomformat └── 1.2.0-1-deb │ └── Dockerfile ├── bioconductor-biostrings └── 2.42.1-1-deb │ └── Dockerfile ├── bioconductor-biovizbase └── 1.22.0-2-deb │ └── Dockerfile ├── bioconductor-bsgenome └── 1.42.0-2-deb │ └── Dockerfile ├── bioconductor-cummerbund └── 2.16.0-2-deb │ └── Dockerfile ├── bioconductor-deseq2 └── 1.14.1-1-deb │ └── Dockerfile ├── bioconductor-dnacopy └── 1.48.0-1-deb │ └── Dockerfile ├── bioconductor-ebseq └── 1.14.0-1-deb │ └── Dockerfile ├── bioconductor-edger └── 3.14.0dfsg-1-deb │ └── Dockerfile ├── bioconductor-ensembldb └── 1.6.2-1-deb │ └── Dockerfile ├── bioconductor-genefilter └── 1.56.0-1-deb │ └── Dockerfile ├── bioconductor-geneplotter └── 1.52.0-2-deb │ └── Dockerfile ├── bioconductor-genomeinfodb └── 1.10.3-1-deb │ └── Dockerfile ├── bioconductor-genomicalignments └── 1.10.0-1b1-deb │ └── Dockerfile ├── bioconductor-genomicfeatures └── 1.26.2-1-deb │ └── Dockerfile ├── bioconductor-genomicranges └── 1.26.2-1b1-deb │ └── Dockerfile ├── bioconductor-go.db └── 3.4.0-1-deb │ └── Dockerfile ├── bioconductor-graph └── 1.52.0-1-deb │ └── Dockerfile ├── bioconductor-gviz └── 1.18.1-1-deb │ └── Dockerfile ├── bioconductor-hilbertvis └── 1.32.0-1-deb │ └── Dockerfile ├── bioconductor-hypergraph └── 1.46.0-1-deb │ └── Dockerfile ├── bioconductor-interactivedisplaybase └── 1.12.0-1-deb │ └── Dockerfile ├── bioconductor-iranges └── 2.8.1-1b1-deb │ └── Dockerfile ├── bioconductor-limma └── 3.30.8dfsg-1-deb │ └── Dockerfile ├── bioconductor-makecdfenv └── 1.50.0-1-deb │ └── Dockerfile ├── bioconductor-mergeomics └── 1.2.0-1-deb │ └── Dockerfile ├── bioconductor-metagenomeseq └── 1.16.0-2-deb │ └── Dockerfile ├── bioconductor-multtest └── 2.30.0-1-deb │ └── Dockerfile ├── bioconductor-phyloseq └── 1.19.1-2-deb │ └── Dockerfile ├── bioconductor-preprocesscore └── 1.36.0-1-deb │ └── Dockerfile ├── bioconductor-qvalue └── 2.6.0-1-deb │ └── Dockerfile ├── bioconductor-rbgl └── 1.50.0dfsg1-1-deb │ └── Dockerfile ├── bioconductor-rsamtools └── 1.26.1-2b1-deb │ └── Dockerfile ├── bioconductor-rtracklayer └── 1.34.1-1-deb │ └── Dockerfile ├── bioconductor-s4vectors └── 0.12.1-2b1-deb │ └── Dockerfile ├── bioconductor-savr └── 1.12.0-1-deb │ └── Dockerfile ├── bioconductor-shortread └── 1.32.0-1b1-deb │ └── Dockerfile ├── bioconductor-snpstats └── 1.24.0dfsg-1-deb │ └── Dockerfile ├── bioconductor-summarizedexperiment └── 1.4.0-2-deb │ └── Dockerfile ├── bioconductor-variantannotation └── 1.20.2-1b1-deb │ └── Dockerfile ├── bioconductor-xvector └── 0.14.0-1b1-deb │ └── Dockerfile ├── biocontainers ├── 1.0.0 │ └── Dockerfile ├── 1.0.0_alpine │ └── Dockerfile ├── 1.1.0 │ └── Dockerfile ├── 1.2.0 │ └── Dockerfile ├── debian-buster-backports │ └── Dockerfile └── debian-stretch-backports │ └── Dockerfile ├── biodocker └── Dockerfile ├── biom-format-tools ├── 2.1.5dfsg-7-deb │ └── Dockerfile └── 2.1.7dfsg-2-deb │ └── Dockerfile ├── biom-format ├── 2.1.5dfsg-7-deb-py2 │ └── Dockerfile ├── 2.1.5dfsg-7-deb-py3 │ └── Dockerfile ├── 2.1.7dfsg-2-deb-py2 │ └── Dockerfile └── 2.1.7dfsg-2-deb-py3 │ └── Dockerfile ├── biomaj-properties └── 1.2.3-11-deb │ └── Dockerfile ├── biomaj └── 1.2.3-11-deb │ └── Dockerfile ├── biomaj3-cli └── 3.1.10-1-deb-py3 │ └── Dockerfile ├── biomaj3-core └── 3.0.15-1-deb-py3 │ └── Dockerfile ├── biomaj3-daemon └── 3.0.17-1-deb-py3 │ └── Dockerfile ├── biomaj3-download └── 3.0.19-1-deb-py3 │ └── Dockerfile ├── biomaj3-process └── 3.0.11-1-deb-py3 │ └── Dockerfile ├── biomaj3-user └── 3.0.6-2-deb-py3 │ └── Dockerfile ├── biomaj3-zipkin └── 0.2.2-1-deb-py3 │ └── Dockerfile ├── biomaj3 └── 3.1.6-1-deb-py3 │ └── Dockerfile ├── bioperl-run ├── 1.7.1-3-deb │ └── Dockerfile └── 1.7.2-4-deb │ └── Dockerfile ├── bioperl ├── 1.7.1-2-deb │ └── Dockerfile └── 1.7.2-3-deb │ └── Dockerfile ├── biopython-sql ├── 1.68dfsg-3-deb-py3 │ └── Dockerfile └── 1.73dfsg-1-deb-py3 │ └── Dockerfile ├── biopython ├── 1.68dfsg-3-deb-py2 │ └── Dockerfile ├── 1.68dfsg-3-deb-py3 │ └── Dockerfile ├── 1.73dfsg-1-deb-py2 │ └── Dockerfile └── 1.73dfsg-1-deb-py3 │ └── Dockerfile ├── bior_annotate └── 2.1.1 │ ├── Dockerfile │ └── annotate │ ├── bior_annotate.sh │ ├── catalogFile.docker │ ├── config │ ├── PED_file.ped │ ├── PED_sample.txt │ ├── catalog_file │ ├── catalog_file.dlmp │ ├── drill_file │ ├── drill_file.dlmp │ ├── memory_info.txt │ ├── targets.genes │ ├── tool_info.minimal.txt │ └── tool_info.txt │ ├── drillFile.docker │ ├── scripts │ ├── AddLinksToVCF.pl │ ├── CompoundHet.pl │ ├── Info_extract2.pl │ ├── Inheritance.pl │ ├── PEDsplit_AddGT.py │ ├── SNPeff_parse.pl │ ├── VCF_remove.pl │ ├── VCF_split.pl │ ├── ba.merge.sh │ ├── ba.program.sh │ ├── bior_vcf2xls.pl │ ├── capture_target_genes.txt │ ├── cava.parse.pl │ ├── new_PED_and_add_genotype.py │ ├── savant.label.pl │ └── shared_functions.sh │ ├── test.vcf │ └── tool_info.minimal.txt ├── biosql ├── 1.68dfsg-3-deb-py2 │ └── Dockerfile └── 1.73dfsg-1-deb-py2 │ └── Dockerfile ├── biosquid-dev └── 1.9gcvs20050121-7-deb │ └── Dockerfile ├── biosquid ├── 1.9gcvs20050121-11-deb │ └── Dockerfile └── 1.9gcvs20050121-7-deb │ └── Dockerfile ├── biosyntax-common └── 1.0.0b-1-deb │ └── Dockerfile ├── biosyntax-example └── 1.0.0b-1-deb │ └── Dockerfile ├── biosyntax-gedit └── 1.0.0b-1-deb │ └── Dockerfile ├── biosyntax-less └── 1.0.0b-1-deb │ └── Dockerfile ├── biosyntax-vim └── 1.0.0b-1-deb │ └── Dockerfile ├── biosyntax └── 1.0.0b-1-deb │ └── Dockerfile ├── biotools ├── 1.2.12-3-deb-py2 │ └── Dockerfile ├── 1.2.12-3-deb-py3 │ └── Dockerfile ├── 1.2.12-3bpo91-deb-py2 │ └── Dockerfile └── 1.2.12-3bpo91-deb-py3 │ └── Dockerfile ├── bitseq └── 0.7.5dfsg-4-deb │ └── Dockerfile ├── blasr ├── 5.3.2dfsg-1.1-deb │ └── Dockerfile └── 5.30-1-deb │ └── Dockerfile ├── blast └── 2.2.31 │ └── Dockerfile ├── blast2 ├── 1-2.6.0-1-deb │ └── Dockerfile └── 1-2.8.1-1-deb │ └── Dockerfile ├── blaze └── 2.2.0 │ └── Dockerfile ├── blixem └── 4.44.1dfsg-3-deb │ └── Dockerfile ├── bolt-lmm-example └── 2.3.2dfsg-3-deb │ └── Dockerfile ├── bolt-lmm └── 2.3.2dfsg-3b1-deb │ └── Dockerfile ├── bowtie ├── 1.1.2 │ └── Dockerfile └── 1.2.2dfsg-4-deb │ └── Dockerfile ├── bowtie2 ├── 2.2.8 │ └── Dockerfile ├── 2.2.9 │ └── Dockerfile ├── 2.3.0-2-deb │ └── Dockerfile ├── 2.3.1 │ └── Dockerfile ├── 2.3.4.3-1-deb │ └── Dockerfile ├── 2.4.1 │ └── Dockerfile └── README.md ├── boxshade ├── 3.3.1-10-deb │ └── Dockerfile └── 3.3.1-12-deb │ └── Dockerfile ├── bppphyview └── 0.6.1-1-deb │ └── Dockerfile ├── bppsuite └── 2.4.1-1-deb │ └── Dockerfile ├── brig ├── 0.95dfsg-1-deb │ └── Dockerfile └── 0.95dfsg-2-deb │ └── Dockerfile ├── burrito ├── 0.9.1-1-deb-py2 │ └── Dockerfile ├── 0.9.1-1-deb-py3 │ └── Dockerfile ├── 0.9.1-3-deb-py2 │ └── Dockerfile └── 0.9.1-3-deb-py3 │ └── Dockerfile ├── bwa ├── 0.7.12 │ └── Dockerfile ├── 0.7.13 │ └── Dockerfile ├── 0.7.15 │ └── Dockerfile ├── 0.7.17-3-deb │ └── Dockerfile └── 0.7.17 │ └── Dockerfile ├── bwakit └── 0.7.15 │ └── Dockerfile ├── bx-tools ├── 0.8.2-1-deb-py2 │ └── Dockerfile └── 0.8.2-1-deb-py3 │ └── Dockerfile ├── bx ├── 0.8.2-1-deb-py2 │ └── Dockerfile └── 0.8.2-1-deb-py3 │ └── Dockerfile ├── bz2file ├── 0.98-1-deb-py2 │ └── Dockerfile ├── 0.98-1-deb-py3 │ └── Dockerfile ├── 0.98-2-deb-py2 │ └── Dockerfile └── 0.98-2-deb-py3 │ └── Dockerfile ├── cadd-scripts-with-envs ├── 1.6.post1 │ ├── Dockerfile │ └── README.md └── 1.6 │ ├── Dockerfile │ └── README.md ├── cain-solvers ├── 1.10dfsg-2-deb │ └── Dockerfile └── 1.10dfsg-3-deb │ └── Dockerfile ├── cain ├── 1.10dfsg-2-deb │ └── Dockerfile └── 1.10dfsg-3-deb │ └── Dockerfile ├── camitk-actionstatemachine ├── 4.0.4-2-deb │ └── Dockerfile └── 4.1.2-3-deb │ └── Dockerfile ├── camitk-config ├── 4.0.4-2-deb │ └── Dockerfile └── 4.1.2-3-deb │ └── Dockerfile ├── camitk-imp ├── 4.0.4-2-deb │ └── Dockerfile └── 4.1.2-3-deb │ └── Dockerfile ├── canu ├── 1.7.1dfsg-1bpo91-deb │ └── Dockerfile └── 1.8dfsg-2-deb │ └── Dockerfile ├── casmoothing └── 0.2-1b1-deb-py2 │ └── Dockerfile ├── cassiopee ├── 1.0.5-1b1-deb │ └── Dockerfile └── 1.0.9-2-deb │ └── Dockerfile ├── cava └── 1.1.1 │ └── Dockerfile ├── ccmetagen └── 1.1.5 │ └── Dockerfile ├── cct ├── 20170919dfsg-1-deb │ └── Dockerfile └── 20170919dfsg-1bpo91-deb │ └── Dockerfile ├── cd-hit ├── 4.6.6-2-deb │ └── Dockerfile └── 4.6.8-2-deb │ └── Dockerfile ├── cdbfasta ├── 0.99-20100722-3-deb │ └── Dockerfile └── 0.99-20100722-5-deb │ └── Dockerfile ├── cellpose ├── 0.6.5 │ ├── Dockerfile │ ├── environment.yml │ └── test │ │ ├── img02.png │ │ ├── img03.png │ │ └── img05.png ├── 2.0.5 │ └── Dockerfile ├── 2.1.1 │ ├── Dockerfile │ └── test │ │ ├── img02.png │ │ ├── img03.png │ │ └── img05.png ├── 2.2.2 │ └── Dockerfile ├── 3.0.1 │ └── Dockerfile └── 3.1.0 │ └── Dockerfile ├── cellprofiler └── 4.2.5 │ └── Dockerfile ├── centrifuge └── 1.0.3-2-deb │ └── Dockerfile ├── cfflib └── 2.0.5-3-deb-py2 │ └── Dockerfile ├── cgview ├── 0.0.20100111-2-deb │ └── Dockerfile └── 0.0.20100111-4-deb │ └── Dockerfile ├── chado-utils ├── 1.31-3-deb │ └── Dockerfile └── 1.31-5-deb │ └── Dockerfile ├── changeo └── 0.4.5-1-deb │ └── Dockerfile ├── chimeraslayer ├── 20101212dfsg1-1-deb │ └── Dockerfile └── 20101212dfsg1-2-deb │ └── Dockerfile ├── chromhmm-example └── 1.18dfsg-1-deb │ └── Dockerfile ├── chromhmm └── 1.18dfsg-1-deb │ └── Dockerfile ├── chromimpute └── 1.0.3dfsg-1-deb │ └── Dockerfile ├── circlator ├── 1.4.1-1-deb │ └── Dockerfile └── 1.5.5-3-deb │ └── Dockerfile ├── circos-tools ├── 0.22-1-deb │ └── Dockerfile └── 0.23-1-deb │ └── Dockerfile ├── circos ├── 0.69.4dfsg-1-deb │ └── Dockerfile └── 0.69.6dfsg-2-deb │ └── Dockerfile ├── clearcut ├── 1.0.9-1b1-deb │ └── Dockerfile └── 1.0.9-3-deb │ └── Dockerfile ├── clips ├── 1.0.7.348clips-2-deb-py2 │ └── Dockerfile └── 1.0.7.348clips-4-deb-py2 │ └── Dockerfile ├── clonalframe ├── 1.2-5-deb │ └── Dockerfile └── 1.2-9-deb │ └── Dockerfile ├── clonalframeml └── 1.11-3-deb │ └── Dockerfile ├── clonalorigin └── 1.0-3-deb │ └── Dockerfile ├── clustal-omega └── 1.2.1 │ └── Dockerfile ├── clustalo ├── 1.2.4-1-deb │ └── Dockerfile └── 1.2.4-2-deb │ └── Dockerfile ├── clustalw ├── 2.1lgpl-5-deb │ └── Dockerfile └── 2.1lgpl-6-deb │ └── Dockerfile ├── clustalx ├── 2.1lgpl-5-deb │ └── Dockerfile └── 2.1lgpl-8-deb │ └── Dockerfile ├── cnvkit └── 0.9.5-3-deb │ └── Dockerfile ├── cobra-data ├── 0.14.1-1-deb-py2 │ └── Dockerfile └── 0.5.9-1-deb-py2 │ └── Dockerfile ├── cobra ├── 0.14.1-1-deb-py3 │ └── Dockerfile ├── 0.5.9-1-deb-py2 │ └── Dockerfile └── 0.5.9-1-deb-py3 │ └── Dockerfile ├── codonw ├── 1.4.4-3b1-deb │ └── Dockerfile └── 1.4.4-4-deb │ └── Dockerfile ├── cogent ├── 1.9-14-deb-py2 │ └── Dockerfile └── 1.9-9-deb-py2 │ └── Dockerfile ├── colormap ├── 1.0.2-1-deb-py2 │ └── Dockerfile └── 1.0.2-1-deb-py3 │ └── Dockerfile ├── colormath └── 3.0.0-1-deb-py3 │ └── Dockerfile ├── comet ├── 2015011 │ └── Dockerfile ├── 2015012 │ └── Dockerfile ├── 2015020 │ └── Dockerfile ├── 2015025 │ └── Dockerfile ├── 2016010 │ └── Dockerfile ├── 2016011 │ └── Dockerfile └── 2016012 │ └── Dockerfile ├── concavity ├── 0.1dfsg.1-1-deb │ └── Dockerfile └── 0.1dfsg.1-4-deb │ └── Dockerfile ├── conodictor ├── 2.2.2 │ └── Dockerfile └── 2.3.1 │ └── Dockerfile ├── consensuscore2 └── 3.3.0dfsg-2.1-deb-py2 │ └── Dockerfile ├── conservation-code ├── 20110309.0-5-deb │ └── Dockerfile └── 20110309.0-7-deb │ └── Dockerfile ├── control-freec └── 11.5 │ └── Dockerfile ├── coregenebuilder └── 1.0 │ ├── Dockerfile │ └── inventory ├── corepywrap ├── 1.005-4b3-deb-py2 │ └── Dockerfile └── 1.005-6-deb-py2 │ └── Dockerfile ├── cpat └── 1.2.4 │ └── Dockerfile ├── crac ├── 2.5.0dfsg-1-deb │ └── Dockerfile └── 2.5.0dfsg-3-deb │ └── Dockerfile ├── crux ├── 2.1 │ └── Dockerfile └── 3.2 │ └── Dockerfile ├── csb ├── 1.2.3dfsg-3-deb-py2 │ └── Dockerfile ├── 1.2.3dfsg-3-deb-py3 │ └── Dockerfile ├── 1.2.5dfsg-3-deb-py2 │ └── Dockerfile ├── 1.2.5dfsg-3-deb-py3 │ └── Dockerfile └── 1.2.5dfsg-3-deb │ └── Dockerfile ├── ctdconverter ├── 2.0-4-deb │ └── Dockerfile └── 2.0-4bpo91-deb │ └── Dockerfile ├── ctdopts ├── 1.2-3-deb-py3 │ └── Dockerfile └── 1.2-3bpo91-deb-py3 │ └── Dockerfile ├── ctn-dev ├── 3.2.0dfsg-5-deb │ └── Dockerfile └── 3.2.0dfsg-6b1-deb │ └── Dockerfile ├── ctn ├── 3.2.0dfsg-5-deb │ └── Dockerfile └── 3.2.0dfsg-6b1-deb │ └── Dockerfile ├── ctsim-help ├── 5.2.0-4-deb │ └── Dockerfile └── 6.0.2-2-deb │ └── Dockerfile ├── ctsim ├── 5.2.0-4-deb │ └── Dockerfile └── 6.0.2-2-deb │ └── Dockerfile ├── cutadapt ├── 1.12-2-deb-py2 │ └── Dockerfile ├── 1.12-2-deb-py3 │ └── Dockerfile ├── 1.12-2-deb │ └── Dockerfile ├── 1.18-1-deb-py2 │ └── Dockerfile ├── 1.18-1-deb-py3 │ └── Dockerfile └── 1.18-1-deb │ └── Dockerfile ├── cwltool ├── 1.0.20170114120503-1-deb │ └── Dockerfile └── 1.0.20181217162649dfsg-10-deb │ └── Dockerfile ├── cycle └── 0.3.1-14-deb │ └── Dockerfile ├── cyvcf2 ├── 0.10.4-1-deb-py2 │ └── Dockerfile └── 0.10.4-1-deb-py3 │ └── Dockerfile ├── daligner ├── 1.020161119-1-deb │ └── Dockerfile └── 1.0git20180524.fd21879-1-deb │ └── Dockerfile ├── danpos └── 2.2.2 │ └── Dockerfile ├── dascrubber ├── 020160601-2-deb │ └── Dockerfile └── 1.1-1-deb │ └── Dockerfile ├── dask └── 2023.10.1-py11-ol9 │ ├── Dockerfile │ ├── conda-env.yml │ ├── config │ └── dask-config.yml │ └── scripts │ ├── determine_ip.sh │ ├── prepare.sh │ ├── startmanager.sh │ ├── startworker.sh │ ├── waitforanyfile.sh │ ├── waitformanager.sh │ └── waitforworkers.sh ├── dawg ├── 1.2-1b1-deb │ └── Dockerfile └── 1.2-2-deb │ └── Dockerfile ├── dazzdb ├── 1.020161112-2-deb │ └── Dockerfile └── 1.0git20180908.0bd5e07-1-deb │ └── Dockerfile ├── dcm2niix ├── 1.0.20161101-1-deb │ └── Dockerfile └── 1.0.20181125-1-deb │ └── Dockerfile ├── dcmtk ├── 3.6.120160216-4-deb │ └── Dockerfile └── 3.6.4-2.1-deb │ └── Dockerfile ├── deepgoplus └── 1.0.0 │ └── Dockerfile ├── deepnano-data └── 0.0git20170813.e8a621e-3-deb │ └── Dockerfile ├── deepnano └── 0.0git20170813.e8a621e-3-deb │ └── Dockerfile ├── delly └── 0.8.1-2-deb │ └── Dockerfile ├── dendropy ├── 4.2.0dfsg-1-deb-py2 │ └── Dockerfile ├── 4.2.0dfsg-1-deb-py3 │ └── Dockerfile ├── 4.4.0-1-deb-py2 │ └── Dockerfile └── 4.4.0-1-deb-py3 │ └── Dockerfile ├── denovogui ├── 1.10.4 │ └── Dockerfile └── 1.5.2 │ └── Dockerfile ├── depinfo └── 1.4.0-1-deb-py3 │ └── Dockerfile ├── dia-umpire ├── 1.4256 │ ├── Dockerfile │ └── input │ │ ├── comet.params │ │ ├── diaumpire.quant_params │ │ ├── diaumpire.se_params │ │ └── diaumpire_v1_4.quant_params └── 2.1.2 │ ├── Dockerfile │ └── input │ ├── DIA_Umpire_Manual_v1.4_pre.pdf │ ├── comet.params │ ├── diaumpire_quant_params.txt │ ├── diaumpire_se_ABSciex_params.txt │ └── diaumpire_se_Thermo_params.txt ├── dialign-tx-data ├── 1.0.2-12-deb │ └── Dockerfile └── 1.0.2-9-deb │ └── Dockerfile ├── dialign-tx ├── 1.0.2-12-deb │ └── Dockerfile └── 1.0.2-9-deb │ └── Dockerfile ├── dialign ├── 2.2.1-10-deb │ └── Dockerfile └── 2.2.1-8-deb │ └── Dockerfile ├── diamond-aligner ├── 0.9.22dfsg-2bpo91-deb │ └── Dockerfile └── 0.9.24dfsg-1-deb │ └── Dockerfile ├── diann ├── 1.8.0 │ └── Dockerfile └── 1.8.1 │ └── Dockerfile ├── dicom3tools ├── 1.0020170109062447-1-deb │ └── Dockerfile └── 1.0020180803063840-1-deb │ └── Dockerfile ├── dicompyler ├── 0.4.2-3-deb │ └── Dockerfile └── 0.4.2.0-2-deb │ └── Dockerfile ├── dicomscope ├── 3.6.0-15-deb │ └── Dockerfile └── 3.6.0-20-deb │ └── Dockerfile ├── dictobj ├── 0.4-1-deb-py2 │ └── Dockerfile └── 0.4-1-deb-py3 │ └── Dockerfile ├── diffexpir └── 0.0.1 │ └── Dockerfile ├── dindel ├── 1.01-wu1-3dfsg-1b1-deb │ └── Dockerfile └── 1.01dfsg-4b1-deb │ └── Dockerfile ├── discosnp ├── 1.2.6-1b2-deb │ └── Dockerfile └── 2.3.0-2-deb │ └── Dockerfile ├── discovar └── 52488 │ └── Dockerfile ├── discovardenovo └── 52488 │ └── Dockerfile ├── disulfinder-data ├── 1.2.11-6-deb │ └── Dockerfile └── 1.2.11-8-deb │ └── Dockerfile ├── disulfinder ├── 1.2.11-6-deb │ └── Dockerfile └── 1.2.11-8-deb │ └── Dockerfile ├── dna-jellyfish └── 2.2.6-1b1-deb-py3 │ └── Dockerfile ├── dnaclust ├── 3-4b2-deb │ └── Dockerfile └── 3-6b1-deb │ └── Dockerfile ├── dotter └── 4.44.1dfsg-3-deb │ └── Dockerfile ├── dssp ├── 2.2.1-3b2-deb │ └── Dockerfile └── 3.0.0-3b1-deb │ └── Dockerfile ├── dwgsim ├── 0.1.11-3b1-deb │ └── Dockerfile └── 0.1.12-2-deb │ └── Dockerfile ├── e-mem └── 1.0.1-2-deb │ └── Dockerfile ├── ea-utils ├── 1.1.2dfsg-4-deb │ └── Dockerfile └── 1.1.2dfsg-5-deb │ └── Dockerfile ├── easydev ├── 0.9.37-1-deb-py2 │ └── Dockerfile └── 0.9.37-1-deb-py3 │ └── Dockerfile ├── ebi-webservice └── 1.0.0 │ └── Dockerfile ├── ecopcr ├── 0.5.0dfsg-1-deb │ └── Dockerfile └── 1.0.1dfsg-1-deb │ └── Dockerfile ├── edfbrowser ├── 1.58-1b1-deb │ └── Dockerfile └── 1.67dfsg-1-deb │ └── Dockerfile ├── edlib-aligner ├── 1.2.3-3bpo91-deb │ └── Dockerfile └── 1.2.4-1-deb │ └── Dockerfile ├── edlib └── 1.2.4-1-deb-py3 │ └── Dockerfile ├── edtsurf ├── 0.2009-4b1-deb │ └── Dockerfile └── 0.2009-6-deb │ └── Dockerfile ├── eido ├── 0.1.6 │ └── Dockerfile ├── 0.1.8 │ └── Dockerfile └── 0.1.9 │ └── Dockerfile ├── eigensoft ├── 6.1.4dfsg-1b1-deb │ └── Dockerfile └── 7.2.1dfsg-1-deb │ └── Dockerfile ├── elastix ├── 4.8-10-deb │ └── Dockerfile ├── 4.8-10b1-deb │ └── Dockerfile └── 4.9.0-1-deb │ └── Dockerfile ├── elph └── 1.0.1-2-deb │ └── Dockerfile ├── embassy-domainatrix ├── 0.1.660-1-deb │ └── Dockerfile └── 0.1.660-3-deb │ └── Dockerfile ├── embassy-domalign ├── 0.1.660-1-deb │ └── Dockerfile └── 0.1.660-3-deb │ └── Dockerfile ├── embassy-domsearch ├── 1-0.1.660-1-deb │ └── Dockerfile └── 1-0.1.660-3-deb │ └── Dockerfile ├── emboss-data ├── 6.6.0dfsg-6-deb │ └── Dockerfile └── 6.6.0dfsg-7-deb │ └── Dockerfile ├── emboss-explorer ├── 2.2.0-10-deb │ └── Dockerfile └── 2.2.0-8-deb │ └── Dockerfile ├── emboss-lib ├── 6.6.0dfsg-6-deb │ └── Dockerfile └── 6.6.0dfsg-7b1-deb │ └── Dockerfile ├── emboss-test ├── 6.6.0dfsg-6-deb │ └── Dockerfile └── 6.6.0dfsg-7-deb │ └── Dockerfile ├── emboss ├── 6.5.7 │ └── Dockerfile ├── 6.6.0dfsg-6-deb │ └── Dockerfile └── 6.6.0dfsg-7b1-deb │ └── Dockerfile ├── entrez-direct └── 7.50.20171103 │ └── Dockerfile ├── eosc-pilot └── 1.0-remastering │ └── Dockerfile ├── epigrass └── 2.4.7-1-deb │ └── Dockerfile ├── estscan └── 3.0.3-3-deb │ └── Dockerfile ├── evidential-gene ├── 22jan14 │ └── Dockerfile └── 23jul15 │ └── Dockerfile ├── examl └── 3.0.21-2-deb │ └── Dockerfile ├── exonerate ├── 2.4.0-2-deb │ └── Dockerfile └── 2.4.0-4-deb │ └── Dockerfile ├── falcon-ms └── 0.1.3 │ └── Dockerfile ├── falcon └── 1.8.6-1.1-deb │ └── Dockerfile ├── famli └── 1.0 │ ├── Dockerfile │ └── tests.bats ├── fast5 ├── 0.5.8-1b2-deb-py2 │ └── Dockerfile ├── 0.5.8-1b2-deb-py3 │ └── Dockerfile ├── 0.6.5-1bpo91-deb │ └── Dockerfile ├── 0.6.5-2-deb │ └── Dockerfile ├── 0.6.5-2b1-deb-py2 │ └── Dockerfile └── 0.6.5-2b1-deb-py3 │ └── Dockerfile ├── fastahack ├── 0.020160702-1b1-deb │ └── Dockerfile └── 0.0git20160702.bbc645fdfsg-6-deb │ └── Dockerfile ├── fastaq ├── 3.14.0-1-deb │ └── Dockerfile └── 3.17.0-2-deb │ └── Dockerfile ├── fastcluster ├── 1.1.22-1-deb-py2 │ └── Dockerfile └── 1.1.22-1-deb-py3 │ └── Dockerfile ├── fastdnaml ├── 1.2.2-11b1-deb │ └── Dockerfile └── 1.2.2-14-deb │ └── Dockerfile ├── fastlink ├── 4.1P-fix100dfsg-1b1-deb │ └── Dockerfile └── 4.1P-fix100dfsg-2-deb │ └── Dockerfile ├── fastml ├── 3.1-3-deb │ └── Dockerfile └── 3.1-4-deb │ └── Dockerfile ├── fastp ├── 0.19.6dfsg-1-deb │ └── Dockerfile └── 0.20.1 │ └── Dockerfile ├── fastqc ├── 0.11.5 │ └── Dockerfile ├── 0.11.8dfsg-2-deb │ └── Dockerfile └── 0.11.9 │ └── Dockerfile ├── fastqtl ├── 2.184dfsg-5-deb │ └── Dockerfile └── 2.184dfsg-6b1-deb │ └── Dockerfile ├── fasttree ├── 2.1.10-2-deb │ └── Dockerfile └── 2.1.9-1-deb │ └── Dockerfile ├── fastx-toolkit ├── 0.0.14-3-deb │ └── Dockerfile └── 0.0.14-6-deb │ └── Dockerfile ├── fastxtools └── 0.0.14 │ └── Dockerfile ├── ffindex ├── 0.9.9.7-3-deb │ └── Dockerfile └── 0.9.9.9-2-deb │ └── Dockerfile ├── figtree ├── 1.4.2dfsg-2-deb │ └── Dockerfile └── 1.4.4-3-deb │ └── Dockerfile ├── filo └── 1.1.0-3b1-deb │ └── Dockerfile ├── fis-gtm-6.3-000a └── 6.3-000A-1-deb │ └── Dockerfile ├── fis-gtm-6.3-007 └── 6.3-007-1-deb │ └── Dockerfile ├── fis-gtm ├── 6.3-000A-1-deb │ └── Dockerfile └── 6.3-007-1-deb │ └── Dockerfile ├── fitbit ├── 0.2.4-1-deb-py2 │ └── Dockerfile ├── 0.3.0-4-deb-py2 │ └── Dockerfile └── 0.3.0-4-deb-py3 │ └── Dockerfile ├── fitgcp ├── 0.0.20150429-1-deb │ └── Dockerfile └── 0.0.20150429-2-deb │ └── Dockerfile ├── flexbar ├── 1-3.4.0-2-deb │ └── Dockerfile └── 2.50-2b1-deb │ └── Dockerfile ├── fml-asm ├── 0.1-2b1-deb │ └── Dockerfile └── 0.1-5-deb │ └── Dockerfile ├── frc_align └── 20150723 │ └── Dockerfile ├── freebayes ├── 1.2.0-1bpo91-deb │ └── Dockerfile └── 1.2.0-2-deb │ └── Dockerfile ├── freecontact ├── 1.0.21-5-deb │ └── Dockerfile ├── 1.0.21-7b1-deb │ └── Dockerfile ├── 1.1-2b2-deb-py2 │ └── Dockerfile ├── 1.1-4-deb-py2 │ └── Dockerfile └── 1.1-4-deb-py3 │ └── Dockerfile ├── freediams-doc-en ├── 0.9.4-1-deb │ └── Dockerfile └── 0.9.4-2-deb │ └── Dockerfile ├── freediams-doc-fr ├── 0.9.4-1-deb │ └── Dockerfile └── 0.9.4-2-deb │ └── Dockerfile ├── freediams ├── 0.9.4-1b1-deb │ └── Dockerfile └── 0.9.4-2-deb │ └── Dockerfile ├── fsa ├── 1.15.9dfsg-3-deb │ └── Dockerfile └── 1.15.9dfsg-4-deb │ └── Dockerfile ├── fsm-lite ├── 1.0-2-deb │ └── Dockerfile └── 1.0-3-deb │ └── Dockerfile ├── fw4spl └── 17.2.0-2-deb │ └── Dockerfile ├── galileo-daemon ├── 0.5.1-4-deb │ └── Dockerfile └── 0.5.1-6-deb │ └── Dockerfile ├── galileo ├── 0.5.1-4-deb │ └── Dockerfile └── 0.5.1-6-deb │ └── Dockerfile ├── gapcloser └── 1.12-r6 │ └── Dockerfile ├── garli-mpi └── 2.1-3-deb │ └── Dockerfile ├── garli ├── 2.1-1-deb │ └── Dockerfile └── 2.1-3-deb │ └── Dockerfile ├── gasic ├── 0.0.r19-1-deb │ └── Dockerfile └── 0.0.r19-4-deb │ └── Dockerfile ├── gatb-core-testdata └── 1.4.1git20181225.44d5a44dfsg-3-deb │ └── Dockerfile ├── gatb-core └── 1.4.1git20181225.44d5a44dfsg-3-deb │ └── Dockerfile ├── gatk └── 3.4 │ ├── Dockerfile │ └── LICENSE ├── gbrowse-calign ├── 2.56dfsg-2-deb │ └── Dockerfile └── 2.56dfsg-4b1-deb │ └── Dockerfile ├── gbrowse-data ├── 2.56dfsg-2-deb │ └── Dockerfile └── 2.56dfsg-4-deb │ └── Dockerfile ├── gbrowse ├── 2.56dfsg-2-deb │ └── Dockerfile └── 2.56dfsg-4-deb │ └── Dockerfile ├── gcta └── 1.24.7 │ └── Dockerfile ├── gdcm ├── 2.6.6-3-deb-py2 │ └── Dockerfile └── 2.8.8-9-deb-py3 │ └── Dockerfile ├── gdpc ├── 2.2.5-6-deb │ └── Dockerfile └── 2.2.5-9-deb │ └── Dockerfile ├── gemma └── 0.98.1dfsg-1-deb │ └── Dockerfile ├── geneocr-api └── 1.0 │ └── Dockerfile ├── geneocr-ui └── 1.0 │ └── Dockerfile ├── genometester └── 4.0git20180508.a9c14a6dfsg-1-deb │ └── Dockerfile ├── genometools-common ├── 1.5.10ds-3-deb │ └── Dockerfile └── 1.5.9ds-4-deb │ └── Dockerfile ├── genometools ├── 1.5.10ds-3-deb-py2 │ └── Dockerfile ├── 1.5.10ds-3-deb │ └── Dockerfile ├── 1.5.9ds-4-deb-py2 │ └── Dockerfile └── 1.5.9ds-4-deb │ └── Dockerfile ├── gentle ├── 1.9cvs20100605dfsg1-5-deb │ └── Dockerfile └── 1.9cvs20100605dfsg1-7b1-deb │ └── Dockerfile ├── getdata └── 0.2-3-deb │ └── Dockerfile ├── gfapy └── 1.0.0dfsg-3-deb-py3 │ └── Dockerfile ├── gff2aplot ├── 2.0-11-deb │ └── Dockerfile └── 2.0-8b1-deb │ └── Dockerfile ├── gff2ps ├── 0.98d-5-deb │ └── Dockerfile └── 0.98l-2-deb │ └── Dockerfile ├── gffutils └── 0.9-1-deb-py3 │ └── Dockerfile ├── ghmm └── 0.9rc3-2-deb │ └── Dockerfile ├── giira ├── 0.0.20140625-1-deb │ └── Dockerfile └── 0.0.20140625-2-deb │ └── Dockerfile ├── ginkgocadx ├── 3.8.4-1-deb │ └── Dockerfile └── 3.8.8-1-deb │ └── Dockerfile ├── glam2 ├── 1064-3b1-deb │ └── Dockerfile └── 1064-5-deb │ └── Dockerfile ├── gnumed-client-de ├── 1.6.11dfsg-3-deb │ └── Dockerfile └── 1.7.5dfsg-3-deb │ └── Dockerfile ├── gnumed-client ├── 1.6.11dfsg-3-deb │ └── Dockerfile └── 1.7.5dfsg-3-deb │ └── Dockerfile ├── gnumed-common ├── 1.6.11dfsg-3-deb │ └── Dockerfile └── 1.7.5dfsg-3-deb │ └── Dockerfile ├── gnumed-server ├── 21.11-1-deb │ └── Dockerfile └── 22.5-1-deb │ └── Dockerfile ├── golang-github-dataence-porter2-dev └── 0.0git20150829.56e4718-2-deb │ └── Dockerfile ├── grabix └── 0.1.7-1-deb │ └── Dockerfile ├── graphlan ├── 1.1-2-deb │ └── Dockerfile └── 1.1.3-1-deb │ └── Dockerfile ├── grinder ├── 0.5.4-1-deb │ └── Dockerfile └── 0.5.4-5-deb │ └── Dockerfile ├── gubbins ├── 2.2.0-1-deb │ └── Dockerfile └── 2.3.4-1-deb │ └── Dockerfile ├── guidance2 └── 2.02 │ └── Dockerfile ├── gwama ├── 2.2.2dfsg-1-deb │ └── Dockerfile └── 2.2.2dfsg-2-deb │ └── Dockerfile ├── gwas-fasp └── v1.0.0 │ ├── Dockerfile │ ├── requirements.txt │ └── scripts │ ├── create_plot.sh │ ├── manhattan_plot.py │ ├── parse_metadata.sh │ └── run_gwas.sh ├── gwyddion-common ├── 2.47-1-deb │ └── Dockerfile └── 2.52-1-deb │ └── Dockerfile ├── gwyddion-plugins ├── 2.47-1-deb │ └── Dockerfile └── 2.52-1-deb │ └── Dockerfile ├── gwyddion ├── 2.47-1-deb │ └── Dockerfile └── 2.52-1-deb │ └── Dockerfile ├── hap-ibd └── 1.0.rev20May22.818 │ └── Dockerfile ├── harvest-tools ├── 1.3-1-deb │ └── Dockerfile └── 1.3-4-deb │ └── Dockerfile ├── hdmedians └── 0.13git20171027.8e0e9e3-1-deb-py3 │ └── Dockerfile ├── hhsuite-data ├── 3.0beta2dfsg-3-deb │ └── Dockerfile └── 3.0beta3dfsg-3-deb │ └── Dockerfile ├── hhsuite ├── 3.0beta2dfsg-3-deb │ └── Dockerfile └── 3.0beta3dfsg-3-deb │ └── Dockerfile ├── hifiadapterfilt └── 2.0.0 │ └── Dockerfile ├── hilive ├── 0.3-2-deb │ └── Dockerfile └── 1.1-2-deb │ └── Dockerfile ├── hinge └── 0.5.0-4-deb │ └── Dockerfile ├── hisat2 ├── 2.0.5-1-deb │ └── Dockerfile └── 2.1.0-2-deb │ └── Dockerfile ├── hl7 ├── 0.3.4-1-deb-py2 │ └── Dockerfile ├── 0.3.4-1-deb-py3 │ └── Dockerfile ├── 0.3.4-3-deb-py2 │ └── Dockerfile └── 0.3.4-3-deb-py3 │ └── Dockerfile ├── hmmer ├── 3.1b2dfsg-5-deb │ └── Dockerfile └── 3.2.1dfsg-1-deb │ └── Dockerfile ├── hmmer2-pvm ├── 2.3.2-13-deb │ └── Dockerfile └── 2.3.2dfsg-6-deb │ └── Dockerfile ├── hmmer2 ├── 2.3.2-13-deb │ └── Dockerfile └── 2.3.2dfsg-6-deb │ └── Dockerfile ├── htseq ├── 0.11.2-1-deb-py2 │ └── Dockerfile ├── 0.11.2-1-deb-py3 │ └── Dockerfile └── 0.6.1p1-4-deb-py2 │ └── Dockerfile ├── htslib-test ├── 1.3.2-2-deb │ └── Dockerfile └── 1.9-11-deb │ └── Dockerfile ├── htslib └── 1.2.1 │ └── Dockerfile ├── hunspell-de-med └── 20160103-3-deb │ └── Dockerfile ├── hunspell-en-med ├── 0.0.20080513-2-deb │ └── Dockerfile └── 0.0.20140410-1-deb │ └── Dockerfile ├── hyphy-common ├── 2.2.7dfsg-1-deb │ └── Dockerfile └── 2.3.14dfsg-1-deb │ └── Dockerfile ├── hyphy-mpi ├── 2.2.7dfsg-1b2-deb │ └── Dockerfile └── 2.3.14dfsg-1-deb │ └── Dockerfile ├── hyphy-pt ├── 2.2.7dfsg-1b2-deb │ └── Dockerfile └── 2.3.14dfsg-1-deb │ └── Dockerfile ├── hyphygui └── 2.2.7dfsg-1b2-deb │ └── Dockerfile ├── i2nca ├── 0.3.0 │ └── Dockerfile └── 0.3.12 │ └── Dockerfile ├── idba ├── 1.1.3-1-deb │ └── Dockerfile └── 1.1.3-3-deb │ └── Dockerfile ├── igor └── 1.3.0dfsg-1-deb │ └── Dockerfile ├── ilastik ├── 1.3.3post3 │ └── Dockerfile ├── 1.4.0 │ ├── Dockerfile │ └── test-cmds.txt └── 1.4.1 │ ├── Dockerfile │ └── test-cmds.txt ├── imagej ├── 1.51idfsg-2-deb │ └── Dockerfile └── 1.52j-1-deb │ └── Dockerfile ├── imagevis3d ├── 3.1.0-5-deb │ └── Dockerfile └── 3.1.0-7b2-deb │ └── Dockerfile ├── imputeme ├── v1.0.4 │ └── Dockerfile ├── v1.0.6 │ └── Dockerfile └── v1.0.7 │ └── Dockerfile ├── indelible ├── 1.03-2b1-deb │ └── Dockerfile └── 1.03-4-deb │ └── Dockerfile ├── infernal ├── 1.1.2-1-deb │ └── Dockerfile └── 1.1.2-2-deb │ └── Dockerfile ├── insighttoolkit4-python ├── 4.10.1-dfsg1-1.1b1-deb │ └── Dockerfile └── 4.12.2-dfsg1-4b1-deb │ └── Dockerfile ├── integron-finder └── 1.5.1 │ └── Dockerfile ├── interproscan └── 5.30-69.0 │ ├── Dockerfile │ └── README.md ├── intervaltree-bio ├── 1.0.1-1-deb-py2 │ └── Dockerfile ├── 1.0.1-1-deb-py3 │ └── Dockerfile ├── 1.0.1-3-deb-py2 │ └── Dockerfile └── 1.0.1-3-deb-py3 │ └── Dockerfile ├── invesalius-bin ├── 3.0.1-1-deb │ └── Dockerfile └── 3.1.99992-3-deb │ └── Dockerfile ├── invesalius ├── 3.0.1-1-deb │ └── Dockerfile └── 3.1.99992-3-deb │ └── Dockerfile ├── ipig ├── 0.0.r5-2-deb │ └── Dockerfile └── 0.0.r5-3-deb │ └── Dockerfile ├── iqtree ├── 1.5.3dfsg-2-deb │ └── Dockerfile └── 1.6.9dfsg-1-deb │ └── Dockerfile ├── isee-galaxy └── 3.13 │ ├── Dockerfile │ └── scripts │ ├── monitor_traffic.sh │ └── run.sh ├── ismrmrd-schema ├── 1.3.3-1-deb │ └── Dockerfile └── 1.4.0-1-deb │ └── Dockerfile ├── ismrmrd-tools ├── 1.3.3-1b1-deb │ └── Dockerfile └── 1.4.0-1-deb │ └── Dockerfile ├── iva ├── 1.0.8ds-1-deb │ └── Dockerfile └── 1.0.9ds-6-deb │ └── Dockerfile ├── jaligner ├── 1.0dfsg-4-deb │ └── Dockerfile └── 1.0dfsg-6-deb │ └── Dockerfile ├── jbrowse └── 1.11.6 │ └── Dockerfile ├── jellyfish ├── 2.2.10-2-deb │ └── Dockerfile ├── 2.2.3 │ └── Dockerfile └── 2.2.6-1b1-deb │ └── Dockerfile ├── jellyfish1 ├── 1.1.11-3bpo91-deb │ └── Dockerfile └── 1.1.11-4-deb │ └── Dockerfile ├── jemboss ├── 6.6.0dfsg-6-deb │ └── Dockerfile └── 6.6.0dfsg-7-deb │ └── Dockerfile ├── jmodeltest ├── 2.1.10dfsg-5-deb │ └── Dockerfile └── 2.1.10dfsg-7-deb │ └── Dockerfile ├── kalign ├── 1-2.0320110620-3-deb │ └── Dockerfile └── 1-2.0320110620-5-deb │ └── Dockerfile ├── kast ├── 1.0.0 │ └── Dockerfile └── 1.0.1 │ └── Dockerfile ├── khmer-common ├── 2.0dfsg-10-deb │ └── Dockerfile └── 2.1.2dfsg-6-deb │ └── Dockerfile ├── khmer ├── 2.0dfsg-10-deb │ └── Dockerfile └── 2.1.2dfsg-6-deb │ └── Dockerfile ├── kineticstools-data ├── 0.6.120161222-1-deb │ └── Dockerfile └── 0.6.1git20180425.27a1878-2-deb │ └── Dockerfile ├── kineticstools ├── 0.6.120161222-1-deb-py2 │ └── Dockerfile ├── 0.6.120161222-1-deb │ └── Dockerfile ├── 0.6.1git20180425.27a1878-2-deb-py2 │ └── Dockerfile └── 0.6.1git20180425.27a1878-2-deb │ └── Dockerfile ├── king-probe ├── 2.13.110909-2-deb │ └── Dockerfile └── 2.16.160404git20180613.a09b012-1-deb │ └── Dockerfile ├── king ├── 2.23.161103dfsg1-1-deb │ └── Dockerfile └── 2.23.161103dfsg1-3-deb │ └── Dockerfile ├── kissplice ├── 2.4.0-p1-1-deb │ └── Dockerfile └── 2.4.0-p1-4-deb │ └── Dockerfile ├── kmc ├── 2.3dfsg-5-deb │ └── Dockerfile └── 2.3dfsg-7-deb │ └── Dockerfile ├── kmer ├── 020150903r2013-3-deb │ └── Dockerfile └── 020150903r2013-6-deb │ └── Dockerfile ├── kraken ├── 0.10.5beta-2b1-deb │ └── Dockerfile └── 1.1-3-deb │ └── Dockerfile ├── krona └── 2.7.1 │ └── Dockerfile ├── lagan ├── 2.0-3-deb │ └── Dockerfile └── 2.0-3bpo91-deb │ └── Dockerfile ├── lamarc └── 2.1.10.1dfsg-3-deb │ └── Dockerfile ├── lambda-align ├── 1.0.1-2-deb │ └── Dockerfile └── 1.0.3-5-deb │ └── Dockerfile ├── lambda-align2 └── 2.0.0-6-deb │ └── Dockerfile ├── last-align ├── 830-1-deb │ └── Dockerfile └── 963-2-deb │ └── Dockerfile ├── leaff ├── 020150903r2013-3-deb │ └── Dockerfile └── 020150903r2013-6-deb │ └── Dockerfile ├── lefse ├── 1.0.8-2-deb │ └── Dockerfile └── 1.020160802-1-deb │ └── Dockerfile ├── logol-bin ├── 1.7.5-1-deb │ └── Dockerfile └── 1.7.9-1-deb │ └── Dockerfile ├── logol ├── 1.7.5-1-deb │ └── Dockerfile └── 1.7.9-1-deb │ └── Dockerfile ├── loki ├── 2.4.7.4-6b1-deb │ └── Dockerfile └── 2.4.7.4-8-deb │ └── Dockerfile ├── ltrsift ├── 1.0.2-7-deb │ └── Dockerfile └── 1.0.2-8-deb │ └── Dockerfile ├── lucy └── 1.20-1-deb │ └── Dockerfile ├── lzstring └── 1.0.4-1-deb-py3 │ └── Dockerfile ├── mace └── 1.2 │ └── Dockerfile ├── macs ├── 2.1.1.20160309-1-deb │ └── Dockerfile └── 2.1.2.1-1-deb │ └── Dockerfile ├── macsyfinder ├── 1.0.2-3-deb │ └── Dockerfile └── 1.0.5-2-deb │ └── Dockerfile ├── maffilter ├── 1.1.0-1dfsg-2b2-deb │ └── Dockerfile └── 1.3.1dfsg-1b1-deb │ └── Dockerfile ├── mafft ├── 7.307-1-deb │ └── Dockerfile ├── 7.394 │ └── Dockerfile └── 7.407-2-deb │ └── Dockerfile ├── magicblast └── 1.3.0 │ └── Dockerfile ├── mapdamage ├── 2.0.6dfsg-2-deb │ └── Dockerfile └── 2.0.9dfsg-1-deb │ └── Dockerfile ├── mapsembler2 ├── 2.2.3dfsg-3b1-deb │ └── Dockerfile └── 2.2.4dfsg-3b1-deb │ └── Dockerfile ├── maq ├── 0.7.1-7-deb │ └── Dockerfile └── 0.7.1-8-deb │ └── Dockerfile ├── maqview ├── 0.2.5-7b1-deb │ └── Dockerfile └── 0.2.5-9-deb │ └── Dockerfile ├── maracluster ├── 1.02.1 │ └── Dockerfile └── 1.04.1 │ └── Dockerfile ├── mash ├── 1.1.1-2-deb │ └── Dockerfile └── 2.1dfsg-2-deb │ └── Dockerfile ├── matplotlib-venn ├── 0.11.5-1-deb-py2 │ └── Dockerfile ├── 0.11.5-1-deb-py3 │ └── Dockerfile ├── 0.11.5-5-deb-py2 │ └── Dockerfile └── 0.11.5-5-deb-py3 │ └── Dockerfile ├── maude ├── 2.7-2b1-deb │ └── Dockerfile └── 2.7-2b2-deb │ └── Dockerfile ├── mauve-aligner ├── 2.4.04734-3-deb │ └── Dockerfile └── 2.4.04736-1-deb │ └── Dockerfile ├── mcl ├── 1-14-137-1b1-deb │ └── Dockerfile └── 1-14-137ds-3-deb │ └── Dockerfile ├── medcon ├── 0.14.1-1b2-deb │ └── Dockerfile └── 0.16.1dfsg-1-deb │ └── Dockerfile ├── megahit └── 1.2.9 │ ├── Dockerfile │ └── env_megahit.yml ├── melting-gui └── 4.3.1dfsg-2-deb │ └── Dockerfile ├── melting ├── 4.3.1dfsg-2b1-deb │ └── Dockerfile └── 5.2.0-1-deb │ └── Dockerfile ├── mencal ├── 3.0-2-deb │ └── Dockerfile └── 3.0-4-deb │ └── Dockerfile ├── meryl ├── 020150903r2013-3-deb │ └── Dockerfile └── 020150903r2013-6-deb │ └── Dockerfile ├── metaphlan2-data ├── 2.6.0ds-2-deb │ └── Dockerfile └── 2.6.0ds-4-deb │ └── Dockerfile ├── metaphlan2 ├── 2.6.0ds-2-deb │ └── Dockerfile └── 2.7.8-1-deb │ └── Dockerfile ├── metastudent-data-2 ├── 1.0.0-2-deb │ └── Dockerfile └── 1.0.0-4-deb │ └── Dockerfile ├── metastudent-data ├── 2.0.1-2-deb │ └── Dockerfile └── 2.0.1-4-deb │ └── Dockerfile ├── metastudent ├── 2.0.1-4-deb │ └── Dockerfile └── 2.0.1-6-deb │ └── Dockerfile ├── mhap ├── 2.1.1dfsg-1-deb │ └── Dockerfile └── 2.1.3dfsg-2-deb │ └── Dockerfile ├── mia-doctools ├── 2.4.3-5-deb │ └── Dockerfile └── 2.4.6-4-deb │ └── Dockerfile ├── mia-tools ├── 2.4.3-5-deb │ └── Dockerfile └── 2.4.6-4-deb │ └── Dockerfile ├── mia-viewit ├── 1.0.4-1b1-deb │ └── Dockerfile └── 1.0.5-2-deb │ └── Dockerfile ├── mia ├── 0.1.9-1-deb-py2 │ └── Dockerfile ├── 0.1.9-1-deb-py3 │ └── Dockerfile ├── 0.1.9-2b1-deb-py2 │ └── Dockerfile └── 0.1.9-2b1-deb-py3 │ └── Dockerfile ├── mialmpick ├── 0.2.13-1-deb │ └── Dockerfile └── 0.2.14-2-deb │ └── Dockerfile ├── micro-sam └── 1.1.1 │ ├── Dockerfile │ └── conda.yml ├── microbegps ├── 1.0.0-2-deb │ └── Dockerfile └── 1.0.0-3-deb │ └── Dockerfile ├── microbiomeutil-data ├── 20101212dfsg1-1-deb │ └── Dockerfile └── 20101212dfsg1-2-deb │ └── Dockerfile ├── microbiomeutil ├── 20101212dfsg1-1-deb │ └── Dockerfile └── 20101212dfsg1-2-deb │ └── Dockerfile ├── minc-tools ├── 2.3.00dfsg-1.1b1-deb │ └── Dockerfile └── 2.3.00dfsg-3b1-deb │ └── Dockerfile ├── mindthegap └── 2.0.1 │ └── Dockerfile ├── minia ├── 1.6906-1b2-deb │ └── Dockerfile └── 1.6906-2-deb │ └── Dockerfile ├── miniasm ├── 0.2dfsg-2b1-deb │ └── Dockerfile └── 0.3dfsg-1-deb │ └── Dockerfile ├── minimac4 └── 1.0.0-2-deb │ └── Dockerfile ├── minimap ├── 0.2-3b1-deb │ └── Dockerfile └── 0.2-4-deb │ └── Dockerfile ├── minimap2 ├── 2.15dfsg-1-deb │ └── Dockerfile └── 2.15dfsg-1bpo91-deb │ └── Dockerfile ├── mipe ├── 1.1-5-deb │ └── Dockerfile └── 1.1-7-deb │ └── Dockerfile ├── mira-assembler ├── 4.9.6-2-deb │ └── Dockerfile └── 4.9.6-4b1-deb │ └── Dockerfile ├── mira-rfam-12s-rrna ├── 4.9.6-2-deb │ └── Dockerfile └── 4.9.6-4-deb │ └── Dockerfile ├── mitohifi ├── 2.2 │ └── Dockerfile └── 3.0.0 │ └── Dockerfile ├── mlv-smile ├── 1.47-4b1-deb │ └── Dockerfile └── 1.47-6-deb │ └── Dockerfile ├── mne ├── 0.13.1dfsg-3-deb-py2 │ └── Dockerfile └── 0.17dfsg-1-deb-py2 │ └── Dockerfile ├── mobyle-programs ├── 5.1.2-1-deb │ └── Dockerfile └── 5.1.2-3-deb │ └── Dockerfile ├── mobyle-tutorials ├── 1.5.0-2-deb │ └── Dockerfile └── 1.5.0-4-deb │ └── Dockerfile ├── mobyle-utils ├── 1.5.5dfsg-2-deb │ └── Dockerfile └── 1.5.5dfsg-6-deb │ └── Dockerfile ├── mobyle ├── 1.5.5dfsg-2-deb │ └── Dockerfile └── 1.5.5dfsg-6-deb │ └── Dockerfile ├── mothur-mpi └── 1.38.1.1-1-deb │ └── Dockerfile ├── mothur ├── 1.38.1.1-1-deb │ └── Dockerfile └── 1.41.21-1-deb │ └── Dockerfile ├── mptp └── 0.2.4-1-deb │ └── Dockerfile ├── mrbayes-mpi ├── 3.2.6dfsg-1b4-deb │ └── Dockerfile └── 3.2.6dfsg-2b1-deb │ └── Dockerfile ├── mrbayes ├── 3.2.6dfsg-1b4-deb │ └── Dockerfile └── 3.2.6dfsg-2b1-deb │ └── Dockerfile ├── mriconvert ├── 1-2.1.0-1-deb │ └── Dockerfile └── 1-2.1.0-3-deb │ └── Dockerfile ├── mrs ├── 6.0.5dfsg-2b2-deb │ └── Dockerfile └── 6.0.5dfsg-7b2-deb │ └── Dockerfile ├── msamanda └── 1.0.0.5242 │ └── Dockerfile ├── msgfp └── 9949 │ └── Dockerfile ├── msisensor2 └── 0.1 │ └── Dockerfile ├── multipletau ├── 0.1.7ds-1-deb-py2 │ └── Dockerfile ├── 0.1.7ds-1-deb-py3 │ └── Dockerfile ├── 0.3.3ds-1-deb-py2 │ └── Dockerfile └── 0.3.3ds-1-deb-py3 │ └── Dockerfile ├── mummer ├── 3.23dfsg-2-deb │ └── Dockerfile └── 3.23dfsg-4-deb │ └── Dockerfile ├── murasaki-common ├── 1.68.6-6-deb │ └── Dockerfile └── 1.68.6-8-deb │ └── Dockerfile ├── murasaki-mpi ├── 1.68.6-6b4-deb │ └── Dockerfile └── 1.68.6-8b1-deb │ └── Dockerfile ├── murasaki ├── 1.68.6-6b4-deb │ └── Dockerfile └── 1.68.6-8b1-deb │ └── Dockerfile ├── muscle ├── 1-3.8.1551-2-deb │ └── Dockerfile └── 1-3.8.31dfsg-2-deb │ └── Dockerfile ├── mustang-testdata ├── 3.2.3-1-deb │ └── Dockerfile └── 3.2.3-3-deb │ └── Dockerfile ├── mustang ├── 3.2.3-1-deb │ └── Dockerfile └── 3.2.3-3-deb │ └── Dockerfile ├── mypy-extensions └── 0.4.1-1-deb-py3 │ └── Dockerfile ├── mypy ├── 0.470-complete-1-deb │ └── Dockerfile ├── 0.670-2-deb-py3 │ └── Dockerfile └── 0.670-2-deb │ └── Dockerfile ├── nanook ├── 1.33dfsg-1-deb │ └── Dockerfile └── 1.33dfsg-1bpo91-deb │ └── Dockerfile ├── nanopolish ├── 0.11.0-2-deb │ └── Dockerfile └── 0.5.0-1b1-deb │ └── Dockerfile ├── nanosv └── 1.2.4 │ └── Dockerfile ├── nast-ier ├── 20101212dfsg1-1b1-deb │ └── Dockerfile └── 20101212dfsg1-2-deb │ └── Dockerfile ├── ncbi-blast-plus-legacy ├── 2.6.0-1-deb │ └── Dockerfile └── 2.8.1-1-deb │ └── Dockerfile ├── ncbi-blast-plus ├── 2.6.0-1-deb │ └── Dockerfile └── 2.8.1-1-deb │ └── Dockerfile ├── ncbi-data ├── 6.1.20170106-2-deb │ └── Dockerfile └── 6.1.20170106-6-deb │ └── Dockerfile ├── ncbi-datasets-cli ├── 14.2.2 │ └── Dockerfile ├── 15.12.0 │ └── Dockerfile └── 16.22.1 │ └── Dockerfile ├── ncbi-entrez-direct ├── 10.9.20190219ds-1b10-deb │ └── Dockerfile └── 6.10.20170123ds-1-deb │ └── Dockerfile ├── ncbi-epcr ├── 2.3.12-1-4-deb │ └── Dockerfile └── 2.3.12-1-7-deb │ └── Dockerfile ├── ncbi-rrna-data ├── 6.1.20170106-2-deb │ └── Dockerfile └── 6.1.20170106-6-deb │ └── Dockerfile ├── ncbi-seg ├── 0.0.20000620-3b1-deb │ └── Dockerfile └── 0.0.20000620-5-deb │ └── Dockerfile ├── ncbi-tools-bin ├── 6.1.20170106-2-deb │ └── Dockerfile └── 6.1.20170106-6-deb │ └── Dockerfile ├── ncbi-tools-x11 ├── 6.1.20170106-2-deb │ └── Dockerfile └── 6.1.20170106-6-deb │ └── Dockerfile ├── ncl-tools ├── 2.1.18dfsg-2b1-deb │ └── Dockerfile └── 2.1.21git20180827.c71b264-2-deb │ └── Dockerfile ├── ncoils ├── 2002-4b1-deb │ └── Dockerfile └── 2002-7-deb │ └── Dockerfile ├── neobio ├── 0.0.20030929-2-deb │ └── Dockerfile └── 0.0.20030929-4-deb │ └── Dockerfile ├── ngs ├── 1.3.0-2-deb-py2 │ └── Dockerfile ├── 1.3.0-2-deb-py3 │ └── Dockerfile ├── 2.9.3-1-deb-py2 │ └── Dockerfile └── 2.9.3-1-deb-py3 │ └── Dockerfile ├── njplot ├── 2.4-7-deb │ └── Dockerfile └── 2.4-8-deb │ └── Dockerfile ├── norsnet ├── 1.0.17-2-deb │ └── Dockerfile └── 1.0.17-4-deb │ └── Dockerfile ├── norsp ├── 1.0.6-2-deb │ └── Dockerfile └── 1.0.6-4-deb │ └── Dockerfile ├── novor └── 1b │ └── Dockerfile ├── nutsqlite ├── 1.9.9.3-2-deb │ └── Dockerfile └── 2.0.6-1-deb │ └── Dockerfile ├── obitools └── 1.2.12dfsg-2-deb │ └── Dockerfile ├── octave-bart ├── 0.4.00-1-deb │ └── Dockerfile └── 0.4.04-2-deb │ └── Dockerfile ├── odil ├── 0.10.0-3-deb-py2 │ └── Dockerfile ├── 0.10.0-3-deb-py3 │ └── Dockerfile ├── 0.10.0-3-deb │ └── Dockerfile ├── 0.7.3-1-deb-py2 │ └── Dockerfile └── 0.7.3-1-deb │ └── Dockerfile ├── oncocnv └── v7.0 │ └── Dockerfile ├── openbugs └── 3.2.3 │ └── Dockerfile ├── opencfu ├── 3.9.0-2-deb │ └── Dockerfile └── 3.9.0-3-deb │ └── Dockerfile ├── openmolar └── 1.0.15-gd81f9e5-1-deb │ └── Dockerfile ├── openms ├── 1.11.1-3 │ └── Dockerfile ├── 2.0.0 │ └── Dockerfile └── 2.2.0 │ └── Dockerfile ├── openslide-tools ├── 3.4.1dfsg-2-deb │ └── Dockerfile └── 3.4.1dfsg-4-deb │ └── Dockerfile ├── openslide ├── 1.1.1-2-deb-py2 │ └── Dockerfile ├── 1.1.1-2-deb-py3 │ └── Dockerfile ├── 1.1.1-4-deb-py2 │ └── Dockerfile └── 1.1.1-4-deb-py3 │ └── Dockerfile ├── orthanc-dev ├── 1.2.0dfsg-1-deb │ └── Dockerfile └── 1.5.6dfsg-1-deb │ └── Dockerfile ├── orthanc-dicomweb ├── 0.3dfsg-1b2-deb │ └── Dockerfile └── 0.6dfsg-1-deb │ └── Dockerfile ├── orthanc-imagej ├── 1.1dfsg-1-deb │ └── Dockerfile └── 1.2dfsg-1-deb │ └── Dockerfile ├── orthanc-mysql └── 2.0-2-deb │ └── Dockerfile ├── orthanc-postgresql ├── 2.0-3b1-deb │ └── Dockerfile └── 3.2-1-deb │ └── Dockerfile ├── orthanc-webviewer ├── 2.2-1b2-deb │ └── Dockerfile └── 2.5-1-deb │ └── Dockerfile ├── orthanc-wsi └── 0.6-2-deb │ └── Dockerfile ├── orthanc ├── 1.2.0dfsg-1-deb │ └── Dockerfile └── 1.5.6dfsg-1-deb │ └── Dockerfile ├── otf-symbols-circos └── 0.69.4dfsg-1-deb │ └── Dockerfile ├── pal2nal └── 14.1-2-deb │ └── Dockerfile ├── paleomix └── 1.2.13.3-1-deb │ └── Dockerfile ├── paml └── 4.9hdfsg-1-deb │ └── Dockerfile ├── pandas └── 1.5.1 │ └── Dockerfile ├── paraclu ├── 9-1b2-deb │ └── Dockerfile └── 9-2-deb │ └── Dockerfile ├── parafly ├── 0.0.2013.01.21-3b1-deb │ └── Dockerfile └── 0.0.2013.01.21-4-deb │ └── Dockerfile ├── parsinsert-testdata └── 1.04-4-deb │ └── Dockerfile ├── parsinsert ├── 1.04-2-deb │ └── Dockerfile └── 1.04-4-deb │ └── Dockerfile ├── parsnp ├── 1.2dfsg-3-deb │ └── Dockerfile └── 1.2dfsg-5-deb │ └── Dockerfile ├── partitionfinder2 └── 2.1.1 │ └── Dockerfile ├── patchwork ├── 0.1.2 │ └── Dockerfile ├── 0.5.0 │ └── Dockerfile └── 0.5.2 │ └── Dockerfile ├── patman └── 1.2.2dfsg-5-deb │ └── Dockerfile ├── pbalign ├── 0.3.0-1-deb-py2 │ └── Dockerfile ├── 0.3.0-1-deb │ └── Dockerfile ├── 0.3.2-1-deb-py2 │ └── Dockerfile └── 0.3.2-1-deb │ └── Dockerfile ├── pbbamtools ├── 0.19.0dfsg-4-deb │ └── Dockerfile └── 0.7.4ds-1-deb │ └── Dockerfile ├── pbbanana ├── 15.8.24dfsg-2-deb-py2 │ └── Dockerfile └── 15.8.24dfsg-3-deb-py2 │ └── Dockerfile ├── pbbarcode ├── 0.8.0-4-deb │ └── Dockerfile └── 0.8.0-5-deb │ └── Dockerfile ├── pbcommand ├── 0.5.3-1-deb-py2 │ └── Dockerfile └── 1.1.1-1-deb-py2 │ └── Dockerfile ├── pbconsensuscore ├── 1.0.2-2-deb-py2 │ └── Dockerfile ├── 1.0.2-2-deb-py3 │ └── Dockerfile ├── 1.1.1dfsg-1-deb-py2 │ └── Dockerfile └── 1.1.1dfsg-1-deb-py3 │ └── Dockerfile ├── pbcore ├── 1.2.11dfsg-1-deb-py2 │ └── Dockerfile └── 1.6.5dfsg-1-deb-py2 │ └── Dockerfile ├── pbdagcon ├── 0.320161121ds-1-deb │ └── Dockerfile └── 0.3git20161121.0000000ds-1.1-deb │ └── Dockerfile ├── pbgenomicconsensus ├── 2.1.0-1-deb-py2 │ └── Dockerfile ├── 2.1.0-1-deb │ └── Dockerfile ├── 2.3.2-5-deb-py2 │ └── Dockerfile └── 2.3.2-5-deb │ └── Dockerfile ├── pbh5tools ├── 0.8.0dfsg-5-deb-py2 │ └── Dockerfile ├── 0.8.0dfsg-5-deb │ └── Dockerfile ├── 0.8.0git20170929.58d54ffdfsg-1-deb-py2 │ └── Dockerfile └── 0.8.0git20170929.58d54ffdfsg-1-deb │ └── Dockerfile ├── pbhoney ├── 15.8.24dfsg-2-deb │ └── Dockerfile └── 15.8.24dfsg-3-deb │ └── Dockerfile ├── pbjelly ├── 15.8.24dfsg-2-deb │ └── Dockerfile └── 15.8.24dfsg-3-deb │ └── Dockerfile ├── pbsim ├── 1.0.3-2-deb │ └── Dockerfile └── 1.0.3git20180330.e014b1ddfsg-1-deb │ └── Dockerfile ├── pbsuite-utils ├── 15.8.24dfsg-2-deb-py2 │ └── Dockerfile └── 15.8.24dfsg-3-deb-py2 │ └── Dockerfile ├── pbsuite ├── 15.8.24dfsg-2-deb │ └── Dockerfile └── 15.8.24dfsg-3-deb │ └── Dockerfile ├── pcalendar ├── 3.4.1-1-deb │ └── Dockerfile └── 3.4.1-3-deb │ └── Dockerfile ├── pdb2pqr ├── 2.1.1dfsg-2-deb │ └── Dockerfile └── 2.1.1dfsg-5-deb │ └── Dockerfile ├── pepnovo └── 20120423 │ └── Dockerfile ├── peptideprophet └── 201510131012 │ └── Dockerfile ├── peptideshaker ├── 1.10.3 │ └── Dockerfile ├── 1.16.16 │ └── Dockerfile └── 1.16.17 │ └── Dockerfile ├── peptimapper └── 2.0.0 │ └── Dockerfile ├── percolator └── 3.0 │ └── Dockerfile ├── perlprimer ├── 1.2.3-1-deb │ └── Dockerfile └── 1.2.4-1-deb │ └── Dockerfile ├── perm ├── 0.4.0-2-deb │ └── Dockerfile └── 0.4.0-4-deb │ └── Dockerfile ├── pftools ├── 3dfsg-3-deb │ └── Dockerfile └── 3dfsg-3bpo91-deb │ └── Dockerfile ├── phast └── 1.4dfsg-1-deb │ └── Dockerfile ├── philosopher └── 2.0.0 │ └── Dockerfile ├── phipack ├── 0.0.20160614-2-deb │ └── Dockerfile └── 0.0.20160614-3-deb │ └── Dockerfile ├── phybin ├── 0.3-1b1-deb │ └── Dockerfile └── 0.3-3-deb │ └── Dockerfile ├── phylip ├── 1-3.696dfsg-5-deb │ └── Dockerfile └── 1-3.697dfsg-1-deb │ └── Dockerfile ├── phylocsf └── latest │ └── Dockerfile ├── phylotools └── 0.2.4 │ ├── Dockerfile │ └── install.R ├── phyml ├── 3-3.2.0dfsg-7b1-deb │ └── Dockerfile └── 3-3.3.20180621-2-deb │ └── Dockerfile ├── physamp ├── 0.2.0-1b1-deb │ └── Dockerfile └── 1.1.0-1-deb │ └── Dockerfile ├── phyutility ├── 2.7.3-1-deb │ └── Dockerfile └── 2.7.3dfsg-2-deb │ └── Dockerfile ├── phyx └── 0.999ds-1-deb │ └── Dockerfile ├── pia-web-server └── 1.1.0-SNAPSHOT │ └── Dockerfile ├── pia ├── 1.1.0-SNAPSHOT │ ├── Dockerfile │ └── runpia.sh ├── 1.3.0 │ ├── Dockerfile │ └── runpia.sh └── 1.3.8 │ ├── Dockerfile │ └── runpia.sh ├── picard-tools ├── 2.18.25dfsg-2-deb │ └── Dockerfile └── 2.8.1dfsg-1-deb │ └── Dockerfile ├── picard ├── 1.139 │ └── Dockerfile ├── 1.141 │ └── Dockerfile └── 2.3.0 │ └── Dockerfile ├── piler ├── 020140707-1b1-deb │ └── Dockerfile └── 020140707-2-deb │ └── Dockerfile ├── pilon ├── 1.22dfsg-1bpo91-deb │ └── Dockerfile ├── 1.22dfsg-2bpo92-deb │ └── Dockerfile └── 1.23dfsg-1-deb │ └── Dockerfile ├── pipdeptree └── 0.13.2-1-deb-py3 │ └── Dockerfile ├── pirs-profiles ├── 2.0.2dfsg-5.1-deb │ └── Dockerfile └── 2.0.2dfsg-8-deb │ └── Dockerfile ├── pirs ├── 2.0.2dfsg-5.1b1-deb │ └── Dockerfile └── 2.0.2dfsg-8-deb │ └── Dockerfile ├── pixelmed-apps ├── 20150917-1-deb │ └── Dockerfile └── 20150917git20151209.36f3174dfsg-1-deb │ └── Dockerfile ├── pixelmed-webstart-apps ├── 20150917-1-deb │ └── Dockerfile └── 20150917git20151209.36f3174dfsg-1-deb │ └── Dockerfile ├── pixelmed-www ├── 20150917-1-deb │ └── Dockerfile └── 20150917git20151209.36f3174dfsg-1-deb │ └── Dockerfile ├── placnet ├── 1.03-2-deb │ └── Dockerfile └── 1.03-3-deb │ └── Dockerfile ├── plasmidomics ├── 0.2.0-5-deb │ └── Dockerfile └── 0.2.0-7-deb │ └── Dockerfile ├── plasmidseeker └── 1.0dfsg-1-deb │ └── Dockerfile ├── plast-example ├── 2.3.1dfsg-4-deb │ └── Dockerfile └── 2.3.2dfsg-1-deb │ └── Dockerfile ├── plast ├── 2.3.1dfsg-4-deb │ └── Dockerfile └── 2.3.2dfsg-1-deb │ └── Dockerfile ├── plastimatch ├── 1.6.5dfsg.1-1-deb │ └── Dockerfile └── 1.7.4dfsg.1-2-deb │ └── Dockerfile ├── plink ├── 1.07-7-deb │ └── Dockerfile └── 1.07dfsg-2-deb │ └── Dockerfile ├── plink1.9 ├── 1.90b3.45-170113-1-deb │ └── Dockerfile └── 1.90b6.6-181012-1-deb │ └── Dockerfile ├── plip ├── 1.3.3dfsg-1-deb │ └── Dockerfile └── 1.4.3bdfsg-2-deb │ └── Dockerfile ├── poa ├── 2.020060928-4b1-deb │ └── Dockerfile └── 2.020060928-7-deb │ └── Dockerfile ├── pondus └── 0.8.0-4-deb │ └── Dockerfile ├── populations └── 1.2.33svn0120106dfsg-2-deb │ └── Dockerfile ├── porechop └── 0.2.4dfsg-1-deb │ └── Dockerfile ├── poretools-data ├── 0.6.0dfsg-2-deb │ └── Dockerfile └── 0.6.0dfsg-3-deb │ └── Dockerfile ├── poretools ├── 0.6.0dfsg-2-deb │ └── Dockerfile └── 0.6.0dfsg-3-deb │ └── Dockerfile ├── pp-popularity-contest ├── 1.0.6-2b4-deb │ └── Dockerfile └── 1.0.6-4b1-deb │ └── Dockerfile ├── praat ├── 6.0.23-1-deb │ └── Dockerfile └── 6.0.48-1-deb │ └── Dockerfile ├── prank ├── 0.0.150803-2-deb │ └── Dockerfile └── 0.0.170427dfsg-2-deb │ └── Dockerfile ├── predictnls ├── 1.0.20-3-deb │ └── Dockerfile └── 1.0.20-5-deb │ └── Dockerfile ├── predictprotein ├── 1.1.07-2-deb │ └── Dockerfile └── 1.1.08-1-deb │ └── Dockerfile ├── prime-phylo ├── 1.0.11-4b3-deb │ └── Dockerfile └── 1.0.11-7b1-deb │ └── Dockerfile ├── primer3 ├── 2.3.7-3-deb │ └── Dockerfile └── 2.4.0-2-deb │ └── Dockerfile ├── proalign ├── 0.603-2-deb │ └── Dockerfile └── 0.603-4-deb │ └── Dockerfile ├── probabel ├── 0.4.5-3b1-deb │ └── Dockerfile └── 0.5.0dfsg-3-deb │ └── Dockerfile ├── probalign ├── 1.4-5-deb │ └── Dockerfile └── 1.4-8-deb │ └── Dockerfile ├── probcons-extra ├── 1.12-11-deb │ └── Dockerfile └── 1.12-12-deb │ └── Dockerfile ├── probcons ├── 1.12-11-deb │ └── Dockerfile └── 1.12-12-deb │ └── Dockerfile ├── proda ├── 1.0-10-deb │ └── Dockerfile └── 1.0-12-deb │ └── Dockerfile ├── prodigal ├── 1-2.6.3-1b1-deb │ └── Dockerfile └── 1-2.6.3-4-deb │ └── Dockerfile ├── profbval ├── 1.0.22-4-deb │ └── Dockerfile └── 1.0.22-6-deb │ └── Dockerfile ├── profisis ├── 1.0.11-3-deb │ └── Dockerfile └── 1.0.11-5-deb │ └── Dockerfile ├── profnet-bval ├── 1.0.22-4-deb │ └── Dockerfile └── 1.0.22-6-deb │ └── Dockerfile ├── profnet-chop ├── 1.0.22-4-deb │ └── Dockerfile └── 1.0.22-6-deb │ └── Dockerfile ├── profnet-con ├── 1.0.22-4-deb │ └── Dockerfile └── 1.0.22-6-deb │ └── Dockerfile ├── profnet-isis ├── 1.0.22-4-deb │ └── Dockerfile └── 1.0.22-6-deb │ └── Dockerfile ├── profnet-md ├── 1.0.22-4-deb │ └── Dockerfile └── 1.0.22-6-deb │ └── Dockerfile ├── profnet-norsnet ├── 1.0.22-4-deb │ └── Dockerfile └── 1.0.22-6-deb │ └── Dockerfile ├── profnet-prof ├── 1.0.22-4-deb │ └── Dockerfile └── 1.0.22-6-deb │ └── Dockerfile ├── profnet-snapfun ├── 1.0.22-4-deb │ └── Dockerfile └── 1.0.22-6-deb │ └── Dockerfile ├── profphd-net ├── 1.0.22-4-deb │ └── Dockerfile └── 1.0.22-6-deb │ └── Dockerfile ├── profphd-utils ├── 1.0.10-3b1-deb │ └── Dockerfile └── 1.0.10-5-deb │ └── Dockerfile ├── profphd ├── 1.0.42-1-deb │ └── Dockerfile └── 1.0.42-3-deb │ └── Dockerfile ├── proftmb ├── 1.1.12-6b1-deb │ └── Dockerfile └── 1.1.12-8-deb │ └── Dockerfile ├── progressive-cactus └── 0.1 │ └── Dockerfile ├── progressivemauve ├── 1.2.04713-2b2-deb │ └── Dockerfile └── 1.2.04713dfsg-4-deb │ └── Dockerfile ├── proteinortho ├── 5.15dfsg-1-deb │ └── Dockerfile └── 5.16.bdfsg-1-deb │ └── Dockerfile ├── proteinprophet └── 201510131012 │ └── Dockerfile ├── proteowizard └── 3_0_9740 │ └── Dockerfile ├── prottest ├── 3.4.2dfsg-2-deb │ └── Dockerfile └── 3.4.2dfsg-3-deb │ └── Dockerfile ├── pscan-chip-data └── 1.1-2-deb │ └── Dockerfile ├── pscan-chip └── 1.1-2-deb │ └── Dockerfile ├── pscan-tfbs └── 1.2.2-3-deb │ └── Dockerfile ├── psortb ├── 3.0.6dfsg-1b1-deb │ └── Dockerfile └── 3.0.6dfsg-1bpo91-deb │ └── Dockerfile ├── pvrg-jpeg ├── 1.2.1dfsg1-4b1-deb │ └── Dockerfile └── 1.2.1dfsg1-6-deb │ └── Dockerfile ├── pybedtools-bin └── 0.8.0-1-deb │ └── Dockerfile ├── pybedtools └── 0.8.0-1-deb-py3 │ └── Dockerfile ├── pycorrfit ├── 0.9.9dfsg-2-deb │ └── Dockerfile └── 1.1.5dfsg-1-deb │ └── Dockerfile ├── pyfaidx ├── 0.4.8.1-1-deb-py2 │ └── Dockerfile ├── 0.4.8.1-1-deb-py3 │ └── Dockerfile ├── 0.5.5.2-1-deb-py2 │ └── Dockerfile └── 0.5.5.2-1-deb-py3 │ └── Dockerfile ├── pyflow └── 1.1.20-1-deb-py2 │ └── Dockerfile ├── pymol-jupiter └── 1.0.0 │ ├── Dockerfile │ ├── ipymol │ └── iPyMol_example.ipynb │ └── jupyter-minimal-notebook │ ├── jupyter_notebook_config.py │ ├── start-notebook.sh │ └── start-singleuser.sh ├── pymummer ├── 0.10.1-1-deb-py3 │ └── Dockerfile └── 0.10.3-2-deb-py3 │ └── Dockerfile ├── pynast ├── 1.2.2-2-deb │ └── Dockerfile └── 1.2.2-4-deb │ └── Dockerfile ├── pyqi ├── 0.3.2dfsg-2-deb │ └── Dockerfile └── 0.3.2dfsg-3-deb │ └── Dockerfile ├── pysam-tests ├── 0.10.0ds-2-deb-py2 │ └── Dockerfile └── 0.15.2ds-2-deb-py2 │ └── Dockerfile ├── pysam ├── 0.10.0ds-2-deb-py2 │ └── Dockerfile ├── 0.10.0ds-2-deb-py3 │ └── Dockerfile ├── 0.15.2ds-2-deb-py2 │ └── Dockerfile └── 0.15.2ds-2-deb-py3 │ └── Dockerfile ├── pyscanfcs ├── 0.2.3-3-deb │ └── Dockerfile └── 0.3.2ds-2-deb │ └── Dockerfile ├── pyvcf ├── 0.6.8-1-deb-py2 │ └── Dockerfile ├── 0.6.8-1-deb-py3 │ └── Dockerfile ├── 0.6.8-1-deb │ └── Dockerfile ├── 0.6.8git20170215.476169c-1-deb-py2 │ └── Dockerfile ├── 0.6.8git20170215.476169c-1-deb-py3 │ └── Dockerfile └── 0.6.8git20170215.476169c-1-deb │ └── Dockerfile ├── qcli ├── 0.1.1-1-deb-py2 │ └── Dockerfile └── 0.1.1-3-deb-py2 │ └── Dockerfile ├── qcumber └── 1.0.14dfsg-1-deb │ └── Dockerfile ├── qrisk2 ├── 0.1.20150729-2-deb │ └── Dockerfile └── 0.1.20150729-4-deb │ └── Dockerfile ├── qsopt-ex ├── 2.5.10.3-1b1-deb │ └── Dockerfile └── 2.5.10.3-2-deb │ └── Dockerfile ├── qtltools-example ├── 1.1dfsg-1-deb │ └── Dockerfile └── 1.1dfsg-3-deb │ └── Dockerfile ├── qtltools ├── 1.1dfsg-1-deb │ └── Dockerfile └── 1.1dfsg-3b1-deb │ └── Dockerfile ├── quorum └── 1.1.1-2-deb │ └── Dockerfile ├── r-metamix └── 0.3 │ └── Dockerfile ├── r-other-mott-happy.hbrem └── 2.4-1-deb │ └── Dockerfile ├── racon ├── 1.3.1-1bpo91-deb │ └── Dockerfile └── 1.3.2-1b1-deb │ └── Dockerfile ├── radiant ├── 2.7dfsg-2-deb │ └── Dockerfile └── 2.7dfsg-2bpo91-deb │ └── Dockerfile ├── rambo-k ├── 1.21dfsg-1-deb │ └── Dockerfile └── 1.21dfsg-2-deb │ └── Dockerfile ├── rampler ├── 1.1.0-1-deb │ └── Dockerfile └── 1.1.0-1bpo91-deb │ └── Dockerfile ├── rapmap-dev └── 0.12.0dfsg-3-deb │ └── Dockerfile ├── rapmap-example-data └── 0.12.0dfsg-3-deb │ └── Dockerfile ├── rapmap ├── 0.12.0dfsg-3b1-deb │ └── Dockerfile └── 0.4.0dfsg-2-deb │ └── Dockerfile ├── raremetalworker └── 4.13.7 │ └── Dockerfile ├── raster3d ├── 3.0-3-2b1-deb │ └── Dockerfile └── 3.0-3-5-deb │ └── Dockerfile ├── rate4site ├── 3.0.0-4b1-deb │ └── Dockerfile └── 3.0.0-6-deb │ └── Dockerfile ├── raxml ├── 8.2.12dfsg-1-deb │ └── Dockerfile └── 8.2.9dfsg-1b1-deb │ └── Dockerfile ├── ray-extra ├── 2.3.1-4-deb │ └── Dockerfile └── 2.3.1-6-deb │ └── Dockerfile ├── ray ├── 2.3.1-4b1-deb │ └── Dockerfile └── 2.3.1-6-deb │ └── Dockerfile ├── rdflib-jsonld ├── 0.4.0-2-deb-py2 │ └── Dockerfile ├── 0.4.0-2-deb-py3 │ └── Dockerfile ├── 0.4.0-4-deb-py2 │ └── Dockerfile └── 0.4.0-4-deb-py3 │ └── Dockerfile ├── rdp-alignment ├── 1.2.0-2-deb │ └── Dockerfile └── 1.2.0-5-deb │ └── Dockerfile ├── rdp-classifier ├── 2.10.2-1-deb │ └── Dockerfile └── 2.10.2-4-deb │ └── Dockerfile ├── rdp-readseq ├── 2.0.2-2-deb │ └── Dockerfile └── 2.0.2-6-deb │ └── Dockerfile ├── readseq ├── 1-11b1-deb │ └── Dockerfile └── 1-13-deb │ └── Dockerfile ├── reapr ├── 1.0.18dfsg-3-deb │ └── Dockerfile └── 1.0.18dfsg-4-deb │ └── Dockerfile ├── relion-bin-plusgui ├── 1.4dfsg-2b2-deb │ └── Dockerfile └── 1.4dfsg-4-deb │ └── Dockerfile ├── relion-bin-plusmpi-plusgui ├── 1.4dfsg-2b2-deb │ └── Dockerfile └── 1.4dfsg-4-deb │ └── Dockerfile ├── relion-bin-plusmpi ├── 1.4dfsg-2b2-deb │ └── Dockerfile └── 1.4dfsg-4-deb │ └── Dockerfile ├── relion-bin ├── 1.4dfsg-2b2-deb │ └── Dockerfile └── 1.4dfsg-4-deb │ └── Dockerfile ├── relion-binplusmpi └── 1.4dfsg-2b2-deb │ └── Dockerfile ├── repeatmasker-recon ├── 1.08-3b1-deb │ └── Dockerfile └── 1.08-4-deb │ └── Dockerfile ├── reprof ├── 1.0.1-4-deb │ └── Dockerfile └── 1.0.1-6-deb │ └── Dockerfile ├── rna-star ├── 2.5.2bdfsg-1-deb │ └── Dockerfile └── 2.7.0adfsg-1-deb │ └── Dockerfile ├── rnahybrid ├── 2.1.2-1b1-deb │ └── Dockerfile └── 2.1.2-5-deb │ └── Dockerfile ├── roary ├── 3.12.0dfsg-2-deb │ └── Dockerfile └── 3.8.0dfsg-1-deb │ └── Dockerfile ├── roguenarok └── 1.0-3-deb │ └── Dockerfile ├── rpg └── 1.1.0 │ └── Dockerfile ├── rsat ├── 20230602 │ └── Dockerfile ├── 20230825 │ └── Dockerfile ├── 20230828 │ └── Dockerfile ├── 20240507 │ └── Dockerfile ├── 20240828 │ └── Dockerfile └── 2025-03-26 │ └── Dockerfile ├── rsem ├── 1.2.31dfsg-1-deb │ └── Dockerfile └── 1.3.1dfsg-1-deb │ └── Dockerfile ├── rstudio-proteomics └── 1.0.0 │ ├── Dockerfile │ ├── installFromBiocViews.R │ └── startx.sh ├── rtax ├── 0.984-5-deb │ └── Dockerfile └── 0.984-6-deb │ └── Dockerfile ├── ruby-rgfa ├── 1.3.1-1-deb │ └── Dockerfile └── 1.3.1dfsg-1-deb │ └── Dockerfile ├── ruffus ├── 2.6.3dfsg-4-deb-py2 │ └── Dockerfile ├── 2.6.3dfsg-4-deb-py3 │ └── Dockerfile ├── 2.8.1-4-deb-py2 │ └── Dockerfile └── 2.8.1-4-deb-py3 │ └── Dockerfile ├── runcircos-gui ├── 0.0git20180828.97703b9-1-deb │ └── Dockerfile └── 0.0git20180828.97703b9-1bpo91-deb │ └── Dockerfile ├── saint ├── 2.5.0dfsg-2b1-deb │ └── Dockerfile └── 2.5.0dfsg-3-deb │ └── Dockerfile ├── saintq └── 0.0.2 │ ├── Dockerfile │ ├── fragment_intensity_analysis │ ├── MSPLIT_frag_level.tsv │ ├── param_MSPLIT_frag_level │ └── scores_list__MSPLIT_frag_level.tsv__.tsv │ ├── peptide_intensity_analysis │ ├── MSPLIT_pep_level.tsv │ ├── param_MSPLIT_pep_level │ └── scores_list__MSPLIT_pep_level.tsv__.tsv │ └── protein_intensity_analysis │ ├── MSPLIT_prot_level.tsv │ ├── param_MSPLIT_prot_level │ └── scores_list__MSPLIT_prot_level.tsv__.tsv ├── salmid ├── 0.1.23-1-deb │ └── Dockerfile └── 0.1.23-1bpo91-deb │ └── Dockerfile ├── salmon ├── 0.12.0ds1-1b1-deb │ └── Dockerfile └── 0.7.2ds1-2b1-deb │ └── Dockerfile ├── samblaster └── 0.1.24-2-deb │ └── Dockerfile ├── samtools-test ├── 1.3.1-3-deb │ └── Dockerfile └── 1.9-4-deb │ └── Dockerfile ├── samtools ├── 1.2 │ └── Dockerfile ├── 1.3.1 │ └── Dockerfile ├── 1.3 │ └── Dockerfile ├── 1.7.0 │ └── Dockerfile └── 1.9-4-deb │ └── Dockerfile ├── sbml5 └── 5.17.2dfsg-3-deb-py3 │ └── Dockerfile ├── sbmltoolbox ├── 4.1.0-3-deb │ └── Dockerfile └── 4.1.0-4-deb │ └── Dockerfile ├── schema-salad ├── 2.2.20170111180227-1-deb-py2 │ └── Dockerfile └── 3.0.20181206233650-2-deb-py3 │ └── Dockerfile ├── scoary ├── 1.6.16-1-deb │ └── Dockerfile └── 1.6.16-1bpo91-deb │ └── Dockerfile ├── screed ├── 0.9-2-deb-py2 │ └── Dockerfile ├── 0.9-2-deb-py3 │ └── Dockerfile └── 1.0-3-deb-py3 │ └── Dockerfile ├── scrm ├── 1.7.2-1b1-deb │ └── Dockerfile └── 1.7.3-1-deb │ └── Dockerfile ├── scythe ├── 0.994-4-deb │ └── Dockerfile └── 0.994git20141017.20d3cff-1-deb │ └── Dockerfile ├── seaborn └── 0.12.2 │ └── Dockerfile ├── searchgui ├── 2.6.0 │ └── Dockerfile └── 2.8.6 │ └── Dockerfile ├── seaview ├── 1-4.6.1.2-2-deb │ └── Dockerfile └── 1-4.7-1-deb │ └── Dockerfile ├── seer ├── 1.1.2-3-deb │ └── Dockerfile └── 1.1.4-2b2-deb │ └── Dockerfile ├── segemehl └── 0.3.4-1-deb │ └── Dockerfile ├── seq_crumbs └── 0.1.9 │ └── Dockerfile ├── seqan-apps ├── 2.3.1dfsg-4-deb │ └── Dockerfile └── 2.4.0dfsg-11-deb │ └── Dockerfile ├── seqan-dev ├── 1.4.2dfsg-2-deb │ └── Dockerfile └── 1.4.2dfsg-3-deb │ └── Dockerfile ├── seqmagick └── 0.7.0-1-deb │ └── Dockerfile ├── seqprep-data ├── 1.3.2-1-deb │ └── Dockerfile └── 1.3.2-3-deb │ └── Dockerfile ├── seqprep ├── 1.3.2-1-deb │ └── Dockerfile └── 1.3.2-3-deb │ └── Dockerfile ├── seqsero ├── 1.0-2bpo91-deb │ └── Dockerfile └── 1.0.1dfsg-1-deb │ └── Dockerfile ├── seqtk ├── 1.2-1-deb │ └── Dockerfile └── 1.3-1-deb │ └── Dockerfile ├── sga ├── 0.10.13 │ └── Dockerfile ├── 0.10.15-2-deb │ └── Dockerfile └── 0.10.15-4-deb │ └── Dockerfile ├── shotmap └── 1.0.0 │ ├── Dockerfile │ └── README.md ├── sibsim4 ├── 0.20-2b1-deb │ └── Dockerfile └── 0.20-4-deb │ └── Dockerfile ├── sickle ├── 1.33-1b1-deb │ └── Dockerfile └── 1.33git20150314.f3d6ae3-1-deb │ └── Dockerfile ├── sigma-align ├── 1.1.3-4b1-deb │ └── Dockerfile └── 1.1.3-6-deb │ └── Dockerfile ├── sim4 ├── 0.0.20121010-4-deb │ └── Dockerfile └── 0.0.20121010-5-deb │ └── Dockerfile ├── sim4db ├── 020150903r2013-3-deb │ └── Dockerfile └── 020150903r2013-6-deb │ └── Dockerfile ├── simpleitk └── 1.0.1-3-deb-py3 │ └── Dockerfile ├── sitplus-data └── 1.0.3-5.1-deb │ └── Dockerfile ├── sitplus └── 1.0.3-5.1-deb │ └── Dockerfile ├── skbio └── 0.5.1-2-deb-py3 │ └── Dockerfile ├── sleepyhead ├── 1.0.0-beta-2dfsg-2b1-deb │ └── Dockerfile └── 1.0.0-beta-2dfsg-6-deb │ └── Dockerfile ├── smalr └── 1.1dfsg-2-deb │ └── Dockerfile ├── smalt ├── 0.7.6-6-deb │ └── Dockerfile └── 0.7.6-8-deb │ └── Dockerfile ├── smithwaterman ├── 0.020160702-1b1-deb │ └── Dockerfile └── 0.0git20160702.2610e25-7-deb │ └── Dockerfile ├── smrtanalysis-dev └── 020161126-deb │ └── Dockerfile ├── smrtanalysis └── 020161126-deb │ └── Dockerfile ├── snakemake ├── 3.10.0-1-deb │ └── Dockerfile └── 5.4.0-1-deb │ └── Dockerfile ├── snap-aligner ├── 1.0beta.18dfsg-1-deb │ └── Dockerfile └── 1.0beta.18dfsg-3-deb │ └── Dockerfile ├── snap ├── 2013-11-29-6-deb │ └── Dockerfile └── 2013-11-29-9-deb │ └── Dockerfile ├── sniffles ├── 1.0.11ds-1-deb │ └── Dockerfile └── 1.0.2ds-1-deb │ └── Dockerfile ├── snp-sites ├── 2.3.2-1-deb │ └── Dockerfile └── 2.4.1-1-deb │ └── Dockerfile ├── snpeff └── 4.1k │ └── Dockerfile ├── snpomatic ├── 1.0-3b1-deb │ └── Dockerfile └── 1.0-4-deb │ └── Dockerfile ├── soapaligner └── 2.20-3-deb │ └── Dockerfile ├── soapdenovo ├── 240 │ └── Dockerfile ├── 1.05-3-deb │ └── Dockerfile └── 1.05-5-deb │ └── Dockerfile ├── soapdenovo2 ├── 240dfsg1-2-deb │ └── Dockerfile └── 241dfsg-3-deb │ └── Dockerfile ├── soapec └── 2.03 │ └── Dockerfile ├── soapsnp └── 1.03-3-deb │ └── Dockerfile ├── sofa-apps ├── 1.0beta4-11b3-deb │ └── Dockerfile └── 1.0beta4-12b2-deb │ └── Dockerfile ├── sofa-data ├── 1.0beta4-11-deb │ └── Dockerfile └── 1.0beta4-12-deb │ └── Dockerfile ├── sofa-tutorials ├── 1.0beta4-11-deb │ └── Dockerfile └── 1.0beta4-12-deb │ └── Dockerfile ├── sortmerna ├── 2.1-1b1-deb │ └── Dockerfile └── 2.1-3-deb │ └── Dockerfile ├── spaced ├── 1.0.2dfsg-1b1-deb │ └── Dockerfile └── 1.2.0-201605dfsg-1-deb │ └── Dockerfile ├── spades ├── 3.13.0dfsg2-2-deb │ └── Dockerfile ├── 3.13.1 │ └── Dockerfile ├── 3.6.0 │ └── Dockerfile └── 3.9.1dfsg-1-deb │ └── Dockerfile ├── spark └── 3.1.3 │ ├── Dockerfile │ └── scripts │ ├── determine_ip.sh │ ├── prepare.sh │ ├── runapp.sh │ ├── startmanager.sh │ ├── startworker.sh │ ├── terminate.sh │ ├── waitformanager.sh │ └── waitforworker.sh ├── spectra-cluster-cli ├── v1.0-beta │ └── Dockerfile └── v1.1.2 │ └── Dockerfile ├── spectra └── 0.0.11-1-deb-py3 │ └── Dockerfile ├── sphinxcontrib-autoprogram ├── 0.1.2-1-deb │ └── Dockerfile └── 0.1.5-1-deb │ └── Dockerfile ├── sphinxcontrib.autoprogram ├── 0.1.2-1-deb-py3 │ └── Dockerfile └── 0.1.5-1-deb-py3 │ └── Dockerfile ├── spoa ├── 1.1.3-2bpo91-deb │ └── Dockerfile └── 1.1.5-1-deb │ └── Dockerfile ├── sprai ├── 0.9.9.22dfsg-1-deb │ └── Dockerfile └── 0.9.9.23dfsg-2-deb │ └── Dockerfile ├── spread-phy ├── 1.0.7dfsg-1-deb │ └── Dockerfile └── 1.0.7dfsg-2-deb │ └── Dockerfile ├── sqlsoup ├── 0.9.1-1-deb-py2 │ └── Dockerfile ├── 0.9.1-1-deb-py3 │ └── Dockerfile ├── 0.9.1-3-deb-py2 │ └── Dockerfile └── 0.9.1-3-deb-py3 │ └── Dockerfile ├── sqt └── 0.8.0-3-deb-py3 │ └── Dockerfile ├── squizz ├── 0.99cdfsg-1-deb │ └── Dockerfile └── 0.99ddfsg-2-deb │ └── Dockerfile ├── sra-toolkit ├── 2.8.1-2dfsg-2-deb │ └── Dockerfile └── 2.9.3dfsg-1b1-deb │ └── Dockerfile ├── srst2 ├── 0.2.0-4-deb │ └── Dockerfile └── 0.2.0-6-deb │ └── Dockerfile ├── ssaha2 └── 2.5.5 │ └── Dockerfile ├── ssake ├── 3.8.4-1-deb │ └── Dockerfile └── 4.0-2-deb │ └── Dockerfile ├── sspace ├── 2.1.1dfsg-2-deb │ └── Dockerfile └── 2.1.1dfsg-4-deb │ └── Dockerfile ├── ssw-align ├── 1.1-1b1-deb │ └── Dockerfile └── 1.1-2-deb │ └── Dockerfile ├── stacks-web ├── 1.44-2-deb │ └── Dockerfile └── 2.2dfsg-1-deb │ └── Dockerfile ├── stacks ├── 1.41 │ └── Dockerfile ├── 1.44-2b1-deb │ └── Dockerfile └── 2.2dfsg-1-deb │ └── Dockerfile ├── staden-common ├── 2.0.0b11-2-deb │ └── Dockerfile └── 2.0.0b11-4-deb │ └── Dockerfile ├── staden-io-lib-utils ├── 1.14.11-6-deb │ └── Dockerfile └── 1.14.8-2-deb │ └── Dockerfile ├── staden ├── 2.0.0b11-2b1-deb │ └── Dockerfile └── 2.0.0b11-4-deb │ └── Dockerfile ├── stitching-spark └── 1.10.0 │ └── Dockerfile ├── strelka └── 2.9.7 │ └── Dockerfile ├── subread-data ├── 1.5.1dfsg-4-deb │ └── Dockerfile └── 1.6.3dfsg-1-deb │ └── Dockerfile ├── subread ├── 1.5.1dfsg-4-deb │ └── Dockerfile └── 1.6.3dfsg-1-deb │ └── Dockerfile ├── suffixfsm └── 0.0git20150829.56e4718-2-deb │ └── Dockerfile ├── suitename ├── 0.3.070628-1b1-deb │ └── Dockerfile └── 0.3.070628-2-deb │ └── Dockerfile ├── sumaclust ├── 1.0.20-1b1-deb │ └── Dockerfile └── 1.0.31-2-deb │ └── Dockerfile ├── sumatra ├── 1.0.20-1b1-deb │ └── Dockerfile └── 1.0.31-2-deb │ └── Dockerfile ├── sumtrees ├── 4.2.0dfsg-1-deb │ └── Dockerfile └── 4.4.0-1-deb │ └── Dockerfile ├── surankco ├── 0.0.r5dfsg-1-deb │ └── Dockerfile └── 0.0.r5dfsg-2-deb │ └── Dockerfile ├── swarm ├── 2.1.12dfsg-1-deb │ └── Dockerfile └── 2.2.2dfsg-2-deb │ └── Dockerfile ├── sweed └── 3.2.1dfsg-1-deb │ └── Dockerfile ├── t-coffee ├── 11.00.8cbe486-5-deb │ └── Dockerfile └── 12.00.7fb08c2-4-deb │ └── Dockerfile ├── tabix ├── 1.3.2-2-deb │ └── Dockerfile └── 1.9-11-deb │ └── Dockerfile ├── talon ├── 4.1 │ └── Dockerfile ├── 4.2 │ └── Dockerfile ├── 4.4.1 │ └── Dockerfile ├── 4.4.2 │ └── Dockerfile ├── 4.4 │ └── Dockerfile └── 5.0 │ └── Dockerfile ├── tandem ├── 10-12-01-1 │ └── Dockerfile ├── 15-12-15-2 │ └── Dockerfile └── 17-02-01-4 │ └── Dockerfile ├── tantan ├── 13-4-deb │ └── Dockerfile └── 22-1-deb │ └── Dockerfile ├── telescoper └── 1.0.0 │ ├── Dockerfile │ └── makefile ├── test-ci ├── 0.0.1 │ ├── Dockerfile │ └── README.md └── 0.0.2 │ └── Dockerfile ├── theseus ├── 3.3.0-5b1-deb │ └── Dockerfile └── 3.3.0-8-deb │ └── Dockerfile ├── tifffile ├── 20151006-1-deb-py2 │ └── Dockerfile └── 20181128-1-deb │ └── Dockerfile ├── tigr-glimmer ├── 3.02b-1-deb │ └── Dockerfile └── 3.02b-2-deb │ └── Dockerfile ├── tm-align ├── 20160521dfsg-2-deb │ └── Dockerfile └── 20170708dfsg-2-deb │ └── Dockerfile ├── tnseq-transit ├── 2.2.1-2bpo91-deb │ └── Dockerfile └── 2.3.4-1-deb │ └── Dockerfile ├── toil └── 3.18.0-2-deb │ └── Dockerfile ├── tophat └── 2.1.1 │ └── Dockerfile ├── toppas └── 1.11.1-3 │ └── Dockerfile ├── toppred ├── 1.10-4-deb │ └── Dockerfile └── 1.10-7-deb │ └── Dockerfile ├── tpmcalculator └── 0.0.1 │ └── Dockerfile ├── tpp ├── 4.8 │ └── Dockerfile ├── 5.0 │ └── Dockerfile └── 5.2 │ └── Dockerfile ├── trace2dbest └── 3.0.1-1-deb │ └── Dockerfile ├── tracetuner └── 3.0.6betadfsg-1-deb │ └── Dockerfile ├── transcriptclean ├── 1.0.7 │ └── Dockerfile ├── 1.0.8 │ └── Dockerfile └── 2.0.2 │ └── Dockerfile ├── transdecoder ├── 3.0.1dfsg-1-deb │ └── Dockerfile └── 5.0.1-2-deb │ └── Dockerfile ├── transrate-tools ├── 1.0.0-1b1-deb │ └── Dockerfile └── 1.0.0-2-deb │ └── Dockerfile ├── transtermhp ├── 2.09-3b1-deb │ └── Dockerfile └── 2.09-4-deb │ └── Dockerfile ├── tree-ppuzzle ├── 5.2-11-deb │ └── Dockerfile └── 5.2-8b3-deb │ └── Dockerfile ├── tree-puzzle ├── 5.2-11-deb │ └── Dockerfile └── 5.2-8b3-deb │ └── Dockerfile ├── treetime └── 0.5.3-1-deb-py3 │ └── Dockerfile ├── treeview ├── 1.1.6.4dfsg1-2-deb │ └── Dockerfile └── 1.1.6.4dfsg1-4-deb │ └── Dockerfile ├── treeviewx ├── 0.5.120100823-4-deb │ └── Dockerfile └── 0.5.1git20100823.7e4d0e9-1-deb │ └── Dockerfile ├── trimmomatic ├── 0.36dfsg-1-deb │ └── Dockerfile └── 0.38dfsg-1-deb │ └── Dockerfile ├── trinityrnaseq ├── 2.2.0dfsg-2b1-deb │ └── Dockerfile └── 2.6.6dfsg-6-deb │ └── Dockerfile ├── tvc └── 5.0.3git20151221.80e144edfsg-2-deb │ └── Dockerfile ├── typed-ast ├── 0.6.3-1-deb-py3 │ └── Dockerfile └── 1.3.1-1-deb-py3 │ └── Dockerfile ├── uc-echo ├── 1.12-11-deb │ └── Dockerfile └── 1.12-9b1-deb │ └── Dockerfile ├── unanimity └── 3.3.0dfsg-2.1-deb │ └── Dockerfile ├── unicycler-data ├── 0.4.7dfsg-1bpo91-deb │ └── Dockerfile └── 0.4.7dfsg-2-deb │ └── Dockerfile ├── unicycler ├── 0.4.7dfsg-1bpo91-deb │ └── Dockerfile └── 0.4.7dfsg-2-deb │ └── Dockerfile ├── varna ├── 3-93ds-1-deb │ └── Dockerfile └── 3-93ds-2-deb │ └── Dockerfile ├── vcftools ├── 0.1.14 │ └── Dockerfile ├── 0.1.15 │ └── Dockerfile └── 0.1.16-1-deb │ └── Dockerfile ├── velvet-example ├── 1.2.10dfsg1-3-deb │ └── Dockerfile └── 1.2.10dfsg1-5-deb │ └── Dockerfile ├── velvet-long ├── 1.2.10dfsg1-3b1-deb │ └── Dockerfile └── 1.2.10dfsg1-5-deb │ └── Dockerfile ├── velvet-tests ├── 1.2.10dfsg1-3-deb │ └── Dockerfile └── 1.2.10dfsg1-5-deb │ └── Dockerfile ├── velvet └── 1.2.10 │ └── Dockerfile ├── velvetoptimiser ├── 2.2.5-5-deb │ └── Dockerfile └── 2.2.6-2-deb │ └── Dockerfile ├── vg └── 1.23.0-plusds-1-deb │ ├── Dockerfile │ └── test-cmds.txt ├── visionegg └── 1.2.1-2-deb-py2 │ └── Dockerfile ├── vsearch ├── 2.10.4-1-deb │ └── Dockerfile └── 2.3.4-1-deb │ └── Dockerfile ├── vtk-dicom-tools ├── 0.7.10-1b2-deb │ └── Dockerfile └── 0.8.9-1-deb │ └── Dockerfile ├── vtk-dicom ├── 0.7.10-1b2-deb-py2 │ └── Dockerfile └── 0.8.9-1-deb-py3 │ └── Dockerfile ├── vtkgdcm ├── 2.6.6-3-deb-py2 │ └── Dockerfile └── 2.8.8-9-deb-py3 │ └── Dockerfile ├── wgerman-medical └── 20160103-3-deb │ └── Dockerfile ├── wigeon ├── 20101212dfsg1-1-deb │ └── Dockerfile └── 20101212dfsg1-2-deb │ └── Dockerfile ├── wise-data ├── 2.4.1-19-deb │ └── Dockerfile └── 2.4.1-21-deb │ └── Dockerfile ├── wise ├── 2.4.1-19-deb │ └── Dockerfile └── 2.4.1-21-deb │ └── Dockerfile ├── xmedcon ├── 0.14.1-1b2-deb │ └── Dockerfile └── 0.16.1dfsg-1-deb │ └── Dockerfile ├── xopen ├── 0.1.1-1-deb-py2 │ └── Dockerfile ├── 0.1.1-1-deb-py3 │ └── Dockerfile ├── 0.5.0-2-deb-py2 │ └── Dockerfile └── 0.5.0-2-deb-py3 │ └── Dockerfile ├── yaggo ├── 1.5.10-2-deb │ └── Dockerfile └── 1.5.9-1-deb │ └── Dockerfile ├── yaha └── 0.1.83-1-deb │ └── Dockerfile ├── zalign ├── 0.9.1-2b3-deb │ └── Dockerfile └── 0.9.1-4-deb │ └── Dockerfile ├── zorro └── 1.0.0 │ └── Dockerfile └── zstd ├── 1.1.2-1-deb └── Dockerfile └── 1.3.8dfsg-3-deb └── Dockerfile /.github/workflows/build.yml: -------------------------------------------------------------------------------- 1 | name: Unit tests and docker build 2 | 3 | on: 4 | push: 5 | branches: 6 | - master 7 | pull_request: 8 | 9 | jobs: 10 | 11 | build: 12 | 13 | runs-on: self-hosted 14 | 15 | steps: 16 | - uses: actions/checkout@v1 17 | - name: Check and build 18 | run: | 19 | echo "Path: ${GITHUB_WORKSPACE}, commit: ${GITHUB_SHA}, ref: ${GITHUB_REF}" 20 | cd $GITHUB_WORKSPACE && biocontainers-build 21 | docker image prune -a -f 22 | -------------------------------------------------------------------------------- /.github/workflows/conda.yml: -------------------------------------------------------------------------------- 1 | # Calls biocontainer-ci repo / bioconda-backup script 2 | # on self hosted node 3 | 4 | name: Bioconda and docker backups 5 | 6 | on: 7 | schedule: 8 | - cron: "0 23 * * * " 9 | 10 | jobs: 11 | 12 | build: 13 | timeout-minutes: 4320 14 | runs-on: self-hosted 15 | steps: 16 | - name: Backup bioconda and docker containers to local and aws registries 17 | run: | 18 | cd /home/debian/sync && node index.js --backup --aws --conda --updated 19 | cd /home/debian/sync && node index.js --aws --docker --updated 20 | -------------------------------------------------------------------------------- /.gitignore: -------------------------------------------------------------------------------- 1 | ### Example user template 2 | 3 | # IntelliJ project files 4 | .idea 5 | *.iml 6 | out 7 | gen### Example user template template 8 | ### Example user template 9 | 10 | # IntelliJ project files 11 | .idea 12 | *.iml 13 | out 14 | gen 15 | 16 | 17 | *.o 18 | .idea/ 19 | 20 | -------------------------------------------------------------------------------- /.gitmodules: -------------------------------------------------------------------------------- 1 | [submodule "metfrag-cli-batch/2.4.3"] 2 | path = metfrag-cli-batch/2.4.3 3 | url = https://github.com/phnmnl/container-metfrag-cli-batch/ 4 | [submodule "ipo/1.7.5"] 5 | path = ipo/1.7.5 6 | url = https://github.com/phnmnl/container-ipo 7 | [submodule "isatab-create/0.9.5"] 8 | path = isatab-create/0.9.5 9 | url = https://github.com/phnmnl/container-isatab-create/ 10 | [submodule "simid/1.0.0"] 11 | path = simid/1.0.0 12 | url = https://github.com/phnmnl/container-simid/ 13 | -------------------------------------------------------------------------------- /adun-core/0.81-9b2-deb/Dockerfile: -------------------------------------------------------------------------------- 1 | FROM biocontainers/biocontainers:debian-stretch-backports 2 | MAINTAINER biocontainers 3 | LABEL software="adun-core" \ 4 | container="adun-core" \ 5 | about.summary="Molecular Simulator" \ 6 | about.home="http://diana.imim.es/Adun" \ 7 | software.version="0.81-9b2-deb" \ 8 | version="1" \ 9 | about.license_file="/usr/share/doc/adun-core/copyright" \ 10 | extra.binaries="/usr/bin/AdunCore,/usr/bin/AdunServer" \ 11 | about.tags="" 12 | 13 | ENV DEBIAN_FRONTEND noninteractive 14 | RUN apt-get update && apt-get install -y adun-core && apt-get clean && apt-get purge && rm -rf /var/lib/apt/lists/* /tmp/* 15 | USER biodocker 16 | -------------------------------------------------------------------------------- /amide/1.0.5-7-deb/Dockerfile: -------------------------------------------------------------------------------- 1 | FROM biocontainers/biocontainers:debian-stretch-backports 2 | MAINTAINER biocontainers 3 | LABEL software="amide" \ 4 | container="amide" \ 5 | about.summary="software for Medical Imaging" \ 6 | about.home="http://amide.sourceforge.net/" \ 7 | software.version="1.0.5-7-deb" \ 8 | version="1" \ 9 | about.copyright="" \ 10 | about.license="GPL-2+" \ 11 | about.license_file="/usr/share/doc/amide/copyright" \ 12 | extra.binaries="/usr/bin/amide" \ 13 | about.tags="field::medicine, field::medicine:imaging, role::program" 14 | 15 | ENV DEBIAN_FRONTEND noninteractive 16 | RUN apt-get update && apt-get install -y amide && apt-get clean && apt-get purge && rm -rf /var/lib/apt/lists/* /tmp/* 17 | USER biodocker 18 | -------------------------------------------------------------------------------- /anfo/0.98-5-deb/Dockerfile: -------------------------------------------------------------------------------- 1 | FROM biocontainers/biocontainers:debian-stretch-backports 2 | MAINTAINER biocontainers 3 | LABEL software="anfo" \ 4 | container="anfo" \ 5 | about.summary="Short Read Aligner/Mapper from MPG" \ 6 | about.home="http://bioinf.eva.mpg.de/anfo/" \ 7 | software.version="0.98-5-deb" \ 8 | version="1" \ 9 | about.copyright=" 2009 Udo Stenzel " \ 10 | about.license="GPL-3+" \ 11 | about.license_file="/usr/share/doc/anfo/copyright" \ 12 | extra.binaries="/usr/bin/anfo,/usr/bin/anfo-tool,/usr/bin/dnaindex,/usr/bin/fa2dna" \ 13 | about.tags="" 14 | 15 | ENV DEBIAN_FRONTEND noninteractive 16 | RUN apt-get update && apt-get install -y anfo && apt-get clean && apt-get purge && rm -rf /var/lib/apt/lists/* /tmp/* 17 | USER biodocker 18 | -------------------------------------------------------------------------------- /atac/020150903r2013-3-deb/Dockerfile: -------------------------------------------------------------------------------- 1 | FROM biocontainers/biocontainers:debian-stretch-backports 2 | MAINTAINER biocontainers 3 | LABEL software="atac" \ 4 | container="atac" \ 5 | about.summary="genome assembly-to-assembly comparison" \ 6 | about.home="http://kmer.sourceforge.net" \ 7 | software.version="020150903r2013-3-deb" \ 8 | version="1" \ 9 | about.copyright=" 2002 PE Corporation (NY) through the Celera Genomics Group" \ 10 | about.license="GPL-2+" \ 11 | about.license_file="/usr/share/doc/atac/copyright" \ 12 | extra.binaries="/usr/bin/atac" \ 13 | about.tags="" 14 | 15 | ENV DEBIAN_FRONTEND noninteractive 16 | RUN apt-get update && apt-get install -y atac && apt-get clean && apt-get purge && rm -rf /var/lib/apt/lists/* /tmp/* 17 | USER biodocker 18 | -------------------------------------------------------------------------------- /autodock-vina/1.1.2-3b6-deb/Dockerfile: -------------------------------------------------------------------------------- 1 | FROM biocontainers/biocontainers:debian-stretch-backports 2 | MAINTAINER biocontainers 3 | LABEL software="autodock-vina" \ 4 | container="autodock-vina" \ 5 | about.summary="docking of small molecules to proteins" \ 6 | about.home="http://vina.scripps.edu" \ 7 | software.version="1.1.2-3b6-deb" \ 8 | version="1" \ 9 | about.license_file="/usr/share/doc/autodock-vina/copyright" \ 10 | extra.binaries="/usr/bin/vina,/usr/bin/vina_split" \ 11 | about.tags="" 12 | 13 | ENV DEBIAN_FRONTEND noninteractive 14 | RUN apt-get update && apt-get install -y autodock-vina && apt-get clean && apt-get purge && rm -rf /var/lib/apt/lists/* /tmp/* 15 | USER biodocker 16 | -------------------------------------------------------------------------------- /avro/1.8.1dfsg-1-deb-py2/Dockerfile: -------------------------------------------------------------------------------- 1 | FROM biocontainers/biocontainers:debian-stretch-backports 2 | MAINTAINER biocontainers 3 | LABEL software="avro" \ 4 | container="avro" \ 5 | about.summary="Apache Avro serialization system ?? Python 2 library" \ 6 | about.home="http://avro.apache.org" \ 7 | software.version="1.8.1dfsg-1-deb-py2" \ 8 | version="1" \ 9 | about.copyright="2010-2015 Apache Software Foundation" \ 10 | about.license="Apache-2.0" \ 11 | about.license_file="/usr/share/doc/avro/copyright" \ 12 | about.tags="" 13 | 14 | ENV DEBIAN_FRONTEND noninteractive 15 | RUN apt-get update && apt-get install -y python-avro && apt-get clean && apt-get purge && rm -rf /var/lib/apt/lists/* /tmp/* 16 | USER biodocker 17 | -------------------------------------------------------------------------------- /avro/1.8.1dfsg-1-deb-py3/Dockerfile: -------------------------------------------------------------------------------- 1 | FROM biocontainers/biocontainers:debian-stretch-backports 2 | MAINTAINER biocontainers 3 | LABEL software="avro" \ 4 | container="avro" \ 5 | about.summary="Apache Avro serialization system ?? Python 3 library" \ 6 | about.home="http://avro.apache.org" \ 7 | software.version="1.8.1dfsg-1-deb-py3" \ 8 | version="1" \ 9 | about.copyright="2010-2015 Apache Software Foundation" \ 10 | about.license="Apache-2.0" \ 11 | about.license_file="/usr/share/doc/avro/copyright" \ 12 | extra.binaries="/usr/bin/avro" \ 13 | about.tags="" 14 | 15 | ENV DEBIAN_FRONTEND noninteractive 16 | RUN apt-get update && apt-get install -y python3-avro && apt-get clean && apt-get purge && rm -rf /var/lib/apt/lists/* /tmp/* 17 | USER biodocker 18 | -------------------------------------------------------------------------------- /ball/1.4.3beta1-3-deb-py2/Dockerfile: -------------------------------------------------------------------------------- 1 | FROM biocontainers/biocontainers:debian-stretch-backports 2 | MAINTAINER biocontainers 3 | LABEL software="ball" \ 4 | container="ball" \ 5 | about.summary="Python bindings for the Biochemical Algorithms Library" \ 6 | about.home="http://www.ball-project.org/" \ 7 | software.version="1.4.3beta1-3-deb-py2" \ 8 | version="1" \ 9 | about.copyright=" 1998-2013 the BALL project group" \ 10 | about.license="GPL-2+" \ 11 | about.license_file="/usr/share/doc/ball/copyright" \ 12 | about.tags="uitoolkit::qt" 13 | 14 | ENV DEBIAN_FRONTEND noninteractive 15 | RUN apt-get update && apt-get install -y python-ball && apt-get clean && apt-get purge && rm -rf /var/lib/apt/lists/* /tmp/* 16 | USER biodocker 17 | -------------------------------------------------------------------------------- /ballview/1.4.3beta1-3-deb-py2/Dockerfile: -------------------------------------------------------------------------------- 1 | FROM biocontainers/biocontainers:debian-stretch-backports 2 | MAINTAINER biocontainers 3 | LABEL software="ballview" \ 4 | container="ballview" \ 5 | about.summary="Python bindings for VIEW-parts of the Biochemical Algorithms Library" \ 6 | about.home="http://www.ball-project.org/" \ 7 | software.version="1.4.3beta1-3-deb-py2" \ 8 | version="1" \ 9 | about.copyright=" 1998-2013 the BALL project group" \ 10 | about.license="GPL-2+" \ 11 | about.license_file="/usr/share/doc/ballview/copyright" \ 12 | about.tags="uitoolkit::qt" 13 | 14 | ENV DEBIAN_FRONTEND noninteractive 15 | RUN apt-get update && apt-get install -y python-ballview && apt-get clean && apt-get purge && rm -rf /var/lib/apt/lists/* /tmp/* 16 | USER biodocker 17 | -------------------------------------------------------------------------------- /bart/0.4.00-1-deb/Dockerfile: -------------------------------------------------------------------------------- 1 | FROM biocontainers/biocontainers:debian-stretch-backports 2 | MAINTAINER biocontainers 3 | LABEL software="bart" \ 4 | container="bart" \ 5 | about.summary="tools for computational magnetic resonance imaging" \ 6 | about.home="https://mrirecon.github.io/bart/" \ 7 | software.version="0.4.00-1-deb" \ 8 | version="1" \ 9 | about.copyright="2013-2016 The Regents of the University of California" \ 10 | about.license="BSD-3-clause" \ 11 | about.license_file="/usr/share/doc/bart/copyright" \ 12 | extra.binaries="/usr/bin/bart" \ 13 | about.tags="" 14 | 15 | ENV DEBIAN_FRONTEND noninteractive 16 | RUN apt-get update && apt-get install -y bart && apt-get clean && apt-get purge && rm -rf /var/lib/apt/lists/* /tmp/* 17 | USER biodocker 18 | -------------------------------------------------------------------------------- /bedtools-test/2.26.0dfsg-3-deb/Dockerfile: -------------------------------------------------------------------------------- 1 | FROM biocontainers/biocontainers:debian-stretch-backports 2 | MAINTAINER biocontainers 3 | LABEL software="bedtools-test" \ 4 | container="bedtools-test" \ 5 | about.summary="test data for the bedtools package" \ 6 | about.home="https://github.com/arq5x/bedtools2" \ 7 | software.version="2.26.0dfsg-3-deb" \ 8 | version="1" \ 9 | extra.identifiers.biotools="bedtools" \ 10 | about.copyright=" 2009,2010,2011 Aaron Quinlan" \ 11 | about.license="GPL-2" \ 12 | about.license_file="/usr/share/doc/bedtools-test/copyright" \ 13 | about.tags="" 14 | 15 | ENV DEBIAN_FRONTEND noninteractive 16 | RUN apt-get update && apt-get install -y bedtools-test && apt-get clean && apt-get purge && rm -rf /var/lib/apt/lists/* /tmp/* 17 | USER biodocker 18 | -------------------------------------------------------------------------------- /bioconductor-annotate/1.52.1dfsg-1-deb/Dockerfile: -------------------------------------------------------------------------------- 1 | FROM biocontainers/biocontainers:debian-stretch-backports 2 | MAINTAINER biocontainers 3 | LABEL software="bioconductor-annotate" \ 4 | container="bioconductor-annotate" \ 5 | about.summary="BioConductor annotation for microarrays" \ 6 | about.home="https://bioconductor.org/packages/annotate/" \ 7 | software.version="1.52.1dfsg-1-deb" \ 8 | version="1" \ 9 | about.copyright=" 2006-2016 R. Gentleman" \ 10 | about.license="Artistic-2.0" \ 11 | about.license_file="/usr/share/doc/bioconductor-annotate/copyright" \ 12 | about.tags="" 13 | 14 | ENV DEBIAN_FRONTEND noninteractive 15 | RUN apt-get update && apt-get install -y r-bioc-annotate && apt-get clean && apt-get purge && rm -rf /var/lib/apt/lists/* /tmp/* 16 | USER biodocker 17 | -------------------------------------------------------------------------------- /bioconductor-dnacopy/1.48.0-1-deb/Dockerfile: -------------------------------------------------------------------------------- 1 | FROM biocontainers/biocontainers:debian-stretch-backports 2 | MAINTAINER biocontainers 3 | LABEL software="bioconductor-dnacopy" \ 4 | container="bioconductor-dnacopy" \ 5 | about.summary="R package: DNA copy number data analysis" \ 6 | about.home="http://www.bioconductor.org/packages/DNAcopy/" \ 7 | software.version="1.48.0-1-deb" \ 8 | version="1" \ 9 | about.copyright="Venkatraman E. Seshan " \ 10 | about.license="GPL-2.0+" \ 11 | about.license_file="/usr/share/doc/bioconductor-dnacopy/copyright" \ 12 | about.tags="" 13 | 14 | ENV DEBIAN_FRONTEND noninteractive 15 | RUN apt-get update && apt-get install -y r-bioc-dnacopy && apt-get clean && apt-get purge && rm -rf /var/lib/apt/lists/* /tmp/* 16 | USER biodocker 17 | -------------------------------------------------------------------------------- /bioconductor-ebseq/1.14.0-1-deb/Dockerfile: -------------------------------------------------------------------------------- 1 | FROM biocontainers/biocontainers:debian-stretch-backports 2 | MAINTAINER biocontainers 3 | LABEL software="bioconductor-ebseq" \ 4 | container="bioconductor-ebseq" \ 5 | about.summary="R package for RNA-Seq Differential Expression Analysis" \ 6 | about.home="https://bioconductor.org/packages/EBSeq/" \ 7 | software.version="1.14.0-1-deb" \ 8 | version="1" \ 9 | about.copyright=" 2013-2016 Ning Leng " \ 10 | about.license="Artistic-2.0" \ 11 | about.license_file="/usr/share/doc/bioconductor-ebseq/copyright" \ 12 | about.tags="" 13 | 14 | ENV DEBIAN_FRONTEND noninteractive 15 | RUN apt-get update && apt-get install -y r-bioc-ebseq && apt-get clean && apt-get purge && rm -rf /var/lib/apt/lists/* /tmp/* 16 | USER biodocker 17 | -------------------------------------------------------------------------------- /bioconductor-genomicalignments/1.10.0-1b1-deb/Dockerfile: -------------------------------------------------------------------------------- 1 | FROM biocontainers/biocontainers:debian-stretch-backports 2 | MAINTAINER biocontainers 3 | LABEL software="bioconductor-genomicalignments" \ 4 | container="bioconductor-genomicalignments" \ 5 | about.summary="BioConductor representation and manipulation of short genomic alignments" \ 6 | about.home="https://bioconductor.org/packages/GenomicAlignments/" \ 7 | software.version="1.10.0-1b1-deb" \ 8 | version="1" \ 9 | about.license_file="/usr/share/doc/bioconductor-genomicalignments/copyright" \ 10 | about.tags="" 11 | 12 | ENV DEBIAN_FRONTEND noninteractive 13 | RUN apt-get update && apt-get install -y r-bioc-genomicalignments && apt-get clean && apt-get purge && rm -rf /var/lib/apt/lists/* /tmp/* 14 | USER biodocker 15 | -------------------------------------------------------------------------------- /bioconductor-genomicranges/1.26.2-1b1-deb/Dockerfile: -------------------------------------------------------------------------------- 1 | FROM biocontainers/biocontainers:debian-stretch-backports 2 | MAINTAINER biocontainers 3 | LABEL software="bioconductor-genomicranges" \ 4 | container="bioconductor-genomicranges" \ 5 | about.summary="BioConductor representation and manipulation of genomic intervals" \ 6 | about.home="https://bioconductor.org/packages/GenomicRanges/" \ 7 | software.version="1.26.2-1b1-deb" \ 8 | version="1" \ 9 | about.license_file="/usr/share/doc/bioconductor-genomicranges/copyright" \ 10 | about.tags="" 11 | 12 | ENV DEBIAN_FRONTEND noninteractive 13 | RUN apt-get update && apt-get install -y r-bioc-genomicranges && apt-get clean && apt-get purge && rm -rf /var/lib/apt/lists/* /tmp/* 14 | USER biodocker 15 | -------------------------------------------------------------------------------- /bioconductor-go.db/3.4.0-1-deb/Dockerfile: -------------------------------------------------------------------------------- 1 | FROM biocontainers/biocontainers:debian-stretch-backports 2 | MAINTAINER biocontainers 3 | LABEL software="bioconductor-go.db" \ 4 | container="bioconductor-go.db" \ 5 | about.summary="annotation maps describing the entire Gene Ontology" \ 6 | about.home="https://bioconductor.org/packages/GO.db/" \ 7 | software.version="3.4.0-1-deb" \ 8 | version="1" \ 9 | about.copyright="2006-2016 Marc Carlson" \ 10 | about.license="Artistic-2.0" \ 11 | about.license_file="/usr/share/doc/bioconductor-go.db/copyright" \ 12 | about.tags="" 13 | 14 | ENV DEBIAN_FRONTEND noninteractive 15 | RUN apt-get update && apt-get install -y r-bioc-go.db && apt-get clean && apt-get purge && rm -rf /var/lib/apt/lists/* /tmp/* 16 | USER biodocker 17 | -------------------------------------------------------------------------------- /bioconductor-iranges/2.8.1-1b1-deb/Dockerfile: -------------------------------------------------------------------------------- 1 | FROM biocontainers/biocontainers:debian-stretch-backports 2 | MAINTAINER biocontainers 3 | LABEL software="bioconductor-iranges" \ 4 | container="bioconductor-iranges" \ 5 | about.summary="GNU R low-level containers for storing sets of integer ranges" \ 6 | about.home="https://bioconductor.org/packages/IRanges/" \ 7 | software.version="2.8.1-1b1-deb" \ 8 | version="1" \ 9 | about.license_file="/usr/share/doc/bioconductor-iranges/copyright" \ 10 | about.tags="" 11 | 12 | ENV DEBIAN_FRONTEND noninteractive 13 | RUN apt-get update && apt-get install -y r-bioc-iranges && apt-get clean && apt-get purge && rm -rf /var/lib/apt/lists/* /tmp/* 14 | USER biodocker 15 | -------------------------------------------------------------------------------- /bioconductor-rsamtools/1.26.1-2b1-deb/Dockerfile: -------------------------------------------------------------------------------- 1 | FROM biocontainers/biocontainers:debian-stretch-backports 2 | MAINTAINER biocontainers 3 | LABEL software="bioconductor-rsamtools" \ 4 | container="bioconductor-rsamtools" \ 5 | about.summary="GNU R binary alignment (BAM), variant call (BCF), or tabix file import" \ 6 | about.home="https://bioconductor.org/packages/Rsamtools/" \ 7 | software.version="1.26.1-2b1-deb" \ 8 | version="1" \ 9 | about.license_file="/usr/share/doc/bioconductor-rsamtools/copyright" \ 10 | about.tags="" 11 | 12 | ENV DEBIAN_FRONTEND noninteractive 13 | RUN apt-get update && apt-get install -y r-bioc-rsamtools && apt-get clean && apt-get purge && rm -rf /var/lib/apt/lists/* /tmp/* 14 | USER biodocker 15 | -------------------------------------------------------------------------------- /bioconductor-s4vectors/0.12.1-2b1-deb/Dockerfile: -------------------------------------------------------------------------------- 1 | FROM biocontainers/biocontainers:debian-stretch-backports 2 | MAINTAINER biocontainers 3 | LABEL software="bioconductor-s4vectors" \ 4 | container="bioconductor-s4vectors" \ 5 | about.summary="BioConductor S4 implementation of vectors and lists" \ 6 | about.home="https://bioconductor.org/packages/S4Vectors/" \ 7 | software.version="0.12.1-2b1-deb" \ 8 | version="1" \ 9 | about.license_file="/usr/share/doc/bioconductor-s4vectors/copyright" \ 10 | about.tags="" 11 | 12 | ENV DEBIAN_FRONTEND noninteractive 13 | RUN apt-get update && apt-get install -y r-bioc-s4vectors && apt-get clean && apt-get purge && rm -rf /var/lib/apt/lists/* /tmp/* 14 | USER biodocker 15 | -------------------------------------------------------------------------------- /bioconductor-savr/1.12.0-1-deb/Dockerfile: -------------------------------------------------------------------------------- 1 | FROM biocontainers/biocontainers:debian-stretch-backports 2 | MAINTAINER biocontainers 3 | LABEL software="bioconductor-savr" \ 4 | container="bioconductor-savr" \ 5 | about.summary="GNU R parse and analyze Illumina SAV files" \ 6 | about.home="https://bioconductor.org/packages/savR/" \ 7 | software.version="1.12.0-1-deb" \ 8 | version="1" \ 9 | about.copyright="2013-2016 R. Brent Calder " \ 10 | about.license="AGPL-3" \ 11 | about.license_file="/usr/share/doc/bioconductor-savr/copyright" \ 12 | about.tags="" 13 | 14 | ENV DEBIAN_FRONTEND noninteractive 15 | RUN apt-get update && apt-get install -y r-bioc-savr && apt-get clean && apt-get purge && rm -rf /var/lib/apt/lists/* /tmp/* 16 | USER biodocker 17 | -------------------------------------------------------------------------------- /bioconductor-shortread/1.32.0-1b1-deb/Dockerfile: -------------------------------------------------------------------------------- 1 | FROM biocontainers/biocontainers:debian-stretch-backports 2 | MAINTAINER biocontainers 3 | LABEL software="bioconductor-shortread" \ 4 | container="bioconductor-shortread" \ 5 | about.summary="GNU R classes and methods for high-throughput short-read sequencing data" \ 6 | about.home="https://bioconductor.org/packages/ShortRead/" \ 7 | software.version="1.32.0-1b1-deb" \ 8 | version="1" \ 9 | about.license_file="/usr/share/doc/bioconductor-shortread/copyright" \ 10 | about.tags="" 11 | 12 | ENV DEBIAN_FRONTEND noninteractive 13 | RUN apt-get update && apt-get install -y r-bioc-shortread && apt-get clean && apt-get purge && rm -rf /var/lib/apt/lists/* /tmp/* 14 | USER biodocker 15 | -------------------------------------------------------------------------------- /bioconductor-variantannotation/1.20.2-1b1-deb/Dockerfile: -------------------------------------------------------------------------------- 1 | FROM biocontainers/biocontainers:debian-stretch-backports 2 | MAINTAINER biocontainers 3 | LABEL software="bioconductor-variantannotation" \ 4 | container="bioconductor-variantannotation" \ 5 | about.summary="BioConductor annotation of genetic variants" \ 6 | about.home="https://bioconductor.org/packages/VariantAnnotation/" \ 7 | software.version="1.20.2-1b1-deb" \ 8 | version="1" \ 9 | about.license_file="/usr/share/doc/bioconductor-variantannotation/copyright" \ 10 | about.tags="" 11 | 12 | ENV DEBIAN_FRONTEND noninteractive 13 | RUN apt-get update && apt-get install -y r-bioc-variantannotation && apt-get clean && apt-get purge && rm -rf /var/lib/apt/lists/* /tmp/* 14 | USER biodocker 15 | -------------------------------------------------------------------------------- /bioconductor-xvector/0.14.0-1b1-deb/Dockerfile: -------------------------------------------------------------------------------- 1 | FROM biocontainers/biocontainers:debian-stretch-backports 2 | MAINTAINER biocontainers 3 | LABEL software="bioconductor-xvector" \ 4 | container="bioconductor-xvector" \ 5 | about.summary="BioConductor representation and manpulation of external sequences" \ 6 | about.home="https://bioconductor.org/packages/XVector/" \ 7 | software.version="0.14.0-1b1-deb" \ 8 | version="1" \ 9 | about.license_file="/usr/share/doc/bioconductor-xvector/copyright" \ 10 | about.tags="" 11 | 12 | ENV DEBIAN_FRONTEND noninteractive 13 | RUN apt-get update && apt-get install -y r-bioc-xvector && apt-get clean && apt-get purge && rm -rf /var/lib/apt/lists/* /tmp/* 14 | USER biodocker 15 | -------------------------------------------------------------------------------- /biom-format/2.1.5dfsg-7-deb-py2/Dockerfile: -------------------------------------------------------------------------------- 1 | FROM biocontainers/biocontainers:debian-stretch-backports 2 | MAINTAINER biocontainers 3 | LABEL software="biom-format" \ 4 | container="biom-format" \ 5 | about.summary="Biological Observation Matrix (BIOM) format (Python 2)" \ 6 | about.home="http://biom-format.org/" \ 7 | software.version="2.1.5dfsg-7-deb-py2" \ 8 | version="1" \ 9 | about.copyright=" 2010-2015 Greg Caporaso " \ 10 | about.license="GPL" \ 11 | about.license_file="/usr/share/doc/biom-format/copyright" \ 12 | about.tags="" 13 | 14 | ENV DEBIAN_FRONTEND noninteractive 15 | RUN apt-get update && apt-get install -y python-biom-format && apt-get clean && apt-get purge && rm -rf /var/lib/apt/lists/* /tmp/* 16 | USER biodocker 17 | -------------------------------------------------------------------------------- /biom-format/2.1.5dfsg-7-deb-py3/Dockerfile: -------------------------------------------------------------------------------- 1 | FROM biocontainers/biocontainers:debian-stretch-backports 2 | MAINTAINER biocontainers 3 | LABEL software="biom-format" \ 4 | container="biom-format" \ 5 | about.summary="Biological Observation Matrix (BIOM) format (Python 3)" \ 6 | about.home="http://biom-format.org/" \ 7 | software.version="2.1.5dfsg-7-deb-py3" \ 8 | version="1" \ 9 | about.copyright=" 2010-2015 Greg Caporaso " \ 10 | about.license="GPL" \ 11 | about.license_file="/usr/share/doc/biom-format/copyright" \ 12 | about.tags="" 13 | 14 | ENV DEBIAN_FRONTEND noninteractive 15 | RUN apt-get update && apt-get install -y python3-biom-format && apt-get clean && apt-get purge && rm -rf /var/lib/apt/lists/* /tmp/* 16 | USER biodocker 17 | -------------------------------------------------------------------------------- /biopython-sql/1.68dfsg-3-deb-py3/Dockerfile: -------------------------------------------------------------------------------- 1 | FROM biocontainers/biocontainers:debian-stretch-backports 2 | MAINTAINER biocontainers 3 | LABEL software="biopython-sql" \ 4 | container="biopython-sql" \ 5 | about.summary="Biopython support for the BioSQL database schema (Python 3)" \ 6 | about.home="http://biopython.org" \ 7 | software.version="1.68dfsg-3-deb-py3" \ 8 | version="1" \ 9 | about.copyright=" 2002-2009 Biopython contributors" \ 10 | about.license="other" \ 11 | about.license_file="/usr/share/doc/biopython-sql/copyright" \ 12 | about.tags="" 13 | 14 | ENV DEBIAN_FRONTEND noninteractive 15 | RUN apt-get update && apt-get install -y python3-biopython-sql && apt-get clean && apt-get purge && rm -rf /var/lib/apt/lists/* /tmp/* 16 | USER biodocker 17 | -------------------------------------------------------------------------------- /biopython/1.68dfsg-3-deb-py3/Dockerfile: -------------------------------------------------------------------------------- 1 | FROM biocontainers/biocontainers:debian-stretch-backports 2 | MAINTAINER biocontainers 3 | LABEL software="biopython" \ 4 | container="biopython" \ 5 | about.summary="Python library for bioinformatics (implemented in Python 3)" \ 6 | about.home="http://biopython.org" \ 7 | software.version="1.68dfsg-3-deb-py3" \ 8 | version="1" \ 9 | about.copyright=" 2002-2009 Biopython contributors" \ 10 | about.license="other" \ 11 | about.license_file="/usr/share/doc/biopython/copyright" \ 12 | about.tags="" 13 | 14 | ENV DEBIAN_FRONTEND noninteractive 15 | RUN apt-get update && apt-get install -y python3-biopython && apt-get clean && apt-get purge && rm -rf /var/lib/apt/lists/* /tmp/* 16 | USER biodocker 17 | -------------------------------------------------------------------------------- /bior_annotate/2.1.1/annotate/catalogFile.docker: -------------------------------------------------------------------------------- 1 | noTCGA_ExAc bior_same_variant /Data/catalogs/2015_05_18/noTCGA_ExAc.tsv.bgz 2 | -------------------------------------------------------------------------------- /bior_annotate/2.1.1/annotate/config/PED_file.ped: -------------------------------------------------------------------------------- 1 | FAM1 NA12878 NA12891 NA12892 2 2 2 | FAM1 NA12891 0 0 1 1 3 | FAM1 NA12892 0 0 2 2 4 | -------------------------------------------------------------------------------- /bior_annotate/2.1.1/annotate/config/PED_sample.txt: -------------------------------------------------------------------------------- 1 | FAM1 NA12878 NA12891 NA12892 2 2 2 | FAM1 NA12891 0 0 1 1 3 | FAM1 NA12892 0 0 2 2 4 | controlFAM new_NA12878 new_NA12891 new_NA12892 2 2 5 | controlFAM new_NA12891 0 0 1 1 6 | controlFAM new_NA12892 0 0 2 2 7 | -------------------------------------------------------------------------------- /bior_annotate/2.1.1/annotate/config/catalog_file: -------------------------------------------------------------------------------- 1 | Clinvar bior_same_variant /data5/bsi/catalogs/user/v1/Clinvar/2015_03_09/Clinvar.tsv.bgz 2 | ExAC bior_same_variant /data5/bsi/catalogs/user/v1/ExAc/2015_05_18/noTCGA_ExAc.tsv.bgz 3 | hgmd_2014.2 bior_same_variant /data5/bsi/catalogs/user/v1/HGMD/2014_07_16/hgmd_pro.tsv.gz 4 | cosmic68 bior_same_variant /data5/bsi/catalogs/bior/v1/cosmic/v68/CosmicCompleteExport_GRCh37.tsv.bgz 5 | dbSNP139 bior_same_variant /data5/bsi/catalogs/bior/v1/dbSNP/139/00-All_GRCh37.tsv.bgz 6 | dbNSFPv2.8 bior_same_variant /data5/bsi/catalogs/user/v1/variant_prediction/dbNSFP/2014_11_24/dbNSFP.all.catalog.gz 7 | BlatED50 bior_overlap /data5/bsi/catalogs/user/v1/BLAT_ED/BlatED50.tsv.bgz 8 | -------------------------------------------------------------------------------- /bior_annotate/2.1.1/annotate/config/drill_file: -------------------------------------------------------------------------------- 1 | Clinvar ClinicalSignificance,RCVaccession,PhenotypeIDs,Guidelines,ReviewStatus 2 | ExAC INFO.AC,INFO.AN,INFO.AF,INFO.AC_NFE 3 | hgmd_2014.2 CLASS,PHEN,OMIM_ID,PubMed 4 | dbSNP139 ID 5 | BlatED50 ED 6 | dbNSFPv2.8 Vest3Score,MetalrPred,MetalrScore,MetasvmPred,MetasvmScore 7 | -------------------------------------------------------------------------------- /bior_annotate/2.1.1/annotate/config/drill_file.dlmp: -------------------------------------------------------------------------------- 1 | Clinvar ClinicalSignificance,RCVaccession,PhenotypeIDs,Guidelines,ReviewStatus 2 | ExAC Info.AC,Info.AN,Info.AF,Info.AC_Het,Info.AC_Hom 3 | hgmd_2014.2 CLASS,PHEN,OMIM_ID,PubMed 4 | cosmic68 Histology_subtype 5 | dbSNP139 ID 6 | dbNSFPv2.8 SiftPred,Polyphen2HdivPred,MutationtasterPred,MutationassessorPred,FathmmPred,MetasvmPred,MetalrPred 7 | ExperienceDB ASSAY,CLASS,NOTES,Submitter 8 | OMIM name 9 | PGx_variants name 10 | ACMG_genes name 11 | -------------------------------------------------------------------------------- /bior_annotate/2.1.1/annotate/config/memory_info.txt: -------------------------------------------------------------------------------- 1 | ######################## 2 | ##### annotation 3 | ####################### 4 | annotate_mem="6G" 5 | annotate_ba_mem="14G" 6 | annotate_ba_merge="1G" 7 | bior_annotate_mem="1G" 8 | 9 | -------------------------------------------------------------------------------- /bior_annotate/2.1.1/annotate/drillFile.docker: -------------------------------------------------------------------------------- 1 | noTCGA_ExAc INFO.AC_NFE,INFO.AC 2 | -------------------------------------------------------------------------------- /bowtie2/README.md: -------------------------------------------------------------------------------- 1 | version 2.3.4.3-1-deb_cv1 broken please use version 2.3.4.3-1-deb_cv2 or later (cf #356) 2 | -------------------------------------------------------------------------------- /brig/0.95dfsg-1-deb/Dockerfile: -------------------------------------------------------------------------------- 1 | FROM biocontainers/biocontainers:debian-stretch-backports 2 | MAINTAINER biocontainers 3 | LABEL software="brig" \ 4 | container="brig" \ 5 | about.summary="BLAST Ring Image Generator" \ 6 | about.home="http://sourceforge.net/projects/brig/" \ 7 | software.version="0.95dfsg-1-deb" \ 8 | version="1" \ 9 | extra.identifiers.biotools="brig" \ 10 | about.copyright="2010-2012 Nabil Alikhan" \ 11 | about.license="GPL-3+" \ 12 | about.license_file="/usr/share/doc/brig/copyright" \ 13 | extra.binaries="/usr/bin/brig" \ 14 | about.tags="" 15 | 16 | ENV DEBIAN_FRONTEND noninteractive 17 | RUN apt-get update && apt-get install -y brig && apt-get clean && apt-get purge && rm -rf /var/lib/apt/lists/* /tmp/* 18 | USER biodocker 19 | -------------------------------------------------------------------------------- /burrito/0.9.1-1-deb-py2/Dockerfile: -------------------------------------------------------------------------------- 1 | FROM biocontainers/biocontainers:debian-stretch-backports 2 | MAINTAINER biocontainers 3 | LABEL software="burrito" \ 4 | container="burrito" \ 5 | about.summary="Python 2 framework for wrapping and controlling command-line applications" \ 6 | about.home="https://github.com/biocore/burrito" \ 7 | software.version="0.9.1-1-deb-py2" \ 8 | version="1" \ 9 | about.copyright="2014-2015 burrito development team " \ 10 | about.license="BSD-3-clause" \ 11 | about.license_file="/usr/share/doc/burrito/copyright" \ 12 | about.tags="" 13 | 14 | ENV DEBIAN_FRONTEND noninteractive 15 | RUN apt-get update && apt-get install -y python-burrito && apt-get clean && apt-get purge && rm -rf /var/lib/apt/lists/* /tmp/* 16 | USER biodocker 17 | -------------------------------------------------------------------------------- /burrito/0.9.1-1-deb-py3/Dockerfile: -------------------------------------------------------------------------------- 1 | FROM biocontainers/biocontainers:debian-stretch-backports 2 | MAINTAINER biocontainers 3 | LABEL software="burrito" \ 4 | container="burrito" \ 5 | about.summary="Python 3 framework for wrapping and controlling command-line applications" \ 6 | about.home="https://github.com/biocore/burrito" \ 7 | software.version="0.9.1-1-deb-py3" \ 8 | version="1" \ 9 | about.copyright="2014-2015 burrito development team " \ 10 | about.license="BSD-3-clause" \ 11 | about.license_file="/usr/share/doc/burrito/copyright" \ 12 | about.tags="" 13 | 14 | ENV DEBIAN_FRONTEND noninteractive 15 | RUN apt-get update && apt-get install -y python3-burrito && apt-get clean && apt-get purge && rm -rf /var/lib/apt/lists/* /tmp/* 16 | USER biodocker 17 | -------------------------------------------------------------------------------- /bz2file/0.98-1-deb-py2/Dockerfile: -------------------------------------------------------------------------------- 1 | FROM biocontainers/biocontainers:debian-stretch-backports 2 | MAINTAINER biocontainers 3 | LABEL software="bz2file" \ 4 | container="bz2file" \ 5 | about.summary="Python library for reading and writing bzip2-compressed files" \ 6 | about.home="https://github.com/nvawda/bz2file" \ 7 | software.version="0.98-1-deb-py2" \ 8 | version="1" \ 9 | about.copyright=" 2012-2015 Nadeem Vawda " \ 10 | about.license="Apache" \ 11 | about.license_file="/usr/share/doc/bz2file/copyright" \ 12 | about.tags="" 13 | 14 | ENV DEBIAN_FRONTEND noninteractive 15 | RUN apt-get update && apt-get install -y python-bz2file && apt-get clean && apt-get purge && rm -rf /var/lib/apt/lists/* /tmp/* 16 | USER biodocker 17 | -------------------------------------------------------------------------------- /bz2file/0.98-1-deb-py3/Dockerfile: -------------------------------------------------------------------------------- 1 | FROM biocontainers/biocontainers:debian-stretch-backports 2 | MAINTAINER biocontainers 3 | LABEL software="bz2file" \ 4 | container="bz2file" \ 5 | about.summary="Python3 library for reading and writing bzip2-compressed files" \ 6 | about.home="https://github.com/nvawda/bz2file" \ 7 | software.version="0.98-1-deb-py3" \ 8 | version="1" \ 9 | about.copyright=" 2012-2015 Nadeem Vawda " \ 10 | about.license="Apache" \ 11 | about.license_file="/usr/share/doc/bz2file/copyright" \ 12 | about.tags="" 13 | 14 | ENV DEBIAN_FRONTEND noninteractive 15 | RUN apt-get update && apt-get install -y python3-bz2file && apt-get clean && apt-get purge && rm -rf /var/lib/apt/lists/* /tmp/* 16 | USER biodocker 17 | -------------------------------------------------------------------------------- /cadd-scripts-with-envs/1.6.post1/README.md: -------------------------------------------------------------------------------- 1 | # Container image for CADD-scripts 2 | 3 | This container image lets you use the CADD scripts snakemake pipeline to annotate variants. 4 | Documentation for CADD-scripts is here: 5 | 6 | https://github.com/kircherlab/CADD-scripts 7 | 8 | 9 | To use this container image you also need to mount the reference data. Assume you have 10 | downloaded the reference data to a directory `$REFPATH`, such that it looks something 11 | like this: 12 | 13 | $ ls $REFPATH 14 | GRCh37_v1.6 15 | 16 | Then use the following options 17 | 18 | Singularity/Apptainer: 19 | 20 | -B $REFPATH:/opt/CADD-scripts-1.6.post1/data/annotations 21 | 22 | Docker: 23 | 24 | -v $REFPATH:/opt/CADD-scripts-1.6.post1/data/annotations 25 | 26 | 27 | -------------------------------------------------------------------------------- /cadd-scripts-with-envs/1.6/README.md: -------------------------------------------------------------------------------- 1 | # Container image for CADD-scripts 2 | 3 | This container image lets you use the CADD scripts snakemake pipeline to annotate variants. 4 | Documentation for CADD-scripts is here: 5 | 6 | https://github.com/kircherlab/CADD-scripts 7 | 8 | 9 | To use this container image you also need to mount the reference data. Assume you have 10 | downloaded the reference data to a directory `$REFPATH`, such that it looks something 11 | like this: 12 | 13 | $ ls $REFPATH 14 | GRCh37_v1.6 15 | 16 | Then use the following options 17 | 18 | Singularity/Apptainer: 19 | 20 | -B $REFPATH:/opt/conda/share/cadd-scripts-1.6-1/data/annotations 21 | 22 | Docker: 23 | 24 | -v $REFPATH:/opt/conda/share/cadd-scripts-1.6-1/data/annotations 25 | 26 | 27 | -------------------------------------------------------------------------------- /cain-solvers/1.10dfsg-2-deb/Dockerfile: -------------------------------------------------------------------------------- 1 | FROM biocontainers/biocontainers:debian-stretch-backports 2 | MAINTAINER biocontainers 3 | LABEL software="cain-solvers" \ 4 | container="cain-solvers" \ 5 | about.summary="solvers for cain" \ 6 | about.home="http://cain.sourceforge.net" \ 7 | software.version="1.10dfsg-2-deb" \ 8 | version="1" \ 9 | about.copyright="1999-2012, California Institute of Technology" \ 10 | about.license="BSD-3-clause" \ 11 | about.license_file="/usr/share/doc/cain-solvers/copyright" \ 12 | about.tags="" 13 | 14 | ENV DEBIAN_FRONTEND noninteractive 15 | RUN apt-get update && apt-get install -y cain-solvers && apt-get clean && apt-get purge && rm -rf /var/lib/apt/lists/* /tmp/* 16 | USER biodocker 17 | -------------------------------------------------------------------------------- /cain/1.10dfsg-2-deb/Dockerfile: -------------------------------------------------------------------------------- 1 | FROM biocontainers/biocontainers:debian-stretch-backports 2 | MAINTAINER biocontainers 3 | LABEL software="cain" \ 4 | container="cain" \ 5 | about.summary="simulations of chemical reactions" \ 6 | about.home="http://cain.sourceforge.net" \ 7 | software.version="1.10dfsg-2-deb" \ 8 | version="1" \ 9 | about.copyright="1999-2012, California Institute of Technology" \ 10 | about.license="BSD-3-clause" \ 11 | about.license_file="/usr/share/doc/cain/copyright" \ 12 | extra.binaries="/usr/bin/cain" \ 13 | about.tags="" 14 | 15 | ENV DEBIAN_FRONTEND noninteractive 16 | RUN apt-get update && apt-get install -y cain && apt-get clean && apt-get purge && rm -rf /var/lib/apt/lists/* /tmp/* 17 | USER biodocker 18 | -------------------------------------------------------------------------------- /casmoothing/0.2-1b1-deb-py2/Dockerfile: -------------------------------------------------------------------------------- 1 | FROM biocontainers/biocontainers:debian-stretch-backports 2 | MAINTAINER biocontainers 3 | LABEL software="casmoothing" \ 4 | container="casmoothing" \ 5 | about.summary="Context-aware mesh smoothing for biomedical applications" \ 6 | about.home="https://github.com/tfmoraes/python-casmoothing" \ 7 | software.version="0.2-1b1-deb-py2" \ 8 | version="1" \ 9 | about.license_file="/usr/share/doc/casmoothing/copyright" \ 10 | about.tags="" 11 | 12 | ENV DEBIAN_FRONTEND noninteractive 13 | RUN apt-get update && apt-get install -y python-casmoothing && apt-get clean && apt-get purge && rm -rf /var/lib/apt/lists/* /tmp/* 14 | USER biodocker 15 | -------------------------------------------------------------------------------- /cassiopee/1.0.5-1b1-deb/Dockerfile: -------------------------------------------------------------------------------- 1 | FROM biocontainers/biocontainers:debian-stretch-backports 2 | MAINTAINER biocontainers 3 | LABEL software="cassiopee" \ 4 | container="cassiopee" \ 5 | about.summary="index and search tool in genomic sequences" \ 6 | about.home="https://github.com/osallou/cassiopee-c" \ 7 | software.version="1.0.5-1b1-deb" \ 8 | version="1" \ 9 | about.license_file="/usr/share/doc/cassiopee/copyright" \ 10 | extra.binaries="/usr/bin/cassiopee,/usr/bin/cassiopeeknife" \ 11 | about.tags="" 12 | 13 | ENV DEBIAN_FRONTEND noninteractive 14 | RUN apt-get update && apt-get install -y cassiopee && apt-get clean && apt-get purge && rm -rf /var/lib/apt/lists/* /tmp/* 15 | USER biodocker 16 | -------------------------------------------------------------------------------- /cellpose/0.6.5/environment.yml: -------------------------------------------------------------------------------- 1 | name: cellpose 2 | dependencies: 3 | - python>3.4,<3.8 4 | - pip 5 | - pip: 6 | - PyQt5 7 | - PyQt5.sip 8 | - numpy>1.14.6,<1.19.4 9 | - numba>=0.43.1 10 | - scipy 11 | - torch>=1.6 12 | - opencv-python-headless 13 | - pyqtgraph>=0.11.0rc0 14 | - natsort 15 | - google-cloud-storage 16 | - tqdm 17 | - tifffile 18 | 19 | -------------------------------------------------------------------------------- /cellpose/0.6.5/test/img02.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/BioContainers/containers/eb5588f9c03e93c54879252645e9f9ded1de4e71/cellpose/0.6.5/test/img02.png -------------------------------------------------------------------------------- /cellpose/0.6.5/test/img03.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/BioContainers/containers/eb5588f9c03e93c54879252645e9f9ded1de4e71/cellpose/0.6.5/test/img03.png -------------------------------------------------------------------------------- /cellpose/0.6.5/test/img05.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/BioContainers/containers/eb5588f9c03e93c54879252645e9f9ded1de4e71/cellpose/0.6.5/test/img05.png -------------------------------------------------------------------------------- /cellpose/2.1.1/test/img02.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/BioContainers/containers/eb5588f9c03e93c54879252645e9f9ded1de4e71/cellpose/2.1.1/test/img02.png -------------------------------------------------------------------------------- /cellpose/2.1.1/test/img03.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/BioContainers/containers/eb5588f9c03e93c54879252645e9f9ded1de4e71/cellpose/2.1.1/test/img03.png -------------------------------------------------------------------------------- /cellpose/2.1.1/test/img05.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/BioContainers/containers/eb5588f9c03e93c54879252645e9f9ded1de4e71/cellpose/2.1.1/test/img05.png -------------------------------------------------------------------------------- /cgview/0.0.20100111-2-deb/Dockerfile: -------------------------------------------------------------------------------- 1 | FROM biocontainers/biocontainers:debian-stretch-backports 2 | MAINTAINER biocontainers 3 | LABEL software="cgview" \ 4 | container="cgview" \ 5 | about.summary="Circular Genome Viewer" \ 6 | about.home="http://wishart.biology.ualberta.ca/cgview/" \ 7 | software.version="0.0.20100111-2-deb" \ 8 | version="1" \ 9 | extra.identifiers.biotools="cgview" \ 10 | about.copyright="2004-2010 Paul Stothard" \ 11 | about.license="GPL-2+" \ 12 | about.license_file="/usr/share/doc/cgview/copyright" \ 13 | extra.binaries="/usr/bin/cgview" \ 14 | about.tags="" 15 | 16 | ENV DEBIAN_FRONTEND noninteractive 17 | RUN apt-get update && apt-get install -y cgview && apt-get clean && apt-get purge && rm -rf /var/lib/apt/lists/* /tmp/* 18 | USER biodocker 19 | -------------------------------------------------------------------------------- /chado-utils/1.31-3-deb/Dockerfile: -------------------------------------------------------------------------------- 1 | FROM biocontainers/biocontainers:debian-stretch-backports 2 | MAINTAINER biocontainers 3 | LABEL software="chado-utils" \ 4 | container="chado-utils" \ 5 | about.summary="tools to add/extract data from Chado" \ 6 | about.home="http://gmod.org/wiki/Chado" \ 7 | software.version="1.31-3-deb" \ 8 | version="1" \ 9 | about.license_file="/usr/share/doc/chado-utils/copyright" \ 10 | about.tags="" 11 | 12 | ENV DEBIAN_FRONTEND noninteractive 13 | RUN apt-get update && apt-get install -y chado-utils && apt-get clean && apt-get purge && rm -rf /var/lib/apt/lists/* /tmp/* 14 | USER biodocker 15 | -------------------------------------------------------------------------------- /clearcut/1.0.9-1b1-deb/Dockerfile: -------------------------------------------------------------------------------- 1 | FROM biocontainers/biocontainers:debian-stretch-backports 2 | MAINTAINER biocontainers 3 | LABEL software="clearcut" \ 4 | container="clearcut" \ 5 | about.summary="extremely efficient phylogenetic tree reconstruction" \ 6 | about.home="http://bioinformatics.hungry.com/clearcut/" \ 7 | software.version="1.0.9-1b1-deb" \ 8 | version="1" \ 9 | about.license_file="/usr/share/doc/clearcut/copyright" \ 10 | extra.binaries="/usr/bin/clearcut" \ 11 | about.tags="" 12 | 13 | ENV DEBIAN_FRONTEND noninteractive 14 | RUN apt-get update && apt-get install -y clearcut && apt-get clean && apt-get purge && rm -rf /var/lib/apt/lists/* /tmp/* 15 | USER biodocker 16 | -------------------------------------------------------------------------------- /clips/1.0.7.348clips-2-deb-py2/Dockerfile: -------------------------------------------------------------------------------- 1 | FROM biocontainers/biocontainers:debian-stretch-backports 2 | MAINTAINER biocontainers 3 | LABEL software="clips" \ 4 | container="clips" \ 5 | about.summary="Python module to interface the CLIPS expert system shell library" \ 6 | about.home="http://sourceforge.net/projects/pyclips/" \ 7 | software.version="1.0.7.348clips-2-deb-py2" \ 8 | version="1" \ 9 | about.copyright="2002-2008 Francesco Garosi/JKS" \ 10 | about.license="LGPL-2" \ 11 | about.license_file="/usr/share/doc/clips/copyright" \ 12 | about.tags="" 13 | 14 | ENV DEBIAN_FRONTEND noninteractive 15 | RUN apt-get update && apt-get install -y python-clips && apt-get clean && apt-get purge && rm -rf /var/lib/apt/lists/* /tmp/* 16 | USER biodocker 17 | -------------------------------------------------------------------------------- /clustalo/1.2.4-1-deb/Dockerfile: -------------------------------------------------------------------------------- 1 | FROM biocontainers/biocontainers:debian-stretch-backports 2 | MAINTAINER biocontainers 3 | LABEL software="clustalo" \ 4 | container="clustalo" \ 5 | about.summary="General purpose multiple sequence alignment program for proteins" \ 6 | about.home="http://www.clustal.org/omega/" \ 7 | software.version="1.2.4-1-deb" \ 8 | version="1" \ 9 | about.copyright="2010 UCD Dublin " \ 10 | about.license="GPL-2+" \ 11 | about.license_file="/usr/share/doc/clustalo/copyright" \ 12 | extra.binaries="/usr/bin/clustalo" \ 13 | about.tags="" 14 | 15 | ENV DEBIAN_FRONTEND noninteractive 16 | RUN apt-get update && apt-get install -y clustalo && apt-get clean && apt-get purge && rm -rf /var/lib/apt/lists/* /tmp/* 17 | USER biodocker 18 | -------------------------------------------------------------------------------- /cobra-data/0.5.9-1-deb-py2/Dockerfile: -------------------------------------------------------------------------------- 1 | FROM biocontainers/biocontainers:debian-stretch-backports 2 | MAINTAINER biocontainers 3 | LABEL software="cobra-data" \ 4 | container="cobra-data" \ 5 | about.summary="constraint-based modeling of biological networks (data)" \ 6 | about.home="http://opencobra.github.io/cobrapy/" \ 7 | software.version="0.5.9-1-deb-py2" \ 8 | version="1" \ 9 | about.copyright="" \ 10 | about.license="GPL-2+ or LGPL-2.0+" \ 11 | about.license_file="/usr/share/doc/cobra-data/copyright" \ 12 | about.tags="" 13 | 14 | ENV DEBIAN_FRONTEND noninteractive 15 | RUN apt-get update && apt-get install -y python-cobra-data && apt-get clean && apt-get purge && rm -rf /var/lib/apt/lists/* /tmp/* 16 | USER biodocker 17 | -------------------------------------------------------------------------------- /cobra/0.5.9-1-deb-py2/Dockerfile: -------------------------------------------------------------------------------- 1 | FROM biocontainers/biocontainers:debian-stretch-backports 2 | MAINTAINER biocontainers 3 | LABEL software="cobra" \ 4 | container="cobra" \ 5 | about.summary="constraint-based modeling of biological networks (Python 2)" \ 6 | about.home="http://opencobra.github.io/cobrapy/" \ 7 | software.version="0.5.9-1-deb-py2" \ 8 | version="1" \ 9 | about.copyright="" \ 10 | about.license="GPL-2+ or LGPL-2.0+" \ 11 | about.license_file="/usr/share/doc/cobra/copyright" \ 12 | about.tags="field::biology, implemented-in::python, science::modelling" 13 | 14 | ENV DEBIAN_FRONTEND noninteractive 15 | RUN apt-get update && apt-get install -y python-cobra && apt-get clean && apt-get purge && rm -rf /var/lib/apt/lists/* /tmp/* 16 | USER biodocker 17 | -------------------------------------------------------------------------------- /cobra/0.5.9-1-deb-py3/Dockerfile: -------------------------------------------------------------------------------- 1 | FROM biocontainers/biocontainers:debian-stretch-backports 2 | MAINTAINER biocontainers 3 | LABEL software="cobra" \ 4 | container="cobra" \ 5 | about.summary="constraint-based modeling of biological networks (Python 3)" \ 6 | about.home="http://opencobra.github.io/cobrapy/" \ 7 | software.version="0.5.9-1-deb-py3" \ 8 | version="1" \ 9 | about.copyright="" \ 10 | about.license="GPL-2+ or LGPL-2.0+" \ 11 | about.license_file="/usr/share/doc/cobra/copyright" \ 12 | about.tags="" 13 | 14 | ENV DEBIAN_FRONTEND noninteractive 15 | RUN apt-get update && apt-get install -y python3-cobra && apt-get clean && apt-get purge && rm -rf /var/lib/apt/lists/* /tmp/* 16 | USER biodocker 17 | -------------------------------------------------------------------------------- /coregenebuilder/1.0/inventory: -------------------------------------------------------------------------------- 1 | [ifb] 2 | localhost 3 | 4 | [ifb:vars] 5 | CGB_CONFIG_PATH=/etc/coregenebuilder/ 6 | -------------------------------------------------------------------------------- /corepywrap/1.005-4b3-deb-py2/Dockerfile: -------------------------------------------------------------------------------- 1 | FROM biocontainers/biocontainers:debian-stretch-backports 2 | MAINTAINER biocontainers 3 | LABEL software="corepywrap" \ 4 | container="corepywrap" \ 5 | about.summary="library that exports C++ mmCIF accessors to Python" \ 6 | about.home="http://sw-tools.rcsb.org/apps/CORE-WRAPPER/index.html" \ 7 | software.version="1.005-4b3-deb-py2" \ 8 | version="1" \ 9 | about.license_file="/usr/share/doc/corepywrap/copyright" \ 10 | about.tags="" 11 | 12 | ENV DEBIAN_FRONTEND noninteractive 13 | RUN apt-get update && apt-get install -y python-corepywrap && apt-get clean && apt-get purge && rm -rf /var/lib/apt/lists/* /tmp/* 14 | USER biodocker 15 | -------------------------------------------------------------------------------- /csb/1.2.3dfsg-3-deb-py2/Dockerfile: -------------------------------------------------------------------------------- 1 | FROM biocontainers/biocontainers:debian-stretch-backports 2 | MAINTAINER biocontainers 3 | LABEL software="csb" \ 4 | container="csb" \ 5 | about.summary="Python framework for structural bioinformatics" \ 6 | about.home="http://csb.codeplex.com/" \ 7 | software.version="1.2.3dfsg-3-deb-py2" \ 8 | version="1" \ 9 | about.copyright="2012-2013 Michael Habeck ," \ 10 | about.license="Expat" \ 11 | about.license_file="/usr/share/doc/csb/copyright" \ 12 | about.tags="" 13 | 14 | ENV DEBIAN_FRONTEND noninteractive 15 | RUN apt-get update && apt-get install -y python-csb && apt-get clean && apt-get purge && rm -rf /var/lib/apt/lists/* /tmp/* 16 | USER biodocker 17 | -------------------------------------------------------------------------------- /csb/1.2.3dfsg-3-deb-py3/Dockerfile: -------------------------------------------------------------------------------- 1 | FROM biocontainers/biocontainers:debian-stretch-backports 2 | MAINTAINER biocontainers 3 | LABEL software="csb" \ 4 | container="csb" \ 5 | about.summary="Python framework for structural bioinformatics (Python3 version)" \ 6 | about.home="http://csb.codeplex.com/" \ 7 | software.version="1.2.3dfsg-3-deb-py3" \ 8 | version="1" \ 9 | about.copyright="2012-2013 Michael Habeck ," \ 10 | about.license="Expat" \ 11 | about.license_file="/usr/share/doc/csb/copyright" \ 12 | about.tags="" 13 | 14 | ENV DEBIAN_FRONTEND noninteractive 15 | RUN apt-get update && apt-get install -y python3-csb && apt-get clean && apt-get purge && rm -rf /var/lib/apt/lists/* /tmp/* 16 | USER biodocker 17 | -------------------------------------------------------------------------------- /cutadapt/1.12-2-deb-py2/Dockerfile: -------------------------------------------------------------------------------- 1 | FROM biocontainers/biocontainers:debian-stretch-backports 2 | MAINTAINER biocontainers 3 | LABEL software="cutadapt" \ 4 | container="cutadapt" \ 5 | about.summary="Clean biological sequences from high-throughput sequencing reads (Python 2)" \ 6 | about.home="http://pypi.python.org/pypi/cutadapt" \ 7 | software.version="1.12-2-deb-py2" \ 8 | version="1" \ 9 | about.copyright="2010-2015 Marcel Martin " \ 10 | about.license="Expat" \ 11 | about.license_file="/usr/share/doc/cutadapt/copyright" \ 12 | about.tags="" 13 | 14 | ENV DEBIAN_FRONTEND noninteractive 15 | RUN apt-get update && apt-get install -y python-cutadapt && apt-get clean && apt-get purge && rm -rf /var/lib/apt/lists/* /tmp/* 16 | USER biodocker 17 | -------------------------------------------------------------------------------- /cutadapt/1.12-2-deb-py3/Dockerfile: -------------------------------------------------------------------------------- 1 | FROM biocontainers/biocontainers:debian-stretch-backports 2 | MAINTAINER biocontainers 3 | LABEL software="cutadapt" \ 4 | container="cutadapt" \ 5 | about.summary="Clean biological sequences from high-throughput sequencing reads (Python 3)" \ 6 | about.home="http://pypi.python.org/pypi/cutadapt" \ 7 | software.version="1.12-2-deb-py3" \ 8 | version="1" \ 9 | about.copyright="2010-2015 Marcel Martin " \ 10 | about.license="Expat" \ 11 | about.license_file="/usr/share/doc/cutadapt/copyright" \ 12 | about.tags="" 13 | 14 | ENV DEBIAN_FRONTEND noninteractive 15 | RUN apt-get update && apt-get install -y python3-cutadapt && apt-get clean && apt-get purge && rm -rf /var/lib/apt/lists/* /tmp/* 16 | USER biodocker 17 | -------------------------------------------------------------------------------- /cwltool/1.0.20170114120503-1-deb/Dockerfile: -------------------------------------------------------------------------------- 1 | FROM biocontainers/biocontainers:debian-stretch-backports 2 | MAINTAINER biocontainers 3 | LABEL software="cwltool" \ 4 | container="cwltool" \ 5 | about.summary="Common workflow language reference implementation" \ 6 | about.home="http://www.commonwl.org" \ 7 | software.version="1.0.20170114120503-1-deb" \ 8 | version="1" \ 9 | about.copyright="No copyright declared" \ 10 | about.license="Apache-2.0" \ 11 | about.license_file="/usr/share/doc/cwltool/copyright" \ 12 | extra.binaries="/usr/bin/cwltool" \ 13 | about.tags="" 14 | 15 | ENV DEBIAN_FRONTEND noninteractive 16 | RUN apt-get update && apt-get install -y cwltool && apt-get clean && apt-get purge && rm -rf /var/lib/apt/lists/* /tmp/* 17 | USER biodocker 18 | -------------------------------------------------------------------------------- /dask/2023.10.1-py11-ol9/conda-env.yml: -------------------------------------------------------------------------------- 1 | channels: 2 | - conda-forge 3 | - defaults 4 | dependencies: 5 | - python=3.11 6 | - pip 7 | - bokeh>=2.4.2,<3 8 | - cachey=0.2.1 9 | - cytoolz>=0.12 10 | - dask=2023.10.1 11 | - distributed=2023.10.1 12 | - h5py 13 | - jq=1.6 14 | - jupyter-server-proxy 15 | - lz4>=4.3.2 16 | - msgpack-python 17 | - nomkl=3.0 18 | - numpy>=1.26.0 19 | - pandas=1.5.1 20 | - psutil>=5.7.2 21 | - python-blosc=1.10.6 22 | - s3fs>=2021.9.0 23 | - scipy>=1.9.1 24 | - streamz=0.6.3 25 | - tblib>=1.6.0 26 | - zarr=2.16.1 27 | - pip: 28 | - cloudpickle==3.0.0 29 | -------------------------------------------------------------------------------- /dask/2023.10.1-py11-ol9/scripts/prepare.sh: -------------------------------------------------------------------------------- 1 | #!/bin/bash -ue 2 | # Prepare the given dir by creating it, or cleaning it 3 | # of Dask content if it already exists. 4 | work_dir=$1 5 | 6 | if [[ ! -d "${work_dir}" ]] ; then 7 | echo "Creating work directory: ${work_dir}" 8 | mkdir -p "${work_dir}" 9 | else 10 | echo "Cleaning existing work directory: ${work_dir}" 11 | rm -rf ${work_dir}/* || true 12 | fi 13 | -------------------------------------------------------------------------------- /dawg/1.2-1b1-deb/Dockerfile: -------------------------------------------------------------------------------- 1 | FROM biocontainers/biocontainers:debian-stretch-backports 2 | MAINTAINER biocontainers 3 | LABEL software="dawg" \ 4 | container="dawg" \ 5 | about.summary="program to simulate the evolution of recombinant DNA sequences" \ 6 | about.home="http://scit.us/projects/dawg" \ 7 | software.version="1.2-1b1-deb" \ 8 | version="1" \ 9 | about.license_file="/usr/share/doc/dawg/copyright" \ 10 | extra.binaries="/usr/bin/dawg" \ 11 | about.tags="" 12 | 13 | ENV DEBIAN_FRONTEND noninteractive 14 | RUN apt-get update && apt-get install -y dawg && apt-get clean && apt-get purge && rm -rf /var/lib/apt/lists/* /tmp/* 15 | USER biodocker 16 | -------------------------------------------------------------------------------- /dendropy/4.2.0dfsg-1-deb-py2/Dockerfile: -------------------------------------------------------------------------------- 1 | FROM biocontainers/biocontainers:debian-stretch-backports 2 | MAINTAINER biocontainers 3 | LABEL software="dendropy" \ 4 | container="dendropy" \ 5 | about.summary="DendroPy Phylogenetic Computing Library (Python 2)" \ 6 | about.home="http://dendropy.org/" \ 7 | software.version="4.2.0dfsg-1-deb-py2" \ 8 | version="1" \ 9 | about.copyright="2014 Jeet Sukumaran " \ 10 | about.license="BSD-3-clause" \ 11 | about.license_file="/usr/share/doc/dendropy/copyright" \ 12 | about.tags="" 13 | 14 | ENV DEBIAN_FRONTEND noninteractive 15 | RUN apt-get update && apt-get install -y python-dendropy && apt-get clean && apt-get purge && rm -rf /var/lib/apt/lists/* /tmp/* 16 | USER biodocker 17 | -------------------------------------------------------------------------------- /dendropy/4.2.0dfsg-1-deb-py3/Dockerfile: -------------------------------------------------------------------------------- 1 | FROM biocontainers/biocontainers:debian-stretch-backports 2 | MAINTAINER biocontainers 3 | LABEL software="dendropy" \ 4 | container="dendropy" \ 5 | about.summary="DendroPy Phylogenetic Computing Library (Python 3)" \ 6 | about.home="http://dendropy.org/" \ 7 | software.version="4.2.0dfsg-1-deb-py3" \ 8 | version="1" \ 9 | about.copyright="2014 Jeet Sukumaran " \ 10 | about.license="BSD-3-clause" \ 11 | about.license_file="/usr/share/doc/dendropy/copyright" \ 12 | about.tags="" 13 | 14 | ENV DEBIAN_FRONTEND noninteractive 15 | RUN apt-get update && apt-get install -y python3-dendropy && apt-get clean && apt-get purge && rm -rf /var/lib/apt/lists/* /tmp/* 16 | USER biodocker 17 | -------------------------------------------------------------------------------- /dia-umpire/2.1.2/input/DIA_Umpire_Manual_v1.4_pre.pdf: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/BioContainers/containers/eb5588f9c03e93c54879252645e9f9ded1de4e71/dia-umpire/2.1.2/input/DIA_Umpire_Manual_v1.4_pre.pdf -------------------------------------------------------------------------------- /dicompyler/0.4.2-3-deb/Dockerfile: -------------------------------------------------------------------------------- 1 | FROM biocontainers/biocontainers:debian-stretch-backports 2 | MAINTAINER biocontainers 3 | LABEL software="dicompyler" \ 4 | container="dicompyler" \ 5 | about.summary="radiation therapy research platform" \ 6 | about.home="http://www.dicompyler.com/" \ 7 | software.version="0.4.2-3-deb" \ 8 | version="1" \ 9 | about.copyright=" 2005-2014 Aditya Panchal " \ 10 | about.license="BSD-3-clause" \ 11 | about.license_file="/usr/share/doc/dicompyler/copyright" \ 12 | extra.binaries="/usr/bin/dicompyler" \ 13 | about.tags="" 14 | 15 | ENV DEBIAN_FRONTEND noninteractive 16 | RUN apt-get update && apt-get install -y dicompyler && apt-get clean && apt-get purge && rm -rf /var/lib/apt/lists/* /tmp/* 17 | USER biodocker 18 | -------------------------------------------------------------------------------- /dictobj/0.4-1-deb-py2/Dockerfile: -------------------------------------------------------------------------------- 1 | FROM biocontainers/biocontainers:debian-stretch-backports 2 | MAINTAINER biocontainers 3 | LABEL software="dictobj" \ 4 | container="dictobj" \ 5 | about.summary="Dictionary where keys can be accessed as instance attributes" \ 6 | about.home="http://pypi.python.org/pypi/dictobj" \ 7 | software.version="0.4-1-deb-py2" \ 8 | version="1" \ 9 | about.copyright="2012-2016 William Grim " \ 10 | about.license="Apache 2.0" \ 11 | about.license_file="/usr/share/doc/dictobj/copyright" \ 12 | about.tags="" 13 | 14 | ENV DEBIAN_FRONTEND noninteractive 15 | RUN apt-get update && apt-get install -y python-dictobj && apt-get clean && apt-get purge && rm -rf /var/lib/apt/lists/* /tmp/* 16 | USER biodocker 17 | -------------------------------------------------------------------------------- /dictobj/0.4-1-deb-py3/Dockerfile: -------------------------------------------------------------------------------- 1 | FROM biocontainers/biocontainers:debian-stretch-backports 2 | MAINTAINER biocontainers 3 | LABEL software="dictobj" \ 4 | container="dictobj" \ 5 | about.summary="Dictionary where keys can be accessed as instance attributes" \ 6 | about.home="http://pypi.python.org/pypi/dictobj" \ 7 | software.version="0.4-1-deb-py3" \ 8 | version="1" \ 9 | about.copyright="2012-2016 William Grim " \ 10 | about.license="Apache 2.0" \ 11 | about.license_file="/usr/share/doc/dictobj/copyright" \ 12 | about.tags="" 13 | 14 | ENV DEBIAN_FRONTEND noninteractive 15 | RUN apt-get update && apt-get install -y python3-dictobj && apt-get clean && apt-get purge && rm -rf /var/lib/apt/lists/* /tmp/* 16 | USER biodocker 17 | -------------------------------------------------------------------------------- /dindel/1.01dfsg-4b1-deb/Dockerfile: -------------------------------------------------------------------------------- 1 | FROM biocontainers/biocontainers:debian-stretch-backports 2 | MAINTAINER biocontainers 3 | LABEL software="dindel" \ 4 | container="dindel" \ 5 | about.summary="determines indel calls from short-read data" \ 6 | about.home="https://sites.google.com/site/keesalbers/soft/dindel" \ 7 | software.version="1.01dfsg-4b1-deb" \ 8 | version="1" \ 9 | about.license_file="/usr/share/doc/dindel/copyright" \ 10 | extra.binaries="/usr/bin/dindel" \ 11 | about.tags="" 12 | 13 | ENV DEBIAN_FRONTEND noninteractive 14 | RUN apt-get update && apt-get install -y dindel && apt-get clean && apt-get purge && rm -rf /var/lib/apt/lists/* /tmp/* 15 | USER biodocker 16 | -------------------------------------------------------------------------------- /discosnp/1.2.6-1b2-deb/Dockerfile: -------------------------------------------------------------------------------- 1 | FROM biocontainers/biocontainers:debian-stretch-backports 2 | MAINTAINER biocontainers 3 | LABEL software="discosnp" \ 4 | container="discosnp" \ 5 | about.summary="discovering Single Nucleotide Polymorphism from raw set(s) of reads" \ 6 | about.home="http://colibread.inria.fr/discosnp/" \ 7 | software.version="1.2.6-1b2-deb" \ 8 | version="1" \ 9 | about.license_file="/usr/share/doc/discosnp/copyright" \ 10 | extra.binaries="/usr/bin/discoSnp_to_csv,/usr/bin/discoSnp_to_genotypes,/usr/bin/kissnp2,/usr/bin/kissreads" \ 11 | about.tags="" 12 | 13 | ENV DEBIAN_FRONTEND noninteractive 14 | RUN apt-get update && apt-get install -y discosnp && apt-get clean && apt-get purge && rm -rf /var/lib/apt/lists/* /tmp/* 15 | USER biodocker 16 | -------------------------------------------------------------------------------- /disulfinder-data/1.2.11-6-deb/Dockerfile: -------------------------------------------------------------------------------- 1 | FROM biocontainers/biocontainers:debian-stretch-backports 2 | MAINTAINER biocontainers 3 | LABEL software="disulfinder-data" \ 4 | container="disulfinder-data" \ 5 | about.summary="data files for predictor of disulfide bonds in proteins" \ 6 | about.home="http://disulfind.dsi.unifi.it/" \ 7 | software.version="1.2.11-6-deb" \ 8 | version="1" \ 9 | about.copyright=" 2011 Alessio Ceroni," \ 10 | about.license="GPL-2+" \ 11 | about.license_file="/usr/share/doc/disulfinder-data/copyright" \ 12 | about.tags="role::app-data" 13 | 14 | ENV DEBIAN_FRONTEND noninteractive 15 | RUN apt-get update && apt-get install -y disulfinder-data && apt-get clean && apt-get purge && rm -rf /var/lib/apt/lists/* /tmp/* 16 | USER biodocker 17 | -------------------------------------------------------------------------------- /dna-jellyfish/2.2.6-1b1-deb-py3/Dockerfile: -------------------------------------------------------------------------------- 1 | FROM biocontainers/biocontainers:debian-stretch-backports 2 | MAINTAINER biocontainers 3 | LABEL software="dna-jellyfish" \ 4 | container="dna-jellyfish" \ 5 | about.summary="count k-mers in DNA sequences (Python bindings of jellyfish)" \ 6 | about.home="http://www.cbcb.umd.edu/software/jellyfish/" \ 7 | software.version="2.2.6-1b1-deb-py3" \ 8 | version="1" \ 9 | about.license_file="/usr/share/doc/dna-jellyfish/copyright" \ 10 | about.tags="" 11 | 12 | ENV DEBIAN_FRONTEND noninteractive 13 | RUN apt-get update && apt-get install -y python3-dna-jellyfish && apt-get clean && apt-get purge && rm -rf /var/lib/apt/lists/* /tmp/* 14 | USER biodocker 15 | -------------------------------------------------------------------------------- /dssp/2.2.1-3b2-deb/Dockerfile: -------------------------------------------------------------------------------- 1 | FROM biocontainers/biocontainers:debian-stretch-backports 2 | MAINTAINER biocontainers 3 | LABEL software="dssp" \ 4 | container="dssp" \ 5 | about.summary="protein secondary structure assignment based on 3D structure" \ 6 | about.home="http://www.cmbi.ru.nl/dssp.html" \ 7 | software.version="2.2.1-3b2-deb" \ 8 | version="1" \ 9 | about.license_file="/usr/share/doc/dssp/copyright" \ 10 | extra.binaries="/usr/bin/dssp,/usr/bin/mkdssp" \ 11 | about.tags="" 12 | 13 | ENV DEBIAN_FRONTEND noninteractive 14 | RUN apt-get update && apt-get install -y dssp && apt-get clean && apt-get purge && rm -rf /var/lib/apt/lists/* /tmp/* 15 | USER biodocker 16 | -------------------------------------------------------------------------------- /dwgsim/0.1.11-3b1-deb/Dockerfile: -------------------------------------------------------------------------------- 1 | FROM biocontainers/biocontainers:debian-stretch-backports 2 | MAINTAINER biocontainers 3 | LABEL software="dwgsim" \ 4 | container="dwgsim" \ 5 | about.summary="short sequencing read simulator" \ 6 | about.home="https://github.com/nh13/DWGSIM/" \ 7 | software.version="0.1.11-3b1-deb" \ 8 | version="1" \ 9 | about.license_file="/usr/share/doc/dwgsim/copyright" \ 10 | extra.binaries="/usr/bin/dwgsim" \ 11 | about.tags="" 12 | 13 | ENV DEBIAN_FRONTEND noninteractive 14 | RUN apt-get update && apt-get install -y dwgsim && apt-get clean && apt-get purge && rm -rf /var/lib/apt/lists/* /tmp/* 15 | USER biodocker 16 | -------------------------------------------------------------------------------- /edtsurf/0.2009-4b1-deb/Dockerfile: -------------------------------------------------------------------------------- 1 | FROM biocontainers/biocontainers:debian-stretch-backports 2 | MAINTAINER biocontainers 3 | LABEL software="edtsurf" \ 4 | container="edtsurf" \ 5 | about.summary="triangulated mesh surfaces for protein structures" \ 6 | about.home="http://zhanglab.ccmb.med.umich.edu/EDTSurf/" \ 7 | software.version="0.2009-4b1-deb" \ 8 | version="1" \ 9 | about.license_file="/usr/share/doc/edtsurf/copyright" \ 10 | extra.binaries="/usr/bin/EDTSurf" \ 11 | about.tags="" 12 | 13 | ENV DEBIAN_FRONTEND noninteractive 14 | RUN apt-get update && apt-get install -y edtsurf && apt-get clean && apt-get purge && rm -rf /var/lib/apt/lists/* /tmp/* 15 | USER biodocker 16 | -------------------------------------------------------------------------------- /eido/0.1.6/Dockerfile: -------------------------------------------------------------------------------- 1 | # Base Image 2 | FROM ubuntu:latest 3 | 4 | # Metadata 5 | LABEL base_image="biocontainers:latest" 6 | LABEL version="1" 7 | LABEL software="eido" 8 | LABEL software.version="0.1.6" 9 | LABEL about.summary="An open source tool used to validate and convert PEP format sample metadata against a schema." 10 | LABEL about.home="http://eido.databio.org/en/latest/" 11 | LABEL about.license="BSD-2-Clause" 12 | LABEL about.tags="PEP, metadata, validation" 13 | LABEL extra.identifiers.biotools=eido-python-package 14 | 15 | # Maintainer 16 | MAINTAINER Nathan Sheffield 17 | 18 | USER root 19 | 20 | RUN apt-get update && \ 21 | apt-get install -y python3 python3-pip && \ 22 | pip3 install eido==0.1.6 23 | -------------------------------------------------------------------------------- /eido/0.1.8/Dockerfile: -------------------------------------------------------------------------------- 1 | # Base Image 2 | FROM ubuntu:latest 3 | 4 | # Metadata 5 | LABEL base_image="biocontainers:latest" 6 | LABEL version="1" 7 | LABEL software="eido" 8 | LABEL software.version="0.1.8" 9 | LABEL about.summary="An open source tool used to validate and convert PEP format sample metadata against a schema." 10 | LABEL about.home="http://eido.databio.org/en/latest/" 11 | LABEL about.license="BSD-2-Clause" 12 | LABEL about.tags="PEP, metadata, validation" 13 | LABEL extra.identifiers.biotools=eido-python-package 14 | 15 | # Maintainer 16 | MAINTAINER Nathan Sheffield 17 | 18 | USER root 19 | 20 | RUN apt-get update && \ 21 | apt-get install -y python3 python3-pip && \ 22 | pip3 install eido==0.1.8 23 | -------------------------------------------------------------------------------- /eido/0.1.9/Dockerfile: -------------------------------------------------------------------------------- 1 | # Base Image 2 | FROM ubuntu:latest 3 | 4 | # Metadata 5 | LABEL base_image="biocontainers:latest" 6 | LABEL version="2" 7 | LABEL software="eido" 8 | LABEL software.version="0.1.9" 9 | LABEL about.summary="An open source tool used to validate and convert PEP format sample metadata against a schema." 10 | LABEL about.home="http://eido.databio.org/en/latest/" 11 | LABEL about.license="BSD-2-Clause" 12 | LABEL about.tags="PEP, metadata, validation" 13 | LABEL extra.identifiers.biotools=eido-python-package 14 | 15 | # Maintainer 16 | MAINTAINER Nathan Sheffield 17 | 18 | USER root 19 | 20 | RUN apt-get update && \ 21 | apt-get install -y python3 python3-pip && \ 22 | pip3 install peppy==0.35.2 && \ 23 | pip3 install eido==0.1.9 24 | -------------------------------------------------------------------------------- /falcon-ms/0.1.3/Dockerfile: -------------------------------------------------------------------------------- 1 | FROM python:3 2 | 3 | LABEL base_image="python:3" 4 | LABEL version="1" 5 | LABEL software="falcon-ms" 6 | LABEL software.version="0.1.3" 7 | LABEL about.summary="Large-scale tandem mass spectrum clustering using fast nearest neighbor searching" 8 | LABEL about.home="https://github.com/bittremieux/falcon" 9 | LABEL about.license="BSD-3-Clause" 10 | LABEL about.license_file="https://github.com/bittremieux/falcon/blob/main/LICENSE.txt" 11 | LABEL about.documentation="https://github.com/bittremieux/falcon/blob/main/README.md" 12 | LABEL maintainer ="olivier.sallou@irisa.fr" 13 | 14 | RUN pip install falcon-ms==v0.1.3 15 | -------------------------------------------------------------------------------- /famli/1.0/tests.bats: -------------------------------------------------------------------------------- 1 | #!/usr/bin/env bats 2 | 3 | @test "FASTX Toolkit 0.0.13" { 4 | v="$(fastq_quality_trimmer -h 2>&1 || true )" 5 | [[ "$v" =~ "FASTX Toolkit 0.0.13" ]] 6 | } 7 | 8 | 9 | @test "AWS CLI" { 10 | v="$(aws --version 2>&1)" 11 | [[ "$v" =~ "aws-cli" ]] 12 | } 13 | 14 | 15 | @test "Curl v7.47.0" { 16 | v="$(curl --version)" 17 | [[ "$v" =~ "7.47.0" ]] 18 | } 19 | 20 | @test "DIAMOND v0.9.10" { 21 | v="$(diamond --version)" 22 | [[ "$v" =~ "0.9.10" ]] 23 | } 24 | 25 | @test "Make sure the run script is in the PATH" { 26 | h="$(famli -h 2>&1)" 27 | 28 | [[ "$h" =~ "FAMLI" ]] 29 | } 30 | -------------------------------------------------------------------------------- /fast5/0.5.8-1b2-deb-py2/Dockerfile: -------------------------------------------------------------------------------- 1 | FROM biocontainers/biocontainers:debian-stretch-backports 2 | MAINTAINER biocontainers 3 | LABEL software="fast5" \ 4 | container="fast5" \ 5 | about.summary="library for reading Oxford Nanopore Fast5 files -- Python 2" \ 6 | about.home="https://github.com/mateidavid/fast5" \ 7 | software.version="0.5.8-1b2-deb-py2" \ 8 | version="1" \ 9 | about.license_file="/usr/share/doc/fast5/copyright" \ 10 | about.tags="" 11 | 12 | ENV DEBIAN_FRONTEND noninteractive 13 | RUN apt-get update && apt-get install -y python-fast5 && apt-get clean && apt-get purge && rm -rf /var/lib/apt/lists/* /tmp/* 14 | USER biodocker 15 | -------------------------------------------------------------------------------- /fast5/0.5.8-1b2-deb-py3/Dockerfile: -------------------------------------------------------------------------------- 1 | FROM biocontainers/biocontainers:debian-stretch-backports 2 | MAINTAINER biocontainers 3 | LABEL software="fast5" \ 4 | container="fast5" \ 5 | about.summary="library for reading Oxford Nanopore Fast5 files -- Python 3" \ 6 | about.home="https://github.com/mateidavid/fast5" \ 7 | software.version="0.5.8-1b2-deb-py3" \ 8 | version="1" \ 9 | about.license_file="/usr/share/doc/fast5/copyright" \ 10 | about.tags="" 11 | 12 | ENV DEBIAN_FRONTEND noninteractive 13 | RUN apt-get update && apt-get install -y python3-fast5 && apt-get clean && apt-get purge && rm -rf /var/lib/apt/lists/* /tmp/* 14 | USER biodocker 15 | -------------------------------------------------------------------------------- /fastahack/0.020160702-1b1-deb/Dockerfile: -------------------------------------------------------------------------------- 1 | FROM biocontainers/biocontainers:debian-stretch-backports 2 | MAINTAINER biocontainers 3 | LABEL software="fastahack" \ 4 | container="fastahack" \ 5 | about.summary="utility for indexing and sequence extraction from FASTA files" \ 6 | about.home="https://github.com/ekg/fastahack" \ 7 | software.version="0.020160702-1b1-deb" \ 8 | version="1" \ 9 | about.license_file="/usr/share/doc/fastahack/copyright" \ 10 | extra.binaries="/usr/bin/fastahack" \ 11 | about.tags="" 12 | 13 | ENV DEBIAN_FRONTEND noninteractive 14 | RUN apt-get update && apt-get install -y fastahack && apt-get clean && apt-get purge && rm -rf /var/lib/apt/lists/* /tmp/* 15 | USER biodocker 16 | -------------------------------------------------------------------------------- /filo/1.1.0-3b1-deb/Dockerfile: -------------------------------------------------------------------------------- 1 | FROM biocontainers/biocontainers:debian-stretch-backports 2 | MAINTAINER biocontainers 3 | LABEL software="filo" \ 4 | container="filo" \ 5 | about.summary="FILe and stream Operations" \ 6 | about.home="https://github.com/arq5x/filo" \ 7 | software.version="1.1.0-3b1-deb" \ 8 | version="1" \ 9 | about.license_file="/usr/share/doc/filo/copyright" \ 10 | extra.binaries="/usr/bin/groupBy" \ 11 | about.tags="" 12 | 13 | ENV DEBIAN_FRONTEND noninteractive 14 | RUN apt-get update && apt-get install -y filo && apt-get clean && apt-get purge && rm -rf /var/lib/apt/lists/* /tmp/* 15 | USER biodocker 16 | -------------------------------------------------------------------------------- /fis-gtm-6.3-000a/6.3-000A-1-deb/Dockerfile: -------------------------------------------------------------------------------- 1 | FROM biocontainers/biocontainers:debian-stretch-backports 2 | MAINTAINER biocontainers 3 | LABEL software="fis-gtm-6.3-000a" \ 4 | container="fis-gtm-6.3-000a" \ 5 | about.summary="package for FIS-GT.M database" \ 6 | about.home="http://sourceforge.net/projects/fis-gtm" \ 7 | software.version="6.3-000A-1-deb" \ 8 | version="1" \ 9 | about.copyright="1987 - 2003 Sanchez Computer Associates" \ 10 | about.license="AGPL-3.0" \ 11 | about.license_file="/usr/share/doc/fis-gtm-6.3-000a/copyright" \ 12 | about.tags="uitoolkit::ncurses" 13 | 14 | ENV DEBIAN_FRONTEND noninteractive 15 | RUN apt-get update && apt-get install -y fis-gtm-6.3-000a && apt-get clean && apt-get purge && rm -rf /var/lib/apt/lists/* /tmp/* 16 | USER biodocker 17 | -------------------------------------------------------------------------------- /fis-gtm/6.3-000A-1-deb/Dockerfile: -------------------------------------------------------------------------------- 1 | FROM biocontainers/biocontainers:debian-stretch-backports 2 | MAINTAINER biocontainers 3 | LABEL software="fis-gtm" \ 4 | container="fis-gtm" \ 5 | about.summary="metapackage for the latest version of FIS-GT.M database" \ 6 | about.home="http://sourceforge.net/projects/fis-gtm" \ 7 | software.version="6.3-000A-1-deb" \ 8 | version="1" \ 9 | about.copyright="1987 - 2003 Sanchez Computer Associates" \ 10 | about.license="AGPL-3.0" \ 11 | about.license_file="/usr/share/doc/fis-gtm/copyright" \ 12 | about.tags="" 13 | 14 | ENV DEBIAN_FRONTEND noninteractive 15 | RUN apt-get update && apt-get install -y fis-gtm && apt-get clean && apt-get purge && rm -rf /var/lib/apt/lists/* /tmp/* 16 | USER biodocker 17 | -------------------------------------------------------------------------------- /flexbar/2.50-2b1-deb/Dockerfile: -------------------------------------------------------------------------------- 1 | FROM biocontainers/biocontainers:debian-stretch-backports 2 | MAINTAINER biocontainers 3 | LABEL software="flexbar" \ 4 | container="flexbar" \ 5 | about.summary="flexible barcode and adapter removal for sequencing platforms" \ 6 | about.home="https://sourceforge.net/projects/flexbar/" \ 7 | software.version="2.50-2b1-deb" \ 8 | version="1" \ 9 | about.license_file="/usr/share/doc/flexbar/copyright" \ 10 | extra.binaries="/usr/bin/flexbar" \ 11 | about.tags="" 12 | 13 | ENV DEBIAN_FRONTEND noninteractive 14 | RUN apt-get update && apt-get install -y flexbar && apt-get clean && apt-get purge && rm -rf /var/lib/apt/lists/* /tmp/* 15 | USER biodocker 16 | -------------------------------------------------------------------------------- /fml-asm/0.1-2b1-deb/Dockerfile: -------------------------------------------------------------------------------- 1 | FROM biocontainers/biocontainers:debian-stretch-backports 2 | MAINTAINER biocontainers 3 | LABEL software="fml-asm" \ 4 | container="fml-asm" \ 5 | about.summary="tool for assembling Illumina short reads in small regions" \ 6 | about.home="https://github.com/lh3/fermi-lite" \ 7 | software.version="0.1-2b1-deb" \ 8 | version="1" \ 9 | about.license_file="/usr/share/doc/fml-asm/copyright" \ 10 | extra.binaries="/usr/bin/fml-asm" \ 11 | about.tags="" 12 | 13 | ENV DEBIAN_FRONTEND noninteractive 14 | RUN apt-get update && apt-get install -y fml-asm && apt-get clean && apt-get purge && rm -rf /var/lib/apt/lists/* /tmp/* 15 | USER biodocker 16 | -------------------------------------------------------------------------------- /freecontact/1.1-2b2-deb-py2/Dockerfile: -------------------------------------------------------------------------------- 1 | FROM biocontainers/biocontainers:debian-stretch-backports 2 | MAINTAINER biocontainers 3 | LABEL software="freecontact" \ 4 | container="freecontact" \ 5 | about.summary="fast protein contact predictor - binding for Python" \ 6 | about.home="http://rostlab.org/" \ 7 | software.version="1.1-2b2-deb-py2" \ 8 | version="1" \ 9 | about.license_file="/usr/share/doc/freecontact/copyright" \ 10 | about.tags="" 11 | 12 | ENV DEBIAN_FRONTEND noninteractive 13 | RUN apt-get update && apt-get install -y python-freecontact && apt-get clean && apt-get purge && rm -rf /var/lib/apt/lists/* /tmp/* 14 | USER biodocker 15 | -------------------------------------------------------------------------------- /freediams-doc-en/0.9.4-1-deb/Dockerfile: -------------------------------------------------------------------------------- 1 | FROM biocontainers/biocontainers:debian-stretch-backports 2 | MAINTAINER biocontainers 3 | LABEL software="freediams-doc-en" \ 4 | container="freediams-doc-en" \ 5 | about.summary="FreeDiams English documentation" \ 6 | about.home="http://www.freemedforms.com/" \ 7 | software.version="0.9.4-1-deb" \ 8 | version="1" \ 9 | about.copyright="2008-2012 by Eric Maeker, MD" \ 10 | about.license="GPL-3+" \ 11 | about.license_file="/usr/share/doc/freediams-doc-en/copyright" \ 12 | about.tags="field::medicine, made-of::html, role::documentation" 13 | 14 | ENV DEBIAN_FRONTEND noninteractive 15 | RUN apt-get update && apt-get install -y freediams-doc-en && apt-get clean && apt-get purge && rm -rf /var/lib/apt/lists/* /tmp/* 16 | USER biodocker 17 | -------------------------------------------------------------------------------- /fsm-lite/1.0-2-deb/Dockerfile: -------------------------------------------------------------------------------- 1 | FROM biocontainers/biocontainers:debian-stretch-backports 2 | MAINTAINER biocontainers 3 | LABEL software="fsm-lite" \ 4 | container="fsm-lite" \ 5 | about.summary="frequency-based string mining (lite)" \ 6 | about.home="https://github.com/nvalimak/fsm-lite" \ 7 | software.version="1.0-2-deb" \ 8 | version="1" \ 9 | about.copyright="2015 Niko Vlimki " \ 10 | about.license="GPL-3" \ 11 | about.license_file="/usr/share/doc/fsm-lite/copyright" \ 12 | extra.binaries="/usr/bin/fsm-lite" \ 13 | about.tags="" 14 | 15 | ENV DEBIAN_FRONTEND noninteractive 16 | RUN apt-get update && apt-get install -y fsm-lite && apt-get clean && apt-get purge && rm -rf /var/lib/apt/lists/* /tmp/* 17 | USER biodocker 18 | -------------------------------------------------------------------------------- /galileo-daemon/0.5.1-4-deb/Dockerfile: -------------------------------------------------------------------------------- 1 | FROM biocontainers/biocontainers:debian-stretch-backports 2 | MAINTAINER biocontainers 3 | LABEL software="galileo-daemon" \ 4 | container="galileo-daemon" \ 5 | about.summary="Utility to securely synchronize a Fitbit device - daemon" \ 6 | about.home="https://bitbucket.org/benallard/galileo/" \ 7 | software.version="0.5.1-4-deb" \ 8 | version="1" \ 9 | about.copyright="2013-2016 Benot Allard" \ 10 | about.license="LGPL-3+" \ 11 | about.license_file="/usr/share/doc/galileo-daemon/copyright" \ 12 | about.tags="" 13 | 14 | ENV DEBIAN_FRONTEND noninteractive 15 | RUN apt-get update && apt-get install -y galileo-daemon && apt-get clean && apt-get purge && rm -rf /var/lib/apt/lists/* /tmp/* 16 | USER biodocker 17 | -------------------------------------------------------------------------------- /garli/2.1-1-deb/Dockerfile: -------------------------------------------------------------------------------- 1 | FROM biocontainers/biocontainers:debian-stretch-backports 2 | MAINTAINER biocontainers 3 | LABEL software="garli" \ 4 | container="garli" \ 5 | about.summary="phylogenetic analysis of molecular sequence data using maximum-likelihood" \ 6 | about.home="https://github.com/Ashod/garli" \ 7 | software.version="2.1-1-deb" \ 8 | version="1" \ 9 | about.copyright="2006-2014 Ashod Nakashian" \ 10 | about.license="GPL-3" \ 11 | about.license_file="/usr/share/doc/garli/copyright" \ 12 | extra.binaries="/usr/bin/garli" \ 13 | about.tags="" 14 | 15 | ENV DEBIAN_FRONTEND noninteractive 16 | RUN apt-get update && apt-get install -y garli && apt-get clean && apt-get purge && rm -rf /var/lib/apt/lists/* /tmp/* 17 | USER biodocker 18 | -------------------------------------------------------------------------------- /gdcm/2.6.6-3-deb-py2/Dockerfile: -------------------------------------------------------------------------------- 1 | FROM biocontainers/biocontainers:debian-stretch-backports 2 | MAINTAINER biocontainers 3 | LABEL software="gdcm" \ 4 | container="gdcm" \ 5 | about.summary="Grassroots DICOM Python bindings" \ 6 | about.home="http://gdcm.sourceforge.net/" \ 7 | software.version="2.6.6-3-deb-py2" \ 8 | version="1" \ 9 | about.copyright="2006-2011 Mathieu Malaterre" \ 10 | about.license="BSD-3-clause-alike-CREATIS" \ 11 | about.license_file="/usr/share/doc/gdcm/copyright" \ 12 | about.tags="" 13 | 14 | ENV DEBIAN_FRONTEND noninteractive 15 | RUN apt-get update && apt-get install -y python-gdcm && apt-get clean && apt-get purge && rm -rf /var/lib/apt/lists/* /tmp/* 16 | USER biodocker 17 | -------------------------------------------------------------------------------- /genometools-common/1.5.9ds-4-deb/Dockerfile: -------------------------------------------------------------------------------- 1 | FROM biocontainers/biocontainers:debian-stretch-backports 2 | MAINTAINER biocontainers 3 | LABEL software="genometools-common" \ 4 | container="genometools-common" \ 5 | about.summary="shared data files for GenomeTools" \ 6 | about.home="http://genometools.org" \ 7 | software.version="1.5.9ds-4-deb" \ 8 | version="1" \ 9 | extra.identifiers.biotools="genometools" \ 10 | about.license_file="/usr/share/doc/genometools-common/copyright" \ 11 | about.tags="role::app-data, uitoolkit::ncurses" 12 | 13 | ENV DEBIAN_FRONTEND noninteractive 14 | RUN apt-get update && apt-get install -y genometools-common && apt-get clean && apt-get purge && rm -rf /var/lib/apt/lists/* /tmp/* 15 | USER biodocker 16 | -------------------------------------------------------------------------------- /genometools/1.5.9ds-4-deb-py2/Dockerfile: -------------------------------------------------------------------------------- 1 | FROM biocontainers/biocontainers:debian-stretch-backports 2 | MAINTAINER biocontainers 3 | LABEL software="genometools" \ 4 | container="genometools" \ 5 | about.summary="Python bindings for genometools" \ 6 | about.home="http://genometools.org" \ 7 | software.version="1.5.9ds-4-deb-py2" \ 8 | version="1" \ 9 | extra.identifiers.biotools="genometools" \ 10 | about.license_file="/usr/share/doc/genometools/copyright" \ 11 | about.tags="devel::lang:python, devel::library, implemented-in::python,:devel-lib" 12 | 13 | ENV DEBIAN_FRONTEND noninteractive 14 | RUN apt-get update && apt-get install -y python-genometools && apt-get clean && apt-get purge && rm -rf /var/lib/apt/lists/* /tmp/* 15 | USER biodocker 16 | -------------------------------------------------------------------------------- /gnumed-common/1.6.11dfsg-3-deb/Dockerfile: -------------------------------------------------------------------------------- 1 | FROM biocontainers/biocontainers:debian-stretch-backports 2 | MAINTAINER biocontainers 3 | LABEL software="gnumed-common" \ 4 | container="gnumed-common" \ 5 | about.summary="medical practice management - common files" \ 6 | about.home="http://www.gnumed.de" \ 7 | software.version="1.6.11dfsg-3-deb" \ 8 | version="1" \ 9 | about.copyright=" 2000-2005 Horst Herb, a.o." \ 10 | about.license="GPL-2+" \ 11 | about.license_file="/usr/share/doc/gnumed-common/copyright" \ 12 | about.tags="field::medicine, made-of::TODO, role::app-data" 13 | 14 | ENV DEBIAN_FRONTEND noninteractive 15 | RUN apt-get update && apt-get install -y gnumed-common && apt-get clean && apt-get purge && rm -rf /var/lib/apt/lists/* /tmp/* 16 | USER biodocker 17 | -------------------------------------------------------------------------------- /gwas-fasp/v1.0.0/requirements.txt: -------------------------------------------------------------------------------- 1 | matplotlib==3.0.1 2 | numpy==1.16.5 3 | pandas==0.24.2 4 | argparse==1.1 5 | seaborn==0.9.0 6 | -------------------------------------------------------------------------------- /gwas-fasp/v1.0.0/scripts/create_plot.sh: -------------------------------------------------------------------------------- 1 | #!/bin/bash 2 | 3 | # args: logistic 4 | 5 | output_basename=$(basename $1 .assoc.logistic) 6 | manhattan_plot.py \ 7 | -i $1 \ 8 | -o ${output_basename}.png 9 | -------------------------------------------------------------------------------- /gwas-fasp/v1.0.0/scripts/run_gwas.sh: -------------------------------------------------------------------------------- 1 | #!/bin/bash 2 | 3 | # args: vcf ids sex phenotypes covariates 4 | 5 | output_basename=$(basename $1 .vcf.gz) 6 | 7 | plink \ 8 | --vcf $1 \ 9 | --maf 0.10 \ 10 | --update-ids $2 \ 11 | --make-bed \ 12 | --out $output_basename 13 | 14 | plink \ 15 | --bfile $output_basename \ 16 | --update-sex $3 \ 17 | --pheno $4 \ 18 | --make-bed \ 19 | --out $output_basename 20 | 21 | plink \ 22 | --bfile $output_basename \ 23 | --covar $5 \ 24 | --dummy-coding \ 25 | --write-covar 26 | 27 | plink \ 28 | --bfile $output_basename \ 29 | --logistic \ 30 | --covar plink.cov \ 31 | --out $output_basename 32 | 33 | sed -i -e 's/\s\+/,/g' -e 's/^,//g' -e 's/,$//g' $output_basename.assoc.logistic 34 | -------------------------------------------------------------------------------- /gwyddion-common/2.47-1-deb/Dockerfile: -------------------------------------------------------------------------------- 1 | FROM biocontainers/biocontainers:debian-stretch-backports 2 | MAINTAINER biocontainers 3 | LABEL software="gwyddion-common" \ 4 | container="gwyddion-common" \ 5 | about.summary="architecture-independent files for Gwyddion SPM analysis tool" \ 6 | about.home="http://gwyddion.net/" \ 7 | software.version="2.47-1-deb" \ 8 | version="1" \ 9 | about.copyright="2003-2016 David Necas (Yeti) " \ 10 | about.license="GPL-2+" \ 11 | about.license_file="/usr/share/doc/gwyddion-common/copyright" \ 12 | about.tags="role::app-data" 13 | 14 | ENV DEBIAN_FRONTEND noninteractive 15 | RUN apt-get update && apt-get install -y gwyddion-common && apt-get clean && apt-get purge && rm -rf /var/lib/apt/lists/* /tmp/* 16 | USER biodocker 17 | -------------------------------------------------------------------------------- /gwyddion-plugins/2.47-1-deb/Dockerfile: -------------------------------------------------------------------------------- 1 | FROM biocontainers/biocontainers:debian-stretch-backports 2 | MAINTAINER biocontainers 3 | LABEL software="gwyddion-plugins" \ 4 | container="gwyddion-plugins" \ 5 | about.summary="plugins for Gwyddion SPM analysis tool" \ 6 | about.home="http://gwyddion.net/" \ 7 | software.version="2.47-1-deb" \ 8 | version="1" \ 9 | about.copyright="2003-2016 David Necas (Yeti) " \ 10 | about.license="GPL-2+" \ 11 | about.license_file="/usr/share/doc/gwyddion-plugins/copyright" \ 12 | about.tags="role::plugin" 13 | 14 | ENV DEBIAN_FRONTEND noninteractive 15 | RUN apt-get update && apt-get install -y gwyddion-plugins && apt-get clean && apt-get purge && rm -rf /var/lib/apt/lists/* /tmp/* 16 | USER biodocker 17 | -------------------------------------------------------------------------------- /hl7/0.3.4-1-deb-py2/Dockerfile: -------------------------------------------------------------------------------- 1 | FROM biocontainers/biocontainers:debian-stretch-backports 2 | MAINTAINER biocontainers 3 | LABEL software="hl7" \ 4 | container="hl7" \ 5 | about.summary="Python library for parsing HL7 messages" \ 6 | about.home="https://github.com/johnpaulett/python-hl7/" \ 7 | software.version="0.3.4-1-deb-py2" \ 8 | version="1" \ 9 | about.copyright="2009-2014 John Paulett " \ 10 | about.license="BSD-3-clause" \ 11 | about.license_file="/usr/share/doc/hl7/copyright" \ 12 | about.tags="" 13 | 14 | ENV DEBIAN_FRONTEND noninteractive 15 | RUN apt-get update && apt-get install -y python-hl7 && apt-get clean && apt-get purge && rm -rf /var/lib/apt/lists/* /tmp/* 16 | USER biodocker 17 | -------------------------------------------------------------------------------- /hl7/0.3.4-1-deb-py3/Dockerfile: -------------------------------------------------------------------------------- 1 | FROM biocontainers/biocontainers:debian-stretch-backports 2 | MAINTAINER biocontainers 3 | LABEL software="hl7" \ 4 | container="hl7" \ 5 | about.summary="Python3 library for parsing HL7 messages" \ 6 | about.home="https://github.com/johnpaulett/python-hl7/" \ 7 | software.version="0.3.4-1-deb-py3" \ 8 | version="1" \ 9 | about.copyright="2009-2014 John Paulett " \ 10 | about.license="BSD-3-clause" \ 11 | about.license_file="/usr/share/doc/hl7/copyright" \ 12 | extra.binaries="/usr/bin/mllp_send" \ 13 | about.tags="" 14 | 15 | ENV DEBIAN_FRONTEND noninteractive 16 | RUN apt-get update && apt-get install -y python3-hl7 && apt-get clean && apt-get purge && rm -rf /var/lib/apt/lists/* /tmp/* 17 | USER biodocker 18 | -------------------------------------------------------------------------------- /htslib-test/1.3.2-2-deb/Dockerfile: -------------------------------------------------------------------------------- 1 | FROM biocontainers/biocontainers:debian-stretch-backports 2 | MAINTAINER biocontainers 3 | LABEL software="htslib-test" \ 4 | container="htslib-test" \ 5 | about.summary="Test data for HTSlib" \ 6 | about.home="https://github.com/samtools/htslib" \ 7 | software.version="1.3.2-2-deb" \ 8 | version="1" \ 9 | extra.identifiers.biotools="htslib" \ 10 | about.copyright=" 2012-2016 Genome Research Ltd." \ 11 | about.license="MIT" \ 12 | about.license_file="/usr/share/doc/htslib-test/copyright" \ 13 | about.tags="role::shared-lib" 14 | 15 | ENV DEBIAN_FRONTEND noninteractive 16 | RUN apt-get update && apt-get install -y htslib-test && apt-get clean && apt-get purge && rm -rf /var/lib/apt/lists/* /tmp/* 17 | USER biodocker 18 | -------------------------------------------------------------------------------- /hyphy-common/2.2.7dfsg-1-deb/Dockerfile: -------------------------------------------------------------------------------- 1 | FROM biocontainers/biocontainers:debian-stretch-backports 2 | MAINTAINER biocontainers 3 | LABEL software="hyphy-common" \ 4 | container="hyphy-common" \ 5 | about.summary="Hypothesis testing using Phylogenies (common files)" \ 6 | about.home="http://hyphy.org/" \ 7 | software.version="2.2.7dfsg-1-deb" \ 8 | version="1" \ 9 | about.copyright="1997-2015 Sergei L Kosakovsky Pond " \ 10 | about.license="MIT" \ 11 | about.license_file="/usr/share/doc/hyphy-common/copyright" \ 12 | about.tags="" 13 | 14 | ENV DEBIAN_FRONTEND noninteractive 15 | RUN apt-get update && apt-get install -y hyphy-common && apt-get clean && apt-get purge && rm -rf /var/lib/apt/lists/* /tmp/* 16 | USER biodocker 17 | -------------------------------------------------------------------------------- /hyphy-mpi/2.2.7dfsg-1b2-deb/Dockerfile: -------------------------------------------------------------------------------- 1 | FROM biocontainers/biocontainers:debian-stretch-backports 2 | MAINTAINER biocontainers 3 | LABEL software="hyphy-mpi" \ 4 | container="hyphy-mpi" \ 5 | about.summary="Hypothesis testing using Phylogenies (MPI version)" \ 6 | about.home="http://hyphy.org/" \ 7 | software.version="2.2.7dfsg-1b2-deb" \ 8 | version="1" \ 9 | about.license_file="/usr/share/doc/hyphy-mpi/copyright" \ 10 | extra.binaries="/usr/bin/hyphympi" \ 11 | about.tags="" 12 | 13 | ENV DEBIAN_FRONTEND noninteractive 14 | RUN apt-get update && apt-get install -y hyphy-mpi && apt-get clean && apt-get purge && rm -rf /var/lib/apt/lists/* /tmp/* 15 | USER biodocker 16 | -------------------------------------------------------------------------------- /hyphy-pt/2.2.7dfsg-1b2-deb/Dockerfile: -------------------------------------------------------------------------------- 1 | FROM biocontainers/biocontainers:debian-stretch-backports 2 | MAINTAINER biocontainers 3 | LABEL software="hyphy-pt" \ 4 | container="hyphy-pt" \ 5 | about.summary="Hypothesis testing using Phylogenies (pthreads version)" \ 6 | about.home="http://hyphy.org/" \ 7 | software.version="2.2.7dfsg-1b2-deb" \ 8 | version="1" \ 9 | about.license_file="/usr/share/doc/hyphy-pt/copyright" \ 10 | extra.binaries="/usr/bin/hyphymp" \ 11 | about.tags="" 12 | 13 | ENV DEBIAN_FRONTEND noninteractive 14 | RUN apt-get update && apt-get install -y hyphy-pt && apt-get clean && apt-get purge && rm -rf /var/lib/apt/lists/* /tmp/* 15 | USER biodocker 16 | -------------------------------------------------------------------------------- /hyphygui/2.2.7dfsg-1b2-deb/Dockerfile: -------------------------------------------------------------------------------- 1 | FROM biocontainers/biocontainers:debian-stretch-backports 2 | MAINTAINER biocontainers 3 | LABEL software="hyphygui" \ 4 | container="hyphygui" \ 5 | about.summary="Hypothesis testing using Phylogenies (GTK+ gui)" \ 6 | about.home="http://hyphy.org/" \ 7 | software.version="2.2.7dfsg-1b2-deb" \ 8 | version="1" \ 9 | about.license_file="/usr/share/doc/hyphygui/copyright" \ 10 | extra.binaries="/usr/bin/hyphygtk" \ 11 | about.tags="uitoolkit::gtk" 12 | 13 | ENV DEBIAN_FRONTEND noninteractive 14 | RUN apt-get update && apt-get install -y hyphygui && apt-get clean && apt-get purge && rm -rf /var/lib/apt/lists/* /tmp/* 15 | USER biodocker 16 | -------------------------------------------------------------------------------- /ilastik/1.4.0/test-cmds.txt: -------------------------------------------------------------------------------- 1 | /opt/ilastik-1.4.0-Linux/run_ilastik.sh --headless --version 2 | -------------------------------------------------------------------------------- /ilastik/1.4.1/test-cmds.txt: -------------------------------------------------------------------------------- 1 | /opt/ilastik-1.4.1-Linux/run_ilastik.sh --headless --version 2 | -------------------------------------------------------------------------------- /indelible/1.03-2b1-deb/Dockerfile: -------------------------------------------------------------------------------- 1 | FROM biocontainers/biocontainers:debian-stretch-backports 2 | MAINTAINER biocontainers 3 | LABEL software="indelible" \ 4 | container="indelible" \ 5 | about.summary="powerful and flexible simulator of biological evolution" \ 6 | about.home="http://abacus.gene.ucl.ac.uk/software/indelible/" \ 7 | software.version="1.03-2b1-deb" \ 8 | version="1" \ 9 | about.license_file="/usr/share/doc/indelible/copyright" \ 10 | extra.binaries="/usr/bin/indelible" \ 11 | about.tags="" 12 | 13 | ENV DEBIAN_FRONTEND noninteractive 14 | RUN apt-get update && apt-get install -y indelible && apt-get clean && apt-get purge && rm -rf /var/lib/apt/lists/* /tmp/* 15 | USER biodocker 16 | -------------------------------------------------------------------------------- /insighttoolkit4-python/4.10.1-dfsg1-1.1b1-deb/Dockerfile: -------------------------------------------------------------------------------- 1 | FROM biocontainers/biocontainers:debian-stretch-backports 2 | MAINTAINER biocontainers 3 | LABEL software="insighttoolkit4-python" \ 4 | container="insighttoolkit4-python" \ 5 | about.summary="Image processing toolkit for registration and segmentation - Python bindings" \ 6 | about.home="http://www.itk.org/" \ 7 | software.version="4.10.1-dfsg1-1.1b1-deb" \ 8 | version="1" \ 9 | about.license_file="/usr/share/doc/insighttoolkit4-python/copyright" \ 10 | about.tags="" 11 | 12 | ENV DEBIAN_FRONTEND noninteractive 13 | RUN apt-get update && apt-get install -y insighttoolkit4-python && apt-get clean && apt-get purge && rm -rf /var/lib/apt/lists/* /tmp/* 14 | USER biodocker 15 | -------------------------------------------------------------------------------- /isee-galaxy/3.13/scripts/monitor_traffic.sh: -------------------------------------------------------------------------------- 1 | #!/bin/bash 2 | 3 | # Copied from https://github.com/shiltemann/phinch-galaxy-ie (thanks!) 4 | 5 | # Take the netstat output the estimate if the client is still connected to 6 | # the Phinch server. The 'CLOSE_WAIT' state will be ignored. 7 | 8 | while true; do 9 | sleep 60 10 | 11 | if [ `netstat -t | grep -v CLOSE_WAIT | grep ':8888' | wc -l` -lt 1 ] 12 | then 13 | pkill Rscript 14 | fi 15 | 16 | done 17 | -------------------------------------------------------------------------------- /isee-galaxy/3.13/scripts/run.sh: -------------------------------------------------------------------------------- 1 | #!/usr/bin/env bash 2 | 3 | # Run isee by passing templated R script to Rscript 4 | # WDIR: /import 5 | 6 | # Automatically kill container when traffic stops 7 | /scripts/monitor_traffic.sh & 8 | 9 | Rscript --vanilla $1 10 | -------------------------------------------------------------------------------- /ismrmrd-schema/1.3.3-1-deb/Dockerfile: -------------------------------------------------------------------------------- 1 | FROM biocontainers/biocontainers:debian-stretch-backports 2 | MAINTAINER biocontainers 3 | LABEL software="ismrmrd-schema" \ 4 | container="ismrmrd-schema" \ 5 | about.summary="schema for ISMRMRD" \ 6 | about.home="http://ismrmrd.github.io/" \ 7 | software.version="1.3.3-1-deb" \ 8 | version="1" \ 9 | about.copyright="2013-2014 Michael S. Hansen " \ 10 | about.license="Expat" \ 11 | about.license_file="/usr/share/doc/ismrmrd-schema/copyright" \ 12 | about.tags="" 13 | 14 | ENV DEBIAN_FRONTEND noninteractive 15 | RUN apt-get update && apt-get install -y ismrmrd-schema && apt-get clean && apt-get purge && rm -rf /var/lib/apt/lists/* /tmp/* 16 | USER biodocker 17 | -------------------------------------------------------------------------------- /jaligner/1.0dfsg-4-deb/Dockerfile: -------------------------------------------------------------------------------- 1 | FROM biocontainers/biocontainers:debian-stretch-backports 2 | MAINTAINER biocontainers 3 | LABEL software="jaligner" \ 4 | container="jaligner" \ 5 | about.summary="Smith-Waterman algorithm with Gotoh's improvement" \ 6 | about.home="https://github.com/ahmedmoustafa/JAligner" \ 7 | software.version="1.0dfsg-4-deb" \ 8 | version="1" \ 9 | about.copyright="Ahmed Moustafa " \ 10 | about.license="GPL-2+" \ 11 | about.license_file="/usr/share/doc/jaligner/copyright" \ 12 | extra.binaries="/usr/bin/jaligner" \ 13 | about.tags="" 14 | 15 | ENV DEBIAN_FRONTEND noninteractive 16 | RUN apt-get update && apt-get install -y jaligner && apt-get clean && apt-get purge && rm -rf /var/lib/apt/lists/* /tmp/* 17 | USER biodocker 18 | -------------------------------------------------------------------------------- /jellyfish/2.2.6-1b1-deb/Dockerfile: -------------------------------------------------------------------------------- 1 | FROM biocontainers/biocontainers:debian-stretch-backports 2 | MAINTAINER biocontainers 3 | LABEL software="jellyfish" \ 4 | container="jellyfish" \ 5 | about.summary="count k-mers in DNA sequences" \ 6 | about.home="http://www.cbcb.umd.edu/software/jellyfish/" \ 7 | software.version="2.2.6-1b1-deb" \ 8 | version="1" \ 9 | about.license_file="/usr/share/doc/jellyfish/copyright" \ 10 | extra.binaries="/usr/bin/jellyfish" \ 11 | about.tags="" 12 | 13 | ENV DEBIAN_FRONTEND noninteractive 14 | RUN apt-get update && apt-get install -y jellyfish && apt-get clean && apt-get purge && rm -rf /var/lib/apt/lists/* /tmp/* 15 | USER biodocker 16 | -------------------------------------------------------------------------------- /kineticstools-data/0.6.120161222-1-deb/Dockerfile: -------------------------------------------------------------------------------- 1 | FROM biocontainers/biocontainers:debian-stretch-backports 2 | MAINTAINER biocontainers 3 | LABEL software="kineticstools-data" \ 4 | container="kineticstools-data" \ 5 | about.summary="detection of DNA modifications -- data files" \ 6 | about.home="https://github.com/PacificBiosciences/kineticsTools" \ 7 | software.version="0.6.120161222-1-deb" \ 8 | version="1" \ 9 | about.copyright="" \ 10 | about.license="PacBio-BSD-3-Clause" \ 11 | about.license_file="/usr/share/doc/kineticstools-data/copyright" \ 12 | about.tags="" 13 | 14 | ENV DEBIAN_FRONTEND noninteractive 15 | RUN apt-get update && apt-get install -y kineticstools-data && apt-get clean && apt-get purge && rm -rf /var/lib/apt/lists/* /tmp/* 16 | USER biodocker 17 | -------------------------------------------------------------------------------- /kineticstools/0.6.120161222-1-deb-py2/Dockerfile: -------------------------------------------------------------------------------- 1 | FROM biocontainers/biocontainers:debian-stretch-backports 2 | MAINTAINER biocontainers 3 | LABEL software="kineticstools" \ 4 | container="kineticstools" \ 5 | about.summary="detection of DNA modifications (Python 2 library)" \ 6 | about.home="https://github.com/PacificBiosciences/kineticsTools" \ 7 | software.version="0.6.120161222-1-deb-py2" \ 8 | version="1" \ 9 | about.copyright="" \ 10 | about.license="PacBio-BSD-3-Clause" \ 11 | about.license_file="/usr/share/doc/kineticstools/copyright" \ 12 | about.tags="" 13 | 14 | ENV DEBIAN_FRONTEND noninteractive 15 | RUN apt-get update && apt-get install -y python-kineticstools && apt-get clean && apt-get purge && rm -rf /var/lib/apt/lists/* /tmp/* 16 | USER biodocker 17 | -------------------------------------------------------------------------------- /kmer/020150903r2013-3-deb/Dockerfile: -------------------------------------------------------------------------------- 1 | FROM biocontainers/biocontainers:debian-stretch-backports 2 | MAINTAINER biocontainers 3 | LABEL software="kmer" \ 4 | container="kmer" \ 5 | about.summary="suite of tools for DNA sequence analysis" \ 6 | about.home="http://kmer.sourceforge.net" \ 7 | software.version="020150903r2013-3-deb" \ 8 | version="1" \ 9 | about.copyright=" 2002 PE Corporation (NY) through the Celera Genomics Group" \ 10 | about.license="GPL-2+" \ 11 | about.license_file="/usr/share/doc/kmer/copyright" \ 12 | about.tags="" 13 | 14 | ENV DEBIAN_FRONTEND noninteractive 15 | RUN apt-get update && apt-get install -y kmer && apt-get clean && apt-get purge && rm -rf /var/lib/apt/lists/* /tmp/* 16 | USER biodocker 17 | -------------------------------------------------------------------------------- /maffilter/1.1.0-1dfsg-2b2-deb/Dockerfile: -------------------------------------------------------------------------------- 1 | FROM biocontainers/biocontainers:debian-stretch-backports 2 | MAINTAINER biocontainers 3 | LABEL software="maffilter" \ 4 | container="maffilter" \ 5 | about.summary="process genome alignment in the Multiple Alignment Format" \ 6 | about.home="http://biopp.univ-montp2.fr/forge/maffilter" \ 7 | software.version="1.1.0-1dfsg-2b2-deb" \ 8 | version="1" \ 9 | about.license_file="/usr/share/doc/maffilter/copyright" \ 10 | extra.binaries="/usr/bin/maffilter" \ 11 | about.tags="" 12 | 13 | ENV DEBIAN_FRONTEND noninteractive 14 | RUN apt-get update && apt-get install -y maffilter && apt-get clean && apt-get purge && rm -rf /var/lib/apt/lists/* /tmp/* 15 | USER biodocker 16 | -------------------------------------------------------------------------------- /maqview/0.2.5-7b1-deb/Dockerfile: -------------------------------------------------------------------------------- 1 | FROM biocontainers/biocontainers:debian-stretch-backports 2 | MAINTAINER biocontainers 3 | LABEL software="maqview" \ 4 | container="maqview" \ 5 | about.summary="graphical read alignment viewer for short gene sequences" \ 6 | about.home="http://maq.sourceforge.net/maqview.shtml" \ 7 | software.version="0.2.5-7b1-deb" \ 8 | version="1" \ 9 | about.license_file="/usr/share/doc/maqview/copyright" \ 10 | extra.binaries="/usr/bin/maqindex,/usr/bin/maqindex_socks,/usr/bin/maqview,/usr/bin/zrio" \ 11 | about.tags="" 12 | 13 | ENV DEBIAN_FRONTEND noninteractive 14 | RUN apt-get update && apt-get install -y maqview && apt-get clean && apt-get purge && rm -rf /var/lib/apt/lists/* /tmp/* 15 | USER biodocker 16 | -------------------------------------------------------------------------------- /mash/1.1.1-2-deb/Dockerfile: -------------------------------------------------------------------------------- 1 | FROM biocontainers/biocontainers:debian-stretch-backports 2 | MAINTAINER biocontainers 3 | LABEL software="mash" \ 4 | container="mash" \ 5 | about.summary="fast genome and metagenome distance estimation using MinHash" \ 6 | about.home="https://mash.readthedocs.io" \ 7 | software.version="1.1.1-2-deb" \ 8 | version="1" \ 9 | about.copyright=" 2015 Battelle National Biodefense Institute (BNBI)" \ 10 | about.license="BSD-3-clause" \ 11 | about.license_file="/usr/share/doc/mash/copyright" \ 12 | extra.binaries="/usr/bin/mash" \ 13 | about.tags="" 14 | 15 | ENV DEBIAN_FRONTEND noninteractive 16 | RUN apt-get update && apt-get install -y mash && apt-get clean && apt-get purge && rm -rf /var/lib/apt/lists/* /tmp/* 17 | USER biodocker 18 | -------------------------------------------------------------------------------- /maude/2.7-2b1-deb/Dockerfile: -------------------------------------------------------------------------------- 1 | FROM biocontainers/biocontainers:debian-stretch-backports 2 | MAINTAINER biocontainers 3 | LABEL software="maude" \ 4 | container="maude" \ 5 | about.summary="high-performance logical framework" \ 6 | about.home="http://maude.cs.uiuc.edu" \ 7 | software.version="2.7-2b1-deb" \ 8 | version="1" \ 9 | about.license_file="/usr/share/doc/maude/copyright" \ 10 | extra.binaries="/usr/bin/maude" \ 11 | about.tags="uitoolkit::ncurses" 12 | 13 | ENV DEBIAN_FRONTEND noninteractive 14 | RUN apt-get update && apt-get install -y maude && apt-get clean && apt-get purge && rm -rf /var/lib/apt/lists/* /tmp/* 15 | USER biodocker 16 | -------------------------------------------------------------------------------- /mauve-aligner/2.4.04734-3-deb/Dockerfile: -------------------------------------------------------------------------------- 1 | FROM biocontainers/biocontainers:debian-stretch-backports 2 | MAINTAINER biocontainers 3 | LABEL software="mauve-aligner" \ 4 | container="mauve-aligner" \ 5 | about.summary="multiple genome alignment" \ 6 | about.home="http://darlinglab.org/mauve/" \ 7 | software.version="2.4.04734-3-deb" \ 8 | version="1" \ 9 | about.copyright="2003 - 2014 Aaron Darling -- darling@cs.wisc.edu" \ 10 | about.license="GPL-2+" \ 11 | about.license_file="/usr/share/doc/mauve-aligner/copyright" \ 12 | extra.binaries="/usr/bin/mauve" \ 13 | about.tags="" 14 | 15 | ENV DEBIAN_FRONTEND noninteractive 16 | RUN apt-get update && apt-get install -y mauve-aligner && apt-get clean && apt-get purge && rm -rf /var/lib/apt/lists/* /tmp/* 17 | USER biodocker 18 | -------------------------------------------------------------------------------- /megahit/1.2.9/env_megahit.yml: -------------------------------------------------------------------------------- 1 | name: biocontainers-megahit 2 | channels: 3 | - conda-forge 4 | - bioconda 5 | dependencies: 6 | - megahit=1.2.9 7 | - conda-forge::procps-ng 8 | - pigz 9 | -------------------------------------------------------------------------------- /mhap/2.1.1dfsg-1-deb/Dockerfile: -------------------------------------------------------------------------------- 1 | FROM biocontainers/biocontainers:debian-stretch-backports 2 | MAINTAINER biocontainers 3 | LABEL software="mhap" \ 4 | container="mhap" \ 5 | about.summary="locality-sensitive hashing to detect long-read overlaps" \ 6 | about.home="http://mhap.readthedocs.org/en/stable/" \ 7 | software.version="2.1.1dfsg-1-deb" \ 8 | version="1" \ 9 | about.copyright="2012-2015 Konstantin Berlin " \ 10 | about.license="Apache-2.0" \ 11 | about.license_file="/usr/share/doc/mhap/copyright" \ 12 | extra.binaries="/usr/bin/mhap" \ 13 | about.tags="" 14 | 15 | ENV DEBIAN_FRONTEND noninteractive 16 | RUN apt-get update && apt-get install -y mhap && apt-get clean && apt-get purge && rm -rf /var/lib/apt/lists/* /tmp/* 17 | USER biodocker 18 | -------------------------------------------------------------------------------- /mia-doctools/2.4.3-5-deb/Dockerfile: -------------------------------------------------------------------------------- 1 | FROM biocontainers/biocontainers:debian-stretch-backports 2 | MAINTAINER biocontainers 3 | LABEL software="mia-doctools" \ 4 | container="mia-doctools" \ 5 | about.summary="Helper scripts for run-time document creation" \ 6 | about.home="http://mia.sourceforge.net" \ 7 | software.version="2.4.3-5-deb" \ 8 | version="1" \ 9 | about.copyright="Gert Wollny " \ 10 | about.license="GPL-3.0+" \ 11 | about.license_file="/usr/share/doc/mia-doctools/copyright" \ 12 | about.tags="" 13 | 14 | ENV DEBIAN_FRONTEND noninteractive 15 | RUN apt-get update && apt-get install -y mia-doctools && apt-get clean && apt-get purge && rm -rf /var/lib/apt/lists/* /tmp/* 16 | USER biodocker 17 | -------------------------------------------------------------------------------- /mia/0.1.9-1-deb-py2/Dockerfile: -------------------------------------------------------------------------------- 1 | FROM biocontainers/biocontainers:debian-stretch-backports 2 | MAINTAINER biocontainers 3 | LABEL software="mia" \ 4 | container="mia" \ 5 | about.summary="Python-2 bindings for the MIA image processing library" \ 6 | about.home="http://mia.sourceforge.net" \ 7 | software.version="0.1.9-1-deb-py2" \ 8 | version="1" \ 9 | about.copyright="Gert Wollny " \ 10 | about.license="GPL-3.0+" \ 11 | about.license_file="/usr/share/doc/mia/copyright" \ 12 | about.tags="" 13 | 14 | ENV DEBIAN_FRONTEND noninteractive 15 | RUN apt-get update && apt-get install -y python-mia && apt-get clean && apt-get purge && rm -rf /var/lib/apt/lists/* /tmp/* 16 | USER biodocker 17 | -------------------------------------------------------------------------------- /mia/0.1.9-1-deb-py3/Dockerfile: -------------------------------------------------------------------------------- 1 | FROM biocontainers/biocontainers:debian-stretch-backports 2 | MAINTAINER biocontainers 3 | LABEL software="mia" \ 4 | container="mia" \ 5 | about.summary="Python-3 bindings for the MIA image processing library" \ 6 | about.home="http://mia.sourceforge.net" \ 7 | software.version="0.1.9-1-deb-py3" \ 8 | version="1" \ 9 | about.copyright="Gert Wollny " \ 10 | about.license="GPL-3.0+" \ 11 | about.license_file="/usr/share/doc/mia/copyright" \ 12 | about.tags="" 13 | 14 | ENV DEBIAN_FRONTEND noninteractive 15 | RUN apt-get update && apt-get install -y python3-mia && apt-get clean && apt-get purge && rm -rf /var/lib/apt/lists/* /tmp/* 16 | USER biodocker 17 | -------------------------------------------------------------------------------- /micro-sam/1.1.1/conda.yml: -------------------------------------------------------------------------------- 1 | name: sam 2 | channels: 3 | - pytorch 4 | - conda-forge 5 | dependencies: 6 | - cpuonly 7 | # This pin is necessary because later nifty versions have import errors on windows. 8 | - nifty =1.2.1=*_4 9 | - imagecodecs 10 | - natsort 11 | - pip 12 | - zarr 13 | - pooch 14 | - protobuf <5 15 | - python-xxhash 16 | - python-elf >=0.4.8 17 | - pytorch >=2.4 18 | - segment-anything 19 | - torchvision 20 | - torch_em >=0.7.0 21 | - tqdm 22 | - timm 23 | - git 24 | - pip: 25 | - git+https://github.com/ChaoningZhang/MobileSAM.git -------------------------------------------------------------------------------- /minia/1.6906-1b2-deb/Dockerfile: -------------------------------------------------------------------------------- 1 | FROM biocontainers/biocontainers:debian-stretch-backports 2 | MAINTAINER biocontainers 3 | LABEL software="minia" \ 4 | container="minia" \ 5 | about.summary="short-read biological sequence assembler" \ 6 | about.home="http://minia.genouest.org/" \ 7 | software.version="1.6906-1b2-deb" \ 8 | version="1" \ 9 | about.license_file="/usr/share/doc/minia/copyright" \ 10 | extra.binaries="/usr/bin/minia" \ 11 | about.tags="" 12 | 13 | ENV DEBIAN_FRONTEND noninteractive 14 | RUN apt-get update && apt-get install -y minia && apt-get clean && apt-get purge && rm -rf /var/lib/apt/lists/* /tmp/* 15 | USER biodocker 16 | -------------------------------------------------------------------------------- /mlv-smile/1.47-4b1-deb/Dockerfile: -------------------------------------------------------------------------------- 1 | FROM biocontainers/biocontainers:debian-stretch-backports 2 | MAINTAINER biocontainers 3 | LABEL software="mlv-smile" \ 4 | container="mlv-smile" \ 5 | about.summary="Find statistically significant patterns in sequences" \ 6 | about.home="http://www-igm.univ-mlv.fr/~marsan/smile_english.html" \ 7 | software.version="1.47-4b1-deb" \ 8 | version="1" \ 9 | about.license_file="/usr/share/doc/mlv-smile/copyright" \ 10 | extra.binaries="/usr/bin/mlv-smile" \ 11 | about.tags="" 12 | 13 | ENV DEBIAN_FRONTEND noninteractive 14 | RUN apt-get update && apt-get install -y mlv-smile && apt-get clean && apt-get purge && rm -rf /var/lib/apt/lists/* /tmp/* 15 | USER biodocker 16 | -------------------------------------------------------------------------------- /mne/0.13.1dfsg-3-deb-py2/Dockerfile: -------------------------------------------------------------------------------- 1 | FROM biocontainers/biocontainers:debian-stretch-backports 2 | MAINTAINER biocontainers 3 | LABEL software="mne" \ 4 | container="mne" \ 5 | about.summary="Python modules for MEG and EEG data analysis" \ 6 | about.home="http://martinos.org/mne" \ 7 | software.version="0.13.1dfsg-3-deb-py2" \ 8 | version="1" \ 9 | about.copyright="2010-2016, MNE-Python Developers" \ 10 | about.license="BSD-3-Clause" \ 11 | about.license_file="/usr/share/doc/mne/copyright" \ 12 | extra.binaries="/usr/bin/mne" \ 13 | about.tags="" 14 | 15 | ENV DEBIAN_FRONTEND noninteractive 16 | RUN apt-get update && apt-get install -y python-mne && apt-get clean && apt-get purge && rm -rf /var/lib/apt/lists/* /tmp/* 17 | USER biodocker 18 | -------------------------------------------------------------------------------- /mobyle-tutorials/1.5.0-2-deb/Dockerfile: -------------------------------------------------------------------------------- 1 | FROM biocontainers/biocontainers:debian-stretch-backports 2 | MAINTAINER biocontainers 3 | LABEL software="mobyle-tutorials" \ 4 | container="mobyle-tutorials" \ 5 | about.summary="program tutorials for the mobyle portal" \ 6 | about.home="https://projets.pasteur.fr/projects/mobyle/wiki/Download" \ 7 | software.version="1.5.0-2-deb" \ 8 | version="1" \ 9 | about.copyright="2011 Herve Menager " \ 10 | about.license="LGPL-2+" \ 11 | about.license_file="/usr/share/doc/mobyle-tutorials/copyright" \ 12 | about.tags="" 13 | 14 | ENV DEBIAN_FRONTEND noninteractive 15 | RUN apt-get update && apt-get install -y mobyle-tutorials && apt-get clean && apt-get purge && rm -rf /var/lib/apt/lists/* /tmp/* 16 | USER biodocker 17 | -------------------------------------------------------------------------------- /mrbayes-mpi/3.2.6dfsg-1b4-deb/Dockerfile: -------------------------------------------------------------------------------- 1 | FROM biocontainers/biocontainers:debian-stretch-backports 2 | MAINTAINER biocontainers 3 | LABEL software="mrbayes-mpi" \ 4 | container="mrbayes-mpi" \ 5 | about.summary="Bayesian Inference of Phylogeny - mpi version" \ 6 | about.home="http://mrbayes.csit.fsu.edu/" \ 7 | software.version="3.2.6dfsg-1b4-deb" \ 8 | version="1" \ 9 | about.license_file="/usr/share/doc/mrbayes-mpi/copyright" \ 10 | extra.binaries="/usr/bin/mb-mpi" \ 11 | about.tags="" 12 | 13 | ENV DEBIAN_FRONTEND noninteractive 14 | RUN apt-get update && apt-get install -y mrbayes-mpi && apt-get clean && apt-get purge && rm -rf /var/lib/apt/lists/* /tmp/* 15 | USER biodocker 16 | -------------------------------------------------------------------------------- /mrbayes/3.2.6dfsg-1b4-deb/Dockerfile: -------------------------------------------------------------------------------- 1 | FROM biocontainers/biocontainers:debian-stretch-backports 2 | MAINTAINER biocontainers 3 | LABEL software="mrbayes" \ 4 | container="mrbayes" \ 5 | about.summary="Bayesian Inference of Phylogeny" \ 6 | about.home="http://mrbayes.csit.fsu.edu/" \ 7 | software.version="3.2.6dfsg-1b4-deb" \ 8 | version="1" \ 9 | about.license_file="/usr/share/doc/mrbayes/copyright" \ 10 | extra.binaries="/usr/bin/mb" \ 11 | about.tags="" 12 | 13 | ENV DEBIAN_FRONTEND noninteractive 14 | RUN apt-get update && apt-get install -y mrbayes && apt-get clean && apt-get purge && rm -rf /var/lib/apt/lists/* /tmp/* 15 | USER biodocker 16 | -------------------------------------------------------------------------------- /mrs/6.0.5dfsg-2b2-deb/Dockerfile: -------------------------------------------------------------------------------- 1 | FROM biocontainers/biocontainers:debian-stretch-backports 2 | MAINTAINER biocontainers 3 | LABEL software="mrs" \ 4 | container="mrs" \ 5 | about.summary="Information Retrieval System for Biomedical databanks" \ 6 | about.home="http://mrs.cmbi.ru.nl/" \ 7 | software.version="6.0.5dfsg-2b2-deb" \ 8 | version="1" \ 9 | about.license_file="/usr/share/doc/mrs/copyright" \ 10 | extra.binaries="/usr/bin/mrs" \ 11 | about.tags="" 12 | 13 | ENV DEBIAN_FRONTEND noninteractive 14 | RUN apt-get update && apt-get install -y mrs && apt-get clean && apt-get purge && rm -rf /var/lib/apt/lists/* /tmp/* 15 | USER biodocker 16 | -------------------------------------------------------------------------------- /multipletau/0.1.7ds-1-deb-py2/Dockerfile: -------------------------------------------------------------------------------- 1 | FROM biocontainers/biocontainers:debian-stretch-backports 2 | MAINTAINER biocontainers 3 | LABEL software="multipletau" \ 4 | container="multipletau" \ 5 | about.summary="multiple-tau algorithm for Python/NumPy" \ 6 | about.home="http://paulmueller.github.io/multipletau" \ 7 | software.version="0.1.7ds-1-deb-py2" \ 8 | version="1" \ 9 | about.copyright="2014 Paul Mueller " \ 10 | about.license="BSD-3-Clause" \ 11 | about.license_file="/usr/share/doc/multipletau/copyright" \ 12 | about.tags="" 13 | 14 | ENV DEBIAN_FRONTEND noninteractive 15 | RUN apt-get update && apt-get install -y python-multipletau && apt-get clean && apt-get purge && rm -rf /var/lib/apt/lists/* /tmp/* 16 | USER biodocker 17 | -------------------------------------------------------------------------------- /multipletau/0.1.7ds-1-deb-py3/Dockerfile: -------------------------------------------------------------------------------- 1 | FROM biocontainers/biocontainers:debian-stretch-backports 2 | MAINTAINER biocontainers 3 | LABEL software="multipletau" \ 4 | container="multipletau" \ 5 | about.summary="multiple-tau algorithm for Python3/NumPy" \ 6 | about.home="http://paulmueller.github.io/multipletau" \ 7 | software.version="0.1.7ds-1-deb-py3" \ 8 | version="1" \ 9 | about.copyright="2014 Paul Mueller " \ 10 | about.license="BSD-3-Clause" \ 11 | about.license_file="/usr/share/doc/multipletau/copyright" \ 12 | about.tags="" 13 | 14 | ENV DEBIAN_FRONTEND noninteractive 15 | RUN apt-get update && apt-get install -y python3-multipletau && apt-get clean && apt-get purge && rm -rf /var/lib/apt/lists/* /tmp/* 16 | USER biodocker 17 | -------------------------------------------------------------------------------- /murasaki-mpi/1.68.6-6b4-deb/Dockerfile: -------------------------------------------------------------------------------- 1 | FROM biocontainers/biocontainers:debian-stretch-backports 2 | MAINTAINER biocontainers 3 | LABEL software="murasaki-mpi" \ 4 | container="murasaki-mpi" \ 5 | about.summary="homology detection tool across multiple large genomes (MPI-version)" \ 6 | about.home="http://murasaki.dna.bio.keio.ac.jp/wiki/" \ 7 | software.version="1.68.6-6b4-deb" \ 8 | version="1" \ 9 | about.license_file="/usr/share/doc/murasaki-mpi/copyright" \ 10 | extra.binaries="/usr/bin/geneparse-mpi,/usr/bin/mbfa-mpi,/usr/bin/murasaki-mpi" \ 11 | about.tags="" 12 | 13 | ENV DEBIAN_FRONTEND noninteractive 14 | RUN apt-get update && apt-get install -y murasaki-mpi && apt-get clean && apt-get purge && rm -rf /var/lib/apt/lists/* /tmp/* 15 | USER biodocker 16 | -------------------------------------------------------------------------------- /murasaki/1.68.6-6b4-deb/Dockerfile: -------------------------------------------------------------------------------- 1 | FROM biocontainers/biocontainers:debian-stretch-backports 2 | MAINTAINER biocontainers 3 | LABEL software="murasaki" \ 4 | container="murasaki" \ 5 | about.summary="homology detection tool across multiple large genomes" \ 6 | about.home="http://murasaki.dna.bio.keio.ac.jp/wiki/" \ 7 | software.version="1.68.6-6b4-deb" \ 8 | version="1" \ 9 | about.license_file="/usr/share/doc/murasaki/copyright" \ 10 | extra.binaries="/usr/bin/geneparse,/usr/bin/mbfa,/usr/bin/murasaki" \ 11 | about.tags="" 12 | 13 | ENV DEBIAN_FRONTEND noninteractive 14 | RUN apt-get update && apt-get install -y murasaki && apt-get clean && apt-get purge && rm -rf /var/lib/apt/lists/* /tmp/* 15 | USER biodocker 16 | -------------------------------------------------------------------------------- /mypy/0.470-complete-1-deb/Dockerfile: -------------------------------------------------------------------------------- 1 | FROM biocontainers/biocontainers:debian-stretch-backports 2 | MAINTAINER biocontainers 3 | LABEL software="mypy" \ 4 | container="mypy" \ 5 | about.summary="Optional static typing for Python" \ 6 | about.home="http://www.mypy-lang.org/" \ 7 | software.version="0.470-complete-1-deb" \ 8 | version="1" \ 9 | about.copyright=" 2015-2016 Jukka Lehtosalo and contributors" \ 10 | about.license="MIT" \ 11 | about.license_file="/usr/share/doc/mypy/copyright" \ 12 | extra.binaries="/usr/bin/mypy,/usr/bin/stubgen" \ 13 | about.tags="" 14 | 15 | ENV DEBIAN_FRONTEND noninteractive 16 | RUN apt-get update && apt-get install -y mypy && apt-get clean && apt-get purge && rm -rf /var/lib/apt/lists/* /tmp/* 17 | USER biodocker 18 | -------------------------------------------------------------------------------- /nanopolish/0.5.0-1b1-deb/Dockerfile: -------------------------------------------------------------------------------- 1 | FROM biocontainers/biocontainers:debian-stretch-backports 2 | MAINTAINER biocontainers 3 | LABEL software="nanopolish" \ 4 | container="nanopolish" \ 5 | about.summary="consensus caller for nanopore sequencing data" \ 6 | about.home="https://github.com/jts/nanopolish" \ 7 | software.version="0.5.0-1b1-deb" \ 8 | version="1" \ 9 | about.license_file="/usr/share/doc/nanopolish/copyright" \ 10 | extra.binaries="/usr/bin/nanopolish" \ 11 | about.tags="" 12 | 13 | ENV DEBIAN_FRONTEND noninteractive 14 | RUN apt-get update && apt-get install -y nanopolish && apt-get clean && apt-get purge && rm -rf /var/lib/apt/lists/* /tmp/* 15 | USER biodocker 16 | -------------------------------------------------------------------------------- /nast-ier/20101212dfsg1-1b1-deb/Dockerfile: -------------------------------------------------------------------------------- 1 | FROM biocontainers/biocontainers:debian-stretch-backports 2 | MAINTAINER biocontainers 3 | LABEL software="nast-ier" \ 4 | container="nast-ier" \ 5 | about.summary="NAST-based DNA alignment tool" \ 6 | about.home="http://microbiomeutil.sourceforge.net/" \ 7 | software.version="20101212dfsg1-1b1-deb" \ 8 | version="1" \ 9 | about.license_file="/usr/share/doc/nast-ier/copyright" \ 10 | extra.binaries="/usr/bin/nast-ier" \ 11 | about.tags="" 12 | 13 | ENV DEBIAN_FRONTEND noninteractive 14 | RUN apt-get update && apt-get install -y nast-ier && apt-get clean && apt-get purge && rm -rf /var/lib/apt/lists/* /tmp/* 15 | USER biodocker 16 | -------------------------------------------------------------------------------- /ncbi-seg/0.0.20000620-3b1-deb/Dockerfile: -------------------------------------------------------------------------------- 1 | FROM biocontainers/biocontainers:debian-stretch-backports 2 | MAINTAINER biocontainers 3 | LABEL software="ncbi-seg" \ 4 | container="ncbi-seg" \ 5 | about.summary="tool to mask segments of low compositional complexity in amino acid sequences" \ 6 | about.home="ftp://ftp.ncbi.nih.gov/pub/seg/seg/" \ 7 | software.version="0.0.20000620-3b1-deb" \ 8 | version="1" \ 9 | about.license_file="/usr/share/doc/ncbi-seg/copyright" \ 10 | extra.binaries="/usr/bin/ncbi-seg" \ 11 | about.tags="" 12 | 13 | ENV DEBIAN_FRONTEND noninteractive 14 | RUN apt-get update && apt-get install -y ncbi-seg && apt-get clean && apt-get purge && rm -rf /var/lib/apt/lists/* /tmp/* 15 | USER biodocker 16 | -------------------------------------------------------------------------------- /ncl-tools/2.1.18dfsg-2b1-deb/Dockerfile: -------------------------------------------------------------------------------- 1 | FROM biocontainers/biocontainers:debian-stretch-backports 2 | MAINTAINER biocontainers 3 | LABEL software="ncl-tools" \ 4 | container="ncl-tools" \ 5 | about.summary="tools to deal with NEXUS files" \ 6 | about.home="http://sourceforge.net/projects/ncl/" \ 7 | software.version="2.1.18dfsg-2b1-deb" \ 8 | version="1" \ 9 | about.license_file="/usr/share/doc/ncl-tools/copyright" \ 10 | extra.binaries="/usr/bin/NCLconverter,/usr/bin/NEXUSnormalizer,/usr/bin/NEXUSvalidator" \ 11 | about.tags="" 12 | 13 | ENV DEBIAN_FRONTEND noninteractive 14 | RUN apt-get update && apt-get install -y ncl-tools && apt-get clean && apt-get purge && rm -rf /var/lib/apt/lists/* /tmp/* 15 | USER biodocker 16 | -------------------------------------------------------------------------------- /ncoils/2002-4b1-deb/Dockerfile: -------------------------------------------------------------------------------- 1 | FROM biocontainers/biocontainers:debian-stretch-backports 2 | MAINTAINER biocontainers 3 | LABEL software="ncoils" \ 4 | container="ncoils" \ 5 | about.summary="coiled coil secondary structure prediction" \ 6 | about.home="http://www.russelllab.org/coils/" \ 7 | software.version="2002-4b1-deb" \ 8 | version="1" \ 9 | about.license_file="/usr/share/doc/ncoils/copyright" \ 10 | extra.binaries="/usr/bin/coils-wrap,/usr/bin/ncoils" \ 11 | about.tags="" 12 | 13 | ENV DEBIAN_FRONTEND noninteractive 14 | RUN apt-get update && apt-get install -y ncoils && apt-get clean && apt-get purge && rm -rf /var/lib/apt/lists/* /tmp/* 15 | USER biodocker 16 | -------------------------------------------------------------------------------- /neobio/0.0.20030929-2-deb/Dockerfile: -------------------------------------------------------------------------------- 1 | FROM biocontainers/biocontainers:debian-stretch-backports 2 | MAINTAINER biocontainers 3 | LABEL software="neobio" \ 4 | container="neobio" \ 5 | about.summary="computes alignments of amino acid and nucleotide sequences" \ 6 | about.home="http://neobio.sourceforge.net/" \ 7 | software.version="0.0.20030929-2-deb" \ 8 | version="1" \ 9 | about.copyright=" 2003 Sergio Anibal de Carvalho Junior" \ 10 | about.license="GPL-2+" \ 11 | about.license_file="/usr/share/doc/neobio/copyright" \ 12 | extra.binaries="/usr/bin/neobio" \ 13 | about.tags="" 14 | 15 | ENV DEBIAN_FRONTEND noninteractive 16 | RUN apt-get update && apt-get install -y neobio && apt-get clean && apt-get purge && rm -rf /var/lib/apt/lists/* /tmp/* 17 | USER biodocker 18 | -------------------------------------------------------------------------------- /ngs/1.3.0-2-deb-py2/Dockerfile: -------------------------------------------------------------------------------- 1 | FROM biocontainers/biocontainers:debian-stretch-backports 2 | MAINTAINER biocontainers 3 | LABEL software="ngs" \ 4 | container="ngs" \ 5 | about.summary="Next Generation Sequencing language Bindings (Python bindings)" \ 6 | about.home="https://github.com/ncbi/ngs" \ 7 | software.version="1.3.0-2-deb-py2" \ 8 | version="1" \ 9 | about.copyright=" 2010-2015 National Center for Biotechnology Information" \ 10 | about.license="public_domain" \ 11 | about.license_file="/usr/share/doc/ngs/copyright" \ 12 | about.tags="" 13 | 14 | ENV DEBIAN_FRONTEND noninteractive 15 | RUN apt-get update && apt-get install -y python-ngs && apt-get clean && apt-get purge && rm -rf /var/lib/apt/lists/* /tmp/* 16 | USER biodocker 17 | -------------------------------------------------------------------------------- /ngs/1.3.0-2-deb-py3/Dockerfile: -------------------------------------------------------------------------------- 1 | FROM biocontainers/biocontainers:debian-stretch-backports 2 | MAINTAINER biocontainers 3 | LABEL software="ngs" \ 4 | container="ngs" \ 5 | about.summary="Next Generation Sequencing language Bindings (Python3 bindings)" \ 6 | about.home="https://github.com/ncbi/ngs" \ 7 | software.version="1.3.0-2-deb-py3" \ 8 | version="1" \ 9 | about.copyright=" 2010-2015 National Center for Biotechnology Information" \ 10 | about.license="public_domain" \ 11 | about.license_file="/usr/share/doc/ngs/copyright" \ 12 | about.tags="" 13 | 14 | ENV DEBIAN_FRONTEND noninteractive 15 | RUN apt-get update && apt-get install -y python3-ngs && apt-get clean && apt-get purge && rm -rf /var/lib/apt/lists/* /tmp/* 16 | USER biodocker 17 | -------------------------------------------------------------------------------- /nutsqlite/1.9.9.3-2-deb/Dockerfile: -------------------------------------------------------------------------------- 1 | FROM biocontainers/biocontainers:debian-stretch-backports 2 | MAINTAINER biocontainers 3 | LABEL software="nutsqlite" \ 4 | container="nutsqlite" \ 5 | about.summary="Dietary nutrition analysis software" \ 6 | about.home="http://nut.sourceforge.net/" \ 7 | software.version="1.9.9.3-2-deb" \ 8 | version="1" \ 9 | about.copyright="(C) Jim Jozwiak" \ 10 | about.license="GPL-2+" \ 11 | about.license_file="/usr/share/doc/nutsqlite/copyright" \ 12 | extra.binaries="/usr/bin/nut,/usr/bin/update-nut" \ 13 | about.tags="" 14 | 15 | ENV DEBIAN_FRONTEND noninteractive 16 | RUN apt-get update && apt-get install -y nutsqlite && apt-get clean && apt-get purge && rm -rf /var/lib/apt/lists/* /tmp/* 17 | USER biodocker 18 | -------------------------------------------------------------------------------- /octave-bart/0.4.00-1-deb/Dockerfile: -------------------------------------------------------------------------------- 1 | FROM biocontainers/biocontainers:debian-stretch-backports 2 | MAINTAINER biocontainers 3 | LABEL software="octave-bart" \ 4 | container="octave-bart" \ 5 | about.summary="Octave bindings for BART" \ 6 | about.home="https://mrirecon.github.io/bart/" \ 7 | software.version="0.4.00-1-deb" \ 8 | version="1" \ 9 | about.copyright="2013-2016 The Regents of the University of California" \ 10 | about.license="BSD-3-clause" \ 11 | about.license_file="/usr/share/doc/octave-bart/copyright" \ 12 | about.tags="" 13 | 14 | ENV DEBIAN_FRONTEND noninteractive 15 | RUN apt-get update && apt-get install -y octave-bart && apt-get clean && apt-get purge && rm -rf /var/lib/apt/lists/* /tmp/* 16 | USER biodocker 17 | -------------------------------------------------------------------------------- /odil/0.7.3-1-deb-py2/Dockerfile: -------------------------------------------------------------------------------- 1 | FROM biocontainers/biocontainers:debian-stretch-backports 2 | MAINTAINER biocontainers 3 | LABEL software="odil" \ 4 | container="odil" \ 5 | about.summary="C++11 library for the DICOM standard (Python wrappers)" \ 6 | about.home="https://github.com/lamyj/odil" \ 7 | software.version="0.7.3-1-deb-py2" \ 8 | version="1" \ 9 | about.copyright=" 2016 Julien Lamy " \ 10 | about.license="CeCILL-B" \ 11 | about.license_file="/usr/share/doc/odil/copyright" \ 12 | about.tags="" 13 | 14 | ENV DEBIAN_FRONTEND noninteractive 15 | RUN apt-get update && apt-get install -y python-odil && apt-get clean && apt-get purge && rm -rf /var/lib/apt/lists/* /tmp/* 16 | USER biodocker 17 | -------------------------------------------------------------------------------- /odil/0.7.3-1-deb/Dockerfile: -------------------------------------------------------------------------------- 1 | FROM biocontainers/biocontainers:debian-stretch-backports 2 | MAINTAINER biocontainers 3 | LABEL software="odil" \ 4 | container="odil" \ 5 | about.summary="C++11 library for the DICOM standard (application)" \ 6 | about.home="https://github.com/lamyj/odil" \ 7 | software.version="0.7.3-1-deb" \ 8 | version="1" \ 9 | about.copyright=" 2016 Julien Lamy " \ 10 | about.license="CeCILL-B" \ 11 | about.license_file="/usr/share/doc/odil/copyright" \ 12 | extra.binaries="/usr/bin/odil" \ 13 | about.tags="" 14 | 15 | ENV DEBIAN_FRONTEND noninteractive 16 | RUN apt-get update && apt-get install -y odil && apt-get clean && apt-get purge && rm -rf /var/lib/apt/lists/* /tmp/* 17 | USER biodocker 18 | -------------------------------------------------------------------------------- /openslide/1.1.1-2-deb-py2/Dockerfile: -------------------------------------------------------------------------------- 1 | FROM biocontainers/biocontainers:debian-stretch-backports 2 | MAINTAINER biocontainers 3 | LABEL software="openslide" \ 4 | container="openslide" \ 5 | about.summary="Python 2 wrapper for reading whole slide image files" \ 6 | about.home="http://openslide.org" \ 7 | software.version="1.1.1-2-deb-py2" \ 8 | version="1" \ 9 | about.copyright=" 2010-2014 Carnegie Mellon University" \ 10 | about.license="LGPL-2.1" \ 11 | about.license_file="/usr/share/doc/openslide/copyright" \ 12 | about.tags="" 13 | 14 | ENV DEBIAN_FRONTEND noninteractive 15 | RUN apt-get update && apt-get install -y python-openslide && apt-get clean && apt-get purge && rm -rf /var/lib/apt/lists/* /tmp/* 16 | USER biodocker 17 | -------------------------------------------------------------------------------- /openslide/1.1.1-2-deb-py3/Dockerfile: -------------------------------------------------------------------------------- 1 | FROM biocontainers/biocontainers:debian-stretch-backports 2 | MAINTAINER biocontainers 3 | LABEL software="openslide" \ 4 | container="openslide" \ 5 | about.summary="Python 3 wrapper for reading whole slide image files" \ 6 | about.home="http://openslide.org" \ 7 | software.version="1.1.1-2-deb-py3" \ 8 | version="1" \ 9 | about.copyright=" 2010-2014 Carnegie Mellon University" \ 10 | about.license="LGPL-2.1" \ 11 | about.license_file="/usr/share/doc/openslide/copyright" \ 12 | about.tags="" 13 | 14 | ENV DEBIAN_FRONTEND noninteractive 15 | RUN apt-get update && apt-get install -y python3-openslide && apt-get clean && apt-get purge && rm -rf /var/lib/apt/lists/* /tmp/* 16 | USER biodocker 17 | -------------------------------------------------------------------------------- /orthanc-dicomweb/0.3dfsg-1b2-deb/Dockerfile: -------------------------------------------------------------------------------- 1 | FROM biocontainers/biocontainers:debian-stretch-backports 2 | MAINTAINER biocontainers 3 | LABEL software="orthanc-dicomweb" \ 4 | container="orthanc-dicomweb" \ 5 | about.summary="Plugin to extend Orthanc with support of WADO and DICOMweb" \ 6 | about.home="http://www.orthanc-server.com/static.php?page=dicomweb" \ 7 | software.version="0.3dfsg-1b2-deb" \ 8 | version="1" \ 9 | about.license_file="/usr/share/doc/orthanc-dicomweb/copyright" \ 10 | about.tags="" 11 | 12 | ENV DEBIAN_FRONTEND noninteractive 13 | RUN apt-get update && apt-get install -y orthanc-dicomweb && apt-get clean && apt-get purge && rm -rf /var/lib/apt/lists/* /tmp/* 14 | USER biodocker 15 | -------------------------------------------------------------------------------- /orthanc-postgresql/2.0-3b1-deb/Dockerfile: -------------------------------------------------------------------------------- 1 | FROM biocontainers/biocontainers:debian-stretch-backports 2 | MAINTAINER biocontainers 3 | LABEL software="orthanc-postgresql" \ 4 | container="orthanc-postgresql" \ 5 | about.summary="Plugins to use PostgreSQL as a database back-end to Orthanc" \ 6 | about.home="http://www.orthanc-server.com/static.php?page=postgresql" \ 7 | software.version="2.0-3b1-deb" \ 8 | version="1" \ 9 | about.license_file="/usr/share/doc/orthanc-postgresql/copyright" \ 10 | about.tags="" 11 | 12 | ENV DEBIAN_FRONTEND noninteractive 13 | RUN apt-get update && apt-get install -y orthanc-postgresql && apt-get clean && apt-get purge && rm -rf /var/lib/apt/lists/* /tmp/* 14 | USER biodocker 15 | -------------------------------------------------------------------------------- /orthanc-webviewer/2.2-1b2-deb/Dockerfile: -------------------------------------------------------------------------------- 1 | FROM biocontainers/biocontainers:debian-stretch-backports 2 | MAINTAINER biocontainers 3 | LABEL software="orthanc-webviewer" \ 4 | container="orthanc-webviewer" \ 5 | about.summary="Web viewer of medical images for Orthanc" \ 6 | about.home="http://www.orthanc-server.com/static.php?page=web-viewer" \ 7 | software.version="2.2-1b2-deb" \ 8 | version="1" \ 9 | about.license_file="/usr/share/doc/orthanc-webviewer/copyright" \ 10 | about.tags="" 11 | 12 | ENV DEBIAN_FRONTEND noninteractive 13 | RUN apt-get update && apt-get install -y orthanc-webviewer && apt-get clean && apt-get purge && rm -rf /var/lib/apt/lists/* /tmp/* 14 | USER biodocker 15 | -------------------------------------------------------------------------------- /paraclu/9-1b2-deb/Dockerfile: -------------------------------------------------------------------------------- 1 | FROM biocontainers/biocontainers:debian-stretch-backports 2 | MAINTAINER biocontainers 3 | LABEL software="paraclu" \ 4 | container="paraclu" \ 5 | about.summary="Parametric clustering of genomic and transcriptomic features" \ 6 | about.home="http://www.cbrc.jp/paraclu/" \ 7 | software.version="9-1b2-deb" \ 8 | version="1" \ 9 | about.license_file="/usr/share/doc/paraclu/copyright" \ 10 | extra.binaries="/usr/bin/paraclu,/usr/bin/paraclu-cut.sh" \ 11 | about.tags="" 12 | 13 | ENV DEBIAN_FRONTEND noninteractive 14 | RUN apt-get update && apt-get install -y paraclu && apt-get clean && apt-get purge && rm -rf /var/lib/apt/lists/* /tmp/* 15 | USER biodocker 16 | -------------------------------------------------------------------------------- /parafly/0.0.2013.01.21-3b1-deb/Dockerfile: -------------------------------------------------------------------------------- 1 | FROM biocontainers/biocontainers:debian-stretch-backports 2 | MAINTAINER biocontainers 3 | LABEL software="parafly" \ 4 | container="parafly" \ 5 | about.summary="parallel command processing using OpenMP" \ 6 | about.home="http://parafly.sourceforge.net" \ 7 | software.version="0.0.2013.01.21-3b1-deb" \ 8 | version="1" \ 9 | about.license_file="/usr/share/doc/parafly/copyright" \ 10 | extra.binaries="/usr/bin/ParaFly" \ 11 | about.tags="" 12 | 13 | ENV DEBIAN_FRONTEND noninteractive 14 | RUN apt-get update && apt-get install -y parafly && apt-get clean && apt-get purge && rm -rf /var/lib/apt/lists/* /tmp/* 15 | USER biodocker 16 | -------------------------------------------------------------------------------- /pbbanana/15.8.24dfsg-2-deb-py2/Dockerfile: -------------------------------------------------------------------------------- 1 | FROM biocontainers/biocontainers:debian-stretch-backports 2 | MAINTAINER biocontainers 3 | LABEL software="pbbanana" \ 4 | container="pbbanana" \ 5 | about.summary="additional utilities for the pbsuite" \ 6 | about.home="http://sourceforge.net/projects/pb-jelly" \ 7 | software.version="15.8.24dfsg-2-deb-py2" \ 8 | version="1" \ 9 | about.copyright="2013 Baylor College of Medicine" \ 10 | about.license="BSD-2-Clause" \ 11 | about.license_file="/usr/share/doc/pbbanana/copyright" \ 12 | about.tags="" 13 | 14 | ENV DEBIAN_FRONTEND noninteractive 15 | RUN apt-get update && apt-get install -y python-pbbanana && apt-get clean && apt-get purge && rm -rf /var/lib/apt/lists/* /tmp/* 16 | USER biodocker 17 | -------------------------------------------------------------------------------- /pbcore/1.2.11dfsg-1-deb-py2/Dockerfile: -------------------------------------------------------------------------------- 1 | FROM biocontainers/biocontainers:debian-stretch-backports 2 | MAINTAINER biocontainers 3 | LABEL software="pbcore" \ 4 | container="pbcore" \ 5 | about.summary="Python library for processing PacBio data files" \ 6 | about.home="https://github.com/PacificBiosciences/pbcore" \ 7 | software.version="1.2.11dfsg-1-deb-py2" \ 8 | version="1" \ 9 | about.license_file="/usr/share/doc/pbcore/copyright" \ 10 | extra.binaries="/usr/bin/pbopen" \ 11 | about.tags="" 12 | 13 | ENV DEBIAN_FRONTEND noninteractive 14 | RUN apt-get update && apt-get install -y python-pbcore && apt-get clean && apt-get purge && rm -rf /var/lib/apt/lists/* /tmp/* 15 | USER biodocker 16 | -------------------------------------------------------------------------------- /pbsuite/15.8.24dfsg-2-deb/Dockerfile: -------------------------------------------------------------------------------- 1 | FROM biocontainers/biocontainers:debian-stretch-backports 2 | MAINTAINER biocontainers 3 | LABEL software="pbsuite" \ 4 | container="pbsuite" \ 5 | about.summary="software for Pacific Biosciences sequencing data" \ 6 | about.home="http://sourceforge.net/projects/pb-jelly" \ 7 | software.version="15.8.24dfsg-2-deb" \ 8 | version="1" \ 9 | about.copyright="2013 Baylor College of Medicine" \ 10 | about.license="BSD-2-Clause" \ 11 | about.license_file="/usr/share/doc/pbsuite/copyright" \ 12 | about.tags="" 13 | 14 | ENV DEBIAN_FRONTEND noninteractive 15 | RUN apt-get update && apt-get install -y pbsuite && apt-get clean && apt-get purge && rm -rf /var/lib/apt/lists/* /tmp/* 16 | USER biodocker 17 | -------------------------------------------------------------------------------- /phybin/0.3-1b1-deb/Dockerfile: -------------------------------------------------------------------------------- 1 | FROM biocontainers/biocontainers:debian-stretch-backports 2 | MAINTAINER biocontainers 3 | LABEL software="phybin" \ 4 | container="phybin" \ 5 | about.summary="binning/clustering newick trees by topology" \ 6 | about.home="http://www.cs.indiana.edu/~rrnewton/projects/phybin/" \ 7 | software.version="0.3-1b1-deb" \ 8 | version="1" \ 9 | about.license_file="/usr/share/doc/phybin/copyright" \ 10 | extra.binaries="/usr/bin/phybin" \ 11 | about.tags="" 12 | 13 | ENV DEBIAN_FRONTEND noninteractive 14 | RUN apt-get update && apt-get install -y phybin && apt-get clean && apt-get purge && rm -rf /var/lib/apt/lists/* /tmp/* 15 | USER biodocker 16 | -------------------------------------------------------------------------------- /phylotools/0.2.4/install.R: -------------------------------------------------------------------------------- 1 | install.packages("devtools") 2 | library(devtools) 3 | install_github("helixcn/phylotools", build_vignettes = FALSE) 4 | -------------------------------------------------------------------------------- /physamp/0.2.0-1b1-deb/Dockerfile: -------------------------------------------------------------------------------- 1 | FROM biocontainers/biocontainers:debian-stretch-backports 2 | MAINTAINER biocontainers 3 | LABEL software="physamp" \ 4 | container="physamp" \ 5 | about.summary="sample sequence alignment according to its corresponding phylogenetic tree" \ 6 | about.home="http://biopp.univ-montp2.fr/forge/physamp" \ 7 | software.version="0.2.0-1b1-deb" \ 8 | version="1" \ 9 | about.license_file="/usr/share/doc/physamp/copyright" \ 10 | extra.binaries="/usr/bin/bppalnoptim" \ 11 | about.tags="" 12 | 13 | ENV DEBIAN_FRONTEND noninteractive 14 | RUN apt-get update && apt-get install -y physamp && apt-get clean && apt-get purge && rm -rf /var/lib/apt/lists/* /tmp/* 15 | USER biodocker 16 | -------------------------------------------------------------------------------- /pia/1.1.0-SNAPSHOT/runpia.sh: -------------------------------------------------------------------------------- 1 | #!/bin/bash 2 | set -e 3 | 4 | if [ "$1" = 'pia' ]; then 5 | shift 6 | exec java -jar "${PIA_JAR}" "$@" 7 | elif [ "$1" = 'compiler' ]; then 8 | shift 9 | exec java -cp "${PIA_JAR}" de.mpc.pia.intermediate.compiler.PIACompiler "$@" 10 | fi 11 | 12 | echo "run either 'pia' or 'compiler' (or anything else to not execute pia but e.g. start the bash)" 13 | exec "$@" 14 | -------------------------------------------------------------------------------- /pia/1.3.0/runpia.sh: -------------------------------------------------------------------------------- 1 | #!/bin/bash 2 | set -e 3 | 4 | if [ "$1" = 'pia' ]; then 5 | shift 6 | exec java -jar "${PIA_JAR}" "$@" 7 | elif [ "$1" = 'compiler' ]; then 8 | shift 9 | exec java -cp "${PIA_JAR}" de.mpc.pia.intermediate.compiler.PIACompiler "$@" 10 | fi 11 | 12 | echo "run either 'pia' or 'compiler' (or anything else to not execute pia but e.g. start the bash)" 13 | exec "$@" 14 | -------------------------------------------------------------------------------- /pia/1.3.8/runpia.sh: -------------------------------------------------------------------------------- 1 | #!/bin/bash 2 | set -e 3 | 4 | if [ "$1" = 'pia' ]; then 5 | shift 6 | exec java -jar "${PIA_JAR}" "$@" 7 | elif [ "$1" = 'compiler' ]; then 8 | shift 9 | exec java -cp "${PIA_JAR}" de.mpc.pia.intermediate.compiler.PIACompiler "$@" 10 | fi 11 | 12 | echo "run either 'pia' or 'compiler' (or anything else to not execute pia but e.g. start the bash)" 13 | exec "$@" 14 | -------------------------------------------------------------------------------- /piler/020140707-1b1-deb/Dockerfile: -------------------------------------------------------------------------------- 1 | FROM biocontainers/biocontainers:debian-stretch-backports 2 | MAINTAINER biocontainers 3 | LABEL software="piler" \ 4 | container="piler" \ 5 | about.summary="genomic repeat analysis" \ 6 | about.home="http://www.drive5.com/piler/" \ 7 | software.version="020140707-1b1-deb" \ 8 | version="1" \ 9 | about.license_file="/usr/share/doc/piler/copyright" \ 10 | extra.binaries="/usr/bin/piler2" \ 11 | about.tags="" 12 | 13 | ENV DEBIAN_FRONTEND noninteractive 14 | RUN apt-get update && apt-get install -y piler && apt-get clean && apt-get purge && rm -rf /var/lib/apt/lists/* /tmp/* 15 | USER biodocker 16 | -------------------------------------------------------------------------------- /pirs-profiles/2.0.2dfsg-5.1-deb/Dockerfile: -------------------------------------------------------------------------------- 1 | FROM biocontainers/biocontainers:debian-stretch-backports 2 | MAINTAINER biocontainers 3 | LABEL software="pirs-profiles" \ 4 | container="pirs-profiles" \ 5 | about.summary="profile basd Illumina pair-end Reads Simulator (profile data)" \ 6 | about.home="https://github.com/galaxy001/pirs" \ 7 | software.version="2.0.2dfsg-5.1-deb" \ 8 | version="1" \ 9 | about.copyright="2011-2016 BGI (http://en.genomics.cn/)" \ 10 | about.license="GPL-2+" \ 11 | about.license_file="/usr/share/doc/pirs-profiles/copyright" \ 12 | about.tags="" 13 | 14 | ENV DEBIAN_FRONTEND noninteractive 15 | RUN apt-get update && apt-get install -y pirs-profiles && apt-get clean && apt-get purge && rm -rf /var/lib/apt/lists/* /tmp/* 16 | USER biodocker 17 | -------------------------------------------------------------------------------- /placnet/1.03-2-deb/Dockerfile: -------------------------------------------------------------------------------- 1 | FROM biocontainers/biocontainers:debian-stretch-backports 2 | MAINTAINER biocontainers 3 | LABEL software="placnet" \ 4 | container="placnet" \ 5 | about.summary="Plasmid Constellation Network project" \ 6 | about.home="http://sourceforge.net/projects/placnet/" \ 7 | software.version="1.03-2-deb" \ 8 | version="1" \ 9 | about.copyright="2013-2015 Val F. Lanza ," \ 10 | about.license="CC-4.0" \ 11 | about.license_file="/usr/share/doc/placnet/copyright" \ 12 | extra.binaries="/usr/bin/placnet" \ 13 | about.tags="" 14 | 15 | ENV DEBIAN_FRONTEND noninteractive 16 | RUN apt-get update && apt-get install -y placnet && apt-get clean && apt-get purge && rm -rf /var/lib/apt/lists/* /tmp/* 17 | USER biodocker 18 | -------------------------------------------------------------------------------- /pp-popularity-contest/1.0.6-2b4-deb/Dockerfile: -------------------------------------------------------------------------------- 1 | FROM biocontainers/biocontainers:debian-stretch-backports 2 | MAINTAINER biocontainers 3 | LABEL software="pp-popularity-contest" \ 4 | container="pp-popularity-contest" \ 5 | about.summary="PredictProtein popularity contest" \ 6 | about.home="http://predictprotein.org/" \ 7 | software.version="1.0.6-2b4-deb" \ 8 | version="1" \ 9 | about.license_file="/usr/share/doc/pp-popularity-contest/copyright" \ 10 | extra.binaries="/usr/bin/pp_popcon_cnt" \ 11 | about.tags="" 12 | 13 | ENV DEBIAN_FRONTEND noninteractive 14 | RUN apt-get update && apt-get install -y pp-popularity-contest && apt-get clean && apt-get purge && rm -rf /var/lib/apt/lists/* /tmp/* 15 | USER biodocker 16 | -------------------------------------------------------------------------------- /proalign/0.603-2-deb/Dockerfile: -------------------------------------------------------------------------------- 1 | FROM biocontainers/biocontainers:debian-stretch-backports 2 | MAINTAINER biocontainers 3 | LABEL software="proalign" \ 4 | container="proalign" \ 5 | about.summary="Probabilistic multiple alignment program" \ 6 | about.home="http://ueg.ulb.ac.be/ProAlign/" \ 7 | software.version="0.603-2-deb" \ 8 | version="1" \ 9 | about.copyright=" 2002-2003 Ari Lytynoja and Michel C. Milinkovitch." \ 10 | about.license="GPL-2+" \ 11 | about.license_file="/usr/share/doc/proalign/copyright" \ 12 | extra.binaries="/usr/bin/proalign" \ 13 | about.tags="" 14 | 15 | ENV DEBIAN_FRONTEND noninteractive 16 | RUN apt-get update && apt-get install -y proalign && apt-get clean && apt-get purge && rm -rf /var/lib/apt/lists/* /tmp/* 17 | USER biodocker 18 | -------------------------------------------------------------------------------- /probabel/0.4.5-3b1-deb/Dockerfile: -------------------------------------------------------------------------------- 1 | FROM biocontainers/biocontainers:debian-stretch-backports 2 | MAINTAINER biocontainers 3 | LABEL software="probabel" \ 4 | container="probabel" \ 5 | about.summary="Toolset for Genome-Wide Association Analysis" \ 6 | about.home="http://www.genabel.org" \ 7 | software.version="0.4.5-3b1-deb" \ 8 | version="1" \ 9 | about.license_file="/usr/share/doc/probabel/copyright" \ 10 | extra.binaries="/usr/bin/pacoxph,/usr/bin/palinear,/usr/bin/palogist,/usr/bin/probabel,/usr/bin/probabel.pl" \ 11 | about.tags="" 12 | 13 | ENV DEBIAN_FRONTEND noninteractive 14 | RUN apt-get update && apt-get install -y probabel && apt-get clean && apt-get purge && rm -rf /var/lib/apt/lists/* /tmp/* 15 | USER biodocker 16 | -------------------------------------------------------------------------------- /prodigal/1-2.6.3-1b1-deb/Dockerfile: -------------------------------------------------------------------------------- 1 | FROM biocontainers/biocontainers:debian-stretch-backports 2 | MAINTAINER biocontainers 3 | LABEL software="prodigal" \ 4 | container="prodigal" \ 5 | about.summary="Microbial (bacterial and archaeal) gene finding program" \ 6 | about.home="http://prodigal.ornl.gov/" \ 7 | software.version="1-2.6.3-1b1-deb" \ 8 | version="1" \ 9 | about.license_file="/usr/share/doc/prodigal/copyright" \ 10 | extra.binaries="/usr/bin/prodigal" \ 11 | about.tags="" 12 | 13 | ENV DEBIAN_FRONTEND noninteractive 14 | RUN apt-get update && apt-get install -y prodigal && apt-get clean && apt-get purge && rm -rf /var/lib/apt/lists/* /tmp/* 15 | USER biodocker 16 | -------------------------------------------------------------------------------- /profnet-bval/1.0.22-4-deb/Dockerfile: -------------------------------------------------------------------------------- 1 | FROM biocontainers/biocontainers:debian-stretch-backports 2 | MAINTAINER biocontainers 3 | LABEL software="profnet-bval" \ 4 | container="profnet-bval" \ 5 | about.summary="neural network architecture for profbval" \ 6 | about.home="http://www.predictprotein.org/" \ 7 | software.version="1.0.22-4-deb" \ 8 | version="1" \ 9 | about.copyright="" \ 10 | about.license="GPL-2+" \ 11 | about.license_file="/usr/share/doc/profnet-bval/copyright" \ 12 | extra.binaries="/usr/bin/profnet_bval" \ 13 | about.tags="" 14 | 15 | ENV DEBIAN_FRONTEND noninteractive 16 | RUN apt-get update && apt-get install -y profnet-bval && apt-get clean && apt-get purge && rm -rf /var/lib/apt/lists/* /tmp/* 17 | USER biodocker 18 | -------------------------------------------------------------------------------- /profnet-chop/1.0.22-4-deb/Dockerfile: -------------------------------------------------------------------------------- 1 | FROM biocontainers/biocontainers:debian-stretch-backports 2 | MAINTAINER biocontainers 3 | LABEL software="profnet-chop" \ 4 | container="profnet-chop" \ 5 | about.summary="neural network architecture for profchop" \ 6 | about.home="http://www.predictprotein.org/" \ 7 | software.version="1.0.22-4-deb" \ 8 | version="1" \ 9 | about.copyright="" \ 10 | about.license="GPL-2+" \ 11 | about.license_file="/usr/share/doc/profnet-chop/copyright" \ 12 | extra.binaries="/usr/bin/profnet_chop" \ 13 | about.tags="" 14 | 15 | ENV DEBIAN_FRONTEND noninteractive 16 | RUN apt-get update && apt-get install -y profnet-chop && apt-get clean && apt-get purge && rm -rf /var/lib/apt/lists/* /tmp/* 17 | USER biodocker 18 | -------------------------------------------------------------------------------- /profnet-con/1.0.22-4-deb/Dockerfile: -------------------------------------------------------------------------------- 1 | FROM biocontainers/biocontainers:debian-stretch-backports 2 | MAINTAINER biocontainers 3 | LABEL software="profnet-con" \ 4 | container="profnet-con" \ 5 | about.summary="neural network architecture for profcon" \ 6 | about.home="http://www.predictprotein.org/" \ 7 | software.version="1.0.22-4-deb" \ 8 | version="1" \ 9 | about.copyright="" \ 10 | about.license="GPL-2+" \ 11 | about.license_file="/usr/share/doc/profnet-con/copyright" \ 12 | extra.binaries="/usr/bin/profnet_con" \ 13 | about.tags="" 14 | 15 | ENV DEBIAN_FRONTEND noninteractive 16 | RUN apt-get update && apt-get install -y profnet-con && apt-get clean && apt-get purge && rm -rf /var/lib/apt/lists/* /tmp/* 17 | USER biodocker 18 | -------------------------------------------------------------------------------- /profnet-isis/1.0.22-4-deb/Dockerfile: -------------------------------------------------------------------------------- 1 | FROM biocontainers/biocontainers:debian-stretch-backports 2 | MAINTAINER biocontainers 3 | LABEL software="profnet-isis" \ 4 | container="profnet-isis" \ 5 | about.summary="neural network architecture for profisis" \ 6 | about.home="http://www.predictprotein.org/" \ 7 | software.version="1.0.22-4-deb" \ 8 | version="1" \ 9 | about.copyright="" \ 10 | about.license="GPL-2+" \ 11 | about.license_file="/usr/share/doc/profnet-isis/copyright" \ 12 | extra.binaries="/usr/bin/profnet_isis" \ 13 | about.tags="" 14 | 15 | ENV DEBIAN_FRONTEND noninteractive 16 | RUN apt-get update && apt-get install -y profnet-isis && apt-get clean && apt-get purge && rm -rf /var/lib/apt/lists/* /tmp/* 17 | USER biodocker 18 | -------------------------------------------------------------------------------- /profnet-md/1.0.22-4-deb/Dockerfile: -------------------------------------------------------------------------------- 1 | FROM biocontainers/biocontainers:debian-stretch-backports 2 | MAINTAINER biocontainers 3 | LABEL software="profnet-md" \ 4 | container="profnet-md" \ 5 | about.summary="neural network architecture for metadisorder" \ 6 | about.home="http://www.predictprotein.org/" \ 7 | software.version="1.0.22-4-deb" \ 8 | version="1" \ 9 | about.copyright="" \ 10 | about.license="GPL-2+" \ 11 | about.license_file="/usr/share/doc/profnet-md/copyright" \ 12 | extra.binaries="/usr/bin/profnet_md" \ 13 | about.tags="" 14 | 15 | ENV DEBIAN_FRONTEND noninteractive 16 | RUN apt-get update && apt-get install -y profnet-md && apt-get clean && apt-get purge && rm -rf /var/lib/apt/lists/* /tmp/* 17 | USER biodocker 18 | -------------------------------------------------------------------------------- /profnet-norsnet/1.0.22-4-deb/Dockerfile: -------------------------------------------------------------------------------- 1 | FROM biocontainers/biocontainers:debian-stretch-backports 2 | MAINTAINER biocontainers 3 | LABEL software="profnet-norsnet" \ 4 | container="profnet-norsnet" \ 5 | about.summary="neural network architecture for norsnet" \ 6 | about.home="http://www.predictprotein.org/" \ 7 | software.version="1.0.22-4-deb" \ 8 | version="1" \ 9 | about.copyright="" \ 10 | about.license="GPL-2+" \ 11 | about.license_file="/usr/share/doc/profnet-norsnet/copyright" \ 12 | extra.binaries="/usr/bin/profnet_norsnet" \ 13 | about.tags="" 14 | 15 | ENV DEBIAN_FRONTEND noninteractive 16 | RUN apt-get update && apt-get install -y profnet-norsnet && apt-get clean && apt-get purge && rm -rf /var/lib/apt/lists/* /tmp/* 17 | USER biodocker 18 | -------------------------------------------------------------------------------- /profnet-prof/1.0.22-4-deb/Dockerfile: -------------------------------------------------------------------------------- 1 | FROM biocontainers/biocontainers:debian-stretch-backports 2 | MAINTAINER biocontainers 3 | LABEL software="profnet-prof" \ 4 | container="profnet-prof" \ 5 | about.summary="neural network architecture for profacc" \ 6 | about.home="http://www.predictprotein.org/" \ 7 | software.version="1.0.22-4-deb" \ 8 | version="1" \ 9 | about.copyright="" \ 10 | about.license="GPL-2+" \ 11 | about.license_file="/usr/share/doc/profnet-prof/copyright" \ 12 | extra.binaries="/usr/bin/profnet_prof" \ 13 | about.tags="" 14 | 15 | ENV DEBIAN_FRONTEND noninteractive 16 | RUN apt-get update && apt-get install -y profnet-prof && apt-get clean && apt-get purge && rm -rf /var/lib/apt/lists/* /tmp/* 17 | USER biodocker 18 | -------------------------------------------------------------------------------- /profnet-snapfun/1.0.22-4-deb/Dockerfile: -------------------------------------------------------------------------------- 1 | FROM biocontainers/biocontainers:debian-stretch-backports 2 | MAINTAINER biocontainers 3 | LABEL software="profnet-snapfun" \ 4 | container="profnet-snapfun" \ 5 | about.summary="neural network architecture for snapfun" \ 6 | about.home="http://www.predictprotein.org/" \ 7 | software.version="1.0.22-4-deb" \ 8 | version="1" \ 9 | about.copyright="" \ 10 | about.license="GPL-2+" \ 11 | about.license_file="/usr/share/doc/profnet-snapfun/copyright" \ 12 | extra.binaries="/usr/bin/profnet_snapfun" \ 13 | about.tags="" 14 | 15 | ENV DEBIAN_FRONTEND noninteractive 16 | RUN apt-get update && apt-get install -y profnet-snapfun && apt-get clean && apt-get purge && rm -rf /var/lib/apt/lists/* /tmp/* 17 | USER biodocker 18 | -------------------------------------------------------------------------------- /profphd-net/1.0.22-4-deb/Dockerfile: -------------------------------------------------------------------------------- 1 | FROM biocontainers/biocontainers:debian-stretch-backports 2 | MAINTAINER biocontainers 3 | LABEL software="profphd-net" \ 4 | container="profphd-net" \ 5 | about.summary="neural network architecture for profphd" \ 6 | about.home="http://www.predictprotein.org/" \ 7 | software.version="1.0.22-4-deb" \ 8 | version="1" \ 9 | about.copyright="" \ 10 | about.license="GPL-2+" \ 11 | about.license_file="/usr/share/doc/profphd-net/copyright" \ 12 | extra.binaries="/usr/bin/phd1994,/usr/bin/profphd_net" \ 13 | about.tags="" 14 | 15 | ENV DEBIAN_FRONTEND noninteractive 16 | RUN apt-get update && apt-get install -y profphd-net && apt-get clean && apt-get purge && rm -rf /var/lib/apt/lists/* /tmp/* 17 | USER biodocker 18 | -------------------------------------------------------------------------------- /profphd-utils/1.0.10-3b1-deb/Dockerfile: -------------------------------------------------------------------------------- 1 | FROM biocontainers/biocontainers:debian-stretch-backports 2 | MAINTAINER biocontainers 3 | LABEL software="profphd-utils" \ 4 | container="profphd-utils" \ 5 | about.summary="profphd helper utilities convert_seq and filter_hssp" \ 6 | about.home="http://www.rostlab.org/" \ 7 | software.version="1.0.10-3b1-deb" \ 8 | version="1" \ 9 | about.license_file="/usr/share/doc/profphd-utils/copyright" \ 10 | extra.binaries="/usr/bin/convert_seq,/usr/bin/filter_hssp" \ 11 | about.tags="" 12 | 13 | ENV DEBIAN_FRONTEND noninteractive 14 | RUN apt-get update && apt-get install -y profphd-utils && apt-get clean && apt-get purge && rm -rf /var/lib/apt/lists/* /tmp/* 15 | USER biodocker 16 | -------------------------------------------------------------------------------- /proftmb/1.1.12-6b1-deb/Dockerfile: -------------------------------------------------------------------------------- 1 | FROM biocontainers/biocontainers:debian-stretch-backports 2 | MAINTAINER biocontainers 3 | LABEL software="proftmb" \ 4 | container="proftmb" \ 5 | about.summary="per-residue prediction of bacterial transmembrane beta barrels" \ 6 | about.home="http://rostlab.org/" \ 7 | software.version="1.1.12-6b1-deb" \ 8 | version="1" \ 9 | about.license_file="/usr/share/doc/proftmb/copyright" \ 10 | extra.binaries="/usr/bin/proftmb" \ 11 | about.tags="" 12 | 13 | ENV DEBIAN_FRONTEND noninteractive 14 | RUN apt-get update && apt-get install -y proftmb && apt-get clean && apt-get purge && rm -rf /var/lib/apt/lists/* /tmp/* 15 | USER biodocker 16 | -------------------------------------------------------------------------------- /pvrg-jpeg/1.2.1dfsg1-4b1-deb/Dockerfile: -------------------------------------------------------------------------------- 1 | FROM biocontainers/biocontainers:debian-stretch-backports 2 | MAINTAINER biocontainers 3 | LABEL software="pvrg-jpeg" \ 4 | container="pvrg-jpeg" \ 5 | about.summary="Stanford PVRG JPEG tool" \ 6 | about.home="http://jpeg.sourceforge.net/" \ 7 | software.version="1.2.1dfsg1-4b1-deb" \ 8 | version="1" \ 9 | about.license_file="/usr/share/doc/pvrg-jpeg/copyright" \ 10 | extra.binaries="/usr/bin/pvrg-jpeg" \ 11 | about.tags="implemented-in::c, interface::commandline, role::program" 12 | 13 | ENV DEBIAN_FRONTEND noninteractive 14 | RUN apt-get update && apt-get install -y pvrg-jpeg && apt-get clean && apt-get purge && rm -rf /var/lib/apt/lists/* /tmp/* 15 | USER biodocker 16 | -------------------------------------------------------------------------------- /pyfaidx/0.4.8.1-1-deb-py2/Dockerfile: -------------------------------------------------------------------------------- 1 | FROM biocontainers/biocontainers:debian-stretch-backports 2 | MAINTAINER biocontainers 3 | LABEL software="pyfaidx" \ 4 | container="pyfaidx" \ 5 | about.summary="efficient random access to fasta subsequences for Python" \ 6 | about.home="https://github.com/mdshw5/pyfaidx" \ 7 | software.version="0.4.8.1-1-deb-py2" \ 8 | version="1" \ 9 | about.copyright="2013-2015 The Johns Hopkins University" \ 10 | about.license="BSD-3-clause" \ 11 | about.license_file="/usr/share/doc/pyfaidx/copyright" \ 12 | about.tags="" 13 | 14 | ENV DEBIAN_FRONTEND noninteractive 15 | RUN apt-get update && apt-get install -y python-pyfaidx && apt-get clean && apt-get purge && rm -rf /var/lib/apt/lists/* /tmp/* 16 | USER biodocker 17 | -------------------------------------------------------------------------------- /pymol-jupiter/1.0.0/jupyter-minimal-notebook/start-notebook.sh: -------------------------------------------------------------------------------- 1 | #!/bin/bash 2 | 3 | # Handle special flags if we're root 4 | if [ $UID == 0 ] ; then 5 | # Change UID of NB_USER to NB_UID if it does not match 6 | if [ "$NB_UID" != $(id -u $NB_USER) ] ; then 7 | usermod -u $NB_UID $NB_USER 8 | chown -R $NB_UID $CONDA_DIR 9 | fi 10 | 11 | # Enable sudo if requested 12 | if [ ! -z "$GRANT_SUDO" ]; then 13 | echo "$NB_USER ALL=(ALL) NOPASSWD:ALL" > /etc/sudoers.d/notebook 14 | fi 15 | 16 | # Start the notebook server 17 | exec su $NB_USER -c "env PATH=$PATH jupyter notebook $*" 18 | else 19 | # Otherwise just exec the notebook 20 | exec jupyter notebook $* 21 | fi 22 | -------------------------------------------------------------------------------- /pymol-jupiter/1.0.0/jupyter-minimal-notebook/start-singleuser.sh: -------------------------------------------------------------------------------- 1 | #!/bin/bash 2 | set -e 3 | 4 | notebook_arg="" 5 | if [ -n "${NOTEBOOK_DIR:+x}" ] 6 | then 7 | notebook_arg="--notebook-dir=${NOTEBOOK_DIR}" 8 | fi 9 | 10 | exec jupyterhub-singleuser \ 11 | --port=8888 \ 12 | --ip=0.0.0.0 \ 13 | --user=$JPY_USER \ 14 | --cookie-name=$JPY_COOKIE_NAME \ 15 | --base-url=$JPY_BASE_URL \ 16 | --hub-prefix=$JPY_HUB_PREFIX \ 17 | --hub-api-url=$JPY_HUB_API_URL \ 18 | ${notebook_arg} \ 19 | $@ 20 | -------------------------------------------------------------------------------- /pymummer/0.10.1-1-deb-py3/Dockerfile: -------------------------------------------------------------------------------- 1 | FROM biocontainers/biocontainers:debian-stretch-backports 2 | MAINTAINER biocontainers 3 | LABEL software="pymummer" \ 4 | container="pymummer" \ 5 | about.summary="Python 3 interface to MUMmer" \ 6 | about.home="https://github.com/sanger-pathogens/pymummer" \ 7 | software.version="0.10.1-1-deb-py3" \ 8 | version="1" \ 9 | about.copyright="2015-2016 Martin Hunt and Nishadi De Silva" \ 10 | about.license="GPL-3.0" \ 11 | about.license_file="/usr/share/doc/pymummer/copyright" \ 12 | about.tags="" 13 | 14 | ENV DEBIAN_FRONTEND noninteractive 15 | RUN apt-get update && apt-get install -y python3-pymummer && apt-get clean && apt-get purge && rm -rf /var/lib/apt/lists/* /tmp/* 16 | USER biodocker 17 | -------------------------------------------------------------------------------- /pynast/1.2.2-2-deb/Dockerfile: -------------------------------------------------------------------------------- 1 | FROM biocontainers/biocontainers:debian-stretch-backports 2 | MAINTAINER biocontainers 3 | LABEL software="pynast" \ 4 | container="pynast" \ 5 | about.summary="alignment of short DNA sequences" \ 6 | about.home="http://pynast.sourceforge.net/" \ 7 | software.version="1.2.2-2-deb" \ 8 | version="1" \ 9 | about.copyright="2010-2013 PyNAST Development Team" \ 10 | about.license="BSD-3-clause" \ 11 | about.license_file="/usr/share/doc/pynast/copyright" \ 12 | extra.binaries="/usr/bin/pynast" \ 13 | about.tags="" 14 | 15 | ENV DEBIAN_FRONTEND noninteractive 16 | RUN apt-get update && apt-get install -y pynast && apt-get clean && apt-get purge && rm -rf /var/lib/apt/lists/* /tmp/* 17 | USER biodocker 18 | -------------------------------------------------------------------------------- /pysam-tests/0.10.0ds-2-deb-py2/Dockerfile: -------------------------------------------------------------------------------- 1 | FROM biocontainers/biocontainers:debian-stretch-backports 2 | MAINTAINER biocontainers 3 | LABEL software="pysam-tests" \ 4 | container="pysam-tests" \ 5 | about.summary="interface for the SAM/BAM sequence alignment and mapping format (test data)" \ 6 | about.home="http://pysam.readthedocs.org/en/latest" \ 7 | software.version="0.10.0ds-2-deb-py2" \ 8 | version="1" \ 9 | about.copyright="2009-2016 Andreas Heger," \ 10 | about.license="MIT" \ 11 | about.license_file="/usr/share/doc/pysam-tests/copyright" \ 12 | about.tags="" 13 | 14 | ENV DEBIAN_FRONTEND noninteractive 15 | RUN apt-get update && apt-get install -y python-pysam-tests && apt-get clean && apt-get purge && rm -rf /var/lib/apt/lists/* /tmp/* 16 | USER biodocker 17 | -------------------------------------------------------------------------------- /pysam/0.10.0ds-2-deb-py2/Dockerfile: -------------------------------------------------------------------------------- 1 | FROM biocontainers/biocontainers:debian-stretch-backports 2 | MAINTAINER biocontainers 3 | LABEL software="pysam" \ 4 | container="pysam" \ 5 | about.summary="interface for the SAM/BAM sequence alignment and mapping format (Python 2)" \ 6 | about.home="http://pysam.readthedocs.org/en/latest" \ 7 | software.version="0.10.0ds-2-deb-py2" \ 8 | version="1" \ 9 | about.copyright="2009-2016 Andreas Heger," \ 10 | about.license="MIT" \ 11 | about.license_file="/usr/share/doc/pysam/copyright" \ 12 | about.tags="" 13 | 14 | ENV DEBIAN_FRONTEND noninteractive 15 | RUN apt-get update && apt-get install -y python-pysam && apt-get clean && apt-get purge && rm -rf /var/lib/apt/lists/* /tmp/* 16 | USER biodocker 17 | -------------------------------------------------------------------------------- /pysam/0.10.0ds-2-deb-py3/Dockerfile: -------------------------------------------------------------------------------- 1 | FROM biocontainers/biocontainers:debian-stretch-backports 2 | MAINTAINER biocontainers 3 | LABEL software="pysam" \ 4 | container="pysam" \ 5 | about.summary="interface for the SAM/BAM sequence alignment and mapping format (Python 3)" \ 6 | about.home="http://pysam.readthedocs.org/en/latest" \ 7 | software.version="0.10.0ds-2-deb-py3" \ 8 | version="1" \ 9 | about.copyright="2009-2016 Andreas Heger," \ 10 | about.license="MIT" \ 11 | about.license_file="/usr/share/doc/pysam/copyright" \ 12 | about.tags="" 13 | 14 | ENV DEBIAN_FRONTEND noninteractive 15 | RUN apt-get update && apt-get install -y python3-pysam && apt-get clean && apt-get purge && rm -rf /var/lib/apt/lists/* /tmp/* 16 | USER biodocker 17 | -------------------------------------------------------------------------------- /pyvcf/0.6.8-1-deb-py2/Dockerfile: -------------------------------------------------------------------------------- 1 | FROM biocontainers/biocontainers:debian-stretch-backports 2 | MAINTAINER biocontainers 3 | LABEL software="pyvcf" \ 4 | container="pyvcf" \ 5 | about.summary="Variant Call Format (VCF) parser for Python" \ 6 | about.home="https://pypi.python.org/pypi/PyVCF" \ 7 | software.version="0.6.8-1-deb-py2" \ 8 | version="1" \ 9 | about.copyright="2011-2015, Population Genetics Technologies Ltd, All rights reserved." \ 10 | about.license="BSD-3-clause" \ 11 | about.license_file="/usr/share/doc/pyvcf/copyright" \ 12 | about.tags="" 13 | 14 | ENV DEBIAN_FRONTEND noninteractive 15 | RUN apt-get update && apt-get install -y python-pyvcf && apt-get clean && apt-get purge && rm -rf /var/lib/apt/lists/* /tmp/* 16 | USER biodocker 17 | -------------------------------------------------------------------------------- /pyvcf/0.6.8-1-deb-py3/Dockerfile: -------------------------------------------------------------------------------- 1 | FROM biocontainers/biocontainers:debian-stretch-backports 2 | MAINTAINER biocontainers 3 | LABEL software="pyvcf" \ 4 | container="pyvcf" \ 5 | about.summary="Variant Call Format (VCF) parser for Python 3" \ 6 | about.home="https://pypi.python.org/pypi/PyVCF" \ 7 | software.version="0.6.8-1-deb-py3" \ 8 | version="1" \ 9 | about.copyright="2011-2015, Population Genetics Technologies Ltd, All rights reserved." \ 10 | about.license="BSD-3-clause" \ 11 | about.license_file="/usr/share/doc/pyvcf/copyright" \ 12 | about.tags="" 13 | 14 | ENV DEBIAN_FRONTEND noninteractive 15 | RUN apt-get update && apt-get install -y python3-pyvcf && apt-get clean && apt-get purge && rm -rf /var/lib/apt/lists/* /tmp/* 16 | USER biodocker 17 | -------------------------------------------------------------------------------- /qcli/0.1.1-1-deb-py2/Dockerfile: -------------------------------------------------------------------------------- 1 | FROM biocontainers/biocontainers:debian-stretch-backports 2 | MAINTAINER biocontainers 3 | LABEL software="qcli" \ 4 | container="qcli" \ 5 | about.summary="separated module of pyqi needed for QIIME package" \ 6 | about.home="https://pypi.python.org/pypi/qcli/0.1.0" \ 7 | software.version="0.1.1-1-deb-py2" \ 8 | version="1" \ 9 | about.copyright="2013-2014 Greg Caporaso " \ 10 | about.license="BSDlike" \ 11 | about.license_file="/usr/share/doc/qcli/copyright" \ 12 | about.tags="" 13 | 14 | ENV DEBIAN_FRONTEND noninteractive 15 | RUN apt-get update && apt-get install -y python-qcli && apt-get clean && apt-get purge && rm -rf /var/lib/apt/lists/* /tmp/* 16 | USER biodocker 17 | -------------------------------------------------------------------------------- /qsopt-ex/2.5.10.3-1b1-deb/Dockerfile: -------------------------------------------------------------------------------- 1 | FROM biocontainers/biocontainers:debian-stretch-backports 2 | MAINTAINER biocontainers 3 | LABEL software="qsopt-ex" \ 4 | container="qsopt-ex" \ 5 | about.summary="Exact linear programming solver" \ 6 | about.home="http://www.dii.uchile.cl/~daespino/ESolver_doc/main.html" \ 7 | software.version="2.5.10.3-1b1-deb" \ 8 | version="1" \ 9 | about.license_file="/usr/share/doc/qsopt-ex/copyright" \ 10 | extra.binaries="/usr/bin/esolver" \ 11 | about.tags="" 12 | 13 | ENV DEBIAN_FRONTEND noninteractive 14 | RUN apt-get update && apt-get install -y qsopt-ex && apt-get clean && apt-get purge && rm -rf /var/lib/apt/lists/* /tmp/* 15 | USER biodocker 16 | -------------------------------------------------------------------------------- /rate4site/3.0.0-4b1-deb/Dockerfile: -------------------------------------------------------------------------------- 1 | FROM biocontainers/biocontainers:debian-stretch-backports 2 | MAINTAINER biocontainers 3 | LABEL software="rate4site" \ 4 | container="rate4site" \ 5 | about.summary="detector of conserved amino-acid sites" \ 6 | about.home="http://www.tau.ac.il/~itaymay/cp/rate4site.html" \ 7 | software.version="3.0.0-4b1-deb" \ 8 | version="1" \ 9 | about.license_file="/usr/share/doc/rate4site/copyright" \ 10 | extra.binaries="/usr/bin/rate4site,/usr/bin/rate4site_doublerep" \ 11 | about.tags="" 12 | 13 | ENV DEBIAN_FRONTEND noninteractive 14 | RUN apt-get update && apt-get install -y rate4site && apt-get clean && apt-get purge && rm -rf /var/lib/apt/lists/* /tmp/* 15 | USER biodocker 16 | -------------------------------------------------------------------------------- /ray-extra/2.3.1-4-deb/Dockerfile: -------------------------------------------------------------------------------- 1 | FROM biocontainers/biocontainers:debian-stretch-backports 2 | MAINTAINER biocontainers 3 | LABEL software="ray-extra" \ 4 | container="ray-extra" \ 5 | about.summary="Scripts and XSL sheets for post-processing for ray" \ 6 | about.home="http://denovoassembler.sourceforge.net/" \ 7 | software.version="2.3.1-4-deb" \ 8 | version="1" \ 9 | extra.identifiers.biotools="ray" \ 10 | about.copyright="2009-2014 Sbastien Boisvert" \ 11 | about.license="GPL-3" \ 12 | about.license_file="/usr/share/doc/ray-extra/copyright" \ 13 | about.tags="" 14 | 15 | ENV DEBIAN_FRONTEND noninteractive 16 | RUN apt-get update && apt-get install -y ray-extra && apt-get clean && apt-get purge && rm -rf /var/lib/apt/lists/* /tmp/* 17 | USER biodocker 18 | -------------------------------------------------------------------------------- /ray/2.3.1-4b1-deb/Dockerfile: -------------------------------------------------------------------------------- 1 | FROM biocontainers/biocontainers:debian-stretch-backports 2 | MAINTAINER biocontainers 3 | LABEL software="ray" \ 4 | container="ray" \ 5 | about.summary="de novo genome assemblies of next-gen sequencing data" \ 6 | about.home="http://denovoassembler.sourceforge.net/" \ 7 | software.version="2.3.1-4b1-deb" \ 8 | version="1" \ 9 | about.license_file="/usr/share/doc/ray/copyright" \ 10 | extra.binaries="/usr/bin/Ray" \ 11 | about.tags="" 12 | 13 | ENV DEBIAN_FRONTEND noninteractive 14 | RUN apt-get update && apt-get install -y ray && apt-get clean && apt-get purge && rm -rf /var/lib/apt/lists/* /tmp/* 15 | USER biodocker 16 | -------------------------------------------------------------------------------- /rdflib-jsonld/0.4.0-2-deb-py2/Dockerfile: -------------------------------------------------------------------------------- 1 | FROM biocontainers/biocontainers:debian-stretch-backports 2 | MAINTAINER biocontainers 3 | LABEL software="rdflib-jsonld" \ 4 | container="rdflib-jsonld" \ 5 | about.summary="rdflib extension adding JSON-LD parser and serializer in Python 2" \ 6 | about.home="https://github.com/RDFLib/rdflib-jsonld" \ 7 | software.version="0.4.0-2-deb-py2" \ 8 | version="1" \ 9 | about.copyright="(c) 2012-2015, RDFLib Team" \ 10 | about.license="BSD-3-clause" \ 11 | about.license_file="/usr/share/doc/rdflib-jsonld/copyright" \ 12 | about.tags="" 13 | 14 | ENV DEBIAN_FRONTEND noninteractive 15 | RUN apt-get update && apt-get install -y python-rdflib-jsonld && apt-get clean && apt-get purge && rm -rf /var/lib/apt/lists/* /tmp/* 16 | USER biodocker 17 | -------------------------------------------------------------------------------- /rdflib-jsonld/0.4.0-2-deb-py3/Dockerfile: -------------------------------------------------------------------------------- 1 | FROM biocontainers/biocontainers:debian-stretch-backports 2 | MAINTAINER biocontainers 3 | LABEL software="rdflib-jsonld" \ 4 | container="rdflib-jsonld" \ 5 | about.summary="rdflib extension adding JSON-LD parser and serializer in Python 3" \ 6 | about.home="https://github.com/RDFLib/rdflib-jsonld" \ 7 | software.version="0.4.0-2-deb-py3" \ 8 | version="1" \ 9 | about.copyright="(c) 2012-2015, RDFLib Team" \ 10 | about.license="BSD-3-clause" \ 11 | about.license_file="/usr/share/doc/rdflib-jsonld/copyright" \ 12 | about.tags="" 13 | 14 | ENV DEBIAN_FRONTEND noninteractive 15 | RUN apt-get update && apt-get install -y python3-rdflib-jsonld && apt-get clean && apt-get purge && rm -rf /var/lib/apt/lists/* /tmp/* 16 | USER biodocker 17 | -------------------------------------------------------------------------------- /reprof/1.0.1-4-deb/Dockerfile: -------------------------------------------------------------------------------- 1 | FROM biocontainers/biocontainers:debian-stretch-backports 2 | MAINTAINER biocontainers 3 | LABEL software="reprof" \ 4 | container="reprof" \ 5 | about.summary="protein secondary structure and accessibility predictor" \ 6 | about.home="http://rostlab.org/" \ 7 | software.version="1.0.1-4-deb" \ 8 | version="1" \ 9 | extra.identifiers.biotools="reprof" \ 10 | about.copyright="" \ 11 | about.license="GPL-3" \ 12 | about.license_file="/usr/share/doc/reprof/copyright" \ 13 | extra.binaries="/usr/bin/reprof" \ 14 | about.tags="" 15 | 16 | ENV DEBIAN_FRONTEND noninteractive 17 | RUN apt-get update && apt-get install -y reprof && apt-get clean && apt-get purge && rm -rf /var/lib/apt/lists/* /tmp/* 18 | USER biodocker 19 | -------------------------------------------------------------------------------- /rstudio-proteomics/1.0.0/startx.sh: -------------------------------------------------------------------------------- 1 | #!/bin/bash 2 | nohup Xvfb :1 -screen 0 800x600x16 > /dev/null 2>&1 & -------------------------------------------------------------------------------- /rtax/0.984-5-deb/Dockerfile: -------------------------------------------------------------------------------- 1 | FROM biocontainers/biocontainers:debian-stretch-backports 2 | MAINTAINER biocontainers 3 | LABEL software="rtax" \ 4 | container="rtax" \ 5 | about.summary="Classification of sequence reads of 16S ribosomal RNA gene" \ 6 | about.home="https://github.com/davidsoergel/rtax/" \ 7 | software.version="0.984-5-deb" \ 8 | version="1" \ 9 | about.copyright=" 2011 Regents of the University of California" \ 10 | about.license="BSD-3-clause" \ 11 | about.license_file="/usr/share/doc/rtax/copyright" \ 12 | extra.binaries="/usr/bin/rtax" \ 13 | about.tags="" 14 | 15 | ENV DEBIAN_FRONTEND noninteractive 16 | RUN apt-get update && apt-get install -y rtax && apt-get clean && apt-get purge && rm -rf /var/lib/apt/lists/* /tmp/* 17 | USER biodocker 18 | -------------------------------------------------------------------------------- /ruffus/2.6.3dfsg-4-deb-py2/Dockerfile: -------------------------------------------------------------------------------- 1 | FROM biocontainers/biocontainers:debian-stretch-backports 2 | MAINTAINER biocontainers 3 | LABEL software="ruffus" \ 4 | container="ruffus" \ 5 | about.summary="Python computation pipeline library widely used in bioinformatics" \ 6 | about.home="http://www.ruffus.org.uk/" \ 7 | software.version="2.6.3dfsg-4-deb-py2" \ 8 | version="1" \ 9 | about.copyright=" 2010-2014 Leo Goodstadt " \ 10 | about.license="MIT" \ 11 | about.license_file="/usr/share/doc/ruffus/copyright" \ 12 | about.tags="" 13 | 14 | ENV DEBIAN_FRONTEND noninteractive 15 | RUN apt-get update && apt-get install -y python-ruffus && apt-get clean && apt-get purge && rm -rf /var/lib/apt/lists/* /tmp/* 16 | USER biodocker 17 | -------------------------------------------------------------------------------- /ruffus/2.6.3dfsg-4-deb-py3/Dockerfile: -------------------------------------------------------------------------------- 1 | FROM biocontainers/biocontainers:debian-stretch-backports 2 | MAINTAINER biocontainers 3 | LABEL software="ruffus" \ 4 | container="ruffus" \ 5 | about.summary="Python3 computation pipeline library widely used in bioinformatics" \ 6 | about.home="http://www.ruffus.org.uk/" \ 7 | software.version="2.6.3dfsg-4-deb-py3" \ 8 | version="1" \ 9 | about.copyright=" 2010-2014 Leo Goodstadt " \ 10 | about.license="MIT" \ 11 | about.license_file="/usr/share/doc/ruffus/copyright" \ 12 | about.tags="" 13 | 14 | ENV DEBIAN_FRONTEND noninteractive 15 | RUN apt-get update && apt-get install -y python3-ruffus && apt-get clean && apt-get purge && rm -rf /var/lib/apt/lists/* /tmp/* 16 | USER biodocker 17 | -------------------------------------------------------------------------------- /saint/2.5.0dfsg-2b1-deb/Dockerfile: -------------------------------------------------------------------------------- 1 | FROM biocontainers/biocontainers:debian-stretch-backports 2 | MAINTAINER biocontainers 3 | LABEL software="saint" \ 4 | container="saint" \ 5 | about.summary="Significance Analysis of INTeractome" \ 6 | about.home="http://saint-apms.sourceforge.net/Main.html" \ 7 | software.version="2.5.0dfsg-2b1-deb" \ 8 | version="1" \ 9 | about.license_file="/usr/share/doc/saint/copyright" \ 10 | extra.binaries="/usr/bin/saint-int-ctrl,/usr/bin/saint-reformat,/usr/bin/saint-spc-ctrl,/usr/bin/saint-spc-noctrl,/usr/bin/saint-spc-noctrl-matrix" \ 11 | about.tags="" 12 | 13 | ENV DEBIAN_FRONTEND noninteractive 14 | RUN apt-get update && apt-get install -y saint && apt-get clean && apt-get purge && rm -rf /var/lib/apt/lists/* /tmp/* 15 | USER biodocker 16 | -------------------------------------------------------------------------------- /saintq/0.0.2/fragment_intensity_analysis/param_MSPLIT_frag_level: -------------------------------------------------------------------------------- 1 | ### SAINTq parameter file 2 | ## use # to mark a line as comment 3 | 4 | ## name of file with intensities 5 | input_filename=MSPLIT_frag_level.tsv 6 | 7 | ## type of intensity 8 | ## valid: protein, peptide, fragment 9 | input_level=fragment 10 | 11 | ## column names 12 | protein_colname=Protein 13 | pep_colname=Peptide 14 | frag_colname=Fragment 15 | 16 | ## control bait selection rules 17 | compress_n_ctrl=100 18 | 19 | ## test bait replicate selection rules 20 | compress_n_rep=100 21 | 22 | ## peptide selection rules 23 | min_n_pep=3 24 | best_prop_pep=0.5 25 | 26 | ## fragment selection rules 27 | min_n_frag=3 28 | best_prop_frag=0.5 29 | -------------------------------------------------------------------------------- /saintq/0.0.2/peptide_intensity_analysis/param_MSPLIT_pep_level: -------------------------------------------------------------------------------- 1 | ### SAINTq parameter file 2 | ## use # to mark a line as comment 3 | 4 | ## name of file with intensities 5 | input_filename=MSPLIT_pep_level.tsv 6 | 7 | ## type of intensity 8 | ## valid: protein, peptide, fragment 9 | input_level=peptide 10 | 11 | ## column names 12 | protein_colname=Protein 13 | pep_colname=Peptide 14 | 15 | 16 | ## control bait selection rules 17 | compress_n_ctrl=100 18 | 19 | ## test bait replicate selection rules 20 | compress_n_rep=100 21 | 22 | ## peptide selection rules 23 | min_n_pep=3 24 | best_prop_pep=0.5 -------------------------------------------------------------------------------- /saintq/0.0.2/protein_intensity_analysis/param_MSPLIT_prot_level: -------------------------------------------------------------------------------- 1 | ### SAINTq parameter file 2 | ## use # to mark a line as comment 3 | 4 | ## name of file with intensities 5 | input_filename=MSPLIT_prot_level.tsv 6 | 7 | ## valid: protein, peptide, fragment 8 | input_level=protein 9 | 10 | ## column names 11 | protein_colname=Protein 12 | 13 | ## control bait selection rules 14 | compress_n_ctrl=100 15 | 16 | ## test bait replicate selection rules 17 | compress_n_rep=100 18 | -------------------------------------------------------------------------------- /salmon/0.7.2ds1-2b1-deb/Dockerfile: -------------------------------------------------------------------------------- 1 | FROM biocontainers/biocontainers:debian-stretch-backports 2 | MAINTAINER biocontainers 3 | LABEL software="salmon" \ 4 | container="salmon" \ 5 | about.summary="wicked-fast transcript quantification from RNA-seq data" \ 6 | about.home="https://github.com/COMBINE-lab/salmon" \ 7 | software.version="0.7.2ds1-2b1-deb" \ 8 | version="1" \ 9 | about.license_file="/usr/share/doc/salmon/copyright" \ 10 | extra.binaries="/usr/bin/salmon" \ 11 | about.tags="" 12 | 13 | ENV DEBIAN_FRONTEND noninteractive 14 | RUN apt-get update && apt-get install -y salmon && apt-get clean && apt-get purge && rm -rf /var/lib/apt/lists/* /tmp/* 15 | USER biodocker 16 | -------------------------------------------------------------------------------- /samtools-test/1.3.1-3-deb/Dockerfile: -------------------------------------------------------------------------------- 1 | FROM biocontainers/biocontainers:debian-stretch-backports 2 | MAINTAINER biocontainers 3 | LABEL software="samtools-test" \ 4 | container="samtools-test" \ 5 | about.summary="test files for the samtools package" \ 6 | about.home="http://www.htslib.org/" \ 7 | software.version="1.3.1-3-deb" \ 8 | version="1" \ 9 | extra.identifiers.biotools="samtools" \ 10 | about.copyright=" 20082016, Genome Research Ltd. (GRL)" \ 11 | about.license="MIT" \ 12 | about.license_file="/usr/share/doc/samtools-test/copyright" \ 13 | about.tags="" 14 | 15 | ENV DEBIAN_FRONTEND noninteractive 16 | RUN apt-get update && apt-get install -y samtools-test && apt-get clean && apt-get purge && rm -rf /var/lib/apt/lists/* /tmp/* 17 | USER biodocker 18 | -------------------------------------------------------------------------------- /sbmltoolbox/4.1.0-3-deb/Dockerfile: -------------------------------------------------------------------------------- 1 | FROM biocontainers/biocontainers:debian-stretch-backports 2 | MAINTAINER biocontainers 3 | LABEL software="sbmltoolbox" \ 4 | container="sbmltoolbox" \ 5 | about.summary="libsbml toolbox for octave and matlab" \ 6 | about.home="http://sbml.org/Software/SBMLToolbox" \ 7 | software.version="4.1.0-3-deb" \ 8 | version="1" \ 9 | about.copyright="2005-2012 Sarah M. Keating" \ 10 | about.license="LGPL-2.1" \ 11 | about.license_file="/usr/share/doc/sbmltoolbox/copyright" \ 12 | about.tags="" 13 | 14 | ENV DEBIAN_FRONTEND noninteractive 15 | RUN apt-get update && apt-get install -y sbmltoolbox && apt-get clean && apt-get purge && rm -rf /var/lib/apt/lists/* /tmp/* 16 | USER biodocker 17 | -------------------------------------------------------------------------------- /screed/0.9-2-deb-py2/Dockerfile: -------------------------------------------------------------------------------- 1 | FROM biocontainers/biocontainers:debian-stretch-backports 2 | MAINTAINER biocontainers 3 | LABEL software="screed" \ 4 | container="screed" \ 5 | about.summary="short nucleotide read sequence utils in Python 2" \ 6 | about.home="https://screed.readthedocs.org" \ 7 | software.version="0.9-2-deb-py2" \ 8 | version="1" \ 9 | about.copyright="2008-2014 Michigan State University" \ 10 | about.license="BSD-3-Clause" \ 11 | about.license_file="/usr/share/doc/screed/copyright" \ 12 | about.tags="" 13 | 14 | ENV DEBIAN_FRONTEND noninteractive 15 | RUN apt-get update && apt-get install -y python-screed && apt-get clean && apt-get purge && rm -rf /var/lib/apt/lists/* /tmp/* 16 | USER biodocker 17 | -------------------------------------------------------------------------------- /screed/0.9-2-deb-py3/Dockerfile: -------------------------------------------------------------------------------- 1 | FROM biocontainers/biocontainers:debian-stretch-backports 2 | MAINTAINER biocontainers 3 | LABEL software="screed" \ 4 | container="screed" \ 5 | about.summary="short nucleotide read sequence utils in Python 3" \ 6 | about.home="https://screed.readthedocs.org" \ 7 | software.version="0.9-2-deb-py3" \ 8 | version="1" \ 9 | about.copyright="2008-2014 Michigan State University" \ 10 | about.license="BSD-3-Clause" \ 11 | about.license_file="/usr/share/doc/screed/copyright" \ 12 | about.tags="" 13 | 14 | ENV DEBIAN_FRONTEND noninteractive 15 | RUN apt-get update && apt-get install -y python3-screed && apt-get clean && apt-get purge && rm -rf /var/lib/apt/lists/* /tmp/* 16 | USER biodocker 17 | -------------------------------------------------------------------------------- /scrm/1.7.2-1b1-deb/Dockerfile: -------------------------------------------------------------------------------- 1 | FROM biocontainers/biocontainers:debian-stretch-backports 2 | MAINTAINER biocontainers 3 | LABEL software="scrm" \ 4 | container="scrm" \ 5 | about.summary="simulator of evolution of genetic sequences" \ 6 | about.home="https://github.com/scrm/scrm" \ 7 | software.version="1.7.2-1b1-deb" \ 8 | version="1" \ 9 | about.license_file="/usr/share/doc/scrm/copyright" \ 10 | extra.binaries="/usr/bin/scrm" \ 11 | about.tags="" 12 | 13 | ENV DEBIAN_FRONTEND noninteractive 14 | RUN apt-get update && apt-get install -y scrm && apt-get clean && apt-get purge && rm -rf /var/lib/apt/lists/* /tmp/* 15 | USER biodocker 16 | -------------------------------------------------------------------------------- /scythe/0.994-4-deb/Dockerfile: -------------------------------------------------------------------------------- 1 | FROM biocontainers/biocontainers:debian-stretch-backports 2 | MAINTAINER biocontainers 3 | LABEL software="scythe" \ 4 | container="scythe" \ 5 | about.summary="Bayesian adaptor trimmer for sequencing reads" \ 6 | about.home="https://github.com/vsbuffalo/scythe" \ 7 | software.version="0.994-4-deb" \ 8 | version="1" \ 9 | about.copyright="2011 Vince Buffalo" \ 10 | about.license="Expat" \ 11 | about.license_file="/usr/share/doc/scythe/copyright" \ 12 | extra.binaries="/usr/bin/scythe" \ 13 | about.tags="" 14 | 15 | ENV DEBIAN_FRONTEND noninteractive 16 | RUN apt-get update && apt-get install -y scythe && apt-get clean && apt-get purge && rm -rf /var/lib/apt/lists/* /tmp/* 17 | USER biodocker 18 | -------------------------------------------------------------------------------- /sickle/1.33-1b1-deb/Dockerfile: -------------------------------------------------------------------------------- 1 | FROM biocontainers/biocontainers:debian-stretch-backports 2 | MAINTAINER biocontainers 3 | LABEL software="sickle" \ 4 | container="sickle" \ 5 | about.summary="windowed adaptive trimming tool for FASTQ files using quality" \ 6 | about.home="https://github.com/najoshi/sickle" \ 7 | software.version="1.33-1b1-deb" \ 8 | version="1" \ 9 | about.license_file="/usr/share/doc/sickle/copyright" \ 10 | extra.binaries="/usr/bin/sickle" \ 11 | about.tags="" 12 | 13 | ENV DEBIAN_FRONTEND noninteractive 14 | RUN apt-get update && apt-get install -y sickle && apt-get clean && apt-get purge && rm -rf /var/lib/apt/lists/* /tmp/* 15 | USER biodocker 16 | -------------------------------------------------------------------------------- /sitplus-data/1.0.3-5.1-deb/Dockerfile: -------------------------------------------------------------------------------- 1 | FROM biocontainers/biocontainers:debian-stretch-backports 2 | MAINTAINER biocontainers 3 | LABEL software="sitplus-data" \ 4 | container="sitplus-data" \ 5 | about.summary="Data files for Sitplus, a framework for ludic-therapeutic activities" \ 6 | about.home="http://sitplus.crea-si.com" \ 7 | software.version="1.0.3-5.1-deb" \ 8 | version="1" \ 9 | about.copyright="2011 Cesar Mauri Loba " \ 10 | about.license="GPL-3.0+" \ 11 | about.license_file="/usr/share/doc/sitplus-data/copyright" \ 12 | about.tags="role::app-data" 13 | 14 | ENV DEBIAN_FRONTEND noninteractive 15 | RUN apt-get update && apt-get install -y sitplus-data && apt-get clean && apt-get purge && rm -rf /var/lib/apt/lists/* /tmp/* 16 | USER biodocker 17 | -------------------------------------------------------------------------------- /skbio/0.5.1-2-deb-py3/Dockerfile: -------------------------------------------------------------------------------- 1 | FROM biocontainers/biocontainers:debian-stretch-backports 2 | MAINTAINER biocontainers 3 | LABEL software="skbio" \ 4 | container="skbio" \ 5 | about.summary="Python3 data structures, algorithms, educational resources for bioinformatic" \ 6 | about.home="https://github.com/biocore/scikit-bio" \ 7 | software.version="0.5.1-2-deb-py3" \ 8 | version="1" \ 9 | about.copyright="2013-2015 scikit-bio development team." \ 10 | about.license="BSD-3-clause" \ 11 | about.license_file="/usr/share/doc/skbio/copyright" \ 12 | about.tags="" 13 | 14 | ENV DEBIAN_FRONTEND noninteractive 15 | RUN apt-get update && apt-get install -y python3-skbio && apt-get clean && apt-get purge && rm -rf /var/lib/apt/lists/* /tmp/* 16 | USER biodocker 17 | -------------------------------------------------------------------------------- /smithwaterman/0.020160702-1b1-deb/Dockerfile: -------------------------------------------------------------------------------- 1 | FROM biocontainers/biocontainers:debian-stretch-backports 2 | MAINTAINER biocontainers 3 | LABEL software="smithwaterman" \ 4 | container="smithwaterman" \ 5 | about.summary="determine similar regions between two strings or genomic sequences" \ 6 | about.home="https://github.com/ekg/smithwaterman" \ 7 | software.version="0.020160702-1b1-deb" \ 8 | version="1" \ 9 | about.license_file="/usr/share/doc/smithwaterman/copyright" \ 10 | extra.binaries="/usr/bin/smithwaterman" \ 11 | about.tags="" 12 | 13 | ENV DEBIAN_FRONTEND noninteractive 14 | RUN apt-get update && apt-get install -y smithwaterman && apt-get clean && apt-get purge && rm -rf /var/lib/apt/lists/* /tmp/* 15 | USER biodocker 16 | -------------------------------------------------------------------------------- /smrtanalysis-dev/020161126-deb/Dockerfile: -------------------------------------------------------------------------------- 1 | FROM biocontainers/biocontainers:debian-stretch-backports 2 | MAINTAINER biocontainers 3 | LABEL software="smrtanalysis-dev" \ 4 | container="smrtanalysis-dev" \ 5 | about.summary="develepment libraries for smrtanalysis" \ 6 | about.home="http://www.pacb.com/products-and-services/analytical-software/smrt-analysis/" \ 7 | software.version="020161126-deb" \ 8 | version="1" \ 9 | about.license_file="/usr/share/doc/smrtanalysis-dev/copyright" \ 10 | about.tags="devel::library, role::devel-lib" 11 | 12 | ENV DEBIAN_FRONTEND noninteractive 13 | RUN apt-get update && apt-get install -y smrtanalysis-dev && apt-get clean && apt-get purge && rm -rf /var/lib/apt/lists/* /tmp/* 14 | USER biodocker 15 | -------------------------------------------------------------------------------- /smrtanalysis/020161126-deb/Dockerfile: -------------------------------------------------------------------------------- 1 | FROM biocontainers/biocontainers:debian-stretch-backports 2 | MAINTAINER biocontainers 3 | LABEL software="smrtanalysis" \ 4 | container="smrtanalysis" \ 5 | about.summary="software suite for single molecule, real-time sequencing" \ 6 | about.home="http://www.pacb.com/products-and-services/analytical-software/smrt-analysis/" \ 7 | software.version="020161126-deb" \ 8 | version="1" \ 9 | about.license_file="/usr/share/doc/smrtanalysis/copyright" \ 10 | about.tags="" 11 | 12 | ENV DEBIAN_FRONTEND noninteractive 13 | RUN apt-get update && apt-get install -y smrtanalysis && apt-get clean && apt-get purge && rm -rf /var/lib/apt/lists/* /tmp/* 14 | USER biodocker 15 | -------------------------------------------------------------------------------- /sofa-data/1.0beta4-11-deb/Dockerfile: -------------------------------------------------------------------------------- 1 | FROM biocontainers/biocontainers:debian-stretch-backports 2 | MAINTAINER biocontainers 3 | LABEL software="sofa-data" \ 4 | container="sofa-data" \ 5 | about.summary="Simulation Open Framework Architecture - data" \ 6 | about.home="http://www.sofa-framework.org/" \ 7 | software.version="1.0beta4-11-deb" \ 8 | version="1" \ 9 | about.copyright="2006-2008 MGH, INRIA, USTL, UJF, CNRS" \ 10 | about.license="LGPL" \ 11 | about.license_file="/usr/share/doc/sofa-data/copyright" \ 12 | about.tags="role::app-data" 13 | 14 | ENV DEBIAN_FRONTEND noninteractive 15 | RUN apt-get update && apt-get install -y sofa-data && apt-get clean && apt-get purge && rm -rf /var/lib/apt/lists/* /tmp/* 16 | USER biodocker 17 | -------------------------------------------------------------------------------- /sortmerna/2.1-1b1-deb/Dockerfile: -------------------------------------------------------------------------------- 1 | FROM biocontainers/biocontainers:debian-stretch-backports 2 | MAINTAINER biocontainers 3 | LABEL software="sortmerna" \ 4 | container="sortmerna" \ 5 | about.summary="tool for filtering, mapping and OTU-picking NGS reads" \ 6 | about.home="http://bioinfo.lifl.fr/RNA/sortmerna/" \ 7 | software.version="2.1-1b1-deb" \ 8 | version="1" \ 9 | about.license_file="/usr/share/doc/sortmerna/copyright" \ 10 | extra.binaries="/usr/bin/indexdb_rna,/usr/bin/sortmerna" \ 11 | about.tags="" 12 | 13 | ENV DEBIAN_FRONTEND noninteractive 14 | RUN apt-get update && apt-get install -y sortmerna && apt-get clean && apt-get purge && rm -rf /var/lib/apt/lists/* /tmp/* 15 | USER biodocker 16 | -------------------------------------------------------------------------------- /spaced/1.0.2dfsg-1b1-deb/Dockerfile: -------------------------------------------------------------------------------- 1 | FROM biocontainers/biocontainers:debian-stretch-backports 2 | MAINTAINER biocontainers 3 | LABEL software="spaced" \ 4 | container="spaced" \ 5 | about.summary="alignment-free sequence comparison using spaced words" \ 6 | about.home="http://spaced.gobics.de/" \ 7 | software.version="1.0.2dfsg-1b1-deb" \ 8 | version="1" \ 9 | about.license_file="/usr/share/doc/spaced/copyright" \ 10 | extra.binaries="/usr/bin/spaced" \ 11 | about.tags="" 12 | 13 | ENV DEBIAN_FRONTEND noninteractive 14 | RUN apt-get update && apt-get install -y spaced && apt-get clean && apt-get purge && rm -rf /var/lib/apt/lists/* /tmp/* 15 | USER biodocker 16 | -------------------------------------------------------------------------------- /spark/3.1.3/scripts/prepare.sh: -------------------------------------------------------------------------------- 1 | #!/bin/bash -ue 2 | # Prepare the given Spark work dir by creating it, or cleaning it 3 | # of Spark content if it already exists. 4 | work_dir=$1 5 | 6 | if [[ ! -d "${work_dir}" ]] ; then 7 | echo "Creating work directory: ${work_dir}" 8 | mkdir -p "${work_dir}" 9 | else 10 | echo "Cleaning existing work directory: ${work_dir}" 11 | rm -f ${work_dir}/spark* || true 12 | fi 13 | -------------------------------------------------------------------------------- /spark/3.1.3/scripts/terminate.sh: -------------------------------------------------------------------------------- 1 | #!/bin/bash -ue 2 | # Send signal to terminate the running cluster 3 | terminate_file_name=$1 4 | 5 | echo "DONE" > ${terminate_file_name} 6 | -------------------------------------------------------------------------------- /sqlsoup/0.9.1-1-deb-py2/Dockerfile: -------------------------------------------------------------------------------- 1 | FROM biocontainers/biocontainers:debian-stretch-backports 2 | MAINTAINER biocontainers 3 | LABEL software="sqlsoup" \ 4 | container="sqlsoup" \ 5 | about.summary="one step database access tool for Python, built on the SQLAlchemy ORM" \ 6 | about.home="https://pypi.python.org/pypi/sqlsoup" \ 7 | software.version="0.9.1-1-deb-py2" \ 8 | version="1" \ 9 | about.copyright="2005-2012 by Jonathan Ellis and Michael Bayer." \ 10 | about.license="Expat" \ 11 | about.license_file="/usr/share/doc/sqlsoup/copyright" \ 12 | about.tags="" 13 | 14 | ENV DEBIAN_FRONTEND noninteractive 15 | RUN apt-get update && apt-get install -y python-sqlsoup && apt-get clean && apt-get purge && rm -rf /var/lib/apt/lists/* /tmp/* 16 | USER biodocker 17 | -------------------------------------------------------------------------------- /sqlsoup/0.9.1-1-deb-py3/Dockerfile: -------------------------------------------------------------------------------- 1 | FROM biocontainers/biocontainers:debian-stretch-backports 2 | MAINTAINER biocontainers 3 | LABEL software="sqlsoup" \ 4 | container="sqlsoup" \ 5 | about.summary="one step database access tool for Python3, built on the SQLAlchemy ORM" \ 6 | about.home="https://pypi.python.org/pypi/sqlsoup" \ 7 | software.version="0.9.1-1-deb-py3" \ 8 | version="1" \ 9 | about.copyright="2005-2012 by Jonathan Ellis and Michael Bayer." \ 10 | about.license="Expat" \ 11 | about.license_file="/usr/share/doc/sqlsoup/copyright" \ 12 | about.tags="" 13 | 14 | ENV DEBIAN_FRONTEND noninteractive 15 | RUN apt-get update && apt-get install -y python3-sqlsoup && apt-get clean && apt-get purge && rm -rf /var/lib/apt/lists/* /tmp/* 16 | USER biodocker 17 | -------------------------------------------------------------------------------- /ssw-align/1.1-1b1-deb/Dockerfile: -------------------------------------------------------------------------------- 1 | FROM biocontainers/biocontainers:debian-stretch-backports 2 | MAINTAINER biocontainers 3 | LABEL software="ssw-align" \ 4 | container="ssw-align" \ 5 | about.summary="Smith-Waterman aligner based on libssw" \ 6 | about.home="https://github.com/mengyao/Complete-Striped-Smith-Waterman-Library" \ 7 | software.version="1.1-1b1-deb" \ 8 | version="1" \ 9 | about.license_file="/usr/share/doc/ssw-align/copyright" \ 10 | extra.binaries="/usr/bin/ssw-align,/usr/bin/ssw_test" \ 11 | about.tags="" 12 | 13 | ENV DEBIAN_FRONTEND noninteractive 14 | RUN apt-get update && apt-get install -y ssw-align && apt-get clean && apt-get purge && rm -rf /var/lib/apt/lists/* /tmp/* 15 | USER biodocker 16 | -------------------------------------------------------------------------------- /stacks/1.44-2b1-deb/Dockerfile: -------------------------------------------------------------------------------- 1 | FROM biocontainers/biocontainers:debian-stretch-backports 2 | MAINTAINER biocontainers 3 | LABEL software="stacks" \ 4 | container="stacks" \ 5 | about.summary="pipeline for building loci from short-read DNA sequences" \ 6 | about.home="http://creskolab.uoregon.edu/stacks/" \ 7 | software.version="1.44-2b1-deb" \ 8 | version="1" \ 9 | about.license_file="/usr/share/doc/stacks/copyright" \ 10 | extra.binaries="/usr/bin/stacks" \ 11 | about.tags="" 12 | 13 | ENV DEBIAN_FRONTEND noninteractive 14 | RUN apt-get update && apt-get install -y stacks && apt-get clean && apt-get purge && rm -rf /var/lib/apt/lists/* /tmp/* 15 | USER biodocker 16 | -------------------------------------------------------------------------------- /staden/2.0.0b11-2b1-deb/Dockerfile: -------------------------------------------------------------------------------- 1 | FROM biocontainers/biocontainers:debian-stretch-backports 2 | MAINTAINER biocontainers 3 | LABEL software="staden" \ 4 | container="staden" \ 5 | about.summary="DNA sequence assembly (Gap4/Gap5), editing and analysis tools" \ 6 | about.home="https://staden.sf.net" \ 7 | software.version="2.0.0b11-2b1-deb" \ 8 | version="1" \ 9 | about.license_file="/usr/share/doc/staden/copyright" \ 10 | extra.binaries="/usr/bin/gap4,/usr/bin/gap5,/usr/bin/pregap4,/usr/bin/staden,/usr/bin/trev" \ 11 | about.tags="" 12 | 13 | ENV DEBIAN_FRONTEND noninteractive 14 | RUN apt-get update && apt-get install -y staden && apt-get clean && apt-get purge && rm -rf /var/lib/apt/lists/* /tmp/* 15 | USER biodocker 16 | -------------------------------------------------------------------------------- /suitename/0.3.070628-1b1-deb/Dockerfile: -------------------------------------------------------------------------------- 1 | FROM biocontainers/biocontainers:debian-stretch-backports 2 | MAINTAINER biocontainers 3 | LABEL software="suitename" \ 4 | container="suitename" \ 5 | about.summary="categorize each suite in an RNA backbone" \ 6 | about.home="http://kinemage.biochem.duke.edu/software/suitename.php" \ 7 | software.version="0.3.070628-1b1-deb" \ 8 | version="1" \ 9 | about.license_file="/usr/share/doc/suitename/copyright" \ 10 | extra.binaries="/usr/bin/suitename" \ 11 | about.tags="" 12 | 13 | ENV DEBIAN_FRONTEND noninteractive 14 | RUN apt-get update && apt-get install -y suitename && apt-get clean && apt-get purge && rm -rf /var/lib/apt/lists/* /tmp/* 15 | USER biodocker 16 | -------------------------------------------------------------------------------- /sumaclust/1.0.20-1b1-deb/Dockerfile: -------------------------------------------------------------------------------- 1 | FROM biocontainers/biocontainers:debian-stretch-backports 2 | MAINTAINER biocontainers 3 | LABEL software="sumaclust" \ 4 | container="sumaclust" \ 5 | about.summary="fast and exact clustering of genomic sequences" \ 6 | about.home="http://metabarcoding.org/sumaclust" \ 7 | software.version="1.0.20-1b1-deb" \ 8 | version="1" \ 9 | about.license_file="/usr/share/doc/sumaclust/copyright" \ 10 | extra.binaries="/usr/bin/sumaclust" \ 11 | about.tags="" 12 | 13 | ENV DEBIAN_FRONTEND noninteractive 14 | RUN apt-get update && apt-get install -y sumaclust && apt-get clean && apt-get purge && rm -rf /var/lib/apt/lists/* /tmp/* 15 | USER biodocker 16 | -------------------------------------------------------------------------------- /sumatra/1.0.20-1b1-deb/Dockerfile: -------------------------------------------------------------------------------- 1 | FROM biocontainers/biocontainers:debian-stretch-backports 2 | MAINTAINER biocontainers 3 | LABEL software="sumatra" \ 4 | container="sumatra" \ 5 | about.summary="fast and exact comparison and clustering of sequences" \ 6 | about.home="http://metabarcoding.org/sumatra" \ 7 | software.version="1.0.20-1b1-deb" \ 8 | version="1" \ 9 | about.license_file="/usr/share/doc/sumatra/copyright" \ 10 | extra.binaries="/usr/bin/sumatra" \ 11 | about.tags="" 12 | 13 | ENV DEBIAN_FRONTEND noninteractive 14 | RUN apt-get update && apt-get install -y sumatra && apt-get clean && apt-get purge && rm -rf /var/lib/apt/lists/* /tmp/* 15 | USER biodocker 16 | -------------------------------------------------------------------------------- /sumtrees/4.2.0dfsg-1-deb/Dockerfile: -------------------------------------------------------------------------------- 1 | FROM biocontainers/biocontainers:debian-stretch-backports 2 | MAINTAINER biocontainers 3 | LABEL software="sumtrees" \ 4 | container="sumtrees" \ 5 | about.summary="Phylogenetic Tree Summarization and Annotation" \ 6 | about.home="http://dendropy.org/" \ 7 | software.version="4.2.0dfsg-1-deb" \ 8 | version="1" \ 9 | about.copyright="2014 Jeet Sukumaran " \ 10 | about.license="BSD-3-clause" \ 11 | about.license_file="/usr/share/doc/sumtrees/copyright" \ 12 | extra.binaries="/usr/bin/sumtrees" \ 13 | about.tags="" 14 | 15 | ENV DEBIAN_FRONTEND noninteractive 16 | RUN apt-get update && apt-get install -y sumtrees && apt-get clean && apt-get purge && rm -rf /var/lib/apt/lists/* /tmp/* 17 | USER biodocker 18 | -------------------------------------------------------------------------------- /test-ci/0.0.1/README.md: -------------------------------------------------------------------------------- 1 | this is a test container for the continiuos integration system 2 | -------------------------------------------------------------------------------- /toppred/1.10-4-deb/Dockerfile: -------------------------------------------------------------------------------- 1 | FROM biocontainers/biocontainers:debian-stretch-backports 2 | MAINTAINER biocontainers 3 | LABEL software="toppred" \ 4 | container="toppred" \ 5 | about.summary="transmembrane topology prediction" \ 6 | about.home="https://github.com/bioinfo-center-pasteur-fr/toppred" \ 7 | software.version="1.10-4-deb" \ 8 | version="1" \ 9 | about.copyright=" 1999-2001 Eric Deveaud " \ 10 | about.license="GPL-2+" \ 11 | about.license_file="/usr/share/doc/toppred/copyright" \ 12 | extra.binaries="/usr/bin/toppred" \ 13 | about.tags="" 14 | 15 | ENV DEBIAN_FRONTEND noninteractive 16 | RUN apt-get update && apt-get install -y toppred && apt-get clean && apt-get purge && rm -rf /var/lib/apt/lists/* /tmp/* 17 | USER biodocker 18 | -------------------------------------------------------------------------------- /transrate-tools/1.0.0-1b1-deb/Dockerfile: -------------------------------------------------------------------------------- 1 | FROM biocontainers/biocontainers:debian-stretch-backports 2 | MAINTAINER biocontainers 3 | LABEL software="transrate-tools" \ 4 | container="transrate-tools" \ 5 | about.summary="helper for transrate" \ 6 | about.home="http://hibberdlab.com/transrate/" \ 7 | software.version="1.0.0-1b1-deb" \ 8 | version="1" \ 9 | about.license_file="/usr/share/doc/transrate-tools/copyright" \ 10 | extra.binaries="/usr/bin/bam-read" \ 11 | about.tags="" 12 | 13 | ENV DEBIAN_FRONTEND noninteractive 14 | RUN apt-get update && apt-get install -y transrate-tools && apt-get clean && apt-get purge && rm -rf /var/lib/apt/lists/* /tmp/* 15 | USER biodocker 16 | -------------------------------------------------------------------------------- /transtermhp/2.09-3b1-deb/Dockerfile: -------------------------------------------------------------------------------- 1 | FROM biocontainers/biocontainers:debian-stretch-backports 2 | MAINTAINER biocontainers 3 | LABEL software="transtermhp" \ 4 | container="transtermhp" \ 5 | about.summary="find rho-independent transcription terminators in bacterial genomes" \ 6 | about.home="http://transterm.cbcb.umd.edu/" \ 7 | software.version="2.09-3b1-deb" \ 8 | version="1" \ 9 | about.license_file="/usr/share/doc/transtermhp/copyright" \ 10 | extra.binaries="/usr/bin/2ndscore,/usr/bin/transterm" \ 11 | about.tags="" 12 | 13 | ENV DEBIAN_FRONTEND noninteractive 14 | RUN apt-get update && apt-get install -y transtermhp && apt-get clean && apt-get purge && rm -rf /var/lib/apt/lists/* /tmp/* 15 | USER biodocker 16 | -------------------------------------------------------------------------------- /trinityrnaseq/2.2.0dfsg-2b1-deb/Dockerfile: -------------------------------------------------------------------------------- 1 | FROM biocontainers/biocontainers:debian-stretch-backports 2 | MAINTAINER biocontainers 3 | LABEL software="trinityrnaseq" \ 4 | container="trinityrnaseq" \ 5 | about.summary="RNA-Seq De novo Assembly" \ 6 | about.home="http://trinityrnaseq.github.io/" \ 7 | software.version="2.2.0dfsg-2b1-deb" \ 8 | version="1" \ 9 | about.license_file="/usr/share/doc/trinityrnaseq/copyright" \ 10 | extra.binaries="/usr/bin/Trinity" \ 11 | about.tags="" 12 | 13 | ENV DEBIAN_FRONTEND noninteractive 14 | RUN apt-get update && apt-get install -y trinityrnaseq && apt-get clean && apt-get purge && rm -rf /var/lib/apt/lists/* /tmp/* 15 | USER biodocker 16 | -------------------------------------------------------------------------------- /typed-ast/0.6.3-1-deb-py3/Dockerfile: -------------------------------------------------------------------------------- 1 | FROM biocontainers/biocontainers:debian-stretch-backports 2 | MAINTAINER biocontainers 3 | LABEL software="typed-ast" \ 4 | container="typed-ast" \ 5 | about.summary="AST with PEP 484 type comments support" \ 6 | about.home="http://www.mypy-lang.org/" \ 7 | software.version="0.6.3-1-deb-py3" \ 8 | version="1" \ 9 | about.copyright=" 2016 David Fisher " \ 10 | about.license="Apache-2.0" \ 11 | about.license_file="/usr/share/doc/typed-ast/copyright" \ 12 | about.tags="" 13 | 14 | ENV DEBIAN_FRONTEND noninteractive 15 | RUN apt-get update && apt-get install -y python3-typed-ast && apt-get clean && apt-get purge && rm -rf /var/lib/apt/lists/* /tmp/* 16 | USER biodocker 17 | -------------------------------------------------------------------------------- /uc-echo/1.12-9b1-deb/Dockerfile: -------------------------------------------------------------------------------- 1 | FROM biocontainers/biocontainers:debian-stretch-backports 2 | MAINTAINER biocontainers 3 | LABEL software="uc-echo" \ 4 | container="uc-echo" \ 5 | about.summary="error correction algorithm designed for short-reads from NGS" \ 6 | about.home="http://uc-echo.sourceforge.net/" \ 7 | software.version="1.12-9b1-deb" \ 8 | version="1" \ 9 | about.license_file="/usr/share/doc/uc-echo/copyright" \ 10 | extra.binaries="/usr/bin/uc-echo" \ 11 | about.tags="" 12 | 13 | ENV DEBIAN_FRONTEND noninteractive 14 | RUN apt-get update && apt-get install -y uc-echo && apt-get clean && apt-get purge && rm -rf /var/lib/apt/lists/* /tmp/* 15 | USER biodocker 16 | -------------------------------------------------------------------------------- /varna/3-93ds-1-deb/Dockerfile: -------------------------------------------------------------------------------- 1 | FROM biocontainers/biocontainers:debian-stretch-backports 2 | MAINTAINER biocontainers 3 | LABEL software="varna" \ 4 | container="varna" \ 5 | about.summary="Visualization Applet for RNA" \ 6 | about.home="http://varna.lri.fr/" \ 7 | software.version="3-93ds-1-deb" \ 8 | version="1" \ 9 | about.copyright=" 2008 Kevin Darty, Alain Denise and Yann Ponty " \ 10 | about.license="GPL-3+" \ 11 | about.license_file="/usr/share/doc/varna/copyright" \ 12 | about.tags="" 13 | 14 | ENV DEBIAN_FRONTEND noninteractive 15 | RUN apt-get update && apt-get install -y varna && apt-get clean && apt-get purge && rm -rf /var/lib/apt/lists/* /tmp/* 16 | USER biodocker 17 | -------------------------------------------------------------------------------- /vg/1.23.0-plusds-1-deb/test-cmds.txt: -------------------------------------------------------------------------------- 1 | vg test 2 | -------------------------------------------------------------------------------- /visionegg/1.2.1-2-deb-py2/Dockerfile: -------------------------------------------------------------------------------- 1 | FROM biocontainers/biocontainers:debian-stretch-backports 2 | MAINTAINER biocontainers 3 | LABEL software="visionegg" \ 4 | container="visionegg" \ 5 | about.summary="Python library for 2D/3D visual stimulus generation" \ 6 | about.home="http://www.visionegg.org" \ 7 | software.version="1.2.1-2-deb-py2" \ 8 | version="1" \ 9 | about.copyright="2001-2003 Andrew Straw" \ 10 | about.license="LGPL 2.1" \ 11 | about.license_file="/usr/share/doc/visionegg/copyright" \ 12 | about.tags="" 13 | 14 | ENV DEBIAN_FRONTEND noninteractive 15 | RUN apt-get update && apt-get install -y python-visionegg && apt-get clean && apt-get purge && rm -rf /var/lib/apt/lists/* /tmp/* 16 | USER biodocker 17 | -------------------------------------------------------------------------------- /vtk-dicom/0.7.10-1b2-deb-py2/Dockerfile: -------------------------------------------------------------------------------- 1 | FROM biocontainers/biocontainers:debian-stretch-backports 2 | MAINTAINER biocontainers 3 | LABEL software="vtk-dicom" \ 4 | container="vtk-dicom" \ 5 | about.summary="DICOM for VTK - Python" \ 6 | about.home="http://github.com/dgobbi/vtk-dicom/" \ 7 | software.version="0.7.10-1b2-deb-py2" \ 8 | version="1" \ 9 | about.license_file="/usr/share/doc/vtk-dicom/copyright" \ 10 | about.tags="" 11 | 12 | ENV DEBIAN_FRONTEND noninteractive 13 | RUN apt-get update && apt-get install -y python-vtk-dicom && apt-get clean && apt-get purge && rm -rf /var/lib/apt/lists/* /tmp/* 14 | USER biodocker 15 | -------------------------------------------------------------------------------- /vtkgdcm/2.6.6-3-deb-py2/Dockerfile: -------------------------------------------------------------------------------- 1 | FROM biocontainers/biocontainers:debian-stretch-backports 2 | MAINTAINER biocontainers 3 | LABEL software="vtkgdcm" \ 4 | container="vtkgdcm" \ 5 | about.summary="Grassroots DICOM VTK/Python bindings" \ 6 | about.home="http://gdcm.sourceforge.net/" \ 7 | software.version="2.6.6-3-deb-py2" \ 8 | version="1" \ 9 | about.copyright="2006-2011 Mathieu Malaterre" \ 10 | about.license="BSD-3-clause-alike-CREATIS" \ 11 | about.license_file="/usr/share/doc/vtkgdcm/copyright" \ 12 | about.tags="" 13 | 14 | ENV DEBIAN_FRONTEND noninteractive 15 | RUN apt-get update && apt-get install -y python-vtkgdcm && apt-get clean && apt-get purge && rm -rf /var/lib/apt/lists/* /tmp/* 16 | USER biodocker 17 | -------------------------------------------------------------------------------- /wise-data/2.4.1-19-deb/Dockerfile: -------------------------------------------------------------------------------- 1 | FROM biocontainers/biocontainers:debian-stretch-backports 2 | MAINTAINER biocontainers 3 | LABEL software="wise-data" \ 4 | container="wise-data" \ 5 | about.summary="data files for the wise package" \ 6 | about.home="http://www.ebi.ac.uk/~birney/wise2/" \ 7 | software.version="2.4.1-19-deb" \ 8 | version="1" \ 9 | extra.identifiers.biotools="wise" \ 10 | about.copyright=" 1996-2001 Genome Research Limited (GRL) and" \ 11 | about.license="GRL" \ 12 | about.license_file="/usr/share/doc/wise-data/copyright" \ 13 | about.tags="" 14 | 15 | ENV DEBIAN_FRONTEND noninteractive 16 | RUN apt-get update && apt-get install -y wise-data && apt-get clean && apt-get purge && rm -rf /var/lib/apt/lists/* /tmp/* 17 | USER biodocker 18 | -------------------------------------------------------------------------------- /xopen/0.1.1-1-deb-py2/Dockerfile: -------------------------------------------------------------------------------- 1 | FROM biocontainers/biocontainers:debian-stretch-backports 2 | MAINTAINER biocontainers 3 | LABEL software="xopen" \ 4 | container="xopen" \ 5 | about.summary="Python module to open compressed files transparently" \ 6 | about.home="https://github.com/marcelm/xopen" \ 7 | software.version="0.1.1-1-deb-py2" \ 8 | version="1" \ 9 | about.copyright="2010-2016 Marcel Martin " \ 10 | about.license="MIT" \ 11 | about.license_file="/usr/share/doc/xopen/copyright" \ 12 | about.tags="" 13 | 14 | ENV DEBIAN_FRONTEND noninteractive 15 | RUN apt-get update && apt-get install -y python-xopen && apt-get clean && apt-get purge && rm -rf /var/lib/apt/lists/* /tmp/* 16 | USER biodocker 17 | -------------------------------------------------------------------------------- /xopen/0.1.1-1-deb-py3/Dockerfile: -------------------------------------------------------------------------------- 1 | FROM biocontainers/biocontainers:debian-stretch-backports 2 | MAINTAINER biocontainers 3 | LABEL software="xopen" \ 4 | container="xopen" \ 5 | about.summary="Python3 module to open compressed files transparently" \ 6 | about.home="https://github.com/marcelm/xopen" \ 7 | software.version="0.1.1-1-deb-py3" \ 8 | version="1" \ 9 | about.copyright="2010-2016 Marcel Martin " \ 10 | about.license="MIT" \ 11 | about.license_file="/usr/share/doc/xopen/copyright" \ 12 | about.tags="" 13 | 14 | ENV DEBIAN_FRONTEND noninteractive 15 | RUN apt-get update && apt-get install -y python3-xopen && apt-get clean && apt-get purge && rm -rf /var/lib/apt/lists/* /tmp/* 16 | USER biodocker 17 | -------------------------------------------------------------------------------- /yaggo/1.5.9-1-deb/Dockerfile: -------------------------------------------------------------------------------- 1 | FROM biocontainers/biocontainers:debian-stretch-backports 2 | MAINTAINER biocontainers 3 | LABEL software="yaggo" \ 4 | container="yaggo" \ 5 | about.summary="generate command line parser using getopt_long" \ 6 | about.home="https://github.com/gmarcais/yaggo" \ 7 | software.version="1.5.9-1-deb" \ 8 | version="1" \ 9 | about.copyright="2012-2014 Guillaume Marais " \ 10 | about.license="GPL-3+" \ 11 | about.license_file="/usr/share/doc/yaggo/copyright" \ 12 | extra.binaries="/usr/bin/yaggo" \ 13 | about.tags="" 14 | 15 | ENV DEBIAN_FRONTEND noninteractive 16 | RUN apt-get update && apt-get install -y yaggo && apt-get clean && apt-get purge && rm -rf /var/lib/apt/lists/* /tmp/* 17 | USER biodocker 18 | -------------------------------------------------------------------------------- /zalign/0.9.1-2b3-deb/Dockerfile: -------------------------------------------------------------------------------- 1 | FROM biocontainers/biocontainers:debian-stretch-backports 2 | MAINTAINER biocontainers 3 | LABEL software="zalign" \ 4 | container="zalign" \ 5 | about.summary="parallel local alignment of biological sequences" \ 6 | about.home="https://launchpad.net/zalign" \ 7 | software.version="0.9.1-2b3-deb" \ 8 | version="1" \ 9 | about.license_file="/usr/share/doc/zalign/copyright" \ 10 | extra.binaries="/usr/bin/mpialign,/usr/bin/zalign" \ 11 | about.tags="" 12 | 13 | ENV DEBIAN_FRONTEND noninteractive 14 | RUN apt-get update && apt-get install -y zalign && apt-get clean && apt-get purge && rm -rf /var/lib/apt/lists/* /tmp/* 15 | USER biodocker 16 | -------------------------------------------------------------------------------- /zstd/1.1.2-1-deb/Dockerfile: -------------------------------------------------------------------------------- 1 | FROM biocontainers/biocontainers:debian-stretch-backports 2 | MAINTAINER biocontainers 3 | LABEL software="zstd" \ 4 | container="zstd" \ 5 | about.summary="fast lossless compression algorithm -- CLI tool" \ 6 | about.home="https://github.com/facebook/zstd" \ 7 | software.version="1.1.2-1-deb" \ 8 | version="1" \ 9 | about.license_file="/usr/share/doc/zstd/copyright" \ 10 | extra.binaries="/usr/bin/pzstd,/usr/bin/unzstd,/usr/bin/zstd,/usr/bin/zstdcat,/usr/bin/zstdgrep,/usr/bin/zstdless,/usr/bin/zstdmt" \ 11 | about.tags="" 12 | 13 | ENV DEBIAN_FRONTEND noninteractive 14 | RUN apt-get update && apt-get install -y zstd && apt-get clean && apt-get purge && rm -rf /var/lib/apt/lists/* /tmp/* 15 | USER biodocker 16 | --------------------------------------------------------------------------------