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https://github.com/dceoy/docker-bio

Dockerfile repository for Bioinformatics
https://github.com/dceoy/docker-bio
Last synced: 10 days ago
JSON representation
Dockerfile repository for Bioinformatics
Host: GitHub
URL: https://github.com/dceoy/docker-bio
Owner: dceoy
License: mit
Created: 2017-04-20T15:31:52.000Z (over 7 years ago)
Default Branch: master
Last Pushed: 2023-12-21T13:38:58.000Z (11 months ago)
Last Synced: 2024-08-01T12:15:57.581Z (3 months ago)
Language: Dockerfile
Homepage:
Size: 215 KB
Stars: 33
Watchers: 5
Forks: 13
Open Issues: 1
Metadata Files:
- Readme: README.md
- Funding: .github/FUNDING.yml
- License: LICENSE
Awesome Lists containing this project

README

        docker-bio

==========

Dockerfile repository for Bioinformatics

[![CI to Docker Hub](https://github.com/dceoy/docker-bio/actions/workflows/docker-publish.yml/badge.svg)](https://github.com/dceoy/docker-bio/actions/workflows/docker-publish.yml)

Docker images

-------------

- Images on Docker Hub:

  - [abra2](https://hub.docker.com/r/dceoy/abra2/)

  - ~alfred~

  - [ascat](https://hub.docker.com/r/dceoy/ascat/)

  - [bamsnap](https://hub.docker.com/r/dceoy/bamsnap/)

  - [bcftools](https://hub.docker.com/r/dceoy/bcftools/)

  - [bedops](https://hub.docker.com/r/dceoy/bedops/)

  - [bedtools](https://hub.docker.com/r/dceoy/bedtools/)

  - [bioconda](https://hub.docker.com/r/dceoy/bioconda/)

  - [bowtie2](https://hub.docker.com/r/dceoy/bowtie2/)

  - [bwa](https://hub.docker.com/r/dceoy/bwa/)

  - [bwa-mem2](https://hub.docker.com/r/dceoy/bwa-mem2/)

  - [cufflinks](https://hub.docker.com/r/dceoy/cufflinks/)

  - [cnvkit](https://hub.docker.com/r/dceoy/cnvkit/)

  - [cnvnator](https://hub.docker.com/r/dceoy/cnvnator/)

  - [cutadapt](https://hub.docker.com/r/dceoy/cutadapt/)

  - [delly](https://hub.docker.com/r/dceoy/delly/)

  - [dicey](https://hub.docker.com/r/dceoy/dicey/)

  - [elprep](https://hub.docker.com/r/dceoy/elprep/)

  - [fastp](https://hub.docker.com/r/dceoy/fastp/)

  - [fastq-dump](https://hub.docker.com/r/dceoy/fastq-dump/)

  - [fastqc](https://hub.docker.com/r/dceoy/fastqc/)

  - [fgbio](https://hub.docker.com/r/dceoy/fgbio/)

  - ~freec~

  - [gatk](https://hub.docker.com/r/dceoy/gatk/)

  - [gencore](https://hub.docker.com/r/dceoy/gencore/)

  - [gffread](https://hub.docker.com/r/dceoy/gffread/)

  - [gridss](https://hub.docker.com/r/dceoy/gridss/)

  - [goleft](https://hub.docker.com/r/dceoy/goleft/)

  - [hisat2](https://hub.docker.com/r/dceoy/hisat2/)

  - ~igv~

  - [igv-webapp](https://hub.docker.com/r/dceoy/igv-webapp/)

  - [jbrowse](https://hub.docker.com/r/dceoy/jbrowse/)

  - [kallisto](https://hub.docker.com/r/dceoy/kallisto/)

  - ~last~

  - ~lumpy~

  - [macs2](https://hub.docker.com/r/dceoy/macs2/)

  - [manta](https://hub.docker.com/r/dceoy/manta/)

  - [miso](https://hub.docker.com/r/dceoy/miso/)

  - [msisensor](https://hub.docker.com/r/dceoy/msisensor/)

  - [msisensor-pro](https://hub.docker.com/r/dceoy/msisensor-pro/)

  - [multiqc](https://hub.docker.com/r/dceoy/multiqc/)

  - [nirvana](https://hub.docker.com/r/dceoy/nirvana/)

  - ~oncotator~

  - [picard](https://hub.docker.com/r/dceoy/picard/)

  - ~pindel~

  - [prinseq](https://hub.docker.com/r/dceoy/prinseq/)

  - [rsem](https://hub.docker.com/r/dceoy/rsem/)

  - ~sambamba~

  - [samplot](https://hub.docker.com/r/dceoy/samplot/)

  - [samtools](https://hub.docker.com/r/dceoy/samtools/)

  - [seqkit](https://hub.docker.com/r/dceoy/seqkit/)

  - ~sequenza~

  - [sigprofiler](https://hub.docker.com/r/dceoy/sigprofiler/)

  - ~smoove~

  - [snpeff](https://hub.docker.com/r/dceoy/snpeff/)

  - [star](https://hub.docker.com/r/dceoy/star/)

  - [strelka](https://hub.docker.com/r/dceoy/strelka/)

  - [svtools](https://hub.docker.com/r/dceoy/svtools/)

  - [trim_galore](https://hub.docker.com/r/dceoy/trim_galore/)

  - [trimmomatic](https://hub.docker.com/r/dceoy/trimmomatic/)

  - [varscan](https://hub.docker.com/r/dceoy/varscan/)

  - [vep](https://hub.docker.com/r/dceoy/vep/)

- Images requiring a user build:

  - annovar

  - bcl2fastq

- Images outside this repository:

  - [deepvariant](https://console.cloud.google.com/gcr/images/deepvariant-docker/GLOBAL/deepvariant)

  - [deepvariant_gpu](https://console.cloud.google.com/gcr/images/deepvariant-docker/GLOBAL/deepvariant_gpu)

Docker Compose

--------------

- Pull an image

  ```sh

  $ docker-compose pull 

  ```

- Build an image

  ```sh

  $ docker-compose build 

  ```

Dependencies

------------

Some images use the following tools:

- print-github-tags

  - Tiny command to fetch repository tags or releases from GitHub

  - [GitHub - dceoy/print-github-tags](https://github.com/dceoy/print-github-tags)

- clir

  - R package manager for command line interface

  - [GitHub - dceoy/clir](https://github.com/dceoy/clir)

  - [DockerHub - dceoy/clir](https://hub.docker.com/r/dceoy/clir)

References

----------

- abra2

  - [GitHub - mozack/abra2](https://github.com/mozack/abra2)

- alfred

  - [GitHub - tobiasrausch/alfred](https://github.com/tobiasrausch/alfred)

  - [www.gear-genomics.com - Alfred](https://www.gear-genomics.com/docs/alfred/)

- annovar

  - [annovar.openbioinformatics.org - ANNOVAR](http://annovar.openbioinformatics.org/)

- ascat

  - [GitHub - Crick-CancerGenomics/ascat](https://github.com/Crick-CancerGenomics/ascat)

  - [The Francis Crick Institute - Allele-Specific Copy number Analysis of Tumours (ASCAT)](https://www.crick.ac.uk/research/labs/peter-van-loo/software)

- bamsnap

  - [bamsnap.readthedocs.io - BamSnap](https://bamsnap.readthedocs.io/en/latest/)

  - [GitHub - parklab/bamsnap](https://github.com/parklab/bamsnap)

- bcftools

  - [samtools.github.io - Bcftools](https://samtools.github.io/bcftools/)

  - [GitHub - samtools/bcftools](https://github.com/samtools/bcftools)

- bcl2fastq

  - [Illumina - bcl2fastq Conversion Software](https://support.illumina.com/sequencing/sequencing_software/bcl2fastq-conversion-software.html)

- bedops

  - [bedops.readthedocs.io - BEDOPS](https://bedops.readthedocs.io/)

  - [GitHub - bedops/bedops](https://github.com/bedops/bedops)

- bedtools

  - [bedtools.readthedocs.io - bedtools2](http://bedtools.readthedocs.io/en/latest/index.html)

  - [GitHub - arq5x/bedtools2](https://github.com/arq5x/bedtools2)

- bioconda

  - [bioconda.github.io - Bioconda](https://bioconda.github.io/)

- bowtie2

  - [bowtie-bio.sourceforge.net - Bowtie 2](http://bowtie-bio.sourceforge.net/bowtie2/index.shtml)

  - [GitHub - BenLangmead/bowtie2](https://github.com/BenLangmead/bowtie2)

- bwa

  - [bio-bwa.sourceforge.net - Burrows-Wheeler Aligner](http://bio-bwa.sourceforge.net/)

  - [GitHub - lh3/bwa](https://github.com/lh3/bwa)

- bwa-mem2

  - [GitHub - bwa-mem2/bwa-mem2](https://github.com/bwa-mem2/bwa-mem2)

- canvas

  - [GitHub - Illumina/canvas](https://github.com/Illumina/canvas)

- cn.mops

  - [Bioconductor - cn.mops](https://bioconductor.org/packages/release/bioc/html/cn.mops.html)

- cnvkit

  - [cnvkit.readthedocs.io - CNVkit](https://cnvkit.readthedocs.io/)

  - [GitHub - etal/cnvkit](https://github.com/etal/cnvkit)

- cufflinks

  - [Trapnell Lab - Cufflinks](http://cole-trapnell-lab.github.io/cufflinks/)

  - [GitHub - cole-trapnell-lab/cufflinks](https://github.com/cole-trapnell-lab/cufflinks)

- cutadapt

  - [cutadapt.readthedocs.io - Cutadapt](http://cutadapt.readthedocs.io/)

  - [GitHub - marcelm/cutadapt](https://github.com/marcelm/cutadapt)

- deepvariant

  - [GitHub -google/deepvariant](https://github.com/google/deepvariant)

  - [Google Cloud Platform - DeepVariant](https://cloud.google.com/genomics/deepvariant)

- delly

  - [GitHub - dellytools/delly](https://github.com/dellytools/delly)

- dicey

  - [GitHub - gear-genomics/dicey](https://github.com/gear-genomics/dicey)

- elprep

  - [GitHub - ExaScience/elprep](https://github.com/ExaScience/elprep)

- fastp

  - [GitHub - OpenGene/fastp](https://github.com/OpenGene/fastp#per-read-cutting-by-quality-score)

- fastq-dump

  - [NCBI - SRA Toolkit](https://www.ncbi.nlm.nih.gov/books/NBK158900/)

- fastqc

  - [Babraham Bioinformatics - FastQC](http://www.bioinformatics.babraham.ac.uk/projects/fastqc/)

- fgbio

  - [GitHub - fulcrumgenomics/fgbio](https://github.com/fulcrumgenomics/fgbio)

  - [fulcrumgenomics.github.io - fgbio](http://fulcrumgenomics.github.io/fgbio/)

- freec

  - [boevalab.inf.ethz.ch - Control-FREEC](http://boevalab.inf.ethz.ch/FREEC/index.html)

  - [GitHub - BoevaLab/FREEC](https://github.com/BoevaLab/FREEC)

- gatk

  - [Broad Institute - Genome Analysis Toolkit](https://software.broadinstitute.org/gatk/)

  - [GitHub - broadinstitute/gatk](https://github.com/broadinstitute/gatk)

- gencore

  - [GitHub - OpenGene/gencore](https://github.com/OpenGene/gencore)

- gffread

  - [GitHub - gpertea/gffread](https://github.com/gpertea/gffread)

- gridss

  - [GitHub - PapenfussLab/gridss](https://github.com/PapenfussLab/gridss)

- goleft

  - [GitHub - brentp/goleft](https://github.com/brentp/goleft)

- hisat2

  - [Johns Hopkins University - HISAT2](http://ccb.jhu.edu/software/hisat2/)

  - [GitHub - infphilo/hisat2](https://github.com/infphilo/hisat2)

- igv:

  - [Broad Institute - Integrative Genomics Viewer](https://igv.org/)

  - [GitHub - igvteam/igv](https://github.com/igvteam/igv)

- igv-webapp:

  - [Broad Institute - Integrative Genomics Viewer](https://igv.org/)

  - [GitHub - igvteam/igv-webapp](https://github.com/igvteam/igv-webapp)

- jbrowse

  - [jbrowse.org - The JBrowse Genome Browser](http://jbrowse.org/)

  - [GitHub - GMOD/jbrowse](https://github.com/GMOD/jbrowse)

- kallisto

  - [pachterlab.github.io - kallisto](https://pachterlab.github.io/kallisto/)

  - [GitHub - pachterlab/kallisto](https://github.com/pachterlab/kallisto)

- last

  - [last.cbrc.jp - LAST](http://last.cbrc.jp/)

- lumpy

  - [GitHub - arq5x/lumpy-sv](https://github.com/arq5x/lumpy-sv)

- macs2

  - [X. Shirley Liu Lab - MACS](http://liulab.dfci.harvard.edu/MACS/)

  - [GitHub - taoliu/MACS](https://github.com/taoliu/MACS)

- manta

  - [GitHub - Illumina/manta](https://github.com/Illumina/manta)

- miso

  - [miso.readthedocs.io - MISO](https://miso.readthedocs.io/en/fastmiso/)

  - [hollywood.mit.edu - MISO](http://hollywood.mit.edu/burgelab/miso/index.html)

  - [GitHub - yarden/MISO](https://github.com/yarden/MISO)

- msisensor

  - [GitHub - ding-lab/msisensor](https://github.com/ding-lab/msisensor)

- msisensor-pro

  - [GitHub - xjtu-omics/msisensor-pro](https://github.com/xjtu-omics/msisensor-pro)

- multiqc

  - [GitHub - ewels/MultiQC](https://github.com/ewels/MultiQC)

- nirvana

  - [GitHub - Illumina/Nirvana](https://github.com/Illumina/Nirvana)

- oncotator

  - [Broad Institute - Oncotator](http://portals.broadinstitute.org/oncotator/)

  - [GitHub - broadinstitute/oncotator](https://github.com/broadinstitute/oncotator)

- picard

  - [broadinstitute.github.io - Picard](https://broadinstitute.github.io/picard/)

  - [GitHub - broadinstitute/picard](https://github.com/broadinstitute/picard)

- pindel

  - [GitHub - genome/pindel](https://github.com/genome/pindel)

- prinseq

  - [prinseq.sourceforge.net - PRINSEQ](http://prinseq.sourceforge.net/)

- rsem

  - [deweylab.github.io - RSEM (RNA-Seq by Expectation-Maximization)](https://deweylab.github.io/RSEM/)

  - [GitHub - deweylab/RSEM](https://github.com/deweylab/RSEM)

- sambamba

  - [GitHub - biod/sambamba](https://github.com/biod/sambamba)

  - [lomereiter.github.io - Sambamba](https://lomereiter.github.io/sambamba/)

- samplot

  - [GitHub - ryanlayer/samplot](https://github.com/ryanlayer/samplot)

- samtools

  - [samtools.sourceforge.net - SAMtools](http://samtools.sourceforge.net/)

  - [GitHub - samtools/samtools](https://github.com/samtools/samtools)

- seqkit

  - [bioinf.shenwei.me - SeqKit](https://bioinf.shenwei.me/seqkit/)

  - [GitHub - shenwei356/seqkit](https://github.com/shenwei356/seqkit/)

- sequenza

  - [CRAN - sequenza](https://cran.r-project.org/web/packages/sequenza/)

  - [sequenzatools.bitbucket.io - Sequenza](https://sequenzatools.bitbucket.io/)

  - [Bitbucket - Sequenza](https://bitbucket.org/sequenzatools/sequenza/)

  - [Bitbucket - Sequenza-utils](https://bitbucket.org/sequenzatools/sequenza-utils/)

  - [sequenza-utils.readthedocs.io - Sequenza-utils](https://sequenza-utils.readthedocs.io/)

- sigprofiler

  - [COSMIC Mutational Signatures - SigProfiler Tools](https://cancer.sanger.ac.uk/cosmic/signatures/sigprofiler.tt)

  - [GitHub - AlexandrovLab/SigProfilerMatrixGenerator](https://github.com/AlexandrovLab/SigProfilerMatrixGenerator)

  - [GitHub - AlexandrovLab/SigProfilerPlotting](https://github.com/AlexandrovLab/SigProfilerPlotting)

  - [GitHub - AlexandrovLab/SigProfilerExtractor](https://github.com/AlexandrovLab/SigProfilerExtractor)

  - [GitHub - AlexandrovLab/SigProfilerSimulator](https://github.com/AlexandrovLab/SigProfilerSimulator)

- smoove

  - [GitHub - brentp/smoove](https://github.com/brentp/smoove)

- snpeff

  - [snpeff.sourceforge.net - SnpEff](http://snpeff.sourceforge.net/index.html)

- star

  - [GitHub - alexdobin/STAR](https://github.com/alexdobin/STAR)

- strelka

  - [GitHub - Illumina/strelka](https://github.com/Illumina/strelka)

- svtools

  - [GitHub - hall-lab/svtools](https://github.com/hall-lab/svtools)

- trim_galore

  - [GitHub - FelixKrueger/TrimGalore](https://github.com/FelixKrueger/TrimGalore)

  - [Babraham Bioinformatics - Trim Galore](https://www.bioinformatics.babraham.ac.uk/projects/trim_galore/)

- trimmomatic

  - [usadellab.org - Trimmomatic](http://www.usadellab.org/cms/?page=trimmomatic)

  - [GitHub - timflutre/trimmomatic](https://github.com/timflutre/trimmomatic)

- varscan

  - [massgenomics.org - VarScan](http://massgenomics.org/varscan)

  - [dkoboldt.github.io - VarScan](http://dkoboldt.github.io/varscan/)

  - [GitHub - dkoboldt/varscan](https://github.com/dkoboldt/varscan)

- vep

  - [www.ensembl.org - Ensembl Variant Effect Predictor (VEP)](https://www.ensembl.org/vep)

  - [GitHub - Ensembl/ensembl-vep](https://github.com/Ensembl/ensembl-vep)