docker-bio

Dockerfile repository for Bioinformatics

Docker images

• Images on Docker Hub:
  • abra2
  • alfred
  • ascat
  • bamsnap
  • bcftools
  • bedops
  • bedtools
  • bioconda
  • bowtie2
  • bwa
  • bwa-mem2
  • cufflinks
  • cnvkit
  • cnvnator
  • cutadapt
  • delly
  • dicey
  • elprep
  • fastp
  • fastq-dump
  • fastqc
  • fgbio
  • freec
  • gatk
  • gencore
  • gffread
  • gridss
  • goleft
  • hisat2
  • igv
  • igv-webapp
  • jbrowse
  • kallisto
  • last
  • lumpy
  • macs2
  • manta
  • miso
  • msisensor
  • msisensor-pro
  • multiqc
  • nirvana
  • oncotator
  • picard
  • pindel
  • prinseq
  • rsem
  • sambamba
  • samplot
  • samtools
  • seqkit
  • sequenza
  • sigprofiler
  • smoove
  • snpeff
  • star
  • strelka
  • svtools
  • trim_galore
  • trimmomatic
  • varscan
  • vep
• Images requiring a user build:
  • annovar
  • bcl2fastq
• Images outside this repository:
  • deepvariant
  • deepvariant_gpu

Docker Compose

• Pull an image

  $ docker-compose pull <name>

• Build an image

  $ docker-compose build <name>

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
• clir
  • R package manager for command line interface
  • GitHub - dceoy/clir
  • DockerHub - dceoy/clir

References

• abra2
  • GitHub - mozack/abra2
• alfred
  • GitHub - tobiasrausch/alfred
  • www.gear-genomics.com - Alfred
• annovar
  • annovar.openbioinformatics.org - ANNOVAR
• ascat
  • GitHub - Crick-CancerGenomics/ascat
  • The Francis Crick Institute - Allele-Specific Copy number Analysis of Tumours (ASCAT)
• bamsnap
  • bamsnap.readthedocs.io - BamSnap
  • GitHub - parklab/bamsnap
• bcftools
  • samtools.github.io - Bcftools
  • GitHub - samtools/bcftools
• bcl2fastq
  • Illumina - bcl2fastq Conversion Software
• bedops
  • bedops.readthedocs.io - BEDOPS
  • GitHub - bedops/bedops
• bedtools
  • bedtools.readthedocs.io - bedtools2
  • GitHub - arq5x/bedtools2
• bioconda
  • bioconda.github.io - Bioconda
• bowtie2
  • bowtie-bio.sourceforge.net - Bowtie 2
  • GitHub - BenLangmead/bowtie2
• bwa
  • bio-bwa.sourceforge.net - Burrows-Wheeler Aligner
  • GitHub - lh3/bwa
• bwa-mem2
  • GitHub - bwa-mem2/bwa-mem2
• canvas
  • GitHub - Illumina/canvas
• cn.mops
  • Bioconductor - cn.mops
• cnvkit
  • cnvkit.readthedocs.io - CNVkit
  • GitHub - etal/cnvkit
• cufflinks
  • Trapnell Lab - Cufflinks
  • GitHub - cole-trapnell-lab/cufflinks
• cutadapt
  • cutadapt.readthedocs.io - Cutadapt
  • GitHub - marcelm/cutadapt
• deepvariant
  • GitHub -google/deepvariant
  • Google Cloud Platform - DeepVariant
• delly
  • GitHub - dellytools/delly
• dicey
  • GitHub - gear-genomics/dicey
• elprep
  • GitHub - ExaScience/elprep
• fastp
  • GitHub - OpenGene/fastp
• fastq-dump
  • NCBI - SRA Toolkit
• fastqc
  • Babraham Bioinformatics - FastQC
• fgbio
  • GitHub - fulcrumgenomics/fgbio
  • fulcrumgenomics.github.io - fgbio
• freec
  • boevalab.inf.ethz.ch - Control-FREEC
  • GitHub - BoevaLab/FREEC
• gatk
  • Broad Institute - Genome Analysis Toolkit
  • GitHub - broadinstitute/gatk
• gencore
  • GitHub - OpenGene/gencore
• gffread
  • GitHub - gpertea/gffread
• gridss
  • GitHub - PapenfussLab/gridss
• goleft
  • GitHub - brentp/goleft
• hisat2
  • Johns Hopkins University - HISAT2
  • GitHub - infphilo/hisat2
• igv:
  • Broad Institute - Integrative Genomics Viewer
  • GitHub - igvteam/igv
• igv-webapp:
  • Broad Institute - Integrative Genomics Viewer
  • GitHub - igvteam/igv-webapp
• jbrowse
  • jbrowse.org - The JBrowse Genome Browser
  • GitHub - GMOD/jbrowse
• kallisto
  • pachterlab.github.io - kallisto
  • GitHub - pachterlab/kallisto
• last
  • last.cbrc.jp - LAST
• lumpy
  • GitHub - arq5x/lumpy-sv
• macs2
  • X. Shirley Liu Lab - MACS
  • GitHub - taoliu/MACS
• manta
  • GitHub - Illumina/manta
• miso
  • miso.readthedocs.io - MISO
  • hollywood.mit.edu - MISO
  • GitHub - yarden/MISO
• msisensor
  • GitHub - ding-lab/msisensor
• msisensor-pro
  • GitHub - xjtu-omics/msisensor-pro
• multiqc
  • GitHub - ewels/MultiQC
• nirvana
  • GitHub - Illumina/Nirvana
• oncotator
  • Broad Institute - Oncotator
  • GitHub - broadinstitute/oncotator
• picard
  • broadinstitute.github.io - Picard
  • GitHub - broadinstitute/picard
• pindel
  • GitHub - genome/pindel
• prinseq
  • prinseq.sourceforge.net - PRINSEQ
• rsem
  • deweylab.github.io - RSEM (RNA-Seq by Expectation-Maximization)
  • GitHub - deweylab/RSEM
• sambamba
  • GitHub - biod/sambamba
  • lomereiter.github.io - Sambamba
• samplot
  • GitHub - ryanlayer/samplot
• samtools
  • samtools.sourceforge.net - SAMtools
  • GitHub - samtools/samtools
• seqkit
  • bioinf.shenwei.me - SeqKit
  • GitHub - shenwei356/seqkit
• sequenza
  • CRAN - sequenza
  • sequenzatools.bitbucket.io - Sequenza
  • Bitbucket - Sequenza
  • Bitbucket - Sequenza-utils
  • sequenza-utils.readthedocs.io - Sequenza-utils
• sigprofiler
  • COSMIC Mutational Signatures - SigProfiler Tools
  • GitHub - AlexandrovLab/SigProfilerMatrixGenerator
  • GitHub - AlexandrovLab/SigProfilerPlotting
  • GitHub - AlexandrovLab/SigProfilerExtractor
  • GitHub - AlexandrovLab/SigProfilerSimulator
• smoove
  • GitHub - brentp/smoove
• snpeff
  • snpeff.sourceforge.net - SnpEff
• star
  • GitHub - alexdobin/STAR
• strelka
  • GitHub - Illumina/strelka
• svtools
  • GitHub - hall-lab/svtools
• trim_galore
  • GitHub - FelixKrueger/TrimGalore
  • Babraham Bioinformatics - Trim Galore
• trimmomatic
  • usadellab.org - Trimmomatic
  • GitHub - timflutre/trimmomatic
• varscan
  • massgenomics.org - VarScan
  • dkoboldt.github.io - VarScan
  • GitHub - dkoboldt/varscan
• vep
  • www.ensembl.org - Ensembl Variant Effect Predictor (VEP)
  • GitHub - Ensembl/ensembl-vep