Tool: list of dockerized bioinformatics apps
This is a forum post to list bioinformatics applications that have been installed into a docker container and are ready for download on a registry URL.
- spades https://registry.hub.docker.com/search?q=spades
- tophat-bowtie2-samtools https://registry.hub.docker.com/u/quagbrain/tophat-bowtie2-samtools/ -
- velvet https://registry.hub.docker.com/search?q=velvet
- bwa https://registry.hub.docker.com/search?q=bwa
- https://registry.hub.docker.com/search?q=soapdenovo - soapdenovo
- https://registry.hub.docker.com/search?q=bedtools&searchfield= - bedtools
- https://registry.hub.docker.com/search?q=cnanorm&searchfield= - cnanorm
- annovar - https://registry.hub.docker.com/u/compbio/ngseasy-annovar/
- gsnap - https://registry.hub.docker.com/u/compbio/ngseasy-gsnap/
- lumpy - https://registry.hub.docker.com/u/compbio/ngseasy-lumpy/
- delly - https://registry.hub.docker.com/u/compbio/ngseasy-delly/
- https://registry.hub.docker.com/u/compbio/ngseasy-freebayes/ - freebayes
- platypus - https://registry.hub.docker.com/u/compbio/ngseasy-platypus/
- novoalign - https://registry.hub.docker.com/u/compbio/ngseasy-novoalign/
- stampy - https://registry.hub.docker.com/u/compbio/ngseasy-stampy/
- vcftools - https://registry.hub.docker.com/u/compbio/ngseasy-vcftools/
- bedtools - https://registry.hub.docker.com/u/compbio/ngseasy-bedtools
- seqtk - https://registry.hub.docker.com/u/compbio/ngseasy-seqtk
- samtools - https://registry.hub.docker.com/u/compbio/ngseasy-samtools
- trimmomatic - https://registry.hub.docker.com/u/compbio/ngseasy-trimmomatic
- picardtools - https://registry.hub.docker.com/u/compbio/ngseasy-picardtools
- ensembl API - https://registry.hub.docker.com/u/gawbul/docker-ensembl
- galaxy - https://github.com/bgruening/docker-galaxy-stable
- sambamba - https://registry.hub.docker.com/u/sbgoliver/sambamba/
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3 answers
If it's in Bioconda, it's in a docker image via the Biocontainers project https://quay.io/organization/biocontainers and https://biocontainers.pro/#/
Also a set of curated, microbially-focused bioinfo tools (I'm a contributor to this project): https://github.com/StaPH-B/docker-builds and dockerhub https://hub.docker.com/u/staphb
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http://dirk.eddelbuettel.com/blog/2014/10/23/#introducing_rocker
WUSTL Genome MuSic https://hub.docker.com/r/zayed/genomemusic/