Tool:list of dockerized bioinformatics apps

Question

[14134125465346445]

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/

[14134125465346445]

https://github.com/johnworth/docker-samtools-bowtie2-tophat

[zx8754]

http://dirk.eddelbuettel.com/blog/2014/10/23/#introducing_rocker

[Zee]

WUSTL Genome MuSic https://hub.docker.com/r/zayed/genomemusic/

Answer 1

[martenson]

• https://registry.hub.docker.com/u/bgruening/galaxy-deeptools/dockerfile/
• https://registry.hub.docker.com/u/bgruening/galaxy-chemicaltoolbox/dockerfile/

More info: https://biostar.usegalaxy.org/p/7375/

Answer 2

[kapsakcj]

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

Answer 3

[Andreas]

• LoFreq - https://registry.hub.docker.com/u/andreaswilm/lofreq/