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docker-builds

This repository contains the Dockerfiles and other assorted files necessary for building Docker images for a variety of programs used by members of the StaPH-B (State Public Health Lab Bioinformatics) consortium. The purpose of this repository is to provide a centralized location for Docker images that is easily accessible for users, with clear documentation on how the containers were built and how to use them.

If you would like to contribute with a Docker image or improve upon the existing images, please fork the repository, make your changes/additions, and submit a pull request. If you are having an issue with an existing image, please submit an issue. We welcome any and all feedback!
See more details on how to contribute here

Docker User Guide

We have also created a user guide that outlines methods and best practices for using and developing docker containers.
Docker User Guide

What about Singularity?

For many people Docker is not an option, but Singularity is. Most Docker containers are compatible with Singularity and can easily be converted to Singularity format. Please see the User Guide linked above to for instructions on how to download docker images from dockerhub and how to run them using Singularity. We've worked hard to ensure that our containers are compatibile with Singularity, but if you find one that isn't, please leave an issue and let us know!

Available Docker images

Build Status (Build only reflects those containers that have been added to the TravisCI tests)

Software Version Link
ABRicate
docker pulls		 0.8.7, 0.8.13, 0.8.13s (+serotypefinder db), 0.9.8, 1.0.0 https://github.com/tseemann/abricate
ARIBA
docker pulls		 2.14.4 https://github.com/sanger-pathogens/ariba
Augur
docker pulls		 6.3.0, 7.0.2, 8.0.0, 9.0.0 https://github.com/nextstrain/augur
Auspice
docker pulls		 2.12.0 https://github.com/nextstrain/auspice
BBTools
docker pulls		 38.76, 38.86 https://jgi.doe.gov/data-and-tools/bbtools/
bcftools
docker pulls		 1.10.2, 1.11 https://github.com/samtools/bcftools
bedtools
docker pulls		 2.29.2 https://bedtools.readthedocs.io/en/latest/
BWA
docker pulls		 0.7.17 https://github.com/lh3/bwa
Canu
docker pulls		 2.0 https://canu.readthedocs.io/en/latest/
https://github.com/marbl/canu
Canu-Racon
docker pulls		 2.0 (Canu) 1.4.3 (Racon) 2.17 (minimap2);
1.9 (Canu) 1.4.3 (Racon) 2.17 (minimap2);
1.9i (Canu) 1.4.3 (Racon) 2.17 (minimap2) (+racon_preprocess.py);
1.7.1 (Canu) 1.3.1 (Racon) 2.13 (minimap2)		 https://canu.readthedocs.io/en/latest/
https://github.com/lbcb-sci/racon
https://github.com/isovic/racon (ARCHIVED)
https://lh3.github.io/minimap2/
centroid
docker pulls		 1.0.0 https://github.com/stjacqrm/centroid
CDC-SPN
docker pulls		 0.1 (no version) https://github.com/BenJamesMetcalf/Spn_Scripts_Reference
cfsan-snp-pipeline
docker pulls		 2.0.2 https://github.com/CFSAN-Biostatistics/snp-pipeline
Circlator
docker pulls		 1.5.6 https://github.com/sanger-pathogens/circlator
Clustalo
docker pulls		 1.2.4 http://www.clustal.org/omega/
cutshaw-report-env
docker pulls		 1.0.0 https://github.com/VADGS/CutShaw
emm-typing-tool
docker pulls		 0.0.1 (no version) https://github.com/phe-bioinformatics/emm-typing-tool
FastANI
docker pulls		 1.1 https://github.com/ParBLiSS/FastANI
FastTree
docker pulls		 2.1.11 http://www.microbesonline.org/fasttree/
FastQC
docker pulls		 0.11.8 https://www.bioinformatics.babraham.ac.uk/projects/fastqc/
https://github.com/s-andrews/FastQC
Filtlong
docker pulls		 0.2.0 https://github.com/rrwick/filtlong
Flye
docker pulls		 2.5, 2.7, 2.8 https://github.com/fenderglass/Flye
iqtree
docker pulls		 1.6.7 http://www.iqtree.org/
iVar
docker pulls		 1.1, 1.1 (+ SARS-CoV2 reference),
1.2.1, 1.2.1 (+ SC2 ref),
1.2.2 (+SC2 ref and artic bedfiles)		 https://github.com/andersen-lab/ivar
kma
docker pulls		 1.2.21 https://bitbucket.org/genomicepidemiology/kma/
Kraken
docker pulls		 1.0, 1.1.1, 1.1.1 (no database) https://github.com/DerrickWood/kraken
Kraken2
docker pulls		 2.0.8-beta (no database),
2.0.8-beta (MiniKraken2_v1_8GB db),
2.0.8-beta_hv (human + virus db),
2.0.9-beta (no db),
2.0.9-beta (Minikraken v2 RefSeq: bacteria, archaea, viral, and human 8GB db)		 https://github.com/DerrickWood/kraken2
kSNP3
docker pulls		 3.1 https://sourceforge.net/projects/ksnp/
legsta
docker pulls		 0.3.7, 0.5.1 https://github.com/tseemann/legsta
Lyve-SET (includes CG-Pipeline scripts and raxml)
docker pulls		 1.1.4f, 2.0.1 (lyve-SET) https://github.com/lskatz/lyve-SET https://github.com/lskatz/CG-Pipeline
MAFFT
docker pulls		 7.450 https://mafft.cbrc.jp/alignment/software/
Mash
docker pulls		 2.1, 2.2 https://github.com/marbl/Mash
mashtree
docker pulls		 0.52.0, 0.57.0, 1.0.4, 1.2.0 https://github.com/lskatz/mashtree
medaka
docker pulls		 0.8.1, 1.0.1 https://github.com/nanoporetech/medaka
minimap2
docker pulls		 2.17 https://github.com/lh3/minimap2
mlst
docker pulls		 2.16.2, 2.17.6, 2.19.0 https://github.com/tseemann/mlst
Mugsy
docker pulls		 1r2.3 http://mugsy.sourceforge.net/
MultiQC
docker pulls		 1.7, 1.8 https://github.com/ewels/MultiQC
NanoPlot
docker pulls		 1.27.0, 1.29.0, 1.30.1, 1.32.0, 1.33.0 https://github.com/wdecoster/NanoPlot
NCBI AMRFinderPlus
docker pulls		 3.1.1b, 3.8.4 https://github.com/ncbi/amr
OrthoFinder
docker pulls		 2.17 https://github.com/davidemms/OrthoFinder
Pangolin
docker pulls		 1.1.14, 2.0.4, 2.0.5 https://github.com/hCoV-2019/pangolin
Pilon
docker pulls		 1.23.0 https://github.com/broadinstitute/pilon
PlasmidSeeker
docker pulls		 1.0 https://github.com/bioinfo-ut/PlasmidSeeker
Prokka
docker pulls		 1.13.4, 1.14.0, 1.14.5 https://github.com/tseemann/prokka
QUAST
docker pulls		 5.0.0, 5.0.2 https://github.com/ablab/quast
racon
docker pulls		 1.4.3 https://github.com/lbcb-sci/racon
https://github.com/isovic/racon (ARCHIVED)
rasusa
docker pulls		 0.1.0, 0.2.0, 0.3.0 https://github.com/mbhall88/rasusa
RAxML
docker pulls		 8.2.12 (RAxML)
0.9.0 (RAxML Next Generation)		 https://github.com/stamatak/standard-RAxML
https://github.com/amkozlov/raxml-ng
Roary
docker pulls		 3.12.0 https://github.com/sanger-pathogens/Roary
SalmID
docker pulls		 0.1.23 https://github.com/hcdenbakker/SalmID
Samtools
docker pulls		 1.9, 1.10, 1.11 https://github.com/samtools/samtools
SeqSero
docker pulls		 1.0.1 https://github.com/denglab/SeqSero
SeqSero2
docker pulls		 0.1.0, 1.0.0, 1.0.2, 1.1.0, 1.1.1 https://github.com/denglab/SeqSero2/
seqtk
docker pulls		 1.3 https://github.com/lh3/seqtk
seqyclean
docker pulls		 1.10.09 https://github.com/ibest/seqyclean
Seroba
docker pulls		 1.0.0 https://github.com/sanger-pathogens/seroba
SerotypeFinder
docker pulls		 1.1 (I think? Bitbucket repo does not list older versions like the one in this docker image) https://bitbucket.org/genomicepidemiology/serotypefinder/
Shovill
docker pulls		 1.0.4, 1.1.0 https://github.com/tseemann/shovill
SISTR
docker pulls		 1.0.2 https://github.com/peterk87/sistr_cmd
SKESA
docker pulls		 2.3.0, 2.4.0 (gfa_connector & kmercounter included) https://github.com/ncbi/SKESA
Snippy
docker pulls		 4.4.5, 4.5.1, 4.6.0 https://github.com/tseemann/snippy
snp-dists
docker pulls		 0.6.2 https://github.com/tseemann/snp-dists
SNP-sites
docker pulls		 2.3.3 https://github.com/sanger-pathogens/snp-sites
SPAdes
docker pulls		 3.8.2, 3.12.0, 3.13.0, 3.14.0, 3.14.1 http://cab.spbu.ru/software/spades/
SRA-toolkit
docker pulls		 2.9.2 https://github.com/ncbi/sra-tools
Staramr
docker pulls		 0.5.1, 0.7.1 https://github.com/phac-nml/staramr
TipToft
docker pulls		 1.0.0, 1.0.2 https://github.com/andrewjpage/tiptoft
Trimmomatic
docker pulls		 0.38, 0.39 http://www.usadellab.org/cms/?page=trimmomatic
Trycycler
docker pulls		 0.3.1, 0.3.2, 0.3.3 https://github.com/rrwick/Trycycler
Unicycler
docker pulls		 0.4.7, 0.4.8 https://github.com/rrwick/Unicycler
VADR
docker pulls		 1.1 https://github.com/nawrockie/vadr
VIBRANT
docker pulls		 1.2.1 https://github.com/AnantharamanLab/VIBRANT
VIGOR4
docker pulls		 4.1.20190131 https://github.com/JCVenterInstitute/VIGOR4
wtdbg2
docker pulls		 2.5 https://github.com/ruanjue/wtdbg2

You can also view the list of images on Docker hub here: https://hub.docker.com/r/staphb/

License

  • GNU GPLv3 license was added 2020-01-16
  • We keep a list of the licenses for the main software within the docker images here: Program_Licenses.md
  • Links to licenses for each program should also be listed as a metadata LABEL within each dockerfile

Authors/Maintainers

Each Dockerfile lists the author(s)/maintainer(s) as a metadata LABEL, but the authors/maintainers of the docker images are:

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