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!

Docker image repositories & hosting

We host all of our docker images on two different repositories and periodically sync the images between the two:

1. Dockerhub - https://hub.docker.com/r/staphb/
2. Quay.io - https://quay.io/organization/staphb/

In November 2020, Docker began to implement pull rate limits for images hosted on dockerhub. This limits the number of docker pull's per time period (e.g. anonymous users allowed 100 pulls per six hours). We applied and were approved for Docker's "Open Source Program," which should have removed the pull rate limits for all staphb docker images! 🎉 🥳 If you encounter an error such as ERROR: toomanyrequests: Too Many Requests. or You have reached your pull rate limit. You may increase the limit by authenticating and upgrading: https://www.docker.com/increase-rate-limits. , please let us know by submitting an issue.

A huge thank you goes to the folks at Docker for supporting our efforts to distribute & share critical tools for public health bioinformatics. This has been especially important during the COVID-19 global pandemic, as many of these tools are used to conduct genomic surveillance on the SARS-CoV-2 virus as well as other important pathogens of public health concern.

To learn more about the docker pull rate limits and the open source software program, please see these blog posts (1, 2, and 3) and Docker documentation (1).

NOTE: In the table below, we do not provide individual links to the various tools on quay.io, please visit the above quay.io link to find all of our docker images.

Available Docker images

Software	Version	Link
ABRicate	0.8.7 0.8.13 0.8.13s (+serotypefinder db) 0.9.8 1.0.0	https://github.com/tseemann/abricate
any2fasta	0.4.2	https://github.com/tseemann/any2fasta
ARIBA	2.14.4	https://github.com/sanger-pathogens/ariba
artic-ncov2019	1.3.0	https://github.com/artic-network/fieldbioinformatics
artic-ncov2019-epi2me	0.3.10	https://github.com/epi2me-labs/wf-artic
artic-ncov2019-medaka	1.1.0	https://github.com/artic-network/artic-ncov2019
artic-ncov2019-nanopolish	1.1.0	https://github.com/artic-network/artic-ncov2019
Augur	6.3.0 7.0.2 8.0.0 9.0.0	https://github.com/nextstrain/augur
Auspice	2.12.0	https://github.com/nextstrain/auspice
BBTools	38.76 38.86 38.95	https://jgi.doe.gov/data-and-tools/bbtools/
bcftools	1.10.2 1.11 1.12 1.13 1.14	https://github.com/samtools/bcftools
bedtools	2.29.2 2.30.0	https://bedtools.readthedocs.io/en/latest/ https://github.com/arq5x/bedtools2
berrywood-report-env	1.0	none
bowtie2	2.4.4	http://bowtie-bio.sourceforge.net/bowtie2/manual.shtml https://github.com/BenLangmead/bowtie2
BWA	0.7.17	https://github.com/lh3/bwa
Canu	2.0 2.1.1 2.2	https://canu.readthedocs.io/en/latest/ https://github.com/marbl/canu
Canu-Racon	1.7.1 (Canu), 1.3.1 (Racon), 2.13 (minimap2) 1.9 (Canu), 1.4.3 (Racon), 2.17 (minimap2) 1.9i (Canu), 1.4.3 (Racon), 2.17 (minimap2), (+racon_preprocess.py) 2.0 (Canu), 1.4.3 (Racon), 2.17 (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	1.0.0	https://github.com/stjacqrm/centroid
CDC-SPN	0.1 (no version)	https://github.com/BenJamesMetcalf/Spn_Scripts_Reference
cfsan-snp-pipeline	2.0.2	https://github.com/CFSAN-Biostatistics/snp-pipeline
Circlator	1.5.6	https://github.com/sanger-pathogens/circlator
Clustalo	1.2.4	http://www.clustal.org/omega/
colorid	0.1.4.3	https://github.com/hcdenbakker/colorid
cutshaw-report-env	1.0.0	https://github.com/VADGS/CutShaw
datasets-sars-cov-2	0.4	https://github.com/CDCgov/datasets-sars-cov-2
emm-typing-tool	0.0.1 (no version)	https://github.com/phe-bioinformatics/emm-typing-tool
FastANI	1.1 1.32 1.33	https://github.com/ParBLiSS/FastANI
FastTree	2.1.11	http://www.microbesonline.org/fasttree/
FastQC	0.11.8 0.11.9	https://www.bioinformatics.babraham.ac.uk/projects/fastqc/ https://github.com/s-andrews/FastQC
fastq-scan	0.4.3 0.4.4	https://github.com/rpetit3/fastq-scan
Filtlong	0.2.0 0.2.1	https://github.com/rrwick/filtlong
Flye	2.5 2.7 2.8 2.9	https://github.com/fenderglass/Flye
Freyja	1.2 1.2.1	https://github.com/andersen-lab/Freyja
GAMBIT	0.3.0	https://github.com/hesslab-gambit/gambit
GAMMA	1.4	https://github.com/rastanton/GAMMA/
hmmer	3.3	http://hmmer.org/
iqtree	1.6.7	http://www.iqtree.org/
iqtree2	2.1.2	http://www.iqtree.org/
iVar	1.1 1.1 (+SARS-CoV2 reference) 1.2.1 1.2.1 (+SC2 ref) 1.2.2 (+SC2 ref and artic bedfiles) 1.3 1.3.1	https://github.com/andersen-lab/ivar
Kleborate	2.0.4 2.1.0	https://github.com/katholt/Kleborate/ https://github.com/katholt/Kaptive/
kma	1.2.21	https://bitbucket.org/genomicepidemiology/kma/
Kraken	1.0 1.0.0_wslh_signed 1.1.1 1.1.1 (no database)	https://github.com/DerrickWood/kraken
Kraken2	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) 2.1.0 (no db) 2.1.1 (no db) 2.1.2 (no db)	https://github.com/DerrickWood/kraken2
kSNP3	3.1	https://sourceforge.net/projects/ksnp/
legsta	0.3.7 0.5.1	https://github.com/tseemann/legsta
Lyve-SET (includes CG-Pipeline scripts and raxml)	1.1.4f 2.0.1	https://github.com/lskatz/lyve-SET https://github.com/lskatz/CG-Pipeline
MAFFT	7.450 7.475	https://mafft.cbrc.jp/alignment/software/
Mash	2.1 2.2 2.3	https://github.com/marbl/Mash
mashtree	0.52.0 0.57.0 1.0.4 1.2.0	https://github.com/lskatz/mashtree
medaka	0.8.1 1.0.1 1.2.0	https://github.com/nanoporetech/medaka
metaphlan	3.0.3-no-db (no database) 3.0.3 (~3GB db)	https://github.com/biobakery/MetaPhlAn/tree/3.0
minimap2	2.17 2.18 2.21 2.22 2.23 2.24	https://github.com/lh3/minimap2
minipolish	0.1.3	https://github.com/rrwick/Minipolish
mlst	2.16.2 2.17.6 2.19.0	https://github.com/tseemann/mlst
Mugsy	1r2.3	http://mugsy.sourceforge.net/
MultiQC	1.7 1.8	https://github.com/ewels/MultiQC
NanoPlot	1.27.0 1.29.0 1.30.1 1.32.0 1.33.0	https://github.com/wdecoster/NanoPlot
NCBI AMRFinderPlus	3.1.1b 3.8.4 3.8.28 3.9.3 3.9.8 3.10.1 3.10.5 3.10.16 3.10.20	https://github.com/ncbi/amr
OrthoFinder	2.17	https://github.com/davidemms/OrthoFinder
Pangolin	Pangolin version & pangoLEARN data release date 1.1.14 2.0.4 & 2020-07-20 2.0.5 & 2020-07-20 2.1.1 & 2020-12-17 2.1.3 & 2020-12-17 2.1.6 & 2021-01-06 2.1.7 & 2021-01-11 2.1.7 & 2021-01-20 2.1.8 & 2021-01-22 2.1.10 & 2021-02-01 2.1.11 & 2021-02-01 2.1.11 & 2021-02-05 2.2.1 & 2021-02-06 2.2.2 & 2021-02-06 2.2.2 & 2021-02-11 2.2.2 & 2021-02-12 2.3.0 & 2021-02-12 2.3.0 & 2021-02-18 2.3.0 & 2021-02-21 2.3.2 & 2021-02-21 2.3.3 & 2021-03-16 2.3.4 & 2021-03-16 2.3.5 & 2021-03-16 2.3.6 & 2021-03-16 2.3.6 & 2021-03-29 2.3.8 & 2021-04-01 2.3.8 & 2021-04-14 2.3.8 & 2021-04-21 2.3.8 & 2021-04-23 2.4 & 2021-04-28 2.4.1 & 2021-04-28 2.4.2 & 2021-04-28 2.4.2 & 2021-05-10 2.4.2 & 2021-05-11 2.4.2 & 2021-05-19 3.0.5 & 2021-06-05 3.1.3 & 2021-06-15 3.1.5 & 2021-06-15 3.1.5 & 2021-07-07-2 3.1.7 & 2021-07-09 3.1.8 & 2021-07-28 3.1.10 & 2021-07-28 3.1.11 & 2021-08-09 3.1.11 & 2021-08-24 3.1.11 & 2021-09-17 3.1.14 & 2021-09-28 3.1.14 & 2021-10-13 3.1.16 & 2021-10-18 3.1.16 & 2021-11-04 3.1.16 & 2021-11-09 3.1.16 & 2021-11-18 3.1.16 & 2021-11-25 3.1.17 & 2021-11-25 3.1.17 & 2021-12-06 3.1.17 & 2022-01-05 3.1.18 & 2022-01-20 3.1.19 & 2022-01-20	https://github.com/cov-lineages/pangolin https://github.com/cov-lineages/pangoLEARN https://github.com/cov-lineages/pango-designation https://github.com/cov-lineages/scorpio https://github.com/cov-lineages/constellations https://github.com/cov-lineages/lineages (archived) https://github.com/hCoV-2019/pangolin (archived)
parallel-perl	20200722	https://www.gnu.org/software/parallel
Piggy	1.5	https://github.com/harry-thorpe/piggy
Pilon	1.23.0	https://github.com/broadinstitute/pilon
PlasmidSeeker	1.0	https://github.com/bioinfo-ut/PlasmidSeeker
pmga	3.0.2	https://github.com/rpetit3/pmga
Prokka	1.13.4 1.14.0 1.14.5	https://github.com/tseemann/prokka
QUAST	5.0.0 5.0.2	https://github.com/ablab/quast
racon	1.4.3 1.4.20	https://github.com/lbcb-sci/racon https://github.com/isovic/racon (ARCHIVED)
rasusa	0.1.0 0.2.0 0.3.0 0.6.0	https://github.com/mbhall88/rasusa
raven	1.5.1	https://github.com/lbcb-sci/raven
RAxML	8.2.12 (RAxML) and 0.9.0 (RAxML Next Generation)	https://github.com/stamatak/standard-RAxML https://github.com/amkozlov/raxml-ng
Roary	3.12.0 3.13.0	https://github.com/sanger-pathogens/Roary
SalmID	0.1.23	https://github.com/hcdenbakker/SalmID
Samtools	1.9 1.10 1.11 1.12 1.13 1.14	https://github.com/samtools/samtools
SeqSero	1.0.1	https://github.com/denglab/SeqSero
SeqSero2	0.1.0 1.0.0 1.0.2 1.1.0 1.1.1 1.2.1	https://github.com/denglab/SeqSero2/
seqtk	1.3	https://github.com/lh3/seqtk
seqyclean	1.10.09	https://github.com/ibest/seqyclean
Seroba	1.0.0 1.0.2 1.0.2_wslh_signed	https://github.com/sanger-pathogens/seroba
SerotypeFinder	1.1 (perl version) 2.0.1 (python version)	https://bitbucket.org/genomicepidemiology/serotypefinder/
Shovill	1.0.4 1.1.0	https://github.com/tseemann/shovill
Shovill-se	1.1.0	https://github.com/rpetit3/shovill/tree/v1.1.0se
SISTR	1.0.2 1.1.1	https://github.com/phac-nml/sistr_cmd
SKESA	2.3.0 2.4.0 (gfa_connector & kmercounter included)	https://github.com/ncbi/SKESA
Snippy	4.4.5 4.5.1 4.6.0	https://github.com/tseemann/snippy
snp-dists	0.6.2 0.8.2	https://github.com/tseemann/snp-dists
SNP-sites	2.3.3 2.5.1	https://github.com/sanger-pathogens/snp-sites
SPAdes	3.8.2 3.12.0 3.13.0 3.14.0 3.14.1 3.15.0 3.15.1 3.15.2 3.15.3	https://github.com/ablab/spades http://cab.spbu.ru/software/spades/
SRA-toolkit	2.9.2	https://github.com/ncbi/sra-tools
Staramr	0.5.1 0.7.1	https://github.com/phac-nml/staramr
TipToft	1.0.0 1.0.2	https://github.com/andrewjpage/tiptoft
Treemmer	0.3	https://git.scicore.unibas.ch/TBRU/Treemmer (archived, moved to GitHub) https://github.com/fmenardo/Treemmer
Trimmomatic	0.38 0.39	http://www.usadellab.org/cms/?page=trimmomatic https://github.com/usadellab/Trimmomatic
Trycycler	0.3.1 0.3.2 0.3.3 0.5.0	https://github.com/rrwick/Trycycler
Unicycler	0.4.7 0.4.8 0.4.9	https://github.com/rrwick/Unicycler
VADR	1.1 1.1.2 1.1.3 1.2 1.2.1 1.3 & SARS-CoV-2 models 1.3-1 1.3 & SARS-CoV-2 models 1.3-2 1.4 & SARS-CoV-2 models 1.3-2 1.4.1 & SARS-CoV-2 models 1.3-2	https://github.com/nawrockie/vadr (archived, now redirects to ncbi/vadr) https://github.com/ncbi/vadr
VIBRANT	1.2.1	https://github.com/AnantharamanLab/VIBRANT
VIGOR4	4.1.20190131	https://github.com/JCVenterInstitute/VIGOR4
VirSorter2	2.1	https://github.com/jiarong/VirSorter2
wtdbg2	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:

• @kapsakcj
• @k-florek
• @garfinjm
• @kevinlibuit
• @erinyoung
• @lskatz
• @stjacqrm
• @AbigailShockey
• @andersgs
• @logan-fink
• @tgallagh
• Kelly Oakeson
• @joacjo
• @rpetit3
• @jvhagey
• @Antonia-Chalka
• @MillironX
• @frankambrosio3
• @HNHalstead
• @fanninpm
• @SarahNadeau
• @DOH-HNH0303