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.

There are several community projects that create and share containers for bioinformatic tools. This repository contains the Dockerfiles and other assorted files necessary for building Docker images for a variety of tools 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.

This is a community resource, built and maintined by users from varied backgrounds and expertise levels. As such, we have provided some templates for contributing to this repository. If you would like to add 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 image repositories & hosting

We host all of our docker images on two different repositories:

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

The development process of creating a new image is summarized as follows:

graph TD
     A[fork staphb/docker-builds repo]-->B[create tool/version directory]
     B-->C[create readme]
     B-->D[create dockerfile]
     D-->G[create app and test layers]
     A-->E[add License to Program_Licenses.md]
     A-->F[add tool to list in this readme]
     E-->H[submit PR]
     F-->H
     G-->H
     C-->H
     H-->I{build to test}
     I--success-->J[PR merged and docker image pushed to dockerhub and quay]
     I--failure-->K[edit dockerfile]
     K-->I

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User Guide

The StaPH-B Docker User Guide was created to outline methods and best practices for using and developing docker containers. There are chapters for:

Contributing
Downloading Docker images
Running Docker containers
Developing Docker images
Useful links

Summarized usage guide for docker

# Build a docker image to the 'test' layer
docker build --tag tool:test --target test <directory to Dockerfile>
docker build --tag samtools:test --target test samtools/1.15

# Download a docker image from dockerhub (most tools have a 'latest' version tag)
docker pull staphb/tool:version
docker pull staphb/shigatyper:2.0.2

# Run the container (don't forget to mount your volumes!)
docker run --rm -u $(id -u):$(id -g) -v <local directory>:/data tool:version <command>
docker run --rm -u $(id -u):$(id -g) -v $(pwd)/amrfinder_test_files:/data amrfinder:3.10 amrfinder --nucleotide 2021CK-01854_contigs.fa --threads 20 --name 2021CK-01854 --output /data/2021CK-01854.txt --organism Klebsiella

Further documentation can be found at docs.docker.com

Templates

Several template files are provided. These are intended to be copied and edited by contributors.

dockerfile-template/Dockerfile is the basic template useful for most images
dockerfile-template/Dockerfile_mamba is a basic template for using the micromamba base image
dockerfile-template/README.md is a basic readme file template to assist others in using the image

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 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!

Summarized usage guide for singularity

# Pulling a container from dockerhub (creates a file)
singularity pull --name <name of singularity file> docker://staphb/bbtools:38.96
singularity pull --name staphb-bbtools-38.96.simg docker://staphb/bbtools:38.96

# Running the container (don't forget to mount your volumes!)
singularity exec --bind <local directory>:/data <name of singularity file> <command>
singularity exec --bind $(pwd)/fastq:/data staphb-bbtools-38.96.simg bbduk.sh in1=sample1_R1.fastq.gz in2=sample1_R2.fastq.gz out1=bbduk/sample1_rmphix_R1.fastq.gz out2=bbduk/sample1_rmphix_R2.fastq.gz outm=bbduk/sample1.matched_phix.fq ref=/opt/bbmap/resources/phix174_ill.ref.fa.gz stats=bbduk/sample1.phix.stats.txt threads=4

Further documentation can be found at docs.sylabs.io

Training

Training materials (slides & exercises) from the North East Bioinformatics Regional Resource 2023 workshop Docker for Public Health Bioinformatics can be located here, within training/NE-BRR-docker-for-PH-bioinformatics-May2023/
Video training from APHL 2024 workshop Intermediate Docker Bioinformatics Workshop can be located in APHL's e-learning resources

Logs

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 1.0.1 (+ A. baumannii plasmid typing db) 1.0.1 (+ InsaFlu db) 1.0.1 (+ Vibrio cholerae db)	https://github.com/tseemann/abricate
ACI	1.4.20240116	https://github.com/erinyoung/ACI
ANIclustermap	1.3.0 1.4.0	https://github.com/moshi4/ANIclustermap
any2fasta	0.4.2	https://github.com/tseemann/any2fasta
ARIBA	2.14.4 2.14.6 2.14.7	https://github.com/sanger-pathogens/ariba
artic	1.2.4-1.11.1 (artic-medaka) 1.2.4-1.12.0 (artic-medaka)	https://github.com/artic-network/fieldbioinformatics
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
assembly_snptyper	0.1.1	https://github.com/boasvdp/assembly_snptyper
Augur	6.3.0 7.0.2 8.0.0 9.0.0 16.0.3 24.2.2 24.2.3 24.3.0 24.4.0 26.0.0	https://github.com/nextstrain/augur
Auspice	2.12.0	https://github.com/nextstrain/auspice
bakta	1.9.2 1.9.2-light 1.9.3 1.9.3-light 1.9.4 1.9.4-5.1-light	https://github.com/oschwengers/bakta
bandage	0.8.1	https://rrwick.github.io/Bandage/
BBTools	38.76 38.86 38.95 38.96 38.97 38.98 38.99 39.00 39.01 39.06 39.10 39.13	https://jgi.doe.gov/data-and-tools/bbtools/
bcftools	1.10.2 1.11 1.12 1.13 1.14 1.15 1.16 1.17 1.18 1.19 1.20 1.20.c 1.21	https://github.com/samtools/bcftools
bedtools	2.29.2 2.30.0 2.31.0 2.31.1	https://bedtools.readthedocs.io/en/latest/ https://github.com/arq5x/bedtools2
berrywood-report-env	1.0	none
blast+	2.13.0 2.14.0 2.14.1 2.15.0 2.16.0	https://www.ncbi.nlm.nih.gov/books/NBK279690/
bowtie2	2.4.4 2.4.5 2.5.1 2.5.3 2.5.4	http://bowtie-bio.sourceforge.net/bowtie2/manual.shtml https://github.com/BenLangmead/bowtie2
Bracken	2.9	https://ccb.jhu.edu/software/bracken/index.shtml?t=manual https://github.com/jenniferlu717/Bracken
BUSCO	5.4.7 5.6.1 5.6.1-prok-bacteria_odb10_2024-01-08 5.7.1 5.7.1-prok-bacteria_odb10_2024-01-08 5.8.0 5.8.0-prok-bacteria_odb10_2024-01-08	https://busco.ezlab.org/busco_userguide.html https://gitlab.com/ezlab/busco
BWA	0.7.17 0.7.18	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/
CAT	5.3	https://github.com/dutilh/CAT
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 2.2.1	https://github.com/CFSAN-Biostatistics/snp-pipeline
CheckM	1.2.2 1.2.3	https://github.com/Ecogenomics/CheckM
CheckM2	1.0.2	https://github.com/chklovski/CheckM2
CheckV	1.0.3	https://bitbucket.org/berkeleylab/checkv/
Circlator	1.5.6 1.5.5	https://github.com/sanger-pathogens/circlator
Circos	0.69-9	https://circos.ca/
CirculoCov	0.1.20240104	https://github.com/erinyoung/CirculoCov
Clair3	1.0.9 1.0.10	https://github.com/HKU-BAL/Clair3
Clustalo	1.2.4	http://www.clustal.org/omega/
colorid	0.1.4.3	https://github.com/hcdenbakker/colorid
Core-SNP-filter	0.2.0	https://github.com/rrwick/Core-SNP-filter
cutshaw-report-env	1.0.0	https://github.com/VADGS/CutShaw
datasets-sars-cov-2	0.6.2 0.6.3 0.7.2	https://github.com/CDCgov/datasets-sars-cov-2
dnaapler	0.1.0 0.4.0 0.5.0 0.5.1 0.7.0 0.8.0 1.0.1	https://github.com/gbouras13/dnaapler
diamond	2.1.9 2.1.10	https://github.com/bbuchfink/diamond
dorado	0.8.0 0.8.3	https://github.com/nanoporetech/dorado
dragonflye	1.0.14 1.1.1 1.1.2 1.2.0 1.2.1	https://github.com/rpetit3/dragonflye
Dr. PRG	0.1.1	https://mbh.sh/drprg/
DSK	0.0.100 2.3.3	https://gatb.inria.fr/software/dsk/
el_gato	1.15.2 1.18.2 1.19.0 1.20.0 1.20.1	https://github.com/appliedbinf/el_gato
emboss	6.6.0 (no version)	http://emboss.sourceforge.net
emmtyper	0.2.0 0.2.0-2412	https://github.com/MDU-PHL/emmtyper
emm-typing-tool	0.0.1 (no version)	https://github.com/phe-bioinformatics/emm-typing-tool
EToKi	1.2.1	https://github.com/zheminzhou/EToKi
FastANI	1.1 1.32 1.33 1.33 + RGDv2 1.34 1.34 + RGDv2	https://github.com/ParBLiSS/FastANI
fasten	0.7.2 0.8.1	https://github.com/lskatz/fasten
Fastp	0.23.2 0.23.4 0.24.0	http://opengene.org/fastp/ https://github.com/OpenGene/fastp
FastTree	2.1.11	http://www.microbesonline.org/fasttree/
FastQC	0.11.8 0.11.9 0.12.1	https://www.bioinformatics.babraham.ac.uk/projects/fastqc/ https://github.com/s-andrews/FastQC
fastq-scan	0.4.3 0.4.4 1.0.0 1.0.1	https://github.com/rpetit3/fastq-scan
Freebayes	1.3.6 1.3.7 1.3.7 1.3.7	https://github.com/freebayes/freebayes
Filtlong	0.2.0 0.2.1	https://github.com/rrwick/filtlong
FLASH	1.2.11	http://ccb.jhu.edu/software/FLASH
Flye	2.5 2.7 2.8 2.9 2.9.1 2.9.2 2.9.3 2.9.4 2.9.5	https://github.com/fenderglass/Flye
Freyja	1.2 1.2.1 1.3.1 1.3.2 1.3.4 1.3.7 1.3.8 1.3.9 1.3.10 1.3.11 1.3.12 1.4.2 1.4.3 1.4.4 1.4.5 1.4.7 1.4.8 1.4.9 1.5.0 1.5.1 1.5.2	https://github.com/andersen-lab/Freyja
GAMBIT	0.3.0 0.4.0 0.5.0 1.0.0	https://github.com/jlumpe/gambit
GAMMA	1.4 2.1 2.2	https://github.com/rastanton/GAMMA/
GenoFLU	1.03	https://github.com/USDA-VS/GenoFLU
geNomad	1.7.4 1.8.0 1.8.1	https://github.com/apcamargo/genomad
GenoVi	0.2.16	https://github.com/robotoD/GenoVi
gfastats	1.3.6 1.3.7	https://github.com/vgl-hub/gfastats
grandeur_ref	4.5	Part of https://github.com/UPHL-BioNGS/Grandeur
Gubbins	3.3.3 3.3.4 3.3.5	https://github.com/nickjcroucher/gubbins
heatcluster	1.0.2c	https://github.com/DrB-S/heatcluster/tree/main
hmmer	3.3 3.3.2 3.4	http://hmmer.org/
homopolish	0.4.1	https://github.com/ythuang0522/homopolish/
hostile [](https://hub.docker.com/r/staphb/hostile	1.1.0	https://github.com/bede/hostile
htslib	1.14 1.15 1.16 1.17 1.18 1.19 1.20 1.20.c 1.21	https://www.htslib.org/
igv-reports	1.12.0	https://github.com/igvteam/igv-reports
Integron Finder	2.0.5	https://github.com/gem-pasteur/Integron_Finder
iqtree	1.6.7	http://www.iqtree.org/
iqtree2	2.1.2 2.2.2.2 2.2.2.6 2.2.2.7 2.3.1 2.3.4 2.3.6	http://www.iqtree.org/
IPA	1.8.0	https://github.com/PacificBiosciences/pbipa
IRMA	1.0.2 1.0.3 1.1.2 1.1.3 1.1.4	https://wonder.cdc.gov/amd/flu/irma/
isPcr	33	https://users.soe.ucsc.edu/~kent/
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 1.3.2 1.4.1 1.4.2 1.4.3	https://github.com/andersen-lab/ivar
Jasmine	2.0.0	https://github.com/PacificBiosciences/jasmine
Kaptive	2.0.0 2.0.3 2.0.5 2.0.8 3.0.0b6	https://github.com/klebgenomics/Kaptive
Kleborate	2.0.4 2.1.0 2.2.0 2.3.2 2.3.2-2023-05 2.4.1 3.1.2	https://github.com/katholt/Kleborate/ https://github.com/katholt/Kaptive/
kma	1.2.21 1.4.10 (no database) 1.4.14 (no database)	https://bitbucket.org/genomicepidemiology/kma/
Kraken	1.0 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) 2.1.3 (no db)	https://github.com/DerrickWood/kraken2
KrakenTools	d4a2fbe	https://github.com/jenniferlu717/KrakenTools
KrakenUniq	1.0.4 (no database)	https://github.com/fbreitwieser/krakenuniq
kSNP3	3.1	https://sourceforge.net/projects/ksnp/
kSNP4	4.0 4.1	https://sourceforge.net/projects/ksnp/
label	0.6.4	https://wonder.cdc.gov/amd/flu/label
legsta	0.3.7 0.5.1	https://github.com/tseemann/legsta
liftoff	1.6.3	https://github.com/agshumate/Liftoff
lima	2.9.0 2.9.0+Rscripts	https://github.com/PacificBiosciences/barcoding
longshot	0.4.5 1.0.0	https://github.com/pjedge/longshot
lrge	0.1.3	https://github.com/mbhall88/lrge
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 7.505 7.520 7.526	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 1.4.6	https://github.com/lskatz/mashtree
MaSuRCA	4.0.8 4.0.9 4.1.0	https://github.com/alekseyzimin/masurca
medaka	0.8.1 1.0.1 1.2.0 2.0.0 2.0.1	https://github.com/nanoporetech/medaka
meningotype	0.8.5	https://github.com/MDU-PHL/meningotype
metaphlan	3.0.3-no-db (no database) 3.0.3 (~3GB db) 4.1.0 (no database) 4.1.1 (no database)	https://github.com/biobakery/MetaPhlAn
MIDAS	1.3.2 (no database)	https://github.com/snayfach/MIDAS
minimap2	2.17 2.18 2.21 2.22 2.23 2.24 2.25 2.26 2.27 2.28	https://github.com/lh3/minimap2
minipolish	0.1.3	https://github.com/rrwick/Minipolish
mlst	2.16.2 2.17.6 2.19.0 2.22.0 2.22.1 2.23.0 2.23.0-2023-07 (databases updated July 2023) 2.23.0-2023-08 (databases updated Aug 2023) 2.23.0-2024-01 (databases updated Jan 2024) 2.23.0-2024-03 (databases updated March 2024)	https://github.com/tseemann/mlst
Mugsy	1r2.3	http://mugsy.sourceforge.net/
MultiQC	1.7 1.8 1.18 1.19 1.22.2 1.22.3 1.25	https://github.com/MultiQC/MultiQC
Mummer	4.0.0 4.0.0 + RGDv2 4.0.0 + RGDv2 + gnuplot	https://github.com/mummer4/mummer
Mykrobe + Genotyphi + sonneityping	0.11.0 (Mykrobe) & 1.9.1 (Genotyphi) 0.12.1 (Mykrobe) & 1.9.1 (Genotyphi) & v20210201 (sonneityping) 0.12.1 (Mykrobe) & 2.0 (Genotyphi) & v20210201 (sonneityping) 0.12.2 (Mykrobe) & 2.0 (Genotyphi) & v20210201 (sonneityping) 0.13.0	https://github.com/Mykrobe-tools/mykrobe https://github.com/typhoidgenomics/genotyphi https://github.com/katholt/sonneityping
NanoPlot	1.27.0 1.29.0 1.30.1 1.32.0 1.33.0 1.40.0 1.41.6 1.42.0	https://github.com/wdecoster/NanoPlot
ngmaster	0.5.8 1.0.0	https://github.com/MDU-PHL/ngmaster
NCBI Datasets	Click to see all datasets versions datasets versions 13.31.0 13.35.0 13.43.2 14.0.0 14.3.0 14.7.0 14.13.2 14.20.0 14.27.0 15.1.0 15.2.0 15.11.0 15.27.1 15.31.0 16.2.0 16.8.1 16.10.3 16.15.0 16.22.1 16.30.0 16.35.0	https://github.com/ncbi/datasets https://www.ncbi.nlm.nih.gov/datasets/docs/v1/
NCBI AMRFinderPlus	AMRFinderPlus & database verion Click to see AMRFinderplus v3.11.4 and older versions! 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 3.10.24 3.10.30 3.10.36 3.10.42 3.11.2 & 2022-12-19.1 3.11.2 & 2023-02-23.1 3.11.4 & 2023-02-23.1 3.11.8 & 2023-02-23.1 3.11.11 & 2023-04-17.1 3.11.14 & 2023-04-17.1 3.11.17 & 2023-07-13.2 3.11.18 & 2023-08-08.2 3.11.20 & 2023-09-26.1 3.11.26 & 2023-11-15.1 3.12.8 & 2024-01-31.1 3.12.8 & 2024-05-02.2 3.12.8 & 2024-07-22.1 4.0.3 & 2024-10-22.1 (includes stxtyper)	https://github.com/ncbi/amr
NCBI table2asn	1.26.678 1.28.943 1.28.1021	https://www.ncbi.nlm.nih.gov/genbank/table2asn/ https://ftp.ncbi.nlm.nih.gov/asn1-converters/versions/2022-06-14/by_program/table2asn/
ONTime	0.2.3 0.3.1	https://github.com/mbhall88/ontime
OrthoFinder	2.17	https://github.com/davidemms/OrthoFinder
Panaroo	1.2.10 1.3.4 1.5.0	https://github.com/gtonkinhill/panaroo
pandas	2.2.3	https://github.com/pandas-dev/pandas
pango_aliasor	0.3.0	https://github.com/corneliusroemer/pango_aliasor
Pangolin	Click to see Pangolin v4.2 and older versions! 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 3.1.20 & 2022-02-02 3.1.20 & 2022-02-28 Pangolin version & pangolin-data version 4.0 & 1.2.133 4.0.1 & 1.2.133 4.0.2 & 1.2.133 4.0.3 & 1.2.133 4.0.4 & 1.2.133 4.0.5 & 1.3 4.0.6 & 1.6 4.0.6 & 1.8 4.0.6 & 1.9 4.1.1 & 1.11 4.1.2 & 1.12 4.1.2 & 1.13 4.1.2 & 1.14 4.1.3 & 1.15.1 4.1.3 & 1.16 4.1.3 & 1.17 4.2 & 1.18 4.2 & 1.18.1 4.2 & 1.18.1.1 4.2 & 1.19 Pangolin version & pangolin-data version 4.3 & 1.20 4.3 & 1.21 4.3.1 & 1.22 4.3.1 & 1.23 4.3.1 & 1.23.1 4.3.1 & 1.23.1 with XDG_CACHE_HOME=/tmp 4.3.1 & 1.24 4.3.1 & 1.25.1 4.3.1 & 1.26 4.3.1 & 1.27 4.3.1 & 1.28 4.3.1 & 1.28.1 4.3.1 & 1.29 4.3.1 & 1.30 4.3.1 & 1.31	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)
panqc	0.4.0	https://github.com/maxgmarin/panqc/releases/tag/0.4.0
parallel-perl	20200722	https://www.gnu.org/software/parallel
parsnp	1.5.6 2.0.4 2.0.5	https://github.com/marbl/parsnp
pasty	1.0.2 1.0.3 2.2.1	https://github.com/rpetit3/pasty
pbmm2	1.13.1	https://github.com/PacificBiosciences/pbmm2
Pavian	1.2.1	https://github.com/fbreitwieser/pavian
pbptyper	1.0.0 1.0.1 1.0.4 2.0.0	https://github.com/rpetit3/pbptyper
pbtk	3.1.1	https://github.com/PacificBiosciences/pbtk
Phyml	3.3.20220408	https://github.com/stephaneguindon/phyml
phyTreeViz	0.1.0 0.2.0	https://github.com/moshi4/phyTreeViz/
Piggy	1.5	https://github.com/harry-thorpe/piggy
Pilon	1.23.0 1.24	https://github.com/broadinstitute/pilon
Piranha	1.0.4	https://github.com/polio-nanopore/piranha
PlasmidFinder	2.1.6 2.1.6_2024-03-07	https://bitbucket.org/genomicepidemiology/plasmidfinder/src/master/
PlasmidSeeker	1.0 1.3	https://github.com/bioinfo-ut/PlasmidSeeker
pmga	3.0.2	https://github.com/rpetit3/pmga
PolkaPox	1.0.0-beta	https://github.com/CDCgov/polkapox
polypolish	0.5.0 0.6.0 0.6.0-bwa	https://github.com/rrwick/Polypolish
PopPUNK	2.4.0 2.5.0 2.6.0 2.6.2 2.6.3 2.6.5	https://github.com/bacpop/PopPUNK
Porechop	0.2.4	https://github.com/rrwick/Porechop
PPanGGOLiN	1.2.105 2.0.3 2.0.5 2.1.2	https://github.com/labgem/PPanGGOLiN
Prokka	1.13.4 1.14.0 1.14.5 1.14.6	https://github.com/tseemann/prokka
pyCirclize	1.0.0 1.2.0 1.5.0 1.6.0 1.71	https://github.com/moshi4/pyCirclize
pyGenomeViz	0.2.2 0.3.2 0.4.2 0.4.3 0.4.4 1.1.0	https://github.com/moshi4/pyGenomeViz
pyMLST	2.1.5 2.1.6	https://github.com/bvalot/pyMLST
pypolca	0.3.1	https://github.com/gbouras13/pypolca
QUAST	5.0.0 5.0.2 5.2.0 5.2.0-slim 5.3.0 5.3.0-slim	https://github.com/ablab/quast
QuickSNP	1.0.1	https://github.com/k-florek/QuickSNP
racon	1.4.3 1.4.20 1.5.0 1.5.0-minimap2	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 0.7.0 0.8.0 2.0.0 2.1.0	https://github.com/mbhall88/rasusa
raven	1.5.1 1.8.1 1.8.3	https://github.com/lbcb-sci/raven
RAxML	8.2.12 8.2.13	https://github.com/stamatak/standard-RAxML
RAxML-NG	1.2.2	https://github.com/amkozlov/raxml-ng
rdp	2.14	https://sourceforge.net/projects/rdp-classifier/files/rdp-classifier/rdp_classifier_2.14.zip/download
ResFinder	4.1.1 4.5.0	https://bitbucket.org/genomicepidemiology/resfinder/src/master/
Roary	3.12.0 3.13.0	https://github.com/sanger-pathogens/Roary
SalmID	0.1.23	https://github.com/hcdenbakker/SalmID
samclip	0.4.0	https://github.com/tseemann/samclip
Samtools	1.9 1.10 1.11 1.12 1.13 1.14 1.15 1.16 1.16.1 1.17 1.17-2023-06 1.18 1.19 1.20 1.20.c	https://github.com/samtools/samtools
SeqFu	1.20.3	https://github.com/telatin/seqfu2
SeqKit	2.3.1 2.6.1 2.7.0 2.8.0 2.8.1 2.8.2	https://github.com/shenwei356/seqkit
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 1.3.1	https://github.com/denglab/SeqSero2/
seqtk	1.3 1.4	https://github.com/lh3/seqtk
seqyclean	1.10.09	https://github.com/ibest/seqyclean
Seroba	1.0.0 1.0.2	https://github.com/sanger-pathogens/seroba
SerotypeFinder	1.1 (perl version) 2.0.1 (python version) 2.0.2	https://bitbucket.org/genomicepidemiology/serotypefinder/
ShigaPass	1.5.0	https://github.com/imanyass/ShigaPass
shigatyper	2.0.1 2.0.2 2.0.3 2.0.4 2.0.5	https://github.com/CFSAN-Biostatistics/shigatyper
ShigEiFinder	1.3.2 1.3.3 1.3.5	https://github.com/LanLab/ShigEiFinder
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 1.1.2	https://github.com/phac-nml/sistr_cmd
SKA	1.0	https://github.com/simonrharris/SKA
SKA2	0.3.6 0.3.7 0.3.10	https://github.com/bacpop/ska.rust
skani	0.2.0 0.2.1 0.2.2	https://github.com/bluenote-1577/skani
SKESA	2.3.0 2.4.0 (`gfa_connector` & `kmercounter` included) skesa.2.4.0_saute.1.3.0_2 (also known as 2.5.1)	https://github.com/ncbi/SKESA
Smalt	0.7.6	https://www.sanger.ac.uk/tool/smalt-0/
snpeff	5.1 5.2a	https://pcingola.github.io/SnpEff
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
SNVPhyl-tools	1.8.2	https://github.com/phac-nml/snvphyl-tools
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 3.15.4 3.15.5 4.0.0	https://github.com/ablab/spades http://cab.spbu.ru/software/spades/
SRA-toolkit	2.9.2 3.0.7	https://github.com/ncbi/sra-tools
SRST2	0.2.0 0.2.0 + custom Vibrio cholerae database	https://github.com/katholt/srst2
Staramr	0.5.1 0.7.1 0.8.0 0.10.0	https://github.com/phac-nml/staramr
stxtyper	1.0.24 1.0.27	https://github.com/ncbi/stxtyper
sylph	0.4.1 0.5.1 0.6.0 0.6.1	https://github.com/bluenote-1577/sylph
TBProfiler	4.3.0 4.4.0 4.4.2 5.0.1 6.2.0 6.2.1 6.3.0 6.4.0 6.4.1	https://github.com/jodyphelan/TBProfiler
TipToft	1.0.0 1.0.2	https://github.com/andrewjpage/tiptoft
Tostadas	0.2.0-beta 3.1.0 4.0.0	https://github.com/CDCgov/tostadas
toulligQC	2.7.1	https://github.com/GenomiqueENS/toulligQC
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 0.5.3 0.5.4 0.5.5	https://github.com/rrwick/Trycycler
Unicycler	0.4.7 0.4.8 0.4.9 0.5.0	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 1.4.2 & SARS-CoV-2 models 1.3-2, MPXV models 1.4.2-1 1.5 & SARS-CoV-2 models 1.3-2, MPXV models 1.4.2-1 1.5.1 & SARS-CoV-2 models 1.3-2, MPXV models 1.4.2-1, RSV models 1.5-2 1.6.3 & SARS-CoV-2 models 1.3-2, MPXV models 1.4.2-1, RSV models 1.5-2, Influenza v1.6.3-1 1.6.3 & SARS-CoV-2 models 1.3-2, MPXV models 1.4.2-1, RSV models 1.5-2, Influenza v1.6.3-1, HAV v1.0.0 1.6.3 & SARS-CoV-2 models 1.3-2, MPXV models 1.4.2-1, RSV models 1.5-2, Influenza v1.6.3-2, HAV v1.0.0	https://github.com/nawrockie/vadr (archived, now redirects to ncbi/vadr) https://github.com/ncbi/vadr
Verkko	2.0 2.1 2.2	https://github.com/marbl/verkko
VIBRANT	1.2.1	https://github.com/AnantharamanLab/VIBRANT
VIGOR4	4.1.20190131 4.1.20200702	https://github.com/JCVenterInstitute/VIGOR4
Viridian	1.2.2 1.3.0	https://github.com/iqbal-lab-org/viridian
VirSorter2	2.1	https://github.com/jiarong/VirSorter2
VirulenceFinder	2.0.4 3.0.0	https://bitbucket.org/genomicepidemiology/virulencefinder/src/master/ https://bitbucket.org/genomicepidemiology/virulencefinder_db/src/master/
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
@koakeson
@joacjo
@rpetit3
@jvhagey
@Antonia-Chalka
@MillironX
@frankambrosio3
@HNHalstead
@fanninpm
@SarahNadeau
@DOH-HNH0303
@jwarnn
@stitam
@tiverson
@sbthandras
@idolawoye
@michellescribner
@cjjossart
@jlumpe
@kissake
@sage-wright
@ankushkgupta
@kyleoconnell
@CTindall-1
@hkunerth
@eetueklund
@wchen190
@shelby-bennett
@cjalcorta
@mndoucette
@jcw349
@poojasgupta
@hollygene
@HarryHung
@sam-baird
@eproctor118
@cimendes
@golden75
@Kincekara
@Haikelnb
@kprus
@arianna-smith
@laura-bankers
@evagunawan
@nawrockie
@stephenturner
@soejun
@taylorpaisie
@fraser-combe

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