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docker-builds

:package: :whale: Dockerfiles and documentation on tools for public health bioinformatics

https://github.com/staph-b/docker-builds

Science Score: 67.0%

This score indicates how likely this project is to be science-related based on various indicators:

  • ✓
    CITATION.cff file
    Found CITATION.cff file
  • ✓
    codemeta.json file
    Found codemeta.json file
  • ✓
    .zenodo.json file
    Found .zenodo.json file
  • ✓
    DOI references
    Found 2 DOI reference(s) in README
  • ✓
    Academic publication links
    Links to: ncbi.nlm.nih.gov
  • ○
    Academic email domains
  • ○
    Institutional organization owner
  • ○
    JOSS paper metadata
  • ○
    Scientific vocabulary similarity
    Low similarity (14.3%) to scientific vocabulary

Keywords

bioinformatics containers docker dockerfiles singularity
Last synced: 6 months ago · JSON representation ·

Repository

:package: :whale: Dockerfiles and documentation on tools for public health bioinformatics

Basic Info
  • Host: GitHub
  • Owner: StaPH-B
  • License: gpl-3.0
  • Language: Dockerfile
  • Default Branch: master
  • Homepage:
  • Size: 108 MB
Statistics
  • Stars: 212
  • Watchers: 11
  • Forks: 134
  • Open Issues: 29
  • Releases: 0
Topics
bioinformatics containers docker dockerfiles singularity
Created over 7 years ago · Last pushed 6 months ago
Metadata Files
Readme Contributing License Code of conduct Citation

README.md

Gitpod ready-to-code

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.

This is a community resource, built and maintained 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:

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

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

mermaid 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

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:

Summarized usage guide for docker

```bash

Build a docker image to the 'test' layer

docker build --tag tool:test --target test 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 :/data tool:version docker run --rm -u $(id -u):$(id -g) -v $(pwd)/amrfindertestfiles:/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.

  1. dockerfile-template/Dockerfile is the basic template useful for most images
  2. dockerfile-template/Dockerfile_mamba is a basic template for using the micromamba base image
  3. 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

```bash

Pulling a container from dockerhub (creates a file)

singularity pull --name 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 :/data singularity exec --bind $(pwd)/fastq:/data staphb-bbtools-38.96.simg bbduk.sh in1=sample1R1.fastq.gz in2=sample1R2.fastq.gz out1=bbduk/sample1rmphixR1.fastq.gz out2=bbduk/sample1rmphixR2.fastq.gz outm=bbduk/sample1.matchedphix.fq ref=/opt/bbmap/resources/phix174ill.ref.fa.gz stats=bbduk/sample1.phix.stats.txt threads=4 ```

Further documentation can be found at docs.sylabs.io

Training

Logs

In December 2024, StaPH-B/docker-builds underwent a structural change where all Dockerfiles were placed in the subdirectory build-files.

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
docker pulls |

Click to see all versions
| https://github.com/tseemann/abricate | | ACI
docker pulls |
Click to see all versions
| https://github.com/erinyoung/ACI | | ANIclustermap
docker pulls |
Click to see all versions
| https://github.com/moshi4/ANIclustermap | | any2fasta
docker pulls |
Click to see all versions
| https://github.com/tseemann/any2fasta | | ARIBA
docker pulls |
Click to see all versions
| https://github.com/sanger-pathogens/ariba | | artic
docker pulls |
Click to see all versions
| https://github.com/artic-network/fieldbioinformatics | | artic-ncov2019
docker pulls |
Click to see all versions
| https://github.com/artic-network/fieldbioinformatics | | artic-ncov2019-epi2me
docker pulls |
Click to see all versions
| https://github.com/epi2me-labs/wf-artic | | artic-ncov2019-medaka
docker pulls |
Click to see all versions
| https://github.com/artic-network/artic-ncov2019 | | artic-ncov2019-nanopolish
docker pulls |
Click to see all versions
| https://github.com/artic-network/artic-ncov2019 | | assembly_snptyper
docker pulls |
Click to see all versions
| https://github.com/boasvdp/assemblysnptyper | | Augur
docker pulls |
Click to see all versions
| https://github.com/nextstrain/augur | | Auspice
docker pulls |
Click to see all versions
| https://github.com/nextstrain/auspice | | Autocycler
docker pulls |
Click to see all versions
| https://github.com/rrwick/Autocycler/ | | bakta
docker pulls |
Click to see all versions
| https://github.com/oschwengers/bakta | | bandage
docker pulls |
Click to see all versions
| https://rrwick.github.io/Bandage/ | | BBTools
docker pulls |
Click to see all versions
| https://jgi.doe.gov/data-and-tools/bbtools/ | | bcftools
docker pulls |
Click to see all versions
| https://github.com/samtools/bcftools | | bedtools
docker pulls |
Click to see all versions
| https://bedtools.readthedocs.io/en/latest/
https://github.com/arq5x/bedtools2 | | berrywood-report-env
docker pulls |
Click to see all versions
| none | | bindashtree
docker pulls |
Click to see all versions
| https://github.com/jianshu93/bindashtree | | blast+
docker pulls |
Click to see all versions
| https://www.ncbi.nlm.nih.gov/books/NBK279690/ | | bowtie2
docker pulls |
Click to see all versions
| http://bowtie-bio.sourceforge.net/bowtie2/manual.shtml
https://github.com/BenLangmead/bowtie2 | | Bracken
docker pulls |
Click to see all versions
| https://ccb.jhu.edu/software/bracken/index.shtml?t=manual
https://github.com/jenniferlu717/Bracken | | BUSCO
docker pulls |
Click to see all versions
| https://busco.ezlab.org/buscouserguide.html
https://gitlab.com/ezlab/busco | | BWA
docker pulls |
Click to see all versions
| https://github.com/lh3/bwa | | Canu
docker pulls|
Click to see all versions
| https://canu.readthedocs.io/en/latest/
https://github.com/marbl/canu | | Canu-Racon
docker pulls |
Click to see all versions
| https://canu.readthedocs.io/en/latest/
https://github.com/lbcb-sci/racon
https://github.com/isovic/racon (ARCHIVED)
https://lh3.github.io/minimap2/ | | CAT
docker pulls |
Click to see all versions
| https://github.com/MGXlab/CATpack | | cbird-util
docker pulls |
Click to see all versions
| https://github.com/Kincekara/C-BIRD | | centroid
docker pulls |
Click to see all versions
| https://github.com/stjacqrm/centroid | | CDC-SPN
docker pulls |
Click to see all versions
| https://github.com/BenJamesMetcalf/SpnScriptsReference | | cfsan-snp-pipeline
docker pulls |
Click to see all versions | https://github.com/CFSAN-Biostatistics/snp-pipeline | | CheckM
docker pulls |
Click to see all versions
| https://github.com/Ecogenomics/CheckM | | CheckM2
docker pulls |
Click to see all versions
| https://github.com/chklovski/CheckM2 | | CheckV
docker pulls |
Click to see all versions
| https://bitbucket.org/berkeleylab/checkv/ | | Circlator
docker pulls |
Click to see all versions
| https://github.com/sanger-pathogens/circlator | | Circos
docker pulls |
Click to see all versions
| https://circos.ca/ | | CirculoCov
docker pulls |
Click to see all versions
| https://github.com/erinyoung/CirculoCov | | Clair3
docker pulls |
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| https://github.com/HKU-BAL/Clair3 | | Clustalo
docker pulls |
Click to see all versions
| http://www.clustal.org/omega/ | | colorid
docker pulls |
Click to see all versions
| https://github.com/hcdenbakker/colorid | | Core-SNP-filter
docker pulls |
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| https://github.com/rrwick/Core-SNP-filter | | cutshaw-report-env
docker pulls |
Click to see all versions
| https://github.com/VADGS/CutShaw | | datasets-sars-cov-2
docker pulls |
Click to see all versions
| https://github.com/CDCgov/datasets-sars-cov-2 | | dnaapler
docker pulls |
Click to see all versions
| https://github.com/gbouras13/dnaapler | | diamond
docker pulls |
Click to see all versions
| https://github.com/bbuchfink/diamond| | dorado
docker pulls |
Click to see all versions
| https://github.com/nanoporetech/dorado | | dragonflye
docker pulls |
Click to see all versions
| https://github.com/rpetit3/dragonflye | | Dr. PRG
docker pulls |
Click to see all versions
| https://mbh.sh/drprg/ | | DSK
docker pulls |
Click to see all versions
| https://gatb.inria.fr/software/dsk/ | | ectyper
docker pulls |
Click to see all versions
| https://github.com/phac-nml/ecoliserotyping | | el_gato
docker pulls |
Click to see all versions
| https://github.com/appliedbinf/elgato https://github.com/CDCgov/elgato | | emboss
docker pulls |
Click to see all versions
| http://emboss.sourceforge.net | | emmtyper
docker pulls |
Click to see all versions
| https://github.com/MDU-PHL/emmtyper | | emm-typing-tool
docker pulls |
Click to see all versions
| https://github.com/phe-bioinformatics/emm-typing-tool | | enaBrowserTools
docker pulls |
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| https://github.com/enasequence/enaBrowserTools | | EToKi
docker pulls |
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| https://github.com/zheminzhou/EToKi | | falco
docker pulls |
Click to see all versions
| https://github.com/smithlabcode/falco | | FastANI
docker pulls |
Click to see all versions
| https://github.com/ParBLiSS/FastANI | | fasten
docker pulls |
Click to see all versions
| https://github.com/lskatz/fasten | | Fastp
docker pulls |
Click to see all versions
| http://opengene.org/fastp/
https://github.com/OpenGene/fastp | | fastplong
docker pulls |
Click to see all versions
| https://github.com/OpenGene/fastplong | | FastTree
docker pulls |
Click to see all versions
| http://www.microbesonline.org/fasttree/ | | FastQC
docker pulls |
Click to see all versions
| https://www.bioinformatics.babraham.ac.uk/projects/fastqc/
https://github.com/s-andrews/FastQC | | fastq-scan
docker pulls |
Click to see all versions
| https://github.com/rpetit3/fastq-scan | | Freebayes
docker pulls |
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| https://github.com/freebayes/freebayes | | Filtlong
docker pulls |
Click to see all versions
| https://github.com/rrwick/filtlong | | FLASH
docker pulls |
Click to see all versions
| http://ccb.jhu.edu/software/FLASH | | Flye
docker pulls |
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| https://github.com/fenderglass/Flye | | Freyja
docker pulls |
Click to see all versions
| https://github.com/andersen-lab/Freyja | | GAMBIT
docker pulls |
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| https://github.com/jlumpe/gambit | | GAMMA
docker pulls |
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| https://github.com/rastanton/GAMMA/ | | GenoFLU
docker pulls |
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| https://github.com/USDA-VS/GenoFLU | | geNomad
docker pulls |
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| https://github.com/apcamargo/genomad | | GenoVi
docker pulls |
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| https://github.com/robotoD/GenoVi | | gfastats
docker pulls |
Click to see all versions
| https://github.com/vgl-hub/gfastats | | grandeur_ref
docker pulls |
Click to see all versions
| Part of https://github.com/UPHL-BioNGS/Grandeur | | Gubbins
docker pulls |
Click to see all versions
| https://github.com/nickjcroucher/gubbins | | heatcluster
docker pulls |
Click to see all versions
| https://github.com/DrB-S/heatcluster/tree/main | | hmmer
docker pulls |
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| http://hmmer.org/ | | hocort
docker pulls |
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| https://github.com/ignasrum/hocort | | homopolish
docker pulls |
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| https://github.com/ythuang0522/homopolish/ | | hostile
docker pulls |
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| https://github.com/bede/hostile | | htslib
docker pulls |
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| https://www.htslib.org/ | | igv-reports
docker pulls |
Click to see all versions
| https://github.com/igvteam/igv-reports | | Integron Finder
docker pulls |
Click to see all versions
| https://github.com/gem-pasteur/IntegronFinder | | iqtree
docker pulls |
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| http://www.iqtree.org/ | | iqtree2
docker pulls |
Click to see all versions
| http://www.iqtree.org/ | | iqtree3
docker pulls |
Click to see all versions
| http://www.iqtree.org/ | | IPA
docker pulls |
Click to see all versions
| https://github.com/PacificBiosciences/pbipa | | IRMA
docker pulls |
Click to see all versions
|
  • https://wonder.cdc.gov/amd/flu/irma/
  • https://github.com/CDCgov/irma
    • | | isPcr
    docker pulls |
    Click to see all versions
    | https://users.soe.ucsc.edu/~kent/ | | iVar
    docker pulls |
    Click to see all versions
    | https://github.com/andersen-lab/ivar | | Jasmine
    docker pulls |
    Click to see all versions
    | https://github.com/PacificBiosciences/jasmine | | Kaptive
    docker pulls |
    Click to see all versions
    | https://github.com/klebgenomics/Kaptive | | Kleborate
    docker pulls |
    Click to see all versions
    | https://github.com/klebgenomics/Kleborate
    https://github.com/klebgenomics/Kaptive | | kma
    docker pulls |
    Click to see all versions
    | https://bitbucket.org/genomicepidemiology/kma/ | | Kraken
    docker pulls |
    Click to see all versions
    | https://github.com/DerrickWood/kraken | | Kraken2
    docker pulls |
    Click to see all versions
    | https://github.com/DerrickWood/kraken2 | | KrakenTools
    docker pulls |
    Click to see all versions
    | https://github.com/jenniferlu717/KrakenTools | | KrakenUniq
    docker pulls |
    Click to see all versions
    | https://github.com/fbreitwieser/krakenuniq | | krocus
    docker pulls |
    Click to see all versions
    | https://github.com/andrewjpage/krocus/ | | Krona
    docker pulls |
    Click to see all versions
    | https://github.com/marbl/Krona | | kSNP3
    docker pulls|
    Click to see all versions
    | https://sourceforge.net/projects/ksnp/ | | kSNP4
    docker pulls|
    Click to see all versions
    | https://sourceforge.net/projects/ksnp/ | | label
    docker pulls|
    Click to see all versions
    | https://wonder.cdc.gov/amd/flu/label | | legsta
    docker pulls|
    Click to see all versions
    | https://github.com/tseemann/legsta | | liftoff
    docker pulls|
    Click to see all versions
    | https://github.com/agshumate/Liftoff | | lima
    docker pulls|
    Click to see all versions
    | https://github.com/PacificBiosciences/barcoding | | longshot
    docker pulls|
    Click to see all versions
    | https://github.com/pjedge/longshot | | lrge
    docker pulls|
    Click to see all versions
    | https://github.com/mbhall88/lrge | | Lyve-SET (includes CG-Pipeline scripts and raxml)
    docker pulls |
    Click to see all versions
    | https://github.com/lskatz/lyve-SET https://github.com/lskatz/CG-Pipeline | | MAFFT
    docker pulls |
    Click to see all versions
    | https://mafft.cbrc.jp/alignment/software/ | | Mash
    docker pulls |
    Click to see all versions
    | https://github.com/marbl/Mash | | mashtree
    docker pulls |
    Click to see all versions
    | https://github.com/lskatz/mashtree | | MaSuRCA
    docker pulls |
    Click to see all versions
    | https://github.com/alekseyzimin/masurca | | medaka
    docker pulls |
    Click to see all versions
    | https://github.com/nanoporetech/medaka | | meningotype
    docker pulls |
    Click to see all versions
    | https://github.com/MDU-PHL/meningotype | | metaphlan
    docker pulls |
    Click to see all versions
    | https://github.com/biobakery/MetaPhlAn | | MIDAS
    docker pulls |
    Click to see all versions

    Owner

    • Name: StaPH-B
    • Login: StaPH-B
    • Kind: organization

    State Public Health Bioinformatics Workgroup

    Citation (CITATION.cff) 

    cff-version: 1.2.0
message: "If you use this software, please cite it as below."
authors:
- family-names: "Florek"
  given-names: "Kelsey R."
  orcid: "https://orcid.org/0000-0002-8743-8579"
- family-names: "Young"
  given-names: "Erin L."
  orcid: "https://orcid.org/0000-0002-7535-006X"
- family-names: "Incekara"
  given-names: "Kutluhan"
  orcid: "https://orcid.org/0000-0001-7915-9847"
- family-names: "Libuit"
  given-names: "Kevin G."
  orcid: "https://orcid.org/0000-0002-0894-1820"
- family-names: "Kapsak"
  given-names: "Curtis J."
  orcid: "https://orcid.org/0000-0002-8735-1190"
title: "StaPH-B/docker-builds"
version: None
doi: None
date-released: N/A
url: "https://github.com/StaPH-B/docker-builds/"
preferred-citation:
  type: article
  authors:
    - family-names: "Florek"
      given-names: "Kelsey R."
      orcid: "https://orcid.org/0000-0002-8743-8579"
    - family-names: "Young"
      given-names: "Erin L."
      orcid: "https://orcid.org/0000-0002-7535-006X"
    - family-names: "Incekara"
      given-names: "Kutluhan"
      orcid: "https://orcid.org/0000-0001-7915-9847"
    - family-names: "Libuit"
      given-names: "Kevin G."
      orcid: "https://orcid.org/0000-0002-0894-1820"
    - family-names: "Kapsak"
      given-names: "Curtis J."
      orcid: "https://orcid.org/0000-0002-8735-1190"
  doi: "10.3201/eid3113.241363"
  journal: "Emerging Infectious Diseases"
  month: 5
  start: S18 # First page number
  end: S21 # Last page number
  title: "Advantages of Software Containerization in Public Health Infectious Disease Genomic Surveillance"
  issue: "13, Supplement"
  volume: 31
  year: 2025

    GitHub Events

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    Last Year
    • Issues event: 96
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    • Pull request review comment event: 128
    • Pull request review event: 338
    • Pull request event: 461
    • Fork event: 16
    • Create event: 46

    Issues and Pull Requests

    Last synced: 6 months ago

    All Time
    • Total issues: 46
    • Total pull requests: 203
    • Average time to close issues: 5 months
    • Average time to close pull requests: 26 days
    • Total issue authors: 9
    • Total pull request authors: 12
    • Average comments per issue: 0.54
    • Average comments per pull request: 0.75
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    Past Year
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    • Pull requests: 200
    • Average time to close issues: about 1 month
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    • Issue authors: 7
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    • Average comments per pull request: 0.68
    • Merged pull requests: 127
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    Dependencies

    docs/Gemfile rubygems
    • github-pages = 193 development
    • jekyll-paginate >= 0
    docs/Gemfile.lock rubygems
    • activesupport 4.2.10
    • addressable 2.8.0
    • coffee-script 2.4.1
    • coffee-script-source 1.11.1
    • colorator 1.1.0
    • commonmarker 0.17.13
    • concurrent-ruby 1.1.9
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