staphb/freyja

Sponsored OSS

Freyja: recover relative lineage abundances from mixed SARS-CoV-2 samples from a sequencing dataset

Image

100K+

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

SoftwareVersionLink
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
any2fasta
docker pulls
  • 0.4.2
https://github.com/tseemann/any2fasta
ARIBA
docker pulls
  • 2.14.4
https://github.com/sanger-pathogens/ariba
artic-ncov2019
docker pulls
  • 1.3.0
https://github.com/artic-network/fieldbioinformatics
artic-ncov2019-epi2me
docker pulls
  • 0.3.10
https://github.com/epi2me-labs/wf-artic
artic-ncov2019-medaka
docker pulls
  • 1.1.0
https://github.com/artic-network/artic-ncov2019
artic-ncov2019-nanopolish
docker pulls
  • 1.1.0
https://github.com/artic-network/artic-ncov2019
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
  • 38.95
https://jgi.doe.gov/data-and-tools/bbtools/
bcftools
docker pulls
  • 1.10.2
  • 1.11
  • 1.12
  • 1.13
  • 1.14
https://github.com/samtools/bcftools
bedtools
docker pulls
  • 2.29.2
  • 2.30.0
https://bedtools.readthedocs.io/en/latest/
https://github.com/arq5x/bedtools2
berrywood-report-env
docker pulls
  • 1.0
none
bowtie2
docker pulls
  • 2.4.4
http://bowtie-bio.sourceforge.net/bowtie2/manual.shtml
https://github.com/BenLangmead/bowtie2
BWA
docker pulls
  • 0.7.17
https://github.com/lh3/bwa
Canu
docker pulls
  • 2.0
  • 2.1.1
  • 2.2
https://canu.readthedocs.io/en/latest/
https://github.com/marbl/canu
Canu-Racon
docker pulls
  • 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
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/
colorid
docker pulls
  • 0.1.4.3
https://github.com/hcdenbakker/colorid
cutshaw-report-env
docker pulls
  • 1.0.0
https://github.com/VADGS/CutShaw
datasets-sars-cov-2
docker pulls
  • 0.4
https://github.com/CDCgov/datasets-sars-cov-2
emm-typing-tool
docker pulls
  • 0.0.1 (no version)
https://github.com/phe-bioinformatics/emm-typing-tool
FastANI
docker pulls
  • 1.1
  • 1.32
  • 1.33
https://github.com/ParBLiSS/FastANI
FastTree
docker pulls
  • 2.1.11
http://www.microbesonline.org/fasttree/
FastQC
docker pulls
  • 0.11.8
  • 0.11.9
https://www.bioinformatics.babraham.ac.uk/projects/fastqc/
https://github.com/s-andrews/FastQC
fastq-scan
docker pulls
  • 0.4.3
  • 0.4.4
https://github.com/rpetit3/fastq-scan
Filtlong
docker pulls
  • 0.2.0
  • 0.2.1
https://github.com/rrwick/filtlong
Flye
docker pulls
  • 2.5
  • 2.7
  • 2.8
  • 2.9
https://github.com/fenderglass/Flye
Freyja
docker pulls
  • 1.2
  • 1.2.1
  • 1.3.1
  • 1.3.2
https://github.com/andersen-lab/Freyja
GAMBIT
docker pulls
  • 0.3.0
https://github.com/hesslab-gambit/gambit
GAMMA
docker pulls
  • 1.4
https://github.com/rastanton/GAMMA/
hmmer
docker pulls
  • 3.3
http://hmmer.org/
iqtree
docker pulls
  • 1.6.7
http://www.iqtree.org/
iqtree2
docker pulls
  • 2.1.2
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)
  • 1.3
  • 1.3.1
https://github.com/andersen-lab/ivar
Kleborate
docker pulls
  • 2.0.4
  • 2.1.0
https://github.com/katholt/Kleborate/
https://github.com/katholt/Kaptive/
kma
docker pulls
  • 1.2.21
https://bitbucket.org/genomicepidemiology/kma/
Kraken
docker pulls
  • 1.0
  • 1.0.0_wslh_signed
  • 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)
  • 2.1.0 (no db)
  • 2.1.1 (no db)
  • 2.1.2 (no 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
https://github.com/lskatz/lyve-SEThttps://github.com/lskatz/CG-Pipeline
MAFFT
docker pulls
  • 7.450
  • 7.475
https://mafft.cbrc.jp/alignment/software/
Mash
docker pulls
  • 2.1
  • 2.2
  • 2.3
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
  • 1.2.0
https://github.com/nanoporetech/medaka
metaphlan
docker pulls
  • 3.0.3-no-db (no database)
  • 3.0.3 (~3GB db)
https://github.com/biobakery/MetaPhlAn/tree/3.0
minimap2
docker pulls
  • 2.17
  • 2.18
  • 2.21
  • 2.22
  • 2.23
  • 2.24
https://github.com/lh3/minimap2
minipolish
docker pulls
  • 0.1.3
https://github.com/rrwick/Minipolish
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
  • 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
docker pulls
  • 2.17
https://github.com/davidemms/OrthoFinder
Pangolin
docker pulls
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
  • 3.1.20 & 2022-02-02
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
docker pulls
  • 20200722
https://www.gnu.org/software/parallel
Piggy
docker pulls
  • 1.5
https://github.com/harry-thorpe/piggy
Pilon
docker pulls
  • 1.23.0
https://github.com/broadinstitute/pilon
PlasmidSeeker
docker pulls
  • 1.0
https://github.com/bioinfo-ut/PlasmidSeeker
pmga
docker pulls
  • 3.0.2
https://github.com/rpetit3/pmga
Prokka
docker pulls
  • 1.13.4
  • 1.14.0
  • 1.14.5
https://github.com/tseema

Docker Pull Command

docker pull staphb/freyja