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

License: GNU General Public License v3.0

Dockerfile 54.00% Perl 1.92% Shell 1.21% Python 0.68% HTML 42.18%

bioinformatics containers docker singularity dockerfiles

docker-builds's Introduction

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:

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

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

# 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

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	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
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	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	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	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	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	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	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/
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
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	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
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
diamond	2.1.9	https://github.com/bbuchfink/diamond
dnaapler	0.1.0 0.4.0 0.5.0 0.5.1 0.7.0	https://github.com/gbouras13/dnaapler
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	https://github.com/appliedbinf/el_gato
emboss	6.6.0 (no version)	http://emboss.sourceforge.net
emmtyper	0.2.0	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	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	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	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	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
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/
htslib	1.14 1.15 1.16 1.17 1.18 1.19 1.20	https://www.htslib.org/
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	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	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	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
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
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	https://github.com/nanoporetech/medaka
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 li>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	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	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	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://hub.docker.com/r/staphb/panaroo)
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	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	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	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	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	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	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	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	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	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
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	https://github.com/samtools/samtools
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/
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	https://github.com/phac-nml/sistr_cmd
SKA	1.0	https://github.com/simonrharris/SKA
SKA2	0.3.6 0.3.7	https://github.com/bacpop/ska.rust
skani	0.2.0 0.2.1	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
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	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	https://github.com/CDCgov/tostadas
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	https://github.com/marbl/verkko
VIBRANT	1.2.1	https://github.com/AnantharamanLab/VIBRANT
VIGOR4	4.1.20190131	https://github.com/JCVenterInstitute/VIGOR4
Viridian	1.2.2	https://github.com/iqbal-lab-org/viridian
VirSorter2	2.1	https://github.com/jiarong/VirSorter2
VirulenceFinder	2.1.4	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:

docker-builds's People

Contributors

Stargazers

Watchers

Forkers

kevinlibuit pythseq mchiapello stjacqrm abigailshockey mackellardrew tgallagh davidealbanese akashpayne theiagen syssynbio joacjo fanninpm rossbalch mokrobial quincy-deng jvhagey rpetit3 matt-plumb nkinash antonia-chalka mxrcon garfinjm frankambrosio3 doh-hnh0303 gashanjakim sarahnadeau vikash84 stitam viv3kanand michellescribner kapsakcj jwarnn tives82 lskatz drb-s liu5796796 sbthandras idolawoye jh36 whottel vidhyanipin olabiyi hirenbioinfo ldipotetjob cjjossart arodzh-sudo jlumpe kissake soniatad sage-wright kyleoconnell ctindall-1 erikwolfsohn smarcellus16 olintoyale hkunerth johnsonj161 creightonma shelby-bennett trevoranz mamunmonir mndoucette danielevansr poojasgupta jcw349 wchen190 cjalcorta eetueklund njphel doh-kew4303 genizamt hollygene jl32587 siddra2021 apcamargo sam-baird neranjan007 eproctor118 emmadoughty jsgro kapsakcjtest cimendes karimartinez1 jlb423 seansierra-patev kincekara golden75 lgagne01 pnnl-projects connercopeland harryhung ybdong919 evagunawan hutchinsonmiri kprus tinalai29 haikelnb kittychasenc arianna-smith

docker-builds's Issues

add Canu 2.0

Any takers? @k-florek ?

https://github.com/marbl/canu/releases/tag/v2.0

Just wanted to make you aware in case you're interested in trying out the new version.

add mashtree 1.0

Review is almost finished up on JOSS. Lee just released v1.0 https://github.com/lskatz/mashtree/releases/tag/v1.0

openjournals/joss-reviews#1762

reduce amount of LABEL statements used across all dockerfiles?

I just learned that you can combine Dockerfile LABEL's. I wonder if this would reduce the amount of layers in an image and thus reduce the overall size? Perhaps not since it is LABEL's are considered metadata and may be treated differently than other Dockerfile commands (RUN, ENV, FROM, etc.)? Any ideas?

From: https://hub.docker.com/r/greatfireball/canu/~/dockerfile/

LABEL maintainer="[email protected]" \
      description="Dockerfile providing the canu assembler for long reads" \
      version=${VERSION} \
      org.label-schema.vcs-ref=${VCS_REF} \
      org.label-schema.build-date=${BUILD_DATE} \
      org.label-schema.vcs-url="https://github.com/greatfireball/ime_canu.git"

LABEL container.version --> LABEL dockerfile.version

LABEL container.version is super vague. It should be LABEL dockerfile.version. Intended for tracking multiple versions of a dockerfile for a single program (and it's single version).

For example if I had to make adjustments to the SPAdes 3.14.1 dockerfile (for which there is only one dockerfile version currently), I would bump to LABEL dockerfile.version=2

add ariba?

Don't know if anyone is interested, but we don't have ariba in our repo.

Sanger-pathogens has a dockerfile and image available, but might be good to have our own with a pinned ariba version since their docker image is built off of the last commit to the master branch.

latest release: https://github.com/sanger-pathogens/ariba/releases/tag/v2.14.4

https://github.com/sanger-pathogens/ariba

https://github.com/sanger-pathogens/ariba/blob/master/Dockerfile

fix quast 5.0.2

TravisCI is failing to build the quast 5.0.2 docker image, and I can't get it to build locally. See travis log here https://travis-ci.com/github/StaPH-B/docker-builds/builds/166582909

Seems to be an error during the python install script: Step 15/16 : RUN cd /quast-5.0.2 && /quast-5.0.2/setup.py install

[...]
Installing icarus.py script to /usr/local/bin
Installing quast.py script to /usr/local/bin

Installed /usr/local/lib/python2.7/dist-packages/quast-5.0.2-py2.7.egg
Processing dependencies for quast==5.0.2
Searching for simplejson
Reading https://pypi.python.org/simple/simplejson/
Download error on https://pypi.python.org/simple/simplejson/: [SSL: CERTIFICATE_VERIFY_FAILED] certificate verify failed (_ssl.c:590) -- Some packages may not be found!
Couldn't find index page for 'simplejson' (maybe misspelled?)
Scanning index of all packages (this may take a while)
Reading https://pypi.python.org/simple/
No local packages or download links found for simplejson
error: Could not find suitable distribution for Requirement.parse('simplejson')

Then after adding apt-get install python-simplejson, I get nearly the same error as TravisCI

Installed /usr/local/lib/python2.7/dist-packages/quast-5.0.2-py2.7.egg
Processing dependencies for quast==5.0.2
Searching for joblib
Reading https://pypi.python.org/simple/joblib/
Best match: joblib 0.15.1
Downloading https://files.pythonhosted.org/packages/57/d2/45a038246a0596fb73af64c07e95578764d0fd115ce67f6b41eb457eed39/joblib-0.15.1.tar.gz#sha256=61e49189c84b3c5d99a969d314853f4d1d263316cc694bec17548ebaa9c47b6e
Processing joblib-0.15.1.tar.gz
Writing /tmp/easy_install-261ygp/joblib-0.15.1/setup.cfg
Running joblib-0.15.1/setup.py -q bdist_egg --dist-dir /tmp/easy_install-261ygp/joblib-0.15.1/egg-dist-tmp-F56mw2
Traceback (most recent call last):
  File "/quast-5.0.2/setup.py", line 268, in <module>
    script_args=args,
  File "/usr/lib/python2.7/distutils/core.py", line 151, in setup
    dist.run_commands()
  File "/usr/lib/python2.7/distutils/dist.py", line 953, in run_commands
    self.run_command(cmd)
  File "/usr/lib/python2.7/distutils/dist.py", line 972, in run_command
    cmd_obj.run()
  File "/usr/lib/python2.7/dist-packages/setuptools/command/install.py", line 67, in run
    self.do_egg_install()
  File "/usr/lib/python2.7/dist-packages/setuptools/command/install.py", line 117, in do_egg_install
    cmd.run()
  File "/usr/lib/python2.7/dist-packages/setuptools/command/easy_install.py", line 414, in run
    self.easy_install(spec, not self.no_deps)
  File "/usr/lib/python2.7/dist-packages/setuptools/command/easy_install.py", line 644, in easy_install
    return self.install_item(None, spec, tmpdir, deps, True)
  File "/usr/lib/python2.7/dist-packages/setuptools/command/easy_install.py", line 695, in install_item
    self.process_distribution(spec, dist, deps)
  File "/usr/lib/python2.7/dist-packages/setuptools/command/easy_install.py", line 740, in process_distribution
    [requirement], self.local_index, self.easy_install
  File "/usr/lib/python2.7/dist-packages/pkg_resources/__init__.py", line 826, in resolve
    dist = best[req.key] = env.best_match(req, ws, installer)
  File "/usr/lib/python2.7/dist-packages/pkg_resources/__init__.py", line 1092, in best_match
    return self.obtain(req, installer)
  File "/usr/lib/python2.7/dist-packages/pkg_resources/__init__.py", line 1104, in obtain
    return installer(requirement)
  File "/usr/lib/python2.7/dist-packages/setuptools/command/easy_install.py", line 663, in easy_install
    return self.install_item(spec, dist.location, tmpdir, deps)
  File "/usr/lib/python2.7/dist-packages/setuptools/command/easy_install.py", line 693, in install_item
    dists = self.install_eggs(spec, download, tmpdir)
  File "/usr/lib/python2.7/dist-packages/setuptools/command/easy_install.py", line 873, in install_eggs
    return self.build_and_install(setup_script, setup_base)
  File "/usr/lib/python2.7/dist-packages/setuptools/command/easy_install.py", line 1101, in build_and_install
    self.run_setup(setup_script, setup_base, args)
  File "/usr/lib/python2.7/dist-packages/setuptools/command/easy_install.py", line 1087, in run_setup
    run_setup(setup_script, args)
  File "/usr/lib/python2.7/dist-packages/setuptools/sandbox.py", line 246, in run_setup
    raise
  File "/usr/lib/python2.7/contextlib.py", line 35, in __exit__
    self.gen.throw(type, value, traceback)
  File "/usr/lib/python2.7/dist-packages/setuptools/sandbox.py", line 195, in setup_context
    yield
  File "/usr/lib/python2.7/contextlib.py", line 35, in __exit__
    self.gen.throw(type, value, traceback)
  File "/usr/lib/python2.7/dist-packages/setuptools/sandbox.py", line 166, in save_modules
    saved_exc.resume()
  File "/usr/lib/python2.7/dist-packages/setuptools/sandbox.py", line 141, in resume
    six.reraise(type, exc, self._tb)
  File "/usr/lib/python2.7/dist-packages/setuptools/sandbox.py", line 154, in save_modules
    yield saved
  File "/usr/lib/python2.7/dist-packages/setuptools/sandbox.py", line 195, in setup_context
    yield
  File "/usr/lib/python2.7/dist-packages/setuptools/sandbox.py", line 243, in run_setup
    DirectorySandbox(setup_dir).run(runner)
  File "/usr/lib/python2.7/dist-packages/setuptools/sandbox.py", line 273, in run
    return func()
  File "/usr/lib/python2.7/dist-packages/setuptools/sandbox.py", line 242, in runner
    _execfile(setup_script, ns)
  File "/usr/lib/python2.7/dist-packages/setuptools/sandbox.py", line 46, in _execfile
    exec(code, globals, locals)
  File "/tmp/easy_install-261ygp/joblib-0.15.1/setup.py", line 6, in <module>
    # All Rights Reserved
  File "/tmp/easy_install-261ygp/joblib-0.15.1/joblib/__init__.py", line 113, in <module>
  File "/tmp/easy_install-261ygp/joblib-0.15.1/joblib/memory.py", line 274
    raise new_exc from exc
                     ^
SyntaxError: invalid syntax

I'm stumped on this one.

Adjust Trimmomatic container to be more easily callable

I did this in the Shovill dockerfile, to make trimmomatic callable from the commandline with simply
docker run staphb/trimmomatic:latest trimmomatic

# install trimmomatic
RUN mkdir trimmomatic &&\
  cd trimmomatic &&\
  wget http://www.usadellab.org/cms/uploads/supplementary/Trimmomatic/Trimmomatic-0.38.zip &&\
  unzip Trimmomatic-0.38.zip &&\
  rm -rf Trimmomatic-0.38.zip &&\
  chmod +x Trimmomatic-0.38/trimmomatic-0.38.jar &&\
  echo "#!/bin/bash" >> trimmomatic &&\
  echo "exec java -jar /trimmomatic/Trimmomatic-0.38/trimmomatic-0.38.jar """"$""@"""" " >> trimmomatic &&\
  chmod +x trimmomatic

saves us from having to do java -jar /path/to/trimmomatic.jar

Add a contributing.md file, move contributing instructions there

https://help.github.com/articles/setting-guidelines-for-repository-contributors/

Very simple example here: https://github.com/dib-lab/sourmash/blob/master/CONTRIBUTING.md

Would be good to move this section to the contributing.md: https://github.com/StaPH-B/docker-auto-builds#how-to-contribute-a-new-docker-image-or-alter-an-existing-image

add staramr 0.7.1

https://github.com/phac-nml/staramr/releases/tag/0.7.1

There's been a few releases since @stjacqrm made the first dockerfile for staramr.

Just putting this on the radar in case anyone wanted to upgrade versions.

hopefully the only change needed in the dockerfile is pip3 install staramr==0.7.1 🤞

add to docs or readme - note about singularity compatibility

add standalone bedtools docker image

bedtools is in a few other docker images, but it would be good to have a standalone container for bedtools.

apt-get versions of bedtools are usually old/out-of-date, but there are a few dockerfiles where bedtools is installed from source code in order to get a more recent version

TY @SESchmedes for the idea!

add Mash 2.2

There's a Mash 2.2.2 release, but there is no binary for it. Probably best to just add Mash 2.2 for now until the next release which includes a binary

https://github.com/marbl/Mash/releases/tag/v2.2

Issue running prokka 1.14.5 in singularity

Just hit an odd problem while running the prokka 1.14.5 docker image using singularity. Not sure if it's a PATH issue or what....

Singularity prokka.1.14.5.simg:/data> prokka --cpus 16 --outdir /data/prokka/ --force medaka/consensus.fasta --prefix bc04-4013
[13:39:31] This is prokka 1.14.5
[13:39:31] Written by Torsten Seemann <[email protected]>
[13:39:31] Homepage is https://github.com/tseemann/prokka
[13:39:31] Local time is Thu Jun 18 13:39:31 2020
[13:39:31] You are pjx8
[13:39:31] Operating system is linux
[13:39:31] You have BioPerl 1.006924
[13:39:31] System has 72 cores.
[13:39:31] Will use maximum of 16 cores.
[13:39:31] Annotating as >>> Bacteria <<<
[13:39:31] Generating locus_tag from 'medaka/consensus.fasta' contents.
[13:39:31] Setting --locustag GMHEDBAA from MD5 061edbaa40a6cb8a52d91b24d2fb3d33
[13:39:31] Re-using existing --outdir /data/prokka/
[13:39:31] Using filename prefix: bc04-4013.XXX
[13:39:31] Setting HMMER_NCPU=1
[13:39:31] Writing log to: /data/prokka//bc04-4013.log
[13:39:31] Command: /prokka-1.14.5/bin/prokka --cpus 16 --outdir /data/prokka/ --force medaka/consensus.fasta --prefix bc04-4013
[13:39:31] Appending to PATH: /prokka-1.14.5/bin/../binaries/linux
[13:39:31] Appending to PATH: /prokka-1.14.5/bin/../binaries/linux/../common
[13:39:31] Appending to PATH: /prokka-1.14.5/bin
[13:39:31] Looking for 'aragorn' - found /prokka-1.14.5/bin/../binaries/linux/aragorn
[13:39:31] Determined aragorn version is 001002 from 'ARAGORN v1.2.38 Dean Laslett'
[13:39:31] Looking for 'barrnap' - found /barrnap-0.9/bin/barrnap
[13:39:31] Determined barrnap version is 000009 from 'barrnap 0.9'
[13:39:31] Looking for 'blastp' - found /prokka-1.14.5/bin/../binaries/linux/blastp
[13:39:32] Determined blastp version is 002009 from 'blastp: 2.9.0+'
[13:39:32] Looking for 'cmpress' - found /prokka-1.14.5/bin/../binaries/linux/cmpress
[13:39:32] Determined cmpress version is 001001 from '# INFERNAL 1.1.2 (July 2016)'
[13:39:32] Looking for 'cmscan' - found /prokka-1.14.5/bin/../binaries/linux/cmscan
[13:39:32] Determined cmscan version is 001001 from '# INFERNAL 1.1.2 (July 2016)'
[13:39:32] Looking for 'egrep' - found /bin/egrep
[13:39:32] Looking for 'find' - found /usr/bin/find
[13:39:32] Looking for 'grep' - found /bin/grep
[13:39:32] Looking for 'hmmpress' - found /usr/bin/hmmpress
[13:39:32] Determined hmmpress version is 003001 from '# HMMER 3.1b2 (February 2015); http://hmmer.org/'
[13:39:32] Looking for 'hmmscan' - found /usr/bin/hmmscan
[13:39:32] Determined hmmscan version is 003001 from '# HMMER 3.1b2 (February 2015); http://hmmer.org/'
[13:39:32] Looking for 'java' - found /usr/bin/java
[13:39:32] Looking for 'makeblastdb' - found /prokka-1.14.5/bin/../binaries/linux/makeblastdb
[13:39:33] Determined makeblastdb version is 002009 from 'makeblastdb: 2.9.0+'
[13:39:33] Looking for 'minced' - found /prokka-1.14.5/bin/../binaries/linux/../common/minced
[13:39:33] Determined minced version is 002000 from 'minced 0.2.0'
[13:39:33] Looking for 'parallel' - found /prokka-1.14.5/bin/../binaries/linux/../common/parallel
[13:39:33] Determined parallel version is 20150122 from 'GNU parallel 20150122'
[13:39:33] Looking for 'prodigal' - found /prokka-1.14.5/bin/../binaries/linux/prodigal
[13:39:33] Determined prodigal version is 002006 from 'Prodigal V2.6.3: February, 2016'
[13:39:33] Looking for 'prokka-genbank_to_fasta_db' - found /prokka-1.14.5/bin/prokka-genbank_to_fasta_db
[13:39:33] Looking for 'sed' - found /bin/sed
[13:39:33] Looking for 'tbl2asn' - found /usr/bin/tbl2asn
[13:39:33] Determined tbl2asn version is 025008 from 'tbl2asn 25.8   arguments:'
[13:39:33] Using genetic code table 11.
[13:39:33] Loading and checking input file: medaka/consensus.fasta
[13:39:34] Wrote 4 contigs totalling 4254266 bp.
[13:39:34] Predicting tRNAs and tmRNAs
[13:39:34] Running: aragorn -l -gc11  -w \/data\/prokka\/\/bc04\-4013\.fna
[13:39:35] 1 tRNA-Ser c[10552,10641] 35 (gga)
[13:39:35] 2 tRNA-Arg c[14063,14139] 35 (cct)
[13:39:35] 3 tRNA-Arg c[17344,17420] 35 (acg)
[13:39:35] 4 tRNA-Ser c[17505,17595] 35 (gct)
[13:39:35] 5 tRNA-Ser c[17616,17706] 36 (tga)
[13:39:35] 6 tRNA-Ser c[18013,18103] 35 (gct)
[13:39:35] 7 tRNA-Ser c[18124,18214] 36 (tga)
[13:39:35] 8 tRNA-Ala c[27852,27927] 34 (tgc)
[13:39:35] 9 tRNA-Met c[27931,28007] 35 (cat)
[13:39:35] 10 tRNA-Glu [75830,75904] 34 (ttc)
[13:39:35] 11 tRNA-Val [75922,75997] 34 (tac)
[13:39:35] 12 tRNA-Asp [76007,76083] 35 (gtc)
[13:39:35] 13 tRNA-Thr [76088,76163] 34 (tgt)
[13:39:35] 14 tRNA-Glu [76169,76243] 34 (ttc)
[13:39:35] 15 tRNA-Val [76262,76337] 34 (tac)
[13:39:35] 16 tRNA-Asp [76345,76421] 35 (gtc)
[13:39:35] 17 tRNA-Glu [76479,76553] 34 (ttc)
[13:39:35] 18 tRNA-Val [76571,76646] 34 (tac)
[13:39:35] 19 tRNA-Asp [76656,76732] 35 (gtc)
[13:39:35] 20 tRNA-Thr [76737,76812] 34 (tgt)
[13:39:35] 21 tRNA-Pro c[133358,133433] 34 (tgg)
[13:39:35] 22 tRNA-Leu [154361,154449] 35 (taa)
[13:39:35] 23 tRNA-Met [154454,154529] 34 (cat)
[13:39:35] 24 tRNA-Met [154534,154610] 35 (cat)
[13:39:35] 25 tRNA-Leu [154642,154730] 35 (taa)
[13:39:35] 26 tRNA-Met [154735,154810] 34 (cat)
[13:39:35] 27 tRNA-Met [154864,154939] 34 (cat)
[13:39:35] 28 tRNA-Met [154950,155026] 35 (cat)
[13:39:35] 29 tRNA-Met [177873,177949] 35 (cat)
[13:39:35] 30 tRNA-Ala [177953,178029] 34 (tgc)
[13:39:35] 31 tRNA-Ile [179843,179919] 35 (gat)
[13:39:35] 32 tRNA-Asn [183111,183185] 33 (gtt)
[13:39:35] 33 tRNA-Asn [183213,183287] 33 (gtt)
[13:39:35] 34 tRNA-Gly [203926,204000] 33 (ccc)
[13:39:35] 35 tRNA-Thr [204019,204094] 34 (ggt)
[13:39:35] 36 tRNA-Trp [413153,413228] 34 (cca)
[13:39:35] 37 tRNA-Pro [484110,484185] 34 (tgg)
[13:39:35] 38 tRNA-Gly [484193,484266] 33 (tcc)
[13:39:35] 39 tRNA-Arg [484273,484349] 35 (tct)
[13:39:35] 40 tRNA-His [484357,484432] 34 (gtg)
[13:39:35] 41 tRNA-Gln [484437,484511] 33 (ttg)
[13:39:35] 42 tRNA-Lys [484515,484590] 34 (ttt)
[13:39:35] 43 tRNA-Leu [484606,484689] 35 (tag)
[13:39:35] 44 tRNA-Gly [484762,484836] 33 (gcc)
[13:39:35] 45 tRNA-Gly [484845,484918] 33 (tcc)
[13:39:35] 46 tRNA-Arg [484925,485001] 35 (tct)
[13:39:35] 47 tRNA-Lys [485007,485082] 34 (ctt)
[13:39:35] 48 tRNA-His [485098,485173] 34 (gtg)
[13:39:35] 49 tRNA-Gln [485178,485252] 33 (ttg)
[13:39:35] 50 tRNA-Lys [485256,485331] 34 (ttt)
[13:39:35] 51 tRNA-Leu [485347,485430] 35 (tag)
[13:39:35] 52 tRNA-Gly [485503,485577] 33 (gcc)
[13:39:35] 53 tRNA-Gly [485586,485659] 33 (tcc)
[13:39:35] 54 tRNA-Arg [485666,485742] 35 (tct)
[13:39:35] 55 tRNA-Lys [485748,485823] 34 (ctt)
[13:39:35] tRNA [485850,485926] is a pseudo/wacky gene - skipping.
[13:39:35] 57 tRNA-Gly [485956,486029] 33 (tcc)
[13:39:35] 58 tRNA-Arg [486054,486130] 35 (tcg)
[13:39:35] 59 tRNA-Val [593279,593354] 34 (tac)
[13:39:35] 60 tRNA-Asp [593360,593436] 35 (gtc)
[13:39:35] 61 tRNA-Phe [593440,593515] 34 (gaa)
[13:39:35] 62 tRNA-Gly [593520,593594] 33 (gcc)
[13:39:35] 63 tRNA-Cys [593604,593677] 33 (gca)
[13:39:35] 64 tRNA-Leu [709714,709800] 35 (caa)
[13:39:35] 65 tRNA-Leu [741135,741219] 35 (gag)
[13:39:35] 66 tRNA-SeC [775727,775823] 35 (tca)
[13:39:35] 67 tRNA-Glu c[3541372,3541446] 34 (ctc)
[13:39:35] 68 tRNA-Asn c[3617986,3618060] 33 (gtt)
[13:39:35] 69 tRNA-Ile c[3621268,3621344] 35 (gat)
[13:39:35] 70 tRNA-Ala c[3621350,3621425] 34 (tgc)
[13:39:35] 71 tmRNA* c[3831181,3831688] 340,420 AEKVLICSLESRLLGLKCTNNNFCI**
[13:39:35] tRNA/tmRNA c[3831181,3831688] is too big (>500bp) - skipping.
[13:39:35] 72 tmRNA c[3831594,3831948] 98,130 ANDNFALAA**
[13:39:35] 73 tRNA-Gln [3885596,3885670] 33 (ctg)
[13:39:35] 74 tRNA-Tyr c[3912022,3912106] 35 (gta)
[13:39:35] 75 tRNA-Thr c[3912112,3912187] 34 (tgt)
[13:39:35] 76 tRNA-Val c[3912205,3912280] 34 (tac)
[13:39:35] 77 tRNA-Tyr c[3912294,3912378] 35 (gta)
[13:39:35] 78 tRNA-Thr c[3912384,3912459] 34 (tgt)
[13:39:35] 79 tRNA-Cys c[4033292,4033365] 33 (gca)
[13:39:35] 80 tRNA-Phe c[4040816,4040891] 34 (gaa)
[13:39:35] 81 tRNA-Phe c[4047878,4047953] 34 (gaa)
[13:39:35] Found 79 tRNAs
[13:39:35] Predicting Ribosomal RNAs
[13:39:35] Running Barrnap with 16 threads
[13:39:37] 1 contig_1_segment0 28019 5S ribosomal RNA
[13:39:37] 2 contig_1_segment0 28227 23S ribosomal RNA
[13:39:37] 3 contig_1_segment0 31345 16S ribosomal RNA
[13:39:37] 4 contig_1_segment0 173027 16S ribosomal RNA
[13:39:37] 5 contig_1_segment0 174757 23S ribosomal RNA
[13:39:37] 6 contig_1_segment0 177751 5S ribosomal RNA
[13:39:37] 7 contig_1_segment0 178251 16S ribosomal RNA
[13:39:37] 8 contig_1_segment0 179995 23S ribosomal RNA
[13:39:37] 9 contig_1_segment0 182988 5S ribosomal RNA
[13:39:37] 10 contig_1_segment0 3618072 5S ribosomal RNA
[13:39:37] 11 contig_1_segment0 3618293 23S ribosomal RNA
[13:39:37] 12 contig_1_segment0 3621566 16S ribosomal RNA
[13:39:37] 13 contig_1_segment0 4034567 5S ribosomal RNA
[13:39:37] 14 contig_1_segment0 4034787 23S ribosomal RNA
[13:39:37] 15 contig_1_segment0 4037906 16S ribosomal RNA
[13:39:37] 16 contig_1_segment0 4040902 5S ribosomal RNA
[13:39:37] 17 contig_1_segment0 4041123 23S ribosomal RNA
[13:39:37] 18 contig_1_segment0 4044245 16S ribosomal RNA
[13:39:37] 19 contig_1_segment0 4047964 5S ribosomal RNA
[13:39:37] 20 contig_1_segment0 4048185 23S ribosomal RNA
[13:39:37] 21 contig_1_segment0 4051306 16S ribosomal RNA
[13:39:37] Found 21 rRNAs
[13:39:37] Skipping ncRNA search, enable with --rfam if desired.
[13:39:37] Total of 99 tRNA + rRNA features
[13:39:37] Searching for CRISPR repeats
[13:39:38] CRISPR1 contig_1_segment0 1725351 with 3 spacers
[13:39:38] CRISPR2 contig_1_segment0 1725765 with 5 spacers
[13:39:38] CRISPR3 contig_1_segment0 2640089 with 5 spacers
[13:39:38] CRISPR4 contig_7_segment0 156403 with 17 spacers
[13:39:38] CRISPR5 contig_7_segment0 157832 with 15 spacers
[13:39:38] Found 5 CRISPRs
[13:39:38] Predicting coding sequences
[13:39:38] Contigs total 4254266 bp, so using single mode
[13:39:38] Running: prodigal -i \/data\/prokka\/\/bc04\-4013\.fna -c -m -g 11 -p single -f sco -q
[13:39:48] Excluding CDS which overlaps existing RNA (rRNA) at contig_1_segment0:3618158..3618754 on + strand
[13:39:48] Excluding CDS which overlaps existing RNA (rRNA) at contig_1_segment0:3618693..3619328 on + strand
[13:39:48] Found 4532 CDS
[13:39:48] Connecting features back to sequences
[13:39:48] Not using genus-specific database. Try --usegenus to enable it.
[13:39:48] Annotating CDS, please be patient.
[13:39:48] Will use 16 CPUs for similarity searching.
[13:39:53] There are still 4532 unannotated CDS left (started with 4532)
[13:39:53] Will use blast to search against /prokka-1.14.5/db/kingdom/Bacteria/IS with 16 CPUs
[13:39:53] Running: cat \/data\/prokka\/\/bc04\-4013\.IS\.tmp\.45937\.faa | parallel --gnu --plain -j 16 --block 36506 --recstart '>' --pipe blastp -query - -db /prokka-1.14.5/db/kingdom/Bacteria/IS -evalue 1e-30 -qcov_hsp_perc 90 -num_threads 1 -num_descriptions 1 -num_alignments 1 -seg no > \/data\/prokka\/\/bc04\-4013\.IS\.tmp\.45937\.blast 2> /dev/null
[13:39:53] Could not run command: cat \/data\/prokka\/\/bc04\-4013\.IS\.tmp\.45937\.faa | parallel --gnu --plain -j 16 --block 36506 --recstart '>' --pipe blastp -query - -db /prokka-1.14.5/db/kingdom/Bacteria/IS -evalue 1e-30 -qcov_hsp_perc 90 -num_threads 1 -num_descriptions 1 -num_alignments 1 -seg no > \/data\/prokka\/\/bc04\-4013\.IS\.tmp\.45937\.blast 2> /dev/null

add SeqSero2 1.1.1

https://github.com/denglab/SeqSero2/releases/tag/v1.1.1

add kma

https://bitbucket.org/genomicepidemiology/kma/src/master/

nanoplot missing python dependency

Got this error when running the NanoPlot 1.27.0 container:

2020-03-17 16:37:51,632 Nanoplotter: orca not found, not creating static image of html. See https://github.com/plotly/orca
2020-03-17 16:37:51,633 Image generation requires the psutil package.

Install using pip:
    $ pip install psutil

Install using conda:
    $ conda install psutil
Traceback (most recent call last):
  File "/usr/local/lib/python3.5/dist-packages/nanoplotter/plot.py", line 60, in save_static
    pio.write_image(self.fig, self.path.replace('html', 'png'))
  File "/usr/local/lib/python3.5/dist-packages/plotly/io/_orca.py", line 1705, in write_image
    fig, format=format, scale=scale, width=width, height=height, validate=validate
  File "/usr/local/lib/python3.5/dist-packages/plotly/io/_orca.py", line 1482, in to_image
    ensure_server()
  File "/usr/local/lib/python3.5/dist-packages/plotly/io/_orca.py", line 1325, in ensure_server
    """
ValueError: Image generation requires the psutil package.

Install using pip:
    $ pip install psutil

Install using conda:
    $ conda install psutil

I'll update the 1.27.0 image and make a new image for the latest version available on pypi NanoPlot 1.29.0 https://pypi.org/project/NanoPlot/

add SPAdes 3.14.1

this one should be easy to make. I'll make at some point if no one else gets to it.

To do - make lyveSET container smaller, use less layers

I found that when I pull the lyveSET v2.0.1 image, it takes much longer to download than the other containers, and seems to have a lot of layers due to the dockerfile. Need to see if we can reduce the number of RUN commands in the dockerfile.

add SeqSero 1.1.0

https://github.com/denglab/SeqSero2/releases/tag/v1.1.0

Looks like there are a good bit of misidentification fixes among some new features

add bbtools to readme

...and any other programs we've added, but forgot to add to the table in the README and Program_licenses.md

add Flye 2.7

https://github.com/fenderglass/Flye/releases/tag/2.7

add cfsan-snp-pipeline to table in README

add links, badge, etc.

MAINTAINER labels are deprecated by docker

https://docs.docker.com/engine/reference/builder/#maintainer-deprecated

Need to change the maintainer labels into normal labels like so:
LABEL maintainer="Curtis Kapsak"
LABEL maintainer.email="[email protected]:

add skesa 2.4.0

https://github.com/ncbi/SKESA/releases/tag/2.4.0

Should be an easy one to tackle

Math::Round not included in lyve-set containers

It looks like the Math::Round perl module is missing from the lyve-set containers, should be a quick fix with cpanm.

I have no name!@4e6d93230ba0:/data$ perl -e "use Math::Round qw/nearest/;"
Can't locate Math/Round.pm in @INC (you may need to install the Math::Round module) (@INC contains: /etc/perl /usr/local/lib/x86_64-linux-gnu/perl/5.22.1 /usr/local/share/perl/5.22.1 /usr/lib/x86_64-linux-gnu/perl5/5.22 /usr/share/perl5 /usr/lib/x86_64-linux-gnu/perl/5.22 /usr/share/perl/5.22 /usr/local/lib/site_perl /usr/lib/x86_64-linux-gnu/perl-base .) at -e line 1.
BEGIN failed--compilation aborted at -e line 1.

Remove unneeded samtools from seqsero2

The seqsero2 Dockerfile installs 2 versions of Samtools, one installed with apt-get and the other (v1.9) installed manually.

The version installed by apt-get is very old, and not necessary to run SeqSero2. It should be removed with the next update.

Prokka image is missing barrnap for rRNA prediction

Just noticed that the prokka 1.13.3 image is missing barrnap. Prokka still runs, but cannot predict rRNAs.
https://github.com/tseemann/barrnap

Barrnap requires:

Perl 5.xx (core modules only)
nhmmer (part of HMMER 3.x)
bedtools >= 2.27.0

Need to include barrnap and its dependencies in dockerfile for Prokka:

# add hmmer to list of things to install with apt-get
RUN apt-get install hmmer gcc

# install bedtools, needs gcc to compile
RUN wget https://github.com/arq5x/bedtools2/releases/download/v2.27.1/bedtools-2.27.1.tar.gz &&\
    tar -xzf bedtools-2.27.1.tar.gz &&\
    rm bedtools-2.27.1.tar.gz &&\
    cd bedtools2/ &&\
    make

# install barrnap
RUN wget https://github.com/tseemann/barrnap/archive/0.9.tar.gz &&\
    tar -zxf 0.9.tar.gz &&\
    rm 0.9.tar.gz &&\
    
ENV PATH="$PATH:/prokka-1.13.3/bin:\
/bedtools2/bin:\
/barrnap-0.9/bin"

Also plan on bumping the dockerfile version to 2 in the dockerfile label

Prokka and it's dependencies make it quite a large image. One of our largest at ~2.1 GB

add colorid 0.1.4.3

https://github.com/hcdenbakker/colorid/releases/tag/v0.1.4.3

Pretty easy to make by downloading the precompiled linux binary, renaming it as colorid, and putting it in the PATH somewhere.

I'll take this one

add bcftools

Would be good to follow the style of the recent samtools install steps (samtools 1.10)

I imagine that the install steps will be very similar

https://github.com/StaPH-B/docker-builds/blob/master/samtools/1.10/Dockerfile

add abricate 1.0.0 dockerfile

https://github.com/tseemann/abricate/releases/tag/v0.9.9

Any takers? :)

add kraken2?

I started a dev branch for this, but didn't get very far....don't know if anyone is interested in this or not.

One minor issue is that there are no releases for kraken2, only pre-releases: https://github.com/DerrickWood/kraken2/releases

Update Abricate Databases Automatically

I was wondering if it is possible to have an abricate dockerfile that force updates the abricate databases every time the image is used in a job/script. I discussed this idea a few months back with Curtis and he added version 0.8.13-db. I notice that this does not work how I originally thought it might. The force update lines included in this version does not capture any changes beyond Aug-16 (when this dockerfile was added).

condense ENV layers into one for all dockerfiles

This:

# set PATH and perl local settings
ENV PATH="${PATH}:/mlst-2.19.0/bin:\
/ncbi-blast-2.9.0+/bin" \
    LC_ALL=C

uses one layer to set env variables, where as the below examples adds an unnecessary layer to the docker image:

ENV PATH="${PATH}:/mlst-2.17.6/bin:\
/ncbi-blast-2.9.0+/bin"

# set perl locale settings
ENV LC_ALL=C

This could be applied across all of our Dockerfiles that has more than one ENV layer

add legsta 0.5.1

@garfinjm just FYI Torsten released this yesterday. Not sure if you're interested in upgrading versions or not.

New dependency - any2fasta. This one is really easy to install:

# get any2fasta
RUN cd /usr/local/bin && \
  wget https://raw.githubusercontent.com/tseemann/any2fasta/master/any2fasta && \
  chmod +x any2fasta

# no need to update PATH since it's in /usr/local/bin

https://github.com/tseemann/legsta/releases/tag/v0.5.1

add latest version of Medaka

I started working on a dockerfile, but had issues with git lfs and the large files that are downloaded as part of the repo.

This one might be a PITA to get building/running correctly :)))))))))))))))))))))))))

add shigatyper

@AndrewLangvt whenever you get a chance 😃

add mlst 2.19.0

https://github.com/tseemann/mlst/releases/tag/v2.19.0

apparently it's what Jason wanted

add metaphlan3

I've never used metaphlan3, but it was requested by @SESchmedes

I think it would make a great addition to the repository

add NCBI AMRFinderPlus 3.8.4

https://github.com/ncbi/amr/releases/tag/amrfinder_v3.8.4

Looks like there have been significant changes, would be worth having a more recent version.

Create and add dockerfiles for Samtools and BWA

These tools are already in the Shovill docker image, but it would be nice to have a smaller, individual image for each

Will involve code that looks somewhat like this:

# I'm not sure what the dependencies are for bwa off the top of my head, but they should be minimal.

# install bwa (mem)
RUN mkdir bwa &&\
  cd bwa &&\
  wget https://github.com/lh3/bwa/releases/download/v0.7.17/bwa-0.7.17.tar.bz2 &&\
  tar -xjf bwa-0.7.17.tar.bz2 &&\
  rm bwa-0.7.17.tar.bz2 &&\
  cd bwa-0.7.17 &&\
  make

and

RUN apt-get update && apt-get install -y libncurses5-dev \
  libbz2-dev \
  liblzma-dev \
  libcurl4-gnutls-dev 
# there may be more, just need to look at the INSTALL file included in the samtools tarball

# install samtools 
RUN mkdir samtools &&\
  cd samtools &&\
  wget https://github.com/samtools/samtools/releases/download/1.9/samtools-1.9.tar.bz2 &&\
  tar -xjf samtools-1.9.tar.bz2 &&\
  rm samtools-1.9.tar.bz2 &&\
  cd samtools-1.9 &&\
  ./configure &&\
  make &&\
  make install

add SPAdes 3.14

http://cab.spbu.ru/software/spades/

3.14 isn't released on GitHub yet, but the linux binary is available ^^

add shovill 1.1.0

https://github.com/tseemann/shovill/releases/tag/v1.1.0

Need to remove mash and add kmc. Also use SPAdes 3.14.0.

Don't know much about kmc but here's some docs on it:
http://sun.aei.polsl.pl/REFRESH/index.php?page=projects&project=kmc&subpage=download

Probably will be easiest to use the binary instead of compiling, but here's the repo https://github.com/refresh-bio/KMC

linux executable/binary: https://github.com/refresh-bio/KMC/releases/download/v3.1.1/KMC3.1.1.linux.tar.gz

tbl2asn expires in all prokka images

affects the following dockerhub tags: 1.13 , 1.14.0, 1.14.0-cv2, 1.14.5, and latest (yes, all of them...)

[14:38:46] Looking for 'tbl2asn' - found /prokka-1.14.0/bin/../binaries/linux/tbl2asn
[tbl2asn] This copy of tbl2asn is more than a year old.  Please download the current version.
[14:38:46] Determined tbl2asn version is 25.7

Can't wait for Torsten to remove tbl2asn as a dependency

tseemann/prokka#453

add sratoolkit 2.10.8

Just realized that their dockerfiles are public: https://github.com/ncbi/sra-tools/tree/master/build/docker

A few different approaches for making the docker image, but it may be best to stick with the simplest as we did with sratools v2.9.2 https://github.com/StaPH-B/docker-builds/blob/master/sratoolkit/2.9.2/Dockerfile

download linux binary
put in PATH
done

add Samtools 1.10

https://github.com/samtools/samtools/releases/tag/1.10

Assigning to myself, but anyone that wants to take it on is welcome to.

I'm just referring to the dockerfile with only samtools, not any of the others that include samtools as a dependency