(view the versioned images on Docker Hub)

Genetics tools Docker image

This image includes common tools for manipulating/QCing common formats of genetic data, and relatedness (GRM/kinship matrices) and ancestry (PC) estimation. Images are built and pushed when the base image is updated.

Included software

• PLINK v1.9 and v2.0
• VCFtools
• BCFtools
• METAL
• Metasoft and ForestPMPlot
• R packages
  • GENESIS and dependencies (gdsfmt, SeqArray, SeqVarTools, etc.)
  • Tidyverse packages (dplyr, tidyr, ggplot2, etc.)
  • plinkFile
• Snakemake

Software is installed with micromamba where possible. See the Dockerfile for details.

Usage

The primary use-case for this image, and the reason it uses snakemake/snakemake as its base image, is to be invoked from a Snakemake workflow. Add the line

container: "docker://broome/genetics-tools"

near the top of your snakefile (to run all rules in this environment), or within a rule definition (to run only for a specific rule); and use the --use-apptainer flag when invoking snakemake.

You can also do docker run broome/genetics-tools. Refer to the docker documentation for executing a specific command or script with docker run.

Building and versioning

This image inherits the <MAJOR>.<MINOR>.<PATCH> version from the snakemake/snakemake base image. Additionally,

• versions of this image are appended with .<RELEASE>. The first release will be appended with .0 e.g. v9.14.5.0, the first update will be tagged with v9.14.5.1, etc.
• The most up-to-date versions of this image will also be tagged with the corresponding major, minor and patch versions, and stable and latest, e.g. v9.14.5.1 from the previous examplewould also be tagged stable, latest, v9.14.5, v9.14 and v9.
  • Image v9.13.7 also still has the tag v9.13 as it was the last image built from a v9.13 image.

If your analysis requires a stable and persistent environment, only refer to the <MAJOR>.<MINOR>.<PATCH>.<RELEASE> tags. These are the only tags that will persistently point to a specific image.

Images are built automatically via GitHub Actions when a new version of snakemake/snakemake is released, to ensure up-to-date images and images with each version of Snakemake are available and so the provenance of the images is verifiable. See logs from the GitHub repo to verify, or build your own image with

git clone git@github.com:broomej/genetics-tools-docker.git
cd genetics-tools-dockers
docker build -t genetics-tools:local .

A note on the image size

Snakemake requires a lot of dependencies, and the base image is > 900MB as of this writing. This image adds additional software and dependencies and is around 1.6GB.

I had started to build smaller, application-focused images with just PLINK, VCFTools or BCFTools, but my workflow requires Snakemake to be installed inside of the container. That meant I had four > 1GB images instead of one 1.6GB image. If these smaller containers would be useful for you, or have ideas about how to keep the image size down, open an issue in the GitHub repo.