Monash Bioinformatics Containers

This is a repository for Dockerfiles and container images (mostly) packaging individual tools.

Your first port of call should usually be the Galaxy Container Depot or BioContainers (eg via the little 'containers|none' badge on a Bioconda package). There is a convenience script here get_biocontainer.sh that will grab the latest Singularity image for a Bioconda package. But sometimes we need our own custom containers.

Quickstart - using an image

Find the image and version you want under Packages.

Run:

NAME=guppy-gpu:6.3.8

singularity pull docker://ghcr.io/monashbioinformaticsplatform/containers/${NAME}

(where ${NAME} is the name:version of the image you want)

This will generate a *.sif file (eg guppy-gpu_6.3.8.sif). You can run the tool in the container with something like:

singularity exec guppy-gpu_6.3.8.sif gupper_basecaller --help

Adding new Dockerfiles, building images

Create a new branch:

git branch myNewContainer
git checkout myNewContainer

Create a Dockerfile at dockerfiles/${tool}/${version}/Dockerfile. (where ${tool} and version might be guppy-gpu and 6.3.8)

Ideally also add a dockerfiles/${tool}/${version}/README.md

Test your docker build -t myNewContainer:1.0 . locally.

Edit the matrix: section at the top of .github/workflows/docker-build-push.yml to add the details for your new tool (follow the established pattern).

Commit and push your branch, then check Actions to see if the image build was successful (all branches automatically build).

If your build is successful, PR / squash and merge into the main branch (we prefer squashing before merging into the main branch to keep the main commit history cleaner).