Monash Bioinformatics Containers
This is a repository for Dockerfiles and container images (mostly) packaging individual tools.
Your first port of call should usually by BioContainers (eg via the little 'containers|none' badge on a Bioconda package). There is a convenience script here
get_biocontainer.shthat 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 ${NAME} is the name:version of the image you want)
This will generate a *.sif file (eg guppy-gpu_6.3.8.sif). You can run the tool in the container with something like:
singularity exec guppy-gpu_6.3.8.sif gupper_basecaller --help
Adding new Dockerfiles, building images
Create a Dockerfile at dockerfiles/${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 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 to the main branch and check Actions to see if the image build was successful.