bio-ansible can be used to build a container with a subset of tools.
To build using your current clone of bio-ansible (eg for testing):
docker build -t bioansible -f docker/Dockerfile-local .Several of the slower steps (r_core, r_extras, blast) are executed as
separate RUN commands so that these get cached as intermediate Docker layers.
This allows a single task to be tested quickly (by tag) by adding it at the
end of the Dockerfile-local. If you want to run all steps from scratch, run
with the --no-cache option:
docker build --no-cache -t bioansible:latest -f docker/Dockerfile-local .To test a specific tag(s) in the bio.yml playbook (eg hisat2 and muscle):
docker build --build-arg TASK_TAGS=hisat2,muscle -t bioansible -f docker/Dockerfile-bio-tags .To build a production image by pulling the master branch:
docker build -t bioansible:latest -f docker/Dockerfile-repo .We also have a Dockerfile for building a lighter-weight container than only runs the RNAsik pipeline:
docker build -t rnasik:latest -f docker/Dockerfile-rnasik .
docker run -t rnasik:latest -help