This directory has scripts to (locally) build and test the Docker/Podman container.

The build-containers.sh script successively builds 4 images, using podman if installed, else docker.

• step 0: base Conda with only Snakemake added (= envs/hamronization_workflow.yaml)
• step 1: step 0 with on top all tools, installed by Snakemake (= envs/*.yaml)
• step 2: step 1 with on top the binary deps (minor step)
• step 3: step 2 with on top the databases (massive final step)

The images all have the same Dockerfile, except that an additional RUN step is added in each. This so that if the build fails at some step, we have the successful image from the prior step for debugging the failing step.

We could have also used Docker's FROM ... to do this, but the idea is that once the build is stable, we can ditch the steps and just have Dockerfile (i.e. the final image).

OTOH, as long as the Dockerfiles are identical up to the penultimate step, they share all their image layers, so none of the earlier steps consume any disc space or build time.

The run-*.sh scripts are convenience wrappers for podman|docker run ..., with the necessary mounts set up.

The test-final.sh script runs the final container against the test data in ../test, writing results and logs to a temporary directory in /tmp.