Minimal comments on Podman/Docker support

[marcodelapierre]

Hi!
I have just run some quick tests with Podman on Ubuntu 18, and they have worked well!

I just have a couple of minimal comments on the modulefile layout (had a look at LUA modules);
I have used my usual biocontainers/samtools:v1.9-4-deb_cv1 as a test.

• Some typos in help screen -- apply also for Docker

  • -v ${PWD} -w ${PWD} is defined also for <tool>-shell and <tool>-exec but not documented

  • --entrypoint /bin/sh is defined for <tool>-shell but not documented

  • for <tool>-exec, help says --entrypoint /bin/sh, but instead it should be --entrypoint ""

  • for aliases, e.g. :

     - samtools:
           podman run --rm -it --entrypoint /usr/bin/samtools --env-file /home/ubuntu/shpc-v0027/modules/biocontainers/samtools/v1.9-4-deb_cv1/99-shpc.sh  -v ${PWD} -w ${PWD} <container> ""
    

    Instead of <container> "", the very last bit of this snippet should be <container> "$@".

Only for Podman:

• I notice that the variables here are called DOCKER_OPTS and DOCKER_COMMAND_OPTS; shouldn't they contain PODMAN instead?

PS: the final implementation you used for entrypoint is the cleanest possible, love it!

[vsoch]

Fixed! (Will come in PR soon). For the environment variable names, since Podman and Docker share the same template file (and the same class base) and Podman is known to be "a shoe in for Docker" - its easier to maintain to just use a standard set of environment variables that both share. As an alternative, we could call them something more generic? It could be something like OCI_OPTS and OCI_COMMAND_OPTS but I thought that Docker was a more suitable name. What do you think?

[marcodelapierre]

Podman is known to be "a shoe in for Docker" - its easier to maintain to just use a standard set of environment variables that both share

you're right, makes sense. I was wondering then ... instead of using DOCKER for Podman, too ... how about using PODMAN for Docker ...? too daring ...? after all SHPC is more focused on HPC, Docker is kind of a free add-on feature