execute miniWDL in a Docker container

Hello,

I’d like to run miniWDL itself in a Docker container.

This doesn’t work as Docker cannot bind the tmp volume when he is called by miniWDL :

docker run \
    --rm \
    --volume /var/run/docker.sock:/var/run/docker.sock \
    python:3.9.7-buster \
    bash -c '
    pip3 install miniwdl==1.4.1
    miniwdl run_self_test
    '

But when mounting the /tmp of my host on /tmp on the container side, it works:

docker run \
    --rm \
    --volume /tmp:/tmp \
    --volume /var/run/docker.sock:/var/run/docker.sock \
    python:3.9.7-buster \
    bash -c '
    pip3 install miniwdl==1.4.1
    miniwdl run_self_test
    '

I believe this is because of this docker-with-socket approach when miniWDL attempts to spin a container and bind volumes, that container is actually started by the daemon at the host level.

I’d like to use containers for miniWDL because it allows simple update everytime a new version of miniWDL comes out, but I’m open to cleaner solutions !

Thank you 😃

[dpark01]

Yes so the docker container (such as the Dockerfile in the gist above) is the space in which you execute miniwdl. That Dockerfile already sets environment variables that tell miniwdl to use udocker instead of docker. All your WDL tasks run inside udocker inside the docker – so no mounting docker sockets because you’re running udocker in userspace in the container.

No guarantees that it doesn’t crash the house.

[Melkaz]

Thanks for this detailed answer @mlin, I’ll think about it.