Dockerfile upgrade

[alexiswl]

• This comment contains a description of changes (with reason)
  • Use alpine:3.13 as base image for multi-arch build of dockerfile
    • Multiarch images can be built through docker buildx like so on a docker swarm running on multiple platforms:

      docker buildx build --platform linux/amd64,linux/arm64 --progress plain --push --tag ewels/multiqc:latest .

    • See docker buildx for more info
  • Maintain *-dev apk packages through installation of multiqc (for packages without pre-compiled binaries (i.e kiwisolver)
    • Although not an issue in the existing master branch of multiqc, the dragen-fastqc pr (Add new module to support DRAGEN-FastQC #1232) has kiwisolver as a requirement in setup.py. Kiwisolver currently has the following bug that means the build apk packages must be present at installation time of multiqc.
  • Added non-root USER for safer container invocation
    • See more info here
  • Moved from ENTRYPOINT to CMD for CWL conformance.
    • See more info here
• CHANGELOG.md has been updated

[ewels]

Thanks for this - looks good, couple of minor questions but otherwise no problems.

Out of curiosity, does the final image size end up being about the same?

Would also be nice to check for a couple of other bonus packages if we're building everything ourselves. For example, ps for Nextflow if it's not already there..

[ewels]

• Removed the matplotlib and numpy installations
• Removed the CMD completely
• Updated the docs

[ewels]

Hmm, I can't get it to build locally - not sure if I broke something or if it was problematic from the start (I'm on a MacBook M1, so docker can have issues sometimes).

Could try adding --prefer-binary from the docs you linked maybe? Bedtime for me..

[ewels]

Ok, it builds ok on GitPod 🎉

I's a fair bit bigger though, half the size again:

gitpod /workspace/MultiQC (dockerfile-update) $ docker image ls
REPOSITORY      TAG       IMAGE ID       CREATED          SIZE
multiqc/new     latest    c07c030d8fe4   24 seconds ago   336MB
ewels/multiqc   latest    6444a526efaa   3 months ago     204MB

Would be nice to try to trim it down a little more, though it's not super important.

It would be cool to set up automated multi-arch builds! This blog post makes it sound very doable..

[ewels]

It would also be nice to use a multi-stage build instead of the huge chained run commands.

[ewels]

ok, I messed around with a few ideas and ended up with #1836 which uses one of the official Python base images.

This still ends up bigger than the existing image, but by a smaller margin:

gitpod /workspace/MultiQC (dockerfile_python_base) $ docker image ls
REPOSITORY      TAG           IMAGE ID       CREATED         SIZE
ewels/multiqc   python-slim   ce6cc07ddaf2   7 minutes ago   277MB
ewels/multiqc   latest        6444a526efaa   3 months ago    204MB

I think I prefer this as going directly from Python feels a bit simpler and hopefully more robust. It's still a multi-arch base image, so can hopefully still set up multi-arch MultiQC images.

What do you think @alexiswl?

[alexiswl]

This looks great!

[ewels]

Multi-arch effort started in #1837