Dockerfile refinements and add Apptainer definition

[orbsmiv]

Brief overview of PR changes

Dockerfile:

• Uses a multi-stage build to minimise the layers and size of the final image. Also allows targeting of dev pkg installs.
• Replace apt (primarily designed for interactive use) with apt-get

Apptainer definition file:

• Broadly replicates Dockerfile process, also using a multi-stage build.
• The current recommendation to build a Docker image and then copy this to an HPC for converting to Apptainer is potentially problematic because...
  • Many HPCs are x86_64 whereas users may be building on more recent ARM-based Apple systems. It is possible to target a specific arch when building an image but this would need to be made clear in the documentation.
  • Not all features from a Docker image are portable to the Apptainer sif format.

Issues:

• triton dependency is only available as compiled x86_64 wheel on pypi.org so ARM-based builds aren't currently possible without moving the triton install into a separate compile step.

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[orbsmiv]

Ideally this would be split into a separate ENTRYPOINT and CMD sections, e.g.

ENTRYPOINT ["python3", "run_alphafold.py"]

CMD ["--help"]

It would then be possible to pass the arguments directly to the Docker command, e.g.

docker run -it alphafold3 --output_dir=/root/af_output

However, this would involve rewriting the documentation and is arguably less intuitive so I'm broadly replicating the current functionality.

[orbsmiv]

This takes a different approach to the existing Dockerfile (which copies the contents from the local repository) and instead allows the Docker build to act as a stand-alone process.

[mmtmn]

lgtm