please provide apptainer howto

[EricDeveaud]

Hello,

docker is forbiden on our cluster. only apptainer (singularity) is allowed.

please provide a comprehensive howto run fantasion using apptainer.
test data, config.yaml and so on.

NB I was unable to find the documenttion for the config.yaml syntax

regards

Eric

[frapercan]

@EricDeveaud,

There are indeed many parameters, but as far as I know each one is at least mentioned somewhere in the documentation. The configuration file is also documented, and the CLI itself explains the available options (and how they map to the YAML / override it).

Also, we already provide SLURM + Apptainer examples in the docs (including complete job scripts and expected folder layout), which should cover most HPC setups with minor path/bind adjustments:

• https://fantasia.readthedocs.io/en/latest/deployment/cesga_job.html
• https://fantasia.readthedocs.io/en/latest/deployment/cesga_array_job.html
• https://fantasia.readthedocs.io/en/latest/appendix/slurm.html

Apptainer can pull Docker images directly on the compute node, and then you can run normally using a cached .sif:

• Reference image: docker://frapercan/fantasia:latest
  https://hub.docker.com/r/frapercan/fantasia

With the default configuration and by following the instructions, everything should run out-of-the-box on most reasonably up-to-date Linux machines. There are no major external requirements beyond Python, CUDA if you want GPU acceleration, and a few standard bioinformatics utilities included in the image.

Could you please take a look at the project docs/CLI help and the example configs first? I’d also strongly recommend running the pipeline locally on the provided test setup before attempting to deploy it on an HPC, so you can validate paths, permissions, and the expected outputs in a controlled environment.

If you have any specific question or a concrete issue (error log, config snippet, environment constraints), feel free to ask.

Regards.
Francisco Miguel