Migrate from Bioconda to container-based distribution for faster release cycles

[gordonkoehn]

Problem

The current Bioconda release cycle is too slow for rapid development workflows. Bioconda packages typically take several days to be released after a new version is tagged, creating friction when deploying updates to cluster environments.

Proposed Solution

Migrate to container-based distribution (Docker/Singularity/Apptainer) for cluster deployments, enabling same-day releases.

Tasks

• Create a Dockerfile for sr2silo
• Set up GitHub Actions workflow to build and push container images on release
• Choose container registry (GitHub Container Registry recommended: ghcr.io/cbg-ethz/sr2silo)
• Add Singularity/Apptainer compatibility (for HPC clusters)
• Update documentation with container usage instructions
• Decide on Bioconda future: deprecate or maintain in parallel?

Acceptance Criteria

• Container image is automatically built and published on each release
• Container works on HPC clusters via Singularity/Apptainer
• Documentation includes container installation and usage
• Release-to-deployment time is reduced to < 1 hour

Notes

• Keep Bioconda package for users who prefer conda ecosystems?
• Consider multi-arch builds (amd64, arm64)?