Galaxy Docker skill

Galaxy Docker skill

Use this skill when working in the bgruening/​docker-galaxy repo to upgrade Galaxy releases or refresh runtime, scheduler, CVMFS, and CI behavior.

Quick start workflow

1. Define targets: Galaxy release, Ubuntu base, scheduler expectations (Slurm/​HTCondor), and CI scope.
2. Update build: galaxy/​Dockerfile (release ARGs, build stages, slurm-drmaa, uv usage, npm cleanup).
3. Update Ansible: galaxy/​ansible/​requirements.yml and playbooks (rabbitmq.yml, condor.yml, slurm.yml, nginx.yml, proftpd.yml).
4. Update runtime: galaxy/​startup.sh, galaxy/​startup2.sh, and galaxy/​ansible/​templates/​export_user_files.py.j2.
5. CVMFS changes: cvmfs/ sidecar + galaxy/​docker-compose.yaml + resolver config.
6. Tests/​CI: test/ scripts and .github/​workflows/ (buildx caches, test orchestration).
7. Run tests: Use both --privileged and non-privileged runs where relevant.

Repo map (files to touch)

• Build: galaxy/​Dockerfile
• Startup: galaxy/​startup.sh, galaxy/​startup2.sh
• Galaxy config export: galaxy/​ansible/​templates/​export_user_files.py.j2
• Ansible roles: galaxy/​ansible/​requirements.yml
• Services: galaxy/​ansible/​rabbitmq.yml, galaxy/​ansible/​condor.yml, galaxy/​ansible/​slurm.yml, galaxy/​ansible/​nginx.yml, galaxy/​ansible/​proftpd.yml
• Slurm config template: galaxy/​ansible/​templates/​configure_slurm.py.j2
• Container resolvers: galaxy/​ansible/​templates/​container_resolvers_conf.yml.j2
• CVMFS sidecar: cvmfs/ and galaxy/​docker-compose.yaml
• Tests: test/​bioblend/, test/​slurm/, test/​gridengine/, test/​cvmfs/, test/​container_resolvers_conf.ci.yml
• CI: .github/​workflows/​*.yml and .github/​workflows/​single.sh

Guardrails and expectations

• Keep Python installs on uv (build and runtime). Avoid pip install directly.
• Prefer buildx cache mounts in Dockerfiles and cache-to/​cache-from in GitHub Actions.
• Use --rm for test containers and clean up by name to avoid conflicts.
• If /​tmp fills up on CI, use TMPDIR=/​var/​tmp for heavy Docker tests.
• Use startup2 for richer diagnostics; keep startup.sh minimal.

CVMFS

• Privileged runs use full CVMFS client + autofs.
• Sidecar is optional via compose profile (cvmfs/ image).
• Container resolver config should include cached mulled paths on both CVMFS and /​export.
• See references/​upgrade-25.1.md for the exact sidecar design and tests.

Slurm

• Ensure Slurm works in containers without systemd/​cgroup v2 requirements.
• configure_slurm.py.j2 writes cgroup.conf with CgroupPlugin=disabled.
• Slurm-DRMAA is built from source when ABI mismatches exist (documented in references).

Tests (typical order)

• test/​slurm/​test.sh (set GALAXY_IMAGE=galaxy:test if needed)
• test/​gridengine/​test.sh (uses ephemeris container for wait)
• test/​bioblend/​test.sh
• test/​cvmfs/​test.sh (sidecar + mount propagation)
• startup2 sanity: docker run --rm --privileged ... /​usr/​bin/​startup2

References

• references/​upgrade-25.1.md for 25.1 upgrade decisions, pins, and pitfalls.