AgentSkillsCN

galaxy-docker

维护和升级bgruening/docker-galaxy项目：提升Galaxy/Ubuntu版本、更新Ansible角色和调度器支持、调整启动/CI/测试，并管理CVMFS。

SKILL.md
--- frontmatter
name: galaxy-docker
description: Maintain and upgrade the bgruening/docker-galaxy project: bump Galaxy/Ubuntu versions, update Ansible roles and scheduler support, adjust startup/CI/tests, and manage CVMFS.

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.