Claude-skill-registry galaxy-docker

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.

install

source · Clone the upstream repo

git clone https://github.com/majiayu000/claude-skill-registry

Claude Code · Install into ~/.claude/skills/

T=$(mktemp -d) && git clone --depth=1 https://github.com/majiayu000/claude-skill-registry "$T" && mkdir -p ~/.claude/skills && cp -r "$T/skills/data/galaxy-docker" ~/.claude/skills/majiayu000-claude-skill-registry-galaxy-docker && rm -rf "$T"

manifest: skills/data/galaxy-docker/SKILL.md

source content

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

Define targets: Galaxy release, Ubuntu base, scheduler expectations (Slurm/HTCondor), and CI scope.
Update build:
```
galaxy/Dockerfile
```
(release ARGs, build stages, slurm-drmaa, uv usage, npm cleanup).

Update Ansible:

galaxy/ansible/requirements.yml

and playbooks (

rabbitmq.yml

condor.yml

slurm.yml

nginx.yml

proftpd.yml

Update runtime:

galaxy/startup.sh

galaxy/startup2.sh

, and

galaxy/ansible/templates/export_user_files.py.j2

CVMFS changes:
```
cvmfs/
```
sidecar +
```
galaxy/docker-compose.yaml
```
+ resolver config.
Tests/CI:
```
test/
```
scripts and
```
.github/workflows/
```
(buildx caches, test orchestration).
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.