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Merged
bgruening merged 5 commits into from
Mar 12, 2026
Merged

update CI #3896

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16231cc
update CI
bgruening Mar 12, 2026
7aca938
Update ci.yaml
bgruening Mar 12, 2026
86c577d
Update ci.yaml
bgruening Mar 12, 2026
e134189
Update ci.yaml
bgruening Mar 12, 2026
83004d4
Update ci.yaml
bgruening Mar 12, 2026
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11 changes: 4 additions & 7 deletions .github/workflows/ci.yaml
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Original file line number Diff line number Diff line change
Expand Up @@ -2,6 +2,7 @@ name: Build image
on: [push, pull_request]
env:
MULLED_NAMESPACE: biocontainers
MULLED_TOOL_UTIL_SOURCE: git+https://github.com/bgruening/galaxy.git@mulled_quay_enhancements#subdirectory=packages/tool_util
jobs:
build-and-test:
runs-on: ubuntu-latest
Expand All @@ -14,16 +15,12 @@ jobs:
- uses: actions/setup-python@v5
with:
python-version: ${{ matrix.python-version }}
- name: Install python dependencies
run: |
#python -m pip install git+https://git@github.com/galaxyproject/galaxy.git@dev#subdirectory=packages/util
#python -m pip install git+https://git@github.com/galaxyproject/galaxy.git@dev#subdirectory=packages/tool_util
python -m pip install galaxy-tool-util
- uses: astral-sh/setup-uv@v7
- run: docker --version
- run: docker info
- name: Build images
run: |
mulled-build-files --check-published --singularity --namespace $MULLED_NAMESPACE build-and-test ./combinations --verbose
uv run --with "$MULLED_TOOL_UTIL_SOURCE" python -m galaxy.tool_util.deps.mulled.mulled_build_files --check-published --singularity --namespace $MULLED_NAMESPACE build-and-test ./combinations --verbose
- name: Upload images (if pushed to master branch)
if: github.ref == 'refs/heads/master' && github.repository_owner == 'BioContainers'
env:
Expand All @@ -34,6 +31,6 @@ jobs:
ssh-keyscan -t rsa depot.galaxyproject.org >> ~/.ssh/known_hosts
ssh-agent -a $SSH_AUTH_SOCK > /dev/null
ssh-add - <<< "${{ secrets.ORVAL_KEY }}"
mulled-build-files --check-published --namespace $MULLED_NAMESPACE --oauth-token ${{ secrets.QUAY_OAUTH_TOKEN }} push ./combinations
uv run --with "$MULLED_TOOL_UTIL_SOURCE" python -m galaxy.tool_util.deps.mulled.mulled_build_files --check-published --namespace $MULLED_NAMESPACE --oauth-token ${{ secrets.QUAY_OAUTH_TOKEN }} push ./combinations
ls -l singularity_import
[ "$(ls -A singularity_import)" ] && echo 'uploading Singularity images' && scp singularity_import/*:* singularity@depot.galaxyproject.org:/srv/nginx/depot.galaxyproject.org/root/singularity/
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