Update Trusted Tools #156
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| name: Update Trusted Tools | |
| on: | |
| pull_request: | |
| branches: | |
| - master | |
| workflow_dispatch: | |
| schedule: | |
| # Runs weekly, every Saturday at 02:00 UTC (alligned with off-peak hours) | |
| - cron: "0 2 * * SAT" | |
| jobs: | |
| build: | |
| runs-on: ubuntu-latest | |
| strategy: | |
| matrix: | |
| python-version: [3.8] | |
| steps: | |
| - name: Checkout | |
| uses: actions/checkout@v4 | |
| with: | |
| fetch-depth: 0 | |
| - name: Set up Python ${{ matrix.python-version }} | |
| uses: actions/setup-python@v5 | |
| with: | |
| python-version: ${{ matrix.python-version }} | |
| - name: Install dependencies | |
| run: | | |
| python -m pip install --upgrade pip | |
| if [ -f requirements.txt ]; then pip install -r requirements.txt; fi | |
| - name: Clone usegalaxy-eu-tools repository | |
| uses: actions/checkout@v4 | |
| with: | |
| repository: usegalaxy-eu/usegalaxy-eu-tools | |
| path: usegalaxy-eu-tools | |
| ref: master | |
| - name: Update tools_iuc.yaml from tools_iuc_eu.yaml | |
| run: | | |
| python3 process_yaml.py --merge_yaml --base_file tools_iuc.yaml --tools_yaml ${GITHUB_WORKSPACE}/usegalaxy-eu-tools/tools_iuc.yaml --out_file tools_iuc.yaml | |
| - name: Deleting usegalaxy-eu-tools repository | |
| run: rm -r usegalaxy-eu-tools | |
| - name: Perform linting | |
| run: | | |
| # Update the trusted tools. | |
| make fix -j $(nproc) | |
| # make lint -j $(nproc) | |
| make update_trusted -j $(nproc) | |
| - name: Show differences | |
| run: "git diff --stat" | |
| - name: Create Pull Request | |
| id: cpr | |
| uses: peter-evans/create-pull-request@v6 | |
| with: | |
| token: ${{ secrets.GITHUB_TOKEN }} | |
| commit-message: Update Galaxy tools | |
| title: "Automatic updating of the tools in tools-iuc.yaml" | |
| body: | | |
| This PR is automatically generated based on changes in the [usegalaxy.* tools](https://github.com/usegalaxy-eu/usegalaxy-eu-tools) tools | |
| and updates to our own tools and new tools added. | |
| Please verify if these changes are valid. | |
| labels: | | |
| automatic PR | |
| branch: tools-update | |
| base: master | |
| - name: Check output | |
| run: | | |
| echo "Pull Request Number - ${{ steps.cpr.outputs.pull-request-number }}" |