Add Galaxy Tool CI/CD pipeline configuration #1
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| name: Galaxy Tool CI/CD Pipeline | ||
| on: | ||
| push: | ||
| branches: [ main, master ] | ||
| pull_request: | ||
| branches: [ main, master ] | ||
| release: | ||
| types: [ published ] | ||
| tag: | ||
| types: [ created ] | ||
| jobs: | ||
| test: | ||
| runs-on: ubuntu-latest | ||
| steps: | ||
| - uses: actions/checkout@v3 | ||
| - name: Set up Python | ||
| uses: actions/setup-python@v4 | ||
| with: | ||
| python-version: '3.9' | ||
| - name: Create Planemo config | ||
| env: | ||
| USER: ${{ secrets.USER }} | ||
| KEY: ${{ secrets.KEY }} | ||
| EMAIL: ${{ secrets.EMAIL }} | ||
| PASS: ${{ secrets.PASS }} | ||
| run: | | ||
| mkdir -p $HOME/.planemo | ||
| cat > $HOME/.planemo.yml << EOF | ||
| shed_username: $USER # your ToolShed username | ||
| sheds: | ||
| toolshed: | ||
| key: $KEY # your ToolShed API key, under 'User > API Keys' | ||
| email: $EMAIL # your ToolShed email | ||
| password: $PASS # your ToolShed password | ||
| EOF | ||
| - name: Install Planemo | ||
| run: pip install planemo | ||
| - name: Lint Galaxy tool | ||
| run: planemo lint structural_validator.xml | ||
| - name: Test Galaxy tool | ||
| run: planemo test structural_validator.xml | ||
| deploy: | ||
| needs: test | ||
| if: startsWith(github.ref, 'refs/tags/v') | ||
| runs-on: ubuntu-latest | ||
| steps: | ||
| - uses: actions/checkout@v3 | ||
| - name: Set up Python | ||
| uses: actions/setup-python@v4 | ||
| with: | ||
| python-version: '3.9' | ||
| - name: Create Planemo config | ||
| env: | ||
| USER: ${{ secrets.USER }} | ||
| KEY: ${{ secrets.KEY }} | ||
| EMAIL: ${{ secrets.EMAIL }} | ||
| PASS: ${{ secrets.PASS }} | ||
| run: | | ||
| mkdir -p $HOME/.planemo | ||
| cat > $HOME/.planemo.yml << EOF | ||
| shed_username: $USER # your ToolShed username | ||
| sheds: | ||
| toolshed: | ||
| key: $KEY # your ToolShed API key, under 'User > API Keys' | ||
| email: $EMAIL # your ToolShed email | ||
| password: $PASS # your ToolShed password | ||
| EOF | ||
| - name: Install Planemo | ||
| run: pip install planemo | ||
| - name: Update Tool Shed | ||
| run: planemo shed_update --shed_target toolshed | ||
