Update to 3.21 and add shutdown script #19
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| name: Build Bioconductor Extension Images | |
| on: | |
| push: | |
| branches: | |
| - devel | |
| - RELEASE_* | |
| paths: | |
| - 'extensions/**' | |
| workflow_dispatch: | |
| inputs: | |
| specific_extension: | |
| description: 'Build only a specific extension (folder name in extensions/)' | |
| required: false | |
| type: string | |
| schedule: | |
| - cron: '0 20 * * 5' # Run every Friday at 8PM UTC | |
| jobs: | |
| build-extensions: | |
| runs-on: ubuntu-latest | |
| steps: | |
| - uses: actions/checkout@v4 | |
| - name: Free root space | |
| uses: almahmoud/free-root-space@main | |
| with: | |
| verbose: true | |
| - name: Set up QEMU | |
| uses: docker/setup-qemu-action@v3 | |
| - name: Set up Docker Buildx | |
| uses: docker/setup-buildx-action@v3 | |
| - name: Login to GHCR | |
| uses: docker/login-action@v3 | |
| with: | |
| registry: ghcr.io | |
| username: ${{ github.actor }} | |
| password: ${{ secrets.GITHUB_TOKEN }} | |
| - name: Login to Dockerhub | |
| uses: docker/login-action@v3 | |
| with: | |
| username: ${{ secrets.DOCKER_USERNAME }} | |
| password: ${{ secrets.DOCKER_PASSWORD }} | |
| - name: Install dependencies | |
| run: | | |
| # Install yq for YAML parsing | |
| wget -qO /usr/local/bin/yq https://github.com/mikefarah/yq/releases/latest/download/yq_linux_amd64 | |
| chmod +x /usr/local/bin/yq | |
| - name: Process and build extensions | |
| run: | | |
| # Get branch name | |
| branch="${GITHUB_REF##*/}" | |
| # Convert repository owner to lowercase for Docker compatibility | |
| REPO_OWNER="${{ github.repository_owner }}" | |
| REPO_OWNER_LOWER=$(echo "$REPO_OWNER" | tr '[:upper:]' '[:lower:]') | |
| # Find extensions based on input or search all | |
| if [[ -n "${{ github.event.inputs.specific_extension }}" ]]; then | |
| if [[ ! -d "extensions/${{ github.event.inputs.specific_extension }}" ]]; then | |
| echo "::error::Extension directory not found: extensions/${{ github.event.inputs.specific_extension }}" | |
| exit 1 | |
| fi | |
| extension_files=$(find extensions/${{ github.event.inputs.specific_extension }} -name 'bioc-extension.yaml') | |
| echo "Building specific extension: ${{ github.event.inputs.specific_extension }}" | |
| else | |
| extension_files=$(find extensions -name 'bioc-extension.yaml' | sort) | |
| echo "Building all available extensions" | |
| fi | |
| # Process each extension file directly | |
| for ext_file in $extension_files; do | |
| ext_dir=$(dirname "$ext_file") | |
| ext_name=$(basename "$ext_dir") | |
| echo "Processing extension: $ext_name from $ext_file" | |
| # Check if Dockerfile exists | |
| if [[ ! -f "$ext_dir/Dockerfile" ]]; then | |
| echo "::warning::No Dockerfile found for extension $ext_name, skipping" | |
| continue | |
| fi | |
| # Parse YAML directly using yq | |
| outname=$(yq '.container.outname' "$ext_file" | tr '[:upper:]' '[:lower:]') | |
| base_image=$(yq '.container.base.image' "$ext_file" | tr '[:upper:]' '[:lower:]') | |
| # Handle tags | |
| tags_count=$(yq '.container.base.tag | length' "$ext_file") | |
| # Build for each tag (or branch name if no tags specified) | |
| if [[ $tags_count -eq 0 ]]; then | |
| tags=("$branch") | |
| else | |
| # Get all tags as an array | |
| tags=() | |
| for (( i=0; i<$tags_count; i++ )); do | |
| tags+=("$(yq ".container.base.tag[$i]" "$ext_file")") | |
| done | |
| fi | |
| # Build for each tag | |
| for tag in "${tags[@]}"; do | |
| echo "Building $outname:$tag from $base_image:$tag using Dockerfile in $ext_dir" | |
| # Build and push with lowercase names | |
| docker buildx build --platform linux/amd64 \ | |
| -t "ghcr.io/$REPO_OWNER_LOWER/$outname:$tag" \ | |
| -t "docker.io/$REPO_OWNER_LOWER/$outname:$tag" \ | |
| --build-arg BASE_IMAGE=$base_image \ | |
| --build-arg TAG=$tag \ | |
| --push \ | |
| "$ext_dir" | |
| build_result=$? | |
| if [ $build_result -ne 0 ]; then | |
| echo "::error::Failed to build $outname:$tag" | |
| exit $build_result | |
| fi | |
| echo "Successfully built and pushed $outname:$tag" | |
| done | |
| done |