Merge pull request #4 from jBeale23/main #26
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| name: QuantMS Containers Build and Sync | |
| on: | |
| push: | |
| branches: [ "main" ] | |
| pull_request: | |
| branches: [ "main" ] | |
| paths: | |
| - 'diann-*/Dockerfile' | |
| - 'relink-*/Dockerfile' | |
| - '.github/workflows/**' | |
| release: | |
| types: [published] | |
| workflow_dispatch: | |
| inputs: | |
| push_images: | |
| description: 'Push images to registry' | |
| required: false | |
| default: true | |
| type: 'boolean' | |
| push_release: | |
| description: 'Push as release version' | |
| required: false | |
| default: false | |
| type: boolean | |
| jobs: | |
| build-diann-2-1-0: | |
| name: Build and Push DiaNN 2.1.0 Docker Images | |
| runs-on: ubuntu-latest | |
| permissions: | |
| contents: read | |
| packages: write | |
| env: | |
| RETRY_TIMES: 3 | |
| RETRY_DELAY: 30 | |
| steps: | |
| - name: Checkout repository | |
| uses: actions/checkout@v4 | |
| - name: Set up Docker Buildx | |
| uses: docker/setup-buildx-action@v3 | |
| - name: Log in to GitHub Container Registry | |
| uses: docker/login-action@v3 | |
| with: | |
| registry: ghcr.io | |
| username: ${{ github.actor }} | |
| password: ${{ secrets.GHCR_TOKEN }} | |
| - name: Extract metadata for Docker | |
| id: meta | |
| uses: docker/metadata-action@v5 | |
| with: | |
| images: ghcr.io/bigbio/diann | |
| tags: | | |
| type=raw,value=latest,enable={{is_default_branch}} | |
| type=raw,value={{date 'YYYY.MM.DD'}} | |
| - name: Set date tag | |
| id: date | |
| run: echo "DATE_TAG=$(date +'%Y.%m.%d')" >> $GITHUB_OUTPUT | |
| - name: Build and Push DiaNN 2.1.0 image (Latest) | |
| uses: docker/build-push-action@v5 | |
| with: | |
| context: ./diann-2.1.0 | |
| push: ${{ (github.event.inputs.push_images == true || github.event.inputs.push_images == '') }} | |
| tags: | | |
| ghcr.io/bigbio/diann:2.1.0 | |
| ghcr.io/bigbio/diann:latest | |
| cache-from: type=gha | |
| cache-to: type=gha,mode=max | |
| provenance: false | |
| - name: Set up Singularity | |
| if: ${{ (github.event.inputs.push_images == true || github.event.inputs.push_images == '') }} | |
| uses: eWaterCycle/setup-singularity@v7 | |
| with: | |
| singularity-version: 3.8.7 | |
| - name: Pull Docker image for Singularity conversion | |
| if: ${{ (github.event.inputs.push_images == true || github.event.inputs.push_images == '') }} | |
| run: | | |
| # Pull the Docker image from GitHub Container Registry | |
| docker pull ghcr.io/bigbio/diann:2.1.0 | |
| # Save the Docker image to a tar file | |
| docker save ghcr.io/bigbio/diann:2.1.0 -o diann-2.1.0.tar | |
| - name: Convert Docker image to Singularity | |
| if: ${{ (github.event.inputs.push_images == true || github.event.inputs.push_images == '') }} | |
| run: | | |
| # Convert Docker tar to Singularity SIF | |
| singularity build diann-2.1.0.sif docker-archive://diann-2.1.0.tar | |
| # Verify the SIF file exists | |
| ls -la diann-2.1.0.sif | |
| - name: Login and Deploy Container | |
| if: (github.event_name != 'pull_request') | |
| env: | |
| IS_RELEASE: ${{ github.event_name == 'release' }} | |
| run: | | |
| echo ${{ secrets.GHCR_TOKEN }} | singularity remote login -u ${{ secrets.GHCR_USERNAME }} --password-stdin oras://ghcr.io | |
| # Push with version tag | |
| singularity push diann-2.1.0.sif oras://ghcr.io/bigbio/diann-sif:2.1.0 | |
| # If this is a release event, also tag as latest | |
| if [[ "${{ env.IS_RELEASE }}" == "true" || "${{ github.event_name }}" == "release" ]]; then | |
| singularity push diann-2.1.0.sif oras://ghcr.io/bigbio/diann-sif:latest | |
| fi | |
| - name: Notify on success | |
| if: success() | |
| run: | | |
| echo "::notice::Successfully built and pushed DiaNN 2.1.0 Docker and Singularity images to ghcr.io/bigbio" | |
| - name: Notify on failure | |
| if: failure() | |
| run: | | |
| echo "::error::Failed to build or push DiaNN 2.1.0 images. Check the logs for details." | |
| build-diann-1-8-1: | |
| name: Build and Push DiaNN 1.8.1 Docker Images | |
| runs-on: ubuntu-latest | |
| permissions: | |
| contents: read | |
| packages: write | |
| env: | |
| RETRY_TIMES: 3 | |
| RETRY_DELAY: 30 | |
| steps: | |
| - name: Checkout repository | |
| uses: actions/checkout@v4 | |
| - name: Set up Docker Buildx | |
| uses: docker/setup-buildx-action@v3 | |
| - name: Log in to GitHub Container Registry | |
| uses: docker/login-action@v3 | |
| with: | |
| registry: ghcr.io | |
| username: ${{ github.actor }} | |
| password: ${{ secrets.GHCR_TOKEN }} | |
| - name: Build and Push DiaNN 1.8.1 image | |
| uses: docker/build-push-action@v5 | |
| with: | |
| context: ./diann-1.8.1 | |
| push: ${{ (github.event.inputs.push_images == true || github.event.inputs.push_images == '') }} | |
| tags: | | |
| ghcr.io/bigbio/diann:1.8.1 | |
| cache-from: type=gha | |
| cache-to: type=gha,mode=max | |
| provenance: false | |
| - name: Set up Singularity | |
| if: ${{ (github.event.inputs.push_images == true || github.event.inputs.push_images == '') }} | |
| uses: eWaterCycle/setup-singularity@v7 | |
| with: | |
| singularity-version: 3.8.7 | |
| - name: Pull Docker image for Singularity conversion | |
| if: ${{ (github.event.inputs.push_images == true || github.event.inputs.push_images == '') }} | |
| run: | | |
| # Pull the Docker image from GitHub Container Registry | |
| docker pull ghcr.io/bigbio/diann:1.8.1 | |
| # Save the Docker image to a tar file | |
| docker save ghcr.io/bigbio/diann:1.8.1 -o diann-1.8.1.tar | |
| - name: Convert Docker image to Singularity | |
| if: ${{ (github.event.inputs.push_images == true || github.event.inputs.push_images == '') }} | |
| run: | | |
| # Convert Docker tar to Singularity SIF | |
| singularity build diann-1.8.1.sif docker-archive://diann-1.8.1.tar | |
| # Verify the SIF file exists | |
| ls -la diann-1.8.1.sif | |
| - name: Login and Deploy Container | |
| if: (github.event_name != 'pull_request') | |
| run: | | |
| echo ${{ secrets.GHCR_TOKEN }} | singularity remote login -u ${{ secrets.GHCR_USERNAME }} --password-stdin oras://ghcr.io | |
| # Push with version tag | |
| singularity push diann-1.8.1.sif oras://ghcr.io/bigbio/diann-sif:1.8.1 | |
| - name: Notify on success | |
| if: success() | |
| run: | | |
| echo "::notice::Successfully built and pushed DiaNN 1.8.1 Docker and Singularity images to ghcr.io/bigbio" | |
| - name: Notify on failure | |
| if: failure() | |
| run: | | |
| echo "::error::Failed to build or push DiaNN 1.8.1 images. Check the logs for details." | |
| build-relink-1-0-0: | |
| name: Build and Push Relink 1.0.0 Docker Images | |
| runs-on: ubuntu-latest | |
| permissions: | |
| contents: read | |
| packages: write | |
| env: | |
| RETRY_TIMES: 3 | |
| RETRY_DELAY: 30 | |
| steps: | |
| - name: Checkout repository | |
| uses: actions/checkout@v4 | |
| - name: Set up Docker Buildx | |
| uses: docker/setup-buildx-action@v3 | |
| - name: Log in to GitHub Container Registry | |
| uses: docker/login-action@v3 | |
| with: | |
| registry: ghcr.io | |
| username: ${{ github.actor }} | |
| password: ${{ secrets.GHCR_TOKEN }} | |
| - name: Build and Push Relink 1.0.0 image | |
| uses: docker/build-push-action@v5 | |
| with: | |
| context: ./relink-1.0.0 | |
| push: ${{ (github.event.inputs.push_images == true || github.event.inputs.push_images == '') }} | |
| tags: | | |
| ghcr.io/bigbio/relink:1.0.0 | |
| ghcr.io/bigbio/relink:latest | |
| cache-from: type=gha | |
| cache-to: type=gha,mode=max | |
| provenance: false | |
| - name: Set up Singularity | |
| if: ${{ (github.event.inputs.push_images == true || github.event.inputs.push_images == '') }} | |
| uses: eWaterCycle/setup-singularity@v7 | |
| with: | |
| singularity-version: 3.8.7 | |
| - name: Pull Docker image for Singularity conversion | |
| if: ${{ (github.event.inputs.push_images == true || github.event.inputs.push_images == '') }} | |
| run: | | |
| # Pull the Docker image from GitHub Container Registry | |
| docker pull ghcr.io/bigbio/relink:1.0.0 | |
| # Save the Docker image to a tar file | |
| docker save ghcr.io/bigbio/relink:1.0.0 -o relink-1.0.0.tar | |
| - name: Convert Docker image to Singularity | |
| if: ${{ (github.event.inputs.push_images == true || github.event.inputs.push_images == '') }} | |
| run: | | |
| # Convert Docker tar to Singularity SIF | |
| singularity build relink-1.0.0.sif docker-archive://relink-1.0.0.tar | |
| # Verify the SIF file exists | |
| ls -la relink-1.0.0.sif | |
| - name: Login and Deploy Container | |
| if: (github.event_name != 'pull_request') | |
| env: | |
| IS_RELEASE: ${{ github.event_name == 'release' }} | |
| run: | | |
| echo ${{ secrets.GHCR_TOKEN }} | singularity remote login -u ${{ secrets.GHCR_USERNAME }} --password-stdin oras://ghcr.io | |
| # Push with version tag | |
| singularity push relink-1.0.0.sif oras://ghcr.io/bigbio/relink-sif:1.0.0 | |
| # If this is a release event, also tag as latest | |
| if [[ "${{ env.IS_RELEASE }}" == "true" || "${{ github.event_name }}" == "release" ]]; then | |
| singularity push relink-1.0.0.sif oras://ghcr.io/bigbio/relink-sif:latest | |
| fi | |
| - name: Notify on success | |
| if: success() | |
| run: | | |
| echo "::notice::Successfully built and pushed Relink 1.0.0 Docker and Singularity images to ghcr.io/bigbio" | |
| - name: Notify on failure | |
| if: failure() | |
| run: | | |
| echo "::error::Failed to build or push Relink 1.0.0 images. Check the logs for details." | |
| sync-openms: | |
| name: Sync OpenMS Containers | |
| needs: [build-diann-2-1-0, build-diann-1-8-1, build-relink-1-0-0] | |
| runs-on: ubuntu-latest | |
| permissions: | |
| contents: read | |
| packages: write | |
| env: | |
| OPENMS_VERSION: "2025.04.14" # Manually defined version for OpenMS | |
| steps: | |
| - name: Checkout repository | |
| uses: actions/checkout@v4 | |
| - name: Set up Docker Buildx | |
| uses: docker/setup-buildx-action@v3 | |
| - name: Log in to GitHub Container Registry | |
| uses: docker/login-action@v3 | |
| with: | |
| registry: ghcr.io | |
| username: ${{ github.actor }} | |
| password: ${{ secrets.GHCR_TOKEN }} | |
| - name: Pull OpenMS Docker container | |
| id: pull_docker | |
| uses: nick-fields/retry@v2 | |
| with: | |
| timeout_minutes: 10 | |
| max_attempts: 3 | |
| retry_wait_seconds: 30 | |
| command: docker pull ghcr.io/openms/openms-tools-thirdparty:latest | |
| - name: Tag and push OpenMS Docker container | |
| if: steps.pull_docker.outcome == 'success' | |
| run: | | |
| # Set container names using the fixed version | |
| SOURCE_CONTAINER="ghcr.io/openms/openms-tools-thirdparty:latest" | |
| TARGET_CONTAINER="ghcr.io/bigbio/openms-tools-thirdparty:${{ env.OPENMS_VERSION }}" | |
| echo "Tagging as $TARGET_CONTAINER" | |
| docker tag $SOURCE_CONTAINER $TARGET_CONTAINER | |
| echo "Pushing $TARGET_CONTAINER" | |
| docker push $TARGET_CONTAINER || { | |
| echo "Failed to push $TARGET_CONTAINER, retrying..." | |
| sleep 30 | |
| docker push $TARGET_CONTAINER | |
| } | |
| # If this is a release push or a GitHub release event, also tag as latest | |
| if [[ "${{ github.event.inputs.push_release }}" == "true" || "${{ github.event_name }}" == "release" ]]; then | |
| LATEST_IMAGE="ghcr.io/bigbio/openms-tools-thirdparty:latest" | |
| docker tag $SOURCE_CONTAINER $LATEST_IMAGE | |
| docker push $LATEST_IMAGE || { | |
| echo "Failed to push $LATEST_IMAGE, retrying..." | |
| sleep 30 | |
| docker push $LATEST_IMAGE | |
| } | |
| echo "Pushed release version as $LATEST_IMAGE" | |
| fi | |
| - name: Set up Singularity | |
| if: success() | |
| uses: eWaterCycle/setup-singularity@v7 | |
| with: | |
| singularity-version: 3.8.7 | |
| - name: Configure Singularity for GitHub Container Registry | |
| if: success() | |
| run: | | |
| # Create Singularity remote endpoint for GitHub Container Registry | |
| singularity remote add --no-login GithubContainer oras://ghcr.io | |
| # Login to GitHub Container Registry | |
| echo "${{ secrets.GHCR_TOKEN }}" | singularity remote login -u ${{ secrets.GHCR_USERNAME }} --password-stdin GithubContainer | |
| - name: Pull OpenMS SIF container | |
| id: pull_sif | |
| if: success() | |
| uses: nick-fields/retry@v2 | |
| with: | |
| timeout_minutes: 15 | |
| max_attempts: 3 | |
| retry_wait_seconds: 60 | |
| command: singularity pull --force openms-tools-thirdparty.sif oras://ghcr.io/openms/openms-tools-thirdparty-sif:latest | |
| - name: Login and Push OpenMS SIF container | |
| if: steps.pull_sif.outcome == 'success' | |
| env: | |
| keepgoing: true | |
| run: | | |
| # Login to GitHub Container Registry | |
| echo ${{ secrets.GHCR_TOKEN }} | singularity remote login -u ${{ secrets.GHCR_USERNAME }} --password-stdin oras://ghcr.io | |
| # Set SIF paths and push with version tag | |
| echo "Pushing OpenMS SIF with version tag" | |
| singularity push openms-tools-thirdparty.sif oras://ghcr.io/bigbio/openms-tools-thirdparty-sif:${{ env.OPENMS_VERSION }} || { | |
| echo "Failed to push with version tag, retrying..." | |
| sleep 60 | |
| singularity push openms-tools-thirdparty.sif oras://ghcr.io/bigbio/openms-tools-thirdparty-sif:${{ env.OPENMS_VERSION }} | |
| } | |
| # If this is a release push or a GitHub release event, also tag as latest | |
| if [[ "${{ github.event.inputs.push_release }}" == "true" || "${{ github.event_name }}" == "release" ]]; then | |
| echo "Pushing OpenMS SIF as latest" | |
| singularity push openms-tools-thirdparty.sif oras://ghcr.io/bigbio/openms-tools-thirdparty-sif:latest || { | |
| echo "Failed to push as latest, retrying..." | |
| sleep 60 | |
| singularity push openms-tools-thirdparty.sif oras://ghcr.io/bigbio/openms-tools-thirdparty-sif:latest | |
| } | |
| fi | |
| - name: Notify on success | |
| if: success() | |
| run: | | |
| echo "::notice::Successfully synced OpenMS containers to BigBio repositories" | |
| - name: Notify on failure | |
| if: failure() | |
| run: | | |
| echo "::error::Failed to sync OpenMS containers. Check the logs for details." |