update samtools version + update actions + clean up (#19) #39
Workflow file for this run
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| name: Docker | |
| on: | |
| push: | |
| # Publish `main` as Docker `latest` image. | |
| branches: | |
| - main | |
| # Publish `v1.2.3` tags as releases. | |
| tags: | |
| - v* | |
| # Run tests for any PRs. | |
| pull_request: | |
| env: | |
| IMAGE_NAME: bioinformatics | |
| jobs: | |
| # Push image to GitHub Packages. | |
| # See also https://docs.docker.com/docker-hub/builds/ | |
| push: | |
| runs-on: ubuntu-latest | |
| if: github.event_name == 'push' | |
| steps: | |
| - uses: actions/checkout@v4 | |
| with: | |
| lfs: true | |
| - name: Checkout LFS objects | |
| run: git lfs checkout | |
| - name: Set Date | |
| run: echo "TODAYS_DATE=$(date +'%Y%m%d')" >> $GITHUB_ENV | |
| - name: Prepare tags | |
| id: prep | |
| run: | | |
| # Docker Registries | |
| GHCR_IMAGE_NAME="ghcr.io/${{ github.repository_owner }}/${{ env.IMAGE_NAME }}" | |
| DOCKER_HUB_IMAGE_NAME="${{ github.repository_owner }}/${{ env.IMAGE_NAME }}" | |
| TAGS="" | |
| FINAL_TAGS="" | |
| # Identify Tags | |
| # Type of tags: | |
| # 1. Scenario 1 - x.y.z.patchedYYYYMMDD | |
| # 2. Scenario 2 - Semver Tags x.y.z | |
| # 3. Scenario 3 - Main Branch | |
| # 4. Scenario 4 - Branches | |
| if [[ $GITHUB_REF == refs/tags/* ]]; then | |
| # If this is a tag push, use the tag name (stripping 'refs/tags/') | |
| FULL_TAG=${GITHUB_REF#refs/tags/} | |
| # Remove leading 'v' from tag if present | |
| if [[ $FULL_TAG == v* ]]; then | |
| FULL_TAG=${FULL_TAG#v} | |
| fi | |
| # Scenario 1 - x.y.z.patchedYYYYMMDD | |
| # Tags | |
| # 1. x.y.z.patchedYYYYMMDD | |
| # 2. x.y.z | |
| # 3. x.y | |
| # 4. x | |
| if [[ $FULL_TAG =~ (.*)\.patched[0-9]+ ]]; then | |
| # Extract the base tag without the .patched segment | |
| BASE_TAG=${BASH_REMATCH[1]} | |
| if [[ $BASE_TAG =~ ^([0-9]+)\.([0-9]+)\.([0-9]+)$ ]]; then | |
| MAJOR=${BASH_REMATCH[1]} | |
| MINOR=${BASH_REMATCH[2]} | |
| PATCH=${BASH_REMATCH[3]} | |
| TAGS="$FULL_TAG,$BASE_TAG,$MAJOR.$MINOR.$PATCH,$MAJOR.$MINOR,$MAJOR" | |
| fi | |
| else | |
| # Scenario 2 - Semver Tags x.y.z | |
| # Tags | |
| # 1. x.y.z | |
| # 2. x.y | |
| # 3. x | |
| if [[ $FULL_TAG =~ ^([0-9]+)\.([0-9]+)\.([0-9]+)$ ]]; then | |
| MAJOR=${BASH_REMATCH[1]} | |
| MINOR=${BASH_REMATCH[2]} | |
| PATCH=${BASH_REMATCH[3]} | |
| TAGS="$MAJOR.$MINOR.$PATCH,$MAJOR.$MINOR,$MAJOR" | |
| fi | |
| fi | |
| elif [[ $GITHUB_REF == refs/heads/main ]]; then | |
| # Scenario 3 - Main Branch | |
| # If this is a push to main, use 'latest' | |
| TAGS="latest" | |
| else | |
| # Scenario 4 - Branches | |
| # Otherwise, use the branch name, replacing non-alphanumeric characters with underscores | |
| TAG=$(echo ${GITHUB_REF#refs/heads/} | sed 's/[^a-zA-Z0-9]/_/g') | |
| TAGS=$TAG | |
| fi | |
| # For each tag, prepend the registry name and output a newline-separated list | |
| for tag in $(echo "$TAGS" | tr ',' '\n'); do | |
| FINAL_TAGS="$FINAL_TAGS $GHCR_IMAGE_NAME:$tag," | |
| FINAL_TAGS="$FINAL_TAGS $DOCKER_HUB_IMAGE_NAME:$tag," | |
| done | |
| FINAL_TAGS=${FINAL_TAGS%,} | |
| echo "tags=${FINAL_TAGS}" >> $GITHUB_OUTPUT | |
| - name: Docker meta | |
| id: meta | |
| uses: docker/metadata-action@v5 | |
| with: | |
| # list of Docker images to use as base name for tags | |
| images: | | |
| ghcr.io/${{ github.repository_owner }}/${{ env.IMAGE_NAME }} | |
| ${{ github.repository_owner }}/${{ env.IMAGE_NAME }} | |
| labels: | |
| org.opencontainers.image.title=${{ env.IMAGE_NAME }} | |
| org.opencontainers.image.description=Bioinformatics Tools | |
| org.opencontainers.image.vendor=Englander Institute for Precision Medicine | |
| maintainer=Andrea Sboner <[email protected]> | |
| org.opencontainers.image.authors=Andrea Sboner <[email protected]> | |
| - name: Set up QEMU | |
| uses: docker/setup-qemu-action@v3 | |
| - name: Set up Docker Buildx | |
| uses: docker/setup-buildx-action@v3 | |
| - name: Log into GitHub Container Registry | |
| uses: docker/login-action@v3 | |
| with: | |
| registry: ghcr.io | |
| username: ${{ secrets.GHCR_SVC_ACCOUNT }} | |
| password: ${{ secrets.GHCR_TOKEN }} | |
| - name: Login to EIPM DockerHub | |
| uses: docker/login-action@v3 | |
| with: | |
| username: ${{ secrets.EIPM_DOCKER_HUB_USERNAME }} | |
| password: ${{ secrets.EIPM_DOCKER_HUB_TOKEN }} | |
| - name: Build and push to Docker Hub and GitHub Container Registry | |
| uses: docker/build-push-action@v5 | |
| with: | |
| context: . | |
| platforms: linux/amd64 | |
| file: ./Dockerfile | |
| sbom: true | |
| push: true | |
| provenance: mode=max | |
| tags: ${{ steps.prep.outputs.tags }} | |
| labels: ${{ steps.meta.outputs.labels }} | |
| cache-from: type=registry,ref=ghcr.io/${{ github.repository_owner }}/${{ env.IMAGE_NAME }}:cache | |
| cache-to: type=registry,ref=ghcr.io/${{ github.repository_owner }}/${{ env.IMAGE_NAME }}:cache,mode=max | |