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update samtools version + update actions + clean up (#19)
* BIO-2033 change env vars to v1.19 * rm transformBAM.sh * rm commented code * rm transformBAM.sh from Dockerfile * rm scripts to test transformBAM.sh * update to new github actions * rm Dockerfile-test * rm checkFileSize.R * rm test-data * don't copy entrypoint.sh because it's gone * update README.md did check versions of packages installed via apt, the correct versions are listed
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@@ -14,7 +14,6 @@ on: | |
| pull_request: | ||
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| env: | ||
| # TODO: Change variable to your image's name. | ||
| IMAGE_NAME: bioinformatics | ||
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| jobs: | ||
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@@ -27,61 +26,137 @@ jobs: | |
| if: github.event_name == 'push' | ||
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| steps: | ||
| - uses: actions/checkout@v2 | ||
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| - name: Build image | ||
| run: docker build . --file Dockerfile --tag $IMAGE_NAME | ||
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| - name: Log into GitHub Container Registry | ||
| run: echo "${{ secrets.GHCR_TOKEN }}" | docker login https://ghcr.io -u ${{ secrets.GHCR_SVC_ACCOUNT }} --password-stdin | ||
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| - name: Push image to GitHub Container Registry | ||
| - uses: actions/checkout@v4 | ||
| with: | ||
| lfs: true | ||
| - name: Checkout LFS objects | ||
| run: git lfs checkout | ||
| - name: Set Date | ||
| run: echo "TODAYS_DATE=$(date +'%Y%m%d')" >> $GITHUB_ENV | ||
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| - name: Prepare tags | ||
| id: prep | ||
| run: | | ||
| IMAGE_ID=ghcr.io/${{ github.repository_owner }}/$IMAGE_NAME | ||
| # Change all uppercase to lowercase | ||
| IMAGE_ID=$(echo $IMAGE_ID | tr '[A-Z]' '[a-z]') | ||
| # Strip git ref prefix from version | ||
| VERSION=$(echo "${{ github.ref }}" | sed -e 's,.*/\(.*\),\1,') | ||
| # Strip "v" prefix from tag name | ||
| [[ "${{ github.ref }}" == "refs/tags/"* ]] && VERSION=$(echo $VERSION | sed -e 's/^v//') | ||
| # Use Docker `latest` tag convention | ||
| [ "$VERSION" == "main" ] && VERSION=latest | ||
| echo IMAGE_ID=$IMAGE_ID | ||
| echo VERSION=$VERSION | ||
| # 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 | ||
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| # 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]} | ||
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| if [[ $BASE_TAG =~ ^([0-9]+)\.([0-9]+)\.([0-9]+)$ ]]; then | ||
| MAJOR=${BASH_REMATCH[1]} | ||
| MINOR=${BASH_REMATCH[2]} | ||
| PATCH=${BASH_REMATCH[3]} | ||
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| TAGS="$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=${BASH_REMATCH[3]} | ||
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| TAGS="$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 | ||
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| # 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 | ||
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| FINAL_TAGS=${FINAL_TAGS%,} | ||
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| echo "tags=${FINAL_TAGS}" >> $GITHUB_OUTPUT | ||
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| - name: Docker meta | ||
| id: meta | ||
| uses: docker/metadata-action@v5 | ||
| with: | ||
| # list of Docker images to use as base name for tags | ||
| images: | | ||
| ghcr.io/${{ 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]> | ||
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| - name: Set up QEMU | ||
| uses: docker/setup-qemu-action@v3 | ||
| - name: Set up Docker Buildx | ||
| uses: docker/setup-buildx-action@v3 | ||
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| docker tag $IMAGE_NAME $IMAGE_ID:$VERSION | ||
| docker push $IMAGE_ID:$VERSION | ||
| - name: Log into GitHub Container Registry | ||
| uses: docker/login-action@v3 | ||
| with: | ||
| registry: ghcr.io | ||
| username: ${{ secrets.GHCR_SVC_ACCOUNT }} | ||
| password: ${{ secrets.GHCR_TOKEN }} | ||
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| - name: Login to EIPM DockerHub | ||
| uses: docker/login-action@v1 | ||
| uses: docker/login-action@v3 | ||
| with: | ||
| username: ${{ secrets.EIPM_DOCKER_HUB_USERNAME }} | ||
| password: ${{ secrets.EIPM_DOCKER_HUB_TOKEN }} | ||
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| - name: Push image to EIPM Docker Hub | ||
| run: | | ||
| IMAGE_ID=eipm/$IMAGE_NAME | ||
| # Change all uppercase to lowercase | ||
| IMAGE_ID=$(echo $IMAGE_ID | tr '[A-Z]' '[a-z]') | ||
| # Strip git ref prefix from version | ||
| VERSION=$(echo "${{ github.ref }}" | sed -e 's,.*/\(.*\),\1,') | ||
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||
| # Strip "v" prefix from tag name | ||
| [[ "${{ github.ref }}" == "refs/tags/"* ]] && VERSION=$(echo $VERSION | sed -e 's/^v//') | ||
| # Use Docker `latest` tag convention | ||
| [ "$VERSION" == "main" ] && VERSION=latest | ||
| echo IMAGE_ID=$IMAGE_ID | ||
| echo VERSION=$VERSION | ||
| docker tag $IMAGE_NAME $IMAGE_ID:$VERSION | ||
| docker push $IMAGE_ID:$VERSION | ||
| - 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 | ||
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| Original file line number | Diff line number | Diff line change |
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| @@ -0,0 +1,48 @@ | ||
| name: Monthly Patching | ||
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| on: | ||
| schedule: | ||
| # Runs at 00:00 on the first day of every month | ||
| - cron: '30 6 29 * *' | ||
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| jobs: | ||
| tag: | ||
| runs-on: ubuntu-latest | ||
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| steps: | ||
| - name: Checkout repository | ||
| uses: actions/checkout@v4 | ||
| with: | ||
| token: ${{secrets.GHCR_TOKEN}} | ||
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| - name: Set up Git | ||
| run: | | ||
| git config --global user.name "eipmgithubsvc1" | ||
| git config --global user.email "[email protected]" | ||
| - name: Get the latest release | ||
| id: latest-release | ||
| uses: actions/github-script@v7 | ||
| with: | ||
| script: | | ||
| const release = await github.rest.repos.getLatestRelease({ | ||
| owner: context.repo.owner, | ||
| repo: context.repo.repo | ||
| }); | ||
| return release.data.tag_name; | ||
| - name: Generate new tag | ||
| run: | | ||
| ORIGINAL_TAG=${{ steps.latest-release.outputs.result }} | ||
| if [[ $ORIGINAL_TAG == *".patched"* ]]; then | ||
| BASE_TAG=${ORIGINAL_TAG%%.patched*} | ||
| else | ||
| BASE_TAG=$ORIGINAL_TAG | ||
| fi | ||
| DATE=$(date +'%Y%m%d') | ||
| echo "NEW_TAG=$BASE_TAG.patched$DATE" >> $GITHUB_ENV | ||
| - name: Create and push tag | ||
| run: | | ||
| git tag $NEW_TAG | ||
| git push origin $NEW_TAG |
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