fix command for json format #339
Workflow file for this run
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| name: Docker | |
| # This workflow uses actions that are not certified by GitHub. | |
| # They are provided by a third-party and are governed by | |
| # separate terms of service, privacy policy, and support | |
| # documentation. | |
| on: | |
| push: | |
| branches: [ "master", "*" ] | |
| # Publish semver tags as releases. | |
| tags: [ 'v*.*.*' ] | |
| paths-ignore: | |
| - 'README.md' | |
| pull_request: | |
| branches: [ "*" ] | |
| # Publish semver tags as releases. | |
| tags: [ 'v*.*.*' ] | |
| paths-ignore: | |
| - 'README.md' | |
| env: | |
| REGISTRY: ghcr.io | |
| IMAGE_NAME: ${{ github.repository }} | |
| jobs: | |
| # adapted from https://docs.github.com/en/actions/learn-github-actions/expressions#example-returning-a-json-object | |
| metadata: | |
| runs-on: ubuntu-latest | |
| outputs: | |
| matrix: ${{ steps.generate-matrix.outputs.matrix }} # contains a list of the module names encoded as json | |
| modulenames: ${{ steps.generate-matrix.outputs.modulenames }} # contains a simple, space-separated list of the module names | |
| steps: | |
| - name: Checkout | |
| uses: actions/checkout@v3 | |
| - name: generate matrix | |
| id: generate-matrix | |
| # adapted from https://stackoverflow.com/a/74829694 | |
| # modulenames="$(ls *.yml | sed 's/.yml//' | paste -s -d ' ')" | |
| run: | | |
| modulenames="chipseq gwas" | |
| echo "modulenames=$modulenames" >> $GITHUB_OUTPUT | |
| # echo $modulenames | tr ' ' '\n' | sed 's/^/type=gha,scope=builder-/' | paste -s | |
| matrix=$(echo $modulenames | jq -R 'split(" ") | map({modulename: .})') | |
| echo "matrix=$(echo $matrix | jq -c)" >> $GITHUB_OUTPUT | |
| build-module-images: | |
| runs-on: ubuntu-latest | |
| permissions: | |
| contents: read | |
| packages: write | |
| needs: [metadata] | |
| strategy: | |
| matrix: ${{ fromJson(needs.metadata.outputs.matrix) }} | |
| steps: | |
| - name: Checkout repository | |
| uses: actions/checkout@v3 | |
| - name: Log in to the Container registry | |
| uses: docker/login-action@v2 | |
| with: | |
| registry: ${{ env.REGISTRY }} | |
| username: ${{ github.actor }} | |
| password: ${{ secrets.GITHUB_TOKEN }} | |
| - name: Set up Docker Buildx | |
| uses: docker/setup-buildx-action@v2 | |
| - name: Extract metadata (tags, labels) for Docker | |
| id: meta | |
| uses: docker/metadata-action@v4 | |
| with: | |
| images: ${{ env.REGISTRY }}/${{ env.IMAGE_NAME }} | |
| - name: prune | |
| run: docker system prune -af | |
| - name: Builder Docker image | |
| id: builder | |
| uses: docker/build-push-action@v3 | |
| with: | |
| context: . | |
| file: Dockerfile | |
| push: false | |
| #tags: ${{ steps.meta.outputs.tags }} # TODO: do we need this? | |
| cache-to: type=gha,mode=max | |
| target: builder | |
| builder-args: | | |
| "modulename=${{ matrix.modulename }}" | |
| build-and-push-image: | |
| runs-on: ubuntu-latest | |
| permissions: | |
| contents: read | |
| packages: write | |
| needs: [metadata, build-module-images] | |
| steps: | |
| - name: Checkout repository | |
| uses: actions/checkout@v3 | |
| - name: Log in to the Container registry | |
| uses: docker/login-action@v2 | |
| with: | |
| registry: ${{ env.REGISTRY }} | |
| username: ${{ github.actor }} | |
| password: ${{ secrets.GITHUB_TOKEN }} | |
| - name: Set up Docker Buildx | |
| uses: docker/setup-buildx-action@v2 | |
| - name: Extract metadata (tags, labels) for Docker | |
| id: meta | |
| uses: docker/metadata-action@v4 | |
| with: | |
| images: ${{ env.REGISTRY }}/${{ env.IMAGE_NAME }} | |
| - name: prune | |
| run: docker system prune -af | |
| - name: Patch Dockerfile | |
| id: patch-dockerfile | |
| # use sed to add instructions to our Dockerfile | |
| run: | | |
| DOCKERFILE_CODE="# copy each of the modules into the current image" | |
| for module in ${{ needs.metadata.outputs.modulenames }}; do | |
| DOCKERFILE_CODE="$DOCKERFILE_CODE\nCOPY --from=builder-$module /opt/env /opt/conda/envs/$module" | |
| DOCKERFILE_CODE="$DOCKERFILE_CODE\nENV PATH=\"/opt/conda/envs/$module/bin:\${PATH}\"" | |
| done | |
| awk -v r="$DOCKERFILE_CODE" '{gsub(/^#KEEP.*$/,r)}1' Dockerfile > Dockerfile.patch | |
| - name: Primary Docker image | |
| id: primary | |
| uses: docker/builder-push-action@v3 | |
| with: | |
| context: . | |
| file: Dockerfile.patch | |
| push: true | |
| tags: ${{ steps.meta.outputs.tags }} | |
| labels: ${{ steps.meta.outputs.labels }} | |
| cache-from: type=gha | |
| cache-to: type=gha,mode=max | |
| target: primary |