Full rocker & bioc build #100
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| # This is a basic workflow to help you get started with Actions | |
| name: Full rocker & bioc build | |
| # Controls when the action will run. Triggers the workflow on push or pull request | |
| # events but only for the master branch | |
| on: | |
| workflow_dispatch: | |
| inputs: | |
| rver: | |
| default: "devel" | |
| biocver: | |
| default: "3.21" | |
| outname: | |
| default: "bioconductor_docker" | |
| schedule: | |
| - cron: '0 18 * * 5' | |
| jobs: | |
| bump: | |
| runs-on: ubuntu-latest | |
| steps: | |
| - uses: actions/checkout@v3 | |
| - name: Push patch bump | |
| uses: nick-fields/retry@v2 | |
| with: | |
| timeout_minutes: 10 | |
| max_attempts: 50 | |
| shell: bash | |
| command: | | |
| set -x | |
| git config --global --add safe.directory "$GITHUB_WORKSPACE" | |
| git config user.name github-actions | |
| git config user.email [email protected] | |
| git pull origin main || git reset --hard origin/main | |
| sed -r -i 's/(^ARG BIOCONDUCTOR_PATCH=)([0-9]+)$/echo "\1$((\2+1))"/ge' Dockerfile | |
| git add Dockerfile | |
| git commit -m "Bump BIOCONDUCTOR_PATCH" | |
| git push | |
| build: | |
| outputs: | |
| registryuser: ${{ steps.defs.outputs.registryuser }} | |
| outname: ${{ steps.defs.outputs.outname }} | |
| rver: ${{ steps.defs.outputs.rver }} | |
| strategy: | |
| matrix: | |
| arch: [amd64, arm64] | |
| runs-on: ubuntu-latest | |
| needs: bump | |
| steps: | |
| # Checks-out your repository under $GITHUB_WORKSPACE, so your job can access it | |
| - uses: actions/checkout@v3 | |
| - name: Free root space | |
| uses: almahmoud/free-root-space@main | |
| with: | |
| verbose: true | |
| - name: Set defaults for schedule | |
| id: defs | |
| run: | | |
| echo outname=$(echo ${{ github.event.inputs.outname || 'bioconductor_docker' }}) >> $GITHUB_OUTPUT | |
| echo rver=$(echo ${{ github.event.inputs.rver || 'devel' }}) >> $GITHUB_OUTPUT | |
| echo biocver=$(echo ${{ github.event.inputs.biocver || '3.21' }}) >> $GITHUB_OUTPUT | |
| echo registryuser=$(echo ${{ github.repository_owner }} | awk '{print tolower($0)}') >> $GITHUB_OUTPUT | |
| echo rockerintermediateprefix=$(echo "ghcr.io/${{ github.repository_owner }}/rocker" | awk '{print tolower($0)}') >> $GITHUB_OUTPUT | |
| - name: Set up QEMU | |
| uses: docker/setup-qemu-action@v2 | |
| with: | |
| platforms: arm64 | |
| if: matrix.arch == 'arm64' | |
| - name: Login to GHCR | |
| uses: docker/login-action@v2 | |
| with: | |
| registry: ghcr.io | |
| username: ${{ github.actor }} | |
| password: ${{ secrets.GITHUB_TOKEN }} | |
| - name: Login to Dockerhub | |
| uses: docker/login-action@v2 | |
| with: | |
| username: ${{ secrets.DOCKER_USERNAME }} | |
| password: ${{ secrets.DOCKER_PASSWORD }} | |
| - name: Extract metadata for container image | |
| id: meta | |
| uses: docker/metadata-action@v4 | |
| with: | |
| images: ${{ steps.defs.outputs.registryuser }}/${{ steps.defs.outputs.outname }} | |
| tags: | | |
| type=raw,value=${{ steps.defs.outputs.rver }}-${{ matrix.arch }} | |
| - name: Set comma-separated list with all repository names | |
| id: images | |
| run: | | |
| IMG=${{ steps.meta.outputs.tags }} | |
| REPOLIST="docker.io/$IMG,ghcr.io/$IMG" | |
| echo ghcr=$(echo "ghcr.io/$IMG") >> $GITHUB_OUTPUT | |
| SUB="_docker" | |
| # Also add alternative without _docker when in name | |
| echo list=$(if [[ $REPOLIST == *$SUB* ]]; then echo "$REPOLIST,$(echo $REPOLIST | sed 's/_docker//g')"; else echo $REPOLIST; fi) >> $GITHUB_OUTPUT | |
| bash .github/scripts/rocker_prep.sh "${{ steps.defs.outputs.rver }}" "${{ steps.defs.outputs.biocver }}" "${{ steps.defs.outputs.rockerintermediateprefix }}" "${{ matrix.arch }}" | |
| - name: Set up Docker Buildx | |
| uses: docker/setup-buildx-action@v2 | |
| with: | |
| platforms: linux/${{ matrix.arch }} | |
| - name: Build and load r-ver | |
| uses: docker/build-push-action@v3 | |
| with: | |
| file: rocker-versioned2/dockerfiles/r-ver_${{ steps.defs.outputs.rver }}.Dockerfile | |
| context: rocker-versioned2 | |
| push: true | |
| tags: ${{ steps.defs.outputs.rockerintermediateprefix }}-r-ver:${{ steps.defs.outputs.rver }}-${{ matrix.arch }} | |
| platforms: linux/${{ matrix.arch }} | |
| - name: Build and load rstudio | |
| uses: docker/build-push-action@v3 | |
| with: | |
| file: rocker-versioned2/dockerfiles/rstudio_${{ steps.defs.outputs.rver }}.Dockerfile | |
| context: rocker-versioned2 | |
| push: true | |
| tags: ${{ steps.defs.outputs.rockerintermediateprefix }}-rstudio:${{ steps.defs.outputs.rver }}-${{ matrix.arch }} | |
| platforms: linux/${{ matrix.arch }} | |
| - name: Build and push container image to all repos both arm64 and amd64 | |
| uses: docker/build-push-action@v3 | |
| with: | |
| build-args: | | |
| BASE_IMAGE=${{ steps.defs.outputs.rockerintermediateprefix }}-rstudio | |
| arm64_tag=${{ steps.defs.outputs.rver }}-${{ matrix.arch }} | |
| amd64_tag=${{ steps.defs.outputs.rver }}-${{ matrix.arch }} | |
| BIOCONDUCTOR_VERSION=${{ steps.defs.outputs.biocver }} | |
| file: Dockerfile | |
| context: . | |
| push: true | |
| tags: ${{ steps.images.outputs.list }} | |
| labels: ${{ steps.meta.outputs.labels }} | |
| platforms: linux/${{ matrix.arch }} | |
| test-built-containers: | |
| strategy: | |
| matrix: | |
| arch: [arm64, amd64] | |
| # The type of runner that the job will run on | |
| runs-on: ubuntu-latest | |
| needs: build | |
| steps: | |
| - name: Get image name | |
| id: image | |
| run: | | |
| IMG=$(echo "${{needs.build.outputs.registryuser}}/${{ needs.build.outputs.outname }}:${{ needs.build.outputs.rver }}-${{ matrix.arch }}") | |
| echo name=$IMG >> $GITHUB_OUTPUT | |
| cat << EOF > test.Dockerfile | |
| FROM $IMG as test | |
| USER root | |
| RUN mkdir -p /tmp/bioc_test && \ | |
| apt list --installed | tee /tmp/bioc_test/aptlist && \ | |
| Rscript -e "BiocManager::install(c('SummarizedExperiment','usethis','data.table','igraph','GEOquery'))" 2>&1 | tee /tmp/bioc_test/packages_install && \ | |
| Rscript -e "BiocManager::install('gert'); require('gert')" 2>&1 | tee /tmp/bioc_test/gert_install | |
| FROM scratch as export | |
| COPY --from=test /tmp/bioc_test /tmp | |
| EOF | |
| - name: Set up QEMU | |
| uses: docker/setup-qemu-action@v2 | |
| with: | |
| platforms: arm64 | |
| if: matrix.arch == 'arm64' | |
| - name: Set up Docker Buildx | |
| uses: docker/setup-buildx-action@v2 | |
| with: | |
| platforms: linux/${{ matrix.arch }} | |
| - name: Login to GHCR | |
| uses: docker/login-action@v2 | |
| with: | |
| registry: ghcr.io | |
| username: ${{ github.actor }} | |
| password: ${{ secrets.GITHUB_TOKEN }} | |
| - name: Test via build | |
| id: dockerbuild | |
| uses: docker/build-push-action@v4 | |
| with: | |
| file: test.Dockerfile | |
| context: . | |
| push: false | |
| load: false | |
| outputs: type=tar,dest=/tmp/image.tar | |
| tags: ${{ steps.image.outputs.name }} | |
| - run: | | |
| mkdir -p /tmp/contents | |
| cd /tmp/contents | |
| tar -xvf /tmp/image.tar | |
| sudo ls tmp/* | xargs -i bash -c "echo 'cat {}' && cat {}" | |