update rna_quantification #102
Workflow file for this run
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| name: Push containers to registries | |
| on: | |
| pull_request_target: | |
| types: [closed] | |
| paths: | |
| - 'container/*/*.yml' | |
| jobs: | |
| setup: | |
| runs-on: ubuntu-latest | |
| strategy: | |
| fail-fast: false | |
| outputs: | |
| matrix: ${{ steps.export-directories.outputs.matrix }} | |
| any_changed: ${{ steps.download-changed-directories.outputs.found_artifact }} | |
| if: github.event.pull_request.merged == true | |
| steps: | |
| - name: Download changed directories | |
| id: download-changed-directories | |
| uses: dawidd6/action-download-artifact@v2 | |
| with: | |
| github_token: ${{ secrets.GITHUB_TOKEN }} | |
| workflow: container_build.yml | |
| name: 'changed_directories_${{ github.event.pull_request.head.sha }}' | |
| name_is_regexp: true | |
| path: /tmp | |
| if_no_artifact_found: warn | |
| - name: Export changed directories | |
| id: export-directories | |
| run: cat /tmp/changed_directories_${{ github.event.pull_request.head.sha }}/changed_directories.json >> "$GITHUB_OUTPUT" | |
| push_docker_containers: | |
| needs: setup | |
| if: needs.setup.outputs.any_changed == 'true' | |
| runs-on: ubuntu-latest | |
| strategy: | |
| fail-fast: false | |
| matrix: ${{ fromJSON(needs.setup.outputs.matrix) }} | |
| permissions: | |
| contents: read | |
| packages: write | |
| steps: | |
| - name: Checkout pull request branch | |
| uses: actions/checkout@v3 | |
| with: | |
| fetch-depth: 0 | |
| - name: Setup up docker buildx | |
| uses: docker/setup-buildx-action@v2 | |
| - name: Get basename | |
| id: context_basename | |
| run: echo "basename=$(basename ${{ matrix.context }})" >> "$GITHUB_OUTPUT" | |
| - name: Log in to ghcr.io with docker | |
| uses: docker/login-action@v2 | |
| with: | |
| registry: ghcr.io | |
| username: ${{github.repository_owner}} | |
| password: ${{ secrets.GITHUB_TOKEN }} | |
| - name: Log in to quay.io with docker | |
| uses: docker/login-action@v2 | |
| with: | |
| registry: quay.io | |
| username: ${{ vars.QUAYIO_USERNAME }} | |
| password: ${{ secrets.QUAYIO_TOKEN }} | |
| - name: Log in to docker.io with docker | |
| uses: docker/login-action@v2 | |
| with: | |
| registry: docker.io | |
| username: ${{ vars.DOCKERIO_USERNAME }} | |
| password: ${{ secrets.DOCKERIO_TOKEN }} | |
| - name: Build and push docker containers | |
| uses: docker/build-push-action@v4 | |
| with: | |
| context: ${{ matrix.context }} | |
| file: .github/docker.df | |
| push: true | |
| tags: | | |
| ghcr.io/${{ github.repository_owner }}/${{ steps.context_basename.outputs.basename }}_docker:latest | |
| quay.io/${{ vars.QUAYIO_USERNAME }}/${{ steps.context_basename.outputs.basename }}_docker:latest | |
| docker.io/${{ vars.DOCKERIO_USERNAME }}/${{ steps.context_basename.outputs.basename }}_docker:latest | |
| push_apptainer_containers: | |
| needs: setup | |
| if: needs.setup.outputs.any_changed == 'true' | |
| runs-on: ubuntu-latest | |
| strategy: | |
| fail-fast: false | |
| matrix: ${{ fromJSON(needs.setup.outputs.matrix) }} | |
| permissions: | |
| contents: read | |
| packages: write | |
| steps: | |
| - name: Checkout pull request branch | |
| uses: actions/checkout@v3 | |
| with: | |
| fetch-depth: 0 | |
| - name: Setup micromamba | |
| uses: mamba-org/setup-micromamba@v1 | |
| with: | |
| environment-name: containers | |
| create-args: apptainer | |
| generate-run-shell: true | |
| - name: Get basename | |
| id: context_basename | |
| run: echo "basename=$(basename ${{ matrix.context }})" >> "$GITHUB_OUTPUT" | |
| - name: Build apptainer containers | |
| shell: micromamba-shell {0} | |
| run: | | |
| pushd ${{ matrix.context}}; \ | |
| apptainer build /tmp/${{ steps.context_basename.outputs.basename }}_apptainer.sif ${{ github.workspace }}/.github/apptainer.def; \ | |
| popd | |
| - name: Log in to ghcr.io with apptainer | |
| shell: micromamba-shell {0} | |
| run: | | |
| apptainer remote login --username ${{ github.repository_owner }} \ | |
| --password ${{ secrets.GITHUB_TOKEN }} \ | |
| docker://ghcr.io/${{ github.repository_owner }} | |
| - name: Push apptainer containers to ghcr.io | |
| shell: micromamba-shell {0} | |
| run: | | |
| apptainer push \ | |
| /tmp/${{ steps.context_basename.outputs.basename }}_apptainer.sif \ | |
| oras://ghcr.io/${{ github.repository_owner }}/${{ steps.context_basename.outputs.basename }}_apptainer:latest | |
| - name: Log in to quay.io with apptainer | |
| shell: micromamba-shell {0} | |
| run: | | |
| apptainer remote login --username ${{ vars.QUAYIO_USERNAME }} \ | |
| --password ${{ secrets.QUAYIO_TOKEN }} \ | |
| docker://quay.io/${{ vars.QUAYIO_USERNAME }} | |
| - name: Push apptainer containers to quay.io | |
| shell: micromamba-shell {0} | |
| run: | | |
| apptainer push \ | |
| /tmp/${{ steps.context_basename.outputs.basename }}_apptainer.sif \ | |
| oras://quay.io/${{ vars.QUAYIO_USERNAME }}/${{ steps.context_basename.outputs.basename }}_apptainer:latest | |
| - name: Log in to docker.io with apptainer | |
| shell: micromamba-shell {0} | |
| run: | | |
| apptainer remote login --username ${{ vars.DOCKERIO_USERNAME }} \ | |
| --password ${{ secrets.DOCKERIO_TOKEN }} \ | |
| docker://docker.io | |
| - name: Push apptainer containers to docker.io | |
| shell: micromamba-shell {0} | |
| run: | | |
| apptainer push \ | |
| /tmp/${{ steps.context_basename.outputs.basename }}_apptainer.sif \ | |
| oras://docker.io/${{ vars.DOCKERIO_USERNAME }}/${{ steps.context_basename.outputs.basename }}_apptainer:latest |