Update to galaxy-bioblend to 1.1.101 #141
Workflow file for this run
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| name: Build and Push miniconda templated containers | |
| on: | |
| push: | |
| branches: | |
| - master | |
| pull_request: | |
| paths: | |
| - "*/templated-conda-env.yaml" | |
| - "*/image_tag" | |
| - "*/pre_install_dockerfile" | |
| - "*/post_install_dockerfile" | |
| - "miniconda_template/*" | |
| - ".github/workflows/miniconda_template.yaml" | |
| jobs: | |
| getchanges: | |
| name: Get changed repos | |
| runs-on: ubuntu-latest | |
| steps: | |
| - uses: actions/checkout@v2 | |
| with: | |
| fetch-depth: 0 | |
| - name: Get changed files | |
| id: changed-files | |
| uses: tj-actions/[email protected] | |
| with: | |
| separator: ',' | |
| - name: Changed base directories for u-mamba based containers | |
| id: changes | |
| run: | | |
| CHANGED_DIRS_JSON=$(echo ${{ steps.changed-files.outputs.all_changed_and_modified_files }} | \ | |
| tr ',' '\n' | \ | |
| awk '{ if ( $0 ~ /\// ) { print $1 } }' | \ | |
| awk -F'/' '{ print $1 }' | sort -u | \ | |
| awk 'system("test -f "$1"/templated-conda-env.yaml")==0 { print $1 }' | \ | |
| jq -R -s -c 'split("\n") | map(select(length > 0))' ) | |
| echo ::set-output name=changeddirsjson::"$CHANGED_DIRS_JSON" | |
| - name: Print changed directories with miniconda based containers | |
| run: | | |
| echo ${{steps.changes.outputs.changeddirsjson}} | |
| outputs: | |
| changeddirs: ${{ steps.changes.outputs.changeddirsjson }} | |
| all_changed_and_modified_files: ${{ steps.changed-files.outputs.all_changed_and_modified_files }} | |
| test: | |
| name: Build image and optionally deploy | |
| runs-on: ubuntu-latest | |
| needs: getchanges | |
| strategy: | |
| matrix: | |
| changed: ${{fromJSON(needs.getchanges.outputs.changeddirs)}} | |
| steps: | |
| - uses: actions/checkout@v2 | |
| - name: Check matrix | |
| run: echo ${{ matrix.changed }} | |
| - name: Check that tag has been modified | |
| run: | | |
| if [[ ! "${{ needs.getchanges.outputs.all_changed_and_modified_files }}" == *"${{ matrix.changed }}/image_tag"* ]]; then | |
| echo "Tag needs to be changed for container in ${{ matrix.changed }}" | |
| exit 1 | |
| fi | |
| - name: Read image | |
| id: gettag | |
| run: echo "::set-output name=image::$(head -n 1 ${{ matrix.changed }}/image_tag | awk -F':' '{ print $1 }' )" | |
| - name: Read tag | |
| id: gettagver | |
| run: echo "::set-output name=tag::$(head -n 1 ${{ matrix.changed }}/image_tag | awk -F':' '{ print $2 }' )" | |
| - name: Assemble Dockerfile | |
| run: miniconda_template/create_dockerfile.sh ${{ matrix.changed }} | |
| - name: Free up some space for building large images | |
| run: | | |
| sudo rm -rf /usr/share/dotnet | |
| sudo rm -rf "$AGENT_TOOLSDIRECTORY" | |
| - name: Build image | |
| id: build-image | |
| uses: redhat-actions/buildah-build@v2 | |
| with: | |
| image: ${{ steps.gettag.outputs.image }} | |
| tags: latest ${{ steps.gettagver.outputs.tag }} | |
| context: ${{ matrix.changed }} | |
| dockerfiles: | | |
| ./${{ matrix.changed }}/Dockerfile | |
| - name: Push to Quay | |
| if: ${{ github.ref == 'refs/heads/master' }} | |
| id: push-to-quay | |
| uses: redhat-actions/push-to-registry@v2 | |
| with: | |
| image: ${{ steps.gettag.outputs.image }} | |
| tags: latest ${{ steps.gettagver.outputs.tag }} | |
| registry: quay.io/ebigxa | |
| username: ${{ secrets.QUAY_USERNAME }} | |
| password: ${{ secrets.QUAY_TOKEN }} | |
| - name: Use the image | |
| if: ${{ github.ref == 'refs/heads/master' }} | |
| run: echo "New image has been pushed to ${{ steps.push-to-quay.outputs.registry-paths }}" |