Update github action to run on prs and install unxz command #48
Workflow file for this run
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| name: Docker Image CI | |
| on: | |
| push: | |
| branches: | |
| - master | |
| - demo-* | |
| pull_request: | |
| # Only use GitHub Actions for testing, because the Docker image with Mutation Assessor data is too big to be built and pushed. | |
| # CircleCI builds and pushes the images to Docker Hub for every new release. | |
| jobs: | |
| build_and_publish_grch37: | |
| if: github.repository == 'genome-nexus/genome-nexus-importer' | |
| runs-on: ubuntu-latest | |
| steps: | |
| - name: 'Checkout git repo' | |
| uses: actions/checkout@v1 | |
| - name: Install xz-utils | |
| run: sudo apt-get update && sudo apt-get install -y xz-utils | |
| - name: Extract branch or tag name | |
| # The GITHUB_REF variable is like "refs/head/branch_name" or | |
| # "refs/tag/tag_name". If the tag is prefixed with v, this is a new | |
| # version and we want to push it with the tag "latest" as well. One can give | |
| # the same image multiple tags by using "," | |
| run: echo "##[set-output name=image_tag_names;]$(echo ${GITHUB_REF##*/} | sed 's/^v/latest,/g')" | |
| id: extract_tags | |
| - name: 'Docker build with cache' | |
| uses: whoan/docker-build-with-cache-action@v5 | |
| with: | |
| image_name: genomenexus/gn-mongo | |
| image_tag: ${{ steps.extract_tags.outputs.image_tag_names }} | |
| push_image_and_stages: false | |
| build_and_publish_grch38: | |
| if: github.repository == 'genome-nexus/genome-nexus-importer' | |
| runs-on: ubuntu-latest | |
| env: | |
| Version: grch38_ensembl95 | |
| steps: | |
| - name: 'Checkout git repo' | |
| uses: actions/checkout@v1 | |
| - name: Install xz-utils | |
| run: sudo apt-get update && sudo apt-get install -y xz-utils | |
| - name: Extract branch or tag name | |
| # The GITHUB_REF variable is like "refs/head/branch_name" | |
| # The format of image tag is e.g. v0.12_grch38_ensembl95 | |
| run: echo "##[set-output name=image_tag_name;]${GITHUB_REF##*/}_${Version}" | |
| id: extract_tag | |
| - name: 'Docker build with cache' | |
| uses: whoan/docker-build-with-cache-action@v5 | |
| with: | |
| build_extra_args: '{"--build-arg": "ARG_REF_ENSEMBL_VERSION=grch38_ensembl95"}' | |
| image_name: genomenexus/gn-mongo | |
| image_tag: ${{ steps.extract_tag.outputs.image_tag_name }} | |
| push_image_and_stages: false | |
| build_and_publish_grcm38: | |
| if: github.repository == 'genome-nexus/genome-nexus-importer' | |
| runs-on: ubuntu-latest | |
| env: | |
| Version: grcm38_ensembl95 | |
| steps: | |
| - name: 'Checkout git repo' | |
| uses: actions/checkout@v1 | |
| - name: Extract branch or tag name | |
| # The GITHUB_REF variable is like "refs/head/branch_name" | |
| # The format of image tag is e.g. v0.12_grch38_ensembl95 | |
| run: echo "##[set-output name=image_tag_names;]$(echo ${GITHUB_REF##*/}_${Version})" | |
| id: extract_tags | |
| - name: 'Docker build with cache' | |
| uses: whoan/docker-build-with-cache-action@v5 | |
| with: | |
| build_extra_args: '--build-arg SPECIES=mus_musculus --build-arg REF_ENSEMBL_VERSION=grcm38_ensembl95' | |
| image_name: genomenexus/gn-mongo | |
| image_tag: ${{ steps.extract_tags.outputs.image_tag_names }} | |
| push_image_and_stages: false | |