Implement filtering of non-canonical chromosomes #111
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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" ] | |
| jobs: | |
| build: | |
| runs-on: self-hosted | |
| environment: DockerHub | |
| permissions: | |
| contents: read | |
| packages: write | |
| # This is used to complete the identity challenge | |
| # with sigstore/fulcio when running outside of PRs. | |
| id-token: write | |
| steps: | |
| - name: Checkout repository | |
| uses: actions/checkout@v3 | |
| - name: Set up JDK 17 | |
| uses: actions/setup-java@v3 | |
| with: | |
| java-version: '17' | |
| distribution: 'corretto' | |
| - name: Compile TEPIC | |
| run: pushd src/main/resources/org/exbio/tfprio/steps/TEPIC/Code && g++ TRAPmulti.cpp -O3 -fopenmp -o TRAPmulti && popd | |
| - name: Install pipeJar | |
| run: ./mvnw org.apache.maven.plugins:maven-install-plugin:2.5.2:install-file -Dfile=lib/pipeJar.jar | |
| - name: Build jar | |
| run: ./mvnw clean compile assembly:single && mkdir -p bin && cp target/TFPRIO-1.0-bin.jar bin/TF-Prioritizer.jar | |
| # Workaround: https://github.com/docker/build-push-action/issues/461 | |
| - name: Setup Docker buildx | |
| uses: docker/setup-buildx-action@79abd3f86f79a9d68a23c75a09a9a85889262adf | |
| - name: Log in to Docker Hub | |
| uses: docker/login-action@f054a8b539a109f9f41c372932f1ae047eff08c9 | |
| with: | |
| username: ${{ secrets.DOCKER_USERNAME }} | |
| password: ${{ secrets.DOCKER_PASSWORD }} | |
| # Extract metadata (tags, labels) for Docker | |
| # https://github.com/docker/metadata-action | |
| - name: Extract Docker metadata | |
| id: meta | |
| uses: docker/metadata-action@98669ae865ea3cffbcbaa878cf57c20bbf1c6c38 | |
| with: | |
| images: nicotru/tf-prioritizer | |
| # Build and push Docker image with Buildx (don't push on PR) | |
| # https://github.com/docker/build-push-action | |
| - name: Build and push Docker image | |
| id: build-and-push | |
| uses: docker/build-push-action@ac9327eae2b366085ac7f6a2d02df8aa8ead720a | |
| with: | |
| context: . | |
| push: ${{ github.event_name != 'pull_request' }} | |
| tags: ${{ steps.meta.outputs.tags }} | |
| labels: ${{ steps.meta.outputs.labels }} | |
| cache-from: type=gha | |
| cache-to: type=gha,mode=max | |
| # - name: Sync readme | |
| # uses: ms-jpq/sync-dockerhub-readme@v1 | |
| # with: | |
| # username: ${{ secrets.DOCKER_USERNAME }} | |
| # password: ${{ secrets.DOCKER_PASSWORD }} | |
| # repository: nicotru/tf-prioritizer | |
| # readme: "README.md" |