feat: add biosample index (#769) #235
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| name: Build and Push to Artifact Registry | |
| "on": | |
| push: | |
| branches: ["*"] | |
| tags: ["*"] | |
| env: | |
| PROJECT_ID: open-targets-genetics-dev | |
| REGION: europe-west1 | |
| GAR_LOCATION: europe-west1-docker.pkg.dev/open-targets-genetics-dev | |
| REPOSITORY: gentropy-app | |
| PYTHON_VERSION_DEFAULT: "3.10.8" | |
| jobs: | |
| build-push-artifact: | |
| runs-on: ubuntu-latest | |
| steps: | |
| - name: "Checkout" | |
| uses: "actions/checkout@v3" | |
| - name: "auth" | |
| uses: "google-github-actions/auth@v2" | |
| with: | |
| credentials_json: "${{ secrets.SERVICE_ACCOUNT_KEY }}" | |
| - name: "Set up Cloud SDK" | |
| uses: "google-github-actions/setup-gcloud@v2" | |
| - name: "Use gcloud CLI" | |
| run: "gcloud info" | |
| - name: Set up QEMU | |
| uses: docker/setup-qemu-action@v3 | |
| - name: Set up Docker Buildx | |
| uses: docker/setup-buildx-action@v3 | |
| - name: "Docker auth" | |
| run: |- | |
| gcloud auth configure-docker ${{ env.REGION }}-docker.pkg.dev --quiet | |
| - name: Quick Docker build (gentropy only, AMD64 only, with layer cache) | |
| uses: docker/build-push-action@v6 | |
| with: | |
| platforms: linux/amd64 | |
| push: true | |
| tags: "${{ env.GAR_LOCATION }}/${{ env.REPOSITORY }}/gentropy:${{ github.ref_name }}" | |
| context: . | |
| cache-from: type=gha | |
| cache-to: type=gha,mode=max | |
| - name: Build and push gentropy image | |
| if: github.ref == 'refs/heads/dev' || startsWith(github.ref, 'refs/tags/v') | |
| uses: docker/build-push-action@v6 | |
| with: | |
| platforms: linux/amd64,linux/arm64 | |
| push: true | |
| tags: "${{ env.GAR_LOCATION }}/${{ env.REPOSITORY }}/gentropy:${{ github.ref_name }}" | |
| context: . | |
| - name: Build and push VEP image | |
| if: github.ref == 'refs/heads/dev' || startsWith(github.ref, 'refs/tags/v') | |
| uses: docker/build-push-action@v6 | |
| with: | |
| platforms: linux/amd64 | |
| push: true | |
| tags: "${{ env.GAR_LOCATION }}/${{ env.REPOSITORY }}/custom_ensembl_vep:${{ github.ref_name }}" | |
| context: . | |
| file: "src/vep/Dockerfile" | |
| - name: Set up Python | |
| uses: actions/setup-python@v4 | |
| with: | |
| python-version: ${{ env.PYTHON_VERSION_DEFAULT }} | |
| - name: Install and configure Poetry | |
| uses: snok/install-poetry@v1 | |
| with: | |
| virtualenvs-create: true | |
| virtualenvs-in-project: true | |
| installer-parallel: true | |
| - name: Build and push spark cluster dependencies | |
| run: | | |
| make build |