add multiome check script #395
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| name: Warp Tools CI | |
| # Controls when the workflow will run | |
| on: | |
| # Triggers the workflow on push or pull request events but only for the "develop" and "master" branch | |
| # Uncomment this block and add your branch name to test without creating a PR | |
| #push: | |
| #branches: [ "kp_github_actions_pd-2113" ] | |
| #paths-ignore: | |
| # - '**/README.md' | |
| pull_request: | |
| branches: [ "develop", "master" ] | |
| paths: | |
| - 'tools/**' | |
| # Allows you to run this workflow manually from the Actions tab | |
| workflow_dispatch: | |
| inputs: | |
| image_tag: | |
| description: 'Docker Image Tag (default: branch_name)' | |
| env: | |
| PROJECT_NAME: WARP Tools | |
| # Github repo name | |
| REPOSITORY_NAME: ${{ github.event.repository.name }} | |
| # Region-specific Google Docker repository where GOOGLE_PROJECT/REPOSITORY_NAME can be found | |
| GOOGLE_CONTAINER_REGISTRY: us.gcr.io | |
| GCR_PATH: broad-gotc-prod/warp-tools | |
| ACR_PATH: warp-tools | |
| TAG: ${{ github.event.inputs.image_tag || github.head_ref || github.ref_name }} | |
| # A workflow run is made up of one or more jobs that can run sequentially or in parallel | |
| jobs: | |
| # The job that builds our container | |
| build-for-gcr: | |
| # The type of runner that the job will run on | |
| runs-on: ubuntu-latest | |
| defaults: | |
| run: | |
| working-directory: tools | |
| # Map a step output to a job output | |
| outputs: | |
| imagePath: ${{ steps.saveImagePath.outputs.url }} | |
| steps: | |
| # Checks-out your repository under $GITHUB_WORKSPACE, so your job can access it | |
| - uses: actions/checkout@v3 | |
| - name: Build the Docker image for GCR | |
| run: docker build . --file Dockerfile --tag ${GOOGLE_CONTAINER_REGISTRY}/${GCR_PATH}:${TAG} | |
| - name: Check working directory' | |
| run: | | |
| echo "Current directory: " | |
| pwd | |
| ls -lht | |
| # Save the image path to an output | |
| - id: 'saveImagePath' | |
| run: echo "url=${GOOGLE_CONTAINER_REGISTRY}/${GCR_PATH}:${TAG}" >> $GITHUB_OUTPUT | |
| # Log into the Google Container registry | |
| - id: 'Auth' | |
| name: Login to GCR | |
| uses: docker/login-action@v2 | |
| with: | |
| registry: ${{ env.GOOGLE_CONTAINER_REGISTRY }} | |
| username: _json_key | |
| password: ${{ secrets.GCR_CI_KEY }} | |
| # Push the image to the Google Container registry | |
| - name: Push image | |
| run: "docker push ${GOOGLE_CONTAINER_REGISTRY}/${GCR_PATH}:${TAG}" | |
| #Runs pytest on all python code in warp-tools/tools | |
| test-python: | |
| needs: build-for-gcr | |
| runs-on: ubuntu-latest | |
| defaults: | |
| run: | |
| working-directory: tools | |
| strategy: | |
| matrix: | |
| python-version: ["3.9", "3.10"] | |
| steps: | |
| - uses: actions/checkout@v3 | |
| - name: Set up Python ${{ matrix.python-version }} | |
| uses: actions/setup-python@v4 | |
| with: | |
| python-version: ${{ matrix.python-version }} | |
| - name: Install dependencies | |
| run: | | |
| python -m pip install --upgrade pip | |
| pip install ruff pytest | |
| if [ -f requirements.txt ]; then pip install -r requirements.txt; fi | |
| - name: Lint with ruff | |
| run: | | |
| # default set of ruff rules with GitHub Annotations | |
| ruff --format=github --target-version=py37 . | |
| continue-on-error: true | |
| - name: Test with pytest | |
| run: | | |
| pytest | |
| test-c: | |
| runs-on: ubuntu-latest | |
| needs: build-for-gcr | |
| container: | |
| image: ${{needs.build-for-gcr.outputs.imagePath}} | |
| # volumes: | |
| # - my_docker_volume:/volume_mount | |
| # options: --cpus 1 | |
| options: "--entrypoint /bin/bash" | |
| steps: | |
| - name: Check for dockerenv file | |
| run: | | |
| (ls /.dockerenv && echo Found dockerenv && cat /.dockerenv) || (echo No dockerenv) | |
| - name: Check directory | |
| run: | | |
| apt-get install tree | |
| whoami | |
| pwd | |
| ls -lhta | |
| tree /warptools | |
| # if test is at the end of the file name in the the test dir -- it gets picked up | |
| - name: Test TagSort | |
| run: | | |
| cd /warptools/TagSort | |
| pwd | |
| ls -lhta | |
| ./fetch_gtest.sh && make test | |
| cd /warptools/TagSort/bin | |
| ls -lht | |
| for f in *test; do ./"$f"; done; | |
| - name: Test FastqPreprocessing | |
| run: | | |
| cd /warptools/fastqpreprocessing | |
| pwd | |
| ls -lhta | |
| ./fetch_gtest.sh && make test | |
| cd /warptools/fastqpreprocessing/bin | |
| ls -lht | |
| for f in *test; do ./"$f"; done; | |
| build-for-acr: | |
| runs-on: ubuntu-latest | |
| defaults: | |
| run: | |
| working-directory: tools | |
| steps: | |
| # checkout the repo | |
| - name: 'Checkout GitHub Action' | |
| uses: actions/checkout@v3 | |
| - name: 'Login via Azure CLI' | |
| uses: azure/login@v1 | |
| with: | |
| creds: ${{ secrets.AZURE_CREDENTIALS }} | |
| - name: 'Build and push image' | |
| uses: azure/docker-login@v1 | |
| with: | |
| login-server: ${{ secrets.REGISTRY_LOGIN_SERVER }} | |
| username: ${{ secrets.REGISTRY_USERNAME }} | |
| password: ${{ secrets.REGISTRY_PASSWORD }} | |
| - run: | | |
| docker build . -t ${{ secrets.REGISTRY_LOGIN_SERVER }}/${ACR_PATH}:${TAG} | |
| docker push ${{ secrets.REGISTRY_LOGIN_SERVER }}/${ACR_PATH}:${TAG} | |