correct detecting cellranger versions and barcode directory #320
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| name: Docker container tests | ||
| on: workflow_dispach | ||
| jobs: | ||
| test: | ||
| runs-on: ubuntu-20.04 | ||
| steps: | ||
| - uses: actions/checkout@v2 | ||
| - name: Login to DockerHub | ||
| uses: docker/login-action@v1 | ||
| with: | ||
| username: ${{ secrets.DOCKER_HUB_USERNAME }} | ||
| password: ${{ secrets.DOCKER_HUB_ACCESS_TOKEN }} | ||
| - name: Run docker | ||
| uses: addnab/docker-run-action@v1 | ||
| with: | ||
| image: docker:latest | ||
| run: echo "hello world" | ||
| test-cellranger: | ||
| runs-on: ubuntu-20.04 | ||
| steps: | ||
| - uses: actions/checkout@v2 | ||
| - uses: docker/setup-buildx-action@v1 | ||
| - uses: docker/login-action@v1 | ||
| with: | ||
| username: ${{ secrets.DOCKER_HUB_USERNAME }} | ||
| password: ${{ secrets.DOCKER_HUB_ACCESS_TOKEN }} | ||
| registry: ${{ env.REGISTRY }} | ||
| - name: Build and push | ||
| uses: docker/build-push-action@v2 | ||
| with: | ||
| context: ./ | ||
| file: ./Dockerfile | ||
| tags: ${{ secrets.DOCKER_HUB_USERNAME }}/universc:test | ||
| push: false | ||
| - name: Hello world | ||
| run: docker run ${{ secrets.DOCKER_HUB_USERNAME }}/cellranger_clean:latest echo "hello world" | ||
| - name: Diagnostics | ||
| run: docker run ${{ secrets.DOCKER_HUB_USERNAME }}/cellranger_clean:latest pwd;ls | ||
| - name: Cell Ranger Call | ||
| run: docker run ${{ secrets.DOCKER_HUB_USERNAME }}/cellranger_clean:latest cellranger count --help | ||
| test-repo: | ||
| runs-on: ubuntu-latest | ||
| steps: | ||
| - uses: actions/checkout@v2 | ||
| - name: What OS is running | ||
| run: uname -a | ||
| - name: Where am i | ||
| run: pwd; ls | ||
| - name: pull updates | ||
| run: git pull --ff-only origin $(git branch --show-current) | ||
| - name: call UniverSC | ||
| run: ls launch_universc.sh | ||
| test-universc: | ||
| runs-on: ubuntu-20.04 | ||
| steps: | ||
| - uses: actions/checkout@v2 | ||
| - name: pull updates | ||
| run: git pull --ff-only origin $(git branch --show-current) | ||
| - uses: docker/setup-buildx-action@v1 | ||
| - uses: docker/login-action@v1 | ||
| with: | ||
| username: ${{ secrets.DOCKER_HUB_USERNAME }} | ||
| password: ${{ secrets.DOCKER_HUB_ACCESS_TOKEN }} | ||
| registry: ${{ env.REGISTRY }} | ||
| - name: Build and push | ||
| uses: docker/build-push-action@v2 | ||
| with: | ||
| context: ./ | ||
| file: ./Dockerfile | ||
| tags: ${{ secrets.DOCKER_HUB_USERNAME }}/universc:test | ||
| push: false | ||
| - name: Hello world | ||
| run: docker run ${{ secrets.DOCKER_HUB_USERNAME }}/universc:test echo "hello world" | ||
| - name: Diagnostics | ||
| run: docker run ${{ secrets.DOCKER_HUB_USERNAME }}/universc:test pwd;ls | ||
| - name: Cell Ranger Call | ||
| run: docker run ${{ secrets.DOCKER_HUB_USERNAME }}/universc:test cellranger count --help | ||
| - name: UniverSC Call | ||
| run: docker run ${{ secrets.DOCKER_HUB_USERNAME }}/universc:test bash /universc/launch_universc.sh -v | ||
| - name: Run test calls | ||
| run: docker run ${{ secrets.DOCKER_HUB_USERNAME }}/universc:test bash /universc/test/test_call.sh | ||
| - name: Git Status | ||
| run: docker run ${{ secrets.DOCKER_HUB_USERNAME }}/universc:test git -C ./universc log --reverse | tail -n 10 | ||
| - name: Pull Updates | ||
| run: docker run ${{ secrets.DOCKER_HUB_USERNAME }}/universc:test git -C ./universc pull --ff-only origin $(git branch --show-current) | ||
| - name: Git Status | ||
| run: docker run ${{ secrets.DOCKER_HUB_USERNAME }}/universc:test git -C ./universc log --reverse | tail -n 10 | ||
