configure inputs for PIP-Seq and VASA-Seq #309
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: 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 | ||
