test calls for GitHub actions (f8ebbc9e) · Commits · github_fork / Universc

.github/workflows/docker-run.yml

+2 −8

Original line number	Diff line number	Diff line
		name: Docker Compose Actions Workflow
		name: Docker Compose Actions
		on: push
		jobs:
		test:
		@@ -9,11 +9,5 @@ jobs:
		run: docker-compose up -d
		- name: Status
		run: echo "build complete"
		- name: Build config
		- name: Build diagnostics
		run: pwd; ls ../; ls ../../
		- name: Paths
		run: which cellranger; echo $PATH
		- name: Call functions
		run: bash test/test_call.sh
		- name: Test docker container
		run: docker run --network container:webapp-frontend appropriate/curl -s --retry 10 --retry-connrefused http://localhost:5000/

.github/workflows/docker-test-call.yml

+52 −0

Original line number	Diff line number	Diff line
		@@ -27,6 +27,30 @@ jobs:
		- name: call Cell Ranger
		run: which cellranger; cellranger -v

		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:latest
		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 -v

		test-universc:
		runs-on: ubuntu-latest
		steps:
		@@ -41,3 +65,31 @@ jobs:
		run: bash /universc/launch_universc.sh -v
		- name: test callas
		run: bash /universc/test/test_call.sh

		test-universc:
		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:latest
		push: false
		- name: Hello world
		run: docker run ${{ secrets.DOCKER_HUB_USERNAME }}/universc:latest echo "hello world"
		- name: Diagnostics
		run: docker run ${{ secrets.DOCKER_HUB_USERNAME }}/universc:latest pwd;ls
		- name: Cell Ranger Call
		run: docker run ${{ secrets.DOCKER_HUB_USERNAME }}/universc:latest cellranger -v
		- name: UniverSC Call
		run: docker run ${{ secrets.DOCKER_HUB_USERNAME }}/universc:latest bash /universc/launch_universc.sh -v
		- name: Run test calls
		run: docker run ${{ secrets.DOCKER_HUB_USERNAME }}/universc:latest bash /universc/test/test_call.sh

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