Merge branch 'master' of github.com:minoda-lab/universc (a658b112) · Commits · github_fork / Universc

.github/workflows/docker-run-tests.yml

0 → 100644

+138 −0

Original line number	Diff line number	Diff line
		name: Run tests in Docker
		on: push
		jobs:
		test:
		runs-on: ubuntu-20.04
		steps:
		-
		name: Login to DockerHub
		uses: docker/login-action@v1
		with:
		username: ${{ secrets.DOCKER_HUB_USERNAME }}
		password: ${{ secrets.DOCKER_HUB_ACCESS_TOKEN }}

		build:
		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

		run:
		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

		call:
		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: Test call
		run: docker run ${{ secrets.DOCKER_HUB_USERNAME }}/universc:latest bash /universc/test/test_call.sh

		test-10x:
		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: Test 10x
		run: docker run ${{ secrets.DOCKER_HUB_USERNAME }}/universc:latest bash /universc/test/run_tests_10x.sh

		test-dropseq:
		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: Test DropSeq
		run: docker run ${{ secrets.DOCKER_HUB_USERNAME }}/universc:latest bash /universc/test/run_tests_dropseq.sh

		test-icell8:
		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: Test ICELL8
		run: docker run ${{ secrets.DOCKER_HUB_USERNAME }}/universc:latest bash /universc/test/run_tests_icell8.sh

.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-10x.yml

+28 −9

Original line number	Diff line number	Diff line
		@@ -28,16 +28,16 @@ jobs:
		file: ./Dockerfile
		tags: ${{ secrets.DOCKER_HUB_USERNAME }}/universc:latest
		push: false
		- name: Run image
		run: docker run docker.pkg.github.com/minoda-lab/universc/universc:latest echo "hello from universc"
		- name: Call UniverSC
		- name: Run image test
		run: docker run ${{ secrets.DOCKER_HUB_USERNAME }}/universc:latest echo "hello from universc"
		- name: Call UniverSC test
		uses: addnab/docker-run-action@v1
		with:
		image: tomkellygenetics/universc:latest
		run: bash /universc/test/test_call.sh
		- name: Run image
		run: docker run docker.pkg.github.com/minoda-lab/universc/universc:latest bash /universc/test/run_tests_10x.sh
		- name: Call UniverSC
		run: echo "hello from universc"
		- name: Call UniverSC from image
		run: docker run ${{ secrets.DOCKER_HUB_USERNAME }}/universc:latest bash /universc/test/run_tests_10x.sh
		- name: Call UniverSC from container
		uses: addnab/docker-run-action@v1
		with:
		image: tomkellygenetics/universc:latest
		@@ -51,5 +51,24 @@ jobs:
		run: docker-compose up -d
		- name: Status
		run: echo "build complete"
		- name: Test runnning on 10x
		run: test/run_tests_10x.sh

		test-10x:
		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: Test 10x
		run: docker run ${{ secrets.DOCKER_HUB_USERNAME }}/universc:latest bash /universc/test/run_tests_10x.sh

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

+2 −2

Original line number	Diff line number	Diff line
		@@ -31,5 +31,5 @@ jobs:
		run: echo ${{ steps.docker_build.outputs.digest }}
		- name: Status
		run: echo "build complete"
		# - name: Call functions
		# run: docker run universc:latest bash /universc/test/test_call.sh
		- name: Call functions
		run: docker run universc:latest bash /universc/test/test_call.sh

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

+52 −13

Original line number	Diff line number	Diff line
		@@ -17,17 +17,30 @@ jobs:
		run: echo "hello world"

		test-cellranger:
		runs-on: ubuntu-latest
		runs-on: ubuntu-20.04
		steps:
		- uses: actions/checkout@v2
		- name: What OS is running
		run: uname -a
		- name: Where am i
		run: pwd; ls
		- name: call Cell Ranger
		run: which cellranger; cellranger -v
		- 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:
		test-repo:
		runs-on: ubuntu-latest
		steps:
		- uses: actions/checkout@v2
		@@ -38,6 +51,32 @@ jobs:
		- name: pull updates
		run: cd universc; git pull origin master
		- name: call UniverSC
		run: bash /universc/launch_universc.sh -v
		- name: test callas
		run: bash /universc/test/test_call.sh
		run: ls /universc/launch_universc.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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