Merge branch 'master' of github.com:minoda-lab/universc (1b0fc528) · Commits · github_fork / Universc

.github/workflows/docker-ci-runner.yml

deleted100644 → 0

+0 −64

Original line number	Diff line number	Diff line
		name: CI to Docker hub runners
		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: Repo diagnostics
		run: docker run ${{ secrets.DOCKER_HUB_USERNAME }}/universc:latest pwd;ls
		- name: Repo size
		run: docker run ${{ secrets.DOCKER_HUB_USERNAME }}/universc:latest pwd; du -sckh *
		- name: Parent directory diagnostics
		run: docker run ${{ secrets.DOCKER_HUB_USERNAME }}/universc:latest pwd;ls ..
		- name: Parent directory size
		run: docker run ${{ secrets.DOCKER_HUB_USERNAME }}/universc:latest pwd; du -sckh ../*
		- name: Root directory diagnostics
		run: docker run ${{ secrets.DOCKER_HUB_USERNAME }}/universc:latest pwd;ls /*
		- name: Root directory size
		run: docker run ${{ secrets.DOCKER_HUB_USERNAME }}/universc:latest pwd; du -sckh /*

.github/workflows/docker-ci.yml

+39 −1

Original line number	Diff line number	Diff line
		name: CI to Docker hub
		name: CI to docker hub
		on: push
		jobs:
		test:
		@@ -49,3 +49,41 @@ jobs:
		tags: ${{ secrets.DOCKER_HUB_USERNAME }}/universc:latest
		push: true


		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: Repo diagnostics
		run: docker run ${{ secrets.DOCKER_HUB_USERNAME }}/universc:latest pwd;ls -d */
		- name: Repo size
		run: docker run ${{ secrets.DOCKER_HUB_USERNAME }}/universc:latest pwd; du -sckh --max=depth=1 *
		- name: Parent directory diagnostics
		run: docker run ${{ secrets.DOCKER_HUB_USERNAME }}/universc:latest pwd;ls -d ../*/
		- name: Parent directory size
		run: docker run ${{ secrets.DOCKER_HUB_USERNAME }}/universc:latest pwd; du -sckh --max-depth=1 ../*
		- name: Grandparent directory diagnostics
		run: docker run ${{ secrets.DOCKER_HUB_USERNAME }}/universc:latest pwd;ls -d ../../*/
		- name: Grandarent directory size
		run: docker run ${{ secrets.DOCKER_HUB_USERNAME }}/universc:latest pwd; du -sckh --max-depth=2 ../../*
		- name: Root directory diagnostics
		run: docker run ${{ secrets.DOCKER_HUB_USERNAME }}/universc:latest pwd;ls -d /*/
		- name: Root directory size
		run: docker run ${{ secrets.DOCKER_HUB_USERNAME }}/universc:latest pwd; du -sckh --max-depth=1 /*

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

0 → 100644

+13 −0

Original line number	Diff line number	Diff line
		name: Docker compose build
		on: push
		jobs:
		test:
		runs-on: ubuntu-20.04
		steps:
		- uses: actions/checkout@v2
		- name: Build the stack
		run: docker-compose up -d
		- name: Status
		run: echo "build complete"
		- name: Build diagnostics
		run: pwd; ls ../; ls ../../

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

+43 −1

Original line number	Diff line number	Diff line
		name: Run tests in Docker
		name: Run all tests in Docker
		on: push
		jobs:
		test:
		@@ -136,3 +136,45 @@ jobs:
		push: false
		- name: Test ICELL8
		run: docker run ${{ secrets.DOCKER_HUB_USERNAME }}/universc:latest bash /universc/test/run_tests_icell8_gh_actions.sh

		test-smart-seq3:
		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 Smart-Seq3
		run: docker run ${{ secrets.DOCKER_HUB_USERNAME }}/universc:latest bash /universc/test/run_tests_smartseq3_gh_actions.sh

		test-indrops-v3:
		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 inDrops v3
		run: docker run ${{ secrets.DOCKER_HUB_USERNAME }}/universc:latest bash /universc/test/run_tests_indropsv3_gh_actions.sh

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

+4 −3

Original line number	Diff line number	Diff line
		name: Docker Test
		name: Docker build image
		on: push
		jobs:
		test:
		@@ -21,15 +21,16 @@ jobs:
		uses: docker/build-push-action@v2
		with:
		context: ./
		builder: ${{ steps.buildx.outputs.name }}
		file: ./Dockerfile
		tags: ${{ secrets.DOCKER_HUB_USERNAME }}/universc:latest
		push: true
		push: false
		cache-from: type=local,src=/tmp/.buildx-cache
		cache-to: type=local,dest=/tmp/.buildx-cache
		- name: Image digest
		run: echo ${{ steps.docker_build.outputs.digest }}
		- name: Status
		run: echo "build complete"
		- name: Hello world
		run: docker run ${{ secrets.DOCKER_HUB_USERNAME }}/universc:latest echo "hello world"
		- name: Call functions
		run: docker run ${{ secrets.DOCKER_HUB_USERNAME }}universc:latest bash /universc/test/test_call.sh

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