Commit c51d4491 authored by TomKellyGenetics's avatar TomKellyGenetics
Browse files

pull branch into testing environment for GitHub Actions

parent 1a53ae47

.github/workflows/docker-ci.yml

+6 −1
Original line number Diff line number Diff line
@@ -15,6 +15,8 @@ jobs: 
    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:
@@ -34,13 +36,14 @@ jobs: 
    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:
@@ -54,6 +57,8 @@ jobs: 
    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:

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

+2 −0
Original line number Diff line number Diff line
@@ -5,6 +5,8 @@ jobs: 
    runs-on: ubuntu-20.04

    steps:

      - uses: actions/checkout@v2

      - name: pull updates

        run: git pull --ff-only origin $(git branch --show-current)

      - name: Build the stack

        run: docker-compose up -d

      - name: Status

.github/workflows/docker-test-10x.yml

+10 −10
Original line number Diff line number Diff line
@@ -36,14 +36,14 @@ jobs: 
        image: tomkellygenetics/universc:test

        run: echo "hello from universc"

    - name: Call UniverSC from image

      timeout-minutes: 15

      run: docker run ${{ secrets.DOCKER_HUB_USERNAME }}/universc:test timeout 10 bash /universc/test/run_tests_10x_gh_actions.sh || code=$?; if [[ $code -ne 124 && $code -ne 0 ]]; then exit $code; fi

      timeout-minutes: 25

      run: docker run ${{ secrets.DOCKER_HUB_USERNAME }}/universc:test timeout 20m git pull --ff-only origin $(git branch --show-current) && bash /universc/test/run_tests_10x_gh_actions.sh || code=$?; if [[ $code -ne 124 && $code -ne 0 ]]; then exit $code; fi

    - name: Call UniverSC from container

      timeout-minutes: 15

      timeout-minutes: 25

      uses: addnab/docker-run-action@v1

      with:

        image: tomkellygenetics/universc:test

        run: timeout 10m bash /universc/test/run_tests_10x_gh_actions.sh || code=$?; if [[ $code -ne 124 && $code -ne 0 ]]; then exit $code; fi

        run: timeout 20m git pull --ff-only origin $(git branch --show-current) && bash /universc/test/run_tests_10x_gh_actions.sh || code=$?; if [[ $code -ne 124 && $code -ne 0 ]]; then exit $code; fi



  build:

    runs-on: ubuntu-20.04
@@ -75,8 +75,8 @@ jobs: 
    - name: clear environment

      run: rm -rf *

    - name: Test Cell Ranger

      timeout-minutes: 45      

      run: docker run ${{ secrets.DOCKER_HUB_USERNAME }}/universc:test timeout 30m bash /universc/test/run_tests_cellranger_gh_actions.sh || code=$?; if [[ $code -ne 124 && $code -ne 0 ]]; then exit $code; fi

      timeout-minutes: 25      

      run: docker run ${{ secrets.DOCKER_HUB_USERNAME }}/universc:test timeout 20m git pull --ff-only origin $(git branch --show-current) && bash /universc/test/run_tests_cellranger_gh_actions.sh || code=$?; if [[ $code -ne 124 && $code -ne 0 ]]; then exit $code; fi



  test-10x-v2:

    runs-on: ubuntu-20.04
@@ -99,8 +99,8 @@ jobs: 
    - name: clear environment

      run: rm -rf *

    - name: Test 10x

      timeout-minutes: 45

      run: docker run ${{ secrets.DOCKER_HUB_USERNAME }}/universc:test timeout 30m bash /universc/test/run_tests_10x_v2_gh_actions.sh || code=$?; if [[ $code -ne 124 && $code -ne 0 ]]; then exit $code; fi

      timeout-minutes: 25

      run: docker run ${{ secrets.DOCKER_HUB_USERNAME }}/universc:test timeout 20m git pull --ff-only origin $(git branch --show-current) && bash /universc/test/run_tests_10x_v2_gh_actions.sh || code=$?; if [[ $code -ne 124 && $code -ne 0 ]]; then exit $code; fi



  test-10x:

    runs-on: ubuntu-20.04
@@ -123,5 +123,5 @@ jobs: 
    - name: clear environment

      run: rm -rf *

    - name: Test 10x

      timeout-minutes: 45

      run: docker run ${{ secrets.DOCKER_HUB_USERNAME }}/universc:test timeout 30m bash /universc/test/run_tests_10x_gh_actions.sh || code=$?; if [[ $code -ne 124 && $code -ne 0 ]]; then exit $code; fi
 
      timeout-minutes: 25

      run: docker run ${{ secrets.DOCKER_HUB_USERNAME }}/universc:test timeout 20m git pull --ff-only origin $(git branch --show-current) && bash /universc/test/run_tests_10x_gh_actions.sh || code=$?; if [[ $code -ne 124 && $code -ne 0 ]]; then exit $code; fi

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

+8 −0
Original line number Diff line number Diff line
@@ -57,6 +57,8 @@ jobs: 
    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:
@@ -80,3 +82,9 @@ jobs: 
      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 log --reverse | tail -n 10

    - name: Pull Updates

      run: docker run ${{ secrets.DOCKER_HUB_USERNAME }}/universc:test git pull --ff-only origin $(git branch --show-current)

    - name: Git Status  

      run: docker run ${{ secrets.DOCKER_HUB_USERNAME }}/universc:test git log --reverse | tail -n 10

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

+1 −1
Original line number Diff line number Diff line
@@ -31,4 +31,4 @@ jobs: 
    - name: clear environment

      run: rm -rf *

    - name: Test DropSeq

      run: docker run ${{ secrets.DOCKER_HUB_USERNAME }}/universc:test timeout 120m bash /universc/test/run_tests_dropseq_gh_actions.sh  || code=$?; if [[ $code -ne 124 && $code -ne 0 ]]; then exit $code; fi
 
      run: docker run ${{ secrets.DOCKER_HUB_USERNAME }}/universc:test timeout 20m git pull --ff-only origin $(git branch --show-current) && bash /universc/test/run_tests_dropseq_gh_actions.sh  || code=$?; if [[ $code -ne 124 && $code -ne 0 ]]; then exit $code; fi

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