Commit 6fbc1911 authored by TomKellyGenetics's avatar TomKellyGenetics
Browse files

configure timeout in min for github actions

parent 089e5b4d

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

+8 −8
Original line number Diff line number Diff line
@@ -94,7 +94,7 @@ jobs: 
        push: false 

    - name: Test 10x timeout

      timeout-minutes: 10      

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

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

    - name: Test 10x

      timeout-minutes: 10

      run: docker run ${{ secrets.DOCKER_HUB_USERNAME }}/universc:latest bash /universc/test/run_tests_cellranger_gh_actions.sh
@@ -119,7 +119,7 @@ jobs: 
        push: false

    - name: Test 10x

      timeout-minutes: 15

      run: timeout 10 docker run ${{ secrets.DOCKER_HUB_USERNAME }}/universc:latest bash /universc/test/run_tests_10x_v2_gh_actions.sh || code=$?; if [[ $code -ne 124 && $code -ne 0 ]]; then exit $code; fi

      run: timeout 10m docker run ${{ secrets.DOCKER_HUB_USERNAME }}/universc:latest bash /universc/test/run_tests_10x_v2_gh_actions.sh || code=$?; if [[ $code -ne 124 && $code -ne 0 ]]; then exit $code; fi



  test-10x-v3:

    runs-on: ubuntu-20.04
@@ -140,7 +140,7 @@ jobs: 
        tags: ${{ secrets.DOCKER_HUB_USERNAME }}/universc:latest

        push: false

    - name: Test 10x

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

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



  test-dropseq:

    runs-on: ubuntu-20.04
@@ -161,7 +161,7 @@ jobs: 
        tags: ${{ secrets.DOCKER_HUB_USERNAME }}/universc:latest

        push: false

    - name: Test DropSeq

      run: timeout 60 docker run ${{ secrets.DOCKER_HUB_USERNAME }}/universc:latest bash /universc/test/run_tests_dropseq_gh_actions.sh || code=$?; if [[ $code -ne 124 && $code -ne 0 ]]; then exit $code; fi

      run: timeout 60m docker run ${{ secrets.DOCKER_HUB_USERNAME }}/universc:latest bash /universc/test/run_tests_dropseq_gh_actions.sh || code=$?; if [[ $code -ne 124 && $code -ne 0 ]]; then exit $code; fi



  test-icell8:

    runs-on: ubuntu-20.04
@@ -182,7 +182,7 @@ jobs: 
        tags: ${{ secrets.DOCKER_HUB_USERNAME }}/universc:latest

        push: false

    - name: Test ICELL8

      run: timeout 15 docker run ${{ secrets.DOCKER_HUB_USERNAME }}/universc:latest bash /universc/test/run_tests_icell8_gh_actions.sh || code=$?; if [[ $code -ne 124 && $code -ne 0 ]]; then exit $code; fi

      run: timeout 15m docker run ${{ secrets.DOCKER_HUB_USERNAME }}/universc:latest bash /universc/test/run_tests_icell8_gh_actions.sh || code=$?; if [[ $code -ne 124 && $code -ne 0 ]]; then exit $code; fi



  test-smart-seq3:

    runs-on: ubuntu-20.04
@@ -203,7 +203,7 @@ jobs: 
        tags: ${{ secrets.DOCKER_HUB_USERNAME }}/universc:latest

        push: false

    - name: Test Smart-Seq3

      run: timeout 15 docker run ${{ secrets.DOCKER_HUB_USERNAME }}/universc:latest bash /universc/test/run_tests_smartseq3_gh_actions.sh || code=$?; if [[ $code -ne 124 && $code -ne 0 ]]; then exit $code; fi

      run: timeout 15m docker run ${{ secrets.DOCKER_HUB_USERNAME }}/universc:latest bash /universc/test/run_tests_smartseq3_gh_actions.sh || code=$?; if [[ $code -ne 124 && $code -ne 0 ]]; then exit $code; fi



  test-indrops-v3:

    runs-on: ubuntu-20.04
@@ -224,7 +224,7 @@ jobs: 
        tags: ${{ secrets.DOCKER_HUB_USERNAME }}/universc:latest

        push: false

    - name: Test inDrops v3

      run: timeout 30 docker run ${{ secrets.DOCKER_HUB_USERNAME }}/universc:latest bash /universc/test/run_tests_indropsv3_gh_actions.sh || code=$?; if [[ $code -ne 124 && $code -ne 0 ]]; then exit $code; fi

      run: timeout 30m docker run ${{ secrets.DOCKER_HUB_USERNAME }}/universc:latest bash /universc/test/run_tests_indropsv3_gh_actions.sh || code=$?; if [[ $code -ne 124 && $code -ne 0 ]]; then exit $code; fi



  test-sci-seq:

    runs-on: ubuntu-20.04
@@ -245,4 +245,4 @@ jobs: 
        tags: ${{ secrets.DOCKER_HUB_USERNAME }}/universc:latest

        push: false

    - name: Test SCI-Seq3

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

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

+5 −5
Original line number Diff line number Diff line
@@ -37,13 +37,13 @@ jobs: 
        run: echo "hello from universc"

    - name: Call UniverSC from image

      timeout-minutes: 15

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

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

    - name: Call UniverSC from container

      timeout-minutes: 15

      uses: addnab/docker-run-action@v1

      with:

        image: tomkellygenetics/universc:latest

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

        run: timeout 10m 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
@@ -74,7 +74,7 @@ jobs: 
        push: false 

    - name: Test 10x timeout

      timeout-minutes: 10      

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

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

    - name: Test 10x

      timeout-minutes: 10

      run: docker run ${{ secrets.DOCKER_HUB_USERNAME }}/universc:latest bash /universc/test/run_tests_cellranger_gh_actions.sh
@@ -99,7 +99,7 @@ jobs: 
        push: false

    - name: Test 10x

      timeout-minutes: 15

      run: timeout 10 docker run ${{ secrets.DOCKER_HUB_USERNAME }}/universc:latest bash /universc/test/run_tests_10x_v2_gh_actions.sh || code=$?; if [[ $code -ne 124 && $code -ne 0 ]]; then exit $code; fi

      run: timeout 10m docker run ${{ secrets.DOCKER_HUB_USERNAME }}/universc:latest bash /universc/test/run_tests_10x_v2_gh_actions.sh || code=$?; if [[ $code -ne 124 && $code -ne 0 ]]; then exit $code; fi



  test-10x:

    runs-on: ubuntu-20.04
@@ -121,4 +121,4 @@ jobs: 
        push: false

    - name: Test 10x

      timeout-minutes: 15

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

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

+1 −1
Original line number Diff line number Diff line
@@ -29,4 +29,4 @@ jobs: 
        tags: ${{ secrets.DOCKER_HUB_USERNAME }}/universc:latest

        push: false

    - name: Test DropSeq

      run: timeout 60 docker run ${{ secrets.DOCKER_HUB_USERNAME }}/universc:latest bash /universc/test/run_tests_dropseq_gh_actions.sh  || code=$?; if [[ $code -ne 124 && $code -ne 0 ]]; then exit $code; fi
 
      run: timeout 60m docker run ${{ secrets.DOCKER_HUB_USERNAME }}/universc:latest bash /universc/test/run_tests_dropseq_gh_actions.sh  || code=$?; if [[ $code -ne 124 && $code -ne 0 ]]; then exit $code; fi

.github/workflows/docker-test-icell8.yml

+1 −1
Original line number Diff line number Diff line
@@ -29,4 +29,4 @@ jobs: 
        tags: ${{ secrets.DOCKER_HUB_USERNAME }}/universc:latest

        push: false

    - name: Test ICELL8

      run: timeout 15 docker run ${{ secrets.DOCKER_HUB_USERNAME }}/universc:latest bash /universc/test/run_tests_icell8_gh_actions.sh  || code=$?; if [[ $code -ne 124 && $code -ne 0 ]]; then exit $code; fi
 
      run: timeout 15m docker run ${{ secrets.DOCKER_HUB_USERNAME }}/universc:latest bash /universc/test/run_tests_icell8_gh_actions.sh  || code=$?; if [[ $code -ne 124 && $code -ne 0 ]]; then exit $code; fi

.github/workflows/docker-test-indropsv3.yml

+1 −1
Original line number Diff line number Diff line
@@ -29,4 +29,4 @@ jobs: 
        tags: ${{ secrets.DOCKER_HUB_USERNAME }}/universc:latest

        push: false

    - name: Test inDrops v3

      run: timeout 30 docker run ${{ secrets.DOCKER_HUB_USERNAME }}/universc:latest bash /universc/test/run_tests_indropsv3_gh_actions.sh || code=$?; if [[ $code -ne 124 && $code -ne 0 ]]; then exit $code; fi
 
      run: timeout 30m docker run ${{ secrets.DOCKER_HUB_USERNAME }}/universc:latest bash /universc/test/run_tests_indropsv3_gh_actions.sh || code=$?; if [[ $code -ne 124 && $code -ne 0 ]]; then exit $code; fi

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