Commit b2aff8ba authored by TomKellyGenetics's avatar TomKellyGenetics
Browse files

configure timeout in min for github actions

parent 78a36319

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

+23 −12
Original line number Diff line number Diff line
@@ -92,12 +92,11 @@ jobs: 
        file: ./Dockerfile

        tags: ${{ secrets.DOCKER_HUB_USERNAME }}/universc:latest

        push: false 

    - name: Test 10x timeout

      timeout-minutes: 15      

      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 echo exit $code; exit $code; fi

    - name: Test 10x

      timeout-minutes: 15

      run: docker run ${{ secrets.DOCKER_HUB_USERNAME }}/universc:latest bash /universc/test/run_tests_cellranger_gh_actions.sh

    - name: clear environment

      run: rm -rf *

    - name: Test Cell Ranger

      timeout-minutes: 45      

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



  test-10x-v2:

    runs-on: ubuntu-20.04
@@ -141,8 +140,10 @@ jobs: 
        file: ./Dockerfile

        tags: ${{ secrets.DOCKER_HUB_USERNAME }}/universc:latest

        push: false

    - name: clear environment

      run: rm -rf *

    - name: Test 10x

      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 echo exit $code; exit $code; fi

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



  test-dropseq:

    runs-on: ubuntu-20.04
@@ -162,8 +163,10 @@ jobs: 
        file: ./Dockerfile

        tags: ${{ secrets.DOCKER_HUB_USERNAME }}/universc:latest

        push: false

    - name: clear environment

      run: rm -rf *

    - name: Test DropSeq

      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 echo exit $code; exit $code; fi

      run: docker run ${{ secrets.DOCKER_HUB_USERNAME }}/universc:latest timeout 120m bash /universc/test/run_tests_dropseq_gh_actions.sh || code=$?; if [[ $code -ne 124 && $code -ne 0 ]]; then echo exit $code; exit $code; fi



  test-icell8:

    runs-on: ubuntu-20.04
@@ -183,8 +186,10 @@ jobs: 
        file: ./Dockerfile

        tags: ${{ secrets.DOCKER_HUB_USERNAME }}/universc:latest

        push: false

    - name: clear environment

      run: rm -rf *

    - name: Test ICELL8

      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

      run: docker run ${{ secrets.DOCKER_HUB_USERNAME }}/universc:latest timeout 30m bash /universc/test/run_tests_icell8_gh_actions.sh || code=$?; if [[ $code -ne 124 && $code -ne 0 ]]; then exit $code; fi



  test-smart-seq3:

    runs-on: ubuntu-20.04
@@ -204,8 +209,10 @@ jobs: 
        file: ./Dockerfile

        tags: ${{ secrets.DOCKER_HUB_USERNAME }}/universc:latest

        push: false

    - name: clear environment

      run: rm -rf *

    - name: Test Smart-Seq3

      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

      run: run ${{ secrets.DOCKER_HUB_USERNAME }}/universc:latest timeout 30m bash /universc/test/run_tests_smartseq3_gh_actions.sh || code=$?; if [[ $code -ne 124 && $code -ne 0 ]]; then exit $code; fi



  test-indrops-v3:

    runs-on: ubuntu-20.04
@@ -225,8 +232,10 @@ jobs: 
        file: ./Dockerfile

        tags: ${{ secrets.DOCKER_HUB_USERNAME }}/universc:latest

        push: false

    - name: clear environment

      run: rm -rf *

    - name: Test inDrops v3

      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

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



  test-sci-seq:

    runs-on: ubuntu-20.04
@@ -246,5 +255,7 @@ jobs: 
        file: ./Dockerfile

        tags: ${{ secrets.DOCKER_HUB_USERNAME }}/universc:latest

        push: false

    - name: clear environment

      run: rm -rf *

    - name: Test SCI-Seq3

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

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

+13 −10
Original line number Diff line number Diff line
@@ -72,12 +72,11 @@ jobs: 
        file: ./Dockerfile

        tags: ${{ secrets.DOCKER_HUB_USERNAME }}/universc:latest

        push: false 

    - name: Test 10x timeout

      timeout-minutes: 10      

      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

    - name: clear environment

      run: rm -rf *

    - name: Test Cell Ranger

      timeout-minutes: 45      

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



  test-10x-v2:

    runs-on: ubuntu-20.04
@@ -97,9 +96,11 @@ jobs: 
        file: ./Dockerfile

        tags: ${{ secrets.DOCKER_HUB_USERNAME }}/universc:latest

        push: false

    - name: clear environment

      run: rm -rf *

    - name: Test 10x

      timeout-minutes: 15

      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

      timeout-minutes: 45

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



  test-10x:

    runs-on: ubuntu-20.04
@@ -119,6 +120,8 @@ jobs: 
        file: ./Dockerfile

        tags: ${{ secrets.DOCKER_HUB_USERNAME }}/universc:latest

        push: false

    - name: clear environment

      run: rm -rf *

    - name: Test 10x

      timeout-minutes: 15

      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
 
      timeout-minutes: 45

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

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

+3 −1
Original line number Diff line number Diff line
@@ -28,5 +28,7 @@ jobs: 
        file: ./Dockerfile

        tags: ${{ secrets.DOCKER_HUB_USERNAME }}/universc:latest

        push: false

    - name: clear environment

      run: rm -rf *

    - name: Test DropSeq

      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
 
      run: docker run ${{ secrets.DOCKER_HUB_USERNAME }}/universc:latest timeout 120m bash /universc/test/run_tests_dropseq_gh_actions.sh  || code=$?; if [[ $code -ne 124 && $code -ne 0 ]]; then exit $code; fi

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

+3 −1
Original line number Diff line number Diff line
@@ -28,5 +28,7 @@ jobs: 
        file: ./Dockerfile

        tags: ${{ secrets.DOCKER_HUB_USERNAME }}/universc:latest

        push: false

    - name: clear environment

      run: rm -rf *

    - name: Test ICELL8

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

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

+3 −1
Original line number Diff line number Diff line
@@ -28,5 +28,7 @@ jobs: 
        file: ./Dockerfile

        tags: ${{ secrets.DOCKER_HUB_USERNAME }}/universc:latest

        push: false

    - name: clear environment

      run: rm -rf *

    - name: Test inDrops v3

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

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