Commit dbbf0071 authored by TomKellyGenetics's avatar TomKellyGenetics
Browse files

pull branch into testing environment for GitHub Actions within test job

parent 1695ac77

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

+8 −8
Original line number Diff line number Diff line
@@ -97,7 +97,7 @@ jobs: 
      run: rm -rf *

    - name: Test 10x

      timeout-minutes: 300

      run: docker run ${{ secrets.DOCKER_HUB_USERNAME }}/universc:test timeout 20m git -C ./universc pull --ff-only origin $(git branch --show-current) 0m bash0m bash bash /universc/test/run_tests_10x_v2_gh_actions.sh || code=$?; if [[ $code -ne 124 && $code -ne 0 ]]; then echo exit $code; exit $code; fi

      run: docker run ${{ secrets.DOCKER_HUB_USERNAME }}/universc:test timeout 20m  /universc/test/run_tests_10x_v2_gh_actions.sh || code=$?; if [[ $code -ne 124 && $code -ne 0 ]]; then echo exit $code; exit $code; fi



  test-10x-v3:

    runs-on: ubuntu-20.04
@@ -120,7 +120,7 @@ jobs: 
    - name: clear environment

      run: rm -rf *

    - name: Test 10x

      run: docker run ${{ secrets.DOCKER_HUB_USERNAME }}/universc:test timeout 30m git -C ./universc pull --ff-only origin $(git branch --show-current) 0m bash0m bash bash /universc/test/run_tests_10x_gh_actions.sh || code=$?; if [[ $code -ne 124 && $code -ne 0 ]]; then echo exit $code; exit $code; fi

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



  test-cellranger:

    runs-on: ubuntu-20.04
@@ -144,7 +144,7 @@ jobs: 
      run: rm -rf *

    - name: Test Cell Ranger

      timeout-minutes: 45      

      run: docker run ${{ secrets.DOCKER_HUB_USERNAME }}/universc:test timeout 30m git -C ./universc pull --ff-only origin $(git branch --show-current) 0m bash0m bash bash /universc/test/run_tests_cellranger_gh_actions.sh || code=$?; if [[ $code -ne 124 && $code -ne 0 ]]; then echo exit $code; exit $code; fi

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



  test-dropseq:

    runs-on: ubuntu-20.04
@@ -167,7 +167,7 @@ jobs: 
    - name: clear environment

      run: rm -rf *

    - name: Test DropSeq

      run: docker run ${{ secrets.DOCKER_HUB_USERNAME }}/universc:test timeout 120m git -C ./universc pull --ff-only origin $(git branch --show-current) 0m bash0m bash bash /universc/test/run_tests_dropseq_gh_actions.sh || code=$?; if [[ $code -ne 124 && $code -ne 0 ]]; then echo exit $code; exit $code; fi

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



  test-icell8:

    runs-on: ubuntu-20.04
@@ -190,7 +190,7 @@ jobs: 
    - name: clear environment

      run: rm -rf *

    - name: Test ICELL8

      run: docker run ${{ secrets.DOCKER_HUB_USERNAME }}/universc:test timeout 30m git -C ./universc pull --ff-only origin $(git branch --show-current) 0m bash0m bash bash /universc/test/run_tests_icell8_gh_actions.sh || code=$?; if [[ $code -ne 124 && $code -ne 0 ]]; then exit $code; fi

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



  test-indrops-v3:

    runs-on: ubuntu-20.04
@@ -213,7 +213,7 @@ jobs: 
    - name: clear environment

      run: rm -rf *

    - name: Test inDrops v3

      run: docker run ${{ secrets.DOCKER_HUB_USERNAME }}/universc:test timeout 30m git -C ./universc pull --ff-only origin $(git branch --show-current) 0m bash0m bash bash /universc/test/run_tests_indropsv3_gh_actions.sh || code=$?; if [[ $code -ne 124 && $code -ne 0 ]]; then exit $code; fi

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



  test-sci-seq:

    runs-on: ubuntu-20.04
@@ -236,7 +236,7 @@ jobs: 
    - name: clear environment

      run: rm -rf *

    - name: Test SCI-Seq3

      run: docker run ${{ secrets.DOCKER_HUB_USERNAME }}/universc:test timeout 30m git -C ./universc pull --ff-only origin $(git branch --show-current) 0m bash0m bash bash /universc/test/run_tests_sciseq_gh_actions.sh || code=$?; if [[ $code -ne 124 && $code -ne 0 ]]; then exit $code; fi

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



  test-smart-seq3:

    runs-on: ubuntu-20.04
@@ -259,5 +259,5 @@ jobs: 
    - name: clear environment

      run: rm -rf *

    - name: Test Smart-Seq3

      run: docker run ${{ secrets.DOCKER_HUB_USERNAME }}/universc:test timeout 30m git -C ./universc pull --ff-only origin $(git branch --show-current) 0m bash0m bash bash /universc/test/run_tests_smartseq3_gh_actions.sh || code=$?; if [[ $code -ne 124 && $code -ne 0 ]]; then exit $code; fi

      run: docker run ${{ secrets.DOCKER_HUB_USERNAME }}/universc:test timeout 30m  /universc/test/run_tests_smartseq3_gh_actions.sh || code=$?; 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: 25

      run: docker run ${{ secrets.DOCKER_HUB_USERNAME }}/universc:test timeout 20m git -C ./universc 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

      run: docker run ${{ secrets.DOCKER_HUB_USERNAME }}/universc:test timeout 20m bash /universc/test/run_tests_10x_gh_actions.sh || code=$?; if [[ $code -ne 124 && $code -ne 0 ]]; then exit $code; fi

    - name: Call UniverSC from container

      timeout-minutes: 25

      uses: addnab/docker-run-action@v1

      with:

        image: tomkellygenetics/universc:test

        run: timeout 20m git -C ./universc 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

        run: timeout 20m 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
@@ -76,7 +76,7 @@ jobs: 
      run: rm -rf *

    - name: Test Cell Ranger

      timeout-minutes: 25      

      run: docker run ${{ secrets.DOCKER_HUB_USERNAME }}/universc:test timeout 20m git -C ./universc 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

      run: docker run ${{ secrets.DOCKER_HUB_USERNAME }}/universc:test timeout 20m bash /universc/test/run_tests_cellranger_gh_actions.sh || code=$?; if [[ $code -ne 124 && $code -ne 0 ]]; then exit $code; fi



  test-10x-v2:

    runs-on: ubuntu-20.04
@@ -100,7 +100,7 @@ jobs: 
      run: rm -rf *

    - name: Test 10x

      timeout-minutes: 25

      run: docker run ${{ secrets.DOCKER_HUB_USERNAME }}/universc:test timeout 20m git -C ./universc 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

      run: docker run ${{ secrets.DOCKER_HUB_USERNAME }}/universc:test timeout 20m bash /universc/test/run_tests_10x_v2_gh_actions.sh || code=$?; if [[ $code -ne 124 && $code -ne 0 ]]; then exit $code; fi



  test-10x:

    runs-on: ubuntu-20.04
@@ -124,4 +124,4 @@ jobs: 
      run: rm -rf *

    - name: Test 10x

      timeout-minutes: 25

      run: docker run ${{ secrets.DOCKER_HUB_USERNAME }}/universc:test timeout 20m git -C ./universc 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
 
      run: docker run ${{ secrets.DOCKER_HUB_USERNAME }}/universc:test timeout 20m bash /universc/test/run_tests_10x_gh_actions.sh || code=$?; if [[ $code -ne 124 && $code -ne 0 ]]; then exit $code; fi

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

+2 −2
Original line number Diff line number Diff line
@@ -83,8 +83,8 @@ jobs: 
    - 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

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

    - name: Pull Updates

      run: docker run ${{ secrets.DOCKER_HUB_USERNAME }}/universc:test git -C ./universc 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
 
      run: docker run ${{ secrets.DOCKER_HUB_USERNAME }}/universc:test git -C ./universc 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 20m git -C ./universc 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
 
      run: docker run ${{ secrets.DOCKER_HUB_USERNAME }}/universc:test timeout 20m bash /universc/test/run_tests_dropseq_gh_actions.sh  || code=$?; 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
@@ -31,4 +31,4 @@ jobs: 
    - name: clear environment

      run: rm -rf *

    - name: Test ICELL8

      run: docker run ${{ secrets.DOCKER_HUB_USERNAME }}/universc:test timeout 15m git -C ./universc pull --ff-only origin $(git branch --show-current) 5m bash5m bash bash /universc/test/run_tests_icell8_gh_actions.sh  || code=$?; if [[ $code -ne 124 && $code -ne 0 ]]; then exit $code; fi
 
      run: docker run ${{ secrets.DOCKER_HUB_USERNAME }}/universc:test timeout 15m bash /universc/test/run_tests_icell8_gh_actions.sh  || code=$?; if [[ $code -ne 124 && $code -ne 0 ]]; then exit $code; fi

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