Commit bd216e14 authored by TomKellyGenetics's avatar TomKellyGenetics
Browse files

configure github actions to test in temporary test container

parent 79d85e87

.github/workflows/docker-ci.yml

+11 −11
Original line number Diff line number Diff line
@@ -27,7 +27,7 @@ jobs: 
      with:

        context: ./

        file: ./Dockerfile

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

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

        push: false



  push:
@@ -46,7 +46,7 @@ jobs: 
      with:

        context: ./

        file: ./Dockerfile

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

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

        push: true
@@ -66,23 +66,23 @@ jobs: 
      with:

        context: ./

        file: ./Dockerfile

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

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

        push: false

    - name: Hello world 

      run: docker run ${{ secrets.DOCKER_HUB_USERNAME }}/universc:latest echo "hello world"

      run: docker run ${{ secrets.DOCKER_HUB_USERNAME }}/universc:test echo "hello world"

    - name: Repo diagnostics

      run: docker run ${{ secrets.DOCKER_HUB_USERNAME }}/universc:latest pwd;ls -d */

      run: docker run ${{ secrets.DOCKER_HUB_USERNAME }}/universc:test pwd;ls -d */

    - name: Repo size

      run: docker run ${{ secrets.DOCKER_HUB_USERNAME }}/universc:latest pwd; du -ckh -d 1 *

      run: docker run ${{ secrets.DOCKER_HUB_USERNAME }}/universc:test pwd; du -ckh -d 1 *

    - name: Parent directory diagnostics

      run: docker run ${{ secrets.DOCKER_HUB_USERNAME }}/universc:latest pwd;ls -d ../*/

      run: docker run ${{ secrets.DOCKER_HUB_USERNAME }}/universc:test pwd;ls -d ../*/

    - name: Parent directory size

      run: docker run ${{ secrets.DOCKER_HUB_USERNAME }}/universc:latest pwd; du -ckh -d 1 ../*

      run: docker run ${{ secrets.DOCKER_HUB_USERNAME }}/universc:test pwd; du -ckh -d 1 ../*

    - name: Grandparent directory diagnostics

      run: docker run ${{ secrets.DOCKER_HUB_USERNAME }}/universc:latest pwd;ls -d ../../*/

      run: docker run ${{ secrets.DOCKER_HUB_USERNAME }}/universc:test pwd;ls -d ../../*/

    - name: Grandarent directory size

      run: docker run ${{ secrets.DOCKER_HUB_USERNAME }}/universc:latest pwd; du -ckh -d 2 ../../*

      run: docker run ${{ secrets.DOCKER_HUB_USERNAME }}/universc:test pwd; du -ckh -d 2 ../../*

    - name: Root directory diagnostics

      run: docker run ${{ secrets.DOCKER_HUB_USERNAME }}/universc:latest pwd;ls -d /*/

      run: docker run ${{ secrets.DOCKER_HUB_USERNAME }}/universc:test pwd;ls -d /*/

    - name: Root directory size

      run: df -h

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

+22 −22
Original line number Diff line number Diff line
@@ -28,7 +28,7 @@ jobs: 
      with:

        context: ./

        file: ./Dockerfile

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

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

        push: false



  run:
@@ -47,12 +47,12 @@ jobs: 
      with:

        context: ./

        file: ./Dockerfile

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

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

        push: false

    - name: Hello world 

      run: docker run ${{ secrets.DOCKER_HUB_USERNAME }}/universc:latest echo "hello world"

      run: docker run ${{ secrets.DOCKER_HUB_USERNAME }}/universc:test echo "hello world"

    - name: Diagnostics

      run: docker run ${{ secrets.DOCKER_HUB_USERNAME }}/universc:latest pwd;ls

      run: docker run ${{ secrets.DOCKER_HUB_USERNAME }}/universc:test pwd;ls



  call:

    runs-on: ubuntu-20.04
@@ -70,10 +70,10 @@ jobs: 
      with:

        context: ./

        file: ./Dockerfile

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

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

        push: false

    - name: Test call

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

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



  test-10x-v2:

    runs-on: ubuntu-20.04
@@ -91,13 +91,13 @@ jobs: 
      with:

        context: ./

        file: ./Dockerfile

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

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

        push: false

    - name: clear environment

      run: rm -rf *

    - name: Test 10x

      timeout-minutes: 300

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

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



  test-10x-v3:

    runs-on: ubuntu-20.04
@@ -115,12 +115,12 @@ jobs: 
      with:

        context: ./

        file: ./Dockerfile

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

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

        push: false

    - name: clear environment

      run: rm -rf *

    - name: Test 10x

      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

      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 echo exit $code; exit $code; fi



  test-cellranger:

    runs-on: ubuntu-20.04
@@ -138,13 +138,13 @@ jobs: 
      with:

        context: ./

        file: ./Dockerfile

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

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

        push: false 

    - 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

      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 echo exit $code; exit $code; fi



  test-dropseq:

    runs-on: ubuntu-20.04
@@ -162,12 +162,12 @@ jobs: 
      with:

        context: ./

        file: ./Dockerfile

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

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

        push: false

    - name: clear environment

      run: rm -rf *

    - name: Test DropSeq

      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

      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 echo exit $code; exit $code; fi



  test-icell8:

    runs-on: ubuntu-20.04
@@ -185,12 +185,12 @@ jobs: 
      with:

        context: ./

        file: ./Dockerfile

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

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

        push: false

    - name: clear environment

      run: rm -rf *

    - name: Test ICELL8

      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

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



  test-indrops-v3:

    runs-on: ubuntu-20.04
@@ -208,12 +208,12 @@ jobs: 
      with:

        context: ./

        file: ./Dockerfile

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

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

        push: false

    - name: clear environment

      run: rm -rf *

    - name: Test inDrops v3

      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

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



  test-sci-seq:

    runs-on: ubuntu-20.04
@@ -231,12 +231,12 @@ jobs: 
      with:

        context: ./

        file: ./Dockerfile

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

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

        push: false

    - name: clear environment

      run: rm -rf *

    - name: Test SCI-Seq3

      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

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



  test-smart-seq3:

    runs-on: ubuntu-20.04
@@ -254,10 +254,10 @@ jobs: 
      with:

        context: ./

        file: ./Dockerfile

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

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

        push: false

    - name: clear environment

      run: rm -rf *

    - name: Test Smart-Seq3

      run: docker 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

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

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

+11 −11
Original line number Diff line number Diff line
@@ -26,23 +26,23 @@ jobs: 
      with:

        context: ./

        file: ./Dockerfile

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

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

        push: false

    - name: Run image test

      run: docker run ${{ secrets.DOCKER_HUB_USERNAME }}/universc:latest echo "hello from universc"

      run: docker run ${{ secrets.DOCKER_HUB_USERNAME }}/universc:test echo "hello from universc"

    - name: Call UniverSC test

      uses: addnab/docker-run-action@v1

      with:

        image: tomkellygenetics/universc:latest

        image: tomkellygenetics/universc:test

        run: echo "hello from universc"

    - name: Call UniverSC from image

      timeout-minutes: 15

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

      run: docker run ${{ secrets.DOCKER_HUB_USERNAME }}/universc:test timeout 10 bash /universc/test/run_tests_10x_gh_actions.sh || code=$?; 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

        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



  build:
@@ -70,13 +70,13 @@ jobs: 
      with:

        context: ./

        file: ./Dockerfile

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

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

        push: false 

    - 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

      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



  test-10x-v2:

    runs-on: ubuntu-20.04
@@ -94,13 +94,13 @@ jobs: 
      with:

        context: ./

        file: ./Dockerfile

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

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

        push: false

    - name: clear environment

      run: rm -rf *

    - name: Test 10x

      timeout-minutes: 45

      run: docker 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

      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



  test-10x:

    runs-on: ubuntu-20.04
@@ -118,10 +118,10 @@ jobs: 
      with:

        context: ./

        file: ./Dockerfile

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

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

        push: false

    - name: clear environment

      run: rm -rf *

    - name: Test 10x

      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
 
      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

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

+4 −4
Original line number Diff line number Diff line
@@ -21,7 +21,7 @@ jobs: 
        with:

          context: ./

          file: ./Dockerfile

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

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

          push: false

          cache-from: type=local,src=/tmp/.buildx-cache

          cache-to: type=local,dest=/tmp/.buildx-cache
@@ -30,7 +30,7 @@ jobs: 
      - name: Status

        run: echo "build complete" 

      - name: Hello world

        run: docker run ${{ secrets.DOCKER_HUB_USERNAME }}/universc:latest echo "hello world"

        run: docker run ${{ secrets.DOCKER_HUB_USERNAME }}/universc:test echo "hello world"





  test-call:
@@ -54,7 +54,7 @@ jobs: 
        with:

          context: ./

          file: ./Dockerfile

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

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

          push: false

          cache-from: type=local,src=/tmp/.buildx-cache

          cache-to: type=local,dest=/tmp/.buildx-cache
@@ -63,5 +63,5 @@ jobs: 
      - name: Status

        run: echo "build complete" 

      - name: Call functions

        run: docker run ${{ secrets.DOCKER_HUB_USERNAME }}universc:latest git pull origin master && bash /universc/test/test_call.sh

        run: docker run ${{ secrets.DOCKER_HUB_USERNAME }}universc:test git pull origin master && bash /universc/test/test_call.sh

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

+7 −7
Original line number Diff line number Diff line
@@ -31,7 +31,7 @@ jobs: 
      with:

        context: ./

        file: ./Dockerfile

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

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

        push: false

    - name: Hello world 

      run: docker run ${{ secrets.DOCKER_HUB_USERNAME }}/cellranger_clean:latest echo "hello world"
@@ -68,15 +68,15 @@ jobs: 
      with:

        context: ./

        file: ./Dockerfile

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

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

        push: false

    - name: Hello world

      run: docker run ${{ secrets.DOCKER_HUB_USERNAME }}/universc:latest echo "hello world"

      run: docker run ${{ secrets.DOCKER_HUB_USERNAME }}/universc:test echo "hello world"

    - name: Diagnostics

      run: docker run ${{ secrets.DOCKER_HUB_USERNAME }}/universc:latest pwd;ls

      run: docker run ${{ secrets.DOCKER_HUB_USERNAME }}/universc:test pwd;ls

    - name: Cell Ranger Call

      run: docker run ${{ secrets.DOCKER_HUB_USERNAME }}/universc:latest cellranger count --help

      run: docker run ${{ secrets.DOCKER_HUB_USERNAME }}/universc:test cellranger count --help

    - name: UniverSC Call

      run: docker run ${{ secrets.DOCKER_HUB_USERNAME }}/universc:latest bash /universc/launch_universc.sh -v

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

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