Commit 26d77b9c authored by TomKellyGenetics's avatar TomKellyGenetics
Browse files

Merge branch 'dev' of https://github.com/minoda-lab/universc into dev

parents bc882509 24a41648

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

+1 −1
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@@ -167,7 +167,7 @@ jobs: 
    - name: clear environment

      run: rm -rf *

    - name: Test DropSeq

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

      run: docker run ${{ secrets.DOCKER_HUB_USERNAME }}/universc:test timeout 45m  /universc/test/run_tests_dropseq_gh_actions.sh || code=$?; if [[ $code -ne 124 && $code -ne 0 ]]; then echo exit $code; exit $code; fi



  test-icell8:

    runs-on: ubuntu-20.04

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

+5 −5
Original line number Diff line number Diff line
@@ -36,10 +36,10 @@ jobs: 
        image: tomkellygenetics/universc:test

        run: echo "hello from universc"

    - name: Call UniverSC from image

      timeout-minutes: 25

      timeout-minutes: 30

      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

      timeout-minutes: 30

      uses: addnab/docker-run-action@v1

      with:

        image: tomkellygenetics/universc:test
@@ -75,7 +75,7 @@ jobs: 
    - name: clear environment

      run: rm -rf *

    - name: Test Cell Ranger

      timeout-minutes: 25      

      timeout-minutes: 30      

      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:
@@ -99,7 +99,7 @@ jobs: 
    - name: clear environment

      run: rm -rf *

    - name: Test 10x

      timeout-minutes: 25

      timeout-minutes: 30

      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:
@@ -123,5 +123,5 @@ jobs: 
    - name: clear environment

      run: rm -rf *

    - name: Test 10x

      timeout-minutes: 25

      timeout-minutes: 30

      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-build.yml

+38 −19
Original line number Diff line number Diff line
@@ -10,12 +10,8 @@ jobs: 
          username: ${{ secrets.DOCKER_HUB_USERNAME }}

          password: ${{ secrets.DOCKER_HUB_ACCESS_TOKEN }}

          registry: ${{ env.REGISTRY }}

      - uses: satackey/action-docker-layer-caching@v0.0.11

        # Ignore the failure of a step and avoid terminating the job.

        continue-on-error: true

      - name: Build the Docker image

        run: docker build . --file Dockerfile --tag my-image-name:$(date +%s)

      - uses: satackey/action-docker-layer-caching@v0.0.11

      - name: Build and push

        uses: docker/build-push-action@v2

        with:
@@ -23,8 +19,6 @@ jobs: 
          file: ./Dockerfile

          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

      - name: Image digest

        run: echo ${{ steps.docker_build.outputs.digest }}

      - name: Status
@@ -32,12 +26,10 @@ jobs: 
      - name: Hello world

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





  test-call:

  test-build-cache:

    runs-on: ubuntu-20.04

    steps:

      - uses: actions/checkout@v2

      - uses: docker/setup-buildx-action@v1

      - uses: docker/login-action@v1

        with:

          username: ${{ secrets.DOCKER_HUB_USERNAME }}
@@ -47,21 +39,48 @@ jobs: 
        # Ignore the failure of a step and avoid terminating the job.

        continue-on-error: true

      - name: Build the Docker image

        run: docker build . --file Dockerfile --tag my-image-name:$(date +%s)

        run: docker build . --file Dockerfile --tag universc:$(date +%s)

      - uses: satackey/action-docker-layer-caching@v0.0.11

      - name: Build and push

        uses: docker/build-push-action@v2

        continue-on-error: true

      - name: Build from cache

        uses: whoan/docker-build-with-cache-action@v5

        with:

          context: ./

          file: ./Dockerfile

          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

          username: ${{ secrets.DOCKER_HUB_USERNAME }} whoan

          password: "${{ secrets.GITHUB_TOKEN }}"

          registry: docker.pkg.github.com

          image_name: test

      - name: Build from cache

        uses: whoan/docker-build-with-cache-action@v5

        with:

          username: ${{ secrets.DOCKER_HUB_USERNAME }}

          password: ${{ secrets.DOCKER_HUB_ACCESS_TOKEN }}

          registry: ${{ env.REGISTRY }}

          dockerfile: ./Dockerfile

          image_name: test

      - name: Image digest

        run: echo ${{ steps.docker_build.outputs.digest }}

      - name: Status

        run: echo "build complete" 

      - name: Hello world

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





  test-call:

    runs-on: ubuntu-20.04

    steps:

      - uses: actions/checkout@v2

      - 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 the Docker image

        run: docker build . --file Dockerfile --tag universc:test

      - name: Image digest

        run: echo ${{ steps.docker_build.outputs.digest }}

      - name: Status

        run: echo "build complete" 

      - name: Call functions

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

        run: docker run universc:test  bash /universc/test/test_call.sh

.version

+1 −1
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1.0.3
 
1.1.0

CHANGELOG

+6 −0
Original line number Diff line number Diff line 
### 1.1.0 (in dev)



- add support for 5' technologies (e.g., Smart-Seq3, ICELL8 5')



- compatilibility with counting reads for non-UMI technologies (e.g., Smart-Seq2)



### 1.0.3



- unit tests for inDrops v3, SCI-Seq, Smart-Seq3

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