Commit 79d85e87 authored by TomKellyGenetics's avatar TomKellyGenetics
Browse files

Merge branch 'master' into dev

parents 9c1c0836 b1cb922d

.gitattributes

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test/cellranger_reference/cellranger-tiny-ref/1.2.0/ filter=lfs diff=lfs merge=lfs -text

test/cellranger_reference/cellranger-tiny-ref/1.2.0/fasta filter=lfs diff=lfs merge=lfs -text

test/cellranger_reference/cellranger-tiny-ref/1.2.0/genes filter=lfs diff=lfs merge=lfs -text

test/cellranger_reference/cellranger-tiny-ref/1.2.0/pickle filter=lfs diff=lfs merge=lfs -text

test/cellranger_reference/cellranger-tiny-ref/1.2.0/reference.json filter=lfs diff=lfs merge=lfs -text

test/cellranger_reference/cellranger-tiny-ref/1.2.0/star filter=lfs diff=lfs merge=lfs -text

test/cellranger_reference/cellranger-tiny-ref/3.0.0 filter=lfs diff=lfs merge=lfs -text

test/cellranger_reference/cellranger-tiny-ref/3.0.0/fasta filter=lfs diff=lfs merge=lfs -text

test/cellranger_reference/cellranger-tiny-ref/3.0.0/genes filter=lfs diff=lfs merge=lfs -text

test/cellranger_reference/cellranger-tiny-ref/3.0.0/pickle filter=lfs diff=lfs merge=lfs -text

test/cellranger_reference/cellranger-tiny-ref/3.0.0/reference.json filter=lfs diff=lfs merge=lfs -text

test/cellranger_reference/cellranger-tiny-ref/3.0.0/star filter=lfs diff=lfs merge=lfs -text

test/cellranger_reference/cellranger-tiny-ref/3.0.0/star/exonGeTrInfo.tab filter=lfs diff=lfs merge=lfs -text

test/cellranger_reference/cellranger-tiny-ref/3.0.0/star/genomeParameters.txt filter=lfs diff=lfs merge=lfs -text

test/cellranger_reference/cellranger-tiny-ref/3.0.0/star/sjdbList.fromGTF.out.tab filter=lfs diff=lfs merge=lfs -text

test/cellranger_reference/cellranger-tiny-ref/3.0.0/fasta/genome.fa filter=lfs diff=lfs merge=lfs -text

test/cellranger_reference/cellranger-tiny-ref/3.0.0/fasta/genome.fa.fai filter=lfs diff=lfs merge=lfs -text

test/cellranger_reference/cellranger-tiny-ref/3.0.0/pickle/genes.pickle filter=lfs diff=lfs merge=lfs -text

test/cellranger_reference/cellranger-tiny-ref/3.0.0/star/chrNameLength.txt filter=lfs diff=lfs merge=lfs -text

test/cellranger_reference/cellranger-tiny-ref/3.0.0/star/Genome filter=lfs diff=lfs merge=lfs -text

test/cellranger_reference/cellranger-tiny-ref/3.0.0/star/SA filter=lfs diff=lfs merge=lfs -text

test/cellranger_reference/cellranger-tiny-ref/3.0.0/star/chrLength.txt filter=lfs diff=lfs merge=lfs -text

test/cellranger_reference/cellranger-tiny-ref/3.0.0/star/exonInfo.tab filter=lfs diff=lfs merge=lfs -text

test/cellranger_reference/cellranger-tiny-ref/3.0.0/star/geneInfo.tab filter=lfs diff=lfs merge=lfs -text

test/cellranger_reference/cellranger-tiny-ref/3.0.0/star/sjdbInfo.txt filter=lfs diff=lfs merge=lfs -text

test/cellranger_reference/cellranger-tiny-ref/3.0.0/star/sjdbList.out.tab filter=lfs diff=lfs merge=lfs -text

test/cellranger_reference/cellranger-tiny-ref/3.0.0/star/transcriptInfo.tab filter=lfs diff=lfs merge=lfs -text

test/cellranger_reference/cellranger-tiny-ref/3.0.0/genes/genes.gtf filter=lfs diff=lfs merge=lfs -text

test/cellranger_reference/cellranger-tiny-ref/3.0.0/star/SAindex filter=lfs diff=lfs merge=lfs -text

test/cellranger_reference/cellranger-tiny-ref/3.0.0/star/chrName.txt filter=lfs diff=lfs merge=lfs -text

test/cellranger_reference/cellranger-tiny-ref/3.0.0/star/chrStart.txt filter=lfs diff=lfs merge=lfs -text

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/home/tom/repos/cellranger_convert/test/shared/icell8-test/72618_KU812_L001_R1_001.fastq.gz filter=lfs diff=lfs merge=lfs -text

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/home/tom/repos/cellranger_convert/test/shared/cellranger-tiny-fastq/3.0.0/tinygex_S1_L002_I1_001.fastq.gz filter=lfs diff=lfs merge=lfs -text

/home/tom/repos/cellranger_convert/test/shared/cellranger-tiny-fastq/3.0.0/tinygex_S1_L002_R1_001.fastq.gz filter=lfs diff=lfs merge=lfs -text

/home/tom/repos/cellranger_convert/test/shared/cellranger-tiny-fastq/3.0.0/tinygex_S1_L002_R2_001.fastq.gz filter=lfs diff=lfs merge=lfs -text

/home/tom/repos/cellranger_convert/test/shared/cellranger-tiny-fastq/1.2.0/read-I1_si-TTTCATGA_lane-008-chunk-001.fastq.gz filter=lfs diff=lfs merge=lfs -text

/home/tom/repos/cellranger_convert/test/shared/cellranger-tiny-fastq/1.2.0/read-RA_si-TTTCATGA_lane-008-chunk-001.fastq.gz filter=lfs diff=lfs merge=lfs -text

/home/tom/repos/cellranger_convert/test/shared/cellranger-tiny-fastq/3.0.0/tinygex_S1_L001_I1_001.fastq.gz filter=lfs diff=lfs merge=lfs -text

/home/tom/repos/cellranger_convert/test/shared/cellranger-tiny-fastq/3.0.0/tinygex_S1_L001_R1_001.fastq.gz filter=lfs diff=lfs merge=lfs -text

/home/tom/repos/cellranger_convert/test/shared/cellranger-tiny-fastq/3.0.0/tinygex_S1_L001_R2_001.fastq.gz filter=lfs diff=lfs merge=lfs -text

test/shared/indrop-v3-test/Undetermined_S0_L001_R2_001.fastq.gz filter=lfs diff=lfs merge=lfs -text

test/shared/indrop-v3-test/Undetermined_S0_L001_R3_001.fastq.gz filter=lfs diff=lfs merge=lfs -text

test/shared/indrop-v3-test/Undetermined_S0_L001_R4_001.fastq.gz filter=lfs diff=lfs merge=lfs -text

test/shared/indrop-v3-test/Undetermined_S0_L002_R1_001.fastq.gz filter=lfs diff=lfs merge=lfs -text

test/shared/indrop-v3-test/Undetermined_S0_L002_R2_001.fastq.gz filter=lfs diff=lfs merge=lfs -text

test/shared/indrop-v3-test/Undetermined_S0_L002_R3_001.fastq.gz filter=lfs diff=lfs merge=lfs -text

test/shared/indrop-v3-test/Undetermined_S0_L002_R4_001.fastq.gz filter=lfs diff=lfs merge=lfs -text

test/shared/indrop-v3-test/Undetermined_S0_L001_R1_001.fastq.gz filter=lfs diff=lfs merge=lfs -text

test/shared/dropseq-test/SRR1873277_Sample1_R1.fastq.gz filter=lfs diff=lfs merge=lfs -text

test/shared/dropseq-test/SRR1873277_Sample1_R2.fastq.gz filter=lfs diff=lfs merge=lfs -text

test/shared/smartseq3-test/Smartseq3_diySpike_I1.fastq.gz filter=lfs diff=lfs merge=lfs -text

test/shared/smartseq3-test/Smartseq3_diySpike_I2.fastq.gz filter=lfs diff=lfs merge=lfs -text

test/shared/smartseq3-test/Smartseq3_diySpike_R1.fastq.gz filter=lfs diff=lfs merge=lfs -text

test/shared/smartseq3-test/Smartseq3_diySpike_R2.fastq.gz filter=lfs diff=lfs merge=lfs -text

test/shared/sciseq-v3-test/SRR7827205_S1_R1.fastq.gz filter=lfs diff=lfs merge=lfs -text

test/shared/sciseq-v3-test/SRR7827205_S1_R2.fastq.gz filter=lfs diff=lfs merge=lfs -text

.github/workflows/docker-ci.yml

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name: CI to docker hub

on: push

jobs:

  test:

    runs-on: ubuntu-20.04

    steps:

      -

        name: Login to DockerHub

        uses: docker/login-action@v1 

        with:

          username: ${{ secrets.DOCKER_HUB_USERNAME }}

          password: ${{ secrets.DOCKER_HUB_ACCESS_TOKEN }}



  build:

    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 and push

      uses: docker/build-push-action@v2

      with:

        context: ./

        file: ./Dockerfile

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

        push: false



  push:

    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 and push

      uses: docker/build-push-action@v2

      with:

        context: ./

        file: ./Dockerfile

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

        push: true





  diagnostics:

    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 and push

      uses: docker/build-push-action@v2

      with:

        context: ./

        file: ./Dockerfile

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

        push: false

    - name: Hello world 

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

    - name: Repo diagnostics

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

    - name: Repo size

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

    - name: Parent directory diagnostics

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

    - name: Parent directory size

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

    - name: Grandparent directory diagnostics

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

    - name: Grandarent directory size

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

    - name: Root directory diagnostics

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

    - name: Root directory size

      run: df -h

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

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name: Docker compose build

on: push

jobs:

  test:

    runs-on: ubuntu-20.04

    steps:

      - uses: actions/checkout@v2

      - name: Build the stack

        run: docker-compose up -d

      - name: Status

        run: echo "build complete" 

      - name: Build diagnostics

        run: pwd; ls ../*; ls ../../*

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

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name: Run all tests in Docker

on: push

jobs:

  test:

    runs-on: ubuntu-20.04

    steps:

      -

        name: Login to DockerHub

        uses: docker/login-action@v1 

        with:

          username: ${{ secrets.DOCKER_HUB_USERNAME }}

          password: ${{ secrets.DOCKER_HUB_ACCESS_TOKEN }}



  build:

    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 and push

      uses: docker/build-push-action@v2

      with:

        context: ./

        file: ./Dockerfile

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

        push: false



  run:

    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 and push

      uses: docker/build-push-action@v2

      with:

        context: ./

        file: ./Dockerfile

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

        push: false

    - name: Hello world 

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

    - name: Diagnostics

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



  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 and push

      uses: docker/build-push-action@v2

      with:

        context: ./

        file: ./Dockerfile

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

        push: false

    - name: Test call

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



  test-10x-v2:

    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 and push

      uses: docker/build-push-action@v2

      with:

        context: ./

        file: ./Dockerfile

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

        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



  test-10x-v3:

    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 and push

      uses: docker/build-push-action@v2

      with:

        context: ./

        file: ./Dockerfile

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

        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



  test-cellranger:

    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 and push

      uses: docker/build-push-action@v2

      with:

        context: ./

        file: ./Dockerfile

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

        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



  test-dropseq:

    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 and push

      uses: docker/build-push-action@v2

      with:

        context: ./

        file: ./Dockerfile

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

        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



  test-icell8:

    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 and push

      uses: docker/build-push-action@v2

      with:

        context: ./

        file: ./Dockerfile

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

        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



  test-indrops-v3:

    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 and push

      uses: docker/build-push-action@v2

      with:

        context: ./

        file: ./Dockerfile

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

        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



  test-sci-seq:

    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 and push

      uses: docker/build-push-action@v2

      with:

        context: ./

        file: ./Dockerfile

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

        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



  test-smart-seq3:

    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 and push

      uses: docker/build-push-action@v2

      with:

        context: ./

        file: ./Dockerfile

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

        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

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