Commit e44705a0 authored by TomKellyGenetics's avatar TomKellyGenetics
Browse files

update test scripts for github actions

parent 50cebbd3

.github/workflows/docker-ci.yml

+1 −2
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@@ -85,5 +85,4 @@ jobs: 
    - name: Root directory diagnostics

    - name: Root directory diagnostics

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

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

    - name: Root directory size

    - name: Root directory size

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

      run: df -h

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

0 → 100644
+32 −0
Original line number Original line Diff line number Diff line 
name: Test SCI-Seq

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" 



  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: Test SCI-Seq

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

test/run_tests_indropsv3_gh_actions.sh

+3 −10
Original line number Original line Diff line number Diff line
@@ -10,19 +10,12 @@ export PATH=${HOME}/local/bin/cellranger-3.0.2:$PATH 
cellrangerversion=`cellranger count --version | head -n 2 | tail -n 1 | cut -f2 -d'(' | cut -f1 -d')'`

cellrangerversion=`cellranger count --version | head -n 2 | tail -n 1 | cut -f2 -d'(' | cut -f1 -d')'`

cellrangerpath=`which cellranger`

cellrangerpath=`which cellranger`





# set up cellranger reference

rm -rf test/cellranger_reference/cellranger-tiny-ref/1.2.0 test/cellranger_reference/cellranger-tiny-ref/3.0.0

if [[ ! -f test/cellranger_reference/cellranger-tiny-ref/3.0.0/star/SA ]] && [[ -f $(dirname $cellrangerpath)/cellranger-tiny-ref/3.0.0/star/SA ]]; then

make -C test/cellranger_reference/cellranger-tiny-ref reference

    ln $(dirname $cellrangerpath)/cellranger-tiny-ref/3.0.0/star/SA test/cellranger_reference/cellranger-tiny-ref/3.0.0/star/SA

rm -rf test/cellranger_reference/cellranger-tiny-ref/1.2.0

fi

if [[ ! -f test/cellranger_reference/cellranger-tiny-ref/1.2.0/star/SA ]] && [[ -f $(dirname $cellrangerpath)/cellranger-tiny-ref/1.2.0/star/SA ]]; then

    ln $(dirname $cellrangerpath)/cellranger-tiny-ref/1.2.0/star/SA test/cellranger_reference/cellranger-tiny-ref/1.2.0/star/SA

fi





rm -rf test/shared/dropseq-test/* test/shared/cellranger-tiny-fastq/* test/shared/mappa-test/ test/shared/icell8-test/ test/shared/smartseq3-test/

rm -rf test/shared/dropseq-test/* test/shared/cellranger-tiny-fastq/* test/shared/mappa-test/ test/shared/icell8-test/ test/shared/smartseq3-test/





rm -rf  test/cellranger_reference/cellranger-tiny-ref/1.2.0

unpigz -f test/shared/indrop-v3-test/*fastq.gz



if [ -d test-indrop-v3 ];then

if [ -d test-indrop-v3 ];then

    rm -rf test-indrop-v3

    rm -rf test-indrop-v3

fi

fi

test/run_tests_sciseq_gh_actions.sh

0 → 100755
+23 −0
Original line number Original line Diff line number Diff line 
#!/bin/bash



# run tests in universc directory (parent of test directory)

cd $(dirname ${BASH_SOURCE[0]})/..

pwd



# used to export to PATH for testing on SGE server

export PATH=${HOME}/local/bin/cellranger-3.0.2:$PATH



cellrangerversion=`cellranger count --version | head -n 2 | tail -n 1 | cut -f2 -d'(' | cut -f1 -d')'`

cellrangerpath=`which cellranger`



rm -rf test/cellranger_reference/cellranger-tiny-ref/1.2.0 test/cellranger_reference/cellranger-tiny-ref/3.0.0

make -C test/cellranger_reference/cellranger-tiny-ref reference

rm -rf test/cellranger_reference/cellranger-tiny-ref/1.2.0



rm -rf  test/shared/dropseq-test/* test/shared/cellranger-tiny-fastq/* test/shared/mappa-test/  test/shared/icell8-test/ test/shared/indrop-v3-test/ test/shared/smartseq3-test/



bash launch_universc.sh --id "test-sciseq" --technology "sciseq" \

 --reference "test/cellranger_reference/cellranger-tiny-ref/3.0.0" \

 --read1 "test/shared/sciseq-test/SRR7827205_S1_R1.fastq" \

 --read2 "test/shared/sciseq-test/SRR7827205_S1_R2.fastq" \

 --jobmode "local" --localcores 1

test/run_tests_smartseq3_gh_actions.sh

+4 −61
Original line number Original line Diff line number Diff line
@@ -10,53 +10,20 @@ export PATH=${HOME}/local/bin/cellranger-3.0.2:$PATH 
cellrangerversion=`cellranger count --version | head -n 2 | tail -n 1 | cut -f2 -d'(' | cut -f1 -d')'`

cellrangerversion=`cellranger count --version | head -n 2 | tail -n 1 | cut -f2 -d'(' | cut -f1 -d')'`

cellrangerpath=`which cellranger`

cellrangerpath=`which cellranger`





# set up cellranger reference

rm -rf test/cellranger_reference/cellranger-tiny-ref/1.2.0 test/cellranger_reference/cellranger-tiny-ref/3.0.0

if [[ ! -f test/cellranger_reference/cellranger-tiny-ref/3.0.0/star/SA ]] && [[ -f $(dirname $cellrangerpath)/cellranger-tiny-ref/3.0.0/star/SA ]]; then

make -C test/cellranger_reference/cellranger-tiny-ref reference

    ln $(dirname $cellrangerpath)/cellranger-tiny-ref/3.0.0/star/SA test/cellranger_reference/cellranger-tiny-ref/3.0.0/star/SA

fi

if [[ ! -f test/cellranger_reference/cellranger-tiny-ref/1.2.0/star/SA ]] && [[ -f $(dirname $cellrangerpath)/cellranger-tiny-ref/1.2.0/star/SA ]]; then

    ln $(dirname $cellrangerpath)/cellranger-tiny-ref/1.2.0/star/SA test/cellranger_reference/cellranger-tiny-ref/1.2.0/star/SA

fi



rm -rf test/shared/cellranger-tiny-fastq/* test/shared/mappa-test/ test/shared/icell8-test/ test/shared/indrop-v3-test/

rm -rf test/cellranger_reference/cellranger-tiny-ref/1.2.0

rm -rf test/cellranger_reference/cellranger-tiny-ref/1.2.0





rm -rf  test/shared/dropseq-test/* test/shared/cellranger-tiny-fastq/* test/shared/mappa-test/  test/shared/icell8-test/ test/shared/indrop-v3-test/



# compress all input files

# compress all input files

if [[ -f test/shared/smartseq3-test/*fastq ]]; then

if [[ -f test/shared/smartseq3-test/*fastq ]]; then

    gzip test/shared/smartseq3-test/*fastq

    gzip test/shared/smartseq3-test/*fastq

fi

fi





# reset test data (compress)

 if [[ -f test/shared/smartseq3-test/Smartseq3_diySpike_S1_L001_R1_001.fastq ]]; then

   gzip -f test/shared/smartseq3-test/Smartseq3_diySpike_S1_L001_R1_001.fastq

fi

if [[ -f test/shared/smartseq3-test/Smartseq3_diySpike_S1_L001_R2_001.fastq ]]; then

    gzip -f test/shared/smartseq3-test/Smartseq3_diySpike_S1_L001_R2_001.fastq

fi

# reset test data (files names)

if [[ ! -f test/shared/smartseq3-test/Smartseq3_diySpike_R1.fastq.gz ]]; then

    mv test/shared/smartseq3-test/Smartseq3_diySpike_S1_L001_R1_001.fastq.gz test/shared/smartseq3-test/Smartseq3_diySpike_R1.fastq.gz

else

    rm test/shared/smartseq3-test/Smartseq3_diySpike_S1_L001_R1_001.fastq.gz

fi

if [[ ! -f test/shared/smartseq3-test/Smartseq3_diySpike_R2.fastq.gz ]]; then

    mv test/shared/smartseq3-test/Smartseq3_diySpike_S1_L001_R2_001.fastq.gz test/shared/smartseq3-test/Smartseq3_diySpike_R2.fastq.gz

else

    rm test/shared/smartseq3-test/Smartseq3_diySpike_S1_L001_R2_001.fastq.gz

fi



## test drop-seq data

# unzip input data

if [[ -f test/shared/smartseq3-test/*fastq.gz ]]; then

    unpigz -f test/shared/smartseq3-test/*fastq.gz

fi

# test manual setup

# test manual setup

bash launch_universc.sh -t "smartseq" --setup

bash launch_universc.sh -t "smartseq" --setup





# remove processed files

if [[ -f SRR1873277_S1_L001_R[12]_001.fastq ]]; then

    rm SRR1873277_S1_L001_R[12]_001.fastq

fi

if [[ -d input4cellranger_test-smartseq3 ]]; then

if [[ -d input4cellranger_test-smartseq3 ]]; then

    rm -rf input4cellranger_test-smartseq3

    rm -rf input4cellranger_test-smartseq3

fi

fi
@@ -70,27 +37,3 @@ bash launch_universc.sh --id "test-smartseq3" --technology "smartseq" \ 
 --read1 "test/shared/smartseq3-test/Smartseq3_diySpike_R1" \

 --read1 "test/shared/smartseq3-test/Smartseq3_diySpike_R1" \

 --read2 "test/shared/smartseq3-test/Smartseq3_diySpike_R2" \

 --read2 "test/shared/smartseq3-test/Smartseq3_diySpike_R2" \

 --jobmode "local" --localcores 1 
 --jobmode "local" --localcores 1 


# reset test data (compress)

 if [[ -f test/shared/smartseq3-test/Smartseq3_diySpike_S1_L001_R1_001.fastq ]]; then

   gzip -f test/shared/smartseq3-test/Smartseq3_diySpike_S1_L001_R1_001.fastq

fi

if [[ -f test/shared/smartseq3-test/Smartseq3_diySpike_S1_L001_R2_001.fastq ]]; then

    gzip -f test/shared/smartseq3-test/Smartseq3_diySpike_S1_L001_R2_001.fastq

fi

# reset test data (files names)

if [[ ! -f test/shared/smartseq3-test/Smartseq3_diySpike_R1.fastq.gz ]]; then

    mv test/shared/smartseq3-test/Smartseq3_diySpike_S1_L001_R1_001.fastq.gz test/shared/smartseq3-test/Smartseq3_diySpike_R1.fastq.gz

else

    rm test/shared/smartseq3-test/Smartseq3_diySpike_S1_L001_R1_001.fastq.gz

fi

if [[ ! -f test/shared/smartseq3-test/Smartseq3_diySpike_R2.fastq.gz ]]; then

    mv test/shared/smartseq3-test/Smartseq3_diySpike_S1_L001_R2_001.fastq.gz test/shared/smartseq3-test/Smartseq3_diySpike_R2.fastq.gz

else

    rm test/shared/smartseq3-test/Smartseq3_diySpike_S1_L001_R2_001.fastq.gz

fi



# compress all input files

if [[ -f test/shared/smartseq3-test/*fastq ]]; then

    gzip test/shared/smartseq3-test/*fastq

fi

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