separate test job for 10x v2 chemistry

#!/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=${HOME}/local/bin/cellranger-2.1.0:$PATH

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

cellrangerpath=`which cellranger`

# set up cellranger reference

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

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

fi

# 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`

# set up cellranger reference

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

    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/dropseq-test/* test/shared/icell8-test/* test/shared/mappa-test/

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

# reset barcodes for test

bash launch_universc.sh -t "10x" --setup

## test 10x data

# unzip input data

ls ${cellrangerpath}-cs/${cellrangerversion}/lib/python/cellranger/barcodes/3M-february-2018.txt*

if [[ ! -f ${cellrangerpath}-cs/${cellrangerversion}/lib/python/cellranger/barcodes/3M-february-2018.txt.gz ]]; then

    gzip -f ${cellrangerpath}-cs/${cellrangerversion}/lib/python/cellranger/barcodes/3M-february-2018.txt

fi

rm -rf ${cellrangerpath}-cs/${cellrangerversion}/lib/python/cellranger/barcodes/3M-february-2018.txt

if [[ -d tiny-test ]]; then

    rm -rf tiny-test

fi

# test cellranger call

if [[ $cellrangerversion == "3.0.2" ]]; then

    cellranger testrun --id="tiny-test"

fi

# unzip input data

if [[ -f test/shared/cellranger-tiny-fastq/3.0.0/*fastq.gz ]]; then

    gunzip -f test/shared/cellranger-tiny-fastq/3.0.0/*fastq.gz

fi

if [[ -f test/shared/cellranger-tiny-fastq/3.0.0/*fastq ]]; then

    rm -rf test/shared/cellranger-tiny-fastq/3.0.0/*fastq.gz

fi

# test cellranger call

if [[ -d tiny-count-v3 ]]; then

    rm -rf tiny-count-v3

fi

if [[ ! -f ${cellrangerpath}-cs/${cellrangerversion}/lib/python/cellranger/barcodes/3M-february-2018.txt.gz ]]; then

    gzip -f ${cellrangerpath}-cs/${cellrangerversion}/lib/python/cellranger/barcodes/3M-february-2018.txt

fi

if [[ -f ${cellrangerpath}-cs/${cellrangerversion}/lib/python/cellranger/barcodes/3M-february-2018.txt ]]; then

    rm -rf ${cellrangerpath}-cs/${cellrangerversion}/lib/python/cellranger/barcodes/3M-february-2018.txt

fi

cellranger count --id="tiny-count-v3" \

 --fastqs="test/shared/cellranger-tiny-fastq/3.0.0/" --sample="tinygex" \

 --transcriptome="test/cellranger_reference/cellranger-tiny-ref/3.0.0" \

 --jobmode "local" --localcores 1 

if [[ -d tiny-count-v2 ]]; then

    rm -rf tiny-count-v2

fi 

if [[ ! -f ${cellrangerpath}-cs/${cellrangerversion}/lib/python/cellranger/barcodes/3M-february-2018.txt.gz ]]; then

    gzip -f ${cellrangerpath}-cs/${cellrangerversion}/lib/python/cellranger/barcodes/3M-february-2018.txt

fi

if [[ -f ${cellrangerpath}-cs/${cellrangerversion}/lib/python/cellranger/barcodes/3M-february-2018.txt ]]; then

    rm -rf ${cellrangerpath}-cs/${cellrangerversion}/lib/python/cellranger/barcodes/3M-february-2018.txt

fi

cellranger count --id="tiny-count-v2" \

 --fastqs="test/shared/cellranger-tiny-fastq/1.2.0/" --sample="" --chemistry="threeprime" \

 --transcriptome="test/cellranger_reference/cellranger-tiny-ref/1.2.0" \

 --jobmode "local" --localcores 1 

# call convert on 10x with multiple lanes

if [[ -d test-10x-v3 ]]; then

    rm -rf test-10x-v3

fi

if [[ -d input4cellranger_test-10x-v3 ]]; then

    rm -rf input4cellranger_test-10x-v3

fi

# unzip input data

if [[ -f test/shared/cellranger-tiny-fastq/3.0.0/tinygex_S1_L001/*fastq.gz ]]; then

    unpigz -f test/shared/cellranger-tiny-fastq/3.0.0/tinygex_S1_L001/*fastq.gz

fi

if [[ -f test/shared/cellranger-tiny-fastq/3.0.0/tinygex_S1_L002/*fastq.gz ]]; then

    unpigz -f test/shared/cellranger-tiny-fastq/3.0.0/tinygex_S1_L002/*fastq.gz

fi

bash launch_universc.sh --id "test-10x-v3" --technology "10x" \

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

 --file "test/shared/cellranger-tiny-fastq/3.0.0/tinygex_S1_L001" \

 "test/shared/cellranger-tiny-fastq/3.0.0/tinygex_S1_L002" \

  --jobmode "local" --localcores 1 

# compress all input files

if [[ -f test/shared/cellranger-tiny-fastq/3.0.0/*fastq ]]; then

    gzip -f test/shared/cellranger-tiny-fastq/3.0.0/*fastq

fi