Commit 436b3425 authored by TomKellyGenetics's avatar TomKellyGenetics
Browse files

correct paths in test jobs

parent ec32f5e2

test/run_tests_10x.sh

+42 −7
Original line number Diff line number Diff line
@@ -4,6 +4,20 @@ 
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

    rsync $(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

    rsync $(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
@@ -11,11 +25,11 @@ cellrangerversion=`cellranger count --version | head -n 2 | tail -n 1 | cut -f2 
cellrangerpath=`which cellranger`



# set up cellranger reference

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

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

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

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

fi

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

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

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

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

fi



# reset barcodes for test
@@ -23,28 +37,49 @@ 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

# test cellranger call

cellranger testrun --id="tiny-test"

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

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

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

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

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"



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

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

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"



# 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

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/run_tests_dropseq.sh

+4 −4
Original line number Diff line number Diff line
@@ -11,11 +11,11 @@ cellrangerversion=`cellranger count --version | head -n 2 | tail -n 1 | cut -f2 
cellrangerpath=`which cellranger`



# set up cellranger reference

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

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

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

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

fi

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

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

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

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

fi



## test drop-seq data

test/run_tests_icell8.sh

+8 −6
Original line number Diff line number Diff line
@@ -11,13 +11,15 @@ cellrangerversion=`cellranger count --version | head -n 2 | tail -n 1 | cut -f2 
cellrangerpath=`which cellranger`



# set up cellranger reference

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

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

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

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

fi

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

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

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

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

fi



unpigz -k test/shared/icell8-test/72618_KU812*fastq.gz



if [ -f test/shared/icell8-test/72618_KU812_S1_L001_R1_001.fastq ]; then

    rename "s/_S1_L001/_L001/" test/shared/icell8-test/72618_KU812_S1_L001_R1_001.fastq

fi
@@ -38,7 +40,7 @@ bash launch_universc.sh --id "test-icell8-72618_KU812-2-lanes" --technology "iCe 
 --read1 "test/shared/icell8-test/72618_KU812_L001_R1_001.fastq" "test/shared/icell8-test/72618_KU812_L002_R1_001.fastq" \

 --read2 "test/shared/icell8-test/72618_KU812_L001_R2_001.fastq" "test/shared/icell8-test/72618_KU812_L002_R2_001.fastq" \

 --barcodefile "test/shared/icell8-test/WellList.txt" \

 --jobmode "sge"

 --jobmode "local"

if [ -f test/shared/icell8-test/72618_KU812_S1_L001_R1_001.fastq ]; then

    rename "s/_S1_L001/_L001/" test/shared/icell8-test/72618_KU812_S1_L001_R1_001.fastq

fi
@@ -53,4 +55,4 @@ bash launch_universc.sh --id "test-icell8-72618_KU812-1-lane" --technology "iCel 
 --read1 "test/shared/icell8-test/72618_KU812_L001_R1_001.fastq" \

 --read2 "test/shared/icell8-test/72618_KU812_L001_R2_001.fastq" \

 --barcodefile "test/shared/icell8-test/WellList.txt" \

 --jobmode "sge"
 
 --jobmode "local"

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