Commit 004cea2b authored by TomKellyGenetics's avatar TomKellyGenetics
Browse files

update test scripts to run in cellranger_convert directory

parent 47e312cc

test/run_tests.sh

+1 −1
Original line number Diff line number Diff line 
#!/bin/bash



# run tests in home directory (writeable)

cd /universc

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



# reset barcodes for test

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

test/run_tests_10x.sh

+23 −18
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@@ -2,33 +2,40 @@ 


# run tests in home directory (writeable)

#cd ~

# run tests in universc directory

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



export PATH=/home/tom/local/bin/cellranger-3.1.0:$PATH

# 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`



# reset barcodes for test

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

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



## test 10x data

# unzip input data

# nzip input data

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

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

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

fi

# test cellranger call

#cellranger testrun --id="tiny-test"

cellranger testrun --id="tiny-test"

# unzip input data

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

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

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 

fi

# test cellranger call

#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"

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"



#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"

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

bash launch_universc.sh --id "test-10x-v3" --technology "10x" \
@@ -36,9 +43,7 @@ bash launch_universc.sh --id "test-10x-v3" --technology "10x" \ 
 --file "test/shared/cellranger-tiny-fastq/3.0.0/tinygex_S1_L001" \

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



#bash launch_universc.sh --id "test-10x-v2" --technology "10x" \

# --reference "test/cellranger_reference/cellranger-tiny-ref/1.2.0" \

# --file "test/shared/cellranger-tiny-fastq/1.2.0/"



# compress all input files

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

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

fi

test/run_tests_dropseq.sh

+10 −4
Original line number Diff line number Diff line
@@ -2,15 +2,20 @@ 


# run tests in home directory (writeable)

#cd ~

# run tests in universc directory

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



#export PATH=/home/tom/local/bin/cellranger-3.1.0:$PATH

# 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`



## test drop-seq data

# unzip input data

gunzip -fk test/shared/dropseq-test/*fastq.gz

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

    gunzip -f test/shared/dropseq-test/*fastq.gz

fi

# test manual setup

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

# call on dropseq with files
@@ -20,5 +25,6 @@ bash launch_universc.sh --id "test-dropseq" --technology "nadia" \ 
 --read2 "test/shared/dropseq-test/SRR1873277_S1_L001_R2_001" 



# compress all input files

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

    gzip -f test/shared/dropseq-test/*fastq

fi

test/run_tests_icell8.sh

+11 −12
Original line number Diff line number Diff line
@@ -2,26 +2,27 @@ 


# run tests in home directory (writeable)

#cd ~

# run tests in universc directory

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



#export PATH=/home/tom/local/bin/cellranger-3.1.0:$PATH

# 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`





## test icell8 data

# unzip input data

#gzip -fk test/shared/icell8-test/*fastq

gunzip -fk test/shared/icell8-test/*fastq.gz

if [[ -f test/shared/icell8-test/*fastq.gz ]]; then

    gunzip -f test/shared/icell8-test/*fastq.gz

fi

# call on icell8 files with default whitelist

#bash launch_universc.sh --id "test-icell8-default" --technology "iCell8" \

bash launch_universc.sh --id "test-icell8-default" --technology "iCell8" \

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

 --read1 "test/shared/icell8-test/iCELL8_01_S1_L001_R1_001.fastq" "test/shared/icell8-test/iCELL8_01_S1_L002_R1_001.fastq" \

 --read2 "test/shared/icell8-test/iCELL8_01_S1_L001_R2_001.fastq" "test/shared/icell8-test/iCELL8_01_S1_L002_R2_001.fastq" \

 --jobmode "sge"

#restore file names for test job

#mv /universc/test/shared/icell8-test/test_FL_S1_L001_R1_001.fastq /universc/test/shared/icell8-test/test_FL_R1.fastq

#mv /universc/test/shared/icell8-test/test_FL_S1_L001_R2_001.fastq /universc/test/shared/icell8-test/test_FL_R2.fastq



# call on icell8 files with custom whitelist and non-standard file names

bash launch_universc.sh --setup -t "icell8"  --barcodefile "test/shared/icell8-test/BarcodeList.txt"
@@ -31,10 +32,8 @@ bash launch_universc.sh --id "test-icell8-custom" --technology "iCell8" \ 
 --read2 "test/shared/icell8-test/iCELL8_01_S1_L001_R2_001.fastq" "test/shared/icell8-test/iCELL8_01_S1_L002_R2_001.fastq" \

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

 --jobmode "sge"

#restore file names for test job

#mv /universc/test/shared/icell8-test/test_FL_S1_L001_R1_001.fastq /universc/test/shared/icell8-test/test_FL_R1.fastq

#mv /universc/test/shared/icell8-test/test_FL_S1_L001_R2_001.fastq /universc/test/shared/icell8-test/test_FL_R2.fastq



# compress all input files

if [[ -f test/shared/icell8-test/*fastq ]]; then

    gzip -f test/shared/icell8-test/*fastq

fi

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