Commit 90b19556 authored by TomKellyGenetics's avatar TomKellyGenetics
Browse files

add test reference from cellranger install

parent dfb1b7f5

test/run_tests_10x.sh

+8 −0
Original line number Diff line number Diff line
@@ -10,6 +10,14 @@ 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 /home/tom/local/bin/cellranger-${cellrangerversion}/cellranger-tiny-ref/3.0.0/star/SA ]] && [[ -f $(dirname $cellrangerpath)/cellranger-tiny-ref/3.0.0/star/SA ]]; then

    rsync $(dirname $cellrangerpath)/cellranger-tiny-ref/3.0.0/star/SA /home/tom/local/bin/cellranger-${cellrangerversion}/cellranger-tiny-ref/3.0.0/star/SA

fi

if [[ ! -f /home/tom/local/bin/cellranger-${cellrangerversion}/cellranger-tiny-ref/1.2.0/star/SA ]] && [[ -f $(dirname $cellrangerpath)/cellranger-tiny-ref/1.2.0/star/SA ]]; then

    rsync $(dirname $cellrangerpath)/cellranger-tiny-ref/1.2.0/star/SA /home/tom/local/bin/cellranger-${cellrangerversion}/cellranger-tiny-ref/1.2.0/star/SA

fi



# reset barcodes for test

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

test/run_tests_dropseq.sh

+8 −0
Original line number Diff line number Diff line
@@ -10,6 +10,14 @@ 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 /home/tom/local/bin/cellranger-${cellrangerversion}/cellranger-tiny-ref/3.0.0/star/SA ]] && [[ -f $(dirname $cellrangerpath)/cellranger-tiny-ref/3.0.0/star/SA ]]; then

    rsync $(dirname $cellrangerpath)/cellranger-tiny-ref/3.0.0/star/SA /home/tom/local/bin/cellranger-${cellrangerversion}/cellranger-tiny-ref/3.0.0/star/SA

fi

if [[ ! -f /home/tom/local/bin/cellranger-${cellrangerversion}/cellranger-tiny-ref/1.2.0/star/SA ]] && [[ -f $(dirname $cellrangerpath)/cellranger-tiny-ref/1.2.0/star/SA ]]; then

    rsync $(dirname $cellrangerpath)/cellranger-tiny-ref/1.2.0/star/SA /home/tom/local/bin/cellranger-${cellrangerversion}/cellranger-tiny-ref/1.2.0/star/SA

fi



## test drop-seq data

# unzip input data

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

test/run_tests_icell8.sh

+8 −0
Original line number Diff line number Diff line
@@ -10,6 +10,14 @@ 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 /home/tom/local/bin/cellranger-${cellrangerversion}/cellranger-tiny-ref/3.0.0/star/SA ]] && [[ -f $(dirname $cellrangerpath)/cellranger-tiny-ref/3.0.0/star/SA ]]; then

    rsync $(dirname $cellrangerpath)/cellranger-tiny-ref/3.0.0/star/SA /home/tom/local/bin/cellranger-${cellrangerversion}/cellranger-tiny-ref/3.0.0/star/SA

fi

if [[ ! -f /home/tom/local/bin/cellranger-${cellrangerversion}/cellranger-tiny-ref/1.2.0/star/SA ]] && [[ -f $(dirname $cellrangerpath)/cellranger-tiny-ref/1.2.0/star/SA ]]; then

    rsync $(dirname $cellrangerpath)/cellranger-tiny-ref/1.2.0/star/SA /home/tom/local/bin/cellranger-${cellrangerversion}/cellranger-tiny-ref/1.2.0/star/SA

fi



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

CRA Git | Maintained and supported by SUSTech CRA and CCSE