Loading launch_universc.sh +5 −2 Original line number Diff line number Diff line Loading @@ -14,7 +14,7 @@ if [[ -z $cellrangerpath ]]; then echo "cellranger command is not found." exit 1 fi cellrangerversion=$(cellranger count --version | head -n 2 | tail -n 1 | cut -f2 -d'(' | cut -f1 -d')') cellrangerversion=$(cellranger --version | head -n 2 | tail -n 1 | rev | cut -f1 -d" " | rev | cut -f2 -d'(' | cut -f1 -d')') ########## Loading Loading @@ -59,6 +59,9 @@ lastcall_b=`echo ${lastcall} | cut -f1 -d' '` lastcall_u=`echo ${lastcall} | cut -f2 -d' '` lastcall_p=`echo ${lastcall} | cut -f3 -d' '` barcodedir=${cellrangerpath}-cs/${cellrangerversion}/lib/python/cellranger/barcodes #folder within cellranger with the whitelist barcodes if [[ $(echo "${cellrangerversion} 4.0.0" | tr " " "\n" | sort -V | tail -n 1) == ${cellrangerversion} ]]; then barcodedir=$(dirname /home/tom/local/bin/cellranger-4.0.0/cellranger)/lib/python/cellranger/barcodes fi barcodefile="" crIN=input4cellranger #name of the directory with all FASTQ and index files given to cellranger whitelistdir=${SDIR}/whitelists #path to whitelists Loading @@ -68,7 +71,7 @@ percellfile="outs/basic_stats.txt" #name of the file with the basic statistics o #####checki if convert and cellranger are writable##### #####checking if convert and cellranger are writable##### #cellranger if ! [[ -w "$barcodedir" ]]; then echo "Error: Trying to run cellranger installed at ${cellrangerpath}" Loading Loading
launch_universc.sh +5 −2 Original line number Diff line number Diff line Loading @@ -14,7 +14,7 @@ if [[ -z $cellrangerpath ]]; then echo "cellranger command is not found." exit 1 fi cellrangerversion=$(cellranger count --version | head -n 2 | tail -n 1 | cut -f2 -d'(' | cut -f1 -d')') cellrangerversion=$(cellranger --version | head -n 2 | tail -n 1 | rev | cut -f1 -d" " | rev | cut -f2 -d'(' | cut -f1 -d')') ########## Loading Loading @@ -59,6 +59,9 @@ lastcall_b=`echo ${lastcall} | cut -f1 -d' '` lastcall_u=`echo ${lastcall} | cut -f2 -d' '` lastcall_p=`echo ${lastcall} | cut -f3 -d' '` barcodedir=${cellrangerpath}-cs/${cellrangerversion}/lib/python/cellranger/barcodes #folder within cellranger with the whitelist barcodes if [[ $(echo "${cellrangerversion} 4.0.0" | tr " " "\n" | sort -V | tail -n 1) == ${cellrangerversion} ]]; then barcodedir=$(dirname /home/tom/local/bin/cellranger-4.0.0/cellranger)/lib/python/cellranger/barcodes fi barcodefile="" crIN=input4cellranger #name of the directory with all FASTQ and index files given to cellranger whitelistdir=${SDIR}/whitelists #path to whitelists Loading @@ -68,7 +71,7 @@ percellfile="outs/basic_stats.txt" #name of the file with the basic statistics o #####checki if convert and cellranger are writable##### #####checking if convert and cellranger are writable##### #cellranger if ! [[ -w "$barcodedir" ]]; then echo "Error: Trying to run cellranger installed at ${cellrangerpath}" Loading
