update paths to support later versions

#####locate cellranger and get cellranger version#####

cellrangerpath=`which cellranger` #location of cellranger

cellrangerpath=$(which cellranger) #location of cellranger

if [[ -z $cellrangerpath ]]; then

    echo "cellranger command is not found."

    exit 1

fi

cellrangerversion=$(cellranger --version | head -n 2 | tail -n 1 | rev | cut -f1 -d" " | rev |  cut -f2 -d'(' | cut -f1 -d')')

## detects version by attempting to parse "cellranger --version" (older versions do not support this by print the help header if invalid args given)

cellrangerversion=$(cellranger --version 2>/dev/null | head -n 2 | tail -n 1 | rev | cut -f1 -d" " | rev |  cut -f2 -d'(' | cut -f1 -d')')

if [[ $verbose ]]; then

    echo $cellrangerversion

fi

##########

#####locate launch_universc.sh, barcode sources, and other tools######

SOURCE="${BASH_SOURCE[0]}"

SDIR=""

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

    mkdir -p $(dirname /home/tom/local/bin/cellranger-4.0.0/cellranger)/${cellrangerpath}-cs/${cellrangerversion}

    ln -sf $(dirname /home/tom/local/bin/cellranger-4.0.0/cellranger)/mro/rna $(dirname /home/tom/local/bin/cellranger-4.0.0/cellranger)/${cellrangerpath}-cs/${cellrangerversion}/mro

    barcodedir=$(dirname $cellrangerpath)/lib/python/cellranger/barcodes

    mkdir -p ${cellrangerpath}-cs/${cellrangerversion}

    ln -sf $(dirname $cellrangerpath)/mro/rna ${cellrangerpath}-cs/${cellrangerversion}/mro

    ln -sf $(dirname $cellrangerpath)/lib ${cellrangerpath}-cs/${cellrangerversion}/lib

fi

barcodefile=""

crIN=input4cellranger #name of the directory with all FASTQ and index files given to cellranger