disable Cell Ranger for testing locally

cellrangerpath=$(which cellranger) #location of Cell Ranger

if [[ -z $cellrangerpath ]]; then

    echo "cellranger command is not found."

    exit 1

#    exit 1

fi

## 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')')

    echo "Install Cell Ranger in a directory with write permissions such as /home/`whoami`/local and export to the PATH"

    echo "The following versions of Cell Ranger are found:"

    echo " `whereis cellranger`"

    exit 1

#    exit 1

fi

#convert

    echo "Error: Trying to run launch_universc.sh installed at $SDIR"

    echo "$SDIR must be writable to run launch_universc.sh"

    echo "Install launch_universc.sh in a directory with write permissions such as /home/`whoami`/local and export to the PATH"

    exit 1

#    exit 1

fi

##########

##########

exit 0

#####running Cell Ranger#####

cellranger count --id=$id \