handle install to git repo or cellranger_convert

#default install location (root)

if [[ -z $prefix ]]; then prefix="/usr/local/share"; fi

echo "installing to: $prefix"

if [[ $1 == "--prefix" ]]

     then

     prefix=$2

fi

if [[ $prefix=="." ]]

    then

    echo "wd"

    prefix=`pwd`

fi

if [[ "universc" == $(echo $prefix | rev | cut -d'/' -f1 | rev) ]]

    then

    echo "prefix in existing convert directory"

    prefix=$(echo $prefix | cut -d'/' -f1-$(($( echo $prefix | grep -o "/" | wc -l))))

    echo $prefix

fi

if [[ ! -d $prefix ]]

    then

        echo "--prefix $prefix must be a directory"

    echo "--prefix $prefix must be a writeable"

    exit 1

fi

fi

if [[ ! -w $prefix ]]

    then

    exit 1

fi

echo "installing to: $prefix"

version=$( cat .version )

if [[ -f inst/.installed ]]

echo prefix=$prefix

version=`cat .version`

# create install directory

INSTALLDIR="${prefix}/universc-${version}"

echo "Installing to $INSTALLDIR"