set up passing a local directory as prefix

reference-clean:

	make -C  test/cellranger_reference/cellranger-tiny-ref clean

	echo "removing pre-generated cellranger reference files"

	@echo "removing pre-generated cellranger reference files"

	rm -Rf  test/cellranger_reference/cellranger-tiny-ref/3.0.0

	rm -Rf  test/cellranger_reference/cellranger-tiny-ref/1.2.0

# Copy to manuals (requires root priviledges

manual:

	bash man/INSTALL

	@bash man/INSTALL

manual-clean:

	bash man/REMOVE

	@bash man/REMOVE

install:

	@if [[ -z $(prefix) ]]; then echo "TRUE"; fi

	@echo "installing to: $(prefix)"

	bash inst/INSTALL

	@bash inst/INSTALL prefix=$(prefix)

remove:

	bash inst/REMOVE

	@bash inst/REMOVE

uninstall: remove clean

#! /bin/sh

#default install location (root)

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

echo "installing to: $prefix"

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

     then

     prefix=$2

     if [[ ! -d $prefix ]]

         then

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

         exit 1

     fi

    if [[ ! -w $prefix ]]

        then

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

        exit 1

    fi

fi

if [[ ! -w $prefix ]]

    then

    echo "$prefix must be a writeable directory"

    echo "try running:"

    echo "    sudo bash $( cd -P "$( dirname ${BASH_SOURCE[0]})" >/dev/null 2>&1 && pwd )/INSTALL"

    echo "    sudo make install"

    exit 1

fi

echo prefix=$prefix

exit 0

if [[ -f /etc/manpath.config ]]

    then 

fi

## check config for Mac

if [[ -f /etc/manpaths ]]

    then CONFIG="/etc/manpaths"

    MANDIR=`tail -n 1 ${CONFIG}`

fi

if [[ -z $CONFIG ]]

    then

    if [[ ! -z $MANPATH ]]

        then

        SHELL_RC=`echo ~/.${0}rc`

        echo "export MANPATH=/usr/local/man" >> $SHELL_RC

        MANDIR=`echo ${MANPATH} | cut -d: -f1`

    fi

fi

#requires root priviledges

if [[ -w ${MANDIR} ]]

    then

    mkdir -p ${MANDIR}/man1

    cp man/launch_universc.sh man/launch_universc.sh.1

    mv man/launch_universc.sh.1 ${MANDIR}/man1/launch_universc.sh.1

    gzip ${MANDIR}/man1/launch_universc.sh.1

else

    echo "Directory ${MANDIR} not writeable"

    echo "Warning: installing manual requires root priviledges"

    echo "  Try running of the following:"

    echo "      sudo bash $( cd -P "$( dirname ${BASH_SOURCE[0]})" >/dev/null 2>&1 && pwd )/INSTALL"

    echo "      sudo make manual"

fi

#! /bin/sh

# add manual directory to PATH if not already found

## check config for Linux

if [[ -f /etc/manpath.config ]]

    then CONFIG="/etc/manpath.config"

    MANDIR=`grep "^MANDATORY_MANPATH" /etc/manpath.config | tail -n 1 | cut -f4`

fi

## check config for Mac

if [[ -f /etc/manpaths ]]

    then CONFIG="/etc/manpaths"

    MANDIR=`tail -n 1 ${CONFIG}`

fi

if [[ -z $CONFIG ]]

    then

    if [[ ! -z $MANPATH ]]

        then

        SHELL_RC=`echo ~/.${0}rc`

        echo "export MANPATH=/usr/local/man" >> $SHELL_RC

        MANDIR=`echo ${MANPATH} | cut -d: -f1`

    fi

fi

if [[ -f  man/launch_universc.sh.1 ]]

    then

    rm man/launch_universc.sh.1

fi

#requires root priviledges

if [[ -w ${MANDIR} ]]

    then

    if [[ -f ${MANDIR}/man1/launch_universc.sh.1 ]]

    then

        rm ${MANDIR}/man1/launch_universc.sh.1

    fi

    if [[ -f ${MANDIR}/man1/launch_universc.sh.1.gz ]] 

        then

        rm ${MANDIR}/man1/launch_universc.sh.1.gz

    fi

else

    echo "Directory ${MANDIR} not writeable"

    echo "Warning: installing manual requires root priviledges"

    echo "  Try running of the following:"

    echo "      sudo bash $( cd -P "$( dirname ${BASH_SOURCE[0]})" >/dev/null 2>&1 && pwd )/REMOVE"

    echo "      sudo make manual-clean"

fi