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20 changes: 10 additions & 10 deletions INSTALL
Original file line number Diff line number Diff line change
Expand Up @@ -4,7 +4,7 @@

# test if we have a argument on the command line

if [ "$#" != "1" ]; then
if [ $# -ne 1 ]; then
echo " "
echo "INSTALL"
echo " purpose: builds the pindel executable "
Expand All @@ -18,23 +18,23 @@ fi

# to make sure, convert relative path to absolute path

ABSPATH=`cd $1; pwd`
ABSPATH=$(cd "$1"; pwd)

ABSPATH="$ABSPATH/"
ABSPATH=$ABSPATH/
echo "path is now: $ABSPATH"
if [ -e "Makefile.local" ];
then LATERRUN="1";
if [ -e Makefile.local ];
then LATERRUN=1;
fi

make HTSLIB=$ABSPATH
make HTSLIB="$ABSPATH"

if [ "$LATERRUN" != "1" ]; then
if [ $LATERRUN -ne 1 ]; then
echo "If this is the first time you're running this install script please wait a moment as we create the Makefile.local"
sleep 10
make HTSLIB=$ABSPATH
make HTSLIB="$ABSPATH"
fi

if [ "$?" -ne 0 ]; then
if [ $? -ne 0 ]; then
echo " "
echo "INSTALL failed"
echo "Possible reasons: "
Expand Down Expand Up @@ -62,4 +62,4 @@ else
echo "For help and background information, see the pindel wiki and its FAQ on https://trac.nbic.nl/pindel/wiki/PindelFaq"
echo "Or contact us on kye@genome.wustl.edu"
echo " "
fi
fi