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|
#!/usr/bin/env bash
CPP_STD=c++14
usage ()
{
echo ""
echo "Usage : "
echo " configure [--boost=BOOST] # root of boost install"
echo " [--swig=SWIG] # location of swig executable"
echo " [--swig-lib=SWIG_LIB] # location of swig library"
echo " [--debug] # build debug library (1)"
echo " [--c++98] # build using old C++98 standard"
echo
echo " (Python only:)"
echo " [--python-include=PYTHON_INCLUDE] # location of Python.h"
echo " [--numpy-include=NUMPY_INCLUDE] # location of numpy/core/include"
echo ""
echo
echo " configure --pbi # use PacBio perforce locations"
echo ""
echo " configure --modules # use PacBio GNU modules"
echo ""
echo
echo " configure --clear # delete configuration"
echo ""
}
configure_pbi ()
{
echo "Configuring based on PacBio P4 depot paths."
SOFTWARE=$(readlink -f ../../../../..) # Path to //depot/software
BOOST=$SOFTWARE/smrtanalysis/prebuilt.out/boost/boost_1_47_0/
SWIG=$SOFTWARE/smrtanalysis/prebuilt.out/swig/swig-2.0.10/ubuntu-1004/bin/swig
SWIG_LIB=$SOFTWARE/smrtanalysis/prebuilt.out/swig/swig-2.0.10/common/share/swig/2.0.10
PYTHON_INCLUDE=
NUMPY_INCLUDE=
DEBUG=
}
configure_modules ()
{
echo "Configuring based on PacBio GNU modules"
echo "(assumes you have already done module load boost, module load swig (selecting your desired versions))"
BOOST=$BOOST_ROOT
SWIG=`which swig`
}
while test x$1 != x; do
case $1 in
--pbi)
configure_pbi
;;
--modules)
configure_modules
;;
--boost=*)
BOOST=`echo $1 | sed 's/--boost=//'`
;;
--swig=*)
SWIG=`echo $1 | sed 's/--swig=//'`
;;
--swig-lib=*)
SWIG_LIB=`echo $1 | sed 's/--swig-lib=//'`
;;
--debug)
DEBUG=1
;;
--c++98)
CPP_STD=c++98
;;
--python-include=*)
PYTHON_INCLUDE=`echo $1 | sed 's/--python-include=//'`
;;
--numpy-include=*)
NUMPY_INCLUDE=`echo $1 | sed 's/--numpy-include=//'`
;;
--help)
usage
exit
;;
--clear)
rm -f make/Config.mk
exit
;;
*)
echo Warning: unknown argument $1 >&2
usage
;;
esac
shift
done
# Find/validate boost and swig
#set -e
BOOST=`tools/find_boost $BOOST` || exit
SWIG=`tools/find_swig $SWIG` || exit
if [ -z $SWIG_LIB ]; then
SWIG_LIB=`$SWIG -swiglib`
fi
echo
echo ConsensusCore configuration summary
echo -----------------------------------
echo " BOOST = $BOOST"
echo " SWIG = $SWIG"
echo " SWIG_LIB = $SWIG_LIB"
echo " PYTHON_INCLUDE = $PYTHON_INCLUDE"
echo " NUMPY_INCLUDE = $NUMPY_INCLUDE"
echo " DEBUG = $DEBUG"
echo " CPP_STD = $CPP_STD"
echo
echo > make/Config.mk
echo "BOOST:=$BOOST" >> make/Config.mk
echo "SWIG:=$SWIG" >> make/Config.mk
echo "SWIG_LIB:=$SWIG_LIB" >> make/Config.mk
echo "PYTHON_INCLUDE:=$PYTHON_INCLUDE" >> make/Config.mk
echo "NUMPY_INCLUDE:=$NUMPY_INCLUDE" >> make/Config.mk
echo "DEBUG?=$DEBUG" >> make/Config.mk
echo "CPP_STD:=$CPP_STD" >> make/Config.mk
|
