config.mf.in

####### Automatic Configuration

#system
SYSTEM_SUFFIX = _@host_os@
PREFIX = @prefix@

# programms
CXX = @CXX@ 
CC = @CC@ 
LD = $(CC)
LEX = @FLEX@
YACC = @BISON@
SED = @SED@
INSTALL = @INSTALL@
SHELL = @SHELL@
HG = @HG@

#flags
# c
CFLAGS = @CFLAGS@ 

#c++
CXXFLAGS = @CXXFLAGS@

#library
SO_SUFFIX = @SO_SUFFIX@
SHARED_FLAGS = @SHARED_FLAGS@
FAST_MATH = @FAST_MATH@
PIC_FLAGS = @PIC_FLAGS@
INSTALL_SHARED_FLAG=@INSTALL_SHARED_FLAG@

#bison
BISON_VERSION_FLAG = @BISON_VERSION_FLAG@

#boost
BOOST_CPPFLAGS = @BOOST_CPPFLAGS@
BOOST_LDFLAGS = @BOOST_LDFLAGS@
BOOST_PROGRAM_OPTIONS_LIB = @BOOST_PROGRAM_OPTIONS_LIB@
BOOST_UNIT_TEST_FRAMEWORK_LIB = @BOOST_UNIT_TEST_FRAMEWORK_LIB@

#gsl
GSL_LIBS = @GSL_LIBS@
GSL_CFLAGS = @GSL_CFLAGS@

# openmp
CXXFLAGS_OPENMP = @OPENMP_CXXFLAGS@

####### Fixed Configuration

AR = ar

#preprocessor
LIB_RT = rtlib
LIB_RNA = librna
LIB_GENERAL = 
INCLUDE_PATH=/include
CPPFLAGS += $(BOOST_CPPFLAGS) \
	 $(CPPFLAGS_EXTRA) \
	 $(RTLIB_CPPFLAGS)

# c
CFLAGS += -DNDEBUG

# c++
CXXFLAGS += -DNDEBUG $(BISON_VERSION_FLAG) $(CXXFLAGS_EXTRA)

# linker
LIB_PATH=/lib
LDFLAGS = $(BOOST_LDFLAGS)  \
	$(LDFLAGS_EXTRA) \
	$(RTLIB_LDFLAGS) \
	$(shell echo " $(BOOST_LDFLAGS) " | sed -e 's/[ ][ ]*[^ ]*\.o[ ]//g' | sed -e 's/\-L/-Xlinker -rpath -Xlinker /g') \
	$(shell echo " $(LDFLAGS_EXTRA) " | sed -e 's/[ ][ ]*[^ ]*\.o[ ]//g' | sed -e 's/\-L/-Xlinker -rpath -Xlinker /g') \
	$(shell echo " $(RTLIB_LDFLAGS) " | sed -e 's/[ ][ ]*[^ ]*\.o[ ]//g' | sed -e 's/\-L/-Xlinker -rpath -Xlinker /g') 

LDLIBS = $(RTLIB_LDLIBS) \
	 $(LDLIBS_EXTRA)



# Options for compling GapC generated code
# set to RTLIB_LDLIBS
RT_LDLIBS = $(GSL_LIBS) -lrna

# set to RTLIB_LDFLAGS
RT_LDFLAGS = -L$(PREFIX)$(LIB_PATH)/$(LIB_GENERAL)

# set to RTLIB_CPPFLAGS
RT_CPPFLAGS = $(GSL_CFLAGS) \
	 -I$(PREFIX)$(INCLUDE_PATH)/$(LIB_GENERAL) \
	 -I$(PREFIX)$(INCLUDE_PATH)/$(LIB_RT) \
	 -I$(PREFIX)$(INCLUDE_PATH)/$(LIB_RNA) \

RTLIB = $(PREFIX)$(INCLUDE_PATH)/$(LIB_RT)