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makefile
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###################################################
#
# Makefile for gcat-omegaMap
#
###################################################
#
# Macros
#
# Header file locations for gcat-project
INCLUDE = -Isrc -I/usr/include/gcat -I/usr/include/gcat/myutils
# C++ compiler
CC = g++
# C++ compiler for MPICH2
MPICC = mpic++
# C++ linker
LD = g++
# C++ standard compiler options
CXXFLAGS = -Wall -w -O3 -g -D __NOEXTERN_FOR_CINCLUDE -D _NOT_MYUTILS_DEBUG
# C++ compiler options for gcat library code
CC_OPTIONS = $(CXXFLAGS) -fPIC
# C++ linker options
#LNK_OPTIONS = -L/mnt/lustre/home/djw/xerces-c-3.0.1-x86_64-linux-gcc-3.4/lib\
# -L/usr/lib64/mpich2\
# -lxerces-c\
# -lgsl\
# -lgslcblas
LNK_OPTIONS = -Wl,--no-as-needed -lxerces-c -L./
#
# Build gcat-omegaMap
#
LIB_OMEGAMAP_OBJECTS = \
./Distribution_omegaMapNCD.o\
./Distribution_omegaMapUnlinked.o\
./MCMC_omegaMapMoves.o\
./RandomVariable_Codon61Count.o\
./RandomVariable_Codon61Sequence.o\
./Transformation_NY98_PDRM.o\
./Transformation_NY98_PDRM_Single.o\
./Transformation_Omega2GammaVector.o\
./Transformation_ParentDependentRateMatrix.o\
./Utility_mutation.o\
./Utility_omegaMapUtils.o\
./Utility_paml.o\
./omegaMapLibrary.o\
./omegaMapXML.o
all : libgcat_omegaMap.so
clean : cleanobj
rm libgcat_omegaMap.so
cleanobj :
rm $(LIB_OMEGAMAP_OBJECTS)
#install : gcat
# cp gcat gcat
libgcat_omegaMap.so : $(LIB_OMEGAMAP_OBJECTS)
$(LD) $(LNK_OPTIONS) -lgsl -lgcat-core -shared -o libgcat_omegaMap.so $(LIB_OMEGAMAP_OBJECTS)
#
# Build the parts of gcat_omegaMap
#
./Distribution_omegaMapNCD.o : src/omegaMap/Distributions/omegaMapNCD.cpp
$(CC) $(CC_OPTIONS) src/omegaMap/Distributions/omegaMapNCD.cpp -c $(INCLUDE) -o ./Distribution_omegaMapNCD.o
./Distribution_omegaMapUnlinked.o : src/omegaMap/Distributions/omegaMapUnlinked.cpp
$(CC) $(CC_OPTIONS) src/omegaMap/Distributions/omegaMapUnlinked.cpp -c $(INCLUDE) -o ./Distribution_omegaMapUnlinked.o
./MCMC_omegaMapMoves.o : src/omegaMap/Inference/MCMC/omegaMapMoves.cpp
$(CC) $(CC_OPTIONS) src/omegaMap/Inference/MCMC/omegaMapMoves.cpp -c $(INCLUDE) -o ./MCMC_omegaMapMoves.o
./RandomVariable_Codon61Count.o : src/omegaMap/RandomVariables/Codon61Count.cpp
$(CC) $(CC_OPTIONS) src/omegaMap/RandomVariables/Codon61Count.cpp -c $(INCLUDE) -o ./RandomVariable_Codon61Count.o
./RandomVariable_Codon61Sequence.o : src/omegaMap/RandomVariables/Codon61Sequence.cpp
$(CC) $(CC_OPTIONS) src/omegaMap/RandomVariables/Codon61Sequence.cpp -c $(INCLUDE) -o ./RandomVariable_Codon61Sequence.o
./Transformation_NY98_PDRM.o : src/omegaMap/Transformations/NY98_PDRM.cpp
$(CC) $(CC_OPTIONS) src/omegaMap/Transformations/NY98_PDRM.cpp -c $(INCLUDE) -o ./Transformation_NY98_PDRM.o
./Transformation_NY98_PDRM_Single.o : src/omegaMap/Transformations/NY98_PDRM_Single.cpp
$(CC) $(CC_OPTIONS) src/omegaMap/Transformations/NY98_PDRM_Single.cpp -c $(INCLUDE) -o ./Transformation_NY98_PDRM_Single.o
./Transformation_Omega2GammaVector.o : src/omegaMap/Transformations/Omega2GammaVector.cpp
$(CC) $(CC_OPTIONS) src/omegaMap/Transformations/Omega2GammaVector.cpp -c $(INCLUDE) -o ./Transformation_Omega2GammaVector.o
./Transformation_ParentDependentRateMatrix.o : src/omegaMap/Transformations/ParentDependentRateMatrix.cpp
$(CC) $(CC_OPTIONS) src/omegaMap/Transformations/ParentDependentRateMatrix.cpp -c $(INCLUDE) -o ./Transformation_ParentDependentRateMatrix.o
./Utility_mutation.o : src/omegaMap/Utilities/mutation.cpp
$(CC) $(CC_OPTIONS) src/omegaMap/Utilities/mutation.cpp -c $(INCLUDE) -o ./Utility_mutation.o
./Utility_omegaMapUtils.o : src/omegaMap/Utilities/omegaMapUtils.cpp
$(CC) $(CC_OPTIONS) src/omegaMap/Utilities/omegaMapUtils.cpp -c $(INCLUDE) -o ./Utility_omegaMapUtils.o
./Utility_paml.o : src/omegaMap/Utilities/paml.c
$(CC) $(CC_OPTIONS) src/omegaMap/Utilities/paml.c -c $(INCLUDE) -o ./Utility_paml.o
./omegaMapLibrary.o : src/omegaMap/omegaMapLibrary.cpp
$(CC) $(CC_OPTIONS) src/omegaMap/omegaMapLibrary.cpp -c $(INCLUDE) -o ./omegaMapLibrary.o
./omegaMapXML.o : src/omegaMap/omegaMapXML.cpp src/omegaMap/gcat_omegaMap1.0.xsd.h
$(CC) $(CC_OPTIONS) src/omegaMap/omegaMapXML.cpp -c $(INCLUDE) -o ./omegaMapXML.o
src/omegaMap/gcat_omegaMap1.0.xsd.h : src/omegaMap/omegaMap1.0.xsd
(cd src/omegaMap && xxd -i omegaMap1.0.xsd > gcat_omegaMap1.0.xsd.h)
##### END RUN ####