Makefile.static

# To compile statistically on your machine, set up correctly the variables INC_MATH, INC_BOOST, LIB_RMATH, LIB_BPO, LIB_BIO 
# before running "make -f Makefile.static"

#compiler
CXX=g++ -std=c++11

#internal paths
VPATH=$(shell for file in `find src -name *.cpp`; do echo $$(dirname $$file); done)
PATH_TABX=lib/Tabix
PATH_EIGN=lib/Eigen

#compiler flags
CXXFLAG_OPTI=-O3 -D_FAST_CORRELATION
CXXFLAG_WARN=-Wall -Wextra -Wno-sign-compare

#linker flags
LDFLAG_OPTI=-O3

#includes
INC_BASE=-Isrc -I$(PATH_TABX) -I$(PATH_EIGN)
INC_MATH=-I/xchip/gtex/francois/R-3.2.4/src/include/
INC_BOOST=-I/broad/software/free/Linux/redhat_6_x86_64/pkgs/boost_1.59.0/

#libraries
LIB_BASE=-Wl,-Bstatic -lz -lblas -lbz2 -Wl,-Bdynamic -lm -lgsl -lgslcblas
LIB_TABX=$(PATH_TABX)/libtabix.a
LIB_RMATH=/xchip/gtex/francois/R-3.2.4/src/nmath/standalone/libRmath.a
LIB_BPO=/broad/software/free/Linux/redhat_6_x86_64/pkgs/boost_1.59.0/lib/libboost_program_options.a
LIB_BIO=/broad/software/free/Linux/redhat_6_x86_64/pkgs/boost_1.59.0/lib/libboost_iostreams.a

#files (binary, objects, headers & sources)
FILE_BIN=bin/fastQTL.static
FILE_O=$(shell for file in `find src -name *.cpp`; do echo obj/$$(basename $$file .cpp).o; done)
FILE_H=$(shell find src -name *.h)
FILE_CPP=$(shell find src -name *.cpp)

#default
all: linux

#linux release
linux: CXXFLAG=$(CXXFLAG_OPTI) $(CXXFLAG_WARN)
linux: IFLAG=$(INC_BASE) $(INC_MATH) $(INC_BOOST)
linux: LIB=$(LIB_RMATH) $(LIB_BPO) $(LIB_BIO) $(LIB_TABX) $(LIB_BASE)
linux: LDFLAG=$(LDFLAG_OPTI)  
linux: $(FILE_BIN)

#compilation
$(LIB_TABX):
	cd $(PATH_TABX) && make && cd ../..

$(FILE_BIN): $(FILE_O) $(LIB_TABX)
	$(CXX) $(LDFLAG) $^ $(LIB) -o $@

obj/%.o: %.cpp $(FILE_H)
	$(CXX) $(CXXFLAG) -o $@ -c $< $(IFLAG)

clean: 
	rm -f obj/*.o $(FILE_BIN)
	
cleanall: clean 
	cd $(PATH_TABX) && make clean && cd ../..