Makefile.in

CXXFLAGS += -std=c++14 -Isrc -I@protobuf@/include -I@capnp@/include

UNAME_S=$(shell uname -s)

ifeq ($(UNAME_S),Darwin)
	CXXFLAGS += -mmacosx-version-min=10.7 -stdlib=libc++
else
	CXXFLAGS += -include src/harvest/memcpyLink.h -Wl,--wrap=memcpy
	CFLAGS += -include src/harvest/memcpyLink.h
endif

SOURCES=\
	src/harvest/AnnotationList.cpp \
	src/harvest/harvest.cpp \
	src/harvest/HarvestIO.cpp \
	src/harvest/LcbList.cpp \
	src/harvest/parse.cpp \
	src/harvest/PhylogenyTree.cpp \
	src/harvest/PhylogenyTreeNode.cpp \
	src/harvest/ReferenceList.cpp \
	src/harvest/TrackList.cpp \
	src/harvest/VariantList.cpp \

OBJECTS=$(SOURCES:.cpp=.o) src/harvest/pb/harvest.pb.o src/harvest/capnp/harvest.capnp.o

all : harvesttools libharvest.a

harvesttools : libharvest.a src/harvest/memcpyWrap.o
	$(CXX) $(CXXFLAGS) $(CPPFLAGS) -o harvesttools src/harvest/memcpyWrap.o libharvest.a @protobuf@/lib/libprotobuf.a @capnp@/lib/libcapnp.a @capnp@/lib/libkj.a -lstdc++ -lz -lm -lpthread

libharvest.a : $(OBJECTS)
	ar -cr libharvest.a $(OBJECTS)
	ranlib libharvest.a

.SUFFIXES :

%.o : %.cpp src/harvest/pb/harvest.pb.h src/harvest/capnp/harvest.capnp.h
	$(CXX) -c $(CXXFLAGS) $(CPPFLAGS) -o $@ $<

%.o : %.c++
	$(CXX) -c $(CXXFLAGS) $(CPPFLAGS) -o $@ $<

%.o : %.cc
	$(CXX) -c $(CXXFLAGS) $(CPPFLAGS) -o $@ $<

src/harvest/memcpyWrap.o : src/harvest/memcpyWrap.c
	$(CC) $(CFLAGS) -c -o $@ $<

src/harvest/pb/harvest.pb.cc src/harvest/pb/harvest.pb.h : src/harvest/pb/harvest.proto
	cd src; @protobuf@/bin/protoc --cpp_out . harvest/pb/harvest.proto

src/harvest/capnp/harvest.capnp.c++ src/harvest/capnp/harvest.capnp.h : src/harvest/capnp/harvest.capnp
	cd src/harvest/capnp;export PATH=@capnp@/bin/:${PATH};capnp compile -I @capnp@/include -oc++ harvest.capnp

install : libharvest.a
	mkdir -p @prefix@/bin/
	mkdir -p @prefix@/lib/
	mkdir -p @prefix@/include/
	mkdir -p @prefix@/include/harvest
	mkdir -p @prefix@/include/harvest/capnp
	mkdir -p @prefix@/include/harvest/pb
	ln -sf `pwd`/harvesttools @prefix@/bin/
	ln -sf `pwd`/libharvest.a @prefix@/lib/
	ln -sf `pwd`/src/harvest/exceptions.h @prefix@/include/harvest/
	ln -sf `pwd`/src/harvest/HarvestIO.h @prefix@/include/harvest/
	ln -sf `pwd`/src/harvest/capnp/harvest.capnp.h @prefix@/include/harvest/capnp/
	ln -sf `pwd`/src/harvest/pb/harvest.pb.h @prefix@/include/harvest/pb/
	ln -sf `pwd`/src/harvest/ReferenceList.h @prefix@/include/harvest/
	ln -sf `pwd`/src/harvest/AnnotationList.h @prefix@/include/harvest/
	ln -sf `pwd`/src/harvest/parse.h @prefix@/include/harvest/
	ln -sf `pwd`/src/harvest/PhylogenyTree.h @prefix@/include/harvest/
	ln -sf `pwd`/src/harvest/PhylogenyTreeNode.h @prefix@/include/harvest/
	ln -sf `pwd`/src/harvest/TrackList.h @prefix@/include/harvest/
	ln -sf `pwd`/src/harvest/LcbList.h @prefix@/include/harvest/
	ln -sf `pwd`/src/harvest/VariantList.h @prefix@/include/harvest/

clean :
	-rm harvesttools
	-rm libharvest.a
	-rm src/harvest/*.o
	-rm src/harvest/capnp/*.o
	-rm src/harvest/capnp/*.c++
	-rm src/harvest/capnp/*.h
	-rm src/harvest/pb/*.o
	-rm src/harvest/pb/*.cc
	-rm src/harvest/pb/*.h