Makefile

ifndef SMITHLAB_CPP
$(error Must define SMITHLAB_CPP variable)
endif

PROGS = subsample-epireads

SOURCES = $(wildcard *.cpp)

INCLUDEDIRS = $(SMITHLAB_CPP)
INCLUDEARGS = $(addprefix -I,$(INCLUDEDIRS))

LIBS += -lgsl -lgslcblas

CXX = g++
CXXFLAGS = -Wall -fmessage-length=50
OPTFLAGS = -O2
DEBUGFLAGS = -g

ifeq "$(shell uname)" "Darwin"
CFLAGS += -arch x86_64
endif

ifdef DEBUG
CXXFLAGS += $(DEBUGFLAGS)
endif

ifdef OPT
CXXFLAGS += $(OPTFLAGS)
endif

all: $(PROGS)

$(PROGS): $(addprefix $(SMITHLAB_CPP)/, GenomicRegion.o smithlab_os.o \
	smithlab_utils.o OptionParser.o)

$(PROGS): \
	$(addprefix $(SMITHLAB_CPP)/, RNG.o)

%.o: %.cpp %.hpp
	$(CXX) $(CXXFLAGS) -c -o $@ $< $(INCLUDEARGS)

%: %.cpp
	$(CXX) $(CXXFLAGS) -o $@ $^ $(INCLUDEARGS) $(LIBS)

clean:
	@-rm -f $(PROGS) *.o *.so *.a *~

.PHONY: clean