USEREADLINE ?= yes
USEBOOST ?= yes
VERSION = "\"1.47.0\""
RELEASE_DATE = "\"1/21/22\""
MOTHUR_TOOLS="\"/nfs/turbo/schloss-lab/bin/mothur_src/tools/\"" 

# Optimize to level 3:
	CXXFLAGS += -O3 -std=c++11 -pthread -mtune=generic -DVERSION=${VERSION} -DRELEASE_DATE=${RELEASE_DATE} -DMOTHUR_TOOLS=${MOTHUR_TOOLS}
	LDFLAGS += -std=c++11 -pthread

# if you do not want to use the readline library, set this to no.
# make sure you have the library installed
ifeq  ($(strip $(USEREADLINE)),yes)
	CXXFLAGS += -DUSE_READLINE
	LIBS += -lreadline
endif

#The boost libraries allow you to read gz files.
ifeq  ($(strip $(USEBOOST)),yes)
	#statically link so the boost install is not required on users machine
	LDFLAGS += -L ${BOOST_LIBRARY_DIR}

    LIBS += -lboost_iostreams -lboost_system -lboost_filesystem -lz
    CXXFLAGS += -DUSE_BOOST -I ${BOOST_INCLUDE_DIR}
endif



#
# INCLUDE directories for mothur
#
#
	VPATH=source/calculators:source/chimera:source/classifier:source/clearcut:source/commands:source/communitytype:source/datastructures:source/metastats:source/read:source/svm:source/engines
    skipUchime := source/uchime_src/
    subdirs :=  $(sort $(dir $(filter-out  $(skipUchime), source/, $(wildcard source/*/))))
	subDirIncludes = $(patsubst %, -I %, $(subdirs))
	subDirLinking =  $(patsubst %, -L%, $(subdirs))
	CXXFLAGS += -I. $(subDirIncludes)
	LDFLAGS += $(subDirLinking)


#
# Get the list of all .cpp files, rename to .o files
#
	OBJECTS=$(patsubst %.cpp,%.o,$(wildcard $(addsuffix *.cpp,$(subdirs))))
	OBJECTS+=$(patsubst %.c,%.o,$(wildcard $(addsuffix *.c,$(subdirs))))
	OBJECTS+=$(patsubst %.cpp,%.o,$(wildcard *.cpp))
	OBJECTS+=$(patsubst %.c,%.o,$(wildcard *.c))

mothur : $(OBJECTS) 
	$(CXX) $(LDFLAGS) $(TARGET_ARCH) -o $@ $(OBJECTS)  $(LIBS)
	strip mothur


install : mothur


%.o : %.c %.h
	$(COMPILE.c) $(OUTPUT_OPTION) $<
%.o : %.cpp %.h
	$(COMPILE.cpp) $(OUTPUT_OPTION) $<
%.o : %.cpp %.hpp
	$(COMPILE.cpp) $(OUTPUT_OPTION) $<



clean :
	@rm -f $(OBJECTS)
