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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)
|
