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| 64BIT_VERSION ?= yes | |
| USEREADLINE ?= yes | |
| USEBOOST ?= yes | |
| RELEASE_DATE = "\"4/05/2015\"" | |
| VERSION = "\"1.37.0\"" | |
| # Optimize to level 3: | |
| CXXFLAGS += -O3 | |
| ifeq ($(strip $(64BIT_VERSION)),yes) | |
| #if you are a mac user use the following line | |
| #TARGET_ARCH += -arch x86_64 | |
| #if you using cygwin to build Windows the following line | |
| #CXX = x86_64-w64-mingw32-g++ | |
| #CC = x86_64-w64-mingw32-g++ | |
| #TARGET_ARCH += -m64 -static | |
| #if you are a linux user use the following line - specific processor builds in future?? | |
| #CXXFLAGS += -mtune=generic | |
| CXXFLAGS += -DBIT_VERSION | |
| endif | |
| CXXFLAGS += -DRELEASE_DATE=${RELEASE_DATE} -DVERSION=${VERSION} | |
| # if you do not want to use the readline library, set this to no. | |
| # make sure you have the library installed | |
| ifeq ($(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 | |
| BOOST_INCLUDE_DIR="/usr/local/include" | |
| BOOST_LIBRARY_DIR="/usr/local/lib" | |
| CXXFLAGS += -DUSE_BOOST | |
| LIBS += ${BOOST_LIBRARY_DIR}/libboost_iostreams.a | |
| #if mac | |
| LIBS += ${BOOST_LIBRARY_DIR}/zlib.a | |
| #if linux or windows | |
| #LIBS += ${BOOST_LIBRARY_DIR}/libz.a | |
| endif | |
| # | |
| # INCLUDE directories for mothur | |
| # | |
| # | |
| VPATH=source/calculators:source/chimera:source/classifier:source/clearcut:source/commands:source/communitytype:source/datastructures:source/metastats:source/randomforest:source/read:source/svm | |
| skipUchime := source/uchime_src/ | |
| subdirs := $(sort $(dir $(filter-out $(skipUchime), $(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) uchime | |
| $(CXX) $(LDFLAGS) $(TARGET_ARCH) -o $@ $(OBJECTS) $(LIBS) | |
| strip mothur | |
| uchime: | |
| cd source/uchime_src && ./mk && mv uchime ../../ && cd .. | |
| 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) | |
| @rm -f uchime |