1 ###################################################
4 # Created: June 29, 2010
6 ###################################################
17 MOTHUR_FILES="\"Enter_your_default_path_here\""
18 RELEASE_DATE = "\"10/16/2013\""
19 VERSION = "\"1.32.1\""
20 FORTAN_COMPILER = gfortran
23 # Optimize to level 3:
26 ifeq ($(strip $(64BIT_VERSION)),yes)
27 #if you are using centos uncomment the following lines
30 #if you are a mac user use the following line
31 TARGET_ARCH += -arch x86_64
33 #if you using cygwin to build Windows the following line
34 #CXX = x86_64-w64-mingw32-g++
35 #CC = x86_64-w64-mingw32-g++
36 #FORTAN_COMPILER = x86_64-w64-mingw32-gfortran
37 #TARGET_ARCH += -m64 -static
39 #if you are a linux user use the following line
40 #CXXFLAGS += -mtune=native -march=native
42 CXXFLAGS += -DBIT_VERSION
46 CXXFLAGS += -DRELEASE_DATE=${RELEASE_DATE} -DVERSION=${VERSION}
48 ifeq ($(strip $(MOTHUR_FILES)),"\"Enter_your_default_path_here\"")
50 CXXFLAGS += -DMOTHUR_FILES=${MOTHUR_FILES}
53 ifeq ($(strip $(CYGWIN_BUILD)),yes)
54 CXXFLAGS += -mno-cygwin
55 LDFLAGS += -mno-cygwin
58 # if you do not want to use the readline library, set this to no.
59 # make sure you have the library installed
62 ifeq ($(strip $(USEREADLINE)),yes)
63 CXXFLAGS += -DUSE_READLINE
70 ifeq ($(strip $(USEMPI)),yes)
75 # if you want to enable reading and writing of compressed files, set to yes.
76 # The default is no. this may only work on unix-like systems, not for windows.
79 ifeq ($(strip $(USECOMPRESSION)),yes)
80 CXXFLAGS += -DUSE_COMPRESSION
84 # INCLUDE directories for mothur
90 # Get the list of all .cpp files, rename to .o files
93 OBJECTS=$(patsubst %.cpp,%.o,$(wildcard *.cpp))
94 OBJECTS+=$(patsubst %.c,%.o,$(wildcard *.c))
95 OBJECTS+=$(patsubst %.f,%.o,$(wildcard *.f))
97 mothur : fortranSource $(OBJECTS) uchime
98 $(CXX) $(LDFLAGS) $(TARGET_ARCH) -o $@ $(OBJECTS) $(LIBS)
103 cd uchime_src && ./mk && mv uchime .. && cd ..
106 ${FORTAN_COMPILER} -c $(FORTRAN_FLAGS) *.f
109 # cp mothur ../Release/mothur
112 $(COMPILE.c) $(OUTPUT_OPTION) $<
114 $(COMPILE.cpp) $(OUTPUT_OPTION) $<
116 $(COMPILE.cpp) $(OUTPUT_OPTION) $<