1 ###################################################
4 # Created: June 29, 2010
6 ###################################################
17 MOTHUR_FILES="\"Enter_your_default_path_here\""
18 RELEASE_DATE = "\"12/7/2011\""
19 VERSION = "\"1.22.0\""
20 FORTAN_COMPILER = gfortran
22 # Optimize to level 3:
25 ifeq ($(strip $(64BIT_VERSION)),yes)
26 #if you are using centos uncomment the following lines
29 #if you are a mac user use the following line
30 TARGET_ARCH += -arch x86_64
32 #if you using cygwin to build Windows the following line
33 #CXX = x86_64-w64-mingw32-g++
34 #CC = x86_64-w64-mingw32-g++
35 #TARGET_ARCH += -m64 -static
37 #if you are a linux user use the following line
38 #CXXFLAGS += -mtune=native -march=native -m64
40 CXXFLAGS += -DBIT_VERSION
44 CXXFLAGS += -DRELEASE_DATE=${RELEASE_DATE} -DVERSION=${VERSION}
46 ifeq ($(strip $(MOTHUR_FILES)),"\"Enter_your_default_path_here\"")
48 CXXFLAGS += -DMOTHUR_FILES=${MOTHUR_FILES}
51 ifeq ($(strip $(CYGWIN_BUILD)),yes)
52 CXXFLAGS += -mno-cygwin
53 LDFLAGS += -mno-cygwin
56 # if you do not want to use the readline library, set this to no.
57 # make sure you have the library installed
60 ifeq ($(strip $(USEREADLINE)),yes)
61 CXXFLAGS += -DUSE_READLINE
68 ifeq ($(strip $(USEMPI)),yes)
73 # if you want to enable reading and writing of compressed files, set to yes.
74 # The default is no. this may only work on unix-like systems, not for windows.
77 ifeq ($(strip $(USECOMPRESSION)),yes)
78 CXXFLAGS += -DUSE_COMPRESSION
82 # INCLUDE directories for mothur
88 # Get the list of all .cpp files, rename to .o files
91 OBJECTS=$(patsubst %.cpp,%.o,$(wildcard *.cpp))
92 OBJECTS+=$(patsubst %.c,%.o,$(wildcard *.c))
93 OBJECTS+=$(patsubst %.f,%.o,$(wildcard *.f))
95 mothur : fortranSource $(OBJECTS) uchime
96 $(CXX) $(LDFLAGS) $(TARGET_ARCH) -o $@ $(OBJECTS) $(LIBS)
101 cd uchime_src && ./mk && mv uchime .. && cd ..
104 ${FORTAN_COMPILER} -c *.f
107 # cp mothur ../Release/mothur
110 $(COMPILE.c) $(OUTPUT_OPTION) $<
112 $(COMPILE.cpp) $(OUTPUT_OPTION) $<
114 $(COMPILE.cpp) $(OUTPUT_OPTION) $<