1 ###################################################
4 # Created: June 29, 2010
6 ###################################################
17 MOTHUR_FILES="\"Enter_your_default_path_here\""
18 RELEASE_DATE = "\"10/18/2011\""
19 VERSION = "\"1.22.0\""
21 # Optimize to level 3:
24 ifeq ($(strip $(64BIT_VERSION)),yes)
25 #if you are using centos uncomment the following lines
28 #if you are a mac user use the following line
29 TARGET_ARCH += -arch x86_64
31 #if you using cygwin to build Windows the following line
32 #CXX = x86_64-w64-mingw32-g++
33 #CC = x86_64-w64-mingw32-g++
34 #TARGET_ARCH += -m64 -static
36 #if you are a linux user use the following line
37 #CXXFLAGS += -mtune=native -march=native -m64
39 CXXFLAGS += -DBIT_VERSION
43 CXXFLAGS += -DRELEASE_DATE=${RELEASE_DATE} -DVERSION=${VERSION}
45 ifeq ($(strip $(MOTHUR_FILES)),"\"Enter_your_default_path_here\"")
47 CXXFLAGS += -DMOTHUR_FILES=${MOTHUR_FILES}
50 ifeq ($(strip $(CYGWIN_BUILD)),yes)
51 CXXFLAGS += -mno-cygwin
52 LDFLAGS += -mno-cygwin
55 # if you do not want to use the readline library, set this to no.
56 # make sure you have the library installed
59 ifeq ($(strip $(USEREADLINE)),yes)
60 CXXFLAGS += -DUSE_READLINE
67 ifeq ($(strip $(USEMPI)),yes)
72 # if you want to enable reading and writing of compressed files, set to yes.
73 # The default is no. this may only work on unix-like systems, not for windows.
76 ifeq ($(strip $(USECOMPRESSION)),yes)
77 CXXFLAGS += -DUSE_COMPRESSION
81 # INCLUDE directories for mothur
87 # Get the list of all .cpp files, rename to .o files
90 OBJECTS=$(patsubst %.cpp,%.o,$(wildcard *.cpp))
91 OBJECTS+=$(patsubst %.c,%.o,$(wildcard *.c))
93 mothur : $(OBJECTS) uchime
94 $(CXX) $(LDFLAGS) $(TARGET_ARCH) -o $@ $(OBJECTS) $(LIBS)
99 cd uchime_src && ./mk && mv uchime .. && cd ..
102 # cp mothur ../Release/mothur
105 $(COMPILE.c) $(OUTPUT_OPTION) $<
107 $(COMPILE.cpp) $(OUTPUT_OPTION) $<
109 $(COMPILE.cpp) $(OUTPUT_OPTION) $<