# Macros
#
+USEMPI ?= no
+64BIT_VERSION ?= yes
+USEREADLINE ?= yes
+CYGWIN_BUILD ?= no
+USECOMPRESSION ?= no
+MOTHUR_FILES="\"Enter_your_default_path_here\""
+RELEASE_DATE = "\"5/29/2013\""
+VERSION = "\"1.31.1\""
+FORTAN_COMPILER = gfortran
+FORTRAN_FLAGS =
+
# Optimize to level 3:
+CXXFLAGS += -O3
-CXXFLAGS += -O3
+ifeq ($(strip $(64BIT_VERSION)),yes)
+ #if you are using centos uncomment the following lines
+ #CXX = g++44
+
+ #if you are a mac user use the following line
+ TARGET_ARCH += -arch x86_64
+
+ #if you using cygwin to build Windows the following line
+ #CXX = x86_64-w64-mingw32-g++
+ #CC = x86_64-w64-mingw32-g++
+ #FORTAN_COMPILER = x86_64-w64-mingw32-gfortran
+ #TARGET_ARCH += -m64 -static
+
+ #if you are a linux user use the following line
+ #CXXFLAGS += -mtune=native -march=native -m64
+
+ CXXFLAGS += -DBIT_VERSION
+ FORTRAN_FLAGS = -m64
+endif
+
+
+CXXFLAGS += -DRELEASE_DATE=${RELEASE_DATE} -DVERSION=${VERSION}
-MOTHUR_FILES = "\"Enter_your_default_path_here\""
ifeq ($(strip $(MOTHUR_FILES)),"\"Enter_your_default_path_here\"")
else
CXXFLAGS += -DMOTHUR_FILES=${MOTHUR_FILES}
endif
-CYGWIN_BUILD ?= no
ifeq ($(strip $(CYGWIN_BUILD)),yes)
CXXFLAGS += -mno-cygwin
LDFLAGS += -mno-cygwin
endif
-64BIT_VERSION ?= yes
-
-ifeq ($(strip $(64BIT_VERSION)),yes)
- TARGET_ARCH += -arch x86_64
- CXXFLAGS += -DBIT_VERSION
-
- #if you are using centos uncomment the following lines
- #CC = g++44
- #CXXFLAGS += -mtune=native -march=native -m64
-endif
-
# if you do not want to use the readline library, set this to no.
# make sure you have the library installed
-USEREADLINE ?= yes
ifeq ($(strip $(USEREADLINE)),yes)
CXXFLAGS += -DUSE_READLINE
- LDFLAGS += \
+ LIBS = \
-lreadline\
-lncurses
endif
-USEMPI ?= no
ifeq ($(strip $(USEMPI)),yes)
CXX = mpic++
CXXFLAGS += -DUSE_MPI
endif
+# if you want to enable reading and writing of compressed files, set to yes.
+# The default is no. this may only work on unix-like systems, not for windows.
+
+
+ifeq ($(strip $(USECOMPRESSION)),yes)
+ CXXFLAGS += -DUSE_COMPRESSION
+endif
+
#
# INCLUDE directories for mothur
#
#
OBJECTS=$(patsubst %.cpp,%.o,$(wildcard *.cpp))
+OBJECTS+=$(patsubst %.c,%.o,$(wildcard *.c))
+OBJECTS+=$(patsubst %.f,%.o,$(wildcard *.f))
-mothur : $(OBJECTS)
- $(CXX) $(LDFLAGS) $(TARGET_ARCH) -o $@ $(OBJECTS)
+mothur : fortranSource $(OBJECTS) uchime
+ $(CXX) $(LDFLAGS) $(TARGET_ARCH) -o $@ $(OBJECTS) $(LIBS)
+
+ strip mothur
+
+uchime:
+ cd uchime_src && ./mk && mv uchime .. && cd ..
+
+fortranSource:
+ ${FORTAN_COMPILER} -c $(FORTRAN_FLAGS) *.f
install : mothur
- cp mothur ../Release/mothur
-
+# cp mothur ../Release/mothur
+
+%.o : %.c %.h
+ $(COMPILE.c) $(OUTPUT_OPTION) $<
%.o : %.cpp %.h
$(COMPILE.cpp) $(OUTPUT_OPTION) $<
%.o : %.cpp %.hpp
clean :
@rm -f $(OBJECTS)
+ @rm -f uchime