# Macros
#
-# Optimize to level 3:
-
-CXXFLAGS += -O3
-
+USEMPI ?= no
64BIT_VERSION ?= yes
+USEREADLINE ?= yes
+CYGWIN_BUILD ?= no
+USECOMPRESSION ?= no
+MOTHUR_FILES="\"Enter_your_default_path_here\""
+RELEASE_DATE = "\"2/12/2013\""
+VERSION = "\"1.29.2\""
+FORTAN_COMPILER = gfortran
+FORTRAN_FLAGS =
+
+# Optimize to level 3:
+CXXFLAGS += -O3
ifeq ($(strip $(64BIT_VERSION)),yes)
#if you are using centos uncomment the following lines
#if you are a mac user use the following line
TARGET_ARCH += -arch x86_64
+ #if you using cygwin to build Windows the following line
+ #CXX = x86_64-w64-mingw32-g++
+ #CC = x86_64-w64-mingw32-g++
+ #FORTAN_COMPILER = x86_64-w64-mingw32-gfortran
+ #TARGET_ARCH += -m64 -static
+
#if you are a linux user use the following line
#CXXFLAGS += -mtune=native -march=native -m64
- CXXFLAGS += -DBIT_VERSION
+ CXXFLAGS += -DBIT_VERSION
+ FORTRAN_FLAGS = -m64
endif
-MOTHUR_FILES = "\"../release\""
-
-RELEASE_DATE = "\"11/02/2010\""
-VERSION = "\"1.14.0\""
CXXFLAGS += -DRELEASE_DATE=${RELEASE_DATE} -DVERSION=${VERSION}
CXXFLAGS += -DMOTHUR_FILES=${MOTHUR_FILES}
endif
-CYGWIN_BUILD ?= no
ifeq ($(strip $(CYGWIN_BUILD)),yes)
CXXFLAGS += -mno-cygwin
LDFLAGS += -mno-cygwin
# if you do not want to use the readline library, set this to no.
# make sure you have the library installed
-USEREADLINE ?= yes
ifeq ($(strip $(USEREADLINE)),yes)
CXXFLAGS += -DUSE_READLINE
-lncurses
endif
-USEMPI ?= no
ifeq ($(strip $(USEMPI)),yes)
CXX = mpic++
# if you want to enable reading and writing of compressed files, set to yes.
# The default is no. this may only work on unix-like systems, not for windows.
-USECOMPRESSION ?= no
ifeq ($(strip $(USECOMPRESSION)),yes)
CXXFLAGS += -DUSE_COMPRESSION
OBJECTS=$(patsubst %.cpp,%.o,$(wildcard *.cpp))
OBJECTS+=$(patsubst %.c,%.o,$(wildcard *.c))
+OBJECTS+=$(patsubst %.f,%.o,$(wildcard *.f))
-mothur : $(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) $<
clean :
@rm -f $(OBJECTS)
+ @rm -f uchime