working on windows paralellization, added trimOligos class to be used by trim.flows...

[mothur.git] / makefile

diff --git a/makefile b/makefile
index 278a3adc659ac0d8e6d5afd9815ad0adac7dafd6..3f6431210735a622f8c0e416a088581d331ed714 100644 (file)
--- a/makefile
+++ b/makefile
@@ -9,14 +9,36 @@
 # Macros
 #
 
+USEMPI ?= no
+64BIT_VERSION ?= yes
+USEREADLINE ?= yes
+CYGWIN_BUILD ?= no
+USECOMPRESSION ?= no
+MOTHUR_FILES="\"/Users/Sarahswork/desktop/release\""
+RELEASE_DATE = "\"7/25/2011\""
+VERSION = "\"1.21.0\""
+
 # Optimize to level 3:
+CXXFLAGS += -03 -g
 
-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++
+       #TARGET_ARCH += -m64
 
-MOTHUR_FILES = "\"Enter_your_default_path_here\""
+       #if you are a linux user use the following line
+       #CXXFLAGS += -mtune=native -march=native -m64
+       
+        CXXFLAGS += -DBIT_VERSION
+endif
 
-RELEASE_DATE = "\"9/9/2010\""
-VERSION = "\"1.13.0\""
 
 CXXFLAGS += -DRELEASE_DATE=${RELEASE_DATE} -DVERSION=${VERSION}
 
@@ -25,42 +47,36 @@ 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
-       #CXX = 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
 #
@@ -72,13 +88,18 @@ endif
 #
 
 OBJECTS=$(patsubst %.cpp,%.o,$(wildcard *.cpp))
+OBJECTS+=$(patsubst %.c,%.o,$(wildcard *.c))
 
 mothur : $(OBJECTS)
-       $(CXX) $(LDFLAGS) $(TARGET_ARCH) -o $@ $(OBJECTS)
+       $(CXX) $(LDFLAGS) $(TARGET_ARCH) -o $@ $(OBJECTS) $(LIBS)
+       
+       strip mothur
 
 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