X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=makefile;h=df165b3e4195420a3543c352cd3d02c8df6b7dbc;hb=92de7f976371d41441ad41f02ca83af8b43cef5c;hp=ffee66ec76967b2f69f376706ae72d24e78911e1;hpb=afcbef163b4f32d0ff25a834cb9af8eef8d06ffa;p=mothur.git

diff --git a/makefile b/makefile
index ffee66e..df165b3 100644
--- a/makefile
+++ b/makefile
@@ -9,14 +9,31 @@
 # Macros
 #
 
-# Optimize to level 3:
+USEMPI ?= no
+64BIT_VERSION ?= yes
+USEREADLINE ?= yes
+CYGWIN_BUILD ?= no
+USECOMPRESSION ?= no
+MOTHUR_FILES="\"../release\""
+RELEASE_DATE = "\"2/7/2011\""
+VERSION = "\"1.16.0\""
 
+# Optimize to level 3:
 CXXFLAGS += -O3
 
-MOTHUR_FILES = "\"../Release\""
+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 are a linux user use the following line
+	#CXXFLAGS += -mtune=native -march=native -m64
+	
+	 CXXFLAGS += -DBIT_VERSION
+endif
 
-RELEASE_DATE = "\"8/30/2010\""
-VERSION = "\"1.13.0\""
 
 CXXFLAGS += -DRELEASE_DATE=${RELEASE_DATE} -DVERSION=${VERSION}
 
@@ -25,42 +42,36 @@ 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 +83,18 @@ 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