removed parse.sff command and made its functionality part of sffinfo command. fixed...

[mothur.git] / makefile

diff --git a/makefile b/makefile
index dc5065db04a20db83b186cfcc3fe81e2d5901356..266c0c347d82ad54aa55b2c0edf5ae8a5a3d6c03 100644 (file)
--- a/makefile
+++ b/makefile
@@ -13,10 +13,25 @@
 
 CXXFLAGS += -O3
 
-MOTHUR_FILES = "\"../Release\""
+64BIT_VERSION ?= yes
 
-RELEASE_DATE = "\"8/5/2010\""
-VERSION = "\"1.12.3\""
+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
+
+MOTHUR_FILES = "\"../release\""
+
+RELEASE_DATE = "\"12/10/2010\""
+VERSION = "\"1.15.0\""
 
 CXXFLAGS += -DRELEASE_DATE=${RELEASE_DATE} -DVERSION=${VERSION}
 
@@ -31,17 +46,6 @@ ifeq  ($(strip $(CYGWIN_BUILD)),yes)
     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
 
@@ -49,7 +53,7 @@ USEREADLINE ?= yes
 
 ifeq  ($(strip $(USEREADLINE)),yes)
     CXXFLAGS += -DUSE_READLINE
-    LDFLAGS += \
+    LIBS = \
       -lreadline\
       -lncurses
 endif
@@ -61,6 +65,15 @@ ifeq  ($(strip $(USEMPI)),yes)
     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.
+
+USECOMPRESSION ?= no
+
+ifeq  ($(strip $(USECOMPRESSION)),yes)
+  CXXFLAGS += -DUSE_COMPRESSION
+endif
+
 #
 # INCLUDE directories for mothur
 #
@@ -72,13 +85,18 @@ 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