X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=makefile;h=92c20134b7911b1cb2aa570da7c2e95cdc1b119b;hb=4745a956b3116a719f52f341d2a2db84df4817da;hp=efac3fb5b84fc3bde1178520a8ca15009b1ef3dd;hpb=956cdff34f2d609a7736838b1631cd7957580b8b;p=mothur.git

diff --git a/makefile b/makefile
index efac3fb..92c2013 100644
--- a/makefile
+++ b/makefile
@@ -1,74 +1,102 @@
-###################################################
-#
-# Makefile for mothur
-# Created: June 29, 2010
-#
-###################################################
-
-#
-# Macros
-#
-
-# Optimize to level 3:
-
-CXXFLAGS += -O3
-
-CYGWIN_BUILD ?= no
-ifeq  ($(strip $(CYGWIN_BUILD)),yes)
-    CXXFLAGS += -mno-cygwin
-    LDFLAGS += -mno-cygwin 
-endif
-
-64BIT_VERSION ?= yes
-
-ifeq  ($(strip $(64BIT_VERSION)),yes)
-    TARGET_ARCH += -arch x86_64
-	 CXXFLAGS += -DBIT_VERSION
-endif
-
-# if you do not want to use the readline library, set this to no.
-# make sure you have the library installed
-
-USEREADLINE ?= yes
-
-ifeq  ($(strip $(USEREADLINE)),yes)
-    CXXFLAGS += -DUSE_READLINE
-    LDFLAGS += \
-      -lreadline\
-      -lncurses
-endif
-
-USEMPI ?= no
-
-ifeq  ($(strip $(USEMPI)),yes)
-    CXX = mpic++
-    CXXFLAGS += -DUSE_MPI
-endif
-
-#
-# INCLUDE directories for mothur
-#
-
-     CXXFLAGS += -I.
-
-#
-# Get the list of all .cpp files, rename to .o files
-#
-
-OBJECTS=$(patsubst %.cpp,%.o,$(wildcard *.cpp))
-
-mothur : $(OBJECTS)
-	$(CXX) $(LDFLAGS) $(TARGET_ARCH) -o $@ $(OBJECTS)
-
-install : mothur
-	cp mothur ../Release/mothur
-
-%.o : %.cpp %.h
-	$(COMPILE.cpp) $(OUTPUT_OPTION) $<
-%.o : %.cpp %.hpp
-	$(COMPILE.cpp) $(OUTPUT_OPTION) $<
-
-
-clean :
-	@rm -f $(OBJECTS)
-
+###################################################
+#
+# Makefile for mothur
+# Created: June 29, 2010
+#
+###################################################
+
+#
+# Macros
+#
+
+# Optimize to level 3:
+
+CXXFLAGS += -O3
+
+MOTHUR_FILES = "\"../Release\""
+
+RELEASE_DATE = "\"9/17/2010\""
+VERSION = "\"1.13.0\""
+
+CXXFLAGS += -DRELEASE_DATE=${RELEASE_DATE} -DVERSION=${VERSION}
+
+ifeq  ($(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 $(64BIT_VERSION)),yes)
+    TARGET_ARCH += -arch x86_64
+	 CXXFLAGS += -DBIT_VERSION
+	
+	#if you are using centos uncomment the following lines
+	#CXX = g++44
+	#CXXFLAGS += -mtune=native -march=native -m64
+endif
+
+# if you do not want to use the readline library, set this to no.
+# make sure you have the library installed
+
+USEREADLINE ?= yes
+
+ifeq  ($(strip $(USEREADLINE)),yes)
+    CXXFLAGS += -DUSE_READLINE
+    LDFLAGS += \
+      -lreadline\
+      -lncurses
+endif
+
+USEMPI ?= no
+
+ifeq  ($(strip $(USEMPI)),yes)
+    CXX = mpic++
+    CXXFLAGS += -DUSE_MPI
+endif
+
+# if you want to enable reading and writing of compressed files, set to yes.
+# The default is no.  this may only work on unix-like systems.
+
+USECOMPRESSION ?= no
+
+ifeq  ($(strip $(USECOMPRESSION)),yes)
+  CXXFLAGS += -DUSE_COMPRESSION
+endif
+
+#
+# INCLUDE directories for mothur
+#
+
+     CXXFLAGS += -I.
+
+#
+# Get the list of all .cpp files, rename to .o files
+#
+
+OBJECTS=$(patsubst %.cpp,%.o,$(wildcard *.cpp))
+OBJECTS+=$(patsubst %.c,%.o,$(wildcard *.c))
+
+mothur : $(OBJECTS)
+	$(CXX) $(LDFLAGS) $(TARGET_ARCH) -o $@ $(OBJECTS)
+
+install : mothur
+	cp mothur ../Release/mothur
+	
+%.o : %.c %.h
+	$(COMPILE.c) $(OUTPUT_OPTION) $<
+%.o : %.cpp %.h
+	$(COMPILE.cpp) $(OUTPUT_OPTION) $<
+%.o : %.cpp %.hpp
+	$(COMPILE.cpp) $(OUTPUT_OPTION) $<
+
+
+clean :
+	@rm -f $(OBJECTS)
+