X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=makefile;h=a8a0170db2642bf436dbace2f002a2f370c76d23;hb=0b99c6b6ea875e13febda76903fd4d9cda7add7d;hp=efac3fb5b84fc3bde1178520a8ca15009b1ef3dd;hpb=956cdff34f2d609a7736838b1631cd7957580b8b;p=mothur.git

diff --git a/makefile b/makefile
index efac3fb..a8a0170 100644
--- a/makefile
+++ b/makefile
@@ -1,74 +1,84 @@
-###################################################
-#
-# 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 $(OBJECTS)
-
+###################################################
+#
+# Makefile for mothur
+# Created: June 29, 2010
+#
+###################################################
+
+#
+# Macros
+#
+
+# Optimize to level 3:
+
+CXXFLAGS += -O3
+
+MOTHUR_FILES = "\"Enter_your_default_path_here\""
+ifeq  ($(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 $(USEMPI)),yes)
+    CXX = mpic++
+    CXXFLAGS += -DUSE_MPI
+endif
+
+#
+# INCLUDE directories for mothur
+#
+
+     CXXFLAGS += -I.
+
+#
+# Get the list of all .cpp files, rename to .o files
+#
+
+OBJECTS=$(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)
+