added compile time default path

[mothur.git] / makefile

diff --git a/makefile b/makefile
index 8ea410e02545278774c6b5f922c8ac40f68f946e..3f0893c5ad82d811fb4c5cf05f86f0326b4561c8 100644 (file)
--- a/makefile
+++ b/makefile
@@ -1,78 +1,84 @@
-###################################################\r
-#\r
-# Makefile for mothur\r
-# Created: June 29, 2010\r
-#\r
-###################################################\r
-\r
-#\r
-# Macros\r
-#\r
-\r
-# Optimize to level 3:\r
-\r
-CXXFLAGS += -O3\r
-\r
-CYGWIN_BUILD ?= no\r
-ifeq  ($(strip $(CYGWIN_BUILD)),yes)\r
-    CXXFLAGS += -mno-cygwin\r
-    LDFLAGS += -mno-cygwin \r
-endif\r
-\r
-64BIT_VERSION ?= yes\r
-\r
-ifeq  ($(strip $(64BIT_VERSION)),yes)\r
-    TARGET_ARCH += -arch x86_64\r
-        CXXFLAGS += -DBIT_VERSION\r
-       \r
-       #if you are using centos uncomment the following lines\r
-       #CC = g++44\r
-       #CXXFLAGS += -mtune=native -march=native -m64\r
-endif\r
-\r
-# if you do not want to use the readline library, set this to no.\r
-# make sure you have the library installed\r
-\r
-USEREADLINE ?= yes\r
-\r
-ifeq  ($(strip $(USEREADLINE)),yes)\r
-    CXXFLAGS += -DUSE_READLINE\r
-    LDFLAGS += \\r
-      -lreadline\\r
-      -lncurses\r
-endif\r
-\r
-USEMPI ?= no\r
-\r
-ifeq  ($(strip $(USEMPI)),yes)\r
-    CXX = mpic++\r
-    CXXFLAGS += -DUSE_MPI\r
-endif\r
-\r
-#\r
-# INCLUDE directories for mothur\r
-#\r
-\r
-     CXXFLAGS += -I.\r
-\r
-#\r
-# Get the list of all .cpp files, rename to .o files\r
-#\r
-\r
-OBJECTS=$(patsubst %.cpp,%.o,$(wildcard *.cpp))\r
-\r
-mothur : $(OBJECTS)\r
-       $(CXX) $(LDFLAGS) $(TARGET_ARCH) -o $@ $(OBJECTS)\r
-\r
-install : mothur\r
-       cp mothur ../Release/mothur\r
-\r
-%.o : %.cpp %.h\r
-       $(COMPILE.cpp) $(OUTPUT_OPTION) $<\r
-%.o : %.cpp %.hpp\r
-       $(COMPILE.cpp) $(OUTPUT_OPTION) $<\r
-\r
-\r
-clean :\r
-       @rm -f $(OBJECTS)\r
-\r
+###################################################
+#
+# Makefile for mothur
+# Created: June 29, 2010
+#
+###################################################
+
+#
+# Macros
+#
+
+# Optimize to level 3:
+
+CXXFLAGS += -O3
+
+MOTHUR_FILES = "\"Enter_your_default_path_here\""
+ifeq  ($(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 $(64BIT_VERSION)),yes)
+    TARGET_ARCH += -arch x86_64
+        CXXFLAGS += -DBIT_VERSION
+       
+       #if you are using centos uncomment the following lines
+       #CC = g++44
+       #CXXFLAGS += -mtune=native -march=native -m64
+endif
+
+# if you do not want to use the readline library, set this to no.
+# make sure you have the library installed
+
+USEREADLINE ?= yes
+
+ifeq  ($(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)
+