X-Git-Url: https://git.donarmstrong.com/?p=mothur.git;a=blobdiff_plain;f=makefile;h=42e71a0e42bb0341c3cff63a8c616d6572537f4b;hp=af46fd97ab6bcd26392de438592e9d03678f3948;hb=cf9987b67aa49777a4c91c2d21f96e58bf17aa82;hpb=bc4c4d63e983a3e91e74b5038bfec6705e1a3a2e

diff --git a/makefile b/makefile
index af46fd9..42e71a0 100644
--- a/makefile
+++ b/makefile
@@ -1,69 +1,122 @@
-###################################################
-#
-# Makefile for mothur
-# Created: June 29, 2010
-#
-###################################################
-
-#
-# Macros
-#
-
-# Optimize to level 3:
-
-CXXFLAGS += -O3
-
-CYGWIN_BUILD ?= no
-ifeq  ($(strip $(CYGWIN_BUILD)),yes)
-    CXXFLAGS += -mno-cygwin
-    LDFLAGS += -mno-cygwin 
-#-lpsapi
-endif
-
-64BIT_VERSION ?= yes
-
-ifeq  ($(strip $(64BIT_VERSION)),yes)
-    TARGET_ARCH += -arch x86_64
-endif
-
-# if you do not want to use the readline library, set this to no.
-# make sure you have the library installed
-
-USEREADLINE ?= yes
-
-ifeq  ($(strip $(USEREADLINE)),yes)
-    CXXFLAGS += -DUSE_READLINE
-    LDFLAGS += \
-      -lreadline\
-      -lncurses\
-      -L../readline-6.0
-endif
-
-USEMPI ?= no
-
-ifeq  ($(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
-
-clean :
-	@rm -f $(OBJECTS)
-
+###################################################
+#
+# Makefile for mothur
+# Created: June 29, 2010
+#
+###################################################
+
+#
+# Macros
+#
+
+USEMPI ?= no
+64BIT_VERSION ?= yes
+USEREADLINE ?= yes
+CYGWIN_BUILD ?= no
+USECOMPRESSION ?= no
+MOTHUR_FILES="\"Enter_your_default_path_here\""
+RELEASE_DATE = "\"10/16/2013\""
+VERSION = "\"1.32.1\""
+FORTAN_COMPILER = gfortran
+FORTRAN_FLAGS = 
+
+# Optimize to level 3:
+CXXFLAGS += -O3 
+
+ifeq  ($(strip $(64BIT_VERSION)),yes)
+	#if you are using centos uncomment the following lines
+	#CXX = g++44
+	
+	#if you are a mac user use the following line
+	TARGET_ARCH += -arch x86_64
+	
+	#if you using cygwin to build Windows the following line
+	#CXX = x86_64-w64-mingw32-g++
+	#CC = x86_64-w64-mingw32-g++
+	#FORTAN_COMPILER = x86_64-w64-mingw32-gfortran
+ 	#TARGET_ARCH += -m64 -static
+
+	#if you are a linux user use the following line
+	#CXXFLAGS += -mtune=native -march=native 
+	
+	CXXFLAGS += -DBIT_VERSION 
+endif
+
+
+CXXFLAGS += -DRELEASE_DATE=${RELEASE_DATE} -DVERSION=${VERSION}
+
+ifeq  ($(strip $(MOTHUR_FILES)),"\"Enter_your_default_path_here\"")
+else
+	CXXFLAGS += -DMOTHUR_FILES=${MOTHUR_FILES}
+endif
+
+ifeq  ($(strip $(CYGWIN_BUILD)),yes)
+    CXXFLAGS += -mno-cygwin
+    LDFLAGS += -mno-cygwin 
+endif
+
+# if you do not want to use the readline library, set this to no.
+# make sure you have the library installed
+
+
+ifeq  ($(strip $(USEREADLINE)),yes)
+    CXXFLAGS += -DUSE_READLINE
+    LIBS = \
+      -lreadline\
+      -lncurses
+endif
+
+
+ifeq  ($(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 $(USECOMPRESSION)),yes)
+  CXXFLAGS += -DUSE_COMPRESSION
+endif
+
+#
+# INCLUDE directories for mothur
+#
+
+     CXXFLAGS += -I.
+
+#
+# Get the list of all .cpp files, rename to .o files
+#
+
+OBJECTS=$(patsubst %.cpp,%.o,$(wildcard *.cpp))
+OBJECTS+=$(patsubst %.c,%.o,$(wildcard *.c))
+OBJECTS+=$(patsubst %.f,%.o,$(wildcard *.f))
+
+mothur : fortranSource $(OBJECTS) uchime
+	$(CXX) $(LDFLAGS) $(TARGET_ARCH) -o $@ $(OBJECTS) $(LIBS)
+	
+	strip mothur
+ 
+uchime:
+	cd uchime_src && ./mk && mv uchime .. && cd ..
+	
+fortranSource:
+	${FORTAN_COMPILER} -c $(FORTRAN_FLAGS) *.f
+
+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)
+	@rm -f uchime
+