X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=makefile;h=44d8a81a5e7b5a92d70df3dc6618daf5e505f7d7;hb=74dc92cf53df65fd8b14d8eaf35489bbecbccac6;hp=3d0e18de0e40d3b035f101c857c6def36e8cbdfd;hpb=134a9c1275862a6b3ea10a2c0f11965c0a535854;p=mothur.git

diff --git a/makefile b/makefile
index 3d0e18d..44d8a81 100644
--- a/makefile
+++ b/makefile
@@ -9,12 +9,18 @@
 # Macros
 #
 
-# Optimize to level 3:
+USEMPI ?= no
+64BIT_VERSION ?= yes
+USEREADLINE ?= yes
+CYGWIN_BUILD ?= no
+USECOMPRESSION ?= no
+MOTHUR_FILES="\"Enter_your_default_path_here\""
+RELEASE_DATE = "\"10/18/2011\""
+VERSION = "\"1.22.0\""
 
+# Optimize to level 3:
 CXXFLAGS += -O3
 
-64BIT_VERSION ?= yes
-
 ifeq  ($(strip $(64BIT_VERSION)),yes)
 	#if you are using centos uncomment the following lines
 	#CXX = g++44
@@ -22,16 +28,17 @@ ifeq  ($(strip $(64BIT_VERSION)),yes)
 	#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++
+ 	#TARGET_ARCH += -m64 -static
+
 	#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 = "\"10/26/2010\""
-VERSION = "\"1.14.0\""
 
 CXXFLAGS += -DRELEASE_DATE=${RELEASE_DATE} -DVERSION=${VERSION}
 
@@ -40,7 +47,6 @@ else
 	CXXFLAGS += -DMOTHUR_FILES=${MOTHUR_FILES}
 endif
 
-CYGWIN_BUILD ?= no
 ifeq  ($(strip $(CYGWIN_BUILD)),yes)
     CXXFLAGS += -mno-cygwin
     LDFLAGS += -mno-cygwin 
@@ -49,7 +55,6 @@ 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 $(USEREADLINE)),yes)
     CXXFLAGS += -DUSE_READLINE
@@ -58,7 +63,6 @@ ifeq  ($(strip $(USEREADLINE)),yes)
       -lncurses
 endif
 
-USEMPI ?= no
 
 ifeq  ($(strip $(USEMPI)),yes)
     CXX = mpic++
@@ -66,9 +70,8 @@ ifeq  ($(strip $(USEMPI)),yes)
 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.
+# The default is no.  this may only work on unix-like systems, not for windows.
 
-USECOMPRESSION ?= no
 
 ifeq  ($(strip $(USECOMPRESSION)),yes)
   CXXFLAGS += -DUSE_COMPRESSION
@@ -87,11 +90,16 @@ endif
 OBJECTS=$(patsubst %.cpp,%.o,$(wildcard *.cpp))
 OBJECTS+=$(patsubst %.c,%.o,$(wildcard *.c))
 
-mothur : $(OBJECTS)
+mothur : $(OBJECTS) uchime
 	$(CXX) $(LDFLAGS) $(TARGET_ARCH) -o $@ $(OBJECTS) $(LIBS)
+	
+	strip mothur
+
+uchime:
+	cd uchime_src && ./mk && mv uchime .. && cd ..
 
 install : mothur
-	cp mothur ../Release/mothur
+#	cp mothur ../Release/mothur
 	
 %.o : %.c %.h
 	$(COMPILE.c) $(OUTPUT_OPTION) $<
@@ -103,4 +111,5 @@ install : mothur
 
 clean :
 	@rm -f $(OBJECTS)
+	@rm -f uchime