added processors to pre.cluster for mac and windows. Fixed bug in reNameFile function...

[mothur.git] / makefile

diff --git a/makefile b/makefile
index 7cc71f0e9a4064a2163707f3f7bc08da36af2b5e..44d8a81a5e7b5a92d70df3dc6618daf5e505f7d7 100644 (file)
--- a/makefile
+++ b/makefile
@@ -14,9 +14,9 @@ USEMPI ?= no
 USEREADLINE ?= yes
 CYGWIN_BUILD ?= no
 USECOMPRESSION ?= no
-MOTHUR_FILES = "\"../release\""
-RELEASE_DATE = "\"2/7/2011\""
-VERSION = "\"1.16.0\""
+MOTHUR_FILES="\"Enter_your_default_path_here\""
+RELEASE_DATE = "\"10/18/2011\""
+VERSION = "\"1.22.0\""
 
 # Optimize to level 3:
 CXXFLAGS += -O3
@@ -28,6 +28,11 @@ 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
        
@@ -85,11 +90,14 @@ 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
        
@@ -103,4 +111,5 @@ install : mothur
 
 clean :
        @rm -f $(OBJECTS)
+       @rm -f uchime