changing command name classify.shared to classifyrf.shared

[mothur.git] / makefile

diff --git a/makefile b/makefile
index df165b3e4195420a3543c352cd3d02c8df6b7dbc..163db6bd0c547f2b73055ab5b4498dbd82ebfea3 100644 (file)
--- a/makefile
+++ b/makefile
@@ -14,12 +14,14 @@ 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 = "\"5/29/2013\""
+VERSION = "\"1.31.1\""
+FORTAN_COMPILER = gfortran
+FORTRAN_FLAGS = 
 
 # Optimize to level 3:
-CXXFLAGS += -O3
+CXXFLAGS += -O3 
 
 ifeq  ($(strip $(64BIT_VERSION)),yes)
        #if you are using centos uncomment the following lines
@@ -28,10 +30,17 @@ ifeq  ($(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++
+       #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 -m64
        
-        CXXFLAGS += -DBIT_VERSION
+       CXXFLAGS += -DBIT_VERSION 
+    FORTRAN_FLAGS = -m64
 endif
 
 
@@ -84,11 +93,18 @@ endif
 
 OBJECTS=$(patsubst %.cpp,%.o,$(wildcard *.cpp))
 OBJECTS+=$(patsubst %.c,%.o,$(wildcard *.c))
+OBJECTS+=$(patsubst %.f,%.o,$(wildcard *.f))
 
-mothur : $(OBJECTS)
+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
@@ -103,4 +119,5 @@ install : mothur
 
 clean :
        @rm -f $(OBJECTS)
+       @rm -f uchime