fixed bug in make.biom with picrust that didn’t allow for unclassified OTUs. fixed...

[mothur.git] / makefile

diff --git a/makefile b/makefile
index 476070eb2fbb654d054238c45ee335b2ce8fe0eb..c67f0ba6bd2d5a3baf675edef32fbd15679259fc 100644 (file)
--- a/makefile
+++ b/makefile
@@ -12,12 +12,12 @@
 USEMPI ?= no
 64BIT_VERSION ?= yes
 USEREADLINE ?= yes
-CYGWIN_BUILD ?= no
 USECOMPRESSION ?= no
 MOTHUR_FILES="\"Enter_your_default_path_here\""
-RELEASE_DATE = "\"1/9/2012\""
-VERSION = "\"1.23.0\""
+RELEASE_DATE = "\"2/12/2014\""
+VERSION = "\"1.33.0\""
 FORTAN_COMPILER = gfortran
+FORTRAN_FLAGS = 
 
 # Optimize to level 3:
 CXXFLAGS += -O3 
@@ -36,9 +36,9 @@ ifeq  ($(strip $(64BIT_VERSION)),yes)
        #TARGET_ARCH += -m64 -static
 
        #if you are a linux user use the following line
-       #CXXFLAGS += -mtune=native -march=native -m64
+       #CXXFLAGS += -mtune=native -march=native 
        
-        CXXFLAGS += -DBIT_VERSION
+       CXXFLAGS += -DBIT_VERSION 
 endif
 
 
@@ -49,10 +49,6 @@ 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
@@ -97,12 +93,12 @@ 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 *.f
+       ${FORTAN_COMPILER} -c $(FORTRAN_FLAGS) *.f
 
 install : mothur
 #      cp mothur ../Release/mothur