X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=makefile;h=c67f0ba6bd2d5a3baf675edef32fbd15679259fc;hb=cbbf2f185fc7289910bb69421095c1de024c5225;hp=3f6431210735a622f8c0e416a088581d331ed714;hpb=ae57e166b2ed7b475ec3f466106bd76fabadd063;p=mothur.git

diff --git a/makefile b/makefile
index 3f64312..c67f0ba 100644
--- a/makefile
+++ b/makefile
@@ -12,14 +12,15 @@
 USEMPI ?= no
 64BIT_VERSION ?= yes
 USEREADLINE ?= yes
-CYGWIN_BUILD ?= no
 USECOMPRESSION ?= no
-MOTHUR_FILES="\"/Users/Sarahswork/desktop/release\""
-RELEASE_DATE = "\"7/25/2011\""
-VERSION = "\"1.21.0\""
+MOTHUR_FILES="\"Enter_your_default_path_here\""
+RELEASE_DATE = "\"2/12/2014\""
+VERSION = "\"1.33.0\""
+FORTAN_COMPILER = gfortran
+FORTRAN_FLAGS = 
 
 # Optimize to level 3:
-CXXFLAGS += -03 -g
+CXXFLAGS += -O3 
 
 ifeq  ($(strip $(64BIT_VERSION)),yes)
 	#if you are using centos uncomment the following lines
@@ -31,12 +32,13 @@ ifeq  ($(strip $(64BIT_VERSION)),yes)
 	#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
+	#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 += -mtune=native -march=native 
 	
-	 CXXFLAGS += -DBIT_VERSION
+	CXXFLAGS += -DBIT_VERSION 
 endif
 
 
@@ -47,10 +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
@@ -89,11 +87,18 @@ 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
@@ -108,4 +113,5 @@ install : mothur
 
 clean :
 	@rm -f $(OBJECTS)
+	@rm -f uchime