bug fixes

[mothur.git] / makefile

diff --git a/makefile b/makefile
index dccd2c3d3dd12235530bba90da5ffeaa53b670cc..92c20134b7911b1cb2aa570da7c2e95cdc1b119b 100644 (file)
--- a/makefile
+++ b/makefile
@@ -14,6 +14,12 @@
 CXXFLAGS += -O3
 
 MOTHUR_FILES = "\"../Release\""
+
+RELEASE_DATE = "\"9/17/2010\""
+VERSION = "\"1.13.0\""
+
+CXXFLAGS += -DRELEASE_DATE=${RELEASE_DATE} -DVERSION=${VERSION}
+
 ifeq  ($(strip $(MOTHUR_FILES)),"\"Enter_your_default_path_here\"")
 else
        CXXFLAGS += -DMOTHUR_FILES=${MOTHUR_FILES}
@@ -32,14 +38,14 @@ ifeq  ($(strip $(64BIT_VERSION)),yes)
         CXXFLAGS += -DBIT_VERSION
        
        #if you are using centos uncomment the following lines
-       #CC = g++44
+       #CXX = g++44
        #CXXFLAGS += -mtune=native -march=native -m64
 endif
 
 # if you do not want to use the readline library, set this to no.
 # make sure you have the library installed
 
-USEREADLINE ?= no
+USEREADLINE ?= yes
 
 ifeq  ($(strip $(USEREADLINE)),yes)
     CXXFLAGS += -DUSE_READLINE
@@ -48,13 +54,22 @@ ifeq  ($(strip $(USEREADLINE)),yes)
       -lncurses
 endif
 
-USEMPI ?= yes
+USEMPI ?= no
 
 ifeq  ($(strip $(USEMPI)),yes)
     CXX = mpic++
     CXXFLAGS += -DUSE_MPI
 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.
+
+USECOMPRESSION ?= no
+
+ifeq  ($(strip $(USECOMPRESSION)),yes)
+  CXXFLAGS += -DUSE_COMPRESSION
+endif
+
 #
 # INCLUDE directories for mothur
 #
@@ -66,13 +81,16 @@ endif
 #
 
 OBJECTS=$(patsubst %.cpp,%.o,$(wildcard *.cpp))
+OBJECTS+=$(patsubst %.c,%.o,$(wildcard *.c))
 
 mothur : $(OBJECTS)
        $(CXX) $(LDFLAGS) $(TARGET_ARCH) -o $@ $(OBJECTS)
 
 install : mothur
        cp mothur ../Release/mothur
-
+       
+%.o : %.c %.h
+       $(COMPILE.c) $(OUTPUT_OPTION) $<
 %.o : %.cpp %.h
        $(COMPILE.cpp) $(OUTPUT_OPTION) $<
 %.o : %.cpp %.hpp