working on pam

[mothur.git] / makefile

diff --git a/makefile b/makefile
index af46fd97ab6bcd26392de438592e9d03678f3948..42e71a0e42bb0341c3cff63a8c616d6572537f4b 100644 (file)
--- a/makefile
+++ b/makefile
@@ -1,69 +1,122 @@
-###################################################\r
-#\r
-# Makefile for mothur\r
-# Created: June 29, 2010\r
-#\r
-###################################################\r
-\r
-#\r
-# Macros\r
-#\r
-\r
-# Optimize to level 3:\r
-\r
-CXXFLAGS += -O3\r
-\r
-CYGWIN_BUILD ?= no\r
-ifeq  ($(strip $(CYGWIN_BUILD)),yes)\r
-    CXXFLAGS += -mno-cygwin\r
-    LDFLAGS += -mno-cygwin \r
-#-lpsapi\r
-endif\r
-\r
-64BIT_VERSION ?= yes\r
-\r
-ifeq  ($(strip $(64BIT_VERSION)),yes)\r
-    TARGET_ARCH += -arch x86_64\r
-endif\r
-\r
-# if you do not want to use the readline library, set this to no.\r
-# make sure you have the library installed\r
-\r
-USEREADLINE ?= yes\r
-\r
-ifeq  ($(strip $(USEREADLINE)),yes)\r
-    CXXFLAGS += -DUSE_READLINE\r
-    LDFLAGS += \\r
-      -lreadline\\r
-      -lncurses\\r
-      -L../readline-6.0\r
-endif\r
-\r
-USEMPI ?= no\r
-\r
-ifeq  ($(strip $(USEMPI)),yes)\r
-    CXX = mpic++\r
-    CXXFLAGS += -DUSE_MPI\r
-endif\r
-\r
-#\r
-# INCLUDE directories for mothur\r
-#\r
-\r
-     CXXFLAGS += -I.\r
-\r
-#\r
-# Get the list of all .cpp files, rename to .o files\r
-#\r
-\r
-OBJECTS=$(patsubst %.cpp,%.o,$(wildcard *.cpp))\r
-\r
-mothur : $(OBJECTS)\r
-       $(CXX) $(LDFLAGS) $(TARGET_ARCH) -o $@ $(OBJECTS)\r
-\r
-install : mothur\r
-       cp mothur ../Release/mothur\r
-\r
-clean :\r
-       @rm -f $(OBJECTS)\r
-\r
+###################################################
+#
+# Makefile for mothur
+# Created: June 29, 2010
+#
+###################################################
+
+#
+# Macros
+#
+
+USEMPI ?= no
+64BIT_VERSION ?= yes
+USEREADLINE ?= yes
+CYGWIN_BUILD ?= no
+USECOMPRESSION ?= no
+MOTHUR_FILES="\"Enter_your_default_path_here\""
+RELEASE_DATE = "\"10/16/2013\""
+VERSION = "\"1.32.1\""
+FORTAN_COMPILER = gfortran
+FORTRAN_FLAGS = 
+
+# Optimize to level 3:
+CXXFLAGS += -O3 
+
+ifeq  ($(strip $(64BIT_VERSION)),yes)
+       #if you are using centos uncomment the following lines
+       #CXX = g++44
+       
+       #if you are a mac user use the following line
+       TARGET_ARCH += -arch x86_64
+       
+       #if you using cygwin to build Windows the following line
+       #CXX = x86_64-w64-mingw32-g++
+       #CC = x86_64-w64-mingw32-g++
+       #FORTAN_COMPILER = x86_64-w64-mingw32-gfortran
+       #TARGET_ARCH += -m64 -static
+
+       #if you are a linux user use the following line
+       #CXXFLAGS += -mtune=native -march=native 
+       
+       CXXFLAGS += -DBIT_VERSION 
+endif
+
+
+CXXFLAGS += -DRELEASE_DATE=${RELEASE_DATE} -DVERSION=${VERSION}
+
+ifeq  ($(strip $(MOTHUR_FILES)),"\"Enter_your_default_path_here\"")
+else
+       CXXFLAGS += -DMOTHUR_FILES=${MOTHUR_FILES}
+endif
+
+ifeq  ($(strip $(CYGWIN_BUILD)),yes)
+    CXXFLAGS += -mno-cygwin
+    LDFLAGS += -mno-cygwin 
+endif
+
+# if you do not want to use the readline library, set this to no.
+# make sure you have the library installed
+
+
+ifeq  ($(strip $(USEREADLINE)),yes)
+    CXXFLAGS += -DUSE_READLINE
+    LIBS = \
+      -lreadline\
+      -lncurses
+endif
+
+
+ifeq  ($(strip $(USEMPI)),yes)
+    CXX = mpic++
+    CXXFLAGS += -DUSE_MPI
+endif
+
+# if you want to enable reading and writing of compressed files, set to yes.
+# The default is no.  this may only work on unix-like systems, not for windows.
+
+
+ifeq  ($(strip $(USECOMPRESSION)),yes)
+  CXXFLAGS += -DUSE_COMPRESSION
+endif
+
+#
+# INCLUDE directories for mothur
+#
+
+     CXXFLAGS += -I.
+
+#
+# Get the list of all .cpp files, rename to .o files
+#
+
+OBJECTS=$(patsubst %.cpp,%.o,$(wildcard *.cpp))
+OBJECTS+=$(patsubst %.c,%.o,$(wildcard *.c))
+OBJECTS+=$(patsubst %.f,%.o,$(wildcard *.f))
+
+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
+       
+%.o : %.c %.h
+       $(COMPILE.c) $(OUTPUT_OPTION) $<
+%.o : %.cpp %.h
+       $(COMPILE.cpp) $(OUTPUT_OPTION) $<
+%.o : %.cpp %.hpp
+       $(COMPILE.cpp) $(OUTPUT_OPTION) $<
+
+
+clean :
+       @rm -f $(OBJECTS)
+       @rm -f uchime
+