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Makefile options

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If you are building mothur instead of downloading one of our executables, there are several options for you to consider.

Setting a default location

You can set a default location for mothur to look for input files, if they are not found. This will allow you to keep your reference files in one location and save time typing lengthy filenames. This location can be overridden using the set.dir command at run time.

To do this: change Enter_your_default_path_here to the location you would like to use as a default.

MOTHUR_FILES = "\"Enter_your_default_path_here\""
ifeq  ($(strip $(MOTHUR_FILES)),"\"Enter_your_default_path_here\"")

Building a 64bit version

In order to take advantage of your 64bit architecture, you want to build a 64 version of mothur. You do this by changing the "no" to a "yes" below. Note: if you are a linux user, comment out the TARGET_ARCH line and uncomment the CXXFLAGS line.

 64BIT_VERSION ?= yes
  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 lines
 	#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
    FORTRAN_FLAGS = -m64

Readline Library

The readline library is not required to run mothur, but it will allow you to scroll through the commands you have entered if you are running mothur in interactive mode. If you do not want to use the readline library, change the yes to no below. If you are going to use it, make sure you have the readline library and ncurses library installed on your machine.

 ifeq  ($(strip $(USEREADLINE)),yes)
     LDFLAGS += \