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Makefile options
From mothur
If you are building mothur instead of downloading one of our executables, there are several options for you to consider.
Contents |
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 $(MOTHUR_FILES)),"\"Enter_your_default_path_here\"")
else
CXXFLAGS += -DMOTHUR_FILES=${MOTHUR_FILES}
endif
Using cygwin to build
If you are using cygwin to build you will want to include the appropriate flags, so change the "no" to a "yes" below.
CYGWIN_BUILD ?= no
ifeq ($(strip $(CYGWIN_BUILD)),yes)
CXXFLAGS += -mno-cygwin
LDFLAGS += -mno-cygwin
endif
Building a 64bit version
In order to take advantage of your 64bit architecture, you want to build a 64 version of mothur. You do this by changing the "no" to a "yes" below. Note: if you are a linux user, comment out the TARGET_ARCH line and uncomment the CXXFLAGS line.
64BIT_VERSION ?= yes
ifeq ($(strip $(64BIT_VERSION)),yes)
#if you are using centos uncomment the following lines
#CXX = g++44
#if you are a mac user use the following line
TARGET_ARCH += -arch x86_64
#if you using cygwin to build Windows the following lines
#CXX = x86_64-w64-mingw32-g++
#CC = x86_64-w64-mingw32-g++
#FORTAN_COMPILER = x86_64-w64-mingw32-gfortran
#TARGET_ARCH += -m64 -static
#if you are a linux user use the following line
#CXXFLAGS += -mtune=native -march=native -m64
CXXFLAGS += -DBIT_VERSION
FORTRAN_FLAGS = -m64
endif
Readline Library
The readline library is not required to run mothur, but it will allow you to scroll through the commands you have entered if you are running mothur in interactive mode. If you do not want to use the readline library, change the yes to no below. If you are going to use it, make sure you have the readline library and ncurses library installed on your machine.
USEREADLINE ?= yes
ifeq ($(strip $(USEREADLINE)),yes)
CXXFLAGS += -DUSE_READLINE
LDFLAGS += \
-lreadline\
-lncurses
endif
MPI Version
If you would like to build a mpi-enabled version of mothur, you will want to change the no to yes below. If you are running mothur on a single machine and not a cluster, the mpi-enabled version is slower than using the non-mpi enabled version.
USEMPI ?= no
ifeq ($(strip $(USEMPI)),yes)
CXX = mpic++
CXXFLAGS += -DUSE_MPI
endif
Use Compression
If you would like mothur to compress distance files after dist.seqs creates them, then you will need to set USECOMPRESSION ?= yes.
USECOMPRESSION ?= no ifeq ($(strip $(USECOMPRESSION)),yes) CXXFLAGS += -DUSE_COMPRESSION endif
Fortran compiler
You will need a fortran compiler to compile some of mothur's source code. By default the makefile looks for gfortran, but if you would like to use another compiler you must set the FORTAN_COMPILER option.
FORTAN_COMPILER = yourCompiler
