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Installation

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Mac OSX

In the Mac OSX and Linux-type environments, you need to have a C++ compiler installed. These are typically installed with most linux-type operating systems and is on the Mac OSX installation CD/DVD. For Mac OSX users, you need to install the Xcode developer's tools. After downloading mothur, decompress it. If you want to house mothur off of your home folder (because don't we all want to live with our moms forever?), open a terminal window and enter:

escriba:~ pschloss$ unzip mothur.zip

This will generate a mothur folder. Now move into the mothur folder and compile mothur:

escriba:~ pschloss$ cd mothur
escriba:~ pschloss$ make

Go ahead and try to run mothur:

escriba:~ pschloss$ ./mothur

Hopefully, mothur will open in the interactive mode. For now type quit() at the mothur prompt. mothur is installed.

If you are analyzing large data sets (e.g. from pyrosequencing) in OS X and you have more than 2 GB of RAM in your computer, you can add a flag to the make file to use 64-bit pointers by opening the makefile and changing the lines that read:

CC_OPTIONS = -O3
LNK_OPTIONS = 

to

CC_OPTIONS = -O3 -arch x86_64
LNK_OPTIONS = -arch x86_64

Save the makefile and re-do the make command. The flag to compile with 64-bit pointers seems dependent on the architecture of your processor; replace x86_64 with ppc64 to compile for 64-bit PowerPC architecture.

If you would like to build a mpi-enabled version of mothur you must set 2 options:

CC = mpic++

and

USEMPI ?= yes


Linux/Unix

In Linux-type environments, you need to have a C++ compiler installed. These are typically pre-installed with most linux-type operating systems, and are always in a repository for a distribution (the package is named build-essential in Debian and Ubuntu). After downloading mothur, decompress it. If you want to house mothur off of your home folder (because don't we all want to live with our moms forever?), open a terminal window and enter:

 mkdir mothur
 cd mothur
 unzip ../Mothur.source.zip
 make

There are numerous errors that say "warning: no newline at end of file", but they do not cause a problem.

To run mothur:

 ./mothur

Hopefully, mothur will open in the interactive mode. For now type quit() at the mothur prompt. mothur is installed.

If you are analyzing large data sets (e.g. from pyrosequencing) on a 64bit system and you have more than 2 GB of RAM in your computer, you can add a flag to the make file to use 64-bit pointers by opening the makefile and changing the line that reads:

 CC_OPTIONS = -O3

to

 CC_OPTIONS = -O3 -mtune=native -march=native -m64

Save the makefile and re-do the make command. The flag to compile with 64-bit pointers seems dependent on the architecture of your processor.

If you have complied problem with readline, try to install the library first (Ubuntu for example)

 sudo apt-get install libreadline-dev

If you are sure you have the readline library installed already, try to add -lncurses after -lreadline in the makefile

 LNK_OPTIONS = \
     -lreadline\
     -lncurses\
     -L../readline-6.0

Alternatively, open the makefile and remove the lines that refer to the readline library and recompile.

Windows

See the downloads page to obtain the Window's executable version of mothur. Mothur comes as a compressed file known as a ZIP file. To decompress this file, double click on it and follow the instructions. Consider decompressing mothur to a directory such as C:\mothur.