Installation
From mothur
Makefile options to consider before you get started.
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:
64BIT_VERSION ?= no
to
64BIT_VERSION ?= yes
This will add -arch x86_64 to the compiling and linking flags.
Save the makefile and run make clean, then 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 change:
USEMPI ?= no
to
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.
You can also add mothur to system PATH, this will enable you to run mothur from within any folder on your computer without having to move the binary everytime. For Ubuntu users, you can do so by editing the .bashrc file, a hidden file in your Home folder. Open the file in edit mode and enter the following at the end (replace path_to_mothur_binary_folder with the real path):
# User specific environment and startup programs
PATH=~/path_to_mothur_binary_folder:${PATH}
To run mothur from within any folder:
mothur
If you are analyzing large data sets (e.g. from pyrosequencing) on a 64bit system and you have more than 2 GB of RAM in your computer, you can add a flag to the make file to use 64-bit pointers by opening the makefile and changing the line that reads:
CC_OPTIONS = -O3
to
CC_OPTIONS = -O3 -mtune=native -march=native -m64
Save the makefile and re-do the make command. The flag to compile with 64-bit pointers seems dependent on the architecture of your processor.
If you have complied problem with readline, try to install the ncurses and readline development libraries first:
On Ubuntu:
sudo apt-get install libreadline-dev libreadline5-dev
On RedHat / Centos (as root):
yum install readline-devel ncurses-devel
If you are sure you have the readline library installed already, try to add -lncurses after -lreadline in the makefile
LNK_OPTIONS = \
-lreadline\
-lncurses\
-L../readline-6.0
Alternatively, open the makefile and remove the lines that refer to the readline library and recompile.
Additional notes for compiling v1.9.0: Make sure that you have installed the openMPI package from your software repository on your desktop. For Ubuntu users, this is available in the Synaptic Package Manager under System> Administration>
Alternatively install the following package using apt-get in Ubuntu. This will work in Karmic Koala (9.10) other versions of Ubuntu might use different package names or have different package versions.
sudo apt-get install openmpi-bin openmpi-common libopenmpi-dbg libopenmpi-dev libopenmpi1.3
CentOS tips (32-bit and 64-bit is similar)
Edit by Hoytpr: mpi is not installed by default using CentOS 5.4. If you are running CentOS 5.4 on a 32-bit machine, you can use the command:
yum –y install openmpi openmpi-devel
You will see that only the openmpi-1.3.2-gcc-i386 and openmpi-1.3.2-gcc-i386-devel will install.
Then type use the mpi-selector-menu to select the newly installed mpi as the default
[hoyt@biochem5]$ mpi-selector-menu Current System default: <none> "u" and "s" modifiers can be added to numeric and "U" commands to specify "user" or "system-wide". 1. openmpi-1.3.2-gcc-i386 U. Unset default Q. Quit Selection (1[us], U[us], Q):
Answer "1s" to get the mpi and system-wide default, then Q; to Quit. Logout, then log back in and type <which mpic++>
[hoyt@biochem5 ~]$ which mpic++
/usr/lib/openmpi/1.3.2-gcc/bin/mpic++
Looks good, but you are not quite finished! Two steps: FIRST STEP is to compile mothur using the <make> command from within the mothur directory. You will get lots of errors, but ignore them for now. Once the makefile is done, if you try to run mothur, you will get an ERROR like this:
[hoyt@biochem5 mothur]$ ./mothur librdmacm: couldn't read ABI version. librdmacm: assuming: 4 libibverbs: Fatal: couldn't read uverbs ABI version. CMA: unable to open /dev/infiniband/rdma_cm -------------------------------------------------------------------------- WARNING: Failed to open "OpenIB-cma" [DAT_INTERNAL_ERROR:]. This may be a real error or it may be an invalid entry in the uDAPL Registry which is contained in the dat.conf file. Contact your local System Administrator to confirm the availability of the interfaces in the dat.conf file. --------------------------------------------------------------------------
SECOND STEP: You must change the file etc/openmpi-mca-params.conf (it might be in a different location on your machine). To make the change, add the line:
btl=self
to the end of the file. Now you can run mothur!
The problem is that it's looking for an infiniband card in your machine, so this tells it that you're just using the same machine. (Thanks to my great friend and computer guru Dana for this tip!)
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.
