# Installation

## Quick and Easy Install

Most of our users choose to download the prebuilt executable. This option does not require you to have a compiler or any other tools installed on your machine. You simply download a zip file. Decompress it and start using mothur. Sound good? You can download our latest executable versions here.

## Building From Scratch

makefile options to consider before you get started.

### Dependencies

mothur can be built and run WITHOUT any dependancies. But some additional features may be useful for your specific applications. You can include these extra features by installing the following dependancies and compiling mothur with the flags set to yes. Dependency Install

#### Boost

mothur uses the boost library to read compressed files in the make.contigs command. It is not required. If you would like to be able to use this option, you must install Boost and set the boost flags in the makefile.

USEBOOST ?= yes
BOOST_LIBRARY_DIR ?= ""/usr/local/lib""
BOOST_INCLUDE_DIR ?= ""/usr/local/include""


#### HDF5

mothur uses the HDF5 library to read biom files in HDF5 format. These libraries are used by the biom.info command to read biom files in hdf5 format. It is not required. If you would like to use biom files in this format within mothur, you must install the HDF5 library and set the HDF5 flags.

USEHDF5 ?= yes
HDF5_LIBRARY_DIR ?= ""/usr/local/hdf5/lib""
HDF5_INCLUDE_DIR ?= ""/usr/local/hdf5/include""


#### GSL

mothur uses the GSL library to run the estimator.single command. It is not required. If you would like to use the estimator.single command, you must install the GSL library and set the GSL flags.

USEGSL ?= yes
GSL_LIBRARY_DIR ?= ""/usr/local/gsl/lib""
GSL_INCLUDE_DIR ?= ""/usr/local/gsl/include""

ifeq  ($(strip$(USEGSL)),yes)

LDFLAGS += -L ${GSL_LIBRARY_DIR} LIBS += -lgsl -lgslcblas -lm CXXFLAGS += -DUSE_GSL -I${GSL_INCLUDE_DIR}

endif


### 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:

$unzip mothur.zip  This will generate a mothur folder. Now move into the mothur folder and compile mothur: $ cd mothur
$make  Go ahead and try 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) 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


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*:${PATH}  To run mothur from within any folder:  mothur  If you are analyzing large data sets (e.g. from pyrosequencing) on a 64bit system and you have more than 2 GB of RAM in your computer, you can add a flag to the make file to use 64-bit pointers by opening the makefile and changing the line that reads: 64BIT_VERSION ?= no  to 64BIT_VERSION ?= yes  You will also need to uncomment a few lines in the makefile, for a more detailed explanation of makefile options see, Makefile options: ifeq ($(strip $(64BIT_VERSION)),yes) #if you are using linux user uncomment the following lines CXX = g++44 CXXFLAGS += -mtune=native -march=native -m64 #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 CXXFLAGS += -DBIT_VERSION FORTRAN_FLAGS = -m64 endif  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 having trouble with the readline libraries, try this How to Resolve Readline Issues. 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 $ 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++>

    $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 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: $ ./mothur
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.

Alternatively, you can build mothur from source using a tool like cygwin:

• Run cygwin setup-x86_64.
• Choose the mingw64x86_64 compliers for c++ and c - under the devel category.
• Install make utility - under the devel category
• Include any additional packages cygwin recommends installing.

#### Alter mothur makefile

64BIT_VERSION ?= yes
USEBOOST ?= no
RELEASE_DATE = ""3/6/2017""
VERSION = ""1.39.4""

# Optimize to level 3:
CXXFLAGS += -O3 -std=c++0x

ifeq  ($(strip$(64BIT_VERSION)),yes)
#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++
TARGET_ARCH += -m64 -static

#if you are a linux user use the following line - specific processor builds in future??
#CXXFLAGS += -mtune=generic

CXXFLAGS += -DBIT_VERSION
endif


#### Building with Cygwin

• Open Cygwin64Terminal program
• cd to directory with mothur’s source
• Run make clean, then make.