Installation

breseq is a command line tool implemented in Perl, C++, and R. It will compile and function on a variety of Unix platforms, including MacOSX.

1. Install external dependencies

Several external packages and software programs need to be installed to compile and use breseq:

  • GCC (or other C++ compiler) already installed on some systems
  • Perl (version 5.8 or higher) already installed on most systems
  • BioPerl (version 1.4 or higher)
  • SSAHA2 read mapping program
  • R (version 2.10 or higher) statistical programming language
  • Boost (version 1.42 or higher) C++ libraries

To install each missing dependency, use your system’s package manager or visit the respective web pages linked above and follow the instructions for your platform. More specific directions are available below for some platforms. You must make sure that the executables for SSAHA2 and R are in your environment’s $PATH for breseq to function.

MacOSX Instructions

You will need administrator privileges to install breseq dependencies using these instructions. We recommend that you install and use the package manager MacPorts to simplfy some installation steps.

  • GCC: download and install Apple Developer tools.
  • Perl: is already installed on MacOSX systems.
  • BioPerl: download and install according to the directions at BioPerl.org
  • SSAHA2: download and install the MacOSX package from the Sanger Center.
  • R: install with MacPorts terminal command: sudo port install R
  • Boost: install with MacPorts terminal command: sudo port install boost

2. Build breseq

Now, open a terminal window, change directory to the root of the breseq source distribution. If you have admin privileges on your computer, you can run these commands to install breseq:

./configure
make
sudo make install

If you do not have admin privileges on your computer, then see Installing in a user location.

These commands compile and install not only breseq, but also some open-source code developed by others. These packages are included in the breseq source distribution under extern:

Warning

These commands will overwrite any other versions of SAMtools or the Perl module Bio::DB::Sam that you have in the default ./configure install locations. To avoid this, you can follow the instructions in Installing in a user location to safely install breseq elsewhere.

Finally, we recommend that you test that your breseq installation functions with this command:

make test

This should take 5-10 minutes to run and report success at the end if everything is operating correctly.

Installing in a user location

If you do not have admin privileges on your computer, then you need to specify a location in your home directory to install in. We’ll assume that you’ve chosen to install breseq in /mnt/home/me/local, in which case you would use these commands:

./configure --prefix=/mnt/home/me/local
make
make install

Before you test or use this kind of installation, you will need to tell your shell that /mnt/home/me/local contains a usual UNIX grouping of program directories (with sub-directories like bin, lib, man, etc). To do this you can use these commands, if you are using a bash shell:

echo "export PATH=\$PATH:/mnt/home/me/local/bin" >> ~/.profile
echo "export LD_LIBRARY_PATH=\$PATH:/mnt/home/me/local/lib" >> ~/.profile

Now, you should be able to invoke breseq commands if you open a new terminal window.

Common installation problems

None known yet. If you have a problem, please contact jeffrey.e.barrick@gmail.com.

Table Of Contents

Previous topic

Introduction

Next topic

Usage

This Page