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.

MacOS X Instructions

You will need administrator privileges to install breseq 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, and run these commands:

./configure
make
make install

Optionally, you can test your breseq installation with this command:

make test

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:

In order to not interfere with other versions of these tools that you may have installed, these files are not copied into common system-wide paths. All of the files required for breseq to function will be in the newly created breseq directory within the source path after installation. After you have successfully built breseq, you can move the entirety of this directory to any location on your system and breseq will continue to function.

3. Add breseq to your $PATH

breseq can now be run by invoking the executables located under breseq/bin. For convenience, you may want to add this directory to your environment’s $PATH variable so that you can invoke breseq commands from a shell without typing the full path.

For a bash shell, you can do this by running the command:

echo "export PATH=\$PATH:[LOCATION]/breseq/bin" >> ~/.profile

replacing [LOCATION] with the absolute path to the root of the breseq source archive, for example, to make /Users/me/my_programs/breseq/bin. You will need to open a new shell after you do this for the change to take effect.

If you already have SAMtools installed on your system, be careful about the order of paths in your $PATH environmental variable. Include the breseq path last, so that you will not override your previously installed version.

Common installation problems

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

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