Installation

breseq is a command line tool implemented in C++ and R. It will compile and function on a variety of UNIX platforms, including MacOSX. breseq installation from the source code requires some basic familiarity with UNIX commands and environments.

1. Download source code

The most recent breseq source code packages are available for download from Google Code.

2. 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 many systems
• Bowtie2 (version 2.0.0-beta7 or higher) read mapping program
• R (version 2.1.0 or higher) statistical programming language

To install each 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 Bowtie2 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 simplify these installation steps. Using MacPorts will generally take longer than downloading and installing the packages in other ways, but it greatly simplifies the searching you might otherwise have to do to track down all the prerequisites.

• GCC: Download and install Apple Developer tools (available from the App store).
• Bowtie2: Download and install the executable for your systems’s architecture from the Bowtie2 SourceForge site.

You can find out your system’s architecture using this command:

arch

It will return something like i386 or x86_64.

You will need to move the executables to where your system can use them. If you change into the downloaded Bowtie2 directory, you can use this command, for example:

sudo cp bowtie2* /usr/local/bin

If you type this command in the terminal:

which bowtie2

You should now get a message like this, telling you that the system can find your Bowtie2 executable:

/usr/local/bin/bowtie2

• R: Download the installer package from http://www.r-project.org/.

3. Compile and install breseq

If you have admin privileges and want to install breseq in a standard location accessible to all users of a computer, then see Installing in a system-wide location. If you do not have admin privileges on your computer, then see Installing in the source directory or Installing in a custom location.

Note

If you encounter problems with one of the other install methods, we recommend that you try Installing in the source directory.

Installing in a system-wide location

This method requires that you have admin privileges on your machine. After installation, all users of the machine will be able to run breseq.

Open a terminal window and change directory to the root of the breseq source distribution. Then, run these commands:

./configure
make
make test
sudo make install

make test is optional, but recommended. It should take less than 5 minutes to run and report success at the end if everything is operating correctly.

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:

• SAMtools

Warning

Installing breseq will overwrite any other versions of SAMtools that you have in the default ./configure install locations. To avoid this, you can follow the instructions in Installing in the source directory or Installing in a custom location to safely install breseq elsewhere.

Installing in the source directory

This is the most robust way to install breseq if you do not have admin privileges on a system. All of the compiled programs and libraries will be self-contained in the original source tree.

Open a terminal window and change directory to the root of the breseq source distribution. Then, run these commands:

./configure --prefix=${PWD}
make
make test
make install

After installation, if you want to be able to call breseq commands without specifying the entire path to them, you will need to add the newly created “bin” directory within the breseq source to your $PATH.

For a bash shell you can usually use a command like this:

echo "export PATH=\$PATH:${PWD}/bin" >> ~/.bashrc

But the exact way to do this may depend on your system. Once you open a new terminal window so that it registers this change to your $PATH, you should be able to invoke breseq commands.

Installing in a custom location

We’ll assume that you’ve chosen to install breseq in /mnt/home/me/local. Open a terminal window and change directory to the root of the breseq source distribution. Then, run these commands:

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

This will create a usual UNIX grouping of program directories (with sub-directories like bin, lib, man, etc).

After installation, if you want to be able to call breseq commands without specifying the entire path to them, you will need to add the newly created “bin” directory within the breseq source to your $PATH.

For a bash shell you can usually use a command like this:

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

But the exact way to do this may depend on your system. You may also want to similarly update your $MANPATH, $CPPFLAGS, $LD_FLAGS, etc. Now you should be able to invoke breseq commands once you open a new terminal window.

Common installation problems

Dependencies installed in custom locations

In general, you will need to be sure that your environment is set up correctly to find and use each dependency. This will likely be taken care of for you if you use an installer package. If you install some dependencies from source or in custom locations, and run into problems with breseq installation, be sure to check that:

1. R is in your $PATH.
2. Bowtie2 is in your $PATH.

Note

You may need to use absolute paths (i.e. /absolute/path) rather than paths relative to your home directory (i.e ~/path/relative/to/home) for these settings.

Other problems

If you have a problem installing breseq, please send a detailed report to jeffrey.e.barrick@gmail.com.

Developers

If you are working with a development version of breseq downloaded directly from the Google Code Mercurial repository, then you will need to run some additional commands and have additional tools installed in order to get it to compile or work with the XCode project.

These are detailed in the DEVELOPER text file found in the main directory of the source code.