Installation

breseq is a command line tool implemented in C++ and R. It is compatible with a variety of UNIX-like platforms, including Linux, MacOSX, and Cygwin.

The most recent breseq binary distributions and source code packages are available for download from GitHub.

Install external dependencies

breseq requires these software programs to be installed on your system:

  • Bowtie2 (version 2.1.0 or higher) read mapping program
  • R (version 2.1.4 or higher) statistical programming language

To install each dependency, visit the respective web pages linked above and follow the instructions for your platform. You must make sure that the executables for Bowtie2 and R are in your environment’s $PATH for breseq to function.

Method 1. Binary distribution

Linux and MacOSX packages with precompiled executables are available for download. Using these is the quickest and easiest install option that should be used by most users.

You should be able to immediately run breseq from within the unarchived directory structure.

For example, run this command to get breseq help:

$ bin/breseq

You may also run this command to test the breseq install:

$ ./run_tests.sh

Note

If you relocate the executable files in the bin directory, then you must also relocate the files in the share directory to the same location relative to the binaries (e.g., bin/../share/breseq).

Method 2. Source code package

breseq installation from the source code requires some basic familiarity with UNIX commands and environments.

In addition to the normal dependencies, you must also have a C++ compiler installed on your system. For example: GCC.

MacOSX does not have a C++ compiler installed by default. You must first download and install the Apple Developer tools (available from the App store). Be sure that you also complete any additional steps that are necessary to install the “command-line tools”.

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.

The breseq source distribution relies on open-source code developed by others. This code is included in the breseq distribution under /extern:

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.

Installing in the source directory

This is the most robust way to compile and 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.

Method 3. Development source code

If you are working with a development version of breseq cloned from the GitHub code repository, then you will need to run some additional commands and have other tools installed on your system in order to get it to compile or work with the XCode project.

These requirements and commands are detailed in the DEVELOPER text file located in the main directory of the source code.

Installing on Cygwin (Windows)

It is possible to compile and install breseq and all of its dependencies in the Cygwin environment on a Windows computer. We do not currently provide a binary installer for Cygwin and are unable to help troubleshoot these installs, but here is what has worked for other users.

Before you start, use the Cygwin package manager to install these packages (which provide libraries needed to compile breseq and Bowtie2). When prompted whether to install further dependencies of a package, answer yes.

R                    libncurses-devel
gcc-core             zlib-devel
gcc-g++              byacc
gcc-objc++           bool
python               pkg-config
m4                   perl-File-Copy-Recursive
make                 perl-Config-AutoConf
automake             perl-ExtUtils-PkgConfig
autoconf             mingw-pthreads
diffutils            mingw64-x86_64-pthreads
libiconv             mingw64-x86_64-winpthreads

Now, compile and install Bowtie2 from source code and use the Method 2. Source code package instructions to install breseq.

If the configure or make steps in either install fail, try to diagnose which dependencies are missing from the warnings and install further packages as necessary.

Troubleshooting installation

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