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. breseq installation from the source code requires some basic familiarity with UNIX commands and environments.
Several external packages and software programs need to be installed to compile and use breseq:
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 $PATH for breseq to function.
You will need administrator privileges to install breseq dependencies using these instructions. We recommend that you install and use the package manager MacPorts to simplfy some installation steps.
If you have admin privileges and want to install breseq in a standard location accessible to all users of a computer, then see Installing in a system-wide location. If you do not have admin privileges on your computer, then see Installing in the source directory or Installing in a custom location.
Note
If you encounter problems with one of the other install methods, we recommend that you try Installing in the source directory.
This method requires that you have admin privileges on your machine. After installation, all users of the machine will be able to run breseq.
Open a terminal window and change directory to the root of the breseq source distribution. Then, run these commands:
./configure
make
sudo make install
These commands compile and install not only breseq, but also some open-source code developed by others. These packages are included in the breseq source distribution under /extern:
Warning
Installing breseq will overwrite any other versions of SAMtools or the Perl module Bio::DB::Sam that you have in the default ./configure install locations. To avoid this, you can follow the instructions in Installing in the source directory or Installing in a custom location to safely install breseq elsewhere.
Finally, we recommend that you test that your breseq installation functions with this command:
make test
This should take 5-10 minutes to run and report success at the end if everything is operating correctly.
This is the most robust way to install breseq if you do not have admin privileges on a system. All of the compiled programs and libraries will be self-contained in the original source tree.
Open a terminal window and change directory to the root of the breseq source distribution. Then, run these commands:
./configure --prefix=${PWD}
make
make install
make test
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.
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 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.
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 a package manager or 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:
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.
Some version of Perl do not have recent versions of required Perl Modules.
If you get an error like this:
Can't locate Module/Build.pm in @INC
Or this:
File::Path version 2.0605 required--this is only version 2.04_02
Then you will need to install or update a missing Perl Module (Module::Build and File::Path in these two cases). On most systems you can use the CPAN shell.
If you have a problem installing breseq, please send a detailed report to jeffrey.e.barrick@gmail.com.