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