epitopefinder is written in Python. It requires no external Python packages outside of the standard Python library, although it can optionally do some plotting that requires installation of matplotlib. A few of the plotting functionalities also require the installation of scipy.
epitopefinder has been tested on Mac OS X 10.6.8 with Python 2.6.7, matplotlib 1.0.0, and scipy 0.11. However, it should work with other similar versions as well and on other platforms as well.
Alignments are performed using MUSCLE, which must be downloaded and installed separately. Scripts that utilize MUSCLE will require you to specify the location of the MUSCLE executable in the script input file.
To install epitopefinder, first download the source ZIP repository on GitHub. After unzipping the file, run the following commands:
cd epitopefinder
python setup.py build
python setup.py install
The last command might require you to use:
sudo python setup.py install
if you do not have privileges to the default installation directory, you might want to install to your local installation directory using:
python setup.py install --user
These commands install the Python modules and and scripts. The scripts provide the most convenient high-level interface into the epitopefinder package. These scripts should be installed to be executable; they are present in the scripts subdirectory of the main package directory contained in the ZIP repository. The source code for the package is in the src subdirectory. There is also an examples subdirectory that contains examples. This documentation is found in the docs directory.