Skip to content

Installation

Jump to bottom
Damien Farrell edited this page Jun 2, 2017 · 6 revisions

Install on pip using:

pip install epitopepredict

Dependencies pandas and biopython should be installed automatically.

netMHCIIpan

To use netMHCIIpan you must download the program separately as it requires an academic license (free). (Download here: http://www.cbs.dtu.dk/cgi-bin/nph-sw_request?netMHCIIpan). You then need in install and add the path of the executable to your PATH. If you get the following error: bash: /local/bin/netMHCIIpan: /bin/tcsh: bad interpreter:, it means you are missing tcsh and should install it with your package manager.

In Ubuntu: sudo apt-get install tcsh

IEDB tools

You can download this software for MHC-I or MHC-II prediction here: http://tools.iedb.org/mhcii/

Place the required software in a folder on your hard drive. This should then be set before calling the prediction methods:

eg:

from mhcpredict import base
base.iedbmhc1path = '/local/iedbmhc1'
base.iedbmhc2path = '/local/iedbmhc2'
base.iedbbcellpath = '/local/iedbbcell/'

You might also need to install gawk: sudo apt-get install gawk

Clone this wiki locally