Genecentric - A package to uncover graph-theoretic structure in high-throughput epistasis data.

Dependencies

Python 2.6 w/ argparse or Python 2.7.
An Internet connection to perform GO enrichment.

We do not currently support versions older than Python 2.6 at this time.

If you're running Python 2.6, 'argparse' can be installed from PyPI:

easy_install-2.6 argparse

For Linux

Download Genecentric for Linux.

Extract the tar archive and `cd` into the new directory:

tar zxf genecentric-1.0.3.tar.gz cd genecentric-1.0.3

You can now install it directly:

(NOTE: Depending upon how Python is set up on your system, you may need to change python2 below to python or python2.7.)

python2 setup.py install

Or, if you have easy_install installed:

easy_install ./

The easy_install approach works well if you're installing Genecentric in an environment where you don't have root access.

You should now be able to run genecentric-bpms --help and see the command line documentation.

For Mac

See the installation instructions for Linux.

For Windows

Nothing here yet.

No Installation

It is also possible to use Genecentric without installing it to your system. This may be desirable when you don't have root access to your system, or if you don't want to set up a virtual environment.

First, like the other steps, download Genecentric for your operating system and extract it to some directory. (On Linux/Mac, use tar zxf genecentric-1.0.3.tar.gz, and on Windows, use your preferred program to unzip files like WinRAR or Winzip.)

Secondly, change into the directroy that you unzipped Genecentric to (On Linux/Mac use a terminal, and on Windows use cmd.) You should now be able to run any of the Genecentric executables in the directory like so:

python2 genecentric-bpms --help

Or if that doesn't work, try:

python genecentric-bpms --help

Or:

python2.7 genecentric-bpms --help

The name of Python on your system will vary depending upon how it is set up. For Windows users, you will have to make sure that the path to the Python executable is in your PATH environment variable, or else you'll need to write out the full path. Which might look something like C:/Python27/python.exe.