Installation

1. Installation (git)

Installation via git is the best way to keep your copy of cmonkey-python up-to-date. However, there are additional dependencies that you will need to install separately. On Ubuntu, these can all be installed using

sudo apt-get install python-numpy python-scipy python-rpy2 python-beautifulsoup python-mysqldb

Install git, and download and test the package:

sudo apt-get install git
git clone https://github.com/weiju/cmonkey-python.git
cd cmonkey-python
./run_tests.sh

If you will be running the cmonkey viewer/monitor, you will need two extra packages:

sudo apt-get install python-cherrypy3 python-routes

1. Installation (Debian package)

To simplify system setup for Debian and Ubuntu users, cmonkey-python is also made available as a [Debian package](http://networks.systemsbiology.net/gaggle/cmonkey-python_1.0.1-1_all.deb).

You can install this together with its dependencies using

sudo dpkg -i cmonkey-python*.deb

Depending on your configuration, this might result in dpkg reporting dependency issues. In this case, execute

sudo apt-get -f install

to instruct your Debian/Ubuntu system to install the required dependencies.

1. MEME for motif finding

Note that in order to use MEME, you will need to have MEME installed and available in your $PATH. MEME is available [here](http://ebi.edu.au/ftp/software/MEME/index.html).

The cmonkey-python distribution contains a MEME installation script which will download, configure, compile, and locally install the relevant MEME suite tools in the current working directory. MEME requires csh. Simply execute

sudo apt-get install csh   ## or tcsh
tools/install_meme.sh

1. Usage

Using the Debian package will make the cmonkey-python command available. It is recommended that you create a project directory for your run containing your gene expression file and run it from there. cmonkey-python creates a cache and out directory in that directory by default.

cmonkey-python --organism <your organism> --ratios <your_ratios.tsv>

1. Uninstall cmonkey-python from your system

dpkg -r cmonkey-python