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Installation
Installation via git is the best way to keep your copy of cMonkey2 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 python-xmlrunner python-biopython
Install git, and download and test the package:
sudo apt-get install git
git clone https://github.com/baliga-lab/cmonkey2.git
cd cmonkey2
./run_tests.sh
If you will be running the cmonkey viewer/monitor, you will need three extra python packages:
sudo apt-get install python-cherrypy3 python-routes python-jinja2
To simplify system setup for Debian-based systems (including Ubuntu, Mint, etc.), we have also made cMonkey2 available as a Debian package (last update: 12/12/2014).
You can install this together with all dependencies listed above, using
sudo dpkg -i cmonkey2*.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. Then, to reinstall from nothing, you will have to execute
sudo rm /usr/lib/python2.7/dist-packages/cmonkey
sudo dpkg -i cmonkey2*.deb
Note that in order to use MEME, you will need to have MEME installed and available in your $PATH. MEME is available here. cMonkey2 is compatible with MEME versions 4.3.0, 4.8.x, 4.9.x and 4.10.x.
The cMonkey2 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
Using the Debian package will make the cmonkey2 command available. It is recommended that you create a project directory for your run containing your gene expression file and run it from there. cmonkey2 creates a cache and out directory in that directory by default.
cmonkey2 --organism <your organism> --ratios <your_ratios.tsv>
dpkg -r cmonkey2
You can then uninstall all dependencies as needed.