OS X installation

This section describes the installation process on OS X. The installation below has been tested on a MacBook Pro running OS X 10.8.5.

Begin by installing homebrew by following these instructions

Next, install various packages:

brew install mysql
brew install gfortran
brew install freetype
brew install Mercurial
brew install python --with-brewed-openssl

Install the R package from here and bedtools:

wget http://bedtools.googlecode.com/files/BEDTools.v2.17.0.tar.gz
tar -xvzf http://bedtools.googlecode.com/files/BEDTools.v2.17.0.tar.gz
cd bedtools-2.17.0/
make
cp bin/* /usr/local/bin/

Next install and set up a virtual environment:

pip install virtualenv

CGAT depends on numerous other python packages not all of which might install cleanly. Here, we give some more detailed instructions. Generally we recommend when troubleshooting CGAT installation to do so within a virtual environment. To create a clean environment, type:

virtualenv --no-site-packages cgat-python
source cgat-python/bin/activate

Now, download the list of required packages:

wget https://raw.github.com/CGATOxford/cgat/master/requires.txt

To install the required basic packages:

pip install -r requires.txt

Also, bx-python needs to be installed. The current version on pypi is currently out of date, so to install, do:

pip install https://bitbucket.org/james_taylor/bx-python/get/tip.tar.bz2

If all of that works, installing the CGAT tools should now be straight-forward:

pip install cgat