BOL

It seems odd to me as you ask question without any explanation. I presume, you are working on Linux. You can use following commands to install it smoothly 

wget https://raw.github.com/CGATOxford/cgat/master/install-CGAT-tools.sh
chmod +x install-CGAT-tools.sh
./install-CGAT-tools.sh --install-os-packages

./install-CGAT-tools.sh --cgat-scripts --lite --location .

#
# To activate this environment, use:
# > source activate cgat-s
#
# To deactivate this environment, use:
# > source deactivate cgat-s
#

source ./conda-install/bin/activate cgat-s
cgat --help
cgat --help all

I had some problem with it as well. It work only on Ubuntu v12.