I think you have to install the CGAT tools as indicated on the main project page before you can use the individual programs: https://github.com/CGATOxford/cgat/
It looks like you need "pip" installer: http://www.pip-installer.org/en/latest/ for installing CGAT tools
It looks like you need "pip" installer: http://www.pip-installer.org/en/latest/ for installing CGAT tools
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