4 Installing Zanardi

Zanardi is for users running Linux/Unix or Mac operative systems only, and only runs over 64bit infrastructures. As stated in the previous section, the o nly pre-requirements to run this pipeline are: Python 2.7+, Java 1.7+ (to run Beagle) and R 3+ (+ ggplot2 installed for some options), which are ~ default in any up-to-date computer used for scientific research. The fastest and most clever way of getting this pipeline and all accessory files is installing Git and cloning this repository. Further informatio n on how to install Git can be found at http://git-scm.com/book/en/v2/Getting-Started-Installing-Git. An example of cloning command using command line is:

git clone --recursive https://github.com/bioinformatics-ptp/Zanardi.git

Important warning to Windows users: Our advice for Windows users is to install a virtual machine (e.g. VirtualBox) + Linux (Ubuntu) and run Zanardi in there. PLEASE DO NOT TRY USING Zanardi under Cygwin, as it will NOT work. Cygwin uses a twisted way of building linux-like (?) paths.