What's in this package

• R - R code. Sub-folder GCAT contains the GCAT package
• Rails - Rails code
• Testing - testing code, data and documents, outside of any regression tests that may be incorporated directly into R packages or Rails applications

Getting started

Stand-alone R package

If all you want is the R package, you can install it from file R/GCAT_N.N.N.tar.gz using R CMD INSTALL. You can also install it in RStudio, using menu Tools ==> Install Packages ==> Package Archive File.

Virtual machine (VM)

A Ubuntu VirtualBox VM built by Fernando Marotta is available at https://drive.google.com/open?id=1ZSlJozj8cgZ66BR_6_V3G3OVeBdEomNN. Download and unzip the archive. Once VirtualBox is installed (see below), you should be able to launch the VM by double-clicking file Ubuntu.vbox. Password for the user Dolo is dolito.

Install VirtualBox software

This is necessary to run the VM. See https://www.virtualbox.org/wiki/Downloads.

Change system language

This VM's language is Spanish. If you wish to change to another language, see instructions here: https://websiteforstudents.com/how-to-change-to-your-native-language-on-ubuntu-17-10/ Search in system settings for idioma --> select Region e idioma menu. Click on Idioma --> select the language you want --> Click the green Hecho button --> Click Reiniciar… --> Click Cerrar la session --> Log in again --> A dialog pops up: Update standard folders to current language? Choose Update Names

Install guest additions

In the Virtual box menu, go to Devices --> Insert Guest Additions CD Image… --> Run (See https://help.ubuntu.com/community/VirtualBox/GuestAdditions)

Enable exchanging files with the host system by drag-and-drop

In the Virtual box menu, go to Devices --> Drag and Drop --> select Bidirectional You should now be able to drag and drop files from the host to the VM and back. If it doesn’t work, reboot the VM.

Access GCAT

Launch Firefox. Type localhost into the address bar and click Enter

Install your own GCAT server

To get GCAT web server, you will need to install Ruby and Ruby on Rails. I suggest using RVM. Documentation for RVM can be found at: http://rvm.io.

You will need:

• Ruby version 1.9.3p194 and Rails 3.2.15
• R version 3.2.2 or later
• Linux packages: Ruby-dev, libsqlite3-dev, enca

Installation

The R package is in subfolder R. To install, do the following: Open a terminal in the R folder

$  sudo R CMD REMOVE GCAT # do this if an older version of GCAT has been installed
$  sudo R CMD INSTALL GCAT

The rails application is in subfolder Rails. It runs under Rails 3.2.15. To run it locally using the default Rails WEBrick web server do the following: Open a terminal in the Rails folder

bash
$ bundle install
$ rails s

Open http://0.0.0.0:3000 in a web browser