GCAT README
===========

Genome Comparison and Analysis Toolkit
Version 0.81

An adaptable and efficient toolkit for large-scale evolutionary comparative
genomics analysis. Written in the Perl programming language, GCAT utilizes 
the BioPerl, Perl EnsEMBL and R Statistics APIs.

Part of a PhD thesis entitled "Evolutionary Genomics of Organismal Diversity".

Coded by Steve Moss
gawbul@gmail.com
http://gawbul.github.io/

C/o Dr David Lunt and Dr Domino Joyce
Evolutionary Biology Group
The University of Hull

http://www.hull.ac.uk/evolution/
http://davelunt.net/

DEPENDENCIES
------------

Perl 5.12.4+
Bio - BioPerl 1.6.1+
Bio::EnsEMBL - EnsEMBL Perl APIs release 64+
Bio::Phylo 0.45+
R 2.13.1+
MySQL
libmysqlclient-dev 16+
DBI
DBD::mysql
Log::Log4perl
Parallel::ForkManager
Statistics::Descriptive
Statistics::R
Time::HiRes
Set::IntSpan::Fast
Set::IntSpan::Fast::XS
Text::CSV
Text::CSV_XS
Text::FormatTable
Tie::IxHash

DOWNLOAD
--------

You can download from https://bitbucket.org/gawbul/gcat by clicking get source and downloading 
in the preferred format. We recommend zip for the purposes of the installation instructions in 
this document. You can also download from https://github.com/gawbul/gcat and click on the ZIP 
icon to download the source.

Additionally you can checkout the code from bitbucket using Mercurial by running

	hg clone ssh://hg@bitbucket.org/gawbul/gcat

Or from github by running

	git clone git://github.com/gawbul/gcat.git

INSTALLATION
------------

We recommend installing the toolkit on Ubuntu Linux version 10.04+ or OS X 10.5+, as these are
the machines it has been tested and developed on. Support for Windows is unlikely in the future.
Should you require running this software on a Windows machine, then we recommend downloading
VirtualBox from http://www.virtualbox.org and installing BioLinux or Ubuntu as a virtual machine.
We may make a virtual machine available with the software preconfigured in the future. 

To install from source you should simply extract the archive to an appropriate directory for 
example your home directory i.e. /home/stevemoss or /Users/stevemoss. The * in the following 
text represents the revision id e.g. daacf7a00ab8

	mv ~/Downloads/gawbul-gcat-*.zip ~/
	unzip gawbul-gcat-*.zip
	nano ~/.bashrc
	
	Add the following lines to your .bashrc (or .profile) file
	
	PERL5LIB=$PERL5LIB:/home/stevemoss/gawbul-gcat-*/modules
	export PERL5LIB
	
	You should also do the same for the location of the EnsEMBL Perl APIs e.g.

	PERL5LIB=$PERL5LIB:/home/stevemoss/ensembl/ensembl/modules
	PERL5LIB=$PERL5LIB:/home/stevemoss/ensembl/ensembl-compara/modules
	PERL5LIB=$PERL5LIB:/home/stevemoss/ensembl/ensembl-functgenomics/modules
	PERL5LIB=$PERL5LIB:/home/stevemoss/ensembl/ensembl-variation/modules
	export PERL5LIB

TESTING
-------

gawbul-gcat-*/t contains tests of the pipeline functionality. You can run the shell 
script do_tests.sh using

	sh gcat_tests.sh
	
to run all the tests currently implemented.


SUPPORT AND DOCUMENTATION
-------------------------

After installing, you can find documentation for this module at the GCAT Wiki.

	https://bitbucket.org/gawbul/gcat/wiki/

You can report issues with the code at:

	https://bitbucket.org/gawbul/gcat/issues
	
The Wiki has been disabled at the github page, as bitbucket is the primary development 
repository. The github clone is provided for convenience, but provides the exact same 
functionality.

LICENSE AND COPYRIGHT
---------------------

Copyright (C) 2010-2014 "Steve Moss"

This program is free software; you can redistribute it and/or modify it
under the terms of either: the GNU General Public License as published
by the Free Software Foundation; or the Artistic License.

See http://dev.perl.org/licenses/ for more information.