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.