Installing and running GOtcha
=============================

Environment:

It is much easier if the environment variable GOTCHA_LIB is set to the root 
directory for the GOtcha installation. This will make command lines a lot 
shorter as many options no longer need to be set explicitly. A line such as

export GOTCHA_LIB=/path/to/GOtcha
export PERL5LIB=$PERL5LIB:$GOTCHA_LIB/lib

should be included in the .bashrc (for local install) or /etc/profile (for global install).

or for csh users

setenv GOTCHA_LIB /path/to/GOtcha
setenv PERL5LIB $PERL5LIB:$GOTCHA_LIB/lib

in the .cshrc file (local) or /etc/cshrc (global) 

Install directory:

The install directory /path/to/GOtcha is structured as:

	/lib  	Perl modules
		
	/data	GOtcha format tables for GO and score calculation
	
	/db 	Blast databases
	
	/bin	Perl scripts.

	/doc 	Manual and other documentation including an example gotcha.conf file.


Installation:

1. Create a directory in which to install GOtcha.

2. Move to this directory and unpack the distribution there. This should create
the directory structure above.

3. Check the list of Perl dependencies and ensure all the necessary modules are
installed.

4. Determine where the local Perl interpreter is. You may need to edit the 
first line in each of the scripts in the /bin directory to reflect the location
of Perl.

5. Determine where any site-specific installations of Perl modules are and 
amend the 'use lib' lines appropriately or append these to the $PERL5LIB 
environment variable.

6. Add the $GOTCHA_LIB/bin directory to your path.
	export PATH=$PATH:$GOTCHA_LIB/bin

7. Add the GOtcha perl modules to the PERL5LIB variable.
	export PERL5LIB=$PERL5LIB:$GOTCHA_LIB/lib

8. Ensure the GOtcha scripts are executable
	chmod +x $GOTCHA_LIB/bin/*.pl

9. Try executing GOtcha as 
	rungotcha.pl --help

You should get a help screen indicating the many command line options for running GOtcha.


Dependencies:

GOtcha requires the following Perl Modules. Many are part of the standard Perl distribution.

	BioPerl 	(Tested with 0.7 but newer versions should work) www.bioperl.org
	Archive::Tar 	(This may be problematic. Tar archive support is unreliable)
	GD		(required for the graphics drawing. A newer version that supports PNG is required.)

GOtcha also requires the following software to be available in the PATH
	blastall 	from the NCBI BLAST2 suite (www.ncbi.nih.gov)
	seqret		from the EMBOSS suite (www.emboss.org)
	infoseq		from the EMBOSS suite (www.emboss.org)
 
License:
	GOtcha is currently made availble under an academic collaboration license. 
You may use and modify GOtcha but may not distribute it without permission from the author.

If you wish to publish work that has made use of GOtcha then please contact the author, 
Dr David Martin <david@compbio.dundee.ac.uk> for appropriate citation details.


Running GOtcha:

GOtcha needs to know the following:

	Which databases you wish to use for annotation?
	Which evidence codes you wish to include/exclude (deafult: all included)?
	
If GOTCHA_LIB is set then GOtcha can find the databases and data files in the 
GOtcha installation. All these locations can be overwritten on the command line.

GOtcha will automatically attempt to read the sequence format and type. Sequence type can be overridden (Nucleic acid, Protein or Auto (default)) on the comamnd line.

See the full manual in docs/Manual.pdf for further information.