GeneDesign development branch
GeneDesign is a group of cgi scripts fronting a nucleotide manipulation library.  It is entirely implemented in perl.

To install locally as a webserver, you have two options.

a) Easy but breaks version control:
	put the gd folder from cgi-bin into your CGI-Executables folder, 
	and the gd folder from documents into your Documents folder.
	Then change the values $linkpath and $docpath at the top of 
	GeneDesign.pm to the appropriate values for your webserver.

b) More difficult but maintains version control:
	You must edit the configuration file for your web server. The
	following instructions assume you are using apache2.
	let /path/to/your/ represent the absolute path to the 
	parent directory of your git repository.
	the configuration file is at 
	 Ubuntu: /etc/apache2/sites-available/default 
	 Mac OS X: /etc/apache2/httpd.conf
	 Windows: Program Files\Apache Group\Apache2\conf\httpd.conf
 
	add the following after the main Directory listing
		<Directory "/path/to/your/GeneDesign.git/documents/gd">
			Options Indexes MultiViews FollowSymLinks
			AllowOverride All
			Order allow,deny
			Allow from all
		</Directory>

	add the following after the main cgi-bin Directory listing
               <Directory "/path/to/your/GeneDesign.git/cgi-bin/gd"> 
			AllowOverride None
			Options ExecCGI
			Order allow,deny
			Allow from all
		</Directory>

	add the following BEFORE the cgi ScriptAlias Listing
                ScriptAlias /cgi-bin/gd/ "/path/to/your/GeneDesign.git/cgi-bin/gd/"

	add the following in the Alias section
		Alias /gd /path/to/your/documents/gd

	restart the server


installation prereqs (all available from CPAN): 
CGI
GD::Graph 
Text::Wrap
Perl6::Slurp
List::Util 
List::MoreUtils

gdOliReDes and gdFusionDes are not currently under development.


To Do:
-put all variables into hash that makes carrying through "design a gene" much much simpler"