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"