I suggest you test GBrowse from its development directory rather than
doing "make install". The reason for this is that the installation
scripts haven't been updated in a while, and probably won't work!

Assuming that you have unpacked GBrowse into
/home/fred/src/Generic-Genome-Browser, here is a template Apache
configuration devoted to GBrowse testing:

   Listen 8080
   NameVirtualHost *:8080
   <VirtualHost *:8080>
        ServerAdmin webmaster@localhost

	DocumentRoot /home/fred/src/Generic-Genome-Browser/htdocs/
	<Directory />
		Options FollowSymLinks
		AllowOverride None
	</Directory>

	<Directory /home/fred/src/Generic-Genome-Browser/htdocs/>
		Options Indexes FollowSymLinks MultiViews
		AllowOverride None
		Order allow,deny
		allow from all
	</Directory>

	ScriptAlias /cgi-bin/ /home/fred/src/Generic-Genome-Browser/cgi-bin/
	<Directory "/home/fred/src/Generic-Genome-Browser/cgi-bin/">
		SetEnv PERL5LIB /home/fred/src/Generic-Genome-Browser/libnew:/home/fred/src/bioperl-live
		SetEnv GBROWSE_MASTER GBrowse.conf
                SetEnv GBROWSE_CONF   /home/fred/src/Generic-Genome-Browser/conf
                SetEnv GBROWSE_DOCS   /home/fred/src/Generic-Genome-Browser/htdocs
                SetEnv GBROWSE_ROOT   /
	        AllowOverride None
                Options +ExecCGI -MultiViews +SymLinksIfOwnerMatch
                Order allow,deny
                Allow from all
        </Directory>

        ErrorLog /var/log/apache2/error.log
	LogLevel warn
	CustomLog /var/log/apache2/access.log combined
	ServerSignature On
   </VirtualHost>

This will create a virtual host listening on port 8080.

Please make note of all occurrences of
/home/fred/src/Generic-Genome-Browser. This will need to be replaced
with the path in which you unpacked GBrowse. Also be sure to replace
/var/log/apache2/ with the location of your error logs and
/home/fred/src/bioperl-live with the location of bioperl-live, if you
have not installed it.

Lincoln Stein
August 2008
