Setting up authentication and encryption
GenomeView supports BasicAuth for webservers
To create pasword files you can use htpasswd: http://httpd.apache.org/docs/2.0/programs/htpasswd.html
htpasswd -c /location/of/.htpasswd username
Explanation how to setup .htaccess to a folder: http://httpd.apache.org/docs/2.2/howto/htaccess.html#auth
AuthUserFile /location/of/.htpasswd AuthType Basic AuthName “My Files" Require valid-user
Important is that you put the password file outside the document root that is accessible through the web.
That should get you up and running.
GenomeView support SSL encrypted connections. It will use the certificate that is presented, but it will not verify the integrity of the key-chain.