Authentication

GenomeView supports BasicAuth for webservers

Explanation how to setup .htaccess to a folder:
http://httpd.apache.org/docs/2.2/howto/htaccess.html#auth

To create pasword files you can use htpasswd:
http://httpd.apache.org/docs/2.0/programs/htpasswd.html

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.

Encryption

GenomeView support SSL encrypted connections. It will use the certificate that is presented, but it will not verify the integrity of the key-chain.