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I'm looking to run either GeoNode or GeoServer on Ubuntu server 14.04 using Hiawatha, but both are only supported for use with Apache. Has anyone tried using either of them with Hiawatha? Is it possible? Would I have to jump through hoops in order to get it to work? Even the official installation automatically looks for apache2. Thanks.

I've never heard of GeoNode or GeoServer. But if it's a normal CGI application, I'm sure it will work with Hiawatha.

It's GIS software. They evidently use Java, officially supported with Tomcat. Does Hiawatha have any servlet capabilities, or am I best off putting it on another server with Apache while keeping the rest of my site on Hiawatha?

Hiawatha does not support Java. If you want to run Java webapps, you're stuck with Tomcat.