Based on a quick metacpan search, it appears that Java::JCR::Jackrabbit defaults to constructing a Derby-based repository if not instructed to do otherwise. So I guess that could provide some example code for you.

This and a URI::derby in the URI-db distribution (which just sets default_port to 1527) are the only evidence of Apache Derby that I can find in the CPAN repository.

And here I was hoping for a discussion about putting wheels on web servers and racing them.