  The UCSC Genome Browser is a popular tool for the exploration and analysis of
reference genomes. Mirrors of the UCSC Genome Browser and its contents exist at
multiple geographic locations, and this mirror procedure has been modified to
support genome sequences not maintained by UCSC and generated by individual
researchers. While straightforward, this procedure is lengthy and tedious and
would benefit from automation, especially when processing many genome
sequences. We present a Unix shell program that facilitates the creation of
custom instances of the UCSC Genome Browser for genome sequences not being
maintained by UCSC. It automates many steps of the browser creation process,
provides password protection for each browser instance, and automates the
creation of basic annotation tracks. As an example we generate a custom UCSC
Genome Browser for a bacterial genome obtained from a massively parallel
sequencing platform.
