Gtracks: A Framework for Creating and Maintaining UCSC Track Databases Using Google Spreadsheets

The UCSC Genome Browser is a web-based platform that offers a rapid, intuitive, and centralized means of viewing various types of genomic data mapped to a reference genome. The browser also allows users to maintain large catalogs of private data tracks in "track hubs". Despite its great utility, the browser hosted at UCSC is primarily for vertebrate genomes. However, the "assembly hubs" feature allows the use of custom genomes. Users with large numbers of custom genomes may also benefit from the installation of a self-hosted instance of the browser. However, track and assembly hubs require configuration files that are difficult to setup and maintain for many custom datasets. Installing a self-hosted instance of the browser is even more challenging, requiring extensive knowledge of the unix command line and system administration. To address these challenges, we have developed two tools, gtracks (http://github.com/FSUgenomics/gtracks) and cruize (https://github.com/FSUgenomics/cruize), to easily and quickly setup and maintain track hubs, assembly hubs, and genome browser installations. The gtracks approach simplifies the creation and maintenance of complex configuration files and databases through easily-maintainable google spreadsheets. Cruize, composed of scripts and dockerfiles, streamlines the deployment of genome browser installations and the loading of custom genomes and datasets. We use the maize genome and several available maize genomic datasets to show how these tools facilitate the creation of a UCSC browser installation and track hubs.