Supplementary Figure 2: Anatomy of a dynamic Galaxy External Display Application utilizing filters and templates.

(I) A dynamic GEDA is initially defined in the usual manner (see figure S1) for standard text-based VCF files. (II) A set of “dynamic_links” are defined according to the entries contained within an internal Galaxy system “site_type”. Additional (III) dynamic parameters are defined in a named fashion from the content of the site_type entry. The third parameter, “builds” is generated as a list from a comma-separated value within the site_type entry. (IV) Two filters are applied to determine if a GEDA link will be generated for the dataset. First to confirm that this UCSC Genome Browser site (e.g. main, mirror, or domain specific) has been enabled by the Galaxy Administrator. And, secondly, to confirm that this dataset belongs to a genome build that is valid for this particular UCSC Genome Browser site. Should any of the filters fail, then the GEDA will not be available and the link will not be generated for the user. The resource URL (V) is generated dynamically with the Galaxy content being defined using a UCSC Track definition file syntax (“track” template parameter) using the bigDataUrl mechanism. This GEDA is designed to work for standard VCF files, and (VI) we use Galaxy’s automatic datatype conversion system twice. First to bgzip the text-based VCF file and then to build a Tabix index on the bgzip VCF file. We (VII) define a template-type parameter named “track” that will be dynamically generated and presented as an externally viewable file to the external resource. This Track file provides the track type, a track name, dbkey (genome build), and a bigDataUrl value that references the bgzip VCF dataset content. This approach enables the UCSC Genome Browser to make efficient, semi-random access to the user’s dataset by only transferring the subset of data required for a particular user view. Reference: Kent WJ, Sugnet CW, Furey TS, Roskin KM, Pringle TH, Zahler AM, et al. The human genome browser at UCSC. Genome Res 2002;12:996–1006. https://doi.org/10.1101/gr.229102.