Search the Genome Browser help pages:
Search the entire Genome Browser website: @@ -1377,16 +1378,84 @@ Track hubs are web-accessible directories of genomic data that can be viewed on the UCSC Genome Browser alongside native annotation tracks. Hubs are a useful tool for visualizing a large number of genome-wide data sets. The Track Hub utility allows efficient access to data sets from around the world through the familiar Genome Browser interface. Browser users can display tracks from any public track hub that has been registered with UCSC. Additionally, users can import data from unlisted hubs or can set up, display, and share their own track hubs.
For information on using the Track Hub features, refer to the Genome Browser Track Hub User Guide. For specific information on configuring your trackDb.txt file, refer to the Track Database Definition Document. See also the Basic Hub Quick Start Guide and Quick Start Guide to Organizing Track Hubs into Groupings.
+Historically, a hub needed a set of text files to specify properties for a track hub and each of +the data tracks within the hub. The track hub settings were stored in a three file structure: +hub.txt, genomes.txt, and trackDb.txt
+myHub/ - directory containing track hub files +* hub.txt - a short description of hub properties +* genomes.txt - list of genome assemblies included in the hub data +* hg19/ - directory of data for the hg19 (GRCh37) human assembly +** trackDb.txt - display properties for tracks in this directory +
+Now, there is a trackDb option to have your entire track hub inside of one file, +useOneFile on. Adding the useOneFile on line to the hub.txt section of the +file allows the contents of all three files to be referenced inside of one file. The order of the +file contents is essential and needs to be in the following order to work: hub.txt, genomes.txt, +then trackDb.txt. +
useOneFile on
+hub myExampleHub +shortLabel Example Hub +longLabel Example Hub for useOneFile option +useOneFile on +email genome-www@soe.ucsc.edu + +genome hg19 + +track vcfExample +shortLabel VCF example +longLabel VCF: 1000 Genomes phase 1 interim SNVs +visibility pack +type vcfTabix +maxWindowToDraw 200000 +bigDataUrl http://genome.ucsc.edu/goldenPath/help/examples/vcfExample.vcf.gz + +track bamExample +shortLabel BAM example +longLabel Bam: 1000 Genomes read alignments (individual NA12878) +visibility squish +type bam +pairSearchRange 10000 +bamColorMode grey +maxWindowToDraw 200000 +bigDataUrl http://genome.ucsc.edu/goldenPath/help/examples/bamExample.bam +
+The hub above can be accessed using the following URL to the single file, +singleFileHubExample.txt.
+Unfortunately, the useOneFile on setting limits the hub to one assembly. The +useOneFile on setting works by having the genomes.txt file point to only one +trackDb.txt file, which is the file itself. Although this method limits you to one genome assembly, +using the setting grants the advantage of not embedding file names in the hub architecture. So a +simple name change to a hub file will no longer require editing the contents inside the hub.txt and +genomes.txt files.
+Converting an existing track hub to use the new setting does not require much editing. Simply +concatenate the three files into one, with the contents of hub.txt, genomes.txt, and trackDb.txt, in +that order. Using the URL to the single file on the +My Hubs page will allow you to view your +track hub.