The files are placed on the server in a file hierarchy like the one shown in Example 1. Users experienced in setting up Genome Browser mirrors that contain their own data will find that setting up a track hub is similar, but is usually much easier. Depending on the number and complexity of the data sets, a track hub can typically be set up in a day or two. It is generally easiest to run the command-line data formatting programs in a Linux programming environment, although it's possible to manipulate smaller data sets using Mac OS-X as well.
+Note: there is now a useOneFile on hub setting that allows the hub
+properties to be specified in a single file. More information about this setting can be found on the
+Genome Browser User Guide.
Example 1: Directory hierarchy for a hub containing DNase and RNAseq data for the hg18 and hg19 human genome assemblies. The hg18/ and hg19/ subdirectories contain the assembly-specific data files.
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
dnase.html - description text for a DNase track
dnaseLiver.bigWig - wiggle plot of DNase in liver
dnaseLiver.bigBed - regions of active DNase
liverGenes.bigGenePred - gene annotations of genes over-expressed in liver tissue
dnaseLung.bigWig - wiggle plot of DNase in lung
dnaseLung.bigWig - regions of active DNase
@@ -338,30 +342,34 @@
VCF - VCF (Variant Call Format) files can contain annotations of single nucleotide
variants, insertions/deletions, copy number variants, structural variants and other types of genomic
variation. When a VCF file is compressed and indexed using
tabix (available
here), it can be
used as a data track file. Unlike bigWig and bigBed formats, the tabix index is in a separate file,
which the track hub expects to be in the same directory with the same root name as the VCF file with
the addition of a .tbi suffix. See the VCF Track Format help page
for more information.
Step 2. Create the track hub directory
Create a track hub directory in an Internet-accessible location on your web or ftp server. This
directory will contain the hub.txt and genomes.txt files that define properties of the track hub and
a subdirectory for each of the genome assemblies covered by the hub track data.
+
+Note: there is now a useOneFile on hub setting that allows the hub
+properties to be specified in a single file. More information about this setting can be found on the
+Genome Browser User Guide.
Step 3. Place the track data files in an Internet-accessible location
The data files underlying a track in a hub do not have to reside in the track hub directory or even
on the same server, but they must be accessible via the Internet. The track hub utility supports
Internet protocols such as http://, https://, and ftp://, as well as file paths relative to the hub
directory hierarchy. The location of a track file is defined by its bigDataUrl tag in the
associated trackDb.txt file (Step 7).
Step 4. Create the hub.txt file
Within the hub directory, create a hub.txt file containing a single stanza with up to six fields
that define properties of the track hub:
hub hub_name
shortLabel hub_short_label