Quick Start Guide to Organizing Track Hubs into Groupings
Track hubs allow for displaying many tracks, therefore organizing your tracks using
grouping settings
will help your users find related information. Below is a basic example hub illustrating
the use of container multiWig,
compositeTrack on,
and superTrack on lines.
STEP 1: In a publicly-accessible directory, copy the hub.txt, genomes.txt,
trackDb.txt, and examplePage.html files using the following command:
wget -r --no-parent --reject "index.html*" -nH --cut-dirs=3 http://genome.ucsc.edu/goldenPath/help/examples/hubExamples/hubGroupings/
Alternatively, if you do not have wget installed, use curl:
curl -O http://genome.ucsc.edu/goldenPath/help/examples/hubExamples/hubGroupings/hub.txt
curl -O http://genome.ucsc.edu/goldenPath/help/examples/hubExamples/hubGroupings/genomes.txt
mkdir hg19
cd hg19
curl -O http://genome.ucsc.edu/goldenPath/help/examples/hubExamples/hubGroupings/hg19/trackDb.txt
curl -O
http://genome.ucsc.edu/goldenPath/help/examples/hubExamples/hubGroupings/hg19/examplePage.html
If you do not have curl, you can use a text editor and directly recreate the above three files.
STEP 2: Paste your hub.txt link (http://yourURL/hub.txt
) into the
My Hubs tab of the Track Data Hubs page,
then click the "Genome Browser" link from the top bar. Alternatively build a URL that will
directly load your hub in hgTracks:
http://genome.ucsc.edu/cgi-bin/hgTracks?db=hg19&hubUrl=http://yourURL/hub.txt
The URL should work the same as using the original data just copied:
http://genome.ucsc.edu/cgi-bin/hgTracks?db=hg19&hubUrl=http://genome.ucsc.edu/goldenPath/help/examples/hubExamples/hubGroupings/hub.txt
STEP 3: Congratulations! Your hub should display!
If you are having problems, be sure all your files and the hg19 directory are publicly accessible.
For hubs to work, your server must also accept byte-ranges. You can check using the following
command to verify "Accept-Ranges: bytes" displays:
curl -I http://yourURL/hub.txt
The three types of track groupings
Now that you have the hub copied from above, start to edit some of the trackDb.txt settings to
understand how they work. Read more about trackDb settings in the definition document. Note that the Browser waits 5
minutes before checking for any changes to these files. When editing hub.txt, genomes.txt,
trackDb.txt, and related hub files shorten this delay by adding udcTimeout=1
to your
URL. For more information, please see the Debugging and Updating Track Hubs section of the Track Hub User Guide. For more detailed instructions on setting up a hub, please
see the Setting Up Your Own Track Hub
section of the Track Hub User Guide.
Resources
Understanding multiWig tracks
track multiWigUniqueTrackName
type bigWig
container multiWig
aggregate transparentOverlay
showSubtrackColorOnUi on
maxHeightPixels 500:100:8
...
track uniqueNameWithoutSpaces
type bigWig
parent multiWigUniqueTrackName
color 255,0,0
A multiWig starts with a few related bigWig files that you want to display together. The
container multiWig
line allows for this track to be later
referenced as parent multiWigUniqueTrackName
in each of the related
bigWig files. The aggregate transparentOverlay
line defines the way
the multiWigs should appear with options being transparentOverlay/stacked/solidOverlay
.
The showSubtrackColorOnUi on
line shows the track colors on the track
setting page and the maxHeightPixels 500:100:8
sets the maximum (500), default (100), and minimum (8) pixel heights for the track.
Read all about multiWigs here. See an
example trackDb.txt.
Understanding composite tracks
track uniqueCompositeTrackName
compositeTrack on
...
track uniqueNameWithoutSpaces
parent uniqueCompositeTrackName on
...
track newUniqueNameWithoutSpaces
parent uniqueCompositeTrackName off
A composite track starts with related files, usually all of the same type, that you want to group
and display together (referred to as "subtracks"). The
compositeTrack on
line defines the parent track that will be later
referenced as parent uniqueCompositeTrackName off
in each subtrack's
stanza. Either "on" or "off" can be used to set a subtrack to be displayed or not
displayed by default. Composite tracks can be broken apart further to group very similar tracks with
the trackDb use of subGroups and
views, not demonstrated here. Read
all about composite
tracks here. See an
example trackDb.txt.
Understanding super-tracks
track uniqueSuperTrackName
superTrack on show
...
track uniqueNameWithoutSpaces
parent uniqueSuperTrackName
...
track newUniqueNameWithoutSpaces
parent uniqueSuperTrackName
...
track uniqueCompositeTrackNameInSuperTrack
compositeTrack on
parent uniqueSuperTrackName
...
track uniqueNameWithoutSpaces
parent uniqueCompositeTrackNameInSuperTrack on
...
track newUniqueNameWithoutSpaces
parent uniqueCompositeTrackNameInSuperTrack off
A super-track starts with several different types of track data that you want to group together in
a high level folder. Super-tracks can contain composite tracks and container multiWigs, but not vice
versa. The superTrack on show
line allows for this track to be later
referenced as parent uniqueSuperTrackName
in each of the children
subtracks (note how it is only required for direct children, and not for subtracks contained in a
composite inside the super-track). The "show" is optional and sets the super-track to
display by default. Read all about
super-tracks here. See an
example trackDb.txt.