URL to view tracks set in hgt.customText without a user's previously uploaded tracks

[Ben Shirley]

UCSC support group,

We have a website where as part of a larger process a user generates a set of genome browser tracks. They're joined together into a single gff file and we'd like to allow users to view this gff file on UCSC by clicking a single link. Using the URL below, this works correctly and the tracks are displayed.

http://genome.ucsc.edu/cgi-bin/hgTracks?db=hg19&org=human&position=chr22&hgt.customText=http://path-to-our-gff-file

The issue is, the track names in the gff file are dynamically generated and describe the contents of the track. These names change for each execution of our tool, so if a user views the tracks on UCSC after one execution of the tool, when they view the tracks after a second execution using different input, all of the tracks related to both executions are visible in the genome browser itself and if the "manage custom tracks" button is clicked.

Is there a way to create a URL that is self-contained? As in, a URL users could visit which would not contain other custom tracks except those in the current file specified by hgt.customText? I looked into sessions as a way to do this, as it would seem to be the logical way to do it, but I wasn't able to find a way to create a new (temporary) session for each results set using a URL.

Ben

[Steve Heitner]

Hello, Ben.

One possible solution would be configure the tool to first execute a cart reset on the user’s cart each time which would set the Browser back to its default state before loading up a new set of custom tracks.  This would be considered something of an extreme solution.

I think a better option would be to dynamically generate track hubs rather than custom tracks.  You could then use the hubClear feature to clear old hubs when loading new ones.  This process is documented at https://genome.ucsc.edu/goldenPath/help/hgTrackHubHelp.html#Session.  If you are unfamiliar with track hubs, you should definitely read through the track hub help doc at https://genome.ucsc.edu/goldenPath/help/hgTrackHubHelp.html.

Please contact us again at gen...@soe.ucsc.edu if you have any further questions.  All messages sent to that address are archived on a publicly-accessible Google Groups forum.  If your question includes sensitive data, you may send it instead to genom...@soe.ucsc.edu.

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Steve Heitner
UCSC Genome Bioinformatics Group

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