Correcting "accidental typos" in hg18 / hg19 data hubs ?
Jelena Telenius
bioinformatician
MRC Department of Molecular Haematology
Weatherall Institute Of Molecular Medicine
Jonathan Casper
Hello Jelena,
Thank you for your question about issues with your track hubs. That certainly does sound puzzling!
The hubCheck utility does not interact with UCSC's cache of your data files (hubCheck makes its own local cache on your computer), so running hubCheck -clear will not cause the Genome Browser to immediately reload your hub files. The -clear option has actually been removed completely from the most recent version of hubCheck - it might be worth updating and seeing if that resolves any of your issues. All the same, 2 weeks is excessive.
We cache the hub.txt and related hub files on our servers, and refresh them if they're visited after 5 minutes since our last update. There is no "similar enough" - we just download the new file completely and replace our old copy. If you make a change to your hub, you can force our servers to reload your hub sooner by adding the URL parameter &udcTimeout=N, where N is the number of seconds to cache the hub files for before reloading. For example, you could load your hub onto the UCSC Genome Browser, then click in the location bar for hgTracks (e.g., http://genome.ucsc.edu/cgi-bin/hgTracks?http://genome.ucsc.edu/cgi-bin/hgTracks?db=danRer7&position=chr13%3A25004825-25082273&hgsid=441095055_Mr9cJhXXvWZd78i6fAOeHA8quJXH), paste "&udcTimeout=5" on the end of it, and then press enter to load that URL. The Genome Browser should now reload your hub files after 5 seconds, and will show a message at the top of every page as follows:
The Genome Browser cart currently includes the "udcTimeout" string. While this is useful for debugging hubs, it may negatively impact performance. To clear this variable, click here.
As an aside, using udcTimeout=1 forcees the browser to reload the hub pretty much every time you refresh the page on the Genome Browser. That is a rather excessive amount of refresh, and we recommend that you only use it for testing and remove it as soon as you're done. Otherwise it generates a significant amount of additional traffic between our servers.
It looks like you're already aware of at least some of this, but I wanted to make sure we're on the same page. If you are still having issues, my next thought would be that something in your cart might be interfering. You might try going to the gateway page at http://genome.ucsc.edu/cgi-bin/hgGateway and clicking the "cart reset" button. That should clear out any existing settings (including loaded hubs). Then you can click on the track hubs button and paste the URL to your hub to load it again fresh. Note that performing a cart reset will also clear the udcTimeout option, so you will have to set that again before loading your hub. You can also try visiting the public URL of your hub files in your web browser to confirm that your changes are visible to UCSC.
If you change the URL to your hub, the new URL is treated as a completely new and separate hub. That should prevent the contents of the old file from having any affect on the hub with the new URL. I would love to see this in action. Are you able to share the URL of one of these hubs with me? Or a saved session with the hub loaded?
I hope this is helpful. If you have any further questions, please reply to gen...@soe.ucsc.edu or genome...@soe.ucsc.edu. Questions sent to those addresses will be archived in publicly-accessible forums for the benefit of other users. If your question contains sensitive data, you may send it instead to genom...@soe.ucsc.edu.
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Jonathan Casper
UCSC Genome Bioinformatics Group
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Jelena Telenius
p. +358 50 539 5225 (Finnish number)