udcTimeout not working

[Bogutz, Aaron Blair]

Hi there,

First off thanks so much for all your work on the genome browser, it's an indispensable tool for our research and enables such easy collaboration. I do a lot of track hub development for our lab, and it seems like the udcTimeout=5& command hasn't been working over the last couple of weeks. I've been running into some other trouble more recently but not being able to refresh rapidly has made troubleshooting much more difficult. Basically when I paste the above into the url it doesn't display the message to remove it anymore, and it doesn't seem to refresh. Any help you could provide on this would be most appreciated.

If you need more information or have any questions please let me know!

Thanks,

Aaron Bogutz  (He, Him, His)
Lab Manager, Lefebvre and Lorincz Labs; Manager, LSI Cryostorage Facility; Manager, LSI qPCR Facility
Faculty of Medicine | Medical Genetics
The University of British Columbia | Vancouver Campus
Life Sciences Institute | Vancouver BC | V6T1Z3 Canada
Phone 604 822 1798
aaron....@ubc.ca

[Jairo Navarro Gonzalez]

Hello,

Thank you for using the UCSC Genome Browser and reporting your issues.

You have discovered a bug in our code that prevents the udcTimeout dialogue box from appearing, although the udcTimeout setting is active. The bug fix will be released to the live servers in the next software update, which will be released on September 26th. Thank you again for bringing this issue to our attention.

I hope this is helpful. If you have any further questions, please reply to gen...@soe.ucsc.edu.
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.

Jairo Navarro
UCSC Genome Browser

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[Bogutz, Aaron Blair]

Hi Jairo,

That's fantastic, happy to have contributed in some way. Now that I can tell that stuff is refreshing, I have another issue: in my track hubs, I have RNAseq data broken into multiWig containers with positive and negative strand information. Very recently, like in the last 2-3 days, none of the tracks seem to be showing positive and negative strand information any more. Both tracks will show up on the positive or negative strand, the multiwig won't be showing differences between them. I'm hoping this will also be an easy fix, I've banged my head against this for a couple hours and it doesn't seem to be anything I've done as older track hubs are broken as well.

If you need more info please let me know. An example track hub can be found here: https://datahub-105-c22.p.genap.ca/ABB/Nsd1-Adjacent-Hub/ I was playing around with the trackDb.txt in mm10 to see if I could reproduce this behaviour and it seems to stand true for this one as well.

Thanks again,

Aaron

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From: Jairo Navarro Gonzalez <jnav...@ucsc.edu>
Sent: Tuesday, August 29, 2023 2:27 PM
To: Bogutz, Aaron Blair
Cc: gen...@soe.ucsc.edu
Subject: Re: [genome] udcTimeout not working

 

[CAUTION: Non-UBC Email]

[Matthew Speir]

Hello, Aaron.

Thank you for reporting this bug with multiWig tracks. 

This an issue with the way settings are handled in these container tracks. The "negateValues" setting works for the subtracks and displays as expected after initially loading the hub. However, if you change the track configuration for the multiWig (or even go to the track configuration page) the subtrack settings are overwritten with those of the multiWig container. We hope to fix this in the future, though we don't have an estimate of when that might be.

In the meantime, there are a few work-arounds:

• After you load the hub, don't change the configuration for that multiWig track via the Genome Browser interface.
• Convert the values in the negative strand wig to be negative values in the file itself rather than using the "negateValues" setting. This would require a bit of scripting.

If you have any further questions, please reply to gen...@soe.ucsc.edu. 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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Matthew Speir

UCSC Genome Browser, User Support

UC Santa Cruz Genomics Institute

Revealing life’s code.

To view this discussion on the web visit https://groups.google.com/a/soe.ucsc.edu/d/msgid/genome/3f3c1b07412a43478eff0559b790c64c%40ubc.ca.

[Bogutz, Aaron Blair]

Hi Matthew,

This matches exactly with my observations, thanks for the confirmation. I've told all my users to be careful about modifying the container tracks, hopefully we don't run into this issue in the future.

Thanks so much for following up on this!

-Aaron

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From: Matthew Speir <msp...@ucsc.edu>
Sent: Thursday, September 7, 2023 1:06:38 PM
To: Bogutz, Aaron Blair
Cc: Jairo Navarro Gonzalez; gen...@soe.ucsc.edu