track colors

[Belinda M Giardine]

I have been using itemRgb in our track hubs and recently the tracks lost the color.  I found it was because I also had the color set for the tracks.  This used to work by making the labels be the color I set in the trackDb entry and the items were colored by the rgb values in the bed file.  Is this no longer supported?

Thanks,
Belinda

[Luis Nassar]

Hi, Belinda.

That should all still work. Could you share your hub with us so that we can take a look?

Keep in mind this is a public mailing list; if you would like to keep your hub private, you can send it to us at genom...@soe.ucsc.edu.

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Lou Nassar
UCSC Genomics Institute

[Belinda M Giardine]

It is our public VISION hub https://usevision.org/data/trackHub/hub.txt 
The colors are essential to the tracks so I removed the color setting in the trackDb entries.  You can see how it was, as I just commented out the lines in https://usevision.org/data/trackHub/hg38/ideasJointMay2021.hg38.txt as a work around.

Belinda

On 8/4/25 7:56 PM, Luis Nassar wrote:

You don't often get email from lrna...@ucsc.edu. Learn why this is important

[Matthew Speir]

Hello, Belinda.

Looking at a version of the Genome Browser software from early last year, we can confirm the behavior you saw previously: using "itemRgb on" with the "color" setting allowed one to have the track label colored by "color" and items by itemRgb. While we switched "itemRgb on" to be the default behavior in the last 12 months, some testing doesn't seem to implicate that as the immediate cause of the change in behavior, so we'll have to look into it a little further.

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

To view this discussion visit https://groups.google.com/a/soe.ucsc.edu/d/msgid/genome/50506974-97ca-4110-af42-b8c1bc53dea7%40psu.edu.

[Brian Lee]

Dear Belinda,

I saw your message this afternoon and it made me curious to investigate your problem. Try removing the parent reference lines.   

The below is a version of the shared trackDb that with a ''grep -v parent'  removes those lines and it will load the colors.   The rest of the command is putting a feature called "useOneFile on" that can turn a trackDb.txt into a full hub, provided some expected hub-language is added to the trackDb.txt.


echo -e "hub myExampleHub\nshortLabel Example Hub\nlongLabel Example Hub Longer Description\nemail email@here\nuseOneFile on\n\ngenome hg38\n" > hubTest.txt ; curl https://usevision.org/data/trackHub/hg38/ideasJointMay2021.hg38.txt | grep -v parent |  sed -e 's#states/#https://usevision.org/data/trackHub/hg38/states/#' >> hubTest.txt

All the best,
Brian Lee