Troubleshooting Galaxy dataset link-outs to UCSC Genome Browser

[justme]

Hi,
Today, the link to UCSC genome browser in the visualization window (bigwig file) has disappeared.
How can I visualise my file again in this browser that I prefer above IGB or IGV?

I tried:

• “Build custom track for UCSC genome browser (Galaxy Version 1.0.1)” but this resulted in an error.
• “bigWigToBedGraph Convert from bigWig to bedGraph format (Galaxy Version 0.1.0)” but the visualisation window just addad the Ensembl link

Thanks for suggestions.

[jennaj]

Hi @justme

Thanks for reporting the problem. Few questions to get oriented:

1. Does your dataset contain a database metadata attribute? Changing database/build (dbkey)
2. Is that database supported by UCSC? That application will name the same attribute as dbkey. The listing of all can be found here: UCSC Genome Browser Downloads
3. Where are you using Galaxy? URL of the public server please, or describe if other. Troubleshooting errors

You can post back your details plus a screenshot of the expanded dataset for more help

[justme]

Hi,

Thanks for looking into my issue.

In fact, I always used the Galaxy Europe (usegalaxy.eu) site, which displayed the option to visualize the bigwig file to UCSC genome browser. The usegalaxy.org site still does:

[jennaj]

Hi @justme

Thanks for posting back more details. That dataset should have the UCSC link out based on the datatype and database assignments. My test using hg38 instead of hg19 is also missing the UCSC link out, so the problem is likely server side.

The quick solution would be to move the data over to UseGalaxy.org or UseGalaxt.org.au until the functionality is repaired. Thanks for the followup!

Ping for EU support/admin @wm75 @gallardoalba + @dannon in case release related

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Update: I decided to post this over to the EU chat. They make reply here or there, and feel free to join. You're invited to talk on Matrix

[imolineris]

I have the same problem, any news?

[jennaj]

Hi @imolineris

Not sure if this was resolved already or not … but all of the link outs are showing up for me in that same example history as before. This is the history import link if you want to check it out in more detail, or maybe the screenshot helps by itself. Galaxy | Europe

[jennaj]

Merging with No link to UCSC to visualise datasets - #3 by dgarrick