No link to UCSC to visualise datasets

usegalaxy.eu support
1

In Galaxy Europe, I have histories generated previously containing bigwig datasets that I was able to visualise in UCSC with no problem. But now, with the same bigwig files, I do not have the “Display at UCSC” link. I am not sure why this link is no longer present. Thanks for any advice.

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@dgarrick please make sure you have a database associated. This is the genome identifier, e.g. hg19, mm10 or similar.

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Yes they are hg38

4

Same problem for bam for the dm6 genome. Any news?

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Hi @imolineris

I can confirm – dm6 doesn’t have the link outs. Ping @bjoern.gruening

Both of the human genomes (hg19, hg38) are okay. Let’s combine the other post with this one, ref Troubleshooting Galaxy dataset link-outs to UCSC Genome Browser - #6 by jennaj

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The problem for dm6 still persist

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Hi @imolineris

Good catch! I see the problem, but only at UseGalaxy.eu. It works as expected at UseGalaxy.org.

Please follow this ticket for updates: Link to UCSC for dm6 is disconnected at UseGalaxy.eu · Issue #648 · galaxyproject/usegalaxy-tools · GitHub

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The problem still persists. On Link to UCSC for dm6 is disconnected at UseGalaxy.eu · Issue #648 · galaxyproject/usegalaxy-tools · GitHub they say that is ain’t the right place to report it.

I foud a workaround:

  1. On usegnalaxy.eu edit the bam file attribute, change dm6 to dm3 in the Database/Build field
  2. Now the ucsc visualization work, clik on the visualization button and go to ucsc.
  3. On genome.ucsc.edu Edit the custom track in ucsc, copy the text that define the track.
  4. Edit the text canging dm3 to dm6.
  5. Open the uscc genome browser on dm6 genome.
  6. Add a custom track.
  7. Paste the trak definition you found.
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9

Hi @imolineris

The correction is in progress now. Please wait about 12 more hours from now, then try again to see if that fixed dm6 at the EU server. I’ll be doing the same tomorrow my time.

In the future, yes, please keep reporting issues here for triage and we’ll work it out on our side. Apologies for the recent troubles.

10

@imolineris this should be resolved now.

Thanks for your patience and the created post here, it helped us to track down the problem.

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11

I confirm that the problem is solved.

Thank you very much

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