JBrowse hasn't worked for 3 days!

usegalaxy.org support
1

I used JBrowse to visualize genome mapping. It always work until Feb, 27th. Could anyone suggest me what to do?

2

Welcome @OrawanThepmanee

This is important to learn more about!!

We are working through a new release. Perhaps something is not configured correctly.

Would you be able to share some details about what you doing? You can either specify the details as below or share your history with the inputs plus a screenshot of the tool settings on a form or the full job details error report (if you got that far! since this captures everything). Technical details are very helpful.

Details

  1. Server: UseGalaxy.org
  2. Tool/version:
    • JBrowse genome browser (Galaxy Version 1.16.11+galaxy1)
    • or, JBrowse2 genome browser (Galaxy Version 3.7.0+galaxy0)
  3. Inputs: new? existing? If existing, which version was used to create the artifact?
  4. Reference genome options: server index (which?) or a fasta from the history? A new fasta or one that has worked before?
  5. Then, is there anything special about this data? Was this data downloaded/uploaded or created in the same session?

I’ll also give this a try to see if I can reproduce with some default testing data but some details to narrow it down (as needed) would be appreciated! My initial guess is a problem with the versions or possibly the reference data but I’ll be able to comment more once I test, then we can explore more with your example.

Thank you for writing in to let us know! Let’s get this resolved! :hammer_and_wrench:

3

Update.

This is my testing history with a few combinations using the current versions of the tools. The jobs run correctly but the Preview display (eye icon) never resolves.

I am getting feedback about this internally. Would you be able to clarify if this is also what you notice going wrong? The display of the instance?

Thanks and more soon. :slight_smile:

Update 2

Ticket → Bug: Jbrowse fails to find HTML outputs for Preview in 26.0 · Issue #1380 · galaxyproject/usegalaxy-tools · GitHub

We are still sorting out where this is coming from! More updates will follow and thanks again for lettings us know!

4

Dear Jennifer,

Thank you for your fast reply. It is also the case for me. I could run JBrowse and the results was displayed normally until Feb, 27th. Since then, the display hasn’t worked.

Best,
Orawan

1 Like
5

Great! Thanks for confirming @OrawanThepmanee

I was able to triage to the development team working on the release. A correction has been made and this will flow out to the server at UseGalaxy.org (and any other servers that update soon).

This is not live yet but I expect the server to update soon. I’ll keep an eye on it and update back here.

You have been so helpful! Thank you! :slight_smile: