JBrowse failing to show output

[cjkeist]

I have new Galaxy 22.05 running on Centos 7 server. The user is having an issue getting JBrowser to display any output. This is the error:

JBrowse window.onerror=function(msg){ if( document.body ) document.body.setAttribute(“JSError”,msg); } if(window.process&&process.versions&&process.versions.electron) { window.electronRequire = require; delete window.require; } html, body, div.jbrowse { margin: 0; padding: 0; height: 100%; width: 100%; }

Loading…

JBrowseDefaultMainPage

I’m uploading a screenshot of how they submitted

the job if this helps.

[igor]

Hi @cjkeist
based on ‘green’ status, JBrowse job has been completed. The tracks might not be visible by default.

Galaxy Training: Genomic Data Visualisation with JBrowse

Hope that helps.
Kind regards,
Igor

[cjkeist]

Thank you. I get the same error trying to follow the tutorial. See attached pics. The version of JBrowse I installed is 44. Should I try installing older versions?

[cjkeist]

Update, I now have something coming up. Not sure what I did. I found another thread about tools not displaying HTML. From that they stated to make sure the tool set is listed in the Manage Allowlist. When I went to that page, it did list several tool sets there including JBrowse. However when I click on one of the buttons, I think owner, everything in the manage list got removed. So now my manage list is emply, but JBrowse is displaying. But it never displays any data, it looks to be stuck on “loading”.

[igor]

Hi @cjkeist
I am confused now. The original message is tagged ‘usegalaxy.org’, while you somehow can access Allowlist. Do you use a personal Galaxy with admin access? I believe JBrowse should be in Allowlist to show the content.
Kind regards,
Igor

[igor]

I am truly sorry: you clearly stated that you have a new Galaxy. I was confused by ‘usegalaxy.org’ tag.
Kind regards,
Igor

[cjkeist]

Sorry, yes this is our own Galaxy server we are running. Didn’t realize the tag for the usegalaxy.org site, thought it was for general questions on Galaxy server. I have tried installing different versions of JBrowse but nothing has worked yet. Thinking it might be a permissions problem but I’m not sure where the data is saved on the server. The installation was done by the Galaxy user account on our server so I would assume all permissions should be set for that account to read/write.

[cjkeist]

If there is a different forum I should be posting this to for running your own Galaxy server let me know.

Thanks…

[igor]

Hi @cjkeist
it is a proper forum for issues like this one, but you need an input from a person with Galaxy admin skills. I have not dealt with local Galaxy for years.
Kind regards,
Igor