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usegalaxy-no / galaxyadmin

A repository for managing the work of the usegalaxy.no GalaxyAdmin team
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Jbrowse in usegalaxy #64

Closed ehj000 closed 1 year ago

ehj000 commented 2 years ago

A user is not able to visualize data using Jbrowse. The problem is reproducible. Has anyone been able to visualize data with jbrowse in usegalaxy.no?

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

kjetilkl commented 2 years ago

It could be because the JBrowse tool was not added to the "allowlist" which allows it to display unsanitized HTML. I have added it now, and I am able to see the genome browser

kjetilkl commented 2 years ago

Although sometimes I still get the same error, but when I reload the page in the middle frame it suddenly works again...

ehj000 commented 2 years ago

I think I did add it to the allow list before testing, but it works now when reloading. Thank you Kjetil

sveinugu commented 2 years ago

Although sometimes I still get the same error, but when I reload the page in the middle frame it suddenly works again...

Autoupdates of config while a server is running is not managed properly when there are more than one web server process running (at least this used to be the case). Reloading the web browser might connect to another web server which has not loaded new configs, hence such strange behaviour. A full restart should fix the issue.

tothuhien commented 1 year ago

I have the same problem now, and it does not work when I reload the page. By the way, is there any other alternative? IGV seems to not working neither.

kjetilkl commented 1 year ago

JBrowse version 1.16.11 had not yet been whitelisted, only 1.16.10 and 1.16.9. See if it works now.

tothuhien commented 1 year ago

awesome! Thanks.