QuPath is unable to save data

usegalaxy.eu support
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Hi, I was using the interactive tool QuPath (following this galaxy tutorial). The problem is that after I am finished with the analyses in QuPath I am unable to save the results (or anything). Saving the geojson gives me unidentified error (the error is not saved in the QuPath log) and trying to save the image returns “permission denied”. So it seems I am unable to write anything to the output directory and the problem might be in the galaxy settings…?

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Hi @vojtech

Thanks for sharing the tutorial link (very helpful!) and for explaining. Have you solved this yet or still having problems? As a first pass solution, I would suggest trying to save again. Maybe the server had a small hiccup and things are resolved now.

For this part

are you following the method as described in the tutorial? And with the tutorial data?

  1. Export the annotations as a GeoJSON file:
  • Click File → Export objects as GeoJSON
  • Choose Export as FeatureCollection
  • Click Save

The permissions denied error suggests that the interactive tool is not communicating with your Galaxy history properly, so I have a few more questions to narrow things down:

  1. working at UseGalaxy.eu? or somewhere else?
  2. you registered and are logged into your Galaxy account?
  3. this is happening with the tutorial data? or your own data?

Meanwhile, I am going to run a quick test with all three (as a Yes) to see if I can reproduce the problem. If yes, we can report it. If not, I’ll need to see your reply before we can troubleshoot further. Example: maybe an annotation is “not complete”, that state isn’t fully trapped by the tool, and the tool cannot save the intermediate data without more changes. But I can get started with a simple test meanwhile, more soon! :slight_smile:

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Update!

I was able to confirm the issue and have reported to the EU administrators here with some details. → Error interactive_tool_qupath: "permission denied" upon save · Issue #1836 · usegalaxy-eu/infrastructure-playbook · GitHub

Thanks for reporting the issue and let’s see what they think! They’ll comment on the ticket and likely back here once resolved. :slight_smile:

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Thank you jennaj for reproducing it and reporting it further. It is now fixed and working!

1 Like
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Great! let’s mark that as the solution. :slight_smile: