"PPanGGOLiN all" error in https://usegalaxy.eu

usegalaxy.eu support
,
1

Hello,
PPanGGOLiN is installed on https://usegalaxy.fr and seems to work fine. Our local tests are also good and do not show any error. But on https://usegalaxy.eu, there is a strange error during the execution of PPanGGOLiN all (see attached file), maybe a galaxy configuration problem ?
Best,
Thomas

Capture d’écran du 2025-02-12 15-34-02
Capture d’écran du 2025-02-12 15-34-022357×1060 500 KB

2

Hi @thomas_lacroix

Maybe, but it is hard to tell. Would you like to post back a share link to a history with an example? Small is great, so maybe just a slice of the data only run through this tool is fine. How to generate the link is in the banner of this forum, also here → How to get faster help with your question

Let’s start there, thanks! :slight_smile:

Update: to get this started, I am running the tool test at the EU server. I ran it twice – individual files and a collection of files – sometimes that reveals a small issue with a newer tool like this.

One note: the form was really exact about how the files need to be named, since the underlying tool is probably using that as a “sample identifier”. This means that if your input genome files originally have whitespace in the names (maybe from an upstream tool) you can either rename individual files with the pencil icon, or add the files into a list collection (the element identifiers will be used instead, and those never have spaces).

That will take some time to run. And I used some jargon here as you seem to know your way around Galaxy, but please ask about anything not clear!

3

Hi @jennaj ,
Thanks, here is my shared history:

I see you used fasta files and it seems to work fine, I used file in Genbank format and got the error. None of the file name contains whitespace.
What is strange is that I have used the same dataset to test on
https://usegalaxy.fr, https://galaxy.migale.inra.fr, and my local instance of Galaxy and I do not see this error.
Best,
Thomas

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4

Hi @thomas_lacroix

Ok great, thanks for explaining! I’m reviewing now.

5

Hi,

I discussed this with our team and there is a merged pull request that we think solved the problem.

I hope all is working now.

Best,
Armin

1 Like
6

Hi,
It works, thanks !
Best,
Thomas

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