Groot update DM path - Githubissues

galaxyproject / tools-iuc

Tool Shed repositories maintained by the Intergalactic Utilities Commission

https://galaxyproject.org/iuc

MIT License

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Groot update DM path #6563

Closed hugolefeuvre closed 4 days ago

hugolefeuvre commented 1 week ago

FOR CONTRIBUTOR:

[x] I have read the CONTRIBUTING.md document and this tool is appropriate for the tools-iuc repo.
[x] License permits unrestricted use (educational + commercial)
[ ] This PR adds a new tool or tool collection
[x] This PR updates an existing tool or tool collection
[ ] This PR does something else (explain below) DM path was not the same in command wrapper and json file

bernt-matthias commented 4 days ago

What's wrong with the old path?

hugolefeuvre commented 4 days ago

What's wrong with the old path?

In the command part of the DM xml, data are downloaded into a repository called arg-annot.90 (in the case of arg-annot database), but in the json, at the end the path was in a repository called groot_database/data/arg-annot.90-1.1.2-13112024. I'm not sure if the error stems from that, but it's the only difference with the tests I run in the tools section. The tool was integrated into Galaxy because the tests passed but once on the platform I encounter an error, you can find them here : https://usegalaxy.fr/u/hugo-lefeuvre/h/test-groot

hugolefeuvre commented 4 days ago

Likely the problem is that the data manager tool needs to place the files in a directory $out_file.extra_file_path instead of the job working directories.

I made the same error in a few data managers. See the fix here Helmholtz-UFZ/galaxy-tools#71

I made the change in the last commit, hope I've done it right

hugolefeuvre commented 4 days ago

Sorry. Must have overlooked this :)

No problem, thanks for the review !