Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Fix bioformats2raw tool #102

Merged
merged 2 commits into from
Feb 26, 2024
Merged

Fix bioformats2raw tool #102

merged 2 commits into from
Feb 26, 2024

Conversation

kostrykin
Copy link
Member

@kostrykin kostrykin commented Feb 26, 2024

bioformats2raw was producing blank outputs on Galaxy EU but running fine locally and in CI.

The issue boiled down to a known Java issue with NFS volumes: https://issues.apache.org/jira/browse/KAFKA-6647

The fix is to redirect temporary output to a directory within the Docker container.

Much thanks to @bgruening for hunting down this bug! 🎉 🎉

xref #72


FOR CONTRIBUTOR:

  • - I have read the CONTRIBUTING.md document and this tool is appropriate for the galaxy-image-analysis repo.
  • - License permits unrestricted use (educational + commercial)
  • - This PR adds a new tool or tool collection
  • - This PR updates an existing tool or tool collection
  • - This PR does something else (explain below)
  • - Tools added/updated by this PR (if any) comply with the Naming and Annotation Conventions for Tools in the Image Community in Galaxy (or please explain why they do not)

The fix is to redirect temporary output to a directory within the Docker container.
This is due to a known Java issue with NFS volumes:

https://issues.apache.org/jira/browse/KAFKA-6647
@kostrykin
Copy link
Member Author

<param name="output_name" type="text" value="output.ome.zarr" label="Output zarr data"/>

@bugraoezdemir This label seems a bit unspecific. Can we change this to be more expressive?

@kostrykin kostrykin merged commit ae73350 into BMCV:master Feb 26, 2024
10 checks passed
@kostrykin kostrykin deleted the fix-bf2raw branch February 26, 2024 19:50
Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Labels
None yet
Projects
None yet
Development

Successfully merging this pull request may close these issues.

2 participants