Closed bugraoezdemir closed 10 months ago
Files larger than 1M found tools/bioformats2raw/test-data/filament.tif tools/bioformats2raw/test-data/xy_12bit__plant.oir Error: Process completed with exit code 1.
Files larger than 1M found tools/bioformats2raw/test-data/filament.tif tools/bioformats2raw/test-data/xy_12bit__plant.oir Error: Process completed with exit code 1.
OK, I will replace them with smaller files.
Files larger than 1M found tools/bioformats2raw/test-data/filament.tif tools/bioformats2raw/test-data/xy_12bit__plant.oir Error: Process completed with exit code 1.
OK, I will replace them with smaller files.
@kostrykin I have changed the test data.
Thanks, @bugraoezdemir!
Regarding this, I tried changing the output format to ome.zarr
, which works (the tests pass), but there is a warning:
WARNING:galaxy.model:Datatype class not found for extension 'ome.zarr'
I'm not sure what the state of this is in Galaxy. Shall we keep it on html
or change to ome.zarr
?
Thanks, @bugraoezdemir!
Regarding this, I tried changing the output format to
ome.zarr
, which works (the tests pass), but there is a warning:WARNING:galaxy.model:Datatype class not found for extension 'ome.zarr'
I'm not sure what the state of this is in Galaxy. Shall we keep it on
html
or change toome.zarr
?
@kostrykin The fact that it passes the tests is a bit deceptive. I have locally tested it with planemo serve
and the output was an empty file. So I would suggest that we keep this version with html
and when ome.zarr
is fully established as a Galaxy data type, we can update the tool accordingly.
ome.zarr is unfortunately not ready yet as a datatype :(
Alright, thank you all!
Deployment to toolshed failed due to the following error:
Could not update bioformats2raw Failed to find repository for owner/name euro-bioimaging/bioformats2raw Repository bioformats2raw updated successfully. Could not update bioformats2raw Failed to find repository for owner/name euro-bioimaging/bioformats2raw Unexpected HTTP status code: 400: {"err_msg": "You already own a repository named bioformats2raw, please choose a different name.", "err_code": 400008} Repository [bioformats2raw] does not exist in the targeted Tool Shed. Failed to update metadata for repository 'bioformats2raw' on the main Tool Shed. Repository contents updated but failed to update metadata for repository 'bioformats2raw' on the main Tool Shed.
https://github.com/BMCV/galaxy-image-analysis/actions/runs/6879105347/job/18710524827#step:6:224
I find the error message somewhat confusing. @bgruening You maybe know what this means?
My interpretation is that "Failed to find repository for owner/name euro-bioimaging/bioformats2raw" is the root cause? Does such a repository exist in the ToolShed?
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