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bgruening / galaxytools

:microscope::books: Galaxy Tool wrappers
MIT License
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applies the new conventions for imaging tools agreed at BioHackEU23 #1346

Closed kostrykin closed 8 months ago

kostrykin commented 8 months ago

xref https://github.com/elixir-europe/biohackathon-projects-2023/blob/main/16/conventions.md

bgruening commented 8 months ago

Nice, ready to merge when you are!

kostrykin commented 8 months ago

Nice, ready to merge when you are!

@bgruening ready! 🚀

bgruening commented 8 months ago

can you maybe increse the diff-size for cellprofiler4

Collection element AS_09125_050116030001_D03f00d0_Overlay of collection pipeline_output: different than expected Expected file size of 168221+-0 found 182983

kostrykin commented 8 months ago

can you maybe increse the diff-size for cellprofiler4

Collection element AS_09125_050116030001_D03f00d0_Overlay of collection pipeline_output: different than expected Expected file size of 168221+-0 found 182983

@bgruening sorry I have absolutely no idea what you mean :)

bgruening commented 8 months ago

Cellprofiler 4 has in its test some check for the file size and this is failing here, because the size changed.

kostrykin commented 8 months ago

@sunyi000 can you maybe have a look at this?

sunyi000 commented 8 months ago

@sunyi000 can you maybe have a look at this?

i think it's line 148 of cellprofiler.xml, change the number to 182983. or put a delta with some values.

something like

or just

kostrykin commented 8 months ago

Thanks @sunyi000, makes totally sense if you know what to look for :) hopefully this solves the issue!

bgruening commented 8 months ago

There are 3 other tests with the same problem.

kostrykin commented 8 months ago

seems to be fine now

bgruening commented 8 months ago

Thanks.

kostrykin commented 8 months ago

The new tool versions are not found by update-tool.py from the usegalaxy-eu/usegalaxy-eu-tools repo.

For example:

python scripts/update-tool.py --owner bgruening --name cp_cellprofiler4 imaging.yaml
INFO:root:Fetching updates for bgruening/cp_cellprofiler4

I guess this is due to the following error in the CI:

Unsuccessful tests found, inspect the 'All tool test results' artifact for details.

Errored Tests ❌ cp_mask_image (Test #1) Execution Problem: Input staging problem: History not found

Strangely the error was not reported by the PR CI.

I have no clue what "Input staging problem: History not found" means, any ideas? @bgruening