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@natefoo natefoo commented Sep 8, 2025

Although the quoting is valid, I think the way it's done prevents Pulsar from implicitly copying the wrapper script? On .org we're getting:

python: can't open file '/jetstream2/scratch/main/jobs-vgp/70483536/tool_files/add_input_name_as_column.py': [Errno 2] No such file or directory

This adjusts the quoting and adds required_files for good measure. No tool version change because there's no change in functionality, just a fix for running with Pulsar.

FOR CONTRIBUTOR:

  • I have read the CONTRIBUTING.md document and this tool is appropriate for the tools-iuc 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)

@natefoo
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natefoo commented Sep 8, 2025

Heh, lint failed because I didn't update the version.

I do get why we require this but it's a bit annoying to have two identical versions installed except one works half the time and the other doesn't. Obviously I can deal with this on my end in multiple ways, however.

@bernt-matthias
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We can merge. The linter is skipped when merging.

Now that the older version can not be used anymore.

@bernt-matthias
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Do all tools that use __tool_directory__ should have required_files?

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natefoo commented Sep 9, 2025

Someone (@jmchilton) correct me if I'm wrong, but yes I believe that is the desired state. Pulsar will implicitly find, transfer, and rewrite files used in the <command>, but going forward I believe the goal is to have them explicitly referenced.

@bernt-matthias bernt-matthias merged commit 1775d01 into galaxyproject:main Oct 14, 2025
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