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@nilchia nilchia commented Nov 13, 2025

This PR adds the spatialdata tool to galaxy.

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)

@nilchia nilchia marked this pull request as ready for review November 13, 2025 13:17
@nilchia nilchia marked this pull request as draft November 13, 2025 13:17
@nilchia nilchia marked this pull request as ready for review November 13, 2025 13:17
@nilchia nilchia moved this from In progress to Ready in Galaxy Tool Developers SIG Board Nov 13, 2025
@nilchia nilchia moved this from Ready to In progress in Galaxy Tool Developers SIG Board Nov 13, 2025
@bgruening
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.. WARNING (TestsMissing): No tests found, most tools should define test cases.
.. INFO (OutputsNumber): 0 outputs found.
.. INFO (InputsNum): Found 5 input parameters.
.. WARNING (HelpEmpty): Help section appears to be empty.

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nilchia commented Dec 2, 2025

It passes locally but here fails with:

Job in error state.. tool_id: spatialdata_io, exit_code: 1, stderr: /home/runner/.planemo/gx_venv_3.11_release_25.1/bin/python3: No module named spatialdata_io

<token name="@PROFILE@">25.0</token>
<xml name="requirements">
<requirements>
<!-- <requirement type="package" version="@TOOL_VERSION@">spatialdata</requirement> -->
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are those needed? You want to clean this up?

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yes, they are needed for the tool suit. But at the moment they are incompatible with each other in conda.
I have to wrap to mroe dependencies

@nilchia nilchia marked this pull request as draft December 3, 2025 12:11
@github-project-automation github-project-automation bot moved this from In progress to Done in Galaxy Tool Developers SIG Board Dec 5, 2025
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2 participants