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Add simorgh - #1964

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nilchia wants to merge 20 commits into
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nilchia:add_simorgh
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Add simorgh#1964
nilchia wants to merge 20 commits into
bgruening:masterfrom
nilchia:add_simorgh

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@nilchia

@nilchia nilchia commented Aug 23, 2026

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Add a new Galaxy tool wrapper for SIMORGH, a method for predicting apo-state and cryptic ligand binding sites in protein structures.

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)

There are two labels that allow to ignore specific (false positive) tool linter errors:

  • skip-version-check: Use it if only a subset of the tools has been updated in a suite.
  • skip-url-check: Use it if github CI sees 403 errors, but the URLs work.

@nilchia

nilchia commented Aug 23, 2026

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@amisteromid; This is the first draft.

Please check if the parameters are explained correctly and the pipeline is correct.

@nilchia

nilchia commented Aug 23, 2026

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The container has not yet been pushed to Docker Hub. I'll update the requirement once it is available online.

Comment thread tools/simorgh/test-data/multi_model.pdb
Comment thread tools/simorgh/macros.xml Outdated
Comment thread tools/simorgh/simorgh.xml Outdated
Comment thread tools/simorgh/simorgh.xml Outdated
Comment thread tools/simorgh/simorgh.xml Outdated
Comment thread tools/simorgh/simorgh.xml
Comment thread tools/simorgh/.shed.yml Outdated
Comment thread tools/simorgh/.shed.yml Outdated
nilchia and others added 8 commits August 23, 2026 13:51
Co-authored-by: Omid Mokhtari <60341517+amisteromid@users.noreply.github.com>
Co-authored-by: Omid Mokhtari <60341517+amisteromid@users.noreply.github.com>
Co-authored-by: Omid Mokhtari <60341517+amisteromid@users.noreply.github.com>
Co-authored-by: Omid Mokhtari <60341517+amisteromid@users.noreply.github.com>
Co-authored-by: Omid Mokhtari <60341517+amisteromid@users.noreply.github.com>
Co-authored-by: Omid Mokhtari <60341517+amisteromid@users.noreply.github.com>
@nilchia
nilchia marked this pull request as draft August 23, 2026 12:24
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2 participants