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Update PeptideShaker recipe to 3.0.13 - #66603

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BioGeek:peptide-shaker-3.0.13
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BioGeek:peptide-shaker-3.0.13

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@BioGeek

@BioGeek BioGeek commented Jun 23, 2026

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This PR updates the Bioconda peptide-shaker recipe to the PeptideShaker release that contains the merged InstaNovo import and no-FASTA de novo project support.

The PeptideShaker integration depends on the Compomics Utilities and PeptideShaker PRs being merged and released first.

Changes

  • Updates the PeptideShaker version.
  • Updates the source checksum.
  • Updates the wrapper script jar filename.
  • Updates package description text to mention de novo workflows including InstaNovo, InstaNovo+, and InstaNovo with refinement.

Merge Order

Recommended order:

  1. Add InstaNovo and InstaNovo+ import support CompOmics/compomics-utilities#73
  2. Add SearchGUI support for InstaNovo and InstaNovo+ CompOmics/searchgui#387
  3. Add PeptideShaker import UI support for InstaNovo result files CompOmics/peptide-shaker#570
  4. Add DeNovoGUI compatibility APIs to Utilities CompOmics/compomics-utilities#74
  5. Add InstaNovo support to DeNovoGUI CompOmics/denovogui#53
  6. Update SearchGUI recipe to 4.3.17 #66604
  7. This PR
  8. Expose InstaNovo workflows in online input form barsnes-group/peptide-shaker-online#30
  9. Bump PeptideShaker wrappers for InstaNovo support galaxyproteomics/tools-galaxyp#828

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