Add InstaNovo support to DeNovoGUI

[BioGeek]

Add InstaNovo support to DeNovoGUI

InstaNovo is a de novo peptide sequencing tool.

This PR adds DeNovoGUI support for InstaNovo v1.2.2 in three modes:

• InstaNovo: de novo peptide sequencing with the transformer-based InstaNovo model.
• InstaNovo+: de novo peptide sequencing with the diffusion-based InstaNovo+ model.
• InstaNovo with refinement: InstaNovo predictions refined with InstaNovo+.

Changes

• Adds GUI and CLI selection for:
  • InstaNovo
  • InstaNovo+
  • InstaNovo with refinement
• Adds an InstaNovo execution job matching the SearchGUI command behavior.
• Adds support for selecting a local InstaNovo checkout/installation folder.
• Adds result discovery/import/export support for the three InstaNovo CSV result types.
• Updates DeNovoGUI to the newer Utilities line needed for InstaNovo advocates and readers.
• Removes the old Log4j 1.x path by moving local logging usage to Log4j 2 APIs. Closes Apache log4j-1.2.12 no longer supported #51

Notes

DeNovoGUI appears less actively maintained than SearchGUI, and @hbarsnes has mentioned SearchGUI is the newer route for these workflows. This PR is therefore best treated as legacy/parallel support after the SearchGUI and PeptideShaker integration has landed.

Screenshots

Tests

Ran:

mvn -DskipTests -Dmaven.javadoc.skip=true package
mvn -Dtest=com.compomics.denovogui.execution.jobs.InstaNovoJobTest test

Covered by the focused test:

• InstaNovo executable resolution for Unix and Windows virtual environments.
• Result-file naming for InstaNovo, InstaNovo+, and refinement.
• Refined workflow command construction.

Merge Order

Recommended order:

1. Add InstaNovo and InstaNovo+ import support compomics-utilities#73
2. Add SearchGUI support for InstaNovo and InstaNovo+ searchgui#387
3. Add PeptideShaker import UI support for InstaNovo result files peptide-shaker#570
4. Add DeNovoGUI compatibility APIs to Utilities compomics-utilities#74
5. This PR
6. Update SearchGUI recipe to 4.3.17 bioconda/bioconda-recipes#66604
7. Update PeptideShaker recipe to 3.0.13 bioconda/bioconda-recipes#66603
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