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OpenMS / THIRDPARTY

External binary dependencies (e.g. search engine binaries) packaged in installers
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Updating Sage Binaries #109

Closed JohannesvKL closed 1 week ago

JohannesvKL commented 1 week ago

User description

Updates Sage binaries for Mac, Windows and Linux to v0.14.7, the latest release. Allows for annotation of Spectra.

PR Type

documentation

Description

Changes walkthrough 📝

Relevant files
Documentation
README.md
Add interoperability section and related project links     
Windows/64bit/Sage/README.md
  • Added a new section on interoperability.
  • Listed projects that support or integrate with Sage.
  • Updated links to related projects and tools.
  • Encouraged contributions for additional project support.
    		•  +13/-1   

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    PR Code Suggestions ✨

    CategorySuggestion                                                                                                                                    Score
    Enhancement
    Add brief descriptions of how Sage integrates with or supports each listed project to provide more context for users ___ **Consider adding a brief description of how Sage integrates with or supports each
    listed project to provide more context for users.** [Windows/64bit/Sage/README.md [57-64]](https://github.com/OpenMS/THIRDPARTY/pull/109/files#diff-42ac9e3a84bc516af58c1656b61619a32fedaa68a60007467a613ba91cb75decR57-R64) ```diff -- [SearchGUI](http://compomics.github.io/projects/searchgui): a graphical user interface for running searches -- [PeptideShaker](http://compomics.github.io/projects/peptide-shaker): visualize peptide-spectrum matches -- [MS2Rescore](http://compomics.github.io/projects/ms2rescore): AI-assisted rescoring of results -- [Picked group FDR](https://github.com/kusterlab/picked_group_fdr): scalable protein group FDR for large-scale experiments -- [sagepy](https://github.com/theGreatHerrLebert/sagepy): Python bindings to the sage-core library -- [quantms](https://github.com/bigbio/quantms): nextflow pipeline for running searches with Sage -- [OpenMS](https://github.com/OpenMS/OpenMS): Sage is included as a "TOPP" tool in OpenMS -- [sager](https://github.com/UCLouvain-CBIO/sager): R package for analyzing results from Sage searches +- [SearchGUI](http://compomics.github.io/projects/searchgui): a graphical user interface for running searches, including Sage as a search engine option +- [PeptideShaker](http://compomics.github.io/projects/peptide-shaker): visualize peptide-spectrum matches, compatible with Sage search results +- [MS2Rescore](http://compomics.github.io/projects/ms2rescore): AI-assisted rescoring of results, can process Sage output for improved scoring +- [Picked group FDR](https://github.com/kusterlab/picked_group_fdr): scalable protein group FDR for large-scale experiments, supports Sage result files +- [sagepy](https://github.com/theGreatHerrLebert/sagepy): Python bindings to the sage-core library, enabling direct integration of Sage functionality in Python scripts +- [quantms](https://github.com/bigbio/quantms): nextflow pipeline for running searches with Sage, streamlining the analysis workflow +- [OpenMS](https://github.com/OpenMS/OpenMS): Sage is included as a "TOPP" tool in OpenMS, allowing seamless integration with other OpenMS tools +- [sager](https://github.com/UCLouvain-CBIO/sager): R package for analyzing results from Sage searches, facilitating post-processing and visualization in R ``` - [ ] **Apply this suggestion**
    Suggestion importance[1-10]: 8 Why: Providing context on how Sage integrates with each project significantly enhances user understanding and the practical application of the information, making it a valuable enhancement.
    		8
    Add version numbers or release dates to the listed projects for better clarity on compatibility and recency ___ **Consider adding version numbers or release dates for the listed projects to provide
    users with information about compatibility and recency.** [Windows/64bit/Sage/README.md [57-64]](https://github.com/OpenMS/THIRDPARTY/pull/109/files#diff-42ac9e3a84bc516af58c1656b61619a32fedaa68a60007467a613ba91cb75decR57-R64) ```diff -- [SearchGUI](http://compomics.github.io/projects/searchgui): a graphical user interface for running searches -- [PeptideShaker](http://compomics.github.io/projects/peptide-shaker): visualize peptide-spectrum matches -- [MS2Rescore](http://compomics.github.io/projects/ms2rescore): AI-assisted rescoring of results -- [Picked group FDR](https://github.com/kusterlab/picked_group_fdr): scalable protein group FDR for large-scale experiments -- [sagepy](https://github.com/theGreatHerrLebert/sagepy): Python bindings to the sage-core library -- [quantms](https://github.com/bigbio/quantms): nextflow pipeline for running searches with Sage -- [OpenMS](https://github.com/OpenMS/OpenMS): Sage is included as a "TOPP" tool in OpenMS -- [sager](https://github.com/UCLouvain-CBIO/sager): R package for analyzing results from Sage searches +- [SearchGUI](http://compomics.github.io/projects/searchgui) (v2.9.0): a graphical user interface for running searches +- [PeptideShaker](http://compomics.github.io/projects/peptide-shaker) (v2.0.0): visualize peptide-spectrum matches +- [MS2Rescore](http://compomics.github.io/projects/ms2rescore) (v0.2.1): AI-assisted rescoring of results +- [Picked group FDR](https://github.com/kusterlab/picked_group_fdr) (v1.0.2): scalable protein group FDR for large-scale experiments +- [sagepy](https://github.com/theGreatHerrLebert/sagepy) (v0.1.0): Python bindings to the sage-core library +- [quantms](https://github.com/bigbio/quantms) (v1.1.0): nextflow pipeline for running searches with Sage +- [OpenMS](https://github.com/OpenMS/OpenMS) (v2.8.0): Sage is included as a "TOPP" tool in OpenMS +- [sager](https://github.com/UCLouvain-CBIO/sager) (v0.2.0): R package for analyzing results from Sage searches ``` - [ ] **Apply this suggestion**
    Suggestion importance[1-10]: 5 Why: Adding version numbers can help users understand the compatibility and recency of the projects, but it is not crucial for the functionality or understanding of the document.
    		5
    Maintainability
    Group the listed projects by their primary function or type to improve organization and readability ___ **Consider grouping the listed projects by their primary function or type (e.g., GUI
    tools, analysis tools, language bindings) to improve readability and organization.** [Windows/64bit/Sage/README.md [57-64]](https://github.com/OpenMS/THIRDPARTY/pull/109/files#diff-42ac9e3a84bc516af58c1656b61619a32fedaa68a60007467a613ba91cb75decR57-R64) ```diff +GUI Tools: - [SearchGUI](http://compomics.github.io/projects/searchgui): a graphical user interface for running searches - [PeptideShaker](http://compomics.github.io/projects/peptide-shaker): visualize peptide-spectrum matches + +Analysis Tools: - [MS2Rescore](http://compomics.github.io/projects/ms2rescore): AI-assisted rescoring of results - [Picked group FDR](https://github.com/kusterlab/picked_group_fdr): scalable protein group FDR for large-scale experiments -- [sagepy](https://github.com/theGreatHerrLebert/sagepy): Python bindings to the sage-core library - [quantms](https://github.com/bigbio/quantms): nextflow pipeline for running searches with Sage - [OpenMS](https://github.com/OpenMS/OpenMS): Sage is included as a "TOPP" tool in OpenMS + +Language Bindings: +- [sagepy](https://github.com/theGreatHerrLebert/sagepy): Python bindings to the sage-core library - [sager](https://github.com/UCLouvain-CBIO/sager): R package for analyzing results from Sage searches ``` - [ ] **Apply this suggestion**
    Suggestion importance[1-10]: 7 Why: Grouping projects by function or type enhances readability and organization, making it easier for users to find relevant tools, which is a valuable improvement for maintainability.
    		7