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galaxyproject

@galaxyproject source repo

14 published skills

  1. ▌
    Workflow Reports · galaxyproject bundle
    Use this skill when asked to create, draft, or write a Galaxy workflow report template for the Workflow Editor's Report tab. Triggers on requests like "create a report for this workflow", "draft a workflow report template", "write a Galaxy report for workflow <id/url>".
    1 install
  2. ▌
    Galaxy Integration · galaxyproject bundle
    Router for Galaxy MCP, JupyterLite notebooks, and BioBlend automation
    1 install
  3. ▌
    Galaxy Transform Collection · galaxyproject bundle
    Galaxy Collection Transformation Command - transform Galaxy dataset collections reproducibly using Galaxy's native tools. Use when asked to filter, sort, relabel, restructure, flatten, nest, merge, or otherwise manipulate Galaxy collections.
    1 install
  4. ▌
    Jupyterlite Galaxy · galaxyproject bundle
    Write JupyterLite notebooks for Galaxy dataset interaction using gxy package
    1 install
  5. ▌
    Tool Selection Diagram · galaxyproject bundle
    Generate a tool selection flowchart diagram (PNG) for a Galaxy tool suite from a JSON definition. Use when creating visual guides that help users pick the right tool in a multi-tool suite.
    1 install
  6. ▌
    Galaxy MCP Reference · galaxyproject bundle
    Galaxy MCP server tools reference for histories, datasets, tools, and workflows
    3 installs
  7. ▌
    Nf Process To Galaxy Tool · galaxyproject
    Convert a single Nextflow process to a Galaxy tool XML
    1 install
  8. ▌
    Nf Pipeline To Galaxy Workflow · galaxyproject
    Convert a complete Nextflow pipeline to Galaxy
    1 install
  9. ▌
    Nf Subworkflow To Galaxy Workflow · galaxyproject
    Convert a Nextflow subworkflow to a Galaxy workflow
    1 install
  10. ▌
    Tool Dev · galaxyproject bundle
    Galaxy tool development reference — creating new tools, testing, IUC review preparation, and updating existing tools. Use when authoring or modifying Galaxy tool wrappers for tools-iuc.
    1 install
  11. ▌
    Trackhubs · galaxyproject bundle
    Building UCSC Track Hubs (track hubs and assembly hubs) — bigBed/bigChain/bigMaf format requirements, composite-track rules, hub.txt / genomes.txt / trackDb.txt structure. Use when emitting a UCSC hub from Galaxy outputs, wrapping a hub-publishing tool, or debugging hubCheck failures.
    1 install
  12. ▌
    Udt Authoring · galaxyproject bundle
    Use when authoring a Galaxy User-Defined Tool (UDT) -- a `class: GalaxyUserTool` YAML definition that wraps a container and command into a tool a non-admin user creates and runs (e.g. via Galaxy MCP create_user_tool / run_user_tool, or POST /api/unprivileged_tools). Not for classic XML/ToolShed tool wrappers.
    1 install
  13. ▌
    Hub News Posts · galaxyproject bundle
    This skill should be used when creating Galaxy Hub news posts, writing content for galaxyproject.org/news, or converting content to Galaxy Hub markdown format.
    1 install
  14. ▌
    Reproduciblify · galaxyproject bundle
    Use this skill to "reproduciblify" a Galaxy history — re-execute a real (often messy) analysis as a clean, fully on-graph, collection-structured history and author a Galaxy Notebook that extracts cleanly into a reusable, sample-agnostic workflow. Triggers on "reproduciblify this history", "make this history reproducible/extractable", "rebuild this analysis on-graph", "turn this history into a clean notebook/workflow".
    1 install