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galaxy-skills

v2026.9.17

Curated Galaxy skills for running an analysis: connecting to a Galaxy server, the MCP tool surface, dataset collections, user-defined tools, workflow reports and turning an ad-hoc history into a reusable workflow. Mirror of galaxyproject/galaxy-skills (skills/).

CodexClaude Code6 Skills

By The Galaxy ProjectLicense: MIT0 GitHub starsUpdated 5 days ago

Directory evidence

Runtimes
Codex and Claude Code
Parsed components
6 skill or MCP entries
Source updated
Sep 18, 2026
Manifest status
Canonical path parsed

The directory validates manifest shape and source location. It does not execute the plugin or provide a security endorsement. Review the indexing methodology →

Install galaxy-skills for Codex and Claude Code

Installs for the current user
codex plugin marketplace add galaxyproject/agentic-plugins
codex plugin marketplace upgrade galaxyproject
codex plugin add galaxy-skills@galaxyproject

Paste and run these commands in a terminal with Codex. They add and refresh the galaxyproject catalog, then install this plugin.

Compatibility: the page URL and API slug “galaxy-skills” remain stable.

  • Codex: galaxy-skills@agent-plugin-marketplace → galaxy-skills@galaxyproject

The installer fetches third-party code from the source repository shown on this page. This directory validates manifest structure and source location, but does not perform a security audit; review the manifest, components, and source before installing.

Get the source manually
git clone https://github.com/galaxyproject/agentic-plugins

Clone the source repository, then follow its setup instructions to add the plugin to a compatible client. The plugin root is plugins/galaxy-skills/.

Plugin files

plugins/galaxy-skills/
├── .codex-plugin/plugin.json
├── .claude-plugin/plugin.json
├── skills/collection-manipulation/SKILL.md
├── skills/galaxy-integration/SKILL.md
├── skills/galaxy-mcp-reference/SKILL.md
├── skills/reproduciblify/SKILL.md
├── skills/udt-authoring/SKILL.md
└── skills/workflow-reports/SKILL.md

Included Skills6

collection-manipulationskills/collection-manipulation/SKILL.md

Transform Galaxy dataset collections reproducibly using Galaxy's native tools. Use when asked to filter, sort, relabel, restructure, flatten, nest or merge a collection, build a list or paired collection, run a tool over every sample (map over a collection), or work with element identifiers.

galaxy-integrationskills/galaxy-integration/SKILL.md

Use when setting up or choosing how an agent talks to a Galaxy instance -- first-time connection (server URL, API key, verifying access), then picking between Galaxy MCP for interactive work, JupyterLite notebooks for analysis against Galaxy datasets, and BioBlend scripts for batch or CI. Start here to use Galaxy when not yet connected.

galaxy-mcp-referenceskills/galaxy-mcp-reference/SKILL.md

Use when driving a Galaxy server through its MCP tools -- connecting to an instance, listing or creating histories, uploading data, finding and running tools, invoking workflows, inspecting datasets and jobs. Read before the first Galaxy MCP call in a session; covers which tool to reach for and the common traps (id vs name, history vs dataset ids, collection shapes).

reproduciblifyskills/reproduciblify/SKILL.md

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".

udt-authoringskills/udt-authoring/SKILL.md

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.

workflow-reportsskills/workflow-reports/SKILL.md

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>".

Plugin manifests2

plugins/galaxy-skills/.codex-plugin/plugin.json
{
  "name": "galaxy-skills",
  "version": "2026.9.17",
  "description": "Curated Galaxy skills for running an analysis: connecting to a Galaxy server, the MCP tool surface, dataset collections, user-defined tools, workflow reports and turning an ad-hoc history into a reusable workflow. Mirror of galaxyproject/galaxy-skills (skills/).",
  "author": {
    "name": "The Galaxy Project",
    "url": "https://galaxyproject.org"
  },
  "homepage": "https://github.com/galaxyproject/galaxy-skills",
  "repository": "https://github.com/galaxyproject/agentic-plugins",
  "license": "MIT",
  "keywords": [
    "galaxy",
    "bioinformatics",
    "skills",
    "collections",
    "user-defined-tools"
  ],
  "skills": "./skills/",
  "interface": {
    "displayName": "Galaxy Skills",
    "shortDescription": "Curated Galaxy skills for running analyses",
    "longDescription": "Skills that teach an agent to drive a real Galaxy server well: connecting to an instance and choosing a client, the Galaxy MCP tool surface and its pitfalls, structuring dataset collections, authoring user-defined tools when no tool exists, drafting workflow reports, and rebuilding an ad-hoc history as a reusable workflow. Mirrored from galaxyproject/galaxy-skills.",
    "developerName": "The Galaxy Project",
    "category": "Developer Tools",
    "capabilities": [
      "Read",
      "Write"
    ],
    "websiteURL": "https://galaxyproject.org/",
    "defaultPrompt": [
      "Upload these FASTQ files to Galaxy and run FastQC on all of them.",
      "Filter this Galaxy collection to the samples matching a pattern.",
      "Turn this messy history into a reusable workflow."
    ]
  }
}
plugins/galaxy-skills/.claude-plugin/plugin.json
{
  "name": "galaxy-skills",
  "version": "2026.9.17",
  "description": "Curated Galaxy skills for running an analysis: connecting to a Galaxy server, the MCP tool surface, dataset collections, user-defined tools, workflow reports and turning an ad-hoc history into a reusable workflow. Mirror of galaxyproject/galaxy-skills (skills/).",
  "author": {
    "name": "The Galaxy Project",
    "url": "https://galaxyproject.org"
  },
  "homepage": "https://github.com/galaxyproject/galaxy-skills",
  "repository": "https://github.com/galaxyproject/agentic-plugins",
  "license": "MIT",
  "keywords": [
    "galaxy",
    "bioinformatics",
    "skills",
    "collections",
    "user-defined-tools"
  ],
  "skills": [
    "./skills/galaxy-integration/jupyterlite"
  ]
}

For maintainers

If you maintain this plugin, link to this source-backed listing from your README so users can review its manifest and indexed components.

[galaxy-skills on Agent Plugins Marketplace](https://pluginsmp.com/plugins/galaxy-skills)