This is a space for depositing various helpful artifacts (skills, commands, etc.) for various agentic things like Claude Code or Gemini Code Agent. The idea is that by iterating over this we will create a robust set of community curated "skills" that would ultimately create guardrails preventing LLMs from doing crazy 💩 and ensuring best practices. Should probably be called Intergalactic LLM-taming commision (ILT).
This was not written by Claude.
this is complementary to https://github.com/galaxyproject/galaxy-mcp
Skills are structured instructions that help AI agents work effectively with Galaxy development. They provide:
- Best practices - The right way to build Galaxy tools, workflows, and content
- Patterns - Common solutions to common problems
- Examples - Concrete references to learn from
- Guardrails - Preventing common mistakes
Important: This repo is for developers building Galaxy infrastructure. End-user analysis should happen in Galaxy itself to leverage its reproducibility and tracking features.
| Repository | Purpose | Use For |
|---|---|---|
| skills (this repo) | Knowledge - How to build things well | Tool development, workflow conversion, content creation |
| galaxy-mcp | Capabilities - Interact with Galaxy programmatically | Testing, automation, CI/CD |
Use both together for best results.
Skills are automatically available. Just clone this repo into your workspace or add to .claude/skills/:
# Personal skills (available in all projects)
cd ~/.claude/skills
git clone https://github.com/galaxyproject/skills galaxy
# Project skills (specific to one project)
cd your-project/.claude/skills
git clone https://github.com/galaxyproject/skills galaxyClaude will automatically discover and use skills when relevant.
# Install openskills
npm i -g openskills
# Install Galaxy skills
openskills install galaxyproject/skills
# Load a specific skill when needed
openskills read tool-updatesClone this repo into your workspace and reference skills in your prompts:
git clone https://github.com/galaxyproject/skillsThe LLM can read skill files directly from the workspace.
tool-dev ✅
Create and update Galaxy tool wrappers.
- Comprehensive SKILL.md covering tool creation, testing, IUC review, and updates
- references/ - Standalone testing and tool placement guides (also used by other skills)
- tool-selection-diagram/ - Generate "which tool?" flowchart PNGs for multi-tool suites
udt-authoring ✅
Author Galaxy User-Defined Tools (UDTs) — the class: GalaxyUserTool YAML format a non-admin user creates and runs (distinct from classic XML/ToolShed wrappers).
- SKILL.md with the authoring loop and offline/server validation tiers
- references/ - UserToolSource schema,
$(...)templating, common mistakes checklist - scripts/validate.py - offline validate + lint via galaxy-tool-util
- examples/ - seven complete UDTs, simple to complex
hub-news-posts ✅
Write news posts for the Galaxy Project website (galaxyproject.org).
- Frontmatter templates
- Image handling
- Vega charts
- Styled tables
nf-to-galaxy ✅
Convert Nextflow processes and workflows to Galaxy tools and workflows.
- Process → Tool XML
- Container → bioconda mapping
- Workflow → .ga files
- Test with planemo and galaxy-mcp
galaxy-integration ✅
Interact with Galaxy instances via MCP, JupyterLite, or BioBlend.
- jupyterlite/ - Write notebooks using gxy package
- mcp-reference/ - Complete MCP tools reference
- Tool checking and workflow testing examples
- BioBlend automation scripts
update-usegalaxy-tool ✅
Add or update ToolShed tool revisions in the usegalaxy-tools repository.
- Resolve changeset revisions via ToolShed API
- Edit
.yml/.yml.locktoolset files - Handle adds, updates, moves, and removals across sections
- Lint with
fix_lockfile.py
collection-manipulation ✅
Transform Galaxy dataset collections reproducibly using native tools.
- Filter, sort, relabel, merge, flatten, nest collections
- 26 collection operation tools
- Apply Rules DSL for complex restructuring
- API patterns and pitfall avoidance
skills/
├── README.md # This file
├── CONTRIBUTING.md # How to add new skills
├── AGENTS.md # Agent routing instructions
│
├── tool-dev/ # ✅ Galaxy tool development
│ ├── SKILL.md # Comprehensive tool dev reference
│ ├── references/ # Testing, tool placement guides
│ └── tool-selection-diagram/ # Flowchart diagram generator for multi-tool suites
│
├── udt-authoring/ # ✅ Author User-Defined Tools (GalaxyUserTool YAML)
│ ├── SKILL.md # Authoring loop + validation tiers
│ ├── references/ # Schema, templating, common mistakes
│ ├── scripts/ # validate.py (offline validate + lint)
│ └── examples/ # Seven complete UDTs
│
├── hub-news-posts/ # ✅ Galaxy Hub posts
│
├── nf-to-galaxy/ # ✅ Nextflow → Galaxy conversion
│
├── galaxy-integration/ # ✅ Galaxy instance integration
│ ├── jupyterlite/ # JupyterLite notebooks (gxy package)
│ └── mcp-reference/ # MCP tools reference
│
├── update-usegalaxy-tool/ # ✅ UseGalaxy tool management
│ ├── SKILL.md # Main command (add/update ToolShed revisions)
│ └── references/ # YAML file formats, ToolShed API, lint script
│
└── collection-manipulation/ # ✅ Collection transformations
├── SKILL.md # Main command (filter, sort, restructure, etc.)
└── references/ # Tools catalog, Apply Rules DSL, API, tests
We welcome contributions! See CONTRIBUTING.md for:
- How to create a new skill
- Skill structure and format
- Testing and validation
- Submission guidelines
User: "Update the ncbi-datasets tool to version 18.13.0"
AI: [Loads tool-updates skill]
[Follows workflow: research upstream → update version → fix bugs → test]
[Uses planemo for validation]
User: "Convert this Nextflow process to a Galaxy tool"
AI: [Loads nf-to-galaxy skill]
[Maps container → bioconda package]
[Generates Galaxy tool XML]
[Tests with planemo lint]
[Optionally tests on Galaxy instance via galaxy-mcp]
- galaxy-mcp - MCP server for Galaxy interaction
- planemo - Galaxy tool development toolkit
- Galaxy - Main Galaxy platform
- IWC - Intergalactic Workflow Commission