AgentSkillsCN

galaxy-integration

Galaxy MCP、JupyterLite笔记本以及BioBlend自动化流程的路由工具。

SKILL.md
--- frontmatter
name: galaxy-integration
description: Router for Galaxy MCP, JupyterLite notebooks, and BioBlend automation
user_invocable: true

Galaxy Integration Skill

Use Galaxy MCP and BioBlend-based scripts to interact with a Galaxy instance for tool discovery, workflow validation, and workflow testing.

Sub-Skills

Route to the appropriate sub-skill based on task:

TaskSub-SkillLocation
Write JupyterLite notebookjupyterlite-galaxyjupyterlite/SKILL.md
MCP tools referencegalaxy-mcp-referencemcp-reference/SKILL.md
History/dataset access-mcp-reference/history-access.md
Common gotchas-mcp-reference/gotchas.md
BioBlend batch scripts-scripts/galaxy_tool_checker.py
Tool checking examples-examples/tool-checking.md
Workflow testing examples-examples/workflow-testing.md

When to Use

  • •Query tools installed on a Galaxy instance
  • •Inspect tool I/O and parameters
  • •Create histories, upload data, run tools/workflows
  • •Debug workflow/tool issues with fast, interactive feedback
  • •Write JupyterLite notebooks that interact with Galaxy datasets

Prerequisites

Galaxy URL

The base URL of the Galaxy server:

  • •https://usegalaxy.org/
  • •https://usegalaxy.eu/
  • •http://localhost:8080/

Galaxy API Key

In Galaxy UI: User -> Preferences -> Manage API Key

Repository .env (recommended)

bash
cp .env.example .env
nano .env

Set:

bash
GALAXY_URL=https://usegalaxy.org/
GALAXY_API_KEY=your_actual_api_key_here

When to Use MCP vs Scripts

Galaxy MCP when:

  • •Interactive exploration (find a tool, inspect exact tool IDs)
  • •Debugging a workflow with fast iteration

BioBlend script (scripts/galaxy_tool_checker.py) when:

  • •Batch checks across many tools
  • •Repeatable validation/testing as part of CI-like flow

Core MCP Workflow

  1. •

    Confirm MCP connectivity

    • •If not connected, see README.md for configuration
  2. •

    Tool discovery

    code
    search_tools_by_name(query=...)
get_tool_details(tool_id=..., io_details=True)
  3. •

    Workflow testing loop

    code
    create_history(history_name=...)
invoke_workflow(workflow_id=..., inputs=..., history_id=...)
get_history_contents(history_id=...)
# Fix and repeat

Output Expectations

When reporting MCP results:

  • •Provide full Galaxy tool ID (ToolShed-style)
  • •Include tool version
  • •Note whether tool is installed vs only available in repository

References