MCP Server: Galaxy Tool Utilities

This project provides an MCP (Model Context Protocol) server that exposes utilities for working with Galaxy tool XML files.

Features (More Coming Soon)

• Validate Galaxy Tool XML: Check if a Galaxy tool XML file is valid according to the official schema.
• Generate Basic Template: Instantly create a boilerplate Galaxy tool XML file.

Requirements

• Python 3.8+
• uv (for running the server, or use your preferred Python environment)
• Cline (or any MCP-compatible agent)

Installation

1. Clone this repository:

   git clone https://github.com/yourusername/mcp-server-galaxy-tool.git
   cd mcp-server-galaxy-tool
   

2. Install dependencies:

   uv sync
   

Configuring the MCP Server in Cline

To use this MCP server with Cline in VSCode, add it to your Cline MCP configuration. Here’s how:

1. Install Cline in VSCode by searching for it in the Extensions marketplace and installing it.

2. Follow the Cline documentation to add a new server entry. Here is an example MCP servers config:

   {
     "mcpServers": {
       "Galaxy Tools": {
         "disabled": false,
         "timeout": 60,
         "command": "<path to your uv>",
         "args": [
           "--directory",
           "</path/to/this/repo/mcp-server-galaxy-tool>",
           "run",
           "main.py"
         ],
         "transportType": "stdio"
       }
     }
   }
   

• Make sure the command and workingDirectory match your local setup.
• Save the file and restart Cline if necessary.

Usage

Once the server is running and configured in Cline, you can try this example in Cline:

Create a Galaxy tool that uses PyCaret to perform regression on tabular data.

Project Structure

• main.py — MCP server entry point
• galaxy.xsd — Official Galaxy tool XML schema
• pyproject.toml — Python project configuration
• README.md — This documentation

License

MIT License

Acknowledgments

• Galaxy Project
• Model Context Protocol (MCP)
• Cline