What is Mcp Server Galaxy Tool

mcp-server-galaxy-tool is an MCP server designed to provide utilities for generating and validating Galaxy tool XML files, which are essential for integrating tools into the Galaxy platform.

Use cases

Use cases include creating Galaxy tools for data processing, integrating machine learning models into Galaxy workflows, and validating existing Galaxy tool XML files.

How to use

To use mcp-server-galaxy-tool, clone the repository, install the required dependencies, and configure the server in Cline. Once set up, you can run the server and create Galaxy tools using the provided commands.

Key features

Key features include validating Galaxy tool XML files against the official schema and generating basic template XML files for Galaxy tools.

Where to use

mcp-server-galaxy-tool is primarily used in bioinformatics and computational biology, where Galaxy is a popular platform for data analysis and workflow management.

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