goeckslab/mcp-server-galaxy-tool
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This project provides an MCP server that exposes utilities for working with Galaxy tool XML files.
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
-
Clone this repository:
git clone https://github.com/yourusername/mcp-server-galaxy-tool.git cd mcp-server-galaxy-tool -
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:
-
Install Cline in VSCode by searching for it in the Extensions marketplace and installing it.
-
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
commandandworkingDirectorymatch 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 pointgalaxy.xsd— Official Galaxy tool XML schemapyproject.toml— Python project configurationREADME.md— This documentation
License
MIT License
