该项目提供了一个模型上下文协议（MCP）服务器，用于与 Galaxy 生物信息学平台交互。它使 AI 助手和其他客户端能够连接到 Galaxy 实例，搜索和执行工具，管理工作流程，并访问 Galaxy 生态系统的其他功能。

项目概述

该仓库包含两个独立实现的同一个银河操作集，以及 让他们步调一致的契约：

• python/ —— Python MCP 服务器，发布给 PyPI 的编号为 galaxy-mcp。它 通过BioBlend到达银河。参见Python的README。
• typescript/ —— 发布给 NPM 的 PNPM 工作区 @galaxyproject/galaxy-ops、galaxy-cli 和 galaxy-mcp：一个无框架的核心 （[galaxy-ops）并配有命令行和一个stdio MCP服务器。参见 TypeScript README。
• contract/ ——两者都被束缚：蟒蛇表面显现，金色 结果通过两者重播，银河内置服务器的快照，以及 已知差异登记处。详见合同README。

两者旨在保持一致：一个操作保持其名称和意义 两者都是。不过它们仍然是独立的代码库，各自发布了不同的列车，所以每个版本

Galaxy MCP Server

This project provides a Model Context Protocol (MCP) server for interacting with the Galaxy bioinformatics platform. It enables AI assistants and other clients to connect to Galaxy instances, search and execute tools, manage workflows, and access other features of the Galaxy ecosystem.

Project Overview

The repository holds two independent implementations of the same Galaxy operation set, and the contract that keeps them in step:

• python/ – the Python MCP server, published to PyPI as galaxy-mcp. It reaches Galaxy through BioBlend. See the Python README.
• typescript/ – a pnpm workspace published to npm as @galaxyproject/galaxy-ops, galaxy-cli and galaxy-mcp: one framework-free core (galaxy-ops) with a command line and a stdio MCP server on top. See the TypeScript README.
• contract/ – what both are held to: the Python surface manifest, golden results replayed through both, the snapshot of Galaxy’s built-in server, and the registry of known differences. See the contract README.

The two are meant to stay in step: an operation keeps its name and its meaning across both. They are still separate codebases with separate release trains, though, so each README lists the operations that surface actually has – read the one you are using.

ROADMAP.md explains why there are two implementations, how they relate to Galaxy’s built-in MCP server, and what comes next. PARITY.md is the generated, CI-checked record of where they differ.

Key Features

• Galaxy Connection: Connect to any Galaxy instance with a URL and API key
• OAuth Login (optional): Offer browser-based sign-in that exchanges credentials for temporary Galaxy API keys
• Server Information: Retrieve comprehensive server details including version, configuration, and capabilities
• Tools Management: Search the tool catalog, inspect a tool’s inputs, and execute Galaxy tools
• User-Defined Tools: Create, list, run, and deactivate unprivileged user-defined tools
• Workflow Integration: Find and import workflows from the Intergalactic Workflow Commission (IWC), then invoke them and follow their invocations
• History Operations: Manage Galaxy histories, datasets, and collections, and inspect the jobs behind them
• File Management: Upload files to Galaxy from local storage or from a URL, and download results back
• Pages: Read and write Galaxy-flavored markdown pages – history-attached notebooks and standalone reports – including their revision history
• Verified Container Recommendation (optional): Resolve a real quay.io/biocontainers image for a set of conda packages instead of guessing one – see Optional extras