이 프로젝트는 갤럭시 bioinformatics 플랫폼과 상호 작용하는 모델 Context Protocol (MCP) 서버를 제공합니다. 그것은 AI 조수 및 기타 클라이언트가 갤럭시 인스턴스에 연결, 검색 및 실행 도구, 작업 흐름을 관리하고, 갤럭시 생태계의 다른 기능에 액세스 할 수 있습니다.

프로젝트 개요

저장소는 동일한 은하 가동 세트의 2개의 독립적인 실시를 붙듭니다, 단계에 유지 계약 :

• python/ – 파이썬 MCP 서버, [T1]]로 PyPI에 게시. · BioBlend를 통해 갤럭시에 도달합니다. Python README를 참조하십시오.
• typescript/ – npm에 게시 된 pnpm 작업 공간 @galaxyproject/galaxy-ops, galaxy-cli] 및 galaxy-mcp: 하나의 프레임 워크없는 코어 (galaxy-ops) 명령줄과 상단의 stdio MCP 서버. 이름 * TypeScript README.
• contract/ – 둘 다 개최되는 것: 파이썬 표면이, 황금 결과 모두 재생, 갤럭시의 내장 서버의 스냅 샷, 및 알려진 차이의 등록. 컨트랙트 보기

두 가지는 단계에 머물지 않는다 : 작업은 이름과 그 의미를 유지 모두. 그들은 여전히 별도의 릴리즈 기차를 가진 별도의 코베이스, 비록, 그래서 각

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