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galaxyprojectgalaxyprojectOfficial·1 Agent Skills Included

galaxy-mcp

Connect, run, and manage Galaxy bioinformatics workflows

Connects to any Galaxy bioinformatics server to search tools, run analyses, and manage workflows. Handles histories, datasets, and file uploads without manual clicking through the Galaxy web interface. Imports ready-made workflows from the IWC catalog and supports secure OAuth login for shared servers. Lets researchers complete genomics and data analysis tasks through simple natural language requests.
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npx skills add galaxyproject/galaxy-mcp --all -g -y

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release

Bump version, build artifacts, and publish galaxy-mcp to PyPI.

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Frequently Asked Questions

FAQPage Schema
How to install galaxy-mcp?▼

Run `npx skills add galaxyproject/galaxy-mcp --all -g -y` in your terminal to install all skills in this repository globally.

What does galaxy-mcp do?▼

It connects your AI client to the Galaxy bioinformatics platform so you can search tools, execute analyses, manage histories, and run workflows using plain language.

How do I connect galaxy-mcp to my Galaxy server?▼

Set the GALAXY_URL and GALAXY_API_KEY environment variables, or use the built-in OAuth login flow for browser-based sign-in with temporary credentials.

Does galaxy-mcp work with Claude Desktop?▼

Yes. Add it to your Claude Desktop config as an MCP server with your Galaxy URL and API key, then ask Claude to connect to Galaxy.

Can I run Galaxy workflows without using the web interface?▼

Yes. You can import workflows from the IWC catalog, upload files, and execute full analyses directly through conversational requests.

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