Execute bioinformatics tools and manage workflows on a Galaxy instance via API. For developers integrating Galaxy automation into AI agents or building programmatic analysis pipelines.
io.github.galaxyproject/galaxy-mcp
Local install
STDIO
2 required env vars
How models use it and what it is built for.
Execute bioinformatics tools and manage workflows on a Galaxy instance via API. For developers integrating Galaxy automation into AI agents or building programmatic analysis pipelines.
Local install — runs as a subprocess.
Configuration this server reads at startup.
URL of the Galaxy instance to connect to (e.g., https://usegalaxy.org)
API key for authenticating with the Galaxy instance
Where to find authoritative docs and source for Galaxy.
Paste any of these into Agent Studio after connecting Galaxy.
Common questions about connecting and running Galaxy.
What Galaxy instance can I connect to?
Any Galaxy instance you have network access to and valid credentials for. Set GALAXY_URL to your instance URL (e.g., https://usegalaxy.org) and provide a GALAXY_API_KEY for authentication.
How do I get a Galaxy API key?
Log into your Galaxy instance, go to User > Preferences > Manage API Key, and generate a new key. Store it securely and pass it to the MCP server via the GALAXY_API_KEY environment variable.
Can I run existing Galaxy workflows?
Yes. The server can execute tools and manage workflows on your Galaxy instance. Refer to the Galaxy API documentation for workflow invocation details and supported parameters.
What bioinformatics tools are available?
Any tool installed in your Galaxy instance is available. Common tools include FastQC, BWA, GATK, and thousands of others from the Galaxy ToolShed. Use the server to list tools dynamically.
Do I need to install Galaxy locally?
No. You connect to an existing Galaxy instance via its URL and API key. The MCP server communicates remotely—no local Galaxy installation required.
MCP Playground runs 10,000+ hosted MCP servers — GitHub, Linear, Notion, Stripe, Sentry and more — across Claude, GPT, Gemini, DeepSeek and 60+ AI models. Compare model answers side-by-side, save agent presets, share runs. Zero install.
Open Agent StudioJudges Panel
45 judges that evaluate AI-generated code for security, cost, and quality with built-in AST.
Addozhang Nexus
Query Sonatype Nexus Repository (OSS/Pro) for Maven, Python, and Docker artifacts
Cyanheads MCP Ts Template
TypeScript template for building MCP servers with declarative tooling, observability, and auth.
Chernistry Bernstein
Declarative agent orchestration for engineering teams