Genefoundry MCP server

genefoundry-router

A thin FastMCP 3.x aggregator that federates the GeneFoundry -link MCP fleet behind a single Streamable-HTTP endpoint. A host adds one server — genefoundry — and gets every biomedical backend with collision-free naming and search-based discovery.

[!IMPORTANT]

Research use only. Not clinical decision support. Do not use for diagnosis,

treatment, triage, or patient management.

Why

An MCP host that mounted all 21 backends directly would face a wall of several hundred tools — more than a model can reason over, and a guarantee of name collisions. The router collapses that into one endpoint and replaces the flat catalog with a search surface, so a model finds the right tool by intent instead of by scrolling.

It is a client to each backend and a server to hosts: it namespaces and shapes the surface, but never rewrites a backend's data. The caller's token is never forwarded upstream.

Quick start

The fleet is hosted — no install required:

claude mcp add --transport http genefoundry https://genefoundry.org/mcp

Health check: genefoundry.org/health.

To run your own against the live fleet (Python 3.12+, uv):

uv sync --group dev
cp .env.example .env                    # set GF_*_URL backend URLs and GF_AUTH_MODE
uv run genefoundry-router run --host 127.0.0.1 --port 8000
curl -s localhost:8000/health | python -m json.tool

An offline fake fleet (make dev-fleet + make run-dev, or one-shot make test-e2e) runs the real router against impersonated backends over real Streamable-HTTP — no Docker, no network.

Tools

The router does not surface the federated catalog flat. A model sees three things:

search_tools(query="splicing prediction")   # → spliceai_predict_splicing (+ schema)
call_tool(name="spliceai_predict_splicing", arguments={...})

Pinning makes each domain's canonical tool reachable deterministically rather than by relevance luck. See How discovery works — including the two traps that bite MCP clients.

Federated backends

<!-- BEGIN GENERATED: fleet-inventory --> 22 backends, 285 tools, each surfaced namespaced — e.g. gnomadsearchgenes.

Shortened. The full README is on GitHub.