Rotifer Protocol MCP

@rotifer/mcp-server

Build, compose, and run AI agents — directly from your IDE.

Search genes, create agents with composable genomes, run pipelines in a WASM sandbox, and compete in the Arena. Zero config. Works with Cursor, Claude Desktop, Windsurf, and any MCP-compatible client.

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Quick Start

Cursor

Add to .cursor/mcp.json:

{

"mcpServers": { "rotifer": { "command": "npx", "args": ["@rotifer/mcp-server"] } } }

Claude Desktop

Add to claude_desktop_config.json:

{

"mcpServers": { "rotifer": { "command": "npx", "args": ["@rotifer/mcp-server"] } } }

Windsurf / Other MCP Clients

Use the same npx command — any client that supports MCP stdio transport will work.

What Can It Do?

Create and run an agent in one conversation

You: "Build me an agent for code security scanning"

AI: → create_agent({ agent_name: "sec-bot", gene_ids: ["security-scanner", "genesis-code-format"], composition: "Seq" }) Agent 'sec-bot' created with 2-gene Seq genome.

You: "Run it on my project" AI: → agent_run({ agent_name: "sec-bot", input: "{\"path\":\"./src\"}" }) Pipeline complete — 3 findings, 0 critical.

Search, compare, and compose genes

You: "Find the best gene for web search"

AI: → search_genes({ query: "web search" }) Found 8 genes. Top match: genesis-web-search (F(g) = 0.87, Native)

You: "Compare it against the lite version" AI: → compare_genes({ gene_ids: ["...", "..."] }) Side-by-side: success rate, latency, fitness breakdown

Full gene lifecycle from your IDE

You: "Wrap my function as a gene"

AI: → wrap_gene({ gene_name: "my-search", domain: "search.web", fidelity: "Wrapped" }) → compile_gene({ gene_name: "my-search" }) → test_gene({ gene_name: "my-search", compliance: true }) → publish_gene({ gene_name: "my-search", changelog: "Initial release" })

Tools (31)

Discovery & Analytics

Local Workspace

Gene Lifecycle

Agent Composition

Authentication & Analytics

Resources (7)

MCP Resources let AI clients reference Rotifer data as context:

Each resource returns what the tool of the same job returns, so a declared tool set covers both: with --tools=evolve, rotifer://genes/{gene_id}/stats, rotifer://developers/{username} and rotifer://leaderboard disappear from the listing and are refused if read directly, because get_gene_stats, get_developer_profile and get_leaderboard were not asked for. rotifer://version always answers — it is the server describing itself, not a capability. Before 0.16.0 these were reachable whatever the tool set said.

Prompts (4)

MCP Prompts give AI clients guided workflows for common tasks:

Try asking your AI: *"Use the rotifer-hello prompt to build me an agent"* or *"Use rotifer-architect to design an agent for document Q&A"*.

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Architecture

┌─────────────────────────────────────────────────┐

│ AI IDE (Cursor / Claude / Windsurf) │ │ │ │ "Find genes for code formatting" │ │ │ │ │ ▼ │ │ ┌─────────────────────┐ │ │ │ MCP Client │ │ │ │ (stdio transport) │ │ │ └────────┬────────────┘ │ └───────────┼─────────────────────────────────────┘ │ MCP Protocol ▼ ┌─────────────────────────────────────────────────┐ │ @rotifer/mcp-server │ │ │ │ 31 Tools 7 Resources 4 Prompts Local Scanner│ │ ┌──────────┐ ┌───────────┐ ┌────────────┐ │ │ │ discover │ │rotifer:// │ │ ./genes/ │ │ │ │ lifecycle│ │genes/stats│ │ phenotype │ │ │ │ agents │ │developers │ │ agents │ │ │ │ auth │ │leaderboard│ └────────────┘ │ │ └────┬─────┘ └─────┬─────┘ │ │ └───────┼──────────────┼────────────────┼─────────┘ │ │ │ ▼ ▼ ▼ ┌─────────────────────────────────────────────────┐ │ Rotifer Cloud API Local File System │ │ (Supabase) (genes/, .rotifer/) │ └─────────────────────────────────────────────────┘

Configuration

Zero-config by default — connects to the public Rotifer Cloud API.

To use a custom endpoint, create ~/.rotifer/cloud.json:

{

"endpoint": "https://your-supabase-instance.supabase.co", "anonKey": "your-anon-key" }

Or set environment variables:

ROTIFER_CLOUD_ENDPOINT=https://your-instance.supabase.co

ROTIFER_CLOUD_ANON_KEY=your-anon-key

Choosing which tools to expose

All thirty-one tools are available by default. ROTIFER_MCP_TOOLS narrows that to what a given integration actually needs — useful when the server is attached to an assistant that should not be able to publish or log in on your behalf:

npx @rotifer/mcp-server --tools=evolve          # the rank-and-swap preset (10 tools)

npx @rotifer/mcp-server --tools=readonly # nothing that writes (14 tools) ROTIFER_MCP_TOOLS=search_genes,get_gene_detail # an exact list ROTIFER_MCP_TOOLS=evolve,vg_scan # a preset plus one

A name that is neither a preset nor a tool here is ignored, with a note on stderr. If none of the names are, the server does not start: it lists the presets and exits with code 2, rather than running with no tools at all.

The flag and the variable do the same thing, and the flag wins if both are set. Both exist because callers differ in what they can reach: a shell user sets the variable, while something launching this server from a manifest controls only the command line.

A declared set covers the whole surface, not just tools/list. Tools outside it are refused when called by name; resources that duplicate an excluded tool are dropped from the listing and refused when read; and the sandbox escape hatches below stay off unless separately declared. A restriction with an unlisted way around it is not a restriction.

Tools outside the set disappear from listTools and are refused if called anyway. The refusal says how to add the tool back and, where one exists, the rotifer CLI command that does the same job — so a narrowed set is a boundary you can see and cross deliberately, not a dead end.

Leave it unset and nothing changes.

Switching off the sandbox

agent_run and run_gene take no_sandbox, and run_gene also takes trust_unsigned — options that run Gene code as plain Node.js instead of inside the WASM sandbox. Narrowing the tool set would mean little if a tool inside the narrowed set could still do that, so these are refused unless declared at launch:

npx @rotifer/mcp-server --allow=no-sandbox