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The Claude Agent SDK supports MCP servers natively. Pass Runlayer MCP servers to query() and allow their tools with allowedTools.

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Installation

npm install @anthropic-ai/claude-agent-sdk
Set your Anthropic API key: 
export ANTHROPIC_API_KEY=your-anthropic-key

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HTTP Transport (Production)

Use HTTP transport for production deployments with remote MCP servers: 
import { query } from "@anthropic-ai/claude-agent-sdk";

for await (const message of query({
  prompt: "Get info about the vercel/ai repository",
  options: {
    mcpServers: {
      github: {
        type: "http",
        url: "https://mcp.runlayer.com/github-a1b2c3/mcp",
        headers: {
          "x-runlayer-api-key": process.env.RUNLAYER_API_KEY!
        }
      }
    },
    allowedTools: ["mcp__github__*"]
  }
})) {
  if (message.type === "result" && message.subtype === "success") {
    console.log(message.result);
  }
}
The server key sets the tool prefix. A server named github exposes tools as mcp__github__<tool>, so mcp__github__* allows all tools from that server.

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Python Example

The Python SDK uses the same mcp_servers and allowed_tools shape: 
import asyncio
import os
from claude_agent_sdk import ClaudeAgentOptions, ResultMessage, query


async def main():
    options = ClaudeAgentOptions(
        mcp_servers={
            "github": {
                "type": "http",
                "url": "https://mcp.runlayer.com/github-a1b2c3/mcp",
                "headers": {"x-runlayer-api-key": os.environ["RUNLAYER_API_KEY"]},
            }
        },
        allowed_tools=["mcp__github__*"],
    )

    async for message in query(
        prompt="Get info about the vercel/ai repository",
        options=options,
    ):
        if isinstance(message, ResultMessage) and message.subtype == "success":
            print(message.result)


asyncio.run(main())

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Multiple MCP Servers

Add each server to mcpServers and allow each server’s tools: 
import { query } from "@anthropic-ai/claude-agent-sdk";

for await (const message of query({
  prompt: "Create a GitHub issue and a Linear ticket for the bug report",
  options: {
    mcpServers: {
      github: {
        type: "http",
        url: "https://mcp.runlayer.com/github-a1b2c3/mcp",
        headers: { "x-runlayer-api-key": process.env.RUNLAYER_API_KEY! }
      },
      linear: {
        type: "http",
        url: "https://mcp.runlayer.com/linear-d4e5f6/mcp",
        headers: { "x-runlayer-api-key": process.env.RUNLAYER_API_KEY! }
      }
    },
    allowedTools: ["mcp__github__*", "mcp__linear__*"]
  }
})) {
  if (message.type === "result" && message.subtype === "success") {
    console.log(message.result);
  }
}

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Agent Accounts

Use Agent Accounts when your Claude app should authenticate as an agent, not a user API key. Fetch an M2M token, then pass it to Runlayer’s MCP proxy: 
import { query } from "@anthropic-ai/claude-agent-sdk";

const tokenResponse = await fetch(`${process.env.RUNLAYER_URL}/api/v1/oauth/token`, {
  method: "POST",
  headers: { "Content-Type": "application/x-www-form-urlencoded" },
  body: new URLSearchParams({
    grant_type: "client_credentials",
    client_id: process.env.RUNLAYER_CLIENT_ID!,
    client_secret: process.env.RUNLAYER_CLIENT_SECRET!
  })
});

const { access_token: accessToken } = await tokenResponse.json();

for await (const message of query({
  prompt: "List recent GitHub issues",
  options: {
    mcpServers: {
      github: {
        type: "http",
        url: `${process.env.RUNLAYER_URL}/api/v1/proxy/${process.env.SERVER_ID}/mcp`,
        headers: { Authorization: `Bearer ${accessToken}` }
      }
    },
    allowedTools: ["mcp__github__*"]
  }
})) {
  if (message.type === "result" && message.subtype === "success") {
    console.log(message.result);
  }
}
For on-behalf-of user calls, pass the delegated user’s email as subject_token: 
body: new URLSearchParams({
  grant_type: "client_credentials",
  client_id: process.env.RUNLAYER_CLIENT_ID!,
  client_secret: process.env.RUNLAYER_CLIENT_SECRET!,
  subject_token: userEmail,
  subject_token_type: "urn:runlayer:token-type:user-email"
})
See Agent Account Authentication Recipes for UUID and WorkOS OBO variants.

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