How to integrate Fly MCP with LlamaIndex

This guide walks you through connecting Fly to LlamaIndex using the Composio tool router. By the end, you'll have a working Fly agent that can deploy latest image to fly in tokyo, list all running fly apps by region, scale up your fly app to 3 instances through natural language commands. This guide will help you understand how to give your LlamaIndex agent real control over a Fly account through Composio's Fly MCP server. Before we dive in, let's take a quick look at the key ideas and tools involved.

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Introduction

This guide walks you through connecting Fly to LlamaIndex using the Composio tool router. By the end, you'll have a working Fly agent that can deploy latest image to fly in tokyo, list all running fly apps by region, scale up your fly app to 3 instances through natural language commands.

This guide will help you understand how to give your LlamaIndex agent real control over a Fly account through Composio's Fly MCP server.

Before we dive in, let's take a quick look at the key ideas and tools involved.

Also integrate Fly with

TL;DR

Here's what you'll learn:
  • Set your OpenAI and Composio API keys
  • Install LlamaIndex and Composio packages
  • Create a Composio Tool Router session for Fly
  • Connect LlamaIndex to the Fly MCP server
  • Build a Fly-powered agent using LlamaIndex
  • Interact with Fly through natural language

What is LlamaIndex?

LlamaIndex is a data framework for building LLM applications. It provides tools for connecting LLMs to external data sources and services through agents and tools.

Key features include:

  • ReAct Agent: Reasoning and acting pattern for tool-using agents
  • MCP Tools: Native support for Model Context Protocol
  • Context Management: Maintain conversation context across interactions
  • Async Support: Built for async/await patterns

What is the Fly MCP server, and what's possible with it?

The Fly MCP server is an implementation of the Model Context Protocol that connects your AI agent and assistants like Claude, Cursor, etc directly to your Fly account. It provides structured and secure access so your agent can perform Fly operations on your behalf.

What is the Composio tool router, and how does it fit here?

What is Composio SDK?

Composio's Composio SDK helps agents find the right tools for a task at runtime. You can plug in multiple toolkits (like Gmail, HubSpot, and GitHub), and the agent will identify the relevant app and action to complete multi-step workflows. This can reduce token usage and improve the reliability of tool calls. Read more here: Getting started with Composio SDK

The tool router generates a secure MCP URL that your agents can access to perform actions.

How the Composio SDK works

The Composio SDK follows a three-phase workflow:

  1. Discovery: Searches for tools matching your task and returns relevant toolkits with their details.
  2. Authentication: Checks for active connections. If missing, creates an auth config and returns a connection URL via Auth Link.
  3. Execution: Executes the action using the authenticated connection.

Step-by-step Guide

Step by step10 STEPS
1

Prerequisites

Before you begin, make sure you have:
  • Python 3.8/Node 16 or higher installed
  • A Composio account with the API key
  • An OpenAI API key
  • A Fly account and project
  • Basic familiarity with async Python/Typescript
2

Getting API Keys for OpenAI, Composio, and Fly

OpenAI API key (OPENAI_API_KEY)
  • Go to the OpenAI dashboard
  • Create an API key if you don't have one
  • Assign it to OPENAI_API_KEY in .env
Composio API key and user ID
  • Log into the Composio dashboard
  • Copy your API key from Settings
    • Use this as COMPOSIO_API_KEY
  • Pick a stable user identifier (email or ID)
    • Use this as COMPOSIO_USER_ID
3

Installing dependencies

npm install @composio/llamaindex @llamaindex/openai @llamaindex/tools @llamaindex/workflow dotenv

Create a new Typescript project and install the necessary dependencies:

  • @composio/llamaindex: Composio's LlamaIndex integration
  • @llamaindex/openai: OpenAI LLM integration
  • @llamaindex/tools: MCP client for LlamaIndex
  • @llamaindex/workflow: Workflow framework for LlamaIndex
  • dotenv: Environment variable management
4

Set environment variables

bash
OPENAI_API_KEY=your-openai-api-key
COMPOSIO_API_KEY=your-composio-api-key
COMPOSIO_USER_ID=your-user-id

Create a .env file in your project root:

These credentials will be used to:

  • Authenticate with OpenAI's GPT-5 model
  • Connect to Composio's Tool Router
  • Identify your Composio user session for Fly access
5

Import modules

import "dotenv/config";
import readline from "node:readline/promises";
import { stdin as input, stdout as output } from "node:process";

import { Composio } from "@composio/core";

import { mcp } from "@llamaindex/tools";
import { agent as createAgent } from "@llamaindex/workflow";
import { openai } from "@llamaindex/openai";

dotenv.config();

Create a new file called fly_llamaindex_agent.ts and import the required modules:

Key imports:

  • dotenv.config loads .env at runtime
  • readline gives us a simple CLI chat loop
  • Composio is the main Composio SDK client
  • mcp connects to an MCP endpoint
  • createAgent builds a LlamaIndex agent
  • openai configures the LLM backend
6

Load environment variables and initialize Composio

const OPENAI_API_KEY = process.env.OPENAI_API_KEY;
const COMPOSIO_API_KEY = process.env.COMPOSIO_API_KEY;
const COMPOSIO_USER_ID = process.env.COMPOSIO_USER_ID;

if (!OPENAI_API_KEY) throw new Error("OPENAI_API_KEY is not set");
if (!COMPOSIO_API_KEY) throw new Error("COMPOSIO_API_KEY is not set");
if (!COMPOSIO_USER_ID) throw new Error("COMPOSIO_USER_ID is not set");

What's happening:

This ensures missing credentials cause early, clear errors before the agent attempts to initialise.

7

Create a Tool Router session and build the agent function

async function buildAgent() {

  console.log(`Initializing Composio client...${COMPOSIO_USER_ID!}...`);
  console.log(`COMPOSIO_USER_ID: ${COMPOSIO_USER_ID!}...`);

  const composio = new Composio({
    apiKey: COMPOSIO_API_KEY,
    provider: new LlamaindexProvider(),
  });

  const session = await composio.create(
    COMPOSIO_USER_ID!,
    {
      toolkits: ["fly"],
    },
  );

  const mcpUrl = session.mcp.url;
  console.log(`Composio Tool Router MCP URL: ${mcpUrl}`);

  const server = mcp({
    url: mcpUrl,
    clientName: "composio_tool_router_with_llamaindex",
    requestInit: {
      headers: {
        "x-api-key": COMPOSIO_API_KEY!,
      },
    },
    // verbose: true,
  });

  const tools = await server.tools();

  const llm = openai({ apiKey: OPENAI_API_KEY, model: "gpt-5" });

  const agent = createAgent({
    name: "composio_tool_router_with_llamaindex",
        description : "An agent that uses Composio Tool Router MCP tools to perform actions.",
    systemPrompt:
      "You are a helpful assistant connected to Composio Tool Router."+
"Use the available tools to answer user queries and perform Fly actions." ,
    llm,
    tools,
  });

  return agent;
}

What's happening here:

  • We create a Composio client using your API key and configure it with the LlamaIndex provider
  • We then create a tool router MCP session for your user, specifying the toolkits we want to use (in this case, fly)
  • The session returns an MCP HTTP endpoint URL that acts as a gateway to all your configured tools
  • LlamaIndex will connect to this endpoint to dynamically discover and use the available Fly tools.
  • The MCP tools are mapped to LlamaIndex-compatible tools and plug them into the Agent.
8

Create an interactive chat loop

async function chatLoop(agent: ReturnType<typeof createAgent>) {
  const rl = readline.createInterface({ input, output });

  console.log("Type 'quit' or 'exit' to stop.");

  while (true) {
    let userInput: string;

    try {
      userInput = (await rl.question("\nYou: ")).trim();
    } catch {
      console.log("\nAgent: Bye!");
      break;
    }

    if (!userInput) {
      continue;
    }

    const lower = userInput.toLowerCase();
    if (lower === "quit" || lower === "exit") {
      console.log("Agent: Bye!");
      break;
    }

    try {
      process.stdout.write("Agent: ");

      const stream = agent.runStream(userInput);
      let finalResult: any = null;

      for await (const event of stream) {
        // The event.data contains the streamed content
        const data: any = event.data;

        // Check for streaming delta content
        if (data?.delta) {
          process.stdout.write(data.delta);
        }

        // Store final result for fallback
        if (data?.result || data?.message) {
          finalResult = data;
        }
      }

      // If no streaming happened, show the final result
      if (finalResult) {
        const answer =
          finalResult.result ??
          finalResult.message?.content ??
          finalResult.message ??
          "";
        if (answer && typeof answer === "string" && !answer.includes("[object")) {
          process.stdout.write(answer);
        }
      }

      console.log(); // New line after streaming completes
    } catch (err: any) {
      console.error("\nAgent error:", err?.message ?? err);
    }
  }

  rl.close();
}

What's happening:

  • We're creating a direct terminal interface to chat with Fly
  • The LLM's responses are streamed to the CLI for faster interaction.
  • The agent uses context to maintain conversation history
  • The agent processes the request, selects appropriate Fly tools, and returns a result
  • We extract the answer from the result data structure and display it to the user
  • You can type 'quit' or 'exit' to stop the chat loop gracefully
  • Agent responses and any errors are streamed in a clear, readable format
9

Define the main entry point

async function main() {
  try {
    const agent = await buildAgent();
    await chatLoop(agent);
  } catch (err) {
    console.error("Failed to start agent:", err);
    process.exit(1);
  }
}

main();

What's happening here:

  • We're orchestrating the entire application flow
  • The agent gets built with proper error handling
  • Then we kick off the interactive chat loop so you can start talking to Fly
10

Run the agent

npx ts-node llamaindex-agent.ts

When prompted, authenticate and authorise your agent with Fly, then start asking questions.

Complete Code

Here's the complete code to get you started with Fly and LlamaIndex:

import "dotenv/config";
import readline from "node:readline/promises";
import { stdin as input, stdout as output } from "node:process";

import { Composio } from "@composio/core";
import { LlamaindexProvider } from "@composio/llamaindex";

import { mcp } from "@llamaindex/tools";
import { agent as createAgent } from "@llamaindex/workflow";
import { openai } from "@llamaindex/openai";

dotenv.config();

const OPENAI_API_KEY = process.env.OPENAI_API_KEY;
const COMPOSIO_API_KEY = process.env.COMPOSIO_API_KEY;
const COMPOSIO_USER_ID = process.env.COMPOSIO_USER_ID;

if (!OPENAI_API_KEY) {
    throw new Error("OPENAI_API_KEY is not set in the environment");
  }
if (!COMPOSIO_API_KEY) {
    throw new Error("COMPOSIO_API_KEY is not set in the environment");
  }
if (!COMPOSIO_USER_ID) {
    throw new Error("COMPOSIO_USER_ID is not set in the environment");
  }

async function buildAgent() {

  console.log(`Initializing Composio client...${COMPOSIO_USER_ID!}...`);
  console.log(`COMPOSIO_USER_ID: ${COMPOSIO_USER_ID!}...`);

  const composio = new Composio({
    apiKey: COMPOSIO_API_KEY,
    provider: new LlamaindexProvider(),
  });

  const session = await composio.create(
    COMPOSIO_USER_ID!,
    {
      toolkits: ["fly"],
    },
  );

  const mcpUrl = session.mcp.url;
  console.log(`Composio Tool Router MCP URL: ${mcpUrl}`);

  const server = mcp({
    url: mcpUrl,
    clientName: "composio_tool_router_with_llamaindex",
    requestInit: {
      headers: {
        "x-api-key": COMPOSIO_API_KEY!,
      },
    },
    // verbose: true,
  });

  const tools = await server.tools();

  const llm = openai({ apiKey: OPENAI_API_KEY, model: "gpt-5" });

  const agent = createAgent({
    name: "composio_tool_router_with_llamaindex",
    description:
      "An agent that uses Composio Tool Router MCP tools to perform actions.",
    systemPrompt:
      "You are a helpful assistant connected to Composio Tool Router."+
"Use the available tools to answer user queries and perform Fly actions." ,
    llm,
    tools,
  });

  return agent;
}

async function chatLoop(agent: ReturnType<typeof createAgent>) {
  const rl = readline.createInterface({ input, output });

  console.log("Type 'quit' or 'exit' to stop.");

  while (true) {
    let userInput: string;

    try {
      userInput = (await rl.question("\nYou: ")).trim();
    } catch {
      console.log("\nAgent: Bye!");
      break;
    }

    if (!userInput) {
      continue;
    }

    const lower = userInput.toLowerCase();
    if (lower === "quit" || lower === "exit") {
      console.log("Agent: Bye!");
      break;
    }

    try {
      process.stdout.write("Agent: ");

      const stream = agent.runStream(userInput);
      let finalResult: any = null;

      for await (const event of stream) {
        // The event.data contains the streamed content
        const data: any = event.data;

        // Check for streaming delta content
        if (data?.delta) {
          process.stdout.write(data.delta);
        }

        // Store final result for fallback
        if (data?.result || data?.message) {
          finalResult = data;
        }
      }

      // If no streaming happened, show the final result
      if (finalResult) {
        const answer =
          finalResult.result ??
          finalResult.message?.content ??
          finalResult.message ??
          "";
        if (answer && typeof answer === "string" && !answer.includes("[object")) {
          process.stdout.write(answer);
        }
      }

      console.log(); // New line after streaming completes
    } catch (err: any) {
      console.error("\nAgent error:", err?.message ?? err);
    }
  }

  rl.close();
}

async function main() {
  try {
    const agent = await buildAgent();
    await chatLoop(agent);
  } catch (err: any) {
    console.error("Failed to start agent:", err?.message ?? err);
    process.exit(1);
  }
}

main();

Conclusion

You've successfully connected Fly to LlamaIndex through Composio's Tool Router MCP layer. Key takeaways:
  • Tool Router dynamically exposes Fly tools through an MCP endpoint
  • LlamaIndex's ReActAgent handles reasoning and orchestration; Composio handles integrations
  • The agent becomes more capable without increasing prompt size
  • Async Python provides clean, efficient execution of agent workflows
You can easily extend this to other toolkits like Gmail, Notion, Stripe, GitHub, and more by adding them to the toolkits parameter.
TOOLS

Supported Tools

Every Fly action and event your agent gets out of the box.

Add WireGuard Peer

Tool to add a WireGuard peer connection to a Fly.

Check App Name Availability

Tool to validate an app name for Fly.

Check Jobs

Execute GraphQL queries against the Fly.

Check User Only Token

Check whether the authentication token only allows user access.

Create Health Check Job

Tool to create a health check job for monitoring application endpoints in Fly.

Create Check Job Run

Triggers a run of an existing health check job on Fly.

Create Delegated WireGuard Token

Tool to create a delegated WireGuard token for peer management in a Fly.

Create Third-Party Configuration

Tool to create a third-party service configuration for discharging macaroon caveats.

Delete Delegated WireGuard Token

Tool to delete a delegated WireGuard token from a Fly.

Delete Organization

Tool to delete a Fly.

Delete Remote Builder

Tool to delete a remote builder configuration for a Fly.

Delete Third Party Configuration

Tool to delete a third-party service configuration from Fly.

Detach Postgres Cluster

Tool to detach a Postgres cluster from a Fly.

Establish SSH Key

Tool to establish an SSH key for a Fly.

Fetch Nodes by IDs

Fetches a list of node objects from Fly.

Get Add-On

Tool to find a Fly.

Get Add-On Provider

Tool to query information about a specific Fly.

Get app details

Tool to retrieve detailed information about a specific Fly.

Get Certificate

Tool to retrieve a certificate by its ID from Fly.

Get Current Token Info

Tool to get information about the current authentication token.

Get Latest Image Details

Tool to retrieve the latest available tag details for a given image repository from Fly.

Get Latest Image Tag

Tool to retrieve the latest available image tag for a Fly.

Get Machine

Tool to get a single machine by ID from Fly.

Get Nearest Region

Tool to retrieve the nearest Fly.

Get Node by ID

Tool to fetch an object by its globally unique ID using Fly.

Get Organization

Tool to find a Fly.

Get Personal Organization

Tool to retrieve the user's personal organization details from Fly.

Get Placements

Tool to get placement recommendations for Machines in Fly.

Get Platform Information

Tool to retrieve Fly.

Get Products and Pricing

Tool to retrieve Fly.

Get Regions

Tool to get the list of available Fly.

Get Viewer Info

Tool to retrieve the authenticated user's account information from Fly.

Issue Certificate

Tool to issue an SSH certificate for accessing Fly.

List Add-On Plans

Tool to list available add-on service plans from Fly.

List Add-Ons

Tool to list add-ons associated with an organization in Fly.

List Apps

Tool to list all Fly Apps in an organization.

List Apps via GraphQL

List all Fly.

Check Locations

Retrieve all available Fly.

List Machines

Tool to list Fly.

List Organization Machines

Tool to list all Machines across all apps in a Fly organization.

Remove WireGuard Peer

Tool to remove a WireGuard peer connection from a Fly.

Set Apps V2 Default

Tool to configure whether new apps in an organization use Apps V2 by default on Fly.

Update Third-Party Configuration

Tool to update an existing third-party service configuration for discharging macaroon caveats.

Validate Config

Tool to validate a Fly.

Validate WireGuard Peers

Tool to validate WireGuard peer IP addresses in a Fly.

FAQ

Frequently asked questions

With a standalone Fly MCP server, the agents and LLMs can only access a fixed set of Fly tools tied to that server. However, with the Composio Tool Router, agents can dynamically load tools from Fly and many other apps based on the task at hand, all through a single MCP endpoint.

Yes, you can. LlamaIndex fully supports MCP integration. You get structured tool calling, message history handling, and model orchestration while Tool Router takes care of discovering and serving the right Fly tools.

Yes, absolutely. You can configure which Fly scopes and actions are allowed when connecting your account to Composio. You can also bring your own OAuth credentials or API configuration so you keep full control over what the agent can do.

All sensitive data such as tokens, keys, and configuration is fully encrypted at rest and in transit. Composio is SOC 2 Type 2 compliant and follows strict security practices so your Fly data and credentials are handled as safely as possible.

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