How to integrate Fly MCP with LlamaIndex

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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 my 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.

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.

Supported Tools & Triggers

Tools
Add WireGuard PeerTool to add a WireGuard peer connection to a Fly.
Check App Name AvailabilityTool to validate an app name for Fly.
Check JobsExecute GraphQL queries against the Fly.
Check User Only TokenCheck whether the authentication token only allows user access.
Create Health Check JobTool to create a health check job for monitoring application endpoints in Fly.
Create Check Job RunTriggers a run of an existing health check job on Fly.
Create Delegated WireGuard TokenTool to create a delegated WireGuard token for peer management in a Fly.
Create Third-Party ConfigurationTool to create a third-party service configuration for discharging macaroon caveats.
Delete Delegated WireGuard TokenTool to delete a delegated WireGuard token from a Fly.
Delete OrganizationTool to delete a Fly.
Delete Remote BuilderTool to delete a remote builder configuration for a Fly.
Delete Third Party ConfigurationTool to delete a third-party service configuration from Fly.
Detach Postgres ClusterTool to detach a Postgres cluster from a Fly.
Establish SSH KeyTool to establish an SSH key for a Fly.
Fetch Nodes by IDsFetches a list of node objects from Fly.
Get Add-OnTool to find a Fly.
Get Add-On ProviderTool to query information about a specific Fly.
Get app detailsTool to retrieve detailed information about a specific Fly.
Get CertificateTool to retrieve a certificate by its ID from Fly.
Get Current Token InfoTool to get information about the current authentication token.
Get Latest Image DetailsTool to retrieve the latest available tag details for a given image repository from Fly.
Get Latest Image TagTool to retrieve the latest available image tag for a Fly.
Get MachineTool to get a single machine by ID from Fly.
Get Nearest RegionTool to retrieve the nearest Fly.
Get Node by IDTool to fetch an object by its globally unique ID using Fly.
Get OrganizationTool to find a Fly.
Get Personal OrganizationTool to retrieve the user's personal organization details from Fly.
Get PlacementsTool to get placement recommendations for Machines in Fly.
Get Platform InformationTool to retrieve Fly.
Get Products and PricingTool to retrieve Fly.
Get RegionsTool to get the list of available Fly.
Get Viewer InfoTool to retrieve the authenticated user's account information from Fly.
Issue CertificateTool to issue an SSH certificate for accessing Fly.
List Add-On PlansTool to list available add-on service plans from Fly.
List Add-OnsTool to list add-ons associated with an organization in Fly.
List AppsTool to list all Fly Apps in an organization.
List Apps via GraphQLList all Fly.
Check LocationsRetrieve all available Fly.
List MachinesTool to list Fly.
List Organization MachinesTool to list all Machines across all apps in a Fly organization.
Remove WireGuard PeerTool to remove a WireGuard peer connection from a Fly.
Set Apps V2 DefaultTool to configure whether new apps in an organization use Apps V2 by default on Fly.
Update Third-Party ConfigurationTool to update an existing third-party service configuration for discharging macaroon caveats.
Validate ConfigTool to validate a Fly.
Validate WireGuard PeersTool to validate WireGuard peer IP addresses in a Fly.

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

What is Tool Router?

Composio's Tool Router 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 Tool Router

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

How the Tool Router works

The Tool Router 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

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

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

Installing dependencies

pip install composio-llamaindex llama-index llama-index-llms-openai llama-index-tools-mcp python-dotenv

Create a new Python project and install the necessary dependencies:

  • composio-llamaindex: Composio's LlamaIndex integration
  • llama-index: Core LlamaIndex framework
  • llama-index-llms-openai: OpenAI LLM integration
  • llama-index-tools-mcp: MCP client for LlamaIndex
  • python-dotenv: Environment variable management

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

Import modules

import asyncio
import os
import dotenv

from composio import Composio
from composio_llamaindex import LlamaIndexProvider
from llama_index.core.agent.workflow import ReActAgent
from llama_index.core.workflow import Context
from llama_index.llms.openai import OpenAI
from llama_index.tools.mcp import BasicMCPClient, McpToolSpec

dotenv.load_dotenv()

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

Key imports:

  • asyncio: For async/await support
  • Composio: Main client for Composio services
  • LlamaIndexProvider: Adapts Composio tools for LlamaIndex
  • ReActAgent: LlamaIndex's reasoning and action agent
  • BasicMCPClient: Connects to MCP endpoints
  • McpToolSpec: Converts MCP tools to LlamaIndex format

Load environment variables and initialize Composio

OPENAI_API_KEY = os.getenv("OPENAI_API_KEY")
COMPOSIO_API_KEY = os.getenv("COMPOSIO_API_KEY")
COMPOSIO_USER_ID = os.getenv("COMPOSIO_USER_ID")

if not OPENAI_API_KEY:
    raise ValueError("OPENAI_API_KEY is not set in the environment")
if not COMPOSIO_API_KEY:
    raise ValueError("COMPOSIO_API_KEY is not set in the environment")
if not COMPOSIO_USER_ID:
    raise ValueError("COMPOSIO_USER_ID is not set in the environment")

What's happening:

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

Create a Tool Router session and build the agent function

async def build_agent() -> ReActAgent:
    composio_client = Composio(
        api_key=COMPOSIO_API_KEY,
        provider=LlamaIndexProvider(),
    )

    session = composio_client.create(
        user_id=COMPOSIO_USER_ID,
        toolkits=["fly"],
    )

    mcp_url = session.mcp.url
    print(f"Composio MCP URL: {mcp_url}")

    mcp_client = BasicMCPClient(mcp_url, headers={"x-api-key": COMPOSIO_API_KEY})
    mcp_tool_spec = McpToolSpec(client=mcp_client)
    tools = await mcp_tool_spec.to_tool_list_async()

    llm = OpenAI(model="gpt-5")

    description = "An agent that uses Composio Tool Router MCP tools to perform Fly actions."
    system_prompt = """
    You are a helpful assistant connected to Composio Tool Router.
    Use the available tools to answer user queries and perform Fly actions.
    """
    return ReActAgent(tools=tools, llm=llm, description=description, system_prompt=system_prompt, verbose=True)

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.

Create an interactive chat loop

async def chat_loop(agent: ReActAgent) -> None:
    ctx = Context(agent)
    print("Type 'quit', 'exit', or Ctrl+C to stop.")

    while True:
        try:
            user_input = input("\nYou: ").strip()
        except (KeyboardInterrupt, EOFError):
            print("\nBye!")
            break

        if not user_input or user_input.lower() in {"quit", "exit"}:
            print("Bye!")
            break

        try:
            print("Agent: ", end="", flush=True)
            handler = agent.run(user_input, ctx=ctx)

            async for event in handler.stream_events():
                # Stream token-by-token from LLM responses
                if hasattr(event, "delta") and event.delta:
                    print(event.delta, end="", flush=True)
                # Show tool calls as they happen
                elif hasattr(event, "tool_name"):
                    print(f"\n[Using tool: {event.tool_name}]", flush=True)

            # Get final response
            response = await handler
            print()  # Newline after streaming
        except KeyboardInterrupt:
            print("\n[Interrupted]")
            continue
        except Exception as e:
            print(f"\nError: {e}")

What's happening here:

  • We're creating a direct terminal interface to chat with your Fly database
  • The LLM's responses are streamed to the CLI for faster interaction.
  • The agent uses context to maintain conversation history
  • You can type 'quit' or 'exit' to stop the chat loop gracefully
  • Agent responses and any errors are displayed in a clear, readable format

Define the main entry point

async def main() -> None:
    agent = await build_agent()
    await chat_loop(agent)

if __name__ == "__main__":
    # Handle Ctrl+C gracefully
    signal.signal(signal.SIGINT, lambda s, f: (print("\nBye!"), exit(0)))
    try:
        asyncio.run(main())
    except KeyboardInterrupt:
        print("\nBye!")

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

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 asyncio
import os
import signal
import dotenv

from composio import Composio
from composio_llamaindex import LlamaIndexProvider
from llama_index.core.agent.workflow import ReActAgent
from llama_index.core.workflow import Context
from llama_index.llms.openai import OpenAI
from llama_index.tools.mcp import BasicMCPClient, McpToolSpec

dotenv.load_dotenv()

OPENAI_API_KEY = os.getenv("OPENAI_API_KEY")
COMPOSIO_API_KEY = os.getenv("COMPOSIO_API_KEY")
COMPOSIO_USER_ID = os.getenv("COMPOSIO_USER_ID")

if not OPENAI_API_KEY:
    raise ValueError("OPENAI_API_KEY is not set")
if not COMPOSIO_API_KEY:
    raise ValueError("COMPOSIO_API_KEY is not set")
if not COMPOSIO_USER_ID:
    raise ValueError("COMPOSIO_USER_ID is not set")

async def build_agent() -> ReActAgent:
    composio_client = Composio(
        api_key=COMPOSIO_API_KEY,
        provider=LlamaIndexProvider(),
    )

    session = composio_client.create(
        user_id=COMPOSIO_USER_ID,
        toolkits=["fly"],
    )

    mcp_url = session.mcp.url
    print(f"Composio MCP URL: {mcp_url}")

    mcp_client = BasicMCPClient(mcp_url, headers={"x-api-key": COMPOSIO_API_KEY})
    mcp_tool_spec = McpToolSpec(client=mcp_client)
    tools = await mcp_tool_spec.to_tool_list_async()

    llm = OpenAI(model="gpt-5")
    description = "An agent that uses Composio Tool Router MCP tools to perform Fly actions."
    system_prompt = """
    You are a helpful assistant connected to Composio Tool Router.
    Use the available tools to answer user queries and perform Fly actions.
    """
    return ReActAgent(
        tools=tools,
        llm=llm,
        description=description,
        system_prompt=system_prompt,
        verbose=True,
    );

async def chat_loop(agent: ReActAgent) -> None:
    ctx = Context(agent)
    print("Type 'quit', 'exit', or Ctrl+C to stop.")

    while True:
        try:
            user_input = input("\nYou: ").strip()
        except (KeyboardInterrupt, EOFError):
            print("\nBye!")
            break

        if not user_input or user_input.lower() in {"quit", "exit"}:
            print("Bye!")
            break

        try:
            print("Agent: ", end="", flush=True)
            handler = agent.run(user_input, ctx=ctx)

            async for event in handler.stream_events():
                # Stream token-by-token from LLM responses
                if hasattr(event, "delta") and event.delta:
                    print(event.delta, end="", flush=True)
                # Show tool calls as they happen
                elif hasattr(event, "tool_name"):
                    print(f"\n[Using tool: {event.tool_name}]", flush=True)

            # Get final response
            response = await handler
            print()  # Newline after streaming
        except KeyboardInterrupt:
            print("\n[Interrupted]")
            continue
        except Exception as e:
            print(f"\nError: {e}")

async def main() -> None:
    agent = await build_agent()
    await chat_loop(agent)

if __name__ == "__main__":
    # Handle Ctrl+C gracefully
    signal.signal(signal.SIGINT, lambda s, f: (print("\nBye!"), exit(0)))
    try:
        asyncio.run(main())
    except KeyboardInterrupt:
        print("\nBye!")

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.

How to build Fly MCP Agent with another framework

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Vercel AI SDK

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Mastra AI

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CrewAI

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Claude Code

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Codex

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FAQ

What are the differences in Tool Router MCP and Fly MCP?

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.

Can I use Tool Router MCP with LlamaIndex?

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.

Can I manage the permissions and scopes for Fly while using Tool Router?

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.

How safe is my data with Composio Tool Router?

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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