How to integrate GitHub MCP with Atomic Agent

Connect Atomic Agent to GitHub MCP. List all open issues assigned to me, create pull request from your branch, and more using natural language, with authentication handled for you.

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Api Key

GitHub MCP is GitHub's managed API surface for repositories, issues, pull requests, users, actions, projects, and notifications. Use it to let AI agents interact with your code and project data securely and at scale.

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Introduction

Atomic Agent is an open-source AI agent that runs on your machine and supports local models through llama.cpp. Connect it to 1,500+ apps through Composio, including GitHub.

This guide uses Atomic Agent's built-in Composio integration. You need Atomic Agent v0.5.6 or later, your own Composio API key, and a GitHub account. See the Atomic Agent documentation for installation instructions.

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How Atomic Agent connects to GitHub

Atomic Agent connects to Composio's Tool Router over Streamable HTTP MCP. It discovers the tools needed for your request, and Composio handles account authentication.

Execution and account-connection tools follow Atomic Agent's configured approval policy. Review any approval prompt before allowing an action on your connected account.

Connect GitHub to Atomic Agent

  1. Sign up or sign in to the Composio dashboard. Copy your API key.
  2. In Atomic Agent, open the Integrations tab and select Composio. Select API key, press e, paste the key, and press Enter. The tools become available immediately, without a restart.
  3. Ask Atomic Agent to do something in GitHub. It searches Composio for the right tool.
  4. On first use, open the sign-in link returned in the chat. Connect your GitHub account, then return to Atomic Agent to continue.

Headless setup

Add the following line to ~/.atomic-agent/.env, replacing YOUR_COMPOSIO_API_KEY with your key. Start Atomic Agent after saving the file.

bash
COMPOSIO_API_KEY=YOUR_COMPOSIO_API_KEY

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

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

Use GitHub from Atomic Agent

With your account connected, ask Atomic Agent to work with GitHub in natural language. You can connect more apps through the same Composio integration as you need them.

Visit the Atomic Agent website or inspect the Atomic Agent source code.

Troubleshooting

Why is my API key rejected?

Copy the key directly from the Composio dashboard. Atomic Agent requires ASCII characters because it sends the key in an HTTP header. Remove any extra characters introduced when copying.

Why are Composio tools unavailable after saving a key?

Check that you use Atomic Agent v0.5.6 or later and that Composio is enabled in your configuration. A "composio": { "enabled": false } setting disables the integration while keeping the saved key on disk.

Does Composio have a free plan?

The Hobby plan includes 100,000 tool calls per month. Composio-managed OAuth apps have a lower included allowance. See Composio pricing for the current limits that apply to your connection.

TOOLS

Supported Tools

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

Add comment to pending review

Add review comment to the requester's latest pending pull request review.

Add issue comment

Add a comment and/or reaction to a specific issue or issue comment in a GitHub repository.

Add reply to pull request comment

Add a reply and/or reaction to an existing pull request comment.

Create branch

Create a new branch in a GitHub repository

Create or update file

Create or update a single file in a GitHub repository.

Create pull request

Create a new pull request in a GitHub repository.

Create repository

Create a new GitHub repository in your account or specified organization

Delete file

Delete a file from a GitHub repository

Fork repository

Fork a GitHub repository to your account or specified organization

Get commit

Get details for a commit from a GitHub repository

Get file contents

Get the contents of a file or directory from a GitHub repository

Get label

Get a specific label from a repository.

Get latest release

Get the latest release in a GitHub repository

Get me

Get details of the authenticated GitHub user.

Get release by tag

Get a specific release by its tag name in a GitHub repository

Get tag

Get details about a specific git tag in a GitHub repository

Get team members

Get member usernames of a specific team in an organization.

Get teams

Get details of the teams the user is a member of.

Issue read

Get information about a specific issue in a GitHub repository.

Issue write

Create a new or update an existing issue in a GitHub repository.

List branches

List branches in a GitHub repository

List commits

Get list of commits of a branch in a GitHub repository.

List issue fields

List issue fields for a repository or organization.

List issues

List issues in a GitHub repository.

List issue types

List supported issue types for a repository or its owner organization.

List pull requests

List pull requests in a GitHub repository.

List releases

List releases in a GitHub repository

List repository collaborators

List collaborators of a GitHub repository.

List tags

List git tags in a GitHub repository

Merge pull request

Merge a pull request in a GitHub repository.

Pull request read

Get information on a specific pull request in GitHub repository.

Pull request review write

Create and/or submit, delete review of a pull request.

Push files

Push multiple files to a GitHub repository in a single commit

Request copilot review

Request a GitHub Copilot code review for a pull request.

Run secret scanning

Scan files, content, or recent changes for secrets such as API keys, passwords, tokens, and credentials.

Search code

Fast and precise code search across ALL GitHub repositories using GitHub's native search engine.

Search commits

Search for commits across GitHub repositories using GitHub's commit search syntax.

Search issues

Search issues using natural-language semantic matching.

Search pull requests

Search for pull requests in GitHub repositories using issues search syntax already scoped to is:pr

Search repositories

Find GitHub repositories by name, description, readme, topics, or other metadata.

Search users

Find GitHub users by username, real name, or other profile information.

Sub issue write

Add a sub-issue to a parent issue in a GitHub repository.

Update pull request

Update an existing pull request in a GitHub repository.

Update pull request branch

Update the branch of a pull request with the latest changes from the base branch.

FAQ

Frequently asked questions

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

Yes, you can. Atomic Agent 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 GitHub tools.

Yes, absolutely. You can configure which GitHub 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 GitHub data and credentials are handled as safely as possible.

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