# How to integrate GitHub MCP with Atomic Agent

```json
{
  "title": "How to integrate GitHub MCP with Atomic Agent",
  "toolkit": "GitHub MCP",
  "toolkit_slug": "github_mcp",
  "framework": "Atomic Agent",
  "framework_slug": "atomic-agent",
  "url": "https://composio.dev/toolkits/github_mcp/framework/atomic-agent",
  "markdown_url": "https://composio.dev/toolkits/github_mcp/framework/atomic-agent.md",
  "updated_at": "2026-09-24T15:41:48.338Z"
}
```

## 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](https://atomicagent.io/docs/?cta_placement=atomic-agent-docs) for installation instructions.

## Also integrate GitHub MCP with

- [ChatGPT](https://composio.dev/toolkits/github_mcp/framework/chatgpt)
- [Claude Cowork](https://composio.dev/toolkits/github_mcp/framework/claude-cowork)
- [Hermes](https://composio.dev/toolkits/github_mcp/framework/hermes-agent)

## TL;DR

### 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 MCP to Atomic Agent

### Connect GitHub to Atomic Agent
- Sign up or sign in to the [Composio dashboard](https://dashboard.composio.dev/?cta_placement=atomic-agent-api-key). Copy your API key.
- 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.
- Ask Atomic Agent to do something in GitHub. It searches Composio for the right tool.
- 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.

## Supported Tools

| Tool slug | Name | Description |
|---|---|---|
| `GITHUB_MCP_ADD_COMMENT_TO_PENDING_REVIEW` | Add comment to pending review | Add review comment to the requester's latest pending pull request review. A pending review needs to already exist to call this (check with the user if not sure). |
| `GITHUB_MCP_ADD_ISSUE_COMMENT` | Add issue comment | Add a comment and/or reaction to a specific issue or issue comment in a GitHub repository. Use this tool with pull requests as well (in this case pass pull request number as issue_number), but only if user is not asking specifically to add or react to review comments. At least one of body or reaction is required. |
| `GITHUB_MCP_ADD_REPLY_TO_PULL_REQUEST_COMMENT` | Add reply to pull request comment | Add a reply and/or reaction to an existing pull request comment. This can create a new comment linked as a reply to the specified comment, add an emoji reaction to the specified comment, or do both. At least one of body or reaction is required. |
| `GITHUB_MCP_CREATE_BRANCH` | Create branch | Create a new branch in a GitHub repository |
| `GITHUB_MCP_CREATE_OR_UPDATE_FILE` | Create or update file | Create or update a single file in a GitHub repository. If updating, you should provide the SHA of the file you want to update. Use this tool to create or update a file in a GitHub repository remotely; do not use it for local file operations. In order to obtain the SHA of original file version before updating, use the following git command: git rev-parse : SHA MUST be provided for existing file updates. |
| `GITHUB_MCP_CREATE_PULL_REQUEST` | Create pull request | Create a new pull request in a GitHub repository. |
| `GITHUB_MCP_CREATE_REPOSITORY` | Create repository | Create a new GitHub repository in your account or specified organization |
| `GITHUB_MCP_DELETE_FILE` | Delete file | Delete a file from a GitHub repository |
| `GITHUB_MCP_FORK_REPOSITORY` | Fork repository | Fork a GitHub repository to your account or specified organization |
| `GITHUB_MCP_GET_COMMIT` | Get commit | Get details for a commit from a GitHub repository |
| `GITHUB_MCP_GET_FILE_CONTENTS` | Get file contents | Get the contents of a file or directory from a GitHub repository |
| `GITHUB_MCP_GET_LABEL` | Get label | Get a specific label from a repository. |
| `GITHUB_MCP_GET_LATEST_RELEASE` | Get latest release | Get the latest release in a GitHub repository |
| `GITHUB_MCP_GET_ME` | Get me | Get details of the authenticated GitHub user. Use this when a request is about the user's own profile for GitHub. Or when information is missing to build other tool calls. |
| `GITHUB_MCP_GET_RELEASE_BY_TAG` | Get release by tag | Get a specific release by its tag name in a GitHub repository |
| `GITHUB_MCP_GET_TAG` | Get tag | Get details about a specific git tag in a GitHub repository |
| `GITHUB_MCP_GET_TEAM_MEMBERS` | Get team members | Get member usernames of a specific team in an organization. Limited to organizations accessible with current credentials |
| `GITHUB_MCP_GET_TEAMS` | Get teams | Get details of the teams the user is a member of. Limited to organizations accessible with current credentials |
| `GITHUB_MCP_ISSUE_READ` | Issue read | Get information about a specific issue in a GitHub repository. |
| `GITHUB_MCP_ISSUE_WRITE` | Issue write | Create a new or update an existing issue in a GitHub repository. |
| `GITHUB_MCP_LIST_BRANCHES` | List branches | List branches in a GitHub repository |
| `GITHUB_MCP_LIST_COMMITS` | List commits | Get list of commits of a branch in a GitHub repository. Returns at least 30 results per page by default, but can return more if specified using the perPage parameter (up to 100). |
| `GITHUB_MCP_LIST_ISSUE_FIELDS` | List issue fields | List issue fields for a repository or organization. Returns field definitions including name, type (text, number, date, single_select), and for single_select fields the list of valid option names. When repo is omitted, returns org-level fields directly. |
| `GITHUB_MCP_LIST_ISSUES` | List issues | List issues in a GitHub repository. For pagination, use the 'endCursor' from the previous response's 'pageInfo' in the 'after' parameter. |
| `GITHUB_MCP_LIST_ISSUE_TYPES` | List issue types | List supported issue types for a repository or its owner organization. When repo is omitted, returns org-level issue types directly. |
| `GITHUB_MCP_LIST_PULL_REQUESTS` | List pull requests | List pull requests in a GitHub repository. If the user specifies an author, then DO NOT use this tool and use the search_pull_requests tool instead. |
| `GITHUB_MCP_LIST_RELEASES` | List releases | List releases in a GitHub repository |
| `GITHUB_MCP_LIST_REPOSITORY_COLLABORATORS` | List repository collaborators | List collaborators of a GitHub repository. Results are paginated; the response includes `nextPage`, `prevPage`, `firstPage`, and `lastPage` fields. To get the next page, use the `nextPage` value as the `page` parameter. |
| `GITHUB_MCP_LIST_TAGS` | List tags | List git tags in a GitHub repository |
| `GITHUB_MCP_MERGE_PULL_REQUEST` | Merge pull request | Merge a pull request in a GitHub repository. |
| `GITHUB_MCP_PULL_REQUEST_READ` | Pull request read | Get information on a specific pull request in GitHub repository. |
| `GITHUB_MCP_PULL_REQUEST_REVIEW_WRITE` | Pull request review write | Create and/or submit, delete review of a pull request. Available methods: - create: Create a new review of a pull request. If "event" parameter is provided, the review is submitted. If "event" is omitted, a pending review is created. - submit_pending: Submit an existing pending review of a pull request. This requires that a pending review exists for the current user on the specified pull request. The "body" and "event" parameters are used when submitting the review. - delete_pending: Delete an existing pending review of a pull request. This requires that a pending review exists for the current user on the specified pull request. - resolve_thread: Resolve a review thread. Requires only "threadId" parameter with the thread's node ID (e.g., PRRT_kwDOxxx). The owner, repo, and pullNumber parameters are not used for this method. Resolving an already-resolved thread is a no-op. - unresolve_thread: Unresolve a previously resolved review thread. Requires only "threadId" parameter. The owner, repo, and pullNumber parameters are not used for this method. Unresolving an already-unresolved thread is a no-op. |
| `GITHUB_MCP_PUSH_FILES` | Push files | Push multiple files to a GitHub repository in a single commit |
| `GITHUB_MCP_REQUEST_COPILOT_REVIEW` | Request copilot review | Request a GitHub Copilot code review for a pull request. Use this for automated feedback on pull requests, usually before requesting a human reviewer. |
| `GITHUB_MCP_RUN_SECRET_SCANNING` | Run secret scanning | Scan files, content, or recent changes for secrets such as API keys, passwords, tokens, and credentials. This tool is intended for targeted scans of specific files, snippets, or diffs provided directly as content. The files parameter accepts either a single string or an array of strings containing raw file contents or diff hunks, and returns detected secrets with their locations and related secret scanning metadata. Content must not be empty. For full repository scanning, other mechanisms are available. Caveats: - Only files within the codebase should be scanned. Files outside of the codebase should not be sent. - Files listed in .gitignore should be skipped. |
| `GITHUB_MCP_SEARCH_CODE` | Search code | Fast and precise code search across ALL GitHub repositories using GitHub's native search engine. Best for finding exact symbols, functions, classes, or specific code patterns. |
| `GITHUB_MCP_SEARCH_COMMITS` | Search commits | Search for commits across GitHub repositories using GitHub's commit search syntax. Useful for finding specific changes, authors, or messages across one or many repositories. Searches the default branch only. |
| `GITHUB_MCP_SEARCH_ISSUES` | Search issues | Search issues using natural-language semantic matching. Best for conceptual or paraphrased queries (e.g. "login fails after password reset"). Already scoped to is:issue. |
| `GITHUB_MCP_SEARCH_PULL_REQUESTS` | Search pull requests | Search for pull requests in GitHub repositories using issues search syntax already scoped to is:pr |
| `GITHUB_MCP_SEARCH_REPOSITORIES` | Search repositories | Find GitHub repositories by name, description, readme, topics, or other metadata. Perfect for discovering projects, finding examples, or locating specific repositories across GitHub. |
| `GITHUB_MCP_SEARCH_USERS` | Search users | Find GitHub users by username, real name, or other profile information. Useful for locating developers, contributors, or team members. |
| `GITHUB_MCP_SUB_ISSUE_WRITE` | Sub issue write | Add a sub-issue to a parent issue in a GitHub repository. |
| `GITHUB_MCP_UPDATE_PULL_REQUEST` | Update pull request | Update an existing pull request in a GitHub repository. |
| `GITHUB_MCP_UPDATE_PULL_REQUEST_BRANCH` | Update pull request branch | Update the branch of a pull request with the latest changes from the base branch. |

## Supported Triggers

None listed.

## 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](/pricing) for the current limits that apply to your connection.

## Complete Code

None listed.

## Conclusion

### 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](https://atomicagent.io/?cta_placement=atomic-agent-site) or inspect the [Atomic Agent source code](https://github.com/AtomicBot-ai/atomic-agent?cta_placement=atomic-agent-repo).

## How to build GitHub MCP Agent with another framework

- [ChatGPT](https://composio.dev/toolkits/github_mcp/framework/chatgpt)
- [Claude Cowork](https://composio.dev/toolkits/github_mcp/framework/claude-cowork)
- [Hermes](https://composio.dev/toolkits/github_mcp/framework/hermes-agent)

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## Frequently Asked Questions

### What are the differences in Tool Router MCP and GitHub MCP?

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.

### Can I use Tool Router MCP with Atomic Agent?

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.

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

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.

### 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 GitHub data and credentials are handled as safely as possible.

---
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