GitHub MCP Setup

Connect your agents to GitHub repositories, issues, and pull requests

What You’ll Learn

This guide shows you how to integrate GitHub with Junis using the official GitHub MCP Server. Your agents will be able to:

• Browse and search repositories
• Read and create issues
• Manage pull requests
• View commits and branches
• Create and update files

Prerequisites:

• GitHub account with repository access
• Admin role in Junis (for organization-level setup)
• Basic understanding of GitHub Personal Access Tokens

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Quick Setup (5 Minutes)

1. Generate GitHub Personal Access Token

   1. Go to GitHub Settings → Tokens
   2. Click “Generate new token (classic)”
   3. Select scopes based on your needs:
      • repo - Full repository access (recommended)
      • read:org - Read organization info
      • read:user - Read user info
   4. Click “Generate token” and copy it immediately (shown only once!)
2. Add GitHub Platform to Junis

   Navigate to Team > MCP in Junis and find the GitHub card.

   If GitHub is already configured (globe icon 🌍), skip to Step 3.

   Otherwise, click “Connect” and fill in:

   • Platform Name: GitHub
   • MCP Server URL: https://api.githubcopilot.com/mcp/
   • Transport Type: Streamable HTTP ⚠️ Important: Must be HTTP, not SSE!
3. Add Your Credentials

   Click “Add Auth” on the GitHub card and paste your Personal Access Token.

   Click “Test Connection” to verify it works.

4. Enable for Your Agents

   Go to Admin > Agents, edit the agent you want to connect, and check “GitHub” in the MCP Platforms section.

   Save and test by asking: “List repositories in the JunisAI organization”

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Authentication Levels

GitHub MCP supports all three authentication levels:

👤 User-Level (Personal GitHub)

Use Case: Access your personal repositories and private GitHub account

Setup: User Settings > MCP Credentials > GitHub

Example:

• Your personal projects
• Private repos under your account
• Creating issues in repos you own

Scopes Needed: repo, read:user

🏢 Organization-Level (Shared)

Use Case: Access company/team repositories shared by all team members

Setup: Admin > MCP > GitHub > Organization Credentials (Admin only)

Example:

• Company repositories
• Team projects
• Shared organization resources

Scopes Needed: repo, read:org, read:user

🌍 System-Level (Global Default)

Use Case: Fallback authentication when no user/org credentials exist

Setup: Automatically configured by Junis Super Admins

Example:

• Public repositories
• Trial/demo purposes

Scopes Needed: public_repo (read-only)

Priority: User > Organization > System (highest to lowest)

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GitHub PAT Scopes Explained

Minimal Scopes (Read-Only)

✅ repo:status - Repository status
✅ public_repo - Public repositories only

Good for: Browsing public repos, reading issues (no write access)

Recommended Scopes (Read + Write)

✅ repo - Full repository access (includes private repos)
✅ read:org - Read organization information
✅ read:user - Read user profile

Good for: Full agent capabilities (create issues, PRs, commit files)

Optional Scopes (Advanced)

✅ workflow - Manage GitHub Actions workflows
✅ admin:repo_hook - Manage repository webhooks
✅ delete_repo - Delete repositories (⚠️ Use with caution!)

Good for: Advanced automation and repository management

Security Best Practice: Only grant the minimum scopes your agents need. You can always create a new token with more scopes later.

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Available GitHub Tools

Your agents can use these GitHub MCP tools:

Repositories

github_list_repositories

List all repositories for a user or organization

github_get_repository

Get detailed information about a specific repository

github_search_repositories

Search repositories by keyword or criteria

github_create_repository

Create a new repository

Issues

github_list_issues

List issues in a repository

github_get_issue

Get details of a specific issue

github_create_issue

Create a new issue

github_update_issue

Update an existing issue (title, body, labels, assignees)

Pull Requests

github_list_pull_requests

List pull requests in a repository

github_get_pull_request

Get details of a specific PR

github_create_pull_request

Create a new pull request

github_merge_pull_request

Merge a pull request

File Operations

github_get_file_contents

Read file contents from a repository

github_create_or_update_file

Create or update a file in a repository

github_push_files

Push multiple files in a single commit

Commits & Branches

github_list_commits

View commit history

github_get_commit

Get details of a specific commit

github_list_branches

List all branches

github_create_branch

Create a new branch

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Example Use Cases

DevOps Automation Agent

Agent Prompt:

You are a DevOps automation agent. Monitor GitHub repositories for:
- New issues and pull requests
- Failed CI/CD builds
- Pending code reviews

When you detect issues, create reports and notify the team.

Connected MCP: GitHub + Slack

Example Interaction:

User: "Check if there are any failed builds in the main branch"
Agent: [Uses github_list_commits + GitHub Actions status]
       "Found 3 failed builds in the last 24 hours. Creating a report..."

Code Review Assistant

Agent Prompt:

You are a code review assistant. When given a pull request URL:
1. Fetch the PR details and changed files
2. Analyze code quality and potential issues
3. Leave constructive review comments

Connected MCP: GitHub only

Example Interaction:

User: "Review PR #123 in the junis-ai repo"
Agent: [Uses github_get_pull_request, github_get_file_contents]
       "Reviewed 5 changed files. Here are my suggestions:
       - Add error handling in api.py (line 45)
       - Consider using async/await in database.py
       ..."

Issue Triage Agent

Agent Prompt:

You help triage GitHub issues by:
- Reading new issues
- Analyzing content and assigning labels
- Assigning to appropriate team members
- Prioritizing based on severity

Connected MCP: GitHub + Notion (for team member database)

Example Interaction:

User: "Triage all new issues from the last 3 days"
Agent: [Uses github_list_issues, github_update_issue]
       "Triaged 12 new issues:
       - 5 bugs (assigned to engineering team)
       - 4 feature requests (added to backlog)
       - 3 documentation updates (assigned to tech writers)"

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Troubleshooting

Error: 405 Method Not Allowed

Symptom: Connection fails with 405 Method Not Allowed for url 'https://api.githubcopilot.com/mcp/'

Cause: Transport type is set to sse instead of streamable-http

Solution:

1. Go to Admin > MCP > GitHub
2. Edit the platform configuration
3. Change Transport Type to “Streamable HTTP”
4. Save and test connection

Error: 401 Unauthorized

Symptom: Tools load but API calls fail with 401 errors

Cause: Invalid or expired Personal Access Token

Solution:

1. Generate a new PAT at https://github.com/settings/tokens
2. Update your MCP credentials in Junis
3. Test connection again

Error: 403 Forbidden

Symptom: Some operations fail with 403 errors

Cause: PAT lacks necessary scopes (permissions)

Solution:

1. Check which operation failed (e.g., creating issues)
2. Generate a new PAT with additional scopes:
   • Issues: repo scope
   • Private repos: repo scope
   • Organization: read:org scope
3. Update credentials and retry

Tools Not Showing Up

Symptom: Agent is connected to GitHub but no tools appear

Possible Causes:

• MCP connection failed
• Agent cache not refreshed
• Transport type misconfigured

Solution:

1. Check logs: Admin > Dashboard > Recent Activity
2. Look for error messages mentioning “GitHub” or “MCP”
3. Verify connection in Team > MCP > GitHub > Test Connection
4. If all looks good, restart the agent (edit and save without changes)

Rate Limit Exceeded

Symptom: API calls start failing after many requests

Cause: GitHub API rate limit reached (5,000 requests/hour for authenticated users)

Solution:

• Short-term: Wait 1 hour for rate limit reset
• Long-term: Implement caching in your agent logic to reduce API calls
• Check status: Ask agent “What’s my GitHub API rate limit status?”

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Security Best Practices

✅ DO:

• Use user-level credentials for personal repositories
• Use organization-level credentials for shared team resources
• Rotate PATs every 90 days
• Grant only the minimum required scopes
• Store PATs in a password manager

❌ DON’T:

• Share your Personal Access Token with anyone
• Commit PATs to code repositories
• Use admin-level tokens for routine operations
• Grant delete_repo scope unless absolutely necessary

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Advanced Configuration

Using GitHub Enterprise Server

If your organization uses GitHub Enterprise Server:

{
  "mcp_server_url": "https://github.your-company.com/api/mcp/",
  "transport_type": "streamable-http",
  "additional_auth_config": {
    "headers": {
      "Authorization": "Bearer ghp_your_enterprise_token"
    }
  }
}

Rate Limit Monitoring

Create an agent that monitors GitHub API rate limits:

Agent Instruction:

When asked about rate limits, use the github_get_rate_limit tool
to check remaining API calls and reset time.

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What’s Next?

Firecrawl MCP

Web scraping and crawling

Custom MCP Servers

Build your own MCP integrations

MCP Overview

Back to MCP Integration overview

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Additional Resources

• GitHub MCP Server: https://github.com/github/github-mcp-server
• GitHub PAT Guide: https://docs.github.com/en/authentication/keeping-your-account-and-data-secure/creating-a-personal-access-token
• GitHub API Docs: https://docs.github.com/en/rest
• MCP Protocol: https://modelcontextprotocol.io/

Need Help? Contact us at [e-mail] for assistance with GitHub automation workflows and integration support.