GitHub MCP Setup

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

Quick Setup (5 Minutes)

Generate GitHub Personal Access Token

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

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!

Add Your Credentials

Click “Add Auth” on the GitHub card and paste your Personal Access Token.Click “Test Connection” to verify it works.

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”

Authentication Levels

GitHub MCP supports all three authentication levels:

👤 User-Level (Personal GitHub)
🏢 Organization-Level (Shared)
🌍 System-Level (Global Default)

Use Case: Access your personal repositories and private GitHub accountSetup: User Settings > MCP Credentials > GitHubExample:

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

Scopes Needed: repo, read:user

Use Case: Access company/team repositories shared by all team membersSetup: Admin > MCP > GitHub > Organization Credentials (Admin only)Example:

Company repositories
Team projects
Shared organization resources

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

Use Case: Fallback authentication when no user/org credentials existSetup: Automatically configured by Junis Super AdminsExample:

Public repositories
Trial/demo purposes

Scopes Needed: public_repo (read-only)

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

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.

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

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:
Fetch the PR details and changed files
Analyze code quality and potential issues
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)"

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-httpSolution:

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

Error: 401 Unauthorized

Symptom: Tools load but API calls fail with 401 errorsCause: Invalid or expired Personal Access TokenSolution:

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

Error: 403 Forbidden

Symptom: Some operations fail with 403 errorsCause: PAT lacks necessary scopes (permissions)Solution:

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

Tools Not Showing Up

Symptom: Agent is connected to GitHub but no tools appearPossible Causes:

MCP connection failed
Agent cache not refreshed
Transport type misconfigured

Solution:

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

Rate Limit Exceeded

Symptom: API calls start failing after many requestsCause: 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?”

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

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.

What’s Next?

Firecrawl MCP

Web scraping and crawling

Custom MCP Servers

Build your own MCP integrations

MCP Overview

Back to MCP Integration overview

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 contact@junis.ai for assistance with GitHub automation workflows and integration support.

User Guides

​What You’ll Learn

​Quick Setup (5 Minutes)

​Authentication Levels

​GitHub PAT Scopes Explained

​Minimal Scopes (Read-Only)

​Recommended Scopes (Read + Write)

​Optional Scopes (Advanced)

​Available GitHub Tools

​Repositories

github_list_repositories

github_get_repository

github_search_repositories

github_create_repository

​Issues

github_list_issues

github_get_issue

github_create_issue

github_update_issue

​Pull Requests

github_list_pull_requests

github_get_pull_request

github_create_pull_request

github_merge_pull_request

​File Operations

github_get_file_contents

github_create_or_update_file

github_push_files

​Commits & Branches

github_list_commits

github_get_commit

github_list_branches

github_create_branch

​Example Use Cases

​DevOps Automation Agent

​Code Review Assistant

​Issue Triage Agent

​Troubleshooting

​Security Best Practices

​Advanced Configuration

​Using GitHub Enterprise Server

​Rate Limit Monitoring

​What’s Next?

Firecrawl MCP

Custom MCP Servers

MCP Overview

​Additional Resources

What You’ll Learn

Quick Setup (5 Minutes)

Authentication Levels

GitHub PAT Scopes Explained

Minimal Scopes (Read-Only)

Recommended Scopes (Read + Write)

Optional Scopes (Advanced)

Available GitHub Tools

Repositories

Issues

Pull Requests

File Operations

Commits & Branches

Example Use Cases

DevOps Automation Agent

Code Review Assistant

Issue Triage Agent

Troubleshooting

Security Best Practices

Advanced Configuration

Using GitHub Enterprise Server

Rate Limit Monitoring

What’s Next?

Additional Resources