Working with Private Repositories¶

Use GitHub to MCP with private repositories using authentication.

GitHub Token Setup¶

To access private repositories, you need a GitHub Personal Access Token (PAT).

Creating a Token¶

1. Go to GitHub Settings → Developer Settings → Personal Access Tokens
2. Click "Generate new token (classic)"
3. Give it a descriptive name (e.g., "GitHub to MCP")
4. Select scopes:
5. repo - Full control of private repositories
6. Or read:packages for read-only access
7. Click "Generate token"
8. Copy the token immediately (you won't see it again!)

Token Scopes¶

Using Your Token¶

Environment Variable (Recommended)¶

Set the GITHUB_TOKEN environment variable:

# Add to ~/.bashrc or ~/.zshrc
export GITHUB_TOKEN=ghp_xxxxxxxxxxxxx

$env:GITHUB_TOKEN="ghp_xxxxxxxxxxxxx"

set GITHUB_TOKEN=ghp_xxxxxxxxxxxxx

Then use normally:

npx @nirholas/github-to-mcp https://github.com/your-org/private-repo

CLI Flag¶

Pass the token directly:

npx @nirholas/github-to-mcp https://github.com/your-org/private-repo \
  --token ghp_xxxxxxxxxxxxx

Programmatic¶

import { generateFromGithub } from '@nirholas/github-to-mcp';

const result = await generateFromGithub(
  'https://github.com/your-org/private-repo',
  { token: process.env.GITHUB_TOKEN }
);

Web UI Authentication¶

On the web interface:

1. Click the "Settings" gear icon
2. Enter your GitHub token in the "GitHub Token" field
3. The token is stored locally in your browser (not sent to servers)
4. Generate private repos normally

GitHub Enterprise¶

For GitHub Enterprise Server, use the full URL:

npx @nirholas/github-to-mcp https://github.your-company.com/org/repo \
  --token ghp_xxxxxxxxxxxxx

Rate Limits¶

Organization Repositories¶

SSO-Enabled Organizations¶

If your organization uses SAML SSO:

1. Create your token normally
2. Go to Token Settings
3. Find your token and click "Enable SSO"
4. Authorize for your organization

Fine-Grained Tokens¶

For better security, use fine-grained tokens:

1. Go to Fine-grained tokens
2. Click "Generate new token"
3. Select specific repositories
4. Choose minimal permissions:
5. Contents: Read-only
6. Metadata: Read-only

Security Best Practices¶

1. Rotate Tokens Regularly¶

Set a reminder to regenerate tokens every 90 days.

2. Use Minimum Scopes¶

Only request the permissions you need.

3. Never Commit Tokens¶

Add to .gitignore:

.env
.env.local
*.token

4. Use Environment Variables¶

Never hardcode tokens in your code.

5. Audit Token Usage¶

Check Security Log for token activity.

Troubleshooting¶

"Bad credentials" Error¶

• Token may be expired
• Token may lack required scopes
• SSO may not be authorized

"Not Found" Error¶

• Repo doesn't exist or is private
• Token lacks repo scope
• Token not authorized for organization

Rate Limit Exceeded¶

• Wait for the limit to reset (usually 1 hour)
• Use a token if not already
• Check for API-heavy operations

Check Token Validity¶

curl -H "Authorization: token ghp_xxxxx" \
  https://api.github.com/user

Should return your user information.

Example: Private Repo Workflow¶

Complete workflow for a private repository:

# 1. Set token
export GITHUB_TOKEN=ghp_xxxxxxxxxxxxx

# 2. Generate MCP server
npx @nirholas/github-to-mcp https://github.com/my-company/internal-api \
  -o ~/mcp-servers/internal-api

# 3. Install dependencies
cd ~/mcp-servers/internal-api
npm install

# 4. Test the server
npm start

# 5. Add to Claude Desktop
# Edit claude_desktop_config.json

Next Steps¶

• Custom Tools - Extend your MCP server
• Claude Desktop - Connect your server
• Configuration - More options