How to Connect a Private GitHub Repository to cPanel Git Version Control

Category: cPanel / Git / Website Development
Audience: cPanel Users, Website Developers
Applies to: cPanel hosting accounts with Git Version Control

Overview

cPanel provides Git Version Control, allowing you to connect your website to a GitHub repository and manage your website's code directly from your hosting account.

This guide explains how to connect a private GitHub repository to cPanel using a secure SSH Deploy Key.

This method is recommended when your GitHub repository is private and you want cPanel to securely clone and manage the repository.

What You Will Need

Before starting, make sure you have:

• An active cPanel hosting account

• A GitHub account

• Access to the GitHub repository

• Permission to add a Deploy Key to the GitHub repository

• Access to cPanel → Git Version Control

You should also know the GitHub repository you want to deploy.

Example:

GitHub Repository:
[email protected]:yourcompany/your-project.git

Step 1 — Open cPanel Git Version Control

Log in to your cPanel account.

Go to:

cPanel → Files → Git Version Control

Click:

Create

This will open the repository creation form.

Step 2 — Generate an SSH Key in cPanel

If your cPanel account provides the SSH Access or Manage SSH Keys feature, you can generate an SSH key from:

cPanel → Security → SSH Access

Select:

Manage SSH Keys

Then click:

Generate a New Key

Use the following recommended settings:

Key Name

github_deploy

Key Type

RSA

or, if available:

ED25519

Passphrase

For automated Git deployments, the key normally needs to be available without an interactive passphrase.

If your hosting provider's Git deployment configuration requires an empty passphrase, leave this field blank.

Click:

Generate Key

Step 3 — Authorize the SSH Key

After generating the key, locate:

github_deploy

under Public Keys.

Click:

Manage

Then click:

Authorize

The key must be authorized before it can be used for SSH authentication.

Step 4 — Obtain the Public Key

Go back to:

SSH Access → Manage SSH Keys

Locate:

github_deploy

Under Public Keys, select:

View/Download

Copy the complete public key.

A public key normally looks similar to:

ssh-ed25519 AAAAC3NzaC1lZDI1NTE5AAAA... user@server

or:

ssh-rsa AAAAB3NzaC1yc2EAAAADAQABAAABAQ... user@server

Important

Only copy the public key.

Never provide or publish your private key.

Step 5 — Add the Public Key to GitHub

Log in to GitHub and open the repository you want to connect.

Go to:

Repository → Settings → Deploy keys

Click:

Add deploy key

Enter a descriptive title.

For example:

cPanel Production Server

Paste the public key you copied from cPanel.

For normal website deployments, leave:

Allow write access

disabled.

This gives the cPanel server read-only access to the repository.

Click:

Add key

Step 6 — Obtain the GitHub SSH Repository URL

Open the GitHub repository.

Click:

Code

Select:

SSH

Copy the SSH repository URL.

Example:

[email protected]:yourcompany/your-project.git

Use the SSH URL

For private repositories, use:

[email protected]:yourcompany/your-project.git

Avoid using:

https://github.com/yourcompany/your-project.git

when following this SSH Deploy Key configuration.

Step 7 — Create the Repository in cPanel

Return to:

cPanel → Git Version Control → Create

Enable:

Clone a Repository

Clone URL

Paste the GitHub SSH URL.

Example:

[email protected]:yourcompany/your-project.git

Repository Path

Specify where cPanel should store the repository.

For example:

repositories/my-project

or:

public_html/my-project

depending on your website's deployment structure.

Important: Do not place the repository directly inside an existing directory containing unrelated website files unless you understand how Git will manage that directory.

Repository Name

Enter a descriptive name, for example:

my-project

Click:

Create

Step 8 — Wait for the Repository to Clone

cPanel may display a message similar to:

The system successfully initiated the clone process. The system may require more time to clone large remote repositories.

This is normal.

Once the process completes, the repository should appear under:

cPanel → Git Version Control

You should see information such as:

• Repository name

• Repository path

• Branch

• Remote URL

• Repository status

Step 9 — Verify the Repository

Open:

cPanel → Git Version Control

Locate the repository you created.

Click:

Manage

Verify that the repository shows the expected:

Remote URL:
[email protected]:yourcompany/your-project.git

You can also use File Manager to confirm that the repository files were downloaded.

Step 10 — Configure Deployment

After the repository has been successfully cloned, cPanel can be configured to deploy changes from GitHub to your website.

Open:

cPanel → Git Version Control → Manage

Depending on your hosting configuration, you may see deployment-related options such as:

Deploy HEAD Commit

or deployment configuration options.

The exact deployment setup depends on your application.

For a simple PHP website, the repository can often be deployed directly to the website's document root.

For frameworks such as:

• Laravel

• Django

• Node.js

• Python applications

• Other application frameworks

additional application configuration may be required.

Recommended Repository Structure

For a typical website, you may use:

/home/CPANEL_USERNAME/repositories/my-project

with the website deployed to:

/home/CPANEL_USERNAME/public_html

For example:

/home/exampleuser/
│
├── repositories/
│   └── my-project/
│       ├── .git/
│       ├── index.php
│       ├── assets/
│       └── ...
│
└── public_html/

Your developer or hosting administrator may recommend a different structure depending on the application.

Common Problems

"Could not read Username for https://github.com"

You may see an error similar to:

fatal: could not read Username for 'https://github.com':
No such device or address

Cause

The repository was configured using an HTTPS URL:

https://github.com/company/project.git

instead of the SSH URL.

Solution

Use:

[email protected]:company/project.git

and make sure the corresponding SSH public key has been added to the GitHub repository's Deploy keys.

"Permission denied (publickey)"

Example:

Permission denied (publickey).

Possible causes

• The public key has not been added to GitHub.

• The wrong public key was added.

• The SSH key has not been authorized in cPanel.

• The GitHub Deploy Key belongs to a different repository.

• The repository URL is incorrect.

Check the following

1. Open the GitHub repository.

2. Go to Settings → Deploy keys.

3. Confirm that the correct public key is listed.

4. Confirm that the key belongs to the cPanel account.

5. Confirm that the repository URL is correct.

"Repository not found"

Example:

ERROR: Repository not found.

Check:

• GitHub repository owner

• Repository name

• Repository spelling

• Repository visibility

• Deploy Key configuration

For example:

[email protected]:synqbox/odessee.git

must point to the correct GitHub repository.

Host Key Verification Error

You may encounter:

Host key verification failed.

If this occurs, contact your hosting provider's technical support team.

The hosting server may require additional SSH configuration for GitHub.

Security Recommendations

For private GitHub repositories:

1. Use Deploy Keys

A GitHub Deploy Key is dedicated to repository access.

2. Use Read-Only Access

For normal deployments, leave:

Allow write access

disabled.

The server generally only needs to download repository changes.

3. Never Share Your Private Key

Never provide the private SSH key to:

• Support tickets

• Public forums

• Chat messages

• Email

• GitHub repositories

• Website files

Only the public key should be added to GitHub.

4. Use Separate Keys Where Appropriate

For different production servers, projects, or hosting accounts, use separate SSH keys whenever practical.

This allows access to be revoked independently.

Quick Setup Checklist

Before creating the cPanel repository, confirm:

☐ cPanel account is active

☐ SSH key generated

☐ SSH key authorized in cPanel

☐ Public key copied

☐ Public key added to GitHub Deploy Keys

☐ GitHub repository is accessible

☐ GitHub SSH URL copied

☐ cPanel Git Version Control opened

☐ "Clone a Repository" selected

☐ SSH repository URL used

The GitHub URL should look like:

[email protected]:OWNER/REPOSITORY.git

After creation:

☐ Repository appears in Git Version Control

☐ Repository files are present

☐ Correct branch is selected

☐ Deployment configuration completed

Important Note for cPanel Users

If your hosting server uses a custom SSH port, you normally do not need to change anything on your cPanel account.

The hosting provider may already have the required GitHub SSH configuration in place.

If:

ssh -T [email protected]

or the cPanel Git Version Control process produces an SSH connection or host-key error, contact your hosting provider's technical support team rather than changing server SSH settings yourself.

Summary

The basic workflow is:

GitHub Private Repository
        ↓
Generate SSH Key
        ↓
Authorize SSH Key in cPanel
        ↓
Copy Public Key
        ↓
GitHub → Repository → Settings → Deploy Keys
        ↓
Add Public Key
        ↓
Copy GitHub SSH URL
        ↓
cPanel → Git Version Control
        ↓
Create / Clone Repository
        ↓
Deploy

Recommended GitHub URL format

[email protected]:OWNER/REPOSITORY.git

Using SSH Deploy Keys provides a secure way for cPanel to access a private GitHub repository without storing a GitHub username and password in your hosting account.