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Cloning Private GitHub Repositories on a Server (The Right Way, With SSH)

#github #git #devops #tutorial

At some point, most developers hit this wall:

You’re logged into a server, you run:

git clone git@github.com:your-org/your-repo.git
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…and Git responds with:

Permission denied (publickey).
fatal: Could not read from remote repository.
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You know the repo exists.
You know you have access.
So what gives?

This post walks through why this happens, and how to fix it cleanly and securely, without leaking credentials or cutting corners.

The Core Problem (In Plain English)

GitHub doesn’t care who you are.
It cares which SSH key you’re presenting.

When you run git clone from a server:

  • GitHub sees an SSH key
  • It checks whether that key is authorized
  • If it doesn’t recognize it → access denied

That’s it. No magic.

Step 1: Understand What Machine You’re On

There are three identities involved:

  1. Your laptop (already authenticated with GitHub)
  2. Your server (a completely different machine)
  3. A Linux user on that server (e.g. app, bot, or deploy)

Even if:

  • the repo is yours
  • your laptop has access
  • you’re “the same person”

👉 The server has its own identity.

You must explicitly grant it access.

Step 2: Generate an SSH Key on the Server

Log into the server as the user that will run the project:

ssh app@your-server-ip
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Then generate a new SSH key:

ssh-keygen -t ed25519 -C "app-server-repo-access"
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When prompted:

  • Press Enter to accept the default location
  • Leave the passphrase empty (recommended for non-interactive servers)

This creates:

~/.ssh/id_ed25519        (private key)
~/.ssh/id_ed25519.pub    (public key)
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Step 3: Copy the Public Key

Display the public key:

cat ~/.ssh/id_ed25519.pub
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You’ll see a single line starting with:

ssh-ed25519 AAAAC3NzaC1lZDI1NTE5AAAAI...
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Copy the entire line.

Step 4: Add the Key to GitHub (Deploy Key Method)

This is the recommended approach for servers.

In GitHub:

  1. Open the repository
  2. Go to Settings
  3. Click Deploy keys
  4. Click Add deploy key
  5. Give it a name (e.g. app-server)
  6. Paste the public key
  7. Enable write access only if the server needs to push
  8. Save

This key now:

  • works only for this repo
  • cannot access anything else
  • is safe to revoke anytime

Step 5: Test SSH Connectivity

Back on the server:

ssh -T git@github.com
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If successful, you’ll see something like:

Hi! You've successfully authenticated, but GitHub does not provide shell access.
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That’s a good thing.

Step 6: Clone the Repository

Now retry:

git clone git@github.com:your-org/your-repo.git
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This time, it should work without errors.

Common Pitfall: “But I Can Clone From My Laptop”

That’s expected.

Your laptop:

  • has its own SSH key
  • already registered with GitHub

Your server:

  • is a different machine
  • needs its own key

SSH access is machine-based, not user-based.

Alternative: HTTPS (When It Makes Sense)

If the repo is public, you can always do:

git clone https://github.com/your-org/your-repo.git
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For private repos, HTTPS requires:

  • a GitHub token
  • storing credentials on the server

For long-running services, SSH deploy keys are cleaner and safer.

Why This Setup Is Best Practice

Using deploy keys means:

  • no shared credentials
  • no copying laptop keys to servers
  • repo-scoped access
  • easy rotation and revocation

This is how CI systems, deployment bots, and production servers are meant to work.

Final Takeaway

If git clone fails on a server, it’s almost never a Git issue.

It’s an identity issue.

Once you understand that:

Servers authenticate themselves to GitHub using SSH keys,

the fix becomes straightforward, secure, and repeatable.

Happy deploying 🚀

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