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What cloning does on a server
git clone creates a new local copy from a remote repository. Unless you provide a destination directory, Git derives the new directory name from the repository name in the URL. The resulting directory is a normal working tree containing a hidden .git directory, so you can run commands such as git status, git log, and git fetch inside it.
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In a non-bare clone, the branch selected by --branch becomes the branch to which HEAD points and is checked out into the working tree. Without that option, Git uses the remote repository’s default branch. A clone is not a one-time archive: it retains the remote named origin, allowing later fetches and updates.
Before you run the command
- Git must be available on the server. Confirm with
git --version. The exact package-install command depends on the Linux distribution; this guide does not assume Debian, Ubuntu, RHEL, or another specific family. - Choose a location writable by the account that will run Git. Deployment users commonly work in an application directory under their home directory or in a service-owned release path. Do not clone as a different account and expect the deployment account to update the files later.
- Have the complete remote URL. HTTPS and SSH URLs use different credential mechanisms. For a public repository, either may work; a private repository requires credentials that the server can use non-interactively.
- Check available disk space. A full clone includes repository history and can be substantially larger than the checked-out files. A shallow clone can reduce the initial transfer when history is not needed.
- Decide whether the server needs history. Runtime deployments and many CI jobs only need the files at one revision. Builds that calculate changelogs, inspect tags, run history-based versioning, or create patches need more history.
Clone a public repository
Use the default branch
Change to the parent directory and run:
cd /path/where/the/project-should-live
git clone <url>Replace <url> with the repository’s HTTPS or SSH URL. Git creates a directory based on the repository name. Enter it and verify the working tree:
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cd repository-name
git status
git remote -vgit status should report the checked-out branch and a clean tree immediately after a successful clone. git remote -v shows the fetch and push URLs recorded for origin.
Choose the destination directory explicitly
Pass a second argument when the directory name must differ from the repository name:
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Clone a specific branch
Use --branch (or its short form, -b) to select the branch at clone time:
git clone --branch staging <url>For a non-bare repository, this both points HEAD at staging and checks that branch out. The command still downloads the repository data needed by the clone unless you also limit the history or branch scope.
If the branch name contains characters that your shell treats specially, quote the argument:
git clone --branch 'release/2.4' <url>A misspelled or nonexistent branch causes the clone to fail rather than silently selecting another branch. Confirm the name in the remote repository before putting the command in an automated deployment script.
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Use a single-branch shallow clone for deployments
Latest commit only
When the server only needs the current files from one branch, use:
git clone --depth 1 --branch main --single-branch <url>--depth 1 truncates history to one commit. The explicit --single-branch limits the clone to the history leading to the tip of main. This is useful for deploy and CI work where old commits, unrelated branches, and most repository metadata are unnecessary.
The result is a shallow repository. Commands that require ancestors outside the downloaded boundary can report incomplete history, and tools that expect every tag or commit may not work as they do in a full clone. Treat the clone as an intentionally limited checkout, not as a complete backup.
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Choose a larger depth
Set another positive number when a build needs a small amount of recent history:
git clone --depth 20 --branch main --single-branch <url>The number is a commit count, not a number of days or megabytes. The appropriate value depends on the task: a deployment that only reads files can use one commit, while a changelog step may need enough commits to cover the release range.
Using --depth implies single-branch behavior unless you explicitly add --no-single-branch. Add that override only when a shallow clone must include history from more than the selected branch; it can increase the transfer and storage cost.
Deepen a shallow clone later
You do not have to discard a shallow checkout to obtain more history. From inside the clone, fetch additional commits:
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cd /path/to/repository
git fetch --depth 20 origin mainThis requests a history reaching a depth of 20 for main. Git’s fetch options also support deepening relative to the current shallow boundary; use the fetch documentation for the exact deepening or shortening mode required by your workflow. After fetching, inspect the available history with git log before relying on it in a build.
Clone a private repository with an SSH deploy key
Why a deploy key fits a single repository
A deploy key is an SSH key pair installed on the server and authorized for one repository. On GitHub, deploy keys are read-only by default. Write access is an explicit option, and a key is scoped to that one repository rather than to every repository belonging to a user account.
For a server that only pulls source code, keep the key read-only. A 2025 report from Read the Docs described deploy keys with write access being disabled after a security risk involving SSH-agent access. A write-capable key also turns a compromised server into a potential source of unauthorized repository changes.
Generate the key on the server
Log in as the account that will perform the clone and create the key pair there:
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Keep the private key on the server and never paste it into repository settings, tickets, logs, or deployment output. Display or copy only the public-key file when authorizing the repository:
cat ~/.ssh/repo_deploy.pubAuthorize it in the repository settings
- Open the private repository’s settings.
- Choose Deploy keys.
- Add the complete contents of
repo_deploy.pub. - Leave Allow write access unchecked for a pull-only server.
Each deploy key works for one repository. If the same server must read several private repositories, do not assume one repository’s deploy key automatically grants access to the others. GitHub recommends considering a GitHub App with scoped, short-lived tokens when access to multiple repositories is required. That model can reduce the exposure of long-lived private keys, but its setup is outside this clone procedure.
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Tell SSH which key to use
Create or edit ~/.ssh/config for the deployment account:
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Host github-repo-deploy
HostName github.com
User git
IdentityFile ~/.ssh/repo_deploy
IdentitiesOnly yesThe alias lets you select this key without changing the host-wide SSH defaults. IdentitiesOnly yes tells SSH to use the identity specified for this host entry instead of trying unrelated keys from an agent. Protect the configuration and private key with the account’s normal SSH file permissions, and ensure the deployment process runs as the same account whose home directory contains these files.
Test authentication before cloning:
ssh -T [email protected]A successful test confirms that SSH can reach the host and present an accepted identity. The test does not clone a repository and does not prove that the key has access to every repository; repository authorization is still checked during git clone.
Clone through the SSH alias
Use the alias from the configuration in the repository URL:
git clone git@github-repo-deploy:OWNER/REPOSITORY.gitReplace OWNER/REPOSITORY.git with the path for the authorized repository. You can combine the alias with branch and depth options:
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git clone --depth 1 --branch main --single-branch
git@github-repo-deploy:OWNER/REPOSITORY.git
/srv/apps/my-gameThis pattern keeps the private key selection in SSH configuration while making the Git command suitable for a deployment script.
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The choice is primarily about how the server proves its identity and how much repository access that credential carries.
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| Property | HTTPS clone | SSH deploy-key clone |
|---|---|---|
| Credential form | An HTTPS credential supplied through the host’s supported authentication method | A private SSH key paired with a public key authorized in repository settings |
| Typical scope | Depends on the token or account mechanism used | One repository per deploy key |
| Server storage | Requires a safe method for supplying and rotating the HTTPS credential | Private key remains on the server; it is often unprotected by a passphrase for unattended jobs |
| Write permission | Determined by the HTTPS credential’s scopes | Read-only by default; write access must be explicitly enabled |
| Multiple repositories | Can be practical with a carefully scoped token, depending on the host | Separate keys are needed for separately authorized repositories, or use a host-supported app/token model |
Neither transport makes a compromised server safe. A long-lived, passphrase-less deploy key is convenient for unattended pulls but remains usable until it is removed from the repository or replaced. Keep the key read-only, restrict the server account, and remove the key when the machine or deployment is retired.
Verify the clone before deploying files
- Check the directory: run
pwdandgit rev-parse --show-toplevelto confirm that the process is operating in the intended checkout. - Check the selected branch: run
git branch --show-current. This catches a destination or branch mistake before files are copied into a service directory. - Check the remote: run
git remote -vand confirm that the URL points to the expected host and repository. - Check the worktree: run
git status. A newly cloned tree should not contain edits created by an earlier deployment. - Check shallow status when relevant: if the clone used
--depth, treat history-dependent build steps as unverified until you confirm that the required commits or tags are present.
Only after these checks should an automation script link the checkout into a running service, build artifacts from it, or replace an existing release.
Common failures and fixes
git: command not found
Git is not installed or is not on the service account’s PATH. Install Git using the procedure for the server’s distribution, then start a new session or use the fully qualified binary path if your service environment has a restricted path.
Permission denied while creating the destination
The current account cannot write to the parent directory. Choose a directory owned or writable by that account, or correct ownership and permissions according to your server’s deployment policy. Avoid running the clone as root merely to bypass a permissions error; that commonly leaves files that the application account cannot update.
SSH authentication fails
- Confirm that the public key copied into Deploy keys is the contents of the matching
.pubfile, not the private key. - Run
ssh -T [email protected]as the same account that will run Git. - Check that the SSH configuration’s
IdentityFilepath is correct and that the alias used in the Git URL exactly matches theHostentry. - Make sure the key was added to the intended repository and that write access was not enabled unnecessarily.
The repository or branch cannot be found
Check spelling, capitalization, owner, and repository visibility. A private repository can return an access-related error that resembles a missing repository when the key is not authorized. For a branch error, verify the branch name and repeat the clone with the correct value after removing the failed destination directory.
The clone is unexpectedly large or slow
A full clone downloads history that a deployment may never use. Select the required branch and use an appropriate --depth value. If a later build fails because it needs older commits, deepen the existing clone with git fetch --depth rather than starting over.
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That is an expected limitation of a shallow clone. Increase the depth, fetch the required branch history, or use a full clone for that job. Do not silently treat a shallow checkout as equivalent to a complete repository.
Quick Recap
Operational checklist
- Run Git as the intended non-root deployment account.
- Use
--branchwhen the default branch is not the release branch. - Use
--depthonly when the build does not require complete history. - For a private repository, generate the SSH key on the server and authorize its public half for that repository.
- Keep deploy keys read-only unless a documented operation genuinely requires writes.
- Use an SSH
Hostentry andIdentitiesOnly yeswhen the server has several identities. - Test SSH authentication before embedding the clone command in automation.
- Verify branch, remote, path, and worktree status before activating the checkout.
- Remove or rotate the deploy key when the server is decommissioned or the deployment design changes.
Command reference
| Goal | Command |
|---|---|
| Clone the default branch | git clone <url> |
| Clone and check out one branch | git clone --branch <branch> <url> |
| One-commit deployment clone | git clone --depth 1 --branch main --single-branch <url> |
| Shallow clone with 20 commits | git clone --depth 20 --branch main --single-branch <url> |
| Deepen an existing clone | git fetch --depth 20 origin main |
| Generate an RSA deploy-key pair | ssh-keygen -t rsa -f ~/.ssh/repo_deploy |
| Test SSH authentication | ssh -T [email protected] |
| Clone with a configured SSH alias | git clone git@github-repo-deploy:OWNER/REPOSITORY.git |
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