How to copy directory in Linux

Written by Bits Lovers on 06 May 2021

Copying files and directories is one of those things I do every day on Linux. Whether I’m backing up config files, moving photos around, or deploying code to servers, knowing how to copy stuff properly is essential.

Let me walk you through what I’ve learned about using cp, rsync, and why you probably shouldn’t use scp anymore.

The cp Command

The cp command is your basic workhorse for copying files and directories locally. It’s simple, reliable, and does exactly what you’d expect.

Basic syntax:

cp [OPTIONS] SOURCE... DESTINATION

Copy a single file:

cp fileA fileA.bkp

Copy a directory recursively:

cp -R source destination

That -R flag is crucial when copying directories—it tells cp to copy everything inside, not just the folder itself.

Real-World Example

Here’s something I actually do: backing up my home directory to an external USB drive before reinstalling Linux.

cp -R /home/bitslovers /mnt/media/usb01

My USB drive happens to be mounted at /mnt/media/usb01, so this copies everything in my home directory there.

Copy Multiple Files at Once

You can specify multiple files and a destination directory:

cp file1 file2 file3 destination-folder/

Copy Directory Contents Only

Sometimes I want to copy the files inside a directory without the directory itself. Like when I’m organizing photos by year from a camera’s SD card.

Using wildcard:

cp -R /mnt/media/usb01/DCM0001/* /home/bitslovers/Pictures/2021

The issue with wildcards? They skip hidden files (those starting with a dot).

Using -T flag:

cp -RT /mnt/media/usb01/DCM0001 /home/bitslovers/Pictures/2021

This copies everything including hidden files, but not the source directory itself.

Don’t Overwrite Existing Files

I’ve accidentally overwritten files more times than I care to admit. Here’s how to avoid that:

Skip existing files (-n):

cp -n /home/bitslovers/backup-apache2.sh /home/bitslovers/backup-scripts

Prompt before overwriting (-i):

cp -i /home/bitslovers/backup-apache2.sh /home/bitslovers/backup-scripts

You’ll see a prompt like:

cp: overwrite '/home/bitslovers/backup-apache2.sh'?

Type y or n to confirm.

Copy Multiple Directories

Need to copy several directories at once? Just list them all:

cp -R /etc /home/bitslovers /mnt/media/DCM0001

This copies both /etc and /home/bitslovers to the USB drive.

Preserve Permissions and Timestamps

When you copy files, they get new ownership and timestamps by default. That’s usually fine, but sometimes you need to preserve everything exactly as-is.

Preserve mode, ownership, and timestamps (-p):

sudo cp -p /home/bitslovers/.bashrc /home/bitslovers/backup

Preserve only timestamps:

sudo cp --preserve=timestamps /home/bitslovers/.bashrc /home/bitslovers/backup

Force Copy

Sometimes you need to force a copy operation:

cp -f ~/.bashrc /tmp

Copy Symbolic Links

By default, cp follows symbolic links and copies the actual files. If you want to copy the links themselves:

cp -d /home/bitslovers/backup-apache2.sh /usr/bin/

Dereference Links (Copy Actual Files)

If you want to copy what symlinks point to instead of the links:

cp -rL /tmp/docs/ /home/bitslovers/

Copy Only Newer Files

Handy for incremental backups—only copy files that have changed:

cp -ru /tmp/docs/ /home/bitslovers/

Create Hard Links Instead of Copying

This is a cool trick. Hard links point to the same data on disk, so changes in one location appear in the other. Unlike symlinks, hard links don’t break if you move or delete the original file.

cp -lr ~/Documents /tmp

I use this for quick local backups where I want changes to sync automatically between locations.

Copy Files by Extension

Combine ls and xargs to copy specific file types:

ls *.png | xargs -n1 -i cp {} /home/bitslovers/Pictures

Copying to Remote Servers

This is where things get interesting. You’ve got options, and some are better than others.

rsync: My Go-To for Remote Copies

rsync is fantastic. It’s fast, efficient, and has been around forever for good reason.

Check if you have it:

whereis rsync

Install if needed:

# Ubuntu/Debian
sudo apt-get install -y rsync

# CentOS/RHEL/Fedora
sudo yum install -y rsync

Basic syntax:

rsync -ar <origin-folder> <user>@<host>:<path>

Real example—backing up Apache configs:

rsync -ar /etc/apache2 [email protected]:/home/bitslovers/apache2_backup

The -a flag preserves permissions, timestamps, and other attributes. The -r flag makes it recursive.

Copy directory contents only:

rsync -ar /etc/apache2/* [email protected]:/home/bitslovers/apache2/

scp: Deprecated, Avoid Using It

Here’s the thing—scp is deprecated. OpenSSH 8.0 (released in 2019) downgraded the SCP protocol due to security vulnerabilities. Modern scp commands are actually wrappers around sftp internally.

If you’re still using scp, it’s time to switch.

Old way (don’t use):

scp -r /etc/apache2 [email protected]:/home/bitslovers/apache2

New way (use rsync instead):

rsync -avz /etc/apache2 [email protected]:/home/bitslovers/apache2

Why rsync Beats scp

rsync only copies changed files—huge time savings for large directories
rsync can resume interrupted transfers
rsync has more options for compression, permissions, filtering
rsync shows better progress information

The only advantage scp had was simplicity, but rsync isn’t exactly complicated.

Modern Alternatives to Consider

If you’re working with cloud storage or need something more modern:

rclone—Excellent for cloud storage (S3, Google Drive, Dropbox, etc.) but works over SSH/SFTP too:

rclone copy /local/path remote:bucket/path

sftp—For interactive file transfers:

sftp user@host
# Then use: put, get, mput, mget commands

Practical Tips from Experience

After years of copying files around, here’s what I’ve learned:

For local copies: Stick with cp. It’s fast, simple, and reliable.

For remote copies: Use rsync. The delta-transfer algorithm alone saves massive amounts of time.

For cloud storage: Check out rclone. It handles retries, checksums, and bandwidth limiting automatically.

For big transfers: Compress first. A single tar.gz file transfers faster than thousands of small files:

tar czf backup.tar.gz /path/to/files
rsync -avz backup.tar.gz user@host:/backups/

What Changed Since 2021?

scp is now officially deprecated—use rsync or sftp instead
GNU coreutils got a Rust rewrite (uutils)—faster and safer, though your distro might still use the C version
rclone matured significantly—if you work with cloud storage, it’s worth checking out
Better progress tools—progress (coreutils viewer) shows progress for cp, mv, dd, and other commands

Final Thoughts

Copying files isn’t glamorous, but getting it right saves headaches later. Use cp for local stuff, rsync for everything remote, and don’t touch scp anymore unless you absolutely have to.

Want to dive deeper? Check the man pages:

man cp
man rsync

Or combine cp with find for more complex operations. And if you’re moving lots of files, consider zipping them first or using tar.gz to speed things up.