Basic server commands (Linux)

This page lists common commands to navigate on a server, manage files, and understand permissions.

Opening a terminal and pasting

  • Copy text: usually Ctrl + Shift + C (or just select text, depending on your terminal)
  • Paste text into the terminal:
    • Often: Ctrl + Shift + V
    • In many terminal apps: right mouse button (right-click) pastes
    • Sometimes: middle mouse button (mouse wheel click) pastes

Be careful when pasting commands from anywhere (email, chat, web). Always read the command before pressing Enter.

Where am I? (navigation)

Show current directory 

pwd

List files 

ls
ls -l      # long view (permissions, owner, size, date)
ls -lah    # long view + human-readable sizes + show hidden files

Change directory 

cd /path/to/somewhere
cd ..      # go one directory up
cd -       # go back to the previous directory
cd ~       # go to your home directory

{: .note }Tab completion (very useful). Start typing a path/filename and press Tab to auto-complete. And double tab to see options to complete.

Creating directories and files

Create a directory 

mkdir my_folder
mkdir -p projects/2026-05-05_project1/results   # create nested folders if needed

Create an empty file 

touch notes.txt

Copy, move, rename, delete

Copy files 

cp file1.txt copy_of_file1.txt
cp file1.txt /path/to/destination/

Copy a directory (and everything inside):

cp -r my_folder my_folder_backup

Move / rename

mv is used for both moving and renaming.

Rename a file:

mv oldname.txt newname.txt

Move a file to another directory:

mv myfile.txt /path/to/destination/

Delete (be careful)

Delete a file:

rm myfile.txt

Delete a directory (and everything inside):

rm -r my_folder

rm permanently deletes files (there is usually no “Recycle Bin” on servers). Double-check before running rm -r.

Viewing file contents

Show a short text file:

cat file.txt

View long files page-by-page:

less file.txt

Useful inside less:

  • q = quit
  • /word = search for “word”
  • n = next match

Show the first / last lines:

head file.txt
tail file.txt
tail -f logfile.txt   # follow a file that is growing (logs)

Searching

Search for a file by name (in the current directory and below):

find . -name "*.fastq.gz"

Search for text inside files:

grep "ERROR" logfile.txt
grep -R "some_text" .   # recursive search in all files under current directory

Permissions (who can read/write/execute)

Read permissions with ls -l

Example output:

ls -l
# -rw-r----- 1 user group  1200 May  5  file.txt
# drwxr-x--- 2 user group  4096 May  5  my_folder

The permission string has 3 blocks:

  • user (owner)
  • group
  • others (everyone else)

And 3 permission types:

  • r = read (see file contents / list directory)
  • w = write (edit file / create/delete inside directory)
  • x = execute (run a program / enter a directory)

Changing permissions with chmod

Make a script executable:

chmod +x myscript.sh

Remove write permission for others:

chmod o-w file.txt

(Advanced) numeric mode example:

chmod 640 file.txt
# 6 = rw- (user)
# 4 = r-- (group)
# 0 = --- (others)

Changing owner/group (often restricted) 

chown user file.txt
chgrp group file.txt
chown user:group file.txt

On many servers, only admins can change owners.

Ownership: who owns a file? 

ls -l file.txt

If you see permission problems (“Permission denied”), check:

  • Are you in the right directory?
  • Do you have write permission where you are trying to create/edit?
  • Is the file owned by someone else or a different group?

Helpful “safety” tips

  • Prefer cp for safety when you’re unsure; use mv when you’re confident.
  • Use ls before and after a command to confirm what changed.
  • Avoid spaces in file/folder names; use _ instead (e.g. raw_data_2026).

Quick cheat sheet 

pwd                  # where am I
ls -lah              # list files (detailed)
cd <dir>             # go to directory
mkdir -p <dir>       # create directory (nested ok)
cp <src> <dst>       # copy
mv <src> <dst>       # move/rename
rm <file>            # delete file
rm -r <dir>          # delete directory (danger)
less <file>          # view file
grep -R "text" .     # search text in files
find . -name "*.txt" # find by name
chmod +x <file>      # make executable