Linux and the Command Line

Linux is a family of open-source Unix-like operating systems based on the Linux kernel. It's typically packaged in a distribution, which includes the Linux kernel along with a set of software tools and utilities. There are many different distributions of Linux, such as Ubuntu, Fedora, Red Hat, and CentOS.

Linux distributions all run a shell, which is a program that interprets and executes programs. The "command line" refers to the interface between you and the shell.

Concepts

• Operating System: The software that manages resources of a computer.
• Architecture: The type of CPU (e.g., x86, x86_64, ARM).
• Distribution: A version of the Linux operating system.
• Terminal: The window in which you type commands.
• Shell: The program that interprets and executes commands.

Terminal

The "terminal" is the interface between you and the shell. It's also referred to as the "command line" or the "console". Various programs can serve as a terminal, such as:

• iTerm on macOS
• cmd on Windows
• EC2 Serial Console
• The "Terminal" tab in RStudio

Shell

The "shell" is the program that interprets and executes commands. Examples include:

• bash (most common on Linux systems)
• zsh (the default on macOS)

Read through the bash guide for more information on the writing and executing shell scripts.

Windows Subsystem for Linux (WSL)

Windows users can run a Linux distribution on Windows using WSL. This allows you to run Linux command-line tools and utilities directly on Windows without needing a virtual machine or dual-boot setup. If you want to use WSL, follow the installation instructions.

Linux Command Line Interface (CLI)

To check your bash version:

bash --version

Example output:

GNU bash, version 5.1.16(1)-release (x86_64-pc-linux-gnu)
Copyright (C) 2020 Free Software Foundation, Inc.
License GPLv3+: GNU GPL version 3 or later <http://gnu.org/licenses/gpl.html>

To verify if bash is running:

echo $SHELL

User Management

Set a password for the ubuntu user

sudo passwd ubuntu

Adding a user to sudoers

sudo adduser username sudo

Configure no-password sudo

Open the sudoers file for editing:

sudo visudo

[!NOTE] > visudo is a special command that edits the sudoers file safely. If the environment variable $EDITOR is not set, it will use vi.

Uncomment or add these lines:

# Members of the admin group may gain root privileges
%admin ALL=(ALL) ALL

# Allow members of group sudo to execute any command
%sudo   ALL=(ALL:ALL) ALL

# Add to run any command without a password
username ALL=(ALL) NOPASSWD: ALL

SSH Operations

Installing OpenSSH server

sudo apt install openssh-server

Connecting to a remote server

ssh username@hostname

Copying files to/from a remote server

scp username@hostname:/path/to/remote/file /path/to/local/file
scp /path/to/local/file username@hostname:/path/to/remote/file

Setting up passwordless SSH

1. Generate a new SSH key pair:

ssh-keygen -t rsa -b 4096 -C "a comment"

1. Copy the public key to the remote server:

ssh-copy-id -i <identity_file >username@hostname

1. Modify the ~/.ssh/config file:

Host hostname
User username
HostName hostname
IdentityFile ~/.ssh/identity_file

Now you can log in without a password:

ssh username@hostname

Quick Reference of common Linux commands

Command	Description
pwd	print working directory
ls	list files and directories in the current directory
cd	change directory
cp	copy files or directories
mv	move or rename files or directories
touch	create an empty file
mkdir	make a new directory
rm	remove files or directories
wc	word count
less	view the contents of a file
head	view the first few lines of a file
tail	view the last few lines of a file
gzip	compress a file
gunzip	decompress a file
curl	download the contents of a website
echo	print text to the terminal
cat	concatenate and print files
man	view the manual for a command

Created by Ryan D. Najac for the Palomero Lab at the Institute for Cancer Genetics.
Page last updated on 2025-03-13.