Installing Software with apt

Ubuntu uses apt to install, update, and remove software. It downloads packages from official repositories and handles all dependencies automatically. Most bioinformatics tools that run on Linux can be installed this way.

Updating the package list

Before installing anything, update the list of available packages. This tells apt about the latest versions.

$ sudo apt update

This does not install or upgrade anything. It only refreshes the catalog. Run this before every install session.

Installing packages

# Install a single package
$ sudo apt install samtools

# Install multiple packages at once
$ sudo apt install samtools bcftools bedtools

# Say yes automatically
$ sudo apt install -y fastqc

The -y flag skips the confirmation prompt. This is useful in scripts.

Searching for packages

# Search for a package by name
$ apt search samtools

# Show details about a package
$ apt show samtools

The search and show commands do not require sudo because they only read information.

Upgrading installed packages

# Upgrade all installed packages to their latest versions
$ sudo apt upgrade

# Update the list and upgrade in one step
$ sudo apt update && sudo apt upgrade -y

Run this regularly to get security patches and bug fixes.

Removing packages

# Remove a package but keep its configuration files
$ sudo apt remove samtools

# Remove a package and its configuration files
$ sudo apt purge samtools

# Clean up packages that were installed as dependencies but are no longer needed
$ sudo apt autoremove

Common packages for bioinformatics

Some tools are available directly from Ubuntu repositories.

# Essential build tools for compiling software
$ sudo apt install build-essential

# Common bioinformatics tools
$ sudo apt install samtools bcftools bedtools

# Python and development headers
$ sudo apt install python3 python3-dev python3-venv

# R base
$ sudo apt install r-base r-base-dev

# Utilities you will use often
$ sudo apt install curl wget git htop tree

Not every bioinformatics tool is in the Ubuntu repositories. For those, you will use other package managers like conda, uv, or install from source. Containers are another option covered in the next section.

Adding external repositories

Some software requires adding a third-party repository first. This is common for newer versions of R, specialized tools, or commercial software.

# Add a repository
$ sudo add-apt-repository ppa:some/repository

# Update the package list to include the new repository
$ sudo apt update

# Now install the package
$ sudo apt install new-package

Be careful with third-party repositories. Only add repositories from sources you trust.

Checking what is installed

# List all installed packages
$ apt list --installed

# Check if a specific package is installed
$ apt list --installed | grep samtools

# Check which version is installed
$ apt show samtools | grep Version

Quick reference

Command	What it does
sudo apt update	Refresh the package catalog
sudo apt install pkg	Install a package
sudo apt install -y pkg	Install without confirmation
sudo apt upgrade	Upgrade all packages
sudo apt remove pkg	Remove a package
sudo apt purge pkg	Remove a package and its config
sudo apt autoremove	Remove unused dependencies
apt search name	Search for a package
apt show name	Show package details
apt list --installed	List installed packages

Next steps

With software installation covered, the next page explains how to connect to remote servers with SSH.