Setup for this course

In this course, we will use the Linux/Unix operating system to teach practical lessons

For you to benefit completely from the learning on this course, it will be necessary to have some prior knowledge of how to use Linux. There are many online introductory guides on the UNIX/Linux operating system and command line, including the introductory WCS MOOC course Bioinformatics for Biologists: An Introduction to Linux, Bash scripting and R.

System Requirements for the course:

You will need access to a Linux based operating system which can run commands via a terminal. You will need administrator permission on this computer to enable you to install software.

The minimum system requirements of a computer are:

• Access to a Linux/unix terminal (Linux standalone, macOS, Windows Subsystem for Linux (WSL2))
• Processor of i5 or equivalent (M chip Macs see below*)
• 8 Gigabytes of RAM
• At least 50 Gigabytes of hard disk space should be available
• Administrator rights for you, the user
• Access to the internet with a minimum speed of 2Mbps (slower speeds will mean longer download and install times)

NB – *Conda and Virtual Machines are unlikely to work on M chip Macs

Recommended system for this course:

This course material has been tested on an Ubuntu 22.04 LTS system.

We recommend downloading and installing this operating system as a virtual machine by following this guide: https://ubuntu.com/tutorials/how-to-run-ubuntu-desktop-on-a-virtual-machine-using-virtualbox#1-overview

This should take between 1-2 hours depending on your internet speed and computer specifications.

NB – always backup important files and information before making big changes to your operating system.

NB – M chip Macs are not supported by VirtualBox. Conda also may encounter errors, you will need to use Homebrew, as explained below.

How to use the terminal on MacOS and Linux

a. MacOS

Try the following to launch Terminal: Utilize the computer’s Spotlight search feature on a Mac. Using the Return key, enter Terminal.

b. Linux

Bash is typically the default Unix Shell for Linux operating systems. It can be accessed by launching the Gnome Terminal, KDE Konsole, or Xterm, which can be located via the program’s menu or the search bar on most Linux distributions. You may execute it by opening a terminal and typing bash if your computer is configured to use something different from Bash.

We recommend using UNIX-based operating systems (Linux and macOS) for this course. Please use the links attached to install a Linux Virtual machine for those with a Windows Operating system.

a. Linux Virtual box Image https://ubuntu.com/tutorials/how-to-run-ubuntu-desktop-on-a-virtual-machine-using-virtualbox#1-overview

b. Windows Subsystem for Linux https://learn.microsoft.com/en-us/windows/wsl/install#install-wsl-command

FAQ

For some of the frequently asked questions on VirtualBox and virtual disk issues, please see the document attached at the end of the step.