Chapter 2 Linux

Operating systems are important, they sit between you and your computer and define what you can do with your computer, and how you can do this. One of the earliest ways for people to interact with their computers was the Unix shell, which as been around since the 1970ies¹. Unix systems scale well in multitasking, and they support a large amount of users. Because of its stability, software written in Unix will stay compatible with future computers for a long time. Knowing Unix will prepare you for using various computational hardware, from your laptop to a departmental server or university computation cluster.

2.1 How to get linux

Because linux is free and open for people to change and adapt, there are a lot of specialised linux systems. The beginning user may suffer decision paralysis! Luckily for us, there are a few versions that are more general. One of these is ubuntu, which you can download and edit for free, but a enteprise version is also developed for companies. In this guide, we will focus on installing this system because it is quite windows like, and widely supported.

2.1.1 On windows

The most safe and simple way to install linux on your computer is to install it as a virtual system. This means that linux will sit inside a ‘box’ within your linux system, and you will not accidentally delete important data. You will need 5 GB of free storage and an internet connection. This guide has been verified with windows 10 and 11 systems. You will also need administration rights.

Verify that your windows is configured for using virtual machines.
1. Click
2. Type ‘Control panel’, click it
3. Click Programs then click Turn windows features on or off
4. Turn on the following features
5. PressOK.
6. Restart your computer.
Go to the windows store and download the latest version of the ubunu subsystem.
Enable the wsl (windows subsystem).
1. Click .
2. Type powershell, open any versions of powershell that appear.
3. Type wsl --install
4. Type wsl --update
Make a new linux account.
1. Open linux (ubuntu).
2. Type your username (no uppercase, no spaces).
3. Type your password twice (once to select, second type to confirm). Take care that the screen does not show letters while you type!

2.1.2 From a flash drive

The ubuntu coorperation has a guide about installing linxu on a PC that does not yet have an opterating system.

2.2 Basic Linux

In this section you will see the commands needed to operate basic linux software, and get an idea of how the file system works.

2.2.1 The file system

In the linux system, files are placed in directories, just like in a windows computer. However, the directories you’ll find on a linux computer are a bit different than those from a windows one.

Linux directory structure. The directory structure is a tree with / being the top-level folder. From Cornell virtual workshop

User data (that means your data) is stored in the /home/<username> folder. For example if your username is jack06, then your data will be found in /home/jack06. As a short cut, ~/ is the same as /home/<username>.

2.2.2 Navigating and interacting with your files

When I open my Unix shell, my command prompt looks like this:

sibbe@sibbe-ThinkPad-T15-Gen-2i ~/Documents $ 
^^^^^|                        | ^^^^^^^^^^^   ^^^^^
  |  |                        |       |  Space for a command
  |   \_______________________/ Your current directory ($PWD)
  |               |
The user name     The name of your computer

You’ll most find yourself using cd (change directory) and ls (list files), which can be used to move between locations on your computer and to view the content of each location.

2.3 Bibliography

This chapter was inspired by Eric’s bioinformatic guide

See Unix on wikipedia ↩︎