Introducing the Shell

Last updated on 2023-08-15 | Edit this page



  • What is a command shell and why would I use one?
  • How can I move around on my computer?
  • How can I see what files and directories I have?
  • How can I specify the location of a file or directory on my computer?


  • Describe key reasons for learning shell.
  • Navigate your file system using the command line.
  • Access and read help files for bash programs and use help files to identify useful command options.
  • Demonstrate the use of tab completion, and explain its advantages.

What is a shell and why should I care?

A shell is a computer program that presents a command line interface which allows you to control your computer using commands entered with a keyboard instead of controlling graphical user interfaces (GUIs) with a mouse/keyboard/touchscreen combination.

There are many reasons to learn about the shell:

  • Many bioinformatics tools can only be used through a command line interface. Many more have features and parameter options which are not available in the GUI. BLAST is an example. Many of the advanced functions are only accessible to users who know how to use a shell.
  • The shell makes your work less boring. In bioinformatics you often need to repeat tasks with a large number of files. With the shell, you can automate those repetitive tasks and leave you free to do more exciting things.
  • The shell makes your work less error-prone. When humans do the same thing a hundred different times (or even ten times), they’re likely to make a mistake. Your computer can do the same thing a thousand times with no mistakes.
  • The shell makes your work more reproducible. When you carry out your work in the command-line (rather than a GUI), your computer keeps a record of every step that you’ve carried out, which you can use to re-do your work when you need to. It also gives you a way to communicate unambiguously what you’ve done, so that others can inspect or apply your process to new data.
  • Many bioinformatic tasks require large amounts of computing power and can’t realistically be run on your own machine. These tasks are best performed using remote computers or cloud computing, which can only be accessed through a shell.

In this lesson you will learn how to use the command line interface to move around in your file system.

How to access the shell

On a Mac or Linux machine, you can access a shell through a program called “Terminal”, which is already available on your computer. The Terminal is a window into which we will type commands. If you’re using Windows, you’ll need to download a separate program to access the shell.

To save time, we are going to be working on a remote server where all the necessary data and software available. When we say a ‘remote server’, we are talking about a computer that is not the one you are working on right now. You will access the Carpentries remote server where everything is prepared for the lesson. We will learn the basics of the shell by manipulating some data files. Some of these files are very large , and would take time to download to your computer. We will also be using several bioinformatic packages in later lessons and installing all of the software would take up time even more time. A ‘ready-to-go’ server lets us focus on learning.

How to access the remote server

You can log-in to the remote server using the instructions from the Introduction to Cloud Computing for Genomics lesson. Your instructor will supply to you the ip_address and password that you need to login.

Each of you will have a different ip_address. This will prevent us from accidentally changing each other’s files as we work through the exercises. The password will be the same for everyone.

After logging in, you will see a screen showing something like this:


Welcome to Ubuntu 20.04.5 LTS (GNU/Linux 5.4.0-137-generic x86_64)

 * Documentation:
 * Management:
 * Support:

  System information as of Mon 13 Mar 2023 03:57:46 AM UTC

  System load:  0.0                Processes:             192
  Usage of /:   20.3% of 98.27GB   Users logged in:       0
  Memory usage: 25%                IPv4 address for eth0:
  Swap usage:   0%

  Get cloud support with Ubuntu Advantage Cloud Guest:

178 updates can be applied immediately.
108 of these updates are standard security updates.
To see these additional updates run: apt list --upgradable

Last login: Fri Mar 10 03:14:44 2023 from

This provides a lot of information about the remote server that you’re logging into. We’re not going to use most of this information for our workshop, so you can clear your screen using the clear command.

Type the word clear into the terminal and press the Enter key.


$ clear

This will scroll your screen down to give you a fresh screen and will make it easier to read. You haven’t lost any of the information on your screen. If you scroll up, you can see everything that has been output to your screen up until this point.


Hot-key combinations are shortcuts for performing common commands. The hot-key combination for clearing the console is Ctrl+L. Feel free to try it and see for yourself.


We now know how to move around our file system using the command line. This gives us an advantage over interacting with the file system through a GUI as it allows us to work on a remote server, carry out the same set of operations on a large number of files quickly, and opens up many opportunities for using bioinformatic software that is only available in command line versions.

In the next few episodes, we’ll be expanding on these skills and seeing how using the command line shell enables us to make our workflow more efficient and reproducible.


  • The shell gives you the ability to work more efficiently by using keyboard commands rather than a GUI.
  • Useful commands for navigating your file system include: ls, pwd, and cd.
  • Most commands take options (flags) which begin with a -.
  • Tab completion can reduce errors from mistyping and make work more efficient in the shell.