A Brief Introduction to Linux

Introduction

Unix-like operating systems are built under the model of free and open-source development and distribution. They often come with a graphical user interface (GUI) and can be run from the command line (CLI) or terminal. The CLI is a text-based interface that works exactly the same way as you would use your mouse, but you use words. It can be intimidating at first, but once you have mastered the basics, it’s really not different than using your mouse!

It is important to know how to use the terminal as all servers, and most bioinformatics tools do not have a GUI and rely on the use of the terminal.

Warning

MacOS and Linux, and Windows have significant differences in their syntax. Where we do things locally, we will point out some of the differences, but for the most part, we will provide Windows users with a local Linux platform so that this course can run as smoothly as possible

For this course, we do not expect you to be masters of Linux, but we will need some knowledge of how to find files, and some other basic Linux commands.

Filesystem Architecture

Linux uses a hierarchical filesystem, similar to Windows and Mac. In this figure from TecAdmin, there is a representation of this.

We can see here that the root or / folder is at the top of the hierarchy, with all other folders, like home/ and var/ inside of it.

Note

We use / at the end of a folder name to show that it is a folder.

There are two different ways for us to know where our file is within the operating system. The first is the absolute path and the second is the relative path. The absolute path gives us information that is true anywhere on your operating system. Whether your terminal is open in /usr/bin/something/ or /var/tmp/, a file will always be located at /usr/Documents/sequence.fasta as it is the true or absolute location. The relative path, as the name suggests, is relative to where you currently are on the file tree. If your terminal is open in /usr/Documents/paper/figures/, the file from before, sequence.fasta will be two folders up from where you are. If you were in /var/bin/something/ it would three folder up, one to the side, and two folders down.

Tip

It is often good practice to use absolute paths when you set pipelines up to run- this way, your programs know where to go looking for the files they’re supposed to work on

Connecting to a Server

There are many different ways you can connect to a server with SSH. At SLUBI, we have a strong preference towards Visual Studio Code or its open-source alternative, VSCodium. It provides a graphical user interface where you can create, edit, and view files, and see the file system.

To be able to connect to a server, you need to install an extension called Remote-SSH from the extensions market place.

Now we need to add a host to our list of known hosts. There are several ways of doing this, and all ways lead to establishing a connection.

Under the previously shown View option, navigate to the Command Palette. A dropdown menu at the top will start with a >. Type Remote-SSH and select add new host. Here we will input our credentials. This will populate a file in a hidden folder, .ssh in your local home directories called known_hosts.
You can also write all of these lines manually. This way, you can also specify SSH keys that may be needed to log on to particular servers. We won’t be covering that in this course, though.

After a host has been added, you can connect to it. You can do this either through the Command Palette, or through the small blue backwards and forwards arrows in the bottom left corner of VSCode. You will receive a list of known hosts that you can connect to. If you need to connect with a password, a password prompt will be shown.

Once connected, you can open the file manager on the left.

For privacy concerns, we will share the exact commands locally in the room.

Important

Remeber to only open either your home directories or the folder for your projects with the file manager. If you try to open folders that are too large, you will cause VSCode to crash (and you may cause significant problems for your system administrator!)

Navigating with the terminal

For this part of the session, we will do some hands-on practice! For this, we will open a terminal. You can do this through the Command Palette by using the View: Toggle Terminal function, or clicking the box with a dark bottom half and an empty top half in the top right corner of VSCode.

Note

For Windows Users If you are using a Windows operating system, you can install the free Home edition of MobaXterm when your access to this server is removed if you want to continue practicing your Linux skills.

To use MobaXterm as a Linux shell, click on New Session and select a bash shell. There will probably be a prompt that you have to installl an extension. Click on the link it will provide, or copy the extension it needs and search it on Google (or your preferred search engine) and install it. Then try starting a new session again.

To see where we currently are in the filesystem, we use the present working directory command. This will give us the absolute path of the directory that our terminal open in.

pwd

To see the files that are currently in the directory we use the list command.

ls

To make a directory, we use the make directory command, followed by the name we would like our directory to have. Here we will make a directory called sida_training.

mkdir sida_training

Tip

When we give files and folders names, we don’t use spaces or special characters. It makes it really difficult to access files. We can use different ways to name our files and folders 1. youcanbechaoticandusenothing 2. YouCanUseCapitalLetters 3. you_can_use_underscores 4. you-can-use-dashes The most important thing is to be consistent with what you use, and to use descriptive names that are not too long. Future you will thank past you!

To enter the sida_training directory, we will use the change directory command.

cd sida_training

We can use the pwd command again just to make sure that we are indeed in the right folder.

To go back to the folder we were in previously, we can use a shortcut rather than the absolute path.

cd ..

Tip

There are no limits to the amount of directories you can go back (provided they are in your filesystem). If you wanted to go up 3 directories, you’d use

cd ../../..

To delete files and folder you use the remove command. If you want to remove a folder, you need a recursive flag.

rm -r sida_training

If we had a file to look at, we could use the less command. In the interface, we press q to quit.

less filename

With these Linux basics, you will certainly be able to follow our course. If you would like to learn more, Data Carpentry and Software Carpentry have excellent tutorials on using the terminal in more detail, and we can only recommend them!