Get started

Learning command line can bring some flexibility into how you manage and do your analysis, or even if you are just curious about programming this is the place to be. The command line language we are going to use is called Bash, and we will guide you in this initiation.

In this page you will find one session to get ready for the course and a second session in case you want to get Linux installed on your computer to go beyond the exercises.

Get ready for the course

Use Linux on the Vlaamse SuperComputer

The VSC (Vlaamse SuperComputer) can be accessed by all Flemish academics.

If you have an account yet, you create one following the instructions on the vscentrum website and steps 1-5 that are described below.

If you do have a VSC account skip steps 1-5 below and start at step 6.

1. Create a VSC account

You can create an account via the vscentrum website.

VSC accounts are created at your institution (Ugent for Ugent personnel, KULeuven for KULeuven personnel…) but they allow to access the VSC from any site, so UGent personnel can use their VSC number to access the KULeuven VSC clusters and vice versa. In the examples below I will be using KULeuven VSC but the procedure is exactly the same for the other VSC locations.

2. Generate a SSH key

Linux and Mac users can use a terminal for this.
Windows users should install VSCode

  • Open a terminal. In VSCode this is done by clicking Terminal in the top menu and selecting New Terminal
Open terminal in VSCode
  • Run the following code on the terminal:
ssh-keygen -t rsa -b 4096

This will generate a file called id_rsa.pub in the folder user/name/.ssh/

3. Access your VSC account

Edit VSC account

4. Add SSH key to VSC account

  • In the section Add public key click Choose File.
  • Select the id_rsa.pub file.
  • Click the yellow Update button.
Add SSH key to VSC account

5. Check VSC number

  • Click View account in the top menu.

The Uid shows your VSC number. It consists of the letters vsc followed by a 5-digit integer.

Check VSC number

6. Access a Linux shell on VSC

You can access a Linux shell on the VSC via Open Ondemand. As you can see each VSC location has a Open Ondemand website.

  • Log in with your VSC account
  • You see an overview of apps (tools) to use on the VSC. Click Login Server Shell Access.
  • This opens a Linux shell where you can type commands. The first command that you type should take you to your data folder on the VSC (upon access you end up in your home folder but you are very discouraged to use this for analysis since it’s very small).

To go to your data folder type:

cd $VSC_DATA

7. Upload the data of the course to your data folder

  • In the Open Ondemand dashboard go to Files in the top menu: you can only access your home folder and your data folder: choose your data folder
  • When you go to the Data directory, you can use the Upload and Download buttons
  • First use the New Directory button (next to Upload) to create a folder called Linux. It will appear in the list of files and folders in your data folder.
  • Click Linux to access it and then click the Upload button to upload this file. You should see the file (linux-intro-course.tar.gz) in the Linux folder.
  • We need to extract the file using the following commands in the Linux shell:
cd Linux
tar -xvzf linux-intro-course.tar.gz

You are now ready to do the exercises of this course.

Go beyond

There are several ways to use Linux or Bash commands on your computer. You can replace your system and work entirely on the Linux OS, using their interface additionally to the command line (Live modus). You can also have a Virtual machine, that will be a “program” that allows you to create a virtual computer where you can install a different OS to use inside of your current system. You can create a partition on your personal computer and make it Dual boot, in this case you are going to have two OS working in your computer and you can choose to access one or the other. And if you want a simplified version you can just install GitBash, meant for those who will use Git & GitHub, but it is a bash-command terminal system, as you could guess by the name.

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GitBash

GitBash is a software that will create a terminal where you can code (more about this vocbaulary in the next session). This terminal is meant to help you using Git, will all the Git commands, but it is Linux-based and therefore allow to use and test many resources. It will though, differently from the above options, have limitations where some of the commands and resources are not working, osme can be installed, others can not. So it is advised if you want an easy and simplified start, or if you are joining our Git & GitHub live training session. Otherwise the other options will better fulfill your needs and curiosities.

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Live modus

Want to test a Linux distribution? Follow this procedure:

  • Grab an USB key and put your Linux distribution (e.g. Ubuntu) on it.
  • Boot your computer from that bootable USB key, and you have a full linux OS to play around with. This ‘live modus’ is an easy way to test the new stuff linux has to offer.
  • Before you test anything else, check if your hardware works (printer, sound,…) and check internet connection.
  • Secondly, do you like the desktop environment? Does it suit your needs? Play around and test. Done testing? Just reboot your computer, remove the USB key, and the original operating system will start up again as if nothing has happened…

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Virtual machine

Go to https://www.virtualbox.org and choose Downloads. Download the correct installer for your platform and install VirtualBox on your computer. Sometimes VirtualBox displays errors when starting. Or trying VirtualBox for the first time, a virtual machine might not start. These problems might be related to not having virtualization enabled on your CPU.

All the latest processors and motherboards support virtualization technology (vt-x/amd-v). It many cases, VirtualBox requires this to be enabled. To do so, you have to reboot your computer, and get into the BIOS menu, what is slightly different for each computer. In the BIOS menu, you should enable virtualization. Where this setting is located is also different between computers, so check your hardware vendor for the BIOS options, or browse around in your BIOS menu until you find it. Most of the times it is named in a decent way. Enable the option, and boot your computer.

We need to download an .iso file, which is a (binary) copy of an installation DVD containing your distribution of choice. You can find it in the downloads section of the distribution’s web page. You can download it using a direct download, depending on your preference and the options offered by the distribution’s web page. You can run Linux in ‘live modus’ (see instructions above) and install it directly on your virtual machine. Afterwards you have to reboot your virtual machine to get out of the live modus.

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Dual boot

Multi-booting allows more than one operating system to reside on one computer, for example if you have a primary operating system and an alternate system that you use less frequently. Another reason for multi-booting can be to investigate or test a new operating system without switching completely. Multi-booting allows a new operating system to configure all applications needed, and migrate data before removing the old operating system. Here you can check in opensource.com describing one way to do it.

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