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Installation/ Setup of Linux/ a Linux-like Environment and Data Download

How to set up Linux or a Linux-like environment for this course and download data for the course
© Wellcome Genome Campus Advanced Courses and Scientific Conferences

For this course, you will first need to download data files that will be used in different exercises throughout the course and to provide a Linux or Linux-like environment of your choice

Please use this link:

ftp://ftp.sanger.ac.uk/pub/resources/coursesandconferences/Online_Courses/BfB_Linux_Bash_R/

to reach and download the course folder with the data needed. Important – you may need to copy and paste the link into your internet browser, rather than just clicking on it. We recommend use of Chrome or Firefox browsers for downloading data files.

Using the command line on different platforms

Mac: Terminal

On a Mac first select Spotlight Search, which is highlighted here with a yellow box.

image of the spot light search function on Mac

Then type terminal and press the enter key.

terminal command typed into the search box

A terminal will then be launched.

image of the open terminal

Linux: Terminal

In Ubuntu, select the square in the bottom left hand corner. This will show an applications screen.

ubuntu desktop screenshot

In the search box type terminal

ubuntu search box

A terminal icon will appear. Select the application by clicking on it.

ubuntu terminal icon appearance

The terminal application will then launch.

image of the ubuntu terminal launched

Windows: Ubuntu App

Install the Ubuntu app from the Microsoft Store.

https://www.microsoft.com/en-us/p/ubuntu/9nblggh4msv6?activetab=pivot:overviewtab

Ubuntu on Windows allows you to use Ubuntu Terminal and run Ubuntu command line utilities including bash, ssh, git, apt and many more.

Please note that Windows 10 S does not support running this app.

To use the Ubuntu app, one first needs to use “Turn Windows features on or off” and select “Windows Subsystem for Linux”, click OK, reboot and use this app,

operating system features settings screen

The above step can also be performed using Administrator PowerShell prompt: Enable-WindowsOptionalFeature -Online -FeatureName Microsoft-Windows-Subsystem-Linux

This app installs the Ubuntu 20.04 LTS release on Windows.

Start the Ubuntu app

To launch, use “ubuntu” on the command-line prompt (cmd.exe), or click on the Ubuntu tile in the Start Menu.

image of the ubuntu terminal on win os

 Browser options

To practise, you can also use this browser based option:

https://bellard.org/jslinux/ choosing the Alpine Linux 3.12.0 Console link.

or

https://bellard.org/jslinux/vm.html?url=alpine-x86.cfg&mem=192

© Wellcome Genome Campus Advanced Courses and Scientific Conferences
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Bioinformatics for Biologists: An Introduction to Linux, Bash Scripting, and R

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