Introduction to Bioinformatics online course: IBT
Consolidation Session Exercise
Module topic: Linux
Contact session title: Permissions, groups, and process control
Trainer: Sumir Panji and Amel Ghouila
Participant: YONLI Yemboani Emile
Date: 09/06/2025
Permissions, groups, and process control
Introduction
The aim of this consolidation session exercise is to practise and better understand the files
permissions and how to change them and help you start writing your first shell scripts to
automate tasks.
Tools used in this session
If you do have a Linux system installed on your machine, make use of your system terminal.
If you are a Windows user, we highly recommend the use of the wsl or Ubuntu. You can find
more information about installing Linux using Windows PowerShell via this link:
[Link] OR install Gitbash: Git - Downloads.
Instructions on installing Gitbash can be found here: What is Git Bash and How to Install it
on Windows?
Ensure that you are using Ubuntu-22.04 or Ubuntu-24.04 on your PowerShell to get access
to the text editor, nano. Apple or MAC users do not need to install WSL, as a terminal is pre-
installed on their devices.
Always remember these rules while working with the Linux terminal
● Make sure you separate your command name, arguments and options using spaces
● Each option is preceded by - (examples: -l, -r, -lh)
● You can combine different options: -lh for example means a combination of -l and -h
● Linux is case-sensitive: A and a are different (some Mac OS terminals)
● Make use of these Wildcards while working with the command lines
Please note
Introduction to Bioinformatics online course: IBT
● Hand-in information If you are formally enrolled in the IBT course: please note that
you are NOT required to upload this exercise to the Vula ‘Practical Assignments’ tab.
HOWEVER, the content covered in the consolidation session (both the lectures and
this exercise) may be tested in the module assessment. Therefore, it is important to
take the consolidation session exercise seriously as part of your learning.
Instructions
1. Create a new sub-directory Scripting under Linux
2. Create a shell script named Assignment1 (under Scripting), which should clear the
screen. Then print any message on the screen. Write down the different steps that
would allow you to do this.
3. What were the default permissions for the different users when you first created
your script?
4. What did you change to make it work?
5. Change the permissions again to give the execution right to anyone belonging to the
user group. Write down 2 possible commands that could be used to do this.
6. Retrieve all the permissions from all the users who don't belong to the same group
as the owner of the file.
7. What are the values of your HOME and PWD variables?
8. What is the difference between PWD and pwd?
9. Write a new script that will allow you to create automatically (in your scripting
directory) 5 different files named: [Link], [Link], [Link], [Link] and [Link]
10. Remember the [Link] file you created during the last session? Write a new
script "testfasta" that would:
- Display the message: the fasta file I have created is [Link]
- Display the message: My fasta ‘filename’ contains ‘X’ sequences
(‘filename’ should be replaced by the real name and ‘X’ should be replaced by the
real number of sequences in your file)
