Introduction to the Linux shell

QIMR Berghofer

Apr 12, 2023

8:45am - 2:30pm AEST

Instructors: Conrad Leonard, Scott Wood

Helpers: Rebecca Johnston, Sharon Hoyte

General Information

Software Carpentry aims to help researchers get their work done in less time and with less pain by teaching them basic research computing skills. This hands-on introductory workshop will cover basic concepts and tools including navigating the file system and task automation using the shell. Participants will be encouraged to help one another and to apply what they have learned to their own research problems.

For more information on what we teach and why, please see our paper "Best Practices for Scientific Computing".

Who: The course is aimed at graduate students and other researchers at QIMR Berghofer MRI. You don't need to have any previous knowledge of the tools that will be presented at the workshop.

Where: Room 311 ITS training, Education Level 3 Central, 300 Herston Rd Herston QLD. Get directions with OpenStreetMap or Google Maps.

When: 8:45 am Apr 12, 2023. Add to your Google Calendar. The workshop lesson material starts at 9am sharp; please arrive 15 minutes beforehand to allow time for setting up your laptop and downloading the lesson data.

Requirements:

Participants must bring a laptop with a Mac, Linux, or Windows operating system (not a tablet, Chromebook, etc.). ITS has a limited number of training laptops available if you don't have your own; let the organizers know if you need one of these and they will be allocated on a first-come, first-served basis.
If you'll be using Windows, you need the Git BASH emulator installed with Git for Windows. Assuming you don't have it installed already:
- For personal laptops, please install this yourself.
- For Institute laptops, please contact ITS and request them to install it via the software downloads page in the ticket system.
Participants are required to abide by Code of Conduct.

Accessibility: We are committed to making this workshop accessible to everybody. The workshop organizers have checked that:

The room is wheelchair / scooter accessible.
Accessible restrooms are available.

Contact: Please email conrad.leonard@qimrberghofer.edu.au for more information.

Who can attend?: This workshop is open to students and staff of QIMR Berghofer MRI.

Collaborative Notes

We will use this collaborative document for chatting, taking notes, and sharing URLs and bits of code.

Setup

Download the shell-lesson-data.zip file and extract it to your desktop.

Schedule

		Setup	Download files required for the lesson
Day 1	09:00	1. Introducing the Shell	What is a command shell and why would I use one?
	09:05	2. Navigating Files and Directories	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?
	09:45	3. Working With Files and Directories	How can I create, copy, and delete files and directories? How can I edit files?
	10:35	4. Morning Coffee	Break
	11:00	5. Pipes and Filters	How can I combine existing commands to do new things?
	11:35	6. Loops	How can I perform the same actions on many different files?
	12:25	7. Lunch	Break
	13:00	8. Shell Scripts	How can I save and re-use commands?
	13:45	9. Finding Things	How can I find files? How can I find things in files?
	14:30	Finish

The actual schedule may vary slightly depending on the topics and exercises chosen by the instructors.