Instructors:
Dr. Didier Barradas-Bautista, Mohamed ElGharawy
Registration
General Information
The KAUST Visualization Core Lab (KVL) will host an Introduction to the Shell for (Data) Scientists
workshop. KVL staff will provide an introduction to shell commands designed for
learners with little or no previous experience working with shell commands.
The Unix shell has been around longer than most of its users have been alive. It has survived so
long because it’s a power tool that allows people to do complex things with just a few
keystrokes. More importantly, it helps them combine existing programs in new ways and automate
repetitive tasks so they aren’t typing the same things over and over again. Use of the shell is
fundamental to using a wide range of other powerful tools and computing resources with clusters
either locally at KAUST (i.e., Ibex, Nesser, Shaheen, etc) or in the cloud (GCP, AWS, Azure, etc).
Topics covered will include
Navigating files and directories
Working with files and directories
Pipes and filters
Loops
Shell scripting
This hands-on lesson is part of the Introduction to Data Science Workshop Series
being offered by KVL as part of our on-going efforts to build
capacity in core data science skills both at KAUST and within the Kingdom of Saudi Arabia (KSA).
The workshop curriculum largely follows the
curriculum developed by
Software Carpentry, a volunteer project dedicated to helping
researchers get their work done in less time and with less pain by teaching them basic research
computing skills.
This is a live-coding based workshop and learners are expected to work along with the instructor using freely
available cloud resources provided by the Binder project.
Who:
The course is aimed at graduate students and other researchers.
You don't need to have any previous knowledge of the tools
that will be presented at the workshop.
Where:
Auditorium 0215 between building 2 and 3 , KAUST, Thuwal, SA.
Get directions with
OpenStreetMap
or
Google Maps.
Requirements:
Participants must bring a laptop with a
Mac, Linux, or Windows operating system (not a tablet, Chromebook, etc.) that they have administrative privileges on.
For KAUSTians :
The University provides several resources for the participants to use during the workshop but you have to request the service the first time you use it here :
For remote students:
Participants must have access to a computer with a
Mac, Linux, or Windows operating system (not a tablet, Chromebook, etc.) that they have administrative privileges on.
as well as a stable internet connection. Optionally, they can use the following resource Binder to run the code in the cloud.
They should have a few specific software packages installed (listed below).
Accessibility:
We are committed to making this workshop
accessible to everybody. For workshops at a physical location, the workshop organizers have checked that:
Roles:
To learn more about the roles at the workshop (who will be doing what),
refer to our Workshop FAQ.
Code of Conduct
Everyone who participates in Carpentries activities is required to conform to the Code of Conduct. This document also outlines how to report an incident if needed.
Collaborative Notes
We will use this collaborative document for chatting, taking notes, and sharing URLs and bits of code.
Surveys
Please be sure to complete these surveys before and after the workshop.
To participate in a
Software Carpentry
workshop,
you will need access to software as described below.
In addition, you will need an up-to-date web browser.
Click on "Next" four times (two times if you've previously
installed Git). You don't need to change anything
in the Information, location, components, and start menu screens.
From the dropdown menu, "Choosing the default editor used by Git", select "Use the Nano editor by default" (NOTE: you will need to scroll up to find it) and click on "Next".
On the page that says "Adjusting the name of the initial branch in new repositories", ensure that
"Let Git decide" is selected. This will ensure the highest level of compatibility for our lessons.
Ensure that "Git from the command line and also from 3rd-party software" is selected and
click on "Next". (If you don't do this Git Bash will not work properly, requiring you to
remove the Git Bash installation, re-run the installer and to select the "Git from the
command line and also from 3rd-party software" option.)
Select "Use bundled OpenSSH".
Ensure that "Use the native Windows Secure Channel Library" is selected and click on "Next".
Ensure that "Checkout Windows-style, commit Unix-style line endings" is selected and click on "Next".
Ensure that "Use Windows' default console window" is selected and click on "Next".
Ensure that "Default (fast-forward or merge) is selected and click "Next"
Ensure that "Git Credential Manager" is selected and click on "Next".
Ensure that "Enable file system caching" is selected and click on "Next".
Click on "Install".
Click on "Finish" or "Next".
If your "HOME" environment variable is not set (or you don't know what this is):
Open command prompt (Open Start Menu then type cmd and press Enter)
Type the following line into the command prompt window exactly as shown:
setx HOME "%USERPROFILE%"
Press Enter, you should see SUCCESS: Specified value was saved.
Quit command prompt by typing exit then pressing Enter
This will provide you with both Git and Bash in the Git Bash program.
Video Tutorial
The default shell in some versions of macOS is Bash, and
Bash is available in all versions, so no need to install anything.
You access Bash from the Terminal (found in
/Applications/Utilities).
See the Git installation video tutorial
for an example on how to open the Terminal.
You may want to keep Terminal in your dock for this workshop.
To see if your default shell is Bash type echo $SHELL
in Terminal and press the Return key. If the message
printed does not end with '/bash' then your default is something
else and you can run Bash by typing bash
If you want to change your default shell, see
this Apple Support article and follow the instructions on "How to change your default shell".
Video Tutorial
The default shell is usually Bash and there is usually no need to
install anything.
To see if your default shell is Bash type echo $SHELL in
a terminal and press the Enter key. If the message printed
does not end with '/bash' then your default is something else and you
can run Bash by typing bash.
Text Editor
When you're writing code, it's nice to have a text editor that is
optimized for writing code, with features like automatic
color-coding of key words. The default text editor on macOS and
Linux is usually set to Vim, which is not famous for being
intuitive. If you accidentally find yourself stuck in it, hit
the Esc key, followed by :+Q+!
(colon, lower-case 'q', exclamation mark), then hitting Return to
return to the shell.
nano is a basic editor and the default that instructors use in the workshop.
It is installed along with Git.
nano is a basic editor and the default that instructors use in the workshop.
See the Git installation video tutorial
for an example on how to open nano.
It should be pre-installed.
Video Tutorial
nano is a basic editor and the default that instructors use in the workshop.
It should be pre-installed.