Introduction to UNIX

Introduction to UNIX#

Course Description#

The Unix system and the shell predate most computational interfaces (e.g. the graphical user interface). Although very old, Unix based systems and the shell are one of the most powerful ways to use computers whether it is your laptop or a supercomputer. This course is an introduction to navigating your way around the shell and demonstrating how it can improve your workflow. This can be in the form of data processing, executing code, using a huge range of built-in tools, and creating pipelines.

Course Objectives#

Describe what the shell is and how you access it
Navigate around the unix filesystem
Inspect and manipulate files
Automate tasks via scripts
Run programs outside of IDEs and notebooks

Pre-requisite Knowledge#

No pre-requisite knowledge required. The attendees will require access to a Unix-like system. There are number of options here: MacOS, WSL2 on Windows, Linux, HPC (ISCA).

Installation Guide#

Download files#

You need to download some files to follow this lesson.

Download [course_materials/shell-lesson-data.zip][zip-file] and move the file to your Desktop.
Unzip/extract the file. Let your instructor know if you need help with this step. You should end up with a new folder called shell-lesson-data on your Desktop.

Install software#

If you do not already have the shell software installed, you will need to download and install it.

Windows#

Computers with Windows operating systems do not automatically have a Unix Shell program installed.

In this lesson, we encourage you to use an emulator included in [Git for Windows][install_shell], which gives you access to both Bash shell commands and Git. Once installed, you can open a terminal by running the program Git Bash from the Windows start menu.

For advanced users, as an alternative to Git for Windows, you may wish to [Install the Windows Subsystem for Linux][wsl] which gives access to a Bash shell command-line tool in Windows 10. Please note that commands in the Windows Subsystem for Linux (WSL) may differ slightly from those shown in the lesson or presented in the workshop.

MacOS#

For a Mac computer running macOS Mojave or earlier releases, the default Unix Shell is Bash. For a Mac computer running macOS Catalina or later releases, the default Unix Shell is Zsh. Your default shell is available via the Terminal program within your Utilities folder.

To open Terminal, try one or both of the following:

In Finder, select the Go menu, then select Utilities. Locate Terminal in the Utilities folder and open it.
Use the Mac ‘Spotlight’ computer search function. Search for: Terminal and press Return.

To check if your machine is set up to use something other than Bash, type echo $SHELL in your terminal window.

If your machine is set up to use something other than Bash, you can run it by opening a terminal and typing bash.

Here are instruction on [how to Use Terminal on a Mac][mac-terminal]

Linux#

The default Unix Shell for Linux operating systems is usually Bash. On most versions of Linux, it is accessible by running the [Gnome Terminal][gnome-terminal] or [KDE Konsole][kde-konsole] or [xterm][xterm], which can be found via the applications menu or the search bar. If your machine is set up to use something other than Bash, you can run it by opening a terminal and typing bash.

Open a new shell#

After installing the software 3. Open a terminal. If you’re not sure how to open a terminal on your operating system, see the instructions under Install Software above. 4. In the terminal type cd then press the Return key. This step will make sure you start with your home folder as your working directory.

In the lesson, you will find out how to access the data files in this folder.

[zip-file]: /data/shell-lesson-data.zip [wsl]: https://docs.microsoft.com/en-us/windows/wsl/install-win10 [mac-terminal]: http://www.macworld.co.uk/feature/mac-software/how-use-terminal-on-mac-3608274/ [gnome-terminal]: https://help.gnome.org/users/gnome-terminal/stable/ [kde-konsole]: https://konsole.kde.org/ [xterm]: https://en.wikipedia.org/wiki/Xterm [install_shell]: https://carpentries.github.io/workshop-template/#shell