Summary and Setup

The Unix shell has been around longer than most of its users have been alive. It has survived because it’s a powerful tool that allows users to perform complex and powerful tasks, often with just a few keystrokes or lines of code. It helps users automate repetitive tasks and easily combine smaller tasks into larger, more powerful workflows.

Use of the shell is fundamental to a wide range of advanced computing tasks, including high-performance computing. These lessons will introduce you to this powerful tool.

Please note that these materials were imported and modified from the Software Carpentry shell-novice repository. The original Creative Commons license can be found here. Software Carpentry does not endorse HPCBio’s version of this lesson.

Prerequisites

This lesson guides you through the basics of file systems and the shell. If you have stored files on a computer at all and recognize the word “file” and either “directory” or “folder” (two common words for the same thing), you’re ready for this lesson.

If you’re already comfortable manipulating files and directories, searching for files with grep and find, and writing simple loops and scripts, you probably want to explore the next lesson: shell-extras.

Download files

You need to download some files to follow this lesson.

  1. Download shell-lesson-data.zip and move the file to your Desktop.
  2. 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. Please follow the directions under “The Bash Shell” section and select the tab that reflects your operating system.

Open a new shell

After installing the software

  1. Open a terminal. If you’re not sure how to open a terminal on your operating system, see the instructions below.
  2. 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.

Where to type commands: How to open a new shell

The shell is a program that enables us to send commands to the computer and receive output. It is also referred to as the terminal or command line.

Some computers include a default Unix Shell program. The steps below describe some methods for identifying and opening a Unix Shell program if you already have one installed. There are also options for identifying and downloading a Unix Shell program, a Linux/UNIX emulator, or a program to access a Unix Shell on a server.

If none of the options below address your circumstances, try an online search for: Unix shell [your computer model] [your operating system].

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, 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 which gives access to a Bash shell command-line tool in Windows 10 and above.

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.

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.

How to Use Terminal on a Mac

The default Unix Shell for Linux operating systems is usually Bash. On most versions of Linux, it is accessible by running the Gnome Terminal or KDE Konsole or 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.

Additional HPCBio Resources

If you are signed up for an HPCBio workshop, you will have additional resources that you can utilize that will be noted throughout the lessons. These resources are listed below. Make sure to confirm that you have access to both of them. If you’re not signed up for an HPCBio workshop, then you will not have permission to access these. See our website for more workshop information here.

  1. Slack Workshop Group: You should have received an email with an invitation to join our HPCBio Workshops Slack page. Here you can ask HPCBio staff questions related to this material under the channel named # intro-linux-swc.
  2. Video Channel: You should have also received an email containing a link to our video playlist. This includes recordings of HPCBio staff teaching this material if you prefer to listen and follow along with these materials rather than read through the lessons on your own.