Instructor Notes

Lesson motivation and learning objectives

Many researchers making the transition into genomics research (whether from another field or as their first research project) have not had prior experience with command-line tools. They may quickly run into situations in which they need to use command-line tools either because there is no good alternative for the type of analysis they want to do or because they have so many data files that doing things manually on individual files is unfeasible.

This lesson will introduce learners to fundamental skills needed for working with their computers through a command-line interface (using the bash shell). They will learn how to navigate their file system, computationally manipulate their files (e.g. copying, moving, renaming), search files, redirect output and write shell scripts. By the end of the lesson, learners will be prepared to move on to using more advanced bioinformatics command line tools (see the lesson on Data Wrangling and Processing).

Lesson design

This lesson is meant to be taught in its entirety. For novice learners, schedule around 4 hours for this lesson. If your learners are already somewhat familiar with the bash shell, the earlier episodes can be condensed.

Technical tips and tricks

Command Prompt Editing

Instructors might find it helpful to shorten their command prompt to allow better visibility of the commands they are typing. This is because the prompt mayl contain additional information including the username and login for the instance, as well as filesystem location. This is especially useful when teaching the material online, as many learners may be splitting their screens and text wrapping may make the commands more difficult to identify if the prompt takes up a lot of space.

In order to edit your command prompt, type PS1='$ ' into your shell and press enter. This will produce the simple “dollar space” prompt visible in the lesson content.

In order to reset the command prompt, type source .bashrc in order to source the bash profile, or type PS1="\u@\h:\w $ " in order to set the prompt to show username, “@”, hostname, “:”, and current working directory (ie. the user’s current location within the filesystem).

NOTE: Editing the prompt is discussed in 1. Introducing the Shell. This explains how to edit the prompt via PS1='$ ' as here, so it would perhaps be best to start the lesson with the default prompt (as all the learners will and they can see that their screen will reassuringly match the instructor’s screen at this point), and then instructors can choose to edit their prompt and talk through how they’re doing that for learners’ benefit at this section, or the instructor can just make the change early in the lesson for the visibility benefit, and explain to learners that they can find out how to do this in the lesson materials.

Resetting the command prompt is not currently included in the lesson materials, so it might be useful to be familiar with this beforehand in case of learners’ questions.

Tips and Tricks from Library Carpentries lesson

Making a handout

To make a handout for this lesson, adapt/print from https://jlchang.github.io/2024-05-09-Unix_Shell_pilot/shellCheatSheet.html.

Differences between platforms

Some of the commands used in this lesson behave differently depending on whether they are run on Git Bash for Windows, macOS X or Linux. Be prepared to manage these differences. Here are some examples from Library Carpentries “The UNIX Shell” episode 5, “Counting and mining with the shell”:

  • grep -E on macOS X acts like grep -P on other platforms. On Windows and Linux, grep -E is halfway between grep -P and grep: it only does what grep can do, but uses Perl-compatible syntax to do it.

  • The grep on Git Bash for Windows prior to version 2.19.0 (September 2018) did not support the -o flag. If someone gets an error “invalid option – o”, they are most likely trying to use one of these older versions. They should probably just skip the exercises that use it and upgrade later.

  • The episode uses date +%Y-%m-%d because date -I is not available on macOS X.

  • date --help is not available on macOS X so man date should be used instead.

As noted below, you should avoid demonstrating any more options that only work on certain platforms.

General notes on shell

  • Why do we learn to use the shell?
    • Allows users to automate repetitive tasks
    • And capture small data manipulation steps that are normally not recorded to make research reproducible
  • The Problem
    • Running the same workflow on several samples can be unnecessarily labour intensive
    • Manual manipulation of data files:
      • is often not captured in documentation
      • is hard to reproduce
      • is hard to troubleshoot, review, or improve
  • The Shell
    • Workflows can be automated through the use of shell scripts
    • Built-in commands allow for easy data manipulation (e.g. sort, grep, etc.)
    • Every step can be captured in the shell script and allow reproducibility and easy troubleshooting

Overall

Many people have questioned whether we should still teach the shell. After all, anyone who wants to rename several thousand data files can easily do so interactively in the Python interpreter, and anyone who’s doing serious data analysis is probably going to do most of their work inside the iPython Notebook or RStudio. So why teach the shell?

The first answer is, “Because so much else depends on it.” Installing software, configuring your default editor, and controlling remote machines frequently assume a basic familiarity with the shell, and with related ideas like standard input and output. Many tools also use its terminology (for example, the %ls and %cd magic commands in iPython).

The second answer is, “Because it’s an easy way to introduce some fundamental ideas about how to use computers.” As we teach people how to use the Unix shell, we teach them that they should get the computer to repeat things (via tab completion,! followed by a command number, and for loops) rather than repeating things themselves. We also teach them to take things they’ve discovered they do frequently and save them for later re-use (via shell scripts), to give things sensible names, and to write a little bit of documentation (like comment at the top of shell scripts) to make their future selves’ lives better.

The third answer is, “Because it enables use of many domain-specific tools and compute resources researchers cannot access otherwise.” Familiarity with the shell is very useful for remote accessing machines, using high-performance computing infrastructure, and running new specialist tools in many disciplines. We do not teach HPC or domain-specific skills here but lay the groundwork for further development of these skills. In particular, understanding the syntax of commands, flags, and help systems is useful for domain specific tools and understanding the file system (and how to navigate it) is useful for remote access.

Finally, and perhaps most importantly, teaching people the shell lets us teach them to think about programming in terms of function composition. In the case of the shell, this takes the form of pipelines rather than nested function calls, but the core idea of “small pieces, loosely joined” is the same.

All of this material can be covered in three hours as long as learners using Windows do not run into roadblocks such as:

  • not being able to figure out where their home directory is (particularly if they’re using Cygwin);
  • not being able to run a plain text editor; and
  • the shell refusing to run scripts that include DOS line endings.

Preparing to Teach

  • Use the data directory for in-workshop exercises and live coding examples. You can clone the shell-novice directory or use the Download ZIP button on the right to get the entire repository. We also now provide a zip file of the data directory that can be downloaded on its own from the repository by right-click + save or see the “setup” page on the lesson website for more details.

  • Website: various practices have been used.

    • Option 1: Can give links to learners before the lesson so they can follow along, catch up, and see exercises (particularly if you’re following the lesson content without many changes).
    • Option 2: Don’t show the website to the learners during the lesson, as it can be distracting: students may read instead of listen, and having another window open is an additional cognitive load.
    • In any case, make sure to point to website as a post-workshop reference.

  • Content:

    • Unless you have a truly generous amount of time (4+ hours), it is likely that you will not cover ALL the material in this lesson in a single half-day session. Plan ahead on what you might skip, what you really want to emphasize, etc.

  • Exercises:

    • Think in advance about how you might want to handle exercises during the lesson. How are you assigning them (website, slide, handout)? Do you want everyone to try it and then you show the solution? Have a learner show the solution? Have groups each do a different exercise and present their solutions?

  • Other preparation:

    • Feel free to add your own examples or side comments, but know that it shouldn’t be necessary: the topics and commands can be taught as given on the lesson pages. If you think there is a place where the lesson is lacking, feel free to file an issue or submit a pull request.

Teaching Notes

  • Super cool online resource! https://explainshell.com/ will dissect any shell command you type in and display help text for each piece. Additional nice manual tool could be https://tldr.sh/ with short very descriptive manuals for shell commands, useful especially on Windows while using Git BASH where man could not work.

  • Another super cool online resource is https://www.shellcheck.net, which will check shell scripts (both uploaded and typed in) for common errors.

  • Resources for “splitting” your shell so that recent commands remain in view: https://github.com/rgaiacs/swc-shell-split-window.

  • Running a text editor from the command line can be the biggest stumbling block during the entire lesson: many will try to run the same editor as the instructor or will not know how to navigate to the right directory to save their file, or will run a word processor rather than a plain text editor. The quickest way past these problems is to have more knowledgeable learners help those who need it.

  • Introducing and navigating the filesystem in the shell (covered in Navigating Files and Directories section) can be confusing. You may have both terminal and GUI file explorer open side by side so learners can see the content and file structure while they’re using terminal to navigate the system.

  • Tab completion sounds like a small thing: it isn’t. Re-running old commands using !123 or !wc isn’t a small thing either, and neither are wildcard expansion and for loops. Each one is an opportunity to repeat one of the big ideas of Software Carpentry: if the computer can repeat it, some programmer somewhere will almost certainly have built some way for the computer to repeat it.

  • Building up a pipeline with four or five stages, then putting it in a shell script for re-use and calling that script inside a for loop, is a great opportunity to show how “seven plus or minus two” connects to programming. Once we have figured out how to do something moderately complicated, we make it re-usable and give it a name so that it only takes up one slot in working memory rather than several. It is also a good opportunity to talk about exploratory programming: rather than designing a program up front, we can do a few useful things and then retroactively decide which are worth encapsulating for future re-use.

  • If everything is going well, you can drive home the point that file extensions are essentially there to help computers (and human readers) understand file content and are not a requirement of files (covered briefly in Navigating Files and Directories). This can be done in the Pipes and Filters section by showing that you can redirect standard output to a file without the .txt extension (e.g., lengths), and that the resulting file is still a perfectly usable text file. Make the point that if double-clicked in the GUI, the computer will probably ask you what you want to do.

  • We have to leave out many important things because of time constraints, including file permissions, job control, and SSH. If learners already understand the basic material, this can be covered instead using the online lessons as guidelines. These limitations also have follow-on consequences:

    • It’s hard to discuss #! (shebang) without first discussing permissions, which we don’t do. #! is also pretty complicated, so even if we did discuss permissions, we probably still wouldn’t want to discuss #!.

  • Stay within POSIX-compliant commands, as all the teaching materials do. Your particular shell may have extensions beyond POSIX that are not available on other machines, especially the default OSX bash and Windows bash emulators. For example, POSIX ls does not have an --ignore= or -I option, and POSIX head takes -n 10 or -10, but not the long form of --lines=10.

Windows

Installing Bash and a reasonable set of Unix commands on Windows always involves some fiddling and frustration. Please see the latest set of installation guidelines for advice, and try it out yourself before teaching a class. Options we have explored include:

  1. Git Bash,
  2. Cygwin,
  3. using a desktop virtual machine, and
  4. having learners connect to a remote Unix machine (typically a VM in the cloud).

Cygwin was the preferred option until mid-2013, but once we started teaching Git, Git Bash proved to work better. Desktop virtual machines and cloud-based VMs work well for technically sophisticated learners, and can reduce installation and configuration at the start of the workshop, but:

  1. they don’t work well on underpowered machines,
  2. they’re confusing for novices (because simple things like copy and paste work differently),
  3. learners leave the workshop without a working environment on their operating system of choice, and
  4. learners may show up without having downloaded the VM or the wireless will go down (or become congested) during the lesson.

Whatever you use, please test it yourself on a Windows machine before your workshop: things may always have changed behind your back since your last workshop. And please also make use of our Software Carpentry Windows Installer.

Windows Notes

  • On Windows machines if nano hasn’t been properly installed with the Software Carpentry Windows Installer it is possible to use notepad as an alternative. There will be a GUI interface and line endings are treated differently, but otherwise, for the purposes of this lesson, notepad and nano can be used almost interchangeably.

  • On Windows, it appears that:

    BASH 

    cd
cd Desktop

    … will always put someone on their desktop. Have them create the example directory for the shell exercises there so that they can find it easily and watch it evolve.

    • On Windows, Microsoft OneDrive may appear in the home directory list. Desktop is often found inside the OneDrive directory.

Introducing the Shell

Navigating Files and Directories

Working with Files and Directories

Redirection

Writing Scripts and Working with Data

Project Organization