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<!DOCTYPE html>
<!-- START: inst/pkgdown/templates/layout.html --><!-- Generated by pkgdown: do not edit by hand --><html lang="en" data-bs-theme="auto"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><title>The Unix Shell: Introducing the Shell</title><meta name="viewport" content="width=device-width, initial-scale=1"><script src="assets/themetoggle.js"></script><link rel="stylesheet" type="text/css" href="assets/styles.css"><script src="assets/scripts.js" type="text/javascript"></script><!-- mathjax --><script type="text/x-mathjax-config">
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<h1>Introducing the Shell</h1>
<p>Last updated on 2023-06-09 |
<a href="https://github.com/swcarpentry/shell-novice/edit/main/episodes/01-intro.md" class="external-link">Edit this page <i aria-hidden="true" data-feather="edit"></i></a></p>
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<div class="overview card">
<h2 class="card-header">Overview</h2>
<div class="row g-0">
<div class="col-md-4">
<div class="card-body">
<div class="inner">
<h3 class="card-title">Questions</h3>
<ul><li>What is a command shell and why would I use one?</li>
</ul></div>
</div>
</div>
<div class="col-md-8">
<div class="card-body">
<div class="inner bordered">
<h3 class="card-title">Objectives</h3>
<ul><li>Explain how the shell relates to the keyboard, the screen, the
operating system, and users’ programs.</li>
<li>Explain when and why command-line interfaces should be used instead
of graphical interfaces.</li>
</ul></div>
</div>
</div>
</div>
</div>
<div class="section level3">
<h3 id="background">Background<a class="anchor" aria-label="anchor" href="#background"></a></h3>
<p>Humans and computers commonly interact in many different ways, such
as through a keyboard and mouse, touch screen interfaces, or using
speech recognition systems. The most widely used way to interact with
personal computers is called a <strong>graphical user interface</strong>
(GUI). With a GUI, we give instructions by clicking a mouse and using
menu-driven interactions.</p>
<p>While the visual aid of a GUI makes it intuitive to learn, this way
of delivering instructions to a computer scales very poorly. Imagine the
following task: for a literature search, you have to copy the third line
of one thousand text files in one thousand different directories and
paste it into a single file. Using a GUI, you would not only be clicking
at your desk for several hours, but you could potentially also commit an
error in the process of completing this repetitive task. This is where
we take advantage of the Unix shell. The Unix shell is both a
<strong>command-line interface</strong> (CLI) and a scripting language,
allowing such repetitive tasks to be done automatically and fast. With
the proper commands, the shell can repeat tasks with or without some
modification as many times as we want. Using the shell, the task in the
literature example can be accomplished in seconds.</p>
</div>
<div class="section level3">
<h3 id="the-shell">The Shell<a class="anchor" aria-label="anchor" href="#the-shell"></a></h3>
<p>The shell is a program where users can type commands. With the shell,
it’s possible to invoke complicated programs like climate modeling
software or simple commands that create an empty directory with only one
line of code. The most popular Unix shell is Bash (the Bourne Again
SHell — so-called because it’s derived from a shell written by Stephen
Bourne). Bash is the default shell on most modern implementations of
Unix and in most packages that provide Unix-like tools for Windows. Note
that ‘Git Bash’ is a piece of software that enables Windows users to use
a Bash like interface when interacting with Git.</p>
<p>Using the shell will take some effort and some time to learn. While a
GUI presents you with choices to select, CLI choices are not
automatically presented to you, so you must learn a few commands like
new vocabulary in a language you’re studying. However, unlike a spoken
language, a small number of “words” (i.e. commands) gets you a long way,
and we’ll cover those essential few today.</p>
<p>The grammar of a shell allows you to combine existing tools into
powerful pipelines and handle large volumes of data automatically.
Sequences of commands can be written into a <em>script</em>, improving
the reproducibility of workflows.</p>
<p>In addition, the command line is often the easiest way to interact
with remote machines and supercomputers. Familiarity with the shell is
near essential to run a variety of specialized tools and resources
including high-performance computing systems. As clusters and cloud
computing systems become more popular for scientific data crunching,
being able to interact with the shell is becoming a necessary skill. We
can build on the command-line skills covered here to tackle a wide range
of scientific questions and computational challenges.</p>
<p>Let’s get started.</p>
<p>When the shell is first opened, you are presented with a
<strong>prompt</strong>, indicating that the shell is waiting for
input.</p>
<div class="codewrapper sourceCode" id="cb1">
<h3 class="code-label">BASH<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
</h3>
<pre class="sourceCode bash" tabindex="0"><code class="sourceCode bash"><span id="cb1-1"><a href="#cb1-1" tabindex="-1"></a><span class="ex">$</span></span></code></pre>
</div>
<p>The shell typically uses <code>$</code> as the prompt, but may use a
different symbol. In the examples for this lesson, we’ll show the prompt
as <code>$</code>. Most importantly, <em>do not type the prompt</em>
when typing commands. Only type the command that follows the prompt.
This rule applies both in these lessons and in lessons from other
sources. Also note that after you type a command, you have to press the
<kbd>Enter</kbd> key to execute it.</p>
<p>The prompt is followed by a <strong>text cursor</strong>, a character
that indicates the position where your typing will appear. The cursor is
usually a flashing or solid block, but it can also be an underscore or a
pipe. You may have seen it in a text editor program, for example.</p>
<p>Note that your prompt might look a little different. In particular,
most popular shell environments by default put your user name and the
host name before the <code>$</code>. Such a prompt might look like,
e.g.:</p>
<div class="codewrapper sourceCode" id="cb2">
<h3 class="code-label">BASH<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
</h3>
<pre class="sourceCode bash" tabindex="0"><code class="sourceCode bash"><span id="cb2-1"><a href="#cb2-1" tabindex="-1"></a><span class="ex">nelle@localhost</span> $</span></code></pre>
</div>
<p>The prompt might even include more than this. Do not worry if your
prompt is not just a short <code>$</code>. This lesson does not depend
on this additional information and it should also not get in your way.
The only important item to focus on is the <code>$</code> character
itself and we will see later why.</p>
<p>So let’s try our first command, <code>ls</code>, which is short for
listing. This command will list the contents of the current
directory:</p>
<div class="codewrapper sourceCode" id="cb3">
<h3 class="code-label">BASH<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
</h3>
<pre class="sourceCode bash" tabindex="0"><code class="sourceCode bash"><span id="cb3-1"><a href="#cb3-1" tabindex="-1"></a><span class="ex">$</span> ls</span></code></pre>
</div>
<div class="codewrapper">
<h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
</h3>
<pre class="output" tabindex="0"><code>Desktop Downloads Movies Pictures
Documents Library Music Public</code></pre>
</div>
<div id="command-not-found" class="callout">
<div class="callout-square">
<i class="callout-icon" data-feather="bell"></i>
</div>
<div id="command-not-found" class="callout-inner">
<h3 class="callout-title">Command not found</h3>
<div class="callout-content">
<p>If the shell can’t find a program whose name is the command you
typed, it will print an error message such as:</p>
<div class="codewrapper sourceCode" id="cb5">
<h3 class="code-label">BASH<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
</h3>
<pre class="sourceCode bash" tabindex="0"><code class="sourceCode bash"><span id="cb5-1"><a href="#cb5-1" tabindex="-1"></a><span class="ex">$</span> ks</span></code></pre>
</div>
<div class="codewrapper">
<h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
</h3>
<pre class="output" tabindex="0"><code>ks: command not found</code></pre>
</div>
<p>This might happen if the command was mis-typed or if the program
corresponding to that command is not installed.</p>
</div>
</div>
</div>
</div>
<section><h2 class="section-heading" id="nelles-pipeline-a-typical-problem">Nelle’s Pipeline: A Typical Problem<a class="anchor" aria-label="anchor" href="#nelles-pipeline-a-typical-problem"></a></h2>
<hr class="half-width"><p>Nelle Nemo, a marine biologist, has just returned from a six-month
survey of the <a href="https://en.wikipedia.org/wiki/North_Pacific_Gyre" class="external-link">North Pacific
Gyre</a>, where she has been sampling gelatinous marine life in the <a href="https://en.wikipedia.org/wiki/Great_Pacific_Garbage_Patch" class="external-link">Great
Pacific Garbage Patch</a>. She has 1520 samples that she’s run through
an assay machine to measure the relative abundance of 300 proteins. She
needs to run these 1520 files through an imaginary program called
<code>goostats.sh</code>. In addition to this huge task, she has to
write up results by the end of the month, so her paper can appear in a
special issue of <em>Aquatic Goo Letters</em>.</p>
<p>If Nelle chooses to run <code>goostats.sh</code> by hand using a GUI,
she’ll have to select and open a file 1520 times. If
<code>goostats.sh</code> takes 30 seconds to run each file, the whole
process will take more than 12 hours of Nelle’s attention. With the
shell, Nelle can instead assign her computer this mundane task while she
focuses her attention on writing her paper.</p>
<p>The next few lessons will explore the ways Nelle can achieve this.
More specifically, the lessons explain how she can use a command shell
to run the <code>goostats.sh</code> program, using loops to automate the
repetitive steps of entering file names, so that her computer can work
while she writes her paper.</p>
<p>As a bonus, once she has put a processing pipeline together, she will
be able to use it again whenever she collects more data.</p>
<p>In order to achieve her task, Nelle needs to know how to:</p>
<ul><li>navigate to a file/directory</li>
<li>create a file/directory</li>
<li>check the length of a file</li>
<li>chain commands together</li>
<li>retrieve a set of files</li>
<li>iterate over files</li>
<li>run a shell script containing her pipeline</li>
</ul><div id="keypoints1" class="callout keypoints">
<div class="callout-square">
<i class="callout-icon" data-feather="key"></i>
</div>
<div class="callout-inner">
<h3 class="callout-title">Key Points</h3>
<div class="callout-content">
<ul><li>A shell is a program whose primary purpose is to read commands and
run other programs.</li>
<li>This lesson uses Bash, the default shell in many implementations of
Unix.</li>
<li>Programs can be run in Bash by entering commands at the command-line
prompt.</li>
<li>The shell’s main advantages are its high action-to-keystroke ratio,
its support for automating repetitive tasks, and its capacity to access
networked machines.</li>
<li>A significant challenge when using the shell can be knowing what
commands need to be run and how to run them.</li>
</ul></div>
</div>
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