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01-intro.md

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### Background
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### What is the Shell?
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Humans and computers commonly interact in many different ways, such as through a keyboard and mouse,
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touch screen interfaces, or using speech recognition systems.
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With a GUI, we give instructions by clicking a mouse and using menu-driven interactions.
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While the visual aid of a GUI makes it intuitive to learn,
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this way of delivering instructions to a computer scales very poorly.
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this way of interacting scales very poorly for some tasks.
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A **command-line interface** (CLI) allows users to to interact with computer by reading
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and writing text. It excels at making repetitive tasks automatic and fast.
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A **shell** is a particular program that lets you type commands.
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In this workshop, we will be using "Bash" which is the most popular Unix shell.
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Bash is often the default shell on Unix and in Unix-like tools for Windows.
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### Why use the shell?
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Imagine the following task:
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for a literature search, you have to copy the third line of one thousand text files in one thousand
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different directories and paste it into a single file.
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Using a GUI, you would not only be clicking at your desk for several hours,
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but you could potentially also commit an error in the process of completing this repetitive task.
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This is where we take advantage of the Unix shell.
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The Unix shell is both a **command-line interface** (CLI) and a scripting language,
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allowing such repetitive tasks to be done automatically and fast.
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With the proper commands, the shell can repeat tasks with or without some modification
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as many times as we want.
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Using the shell, the task in the literature example can be accomplished in seconds.
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### The Shell
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The shell is a program where users can type commands.
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With the shell, it's possible to invoke complicated programs like climate modeling software
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or simple commands that create an empty directory with only one line of code.
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The most popular Unix shell is Bash (the Bourne Again SHell ---
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so-called because it's derived from a shell written by Stephen Bourne).
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Bash is the default shell on most modern implementations of Unix and in most packages that provide
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Unix-like tools for Windows.
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Note that 'Git Bash' is a piece of software that enables Windows users to use a Bash like interface
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when interacting with Git.
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Using a CLI, you can write a series of commands that does this consistently and nearly instantly.
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The shell can be used for simple tasks like creating an empty folder
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and for launching (even complex) programs with a single command.
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In fact, some tools and resources such as cloud computing systems
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usually require users to be familiar with the shell.
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Shell commands can be combined together and saved into reproducible *scripts*
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that handle large volumes of data automatically.
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Using the shell will take some effort and some time to learn.
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While a GUI presents you with choices to select, CLI choices are not automatically presented to you,
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so you must learn a few commands like new vocabulary in a language you're studying.
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However, unlike a spoken language, a small number of "words" (i.e. commands) gets you a long way,
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and we'll cover those essential few today.
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The grammar of a shell allows you to combine existing tools into powerful
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pipelines and handle large volumes of data automatically. Sequences of
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commands can be written into a *script*, improving the reproducibility of
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workflows.
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In addition, the command line is often the easiest way to interact with remote machines
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and supercomputers.
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Familiarity with the shell is near essential to run a variety of specialized tools and resources
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including high-performance computing systems.
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As clusters and cloud computing systems become more popular for scientific data crunching,
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being able to interact with the shell is becoming a necessary skill.
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We can build on the command-line skills covered here
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to tackle a wide range of scientific questions and computational challenges.
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Let's get started.
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While a GUI presents you with choices to select, CLI choices are not automatically presented to you.
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It can be daunting at first, but once you've come familliar with this different style
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of iteracting, you will be able to find and use the information you need to accomplish
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a huge variety of tasks.
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### Let's get started.
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When the shell is first opened, you are presented with a **prompt**,
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indicating that the shell is waiting for input.

md5sum.txt

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"LICENSE.md" "05e8a3f0bb4e703d7e706da51fca827e" "site/built/LICENSE.md" "2025-01-25"
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"config.yaml" "7e947da357206469f1a2c8a159290d19" "site/built/config.yaml" "2023-05-02"
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"index.md" "0cffd2ceffc82b3f91dbfc4038b7f099" "site/built/index.md" "2025-06-18"
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"episodes/01-intro.md" "f9424965b4e7855f0e569be741c5e88e" "site/built/01-intro.md" "2023-06-09"
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"episodes/01-intro.md" "2b3e0624bd03f071af64e9b44bc9e9b3" "site/built/01-intro.md" "2025-11-12"
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"episodes/02-filedir.md" "09fc51c863aced82bb76d0c9e979865e" "site/built/02-filedir.md" "2025-10-25"
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"episodes/03-create.md" "60df093284472799f26926d6676f4883" "site/built/03-create.md" "2025-09-15"
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"episodes/04-pipefilter.md" "a53169dd94d8546082a0b923ca7060d9" "site/built/04-pipefilter.md" "2025-07-25"

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