source commit: 8a1aa97

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01-intro.md

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+---
+title: Introducing the Shell
+teaching: 5
+exercises: 0
+---
+
+::::::::::::::::::::::::::::::::::::::: objectives
+
+- Explain how the shell relates to the keyboard, the screen, the operating system, and users' programs.
+- Explain when and why command-line interfaces should be used instead of graphical interfaces.
+
+::::::::::::::::::::::::::::::::::::::::::::::::::
+
+:::::::::::::::::::::::::::::::::::::::: questions
+
+- What is a command shell and why would I use one?
+
+::::::::::::::::::::::::::::::::::::::::::::::::::
+
+### Background
+
+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
+**graphical user interface** (GUI).
+With a GUI, we give instructions by clicking a mouse and using menu-driven interactions.
+
+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 **command-line interface** (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.
+
+### The Shell
+
+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.
+
+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.
+
+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 *script*, improving the reproducibility of
+workflows.
+
+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.
+
+Let's get started.
+
+When the shell is first opened, you are presented with a **prompt**,
+indicating that the shell is waiting for input.
+
+```bash
+$
+```
+
+The shell typically uses `$ ` as the prompt, but may use a different symbol.
+In the examples for this lesson, we'll show the prompt as `$ `.
+Most importantly, *do not type the prompt* 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.
+
+The prompt is followed by a **text cursor**, 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.
+
+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 `$`. Such
+a prompt might look like, e.g.:
+
+```bash
+nelle@localhost $
+```
+
+The prompt might even include more than this. Do not worry if your prompt is not
+just a short `$ `. 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 `$ `
+character itself and we will see later why.
+
+So let's try our first command, `ls`, which is short for listing.
+This command will list the contents of the current directory:
+
+```bash
+$ ls
+```
+
+```output
+Desktop     Downloads   Movies      Pictures
+Documents   Library     Music       Public
+```
+
+:::::::::::::::::::::::::::::::::::::::::  callout
+
+## Command not found
+
+If the shell can't find a program whose name is the command you typed, it
+will print an error message such as:
+
+```bash
+$ ks
+```
+
+```output
+ks: command not found
+```
+
+This might happen if the command was mis-typed or if the program corresponding to that command
+is not installed.
+
+
+::::::::::::::::::::::::::::::::::::::::::::::::::
+
+## Nelle's Pipeline: A Typical Problem
+
+Nelle Nemo, a marine biologist,
+has just returned from a six-month survey of the
+[North Pacific Gyre](https://en.wikipedia.org/wiki/North_Pacific_Gyre),
+where she has been sampling gelatinous marine life in the
+[Great Pacific Garbage Patch](https://en.wikipedia.org/wiki/Great_Pacific_Garbage_Patch).
+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 `goostats.sh`.
+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 *Aquatic Goo Letters*.
+
+If Nelle chooses to run `goostats.sh` by hand using a GUI,
+she'll have to select and open a file 1520 times.
+If `goostats.sh` 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.
+
+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 `goostats.sh` program,
+using loops to automate the repetitive steps of entering file names,
+so that her computer can work while she writes her paper.
+
+As a bonus,
+once she has put a processing pipeline together,
+she will be able to use it again whenever she collects more data.
+
+In order to achieve her task, Nelle needs to know how to:
+
+- navigate to a file/directory
+- create a file/directory
+- check the length of a file
+- chain commands together
+- retrieve a set of files
+- iterate over files
+- run a shell script containing her pipeline
+
+
+
+:::::::::::::::::::::::::::::::::::::::: keypoints
+
+- A shell is a program whose primary purpose is to read commands and run other programs.
+- This lesson uses Bash, the default shell in many implementations of Unix.
+- Programs can be run in Bash by entering commands at the command-line prompt.
+- 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.
+- A significant challenge when using the shell can be knowing what commands need to be run and how to run them.
+
+::::::::::::::::::::::::::::::::::::::::::::::::::
+
+