Merge pull request #11 from AFM-SPM/ns-rse/2-unix-shell-intro

config.yaml

@@ -59,7 +59,10 @@ contact: '[email protected]' # FIXME
 
 # Order of episodes in your lesson
 episodes:
-- introduction.md
+- 01-command-line.md
+- 02-filedir.md
+- 03-create.md
+# - introduction.md
 
 # Information for Learners
 learners:

episodes/01-command-line.md

@@ -0,0 +1,167 @@
+---
+title: "Introducing the Command Line"
+teaching: 20
+exercises: 3
+---
+
+:::::::::::::::::::::::::::::::::::::: questions
+
+- What is a command shell and why would I use one?
+
+::::::::::::::::::::::::::::::::::::::::::::::::
+
+::::::::::::::::::::::::::::::::::::: objectives
+
+- Explain when and why command-line interfaces should be used instead of graphical interfaces.
+
+::::::::::::::::::::::::::::::::::::::::::::::::
+
+### 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.
+
+::::::::::::::::::::::::::::::::::::::::::::::::::
+
+
+This chapter is from "[Software Carpentry The Unix Shell][swcarpentry-unix]". It is licensed under the
+[CC-BY-4.0][cc-by-4].
+
+
+[swcarpentry-unix]: https://swcarpentry.github.io/shell-novice/
+[cc-by-4]: https://creativecommons.org/licenses/by-sa/4.0/