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01-shell-intro.qmd
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01-shell-intro.qmd
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---
title: "The Unix Shell"
format:
revealjs:
chalkboard: false
logo: /images/ScPo-logo.png
footer: ScPo Intro To Programming 2023
incremental: false
code-line-numbers: false
highlight-style: github
author: Florian Oswald and Software Carpentry
---
## Intro
::::: {.callout-note}
# Question
* What is a command shell and why would I use one?
:::::
::::: {.callout-tip}
# 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.
::::::
---
## Do You GUI?
::: {.callout-tip}
# What's a GUI
A *Graphical User Interface* (GUI) lets the user interact by clicking with a mouse and using menus.
:::
. . .
* I love 😍 a good Graphical User Interface (GUI)
. . .
* But. Bad things can happen.
. . .
* ☠️
---
## {background-image="/images/bad.gif" background-size="cover"}
---
## Bad.
::::: {.columns}
::::: {.column width="50%"}
::: {.callout-warning}
# No More than 65,536 Rows
* Public Health England [missed 14.000 covid cases](https://www.influentialsoftware.com/how-an-nhs-test-and-trace-excel-error-lost-16000-covid-19-cases/)
* They used `.xls` document to collect data.
:::
:::::
::::: {.column width="50%"}
::: {.callout-warning}
# No Growth with High Debt?
* [Reinhardt and Rogoff controversy](https://theconversation.com/the-reinhart-rogoff-error-or-how-not-to-excel-at-economics-13646).^[Both are eminent researchers and we do *not* imply misconduct.]
* Inadvertently did not select all relevant countries on spreadsheet.
:::
:::::
:::::
---
## Or Do you CLI?
::: {.callout-tip}
# What's a CLI
A *Command Line Interface* (CLI) allows interaction via (text) commands.
:::
* CLIs can collect commands somewhere - *reproducible*
* But one has to learn a *language*.
* They are great for *long, repetitive tasks*.
* It's often the **only** way to interact with high-performance computing. --> Show!
---
## The Shell {.smaller}
* The *shell* is a program where we can type in commands and get output.
* We often use very simple programs - good for just one thing.
* There is tremendous power in *combining* those little programs.
* It's a *platform* approach to an Operating System.
::: {.callout-tip}
# Unix is a Platform
A protocol and many small program who interact according to the rules with each other
:::
![[email protected] Larry Ewing and The GIMP, Attribution, via Wikimedia Commons](/images/Tux.png)
---
## Go! 🚀
1. Open your terminal! (`GitBash` on Windows)
2. You should see something like
```bash
$
```
which is called the **prompt**.
3. You **don't have to type** the `$`!
3. next to it, you see a cursor.
---
## First command: `ls`
* type `ls` and hit enter
* you see something like this as output:
```
Desktop Downloads Movies Pictures
Documents Library Music Public
```
* By default, the terminal opens in your home directory.
* `ls` *lists* the content of that directory.
---
## First Error!
::: {.callout-caution}
* If you mistype a command, or look for a program that is not installed, you get an error. Like:
```
bash-3.2$ ks
```
```
bash: ks: command not found
```
:::
* Look for a spelling mistake (it's `ls` not `ks`)
* Or install the required program.
## Nelle's Pipeline: A Typical Problem {.smaller}
* Nelle Nemo is a marine biologist. 🌊 🐡
* Just sampled gelatinous marine life in the
[Great Pacific Garbage Patch](http://en.wikipedia.org/wiki/Great_Pacific_Garbage_Patch).
* From 1520 samples she obtained measures of the relative abundance of 300 proteins.
* Her supervisor, *Professor Jones*, handed down to hear a program called `goostats.sh`.
* `goostats.sh` needs to be run on each of the 1520 samples.
* Paper needs to be ready by the end of the month.
---
## {background-image="/images/PHD.png" background-size="50%" background-position="center"}
---
## Battle Plan
* Using a GUI to run `goostats.sh`, Nelle will have to use her mouse to select and open a file 1520 times.
* If `goostats.sh` takes 30 secs to run, this will take more than 12 hours of Nelle's *active time*.
* With the help of the shell, Nelle could make her computer go through that list of files instead.
* **Bonus** : she will have a working pipeline, that can be re-run each time need be.
---
## What Does Nelle Need {.smaller}
Nelle has needs to learn the following things:
- 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
And we will be right next to her. 🙂
---
##
::: {.callout-tip}
# Key Points
- 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.
- The shell's main disadvantages are its primarily textual nature and how cryptic its commands and operation can be.
:::