linux101.qmd

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code: HPC 0
name: Introduction to Linux for HPC
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{{< include _title.qmd >}}

# Introduction section

## Introduction to Linux

Aims of this training:

- Introduce you to using command line interface (CLI) Linux
- Build your confidence in navigating Linux file systems using the command line
- Enable you to use Linux without a graphical user interface (GUI)
- Prepare you for [HPC1: Introduction to High Performance Computing](https://arc.leeds.ac.uk/training/courses/hpc1/)

::: {.notes}
- This is a brief, introductory level session. 
- Do not assume knowledge of file systems/directory structures/other computing background.
:::

## Format of this course

- This is a **2.5 hour tutorial**. We will be trying out what we are learning, so be ready for some typing!

- These lecture slides are based on the [Software Carpentries documentation on Unix Shell basics](https://swcarpentry.github.io/shell-novice/), but is a shorter course and uses different examples.

- Once you finish this tutorial, we recommend you read through the Software Carpentries material and follow through the tutorial there: you can do this work from the same *virtual machine* we will be using today.

::: {.notes}
- We include notes at the end on how to use our virtual machine to run the Software Carpentries material
:::

## Format of these slides {.smaller}

- Everything you need for this session is in these slides.
- We recommend you have a copy open on your computer.
- If you have enough room on your screen, have these notes and your command line side-by-side.
- These notes should also be viewable via mobile if you don't mind not being able to copy and paste!
- There is a quick reference [cheat sheet](#cheat-sheet) linked in the footer; you can return to your place in the slideshow from this cheat sheet using the back button.

::: {.notes}

- The cheat sheet can be used from any point in the tutorial; you can just click the back arrow
and return to the exact point in the slides

:::

## Syllabus

- Interacting with a computer: operating systems, GUIs and CLIs, bash
- File systems on Linux
- Navigating filesystems from the command line
- Creating and editing files and directories
- Running simple scripts

::: {.notes}
- If we don't manage to cover all these topics, you will be able to follow on at home.
:::

## Learning method {.smaller}

The aim *is not for you to leave knowing loads of Linux Bash commands*!

- There are many fantastically
useful commands we won't cover today (read through the [Software Carpentries course](https://swcarpentry.github.io/shell-novice/)
after this for some extra commands);
- The aim is for you to get a feel for how Linux's command line works,
to be able to problem solve and find the commands you need.
- This is an introductory course for complete beginners: of course, you're welcome here if you want a refresher, but expect for
the course to be slow-paced.

::: {.notes}

- Emphasise that the point is *not* to teach lots of shortcuts and commands.
- It's ok not to remember commands from today - the point is that if you want to do something on Linux,
you'll be better able to search for and then understand the answer.

:::

## PRIMM method {.smaller}

It's helpful for you as a learner to understand the PRIMM structure so you can apply it while working through this course. Not every step
will be relevant or used at every stage of the course!

::: {.panel-tabset}

### What's PRIMM?

PRIMM is a pedagogical method specifically aimed at teaching text-based programming. While research into adult programming
learners is very limited (especially in terms of demographics; many key studies that are cited have overwhelmingly homogenous test groups),
the PRIMM method has a few key benefits:

- It supports learners with different ability levels and who learn at different speeds;
- It can be applied by learners even if the course materials are not specifically built with it in mind;
- It can be applied to asynchronous learning materials (for example, if you are using these notes online on your own).

### P

The **P** in PRIMM stands for **predict**:

When you first see a command, script, or piece of code, before running it, predict what you think it will
do. It's ok to get this wrong: the important thing is to get into the habit of predicting! This
helps to keep you actively engaged and focused, and begins to build an intuitive sense about the structure of commands.

- What do you think the code is going to do generally?
- What do you think the output in your terminal is going to look like?

### R 

The **R** in PRIMM stands for **run**:

- Run the code or program;
- How does the output/effect compare to your prediction?
  - What did you get right?
  - What did you misinterpret?
- Do you understand what happened?

### I 

The **I** in PRIMM stands for **investigate**:

Let's dig a little deeper into the *structure* of code you've used.

- What options or arguments did you use, and what effect did they have?
- Can you find some documentation on the command you used?
  - Does the description match how you would describe the code?
    - If no, why does your understanding of it diverge?
  - What other options or features are available?



### M 

The first **M** in PRIMM stands for **modify**:

- Try running the code with different options:
  - Change only a small thing at a time;
  - Always predict what you think the output will be!
  - Compare the actual output with your prediction;
  - Compare your understanding to the available documentation.

This stage helps you to gradually increase the difficultly of the tasks you are doing!

### M

The second **M** in PRIMM stands for **make**:

This stage is about making the code your own.

- At this stage, you can try implementing snippets of code you've already learned, but to solve a new or different problem;
- Again, use the previous stages when you are writing your code: *predict* what you think will happen, *run* the code and compare
the output to your predictions, and *investigate* the structure of it, especially if it does not behave how you intended!

### Key notes

**Read before you write** - research has proven repeatedly the importance of reading and predicting the output of code as
a method of learning, over just *getting straight into it* and writing code.

- Novice programmers need to acquire accuracy in tracing code *before* they can program independently
- Trying to write code first leads to frustration and confusion

**Learn in a way that suits you** - if that is copying and pasting commands
from the slides instead of trying to keep up with typing, *that's ok!*

:::

# Ways of interacting with a computer

::: {.notes}
- Our first section is going to cover some very high-level concepts about how we use computers

:::

## Interacting with a computer {.smaller}

When we use a computer, we interact with the hardware through an **operating system** or **OS**.

Common operating systems for research computers include:

- Microsoft Windows
- MacOS
- Linux

We are going to be looking at Linux today, which is a family of operating systems that are **Open Source** and are widely used in research, for example on **High Performance Computing** platforms like ARC4 or Aire.

## Interacting with a computer {.smaller}

When we use a computer, like our desktop or laptop, we often use a **Graphical User Interface** or a **GUI**.

- GUIs allow us to interact with a computer through graphical means: icons, text, buttons, windows. GUIs usually involve using a mouse and clicking into menus.
- The Windows desktop and MacOS desktop are GUIs that let you control the computer graphically.
- Many computer programs also have GUIs: for example, Excel.

![](assets/img/linux101/excel-gui.png){fig-align="center" fig-alt="A screenshot of Excel."}

::: {.notes}
- What are some of the benefits of GUIs? See if people have suggestions.
- What are some of the downsides of using GUIs?
:::

## Interacting with a computer {.smaller}

As well as using a GUI, we can also interact with computers using a **Command Line Interface** or a **CLI**.

- CLIs allow us to interact with a computer through text-based commands typed into the command-line.
- While GUIs can be simple and intuitive to use, they can make it difficult to reproduce workflows:
  - Sometimes you have to record by hand (or with a screen recording) what sub-options from different menus you used;
  - Updates to GUIs can make it difficult to find the same menu options;
  - A workflow with multiple steps can be tedious to repeat for multiple datasets (having to click through multiple layers of menu options for each dataset).
- Many large research machines (such as the HPC machines ARC4 and Aire here at Leeds) *do not have a GUI* and so you need to interact with them through a **CLI**.

## Command Line Interfaces {.smaller}

- There are multiple different CLIs available:
  - General-purpose CLIs are available for each **Operating System** for general computer control:
    - Windows Command Prompt;
    - Windows Powershell;
    - Mac Terminal;
  - Some specific programs have their own custom CLIs:
    - Anaconda Prompt for Windows;
    - Git Bash for Windows;
- Today, we are going to be using a **Unix Shell**:
  - This is the general-purpose CLI that underpins both Linux and Mac;
  - We will use Bash, a popular Unix Shell.

::: {.notes}
- Essentially, there are many different ways to access a command line, and there are different types
of command line interfaces!
- We are teaching you one today that is easy to access, and is used on research HPC systems
:::

## Poll

Throughout this presentation, we will be using quick polls to gauge your familiarity with concepts.

Let's test it out:

[Click here to go to Poll](https://universityofleeds.display.vevox.com#/present/696636/ULXGUZROA4XT20VKGCAZ){target="_blank"}

::: {.notes}
- Open up vevox session and activate relevant poll
:::

## Bash {.smaller}

How do we access Bash?

- Bash is the default shell on Unix systems like Linux or Mac
- Bash is also available through many command-line tools for Windows:
  - Git Bash for Windows
  - Anaconda Prompt

We're going to use a **virtual machine** for this course: this is a Linux machine running in the cloud.

This means that everyone here can run it with the exact same set-up; you only need a browser.

# Linux filesystems

::: {.notes}
- Before we open up our virtual machine, we are going to talk a little bit about how Linux filesystems work.
- It's important for us to build a little bit of a mental map before we start using the command line,
just to make it less confusing.
- This might seem familiar, if you're used to navigating filesystems on Windows or Mac already!
:::

## File system on Linux

```{mermaid}
%%| fig-align: center
---
config:
  look: handDrawn
---
%%{init: {'themeVariables': { 'fontSize': '32px', 'padding': '40px'}}}%%
flowchart
    
    / o--obin
    / o--odev
    / o--oetc
    / o--ohome
    home o--omy-username
    home o--omy-friend
    / o--otmp

    my-username o--o all_my_files
```

Each rectangle is a folder or **directory** (**dir** for short)

::: {.notes}
- This shows a sketch of a file system.
- We have a hierarchy of folders or directories sitting inside one another.
- Folders are usually called "directories" on Linux systems, but they mean the same thing.
:::

## File system on Linux

```{mermaid}
%%| fig-align: center
---
config:
  look: handDrawn
---
%%{init: {'themeVariables': { 'fontSize': '32px', 'padding': '40px'}}}%%
flowchart
    
    / o--obin
    / o--odev
    / o--oetc
    / o--ohome
    home o--omy-username
    home o--omy-friend
    / o--otmp

    my-username o--o all_my_files

    style / fill:#f9f,stroke:#333,stroke-width:10px,color:#333
```

Each rectangle is a folder or **directory** (**dir** for short)

::: {.notes}
- This branching system starts from the root (the forward slash) at the very top, highlighted in pink.
- Inside this root directory, we have a bunch of system folders - we don't need to worry about these now.
:::

## File system on Linux

```{mermaid}
%%| fig-align: center
---
config:
  look: handDrawn
---
%%{init: {'themeVariables': { 'fontSize': '32px', 'padding': '40px'}}}%%
flowchart
    
    / o--obin
    / o--odev
    / o--oetc
    / o--ohome
    home o--omy-username
    home o--omy-friend
    / o--otmp

    my-username o--o all_my_files

    style home fill:#f9f,stroke:#333,stroke-width:10px,color:#333
```

Each rectangle is a folder or **directory** (**dir** for short)

::: {.notes}
- One of the directories is called "home": this contains all the home directories of users.
- The home directories are usually called after their owner's username.
- If you look in this directory on a personal or family computer, you might find a handful of user home directories
- If you look at this directory on a university HPC system, like Aire, you'll find hundreds of user home directories
:::

## File system on Linux

```{mermaid}
%%| fig-align: center
%%| fig-width: 100%
---
config:
  look: handDrawn
---
%%{init: {'themeVariables': { 'fontSize': '32px', 'padding': '40px'}}}%%
flowchart
    
    / o--obin
    / o--odev
    / o--oetc
    / o--ohome
    home o--omy-username
    home o--omy-friend
    / o--otmp

    my-username o--o all_my_files

    style my-username fill:#f9f,stroke:#333,stroke-width:10px,color:#333
```

The `my-username` folder is your **user home directory**

::: {.notes}
- Confusingly, we refer to this highlighted directory as your *home* directory
- Even though there is a folder one level up that is called home!
:::

## File system on Linux

```{mermaid}
%%| fig-align: center
%%| fig-width: 100%
---
config:
  look: handDrawn
---
%%{init: {'themeVariables': { 'fontSize': '32px', 'padding': '40px'}}}%%
flowchart
    
    / o--obin
    / o--odev
    / o--oetc
    / o--ohome
    home o--omy-username
    home o--omy-friend
    / o--otmp

    my-username o--o all_my_files

    style my-username fill:#f9f,stroke:#333,stroke-width:10px,color:#333
```

How do we describe the address of this home directory?

::: {.notes}
- How do we describe where this directory or folder is?
- We describe it in a similar way to a website URL, using it's path
- We need to know all the folders directly above it.
:::

## File system on Linux

```{mermaid}
%%| fig-align: center
%%| fig-width: 100%
---
config:
  look: handDrawn
---
%%{init: {'themeVariables': { 'fontSize': '32px', 'padding': '40px'}}}%%
flowchart
    
    / o--obin
    / o--odev
    / o--oetc
    / o--ohome
    home o--omy-username
    home o--omy-friend
    / o--otmp

    my-username o--o all_my_files

    style my-username fill:#f9f,stroke:#333,stroke-width:10px,color:#333
    style home fill:#f9f,stroke:#333,stroke-width:10px,color:#333
    style / fill:#f9f,stroke:#333,stroke-width:10px,color:#333
```

The folders in the address are `/`, `home` and `my-username`

::: {.notes}
- Above our username directory, we have home and the root (which is denoted by just a forward slash)
:::

## File system on Linux

```{mermaid}
%%| fig-align: center
%%| fig-width: 100%
---
config:
  look: handDrawn
---
%%{init: {'themeVariables': { 'fontSize': '32px', 'padding': '40px'}}}%%
flowchart
    
    / o--obin
    / o--odev
    / o--oetc
    / o--ohome
    home o--omy-username
    home o--omy-friend
    / o--otmp

    my-username o--o all_my_files

    style my-username fill:#f9f,stroke:#333,stroke-width:10px,color:#333
    style home fill:#f9f,stroke:#333,stroke-width:10px,color:#333
    style / fill:#f9f,stroke:#333,stroke-width:10px,color:#333
```

Stick them together like a URL: `/home/my-username`

::: {.notes}
- We just have to put them together like a web address (because the internet is basically just a giant file structure)
:::

## File system on Linux

On Windows, file paths use backlashes ( `\` ) instead of forward slashes (`/`)!

- This can cause confusion and errors if you are writing scripts that load in data from certain file paths, and need to use both Windows and Linux!
- Thankfully there are lots of ways around this, including libraries for handling paths in Python and R

::: {.notes}
- It's useful to note that Windows uses slashes in the opposite direction for file paths.
- We're not going to focus on this today as we are using only Linux
- But if you get an error while coding it's useful to keep this in mind.
:::

## File system on Linux

```{mermaid}
%%| fig-align: center
%%| fig-width: 100%
---
config:
  look: handDrawn
---
%%{init: {'themeVariables': { 'fontSize': '32px', 'padding': '40px'}}}%%
flowchart
    
    / o--obin
    / o--odev
    / o--oetc
    / o--ohome
    home o--omy-username
    home o--omy-friend
    / o--otmp

    my-username o--o all_my_files

    style my-username fill:#f9f,stroke:#333,stroke-width:10px,color:#333
    style home fill:#f9f,stroke:#333,stroke-width:10px,color:#333
    style / fill:#f9f,stroke:#333,stroke-width:10px,color:#333
```

Stick them together like a URL: `/home/my-username`

::: {.notes}
- Back to our file system.
- Today, everything we are doing will be in our home directory, so let's just focus on that!
- When you log in to a linux system, this is usually where you will be dropped!
:::

## File system on Linux

```{mermaid}
%%| fig-align: center
%%| fig-width: 100%
---
config:
  look: handDrawn
---
%%{init: {'themeVariables': { 'fontSize': '32px', 'padding': '40px'}}}%%
flowchart
    
    / o--ohome
    home o--omy-username

    my-username o--o all_my_files

    style my-username fill:#f9f,stroke:#333,stroke-width:10px,color:#333
    style home fill:#f9f,stroke:#333,stroke-width:10px,color:#333
    style / fill:#f9f,stroke:#333,stroke-width:10px,color:#333
```

`/home/my-username/all_my_files` is a bit long...

::: {.notes}
- Typing the full path to our files and folders is a bit tedious
- lets look at a shorter way
:::

## File system on Linux

::: {layout-ncol=2}
```{mermaid}
%%| fig-align: center
%%| fig-width: 100%
---
config:
  look: handDrawn
---
%%{init: {'themeVariables': { 'fontSize': '32px', 'padding': '40px'}}}%%
flowchart
    
    / o--ohome
    home o--omy-username

    my-username o--o all_my_files

    style my-username fill:#f9f,stroke:#333,stroke-width:10px,color:#333
    style home fill:#f9f,stroke:#333,stroke-width:10px,color:#333
    style / fill:#f9f,stroke:#333,stroke-width:10px,color:#333
```

```{mermaid}
%%| fig-align: center
%%| fig-width: 100%
---
config:
  look: handDrawn
---
%%{init: {'themeVariables': { 'fontSize': '32px', 'padding': '40px'}}}%%
flowchart
    
    home["~"] o--o all_my_files

    style home fill:#f9f,stroke:#333,stroke-width:10px,color:#333

```
:::

`/home/my-username/all_my_files` is a bit long...

::: {.notes}
- Typing the full path to our files and folders is a bit tedious
- lets look at a shorter way
:::

## File system on Linux

```{mermaid}
%%| fig-align: center
%%| fig-width: 100%
---
config:
  look: handDrawn
---
%%{init: {'themeVariables': { 'fontSize': '32px', 'padding': '40px'}}}%%
flowchart
    
    home["~"] o--o all_my_files

    style home fill:#f9f,stroke:#333,stroke-width:10px,color:#333
```


- To save us from typing out `/home/my-username` every time we refer to a directory or file, we can use the shortcut `~`, called a *tilde*
- This turns `/home/my-username/all_my_files` to `~/all_my_files`

## Poll

Let's test your familiarity with Linux file paths!

[Click here to go to Poll](https://universityofleeds.display.vevox.com#/present/696636/ULXGUZROA4XT20VKGCAZ){target="_blank"}

## Let's explore some files!

Time to explore some files on a Linux system!

```{mermaid}
%%| fig-align: center
%%| fig-width: 100%
---
config:
  look: handDrawn
---
%%{init: {'themeVariables': { 'fontSize': '28px'}}}%%
flowchart TD
    A["/home/vscode/ <br> or ~"] o--o B[red-folder]
    A o--o C[pink-folder]
    A o--o D[blue-folder]

    B o--o r1([red-1.txt ])
    B o--o r2([red-2.txt ])
    B o--o r3([red-3.txt ])

    C o--o P1[pink-sub-folder]
    C o--o p2(["pink-file.md <br>"])
    C o--o p3{{"say_hi.sh <br>"}}

    P1 o--o p4(["**helloworld.py** <br>"])
    P1 o--o p5(["pink-data.csv <br>"])

    D o--o b1(["**blue.r** <br>"])

```

# First steps in bash

## Using our custom virtual machine {.smaller}

For this course, we've built a custom virtual machine for you to use.

This requires a **GitHub** account which you were asked to set up before this course.

(Don't worry if you haven't - please go and quickly sign up to [GitHub](https://github.com/signup) now!)

- There are many other ways to access the bash shell, such as on one of the HPC systems here at Leeds, or by installing [git bash](https://git-scm.com/downloads/win) on Windows, or using the terminal on Linux or Mac.
- We want everyone in the class to have the same directory structure and environment which is why we are using a virtual machine!

## Launch virtual machine

::::: {.panel-tabset}

### Step 1

One of the pre-requisites for this course was signing up for an account with GitHub,
as this is the service we use to host the virtual Linux machines for teaching this session.

[Log in to GitHub now (or sign up if you haven't already).](https://github.com/)

### Step 2

[Follow this link to open the course repository.](https://github.com/ARCTraining/linux-101)

### Step 3

There will be a green button with the word "Code", which will then bring up a menu when clicked.

:::: {layout="[ 30, 70 ]"}

::: {#first-column}

![](assets/img/linux101/code_button.png){fig-align="center" fig-alt="A green button with the word 'Code'."}

↑ [Click this button,]{style="font-size: 0.95em;"}
[this menu opens ]{style="font-size: 0.95em;"} →
:::

::: {#second-column}
![](assets/img/linux101/codespaces-2.png){fig-align="center" fig-alt="A green button with the word 'Code'."}
:::

::::






:::::

## The terminal

Once you've launched your virtual machine, you will see a terminal window something like this:

::: {style="font-size: 0.7em; text-align: left; background-color: black; color: white; font-family: monospace"}

[_ ]{style="color: black"}

[_ ]{style="color: black"}[\@username]{style="color: #00FF00"} **→** [/workspaces/bash-codespaces-template]{style="color: #00FFFF"} [(main)]{style="color: #FF7F50"} [$ ▮]{style="color: white"}

[_ ]{style="color: black"}
:::

:::::{.fragment .fade-in}



::: {style="font-size: 0.7em; text-align: left; background-color: black; color: white; font-family: monospace"}

[_ ]{style="color: black"}

[_ ]{style="color: black"}[\@username]{style="color: #00FF00"} **→** [<u>/workspaces/bash-codespaces-template</u>]{style="color: #00FFFF"} [(main)]{style="color: #FF7F50"} [$ ▮]{style="color: white"}

[_ ]{style="color: black"}
:::

The <u>underlined section</u> is your directory *path*.

:::::

## The terminal

Once you've launched your virtual machine, you will see a terminal window something like this:

::: {style="font-size: 0.7em; text-align: left; background-color: black; color: white; font-family: monospace"}

[_ ]{style="color: black"}

[_ ]{style="color: black"}[\@username]{style="color: #00FF00"} **→** [/workspaces/bash-codespaces-template]{style="color: #00FFFF"} [(main)]{style="color: #FF7F50"} [$ ▮]{style="color: white"}

[_ ]{style="color: black"}
:::

:::::{.fragment .fade-in}



::: {style="font-size: 0.7em; text-align: left; background-color: black; color: white; font-family: monospace"}

[_ ]{style="color: black"}

[_ ]{style="color: black"}[\@username]{style="color: #00FF00"} **→** [/workspaces/bash-codespaces-template]{style="color: #00FFFF"} [<u>(main)</u>]{style="color: #FF7F50"} [$ ▮]{style="color: white"}

[_ ]{style="color: black"}
:::

The <u>underlined section</u> has to do with the **git version control system**: not a topic for today, but you can learn about this in SWD2!

:::::

## The terminal

Once you've launched your virtual machine, you will see a terminal window something like this:

::: {style="font-size: 0.7em; text-align: left; background-color: black; color: white; font-family: monospace"}

[_ ]{style="color: black"}

[_ ]{style="color: black"}[\@username]{style="color: #00FF00"} **→** [/workspaces/bash-codespaces-template]{style="color: #00FFFF"} [(main)]{style="color: #FF7F50"} [$ ▮]{style="color: white"}

[_ ]{style="color: black"}
:::

:::::{.fragment .fade-in}

::: {style="font-size: 0.7em"}
The dollar symbol ($) and rectangle (▮) on the right hand side are the end of the prompt and the cursor.

- The $ tells you where the computer's message ends, and where you can enter your commands.
- The ▮ (which will probably be slowly flashing) tells you where the cursor is; this often looks more like a vertical line ( | ) in other programs like Word.
:::

:::::

## The terminal

If you click on the [▮]{style="color: white; background-color: black"} or the space just to the right of the [$]{style="color: white; background-color: black"} you can type in your message:

::: {style="font-size: 0.7em; text-align: left; background-color: black; color: white; font-family: monospace"}

[_ ]{style="color: black"}

[_ ]{style="color: black"}[\@username]{style="color: #00FF00"} **→** [/workspaces/bash-codespaces-template]{style="color: #00FFFF"} [(main)]{style="color: #FF7F50"} [$ hello▮]{style="color: white"}

[_ ]{style="color: black"}
:::


Anything you type will be in **white** text in the terminal; the cursor will blink at the end of the text.

To *send* the argument or message, you need to press ENTER on your keyboard.

## The terminal

If you click on the [▮]{style="color: white; background-color: black"} or the space just to the right of the [$]{style="color: white; background-color: black"} you can type in your message:

::: {style="font-size: 0.7em; text-align: left; background-color: black; color: white; font-family: monospace"}

[_ ]{style="color: black"}

[_ ]{style="color: black"}[\@username]{style="color: #00FF00"} **→** [/folders]{style="color: #00FFFF"} [(main)]{style="color: #FF7F50"} [$]{style="color: grey"} [**this is the code you type**]{style="color: white"} [↵]{style="color: #DDA0DD; font-size: 1.5em;"}

[_ ]{style="color: black"}
:::

- The code you need to type/copy and paste is shown in **bold** white
- We will hide the cursor and fade the prompt ($) to grey
- We will show an ENTER symbol in pink to remind you how to enter the command (↵)

## Very first command: `cd`

We're going to use the `cd` command to bring us to our home directory.

::::: {style="font-size: 1.2em; text-align: left; background-color: black; color: white; font-family: monospace"}
[_ ]{style="color: black"}

[_ ]{style="color: black"}[\@username]{style="color: #00FF00"} **→** [/folders]{style="color: #00FFFF"} [(main)]{style="color: #FF7F50"} [$]{style="color: grey"} [▮]{style="color: white"}

:::{.fragment .fade-in}
[_ ]{style="color: black"}[\@username]{style="color: #00FF00"} **→** [/folders]{style="color: #00FFFF"} [(main)]{style="color: #FF7F50"} [$]{style="color: grey"} [**cd**]{style="color: white"} [↵]{style="color: #DDA0DD; font-size: 1.5em;"}
:::

:::{.fragment .fade-in}
[_ ]{style="color: black"}[\@username]{style="color: #00FF00"} **→** [~]{style="color: #00FFFF"} [$]{style="color: grey"} [▮]{style="color: white"}
:::

[_ ]{style="color: black"}
:::::

## Very first command: `cd`

- `cd` stands for *change directory*
- It brings us back to our *home directory*, `~` or `/home/vscode`

:::{.fragment .fade-in}
- Our virtual machine is a little bit weird because it starts us off in a different folder: on most Linux systems, when you log in, you will immediately be in your home directory
:::

::::: {style="font-size: 1.2em; text-align: left; background-color: black; color: white; font-family: monospace"}
[_ ]{style="color: black"}[\@username]{style="color: #00FF00"} **→** [~]{style="color: #00FFFF"} [$]{style="color: grey"} [▮]{style="color: white"}
:::::

## What's in this folder?

Now that you know how to find home (from wherever in the file system you are), you need to know what's *in* your home directory.

- You can *list* out the files and folders in your directory with the command `ls`

## What's in this folder? `ls` to list

Using the `ls` command to list out the contents of the directory:

::::: {style="font-size: 1.2em; text-align: left; background-color: black; color: white; font-family: monospace"}
[_ ]{style="color: black"}

[_ ]{style="color: black"}[\@username]{style="color: #00FF00"} **→** [~]{style="color: #00FFFF"} [$]{style="color: grey"} [▮]{style="color: white"}

:::{.fragment .fade-in}
[_ ]{style="color: black"}[\@username]{style="color: #00FF00"} **→** [~]{style="color: #00FFFF"} [$]{style="color: grey"} [**ls**]{style="color: white"} [↵]{style="color: #DDA0DD; font-size: 1.5em;"}
:::

:::{.fragment .fade-in}
[_ ]{style="color: black"}[blue-folder    pink-folder    red-folder]{style="color: #00FFFF"}

[_ ]{style="color: black"}[\@username]{style="color: #00FF00"} **→** [~]{style="color: #00FFFF"} [$]{style="color: grey"} [▮]{style="color: white"}
:::

[_ ]{style="color: black"}
:::::

## What's in this folder? `ls` to list

How do we know if `blue-folder` is a file or a directory? (imagine it has a less descriptive name)

::::: {style="font-size: 1.2em; text-align: left; background-color: black; color: white; font-family: monospace"}

[_ ]{style="color: black"}[\@username]{style="color: #00FF00"} **→** [~]{style="color: #00FFFF"} [$]{style="color: grey"} [**ls**]{style="color: white"} [↵]{style="color: #DDA0DD; font-size: 1.5em;"}

[_ ]{style="color: black"}[blue-folder    pink-folder    red-folder]{style="color: #00FFFF"}

[_ ]{style="color: black"}[\@username]{style="color: #00FF00"} **→** [~]{style="color: #00FFFF"} [$]{style="color: grey"} [▮]{style="color: white"}

:::{.fragment .fade-in}
[_ ]{style="color: black"}[\@username]{style="color: #00FF00"} **→** [~]{style="color: #00FFFF"} [$]{style="color: grey"} [**ls -F**]{style="color: white"} [↵]{style="color: #DDA0DD; font-size: 1.5em;"}
:::

:::::

## What's in this folder? `ls` to list

We can use `ls -F`: this tells us the category of the "things" in the directory

- If the name ends in a trailing forward slash (like `this/`) then the item is a directory or folder

::::: {style="font-size: 1.2em; text-align: left; background-color: black; color: white; font-family: monospace"}

[_ ]{style="color: black"}[\@username]{style="color: #00FF00"} **→** [~]{style="color: #00FFFF"} [$]{style="color: grey"} [**ls -F**]{style="color: white"} [↵]{style="color: #DDA0DD; font-size: 1.5em;"}

[_ ]{style="color: black"}[blue-folder/    pink-folder/    red-folder/]{style="color: #00FFFF"}

[_ ]{style="color: black"}[\@username]{style="color: #00FF00"} **→** [~]{style="color: #00FFFF"} [$]{style="color: grey"} [▮]{style="color: white"}


:::::

## What's in this folder? `ls` to list

This is what we expected: we saw in our directory map that we have three directories in our home (`~`): `red-folder`, `pink-folder`, and `blue-folder`.

```{mermaid}
%%| fig-align: center
%%| fig-width: 100%
---
config:
  look: handDrawn
---
%%{init: {'themeVariables': { 'fontSize': '28px'}}}%%
flowchart TD
    A["/home/vscode/ <br> or ~"] o--o B[red-folder]
    A o--o C[pink-folder]
    A o--o D[blue-folder]

    B o--o r1([red-1.txt ])
    B o--o r2([red-2.txt ])
    B o--o r3([red-3.txt ])

    C o--o P1[pink-sub-folder]
    C o--o p2(["pink-file.md <br>"])
    C o--o p3{{"say_hi.sh <br>"}}

    P1 o--o p4(["**helloworld.py** <br>"])
    P1 o--o p5(["pink-data.csv <br>"])

    D o--o b1(["**blue.r** <br>"])

```

## What's in this folder? `ls` to list

Let's list what's inside `pink-folder`...

```{mermaid}
%%| fig-align: center
%%| fig-width: 100%
---
config:
  look: handDrawn
---
%%{init: {'themeVariables': { 'fontSize': '28px'}}}%%
flowchart TD
    A["/home/vscode/ <br> or ~"] o--o B[red-folder]
    A o--o C[pink-folder]
    A o--o D[blue-folder]

    B o--o r1([red-1.txt ])
    B o--o r2([red-2.txt ])
    B o--o r3([red-3.txt ])

    C o--o P1[pink-sub-folder]
    C o--o p2(["pink-file.md <br>"])
    C o--o p3{{"say_hi.sh <br>"}}

    P1 o--o p4(["**helloworld.py** <br>"])
    P1 o--o p5(["pink-data.csv <br>"])

    D o--o b1(["**blue.r** <br>"])

```

## What's in this folder? `ls` to list

We can use `ls name-of-folder` to tell us what's in a sub-directory.

What will the output be?

::::: {style="font-size: 1.2em; text-align: left; background-color: black; color: white; font-family: monospace"}

[_ ]{style="color: black"}[\@username]{style="color: #00FF00"} **→** [~]{style="color: #00FFFF"} [$]{style="color: grey"} [**ls pink-folder**]{style="color: white"} [↵]{style="color: #DDA0DD; font-size: 1.5em;"}

:::{.fragment .fade-in}
[_ ]{style="color: black"}[pink-file.md ]{style="color: white"} [  pink-subfolder  ]{style="color: #00FFFF"} [  say_hi.sh  ]{style="color: #00FF00"}
:::

:::::

## What's in this folder? `ls` to list

We can use `ls -F name-of-folder` to tell us what's in a sub-directory and what category the items are.

What will the output be?

::::: {style="font-size: 1.0em; text-align: left; background-color: black; color: white; font-family: monospace"}

[_ ]{style="color: black"}[\@username]{style="color: #00FF00"} **→** [~]{style="color: #00FFFF"} [$]{style="color: grey"} [**ls -F pink-folder**]{style="color: white"} [↵]{style="color: #DDA0DD; font-size: 1.5em;"}

:::{.fragment .fade-in}
[_ ]{style="color: black"}[pink-file.md ]{style="color: white"} [  pink-subfolder/  ]{style="color: #00FFFF"} [  say_hi.sh*  ]{style="color: #00FF00"}
:::

:::::

:::{.fragment .fade-in}
- Files get no added symbols;
- Folders or directories get a trailing forward slash (`/`);
- *Executables* get an asterisk (`*`);
:::

## Poll

Let's test your familiarity with these commands!

[Click here to go to Poll](https://universityofleeds.display.vevox.com#/present/696636/ULXGUZROA4XT20VKGCAZ){target="_blank"}


## Recap

So far, we've used:

- `cd` on it's own to go to our home directory;
- `ls` on it's own to list out the contents of our current directory (our home);
- `ls -F` (`ls` with the *flag or option* `-F`) to list out the categories of the content in the directory;
- `ls dir-name` (`ls` with the *argument* `dir-name`) to list out the content of the sub-directory `dir-name`;

# Navigating filesystems with bash

## Format of bash commands

You've already cracked how bash works with these few commands!

::::: {style="font-size: 1.7em; text-align: left; background-color: black; color: white; font-family: monospace"}

[_ ]{style="color: black"}[$]{style="color: white"} [ls]{style="color: #00FFFF"} [-F]{style="color: #00FF00"} [dir-name]{style="color: #DDA0DD;"}

:::: {style="font-size: 0.7em;"}
:::{.fragment .fade-in}

- [$ → prompt]{style="color: white;"}
- [ls → command]{style="color: #00FFFF;"}
- [-F → option]{style="color: #00FF00;"}
- [dir-name → argument]{style="color: #DDA0DD;"}

:::
::::

:::::

## Adding arguments to `cd`

We've used `cd` on it's own to access our home directory - what happens when we give it an argument?

What will the output be?

::::: {style="font-size: 1.2em; text-align: left; background-color: black; color: white; font-family: monospace"}

[_ ]{style="color: black"}[\@username]{style="color: #00FF00"} **→** [~]{style="color: #00FFFF"} [$]{style="color: grey"} [**cd pink-folder**]{style="color: white"} [↵]{style="color: #DDA0DD; font-size: 1.5em;"}

:::{.fragment .fade-in}

[_ ]{style="color: black"}[\@username]{style="color: #00FF00"} **→** [~/pink-folder]{style="color: #00FFFF"} [$]{style="color: grey"} [▮]{style="color: white"}
:::

:::::

:::{.fragment .fade-in}
We've moved *down* our directory structure, into the directory `pink-folder`
:::

## Explore with `cd` and `ls`

- Remember, you can return to home from anywhere with `cd` and no options or arguments
- Use `ls` to find out what is in the different directories
- Use `cd name-of-dir` to move to a subdirectory
- Use the [directory map](#map) if lost
- Use the `clear` command to clean up your terminal screen if it's getting too messy:


::::: {style="font-size: 1.2em; text-align: left; background-color: black; color: white; font-family: monospace"}

[_ ]{style="color: black"}[\@username]{style="color: #00FF00"} **→** [~]{style="color: #00FFFF"} [$]{style="color: grey"} [**clear**]{style="color: white"} [↵]{style="color: #DDA0DD; font-size: 1.5em;"}

:::::

## Getting help

There are two different ways of getting information about commands and their options and arguments within the shell:

- `man arg`
- `arg --help`

On our virtual machine, we are going to use the section option, `arg --help`. Try running `ls --help`:

::::: {style="font-size: 1.2em; text-align: left; background-color: black; color: white; font-family: monospace"}

[_ ]{style="color: black"}[\@username]{style="color: #00FF00"} **→** [~]{style="color: #00FFFF"} [$]{style="color: grey"} [**ls --help**]{style="color: white"} [↵]{style="color: #DDA0DD; font-size: 1.5em;"}

:::::

## Getting help

You'll be faced with a wall of text and will have to scroll to find the top of it:

::::: {style="font-size: 0.7em; text-align: left; background-color: black; color: white; font-family: monospace"}

[_ ]{style="color: black"}[\@username]{style="color: #00FF00"} **→** [~]{style="color: #00FFFF"} [$]{style="color: grey"} [**ls --help**]{style="color: white"} [↵]{style="color: #DDA0DD; font-size: 1.5em;"}

Usage: ls [OPTION]... [FILE]...

List information about the FILEs (the current directory by default).

Sort entries alphabetically if none of -cftuvSUX nor --sort is specified.


Mandatory arguments to long options are mandatory for short options too.

  -a, --all :                 do not ignore entries starting with .

  -A, --almost-all :          do not list implied . and ..

[and on, and on, and on...]{style="color: #DDA0DD; font-size: 1.5em;"}
:::::

## Getting help {.smaller}

This can be really useful for quickly checking the arguments and options to commands you half-remember,
but can also be incredibly unhelpful and overwhelming if you don't know what you're looking at!

- *Searching online is your friend!*
- If you know the argument name, say `ls`, wrap it in quotation marks in your search to require it;
- Search the term alongside terms like *bash*, *linux*, *command line*, *explanation*;
- For example, I might search **"ls -F" explanation**
- Stack Overflow and Stack Exchange (Q&A forums) can be useful sources, usually with a bit of conversation back and forth and likely some disagreement/argument about the *best* way of doing something.

## Getting help

- What does the command `ls -a` do?
  - Can you find an answer with `ls --help`?
  - What happens if you run `ls -a` inside `pink-folder`?
  - Can you find an answer by searching online?

::::: {style="font-size: 1em; text-align: left; background-color: black; color: white; font-family: monospace"}

[_ ]{style="color: black"}[\@username]{style="color: #00FF00"} **→** [~/somewhere]{style="color: #00FFFF"} [$]{style="color: grey"} [**cd**]{style="color: white"} [↵]{style="color: #DDA0DD; font-size: 1.5em;"} [go back to home]{style="color: grey; font-size: 0.8em;"}

[_ ]{style="color: black"}[\@username]{style="color: #00FF00"} **→** [~]{style="color: #00FFFF"} [$]{style="color: grey"} [**cd pink-folder**]{style="color: white"} [↵]{style="color: #DDA0DD; font-size: 1.5em;"}  [go to folder]{style="color: grey; font-size: 0.8em;"}

[_ ]{style="color: black"}[\@username]{style="color: #00FF00"} **→** [~/pink-folder]{style="color: #00FFFF"} [$]{style="color: grey"} [**ls -a**]{style="color: white"} [↵]{style="color: #DDA0DD; font-size: 1.5em;"} [???]{style="color: grey; font-size: 0.8em;"}

:::::

# More complex directory structures

## `ls -a` {.smaller}

::::: {style="font-size: 0.7em; text-align: left; background-color: black; color: white; font-family: monospace"}

[_ ]{style="color: black"}[\@username]{style="color: #00FF00"} **→** [~/pink-folder]{style="color: #00FFFF"} [$]{style="color: grey"} [**ls -a**]{style="color: white"} [↵]{style="color: #DDA0DD; font-size: 1.5em;"}

:::{.fragment .fade-in}
[_ ]{style="color: black"} [ .  ..]{style="color: #00FFFF"} [pink-file.md ]{style="color: white"} [  pink-subfolder  ]{style="color: #00FFFF"} [  say_hi.sh  ]{style="color: #00FF00"} [.super-secret-hidden-file]{style="color: white"}  [.super-secret-hidden-folder]{style="color: #00FFFF"} 
:::

:::{.fragment .fade-in}
[_ ]{style="color: black"}[\@username]{style="color: #00FF00"} **→** [~/pink-folder]{style="color: #00FFFF"} [$]{style="color: grey"} [**ls -F -a**]{style="color: white"} [↵]{style="color: #DDA0DD; font-size: 1.5em;"}

:::

:::{.fragment .fade-in}
[_ ]{style="color: black"} [ ./  ../]{style="color: #00FFFF"} [pink-file.md ]{style="color: white"} [  pink-subfolder/  ]{style="color: #00FFFF"} [  say_hi.sh*  ]{style="color: #00FF00"} [.super-secret-hidden-file]{style="color: white"}  [.super-secret-hidden-folder/]{style="color: #00FFFF"} 
:::

:::::

:::{.fragment .fade-in}
What's in these weird directories `.` and `..`?

- Try exploring them with `ls .` and `ls ..`
- Try going to them using `cd .` and `cd ..`
- You can use the command `pwd` (path to the working directory) to print out exactly where you are (using `/home/vscode` instead of `~`)
:::

## `ls -a` {.smaller}

> What's in these weird directories `.` and `..`?
> 
> - Try exploring them with `ls .` and `ls ..`
> - Try going to them using `cd .` and `cd ..`
> - You can use the command `pwd` (path to the working directory) to print out exactly where you are (using `/home/vscode` instead of `~`)


- The single dot `.` stands for the current directory - the place you get when you use `pwd`
- The double dot `..` stands for the directory above the current directory.
- If you are currently in `~/pink-folder/pink-subfolder`:
  - The single dot `.` is the folder `~/pink-folder/pink-subfolder`
  - The double dot `..` is the folder `~/pink-folder`


## Relative paths

So far, we've looked at *absolute paths* that start up at `~` or `/home/vscode`.

```{mermaid}
%%| fig-align: center
%%| fig-width: 100%
---
config:
  look: handDrawn
---
%%{init: {'themeVariables': { 'fontSize': '28px'}}}%%
flowchart TD
    A["/home/vscode/ <br> or ~"] o--o B[red-folder]
    A o--o C[pink-folder]
    A o--o D[blue-folder]

    B o--o r1([red-1.txt ])
    B o--o r2([red-2.txt ])
    B o--o r3([red-3.txt ])

    C o--o P1[pink-sub-folder]
    C o--o p2(["pink-file.md <br>"])
    C o--o p3{{"say_hi.sh <br>"}}

    P1 o--o p4(["**helloworld.py** <br>"])
    P1 o--o p5(["pink-data.csv <br>"])

    D o--o b1(["**blue.r** <br>"])

```

## Relative paths

So far, we've looked at *absolute paths* that start up at `~` or `/home/vscode`.

```{mermaid}
%%| fig-align: center
%%| fig-width: 100%
---
config:
  look: handDrawn
---
%%{init: {'themeVariables': { 'fontSize': '28px'}}}%%
flowchart TD
    A["/home/vscode/ <br> or ~"] o--o B[red-folder]
    A o--o C[pink-folder]
    A o--o D[blue-folder]

    B o--o r1([red-1.txt ])
    B o--o r2([red-2.txt ])
    B o--o r3([red-3.txt ])

    C o--o P1[pink-sub-folder]
    C o--o p2(["pink-file.md <br>"])
    C o--o p3{{"say_hi.sh <br>"}}

    P1 o--o p4(["**helloworld.py** <br>"])
    P1 o--o p5(["pink-data.csv <br>"])

    D o--o b1(["**blue.r** <br>"])

    style A fill:#f9f,stroke:#333,stroke-width:10px,color:#333
    style C fill:#f9f,stroke:#333,stroke-width:10px,color:#333
    style P1 fill:#f9f,stroke:#333,stroke-width:10px,color:#333
    style p4 fill:#f9f,stroke:#333,stroke-width:10px,color:#333

```

`~/pink-folder/pink-sub-folder/helloworld.py`

## Relative paths

But if we are already in `pink-folder` (if it's our *working directory*), we can use a relative path:

```{mermaid}
%%| fig-align: center
%%| fig-width: 100%
---
config:
  look: handDrawn
---
%%{init: {'themeVariables': { 'fontSize': '28px'}}}%%
flowchart TD
    A["/home/vscode/ <br> or ~"] o--o B[red-folder]
    A o--o C[pink-folder]
    A o--o D[blue-folder]

    B o--o r1([red-1.txt ])
    B o--o r2([red-2.txt ])
    B o--o r3([red-3.txt ])

    C o--o P1[pink-sub-folder]
    C o--o p2(["pink-file.md <br>"])
    C o--o p3{{"say_hi.sh <br>"}}

    P1 o--o p4(["**helloworld.py** <br>"])
    P1 o--o p5(["pink-data.csv <br>"])

    D o--o b1(["**blue.r** <br>"])

    style C fill:#f9f,stroke:#333,stroke-width:10px,color:#333
    style P1 fill:#f9f,stroke:#333,stroke-width:10px,color:#333
    style p4 fill:#f9f,stroke:#333,stroke-width:10px,color:#333

```

`pink-sub-folder/helloworld.py`

## Relative paths

But if we are already in `pink-subfolder` (if it's our *working directory*), we can use a relative path:

```{mermaid}
%%| fig-align: center
%%| fig-width: 100%
---
config:
  look: handDrawn
---
%%{init: {'themeVariables': { 'fontSize': '28px'}}}%%
flowchart TD
    A["/home/vscode/ <br> or ~"] o--o B[red-folder]
    A o--o C[pink-folder]
    A o--o D[blue-folder]

    B o--o r1([red-1.txt ])
    B o--o r2([red-2.txt ])
    B o--o r3([red-3.txt ])

    C o--o P1[pink-sub-folder]
    C o--o p2(["pink-file.md <br>"])
    C o--o p3{{"say_hi.sh <br>"}}

    P1 o--o p4(["**helloworld.py** <br>"])
    P1 o--o p5(["pink-data.csv <br>"])

    D o--o b1(["**blue.r** <br>"])

    style P1 fill:#f9f,stroke:#333,stroke-width:10px,color:#333
    style p4 fill:#f9f,stroke:#333,stroke-width:10px,color:#333

```

`helloworld.py`

## Relative paths

What if we are in `pink-subfolder` (if it's our *working directory*), and want the path to `pink-file.md`?

```{mermaid}
%%| fig-align: center
%%| fig-width: 100%
---
config:
  look: handDrawn
---
%%{init: {'themeVariables': { 'fontSize': '28px'}}}%%
flowchart TD
    A["/home/vscode/ <br> or ~"] o--o B[red-folder]
    A o--o C[pink-folder]
    A o--o D[blue-folder]

    B o--o r1([red-1.txt ])
    B o--o r2([red-2.txt ])
    B o--o r3([red-3.txt ])

    C o--o P1[pink-sub-folder]
    C o--o p2(["pink-file.md <br>"])
    C o--o p3{{"say_hi.sh <br>"}}

    P1 o--o p4(["**helloworld.py** <br>"])
    P1 o--o p5(["pink-data.csv <br>"])

    D o--o b1(["**blue.r** <br>"])

    style P1 fill:#f9f,stroke:#333,stroke-width:10px,color:#333
    style p2 fill:#ff0,stroke:#333,stroke-width:10px,color:#333

```

Hint: what can we see with `ls .. ` from the current directory?

## Poll

What if we are in `pink-subfolder` (if it's our *working directory*), and want the path to `pink-file.md`?


[Click here to go to Poll](https://universityofleeds.display.vevox.com#/present/696636/ULXGUZROA4XT20VKGCAZ){target="_blank"}


## Relative paths

`../pink-file.md`

```{mermaid}
%%| fig-align: center
%%| fig-width: 100%
---
config:
  look: handDrawn
---
%%{init: {'themeVariables': { 'fontSize': '28px'}}}%%
flowchart TD
    A["/home/vscode/ <br> or ~"] o--o B[red-folder]
    A o--o C[pink-folder]
    A o--o D[blue-folder]

    B o--o r1([red-1.txt ])
    B o--o r2([red-2.txt ])
    B o--o r3([red-3.txt ])

    C o--o P1[pink-sub-folder]
    C o--o p2(["pink-file.md <br>"])
    C o--o p3{{"say_hi.sh <br>"}}

    P1 o--o p4(["**helloworld.py** <br>"])
    P1 o--o p5(["pink-data.csv <br>"])

    D o--o b1(["**blue.r** <br>"])

    style P1 fill:#f9f,stroke:#333,stroke-width:10px,color:#333
    style p2 fill:#ff0,stroke:#333,stroke-width:10px,color:#333

```

We can use the command `cat` with a path to a file to read out the contents: try `cat ../pink-file.md`

## Recap

We've covered an awful lot of commands now!

- If at any point in the course you need a refresher, just click the link at the bottom of the screen to the **Cheat Sheet**
which lists useful commands.

# Creating and editing files and directories

## Making files and directories

- You can create a directory with the command `mkdir` (*make directory*), and the name of the new directory as an argument:
  - `mkdir new-dir-name`
- You can create files with the command `touch`, and the name of the new file as an argument:
 - `touch new-file-name.txt`
- You can provide a path (absolute or relative) instead of a name if you want to create the folder or file somewhere other that the current working directory.

## Rules for file and directory names {.smaller}

1. Don't use spaces in names; Linux will think you are entering two separate arguments to a command.
  - Break up words with hyphens or underscores instead `like_this` `or-this`!
2. Don't begin a name with a hyphen/dash (so no files called `-this`); Linux will think this is a flag/option to a command.
3. Stick with numbers, letters, full stops, dashes/hyphens and underscores.
  - Special characters like $, %, &, *, / etc. have special meanings on the command line and can lead to confusion!
4. When naming files, give them a sensible file ending: `.txt`, `.md`, `.py` etc.

If you're working with old files/directories that have spaces in their names, you'll need to wrap the path in single quotation marks, `'like this.txt'`

## Poll

Choose some sensible Linux file and folder names!

[Click here to go to Poll](https://universityofleeds.display.vevox.com#/present/696636/ULXGUZROA4XT20VKGCAZ){target="_blank"}


## Making files and directories {.smaller}

- Try creating some folders and files in your home directory (`~`)
  - `mkdir path-to-new-folder`
  - `touch path-to-new-file`
- If you want to create multiple nested folders at once, you can use the `-p` option:

::::: {style="font-size: 1em; text-align: left; background-color: black; color: white; font-family: monospace"}
[_ ]{style="color: black"}[\@username]{style="color: #00FF00"} **→** [~]{style="color: #00FFFF"} [$]{style="color: grey"} [**mkdir -p new1/new2/new3**]{style="color: white"} [↵]{style="color: #DDA0DD; font-size: 1.5em;"}
:::::

- You can create multiple new folders in the same directory by just listing all the new names, separate by spaces:

::::: {style="font-size: 1em; text-align: left; background-color: black; color: white; font-family: monospace"}
[_ ]{style="color: black"}[\@username]{style="color: #00FF00"} **→** [~]{style="color: #00FFFF"} [$]{style="color: grey"} [**mkdir new1 new2 new3**]{style="color: white"} [↵]{style="color: #DDA0DD; font-size: 1.5em;"}
:::::

## Editing files

::::: {style="font-size: 0.7em;"}

Oftentimes, when you're doing research on a platform like Aire, you don't need to do extensive manual editing of files;
for example, if you are running multiple R scripts, you would write and test these on your desktop computer and then transfer
them over to Aire.
:::::

- Sometimes, you might need to edit a file from the command line.
- One popular tool that is installed on almost all systems is Nano
- To launch Nano, you just need to type the `nano` command followed by the name of a file (this can be a new or existing file; Nano will create a file for you if it doesn't exist)

## Editing files with Nano

::::: {style="font-size: 1em; text-align: left; background-color: black; color: white; font-family: monospace"}
[_ ]{style="color: black"}[\@username]{style="color: #00FF00"} **→** [~]{style="color: #00FFFF"} [$]{style="color: grey"} [**nano new-file.txt**]{style="color: white"} [↵]{style="color: #DDA0DD; font-size: 1.5em;"}
:::::

This will open up a new screen in your terminal...

## Editing files with Nano

::::: {style="font-size: 1em; text-align: left; background-color: black; color: white; font-family: monospace"}

[_ ]{style="color: black"} [ &nbsp; GNU nano 7.2 &nbsp; &nbsp;  &nbsp;   new-file.txt &nbsp; &nbsp; &nbsp; &nbsp; &nbsp;]{style="color: black; background-color: white; text-align: center;"}

[▮]{style="color: white"}

[_ ]{style="color: black"}

[_ ]{style="color: black"}

[_ ]{style="color: black"}

[_ ]{style="color: black"}

::: {style="text-align: center;"}

[New File]{style="color: black; background-color: white; text-align: center;"}

[\^G]{style="color: black; background-color: white;"} Help &nbsp; &nbsp; [\^O]{style="color: black; background-color: white;"} Write Out &nbsp; &nbsp; [\^X]{style="color: black; background-color: white;"} Exit

:::

:::::

The cursor is shown by the rectangle symbol [▮]{style="color: white; background-color: black;"}

## Editing files with Nano

::::: {style="font-size: 1em; text-align: left; background-color: black; color: white; font-family: monospace"}

[_ ]{style="color: black"} [ &nbsp; GNU nano 7.2 &nbsp; &nbsp;  &nbsp;   new-file.txt &nbsp; &nbsp; &nbsp; &nbsp; &nbsp;]{style="color: black; background-color: white; text-align: center;"}

You can type in this file;

you don't need to click on it.▮


[_ ]{style="color: black"}

[_ ]{style="color: black"}

[_ ]{style="color: black"}

::: {style="text-align: center;"}

[New File]{style="color: black; background-color: white; text-align: center;"}

[\^G]{style="color: black; background-color: white;"} Help &nbsp; &nbsp; [\^O]{style="color: black; background-color: white;"} Write Out &nbsp; &nbsp; [\^X]{style="color: black; background-color: white;"} Exit

:::

:::::

You can start typing.

## Editing files with Nano

::::: {style="font-size: 1em; text-align: left; background-color: black; color: white; font-family: monospace"}

[_ ]{style="color: black"} [ &nbsp; GNU nano 7.2 &nbsp; &nbsp;  &nbsp;   new-file.txt &nbsp; &nbsp; &nbsp; &nbsp; &nbsp;]{style="color: black; background-color: white; text-align: center;"}

To save your edits,

hit \^O to write out.

This means CTRL and o▮

[_ ]{style="color: black"}

[_ ]{style="color: black"}

::: {style="text-align: center;"}

[New File]{style="color: black; background-color: white; text-align: center;"}

[\^G]{style="color: black; background-color: white;"} Help &nbsp; &nbsp; [\^O]{style="color: black; background-color: white;"} Write Out &nbsp; &nbsp; [\^X]{style="color: black; background-color: white;"} Exit

:::

:::::

## Editing files with Nano

::::: {style="font-size: 1em; text-align: left; background-color: black; color: white; font-family: monospace"}

[_ ]{style="color: black"} [ &nbsp; GNU nano 7.2 &nbsp; &nbsp;  &nbsp;   new-file.txt &nbsp; &nbsp; &nbsp; &nbsp; &nbsp;]{style="color: black; background-color: white; text-align: center;"}

To save your edits,

hit \^O to write out.

This means CTRL and o▮

[_ ]{style="color: black"}

[&nbsp; *Hit ENTER to accept the filename*]{style="color: #00FF00; font-size: 0.7em;"}



[File Name to write: new-file.txt &nbsp; &nbsp;]{style="color: black; background-color: white;"}

::: {style="text-align: center;"}

[\^G]{style="color: black; background-color: white;"} Help &nbsp; &nbsp; [\^C]{style="color: black; background-color: white;"} Cancel

:::

:::::

## Editing files with Nano

::::: {style="font-size: 1em; text-align: left; background-color: black; color: white; font-family: monospace"}

[_ ]{style="color: black"} [ &nbsp; GNU nano 7.2 &nbsp; &nbsp;  &nbsp;   new-file.txt &nbsp; &nbsp; &nbsp; &nbsp; &nbsp;]{style="color: black; background-color: white; text-align: center;"}

To save your edits,

hit \^X to exit.

This means CTRL and x▮

[_ ]{style="color: black"}

[_ ]{style="color: black"}

::: {style="text-align: center;"}

[Wrote 3 lines]{style="color: black; background-color: white; text-align: center;"}

[\^G]{style="color: black; background-color: white;"} Help &nbsp; &nbsp; [\^O]{style="color: black; background-color: white;"} Write Out &nbsp; &nbsp; [\^X]{style="color: black; background-color: white;"} Exit

:::

:::::

This will close the Nano text editor and return you to the command line.

## Poll

How comfortable are you using Nano?

[Click here to go to Poll](https://universityofleeds.display.vevox.com#/present/696636/ULXGUZROA4XT20VKGCAZ){target="_blank"}



## Using arrow keys ↑ ↓

- In the Nano text editor, you cannot click on the text to move the cursor: 
  - You need to use the arrow keys on your keyboard to navigate the text.  ← ↑	→	↓
- What happens when you use the up and down arrows when you have exited from Nano and are back in the shell?

:::{.fragment .fade-in}

::::: {style="font-size: 0.7em;"}

- The arrow keys allow you to "scroll" through previous commands you've used
- If you don't want to use a previous command and want to stop scrolling, use \^C to cancel (CTRL and c at the same time)

:::::

:::

## Modifying files and directories: `mv`

The `mv` (move) command allows us to move a file or folder to a specified location:

- Move the file `file-name` to the directory `new-location`: `mv file-name new-location`
- Move the directory `dir-name` to the directory `new-location`: `mv dir-name new-location`

If you move the file or directory to the same location it's already in, it renames it.

## Modifying files and directories: `mv`

::::: {style="font-size: 0.7em; text-align: left; background-color: black; color: white; font-family: monospace"}

[_ ]{style="color: black"}[\@username]{style="color: #00FF00"} **→** [~/somewhere]{style="color: #00FFFF"} [$]{style="color: grey"} [**cd**]{style="color: white"} [↵]{style="color: #DDA0DD; font-size: 1.5em;"}


:::{.fragment .fade-in}
[_ ]{style="color: black"}[\@username]{style="color: #00FF00"} **→** [~]{style="color: #00FFFF"} [$]{style="color: grey"} [**touch test-file.txt**]{style="color: white"} [↵]{style="color: #DDA0DD; font-size: 1.5em;"}

:::

:::{.fragment .fade-in}
[_ ]{style="color: black"}[\@username]{style="color: #00FF00"} **→** [~]{style="color: #00FFFF"} [$]{style="color: grey"} [**ls -F**]{style="color: white"} [↵]{style="color: #DDA0DD; font-size: 1.5em;"}

:::

:::{.fragment .fade-in}
[_ ]{style="color: black"}[blue-folder/  pink-folder/ red-folder/]{style="color: #00FFFF"} [test-file.txt]{style="color: white"}

:::

:::{.fragment .fade-in}
[_ ]{style="color: black"}[\@username]{style="color: #00FF00"} **→** [~]{style="color: #00FFFF"} [$]{style="color: grey"} [**mv test-file.txt test-file.md**]{style="color: white"} [↵]{style="color: #DDA0DD; font-size: 1.5em;"}

:::

:::{.fragment .fade-in}
[_ ]{style="color: black"}[\@username]{style="color: #00FF00"} **→** [~]{style="color: #00FFFF"} [$]{style="color: grey"} [**ls -F**]{style="color: white"} [↵]{style="color: #DDA0DD; font-size: 1.5em;"}

:::

:::{.fragment .fade-in}
[_ ]{style="color: black"}[blue-folder/  pink-folder/ red-folder/]{style="color: #00FFFF"} [test-file.md]{style="color: white"}

:::

:::{.fragment .fade-in}
[_ ]{style="color: black"}[\@username]{style="color: #00FF00"} **→** [~]{style="color: #00FFFF"} [$]{style="color: grey"} [**mv test-file.md blue-folder**]{style="color: white"} [↵]{style="color: #DDA0DD; font-size: 1.5em;"}

:::

:::::

:::{.fragment .fade-in}
What's the result of `ls` and `ls blue-folder` now? Repeat this with a new directory in your home directory.
:::

## Modifying files and directories: `mv` {.smaller}

- Do you use the same *syntax* to move directories and files?
  - Yes, `mv` works *recursively* and moves directories (and everything in them).

After this course, experiment with moving directories around the virtual machine.

- Don't worry about messing up the directory structure - you can rebuild a new VM at any point.
- This is a safe sandbox to experiment in!

**BUT, it's important to note that you can accidentally overwrite files using `mv`: this is why it's useful to practise and get used to using this command in a safe place!**

## Modifying files and directories: `cp` {.smaller}

The `cp` or copy command allows us to copy files or directories to specified locations.

::::: {style="font-size: 1em; text-align: left; background-color: black; color: white; font-family: monospace"}

[_ ]{style="color: black"}[\@username]{style="color: #00FF00"} **→** [~/somewhere]{style="color: #00FFFF"} [$]{style="color: grey"} [**cd**]{style="color: white"} [↵]{style="color: #DDA0DD; font-size: 1.5em;"}


:::{.fragment .fade-in}
[_ ]{style="color: black"}[\@username]{style="color: #00FF00"} **→** [~]{style="color: #00FFFF"} [$]{style="color: grey"} [**touch new-test.txt**]{style="color: white"} [↵]{style="color: #DDA0DD; font-size: 1.5em;"}

[_ ]{style="color: black"} [You can us ls or ls -F to check the file is created]{style="color: #DDA0DD; font-size: 0.9em;"}

:::

:::{.fragment .fade-in}
[_ ]{style="color: black"}[\@username]{style="color: #00FF00"} **→** [~]{style="color: #00FFFF"} [$]{style="color: grey"} [**nano new-test.txt**]{style="color: white"} [↵]{style="color: #DDA0DD; font-size: 1.5em;"}

[_ ]{style="color: black"} [Add some text to the file. After saving, check the content with cat:]{style="color: #DDA0DD; font-size: 0.9em;"}

[_ ]{style="color: black"}[\@username]{style="color: #00FF00"} **→** [~]{style="color: #00FFFF"} [$]{style="color: grey"} [**cat new-test.txt**]{style="color: white"} [↵]{style="color: #DDA0DD; font-size: 1.5em;"}
:::

:::{.fragment .fade-in}
[_ ]{style="color: black"}[\@username]{style="color: #00FF00"} **→** [~]{style="color: #00FFFF"} [$]{style="color: grey"} [**cp new-test.txt new-test-2.txt**]{style="color: white"} [↵]{style="color: #DDA0DD; font-size: 1.5em;"}

[_ ]{style="color: black"} [Check the content of new-test-2.txt with cat]{style="color: #DDA0DD; font-size: 0.9em;"}
:::

:::::

## Modifying files and directories: `cp` {.smaller}

The `cp` or copy command allows us to copy files or directories to specified locations.

::::: {style="font-size: 0.9em; text-align: left; background-color: black; color: white; font-family: monospace"}

[_ ]{style="color: black"}[\@username]{style="color: #00FF00"} **→** [~]{style="color: #00FFFF"} [$]{style="color: grey"} [**mkdir -p test-dir/sub-dir/sub-sub-dir other-test-dir**]{style="color: white"} [↵]{style="color: #DDA0DD; font-size: 1.5em;"}

:::{.fragment .fade-in}

[_ ]{style="color: black"} [Explore your new dirs with cd and ls, then return to ~]{style="color: #DDA0DD; font-size: 0.9em;"}
:::

:::{.fragment .fade-in}

[_ ]{style="color: black"}[\@username]{style="color: #00FF00"} **→** [~]{style="color: #00FFFF"} [$]{style="color: grey"} [**cp test-dir/sub-dir/sub-sub-dir other-test-dir**]{style="color: white"} [↵]{style="color: #DDA0DD; font-size: 1.5em;"}

:::

:::{.fragment .fade-in}

[_ ]{style="color: black"} cp: -r not specified; omitting directory 'test-dir/sub-dir/sub-sub-dir'

[_ ]{style="color: black"} [We need to add a -r to our command, which means "recursive"]{style="color: #DDA0DD; font-size: 0.9em;"}
:::

:::{.fragment .fade-in}

[_ ]{style="color: black"}[\@username]{style="color: #00FF00"} **→** [~]{style="color: #00FFFF"} [$]{style="color: grey"} [**cp -r test-dir/sub-dir/sub-sub-dir other-test-dir**]{style="color: white"} [↵]{style="color: #DDA0DD; font-size: 1.5em;"}

:::

:::::

## Poll

How comfortable are you with exploring and handling directories using the commands we have covered?

[Click here to go to Poll](https://universityofleeds.display.vevox.com#/present/696636/ULXGUZROA4XT20VKGCAZ){target="_blank"}


## Deleting with `rm`

Almost everyone who's used Linux before will have a horror story about the command `rm` (remove), and accidentally deleting files they didn't mean to.

**But** being able to delete and clean up files is very important, especially when using a shared resource (like Aire) that has **storage quotas**.

Let's clean up all the test files we just made.

::::: {style="font-size: 0.7em; text-align: left; background-color: black; color: white; font-family: monospace"}

[_ ]{style="color: black"}[\@username]{style="color: #00FF00"} **→** [~]{style="color: #00FFFF"} [$]{style="color: grey"} [**ls**]{style="color: white"} [↵]{style="color: #DDA0DD; font-size: 1.5em;"} [Check what files you want to delete]{style="color: #DDA0DD; font-size: 0.9em;"}

:::{.fragment .fade-in}

[_ ]{style="color: black"}[\@username]{style="color: #00FF00"} **→** [~]{style="color: #00FFFF"} [$]{style="color: grey"} [**rm new-test.txt new-test-2.txt**]{style="color: white"} [↵]{style="color: #DDA0DD; font-size: 1.5em;"}
:::

:::::

## Deleting with `rm`

Deleting directories

::::: {style="font-size: 0.7em; text-align: left; background-color: black; color: white; font-family: monospace"}

[_ ]{style="color: black"}[\@username]{style="color: #00FF00"} **→** [~]{style="color: #00FFFF"} [$]{style="color: grey"} [**rm test-dir**]{style="color: white"} [↵]{style="color: #DDA0DD; font-size: 1.5em;"} [Delete a directory]{style="color: #DDA0DD; font-size: 0.9em;"}

:::{.fragment .fade-in}

[_ ]{style="color: black"} rm: cannot remove 'test-dir/': Is a directory

[Like cp, we need to tell rm we want it to act recursively, with -r]{style="color: #DDA0DD; font-size: 0.9em;"}
:::

:::{.fragment .fade-in}

[_ ]{style="color: black"}[\@username]{style="color: #00FF00"} **→** [~]{style="color: #00FFFF"} [$]{style="color: grey"} [**rm -r test-dir**]{style="color: white"} [↵]{style="color: #DDA0DD; font-size: 1.5em;"} [Delete a directory]{style="color: #DDA0DD; font-size: 0.9em;"}

:::

:::::

This is very powerful and can quickly delete directories of important data!


**`rm` does not send things to the *recycling bin* or equivalent: it hard-deletes them; data is usually not recoverable.**

## Deleting with `rm`

A cautionary exercise

Look at the following command and try to predict what it does:

::::: {.panel-tabset}

### Breaking it down

 **Do not run the following snippet!** 

`rm -rf *`

:::{.fragment .fade-in style="font-size: 0.7em;"}

- `rm`: the delete command (remove)
- `-r`: recursive, so will eat through directories
- `-f`: force - do not ask for clarification, just delete
- `*`: a "wildcard" character; instead of providing a file or directory name, this essentially means **everything**
:::

### Face the fear

Before we go on a break, `cd` back to your home directory, and experience the abject horror of `rm`.

:::{.fragment .fade-in style="font-size: 0.7em;"}

**Run `rm -rf *` from `/home/vscode`.  Only do this in your virtual machine on codespaces, never on a research machine**

:::

:::{.fragment .fade-in style="font-size: 0.7em;"}

Use `cd` and `ls` to look around - what does your home directory look like now?

:::

:::::

## Rebuild codespaces

- Click on the `>< Codespaces` button in the lower left of your screen, then select "Rebuild Container" from the menu that pops up.
- Take a break while it's re-building (remember to lock your screen if leaving your pc unattended)

# Interactive scripts

## Bash scripts

- Use `ls -F` to list out the contents of `~/pink-folder`
- What are the three categories of content?
  - What kind of file is `say_hi.sh`?

:::{.fragment .fade-in}

**This is an *executable* file - like a Windows `.exe` file - you can run it.**

Let's read it first and predict what it will do:

- Use `cat say_hi.sh` to print out the contents

:::

## Bash scripts
What's in `say_hi.sh`?

```{.bash code-line-numbers="1|2|3|4|5|6"}
#!/bin/sh
echo "hello!"
echo "Running this file prints out a number of greetings"
echo "What's your name? (type your name in below)"
read yourname
echo "Nice to meet you, $yourname!"
```

:::{style="font-size: 0.6em;"}
- `#!/bin/bash`: this is known as "shebang bin bash" tells Linux to use Bash to parse the file - we don't need to worry about this, beyond knowing to include it at the beginning of a shell script.
- The `echo` will just print out (or echo back) any arguments after it.
  - Try running `echo Hello` in your terminal
- The `read` command waits for you to type input and press enter, then saves it to a variable
  - Try running `read greeting` and pressing enter
  - On the next line, type `Hello`, and press enter
  - Now, type `echo $greeting` and press enter
- Variables generally start with `$`

:::

## Bash scripts
What's in `say_hi.sh`?

```{.bash}
#!/bin/sh
echo "hello!"
echo "Running this file prints out a number of greetings"
echo "What's your name? (type your name in below)"
read yourname
echo "Nice to meet you, $yourname!"
```

What do we predict it's going to do?

::::: {style="font-size: 0.7em; text-align: left; background-color: black; color: white; font-family: monospace"}

[_ ]{style="color: black"}[\@username]{style="color: #00FF00"} **→** [~/pink-folder]{style="color: #00FFFF"} [$]{style="color: grey"} [**./say_hi.sh**]{style="color: white"} [↵]{style="color: #DDA0DD; font-size: 1.5em;"}

[Run using ./ in front of the script name]{style="color: #DDA0DD; font-size: 0.9em;"}
:::::

## Bash scripts

Let's create a simple bash script. `cd` to home and open a new file with Nano:

::::: {style="font-size: 0.7em; text-align: left; background-color: black; color: white; font-family: monospace"}

[_ ]{style="color: black"}[\@username]{style="color: #00FF00"} **→** [~/pink-folder]{style="color: #00FFFF"} [$]{style="color: grey"} [**cd**]{style="color: white"} [↵]{style="color: #DDA0DD; font-size: 1.5em;"}

[_ ]{style="color: black"}[\@username]{style="color: #00FF00"} **→** [~]{style="color: #00FFFF"} [$]{style="color: grey"} [**nano test-script.sh**]{style="color: white"} [↵]{style="color: #DDA0DD; font-size: 1.5em;"}
:::::


```{.bash code-line-numbers="1|2|3|4|5|6"}
#!/bin/bash
touch test-file-auto.txt
mkdir new-dir-auto
cp test-file-auto.txt new-dir-auto
echo "Put this text in the job report" > job-report.txt

```

Save the file with Nano.

## Bash scripts {.smaller}

- Check the contents of your home directory using `ls -F`
  - What category does your new script show as?
- Try using `ls -l`

:::{.fragment .fade-in}

It's just a regular file: we need to make it executable!

::::: {style="font-size: 1em; text-align: left; background-color: black; color: white; font-family: monospace"}
[_ ]{style="color: black"}[\@username]{style="color: #00FF00"} **→** [~]{style="color: #00FFFF"} [$]{style="color: grey"} [**chmod +x test-script.sh**]{style="color: white"} [↵]{style="color: #DDA0DD; font-size: 1.5em;"}
:::::

The `chmod` command changes or modifies file permissions: you need permission to be able to execute a bash script.

- `+x` add executable permissions
- `test-script.sh` is the name of the script you want to apply permissions to.

Now, try `ls -F` again!
:::

## Run your Bash script

::::: {style="font-size: 1em; text-align: left; background-color: black; color: white; font-family: monospace"}
[_ ]{style="color: black"}[\@username]{style="color: #00FF00"} **→** [~]{style="color: #00FFFF"} [$]{style="color: grey"} [**./test-script.sh**]{style="color: white"} [↵]{style="color: #DDA0DD; font-size: 1.5em;"}
:::::

What did it do?

::: {.incremental}
- What did the line `echo "Put this text in the job report" > job-report.txt` do?
  - The `>` operator directs the output from `echo "your message"` to the file `job-report.txt`
:::

## Run your Bash script

::: {.incremental}
- Try to  rerun the code, what happens?
- Replace the line `mkdir new-dir-auto` with `mkdir -p new-dir-auto` and rerun, what happens?
  - The `-p` option (in addition to allowing you to create nested files) also allows you to try to make a folder, and if it already exists, doesn't fail
:::

## Run your Bash script

::: {.incremental}
- Change the line `echo "Put this text in the job report" > job-report.txt` to `echo "Put this text in the job report" >> job-report.txt`, what does this do?
  - The message now gets *appended* to the file instead of overwriting
- Add more messages by repeating `echo "message" > job-report.txt` or `echo "message" >> job-report.txt` and seeing how they behave.
:::

## Other scripts

In general, on the HPC system, you will want to run scripts in other languages, like `R` or `Python` (amongst many, many others).

- The way you load in a certain language varies depending on the system
  - You'll learn how to do this on Aire at HPC 1
- Our system is very simple but has Python and R installed
- Often times, you will want to write a bash script that tells other scripts (written in R, Python etc.) to run

## R scripts

`cd` home, and then into the directory `blue-folder`:

::::: {style="font-size: 0.7em; text-align: left; background-color: black; color: white; font-family: monospace"}

[_ ]{style="color: black"}[\@username]{style="color: #00FF00"} **→** [~/wherever]{style="color: #00FFFF"} [$]{style="color: grey"} [**cd**]{style="color: white"} [↵]{style="color: #DDA0DD; font-size: 1.5em;"}

::: {.fragment .fade-in}
[_ ]{style="color: black"}[\@username]{style="color: #00FF00"} **→** [~]{style="color: #00FFFF"} [$]{style="color: grey"} [**cd blue-folder**]{style="color: white"} [↵]{style="color: #DDA0DD; font-size: 1.5em;"}
:::

::: {.fragment .fade-in}
[_ ]{style="color: black"}[\@username]{style="color: #00FF00"} **→** [~/blue-folder]{style="color: #00FFFF"} [$]{style="color: grey"} [**ls**]{style="color: white"} [↵]{style="color: #DDA0DD; font-size: 1.5em;"}
:::

::: {.fragment .fade-in}
[_ ]{style="color: black"}[blue.R]{style="color: white"}

[This is an R script; if R is installed on the system it can be run with the command Rscript. Check what is in the file before running it with the command cat.]{style="color: #DDA0DD; font-size: 0.9em;"}
:::

::: {.fragment .fade-in}
[_ ]{style="color: black"}[\@username]{style="color: #00FF00"} **→** [~/blue-folder]{style="color: #00FFFF"} [$]{style="color: grey"} [**cat blue.R**]{style="color: white"} [↵]{style="color: #DDA0DD; font-size: 1.5em;"}
:::

::: {.fragment .fade-in}
[_ ]{style="color: black"}[print("Hello World")]{style="color: white"} [Ok, lets run it]{style="color: #DDA0DD; font-size: 0.9em;"}
:::

::: {.fragment .fade-in}
[_ ]{style="color: black"}[\@username]{style="color: #00FF00"} **→** [~/blue-folder]{style="color: #00FFFF"} [$]{style="color: grey"} [**Rscript blue.R**]{style="color: white"} [↵]{style="color: #DDA0DD; font-size: 1.5em;"}
:::

:::::

## R scripts

::: {.incremental}
- The R script ran, and printed the results out onto the screen

What if we wanted the results saved to a text file?

- In general, it's a good idea to do this in R and ensure all your results are saved in the correct data format etc.
- However, it can be useful to save printed messages to a file for safe keeping: use a bash script

What if we wanted to run multiple R scripts?

- We could write a bash script to do this!

:::

## R scripts + bash

Let's create a bash script called `r-bash.sh` and save it alongside `blue.R`; remember you'll need to do `chmod +x r-bash.sh`.

```{.bash}
#!/bin/bash

Rscript blue.R

```

Run this: `./r-bash.sh` ; what happens?

::: {.fragment .fade-in}

```{.bash}
#!/bin/bash

Rscript blue.R >> output_log.txt

```

Run this: `./r-bash.sh` ; what happens? Use `cat` to read the output of `output_log.txt`

:::

## Python scripts

We can do the exact same with Python scripts; we only need slightly different commands to run the `.py` script.

## Python scripts

`cd` home, and then into the directory `pink-folder/pink-sub-folder`:

::::: {style="font-size: 0.7em; text-align: left; background-color: black; color: white; font-family: monospace"}

[_ ]{style="color: black"}[\@username]{style="color: #00FF00"} **→** [~/wherever]{style="color: #00FFFF"} [$]{style="color: grey"} [**cd**]{style="color: white"} [↵]{style="color: #DDA0DD; font-size: 1.5em;"}

::: {.fragment .fade-in}
[_ ]{style="color: black"}[\@username]{style="color: #00FF00"} **→** [~]{style="color: #00FFFF"} [$]{style="color: grey"} [**cd pink-folder/pink-sub-folder**]{style="color: white"} [↵]{style="color: #DDA0DD; font-size: 1.5em;"}
:::

::: {.fragment .fade-in}
[_ ]{style="color: black"}[\@username]{style="color: #00FF00"} **→** [~/pink-folder/pink-subfolder]{style="color: #00FFFF"} [$]{style="color: grey"} [**ls**]{style="color: white"} [↵]{style="color: #DDA0DD; font-size: 1.5em;"}
:::

::: {.fragment .fade-in}
[_ ]{style="color: black"}[helloworld.py  pink-data.csv]{style="color: white"}

[Check what is in the Python file before running it with the command cat.]{style="color: #DDA0DD; font-size: 0.9em;"}
:::

::: {.fragment .fade-in}
[_ ]{style="color: black"}[\@username]{style="color: #00FF00"} **→** [~/pink-folder/pink-subfolder]{style="color: #00FFFF"} [$]{style="color: grey"} [**cat helloworld.py**]{style="color: white"} [↵]{style="color: #DDA0DD; font-size: 1.5em;"}
:::

::: {.fragment .fade-in}
[_ ]{style="color: black"}[print("Hello World")]{style="color: white"} [Ok, lets run it]{style="color: #DDA0DD; font-size: 0.9em;"}
:::

::: {.fragment .fade-in}
[_ ]{style="color: black"}[\@username]{style="color: #00FF00"} **→** [~/pink-folder/pink-subfolder]{style="color: #00FFFF"} [$]{style="color: grey"} [**python helloworld.py**]{style="color: white"} [↵]{style="color: #DDA0DD; font-size: 1.5em;"}
:::

:::::

## Python + bash scripts

Write a bash script that runs the Python script `helloworld.py` and saves the output to a text file.

- Remember to always start with `#!/bin/bash`
- Change the permissions on your bash script with `chmod +x name-of-script.sh`

::: {.fragment .fade-in}

```{.bash}
#!/bin/bash

python helloworld.py >> output_log.txt

```

Run this with `./script-name.sh` and check the contents of `output_log.txt`

:::

## Executable scripts

- Always check the contents of any files/scripts you want to run, to ensure you understand what they are doing.
- Use `chmod +x script-name.sh` to make a bash file executable.
- When running Python or R scripts for research, you will need to carefully specify what version of the language (and any libraries/packages) are being used
- Be careful of overwriting data using `>` to write files.

## Next steps {.smaller}

- A three hour session can introduce the basics, but is not enough to make you
feel like a Linux shell expert!
- Your homework: work through the tutorial/session notes for [The Unix Shell](https://swcarpentry.github.io/shell-novice/index.html)
created by the software carpentry.
- In order to download the files they use (so that you can follow along all the sessions),
we just need the URL of the files: *https://swcarpentry.github.io/shell-novice/data/shell-lesson-data.zip* 

::::: {style="font-size: 0.95em; text-align: left; background-color: black; color: white; font-family: monospace"}

[_ ]{style="color: black"}[\@username]{style="color: #00FF00"} **→** [~/wherever]{style="color: #00FFFF"} [$]{style="color: grey"} [**cd**]{style="color: white"} [↵]{style="color: #DDA0DD; font-size: 1.5em;"}
[Or to wherever you want to download the files]{style="color: #DDA0DD; font-size: 0.7em;"}

::: {.fragment .fade-in}
[_ ]{style="color: black"}[\@username]{style="color: #00FF00"} **→** [~]{style="color: #00FFFF"} [$]{style="color: grey"} [**wget https://swcarpentry.github.io/shell-novice/data/shell-lesson-data.zip**]{style="color: white"} [↵]{style="color: #DDA0DD; font-size: 1.5em;"}
[Download the zip file (expect lots of output)]{style="color: #DDA0DD; font-size: 0.7em;"}
:::

::: {.fragment .fade-in}
[_ ]{style="color: black"}[\@username]{style="color: #00FF00"} **→** [~]{style="color: #00FFFF"} [$]{style="color: grey"} [**unzip shell-lesson-data.zip**]{style="color: white"} [↵]{style="color: #DDA0DD; font-size: 1.5em;"}
[Unzip the folder (expect lots of output)]{style="color: #DDA0DD; font-size: 0.7em;"}
:::

:::::

## Next steps {.smaller}

::: {.panel-tabset}

### `wget`

- `wget` is a really useful command for downloading data from the internet. It can take a range of different *options* and *arguments*:
  - Basic use: `wget url-to-data`: this downloads the data to the current working directory, with the folder/file name provided by the URL .
  - You can provide a different file name for the download either: `wget -O new-nap.zip url-to-data`.
  - You can provide a location for the file to download to (not the current working directory): `wget -P path/to/folder url-to-data`.
  - These are only some of the many, many options available!

### `unzip`

- `unzip` is necessary if you are downloading compressed/zipped archives (that end in `.zip`)
  - Basic use: `unzip filename.zip`; this will unzip the file in the current working directory, into a folder called `filename`.
  - Check contents: `unzip -l filename.zip` will list the contents of the archive without extracting them.

:::

## Directory map {.smaller .scrollable #map}

Use the back button in your browser to return to the slide you were previously on.
```{mermaid}
flowchart TD
    START:::hidden --> |cd|A
    A[/home/vscode/] -->|cd red-folder| B[red-folder/ ]
    A[/home/vscode/] -->|cd pink-folder| C[pink-folder/ ]
    A[/home/vscode/] -->|cd blue-folder| D[blue-folder/ ]

    B --- r1([red-1.txt ])
    B --- r2([red-2.txt ])
    B --- r3([red-3.txt ])

    C --- |cd pink-sub-folder|P1[pink-sub-folder/ ]
    C --- p2([pink-file.md ])
    C --- |./say_hi.sh|p3{{say_hi.sh }}

    P1 --- |python helloworld.py|p4([**helloworld.py** ])
    P1 --- p5([pink-data.csv ])

    D --- |Rscript blue.r|b1([**blue.r** ])

```

Scroll down to see key:

```{mermaid}
flowchart TD
  E[folder] -->|CLI argument|F([file])
  E[folder] -->|CLI argument|G{{executable}}
```

You can use `cat filename` to print out the content of a file, or `nano filename` to open the nano text editor.
You can also use `code filename` to open it in vscode on your virtual machine.

On the HPC system, you'll likely use `nano` to edit code if you ever need to.


## Cheat Sheet {.smaller .scrollable #cheat-sheet background-color="#f5e0fd"}

Use the back button in your browser to return to the slide you were previously on.

**If you are lost, you can always `cd` home!**

| Command | Description |
| :--- | :--- |
| `cd` | Change directory to home |
| `cd dir-name` | Change directory to `dir-name` |
| `pwd` | Print the current working directory - where am I? |
| `name --help` | Load the manual for `name` - on Codespaces |
| `man name` | Load the manual for `name` - on Aire/ARC |
| `ls` | List the contents of a directory |
| `cat file-name` | Print out the contents of a file called `file-name` |
| `mkdir dir-name` | Make a new directory called `dir-name` |
| `touch file-name` | Make a new file/update the last-edited date of a file called `file-name` |

Some more `cd` commands:

| Command | Description |
| :--- | :--- |
| `cd ..` | Go up a level to the parent directory |
| `cd -` | Go back to the previous directory |
| `cd ~/dir-name` | Go to `dir-name`, a directory in the home directory |

Some more `ls` commands:

| Command | Description |
| :--- | :--- |
| `ls -F` | List the contents of a dir, with symbols for content type |
| `ls -a` | List *all* contents, including hidden files and directories |
| `ls -l` | List contents, including permissions, the owner and their "group", and when the content was edited |


Commands for working with files and directories:

| Command | Description |
| :--- | :--- |
| `cp` |  |
| `mv` |  |
| `rm` |  |
| `mkdir -p dir-name` | Make a new directory call `dir-name` if it doesn't already exist |

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