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new slides for linux binf intro started
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SamueleSoraggi committed May 13, 2024
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70 changes: 70 additions & 0 deletions resources/Slides/linuxbasic/slides.qmd
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---
title: "Introduction to `bash` command line for Bioinformatics"
subtitle: https://hds-sandbox.github.io/GDKworkshops
author:
- "Samuele Soraggi"
- "Dan Søndergaard"
institute:
- Health Data Science sandbox, BiRC
- GenomeDK, Health
date: 13.may 2024
format: revealjs
scrollable: true
small: true
toc: true
toc-depth: 1
slide-number: h.v
code-line-numbers: false
logo: img/logos.png
navigation-mode: vertical

---

# Bash command line introduction

:::{.callout-caution icon="false" appearance=simple}

"What is a shell, a terminal, a command-line, and what is bash?"

 

"How do these concepts connect to my computer and a computing cluster?"
:::

## Interaction with hardware

Computer hardware can act on files and softwares through:

![](img/GUIandCLI.png){height="7cm"}

- a **Graphical User Interface (GUI)**, such as your point-and-click operating system
- a **Command Line Interface (CLI) or terminal**, where commands are interpreted and translated into actions

---

- Linux and Mac already have a terminal application

 

- For Windows, you can use
- WSL (windows Subsystem for Linux), which integrates a Linux virtual machine in Windows
- One of many terminal softwares such as
- gitbash
- MobaXterm

## Bash CLI on GenomeDK

When logging in on GenomeDK from the terminal, you are presented with the cluster's CLI.



From this, you can access files and software using the bash language.



Computer hardware can act on files and softwares through:

![](img/GUIandCLI.png){height="7cm"}

- a **Graphical User Interface (GUI)**, such as your point-and-click operating system
- a **Command Line Interface (CLI) or terminal**, where commands are interpreted and translated into actions

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