Slides - Introduction to Unix Workshop

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# Introduction to Unix
## Hands-on workshop

???

**p**: toggles **presenter** mode

**c**: creates a **clone** for dual screen

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# Melbourne
# Bioinformatics

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* High-end Computing
* Life Science Computing Expertise

<u>melbournebioinformatics.org.au</u>

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# Why Unix?

* Powerful
* Big data
* Flexible
* Automation
* Pipelines
* Science Software

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* Powerful: lots of CPU's and Memory, GUI wastes
* Big data: excel has limits
* Flexible: no need to click, copy paste; tell computer to do it
* Automation: for loops
* Pipelines: connect applications together
* Science Software: lots, because of ^points

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# User Interface

<div style="width: 48%; display: inline-block;">
	<h4>Graphical User Interface (GUI)</h4>
	<img width="100%" src="media/windows-screen.png" />
</div>
<div style="width: 48%; display: inline-block; margin-left: 2%; height: 380px; vertical-align: top;">
	<h4>Command Line Interface (CLI)</h4>
	<img width="100%" src="media/unix-screen.png" />
</div>

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* My Documents -> Home dir
* Double click folder -> cd folder

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# Command prompt

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* Time: when last command finished
* Username: you
* Hostname: the computer you are connected to (useful in HPC course)
* Current Working Directory: like the "location" bar at top of file explorer
* Prompt: Give me something to do!

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# Command line

* space separation
* quote spaces

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* Simplified the prompt to just *$*
* space separation: 
	* 1+ spaces, 
	* don't put spaces in filenames
* parts:
	* command: the program/app running
	* flag: a *-* followed by a *letter*, turns feature on (or off)
	* long-flag: same as flage but *--* and a word
	* option: a (long-)*flag* followed by value.
	* anonymous options: values without a flag. (aka positional)
* quote spaces: wrap with single/double

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# File System

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* (Up-side-down) Tree
	* Root ~> (My) Computer
	* Directory == Folder
	* Dir in dir
	* /home/user1/ == Home ~= Documents
* Absolute path for settings file

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# Absolute File Name

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* Absolute <-> Full
* Uniquely ID file/dir

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# Absolute File Name

* /settings

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# Absolute File Name

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# Absolute File Name

* /home/user1/file01.txt

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# Absolute File Name

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# Absolute File Name

* /home/user2
	* Trailing "/" ignored

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* Correct answer (no /)
* Absolute = lots of typing

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# Current Working Directory

* Position in filesystem
* Starts at *Home*

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* Position
* Home
* Reminder in Prompt

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# Relative File Name

* **CWD**: /home

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* Relative to CWD
	* leave off first part

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# Relative File Name

* **CWD**: /home
* user1/muscle.fq

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# Special File Names

* **~** = *Home directory*
* **.** = *CWD*
* **..** = *Parent* of *CWD*
* **...** = ??

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# Special File Names

* **~** = *Home directory*
* **.** = *CWD*
* **..** = *Parent* of *CWD*
* **...** = ERROR, use **../..** instead

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# Relative File Name

* **CWD**: /home/user2

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# Relative File Name

* **CWD**: /home/user2
* ../user1/muscle.fq

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# Before we start

* Q/A style
* Incremental Hints
* Think > Hint > Answer

#### What is the answer to Life?

<div class="md-typeset">
<details>
  <summary>Hint</summary>
  What is the answer to everything?
  <br/>
  As featured in <em>The Hitchhiker's Guide to the Galaxy</em>
</details>

<details>
  <summary>Answer</summary>
  <strong>Answer</strong>: 42
  <br/>
  Ref: <a href="http://en.wikipedia.org/wiki/42_%28number%29">Number 42 (Wikipedia)</a>
</details>
</div>

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# Ready, Set, Go

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* Pairs?

.giant-url2[bit.ly/2J82JH1]

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* Pairs: 
	* Recommend, 
	* Alternate *driving* responsibilities
	* Make sure both understand what is happening