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UNIX Tutorial
#Introduction(UNDER DEVELOPMENT)
UNIX is a command line operating system (OS)
- It is the backbone of popular graphical OS's like Apple's OS X and Linux
Unix is built on a simple modular philosophy
- UNIX is based on files and processes. In other words, all the OS 'sees' are files and processes even though there are directories and other types, they are all viewed by the OS as a file. This is useful as it makes it easier to pass files around the system.
- The OS provides a unified filesystem to facilitate communication between programs
- The OS operates on a set of simple programs that each provide a single well defined function.
##The Kernel
The kernel is the hub of the OS. It does all of the work behind the scenes.
- The kernel executes programs
- Allocates time and memory to programs
##The shell
The shell is the interface between the kernel and the user.
- Is a command line interpreter -- It has a defined syntax to execute processes
- Can be customized to user preferences
- Provides shortcuts for usability (tab completion)
- Stores a history of all commands run. Try
history
or press the up arrow in the terminal
#Commands
To get started open a terminal.
##Navigating the filesystem
Let's start by learning how to get around in unix. Before we get started there are a few things that you need to know. This first is your home directory. Your home directory is where you start when you open a new terminal. I is a folder that has the same name as your username. This is where you will store all your files on the system. There are a few other places that you need to know. One in / (yes, slash), this is the root directory for your system and is where you would go to find any system-wide files.
###pwd
pwd
stands for print working directory. Entering pwd
should print your home directory to your screen because that is where you start out
###ls
ls
stands for list. ls
will list all of the files in your current directory. ls
can also take arguments. To see the contents of your Documents folder type ls Documents
.
###cd
cd
stands for change directory. Entering cd
with no arguments will always take you home if you get lost. cd Documents
will change your current working directory into your Documents folder.
The .
in UNIX is useful because it provides a relative location to where you are. .
is a shortcut for your current directory. Compare the output of ls
to ls .
.
..
in UNIX is the location one directory above your current working directory.
~
is a shortcut for you home directory and can be use in any path to reduce typing. For example cd ~/Documents
will take you into you Documents folder from anywhere in the system.
mkdir
stands for make directory. Entering this command will create a new directory. Let's make a playground folder in our home directory. To do this enter cd
to take you home, then enter mkdir playground
to create a playground folder. Change into your playground folder by cd playground
.
The touch
command creates an empty file. Let's create one, enter touch file1
. then enter ls
to see your file
##Note: The current version of this tutorial is now at www.rnaseq.wiki
Table of Contents
Module 0: Authors | Citation | Syntax | Intro to AWS | Log into AWS | Unix | Environment | Resources
Module 1: Installation | Reference Genomes | Annotations | Indexing | Data | Data QC
Module 2: Adapter Trim | Alignment | IGV | Alignment Visualization | Alignment QC
Module 3: Expression | Differential Expression | DE Visualization
Module 4: Ref Guided | De novo | Merging | Differential Splicing | Splicing Visualization
Module 5: Kallisto
Appendix: Abbreviations | Lectures | Practical Exercise Solutions | Integrated Assignment | Proposed Improvements | AWS Setup