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Introduction to UNIX, Linux and scripting with Bash
Overview
1
Introduction
1.1
BASH ?? Never heard!
1.2
BASH is awesome!
1.3
Installing Bash
1.4
Using BASH and Getting Help
1.5
Basic Usage and Syntax
1.6
Exercises
2
Files and Folders
2.1
Create and change directory: mkdir, cd
2.2
List and create empty files:ls, touch
2.3
Copy and move files: cp, mv
2.4
Delete files and directories: rm
2.5
Exercises
3
Redirection
3.1
Input, Output and Redirection
3.2
Appending: “>>”
3.3
Redirecting: “<”
3.4
Redirecting
STDOUT
to
STDIN
: “|”
3.5
Exercises
4
Variables
4.1
Assigning data to variables
4.2
Accessing data stored in variables
4.3
Creating variables from STDOUT
4.4
Exercises
5
Conditionals and Loops
5.1
Conditionals
5.2
For Loops
5.3
While Loops
5.4
Evaluation of commands on the fly
5.5
Exercises
6
BASH Scripts
6.1
Using
echo
6.2
Using command line text editors
6.3
Using a text editor with a GUI
6.4
Execute a BASH script
6.5
The Unix permission system
6.6
Changing permissions
6.7
Paths
6.8
Passing arguments to a script
6.9
Exercises
7
Text files
7.1
Encoding
7.2
Looking at files
7.3
Comparing Files
7.4
Exercises
8
File Compression
8.1
Zipping files: gzip
8.2
Compressing multiple files: tar
8.3
Looking at zipped files
8.4
Zipping from STDOUT
8.5
Exercises
9
Filtering and Editing Files
9.1
grep
9.2
tr
9.3
sed
9.4
Regular expressions
9.5
Sorting and unique lines: sort, unique
9.6
Matching: join
9.7
Exercises
10
AWK
10.1
Basic structure
10.2
Variables in awk
10.3
Functions
10.4
Extended matching
10.5
If-Else
10.6
Exercises
11
Using R with BASH
11.1
Exercises
12
Solutions to Exercises
References
Prepared by the Wegmann Lab - from noobs for noobs
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FriBASH - Introduction to UNIX and Bash
Chapter 4
Variables
