Table of content

File names

• ls
• Change File Name by Shell
• Get file's base name
• find command
• Find a file

File content

• grep
• awk
• sed
• cut, paste, join
• join
• tr - translate characters
• printf
• Bash print specific line of file
• Convert newline between systems
• How to Convert DOS and UNIX text files
• Randomize lines in file
• Split a file
• Compare two files line by line

Manipilate Files

• Remove a certain list of files
• Create a file of specified size
• ln
• tar, gzip
• How to Backup with date, find, tar and gzip
• cp

Directory

• Print Directory tree

Job control

• Kill all your process
• Proces ID: $$
• Schedule jobs in Unix
• screen
• script command
• watch in shell

Data structure

• String in Bash
• Arrays in Bash
• Dictionary in Bash

Variables

• Variable in shell
• Bash random number

Programming

• Loop and Conditionals
• Logical operators and simple flow control
• Bash Function
• Bash getopts
• Pass an argument into shell script
• Go to the directory of current shell script

I/O Redirection

• Bash redirections
• Bash read file
• Bash prompt

Math

• Math in Bash
• Bash combinations
• Use awk to sum a column of numbers

Network

• Send email attahment
• Password-less SSH
• iftop for monitoring network traffic

Other commands

• Unix Command Summary
• Time difference in bash
• convert a PDF file to images

Scripts

• A safe rm
• Clustalw.sh

References and Tutorials

• [http://www.linuxtopia.org/online_books/advanced_bash_scripting_guide/index.html Advanced Bash-Scripting Guide]
• [http://mercury.chem.pitt.edu/~sasha/LinuxFocus/English/September2001/article216.shtml lf216, UNIX Basics: Shell Programming]
• [http://www.grymoire.com/Unix/Sh.html Sh - the Bourne Shell]
• [http://tldp.org/LDP/abs/html/ Advanced Bash-Scripting Guide by Mendel Cooper]
• [http://www.freeos.com/guides/lsst/ Linux Shell Scripting Tutorial v1.05r3 A Beginner's handbook]
• A Bioinformatician's UNIX Toolbox
• http://lifehacker.com/5743814/become-a-command-line-ninja-with-these-time+saving-shortcuts