Linux Basics Tutorial

Linux is a type of Unix operating system, designed and developed by Linus Torvalds while studying at the University of Helsinki in 1991. Today, the Linux family has nearly 140 different versions that all use the Linux kernel.

Advantages of Linux Operating System

Free and Open Source: Open source code

Security: No need for antivirus software, no need to block adware and Trojans

Stability: Linux systems can run without failure for years

Multithreading, Multi-user: Support for multiple users and parallel operations

High Compatibility: Supports most biological software

Once the Linux server is established, we can log in to the server from a PC using commands or tools.

1) Use software: putty

2) Download link:

https://pan.baidu.com/s/1aOKwMZvQGIqQ2xn25MlNBg Extract code: rspi

Image credit: Teacher Ju Jia

3) Log out: exit

Directory: Equivalent to a folder in Windows

File: Equivalent to a document or application in Windows

Path: The storage address of files or directories composed of various levels of directories

man [command_name]

1. A typical man manual includes the following sections:

NAME: The name of the command.

SYNOPSIS: A brief description of how to use the command.

DESCRIPTION: Detailed description of the command’s usage, including the functions of various parameter options.

SEE ALSO: Lists other related manual page entries that may be useful.

AUTHOR, COPYRIGHT: Information about the author and copyright.

2. Exit man command: q

help [built-in_command]

Used to view help for built-in Linux commands

Help outputs all built-in commands

Display current path: pwd

Change path: cd [directory]

Two methods to enter the basic folder:

1. Absolute path

2. Relative path

Two ways to represent paths

1. Absolute path:

Starts from the root directory “/”, separated by “/” for each level of directories

2. Relative path:

The position of the target directory relative to the current directory

Enter the parent directory:

Return to the previous directory before switching:

Enter the personal home directory:

Display the contents of a specified directory in tree form: tree [directory]

tree displays the files and subdirectories in the current directory (default)

tree dir displays the files and subdirectories in the dir directory

Create directory: mkdir [directory]

mkdir dir0 creates dir0 directory in the current directory

mkdir -p dir0/sub1/sub2 recursively creates directories

Delete directory: rm –r [directory]

rm -r dir0 deletes directory dir0

List files or subdirectories: ls [directory]

ls displays information in the current path

ls -l displays detailed information in long format

ls -t displays information in chronological order

Image credit: Teacher Ju Jia

Copy files or directories: cp

cp file temp creates a copy of file as temp

cp file ./dir1 copies file to dir1 directory

cp -r ./dir1 ./dir2 copies directory dir1 to dir2 directory

Delete files or directories: rm

rm temp deletes file temp

rm -r ./dir2 deletes directory dir2 and its contents

Change file or directory name: mv

mv file1 file2 renames file1 to file2

mv ./dir ./DIR if the target folder ./DIR does not exist, renames dir to DIR

Move files or directories: mv

mv file ./dir file1 moves to dir

mv ./dir1 ./dir2 if the target folder ./dir2 exists, moves dir1 into dir2

View file content:

1. Display all: cat [file]

2. Display page by page: more [file] (Enter moves one line; Space moves one page, q to exit)

3. Scroll display: less [file] (Use up and down keys to navigate; q to exit view; can also view content in directory)

View part of a file:

1. Display first N lines (default 10 lines): head [-N] [file]

2. Display last N lines (default 10 lines): tail [-N] [file]

Display the number of lines in a file: wc -l [file]

Display specified columns or fields in a file: cut [file]

cut -f1,3-5 refGene displays the 1st column and the 3rd to 5th columns in the file (default tab-separated)

sort [file]: Sort the contents of the file in alphabetical order and output

uniq [file]: Compare adjacent lines and display non-repeating lines

Note: The uniq command only removes adjacent duplicate lines; non-adjacent lines are not filtered.

uniq is often used with the sort command

Common Operators

1. “|” Pipe operator

2. “>” Output redirection operator

3. “>>” Append operator

File Compression Backup: tar

1. Compress: tar zcf china.tar.gz china

2. Decompress: tar zxf china.tar.gz

Image credit: Teacher Ju Jia

Image credit: Teacher Ju Jia

No such file or directory: Path or file name error, the computer cannot find it

Permission denied: Path or file name is correct, but operating in an inappropriate path, permission is not allowed

Command not found: Check for correct spelling; whether it is uppercase; whether there is a space between commands and between command and file name

vi editor: The most famous editor under Linux, and a tool that we must master when learning Linux

Edit a file or create a new file

1. Command mode: In this mode, you can save, exit, cut, paste, and perform other operations on the file. Any characters entered are treated as commands

2. Input mode: Used to input and edit files, the user’s typing will be displayed on the screen, written as text to the user’s file

Start vi: vi [filename]

For example: vi test.txt

Edit File

Press the 【i】 key to edit the file

You can use the keyboard’s up and down arrows to move the cursor

Save and Exit vi

Press the 【Esc】 key, then type “:wq” or “:q!”, and press 【Enter】

:wq Save and Exit

:q! Exit without saving

Common Commands

Need to be used in command mode, press 【Esc】 and then type the command

Image credit: Teacher Ju Jia

vi editor is the most commonly used text editor under Linux

vi editor has two working modes: input mode and command mode

As a bioinformatics worker, it is essential to master the above content!

1. Free Course | Linux Basics

2. Bioinformatics Training | Professional Skills Training for Genomic Data Analysis