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Basic linux commands

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Basic Commands for BioInformatics Students
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BASIC LINUX COMMANDS Welcome to the Linux World
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Page 1: Basic linux commands

BASIC LINUX COMMANDS

Welcome to the Linux World

Page 2: Basic linux commands

What are linux commands

Linux commands are just simple programs like a program in windows. Typing command is like clicking an icon in windows.

Sometimes commands take some extra parameters to do extra work, we call them flags.

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man (Your best friend!)

man means manual pages, its like reading a manual of any home appliance. In software it means reading documentation. Good softwares have always a good documentation part.

$ man <command>$ man clear

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ls (list items)

● The ls command ( lowercase L and lowercase S ) lists the contents of your current working directory.

● ls by default does not show hidden files

● to see all files use ls -al● -al is flag in this case

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mkdir (make directory)

● creates a directory● use -p to create as many directories.● $ mkdir first/second/third -p● $ cd first/second/third

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cd (change directory)

● changes the current directory ● cd . to remain inside same directory● cd .. to go back one directory

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pwd (print working directory)

For example, to find out the absolute pathname of your home-directory, type cd to get back to your home-directory and then type

$ pwdit will print current directory

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~ Your Home Directory

By typing cd ~ in terminal it will take you to the home directory of current user$ cd ~

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cp (copy)

copies a file or entire directory to another pathIf you want to copy files from another directory to current directory use a . for destination$ cp <source_file> <destination_file>Tip: Always read the error carefully and please don't freak out :)

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mv (move file)

move command renames or move a file

use -r flag to recursively move all files

$ mv file1.txt file2.txt

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rm (remove)

rm removes a file or entire directory with -r flag

$ rm <file>$ rm <directory> -r

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clear

clears your screen

$ clear

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cat

displays the content of files on screen.

$ cat file.txt

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less

Iess is similar to cat but it displays content one page at a time

$ less file.txt

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head

head is a short version of less command. It prints only first 10 lines.

You can set the number of lines by giving a -<number> flag e.x$ head -5 file.txt

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tail

tail is opposite to head, it shows last 10 lines of the file.

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searching within text

You can use less command to search within text. Do you remember what less command do?After executing the less command use / and type your required text to search$ less file.txt/science

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grep (don't ask what that’s called :) )

This command search a file for specific word or a pattern. for examplegrep Science file.txt will search string Science in file.txt

grep command by default is case sensitive

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wc (word count)

counts number of words in a given file.

to find number of lines set the -l flag

$ wc -l file.txt

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Writing input to output

type the cat command without file name. It will start taking your text into output memory. Once you press Ctrl + d the output will be printed on screen.$ cat$ alpha $ Ctrl + d

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use cat to write a file

$ cat > file.txtThis will take your input and write to a file by name file.txt from your input until Ctrl+d is pressed.

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Pipes

Piping means passing result of one command to another command.

You can search in first 10 lines by using head and grep command by piping$ head file.txt | grep science

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The wildcard *

The * character is a wildcard character. It means it will ignore the part after and before where its used$ ls list*will list all files starting with string list$ ls *listwill list all files ending with string list

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UNIX File System

Type ls -l and see the result

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UNIX File SystemIn the left-hand column is a 10 symbol string consisting of the symbols d, r, w, x, -, and,

occasionally, s or S. If d is present, it will be at the left hand end of the string, and indicates a

directory: otherwise - will be the starting symbol of the string.

The 9 remaining symbols indicate the permissions, or access rights, and are taken as three groups of

3.

● The left group of 3 gives the file permissions for the user that owns the file (or directory) (thirdknife in the above example);

● the middle group gives the permissions for the group of people to whom the file (or directory) belongs (staff in the above example);

● the rightmost group gives the permissions for all others.The symbols r, w, etc., have slightly different meanings depending on whether they refer to a simple

file or to a directory.

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chmod (changing file mode)

Only owner can change the mode.Symbol Meaning

u user

g group

o other

a all

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chmod (changing file mode)Symbol Meaning

r read

w write (and delete)

x execute (and access directory)

+ add permission

- remove permission

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Example

$ chmod a+rw file.txtthis will give read and write access to all user, group and others

-rwxrwxrwx 1 thirdknife staff 5 Nov 27 23:09 text.txt

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making file executable and runnable

For any file to be executable you have to make it x using chmod, e.g$ chmod a+x file.txt this will make file.txt executable for all (user, group and others)to execute a file use ./<filename>

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sudo (execute commands as others)

Use this command to do as a different user.

$sudo su lswill list files as root user $sudo su - shakeel ls will list files as shakeel user

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Tips

Always use manual pages for help.I understand they are boring but believe me thats where I learned the most. Second friend is google :)

Try to understand the error statement.

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Contact

[email protected]


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