Basic linux commands

Post on 09-Jul-2015

414 Views

Category:

Software

3 Downloads

Preview:

Click to see full reader

DESCRIPTION

Basic Commands for BioInformatics Students

Transcript

BASIC LINUX COMMANDS

Welcome to the Linux World

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.

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

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

mkdir (make directory)

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

cd (change directory)

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

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

~ Your Home Directory

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

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 :)

mv (move file)

move command renames or move a file

use -r flag to recursively move all files

$ mv file1.txt file2.txt

rm (remove)

rm removes a file or entire directory with -r flag

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

clear

clears your screen

$ clear

cat

displays the content of files on screen.

$ cat file.txt

less

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

$ less file.txt

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

tail

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

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

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

wc (word count)

counts number of words in a given file.

to find number of lines set the -l flag

$ wc -l file.txt

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

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.

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

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

UNIX File System

Type ls -l and see the result

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.

chmod (changing file mode)

Only owner can change the mode.Symbol Meaning

u user

g group

o other

a all

chmod (changing file mode)Symbol Meaning

r read

w write (and delete)

x execute (and access directory)

+ add permission

- remove permission

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

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>

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

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.

Contact

shakeel@creanyx.com

top related