Basic Commands for BioInformatics Students

1. BASIC LINUX
COMMANDS
Welcome to the Linux World

2. 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.

3. 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

4. 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

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

6. cd (change directory)
● changes the current directory
● cd . to remain inside same directory
● cd .. to go back one directory

7. 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
$ pwd
it will print current directory

8. ~ Your Home Directory
By typing cd ~ in terminal it will take you to the
home directory of current user
$ cd ~

9. cp (copy)
copies a file or entire directory to another path
If 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 :)

10. mv (move file)
move command renames or move a file
use -r flag to recursively move all files
$ mv file1.txt file2.txt

11. rm (remove)
rm removes a file or entire directory with -r flag
$ rm <file>
$ rm <directory> -r

12. clear
clears your screen
$ clear

13. cat
displays the content of files on screen.
$ cat file.txt

14. less
Iess is similar to cat but it displays content one
page at a time
$ less file.txt

15. 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

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

17. 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

18. grep (don't ask what that’s called :) )
This command search a file for specific word or
a pattern. for example
grep Science file.txt will search string Science
in file.txt
grep command by default is case sensitive

19. wc (word count)
counts number of words in a given file.
to find number of lines set the -l flag
$ wc -l file.txt

20. 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

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

22. 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

23. 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 *list
will list all files ending with string list

24. UNIX File System
Type ls -l and see the result

25. UNIX File System
In 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.

26. chmod (changing file mode)
Only owner can change the mode.
Symbol Meaning
u user
g group
o other
a all

27. chmod (changing file mode)
Symbol Meaning
r read
w write (and delete)
x execute (and access directory)
+ add permission
- remove permission

28. Example
$ chmod a+rw file.txt
this will give read and write access to all user,
group and others
-rwxrwxrwx 1 thirdknife staff 5 Nov 27 23:09
text.txt

29. 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>

30. sudo (execute commands as others)
Use this command to do as a different user.
$sudo su ls
will list files as root user
$sudo su - shakeel ls
will list files as shakeel user

31. 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.

32. Contact
shakeel@creanyx.com