Transcript Introduction to Linux/Unix

Outline
1.0
What to expect
1.1
1.2
1.3
1.4
1.5
Introduction to programming: Hardware VS Software
Types of programming Languages
Types of Operating systems
Introduction to Linux/Unix
SSH
• Introduction to Linux/Unix
• working on Linux/Unix system
• logging in
• managing passwords
• navigating the Linux/Unix file system
•Core PERL
• Basic language syntax
•Applied PERL
• Using perl to do bioinformatics
 Computer


Device capable of performing computations and making
logical decisions at speeds millions of times faster than
human beings
Computers process data under the control of sets of
instructions called computer programs, or scripts.
 Has
•
Hardware
–
•
two inseparable components
The various physical components comprising a computer
• Keyboard, screen, mouse, disks, memory,
• CD-ROM, central processing units
Software
–
Tested and working step-by-step instructions that are bundled
as a unit and can run on a computer
Six logical units in every computer:
1.
Input unit

2.
Output unit

3.
Performs arithmetic calculations and logical decisions
Central processing unit (CPU)

6.
Rapid access, low capacity, stores input information
Arithmetic and logic unit (ALU)

5.
Outputs information (to screen, to printer, to control other
devices)
Memory unit

4.
Obtains information from input devices (keyboard, mouse)
Supervises, coordinates and prioritizes computing jobs
Secondary storage unit


Cheap, long-term, high-capacity storage
Stores programs and data for loading and processing by
ALU/CPU

Three types of programming languages
1.
Machine languages


Strings of numbers giving machine specific
instructions
Example:
+1300042774 (100111101011001001010)
+1400593419 (101010101111100010001)
+1200274027 (100100101000010010010)
2.
Assembly languages


English-like abbreviations representing elementary
computer operations (translated via assemblers)
Example:
LOAD
ADD
STORE
BASEPAY
OVERPAY
GROSSPAY
3.
High-level languages
Code that is:

Written in non redundant, unambiguous subset of
everyday English and Mathematical notations

Human readable

Incomprehensible to computers unless translated by
compiler or interpreter programs

Example:
grossPay = basePay + overTimePay
 Examples

C, C++, C#, Java


Used to manipulate large amounts of data
Pascal


Used for scientific and engineering applications
COBOL


Used for major applications in various fields
FORTRAN


of high-level languages
Intended for academic /instructional use
Perl, Python, Ruby …


Interpreted , good for the web applications,
Fast text and data manipulation …
 What
is Linux/Unix
 An architecture independent Operating system:
- Multiuser
- Multitasking
- Secure mode
*Each user restricted to his/her home directory:
*Can’t access other peoples home directory
 Secure
login shell
 Case sensitive
 Uses forward slash as directory separator “/”
 Prime development environment for bioinformatics
software, webserver applications

Logging in/out




Password resetting:





Type username at prompt
Supply password when prompted
Issue exit/logout command to exit
Type passwd at the command prompt
Issue current password when prompted
Issue new password when prompted
Re-issue new password to confirm
Choose a good password
Longer than six letters & digits
 Mix upper case, lowercase, digit and punctuation
marks


http://www.linux-tutorial.info/modules.php?name=MContent&pageid=5
1.
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5.
6.
7.
Overview of the Linux System
Basic Commands
Relative & Absolute Path
Redirection and Pipe
File/Directory Permissions
Process Management
The nano Text Editor

Kernel is a main program of Unix system.
it controls hard wares, CPU, memory, hard
disk, network card etc.

Shell is an interface between user and
kernel. Shell interprets your input as
commands and pass them to kernel.
User
input
Shell
Kernel
Directory Structure



Files are placed in directories/folders.
All directories are in a tree like hierarchical structure.
Users can add and remove files and directories on the tree



If they have proper level of authority.
Top Most directory is “/”, which is called or root.
Users have their own directory called home directory
Users can create and delete files and folders they own
 Users can give permission to others on their files and folders


When you log on too Linux machines, you will see a prompt
 On cisunix/wildcats it is a % with a blinking cursor
 On other machines it looks like: [user@host ~]$
[feseha@perl ~]$
The prompt is called a shell prompt and waits for user commands
User commands consists of three basic parts (in order):
 command name eg. ls
 options (modifiers) eg. -la (l= long form, a = all file types)
 arguments the entity to be acted upon

eg: /usr/local/bin
NB: options and arguments are optional
[user@host ~]$ ls –la /usr/local/bin

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
ls
cd
cp
mv
rm
pwd
mkdir
rmdir
less
more
show files in current position
change directory
copy file or directory
move file or directory
remove file or directory
print Working directory
create directory
remove directory
display file contents one screen full at a time
display file contents one screen full at a time
(with less and more: press space bar to see next screen full
or press the letter ‘q’ to quit and get the prompt back)

cat
concatenates and display contents of one or more files
(pipe it to more or less to prevent continuous flow and read contents)

man
display online manual

passwd change password (following its instruction)

head
show the top 10, or more with options, lines of a file

tail
show the bottom 10, or more with options, lines of a file

sort
Sort file contents by the first field in ascending
alphabetical order

grep
search file and retrieve lines containing pattern

wc
word or line count

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
Path refers to the position of a file / folder in the directory tree.
Paths can be expressed as relative path or absolute path.
Relative path expression:
the path is not defined uniquely
 expressed relative to current position.






../../../fileName
FileName is two directories up!
../foldername/fileName
File is in folderName one directory up!
Absolute path expression:
 the path is defined uniquely
 does not depend on your current path
 It goes all the way from root position to the target file/folder
position
 Eg. /home/feseha/public_html/cgi-bin/w777/junk.txt
By default, output of commands, if any, is displayed on screen.


Output can be directed to:
 File
 Other commands to process it further
Use: >fileName to redirect command output from screen to a file.


NB: “>” also means overwrite the file if it exists so pay attention to what you write to!
Using “>>” instead of “>” appends the output to the end of the file if the file already
exists or creates a new file if it doesn’t exist.
Output can be redirected to other commands via a pipe “|”
Eg. 1. If the output of a command is longer than the screen size, you can pipe it to less
or more so that one screen full can be viewed at a time
ls –l | more
Eg. 2. If you want to peruse a many concatenated documents spanning more than one
screen, pipe it to “more” or “less” to view one screen full at a time
head *.pl | more
(* = anything so *.pl means all files ending in “.pl” i.e. perl scripts)
Eg. 3. You just want to know how many lines are in the output of ls. You
can pipe its output to wc –l as follows
ls | wc –l
Eg. 4. You want to see the lines 250 to 265 in a file that has 1000 lines in
it.
You can use head to get the first 265 line and pipe it to tail to get the
last 15 lines
head -265 targetFile.txt | tail -15
If you want the lines saved to result.txt instead of the screen, redirect it
with >
head -265 targetFile.txt | tail -15 > result.txt
sort

Sorts a file /list with the first field of each line.
Options:

-n numerical sorting on first fiels

-k sort by field number following k

-r sort in reverse descending order ( z – a or say 100 to 1)

-n
Sorts considering the numeric value of the strings

-k3
Sorts using the third field of each line

-rnk3 Sorts in reverse order, using the numeric value of field # 3

What does the following command achieve?
ls –la /bin/ | sort –nk5 | tail -1
First figure out what each command is supposed to do …
ls – la /bin/
sort –nk5
tail -1

All of files and directories have specific owner and permission.

There are three types of permission:
Readable, r
 Writeable, w and
 eXecutable, x


Permissions are set at three user levels:
owner, u (u from user)
 group member, g and
 World, o (All Others outside owner and owner’s group).
 ALL, a i.e u+g+o

Example:
ls -l .bash_profile
-rw-r--r-
1 cnotred
cnotred
191 Jan 4 13:11 .bash_profile
r:readable, w:writable, x: executable
Command
Outcome_____________________
chmod
chown
change file mode, add or remove permission
change owner of the file


Examples:
chmod a+w filename
add writable permission to all users
chmod o-x filename
remove executable permission from others
chmod a+x
Gives permission to the user to execute a file

u: user (owner),
a: all
g: group,
o: others

r = 4,
w = 2,
x=1
rwx rwx rwx
 421 421 421

7
7
7


a+rwx
421 001 001
 rwx --x –x

Command line usage:
 chmod 711 fileName


Set the permission at three levels
chown userName myFile.txt

(I passed ownership to another user!)

Check permission
ls –l .bash_profile
cp .bash_profile sample.txt
ls –l sample.txt

Remove readable permission from all.
chmod a-r sample.txt
ls –l sample.txt
less sample.txt

Add readable & writable premissions to file owner.
chmod u+rw sample.txt
ls –l sample.txt
less sample.txt
rm sample.txt
Nano is a user friendly text editor!

Arrow-keys
CTRL+a
CTRL+e
CTRL+v
CTRL+y
CTRL+w
CTRL+d
CTRL+k
CTRL+u
CTRL+o
Move cursor____________________________
Move to the beginning of the current line.
Move to the end of the current line.
Move forward one page.
Move backward one page.
Search for text.
Delete the current character.
Remove (cut) current line or selected text.
Paste (uncut) last cut text at the cursor position.
Save (output) the file.

CTRL+x
Exit nano, saving the file.
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
Create the file Hello.pl
nano hello.pl

Write hello.pl as follows.
#!/usr/bin/perl
print “Hello World\n”;


Make it executable
chmod u+x hello.pl
Run it!
./hello.pl