********************************************************************************
Introduction
********************************************************************************
Facts you should know about linux:
Linux is an implementation of Unix
	About 38 years ago,  Bell Labs developed a new operating system,
	called "UNIX"
	About 15 years ago, home PC became popular. There is need to run unix
	on PC. Linux Torvalds, began to work on linux.
Linux is written with C.
Linux is an ideal operating system for power-users and programmers,
Linux is free.
Linux is secure and versatile.
There is a Linux for everyone.
	Currently, there are many versions of linux. Redhat(Fedora),
	Debian,Gentoo, Knoppix, Mandrva, Slackware, SUSE, Ubuntu, and more.
	Downloadable ISO-images can be obtained from Linux.com.
Linux is open source, it uses GNU tools, a set of freely available standard tools for handling the operating system.

Linux comprises of two parts:  the kernel and the shell.

The kernel part carries out basic operating system functions such as accessing files, 
allocating memory and handling communications.
A shell provides the user interface to the kernel. A number of shells are available 
on the Unix operating system including the Bourne shell and the C shell. The shell 
is basically an extensive program that runs all the time that you are logged on to 
the computer, and provides an interactive interface between the user and the computer 
functions. A modernized version of Bourne Shell is called the Bourne Again Shell, or bash. 
For C-shell, we have an extended one: tcsh.
********************************************************************************
File and Directory commands
********************************************************************************
The most used commands:
ls - lists all files in current directory
	Format: ls [option] [FILE]
	option:	-l	list in long format
		-a	list all files( including hiden files starting with ".")
		-d	list directories
		-t	sort by modification time
		-r	reverse order while sorting
		-p	append / indicator to directories
	examples:	ls -la
			ls -lrtp
	format of FILE: *(any string),?(any one character)
			*.c, test.?, ...
	
pwd - show your current directory that you are in.

mkdir - create a directory

cd - changes directory
	. current directory
	.. parent directory
	~ your home directory
	/ separate different level of directories
	\ for some special symbols

rmdir - deletes a directory that is empty.

cp - copies files
	Format: cp [option] file1 file2
	option: -i	prompts for confirmation before overwriting an existing file.
		-r	copy recursively
		-f	force. Overwrites without promption.
rm - deletes files.
	Format: rm [option] file
	option: -i	prompts for confirmation before deleting.
		-r	deletes the directory and its contents.
		-f	force. Deletes without promption

mv - moves files from source to target. Difference with cp?
	also used to change file/directory name.

Now, here are some commands to list file contents:

cat - outputs file contents on the screen
	Format: cat [option] file
	option:	-n	number the lines
		-v	display non printing characters.

head - outputs the first few lines of the file on the screen.
	Format: head [option] file
	option: -n	outputs first n lines

tail - outputs the last few lines of a file on the screen.
	Format: tail [option] file
	option: -n outputs the last n lines
		-f outputs appended data as the file grows.

more - outputs the contents of a file on the screen page by page.

?????? First lecture stops here ??????
how to connect linux?
	softweb.cc.sunysb.edu
	ssh
where is terminal?
more on cp (file/dir)
file type and how to open.
.exe?
You can always get help about commands by 'man command' or 'command --help'
********************************************************************************
Text Editor -- Vi(Vim)
Lecture 2, by Lingling Wu
vimtutor
********************************************************************************
More on files and directories
********************************************************************************
chmod	change file access permissions
	chmod [option] MODE FILE
		MODE '[ugoa]*([-+=]([rwxXst]*|[ugo]))+'
	or	chmod 755 FILE
find	search for files in a directory hierarchy
	find [path] [expression]
	    path can be empty, default is current directory
            -regex     use regular expression
	    -name pattern
	    -mtime [+-]n	modified in the last n days
	    -mmin [+-]n		modified in the last n minutes
	    -size [+-]n		
	examples
		 find . -name "*.c"
ln
	make links between files
locate	list files in databases that match a pattern
touch	change file timestamps
whatis	display a oneline summary about a command
	quite useful when you forget what one command should used to do
which	locate a command
whereis locate the binary, source, and manual page files for a command
df	display number of free disk blocks and files
du	summary disk usage
********************************************************************************
Networking and Communications
********************************************************************************
telnet - used to communicate with another host.
	Format:	telnet [options] hostname
	option:	-l	username

rlogin - used to communicate with another host. The difference with telnet is that it logs you into the host with the same username as you are logged on with.

rsh - connects to the specified hostname and executes the specified command.
	Format: rsh [option] hostname command
	option:	-l	username

ssh - OpenSSH secure shell client
	Format: ssh [option] user@hostname
	ssh -l abc ams.sunysb.edu
	ssh abc@ams.sunysb.edu
	pine

scp - secure copy
	Format: scp [option] user1@host1:file1 user2@host2:file2

ftp - File Transfer Protocol
	cd
	get
	put
	exit

sftp - secure file transfer program
	Format: sftp [option] user@hostname

lftp - sophisticated file transfer program

talk - used to communicate with another user who is on the machine with name hostname. 
	Format: talk user@hostname
	Mathlab may not work for this command.

write - send a message to another user

finger - display data about a user, including information listed in his/her .plan file.
	parameter could be user name, last name or first name
whoami	print effective userid
w,who	show who is logged on

********************************************************************************
clear	clear the terminal screen
grep	print lines matching a pattern
	grep [options] PATTERN [FILE...]
	useful option	-n 	display line number
			-v	invert match
	basicly, grep string filename
	more complicated search can use regular expression
		^word	begin with
		word$	end with
		[0-9]	numerate number
		*	Matches the preceding element zero or more times. 
		+ 	Matches the preceding element one or more times. For example, ba+ matches "ba", "baa", "baaa", and so on.
		?	Matches the preceding element zero or one time. For example, ba? matches "b" or "ba".
		.	any single character
		\.	dot
	examples
		grep -n root /etc/passwd
		grep return *.c
tar	create tape archives and add or extract files
	tar cvf backup.tar file/dirname
	tar xvf backup.tar
	tar xvzf backup.tar.gz
gzip	gzip filename
gunzip	gunzip filename.gz
zip	
unzip	unzip filename.zip
unrar	unrar x file.rar
PIPE	|
>	redirect
>>	append
top	display linux tasks
ps	report a snapshot of the current processes
kill	send a signal to a process
	kill [ -signal | -s signal ] pid ...
	kill -9 pid
Printing ...
lpr	submit print requests
	lpr [ -P printer ] files
lpq	display the print queue
lprm	remove print jobs from the print queue
	lprm [ -P printer ] job-ID

super user commands
google it and practice in your own linux.
Do not practice super user commands in mathlab, else your account will be cancelled.
********************************************************************************
Shell Configuration:
********************************************************************************
Two popular shells: tcsh and bash
	there are many different shells available, but others tend to be very similar to one or both of these
	Most of the commands that we use are common.
Check your shell type
	echo $SHELL
command 'echo' comes with a return automatically, option '-n' will suppress the return.
Change Shell
you can always type the name of the shell to switch.(bash,csh,sh,tcsh)
If you want to change permantly, (change your login shell), you can do this:
chsh or ypchsh
(chsh -s bash)
Some nice feature of modern shells:
	command line editing
	file name completion (Tab key)
startup file
	.cshrc .bashrc
assignment
	${var}	reference to value of the variable
	${#var}	length of the value as a string
	tcsh: set name=value
	      inherited environment variables: setenv name value
	bash: name=value
              inherited environment variables: export name=value
shell variables:
	$cwd,$PWD	This variable consists of a string which records the name of the current directory.
	$term,$TERM	The terminal type.
	$path,$PATH	an environment variable listing a set of paths to directories where executables may be found
              $HOME     your home directory
		set path in tcsh:
		set path = ($path /a/b/c )
		set path in bash:
		path = $path:/a/b/c
        all variables are set as strings in default, if want to evaluate the numeric value use $(( )), like $(($var1+$var2)), but integers only.
	prompt
	    variables or commands could be part of prompt
	    tcsh
		set prompt = "options"
		options:	%/	full path of current directory
				%c,%.	trailing component of the current directory
				%h,%!,!	current history number
				%t,%@	time
				%n	user name
				%d	week day
				%w	month
				%y	year
		examples
			set prompt = "%n.%.> "
	    bash
		PS1 = "options"
			\w	full path of current directory
			\W	base name of current directory
			\u	user name
			\h	host name
alias:
	bash: alias name='command'
        tcsh: alias name 'command'
      example:
	alias print 'lpr \!* -Pps5'
	print part1.ps glossary.ps figure.ps
	The notation !* causes each argument given to the alias print to be inserted in the command at this point. The command that is carried out is:
	lpr part1.ps glossary.ps figure.ps -Pps5

        an alias can override an existing command, like
        alias ls = 'ls --color'
        but the originally defined command can also be used by 'ls' or \ls 
unalias:remove a defined alias

#:	ignore words after it.
source:	evaluate a file
Write or modify your own shell start up file.

Shell script:
usually begins with shebang: #!/bin/shellname
more powerful: Perl
********************************************************************************