User manual | UNIX and Linux – An Introduction CHARMM – CERM/PROTEO workshop

UNIX and Linux –
An Introduction
CHARMM – CERM/PROTEO workshop
Condordia University, March 2010
Olivier Fisette
<[email protected]>
Département de biochimie
et de microbiologie
Université Laval
UNIX – An operating system
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The original UNIX is an operating system
developed in 1969 at the AT&T Bell Labs
It implemented revolutionnary ideas
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Concurent users and tasks
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Remote access and networking
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File orientation
UNIX philosophy
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Many small tools combine to perform a task
UNIX - An operating system
family
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Many vendors developed derivatives and
clones
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HP UNIX
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Sun Solaris
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Mac OS X
Academic and free projects did the same
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BSD (University of Berkeley, California)
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Minix
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Linux
A family of UNIX-like operating systems
UNIX - A standardised OS
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The POSIX standard by the Open Group
defines what is UNIX today
UNIX and UNIX-like are generic terms for
any operating system that is reasonably
compatible with the standard
What you learn on Linux or another UNIX
is transferable
First steps with UNIX
Ex. 1
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Open a terminal application
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Meet the shell (command-line interpreter)
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UNIX is a text-based operating system
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The Linux shell is bash
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A graphical interface is built on top of the basic
OS
Type a few commands
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date, whoami, who, ps, ls, pwd
The UNIX filesystem
The UNIX file system
Files and paths
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Everything in UNIX is a file
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Even directories are specialised files
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Files are organised in a hierarchical fashion
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A path is the address of a file
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Paths can be absolute...
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/home/tux/test.c
… or relative (to /home/tux in these
examples)
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test.c
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../../etc/
File management in UNIX
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A variety of commands are used to
create, delete, show and manipulate files
in UNIX
Download the exercice archive
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tar xjf ws-2010-03.tar.bz2
Check the newly uncompressed files
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wget www.proteo.ca/ws-2010-03.tar.bz2
Unpack the archive
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Ex. 2
ls
Files are in the
ws-2010-03
directory
File management in UNIX
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Basic file management commands:
: Show the working directory
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pwd
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cd
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ls [dir]
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cat <file>
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touch <file>
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mkdir <dir>
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rm <file>
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rmdir <dir>
: Change the working directory
: Show directory contents
: Show file contents
: Create an empty file
: Create an empty directory
: Delete a file (except a directory)
: Delete an empty directory
Ex. 2
File management in UNIX
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Ex. 3
More basic file management
: Copy a file
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cp [file1] [file2]
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cp -r [file1] [file2]
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mv [file1] [file2]
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mv [file] [directory]
directory
: Move a file
: Move a file inside a
: Remove a directory
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rm -r [file]
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ls -l -a -h (ls -lah)
file listing
: Copy a directory
: Detailed, complete, readable
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less [file]
: Show a file, one page at a time
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nano [file]
: Edit a file
Path expansion in bash
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Ex. 4
Several characters can be used to match
one or more paths in bash
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? Matches any single character
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* Matches any string of characters (or nothing)
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~ Expanded to your home directory
Also remember the standard UNIX
characters for special directories
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.. Parent directory
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. The current directory
Getting help with UNIX and
bash
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Manual pages are available for UNIX
commands.
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Help is available for bash built-in
commands
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man [program]
help [command]
Unknown files can be identified
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file [file]
Ex. 5
Working efficiently with
bash
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Ex. 6
Key bindings for command edition
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Ctrl+A, Ctrl+E : Go to start or end of line
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Ctrl+B, Ctrl+F : Move one character right or left
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Ctrl+P, Ctrl+N : Previous or next command in
history
Using completion
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Tab : Attempt to complete the current word
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Tab+Tab : Attempt to complete the current
word, then show possible choices
Other key bindings
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Ctrl+D : Exit shell (like the exit command)
Text manipulation
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UNIX is very much text oriented; a wide
array of commands is available to analyse
and manipulate text
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head [file]
: Show the first lines of a text
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tail [file]
: Show the last lines of a text
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grep [pattern] [file]
: Search for matching lines
in a text
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grep supports regular expressions
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^ and $ match beginning and end of lines
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Ex. 7
Enclose RE and expressions with whitespace
characters in 'quotes'
sort [file]
: Sort lines of text alphabetically
These are UNIX filter commands
Communication channels
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There are three standard communication
channels in UNIX
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Standard input (stdin) : What you type
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Standard output (stdout) : Program or command
output
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Standard error (stderr) : Warnings and error
messages from commands
The last two are both shown on the
terminal
–
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Ex. 8
They can be separated
Filter commands operate on files or on
stdin
Communication channels
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Ex. 9
Input and output redirection
Output redirection sends the output of a
command to a file
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[command] > [file]
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Standard error is still shown on screen (but not
with >&)
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File is overwritten (but not with >>)
Input redirection sends the contents of a
file to the input of a command
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[command] < [file]
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Seldom used, since UNIX filters accept files as
arguments
Communication channels
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Ex. 10
UNIX pipes send the output of a
command to the input of another
command
–
[command1] | [command2]
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They can be chained and combined with
redirections
Using only filters, redirections and pipes,
one can achieve powerful text
manipulation
Process management
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UNIX allows many programs to run
simultanously
Commands are available to list and
manage processes (running programs)
: List user processes in the current session
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ps
–
ps -ef
: List all processes in the system
Each process has an identifier (PID) and a
parent
Bash keeps a list of processes started
within the current shell (jobs) for
convenient process management
Process management
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Terminate process :
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Or with a bash task: kill %[job]
Interactive process management:
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kill [pid]
top
Use q and k to quit and terminate process,
respectively
Run command with a different priority
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nice - n [i] [command]
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Where -20 is the lowest priority and 19 the
highest
Change process priority
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renice -n [i] [pid]
Process management
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Run process in background
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Ex. 11
[command] &
Job management key-bindings
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Ctrl+C : Terminate foreground process
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Ctrl+Z : Pause foreground process and send to
background
Other job management commands
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bg %[job]
: Restart process in background
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fg %[job]
: Restart process in foreground
Shell scripts
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A bash shell script is a file containing
bash commands
The commands are excuted when the
script is run
Anything one can type in an interactive
shell can also be put in a bash script
Bash script have many usages:
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Gluing together individual UNIX tools
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Reusing complex commands
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Automating tasks
My First Shell ScriptTM
#!/bin/bash
date
whoami
echo 'This is my first shell script!'
Running a shell script
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In UNIX, each file has an owner and
permissions
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This makes the system more secure
–
It is sometimes confusing for users coming from
Windows
Shell scripts must be executable
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Shell scripts not in the PATH environment
variable must be called explicitly
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chmod +x [file]
./script.sh
The shebang line specifies the interpreter
Environment variables
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Environment variables give UNIX
programs information that is specific to
the current session
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USER
: User name
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HOME
: Home directory
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PATH
: List of program directories
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Print environment with
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Set an environment variable
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Ex. 12
env
and
echo
export VAR=value
The file .bashrc in the home directory
contains instructions for bash to execute
on startup
Variables
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Variables in bash can be assigned with =
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var=value
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No spaces!
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Variables are untyped
Variable substitution with
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${var}
echo ${var}
Do not confuse bash and environment
variables
Variables are especially useful in scripts
Calculations
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let command
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let 'result = (5 +3) * (4 - 2) + 2**3'
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let 'result *= 4'
Arithmetic expansion
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$((expression))
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echo $(( (5 +3) * (4 - 2) + 2**3 ))
Quoting and chain literals
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Bash parses each word as a separate
entity; Whitespaces separate words
Quotes are used to group words that
should belong to the same entity
There are two types of quotes in bash
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'single quotes' group words and prevent all
substitution and expansion
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"double quotes" group words but allow some
limited substitution and expansion (such as
variable expansion)
Control flow
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With bash, you can do tests, conditions
and loops
Combined with variables and UNIX
programs, this makes bash a full-fledged
programming language
#!/bin/bash
nwarn=$(( grep WARNING "${1}" | wc -l ))
if [[ nwarn == 0 ]]; then
echo "You are ready to graduate!"
else
echo "${nwarn} warnings; better double-check, mate"
Remote access with SSH
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The ssh command allows you to connect
to a remote host and work inside its UNIX
environment.
Files can be transfered using the
command.
scp
SSH and SFTP clients exist for most
operating systems, including Windows.
What is Linux and GNU?
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In 1983, Richard M.
Stallman, an MIT worker,
announces the GNU
project.
He was frustrated by the
then recent trend of
UNIX vendors to close
their source code.
GNU is a free software
UNIX clone, which
everyone is free to use,
What is Linux and GNU?
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Linus Torvalds, a student
at Helsinki University,
Finland, started working
on Linux in 1991.
Linux is a free software
operating system kernel,
initially for PC
computers.
Together with GNU, Linux
makes it possible to run
a free UNIX OS on pretty
much any computer.
What is Linux and GNU?
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Since Linux and GNU are free software,
anyone is allowed to package it and
redistribute it.
There are therefore many flavours of
Linux, called Linux distributions. These
include the kernel, the GNU projects,
desktop environments, etc.
Ubuntu is a Linux distribution founded by
Mark Shuttleworth in 1999.
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One of its key objectives is to make Linux easy
to use for beginners.
UNIX/Linux and bash
resources
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A concise Linux/UNIX quick reference is
available is distributed in the exercice
archive (you also have a hand-out)
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A copy of the slides is in the exercise
archive
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http://fosswire.com/post/2007/8/unixlinux-command-cheat-sheet/
http://www.proteo.ca/ws-2010-03.tar.bz2
BASH Programming - Introduction HOWTO
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http://tldp.org/HOWTO/Bash-Prog-Intro-HOWTO.html
Advanced bash scripting guide

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