Developing Bioinformatics
Computer Skills 1
Outline
1. What Bioinformatics Skills?
1. Operating Systems
1. Why UNIX/LINUX?
1. UNIX/LINUX basics
Developing Bioinformatics Computer
Skills
Developing Bioinformatics Computer Skills
Biological research using the web
• NCBI - National Center for Biotechnology Information
• ExPASy - (Expert Protein Analysis System) proteomics
server of the Swiss Institute of Bioinformatics
• Many other examples
Methods -
Web browser - Interactive
API/screen scrapping - Scriptable
ftp - Interactive/scriptable
4
Developing Bioinformatics Computer Skills
• Visualizing protein structures and computing structural
properties
• Predicting protein structure and function from sequence
• Tools for genomics and proteomics
• Automating data analysis
• Building biological databases
• Visualization and data mining
5
What do bioinformaticists do? (1)
• Computer stuff
• Internet stuff
• Database stuff
• Program
• Design user interfaces
• Visualization
6
What do bioinformaticists do ?(2)
• Science!
• Project management
• Interdisciplinary communication
• Data management
• Data analysis
• Data mining
7
What do bioinformaticists do? (3)
• Model development
• Statistical analysis
• Machine learning
8
Outline
1. What Bioinformatics Skills?
1. Operating Systems
1. Why UNIX/LINUX?
1. UNIX/LINUX basics
Various Operating Systems
Comparison of Operation Systems
Name Creator First public Predecessor Latest stable Latest release Cost/Availabili Preferred Target system
release version date ty license1 type
AIX IBM 1986-?-? System V R3 6.1 2007-11-? Bundled with Proprietary Server,
hardware NetApp,
Workstation
FreeBSD The FreeBSD 1993-12-? 386BSD 7.2 2009-05-04 Free BSD Server,
Project Workstation,
NetApp,
Embedded
HP-UX Hewlett- 1983-?-? Unix 11.31 "11i v3" 2007-02-15 $400 Proprietary Server,
Packard Workstation
IBM i IBM 1988-?-? OS/400 V6R1 2008-04-? Bundled with Proprietary Server
hardware
IRIX SGI 1988-?-? Unix 6.5.30 2006-08-16 Bundled with Proprietary Server,
hardware Workstation
GNU/Linux Linus Torvalds, 1992-08-25 Unix4, Minix5 Linux kernel 2008-12-14; Free GNU GPL, See:
et al. 2.6.30; GNU C 2007-10-23 GNU LGPL Comparison
Library 2.7 of Linux
distributions
Mac OS Apple Inc. 1984-01-24 None2 7 9.2.2 2002-05-12 Bundled with Proprietary Works
68K and
PowerPC
Macs; versions
7-9
Mac OS X Apple Inc 2001-03-24 NeXTStep 10.6.0 2009-08-28 $169 Open source Workstation,
core Desktop
NetBSD The NetBSD 1993-05 386BSD 5.0 2009-04-29 Free BSD Server,
Project Workstation
Microsoft Microsoft 1985-11-20 MS-DOS, Windows 7 Propriertary Desktop
Windows OS/2,
Windows
Bioinformatics:
Beyond Using Websites
• You can do a lot of sophisticated bioinformatics using
public websites
• But at some point you may be faced with a LOT of data
• The only solution is to have your own bioinformatics
computer, database, and custom programs.
• Needs more processor power and more hard drive space
than a typical desktop personal computer
Bioinformatics Requires Powerful
Computers
• One definition of bioinformatics is "the use of
computers to analyze biological problems.”
• As biological data sets have grown larger and
biological problems have become more complex, the
requirements for computing power have also grown.
• Computers that can provide this power generally use
the Unix operating system - so you must learn Unix
Unix Runs the Internet
• Unix is a command line interface, used by most large,
powerful computers.
• In fact, Unix is the underlying structure for most of the
Internet and most large scale bioinformatics operations.
• A knowledge of Unix is likely to be helpful in your future
career, regardless of where you pursue it.
Web Server Statistics
Outline
1. What Bioinformatics Skills?
1. Operating Systems
1. Why UNIX/LINUX?
1. UNIX/LINUX basics
Unix Advantages
• It is very popular, so it is easy to find information
and get help
• pick up books at the local bookstore (or street vendor)
• plenty of helpful websites
• USENET discussions and e-mail lists
• most Comp. Sci. students know Unix
• Unix can run on virtually any computer
(IBM, Sun, Compaq, Macintosh, etc)
• Unix is free or nearly free
• Linux/open source software movement
• RedHat, FreeBSD, MKLinux, LinuxPPC, etc.
Stable and Efficient
• Unix is very stable - computers running Unix almost
never crash
• Unix is very efficient
• it gets maximum number crunching power out
of your processor (and multiple processors)
• it can smoothly manage extremely huge
amounts of data
• it can give a new life to otherwise obsolete
Macs and PCs
• Most new bioinformatics software is created for Unix
- its easy for the programmers
UUNIX Philosophy
• Write programs that do one thing and do it well
• Write programs to work together
• Write programs to handle text streams, because
that is a universal interface
Doug Mcllroy (1978)
UNIX Philosophy
1. Rule of Modularity: Write simple parts connected by clean interfaces
2. Rule of Clarity: Clarity is better than cleverness
3. Rule of Composition: Design programs to be connected to other programs
4. Rule of Separation: Separate policy from mechanism; separate interfaces from engines
5. Rule of Simplicity: Design for simplicity; add complexity only where you must
6. Rule of Parsimony: Write a big program only when it is clear by demonstration that
nothing else will do
7. Rule of Transparency: Design for visibility to make inspection and debugging easier
8. Rule of Robustness: Robustness is the child of transparency and simplicity.
Eric, Raymond (2003) The Art of UNIX Programming
UNIX Philosophy (continued)
9. Rule of Representation: Fold knowledge into data so program logic can be stupid and robust
10. Rule of Least Surprise: In interface design, always do the least surprising thing
11. Rule of Silence: When a program has nothing surprising to say, it should say nothing
12. Rule of Repair: When you must fail, fail noisily and as soon as possible
13. Rule of Economy: Programmer time is expensive; conserve it in preference to machine time
14. Rule of Generation: Avoid hand-hacking; write programs to write programs when you can
15. Rule of Optimization: Prototype before polishing. Get it working before you optimize it
16. Rule of Diversity: Distrust all claims for “one true way”
17. Rule of Extensibility: Design for the future, because it will be here sooner than you think .
Unix has some Drawbacks
• Unix computers are controlled by a command line
interface
• NOT user-friendly
• difficult to learn, even more difficult to truly master
• Hackers love Unix
• there are lots of security holes
• most computers on the Internet run Unix , so hackers can
apply the same tricks to many different computers
• There are many different versions of Unix with subtle (or
not so subtle) differences
Open Source Bioinformatics
• Almost all of the bioinformatics software that you need
to do complex analyses is free for UNIX computers
• The Open Source software ethic is very strong among
biologists
– Bioinformatics.org
– Bioperl.org
– Open-bio.org
• New algorithms generally appear first as free software
(a publication requirement)
Free Software
• Linux operating system, MySQL database
• Perl - programming language
• Blast and Fasta - similarity search
• Clustal - multiple alignment
• Phylip - phylogenetics
• Phred/Phrap/Consed - sequence assembly and
SNP detection
• EMBOSS - a complete sequence analysis
package created by the EMBL (like GCG)
Computer Hardware is not Free
• However, you can build a powerful Linux
server/cluster for $20-50K
(depending on how much power you need)
• The real cost is for a person to manage the
machines, install the software, and train scientists
to use it.
• Small schools can join together or affiliate with a
larger neighbor.
Do Biologists have to become
Programmers?
• No, but it can give you a big advantage
• More and more of biology is becoming
computer aided design of experiments,
automated equipment, and computational
analysis of the results
• “I just want to say one word to you ... Databases”
Linux – An Operating System
• A kernel
• Surrounded by utilities and applications
• Strictly speaking, Linux is the kernel of a Unix-
like operating system originally created by
Linus Torvalds in 1991
Timeline
• 1971 - The first edition of the Unix server operating system emerges from
Bell Labs
• 1985 - Richard Stallman publishes his famous "GNU Manifesto", one of the
first documents of the open-source revolution
• 1991 - In August, Torvalds announces his plans to create a free operating
system on the Minix users newsgroup. He modestly notes in his posting that
his OS is "just a hobby”. In October, Linux 0.01 is released on the Internet
under a GNU public license
• 1993 – 100,000 users. Start of Slackware and Debian projects
• 1999 – 15,000,000+ users. RedHat IPO
How Linux Came to Be –
Intentional and Evolutionary
• "Linux, it turns out, was no intentional masterstroke,
but an incremental process, a combination of
experiments, ideas, and tiny scraps of code that
gradually coalesced into an organic whole." - Glyn
Moody, Wired
• “Once the system is at the edge of chaos, we are
bound to see surprises. Linux is one such system that
has come to dazzle us all. “ – Ko Kuwabara
Outline
1. What Bioinformatics Skills?
1. Operating Systems
1. Why UNIX/LINUX?
1. UNIX/LINUX basics
General Unix Tips
• UNIX is case sensitive!!
– myfile.txt and MyFile.txt do not mean the same
thing
– I like to use capital letters for directory names - it puts
them at the top of an alphabetical listing
• Every program is independent
– the core operating system (known as the kernel)
manages each program as a distinct process with its
own little chunk of dedicated memory.
– If one program runs into trouble, it dies, but does not
affect the affect the kernel or the other programs
running on the computer.
The Unix Shell
• You communicate with a Unix computer through a
command program known as a shell.
• The shell interprets the commands that you type on
the keyboard.
• There are actually many different shells available for
Unix computers, and on some systems you can
choose the shell in which you wish to work.
• You can use shell commands to write simple
programs (scripts) to automate many tasks
Simple Programs
• You can use the Unix shell to run programs right from
the command line, or save them as shell scripts
• Simple loops can run a GCG command (such as Blast or
FASTA) on many sequence files
• Then you can check the output files for specific results,
and use if statements to sort or take other actions
Unix Commands
• Unix commands are short and cryptic like
vi or rm.
• Computer geeks like it that way; you will get used to it
• Every command has a host of modifiers which are
generally single letters preceded by a hyphen:
ls -l or mv -R
• Capital letters have different functions than small letters,
often completely unrelated.
• A command also generally requires an argument, meaning
some file on which it will act:
cat -n mygene.seq
Wildcards
• You can substitute the * as a wildcard symbol for any
number of characters in any filename
• If you type just * after a command, it stands for all files
in the current directory:
lpr * will print all files
• You can mix the * with other characters to form a search
pattern:
ls a*.txt will list all files that start with “a” and end in “.txt”
• The “?” wildcard stands for any single character:
cp draft?.doc will copy draft1.doc, draft2.doc, draftb.doc, etc.
Typing Mistakes
• Unix is remarkably unforgiving of typing mistakes
• You can do a lot with just a few keystrokes, but it can be
hard or impossible to undo
• If you have not yet hit „return‟
• The „delete‟ key removes the characters that you just typed
• Which key on your keyboard will actually function as “delete”
will vary depending on the type of computer that you are
using, the Telnet program and the Unix shell that you are
using, or if you are running a specific Unix program
Control Characters
• You type Control characters by holding down
the „control‟ key while also pressing the
specified character
• While you are typing a command:
• ctrl-W erases the previous word
• ctrl-U erases the whole command line
• Control commands that work (almost) any time
• ctrl-S suspends (halts) output scrolling up on your
terminal screen
• ctrl-Q resumes the display of output on your screen
• ctrl-C will abort any program
Getting Help in Unix
• Unix is not a user-friendly computer system.
– While not actively user-hostile, it is perfectly happy to sit
there and taunt you with a blank screen and a blinking >
cursor.
• There is a rudimentary Help system which consists of
a set of "manual” pages for every Unix command
• The man pages tell you which options a particular
command can take, and how each option modifies
the behavior of the command
• Type man and the name of a command to read the
manual page for that command.
> man ls
Reformatting page. Please wait... completed
ls(1) ls(1)
NAME
ls - Lists and generates statistics for files
SYNOPSIS
ls [-aAbcCdfFgilLmnopqrRstux1] [file...|directory...]
STANDARDS
Interfaces documented on this reference page conform to industry standards
as follows:
ls: XPG4, XPG4-UNIX
Refer to the standards(5) reference page for more information about indus-
try standards and associated tags.
OPTIONS
-a Lists all entries in the directory, including the entries that begin
with a . (dot). Entries that begin with a . are not displayed unless
you refer to them specifically, or you specify the -a option.
-A [Compaq] Lists all entries, except . (dot) and .. (dot-dot). If you
issue the ls command as the superuser, it behaves as if you specified
this option.
-b [Compaq] Displays nonprintable characters in octal notation.
-c Uses the time of last inode modification (file created, mode changed,
and so on) for sorting when used with the -t option. Displays the time
of last inode modification (instead of the time at which the file's
contents were last modified) when used with the -l option. This option
has effect only when used with either -t or -l or both.
manaacsba (10%)
More Help (?)
• The man pages, such as they are, give information
about specific commands
• So what if you don‟t know what command you need?
• There is a command called apropos that will give you a
list of commands that contain a given keyword in their
man page header:
apropos password
– The man command with the -k modifier gives a similar result to
apropos
• Get yourself a good "Intro to Unix" book
Unix Help on the Web
Here is a list of a few online Unix tutorials:
• Unix for Beginners
http://www.ee.surrey.ac.uk/Teaching/Unix/
• Introduction to Unix (OSU)
http://8help.osu.edu/wks/unix_course/intro-1.html
• Unix Guru Universe
http://www.ugu.com/sui/ugu/show?help.beginners
• Getting Started With The Unix Operating
System
http://www.leeds.ac.uk/iss/documentation/beg/beg8/beg8.html
Unix Filenames
• Unix is cAsE sEnsItiVe
• UNIX filenames contain only letters, numbers, and the _
(underscore), . (dot), and - (dash) characters
• Unix does not allow two files to exist in the same
directory with the same name.
• Whenever a situation occurs where a file is about to be
created or copied into a directory where another file has
that exact same name, the new file will overwrite (and
delete) the older file.
• Unix will generally alert you when this is about to happen,
but it is easy to ignore the warning.
Filename Extensions
• Most UNIX filenames start with a lower case letter and
end with a dot followed by one, two, or three letters:
myfile.txt
• However, this is just a common convention and is not
required.
• It is also possible to have additional dots in the filename
• The part of the name following the dot is called the
“extension.”
• The extension is often used to designate the type of file.
Some Common Extensions
• By convention:
– files that end in .txt are text files
– files that end in .c are source code in the "C” language
– files that end in .html are HTML files for the Web
– Compressed files have the .zip or .gz extension
• Unix does not require these extensions (unlike
Windows), but it is a sensible idea and one that
you should follow
Files and Directories:
Naming something gives you power over it.
Absolute Addressing
Addressing relative to your home dir.
Addressing relative to your current dir.
Working with Directories
• Directories are a means of organizing your files
on a Unix computer.
– They are equivalent to folders on Windows and
Macintosh computers
• Directories contain files, executable programs,
and sub-directories
• Understanding how to use directories is crucial to
manipulating your files on the Unix system.
Your Home Directory
• When you login to the server, you always start
in your Home directory
• Create sub-directories to store specific projects
or groups of information, just as you would
place folders in a filing cabinet
• Do not accumulate thousands of files with
cryptic names in your Home directory
File & Directory Commands
• This is a minimal list of Unix commands that
you must know for file management:
ls (list) mkdir (make directory)
cd (change directory) rmdir (remove directory)
cp (copy) pwd (present working directory)
mv (move) more (view by page)
rm (remove) cat (view entire file on screen)
• All of these commands can be modified with
many options. Learn to use Unix „man‟ pages
for more information.
Navigation
• pwd (present working directory) shows the name and
location of the directory where you are currently working:
> pwd
/u/browns02
– This is a “pathname,” the slashes indicate sub-directories
– The initial slash is the “root” of the whole filesytem
• ls (list) gives you a list of the files in the current directory:
> ls
assembin4.fasta Misc test2.txt
bin temp testfile
– Use the ls -l (long) option to get more information about each file
> ls -l
total 1768
drwxr-x--- 2 browns02 users 8192 Aug 28 18:26 Opioid
-rw-r----- 1 browns02 users 6205 May 30 2000 af124329.gb_in2
-rw-r----- 1 browns02 users 131944 May 31 2000 af151074.fasta
Sub-directories
• cd (change directory) moves you to another
directory
>cd Misc
> pwd
/u/browns02/Misc
• mkdir (make directory) creates a new
sub-directory inside of the current directory >
ls
assembler phrap space
> mkdir subdir
> ls
assembler phrap space subdir
• rmdir (remove directory) deletes a sub-directory,
but the sub-directory must be empty
> rmdir subdir
> ls
assembler phrap space
Shortcuts
• There are some important shortcuts in
Unix for specifying directories
• . (dot) means "the current directory"
• .. means "the parent directory" - the directory one
level above the current directory, so cd .. will move
you up one level
• ~ (tilde) means your Home directory, so cd ~ will
move you back to your Home.
– Just typing a plain cd will also bring you back to your
home directory
Unix File Protections
• File protection (also known as permissions)
enables the user to set up a file so that only
specific people can read (r), write/delete (w),
and execute (x) it
• Write and delete privilege are the same on a
Unix system since write privilege allows
someone to overwrite a file with a different one.
File Owners and Groups
• Unix file permissions are defined according to
ownership. The person who creates a file is its owner.
• You are the owner of files in your Home directory and all its
sub-directories
• In addition, there is a concept known as a Group.
• Members of a group have privileges to see each other's files.
• We create groups as the members of a single lab - the
students, technicians, postdocs, visitors, etc. who work for a
given PI.
View File Permissions
• Use the ls -l command to see the permissions for all files in a
directory:
> ls -l
drwxr-x--- 2 browns02 users 8192 Aug 28 18:26 Opioid
-rw-r----- 1 browns02 users 6205 May 30 2000 af124329.gb_in2
-rw-r----- 1 browns02 users 131944 May 31 2000 af151074.fasta
– The username of the owner is shown in the third column. (The owner of the files
listed above is browns02)
– The owner belongs to the group “users”
• The access rights for these files is shown in the first column. This
column consists of 10 characters known as the attributes of the file:
r, w, x, and -
r indicates read permission
w indicates write (and delete) permission
x indicates execute (run) permission
- indicates no permission for that operation
> ls -l
drwxr-x--- 2 browns02 users 8192 Aug 28 18:26 Opioid
-rw-r----- 1 browns02 users 6205 May 30 2000 af124329.gb_in2
-rw-r----- 1 browns02 users 131944 May 31 2000 af151074.fasta
• The first character in the attribute string indicates if a file is a
directory (d) or a regular file (-)
• The next 3 characters (rwx) give the file permissions for the owner
of the file
• The middle 3 characters give the permissions for other members
of the owner's group
• The last 3 characters give the permissions for everyone else
(others)
• The default protections assigned to new files on our system is: -
rw-r----- (owner=read and write,
group =read, others=nothing)
Change Protections
• Only the owner of a file can change its protections
• To change the protections on a file use the chmod (change mode)
command
[Beware, this is a confusing command.]
– First you have to decide for whom you will change the access permissions:
» the file owner (u)
» the members of your group (g)
» others (o) (ie. anyone with an RCR account)
– Next you have to decide if you are adding (+), removing (-), or setting (=)
permissions.
• Taken all together, it looks like this:
> chmod u=rwx g+r o-x myfile.txt
This will set the owner to have read, write, and execute permission;
add the permission for the group to read;
and remove the permission for others to execute the file named myfile.txt.
Commands for Files
• Files are used to store information, for example,
data or the results of some analysis.
– You will mostly deal with text files
– Files on the RCR Alpha are automatically backed up to tape
every night
• cat dumps the entire contents of a file onto the
screen.
– For a long file this can be annoying, but it can also be helpful if
you want to copy and paste (use the buffer of your telnet
program)
more
• Use the command more to view at the contents of a file
one screen at a time:
> more t27054_cel.pep
!!AA_SEQUENCE 1.0
P1;T27054 - hypothetical protein Y49E10.20 - Caenorhabditis elegans
Length: 534 May 30, 2000 13:49 Type: P Check: 1278 ..
1 MLKKAPCLFG SAIILGLLLA AAGVLLLIGI PIDRIVNRQV IDQDFLGYTR
51 DENGTEVPNA MTKSWLKPLY AMQLNIWMFN VTNVDGILKR HEKPNLHEIG
101 PFVFDEVQEK VYHRFADNDT RVFYKNQKLY HFNKNASCPT CHLDMKVTIP
t27054_cel.pep (87%)
– Hit the spacebar to page down through the file
– Ctrl-U moves back up a page
– At the bottom of the screen, more shows how much of the file has
been displayed
• More sophisticated options for viewing text files are
available in a text editor (next week).
Copy & Move
• cp lets you copy a file from any directory to any other
directory, or create a copy of a file with a new name in
one directory
• cp filename.ext newfilename.ext
• cp filename.ext subdir/newname.ext
• cp /u/jdoe01/filename.ext ./subdir/newfilename.ext
• mv allows you to move files to other directories, but it is
also used to rename files.
– Filename and directory syntax for mv is exactly the same as for
the cp command.
• mv filename.ext subdir/newfilename.ext
– NOTE: When you use mv to move a file into another directory,
the current file is deleted.
Delete
• Use the command rm (remove) to delete files
• There is no way to undo this command!!!
– We have set the RCR server to ask if you really want
to remove each file before it is deleted.
– You must answer “Y” or else the file is not deleted.
> ls
af151074.gb_pr5 test.seq
> rm test.seq
rm: remove test.seq? y
> ls
af151074.gb_pr5
Moving Files between
Computers
• You will often need to move files between
computers - desktop to server and back
• There are several options
– Sneaker net (floppy, zip, writeable CD, USB)
– E-mail
– Network filesharing
– FTP
FTP is Simple
• File Transfer Protocol is standard for all
computers on any network
• The best way to move lots of data to and from
remote machines:
– put raw data onto the server for analysis
– get results back to the desktop for use in papers and
grants
• Graphical FTP applications for desktop PCs
– On a Mac, use Fetch, RBrowserLite, Filezilla
– On a Windows PC, use WS_FTP, Filezilla
FTP Login
• When you open an FTP program, you connect
to mendel just as you would with a telnet client.
• Your username and password are the same.
• You will automatically end up in your home
directory.
• Put files from you PC to the server, Get files
from the server to your desktop machine.
File system commands
• pwd - report your current directory
• cd - change your current directory
• ls -list contents of directory
• cp - copy
• mv - move (or rename)
• rm -delete a file
• mkdir -make a directory
• rmdir -remove an empty directory
getting recursive
• remove a directory and its contents:
rm -r
• copy a directory and its contents:
cp -r
(un)aliasing
• create shortcuts for yourself
~>alias ll “ls -la”
• Use alias with no arguments to discover
current aliases
~>alias
rm rm -i
ll ls -la
• Type “unalias rm” to remove alias.
PATH: a very important shell variable
>echo $PATH
/home/d/da/darin/bin:/opt/local/bin:/opt/local/bin/pbmutils:/usr/bin
:/usr/sbin:/opt/SUNWspro/bin:/usr/ccs/bin:/opt/local/X11/bin:/usr
/dt/bin:/usr/openwin/bin:/opt/local/gnu/bin:/opt/local/games/bin:
/usr/ucb:./
• If a program (like ls) is in one directory found in your
path, then typing it (~>ls ) will execute it.
• Otherwise you can type the full absolute address to
execute a program (~>/usr/bin/ls )
finding things in your PATH.
• Type “which ” to find the location of the
program which would be run when you type
.
• If you don‟t remember if it was chgrp or chgroup, type
“ch” to get a list of commands that starts
with ch.
• when all else fails, use “find” to find a file.
~>find -name “*.doc”
Shell scripts.
• If you have a bunch of commands you‟d like to
automate, you can put them on separate lines of a file.
Then type “source ” to run the script.
• If the first line of your script looks like
#!
then you can make the script executable. When it
executes, it uses to interpret the
contents of the script.
Login scripts
• Most people have a script that executes when
they log in. It is commonly used to set up one‟s
PATH and aliases.
• Ask someone to help you start your own login
script.
What not to use.
• telnet, ftp, rlogin
• all your data (including your password) is
transmitted plain text over the network.
• from library machines you can use the java ssh
client from a web browser.
using ssh keys
• use “ssh-keygen” to generate a public/private
set of keys. You keep the private key and
append the public key to authorized_keys.
• You can now log in using either your
password or the private key file.
using secure copy: scp
• copy local to remote
scp
user@machine:
• copy remote to local
scp user@machine:
pico - the pine composer
• the simplest visual editor available on
most Unix systems.
• all possible commands displayed at
bottom of screen. (control-somethings)
• no real surprises
STD*
• All terminal programs have:
– standard output, which is usually your screen
– standard input, which is usually your
keyboard
– standard error, which is also the screen
redirect output to a file with >
• If you type who at the prompt, you will get a
list of who is logged into the system.
• If you type who >f, a file named f will be
created and the standard output of who will be
placed in that file instead of to your screen.
> vers >>
• By default, who >f will overwrite the file
f.
• Use who >>f to append to f rather
than overwriting it.
redirecting input from a file
with file2
The output of one program
can be the input to another.
who | sort
• The output of who is sorted and
shown on your terminal screen.
grep
• grep shows only those lines containing
its search pattern.
• To see all lines in a file containing „bob‟:
grep „bob‟ output &
• big_program will not have input!
managing jobs
• To suspend the currently active program, use
.
• To return to the program you just suspended,
type “fg”
• To put the program you just suspended in the
background, type “bg”
To see a list of your programs
running, type “ps”.
>ps
PID TTY TIME CMD
866 pts/1 00:00:00 tcsh
872 pts/1 00:00:00 ps
use kill to end a process
>ps
PID TTY TIME CMD
866 pts/1 00:00:00 tcsh
874 pts/1 00:00:00 cat
875 pts/1 00:00:00 ps
>kill 874
[1] Terminated cat
Linux Commands
UNIX Commands
A command is a program which interacts with the kernel
to provide the environment and perform the functions
called for by the user.
A command can be: a built-in shell command; an
executable shell file, known as a shell script; or a source
compiled, object code file.
The shell is a command line interpreter. The user
interacts with the kernel through the shell. You can write
ASCII (text) scripts to be acted upon by a shell.
Linux Commands
UNIX Shell
The shell sits between you and the operating system,
acting as a command interpreter.
It reads your terminal input and translates the
commands into actions taken by the system. The shell is
analogous to command.com in DOS.
When you log into the system you are given a default
shell.
When the shell starts up it reads its startup files and may
set environment variables, command search paths, and
command aliases, and executes any commands specified
in these files.
Linux Commands
UNIX Shell
The original shell was the Bourne shell, sh.
Every Unix platform will either have the Bourne shell,
or a Bourne compatible shell available.
The default prompt for the Bourne shell is $ (or #, for
the root user).
Another popular shell is C Shell. The default prompt
for the C shell is %.
Linux Commands
UNIX Shell
Numerous other shells are available from the
network. Almost all of them are based on either sh or
csh with extensions to provide job control to sh,
allow in-line editing of commands, page through
previously executed commands, provide command
name completion and custom prompt, etc.
Some of the more well known of these may be on
your favorite Unix system: the Korn shell, ksh, by
David Korn and the Bourne Again SHell, bash, from
the Free Software Foundations GNU project, both
based on sh, the T-C shell, tcsh, and the extended C
shell, cshe, both based on csh.
Linux Commands
Shell Programming
You can write shell programs by creating scripts
containing a series of shell commands.
The first line of the script should start with #! which
indicates to the kernel that the script is directly
executable.
You immediately follow this with the name of the shell,
or program (spaces are allowed), to execute, using the
full path name. So to set up a Bourne shell script the first
line would be: #! /bin/sh
Linux Commands
Shell Programming
The first line is followed by commands
Within the scripts # indicates a comment from that point
until the end of the line, with #! being a special case if
found as the first characters of the file.
#!/bin/bash
cd /tmp
mkdir t
You also need to specify that the script is executable by
setting the proper bits on the file with chmod, e.g.:
$ chmod +x shell_script
Linux Commands
LINUX COMMANDS
File Management and Viewing
Filesystem Mangement
Help, Job and Process Management
Network Management
System Management
User Management
Printing and Programming
Document Preparation
Miscellaneous
Linux Commands
Command Structure
Command
Multiple commands separated by ; can be
executed one after the other
Linux Commands
Help Facilities for Commands
To understand the working of the command and
possible options use (man command)
Using the GNU Info System (info, info command)
Listing a Description of a Program (whatis
command)
Many tools have a long−style option, `−−help', that
outputs usage information about the tool, including
the options and arguments the tool takes. Ex:
whoami --help
Linux Commands
Pipes
An important early development in Unix was the
invention of "pipes," a way to pass the output of
one tool to the input of another.
eg. $ who | wc −l
By combining these two tools, giving the wc
command the output of who, you can build a new
command to list the number of users currently on
the system
Linux Commands
Linux File Management and Viewing
File and Directory management
cd Change the current directory. With no arguments "cd" changes
to the users home directory. (cd )
chmod Change the file permissions.
Ex: chmod 751 myfile : change the file permissions to rwx for owner,
rx for group and x for others
Ex: chmod go=+r myfile : Add read permission for the group and
others (character meanings u-user, g-group, o-other, + add
permission,-remove,r-read,w-write,x-exe)
Ex: chmod +s myfile - Setuid bit on the file which allows the
program to run with user or group privileges of the file.
Linux Commands
Linux File Management and Viewing
There are three such special permissions within Linux. They are:
setuid — used only for applications, this permission indicates that the
application is to run as the owner of the file and not as the user executing
the application. It is indicated by the character s in place of the x in the
owner category. If the owner of the file does not have execute permissions,
the S is capitalized to reflect this fact.
setgid — used primarily for applications, this permission indicates that the
application is to run as the group owning the file and not as the group of
the user executing the application. The setgid permission is indicated by
the character s in place of the x in the group category. If the group owner of
the file or directory does not have execute permissions, the S is capitalized
to reflect this fact.
sticky bit — used primarily on directories, this bit dictates that a file
created in the directory can be removed only by the user that created the
file. It is indicated by the character t in place of the x in the everyone
category. If the everyone category does not have execute permissions, the
T is capitalized to reflect this fact.
Linux Commands
Linux File Management and Viewing
chown Change owner.
Ex: chown : Change ownership
of a file to owner1.
chgrp Change group.
Ex: chgrp : Change group of a file
to group1.
cp Copy a file from one location to another.
Ex: cp file1 file2 : Copy file1 to file2
Ex: cp –R dir1 dir2 : Copy dir1 to dir2
md5sum Prints the MD5 Checksum
Linux Commands
Linux File Management and Viewing
ls List contents of a directory.
Ex: ls, ls –l , ls –al, ls –ld, ls –R
(-rwxrwxr-x 1 juan juan 0 Sep 26 12:25 foo )
|more will list page wise
mkdir Make a directory.
Ex: mkdir : Makes a directory
Ex mkdir –p /www/chache/var/log will create all the
directories starting from www.
mv Move or rename a file or directory.
Ex: mv
Linux Commands
Linux File Management and Viewing
find Find files (find -name -print)
Ex: find /home –name readme -print
(Search for readme starting at home and output full path.)
―/home" = Search starting at the home directory and proceed
through all its subdirectories
"-name readme" = Search for a file named readme
"-print" = Output the full path to that file
locate File locating program that uses the slocate database.
Ex: locate –u to create the database,
locate to find file/directory
Linux Commands
Linux File Management and Viewing
pwd Print or list the present working directory with full
path.
rm Delete files (Remove files). (rm –rf )
rmdir Remove a directory. The directory must be empty.
(rmdir )
touch Change file timestamps to the current time.
Make the file if it doesn't exist. (touch )
whereis Locate the binary and man page files for a
command. (whereis )
which Show full path of commands where given
commands reside. (which )
Linux Commands
Linux File Management and Viewing
File viewing and editing
emacs Full screen editor.
pico Simple text editor.
vi Editor with a command mode and text mode. Starts in
command mode.
gedit GUI Text Editor
tail Look at the last 10 lines of a file.
Ex: tail –f ,
Ex: tail -100
head Look at the first 10 lines of a file. (head
)
Linux Commands
Linux File Management and Viewing
File compression, backing up and restoring
compress Compress data.
uncompress Expand data.
cpio Can store files on tapes. to/from archives.
gzip - zip a file to a gz file.
gunzip - unzip a gz file.
tar Archives files and directories. Can store files and
directories on tapes.
Ex: tar -zcvf - Archive
copy groups of files. tar –zxvf to
uncompress
zip – Compresses a file to a .zip file.
unzip – Uncompresses a file with .zip extension.
Linux Commands
Linux File Management and Viewing
cat View a file
Ex: cat filename
cmp Compare two files.
cut Remove sections from each line of files.
diff Show the differences between files.
Ex: diff file1 file2 : Find differences between file1 & file2.
echo Display a line of text.
Linux Commands
Linux File Management and Viewing
grep List all files with the specified expression.
(grep pattern )
Ex: ls –l |grep sidbi : List all lines with a sidbi in them.
Ex: grep " R " : Search for R with a space on each side
sleep Delay for a specified amount of time.
sort Sort a file alphabetically.
uniq Remove duplicate lines from a sorted file.
wc Count lines, words, characters in a file. (wc –c/w/l
).