VIEWS: 30 PAGES: 114 POSTED ON: 12/2/2011
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 <to where> - change your current directory • ls <directory> -list contents of directory • cp <old file> <new file> - copy • mv <old file> <new file> - move (or rename) • rm <file> -delete a file • mkdir <new directory name> -make a directory • rmdir <directory> -remove an empty directory getting recursive • remove a directory and its contents: rm -r <directory> • copy a directory and its contents: cp -r <directory> (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 <enter>) will execute it. • Otherwise you can type the full absolute address to execute a program (~>/usr/bin/ls <enter>) finding things in your PATH. • Type “which <command>” to find the location of the program which would be run when you type <command>. • If you don‟t remember if it was chgrp or chgroup, type “ch<control-d>” to get a list of commands that starts with ch. • when all else fails, use “find” to find a file. ~>find <start dir> -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 <file>” to run the script. • If the first line of your script looks like #!<program name> then you can make the script executable. When it executes, it uses <program name> 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 <source file> user@machine:<path> • copy remote to local scp user@machine:<path> <source file> 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 < • The program sort will sort its standard input and then print it on standard out. • To sort the lines of file1 and display: sort < file1 • To sort the lines of file1 and save in file2: sort < file1 > 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‟ < file1 The cat command • the arguments to cat are concatenated together and displayed on stdout. To view a file: cat file1 • if no arguments, cat puts on stdout whatever you type on stdin, so this does the same thing: cat < file1 To start a process in the background, use “&”. • example: big_program > output & • big_program will not have input! managing jobs • To suspend the currently active program, use <control-z>. • 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  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 <Options> <Arguments> 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 <directory path>) 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 <owner1> <filename> : Change ownership of a file to owner1. chgrp Change group. Ex: chgrp <group1> <filename> : 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 <directory name> : 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 <source> <destination> Linux Commands Linux File Management and Viewing find Find files (find <start directory> -name <file 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 <file/directory> 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 <directory/file>) rmdir Remove a directory. The directory must be empty. (rmdir <directory>) touch Change file timestamps to the current time. Make the file if it doesn't exist. (touch <filename>) whereis Locate the binary and man page files for a command. (whereis <program/command>) which Show full path of commands where given commands reside. (which <command>) 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 <filename> , Ex: tail -100 <filename> head Look at the first 10 lines of a file. (head <filename>) 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 <destination> <files/directories> - Archive copy groups of files. tar –zxvf <compressed file> 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 <filename/directorypath>) 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 <filename>).
Pages to are hidden for
"Unix"Please download to view full document