Introduction to Linux operating system. module Basic Bioinformatics PBF

Transcription

1 Introduction to Linux operating system module Basic Bioinformatics PBF

2 What is Linux? A Unix-like Operating System A famous open source project Free to use, distribute, modify under a compatible licence Produced by a large developer and user community A combination of many projects Cost of commercial development estimated at USD 7 billion Companies often make money by selling: o Support o Training o Custom changes

3 Linux distributions - Ubuntu - Debian - Fedora - Redhat - CentOS - SuSE - Big list at:

4 Linux FUD hard to install, support for different hardware try recent distribution (eg. Ubuntu) it's ugly Gnome, KDE, XFCE... (are they all ugly?) something free can't be good? it works different than Windows some would call this benefit :-)

5 What can it do for you? Full operating system Works well on a variety of hardware, including older hardware You can adapt it to fit your needs Thousands of programs available Secure by design LAMP stack (Linux, Apache, MySQL, PHP) Supports a wide range of programming languages Scalable

6 Where might you find Linux?

7 GPL licence and source code GPL is viral: sharing of changes in GPL software is requirement to the benefit of community When programmers on the Internet can read, redistribute, and modify the source for a piece of software, it evolves People improve it, people adapt it, people fix bugs. And this can happen at a speed that, compared to conventional software development, seems astonishing

8 History GNU project started 1984 to produce a Unix-like OS Founded by Richard Stallman Wrote the GNU manifesto in 1985 outlining philosophy Software that is free means more than free of charge "It means that much wasteful duplication of system programming effort will be avoided. This effort can go instead into advancing the state of the art." By early 1990s many of the GNU OS utilities were complete Meanwhile... Linus Torvalds starts work on the Linux Kernel First version released in 1991 Changes Linux to GPL licence in 1992 Combined with GNU to make an OS The first Distros MCC Interim Linux Softlanding Linux System (SLS) Debian

9 Linux Today High profile adoptions: French Police French Parliament City of Munich Amazon Google Dreamworks (to produce Shrek) Preinstalled: Sub notebooks: EEE & OLPC 99 laptop Dell Server hardware Better support for Linux users

10 Bioinformatics Information technologies used for biology, BLAST, HMMER, CLUSTALW... Lots of data, lots of challenges different programming languages specialized libraries BioPerl BioJava BioPython BioBike (LISP)

11 Case Study: SecondLife Linden Labs uses Linux for SecondLife Servers Uses 2000 servers Servers located in San Francisco and Dallas Uses Debian Linux CTO: Cory Ondrejka said Debian chosen as can scale massively with a small number of IT staff Each geographic area corresponds to a processor running software known as a sim Have plans to use more open source tools

12 Linux on the desktop Different desktop systems available Choose the one you like the best! Can adapt to Mac & Windows styles of operation

13 Naming Files Files are named by naming each containing directory starting at the root This is known as the pathname /etc/conf1 /home/pero/b

14 Some Special File Names Some file names are special: / The root directory (not to be confused with the root user). The current directory.. The parent (previous) directory ~ My home directory Examples:./a same as a../pero/x go up one level then look in directory pero for x

15 Linux Command Basics To execute a command, type its name and arguments at the command line ls -l /etc Command name Options (flags) Arguments

16 Command: ls List directory contents ls has many options -l long list (displays lots of info) -t sort by modification time -S sort by size -h list file sizes in human readable format -r reverse the order man ls for more options Options can be combined: ls -ltr

17 Redirecting Output The output of a command may be sent (piped) to a file: ls -l > output > is used to specify the output file

18 Redirecting Input The input of a command may come (be piped) from a file: wc < input < is used to specify the input file

19 General Syntax: * * can be used as a wildcard in unix/linux

20 File Commands cp <fromfile> <tofile> Copy from the <fromfile> to the <tofile> mv <fromfile> <tofile> Move/rename the <fromfile> to the <tofile> rm <file> Remove the file named <file> mkdir <newdir> Make a new directory called <newdir> rmdir <dir> Remove an (empty) directory

21 Other commands whoami print the name of the current user id print information about the current user who print a list of other users who are logged in date print the current date and time on the server cal print a calendar for the current month echo print a text string to the screen

22 Where to Get Help You can always read the manual! To see the man page for the ls command: man ls

23 Windows console Start -> Run -> cmd d: cd <path> dir > dirlist.txt help dir notepad exit

24 Download PuTTY file: putty.exe host: bioserv7.bioinfo.pbf.hr

25 Linux commands whoami print effective userid ls list directory contents ls a man ls an interface to the on-line reference manuals whatis ls display simple manual page descriptions pwd print name of current/working directory cd change directory