INTRODUCTION TO UNIX

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1 INTRODUCTION TO UNIX Vivek Krishnakumar JCVI Genmic Science and Leadership Wrkshp Presented n: 05/26/2016

2 Overview What is Unix? Where is it used? Biinfrmatics and Unix Paradigm f Lcal Cmputers vs Remte Servers Unix Cmmand Line Interface (CLI) Issuing cmmands Brief verview f Directry structures Brief verview f Unix File permissins General Unix rules FIN Skim thrugh Supplementary slides (will serve as reference material fr hands-n)

3 WHAT IS UNIX? Prtable, multi-tasking, multi-user, time-sharing perating system It is the leading perating system f chice fr servers such as supercmputers. Mre than 90% f the tp 500 fastest cmputers are based n Unix. Available fr free (Open Surce) r nearly free: Unix-like OSs like Linux, Minix, BSD, Andrid Mac cmputers are related t Unix because they are als based n Unix Depending n the purpse f the Unix machine, it may r may nt have a Desktp envirnment that we are familiar with n ur persnal cmputers. Unix uses X Windw System t prvide the Desktp envirnment.

4 Surce:

5 BIOINFORMATICS AND UNIX Many biinfrmatics cre tls are written fr use with Unix BLAST, CLUSTALW, PHRAP, etc. Many web applicatins are als supprted n web servers hsted n Unix-based machines Unix supprts develpment and use f sftware using many different prgramming languages (Pythn, Perl, Java, R, C, C++). Multiple users can lg in at the same time A user lgging in ver the netwrk can d just abut anything a user sitting in frnt f the cmputer can d. Which means it can multitask (run many prcesses in parallel).

6 APPLICATIONS AND SERVERS Server/Remte Cmputer (Unix) BLAST DB WEB Data files SSH WEB SCP App Service Terminal IGV Data files Windw Thanks t Manpreet Katari (NYU) fr slide(s) Persnal/Lcal Cmputer (Mac/Windws/Unix)

7 UNIX COMMAND LINE INTERFACE (SHELL) Users cmmunicate with the OS via the shell The shell interprets the cmmands typed by the user n the keybard Different shells are available fr Unix systems sh - burne shell csh - C shell bash - burne-again shell zsh - Z shell Yu can type the cmmands directly at the shell r build scripts t accmplish certain tasks * During the wrkshp hands-n sessins, we will be wrking with the bash shell, ne f the mst ppular unix shells.

8 ISSUING COMMANDS The cmmand prmpt (signified by a $ symbl) requires that yu enter/type the cmmand fllwed by arguments (if necessary) If there is an utput t the prgram, it usually prints it n the screen, ften referred t as standard utput (stdut)

9 DIRECTORY STRUCTURES IN UNIX Directries are used t rganize files. Analgus t flders in Windws and Mac OS. Imprtant diretries: / - 'rt /hme Persnal user directries /bin - Cmmn prgrams, shared by the system and users /lib - Library files required by the prgrams /usr - Prgrams, libraries, dcumentatin etc. fr all user-related prgrams /mnt - Munt pint fr external file systems /tmp - Temprary space; cleaned up peridically and n rebt Reference:

10 GRANULAR FILE PERMISSIONS READ (R), WRITE (W), EXECUTE (X) Learn mre:

11 GENERAL UNIX RULES Unix is CaSe sensitive file.txt and File.txt are nt ne and the same This applies t the cmmands as well (e.g.: ls is nt Ls) In any directry, yu can have nly ne file with a given name Filenames shuld nly cntain letters [A-z], numbers [0-9], underscres [_], dts [.] and hyphens [-]. Abslutely n-spac3s_what_s.ever File extensins are ptinal but recmmended because mst prgrams fllw sme standards. Example:.txt - File cntaining plain text data.sh - File cntaining cmmands t be executed.pl/.py - Perl/Pythn scripts

12 Fllwing slides are fr yur reference T be used in the Hands-On Sessin(s)

13 GETTING HELP IN UNIX Unix is nt a very user-friendly system The whatis database prvides a descriptin fr each cmmand: If yu dn't knw what cmmand t use, search by keywrd: $ aprps KEYWORD Similar t a 'User Manual' which yu get with husehld appliances and electrnic devices, Unix als ffers help in the frm f "manual" pages fr every cmmand These man pages describe all available cmmand line ptins and hw each ptin mdifies its behavir Fr help at the shell, type man fllwed by the name f the cmmand: $ man ls

14 AUTO-COMPLETION & HISTORY Unix ffers file/directry name aut-cmpletin When typing ut a file/directry name partially, hit the <tab> key fr pssible matches Unix shell tracks the cmmand histry (upt a certain limit, size can be cntrlled by envirnment variables). Get the last 5 executed cmmands $ histry tail -n5 Re-execute the 25th cmmand $!25 $ cd /exprt

15 NAVIGATING THRU DIRECTORIES pwd - Print the present wrking directry (smetimes yur pwd will be visible at the prmpt) cd DIR - Change t specified directry cd.. - Change directry t ne level up cd r cd ~ - Change directry t the user hme. (current directry).. (parent directry) ~ (hme directry) mkdir DIR - Make a directry rmdir DIR - Remve a directry (nly if it is empty)

16 VIEWING FILE CONTENTS less FILE - Page thrugh a file (alternative t mre). less allws yu t navigate up/dwn with the arrw keys n the keybard. space t page dwn. Esc t exit cat FILE - Dump the entire file cntents t standard ut (stdut) wc FILE Perfrm a wrd cunt n the file(s) (line, wrd, byte cunt) head FILE - Shw first 10 lines f a file (-n t cntrl the number f lines) tail FILE - Shw last 10 lines f a file (-n t cntrl the number f lines)

17 PIPING & FILE REDIRECTIONS Unix allws serializing cmmands using the pipe (I) peratr and redirectin f the standard input/utput streams (>, >> and <) Retrieve lines 15 thrugh 20 f the file > Redirect standard utput (stdut) t file >> Append stdut t file < Redirect standard input (stdin) t cmmand cat Cncatenate t stdut

18 PATTERN SEARCHING (GREP) Searches thrugh a file r standard input (stdin) stream fr patterns All matched lines are returned t standard utput (stdut) Syntax: grep [-ptins] <pattern> <file name> Optins: -c - Cunt the number f matches -i - Make search case-insensitive -v - Invert-match Prviding search cntext: -A4 - extract 4 lines after match -B3 - extract 3 lines befre match -C4 - extract 4 lines befre and after match Pattern (Plaintext string r Regular Expressins) ^ - Specify the beginning f a line $ - Specify the end f a line Nice intrductry article t using regular expressins with grep

19 CUTTING & PASTING cut - Extract specific clumns frm a multi-clumn delimited file Syntax: cut [-ptins] FILE Available ptins: -f1,2,3,6 - Specify the index f the clumns -d"," - specify the input clumn delimiter --utput-delimiter="\t" - used t mdify the utput delimiter paste - Jin multiple files in desired rder Syntax: paste FILE1 FILE2... It writes lines which cnsists f sequentially crrespnding lines frm each input FILE[12...]

20 SORTING & UNIQ-ING srt is a prgram used t srt the lines f standard input Syntax: srt [-ptins] FILE Several ptins available (investigate using man r invke --help): -k2,2 - srt file by 2nd clumn -n - srt by numeric rder -r - reverse the srt rder -t; - specify an alternative field separatr -u - print nly unique (uniq) lines uniq is a prgram used t discard all but ne successive identical lines frm the input Syntax: uniq [-ptins] FILE Available ptins: -c - prefix line with cunt f number f ccurrences -d - print ut nly duplicate lines

21 STRING SUBSTITUTION USING SED sed (stream editr) is used t mdify input streams (stdin r file cntents) Syntax: sed [-ptins] PATTERN FILE Sme example cmmands $ sed s/exn/cds/ ld.gff > new.gff There are fur parts t this substitute cmmand: s Substitute cmmand /../../ Delimiter exn Search Pattern CDS Replacement string Changes made nly t the first ccurrence f the pattern n each line Sme mre examples: $ sed s/exn/cds/ -i ld.gff # in-place change $ sed s/exn/cds/g -i ld.gff # change glbally $ sed '1/50 s/exn/cds' ld.gff # mdify first 50 lines Enclse the substitute cmmand within qutes when dealing with cmplex patterns Cmprehensive sed manual:

22 FINDING/LOCATING FILES Syntax: find PATH EXP Searches recursively thrugh all subflders Optins: -name specify file/flder name -iname fr case insensitive search -type f finds nly files and -type d nly flders -print will print ut that path f the file(s) fund -exec allws yu t execute a cmmand n the files fund Examples $ find /hme/train01 -name file.txt $ find. -type f -iname "*.sh" $ find. -name "rc.cnf" -print $ find. -name "*.sh" \ -exec chmd +x '{}' \;

23 USEFUL KEYBOARD SHORTCUTS Manipulate the current cmmand Ctrl + A G t the beginning f the cmmand prmpt line Ctrl + E Ctrl + L Ctrl + U Ctrl + K Ctrl + W Search Ctrl + R Jb Cntrl Ctrl + C Ctrl + Z Ctrl + D G t the end f the cmmand prmpt line Clears the screen, similar t the clear cmmand Clears the line befre the cursr psitin Clears the line after the cursr psitin Deletes the wrd befre the cursr psitin Lets yu search thrugh previusly used cmmands Kills the currently running jb Puts the current jb int a suspended state Exits the current shell

24 JOB CONTROL The jbs cmmand shws yu all the jbs running in the current terminal (with status inf) $ jbs [1]- Stpped vi run.sh [2]+ Stpped less file.txt Each jb is given a number. They can be run in the backgrund r fregrund: $ bg 2 # Run in bg and gives yu cntrl f the shell $ fg 2 # Run in the fregrund Launch a jb in the backgrund directly like s: $ run.sh & List all running jbs (filter by user if necessary): $ ps -u train01 PID TTY TIME CMD pts/21 00:00:00 vi pts/21 00:00:00 less Kill any jb (by PID, name r jb number) $ kill $ kill %2 $ killall less

25 QUESTIONS?

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