Linux Introduc)on to Linux and Unix and the …on to Bioinformacs online course: IBT Linux | Amel Ghouila Linux Introduc)on to Linux and Unix and the command line Introduc)on to Bioinformacs

Introduc)ontoBioinforma)csonlinecourse:IBTLinux|AmelGhouila

LinuxIntroduc)ontoLinuxandUnixandthe

commandline

Introduc)ontoBioinforma)csonlinecourse:IBT


LearningObjec)ves

① UnderstandtheUnixfilestructure② Understandfullvsrela5vepaths:whenand

howtousethem③ Learnhowtocreatedirectoriesandnavigate

throughthefilestructure④ Learnsomeusefulshortcuts


LearningOutcomes

① Beabletocreateafilestructure② Beabletonavigatethroughthefilestructure③ Beabletocreatetextfilesandviewtheir

content④ Beabletousesimpleshortcuts


Introduc)ontoLinuxandUNIX

4

Part1


WhatisLinux?

•  UNIXisanOpera5ngSystem(OS)ini5allydevelopedinthe1960.

•  There are many different versions of UNIX, thatsharecommonsimilari5es.

•  Themostpopularvarie5esofUNIXareSolaris,LinuxandMacOS.

•  UNIX systemshaveagraphicaluser interface (GUI)makingthemeasiertouse.


LinuxvsUnix

•  Linux is a “clone” of the original Unix but doesn’tcontainitscode

•  Linux is free and open source, the original Unix isnot(butsomeofitsderiva5vesare)

•  Allcommandlinesworkthesameonboth


•  Linuxisfreeandthemostpopulardistribu5onsareUbuntu,Fedora/RedHat,Mandriva,etc.

•  Lowcostandverystablesystem•  MostsecureOS•  Bestmul5-userandmul5taskingOS•  Theworld’sfastestsupercomputersrunLinux•  FastdevelopingOS(manydevelopers)

VerypopularasserversOS

7

WhyLinux?


Linuxdistribu)ons

•  DifferentLinuxdistribu5onsareavailablehap://distrowatch.com/

•  Ubuntudistribu5oniseasyandconvenienttouseforbeginners

•  AsimpleguidetoinstallUbuntuinyourmachine:hap://www.ubuntu.com/download/desktop/install-ubuntu-desktop


Adaptedfrom:www.usna.edu

AccessibleviatheTerminal

Thecoreopera)ngsystem

ProgramsandsoJwares


10

TheTerminal

•  Aterminalreferstoawrapperprogramwhichrunsashell

•  TherearemanydifferentUnixshells,themostpopularshellforinterac5veuseincludeBash:thedefaultonmostLinuxinstalla5ons


ShellpromptMachinename

Username Eventhoughitisacommandlineinterface,themouseiss5llhandy(scroll,copy,paste,etc.)

11

TheTerminal


File-systemunderUNIX

12

Part2


home dev bin etc Configura5onfiles

Devicefiles

Usershomedirectories

Essen5alusercommandsbinaries

Rootdirectoryoftheen5refilesystem

WatsonCrick

Desktop Documents

Sanger

IBT2017

Linux

Session1 Session2

Genomics

Wastsonfiles

13

Linuxfilesstructure


home

Watson

Desktop Documents IBT2017

Linux

Session1 Session2

Genomics

file1 file2

Directoriesfiles

14

fileX

Ordinaryfiles


Homedirectoryandworkingdirectory

•  When you first log in on aUNIX system, theworkingdirectoryisyourhomedirectory.

•  Whileworkingyouwillbeassociatedtoonedirectorycalledtheworkingdirectoryorthecurrentdirectory

•  An abbrevia5on of theworking directory is displayedaspartofthepromptonyourterminal

•  The command pwd gives the absolute path of theworkingdirectory


Whatisapathorapathname?

•  A path locates a given file in the systemhierarchy

•  Anabsolutepath in thefile systemhierarchyforagivenfileorfolderdescribestheparentsallthewayuptotheroot

•  A rela5ve path describes the path to the filestar5ngfromthecurrentworkingdirectory


~(yourhomedirectory)

•  ~referstothehomedirectoryinagivenfilesystem

•  The5lde~charactercanbeusedtospecifypathsstar5ngatyourhomedirectory


Absoultepath?/

home

Watson


Linux

Session1 Session2

Genomics

file1 file2

Thefullpathtofile1is:/home/Watson/IBT2017/Linux/Session1/file1


Absoultepath?/

home

Watson


Linux

Session1 Session2

Genomics

file1 file2

/

/home

/home/Watson

/home/Watson/IBT2017

/home/Watson/IBT2017/Linux

/home/Watson/IBT2017/Linux/Session1

/home/Watson/IBT2017/Linux/Session1/file1


Everydirectoryhastwospecialsub-directories:

u . (dot): thecurrentdirectory

u .. (dot-dot): theparentdirectory

IBT2017

Genomics Linux

Session2Session1

. ..

20

RefertotheparentandcurrentdirectoriesRefertotheparentandcurrent

directories


/

home

Watson


Linux

Session1 Session2

Genomics

file1 file2

./Linux

./Linux/Session1

./Linux/Session1/file1

Currentworkingdirectory

. referstothecurrentdirectory

21

RefertotheparentandcurrentRela)vepath?


Firsttestoftheterminal

•  OpentheTerminalonyoursystem•  Theshellpromptwillappear

Ok,let’strysometyping!


Crea)ngdirectoriesandnaviga)ngthroughthefilestructure

Part3


Commandsformanipula)ngdirectories

mkdir Makedirectory:createsanewdirectory

rmdir Removesadirectory

pwd Displaystheabsolutepathofthecurrentworkingdirectory

cd Changedirectory:allowsmovingfromonedirectorytoanother

ls Listsadirectorycontent


pwdcommand

•  pwd:printworkingdirectory•  Displaystheabsolutepathofyourcurrentloca5oninthefilesystem

•  Trypwdonyourterminal•  Youshouldsee:/home/YourUsername


lscommand

•  lsliststhecontentofthecurrentdirectorybydefault

•  Commandstructurels[OPTION][dirname]•  Someusefulop5ons:

•  -l:showssizes,modifieddateand5me,fileorfoldernameandowneroffileandpermissions•  -a:Listallfilesincludinghiddenfilestar5ngwith‘.’•  -lh:showssizesineasierreadableformat•  -R:recursivelylistssub-directories•  -lS:sor5ngbyfilesizes


Createadirectory

•  mkdir:makesadirectory•  Commandstructure:mkdirdirname[path]

•  mkdirdirname:wouldcreateadirectorywiththespecifieddirname

•  Thenewcreateddirectorywillbecreatedinyourcurrentworkingdirectory

•  Ifyouwanttocreateitelsewhere,youhavetospecifythepath:mkdirdirnamepath


Commandsbasicstructure

command[–op5ons][arguments]Example:

ls–lh/home/Watson/IBT2016 pwd mkdirTest1


WhatyoushouldknowaboutfilenamesinLinux

•  No real dis5nc5on between the names ofordinaryfilesandthenamesofdirectoryfiles.

•  No twofiles in the samedirectory canhave thesamename.

•  Files in different directories can have the samename.

•  Linux is case-sensi5ve: Sanger, sanger andSANGERaredifferentandwouldrepresentthreedis5nctfiles.

•  In most cases, file extensions are op5onal(.txt,.exe,etc.)


Moveinthefilessystem

•  cd:changetheworkingdirectory•  Commandstructure:cd<path>

•  Thepathnameofthedirectoryyouwanttomovetoshouldbespecified

•  Youcanspecifyeithertheabsolutepathortherela5vepath


Moveinthefilessystem:example

/

home

Watson

IBT2017Currentworking

directory

•  MovetoWatsondirectory

1.  cd/home/Watson2.  cd../..3.  cd..+cd..

•  MovetoGenomicsdirectory

1.  cd/home/Watson/IBT2017/Genomics2.  cd../Genomics3.  cd..+cdGenomics

LinuxGenomics


Removeadirectory

•  rmdir:removesadirectory•  Commandstructure:rmdirdirname[path]•  Itwouldremovethedirnamedirectory•  Thedirectoryshouldbeinyourcurrentworkingdirectory

•  Ifyouwanttoremoveitfromelsewhere,youhavetospecifythepath:rmdirdirnamepathtothedirectory

•  rmdirworksifthereisnocontentsinthedirectory


Removeadirectory

•  rmdirworksifthereisnocontentsinthedirectory

•  Ifthedirectorycontainsfilesorsub-directories,anerrormessagewillappear:“Directorynotempty”

•  Thereisanop5ontoremove-r,whichstandsforrecursive,thatwillrecursivelyremoveadirectoryanditscontents


Howtogethelpforacommandfromtheterminal?

•  mancommandnamedisplays


Part4

SomeusefulshortcutsandLinks


UsefulLinks

•  cd:cdfollowedbynothingwillchangetheworkingdirectorytoyourhomedirectory

•  cd~user_name:movestothespecifieduserhomedirectory


Linux,someusefulCLIkeycombina)ons

•  Ctrl+A:movethecursortothebeginningofthecommandline

•  Ctrl+C:endarunningprogramandreturntotheprompt

•  Ctrl+D:logoutfromthecurrentshellsession:equivalenttoexit

•  Tab:autocompleteafilename•  TabTab:displayscommandcomple5onpossibli5es

•  Ctrl+L:cleartheterminal


Thanks

•  ShaunAron&SumirPanji