HowtoUseCLCatLeibnizSupercomputingCentreStep-by-stepGuideThefollowingisastep-by-stepguidetolaunchCLCgenomicworkbenchonLRZinfrastructure.Thenewmodulecanbeloadedbyusingmodule load CLC/10.1.1 Please change the corresponding command in the screen shots below.

1) Gotohttps://rvs.lrz.de/vnc/

2) Onthetoppanel,clickonthebutton 3) Set your VNC session reserved time to 4 hours and set your VNC

password,pleasenotethisVNCpasswordisnotyourLRZpassword.Oncethe VNC password has been set up, you can use it for upcoming VNCsessionsaslongasyouwant.Forsecurityreasons,youareencouragedtochange your VNC password periodically. Youmaywant to reserve lessthan4hours.ThemaximumrunningtimeforonesessionofCLCgenomicworkbenchis4hours,ifyoureservemorethan4hoursVNCsession,youwon’tbeabletorunCLCgenomicworkbenchafteryoulogin.

4) EnteryourLRZaccountandthecorrespondingpassword,thenclickonLogin.

5) Youwillberemindedthatyoushouldallowpopupsforyourbrowser.

6)Insomesecondsanewwindoworanewtabwillbeopenonyourbrowser,depending on your browser configuration. “noVNC” is a browser based VNCclient implementedusingHTML5CanvasandWebSockets.Youprobablynoticethatthename“noVNC”isasconfusingasitcouldpossiblybe.YouwillbeaskedtoenteryourVNCpassword,whichshouldbesetupbyyouonStep3.

7)AfteryouenteryourVNCpassword,yourVNCsessionwillstart.

8)Ontheleftlowercorner,clickonXTermbutton.Ifyoudon’tfindthisbutton,youneedtoeitherenlargeyourbrowserwindoworscrolldown.

9)Nowyouhaveaterminalwindowatyourdisposal.

10)Typeincommand“moduleloadCLC/10.1.1”(withoutdoublequote).

11)NowCLCgenomicworkbenchhasbeenmadeavailable,youcaneithertypein$CLCorclcgenomicwb10.

12)CLCgenomicworkbenchstartstorun, itwillconnectotheLRZCLCgenomic server. If it doesn’t, you can always connect it to the serveryourself.

13) On the certificate we used to connect the CLC genomic server, wehave used “clc-bio.srv.lrz.de” as the server name. If you connect to theserver by using the ip address of the server, you may get a warningmessage as below. Just click on OK button to start to use CLC genomicworkbench.

15)NowyoucanstarttouseCLCgenomicworkbench.

16)IfyouarenotconnectedtotheCLCgenomicserver,youcanclickon“File”ontheleftuppercorner.Youwillgetapulldownmenulikebelow,pleaseclickon“CLCServerLogin”.

17)ApopupwindowwillbeshownonCLCgenomicworkbench.Youcanfill in your LRZ Linux cluster user name and password (Important, youhave tohavea validLRZLinux clusterusername, yournormalTUMorLMU account does not work. Please confirm with your local systemadmin.https://www.lrz.de/services/compute/antrag/).

18) Tips. When CLC genomic workbench starts to run, it occupies thewhole desktop. In order to resize the window, you can go to the rightuppercorner.Therearethreebuttons,asshowinthefigurebelow.Clickonthemiddlebuttonandthewholedesktopmodewillbedisabled.Nowyou can move the window by clicking and holding the top bar of thewindowandresizethewindowasyouwish.

HowtouploaddatatoLRZCLCgenomicworkbenchToaccessyourdatafromCLCgenomicworkbench,youwillhavetofirstuploadyour data to your LRZ storage. LRZ storage can be accessed from the Linux

cluster(http://tinyurl.com/gpc4qnr).Pleasenote therearedifferent typesofdiskresourcesand file system layout (http://tinyurl.com/nfprutg).Thebasicdirectoriesyoucanuseareyourhomedirectory($HOME,100GByte,backupbyLRZ)andprojectdirectory ($WORK,5TByte, selfbackuppossible). If youhavemore data to analyze, you may be interested in a big data storage option(http://tinyurl.com/jhcpt8n).YouareencouragedtotransferyourdatatoLRZby using Globus (http://tinyurl.com/nrzgzn8) or you can simply transfer byconnectingtoLRZlinuxclusterbyssh(putty inWindows).PleaseconsultyourlocalsystemadministratorsifyouarenotfamiliarwithLinuxsystems.Onceyouremotely transfer your data to LRZ, you can import them from CLC genomicworkbench,gotoFile->Import->StandardImport.

YoucanbrowsetheLinuxfilesystemtoimportyourdataeitherfrom$HOMEor$WORK(/naslx/projects/your_project/your_account).