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CLC Genomics Server

1. CLC Genomics Server User manual Manual for CLC Genomics Server 4 5 Windows Mac OS X and Linux June 12 2012 This software is for research purposes only CLC bio Finlandsgade 10 12 DK 8200 Aarhus N gt Denmark ke il bio Contents 1 Introduction 4 2 Using the server from a CLC Workbench 6 2 1 Installing relevant plug ins in the Workbench 2 2 ae eee e enn ene sn 6 2 2 Log into the server ced cos tee bee we ewe Gwe oe we ee RE we 6 2 3 Browsing and searching data from the workbench 206 7 2 4 Running analyses on the server 2 2 a ee ee se 8 2 5 Accessing files on and writing to areas of the server filesystem 9 2 6 Monitoring processes noaoo ee a 11 3 Using a web browser as client 13 3 1 Browsing and searching data 2 444566 ee eee eRe EE HSE EE Es 13 3 2 Upload and download s s sss ss arer errin be Hee eee KE ad 14 Chapter 1 Introduction The CLC Server is the central part of CLC bio s enterprise solutions You can see an overview of the server solution in figure 1 1 The basic idea is that you can have the Server store data and run jobs centrally and thereby off load personal and typically smaller computers For the user the difference between working just with a Workbench and working with a Workbench and a server is very small All the mechanisms for managing data using the tools and visualizing the data are the same This user manual is intended to show how to
2. will allow you to enter the host and port for the server as shown in figure 2 2 In addition you can choose to save user name and password and automatically log in to the In order to install plug ins on Windows Vista the Workbench must be run in administrator mode Right click the program shortcut and choose Run as Administrator Then follow the procedure described below CHAPTER 2 USING THE SERVER FROM A CLC WORKBENCH 7 amp CLC Server Login User name testuser H Advanced Figure 2 1 Expand the login dialog by clicking Advanced CLC Server Login User name bestuser Password Advanced Server hast hostname Server port 7777 Save user name and password Automatic login Figure 2 2 Specifying host and port server when the Workbench starts Note that you need to get information used to log in from your server administrator When you press Login the Workbench connects to the server You will see a progress bar in the login dialog If the login is successful the dialog will disappear and you will be able to use the server as described below 2 3 Browsing and searching data from the workbench Once you have logged in the data locations on the server are shown in the Navigation Area see figure 2 3 Once logged in the server data locations can be used in the same way as local data locations We refer to the users manual of the Workbench for information about using the Navigation Are
3. Figure 2 7 Deciding source for high throughput sequencing data files presented with a file browser for the selected parts of the server file system that the administator has configured as an Import export location See figure 2 8 g SOLID on Server 1 Choose import files ee dk 2 location Navigation Area Selected Elements 2 2 Import Files and options 5 Server safe locations SHIRAZ_20080320_MP_2_Sample1_R3 csfasta NGS SHIRAZ 20080320 MP 2 Sample1_F3 csfasta H ticket data B k data a benchmark data w databases knowngenes gtf a program FH project data a temporary_data itest data a ticket data project data General options Read orientation _ Paired reads Discard read names Discard quality scores Figure 2 8 Selecting files on server file system Note Import Export locations should NOT be set to subfolders of any defined CLC file or data locations CLC file and data locations should be used for CLC data and data should only be added or removed from these areas by CLC tools By definition an Import Export folder is meant for holding non CLC data for example sequencing data that will be imported data that you export from the Genomics Server or blast databases Note that your server administrator needs to configure the server to import files directly from the server file system 2 6 Monitoring processes Just as for processes running locally you will be able to monitor process ru
4. analysis is performed on the server This means that you can close the Workbench or disconnect the computer from the server and the analysis will continue to run When you log in after the analysis is done you will get a notification in the Workbench A special case is the tools for importing high throughput sequencing data on the server only for Genomics Workbench and Server Depending on your choice the first part of the import is uploading the data to the server and during this part the Workbench has to maintain connection to the server If you try close the Workbench during upload you will get a warning dialog The upload runs as a local process in Processes tab in the lower left corner and when the upload is done a new process is started that has a server icon and runs on the server If you need help on the analyses themselves please click the Help 7 button in the dialog That will take you to the relevant part of the user manual of the Workbench 2 5 Accessing files on and writing to areas of the server filesystem There are circumstance when it is beneficial to be able to interact with non CLC files directly on your server filesystem A common circumstance would be importing high throughput sequencing data from folders where it is stored on the same system that your CLC Genomics Server is CHAPTER 2 USING THE SERVER FROM A CLC WORKBENCH 10 running on This could eliminate the need for each user to copy large sequence data fi
5. take advantage of the server as a user For information about administrating the server please see the Administrator Manual The CLC Genomics Server is shipped with the following tools and analyses that can be started from the CLC Genomics Workbench e Import e Trimming e Sequencing Data QC Report e Map reads to reference e De novo assembly e All tools for re sequencing analysis e Download genomes e All tools for track management and filtering e Create detailed mapping report e ChIP Seq e RNA Seq e Extract and count small RNA e Annotate small RNA CHAPTER 1 INTRODUCTION 5 Clients CLC Genomics m Ee Browser Workbench UOI EZIWO SN 2 0 amp Job Nodes i Scalability i 8 ses S amp S Sa Bioinformatics Database database schemas Data backend Figure 1 1 An overview of the server solution from CLC bio Note that not all features are included with all license models e Process tagged sequences de multiplexing e External applications integrating with 3rd party programs on the server e BLAST creation of databases download of databases and running BLAST against local data or NCBI Find primer binding sites Annotate secondary peaks Sanger data Extract sequences e Additional alignments plug in The functionality of the CLC Genomics Server can be extended by installation of Server plug ins The available plug ins can be found at http www clcbio com server_plugin
6. a click the location and press Fi on the keyboard to get context help You may also wish to have a look at the search chapter Searching your data in the workbench user manual press F1 and look for Searching your data It is possible to have both local and server locations added at the same time This means that you can work on e g temporary sequences located on your own computer and then when you have more complete results you can drag the elements to a folder in the server location CHAPTER 2 USING THE SERVER FROM A CLC WORKBENCH H E nobackup a pa CLC Data H E My Sgl clodbi storage office Hg Oracle orcl storage office EEG presentation Hg test H E training el Er tutorials Figure 2 3 Three server locations on the server appears in the Navigation Area There are also five local file locations that exist in the Workbench independent of the server 2 4 Running analyses on the server The tools available on the server are listed in the introduction see section 1 For more information on the tools please see the manual for CLC Genomics Workbench at http www clcbio com usermanuals or click the Help button in the dialogs that are shown when you run the tools The high throughput sequencing data import tools are also available on the server as shown in figure 2 4 rew Toolbox Workspace Help lee aE GE GR import MGS Import Export Greohics Frnt Undo Redo bee RE Roche 454 R Illu
7. ats as shown in figure 3 3 Clicking one of the buttons will start the download of the sequence in the selected format You can also put data into the server data location select the folder where you want the data to be and click Upload E see figure 3 4 Click the Browse button to select a file and click Upload File The server will automatically recognize the file format and interpret the file If this does not work as expected you can try to select the file format in the drop down list above the Upload File button where it says Automatic in figure 3 4 CHAPTER 3 USING A WEB BROWSER AS CLIENT logout root CLC Science Server 9 Element Info LI History Sequence Text NEN ES Upload 669 Admin XX aTPSal genomic segue XX ATPBal mRNA Choose download format for ATPSa1 ATP8al Download as CLC clc Cloning Primers Download as DNA Strider files str strider Protein analyses Download as FASTA fa fsa fasta Protein orthologs Download as GenBank gbk gb gp amp RNA secondary structu F YED bv fy ly EF lt gt Download as Nexus data nxs nexus e Download as PIR pir lt enter search term gt EN Download as SwissProt swp Figure 3 3 Downloading a sequence from the server logout root CLC Science Server F Element Info LI History Sequence Text F Download BF Unload XE ATPSal genomic
8. er address eQ X 3 A El B http fservertest clcbio com 7777 V IG Google 5 CLC Science Server Figure 3 1 The web interface of the server 3 1 Browsing and searching data To the left you will see the data locations connected to the server You can browse the folder hierarchy of the data location When you click an element in the tree a number of options are available e Click the Element Info tab to see the properties of this element Note that you can edit the information in this view e Click the History Li tab to see the history of this element 13 CHAPTER 3 USING A WEB BROWSER AS CLIENT 14 e Click the Sequence Text tab to see a textual representation of this element only works for Sequences An example of a protein sequence in the text view is shown in figure 3 2 CLC Science Server XE ATPBal mRNA 1 A F Element Info LI History RESTEN EEG Download FS Upload 2 9 Admin XX ATP8al mRNA AW ATPBal Clonin LOCUS ATPSal 1149 aa linear ROD OS FEB 2Z008 NI 9 DEFINITION Probable phospholipid transporting ATPase IA Chromaffin granule E primers ATPase II ATPase class I type SA member 1l men ACCESSION P70704 Protein analyses VERSION P 70704 1 GI 8134322 D A i DBSOURCE swissprot locus ATSAl MOUSE accession P70704 J Protein orthologs Sieh ocean D RNA secondary structe created May 30 2000 sequence updated Feb 1 1997 J Seque
9. figuration Remove Path mnt test_cledata configuration Remove Path usr local cledata configuration Remove Path mnt CLCTmpArea configuration HTTP settings Audit log settings Figure 2 6 Defining source folders that should be available for browsing from the Workbench Press the Add new import export directory location button to specify a path to a folder on the server This folder and all its subfolders will then be available for browsing in the Workbench for certain activities e g importing data functions For example in the case where a directory has been set up an Import export location and a user logged into the CLC Genomics Server via their CLC Workbench wishes to import some high throughput sequencing data they would see an option like that shown in figure 2 7 On my local disk or a place have access to means that the user will be able to select files from the file system of the machine their CLC Workbench is installed on These files will then be transferred over the network to the server and placed as temporary files for importing If the user chooses instead the option On the server or a place the server has access to the user is CHAPTER 2 USING THE SERVER FROM A CLC WORKBENCH 11 4 SOLID on Server 1 Choose import files Setparameters location Where are your Files located On my local disk or a place I have access to G On the server or a place that the server has access to i
10. les onto the machine their CLC Workbench is running on before importing the data into a CLC Genomics Server CLC server data area Another example is if you wished to export data from CLC format to other formats and save those files on your server machine s filesystem as opposed to saving the files onto the system your Workbench is running on From the administrator s point of view this is about configuring folders that are safe for the CLC Genomics Server to read and write to on the server machine system This means that users logged into the CLC Genomics Server from their Workbench will be able to access files in that area and potentially write files to that area Note that the CLC Genomics Server will be accessing the file system as the user running the server process not as the user logged into the Workbench This means that you should be careful when opening access to the server filesystem in this way Certainly only folders that do not contain sensitive information should be added Folders to be added for this type of access are configured in the web administration interface in the Main configuration tab under Import export directories see figure 2 6 Earlier versions of the server software referred to these locations as High throughput sequencing data import locations 79 Main configuration File system locations YF importexport directories Add new import export directory configuration Remove Path mint cledata con
11. mina vats SOLID in 0 R Fasta R Sanger SAM BAM Mapping Files Tabular Mapping Files Figure 2 4 Once logged in the import tools on the server become active When you run the analyses you will be faced with an initial dialog with two choices e Workbench This will run the analysis on your computer e Server This will run the analysis on the server CHAPTER 2 USING THE SERVER FROM A CLC WORKBENCH 9 An example of such a dialog is shown in figure 2 5 r g Simple variant detection and annotation xs 1 Choose where to run a AF SS RD Grid oge nightly branch Remember setting and skip this step Figure 2 5 Selecting where to run the analysis Note that you can check the Remember setting and skip this step option to always use the selected option when the analysis dialog is shown If you change your mind later on and want to switch simply click Previous in the dialog and you will be able to change the setting Running the analyses on the server is identical to running the same analyses in the Workbench with three exceptions e You can only select data from the data locations connected to the server This means that the Navigation Area is filtered to only show these locations e You have to save the result In the last step you can normally choose between Open and Save but for the analyses performed on the server you have to choose Save e When you click Finish the
12. ncing data annotation updated Feb 5 2008 xrefs U7S3Z1 1 AAB18627 1 T30869 NP_033857 1 ATP8al mRNA refe xrefs mon sequence databases UniGene Mm 153230 Ensembl ENSMUSGOO000037685 GeneID 11980 MGI 1330848 ArrayExpress P70704 GermOnline ENSMUSGOOOO00037685 EH E Example Data 1 J InterPro IPROOL S InterPro IPROOS834 InterPro IPROO8Z50 InterPro IPROO6539 PANTHER PTHR11939 Pfam PFOO1ZZ Pfam PFOO OZ i 2 PRINTS PR00119 TIGRFAMs TIGRO1652 TIGRFAMs TIGRO1494 PROSITE PS00154 KEYWORDS ATP binding Cytoplasmic vesicle Hydrolase Maqnesium Membrane A Metal binding Nucleotide binding Phosphoprotein Transmembrane SOURCE Mus musculus house mouse ORGANISM Mus musculus Eukaryota Metazoa Chordata Craniata Vertebrata Euteleostomi Mammalia Eutheria Euarchontoglires Glires Rodentia Sciurognathi Muroidea Muridae Murinae Mus REFERENCE l residues 1 to 1149 AUTHORS Halleck M S Pradhan D Blackman C Berkes C Williamson P and Schlegel R A TITLE Multiple members of a third subfamily of P type ATPases identified v lt amp Figure 3 2 Inspecting the text view of a protein sequence El Sequencing reads lt enter search term gt Note that these views are a subset of the views that you find in the CLC Workbench 3 2 Upload and download If you wish to download one of the elements from the server simply select it and click Download E3 That will present a list of file form
13. nning on the server Click the Processes tab next to the Toolbox and you will see the list of processes See figure 2 9 CHAPTER 2 USING THE SERVER FROM A CLC WORKBENCH 12 mRNA Sequencing Building contigs tt He Set Up Experiment CT 100 S mRNA Sequencing Done 25 CONN N NATTA 100 SNP Detection number 2 in queue 6 E De Novo Assembly number 1 in queue oC W Reference Assembly Building contigs on xx Processes Toolbox Figure 2 9 Monitoring processes Note that the processes running on the server have a server icon iG or ER whereas the processes running locally have specific icons like 2 and Fan You can also see that two of the server processes are queued Contrary to processes running locally running server processes will appear even if you restart the Workbench and log in to the server Server processes that are finished when you close the Workbench will not be shown when you start the Workbench again Chapter 3 Using a web browser as client Besides using the CLC Workbench as client you also have access to the server from the web interface The web interface gives you access to browsing and searching data and up and downloading data Simply type the address of the server into your browser follow by the port number and you will see the login dialog see figure 3 1 you will need to get information from your server administrator about the serv
14. s Chapter 2 Using the server from a CLC Workbench 2 1 Installing relevant plug ins in the Workbench In order to use the CLC Genomics Server from a CLC Workbench you need to install a plug in to the Workbench If you connect to the server from a CLC Genomics Workbench you should install the CLC Genomics Server Plug in If you are using e g CLC Main Workbench you should install the generic CLC Server Plug in Both plug ins allow you to log in to the server and access data from the server data locations but the CLC Genomics Server Plug in also includes the tools to access the analyses on the server e g assembly RNA Seq The plug ins can be found on the same web page as the server installer or at http www clobio com plugins Plug ins are installed using the plug in manager Help in the Menu Bar Install Plug ins 22 or Plug ins 2 in the Toolbar Install the plug in by clicking the Install from File button at the bottom of the dialog This will open a dialog where you can browse for the plug in The plug in file is provided by CLC bio on the page where you downloaded the server installation You need to restart the Workbench before the plug in is ready for use 2 2 Log in to the server Once the plug in is installed log in to the server File CLC Server Login That will bring up a login dialog as shown in figure 2 1 The first time you log in to the server you have to expand the dialog by clicking Advanced That
15. seque AS ATPGal mRNA Choose a File to be uploaded into a Cloning Aall Browse Browse Ea Cloning f primers J ET Protein analyses Upload File H H a E ET Protein orthologs H RNA secondary structe i mM mm lS a ae jili gt La tenter search term iii gt Figure 3 4 Uploading sequences to the server 15

CLC Genomics Server

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