Deployment Manual
Contents
1. 008 20 8 3 1 Temporary data ass a au woe a a a a en a 20 8 3 2 Disk space requirements 2 2 nn u nn e 20 9 System resources 22 9 1 Setting the amount of memory available forthe JVM 22 92 Setting the number of coresto use ken ke aha ana a neh ae a 23 10 Overview where do we put things 24 10 1 Computer level information 22222 22 nn u mann 24 10 2 Userlevel information 2 22 2 2m o nn 25 Index 25 Chapter 1 Introduction If you are in charge of installing and maintaining CLC Workbenches in your organization you probably have a lot of questions about installers licenses and where do we put files for this and that This manual is written to answer these questions It is primarily aimed towards client installations i e the CLC Workbenches For installing the CLC Bioinformatics Database and CLC Server please refer to the installation chapter in the respective user manuals see http www clcbio com usermanuals At the moment the CLC Workbenches are e CLC Main Workbench e CLC Genomics Workbench In addition there is the CLC Sequence Viewer which is very similar to the other Workbenches except when it comes to licensing it is free and plug ins Some plug ins cannot be installed in the CLC Sequence Viewer In the first part of this manual we take a closer look at the installer what does it do what are the options etc Then we go into details of the license system followe2. 2 3 1 Extracting and copying files to the installation directory The Workbench is installed into the following directory per default we use CLC Main Workbench 5 as example Windows C Program files Main Workbench 5 Mac OS X Applications Main Workbench 5 Note that each major version of a Workbench has its own installation directory This means that when upgrading from e g CLC Main Workbench 5 to CLC Main Workbench 6 the old installation directory of version 4 will be left untouched when you install CLC Main Workbench 6 If you wish to remove the old installation please run the Uninstall program Minor updates will use the existing installation directory of the Workbench The installation directory can be defined during installation the above are the default installation directories see section 2 4 for more information on how to define the installation directory CHAPTER 2 INSTALLATION 10 2 3 2 Setting the amount of memory available The installer investigates the amount of RAM during installation and sets the amount of memory that the Workbench can use Read more in section 9 1 2 3 3 Shortcuts and file associations The installer also creates shortcuts for starting the Workbench and it creates file associations so that clc files will be opened by the Workbench 2 4 Silent installation The installer also has a silent installation mode which is activated by the q parameter when running the installer from a command li
3. mapping and analysis tasks The requirements suggested are based on the genome size CHAPTER 2 INSTALLATION 8 E coli K12 4 6 megabases x Minimum 2Gb RAM x Recommended 4Gb RAM C elegans 100 megabases and Arabidopsis thaliana 120 megabases x Minimum 4Gb RAM Recommended 8Gb RAM Zebrafish 1 5 gigabases x Minimum 8Gb RAM x Recommended 16Gb RAM Human 3 2 gigabases and Mouse 2 7 gigabases x Minimum 24Gb RAM x Recommended 48Gb RAM e Special requirements for de novo assembly De novo assembly may need more memory than stated above this depends both on the number of reads and the complexity and size of the genome See http www clcbio com white paper for examples of the memory usage of various data sets e 64 bit computer and operating system required to use more than 2GB RAM 2 2 Available installers There are installers available for each platform Windows Mac OS X and Linux Each of these installers is available in a 32 bit and a 64 bit version except for the Mac OS X installer For Linux there is both a sh installer and an rpm package 2 2 1 Java The Workbenches are based on Java and this means that there has to be a Java Runtime Environment JRE on the computer to run the Workbench For both Linux and Windows the installers have a built in JRE that will be installed in the installation directory of the Workbench The advantage of this is twofold 1 For computers who do not already ha
4. is not a guarantee that the Workbench will never use more but that will be for very brief and infrequent peaks and should not affect performance of other applications running on your system The only exception is when a user starts several jobs to run simultaneously You can download a sample cpu properties file at http clcbio com files deployment cpu properties Chapter 10 Overview where do we put things This part gives you an overview of all the parts of a CLC Workbench installation Some parts are at the level of the computer i e shared by all users whereas other parts are at the user level 10 1 Computer level information In the Workbench installation directory you will find the following Licenses The license information depends on what kind of license you use Fixed licenses Stored in the licenses folder they are unique for each computer Floating licenses Information about the license server connection is stored inthe license propertie file in the settings folder Plug ins are stored in the plug ins folder and can be copied to other computers running the same version of the Workbench Resources are stored in the resource folder and can be copied to other computers running the same version of the Workbench Security policy is stored in a properties file in the settings folder Path for default location and temporary data is stored in a properties file in the settings folder Information on server port an
5. users access to e Tools accessing services on the internet This includes NCBI BLAST NCBI and Uniprot Searches e Notifications about updates Update notifications on new Workbench and plug in versions e Plug in management Installation of plug ins The configuration is specified in a simple properties file called policy properties that resides in the settings folder of the installation directory e g C Program Files CLC Main Workbench 6 settings on Windows Note that users without administrator access will not be able to change the contents of this file Each of the following keys can be followed be either allow or deny workbench_version_check Controls whether notifications for Workbench updates should be shown plugin_version_check Controls whether notifications for plug in updates should be shown Note that if plugin_download is not allowed plug in update notifications will not be shown regardless of this setting online_ncbi_search Controls whether the Search for Sequences at NCBI ga in the Download menu should be available this can be used to search for and download sequences from NCBI online_structure_search Controls whether the Search for Structures at NCBI Ei in the Download menu should be available this can be used to search for and download 3D structures from NCBI online_uniprot_search Controls whether the Search for Sequences in UniProt E in the Download menu should be available this can be used t
6. Deployment Manual CLC Workbenches Manual for CLC Workbenches deployment and technical information version 1 6 Windows Mac OS X and Linux August 8 2012 This software is for research purposes only CLC bio Finlandsgade 10 12 DK 8200 Aarhus N LE bio Denmark Contents 1 Introduction 1 1 Deployment Strategies caca we ca ae a Sc a a sw Siw a ee we et 5 2 Installation 7 2 1 System requirements ee 7 2 2 Available installers oo s ar a a a et ee 8 a NN 8 Java Of Mat i o a aan ee Pb we ee ba bee Be ee Sb 9 2 2 2 Overview of available installers 0 00002 eee eeae 9 2 3 What does tdo aaa aa aha e ee a aa a A 9 2 3 1 Extracting and copying files to the installation directory 9 2 3 2 Setting the amount of memory available 10 2 3 3 Shortcuts and file associations 6 ana eee a aaa 10 24 Silent installation s a au ua aaa a a e ee a 10 3 License 11 3 1 License server set up on clients soono eee ee es 11 4 Plug ins and resources 13 5 Workflows 14 6 Connecting to a CLC Server 15 7 Security policies 16 8 Storing and backing up data 18 Sol STONE Cala au o ERA E O A O ee 18 CONTENTS 4 SL L Data Structure u e we saora ee wee ee ae we ae ae 18 8 1 2 Changing the default location 2 sss sosis baw ee ee ee ee ne 19 8 2 Backup Ofdata lt sii a saion aea m da ORD eee ee Ree e eS 19 8 3 Special configurations for large amounts of data
7. also be included in the back up see section 10 2 CHAPTER 8 STORING AND BACKING UP DATA 20 8 3 Special configurations for large amounts of data Especially the CLC Genomics Workbench is often used with large amounts of data This means that special configurations often need to be made This concerns locations for temporary data and disk space in general 8 3 1 Temporary data The Workbench has a built in cache system that intends to make sure that the Workbench does not run out of memory even for large data sets During various processes such as assembly and RNA Seq analysis the Workbench often writes temporary files to the disk Depending on the data set these temporary files can take up a lot of disk space If there is not enough space in the default tmp directory the tmp directory can be re directed Create a text file called path properties and save it in the settings folder in the Workbench installation directory The file should include one line like this tmpdir path to temp Instead of path to temp you write the absolute path to the new tmp directory When the Workbench is restarted it will then use the new directory for storing temporary data You can download a sample path properties file athttp clcbio com files deployment path properties Note It is imperative for acceptable performance that data transfer to the temp directory is not over a network connection Since the Workbench will spend a lot of time w
8. anager Resources are installed in the same way as plug ins Resources can be e g PFAM databases used by the Workbench s PFAM Domain Search gt Installing a plug in is basically just a matter of putting files in the right folder All plug in files are put in plugins and all resources in resource in the installation directory This means that the contents of these folders can be copied to other computers and they will have the plug ins installed Licenses for the plug ins are handled the same way as the Workbench licenses see section 3 13 Chapter 5 Workflows There is a graphical user interface to install workflows called Workflows which is invoked in the Help menu see figure Manage Workflows u Manage Workfiows 5 Simple variant detection and annotation Description Preview Workflow id CLC bio Simple variant detection and annotation 1 2 fp Support support dcbio com SEE 12 Sequencing reads The workflow needs to be configured before execution is i possible E Configure Rename Uninstall _Renome_ _uninstat_ a Sl er A Sa o AA A Probabilistic Variant Detection Mapping E A Y EEE varistonrack variaton able A input track aminoscidchange annotate Amino Acid Changes refined track aminoaci change snnotate 7 C Figure 5 1 The workflow manager Workflows can be created in any workbench and distr
9. cause of overheads in memory management If you do not wish to use the installer on each computer and use an image instead either make sure all computers have the same amount of RAM or set the number to 50 of the computer with the smallest amount of RAM this value should not be lower than 200 MB and for genomics scale data it should be significantly higher You can manually change the contents if you want to raise or lower this value In case you get an out of memory error you may need to allocate a higher amount of memory by increasing the number in the vmoptions file In case you get a java exception saying The JVM could not be started The main method may have thrown an exception you may need to decrease the value in the vmoptions file 22 CHAPTER 9 SYSTEM RESOURCES 23 9 2 Setting the number of cores to use A number of the algorithms in the CLC Genomics Workbench in the case of large jobs use all the cores available on your system to make the analysis as fast as possible If you wish to restrict this to a predefined number of cores this can be done with a properties file Create a text file called cpu properties and save it in the settings folder in the Workbench installation directory The file should include one line like this maxcores 1 Instead of 1 you write the maximum number of cores that the Workbench is allowed to use When the Workbench is restarted it will comply with this setting Please note that this
10. d by an explanation of the concept of plug ins Finally there is an overview chapter which tells you where to find all the different files in a client installation This is useful when deploying the Workbench but also for back up purposes We will not go into details of Linux installations but if you need these details please contact us Questions comments and feedback on this manual are very welcome at Support clcbio com 1 1 Deployment strategies Deployment strategies should be developed so that they fit your existing IT set up However the following solution has proven to work in many cases Note that this is a brief summary of the steps to take and that the rest of this manual is devoted to more detailed information 1 On a single computer with the same OS as the target computers complete a full installation including CHAPTER 1 INTRODUCTION 6 Running the installer Set up license server connection t Install plug ins and resources e Configure security policies path for temporary data and default location See more information in this manual e Specify proxy server information if needed 2 Run the installer in silent mode q on all the target computers 3 Copy the following files from the installation in 1 to the target computers e All files from the settings folder in the installation directory e plugins and resource folder from the installation directory We recommend you tailor this strategy to your own organ
11. d host is stored in a properties file in the settings folder Memory allocation for the VM is stored in the workbenchname vmoptions file Proxy settings Information about proxy server when the Workbench needs access to online services is stored in the proxy properties file in the settings folder the file will only be created if a proxy server has been specified In addition file associations for clc files are stored in the registry database on Windows 24 CHAPTER 10 OVERVIEW WHERE DO WE PUT THINGS 25 10 2 User level information The user level information is found in the application data folder Windows 2000 and XP c Documents and settings username Application data CLC bio Windows Vista and 7 C Users username Appdata Roaming CLC bio Mac OS X User home Library Application Support CLC bio Linux SHOME clcbio In this folder the following information may be useful to you User settings The user settings file stores information such as view settings parameters workspaces user name and password to server log ins and other settings customized by the user The user settings file is found in the application data folder under settings workbench name version name It is recommended to back up the user settings file When upgrading to a new version of the Workbench the user s old user settings file is copied by the Workbench the first time it is run Locations Information about which locations the user has added in the Nav
12. e and place it in the settings folder update the relevant values and the new policy will take effect next time the Workbench is started Chapter 8 Storing and backing up data This chapter explains how data is stored gives general guidance on size of data and outlines configurations needed for running analyses on large amounts of data 8 1 Storing data 8 1 1 Data structure The data in the Navigation Area is organized into a number of Locations When the the CLC workbenches except the CLC Genomics Workbench is started for the first time there is one location called CLC_Data unless your computer administrator has configured the installation otherwise A location represents a folder on the computer The data shown under a location in the Navigation Area is stored on the computer in the folder which the location points to This is explained visually in figure 8 1 B CLC Data Eile Edit View Favorites Tools Help ay Q Back y Search 7 javigation rear 1 e g A Y Address C Documents and Settings clcuserfCLC_Data Y Go a Ya ta x faja CLC_Data posers Example data E cic_pata a a Extra Example data Nucleotide Extra a Assembly E Nucleotide 9 Cloning Assembly W E More data Cloning E ta Primer design More data W E Restriction analysis 2 Primer design wm u Sequences Restriction analysis Eu wen D Sequences E 3D structures ab ee W E More data pi w Sequences a 3D struct
13. ge 8 Security policies 16 Server connection 15 sh Linux installer 8 Silent installation 10 System requirements 7 System resources 22 Temporary data 20 User settings 25 VM Virtual Machine 8 vmoptions memory allocation 22 Workflows 14 Xmx argument 22 26
14. ibuted as an installer file that can be installed in any workbench or server A workflow is always installed per user The workflow definition is stored in the user home see section 10 2 The ability to install workflows can be disabled by the policy see section 7 When the workbench is part of a CLC Genomics Server set up it will be a great advantage to manage workflows to be used by all users on the server which means no local deployment when workflows are updated see more in the user manual at http www clcbio com usermanuals 14 Chapter 6 Connecting to a CLC Server Information about server name and port can be stored ina file called serverinfo properties in the settings folder in the Workbench installation directory When the user opens the log in dialog the Workbench will read in the information from this file If the file does not exist the information that the user enters will be saved in the user settings The user name and password is stored with the user settings The serverinfo properties file contains the following port 7777 host hostname Since all this information is stored in a file in the installation directory it can easily be copied to all clients You can download a sample serverinfo properties file at http clcbio com files deployment serverinfo properties 15 Chapter 7 Security policies The Workbench has a security policy configuration that enables administrators to restrict
15. igation Area is stored in the model_settings_300 xml file in the settings folder Error logs to be sent to support clcbio com for use in case of program errors are output log and error log and they are found in the log folder Workflows Workflows are saved in a workflows workbench name version name folder When upgrading to a new version of the Workbench the user s old workflows are copied by the Workbench the first time it is run unless there are major changes to the workflow framework that breaks compatibility Index CLC Bioinformatics Database 5 CLC Server 5 32 bit installer 8 64 bit installer 8 Back up user settings 25 Back up 19 Block access to internet 16 Command line installation 10 Cores restrict usage 23 CPU restrict usage of 23 Data storage 18 Data structure 18 Database local 18 Error log 25 Floating license 11 GHOST image 6 Image copy 6 Install plug ins 13 resources 13 workflows 14 Installers overview 9 Introduction 5 Java 8 JRE Java Runtime Environment 8 JVM Java Virtual Machine 8 License order ID 11 License server 11 setup on clients 11 Licenses 11 for plug ins 11 Linux 5 Linux installer vs package 8 Locations 25 Memory allocation 22 Online tools block access to 16 Output log 25 Plug in licenses 11 Plug in Manager 13 Plug ins 13 Policy 16 Proxy server 24 Quiet installation 10 RAM 22 Resources 13 rpm Linux packa
16. ization this is just an example of how it can be done Creating a GHOST image or similar to copy to all the target computers is also a possibility but there are a few routines performed by the installer that need to be taken into acount especially allocating memory see section 9 1 and the creation of shortcuts and file associations 11f you do not use a license server you will have to activate licenses on each computer Chapter 2 Installation This chapter deals with the installer and related information about the installation process 2 1 System requirements The system requirements of the CLC workbenches except the CLC Genomics Workbench are these e Windows XP Windows Vista or Windows 7 Windows Server 2003 or Windows Server 2008 e Mac OS X 10 6 or later Intel CPU required However Mac OS X 10 5 8 is supported on 64 bit Intel systems e Linux RedHat 5 or later SUSE 10 or later e 32 or 64 bit e 256 MB RAM required e 512 MB RAM recommended e 1024 x 768 display recommended The requirements for the CLC Genomics Workbench are e Windows XP Windows Vista or Windows 7 Windows Server 2003 or Windows Server 2008 e Mac OS X 10 6 or later Intel CPU required However Mac OS X 10 5 8 is supported on 64 bit Intel systems e Linux RedHat 5 or later SUSE 10 or later e 1024 x 768 display recommended e Intel or AMD CPU required e Memory The numbers below give minimum and recommended amounts for systems running
17. ne e g CLCMainWorkbench_5_6 exe q On Windows if you wish to have console output console can be appended as the second parameter this is only needed when running on Windows where there is no output per default CLCMainWorkbench_5_6 exe q console You can also in silent mode define a different installation directory dir CLCMainWorkbench_5_6 exe q console dir c bioinformatics clc Note Both the console and the dir options only work when the installer is run in silent mode The q and the console options work for the Uninstall program as well Chapter 3 License There are fundamentally two kinds of licenses for the Workbenches Fixed license A license order ID has to be activated against our server for each computer The license will then be fixed to this computer This requires manual intervention for each activation Floating license A license server is installed in your organization It hosts a number of licenses which can be shared among all computers Note that the license server is available for both Linux Windows and Mac OS X For large installations the floating license is by far the best option since all the license administration takes place on the server find the manual for the license server together with the server distribution The fixed license requires manual work during installation and also if the licenses need to be updated For information on how to use the floating license please refer t
18. o search for and download sequences from Swissprot UniProt online_ncbi_blast Controls whether all the tools performing BLAST at NCBI s servers should be available This is NCBI BLAST both from the Toolbox and from sequence selections 16 CHAPTER 7 SECURITY POLICIES 17 plugin_manage Controls whether the Plug ins and Resources manager should be available for the user Note that users can still install plug in updates if plugin_download and plugin_version_check are allowed plugin_file_install Controls whether this user should be allowed to install plug ins and resources from a local file plugin_download Controls whether this user should be allowed to install CLC plug ins and resources downloaded directly within the plug in manager dialog This also includes manually checking for updated plug ins in the Plug ins and Resources manager dialog and also the automatic check for plug in updates at start up workflow_file_install Controls whether the user should be allowed to install workflows from a file workflow_manage Controls whether the user should be allowed to manage workflows workflow_download Controls whether the user should be allowed to download and install workflows form the CLC workflows repository Per default there is no policy properties file so everything is allowed A commented sample file that you can download and edit is located at http clcbio com files deployment 2 policy properties Download the fil
19. o the user manual for the relevant Workbench see http www clcbio com manuals Plug ins use the same licensing system as the Workbenches so all the concepts described here also apply to the plug in licenses 3 1 License server set up on clients The connection to the license server can be set up as described in the Workbench user manual see also figure 3 1 The license server information is stored in a file called 1icense properties in the settings folder in the Workbench installation directory This means that you need write access to the installation directory with the default installation directory you need to be an administrator to have this write access in order to set up a connection to the license server The file contains the following 11 CHAPTER 3 LICENSE 12 License Wizard E Mm CLC Main Workbench Configure License Server connection Please choose how you would like to connect to your CLC License server F Enable license server connection Automatically detect license server Manually specify license server Disable license borrowing Tf you choose this option users of this computer will not be able to borrow licenses From the License Server Ifyou experience any problems please contact The CLC Support Team Figure 3 1 Connecting to a license server serverip serverport 6200 disableborrow false autodiscover true useserver true Since all this information is
20. riting and reading these files disk speed has a great impact on overall performance when working with large data sets 8 3 2 Disk space requirements It is hard to give general guidance on disk space requirements but we have made an example of a typical work flow for CLC Genomics Workbench to illustrate For calculating disk space for next generation sequencing data you need to consider the following e Reads are imported and take up space as raw reads see details below Once imported you can delete the original sequence file if you do not need it for other purposes e When the data has been assembled either de novo or against a reference they take up space once again this time more space since there is also information about where they map etc e Reference sequences also take up space e The computer doing the analysis needs space for tmp files Once the assembly is done the temporary files are deleted The temporary files usually do not take up more space than the final result The formulae giving the disk space usage CHAPTER 8 STORING AND BACKING UP DATA 21 Bytes per read 28 length of read name 0 25 x length of read Note that you can discard read names during import If quality scores are present add 6 length of read If color space encoding is present add 7 As an example a data set of 5 2 million 35 bp reads imported by CLC Genomics Workbench using the Discard sequence names option including qualit
21. stored in a file in the installation directory it can easily be copied to all clients and the license configuration is completed When the Workbench is started it will look in this file and if useserver true then it will try to connect to the license server and no license dialogs will be shown to the user You can download a sample license properties file at http clcbio com files deployment license properties Chapter 4 Plug ins and resources There is a graphical user interface to install plug ins called the Plug in Manager which is invoked in the Help menu see figure 5 1 e E Manage Resources Download Resources O additional allignments Version 1 02 Description Per ments with many different programs from within the FFT MacfLi ign MacfLin Additional information More information is available on the Additional aianments plugin website Usage Located in Toolbox gt Alignments and Trees gt Additional Alignments E Help _ _Proxy Settings Check for updates _installfrom File Figure 4 1 The Plug in Manager Plug ins are either general modules or extensions provided by CLC bio see http www clcbio com plugins or can be custom made plug ins specific to your organization Plug ins can either be downloaded and installed directly in the Plug in Manager or they can be installed from a file Install from File button at the bottom of the Plug in M
22. the home directory of the current user Sproduct the short name of the workbench example clegenomicswb or clemainwb A few examples datadir Shome CLC_Data default datadir X clcstorage Suser seperate disk network mount in Windows Note that the folder does not need to exist it will be created if needed You can use both slash normally used on Mac and Linux and backslash normally used on Windows in the configuration file the Workbench will use the appropriate one depending on the platform Note that the default location is only considered the very first time the Workbench starts When the Workbench closes the first time the model_settings_300 xml file is created and this is where it will look for the locations further on Deleting this file will make the Workbench look for the datadir property in the path properties file The model_settings_300 xml file is located in the settings folder in the user home see section 10 2 You can download a sample path properties file at http clcbio com files deployment path properties 8 2 Back up of data Since all data used in the Workbench is stored as files in the locations specified a back up procedure has to include all the locations If the data needs to be restored from a back up simply copy the files back into the folder locations and start the Workbench Database locations needs a different back up procedure Besides the data itself user level settings should
23. ures README More data Emmi mRecycle bin 0 O Sequences Figure 8 1 In this example the location called CLC_Data points to the folder at C Documents and settings clcuser CLC_Data If the Workbench is connected to a CLC Server the server s locations will automatically show up when the user is logged in This chapter does not deal with server locations please refer to the server user manual at http www clcbio com usermanuals 18 CHAPTER 8 STORING AND BACKING UP DATA 19 The list of locations is stored in a file called model_settings_300 xml in the settings folder in the user home see section 10 2 We do not recommend manual editing of this file although it is standard xml 8 1 2 Changing the default location In some set ups storing data in the default location CLC_Data in the user home is not desired This could be for roaming user profiles or in situations where there is a quota on this disk The default location that is used the first time the Workbench starts can be configured in the path properties file that resides in the settings folder of the installation directory e g C Program Files CLC Main Workbench 5 settings on Windows Add a line like this to the file to change the default location The file should include one line like this datadir c clcdata The following variables can be used to construct the path to the desired location Suser the user name of the current user Shome
24. ve a JRE installed the need for downloading and installing a JRE is eliminated 2 for computers who already have a JRE installed there will never be compatibility problems because the Workbench always uses its own JRE The built in JRE is the latest Java 6 JRE from Sun Microsystems http java sun com The JRE used for running the CLC Workbench will not interfere with existing JREs on the computer CHAPTER 2 INSTALLATION 9 Java on Mac Since the Workbench uses Apple s JRE there is no JRE included in the installer When running the Workbench on 64 bit systems please make sure that the 64 bit Java is used for launching applications Go to Applications Utilties Java and double click on Java Preferences In the Java application versions reorder the list to have JREG 64 bit at the top Note that this may change the behavior of other Java based programs on the computer Note After setting the Java preference you can either uninstall and reinstall the workbench and the memory will be adjusted automatically or you can set the memory yourself See section 9 1 2 2 2 Overview of available installers The table below shows an overview of the installers that are available Platform Windows 2000 XP Vista and 7 Mac OS X 10 6 or later Intel CPU required However Mac OS X 10 5 8 is supported on 64 bit Intel systems Linux installer Linux package 2 3 What does it do The installer performs the following tasks
25. y scores takes up 5 244 764 x 28 O 0 25 x 35 6 35 389 MB When mapped to a 4 7 Mbp annotated reference sequence the mapping results takes up 473 MB Chapter 9 System resources You can specify the amount of system resources that the Workbench is allowed to use This can be done for both memory and CPU 9 1 Setting the amount of memory available for the JVM When running the Workbench the Java Virtual Machine JVM needs to know how much memory it can use This depends on the amount of physical memory RAM and can thus be different from computer to computer Therefore the installer investigates the amount of RAM during installation and sets the amount of memory that the JVM can use when running the Workbench On Windows and Linux this value is stored in a property file called workbenchname vmoptions e g clcmainwb vmoptions which contains a text like this Xmx1400m The number 1400 is the amount of memory the Workbench is allowed to use The file is placed in the installation folder e g C Program Files CLC Main Workbench 6 clcmainwb vmoptions On Mac OS X the Xmx value is stored in Info plist in the application bundle Control click the application and choose Show Package Contents The value is set to 50 of the computers RAM per default and at a maximum of 1400 MB for 32 bit systems and a maximum at 50GB for 64 bit systems at this point there is no performance increase by setting it higher be
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