Deployment Manual - Cooke Lab Web Services
Contents
1. Mac OS X User home Library Application Support CLC bio 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 log in information to database locations 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 Navigation Area is stored in the model_settings_300 xml file in the settings folder Index CLC Bioinformatics Database 5 Plug in licenses 11 CLC Genomics Server 5 Plug in Manager 13 32 bit installer 8 Plug ins 13 64 bit installer 8 Proxy server 17 Back up Quiet installation 10 user settings 18 RAM 9 Command line installation 10 Resources 13 rpm Linux package 8 Data structure 14 Database sh Linux installer 8 local 14 Silent installation 10 System requirements 7 Error log 17 User settings 18 Floating license 11 VM Virtual Machine 8 GHOST image 6 vmoptions memory allocation 9 Image copy 6 Xmx argument 9 Install plug ins 13 resources 13 Installers overview 9 Introduction 5 Java 8 JRE Java Runtime Environment 82. XP and Vista Yes Yes Mac OS X 10 4 and 10 5 No No Linux installer Yes Yes Linux package Yes Yes 2 3 What does it do The installer performs the following tasks 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 2 3 2 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
3. 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 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 CHAPTER 2 INSTALLATION 10 The value is set to 75 of the computers RAM per default and at a maximum of 1400 MB for 64 bit systems there is no maximum 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 75 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 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 line e g CLCMainWorkbench 5 0 1 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 CLCMa
4. 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 license properties inthe 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 Mm CLC Main Workbench Configure License Server connection Please choose how you would like to connect to your CLC License server E License Wizard F Enable license server connection Automatically detect license server Manually specify license server Hostname IP address 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 Proxy Settings Previous Cancel Figure 3 1 Connecting to a license server License Settings Mon Aug 04 09 57 26 CEST 2008 serverip serverport 6200 disableborrow false autodiscover true useserver tru Since all this information is stored in a file in the installation directory it can easily be copied to all client
5. Deployment Manual CLC Workbenches Manual for CLC Workbenches deployment and technical information version 1 2 Windows Mac OS X and Linux August 10 2009 CLC bio Finlandsgade 10 12 DK 8200 Aarhus N gt Denmark _ tC bio Contents 1 Introduction 1 1 Deployment Strategies a caco a we ca a Bac ae a ks wt Siw a tee we et 2 Installation 2 1 System requirements m nn nn 2 2 Available installers 22 s mm mm Java On MAE x ss ds 84 be ee bad a ed 2 2 2 Overview of avallable installers o ss ssa Em Re SE Se eS 2 3 What does dO soc cs a aapea au eee eee ed aa EE RR 2 3 1 Extracting and copying files to the installation directory 2 3 2 Setting the amount of memory available forthe JVM 2 3 3 Shortcuts ana file associationS Haas su ee ee ee eee ga 24 Silent installation kw Xe sa en 3 License 3 1 License server set up on clients 22 2 222 nn 4 Plug ins and resources 5 Storing and backing up data SL Data SUCUS a 0 aos aa AP es A Om AD a A a E e 52 BaAGkup OT CALA ae ade wi ce a A O we re E 5 3 Special configurations for large amounts of data Bio Tempra Gala casa alk poe wa aa BRE ee am Res wt RE DO Lao ES an 5 3 2 Disk space requirements 2 nn nm nn nn O o OO O O 00 00 00 N N 10 CONTENTS 6 Overview where do we put things 6 1 Computerlevel information un u a aaa Be as foi a a a ao 6 2 Userlevel informat
6. 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 18 Memory allocation 9 Output log 17 19
7. atter 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 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 5 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 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 5 1 CLC Data DER File Edit View Favorites Tools Help ay EZ 4 B 7 SEEN MA n gt ES Y Address C Documents and SettingsiclcuserpCLC Data Y Go gt Ea Lal N AR x Bt js CLC_Data Folders Example data El CLC_Data A 5 Extra Example data gt Nucleotide Extra Ef Assembly El Nucleotide 89 Cloning Assembly Cloning E More data E Primer design 3 More data W E Primer design W Restriction analy
8. e user level 6 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 Memory allocation for the VM is stored in the workbenchname vmoptions file Error logs to be sent to support clcbio com for use in case of program errors are output log and error log 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 6 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 17 CHAPTER 6 OVERVIEW WHERE DO WE PUT THINGS 18 Windows Vista C Users username Appdata Roaming CLC bio
9. 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 2000 Windows XP or Windows Vista e Mac OS X 10 4 or newer e Linux Redhat or SuSE 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 2000 Windows XP or Windows Vista e Mac OS X 10 4 or newer e Linux Redhat or SuSE e 256 MB RAM required e 512 MB RAM recommended e 1024 x 768 display recommended e Intel or AMD CPU required e Assembly and analysis of genomes up to 10 mega bases CHAPTER 2 INSTALLATION 8 2 GB RAM required 4 GB RAM recommended e Assembly and analysis of larger genomes 2 GB RAM required 8 GB RAM recommended 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 Linu
10. inWorkbench 5 0 1 exe q console You can also in silent mode define a different installation directory dir CLCMainWorkbench 5 0 1 exe q console dir c program files bioinformatics clc clcmainwb 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 to the user manual of the Workbenches see http www clcio com usermanuals Plug ins use the same licensing system as the Workbenches so all the concepts described here also apply to the plug
11. ion 2 222mm Index 17 17 17 18 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 Genomics Server please refer to the installation chapter in the respective user manuals See http www clcio com usermanuals At the moment the CLC Workbenches are e CLC Main Workbench e CLC Protein Workbench e CLC DNA Workbench e CLC RNA 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 followed 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
12. is concerns locations for temporary data and disk space in general 5 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 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 writing and reading these files disk speed has a great impact on overall performance when working with large data sets 5 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 follo
13. s 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 Chapter 4 Plug ins and resources There is a graphical user interface to install plug ins called the Plug in Manager 69 which is invoked in the Help menu see figure 4 1 NA 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 aigrments plugin website Usage Located in Toolbox gt Alignments and Trees gt Additional Alignments E Help Proxy Settings checkforupdetes _installfromFile_ 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 Manager 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 m
14. sis H H Sequences Protein Restriction analysis 3 Sequences E Protein 3D structures README w 3D structures 5 More data w Sequences More data 2 0 EE D Sequences Figure 5 1 In this example the location called CLC_Data points to the folder at C Documents and settings clcuser CLC_Data If the database plug in is installed you will be able to add database locations in a similar way as described in the manual for the CLC Bioinformatics Database see http www clcio com usermanuals The list of locations is stored in a file called model_settings_300 xml in the settings folder in the user home see section 6 2 We do not recommend manual editing of this file 14 CHAPTER 5 STORING AND BACKING UP DATA 15 although it is standard xml 5 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 also be included in the back up see section 6 2 5 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 Th
15. us Questions comments and feedback on this manual are very welcome at Support clcbio com CHAPTER 1 INTRODUCTION 6 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 Ona single computer with the same OS as the target computers complete a full installation including Running the installer e Set up license server connection 1 Install plug ins and resources 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 license properties and proxy properties 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 organization 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 2 3 2 and the creation of shortcuts and file associations 11f you do not use a license server you will have to activate licenses on
16. wing 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 CHAPTER 5 STORING AND BACKING UP DATA 16 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 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 3 6 1 using the Discard sequence names option including quality scores takes up 5 244 764 x 28 0 0 25 x 35 6 35 389 MB When assembled to a 4 7 Mbp annotated reference sequence the contig takes up 511 MB Chapter 6 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 th
17. x 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 have 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 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 232 CHAPTER 2 INSTALLATION 9 2 2 2 Overview of available installers The table below shows an overview of the installers that are available Platform JRE included Special 64 bit version Windows 2000
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