Agilent GeneSpring - Installation Guide.fm
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1. Enter your new Order IDs for the appropriate modules here GeneSpring GX Order ID VFG0 6077 4824 Mass Profiler Professional Ord AZO0 6087 4824 GeneSpring NGS Order ID BET0 6087 4824 Pathway Architect Order ID Figure 13 Change License dialog box GeneSpring confirms the activation of the licenses associated with the new or changed OrderIDs with a confirmation message Agilent GeneSpring Installation Guide 21 22 a i Your license has been successfully changed Please relaunch your tool i Cancel Figure 14 Successful license change confirmation 4 Click OK to acknowledge the successful license change GeneSpring shuts down Restart GeneSpring to start using the features of the new module for which you added a new OrderID If you changed your license type from a trial license to a purchased license this change is now reflected in the new expiry date displayed in the License Manager dialog box see Figure 8 on page 17 Add or change a license manually If the automatic procedure to add or change a license fails you can add or change your license manually using the following procedure 1 Click Yes in the dialog box indicating that the automatic change license operation failed Es i Automatic Change License Operation has failed Do you want to proceed manually Figure 15 Automatic change license operation failed message 2 Click the web link for the Agilent manual activation web page2. http lcosgens cos agilent com gsLicense MultipleActivate html in the dialog box that opens Make a note of the location of the manualActivation txt file which is displayed in the same dialog box You have to know the location of this file in Step 4 of this procedure Click OK Agilent GeneSpring Installation Guide Ci To activate manually please go to z http Icosgens cos agilent com gsLicense MultipleActivate html and upload this file C Program Files Agilent GeneSpring bin license manualActivation txt Figure 16 Manual change license operation details message 3 On the GeneSpring License Request website provide the OrderID for each of the modules for which you want to add or change your license in the corresponding fields of the website form 4 Specify the manualActivation txt file in the Activation file field This file is located in the bin folder of the GeneSpring installation directory You made a note of the exact location in Step 2 of this procedure 5 Click Submit You will receive an activation license file lic corresponding to each module you wanted to change by email from GeneSpring technical support The support team uses the email address that you provided when you purchased GeneSpring or registered for a free trial 6 Save the lic files in the bin license folder of your GeneSpring installation directory 7 Restart GeneSpring Your license is now activated If you have followed
3. the steps above and launching GeneSpring produces an error please send an email to GeneSpring technical support informatics_support agilent com with the subject Activation Failure and provide the Error code displayed in the License Error dialog box The support team will respond to your email within four hours If you cannot access the Agilent Manual License Activation website or did not receive the lic file please send an email to GeneSpring technical support informatics_support agilent com with the subject Registration Request and attach the activation file Agilent GeneSpring Installation Guide 23 manualActivation text The support team will generate the activation license file and reply to your email with the new activation license file as an attachment within four hours To reactivate a license If your license period was extended by GeneSpring technical support reactivate your license for the extension to take effect Follow the steps described in this section to reactivate your license 1 Select Help gt License Manager from the main menu see Figure 7 on page 16 2 Click Re activate in the License Manager dialog box see Figure 8 on page 17 3 Click Yes in the License Re activation dialog box License Re activation i This operation allows you to re activate your OrderIds for the application After re activation the application will be automatically closed Are you sure you want to re a
4. GB at least 16 MB not required Following installation GeneSpring will only be available from the user account in which it was installed e Red Hat Enterprise Linux 5 Debian GNU Linux 4 0rl Pentium 4 with 1 5 GHz 1 GB 1 5 GB at least 16 MB not required Following installation GeneSpring will only be available from the user account in which it was installed Agilent GeneSpring Installation Guide Actual system requirements vary depending on the experiment type number of samples and sample size of your data especially for NGS experiments as well as Copy Number and Association experiments see Table 2 Table 2 Recommended system specifications for NGS Copy Number and Association experiment types NGS experiments Copy Number and Association experiments Hardware architecture and processor Available memory Hard disk space 64 bit quad core at least 32 bit ideally 64 bit at least 4 GB ideally 8 GB at least 2 GB ideally 4 GB 30 GB or more depending at least 25 GB ideally 5x the total file size of all the samples on sample size and number to be loaded into GeneSpring in Methyl Seq minimum requirements stated here are based on 75 experiments these samples from an Affymetrix Genome Wide Human SNP specifications are sufficient Array 6 0 to work with up to 6 samples with 50 million reads each b Identify the appropriate installation file for your system Agilent provides diff
5. ctivate Figure 17 License Re activation dialog box 4 Click OK to acknowledge the successful license re activation GeneSpring shuts down The next time you start GeneSpring the extension of your license duration is reflected in the new expiry date displayed in the License Manager dialog box see Figure 8 on page 17 Reactivate a license manually If the automatic process to reactivate a license fails you can reactivate that license manually using the following procedure Agilent GeneSpring Installation Guide 1 Click Yes in the Automatic License Reactivation Failed dialog box Automatic License Reactivation Failed eal e Automatic license reactivation has Failed Do you want to reactivate the license manually Figure 18 Automatic License Reactivation Failed dialog box 2 The remaining steps are the same as Steps 1 to 6 of the manual license activation procedure see Manual License Activation on page 13 The next time you start GeneSpring the new license expiry date is reflected in the License Manager dialog box Agilent GeneSpring Installation Guide 25 Upgrading Agilent GeneSpring to a New Version Agilent continues to improve the GeneSpring suite of products to enable you to analyze and visualize the latest data types generated in the laboratory environment In addition to such new features upgrades also contain enhancements to existing features as well as bug fixes We therefore recommend that
6. documentation index opens in your default browser You can access the available GeneSpring user manuals and quick start guides from this page A shortcut to start GeneSpring is now available on your desktop Following installation you will only be able to start using GeneSpring once you have activated it with your license key see Step 3 Activating the software on page 11 Return to the Flowchart for installation Agilent GeneSpring Installation Guide Step 3 Activating the software When starting GeneSpring for the first time you have to provide a license key OrderID for each of the modules for which you have a license This will activate your software installation and enables all the available features associated with the activated module Agilent GeneSpring software imposes a node locked desktop license This means the software can only be used on the machine that it was installed on See Managing Licenses on page 16 for more information on how you can transfer your license to an installation of GeneSpring on another computer Follow the steps below to activate your installation of GeneSpring 1 Have your valid OrderID ready and make sure you are connected to the internet You should have received your OrderlD when you purchased the license For a free trial of the software register at www genespring support com and apply for a free trial You will receive a valid OrderlD by email 2 Double click the GeneSpr
7. e e l l e ee Agilent GeneSpring Software TF 9 i n Installation Guide Quick Start Installation of Agilent GeneSpring 3 Detailed Instructions for Installing Agilent GeneSpring 5 Managing Licenses 16 Upgrading Agilent GeneSpring to a New Version 27 Migrating data from previous versions 29 Getting help 30 Agg Agilent Technologies Agilent GeneSpring provides powerful accessible tools for statistical analysis and visualization of genomics transcriptomics proteomics and metabolomics data Agilent GeneSpring Installation Guide Quick Start Installation of Agilent GeneSpring Agilent GeneSpring software can be installed on any desktop computer with Windows Mac or Linux operating systems The following flowchart describes the general steps for installing Agilent GeneSpring Make sure to follow the steps in the order they are shown Detailed instructions for each step and the differences if any for the varying operating systems are provided later in this guide Click the See links to jump to the detailed topics If you want to upgrade to a new version read Upgrading Agilent GeneSpring to a New Version on page 26 If you have been working with version 7 3 and you want to move to the latest version of GeneSpring please refer to Chapter 4 in the GeneSpring User Manual for information on how to migrate your data In Windows you cannot run two different versions of GeneSpring on the same co
8. er programs that are running on your computer Browse your hard drive for the installation file which you downloaded from the GeneSpring support portal Double click the lt installation file name gt icon In Mac systems if downloading the file in any other browser than Safari The first double click uncompresses the installation file and creates a app file in the same location Make sure this file has executable permission Double click this file to start the installation The InstallAnywhere dialog box see Figure 3 indicates the progress of preparing the installation wizard InstallAnywhere 4 Install nywhere is preparing to install 25 Cancel C 2002 2006 Macrovision Europe Ltd and or Macrovision Corporation Figure 3 Install Anywhere dialog box preparing to install Agilent GeneSpring Installation Guide The installation wizard starts Click Next to move on to a next step Click Previous to review information in a previous step If you no longer want to install GeneSpring you can click Cancel at any time 6 Review the information provided in the Introduction and System Requirements steps of the installation wizard 7 Inthe License Agreement step review the license agreement If you agree to the terms of the agreement select I accept the terms of the License Agreement from the options at the bottom of the page The installation only continues if you accept these terms 8 In the Choose Install F
9. erent installation files optimized for the different platforms and relevant system types Before downloading the installation file from the GeneSpring support portal or requesting the installation files from your Agilent account manager follow these steps to identify your operating system s system type In Windows operating systems 1 Click the Start button 2 In Windows 7 and Vista select Control Panel In Windows XP select Settings gt Control Panel 3 Click Systems Your version of the operating system and system type 82 bit or 64 bit are specified in the Systems page of the Control Panel browser window see Figure 2 on page 7 In the Windows XP system the system type is only explicitly mentioned for the 64 bit type Agilent GeneSpring Installation Guide gt All Control Panel Items System Da Search Control Pane Pp View basic information about your computer Windows edition Windows 7 Home Premium Copyright 2009 Microsoft Corporation All rights reserved m Service Pack 1 Get more features with a new edition of Windows 7 System Rating Bi Windows Experience Index Processor Intel R Core TM 2 Duo CPU T58 00GHz 2 00 GHz Installed memory RAM 2 00 GB System type 32 bit Operating System Pen and Touch No Pen or Touch Input is available for this Display Figure 2 Systems information for Windows 7 installation In Linux operating systems 1 Launch a Terminal via A
10. hed If the automatic activation process failed you can activate your license manually as described under Manual License Activation on page 13 12 Agilent GeneSpring Installation Guide Manual License Activation If automatic license activation fails you can manually activate your license through the Agilent Manual License Activation website You will need an active internet connection your Orderlds and the activation file that is provided in the installation directory of GeneSpring To complete manual activation follow the steps below 1 Go to the GeneSpring License Request website http lcosgens cos agilent com gsLicense MultipleActivate html by clicking on this link or on the link provided in the License Error dialog box 2 Enter the OrderIDs for the modules that you want to activate in the field provided on the website 3 Browse for the activation file manualActivation txt in the lt installation directory gt bin license folder 4 Click Submit You will receive an activation license file for each module gs lic mpp lic ss lic or pw lic at your email address that you provided when you purchased GeneSpring or registered for a free trial 5 Save the lic files to the bin license folder in your GeneSpring installation directory 6 Restart GeneSpring Your licenses are now activated and GeneSpring is launched If you have followed the steps above and launching GeneSpring still produces an error plea
11. here you installed GeneSpring Click OK GeneSpring performs the upgrade The progress bar at the bottom of the Automatic Software Update dialog box indicates the progress of the upgrade process 5 Click OK in the Update dialog box to acknowledge completion of the upgrade You have successfully upgraded to the new version of GeneSpring The GeneSpring Update Product feature upgrades your installation one update at a time If you have skipped previous version updates and would now like to upgrade to the latest version repeat the steps described here until you have upgraded to the latest version Agilent GeneSpring Installation Guide 27 Migrating data from previous versions Due to the completely new data organization in GeneSpring GX 9 and later versions when compared to previous versions data that was saved in GeneSpring GX 7 is not automatically available in version 9 or later To allow you to move genomes from version 7 to later versions a migration tool is available in all versions of GeneSpring from GX 9 onwards Please refer to Chapter 4 of the GeneSpring User Manual for the detailed procedure to migrate your data 28 Agilent GeneSpring Installation Guide Getting help Online help Documents Press F1 To get more information about a menu toolbar window or dialog box place the cursor on the part of the menu toolbar window or dialog box of interest and press the F1 key Help menu Click Help gt Documentation Index
12. ick the Uninstall shortcut icon amp The Uninstall wizard opens Uninstall GeneSpring a Uninstall GeneSpring Introduction About to uninstall Uninstalling Senssod eneSpring Uninstall Complete This will remove features installed by InstallAnywhere It will not remove files and folders created after the installation Multi Omic Analysis EE Agilent Technologies InstallAnywhere by Macrovision Cancel Previous Figure 5 Uninstall GeneSpring dialog box 4 Click Uninstall in the Uninstall GeneSpring dialog box Agilent GeneSpring Installation Guide You can follow the progress of the uninstalling process in the same dialog box 5 Click Done in the Uninstall GeneSpring dialog box when the uninstall process is completed SW UninstallGeneSpring a kodola Uninstall Complete Introduction Alliterns were successfully uninstalled Uninstalling Uninstall Complete Multi Omic Analysis fe Agilent Technologies InstallAnywhere by Macrovision Figure 6 Uninstall GeneSpring dialog box Uninstall Complete GeneSpring is uninstalled from your computer The following folders remain in your installation folder e app e logs e marray logs e samples If you want to remove everything related to GeneSpring from your computer delete these folders as you delete any other folders containing information you no longer require Agilent GeneSpring Instal
13. ing shortcut icon that was added to your desktop during installation to start GeneSpring The GeneSpring License Activation dialog box see Figure 4 on page 12 opens 3 Select the modules GeneSpring GX Mass Profiler Professional GeneSpring NGS and Pathway Architect that you would like to activate and enter the corresponding OrderIDs Optional If your system is behind a proxy server provide the proxy host and proxy port in the Proxy settings area of the License Activation dialog box If your proxy server supports authentication you also have to provide your proxy user name and password Agilent GeneSpring Installation Guide 11 Select License Type Please choose your license type individual license M Order ID You should have valid OrderlDs to activate GeneSpring 12 5 over the web To get OrderiDs write to the support team at informatics_support agilent com _ Gene Spring GX OrderiD Mass Profiler Professional OrderiD __ GeneSpring NGS OrderiD Pathway Architect OrderlD Example ABC1 2345 6789 Proxy settings Use proxy C Authenticate Lo Cancel Figure 4 GeneSpring License Activation dialog box 4 Click the OK button GeneSpring obtains the information associated with your OrderID validity and license duration by connecting to the Agilent license server over the internet Successful completion of this process activates your installation and GeneSpring is launc
14. lation Guide 15 Managing Licenses The GeneSpring License Manager provides an easy way for you to manage your licenses for all the available modules see Step 3 Activating the software on page 11 Select Help gt License Manager from the main menu bar to access the License Manager Help Help Documentation Index License Manager Contact Technical Support GeneSpring Extras Update Product gt About Figure 7 License Manager is available within the Help menu from the menu bar The GeneSpring License Manager see Figure 8 on page 17 allows you to e Surrender a license when you want to move your license to another computer see To surrender a license on page 18 e Add Change a license for example when you purchased GeneSpring and want to replace your trial license see To add or change a license on page 21 e Re activate a license for example if the duration of your license has changed see To reactivate a license on page 24 16 Agilent GeneSpring Installation Guide Managing Licenses Order ID GeneSpring GX PXK9 8174 4214 Mass Profiler Professional MSG0 9285 5325 GeneSpring NGS BOES 4740 0870 Pathway Architect PNT3 2528 8658 License Status Updates Status Expires On 21 Dec 2012 pires On 11 Dec 2012 Pathway Architect Figure 8 License Manager dialog box The following sections describe how to perform each of the
15. mputer at the same time The only exception is a combination of version 7 3 and any of the later versions of GeneSpring due to the fact that version 7 3 is based on a different software platform Agilent GeneSpring Installation Guide 3 Quick Start Installation of Agilent GeneSpring Flowchart for installation Figure 1 Flowchart for installing Agilent GeneSpring 4 Agilent GeneSpring Installation Guide Detailed Instructions for Installing Agilent GeneSpring This section contains more detailed instructions and important notes about each step of the installation process outlined in the installation flow chart shown in Figure 1 on page 4 You can click on the link at the end of each topic to return to the flow chart Step 1 Prepare for installation Table 1 a Check system requirements before you start Before installing GeneSpring make sure that your computer system meets the minimum requirements specified in Table 1 System Requirements by Different Platforms Microsoft Windows Apple Mac OS X Linux Operating system Processor Available memory RAM Hard disk space Video Memory Administrator privileges 7 Professional XP Service Pack 3 e Vista Pentium 4 with 1 5 GHz 1GB 1 5 GB at least 16 MB required Following installations all other users of this machine will also be able to use GeneSpring Snow Leopard v10 6 Lion v10 7 e Mountain Lion v10 8 1 5 GHz 1 GB 1 5
16. neSpring License Request website provide the OrderID for each of the modules for which you want to surrender your license in the corresponding fields of the website form 4 Specify the surrender bin directory in the Surrender file field This directory is located in the bin folder of the GeneSpring installation directory You made a note of the exact location in Step 2 of this procedure 5 Click Submit The licenses are surrendered You can now proceed with activating the license in another installation on a different computer Step 3 Activating the software on page 11 Agilent GeneSpring Installation Guide To add or change a license There are a number of different license types available for GeneSpring for example a trial license or purchased licenses for any of the four available GeneSpring modules Use this procedure if you want to add a license for a new module or if you want to change a trial license to a purchased license 1 Select Help gt License Manager from the main menu see Figure 7 on page 16 2 Click Add Change in the License Manager dialog box see Figure 8 on page 17 The Change License dialog box opens and displays all the existing licenses currently associated with the available modules 3 Provide the new OrderIDs for the corresponding modules Click OK Change License Change License New Order IDs are required to change your license Please contact informatics_support agilent com for help
17. older step of the installation wizard click Choose to specify an installation folder other than the folder chosen by the installation wizard By default Agilent GeneSpring is installed in these directories in Windows systems C Program Files Agilent GeneSpring in Linux systems HOME Agilent GeneSpring in Mac systems HOME Applications Agilent GeneSpring When specifying the installation folder consider the hard disk space requirements for your experiments see Table 1 on page 5 and Table 2 on page 6 9 Review the installation details including the installation folder and where the shortcut to start GeneSpring is created in the Pre Installation Summary step This step also indicates the exact hard disk space required for installing GeneSpring and the available space in the selected installation folder If the available space is less than the required space click Previous to return to the Choose Install Folder step see step 8 and specify another location that has sufficient space When you are ready to continue with the installation click Install 10 The installation process begins You can find out more about any new and existing features of this version of GeneSpring from the peeling pages displayed in the installation window 11 The Install Complete step confirms when the installation process has finished Click Done to complete the installation and close the wizard Agilent GeneSpring Installation Guide 9 10 The
18. pplications gt Accessories lt Terminal from the main menu 2 Type uname a and press Enter Your version of the operating system and system type can be found at the end of the Terminal response for example e for a 32 bit system type and Debian GNU Linux 4 0 system the response ends like this i686 GNU Linux e for a 64 bit system type and Debian GNU Linux 4 0 system the response ends like this x86_64 GNU Linux In Mac OS X operating systems The installation file provided by Agilent for Mac is compatible with all supported operating system versions and all system types You do not have to identify the system type first Return to the Flowchart for installation Agilent GeneSpring Installation Guide Step 2 Install the software on your desktop computer The installation process for GeneSpring described in this section is applicable for all three supported platforms see Table 1 on page 5 Where the instructions differ for a particular platform this is indicated in the details of each step where applicable 1 Before beginning to install Agilent GeneSpring make sure you have completed all the pre installation steps outlined in Step 1 Prepare for installation on page 5 Login to the system where you want to install Agilent GeneSpring In Windows systems use an account that has administrator privileges In Linux and Mac systems administrator privileges are not required Close any oth
19. se license management tasks Agilent GeneSpring Installation Guide 17 To surrender a license You can move a license to an installation of GeneSpring on another computer by surrendering the license on the current computer and activating it on the other computer Use this procedure if you want to activate an installation of GeneSpring on a different computer with the same license Make a note of your OrderlDs before surrendering them If you want to activate the associated licenses again at a later date see Step 3 Activating the software on page 11 you have to enter these OrderlDs in the GeneSpring License Activation dialog box 1 Select Help gt License Manager from the main menu see Figure 7 on page 16 2 Click Surrender in the License Manager dialog box see Figure 8 on page 17 3 Select GeneSpring GX and any other products orderIDs for which you want to surrender the license Bl E Choose the products orderIDs to surrender Choose Product V GeneSpring GX V Mass Profiler Professional V GeneSpring NGS V Pathway Architect Cox cancel Figure 9 Product selection dialog box 4 Click OK You can confirm or decline surrendering your licenses in the next dialog box 5 Click Yes in the Confirm Surrender dialog box 18 Agilent GeneSpring Installation Guide Confirm Surrender 2 This operation allows you to use the application with i the same OrderId on another computer Are you
20. se send an email to GeneSpring technical support informatics_support agilent com with the subject Activation Failure and provide the Error code displayed in the License Error dialog box The support team will respond to your email within four hours If you cannot access the Agilent Manual License Activation website or did not receive the strand lic file please send an email to GeneSpring technical support informatics_support agilent com with the subject Registration Request and attach the activation file manualActivation text The support team will generate the activation license file and reply your email with the file as an attachment within four hours Agilent GeneSpring Installation Guide 13 14 Uninstalling GeneSpring Your installation of GeneSpring includes an uninstall facility Before uninstalling please contact GeneSpring technical support to get more information on how to backup your data and experiments If you are planning to use your licenses on another computer surrender the licenses before uninstalling see To surrender a license on page 18 Follow these steps to uninstall GeneSpring from your computer 1 Ina Windows system log in to an account with administrator privileges on the computer where you installed GeneSpring In Mac and Linux systems log in to the account where you installed GeneSpring Administrator privileges are not required Go to the GeneSpring installation folder Double cl
21. sure you want to surrender the license Figure 10 Confirm Surrender dialog box 6 Click OK in the Automatic Surrender Operation Successful dialog box Automatic Surrender Operation Successful Ea i Your license has been surrendered successfully Figure 11 Automatic Surrender Operation Successful dialog box The license is surrendered and GeneSpring shuts down You can now proceed with activating the license in another installation on a different computer Step 3 Activating the software on page 11 Surrender a license manually If the automatic surrender process described in To surrender a license on page 18 fails you can surrender a license or licenses manually as described in this section Agilent GeneSpring Installation Guide 19 1 Click Yes in the Automatic Surrender Operation Failed dialog box Automatic Surrender Operation Failed Automatic Surrender Operation has Failed i Pathway Architect Failed Do you want to surrender manually Figure 12 Automatic Surrender Operation Failed dialog box 2 Click the web link for the Agilent manual surrender web page http lcosgens cos agilent com gsLicense MultipleSurrender html in the Manual Surrender Operation dialog box Make a note of the location of the surrender bin directory displayed in the same dialog box You have to know the location of this directory in Step 4 of this procedure Click OK GeneSpring shuts down 3 On the Ge
22. to access the release notes quick start guides and HTML and PDF versions of the GeneSpring manual Online support portal Visit www genespring support com to contact the GeneSpring support team and access additional demo data sets user guides and video tutorials E seminars Visit our e seminar calendar to register for live seminars on available features in GeneSpring GeneSpring manual Agilent GeneSpring User Manual Agilent publication n a August 2012 Agilent GeneSpring Installation Guide 29 www agilent com In this Book This book tells you how to install Agilent GeneSpring on your computer Agilent Technologies Inc 2012 Printed in United States of America 10 2012 001 G9220 Agilent Technologies
23. you upgrade your GeneSpring installation whenever a new product update becomes available CAUTION Always use the procedure described here to upgrade to a new version Do not uninstall the current version and install the new one as you risk losing access to parts or all of your analyses performed in the current version Every time you start GeneSpring while you are connected to the internet GeneSpring connects to the Agilent Server to retrieve information about available updates to technologies annotations and product updates An Update dialog box opens immediately after GeneSpring has launched to inform you of the availability of a product update To upgrade to the new version follow these steps 1 In GeneSpring select Help gt Update Product gt Update from Agilent Server from the main menu 2 Click Yes in the Updates dialog box to confirm that you want to go ahead with the update Your current session closes and GeneSpring retrieves the update from the Agilent server 3 Select the product update in the Automatic Software Update dialog box Details about the selected update including a list of new features enhancements and bug fixes are available in the lower panel of this dialog box Click Update An information dialog box informs you about the space requirements to perform the update 26 Agilent GeneSpring Installation Guide 4 Before continuing make sure there is sufficient space for the upgrade in the folder w
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