Agilent Genomic Workbench 6...To uninstall Agilent Genomic Workbench server without removing database schema 27 To uninstall Agilent Genomic Workbench server, the database schema and

Agilent Genomic Workbench 6.0

Standard Edition

Installation Guide

2 Agilent Genomic Workbench 6.0Standard Edition Installation Guide

Notices © Agilent Technologies, Inc. 2010

No part of this manual may be reproduced in any form or by any means (including electronic storage and retrieval or translation into a foreign language) without prior agreement and written consent from Agilent Technologies, Inc. as governed by United States and international copyright laws.

Revision Revision A, February 2010

Agilent Technologies, Inc. 5301 Stevens Creek Blvd. Santa Clara, CA 95051

Microsoft ® is a U.S. registered trademark of Microsoft Corporation in the USA and other countries.

Software Revision This guide is valid for 6.0 and later revisions of the Agilent Genomic Workbench 6.0 software, until superseded.

Warranty The material contained in this document is provided “as is,” and is subject to being changed, without notice, in future editions. Further, to the maximum extent permitted by applicable law, Agilent disclaims all warranties, either express or implied, with regard to this manual and any information contained herein, including but not limited to the implied warranties of merchantability and fitness for a particular purpose. Agilent shall not be liable for errors or for incidental or consequential damages in connection with the furnishing, use, or performance of this document or of any information contained herein. Should Agilent and the user have a separate written agreement with warranty terms covering the material in this document that conflict with these terms, the warranty terms in the separate agreement shall control.

Technology Licenses The hardware and/or software described in this document are furnished under a license and may be used or copied only in accordance with the terms of such license.

Restricted Rights Legend If software is for use in the performance of a U.S. Government prime contract or subcontract, Software is delivered and licensed as “Commercial computer software” as defined in DFAR 252.227-7014 (June 1995), or as a “commercial item” as defined in FAR 2.101(a) or as “Restricted computer software” as defined in FAR 52.227-19 (June 1987) or any equivalent agency regulation or contract clause. Use, duplication or disclosure of Software is subject to Agilent Technologies’ standard commercial license terms, and non-DOD Departments and Agencies of the U.S. Government will receive no greater than Restricted Rights as defined in FAR 52.227-19(c)(1-2) (June 1987). U.S. Government users will receive no greater than Limited Rights as defined in FAR 52.227-14 (June 1987) or DFAR 252.227-7015 (b)(2) (November 1995), as applicable in any technical data.

Safety Notices

A CAUTION notice denotes a hazard. It calls attention to an operating procedure, practice, or the like that, if not correctly performed or adhered to, could result in damage to the product or loss of important data. Do not proceed beyond a CAUTION notice until the indicated conditions are fully understood and met.

A WARNING notice denotes a hazard. It calls attention to an operating procedure, practice, or the like that, if not correctly performed or adhered to, could result in personal injury or death. Do not proceed beyond a WARNING notice until the indicated conditions are fully understood and met.

CAUTION

WARNING

3 Agilent Genomic Workbench 6.0 Standard Edition Installation Guide

Contents

1 Installing Agilent Genomic Workbench Server Software Components 4

Step 1. Check system requirements before you start 4

Step 2. Set up a Windows user account with administrator privileges 4

Step 3. Set up a common storage directory 6

Examples of UNC notation for path names 7 How common storage is used 7

Step 4. Install Agilent Genomic Workbench server for the first time 9

Backing up the MySQL database 15

2 Installing Agilent Genomic Workbench Client 16

Step 1. Check these items before you start 16

Step 2. Disable User Account Control (UAC) in Windows Vista 16

Step 3. Install Agilent Genomic Workbench client 17

Step 4. Enable User Account Control (UAC) in Windows Vista 21

3 Starting Agilent Genomic Workbench Software 22

4 Using Agilent Genomic Workbench Services 24

RemoteTaskManager Service 24

DataTransfer Service 24

Writer Service 24

ProbeUpload Service 25

Starting and stopping services 25

To start and stop services from the Control Panel 25 To start or stop a service using batch files 26 To check memory usage 26

5 Uninstalling or Reinstalling Genomic Workbench Server 27

To uninstall Agilent Genomic Workbench server without removing database schema 27

To uninstall Agilent Genomic Workbench server, the database schema and its contents 29

To reinstall Agilent Genomic Workbench server with an existing database 31

6 Configuring MySQL Server (Reference information) 34


1 Installing Agilent Genomic Workbench Server Software Components

This section includes the following topics:

Step 1. Check system requirements before you start

Step 2. Set up a Windows user account with admin privileges

Step 3. Set up a common storage directory

Step 4. Install Agilent Genomic Workbench server for the first time

Step 1. Check system requirements before you start

1 Check to make sure that your computer system meets the following minimum requirements. The requirements listed here are for Agilent Genomic Workbench Server software components. See page 16 for a list of system requirements for Agilent Genomic Workbench client software.

Operating System: Windows XP 64- bit or Windows Vista 64- bit

NOTE Genomic Workbench server will also run on Windows XP 32-bit, with limited performance.

Processor: Intel Core 2 Duo CPU

Available Memory (RAM): 4 GB

Hard Disk Space: 200 GB

Display Resolution: 1280 X 800

Internet Connectivity: T1 or T3 connection (1.5 Mbps)

2 If MySQL is already installed on the computer, make sure it is version 5.1 Pro.

Otherwise MySQL will be installed with Genomic Workbench. MySQL server configuration is done automatically during the installation of Agilent Genomic Workbench Server software as described on page 9.

Step 2. Set up a Windows user account with administrator privileges

Agilent Genomic Workbench registers several Windows services which are automatically started when the server machine starts. These services handle data transfer between eArray Web site and the Agilent Genomic Workbench server software, as well as performing file processing for eArrayXD. The installation of Agilent Genomic Workbench server software requires the user to have administrative privileges on the machine. It requires the current user to have administrative privileges. Contact your System Administrator to learn how to give administrator privileges to this Windows user account. Do this before you install the Agilent Genomic Workbench server. Otherwise, the installation program will finish but the required services won’t be registered and the software won’t run.

Installing Agilent Genomic Workbench Server Software Components

Agilent Genomic Workbench 6.0 Standard Edition Installation Guide 5



Step 3. Set up a common storage directory

Agilent Genomic Workbench server and client application require a common file storage set up with appropriate access so that it can store/access files created during various operations.

1 Create a directory to assign as your Common Storage Directory during installation of Agilent Genomic Workbench.

Create the directory in a disk in file system with at least 400 GB of available space.

Create the directory in a shared location on the network with read- write access from the computer where Agilent Genomic Workbench server will be installed. Please contact your System Administrator to learn how to set up a shared directory with read-write access.

Create the directory without any spaces in the name. For example, name the directory ‘AgilentCommon’ instead of ‘Agilent Common’.

NOTE The directory can be located on a different computer than the one where Agilent Genomic Workbench server is being installed. It can even be a Network Access Storage (NAS-box) set up with appropriate configuration.

2 Give read- write access to all users who will be installing the Genomic Workbench client in your workgroup and sharing the Agilent Genomic Workbench server that you are installing.

To set up read- write access to a shared folder on Windows XP:

Right- click on the common directory and select Sharing and Security.

On the Sharing tab, click Share this folder on the network.

Click the Permissions button.

Set the Share Permissions options as follows in the figure below, then click OK.

To set up read- write access to a shared folder on Windows Vista:

Right- click on the common directory and select Properties.

On the Sharing tab, click Advanced Sharing.

Check the box labelled Share this folder.

Click the Permissions button.

Set the Share Permissions options as follows, then click OK.



3 Determine the UNC path name for the Common Storage Directory.

During installation, you are prompted to enter the Common Storage Directory path in UNC standard notation. This is the case even if you are installing Agilent Genomic Workbench on the computer where the common storage directory is located (see Example 2 below).

Examples of UNC notation for path names

Example 1: Suppose you are installing Agilent Genomic Workbench on a computer named 'machine1' while you configured a directory named 'AgilentCommon' on another computer named 'machine2' with read- write access to it from 'machine1'. The UNC standard name for this directory would be \\machine2\AgilentCommon.

Example 2: If you are installing Agilent Genomic Workbench on a computer named 'machine1' that has a shared directory on its D:\ drive named 'AgilentCommon', then you will enter the Common Storage Directory path during installation as:

Correct: \\machine1\AgilentCommon

Incorrect: D:\AgilentCommon

How common storage is used

The common storage is used by Agilent Genomic Workbench to store the following files:

Design/Annotation files written for microarray designs created using eArrayXD.

Design/Annotation files downloaded from eArray Web site upon request.



Input files when you use eArrayXD, such as probe files that you uploaded through Probe Upload, target sequence files that you uploaded for gene expression probe design, custom genome files that you imported, etc.

Error reports created during probe upload process.

Various temporary files used to update database and communicate with eArray Web site.

Index files for displaying information on user interface.

Track files that you can download for various DNA tracks.



Step 4. Install Agilent Genomic Workbench server for the first time

1 Before beginning to install Agilent Genomic Workbench server, be sure you have a valid eArray login and that you are a registered user on eArray Web site. You must provide your eArray Web site login name and password during the installation of the software. To become a registered user, go to earray.chem.agilent.com, then click Request for Registration. For details, see the online help on the site.

2 Login to the Windows system where you want to install Agilent Genomic Workbench server. Use an account that has administrator privileges.

3 Select the correct installer for your platform and operating system. If you are installing on Windows XP, double- click the Installer.exe file. If you are installing on Windows Vista, you must elevate your installation permissions. To do so:

Right- click the Installer.exe file.

Select Run as administrator…

Accept the User Account Control dialogs to proceed with the installation.

The following message is displayed.

The installer appears in a new dialog box.

4 Enter the information for the installer as described below. When you complete the information in a section, click Next to display the next section. You can click Previous to review information in a previous section.



Read the introductory information, then click Next.

When the MySQL Installation Option pane appears, select one of the following options, then click Next.

If you already have MySQL 5.1 or later installed on this machine, click Skip MySQL Installation.

If you don’t already have MySQL 5.1 or later installed, click Install MySQL 5.1.

Note: The MySQL version must be 5.1 or later to work with Agilent Genomic Workbench 6.0.

If you selected Skip MySQL Installation in the previous screen, enter the following MySQL Configuration information. Otherwise skip to the next screen.

MySQL Installation path – Browse to select the directory where MySQL 5.1 is installed.

Port Number – Enter the port number that MySQL uses to communicate. The default port is 3306, but may be different on your system.

MySQL Service Name –Enter the MySQL service name used on your system, The default service name is MySQL, but may be different on your system.

MySQL root password – Enter the root password for MySQL on your system.

Click Next to continue.



If you selected Install MySQL 5.1 on the MySQL Installation Option screen, enter the following MySQL Configuration information.

Note: Skip this step if you selected Skip MySQL Installation on the MySQL Installation Option screen. This pane applies to a new MySQL installation only.

MySQL Installation path – Browse to select the directory where you want to install MySQL.

Note: In Windows XP, the MySQL Installation path must not contain any empty spaces. For example, use ‘C:\mysql’ instead of ‘C:\Program Files\mysql’.

In Windows Vista, the MySQL Installation path must be a folder for which you have both full administrative read/write priviledges and which contains no empty spaces. In other words, the MySQL Installation path should be a folder created in an area other than Windows install directories such as ‘Program Files’ or ‘Windows’.

Port Number – Accept the default port number, unless you have a reason to change it.

MySQL Service Name –Accept the default MySQL service name, unless you have a reason to change it.


The following versions of MySQL will be installed:

5.1.36 (64-bit Agilent Genomic Workbench server) 5.1.30 (32-bit Agilent Genomic Workbench server)

Enter the following information for Common Storage:

Common Storage Path – Enter the Common Storage path that you set up for use with Agilent Genomic Workbench Software as described on page 6.

Note: Make sure that the value you provide follows UNC Standard format, that is:

\\<machine name>\<shared directory name>

This format must be used even if the common storage directory is on the same computer where you are installing Agilent Genomic Workbench server.




When the Proxy Server Configuration pane appears, click one of the following options:

No Proxy

Use Proxy Server

For normal operation, use the No Proxy option.

If you select to use a proxy server, see your system administrator to find out the Proxy user, password, host, and port information to enter on this screen.

Note: If problems arise, the proxy settings can be changed from the Miscellaneous tab in the User Preferences dialog box, after Agilent Genomic Workbench Standard Edition software is installed. See the Product Overview Guide for more information.


Enter your eArray User Name and Password, then click Next to continue.

The program tries to authenticate the user name and password, which takes a minute or so.

Indicate your preference for automatic updates:

If you want to have your system automatically detect and download the latest version of Agilent Genomic Workbench software, then mark the I would like to automatically receive Agilent Genomic Workbench software updates check box. Automatic updates are done only for minor release versions of the software. Major release versions must be downloaded manually from the eArray Web site.

If you don’t want to receive automatic updates, then clear the I would like to automatically receive Agilent Genomic Workbench software updates check box.

Click Next.



If you have entered valid credentials and authentication is successful, the License Agreement pane appears.

Read the License Agreement. Click I accept the terms of the License

Agreement. Click Next.

Select the location to install the Agilent Genomic Workbench server on your system.

Click Choose to change the default location of the installation on your system or click Next to accept the default location.

Note: In Windows XP, the MySQL Installation path must not contain any empty spaces. For example, use ‘C:\AgilentGenomicWorkbench’ instead of ‘C:\Program Files\Agilent Genomic Workbench’.

In Windows Vista, the MySQL Installation path must be a folder for which you have both full administrative read/write privileges and which contains no empty spaces. In other words, the MySQL Installation path should be a folder created in an area other than Windows install directories such as ‘Program Files’ or ‘Windows’.



The installer creates a shortcut that you can use to conveniently start the server software. By default, the installer creates this shortcut in a program group Agilent Genomic Workbench Server. Click Next to accept this shortcut or select one of the following other options if desired:

In a new Program Group – Type in the name of a new program group for the shortcut.

In an existing program group – Select the existing program group where you want to put the shortcut.

In the Start Menu - Puts the shortcut in the Windows Start Menu.

On the Desktop - Puts the shortcut on your desktop.

In the Quick Launch Bar - Puts the shortcut in the Quick Launch Bar.

Other - Puts the shortcut in a new or existing folder that you select.

Don’t create icons – No shortcut is created.

Note: Mark the check box for Create Icons for All Users at the bottom of the pane. This will create a program shortcut that is available to all user accounts on your computer. Otherwise, the shortcut will only be available in your user account. This option applies to program icons created in a New Program Group, the Windows Start Menu, or On the Desktop only.

5 Review the installation settings shown on the Installation Summary pane. You will have to scroll down to see all of the information provided. To make changes, click Previous to go back to any sections you want to change.

6 Click the Install button to start the installation program.

7 A progress bar and various progress messages are displayed as Agilent Genomic Workbench server components are installed, such as the following:

You will get error messages if any of the following things fail during the install process:

A connection can’t be made to the MySQL database.

The program can’t access the Common Storage location.

Read- write access is not available over the directory from the computer where installation is running.

8 When the Install Complete pane appears, click Done .



Once installation is complete, the installer will automatically start the required services on the host computer. For more information, see Using Agilent Genomic Workbench Services on page 24.

9 Proceed to install the Agilent Genomic Workbench client in the next section.

NOTE Although you can install client software immediately after the Agilent Genomic Workbench server software is installed, the client software cannot be used immediately. It takes some time for the server program to retrieve all of the custom content of your workgroup from the eArray Web site. This download process can take as long as several days or more, especially for workgroups with extensive custom content stored on the eArray Web site.

Backing up the MySQL database

It is important that you regularly back up the MySQL database on your system. Please see the MySQL 5.1 documentation for how to do this or ask your system administrator for help. Agilent Genomic Workbench 6.0 does not have a utility for backing up the MySQL database.

CAUTION There is a risk of significant loss of data if your system has a serious hardware failure and you are unable to restore the MySQL database from a recent backup.

Installing Agilent Genomic Workbench Client


2 Installing Agilent Genomic Workbench Client

This section includes the following topics:

Step 1. Check these items before you start

Step 2. Install the Agilent Genomic Workbench client

Step 1. Check these items before you start

The requirements below must be met before you start the installation of Genomic Workbench Standard Edition client.

1 Check that your computer system meets the following minimum requirements:

Operating System: Windows XP or Vista (32- bit or 64-bit)

Processor: Intel Core 2 Duo CPU

Available Memory (RAM): 2 GB

Hard Disk Space: 100 GB

Display Resolution: 1280 X 800

Internet Connectivity: T1

2 Verify that Agilent Genomic Workbench server has been installed .

Your computer must be connected to this server during the installation of the Agilent Genomic Workbench client, and also whenever you use the program.

You will be asked to enter the network name of this computer during the installation of the Agilent Genomic Workbench client.

Installation of the Agilent Genomic Workbench server is described previously in this document, starting on page 9.

3 Download the installer file from Agilent:

Genomic_Workbench_Installer_x.x.x.x This installer installs files for all of the programs in the Agilent Genomic Workbench Standard Edition suite.

Step 2. Disable User Account Control (UAC) in Windows Vista

On Windows Vista (both 32 and 64 bit versions), you must disable User Account Control before you install the Genomic Workbench client. If User Access Control (UAC) is enabled, the software can fail to install the Feature Extraction module because the required system registry will not be accessible.

1 Click the Start button in Windows Vista

2 Select Control Panel. The Control Panel window opens.

3 Select User Accounts. The User Accounts window opens.



4 Select User Accounts again.

5 Select Turn User Account Control on or off. The User Account Control dialogue window opens. Click Continue to allow changes to be made to your computer.

6 Uncheck the box labeled Use User Account Control (UAC) to help protect your computer.

7 Click OK to continue.

Step 3. Install Agilent Genomic Workbench client

The client program is part of the Agilent Genomic Workbench Standard Edition suite. You install all of the programs in the suite together. Note that some programs in the suite require that you must purchase additional licenses from Agilent.

1 Double- click the Genomic_Workbench_Installer_x_x_x_xx.exe icon .







Enter the following information about your MySQL Server installation, then click Next:

Database Host – Enter the host name or IP address of the computer where MySQL Server is installed. For example, if MySQL Server 5.1 is installed on a computer named ‘dbmachine’, enter the value dbmachine or its IP address in Host textbox.

Note: Do not enter ‘localhost’ or ‘127.0.0.1’ as value for host even if your MySQL Server 5.1 installation resides on same computer where Agilent Genomic Workbench server is being installed.

Database Port – Enter the port number on which MySQL Server 5.1 listens for its clients. The default port number that MySQL uses (3306) is displayed as a default. If your uses a different port, ask your database administrator for the exact port number. The port number must be entered as a number.

The Installer does the following tests with the information you entered:

Tries to establish a test connection to the MySQL database. Tries to access the Common Storage location. Checks if read-write access is available over the directory from the computer where installation is running.

If any of these checks fails, an appropriate error message is displayed.



If you have entered valid credentials and authentication is successful, the License Agreement pane appears.

Read the License Agreement. Click I accept the terms of the License

Agreement. Click Next.

Select the location to install the Agilent Genomic Workbench client on your system.

Click Choose to change the default location of the installation on your system or click Next to accept the default location.



The installer creates a shortcut that you can use to conveniently start the client software. By default, the installer creates this shortcut in a program group Agilent Genomic Workbench Enterprise Edition. Click Next to accept this shortcut or select one of the following other options if desired:

In a new Program Group – Type in the name of a new program group for the shortcut.

In an existing program group – Select the existing program group where you want to put the shortcut.

In the Start Menu - Puts the shortcut in the Windows Start Menu.

On the Desktop - Puts the shortcut on your desktop.

In the Quick Launch Bar - Puts the shortcut in the Quick Launch Bar.

Other - Puts the shortcut in a new or existing folder that you select.

Don’t create icons – No shortcut is created.

Note: Mark the check box for Create Icons for All Users at the bottom of the pane. This will create a program shortcut that is available to all user accounts on your computer. Otherwise, the shortcut will only be available in your user account. This option applies to program icons created in a New Program Group, the Windows Start Menu, or On the Desktop only.

3 Review the installation settings shown on the Pre- Installation Summary pane. You will have to scroll down to see all of the information provided. Click Previous to go back to any sections you want to change.


A progress bar and various progress messages are displayed as Agilent Genomic Workbench client is installed, including the one shown below for Feature Extraction:



5 Click Done when the Install Complete pane appears.

Step 4. Enable User Account Control (UAC) in Windows Vista

Following successful installation on Windows Vista, you should re-enable the User Account Control (UAC) to protect your computer.

1 Click the Start button in Windows Vista.

2 Select Control Panel. The Control Panel window opens.

3 Select User Accounts. The User Accounts window opens.

4 Select User Accounts again.

5 Select Turn User Account Control on or off. The User Account Control dialogue window opens. Click Continue to allow changes to be made to your computer.

6 Check the box labeled Use User Account Control (UAC) to help protect your computer.

7 Click OK to continue.

Starting Agilent Genomic Workbench Software


3 Starting Agilent Genomic Workbench Software

After you have installed Agilent Genomic Workbench Standard Edition as described in this manual, start the program as described below.

1 Double- click the Agilent Genomic Workbench Standard Edition 6.0 icon from your desktop or select Agilent Genomic Workbench Standard Edition 6.0 from the Windows Start menu.

How you start the program depends on the choice you made for Shortcut Folder during installation of the Agilent Genomic Workbench Client.

2 If this is the first time you have opened Agilent Genomic Workbench after installation, you are presented with a license agreement. Read the license and click “I accept” to proceed.

3 Enter your eArray User Name and Password, then click OK.

4 Select an application type, then click OK. If you get an invalid

license message, ignore it for now. You will get a chance to enter your license later (see Step 8).

5 If your workgroup has recently installed the Agilent Genomic Workbench server, you may see the following message:

a If you click Yes, the following screen is displayed in a separate

window.

Starting Agilent Genomic Workbench Software


b Wait awhile, then try starting up Agilent Genomic Workbench Standard Edition 6.0 as described in Step 1 until the program opens.

NOTE It takes some time for the server program to retrieve all of the custom content of your workgroup from the eArray Web site after the Agilent Genomic Workbench server software is installed. The download process can take up to several days, if your workgroup has extensive custom content stored on the eArray Web site.

6 When the Open Application window appears, click Product Overview.

7 Read the Product Overview Guide.

8 If your application requires a license, follow the instructions in the Product Overview Guide to enter its licence information.

9 Follow the instructions in the Product Overview Guide to open your application.

Using Agilent Genomic Workbench Services


4 Using Agilent Genomic Workbench Services

Agilent Genomic Workbench server registers the following services on the Windows computer where it is being installed. These services are described in this section.

RemoteTask Manager

DataTransfer

ProbeUpload

Writer

RemoteTaskManager Service

This service does those tasks that require remote processing. They include loading Catalog and Workgroup data at start- up, checking for updates on eArray Web site, transferring updated data, sending out remote search requests (such as HD Search and Probe Design requests) and loading the search results, and submitting a Microarray design on eArray Web site. This service coordinates with DataTransfer service for sending/receiving files. Unless this service retrieves existing user workgroup data and catalog data from the local system, the Writer and ProbeUpload services won’t be able to do their work. Client applications won’t start in this case either.

Only one instance of RemoteTaskManager service can run at a time for a given Workgroup. If you try to manually start another instance, an error message is displayed that says that another instance is already running.

As it runs, the RemoteTaskManager service creates log files in the directory: <Installation- directory>/RemoteTaskManager/log/.

DataTransfer Service

This service sends and receives data in the form of files from the local system to the eArray Web site and from eArray Web site back to the local system. Files transferred from the eArray Web site are then processed by the RemoteTaskManager service for various purposes. This service does not process files that it sends out or receives.

Only one instance of DataTransfer service can run at a time for a given Workgroup. If you try to manually start another instance, an error message is displayed that says that another instance is already running.

As it runs, the DataTransfer service creates log files in the directory: <Installation- directory>/DataTransfer/log/.

Writer Service

This service creates the design files for Microarray designs created by users on the local system. This service requires all Catalog and Workgroup data to be present in the local database before it can create the design files. Requests are not processed until catalog and workgroup data is processed and transferred to the local system by the RemoteTaskManager. Writer service processes one request at a time if multiple microarray design output requests are submitted concurrently.



Only one instance of Writer service can run at a time for a given Workgroup. If you try to manually start another instance, an error message is displayed that says that another instance is already running.

As it runs, Writer service creates log files in the directory: <Installation-directory>/Writer/log/.

ProbeUpload Service

This service transfers the probes submitted by users to the database. It processes the input file (.txt and .xls files) and loads the probes into database. These files are kept on Common Storage temporarily once they are uploaded by the user from the user interface. It will not process any request until RemoteTaskManager service processes and transfers Catalog and Workgroup data to the local system, as it first checks to see if the probe is already present in the system.

Only one instance of ProbeUpload service can run at a time for a given Workgroup. If you try to manually start another instance, an error message is displayed that says that another instance is already running.

As it runs, ProbeUpload generates log files in the directory: <Installation-directory>/ProbeUpload/log/.

Starting and stopping services

Services installed by Agilent Genomic Workbench server are started automatically when installation is complete and also whenever the computer is rebooted. You can also start and stop the services manually as described in this section. For example, suppose you find out that a service stopped after an exception and you want to start it again. Or, you might want to stop all the services to upgrade your MySQL installation, and need to start them again once the MySQL upgrade is complete.

To start and stop services from the Control Panel

1 Open the Services window from the Windows Control Panel.

2 Scroll to find the Agilent Genomic Workshop services.

3 Click on the service of interest, then click Start or Stop from the Action menu.



To start or stop a service using batch files

Agilent Genomic Workbench server includes one- click batch files to let you start and stop services manually, as needed.

1 Find the batch files in Windows Explorer. They are located in the directory you selected during installation.

2 Double- click the batch file name of interest, depending on whether you want to start or stop a service.

start_DataTransfer_service.bat

start_ProbeUpload_service.bat

start_RemoteTaskManager_service.bat

start_Writer_service.bat

stop_DataTransfer_service.bat

stop_ProbeUpload_service.bat

stop_RemoteTaskManager_service.bat

stop_Writer_service.bat

To check memory usage

1 Open the Task Manager window.

2 Click the Processes tab and view the value in the Mem Usage column for the processes of interest.

Uninstalling or Reinstalling Genomic Workbench Server


5 Uninstalling or Reinstalling Genomic Workbench Server

To uninstall Agilent Genomic Workbench server without removing database schema

This option lets you uninstall the Agilent Genomic Workbench server software without removing the database schema that it created during installation and data that was added to it by users.

1 Log in to the Windows system where you installed the application. Use an account that has administrator privileges.

2 Run the Uninstall Agilent Genomic Workbench Server program, which is located in the Shortcut Folder you selected during the Agilent Genomic Workbench Server installation. A message is displayed while the Uninstall program starts up.

3 When the Uninstaller program dialog box appears, enter the information for the Uninstaller as described below.


Select Uninstall Application, do not remove Database, then click Uninstall.



The following warning message is displayed.

Click OK to continue.

Enter the following information about your MySQL server installation.

Host – Enter the host name or IP address of the computer where MySQL server is installed. For example, if MySQL Server 5.1 is installed on a computer named ‘dbmachine’, enter the value dbmachine or its IP address. Do not enter ‘localhost’ or ‘127.0.0.1’ .

Port – Enter the port number where MySQL Server 5.1 listens for its clients. The default port number that MySQL uses (3306) is displayed as a default. If your Database Administrator has set up MySQL Server 5.1 to listen on different port than default, ask your database administrator for the exact port number. Don’t enter an alpha-numeric value for port number.

4 Click the Uninstall button.

A progress bar and various progress messages are displayed as Agilent Genomic Workbench client is uninstalled.

5 When the Uninstall Complete pane appears, click Done .

6 Manually remove the directories and files in the Common Storage directory, if desired.



To uninstall Agilent Genomic Workbench server, the database schema and its contents

This option removes the application along with the database schema that it created during installation and data that was added to it by users.

1 Login to the Windows system where you installed the application. Use an account that has administrator privileges.

2 Run the Uninstall Agilent Genomic Workbench Server program, which is located in the Shortcut Folder you selected during the Agilent Genomic Workbench Server installation.

When the program is ready, the Uninstaller appears in a new dialog box.

3 Enter the information for the Uninstaller as described below.


Select Uninstall Database and all its contents along with application, then click Uninstall.



A Warning message is displayed to make sure you want to remove the database.

If so, click OK to continue.

Enter the following information about your MySQL server installation.

Host – Enter the host name or IP address of the computer where MySQL server is installed. For example, if MySQL Server 5.1 is installed on a computer named ‘dbmachine’, enter the value dbmachine or its IP address. Do not enter ‘localhost’ or ‘127.0.0.1’ .

Port – Enter the port number where MySQL Server 5.1 listens for its clients. The default port number that MySQL uses (3306) is displayed as a default. If your Database Administrator has set up MySQL Server 5.1 to listen on different port than this default, ask your database administrator for the exact port number. Don’t enter an alpha-numeric value for port number.

Root password – Enter the root password for MySQL on your system.

4 Click the Uninstall button.

A progress bar and various progress messages are displayed as Agilent Genomic Workbench server and the MySQL database are uninstalled.

5 When the Uninstall Complete pane appears, click Done.

You may see a list of some items, usually directories, that could not be removed by the uninstall program.

6 Manually remove the directories and files in the Common Storage directory, if desired.



To reinstall Agilent Genomic Workbench server with an existing database

Use this procedure if you have an existing database or have just uninstalled Agilent Genomic Workbench server, without removing the database, as described on page 27.

1 Login to the Windows computer where you want to install Agilent Genomic Workbench server. Use an account that has administrator privileges.

2 Select the correct installer for your platform and operating system. Then double- click the Installer.exe file.







This screen shows the Agilent Genomic Workbench client applications that are currently connected to this server.

If possible, try to contact each client user before continuing, so that they may close their application. Otherwise, reinstalling the server software with client sessions in progress my result in unexpected behavior or results for the client. For example, if a CGH analysis workflow is running on one of the clients, the server update may interrupt the process and cause errors.

Click the RETRY button to update the list of client applications that are currently connected to the server.


4 Fill out the following screens as described previously for

server installation and click Next to display the next screen:

Automatic Updates

License Agreement

Choose Install Folder

Choose Shortcut Folder

5 Review the installation settings shown on the Installation Summary pane. You will have to scroll down to see all of the information provided. To make changes, click Previous to go back to any sections you want to change.


A progress bar and various progress messages are displayed as Agilent Genomic Workbench server components are installed, such as the following:

You will get error messages if any of the following things fail during the install process:

A connection can’t be made to the MySQL database.

The program can’t access the Common Storage location.

Read- write access is not available over the directory from the computer where installation is running.

7 When the Install Complete pane appears, click Done .



Once installation is complete, the installer will automatically start the required services on the host computer. For more information, see Using Agilent Genomic Workbench Services on page 24.

Configuring MySQL Server (Reference information)


6 Configuring MySQL Server (Reference information)

MySQL server configuration is done automatically during the installation of Agilent Genomic Workbench Server software components.

NOTE Under normal operation and circumstances, you won’t need to perform the manual configuration steps described in this section. The information is included here in case there is a problem.

Consider backing up your existing MySQL databases if you are using the same MySQL Server installation for other purposes.

Genomic Workbench software must be able to log in using MySQL’s ‘root’ user (database user) from any host so that it can create its own database, database user and grant appropriate privileges to its new database user.

MySQL automatically creates ‘root’ user account for logging in to MySQL server from the computer where MySQL Server is installed. In addition to the default ‘root’ account, Genomic Workbench also requires a ‘root’ account for logging in from any other host with proper privileges. This is true even if you are running the Agilent Genomic Workbench server software installer on the same computer where the MySQL server is currently installed. Agilent recommends that you install MySQL server and Agilent Genomic Workbench server on the same computer.

1 Check that MySQL is configured to accept ‘root’ user login from other hosts.

a. Log in to the computer where MySQL server is installed.

b. Open a command prompt.

c. Execute the command: mysql - u root mysql - p

If the error message: ' mysql ' is not recognized as an internal or external command, operable program or batch file, check that the MySQL Server installer's bin directory is included in your PATH environment variable. For help setting PATH variable, see http://dev.mysql.com/doc/refman/5.1/en/server- system-variables.html.

d. When MySQL asks you to enter your password, type the root user password and press Enter.

e. After MySQL displays a message that says you are now logged in, execute the following command including the semicolon at the end of the line: select user, host from user where user = 'root';

If the following information is displayed, continue with Step 3, as this means that MySQL is configured to accept log in from other hosts.

+- - - - - - - - +- - - - - - - - - - - - - - - - - - + | user | host | +- - - - - - - - +- - - - - - - - - - - - - - - - - - + | root | % |



| root | localhost | +- - - - - - - - +- - - - - - - - - - - - - - - - - - +

If only one record is returned as shown below, then continue with Step 2 to configure MySQL to a log in from other hosts.

+- - - - - - - - +- - - - - - - - - - - - - - - - - - + | user | host | +- - - - - - - - +- - - - - - - - - - - - - - - - - - + | root | localhost | +- - - - - - - - +- - - - - - - - - - - - - - - - - - +

f. Execute the command: exit;

2 Configure access to MySQL from other hosts using 'root' user, if you find this is necessary from Step 1.

a. Log in to the computer where MySQL server is installed.


c. Execute the following command: mysql - u root mysql - p



e. After MySQL displays a message that says you are now logged in, execute the following command including the semicolon at the end of the line:

grant all on *.* to 'root'@'%' identified by '<your- root- password>';

where <your- root- password> is the root password that you entered while logging in to MySQL. Note that the < and > characters are not part of the command, but the single quotation marks ( ' ) are.

The system should respond with:

Query OK, 0 rows affected

f. Execute the following command: exit;

3 Grant appropriate privileges to the 'root' user (configured for other hosts).

a. Login to the computer where MySQL server is installed.


c. Execute following command:

mysql - u root mysql - p







e. After MySQL displays a message that says you are now logged in, execute the following commands including the semicolon at the end of the line. Skip the first command if you did it in Step 2.

Command Expected Response grant all on *.* to 'root'@'%'; Query OK, 0 rows affected

update user set Grant_priv = 'Y' where user='root' and host = '%';

Query OK, 1 row affected (0.00 sec) Rows matched: 1 Changed: 1 Warnings: 0

commit; Query OK, 0 rows affected

flush privileges; Query OK, 0 rows affected

exit;

4 Set MySQL configuration parameters.

a. Stop the MySQL service.

b. Open the my.ini file located in your MySQL server installation directory.

c. Modify/Add the following configuration to the my.ini file:

max_allowed_packet=64M

innodb_buffer_pool_size=512M

tmpdir="=<new- location>"

where <new- location> is where you want to put temporary files from MySQL. Note that the < and > characters are not part of the command, but the quotation marks ( ") are.

d. Save the file and close it.

e. Start the MySQL service.

5 Make sure you have enough space in your MySQL data directory.

Agilent Genomic Workbench uses large scientific data that includes your own customized data and Agilent Catalog data. Because of this, your MySQL server installation must be on a high- end computer with sufficient disk space that is configured to make use of available disk space. If your MySQL data directory is not set to a location with sufficient disk space, then MySQL will not be able to hold data that is created with Agilent Genomic Workbench.

Though MySQL makes use of available disk space, eventually the disk may get full and you will need to add data files to your database or set up MySQL data directory to some other location.

Please visit http://dev.mysql.com/doc/refman/5.1/en/windows- create-option- file.html for information on how to set up a MySQL data directory for your MySQL installation. Or visit http://dev.mysql.com/doc/refman/5.0/en/adding- and- removing.html for information on how to add a new data file to your MySQL database. You may want your Database Administrator to perform these tasks for you.



If you change the location of your MySQL data directory after some data is already stored in the database, you will need to manually copy the contents of the previous data directory to the new data directory before you start the MySQL service again.

NOTE If your MySQL installation runs out of disk space and is cannot hold additional data, you will see exceptions in the application log files. Please refer to page 24for more information on Agilent Genomic Workbench services.

6 Set up a temporary directory for MySQL.

Agilent Genomic Workbench uses some MySQL features for bulk entry of data into a database. These features require a 'temp' directory for MySQL with sufficient available disk space. This disk space is used when bulk data is loaded and becomes available again after the data is saved to the database. If a temp directory is not set up, data loading operations for large datasets may fail, which will cause abnormal or unexpected behavior. If MySQL does run out of temporary disk space, the following exception is written to the appropriate application log files.

Caused by: java.sql.SQLException: Incorrect key file for table '<temp-directory- location>\#sql_6c0_0.MYI'; try to repair it

where <temp- directory- location> is location of the temporary directory and the .MYI file name after it may vary.

See http://dev.mysql.com/doc/refman/5.0/en/temporary- files.html to learn how to set up a temp directory location for MySQL server.

The following procedure describes how to set up a one- time temp directory for MySQL.

a Stop the MySQL service.

b Open my.ini file located in your MySQL server installation directory.

c Look for an entry such as tmpdir=<some- location>.

If you find one, edit the <some- location> to the location you want to configure as the temp directory.

If you don’t find one, add an entry with tmpdir=<new- location>.

Remember to use forward (/) slashes rather than backslashes for identifying Windows path names. If you do use backslashes, you must double them.

d Save the file and close it.

e Start the MySQL service.

Agilent Technologies, Inc. 2010 Revision A, February 2010

*G3800-90011* G3800-90011

Agilent Technologies

www.agilent.com

Documents

Agilent Genomic Workbench 6...To uninstall Agilent Genomic Workbench server without removing database schema 27 To uninstall Agilent Genomic Workbench server, the database schema and