Seurat Windows Quick Start Guide

Synaptic Science LLC

Last Updated January 2008

 

 

 

 

 

If you encounter any problems trying to follow the instructions in this guide please contact us at support@synapticscience.com or post a question to our technical support forum http://synapticscience.com/phpBB2/index.php

 

 

Seurat Windows Quick Start Guide  1

Synaptic Science LLC   1

Last Updated January 2008  1

1      Assumptions  2

2      Installation Requirements  2

3      Installation steps  3

3.1       Seurat Server 3

3.2       Seurat Client using Windows Installer (Option 1) 5

3.2.1        Install Seurat Server as Windows Service  8

3.3       Seurat Client using Webstart Installer (Option 2) 9

3.3.1        Installing jetty as windows service  10

3.3.2        Starting jetty as windows service  10

3.3.3        Stopping jetty as windows service  10

3.3.4        Removing jetty as windows service  10

4      Troubleshooting  10

4.1       Seurat Server Installation  11

4.1.1        PostgreSQL Installation Automatically Uninstalls Itself  11

 

1       Assumptions

This guide is meant to get you up and running quickly with Seurat. To do this it makes several assumptions about how you will install Seurat.  If your situation does not match these assumptions then please refer to our more detailed Installation and Administration Guides on our website at www.synapticscience.com

 

In this guide we are assuming:

 

  1. That you will install the Seurat Client and Seurat Server both onto the same Windows Vista, XP Professional - SP2, 2000, 2000 server or 2003 server machine.
  2. That you will be using the Synaptic Science native database schema that comes with Seurat. If you want to configure Seurat to talk to your existing database please refer to the Seurat Database Mapping Guide on our website.
  3. You will load the test cMet dataset as the test data for use with Seurat.
  4. This is the first time you are installing Seurat. IF you are upgrading from an earlier version then you will need to read the Installation and Administration guides for Seurat.

2       Installation Requirements

As SEURAT is a pure Java application it can run on any platform supporting a Java 1.5 or greater JVM. Starting with version 5.0 of SEURAT you must use at least a 1.5 JVM.

 

The SEURAT Server has been successfully deployed under Windows, AIX and Linux. The SEURAT client has been successfully deployed under Windows (Vista, XP, 2000, 2003 Server), AIX, Linux and Mac OSX.

 

If your particular platform or configuration does not seem to be supported please contact us at sales@syanpticscience.com. As long as your platform supports 1.5 JVM or greater Seurat will be able to run on your platform.

 

The installation requirements for Windows are:

 

 

3       Installation steps

3.1    Seurat Server

  1. Download the client and server installers for windows from the download link on our website at www.synapticscience.com

 

  1. Run the server installer taking all the defaults with the exception of changing the port the PostgreSQL database will run on within the “Initialize database cluster” screen to 3247.

 

    1. NOTE: For Windows Vista installations you MUST use right mouse click -> run as administrator when running the downloaded installers otherwise the SEURAT installers for the client and server will fail to run.

 

  1. Make sure you write down the postgreSQL super user account password you are prompted to supply on this same screen as you will need it later on when loading the cMet test data set into the database.

 

  1. Upon completion of the Seurat Server installer navigate to the C:\Program Files\SynapticScience\SeuratServer directory and rename the following files:

 

    1. Make a copy of the pri_mappings.properties.example file and rename that copy to pri_mappings.properties
    2. Make a copy of roles.properties.examaple file and rename that copy to roles.properties

 

  1. Starting with version 4.4 of Seurat, license management is performed by the Seurat Server. If you are using version 4.4 of Seurat or later then save the license file supplied to you by Synaptic Science into the  C:\Program Files\SynapticScience\SeuratServer\bin directory and name it seurat.lic

 

  1. Navigate to the C:\Program Files\SynapticScience\SeuratServer\data directory

 

  1. Double click on the installCmetSampleData.bat batch file. This will issue a command to load the cMet test data set into the PostgreSQL database that was installed as part of the Seurat Server installation process.

 

  1. You will be prompted for the PostgreSQL databases postgreSQL super user account password. Enter it and then wait for the data load script to run to completion. You will see a few errors about objects already existing which can be ignored.

 

  1. Select the Start->All Programs->Seurat Server->Interactive Seurat Server menu option created by the Seurat Server installer and if everything is configured correctly you should see a screen like the one shown below:

 

 

 

3.2    Seurat Client using Windows Installer (Option 1)

  1. Run the downloaded Seurat Client installer for Windows and accept all defaults for the Seurat Client as well as for the PyMol installation screens that will be kicked off by the installer.

 

  1. To start the Seurat client select the Start->All Programs->Seurat Client->Seurat Client menu option and after a few moments and the presentation of a splash screen you should be presented with the Seurat login in screen as shown below

 

 

  1. With versions of Seurat prior to and including 4.3 license management is performed in the client. If however you are using version 4.4 or later of Seurat then license management is performed in the server and you can skip steps 12 and 13. If you are using version 4.3 or earlier before you can login you will need to tell Seurat where to find your license file. To do this click the “Prefs…” button and you will be presented with a screen like the one below

 

 

  1. Switch to the License tab, click the “Browse…” button and then select the license file for Seurat that you were sent earlier. Once you have selected the license file click the “OK” button and you will be returned to the login window of Seurat.
    1. NOTE: If you do not yet have a Seurat license file then please go to the Contact Us link on our website and fill out a form requesting a license or if you have already purchased Seurat contact us at sales@synapticscience.com.

 

  1. In the login window enter a username of demo and a password of demo and click Connect. Note that the demo user account was created as part of the script that loads the cMet test data set

 

  1. Once logged in you will see the List Manager (initial) screen within Seurat.

 

 

  1. Click on the Quick Search  button and on the Quick Search (as shown below) enter the identifiers 31137, 31437 and hit return (or click get results).

 

 

  1. You should see a screen like the following after a few seconds

 

 

  1. To learn about how to use the full set of Seurat features please refer to the Seurat Users Guide on our website.

 

If you encounter any problems following these steps please report them to support@synapticscience.com, post a question to the forum link on our website or call our offices at 301 915 0274.

 

To learn how to configure Seurat and how to share your results with your colleagues please refer to the Seurat Administrators Guide, Seurat Database Mapping Guide and the Seurat Users guide on our website www.synapticscience.com

 

3.2.1      Install Seurat Server as Windows Service

If you want to setup the Seurat Server so that it will automatically restart after the machine on which it is installed is rebooted execute the following steps:

 

 

1.       Open a windows command window and cd to the Seurat Server bin directory (which is C:\Program Files\SynapticScience\SeuratServer\bin by default).

 

2.       Define the environment variable JAVA_HOME to point to the top level directory of an installed version of the j2sdk1.4.2_12 SDK. So for example if you had the SDK installed in C:\j2sdk1.4.2_12 you would need to issue the command “set JAVA_HOME= C:\j2sdk1.4.2_12”

a.       NOTE: Pointing JAVA_HOME to the jre that comes bundled with the Seurat Client and Seurat Server after installation for this step WILL NOT WORK as the JavaService.exe program we are using to install Seurat as a service requires the tools.jar jar file that only comes with the JDK. You will need to go to the sun website and download and install the SDK and then make JAVA_HOME point to the install location you choose.

 

3.       Define the environment variable SEURAT_HOME to point to the top level directory of the Seurat Server. Assuming an installation into the default directory that would be achieved by the command “set SEURAT_HOME=C:\Program Files\SynapticScience\SeuratServer”

a.       NOTE: DO NOT put double quotes around the path specified in the setting of the SEURAT_HOME environment variable as the InstallSeuratAsService.bat file will take care of dealing with the spaces in the name.

 

4.       Assuming you installed the Seurat Server into its default location issue the command “.\InstallSeuratAsService.bat pgsql-8.1 –auto” to install the Seurat Server as a service. The service will appear in the Services window under the Administrative Tools section of the Control Panel with the name “SeuratServer”

a.       Note that although this will create a service to run the Seurat Server that will start automatically upon system restart you still have to manually start the service after it has been installed (or you could reboot the machine to test that it starts automatically). You can start the SeuratServer service once installed either by issuing the command “net start SeuratServer” or by navigating to the Services window of the Administrative Tools section in the Control panel and using the GUI there to start the service from the list of Windows Services.

b.       The first argument pgsql-8.1 passed to the command to install the SeuratServer service is the name of the PostgreSQL database service and denotes the fact that the SeuratServer service depends upon the PostgreSQL service having been started before it will itself be started. This means that the SeuratServer service will not start unless the PostgreSQL database service is running.

c.        If you chose to install the Seurat Server into other than the default directory then make sure you set SEURAT_HOME appropriately.

 

If you ever want to uninstall the SeuratServer service created in step 5 then issue the command “JavaService -uninstall SeuratServer” from the same directory in which you issued the InstallSeuratAsService.bat command with all the same environment variables defined.

3.3    Seurat Client using Webstart Installer (Option 2)

An alternative to running the supplied Seurat Client installer (which is optimized for a single user evaluation environment) is to use the WebStart version of the Seurat Client.

 

The WebStart version allows a team to evaluate the collaborative features (emailing of job links to colleagues, easy web based deployment of documents and upgrades, etc…) of Seurat in greater depth.

To install and run the WebStart version of the Seurat Client do the following:

 

  1. Download the latest WebStart Seurat Client version from the downloads page of the Synaptic Science website (named SeuratClientWebstart_VX.X.jar where X.X represents the current version).
  2. Unzip or unjar the contents of the file to create a directory named seurat-jetty in the directory into which you decide to unjar the jar file contents.
  3. Open a windows command window.
  4. Change directory into the seurat-jetty directory created by unjar’ing the contents of the jar file.
  5. Issue the command “java –jar start.jar” (omitting the double quotes used here for emphasis)
  6. Open a web browser (Firefox, IE or Safari) and enter the URL http://localhost:9080/seurat/chemwb.jnlp
  7. You will then be presented with a sequence of WebStart dialogs as the Seurat Client is downloaded form the jetty webserver hosting the WebStart version of the Seurat Client and will be asked to trust the appliction.
    1. Please answer yes/allow to all such questions.
  8. You will then be presented with the Seurat Login window.
  9. Continue on to the next section if you want to learn how to install the jetty web server as a windows service so that it will always automatically be running after a server machine restart.

3.3.1      Installing jetty as windows service

(in your  <jetty-root>/bin)
Jetty-Service.exe --install jetty-service.conf
or
Jetty-Service.exe -i jetty-service.conf

3.3.2      Starting jetty as windows service

(in your  <jetty-root>/bin)
Jetty-Service.exe --start jetty-service.conf
or
Jetty-Service.exe -t jetty-service.conf

3.3.3       Stopping jetty as windows service

(in your  <jetty-root>/bin)
Jetty-Service.exe --stop jetty-service.conf
or
Jetty-Service.exe -p jetty-service.conf

3.3.4       Removing jetty as windows service

(in your  <jetty-root>/bin)
Jetty-Service.exe --remove jetty-service.conf
or
Jetty-Service.exe -r jetty-service.conf

Note: The above application (Jetty-Service.exe) must execute with administrator rights otherwise, it fails.
In Vista, even with administrator account the service fails to install. Giving an error 'OpenSCManager failed'.
Below is the solution to this problem. This will now open a command prompt window with administrator rights.

Go to Start | All Programs | Accessories, then right-click on "Command Prompt", and select "Run as administrator".

4       Troubleshooting

This trouble shooting section only documents problems that may be encountered during the installation process.

 

For troubleshooting tips on administering the SEURAT platform see the Troubleshooting section of the Seurat Administrators Guide which is available from the “Start->All Programs->Seurat Server->Administrators Guide” menu item.

 

For troubleshooting tips on using SEURAT in general see the Troubleshooting section of the Seurat Users Guide which is available from the “Start->All Programs->Seurat Client->Users Guide menu item.

 

4.1    Seurat Server Installation

4.1.1      PostgreSQL Installation Automatically Uninstalls Itself

 

4.1.1.1  Description

At the very end of the PostgreSQL installation wizard the PostgreSQL installer issues an error and automatically uninstalls itself.

 

4.1.1.2  Cause

You are attempting to install the Seurat Server from a non windows administrator account or an account that cannot grant the “Log on as a service” and “Log on locally” rights to the windows service account the PostgreSQL installer tried to create during installation (or the account you created before installation and specified to the installer did not have these rights).

 

4.1.1.3  Solution

Please log into the machine as a windows administrator and re-run the installer.