Running Array Server in Windows

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Most of our clients are setting up ArrayServer on a Linux machine, which can easily enable HPC cluster and external tool integration. However, ArrayServer is much easier to setup on Windows OS, where most dependencies are already in OS.

Installing Array Server Service

Important: If you have been using ArrayServer, first stop the server and then backup the ArrayServer BaseDirectory (listed in ArrayServer.cfg). At a minimum, back up the data in BaseDirectory/Database.

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Download and install

  1. Download and save the ArrayServerServiceInstaller.msi in any folder
  2. Double click ArrayServerServiceInstaller.msi to install the service. You will be asked to choose where you want this service be installed (e.g. C:\Program Files\Omicsoft\Array Server Service). If installed successfully, ArrayServerService.exe, as well as some .dll files, should be in the folder you choose.

Update to the latest version

Go to the Array Server installation directory (e.g. C:\Program Files\Omicsoft\Array Server Service), right click on the file OmicsoftUpdater.exe, and select "Run as administrator".


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Configuring ArrayServer

Download configuration templates. Unzip and save them in the same folder where your service is installed (e.g. C:\Program Files\Omicsoft\Array Server Service).

Admin will have to modify three important configuration files based on downloaded template:

  • ArrayServer.cfg is the key configuration file. A few important options are :
    • Port, Port2 and Port3 define the port number for data communication between ArrayStudio client and ArrayServer. Make sure to open these ports on firewall.
    • DataPortBegin and DataPortEnd define the port range for Threaded Ftp data transfer. Make sure to open the port range on firewall.
    • BaseDirectory: this will be the working directory of the array server, storing all the raw and possessed data. Depending on the projects, it can take huge amount of disk space.
    • OmicsoftDirectory: This directory can sit locally or on a network drive. All the reference genomes, gene models, Affymetrix CDF files, log files, etc. are stored in this folder.
    • TempDirectory: This should be a local directory (i.e. NOT a network drive) for fast read and write access. It can take twice the size of an unzipped fastq file in some NGS tasks (we would suggest use a drive with at least 100GB storage).
    • The Folder section defines additional local or network folders monitored and available for access by array server users.
    • For a full list of options, see ArrayServer.cfg for more details.
    • For master-analytic server setup, please read Master Server and Analytic Server for more details.
  • default.template: it defines project level meta data, such as requiring project title, and list organism. Admin can customize the project meta data based on this template file and even enforce controlled vocabulary. For first time setup, the default values we prepared should be good to go. Admin can further customized based on the understanding of default.template wiki article.
  • sample.template: it defines sample level meta data, such as requiring users to fill organism and tissue for each samples in sample registration. Admin can customize the sample meta based on this template file and even enforce controlled vocabulary. For first time setup, the default values we prepared should be good to go. Admin can further customize based on the understanding of sample.template wiki article.
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Start Service

Right click on Computer or This PC (on the desktop, or the windows start menu), then click on Manage to open the Computer Manage window. You will see a service named "Array Server Service".


  1. Before starting the service, you should set the array server service user account. Right click on "Array Server Service | Property", then go to the Log On tab and select a user account, e.g. "MikeSmith". Note: This user account needs to have access rights to all the network drives monitored by the Array Server.
  2. Mouse right click to start Array Server Service. The first time starting the array server service may take hours, depending on the sizes of existing projects if it is a server migration.
  3. While the service starting is in progress, check the status in ArrayServerService.log in the installation folder (e.g. C:\Program Files\Omicsoft\Array Server Service).
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Updating Array Server Service

If you already have Array Server Service installed and want to update to the latest release version, please follow these steps:

  1. Stop the Array Server Service. Right click on Array Server Service in Computer Manage window and click stop (see above).
  2. Backup the Array Server BaseDirectory (listed in ArrayServer.cfg). At a minimum, back up the data in BaseDirectory/Database.
  3. Run OmicsoftUpdater.exe as administrator (see below). The file should be located in the same folder as ArrayServerService.exe (e.g. C:\Program Files\Omicsoft\Array Server Service )
  4. Restart the service by right clicking on Array Server Service in Computer Manage window, and click start.
Note: Whenever the array server service is updated, or configuration files are modified, a service restart is necessary to make the change effective.
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Uninstall Array Server Service

This is usually NOT necessary, but just in case one wants to completely remove the old version.
1. Delete the service by running the following command as administrator:

sc delete ArrayServerService

2. In Windows Control Panel -> Programs -> Programs and Features, uninstall the ArrayServerService.

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Command lines (Advanced)

Advanced windows users may run these commands to manage services:

1. Start Service

Net start ArrayServerService

2. Stop Service

Net stop ArrayServerService

3. Delete Service

sc delete ArrayServerService
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