Modifying Server Settings  Print-icon

To modify the configuration of your GenePattern server, use the Server Settings page:

  1. Click Administration>Server Settings to display the Server Settings page.
  2. From the Server Settings pane, select the server setting that you want to modify. GenePattern displays a page of related server configuration options.
  3. Modify and save the server configuration options.
  4. Optionally, return to step 2 to change additional settings.

The following table summarizes the server settings. For more detail, click a link in the table.

Access

Specify which clients have access to the server.

Advanced

Specify software source directories and other low-level configuration options.

Command Line Prefix

Specify commands and qualifiers to be prepended to the command line used to invoke a module or pipeline.

Custom

Create new server configuration options.

Database

Specify configuration options for the GenePattern database.

File Purge

Specify how long files remain on the server before being deleted.

GenePattern Log

Display the log file for the GenePattern server.

Job Configuration

Work with a job queue that you have configured for use with a queuing system, such as the Load Sharing Facility (LSF) and the Sun Grid Engine (SGE).

Programming Languages

Specify the root directories for the programming languages used by GenePattern and the Java flags to be added to Java command lines executed by the server.

Proxy

If your organization has a web proxy between the GenePattern server and the internet, specify the proxy information required to access the internet.

Repositories

Specify the URL used to access the module repository and the suite repository.

Shut Down Server

Shut down the GenePattern server.

System Message

Broadcast a message to all users logged into the GenePattern server.

Task Info

Display the LSID of each module and pipeline installed on the GenePattern server.

Uploaded Files

Display the account information and uploaded files of a selected user.

Users and Groups

Display account information for all users, including the groups to which they belong.

Web Server Log

Display the log file for the web server used by the GenePattern server.

Access

Use the Access page to define which GenePattern clients have access to the GenePattern server. The localhost (127.0.0.1) computer cannot be denied access to the locally installed GenePattern server. This prevents you from inadvertently denying yourself access to the server.

Using the Access page to control which computers have access to the GenePattern server is the simplest way to secure your server. You can also control access to your server based on user authentication and user permissions, as described in Securing the Server. The Access page filters are applied before any user-specific authentication or permissions are checked. If your computer cannot access the server, you cannot access the server regardless of your username/password or permissions.

Access

Click Save to save your changes. Click Restore to return to the value set at installation.

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Advanced

The Advanced page contains directory specifications for the GenePattern source files and other low-level configuration options. You rarely need to modify these options.

Advanced Configurations

Click Save to save your changes. Click Restore to return to the values set at installation.

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Command Line Prefix

The Command Line Prefix page allows you to prepend text to the command line used to execute a module. You can prepend the same text to all module command lines or prepend text for a specific module.

Note: Prior to GenePattern 3.2.3 (June 2010), administrators used the command line prefix for connecting to an external queuing system. GenePattern now provides the CommandExecutor interface for that purpose. For more information, see Using a Queuing System.

Command Line Prefix

To prepend text to all (or most) command lines executed by the GenePattern server:

  1. Enter the desired commands and qualifiers in the Default Command Prefix field.
  2. Click save default. GenePattern displays the updated content of the default prefix. The name/content table in the middle of the form lists the default prefix and its content. The previous illustration shows the default prefix with no content.
    When GenePattern executes a module or pipeline, it constructs the appropriate command line, prepends the default prefix to that command line, and then executes the command line.

To prepend text only to command lines that invoke specific modules or pipelines:

  1. In the Add New Prefix field, enter a name for the prefix and the commands and qualifiers to prepend to the command line.
  2. Click add prefix. GenePattern creates the new prefix, updates its content, and adds the prefix to the name/content table in the middle of the form.
  3. At the bottom of the form, select one or more module(s)/pipeline(s), select your new prefix, and click add mapping. GenePattern adds the prefix information to the module/command prefix name table.
    When GenePattern executes a module or pipeline listed in the module/command prefix name table, it constructs the appropriate command line, prepends the specified prefix to that command line, and then executes the command line. (When GenePattern executes a module or pipeline not listed in that table, it constructs the appropriate command line, prepends the default prefix to that command line, and then executes the command line.)

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Custom

Use the Custom page to define your own configuration options.

When you create a module, the custom configuration options are available as substitution variables in the module command line. For example, if you define a custom property "foo", you can use <foo> in the command line to pass the value of the custom configuration option to your module. In the Broad repository, for example, the LandmarkMatching and PeakMatch modules use the custom configuration option pepperPrefix. For more information, see Creating Modules in GenePattern.

Custom Settings

  1. In the name field, enter a name for the configuration option.
  2. In the content field, enter a value for the configuration option.
  3. Click add setting. GenePattern adds the option to the table at the bottom of the form.

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Database

Use the Database Parameters page to set configuration options for the GenePattern database. The following figure shows the HSQL options. You rarely need to change these options.

For information about modifying the database, see Changing the GenePattern Database (HSQL to Oracle).

Database Parameters

Click Save to save your changes. Click Restore to return to the value set at installation.

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File Purge

Use the File Purge page to specify when analysis result files are deleted from the server:

File Purge Settings

Click Save to save your changes. Click Restore to return to the values set at installation.

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GenePattern Log

Use the GenePattern Log page to view warnings and messages generated by the GenePattern server. (Use the Web Server Log page to view messages generated by the web server that GenePattern uses.)

GenePattern Log

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Job Configuration

If you have configured your GenePattern system to work with a queuing system, such as the Load Sharing Facility (LSF) and the Sun Grid Engine (SGE), the Job Configuration page helps you control the queue and reload your configuration files. For more information, see Using a Queuing System.

Use the Job Configuration section to control the GenePattern internal job queue:

Use the Command Executors section to identify each of the command executors currently installed on the GenePattern server.

Use the Configuration File section to identify and review the .yaml configuration file currently active on the GenePattern server.

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Programming Languages

The Programming Languages page contains two sections. After making changes, click Save to save them or Restore to return to the value set at installation.

Use Programming Language Configurations to specify the root directories for the programming languages used by GenePattern:

Programming Language Configurations

When you install GenePattern, you install the programming languages used by GenePattern. If you have alternate programming language installations that you prefer to use, use this page to point to those installations. If you would like to use more recent versions of R, see Using Different Versions of R.

Use Programming Language Options to increase the memory allocated to modules written in Java and R:

Programming Language Options

You can also increase the amount of memory allocated to the GenePattern server or client. For more information, see Increasing Memory Allocation.

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Proxy

If your server is behind a firewall, use the Proxy page to set the HTTP and FTP Proxy information. Without the proxy information, the server cannot download modules, pipelines, or suites from the repository maintained by the Broad Institute. If you do not know the proxy information, contact your systems administrator.

Proxy Settings

Click Save to save your changes. Click Restore to return to the values set at installation.

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Repositories

Use the Repositories page to identify the location of the repository to be accessed by the GenePattern server when you install modules and pipelines or suites from the repository. By default, it points to the module repository maintained by the Broad Institute. For information about implementing a module repository at your site, see the In-Depth Article Setting Up a Module Repository.

Click Save to save your changes. Click Restore to return to the values set at installation. Click Remove to delete the selected URL from the list.

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Shut Down Server

You can shut down the GenePattern server by clicking the link on this page. Alternatively, double-click the Stop GenePattern Server icon on your desktop.

Shut Down Server

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System Message

Use the System Message page to broadcast a message to all users logged into the GenePattern server. The message text that you enter can include simple HTML formatting commands, such as <b> and <em>.

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Task Info

The Task Info page lists every module and pipeline installed on the GenePattern server. It can be useful in sorting out the confusion that can occur when modules and pipelines share the same name.

The Clear TaskInfo Cache link clears an internal GenePattern cache, which can be useful for GenePattern development. Clicking the link has no visible impact on GenePattern operations.

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Uploaded Files

The Uploaded Files page displays basic information about a user and their uploaded files (see Uploading Files). By default, the page displays information about the user logged into the GenePattern web client. To view information for another user, enter their username and click Select User.

If a user manually adds or removes files from the Uploads directory on the file server:

  1. Enter their username and click Select User to display their information.
  2. Click Resync Files to update (resynchronize) their uploaded files based on their Uploads directory on the file server.
  3. Enter their username and click Select User to display the updated information.

This allows you to synchronize the user interface with the modified uploads directory on the file server without restarting the GenePattern server.

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Users and Groups

Use the Users and Groups page to view user account information, including the groups to which a user belongs. This page shows only registered users. An administrator can add users to a group (Creating Groups and Administrators) before they register, but the users are not listed on this page until they have created a GenePattern account by clicking the Registration link on the GenePattern login page. If you update the userGroups.xml file, click Reload Users and Groups to update (resynchronize) the GenePattern web interface. This allows you to update users and groups without restarting the GenePattern server.

When you start the GenePattern server, the server populates the Uploads tab for each user by reviewing the Uploads directory on the file server. Typically, users add and remove uploaded files from the GenePattern web client interface. If a user adds or removes files from the Uploads directory on the file server, enter their username and click Resync Uploads to update (resynchronize) their Uploads tab based on their Uploads directory on the file server. This allows you to synchronize the user interface with the modified uploads directory on the file server without restarting the GenePattern server.

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Web Server Log

Use the Web Server Log page to view messages generated by the web server that GenePattern uses. (Use the GenePattern Log page to view warnings and messages generated by the GenePattern server.)

Web Server Log

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Updated on September 05, 2012 13:29