Modifying Server Settings  

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

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.

• Click Standalone to allow only local clients to connect to the server; that is, you can access this GenePattern server only from the computer that it is running on.
• Click Any Computer (default) to allow any client to connect to the server.
• Click These Domains to allow only clients from specific domains to connect to the server. Enter a comma-separated list of domains or IP addresses in the text box, for example: broadinstitute.org,dfci.harvard.edu,mit.edu.
  GenePattern scans all incoming connection attempts. If they match in whole or in part any domain name or IP address in this list, the server allows access; otherwise, the server redirects the connection to a page indicating that the server does not allow 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.

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.

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.

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).

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:

• Use Purge Jobs After to specify the number of days the server keeps the analysis result files. To prevent the server from automatically deleting the files, set this value to -1.
• Use Purge Time to specify what time of day (24-hour format) the server deletes the files.

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.)

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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:

• Suspend/Resume internal job queue. When the queuing system fails or requires maintenance, use this option to temporarily halt the internal GenePattern job queue. When the queuing system has been restarted, resume the internal GenePattern job queue.
• Shut down/Restart job execution engine. When you modify the .yaml file that configures GenePattern for use with your queuing system, you must reload that configuration file. Rather than stopping and restarting the GenePattern server, you can use this option to stop the job execution engine, click Reload job configuration to reload the configuration file, and then use this option to restart the job execution engine.
• Reload job configuration. Used in conjunction with Shut down/Restart job execution engine.

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:

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:

• In the Java VMOptions field, modify the Java -X flag to increase the memory allocated for Java modules run on the server (non-visualizer modules); for example, -Xmx1024M doubles the amount of memory allocated. You can specify up to the maximum memory size of your server machine. Changes take effect when you stop and restart the server.
• In the Java Visualizer VMOptions field, modify the Java -X flag to increase the memory allocated by default for modules run on the client (visualizer modules). Changes take effect when you next run a visualizer module.
  GenePattern users can customize the memory allocated to visualizer modules based on the amount of memory available on their desktop PCs. To customize the memory allocated to visualizer modules run on your own desktop: select My Settings, select Visualizer Memory, and modify the Java -X flag to specify the amount of memory to be allocated to visualizer modules run on your desktop.
• In the R Options field, add the --max-mem-size flag to specify the maximum amount of memory to be used by R modules running on the server; for example, --max-mem-size=1G allocates a gigabyte. You can specify up to the maximum memory size of your server machine. The --max-mem-size flag affects only Windows operating systems. Changes take effect when you stop and restart the server.

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.

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.

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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.)

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