Creating Modules: The Module Integrator  Print-icon

Only the GenePattern team can create, edit, or install modules on the GenePattern public server. Therefore, to create a module, you must have a local GenePattern server installed (see Starting Your Own GenePattern Server).

Creating a GenePattern module is a multi-step process:

  1. Find or write a program that executes the desired function. Any program that can be executed from the command line can be run as a GenePattern module. If you are writing the program, you can use any programming language; for example, you can use a compiled language, such as C, to create an executable or use a scripting language, such as Perl, to create a script that is run by an interpreter. For more information, see Writing Modules for GenePattern.
  2. Use GenePattern to create a module that invokes the program that you have written. It takes just a few minutes to enter the necessary information. You can decide which parameters from the algorithm to expose to the user and can replace command line parameter names that are hard to remember with names that are self-explanatory. You can also create drop-down list choices for parameters to reduce the possibility of invoking the module with incorrect values. This section provides information on how to create and edit modules in GenePattern.
  3. Run the module several times, testing it thoroughly before making it available to other GenePattern users.

Malicious code: By adding a module, a user can execute arbitrary code on the GenePattern server. Because arbitrary code may include malicious code, take precautions to protect your server: for example, employ virus scanner software and restrict access to appropriately privileged (non-root) users. For more information about securing your server, see Securing the Server.

Creating a Module

To create a module in GenePattern:

  1. Click Modules & Pipelines>New Module. GenePattern displays the module integrator.
  2. Enter values for the module properties. For more information, click the Help icon.
  3. Click Save to create the module. GenePattern checks the following:
    • Every parameter not marked as optional is included in the command line.
    • Every parameter in the command line is a parameter, environment variable, or system property.
    • Module parameter names are valid.

    If no errors are found, GenePattern copies the support files to the server and makes the module available to the GenePattern clients.

The in-depth article Creating a GenePattern Module provides a hands-on tutorial that walks you through the process of creating a GenePattern module.

Licensed Modules

Modules can have end-user license agreements (EULAs) attached to them.  In order to run a licensed module (either standalone or within a pipeline), users must view and accept the license terms; GenePattern will display the license and prompt the user to accept it.  After a user accepts a licensed module's terms, that user can run the module and GenePattern will not prompt the user to re-accept the license on subsequent runs.  However, a user will need to re-accept the license whenever the licensed module is updated to a new version.  The GenePattern Server records each acceptance of a licensed module's terms and reports these records to a database application hosted at the Broad Institute.  If this module will only be on your GenePattern server and you need to maintain your own database for the terms agreements, contact the GenePattern development team for assistance. 

Academic users can agree to the license and use the module.  Commercial users, however, need to contact the GenePattern team to work out terms for use, particularly if commercial users are establishing their own GenePattern server on which to host the licensed module.

The EULA terms need to be in a text document (.txt).  You can add a EULA to your module in the module integrator by clicking Add License File.

Editing Modules

To edit a module:

  1. Click Modules & Pipelines  to display the GenePattern home page.
  2. Open the module integrator in one of the following ways:
    • Select a module that you created. When GenePattern displays the module parameters, click Edit.
    • Select a public module. When GenePattern displays the module parameters, click Properties. When GenePattern displays the module properties, click Clone to create a copy of the module. Enter a name for the new copy of the module. When GenePattern displays the properties of the new module, click Edit.
  3. Enter values for the module properties. For more information, click the Help icon.
  4. Click Save to create a new version of the module.

Module Properties

When you create or edit a module, GenePattern displays its properties in the module integrator. Click the Help icon to display descriptions of each property and its valid values. The help text is provided here for your convenience.


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Updated on December 06, 2012 16:07