Managing Modules, Pipelines, and Suites  Print-icon

An analysis module runs a single analysis. A pipeline runs a series of analysis modules. Suites group modules and pipelines into packages that have related functionality, which helps you to organize and work with modules and pipelines. If you are unfamiliar with GenePattern modules, pipelines, and suites, see Concepts.

Installing Modules & Pipelines from the Repository

The Broad Institute maintains a repository of modules and pipelines that are freely available to the public. Most of these modules and pipelines are available on the GenePattern public server. To install these modules and pipelines on your local GenePattern server:

  1. Click Modules & Pipelines>Install from Repository. GenePattern displays the Install Modules & Pipelines from Repository page, as shown below.
  2. Select the repository from which you want to install. By default, the Broad Production Repository is displayed. Default server configuration also includes the Broad Beta Repository and GPARC as choices.
  3. Select the modules and pipelines to install. Filtering Options are described below.
  4. Click Install Checked

Install from Repository

Use the top section of the form to find the modules to install. To update the list of modules/pipelines, select the modules/pipelines to search for and click Update View:

Note: To install an older version of a module already installed on your server, check the "Show latest versions of all modules" box under Filtering Options, then Update View. This will show all modules in the repository. The checkbox underneath Update View and next to "Name (Version)" allows you to select/deselect all modules in the displayed list. Then you can use the dropdown under the module to select the version you wish to install.

For each module and pipeline, GenePattern displays similar information:

Exporting and Installing Modules & Pipelines Using Zip Files

Zip files provide a convenient means of sending your modules and pipelines to other GenePattern users. You can export a module or pipeline to a zip file. The zip file can then be used to install the module or pipeline on another GenePattern server.

To export a module or pipeline to a zip file:

  1. Click Modules & Pipelines to display the GenePattern home page.
  2. In the Modules & Pipelines pane, select the module or pipeline to export. GenePattern displays the analysis parameters (if any).
  3. Click the gear icon in the upper right corner of the module page, then select Export.
  4. If you are exporting a pipeline, GenePattern displays the following dialog:
    pipeline export prompt
    • Click Include modules to create a zip file that includes all modules in the pipeline.
    • Click Pipeline only to create a zip file that contains only the pipeline definition. (If you install a pipeline without installing the modules that it uses, when you run the pipeline, GenePattern lists the missing modules and prompts you to edit the pipeline or install the modules.)
  5. GenePattern creates a zip file that contains the module/pipeline and prompts you to save the file to your local drive.

To install a module or pipeline from a zip file:

  1. Click Modules & Pipelines>Install from zip. GenePattern displays the Install Modules & Pipelines page, as shown below.
  2. Select the file to install in one of two ways:
    • To select a zip file from a directory, click Browse.
    • To select a zip file from a web site, enter the URL for the zip file.
  3. Use the Visible to radio buttons to select a private or public installation:
    • Your user name: Choose this option for a private installation. Only you (or an administrator) can view and run the module/pipeline.
    • All users (default): Choose this option for public installation. Any user connected to this server can view or run the module/pipeline.
  4. Click Install.

install from zip

Managing Modules & Pipelines

Click Modules & Pipelines>Manage to display the Manage Modules & Pipelines page. From this page, you can

manage module

Installing Suites from the Repository

The Broad Institute maintains a repository of suites that are freely available to the public. To install these suites on your GenePattern server:

  1. Click Suites>Install from Repository. GenePattern displays the Install Suites from Repository page, as shown below.
  2. Select the suites to install.
    Installing a suite installs its modules, if they are not yet installed on the server.
  3. Click Install Checked.

Install Suites from Repository

Use the top section of the form to find the suites to install. To update the list of suites, select the suites to search for and click Search:

For each suite, GenePattern displays similar information:

Exporting and Installing Suites Using Zip Files

Zip files provide a convenient means of sending your suites to other GenePattern users. You can export a suite to a zip file. The zip file can then be used to install the suite on another GenePattern server.

To export a suite to a zip file:

  1. Click Suites>Manage.
  2. Click the menu icon menu icon following the name of the suite that you want to export. GenePattern displays the suite menu.
  3. Click one of the following:
    • Export excluding dependents: Creates a zip file that contains the definition of the suite, but not the modules or pipelines in the suite. Installing the suite from this zip file will not install any modules or pipelines in the suite; they must already be installed on the GenePattern server or be installed separately.
    • Export Including dependents: Creates a zip file that contains the definition of the suite, as well as the modules and/or pipelines in the suite. Installing the suite from this zip file will also install the modules and pipelines in the suite (unless they are already installed on the GenePattern server).

To install a suite from a zip file:

  1. Click Suites>Install from zip.
  2. Select the file to install. You can identify the zip file using a file specification or a URL.
  3. Use the Visible to radio buttons to select a private or public installation:
    • Your user name: Choose this option for a private installation. Only you (or an administrator) can view and run the module/pipeline.
    • All users (default): Choose this option for public installation. Any user connected to this server can view or run the module/pipeline.
  4. Click Install.

install suite from zip

Managing Suites

Click Suites>Manage to display the Manage Suites page. From this page, you can

manage suite

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Updated on April 10, 2014 11:01