Managing Modules, Pipelines, and Suites  

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
• Exporting and Installing Modules & Pipelines Using Zip Files
• Managing Modules & Pipelines
• Installing Suites from the Repository
• Exporting and Installing Suites Using Zip Files
• Managing Suites

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 modules and pipelines to install.
   The search fields at the top of the page allow you to select any version of a module that is not installed on your server or more recent versions of any module already installed on your server. To install an older version of a module already installed on your server, delete the current version(s) installed on your server (see Managing Modules & Pipelines). You can then use this page to install any version of the module (which is no longer installed on your server).
3. Click Install Checked.

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 Search:

• Search for new modules to install: Displays modules and pipelines that are in the Broad repository and not on your server.
• Search for updates of the currently installed modules: Displays modules and pipelines where the Broad repository contains a more recent version than the version installed on your server.
• Search for up to date modules: Displays modules and pipelines where the Broad repository contains versions not installed on your server.
• Operating system: Filters the search results to display only modules and pipelines that run the selected operating system platform(s).

For each module and pipeline, GenePattern displays similar information:

• In the Name (Version) column:
  • Module/pipeline name.
  • Drop-down list of available versions. By default, the most recent version is selected.
  • Brief description of the module/pipeline.
  • documentation link, which displays the module/pipeline documentation.
  • download zip link, which downloads a zip file of the module/pipeline. Downloading the zip file allows you to examine the source files before installing them on your server. You can then install the module/pipeline from the zip file, as described in Exporting and Installing Suites Using Zip Files.
• In the Module type column, the category label assigned to the module/pipeline.
• In the Details column, the author, size, and operating system requirements for the module/pipeline.

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 Export.
4. If you are exporting a pipeline, GenePattern displays the following dialog:
   
   • 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.

Managing Modules & Pipelines

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

• View the modules/pipelines installed on your GenePattern server. To display only your own modules/pipelines, clear the show everyone’s modules check box. To display all modules/pipelines, select the check box. Private modules owned by other users are not visible unless you are an administrator.
• Delete modules/pipelines from your GenePattern server.
  Note: If the check box next to the module/pipeline is grayed out, you cannot delete it. Typically, this occurs when the module/pipeline is used by another module, pipeline, or suite. To delete the module/pipeline, you must first delete the module, pipeline, or suite that uses it or remove it from that module, pipeline, or suite.

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.

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:

• Search for new suites to install: Displays suites that are in the Broad repository and not on your server.
• Search for updates of the currently installed suites: Displays suites where the Broad repository contains a more recent version than the version installed on your server.
• Search for up to date suites: Displays suites where the Broad repository contains versions not installed on your server.

For each suite, GenePattern displays similar information:

• In the Name (Version) column:
  • Suite name. Click the menu icon next to the name to display the suites menu.
  • Drop-down list of available versions. By default, the most recent version is selected.
  • One-line description of the suite.
  • download zip link, which downloads a zip file of the suite. Downloading the zip file allows you to examine the source files before installing them on your server. You can then install the suite from the zip file, as described in Exporting and Installing Suites Using Zip Files.
• In the Modules column, a list of the modules and pipelines in the suite.

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 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.

Managing Suites

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

• View the suites installed on your GenePattern server.
• Delete suites from your GenePattern server. If the check box next to the module/pipeline is grayed out, you cannot delete it. Deleting a suite does not delete its modules.
• Click the menu icon next to a suite name to display the suites menu.

<< Working with Suites | Up | >>