This topic explains how to configure a project to use the Enterprise Pipeline. This example configures it for MS1 and MS2 searches. For these instructions, we will create a new project and configure a pipeline for it.

Before performing the tasks below, you must:

Create a New Project to Test the Enterprise Pipeline

You can skip this step if a project already exists that you would rather use.

  • Log on to your LabKey Server using a Site Admin account
  • Create a new project with the following options:
    • Project Name: PipelineTest
    • Folder Type: MS2
  • Accept the default settings during the remaining wizard panels

For more information see Create a Project or Folder.

Configure the Project to use the Enterprise Pipeline

The following information will be required in order to configure this project to use the Enterprise Pipeline:

  • Pipeline Root Directory

Set Up the Pipeline

  • In the Data Pipeline web part, click Setup.
  • Enter the following information:
    • Path to the desired pipeline root directory on the web server
    • Specific settings and parameters for the relevant sections
  • Click Save.
  • Return to the MS2 Dashboard by clicking the PipelineTest link near the top of the page.

Run the Enterprise Pipeline

To test the Enterprise Pipeline:

  • In the Data Pipeline web part, click Process and Upload Data.
  • Navigate to and select an mzXML file, then click X!Tandem Pepitide Search.

Most jobs are configured to run single-threaded. The pipeline assigns work to different thread pools. There are two main ones for work that runs on the web server, each with one thread in it. The pipeline can be configured to run with more threads or additional thread pools if necessary. In many scenarios, trying to run multiple imports in parallel or some third-party tools in parallel degrades performance vs running them sequentially.

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