The Enterprise Pipeline is a special configuration of the data processing pipeline. Instead of running all of the tasks on the same machine as your LabKey Server instance, it runs some of them on a remote pipeline server. While many examples in this section use mass spectrometry scenarios, the enterprise pipeline is not specific to that application.

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Assumptions

This documentation assumes the LabKey Server and the Enterprise Pipeline will be configured to work in the following architecture:

  • All files (both sample files and result files from searches) will be stored on a Shared File System
  • LabKey Server will mount the Shared File System.
    • Some third party tools may require a Windows installation of LabKey Server, but a LabKey remote server can be deployed on any platform that is supported by LabKey Server itself.
  • Conversion of RAW files to mzXML format will be included in the pipeline processing
    • The remote server running the conversion will mount the Shared File System
  • MS2 pipeline analysis tools (X!Tandem, TPP, etc) can be executed on a remote server
    • Remote servers will mount the Shared File System

Prerequisites

Install prerequisites for using the Enterprise Pipeline:

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