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.



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


Install prerequisites for using the Enterprise Pipeline:


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