The enterprise pipeline is like the data processing pipeline, but, instead of running on the same machine as your LabKey Server instance, it runs on a remote pipeline server.

The topics below show you how to install and use the enterprise pipeline:

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 is running on a Windows Server
    • LabKey Server will mount the Shared File System
  • Conversion of RAW files to mzXML format will be included in the pipeline processing
    • Conversion Server will mount the Shared File System
  • MS1 and MS2 pipeline analysis tools (xtandem, tpp, msInspect, etc) will be executed on Cluster
    • Cluster execution nodes will mount the Shared File System
    • Instructions for SGE and PBS based clusters are available.


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