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.

Topics

• Configure LabKey Server to use the Enterprise Pipeline
• Configure the Conversion Service
• Use the Enterprise Pipeline
• Troubleshoot the Enterprise Pipeline

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:

• Working installation of LabKey Server
• JMS Queue (ActiveMQ)
• RAW to mzXML Converters (convert MS2 output to mzXML). Optional. Only required if you plan to convert files to mzXML format in your pipeline