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:

• Install Prerequisites for 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
• Configure LabKey Server to use the Enterprise Pipeline
• Configure the Conversion Service
• Use the Enterprise Pipeline
• Troubleshoot 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.