Configure LabKey Server to use the Enterprise Pipeline

Documentation: Version 20.7
Before performing the tasks below, you must complete the steps in this topic:

This topic covers configuring LabKey Server to use the Enterprise Pipeline. If necessary, you will also create the LabKey Tool directory where programs such as the MS2 analysis tools will be installed.


The Enterprise Pipeline allows work to be distributed to remote servers, separate from the LabKey Server web server. The following assumptions and prerequisites apply:

  • Use of a Network File System: The LabKey web server and remote servers must be able to mount the following resources:
    • Pipeline directory (location where mzXML, pepXML, etc files are located)
    • Pipeline bin directory (location where third-party tools (TPP, Xtandem, etc) are located
  • MS2 analysis tools will be run on a separate server.
  • A version of Java supported by your version of LabKey Server for each location that will be running tasks.
  • You have downloaded or built from source the following files:
    • LabKey Server
    • Labkey Server Enterprise Pipeline Configuration files

Enable Communication with the ActiveMQ JMS Queue

You will need to add the following settings to the LabKey configuration file. Before adding this section, check to see if it is already present but commented out, and if so simply uncomment it:

<Resource name="jms/ConnectionFactory" auth="Container"
description="JMS Connection Factory"

You will need to change the setting for brokerURL to point to the location of your ActiveMQ installation (i.e. replace @@JMSQUEUE@@ with the hostname of the server running the ActiveMQ software).

Set the Enterprise Pipeline Configuration Directory (Optional)

By default, the system looks for the pipeline configuration files in the following directory: LABKEY_HOME/config.

To specify a different location, add (or uncomment) the following parameter to the LabKey configuration file:

<Parameter name="org.labkey.api.pipeline.config" value="C:/path-to-config"/>

Set this to the location of your Enterprise Pipeline configuration directory.

Create the Enterprise Pipeline Configuration Files

  • Unzip the Enterprise Pipeline Configuration distribution and copy the webserver configuration file to the Pipeline Configuration directory specified in the last step (ie <LABKEY_HOME>/config).
  • The configuration file is ms2config.xml which includes:
    • Where MS2 searches will be performed (on a remote server or locally on the web server)
    • Where the Conversion of raw files to mzXML will occur (if required)
    • Which analysis tools will be executed during a MS2 search

Restart LabKey Server

In order for the LabKey Server to use the new Enterprise Pipeline configuration settings, the Tomcat process will need to be restarted. Confirm that the server started up with no errors:

  • Log on to your LabKey Server using a Site Admin account.
  • Select (Admin) > Site > Admin Console.
  • Under Diagnostics, click View all site errors.
  • Check to see that no errors have occurred after the restart.

Create the LABKEY_TOOLS Directory

The <LABKEY_TOOLS> directory will contain all the files necessary to perform MS2 searches on the remote server. The directory will contain:

  • Required LabKey software and configuration files
  • TPP tools
  • XTandem search engine
  • Additional MS2 analysis tools

Create the <LABKEY_TOOLS> Directory

Create the <LABKEY_TOOLS> directory on the remote server. It can be on the local file system, or available as a network file share.

Download the Required LabKey Software

  1. Unzip the LabKey Server distribution into the directory <LABKEY_TOOLS>/labkey/dist
  2. Unzip the LabKey Server Pipeline Configuration distribution into the directory <LABKEY_TOOLS>/labkey/dist/conf
NOTE: For the next section you will need to know the paths to the <LABKEY_TOOLS>/labkey directory and the <LABKEY_TOOLS>/external directory on the remote server.

Install the LabKey Software into the <LABKEY_TOOLS> Directory

Copy the following to the <LABKEY_TOOLS>/labkey directory

  • The directory <LABKEY_TOOLS>/labkey/dist/LabKey<VERSION>/labkeywebapp
  • The directory <LABKEY_TOOLS>/labkey/dist/LabKey<VERSION>/modules
  • The directory <LABKEY_TOOLS>/labkey/dist/LabKey<VERSION>/pipeline-lib
  • The file <LABKEY_TOOLS>/labkey/dist/LabKey<VERSION>/tomcat-lib/labkeyBootstrap-X.Y.jar
Expand all modules in the <LABKEY_TOOLS>/labkey/modules directory by running:

cd <LABKEY_TOOLS>/labkey/
java -jar labkeyBootstrap-X.Y.jar

Create the Enterprise Pipeline Configuration Files

There are 2 configuration files used on the Remote Server:

  • pipelineConfig.xml
  • ms2Config.xml

Install the MS2 Analysis Tools

These tools will be installed in the <LABKEY_TOOLS>/bin directory on the Remote Server.

Test the Configuration

There are a few simple tests that can be performed at this stage to verify that the configuration is correct. These tests are focused on ensure that a remote server can perform an MS2 search

  1. Can the remote server see the Pipeline Directory and the <LabKey_Tools> directory?
  2. Can the remote server execute Xtandem?
  3. Can the remote server execute the Java binary?
  4. Can the remote server execute a Xtandem search against an mzXML file located in the Pipeline Directory?
  5. Can the remote server execute a PeptideProphet search against the resultant pepXML file?
  6. Can the remote server execute the Xtandem search again, but this time using the LabKey Java code located on the remote server?
Once all these tests are successful, you will have a working Enterprise Pipeline. The next step is to configure a new Project on your LabKey Server and configure the Project's pipeline to use the Enterprise Pipeline.


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