This page explains how to configure the LabKey Server Enterprise Pipeline Remote Server. The Remote Server can be used to execute X!Tandem or SEQUEST MS/MS searches on a separate computer from LabKey Server. It can also be used run a raw data file to mzXML conversion server, or run other pipeline configured tools.


  • Use of a Shared File System: The LabKey Remote Server must be able to mount the following resources
    • Pipeline directory (location where mzXML, pepXML, etc files are located)
  • Java is installed. It must be a supported version for the version of LabKey Server that is being deployed, and match the version being used for the web server.
  • You have downloaded the version of LabKey Server you wish to deploy

Install the Enterprise Pipeline

Download and expand LabKey Server

NOTE: You will use the same distribution software for this server as you use for the LabKey Server web server. We recommend simply copying the downloaded distribution files from your LabKey Server.

  • Create the <LABKEY_HOME> directory
    • On Windows: LabKey recommends you use c:\LabKey
    • On Linux or OSX: LabKey recommends you use /usr/local/labkey
  • Unzip the LabKey Server distribution into the directory <LABKEY_HOME>\src

Install the LabKey Software

Copy the following to the <LABKEY_HOME> directory

  • The directory <LABKEY_HOME>\src\LabKeyX.X-xxxxx-Bin\labkeywebapp
  • The directory <LABKEY_HOME>\src\LabKeyX.X-xxxxx-Bin\modules
  • The directory <LABKEY_HOME>\src\LabKeyX.X-xxxxx-Bin\pipeline-lib
  • The directory <LABKEY_HOME>\src\LabKeyX.X-xxxxx-Bin\bin
  • The file <LABKEY_HOME>\src\LabKeyX.X-xxxxx-Bin\tomcat-lib\labkeyBootstrap.jar

Create the Configuration directory

  • Create the directory <LABKEY_HOME>\config

Create the Temporary Working directory for this server

  • Create the directory <LABKEY_HOME>\RemoteTempDirectory

Create the directory to hold the FASTA indexes for this server (for installations using Sequest)

  • Create the directory <LABKEY_HOME>\FastaIndices

Create the logs directory

  • Create the directory <LABKEY_HOME>\logs

Install the Pipeline Configuration Files

There are XML files that need to be configured on the Remote Server. The configuration settings will be different depending on the use of the LabKey Remote Pipeline Server.

Download the Enterprise Pipeline Configuration Files

Configuration Settings for using the Enhanced Sequest MS2 Pipeline

pipelineConfig.xml: This file holds the configuration for the pipeline. To install:

  1. Copy <LABKEY_HOME>\src\LabKeyX.X-xxxxx-PipelineConfig\remote\pipelineConfig.xml to <LABKEY_HOME>\config
  2. Copy <LABKEY_HOME>\src\LabKeyX.X-xxxxx-PipelineConfig\webserver\ms2Config.xml to <LABKEY_HOME>\config

There are a few important settings that may need to be changed:

  • tempDirectory: set to <LABKEY_HOME>\RemoteTempDirectory
  • toolsDirectory: set to <LABKEY_HOME>\bin
  • location: set to sequest
  • Network Drive Configuration: You will need to the set the variables in this section of the configuration. In order for the Enhanced SEQUEST MS2 Pipeline to function, the LabKey Remote Pipeline Server will need to be able to access same files as the LabKey Server via a network drive. The configuration below will allow the LabKey Remote Pipeline Server to create a new Network Drive.
    <property name="appProperties"> 
    <bean class="">
    <property name="networkDriveLetter" value="t" />
    <property name="networkDrivePath" value="\\@@SERVER@@\@@SHARE@@" />
    <!-- Map the network drive manually in dev mode, or supply a user and password -->
    <property name="networkDriveUser" value="@@USER@@" />
    <property name="networkDrivePassword" value="@@PASSWORD@@" />
  • Enable Communication with the JMS Queue by changing @@JMSQUEUE@@ to be the name of your JMS Queue server in the code that looks like:
    <bean id="activeMqConnectionFactory" class="org.apache.activemq.ActiveMQConnectionFactory"> 
    <constructor-arg value="tcp://@@JMSQUEUE@@:61616"/>
    • Change @@JMSQUEUE@@ to be the hostname of the server where you installed the ActiveMQ software.

ms2Config.xml: This file holds the configuration settings for MS2 searches. Change the configuration section:

<bean id="sequestTaskOverride" class="org.labkey.ms2.pipeline.sequest.SequestSearchTask$Factory"> 
<property name="location" value="sequest"/>
<bean id="sequestTaskOverride" class="org.labkey.ms2.pipeline.sequest.SequestSearchTask$Factory"> 
<property name="sequestInstallDir" value="C:\Program Files (x86)\Thermo\Discoverer\Tools\Sequest"/>
<property name="indexRootDir" value="C:\FastaIndices"/>
<property name="location" value="sequest"/>

Configuration Settings for executing X!Tandem searches on the LabKey Remote Pipeline Server

If you are attempting to enable this configuration, you may find assistance by searching the inactive Proteomics Discussion Board, or contact us on the Community Support Forum.

Install the LabKey Remote Server as a Windows Service

LabKey uses procrun to run the Remote Server as a Windows Service. This means you will be able to have the Remote Server start up when the server boots and be able to control the Service via the Windows Service Control Panel.

Set the LABKEY_ROOT environment variable

In the System Control Panel, create the LABKEY_ROOT environment variable and set it to <LABKEY_HOME> . This should be a System Environment Variable.

Install the LabKey Remote Service

This assumes that you are running a 64-bit version of Windows, have a 64-bit Java Virtual Machine.

  • Copy *.bat from the directory <LABKEY_HOME>\dist\LabKeyX.X-xxxxx-PipelineConfig\remote to <LABKEY_HOME>\bin
  • Download the latest version of the Apache Commons Daemon to <LABKEY_HOME>\dist
  • Expand the downloaded software
  • Copy the following from the expanded directory to <LABKEY_HOME>\bin
    • prunmgr.exe to <LABKEY_HOME>\bin\prunmgr.exe
    • amd64\prunsrv.exe to <LABKEY_HOME>\bin\prunsrv.exe
    • amd64\prunsrv.exe to <LABKEY_HOME>\bin\procrun.exe
  • Install the Windows Service by running the following from the Command Prompt:
where <LABKEY_HOME> is the directory where labkey is installed. For example, if installed in c:\labkey, then the command is
set LABKEY_ROOT=c:\labkey

If the installService.bat command succeeded, it should have created a new Windows Service named LabKeyRemoteServer.

Starting and Stopping the LabKey Remote Windows Service

To start the service, from a command prompt, run:

net start LabKeyRemoteServer

To stop the service, from a command prompt, run:

net stop LabKeyRemoteServer

Log File Locations

All logs from the LabKey Remote Server are located in <LABKEY_HOME>\logs

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