Before performing the tasks below, you must:

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 Binary to mzXML conversion server.

 
 

Assumptions


  • Use of a Shared File System: The LabKey Conversion Server must be able to mount the following resources
    • Pipeline directory (location where mzXML, pepXML, etc files are located)
  • Sun Java 1.5 or greater is installed
  • You have downloaded (or built from the subversion tree) the following files
    • LabKey Server
    • Labkey Server Enterprise Pipeline Configuration files

 
 

Install the Enterprise Pipeline Remote Server


Download and expand the LabKey Software

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

  1. Create the <LABKEY_HOME> directory
    • On Windows: LabKey recommends you use c:\LabKey
    • On Linux, Solaris or MacOSX: LabKey recommends you use /usr/local/labkey
  2. 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

  • Create the directory <LABKEY_HOME>\FastaIndices

 

Create the logs directory

  • Create the directory <LABKEY_HOME>\logs

 
 

Install the Pipeline Configuration Files


There are currently 3 important configuration 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

  1. Goto the Download Page
    • Download the Pipeline Configuration(zip) zip file
  2. Unzip the LabKey Server distribution into the directory <LABKEY_HOME>\src

 

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="org.labkey.pipeline.api.properties.ApplicationPropertiesImpl"> 
      <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"/> 
    </bean> 
    • 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>

to

<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"/> 
</bean> 

 

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

If you are attempting to enable this configuration, please contact us on the Support Discussion Board

 
 

Install the LabKey Remote Server as a Windows Service


If you are installing the Remote Server on a non-Windows operating system, see the next section, Configure the LabKey Remote Server to start at boot-time on Linux Server.

LabKey uses procrun to run the Conversion Service as a Windows Service. This means you will be able to have the Conversion Service 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 on 32bit Windows

  • Copy *.exe and *.bat from the directory <LABKEY_HOME>\dist\LabKeyX.X-xxxxx-PipelineConfig\remote to <LABKEY_HOME>\bin
  • Install the Windows Service by running the following from the Command Prompt

    set LABKEY_ROOT=<LABKEY_HOME> 
    <LABKEY_HOME>\bin\service\installService.bat
    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 then it should have created a new Windows Service named LabKeyRemoteServer

 

Install the LabKey Remote Service on 64bit Windows

If you are running a a 64bit version of Windows, then you will need to follow the instructions below

  • 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\amd64\prunsrv.exe
    • amd64\prunsrv.exe to <LABKEY_HOME>\bin\amd64\procrun.exe
  • Install the Windows Service by running the following from the Command Prompt

    set LABKEY_ROOT=<LABKEY_HOME> 
    <LABKEY_HOME>\bin\service\installService.bat 
    
    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.

 

How to Start the LabKey Remote Windows Service

How to start the service From the command prompt you can run

 net start LabKeyRemoteServer 

 
How to stop the service From the command prompt you can run

 net stop LabKeyRemoteServer 

 

Where are the log files located

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

 
 

Configure the LabKey Remote Server to start at boot-time on Linux Server


If you are attempting to enable this configuration, please contact us on the Support Discussion Board

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