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.
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
Copy the following to the <LABKEY_HOME> directory
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.
pipelineConfig.xml This file holds the configuration for the pipeline. To install,
There are a few important settings that may need to be changed
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>
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>
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.
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.
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 Windows Service by running the following from the Command Prompt
set LABKEY_ROOT=<LABKEY_HOME> <LABKEY_HOME>\bin\service\installService.batwhere
<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
If you are running a a 64bit version of Windows, then you will need to follow the instructions below
Install the Windows Service by running the following from the Command Prompt
set LABKEY_ROOT=<LABKEY_HOME> <LABKEY_HOME>\bin\service\installService.batwhere
<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.
To start the service, from a command prompt, run:
net start LabKeyRemoteServer
To stop the service, from a command prompt, run:
net stop LabKeyRemoteServer
All logs from the LabKey Remote Server are located in <LABKEY_HOME>\logs\output.log
If you are attempting to enable this configuration, please contact us on the Support Discussion Board