Configure Remote Pipeline Server: /home/

Configure Remote Pipeline Server

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.

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)

Oracle Java 8 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

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
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

Goto the Download Page
- Download the Pipeline Configuration(zip) zip file
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,

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

<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, 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

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
- http://newverhost.com/pub//commons/daemon/binaries/1.0.5/
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.

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\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

LabKey Support

LabKey Support