There are 2 ways that the Enhanced Sequest Pipeline can be installed. The first is to install the LabKey Remote Pipeline Server software on an existing computer with Proteome Discoverer installed. The second is to install Proteome Discoverer on the same computer as the LabKey Server.

Install the LabKey Remote Pipeline Server on an existing computer with Proteome Discoverer

In this option, you will install LabKey Remote Pipeline Server software on a computer that is currently running Proteome Discoverer software. This is our recommended solution. See Enterprise Pipeline for more information on the Enterprise Pipeline.

Install JAVA on the computer running Proteome Discoverer 1.1

• Download the Java Runtime Environment (JRE) from http://www.oracle.com/technetwork/java/javase/downloads/index.html
• Install the JRE to the chosen directory.
• Create the JAVA_HOME environmental variable to point at your installation directory.

Install the LabKey Remote Pipeline Server Software

Define the Location of the Remote Pipeline Server

<property name="remoteServerProperties">
    <bean class="org.labkey.pipeline.api.properties.RemoteServerPropertiesImpl">
         <property name="location" value="mzxmlconvert"/>
    </bean>
</property>

to

<property name="remoteServerProperties">
    <bean class="org.labkey.pipeline.api.properties.RemoteServerPropertiesImpl">
         <property name="location" value="sequest"/>
    </bean>
</property>

Enable Sequest Integration

<!-- Enable Sequest integration and configure it to run on a remote pipeline server (using "sequest" as its location
     property value in its pipelineConfig.xml file). Give pointers to the directory where Sequest is installed,
     and a directory to use for storing FASTA index files. -->
<!--
<bean id="sequestTaskOverride" class="org.labkey.ms2.pipeline.sequest.SequestSearchTask$Factory">
    <property name="location" value="sequest"/>
    <property name="sequestInstallDir" value="C:\Program Files (x86)\Thermo\Discoverer\Tools\Sequest" />
    <property name="indexRootDir" value="C:\FastaIndices" />
</bean>
-->

to

<!-- Enable Sequest integration and configure it to run on a remote pipeline server (using "sequest" as its location
     property value in its pipelineConfig.xml file). Give pointers to the directory where Sequest is installed,
     and a directory to use for storing FASTA index files. -->

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

Also change the sequestInstallDir property value to be the location of the Sequest binary on your server.

Change the values for all location properties in the file to be webserver

1. Find all places in the file that contain a line that starts with <property name="location"...
1. Do not change location value in the sequestTaskOverride bean, shown above, that should stay as sequest
2. On each line, change the value to be webserver
3. Save the file

Install a JMS Queue for use with the Enterprise Pipeline

Configure your LabKey Server to use the Enterprise Pipeline

1) Enable Communication with the ActiveMQ JMS Queue:

You will need to uncomment the JMS configuration settings in the LabKey configuration file (labkey.xml). The labkey.xml is normally located in CATALINA_HOME/conf/Catalina/localhost/labkey.xml. Change

<!-- <Resource name="jms/ConnectionFactory" auth="Container"
        type="org.apache.activemq.ActiveMQConnectionFactory"
        factory="org.apache.activemq.jndi.JNDIReferenceFactory"
        description="JMS Connection Factory"
        brokerURL="vm://localhost?broker.persistent=false&amp;broker.useJmx=false"
        brokerName="LocalActiveMQBroker"/> -->

to

<Resource name="jms/ConnectionFactory" auth="Container"
        type="org.apache.activemq.ActiveMQConnectionFactory"
        factory="org.apache.activemq.jndi.JNDIReferenceFactory"
        description="JMS Connection Factory"
        brokerURL="tcp://@@JMSQUEUE@@:61616"
        brokerName="LocalActiveMQBroker"/>

• where @@JMSQUEUE@@ is the hostname or IP address of the server where you installed the ActiveMQ software.

Create the Enterprise Pipeline configuration directory for your server. The recommended location for this directory is LABKEY_HOME/config. Where LABKEY_HOME is the directory where LabKey Server is installed.

3) Enable the Enterprise Pipeline configuration directory

To configure the Enterprise Pipeline configuration directory, open the LabKey configuration file (labkey.xml) and change

<!-- Pipeline configuration -->
    <!--    <Parameter name="org.labkey.api.pipeline.config" value="C:\proj\labkey\docs\mule\config-demo"/> -->

to

<!-- Pipeline configuration -->
    <Parameter name="org.labkey.api.pipeline.config" value="@@LABKEY_HOME@@\config"/>

• where @@LABKEY_HOME@@\config is the configuration directory location. The default setting is LABKEY_HOME\config. (i.e., replace @@LABKEY_HOME@@ with the full path to the LABKEY_HOME directory for your installation)

Restart your LabKey Server

Install Proteome Discoverer on LabKey Server

Install Proteome Discoverer 1.1

Download and Expand the Enterprise Pipeline Configuration files

1. Goto the LabKey Download Page
2. Download the Pipeline Configuration(zip) zip file
3. Expand the downloaded file.

Enable SEQUEST support in LabKey Server

Create the Enterprise Pipeline configuration directory

1. Open Windows Explorer and goto the installation directory for your LabKey Server
2. Create a new directory named config
3. Write down the full path of this new directory

1. Goto to the Enterprise Pipeline Configuration files that were downloaded above.
2. Open the webserver directory
3. Copy the ms2Config.xml file to configuration directory created in the previous step

Enable Sequest Integration by going to the bottom of the file and change the text

<!-- Enable Sequest integration and configure it to run on a remote pipeline server (using "sequest" as its location
     property value in its pipelineConfig.xml file). Give pointers to the directory where Sequest is installed,
     and a directory to use for storing FASTA index files. -->
<!--
<bean id="sequestTaskOverride" class="org.labkey.ms2.pipeline.sequest.SequestSearchTask$Factory">
    <property name="location" value="sequest"/>
    <property name="sequestInstallDir" value="C:\Program Files (x86)\Thermo\Discoverer\Tools\Sequest" />
    <property name="indexRootDir" value="C:\FastaIndices" />
</bean>
-->

to

<!-- Enable Sequest integration and configure it to run on a remote pipeline server (using "sequest" as its location
     property value in its pipelineConfig.xml file). Give pointers to the directory where Sequest is installed,
     and a directory to use for storing FASTA index files. -->

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

in addition:

• change the sequestInstallDir property value to be the installation of the Sequest binary on your server.
• change the location value to be webserver

1. Find all places in the file that contain a line that starts with <property name="location"...
2. On each line, change the value to be webserver
3. Save the file

Enable the Enterprise Pipeline configuration directory

To configure the Enterprise Pipeline configuration directory, open the LabKey configuration file (labkey.xml) and change

<!-- Pipeline configuration -->
    <!--    <Parameter name="org.labkey.api.pipeline.config" value="C:\proj\labkey\docs\mule\config-demo"/> -->

to

<!-- Pipeline configuration -->
    <Parameter name="org.labkey.api.pipeline.config" value="@@LABKEY_HOME@@\config"/>

• where @@LABKEY_HOME@@\config is the configuration directory location. The default setting is LABKEY_HOME\config. (i.e., replace @@LABKEY_HOME@@ with the full path to the LABKEY_HOME directory for your installation)

Restart your LabKey Server

Supported versions of Proteome Discoverer

How to Upgrade the Enhanced Sequest MS2 Pipeline

This page is currently under development: If you need assistance with an upgrade, please contact us on the Support Discussion Board

Additional Features

• The Enhanced MS2 Sequest Pipeline includes the capability of indexing FASTA files using the makedb.exe utility.&nbsp; This makes your searches faster. It only works for Sequest. To tell Sequest to use indexed FASTA files, set the appropriate parameter on the MS2 search settings dialog. See the following for more information
• Search and Process MS2 Data
• Configure Sequest Parameters
• API for submitting jobs