Introduction

The LabKey Enterprise Pipeline gives you are the ability to specify the version of Proteomics Search tools to be used during your analysis. The version of the Proteomics Search tools to be used can be set at the Server, Pipeline and/or individual search level. The tools covered on this page:
  • X!Tandem
  • Trans Proteomic Pipeline
  • msconvert and other ProteoWizard tools
These instructions will show you how to change the:
  1. Server-wide default version of tools
  2. Pipeline-default version of tools
  3. Version used during a Search

Prerequisites

The new version(s) of the Search Tools must be installed on your Enterprise Pipeline Servers.

The name of the installation directory for each tool is very important. LabKey uses the following naming convention for each of the tools:

  • X!Tandem
    • Installation directory name = `tandem.VERSIONNUMBER`
    • where VERSIONNUMBER is the version of the X!Tandem binary contained in the directory (e.g.. `tandem.2009.10.01.1`)
  • Trans Proteomic Pipeline
    • Installation directory name = `tpp.VERSIONNUMBER`
    • where VERSIONNUMBER is the version of the TPP binaries contained in the directory (e.g. `tpp.4.3.1`)

How to Change the Server-Wide Default Versions of the Tools

X!Tandem

For the sake of this documentation, let's assume

  • Version 2009.10.10.1 will be the new default version
  • Version 2009.10.01.1 is installed in the directory `/opt/labkey/bin/tandem.2009.10.01.1`
By default, the LabKey Enterprise Pipeline will execute the following during a X!Tandem Search
	/opt/labkey/bin/tandem/tandem.exe

To set `X!Tandem 2009.10.01.1` as the default version, perform the following steps

  • Ensure that no Enterprise Pipeline jobs are currently running
  • Stop all Pipeline jobs from running on the cluster using your cluster management tools
  • Perform the following steps
sudo su - labkey 
cd /opt/labkey/bin/
mv tandem/ tandem.old
cp -R tandem.2009.10.01.1 tandem
  • The default version of X!Tandem has now been changed. Please perform a test search and verify that is working properly.
  • After testing is complete run
rm -r tandem.old

Trans Proteomic Pipeline Toolset

For the sake of this documentation, let's assume

  • Version 4.3.1 will be the new default version
  • Version 4.3.1 is installed in the directory `/opt/labkey/bin/tpp.4.3.1`
By default the LabKey Enterprise Pipeline will execute the TPP tools located in the following directory
/opt/labkey/bin/tpp/bin

To set TPP 4.3.1 as the default version, perform the following steps

  • Log into medusa.tgen.org
  • Ensure that no Enterprise Pipeline jobs are currently running
  • Stop all Pipeline jobs from running on the cluster using your cluster management tools
  • Perform the following steps
sudo su - labkey 
cd /opt/labkey/bin/
mv tpp/ tpp.old
cp -R tpp.4.3.1 tpp
  • The default version of TPP has now been changed. Please perform a test search and verify that is working properly.
  • After testing is complete run
rm -r tpp.old

ReAdW.exe Conversion utility (backwards compatibility only, ProteoWizard strongly recommended instead)

For the sake of this documentation, let's assume

  • Version 4.3.1 will be the new default version
  • Version 4.3.1 is installed in the directory `c:labkeybin`
By default the LabKey Enterprise Pipeline will execute the tools in the following directory
c:labkeybinReAdW.exe

To set ReAdW 4.3.1 as the default version, perform the following steps

  • Log into cpas-xp-conv01 using RDP
  • Stop the LabKey Remote Pipeline Server
    • Open a command prompt window
    • execute
net stop "LabKey Remote Pipeline Server"
  • Make a backup of the Enterprise Pipeline Configuration file `c:labkeyconfigms2config.xml`
  • Edit `c:labkeyconfigms2config.xml`
[change]
<bean class="org.labkey.api.pipeline.cmd.EnumToCommandArgs">
<property name="parameter" value="pipeline, readw version"/>
<property name="default" value="1.2"/>

[to]
<bean class="org.labkey.api.pipeline.cmd.EnumToCommandArgs">
<property name="parameter" value="pipeline, readw version"/>
<property name="default" value="4.3.1"/>
  • Start the LabKey Remote Pipeline Server
    • Open a command prompt window
    • execute
net start "LabKey Remote Pipeline Server"
  • Review the log file at `c:labkeylogsoutput.log` for any error messages. If the server starts without any problems then
  • Copy the `c:labkeyconfigms2config.xml` to
    • `c:labkeyconfigms2config.xml` on cpas-web01
    • `/opt/labkey/config/msconfig.xml` on medusa.tgen.org
  • The default version of ReAdW has now been changed. Please perform a test search and verify that is working properly.

How to Change the Pipeline Default Versions of the Tools

For the sake of this documentation, let's assume we will be setting the default options on the pipeline for the MyAdmin project

  1. Log on to your LabKey Server as a user with Site Admin privileges
  2. Goto to the Database Pipeline Setup Page for the pipeline you would like to edit
  3. Click on the Set Defaults link under "X! Tandem specific settings:"
Now we are ready to set the Pipeline default settings

X!Tandem

  • Verify that there are no defaults set already by searching in the text box for
<note type="input" label="pipeline tandem, version">
  • If there is a default already configured, then change the version specified. The result should look like
<note type="input" label="pipeline tandem, version">2009.10.01.1</note>
  • If there is no default configured, then add the following text to the bottom of the file, above the line containing`</bioml>`
<note type="input" label="pipeline tandem, version">2009.10.01.1</note>
<note>Set the default version of X!Tandem used by this pipeline</note>

If there are no other changes, than hit the Set Defaults button and you are done.

TPP

  • Verify that there are no defaults set already by searching in the text box for
<note type="input" label="pipeline tpp, version">
  • If there is a default already configured, then change the version specified. The result should look like
<note type="input" label="pipeline tpp, version">4.3.1</note>
  • If there is no default configured, then add the following text to the bottom of the file, above the line containing`</bioml>`
<note type="input" label="pipeline tpp, version">4.3.1</note>
<note>Set the default version of TPP used by this pipeline</note>
If there are no other changes, than hit the *Set Defaults* button and you are done.

ReAdW

  • Verify that there are no defaults set already by searching in the text box for
<note type="input" label="pipeline, readw version">
  • If there is a default already configured, then change the version specified. The result should look like
<note type="input" label="pipeline, readw version">4.3.1</note>
  • If there is no default configured, then add the following text to the bottom of the file, above the line containing`</bioml>`
<note type="input" label="pipeline, readw version">4.3.1</note>
<note>Set the default version of ReAdW used by this pipeline</note>
If there are no other changes, than hit the *Set Defaults* button and you are done.

How to Change the version of the tools to use for an individual search

When a search is being submitted, you are able to specify the version of the Search tool on the Search MS2 Data page, where you specify the MS2 Search Protocol to be used for this search.

X!Tandem

Enter the following configuration settings in the X! Tandem XML: text box. Enter it below the line containing `<!-- Override default parameters here. -->`

<note type="input" label="pipeline tandem, version">VERSIONNUMBER</note>
where `VERSIONNUMBER` is the version of X!Tandem you would like to use.

TPP

Enter the following configuration settings in the X! Tandem XML: text box. Enter it below the line containing `<!-- Override default parameters here. -->`

<note type="input" label="pipeline tpp, version">VERSIONNUMBER</note>
where `VERSIONNUMBER` is the version of TPP you would like to use.

ReAdW

Enter the following configuration settings in the X! Tandem XML: text box. Enter it below the line containing `<!-- Override default parameters here. -->`

<note type="input" label="pipeline, readw version">VERSIONNUMBER</note>
where `VERSIONNUMBER` is the version of X!Tandem you would like to use.

Discussion

previousnext
 
expand all collapse all