Installation Requirements

• Install CPAS and the MS2 cluster pipeline. (Currently the mzXML Conversion Service is only available with the MS2 cluster pipeline.)
• Choose a machine on which to run the conversion server:
  • The machine must be running Windows.
  • The server can run on the same machine as CPAS itself, if it is running Windows (or VMWare with Windows VM?)
• Install the Java 1.5 runtime and Tomcat 5 web server.
• Install vendor software for the converters you will use.  (Currently only ThermoFinnigan and Waters are supported.)
• Install mzXML converter EXEs by extracting the attached Converters.zip:
  • ReAdW.exe for ThermoFinnigan
  • wolf.exe for Waters
• Make sure these executables are on the path for the service running Tomcat.

Installing the Conversion Service

• Place the attached ConversionQueue.war in <tomcat-root>/webapps
• Place the attached ConversionQueue.xml in <tomcat-root>/conf/Catalina/localhost
• Edit the properties marked with @@ in the ConversionQueue.xml to match your system:
  • Set @@conversionQueueDocBase@@ to the directory where the WAR is exploded
  • Set @@networkDriveLetter@@ to the drive leter of your choosing.
    (NB: If you are running CPAS on a Windows server, this should be the same drive chosen for the CPAS installation.)
  • Set @@networkDrivePath@@ to the UNC path where your raw data will be placed (e.g. \\large\storage)
    (NB: If you are running CPAS on a Windows server, this should be the same path chosen for the CPAS installation.)
  • Set @@networkDriveUser@@ to the user name used to log onto this share (e.g. DOMAIN\labkey)
  • Set @@networkDrivePassword@@ to the password for the specified user
  • Set @@smtpHost@@ to the SMTP server that may be used for system errors
  • Set @@smtpUser@@ to the user name used for SMTP communication
  • Set @@smtpPort@@ to the port used by the SMTP service on the specified server
• Restart the Tomcat server.

Testing the Conversion Service

• First make sure Tomcat is now aware of the web app by pointing a browser at
  http://myserver/ConversionQueue/
  You should get a HTML page back.  Browse a couple links on the page.
• Next test your network drive by pointing to a raw data file to convert, e.g.
  http://myserver/ConversionQueue/ConvertSpectrum/submit.post?type=thermo&infile=T:\test\Test.RAW
  You should get a single line of text "Succeeded".
• Check the contents of the queue
  http://myserver/ConversionQueue/ConvertSpectrum/list.view
  You should see the request you just made.  Refresh until the job appears complete.
• Acknowledge completion of the conversion
  http://myserver/ConversionQueue/ConvertSpectrum/acknowledge.post?infile=T:\test\Test.RAW
  You should get a single line of text "Acknowledged".
• If any of the above fail, consult the Tomcat log file conversion.log in <tomcat-home>/logs.

Connecting the Cluster Pipeline

• To connect your MS2 cluster pipeline to the mzXML conversion service, edit the "params.xml" file in the directory where you installed pipe.pl.
  • Set "pipeline config, conversion server" to point to the server you just installed.
  • If your CPAS server is not running on Windows, make sure you set the "pipeline config, windows path prefix" and "pipeline config, unix path prefix" to correctly map paths between your Unix cluster and the conversion server Windows drive mapping.

Testing Conversion in the Cluster Pipeline

• You may want to set up a new pipeline root with a pipe.sh debug parameters like "--v --v --i --t=15", and run this script in a command window, rather than using an existing production pipeline that runs as a cron job.
• Place a raw data file in a folder under this debug pipeline root.
• Set up a CPAS project to point to this pipeline root directory.
• Click on the "Process and Upload Data" button, and navigate to the directory containing your raw data file.
• Initiate a simple peptide search.
• If everything is set up correctly, the pipeline should progress to completion without error.
• If you get errors, review the logs and the output in your pipeline command console.