Hi Parag,

My understanding is that the RAW file from MS2 needs to be converted to mzXML for it to be read by LabKey.

Have you had a chance to look at the following documentation on converting RAW to mzXML?

https://www.labkey.org/Documentation/wiki-page.view?name=conversionSoftware

Although you are not using the enterprise pipeline to have LabKey do the conversion using the ProteoWizard utilities, I think you can still use the msconvert.exe program from ProteoWizard manually to convert the RAW file to mzXML and then manually process it within LabKey.

http://proteowizard.sourceforge.net/downloads.shtml

Regards,

Jon

Hi Parag,

There's not a strict line between the "enterprise" pipeline and other configurations you might do to the pipeline on a given server, so some of the relevant documentation is filed under "Enterprise".

If you just want to use msconvert on the web server itself, the setup is much simpler. You don't need ActiveMQ (which is what coordinates messaging across multiple servers), nor do you need to install the LabKey Remote Service.

You really just need to toss msconvert and related dependencies in the tools directory along with the TPP, etc, and tell the server it should run them. You can do this by placing a ms2Config.xml file in your LABKEY_ROOT/config directory. The one shown on this page:

https://www.labkey.org/Documentation/wiki-page.view?name=configureConversionService

is basically what you want, except for the third-to-last line, which assigns the task to run on a different server. Since you're running everything on the web server, you can just delete that line.

Restart Tomcat, and you should see messages in labkey.log that indicate the server is loading from the new XML file. When you browse files, you should see the actions wired up to .raw files.

Thanks,
Josh