Hi Vitor,

When I translated the "pipeline quantitation" parameters from the Perl Cluster Pipeline, I left Q3 in there, but never really tested it, as the only people I knew using Q3 were members of the Hanash Lab, and none of you had ever made any requests of the single-machine installation.

If you make it past the java.exe issue you are likely to run into the problem that we do not install viewerApp.jar, nor does the code make any attempt to locate a viewerApp.jar, making the java command-line somewhat lacking.

I have had to fix this last problem for the MS1 pipeline to be shipped with our next release, so I should also be able to fix Q3. I'll do my best to make v8.1 handle Q3 from a simple single-machine installation. Sorry to lead you on by actually generating a "java ..." command line, rather than emitting a "Not yet implemented" error, as would be more accurate in v2.3.

Thanks for the bug report. It would certainly impact the MS1 pipeline to not have java.exe on the system path inside the labkey server application.

--Brendan