If anyone's interested, I finally got msconvert to work, but it takes extra effort to do when you have your pipeline running on a UNIX machine.
I tried running msconvert under wine, but it or its dependencies kept crashing, so we decided to set up msconvert on a Windows computer and create a dedicated server. That way the Linux computer sends the file to the Windows computer, where msconvert transforms it into an mzML file, and then sends it back to the Linux computer. -- You received this message because you are subscribed to the Google Groups "spctools-discuss" group. To post to this group, send email to [email protected]. To unsubscribe from this group, send email to [email protected]. For more options, visit this group at http://groups.google.com/group/spctools-discuss?hl=en.
