Setting up ReAdW and Wine

Here are the relatively simple steps needed to run ReAdW under Wine. This will let you perform mzXML conversions of Thermo RAW files on your linux box. If you need to install Wine, do so (e.g. "yum install wine").

A. Grab the latest ReAdW binary compiled with MS File Reader support.
https://github.com/PedrioliLab/ReAdW/blob/master/bin/ReAdW.2016010.msfilereader.exe

B. Log into Thermo's mass spectrometry software site:
https://thermo.flexnetoperations.com/control/thmo/login

C. Then get "MS File Reader 3.0 SP3" from Thermo from this page:
https://thermo.flexnetoperations.com/control/thmo/download?element=6306677

Note that latest MSFileReader 3.1 is 64-bit and won't install under Wine for me as my default Wine installation must just support 32-bit Windows. Actually I did find another box with a 64-bit install of Wine and still can't install MSFileReader 3.1 as it complains it is not supported on a 32-bit operating system even though I have set WINEARCH=win64.

D. install MSFileReader (which installs vcrun2008 + vcrun2010):  wine /path/to/MSFileReader_x86_x64.exe

That's it! Now try to run a conversion:  wine /path/to/ReAdW.2016010.msfilereader.exe --centroid somefile.raw

Actually also set the following environment variable to suppress all Wine debug output: export WINEDEBUG=-all