Re: [proteowizard-support] Issue with Thermo RAW reader for Linux (msconvert)

[Chambers, M. <mat...@gm...>]

Hi Simon,

To use msconvert with vendor readers on Linux, you need to use the Docker container:
https://hub.docker.com/r/proteowizard/pwiz-skyline-i-agree-to-the-vendor-licenses

Hope this helps,
-Matt


On 5/7/2023 6:59 AM, SImon Michau wrote:
>
> Dear ProteoWizard Team,
>
> while working on a new Data Analysis Pipeline for Orbitrap in Linux I encountered a problem with msconvert when trying to convert a .raw 
> file to .mzML using the command `msconvert data.RAW` (see log below).
>
> I also tried the same in Windows where it works flawless. Is there a workaround to make this work in Linux? And if not do you have any 
> recommendations for raw to mzML conversion via CLI?
>
>
> *[ReaderFail] [Reader_Thermo::read()] Thermo RAW reader not implemented: Thermo DLLs only work on Windows*
> Error processing file data.RAW
>