Add support for raw files

ProtProtocols / IsoProt

Protocol of the analysis of iTRAQ/TMT proteomics data including quantification, statistical analysis and maybe clustering

https://protprotocols.github.io

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Add support for raw files #71

Open veitveit opened 5 years ago

veitveit commented 5 years ago

This seems to work:https://github.com/compomics/ThermoRawFileParser

jgriss commented 5 years ago

Yes, Thermo ported their RawFileReader and also supports linux now.

iustin94 commented 5 years ago

What about the raw files CLI application from proteowizard? They have the GUI only for windows but it looks that the msconvert CLI can be built on linux and added in the the workflow.

jgriss commented 5 years ago

On Linux, msconvert can currently not use vendor libraries. This can lead to issues. There is now a Java CLI available for the Thermo reader which I think will be the best option.