Bioinformatics Asked on August 19, 2021
MaxQuant is a software package for mass spectroscopy and proteomics. There is a windows version and a linux version. To run on linux you have to use a program that is called mono. I think, it is developed by Microsoft, which I find quite nice from them. I installed mono on Linux and started MaxQuant.
mono MaxQuant.exe
The documentation claims it is for running MaxQuant in commandline mode, though a GUI is started anyway. How can I start the program in commandline mode to perform batch analysis? I think, there is not enough information given on the web-page.
Give
mono MaxQuantCmd.exe [OPTIONS]
a try.
University of Oslo description of how to use the tool in their infrastructure.
Correct answer by Kohl Kinning on August 19, 2021
You can now install MaxQuant (v. 1.6.10.43) with anaconda:
conda install -c bioconda maxquant
and to run MaxQuant simply with:
maxquant.sh mqpar.xml
Answered by Sören on August 19, 2021
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