I have been running MaxQuant quite frequently on Linux. I would use conda to create a dedicated environment and install
# create the environment
conda create -n maxquant -c conda-forge mono
# activate the environment
conda activate maxquant
# run any maxquant version
mono /path/to/maxuant/MaxQuantCmd.exe mqpar.xml
This installs a conda environment with
mono which is a
.NET framework for Linux. I had problems in the past running certain MaxQuant versions that way.
mqpar.xml that is required can be created with the MaxQuant GUI. And then the path for input files needs to be contained correctly. The path to the fasta file and the raw file. I would create a template file and then parse these filenames into the specific locations.
The combination of
mono=5.14 worked and a few other versions. Some versions between 1.6 and 2.x did not work at all.
Specific versions of MaxQuant are also available directly via
conda and there is no need to download the zip file. Instead, you can simply install it with:
conda install -c conda-forge -c bioconda maxquant mono=5.14
Recently MaxQuant 2 has been added, and not all previous versions are available and run maxquant with: