biodavidjm / maxquant_linux_guide

A guide to running MaxQuant in Linux

MaxQuant for Linux Guide

Read my blog post here: http://atchen.me/research/2019/03/21/mq-linux.html

The goal of the gen_mqpar.py script is to create MaxQuant configuration files (mqpar.xml files) in a console environment without having to transfer one over or edit the XML manually. The example given has some hard-coded stuff and makes assumptions about your filesystem, so please follow the steps below to get started.

1. Verify that Mono is installed.

Note, If searching Bruker timsTOF data, you need gcc version 8.3+. Check the version with gcc --version. You can install gcc8 with these commands:

# For CentOS 7:

yum install centos-release-scl
yum install devtoolset-8
scl enable devtoolset-8 -- bash

# Enable the tools (put this into .bash_profile)
source /opt/rh/devtoolset-8/enable

(Thanks to @cscaife for identifying this step, and https://stackoverflow.com/a/55876012 for the install instructions)

2. Create template mqpar.xml files – representing configurations for MaxQuant searches you routinely run on your experiments. I put a bunch of my templates in a folder, templates/ for easy access.
   • I recommend generating these first in the MaxQuant GUI, as it's easier and you can verify that the configuration file is valid before moving it to your Linux instance.
   • Don't worry about the raw files, folder paths, or FASTA file paths in the template file – they will be replaced by the script
3. Move the MaxQuant files onto your Linux instance. My setup has MaxQuant versions separately in a folder MQ/, i.e., MQ/MaxQuant_1_7_0. I then map this path to an environment variable in my .bash_profile, with export MQ_1_7_0=~/MQ_1_7_0/bin/MaxQuantCmd.exe. You can manage your MaxQuant versions however you like, just make sure that it's reflected in the gen_mqpar.py script.
4. Move your protein FASTA files over to the Linux instance. The current gen_mqpar.py script has the path to the FASTA file hard-coded, and it's straightforward to change this or make it argument-driven.

Run:

./gen_mqpar.py <path/to/template> <path/to/raw_file_folder> -o <path/to/output_mqpar.xml> -t <num_threads>
# for example,
./gen_mqpar.py templates/SILAC.xml raw_files/FP93 -o fp93_silac.xml -t 6

If you're getting errors with starting MaxQuant with the generated mqpar files, then I would manually check all of the paths in the XML file first.