Quickstart

Calling MaxQuant locally

blubb.

Calling MaxQuant on a dedicated Windows machine

Suppose the two hosts win_host and linux_host are in a network and we would like to call MaxQuant on the win_host, but control the process and provide the input and parameter files from the linux machine.

In this tutorial I will assume that MaxQuant is already installed on win_host and that a share has been setup: /mnt/win_share should be accessable from win_host as Z:\\. There are countless tutorials for this setup, but you can find a quick description for this in (:todo:`not yet`).

First we need to install python3.3 or later on the windows machine. Download the msi installer from the Python download page and install Python. For ease of use, the option to add the executables to the PATH should be enabled. (:todo:`check that this option exists...`)

Next, install mqrun on both machines:

pip install mqrun

On linux this needs administrator priviliges, although a local installation with virtualenv is possible.

Note

python2.7 is ok on linux, the windows version needs at least python3.3

Start the mqrun.mqdaemon server process on the windows machine:

cd Z:
mkdir requests
mqdaemon -h  # have a look at the options...
mqdaemon --mqpath C:\\path\to\MaxQuant\dir --logfile maxquant.log requests

You can now run MaxQuant from linux (using python):

from mqrun import mqclient
import json

with open('paramfile.json') as f:
    params = json.load(f)

path_data = {
    "raw_file1": "/path/to/raw/file",
    "raw_file2": "/path/to/raw/file2",
    "fasta_file": "/path/to/fasta/file",
}

maxquant = mqclient.mqrun(params, path_data, share='/mnt/win_share_requests')

maxquant.wait()
try:
    outfiles = maxquant.result()
except TimeoutError:
    print("Connection lost or server overloaded")
except Exception as e:
    print("Error executing MaxQuant: " + str(e))
else:
    print(outfiles)

print("Logfile\n=======\n")
print(maxquant.log)  # print the logging output of the server

The format of the parameter file is explained in mqrun.mqparams.

Use MaxQuant on an virtual machine

Requirements:

• qemu with kvm enabled on the linux machine
• guestfs + python wrappers on linux
• A windows virtual machine image

Configure the windows machine

Start the windows machine with qemu and the software image at (TODO)

qemu -hda winvm.img -boot c -hdb mqrun_image.img -enable-kvm -m 1024

and execute the file install.bat on d:\\.

Execute MaxQuant exactly as in the example above, but replace the keyword argument share in the mqclient.mqrun call by img=path/to/win/image.