DESCRIPTION.rst

MaxQuant is a quantitative proteomics software package that unfortunatly only runs on Windows and is designed for use with a graphical user interface. Both make it hard to integrate into a larger workflow.

mqrun consists of four parts, that try to mitigate those problems:

:mod:`mqrun.mqparams`

This is a small library that converts user supplied json-parameter files into the rather peculiar configuration files of MaxQuant and supplies a small helper function that calles the MaxQuant executable with this configuration. The format of the parameter file is documented in :doc:`param_format`. Since the format of the MaxQuant configuration file keeps changing, mqparams supports one version of MaxQuant only.

:mod:`mqrun.fscall`

fscall is a library that handles requests to another machine, where the filesystem is the only communication channel. It provides status messages, simple error handling, access to logfiles and a heartbeat that tells the client that the server is still working on a request.

:mod:`mqrun.mqdaemon`

mqdaemon uses fscall to provide a server that can run on a Windows machine and handles requests for MaxQuant. It includes basic load balancing. See mqdaemon -h for options.

:mod:`mqrun.mqclient`

mqclient is a small client library that wraps the fscall routines to provide a convenient interface for programs running on linux (or windows) machines, that want to run MaxQuant.

If configured correctly it can also start a virtual machine running Windows and use that to run MaxQuant without the need for a dedicated Windows machine.