A Python file monitor that converts raw data files to mzML format and adds them to Stasis, our processing tracking system. This software can only be run on Windows based computers.
We use ProteoWizard for the conversion, and use only a subset of ProteoWizard's supported formats
- Agilent .d
- Thermo .raw
- Waters .raw
- Open formats (no need to convert)
- .mzML
Install from source by cloning our repository source code
$ git clone git://bitbucket.com/fiehnlab/monitor.git
Then run the following to install all the dependencies:
$ cd monitor
$ pip install -r requirements
$ pip install ./
Python versions 3.8 and newer are supported.
Please adjust the values in appconfig.yml and appconfig-test.yml to match your system and/or needs.
Tests can be run using
$ pytest tests
Please note this tool depends on ProteoWizard being installed on the same host.
Configure ProteoWizard's installation folder in appconfig.yml
This application can be run as follows:
$ python launch.py [options]
Before running, please ensure you update the config file to your needs.
Please use
$ python launch.py -h
to get a list of the available options.
To terminate the application press: Ctrl+C
NOTE: It is suggested to use a 'service wrapper' (like nssm) to run this app.
NOT FULLY IMPLEMENTED!!!
Please download and save the following files in 'docker' folder:
- pwiz-3.0.21209.zip
- MinGit-2.32.0-64-bit.zip
The docker folder contains a Dockerfile to build an image that can run the application. Currently pip has issues cloning some git dependencies needed for the proper running of the monitor.
This module was written by Diego Pedrosa.