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PyFGCZ contains BioBeamer and FCC python code.

Project description

BioBeamer helps to collect vast amounts of instrument data (M|G|TBytes). An example configuration collecting mass spectrometric measurement of more then a dozen devices can be seen through http://fgcz-ms.uzh.ch/config/BioBeamer.xml.

FCC is a minimalistic workflow engine. The specification/properties of the program are as follow:

  • converting instrument files, e.g., RAW-files to all kinds of formats
  • being generic
  • follows FGCZ hierarch storage granularity: project, user, instrument, time range
  • multi-platform, host, task
  • configurable through XML file which means new converter by new tag in XML file NO CODE CHANGE!
  • stdout and errout through Syslog

A current configuration can be found through http://fgcz-ms.uzh.ch/config/fcc_config.xml.

Install

::
pip3 install PyFGCZ

Usage

adapt the following scripts

Linux

::
fcc_run_linux.py –ncpu 1 –hostname fgcz-s-021 –output __runme.bash –exec –loop

Windows

::
C:Python37python.exe c:FGCZfccfcc_run_windows.py –ncpu 1 –exec –loop

References

FCC - An automated rule-based processing tool for life science data, Simon Barkow-Oesterreicher, Can Türker and Christian Panse, Source Code for Biology and Medicine20138:3 DOI: 10.1186/1751-0473-8-3.

Project details


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Files for PyFGCZ, version 3.0.1
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