fgcz / PyFGCZ

Move and Convert Mass Spectrometry Data using BioBeamer and FCC

PyFGCZ

BioBeamer helps to collect vast amounts of instrument data (MTBytes). 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:\Python37\python.exe c:\FGCZ\fcc\fcc_run_windows.py --ncpu 1 --exec --loop

See also

• https://github.com/fgcz/BioBeamer
• https://github.com/fgcz/fcc

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.