PyFGCZ contains BioBeamer and FCC python code.
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.
- pip3 install PyFGCZ
adapt the following scripts
- fcc_run_linux.py –ncpu 1 –hostname fgcz-s-021 –output __runme.bash –exec –loop
- C:Python37python.exe c:FGCZfccfcc_run_windows.py –ncpu 1 –exec –loop
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.
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