PyFGCZ
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.
Usage
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
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.
