fgcz / pyfgcz

Move and Convert Mass Spectrometry Data using BioBeamer and FCC

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.

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.

pyfgcz's Issues

add `$HOME/.fcc.rc`

for configuring

• syslog server
• instrument pattern

add number of pending jobs