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https://github.com/fgcz/pyfgcz
Move and Convert Mass Spectrometry Data using BioBeamer and FCC
https://github.com/fgcz/pyfgcz
automation data-processing high-throughput python3 robot staging-algorithm workflow-engine
Last synced: 4 days ago
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Move and Convert Mass Spectrometry Data using BioBeamer and FCC
- Host: GitHub
- URL: https://github.com/fgcz/pyfgcz
- Owner: fgcz
- License: gpl-3.0
- Created: 2016-09-26T05:02:16.000Z (about 8 years ago)
- Default Branch: python3
- Last Pushed: 2020-08-11T13:55:58.000Z (over 4 years ago)
- Last Synced: 2024-10-07T08:45:26.709Z (about 1 month ago)
- Topics: automation, data-processing, high-throughput, python3, robot, staging-algorithm, workflow-engine
- Language: Python
- Homepage: https://pypi.python.org/pypi/PyFGCZ
- Size: 66.4 KB
- Stars: 2
- Watchers: 5
- Forks: 1
- Open Issues: 2
-
Metadata Files:
- Readme: README.rst
- License: LICENSE
Awesome Lists containing this project
README
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 PyFGCZUsage
-----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 --loopSee 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`__.__ http://dx.doi.org/10.1186%2F1751-0473-8-3