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FCC - FGCZ Converter Control

Description

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

Install

  1. use python version 3.7 or higher
  2. see https://pypi.org/project/PyFGCZ/ and run pip3 install PyFGCZ
  3. adapt the fcc_run.py script to your needs.

Synopsis

on Microsoft OS

c:\Python27\python.exe fcc_run_windows.py --output __runme.bat --ncpu 2 --exec

on UNIX

# use python 2.7.x
$ python fcc_run_linux.py --hostname fgcz-s-021 --output out-20150824.bash --ncpu 1 --exec --loop

Arguments:

  • --output <file> writes a batch file to run later manually
  • --exec automatically triggers the execution of the generated converter commands
  • --loop the FCC automatically restarts after it has finished one crawling round
  • --ncpu number of jobs should be used
  • --hostname <host configuration> tells fcc which host configuration should be used.

Authors

Simon Barkow-Oesterreicher [email protected] and Christian Panse [email protected]

#maintainer

[email protected]

Configuration

the current FCGZ configuration can be found here.

 <controllerRuleSet>
    <rule converterID='000' 
    project='p103' 
    omics='Proteomics' 
    user='' instrument='ORBI_2' 
    beginDate='20080901' 
    endDate='20990101' 
    keyword="iTRAQ">
    </rule>
</controllerRuleSet>
    
<converterList>
    <converter converterID='000' 
    converterDir= 'mgf__low_res_MS2_iTRAQ' 
    converterCmd='cscript "C:\FGCZ\fgcz-proteomics\stage\mascot_distiller\fgczRaw2Mgf.vbs"'         converterOptions='"C:\FGCZ\fgcz-proteomics\stage\generalRawFileConverterRobot\MascotDistillerOPTs\Orbitrap_low_res_MS2_iTRAQ.opt"' 
    toFileExt='.mgf' 
    hostname='fgcz-s-034'> 
    </converter>
</converterList>

TODO

  • provide cmd argv for log file name
  • unit test - no glue how to do that
  • ensure that no process is killed by CTRL-C. add a pool wait at the right position on the code when CTRL-C is pressed or give at least a warning.
  • write a pid file to ensure that only one fcc is running

Branches

See also