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

• fgcz (default)

See also

• FCC - An automated rule-based processing tool for life science data. Barkow-Oesterreicher S1, Türker C, Panse C. Source Code Biol Med. 2013 Jan 11;8(1):3. doi:10.1186/1751-0473-8-3, PMC3614436, PMID: 23311610
• FCC configuration @ FGCZ