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https://github.com/fgcz/fcc

An automated rule-based processing tool for life science data.

https://github.com/fgcz/fcc

Science Score: 23.0%

This score indicates how likely this project is to be science-related based on various indicators:

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    CITATION.cff file
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    codemeta.json file
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    .zenodo.json file
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    DOI references
    Found 1 DOI reference(s) in README
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    Academic publication links
    Links to: ncbi.nlm.nih.gov
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    Academic email domains
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    Institutional organization owner
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    Scientific vocabulary similarity
    Low similarity (11.5%) to scientific vocabulary

Keywords

automation instrument life-science-data python reproducible-science
Last synced: 4 months ago · JSON representation

Repository

An automated rule-based processing tool for life science data.

Basic Info
  • Host: GitHub
  • Owner: fgcz
  • Language: Python
  • Default Branch: fgcz
  • Homepage:
  • Size: 104 KB
Statistics
  • Stars: 2
  • Watchers: 4
  • Forks: 1
  • Open Issues: 0
  • Releases: 0
Topics
automation instrument life-science-data python reproducible-science
Created about 11 years ago · Last pushed over 5 years ago
Metadata Files
Readme

README.md

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

```sh

use python 2.7.x

$ python fccrunlinux.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 simon@uberchord.com and Christian Panse cp@fgcz.ethz.ch

maintainer

cp@fgcz.ethz.ch

Configuration

the current FCGZ configuration can be found here.

```xml

```

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

Owner

  • Name: Functional Genomics Center UZH|ETH Zurich
  • Login: fgcz
  • Kind: organization
  • Email: protinf@fgcz.ethz.ch
  • Location: Switzerland

proteome informatics FGCZ

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