bein,bbcf

bein's Introduction

bein 1.1.0
Copyright 2011 EPFL BBCF <webmaster dot bbcf at epfl dot ch>

Bein is a workflow manager and miniature LIMS system built in the
Bionformatics and Biostatistics Core Facility of the EPFL.  It fills
the gap for the working scientist between the classical shell and big
workflow managers like KNIME or Galaxy and major LIMS systems like
OpenBIS.

Bein is released under the GNU General Public License 3.0.  A copy of
this license is in the LICENSE file.

Installation
------------

You will need to have Python >= 2.5 installed on your system.  Some of the functions in bein.utils require numpy, matplotlib, pytables, and pysam, but will simply be unavailable if those libraries are not installed.

To install bein, in the bein directory, run

$ python setup.py build
$ sudo python setup.py install

Acknowledgements
----------------

The development of bein was supported by The Bioinformatics and
Biostatistics Core Facility of the EPFL (http://bbcf.epfl.ch/) and
SyBit (http://www.systemsx.ch/projects/systemsxch-projects/sybit/).

Features to add someday
-----------------------

* A MiniLIMS based on PostgreSQL for scaling up MiniLIMS repositories.
* A fancier MiniLIMS client.
* Refactor bein.util into submodules based on domain.

bein's People

Contributors

Stargazers

Watchers

bein's Issues

bein and BBCF LSF queue

Make BBCF lsf queue the default queue when running jobs on the cluster

bein.search_executions

Would be nice to add an option to filter on executions that succeded only ?
Greg

fetch_file and description

fetch_file(id)["description"] is returned as a long string though it is set through execution() as dictionary.
I guess it would be better to keep it as a dict.