bein: Bein is a provenance and workflow management system for bioinformatics.

[ application, deprecated, gpl, program ] [ Propose Tags ]

To avoid having thousands of files produced in a random way from a bunch of scripts, as is typically the case for a bioinformaticist, Bein keeps track of scripts, and their executions on various inputs. It provides a web front end, and will integrate with LSF clusters.

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Versions [RSS] 0.1, 0.2, 0.3, 0.3.1, 0.3.2, 0.3.3
Dependencies base (>=3 && <5), bytestring, containers, convertible, Crypto, directory, filepath, happstack-server, happstack-util, hdaemonize (>=0.4), HDBC, HDBC-postgresql, hsyslog, mtl, network, old-locale, parsec, process, random, stm, time, unix, utf8-string, xhtml [details]
License GPL-3.0-only
Author Fred Ross
Category Application
Uploaded by FrederickRoss at 2010-05-28T12:27:47Z
Reverse Dependencies 1 direct, 0 indirect [details]
Executables beinhttpd, beinminion, beinclient, beind, beinctl
Downloads 4772 total (15 in the last 30 days)
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Status Docs not available [build log]
All reported builds failed as of 2016-10-27 [all 10 reports]

Readme for bein-0.3.3

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Bein is a provenance and workflow system for bioinformatics.  Typically a bioinformaticist ends up with a dozen scripts and a thousand or so files from running the scripts with slightly varying parameters and no way to keep track of what came from where.  Bein resolves this by keeping scripts, and their executions on inputs and the resulting outputs, in a database, and providing a web interface to the system.

Organization of the build directory

The build directory contains the following items:

bein.cabal    -- The equivalent of a Makefile for Haskell
doc/          -- Documentation for the system
priv/files/   -- A default directory for data files stored in Bein
priv/scratch/ -- A default working directory for scripts run by Bein
Setup.lhs     -- Part of the infrastructure needed by bein.cabal.  DO NOT EDIT.
sql/          -- All code for setting up the PostgreSQL database
src/	      -- Haskell source code
templates/    -- Template files for the web interface