Bioperl Pipeline
The item described in this page is not (or is no longer) supported by
the GMOD project.
This page is included only for reference purposes.
See Ergatis,
Galaxy, Genome grid,
DIYA and MAKER for currently supported
workflow and analysis packages.
Contents
Description
The Bioperl pipeline framework is a
flexible workflow system that complements the Bioperl package by
providing job management facilities for high throughput sequence
analysis. It also known as Biopipe. This system is heavily inspired by
the EnsEMBL Pipeline system.
- Handling of various input and output data formats from various
databases.
- A bioperl interface to non-specific loadsharing software (LSF,PBS etc)
to ensure that the various analysis programs are run in proper order
and are successfully completed while re-running those that fail.
- A flexible pluggable bioperl interface that allows programs to be
‘pipeline-enabled’. Setting up bioinformatics pipeline is not trivial.
This tutorial introduces some aspects of biopipe through setting up a
very simple blast pipeline and a protein analysis pipeline.It is hope
that through this tutorial, two objectives are achieved:
- Iron out installation issues using a simple example.
- Familiarization with the biopipe system and introduction of the XML
system we have develop to ameliorate some of the complexities involve
in setting up.
Requirements
Getting the Software
You can download the CVS version of bioperl-pipeline from
Bioperl CVS
cvs -d :pserver:cvs@cvs.open-bio.org:/home/repository/bioperl co bioperl-pipeline
Mailing List
Mailing list
Affiliated projects
Maize annotation project
system registry cleaner
ParameciumDB
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