Bioperl Pipeline
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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.
Warning: The BioPipe workflow management system is no longer supported by GMOD due to lack of support.
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
- Perl 5.6 or later
- MySQL
- Bioperl Packages Browse CVS]
bioperl-pipeline
bioperl-live
bioperl-run
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
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