Difference between revisions of "Bioperl Pipeline"

Jump to: navigation, search
(New page: == Description == The [http://www.genome.org/cgi/content/full/13/8/1904 Bioperl pipeline framework ]is a flexible workflow system that complements the Bioperl package by providing job ...)
Line 15: Line 15:
* [http://www.perl.com/ Perl 5.6 or later]
* [http://www.perl.com/ Perl 5.6 or later]
* [http://www.mysql.com/ MySQL]
* [http://www.mysql.com/ MySQL]
* [http://bioperl.org/wiki/Main_Page Bioperl Packages] [[[http://code.open-bio.org/cgi/viewcvs.cgi/ Browse CVS]]]<br /> bioperl-pipeline<br /> bioperl-live<br /> bioperl-run
* [http://bioperl.org/wiki/Main_Page Bioperl Packages] [[Browse CVS]]]<br /> bioperl-pipeline<br /> bioperl-live<br /> bioperl-run
== Getting the Software ==
== Getting the Software ==
Line 34: Line 34:
* [[1_documentation 1. Documentation]]
* [[1. Documentation]]
* [[2_development 2. Development]]
* [[2. Development]]

Revision as of 18:39, 25 January 2007


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.


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
Paramecium genome curation project
Ciona savignyi genome project