Difference between revisions of "Bioperl Pipeline"

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See [[Ergatis]], [[Galaxy]], [[Genome grid]], [[DIYA]] and [[MAKER]] for currently supported workflow and analysis packages.
  
 
== Description ==
 
== Description ==
  
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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 management facilities for high throughput sequence analysis. It also known as Biopipe. This system is heavily inspired by the EnsEMBL Pipeline system.
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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 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.
 
* Handling of various input and output data formats from various databases.
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* [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]
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* [http://bioperl.org/wiki/Main_Page Bioperl Packages] [[Browse CVS]]]<br /> bioperl-pipeline<br /> bioperl-live<br /> bioperl-run
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* [http://bioperl.org/wiki/Main_Page Bioperl Packages]:
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** bioperl-pipeline
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** bioperl-live
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** bioperl-run
  
 
== Getting the Software ==
 
== Getting the Software ==
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You can download the CVS version of bioperl-pipeline from [http://code.open-bio.org/cgi/viewcvs.cgi/ Bioperl CVS]
 
You can download the CVS version of bioperl-pipeline from [http://code.open-bio.org/cgi/viewcvs.cgi/ Bioperl CVS]
  
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  cvs -d :pserver:cvs@cvs.open-bio.org:/home/repository/bioperl co bioperl-pipeline
 
  cvs -d :pserver:cvs@cvs.open-bio.org:/home/repository/bioperl co bioperl-pipeline
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== Mailing List ==
 
== Mailing List ==
  
 
[http://bioperl.org/mailman/listinfo/bioperl-pipeline Mailing list]
 
[http://bioperl.org/mailman/listinfo/bioperl-pipeline Mailing list]
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== Affiliated projects ==
 
== Affiliated projects ==
  
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[http://www.maizegdb.org/ Maize annotation project]<br />[http://paramecium.cgm.cnrs-gif.fr/db/about_project Paramecium genome curation project]<br />[http://pre.ensembl.org/Ciona_savignyi/index.html Ciona savignyi genome project]
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[http://www.maizegdb.org/ Maize annotation project]
  
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[http://www.top-registry-cleaner.org/ system registry cleaner]
  
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[[ParameciumDB]]
  
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* [[1. Documentation]]
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[[Category:BioPerl]]
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* [[2. Development]]
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Latest revision as of 12:53, 29 December 2010

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.

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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