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Revision as of 13:51, 17 June 2011 (view source) Roczei (Talk | contribs) ← Older edit		Revision as of 13:46, 28 June 2011 (view source) Roczei (Talk | contribs) (→Recommendations for Configuration and Usage) Newer edit →
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	== Recommendations for Configuration and Usage ==		== Recommendations for Configuration and Usage ==
-	Please describe here any common settings, configurations or conventions that would make the usage of this resource (library or tool) more interoperable or scalable across the HP-SEE resources. These recommendations should include anything that is related to the resource and is agreed upon by administrators and users, or across sites and applications. These recommendations should emerge from questions or discussions opened by site administrators or application developers, at any stage, including installation, development, usage, or adaptation for another HPC centre.	+	Need to be installed to user space.
-		+
-	Provided descriptions should describe general or site specific aspects of resource installation, configuration and usage, or describe the guidelines or convention for deploying or using the resource within the local (user/site) or temporary environment (job). Examples are:	+
-		+
-	* Common configuration settings of execution environment	+
-	* Filesystem path or local access string	+
-	* Environment variables to be set or used by applications	+
-	* Options (e.g. additional modules) that are needed or required by applications and should be present	+
-	* Minimum quantitative values (e.g. quotas) offered by the site	+
-	* Location and format of some configuration or usage hint instructing applications on proper use of the resource or site specific policy	+
-	* Key installation or configuration settings that should be set to a common value, or locally tweaked by local site admins	+
-	* Conventions for application or job bound installation and usage of the resource	+

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Revision as of 13:46, 28 June 2011

Contents 1 Information 1.1 Authors/Maintainers 1.2 Summary 1.3 Features 1.4 Architectural/Functional Overview 1.5 Usage Overview 1.6 Dependacies 1.7 HP-SEE Applications 1.8 Resource Centers 1.9 Usage by other projects and communities 1.10 Recommendations for Configuration and Usage

Information

• Web site: http://www.bioperl.org/
• Described version: 1.6.1
• Licensing: Dual - Perl Artistic License or GNU General Public License v3
• User documentation: http://www.bioperl.org/wiki/Category:Documentation
• Download: http://www.bioperl.org/wiki/Getting_BioPerl#BioPerl_Releases
• Source code: http://bioperl.org/DIST/BioPerl-1.6.1.tar.gz

Authors/Maintainers

• Main developers: Windiwsch Gergely, OU
• Co-developers: Judit Marton, Kemenyfi Timea

Summary

BioPerl is a toolkit of perl modules useful in building bioinformatics solutions in Perl. It is built in an object-oriented manner so that many modules depend on each other to achieve a task. The collection of modules in the BioPerl-live repository consist of the core of the functionality of BioPerl. Additionally auxiliary modules for creating graphical interfaces (bioperl-gui), persistent storage in RDMBS (bioperl-db), running and parsing the results from hundreds of bioinformatics applications (Run package), software to automate bioinformatic analyses (bioperl-pipeline) are all available as Git modules. Bioperl is a collection of Perl modules that facilitate the development of Perl scripts for bioinformatics applications. As such, it does not include ready to use programs in the sense that many commercial packages and free web-based interfaces do (e.g. Entrez, SRS). On the other hand, Bioperl does provide reusable Perl modules that facilitate writing Perl scripts for sequence manipulation, accessing of databases using a range of data formats and execution and parsing of the results of various molecular biology programs including Blast, clustalw, TCoffee, genscan, ESTscan and HMMER. Consequently, BioPerl enables one to develop scripts that can analyze large quantities of sequence data in ways that are typically difficult or impossible with web based systems.

Features

• Listed features

Architectural/Functional Overview

• high level design info, how it works, performance - may be a link, or several links

Usage Overview

• Installation on Unix and on Windows
• HowTo
• Tutorial and tutorial documents

Dependacies

• Unix
  • Perl 5.6.1 or later; version 5.8 or greater is recommended.
  • make. For Mac OS X, this requires installing the Xcode Developer Tools.
• Windows
  • ActivePerl >= 5.8.8.819

other dependencies

HP-SEE Applications

• DeepAligner (Deep sequencing for short fragment alignment)
• DiseaseGene (In-silico Disease Gene Mapper)

Resource Centers

• RCs supporting it (with version number if not the same as above)

Usage by other projects and communities

• If any

Recommendations for Configuration and Usage

Need to be installed to user space.