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BioPerl.pm  view on Meta::CPAN

  cpan> install Bundle::BioPerl
  cpan> quit

Just like the manual installation of perl modules, the user may
need root access during this process to insure write permission 
is allowed within the intstallation directory.


=head1 CONTENTS

    Algorithm::Munkres

    Bio::Phylo

    Class::AutoClass 1.01

    Clone

    Convert::Binary::C

    Data::Stag::Writer
    
    DB_File

    DBD::mysql

    GD::SVG	- Optional, used to generate SVG output in Bio::Graphics

    GD 1.3	- Used only for drawing things within the Bio::Graphics modules

    Graph::Directed	- This module is used for Ontology Engine implementation for the GO parser

    GraphViz

    HTML::Entities

    HTML::HeadParser

    HTML::Parser 3.0	- recommended, used to parse GDP page in Bio::DB::GDP

    HTML::TableExtract

    HTTP::Request::Common - recommended, used for web access (part of libwww-perl)

    IO::String

    IO::Scalar

    List::MoreUtils

    LWP::UserAgent	- recommended, used for web access

    PostScript::TextBlock

    Scalar::Util

    Set::Scalar

    SOAP::Lite	- Used for bibliographic queries & XEMBLService modules

    Sort::Naturally

    Spreadsheet::ParseExcel

    Storable	- recommended for all bioperl releases after 0.7.2. Used for persistant storage of objects and local file caching

    SVG 2.26	- Optional, used to generate SVG output in Bio::Graphics

    SVG::Graph 0.01	- Optional, used to generate SVG output in Bio::Graphics

    Text::ParseWords	- Recommended, used in Bio::Graphics

    XML::DOM

    XML::DOM::XPath

    XML::LibXML

    XML::Parser

    XML::Parser::PerlSAX	- recommended for all bioperl releases after 0.6.2

    XML::SAX

    XML::SAX::Writer

    XML::Simple

    XML::Twig	- recommended for all bioperl releases after 0.6.2

    XML::Writer	- recommended for all bioperl releases after 0.6.2

    YAML

=head1 DESCRIPTION

The BioPerl distribution from http://bioperl.org contains code and
modules that may use or require additional 'external' perl modules 
for advanced functionality. Many of the external modules are not
contained within the standard Perl distribution. These external 
modules can be obtained from the Comprehensive Perl Archive 
Network (CPAN) located at http://www.cpan.org. 

NOTE: The latest release of this bundle includes all of the
external CPAN modules that are listed as dependencies of the
official BioPerl 1.5.2 codebase release. 

The only exceptions are the DBD:: and DBI:: modules which are really 
best off installed on their own if you have a need to load and 
query relational. databases.

These modules are not required - they greatly extend the functionality
of bioperl in various ways. To get the best use of bioperl, particularly
after the release of BioPerl 1.0 we recommend at least having the
LWP:: network access and the XML:: related modules installed. 

This perl module (Bundle::BioPerl) contains NO functionality
or real code at all. It is essentially a special perl module
meant to be used by the CPAN.pm module to simplify the task of
automatically installing multiple modules in one easy step.