Bundle::BioPerl - A bundle to install external CPAN modules used by BioPerl
Perl one liner using CPAN.pm:
perl -MCPAN -e 'install Bundle::BioPerl'
Use of CPAN.pm in interactive mode:
$> perl -MCPAN -e shell 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.
Bundle::LWP - recommended, used for network access
File::Temp - Already present in modern versions of perl
File::Spec - Already present in modern versions of perl
IO::Scalar - optional, used only in Bio::Tools::Blast::Run::WebBlast.pm
IO::String - recommended, used by Bio::DB:WebDBSeqI
HTML::Entities - recommended, used for web RemoteBlast access
HTML::Parser - recommended, used to parse GDP page in Bio::DB::GDP
HTTP::Request::Common - recommended, used for web access
HTTP::Status - recommended, used for web access
LWP::UserAgent - recommended, used for web access
URI::Escape - recommended, used for web access
XML::Parser - recommended for all bioperl releases after 0.6.2
XML::Parser::PerlSAX - recommended for all bioperl releases after 0.6.2
XML::Writer - recommended for all bioperl releases after 0.6.2
XML::Node - recommended for all bioperl releases after 0.6.2
XML::Twig - recommended for all bioperl releases after 0.6.2
Text::Iconv - dependency for XML::Twig
Scalar::Util - dependency for XML::Twig
XML::DOM - used only by SeqIO::bsml
SOAP::Lite - Used for bibliographic queries & XEMBLService modules
GD - Used only for drawing things within the Bio::Graphics modules
GD::SVG - Optional, used to generate SVG output in Bio::Graphics
SVG - Optional, used to generate SVG output in Bio::Graphics
SVG::Graph - Optional, used to generate SVG output in Bio::Graphics
Storable - recommended for all bioperl releases after 0.7.2. Used for persistant storage of objects and local file caching
Text::Shellwords - Recommended, used in Bio::Graphics
Data::Stag - This module is used by our SeqIO/chado* modules.
Graph::Directed - This module is used for Ontology Engine implementation for the GO parser
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 1.4 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.
Essentially users can tell CPAN.pm to 'install Bundle::BioPerl' and CPAN.pm will download, install and configure all of the modules listed in the BioPerl Bundle module. See the SYNOPSIS section or do
perldoc CPAN to learn about how to use the CPAN.pm module to install bundles.
NOTE: This process is complicated by the fact that some BioPerl external modules themselves have their own dependencies and prerequisites. In particular the XML::Parser module requires the prior installation of the 'xpat' package which resides outside of CPAN at http://sourceforge.net/projects/expat/.
install Bundle::BioPerl process may need to be repeated several times to complete the full installation of all listed modules. Some external modules are complicated or may themselves have dependencies.
NOTE: This Bundle does not install BioPerl :) Just the additional modules that BioPerl code ocasionally makes use of. You will still need to get the BioPerl distribution from CPAN or http://bioperl.org and install it the usual way:
perl Makefile.PL make make test make install
CPAN.pm has many features - including the ability to download but not install the modules listed in the BioPerl bundle.
perldoc CPAN is your friend :)
Chris Dagdigian <email@example.com> (Author only of this bundle, not any the modules it lists)