[an error occurred while processing this directive] Bioperl external package dependencies [an error occurred while processing this directive] [an error occurred while processing this directive] [an error occurred while processing this directive] [an error occurred while processing this directive] [an error occurred while processing this directive] [an error occurred while processing this directive] [an error occurred while processing this directive] [an error occurred while processing this directive] External package dependencies
The core bioperl distribution will work fine by itself, however, there are portions of the code that can make use of third party packages and code in order to add functionality and provide additional features.

Third party applications

Bioperl contains wrappers, parsers and modules that can make use of several third party applications. Parts of our pre-install test suite may try to check for the presense and behaviour of these applications so you may see mention of them during the bioperl 'make test' installation step. Don't worry about them if you don't need or or use them.

Perl Modules

MySQL database driver and interface modules
DBD::mysql and DBI::mysql, OR DBI::mysqlopt. Some parts of the core bioperl package (and the related bioperl-db codebase) can make use of MySQL relational databases. For example, the Bio::DB:GFF modules can load and query MySQL based GFF feature databases. Given the choice the optimized DBI::mysqlopt driver module is recommended.

AcePerl Modules
In order for bioperl objects to talk to local and remote AceDB databases Lincoln Stein's AcePerl package must be installed prior to bioperl installation. Lincoln Stein's website is http://stein.cshl.org. The AcePerl package is only required if AceDB connectivity is desired.

SOAP::Lite module (only for Bioperl 1.0 and later)
The Biblio:: modules used for bibliographic queries and the XEMBLService module will make use of SOAP::Lite in future releases of bioperl.

File::Temp and File::Spec Modules
These modules will be already present if you are using a recent version of perl.

IO::Scalar
IO::Scalar (contained in the "IO-Stringy" CPAN perl module) is used only in the depreciated Bio::Tools::Blast::Run::Webblast.pm module

IO::String Modules
IO::String (contained in the "IO-String" CPAN perl module) is used in Bio::DB::WebDBSeqI

LWP:: Modules
In order to perform remote blast searches via a network the following modules are required - HTTP::Request::Common and LWP::UserAgent. These modules are both contained in the libwww-perl distribution. The only complication is that libwww-perl in turn also has some dependencies which must be present prior to installation:

XML Enabling Modules
The current bioperl-live CVS codebase and future releases of bioperl (after 0.6.2) will include significant XML related functionality. The following external CPAN modules are recommended and may be required for the use of some bioperl modules:

GD
- Used by the Bio::Graphics modules for drawing images only in bioperl 1.0 releases and later

Storable
- Recommended for all releases after bioperl-0.7.2. This module used for persistant object storage and local file caching.

Text::Shellwords
- Used only within the bioperl graphics package.

Bioperl XS extentions

The bioperl-ext package contains modules that include C code that is compiled and made available to perl via the XS mechanism. The current bioperl-ext-06 package contains the Bio::Tools::pSW and Bio::SearchDist modules. The pSW module adds protein Smith-Waterman comparison functionality to bioperl. SearchDist deals with EVD fitting of extreme value distributions. Users who do not need pSW or SearchDist functionality do not need the bioperl-ext package.

For your convenience

All of the various external packages mentioned here are available via FTP from our server. The URL is ftp://bioperl.org/pub/external/

BEWARE that the versions we have available for FTP may not be the most recent versions available. Users may just want to download directly from CPAN and other source sites to insure the most up to date code is used. You have been warned.

  Easy installation of perl modules with CPAN.pm and Bundle::Bioperl Newer versions of Perl ship with a highly functional CPAN.pm module as part of the default installation. This module can be an invaluable assistant when downloading, installing or upgrading installed CPAN modules. In particular CPAN.pm supports the concept of CPAN Bundles which are specialized files listing convenient module groups. The use of CPAN.pm makes downloading and installation of multiple independent CPAN packages an easy excercise.

There is a Bundle::BioPerl (README) module within CPAN that lists all the CPAN resident modules that BioPerl can make use of as (optional) dependencies. The bundle file can be used to simplify and automate the installation of our dependencies.

Before using Bundle::BioPerl users should be familiar with use and operation of the CPAN.pm module. Bundle::BioPerl WILL NOT install the Bioperl distribution -- only the external perl packages that Bioperl may be dependent on.

Installation of the XML related modules listed in the bundle will fail if the 'expat' package is not previously installed. This is not a problem with the bundle, merely a prerequisite of the XML modules. CPAN.pm can be used multiple times to install Bundle::BioPerl with no ill effects. Some users have reported that CPAN.pm will ocasionally attempt to upgrade their systems to the latest version of perl. This may not be a desired thing on a production system :) so be careful about blindly hitting the 'y' key when using CPAN.pm.

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Last Modified: $Date: 2002/07/15 22:30:26 $

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