[Bioperl-l] help test Bundle::BioPerl

Chris Dagdigian dag@sonsorol.org
Fri, 15 Dec 2000 14:54:04 -0500 (EST)

Hi folks,

BioPerl::Bundle 1.0 is not in CPAN yet but is available at

If you would like to help test the bundle all you need to do is download
and install the module locally. Then you can use CPAN.pm  to test it's


perl -MCPAN -e 'install Bundle::BioPerl'

The POD docs are appended below. Things get really messy when CPAN.pm
tries to install the XML modules without the presense of expat...

After the module has been uploaded to CPAN anyone will be able to run the
command 'install Bundle::BioPerl'....



    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 - recommended, used for safe/portable tempfile

    IO::Scalar - optional, used only in

    IO::String - recommended, used by Bio::DB:WebDBSeqI

    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 bioperl releases after 0.6.2

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

    XML::Writer - recommended for bioperl releases after 0.6.2

    XML::Node - recommended for bioperl releases after 0.6.2

    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.

    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/.

    The `install Bundle::BioPerl' process may need to be repeated
    several times to complete the full installation of all listed

    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 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 <dag@sonsorol.org> (Author only of this bundle,
    not any the modules it lists)