[Bioperl-l] dependencies in Makefile.PL

Chris Fields cjfields at uiuc.edu
Tue Sep 26 14:52:42 UTC 2006

Just to note, there are several Bundle-* packages available via PPM;
Bundle-Test, Bundle-WikiConverter, and others.  It is entirely possible to
create a Bundle-Bioperl PPM if the packages are all available as a PPM on
one repository or another.  And, I can personally attest, every one is
either available or can be made into a PPM.  

We should keep Bundle::Bioperl, at least for now.  Using Bundle::Bioperl
enables you to split modules into 'required' prereqs vs. 'optional' ones.
The Bundle::Bioperl description in CPAN seems to indicate this:


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...

So, it's basically a convenient way to get full Bioperl functionality.

The missing WinXP PPMs not present on any repository that can be made into a
PPM are:

Bio::ASN1::EntrezGene (needed for Bio::SeqIO::entrezgene)
Class::AutoClass (which may be removed at some point)

There may be a few more, but I think those two are it.  They both work based
on 'nmake test'.

GD::SVG is available on the bioperl repository.  A few more
Bioperl::Bundle-related PPM's, like Text::ShellWords, can be found here
(note that a newer Bioperl core PPM is also here):


We could also make PPM distributions for bioperl-run, bioperl-db,
bioperl-network, etc, if requested.  I wouldn't attempt bioperl-ext,

Christopher Fields
Postdoctoral Researcher - Switzer Lab
Dept. of Biochemistry
University of Illinois Urbana-Champaign 

> -----Original Message-----
> From: bioperl-l-bounces at lists.open-bio.org [mailto:bioperl-l-
> bounces at lists.open-bio.org] On Behalf Of Sendu Bala
> Sent: Tuesday, September 26, 2006 3:38 AM
> To: bioperl-l
> Subject: Re: [Bioperl-l] dependencies in Makefile.PL
> Nathan S. Haigh wrote:
> > Under Windows, the dependencies could be included in Bioperls PPD
> > directly, or have them in Bundle::BioPerl PPD, and have Bioperl depend
> > on Bundle::BioPerl - either is straight forward to do. Which to do, I
> > suppose, depends on whether there are any benefits to maintaining a
> > separate Bundle::BioPerl or not. If there is a benefit to keeping
> > Bundle::BioPerl, then the only decision would be if any dependencies
> > should definitely be with Bioperl rather than Bundle::BioPerl. Otherwise
> > Bundle::BioPerl would become obsolete.
> If (after your changes to PPDs, Makefile.PL et al.) you can easily get
> to a complete working install without Bundle::BioPerl on all platforms,
> then I don't see any benefit to having it. It needs to hang around
> unchanged for people who want to install 1.4, however.
> (Or if there's a reason to stay with Bundle::BioPerl, we'll need
> multiple versions of it for different Bioperl releases - ugh.)
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