[Bioperl-l] Cleanup of BioPerl distribution website

Chris Fields cjfields at uiuc.edu
Sun Sep 17 13:56:54 UTC 2006

On Sep 17, 2006, at 5:09 AM, Nathan S. Haigh wrote:
> I don't have any immediate problems about the changes either. I've  
> seen
> a few posts recently about installing Bioperl on Windows - how soon  
> will
> 1.5.2 been released? It's not too difficult to generate a new ppd file
> etc so I could make a barebones ppd for 1.5.1?
> I know when I made the ppd file for 1.5 I included a lot of prereqs to
> ensure that most of bioperl would work without the need to manually
> install the modules later once the user found out that something  
> didn't
> work. Personally, despite the need to download and install a lot more
> packages in one sitting, I thought this was important since Windows
> users that install bioperl are probably (or more likely) not from a
> programming background (no offence intended if your a whiz programmer
> working in Windows! :o) ). Therefore, their first experience of  
> bioperl
> would get off to a better start if everything worked out of the hat
> after its installation, despite having a longer/bigger install.  
> What do
> you think?

I'm not sure how the new GUI version of PPM (PPM4) affects  
installation.  If we keep the prereqs in we might want to remove the  
version requirements; a previous poster stated that when they  
attempted installation of Bioperl 1.4 it wanted to downgrade the  
dependencies, likely to the versions listed in the ppd.  I have never  
seen it do that before, so it could be something to do with the new  
PPM version.


> What is the state of play with regards to tracking dependencies? I've
> just noticed that Makefile.PL has a lot more packages in %packages, is
> this a complete list of prereqs? If so, could they be added to  
> in the WriteMakefile sub in order to make it easier for generating  
> a ppd
> with a complete prereqs list?
> Nath

Many of those are included with current versions of ActivePerl, like  
XML::Simple, libwww-perl, etc.  We are also planning on having a  
minimal requirement of perl 5.6.1 (Features parsing requires  
recursive regexes, which aren't found before 5.6.1).  All the tests  
pass so far with ActivePerl.  I haven't tried anything with CygWin,  

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

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