[Bioperl-l] Re: Installing Bioperl on Windows 98 [AND] Cygwin vs ActiveState Perl Programs

[Elizabeth Bowen]

> Message: 6
> From: "Jurgen Pletinckx" <jurgen.pletinckx@algonomics.com>
> To: <bioperl-l@bioperl.org>
> Subject: RE: [Bioperl-l] Installing Bioperl on Windows 98
> Date: Tue, 18 Dec 2001 11:39:08 +0100
> 
> Oh dear. 
> 
> It seems that, by following my advice on the windows-bioperl
> page, you found "XML-LibXML" (latest is 
> http://www.cpan.org/modules/by-module/XML/XML-LibXML-1.31.tar.gz),
> 
> rather than "libxml-perl" (latest is still 
> http://www.cpan.org/modules/by-module/XML/libxml-perl-0.07.tar.gz)
> 
> The former uses the C library libxml2, which is why you get the 
> error. Mind you, even if you do get it to work (and it seems Active-
> State hasn't ported that particular module collection for Windows),
> it won't be any use to get bioperl up and running, as bioperl needs
> one or more of the modules inside libxml-perl.
> 
> On the bright side, libxml-perl is still available, and can now 
> apparently be installed through PPM. That leaves XML::Node as the
> only module to be installed 'by hand'. And bioperl itself, of course.


Yes, that was the problem.  I'm afraid that when I looked up LibXML on CPAN, I found the XML::LibXML module first instead of the LibXML-Perl module.  So it wasn't your fault on the windows-bioperl page, but instead, my over-eagerness to get Bioperl up and running.

Thank you very much for your help, and thank you as well to everyone else for their advice.


> Two non-bioperl questions of my own:
> * search.cpan.org doesn't report libxml-perl when querying for 'libxml'
> or 'libxml-perl'. The FAQ for s.c.o mentions that it "only indexes 
> distributions that unpack to a single top-level directory, i.e. a 
> distribution that unpacks into its own directory instead of dumping 
> into the current working directory."
> Can that be the reason here, or should I notify the maintainers?
> 
> * The existence of the following file
> http://www.activestate.com/PPMPackages/5.6plus/XML-Node.ppd
> hints that XML-Node ought to be installable through PPM. Anyone have
> a guess why it isn't (at least for me)?
> 
> -- 
> Jurgen Pletinckx
> AlgoNomics NV 


I also have my own non-bioperl question.  While I was waiting for the next Bioperl Digest to come out to solve my LibXML/libxml-perl dilemma, I went ahead and downloaded Cygwin (a Unix environment for Windows that happens to contain Perl) from http://sources.redhat.com/cygwin/.  I was then able to install the bioperl external CPAN modules as well as bioperl itself rather easily.  (The CPAN.pm module in Cygwin makes life so much easier, rather than having to install manually if it is not available with ppm as with ActiveState Perl.)

I was just wondering, since most BioPerl people tend to use ActiveState, if there were any issues between using either Cygwin or ActiveState for BioPerl which makes one more advantageous than the other, or is it just a matter of choice?

Thanks again!
Elizabeth Bowen

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