[Bioperl-l] About Bioperl - patch - installation Windows
cjfields at illinois.edu
Sat Oct 31 11:11:06 EDT 2009
On Oct 30, 2009, at 8:00 AM, djibrilo wrote:
> There are some problems about bioperl installation on Windows.
> I am using bioperl on Windows XP, Vista, ... and I use activeperl
> 5.8 and some times 5.10. for module installation
> , I use ppm on Windows system and sometimes I use cpan or build via
> The problem now is about ppm.
In general, I understand that mixing perl versions on Windows is NOT
recommended unless you know what you are doing. Not sure about
upgrading, but this is problematic through PPM for many reasons, first
being PPMs are missing (DB_File is a dummy PPM on ActivePerl) and
others are problematic (SOAP::Lite is apparently an issue).
> There are 2 repositories to install bioperl :
> 1- trouchelle, there are :
> - bioperl 1.4, 1.5.2_100
> - bioperl-db 0.01, 1.5.2_100
> - bioperl-run 1.2.2
> 2- BioPerl ( http://bioperl.org/DIST), there are :
> - BioPerl 1.6.1
> - bioperl-db 1.5.2_100
> - bioperl-network 1.5.2_100
> - bioperl-run 1.5.2_100
> - Bundle-BioPerl-Core 1.6.1
> I have seen the package.XML of BioPerl repository :
> <SOFTPKG NAME="GD-SVG" VERSION="0.25">
> <SOFTPKG NAME="SVG-Graph" VERSION="0.01">
> <SOFTPKG NAME="Bio-ASN1-EntrezGene" VERSION="1.09">
> <SOFTPKG NAME="Class-AutoClass" VERSION="1.01">
> <SOFTPKG NAME="Graph" VERSION="0.80">
> <SOFTPKG NAME="GraphViz" VERSION="2.04">
> <SOFTPKG NAME="bioperl-db" VERSION="1.5.2_100" DATE="2006-12-6">
> <SOFTPKG NAME="Bundle-BioPerl-Db" VERSION="1.5.2_100"
> <SOFTPKG NAME="bioperl-network" VERSION="1.5.2_100" DATE="2006-12-6">
> <SOFTPKG NAME="Bundle-BioPerl-Network" VERSION="1.5.2_100"
> <SOFTPKG NAME="bioperl-run" VERSION="1.5.2_100" DATE="2006-12-6">
> <SOFTPKG NAME="Bundle-BioPerl-Run" VERSION="1.5.2_100"
> <SOFTPKG NAME="BioPerl" VERSION="1.6.1" DATE="2009-9-29">
> <SOFTPKG NAME="Bundle-BioPerl-Core" VERSION="1.6.1" DATE="2009-9-29">
> The file have been updated at 10 October 2009 but some files are
> old. Then, it is impossible to many people using bioperl on Windows to
> update correctly bioperl. And, it is difficult to me to send you a
> patch about clustalw and primer3 modules because I can not install
> BioPerl-run-1.6.1 on my Windows PC.
I'll remove the older ones. Just to note, I haven't uploaded the
final CPAN releases and the PPMs for BioPerl-DB, BioPerl-Run, and
BioPerl-Network to the repo yet, for many various reasons (I haven't
had a chance to test them on Win being one of them).
To acknowledge something Robert said in another post, Perl is
generally configured to work best with UNIX'y flavors, but support for
a UNIX-like Perl on Windows is growing, particularly with Strawberry
> I have seen another BioPerl repository ( http://bioperl.org/DIST/RC)
> and there are the same problems.
Those are release candidates, and should be removed (they haven't been
tested yet). The package.xml In the meantime, you can try out code
very easily by setting your local PERL5LIB, or having a 'use lib'
directive (this also works for bioperl-live).
> Nevertheless there are PPM-BioPerl-Run-1.6.1_001.tar.gz, PPM-
> BioPerl-DB-1.6.0_001.tar.gz, PPM-BioPerl-Network-1.6.0_001.tar.gz
> Can you try to update all your ppd files on your repositories
> because it is a real problem
> to many lab and user wich try to updated bioperl and use it on
> Windows server.
> Best Regards,
> Djibril Ousmanou
We appreciate pointing these things out, I'll file them as a bug for
tracking. This is probably the best way to address problems in the
Also, realize this is a completely volunteer project. It takes an
inordinate amount of our (not so free) time to work on BioPerl and
related projects, so any help towards this end would be greatly
appreciated, including contributing back. Personally, I am a Linux/OS
X user and generally avoid anything Win-related (my preference) unless
needed. I believe a large number of users here fall in the same
category; we only have a couple of active Win users who have time to
work on portability issues.
I myself managed to get PPM and CPAN installation working by testing
via Remote Desktop and (soonish) VM, but that's hardly optimal and is
based on my schedule, which has been very busy as of late. To that
end, we would really appreciate anyone volunteering and dedicating
some time towards getting the Windows bits to work, otherwise Windows
support will always be determined on how much time we dedicate to it
(at the moment, that being very little).
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