[Bioperl-l] About Bioperl - patch - installation Windows

djibrilo djibrilo at yahoo.fr
Fri Oct 30 09:00:32 EDT 2009


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 compilation.

The problem now is about ppm.

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="Bio-ASN1-EntrezGene" VERSION="1.09">
<SOFTPKG NAME="Class-AutoClass" VERSION="1.01">
<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" DATE="2006-12-6">
<SOFTPKG NAME="bioperl-network" VERSION="1.5.2_100" DATE="2006-12-6">
<SOFTPKG NAME="Bundle-BioPerl-Network" VERSION="1.5.2_100" DATE="2006-12-6">
<SOFTPKG NAME="bioperl-run" VERSION="1.5.2_100" DATE="2006-12-6">
<SOFTPKG NAME="Bundle-BioPerl-Run" VERSION="1.5.2_100" DATE="2006-12-6">
<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 have seen another BioPerl repository ( http://bioperl.org/DIST/RC) and there are the same problems.


<SOFTPKG NAME="BioPerl-Run" VERSION="1,006000_001,0,0">

    <ABSTRACT>BioPerl-Run - wrapper toolkit</ABSTRACT>
    <AUTHOR>BioPerl Team &lt;bioperl-l at bioperl.org&gt;</AUTHOR>
        <DEPENDENCY NAME="Bio-Root-Version" VERSION="1,006001,0,0" />
        <CODEBASE HREF="PPM-BioPerl-Run-1.006000_001.tar.gz" />

<SOFTPKG NAME="BioPerl-DB" VERSION="1,006000_001,0,0">
    <ABSTRACT>BioPerl-DB - package for biological databases</ABSTRACT>
    <AUTHOR>BioPerl Team &lt;bioperl-l at bioperl.org&gt;</AUTHOR>
        <DEPENDENCY NAME="Bio-Root-Version" VERSION="1,006001,0,0" />
        <DEPENDENCY NAME="DBI" VERSION="0,0,0,0" />
        <CODEBASE HREF="PPM-BioPerl-DB-1.006000_001.tar.gz" />


<SOFTPKG NAME="BioPerl-Network" VERSION="1,006000_001,0,0">
    <ABSTRACT>BioPerl-Network - package for biological networks</ABSTRACT>
    <AUTHOR>BioPerl Team &lt;bioperl-l at bioperl.org&gt;</AUTHOR>
        <DEPENDENCY NAME="Bio-Root-Version" VERSION="1,006001,0,0" />
        <DEPENDENCY NAME="Graph" VERSION="0,86,0,0" />
        <CODEBASE HREF="PPM-BioPerl-Network-1.006000_001.tar.gz" />

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


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