[Bioperl-l] PPM4 PPD + server configuration

Nathan S. Haigh n.haigh at sheffield.ac.uk
Tue Sep 26 21:16:50 UTC 2006

I've now have working packages for Bioperl 5.6.2-c, and Bundle::BioPerl
2.6.(if it's decided that we need it) and a few other modules
(Bio-ASN1-EntrezGene 1.09, Class-AutoClass 1.01, GD-SVG 0.28 and
SVG-Graph 0.01). Please comment on the Bioperl and Bundle::BioPerl
packages with respect to thoe modules I've included as being "core" to
Bioperl, and those I've put into Bundle::bioPerl - relevant PPD XML code
at the bottom. Once, I've had feedback I'll also update the PREREQ_PM in

During this time, I stumbled across a bug in PPM4:
http://bugs.activestate.com/show_bug.cgi?id=50728. In short, PPM4 tries
to get some of the dependencies that are actually in ActiveStates repo
from the repo that the package is being installed from. For example, if
You were to try and install Bioperl 1.5.2 from the bioperl repo
(http://bioperl.org/DIST/) it will also try to get some dependencies
from this repo (which aren't there) instead of ActiveStates repo. A
workaround is to set up a redirect in the servers httpd.conf file,
something like the following should work for the Bioperl server:

RedirectMatch /DIST/MSWin32-x86-multi-thread-5.8/(.*)

The bug has been fixed since I wrote the draft of this e-mail and will
be fixed in ActivePerl However, they tell me, this won't be
released for at least a few months. Therefore, we need to implement the
above workaround until then - a volunteer?


-- start package.xml code --
   <SOFTPKG NAME="bioperl" VERSION="1.5.2-c" DATE="2006-09-25">
   <PROVIDE NAME="bioperl::" VERSION="1.5.2"/>
   <ABSTRACT>Bioinformatics Toolkit</ABSTRACT>
   <AUTHOR>Bioperl Team (bioperl-l at bioperl.org)</AUTHOR>
     <ARCHITECTURE NAME="MSWin32-x86-multi-thread-5.8"/>
     <CODEBASE HREF="bioperl-1.5.2-ppm.tar.gz"/>
     <REQUIRE NAME="IO::String" VERSION=""/>
     <REQUIRE NAME="HTML::Entities" VERSION=""/>
     <REQUIRE NAME="DB_File::" VERSION=""/>
     <REQUIRE NAME="BerkeleyDB::" VERSION=""/>
     <REQUIRE NAME="Bundle::BioPerl" VERSION="2.1.6-c"/>

<SOFTPKG NAME="Bundle-BioPerl" VERSION="2.1.6-c" DATE="2006-09-25">
   <PROVIDE NAME="Bundle::BioPerl" VERSION="2.1.6-c"/>
   <ABSTRACT>A Bundle to install dependencies for Bioperl 1.5.2</ABSTRACT>
Chris Dagdigian (dag at sonsorol.org) (Author only of this bundle, not any
the modules it lists)
     <ARCHITECTURE NAME="MSWin32-x86-multi-thread-5.8"/>
     <CODEBASE HREF="Bundle-BioPerl-2.1.6-ppm.tar.gz"/>
     <REQUIRE NAME="Ace::" VERSION=""/>
     <REQUIRE NAME="Bio::ASN1::EntrezGene" VERSION=""/>
     <REQUIRE NAME="Class::AutoClass" VERSION="1.01"/>
     <REQUIRE NAME="Clone::" VERSION=""/>
     <REQUIRE NAME="Convert::Binary::C" VERSION=""/>
     <REQUIRE NAME="Data::Stag::Writer" VERSION=""/>
     <REQUIRE NAME="DBD::mysql" VERSION=""/>
     <REQUIRE NAME="GD::" VERSION="1.3"/>
     <REQUIRE NAME="Graph::Directed" VERSION=""/>
     <REQUIRE NAME="HTML::Parser" VERSION="3.0"/>
     <REQUIRE NAME="HTTP::Request::Common" VERSION=""/>
     <REQUIRE NAME="LWP::UserAgent" VERSION=""/>
     <REQUIRE NAME="Set::Scalar" VERSION=""/>
     <REQUIRE NAME="Spreadsheet::ParseExcel" VERSION=""/>
     <REQUIRE NAME="Storable::" VERSION=""/>
     <REQUIRE NAME="SVG::" VERSION="2.26"/>
     <REQUIRE NAME="SVG::Graph" VERSION="0.01"/>
     <REQUIRE NAME="Text::Shellwords" VERSION=""/>
     <REQUIRE NAME="XML::Parser::PerlSAX" VERSION=""/>
     <REQUIRE NAME="XML::SAX::Writer" VERSION=""/>
     <REQUIRE NAME="XML::Simple" VERSION=""/>
     <REQUIRE NAME="XML::Writer" VERSION=""/>
-- end package.xml code --

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