[Bioperl-l] A new Bundle::BioPerl

Conrad Halling chhalling at verizon.net
Mon Nov 27 22:51:14 EST 2006


After experimenting with the existing Bundle::BioPerl version 2.1.8 
under Perl 5.8.8 and Mac OS X 10.4.8, I found that it could not install 
all of the BioPerl dependencies unless run multiple times.

I edited the the order that the dependencies were listed so I could get 
all the dependencies to install on the first try.

Then I got carried away and ran some grep commands on the bioperl-live 
source code to identify all of the dependencies that are use'd or 
require'd, and I added these dependencies to the Bundle::BioPerl 
package. Many of these dependencies are core Perl modules, which it 
doesn't hurt to update.

After a few rounds of testing during Thanksgiving weekend festivities, I 
have completed a new Bundle::BioPerl package that installs virtually all 
of the dependencies on the first try.

There are two modules that won't install. The first is 
Bio::ASN1::EntrezGene, and the second is CORBA::ORBit. 
Bio::ASN1::EntrezGene won't install because it is dependent on 
Bio::Index::AbstractSeq, which is part of BioPerl. CORBA::ORBit won't 
install because its tarball appears to be corrupted. The cpan utility 
also reports that Math::Trig and Text::Balanced didn't install, but this 
is an error, because they are installed correctly.

The cpan commands for installing the BioPerl dependencies, 
Bio::ASN1::EntrezGene, and BioPerl 1.5.2 RC5, will become:

 cpan> install Bundle::BioPerl
 cpan> force install Bio::ASN1::EntrezGene
 cpan> install S/SE/SENDU/bioperl-1.5.2_005-RCb.tar.gz

I have filed a Bugzilla bug report (bug #2153) and attached my 
Bundle::BioPerl package (attachment #508) to it for consideration.

-- 
Conrad Halling
chhalling at verizon.net



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