[Bioperl-l] BioDB.pm

[Hilmar Lapp]

Did the test script that you ran come with bioperl? Bio::DB::BioDB 
comes with bioperl-db, and is not needed for anything else. Also, 
bioperl-db is not included in the bioperl 1.4 distribution. If you want 
it, you do need to obtain from CVS at this point. Let me know if you 
have problems with that.

Also, if you do want to use bioperl-db I do recommend you obtain 
bioperl 1.4 from the CVS branch as well, or otherwise wait for the 1.5 
release. The 1.4.0 release has problems in the interpro and GO ontology 
parsers, and 1.4.1 was never released in anticipation of 1.5.

	-hilmar

On Jan 10, 2005, at 5:10 PM, Barry Moore wrote:

> I've just installed bioperl 1.4 (bioperl-core, bioperl-run and 
> bioperl-db) on a new system (Debian woody). I run a test script that 
> works fine on my old system and get an error that BioDB.pm can't be 
> found.  Sure enough BioDB.pm isn't on my new system, but it is on the 
> old (also bioperl 1.4 Debian woody).  I look in cvs and BioDB.pm is 
> there, but I look in the distribution downloaded from bioperl.org and 
> it seems to be missing BioDB.pm and several other files?  I can get 
> the files from cvs, but is this an error in the distribution file?
>
> Barry
>
> -- 
> Barry Moore
> Dept. of Human Genetics
> University of Utah
> Salt Lake City, UT
>
>
>
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-- 
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Hilmar Lapp                            email: lapp at gnf.org
GNF, San Diego, Ca. 92121              phone: +1-858-812-1757
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