Re: Error in gmod_bulk_load_gff3.pl

Hi Richard,

That is a bioperl problem.  I haven't tried the official 1.6 release
with chado, but it was working from cvs not that long ago.  I'll do
some testing with the official release and get back to you.

Scott

On Tue, Feb 10, 2009 at 8:08 AM, Richard Smith <richard <at> flymine.org> wrote:
> Hi all,
> I am trying to load some gff files into a new chado database using
> gmod_bulk_load_gff3.pl and have got an error.
>
> I downloaded gmod-1.0 and followed the INSTALL.Chado instructions - this
> was a clean install on mac OS X Leopard, I installed the latest versions
> of all required perl modules from CPAN.
>
> Setting up the chado database and loading up the sequence ontology, etc
> was fine.  Running:
>
> ~/gmod-1.0/load/bin/gmod_bulk_load_gff3.pl --organism dicty --gfffile
> chromosome_1.gff.sorted --noexon
>
> Produced the error:
>
> Can't locate object method "value" via package "Bio::Annotation::Target"
> at /Users/rns/gmod-1.0/load/bin/gmod_bulk_load_gff3.pl line 808, <GEN0>
> line 11.
>
>
> Is this due to the version of BioPerl I installed?  It looks like there
> is no value method on Bio::Annotation::Target.  I got the latest BioPerl
> by installing CJFIELDS/BioPerl-1.6.0.tar.gz with CPAN, the GMOD
> INSTALL.Chado docs said any version greater than 1.5.2.
>
> Do you think I should I install an older version of BioPerl or try GMOD
> scripts from cvs?
>
>
> Thanks,
> Richard.
>
> ------------------------------------------------------------------------------
> Create and Deploy Rich Internet Apps outside the browser with Adobe(R)AIR(TM)
> software. With Adobe AIR, Ajax developers can use existing skills and code to
> build responsive, highly engaging applications that combine the power of local
> resources and data with the reach of the web. Download the Adobe AIR SDK and
> Ajax docs to start building applications today-http://p.sf.net/sfu/adobe-com
> _______________________________________________
> Gmod-schema mailing list
> Gmod-schema <at> lists.sourceforge.net
> https://lists.sourceforge.net/lists/listinfo/gmod-schema
>

--

-- 
------------------------------------------------------------------------
Scott Cain, Ph. D.                                   scott at scottcain dot net
GMOD Coordinator (http://gmod.org/)                     216-392-3087
Ontario Institute for Cancer Research

------------------------------------------------------------------------------
Create and Deploy Rich Internet Apps outside the browser with Adobe(R)AIR(TM)
software. With Adobe AIR, Ajax developers can use existing skills and code to
build responsive, highly engaging applications that combine the power of local
resources and data with the reach of the web. Download the Adobe AIR SDK and
Ajax docs to start building applications today-http://p.sf.net/sfu/adobe-com