[Bioperl-l] bioperl 1.6. and Perl API

[Fields, Christopher J]

The below error is from the Ensembl code, not from bioperl (they're two separate things).  You need to install the Ensembl Perl API.

Re:bioperl versions, there is an explanation out there somewhere lurking in the Ensembl mail lists, I can't recall the details, but from what I understand more recent bioperl versions work unless you intend using the code for setting up Ensembl locally and processing your own data.  Otherwise if you are just accessing the ensembl database it should just work.

chris

On May 8, 2012, at 3:30 PM, Hermann Norpois wrote:

> Hello,
> 
> I installed bioperl 1.6.901-1 on ubuntu. Is it compatible with Perl API?
> Ensembl seems to prefer an older version:
> http://www.ensembl.org/info/docs/api/api_installation.html. I downloaded
> the four API packages and put them in /usr/share/perl5 (location of the
> already installes bio-perl-modules).
> If I start my testscript I get:
> 
> Can't locate Bio/EnsEMBL/Registry.pm in @INC (@INC contains: /etc/perl
> /usr/local/lib/perl/5.12.4 /usr/local/share/perl/5.12.4 /usr/lib/perl5
> /usr/share/perl5 /usr/lib/perl/5.12 /usr/share/perl/5.12
> /usr/local/lib/site_perl .)
> 
> 
> But @INV contains:
> /etc/perl
> /usr/local/lib/perl/5.12.4
> /usr/local/share/perl/5.12.4
> /usr/lib/perl5
> /usr/share/perl5
> /usr/lib/perl/5.12
> /usr/share/perl/5.12
> /usr/local/lib/site_perl
> 
> So principally the module should be found.
> 
> Thanks
> Hermann Norpois
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