[Bioperl-l] problem with Bio::Tools::EMBOSS

[Chris Fields]

On Mar 3, 2008, at 1:34 PM, Dave Messina wrote:

> Hi Anjan,
>
> Bio::Factory::EMBOSS is not part of the BioPerl core distribution, but
> rather part of bioperl-run. For some reason CPAN went for the old  
> (1.4)
> version of bioperl-run rather than the current 1.5.2.
>
> And indeed, I seem to run into the same problem:
> cpan> d /bioperl/
>
> Distribution    BIRNEY/bioperl-1.2.1.tar.gz
> Distribution    BIRNEY/bioperl-1.2.2.tar.gz
> Distribution    BIRNEY/bioperl-1.2.3.tar.gz
> Distribution    BIRNEY/bioperl-1.2.tar.gz
> Distribution    BIRNEY/bioperl-1.4.tar.gz
> Distribution    BIRNEY/bioperl-db-0.1.tar.gz
> Distribution    BIRNEY/bioperl-ext-1.4.tar.gz
> Distribution    BIRNEY/bioperl-gui-0.7.tar.gz
> Distribution    BIRNEY/bioperl-run-1.2.2.tar.gz
> Distribution    BIRNEY/bioperl-run-1.4.tar.gz
> Distribution    BOZO/Fry-Lib-BioPerl-0.15.tar.gz
> Distribution    CRAFFI/Bundle-BioPerl-2.1.8.tar.gz
> 12 items found
>
> but when I ask in a different way the right distributions show up.  
> [Sendu,
> any idea what's going on here?]

It's marked as a developer release, which I think requires a full path  
(as you have below) and not just the package name.

chris

> cpan> ls
> SENDU
> 5919092 2007-02-14 SENDU/bioperl-1.5.2_102.tar.gz
>  320154 2006-12-06 SENDU/bioperl-db-1.5.2_100.tar.gz
>   99082 2006-12-06 SENDU/bioperl-network-1.5.2_100.tar.gz
>  942093 2006-12-06 SENDU/bioperl-run-1.5.2_100.tar.gz
>
> So try doing
>
> cpan> install SENDU/bioperl-run-1.5.2_100.tar.gz
>
> Or if CPAN refuses to cooperate, you can grab it from here:
> http://www.bioperl.org/wiki/Getting_BioPerl#Bioperl_1.5.2.2C_Developer_Release
>
>
> Dave