[Bioperl-l] Modern BioPerl vs. Ensembl

[Chris Fields]

On Aug 24, 2009, at 7:12 PM, George Hartzell wrote:

>
> There's a warning at Ensembl about the perl api code depending on an
> old version of bioperl (1.2.3)
>
>  http://www.ensembl.org/info/docs/webcode/install/ensembl-code.html
>
> Does anyone have current information about that dependency?
>
> My quick-n-dirty tests suggest that one can't build an app that uses
> both new Bioperl and the ensembl api without ensembl picking up the
> newer bioperl libraries (or your app getting the older ones).  It's
> not clear what parts of the ensembl world depend on the older BioPerl.

I've asked this question several times of the ensembl folk w/o an  
adequate response.  My general feeling is even they may not really  
know for sure (though I recall ewan saying something about feature/ 
annotation changes around then, and maybe something about the  
blastreporter).

Saying that, the ensembl perl API worked for me using bioperl-live  
(and bioperl 1.6) as of a couple months ago.  You might eventually run  
into some issues; if so report them back here and to the ensembl list.

> Anyone have any recipes to make it work?
>
> Any info on a possible modernization of the ensembl code?

That is completely up to the ensembl folks.  bioperl 1.2.3 is full  
enough of bugs, and I don't plan on backporting any changes to that  
branch (seems kind of silly, as that branch is now about six yrs old).

> Thanks,
>
> g.


np!

-chris