[Bioperl-l] Modern BioPerl vs. Ensembl

[William Spooner]

On 25 Aug 2009, at 03:29, Chris Fields wrote:

> 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.

I'm not sure of the full list of dependencies, but my feeling is that  
most are related to the Ensembl application/web code; the blast  
interface in particular. I can support Chris's findings that the API  
works (AFAIK) with bioperl-live, but this is obviously untested.


>
>> 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).

It would be nice if someone at Ensembl could compile a list of BioPerl  
dependencies. At least that would give a feel for the scope of the  
problem...

Will