[ensembl-dev] installing perl api and its dependency on bioperl

Will Spooner whs at eaglegenomics.com
Thu Oct 28 18:10:39 BST 2010


Hi Chris,

I recall it having something to do with the Bio::SearchIO::_eventHandler and register_factory methods. I should really have a go at fixing it; I think that this will be easier on the Ensembl side than the BioPerl side. We would also like to see Ensembl use an up-to-date BioPerl.

Will


On 28 Oct 2010, at 17:34, Chris Fields wrote:

> Anyone know specifically what that dependency is?  I can start possibly looking at it from the BioPerl end.
> 
> chris
> 
> On Oct 28, 2010, at 11:07 AM, Will Spooner wrote:
> 
>> The latest bioperl version works fine with the Ensembl APIs. There is one remaining dependancy on BioPerl 1.2.3 in the Ensembl code, specifically the BlastView result parsing.
>> 
>> Will
>> 
>> On 28 Oct 2010, at 13:57, Andrea Edwards wrote:
>> 
>>> Hi
>>> 
>>> Just a quick question - on the installation instructions for ensembl perl api it says to install bioperl 1.2.3. Does it have to be that specific version of bioperl or anything later than that?
>>> 
>>> thanks
>>> 
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>> 
>> --
>> William Spooner
>> whs at eaglegenomics.com
>> http://www.eaglegenomics.com
>> 
>> 
>> 
>> 
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> 

--
William Spooner
whs at eaglegenomics.com
http://www.eaglegenomics.com







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