[Bioperl-l] Next-gen modules

Chris Fields cjfields at illinois.edu
Wed Jun 17 15:05:03 EDT 2009

On Jun 17, 2009, at 12:49 PM, Elia Stupka wrote:

> I would suggest developing the "standard" version first, then moving  
> onto potential optimizations.

Yes, agreed.

> When we went through a similar argument in Ensembl about 8 years ago  
> we ended up dropping Bio::Root completely...

They (strangely enough) still use it in a few modules and require  
bioperl 1.2.3, but (in my experience) the latest bioperl works just  
fine.  I asked about that and never got a response.

> If one is truly after performance for these large next-gen projects,  
> it'd be down to pure piping, shell, and worrying about location and  
> copying of files, sticking to systems-level as much as possible, and  
> quite far from Bioperl altogether, so I think it's a whole different  
> level of optimization issues, probably outside the scope of Bioperl.
> Elia

In the end I don't think we can run it using perl alone, no, and I  
believe using BioPerl by itself will not be the optimal solution, but  
it can probably interface with something that is.


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