[Bioperl-l] Next-gen modules
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.
> 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.
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.
More information about the Bioperl-l