[ensembl-dev] BioPerl version

[Fields, Christopher J]

I think Ensembl still insists on BioPerl 1.2.3.  AFAIK there are only a few conflicts causing this, namely BLAST-related modules.

We're (meaning BioPerl) have started work on modularizing the code base; I think this will make some of these issues easier to fix (namely, moving code out into specific self-contained repositories for better maintenance).  This includes everything down to Bio::Root.  If there are specific conflicts, we could feasibly package the right light-weight combination of modules for Ensembl more readily so you get the latest code, but we'll need input from the Ensembl folks on what areas to focus on for such an endeavor.  We already have our hands full with tweezing out the dependency graph as it is.

chris

On May 10, 2013, at 9:44 AM, "Youens-Clark, Ken" <kclark at cshl.edu>
 wrote:

> I have the v70 Ensembl BLAST code installed on a machine.  BioPerl 1.2.3 is linked in as the "bioperl-live" directory, but 1.6.9 is also installed into the standard Perl library.  I believe this is causing conflicts.  Which is the recommended version?
> 
> --
> Ken Youens-Clark
> kclark at cshl.edu
> Ware Lab/CSHL/USDA-ARS
> 
> 
> 
> 
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