[ensembl-dev] variation effect pipeline module bug?

[Graham Ritchie]

Hi Sharon,

Yes, we actually have that exact fix in the current version of our code! It must not have made it into the release 65 branch somehow, sorry about that. Let us know if you find any other issues running the pipeline.

Cheers,

Graham


On 7 Feb 2012, at 17:16, Sharon Wei wrote:

> Hi Ensembl Variation Developers,
> 
> I think the following code in BaseVariationProcess needs an eval to catch the exceptions. Otherwise the pipeline will quit before gets its chance to load the reg_file.
> This is ensembl-variation branch-ensembl-65 code base.
> 
> [weix at blade170 Pipeline]$ cvs diff BaseVariationProcess.pm
> Index: BaseVariationProcess.pm
> ===================================================================
> RCS file: /cvsroot/ensembl/ensembl-variation/modules/Bio/EnsEMBL/Variation/Pipeline/BaseVariationProcess.pm,v
> retrieving revision 1.4
> diff -r1.4 BaseVariationProcess.pm
> 
> 80c80,82
> <     my $dba = Bio::EnsEMBL::Registry->get_DBAdaptor($species, $group);
> ---
> >     my $dba;
> >
> >     eval{$dba = Bio::EnsEMBL::Registry->get_DBAdaptor($species, $group)};
> 
> Sharon
> 
> _______________________________________________
> Dev mailing list    Dev at ensembl.org
> List admin (including subscribe/unsubscribe): http://lists.ensembl.org/mailman/listinfo/dev
> Ensembl Blog: http://www.ensembl.info/