[ensembl-dev] VEP regulatory cache

[Will McLaren]

Hello,

The most crucial thing is the API, as this is where the majority of the
code resides.

The script itself basically just parses your command line flags and sets up
database connections etc.

If you have something tagged as 2.6 then chances are that it is 2.6 -
perhaps the download is pointing to the wrong place. Are you downloading
from the Download page of the documentation or from CVS?

Will


On 5 December 2012 11:37, <cj5 at sanger.ac.uk> wrote:

> Hi Will,
>
> Thanks, we are using version v2.4 because we want to remain with Ensembl
> 66 for now.
> I just downloaded v2.4 again and I note that has been modified from my
> original download, so I'll give it a try.
>
> I also noticed however that it is tagged as version 2.6 - I presume this
> is a typo?
>
> Thanks
> Chris
>
> > Hi Chris,
> >
> > I think that's a bug that's been patched on the 66 CVS branch; the
> version
> > of the library you are using has not been patched. I don't know who
> > monitors/updates these, but a CVS update should fix it.
> >
> > Is there any reason why you're not using the latest version of VEP (2.7,
> > Ensembl API 69)?
> >
> > Regards
> >
> > Will McLaren
> > Ensembl Variation
> >
> >
> > On 5 December 2012 09:12, <cj5 at sanger.ac.uk> wrote:
> >
> >> Hi
> >>
> >> I am running the VEP, version 2.4 with the following options:
> >> --regulatory
> >> --offline
> >> --sift b
> >> --polyphen b
> >> --condel b
> >> --gene
> >> --hgnc
> >> --format vcf
> >> --force_overwrite
> >> --cache
> >> --dir <dir to human cache>
> >>
> >> and the script crashes with:
> >>
> >> Can't call method "length" on unblessed reference
> >> at
> >>
> /software/vertres/lib/all/ensembl/66/ensembl-variation/modules/Bio/EnsEMBL/Variation/Utils/VEP.pm
> >> line 1919, <STDIN> line 2154.
> >>
> >> Removing the --offline option solves it, I guess the regulatory cache is
> >> incomplete?
> >>
> >> Thanks
> >> Chris
> >>
> >>
> >>
> >>
> >>
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>
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