[ensembl-dev] VEP regulatory cache

[Will McLaren]

Looks like there's some mangling of versions in our CVS.

However, you should be OK to continue using the script that you have - as I
have said it is important that API is up to date, not necessarily the
script.

Will


On 5 December 2012 12:08, <cj5 at sanger.ac.uk> wrote:

> Hi Will,
>
> I'm following the 'Download version 2.4' link here:
>
> http://www.ensembl.org/info/docs/variation/vep/vep_script.html#download
>
> The script is documented as v 2.6, amongst other changes from my original
> 2.4 script the --gene option has been removed.
>
> If you could instruct how to get from CVS instead that would be good.
>
> Thanks
> Chris
>
> > 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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>
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