[ensembl-dev] VEP regulatory cache

[cj5 at sanger.ac.uk]

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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