[ensembl-dev] VEP regulatory cache

[cj5 at sanger.ac.uk]

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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