[ensembl-dev] Bulding cache for vep script

Will McLaren wm2 at ebi.ac.uk
Tue Nov 22 10:34:31 GMT 2011


Hi Duarte,

Looks like your script is having a problem disconnecting its DB
connections before it tries to dump the data out.

You might be able to fix this by skipping the step that caches the
adaptors - can you comment out line 560 in variant_effect_predictor.pl
such that it reads:

# &dump_adaptor_cache($config) if defined($config->{write_cache})

Let me know if this fixes the problem, since I can't replicate the
issue when using our code and servers.

NB: you don't need to specify -cache, -write_cache or -i when using -build

Cheers

Will McLaren
Ensembl Variation

On 21 November 2011 15:57, Duarte Molha <Duarte.Molha at ogt.co.uk> wrote:
> Dear Devs
>
>
>
> I want to build my own cach from my local version of the ensembl database...
> I used the command:
>
> variant_effect_predictor.pl -cache -dir
> /ReferenceData/ensembl_cache/our_cache --write_cache --build all  -i
> input.txt -host myHOST_SERVER  --password myPassword --user ensembl --port
> 3306
>
>
>
> but I get back this error message:
>
>
>
> Can't store CODE items at ../../lib/Storable.pm (autosplit into
> ../../lib/auto/Storable/_store_fd.al) line 304, at
> /array/dept/compbio/ensembl/current_api/ensembl-variation/modules/Bio/EnsEMBL/Variation/Utils/VEP.pm
> line 1978
>
>
>
> Can you tell me what might be wrong?
>
>
>
> Cheers
>
>
>
> Duarte Molha
>
>
>
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