[ensembl-dev] question about VEP cache for human-refseq

[Will McLaren]

Hi Pablo,

There's an issue with the setup and install of the RefSeq cache which is
being fixed for version 75.

Both cache files have the directory structure homo_sapiens/74, which means
the second one attempts to overwrite the first.

To get around this, you should install each separately in a different
directory - use --CACHE_DIR with INSTALL.pl to change the directory. You
then have to point VEP to this directory when you run it with --dir (or
--cache_dir if you have plugins in use).

As I said, this shouldn't be an issue for 75 when it rolls out.

Regards

Will


On 25 February 2014 01:21, pmg <pablo.marin at uv.es> wrote:

> Hello Will and Co.
>
> When installing VEP with cache I have a list of cache files. I have chosen
> 26 and 27 (assuming that there are two sets of cache. One for refseq
> transcripts and another for ensembl transcripts), but when installing VEP,
>  cache number 27 overwrites 26:
>
> -------------
> list of caches for installing:
>
> 26 : homo_sapiens_refseq_vep_74.tar.gz
> 27 : homo_sapiens_vep_74.tar.gz
>
> ? 26 27
>
>  - downloading
> ftp://ftp.ensembl.org/pub/release-74/variation/VEP/homo_sapiens_refseq_vep_74.tar.gz
> ** GET
> ftp://ftp.ensembl.org:21/pub/release-74/variation/VEP/homo_sapiens_refseq_vep_74.tar.gz==> 200 OK (220s)
>  - unpacking homo_sapiens_refseq_vep_74.tar.gz
>
> WARNING: It looks like you already have the cache for homo_sapiens (v74)
> installed.
> If you continue the existing cache will be overwritten.
> Are you sure you want to continue (y/n)?
> -----------
>
> Are both cache really the same? are they mutually exclusive having both
> the same key? or any of them contains the information for both ensembl and
> refseq transcripts?
>
> Pablo
>
>
>
>
> =============================================================
> Pablo Marin-Garcia, PhD
> UNIDAD DE GENOTIPADO Y DIAGNOSTICO GENETICO
> FUNDACIÓN INVESTIGACIÓN CLÍNICO DE VALENCIA-INCLIVA
> Avda. Menéndez Pelayo 4 accesorio
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>
> TELF. 96 197 35 19
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> e-mail: pablo.marin at uv.es
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> http://pablomarin-garcia.blogspot.com.es
>
>
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