[ensembl-dev] VEP cache files for barley (Hordeum vulgare)

[Fred Peng]

Hi Will

Thanks very much for your suggestion! It works!

However, it seems hard to load VEP_summary.html completely into a web
browser (I use Safari). I can only see VEP Run Stats and General Stats on
the web page, and no links can be clicked. Is this a browser issue? but I
will try another one (e.g. IE) when I have a chance. BTW, the HTML file is
~63 MB and should not be a problem.

Cheers
Fred Peng

On 19 November 2014 02:04, Will McLaren <wm2 at ebi.ac.uk> wrote:

> Hello,
>
> By default when using --cache the VEP checks in with the DB server at
> ensembldb.ensembl.org at the beginning of its run; barley is located on a
> different server, which you can have the VEP connect to using --genomes
> (see
> http://www.ensembl.org/info/docs/tools/vep/script/vep_options.html#opt_genomes
> )
>
> You can also bypass this connection completely by using --offline (with
> limitations, see
> http://www.ensembl.org/info/docs/tools/vep/script/vep_cache.html#limitations),
> though note in this case you must use the latin name for the species e.g.
> --species hordeum_vulgare
>
> In both the above cases you will also need to specify the e!Genomes cache
> version using --cache_version 24, since the e!Genomes version numbers
> differ from the main Ensembl version numbers (see
> http://www.ensembl.org/info/docs/tools/vep/script/vep_options.html#opt_cache_version
> )
>
> So, in summary, you can use either:
>
> perl variant_effect_predictor.pl --cache --cache_version 24 --species
> barley --genomes
>
> or
>
> perl variant_effect_predictor.pl --offline --cache_version 24 --species
> hordeum_vulgare
>
> Regards
>
> Will McLaren
> Ensembl Variation
>
> On 18 November 2014 21:37, Fred Peng <fredyfpeng at ualberta.ca> wrote:
>
>> Dear Developer,
>>
>> I am running VEP on barley (Hordeum vulgare L.) but could not make it
>> work, with a message like: Hordeum_vulgare is not a valid species name
>> (check DB and API version). I downloaded the cache file for barley
>> hordeum_vulgare_vep_24_082214v1.tar.gz and unpacked it into ~/.vep
>> directory. I run VEP with --cache option and specified --species
>> Hordeum_vulgare.
>>
>> Any help (especially regarding cache file prep, how to specify a species
>> -- common name or Latin name?) is appreciated.
>>
>> Cheers,
>> Fred Peng
>>
>>
>>
>> _______________________________________________
>> Dev mailing list    Dev at ensembl.org
>> Posting guidelines and subscribe/unsubscribe info:
>> http://lists.ensembl.org/mailman/listinfo/dev
>> Ensembl Blog: http://www.ensembl.info/
>>
>>
>
> _______________________________________________
> Dev mailing list    Dev at ensembl.org
> Posting guidelines and subscribe/unsubscribe info:
> http://lists.ensembl.org/mailman/listinfo/dev
> Ensembl Blog: http://www.ensembl.info/
>
>
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://mail.ensembl.org/pipermail/dev_ensembl.org/attachments/20141119/11e222bd/attachment.html>