[ensembl-dev] VEP plugin Conservation

[Will McLaren]

Hi Kirsley,

The only parameter you have to change for GRCh37 is the port, by adding
"--port 3337" to your VEP command. The plugin will only work when using
--cache (recommended) or --database; it will not work with --offline.

You also need the ensembl-compara API installed, which is not installed by
the VEP installer script.

https://github.com/Ensembl/ensembl-compara

http://www.ensembl.org/info/docs/api/api_installation.html

Will

On 13 August 2015 at 14:36, Kirsley Chennen <kchennen at unistra.fr> wrote:

> Hi Will,
>             Am still having the same issue with the latest version of the
> Convervation.pm plugin :
>
> 2015-08-13 15:31:17 - Failed to instantiate plugin Conservation: Failed to
> connect to compara database
>
>
> Do we have to the config for the database in the vep.ini file?
>
>     # reconnect to DB without species param
>     my $config = $self->{config};
>     $reg->load_registry_from_db(
>         -host       => $config->{host},
>         -user       => $config->{user},
>         -pass       => $config->{password},
>         -port       => $config->{port},
>         -db_version => $config->{db_version},
>         -no_cache   => $config->{no_slice_cache},
>     );
>
> If that's so, what are the parameters for the GRCh37 human assembly?
>
> Regards
> Kirsley
>
>
>
> On 13/08/2015 14:46, Will McLaren wrote:
>
> Hi Guillermo,
>
> Thanks for the report, I've pushed a fix to the plugin on GitHub.
>
> Regards
>
> Will
>
> On 13 August 2015 at 12:36, Guillermo Marco Puche <
> guillermo.marco at sistemasgenomicos.com> wrote:
>
>> Dear devs,
>>
>> I'm using latest version of VEP Conservation plugin available in github.
>> However it's not working for me:
>>
>> 2015-08-13 13:35:17 - Failed to instantiate plugin Conservation: Failed
>> to connect to compara database
>>
>> Is this a bug?
>>
>> Regards,
>> Guillermo.
>>
>>
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>
>
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