[ensembl-dev] VEP: Bug when using plugins from command line and config file

[Will McLaren]

Hi Guillermo,

If you pull release/88 you will by default get the latest sub-version
(88.9). You may check out specific sub-versions e.g. release/88.x; these
are tags on the git repo to aid reproducibility.

Will

On 24 May 2017 at 07:45, Guillermo Marco Puche <
guillermo.marco at sistemasgenomicos.com> wrote:

> Hi Will,
>
> Thank you for the quick fix. Should we wait for the changes in
> release/88.9 to be merged in release/88 or will they be merged in release
> 89? Or work with release 88.9?
>
> Regards,
>
> On 05/22/2017 04:21 PM, Will McLaren wrote:
>
> Hi Guillermo,
>
> Thanks for spotting this. The issue is fixed in ensembl-vep 88.9 (
> https://github.com/Ensembl/ensembl-vep/commit/
> 21069f158e4081ffc44d5389852a0e3da71fd7ff).
>
> Regards
>
> Will McLaren
> Ensembl Variation
>
> On 17 May 2017 at 07:45, Guillermo Marco Puche <guillermo.marco@
> sistemasgenomicos.com> wrote:
>
>> Dear devs,
>>
>> I've noticed a bug in latest VEP 88 version. If you activate more than
>> one plugin, one in the config file and other directly in command line all
>> the annotation fields produced by plugins are rendered empty. See the
>> example below (my.conf would be the config file containing a line
>> activating plugin):
>>
>> *vep -i input.vcf -o output.vcf -config my.conf -dir_plugins  dir_plugins -dir_cache .vep -plugin Test*
>>
>> I've managed to make this work "calling" all the plugins from command
>> line.
>>
>> Regards,
>> Guillermo
>>
>>
>>
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>
>
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