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

[Guillermo Marco Puche]

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 at sistemasgenomicos.com 
> <mailto:guillermo.marco at 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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