[ensembl-dev] WARNNING FunMotifs Plugin

[Andrew Parton]

Hi Souhila,

Thanks for this report. This is a bug in the FunMotifs plugin caused when using a more recent perl version.

We’ve implemented a fix for release/100. You can access the plugin early from here: https://github.com/Ensembl/VEP_plugins/blob/release/100/FunMotifs.pm <https://github.com/Ensembl/VEP_plugins/blob/release/100/FunMotifs.pm>

Kind Regards,
Andrew

> On 6 Apr 2020, at 18:40, Souhila Amanzougarene <souhila.amanzougarene at cnrs.fr> wrote:
> 
> Hello,
> 
> I'm Souhila AMANZOUGARENE, a bioinformatician in the UMR 8199 from CNRS (France).
> I'm using VEP to annotate SNPs in human data and I use many plugins to do this. I have tried FunMotifs plugin, but it doesn't seem to work.
> 
> Here is the error warning:
> 
> WARNING: Failed to compile plugin FunMotifs: Experimental shift on scalar is now forbidden at /media/Data/Ensembl_hg19/EnsemblVepCache/Plugins/FunMotifs.pm line 106, near "$params if"
> 
> Compilation failed in require at (eval 79) line 2.
> 
> BEGIN failed--compilation aborted at (eval 79) line 2.
> 
> I have modified the line 106 code:
> 
> shift $params if ($params->[0] =~ /.gz/i); #Removes filename
> 
> by:
> 
> shift @{$params} if ($params->[0] =~ /.gz/i); #Removes filename
> 
> After this change, I do not get a warning but it doesn't annotate with the file funmotifs_sorted.bed.gz, and I have blank column for all SNPs.
> 
> Could you help me please to find a solution to this problem?
> 
> 
> Best regards
> 
> -- 
> Souhila Amanzougarene
> 
> Bio-Informaticienne
> 
> UMR CNRS 1283
> (Epi)génomique Fonctionnelle et Physiologie Moléculaire Du Diabète et Maladies Associées
> 
> FR3508 European Genomic Institute for Diabetes (E.G.I.D.)
> Faculté de médecine - Pôle Recherche
> 
> sous sol, Aile Ouest
> 1 place de Verdun
> 59045 LILLE CEDEX
> FRANCE
> souhila.amanzougarene at cnrs.fr
> 03 74 00 81 05
> 
> http://www.good.cnrs.fr/ - http://www.egid.fr/
> 
> 
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