[ensembl-dev] Condel Plugin

[Koul, Sunita]

Thanks –It is working now


From: dev-bounces at ensembl.org [mailto:dev-bounces at ensembl.org] On Behalf Of Will McLaren
Sent: Wednesday, June 20, 2012 10:34 AM
To: Ensembl developers list
Subject: Re: [ensembl-dev] Condel Plugin

Hi Sunita,

This Condel.pm file is not the plugin - it is part of the API. It will be removed in the next release of Ensembl as it has been deprecated.

The Condel.pm you should be using is the one from the GitHub repository:

https://github.com/ensembl-variation/VEP_plugins

There you will see the Condel.pm file and the config/ directory. If you clone the whole plugins repository you should get the files you need.

Cheers

Will McLaren
Ensembl Variation

On 20 June 2012 15:46, Koul, Sunita <sunita at pathology.wustl.edu<mailto:sunita at pathology.wustl.edu>> wrote:
Thanks Michael for the response.
Please bear with me as I am little confused about the config directory
Condel.pm is under
\Bio\ensembl-variation\modules\Bio\EnsEMBL\Variation\Utils directory.
I see a Config.pm file under that besides condel.pm<http://condel.pm>
There is no config directory as such.

Thanks
Sunita

From: Michael Yourshaw [mailto:myourshaw at ucla.edu<mailto:myourshaw at ucla.edu>]
Sent: Friday, June 15, 2012 5:38 PM
To: Koul, Sunita
Cc: Ensembl developers list
Subject: Re: [ensembl-dev] Condel Plugin

You need to specify some parameters for the Condel plugin

--plugin Condel,/path/to/VEP_plugins/config/Condel/config,b,2

ॐ

Michael Yourshaw
UCLA Geffen School of Medicine
Department of Human Genetics, Nelson Lab
695 Charles E Young Drive S
Gonda 5554

Los Angeles CA 90095-8348 USA

myourshaw at ucla.edu<mailto:myourshaw at ucla.edu>

970.691.8299<tel:970.691.8299>

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On Jun 15, 2012, at 15:04, Koul, Sunita wrote:

Hi
I am trying to run Condel using the variant effect predictor using the following command
perl variant_effect_predictor.pl<http://variant_effect_predictor.pl> -i input.vcf --plugin Condel

I get the error
Can't locate loadable object for module Win32 in @INC (@INC contains: E:\Perl\variant_effect_predictor\Bio\bioperl-1.2.3 E:\Perl\variant_effect_predictor\Bio\ensembl\modules E:\Perl\variant_effect_predictor\Bio\ensembl-compara\modules
E:\Perl\variant_effect_predictor\Bio\ensembl-variation\modules E:\Perl\variant_effect_predictor\Bio\ensembl-functgenomics\modules E:\Perl\variant_effect_predictor\Bio\ensembl-variation\modules\Bio\EnsEMBL\Variation\Utils ---

Any idea why this is happening(I am using Windows to run this tool)


Sunita


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