[ensembl-dev] Condel Plugin

[Will McLaren]

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> 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****
>
> There is no config directory as such.****
>
> ** **
>
> Thanks****
>
> Sunita****
>
> ** **
>
> *From:* Michael Yourshaw [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****
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> ** **
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>
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> ****
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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 -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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