[ensembl-dev] Vraint Effect Predictor

[Koul, Sunita]

I will look into this option. I was able to get the VEP code running after setting the Lib path to point to the Bio modules.
I am currently looking for ways  on how to get the Condel scores as an output just like the SIFT and Polyphen  for a given VCF file.
Any help in that direction will be helpful.
Thanks again
Sunita

From: dev-bounces at ensembl.org [mailto:dev-bounces at ensembl.org] On Behalf Of Fiona Cunningham
Sent: Friday, June 01, 2012 10:02 AM
To: Ensembl developers list
Subject: Re: [ensembl-dev] Vraint Effect Predictor

Dear Sunita,

We have also just released code for an Ensembl Virtual Machine which has all the code for the API and VEP already installed. Maybe this will be easier for you. For instructions see here:
http://www.ensembl.org/info/data/virtual_machine.html

and announcement here:
http://www.ensembl.info/blog/2012/05/10/ensembl-67-has-been-released/

Best wishes,

Fiona

-----------------------------------------------------------------------------------
Fiona Cunningham
Ensembl Coordinator, Ensembl Variation Project Leader.
EMBL-EBI, Genome Campus, Hinxton, UK
www.ensembl.org<http://www.ensembl.org> || www.lrg-sequence.org<http://www.lrg-sequence.org>
fiona at ebi.ac.uk<mailto:fiona at ebi.ac.uk>   || t: +44 1223 494612

On 1 June 2012 09:32, Will McLaren <wm2 at ebi.ac.uk<mailto:wm2 at ebi.ac.uk>> wrote:
Hello Sunita,

It looks like you are using a Windows machine; the VEP is not well tested on Windows and I'm not sure if the installer script will work.

You may still be able to get the VEP running by installing the Ensembl API manually; see here for details:

http://www.ensembl.org/info/docs/api/api_installation.html

You will need the ensembl, ensembl-variation and ensembl-functgenomics modules installed.

Hope this helps!

Cheers

Will
On 31 May 2012 17:17, Koul, Sunita <sunita at pathology.wustl.edu<mailto:sunita at pathology.wustl.edu>> wrote:
Hi,
I am trying to install the perl API for Variant Effect Predictor.
When I run the INSTALL.pl (as per instructions in  http://useast.ensembl.org/info/docs/variation/vep/vep_script.html#run_install)

I am getting the following error
Testing VEP script
ERROR: Testing VEP script failed with the following error
Can't locate Bio/EnsEMBL/Variation/Utils/Sequence.pm in @INC (@INC contains: E:/
Perl/variant_effect_predictor C:/Perl/site/lib C:/Perl/lib .) at variant_effect_
predictor.pl<http://predictor.pl> line 40.
BEGIN failed--compilation aborted at variant_effect_predictor.pl<http://variant_effect_predictor.pl> line 40.


Any idea why I am getting this error


Sunita


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