[ensembl-dev] VEP 79 API problems

[Guillermo Marco Puche]

Hi Will,

I've been checking and I can't see any unintended whitespace or problem 
with tabulations.
I've no issues with old vep 75 script and API. I've updated the Bioperl 
lib in $PERL5LIB variable from 1.2.3 to 1.6.1 (I didn't see this change 
before sorry) however I'm still getting all those errors.

Here's a link where you can download the VCF I'm using as input: 
https://www.dropbox.com/sh/felwyoo5kl2mgty/AAC177Digqy-_mEmyk9WvmYba/input.vcf?dl=0

Thank you.

Best regards,
Guille.

On 03/06/15 17:30, Will McLaren wrote:
> Hi Guille,
>
> It looks to me like your input is not being parsed properly.
>
> Check the formatting of your input VCF; double check that it is valid 
> VCF, and that you haven't got any unintended whitespace on any of the 
> lines.
>
> If you still have an issue, can you send a line or two of the input 
> that recreates these issues?
>
> Thanks
>
> Will McLaren
> Ensembl Variation
>
>
> On 3 June 2015 at 16:16, Guillermo Marco Puche 
> <guillermo.marco at sistemasgenomicos.com 
> <mailto:guillermo.marco at sistemasgenomicos.com>> wrote:
>
>     Dear devs,
>
>     I'm trying ensembl 79 VEP.
>
>     This is my dummy input VCF: http://pastebin.com/kFKWH50q#
>
>     I've cloned and installed API from github as always (this step is
>     repeated for variaton, funcgen and compara):
>
>       * git clone --branch release/79
>         https://github.com/Ensembl/ensembl.git ensembl_79
>
>     PERL5LIB env variable is correctly pointing to the cloned API:
>
>       * echo $PERL5LIB
>         /share/apps/local/bioperl-live:/share/apps/src/ensembl_79/modules:/share/apps/src/ensembl_79-compara/modules:/share/apps/src/ensembl_79-variation/modules:/share/apps/src/ensembl_79-functgenomics/modules
>
>     However I'm getting a lot of errors I really don't understand. It
>     seems like a bug with API installation with me. If I change
>     $PERL5LIB variable to point to 75 API (previous version I was
>     using) I can't reproduce the errors VEP script works for this old
>     75 version.
>
>     I've been reading the docs again and I can't seen any additional
>     PERL library requirement.
>
>     Here's the error log: http://pastebin.com/VvQrkEQZ
>
>
>     Thank you!
>
>     Best regards,
>     Guille.
>
>
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