[ensembl-dev] VEP 79 API problems

[Will McLaren]

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> 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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