[ensembl-dev] Problem with VEP

[Ivan Smirnov]

Hi Daniel,

I used the links from the page
http://www.ensembl.org/info/docs/api/api_installation.html. They do
point to version 64, but actual tar.gz files are sent back for version
65. This issue was already pointed in October, but was never fixed.
Anyway, I am glad that at CVS installation works correctly.

Thanks
Ivan

On Fri, Nov 18, 2011 at 5:11 PM,  <sobral at ebi.ac.uk> wrote:
> You seem to have an incorrect instalation of the API.
> You probably installed from the HEAD code instead of the release branch.
> The HEAD code is already pointing to the future databases of release 65
> (out in early December).
>
> You need to install it as described here:
> http://www.ensembl.org/info/docs/api/api_cvs.html
>
> Hope this helps.
> Daniel
>
>
>> I have downloaded latest API and variant_effect_predictor.pl (v.2.2),
>> and when I try to run it I am getting errors:
>>
>> -------------------- WARNING ----------------------
>> MSG: homo_sapiens is not a valid species name (check DB and API version)
>> FILE: Bio/EnsEMBL/Registry.pm LINE: 1159
>> CALLED BY: ./variant_effect_predictor.pl  LINE: 462
>> Ensembl API version = 65
>> ---------------------------------------------------
>>
>> -------------------- WARNING ----------------------
>> MSG: homo_sapiens is not a valid species name (check DB and API version)
>> FILE: Bio/EnsEMBL/Registry.pm LINE: 1159
>> CALLED BY: Bio/EnsEMBL/Registry.pm  LINE: 953
>> Ensembl API version = 65
>> ---------------------------------------------------
>>
>> -------------------- EXCEPTION --------------------
>> MSG: Can not find internal name for species 'homo_sapiens'
>> STACK Bio::EnsEMBL::Registry::get_adaptor
>> /home/isadmin/arch/Perl/ensembl/modules/Bio/EnsEMBL/Registry.pm:955
>> STACK main::get_adaptors ./variant_effect_predictor.pl:707
>> STACK main::configure ./variant_effect_predictor.pl:559
>> STACK toplevel ./variant_effect_predictor.pl:61
>> Ensembl API version = 65
>> ---------------------------------------------------
>>
>>
>> Another strange thing is that when I was downloading API the link says
>> version 64, as in:
>> http://cvs.sanger.ac.uk/cgi-bin/viewvc.cgi/ensembl.tar.gz?root=ensembl&only_with_tag=branch-ensembl-64&view=tar
>> but from the error message it seems that the version is 65??
>>
>> Help!
>> Ivan
>>
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>>
>
>
>