[ensembl-dev] VEP 89 gets files and caches for 88

[Will McLaren]

Thanks for spotting that link - will get it updated.

Regarding the test failures, it looks like the tests are picking up an
out-of-date version of the ensembl-variation API - do you have this
installed somewhere else and added to your PERL5LIB? If so you may want to
update it (and any other API modules) to release/89. VEP *should* use the
modules downloaded by INSTALL.pl to the ensembl-vep directory, but it looks
like the test run is not picking these up.

Will

On 1 June 2017 at 15:47, Nicolas Thierry-Mieg <
Nicolas.Thierry-Mieg at univ-grenoble-alpes.fr> wrote:

> oups! I had missed that.
>
> You might want to update the "Download latest version" (under "Standalone
> perl script") on this page then:
> http://www.ensembl.org/info/docs/tools/vep/index.html
>
>
> Unfortunately the latest version obtained with git clone fails to INSTALL
> for me. It ends with:
> Result: FAIL
> Failed 25/38 test programs. 26/800 subtests failed.
>
>
> Looking at the stderr output, it seems many of the failures are due to:
>
> #     Error:  "trim_sequences" is not exported by the
> Bio::EnsEMBL::Variation::Utils::Sequence module
>
>
> Any ideas?
> Thanks
>
>
>
> On 06/01/2017 04:16 PM, Will McLaren wrote:
>
>> Hi Nicolas,
>>
>> The version of VEP in ensembl-tools is no longer supported and will be
>> phased out soon.
>>
>> Please switch to using the ensembl-vep repository instead.
>>
>> http://www.ensembl.org/info/docs/tools/vep/script/index.html
>>
>> Regards
>>
>> Will McLaren
>> Ensembl Variation
>>
>> On 1 June 2017 at 15:10, Nicolas Thierry-Mieg
>> <Nicolas.Thierry-Mieg at univ-grenoble-alpes.fr
>> <mailto:Nicolas.Thierry-Mieg at univ-grenoble-alpes.fr>> wrote:
>>
>>     Hi,
>>
>>     I just installed the latest VEP from ensembl-tools-release-89.zip ,
>>     perl INSTALL claims it "is configured to install v88 of the Ensembl
>>     API for use by the VEP" [NOTE: v88 not v89]. It then grabs a lot of
>>     stuff that has 88 in it's name or path, and when I install the human
>>     refseq cache it gets:
>>      - downloading
>>     ftp://ftp.ensembl.org/pub/release-88/variation/VEP/homo_sapi
>> ens_refseq_vep_88_GRCh37.tar.gz
>>     <ftp://ftp.ensembl.org/pub/release-88/variation/VEP/homo_sap
>> iens_refseq_vep_88_GRCh37.tar.gz>
>>
>>
>>     I guess someone forgot to increment something somewhere ;-)
>>
>>     Regards,
>>     Nicolas
>>
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> --
> -----------------------------------------------------------
> Nicolas Thierry-Mieg
> Laboratoire TIMC-IMAG/BCM, CNRS UMR 5525
> Pavillon Taillefer, Faculte de Medecine
> 38700 La Tronche, France
> tel: (+33)456.520.067, fax: (+33)456.520.055
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