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

[Nicolas Thierry-Mieg]

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_sapiens_refseq_vep_88_GRCh37.tar.gz
>     <ftp://ftp.ensembl.org/pub/release-88/variation/VEP/homo_sapiens_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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