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

Nicolas Thierry-Mieg Nicolas.Thierry-Mieg at univ-grenoble-alpes.fr
Thu Jun 1 16:36:59 BST 2017


Spot on, thanks! I indeed had a symlink in /usr/local/lib64/perl5/ 
pointing to my previous ensembl-tools-release-*/ stuff. Cleaning this up 
fixed my issue.
INSTALL then works flawlessly, it's downloading the caches as I type.



On 06/01/2017 04:53 PM, Will McLaren wrote:
> 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 out-of-date version of the ensembl-variation API - do you have this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
> <mailto: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
>     <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
>         <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>
>         <mailto: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>
>
>         <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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