[ensembl-dev] Ensembl release 82 is out!

Fri Oct 2 09:32:03 BST 2015

No, the script version should match the API/DB version - perhaps at some
point 80 is getting inserted instead of 82?

Will

On 2 October 2015 at 00:12, Ivan Adzhubey <iadzhubey at rics.bwh.harvard.edu>
wrote:

> Hi Will,
>
> Updating the API installation did help, no more noisy warning messages.
> Thanks
> you!
>
> One more question. After the upgrade, is this normal:
>
> $ variant_effect_predictor.pl
> #----------------------------------#
> # ENSEMBL VARIANT EFFECT PREDICTOR #
> #----------------------------------#
>
> version 80
> by Will McLaren (wm2 at ebi.ac.uk)
>
> Help: dev at ensembl.org , helpdesk at ensembl.org
> Twitter: @ensembl , @EnsemblWill
> <...>
>
> Note the script version which does not match the API/database one.
>
> Thanks,
> Ivan
>
> On Thursday, October 01, 2015 11:01:35 AM Will McLaren wrote:
> > Hi Ivan
> >
> > Thanks for the report. We have a data bug in the GRCh37 VEP cache that
> > means some protein domain descriptions are incomplete.
> >
> > I've added a fix to the VEP code to suppress the warning you are seeing
> > (re-run INSTALL.pl to pick it up); it may be that we are able to update
> the
> > cache at a later date with the missing data.
> >
> > Regards
> >
> > Will McLaren
> > Ensembl Variation
> >
> > On 30 September 2015 at 23:41, Ivan Adzhubey <
> iadzhubey at rics.bwh.harvard.edu
> > > wrote:
> > >
> > > Hi,
> > >
> > > $ variant_effect_predictor.pl --offline --cache --assembly GRCh37
> > > --format vcf -i
> > > example_GRCh37.vcf --everything -o example_annotated_GRCh37.vcf
> > >
> > > 2015-09-30 17:39:59 - Read existing cache info
> > > 2015-09-30 17:39:59 - INFO: Disabling --hgvs; using --offline and no
> FASTA
> > > file
> > > found
> > > 2015-09-30 17:39:59 - Starting...
> > > 2015-09-30 17:39:59 - Read 173 variants into buffer
> > > 2015-09-30 17:39:59 - Checking for existing variations
> > > <...>
> > > Use of uninitialized value in concatenation (.) or string at
> > > /net/apps/noarch/vep/Bio/EnsEMBL/Variation/Utils/VEP.pm line 2757.
> > > [============================>
> > > ]   [ 23% ]Use of uninitialized value in concatenation (.) or string at
> > > /net/apps/noarch/vep/Bio/EnsEMBL/Variation/Utils/VEP.pm line 2757.
> > > Use of uninitialized value in concatenation (.) or string at
> > > /net/apps/noarch/vep/Bio/EnsEMBL/Variation/Utils/VEP.pm line 2757.
> > > Use of uninitialized value in concatenation (.) or string at
> > > /net/apps/noarch/vep/Bio/EnsEMBL/Variation/Utils/VEP.pm line 2757.
> > > Use of uninitialized value in concatenation (.) or string at
> > > /net/apps/noarch/vep/Bio/EnsEMBL/Variation/Utils/VEP.pm line 2757.
> > > Use of uninitialized value in concatenation (.) or string at
> > > /net/apps/noarch/vep/Bio/EnsEMBL/Variation/Utils/VEP.pm line 2757.
> > > Use of uninitialized value in concatenation (.) or string at
> > > /net/apps/noarch/vep/Bio/EnsEMBL/Variation/Utils/VEP.pm line 2757.
> > > Use of uninitialized value in concatenation (.) or string at
> > > /net/apps/noarch/vep/Bio/EnsEMBL/Variation/Utils/VEP.pm line 2757.
> > > Use of uninitialized value in concatenation (.) or string at
> > > /net/apps/noarch/vep/Bio/EnsEMBL/Variation/Utils/VEP.pm line 2757.
> > > Use of uninitialized value in concatenation (.) or string at
> > > /net/apps/noarch/vep/Bio/EnsEMBL/Variation/Utils/VEP.pm line 2757.
> > > Use of uninitialized value in concatenation (.) or string at
> > > /net/apps/noarch/vep/Bio/EnsEMBL/Variation/Utils/VEP.pm line 2757.
> > > Use of uninitialized value in concatenation (.) or string at
> > > /net/apps/noarch/vep/Bio/EnsEMBL/Variation/Utils/VEP.pm line 2757.
> > > Use of uninitialized value in concatenation (.) or string at
> > > /net/apps/noarch/vep/Bio/EnsEMBL/Variation/Utils/VEP.pm line 2757.
> > > <...>
> > >
> > > On Wednesday, September 30, 2015 01:41:00 PM Thomas Maurel wrote:
> > > > We are pleased to announce that the latest Ensembl update (e!82) has
> > > > been
> > > > released: http://www.ensembl.org/ <http://www.ensembl.org/>
> > > >
> > > > Highlights of this release include:
> > > >
> > > > Ensembl mobile website <http://m.ensembl.org/>
> > > > Support of VEP Plugins through the web interface, script and REST
> > > > Improved Variation tables
> > > > <
> > >
> > >
> http://e82.ensembl.org/Homo_sapiens/Gene/Variation_Gene/Table?g=ENSG000001
> > >
> > > > 39618;r=13:32315474-32400266> RNASeq data set of Zebrafish
> > > > <http://e82.ensembl.org/Danio_rerio/Info/Index> developmental stages
> > > > Marking a region on images
> > > > LastZ replaced TBlat for pairwise alignments
> > > > Human variation data updates to dbSNP (144) including variants from
> the
> > > > Exome Aggregation Consortium (ExAC <http://exac.broadinstitute.org/
> >)
> > >
> > > Mouse
> > >
> > > > <http://e82.ensembl.org/Mus_musculus/Info/Index>: updated to
> GENCODE M7
> > > > including HAVANA annotation. Improved data upload form
> > > > Improvements to PDF export
> > > > Export mode for projectors and print
> > > > Phenotype data updated for several species, including human
> > > > <http://e82.ensembl.org/Homo_sapiens/Phenotype/Locations?ph=5815>,
> mouse
> > > > <http://e82.ensembl.org/Mus_musculus/Phenotype/Locations?ph=225>,
> rat
> > > > <http://e82.ensembl.org/Rattus_norvegicus/Phenotype/Locations?ph=73>
> and
> > > > horse <http://e82.ensembl.org/Equus_caballus/Info/Index>
> > > >
> > > > A complete list of the changes in release 82 can be found at
> > > > http://www.ensembl.org/info/website/news.html
> > > > <http://www.ensembl.org/info/website/news.html>
> > > >
> > > > For the latest news from the Ensembl project visit our blog at
> > > > http://www.ensembl.info <http://www.ensembl.info/>
> > > >
> > > > The release 82 blog post can be viewed here:
> > > >
> http://www.ensembl.info/blog/2015/09/30/ensembl-82-has-been-released/
> > > > <
> http://www.ensembl.info/blog/2015/09/30/ensembl-82-has-been-released/>
> > > >
> > > > The e82 webinar is planned for Wednesday 7th Oct at 16:00 GMT+1,
> please
> > > > register using the following URL (registration is free):
> > > > http://www.ebi.ac.uk/training/events/2015/ensembl-release-82-webinar
> > > > <https://attendee.gototraining.com/r/1571390501370151169>
> > > >
> > > >
> > > > Best Regards,
> > > > Thomas
>
>
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