[ensembl-dev] Ensembl release 82 is out!
Will McLaren
wm2 at ebi.ac.uk
Mon Oct 5 09:40:23 BST 2015
Thanks Ivan, a useful improvement.
I don't understand what might have happened when you've run the installer -
your output from ls suggests that even INSTALL.pl has been deleted somehow?
Did you run it with the -n or --UPDATE flag? You should only do this if you
want to find if there is a new version available - you already have the
latest with 82.
I'd start from scratch again, I can't replicate the issue that you're
seeing.
Regards
Will
On 2 October 2015 at 20:01, Ivan Adzhubey <iadzhubey at rics.bwh.harvard.edu>
wrote:
> I would also suggest the following changes to variant_effect_predictor.pl:
>
> --- original/variant_effect_predictor.pl 2015-09-30 11:00:42.000000000
> -0400
> +++ patched/variant_effect_predictor.pl 2015-10-02 14:55:21.211776330
> -0400
> @@ -43,8 +43,8 @@ use strict;
> use Getopt::Long;
> use FileHandle;
> use CGI qw/:standard/;
> -use FindBin qw($Bin);
> -use lib $Bin;
> +use FindBin qw($RealBin);
> +use lib $RealBin;
>
> This would allow using symbolic links with the script.
>
> Thanks,
> Ivan
>
> On Friday, October 02, 2015 02:20:51 PM Ivan Adzhubey wrote:
> > Hi Will,
> >
> > On Friday, October 02, 2015 09:32:03 AM Will McLaren wrote:
> > > No, the script version should match the API/DB version - perhaps at
> some
> > > point 80 is getting inserted instead of 82?
> >
> > I have set aside (renamed) old installation directory, re-downloaded
> 82.zip
> > archive once again, unzipped it and re-run INSTALL.pl from scratch.
> >
> > This time I did not get *any* of the scripts copied to the installation
> > directory at all. Below is file listing of the target directory after the
> > successful installation (no errors reported, all tests PASSed):
> >
> > $ ls -lh
> > total 80K
> > drwxrwxr-x 45 ivan ivan 4.0K Oct 2 14:09 Bio
> > drwxrwxr-x 6 ivan ivan 4.0K Oct 2 14:09 FAIDX
> > -rw-rw-r-- 1 ivan ivan 2.0K Oct 2 14:09 Faidx.pm
> > -rw-rw-r-- 1 ivan ivan 60K Oct 2 14:09 Faidx.so
> > drwxr-xr-x 6 ivan ivan 4.0K Oct 2 14:09 htslib
> > drwxrwxr-x 3 ivan ivan 4.0K Oct 2 13:55 t
> >
> > As you can see, variant_effect_predictor.pl is nowhere to be found.
> >
> > So, the INSTALL.pl seems to be broken in this release.
> >
> > Best,
> > Ivan
> >
> > > 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=ENSG0000
> > > > 01
> > > >
> > > > > > > 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=7
> > > > > > > 3>
> > > >
> > > > 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-webin
> > > > > > > ar
> > > > > > > <https://attendee.gototraining.com/r/1571390501370151169>
> > > > > > >
> > > > > > >
> > > > > > > Best Regards,
> > > > > > > Thomas
>
>
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