[ensembl-dev] Ensembl release 82 is out!

Ivan Adzhubey iadzhubey at rics.bwh.harvard.edu
Fri Oct 2 20:01:41 BST 2015 

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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