[ensembl-dev] Ensembl release 82 is out!

Mon Oct 5 11:05:15 BST 2015

Hi Ivan

Was the -d option specified with INSTALL.pl? This is where downloaded code modules end up. Using this would give the listing as specified below but 
the location of the ensembl-tools scripts would still be where the ensembl-tools archive was unzipped.

Regards

Rishi

On 02/10/2015 19:20, 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=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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