[ensembl-dev] Ensembl release 82 is out!

[Will McLaren]

Hi Ivan

On 6 October 2015 at 02:06, Ivan Adzhubey <iadzhubey at rics.bwh.harvard.edu>
wrote:

> Hi Rishi,
>
> On Monday, October 05, 2015 11:05:15 AM Rishi Nag wrote:
> > Hi Ivan
> >
> > Was the -d option specified with INSTALL.pl?
>
> Yep.
>
> > 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.
>
> Hmm, looks like the INSTALL.pl used to also copy the executables in the
> directory specified by the -d switch, at least up to version 80. That's the
> version of the script(s) I found stuck on my system.
>

I don't believe that is the case - the behaviour has always been the same.


>
> Anyway, not actually installing the executables into target location
> specified
> (explicitly) looks like a very counter-intuitive behavior to me. At least
> it
> should be clearly documented.
>

I agree, this is not very intuitive - I will update the documentation.


>
> One more question, here's the header excerpt from the example VCF
> generated by
> the test run:
>
> $ head -7 example_annotated_GRCh37.vcf
> ## ENSEMBL VARIANT EFFECT PREDICTOR v82
> ## Output produced at 2015-10-05 20:54:32
> ## Using cache in /net/data/vep/homo_sapiens/82_GRCh37
> ## Using API version 82, DB version ?
> ## polyphen version 2.2.2
> ## sift version sift5.2.2
> ## COSMIC version 71
>
> Why the DB version is reported as missing (?) on line 4? Is this normal?
> The
> cache path specified is correct.
>

If you are using --offline then the VEP script makes no DB connection, so
the database version won't be checked. If you use --cache or --database
then you will see the version populated. Perhaps it would be clearer to
remove that statement from the header if no DB connection is made.

Regards

Will


>
> Thanks,
> Ivan
>
>
> --
> Ivan Adzhubey, Ph.D.
> Instructor
> Division of Genetics, Dept of Medicine
> Brigham & Women's Hospital
> Harvard Medical School
> New Research Building, Room 0464C
> 77 Avenue Louis Pasteur
> Boston, MA 02115
> tel.: (617) 525-4728
> fax:  (617) 525-4705
> web: http://genetics.bwh.harvard.edu/wiki/sunyaevlab/
>
>
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