[ensembl-dev] Ensembl release 82 is out!

[Ivan Adzhubey]

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.

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.

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.

Thanks,
Ivan


-- 
Ivan Adzhubey, Ph.D.
Instructor
Division of Genetics, Dept of Medicine
Brigham & Women's Hospital
Harvard Medical School
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