[ensembl-dev] Release 81 installation problems

[Cyriac Kandoth]

Hi Nikolas,

The only fix in those commands is to download the v81 cache instead of v79.
See the highlighted fix below...

rsync -zvh rsync://
ftp.ensembl.org/ensembl/pub/release-81/variation/VEP/homo_sapiens_vep_*81*_GRCh{37,38}.tar.gz
$VEP_DATA

Also note that these instructions are just for installing VEP locally to
run offline. You won't install all of Ensembl's API and tools.

~Cyriac

On Mon, Jul 20, 2015 at 9:58 PM, Balanis, Nikolas G. <
NBalanis at mednet.ucla.edu> wrote:

>  Hello I am looking for the solution to this problem. *I googled and
> looked on throught the archives but I am not sure how to fix this. *I am
> installing vep based on the instructions from
> https://github.com/ckandoth/vcf2maf
>
> export VEP_PATH=~/vep
> export VEP_DATA=~/.vep
>
>
> mkdir $VEP_PATH; cd $VEP_PATH
> curl -LO https://github.com/Ensembl/ensembl-tools/archive/release/81.tar.gz
> tar -zxf 81.tar.gz --starting-file variant_effect_predictor --transform='s|.*/|./|g'
>
> rsync -zvh rsync://ftp.ensembl.org/ensembl/pub/release-81/variation/VEP/homo_sapiens_vep_79_GRCh{37,38}.tar.gz <http://ftp.ensembl.org/ensembl/pub/release-81/variation/VEP/homo_sapiens_vep_79_GRCh%7B37,38%7D.tar.gz> $VEP_DATA
> cat $VEP_DATA/*.tar.gz | tar -izxf - -C $VEP_DATA
>
>
> cd $VEP_PATH
> perl INSTALL.pl --AUTO af --SPECIES homo_sapiens --ASSEMBLY GRCh37 --DESTDIR $VEP_PATH --CACHEDIR $VEP_DATA
> perl INSTALL.pl --AUTO af --SPECIES homo_sapiens --ASSEMBLY GRCh38 --DESTDIR $VEP_PATH --CACHEDIR $VEP_DATA
>
> I get this warning message below when I perform either of the last 2 instructions.  I can't
> seem to figure this out. Everything should be release 81 so I am quite confused.
> What are the steps to fix this?
>
>
>
> *For homo_sapiens_core_80_38 there is a difference in the software release
> (81) and the database release (80). You should update one of these to
> ensure that your script does not crash. For homo_sapiens_variation_80_38
> there is a difference in the software release (81) and the database release
> (80). You should update one of these to ensure that your script does not
> crash. *
>
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