[ensembl-dev] virtual machine update/ensembl API

[Will McLaren]

Hi Juha,

You can use the INSTALL.pl script in
$HOME/ensembl-api-folder/ensembl-tools/scripts/variant_effect_predictor/ to
retrieve the latest cache files after you have done the CVS update as
suggested by Andy.

Regards

Will McLaren
Ensembl Variation


On 8 November 2012 13:02, Andy Yates <ayates at ebi.ac.uk> wrote:

> Hi Juha,
>
> Currently our update procedure is to download a fresh VM from our FTP site
> with each release as we will be introducing more things into it as we merge
> our various internal VMs. However the APIs on the VMs are just CVS
> checkouts with little dependency on the underlying OS so you can update say
> the 68 API to 69 by doing:
>
> cd $HOME/ensembl-api-folder
> for d in ensembl*; do
> echo Updating $d
> cd $d && cvs -q update -dP -A -r branch-ensembl-69 && cd -
> done
>
> The VEP cache files need to be re-downloaded but there should be no OS
> dependency issues with them
>
> Regards,
>
> Andy
>
> Andrew Yates                   Ensembl Core Software Project Leader
> EMBL-EBI                       Tel: +44-(0)1223-492538
> Wellcome Trust Genome Campus   Fax: +44-(0)1223-494468
> Cambridge CB10 1SD, UK         http://www.ensembl.org/
>
> On 8 Nov 2012, at 05:27, juha.muilu at kolumbus.fi wrote:
>
> >
> > Hi
> > Wondering what  is the best procedure to update existing ensemble
> virtual machine to the latest release.  Are there any dependencies with
> operating system or cache settings variation api is using for example?
> >
> > Best regards, Juha
> >
> >
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