[ensembl-dev] virtual machine update/ensembl API

[Will McLaren]

Hi Juha,

You shouldn't need to no, the version of BioPerl that the Ensembl API uses
has been stable for a long time.

There is one proviso to this - if you intend on using the --fasta option
with the VEP and a large (>4gig unpacked) FASTA file, then you should
install the latest (>=1.6) version of BioPerl in place since it fixes a bug
in handling these large files.

Regards

Will


On 8 November 2012 13:47, <juha.muilu at kolumbus.fi> wrote:

> Hi Will and Andy, Great thanks for the help!  Should I update the bio-perl
> API as well ?
> Cheers, Juha
>
> Will McLaren [wm2 at ebi.ac.uk] kirjoitti:
>
>> 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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