Hi Juha,<div><br></div><div>You shouldn't need to no, the version of BioPerl that the Ensembl API uses has been stable for a long time.</div><div><br></div><div>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.</div>
<div><br></div><div>Regards</div><div><br></div><div>Will</div><div class="gmail_extra"><br><br><div class="gmail_quote">On 8 November 2012 13:47, <span dir="ltr"><<a href="mailto:juha.muilu@kolumbus.fi" target="_blank">juha.muilu@kolumbus.fi</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">Hi Will and Andy, Great thanks for the help! Should I update the bio-perl API as well ?<br>
Cheers, Juha<br>
<br>
Will McLaren [<a href="mailto:wm2@ebi.ac.uk" target="_blank">wm2@ebi.ac.uk</a>] kirjoitti: <br><div class="HOEnZb"><div class="h5">
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
Hi Juha,<br>
<br>
You can use the INSTALL.pl script in<br>
$HOME/ensembl-api-folder/<u></u>ensembl-tools/scripts/variant_<u></u>effect_predictor/ to<br>
retrieve the latest cache files after you have done the CVS update as<br>
suggested by Andy.<br>
<br>
Regards<br>
<br>
Will McLaren<br>
Ensembl Variation<br>
<br>
<br>
On 8 November 2012 13:02, Andy Yates <<a href="mailto:ayates@ebi.ac.uk" target="_blank">ayates@ebi.ac.uk</a>> wrote:<br>
<br>
> Hi Juha,<br>
><br>
> Currently our update procedure is to download a fresh VM from our FTP site<br>
> with each release as we will be introducing more things into it as we merge<br>
> our various internal VMs. However the APIs on the VMs are just CVS<br>
> checkouts with little dependency on the underlying OS so you can update say<br>
> the 68 API to 69 by doing:<br>
><br>
> cd $HOME/ensembl-api-folder<br>
> for d in ensembl*; do<br>
> echo Updating $d<br>
> cd $d && cvs -q update -dP -A -r branch-ensembl-69 && cd -<br>
> done<br>
><br>
> The VEP cache files need to be re-downloaded but there should be no OS<br>
> dependency issues with them<br>
><br>
> Regards,<br>
><br>
> Andy<br>
><br>
> Andrew Yates Ensembl Core Software Project Leader<br>
> EMBL-EBI Tel: <a href="tel:%2B44-%280%291223-492538" value="+441223492538" target="_blank">+44-(0)1223-492538</a><br>
> Wellcome Trust Genome Campus Fax: <a href="tel:%2B44-%280%291223-494468" value="+441223494468" target="_blank">+44-(0)1223-494468</a><br>
> Cambridge CB10 1SD, UK <a href="http://www.ensembl.org/" target="_blank">http://www.ensembl.org/</a><br>
><br>
> On 8 Nov 2012, at 05:27, <a href="mailto:juha.muilu@kolumbus.fi" target="_blank">juha.muilu@kolumbus.fi</a> wrote:<br>
><br>
> ><br>
> > Hi<br>
> > Wondering what is the best procedure to update existing ensemble<br>
> virtual machine to the latest release. Are there any dependencies with<br>
> operating system or cache settings variation api is using for example?<br>
> ><br>
> > Best regards, Juha<br>
> ><br>
> ><br>
> > ______________________________<u></u>_________________<br>
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> > Ensembl Blog: <a href="http://www.ensembl.info/" target="_blank">http://www.ensembl.info/</a><br>
><br>
><br>
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><br>
<br>
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<br>
</blockquote>
<br>
<br>
<br>
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</div></div></blockquote></div><br></div>