<html><head><meta http-equiv="content-type" content="text/html; charset=utf-8"></head><body dir="auto"><div>Hi</div><div><br></div><div>It only appends it for the lifetime of the running process IIRC. So it would reset once the vep had finished</div><div><br></div><div>Andy <br><br>Sent from my mobile.</div><div><br>On 15 May 2013, at 11:52, Duarte Molha <<a href="mailto:duartemolha@gmail.com">duartemolha@gmail.com</a>> wrote:<br><br></div><blockquote type="cite"><div><div dir="ltr">Yes... I could... but would that not append to the PERL5LIB permanently (or at least until the end of the terminal session?</div><div class="gmail_extra"><br clear="all"><div><font style="background-color:rgb(255,255,255)" color="#999999">=========================<br>
Duarte Miguel Paulo Molha <br></font><div><font style="background-color:rgb(255,255,255)" color="#999999"> <a href="http://about.me/duarte" target="_blank">http://about.me/duarte</a> <br>=========================</font></div>
</div>
<br><br><div class="gmail_quote">On Wed, May 15, 2013 at 11:50 AM, Andy Yates <span dir="ltr"><<a href="mailto:ayates@ebi.ac.uk" target="_blank">ayates@ebi.ac.uk</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
Hi Duarte,<br>
<br>
You can also modify ENV variables just before program execution so there's need to alter your system PERL5LIB or to run the VEP script with a perl interpreter e.g.<br>
<br>
PERL5LIB=/path/to/modules:$PERL5LIB ./<a href="http://variant_effect_predictor.pl" target="_blank">variant_effect_predictor.pl</a><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">+44-(0)1223-492538</a><br>
Wellcome Trust Genome Campus Fax: <a href="tel:%2B44-%280%291223-494468" value="+441223494468">+44-(0)1223-494468</a><br>
Cambridge CB10 1SD, UK <a href="http://www.ensembl.org/" target="_blank">http://www.ensembl.org/</a><br>
<div class="HOEnZb"><div class="h5"><br>
On 15 May 2013, at 11:46, Duarte Molha <<a href="mailto:duartemolha@gmail.com">duartemolha@gmail.com</a>> wrote:<br>
<br>
> Thanks for the tip.<br>
><br>
> However I think it would be neater if the plugin location argument was included.<br>
> But I understand it there are other priorities. In my way of working I like to keep the PERL5LIB argument only for system modules and dependencies and I like to be able to control all the script workflow and data from arguments parsed in the script itself.<br>
><br>
> But I understand if you feel that this is not necessary (because it isn't) ... It is probably me just being a bit OCD about it :-)<br>
><br>
> Thanks<br>
><br>
> Duarte<br>
><br>
> =========================<br>
> Duarte Miguel Paulo Molha<br>
> <a href="http://about.me/duarte" target="_blank">http://about.me/duarte</a><br>
> =========================<br>
><br>
><br>
> On Wed, May 15, 2013 at 11:40 AM, Will McLaren <<a href="mailto:wm2@ebi.ac.uk">wm2@ebi.ac.uk</a>> wrote:<br>
> You can easily enough add directories to your INC by using:<br>
><br>
> perl -I /path/to/modules <a href="http://variant_effect_predictor.pl" target="_blank">variant_effect_predictor.pl</a><br>
><br>
> This is how I maintain various head and branch installations of the Ensembl API when testing code.<br>
><br>
> Will<br>
><br>
><br>
> On 15 May 2013 11:31, Duarte Molha <<a href="mailto:duartemolha@gmail.com">duartemolha@gmail.com</a>> wrote:<br>
> I much preferred to have a way of specifying it on the arguments. Yes we could use the PERL5LIB... but I was thinking more in terms of being able to quickly change from production ready plugins to testing plugins by specifying a different location.<br>
><br>
> If you wish to maintain backwards compatibility I suggest that to keep the –dir argument as an overriding argument (if present the script expects both cache and plugins in the same directory) and add only 1 additional argument --dir_plugins<br>
><br>
> if you want to specify a different location.<br>
><br>
> I personally prefer to to have control over my run environment without having to be dependent on the system path environment and can be different for different users, servers,etc...<br>
><br>
> Thanks<br>
><br>
><br>
> Duarte<br>
><br>
><br>
><br>
><br>
> =========================<br>
> Duarte Miguel Paulo Molha<br>
> <a href="http://about.me/duarte" target="_blank">http://about.me/duarte</a><br>
> =========================<br>
><br>
><br>
> On Wed, May 15, 2013 at 11:20 AM, Will McLaren <<a href="mailto:wm2@ebi.ac.uk">wm2@ebi.ac.uk</a>> wrote:<br>
> Hi Duarte,<br>
><br>
> It has been pointed out to me that the VEP will actually look for plugins anywhere in $PERL5LIB, so you could simply add you plugins dir (if separate) to $PERL5LIB and then --dir will be used to look up the cache directory.<br>
><br>
> Would this suit your purposes?<br>
><br>
> Cheers<br>
><br>
> Will<br>
><br>
><br>
> On 15 May 2013 11:11, Duarte Molha <<a href="mailto:Duarte.Molha@ogt.com">Duarte.Molha@ogt.com</a>> wrote:<br>
> Much appreciated<br>
><br>
><br>
><br>
> From: <a href="mailto:dev-bounces@ensembl.org">dev-bounces@ensembl.org</a> [mailto:<a href="mailto:dev-bounces@ensembl.org">dev-bounces@ensembl.org</a>] On Behalf Of Will McLaren<br>
> Sent: 15 May 2013 11:09<br>
> To: Ensembl developers list<br>
> Subject: Re: [ensembl-dev] VEP feature request - different plugin and cache folder locations<br>
><br>
><br>
><br>
> Hi Duarte,<br>
><br>
><br>
><br>
> Yes, a very reasonable suggestion.<br>
><br>
><br>
><br>
> I'll look into it.<br>
><br>
><br>
><br>
> Will<br>
><br>
><br>
><br>
> On 15 May 2013 10:50, Duarte Molha <<a href="mailto:duartemolha@gmail.com">duartemolha@gmail.com</a>> wrote:<br>
><br>
> Dear Devs<br>
><br>
><br>
><br>
> I would like to ask that the vep cache directory and the vep plugin directory be decoupled in the script.<br>
><br>
><br>
><br>
> It doesn't make sense (at least to me) that both these disparate sets of data have to be put in the same folder.<br>
><br>
><br>
><br>
> Sure I can hack the code myself, but I do not want to have to make this change everytime a new version comes out<br>
><br>
><br>
><br>
> All I am asking is that you be given options like:<br>
><br>
><br>
><br>
> --dir_cache /vep_dache<br>
><br>
> --dir_plugins /vep_plugins<br>
><br>
><br>
><br>
> Is this something you would be willing to change?<br>
><br>
><br>
><br>
> Thanks<br>
><br>
><br>
> Duarte<br>
><br>
><br>
><br>
> =========================<br>
> Duarte Miguel Paulo Molha<br>
><br>
> <a href="http://about.me/duarte" target="_blank">http://about.me/duarte</a><br>
> =========================<br>
><br>
><br>
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