[ensembl-dev] VEP feature request - different plugin and cache folder locations

[Andy Yates]

Hi Duarte,

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.

PERL5LIB=/path/to/modules:$PERL5LIB ./variant_effect_predictor.pl

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 15 May 2013, at 11:46, Duarte Molha <duartemolha at gmail.com> wrote:

> Thanks for the tip. 
> 
> However I think it would be neater if the plugin location argument was included. 
> 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. 
> 
> 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 :-)
> 
> Thanks
> 
> Duarte
> 
> =========================
>      Duarte Miguel Paulo Molha      
>          http://about.me/duarte         
> =========================
> 
> 
> On Wed, May 15, 2013 at 11:40 AM, Will McLaren <wm2 at ebi.ac.uk> wrote:
> You can easily enough add directories to your INC by using:
> 
> perl -I /path/to/modules variant_effect_predictor.pl
> 
> This is how I maintain various head and branch installations of the Ensembl API when testing code.
> 
> Will
> 
> 
> On 15 May 2013 11:31, Duarte Molha <duartemolha at gmail.com> wrote:
> 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.
> 
> 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
> 
> if you want to specify a different location.
> 
> 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...
> 
> Thanks
> 
> 
> Duarte
> 
> 
> 
> 
> =========================
>      Duarte Miguel Paulo Molha      
>          http://about.me/duarte         
> =========================
> 
> 
> On Wed, May 15, 2013 at 11:20 AM, Will McLaren <wm2 at ebi.ac.uk> wrote:
> Hi Duarte,
> 
> 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.
> 
> Would this suit your purposes?
> 
> Cheers
> 
> Will
> 
> 
> On 15 May 2013 11:11, Duarte Molha <Duarte.Molha at ogt.com> wrote:
> Much appreciated
> 
>  
> 
> From: dev-bounces at ensembl.org [mailto:dev-bounces at ensembl.org] On Behalf Of Will McLaren
> Sent: 15 May 2013 11:09
> To: Ensembl developers list
> Subject: Re: [ensembl-dev] VEP feature request - different plugin and cache folder locations
> 
>  
> 
> Hi Duarte,
> 
>  
> 
> Yes, a very reasonable suggestion.
> 
>  
> 
> I'll look into it.
> 
>  
> 
> Will
> 
>  
> 
> On 15 May 2013 10:50, Duarte Molha <duartemolha at gmail.com> wrote:
> 
> Dear Devs
> 
>  
> 
> I would like to ask that the vep cache directory and the vep plugin directory be decoupled in the script.
> 
>  
> 
> It doesn't make sense (at least to me) that both these disparate sets of data have to be put in the same folder.
> 
>  
> 
> Sure I can hack the code myself, but I do not want to have to make this change everytime a new version comes out
> 
>  
> 
> All I am asking is that you be given options like:
> 
>  
> 
> --dir_cache /vep_dache
> 
> --dir_plugins /vep_plugins
> 
>  
> 
> Is this something you would be willing to change?
> 
>  
> 
> Thanks
> 
> 
> Duarte
> 
>  
> 
> =========================
>      Duarte Miguel Paulo Molha      
> 
>          http://about.me/duarte         
> =========================
> 
> 
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