[ensembl-dev] VEP feature request - different plugin and cache folder locations
Duarte Molha
duartemolha at gmail.com
Wed May 15 11:52:33 BST 2013
Yes... I could... but would that not append to the PERL5LIB permanently (or
at least until the end of the terminal session?
=========================
Duarte Miguel Paulo Molha
http://about.me/duarte
=========================
On Wed, May 15, 2013 at 11:50 AM, Andy Yates <ayates at ebi.ac.uk> wrote:
> 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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