[ensembl-dev] VEP feature request - different plugin and cache folder locations
LAW Andy
andy.law at roslin.ed.ac.uk
Wed May 15 11:55:40 BST 2013
Or you could just throw in a quick, optional pair of -dir_cache/-dir_plugins flags, add a quick USAGE response to the script and have everything self-contained and logical for normal people to use?
:o}
On 15 May 2013, at 11:50, 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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>>
>>
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Later,
Andy
--------
Yada, yada, yada...
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