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

[Duarte Molha]

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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>>>
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