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

[Duarte Molha]

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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