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

Will McLaren wm2 at ebi.ac.uk
Wed May 15 11:40:30 BST 2013


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
>>> =========================****
>>>
>>>
>>> _______________________________________________
>>> Dev mailing list    Dev at ensembl.org
>>> Posting guidelines and subscribe/unsubscribe info:
>>> http://lists.ensembl.org/mailman/listinfo/dev
>>> Ensembl Blog: http://www.ensembl.info/****
>>>
>>> ** **
>>>
>>> _______________________________________________
>>> Dev mailing list    Dev at ensembl.org
>>> Posting guidelines and subscribe/unsubscribe info:
>>> http://lists.ensembl.org/mailman/listinfo/dev
>>> Ensembl Blog: http://www.ensembl.info/
>>>
>>>
>>
>> _______________________________________________
>> Dev mailing list    Dev at ensembl.org
>> Posting guidelines and subscribe/unsubscribe info:
>> http://lists.ensembl.org/mailman/listinfo/dev
>> Ensembl Blog: http://www.ensembl.info/
>>
>>
>
> _______________________________________________
> Dev mailing list    Dev at ensembl.org
> Posting guidelines and subscribe/unsubscribe info:
> http://lists.ensembl.org/mailman/listinfo/dev
> Ensembl Blog: http://www.ensembl.info/
>
>
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://mail.ensembl.org/pipermail/dev_ensembl.org/attachments/20130515/9a0b2c68/attachment.html>


More information about the Dev mailing list