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

[Will McLaren]

Thanks, well spotted.

Fixed. It will now only add on '/Plugins' if you are using --dir or the
default directory.

Will


On 15 May 2013 13:35, Duarte Molha <duartemolha at gmail.com> wrote:

> Will I believe there is an error in your code line 525
>
> 1262:  unshift @INC, $config->{dir_plugins}."/Plugins";
>
>
> If you have already defined the plugins location using the argument,  (for
> example: "--dir_plugins /vep_plugins"), this line will make the script look
> for the plugins in  /vep_plugins/Plugins
>
> I am sure this is not the intended behavior
>
> Best regards
>
> Duarte
>
>
>
> =========================
>      Duarte Miguel Paulo Molha
>          http://about.me/duarte
> =========================
>
>
> On Wed, May 15, 2013 at 1:15 PM, Duarte Molha <duartemolha at gmail.com>wrote:
>
>> Thanks...
>>
>> It was right in front of my face but I wasn't able to see it :)
>>
>> However, please correct me if I am wrong... but the
>>
>> http://www.ensembl.org/info/docs/variation/vep/vep_script.html#top
>>
>> Version is the one in head right? So that one would not have the new
>> arguments right?
>>
>> Thanks
>>
>> Duarte
>>
>>
>> =========================
>>      Duarte Miguel Paulo Molha
>>          http://about.me/duarte
>> =========================
>>
>>
>> On Wed, May 15, 2013 at 1:12 PM, Will McLaren <wm2 at ebi.ac.uk> wrote:
>>
>>> You just need the script from the ensembl-tools module.
>>>
>>> You could just download from the web page too:
>>>
>>> http://www.ensembl.org/info/docs/variation/vep/vep_script.html#top
>>>
>>> Will
>>>
>>>
>>> On 15 May 2013 12:56, Duarte Molha <duartemolha at gmail.com> wrote:
>>>
>>>> I am terrible sorry ... But I just downloaded you CSV repository. Where
>>>> in the branch 71 can I checkout your code?
>>>>
>>>> Thanks
>>>>
>>>> Duarte
>>>>
>>>> =========================
>>>>      Duarte Miguel Paulo Molha
>>>>          http://about.me/duarte
>>>> =========================
>>>>
>>>>
>>>> On Wed, May 15, 2013 at 12:26 PM, Will McLaren <wm2 at ebi.ac.uk> wrote:
>>>>
>>>>> --dir_cache and --dir_plugins are now available on branch 71.
>>>>>
>>>>> Will
>>>>>
>>>>>
>>>>> On 15 May 2013 12:13, LAW Andy <andy.law at roslin.ed.ac.uk> wrote:
>>>>>
>>>>>>
>>>>>> On 15 May 2013, at 12:08, Duarte Molha <duartemolha at gmail.com> wrote:
>>>>>>
>>>>>> >
>>>>>> > I would not call myself "normal" but I agree with Andy Law that
>>>>>> users would appreciate the option :)
>>>>>> >
>>>>>>
>>>>>> No-one that knows me thinks *I'm* normal, but when a discussion
>>>>>> descends into suggesting esoteric manipulation of environment variables
>>>>>> relating to Perl installations as an acceptable alternative to introducing
>>>>>> simple and logical command-line arguments into a script, I think a bit of a
>>>>>> reality check is perhaps in order.
>>>>>>
>>>>>>
>>>>>> Later,
>>>>>>
>>>>>> Andy
>>>>>> --------
>>>>>> Yada, yada, yada...
>>>>>>
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>>>>>>
>>>>>>
>>>>>>
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>>>>>>
>>>>>>
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>>>>>
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