[ensembl-dev] VEP Conservation Plugin error

[James Walker]

I did a fresh install of API + Plugins directory.
Works fine now, thank you Will.

Regards,
James.


2013/10/14 James Walker <walker.james.kerrigan at gmail.com>

> Hello Will,
>
> I've installed API from
> http://www.ensembl.org/info/docs/api/api_installation.html
>
>
> 2013/10/14 Will McLaren <wm2 at ebi.ac.uk>
>
>> Hi James,
>>
>> If you used CVS to install the ensembl-compara API module, then if you
>> don't specify a branch number when you checkout the code, by default CVS
>> will fetch the bleeding-edge or "head" code, which is not intended for
>> external use.
>>
>> On the instructions on this page:
>>
>> http://www.ensembl.org/info/docs/api/api_cvs.html
>>
>> if you miss off the "-r branch-ensembl-73" in your CVS checkout command,
>> you will get head code.
>>
>> If you have installed from the tar.gz archives (as per
>> http://www.ensembl.org/info/docs/api/api_installation.html) then you
>> won't be at risk of this.
>>
>> The change you have made to the plugin code won't make any difference, it
>> just suppresses a warning from the VEP.
>>
>> Will
>>
>>
>> On 14 October 2013 16:07, James Walker <walker.james.kerrigan at gmail.com>wrote:
>>
>>> Hello Will,
>>>
>>> I'm using vep cache plus local ensembl database to annotate variants.
>>>
>>> I don't really understand what do you refer with: "Is there any chance
>>> you have accidentally checked out head code (instead of branch 73) for the
>>> ensembl-compara API?"
>>>
>>> I've modified code in the script from:
>>>
>>>
>>>
>>> sub version {
>>>     return '2.3';
>>>
>>>
>>> }
>>>
>>> to
>>>
>>> sub version {
>>>
>>>     return '73';
>>> }
>>>
>>> Regards,
>>> James.
>>>
>>>
>>>
>>> 2013/10/14 Will McLaren <wm2 at ebi.ac.uk>
>>>
>>>> Hi James, Guillermo,
>>>>
>>>> We're struggling to recreate the problem at our end.
>>>>
>>>> While we do still see the warning message (which will disappear in 74
>>>> as Matthieu says), the plugin seems to be working fine.
>>>>
>>>> I've tested it on the example.vcf supplied with the VEP and a larger
>>>> set of ~3500 exonic variants from the 1000 genomes project, and I see
>>>> Conservation scores in the output for every variant in my test set.
>>>>
>>>> Are you seeing any other error messages? Are you using a local database
>>>> copy, or relying on the ensembldb connection (the default when using VEP)?
>>>>
>>>> Is there any chance you have accidentally checked out head code
>>>> (instead of branch 73) for the ensembl-compara API?
>>>>
>>>> MethodLinkSpeciesSet is not deprecated, although a couple of deprecated
>>>> methods in it were removed in 73, though these are not used by the plugin.
>>>>
>>>> Some more information would be useful!
>>>>
>>>> Thanks
>>>>
>>>> Will
>>>>
>>>>
>>>> On 14 October 2013 15:10, James Walker <walker.james.kerrigan at gmail.com
>>>> > wrote:
>>>>
>>>>> I'm experiencing the exact same problem. Plugin seems to be broken.
>>>>>
>>>>>
>>>>>
>>>>>
>>>>>
>>>>> James.
>>>>>
>>>>>
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>>>>
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>>>
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>>
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>
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