[ensembl-dev] VEP Conservation Plugin error

[James Walker]

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.
>>>>
>>>>
>>>> _______________________________________________
>>>> 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/20131014/880390ae/attachment.html>