[ensembl-dev] VEP Conservation Plugin error

Will McLaren wm2 at ebi.ac.uk
Mon Oct 14 16:38:33 BST 2013


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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