[ensembl-dev] VEP Conservation Plugin error

[Guillermo Marco Puche]

Hello,

I fixed it by downloading fresh Conservation plugin from VEP Github too.
Someone pushed a commit into my local repository and modified badly the 
script. That's why no conservation score was appearing.

Thank you and sorry for inconvenience.

Best regards,
Guillermo.

On 10/15/2013 09:09 AM, James Walker wrote:
> 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 
> <mailto: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 <mailto: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
>         <mailto: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 <mailto: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
>                 <mailto:walker.james.kerrigan at gmail.com>> wrote:
>
>>                     I'm experiencing the exact same problem. Plugin seems to be broken.
>>
>>
>>
>>
>>
>>
>>                     James.
>
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