[ensembl-dev] VEP FATHMM plugin

[Will McLaren]

Hi Michael,

Thanks for finding this; I've committed a fix to the CVS (branch 73).

It should work now if you use quotes - it won't work if you don't have
quotes due to the way the config parser has to work.

Regards

Will McLaren
Ensembl Variation


On 13 November 2013 02:43, Michael Yourshaw <myourshaw at ucla.edu> wrote:

> I’m having a problem with the FATHMM plugin parameters. I think this will
> affect all plugins that need a space in the text when the plugin is
> specified in a configuration file.
>
> The plugin wants to be specified like this:
> FATHMM,"python /path/to/fathmm/fathmm.py”
>
> I am using a configuration file with parameters in that form, but the
> VEP read_config_from_file subroutine seems to be splitting on the space
> between ‘python’ and ‘/path/to’. This happens whether I use the enclosing
> double quotes or not.
>
> The space in a plugin parameter isn’t a problem on the command line, just
> in a config file.
>
>
>
> ॐ
>
> Michael Yourshaw
> UCLA Geffen School of Medicine
> Department of Human Genetics, Nelson Lab
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