Deploying custom genome in Galaxy for use with ANNOVAR

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Deploying custom genome in Galaxy for use with ANNOVAR

David Kovalic
All,

From my read of the command line docs for ANNOVAR I believe that the program needs so ancillary files for its operation (e.g. GenePred file, transcripts fasta file, etc...).

Does anyone have any experience deploying custom genomes in Galaxy for use with ANNOVAR? Specifically what files need to go where in order to enable the Galaxy ANNOVAR front end?

Thanks,

David

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Re: Deploying custom genome in Galaxy for use with ANNOVAR

Peter Briggs
Hello David

I don't think it will answer all your questions, however: I wrote up my
experiences with installing ANNOVAR in Galaxy last year which might be
useful as a starting point:

http://galacticengineer.blogspot.co.uk/2015/03/installing-annovar-in-galaxy.html

As I recall all the databases we installed were standard ones from
ANNOVAR. However the above instructions might be useful in at least
getting started.

Apologies if I've misunderstood your question and this doesn't help,

Best wishes

Peter

On 07/06/16 17:48, David Kovalic wrote:

> All,
>
>  From my read of the command line docs for ANNOVAR I believe that the
> program needs so ancillary files for its operation (e.g. GenePred file,
> transcripts fasta file, etc...).
>
> Does anyone have any experience deploying custom genomes in Galaxy for
> use with ANNOVAR? Specifically what files need to go where in order to
> enable the Galaxy ANNOVAR front end?
>
> Thanks,
>
> David
>
>
> ___________________________________________________________
> Please keep all replies on the list by using "reply all"
> in your mail client.  To manage your subscriptions to this
> and other Galaxy lists, please use the interface at:
>    https://lists.galaxyproject.org/
>
> To search Galaxy mailing lists use the unified search at:
>    http://galaxyproject.org/search/mailinglists/
>

--
Peter Briggs [hidden email]
Bioinformatics Core Facility University of Manchester
B.1083 Michael Smith Bldg Tel: (0161) 2751482
___________________________________________________________
Please keep all replies on the list by using "reply all"
in your mail client.  To manage your subscriptions to this
and other Galaxy lists, please use the interface at:
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To search Galaxy mailing lists use the unified search at:
  http://galaxyproject.org/search/mailinglists/