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


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Peter Briggs peter.bri...@manchester.ac.uk
Bioinformatics Core Facility University of Manchester
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