Re: [galaxy-dev] Deploying custom genome in Galaxy for use with ANNOVAR (Peter Briggs)
Peter, Thanks! The blog post is very helpful. David > -- Forwarded message -- > From: Peter Briggs <peter.bri...@manchester.ac.uk> > To: galaxy-dev@lists.galaxyproject.org > Cc: > Date: Wed, 8 Jun 2016 08:25:03 +0100 > Subject: Re: [galaxy-dev] Deploying custom genome in Galaxy for use with > ANNOVAR > 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 peter.bri...@manchester.ac.uk > 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: https://lists.galaxyproject.org/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-dev] Deploying custom genome in Galaxy for use with ANNOVAR
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 peter.bri...@manchester.ac.uk 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: https://lists.galaxyproject.org/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
[galaxy-dev] Deploying custom genome in Galaxy for use with ANNOVAR
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/
