Re: [GMOD-devel] [Gmod-gbrowse] help with conf file

[Scott C. <sc...@sc...>]

Hi Pushkala,

Are there any messages in the error log?

Scott




On Tue, May 25, 2010 at 2:25 PM, Jayaraman, Pushkala <pja...@mc...> wrote:
> Hello after resolving issues with database access, I see that I get this
> when I try accessing gborwse2
>
> http://rgddev.mcw.edu/cgi-bin/gbrowse/03.rgd_904_gb2/?source=03.rgd_904_gb2
>
>
>
> I am not able to see the overview/region/detail panels..
>
>
>
> I know there is something wrong with the config file.. but I am just not
> sure what..
>
>
>
> Herewith is my config file:
>
>
>
>
>
>
>
>
>
> [GENERAL]
>
> description   = Rat Genome V3.4 Assembly
>
> db_adaptor    = Bio::DB::GFF
>
> db_args       = -adaptor dbi::mysql
>
>                 -dsn
> dbi:mysql:database=rgd_904_test;host=forte.hmgc.mcw.edu;port=3306
>
>                                 -user rgdselect
>
>                                 -pass rgdselusrdv1a
>
>
>
> # examples to show in the introduction
>
> examples = proteinuria
>
>            Grik1
>
>            RGD620956
>
>
>
> # Default track settings
>
> [TRACK DEFAULTS]
>
> glyph       = generic
>
> height      = 8
>
> bgcolor     = cyan
>
> fgcolor     = cyan
>
> font2color  = black
>
> label density = 25
>
>
>
> ### Individual track settings ####
>
> [PSEUDOGENE:overview]
>
> category     = GENE MODELS
>
> feature      = pseudogene:GenBank
>
> glyph        = arrow
>
> fgcolor      = blue
>
> linewidth    = 2
>
> height       = 6
>
> link   = sub {
>
>                   my $f=shift;
>
>                   if ($f->attributes->{'Dbxref'} eq "") {
>
>                       return;
>
>                   }
>
>                   my $xdb=join(",", @{$f->attributes->{Dbxref}});
>
>                   my $ncbiId;
>
>                   if ($xdb =~/GeneID:(\d+)/) {
>
>                     $ncbiId=$1;
>
>                   }
>
>                   return
> "http://www.ncbi.nlm.nih.gov/sites/entrez?db=gene&cmd=search&term=$ncbiId";
>
>                 }
>
> key          =  Entrez Pseudogenes
>
> citation     = This track shows pseudogenes labeled as such at <a
> href="http://www.ncbi.nlm.nih.gov/Genbank/"> GenBank</a>. Hovering over a
> feature provides additional annotation including the EntrezGeneID, Name,
> Description, and Source. Clicking on a features links to the appropriate
> EntrezGene record.
>
>
>
>
>
>
>
> I know there is absolutely nothing here..
>
> But I am just not able to see the Overview/Region/detail panels or the
> glyphs.. I can see the section that allows you to search for keywords/click
> on what tracks you need ON/select datasource.
>
> I can even see the Overview/Region/Detail sections when I chose some of the
> sample datasets provided eg Yeast Basic and yeast Advanced..
>
>
>
> Where am I going wrong?
>
>
>
> Pushkala Jayaraman
>
> Programmer/Analyst
>
> Rat Genome Database
>
> Human and Molecular Genetics Center
>
> Medical College of Wisconsin
>
> Email: pja...@mc...
>
> Work: 414-955-2229
>
> www.rgd.mcw.edu
>
>
>
> ------------------------------------------------------------------------------
>
>
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>
>



-- 
------------------------------------------------------------------------
Scott Cain, Ph. D.                                   scott at scottcain dot net
GMOD Coordinator (http://gmod.org/)                     216-392-3087
Ontario Institute for Cancer Research