[Gmod-help] Re: [Gmod-gbrowse] multiple database configuration problems

[Miquel Ramia]

Sorry for being ambiguous, here's a screenshot attached

This only happens when the page is loaded for the first time or with  
the reset button: Some parts of the header like the example links, 
bookmark, download pdf, send to galaxy, etc. disappears , it doesn't go 
to the specified initial landmark and no default tracks selected as well.

Then I can go manually to a region and all the options appear again, all 
working fine except the example links still not shown.



Dave Clements, GMOD Help Desk wrote:
> Hi Miquel,
>
> What does GBrowse look like?  Are the broken tracks missing, empty, or
> something else.  What do you mean by "doesn't work"?  A screenshot
> might help here.
>
> Also, have tried commenting out one of the databases and just
> displaying tracks from the remaining database.
>
> I don't see anything wrong but I'm not sure what behaviour you are seeing.
>
> Thanks,
>
> Dave C.
>
> On Wed, Jul 1, 2009 at 8:45 AM, Miquel Ramia<miquel.ramia at uab.cat> wrote:
>   
>> Hi,
>>
>> I'm trying to use multiple databases in one .conf file with Gbrowse2,
>> but with this configuration, the  "examples", "default tracks"  and the
>> "initial landmark"  doesn't work:
>>
>> _______________________________________
>>
>> [GENERAL]
>> description   = Dmelgff3
>>
>> [annotations:database]
>> db_adaptor    = Bio::DB::SeqFeature::Store
>> db_args       = -adaptor DBI::mysql
>>                -dsn     dmelgff3_2
>>                -user    nobody
>>
>> [test_db:database]
>> db_adaptor    = Bio::DB::SeqFeature::Store
>> db_args       = -adaptor memory
>>                -dir    /home/mike/Desktop/snp.gff3
>>
>>
>>
>> search options = default
>>
>> initial landmark = 2L:80000..120000
>>
>> default tracks = DNA_CG Genes mRNAs ncRNA
>>
>>
>> # examples to show in the introduction
>> examples = 2L 2R 3L 3R X 4 U dmel_mitochondrion_genome
>>
>> # bring in the special Submitter plugin
>> plugins   = FastaDumper RestrictionAnnotator SequenceDumper TrackDumper
>> Submitter
>>
>> # "automatic" classes to try when an unqualified identifier is given
>> automatic classes = Symbol Gene Clone
>>
>> [...]
>>
>> [TRACK DEFAULTS]
>> [...]
>> database = annotations
>> [...]
>>
>> _____________________________
>>
>>
>> I've to define the databases in another place?
>>
>> If I make a new stanza with my other database it doesn't work, it's related?
>>
>> thanks
>>
>> ------------------------------------------------------------------------------
>> _______________________________________________
>> Gmod-gbrowse mailing list
>> Gmod-gbrowse at lists.sourceforge.net
>> https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse
>>
>>     
>
>
>
>   

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