Re: [Gmod-gbrowse] documentation on configuration file?

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

Ah, weird.  I don't remember seeing that before.  Amusingly, if you
are using the yeast sample data, with a track whose "real" name is
"Genes" (but whose display name is "Named genes"), the spurious Genes
track is not present, but but if the Named genes track is taken out,
the FilterTest-derived track appears.

Thanks for pointing that out so I can get to sleep at a reasonable
hour tonight :-)

Scott


On Tue, Oct 27, 2009 at 7:47 PM, Wes Barris <wes...@cs...> wrote:
> Ryan Golhar wrote:
>> Here is the config file I'm using.  There are no tracks listed, its a
>> blank template, yet Genes is still listed under General
>
> Remove the "FilterTest" plugin from the .conf file and your "Gene"
> track will go away.  I don't know what the FilterTest plugin does.
> I ran into this same problem a while ago.
>
>> Scott Cain wrote:
>>> Hi Ryan,
>>>
>>> You can send the configuration file to the mailing list for us to look
>>> at if you want.  Debugging without it is difficult.
>>>
>>> Scott
>>>
>>>
>>> On Tuesday, October 27, 2009, Ryan Golhar <gol...@um...> wrote:
>>>> Thanks Scott.  Removing the RestrictionAnnotator did the trick for the
>>>> Restriction Sites.
>>>>
>>>> I don't think the Genes track is being cached, only because the
>>>> Restriction sites came off and I've been adding other tracks and they
>>>> show up.  I've tried viewing the site from another computer and I still
>>>> see Genes.  Could it be from another plugin?
>>>>
>>>> Scott Cain wrote:
>>>>> Hello Ryan,
>>>>>
>>>>> If you go to http://localhost/gbrowse (i.e., the computer where you have
>>>>> GBrowse installed local to you), you will find a page that points to
>>>>> several documentation items, including the link to the GBrowse
>>>>> Configuration HOWTO on gmod.org:
>>>>>
>>>>>   http://gmod.org/wiki/CONFIGURE_HOWTO
>>>>>
>>>>> As for your specific questions, two things:
>>>>>
>>>>> * the Analysis section, that comes from plugins.  Remove
>>>>> RestrictionAnnotator from the list of plugins.
>>>>>
>>>>> * For the Genes track, I suspect that you may not be looking at the
>>>>> correct url for the configuration file you are editing, or perhaps the
>>>>> page is being cached.
>>>>>
>>>>> Scott
>>>>>
>>>>>
>>>>> On Oct 27, 2009, at 12:41 PM, Ryan Golhar wrote:
>>>>>
>>>>>> Is there documentation on the configuration file?  I can't seem to find
>>>>>> it from gbrowse.org.
>>>>>>
>>>>>> Also, I've removed everything related to track configurations and
>>>>>> default features thinking I would have a clean display with no tracks.
>>>>>> However, I consistently get Genes listed unnder the General for
>>>>>> available tracks and Restriction Sites under Analysis.
>>>>>>
>>>>>> I don't have any mention of these tracks in my configuration file.  Is
>>>>>> this defaulting from somewhere?
>>>>>>
>>>>>> ------------------------------------------------------------------------------
>>>>>>
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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
>>>>>
>>>>>
>>>>>
>>>>>
>>>>>
>>>> ------------------------------------------------------------------------------
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>
>
> --
> Wes Barris <wes...@cs...>
>
> ------------------------------------------------------------------------------
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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