[Gmod-help] Re: [Gmod-gbrowse] wiggle tracks in gbrowse

Thu Mar 19 19:15:47 EDT 2009

Hi Dave,
I was able to change the viewlimits by setting max_score and min_score, 
so I know that at least some settings can be modified through the "?" 
interface.
I think I was unclear in my original post. I am just a researcher trying 
to use a website, and I have no affiliation with the site that hosts the 
gbrowse instance I'm wrestling with.
So, I'm assuming that the config file in the apache directory is 
inaccessible to me.
I have asked the folks who run the website if they can update the 
Bio::Graphics module as per Lincoln's suggestion, and I currently remain 
optimistic that this will solve the problem.
regards,
Nina

Dave Clements, GMOD Help Desk wrote:
> Hi Nina,
>
> Clicking on the question mark does show most (maybe all?) settings
> from the config file.  However, I'm not sure you can add new settings
> through that interface.  The config file is usually installed
> somewhere under your apache directory.  On my Ubuntu installation the
> GBrowse config files reside in the /etc/apache2/gbrowse.conf/
> directory.
>
> Find your .conf directory there and modify the track definition there
> to conform to Lincoln's suggestions.  Then try loading a region of the
> genome you haven't seen before (to avoid caching issues).
>
> Dave C.
>
> Was this helpful?  Let us know at http://gmod.org/wiki/Help_Desk_Feedback
>
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> On Thu, Mar 19, 2009 at 3:52 PM, Nina Thiessen <nthiessen at bcgsc.ca> wrote:
>   
>> Hi Dave,
>> Thank you for your suggestions.
>> I am not totally sure what the conf file is (I certainly do not provide the
>> file), but I suspect that that is what I can modify when I click on the "?"
>> associated with my track -- what I see is these settings:
>> [001]
>> glyph       = wiggle_xyplot
>> key         = TEST_chr_LG_XIII
>> description = TEST_chr_LG_XIII
>> pos_color=red
>> neg_color=blue
>> height  = 40
>>
>> reference=LG_XIII
>> 001 LG_XIII.data 118980..119605
>> Name=TEST_chr_LG_XIII;Note=TEST_chr_LG_XIII;wigfile=/var/www/gbrowse/tmp/Poptr1.1/uploaded_file/cf3a76bda0f9b059c80427ffcc63df8d/track_001.LG_XIII.1237246714.wig
>>
>> Unfortunately, inserting autoscale=global or autoscale=local into the above
>> config did not change the display at all.
>> Please let me know if you have any other ideas.
>>
>> regards,
>> Nina
>>
>> Dave Clements, GMOD Help Desk wrote:
>>     
>>> Hi Nina,
>>>
>>> As I read the documentation, setting viewLimits should do the trick.
>>> What does the stanza for this track look like in the GBrowse
>>> configuation file?  Have you tried setting autoscale = global in the
>>> conf file?  Although, it sounds like the global max is being
>>> incorrectly set, so maybe try autoscale = local instead.
>>>
>>> Dave C.
>>>
>>> Was this helpful?  Let us know at http://gmod.org/wiki/Help_Desk_Feedback
>>>
>>>
>>>
>>> On Mon, Mar 16, 2009 at 5:08 PM, Nina Thiessen <nthiessen at bcgsc.ca> wrote:
>>>
>>>       
>>>> greetings,
>>>> (I tried looking through the archives for this mailing list, but could
>>>> not find the answer to my question....probably because I was just not
>>>> using the correct keywords or something because I can't believe I'm the
>>>> first person to have encountered this....)
>>>>
>>>> I am trying to view "peaks" data encoded in a fixed-step, step size=1
>>>> wig formatted file using a version of gbrowse on this website
>>>> http://www.popgenie.db.umu.se/popgenie/index.php
>>>> and have encountered a most vexing problem.
>>>>
>>>> I have found that no matter what I do, the maximum obtained value in the
>>>> series of values associated with the first fixedStep determines the max
>>>> display height, and so any data above that height in subsequent peaks
>>>> appears truncated. (I am viewing the data in "full" mode so the peaks
>>>> will look like bar charts) Note that the first peak in the file can be
>>>> well outside the region I am currently viewing and the truncation will
>>>> still occur.
>>>>
>>>> Setting the viewLimits in the track line does not affect anything.
>>>> Including the span=1 in the fixedStep line does not change anything.
>>>> If I change the elements to variableStep format instead of using
>>>> fixedStep, this does not change anything
>>>>
>>>> I confirmed there was nothing wrong with the format of the file by
>>>> changing the chromosome name in my test file to a more standard name
>>>> (chr2), and was able to load my test file into the ucsc genome browser
>>>> (and the display height problem does not happen there.)
>>>>
>>>> Any ideas how I can get this to work right?
>>>>
>>>> --- File format details ---
>>>> ("track" to "40:40:2" is all one line)
>>>> eg:
>>>> track type="wiggle_0" name="TEST_chr_LG_XIII"
>>>> description="TEST_chr_LG_XIII" color=50,50,150 yLineMark=0.0
>>>> yLineOnOff=on visibility=full priority=1 maxHeightPixels=40:40:2
>>>> fixedStep chrom=LG_XIII start=119600 step=1
>>>> 1
>>>> 1
>>>> 2
>>>> 3
>>>> 3
>>>> 5
>>>> 4
>>>> 2
>>>> 2
>>>> 1
>>>> fixedStep chrom=LG_XIII start=119653 step=1
>>>> 1
>>>> 1
>>>> 2
>>>> 3
>>>> 5
>>>> 10
>>>> 15
>>>> 20
>>>> 17
>>>> 10
>>>> 8
>>>> 5
>>>> 3
>>>> 2
>>>> 1
>>>>
>>>> (in the this example, the second peak will be truncated to be 5 units
>>>> tall)
>>>>
>>>> regards,
>>>> Nina
>>>>
>>>>
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>>>>         
>>     