[Gmod-help] Re: [Gmod-gbrowse] user upload of wiggle formatted files

[cwilks]

Hi Dave,

Thanks for looking into this further, we appreciate it.

I checked the permissions issue, and it's ok.  However, your mention of the 
apache log made me think I should go check it out.
Either I never checked it before (which is dumb if I hadn't, its obviously a 
good first place to check for any apache issue) or I missed this, but there 
was an error:

[Tue Aug 18 11:48:07 2009] [error] [client 10.20.20.10] Can't locate object 
method "new" via package "Bio::Graphics::Wiggle::Loader" at 
/var/www/gbrowse/htdocs/../lib/x86_64-linux/Bio/Graphics/Browser/RemoteDataBase.pm 
line 43, <fh00001test_wig_file.wig> chunk 1., referer: 
http://www.arabidopsis.org/cgi-bin/gbrowse/arabidopsis/

Anyway, turns out that this was being caused by us missing a required 
module: Statistics::Descriptive.
I've since installed this module on our server and the test wig track I'm 
using now shows up.

I've looked around at the docs, and Statistics::Descriptive is mentioned as 
a needed perl module for Gbrowse 2.0 and for previous versions if the 
"Spectrogram plugin to calculate Fast Fourier Transforms" option is desired, 
but not in terms of loading Wiggle tracks.
There's also an email from Scott Cain referring to it.  So I took the 
liberty of updating the gmod wiggle wiki 
(http://gmod.org/wiki/GBrowse/Uploading_Wiggle_Tracks) with this 
requirement.

Thanks again for the help,
Chris


----- Original Message ----- 
From: "Dave Clements, GMOD Help Desk" <gmodhelp at googlemail.com>
To: "cwilks" <cwilks at stanford.edu>
Cc: <gmod-gbrowse at lists.sourceforge.net>
Sent: Friday, August 14, 2009 8:07 AM
Subject: Re: [Gmod-help] Re: [Gmod-gbrowse] user upload of wiggle formatted 
files


Hi Chris,

I took the exact sample from your email and uploaded it to WormBase,
which is running 1.70, and yep, it worked.  It also worked in my
default 1.70 yeast instance.  (Although I'd still say overlapping is
undefined.)

I didn't do anything special to enable wig file processing on my
default instance.

If GBrowse can't find the wig processing script, or if the script has
a problem, I would expect it to show up in the Apache log file.  On my
default instance, the processed wig file goes in
wigfile=/var/www/gbrowse/tmp/yeast/uploaded_file/

In wormbase it goes in
/usr/local/wormbase/website-classic/html/tmp/gbrowse/brie3/c_elegans/uploaded_file/

What is tmpimages set to in the configuration file?  I'm wondering if
there is a permissions problem?  the tmpimages directory should be
writable by the Apache user.

Hope this helps,

Dave C.

On Thu, Jul 30, 2009 at 1:22 PM, cwilks<cwilks at stanford.edu> wrote:
> Hi Dave,
>
> Thanks for the response. I tried that (lowered the span to 10 so they
> wouldn't overlap). Still didn't appear to work (same issues as before). A
> user who submitted the original sample said it worked fine on wormbase, so
> I'm wondering what we're doing wrong (or not doing) here on our gbrowse
> instance.
>
> Chris
>
>
> Dave Clements, GMOD Help Desk wrote:
>
>> Hi Chris,
>>
>> I don't have an obvious solution to this. However, I did notice that
>> some of the positions (+ step) given in the example data overlap with
>> each other. I don't know if the behavior of overlapping spans is
>> defined. Does the problem go away if the regions no longer overlap?
>>
>> Dave C.
>>
>> On Tue, Jul 28, 2009 at 4:20 PM, cwilks<cwilks at stanford.edu> wrote:
>>
>>>
>>> Hi Folks,
>>>
>>> We've upgraded to Gbrowse 1.7 currently on our web server. However,
>>> we're still having trouble allowing user uploads of wiggle formatted
>>> data (even a very small sample file). We were wondering if there was
>>> anything special to be done: a) on the gbrowse configuration and/or b)
>>> with apache's configuration to allow this to happen?
>>>
>>> The problem we're seeing is that when a user uploads a file, the refresh
>>> of the gbrowse page either displays a completely white screen or it
>>> displays only the header or top part of the page above where the region
>>> image is normally displayed. I've checked the apache logs and there's
>>> nothing specific regarding this.
>>>
>>> I'm pasting sample wiggle text which we've tried, unsuccessfully to
>>> upload:
>>>
>>> track type=wiggle_0 name="testWIG1"
>>> variableStep chrom=Chr1 span=25
>>> 79 23.0
>>> 91 4.0
>>> 308 6.0
>>> 477 22.0
>>> 651 30.0
>>> 663 45.0
>>> 880 60.0
>>> 1000 75.0
>>>
>>> Thanks for any help,
>>> Chris Wilks
>>> TAIR
>>>
>>>
>>>
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>>>
>>
>>
>>
>>
>



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