[Gmod-help] Re: [Gmod-gbrowse] Hi-Res images of conservation tracks have the background turn blue.

[Scott Cain]

Hi all,

Could this be a bad interaction between the plug in and GD::SVG or
inkscape (depending on what sort of hi res image you are getting)?
For example, I think that GD::SVG has a hard time with alpha channels.

Scott


On Fri, May 29, 2009 at 10:31 AM, mark meyer <mmeyerposting at gmail.com> wrote:
> Hi Angie,
>
> Bill is out of the office today, but I can try to answer your questions.
> Attached are the two screen shots, one is what the plugin looks like in the
> gbrowse, just fine as it looks in UCSC.  The second is what happens when you
> click on high-res image.
>
> We are running gbrowse v1.69.  The plugin code was implemented and
> downloaded about 1 month ago, just recently ran into this issue since we are
> trying to make some publication figures from our Gbrowse data.
>
> I can access conf files, etc. if you need to see them and try to do my best
> to answer questions, but I may not be able to answer very detailed questions
> in Bill's absence since he has been the one configuring this.
>
> Thanks for checking into this for us,
>
> Mark
>
> On Thu, May 28, 2009 at 5:29 PM, Angie Hinrichs <angie at soe.ucsc.edu> wrote:
>>
>> Dave - yes, that sounds likely.
>>
>> Bill, what version of GBrowse are you running?  How recently did you
>> grab the plugin code?  I didn't get the screenshot attachment so if
>> you wouldn't mind sending that to me, that would be helpful.  If your
>> GBrowse is on a public server, can you send the URL?
>>
>> Angie
>>
>> On Thu, 28 May 2009, Dave Clements, GMOD Help Desk wrote:
>>
>> > Hi Bill,
>> >
>> > I have no particular insight on why this is happening.  My guess is
>> > that it is due some obscure interaction between the UCSC plugin and
>> > core GBrowse, but I don't actually know.
>> >
>> > I've CC'd Angie at UCSC to see if she may have any insight.
>> >
>> > Dave C.
>> >
>> >
>> >
>> > On Tue, May 26, 2009 at 2:25 PM, Bill Pulec <wpulec at gmail.com> wrote:
>> > > Hi All,
>> > > I am attempting to view high-res images of conservation tracks but the
>> > > background of these tracks in high-res is blue. This isn't the case
>> > > when
>> > > these tracks are displayed in gbrowse normally, it only happens when
>> > > viewed
>> > > as high-res. Also all the non-conservation tracks are fine in high
>> > > res. Is
>> > > there any reason why outputting these images in high-res would do
>> > > this? Has
>> > > anyone encountered other tracks doing this in high-res? Any insight
>> > > would be
>> > > appreciated. I have attached an example image of the track below.
>> > >
>> > > Thanks,
>> > > Bill
>> > >
>> > >
>> > >
>> >
>> > Was this helpful?  Let us know at
>> > http://gmod.org/wiki/Help_Desk_Feedback
>> >
>> > Learn more about GMOD at:
>> >   SMBE:
>> > http://ccg.biology.uiowa.edu/smbe/symposia.php?action=view&sym_ID=27
>> >   Arthropod Genomics: http://www.k-state.edu/agc/symp2009/seminar.html
>> >   AGA Next Gen Seq in Non-Models:
>> > http://www.regonline.com/Nextgeneration
>> >
>>
>>
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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