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

[mark meyer]

We use the GD::SVG and was never able to get the inkscape (pdf generation)
operational, if that helps any.

On Fri, May 29, 2009 at 9:52 AM, Scott Cain <scott at scottcain.net> wrote:

> 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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> >> Gmod-gbrowse at lists.sourceforge.net
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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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