gbrowse 2.13 flip doesn't work properly

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gbrowse 2.13 flip doesn't work properly

Hector Andres Urbina Saavedra
Hello,

I have GBrowse 2.13 running since a while.  Just today I realized that
the flip method is not working properly.  When I click on it, just the
rule change its orientation, not the glyphs.

Has anyone else had this problem?  I don't have error messages in apache
or gbrowse_slave logs.  Is the flipping proccess handled by the browser
instead?

Thank you for your help,

Héctor.



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Re: gbrowse 2.13 flip doesn't work properly

Lincoln Stein
Hi Hector,

I just checked this and it seems that most glyphs do flip, but the quantitative glyphs based on the xyplot do not. This is a problem in Bio::Graphics and I'll get it fixed in a few days.

Lincoln

On Mon, Aug 30, 2010 at 9:14 PM, Hector Andres Urbina Saavedra <[hidden email]> wrote:
Hello,

I have GBrowse 2.13 running since a while.  Just today I realized that
the flip method is not working properly.  When I click on it, just the
rule change its orientation, not the glyphs.

Has anyone else had this problem?  I don't have error messages in apache
or gbrowse_slave logs.  Is the flipping proccess handled by the browser
instead?

Thank you for your help,

Héctor.



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Lincoln D. Stein
Director, Informatics and Biocomputing Platform
Ontario Institute for Cancer Research
101 College St., Suite 800
Toronto, ON, Canada M5G0A3
416 673-8514
Assistant: Renata Musa <[hidden email]>

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Re: gbrowse 2.13 flip doesn't work properly

Lincoln Stein
In reply to this post by Hector Andres Urbina Saavedra
Hi,

Version 2.12 of Bio::Graphics (available within a few hours from CPAN), fixes the issues with flipping on xyplot glyphs. Please let me know if after upgrading you find still other glyphs that do not respect the glyph setting. 

Lincoln

On Mon, Aug 30, 2010 at 9:14 PM, Hector Andres Urbina Saavedra <[hidden email]> wrote:
Hello,

I have GBrowse 2.13 running since a while.  Just today I realized that
the flip method is not working properly.  When I click on it, just the
rule change its orientation, not the glyphs.

Has anyone else had this problem?  I don't have error messages in apache
or gbrowse_slave logs.  Is the flipping proccess handled by the browser
instead?

Thank you for your help,

Héctor.



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--
Lincoln D. Stein
Director, Informatics and Biocomputing Platform
Ontario Institute for Cancer Research
101 College St., Suite 800
Toronto, ON, Canada M5G0A3
416 673-8514
Assistant: Renata Musa <[hidden email]>

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Re: gbrowse 2.13 flip doesn't work properly

Lincoln Stein
In reply to this post by Hector Andres Urbina Saavedra
Hi Everyone,

Hector sent me a link that demonstrates that flip does not work at all on his installation. I cannot replicate the problem locally. Has anyone else encountered this problem?

Lincoln

On Mon, Aug 30, 2010 at 9:14 PM, Hector Andres Urbina Saavedra <[hidden email]> wrote:
Hello,

I have GBrowse 2.13 running since a while.  Just today I realized that
the flip method is not working properly.  When I click on it, just the
rule change its orientation, not the glyphs.

Has anyone else had this problem?  I don't have error messages in apache
or gbrowse_slave logs.  Is the flipping proccess handled by the browser
instead?

Thank you for your help,

Héctor.



------------------------------------------------------------------------------
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Enter the Intel(R) Threading Challenge 2010.
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--
Lincoln D. Stein
Director, Informatics and Biocomputing Platform
Ontario Institute for Cancer Research
101 College St., Suite 800
Toronto, ON, Canada M5G0A3
416 673-8514
Assistant: Renata Musa <[hidden email]>

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Re: gbrowse 2.13 flip doesn't work properly

Fields, Christopher J
Running Gbrowse 2.14, I see the gene features flipping w/o problems, but rna-seq coverage doesn't.  Could just be my conf file :)

Before:




After:





chris

On Aug 31, 2010, at 4:19 PM, Lincoln Stein wrote:

> Hi Everyone,
>
> Hector sent me a link that demonstrates that flip does not work at all on his installation. I cannot replicate the problem locally. Has anyone else encountered this problem?
>
> Lincoln
>
> On Mon, Aug 30, 2010 at 9:14 PM, Hector Andres Urbina Saavedra <[hidden email]> wrote:
> Hello,
>
> I have GBrowse 2.13 running since a while.  Just today I realized that
> the flip method is not working properly.  When I click on it, just the
> rule change its orientation, not the glyphs.
>
> Has anyone else had this problem?  I don't have error messages in apache
> or gbrowse_slave logs.  Is the flipping proccess handled by the browser
> instead?
>
> Thank you for your help,
>
> Héctor.
>
>
>
> ------------------------------------------------------------------------------
> This SF.net Dev2Dev email is sponsored by:
>
> Show off your parallel programming skills.
> Enter the Intel(R) Threading Challenge 2010.
> http://p.sf.net/sfu/intel-thread-sfd
> _______________________________________________
> Gmod-gbrowse mailing list
> [hidden email]
> https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse
>
>
>
> --
> Lincoln D. Stein
> Director, Informatics and Biocomputing Platform
> Ontario Institute for Cancer Research
> 101 College St., Suite 800
> Toronto, ON, Canada M5G0A3
> 416 673-8514
> Assistant: Renata Musa <[hidden email]>
> ------------------------------------------------------------------------------
> This SF.net Dev2Dev email is sponsored by:
>
> Show off your parallel programming skills.
> Enter the Intel(R) Threading Challenge 2010.
> http://p.sf.net/sfu/intel-thread-sfd_______________________________________________
> Gmod-gbrowse mailing list
> [hidden email]
> https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse

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Re: gbrowse 2.13 flip doesn't work properly

Timothy Parnell
In reply to this post by Lincoln Stein
Generic, CDS, processed transcript, and xyplot (driven by Bio::DB::SeqFeature::Store) glyphs flip properly for me.

BAM coverage and BigWig whisker xyplots do not flip.

Tim

--

Timothy J Parnell, PhD.
Research Associate
Howard Hughes Medical Institute
Department of Oncology
Huntsman Cancer Institute
University of Utah
Salt Lake City, UT 84112


On 8/31/10 3:19 PM, "Lincoln Stein" <[hidden email]> wrote:

Hi Everyone,

Hector sent me a link that demonstrates that flip does not work at all on his installation. I cannot replicate the problem locally. Has anyone else encountered this problem?

Lincoln

On Mon, Aug 30, 2010 at 9:14 PM, Hector Andres Urbina Saavedra <[hidden email]> wrote:
Hello,

I have GBrowse 2.13 running since a while.  Just today I realized that
the flip method is not working properly.  When I click on it, just the
rule change its orientation, not the glyphs.

Has anyone else had this problem?  I don't have error messages in apache
or gbrowse_slave logs.  Is the flipping proccess handled by the browser
instead?

Thank you for your help,

Héctor.



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Enter the Intel(R) Threading Challenge 2010.
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Re: gbrowse 2.13 flip doesn't work properly

Frédéric Sapet
In reply to this post by Lincoln Stein
Hello

I've just tried and I've got the same problem (GBrowse 2.13)

Fred

2010/8/31 Lincoln Stein <[hidden email]>
Hi Everyone,

Hector sent me a link that demonstrates that flip does not work at all on his installation. I cannot replicate the problem locally. Has anyone else encountered this problem?

Lincoln

On Mon, Aug 30, 2010 at 9:14 PM, Hector Andres Urbina Saavedra <[hidden email]> wrote:
Hello,

I have GBrowse 2.13 running since a while.  Just today I realized that
the flip method is not working properly.  When I click on it, just the
rule change its orientation, not the glyphs.

Has anyone else had this problem?  I don't have error messages in apache
or gbrowse_slave logs.  Is the flipping proccess handled by the browser
instead?

Thank you for your help,

Héctor.



------------------------------------------------------------------------------
This SF.net Dev2Dev email is sponsored by:

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Enter the Intel(R) Threading Challenge 2010.
http://p.sf.net/sfu/intel-thread-sfd
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--
Lincoln D. Stein
Director, Informatics and Biocomputing Platform
Ontario Institute for Cancer Research
101 College St., Suite 800
Toronto, ON, Canada M5G0A3
416 673-8514
Assistant: Renata Musa <[hidden email]>

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