Taner Z. Sen | 5 May 16:35 2008

Scroll buttons, negative coordinates, key positions

I installed GBrowse and uploaded some maize data.
http://grinch8-2.gdcb.iastate.edu/cgi-bin/gbrowse/maize/

I have a few problems with the data display:

1) The scroll buttons don't work:
  a) go to http://grinch8-2.gdcb.iastate.edu/cgi-bin/gbrowse/maize/
  b) click example "2:2,000,000..4,000,000"
  c) Click left or right arrows of the "scroll".  They don't work.

2) Negative coordinates appear:
  a) go to http://grinch8-2.gdcb.iastate.edu/cgi-bin/gbrowse/maize/
  b) click example " BAC:AC177838"
  c) Choose "show 500kbp"

There are negative coordinates on the left hand side.

3) I want key positions to appear on the left when the page first 
loads. It seems that there are only two options for "keystyle": 
beneath and between to put in the conf file. Is there any other way 
except choosing the corresponding radio button in the "display 
settings" after the page loads? (keystyle=left didn't work)

Do you have any suggestion to fix these issues?

Thank you very much,
Taner
taner@...

-------------------------------------------------------------------------
(Continue reading)

Lincoln Stein | 5 May 17:25 2008
Picon

Re: Scroll buttons, negative coordinates, key positions

Hi,

The usual cause for this is not including a line for the full-length chromosome or contig in the data file.

Lincoln

On Mon, May 5, 2008 at 10:35 AM, Taner Z. Sen <taner-KgB/ygH5PX6Vc3sceRu5cw@public.gmane.org> wrote:
I installed GBrowse and uploaded some maize data.
http://grinch8-2.gdcb.iastate.edu/cgi-bin/gbrowse/maize/

I have a few problems with the data display:

1) The scroll buttons don't work:
 a) go to http://grinch8-2.gdcb.iastate.edu/cgi-bin/gbrowse/maize/
 b) click example "2:2,000,000..4,000,000"
 c) Click left or right arrows of the "scroll".  They don't work.

2) Negative coordinates appear:
 a) go to http://grinch8-2.gdcb.iastate.edu/cgi-bin/gbrowse/maize/
 b) click example " BAC:AC177838"
 c) Choose "show 500kbp"

There are negative coordinates on the left hand side.


3) I want key positions to appear on the left when the page first
loads. It seems that there are only two options for "keystyle":
beneath and between to put in the conf file. Is there any other way
except choosing the corresponding radio button in the "display
settings" after the page loads? (keystyle=left didn't work)

Do you have any suggestion to fix these issues?


Thank you very much,
Taner
taner-KgB/ygH5PX6Vc3sceRu5cw@public.gmane.org







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Scott Cain | 5 May 17:35 2008
Picon

Re: Scroll buttons, negative coordinates, key positions

Hi Taner,

The problem you are seeing is almost certainly a result of your
reference sequence not being correct.  The overview panel should show
the entire length of chromosome 2 with a red box around the region you
are looking at in the details panel.  When you see what you are seeing
(an overview that starts and stops where your detail view starts and
stops), it is usually because you don't have a valid reference sequence
line.  Do you have something that defines what '2' is, like this:

2   .  chromsome  1  10000000  .  .  .  ID=2;Name=2

Scott

On Mon, 2008-05-05 at 09:35 -0500, Taner Z. Sen wrote:
> I installed GBrowse and uploaded some maize data.
> http://grinch8-2.gdcb.iastate.edu/cgi-bin/gbrowse/maize/
> 
> I have a few problems with the data display:
> 
> 1) The scroll buttons don't work:
>   a) go to http://grinch8-2.gdcb.iastate.edu/cgi-bin/gbrowse/maize/
>   b) click example "2:2,000,000..4,000,000"
>   c) Click left or right arrows of the "scroll".  They don't work.
> 
> 2) Negative coordinates appear:
>   a) go to http://grinch8-2.gdcb.iastate.edu/cgi-bin/gbrowse/maize/
>   b) click example " BAC:AC177838"
>   c) Choose "show 500kbp"
> 
> There are negative coordinates on the left hand side.
> 
> 
> 3) I want key positions to appear on the left when the page first 
> loads. It seems that there are only two options for "keystyle": 
> beneath and between to put in the conf file. Is there any other way 
> except choosing the corresponding radio button in the "display 
> settings" after the page loads? (keystyle=left didn't work)
> 
> Do you have any suggestion to fix these issues?
> 
> 
> Thank you very much,
> Taner
> taner@...
> 
> 
> 
> 
> 
> 
> 
> -------------------------------------------------------------------------
> This SF.net email is sponsored by the 2008 JavaOne(SM) Conference 
> Don't miss this year's exciting event. There's still time to save $100. 
> Use priority code J8TL2D2. 
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-- 
------------------------------------------------------------------------
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GMOD Coordinator (http://www.gmod.org/)                     216-392-3087
Cold Spring Harbor Laboratory

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Taner Z. Sen | 5 May 21:09 2008

Re: Scroll buttons, negative coordinates, key positions

Hi Scott,

The line was slightly different, but according to your suggestion, I changed it to:
2       assembly         chromosome       1        234607100        .        .        .        Sequence         ID=2;Name=2

(deleting "Sequence" doesn't change results)

But the result is the same.

The full gff files is here:
http://grinch8-2.gdcb.iastate.edu/maize_copy.gff

Any other suggestions?

At 10:35 AM 5/5/2008, Scott Cain wrote:
Hi Taner,

The problem you are seeing is almost certainly a result of your
reference sequence not being correct.  The overview panel should show
the entire length of chromosome 2 with a red box around the region you
are looking at in the details panel.  When you see what you are seeing
(an overview that starts and stops where your detail view starts and
stops), it is usually because you don't have a valid reference sequence
line.  Do you have something that defines what '2' is, like this:

2   .  chromsome  1  10000000  .  .  .  ID=2;Name=2

Scott

On Mon, 2008-05-05 at 09:35 -0500, Taner Z. Sen wrote:
> I installed GBrowse and uploaded some maize data.
> http://grinch8-2.gdcb.iastate.edu/cgi-bin/gbrowse/maize/
>
> I have a few problems with the data display:
>
> 1) The scroll buttons don't work:
>   a) go to http://grinch8-2.gdcb.iastate.edu/cgi-bin/gbrowse/maize/
>   b) click example "2:2,000,000..4,000,000"
>   c) Click left or right arrows of the "scroll".  They don't work.
>
> 2) Negative coordinates appear:
>   a) go to http://grinch8-2.gdcb.iastate.edu/cgi-bin/gbrowse/maize/
>   b) click example " BAC:AC177838"
>   c) Choose "show 500kbp"
>
> There are negative coordinates on the left hand side.
>
>
> 3) I want key positions to appear on the left when the page first
> loads. It seems that there are only two options for "keystyle":
> beneath and between to put in the conf file. Is there any other way
> except choosing the corresponding radio button in the "display
> settings" after the page loads? (keystyle=left didn't work)
>
> Do you have any suggestion to fix these issues?
>
>
> Thank you very much,
> Taner
> taner-KgB/ygH5PX6Vc3sceRu5cw@public.gmane.org
>
>
>
>
>
>
>
> -------------------------------------------------------------------------
> This SF.net email is sponsored by the 2008 JavaOne(SM) Conference
> Don't miss this year's exciting event. There's still time to save $100.
> Use priority code J8TL2D2.
> http://ad.doubleclick.net/clk;198757673;13503038;p?http://java.sun.com/javaone
> _______________________________________________
> Gmod-gbrowse mailing list
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> https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse
--
------------------------------------------------------------------------
Scott Cain, Ph. D.                                         cain-FePsPjn27tw@public.gmane.org
GMOD Coordinator (http://www.gmod.org/ )                     216-392-3087
Cold Spring Harbor Laboratory

Taner Z. Sen, Ph.D.
Computational Biologist, USDA-Agricultural Research Service
Collaborator Assistant Professor, Dept. of Genetics, Development and Cell Biology
Bioinformatics and Computational Biology Program
Iowa State University
1025 Crop Genome Informatics Lab
Ames, IA 50011
Phone: (515) 294-5326
Fax: (515) 294-8280
taner <at> iastate. edu
http://www.public.iastate.edu/~taner/
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Scott Cain | 5 May 21:18 2008
Picon

Re: Scroll buttons, negative coordinates, key positions

Oh, what you have now is a mixture of GFF2 and GFF3.  To make it all
consistent, you want to change the chromosome lines to GFF2, like this:

2  assembly  chromosome  1  234607100   .  .  .  Sequence 2

Where there are 9 tab delimited columns (no tab between the "Sequence"
and the "2").

Scott

On Mon, 2008-05-05 at 14:09 -0500, Taner Z. Sen wrote:
> Hi Scott,
> 
> The line was slightly different, but according to your suggestion, I
> changed it to:
> 2       assembly        chromosome      1       234607100       .       .       .       Sequence        ID=2;Name=2 
> 
> (deleting "Sequence" doesn't change results)
> 
> But the result is the same.
> 
> The full gff files is here:
> http://grinch8-2.gdcb.iastate.edu/maize_copy.gff
> 
> Any other suggestions?
> 
> At 10:35 AM 5/5/2008, Scott Cain wrote:
> > Hi Taner,
> > 
> > The problem you are seeing is almost certainly a result of your
> > reference sequence not being correct.  The overview panel should
> > show
> > the entire length of chromosome 2 with a red box around the region
> > you
> > are looking at in the details panel.  When you see what you are
> > seeing
> > (an overview that starts and stops where your detail view starts and
> > stops), it is usually because you don't have a valid reference
> > sequence
> > line.  Do you have something that defines what '2' is, like this:
> > 
> > 2   .  chromsome  1  10000000  .  .  .  ID=2;Name=2
> > 
> > Scott
> > 
> > On Mon, 2008-05-05 at 09:35 -0500, Taner Z. Sen wrote:
> > > I installed GBrowse and uploaded some maize data.
> > > http://grinch8-2.gdcb.iastate.edu/cgi-bin/gbrowse/maize/
> > > 
> > > I have a few problems with the data display:
> > > 
> > > 1) The scroll buttons don't work:
> > >   a) go to
> > http://grinch8-2.gdcb.iastate.edu/cgi-bin/gbrowse/maize/
> > >   b) click example "2:2,000,000..4,000,000"
> > >   c) Click left or right arrows of the "scroll".  They don't work.
> > > 
> > > 2) Negative coordinates appear:
> > >   a) go to
> > http://grinch8-2.gdcb.iastate.edu/cgi-bin/gbrowse/maize/
> > >   b) click example " BAC:AC177838"
> > >   c) Choose "show 500kbp"
> > > 
> > > There are negative coordinates on the left hand side.
> > > 
> > > 
> > > 3) I want key positions to appear on the left when the page first 
> > > loads. It seems that there are only two options for "keystyle": 
> > > beneath and between to put in the conf file. Is there any other
> > way 
> > > except choosing the corresponding radio button in the "display 
> > > settings" after the page loads? (keystyle=left didn't work)
> > > 
> > > Do you have any suggestion to fix these issues?
> > > 
> > > 
> > > Thank you very much,
> > > Taner
> > > taner@...
> > > 
> > > 
> > > 
> > > 
> > > 
> > > 
> > > 
> > >
> > -------------------------------------------------------------------------
> > > This SF.net email is sponsored by the 2008 JavaOne(SM) Conference 
> > > Don't miss this year's exciting event. There's still time to save
> > $100. 
> > > Use priority code J8TL2D2. 
> > >
> > http://ad.doubleclick.net/clk;198757673;13503038;p?http://java.sun.com/javaone 
> > > _______________________________________________
> > > Gmod-gbrowse mailing list
> > > Gmod-gbrowse@...
> > > https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse
> > -- 
> > ------------------------------------------------------------------------
> > Scott Cain, Ph. D.
> > cain@...
> > GMOD Coordinator (http://www.gmod.org/ )
> > 216-392-3087
> > Cold Spring Harbor Laboratory
> 
> Taner Z. Sen, Ph.D.
> Computational Biologist, USDA-Agricultural Research Service
> Collaborator Assistant Professor, Dept. of Genetics, Development and
> Cell Biology
> Bioinformatics and Computational Biology Program
> Iowa State University
> 1025 Crop Genome Informatics Lab
> Ames, IA 50011
> Phone: (515) 294-5326
> Fax: (515) 294-8280 
> taner <at> iastate. edu 
> http://www.public.iastate.edu/~taner/ 
> 
> -------------------------------------------------------------------------
> This SF.net email is sponsored by the 2008 JavaOne(SM) Conference 
> Don't miss this year's exciting event. There's still time to save $100. 
> Use priority code J8TL2D2. 
> http://ad.doubleclick.net/clk;198757673;13503038;p?http://java.sun.com/javaone
> _______________________________________________ Gmod-gbrowse mailing list
Gmod-gbrowse@... https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse
--

-- 
------------------------------------------------------------------------
Scott Cain, Ph. D.                                   cain.cshl@...
GMOD Coordinator (http://www.gmod.org/)                     216-392-3087
Cold Spring Harbor Laboratory

-------------------------------------------------------------------------
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Taner Z. Sen | 5 May 21:26 2008

Re: Scroll buttons, negative coordinates, key positions

YES, it works!

Thanks Scott  & Lincoln.


At 02:18 PM 5/5/2008, Scott Cain wrote:
Oh, what you have now is a mixture of GFF2 and GFF3.  To make it all
consistent, you want to change the chromosome lines to GFF2, like this:

2  assembly  chromosome  1  234607100   .  .  .  Sequence 2

Where there are 9 tab delimited columns (no tab between the "Sequence"
and the "2").

Scott

On Mon, 2008-05-05 at 14:09 -0500, Taner Z. Sen wrote:
> Hi Scott,
>
> The line was slightly different, but according to your suggestion, I
> changed it to:
> 2       assembly        chromosome      1       234607100       .       .       .       Sequence        ID=2;Name=2
>
> (deleting "Sequence" doesn't change results)
>
> But the result is the same.
>
> The full gff files is here:
> http://grinch8-2.gdcb.iastate.edu/maize_copy.gff
>
> Any other suggestions?
>
> At 10:35 AM 5/5/2008, Scott Cain wrote:
> > Hi Taner,
> >
> > The problem you are seeing is almost certainly a result of your
> > reference sequence not being correct.  The overview panel should
> > show
> > the entire length of chromosome 2 with a red box around the region
> > you
> > are looking at in the details panel.  When you see what you are
> > seeing
> > (an overview that starts and stops where your detail view starts and
> > stops), it is usually because you don't have a valid reference
> > sequence
> > line.  Do you have something that defines what '2' is, like this:
> >
> > 2   .  chromsome  1  10000000  .  .  .  ID=2;Name=2
> >
> > Scott
> >
> > On Mon, 2008-05-05 at 09:35 -0500, Taner Z. Sen wrote:
> > > I installed GBrowse and uploaded some maize data.
> > > http://grinch8-2.gdcb.iastate.edu/cgi-bin/gbrowse/maize/
> > >
> > > I have a few problems with the data display:
> > >
> > > 1) The scroll buttons don't work:
> > >   a) go to
> > http://grinch8-2.gdcb.iastate.edu/cgi-bin/gbrowse/maize/
> > >   b) click example "2:2,000,000..4,000,000"
> > >   c) Click left or right arrows of the "scroll".  They don't work.
> > >
> > > 2) Negative coordinates appear:
> > >   a) go to
> > http://grinch8-2.gdcb.iastate.edu/cgi-bin/gbrowse/maize/
> > >   b) click example " BAC:AC177838"
> > >   c) Choose "show 500kbp"
> > >
> > > There are negative coordinates on the left hand side.
> > >
> > >
> > > 3) I want key positions to appear on the left when the page first
> > > loads. It seems that there are only two options for "keystyle":
> > > beneath and between to put in the conf file. Is there any other
> > way
> > > except choosing the corresponding radio button in the "display
> > > settings" after the page loads? (keystyle=left didn't work)
> > >
> > > Do you have any suggestion to fix these issues?
> > >
> > >
> > > Thank you very much,
> > > Taner
> > > taner-KgB/ygH5PX6Vc3sceRu5cw@public.gmane.org
> > >
> > >
> > >
> > >
> > >
> > >
> > >
> > >
> > -------------------------------------------------------------------------
> > > This SF.net email is sponsored by the 2008 JavaOne(SM) Conference
> > > Don't miss this year's exciting event. There's still time to save
> > $100.
> > > Use priority code J8TL2D2.
> > >
> > http://ad.doubleclick.net/clk;198757673;13503038;p?http://java.sun.com/javaone
> > > _______________________________________________
> > > Gmod-gbrowse mailing list
> > > Gmod-gbrowse-5NWGOfrQmneRv+LV9MX5uipxlwaOVQ5f@public.gmane.org
> > > https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse
> > --
> > ------------------------------------------------------------------------
> > Scott Cain, Ph. D.
> > cain-FePsPjn27tw@public.gmane.org
> > GMOD Coordinator (http://www.gmod.org/ )
> > 216-392-3087
> > Cold Spring Harbor Laboratory
>
> Taner Z. Sen, Ph.D.
> Computational Biologist, USDA-Agricultural Research Service
> Collaborator Assistant Professor, Dept. of Genetics, Development and
> Cell Biology
> Bioinformatics and Computational Biology Program
> Iowa State University
> 1025 Crop Genome Informatics Lab
> Ames, IA 50011
> Phone: (515) 294-5326
> Fax: (515) 294-8280
> taner <at> iastate. edu
> http://www.public.iastate.edu/~taner/
>
> -------------------------------------------------------------------------
> This SF.net email is sponsored by the 2008 JavaOne(SM) Conference
> Don't miss this year's exciting event. There's still time to save $100.
> Use priority code J8TL2D2.
> http://ad.doubleclick.net/clk;198757673;13503038;p?http://java.sun.com/javaone
> _______________________________________________ Gmod-gbrowse mailing list Gmod-gbrowse-5NWGOfrQmneRv+LV9MX5uipxlwaOVQ5f@public.gmane.org https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse
--
------------------------------------------------------------------------
Scott Cain, Ph. D.                                   cain.cshl-Re5JQEeQqe8AvxtiuMwx3w@public.gmane.org
GMOD Coordinator (http://www.gmod.org/ )                     216-392-3087
Cold Spring Harbor Laboratory

Taner Z. Sen, Ph.D.
Computational Biologist, USDA-Agricultural Research Service
Collaborator Assistant Professor, Dept. of Genetics, Development and Cell Biology
Bioinformatics and Computational Biology Program
Iowa State University
1025 Crop Genome Informatics Lab
Ames, IA 50011
Phone: (515) 294-5326
Fax: (515) 294-8280
taner <at> iastate. edu
http://www.public.iastate.edu/~taner/
-------------------------------------------------------------------------
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Alessandra | 7 May 10:27 2008
Picon

error log during loading gbrowse page

hi all,
I use 1.68 GBrowse. I install GBrowse with gbrowse_netinstall.pl without error.
I obtain right gbrowse page but in /var/log/apache2/error.log there
are any errors.
I have got errors with yeast database too when I loading gbrowse page:
[Wed May 07 10:13:16 2008] [error] [client 127.0.0.1] Use of
uninitialized value in length at (eval 105) line 7, <> line 26.,
referer: http://localhost/cgi-bin/virus/gbrowse/Tobacco_mosaic_virus/
[Wed May 07 10:13:16 2008] [error] [client 127.0.0.1] Use of
uninitialized value in join or string at (eval 105) line 9, <> line
26., referer: http://localhost/cgi-bin/virus/gbrowse/Tobacco_mosaic_virus/

I have got errors with yeast database too when I loading reset gbrowse page:

 [Wed May 07 10:13:16 2008] [error] [client 127.0.0.1] param():
attempt to read/write deleted session at
/usr/local/lib/perl/5.8.8/Bio/Graphics/Browser/PageSettings.pm line
52, referer: http://localhost/cgi-bin/virus/gbrowse/Tobacco_mosaic_virus/
[Wed May 07 10:13:16 2008] [error] [client 127.0.0.1] param(): attempt
to read/write deleted session at
/usr/local/lib/perl/5.8.8/Bio/Graphics/Browser/PageSettings.pm line
63, referer: http://localhost/cgi-bin/virus/gbrowse/Tobacco_mosaic_virus/
[Wed May 07 10:13:16 2008] [error] [client 127.0.0.1] param(): attempt
to read/write deleted session at
/usr/local/lib/perl/5.8.8/Bio/Graphics/Browser/PageSettings.pm line
64, referer: http://localhost/cgi-bin/virus/gbrowse/Tobacco_mosaic_virus/
[Wed May 07 10:13:16 2008] [error] [client 127.0.0.1] param(): attempt
to read/write deleted session at
/usr/local/lib/perl/5.8.8/Bio/Graphics/Browser/PageSettings.pm line
52, referer: http://localhost/cgi-bin/virus/gbrowse/Tobacco_mosaic_virus/
[Wed May 07 10:13:16 2008] [error] [client 127.0.0.1] param(): attempt
to read/write deleted session at
/usr/local/lib/perl/5.8.8/Bio/Graphics/Browser/PageSettings.pm line
63, referer: http://localhost/cgi-bin/virus/gbrowse/Tobacco_mosaic_virus/
[Wed May 07 10:13:16 2008] [error] [client 127.0.0.1] param(): attempt
to read/write deleted session at
/usr/local/lib/perl/5.8.8/Bio/Graphics/Browser/PageSettings.pm line
64, referer: http://localhost/cgi-bin/virus/gbrowse/Tobacco_mosaic_virus/
[Wed May 07 10:13:16 2008] [error] [client 127.0.0.1] param(): attempt
to read/write deleted session at
/usr/local/lib/perl/5.8.8/Bio/Graphics/Browser/PageSettings.pm line
52, referer: http://localhost/cgi-bin/virus/gbrowse/Tobacco_mosaic_virus/
[Wed May 07 10:13:16 2008] [error] [client 127.0.0.1] param(): attempt
to read/write deleted session at
/usr/local/lib/perl/5.8.8/Bio/Graphics/Browser/PageSettings.pm line
63, referer: http://localhost/cgi-bin/virus/gbrowse/Tobacco_mosaic_virus/
[Wed May 07 10:13:16 2008] [error] [client 127.0.0.1] param(): attempt
to read/write deleted session at
/usr/local/lib/perl/5.8.8/Bio/Graphics/Browser/PageSettings.pm line
64, referer: http://localhost/cgi-bin/virus/gbrowse/Tobacco_mosaic_virus/
[Wed May 07 10:13:16 2008] [error] [client 127.0.0.1] param(): attempt
to read/write deleted session at
/usr/local/lib/perl/5.8.8/Bio/Graphics/Browser/PageSettings.pm line
52, referer: http://localhost/cgi-bin/virus/gbrowse/Tobacco_mosaic_virus/
[Wed May 07 10:13:16 2008] [error] [client 127.0.0.1] param(): attempt
to read/write deleted session at
/usr/local/lib/perl/5.8.8/Bio/Graphics/Browser/PageSettings.pm line
63, referer: http://localhost/cgi-bin/virus/gbrowse/Tobacco_mosaic_virus/
[Wed May 07 10:13:16 2008] [error] [client 127.0.0.1] param(): attempt
to read/write deleted session at
/usr/local/lib/perl/5.8.8/Bio/Graphics/Browser/PageSettings.pm line
64, referer: http://localhost/cgi-bin/virus/gbrowse/Tobacco_mosaic_virus/
[Wed May 07 10:13:16 2008] [error] [client 127.0.0.1] Session error:
at /usr/lib/cgi-bin/virus/gbrowse line 330., referer:
http://localhost/cgi-bin/virus/gbrowse/Tobacco_mosaic_virus/

I don't understand this errors because tmp directory is readable and writable..
Can you help me?
Regards,

--

-- 
 Alessandra Bilardi
=~=~=~=~=~=~=~=~=~=~=~=~=~=~=~=
 CRIBI, University of Padova, Italy
 http://www.linkedin.com/in/bilardi
=~=~=~=~=~=~=~=~=~=~=~=~=~=~=~=

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Sofia Robb | 8 May 21:40 2008
Picon

Empty Tracks Misaligning and No Track Name Displayed

In reference to my last email and the misaligned empty tracks,  i  
have found out that when the 1024 image width option is selected in  
the "display settings" the tracks align just fine, but the track  
titles are still missing.  they are misaligned when i select 800  
image width.

-------last message-----images found in original message.

Hello Everyone!!

Today we installed Gbrowse-stable from cvs.  The empty tracks look  
weird.  They are misaligned, and the track names are not seen in the  
details panel (miRNA is missing between MAKER mRNAs and H.sapiens).   
see image below.   i am using the default track options in my conf file.

but if i "link to image" it appears the way it should. see below.

Thanks
Sofia

PS.  How would I change the highlight color from yellow back to red  
outline in the overview section.  see below
here is how it looks:

here is what i want it to look like:

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Sofia Robb | 8 May 19:25 2008
Picon

Empty Tracks Misaligning and No Track Name Displayed

Hello Everyone!!

Today we installed Gbrowse-stable from cvs.  The empty tracks look  
weird.  They are misaligned, and the track names are not seen in the  
details panel (miRNA is missing between MAKER mRNAs and H.sapiens).   
see image below.   i am using the default track options in my conf file.


but if i "link to image" it appears the way it should. see below.


Thanks
Sofia

PS.  How would I change the highlight color from yellow back to red  
outline in the oversection.  see below
here is how it looks:

here is what i want it to look like.

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Re: gbrowse genbank format dump?

Hi Geoff

First, I apologize for not getting back to you sooner.  An e-mail from
someone at NCBI reminded me about this question.  This functionality
was added in GBrowse 1.54 (~5 years ago), and is still in GBrowse, and
it appears to work at pseudomonas.org.  Get to GBrowse.  Try: select
"Download Sequence File" from the "Reports & Analysis" pull down.
Click "Configure..."  Select "Genbank" from the "Sequence File Format"
pull down.  Hit "Go".

Hope this helps, and apologies again for the delayed response.

Dave C.

On Fri, Apr 25, 2008 at 10:34 AM, Geoff Winsor <gwinsor@...> wrote:
> Hi,
> We are running gbrowse on www.pseudomonas.com and I recently received an
> inquiry from a user who said that they have lost the ability to dump
> gbrowse annotations in genbank format. I have been using gbrowse for
> quite a while and was not aware this feature even existed. We upgrade to
> new versions regularly so I was wondering if this feature may have been
> in an older version.
> Thanks,
> Geoff
>
> --
> Geoff Winsor
> Lead Database Developer, Bioinformatics
> Brinkman Lab
> IRMACS Centre, Room 10920
> Simon Fraser University, Burnaby, BC, Canada, V5A 1S6
> Phone: 778-782-2061
>
>
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Gmane